clipper-2.1/0000777000374100011300000000000011372264352010016 500000000000000clipper-2.1/config/0000777000374100011300000000000011372264352011263 500000000000000clipper-2.1/config/depcomp0000755000374100011300000004426711372264332012567 00000000000000#! /bin/sh # depcomp - compile a program generating dependencies as side-effects scriptversion=2009-04-28.21; # UTC # Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free # Software Foundation, Inc. # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2, or (at your option) # any later version. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # You should have received a copy of the GNU General Public License # along with this program. If not, see . # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Originally written by Alexandre Oliva . case $1 in '') echo "$0: No command. Try \`$0 --help' for more information." 1>&2 exit 1; ;; -h | --h*) cat <<\EOF Usage: depcomp [--help] [--version] PROGRAM [ARGS] Run PROGRAMS ARGS to compile a file, generating dependencies as side-effects. Environment variables: depmode Dependency tracking mode. source Source file read by `PROGRAMS ARGS'. object Object file output by `PROGRAMS ARGS'. DEPDIR directory where to store dependencies. depfile Dependency file to output. tmpdepfile Temporary file to use when outputing dependencies. libtool Whether libtool is used (yes/no). Report bugs to . EOF exit $? ;; -v | --v*) echo "depcomp $scriptversion" exit $? ;; esac if test -z "$depmode" || test -z "$source" || test -z "$object"; then echo "depcomp: Variables source, object and depmode must be set" 1>&2 exit 1 fi # Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po. depfile=${depfile-`echo "$object" | sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`} tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`} rm -f "$tmpdepfile" # Some modes work just like other modes, but use different flags. We # parameterize here, but still list the modes in the big case below, # to make depend.m4 easier to write. Note that we *cannot* use a case # here, because this file can only contain one case statement. if test "$depmode" = hp; then # HP compiler uses -M and no extra arg. gccflag=-M depmode=gcc fi if test "$depmode" = dashXmstdout; then # This is just like dashmstdout with a different argument. dashmflag=-xM depmode=dashmstdout fi cygpath_u="cygpath -u -f -" if test "$depmode" = msvcmsys; then # This is just like msvisualcpp but w/o cygpath translation. # Just convert the backslash-escaped backslashes to single forward # slashes to satisfy depend.m4 cygpath_u="sed s,\\\\\\\\,/,g" depmode=msvisualcpp fi case "$depmode" in gcc3) ## gcc 3 implements dependency tracking that does exactly what ## we want. Yay! Note: for some reason libtool 1.4 doesn't like ## it if -MD -MP comes after the -MF stuff. Hmm. ## Unfortunately, FreeBSD c89 acceptance of flags depends upon ## the command line argument order; so add the flags where they ## appear in depend2.am. Note that the slowdown incurred here ## affects only configure: in makefiles, %FASTDEP% shortcuts this. for arg do case $arg in -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;; *) set fnord "$@" "$arg" ;; esac shift # fnord shift # $arg done "$@" stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile" exit $stat fi mv "$tmpdepfile" "$depfile" ;; gcc) ## There are various ways to get dependency output from gcc. Here's ## why we pick this rather obscure method: ## - Don't want to use -MD because we'd like the dependencies to end ## up in a subdir. Having to rename by hand is ugly. ## (We might end up doing this anyway to support other compilers.) ## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like ## -MM, not -M (despite what the docs say). ## - Using -M directly means running the compiler twice (even worse ## than renaming). if test -z "$gccflag"; then gccflag=-MD, fi "$@" -Wp,"$gccflag$tmpdepfile" stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile" exit $stat fi rm -f "$depfile" echo "$object : \\" > "$depfile" alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz ## The second -e expression handles DOS-style file names with drive letters. sed -e 's/^[^:]*: / /' \ -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile" ## This next piece of magic avoids the `deleted header file' problem. ## The problem is that when a header file which appears in a .P file ## is deleted, the dependency causes make to die (because there is ## typically no way to rebuild the header). We avoid this by adding ## dummy dependencies for each header file. Too bad gcc doesn't do ## this for us directly. tr ' ' ' ' < "$tmpdepfile" | ## Some versions of gcc put a space before the `:'. On the theory ## that the space means something, we add a space to the output as ## well. ## Some versions of the HPUX 10.20 sed can't process this invocation ## correctly. Breaking it into two sed invocations is a workaround. sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" rm -f "$tmpdepfile" ;; hp) # This case exists only to let depend.m4 do its work. It works by # looking at the text of this script. This case will never be run, # since it is checked for above. exit 1 ;; sgi) if test "$libtool" = yes; then "$@" "-Wp,-MDupdate,$tmpdepfile" else "$@" -MDupdate "$tmpdepfile" fi stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile" exit $stat fi rm -f "$depfile" if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files echo "$object : \\" > "$depfile" # Clip off the initial element (the dependent). Don't try to be # clever and replace this with sed code, as IRIX sed won't handle # lines with more than a fixed number of characters (4096 in # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines; # the IRIX cc adds comments like `#:fec' to the end of the # dependency line. tr ' ' ' ' < "$tmpdepfile" \ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \ tr ' ' ' ' >> "$depfile" echo >> "$depfile" # The second pass generates a dummy entry for each header file. tr ' ' ' ' < "$tmpdepfile" \ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \ >> "$depfile" else # The sourcefile does not contain any dependencies, so just # store a dummy comment line, to avoid errors with the Makefile # "include basename.Plo" scheme. echo "#dummy" > "$depfile" fi rm -f "$tmpdepfile" ;; aix) # The C for AIX Compiler uses -M and outputs the dependencies # in a .u file. In older versions, this file always lives in the # current directory. Also, the AIX compiler puts `$object:' at the # start of each line; $object doesn't have directory information. # Version 6 uses the directory in both cases. dir=`echo "$object" | sed -e 's|/[^/]*$|/|'` test "x$dir" = "x$object" && dir= base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'` if test "$libtool" = yes; then tmpdepfile1=$dir$base.u tmpdepfile2=$base.u tmpdepfile3=$dir.libs/$base.u "$@" -Wc,-M else tmpdepfile1=$dir$base.u tmpdepfile2=$dir$base.u tmpdepfile3=$dir$base.u "$@" -M fi stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" exit $stat fi for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" do test -f "$tmpdepfile" && break done if test -f "$tmpdepfile"; then # Each line is of the form `foo.o: dependent.h'. # Do two passes, one to just change these to # `$object: dependent.h' and one to simply `dependent.h:'. sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile" # That's a tab and a space in the []. sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile" else # The sourcefile does not contain any dependencies, so just # store a dummy comment line, to avoid errors with the Makefile # "include basename.Plo" scheme. echo "#dummy" > "$depfile" fi rm -f "$tmpdepfile" ;; icc) # Intel's C compiler understands `-MD -MF file'. However on # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c # ICC 7.0 will fill foo.d with something like # foo.o: sub/foo.c # foo.o: sub/foo.h # which is wrong. We want: # sub/foo.o: sub/foo.c # sub/foo.o: sub/foo.h # sub/foo.c: # sub/foo.h: # ICC 7.1 will output # foo.o: sub/foo.c sub/foo.h # and will wrap long lines using \ : # foo.o: sub/foo.c ... \ # sub/foo.h ... \ # ... "$@" -MD -MF "$tmpdepfile" stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile" exit $stat fi rm -f "$depfile" # Each line is of the form `foo.o: dependent.h', # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'. # Do two passes, one to just change these to # `$object: dependent.h' and one to simply `dependent.h:'. sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile" # Some versions of the HPUX 10.20 sed can't process this invocation # correctly. Breaking it into two sed invocations is a workaround. sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" | sed -e 's/$/ :/' >> "$depfile" rm -f "$tmpdepfile" ;; hp2) # The "hp" stanza above does not work with aCC (C++) and HP's ia64 # compilers, which have integrated preprocessors. The correct option # to use with these is +Maked; it writes dependencies to a file named # 'foo.d', which lands next to the object file, wherever that # happens to be. # Much of this is similar to the tru64 case; see comments there. dir=`echo "$object" | sed -e 's|/[^/]*$|/|'` test "x$dir" = "x$object" && dir= base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'` if test "$libtool" = yes; then tmpdepfile1=$dir$base.d tmpdepfile2=$dir.libs/$base.d "$@" -Wc,+Maked else tmpdepfile1=$dir$base.d tmpdepfile2=$dir$base.d "$@" +Maked fi stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile1" "$tmpdepfile2" exit $stat fi for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" do test -f "$tmpdepfile" && break done if test -f "$tmpdepfile"; then sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile" # Add `dependent.h:' lines. sed -ne '2,${ s/^ *// s/ \\*$// s/$/:/ p }' "$tmpdepfile" >> "$depfile" else echo "#dummy" > "$depfile" fi rm -f "$tmpdepfile" "$tmpdepfile2" ;; tru64) # The Tru64 compiler uses -MD to generate dependencies as a side # effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'. # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put # dependencies in `foo.d' instead, so we check for that too. # Subdirectories are respected. dir=`echo "$object" | sed -e 's|/[^/]*$|/|'` test "x$dir" = "x$object" && dir= base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'` if test "$libtool" = yes; then # With Tru64 cc, shared objects can also be used to make a # static library. 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We should prefer # $dir$base.o.d over $dir.libs/$base.o.d because the latter is # automatically cleaned when .libs/ is deleted, while ignoring # the former would cause a distcleancheck panic. tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4 tmpdepfile2=$dir$base.o.d # libtool 1.5 tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5 tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504 "$@" -Wc,-MD else tmpdepfile1=$dir$base.o.d tmpdepfile2=$dir$base.d tmpdepfile3=$dir$base.d tmpdepfile4=$dir$base.d "$@" -MD fi stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4" exit $stat fi for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4" do test -f "$tmpdepfile" && break done if test -f "$tmpdepfile"; then sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile" # That's a tab and a space in the []. sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile" else echo "#dummy" > "$depfile" fi rm -f "$tmpdepfile" ;; #nosideeffect) # This comment above is used by automake to tell side-effect # dependency tracking mechanisms from slower ones. dashmstdout) # Important note: in order to support this mode, a compiler *must* # always write the preprocessed file to stdout, regardless of -o. "$@" || exit $? # Remove the call to Libtool. if test "$libtool" = yes; then while test "X$1" != 'X--mode=compile'; do shift done shift fi # Remove `-o $object'. IFS=" " for arg do case $arg in -o) shift ;; $object) shift ;; *) set fnord "$@" "$arg" shift # fnord shift # $arg ;; esac done test -z "$dashmflag" && dashmflag=-M # Require at least two characters before searching for `:' # in the target name. This is to cope with DOS-style filenames: # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise. "$@" $dashmflag | sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile" rm -f "$depfile" cat < "$tmpdepfile" > "$depfile" tr ' ' ' ' < "$tmpdepfile" | \ ## Some versions of the HPUX 10.20 sed can't process this invocation ## correctly. Breaking it into two sed invocations is a workaround. sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" rm -f "$tmpdepfile" ;; dashXmstdout) # This case only exists to satisfy depend.m4. 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This case will never be run, # since it is checked for above. exit 1 ;; none) exec "$@" ;; *) echo "Unknown depmode $depmode" 1>&2 exit 1 ;; esac exit 0 # Local Variables: # mode: shell-script # sh-indentation: 2 # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" # time-stamp-time-zone: "UTC" # time-stamp-end: "; # UTC" # End: clipper-2.1/config/utimbuf.m40000644000374100011300000000250211372264321013107 00000000000000dnl Define HAVE_STRUCT_UTIMBUF if `struct utimbuf' is declared -- dnl usually in . dnl Some systems have utime.h but don't declare the struct anywhere. AC_DEFUN([jm_STRUCT_UTIMBUF], [ AC_CHECK_HEADERS(utime.h) AC_REQUIRE([AC_HEADER_TIME]) AC_CACHE_CHECK([for struct utimbuf], fu_cv_sys_struct_utimbuf, [AC_TRY_COMPILE( [ #ifdef TIME_WITH_SYS_TIME # include # include #else # ifdef HAVE_SYS_TIME_H # include # else # include # endif #endif #ifdef HAVE_UTIME_H # include #endif ], [static struct utimbuf x; x.actime = x.modtime;], fu_cv_sys_struct_utimbuf=yes, fu_cv_sys_struct_utimbuf=no) ]) if test $fu_cv_sys_struct_utimbuf = yes; then if test x = y; then # This code is deliberately never run via ./configure. # This is a hack to make autoheader put the corresponding # HAVE_* undef for this symbol in config.h.in. This saves me the # trouble of having to maintain the #undef in acconfig.h manually. AC_CHECK_FUNCS(STRUCT_UTIMBUF) fi # Defining it this way (rather than via AC_DEFINE) short-circuits the # autoheader check -- autoheader doesn't know it's already been taken # care of by the hack above. ac_kludge=HAVE_STRUCT_UTIMBUF AC_DEFINE_UNQUOTED($ac_kludge) fi ]) clipper-2.1/config/config.guess0000755000374100011300000013226411372264332013525 00000000000000#! /bin/sh # Attempt to guess a canonical system name. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, # 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 # Free Software Foundation, Inc. timestamp='2009-04-27' # This file is free software; you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA # 02110-1301, USA. # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Originally written by Per Bothner . # Please send patches to . Submit a context # diff and a properly formatted ChangeLog entry. # # This script attempts to guess a canonical system name similar to # config.sub. If it succeeds, it prints the system name on stdout, and # exits with 0. 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I hope that # covers most systems running today. This code pipes the CPU # types through head -n 1, so we only detect the type of CPU 0. ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1` case "$ALPHA_CPU_TYPE" in "EV4 (21064)") UNAME_MACHINE="alpha" ;; "EV4.5 (21064)") UNAME_MACHINE="alpha" ;; "LCA4 (21066/21068)") UNAME_MACHINE="alpha" ;; "EV5 (21164)") UNAME_MACHINE="alphaev5" ;; "EV5.6 (21164A)") UNAME_MACHINE="alphaev56" ;; "EV5.6 (21164PC)") UNAME_MACHINE="alphapca56" ;; "EV5.7 (21164PC)") UNAME_MACHINE="alphapca57" ;; "EV6 (21264)") UNAME_MACHINE="alphaev6" ;; "EV6.7 (21264A)") UNAME_MACHINE="alphaev67" ;; "EV6.8CB (21264C)") UNAME_MACHINE="alphaev68" ;; "EV6.8AL (21264B)") UNAME_MACHINE="alphaev68" ;; "EV6.8CX (21264D)") UNAME_MACHINE="alphaev68" ;; "EV6.9A (21264/EV69A)") UNAME_MACHINE="alphaev69" ;; "EV7 (21364)") UNAME_MACHINE="alphaev7" ;; "EV7.9 (21364A)") UNAME_MACHINE="alphaev79" ;; esac # A Pn.n version is a patched version. # A Vn.n version is a released version. # A Tn.n version is a released field test version. # A Xn.n version is an unreleased experimental baselevel. # 1.2 uses "1.2" for uname -r. echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` exit ;; Alpha\ *:Windows_NT*:*) # How do we know it's Interix rather than the generic POSIX subsystem? # Should we change UNAME_MACHINE based on the output of uname instead # of the specific Alpha model? echo alpha-pc-interix exit ;; 21064:Windows_NT:50:3) echo alpha-dec-winnt3.5 exit ;; Amiga*:UNIX_System_V:4.0:*) echo m68k-unknown-sysv4 exit ;; *:[Aa]miga[Oo][Ss]:*:*) echo ${UNAME_MACHINE}-unknown-amigaos exit ;; *:[Mm]orph[Oo][Ss]:*:*) echo ${UNAME_MACHINE}-unknown-morphos exit ;; *:OS/390:*:*) echo i370-ibm-openedition exit ;; *:z/VM:*:*) echo s390-ibm-zvmoe exit ;; *:OS400:*:*) echo powerpc-ibm-os400 exit ;; arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*) echo arm-acorn-riscix${UNAME_RELEASE} exit ;; arm:riscos:*:*|arm:RISCOS:*:*) echo arm-unknown-riscos exit ;; SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*) echo hppa1.1-hitachi-hiuxmpp exit ;; Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*) # akee@wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE. if test "`(/bin/universe) 2>/dev/null`" = att ; then echo pyramid-pyramid-sysv3 else echo pyramid-pyramid-bsd fi exit ;; NILE*:*:*:dcosx) echo pyramid-pyramid-svr4 exit ;; DRS?6000:unix:4.0:6*) echo sparc-icl-nx6 exit ;; DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*) case `/usr/bin/uname -p` in sparc) echo sparc-icl-nx7; exit ;; esac ;; s390x:SunOS:*:*) echo ${UNAME_MACHINE}-ibm-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4H:SunOS:5.*:*) echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*) echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*) eval $set_cc_for_build SUN_ARCH="i386" # If there is a compiler, see if it is configured for 64-bit objects. # Note that the Sun cc does not turn __LP64__ into 1 like gcc does. # This test works for both compilers. if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ grep IS_64BIT_ARCH >/dev/null then SUN_ARCH="x86_64" fi fi echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:6*:*) # According to config.sub, this is the proper way to canonicalize # SunOS6. Hard to guess exactly what SunOS6 will be like, but # it's likely to be more like Solaris than SunOS4. echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:*:*) case "`/usr/bin/arch -k`" in Series*|S4*) UNAME_RELEASE=`uname -v` ;; esac # Japanese Language versions have a version number like `4.1.3-JL'. echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'` exit ;; sun3*:SunOS:*:*) echo m68k-sun-sunos${UNAME_RELEASE} exit ;; sun*:*:4.2BSD:*) UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null` test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3 case "`/bin/arch`" in sun3) echo m68k-sun-sunos${UNAME_RELEASE} ;; sun4) echo sparc-sun-sunos${UNAME_RELEASE} ;; esac exit ;; aushp:SunOS:*:*) echo sparc-auspex-sunos${UNAME_RELEASE} exit ;; # The situation for MiNT is a little confusing. The machine name # can be virtually everything (everything which is not # "atarist" or "atariste" at least should have a processor # > m68000). The system name ranges from "MiNT" over "FreeMiNT" # to the lowercase version "mint" (or "freemint"). Finally # the system name "TOS" denotes a system which is actually not # MiNT. But MiNT is downward compatible to TOS, so this should # be no problem. atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) echo m68k-milan-mint${UNAME_RELEASE} exit ;; hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) echo m68k-hades-mint${UNAME_RELEASE} exit ;; *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) echo m68k-unknown-mint${UNAME_RELEASE} exit ;; m68k:machten:*:*) echo m68k-apple-machten${UNAME_RELEASE} exit ;; powerpc:machten:*:*) echo powerpc-apple-machten${UNAME_RELEASE} exit ;; RISC*:Mach:*:*) echo mips-dec-mach_bsd4.3 exit ;; RISC*:ULTRIX:*:*) echo mips-dec-ultrix${UNAME_RELEASE} exit ;; VAX*:ULTRIX*:*:*) echo vax-dec-ultrix${UNAME_RELEASE} exit ;; 2020:CLIX:*:* | 2430:CLIX:*:*) echo clipper-intergraph-clix${UNAME_RELEASE} exit ;; mips:*:*:UMIPS | mips:*:*:RISCos) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #ifdef __cplusplus #include /* for printf() prototype */ int main (int argc, char *argv[]) { #else int main (argc, argv) int argc; char *argv[]; { #endif #if defined (host_mips) && defined (MIPSEB) #if defined (SYSTYPE_SYSV) printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_SVR4) printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD) printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0); #endif #endif exit (-1); } EOF $CC_FOR_BUILD -o $dummy $dummy.c && dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` && SYSTEM_NAME=`$dummy $dummyarg` && { echo "$SYSTEM_NAME"; exit; } echo mips-mips-riscos${UNAME_RELEASE} exit ;; Motorola:PowerMAX_OS:*:*) echo powerpc-motorola-powermax exit ;; Motorola:*:4.3:PL8-*) echo powerpc-harris-powermax exit ;; Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*) echo powerpc-harris-powermax exit ;; Night_Hawk:Power_UNIX:*:*) echo powerpc-harris-powerunix exit ;; m88k:CX/UX:7*:*) echo m88k-harris-cxux7 exit ;; m88k:*:4*:R4*) echo m88k-motorola-sysv4 exit ;; m88k:*:3*:R3*) echo m88k-motorola-sysv3 exit ;; AViiON:dgux:*:*) # DG/UX returns AViiON for all architectures UNAME_PROCESSOR=`/usr/bin/uname -p` if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ] then if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \ [ ${TARGET_BINARY_INTERFACE}x = x ] then echo m88k-dg-dgux${UNAME_RELEASE} else echo m88k-dg-dguxbcs${UNAME_RELEASE} fi else echo i586-dg-dgux${UNAME_RELEASE} fi exit ;; M88*:DolphinOS:*:*) # DolphinOS (SVR3) echo m88k-dolphin-sysv3 exit ;; M88*:*:R3*:*) # Delta 88k system running SVR3 echo m88k-motorola-sysv3 exit ;; XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) echo m88k-tektronix-sysv3 exit ;; Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) echo m68k-tektronix-bsd exit ;; *:IRIX*:*:*) echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'` exit ;; ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id exit ;; # Note that: echo "'`uname -s`'" gives 'AIX ' i*86:AIX:*:*) echo i386-ibm-aix exit ;; ia64:AIX:*:*) if [ -x /usr/bin/oslevel ] ; then IBM_REV=`/usr/bin/oslevel` else IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} fi echo ${UNAME_MACHINE}-ibm-aix${IBM_REV} exit ;; *:AIX:2:3) if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include main() { if (!__power_pc()) exit(1); puts("powerpc-ibm-aix3.2.5"); exit(0); } EOF if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` then echo "$SYSTEM_NAME" else echo rs6000-ibm-aix3.2.5 fi elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then echo rs6000-ibm-aix3.2.4 else echo rs6000-ibm-aix3.2 fi exit ;; *:AIX:*:[456]) IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'` if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then IBM_ARCH=rs6000 else IBM_ARCH=powerpc fi if [ -x /usr/bin/oslevel ] ; then IBM_REV=`/usr/bin/oslevel` else IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} fi echo ${IBM_ARCH}-ibm-aix${IBM_REV} exit ;; *:AIX:*:*) echo rs6000-ibm-aix exit ;; ibmrt:4.4BSD:*|romp-ibm:BSD:*) echo romp-ibm-bsd4.4 exit ;; ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to exit ;; # report: romp-ibm BSD 4.3 *:BOSX:*:*) echo rs6000-bull-bosx exit ;; DPX/2?00:B.O.S.:*:*) echo m68k-bull-sysv3 exit ;; 9000/[34]??:4.3bsd:1.*:*) echo m68k-hp-bsd exit ;; hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) echo m68k-hp-bsd4.4 exit ;; 9000/[34678]??:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` case "${UNAME_MACHINE}" in 9000/31? ) HP_ARCH=m68000 ;; 9000/[34]?? ) HP_ARCH=m68k ;; 9000/[678][0-9][0-9]) if [ -x /usr/bin/getconf ]; then sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null` sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` case "${sc_cpu_version}" in 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1 532) # CPU_PA_RISC2_0 case "${sc_kernel_bits}" in 32) HP_ARCH="hppa2.0n" ;; 64) HP_ARCH="hppa2.0w" ;; '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20 esac ;; esac fi if [ "${HP_ARCH}" = "" ]; then eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #define _HPUX_SOURCE #include #include int main () { #if defined(_SC_KERNEL_BITS) long bits = sysconf(_SC_KERNEL_BITS); #endif long cpu = sysconf (_SC_CPU_VERSION); switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0"); break; case CPU_PA_RISC1_1: puts ("hppa1.1"); break; case CPU_PA_RISC2_0: #if defined(_SC_KERNEL_BITS) switch (bits) { case 64: puts ("hppa2.0w"); break; case 32: puts ("hppa2.0n"); break; default: puts ("hppa2.0"); break; } break; #else /* !defined(_SC_KERNEL_BITS) */ puts ("hppa2.0"); break; #endif default: puts ("hppa1.0"); break; } exit (0); } EOF (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy` test -z "$HP_ARCH" && HP_ARCH=hppa fi ;; esac if [ ${HP_ARCH} = "hppa2.0w" ] then eval $set_cc_for_build # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler # generating 64-bit code. GNU and HP use different nomenclature: # # $ CC_FOR_BUILD=cc ./config.guess # => hppa2.0w-hp-hpux11.23 # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess # => hppa64-hp-hpux11.23 if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | grep __LP64__ >/dev/null then HP_ARCH="hppa2.0w" else HP_ARCH="hppa64" fi fi echo ${HP_ARCH}-hp-hpux${HPUX_REV} exit ;; ia64:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` echo ia64-hp-hpux${HPUX_REV} exit ;; 3050*:HI-UX:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include int main () { long cpu = sysconf (_SC_CPU_VERSION); /* The order matters, because CPU_IS_HP_MC68K erroneously returns true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct results, however. */ if (CPU_IS_PA_RISC (cpu)) { switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break; case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break; case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break; default: puts ("hppa-hitachi-hiuxwe2"); break; } } else if (CPU_IS_HP_MC68K (cpu)) puts ("m68k-hitachi-hiuxwe2"); else puts ("unknown-hitachi-hiuxwe2"); exit (0); } EOF $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` && { echo "$SYSTEM_NAME"; exit; } echo unknown-hitachi-hiuxwe2 exit ;; 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* ) echo hppa1.1-hp-bsd exit ;; 9000/8??:4.3bsd:*:*) echo hppa1.0-hp-bsd exit ;; *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) echo hppa1.0-hp-mpeix exit ;; hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* ) echo hppa1.1-hp-osf exit ;; hp8??:OSF1:*:*) echo hppa1.0-hp-osf exit ;; i*86:OSF1:*:*) if [ -x /usr/sbin/sysversion ] ; then echo ${UNAME_MACHINE}-unknown-osf1mk else echo ${UNAME_MACHINE}-unknown-osf1 fi exit ;; parisc*:Lites*:*:*) echo hppa1.1-hp-lites exit ;; C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) echo c1-convex-bsd exit ;; C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi exit ;; C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) echo c34-convex-bsd exit ;; C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) echo c38-convex-bsd exit ;; C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) echo c4-convex-bsd exit ;; CRAY*Y-MP:*:*:*) echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*[A-Z]90:*:*:*) echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \ | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ -e 's/\.[^.]*$/.X/' exit ;; CRAY*TS:*:*:*) echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*T3E:*:*:*) echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*SV1:*:*:*) echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; *:UNICOS/mp:*:*) echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'` echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" exit ;; 5000:UNIX_System_V:4.*:*) FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'` echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" exit ;; i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE} exit ;; sparc*:BSD/OS:*:*) echo sparc-unknown-bsdi${UNAME_RELEASE} exit ;; *:BSD/OS:*:*) echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE} exit ;; *:FreeBSD:*:*) case ${UNAME_MACHINE} in pc98) echo i386-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; amd64) echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; *) echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; esac exit ;; i*:CYGWIN*:*) echo ${UNAME_MACHINE}-pc-cygwin exit ;; *:MINGW*:*) echo ${UNAME_MACHINE}-pc-mingw32 exit ;; i*:windows32*:*) # uname -m includes "-pc" on this system. echo ${UNAME_MACHINE}-mingw32 exit ;; i*:PW*:*) echo ${UNAME_MACHINE}-pc-pw32 exit ;; *:Interix*:[3456]*) case ${UNAME_MACHINE} in x86) echo i586-pc-interix${UNAME_RELEASE} exit ;; EM64T | authenticamd | genuineintel) echo x86_64-unknown-interix${UNAME_RELEASE} exit ;; IA64) echo ia64-unknown-interix${UNAME_RELEASE} exit ;; esac ;; [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*) echo i${UNAME_MACHINE}-pc-mks exit ;; i*:Windows_NT*:* | Pentium*:Windows_NT*:*) # How do we know it's Interix rather than the generic POSIX subsystem? # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we # UNAME_MACHINE based on the output of uname instead of i386? echo i586-pc-interix exit ;; i*:UWIN*:*) echo ${UNAME_MACHINE}-pc-uwin exit ;; amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*) echo x86_64-unknown-cygwin exit ;; p*:CYGWIN*:*) echo powerpcle-unknown-cygwin exit ;; prep*:SunOS:5.*:*) echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; *:GNU:*:*) # the GNU system echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'` exit ;; *:GNU/*:*:*) # other systems with GNU libc and userland echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu exit ;; i*86:Minix:*:*) echo ${UNAME_MACHINE}-pc-minix exit ;; arm*:Linux:*:*) eval $set_cc_for_build if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ | grep -q __ARM_EABI__ then echo ${UNAME_MACHINE}-unknown-linux-gnu else echo ${UNAME_MACHINE}-unknown-linux-gnueabi fi exit ;; avr32*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; cris:Linux:*:*) echo cris-axis-linux-gnu exit ;; crisv32:Linux:*:*) echo crisv32-axis-linux-gnu exit ;; frv:Linux:*:*) echo frv-unknown-linux-gnu exit ;; ia64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; m32r*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; m68*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; mips:Linux:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #undef CPU #undef mips #undef mipsel #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) CPU=mipsel #else #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) CPU=mips #else CPU= #endif #endif EOF eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' /^CPU/{ s: ::g p }'`" test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } ;; mips64:Linux:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #undef CPU #undef mips64 #undef mips64el #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) CPU=mips64el #else #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) CPU=mips64 #else CPU= #endif #endif EOF eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' /^CPU/{ s: ::g p }'`" test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } ;; or32:Linux:*:*) echo or32-unknown-linux-gnu exit ;; ppc:Linux:*:*) echo powerpc-unknown-linux-gnu exit ;; ppc64:Linux:*:*) echo powerpc64-unknown-linux-gnu exit ;; alpha:Linux:*:*) case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in EV5) UNAME_MACHINE=alphaev5 ;; EV56) UNAME_MACHINE=alphaev56 ;; PCA56) UNAME_MACHINE=alphapca56 ;; PCA57) UNAME_MACHINE=alphapca56 ;; EV6) UNAME_MACHINE=alphaev6 ;; EV67) UNAME_MACHINE=alphaev67 ;; EV68*) UNAME_MACHINE=alphaev68 ;; esac objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} exit ;; padre:Linux:*:*) echo sparc-unknown-linux-gnu exit ;; parisc:Linux:*:* | hppa:Linux:*:*) # Look for CPU level case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in PA7*) echo hppa1.1-unknown-linux-gnu ;; PA8*) echo hppa2.0-unknown-linux-gnu ;; *) echo hppa-unknown-linux-gnu ;; esac exit ;; parisc64:Linux:*:* | hppa64:Linux:*:*) echo hppa64-unknown-linux-gnu exit ;; s390:Linux:*:* | s390x:Linux:*:*) echo ${UNAME_MACHINE}-ibm-linux exit ;; sh64*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; sh*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; sparc:Linux:*:* | sparc64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; vax:Linux:*:*) echo ${UNAME_MACHINE}-dec-linux-gnu exit ;; x86_64:Linux:*:*) echo x86_64-unknown-linux-gnu exit ;; xtensa*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; i*86:Linux:*:*) # The BFD linker knows what the default object file format is, so # first see if it will tell us. cd to the root directory to prevent # problems with other programs or directories called `ld' in the path. # Set LC_ALL=C to ensure ld outputs messages in English. ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \ | sed -ne '/supported targets:/!d s/[ ][ ]*/ /g s/.*supported targets: *// s/ .*// p'` case "$ld_supported_targets" in elf32-i386) TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu" ;; a.out-i386-linux) echo "${UNAME_MACHINE}-pc-linux-gnuaout" exit ;; "") # Either a pre-BFD a.out linker (linux-gnuoldld) or # one that does not give us useful --help. echo "${UNAME_MACHINE}-pc-linux-gnuoldld" exit ;; esac # Determine whether the default compiler is a.out or elf eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include #ifdef __ELF__ # ifdef __GLIBC__ # if __GLIBC__ >= 2 LIBC=gnu # else LIBC=gnulibc1 # endif # else LIBC=gnulibc1 # endif #else #if defined(__INTEL_COMPILER) || defined(__PGI) || defined(__SUNPRO_C) || defined(__SUNPRO_CC) LIBC=gnu #else LIBC=gnuaout #endif #endif #ifdef __dietlibc__ LIBC=dietlibc #endif EOF eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' /^LIBC/{ s: ::g p }'`" test x"${LIBC}" != x && { echo "${UNAME_MACHINE}-pc-linux-${LIBC}" exit } test x"${TENTATIVE}" != x && { echo "${TENTATIVE}"; exit; } ;; i*86:DYNIX/ptx:4*:*) # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. # earlier versions are messed up and put the nodename in both # sysname and nodename. echo i386-sequent-sysv4 exit ;; i*86:UNIX_SV:4.2MP:2.*) # Unixware is an offshoot of SVR4, but it has its own version # number series starting with 2... # I am not positive that other SVR4 systems won't match this, # I just have to hope. -- rms. # Use sysv4.2uw... so that sysv4* matches it. echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION} exit ;; i*86:OS/2:*:*) # If we were able to find `uname', then EMX Unix compatibility # is probably installed. echo ${UNAME_MACHINE}-pc-os2-emx exit ;; i*86:XTS-300:*:STOP) echo ${UNAME_MACHINE}-unknown-stop exit ;; i*86:atheos:*:*) echo ${UNAME_MACHINE}-unknown-atheos exit ;; i*86:syllable:*:*) echo ${UNAME_MACHINE}-pc-syllable exit ;; i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*) echo i386-unknown-lynxos${UNAME_RELEASE} exit ;; i*86:*DOS:*:*) echo ${UNAME_MACHINE}-pc-msdosdjgpp exit ;; i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*) UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'` if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL} else echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL} fi exit ;; i*86:*:5:[678]*) # UnixWare 7.x, OpenUNIX and OpenServer 6. case `/bin/uname -X | grep "^Machine"` in *486*) UNAME_MACHINE=i486 ;; *Pentium) UNAME_MACHINE=i586 ;; *Pent*|*Celeron) UNAME_MACHINE=i686 ;; esac echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION} exit ;; i*86:*:3.2:*) if test -f /usr/options/cb.name; then UNAME_REL=`sed -n 's/.*Version //p' /dev/null >/dev/null ; then UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')` (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486 (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \ && UNAME_MACHINE=i586 (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \ && UNAME_MACHINE=i686 (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \ && UNAME_MACHINE=i686 echo ${UNAME_MACHINE}-pc-sco$UNAME_REL else echo ${UNAME_MACHINE}-pc-sysv32 fi exit ;; pc:*:*:*) # Left here for compatibility: # uname -m prints for DJGPP always 'pc', but it prints nothing about # the processor, so we play safe by assuming i586. # Note: whatever this is, it MUST be the same as what config.sub # prints for the "djgpp" host, or else GDB configury will decide that # this is a cross-build. echo i586-pc-msdosdjgpp exit ;; Intel:Mach:3*:*) echo i386-pc-mach3 exit ;; paragon:*:*:*) echo i860-intel-osf1 exit ;; i860:*:4.*:*) # i860-SVR4 if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4 else # Add other i860-SVR4 vendors below as they are discovered. echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4 fi exit ;; mini*:CTIX:SYS*5:*) # "miniframe" echo m68010-convergent-sysv exit ;; mc68k:UNIX:SYSTEM5:3.51m) echo m68k-convergent-sysv exit ;; M680?0:D-NIX:5.3:*) echo m68k-diab-dnix exit ;; M68*:*:R3V[5678]*:*) test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;; 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0) OS_REL='' test -r /etc/.relid \ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4.3${OS_REL}; exit; } /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;; 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4; exit; } ;; NCR*:*:4.2:* | MPRAS*:*:4.2:*) OS_REL='.3' test -r /etc/.relid \ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4.3${OS_REL}; exit; } /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;; m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) echo m68k-unknown-lynxos${UNAME_RELEASE} exit ;; mc68030:UNIX_System_V:4.*:*) echo m68k-atari-sysv4 exit ;; TSUNAMI:LynxOS:2.*:*) echo sparc-unknown-lynxos${UNAME_RELEASE} exit ;; rs6000:LynxOS:2.*:*) echo rs6000-unknown-lynxos${UNAME_RELEASE} exit ;; PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*) echo powerpc-unknown-lynxos${UNAME_RELEASE} exit ;; SM[BE]S:UNIX_SV:*:*) echo mips-dde-sysv${UNAME_RELEASE} exit ;; RM*:ReliantUNIX-*:*:*) echo mips-sni-sysv4 exit ;; RM*:SINIX-*:*:*) echo mips-sni-sysv4 exit ;; *:SINIX-*:*:*) if uname -p 2>/dev/null >/dev/null ; then UNAME_MACHINE=`(uname -p) 2>/dev/null` echo ${UNAME_MACHINE}-sni-sysv4 else echo ns32k-sni-sysv fi exit ;; PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort # says echo i586-unisys-sysv4 exit ;; *:UNIX_System_V:4*:FTX*) # From Gerald Hewes . # How about differentiating between stratus architectures? -djm echo hppa1.1-stratus-sysv4 exit ;; *:*:*:FTX*) # From seanf@swdc.stratus.com. echo i860-stratus-sysv4 exit ;; i*86:VOS:*:*) # From Paul.Green@stratus.com. echo ${UNAME_MACHINE}-stratus-vos exit ;; *:VOS:*:*) # From Paul.Green@stratus.com. echo hppa1.1-stratus-vos exit ;; mc68*:A/UX:*:*) echo m68k-apple-aux${UNAME_RELEASE} exit ;; news*:NEWS-OS:6*:*) echo mips-sony-newsos6 exit ;; R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) if [ -d /usr/nec ]; then echo mips-nec-sysv${UNAME_RELEASE} else echo mips-unknown-sysv${UNAME_RELEASE} fi exit ;; BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. echo powerpc-be-beos exit ;; BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. echo powerpc-apple-beos exit ;; BePC:BeOS:*:*) # BeOS running on Intel PC compatible. echo i586-pc-beos exit ;; BePC:Haiku:*:*) # Haiku running on Intel PC compatible. echo i586-pc-haiku exit ;; SX-4:SUPER-UX:*:*) echo sx4-nec-superux${UNAME_RELEASE} exit ;; SX-5:SUPER-UX:*:*) echo sx5-nec-superux${UNAME_RELEASE} exit ;; SX-6:SUPER-UX:*:*) echo sx6-nec-superux${UNAME_RELEASE} exit ;; SX-7:SUPER-UX:*:*) echo sx7-nec-superux${UNAME_RELEASE} exit ;; SX-8:SUPER-UX:*:*) echo sx8-nec-superux${UNAME_RELEASE} exit ;; SX-8R:SUPER-UX:*:*) echo sx8r-nec-superux${UNAME_RELEASE} exit ;; Power*:Rhapsody:*:*) echo powerpc-apple-rhapsody${UNAME_RELEASE} exit ;; *:Rhapsody:*:*) echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE} exit ;; *:Darwin:*:*) UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown case $UNAME_PROCESSOR in unknown) UNAME_PROCESSOR=powerpc ;; esac echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE} exit ;; *:procnto*:*:* | *:QNX:[0123456789]*:*) UNAME_PROCESSOR=`uname -p` if test "$UNAME_PROCESSOR" = "x86"; then UNAME_PROCESSOR=i386 UNAME_MACHINE=pc fi echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE} exit ;; *:QNX:*:4*) echo i386-pc-qnx exit ;; NSE-?:NONSTOP_KERNEL:*:*) echo nse-tandem-nsk${UNAME_RELEASE} exit ;; NSR-?:NONSTOP_KERNEL:*:*) echo nsr-tandem-nsk${UNAME_RELEASE} exit ;; *:NonStop-UX:*:*) echo mips-compaq-nonstopux exit ;; BS2000:POSIX*:*:*) echo bs2000-siemens-sysv exit ;; DS/*:UNIX_System_V:*:*) echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE} exit ;; *:Plan9:*:*) # "uname -m" is not consistent, so use $cputype instead. 386 # is converted to i386 for consistency with other x86 # operating systems. if test "$cputype" = "386"; then UNAME_MACHINE=i386 else UNAME_MACHINE="$cputype" fi echo ${UNAME_MACHINE}-unknown-plan9 exit ;; *:TOPS-10:*:*) echo pdp10-unknown-tops10 exit ;; *:TENEX:*:*) echo pdp10-unknown-tenex exit ;; KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) echo pdp10-dec-tops20 exit ;; XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) echo pdp10-xkl-tops20 exit ;; *:TOPS-20:*:*) echo pdp10-unknown-tops20 exit ;; *:ITS:*:*) echo pdp10-unknown-its exit ;; SEI:*:*:SEIUX) echo mips-sei-seiux${UNAME_RELEASE} exit ;; *:DragonFly:*:*) echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` exit ;; *:*VMS:*:*) UNAME_MACHINE=`(uname -p) 2>/dev/null` case "${UNAME_MACHINE}" in A*) echo alpha-dec-vms ; exit ;; I*) echo ia64-dec-vms ; exit ;; V*) echo vax-dec-vms ; exit ;; esac ;; *:XENIX:*:SysV) echo i386-pc-xenix exit ;; i*86:skyos:*:*) echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//' exit ;; i*86:rdos:*:*) echo ${UNAME_MACHINE}-pc-rdos exit ;; i*86:AROS:*:*) echo ${UNAME_MACHINE}-pc-aros exit ;; esac #echo '(No uname command or uname output not recognized.)' 1>&2 #echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2 eval $set_cc_for_build cat >$dummy.c < # include #endif main () { #if defined (sony) #if defined (MIPSEB) /* BFD wants "bsd" instead of "newsos". 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See the $PACKAGE docs for more information." 1>&2 exit $EXIT_FAILURE ;; esac # Clear the version info if we defaulted, and they specified a release. if test -z "$vinfo" && test -n "$release"; then major= case $version_type in darwin) # we can't check for "0.0" in archive_cmds due to quoting # problems, so we reset it completely verstring= ;; *) verstring="0.0" ;; esac if test "$need_version" = no; then versuffix= else versuffix=".0.0" fi fi # Remove version info from name if versioning should be avoided if test "$avoid_version" = yes && test "$need_version" = no; then major= versuffix= verstring="" fi # Check to see if the archive will have undefined symbols. if test "$allow_undefined" = yes; then if test "$allow_undefined_flag" = unsupported; then $echo "$modename: warning: undefined symbols not allowed in $host shared libraries" 1>&2 build_libtool_libs=no build_old_libs=yes fi else # Don't allow undefined symbols. allow_undefined_flag="$no_undefined_flag" fi fi if test "$mode" != relink; then # Remove our outputs, but don't remove object files since they # may have been created when compiling PIC objects. removelist= tempremovelist=`$echo "$output_objdir/*"` for p in $tempremovelist; do case $p in *.$objext) ;; $output_objdir/$outputname | $output_objdir/$libname.* | $output_objdir/${libname}${release}.*) if test "X$precious_files_regex" != "X"; then if echo $p | $EGREP -e "$precious_files_regex" >/dev/null 2>&1 then continue fi fi removelist="$removelist $p" ;; *) ;; esac done if test -n "$removelist"; then $show "${rm}r $removelist" $run ${rm}r $removelist fi fi # Now set the variables for building old libraries. if test "$build_old_libs" = yes && test "$build_libtool_libs" != convenience ; then oldlibs="$oldlibs $output_objdir/$libname.$libext" # Transform .lo files to .o files. oldobjs="$objs "`$echo "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}'$/d' -e "$lo2o" | $NL2SP` fi # Eliminate all temporary directories. for path in $notinst_path; do lib_search_path=`$echo "$lib_search_path " | ${SED} -e 's% $path % %g'` deplibs=`$echo "$deplibs " | ${SED} -e 's% -L$path % %g'` dependency_libs=`$echo "$dependency_libs " | ${SED} -e 's% -L$path % %g'` done if test -n "$xrpath"; then # If the user specified any rpath flags, then add them. temp_xrpath= for libdir in $xrpath; do temp_xrpath="$temp_xrpath -R$libdir" case "$finalize_rpath " in *" $libdir "*) ;; *) finalize_rpath="$finalize_rpath $libdir" ;; esac done if test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes; then dependency_libs="$temp_xrpath $dependency_libs" fi fi # Make sure dlfiles contains only unique files that won't be dlpreopened old_dlfiles="$dlfiles" dlfiles= for lib in $old_dlfiles; do case " $dlprefiles $dlfiles " in *" $lib "*) ;; *) dlfiles="$dlfiles $lib" ;; esac done # Make sure dlprefiles contains only unique files old_dlprefiles="$dlprefiles" dlprefiles= for lib in $old_dlprefiles; do case "$dlprefiles " in *" $lib "*) ;; *) dlprefiles="$dlprefiles $lib" ;; esac done if test "$build_libtool_libs" = yes; then if test -n "$rpath"; then case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-beos*) # these systems don't actually have a c library (as such)! ;; *-*-rhapsody* | *-*-darwin1.[012]) # Rhapsody C library is in the System framework deplibs="$deplibs -framework System" ;; *-*-netbsd*) # Don't link with libc until the a.out ld.so is fixed. ;; *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) # Do not include libc due to us having libc/libc_r. test "X$arg" = "X-lc" && continue ;; *) # Add libc to deplibs on all other systems if necessary. if test "$build_libtool_need_lc" = "yes"; then deplibs="$deplibs -lc" fi ;; esac fi # Transform deplibs into only deplibs that can be linked in shared. name_save=$name libname_save=$libname release_save=$release versuffix_save=$versuffix major_save=$major # I'm not sure if I'm treating the release correctly. I think # release should show up in the -l (ie -lgmp5) so we don't want to # add it in twice. Is that correct? release="" versuffix="" major="" newdeplibs= droppeddeps=no case $deplibs_check_method in pass_all) # Don't check for shared/static. Everything works. # This might be a little naive. We might want to check # whether the library exists or not. But this is on # osf3 & osf4 and I'm not really sure... Just # implementing what was already the behavior. newdeplibs=$deplibs ;; test_compile) # This code stresses the "libraries are programs" paradigm to its # limits. Maybe even breaks it. We compile a program, linking it # against the deplibs as a proxy for the library. 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fi # Do each of the archive commands. if test "$module" = yes && test -n "$module_cmds" ; then if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then eval test_cmds=\"$module_expsym_cmds\" cmds=$module_expsym_cmds else eval test_cmds=\"$module_cmds\" cmds=$module_cmds fi else if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then eval test_cmds=\"$archive_expsym_cmds\" cmds=$archive_expsym_cmds else eval test_cmds=\"$archive_cmds\" cmds=$archive_cmds fi fi if test "X$skipped_export" != "X:" && len=`expr "X$test_cmds" : ".*"` && test "$len" -le "$max_cmd_len" || test "$max_cmd_len" -le -1; then : else # The command line is too long to link in one step, link piecewise. $echo "creating reloadable object files..." # Save the value of $output and $libobjs because we want to # use them later. 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IN NO EVENT SHALL THE # X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN # AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC- # TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # # Except as contained in this notice, the name of the X Consortium shall not # be used in advertising or otherwise to promote the sale, use or other deal- # ings in this Software without prior written authorization from the X Consor- # tium. # # # FSF changes to this file are in the public domain. # # Calling this script install-sh is preferred over install.sh, to prevent # `make' implicit rules from creating a file called install from it # when there is no Makefile. # # This script is compatible with the BSD install script, but was written # from scratch. nl=' ' IFS=" "" $nl" # set DOITPROG to echo to test this script # Don't use :- since 4.3BSD and earlier shells don't like it. doit=${DOITPROG-} if test -z "$doit"; then doit_exec=exec else doit_exec=$doit fi # Put in absolute file names if you don't have them in your path; # or use environment vars. chgrpprog=${CHGRPPROG-chgrp} chmodprog=${CHMODPROG-chmod} chownprog=${CHOWNPROG-chown} cmpprog=${CMPPROG-cmp} cpprog=${CPPROG-cp} mkdirprog=${MKDIRPROG-mkdir} mvprog=${MVPROG-mv} rmprog=${RMPROG-rm} stripprog=${STRIPPROG-strip} posix_glob='?' initialize_posix_glob=' test "$posix_glob" != "?" || { if (set -f) 2>/dev/null; then posix_glob= else posix_glob=: fi } ' posix_mkdir= # Desired mode of installed file. mode=0755 chgrpcmd= chmodcmd=$chmodprog chowncmd= mvcmd=$mvprog rmcmd="$rmprog -f" stripcmd= src= dst= dir_arg= dst_arg= copy_on_change=false no_target_directory= usage="\ Usage: $0 [OPTION]... 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It does not imply ALL GNU software can. # # This file is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA # 02110-1301, USA. # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Please send patches to . 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The user should be able to distinguish # a failure to support a valid configuration from a meaningless # configuration. # The goal of this file is to map all the various variations of a given # machine specification into a single specification in the form: # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM # or in some cases, the newer four-part form: # CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM # It is wrong to echo any other type of specification. me=`echo "$0" | sed -e 's,.*/,,'` usage="\ Usage: $0 [OPTION] CPU-MFR-OPSYS $0 [OPTION] ALIAS Canonicalize a configuration name. Operation modes: -h, --help print this help, then exit -t, --time-stamp print date of last modification, then exit -v, --version print version number, then exit Report bugs and patches to ." version="\ GNU config.sub ($timestamp) Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." help=" Try \`$me --help' for more information." # Parse command line while test $# -gt 0 ; do case $1 in --time-stamp | --time* | -t ) echo "$timestamp" ; exit ;; --version | -v ) echo "$version" ; exit ;; --help | --h* | -h ) echo "$usage"; exit ;; -- ) # Stop option processing shift; break ;; - ) # Use stdin as input. break ;; -* ) echo "$me: invalid option $1$help" exit 1 ;; *local*) # First pass through any local machine types. echo $1 exit ;; * ) break ;; esac done case $# in 0) echo "$me: missing argument$help" >&2 exit 1;; 1) ;; *) echo "$me: too many arguments$help" >&2 exit 1;; esac # Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any). # Here we must recognize all the valid KERNEL-OS combinations. maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` case $maybe_os in nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \ uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \ kopensolaris*-gnu* | \ storm-chaos* | os2-emx* | rtmk-nova*) os=-$maybe_os basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'` ;; *) basic_machine=`echo $1 | sed 's/-[^-]*$//'` if [ $basic_machine != $1 ] then os=`echo $1 | sed 's/.*-/-/'` else os=; fi ;; esac ### Let's recognize common machines as not being operating systems so ### that things like config.sub decstation-3100 work. We also ### recognize some manufacturers as not being operating systems, so we ### can provide default operating systems below. case $os in -sun*os*) # Prevent following clause from handling this invalid input. ;; -dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \ -att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \ -unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \ -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\ -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \ -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \ -apple | -axis | -knuth | -cray) os= basic_machine=$1 ;; -sim | -cisco | -oki | -wec | -winbond) os= basic_machine=$1 ;; -scout) ;; -wrs) os=-vxworks basic_machine=$1 ;; -chorusos*) os=-chorusos basic_machine=$1 ;; -chorusrdb) os=-chorusrdb basic_machine=$1 ;; -hiux*) os=-hiuxwe2 ;; -sco6) os=-sco5v6 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco5) os=-sco3.2v5 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco4) os=-sco3.2v4 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco3.2.[4-9]*) os=`echo $os | sed -e 's/sco3.2./sco3.2v/'` basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco3.2v[4-9]*) # Don't forget version if it is 3.2v4 or newer. basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco5v6*) # Don't forget version if it is 3.2v4 or newer. basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco*) os=-sco3.2v2 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -udk*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -isc) os=-isc2.2 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -clix*) basic_machine=clipper-intergraph ;; -isc*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -lynx*) os=-lynxos ;; -ptx*) basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'` ;; -windowsnt*) os=`echo $os | sed -e 's/windowsnt/winnt/'` ;; -psos*) os=-psos ;; -mint | -mint[0-9]*) basic_machine=m68k-atari os=-mint ;; esac # Decode aliases for certain CPU-COMPANY combinations. case $basic_machine in # Recognize the basic CPU types without company name. # Some are omitted here because they have special meanings below. 1750a | 580 \ | a29k \ | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \ | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \ | am33_2.0 \ | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \ | bfin \ | c4x | clipper \ | d10v | d30v | dlx | dsp16xx \ | fido | fr30 | frv \ | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ | i370 | i860 | i960 | ia64 \ | ip2k | iq2000 \ | lm32 \ | m32c | m32r | m32rle | m68000 | m68k | m88k \ | maxq | mb | microblaze | mcore | mep | metag \ | mips | mipsbe | mipseb | mipsel | mipsle \ | mips16 \ | mips64 | mips64el \ | mips64octeon | mips64octeonel \ | mips64orion | mips64orionel \ | mips64r5900 | mips64r5900el \ | mips64vr | mips64vrel \ | mips64vr4100 | mips64vr4100el \ | mips64vr4300 | mips64vr4300el \ | mips64vr5000 | mips64vr5000el \ | mips64vr5900 | mips64vr5900el \ | mipsisa32 | mipsisa32el \ | mipsisa32r2 | mipsisa32r2el \ | mipsisa64 | mipsisa64el \ | mipsisa64r2 | mipsisa64r2el \ | mipsisa64sb1 | mipsisa64sb1el \ | mipsisa64sr71k | mipsisa64sr71kel \ | mipstx39 | mipstx39el \ | mn10200 | mn10300 \ | moxie \ | mt \ | msp430 \ | nios | nios2 \ | ns16k | ns32k \ | or32 \ | pdp10 | pdp11 | pj | pjl \ | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \ | pyramid \ | score \ | sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \ | sh64 | sh64le \ | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \ | sparcv8 | sparcv9 | sparcv9b | sparcv9v \ | spu | strongarm \ | tahoe | thumb | tic4x | tic80 | tron \ | v850 | v850e \ | we32k \ | x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \ | z8k | z80) basic_machine=$basic_machine-unknown ;; m6811 | m68hc11 | m6812 | m68hc12) # Motorola 68HC11/12. basic_machine=$basic_machine-unknown os=-none ;; m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k) ;; ms1) basic_machine=mt-unknown ;; # We use `pc' rather than `unknown' # because (1) that's what they normally are, and # (2) the word "unknown" tends to confuse beginning users. i*86 | x86_64) basic_machine=$basic_machine-pc ;; # Object if more than one company name word. *-*-*) echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 exit 1 ;; # Recognize the basic CPU types with company name. 580-* \ | a29k-* \ | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \ | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \ | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \ | arm-* | armbe-* | armle-* | armeb-* | armv*-* \ | avr-* | avr32-* \ | bfin-* | bs2000-* \ | c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \ | clipper-* | craynv-* | cydra-* \ | d10v-* | d30v-* | dlx-* \ | elxsi-* \ | f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \ | h8300-* | h8500-* \ | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \ | i*86-* | i860-* | i960-* | ia64-* \ | ip2k-* | iq2000-* \ | lm32-* \ | m32c-* | m32r-* | m32rle-* \ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \ | m88110-* | m88k-* | maxq-* | mcore-* | metag-* \ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \ | mips16-* \ | mips64-* | mips64el-* \ | mips64octeon-* | mips64octeonel-* \ | mips64orion-* | mips64orionel-* \ | mips64r5900-* | mips64r5900el-* \ | mips64vr-* | mips64vrel-* \ | mips64vr4100-* | mips64vr4100el-* \ | mips64vr4300-* | mips64vr4300el-* \ | mips64vr5000-* | mips64vr5000el-* \ | mips64vr5900-* | mips64vr5900el-* \ | mipsisa32-* | mipsisa32el-* \ | mipsisa32r2-* | mipsisa32r2el-* \ | mipsisa64-* | mipsisa64el-* \ | mipsisa64r2-* | mipsisa64r2el-* \ | mipsisa64sb1-* | mipsisa64sb1el-* \ | mipsisa64sr71k-* | mipsisa64sr71kel-* \ | mipstx39-* | mipstx39el-* \ | mmix-* \ | mt-* \ | msp430-* \ | nios-* | nios2-* \ | none-* | np1-* | ns16k-* | ns32k-* \ | orion-* \ | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \ | pyramid-* \ | romp-* | rs6000-* \ | sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \ | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \ | sparclite-* \ | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \ | tahoe-* | thumb-* \ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* | tile-* \ | tron-* \ | v850-* | v850e-* | vax-* \ | we32k-* \ | x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \ | xstormy16-* | xtensa*-* \ | ymp-* \ | z8k-* | z80-*) ;; # Recognize the basic CPU types without company name, with glob match. xtensa*) basic_machine=$basic_machine-unknown ;; # Recognize the various machine names and aliases which stand # for a CPU type and a company and sometimes even an OS. 386bsd) basic_machine=i386-unknown os=-bsd ;; 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc) basic_machine=m68000-att ;; 3b*) basic_machine=we32k-att ;; a29khif) basic_machine=a29k-amd os=-udi ;; abacus) basic_machine=abacus-unknown ;; adobe68k) basic_machine=m68010-adobe os=-scout ;; alliant | fx80) basic_machine=fx80-alliant ;; altos | altos3068) basic_machine=m68k-altos ;; am29k) basic_machine=a29k-none os=-bsd ;; amd64) basic_machine=x86_64-pc ;; amd64-*) basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'` ;; amdahl) basic_machine=580-amdahl os=-sysv ;; amiga | amiga-*) basic_machine=m68k-unknown ;; amigaos | amigados) basic_machine=m68k-unknown os=-amigaos ;; amigaunix | amix) basic_machine=m68k-unknown os=-sysv4 ;; apollo68) basic_machine=m68k-apollo os=-sysv ;; apollo68bsd) basic_machine=m68k-apollo os=-bsd ;; aros) basic_machine=i386-pc os=-aros ;; aux) basic_machine=m68k-apple os=-aux ;; balance) basic_machine=ns32k-sequent os=-dynix ;; blackfin) basic_machine=bfin-unknown os=-linux ;; blackfin-*) basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; c90) basic_machine=c90-cray os=-unicos ;; cegcc) basic_machine=arm-unknown os=-cegcc ;; convex-c1) basic_machine=c1-convex os=-bsd ;; convex-c2) basic_machine=c2-convex os=-bsd ;; convex-c32) basic_machine=c32-convex os=-bsd ;; convex-c34) basic_machine=c34-convex os=-bsd ;; convex-c38) basic_machine=c38-convex os=-bsd ;; cray | j90) basic_machine=j90-cray os=-unicos ;; craynv) basic_machine=craynv-cray os=-unicosmp ;; cr16) basic_machine=cr16-unknown os=-elf ;; crds | unos) basic_machine=m68k-crds ;; crisv32 | crisv32-* | etraxfs*) basic_machine=crisv32-axis ;; cris | cris-* | etrax*) basic_machine=cris-axis ;; crx) basic_machine=crx-unknown os=-elf ;; da30 | da30-*) basic_machine=m68k-da30 ;; decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn) basic_machine=mips-dec ;; decsystem10* | dec10*) basic_machine=pdp10-dec os=-tops10 ;; decsystem20* | dec20*) basic_machine=pdp10-dec os=-tops20 ;; delta | 3300 | motorola-3300 | motorola-delta \ | 3300-motorola | delta-motorola) basic_machine=m68k-motorola ;; delta88) basic_machine=m88k-motorola os=-sysv3 ;; dicos) basic_machine=i686-pc os=-dicos ;; djgpp) basic_machine=i586-pc os=-msdosdjgpp ;; dpx20 | dpx20-*) basic_machine=rs6000-bull os=-bosx ;; dpx2* | dpx2*-bull) basic_machine=m68k-bull os=-sysv3 ;; ebmon29k) basic_machine=a29k-amd os=-ebmon ;; elxsi) basic_machine=elxsi-elxsi os=-bsd ;; encore | umax | mmax) basic_machine=ns32k-encore ;; es1800 | OSE68k | ose68k | ose | OSE) basic_machine=m68k-ericsson os=-ose ;; fx2800) basic_machine=i860-alliant ;; genix) basic_machine=ns32k-ns ;; gmicro) basic_machine=tron-gmicro os=-sysv ;; go32) basic_machine=i386-pc os=-go32 ;; h3050r* | hiux*) basic_machine=hppa1.1-hitachi os=-hiuxwe2 ;; h8300hms) basic_machine=h8300-hitachi os=-hms ;; h8300xray) basic_machine=h8300-hitachi os=-xray ;; h8500hms) basic_machine=h8500-hitachi os=-hms ;; harris) basic_machine=m88k-harris os=-sysv3 ;; hp300-*) basic_machine=m68k-hp ;; hp300bsd) basic_machine=m68k-hp os=-bsd ;; hp300hpux) basic_machine=m68k-hp os=-hpux ;; hp3k9[0-9][0-9] | hp9[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k2[0-9][0-9] | hp9k31[0-9]) basic_machine=m68000-hp ;; hp9k3[2-9][0-9]) basic_machine=m68k-hp ;; hp9k6[0-9][0-9] | hp6[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k7[0-79][0-9] | hp7[0-79][0-9]) basic_machine=hppa1.1-hp ;; hp9k78[0-9] | hp78[0-9]) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[0-9][13679] | hp8[0-9][13679]) basic_machine=hppa1.1-hp ;; hp9k8[0-9][0-9] | hp8[0-9][0-9]) basic_machine=hppa1.0-hp ;; hppa-next) os=-nextstep3 ;; hppaosf) basic_machine=hppa1.1-hp os=-osf ;; hppro) basic_machine=hppa1.1-hp os=-proelf ;; i370-ibm* | ibm*) basic_machine=i370-ibm ;; # I'm not sure what "Sysv32" means. Should this be sysv3.2? i*86v32) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv32 ;; i*86v4*) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv4 ;; i*86v) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv ;; i*86sol2) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-solaris2 ;; i386mach) basic_machine=i386-mach os=-mach ;; i386-vsta | vsta) basic_machine=i386-unknown os=-vsta ;; iris | iris4d) basic_machine=mips-sgi case $os in -irix*) ;; *) os=-irix4 ;; esac ;; isi68 | isi) basic_machine=m68k-isi os=-sysv ;; m68knommu) basic_machine=m68k-unknown os=-linux ;; m68knommu-*) basic_machine=m68k-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; m88k-omron*) basic_machine=m88k-omron ;; magnum | m3230) basic_machine=mips-mips os=-sysv ;; merlin) basic_machine=ns32k-utek os=-sysv ;; mingw32) basic_machine=i386-pc os=-mingw32 ;; mingw32ce) basic_machine=arm-unknown os=-mingw32ce ;; miniframe) basic_machine=m68000-convergent ;; *mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*) basic_machine=m68k-atari os=-mint ;; mips3*-*) basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'` ;; mips3*) basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown ;; monitor) basic_machine=m68k-rom68k os=-coff ;; morphos) basic_machine=powerpc-unknown os=-morphos ;; msdos) basic_machine=i386-pc os=-msdos ;; ms1-*) basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'` ;; mvs) basic_machine=i370-ibm os=-mvs ;; ncr3000) basic_machine=i486-ncr os=-sysv4 ;; netbsd386) basic_machine=i386-unknown os=-netbsd ;; netwinder) basic_machine=armv4l-rebel os=-linux ;; news | news700 | news800 | news900) basic_machine=m68k-sony os=-newsos ;; news1000) basic_machine=m68030-sony os=-newsos ;; news-3600 | risc-news) basic_machine=mips-sony os=-newsos ;; necv70) basic_machine=v70-nec os=-sysv ;; next | m*-next ) basic_machine=m68k-next case $os in -nextstep* ) ;; -ns2*) os=-nextstep2 ;; *) os=-nextstep3 ;; esac ;; nh3000) basic_machine=m68k-harris os=-cxux ;; nh[45]000) basic_machine=m88k-harris os=-cxux ;; nindy960) basic_machine=i960-intel os=-nindy ;; mon960) basic_machine=i960-intel os=-mon960 ;; nonstopux) basic_machine=mips-compaq os=-nonstopux ;; np1) basic_machine=np1-gould ;; nsr-tandem) basic_machine=nsr-tandem ;; op50n-* | op60c-*) basic_machine=hppa1.1-oki os=-proelf ;; openrisc | openrisc-*) basic_machine=or32-unknown ;; os400) basic_machine=powerpc-ibm os=-os400 ;; OSE68000 | ose68000) basic_machine=m68000-ericsson os=-ose ;; os68k) basic_machine=m68k-none os=-os68k ;; pa-hitachi) basic_machine=hppa1.1-hitachi os=-hiuxwe2 ;; paragon) basic_machine=i860-intel os=-osf ;; parisc) basic_machine=hppa-unknown os=-linux ;; parisc-*) basic_machine=hppa-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; pbd) basic_machine=sparc-tti ;; pbb) basic_machine=m68k-tti ;; pc532 | pc532-*) basic_machine=ns32k-pc532 ;; pc98) basic_machine=i386-pc ;; pc98-*) basic_machine=i386-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentium | p5 | k5 | k6 | nexgen | viac3) basic_machine=i586-pc ;; pentiumpro | p6 | 6x86 | athlon | athlon_*) basic_machine=i686-pc ;; pentiumii | pentium2 | pentiumiii | pentium3) basic_machine=i686-pc ;; pentium4) basic_machine=i786-pc ;; pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*) basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentiumpro-* | p6-* | 6x86-* | athlon-*) basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*) basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentium4-*) basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pn) basic_machine=pn-gould ;; power) basic_machine=power-ibm ;; ppc) basic_machine=powerpc-unknown ;; ppc-*) basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ppcle | powerpclittle | ppc-le | powerpc-little) basic_machine=powerpcle-unknown ;; ppcle-* | powerpclittle-*) basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ppc64) basic_machine=powerpc64-unknown ;; ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ppc64le | powerpc64little | ppc64-le | powerpc64-little) basic_machine=powerpc64le-unknown ;; ppc64le-* | powerpc64little-*) basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ps2) basic_machine=i386-ibm ;; pw32) basic_machine=i586-unknown os=-pw32 ;; rdos) basic_machine=i386-pc os=-rdos ;; rom68k) basic_machine=m68k-rom68k os=-coff ;; rm[46]00) basic_machine=mips-siemens ;; rtpc | rtpc-*) basic_machine=romp-ibm ;; s390 | s390-*) basic_machine=s390-ibm ;; s390x | s390x-*) basic_machine=s390x-ibm ;; sa29200) basic_machine=a29k-amd os=-udi ;; sb1) basic_machine=mipsisa64sb1-unknown ;; sb1el) basic_machine=mipsisa64sb1el-unknown ;; sde) basic_machine=mipsisa32-sde os=-elf ;; sei) basic_machine=mips-sei os=-seiux ;; sequent) basic_machine=i386-sequent ;; sh) basic_machine=sh-hitachi os=-hms ;; sh5el) basic_machine=sh5le-unknown ;; sh64) basic_machine=sh64-unknown ;; sparclite-wrs | simso-wrs) basic_machine=sparclite-wrs os=-vxworks ;; sps7) basic_machine=m68k-bull os=-sysv2 ;; spur) basic_machine=spur-unknown ;; st2000) basic_machine=m68k-tandem ;; stratus) basic_machine=i860-stratus os=-sysv4 ;; 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E}{/rx xr w mul 200 div d/ry yr h mul 200 div d/rx2 rx 2 mul d/ry2 ry 2 mul d NP x rx add y MT x y rx2 ry2 180 -90 x y h add ry2 sub rx2 ry2 270 -90 x w add rx2 sub y h add ry2 sub rx2 ry2 0 -90 x w add rx2 sub y rx2 ry2 90 -90 ARC ARC ARC ARC CP BF QS}ifelse}ifelse}D/E{/h ED/w ED/y ED/x ED mat CM pop x w 2 div add y h 2 div add translate 1 h w div scale NP 0 0 w 2 div 0 360 arc mat SM BF QS}D/A{16 div exch 16 div exch NP ARC QS}D/PIE{/ang2 ED/ang1 ED/h ED/w ED/y ED/x ED NP x w 2 div add y h 2 div add MT x y w h ang1 16 div ang2 16 div ARC CP BF QS}D/CH{16 div exch 16 div exch NP ARC CP BF QS}D/BZ{curveto QS}D /CRGB{255 div 3 1 roll 255 div 3 1 roll 255 div 3 1 roll}D/SV{BSt LWi PSt Cx Cy WFi OMo BCol PCol BkCol/nS nS 1 add d gsave}D/RS{nS 0 gt{grestore/BkCol ED/PCol ED/BCol ED/OMo ED/WFi ED/Cy ED/Cx ED/PSt ED/LWi ED/BSt ED/nS nS 1 sub d}if}D/BC {CRGB BkCol astore pop}D/BR{CRGB BCol astore pop/BSt ED}D/WB{1 W BR}D/NB{0 B BR }D/PE{setlinejoin setlinecap CRGB PCol astore pop/LWi ED/PSt ED LWi 0 eq{0.25 /LWi ED}if}D/P1{1 0 5 2 roll 0 0 PE}D/ST{defM setmatrix concat}D/qtfindfont{ true exch true exch{exch pop exch pop dup 0 get dup findfont dup/FontName get 3 -1 roll eq{exit}if}forall exch}d/qtdefinefont{dup 1 get/fxscale exch def 2 get /fslant exch def exch/fencoding exch def[fxscale 0 fslant 1 0 0]makefont fencoding false eq{}{dup maxlength dict begin{1 index/FID ne{def}{pop pop} ifelse}forall/Encoding fencoding def currentdict end}ifelse definefont pop}d/MF {qtfindfont qtdefinefont}D/MSF{findfont exch/slant exch d[1 0 slant 1 0 0] makefont definefont pop}D/DF{findfont/FONTSIZE 3 -1 roll d[FONTSIZE 0 0 FONTSIZE -1 mul 0 0]makefont d}D/ty 0 d/Y{/ty ED}D/Tl{NP 1 index exch MT 1 index 0 rlineto QS}D/T{PCol SC ty MT 1 index dup length exch stringwidth pop 3 -1 roll exch sub exch div exch 0 exch ashow}D/QI{/C save d pageinit/Cx 0 d/Cy 0 d/OMo false d}D/QP{C restore showpage}D %%EndProlog %%BeginSetup /pageinit { % 210*297mm (portrait) 0 842 translate 1 -1 scale/defM matrix 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Generally T will be the floating point type, but in some cases vectors of \c int are used. Vec3<> also defines various simple arithmetic operations, including addition, subtraction, negation, and scaling. Any coordinate type may be constructed from a Vec3<> by using an explicit constructor. (Implicit conversion is not allowed, since this would allow accidental type conversion between coordinate types). The elements of the vector may be accessed as v[0], v[1], and v[2], however the coordinate types all define type-specific names for the members. Similarly, clipper::Mat33 provides a template class for a 3x3 matrix of values. Matrix-vector and matrix-matrix products are defined. If a vector pre-multiplies a matrix, it is assumed that the vector is a row rather than column vector. Symmetric matrices are common on crystallography, so a type is defined for these; clipper::Mat33sym. This does not define any operations except conversion to or from Mat33. This form is therefore used mainly for packed storage of some quantities, such as anisotropic U values. Rotation-translation operators are provided by the clipper::RTop template class. A rotation-translation operator consists of a rotation defined by a Mat33, and a translation defined by a Vec3. The matrix and vector components may be accessed through the rot() and trn() methods. RTop's may be applied to vectors or combined using the '*' operator. \section s_ctcoord Coordinate types \subsection s_ctrecip Reciprocal space coordinate types \par HKL The integral index (sometimes referred to as a Miller index) of a reflection. It has components h, k, and l. \par Coord_reci_frac Reciprocal space fractional coordinate. This is identical to an HKL, except that the values are floating point. This would commonly be used in rotation function calculations when interpolation is required in reciprocal space. \par Coord_reci_orth Reciprocal space orthogonal coordinate. This is a coordinate defined in inverse Angstroms along three orthogonal axes. The exact convention for selection of these axes is defined by the clipper::Cell class. \subsection ss_ctreal Real space coordinate types \par Coord_orth Orthogonal coordinate in Angstroms. This is a coordinate defined in Angstroms along three orthogonal axes. The exact convention for selection of these axes is defined by the clipper::Cell class. \par Coord_frac Fractional (crystal) coordinate. This is defined as the fractional position in the unit cell, with each component traversing a unique cell over the range (0..1). \par Coord_map Map coordinate. This is a floating point coordinate representing a position in the frame of a map. In the case of a crystallographic map, this will simply be the fractional coordinate scaled by the grid sampling of the unit cell (not the asymmetric unit). However in most cases Coord_frac is used in preference for crystallographic maps. In the case of a non-crystallographic map, fractional coordinates are undefined, but the NXmap will define a conversion between orthogonal and map coordinates. \par Coord_grid Map grid coordinate. This is the integer version of a Coord_map, and represents the index of a grid point in a map. The origin is always at the origin of the coordinate frame of the map, thus for crystallographic maps the origin is the crystallographic origin. For non-crystallographic maps, the origin is the first grid point in the map. \section s_ctderiv Derivative types Derivatives and curvatures may be with respect to orthogonal, fractional, or map coordinates. When performing calculations on a crystallographic map, derivatives are usually with respect to fractional coordinates, however map coordinates may be used if preferred. The resulting derivatives may then be converted to orthogonal coordinates if necessary. When performing calculations on a non-crystallographic map, derivatives are calculated with respect to map coordinates. Derivatives are stored as Vec3<> with the template type matching the type of the map. Curvatures are stored as a Mat33<>. \section s_ctops Operator Types Two types of rotation-translation operators are defined as special cases of RTop<> with a floating point template type. \par RTop_frac This is a rotation-translation operator defined on fractional coordinates. A Crystallographic symmetry operator is an example of this type, and in fact Symop is derived from this class. \par RTop_orth This is a rotation-translation operator defined on orthogonal coordinates. A non-crystallographic symmetry operator is an example of this type. \section s_ctother Other types Anisotropic atomic displacement parameters (ADPs) are also defined. These are derived from Mat33sym<> with a floating point template type. There are two types: \par U_aniso_orth Anisotropic atomic displacement parameters defined on orthogonal Angstrom coordinates, as used in PDB files. The terms have units of inverse angstroms squared. \par U_aniso_frac Anisotropic atomic displacement parameters defined on fractional coordinates. \section s_ctconv Conversion of coordinates and related types Coordinates and related types are converted by the following means: - Any fraction coordinate, gradient, curvature, operator, or ADP (with the \c _frac suffix) may be converted to an orthogonal coordinate, etc. (with the \c _orth suffix) or vice-versa using the appropriate method of the Cell class. The name of the required method is always the return type in lower case. e.g. to convert a clipper::Coord_orth to a clipper::Coord_frac, call the clipper::Cell::coord_frac() method of the appropriate clipper::Cell object. - A real space fractional coordinate, gradient, or curvature may be converted to a map coordinate, gradient, or curvature or vice-versa, by using the appropriate method of the clipper::Grid_sampling class. The name of the required method is always the return type in lower case. Fractional coordinates may also be converted directly to grid coordinates and vice-versa. - Coord_grid can be converted directly to Coord_map using the appropriate constructor. Coord_map can be converted to Coord_grid using a method specifying the type of rounding required. - Coord_map for a non-crystallographic map may be converted to a Coord_orth or vice-versa using the methods of the clipper::NXmap object concerned. */ clipper-2.1/dox/img_container.eps0000644000374100011300000001302110736662154014055 00000000000000%!PS-Adobe-2.0 %%Creator: dot version gviz 1.7.3b (Mon Feb 26 14:10:22 EST 2001) %%For: (cowtan) Kevin Cowtan %%Title: G %%Pages: (atend) %%BoundingBox: 36 36 251 233 %%EndComments %%BeginProlog save /DotDict 200 dict def DotDict begin %%BeginResource: procset /coord-font-family /Times-Roman def /default-font-family /Times-Roman def /coordfont coord-font-family findfont 8 scalefont def /InvScaleFactor 1.0 def /set_scale { dup 1 exch div /InvScaleFactor exch def dup scale } bind def % styles /solid { } bind def /dashed { [9 InvScaleFactor mul dup ] 0 setdash } bind def /dotted { [1 InvScaleFactor mul 6 InvScaleFactor mul] 0 setdash } bind def /invis {/fill {newpath} def /stroke {newpath} def /show {pop newpath} def} bind def /bold { 2 setlinewidth } bind def /filled { } bind def /unfilled { } bind def /rounded { } bind def /diagonals { } bind def % hooks for setting color /nodecolor { sethsbcolor } bind def /edgecolor { sethsbcolor } bind def /graphcolor { sethsbcolor } bind def /nopcolor {pop pop pop} bind def /beginpage { % i j npages /npages exch def /j exch def /i exch def /str 10 string def npages 1 gt { gsave coordfont setfont 0 0 moveto (\() show i str cvs show (,) show j str cvs show (\)) show grestore } if } bind def /set_font { findfont exch scalefont setfont } def % draw aligned label in bounding box aligned to current point % alignfactor tells what fraction to place on the left. % -.5 is centered. /alignedtext { % text labelwidth fontsz alignfactor /alignfactor exch def /fontsz exch def /width exch def /text exch def gsave % even if node or edge is dashed, don't paint text with dashes [] 0 setdash currentpoint newpath moveto text stringwidth pop alignfactor mul fontsz -.3 mul rmoveto text show grestore } def /boxprim { % xcorner ycorner xsize ysize 4 2 roll moveto 2 copy exch 0 rlineto 0 exch rlineto pop neg 0 rlineto closepath } bind def /ellipse_path { /ry exch def /rx exch def /y exch def /x exch def matrix currentmatrix newpath x y translate rx ry scale 0 0 1 0 360 arc setmatrix } bind def /endpage { showpage } bind def /layercolorseq [ % layer color sequence - 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The first stores a list of reflections (HKLs), and the second stores a list of data of some type for each reflection. Why is this division made? Because often, many types of data will be stored for the same reflection list, and duplicating the list of reflections for each data list would be wasteful. The relationship of an HKL_info object and several HKL_data<> objects is shown below. \image html hkl_objs.png \image latex hkl_objs.eps width=8cm These objects handle all the crystallographic symmetry operations associated with storing data in reciprocal space. To the programmer, the data appears to fill a sphere of reciprocal space. However, only a unique set of data is stored, and any changes to a data values are automatically reflected in the symmetry and Friedel related reflections. \section s_hklinf The HKL_info object The HKL_info object stores a list of reflections, transformed into a standard reciprocal space asymmetric unit. For example: - \b P1: data is stored for l>0 or (l=0 and (h>0 or (h=0 and k>=0))) - \b P2: data is stored for k>=0 and (l>0 or (l=0 and h>=0)) - \b P212121: data is stored for h>=0 and k>=0 and l>=0 However, the programmer should never need to know which asymmetric unit is being used, as data in other parts of reciprocal space are generated automatically. The HKL_info object also stores a lookup table, which is used to rapidly determine the location in the list of a given HKL. It also stores lookup tables for the reflection class (HKL_class) and resolution (invresolsq). The reflection list depends upon the spacegroup (which determines the reciprocal asymmetric unit and systematic absences), the cell parameters, and the resolution limit. Therefore to initialise an HKL_info object, objects of types Spacegroup, Cell and Resolution are passed to the constructor or initialiser. \par Reflection classes The 'class' of a reflection is a function of its HKL and the spacegroup, and describes whether it is centric, systematically absent, and what its allowed phase and symmetry enhancement factor or multiplicity are (i.e. epsilon). The class of a reflection is described by the class clipper::HKL_class. \par Reflection resolution The resolution of a reflection is a function of its HKL and the unit cell parameters. It is generally handled in terms of the inverse resolution squared, or 'invresolsq'. This is equal to \f$ 4\sin^2 \theta / \lambda^2 \f$. \section s_hkldata The HKL_data<> object The data object is not much more than an array of data, but it has a number of special methods to make crystallographic operations on that data more convenient. It is defined as a template class, where the template type is the type of crystallographic information to be stored in the object. It simply stores a list of data of that type, and a pointer to the parent HKL_info object, which defined the HKL for each element in the list. Additionally a pointer to a Cell object is stored, which may optionally be used for the case where different data comes from slight different unit cells (e.g. RT and frozen data). Therefore to initialise an HKL_data object, an HKL_info object and optionally a Cell object are passed to the constructor or initialiser. Data types typically include several values. Examples include measured X-ray intensity and its standard deviation (I_sigI), structure factor magnitude and phase (F_sigF), and Hendrickson-Lattman coefficients (ABCD). Data types are derived from a base type (Datatype_base), and should override all the methods of that type. This will allow the data to be automatically transformed about reciprocal space, and imported or exported to a file, as required. Methods are provided to access the data by index or by HKL. Any transformations which must be applied to the data in obtaining a symmetry or Friedel related value are applied automatically. In order to use the class efficiently, some important difficulties must be borne in mind. A problem arises when we wish to apply some transformation to the values stored in a data list. In this case, we must access every unique value in the asymmetric unit once and once only, applying the desired transformation. Only then will the entire data list have been transformed correctly. A second problem arises if we want to access the stored value of the data at some position in reciprocal space, for example to expand to a lower spacegroup. Then it is necessary to search through all the symmetry operators, applying each one in turn to the desired HKL to find the operator which brings the HKL into the stored asymmetric unit, with a Friedel inversion if necessary. Clearly this can be time consuming, especially if there are many symmetry operators. Both these problems are addressed by the use of HKL reference types. These come in two forms: - index-like references (clipper::HKL_info::HKL_reference_index) - coordinate-like references (clipper::HKL_info::HKL_reference_coord) The index-like reference behaves like an index: it stores a reference to an HKL_info object and a position in the reflection list. It is used to loop over all the values in the reflection list, using the HKL_info::first(), and HKL_reference_index::last() and HKL_reference_index::next() methods. The HKL corresponding to the index, its resolution, and reflection class can be returned at any point. The coordinate-like reference behaves like an HKL coordinate: it stores a reference to an HKL_info and an HKL. However to enhance performance it also stores the position in the list corresponding to that HKL, and the number of the symmetry operator used to get back into the stored asymmetric unit, along with a flag to signify Friedel inversion. Since reflections are usually accessed systematically, the next HKL used will commonly require the same symmetry operator, and so that operator is tried first. Methods are provided for incrementing and decrementing along the h, k, and l directions. The differences between the index-like and coordinate-like reference types can be summarised as follows: - index-like types can only refer to the position of a stored datum, i.e. reflection in this list. - coordinate-like types can refer to any possible position, and therefore also store the symmetry transformations required to get back to the stored data. HKL reference types may be shared between any data lists which have the same reflection list. It is the responsibility of the programmer to ensure this restriction is obeyed. \section s_hklcode HKL_data code fragments \subsection ss_hklio Importing and exporting HKL_data Currently objects are provided for import and export to CCP4 '.mtz' files and XtalView/SHELX '.phs' files. (More will be added later). To import a datalist from an MTZ files we need an HKL_info object to hold the reflection list and an HKL_data object to hold the actual data. We also need MTZdataset and MTZcrystal objects to hold the additional information which will be returned from the MTZ file. Then we create a CCP4MTZfile object, open it onto a file, and read the reflection list and data. \code clipper::HKL_info myhkl; // define objects clipper::MTZdataset myset; clipper::MTZcrystal myxtl; clipper::HKL_data fphidata( myhkl, myxtl ); clipper::CCP4MTZfile mtzin; mtzin.open_read( "my.mtz" ); // open new file mtzin.import_hkl_info( myhkl ); // read sg, cell, reso, hkls mtzin.import_hkl_data( fphidata, myset, myxtl, "native/CuKa/[FCAL PHICAL]" ); mtzin.close_read(); \endcode Similar functions are used for accessing XtalView/SHELX .phs files, although the interface is much simpler since these files do not contain labelled data. \subsection ss_hklexp Expanding reflection data to a lower symmetry To expand a list of data to a lower symmetry, we need two reflection lists, one for each spacegroup; and two datalists, one for each reflection list. The lower symmetry list is then filled by looping over all the reflections in that list an requesting the value from the other list for that HKL. \code clipper::HKL_info oldhkl( .... ); clipper::HKL_data olddata(oldhkl); // ---- fill the objects here ---- clipper::HKL_info newhkl( Spacegroup( Spgr_descr( 1 ) ), oldhkl.cell(), oldhkl.resolution() ); clipper::HKL_data newdata(oldhkl); HKL_info::HKL_reference_index ih; for ( ih = newhkl.first(); !ih.last; ih.next() ) { newdata[ih] = olddata[ih.hkl()]; } \endcode Note that the '.hkl' is vital, as we want the data with the corresponding hkl, not the data from the corresponding position in the list. If efficiency is paramount, using an HKL_reference_coord to access the old list will save some searches over the symmetry operators: \code clipper::HKL_info::HKL_reference_index ih; clipper::HKL_info::HKL_reference_coord ik( oldhkl ); for ( ih = newhkl.first(); !ih.last; ih.next() ) { ik.set_hkl( ih.hkl() ); newdata[ih] = olddata[ik]; } \endcode \subsection ss_hklconv Applying simple operations to a whole data list While it is simple to loop through a reflection list and apply some transformation on the data, some simple operations have been automated using built-in C++ arithmetic operators for data of specific types, logical operators for data or any type, comparison operators for flags, and function 'Computation operators' for more complex operations. \par Arithmetic operators. Arithmetic operators are defined for the addition, subtraction, and scaling of map coefficients (i.e. HKL_data), and for the addition and scaling of Hendrickson-Lattman coefficients (class HKL_data). Thus, to add two lists of map coefficients, the following code is required: \code clipper::HKL_data fphi1, fphi2, fphi3; // ---- set data here ---- fphi3 = fphi2 + fphi1; \endcode The columns are added using vector addition. If any values in either list are missing, then the result is missing. Subtraction is similar. Multiplication by a scalar scales the magnitude of every non-missing element in the list. \par Logical operators. Standard C/C++ bitwise logical operators (&, |, ^, !) may be applied to any data list. For each data in the list, the value 'true' will be returned if the data is not missing, or false if it is missing. The result of the operation is a new data list of type HKL_data, containing the results of the logical operation. This may be used in further logical operations, or may be used as a mask to eliminate data from a list using the HKL_data::mask() method. \par Comparison operators. Comparison operators (==, !=, >, <, >=, <=) may be applied to a data lists of flags (i.e. HKL_data), to compare the values in the list with a single integer. This is commonly used in the handling of Free-R test sets. The result is a list of HKL_data, where the value of the flag for each reflection is the result of the compraison of the frag for that reflection and this given integer. So, for example, to make a list of data containing only the values for which the test set is numbered 18 or greater, use the following code: \code clipper::HKL_data fsigf, fsigftest; clipper::HKL_data flag; // ---- set data here ---- fsigftest = fsigf; fsigftest.mask( flag >= 18 ); \endcode \par Computation operators Computation operators handle more complex crystallographic tasks, and will be discussed in more detail. To use a computation operator, call the compute() method of the destination datalist. This method must be supplied with one or two source datalists, and a computation operator. This is an object which performs the computation for an individual reflection, and is usually constructed on the fly. Some computation operators simply convert a datalist of one type to a datalist of another type. For example, you can convert a phase and weight to Hendrickson Lattman coefficients. (Of course C and D will be 0, because a phase and weight can only describe a unimodal distribution). \code clipper::HKL_data myphifom; // ---- set data here ---- clipper::HKL_data myabcd; myabcd.compute( myphifom, clipper::data32::Compute_abcd_from_phifom() ); \endcode Some computation operators take data from two datalists. For example, you can calculate map coefficient (magnitude and phase) from a set of observed magnitudes and a phase and weight: \code clipper::HKL_data myfsig; clipper::HKL_data myphifom; // ---- set data here ---- clipper::HKL_data myfphi; myfphi.compute( myfsig, myphifom, clipper::data32::Compute_fphi_from_fsigf_phifom() ); \endcode Computation operators may operate on a datalist itself, and can also take parameters. These parameters are passed to the constructor of the computation operator. For example, to apply a scale factor of 2.0 and and U-value of 0.5 to a list of reflections, use the following code: \code clipper::HKL_data myfsig; // ---- set data here ---- myfsig.compute( myfsig, clipper::data32::Compute_scale_u( 2.0, 0.5 ) ); \endcode Computation operators are provided for performing addition, subtraction and scaling of map coefficients (i.e. F_phi), addition and computation of Hendrickson Lattman coefficients, and for scaling data. It is fairly simple to define new computation operators, see core/hkl_compute.h. \section s_newdatatype Defining a new reflection datatype Several data types are defined in the file \c hkl_datatypes.h . Defining a new type proceeds as follows: -# Define a struct containing the data which needs to be stored for each reflection. A default constructor should be supplied which initialises all the data to NaN for floats, or an illegal value for ints (e.g. -1 for Free-R flag). -# Defined a member function `void friedel()' which changes the values of the data to the values of the Friedel opposite of the data. (e.g. a magnitude is unchanged, a phase will be negated). -# Defined a member function `void shift_phase(const float)' which chages the values of the data to the value of a symmetry equivalent with the given phase shift from the original. (e.g. a magnitude is unchanged, a phase will have the shift added to it). -# Define a member function `static const string type()' for that struct which returns a `type name' string for this type. This is used to identify the data type and to infer column names in an mtz file. For example, an F_phi group are defined as follows: \code struct F_phi { float f,phi; F_phi() { f=phi=Nan(); } static const String type() { return "F_phi"; } void friedel() { phi=-phi; } void shift_phase(const ftype dphi) { phi+=dphi; } const bool missing() const { return (isnan(f) || isnan(phi)); } }; \endcode The datalist types are constructed from the individual data type by a template class. If you need to store your new datatype in an MTZ file, you must also define an MTZ_iotype by derivation from clipper::MTZ_iotype_base, create a static instance of the new MTZ_iotype, and add it to the mtz_iotype_registry. */ clipper-2.1/dox/hierarchy.eps0000644000374100011300000005425310736662154013231 00000000000000%!PS-Adobe-2.0 %%Creator: dot version 1.7.11 (Fri Nov 16 14:55:37 GMT 2001) %%For: (cowtan) Kevin Cowtan %%Title: inheritance %%Pages: (atend) %%BoundingBox: 35 35 683 377 %%EndComments %%BeginProlog save /DotDict 200 dict def DotDict begin %%BeginResource: procset /coord-font-family /Times-Roman def /default-font-family /Times-Roman def /coordfont coord-font-family findfont 8 scalefont def /InvScaleFactor 1.0 def /set_scale { dup 1 exch div /InvScaleFactor exch def dup scale } bind def % styles /solid { } bind def /dashed { [9 InvScaleFactor mul dup ] 0 setdash } bind def /dotted { [1 InvScaleFactor mul 6 InvScaleFactor mul] 0 setdash } bind def /invis {/fill {newpath} def 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clipper-2.1/dox/conventions.dox0000644000374100011300000001261610736662154013620 00000000000000/*! \page p_conventions Conventions \section s_conv_intro Introduction This page discusses the conventions of coding style and memory management adopted in the Clipper libraries. \section s_notation Notation - Miller indices have componented h, k, l. - Fractional coordinates have components u, v, w. - Orthogonal coordinates have components x, y, z. - The squared distance from the origin in reciprocal space, in A-2, is usually referred to as 'invresolsq'. This is equal to \f$ 4\sin^2 \theta / \lambda^2 \f$ - Temperature factors and anisotrpic displacement parameters are always given as U-values. - Angles are always given in radians. \section s_codingstype Coding Style \subsection ss_dialect Dialect Clipper is written in C++, with extensive use of modern constructs such templates, and in particular the Standard Template Library (STL). The coding style of the library, and its API, both reflect this. In particular, a developer writing code using Clipper objects should be able to do so with minimal or no use of pointers, or of the built-in \c new and \c delete operators. References are used in preference to pointers where possible. Heap objects, with the corresponding dangers of memory leakage, are avoided. (However, for the cases where the developer needs to use heap objects, an optional mechanism is provided for automatic garbage collection). Clipper objects should generally be passed by reference rather than by value. \subsection ss_floatrep Floating-point representation. The package may be compiled to use either \c float or \c double for the representation of floating-point numbers. This is acheived by defining floating-point values with a user-defined type \c ftype. This is set by a \c typedef in lib/clipper_util.h. Data may have a different type. Since data objects may be large, these may be individually typed to save memory or provide additional precision as required. Data types are based on templates in lib/clipper_datatypes.h. The type for Fast-Fourier transforms is dependent on the FFTw library to which Clipper is linked. FFTw may be compiled for \c float or \c double. Since crystallographic FFTs generally have quite short dimensions (< 1000), \c float is recommended. \subsection ss_namespaces Namespaces All Clipper objects belong to the \c Clipper namespace, and can be accessed by using the \c Clipper:: prefix or \code using namespace Clipper; \endcode Templates for reciprocal space datatypes are provided in the \c Clipper::datatypes namespace. Instantiations of these types for \c float and \c double data are provided in \c Clipper::data32 and \c Clipper::data64. Classes are all named with an initial capital letter. Method names are all lowercase, with words separated by underscore ('_'). A handful of top level functions are implemented; these have an initial capital letter to distinguish them from standard library functions. \section s_memory Memory management All Clipper objects are designed to be created on the stack. Such objects are destroyed automatically when they go out of scope. Large or variable-sized data items within an object are generally held in STL vectors, and so are stored on the heap, and automatically destroyed with the associated object. Sometimes it may be useful to create Clipper container objects on the heap. In this case, the developer can arrange for the object to be destroyed when it is no-longer needed. However an alternative, automatic, method for memory management is provided, in the form of a \c destroyed_with_parent flag. If in object is created on the heap (i.e. with \c new), this flag may be set as follows: \code Container* new_container = new Container( parent, "A container" ); new_container->set_destroyed_with_parent(); \endcode Then, as soon as \c parent is destroyed, either by going out of scope, or by a \c delete operator, the new container will also be destroyed. \subsection ss_passing Passing objects Clipper objects should generally be passed by reference rather than by value. In particular passing a container type by value will lead to a container which is orphaned from the tree. Passing or assigning an object always results in a 'deep copy', i.e. all of the data associated with the object is copied. \section s_standards Coding standards Code in the Clipper library should obey the following standards. Some of these are stylistic, but most are simply good practice. Code which does not obey these standards will be rejected from my tree. -# No C-style casts. -# No reinterpret_cast<> except for conversion of external types. -# No static_cast<> without a very strong performance argument. -# No const_cast<>. -# No preprocessor macros, except for a stand-alone portability library. -# No global functions. Useful functions are contained in the Util class. -# Absolutely strict use of const, both for parameters and methods. -# Parameters are passed by reference. -# No pointers in public APIs. -# No pointers internally, expect for - testing for NULL after a dynamic_cast - member variables which point to other objects -# No 'new' or 'malloc'. Use STL containers. (Exception: for explicitly memory managed objects. There are still a couple of 'new's in the MTZ i/o layer). -# 'explicit' is used where necessary to prevent accidental type conversion. -# Access specifiers are ordered public, protected, private. There are a few places where I haven't yet finished implementing all of these standards, but I'm working on it. */ clipper-2.1/dox/clipper_hierarchy.eps0000644000374100011300000001752210736662154014745 00000000000000%!PS-Adobe-2.0 %%Creator: dot version 1.7.11 (Fri Nov 16 14:55:37 GMT 2001) %%For: (cowtan) Kevin Cowtan %%Title: G %%Pages: (atend) %%BoundingBox: 35 35 481 191 %%EndComments %%BeginProlog save /DotDict 200 dict def DotDict begin %%BeginResource: procset /coord-font-family /Times-Roman def /default-font-family /Times-Roman def /coordfont coord-font-family findfont 8 scalefont def /InvScaleFactor 1.0 def /set_scale { dup 1 exch div /InvScaleFactor exch def dup scale } bind def % styles /solid { } bind def /dashed { [9 InvScaleFactor mul dup ] 0 setdash } bind def /dotted { [1 InvScaleFactor mul 6 InvScaleFactor mul] 0 setdash } bind def /invis {/fill {newpath} def /stroke {newpath} def /show {pop newpath} def} bind def /bold { 2 setlinewidth } bind def /filled { } bind def 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The Cell object:
This object describes a unit cell. It holds the cell parameters, and derived information including coordinate conversion matrices and metrics. Any cell object may be used to convert coordinates between orthogonal and fractional forms, and calculate distances in real space and resolutions in reciprocal space.
The Spacegroup object:
This object describes a spacegroup, using information from the 'cctbx' library of Dr Ralph Grosse-Kunstleve. It can be use to generate symmetry coordinates and reflections, phase shifts, centricity, asymmetric units, and so on. \subsection ss_dobj Data objects: These hold actual data. They are written as templates which can hold whatever type of data the developer requires.
The reflection data object:
It is commonly necessary to store several related items of reflection data. Therefore this object is split into two parts; a parent object which holds a list of Miller indices and related data, and then several data objects which hold the actual data associated with each Miller index. The data objects can hold data of arbitrary types: these types will usually consist of several values. For example, a structure factor magnitude and its variance, or all four Hendrickson-Lattman coefficients, are usually held in a single data object. To the user, the data appears to cover the whole of reciprocal space, however in practice only an asymmetric unit is stored. Data is transformed about reciprocal spaces as required. When a new data type is defined, its behavior under transformation is also be defined so that this mapping can be performed.
The crystallographic map object:
This object also implements crystallographic symmetry, and also cell repeat, in a manner which is transparent to the user. It may also hold arbitrary data types: common examples would include bits, real values, complex values, or orthogonal or fractional gradients.
The non-crystallographic map object:
This object is used for map data which does not have symmetry or cell repeat, for example an NCS averaging mask.
\subsection ss_mobj Method objects: These are used to provide additional functionality commonly required in crystallographic calculations. Examples include:
FFT map:
This object holds data which may be represented in either real or reciprocal space. The data may be accessed in either form, and may be transformed between spaces as required.
The resolution function evaluator:
This object creates an arbitrary function of position in reciprocal space, by optimising the parameters of some basis function in order to minimise some target function. This is an extreme generalisation of the idea of 'resolution bins', and can be used for anything from <|F|2>s to sigma-a and beyond.
Import/export objects:
The only import/export objects implemented so far are the MTZfile and MAPfile objects. These stand as proxies for an external file, and can transfer data between the Clipper objects and the file.
\section s_scpt Scripting Automation of crystallographic tasks depends on being able to communicate between successive tasks, and by being able to execute control code to activate tasks and make protocol decisions. This functionality is provided through a scripting interface. A Python interface will be provided through the boost.python library. It is possible that interfaces to C and a range of scripting languages will be provided through other means. All the data and the full functionality of the methods will be available from the scripting layer, allowing full automation and full communication between tasks. Eventually the individual programs should disappear, rather exposing their functionality directly to the scripting layer. At the same time, data will have to move from traditional files into a database, so that each task has immediate access to all the information currently available. \section s_hier Partial class hierarchy (as of 1/2/2001) \image html hierarchy.png \image latex hierarchy.eps width=15cm \section s_ackn Acknowledgments: I would like to thank Ralph Grosse-Kunstleve, Airlie McCoy, Eugene Krissinel, Jan Zelinka and the CCP4 staff for their many and varied contributions to this effort. Clipper stands for 'Cross-crystal Likelihood Phase Probability Estimation and Refinement', which is what I hope to use it for. \section s_refr References: - 'Clipper' code and documentation (K. Cowtan): http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html - 'mmdb' coordinate library (E. Krissinel): http://www.ebi.ac.uk/~keb/cldoc/ - 'cctbx' crystallography toolbox (R. Grosse-Kunstleve): http://cctbx.sourceforge.net See the following pages in the Clipper documentation for further information: - \ref p_class_overview (brief guide to classes) - \ref p_conventions (coding style) - \ref p_coords (Coodinate types) - \ref p_develop (initial example) - \ref p_develop_hkl (reflection data handling and examples) - \ref p_develop_map (map handling and examples) - \ref p_develop_model (model handling) - \ref p_wheretolook (thematic index) - \ref p_installation (and dependencies) */ /*! \namespace clipper All normal clipper objects except data objects are defined in this namespace. */ /*! \namespace clipper::datatypes This namespace is used for templates which will later be instantiated for float or double precision data. 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500 curveto stroke newpath 509 526 moveto 506 536 lineto 505 526 lineto closepath fill endpage grestore %%PageTrailer %%EndPage: 1 %%Trailer %%Pages: 1 end restore %%EOF clipper-2.1/dox/Makefile.am0000644000374100011300000000174611372264321012564 00000000000000# Makefile.am, passed: dox, extracted subdir: dox # in dir /home/cowtan/clipper-autoconf/clipper-2.1/dox ## -*- mode: Makefile; mode: font-lock -*- INCLUDES=${FFTW_CXXFLAGS} library_includedir = $(pkgincludedir) EXTRA_DIST = \ class_overview.dox \ clipper.dox \ clipper_hierarchy.eps \ clipper_hierarchy.png \ container.eps \ container.png \ conventions.dox \ coordtypes.dox \ develop.dox \ develop_hkl.dox \ develop_map.dox \ develop_model.dox \ donors.eps \ donors.png \ hierarchy.eps \ hierarchy.png \ hier_rep.eps \ hier_rep.png \ hkl_objs.eps \ hkl_objs.png \ img_container.eps \ img_container.png \ include.eps \ include.png \ installation.dox \ map_p1.eps \ map_p1.png \ map_p2.eps \ map_p2.png \ minimol1.png \ minimol2.png \ minimol3.png \ wheretolook.dox clipper-2.1/dox/develop_map.dox0000644000374100011300000002721510736662154013547 00000000000000/*! \page p_develop_map Developing using Crystallographic Maps \section s_mapund Understanding Xmaps The most commonly used map object in Clipper is the crystallographic map, or Xmap. This is the map class which is used to describe any function of position in a crystal which obeys the crystal cell repeat and symmetry. Electron density is the most common example. The aim of the Xmap is to provide a fast and efficient way of storing some property, in such a way that the crystallographic symmetry and cell repeat are imposed without any effort from the programmer. Therefore, a clipper::Xmap appears to be infinite in every direction, allowing the map to be queried at any position in crystal space. However, only a unique subregion of a single cell is stored. If a value in the map is changed, then every copy of that value throughout crystal space also changes. \subsection ss_mapgrid Grids Representing the electron density across the whole unit cell is simple enough. A sampling is chosen which is sufficient to represent the electron density to the desired level of detail. The unit cell is then divided into a 3-dimensional grid with the given sampling. The first point is at the origin, and the first point along each line through the array lies on the surface of the unit cell. The last point along each line is the point before the surface of the next cell. Since the cell repeats, there is no point storing each surface twice. There are generally some restrictions on the grid sampling, imposed by the cell dimensions, spacegroup, and FFT requirements. The clipper::Grid_sampling class can be used to select an appropriate grid sampling for any particular problem. The following image shows a slice of a unit cell which has been sampled on a (6x8) grid. 48 points are stored, with fractional coordinates 0...5/6 on the horizontal axis and 0...7/8 on the vertical axis. \image html map_p1.png \image latex map_p1.eps width=5cm The fraction coordinate of any map grid point may therefore be determined by dividing the zero-based grid coordinate by the grid sampling along each direction. \subsection s_mapasu Asymmetric units Unfortunately the general case in crystallography is rather more complex. In addition to the unit cell repeat, most molecules crystallise with some sort of symmetry within the unit cell. Thus the unique region of crystal space, referred to as an asymmetric unit (ASU), is smaller than the the unit cell by a factor equal to the number of symmetry operators. A naive approach to this problem would be to store only an oblong 'brick' within the unit cell. Unfortunately in the general case this does not work, since some symmetry operators are not aligned along grid axes. Even simple cases, such as a single 2-fold rotation axis, can cause problems, as illustrated in the figure below: \image html map_p2.png \image latex map_p2.eps width=5cm The map section shows a sampling of a P2 unit cell. An attempt has been made to select an asymmetric unit using a rectangular subregion of the section. However it can be seen that the origin is related to itself, and the 2-fold axis also relates the points on the left and right-hand edges of the oblong to other points on the same edge. Therefore 26 points are required to store a complete asymmetric unit section, and the brick containing those points is just over half the unit cell wide and contains 32 points. The approach used by the Xmap class is therefore to store a compact brick of density, along with a flag array marking which points within that brick are considered to be part of the ASU, and which are considered to be outside the ASU. \note In actual fact, clipper stores a border of 1 extra cell around the ASU brick. This extra row is used to speed up systematic searches through the density by flagging the edge of the ASU. In addition these extra points cache the number of the symop required to get back into the ASU, making systematic density searches very efficient. \subsection ss_mapcoord Coordinates There are three kinds of coordinates which are commonly used in real space. They are: - Orthogonal (Angstom) coordinates (clipper::Coord_orth) - Fractional (cell) coordinates (clipper::Coord_frac) - Grid coordinates (clipper::Coord_grid) Grid coordinates are always integers, the others are floating point values. Conversion between orthogonal and fractional coordinates is performed using the clipper::Coord_orth::coord_frac() and clipper::Coord_frac::coord_orth() methods, supplying the cell as an argument. e.g. corth.coord_frac(xmap.cell()) Conversion between fractional and grid coordinates is performed using the clipper::Coord_map::coord_frac() and clipper::Coord_frac::coord_map() methods, supplying the grid as an argument. e.g. cfrac.coord_map(xmap.grid_sampling()) \section s_mapxmap The Xmap class The clipper Xmap class therefore holds a flag array and data array corresponding to a compact brick containing at least complete asymmetric unit. The Xmap is constructed by providing a spacegroup, cell, and grid sampling. These are used to determine an appropriate ASU, and allocate an array to store the map data. The data may then be read or written by providing the appropriate grid coordinate. Alternatively, interpolated values and gradients at non-grid locations may be read by providing a fraction coordinate. A variety of interpolation methods are provided for this purpose. In order to use the class efficiently, some important difficulties must be borne in mind. A problem arises when we wish to apply some transformation to the values stored in the map. In this case, we must access every unique value in the asymmetric unit once and once only, applying the desired transformation. Only then will the entire map have been transformed correctly. A second problem arises if we want to access the stored value of the density at some position in crystal space, represented by a grid coordinate. Then it is necessary to search through all the symmetry operators, applying each one in turn to the coordinate to find the operator which brings the coordinate into the stored asymmetric unit. Any cell translations must also be taken into account. The value of the map for that coordinate can then be returned. Clearly this can be time consuming, especially if there are many symmetry operators. Both these problems are addressed by the use of map reference types. These come in two forms: - index-like references (clipper::Xmap_base::Map_reference_index) - coordinate-like references (clipper::Xmap_base::Map_reference_coord) The index-like reference behaves like an index: it stores a reference to a map and an index into that map. It is used to loop over all the values in the asymmetric unit of a map, using the Xmap<>::first(), and Map_reference_index::last() and Map_reference_index::next() methods. The coordinate corresponding to the index can be returned at any point. The coordinate-like reference behaves like a coordinate: it stores a reference to a map and a grid coordinate into that map. However to enhance performance it also stores the index corresponding to that coordinate, and the number of the symmetry operator used to get back into the stored asymmetric unit. Since maps are usually accessed systematically, the next coordinate used will commonly require the same symmetry operator, and so that operator is tried first. An efficient caching mechanism makes incrementing or decrementing the coordinate along the u, v, or w directions particularly fast. The differences between the index-like and coordinate-like reference types can be summarised as follows: - index-like types can only refer to the position of a stored datum, i.e. a coordinate in the stored ASU. - coordinate-like types can refer to any possible position, and therefore also store the symmetry transformations required to get back to the stored data. Use of map reference types is always preferred over requesting a coordinate directly. The accessor methods for the map are designed to encourage efficient usage. Map reference types may be shared between any maps which have the same symmetry and grid sampling. It is the responsibility of the programmer to ensure this restriction is obeyed. \section s_mapcode Xmap code fragments \subsection ss_mapio Importing and exporting Xmaps Importing and exporting Xmaps to or from CCP4 map files couldn't be easier. To import a map, use: \code clipper::CCP4MAPfile file; file.open_read( "my.map" ); file.import_xmap( xmap ); file.close_read(); \endcode The extent and axis order of the input map do not matter, the resulting map will always cover the preferred ASU. However, if there is insufficient information in the input map to obtain an ASU, the remaining portion of the map will be untouched. To export a map, use: \code clipper::CCP4MAPfile file; file.open_write( "my.map" ); file.export_xmap( xmap ); file.close_write(); \endcode \subsection ss_mapexp Expanding a map to a lower symmetry Sometimes it is necessary to expand a map to a lower symmetry. The ASU for the new spacegroup will be larger than the ASU for the old spacegroup, so the additional density values must be generated by applying the symmetry operators from the old spacegroup. This can be handled automatically by the map class. The new map is constructed to share a grid and cell with the old map, but with the new spacegroup. We must ensure that every value in the new map is set, so we loop over the new map using a clipper::Xmap_base::Map_reference_index. The we request the corresponding density from the old map, using the coordinate of the Map_reference_index: \code clipper::Xmap oldmap, newmap; ... newmap.init( newspacegroup, oldmap.cell(), oldmap.grid_sampling() ); clipper::Xmap_base::Map_reference_index ix; for ( ix = newmap.first(); !ix.last(); ix.next() ) { newmap[ ix ] = oldmap.get_data( ix.coord() ); } \endcode This works, but it would be faster to use a Map_reference_coord to access the second map, so that the symmetry operators do not need to be searched every time. The coordinate of the Map_reference_coord can be set from the Map_reference_index into the first map. i.e.: \code clipper::Xmap oldmap, newmap; ... newmap.init( newspacegroup, oldmap.cell(), oldmap.grid_sampling() ); clipper::Xmap_base::Map_reference_index ix; clipper::Xmap_base::Map_reference_coord iy(oldmap); for ( ix = newmap.first(); !ix.last(); ix.next() ) { iy.set_coord( ix.coord() ); newmap[ ix ] = oldmap[ iy ]; } \endcode \subsection ss_mapbloc Looping over a small block of density Sometimes it is necessary to access all of the map values in a cubic or oblong block of the unit cell. To perform this operation efficiently, coordinate-like map references must be used to eliminate the need to search over symmetry operators. Either of the following approaches may be used, depending on the situation: Three map references can be used, one each for looping along the u, v, and w directions. Suppose the loop must run over the box bounded by Coord_grid g0 and Coord_grid g1. This leads to code of the following form: \code clipper::Xmap_base::Map_reference_coord i0, iu, iv, iw; i0 = clipper::Xmap_base::Map_reference_coord( xmap, g0 ); for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) { // ---- access xmap[iw] here ---- } \endcode Alternatively, in most cases it is only necessary to optimise the innermost loop. \code int u, v; clipper::Xmap_base::Map_reference_coord ix( xmap ); for ( u = g0.u(); u <= g1.u(); u++ ) for ( v = g0.v(); v <= g1.v(); v++ ) for ( ix.set_coord(Coord_grid(u,v,g0.w())); ix.coord().w() <= g1.w(); ix.next_w() ) { // ---- access xmap[ix] here ---- } \endcode */ clipper-2.1/dox/hkl_objs.png0000644000374100011300000002161510736662154013037 00000000000000‰PNG  IHDRÛúfŸzD# IDATxÚí=ôºuÇ9É-l8E´¥ÃÚÛ] …µå-Rh«Û¤™q—4)ÒKE>€æ#H€7IF½©Èµ©®d1àNj #€R/ÃG¤8z¥ýÿðàÁ¬^(ytxD ÿçÔ4 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This section describes the documentation which might help when addressing a particular type of problem. \subsection ss_where_theme_all Documentation common to all problems. Some information is common to all tasks in Clipper. Most fundamental are the coordinate types. There are described in the following essay: \ref p_coords. The most commonly used classes are clipper::Coord_orth, clipper::Coord_frac, clipper::Coord_grid and clipper::HKL. All crystallographic tasks depend upon the spacegroup and cell classes, so read their documentation. The cell class is clipper::Cell, and the spacegroup class is clipper::Spacegroup. You may want to look at their parent classes, Cell_descr, and clipper::Spgr_descr, which are used to initialise the classes if the information is not coming from a file. If you are going to need to perform operations on coordinates, then you may want to look at the clipper::RTop_orth documentation. Its counterpart, clipper::RTop_frac is the base class of the symmetry operator clipper::Symop. Often, the parent classes of a class also contain useful methods. For example, the coordinate classes are all derived from clipper::Vec3, and the operators are derived from clipper::RTop. The clipper::Util class may contain some helpful utility functions. The clipper::String class is a trivial extension of the STL std::string. You can use either interchangeably. \subsection ss_where_theme_hkl Documentation for reflection-related problems. First, look at the essay \ref p_develop_hkl, which describes how Clipper handles reciprocal space data. The fundamental types which hold lists of HKL's and lists of associated reflection data (e.g. F's, phases, etc.) are clipper::HKL_info and clipper::HKL_data. clipper::HKL_data is a template class which can be used to hold any kind of data. A range of common datatypes are provided which you can store in this object: Look at the derived classes of clipper::Datatype_base for a list. Alternatively, you can add your own. Most common reflection data conversions have built in methods. Look at the clipper::HKL_data::compute() method. For operators to use with it, look at the class listing for classes labelled clipper::datatypes::Compute_*. Scaling of data is also built in. See clipper::ResolutionFn and the examples on that page, and the derived classes of clipper::BasisFn_base and clipper::TargetFn_base. \subsection ss_where_theme_map Documentation for map-related problems. First, look at the essay \ref p_develop_map, which describes how Clipper handles real space map data. Crystallographic maps are handled by the clipper::Xmap class. Calculation of FFT's to and from reciprocal space is build in to this class, as are interpolation methods. The clipper::Map_stats class provides tools for calculating map statistics. Calculation of maps and masks from atomic coordinates is handled in the contrib package by the EDcalc- and MASKcalc- classes. Filtering of maps and calculation of masks is aided by the MapFilter- classes in the contrib package. Non-crystallographic maps (i.e. maps with no symmetry or cell repeat) are handled by the clipper::NXmap class. Non-crystallographic maps may be referred into a crystallographic frame using the clipper::NXoperator class. \subsection ss_where_theme_model Documentation for model-related problems. First, look at the essay \ref p_develop_model, which describes how Clipper handles atomic models. The clipper::Atom and clipper::Atom_list classes provide basic support for atoms and lists of atoms, or you can use the more advanced MMDB or MiniMol packages. To calculate structure factors, maps, or masks from a coordinate model, look at the SFcalc-, EDcalc-, and MASKcalc- classes in the contrib package.
\section s_where_task Task index This section describes the documentation which might help when addressing a particular crystallographic task. \subsection ss_where_molrep Molecular Replacement. Rotations are handled in a generic form as Quaternions by the clipper::Rotation class. These may be converted to and from Polar angles, Euler angles (24 conventions), and matrix representations. See the clipper::Polar_ccp4, clipper::Euler_ccp4, clipper::Euler, and clipper::Mat33 classes. Rotation-translation operators are handled by the derived classes of clipper::RTop, i.e. clipper::RTop_orth and clipper::RTop_frac. \subsection ss_where_phaseimp Phase improvement (Density modification) Filtering of maps and calculation of masks is aided by the MapFilter- classes in the contrib package. Data scaling and sigmaa estimation can be performed using the clipper::ResolutionFn class and its related classes. \subsection ss_where_refinement Refinement Agarwal coefficients for calculation of refinement residual gradients may be generated using the clipper::AtomShapeFn class. Data scaling and sigmaa estimation can be performed using the clipper::ResolutionFn class and its related classes. \subsection ss_where_modelbuild Model building FFFear-style translation functions may be calculated using the FFFear- classes in the contrib package. */ clipper-2.1/dox/map_p2.png0000644000374100011300000000430610736662154012420 00000000000000‰PNG  IHDR|1€ûEIDATxÚíÜ=nÛJÀqð«ärÁÊ¥J#u _ @J7{žÅ•JB70|Bܪ.Õz\2 Þ#wÄyÑr9 ÿSäs–?ŠK.9ðâÔ‹}QÅþ”Š:>RÏXÝ>Ì[“ø–z€Æêö`ÅÏ8¤Ÿµº=˜²M,ÓÐZÝÌ®MÜ¥ µº=˜m›¸M;@ku{0ůH;@kuƒ0kç#OîWLPw­„q_t¼¿××äùŠ«Õ4u¿8-ŒÓ}¥ó\÷uÕäY«œ|ëDÅ$s€Öê/×u¢â²s€ÖêoðêDÅVÌZ«\Ô‰Š[ó˜´V7¸ˆô‰šÅ\ÌZ«|ìà5Ëÿ¨4V·sÚûDÕ£¨4V7s,+éh«î"”·ðuæ 0ÀŒ<`€ùŸ0?òÍé©yÊç3|<åß›ô?9mþýÉý½ôɦyÄ8´µj{yà“ÍD0›¯¶aBƒN3QamÞTã`€`€¹Ö<ÖJÀüa0væ˜üµI|Þê¬`òÅçWŸøúy1°Ù÷jÕ¼y.«Ë«ŽG=Àîñ0S|~Ìë¿^Ïnm“ewwY¶9 „.Ï?ÀÞñ0ã‡ö÷£ÂeážT;4°Çʼº`ž÷ëÚñc¼ù4äòžåÍóì=F^óM}ìC0§×›ÅâÓy—êi7xþ$Ñæ5Çã¦<¬ÁÜ<tŠÞµí¢w÷1òªx –ýø±˜í¬?©j`ªC÷×M5ÏÓsQL¾ó;•”—ëd“oìVÃô’”7x©.×f`ÔK‚D7xv`Ԝْ Uam0À 0À 0ÌTyæß+c,Ï< s 0À 0À 0ó€™*Ïü’cyæa˜cÌÃÐ熡ÏW€¡ÏW€¡ÏW‚¡ÏW‚¡Ï÷ }¾ôù^iŸoìSD›×[Ðç+ÀÐç+ÀXëóµtU¢Ï÷2˜™-"`€`®$Ïü{%`Œå™‡aŽ`€`€f0Så™_c,Ï< s 0× CŸo†>_†>_†>_ †>_ †>ßs0ôùZïó½h‡/ }¥éó¥ÏWc­Ï×ÎäKŸ¯£ÞàÌ–© kó€`€ó0S噯Œ±<ó0Ì1À 0À 0ÀÌfª<óK`Œå™‡14ÇKçÊcz˜pÝñaÂu0û¹bŸ&\w|˜pÝ>ÌGá‹Ô0BÝÑa„º}˜·&ñ-5ŒPwt¡næP¼¬W«õKqÚbÜ—úRݱaEÓ­Ûƒ)×Ëe–-—ër`‹qÛ@ĺcÔ-L§næyá|¢[<ìoÜÆ!±îØ0»fwæýÖ5‰î6J ™:Oª;6̶…Ùž‡Ù,ÛÄe”¦CužTwl˜¢­[œ‡É|âÊ9—EiSUçeUÉÕpÝèí¬Î× Át‘ Ø;•~÷¹øTêä1ù¶0\®u—knð$– ‹H †Ç ª$m 0< æša¦Ê3ÿ^ cyæa˜c€`€`€™ÌTyæ—ÀË3à 0À3o˜¸/ë/ͳ¹½ãÒ<30±‚.ͳ½…ìÒ<+0Ñ›£ÿ²ÒT0Ýœoþˆmªñ½í4¿¶ÆÜ©deŽaò`¸\K0ÜàI0, $‘À 0³‡™*Ïü{%`Œå™‡aŽ`€`€f0Så™_c,Ï< s 0À 0ÀðR_ CH†Æ¡0Œ¹V³Ø;¬†éüß\s¢ÚY¯æ{àÇ’ÀXo™gòò¬Àp¹–`¸Á“`XH0,"˜ùÀL•gþ½0ÆòÌÃ0Ç 0À 0À3˜©òÌ/ €1–g†9`€`€ÑÃðR? CHÆZãPìVÃtþo®ÕÌ Œ¹æD+0´³¶09ÆÜ©dåªdnòµcîrm†< †%Ã"`þ@˜©òÌ¿WÆXžyæ`€`€`æ3Užù%0ÆòÌÃ0Ç 039–ΕÇô0áºãÄë`ö…sÅ>=L¸îø0áº}˜Â'©a„º£Ãuû0oMâ[j¡îè0BÝÌ¡xY¯Vë—â0´Å¸/õ¥ºcʦ[·S®—Ë,[.×åÀ#·¨ëF†)[˜NÝÞ’àyá|¢[<ìoäÆ!mÝØ0»fwæýÖ5‰î6m«™²nt˜m ³=³Y¶‰Ë´Í‰Rݱ瘢­[t`ºí¬>ñ‹s.KÛΚU%W«~ݱÛY«ŠÕî*aÖNS‡F“çaœÓÁÄŒºæz¦þJס8•êPœJš<©îFyÚün¿âÍåÚï¯ær­É“êŽ ³kaº—ëÐ ÞÃîïÛ7Ý ž&Oª;6LÙÂtoðBK‚j6R- ò\·$ÐäIudž9´0CK¿¨ò¡YDF ¡îØ0RÝàcšÇQC¨;:ŒP7ø ª Õƒª¸a«nà½Ò±št6ㆭº‹ßÙÔÂ<ÌèsŒ‹© k!€!€!€b:˜¯›ÓSó”Ï?=öñT¦ Ÿh|G‡ùab÷Ï|¢ø}2£ÀLSÖ~#0B#0B#0B#0B#0B#0B#0B#0B#0B#0B#0B#0B#0B#0B#Ä?_’bSYŽDù fphidata( myhkl ); \endcode Next, we want to open an MTZ file. I'll assume it is called \c my.mtz . To do this we create an \c clipper::MTZfile object. This is an i/o object which can be linked to an MTZ file by an open command, and can then fill Clipper data objects using the information from that file. \code clipper::CCP4MTZfile mtzin; mtzin.open_read( "my.mtz" ); // open new file \endcode When we created the reflection list object, we did not provide a cell or spacegroup, or generate a reflection list. So we'll get those from the file now. \code mtzin.import_hkl_info( myhkl ); // read sg, cell, reso, hkls \endcode Now we want some actual data. We read a couple of MTZ columns into the data list we created earlier. \code mtzin.import_hkl_data( fphidata, "/native/CuKa/[FCAL,PHICAL]" ); \endcode Note that we create the data-list as a child of the reflection list \c myhkl . (Actually, any descendent will do). The import operation will actually move it, by inserting the appropriate \c CCrystal and \c CDataset objects, according to the information on the file. Note also that we give specify the MTZ columns by giving the full path: crystal, dataset, and column names. The column names are grouped in square brackets. (For older MTZ files, which do not have crystal and dataset entries, the dummy names "unnamed_crystal" and "unnamed_dataset" are used.) Now we close the MTZ file. \b NOTE: No data is actually read until you close the file! \code mtzin.close_read(); \endcode Next, we create a map. For this we need to provide a grid. The grid depends on the spacegroup, cell, and resolution, which we get from the reflection list: \code clipper::Grid_sampling mygrid( myhkl.spacegroup(), myhkl.cell(), myhkl.resolution() ); // define grid \endcode Now we make the map itself, using the spacegroup, cell, and grid. \code clipper::Xmap mymap( myhkl.spacegroup(), myhkl.cell(), mygrid ); // define map \endcode Next, we calculate the map by FFT. \code mymap.fft_from( fphidata ); // generate map \endcode Finally, then map is written out to an output file. \code clipper::CCP4MAPfile mapout; mapout.open_write( "my.map" ); // write map mapout.export_xmap( mymap ); mapout.close_write(); \endcode To summarise, here is the complete program: \code clipper::HKL_info myhkl; clipper::HKL_data fphidata( myhkl ); clipper::CCP4MTZfile mtzin; mtzin.open_read( "my.mtz" ); // open new file mtzin.import_hkl_info( myhkl ); // read sg, cell, reso, hkls mtzin.import_hkl_data( fphidata, "/native/CuKa/[FCAL,PHICAL]" ); mtzin.close_read(); clipper::Grid_sampling mygrid( myhkl.spacegroup(), myhkl.cell(), myhkl.resolution() ); // define grid clipper::Xmap mymap( myhkl.spacegroup(), myhkl.cell(), mygrid ); // define map mymap.fft_from( fphidata ); // generate map clipper::CCP4MAPfile mapout; mapout.open_write( "my.map" ); // write map mapout.export_xmap( mymap ); mapout.close_write(); \endcode \section s_incl Libraries and Include files Which header and library files should you include in your application? The libraries are as follows, and there is an aggregated header file for each library.
Contents Library Include
Reflection, maps, models $PREFIX/lib/libclipper.a $PREFIX/include/clipper/clipper.h
Function objects (e.g. SFcalc) $PREFIX/lib/libclipper-contrib.a $PREFIX/include/clipper/clipper-contrib.h
CCP4 mtz/map i/o $PREFIX/lib/libclipper-ccp4.a $PREFIX/include/clipper/clipper-ccp4.h
SHELX phs i/o $PREFIX/lib/libclipper-phs.a $PREFIX/include/clipper/clipper-phs.h
cctbx interface $PREFIX/lib/libclipper-cctbx.a $PREFIX/include/clipper/clipper-cctbx.h
Alternatively, you can include individual header files from the subdirectories of include/clipper/. The precise header files can be identified by the following include tree: \image html include.png \image latex include.eps \width=10cm */ clipper-2.1/dox/class_overview.dox0000644000374100011300000004226610736662154014312 00000000000000/*! \page p_class_overview Class Overview \section s_classov_intro Introduction This page contains a brief outline of the types of classes provided by the Clipper libraries, followed by a more detailed description of the different classes.
  1. \ref ss_ordi Ordinates include Miller indices (clipper::HKL), orthogonal and fractional coordinates (clipper::Coord_orth, clipper::Coord_frac), and grid coordinates (clipper::Coord_grid). Grids describe the storage of 3D data: The basic grid class (clipper::Grid) describes the dimensions and indexing of a 3D rectangular arrays. The unit cell grid (clipper::Grid_sampling) also provides methods for converting between fractional and grid coordinates, and the map grid (clipper::Grid_range) describes a general sampled map, which is bounded by lower and upper grid coordinates.
  2. \ref ss_crys A crystal is defined by two main classes: a unit cell (clipper::Cell) and a spacegroup (clipper::Spacegroup). These are complex classes which store derived information and provide optimised methods for handling it. Two smaller `descriptor' objects provide a more compact representation for storage and transmission: The cell descriptor (clipper::Cell_descr) holds just the cell edges and angles, and the spacegroup descriptor (clipper::Spgr_descr) hold the Hall code of the spacegroup.
  3. \ref ss_data Data objects hold the actual crystallographic data. They include reciprocal space data (clipper::HKL_info, clipper::HKL_data), crystallographic and non-crystallographic maps (clipper::Xmap, clipper::NXmap), and FFT maps (clipper::FFTmap) The primary design goal of the data objects is that they hide all the bookkeeping associated with crystallographic symmetry (and in real space, cell repeat). Data can be written to and read from any region of real or reciprocal space, and the unique stored copy of the data will be modified correctly. This is all achieved in a computationally efficient manner. The data objects are templates which can hold data of any type. In the case of a map, this type will usually be `double' or `float', however in the case of reciprocal space data the types are often more complex, for example `magnitude and phase' (F_phi) or Hendrickson-Lattman coefficient (ABCD).
  4. \ref ss_io Input/Output objects are used to record the contents of an object in a file or restore the contents from a file. (MTZfile, MAPfile) The crystal descriptors and data objects may be used as stand-alone objects. However, the data objects are related to a particular crystal, and may be related to each other. In order to facilitate the organisation of information, all the objects have `container' variants.
\section s_class Classes The classes which a developer will commonly encounter are as follows: \subsection ss_ordi Ordinates and grids:
  • clipper::HKL Reflection/Miller index. Constructed with 3 integers, h, k and l. Read-write access is provided to these members through the h(), k() and l() methods.
  • clipper::Coord_orth Orthogonal Angstrom coordinate, defined on some unspecified coordinate frame. Constructed from 3 real numbers, x, y, and z. Read access is provided to these members through the x(), y() and z() methods.
  • clipper::Coord_frac Fractional coordinate, defined in fractions of the cell edges. The coordinates are therefore not necessarily orthogonal. Constructed from 3 real numbers, u, v, and w, being fractions of the a, b, and c axes. Read access is provided to these members through the u(), v() and w() methods.
  • clipper::Coord_grid Grid coordinate, defined on some unspecified grid. (Ideally this object should define its own grid, but these things are used so frequently that the overhead would be unacceptable.) Constructed with 3 integers, u, v and w, being grid positions along the a, b and c axes. Read-write access is provided to these members through the u(), v() and w() methods.
  • clipper::Grid A generic grid definition. Constructed with 3 integers, nu, nv and nw, defining the size of a grid along 3 direction. Read access is provided to these members through the nu(), nv() and nw() methods. Methods are provided for simple indexing of a 3D array stored as a 1D list (Like a multidimensional local array in C, or a Fortran array with the indices reversed).
  • clipper::Grid_sampling Derived from clipper::Grid, this class is used for a grid which defines the sampling of a unit cell. Constructor as for clipper::Grid. It provides additional methods for converting between fractional and grid coordinates, and for reducing a coordinate from anywhere in crystal space to the unit cell (0-1,0-1,0-1).
  • clipper::Grid_range Derived from clipper::Grid, this class is used for defining a map grid. The map grid need not cover a unit cell, and need not be based at the origin. It is constructed by two clipper::Coord_grid's, representing the lower and upper bounds of the volume in 3D space. Methods are provided for simple indexing of a 3D array stored as a 1D list.
\subsection ss_crys Crystal information
  • clipper::Cell_descr The cell descriptor class (clipper::Cell_descr) contains the basic information required to describe a unit cell, i.e. the cell edges a, b, and c, and the cell angles, alpha, beta and gamma. It is constructed by providing these 6 values in order. The angles may be given in degrees or radians, if they are less than pi they are assumed to be in radians. If they angles are omitted they are assumed to be 90 degrees.
  • clipper::Cell The cell class (clipper::Cell) is constructed from a cell descriptor (clipper::Cell_descr), but additionally contains derived information, including the cell volume, the orthogonalising and fractionalising matrices (for converting between orthogonal and fractional coordinates) and the metric tensors (for computing the distance between points in real space, or the resolution of a reflection in reciprocal space). It provides methods for conversion between fractional and orthogonal coordinates (frac_to_orth, orth_to_frac), calculating distances in real space (distancesq) and reflection resolutions (invresolsq).
  • clipper::Spgr_descr The spacegroup descriptor class (clipper::Spgr_descr) contains the Hall symbol, which uniquely describes the spacegroup. It can be constructed from a spacegroup number, a traditional Hermann-Maugnuin symbol, or a list of symmetry operators (not implemented).
  • clipper::Spacegroup The spacegroup class (clipper::Spacegroup) is constructed from a spacegroup descriptor (clipper::Spgr_descr), but additionally contains a list of all the symmetry operators, and tables for looking up inverses of symmetry operators. It provides methods for returning symmetry operators, along with other information such as the point group and Laue group. Symmetry operators are represented as a 3x3 matrix and 3x1 vector of either real numbers (Rsymop) or integers (Isymop). For integer symops the translation components are scaled by a factor of 12. Both real and integer symops provide methods for transforming Miller indices (sym_hkl) and fractional coordinates (sym_coord), and for calculating the phase shift associated with the symmetry transformation of a reflection (sym_phase_shift).
\subsection ss_data Data objects Reciprocal space data The reciprocal space data object is divided into two parts: the first part (clipper::HKL_info) handles indexing of reflections and information derived from the Miller indices, and the second part contains the actual data. The reasons for this division are that it is common to have several lists of information for each reflection, so a single list of Miller indices can be used for several lists of data. This also allows the use of optimised tables for looking up reflections, without wasting space duplicating them for several data lists. However, if reciprocal space data are stored which do not have the same list of Miller indices, it is quite possible to provide several clipper::HKL_info objects, one for each list of data.
  • clipper::HKL_info The reflection indexing class (clipper::HKL_info) contains a cell, a spacegroup, and a list of Miller indices. Reflection data is most commonly accessed by looping through each reflection in turn, and so the reflections can be referred to by number, or by coordinate-reference types provided for that purpose. However, it is occasionally necessary to refer to a reflection directly by its Miller index. For this purpose, a fast lookup table is also maintained, allowing efficient access to any reflection. This operation may however require searching through several symmetry equivalents, so there is still some overhead. The overhead is reduced by using the appropriate coordinate-reference type (clipper::HKL_info::HKL_reference_coord), which stores the last use symmetry operator as a guess at which operator will be required next. clipper::HKL_info is constructed by providing a clipper::Spacegroup and clipper::Cell (unless the container version is used). A method is provided to generate a list of unique non-absent reflections to a given resolution (generate_hkl_list), or alternatively a list may be imported using an I/O object. Coordinate-Reference Types are provided for looping through the list of reflections (clipper::HKL_info::HKL_reference_index) or accessing reflections by Miller index (clipper::HKL_info::HKL_reference_coord). The latter is optimised for the case where reflections are taken consecutively from the same region of reciprocal space.
  • clipper::HKL_data The reflection data object is a template object, where the template type is the type of crystallographic information to be stored in the object. It simply stores a list of data of that type. Data types typically include several values. Examples include measured X-ray intensity and its standard deviation (I_sigI), structure factor magnitude and phase (F_sigF), and Hendrickson-Lattman coefficients (ABCD). Data types are derived from a base type (Datatype_base), and should override all the methods of that type. This will allow the data to be automatically transformed about reciprocal space, and imported or exported to a file, as required. The class provides methods for accessing the data by index number, by coordinate-reference type, or by Miller index. The last method should avoided for speed critical tasks. The coordinate-reference types are typedef'ed from those in clipper::HKL_info, and may be used interchangeably with them. However clipper::HKL_data provides an additional method (next_data) for accessing only the non-missing data in a list.
Real space data
  • clipper::Xmap The crystallographic map data object is a template object, with the template type being the type of the data; usually double or float for maps, or int or bool for masks. (In future a specialisation for complex data will be available, with a complex fft method.) The map object is constructed by providing a clipper::Spacegroup and clipper::Cell (unless the container version is used), and the unit cell sampling (clipper::Grid_sampling). Methods are provided to set and get data by grid coordinate (clipper::Coord_grid), however it is more efficient to use coordinate-reference types for this purpose. Coordinate-Reference Types are provided for looping through the unique map grid points (clipper::Xmap_base::Map_reference_index) or accessing map grid points by coordinate (clipper::Xmap_base::Map_reference_coord). The latter is optimised for the case where map values are taken consecutively from the same region of crystal space. Methods are also provided for moving one grid step along any of the cell axes.
  • clipper::NXmap The non-crystallographic map data object is a template object, with the template type being the type of the data; usually double or float for maps, or int or bool for masks. It contains a finite bounded grid of data with no symmetry or repeat. A rotation-translation operator allows the grid coordinates to be related to an arbitrary orthogonal coordinate frame. This will often relate to the orthogonal coordinate representation of a portion of some unit cell to which the map is related. Coordinate-Reference Types are provided for looping through the map grid points (clipper::NXmap_base::Map_reference_index) or accessing map grid points by coordinate (clipper::NXmap_base::Map_reference_coord).
Other objects
  • clipper::FFTmap The FFT map (clipper::FFTmap) is a map used for calculating Fast Fourier transforms. It can hold represent data in either real or reciprocal space, and transform between representations. The data is stored covering the whole of the P1 unit cell in real space, or the L>0 hemisphere in reciprocal space, however the crystallographic symmetry of the data is maintained at all times. This is achieved by setting every symmetry equivalent value when writing to the object. When reading the symmetry is assumed and only the requested value is returned. In general it is not necessary to use an FFT map directly, since one will be created whenever an FFT is required. However if data is being transformed very frequently, or if very fast random access to reflection or map values is required, then it may be beneficial to use an clipper::FFTmap for this purpose.
  • clipper::ResolutionFn The resolution function evaluator is a class for the calculation of arbitrary functions of resolution or position in reciprocal space. It can be used for the generation of Wilson plots, or for the calculation of simple likelihood function such as sigma-a. It is a superior replacement for any calculation which would previously have been performed using resolution bins.
\subsection ss_io Input/Output objects
  • clipper::MTZfile Import/export class for MTZ files.
  • clipper::MAPfile Import/export class for CCP4 maps.
\subsection ss_refer Coordinate-reference types. Coordinate-reference types are provided for accessing data in both real and reciprocal space. Data is commonly referred to in one of two ways: -# by index into a list of unique data, or -# by 3-dimensional coordinate. The coordinate-reference types are designed to make switching between the two forms of reference easier. Two coordinate-reference types are provided in each space - one which behaves more like an index, and one which behaves more like a coordinate. However, either may be asked to return either an index or a coordinate on request. References may also return other useful information, for example the HKL_reference types will return the resolution and reflection class of a reflection (i.e. centricity, phase restriction, multiplicity). The coordinate reference types are as follows: \code clipper::HKL_info::HKL_reference_index clipper::HKL_info::HKL_reference_coord clipper::XMap_base::Map_reference_index clipper::XMap_base::Map_reference_coord clipper::NXMap_base::Map_reference_index clipper::NXMap_base::Map_reference_coord \endcode The index-like reference is simply an index, and a pointer to the parent object, which allows the corresponding coordinate to be looked up. It provides a convenient way to access either every unique reflection in a list, or every unique map grid point in the asymmetric unit, in turn. The coordinate-reference type is usually initialised by assignment from the `first' method in the parent object. It may then be incremented by its own `next' method. Completion is tested by the `last' method. For example, if hklinfo is an object of type clipper::HKL_info and xmap is an object of type clipper::Xmap, then the following loops could be used to access all the data: \code for ( clipper::HKL_info::HKL_reference_index ih = hklinfo.first(); !ih.last(); ih.next ) \endcode However, if the Miller indices of a reflection are are required, the reference type may be queried directly. Other information can also be obtained: \code HKL hkl = ih.hkl(); int index = ih.index(); ftype s = ih.invresolsq(); HKL_class cls = ih.hkl_class(); \endcode Similarly, if hkldata is an object of type clipper::HKL_data, then the following will loop over all non-missing data in the list: \code for ( clipper::HKL_info::HKL_reference_index ih = hkldata.first_data(); !ih.last(); ih.next_data(hkldata) ) \endcode The reference types in real space are equivalent: \code for ( clipper::Xmap_base::Map_reference_index ix = xmap.first(); !ix.last(); ix.next ) { int i = ix.index() Coord_grid coord = ix.coord(); } \endcode The coordinate-like types are more sophisticated. They hold a coordinate and a pointer to the parent object. However, the corresponding index is also stored (if it exists), along with the symmetry operator (and in reciprocal space the Friedel operator) used to obtain it. If an new coordinate is assigned to the reference, then this symmetry operator will be tried first, providing a significant performance gain. The differences between the index-like and coordinate-like reference types can be summarised as follows: - index-like types can only refer to the position of a stored datum, i.e. a coordinate in the stored ASU or a non-absent reflection in the reciprocal ASU. - coodinate-like types can refer to any possible position, and therefore also store the symmetry transformations required to get back to the stored data. 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‘HDðTË¡iÚår…Ãa§ÓIaÆ`0ˆH&“p¹ä£€Åb¯ÊuåYµ øRhF}W×A·û…h4=?ï¬9Ô‘8÷¡=èèÖe+‰ÅbÉd’¢(—Ë&SÂúúzOOËå‚—Žä£ÇãaY–¢(“ɆVŒxŒÙétÒ4„Abcðz½±XLòQœ[8fÆŒ…žwÉg‘_K1 âÎ}ÅÛŒ‘òH$ÒÓÓjU˜ìÞN¸Ý#ÑèÍƆk5UAò ¨5¤Å`¹EX,–L&#N¼Áà=^ZZ+ùh0ä&PœƒøÀãñx<ž=|.·X,0l\ù³ˆeÈçóåÄÓ5õÏË[T^¯†á“É$Ã0Íó¢—¼»*˜ÍÇFGŸŽFÓ5,¦LÃ$Lp Ê`ð‚üÜöQBË6»ØÝ}¨’í QG{‚Û>¶h˜Q™bqwlì¢Õ:TÏ®SÒ6à3‚ *ÓÕu0>›H¬D£iµeAõÁ3‚ š ‘Xõx¾¹¸øU³ù˜Ú² ˆš`AMàpœ˜™Ÿœ¼ÔØÝšDw`A áó1·Yy6‚´ØcFDCÌÌ8!>_¬îœD¯ aFDCtu¼ví\*µ67—P[Q4Ì‚h‹®®ƒW¯ž‹FÓ¤t&¼öÚkjË€ ò Ž9ÜÕuhn.‘ËåŸÞxàÀcjK„ ­ƒ¿Ñ(°Z'!d~Þ…s¨Î]Ù‚h³ùØââ+££C““—ЭtØcFDë$«>_Ìá893ãÀiTHÛƒ†A°±±íñ\.wÃá³èÖFÚte#¢z_?16öF(t£XÜU["iØcFDO$«³³‰bñžÃqÒíÁÞ3Ò~ aFD¤Rkñøj4zÓlîw»GÆÇOâØ3Ò6 an.¸¯»]ïâÞfÚÔµ.€bqÖ!:Ð}ôn;éHNh Ù“GÕ Ía†eY¬H˲„ý–F;iSﺺºNMžš: è±±7z{÷õö~ÿÔ)³Ú¢5…öв'h˜›ŽÅb¡iZm)4A P[„zim¶.ÄX­CVëÐÌŒÃíþڳϚÛCGrÚLkH90*[(Š"„ØíöÆf›L&‡‡‡ …!„eY“ÉÇ)‰P8Uk³uÚNtu|öÙGNhR½#„D"“ÉDQEQ^¯·P( âšAì&~¿¿žËåõÜf³Ùl¶`0Hñz½ápØ`0¨ý”GcÕŠ:m8 ¯w Ã0 ³´´Äó<Ïóƒ!‰ âšAÃÜ X–µÛíКG¦Øív»Ýîr¹(Šêéé‰D"(Iñz½p­àÈ¢(*‰ ¡—&Ð4 ·ƒ÷|mùááaÈz Ãôôô)òû–Αä@ B¿¤• /¡XÜM$V}>æ™gfÔVTtZR­%˶rµÊuZN­rT¨V]ë¢Z5¼ÞƒÁp8l4!‘¦i°ý-SÒnðH3ñûý~¿ßf³Åb1žç3™L8æyJT |e4!QœBÓ4MÓ<Ïg³Y8A¸¼áp˜’Íf…“óù|>Ÿ@þpN6›-)‰ñ9ƒA’Ïóƒ!çóùl6›Éd$ÂCi@V¹ÜÝ……ëÏ7ûú^þÔVWEÚ„ãr:-©VyÙV«V‰NË©U®‘rjÕ».êÑQÃë]Ë'~:¤ÁéRÍÚÚÁ`PRÎEñ<Ímá+!Qœâ÷ûÁÀkB|Ž„õõu»Ýî÷ûÁ·&d+?`Y6  ‹Å·H"Ï\"[&“çy2 “L& !~¿n!\þÒK/Ý¿øÉ'­ËËk·)Ïÿüù3jkL‰¿üËÿøÜs@`‘¼ˆÄÅ+)LyÙÊÕ*×i9µÊ5"Q™pòy^¿º¨GG ¯w&“) }b¨4M7\qð>i×Ð6D]Ù­Àh4BbYVîÑBEW˜8Å`0@Ë=ŸÏÓ4-œS¯×KÓ´Çã1 â7‹»ÝNÓôÒÒ’0ä&—¤dþÂ9òÖ××=O&“‰Åb.—K"|WW!d` wtthtôiµÕRÊ:•¦äcUj­G§DQ­í¡‹r´¬ÞÑ4ír¹o9Ã00œÜ<Å!í N—j±X Æ«ŒFc,“|»¾¾ÞÓÓN`yŠÍfƒkáM!¹VÒúƒƒÁétBÂá°ÉdZñr<Éd"¢X¹$l6›øˆ5r€Ž2D¢Æp8ìt:Å …žÊí2ä¸-ŽÛÜØØ渭åå[ÓÓµu¥Ä{ï}»BJ ÓårIÊÖãñT¨Vš¦å:-7“U¢SÐH9µêZõë¨õÎét …@ QÇî&)i{ЕÝ\öt=)xD[L î«wG\åòK S-*ÜZïº(G…Ï¥zW¹„•?¢wЕ”&™LRŸ¤³?A èÊFJc³Ù4Õ@é°Ç¬2r㧖9D3Ü@$…©bÙ¢ZK¢zW¹„Hç€=æ¦S.j·iƒ ÚF›m  …Gk•|´vÕ"æÿ¥`nU_¿ä}, and provides a template constructor to build an atom list from any vector-like object of atom-like objects. Atom lists can also be constructed using the standard vector methods, e.g. push_back(), insert(). Clipper methods requiring an atom list, e.g. a structure factor calculation may be given a Clipper::Atom_list, any class derived from that class, or a std::vector as an argument.
\section s_model_opt Optional model handling packages Two optional packages are provided for model manipulation. Both require the the 'MMDB' coordinate library by E. Krissinel to be installed (see http://msd.ebi.ac.uk/~keb/cldoc/). \subsection ss_model_mmdb MMDB interface. The MMDB interface is a lightweight interface to allow MMDB to be used with Clipper. It consists of one main class: clipper::MMDBAtom_list. This is a trivial extension of clipper::Atom_list which may be used anywhere an Atom_list would be used. It provides an additional constructor which will build an atom list from an MMDB atom selection (i.e. PPCAtom + count). Other classes are provided which may optionally be used to access information in the MMDB hierarchy in the form of Clipper objects. These are trivial extensions of MMDB objects. The MMDB objects may therefore be cast to the Clipper types to access the additional conversion methods. \subsection ss_model_mini MiniMol package. The MiniMol package is a lightweight, STL based implementation of a small subset of the MMDB functionality. It provides simpler tools for manipulating single models and their constituents. The use of STL-style code means that no memory management is required, and all common operations such as assignment and passing variables have the most obvious effect. The minimum necessary information is stored for each object in the hierarchy, however additional information of any type may be added to any object through use of the clipper::PropertyManager. Basic searching and selection tools are provided, and logical 'and' and 'or' operators may be used to combine models, polymers, and monomers. MiniMol provides an MMDBfile class which may be used to extract models from and store models back into an MMDB, or a file.
\section s_model_which Choosing a model package. If you have very specific model requirements, you may be better off writing your own objects tailored to those requirements, and then deriving an Atom_list class to allow your objects to be communicated to Clipper. Otherwise, consider the following points: - MMDB is a very powerful package, with an enormous range of facilities. However, it requires a good knowledge of C++, and the API can be quite complex. - MiniMol is a very simple package with a concise and intuitive interface. It has a simple API accessible to non-C++ programmers. MiniMol will do simple tasks much more easily than MMDB, but it won't do hard tasks at all. If MiniMol does everything you will need (or can easily be extended to do so), then it is probably a good choice, otherwise use MMDB. */ clipper-2.1/dox/minimol2.png0000644000374100011300000000300310736662154012761 00000000000000‰PNG  IHDRÄ\Mêw¨PLTE """3!33"""333D,U6DDUUfAwLffwwwa8ww8DDDUUUfffwwwˆW™bªl»wˆ‡™˜ª©»º»˜X»»XÌ‚Ýî˜ÿ¢Ì¥`ÌËÝÜîíÿýÿÎwÿþwˆˆˆ™™™ªªª»»»ÌÌÌÝÝÝÿíÌÿÿÌîîîÿÿÿ„¤Ü ÎIDATxÚ훉rÚ0@—Ö@ ¡±$¡¥¸'LjÿÿŸuå_²DÍx‡±ŽHë}’V—'à}6 …h!“Bi!T‘ª_+Ë߇xµ+Ëk QìðуK("ûoðåI)´fw—O`ÛO3{÷E)ˆ™mÏž w#¿‘áFQ´‡ aë“"0]ÛöŸ?ö^-ˆçgûfQ8z¶×=Ìݧ¢$õh?c?…]µ»Qk8ÙÓõŸa~–ÿKDIŠH1íÔrl{úm@°7 šßNEIêÑÞ?†èŠÍNö£oi¢o÷vÙ‰hò=„Ô™½¢ħX'Zˆ¢QˆµP–"[ñû¯?£Ø}ùùõ^Õ­8UܹæDqÓŒbŽ6w›x[3çá0¶6†ðÜáðü¿@8š‘hñ„çq© q3™4Ó)8ü¦–63 á4SFÛ‡@$]š ш{× ‘ri:Dî]+ÄI3ryf~øÚI]ˆ¼å3)Þ[Íî]#„¡)¹4ïHé2 \}@]¨ž3Ðktïº œ¼K³ ˆ{×·îÕq*fѺP£{×ÁðÔBú<ðq¬F-†`tßõ!ØÛQìHW‡àL4,ˆÂ)íÚ—)5¹g=§/„ðóóÍ-.D‹£KZU"vi0æ^!ÄÙÔ¨o˸7¼ÍA“µª"Dâ”×…bˆýmNʽáì¹×…HmH#é"½õï4w® á ’Gσ2x‰ÝŽoòVU€ÈÒਡ”Ha׃È—®O">˜hi"qQ0‰r¦ØH¢+^¹:!ÄϘ¦àÅÀ¹Âê]Bâ´/ A¹chBæÞE"ÛÓ(„Ô ˜DöÞ­I¹»HˆÌêÝ„쵑DI÷–…>áËA”ÛœKBÈÆ$!J½å ò·^Ò%^"A¿«BþjM"¹Ù×¢ÉVJoë„(7qèaH×’œ!L#ýKXðÌ òcÐß_ÂQ Ï–%ÓÖ,µ±#ô¢Ó”„«•Dr{PF âL‚øBd`ÊnÎJ^VøR½>ìYÍ,»ÙסäÇ-×ÔDÇ°:D)Ÿ[`XºªkºÂÕô* U>ùžu!·€ž|ÿ‘ÉxÏêxgUÿý›õW®®ß¹¾{`IËKöÅ/ò:êÔõò™ `ƒ.Æ_–µÙPŠvH&°^ÌW²èŒ·a„€=‘®Ä‹ö1Þ˜XÖjE©“-‚§dy‹MÂL®=] ,:Y€õënÛÅX›[è "èBà6hœ1‚®$ÖÑÛ?(À„àÚéJB,—V XѺ[òÛ¥µ"Õ·[òó‹Xã‚®$Öù_P€ Áµ'áËk¼ãÇŒI¥°ÜåGÛî† AWëèË7“°‚kO¤+ Ä°ÄŽÚvH¥î$ OBX“>‚¦$Ö±ì,É8 p 8ö„ºÒ¤˺[`ƒ£Wu7Y¾`AP•$tàŒÒ™Xa6מ@WBJT]'Zˆ¢…¸@pwºòÛç+ëzoÿVi!T‘Bùÿo“ÇΕe“(333>>>DUfw D 0f08w8:IMD,U6DDUUDD UU(fAwLRfS0ffwwff0wa8ww8DDDFX\UUUXXXQfl]u{fffcoqvvvˆ™ª»ÌÝîÿH™HPªP`Ì`hÝhpîpwÿwhƒŠt’š ©ˆW™bªl»w™|Hˆ‡™˜ª©»º™™HªŠP»˜XªªP»»XÌ‚Ýî˜ÿ¢Ì¥`ÌËÝÜîíÿýÌÌ`ÝÝhîÁpÿÎwîîpÿþwˆˆˆ™™™Žž¢‹¯¸ªªª»»»–½È¢Ì׸ÍÒ­ÚæÌÌÌÝÝÝÌÿÌÔìòÿíÌÿÿÌîîîïøúÿÿÿ÷¬ã¤pIDATxÚí‰cÅÆ'6v7‚HJš—šFUƒØ8‡ÕbÈÑ$¤b“Ø@Š¶‘âzűø¿ïì!iï}³ûföz_Z$y5ûæøiçíÌìzßÑø_—ì#Klé8!WÝ8üëÛ—`‡.ÎÇ¥ÇøbvÔûαKüspø‚€«vH|îts$ì¼ãØö°?zß±ÿº½ô–óæ !WÍHÑKº ÅQs q $¤ RH„)¤æ"±MHäS}Èœÿøcÿ§ÿ½þúir<êƒD¦t=ðÑÒµÞ¤ì<ÕQÍE†‚õ§eçª~j2GGÓXeç«nj6GGfOÓ !5‰££ ‡¢ì¬ÕJÍGâèÈètŒ²3W#µ ‚BHí@‚îHÔ$ ¸Zƒ„sGJõ w˜‚ ÈR«àPô Š,µ w˜‚Æ®ÒÔ:$Š,µ E‡4“ÕJ$hì*M-E‚ HVóà%²¦=@¹ - ')ä UƒJ>CBg¬*—¥kݘM6ÕµFUŒ TòËbÀrÅŽr³ cªA5¨ä3$œö„–+ 6û_KÕ ’ϯãiG \Ö€¡ $£cBå ͇ÑâŽC¸\ù0B¢1ò#!|郂nB#±¡ªˆh’Ô!±Ð¤GPAq(h’”ŠfÎ ‰ˆZ!UË¡ $â4é¶ B"^F§µPIj-„D²Œv.ÑlŒKC>g+Wã5‰Gb€~ÖBÑ$tŽÄXÂy[Es08rÜA ÿTM5 Ó^…+I ]F·TI5 î_Žä|Ĥ¸*UTƒè1‰3Û¶óÚ&„„Þ•xrSﶅ‰!aHWšŽú­`¢~Hüx;A·n%ùËæ§ÿxçÝÛ0¶Yšê‡Äí¡°n×Ñfi"$ªj³4Õ öêpx“ñWÆ6`ñí²¼‰‡Ð&c'®jå4ω›Ãkvó ·XJó\[;‡ˆÌ&?¼LH¨•ÓÁ¿1ä?WïƒȦ}ø!¡VNó ϯ9ýºí/ÜàWj6<÷öpÖ<[ÃΑÍÍáNóÀm½o å6ÏõWg•Ï/â›N{͚ǽªó#çø¯öí-<$ 6mï“:ÅJ¸!<Sâ a6KSS¸º6”ØéFýL6ê3 »J¬žì¦à%*GÕËY(è<„ø hÈð¨ŸÉ¦G:vçèÒD‚¢—¡ªå,…B|Ñq#¿FÁØѤoJ¨³ãï<Ä‚¢«Wµrf‡P ù}ðâÂH8ñÆW¤ñHN•X}ßä¨hPtÕªRÎÆqÓ•ðâ9°o}~&ë3&é÷;ZtâAÑÕª:9Kˆ’!ž ‰€Ÿ™'\9Tf§ë`]¡Š«*9K ›ž;æ8÷3'9“ hÞyT=¦y5r†G+ 'ÛÏT0ÊX“•5U@)J‘Ø^–ø`iÕceMéHX:Ör§báÞ”,Å«ÅÊš’‘,©«h@îgÊo¯<V*˜@`…TñÀ`õWÖ”ˆxPqBí,Iw)ôŠw¥!1`¯Z@ ;È_ŠWñe™%!!¸` $¤h –âU»ó( áS ¡˜Ë_ŠWåΣ$LIcˆ1Çå]U¸óPŽDdö­$˜1Çí¡+¹MVÝa+ÅHH=æ¸Ù“¼+@e‡­”"³Oè1ÇdzÙ0Y²‡­*¶Z Ö€7–Ñ•:d,!æ¸3J!±ÑÌîÆ*w©P‚„Õe}”ÉÎ4Ɉ9Îoþ&36èÔv€ªÆ„ $L;ïñ‘l[JÌñ±ÔÂNØj­bn¦$LÍ.¸üœ¤Ä—k|ܯ ò‘0"XGº!)1ÇeÇŸêƺ•¢Ž„íõ±žnÈÿ%ÈŠ9.;Ö8¿TTŠ‰œHüòPþñòão½÷¿`d8Ùò·ß&Êgyaê?ÿþð2°À0SÁR|wtv”úËVN$~ØÏ¡02¬Ð²DSåÕ_¶‰RL5 öæþþ36{Q‰„彧EUH…¥V$N=ÛÄf/©z¶±ŠŠÜòƒ‹lµpS"¦–BXxð`ÿ!›½<\eìyçÍ)þouÿÑ)v‘m<Øßÿ‚1T$à–ŸíïCB û_¼)„„¢R«{oîÙEr_V÷öÛÛ÷Þð£ö[¶zŠÿÍ.–¿¸X¬ã1Å. !¡¨Â*€ÄþŸ7ì¾Ð}Y}º·ê”dþÆ.ÝþSï’ˆ‹Üò£|1S{N)áH(*…°Š Á/”lö¯w’ÌßxC)H€-_d ÞNÅL=blC 5¥–¢›PT$ÄE7¡¢q‰RL„Deê/[„D)¦ B¢2õ—-<$ž–†ÄÓÌŒÔ _!Ö‰èõcö•óš2Ï+ir‚–MiLôq‹ª'lµ¥wR|†ø°È…”‰¤v‘„°eiL ;½¤­¶º©Û²¡»9‘˜·K$€vî k‚–£‘»-‡˜@‹,>s&‚ˆ;Dܹ¦þÉŽ˜Š5:—¢Hó¥ZüR#´Å"ç·Ül9È^dqÏ™À "çò»q #R¤Œ¹Ré‹kw$€¶häï¼–£‘»S,›þÍñ"‹{ÎNqוˆ?—oíD|ņÈ)cžT_o  3€«°åhäî4˦¶¸½Ç‹,î98AÄ]W"á\ý¹Û’T±Á0"Eʘ#•Ÿˆhm™HXŒDîNµìc/²¸çLàw;‡„s-–b&W¬á‹Q¤Œâ©DDhKD"Èb$rwºåˆ‘Å]g%ˆ¸7*‘t.s6“R±–>ï=Š”Q8UˆhmyH„XŒd?Ãòœ Ę߮3rBoT"ñ\¾;­äŠ5»qúiM""zO$í&4ŽEØM謾<&³æ:('ôF%’Ï5p'À2ŒÜ{"YL5ÈÜïYÖP‚e¿‰#ÄiŽìçBº @V¿èvåbet3GÔ%!byÚÅfmšðôØ™pR0´ŒÀ^Ïr@²la36Í¡.ljõ Ì{ aõ!»Ë@ϲÕ-RYQ¡Msô W€‘œöœ‰u GÂê‚öƒ—€¦e๠Bs&`˜B.–®ÆÜK)ÀE‚Ö%>¸–‘™@r&€¢ t|¾A AA‘×$:Ø–q™@r& ®„-¨‹iËìi¹ ‘àxë |Ëüò›-$gäJØ2E_Ž´ä”^K›Šù[ºe§bµÂôN‘ùÕ9"ñêðèæéåqêMl3¤ÈßÒ-œ(Á$Äòahì'ðHÖ©å±¢Ï'ãDþV`ÙÒ5Á_güi4$D¯V¦&z-vü`©åá%tèp.œÈßJ,[¡><É,Â>لًÓH+Ï„õÄD(‘¿UYžö<ýYÅw;Ìqçcu…KëÄN0Áž'ëƒ/}~§ü9>Ñ7ßÄÿš^±å/?HÉÌò? 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esac ;; gnu*) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH hardcode_into_libs=yes ;; hpux9* | hpux10* | hpux11*) # Give a soname corresponding to the major version so that dld.sl refuses to # link against other versions. version_type=sunos need_lib_prefix=no need_version=no case $host_cpu in ia64*) shrext_cmds='.so' hardcode_into_libs=yes dynamic_linker="$host_os dld.so" shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' if test "X$HPUX_IA64_MODE" = X32; then sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib" else sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64" fi sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec ;; 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irix5* | irix6* | nonstopux*) case $host_os in nonstopux*) version_type=nonstopux ;; *) if test "$lt_cv_prog_gnu_ld" = yes; then version_type=linux else version_type=irix fi ;; esac need_lib_prefix=no need_version=no soname_spec='${libname}${release}${shared_ext}$major' library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}' case $host_os in irix5* | nonstopux*) libsuff= shlibsuff= ;; *) case $LD in # libtool.m4 will add one of these switches to LD *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ") libsuff= shlibsuff= libmagic=32-bit;; *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ") libsuff=32 shlibsuff=N32 libmagic=N32;; *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ") libsuff=64 shlibsuff=64 libmagic=64-bit;; *) libsuff= shlibsuff= libmagic=never-match;; esac ;; esac shlibpath_var=LD_LIBRARY${shlibsuff}_PATH shlibpath_overrides_runpath=no sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}" sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}" hardcode_into_libs=yes ;; 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aCC*) _LT_AC_TAGVAR(archive_cmds, $1)='$rm $output_objdir/$soname~$CC -b ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' # Commands to make compiler produce verbose output that lists # what "hidden" libraries, object files and flags are used when # linking a shared library. # # There doesn't appear to be a way to prevent this compiler from # explicitly linking system object files so we need to strip them # from the output so that they don't get included in the library # dependencies. output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | grep "[[-]]L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; echo $list' ;; *) if test "$GXX" = yes; then _LT_AC_TAGVAR(archive_cmds, $1)='$rm $output_objdir/$soname~$CC -shared -nostdlib -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' else # FIXME: insert proper C++ library support _LT_AC_TAGVAR(ld_shlibs, $1)=no fi ;; esac ;; hpux10*|hpux11*) if test $with_gnu_ld = no; then _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir' _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=: case $host_cpu in hppa*64*|ia64*) ;; *) _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' ;; esac fi case $host_cpu in hppa*64*|ia64*) _LT_AC_TAGVAR(hardcode_direct, $1)=no _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no ;; *) _LT_AC_TAGVAR(hardcode_direct, $1)=yes _LT_AC_TAGVAR(hardcode_minus_L, $1)=yes # Not in the search PATH, # but as the default # location of the library. ;; esac case $cc_basename in CC*) # FIXME: insert proper C++ library support _LT_AC_TAGVAR(ld_shlibs, $1)=no ;; aCC*) case $host_cpu in hppa*64*) _LT_AC_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' ;; ia64*) _LT_AC_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' ;; *) _LT_AC_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' ;; esac # Commands to make compiler produce verbose output that lists # what "hidden" libraries, object files and flags are used when # linking a shared library. # # There doesn't appear to be a way to prevent this compiler from # explicitly linking system object files so we need to strip them # from the output so that they don't get included in the library # dependencies. output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | grep "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; echo $list' ;; *) if test "$GXX" = yes; then if test $with_gnu_ld = no; then case $host_cpu in hppa*64*) _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' ;; ia64*) _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' ;; *) _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' ;; esac fi else # FIXME: insert proper C++ library support _LT_AC_TAGVAR(ld_shlibs, $1)=no fi ;; esac ;; interix[[3-9]]*) _LT_AC_TAGVAR(hardcode_direct, $1)=no _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir' _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc. # Instead, shared libraries are loaded at an image base (0x10000000 by # default) and relocated if they conflict, which is a slow very memory # consuming and fragmenting process. To avoid this, we pick a random, # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link # time. 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(KAI) C++ Compiler # KCC will only create a shared library if the output file # ends with ".so" (or ".sl" for HP-UX), so rename the library # to its proper name (with version) after linking. _LT_AC_TAGVAR(archive_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib' _LT_AC_TAGVAR(archive_expsym_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib ${wl}-retain-symbols-file,$export_symbols; mv \$templib $lib' # Commands to make compiler produce verbose output that lists # what "hidden" libraries, object files and flags are used when # linking a shared library. # # There doesn't appear to be a way to prevent this compiler from # explicitly linking system object files so we need to strip them # from the output so that they don't get included in the library # dependencies. output_verbose_link_cmd='templist=`$CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1 | grep "ld"`; rm -f libconftest$shared_ext; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; echo $list' _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}--rpath,$libdir' _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic' # Archives containing C++ object files must be created using # "CC -Bstatic", where "CC" is the KAI C++ compiler. _LT_AC_TAGVAR(old_archive_cmds, $1)='$CC -Bstatic -o $oldlib $oldobjs' ;; icpc*) # Intel C++ with_gnu_ld=yes # version 8.0 and above of icpc choke on multiply defined symbols # if we add $predep_objects and $postdep_objects, however 7.1 and # earlier do not add the objects themselves. case `$CC -V 2>&1` in *"Version 7."*) _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib' _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' ;; 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templist=`echo $templist | $SED "s/\(^.*ld.*\)\( .*ld .*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; echo $list' ;; *) case `$CC -V 2>&1 | sed 5q` in *Sun\ C*) # Sun C++ 5.9 _LT_AC_TAGVAR(no_undefined_flag, $1)=' -zdefs' _LT_AC_TAGVAR(archive_cmds, $1)='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file ${wl}$export_symbols' _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' _LT_AC_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}--no-whole-archive' # Not sure whether something based on # $CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1 # would be better. output_verbose_link_cmd='echo' # Archives containing C++ object files must be created using # "CC -xar", where "CC" is the Sun C++ compiler. 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This bash problem # is reportedly fixed, but why not run on old versions too? sed '$q' "$ltmain" >> "$cfgfile" || (rm -f "$cfgfile"; exit 1) mv -f "$cfgfile" "$ofile" || \ (rm -f "$ofile" && cp "$cfgfile" "$ofile" && rm -f "$cfgfile") chmod +x "$ofile" ]) else # If there is no Makefile yet, we rely on a make rule to execute # `config.status --recheck' to rerun these tests and create the # libtool script then. ltmain_in=`echo $ltmain | sed -e 's/\.sh$/.in/'` if test -f "$ltmain_in"; then test -f Makefile && make "$ltmain" fi fi ])# AC_LIBTOOL_CONFIG # AC_LIBTOOL_PROG_COMPILER_NO_RTTI([TAGNAME]) # ------------------------------------------- AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_NO_RTTI], [AC_REQUIRE([_LT_AC_SYS_COMPILER])dnl _LT_AC_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)= if test "$GCC" = yes; then _LT_AC_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin' AC_LIBTOOL_COMPILER_OPTION([if $compiler supports -fno-rtti -fno-exceptions], lt_cv_prog_compiler_rtti_exceptions, [-fno-rtti -fno-exceptions], [], [_LT_AC_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)="$_LT_AC_TAGVAR(lt_prog_compiler_no_builtin_flag, $1) -fno-rtti -fno-exceptions"]) fi ])# AC_LIBTOOL_PROG_COMPILER_NO_RTTI # AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE # --------------------------------- AC_DEFUN([AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE], [AC_REQUIRE([AC_CANONICAL_HOST]) AC_REQUIRE([LT_AC_PROG_SED]) AC_REQUIRE([AC_PROG_NM]) AC_REQUIRE([AC_OBJEXT]) # Check for command to grab the raw symbol name followed by C symbol from nm. 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linux* | k*bsd*-gnu) if test "$host_cpu" = ia64; then symcode='[[ABCDGIRSTW]]' lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (lt_ptr) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"\2\", (lt_ptr) \&\2},/p'" fi ;; irix* | nonstopux*) symcode='[[BCDEGRST]]' ;; osf*) symcode='[[BCDEGQRST]]' ;; solaris*) symcode='[[BDRT]]' ;; sco3.2v5*) symcode='[[DT]]' ;; sysv4.2uw2*) symcode='[[DT]]' ;; sysv5* | sco5v6* | unixware* | OpenUNIX*) symcode='[[ABDT]]' ;; sysv4) symcode='[[DFNSTU]]' ;; esac # Handle CRLF in mingw tool chain opt_cr= case $build_os in mingw*) opt_cr=`echo 'x\{0,1\}' | tr x '\015'` # option cr in regexp ;; esac # If we're using GNU nm, then use its standard symbol codes. case `$NM -V 2>&1` in *GNU* | *'with BFD'*) symcode='[[ABCDGIRSTW]]' ;; esac # Try without a prefix undercore, then with it. for ac_symprfx in "" "_"; 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lt_ptr_t address; } lt_preloaded_symbols[[]] = { EOF $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (lt_ptr_t) \&\2},/" < "$nlist" | grep -v main >> conftest.$ac_ext cat <<\EOF >> conftest.$ac_ext {0, (lt_ptr_t) 0} }; #ifdef __cplusplus } #endif EOF # Now try linking the two files. mv conftest.$ac_objext conftstm.$ac_objext lt_save_LIBS="$LIBS" lt_save_CFLAGS="$CFLAGS" LIBS="conftstm.$ac_objext" CFLAGS="$CFLAGS$_LT_AC_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)" if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext}; then pipe_works=yes fi LIBS="$lt_save_LIBS" CFLAGS="$lt_save_CFLAGS" else echo "cannot find nm_test_func in $nlist" >&AS_MESSAGE_LOG_FD fi else echo "cannot find nm_test_var in $nlist" >&AS_MESSAGE_LOG_FD fi else echo "cannot run $lt_cv_sys_global_symbol_pipe" >&AS_MESSAGE_LOG_FD fi else echo "$progname: failed program was:" >&AS_MESSAGE_LOG_FD cat conftest.$ac_ext >&5 fi rm -rf conftest* conftst* # Do not use the global_symbol_pipe unless it works. if test "$pipe_works" = yes; then break else lt_cv_sys_global_symbol_pipe= fi done ]) if test -z "$lt_cv_sys_global_symbol_pipe"; then lt_cv_sys_global_symbol_to_cdecl= fi if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then AC_MSG_RESULT(failed) else AC_MSG_RESULT(ok) fi ]) # AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE # AC_LIBTOOL_PROG_COMPILER_PIC([TAGNAME]) # --------------------------------------- AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_PIC], [_LT_AC_TAGVAR(lt_prog_compiler_wl, $1)= _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)= _LT_AC_TAGVAR(lt_prog_compiler_static, $1)= AC_MSG_CHECKING([for $compiler option to produce PIC]) ifelse([$1],[CXX],[ # C++ specific cases for pic, static, wl, etc. if test "$GXX" = yes; then _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-static' case $host_os in aix*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' fi ;; amigaos*) # FIXME: we need at least 68020 code to build shared libraries, but # adding the `-m68020' flag to GCC prevents building anything better, # like `-m68040'. _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4' ;; 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*) _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac ;; *) _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac else case $host_os in aix[[4-9]]*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' else _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp' fi ;; chorus*) case $cc_basename in cxch68*) # Green Hills C++ Compiler # _LT_AC_TAGVAR(lt_prog_compiler_static, $1)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a" ;; esac ;; darwin*) # PIC is the default on this platform # Common symbols not allowed in MH_DYLIB files case $cc_basename in xlc*) _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-qnocommon' _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' ;; esac ;; dgux*) case $cc_basename in ec++*) _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' ;; ghcx*) # Green Hills C++ Compiler _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; *) ;; esac ;; freebsd* | dragonfly*) # FreeBSD uses GNU C++ ;; hpux9* | hpux10* | hpux11*) case $cc_basename in CC*) _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' if test "$host_cpu" != ia64; then _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='+Z' fi ;; aCC*) _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' case $host_cpu in hppa*64*|ia64*) # +Z the default ;; *) _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='+Z' ;; esac ;; *) ;; esac ;; interix*) # This is c89, which is MS Visual C++ (no shared libs) # Anyone wants to do a port? ;; irix5* | irix6* | nonstopux*) case $cc_basename in CC*) _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' # CC pic flag -KPIC is the default. ;; *) ;; esac ;; linux* | k*bsd*-gnu) case $cc_basename in KCC*) # KAI C++ Compiler _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,' _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; icpc* | ecpc*) # Intel C++ _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; pgCC* | pgcpp*) # Portland Group C++ compiler. _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-fpic' _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; cxx*) # Compaq C++ # Make sure the PIC flag is empty. 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Therefore, libtool *** is disabling shared libraries support. We urge you to upgrade GNU *** binutils to release 2.9.1 or newer. Another option is to modify *** your PATH or compiler configuration so that the native linker is *** used, and then restart. EOF elif $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' else _LT_AC_TAGVAR(ld_shlibs, $1)=no fi ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*) case `$LD -v 2>&1` in *\ [[01]].* | *\ 2.[[0-9]].* | *\ 2.1[[0-5]].*) _LT_AC_TAGVAR(ld_shlibs, $1)=no cat <<_LT_EOF 1>&2 *** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not *** reliably create shared libraries on SCO systems. 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Another option is to modify *** your PATH or compiler configuration so that the native linker is *** used, and then restart. _LT_EOF ;; *) if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='`test -z "$SCOABSPATH" && echo ${wl}-rpath,$libdir`' _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib' _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname,\${SCOABSPATH:+${install_libdir}/}$soname,-retain-symbols-file,$export_symbols -o $lib' else _LT_AC_TAGVAR(ld_shlibs, $1)=no fi ;; esac ;; sunos4*) _LT_AC_TAGVAR(archive_cmds, $1)='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags' wlarc= _LT_AC_TAGVAR(hardcode_direct, $1)=yes _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no ;; *) if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' else _LT_AC_TAGVAR(ld_shlibs, $1)=no fi ;; esac if test "$_LT_AC_TAGVAR(ld_shlibs, $1)" = no; then runpath_var= _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)= _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)= _LT_AC_TAGVAR(whole_archive_flag_spec, $1)= fi else # PORTME fill in a description of your system's linker (not GNU ld) case $host_os in aix3*) _LT_AC_TAGVAR(allow_undefined_flag, $1)=unsupported _LT_AC_TAGVAR(always_export_symbols, $1)=yes _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname' # Note: this linker hardcodes the directories in LIBPATH if there # are no directories specified by -L. _LT_AC_TAGVAR(hardcode_minus_L, $1)=yes if test "$GCC" = yes && test -z "$lt_prog_compiler_static"; then # Neither direct hardcoding nor static linking is supported with a # broken collect2. _LT_AC_TAGVAR(hardcode_direct, $1)=unsupported fi ;; aix[[4-9]]*) if test "$host_cpu" = ia64; then # On IA64, the linker does run time linking by default, so we don't # have to do anything special. aix_use_runtimelinking=no exp_sym_flag='-Bexport' no_entry_flag="" else # If we're using GNU nm, then we don't want the "-C" option. # -C means demangle to AIX nm, but means don't demangle with GNU nm if $NM -V 2>&1 | grep 'GNU' > /dev/null; then _LT_AC_TAGVAR(export_symbols_cmds, $1)='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\[$]2 == "T") || (\[$]2 == "D") || (\[$]2 == "B")) && ([substr](\[$]3,1,1) != ".")) { print \[$]3 } }'\'' | sort -u > $export_symbols' else _LT_AC_TAGVAR(export_symbols_cmds, $1)='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\[$]2 == "T") || (\[$]2 == "D") || (\[$]2 == "B")) && ([substr](\[$]3,1,1) != ".")) { print \[$]3 } }'\'' | sort -u > $export_symbols' fi aix_use_runtimelinking=no # Test if we are trying to use run time linking or normal # AIX style linking. 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then _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $libdir:/usr/lib:/lib' _LT_AC_TAGVAR(allow_undefined_flag, $1)="-z nodefs" _LT_AC_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols" else # Determine the default libpath from the value encoded in an empty executable. _LT_AC_SYS_LIBPATH_AIX _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath" # Warning - without using the other run time loading flags, # -berok will link without error, but may produce a broken library. _LT_AC_TAGVAR(no_undefined_flag, $1)=' ${wl}-bernotok' _LT_AC_TAGVAR(allow_undefined_flag, $1)=' ${wl}-berok' # Exported symbols can be pulled into shared objects from archives _LT_AC_TAGVAR(whole_archive_flag_spec, $1)='$convenience' _LT_AC_TAGVAR(archive_cmds_need_lc, $1)=yes # This is similar to how AIX traditionally builds its shared libraries. _LT_AC_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' fi fi ;; amigaos*) _LT_AC_TAGVAR(archive_cmds, $1)='$rm $output_objdir/a2ixlibrary.data~$echo "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$echo "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$echo "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$echo "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' _LT_AC_TAGVAR(hardcode_minus_L, $1)=yes # see comment about different semantics on the GNU ld section _LT_AC_TAGVAR(ld_shlibs, $1)=no ;; bsdi[[45]]*) _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)=-rdynamic ;; cygwin* | mingw* | pw32*) # When not using gcc, we currently assume that we are using # Microsoft Visual C++. # hardcode_libdir_flag_spec is actually meaningless, as there is # no search path for DLLs. _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)=' ' _LT_AC_TAGVAR(allow_undefined_flag, $1)=unsupported # Tell ltmain to make .lib files, not .a files. libext=lib # Tell ltmain to make .dll files, not .so files. shrext_cmds=".dll" # FIXME: Setting linknames here is a bad hack. _LT_AC_TAGVAR(archive_cmds, $1)='$CC -o $lib $libobjs $compiler_flags `echo "$deplibs" | $SED -e '\''s/ -lc$//'\''` -link -dll~linknames=' # The linker will automatically build a .lib file if we build a DLL. _LT_AC_TAGVAR(old_archive_From_new_cmds, $1)='true' # FIXME: Should let the user specify the lib program. _LT_AC_TAGVAR(old_archive_cmds, $1)='lib -OUT:$oldlib$oldobjs$old_deplibs' _LT_AC_TAGVAR(fix_srcfile_path, $1)='`cygpath -w "$srcfile"`' _LT_AC_TAGVAR(enable_shared_with_static_runtimes, $1)=yes ;; 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AC_DEFUN([LT_AC_PROG_SED], [AC_MSG_CHECKING([for a sed that does not truncate output]) AC_CACHE_VAL(lt_cv_path_SED, [# Loop through the user's path and test for sed and gsed. # Then use that list of sed's as ones to test for truncation. as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for lt_ac_prog in sed gsed; do for ac_exec_ext in '' $ac_executable_extensions; do if AS_EXECUTABLE_P(["$as_dir/$lt_ac_prog$ac_exec_ext"]); then lt_ac_sed_list="$lt_ac_sed_list $as_dir/$lt_ac_prog$ac_exec_ext" fi done done done IFS=$as_save_IFS lt_ac_max=0 lt_ac_count=0 # Add /usr/xpg4/bin/sed as it is typically found on Solaris # along with /bin/sed that truncates output. for lt_ac_sed in $lt_ac_sed_list /usr/xpg4/bin/sed; do test ! -f $lt_ac_sed && continue cat /dev/null > conftest.in lt_ac_count=0 echo $ECHO_N "0123456789$ECHO_C" >conftest.in # Check for GNU sed and select it if it is found. if "$lt_ac_sed" --version 2>&1 < /dev/null | grep 'GNU' > /dev/null; then lt_cv_path_SED=$lt_ac_sed break fi while true; do cat conftest.in conftest.in >conftest.tmp mv conftest.tmp conftest.in cp conftest.in conftest.nl echo >>conftest.nl $lt_ac_sed -e 's/a$//' < conftest.nl >conftest.out || break cmp -s conftest.out conftest.nl || break # 10000 chars as input seems more than enough test $lt_ac_count -gt 10 && break lt_ac_count=`expr $lt_ac_count + 1` if test $lt_ac_count -gt $lt_ac_max; then lt_ac_max=$lt_ac_count lt_cv_path_SED=$lt_ac_sed fi done done ]) SED=$lt_cv_path_SED AC_SUBST([SED]) AC_MSG_RESULT([$SED]) ]) m4_include([config/ccp4.m4]) m4_include([config/clipper.m4]) m4_include([config/fftw.m4]) m4_include([config/gpp4.m4]) m4_include([config/mmdb.m4]) m4_include([config/utimbuf.m4]) clipper-2.1/NEWS0000644000374100011300000000072410736662163010441 00000000000000For latest changes, see ChangeLog Status: The API has been frozen for about 3 months now. However, new material is being added to support application development. Any API changes which are required will now, if possible, involve duplicating existing APIs so that existing programs still work. Optimisations are in the pipeline for reflection data NaN handling, spacegroups, and xmaps. New i/o classes will be made available for CCP4, cif, and other data formats. clipper-2.1/clipper/0000777000374100011300000000000011372264352011454 500000000000000clipper-2.1/clipper/ccp4/0000777000374100011300000000000011372264353012306 500000000000000clipper-2.1/clipper/ccp4/ccp4_utils.cpp0000644000374100011300000001176411144270257015005 00000000000000/* mtz_utils.cpp: ccp4 utils for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "ccp4_utils.h" #include #include #include CCP4CommandInput::CCP4CommandInput( int argc, char** argv, bool echo ) { for ( int arg = 0; arg < argc; arg++ ) { std::string thisarg( argv[arg] ); if ( thisarg.length() > 2 ) if ( thisarg[0] == '-' && thisarg[1] == '-' ) thisarg = thisarg.substr(1); if ( thisarg == "-stdin" ) { std::string line; while ( !std::getline(std::cin,line).eof() ) if ( line.length() > 0 ) if ( line[0] != '#' ) { int i = line.find_first_not_of( " \t" ); if ( i != std::string::npos ) { line = line.substr( i ); i = line.find_first_of( " \t" ); std::string word = line.substr( 0, i ); if ( word[0] != '-' ) word = "-" + word; push_back( word ); if ( i != std::string::npos ) { line = line.substr( i ); i = line.find_first_not_of( " \t" ); if ( i != std::string::npos ) { line = line.substr( i ); i = line.find_last_not_of( " \t" ); push_back( line.substr( 0, i+1 ) ); } } } } } else { push_back( thisarg ); } } if ( echo ) { // echo output for ( int i = 1; i < size(); i++ ) { char c1 = ' ', c2 = ' '; // spot keywords vs negative numbers if ( (*this)[i].length() > 0 ) c1 = (*this)[i][0]; if ( (*this)[i].length() > 1 ) c2 = (*this)[i][1]; if ( c1 == '-' && ( c2 < '0' || c2 > '9' ) ) std::cout << std::endl << (*this)[i].substr(1); // keywords on newline else std::cout << " \t" << (*this)[i]; // args on sameline } std::cout << std::endl; } } CCP4Program::CCP4Program( const char* name, const char* vers, const char* rcsdate ) { name_ = name; html = ( getenv( "CCP_SUPPRESS_HTML" ) == NULL ); summ = ( getenv( "CCP_SUPPRESS_SUMMARY" ) == NULL ); CCP4::ccp4ProgramName( (char*)name ); CCP4::ccp4_prog_vers( (char*)vers ); CCP4::ccp4RCSDate( (char*)rcsdate ); summary_beg(); if ( html ) std::cout << " " << std::endl << "
" << std::endl << "
" << std::endl;
  CCP4::ccp4_banner();
  summary_end();
  CCP4::ccp4ProgramTime(1);
}


CCP4Program::~CCP4Program()
{
  std::cout << std::endl;
  summary_beg();
  std::cout << name_ << ": " << msg_ << std::endl;
  CCP4::ccp4ProgramTime(0);
  if ( html ) std::cout << "
" << std::endl << "" << std::endl; summary_end(); } void CCP4Program::summary_beg() const { if ( summ ) { if ( html ) std::cout << "" << std::endl; else std::cout << "" << std::endl; } } void CCP4Program::summary_end() const { if ( summ ) { if ( html ) std::cout << "" << std::endl; else std::cout << "" << std::endl; } } clipper-2.1/clipper/ccp4/ccp4_mtz_io.cpp0000644000374100011300000014625611371767221015157 00000000000000/* mtz_io.cpp: class file for reflection data mtz importer */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "ccp4_mtz_io.h" #include "../core/hkl_datatypes.h" #include #include #include namespace clipper { char CCP4MTZ_type_registry::names[200][12]; char CCP4MTZ_type_registry::types[200][4]; ftype32 CCP4MTZ_type_registry::scales[200]; CCP4MTZ_type_registry mtz_type_registry; CCP4MTZ_type_registry::CCP4MTZ_type_registry() { for ( int j = 0; j < 200; j++ ) names[j][0] = '\0'; add_type( "I", "J", 1.0 ); add_type( "sigI", "Q", 1.0 ); add_type( "I+", "K", 1.0 ); add_type( "sigI+", "M", 1.0 ); add_type( "I-", "K", 1.0 ); add_type( "sigI-", "M", 1.0 ); add_type( "covI+-", "C", 1.0 ); add_type( "F", "F", 1.0 ); add_type( "sigF", "Q", 1.0 ); add_type( "F+", "G", 1.0 ); add_type( "sigF+", "L", 1.0 ); add_type( "F-", "G", 1.0 ); add_type( "sigF-", "L", 1.0 ); add_type( "covF+-", "C", 1.0 ); add_type( "E", "F", 1.0 ); add_type( "sigE", "Q", 1.0 ); add_type( "E+", "G", 1.0 ); add_type( "sigE+", "L", 1.0 ); add_type( "E-", "G", 1.0 ); add_type( "sigE-", "L", 1.0 ); add_type( "covE+-", "C", 1.0 ); add_type( "A", "A", 1.0 ); add_type( "B", "A", 1.0 ); add_type( "C", "A", 1.0 ); add_type( "D", "A", 1.0 ); add_type( "phi", "P", Util::rad2d(1.0) ); add_type( "fom", "W", 1.0 ); add_type( "flag", "I", 1.0 ); add_type( "Dano", "D", 1.0 ); add_type( "sigDano", "Q", 1.0 ); } void CCP4MTZ_type_registry::add_type( const String& name, const String& type, const ftype32& scale ) { int i, j; for ( j = 0; j < 200; j++ ) if ( names[j][0] == '\0' ) break; if ( j == 200 ) Message::message( Message_fatal( "CCP4MTZ_type_registry: registry full." ) ); for ( i = 0; i < Util::min( int(name.length()), 11 ); i++ ) names[j][i] = name[i]; names[j][i] = '\0'; for ( i = 0; i < Util::min( int(type.length()), 3 ); i++ ) types[j][i] = type[i]; types[j][i] = '\0'; scales[j] = scale; } String CCP4MTZ_type_registry::type( const String& name ) { int j; for ( j = 0; j < 200; j++ ) if ( String( names[j] ) == name ) break; if ( j == 200 ) Message::message( Message_fatal( "CCP4MTZ_type_registry: name not found." ) ); return String( types[j] ); } ftype32 CCP4MTZ_type_registry::scale( const String& name ) { int j; for ( j = 0; j < 200; j++ ) if ( String( names[j] ) == name ) break; if ( j == 200 ) Message::message( Message_fatal( "CCP4MTZ_type_registry: name not found." ) ); return scales[j]; } /* return the mtz path of a column as a string */ String mtz_col_path( CMtz::MTZ* mtz, CMtz::MTZCOL* col ) { char* resultchr = CMtz::MtzColPath( mtz, col ); String resultstr( resultchr ); free(resultchr); return resultstr; } /* build a lookup of columns in a crystal */ std::vector build_lookup( CMtz::MTZ* mtzin ) { std::vector result; for (int x=0; x < CMtz::MtzNxtal(mtzin); x++) { CMtz::MTZXTAL* xtl = CMtz::MtzIxtal(mtzin,x); for (int s=0; s < CMtz::MtzNsetsInXtal(xtl); s++) { CMtz::MTZSET* set = CMtz::MtzIsetInXtal(xtl,s); for (int c=0; c < CMtz::MtzNcolsInSet(set); c++) result.push_back( CMtz::MtzIcolInSet(set,c) ); } } return result; } /* Turn a clipper path name into a list of MTZ column paths. */ const std::vector mtz_assign( const String& assign, const String& type, const String& ftype, const int& f_size ) { // Translate aassignment to mtz column names // ... loop through each list in turn std::vector mtz_names( f_size, "MNF" ); // interpret list name in terms of columns if ( assign.find( "[" ) == String::npos ) { // name is a single path: add type extenders std::vector list = ftype.split(" "); for (int i=0; i < list.size(); i++) mtz_names[i] = assign + "." + type + "." + list[i]; } else { // name is a list of mtz columns: extract column names from list String pref = assign.substr( 0, assign.find("[") ); String post = assign.substr( assign.find("[") + 1, assign.find("]") - assign.find("[") - 1 ); std::vector list = post.split(", "); for (int i=0; i < list.size(); i++) mtz_names[i] = pref + list[i]; } return mtz_names; } /* Check whether a dummy input column name has been given to suppress input or output of some of the data. */ bool is_virtual_col( const String& path ) { // test for virtual column name String name = path.tail(); return ( name=="MNF" || name=="NAN" || name=="mnf" || name=="nan" ); } /* Do glob matching on two strings. The second string may contain '*'. */ bool match_glob( const String& s1, const String& s2 ) { if ( s2.find('*') == String::npos ) return s1 == s2; String s2a = s2.substr( 0, s2.find('*') ); String s2b = s2.substr( s2.find('*') + 1 ); return ( s2a == s1.substr( 0, s2a.length() ) && s2b == s1.substr( s1.length() - s2b.length(), s2b.length() ) ); } /* Read spacegroup info from mtzin */ void read_spacegroup( CMtz::MTZ* mtzin, Spacegroup& sg ) { ftype rsym[4][4]; String symops; for ( int i = 0; i < mtzin->mtzsymm.nsym; i++ ) { for ( int j = 0; j < 4; j++ ) for ( int k = 0; k < 4; k++ ) rsym[j][k] = mtzin->mtzsymm.sym[i][j][k]; symops += Symop(rsym).format() + ";"; } sg.init( Spgr_descr( symops, Spgr_descr::Symops ) ); } /* Write spacegroup info to mtzout */ void write_spacegroup( CMtz::MTZ* mtzout, const Spacegroup& sg ) { // tables of MTZ symbols char mtzlauetab[231][8]={"?","1","-1","2","2","2","m","m","m","m","2/m","2/m","2/m","2/m","2/m","2/m","222","222","222","222","222","222","222","222","222","mm2","mm2","mm2","mm2","mm2","mm2","mm2","mm2","mm2","mm2","mm2","mm2","mm2","mm2","mm2","mm2","mm2","mm2","mm2","mm2","mm2","mm2","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","mmm","4","4","4","4","4","4","-4","-4","4/m","4/m","4/m","4/m","4/m","4/m","422","422","422","422","422","422","422","422","422","422","4mm","4mm","4mm","4mm","4mm","4mm","4mm","4mm","4mm","4mm","4mm","4mm","-4m2","-4m2","-4m2","-4m2","-42m","-42m","-42m","-42m","-42m","-42m","-4m2","-4m2","4/mmm","4/mmm","4/mmm","4/mmm","4/mmm","4/mmm","4/mmm","4/mmm","4/mmm","4/mmm","4/mmm","4/mmm","4/mmm","4/mmm","4/mmm","4/mmm","4/mmm","4/mmm","4/mmm","4/mmm","3","3","3","3","-3","-3","312","321","312","321","312","321","32","3m1","31m","3m1","31m","3m","3m","-31m","-31m","-3m1","-3m1","-3m","-3m","6","6","6","6","6","6","-6","6/m","6/m","622","622","622","622","622","622","6mm","6mm","6mm","6mm","-62m","-62m","-6m2","-6m2","6/mmm","6/mmm","6/mmm","6/mmm","23","23","23","23","23","m-3","m-3","m-3","m-3","m-3","m-3","m-3","432","432","432","432","432","432","432","432","-43m","-43m","-43m","-43m","-43m","-43m","m-3m","m-3m","m-3m","m-3m","m-3m","m-3m","m-3m","m-3m","m-3m","m-3m"}; unsigned int ccp4_code[][2] = { {0x90a34743,1003},{0x7851c0d1,1004},{0x6042abb6,4005},{0x458c0b8c,1005},{0x939daf66,1006},{0xd9a7d85a,1007},{0x5b2a5e1b,1009},{0x9b92779f,1010},{0x31194672,1011},{0x97e84b5c,1012},{0xc9e50c74,1013},{0xdc48ad2f,1014},{0xb0d2ac85,1015},{0xd756eb1b,1017},{0x10e6701,2017},{0xee8326bb,3018},{0x82570fbb,2018},{0xadb55f32,1059},{0xd5a0aa2d,1146},{0xd9a29bac,1148},{0xa20b8591,1155},{0xb951b4f7,1160},{0x219be015,1161},{0x1c80e47a,1166},{0xbb691c91,1167},{0x9b92779f,1010},{0xd9a29bac,1148},{0x1c80e47a,1166} }; String mtzlaue = String("PG")+mtzlauetab[sg.spacegroup_number()]; String mtzsymb = sg.symbol_hm(); if ( sg.symbol_hm_ext() == "H" || sg.symbol_hm_ext() == "R" ) mtzsymb = sg.symbol_hm_ext() + mtzsymb.substr(1); int mtzspgn = sg.spacegroup_number(); for ( int s = 0; s < sizeof(ccp4_code)/sizeof(ccp4_code[0]); s++ ) if ( ccp4_code[s][0] == sg.hash() ) mtzspgn = ccp4_code[s][1]; // now write the records mtzout->mtzsymm.spcgrp = mtzspgn; mtzout->mtzsymm.nsym = sg.num_symops(); mtzout->mtzsymm.nsymp = sg.num_primops(); mtzout->mtzsymm.symtyp = mtzsymb[0]; strncpy( mtzout->mtzsymm.spcgrpname, mtzsymb.c_str(), 11 ); strncpy( mtzout->mtzsymm.pgname, mtzlaue.c_str(), 11 ); for ( int i = 0; i < sg.num_symops(); i++ ) { for ( int j = 0; j < 3; j++ ) for ( int k = 0; k < 3; k++ ) mtzout->mtzsymm.sym[i][j][k] = sg.symop(i).rot()(j,k); for ( int j = 0; j < 3; j++ ) mtzout->mtzsymm.sym[i][j][3] = sg.symop(i).trn()[j]; } /* CSym::ccp4_symop symops[sg.num_symops()]; for ( int i = 0; i < sg.num_symops(); i++ ) { for ( int j = 0; j < 3; j++ ) for ( int k = 0; k < 3; k++ ) symops[i].rot[j][k] = sg.symop(i).rot()(j,k); for ( int j = 0; j < 3; j++ ) symops[i].trn[j] = sg.symop(i).trn()[j]; } CSym::CCP4SPG* cspg = CSym::ccp4_spgrp_reverse_lookup( sg.num_symops(), symops ); if ( cspg != NULL ) { float msymops[192][4][4] = {{{}}}; for ( int i = 0; i < cspg->nsymop; i++ ) CCP4::rotandtrn_to_mat4( msymops[i], cspg->symop[i] ); char symbol[20]; strncpy( symbol, cspg->symbol_xHM, 20 ); CSym::ccp4spg_name_de_colon( symbol ); char lattice[2] = { symbol[0], '\0' }; int err = ccp4_lwsymm( mtzout, cspg->nsymop, cspg->nsymop_prim, msymops, lattice, cspg->spg_ccp4_num, symbol, cspg->point_group ); if ( err == 0 ) Message::message( Message_fatal( "CCP4MTZfile::close_write: Unable to write spacegroup info. lwsymm failed." ) ); CSym::ccp4spg_free( &cspg ); } else { Message::message( Message_fatal( "CCP4MTZfile::close_write: Unable to write spacegroup info.\nCCP4 not configured or unsupported spacegroup." ) ); } */ } /* Read hierarchy from mtzin */ void read_hierarchy( CMtz::MTZ* mtzin, std::vector& crystals ) { crystals.clear(); CCP4MTZfile::crystalinf newxtl; CCP4MTZfile::datasetinf newset; CCP4MTZfile::datacolinf newcol; for (int x=0; x < CMtz::MtzNxtal(mtzin); x++) { CMtz::MTZXTAL* xtl = CMtz::MtzIxtal(mtzin,x); newxtl.crystal = MTZcrystal( xtl->xname, xtl->pname, Cell( Cell_descr( xtl->cell[0], xtl->cell[1], xtl->cell[2], xtl->cell[3], xtl->cell[4], xtl->cell[5] ) ) ); crystals.push_back( newxtl ); for (int s=0; s < CMtz::MtzNsetsInXtal(xtl); s++) { CMtz::MTZSET* set = CMtz::MtzIsetInXtal(xtl,s); newset.dataset = MTZdataset( set->dname, set->wavelength ); crystals.back().datasets.push_back( newset ); for (int c=0; c < CMtz::MtzNcolsInSet(set); c++) { const CMtz::MTZCOL* col = CMtz::MtzIcolInSet(set,c); newcol.label = col->label; newcol.type = col->type; crystals.back().datasets.back().columns.push_back( newcol ); } } } } /* Write columns to mtzout */ void write_hierarchy( CMtz::MTZ* mtzout, std::vector& crystals ) { for (int x = 0; x < crystals.size(); x ++ ) { const MTZcrystal& cxtl = crystals[x].crystal; float cp[6]; cp[0] = cxtl.a(); cp[3] = cxtl.alpha_deg(); cp[1] = cxtl.b(); cp[4] = cxtl.beta_deg(); cp[2] = cxtl.c(); cp[5] = cxtl.gamma_deg(); CMtz::MTZXTAL* mxtl = CMtz::MtzAddXtal( mtzout, cxtl.crystal_name().c_str(), cxtl.project_name().c_str(), cp ); for (int s = 0; s < crystals[x].datasets.size(); s ++ ) { const MTZdataset& cset = crystals[x].datasets[s].dataset; CMtz::MTZSET* mset = CMtz::MtzAddDataset( mtzout, mxtl, cset.dataset_name().c_str(), cset.wavelength() ); for (int c = 0; c < crystals[x].datasets[s].columns.size(); c ++ ) CMtz::MtzAddColumn( mtzout, mset, crystals[x].datasets[s].columns[c].label.c_str(), crystals[x].datasets[s].columns[c].type.c_str() ); } } } /* Build a column cross-reference */ void reference_cols( CMtz::MTZ* mtz, std::vector lookup, std::vector > hkl_data_cols, std::vector >& cols, std::vector >& scls ) { // Lookup the input columns int nlst = hkl_data_cols.size(); cols.clear(); scls.clear(); cols.resize( nlst ); scls.resize( nlst ); // handle each data list in turn. Each may have several mtz cols for ( int lst = 0; lst < nlst; lst++ ) { int ncols = hkl_data_cols[lst].size(); cols[lst].resize( ncols, -1 ); scls[lst].resize( ncols, 1.0 ); // assign the columns to mtz indexes for ( int col = 0; col < ncols; col++ ) // loop over columns in list if ( !is_virtual_col( hkl_data_cols[lst][col].path ) ) { int mcol; // loop over cols in MTZ for ( mcol = 0; mcol < lookup.size(); mcol++ ) if ( hkl_data_cols[lst][col].path == mtz_col_path( mtz, lookup[mcol] ) ) break; if ( mcol == lookup.size() ) Message::message( Message_fatal( "CCP4MTZfile - internal error" ) ); cols[lst][col] = mcol; // store column index scls[lst][col] = hkl_data_cols[lst][col].scale; } } } /*! Look up the crystal, dataset and column corresponding to the given mtz path. True if exact column match found. */ bool CCP4MTZfile::match_path( const String& path, int& x, int& s, int& c ) { std::vector names = path.split("/"); for ( x = 0; x < crystals.size(); x ++ ) if ( match_glob(crystals[x].crystal.crystal_name(),names[0]) ) for ( s = 0; s < crystals[x].datasets.size(); s ++ ) if ( match_glob(crystals[x].datasets[s].dataset.dataset_name(),names[1] ) ) for ( c = 0; c < crystals[x].datasets[s].columns.size(); c ++ ) if ( match_glob(crystals[x].datasets[s].columns[c].label,names[2]) ) return true; c = -1; for ( x = 0; x < crystals.size(); x ++ ) if ( match_glob(crystals[x].crystal.crystal_name(),names[0]) ) for ( s = 0; s < crystals[x].datasets.size(); s ++ ) if ( match_glob(crystals[x].datasets[s].dataset.dataset_name(),names[1] ) ) return false; s = -1; for ( x = 0; x < crystals.size(); x ++ ) if ( match_glob(crystals[x].crystal.crystal_name(),names[0]) ) return false; x = -1; return false; } /*! Constructing an CCP4MTZfile does nothing except flag the object as not attached to any file for either input or output */ CCP4MTZfile::CCP4MTZfile() { mode = NONE; colmode = Default; } /*! Close any files which were left open. This is particularly important since to access the MTZ file efficiently, data reads and writes are deferred until the file is closed. */ CCP4MTZfile::~CCP4MTZfile() { switch ( mode ) { case READ: close_read(); break; case WRITE: close_write(); break; case APPEND: close_append(); break; case NONE: break; } } /*! The file is opened for reading. This CCP4MTZfile object will remain attached to this file until it is closed. Until that occurs, no other file may be opened with this object, however another CCP4MTZfile object could be used to access another file. \param filename_in The input filename or pathname. */ void CCP4MTZfile::open_read( const String filename_in ) { if ( mode != NONE ) Message::message( Message_fatal( "CCP4MTZfile: open_read - File already open" ) ); // read the mtz filename_in_ = filename_in; // open file CMtz::MTZ* mtzin = CMtz::MtzGet( filename_in_.c_str(), 0 ); if ( mtzin == NULL ) Message::message( Message_fatal( "CCP4MTZfile: open_read - File missing or corrupted: "+filename_in_ ) ); CMtz::MtzAssignHKLtoBase( mtzin ); // get the list of column names/paths read_hierarchy( mtzin, crystals ); int x, s, c; match_path( "/HKL_base/HKL_base/H", x, s, c ); if ( x < 0 ) Message::message( Message_fatal( "CCP4MTZfile: No cell! " ) ); cell_ = crystals[x].crystal; // get spacegroup by decoding symops read_spacegroup( mtzin, spacegroup_ ); // get resolution: float minres, maxres; CMtz::MtzResLimits( mtzin, &minres, &maxres ); resolution_.init( 0.9999 / sqrt( Util::max(minres,maxres) ) ); if ( Util::min(minres,maxres) > 0.0 ) reslim_low = ( 1.0001 / sqrt( Util::min(minres,maxres) ) ); else reslim_low = 1000000.0; hkl_sampling_ = HKL_sampling( cell_, resolution_ ); // get title , history title_ = String( mtzin->title, 70 ); history_ = std::vector( mtzin->histlines ); for ( int h = 0; h < history_.size(); h++ ) history_[h] = String( mtzin->hist + MTZRECORDLENGTH*h, MTZRECORDLENGTH ); num_reflections_ = CMtz::MtzNref( mtzin ); // Sort order int isort[5]; CMtz::ccp4_lrsort( mtzin, isort ); sort_order_.assign(isort, isort+5); ccp4_spacegroup_number_ = mtzin->mtzsymm.spcgrp; // close file CMtz::MtzFree( mtzin ); mode = READ; } /*! Close the file after reading. This command also actually fills in the data in any HKL_data structures which have been marked for import. */ void CCP4MTZfile::close_read() { if ( mode != READ ) Message::message( Message_fatal( "CCP4MTZfile: no file open for read" ) ); // close the mtz: // this actually imports the data from the mtz file // - we save up all the work to do it on a single pass HKL hkl; float fdata_i[1000]; // file data: allow up to 1000 columns on file int idata_i[1000]; // flag data: allow up to 1000 columns on file xtype pdata[100]; // program data: allow up to 100 floats per group type float res; int ref, lst, col; // open file CMtz::MTZ* mtzin = CMtz::MtzGet( filename_in_.c_str(), 0 ); if ( mtzin == NULL ) Message::message( Message_fatal( "CCP4MTZfile: close_read - File missing or corrupted: "+filename_in_ ) ); CMtz::MtzAssignHKLtoBase( mtzin ); std::vector lookup_i = build_lookup( mtzin ); // lookup hkl cols int hklcol_i[3] = {0,1,2}; for ( int i = 0; i < lookup_i.size(); i++ ) { if ( mtz_col_path( mtzin, lookup_i[i] ).tail() == "H" ) hklcol_i[0] = i; if ( mtz_col_path( mtzin, lookup_i[i] ).tail() == "K" ) hklcol_i[1] = i; if ( mtz_col_path( mtzin, lookup_i[i] ).tail() == "L" ) hklcol_i[2] = i; } // Lookup the input columns std::vector > cols; std::vector > scls; reference_cols( mtzin, lookup_i, hkl_data_cols, cols, scls ); // update the data lists to ensure size consistency for ( lst = 0; lst < hkl_data_i.size(); lst++ ) hkl_data_i[lst]->update(); // Import the data for ( ref = 0; ref < CMtz::MtzNref( mtzin ); ref++ ) { // read reflection CMtz::ccp4_lrreff( mtzin, &res, fdata_i, idata_i, (const CMtz::MTZCOL**) &lookup_i[0], lookup_i.size(), ref+1 ); hkl = HKL( Util::intr(fdata_i[hklcol_i[0]]), Util::intr(fdata_i[hklcol_i[1]]), Util::intr(fdata_i[hklcol_i[2]]) ); // do each data list for ( lst = 0; lst < cols.size(); lst++ ) { // for each list, grab the relevent columns for ( col = 0; col < cols[lst].size(); col++ ) { // set to NaN unless readable and present Util::set_null( pdata[col] ); //pdata[col] = Util::nanf(); // try and read the data if ( cols[lst][col] >= 0 ) if ( !idata_i[cols[lst][col]] ) pdata[col] = xtype( fdata_i[cols[lst][col]] / scls[lst][col] ); } // now set the data hkl_data_i[lst]->data_import( hkl, pdata ); } } // tidy up CMtz::MtzFree( mtzin ); hkl_data_i.clear(); hkl_data_cols.clear(); crystals.clear(); assigned_paths_.clear(); filename_in_ = filename_out_ = ""; mode = NONE; } /*! The file is opened for writing. This will be a new file, created entirely from data from within the program, rather than by extending an existing file. Similar restrictions apply as for open_read(). In practice the open_append() method is usually preferred. \param filename_out The output filename or pathname. */ void CCP4MTZfile::open_write( const String filename_out ) { if ( mode != NONE ) Message::message( Message_fatal( "CCP4MTZfile: open_write - File already open" ) ); // make the h,k,l columns to the local list crystalinf newxtl; datasetinf newset; datacolinf newcol; newxtl.crystal = MTZcrystal( "HKL_base", "HKL_base", Cell() ); newset.dataset = MTZdataset( "HKL_base", 9.999 ); newcol.label = newcol.type = "H"; // add columns crystals.push_back(newxtl); crystals[0].datasets.push_back(newset); crystals[0].datasets[0].columns.push_back(newcol); newcol.label = "K"; crystals[0].datasets[0].columns.push_back(newcol); newcol.label = "L"; crystals[0].datasets[0].columns.push_back(newcol); // title, history title_ = "From Clipper CCP4MTZfile"; history_.clear(); filename_out_ = filename_out; mode = WRITE; } /*! Close the file after writing. This command also actually writes the data reflection list from the HKL_info object and the data from any HKL_data objects which have been marked for import. */ void CCP4MTZfile::close_write() { if ( mode != WRITE ) Message::message( Message_fatal( "CCP4MTZfile: no file open for write" ) ); // close the mtz: // this actually exports the data from the mtz file // - we save up all the work to do it on a single pass HKL hkl; float fdata[1000]; // file data: allow up to 1000 columns on file int idata[1000]; // flag data: allow up to 1000 columns on file xtype pdata[100]; // program data: allow up to 100 floats per group type int ref, lst, col, c; // set the cell for the HKL crystal crystals[0].crystal = MTZcrystal( "HKL_base", "HKL_base", hkl_info_o->cell()); // NOW THE ACTUAL MTZ STUFF // create the mtz object CMtz::MTZ* mtzout = CMtz::MtzMalloc( 0, 0 ); // write general info mtzout->refs_in_memory = 0; write_spacegroup( mtzout, spacegroup() ); CMtz::ccp4_lwtitl( mtzout, (char*)title_.c_str(), 0 ); std::vector newhist( history_.size()*MTZRECORDLENGTH, ' ' ); for ( int h = 0; h < history_.size(); h++ ) for ( int c = 0; c < history_[h].size(); c++ ) newhist[h*MTZRECORDLENGTH+c] = history_[h][c]; CMtz::MtzAddHistory( mtzout, (const char (*)[MTZRECORDLENGTH])&(newhist[0]), history_.size() ); // add all the stored columns to the mtz list write_hierarchy( mtzout, crystals ); std::vector lookup_o = build_lookup( mtzout ); // Lookup the output columns std::vector > cols; std::vector > scls; reference_cols( mtzout, lookup_o, hkl_data_cols, cols, scls ); // write the data int nref = hkl_info_o->num_reflections(); mtzout->fileout = CMtz::MtzOpenForWrite( filename_out_.c_str() ); for ( ref = 0; ref < nref; ref++ ) { // read/append reflection hkl = hkl_info_o->hkl_of(ref); fdata[0] = float( hkl.h() ); fdata[1] = float( hkl.k() ); fdata[2] = float( hkl.l() ); idata[0] = idata[1] = idata[2] = 0; // output reflection for ( lst = 0; lst < cols.size(); lst++ ) { // for each list, fetch the data hkl_data_o[lst]->data_export( hkl, pdata ); // and copy to the relevent columns for ( col = 0; col < cols[lst].size(); col++ ) { // set to mtz->mnf, unless we have a value for it if ( !Util::is_nan( pdata[col] ) && cols[lst][col] >= 0 ) { idata[ cols[lst][col] ] = 0; fdata[ cols[lst][col] ] = float( pdata[col] * scls[lst][col] ); } else { idata[ cols[lst][col] ] = 1; fdata[ cols[lst][col] ] = 0.0; } } } // write appended record // help: no equivalent to lrrefl! Need idata and lookup for ( c = 0; c < lookup_o.size(); c++ ) if (idata[c]) fdata[c] = CCP4::ccp4_nan().f; CMtz::ccp4_lwrefl( mtzout, fdata, &lookup_o[0], lookup_o.size(), ref+1 ); } // tidy up CMtz::MtzPut( mtzout, filename_out_.c_str() ); CMtz::MtzFree( mtzout ); hkl_data_o.clear(); hkl_data_cols.clear(); crystals.clear(); assigned_paths_.clear(); filename_in_ = filename_out_ = ""; mode = NONE; } /*! A file is opened for appending. One file is opened for reading, and a second is opened for writing. The second file will contain all the information from the first, plus any additional columns exported from HKL_data objects. \param filename_in The input filename or pathname. \param filename_out The output filename or pathname. */ void CCP4MTZfile::open_append( const String filename_in, const String filename_out ) { if ( mode != NONE ) Message::message( Message_fatal( "CCP4MTZfile: open_append - File already open" ) ); // read the mtz filename_in_ = filename_in; filename_out_ = filename_out; // open file CMtz::MTZ* mtzin = CMtz::MtzGet( filename_in_.c_str(), 0 ); if ( mtzin == NULL ) Message::message( Message_fatal( "CCP4MTZfile: open_append - File missing or corrupted: "+filename_in_ ) ); CMtz::MtzAssignHKLtoBase( mtzin ); // get the list of column names/paths read_hierarchy( mtzin, crystals ); int x, s, c; match_path( "/HKL_base/HKL_base/H", x, s, c ); if ( x < 0 ) Message::message( Message_fatal( "CCP4MTZfile: No cell! " ) ); cell_ = crystals[x].crystal; // get spacegroup by decoding symops read_spacegroup( mtzin, spacegroup_ ); // get resolution: float minres, maxres; CMtz::MtzResLimits( mtzin, &minres, &maxres ); resolution_.init( 0.9999 / sqrt( Util::max(minres,maxres) ) ); hkl_sampling_ = HKL_sampling( cell_, resolution_ ); // title, history title_ = String( mtzin->title, 70 ); history_ = std::vector( mtzin->histlines ); for ( int h = 0; h < history_.size(); h++ ) history_[h] = String( mtzin->hist + MTZRECORDLENGTH*h, MTZRECORDLENGTH ); // close file CMtz::MtzFree( mtzin ); mode = APPEND; } /*! Close the files after appending. This command actually copies the input file to the output file, adding data from any HKL_data objects which have been marked for import. */ void CCP4MTZfile::close_append() { if ( mode != APPEND ) Message::message( Message_fatal( "CCP4MTZfile: no file open for append" ) ); // close the mtz: // this actually exports the data from the mtz file // - we save up all the work to do it on a single pass HKL hkl; float fdata_i[1000]; // file data: allow up to 1000 columns on file int idata_i[1000]; // flag data: allow up to 1000 columns on file float fdata[1000]; // file data: allow up to 1000 columns on file int idata[1000]; // flag data: allow up to 1000 columns on file xtype pdata[100]; // program data: allow up to 100 floats per group type float res; int ref, lst, col, c; // NOW THE ACTUAL MTZ STUFF // open file CMtz::MTZ* mtzin = CMtz::MtzGet( filename_in_.c_str(), 0 ); if ( mtzin == NULL ) Message::message( Message_fatal( "CCP4MTZfile: close_append - File missing or corrupted: "+filename_in_ ) ); CMtz::MtzAssignHKLtoBase( mtzin ); std::vector lookup_i = build_lookup( mtzin ); // lookup hkl cols int hklcol_i[3] = {0,1,2}; for ( int i = 0; i < lookup_i.size(); i++ ) { if ( mtz_col_path( mtzin, lookup_i[i] ).tail() == "H" ) hklcol_i[0] = i; if ( mtz_col_path( mtzin, lookup_i[i] ).tail() == "K" ) hklcol_i[1] = i; if ( mtz_col_path( mtzin, lookup_i[i] ).tail() == "L" ) hklcol_i[2] = i; } // create the mtz object CMtz::MTZ* mtzout = CMtz::MtzMalloc( 0, 0 ); // write general info mtzout->refs_in_memory = 0; mtzout->mtzsymm.nsym = mtzin->mtzsymm.nsym; mtzout->mtzsymm.nsymp = mtzin->mtzsymm.nsymp; mtzout->mtzsymm.symtyp = mtzin->mtzsymm.symtyp; mtzout->mtzsymm.spcgrp = mtzin->mtzsymm.spcgrp; strncpy( mtzout->mtzsymm.spcgrpname,mtzin->mtzsymm.spcgrpname, 11 ); strncpy( mtzout->mtzsymm.pgname, mtzin->mtzsymm.pgname , 11 ); for ( int i = 0; i < mtzin->mtzsymm.nsym; i++ ) for ( int j = 0; j < 4; j++ ) for ( int k = 0; k < 4; k++ ) mtzout->mtzsymm.sym[i][j][k] = mtzin->mtzsymm.sym[i][j][k]; CMtz::ccp4_lwtitl( mtzout, (char*)title_.c_str(), 0 ); std::vector newhist( history_.size()*MTZRECORDLENGTH, ' ' ); for ( int h = 0; h < history_.size(); h++ ) for ( int c = 0; c < history_[h].size(); c++ ) newhist[h*MTZRECORDLENGTH+c] = history_[h][c]; CMtz::MtzAddHistory( mtzout, (const char (*)[MTZRECORDLENGTH])&(newhist[0]), history_.size() ); // add all the stored columns to the mtz list write_hierarchy( mtzout, crystals ); std::vector lookup_o = build_lookup( mtzout ); // Lookup the output columns std::vector > cols; std::vector > scls; reference_cols( mtzout, lookup_o, hkl_data_cols, cols, scls ); // make list of data to append std::vector cpcols( lookup_i.size() ); for ( int i = 0; i < lookup_i.size(); i++ ) { String name_i = mtz_col_path( mtzin, lookup_i[i] ); for ( c = 0; c < lookup_o.size(); c++ ) if ( name_i == mtz_col_path( mtzout, lookup_o[c] ) ) break; if ( c == lookup_o.size() ) Message::message( Message_fatal( "CCP4MTZfile - internal error" ) ); cpcols[i] = c; } // write the data int nref = CMtz::MtzNref( mtzin ); mtzout->fileout = CMtz::MtzOpenForWrite( filename_out_.c_str() ); for ( ref = 0; ref < nref; ref++ ) { // read reflection CMtz::ccp4_lrreff( mtzin, &res, fdata_i, idata_i, (const CMtz::MTZCOL**) &lookup_i[0], lookup_i.size(), ref+1 ); hkl = HKL( Util::intr(fdata_i[hklcol_i[0]]), Util::intr(fdata_i[hklcol_i[1]]), Util::intr(fdata_i[hklcol_i[2]]) ); // copy across all data from old file for ( int i = 0; i < cpcols.size(); i++ ) { fdata[cpcols[i]] = fdata_i[i]; idata[cpcols[i]] = idata_i[i]; } // output reflection for ( lst = 0; lst < cols.size(); lst++ ) { // for each list, fetch the data hkl_data_o[lst]->data_export( hkl, pdata ); // and copy to the relevent columns for ( col = 0; col < cols[lst].size(); col++ ) { // set to mtz->mnf, unless we have a value for it if ( !Util::is_nan( pdata[col] ) && cols[lst][col] >= 0 ) { idata[ cols[lst][col] ] = 0; fdata[ cols[lst][col] ] = float( pdata[col] * scls[lst][col] ); } else { idata[ cols[lst][col] ] = 1; fdata[ cols[lst][col] ] = 0.0; } } } // write appended record // help: no equivalent to lrrefl! Need idata and lookup for ( c = 0; c < lookup_o.size(); c++ ) if (idata[c]) fdata[c] = CCP4::ccp4_nan().f; CMtz::ccp4_lwrefl( mtzout, fdata, &lookup_o[0], lookup_o.size(), ref+1 ); } // tidy up CMtz::MtzPut( mtzout, filename_out_.c_str() ); CMtz::MtzFree( mtzin ); CMtz::MtzFree( mtzout ); hkl_data_i.clear(); hkl_data_o.clear(); hkl_data_cols.clear(); crystals.clear(); assigned_paths_.clear(); filename_in_ = filename_out_ = ""; mode = NONE; } /*! Get the spacegroup from the MTZ file. \return The spacegroup. */ const Spacegroup& CCP4MTZfile::spacegroup() const { return spacegroup_; } /*! Get the base cell from the MTZ file. \return The cell. */ const Cell& CCP4MTZfile::cell() const { return cell_; } /*! Get the resolution limit from the MTZ file. \return The resolution. */ const Resolution& CCP4MTZfile::resolution() const { return resolution_; } /*! Get the HKL sampling from the MTZ file. \return The hkl_sampling. */ const HKL_sampling& CCP4MTZfile::hkl_sampling() const { return hkl_sampling_; } /*! Import the list of reflection HKLs from an MTZ file into an HKL_info object. If the resolution limit of the HKL_info object is lower than the limit of the file, any excess reflections will be rejected, as will any systematic absences or duplicates. \param target The HKL_info object to be initialised. */ void CCP4MTZfile::import_hkl_list( HKL_info& target ) { if ( mode != READ ) Message::message( Message_fatal( "CCP4MTZfile: no file open for read" ) ); float fdata[1000], s; // file data: allow up to 1000 columns on file int idata[1000]; // flag data: allow up to 1000 columns on file HKL hkl; std::vector hkls; // open file CMtz::MTZ* mtzin = CMtz::MtzGet( filename_in_.c_str(), 0 ); if ( mtzin == NULL ) Message::message( Message_fatal( "CCP4MTZfile: import_hkl_list - File missing or corrupted: "+filename_in_ ) ); CMtz::MtzAssignHKLtoBase( mtzin ); std::vector lookup_i = build_lookup( mtzin ); // lookup hkl cols int hklcol_i[3] = {0,1,2}; for ( int i = 0; i < lookup_i.size(); i++ ) { if ( mtz_col_path( mtzin, lookup_i[i] ).tail() == "H" ) hklcol_i[0] = i; if ( mtz_col_path( mtzin, lookup_i[i] ).tail() == "K" ) hklcol_i[1] = i; if ( mtz_col_path( mtzin, lookup_i[i] ).tail() == "L" ) hklcol_i[2] = i; } // read the reflections from the mtz ftype slim = target.resolution().invresolsq_limit(); // read the reflections for ( int ref = 0; ref < CMtz::MtzNref( mtzin ); ref++ ) { // read reflection CMtz::ccp4_lrrefl( mtzin, &s, fdata, idata, ref ); hkl = HKL( Util::intr(fdata[hklcol_i[0]]), Util::intr(fdata[hklcol_i[1]]), Util::intr(fdata[hklcol_i[2]]) ); // check the resolution against the master cell bool in_res = hkl.invresolsq(target.cell()) < slim; // also check against any hkl_datas which have been assigned //for (int lst=0; lst < list_map_i.size(); lst++) in_res = in_res || // (hkl.invresolsq(list_map_i[lst].list->base_cell()) < slim); // store reflection if ( in_res ) hkls.push_back( hkl ); } // close file CMtz::MtzFree( mtzin ); target.add_hkl_list( hkls ); } /*! Import a complete HKL_info object. The supplied HKL_info object is examined, and if any of the parameters (spacegroup, cell, or resolution) are unset, then they will be set using values from the file. The reflections list will then be generated (the default), or imported from the file. This method is a shortcut which can generally replace most common combinations of calls to import_spacegroup(), import_cell(), import_resolution() and import_hkl_list(). \param target The HKL_info object to be initialised. \param generate Generate the list of HKLs rather than importing it from the file. */ void CCP4MTZfile::import_hkl_info( HKL_info& target, const bool generate ) { // first check if the HKL_info params are already set Spacegroup s = target.spacegroup(); Cell c = target.cell(); Resolution r = target.resolution(); // import any missing params if ( s.is_null() ) s = spacegroup_; if ( c.is_null() ) c = cell_; if ( r.is_null() ) r = resolution_; target.init( s, c, r ); // now make the HKL list if ( generate ) target.generate_hkl_list(); else import_hkl_list( target ); } /*! \param cxtl The crystal to import. \param mtzpath The mtz path of the crystal. */ void CCP4MTZfile::import_crystal( MTZcrystal& cxtl, const String mtzpath ) { int x, s, c; String colpath = mtzpath; if ( colmode == Legacy ) if ( colpath.find("/")==String::npos && colpath.find("[")==String::npos ) colpath = "/*/*/["+colpath+"]"; if ( colpath.find( "[" ) != String::npos ) { std::vector list = colpath.split( "[], " ); colpath = list[0]+list[1]; } match_path( colpath, x, s, c ); if ( x >= 0 ) cxtl = crystals[x].crystal; else Message::message( Message_fatal("CCP4MTZfile: No such crystal: "+colpath) ); return; } /*! \param cset The dataset to import. \param mtzpath The mtz path of the dataset. */ void CCP4MTZfile::import_dataset( MTZdataset& cset, const String mtzpath ) { int x, s, c; String colpath = mtzpath; if ( colmode == Legacy ) if ( colpath.find("/")==String::npos && colpath.find("[")==String::npos ) colpath = "/*/*/["+colpath+"]"; if ( colpath.find( "[" ) != String::npos ) { std::vector list = colpath.split( "[], " ); colpath = list[0]+list[1]; } match_path( colpath, x, s, c ); if ( x >= 0 && s >= 0 ) cset = crystals[x].datasets[s].dataset; else Message::message( Message_fatal("CCP4MTZfile: No such dataset: "+colpath) ); return; } void CCP4MTZfile::export_crystal( const MTZcrystal& cxtl, const String mtzpath ) { int x, s, c; match_path( mtzpath, x, s, c ); if ( x < 0 ) { crystalinf newxtl; newxtl.crystal = MTZcrystal( mtzpath.split("/")[0], cxtl.project_name(), cxtl ); crystals.push_back( newxtl ); } } void CCP4MTZfile::export_dataset( const MTZdataset& cset, const String mtzpath ){ int x, s, c; match_path( mtzpath, x, s, c ); if ( x < 0 ) Message::message( Message_fatal( "CCP4MTZfile: export_dataset - Missing crystal: "+mtzpath ) ); if ( s < 0 ) { datasetinf newset; newset.dataset = MTZdataset( mtzpath.split("/")[1], cset.wavelength() ); crystals[x].datasets.push_back( newset ); } } /*! Import data from an MTZ file into an HKL_data object. The dataset and crystal information from the first corresponding MTZ column are also returned. An MTZ column type must be present in the MTZ_type_registry for the HKL_data type element name concerned. This routine does not actually read any data, but rather marks the data to be read when the file is closed. For container objects import_chkl_data() is preferred. \param cdata The HKL_data object into which data is to be imported. \param mtzpath The MTZ column names, as a path. See \ref MTZpaths for details. */ void CCP4MTZfile::import_hkl_data( HKL_data_base& cdata, const String mtzpath ) { if ( mode != READ ) Message::message( Message_fatal( "CCP4MTZfile: import_hkl_data - no file open for read" ) ); // legacy column label handling String colpath = mtzpath; if ( colmode == Legacy ) if ( colpath.find("/")==String::npos && colpath.find("[")==String::npos ) colpath = "/*/*/["+colpath+"]"; // add the exported data columns to the local list int ncols = cdata.data_size(); std::vector col_names = mtz_assign( colpath, cdata.type(), cdata.data_names(), ncols ); std::vector dat_names = cdata.data_names().split(" "); std::vector newcols(ncols); // assign the columns to mtz indexes for ( int col=0; col < ncols; col++ ) // loop over columns in list if ( !is_virtual_col( col_names[col] ) ) { int x, s, c; match_path( col_names[col], x, s, c ); if ( c < 0 ) Message::message( Message_fatal( "CCP4MTZfile: import_hkl_data - Missing column, crystal or dataset: "+col_names[col] ) ); String ctype = CCP4MTZ_type_registry::type( dat_names[col] ); String mtype = crystals[x].datasets[s].columns[c].type; if ( ctype != mtype ) Message::message( Message_warn( "CCP4MTZfile: Mtz column type mismatch: "+crystals[x].datasets[s].columns[c].label+" "+mtype+"-"+ctype ) ); newcols[col].path = "/" + crystals[x].crystal.crystal_name() + "/" + crystals[x].datasets[s].dataset.dataset_name() + "/" + crystals[x].datasets[s].columns[c].label; newcols[col].scale = CCP4MTZ_type_registry::scale( dat_names[col] ); assigned_paths_.push_back( // store names for user query "/" + crystals[x].crystal.crystal_name() + "/" + crystals[x].datasets[s].dataset.dataset_name() + "/" + crystals[x].datasets[s].columns[c].label + " " + crystals[x].datasets[s].columns[c].type ); // initialise any uninitialised datasets (CLIPPER2) if ( cdata.is_null() ) { HKL_data flag( spacegroup_, cell_, hkl_sampling_ ); cdata.init( spacegroup_, crystals[x].crystal, hkl_sampling_ ); } } else { newcols[col].path = "NAN"; assigned_paths_.push_back( "/*/*/NAN -" ); // store names for user query } hkl_data_i.push_back( &cdata ); hkl_data_cols.push_back( newcols ); } /*! Export a complete HKL_info object, including spacegroup, cell, and list of reflection HKLs from an HKL_info object to an MTZ file. This is compulsory when writing an MTZ file, but forbidden when appending, since the HKLs will then come from the input MTZ. \param target The HKL_info object to supply the parameters. */ void CCP4MTZfile::export_hkl_info( const HKL_info& target ) { if ( mode != WRITE ) Message::message( Message_fatal( "CCP4MTZfile: export_hkl_info - no file open for write" ) ); spacegroup_ = target.spacegroup(); cell_ = target.cell(); resolution_ = target.resolution(); hkl_info_o = ⌖ } /*! Export data from an HKL_data object into an MTZ file. MTZdataset and crystal information must be supplied, and will be applied to all columns in the output MTZ. An MTZ column type must be present in the MTZ_type_registry for the HKL_data type element name concerned. This routine does not actually write any data, but rather marks the data to be written when the file is closed. Normally export_chkl_data() is preferred. \param cdata The HKL_data object from which data is to be exported. \param mtzpath The MTZ column names, as a path. See \ref MTZpaths for details. */ void CCP4MTZfile::export_hkl_data( const HKL_data_base& cdata, const String mtzpath ) { if ( mode != WRITE && mode != APPEND ) Message::message( Message_fatal( "CCP4MTZfile: export_hkl_data - no file open for write/append" ) ); // add the exported data columns to the local list int ncols = cdata.data_size(); std::vector col_names = mtz_assign( mtzpath, cdata.type(), cdata.data_names(), ncols ); std::vector dat_names = cdata.data_names().split(" "); std::vector newcols(ncols); // assign the columns to mtz indexes for ( int col=0; col < ncols; col++ ) { // loop over columns in list int x, s, c; match_path( col_names[col], x, s, c ); if ( x < 0 || s < 0 ) Message::message( Message_fatal( "CCP4MTZfile: export_hkl_data - Missing crystal or dataset: "+col_names[col] ) ); datacolinf newcol; newcol.label = col_names[col].tail(); newcol.type = CCP4MTZ_type_registry::type( dat_names[col] ); c = crystals[x].datasets[s].columns.size(); crystals[x].datasets[s].columns.push_back(newcol); newcols[col].path = "/" + crystals[x].crystal.crystal_name() + "/" + crystals[x].datasets[s].dataset.dataset_name() + "/" + crystals[x].datasets[s].columns[c].label; newcols[col].scale = CCP4MTZ_type_registry::scale( dat_names[col] ); assigned_paths_.push_back( // store names for user query "/" + crystals[x].crystal.crystal_name() + "/" + crystals[x].datasets[s].dataset.dataset_name() + "/" + crystals[x].datasets[s].columns[c].label + " " + crystals[x].datasets[s].columns[c].type ); } hkl_data_o.push_back( &cdata ); hkl_data_cols.push_back( newcols ); } /*! Import data from an MTZ into a CHKL_data object. If they don't already exist, then CMTZcrystal and CMTZdataset objects will be created to match the MTZ crystal and dataset information for the first MTZ column used. These new objects will be children of the parent CHKL_info object, and this CHKL_data will be moved to become a child of the CMTZdataset object. Thus, to import data into a CHKL_data, you must first create a CHKL_data anywhere below a parent HKL_info. Then call this method, and the object will be moved to a position below the HKL_info corresponding to its position in the data hierarchy in the MTZ file. The following code imports data, dataset, and crystal from an MTZ file: \code CHKL_info myhkl; // must be given cell, spacegroup, and HKL list. ... CHKL_data mydata CCP4MTZfile file = open_read("in.mtz"); file.import_chkl_data( mydata, "native/CuKa/[FP,SIGFP]" ); file.close_read(); \endcode An MTZ column type must be present in the MTZ_type_registry for the HKL_data type element name concerned. This routine does not actually read any data, but rather marks the data to be read when the file is closed. \param target The HKL_data object into which data is to be imported. \param mtzpath The MTZ column names, as a path. See \ref MTZpaths for details. \param path Where to put this in the data hierarchy, overriding the MTZ crystal and dataset. */ void CCP4MTZfile::import_chkl_data( Container& target, const String mtzpath, const String path ) { if ( mode != READ ) Message::message( Message_fatal( "CCP4MTZfile: no file open for read" ) ); // get this object HKL_data_base* hp = dynamic_cast(&target); if ( hp == NULL ) Message::message( Message_fatal( "CCP4MTZfile: import object not HKL_data" ) ); // and the parent hkl_info CHKL_info* chkl = target.parent_of_type_ptr(); if ( chkl == NULL ) Message::message( Message_fatal( "CCP4MTZfile: import HKL_data has no HKL_info" ) ); // now import the data MTZcrystal xtl; MTZdataset set; import_crystal ( xtl, mtzpath ); import_dataset ( set, mtzpath ); import_hkl_data( *hp, mtzpath ); Container *cxtl, *cset; // check for matching crystals String xtlname = path.notail().notail().tail(); if ( xtlname == "" ) xtlname = xtl.crystal_name(); cxtl = chkl->find_path_ptr( xtlname ); if ( cxtl == NULL ) { cxtl = new CMTZcrystal( *chkl, xtlname, xtl ); cxtl->set_destroyed_with_parent(); // (use garbage collection for this obj) } // check for matching datasets String setname = path.notail().tail(); if ( setname == "" ) setname = set.dataset_name(); cset = cxtl->find_path_ptr( setname ); if ( cset == NULL ) { cset = new CMTZdataset( *cxtl, setname, set ); cset->set_destroyed_with_parent(); // (use garbage collection for this obj) } // move the data to the new dataset String datname = path.tail(); if ( datname == "" ) datname = mtzpath.tail(); target.move( cset->path() + "/" + datname ); } /*! Export data from a CHKL_data object to an MTZ. The object must have a parent Cdataset and CMTZcrystal to provide the MTZ crystal and dataset information. The MTZ file will be checked for names matching the names of these objects, and the new MTZ columns will be added to the corresponding dataset if it exists, otherwise it will be created. An MTZ column type must be present in the MTZ_type_registry for the HKL_data type element name concerned. This routine does not actually write any data, but rather marks the data to be written when the file is closed. \param target The HKL_data object from which data is to be exported. \param mtzpath The MTZ column names, as a path. See \ref MTZpaths for details. */ void CCP4MTZfile::export_chkl_data( Container& target, const String mtzpath ) { if ( mode != WRITE && mode != APPEND ) Message::message( Message_fatal( "CCP4MTZfile: no file open for write/append" ) ); // get this object HKL_data_base* hp = dynamic_cast( &target ); if ( hp == NULL ) Message::message( Message_fatal( "CCP4MTZfile: export object not HKL_data" ) ); // get parent objects MTZdataset* dp = target.parent_of_type_ptr(); if ( dp == NULL ) Message::message( Message_fatal( "CCP4MTZfile: HKL_data has no parent MTZdataset" ) ); MTZcrystal* xp = target.parent_of_type_ptr(); if ( xp == NULL ) Message::message( Message_fatal( "CCP4MTZfile: HKL_data has no parent MTZcrystal" ) ); export_crystal( *xp, mtzpath ); export_dataset( *dp, mtzpath ); export_hkl_data( *hp, mtzpath ); } /*! Return a vector of all the columns in the MTZ file, including crystal, dataset and type information. The result is a vector of Strings. Each String contains text of the form '/CrystalName/DatasetName/ColumnName Type'. */ std::vector CCP4MTZfile::column_paths() const { std::vector result; int x, s, c; for ( x = 0; x < crystals.size(); x ++ ) for ( s = 0; s < crystals[x].datasets.size(); s ++ ) for ( c = 0; c < crystals[x].datasets[s].columns.size(); c ++ ) result.push_back( "/" + crystals[x].crystal.crystal_name() + "/" + crystals[x].datasets[s].dataset.dataset_name() + "/" + crystals[x].datasets[s].columns[c].label + " " + crystals[x].datasets[s].columns[c].type ); return result; } /*! Return a vector of all the columns in the MTZ file used for the previous call to import_hkl_data or export_hkl_data. The result is a vector of Strings. Each String contains text of the form '/CrystalName/DatasetName/ColumnName Type'. This function is commonly used to add an output column to the same crystal and dataset as a particular input column. e.g. \code String opcol = mtzfile.assigned_paths()[0].notail() + "/[FWT,PHIWT]"; \endcode */ const std::vector& CCP4MTZfile::assigned_paths() const { return assigned_paths_; } String CCP4MTZfile::title() const { return title_; } void CCP4MTZfile::set_title( const String& title ) { title_ = title; } std::vector CCP4MTZfile::history() const { return history_; } int CCP4MTZfile::num_reflections() const {return num_reflections_;} std::vector CCP4MTZfile::sort_order() const {return sort_order_;} ftype32 CCP4MTZfile::low_res_limit() const {return reslim_low;} int CCP4MTZfile::ccp4_spacegroup_number() const {return ccp4_spacegroup_number_;} void CCP4MTZfile::set_history( const std::vector& history ) { std::vector histnew; histnew.insert( histnew.end(), history.begin() , history.end() ); histnew.insert( histnew.end(), history_.begin(), history_.end() ); history_ = histnew; } void CCP4MTZfile::set_column_label_mode( CCP4MTZcolumn_label_mode mode ) { colmode = mode; } /* old form for compatibility */ void CCP4MTZfile::import_hkl_data( HKL_data_base& cdata, MTZdataset& cset, MTZcrystal& cxtl, const String mtzpath ) { import_crystal ( cxtl, mtzpath ); import_dataset ( cset, mtzpath ); import_hkl_data( cdata, mtzpath ); } /* old form for compatibility */ void CCP4MTZfile::export_hkl_data( const HKL_data_base& cdata, const MTZdataset& cset, const MTZcrystal& cxtl, const String mtzpath ) { export_crystal( cxtl, mtzpath ); export_dataset( cset, mtzpath ); export_hkl_data( cdata, mtzpath ); } /*! Get the column labels from the MTZ file. \return Array of labels. */ std::vector CCP4MTZfile::column_labels() const { std::vector result; for ( int x = 0; x < crystals.size(); x++ ) for ( int s = 0; s < crystals[x].datasets.size(); s++ ) for ( int c = 0; c < crystals[x].datasets[s].columns.size(); c++ ) result.push_back( "/"+crystals[x].crystal.crystal_name()+"/"+crystals[x].datasets[s].dataset.dataset_name()+"/" +crystals[x].datasets[s].columns[c].label+" "+crystals[x].datasets[s].columns[c].type); return result; } } // namespace clipper clipper-2.1/clipper/ccp4/ccp4_map_io.cpp0000644000374100011300000005755711247655136015132 00000000000000/* map_io.cpp: class file for reflection data map importer */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "ccp4_map_io.h" #include namespace clipper { /*! Constructing an CCP4MAPfile does nothing except flag the object as not attached to any file for either input or output */ CCP4MAPfile::CCP4MAPfile() { mode = NONE; } /*! Close any files which were left open. This is particularly important since to access the MAP file efficiently, data reads and writes are deferred until the file is closed. */ CCP4MAPfile::~CCP4MAPfile() { switch ( mode ) { case READ: close_read(); break; case WRITE: close_write(); break; case NONE: break; } } /*! The file is opened for reading. This CCP4MAPfile object will remain attached to this file until it is closed. Until that occurs, no other file may be opened with this object, however another CCP4MAPfile object could be used to access another file. \param filename_in The input filename or pathname. */ void CCP4MAPfile::open_read( const String filename_in ) { if ( mode != NONE ) Message::message( Message_fatal( "CCP4MAPfile: open_read - File already open" ) ); filename = filename_in; mode = READ; // read the file header char symop[81]; int grid[3], orderfms[3], orderxyz[3], dim[3], gfms0[3], gfms1[3]; float cp[6]; CMap_io::CMMFile* file = (CMap_io::CMMFile*)CMap_io::ccp4_cmap_open( filename.c_str(), O_RDONLY ); if ( file == NULL ) Message::message( Message_fatal( "CCP4MAPfile: open_read - File missing or corrupted: "+filename ) ); CMap_io::ccp4_cmap_get_cell( file, cp ); CMap_io::ccp4_cmap_get_grid( file, grid ); CMap_io::ccp4_cmap_get_order( file, orderfms ); CMap_io::ccp4_cmap_get_dim( file, dim ); CMap_io::ccp4_cmap_get_origin( file, gfms0 ); // get grid bound and axis order for ( int i = 0; i < 3; i++ ) gfms1[i] = gfms0[i] + dim[i] - 1; for ( int i = 0; i < 3; i++ ) orderxyz[orderfms[i]-1] = i; // get spacegroup String symops; for ( int i = 0; i < CMap_io::ccp4_cmap_num_symop( file ); i++ ) { CMap_io::ccp4_cmap_seek_symop( file, i, SEEK_SET ); CMap_io::ccp4_cmap_get_symop( file, symop ); symops += String( symop ) + ";"; } CMap_io::ccp4_cmap_close( file ); // store header info spacegroup_ = Spacegroup( Spgr_descr( symops, Spgr_descr::Symops ) ); cell_ = Cell( Cell_descr( cp[0], cp[1], cp[2], cp[3], cp[4], cp[5] ) ); grid_sam_ = Grid_sampling( grid[0], grid[1], grid[2] ); grid_map_ = Grid_range( Coord_grid( gfms0[orderxyz[0]], gfms0[orderxyz[1]], gfms0[orderxyz[2]] ), Coord_grid( gfms1[orderxyz[0]], gfms1[orderxyz[1]], gfms1[orderxyz[2]] ) ); } /*! Close the file after reading. */ void CCP4MAPfile::close_read() { if ( mode != READ ) Message::message( Message_fatal( "CCP4MAPfile: no file open for read" ) ); mode = NONE; } /*! The file is opened for writing. This will be a new file, created entirely from data from within the program, rather than by extending an existing file. Similar restrictions apply as for open_read(). \param filename_out The output filename or pathname. */ void CCP4MAPfile::open_write( const String filename_out ) { if ( mode != NONE ) Message::message( Message_fatal( "CCP4MAPfile: open_write - File already open" ) ); filename = filename_out; mode = WRITE; } /*! Close the file after writing. */ void CCP4MAPfile::close_write() { if ( mode != WRITE ) Message::message( Message_fatal( "CCP4MAPfile: no file open for write" ) ); mode = NONE; } /*! When writing an NXmap, the cell for the output map must be set using set_cell(). Note that the NXmap is rather more general than the CCP4 map, since it can take an arbitrary rotation+skew matrix. The resulting map will only be sensible if the NXmap grid skew matrix reflects the supplied cell. This is not possible in the general case. (Alternatively, opening an equivalent map for read and then closing it again will also set the cell). \param cell The cell description for the output map file. */ void CCP4MAPfile::set_cell( const Cell& cell ) { if ( mode != WRITE ) Message::message( Message_fatal( "CCP4MAPfile: no file open for write" ) ); cell_ = cell; } /*! Get the spacegroup from the MTZ file. \return The spacegroup. */ const Spacegroup& CCP4MAPfile::spacegroup() const { return spacegroup_; } /*! Get the base cell from the MTZ file. \return The cell. */ const Cell& CCP4MAPfile::cell() const { return cell_; } /*! Get the grid sampling from the MTZ file. \return The grid sampling. */ const Grid_sampling& CCP4MAPfile::grid_sampling() const { return grid_sam_; } /*! Import a complete Xmap object. The supplied Xmap object is examined, and if any of the parameters (spacegroup, cell, or grid_sampling) are unset, then they will be set using values from the file. The data is the imported from the file. If the spacegroups mismatch, the resulting map will obey its spacegroup symmetry, but no expansion will be performed if the file has a higher symmetry and only holds an asymmetric unit. \param xmap The Xmap to be imported. */ template void CCP4MAPfile::import_xmap( Xmap& xmap ) const { if ( mode != READ ) Message::message( Message_fatal( "CCP4MAPfile: no file open for read" ) ); // first check if the HKL_info params are already set Spacegroup s = xmap.spacegroup(); Cell c = xmap.cell(); Grid_sampling r = xmap.grid_sampling(); // import any missing params if ( s.is_null() ) s = spacegroup_; if ( c.is_null() ) c = cell_; if ( r.is_null() ) r = grid_sam_; xmap.init( s, c, r ); // read the file header int orderfms[3], orderxyz[3], dim[3], gfms0[3], gfms1[3]; CMap_io::CMMFile* file = (CMap_io::CMMFile*)CMap_io::ccp4_cmap_open( filename.c_str(), O_RDONLY ); if ( file == NULL ) Message::message( Message_fatal( "CCP4MAPfile: import_xmap - File missing or corrupted: "+filename ) ); CMap_io::ccp4_cmap_get_order( file, orderfms ); CMap_io::ccp4_cmap_get_dim( file, dim ); CMap_io::ccp4_cmap_get_origin( file, gfms0 ); int dmode = CMap_io::ccp4_cmap_get_datamode( file ); if ( dmode != 0 && dmode != 2 ) Message::message( Message_fatal( "CCP4CCP4MAPfile: unsupported data mode" ) ); // get grid bound and axis order for ( int i = 0; i < 3; i++ ) gfms1[i] = gfms0[i] + dim[i] - 1; for ( int i = 0; i < 3; i++ ) orderxyz[orderfms[i]-1] = i; // read the map data int n0 = (gfms1[0]-gfms0[0]+1); int n1 = n0 * (gfms1[1]-gfms0[1]+1); std::vector section( n1 ); int index, g[3]; Xmap_base::Map_reference_coord x( xmap ); for ( g[2] = gfms0[2]; g[2] <= gfms1[2]; g[2]++ ) { index = 0; CMap_io::ccp4_cmap_read_section( file, §ion[0] ); if ( dmode == 0 ) for ( int i = n1-1; i >= 0; i-- ) // deal with byte maps section[i] = float(((unsigned char*)§ion[0])[i]); for ( g[1] = gfms0[1]; g[1] <= gfms1[1]; g[1]++ ) { for ( g[0] = gfms0[0]; g[0] <= gfms1[0]; g[0]++ ) { x.set_coord( Coord_grid( g[orderxyz[0]], g[orderxyz[1]], g[orderxyz[2]] ) ); xmap[x] = T( section[ index++ ] ); } } } // done CMap_io::ccp4_cmap_close( file ); } /*! \param xmap The Xmap to be exported. */ template void CCP4MAPfile::export_xmap( const Xmap& xmap ) { if ( mode != WRITE ) Message::message( Message_fatal( "CCP4MAPfile: no file open for write" ) ); const char* title = "From clipper Xmap "; char symop[80]; int grid[3], orderfms[3], orderxyz[3], dim[3], gfms0[3], gfms1[3]; float cp[6]; int spg = xmap.spacegroup().descr().spacegroup_number(); // spacegroup // get axis order switch ( spg ) { case 1: case 2: case 3: case 4: case 10: case 16: case 17: case 18: case 20: case 21: case 23: orderfms[0] = 2; orderfms[1] = 1; orderfms[2] = 3; break; default: orderfms[0] = 3; orderfms[1] = 1; orderfms[2] = 2; break; } for ( int i = 0; i < 3; i++ ) orderxyz[orderfms[i]-1] = i; // grids for ( int i = 0; i < 3; i++ ) { grid[i] = xmap.grid_sampling()[i]; gfms0[orderxyz[i]] = xmap.grid_asu().min()[i]; gfms1[orderxyz[i]] = xmap.grid_asu().max()[i]; } Cell_descr cd = xmap.cell().descr(); cp[0] = cd.a(); cp[3] = cd.alpha_deg(); cp[1] = cd.b(); cp[4] = cd.beta_deg (); cp[2] = cd.c(); cp[5] = cd.gamma_deg(); for ( int i = 0; i < 3; i++ ) dim[i] = gfms1[i] - gfms0[i] + 1; CMap_io::CMMFile* file = (CMap_io::CMMFile*)CMap_io::ccp4_cmap_open( filename.c_str(), O_WRONLY ); if ( file == NULL ) Message::message( Message_fatal( "CCP4MAPfile: export_xmap - File missing or corrupted: "+filename ) ); CMap_io::ccp4_cmap_set_cell( file, cp ); CMap_io::ccp4_cmap_set_grid( file, grid ); CMap_io::ccp4_cmap_set_order( file, orderfms ); CMap_io::ccp4_cmap_set_dim( file, dim ); CMap_io::ccp4_cmap_set_origin( file, gfms0 ); CMap_io::ccp4_cmap_set_spacegroup( file, spg ); CMap_io::ccp4_cmap_set_title( file, title ); CMap_io::ccp4_cmap_set_datamode( file, 2 ); // write symops for ( int i = 0; i < xmap.spacegroup().num_symops(); i++ ) { String strop = xmap.spacegroup().symop(i).format(); for ( int j = 0; j < 80; j++ ) symop[j] = ' '; for ( int j = 0; j < strop.length(); j++ ) symop[j] = strop[j]; CMap_io::ccp4_cmap_set_symop( file, symop ); } // write the map data int n0 = (gfms1[0]-gfms0[0]+1); int n1 = n0 * (gfms1[1]-gfms0[1]+1); std::vector section( n1 ); int index, g[3]; Xmap_base::Map_reference_coord x( xmap ); for ( g[2] = gfms0[2]; g[2] <= gfms1[2]; g[2]++ ) { index = 0; for ( g[1] = gfms0[1]; g[1] <= gfms1[1]; g[1]++ ) { for ( g[0] = gfms0[0]; g[0] <= gfms1[0]; g[0]++ ) { x.set_coord( Coord_grid( g[orderxyz[0]], g[orderxyz[1]], g[orderxyz[2]] ) ); section[ index++ ] = float( xmap[x] ); } } CMap_io::ccp4_cmap_write_section( file, §ion[0] ); } // done CMap_io::ccp4_cmap_close( file ); } /*! \param nxmap The NXmap to be imported. */ template void CCP4MAPfile::import_nxmap( NXmap& nxmap ) const { if ( mode != READ ) Message::message( Message_fatal( "CCP4MAPfile: no file open for read" ) ); nxmap.init( cell_, grid_sam_, grid_map_ ); // read the file header int orderfms[3], orderxyz[3], dim[3], gfms0[3], gfms1[3]; CMap_io::CMMFile* file = (CMap_io::CMMFile*)CMap_io::ccp4_cmap_open( filename.c_str(), O_RDONLY ); if ( file == NULL ) Message::message( Message_fatal( "CCP4MAPfile: import_nxmap - File missing or corrupted: "+filename ) ); CMap_io::ccp4_cmap_get_order( file, orderfms ); CMap_io::ccp4_cmap_get_dim( file, dim ); CMap_io::ccp4_cmap_get_origin( file, gfms0 ); int dmode = CMap_io::ccp4_cmap_get_datamode( file ); if ( dmode != 0 && dmode != 2 ) Message::message( Message_fatal( "CCP4CCP4MAPfile: unsupported data mode" ) ); // get grid bound and axis order for ( int i = 0; i < 3; i++ ) gfms1[i] = gfms0[i] + dim[i] - 1; for ( int i = 0; i < 3; i++ ) orderxyz[orderfms[i]-1] = i; // read the map data int n0 = (gfms1[0]-gfms0[0]+1); int n1 = n0 * (gfms1[1]-gfms0[1]+1); std::vector section( n1 ); int index, g[3]; for ( g[2] = 0; g[2] <= gfms1[2]-gfms0[2]; g[2]++ ) { index = 0; CMap_io::ccp4_cmap_read_section( file, §ion[0] ); if ( dmode == 0 ) for ( int i = n1-1; i >= 0; i-- ) // deal with byte maps section[i] = float(((unsigned char*)§ion[0])[i]); for ( g[1] = 0; g[1] <= gfms1[1]-gfms0[1]; g[1]++ ) { for ( g[0] = 0; g[0] <= gfms1[0]-gfms0[0]; g[0]++ ) { nxmap.set_data( Coord_grid( g[orderxyz[0]], g[orderxyz[1]], g[orderxyz[2]] ), T( section[ index++ ] ) ); } } } // done CMap_io::ccp4_cmap_close( file ); } /*! The cell for the output map must have been set using set_cell_descr(). Note that the NXmap is rather more general than the CCP4 map, since it can take an arbitrary rotation+skew matrix. The resulting map will only be sensible if the NXmap grid skew matrix reflects the supplied cell. This is not possible in the general case. \param nxmap The NXmap to be exported. */ template void CCP4MAPfile::export_nxmap( const NXmap& nxmap ) { if ( mode != WRITE ) Message::message( Message_fatal( "CCP4MAPfile: no file open for write" ) ); const char* title = "From clipper NXmap "; const char* symop = "X, Y, Z "; int grid[3], orderfms[3], orderxyz[3], dim[3], gfms0[3], gfms1[3]; float cp[6]; int spg = 1; // spacegroup orderfms[0] = 2; orderfms[1] = 1; orderfms[2] = 3; // axis order for ( int i = 0; i < 3; i++ ) orderxyz[orderfms[i]-1] = i; /* Because CCP4 maps don't allow an arbitrary skew matrix, we have to jump through hoops to try and fit an NXmap into one. This code will work for those cases where it is possible and produce garbage otherwise. Don't even try to understand this unless you are pretty smart. */ // cell (set by user, or from previous map) cp[0] = cell_.descr().a(); cp[3] = cell_.descr().alpha_deg(); cp[1] = cell_.descr().b(); cp[4] = cell_.descr().beta_deg (); cp[2] = cell_.descr().c(); cp[5] = cell_.descr().gamma_deg(); // grid (calculated to fit with cell provided - assume angles match) Coord_frac c0, c1; c0 = nxmap.coord_orth( Coord_map(0,0,0) ).coord_frac(cell_); c1 = nxmap.coord_orth( Coord_map( nxmap.grid().nu(), nxmap.grid().nv(), nxmap.grid().nw() ) ).coord_frac(cell_); grid_sam_ = Grid_sampling( Util::intr( ftype(nxmap.grid().nu())/(c1.u()-c0.u()) ), Util::intr( ftype(nxmap.grid().nv())/(c1.v()-c0.v()) ), Util::intr( ftype(nxmap.grid().nw())/(c1.w()-c0.w()) ) ); Coord_grid g0 = c0.coord_grid(grid_sam_); Coord_grid g1 = g0 + Coord_grid(nxmap.grid()) - Coord_grid(1,1,1); grid_map_ = Grid_range( g0, g1 ); for ( int i = 0; i < 3; i++ ) { grid[i] = grid_sam_[i]; gfms0[orderxyz[i]] = grid_map_.min()[i]; gfms1[orderxyz[i]] = grid_map_.max()[i]; } for ( int i = 0; i < 3; i++ ) dim[i] = gfms1[i] - gfms0[i] + 1; CMap_io::CMMFile* file = (CMap_io::CMMFile*)CMap_io::ccp4_cmap_open( filename.c_str(), O_WRONLY ); if ( file == NULL ) Message::message( Message_fatal( "CCP4MAPfile: export_nxmap - File missing or corrupted: "+filename ) ); CMap_io::ccp4_cmap_set_cell( file, cp ); CMap_io::ccp4_cmap_set_grid( file, grid ); CMap_io::ccp4_cmap_set_order( file, orderfms ); CMap_io::ccp4_cmap_set_dim( file, dim ); CMap_io::ccp4_cmap_set_origin( file, gfms0 ); CMap_io::ccp4_cmap_set_spacegroup( file, spg ); CMap_io::ccp4_cmap_set_title( file, title ); CMap_io::ccp4_cmap_set_datamode( file, 2 ); // write symops CMap_io::ccp4_cmap_set_symop( file, symop ); // write the map data int n0 = (gfms1[0]-gfms0[0]+1); int n1 = n0 * (gfms1[1]-gfms0[1]+1); std::vector section( n1 ); int index, g[3]; for ( g[2] = 0; g[2] <= gfms1[2]-gfms0[2]; g[2]++ ) { index = 0; for ( g[1] = 0; g[1] <= gfms1[1]-gfms0[1]; g[1]++ ) { for ( g[0] = 0; g[0] <= gfms1[0]-gfms0[0]; g[0]++ ) { section[ index++ ] = float( nxmap.get_data( Coord_grid( g[orderxyz[0]], g[orderxyz[1]], g[orderxyz[2]] ) ) ); } } CMap_io::ccp4_cmap_write_section( file, §ion[0] ); } // done CMap_io::ccp4_cmap_close( file ); } /*! Import a complete Xmap object. The supplied Xmap object is examined, and if any of the parameters (spacegroup, cell, or grid_sampling) are unset, then they will be set using values from the file. The data is the imported from the file. If the spacegroups mismatch, the resulting map will obey its spacegroup symmetry, but no expansion will be performed if the file has a higher symmetry and only holds an asymmetric unit. This version performs a check on the symmatry of the inport map file. If the import map contains less than a complete ASU, or if it contains more than an ASU and symmetry related positions contain inconsistent values, then an error is returned. This function is only available for float or double maps. \param xmap The Xmap to be imported. \return The ASU check flag */ template CCP4MAPfile::ASUerror CCP4MAPfile::import_xmap_check_asu( Xmap& xmap, T missing ) const { if ( mode != READ ) Message::message( Message_fatal( "CCP4MAPfile: no file open for read" ) ); // first check if the HKL_info params are already set Spacegroup s = xmap.spacegroup(); Cell c = xmap.cell(); Grid_sampling r = xmap.grid_sampling(); // import any missing params if ( s.is_null() ) s = spacegroup_; if ( c.is_null() ) c = cell_; if ( r.is_null() ) r = grid_sam_; xmap.init( s, c, r ); // set missing flag T flag; Util::set_null( flag ); xmap = flag; ftype maxerr = 0.0; // read the file header int orderfms[3], orderxyz[3], dim[3], gfms0[3], gfms1[3]; CMap_io::CMMFile* file = (CMap_io::CMMFile*)CMap_io::ccp4_cmap_open( filename.c_str(), O_RDONLY ); if ( file == NULL ) Message::message( Message_fatal( "CCP4MAPfile: import_xmap - File missing or corrupted: "+filename ) ); CMap_io::ccp4_cmap_get_order( file, orderfms ); CMap_io::ccp4_cmap_get_dim( file, dim ); CMap_io::ccp4_cmap_get_origin( file, gfms0 ); int dmode = CMap_io::ccp4_cmap_get_datamode( file ); if ( dmode != 0 && dmode != 2 ) Message::message( Message_fatal( "CCP4CCP4MAPfile: unsupported data mode" ) ); // get grid bound and axis order for ( int i = 0; i < 3; i++ ) gfms1[i] = gfms0[i] + dim[i] - 1; for ( int i = 0; i < 3; i++ ) orderxyz[orderfms[i]-1] = i; // read the map data int n0 = (gfms1[0]-gfms0[0]+1); int n1 = n0 * (gfms1[1]-gfms0[1]+1); std::vector section( n1 ); int index, g[3]; Xmap_base::Map_reference_coord x( xmap ); for ( g[2] = gfms0[2]; g[2] <= gfms1[2]; g[2]++ ) { index = 0; CMap_io::ccp4_cmap_read_section( file, §ion[0] ); if ( dmode == 0 ) for ( int i = n1-1; i >= 0; i-- ) // deal with byte maps section[i] = float(((unsigned char*)§ion[0])[i]); for ( g[1] = gfms0[1]; g[1] <= gfms1[1]; g[1]++ ) { for ( g[0] = gfms0[0]; g[0] <= gfms1[0]; g[0]++ ) { x.set_coord( Coord_grid( g[orderxyz[0]], g[orderxyz[1]], g[orderxyz[2]] ) ); T oldval = xmap[x]; T newval = T( section[ index++ ] ); if ( !Util::is_nan( oldval ) && !Util::is_nan( newval ) ) { maxerr = Util::max( maxerr, fabs( ftype( newval - oldval ) ) ); newval = Util::max( oldval, newval ); } xmap[x] = newval; } } } // done CMap_io::ccp4_cmap_close( file ); // ASU checks typedef Xmap_base::Map_reference_index MRI; ASUerror asuerr = ASUCORRECT; ftype s0(0.0), s1(0.0), s2(0.0); for ( MRI ix = xmap.first(); !ix.last(); ix.next() ) { T val = xmap[ix]; if ( Util::is_null( val ) ) { asuerr = ASUINCOMPLETE; xmap[ix] = missing; } else { s0 += 1.0; s1 += val; s2 += val*val; } } if ( s0 > 0.5 ) s2 = sqrt( s2*s0 - s1*s1 ) / s0; if ( maxerr > 0.01*s2 ) asuerr = ASUINCONSISTENT; return asuerr; } // instantiate the template functions for all reasonable types // xmap import template void CCP4MAPfile::import_xmap( Xmap& xmap ) const; template void CCP4MAPfile::import_xmap( Xmap& xmap ) const; template void CCP4MAPfile::import_xmap( Xmap& xmap ) const; template void CCP4MAPfile::import_xmap( Xmap& xmap ) const; template void CCP4MAPfile::import_xmap( Xmap& xmap ) const; template void CCP4MAPfile::import_xmap( Xmap& xmap ) const; template void CCP4MAPfile::import_xmap( Xmap& xmap ) const; template void CCP4MAPfile::import_xmap( Xmap& xmap ) const; // xmap export template void CCP4MAPfile::export_xmap( const Xmap& xmap ); template void CCP4MAPfile::export_xmap( const Xmap& xmap ); template void CCP4MAPfile::export_xmap( const Xmap& xmap ); template void CCP4MAPfile::export_xmap( const Xmap& xmap ); template void CCP4MAPfile::export_xmap( const Xmap& xmap ); template void CCP4MAPfile::export_xmap( const Xmap& xmap ); template void CCP4MAPfile::export_xmap( const Xmap& xmap ); template void CCP4MAPfile::export_xmap( const Xmap& xmap ); // nxmap import template void CCP4MAPfile::import_nxmap( NXmap& nxmap ) const; template void CCP4MAPfile::import_nxmap( NXmap& nxmap ) const; template void CCP4MAPfile::import_nxmap( NXmap& nxmap ) const; template void CCP4MAPfile::import_nxmap( NXmap& nxmap ) const; template void CCP4MAPfile::import_nxmap( NXmap& nxmap ) const; template void CCP4MAPfile::import_nxmap( NXmap& nxmap ) const; template void CCP4MAPfile::import_nxmap( NXmap& nxmap ) const; template void CCP4MAPfile::import_nxmap( NXmap& nxmap ) const; // nxmap export template void CCP4MAPfile::export_nxmap( const NXmap& nxmap ); template void CCP4MAPfile::export_nxmap( const NXmap& nxmap ); template void CCP4MAPfile::export_nxmap( const NXmap& nxmap ); template void CCP4MAPfile::export_nxmap( const NXmap& nxmap ); template void CCP4MAPfile::export_nxmap( const NXmap& nxmap ); template void CCP4MAPfile::export_nxmap( const NXmap& nxmap ); template void CCP4MAPfile::export_nxmap( const NXmap& nxmap ); template void CCP4MAPfile::export_nxmap( const NXmap& nxmap ); // xmap import and check template CCP4MAPfile::ASUerror CCP4MAPfile::import_xmap_check_asu( Xmap& xmap, ftype32 missing ) const; template CCP4MAPfile::ASUerror CCP4MAPfile::import_xmap_check_asu( Xmap& xmap, ftype64 missing ) const; } // namespace clipper clipper-2.1/clipper/ccp4/Makefile.am0000644000374100011300000000126611372264321014256 00000000000000# Makefile.am, passed: clipper/ccp4, extracted subdir: ccp4 # in dir /home/cowtan/clipper-autoconf/clipper-2.1/clipper/ccp4 ## -*- mode: Makefile; mode: font-lock -*- INCLUDES=${FFTW_CXXFLAGS} library_include_HEADERS = \ ccp4_map_io.h \ ccp4_mtz_io.h \ ccp4_mtz_types.h \ ccp4_utils.h lib_LTLIBRARIES = libclipper-ccp4.la libclipper_ccp4_la_SOURCES = \ ccp4_map_io.cpp \ ccp4_mtz_io.cpp \ ccp4_mtz_types.cpp \ ccp4_utils.cpp library_includedir = $(pkgincludedir)/ccp4 libclipper_ccp4_la_LDFLAGS = -version-info @CLIPPER_LT_VERSION@ libclipper_ccp4_la_LIBADD = \ $(top_builddir)/clipper/core/libclipper-core.la \ $(CCP4_LIBS) clipper-2.1/clipper/ccp4/ccp4_mtz_types.h0000644000374100011300000001013310736662163015344 00000000000000/*! \file lib/mtz_types.h Header file for CCP4 data types for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_MTZ_TYPES #define CLIPPER_MTZ_TYPES #include "../core/container_hkl.h" namespace clipper { //! CCP4 crystal object class MTZcrystal : public Cell { public: //! null constructor MTZcrystal() {} //! constructor: takes crystal+project name and cell MTZcrystal( const String& xname, const String& pname, const Cell& cell ); //! get crystal name const String& crystal_name() const; //! get project name const String& project_name() const; protected: String xname_, pname_; }; //! CCP4 dataset object class MTZdataset { public: //! null constructor MTZdataset() {} //! constructor: takes wavelength MTZdataset( const String& dname, const ftype& wavel ); //! get dataset name const String& dataset_name() const; //! get wavelength const ftype& wavelength() const; protected: String dname_; ftype wavel_; }; //! CMTZcrystal identifier /*! CMTZcrystal: This has a name and a cell. It overrides the base cell for any HKL_datas below it, and mirrors the mtz++ crystal element. */ class CMTZcrystal : public Container, public MTZcrystal { public: //! null constructor CMTZcrystal() {} //! constructor: from MTZcrystal CMTZcrystal( Container& parent, const String& name, const MTZcrystal& xtl ) : Container( parent, name ), MTZcrystal( xtl ) {} }; //! CMTZdataset identifier /*! CMTZdataset: This has a name and a wavelength. It gives the wavelength for any HKL_datas below it, and mirrors the mtz++ dataset element. */ class CMTZdataset : public Container, public MTZdataset { public: //! null constructor CMTZdataset() {} //! constructor: from MTZdataset CMTZdataset( Container& parent, const String& name, const MTZdataset& set ) : Container( parent, name ), MTZdataset( set ) {} }; } // namespace clipper #endif clipper-2.1/clipper/ccp4/ccp4_map_io.h0000644000374100011300000001037511247463260014555 00000000000000/*! \file ccp4/ccp4_map_io.h Header file for reflection data map importer */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_CCP4_MAP_IO #define CLIPPER_CCP4_MAP_IO #include "../core/container_map.h" namespace clipper { //! MAP import/export parent class for clipper objects /*! This is the import/export class which can be linked to a CCP4 map file and be used to transfer data into or out of a Clipper data structure. */ class CCP4MAPfile { public: //! Constructor: does nothing CCP4MAPfile(); //! Destructor: close any file that was left open ~CCP4MAPfile(); //! Open a file for read access void open_read( const String filename_in ); //! Close a file after reading void close_read(); //! Open a file for read access void open_write( const String filename_out ); //! Close a file after reading void close_write(); //! set cell desription (NXmap write only) void set_cell( const Cell& cell ); //! get file spacegroup const Spacegroup& spacegroup() const; //! get file cell const Cell& cell() const; //! get file grid_sampling const Grid_sampling& grid_sampling() const; //! import data to Xmap template void import_xmap( Xmap& xmap ) const; //! export data from Xmap template void export_xmap( const Xmap& xmap ); //! import data to NXmap template void import_nxmap( NXmap& nxmap ) const; //! export data from NXmap template void export_nxmap( const NXmap& nxmap ); enum ASUerror { ASUCORRECT, ASUINCOMPLETE, ASUINCONSISTENT }; //! import data to Xmap and check ASU (float/double only) template ASUerror import_xmap_check_asu( Xmap& xmap, T missing ) const; protected: enum MAPmode { NONE, READ, WRITE }; String filename; //!< filename MAPmode mode; //!< mode ASUerror asuerr; //!< ASU error flag // header info Spacegroup spacegroup_; //!< map spacegroup Cell cell_; //!< map cell Grid_sampling grid_sam_; //!< cell grid sampling Grid_range grid_map_; //!< map grid extent }; } // namespace clipper #endif clipper-2.1/clipper/ccp4/Makefile.in0000644000374100011300000004536611372264332014302 00000000000000# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, # Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY, to the extent permitted by law; without # even the implied warranty of MERCHANTABILITY or FITNESS FOR A # PARTICULAR PURPOSE. @SET_MAKE@ # Makefile.am, passed: clipper/ccp4, extracted subdir: ccp4 # in dir 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clipper-2.1/clipper/ccp4/ccp4_mtz_types.cpp0000644000374100011300000000543110736662163015704 00000000000000/* mtz_types.cpp: ccp4 data types for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "ccp4_mtz_types.h" namespace clipper { MTZcrystal::MTZcrystal( const String& xname, const String& pname, const Cell& cell ) : Cell( cell ) { xname_ = xname; pname_ = pname; } const String& MTZcrystal::crystal_name() const { return xname_; } const String& MTZcrystal::project_name() const { return pname_; } MTZdataset::MTZdataset( const String& dname, const ftype& wavel ) { dname_ = dname; wavel_ = wavel; } const String& MTZdataset::dataset_name() const { return dname_; } const ftype& MTZdataset::wavelength() const { return wavel_; } } // namespace clipper clipper-2.1/clipper/ccp4/ccp4_utils.h0000644000374100011300000000576010736662163014460 00000000000000/*! \file ccp4_utils.h Header file for CCP4 utilities for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_MTZ_UTILS #define CLIPPER_MTZ_UTILS #include #include //! Mini-parser for command line input /*! This class removes any escape characters from the command-line, and if a -stdin option is present reads standard input and adds the result to the argument list. */ class CCP4CommandInput : public std::vector { public: CCP4CommandInput( int argc, char** argv, bool echo = false ); }; //! class for program start and end class CCP4Program { public: CCP4Program( const char* name, const char* vers, const char* rcsdate ); ~CCP4Program(); void summary_beg() const; void summary_end() const; void set_termination_message( std::string msg ) { msg_ = msg; } private: bool html, summ; std::string name_, msg_; }; #endif clipper-2.1/clipper/ccp4/ccp4_mtz_io.h0000644000374100011300000002365611371767243014626 00000000000000/*! \file lib/mtz_io.h Header file for reflection data mtz importer */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_CCP4_MTZ_IO #define CLIPPER_CCP4_MTZ_IO #include "ccp4_mtz_types.h" namespace clipper { //! CCP4MTZ import/export type registry /*! This class acts as a registry of import/export data types, which provide a translation from a data element name to an MTZ column type. The registry is instantiated statically as \c mtz_type_registry and initialised with a list of built-in datatypes. */ class CCP4MTZ_type_registry { public: //! constructor: initialise the registry with some built-in types CCP4MTZ_type_registry(); //! add a new type to the registry static void add_type( const String& name, const String& type, const ftype32& scale ); //! return MTZ column type static String type( const String& name ); //! return MTZ column type static ftype32 scale( const String& name ); private: static char names[200][12]; static char types[200][4]; static ftype32 scales[200]; }; //! MTZ import/export parent class for clipper objects /*! This is the import/export class which can be linked to an mtz file and be used to transfer data into or out of a Clipper data structure. Note that to access the MTZ file efficiently, data reads and writes are deferred until the file is closed. \anchor MTZpaths \par MTZpaths: MTZ column specification Note that the specification of the MTZ column names is quite versatile. The MTZ crystal and dataset must be specified, although the wildcard '*' may replace a complete name. Several MTZ columns will correspond to a single datalist. This may be handled in two ways: -# A simple name. The corresponding MTZ columns will be named after the datalist name, a dot, the datalist type, a dot, and a type name for the indivudal column, i.e. /crystal/dataset/datalist.listtype.coltype This is the default Clipper naming convention for MTZ data. -# A comma separated list of MTZ column names enclosed in square brackets. This allows MTZ data from legacy applications to be accessed. \n Thus, for example, an MTZPATH of \code native/CuKa/fsigfdata \endcode expands to MTZ column names of \code fsigfdata.F_sigF.F fsigfdata.F_sigF.sigF \endcode with a crystal called \c native and a dataset called \c CuKa. An MTZPATH of \code native/CuKa/[FP,SIGFP] \endcode expands to MTZ column names of \code FP SIGFP \endcode with a crystal called \c native and a dataset called \c CuKa. \archor MTZ_iotypes \par MTZ_iotypes: Import/export types For an HKL_data object to be imported or exported, an MTZ_iotype for that datatype must exist in the MTZ_iotypes_registry. MTZ_iotypes are defined for all the built-in datatypes. If you need to store a user defined type in an MTZ file, then register that type with the MTZ_iotypes_registry. */ class CCP4MTZfile { public: enum CCP4MTZcolumn_label_mode { Default, Normal, Legacy }; //! Constructor: does nothing CCP4MTZfile(); //! Destructor: close any file that was left open ~CCP4MTZfile(); //! Open a file for read access void open_read( const String filename_in ); //! Close a file after reading void close_read(); //! Open a file for read access void open_append( const String filename_in, const String filename_out ); //! Close a file after reading void close_append(); //! Open a file for read access void open_write( const String filename_out ); //! Close a file after reading void close_write(); //! get file spacegroup const Spacegroup& spacegroup() const; //! get file cell const Cell& cell() const; //! get file resolution const Resolution& resolution() const; //! get file HKL sampling const HKL_sampling& hkl_sampling() const; //! read the reflection list from the MTZ void import_hkl_list( HKL_info& target ); //! import parameters of HKL_info object from the MTZ void import_hkl_info( HKL_info& target, const bool generate = true ); //! import crystal info from the MTZ void import_crystal( MTZcrystal& cxtl, const String mtzpath ); //! import dataset info from the MTZ void import_dataset( MTZdataset& cset, const String mtzpath ); //! mark a hkl_data for import from MTZ void import_hkl_data( HKL_data_base& cdata, const String mtzpath ); //! write the reflection list to the MTZ (along with cell, spacegroup) void export_hkl_info( const HKL_info& target ); //! export crystal info from the MTZ void export_crystal( const MTZcrystal& cxtl, const String mtzpath ); //! export dataset info from the MTZ void export_dataset( const MTZdataset& cset, const String mtzpath ); //! mark a hkl_data for export to MTZ void export_hkl_data( const HKL_data_base& cdata, const String mtzpath ); //! mark a chkl_data container for import from MTZ void import_chkl_data( Container& target, const String mtzpath, const String path = "" ); //! mark a chkl_data container for export to MTZ void export_chkl_data( Container& target, const String mtzpath ); //! return a vector of strings of the file column names/path std::vector column_paths() const; //! return a vector of strings of column names/paths just allocated const std::vector& assigned_paths() const; //! get title for MTZ file String title() const; //! set title for MTZ file void set_title( const String& title ); //! get history for MTZ file std::vector history() const; //! add to history for MTZ file void set_history( const std::vector& history ); //! return number of reflections in file int num_reflections() const; //! return sort order std::vector sort_order() const; //! return low resolution limits from file (A) ftype32 low_res_limit() const; //! CCP4 space group number int ccp4_spacegroup_number() const; //! set default column label interpretation mode void set_column_label_mode( CCP4MTZcolumn_label_mode mode ); //! \deprecated std::vector column_labels() const; //! \deprecated void import_hkl_data( HKL_data_base& cdata, MTZdataset& cset, MTZcrystal& cxtl, const String mtzpath ); //! \deprecated void export_hkl_data( const HKL_data_base& cdata, const MTZdataset& cset, const MTZcrystal& cxtl, const String mtzpath ); // index from clipper data lists to mtz columns (by name) struct datacolinf{String label; String type;}; struct datasetinf{MTZdataset dataset;std::vector columns;}; struct crystalinf{MTZcrystal crystal;std::vector datasets;}; struct hkldatacol{String path; ftype scale;}; private: enum MTZmode { NONE, READ, WRITE, APPEND }; //! mtz object String filename_in_, filename_out_; std::vector crystals; HKL_info* hkl_info_i; const HKL_info* hkl_info_o; std::vector hkl_data_i; std::vector hkl_data_o; std::vector > hkl_data_cols; std::vector assigned_paths_; //! mode MTZmode mode; CCP4MTZcolumn_label_mode colmode; //! File spacegroup, cell, resolution Spacegroup spacegroup_; Cell cell_; Resolution resolution_; HKL_sampling hkl_sampling_; //! title, history String title_; std::vector history_; //! Number of reflections int num_reflections_; //! Sort order std::vector sort_order_; //! low resolution limit from file header ftype32 reslim_low; //! CCP4 space group number int ccp4_spacegroup_number_; // generic methods bool match_path( const String& path, int& x, int& s, int& c ); }; } // namespace clipper #endif clipper-2.1/clipper/clipper-cif.h0000644000374100011300000000022610736662163013743 00000000000000/* Clipper header file */ /* (C) 2000-2002 Kevin Cowtan */ #ifndef CLIPPER_CIF_H #define CLIPPER_CIF_H #include "clipper/cif/cif_data_io.h" #endif clipper-2.1/clipper/minimol/0000777000374100011300000000000011372264353013121 500000000000000clipper-2.1/clipper/minimol/minimol_seq.h0000644000374100011300000001134110736662163015526 00000000000000/*! \file minimol_seq.h Header file for atomic sequence types */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_MINIMOL_SEQ #define CLIPPER_MINIMOL_SEQ #include "minimol.h" namespace clipper { //! Polymer sequence object /*! The polymer sequence object represents the named sequence of a single chain. */ class MPolymerSequence { public: MPolymerSequence() {} //!< null constructor const String& id() const { return id_; } //!< get sequence ID void set_id( const String& s ); //!< set sequence ID const String& sequence() const { return seq_; } //!< get sequence ID void set_sequence( const String& s ); //!< set sequence ID static String id_tidy( const String& id ) { return id; } //!< convert ID to std format static bool id_match( const String& id1, const String& id2, const MM::MODE& mode ) { return id1 == id2; } //!< compare two ids private: String id_; String seq_; }; //! Molecule sequence object /*! The molecule sequence object is a list of polymer sequence objects representing the named sequences of all the chains in a molecule. */ class MMoleculeSequence { public: //! number of polymer sequences in model int size() const { return children.size(); } //! get polymer sequence const MPolymerSequence& operator[] ( const int& i ) const { return children[i]; } //! set polymer sequence MPolymerSequence& operator[] ( const int& i ) { return children[i]; } //! get polymer sequence by id const MPolymerSequence& find( const String& n, const MM::MODE mode=MM::UNIQUE ) const; //! set polymer sequence by id MPolymerSequence& find( const String& n, const MM::MODE mode=MM::UNIQUE ); //! lookup polymer sequence by id int lookup( const String& str, const MM::MODE& mode ) const; void insert( const MPolymerSequence& add, int pos=-1 ); //!< add polymer sequence bool is_null() const { return (size()==0); } //!< test for null model private: typedef MPolymerSequence CHILDTYPE; std::vector children; }; //! Sequence alignment obeject /*! Provides methods to find an optimal alignment between two sequences. */ class MSequenceAlign { public: enum TYPE { GLOBAL, LOCAL }; MSequenceAlign( TYPE type = GLOBAL, ftype match_score = 1.0, ftype miss_score = -0.5, ftype gap_score = -1.0 ) : type_(type), scrmat(match_score), scrmis(miss_score), scrgap(gap_score) {} std::pair,std::vector > operator() ( const String& seq1, const String& seq2 ) const; private: TYPE type_; ftype32 scrmat, scrmis, scrgap; }; } // namespace clipper #endif clipper-2.1/clipper/minimol/minimol_seq.cpp0000644000374100011300000001350510740720031016045 00000000000000/* minimol_seq.cpp: atomic model types */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "minimol_seq.h" namespace clipper { // PolymerSequence void MPolymerSequence::set_id( const String& s ) { id_ = id_tidy( s ); } void MPolymerSequence::set_sequence( const String& s ) { seq_ = s; } // MoleculeSequence /*! Lookup monomer by ID. If mode=UNIQUE, the insertion code must match, otherwise the first monomer with the same sequence number is returned. \param n The monomer ID. \param mode The search mode. \return The monomer. */ const MPolymerSequence& MMoleculeSequence::find( const String& n, const MM::MODE mode ) const { int i = lookup( n, mode ); if ( i < 0 ) Message::message(Message_fatal("MMolecule: no such monomer")); return children[i]; } /*! See MMolecule::find() */ MPolymerSequence& MMoleculeSequence::find( const String& n, const MM::MODE mode ) { int i = lookup( n, mode ); if ( i < 0 ) Message::message(Message_fatal("MMolecule: no such monomer")); return children[i]; } int MMoleculeSequence::lookup( const String& str, const MM::MODE& mode ) const { String sid = CHILDTYPE::id_tidy( str ); for ( int i = 0; i < children.size(); i++ ) if ( CHILDTYPE::id_match( sid, children[i].id(), mode ) ) return i; return -1; } void MMoleculeSequence::insert( const MPolymerSequence& add, int pos ) { if ( pos < 0 ) children.push_back( add ); else children.insert( children.begin() + pos, add ); } std::pair,std::vector > MSequenceAlign::operator() ( const String& seq1, const String& seq2 ) const { enum dirn { NUL, U, L, UL }; // directions: null, up, left, diag // pad sequences at start to allow first symbol to be aligned std::string s1 = " " + seq1; std::string s2 = " " + seq2; int n1 = s1.length(); int n2 = s2.length(); // initilize matrices. Matrix scores( n1, n2, 0.0 ); Matrix dirns ( n1, n2, NUL ); // now fill first row/col if ( type_ != LOCAL ) { for ( int i1 = 1; i1 < n1; i1++ ) { scores(i1,0) = scores(i1-1,0) + scrgap; dirns(i1,0) = U; } for ( int i2 = 1; i2 < n2; i2++ ) { scores(0,i2) = scores(0,i2-1) + scrgap; dirns(0,i2) = L; } } // fill the rest of the matrix for ( int i1 = 1; i1 < n1; i1++ ) for ( int i2 = 1; i2 < n2; i2++ ) { // calc bonus for a match at this position ftype32 s = ( s1[i1] == s2[i2] ) ? scrmat : scrmis; // calc best score obtainable for this position ftype32 sul = scores(i1-1,i2-1) + s; ftype32 su = scores(i1-1,i2 ) + scrgap; ftype32 sl = scores(i1 ,i2-1) + scrgap; // and select if ( sul >= su && sul >= sl ) { scores(i1,i2) = sul; dirns(i1,i2) = UL; } else if ( su > sl ) { scores(i1,i2) = su; dirns(i1,i2) = U; } else { scores(i1,i2) = sl; dirns(i1,i2) = L; } if ( type_ == LOCAL ) if ( scores(i1,i2) <= 0.0 ) { scores(i1,i2) = 0.0; dirns(i1,i2) = NUL; } } // now trace backwards to build up the best sequence alignment std::vector r1(seq1.length(),-1), r2(seq2.length(),-1); int i1, i2; if ( type_ == LOCAL ) { // local match: start with highest scoring position i1 = i2 = 0; for ( int j1 = 0; j1 < n1; j1++ ) for ( int j2 = 0; j2 < n2; j2++ ) if ( scores(j1,j2) > scores(i1,i2) ) { i1 = j1; i2 = j2; } } else { // global match: start with last element i1 = n1 - 1; i2 = n2 - 1; } while ( dirns(i1,i2) != NUL ) { if ( dirns(i1,i2) == U ) { i1 = i1 - 1; } else if ( dirns(i1,i2) == L ) { i2 = i2 - 1; } else { i1 = i1 - 1; i2 = i2 - 1; r1[i1] = i2; r2[i2] = i1; } } std::pair,std::vector > result(r1,r2); return result; } } // namespace clipper clipper-2.1/clipper/minimol/minimol_utils.h0000644000374100011300000001123010736662163016073 00000000000000/*! \file minimol_utils.h Header file for minimol utils */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_MINIMOL_UTILS #define CLIPPER_MINIMOL_UTILS #include "minimol.h" namespace clipper { //! Class for holding the indices of an atom within a MiniMol molecule class /*! The indices remain valid only while no changes are made to the MiniMol object. */ class MAtomIndex { public: //! null constructor MAtomIndex() { p = -1; } //! constructor: from polymer, monomer and atom numbers. MAtomIndex( const int& polymer, const int& monomer, const int& atom ) : p(polymer), m(monomer), a(atom) {} //! test if object has been initialised bool is_null() const { return p >= 0; } const int& polymer() const { return p; } //!< return polymer index const int& monomer() const { return m; } //!< return monomer index const int& atom() const { return a; } //!< return atom index friend inline bool operator < ( MAtomIndex i1, MAtomIndex i2 ) { return ( i1.p < i2.p || ( i1.p == i2.p && ( i1.m < i2.m || ( i1.m == i2.m && i1.a < i2.a ) ) ) ); } private: int p, m, a; }; //! Class for holding the indices of an atom within a MiniMol molecule class /*! The indices remain valid only while no changes are made to the MiniMol object. This class can also hold the number of a symmetry operator. */ class MAtomIndexSymmetry : public MAtomIndex { public: //! null constructor MAtomIndexSymmetry() {} //! constructor: from polymer, monomer and atom numbers. MAtomIndexSymmetry( const int& polymer, const int& monomer, const int& atom , const int& symm ) : MAtomIndex(polymer,monomer,atom), s(symm) {} const int& symmetry() const { return s; } //!< return symmetry index private: int s; }; //! Find atoms in the vicinity of some coordinate in real space /*! Uses a fast non-bonded atom search. */ class MAtomNonBond { public: //! null constructor MAtomNonBond() {} //! constructor: from MiniMol and grid radius MAtomNonBond( const clipper::MiniMol& mol, double rad = 5.0 ); //! get a list of atoms in the rough vicinity of a coordinate std::vector atoms_near( const clipper::Coord_orth& co, double rad ) const; std::vector operator() ( const clipper::Coord_orth& co, double rad ) const; void debug() const; private: const MiniMol* mol_; double rad_; Spacegroup spgr; Cell cell; Grid_sampling grid; std::vector lookup; std::vector atoms; }; } // namespace clipper #endif clipper-2.1/clipper/minimol/minimol_utils.cpp0000644000374100011300000001476310736662163016444 00000000000000/* minimol_utils.cpp: minimol utils */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "minimol_utils.h" #include namespace clipper { /*! Set up a non-bonding type search database to allow fast access to a list of atoms within a given radius of a given coordinate. Setting up the class takes a litle (but not a great deal) of time, returning coordinates is very fast indeed. You can also specify a radius to the constructor, which determines memory use as (24*cell volume/rad^3) bytes. For small radii, set this to the search radius or larger. For large radii, a smaller value may improve performance. \param mol The MiniMol object containing the atoms. \param rad A radius for sampling crystal space. */ MAtomNonBond::MAtomNonBond( const clipper::MiniMol& mol, double rad ) { // store params mol_ = &mol; rad_ = rad; cell = mol.cell(); spgr = mol.spacegroup(); // pick a grid for the cell grid = Grid_sampling( Util::intc(1.0/(rad_*cell.a_star())), Util::intc(1.0/(rad_*cell.b_star())), Util::intc(1.0/(rad_*cell.c_star()))); // now create a list of atoms in the cell int gi; Coord_frac cf; std::vector > iatoms; for ( int p = 0; p < mol.size(); p++ ) for ( int m = 0; m < mol[p].size(); m++ ) for ( int a = 0; a < mol[p][m].size(); a++ ) if ( !mol[p][m][a].is_null() ) { for ( int s = 0; s < spgr.num_symops(); s++ ) { cf = spgr.symop(s) * mol[p][m][a].coord_orth().coord_frac(cell); gi = cf.coord_grid(grid).unit(grid).index(grid); iatoms.push_back( std::pair( gi, MAtomIndexSymmetry( p, m, a, s ) ) ); } } // sort them by grid coordinate index std::sort( iatoms.begin(), iatoms.end() ); // turn the index into a list of atom indices, indexed by a list of cells lookup.resize( grid.size()+1, iatoms.size() ); atoms.resize( iatoms.size() ); // fill out the atom index for ( int i = 0; i < iatoms.size(); i++ ) { atoms[i] = iatoms[i].second; if ( lookup[iatoms[i].first] == iatoms.size() ) lookup[iatoms[i].first] = i; } // and fill in any missing terms for ( int i = lookup.size()-1; i > 0; i-- ) if ( lookup[i-1] > lookup[i] ) lookup[i-1] = lookup[i]; } /*! Return a list of atom indices in the MiniMol objects, and symop numbers, of atoms within the previously specified radius of the given coordinate. The function always returns all atoms within the specified radius, but also some beyond it. This function is very fast. \param co The coordinate about which to search. \param rad The radius to search. \return A vector of atom indices near the given coordinate. */ std::vector MAtomNonBond::atoms_near( const clipper::Coord_orth& co, double rad ) const { std::vector result; Coord_grid cg = co.coord_frac(cell).coord_grid(grid); Coord_grid c; int d = Util::intc( rad/rad_ - 1.0e-4 ); int gi; for ( int u = cg.u()-d; u <= cg.u()+d; u++ ) for ( int v = cg.v()-d; v <= cg.v()+d; v++ ) for ( int w = cg.w()-d; w <= cg.w()+d; w++ ) { gi = Coord_grid(u,v,w).unit(grid).index(grid); for ( int i = lookup[gi]; i < lookup[gi+1]; i++ ) result.push_back( atoms[i] ); } return result; } /*! Return a list of atom indices in the MiniMol objects, and symop numbers, of atoms within the previously specified radius of the given coordinate. The function only returns atoms within the specified radius. This function is very fast. \param co The coordinate about which to search. \param rad The radius to search. \return A vector of atom indices near the given coordinate. */ std::vector MAtomNonBond::operator() ( const clipper::Coord_orth& co, double rad ) const { std::vector result; std::vector atoms = atoms_near( co, rad ); const MiniMol& mol = *mol_; Coord_frac f1, f2; f1 = co.coord_frac(cell); for ( int i = 0; i < atoms.size(); i++ ) { f2 = spgr.symop(atoms[i].symmetry()) * mol[atoms[i].polymer()][atoms[i].monomer()][atoms[i].atom()].coord_orth().coord_frac(cell); double l2 = ( f2.lattice_copy_near( f1 ) - f1 ).lengthsq( cell ); if ( l2 < rad*rad ) result.push_back( atoms[i] ); } return result; } void MAtomNonBond::debug() const { std::cout << grid.size() << "\t" << atoms.size() << "\n"; for ( int i = 0; i < lookup.size(); i++ ) std::cout << i << "\t" << lookup[i] << "\n"; } } // namespace clipper clipper-2.1/clipper/minimol/minimol_io.h0000644000374100011300000000671610736662163015357 00000000000000/*! \file minimol_io.h Header file for atomic model io types */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_MINIMOL_IO #define CLIPPER_MINIMOL_IO #include "../mmdb/clipper_mmdb.h" #include "minimol_seq.h" namespace clipper { //! MMDB file object for MiniMol i/o /*! This object is an i/o object for MiniMol, representing an interface between MiniMol and PDB or CIF files. It is implemented as an MMDB Manager, so MMDB methods may be additionally used on the MMDBfile object. */ class MMDBfile : public MMDBManager { public: //! load MMDB hierarchy from file void read_file( const String& file ); //! save MMDB hierarchy to file void write_file( const String& file, TYPE type = Default ); //! import MiniMol from MMDB hierarchy void import_minimol( MiniMol& minimol, const int hnd=-1 ); //! export MiniMol to MMDB hierarchy void export_minimol( const MiniMol& minimol ); }; //! SEQ file object for MiniMol sequence i/o class SEQfile { public: //! load SEQ data from file void read_file( const String& file ); //! read a single sequence from the SEQ file void import_polymer_sequence( MPolymerSequence& target ); //! read a molecule from the SEQ file void import_molecule_sequence( MMoleculeSequence& target ); private: String contents; }; } // namespace clipper #endif clipper-2.1/clipper/minimol/minimol_data.h0000644000374100011300000000540010776417512015646 00000000000000/*! \file minimol_data.h Header file for atomic model data */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_MINIMOL_DATA #define CLIPPER_MINIMOL_DATA #include "../core/clipper_precision.h" namespace clipper { namespace data { struct Rotamer_data { const char* resname; int num_rota, rota; ftype32 rota_prob; int num_atom; const char* atomname; ftype32 x, y, z; }; extern Rotamer_data rotamer_data_dunbrack[]; extern int rotamer_data_dunbrack_size; extern Rotamer_data rotamer_data_richardson[]; extern int rotamer_data_richardson_size; } // namespace data } // namespace clipper #endif clipper-2.1/clipper/minimol/minimol.cpp0000644000374100011300000007446611360607134015221 00000000000000/* minimol.cpp: atomic model types */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "minimol.h" #include "minimol_utils.h" extern "C" { #include } namespace clipper { Message_ctor message_ctor_mmodel( " [MModel: constructed]" ); // helper functions namespace MM { std::vector path_split( const clipper::String& s, const clipper::String& sep ) { std::vector splitstr; size_t tokbeg = 0, tokend = 0; if ( s.find_first_of(sep, 0) == 0 ) tokbeg = 1; while (1) { tokend = s.find_first_of(sep, tokbeg); if (tokend == String::npos) break; splitstr.push_back( s.substr(tokbeg, tokend-tokbeg) ); tokbeg = tokend+1; } splitstr.push_back( s.substr(tokbeg) ); return splitstr; } } // Atom MAtom::MAtom( const clipper::Atom& atom ) { set_element( atom.element() ); set_coord_orth( atom.coord_orth() ); set_occupancy( atom.occupancy() ); set_u_iso( atom.u_iso() ); set_u_aniso_orth( atom.u_aniso_orth() ); } void MAtom::set_id( const String& s ) { id_ = id_tidy( s ); } void MAtom::set_name( const String s, const String altconf ) { if ( altconf != "" ) set_id( s + ":" + altconf ); else set_id( s ); } String MAtom::id_tidy( const String& id ) { int pos = id.find( ":" ); if ( pos == String::npos ) pos = id.length(); String name( id.substr( 0, pos ) ); String altc( id.substr( pos ) ); if ( name.length() < 4 ) { name = name + " "; if ( islower( name[1] ) ) name[1] = toupper( name[1] ); else name = " " + name; } return name.substr(0,4) + altc; } /*! copy from other atom. mode can be MM::COPY_M, COPY_P, COPY_MP, COPY_C, COPY_MC, COPY_PC, COPY_MPC, where M means copy members, P means copy PropertyMananger properties, and C means copy children. Children are copied with the same option. The values 'MEMBERS', 'PROPERTIES', 'CHILDREN' can also be used. */ MAtom& MAtom::copy( const MAtom& other, const MM::COPY& mode ) { if ( mode & MM::COPY_M ) atom() = other.atom(); if ( mode & MM::COPY_M ) id_ = other.id_; if ( mode & MM::COPY_P ) PropertyManager::copy( other ); return *this; } bool MAtom::id_match( const String& id1, const String& id2, const MM::MODE& mode ) { if ( mode == MM::UNIQUE ) return ( id1 == id2 ); else return ( id1.substr(0,4) == id2.substr(0,4) ); } // Monomer void MMonomer::set_id( const String& s ) { id_ = id_tidy( s ); } void MMonomer::set_type( const String& s ) { type_ = s; } void MMonomer::set_seqnum( const int s, const String inscode ) { if ( inscode != "" ) set_id( String( s, 4 ) + ":" + inscode ); else set_id( String( s, 4 ) ); } Atom_list MMonomer::atom_list() const { Atom_list list; for ( int a = 0; a < children.size(); a++ ) list.push_back( Atom( children[a] ) ); return list; } void MMonomer::transform( const RTop_orth rt ) { for ( int i = 0; i < children.size(); i++ ) children[i].transform( rt ); } /*! Creates a copy of this monomer containing only the atoms described by the selection string. '*' copies all atoms. The atom selection must contain an atom ID or a comma separated list of atom IDs, or '*' to select all atom. Atom IDs are described in s_mm_atom_id. The selection string must contain an atom ID or a comma separated list of atom IDs. Atom IDs are described in s_mm_atom_id. \param sel The selection string. \param mode MM::UNIQUE forces an exact match, including alternate conformation code. MM::ANY matches every atom with the right name, ignoring alternate conformation codes. \return The selection as a new monomer. */ MMonomer MMonomer::select( const String& sel, const MM::MODE mode ) const { std::vector path = MM::path_split( sel, "/" ); while ( path.size() < 1 ) path.push_back( "*" ); MMonomer result; result.copy( *this, MM::COPY_MP ); if ( path[0].trim() == "*" ) { for ( int i = 0; i < children.size(); i++ ) result.insert( children[i] ); } else { std::vector list = MM::path_split( path[0], "," ); for ( int j = 0; j < list.size(); j++ ) { String sid = CHILDTYPE::id_tidy( list[j] ); for ( int i = 0; i < children.size(); i++ ) if ( CHILDTYPE::id_match( sid, children[i].id(), mode ) ) result.insert( children[i] ); } } return result; } /*! Creates a list of inidices of children matching the given selection string. See select(). \param sel The selection string. \param mode MM::UNIQUE or MM::ANY. \return A vector of integer indices of the matching children. */ std::vector MMonomer::select_index( const String& sel, const MM::MODE mode ) const { std::vector result; if ( sel.trim() == "*" ) { for ( int i = 0; i < children.size(); i++ ) result.push_back( i ); } else { std::vector list = MM::path_split( sel, "," ); for ( int j = 0; j < list.size(); j++ ) { String sid = CHILDTYPE::id_tidy( list[j] ); for ( int i = 0; i < children.size(); i++ ) if ( CHILDTYPE::id_match( sid, children[i].id(), mode ) ) result.push_back( i ); } } return result; } /*! Lookup atom by ID. If mode=UNIQUE, the alternate conformation code must match, otherwise the first atom with the same name is returned. \param n The atom ID. \param mode The search mode. \return The atom. */ const MAtom& MMonomer::find( const String& n, const MM::MODE mode ) const { int i = lookup( n, mode ); if ( i < 0 ) Message::message(Message_fatal("MMonomer: no such atom")); return children[i]; } /*! See MMonomer::find() */ MAtom& MMonomer::find( const String& n, const MM::MODE mode ) { int i = lookup( n, mode ); if ( i < 0 ) Message::message(Message_fatal("MMonomer: no such atom")); return children[i]; } int MMonomer::lookup( const String& str, const MM::MODE& mode ) const { String sid = CHILDTYPE::id_tidy( str ); for ( int i = 0; i < children.size(); i++ ) if ( CHILDTYPE::id_match( sid, children[i].id(), mode ) ) return i; return -1; } void MMonomer::insert( const MAtom& add, int pos ) { if ( pos < 0 ) children.push_back( add ); else children.insert( children.begin() + pos, add ); } /*! \return atoms which are in both monomers. */ MMonomer operator& ( const MMonomer& m1, const MMonomer& m2 ) { MMonomer result; result.copy( m1, MM::COPY_MP ); for ( int i1 = 0; i1 < m1.size(); i1++ ) for ( int i2 = 0; i2 < m2.size(); i2++ ) if ( m1[i1].id() == m2[i2].id() ) { result.insert( m1[i1] ); break; } return result; } /*! \return atoms which are in either monomer. */ MMonomer operator| ( const MMonomer& m1, const MMonomer& m2 ) { MMonomer result; result.copy( m1, MM::COPY_MP ); int i, j; for ( i = 0; i < m1.size(); i++ ) { for ( j = 0; j < result.size(); j++ ) if ( m1[i].id() == result[j].id() ) break; if ( j == result.size() ) result.insert( m1[i] ); } for ( i = 0; i < m2.size(); i++ ) { for ( j = 0; j < result.size(); j++ ) if ( m2[i].id() == result[j].id() ) break; if ( j == result.size() ) result.insert( m2[i] ); } return result; } /*! copy from other atom. mode can be MM::COPY_M, COPY_P, COPY_MP, COPY_C, COPY_MC, COPY_PC, COPY_MPC, where M means copy members, P means copy PropertyMananger properties, and C means copy children. Children are copied with the same option. The values 'MEMBERS', 'PROPERTIES', 'CHILDREN' can also be used. */ MMonomer& MMonomer::copy( const MMonomer& other, const MM::COPY& mode ) { if ( mode & MM::COPY_M ) id_ = other.id_; if ( mode & MM::COPY_M ) type_ = other.type_; if ( mode & MM::COPY_P ) PropertyManager::copy( other ); if ( mode & MM::COPY_C ) { children.resize( other.size() ); for ( int i = 0; i < size(); i++ ) children[i].copy( other[i], mode ); } return *this; } String MMonomer::id_tidy( const String& id ) { int pos = id.find( ":" ); if ( pos == String::npos ) return String( id.i(), 4 ); else return String( id.i(), 4 ) + id.substr( pos ); } bool MMonomer::id_match( const String& id1, const String& id2, const MM::MODE& mode ) { if ( mode == MM::UNIQUE ) return ( id1 == id2 ); else return ( id1.substr(0,4) == id2.substr(0,4) ); } // Polymer void MPolymer::set_id( const String& s ) { id_ = id_tidy( s ); } Atom_list MPolymer::atom_list() const { Atom_list list; for ( int m = 0; m < children.size(); m++ ) for ( int a = 0; a < children[m].size(); a++ ) list.push_back( Atom( children[m][a] ) ); return list; } void MPolymer::transform( const RTop_orth rt ) { for ( int i = 0; i < children.size(); i++ ) children[i].transform( rt ); } /*! Creates a copy of this polymer containing only the monomers and atoms described by the selection string. The selection string must be of the form 'X/Y' where X is a monomer selection and Y is an atom selection, described under MAtom::select(). The monomer selection must contain a monomer ID or a comma separated list of monomer IDs, or '*' to select all monomers. Monomer IDs are described in s_mm_monomer_id. \param sel The selection string. \param mode MM::UNIQUE forces an exact match, including insertion code. MM::ANY matches any monomer with the right sequence number, ignoring insertion code. \return The selection as a new polymer. */ MPolymer MPolymer::select( const String& sel, const MM::MODE mode ) const { std::vector path = MM::path_split( sel, "/" ); while ( path.size() < 2 ) path.push_back( "*" ); MPolymer result; result.copy( *this, MM::COPY_MP ); if ( path[0].trim() == "*" ) { for ( int i = 0; i < children.size(); i++ ) result.insert( children[i].select( path[1], mode ) ); } else { std::vector list = MM::path_split( path[0], "," ); for ( int j = 0; j < list.size(); j++ ) { String sid = CHILDTYPE::id_tidy( list[j] ); for ( int i = 0; i < children.size(); i++ ) if ( CHILDTYPE::id_match( sid, children[i].id(), mode ) ) result.insert( children[i].select( path[1], mode ) ); } } return result; } /*! Creates a list of inidices of children matching the given selection string. See select(). \param sel The selection string. \param mode MM::UNIQUE or MM::ANY. \return A vector of integer indices of the matching children. */ std::vector MPolymer::select_index( const String& sel, const MM::MODE mode ) const { std::vector result; if ( sel.trim() == "*" ) { for ( int i = 0; i < children.size(); i++ ) result.push_back( i ); } else { std::vector list = MM::path_split( sel, "," ); for ( int j = 0; j < list.size(); j++ ) { String sid = CHILDTYPE::id_tidy( list[j] ); for ( int i = 0; i < children.size(); i++ ) if ( CHILDTYPE::id_match( sid, children[i].id(), mode ) ) result.push_back( i ); } } return result; } /*! Lookup monomer by ID. If mode=UNIQUE, the insertion code must match, otherwise the first monomer with the same sequence number is returned. \param n The monomer ID. \param mode The search mode. \return The monomer. */ const MMonomer& MPolymer::find( const String& n, const MM::MODE mode ) const { int i = lookup( n, mode ); if ( i < 0 ) Message::message(Message_fatal("MPolymer: no such monomer")); return children[i]; } /*! See MPolymer::find() */ MMonomer& MPolymer::find( const String& n, const MM::MODE mode ) { int i = lookup( n, mode ); if ( i < 0 ) Message::message(Message_fatal("MPolymer: no such monomer")); return children[i]; } int MPolymer::lookup( const String& str, const MM::MODE& mode ) const { String sid = CHILDTYPE::id_tidy( str ); for ( int i = 0; i < children.size(); i++ ) if ( CHILDTYPE::id_match( sid, children[i].id(), mode ) ) return i; return -1; } void MPolymer::insert( const MMonomer& add, int pos ) { if ( pos < 0 ) children.push_back( add ); else children.insert( children.begin() + pos, add ); } /*! \return monomers and atoms which are in both polymers. */ MPolymer operator& ( const MPolymer& m1, const MPolymer& m2 ) { MPolymer result; result.copy( m1, MM::COPY_MP ); for ( int i1 = 0; i1 < m1.size(); i1++ ) for ( int i2 = 0; i2 < m2.size(); i2++ ) if ( m1[i1].id() == m2[i2].id() ) { result.insert( m1[i1] & m2[i2] ); break; } return result; } /*! \return monomers and atoms which are in either polymer. */ MPolymer operator| ( const MPolymer& m1, const MPolymer& m2 ) { MPolymer result; result.copy( m1, MM::COPY_MP ); int i, j; for ( i = 0; i < m1.size(); i++ ) { for ( j = 0; j < result.size(); j++ ) if ( m1[i].id() == result[j].id() ) break; if ( j == result.size() ) result.insert( m1[i] ); else result[j] = result[j] | m1[i]; } for ( i = 0; i < m2.size(); i++ ) { for ( j = 0; j < result.size(); j++ ) if ( m2[i].id() == result[j].id() ) break; if ( j == result.size() ) result.insert( m2[i] ); else result[j] = result[j] | m2[i]; } return result; } /*! copy from other atom. mode can be MM::COPY_M, COPY_P, COPY_MP, COPY_C, COPY_MC, COPY_PC, COPY_MPC, where M means copy members, P means copy PropertyMananger properties, and C means copy children. Children are copied with the same option. The values 'MEMBERS', 'PROPERTIES', 'CHILDREN' can also be used. */ MPolymer& MPolymer::copy( const MPolymer& other, const MM::COPY& mode ) { if ( mode & MM::COPY_M ) id_ = other.id_; if ( mode & MM::COPY_P ) PropertyManager::copy( other ); if ( mode & MM::COPY_C ) { children.resize( other.size() ); for ( int i = 0; i < size(); i++ ) children[i].copy( other[i], mode ); } return *this; } String MPolymer::id_tidy( const String& id ) { return id; } bool MPolymer::id_match( const String& id1, const String& id2, const MM::MODE& mode ) { return ( id1 == id2 ); } // Model Atom_list MModel::atom_list() const { Atom_list list; for ( int p = 0; p < children.size(); p++ ) for ( int m = 0; m < children[p].size(); m++ ) for ( int a = 0; a < children[p][m].size(); a++ ) list.push_back( Atom( children[p][m][a] ) ); return list; } void MModel::transform( const RTop_orth rt ) { for ( int i = 0; i < children.size(); i++ ) children[i].transform( rt ); } /*! Creates a copy of this model containing only the polymers, monomers and atoms described by the selection string. The selection string must be of the form 'X/Y/Z' where X is a polymer selection, Y is a monomer selection described under MMonomer::select(), and Z is an atom selection described under MAtom::select(). The polymer selection must contain a polymer ID or a comma separated list of polymer IDs, or '*' to select all polymers. Polymer IDs are described in s_mm_monomer_id. See s_mm_selections for examples. \param sel The selection string. \param mode No effect. \return The selection as a new model. */ MModel MModel::select( const String& sel, const MM::MODE mode ) const { std::vector path = MM::path_split( sel, "/" ); while ( path.size() < 3 ) path.push_back( "*" ); MModel result; result.copy( *this, MM::COPY_MP ); if ( path[0].trim() == "*" ) { for ( int i = 0; i < children.size(); i++ ) result.insert( children[i].select( path[1]+"/"+path[2], mode ) ); } else { std::vector list = MM::path_split( path[0], "," ); for ( int j = 0; j < list.size(); j++ ) { String sid = CHILDTYPE::id_tidy( list[j] ); for ( int i = 0; i < children.size(); i++ ) if ( CHILDTYPE::id_match( sid, children[i].id(), mode ) ) result.insert( children[i].select( path[1]+"/"+path[2], mode ) ); } } return result; } /*! Creates a list of inidices of children matching the given selection string. See select(). \param sel The selection string. \param mode MM::UNIQUE or MM::ANY. \return A vector of integer indices of the matching children. */ std::vector MModel::select_index( const String& sel, const MM::MODE mode ) const { std::vector result; if ( sel.trim() == "*" ) { for ( int i = 0; i < children.size(); i++ ) result.push_back( i ); } else { std::vector list = MM::path_split( sel, "," ); for ( int j = 0; j < list.size(); j++ ) { String sid = CHILDTYPE::id_tidy( list[j] ); for ( int i = 0; i < children.size(); i++ ) if ( CHILDTYPE::id_match( sid, children[i].id(), mode ) ) result.push_back( i ); } } return result; } /*! Lookup polymer by ID. Currently, mode is ignored. \param n The monomer ID. \param mode The search mode. \return The polymer. */ const MPolymer& MModel::find( const String& n, const MM::MODE mode ) const { int i = lookup( n, mode ); if ( i < 0 ) Message::message(Message_fatal("MModel: no such polymer")); return children[i]; } /*! See MModel::find() */ MPolymer& MModel::find( const String& n, const MM::MODE mode ) { int i = lookup( n, mode ); if ( i < 0 ) Message::message(Message_fatal("MModel: no such polymer")); return children[i]; } int MModel::lookup( const String& str, const MM::MODE& mode ) const { String sid = CHILDTYPE::id_tidy( str ); for ( int i = 0; i < children.size(); i++ ) if ( CHILDTYPE::id_match( sid, children[i].id(), mode ) ) return i; return -1; } void MModel::insert( const MPolymer& add, int pos ) { if ( pos < 0 ) children.push_back( add ); else children.insert( children.begin() + pos, add ); } /*! \return polymers, monomers and atoms which are in both models. */ MModel operator& ( const MModel& m1, const MModel& m2 ) { MModel result; result.copy( m1, MM::COPY_MP ); for ( int i1 = 0; i1 < m1.size(); i1++ ) for ( int i2 = 0; i2 < m2.size(); i2++ ) if ( m1[i1].id() == m2[i2].id() ) { result.insert( m1[i1] & m2[i2] ); break; } return result; } /*! \return polymers, monomers and atoms which are in either model. */ MModel operator| ( const MModel& m1, const MModel& m2 ) { MModel result; result.copy( m1, MM::COPY_MP ); int i, j; for ( i = 0; i < m1.size(); i++ ) { for ( j = 0; j < result.size(); j++ ) if ( m1[i].id() == result[j].id() ) break; if ( j == result.size() ) result.insert( m1[i] ); else result[j] = result[j] | m1[i]; } for ( i = 0; i < m2.size(); i++ ) { for ( j = 0; j < result.size(); j++ ) if ( m2[i].id() == result[j].id() ) break; if ( j == result.size() ) result.insert( m2[i] ); else result[j] = result[j] | m2[i]; } return result; } /*! copy from other atom. mode can be MM::COPY_M, COPY_P, COPY_MP, COPY_C, COPY_MC, COPY_PC, COPY_MPC, where M means copy members, P means copy PropertyMananger properties, and C means copy children. Children are copied with the same option. The values 'MEMBERS', 'PROPERTIES', 'CHILDREN' can also be used. */ MModel& MModel::copy( const MModel& other, const MM::COPY& mode ) { if ( mode & MM::COPY_P ) PropertyManager::copy( other ); if ( mode & MM::COPY_C ) { children.resize( other.size() ); for ( int i = 0; i < size(); i++ ) children[i].copy( other[i], mode ); } return *this; } /*! Return an atom on the basis of the MAtomIndex. Behaviour is undefined if the index is null. \param index The index of the atom in the heirarchy. \return A reference to the MAtom. */ const MAtom& MModel::atom( const MAtomIndex& index ) const { return children[index.polymer()][index.monomer()][index.atom()]; } /*! Return an atom on the basis of the MAtomIndex. Behaviour is undefined if the index is null. \param index The index of the atom in the heirarchy. \return A reference to the MAtom. */ MAtom& MModel::atom( const MAtomIndex& index ) { return children[index.polymer()][index.monomer()][index.atom()]; } std::vector MModel::select_atom_index( const String& sel, const MM::MODE mode ) const { std::vector result; std::vector path = MM::path_split( sel, "/" ); while ( path.size() < 3 ) path.push_back( "*" ); const std::vector mps = select_index( path[0], mode ); for ( int p = 0; p < mps.size(); p++ ) { const std::vector mms = children[mps[p]].select_index( path[1], mode ); for ( int m = 0; m < mms.size(); m++ ) { const std::vector mas = children[mps[p]][mms[m]].select_index( path[2], mode ); for ( int a = 0; a < mas.size(); a++ ) { result.push_back( MAtomIndex( mps[p], mms[m], mas[a] ) ); } } } return result; } // MiniMol MiniMol::MiniMol() { Message::message( message_ctor_mmodel ); } /*! The object is constructed with no atoms. \param spacegroup the spacegroup. \param cell the cell. */ MiniMol::MiniMol( const Spacegroup& spacegroup, const Cell& cell ) { init( spacegroup, cell ); Message::message( message_ctor_mmodel ); } /*! The object is initialised with no atoms. \param spacegroup the spacegroup. \param cell the cell. */ void MiniMol::init( const Spacegroup& spacegroup, const Cell& cell ) { spacegroup_ = spacegroup; cell_ = cell; } MAtom MiniMol::symmetry_atom( const MAtomIndexSymmetry& index ) { MAtom atom = MModel::atom(index); atom.set_coord_orth((spacegroup_.symop(index.symmetry())*atom.coord_orth().coord_frac(cell_)).coord_orth(cell_)); return atom; } bool MiniMol::is_null() const { return ( spacegroup_.is_null() || cell_.is_null() ); } // UTILITY FUNCTIONS: // e.g. protein specific tools. MMonomer::TYPE MMonomer::default_type_ = MMonomer::Richardson; /*! A carbonyl oxygen is added to this residue if the supplied residue contains an appriate N atom bonded to the C. Otherwise, nothing happens. \param next The next monomer in the chain. */ void MMonomer::protein_mainchain_build_carbonyl_oxygen( const MMonomer& next ) { // check for mainchain atoms int a1 = lookup( " CA ", MM::ANY ); int c1 = lookup( " C ", MM::ANY ); int n2 = next.lookup( " N ", MM::ANY ); if ( a1 < 0 || c1 < 0 || n2 < 0 ) return; // get coordinates and check bonding const clipper::Coord_orth cc1 = children[c1].coord_orth(); const clipper::Coord_orth ca1 = children[a1].coord_orth() - cc1; const clipper::Coord_orth cn2 = next[n2].coord_orth() - cc1; if ( cn2.lengthsq() > 2.2 ) return; double uiso = children[c1].u_iso(); double occ = children[c1].occupancy(); // delete any existing O int o1 = lookup( " O ", MM::ANY ); if ( o1 >= 0 ) children.erase( children.begin()+o1 ); // add the atom const clipper::Vec3<> v0 = ca1.unit(); const clipper::Vec3<> v1 = ( clipper::Vec3<>::cross( v0, clipper::Vec3<>::cross( v0, cn2 ) ) ).unit(); MAtom atm = MAtom::null(); atm.set_id( " O " ); atm.set_element( "O" ); // length 1.24 angle 2.11 atm.set_coord_orth( cc1 + clipper::Coord_orth( -0.637*v0 + 1.064*v1 ) ); atm.set_occupancy( occ ); atm.set_u_iso( uiso ); insert( atm ); } // internal function for fast lookup in rotamer lib int MMonomer::rotamer_find( String res, int rota, TYPE t ) { int rotamer_data_size; if ( t == Dunbrack ) rotamer_data_size = data::rotamer_data_dunbrack_size; else rotamer_data_size = data::rotamer_data_richardson_size; const data::Rotamer_data* rotamer_data; if ( t == Dunbrack ) rotamer_data = data::rotamer_data_dunbrack; else rotamer_data = data::rotamer_data_richardson; if ( res.length() < 3 ) return 0; int p1 = -1; int p2 = rotamer_data_size - 1; while ( p2 - p1 > 1 ) { int p = ( p1 + p2 ) / 2; int s = strncmp( res.c_str(), rotamer_data[p].resname, 3 ); if ( s < 0 || ( s == 0 && rota <= rotamer_data[p].rota ) ) p2 = p; else p1 = p; } if ( strncmp( res.c_str(), rotamer_data[p2].resname, 3 ) == 0 && rota == rotamer_data[p2].rota ) return p2; return -1; } /*! \return The number of stored rotamers for this residue type. 0 if unknown. */ int MMonomer::protein_sidechain_number_of_rotamers( TYPE t ) const { const data::Rotamer_data* rotamer_data; if ( t == Dunbrack ) rotamer_data = data::rotamer_data_dunbrack; else rotamer_data = data::rotamer_data_richardson; int r = rotamer_find( type(), 0, t ); if ( r < 0 ) return 0; return rotamer_data[r].num_rota; } /*! \param n The number of the rotamer required. \return The frequency of the given rotamer. */ ftype MMonomer::protein_sidechain_build_rotamer( const int& n, TYPE t ) { const data::Rotamer_data* rotamer_data; if ( t == Dunbrack ) rotamer_data = data::rotamer_data_dunbrack; else rotamer_data = data::rotamer_data_richardson; int na = lookup( " CA ", MM::ANY ); int nc = lookup( " C ", MM::ANY ); int nn = lookup( " N ", MM::ANY ); if ( na < 0 || nc < 0 || nn < 0 ) return 0.0; clipper::Coord_orth ca = children[na].coord_orth(); clipper::Coord_orth c1 = children[nc].coord_orth() - ca; clipper::Coord_orth c2 = children[nn].coord_orth() - ca; double uiso = children[na].u_iso(); double occ = children[na].occupancy(); // strip old side chain for ( int i = children.size()-1; i >= 0; i-- ) if ( children[i].name() != " CA " && children[i].name() != " N " && children[i].name() != " C " && children[i].name() != " O " ) children.erase( children.begin()+i ); // get rotamer int r = rotamer_find( type(), n, t ); if ( r < 0 ) return 0.0; if ( n >= rotamer_data[r].num_rota ) return -1.0; // get rtop from standard orientation const clipper::Vec3<> v1( (c1.unit()+c2.unit()).unit() ); const clipper::Vec3<> v2( clipper::Vec3<>::cross(c1,c2).unit() ); const clipper::Vec3<> v3( clipper::Vec3<>::cross(v1,v2).unit() ); const clipper::Mat33<> mr( v1[0], v2[0], v3[0], v1[1], v2[1], v3[1], v1[2], v2[2], v3[2] ); clipper::RTop_orth rtop( mr, ca ); // add new atoms MAtom atm = MAtom::null(); for ( int dr = 0; dr < rotamer_data[r].num_atom; dr++ ) { int i = r + dr; String name = rotamer_data[i].atomname; atm.set_id( name ); name = name.substr( 0, 2 ); name = name.trim(); atm.set_element( name ); atm.set_coord_orth( rtop * Coord_orth( rotamer_data[i].x, rotamer_data[i].y, rotamer_data[i].z ) ); atm.set_occupancy( occ ); atm.set_u_iso( uiso ); insert( atm ); } return rotamer_data[r].rota_prob; } /*! Test if the C of residue 1 is bonded to the N of residue 2, within the distance r. \param r1 The first residue. \param r2 The second residue. \param r The maximum allowed bond length. \return true if N and C are present and bonded. */ bool MMonomer::protein_peptide_bond( const MMonomer& m1, const MMonomer& m2, ftype r ) { int c1 = m1.lookup( " C ", MM::ANY ); int n2 = m2.lookup( " N ", MM::ANY ); if ( c1 >= 0 && n2 >= 0 ) if ( ( m1[c1].coord_orth() - m2[n2].coord_orth() ).lengthsq() < r*r ) return true; return false; } /*! Return the Ramachadran angle in radians on -pi...pi. To check the result, see clipper::Util::is_nan() \param r1 The first residue. \param r2 The second residue. \return The torsion angle in radians, or NaN if atoms are missing. */ double MMonomer::protein_ramachandran_phi( const MMonomer& m1, const MMonomer& m2 ) { ftype result = clipper::Util::nan(); int index_cx = m1.lookup( " C ", clipper::MM::ANY ); int index_n = m2.lookup( " N ", clipper::MM::ANY ); int index_ca = m2.lookup( " CA ", clipper::MM::ANY ); int index_c = m2.lookup( " C ", clipper::MM::ANY ); // if we have all three atoms, then add residue if ( index_cx >= 0 && index_ca >= 0 && index_c >= 0 && index_n >= 0 ) { Coord_orth coord_cx = m1[index_cx].coord_orth(); Coord_orth coord_n = m2[index_n ].coord_orth(); Coord_orth coord_ca = m2[index_ca].coord_orth(); Coord_orth coord_c = m2[index_c ].coord_orth(); // ramachandran calc result = Coord_orth::torsion( coord_cx, coord_n, coord_ca, coord_c ); } return result; } /*! Return the Ramachadran angle in radians on -pi...pi. To check the result, see clipper::Util::is_nan() \param r1 The first residue. \param r2 The second residue. \return The torsion angle in radians, or NaN if atoms are missing. */ double MMonomer::protein_ramachandran_psi( const MMonomer& m1, const MMonomer& m2 ) { ftype result = clipper::Util::nan(); int index_n = m1.lookup( " N ", clipper::MM::ANY ); int index_ca = m1.lookup( " CA ", clipper::MM::ANY ); int index_c = m1.lookup( " C ", clipper::MM::ANY ); int index_nx = m2.lookup( " N ", clipper::MM::ANY ); // if we have all three atoms, then add residue if ( index_ca >= 0 && index_c >= 0 && index_n >= 0 && index_nx >= 0 ) { Coord_orth coord_n = m1[index_n ].coord_orth(); Coord_orth coord_ca = m1[index_ca].coord_orth(); Coord_orth coord_c = m1[index_c ].coord_orth(); Coord_orth coord_nx = m2[index_nx].coord_orth(); // ramachandran calc result = Coord_orth::torsion( coord_n, coord_ca, coord_c, coord_nx ); } return result; } } // namespace clipper clipper-2.1/clipper/minimol/Makefile.am0000644000374100011300000000153711372264321015072 00000000000000# Makefile.am, passed: clipper/minimol, extracted subdir: minimol # in dir /home/cowtan/clipper-autoconf/clipper-2.1/clipper/minimol ## -*- mode: Makefile; mode: font-lock -*- INCLUDES=${FFTW_CXXFLAGS} ${MMDB_CXXFLAGS} library_include_HEADERS = \ container_minimol.h \ minimol_data.h \ minimol.h \ minimol_io.h \ minimol_seq.h \ minimol_utils.h lib_LTLIBRARIES = libclipper-minimol.la libclipper_minimol_la_SOURCES = \ container_minimol.cpp \ minimol.cpp \ minimol_data.cpp \ minimol_io.cpp \ minimol_seq.cpp \ minimol_utils.cpp library_includedir = $(pkgincludedir)/minimol libclipper_minimol_la_LDFLAGS = -version-info @CLIPPER_LT_VERSION@ libclipper_minimol_la_LIBADD = \ $(top_builddir)/clipper/mmdb/libclipper-mmdb.la $(top_builddir)/clipper/core/libclipper-core.la clipper-2.1/clipper/minimol/minimol_data.cpp0000644000374100011300000023772410776417434016224 00000000000000/* minimol.cpp: atomic model data */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "minimol_data.h" namespace clipper { namespace data { Rotamer_data rotamer_data_dunbrack[] = { {"ALA", 1, 0, 1.0000, 1," CB ",-0.940,-1.196, 0.000}, {"ARG",16, 0, 0.1099, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",16, 0, 0.1099, 7," CG ",-2.017,-1.162,-1.063}, {"ARG",16, 0, 0.1099, 7," CD ",-2.937,-2.372,-1.071}, {"ARG",16, 0, 0.1099, 7," NE ",-3.939,-2.292,-2.130}, {"ARG",16, 0, 0.1099, 7," CZ ",-4.817,-3.248,-2.399}, {"ARG",16, 0, 0.1099, 7," NH1",-4.823,-4.365,-1.684}, {"ARG",16, 0, 0.1099, 7," NH2",-5.693,-3.090,-3.382}, {"ARG",16, 1, 0.0666, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",16, 1, 0.0666, 7," CG ",-2.007,-1.170,-1.074}, {"ARG",16, 1, 0.0666, 7," CD ",-2.932,-2.375,-1.075}, {"ARG",16, 1, 0.0666, 7," NE ",-2.238,-3.599,-1.465}, {"ARG",16, 1, 0.0666, 7," CZ ",-2.778,-4.809,-1.423}, {"ARG",16, 1, 0.0666, 7," NH1",-4.029,-4.965,-1.009}, {"ARG",16, 1, 0.0666, 7," NH2",-2.072,-5.867,-1.796}, {"ARG",16, 2, 0.0611, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",16, 2, 0.0611, 7," CG ",-2.002,-1.174,-1.079}, {"ARG",16, 2, 0.0611, 7," CD ",-2.913,-2.390,-1.095}, {"ARG",16, 2, 0.0611, 7," NE ",-3.735,-2.475, 0.109}, {"ARG",16, 2, 0.0611, 7," CZ ",-4.472,-3.527, 0.436}, {"ARG",16, 2, 0.0611, 7," NH1",-4.492,-4.595,-0.351}, {"ARG",16, 2, 0.0611, 7," NH2",-5.190,-3.517, 1.550}, {"ARG",16, 3, 0.0602, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",16, 3, 0.0602, 7," CG ",-2.023,-1.158,-1.057}, {"ARG",16, 3, 0.0602, 7," CD ",-2.960,-2.353,-1.046}, {"ARG",16, 3, 0.0602, 7," NE ",-3.928,-2.302,-2.138}, {"ARG",16, 3, 0.0602, 7," CZ ",-5.057,-1.608,-2.102}, {"ARG",16, 3, 0.0602, 7," NH1",-5.367,-0.899,-1.025}, {"ARG",16, 3, 0.0602, 7," NH2",-5.879,-1.619,-3.142}, {"ARG",16, 4, 0.0546, 7," CB ",-0.939,-1.208, 0.008}, {"ARG",16, 4, 0.0546, 7," CG ",-1.888,-1.249, 1.194}, {"ARG",16, 4, 0.0546, 7," CD ",-2.880,-2.399, 1.157}, {"ARG",16, 4, 0.0546, 7," NE ",-3.750,-2.411, 2.330}, {"ARG",16, 4, 0.0546, 7," CZ ",-4.694,-3.315, 2.549}, {"ARG",16, 4, 0.0546, 7," NH1",-4.895,-4.292, 1.673}, {"ARG",16, 4, 0.0546, 7," NH2",-5.439,-3.249, 3.644}, {"ARG",16, 5, 0.0534, 7," CB ",-0.939,-1.208, 0.008}, {"ARG",16, 5, 0.0534, 7," CG ",-2.028,-1.154,-1.052}, {"ARG",16, 5, 0.0534, 7," CD ",-3.091,-2.230,-0.905}, {"ARG",16, 5, 0.0534, 7," NE ",-2.543,-3.570,-1.094}, {"ARG",16, 5, 0.0534, 7," CZ ",-2.396,-4.156,-2.274}, {"ARG",16, 5, 0.0534, 7," NH1",-2.754,-3.520,-3.382}, {"ARG",16, 5, 0.0534, 7," NH2",-1.890,-5.380,-2.352}, {"ARG",16, 6, 0.0480, 7," CB ",-0.939,-1.208, 0.008}, {"ARG",16, 6, 0.0480, 7," CG ",-2.006,-1.171,-1.075}, {"ARG",16, 6, 0.0480, 7," CD ",-2.934,-2.374,-1.073}, {"ARG",16, 6, 0.0480, 7," NE ",-3.958,-2.278,-2.109}, {"ARG",16, 6, 0.0480, 7," CZ ",-3.794,-2.687,-3.359}, {"ARG",16, 6, 0.0480, 7," NH1",-2.642,-3.227,-3.737}, {"ARG",16, 6, 0.0480, 7," NH2",-4.780,-2.560,-4.237}, {"ARG",16, 7, 0.0392, 7," CB ",-0.939,-1.208, 0.008}, {"ARG",16, 7, 0.0392, 7," CG ",-1.995,-1.180,-1.086}, {"ARG",16, 7, 0.0392, 7," CD ",-2.920,-2.385,-1.086}, {"ARG",16, 7, 0.0392, 7," NE ",-3.759,-2.432, 0.108}, {"ARG",16, 7, 0.0392, 7," CZ ",-4.905,-1.779, 0.241}, {"ARG",16, 7, 0.0392, 7," NH1",-5.358,-1.023,-0.751}, {"ARG",16, 7, 0.0392, 7," NH2",-5.603,-1.879, 1.364}, {"ARG",16, 8, 0.0367, 7," CB ",-0.939,-1.208, 0.008}, {"ARG",16, 8, 0.0367, 7," CG ",-1.933,-1.214, 1.158}, {"ARG",16, 8, 0.0367, 7," CD ",-2.916,-2.372, 1.123}, {"ARG",16, 8, 0.0367, 7," NE ",-2.260,-3.655, 1.362}, {"ARG",16, 8, 0.0367, 7," CZ ",-2.830,-4.833, 1.158}, {"ARG",16, 8, 0.0367, 7," NH1",-4.075,-4.900, 0.704}, {"ARG",16, 8, 0.0367, 7," NH2",-2.158,-5.950, 1.404}, {"ARG",16, 9, 0.0321, 7," CB ",-0.939,-1.208, 0.008}, {"ARG",16, 9, 0.0321, 7," CG ",-1.913,-1.230, 1.175}, {"ARG",16, 9, 0.0321, 7," CD ",-2.850,-2.425, 1.179}, {"ARG",16, 9, 0.0321, 7," NE ",-3.754,-2.417, 0.032}, {"ARG",16, 9, 0.0321, 7," CZ ",-4.468,-3.462,-0.361}, {"ARG",16, 9, 0.0321, 7," NH1",-4.391,-4.608, 0.301}, {"ARG",16, 9, 0.0321, 7," NH2",-5.265,-3.364,-1.417}, {"ARG",16,10, 0.0319, 7," CB ",-0.939,-1.208, 0.008}, {"ARG",16,10, 0.0319, 7," CG ",-1.878,-1.256, 1.202}, {"ARG",16,10, 0.0319, 7," CD ",-2.868,-2.409, 1.168}, {"ARG",16,10, 0.0319, 7," NE ",-3.780,-2.383, 2.307}, {"ARG",16,10, 0.0319, 7," CZ ",-3.507,-2.909, 3.493}, {"ARG",16,10, 0.0319, 7," NH1",-2.341,-3.505, 3.703}, {"ARG",16,10, 0.0319, 7," NH2",-4.397,-2.839, 4.473}, {"ARG",16,11, 0.0308, 7," CB ",-0.939,-1.208, 0.008}, {"ARG",16,11, 0.0308, 7," CG ",-1.882,-1.254, 1.199}, {"ARG",16,11, 0.0308, 7," CD ",-2.837,-2.435, 1.190}, {"ARG",16,11, 0.0308, 7," NE ",-2.135,-3.709, 1.314}, {"ARG",16,11, 0.0308, 7," CZ ",-1.706,-4.216, 2.461}, {"ARG",16,11, 0.0308, 7," NH1",-1.909,-3.558, 3.596}, {"ARG",16,11, 0.0308, 7," NH2",-1.075,-5.382, 2.480}, {"ARG",16,12, 0.0292, 7," CB ",-0.939,-1.208, 0.008}, {"ARG",16,12, 0.0292, 7," CG ",-1.909,-1.232, 1.178}, {"ARG",16,12, 0.0292, 7," CD ",-2.849,-2.427, 1.181}, {"ARG",16,12, 0.0292, 7," NE ",-3.759,-2.411, 0.039}, {"ARG",16,12, 0.0292, 7," CZ ",-4.885,-1.715,-0.007}, {"ARG",16,12, 0.0292, 7," NH1",-5.248,-0.968, 1.027}, {"ARG",16,12, 0.0292, 7," NH2",-5.653,-1.760,-1.087}, {"ARG",16,13, 0.0283, 7," CB ",-0.939,-1.208, 0.008}, {"ARG",16,13, 0.0283, 7," CG ",-1.941,-1.222,-1.135}, {"ARG",16,13, 0.0283, 7," CD ",-3.052,-0.194,-1.000}, {"ARG",16,13, 0.0283, 7," NE ",-4.014,-0.279,-2.095}, {"ARG",16,13, 0.0283, 7," CZ ",-5.054, 0.530,-2.238}, {"ARG",16,13, 0.0283, 7," NH1",-5.272, 1.496,-1.355}, {"ARG",16,13, 0.0283, 7," NH2",-5.879, 0.379,-3.265}, {"ARG",16,14, 0.0252, 7," CB ",-0.939,-1.208, 0.008}, {"ARG",16,14, 0.0252, 7," CG ",-1.890,-1.247, 1.193}, {"ARG",16,14, 0.0252, 7," CD ",-2.861,-2.415, 1.171}, {"ARG",16,14, 0.0252, 7," NE ",-3.733,-2.425, 2.343}, {"ARG",16,14, 0.0252, 7," CZ ",-4.864,-1.740, 2.436}, {"ARG",16,14, 0.0252, 7," NH1",-5.270,-0.985, 1.424}, {"ARG",16,14, 0.0252, 7," NH2",-5.594,-1.808, 3.541}, {"ARG",16,15, 0.0237, 7," CB ",-0.939,-1.208, 0.008}, {"ARG",16,15, 0.0237, 7," CG ",-1.949,-1.216,-1.129}, {"ARG",16,15, 0.0237, 7," CD ",-3.023,-0.147,-1.012}, {"ARG",16,15, 0.0237, 7," NE ",-4.031,-0.266,-2.062}, {"ARG",16,15, 0.0237, 7," CZ ",-3.928, 0.291,-3.260}, {"ARG",16,15, 0.0237, 7," NH1",-2.856, 1.009,-3.570}, {"ARG",16,15, 0.0237, 7," NH2",-4.894, 0.131,-4.154}, {"ASN",12, 0, 0.2820, 4," CB ",-0.952,-1.197, 0.006}, {"ASN",12, 0, 0.2820, 4," CG ",-2.060,-1.067,-1.020}, {"ASN",12, 0, 0.2820, 4," OD1",-2.402, 0.037,-1.445}, {"ASN",12, 0, 0.2820, 4," ND2",-2.628,-2.197,-1.425}, {"ASN",12, 1, 0.1860, 4," CB ",-0.952,-1.197, 0.006}, {"ASN",12, 1, 0.1860, 4," CG ",-1.992,-1.122,-1.095}, {"ASN",12, 1, 0.1860, 4," OD1",-2.829,-0.219,-1.113}, {"ASN",12, 1, 0.1860, 4," ND2",-1.944,-2.073,-2.020}, {"ASN",12, 2, 0.0984, 4," CB ",-0.952,-1.197, 0.006}, {"ASN",12, 2, 0.0984, 4," CG ",-1.993,-1.108, 1.105}, {"ASN",12, 2, 0.0984, 4," OD1",-2.320,-0.019, 1.579}, {"ASN",12, 2, 0.0984, 4," ND2",-2.519,-2.255, 1.516}, {"ASN",12, 3, 0.0714, 4," CB ",-0.952,-1.197, 0.006}, {"ASN",12, 3, 0.0714, 4," CG ",-1.970,-1.126, 1.128}, {"ASN",12, 3, 0.0714, 4," OD1",-1.774,-0.416, 2.115}, {"ASN",12, 3, 0.0714, 4," ND2",-3.065,-1.862, 0.980}, {"ASN",12, 4, 0.0705, 4," CB ",-0.952,-1.197, 0.006}, {"ASN",12, 4, 0.0705, 4," CG ",-0.220,-2.524, 0.066}, {"ASN",12, 4, 0.0705, 4," OD1", 1.008,-2.565, 0.131}, {"ASN",12, 4, 0.0705, 4," ND2",-0.974,-3.616, 0.045}, {"ASN",12, 5, 0.0549, 4," CB ",-0.952,-1.197, 0.006}, {"ASN",12, 5, 0.0549, 4," CG ",-1.953,-1.139, 1.143}, {"ASN",12, 5, 0.0549, 4," OD1",-2.749,-0.204, 1.238}, {"ASN",12, 5, 0.0549, 4," ND2",-1.918,-2.141, 2.014}, {"ASN",12, 6, 0.0432, 4," CB ",-0.952,-1.197, 0.006}, {"ASN",12, 6, 0.0432, 4," CG ",-1.928,-1.159, 1.166}, {"ASN",12, 6, 0.0432, 4," OD1",-1.534,-1.274, 2.327}, {"ASN",12, 6, 0.0432, 4," ND2",-3.209,-0.996, 0.857}, {"ASN",12, 7, 0.0416, 4," CB ",-0.952,-1.197, 0.006}, {"ASN",12, 7, 0.0416, 4," CG ",-1.985,-1.128,-1.102}, {"ASN",12, 7, 0.0416, 4," OD1",-1.811,-1.724,-2.165}, {"ASN",12, 7, 0.0416, 4," ND2",-3.067,-0.398,-0.857}, {"ASN",12, 8, 0.0359, 4," CB ",-0.952,-1.197, 0.006}, {"ASN",12, 8, 0.0359, 4," CG ",-0.221,-2.524,-0.046}, {"ASN",12, 8, 0.0359, 4," OD1", 0.618,-2.818, 0.806}, {"ASN",12, 8, 0.0359, 4," ND2",-0.536,-3.334,-1.049}, {"ASN",12, 9, 0.0309, 4," CB ",-0.952,-1.197, 0.006}, {"ASN",12, 9, 0.0309, 4," CG ",-1.888,-1.191, 1.200}, {"ASN",12, 9, 0.0309, 4," OD1",-1.820,-2.068, 2.060}, {"ASN",12, 9, 0.0309, 4," ND2",-2.767,-0.198, 1.257}, {"ASN",12,10, 0.0304, 4," CB ",-0.952,-1.197, 0.006}, {"ASN",12,10, 0.0304, 4," CG ",-1.977,-1.134,-1.109}, {"ASN",12,10, 0.0304, 4," OD1",-2.296,-2.147,-1.732}, {"ASN",12,10, 0.0304, 4," ND2",-2.499, 0.059,-1.366}, {"ASN",12,11, 0.0260, 4," CB ",-0.952,-1.197, 0.006}, {"ASN",12,11, 0.0260, 4," CG ",-0.220,-2.524, 0.064}, {"ASN",12,11, 0.0260, 4," OD1", 0.653,-2.800,-0.759}, {"ASN",12,11, 0.0260, 4," ND2",-0.574,-3.353, 1.039}, {"ASP", 8, 0, 0.3087, 4," CB ",-0.939,-1.208, 0.006}, {"ASP", 8, 0, 0.3087, 4," CG ",-2.062,-1.078,-1.004}, {"ASP", 8, 0, 0.3087, 4," OD1",-2.259, 0.034,-1.536}, {"ASP", 8, 0, 0.3087, 4," OD2",-2.798,-2.034,-1.328}, {"ASP", 8, 1, 0.1945, 4," CB ",-0.939,-1.208, 0.006}, {"ASP", 8, 1, 0.1945, 4," CG ",-1.964,-1.155,-1.109}, {"ASP", 8, 1, 0.1945, 4," OD1",-2.622,-0.105,-1.264}, {"ASP", 8, 1, 0.1945, 4," OD2",-2.178,-2.113,-1.882}, {"ASP", 8, 2, 0.1761, 4," CB ",-0.939,-1.208, 0.006}, {"ASP", 8, 2, 0.1761, 4," CG ",-1.945,-1.157, 1.139}, {"ASP", 8, 2, 0.1761, 4," OD1",-1.903,-0.190, 1.929}, {"ASP", 8, 2, 0.1761, 4," OD2",-2.814,-2.036, 1.318}, {"ASP", 8, 3, 0.1097, 4," CB ",-0.939,-1.208, 0.006}, {"ASP", 8, 3, 0.1097, 4," CG ",-0.191,-2.526, 0.032}, {"ASP", 8, 3, 0.1097, 4," OD1", 1.057,-2.502, 0.069}, {"ASP", 8, 3, 0.1097, 4," OD2",-0.767,-3.635, 0.019}, {"ASP", 8, 4, 0.0872, 4," CB ",-0.939,-1.208, 0.006}, {"ASP", 8, 4, 0.0872, 4," CG ",-1.924,-1.173, 1.158}, {"ASP", 8, 4, 0.0872, 4," OD1",-2.693,-0.193, 1.254}, {"ASP", 8, 4, 0.0872, 4," OD2",-2.003,-2.079, 2.014}, {"ASP", 8, 5, 0.0493, 4," CB ",-0.939,-1.208, 0.006}, {"ASP", 8, 5, 0.0493, 4," CG ",-2.011,-1.105, 1.073}, {"ASP", 8, 5, 0.0493, 4," OD1",-1.657,-0.939, 2.259}, {"ASP", 8, 5, 0.0493, 4," OD2",-3.232,-1.177, 0.819}, {"ASP", 8, 6, 0.0347, 4," CB ",-0.939,-1.208, 0.006}, {"ASP", 8, 6, 0.0347, 4," CG ",-0.191,-2.526, 0.029}, {"ASP", 8, 6, 0.0347, 4," OD1", 0.647,-2.751,-0.869}, {"ASP", 8, 6, 0.0347, 4," OD2",-0.374,-3.397, 0.907}, {"ASP", 8, 7, 0.0208, 4," CB ",-0.939,-1.208, 0.006}, {"ASP", 8, 7, 0.0208, 4," CG ",-0.195,-2.524,-0.100}, {"ASP", 8, 7, 0.0208, 4," OD1", 0.712,-2.764, 0.725}, {"ASP", 8, 7, 0.0208, 4," OD2",-0.448,-3.380,-0.974}, {"CYS", 3, 0, 0.5664, 2," CB ",-0.940,-1.207, 0.007}, {"CYS", 3, 0, 0.5664, 2," SG ",-2.165,-1.207,-1.322}, {"CYS", 3, 1, 0.2742, 2," CB ",-0.940,-1.207, 0.007}, {"CYS", 3, 1, 0.2742, 2," SG ",-2.064,-1.270, 1.421}, {"CYS", 3, 2, 0.1594, 2," CB ",-0.940,-1.207, 0.007}, {"CYS", 3, 2, 0.1594, 2," SG ",-0.101,-2.807, 0.069}, {"GLN",13, 0, 0.1853, 5," CB ",-0.940,-1.207, 0.006}, {"GLN",13, 0, 0.1853, 5," CG ",-2.016,-1.163,-1.066}, {"GLN",13, 0, 0.1853, 5," CD ",-2.891,-2.400,-1.067}, {"GLN",13, 0, 0.1853, 5," OE1",-2.682,-3.315,-0.270}, {"GLN",13, 0, 0.1853, 5," NE2",-3.874,-2.431,-1.962}, {"GLN",13, 1, 0.1466, 5," CB ",-0.940,-1.207, 0.006}, {"GLN",13, 1, 0.1466, 5," CG ",-1.953,-1.212,-1.126}, {"GLN",13, 1, 0.1466, 5," CD ",-2.911,-0.039,-1.058}, {"GLN",13, 1, 0.1466, 5," OE1",-3.449, 0.268, 0.006}, {"GLN",13, 1, 0.1466, 5," NE2",-3.125, 0.619,-2.193}, {"GLN",13, 2, 0.0949, 5," CB ",-0.940,-1.207, 0.006}, {"GLN",13, 2, 0.0949, 5," CG ",-1.888,-1.251, 1.193}, {"GLN",13, 2, 0.0949, 5," CD 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",-1.729,-1.229, 1.186}, {"THR", 3, 0, 0.4886, 3," CB ",-0.946,-1.215, 0.008}, {"THR", 3, 0, 0.4886, 3," OG1",-0.177,-2.423,-0.002}, {"THR", 3, 0, 0.4886, 3," CG2",-1.731,-1.289,-1.292}, {"THR", 3, 1, 0.4364, 3," CB ",-0.946,-1.215, 0.008}, {"THR", 3, 1, 0.4364, 3," OG1",-1.810,-1.160,-1.133}, {"THR", 3, 1, 0.4364, 3," CG2",-1.910,-1.133, 1.182}, {"THR", 3, 2, 0.0751, 3," CB ",-0.946,-1.215, 0.008}, {"THR", 3, 2, 0.0751, 3," OG1",-1.849,-1.114, 1.115}, {"THR", 3, 2, 0.0751, 3," CG2",-0.173,-2.491, 0.303}, {"TRP", 8, 0, 0.3081,10," CB ",-0.938,-1.209, 0.008}, {"TRP", 8, 0, 0.3081,10," CG ",-1.992,-1.157,-1.056}, {"TRP", 8, 0, 0.3081,10," CD1",-1.984,-1.813,-2.254}, {"TRP", 8, 0, 0.3081,10," CD2",-3.212,-0.408,-1.020}, {"TRP", 8, 0, 0.3081,10," NE1",-3.121,-1.516,-2.964}, {"TRP", 8, 0, 0.3081,10," CE2",-3.893,-0.656,-2.229}, {"TRP", 8, 0, 0.3081,10," CE3",-3.801, 0.453,-0.088}, {"TRP", 8, 0, 0.3081,10," CZ2",-5.126,-0.079,-2.526}, {"TRP", 8, 0, 0.3081,10," CZ3",-5.025, 1.025,-0.385}, {"TRP", 8, 0, 0.3081,10," CH2",-5.673, 0.756,-1.594}, {"TRP", 8, 1, 0.1621,10," CB ",-0.938,-1.209, 0.008}, {"TRP", 8, 1, 0.1621,10," CG ",-1.862,-1.242, 1.188}, {"TRP", 8, 1, 0.1621,10," CD1",-1.767,-2.050, 2.285}, {"TRP", 8, 1, 0.1621,10," CD2",-3.024,-0.430, 1.390}, {"TRP", 8, 1, 0.1621,10," NE1",-2.798,-1.792, 3.154}, {"TRP", 8, 1, 0.1621,10," CE2",-3.584,-0.800, 2.630}, {"TRP", 8, 1, 0.1621,10," CE3",-3.654, 0.576, 0.648}, {"TRP", 8, 1, 0.1621,10," CZ2",-4.736,-0.203, 3.140}, {"TRP", 8, 1, 0.1621,10," CZ3",-4.796, 1.167, 1.157}, {"TRP", 8, 1, 0.1621,10," CH2",-5.324, 0.775, 2.390}, {"TRP", 8, 2, 0.1302,10," CB ",-0.938,-1.209, 0.008}, {"TRP", 8, 2, 0.1302,10," CG ",-1.821,-1.274, 1.217}, {"TRP", 8, 2, 0.1302,10," CD1",-3.018,-0.643, 1.396}, {"TRP", 8, 2, 0.1302,10," CD2",-1.577,-2.014, 2.420}, {"TRP", 8, 2, 0.1302,10," NE1",-3.532,-0.942, 2.634}, {"TRP", 8, 2, 0.1302,10," CE2",-2.667,-1.783, 3.283}, {"TRP", 8, 2, 0.1302,10," CE3",-0.544,-2.849, 2.859}, {"TRP", 8, 2, 0.1302,10," CZ2",-2.752,-2.355, 4.551}, {"TRP", 8, 2, 0.1302,10," CZ3",-0.631,-3.416, 4.117}, {"TRP", 8, 2, 0.1302,10," CH2",-1.727,-3.166, 4.948}, {"TRP", 8, 3, 0.1302,10," CB ",-0.938,-1.209, 0.008}, {"TRP", 8, 3, 0.1302,10," CG ",-2.009,-1.143,-1.038}, {"TRP", 8, 3, 0.1302,10," CD1",-2.256,-0.112,-1.898}, {"TRP", 8, 3, 0.1302,10," CD2",-2.979,-2.153,-1.337}, {"TRP", 8, 3, 0.1302,10," NE1",-3.321,-0.417,-2.710}, {"TRP", 8, 3, 0.1302,10," CE2",-3.783,-1.665,-2.388}, {"TRP", 8, 3, 0.1302,10," CE3",-3.255,-3.425,-0.822}, {"TRP", 8, 3, 0.1302,10," CZ2",-4.836,-2.401,-2.929}, {"TRP", 8, 3, 0.1302,10," CZ3",-4.301,-4.152,-1.362}, {"TRP", 8, 3, 0.1302,10," CH2",-5.077,-3.638,-2.404}, {"TRP", 8, 4, 0.0992,10," CB ",-0.938,-1.209, 0.008}, {"TRP", 8, 4, 0.0992,10," CG ",-0.220,-2.524, 0.002}, {"TRP", 8, 4, 0.0992,10," CD1", 0.167,-3.245,-1.091}, {"TRP", 8, 4, 0.0992,10," CD2", 0.201,-3.278, 1.145}, {"TRP", 8, 4, 0.0992,10," NE1", 0.798,-4.400,-0.699}, {"TRP", 8, 4, 0.0992,10," CE2", 0.834,-4.445, 0.670}, {"TRP", 8, 4, 0.0992,10," CE3", 0.106,-3.088, 2.528}, {"TRP", 8, 4, 0.0992,10," CZ2", 1.366,-5.409, 1.523}, {"TRP", 8, 4, 0.0992,10," CZ3", 0.635,-4.047, 3.373}, {"TRP", 8, 4, 0.0992,10," CH2", 1.257,-5.192, 2.868}, {"TRP", 8, 5, 0.0581,10," CB ",-0.938,-1.209, 0.008}, {"TRP", 8, 5, 0.0581,10," CG ",-1.897,-1.215, 1.159}, {"TRP", 8, 5, 0.0581,10," CD1",-2.233,-0.158, 1.956}, {"TRP", 8, 5, 0.0581,10," CD2",-2.649,-2.334, 1.645}, {"TRP", 8, 5, 0.0581,10," NE1",-3.143,-0.550, 2.906}, {"TRP", 8, 5, 0.0581,10," CE2",-3.417,-1.882, 2.738}, {"TRP", 8, 5, 0.0581,10," CE3",-2.751,-3.678, 1.269}, {"TRP", 8, 5, 0.0581,10," CZ2",-4.270,-2.721, 3.452}, {"TRP", 8, 5, 0.0581,10," CZ3",-3.598,-4.508, 1.980}, {"TRP", 8, 5, 0.0581,10," CH2",-4.346,-4.027, 3.058}, {"TRP", 8, 6, 0.0532,10," CB ",-0.938,-1.209, 0.008}, {"TRP", 8, 6, 0.0532,10," CG ",-0.220,-2.524, 0.009}, {"TRP", 8, 6, 0.0532,10," CD1", 0.193,-3.235, 1.100}, {"TRP", 8, 6, 0.0532,10," CD2", 0.171,-3.290,-1.137}, {"TRP", 8, 6, 0.0532,10," NE1", 0.817,-4.392, 0.703}, {"TRP", 8, 6, 0.0532,10," CE2", 0.817,-4.451,-0.666}, {"TRP", 8, 6, 0.0532,10," CE3", 0.044,-3.112,-2.519}, {"TRP", 8, 6, 0.0532,10," CZ2", 1.329,-5.423,-1.523}, {"TRP", 8, 6, 0.0532,10," CZ3", 0.553,-4.078,-3.367}, {"TRP", 8, 6, 0.0532,10," CH2", 1.187,-5.218,-2.866}, {"TRP", 8, 7, 0.0532,10," CB ",-0.938,-1.209, 0.008}, {"TRP", 8, 7, 0.0532,10," CG ",-2.030,-1.126,-1.014}, {"TRP", 8, 7, 0.0532,10," CD1",-3.285,-0.617,-0.838}, {"TRP", 8, 7, 0.0532,10," CD2",-1.966,-1.567,-2.376}, {"TRP", 8, 7, 0.0532,10," NE1",-4.004,-0.715,-2.004}, {"TRP", 8, 7, 0.0532,10," CE2",-3.218,-1.294,-2.965}, {"TRP", 8, 7, 0.0532,10," CE3",-0.977,-2.168,-3.162}, {"TRP", 8, 7, 0.0532,10," CZ2",-3.503,-1.599,-4.294}, {"TRP", 8, 7, 0.0532,10," CZ3",-1.263,-2.470,-4.481}, {"TRP", 8, 7, 0.0532,10," CH2",-2.515,-2.185,-5.033}, {"TYR", 4, 0, 0.4735, 8," CB ",-0.940,-1.206, 0.008}, {"TYR", 4, 0, 0.4735, 8," CG ",-1.983,-1.178,-1.087}, {"TYR", 4, 0, 0.4735, 8," CD1",-3.154,-0.444,-0.938}, {"TYR", 4, 0, 0.4735, 8," CD2",-1.797,-1.885,-2.266}, {"TYR", 4, 0, 0.4735, 8," CE1",-4.110,-0.416,-1.935}, {"TYR", 4, 0, 0.4735, 8," CE2",-2.749,-1.863,-3.269}, {"TYR", 4, 0, 0.4735, 8," CZ ",-3.901,-1.126,-3.099}, {"TYR", 4, 0, 0.4735, 8," OH ",-4.852,-1.102,-4.093}, {"TYR", 4, 1, 0.3248, 8," CB ",-0.940,-1.206, 0.008}, {"TYR", 4, 1, 0.3248, 8," CG ",-1.838,-1.275, 1.223}, {"TYR", 4, 1, 0.3248, 8," CD1",-2.963,-0.466, 1.326}, {"TYR", 4, 1, 0.3248, 8," CD2",-1.561,-2.149, 2.265}, {"TYR", 4, 1, 0.3248, 8," CE1",-3.786,-0.525, 2.434}, {"TYR", 4, 1, 0.3248, 8," CE2",-2.380,-2.215, 3.378}, {"TYR", 4, 1, 0.3248, 8," CZ ",-3.490,-1.403, 3.456}, {"TYR", 4, 1, 0.3248, 8," OH ",-4.307,-1.463, 4.562}, {"TYR", 4, 2, 0.1159, 8," CB ",-0.940,-1.206, 0.008}, {"TYR", 4, 2, 0.1159, 8," CG ",-0.227,-2.539, 0.059}, {"TYR", 4, 2, 0.1159, 8," CD1", 0.141,-3.196,-1.108}, {"TYR", 4, 2, 0.1159, 8," CD2", 0.076,-3.138, 1.274}, {"TYR", 4, 2, 0.1159, 8," CE1", 0.792,-4.414,-1.066}, {"TYR", 4, 2, 0.1159, 8," CE2", 0.727,-4.358, 1.325}, {"TYR", 4, 2, 0.1159, 8," CZ ", 1.083,-4.989, 0.153}, {"TYR", 4, 2, 0.1159, 8," OH ", 1.730,-6.203, 0.198}, {"TYR", 4, 3, 0.0653, 8," CB ",-0.940,-1.206, 0.008}, {"TYR", 4, 3, 0.0653, 8," CG ",-2.004,-1.162,-1.066}, {"TYR", 4, 3, 0.0653, 8," CD1",-2.304, 0.025,-1.724}, {"TYR", 4, 3, 0.0653, 8," CD2",-2.707,-2.305,-1.420}, {"TYR", 4, 3, 0.0653, 8," CE1",-3.276, 0.070,-2.705}, {"TYR", 4, 3, 0.0653, 8," CE2",-3.681,-2.268,-2.401}, {"TYR", 4, 3, 0.0653, 8," CZ ",-3.960,-1.080,-3.040}, {"TYR", 4, 3, 0.0653, 8," OH ",-4.929,-1.037,-4.016}, {"VAL", 3, 0, 0.7390, 3," CB ",-0.945,-1.215, 0.038}, {"VAL", 3, 0, 0.7390, 3," CG1",-1.718,-1.247, 1.347}, {"VAL", 3, 0, 0.7390, 3," CG2",-1.895,-1.189,-1.149}, {"VAL", 3, 1, 0.1870, 3," CB ",-0.945,-1.215, 0.038}, {"VAL", 3, 1, 0.1870, 3," CG1",-1.904,-1.181,-1.141}, {"VAL", 3, 1, 0.1870, 3," CG2",-0.147,-2.510, 0.049}, {"VAL", 3, 2, 0.0740, 3," CB ",-0.945,-1.215, 0.038}, {"VAL", 3, 2, 0.0740, 3," CG1",-0.149,-2.505, 0.153}, {"VAL", 3, 2, 0.0740, 3," CG2",-1.933,-1.086, 1.188}}; int rotamer_data_dunbrack_size = sizeof( rotamer_data_dunbrack ) / sizeof( rotamer_data_dunbrack[0] ); Rotamer_data rotamer_data_richardson[] = { {"ALA", 1, 0, 1.0000, 1," CB ",-0.940,-1.196, 0.000}, {"ARG",19, 0, 0.1157, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19, 0, 0.1157, 7," CG ",-2.007,-1.170,-1.074}, {"ARG",19, 0, 0.1157, 7," CD ",-2.970,-2.346,-1.037}, {"ARG",19, 0, 0.1157, 7," NE ",-3.931,-2.301,-2.135}, {"ARG",19, 0, 0.1157, 7," CZ ",-4.804,-3.262,-2.400}, {"ARG",19, 0, 0.1157, 7," NH1",-4.845,-4.351,-1.643}, {"ARG",19, 0, 0.1157, 7," NH2",-5.642,-3.137,-3.421}, {"ARG",19, 1, 0.0702, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19, 1, 0.0702, 7," CG ",-2.036,-1.147,-1.043}, {"ARG",19, 1, 0.0702, 7," CD ",-3.144,-2.169,-0.844}, {"ARG",19, 1, 0.0702, 7," NE ",-2.651,-3.539,-0.951}, {"ARG",19, 1, 0.0702, 7," CZ ",-2.531,-4.201,-2.093}, {"ARG",19, 1, 0.0702, 7," NH1",-2.866,-3.619,-3.238}, {"ARG",19, 1, 0.0702, 7," NH2",-2.074,-5.446,-2.097}, {"ARG",19, 2, 0.0689, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19, 2, 0.0689, 7," CG ",-1.992,-1.182,-1.089}, {"ARG",19, 2, 0.0689, 7," CD ",-2.970,-2.345,-1.038}, {"ARG",19, 2, 0.0689, 7," NE ",-3.945,-2.288,-2.123}, {"ARG",19, 2, 0.0689, 7," CZ ",-5.052,-1.559,-2.092}, {"ARG",19, 2, 0.0689, 7," NH1",-5.330,-0.815,-1.029}, {"ARG",19, 2, 0.0689, 7," NH2",-5.884,-1.568,-3.126}, {"ARG",19, 3, 0.0624, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19, 3, 0.0624, 7," CG ",-2.022,-1.158,-1.058}, {"ARG",19, 3, 0.0624, 7," CD ",-2.849,-2.430,-1.163}, {"ARG",19, 3, 0.0624, 7," NE ",-2.044,-3.574,-1.580}, {"ARG",19, 3, 0.0624, 7," CZ ",-2.522,-4.799,-1.748}, {"ARG",19, 3, 0.0624, 7," NH1",-3.809,-5.046,-1.538}, {"ARG",19, 3, 0.0624, 7," NH2",-1.716,-5.781,-2.129}, {"ARG",19, 4, 0.0585, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19, 4, 0.0585, 7," CG ",-1.977,-1.194,-1.103}, {"ARG",19, 4, 0.0585, 7," CD ",-2.848,-2.439,-1.156}, {"ARG",19, 4, 0.0585, 7," NE ",-3.668,-2.584, 0.043}, {"ARG",19, 4, 0.0585, 7," CZ ",-4.429,-3.638, 0.302}, {"ARG",19, 4, 0.0585, 7," NH1",-4.476,-4.651,-0.554}, {"ARG",19, 4, 0.0585, 7," NH2",-5.143,-3.685, 1.419}, {"ARG",19, 5, 0.0442, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19, 5, 0.0442, 7," CG ",-1.853,-1.275, 1.220}, {"ARG",19, 5, 0.0442, 7," CD ",-2.836,-2.435, 1.193}, {"ARG",19, 5, 0.0442, 7," NE ",-2.160,-3.727, 1.258}, {"ARG",19, 5, 0.0442, 7," CZ ",-1.755,-4.301, 2.381}, {"ARG",19, 5, 0.0442, 7," NH1",-1.959,-3.700, 3.547}, {"ARG",19, 5, 0.0442, 7," NH2",-1.147,-5.480, 2.346}, {"ARG",19, 6, 0.0429, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19, 6, 0.0429, 7," CG ",-1.853,-1.275, 1.220}, {"ARG",19, 6, 0.0429, 7," CD ",-2.836,-2.435, 1.193}, {"ARG",19, 6, 0.0429, 7," NE ",-3.706,-2.443, 2.366}, {"ARG",19, 6, 0.0429, 7," CZ ",-4.768,-3.224, 2.500}, {"ARG",19, 6, 0.0429, 7," NH1",-5.097,-4.072, 1.533}, {"ARG",19, 6, 0.0429, 7," NH2",-5.504,-3.164, 3.602}, {"ARG",19, 7, 0.0429, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19, 7, 0.0429, 7," CG ",-2.007,-1.170,-1.074}, {"ARG",19, 7, 0.0429, 7," CD ",-2.910,-2.393,-1.098}, {"ARG",19, 7, 0.0429, 7," NE ",-3.932,-2.299,-2.136}, {"ARG",19, 7, 0.0429, 7," CZ ",-3.733,-2.614,-3.407}, {"ARG",19, 7, 0.0429, 7," NH1",-2.546,-3.052,-3.807}, {"ARG",19, 7, 0.0429, 7," NH2",-4.721,-2.497,-4.285}, {"ARG",19, 8, 0.0364, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19, 8, 0.0364, 7," CG ",-1.870,-1.262, 1.208}, {"ARG",19, 8, 0.0364, 7," CD ",-2.770,-2.487, 1.241}, {"ARG",19, 8, 0.0364, 7," NE ",-2.008,-3.723, 1.398}, {"ARG",19, 8, 0.0364, 7," CZ ",-2.481,-4.929, 1.121}, {"ARG",19, 8, 0.0364, 7," NH1",-3.719,-5.071, 0.665}, {"ARG",19, 8, 0.0364, 7," NH2",-1.716,-6.000, 1.295}, {"ARG",19, 9, 0.0338, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19, 9, 0.0338, 7," CG ",-1.853,-1.275, 1.220}, {"ARG",19, 9, 0.0338, 7," CD ",-2.803,-2.462, 1.216}, {"ARG",19, 9, 0.0338, 7," NE ",-3.659,-2.482, 2.399}, {"ARG",19, 9, 0.0338, 7," CZ ",-3.316,-3.027, 3.557}, {"ARG",19, 9, 0.0338, 7," NH1",-2.127,-3.599, 3.698}, {"ARG",19, 9, 0.0338, 7," NH2",-4.159,-3.001, 4.581}, {"ARG",19,10, 0.0325, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19,10, 0.0325, 7," CG ",-1.919,-1.224, 1.170}, {"ARG",19,10, 0.0325, 7," CD ",-2.820,-2.448, 1.205}, {"ARG",19,10, 0.0325, 7," NE ",-3.719,-2.500, 0.056}, {"ARG",19,10, 0.0325, 7," CZ ",-4.879,-1.863,-0.011}, {"ARG",19,10, 0.0325, 7," NH1",-5.288,-1.116, 1.006}, {"ARG",19,10, 0.0325, 7," NH2",-5.634,-1.968,-1.097}, {"ARG",19,11, 0.0286, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19,11, 0.0286, 7," CG ",-1.785,-1.328, 1.265}, {"ARG",19,11, 0.0286, 7," CD ",-2.765,-0.182, 1.465}, {"ARG",19,11, 0.0286, 7," NE ",-3.553,-0.342, 2.683}, {"ARG",19,11, 0.0286, 7," CZ ",-3.160, 0.061, 3.883}, {"ARG",19,11, 0.0286, 7," NH1",-1.984, 0.656, 4.033}, {"ARG",19,11, 0.0286, 7," NH2",-3.943,-0.127, 4.938}, {"ARG",19,12, 0.0286, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19,12, 0.0286, 7," CG ",-1.820,-1.301, 1.243}, {"ARG",19,12, 0.0286, 7," CD ",-2.737,-0.105, 1.443}, {"ARG",19,12, 0.0286, 7," NE ",-3.594,-0.262, 2.615}, {"ARG",19,12, 0.0286, 7," CZ ",-4.241, 0.733, 3.203}, {"ARG",19,12, 0.0286, 7," NH1",-4.136, 1.968, 2.729}, {"ARG",19,12, 0.0286, 7," NH2",-5.000, 0.498, 4.266}, {"ARG",19,13, 0.0286, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19,13, 0.0286, 7," CG ",-1.919,-1.224, 1.170}, {"ARG",19,13, 0.0286, 7," CD ",-2.915,-2.372, 1.126}, {"ARG",19,13, 0.0286, 7," NE ",-3.818,-2.358, 2.273}, {"ARG",19,13, 0.0286, 7," CZ ",-4.913,-1.617, 2.350}, {"ARG",19,13, 0.0286, 7," NH1",-5.253,-0.824, 1.341}, {"ARG",19,13, 0.0286, 7," NH2",-5.677,-1.667, 3.434}, {"ARG",19,14, 0.0260, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19,14, 0.0260, 7," CG ",-0.227,-2.546, 0.116}, {"ARG",19,14, 0.0260, 7," CD ",-1.150,-3.751, 0.027}, {"ARG",19,14, 0.0260, 7," NE ",-0.427,-5.009, 0.184}, {"ARG",19,14, 0.0260, 7," CZ ", 0.215,-5.626,-0.797}, {"ARG",19,14, 0.0260, 7," NH1", 0.232,-5.100,-2.016}, {"ARG",19,14, 0.0260, 7," NH2", 0.847,-6.769,-0.565}, {"ARG",19,15, 0.0247, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19,15, 0.0247, 7," CG ",-2.036,-1.147,-1.043}, {"ARG",19,15, 0.0247, 7," CD ",-2.926,-2.379,-1.084}, {"ARG",19,15, 0.0247, 7," NE ",-3.680,-2.552, 0.154}, {"ARG",19,15, 0.0247, 7," CZ ",-4.828,-1.946, 0.417}, {"ARG",19,15, 0.0247, 7," NH1",-5.367,-1.123,-0.475}, {"ARG",19,15, 0.0247, 7," NH2",-5.447,-2.162, 1.571}, {"ARG",19,16, 0.0234, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19,16, 0.0234, 7," CG ",-0.225,-2.549,-0.053}, {"ARG",19,16, 0.0234, 7," CD ",-1.151,-3.750, 0.051}, {"ARG",19,16, 0.0234, 7," NE ",-0.415,-5.011, 0.035}, {"ARG",19,16, 0.0234, 7," CZ ",-0.986,-6.207, 0.055}, {"ARG",19,16, 0.0234, 7," NH1",-2.308,-6.313, 0.088}, {"ARG",19,16, 0.0234, 7," NH2",-0.238,-7.303, 0.039}, {"ARG",19,17, 0.0208, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19,17, 0.0208, 7," CG ",-2.022,-1.158,-1.058}, {"ARG",19,17, 0.0208, 7," CD ",-2.970,-2.347,-1.036}, {"ARG",19,17, 0.0208, 7," NE ",-2.289,-3.597,-1.361}, {"ARG",19,17, 0.0208, 7," CZ ",-1.940,-4.509,-0.465}, {"ARG",19,17, 0.0208, 7," NH1",-2.210,-4.317, 0.820}, {"ARG",19,17, 0.0208, 7," NH2",-1.322,-5.618,-0.850}, {"ARG",19,18, 0.0208, 7," CB ",-0.939,-1.208, 0.007}, {"ARG",19,18, 0.0208, 7," CG ",-0.225,-2.547, 0.092}, {"ARG",19,18, 0.0208, 7," CD ",-1.155,-3.750, 0.051}, {"ARG",19,18, 0.0208, 7," NE ",-0.425,-5.010, 0.159}, {"ARG",19,18, 0.0208, 7," CZ ",-0.117,-5.596, 1.306}, {"ARG",19,18, 0.0208, 7," NH1",-0.477,-5.040, 2.456}, {"ARG",19,18, 0.0208, 7," NH2", 0.551,-6.743, 1.310}, {"ASN", 7, 0, 0.4154, 4," CB ",-0.952,-1.197, 0.006}, {"ASN", 7, 0, 0.4154, 4," CG ",-2.069,-1.060,-1.010}, {"ASN", 7, 0, 0.4154, 4," OD1",-2.411, 0.046,-1.427}, {"ASN", 7, 0, 0.4154, 4," ND2",-2.643,-2.187,-1.414}, {"ASN", 7, 1, 0.1633, 4," CB ",-0.952,-1.197, 0.006}, {"ASN", 7, 1, 0.1633, 4," CG ",-2.012,-1.092, 1.086}, {"ASN", 7, 1, 0.1633, 4," OD1",-2.435, 0.004, 1.451}, {"ASN", 7, 1, 0.1633, 4," ND2",-2.446,-2.236, 1.602}, {"ASN", 7, 2, 0.1267, 4," CB ",-0.952,-1.197, 0.006}, {"ASN", 7, 2, 0.1267, 4," CG ",-1.920,-1.165, 1.173}, {"ASN", 7, 2, 0.1267, 4," OD1",-1.682,-0.488, 2.173}, {"ASN", 7, 2, 0.1267, 4," ND2",-3.019,-1.900, 1.051}, {"ASN", 7, 3, 0.0945, 4," CB ",-0.952,-1.197, 0.006}, {"ASN", 7, 3, 0.0945, 4," CG ",-0.220,-2.524, 0.052}, {"ASN", 7, 3, 0.0945, 4," OD1", 0.840,-2.640, 0.667}, {"ASN", 7, 3, 0.0945, 4," ND2",-0.783,-3.533,-0.602}, {"ASN", 7, 4, 0.0845, 4," CB ",-0.952,-1.197, 0.006}, {"ASN", 7, 4, 0.0845, 4," CG ",-2.069,-1.060,-1.010}, {"ASN", 7, 4, 0.0845, 4," OD1",-3.022,-0.310,-0.804}, {"ASN", 7, 4, 0.0845, 4," ND2",-1.956,-1.787,-2.115}, {"ASN", 7, 5, 0.0737, 4," CB ",-0.952,-1.197, 0.006}, {"ASN", 7, 5, 0.0737, 4," CG ",-0.219,-2.524, 0.027}, {"ASN", 7, 5, 0.0737, 4," OD1", 0.989,-2.583,-0.201}, {"ASN", 7, 5, 0.0737, 4," ND2",-0.949,-3.599, 0.302}, {"ASN", 7, 6, 0.0415, 4," CB ",-0.952,-1.197, 0.006}, {"ASN", 7, 6, 0.0415, 4," CG ",-1.966,-1.142,-1.119}, {"ASN", 7, 6, 0.0415, 4," OD1",-2.175,-2.125,-1.830}, {"ASN", 7, 6, 0.0415, 4," ND2",-2.603, 0.011,-1.286}, {"ASP", 5, 0, 0.5330, 4," CB ",-0.939,-1.208, 0.006}, {"ASP", 5, 0, 0.5330, 4," CG ",-2.047,-1.090,-1.022}, {"ASP", 5, 0, 0.5330, 4," OD1",-2.264, 0.026,-1.538}, {"ASP", 5, 0, 0.5330, 4," OD2",-2.752,-2.059,-1.376}, {"ASP", 5, 1, 0.2146, 4," CB ",-0.939,-1.208, 0.006}, {"ASP", 5, 1, 0.2146, 4," CG ",-1.885,-1.202, 1.191}, {"ASP", 5, 1, 0.2146, 4," OD1",-1.825,-0.250, 1.997}, {"ASP", 5, 1, 0.2146, 4," OD2",-2.722,-2.106, 1.397}, {"ASP", 5, 2, 0.0994, 4," CB ",-0.939,-1.208, 0.006}, {"ASP", 5, 2, 0.0994, 4," CG ",-0.191,-2.526,-0.005}, {"ASP", 5, 2, 0.0994, 4," OD1", 1.054,-2.504,-0.095}, {"ASP", 5, 2, 0.0994, 4," OD2",-0.764,-3.634, 0.072}, {"ASP", 5, 3, 0.0950, 4," CB ",-0.939,-1.208, 0.006}, {"ASP", 5, 3, 0.0950, 4," CG ",-0.192,-2.524, 0.093}, {"ASP", 5, 3, 0.0950, 4," OD1", 1.035,-2.499, 0.318}, {"ASP", 5, 3, 0.0950, 4," OD2",-0.750,-3.633,-0.051}, {"ASP", 5, 4, 0.0578, 4," CB ",-0.939,-1.208, 0.006}, {"ASP", 5, 4, 0.0578, 4," CG ",-1.835,-1.240, 1.229}, {"ASP", 5, 4, 0.0578, 4," OD1",-2.678,-0.331, 1.373}, {"ASP", 5, 4, 0.0578, 4," OD2",-1.768,-2.136, 2.098}, {"CYS", 3, 0, 0.5071, 2," CB ",-0.940,-1.207, 0.007}, {"CYS", 3, 0, 0.5071, 2," SG ",-2.178,-1.197,-1.309}, {"CYS", 3, 1, 0.2642, 2," CB ",-0.940,-1.207, 0.007}, {"CYS", 3, 1, 0.2642, 2," SG ",-2.069,-1.265, 1.417}, {"CYS", 3, 2, 0.2285, 2," CB ",-0.940,-1.207, 0.007}, {"CYS", 3, 2, 0.2285, 2," SG ",-0.110,-2.801,-0.180}, {"GLN", 7, 0, 0.3994, 5," CB ",-0.940,-1.207, 0.006}, {"GLN", 7, 0, 0.3994, 5," CG ",-2.009,-1.169,-1.073}, {"GLN", 7, 0, 0.3994, 5," CD ",-2.874,-2.412,-1.082}, {"GLN", 7, 0, 0.3994, 5," OE1",-2.446,-3.477,-0.636}, {"GLN", 7, 0, 0.3994, 5," NE2",-4.096,-2.281,-1.590}, {"GLN", 7, 1, 0.1839, 5," CB ",-0.940,-1.207, 0.006}, {"GLN", 7, 1, 0.1839, 5," CG ",-1.936,-1.214, 1.154}, {"GLN", 7, 1, 0.1839, 5," CD ",-2.956,-2.327, 1.036}, {"GLN", 7, 1, 0.1839, 5," OE1",-2.981,-3.051, 0.040}, {"GLN", 7, 1, 0.1839, 5," NE2",-3.801,-2.468, 2.053}, {"GLN", 7, 2, 0.1668, 5," CB ",-0.940,-1.207, 0.006}, {"GLN", 7, 2, 0.1668, 5," CG ",-1.994,-1.181,-1.088}, {"GLN", 7, 2, 0.1668, 5," CD ",-2.899, 0.030,-0.998}, {"GLN", 7, 2, 0.1668, 5," OE1",-3.293, 0.439, 0.095}, {"GLN", 7, 2, 0.1668, 5," NE2",-3.232, 0.608,-2.148}, {"GLN", 7, 3, 0.1024, 5," CB ",-0.940,-1.207, 0.006}, {"GLN", 7, 3, 0.1024, 5," CG ",-1.920,-1.226, 1.167}, {"GLN", 7, 3, 0.1024, 5," CD ",-2.891,-0.065, 1.131}, {"GLN", 7, 3, 0.1024, 5," OE1",-3.648, 0.090, 0.172}, {"GLN", 7, 3, 0.1024, 5," NE2",-2.875, 0.755, 2.178}, {"GLN", 7, 4, 0.0486, 5," CB ",-0.940,-1.207, 0.006}, {"GLN", 7, 4, 0.0486, 5," CG ",-0.229,-2.549, 0.065}, {"GLN", 7, 4, 0.0486, 5," CD ",-1.190,-3.719, 0.070}, {"GLN", 7, 4, 0.0486, 5," OE1",-2.347,-3.583,-0.331}, {"GLN", 7, 4, 0.0486, 5," NE2",-0.715,-4.875, 0.523}, {"GLN", 7, 5, 0.0315, 5," CB ",-0.940,-1.207, 0.006}, {"GLN", 7, 5, 0.0315, 5," CG ",-1.978,-1.193,-1.103}, {"GLN", 7, 5, 0.0315, 5," CD ",-1.454,-1.770,-2.401}, {"GLN", 7, 5, 0.0315, 5," OE1",-0.299,-2.189,-2.480}, {"GLN", 7, 5, 0.0315, 5," NE2",-2.303,-1.796,-3.424}, {"GLN", 7, 6, 0.0289, 5," CB ",-0.940,-1.207, 0.006}, {"GLN", 7, 6, 0.0289, 5," CG ",-1.978,-1.193,-1.103}, {"GLN", 7, 6, 0.0289, 5," CD ",-2.960,-0.048,-0.969}, {"GLN", 7, 6, 0.0289, 5," OE1",-2.828, 0.974,-1.644}, {"GLN", 7, 6, 0.0289, 5," NE2",-3.951,-0.214,-0.098}, {"GLU", 7, 0, 0.3614, 5," CB ",-0.939,-1.208, 0.006}, {"GLU", 7, 0, 0.3614, 5," CG ",-2.008,-1.170,-1.075}, {"GLU", 7, 0, 0.3614, 5," CD ",-2.872,-2.417,-1.082}, {"GLU", 7, 0, 0.3614, 5," OE1",-2.524,-3.387,-0.377}, {"GLU", 7, 0, 0.3614, 5," OE2",-3.898,-2.427,-1.794}, {"GLU", 7, 1, 0.2613, 5," CB ",-0.939,-1.208, 0.006}, {"GLU", 7, 1, 0.2613, 5," CG ",-1.887,-1.252, 1.195}, {"GLU", 7, 1, 0.2613, 5," CD ",-2.833,-2.436, 1.140}, {"GLU", 7, 1, 0.2613, 5," OE1",-2.723,-3.244, 0.194}, {"GLU", 7, 1, 0.2613, 5," OE2",-3.689,-2.558, 2.042}, {"GLU", 7, 2, 0.1471, 5," CB ",-0.939,-1.208, 0.006}, {"GLU", 7, 2, 0.1471, 5," CG ",-1.978,-1.194,-1.104}, {"GLU", 7, 2, 0.1471, 5," CD ",-2.853, 0.045,-1.065}, {"GLU", 7, 2, 0.1471, 5," OE1",-3.232, 0.472, 0.045}, {"GLU", 7, 2, 0.1471, 5," OE2",-3.163, 0.589,-2.146}, {"GLU", 7, 3, 0.0679, 5," CB ",-0.939,-1.208, 0.006}, {"GLU", 7, 3, 0.0679, 5," CG ",-1.887,-1.252, 1.195}, {"GLU", 7, 3, 0.0679, 5," CD ",-2.875,-0.100, 1.192}, {"GLU", 7, 3, 0.0679, 5," OE1",-2.988, 0.586, 0.155}, {"GLU", 7, 3, 0.0679, 5," OE2",-3.535, 0.121, 2.229}, {"GLU", 7, 4, 0.0657, 5," CB ",-0.939,-1.208, 0.006}, {"GLU", 7, 4, 0.0657, 5," CG ",-1.978,-1.194,-1.104}, {"GLU", 7, 4, 0.0657, 5," CD ",-1.447,-1.772,-2.403}, {"GLU", 7, 4, 0.0657, 5," OE1",-0.253,-2.131,-2.451}, {"GLU", 7, 4, 0.0657, 5," OE2",-2.226,-1.865,-3.375}, {"GLU", 7, 5, 0.0597, 5," CB ",-0.939,-1.208, 0.006}, {"GLU", 7, 5, 0.0597, 5," CG ",-0.225,-2.550, 0.041}, {"GLU", 7, 5, 0.0597, 5," CD ",-1.182,-3.721,-0.075}, {"GLU", 7, 5, 0.0597, 5," OE1",-2.393,-3.526, 0.157}, {"GLU", 7, 5, 0.0597, 5," OE2",-0.722,-4.837,-0.397}, {"GLU", 7, 6, 0.0238, 5," CB ",-0.939,-1.208, 0.006}, {"GLU", 7, 6, 0.0238, 5," CG ",-0.238,-2.538, 0.234}, {"GLU", 7, 6, 0.0238, 5," CD ", 0.437,-3.061,-1.020}, {"GLU", 7, 6, 0.0238, 5," OE1", 0.439,-2.342,-2.040}, {"GLU", 7, 6, 0.0238, 5," OE2", 0.963,-4.194,-0.985}, {"HIS", 8, 0, 0.3096, 6," CB ",-0.940,-1.207, 0.007}, {"HIS", 8, 0, 0.3096, 6," CG ",-1.882,-1.247,-1.154}, {"HIS", 8, 0, 0.3096, 6," ND1",-2.913,-0.344,-1.309}, {"HIS", 8, 0, 0.3096, 6," CD2",-1.949,-2.080,-2.219}, {"HIS", 8, 0, 0.3096, 6," CE1",-3.575,-0.621,-2.418}, {"HIS", 8, 0, 0.3096, 6," NE2",-3.012,-1.669,-2.990}, {"HIS", 8, 1, 0.1672, 6," CB ",-0.940,-1.207, 0.007}, {"HIS", 8, 1, 0.1672, 6," CG ",-1.853,-1.255, 1.191}, {"HIS", 8, 1, 0.1672, 6," ND1",-2.788,-0.275, 1.452}, {"HIS", 8, 1, 0.1672, 6," CD2",-1.977,-2.165, 2.186}, {"HIS", 8, 1, 0.1672, 6," CE1",-3.446,-0.580, 2.556}, {"HIS", 8, 1, 0.1672, 6," NE2",-2.975,-1.721, 3.022}, {"HIS", 8, 2, 0.1387, 6," CB ",-0.940,-1.207, 0.007}, {"HIS", 8, 2, 0.1387, 6," CG ",-1.974,-1.174,-1.073}, {"HIS", 8, 2, 0.1387, 6," ND1",-1.721,-1.598,-2.361}, {"HIS", 8, 2, 0.1387, 6," CD2",-3.266,-0.770,-1.058}, {"HIS", 8, 2, 0.1387, 6," CE1",-2.812,-1.454,-3.092}, {"HIS", 8, 2, 0.1387, 6," NE2",-3.765,-0.954,-2.327}, {"HIS", 8, 3, 0.1138, 6," CB ",-0.940,-1.207, 0.007}, {"HIS", 8, 3, 0.1138, 6," CG ",-1.932,-1.194, 1.127}, {"HIS", 8, 3, 0.1138, 6," ND1",-1.618,-1.602, 2.407}, {"HIS", 8, 3, 0.1138, 6," CD2",-3.233,-0.820, 1.161}, {"HIS", 8, 3, 0.1138, 6," CE1",-2.683,-1.481, 3.179}, {"HIS", 8, 3, 0.1138, 6," NE2",-3.677,-1.009, 2.449}, {"HIS", 8, 4, 0.0907, 6," CB ",-0.940,-1.207, 0.007}, {"HIS", 8, 4, 0.0907, 6," CG ",-0.232,-2.525,-0.030}, {"HIS", 8, 4, 0.0907, 6," ND1", 0.356,-3.023,-1.173}, {"HIS", 8, 4, 0.0907, 6," CD2",-0.016,-3.448, 0.936}, {"HIS", 8, 4, 0.0907, 6," CE1", 0.901,-4.197,-0.910}, {"HIS", 8, 4, 0.0907, 6," NE2", 0.691,-4.479, 0.363}, {"HIS", 8, 5, 0.0782, 6," CB ",-0.940,-1.207, 0.007}, {"HIS", 8, 5, 0.0782, 6," CG ",-1.929,-1.210,-1.115}, {"HIS", 8, 5, 0.0782, 6," ND1",-2.653,-2.330,-1.468}, {"HIS", 8, 5, 0.0782, 6," CD2",-2.317,-0.230,-1.964}, {"HIS", 8, 5, 0.0782, 6," CE1",-3.442,-2.039,-2.486}, {"HIS", 8, 5, 0.0782, 6," NE2",-3.259,-0.772,-2.808}, {"HIS", 8, 6, 0.0551, 6," CB ",-0.940,-1.207, 0.007}, {"HIS", 8, 6, 0.0551, 6," CG ",-1.853,-1.255, 1.191}, {"HIS", 8, 6, 0.0551, 6," ND1",-2.523,-2.400, 1.571}, {"HIS", 8, 6, 0.0551, 6," CD2",-2.208,-0.300, 2.083}, {"HIS", 8, 6, 0.0551, 6," CE1",-3.251,-2.146, 2.643}, {"HIS", 8, 6, 0.0551, 6," NE2",-3.079,-0.881, 2.976}, {"HIS", 8, 7, 0.0462, 6," CB ",-0.940,-1.207, 0.007}, {"HIS", 8, 7, 0.0462, 6," CG ",-0.232,-2.525,-0.006}, {"HIS", 8, 7, 0.0462, 6," ND1", 0.347,-3.071, 1.121}, {"HIS", 8, 7, 0.0462, 6," CD2",-0.010,-3.408,-1.007}, {"HIS", 8, 7, 0.0462, 6," CE1", 0.896,-4.232, 0.812}, {"HIS", 8, 7, 0.0462, 6," NE2", 0.694,-4.461,-0.472}, {"ILE", 5, 0, 0.6043, 4," CB ",-0.946,-1.216, 0.008}, {"ILE", 5, 0, 0.6043, 4," CG1",-1.969,-1.104,-1.124}, {"ILE", 5, 0, 0.6043, 4," CG2",-1.645,-1.338, 1.354}, {"ILE", 5, 0, 0.6043, 4," CD1",-2.764,-2.369,-1.355}, {"ILE", 5, 1, 0.1472, 4," CB 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", 0.113,-2.228,-0.862}, {"PRO", 3, 0, 0.4696, 3," CD ", 1.345,-1.430,-1.153}, {"PRO", 3, 1, 0.4609, 3," CB ",-0.784,-1.311,-0.107}, {"PRO", 3, 1, 0.4609, 3," CG ",-0.916,-1.555,-1.569}, {"PRO", 3, 1, 0.4609, 3," CD ",-0.221,-0.406,-2.229}, {"PRO", 3, 2, 0.0693, 3," CB ",-0.784,-1.311,-0.107}, {"PRO", 3, 2, 0.0693, 3," CG ", 0.123,-2.236,-0.840}, {"PRO", 3, 2, 0.0693, 3," CD ", 1.360,-1.442,-1.120}, {"SER", 3, 0, 0.4890, 2," CB ",-0.939,-1.208, 0.010}, {"SER", 3, 0, 0.4890, 2," OG ",-0.209,-2.421, 0.068}, {"SER", 3, 1, 0.2907, 2," CB ",-0.939,-1.208, 0.010}, {"SER", 3, 1, 0.2907, 2," OG ",-1.878,-1.128,-1.048}, {"SER", 3, 2, 0.2202, 2," CB ",-0.939,-1.208, 0.010}, {"SER", 3, 2, 0.2202, 2," OG ",-1.710,-1.242, 1.199}, {"THR", 3, 0, 0.4936, 3," CB ",-0.946,-1.215, 0.008}, {"THR", 3, 0, 0.4936, 3," OG1",-0.178,-2.422,-0.051}, {"THR", 3, 0, 0.4936, 3," CG2",-1.769,-1.260,-1.270}, {"THR", 3, 1, 0.4368, 3," CB ",-0.946,-1.215, 0.008}, {"THR", 3, 1, 0.4368, 3," OG1",-1.819,-1.152,-1.125}, {"THR", 3, 1, 0.4368, 3," CG2",-1.900,-1.141, 1.191}, {"THR", 3, 2, 0.0695, 3," CB ",-0.946,-1.215, 0.008}, {"THR", 3, 2, 0.0695, 3," OG1",-1.883,-1.087, 1.083}, {"THR", 3, 2, 0.0695, 3," CG2",-0.183,-2.484, 0.359}, {"TRP", 7, 0, 0.3339,10," CB ",-0.938,-1.209, 0.008}, {"TRP", 7, 0, 0.3339,10," CG ",-2.015,-1.139,-1.031}, {"TRP", 7, 0, 0.3339,10," CD1",-1.991,-1.692,-2.279}, {"TRP", 7, 0, 0.3339,10," CD2",-3.279,-0.475,-0.913}, {"TRP", 7, 0, 0.3339,10," NE1",-3.160,-1.413,-2.944}, {"TRP", 7, 0, 0.3339,10," CE2",-3.969,-0.668,-2.128}, {"TRP", 7, 0, 0.3339,10," CE3",-3.902, 0.266, 0.097}, {"TRP", 7, 0, 0.3339,10," CZ2",-5.243,-0.150,-2.357}, {"TRP", 7, 0, 0.3339,10," CZ3",-5.165, 0.779,-0.133}, {"TRP", 7, 0, 0.3339,10," CH2",-5.821, 0.569,-1.349}, {"TRP", 7, 1, 0.1866,10," CB ",-0.938,-1.209, 0.008}, {"TRP", 7, 1, 0.1866,10," CG ",-1.850,-1.251, 1.196}, {"TRP", 7, 1, 0.1866,10," CD1",-3.079,-0.669, 1.310}, {"TRP", 7, 1, 0.1866,10," CD2",-1.605,-1.913, 2.443}, {"TRP", 7, 1, 0.1866,10," NE1",-3.613,-0.925, 2.550}, {"TRP", 7, 1, 0.1866,10," CE2",-2.729,-1.689, 3.265}, {"TRP", 7, 1, 0.1866,10," CE3",-0.548,-2.674, 2.953}, {"TRP", 7, 1, 0.1866,10," CZ2",-2.823,-2.196, 4.560}, {"TRP", 7, 1, 0.1866,10," CZ3",-0.644,-3.176, 4.238}, {"TRP", 7, 1, 0.1866,10," CH2",-1.773,-2.935, 5.026}, {"TRP", 7, 2, 0.1712,10," CB ",-0.938,-1.209, 0.008}, {"TRP", 7, 2, 0.1712,10," CG ",-1.783,-1.303, 1.242}, {"TRP", 7, 2, 0.1712,10," CD1",-1.620,-2.165, 2.287}, {"TRP", 7, 2, 0.1712,10," CD2",-2.928,-0.502, 1.560}, {"TRP", 7, 2, 0.1712,10," NE1",-2.592,-1.952, 3.234}, {"TRP", 7, 2, 0.1712,10," CE2",-3.408,-0.935, 2.814}, {"TRP", 7, 2, 0.1712,10," CE3",-3.601, 0.540, 0.913}, {"TRP", 7, 2, 0.1712,10," CZ2",-4.522,-0.366, 3.427}, {"TRP", 7, 2, 0.1712,10," CZ3",-4.706, 1.103, 1.525}, {"TRP", 7, 2, 0.1712,10," CH2",-5.155, 0.650, 2.768}, {"TRP", 7, 3, 0.1147,10," CB ",-0.938,-1.209, 0.008}, {"TRP", 7, 3, 0.1147,10," CG ",-0.223,-2.523,-0.075}, {"TRP", 7, 3, 0.1147,10," CD1", 0.163,-3.180,-1.208}, {"TRP", 7, 3, 0.1147,10," CD2", 0.195,-3.343, 1.023}, {"TRP", 7, 3, 0.1147,10," NE1", 0.792,-4.357,-0.883}, {"TRP", 7, 3, 0.1147,10," CE2", 0.827,-4.481, 0.480}, {"TRP", 7, 3, 0.1147,10," CE3", 0.100,-3.234, 2.415}, {"TRP", 7, 3, 0.1147,10," CZ2", 1.356,-5.496, 1.276}, {"TRP", 7, 3, 0.1147,10," CZ3", 0.627,-4.242, 3.202}, {"TRP", 7, 3, 0.1147,10," CH2", 1.246,-5.357, 2.631}, {"TRP", 7, 4, 0.0821,10," CB ",-0.938,-1.209, 0.008}, {"TRP", 7, 4, 0.0821,10," CG ",-1.971,-1.173,-1.076}, {"TRP", 7, 4, 0.0821,10," CD1",-2.185,-0.168,-1.975}, {"TRP", 7, 4, 0.0821,10," CD2",-2.934,-2.191,-1.378}, {"TRP", 7, 4, 0.0821,10," NE1",-3.222,-0.497,-2.815}, {"TRP", 7, 4, 0.0821,10," CE2",-3.698,-1.734,-2.471}, {"TRP", 7, 4, 0.0821,10," CE3",-3.231,-3.445,-0.834}, {"TRP", 7, 4, 0.0821,10," CZ2",-4.734,-2.483,-3.027}, {"TRP", 7, 4, 0.0821,10," CZ3",-4.259,-4.186,-1.388}, {"TRP", 7, 4, 0.0821,10," CH2",-4.997,-3.703,-2.472}, {"TRP", 7, 5, 0.0582,10," CB ",-0.938,-1.209, 0.008}, {"TRP", 7, 5, 0.0582,10," CG ",-0.221,-2.524,-0.027}, {"TRP", 7, 5, 0.0582,10," CD1", 0.168,-3.278, 1.043}, {"TRP", 7, 5, 0.0582,10," CD2", 0.196,-3.243,-1.194}, {"TRP", 7, 5, 0.0582,10," NE1", 0.801,-4.419, 0.614}, {"TRP", 7, 5, 0.0582,10," CE2", 0.830,-4.424,-0.755}, {"TRP", 7, 5, 0.0582,10," CE3", 0.100,-3.010,-2.570}, {"TRP", 7, 5, 0.0582,10," CZ2", 1.362,-5.362,-1.638}, {"TRP", 7, 5, 0.0582,10," CZ3", 0.627,-3.943,-3.444}, {"TRP", 7, 5, 0.0582,10," CH2", 1.250,-5.103,-2.975}, {"TRP", 7, 6, 0.0530,10," CB ",-0.938,-1.209, 0.008}, {"TRP", 7, 6, 0.0530,10," CG ",-2.029,-1.128,-1.015}, {"TRP", 7, 6, 0.0530,10," CD1",-3.248,-0.531,-0.872}, {"TRP", 7, 6, 0.0530,10," CD2",-2.000,-1.663,-2.344}, {"TRP", 7, 6, 0.0530,10," NE1",-3.980,-0.663,-2.027}, {"TRP", 7, 6, 0.0530,10," CE2",-3.237,-1.353,-2.948}, {"TRP", 7, 6, 0.0530,10," CE3",-1.055,-2.377,-3.089}, {"TRP", 7, 6, 0.0530,10," CZ2",-3.548,-1.729,-4.253}, {"TRP", 7, 6, 0.0530,10," CZ3",-1.367,-2.748,-4.384}, {"TRP", 7, 6, 0.0530,10," CH2",-2.602,-2.424,-4.952}, {"TYR", 4, 0, 0.4382, 8," CB ",-0.940,-1.206, 0.008}, {"TYR", 4, 0, 0.4382, 8," CG ",-1.972,-1.188,-1.098}, {"TYR", 4, 0, 0.4382, 8," CD1",-3.187,-0.534,-0.929}, {"TYR", 4, 0, 0.4382, 8," CD2",-1.730,-1.823,-2.307}, {"TYR", 4, 0, 0.4382, 8," CE1",-4.131,-0.515,-1.936}, {"TYR", 4, 0, 0.4382, 8," CE2",-2.670,-1.809,-3.322}, {"TYR", 4, 0, 0.4382, 8," CZ ",-3.868,-1.154,-3.131}, {"TYR", 4, 0, 0.4382, 8," OH ",-4.809,-1.138,-4.135}, {"TYR", 4, 1, 0.3446, 8," CB ",-0.940,-1.206, 0.008}, {"TYR", 4, 1, 0.3446, 8," CG ",-1.763,-1.334, 1.271}, {"TYR", 4, 1, 0.3446, 8," CD1",-2.872,-0.524, 1.484}, {"TYR", 4, 1, 0.3446, 8," CD2",-1.431,-2.263, 2.246}, {"TYR", 4, 1, 0.3446, 8," CE1",-3.627,-0.637, 2.636}, {"TYR", 4, 1, 0.3446, 8," CE2",-2.181,-2.384, 3.403}, {"TYR", 4, 1, 0.3446, 8," CZ ",-3.277,-1.569, 3.592}, {"TYR", 4, 1, 0.3446, 8," OH ",-4.026,-1.682, 4.741}, {"TYR", 4, 2, 0.1290, 8," CB ",-0.940,-1.206, 0.008}, {"TYR", 4, 2, 0.1290, 8," CG ",-0.227,-2.540, 0.045}, {"TYR", 4, 2, 0.1290, 8," CD1", 0.109,-3.136, 1.255}, {"TYR", 4, 2, 0.1290, 8," CD2", 0.108,-3.200,-1.128}, {"TYR", 4, 2, 0.1290, 8," CE1", 0.759,-4.353, 1.293}, {"TYR", 4, 2, 0.1290, 8," CE2", 0.760,-4.420,-1.099}, {"TYR", 4, 2, 0.1290, 8," CZ ", 1.083,-4.991, 0.113}, {"TYR", 4, 2, 0.1290, 8," OH ", 1.733,-6.204, 0.148}, {"TYR", 4, 3, 0.0879, 8," CB ",-0.940,-1.206, 0.008}, {"TYR", 4, 3, 0.0879, 8," CG ",-1.956,-1.200,-1.112}, {"TYR", 4, 3, 0.0879, 8," CD1",-2.614,-0.029,-1.472}, {"TYR", 4, 3, 0.0879, 8," CD2",-2.256,-2.362,-1.807}, {"TYR", 4, 3, 0.0879, 8," CE1",-3.542,-0.019,-2.494}, {"TYR", 4, 3, 0.0879, 8," CE2",-3.185,-2.361,-2.833}, {"TYR", 4, 3, 0.0879, 8," CZ ",-3.824,-1.188,-3.172}, {"TYR", 4, 3, 0.0879, 8," OH ",-4.750,-1.181,-4.189}, {"VAL", 3, 0, 0.7353, 3," CB ",-0.945,-1.215, 0.038}, {"VAL", 3, 0, 0.7353, 3," CG1",-1.702,-1.260, 1.357}, {"VAL", 3, 0, 0.7353, 3," CG2",-1.910,-1.177,-1.137}, {"VAL", 3, 1, 0.2003, 3," CB ",-0.945,-1.215, 0.038}, {"VAL", 3, 1, 0.2003, 3," CG1",-1.941,-1.152,-1.108}, {"VAL", 3, 1, 0.2003, 3," CG2",-0.149,-2.511,-0.009}, {"VAL", 3, 2, 0.0643, 3," CB ",-0.945,-1.215, 0.038}, {"VAL", 3, 2, 0.0643, 3," CG1",-0.148,-2.509, 0.091}, {"VAL", 3, 2, 0.0643, 3," CG2",-1.892,-1.116, 1.225}}; int rotamer_data_richardson_size = sizeof( rotamer_data_richardson ) / sizeof( rotamer_data_richardson[0] ); } // namespace data } // namespace clipper clipper-2.1/clipper/minimol/minimol.h0000644000374100011300000003623711350423210014646 00000000000000/*! \file minimol.h Header file for atomic model types */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_MINIMOL #define CLIPPER_MINIMOL #include "../core/coords.h" #include "minimol_data.h" namespace clipper { // Forward definitions class MAtomIndex; class MAtomIndexSymmetry; //! dummy namespace to hold search modes namespace MM { enum MODE { UNIQUE, ANY }; enum COPY { COPY_NONE, COPY_M, COPY_P, COPY_MP, COPY_C, COPY_MC, COPY_PC, COPY_MPC, MEMBERS=COPY_M, PROPERTIES=COPY_P, CHILDREN=COPY_C }; } //! MiniMol atom object /*! The MiniMol atom is derived from the basic clipper::Atom, with the addition of an 'id', which is a unique identifier within a monomer in accordance with the mmCIF definition. In addition, it is a clipper::PropertyManager, which means you can add labelled properties of any type to the object. These may be simple strings, or complex objects such as maps, function objects, or whatever. The most commonly used properties are: - "CID" The original CID of this atom in an MMDB heirarchy. The id() is the unique key which identifies an atom. */ class MAtom : public Atom, public PropertyManager { public: MAtom() {} //!< null constructor MAtom( const clipper::Atom& atom ); //!< constructor: from clipper::Atom //! get atom ID, e.g. " N ", " CA ", " CG1", " CA :A" const String& id() const { return id_; } void set_id( const String& s ); //!< set atom ID //! get atom name, i.e. the ID, omitting any alternate conformation code String name() const { return id_.substr(0,4); } void set_name( const String s, const String altconf="" ); //!< set full id //-- const String& element() const; //!< get element e.g. H, C, Zn2+ //-- const Coord_orth& coord_orth() const; //!< get orth coordinate //-- const ftype& occupancy() const; //!< get occupancy //-- const ftype& u_iso() const; //!< get isotropic U //-- const U_aniso_orth& u_aniso_orth() const; //!< get anisotropic U //-- void set_element( const String& s ); //!< set element //-- void set_coord_orth( const Coord_orth& s ); //!< set coord_orth //-- void set_occupancy( const ftype& s ); //!< set occupancy //-- void set_u_iso( const ftype& s ); //!< set u_iso //-- void set_u_aniso_orth( const U_aniso_orth& s ); //!< set u_aniso //-- void transform( const RTop_orth rt ); //!< apply transform to object const Atom& atom() const { return *this; } //!< explicitly get atom Atom& atom() { return *this; } //!< explicitly set atom //! configureable copy function MAtom& copy( const MAtom& other, const MM::COPY& mode ); static String id_tidy( const String& id ); //!< convert ID to std format static bool id_match( const String& id1, const String& id2, const MM::MODE& mode ); //!< convert ID to std format private: String id_; }; //! MiniMol monomer (e.g. residue) object /*! The MiniMol monomer object contains a list of clipper::MAtom. It has two properties: a sequence number and a type. The sequence number need not reflect the order in which the monomers are stored in a polymer. MResidue is an alias for MMonomer. In addition, it is a clipper::PropertyManager, which means you can add labelled properties of any type to the object. These may be simple strings, or complex objects such as maps, function objects, or whatever. The most commonly used properties are: - "CID" The original CID of this atom in an MMDB heirarchy. The id() is the unique key which identifies a monomer. */ class MMonomer : public PropertyManager { public: const String& id() const { return id_; } //!< get monomer ID void set_id( const String& s ); //!< set monomer ID const String& type() const { return type_; } //!< get monomer type void set_type( const String& s ); //!< set monomer type, e.g. LYS, VAL, G int seqnum() const { return id_.i(); } //!< get monomer seq number void set_seqnum( const int s, const String inscode="" ); //!< set full id // the following methods are similar for all levels of the hierarchy Atom_list atom_list() const; //!< return list of contained atoms void transform( const RTop_orth rt ); //!< apply transformation to object //! number of atoms in monomer int size() const { return children.size(); } //! get atom const MAtom& operator[] ( const int& i ) const { return children[i]; } //! set atom MAtom& operator[] ( const int& i ) { return children[i]; } //! get atom by id const MAtom& find( const String& n, const MM::MODE mode=MM::UNIQUE ) const; //! set atom by id MAtom& find( const String& n, const MM::MODE mode=MM::UNIQUE ); //! create selection MMonomer select( const String& sel, const MM::MODE mode=MM::UNIQUE ) const; //! get child indices matching a selection criteria std::vector select_index( const String& sel, const MM::MODE mode=MM::UNIQUE ) const; //! lookup atom by id int lookup( const String& str, const MM::MODE& mode ) const; void insert( const MAtom& add, int pos=-1 ); //!< add atom //! and operator friend MMonomer operator& ( const MMonomer& m1, const MMonomer& m2 ); //! or operator friend MMonomer operator| ( const MMonomer& m1, const MMonomer& m2 ); //! configureable copy function MMonomer& copy( const MMonomer& other, const MM::COPY& mode ); static String id_tidy( const String& id ); //!< convert ID to std format static bool id_match( const String& id1, const String& id2, const MM::MODE& mode ); //!< convert ID to std format //! Rotamer library type enum TYPE { Default, Dunbrack, Richardson }; //! UTILITY: Build carbonyl oxygen, give next residue in chain void protein_mainchain_build_carbonyl_oxygen( const MMonomer& next ); //! UTILITY: get number of rotamers for protein sidechain int protein_sidechain_number_of_rotamers( TYPE t = default_type_ ) const; int protein_sidechain_number_of_rotomers() const { return protein_sidechain_number_of_rotamers(); } //! UTILITY: build numbered rotamer for protein sidechain ftype protein_sidechain_build_rotamer( const int& n, TYPE t = default_type_ ); ftype protein_sidechain_build_rotomer( const int& n ) { return protein_sidechain_build_rotamer( n ); } //! UTILITY: test if two peptide are adjacent static bool protein_peptide_bond( const MMonomer& m1, const MMonomer& m2, ftype r = 1.5 ); //! UTILITY: return Ramachandran phi, or NaN if atoms missing static double protein_ramachandran_phi( const MMonomer& m1, const MMonomer& m2 ); //! UTILITY: return Ramachandran psi, or NaN if atoms missing static double protein_ramachandran_psi( const MMonomer& m1, const MMonomer& m2 ); static TYPE& default_type() { return default_type_; } private: typedef MAtom CHILDTYPE; std::vector children; String id_, type_; static TYPE default_type_; static int rotamer_find( String res, int rota, TYPE t ); }; //! MiniMol polymer (e.g. chain) object /*! The MiniMol polymer object has one property: an identifying name. It contains a list of clipper::MMonomer. In addition, it is a clipper::PropertyManager, which means you can add labelled properties of any type to the object. These may be simple strings, or complex objects such as maps, function objects, or whatever. The most commonly used properties are: - "CID" The original CID of this atom in an MMDB heirarchy. The id() is the unique key which identifies a polymer. */ class MPolymer : public PropertyManager { public: const String& id() const { return id_; } //!< get polymer ID void set_id( const String& s ); //!< set polymer ID // the following methods are similar for all levels of the hierarchy Atom_list atom_list() const; //!< return list of contained atoms void transform( const RTop_orth rt ); //!< apply transformation to object //! number of monomers in polymer int size() const { return children.size(); } //! get monomer const MMonomer& operator[] ( const int& i ) const { return children[i]; } //! set monomer MMonomer& operator[] ( const int& i ) { return children[i]; } //! get monomer by id const MMonomer& find( const String& n, const MM::MODE mode=MM::UNIQUE ) const; //! set monomer by id MMonomer& find( const String& n, const MM::MODE mode=MM::UNIQUE ); //! create selection MPolymer select( const String& sel, const MM::MODE mode=MM::UNIQUE ) const; //! get child indices matching a selection criteria std::vector select_index( const String& sel, const MM::MODE mode=MM::UNIQUE ) const; //! lookup monomer by id int lookup( const String& str, const MM::MODE& mode ) const; void insert( const MMonomer& add, int pos=-1 ); //!< add monomer //! and operator friend MPolymer operator& ( const MPolymer& m1, const MPolymer& m2 ); //! or operator friend MPolymer operator| ( const MPolymer& m1, const MPolymer& m2 ); //! configureable copy function MPolymer& copy( const MPolymer& other, const MM::COPY& mode ); static String id_tidy( const String& id ); //!< convert ID to std format static bool id_match( const String& id1, const String& id2, const MM::MODE& mode ); //!< convert ID to std format private: typedef MMonomer CHILDTYPE; std::vector children; String id_; }; //! MiniMol model object /*! The MiniMol model object constains a list of clipper::MPolymer. In addition, it is a clipper::PropertyManager, which means you can add labelled properties of any type to the object. These may be simple strings, or complex objects such as maps, function objects, or whatever. The most commonly used properties are: - "CID" The original CID of this atom in an MMDB heirarchy. */ class MModel : public PropertyManager { public: // the following methods are similar for all levels of the hierarchy Atom_list atom_list() const; //!< return list of contained atoms void transform( const RTop_orth rt ); //!< apply transformation to object //! number of polymers in model int size() const { return children.size(); } //! get polymer const MPolymer& operator[] ( const int& i ) const { return children[i]; } //! set polymer MPolymer& operator[] ( const int& i ) { return children[i]; } //! get polymer by id const MPolymer& find( const String& n, const MM::MODE mode=MM::UNIQUE ) const; //! set polymer by id MPolymer& find( const String& n, const MM::MODE mode=MM::UNIQUE ); //! create selection MModel select( const String& sel, const MM::MODE mode=MM::UNIQUE ) const; //! get child indices matching a selection criteria std::vector select_index( const String& sel, const MM::MODE mode=MM::UNIQUE ) const; //! lookup polymer by id int lookup( const String& str, const MM::MODE& mode ) const; void insert( const MPolymer& add, int pos=-1 ); //!< add polymer //! and operator friend MModel operator& ( const MModel& m1, const MModel& m2 ); //! or operator friend MModel operator| ( const MModel& m1, const MModel& m2 ); //! configureable copy function MModel& copy( const MModel& other, const MM::COPY& mode ); //! Return atom by MAtomIndex const MAtom& atom( const MAtomIndex& index ) const; //! Return atom by MAtomIndex MAtom& atom( const MAtomIndex& index ); //! Select and return MAtomIndex values std::vector select_atom_index( const String& sel, const MM::MODE mode=MM::UNIQUE ) const; private: typedef MPolymer CHILDTYPE; std::vector children; }; //! MiniMol lightweight coordinate model object /*! A MiniMol object is a model (clipper::MModel) embedded in a crystal frame, i.e. with additional spacegroup and cell information. The design of this object was inspired by and contributed to by Paul Emsley. */ class MiniMol : public MModel { public: enum MODE { UNIQUE, ANY }; //!< mode to use when matching IDs //! null constructor MiniMol(); //! constructor: from spacegroup and cell MiniMol( const Spacegroup& spacegroup, const Cell& cell ); //! initialiser: from spacegroup and cell void init( const Spacegroup& spacegroup, const Cell& cell ); //! get the cell const Cell& cell() const { return cell_; } //! get the spacegroup const Spacegroup& spacegroup() const { return spacegroup_; } const MModel& model() const { return *this; } //!< explicitly get model MModel& model() { return *this; } //!< explicitly set model //! Return symmetry atom by MAtomIndexSymmetry MAtom symmetry_atom( const MAtomIndexSymmetry& index ); bool is_null() const; //!< test for null model private: Spacegroup spacegroup_; Cell cell_; }; //! MResidue: an alternative name for an MMonomer typedef MMonomer MResidue; //! 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mostlyclean-libtool pdf pdf-am ps ps-am tags uninstall \ uninstall-am uninstall-libLTLIBRARIES \ uninstall-library_includeHEADERS # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: clipper-2.1/clipper/minimol/container_minimol.cpp0000644000374100011300000000751710736662163017265 00000000000000/* container_minimol.cpp: atomic model types */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "container_minimol.h" namespace clipper { // CMiniMol /*! The object is constructed at the given location in the hierarchy. An attempt is made to initialise the object using information from its parents in the hierarchy. \param parent An object in the hierarchy (usually the parent of the new object). \param name The path from \c parent to the new object (usually just the name of the new object). */ CMiniMol::CMiniMol( Container& parent, const String name ) : Container( parent, name ) { init( NullSpacegroup, NullCell ); } /*! An attempt is made to initialise the object using information from the supplied parameters, or if they are Null, from its parents in the hierarchy. \param spacegroup The spacegroup for the model. \param name The cell for the model. */ void CMiniMol::init( const Spacegroup& spacegroup, const Cell& cell ) { // use supplied values by default const Spacegroup* sp = &spacegroup; // use pointers so we can reassign const Cell* cp = &cell; // otherwise get them from the tree if ( sp->is_null() ) sp = parent_of_type_ptr(); if ( cp->is_null() ) cp = parent_of_type_ptr(); // initialise if ( sp != NULL && cp != NULL ) if ( !sp->is_null() && !cp->is_null() ) MiniMol::init( *sp, *cp ); Container::update(); } /*! Hierarchical update. If this object is uninitialised, an attempt is made to initialise the object using information from its parents in the hierarchy. The childen of the object are then updated. */ void CMiniMol::update() { if ( CMiniMol::is_null() ) init( NullSpacegroup, NullCell ); else Container::update(); } } // namespace clipper clipper-2.1/clipper/minimol/minimol_io.cpp0000644000374100011300000003462511205471346015703 00000000000000/* minimol_io.cpp: atomic model types */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "minimol_io.h" #include #include extern "C" { #include } namespace clipper { // MMDBfile // local types for referencing between MMDB and minimol struct SAtom { mmdb::PCAtom db; const MAtom* mm; }; struct SMono { mmdb::PCResidue db; const MMonomer* mm; std::vector data; }; struct SPoly { mmdb::PCChain db; const MPolymer* mm; std::vector data; }; struct SModl { mmdb::PCModel db; const MModel* mm; std::vector data; }; /*! The file may be either a PDB or mmCIF file. If the spacegroup or cell are not set, they will be taken from the file, otherwise the existing values override the ones in the file. \param file The filename (or pathname) of the file to read. */ void MMDBfile::read_file( const String& file ) { int err = ReadCoorFile( (char *)file.c_str() ); if (err) Message::message( Message_fatal( "MMDBfile: read_file error: "+file+" : "+String(err) ) ); } /*! The output file type will be the same as the file read, otherwise PDB. \param file The filename (or pathname) of the file to write. \param type 0=PDB, 1=CIF, 2=binary, default=same as input file, or PDB. */ void MMDBfile::write_file( const String& file, TYPE type ) { const TYPE types[3] = { PDB, CIF, Binary }; int rtype = GetFileType(); if ( type == Default && rtype >= 0 && rtype <= 2 ) type = types[ rtype ]; int err; switch ( type ) { case Binary: err = WriteMMDBF( (char *)file.c_str() ); break; case CIF: err = WriteCIFASCII( (char *)file.c_str() ); break; case PDB: default: err = WritePDBASCII( (char *)file.c_str() ); break; } if (err) Message::message( Message_fatal( "MMDBfile: write_file error: "+file+" : "+String(err) ) ); } /*! Import data from the MMDB hierarchy into a MiniMol object. All the atoms, residues and chains are imported unless a selection handle is supplied, in which case only the selected atoms and their containers are imported. Each data is tagged with an optional Property (see clipper::PropertyManager), called "CID", which describes the position in the MMDB hierarchy from which it was taken. This may (optionally) be used later to put a modified element back into the hierarchy. Any atoms which have alternate conformation codes will also be given an "AltConf" Property. For more details, see clipper::PropertyManager::exists_property(), clipper::PropertyManager::get_property(). \param minimol The minimol to import. \param hnd (optional) MMDB selection handle. */ void MMDBfile::import_minimol( MiniMol& minimol, const int hnd ) { // clear the model minimol = MiniMol( spacegroup(), cell() ); // make atom, residue, chain selections int h_atm = NewSelection(); int h_res = NewSelection(); int h_chn = NewSelection(); int h_mod = NewSelection(); if ( hnd < 0 ) { SelectAtoms( h_atm, 0, 0, SKEY_NEW ); } else { Select( h_atm, STYPE_ATOM, hnd, SKEY_NEW ); } Select( h_res, STYPE_RESIDUE, h_atm, SKEY_NEW ); Select( h_chn, STYPE_CHAIN, h_atm, SKEY_NEW ); Select( h_mod, STYPE_MODEL, h_atm, SKEY_NEW ); // now import objects char txt[256]; MModel& mol = minimol.model(); mmdb::PCModel p_mod = GetModel(1); if ( p_mod != NULL ) { for ( int c = 0; c < p_mod->GetNumberOfChains(); c++ ) { mmdb::PCChain p_chn = p_mod->GetChain(c); if ( p_chn != NULL ) if ( p_chn->isInSelection( h_chn ) ) { // import the chain MPolymer pol; for ( int r = 0; r < p_chn->GetNumberOfResidues(); r++ ) { mmdb::PCResidue p_res = p_chn->GetResidue(r); if ( p_chn != NULL ) if ( p_res->isInSelection( h_res ) ) { // import the residue MMonomer mon; for ( int a = 0; a < p_res->GetNumberOfAtoms(); a++ ) { mmdb::PCAtom p_atm = p_res->GetAtom(a); if ( p_atm != NULL ) if ( p_atm->isInSelection( h_atm ) ) if ( !p_atm->Ter ) { // import the atom MAtom atm( Atom::null() ); atm.set_name( p_atm->GetAtomName(), p_atm->altLoc ); atm.set_element( p_atm->element ); if ( p_atm->WhatIsSet & ASET_Coordinates ) atm.set_coord_orth( Coord_orth( p_atm->x, p_atm->y, p_atm->z ) ); if ( p_atm->WhatIsSet & ASET_Occupancy ) atm.set_occupancy( p_atm->occupancy ); if ( p_atm->WhatIsSet & ASET_tempFactor ) atm.set_u_iso( Util::b2u( p_atm->tempFactor ) ); if ( p_atm->WhatIsSet & ASET_Anis_tFac ) atm.set_u_aniso_orth( U_aniso_orth( p_atm->u11, p_atm->u22, p_atm->u33, p_atm->u12, p_atm->u13, p_atm->u23 ) ); p_atm->GetAtomID( txt ); atm.set_property("CID",Property(String(txt))); if ( p_atm->altLoc[0] != '\0' ) atm.set_property("AltConf", Property(String(p_atm->altLoc))); mon.insert( atm ); // store the atom } } mon.set_seqnum( p_res->GetSeqNum(), String(p_res->GetInsCode()) ); mon.set_type( p_res->GetResName() ); p_res->GetResidueID( txt ); mon.set_property("CID",Property(String(txt))); pol.insert( mon ); // store the residue } } pol.set_id( p_chn->GetChainID() ); p_chn->GetChainID( txt ); pol.set_property("CID",Property(String(txt))); mol.insert( pol ); // store the chain } } p_mod->GetModelID( txt ); mol.set_property("CID",Property(String(txt))); } // clean up DeleteSelection( h_atm ); DeleteSelection( h_res ); DeleteSelection( h_chn ); DeleteSelection( h_mod ); } /*! Export data to the MMDB hierarchy from a MiniMol object. All the atoms, residues and chains are exported. If any MiniMol object has a "CID" Property (see clipper::PropertyManager), then the information from that object will be used to update the corresponding object in the MMDB hierarchy, if it exists. If there is no such entry in the MMDB hierarchy, or if no "CID" Property exists, then a new object will be created in the MMDB hierarchy. */ void MMDBfile::export_minimol( const MiniMol& minimol ) { // export spacegroup/cell if ( !minimol.spacegroup().is_null() ) set_spacegroup( minimol.spacegroup() ); if ( !minimol.cell().is_null() ) set_cell( minimol.cell() ); // create structure for relationships between Minimol and MMDB SModl smod; clipper::String cid; // fill structure smod.mm = &(minimol.model()); smod.db = NULL; smod.data.resize( smod.mm->size() ); for ( int p = 0; p < smod.data.size(); p++ ) { // loop over chains SPoly& spol = smod.data[p]; spol.mm = &((*smod.mm)[p]); spol.db = NULL; spol.data.resize( spol.mm->size() ); for ( int r = 0; r < spol.data.size(); r++ ) { // loop over residues SMono& smon = spol.data[r]; smon.mm = &((*spol.mm)[r]); smon.db = NULL; smon.data.resize( smon.mm->size() ); for ( int a = 0; a < smon.data.size(); a++ ) { // loop over atoms SAtom& satm = smon.data[a]; satm.mm = &((*smon.mm)[a]); satm.db = NULL; } } } // make the MMDB references by CID if present if ( smod.mm->exists_property("CID") ) { cid = dynamic_cast&>( smod.mm->get_property("CID") ).value() + "/A/0/A"; smod.db = GetModel( (char*)cid.c_str() ); } if ( smod.db != NULL ) for ( int p = 0; p < smod.data.size(); p++ ) { // loop over chains SPoly& spol = smod.data[p]; if ( spol.mm->exists_property("CID") ) { cid = dynamic_cast&>( spol.mm->get_property("CID") ).value() + "/0/A"; spol.db = GetChain( (char*)cid.c_str() ); } if ( spol.db != NULL ) for ( int r = 0; r < spol.data.size(); r++ ) { // loop over residues SMono& smon = spol.data[r]; if ( smon.mm->exists_property("CID") ) { cid = dynamic_cast&>( smon.mm->get_property("CID") ).value() + "/A"; smon.db = GetResidue( (char*)cid.c_str() ); } if ( smon.db != NULL ) for ( int a = 0; a < smon.data.size(); a++ ) { // loop over atoms SAtom& satm = smon.data[a]; if ( satm.mm->exists_property("CID") ) { cid = dynamic_cast&>( satm.mm->get_property("CID") ).value(); satm.db = GetAtom( (char*)cid.c_str() ); } } } } // Now create MMDB objects for anything which is missing if ( smod.db == NULL ) { smod.db = new CModel(); AddModel( smod.db ); } for ( int p = 0; p < smod.data.size(); p++ ) { // loop over chains SPoly& spol = smod.data[p]; if ( spol.db == NULL ) { spol.db = new CChain(); smod.db->AddChain( spol.db ); } for ( int r = 0; r < spol.data.size(); r++ ) { // loop over residues SMono& smon = spol.data[r]; if ( smon.db == NULL ) { smon.db = new CResidue(); spol.db->AddResidue( smon.db ); } for ( int a = 0; a < smon.data.size(); a++ ) { // loop over atoms SAtom& satm = smon.data[a]; if ( satm.db == NULL ) { satm.db = new CAtom(); smon.db->AddAtom( satm.db ); } } } } // now fill in information in mmdb from MiniMol for ( int p = 0; p < smod.data.size(); p++ ) { // loop over chains SPoly& spol = smod.data[p]; spol.db->SetChainID( (char*)spol.mm->id().substr(0,9).c_str() ); // set id for ( int r = 0; r < spol.data.size(); r++ ) { // loop over residues SMono& smon = spol.data[r]; smon.db->seqNum = smon.mm->seqnum(); // set residue info smon.db->SetResName( (char*)smon.mm->type().substr(0,19).c_str() ); int pos = smon.mm->id().find( ":" ); if ( pos != String::npos ) strcpy( smon.db->insCode, smon.mm->id().substr(pos+1,9).c_str() ); for ( int a = 0; a < smon.data.size(); a++ ) { // loop over atoms SAtom& satm = smon.data[a]; if ( !satm.mm->coord_orth().is_null() ) { // set atom coord satm.db->x = satm.mm->coord_orth().x(); satm.db->y = satm.mm->coord_orth().y(); satm.db->z = satm.mm->coord_orth().z(); satm.db->WhatIsSet |= ASET_Coordinates; } if ( !Util::is_nan( satm.mm->occupancy() ) ) { // set atom occ satm.db->occupancy = satm.mm->occupancy(); satm.db->WhatIsSet |= ASET_Occupancy; } if ( !Util::is_nan( satm.mm->u_iso() ) ) { // set atom u_iso satm.db->tempFactor = Util::u2b( satm.mm->u_iso() ); satm.db->WhatIsSet |= ASET_tempFactor; } if ( !satm.mm->u_aniso_orth().is_null() ) { // set atom u_aniso satm.db->u11 = satm.mm->u_aniso_orth()(0,0); satm.db->u22 = satm.mm->u_aniso_orth()(1,1); satm.db->u33 = satm.mm->u_aniso_orth()(2,2); satm.db->u12 = satm.mm->u_aniso_orth()(0,1); satm.db->u13 = satm.mm->u_aniso_orth()(0,2); satm.db->u23 = satm.mm->u_aniso_orth()(1,2); satm.db->WhatIsSet |= ASET_Anis_tFac; } if ( satm.mm->id() != "" ) // atom id satm.db->SetAtomName( (char*)satm.mm->id().substr(0,19).c_str() ); if ( satm.mm->element() != "" ) // atom element satm.db->SetElementName( (char*)satm.mm->element().substr(0,19).c_str() ); if ( satm.mm->exists_property("AltConf") ) { // alt conf code String a = dynamic_cast&>( satm.mm->get_property("AltConf") ).value(); if ( a != "" ) strcpy( satm.db->altLoc, a.substr(0,19).c_str() ); } } } } FinishStructEdit(); } void SEQfile::read_file( const String& file ) { std::ifstream seqfile( file.c_str() ); std::ostringstream s; s << seqfile.rdbuf(); contents = s.str(); //non-portable to old Sun //contents = std::string(std::istreambuf_iterator(seqfile), // std::istreambuf_iterator()); } void SEQfile::import_polymer_sequence( MPolymerSequence& target ) { MMoleculeSequence mms; import_molecule_sequence( mms ); target = mms[0]; } void SEQfile::import_molecule_sequence( MMoleculeSequence& target ) { std::vector lines = contents.split("\n"); clipper::String id, seq = ""; for ( int l = 0; l < lines.size(); l++ ) { clipper::String line = lines[l].trim(); if ( line[0] == '>' ) { if ( seq != "" ) { MPolymerSequence s; s.set_id( id ); s.set_sequence( seq ); target.insert( s ); } id = line.substr(1); id = id.trim(); seq = ""; } else if ( isalpha(line[0]) ) { for ( int i = 0; i < line.length(); i++ ) if ( isalpha(line[i]) ) seq += toupper(line[i]); } } if ( seq != "" ) { MPolymerSequence s; s.set_id( id ); s.set_sequence( seq ); target.insert( s ); } } } // namespace clipper clipper-2.1/clipper/minimol/container_minimol.h0000644000374100011300000000552710736662163016731 00000000000000/*! \file container_minimol.h Header file for atomic model types */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_CONTAINER_MINIMOL #define CLIPPER_CONTAINER_MINIMOL #include "../core/container_types.h" #include "minimol.h" namespace clipper { //! MiniMol container /*! See clipper::MiniMol for method descriptions. */ class CMiniMol : public Container, public MiniMol { public: //! null constructor CMiniMol() {} //! constructor: inherit spacegroup, cell CMiniMol( Container& parent, const String name = "" ); //! initialiser: supply or inherit spacegroup, cell void init( const Spacegroup& spacegroup, const Cell& cell ); //! hierarchical update void update(); }; } // namespace clipper #endif clipper-2.1/clipper/phs/0000777000374100011300000000000011372264353012247 500000000000000clipper-2.1/clipper/phs/phs_io.h0000644000374100011300000000775110736662163013633 00000000000000/*! \file lib/phs_io.h Header file for reflection data phs importer */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_PHS_IO #define CLIPPER_PHS_IO #include "../core/hkl_datatypes.h" namespace clipper { //! PHS import/export parent class for clipper objects /*! This is the import/export class which can be linked to an phs file and be used to transfer data into or out of a Clipper data structure. */ class PHSfile { public: //! Constructor: does nothing PHSfile(); //! Destructor: close any file that was left open ~PHSfile(); //! Open a file for read access void open_read( const String filename_in ); //! Close a file after reading void close_read(); //! Open a file for write access void open_write( const String filename_out ); //! Close a file after writing void close_write(); //! get file resolution Resolution resolution( const Cell& cell ) const; //! read the reflection list from the PHS file void import_hkl_info( HKL_info& target ); //! mark a hkl_data for import from PHS file void import_hkl_data( HKL_data_base& cdata ); //! write the reflection list to the PHS file void export_hkl_info( const HKL_info& target ); //! mark a hkl_data for export to PHS file void export_hkl_data( const HKL_data_base& cdata ); private: enum PHSmode { NONE, READ, WRITE }; PHSmode mode; //!< file mode String filename; //!< input/output file HKL_data_base* f_sigf_i; //!< input HKL_data object HKL_data_base* phi_wt_i; //!< input HKL_data object const HKL_data_base* f_sigf_o; //!< output HKL_data object const HKL_data_base* phi_wt_o; //!< output HKL_data object //! object which supplies the hkl list (write mode only) const HKL_info* hkl_ptr; }; } // namespace clipper #endif 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distclean-compile distclean-generic distclean-libtool \ distclean-tags distdir dvi dvi-am html html-am info info-am \ install install-am install-data install-data-am install-dvi \ install-dvi-am install-exec install-exec-am install-html \ install-html-am install-info install-info-am \ install-libLTLIBRARIES install-library_includeHEADERS \ install-man install-pdf install-pdf-am install-ps \ install-ps-am install-strip installcheck installcheck-am \ installdirs maintainer-clean maintainer-clean-generic \ mostlyclean mostlyclean-compile mostlyclean-generic \ mostlyclean-libtool pdf pdf-am ps ps-am tags uninstall \ uninstall-am uninstall-libLTLIBRARIES \ uninstall-library_includeHEADERS # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: clipper-2.1/clipper/phs/phs_io.cpp0000644000374100011300000002467610736662163014173 00000000000000/* phs_io.cpp: class file for reflection data phs importer */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "phs_io.h" extern "C" { #include } namespace clipper { /*! Constructing an PHSfile does nothing except flag the object as not attached to any file for either input or output */ PHSfile::PHSfile() { mode = NONE; } /*! Close any files which were left open. This is particularly important since to access the PHS file efficiently, data reads and writes are deferred until the file is closed. */ PHSfile::~PHSfile() { switch ( mode ) { case READ: close_read(); break; case WRITE: close_write(); break; case NONE: break; } } /*! The file is opened for reading. This PHSfile object will remain attached to this file until it is closed. Until that occurs, no other file may be opened with this object, however another PHSfile object could be used to access another file. \param filename_in The input filename or pathname. */ void PHSfile::open_read( const String filename_in ) { if ( mode != NONE ) Message::message( Message_fatal( "PHSfile: open_read - File already open" ) ); // open the phs f_sigf_i = NULL; phi_wt_i = NULL; filename = filename_in; FILE* phs = fopen( filename.c_str(), "r" ); if ( phs == NULL ) Message::message( Message_fatal( "PHSfile: open_read - Could not read: "+filename ) ); fclose( phs ); mode = READ; } /*! Close the file after reading. This command also actually fills in the data in any HKL_data structures which have been marked for import. */ void PHSfile::close_read() { if ( mode != READ ) Message::message( Message_fatal( "PHSfile: no file open for read" ) ); // make sure the data list is sized if ( f_sigf_i != NULL ) f_sigf_i->update(); if ( phi_wt_i != NULL ) phi_wt_i->update(); int h, k, l; HKL hkl; xtype x1[2], x2[2]; float f1, f2, f3, f4; char line[240]; FILE* phs = fopen( filename.c_str(), "r" ); if ( phs == NULL ) Message::message( Message_fatal( "PHSfile: import_hkl_data - Could not read: "+filename ) ); // read the data from the PHS while ( fgets( line, 240, phs ) != NULL ) { f1 = f2 = f3 = f4 = 0.0; // default sigf to 0 in case missing sscanf( line, " %i %i %i %f %f %f %f", &h, &k, &l, &f1, &f2, &f3, &f4 ); hkl = HKL( h, k, l ); x1[0] = xtype(f1); x1[1] = xtype(f4); x2[0] = xtype(Util::d2rad(ftype(f3))); x2[1] = xtype(f2); if ( f_sigf_i != NULL ) f_sigf_i->data_import( hkl, x1 ); if ( phi_wt_i != NULL ) phi_wt_i->data_import( hkl, x2 ); } fclose( phs ); mode = NONE; } /*! The file is opened for writing. This will be a new file, created entirely from data from within the program, rather than by extending an existing file. Similar restrictions apply as for open_read(). \param filename_out The output filename or pathname. */ void PHSfile::open_write( const String filename_out ) { if ( mode != NONE ) Message::message( Message_fatal( "PHSfile: open_write - File already open" ) ); // open the output phs hkl_ptr = NULL; f_sigf_o = NULL; phi_wt_o = NULL; filename = filename_out; FILE* phs = fopen( filename.c_str(), "w" ); if ( phs == NULL ) Message::message( Message_fatal( "PHSfile: open_write - Could not write: "+filename ) ); fclose( phs ); mode = WRITE; } /*! Close the file after writing. This command also actually writes the data reflection list from the HKL_info object and the data from any HKL_data objects which have been marked for import. */ void PHSfile::close_write() { if ( mode != WRITE ) Message::message( Message_fatal( "PHSfile: close_write - no file open for write" ) ); // export the marked list data to an phs file if ( hkl_ptr == NULL ) Message::message( Message_fatal( "PHSfile: close_write - no refln list exported" ) ); const HKL_info& hklinf = *hkl_ptr; HKL hkl; xtype x1[2], x2[2]; float f1, f2, f3, f4; f1 = f2 = f3 = f4 = 0.0; FILE* phs = fopen( filename.c_str(), "w" ); if ( phs == NULL ) Message::message( Message_fatal( "PHSfile: close_write - Could not write: "+filename ) ); HKL_info::HKL_reference_index ih; for ( ih = hklinf.first(); !ih.last(); ih.next() ) { hkl = ih.hkl(); if ( f_sigf_o != NULL ) f_sigf_o->data_export( hkl, x1 ); if ( phi_wt_o != NULL ) phi_wt_o->data_export( hkl, x2 ); f1 = float(x1[0]); f4 = float(x1[1]); f3 = float(Util::rad2d(ftype(x2[0]))); f2 = float(x2[1]); fprintf( phs, "%6i %6i %6i %11.3f %11.3f %11.3f %11.3f\n", hkl.h(), hkl.k(), hkl.l(), f1, f2, f3, f4 ); } fclose( phs ); mode = NONE; } /*! Get the resolution limit from the PHS file. Since a PHS file does not contain cell information, a Cell object must be supplied, which will be used to determine the resultion. The result is the resolution determined by the most extreme reflection in the file. \return The resolution. */ Resolution PHSfile::resolution( const Cell& cell ) const { if ( mode != READ ) Message::message( Message_fatal( "PHSfile: resolution - no file open for read" ) ); HKL hkl; int h, k, l; char line[240]; FILE* phs = fopen( filename.c_str(), "r" ); if ( phs == NULL ) Message::message( Message_fatal( "PHSfile: resolution - Could not read: "+filename ) ); // read the reflections from the phs ftype slim = 0.0; while ( fgets( line, 240, phs ) != NULL ) { sscanf( line, " %i %i %i", &h, &k, &l ); hkl = HKL( h, k, l ); slim = Util::max( slim, hkl.invresolsq(cell) ); } fclose( phs ); return Resolution( 1.0/sqrt(slim) ); } /*! Import the list of reflection HKLs from an PHS file into an HKL_info object. If the resolution limit of the HKL_info object is lower than the limit of the file, any excess reflections will be rejected, as will any systematic absences or duplicates. \param target The HKL_info object to be initialised. */ void PHSfile::import_hkl_info( HKL_info& target ) { if ( mode != READ ) Message::message( Message_fatal( "PHSfile: import_hkl_info - no file open for read" ) ); std::vector hkls; HKL hkl; int h, k, l; char line[240]; FILE* phs = fopen( filename.c_str(), "r" ); if ( phs == NULL ) Message::message( Message_fatal( "PHSfile: import_hkl_info - Could not read: "+filename ) ); // read the reflections from the phs ftype slim = target.resolution().invresolsq_limit(); while ( fgets( line, 240, phs ) != NULL ) { sscanf( line, " %i %i %i", &h, &k, &l ); hkl = HKL( h, k, l ); if ( hkl.invresolsq(target.cell()) < slim ) hkls.push_back( hkl ); } fclose( phs ); target.add_hkl_list( hkls ); } /*! Import data from an PHS file into an HKL_data object. This routine does not actually read any data, but rather marks the data to be read when the file is closed. The data to be read (F_sigF or Phi_fom) will be selected based on the type of the HKL_data object. \param cdata The HKL_data object into which data is to be imported. */ void PHSfile::import_hkl_data( HKL_data_base& cdata ) { if ( mode != READ ) Message::message( Message_fatal( "PHSfile: import_hkl_data - no file open for read" ) ); if ( cdata.type() == data32::F_sigF::type() ) f_sigf_i = &cdata; else if ( cdata.type() == data32::Phi_fom::type() ) phi_wt_i = &cdata; else Message::message( Message_fatal( "PHSfile: import_hkl_data - data must be F_sigF or Phi_fom" ) ); } /*! Export the list of reflection HKLs to an PHS file from an HKL_info object. */ void PHSfile::export_hkl_info( const HKL_info& target ) { if ( mode != WRITE ) Message::message( Message_fatal( "PHSfile: export_hkl_info - no file open for write" ) ); hkl_ptr = ⌖ } /*! Export data from an HKL_data object into an PHS file. This routine does not actually write any data, but rather marks the data to be written when the file is closed. The data to be read (F_sigF or Phi_fom) will be selected based on the type of the HKL_data object. \param cdata The HKL_data object from which data is to be exported. */ void PHSfile::export_hkl_data( const HKL_data_base& cdata ) { if ( mode != WRITE ) Message::message( Message_fatal( "PHSfile: export_hkl_data - no file open for write" ) ); if ( cdata.type() == data32::F_sigF::type() ) f_sigf_o = &cdata; else if ( cdata.type() == data32::Phi_fom::type() ) phi_wt_o = &cdata; else Message::message( Message_fatal( "PHSfile: export_hkl_data - data must be F_sigF or Phi_fom" ) ); } } // namespace clipper clipper-2.1/clipper/clipper-phs.h0000644000374100011300000000022110736662163013767 00000000000000/* Clipper header file */ /* (C) 2000-2002 Kevin Cowtan */ #ifndef CLIPPER_PHS_H #define CLIPPER_PHS_H #include "clipper/phs/phs_io.h" #endif clipper-2.1/clipper/minimal-clipper-hkl.h0000644000374100011300000000046710736662163015413 00000000000000/* Clipper header file */ /* (C) 2000-2002 Kevin Cowtan */ #ifndef CLIPPER_CORE_H #define CLIPPER_CORE_H #include "clipper/core/container_hkl.h" #include "clipper/core/rotation.h" #include "clipper/core/hkl_compute.h" #include "clipper/core/hkl_operators.h" #include "clipper/core/resol_targetfn.h" #endif clipper-2.1/clipper/cif/0000777000374100011300000000000011372264353012216 500000000000000clipper-2.1/clipper/cif/Makefile.am0000644000374100011300000000105311372264321014160 00000000000000# Makefile.am, passed: clipper/cif, extracted subdir: cif # in dir /home/cowtan/clipper-autoconf/clipper-2.1/clipper/cif ## -*- mode: Makefile; mode: font-lock -*- INCLUDES=${FFTW_CXXFLAGS} ${MMDB_CXXFLAGS} library_include_HEADERS = \ cif_data_io.h lib_LTLIBRARIES = libclipper-cif.la libclipper_cif_la_SOURCES = \ cif_data_io.cpp library_includedir = $(pkgincludedir)/cif libclipper_cif_la_LDFLAGS = -version-info @CLIPPER_LT_VERSION@ libclipper_cif_la_LIBADD = \ $(top_builddir)/clipper/core/libclipper-core.la \ $(MMDB_LIBS) clipper-2.1/clipper/cif/cif_data_io.h0000644000374100011300000001113511204767172014526 00000000000000/*! \file cif/cif_data_io.h Header file for reflection data cif importer */ //c Copyright (C) 2000-2006 Paul Emsley, Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_CIF_IO #define CLIPPER_CIF_IO #include "../core/hkl_datatypes.h" namespace clipper { //! CIF import/export parent class for clipper objects /*! This is the import class which can be linked to an cif data file and be used to transfer data into a Clipper data structure. It is currently a read-only class. */ class CIFfile { public: //! Constructor: does nothing CIFfile(); //! Destructor: close any file that was left open ~CIFfile(); //! Open a file for read access void open_read( const String filename_in ); //! Close a file after reading void close_read(); //! get file spacegroup const Spacegroup& spacegroup() const; //! get file cell const Cell& cell() const; //! get file resolution const Resolution& resolution() const; //! get file HKL sampling const HKL_sampling& hkl_sampling() const; //! get file resolution Resolution resolution( const Cell& cell ) const; //! read the reflection list from the PHS file void import_hkl_info( HKL_info& target ); //! mark a hkl_data for import from PHS file void import_hkl_data( HKL_data_base& cdata ); //! contains phases predicate bool contains_phases_p() const; private: enum CIFmode { NONE, READ}; CIFmode mode; //!< file mode String filename; //!< input/output file HKL_data_base* f_sigf_i; //!< input HKL_data object HKL_data_base* f_phi_i; //!< input HKL_data object (calc sfs) const HKL_data_base* f_sigf_o; //!< output HKL_data object const HKL_data_base* phi_wt_o; //!< output HKL_data object //! object which supplies the hkl list (write mode only) const HKL_info* hkl_ptr; Spacegroup space_group; Cell cell_; Resolution resolution_; HKL_sampling hkl_sampling_; int set_cell_symm_reso(std::string cif_file_name); int set_cell_symm_reso_by_cif(std::string cif_file_name); int set_cell_symm_reso_by_kludge(std::string cif_file_name); // internal variables, due to the strange and variable nature of // mmCIF files, sometime these things are in the file, sometimes // not... // short int clipper_cell_set_flag; short int clipper_reso_set_flag; short int clipper_symm_set_flag; }; } // namespace clipper #endif // CLIPPER_CIF_IO clipper-2.1/clipper/cif/Makefile.in0000644000374100011300000004450211372264332014201 00000000000000# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, # Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy 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clipper-2.1/clipper/cif/cif_data_io.cpp0000644000374100011300000006107011204770746015065 00000000000000 /* cif_io.cpp: class file for reflection data cif importer */ //c Copyright (C) 2000-2006 Paul Emsley, Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "cif_data_io.h" extern "C" { #include #include #include } #include #include #ifndef __MMDB_MMCIF__ #include #endif namespace clipper { /*! Constructing an CIFfile does nothing except flag the object as not attached to any file for either input or output */ CIFfile::CIFfile() { mode = NONE; // Argh, bug. It's things like this that make me dislike object // oriented programming - "Magic happens behind your back". The // problem was that we were trying to import into f_phi_i in // close_read() when f_phi_i had not been initialised by calling // import_hkl_data for it (because it comes from a function that // will calculate the phases from the model itself). So what do we // do? We will set flags in the CIFfile object that mean that the // HKL_data is not to be read into. That value is null. When we // call import_hkl_data, those values get modified to be pointers // to HKL_data. We will add tests for non-nullness to close_read // before we import into those HKL_data. f_sigf_i = NULL; f_phi_i = NULL; // set these when we find them.... clipper_cell_set_flag = 0; clipper_reso_set_flag = 0; clipper_symm_set_flag = 0; } /*! Close any files which were left open. This is particularly important since to access the CIF file efficiently, data reads and writes are deferred until the file is closed. */ CIFfile::~CIFfile() { switch ( mode ) { case READ: close_read(); break; // case WRITE: // close_write(); break; case NONE: break; } } /*! The file is opened for reading. This CIFfile object will remain attached to this file until it is closed. Until that occurs, no other file may be opened with this object, however another CIFfile object could be used to access another file. \param filename_in The input filename or pathname. */ void CIFfile::open_read( const String filename_in ) { if ( mode != NONE ) Message::message( Message_fatal( "CIFfile: open_read - File already open" ) ); // open the cif f_sigf_i = NULL; f_phi_i = NULL; filename = filename_in; FILE* cif = fopen( filename.c_str(), "r" ); if ( cif == NULL ) Message::message( Message_warn( "CIFfile: open_read - Could not read: "+filename ) ); fclose( cif ); mode = READ; filename = filename_in; set_cell_symm_reso(filename); if ( clipper_cell_set_flag && !clipper_reso_set_flag ) { resolution_ = resolution( cell_ ); clipper_reso_set_flag = 1; } if ( clipper_cell_set_flag && clipper_reso_set_flag ) { hkl_sampling_ = clipper::HKL_sampling( cell_, resolution_ ); } } bool CIFfile::contains_phases_p() const { return 0; } /*! Close the file after reading. This command also actually fills in the data in any HKL_data structures which have been marked for import. Note that we attempt to read in calculated structure factors too. These rely on the tags "F_calc" or "F_calc_au" and "phase_calc". http://pdb.rutgers.edu/mmcif/dictionaries/cif_mm.dic/Categories/refln.html It is quite usual then for the HKL_data vector of type F_sigF to have a different size to the HKL_data for the F_phi's (often this will be zero). I hope that this will not be a problem. We test for f_phi_i being non-null before we import data into it - CIFfiles can be used with or without reading calculated phases. Note to self: how about we make a function of a CIFfile that says whether or not it contains phases... Note to self: this text need to be properly marked up in doxygen format. */ void CIFfile::close_read() { if ( mode != READ ) Message::message( Message_fatal( "CIFfile: no file open for read" ) ); // make sure the data list is sized if ( f_sigf_i != NULL ) f_sigf_i->update(); if ( f_phi_i != NULL ) f_phi_i->update(); //xtype x1[2]; int ret_val = 0; int n_calc_data = 0; InitMatType(); // read the data from the CIF file // stat cif_file_name.c_str() here, make sure it exists, is readable. CMMCIFFile ciffile; int ierr = ciffile.ReadMMCIFFile((char *)filename.c_str()); int ierr_f; int ierr_calc; if (ierr!=CIFRC_Ok) { std::string mess = "CIFfile: close_read - Could not read: "; mess += filename.c_str(); mess += " Dirty mmCIF file? "; Message::message( Message_warn( mess )); } else { for(int i=0; iGetNumberOfCategories(); icat++) { PCMMCIFCategory cat = data->GetCategory(icat); std::string cat_name(cat->GetCategoryName()); PCMMCIFLoop mmCIFLoop = data->GetLoop( (char *) cat_name.c_str() ); if (mmCIFLoop == NULL) { } else { if (cat_name == "_refln") { // success: ret_val = 1; int h,k,l; realtype F, sigF, Fcalc, phi; xtype x1[2]; for (int j=0; jGetLoopLength(); j++) { // Eeuck! (much "modification of reference" code) // ierr = mmCIFLoop->GetInteger(h, "index_h", j); ierr += mmCIFLoop->GetInteger(k, "index_k", j); ierr += mmCIFLoop->GetInteger(l, "index_l", j); if ( !ierr ) { // Measured data can be given using F_meas or // F_meas_au (arbitary units). So lets try to // read a F_meas first then try F_meas_au if that // fails. ierr_f = mmCIFLoop->GetReal( F, "F_meas",j); ierr_f += mmCIFLoop->GetReal(sigF, "F_meas_sigma", j); if (ierr_f) { ierr_f = mmCIFLoop->GetReal( F, "F_meas_au",j); ierr_f += mmCIFLoop->GetReal(sigF, "F_meas_sigma_au", j); } if ( F < -0.9e10 || sigF < -0.9e10 ) ierr_f++; ierr_calc = mmCIFLoop->GetReal(Fcalc, "F_calc", j); if ( ierr_calc ) { ierr_calc = mmCIFLoop->GetReal(Fcalc, "F_calc_au", j); } ierr_calc += mmCIFLoop->GetReal(phi, "phase_calc", j); if ( Fcalc < -0.9e10 || phi < -0.9e10 ) ierr_calc++; if ( !ierr_f ) { if ( f_sigf_i != NULL ) if ( !f_sigf_i->is_null() ) { x1[0] = F; x1[1] = sigF; f_sigf_i->data_import( HKL(h,k,l), x1 ); } } if (! ierr_calc ) { if ( f_phi_i != NULL ) if ( !f_phi_i->is_null() ) { x1[0] = Fcalc; x1[1] = clipper::Util::d2rad(phi); f_phi_i->data_import( HKL(h,k,l), x1); n_calc_data++; } } } } } } } } } if (f_phi_i != NULL) std::cout << n_calc_data << " calculated data read on close_read()" << std::endl; mode = NONE; } /*! Get the spacegroup from the MTZ file. \return The spacegroup. */ const Spacegroup& CIFfile::spacegroup() const { return space_group; } /*! Get the base cell from the MTZ file. \return The cell. */ const Cell& CIFfile::cell() const { return cell_; } /*! Get the resolution limit from the MTZ file. \return The resolution. */ const Resolution& CIFfile::resolution() const { return resolution_; } /*! Get the HKL sampling from the MTZ file. \return The hkl_sampling. */ const HKL_sampling& CIFfile::hkl_sampling() const { return hkl_sampling_; } /*! Get the resolution limit from the CIF file. Since a CIF file does not contain cell information, a Cell object must be supplied, which will be used to determine the resultion. The result is the resolution determined by the most extreme reflection in the file. \return The resolution. */ Resolution CIFfile::resolution( const Cell& cell ) const { if ( mode != READ ) Message::message( Message_fatal( "CIFfile: resolution - no file open for read" ) ); HKL hkl; int h, k, l; //char line[240]; ftype slim = 0.0; FILE* cif = fopen( filename.c_str(), "r" ); if ( cif == NULL ) Message::message( Message_warn( "CIFfile: resolution - Could not read: "+filename ) ); CMMCIFFile ciffile; int ierr = ciffile.ReadMMCIFFile((char *)filename.c_str()); if (ierr!=CIFRC_Ok) { std::string mess = "CIFfile: resolution - Could not read: "; mess += filename.c_str(); mess += ". Dirty mmCIF file? "; Message::message( Message_warn( mess )); } else { // read the reflections from the phs for(int i=0; iGetNumberOfCategories(); icat++) { PCMMCIFCategory cat = data->GetCategory(icat); std::string cat_name(cat->GetCategoryName()); PCMMCIFLoop mmCIFLoop = data->GetLoop( (char *) cat_name.c_str() ); if (mmCIFLoop == NULL) { } else { if (cat_name == "_refln") { for (int j=0; jGetLoopLength(); j++) { ierr = mmCIFLoop->GetInteger(h, "index_h", j); ierr += mmCIFLoop->GetInteger(k, "index_k", j); ierr += mmCIFLoop->GetInteger(l, "index_l", j); if (!ierr) { hkl = HKL( h, k, l ); slim = Util::max( slim, hkl.invresolsq(cell) ); } } } } } } } fclose( cif ); return Resolution( 1.0/sqrt(slim) ); } /*! Import the list of reflection HKLs from an CIF file into an HKL_info object. At the start of the routine try to determine the space group, cell and resolution. If the resolution limit was found and if the resolution limit of the HKL_info object is lower than the limit of the file, any excess reflections will be rejected, as will any systematic absences or duplicates. If the resolution is not found then the resolution will be determined from the input hkl data and \parm target will be init()ed before returning from this function. \param target The HKL_info object to be initialised. */ void CIFfile::import_hkl_info( HKL_info& target ) { std::vector hkls; //int h, k, l; if ( mode != READ ) Message::message( Message_warn( "CIFfile: import_hkl_info - no file open for read" ) ); std::string new_str = filename; //std::cout << "checking set_cell_symm_reso filename " // << filename << std::endl; //std::cout << "checking set_cell_symm_reso new_str " // << new_str << std::endl; int icell = set_cell_symm_reso(new_str); if (! icell) { if (! clipper_cell_set_flag) Message::message( Message_warn( "CIFfile: import_hkl_info - error getting cell" ) ); if (! clipper_symm_set_flag) Message::message( Message_warn( "CIFfile: import_hkl_info - error getting symm" ) ); } else { // we have the cell and symmetry, proceed. if (! clipper_reso_set_flag) resolution_.init(2.0); // just a dummy value, we will set it to // the right value once we know it after // we have read in all the reflection // hkls. If clipper_reso_set_flag *was* // set, then we have initialised // resolution already. // import any missing params target.init( space_group, cell_, resolution_ ); // char line[241]; not used FILE* cif = fopen( filename.c_str(), "r" ); if ( cif == NULL ) Message::message( Message_warn( "CIFfile: import_hkl_info - Could not read: "+filename ) ); // read the reflections from the cif ftype slim = target.resolution().invresolsq_limit(); ftype tmp_lim = 0.0; CMMCIFFile ciffile; int ierr = ciffile.ReadMMCIFFile((char *)filename.c_str()); if (ierr!=CIFRC_Ok) { std::string mess = "CIFfile: import_hkl_data - Could not read: "; mess += filename.c_str(); mess += ". Dirty mmCIF file? "; Message::message( Message_warn( mess )); } else { for(int i=0; iGetNumberOfCategories(); icat++) { PCMMCIFCategory cat = data->GetCategory(icat); std::string cat_name(cat->GetCategoryName()); PCMMCIFLoop mmCIFLoop = data->GetLoop( (char *) cat_name.c_str() ); if (mmCIFLoop) { if (cat_name == "_refln") { int h,k,l; //realtype F, sigF; for (int j=0; jGetLoopLength(); j++) { // Eeuck! (much "modification of reference" code) // ierr = mmCIFLoop->GetInteger(h, "index_h", j); ierr += mmCIFLoop->GetInteger(k, "index_k", j); ierr += mmCIFLoop->GetInteger(l, "index_l", j); // std::cout << "import_hkl_info ierr: " << ierr << std::endl; if (!ierr) { HKL hkl(h,k,l); if (clipper_reso_set_flag) { if ( hkl.invresolsq(target.cell()) < slim ) { hkls.push_back(hkl); } } else { // resolution had not been set hkls.push_back(hkl); if (hkl.invresolsq(target.cell()) > tmp_lim) { tmp_lim = hkl.invresolsq(target.cell()); } } } } } } } } } // CMMCIFFile is closed on destruction of ciffile. // Now we can initialise target properly, if we OK reading the hkls. if (!clipper_reso_set_flag) { if (tmp_lim > 0.0) { // the starting value resolution_.init( 1/sqrt(tmp_lim)); // 210170 // just above target.init( space_group, cell_, resolution_ ); std::cout << "Resolution limit set to " << resolution_.limit() << std::endl; } else { std::cout << "Disaster couldn't set resolution" << std::endl; } } } std::cout << "import_hkl_info read " << hkls.size() << " hkls" << std::endl; target.add_hkl_list( hkls ); } /*! Import data from an CIF file into an HKL_data object. This routine does not actually read any data, but rather marks the data to be read when the file is closed. The data to be read (F_sigF or Phi_fom) will be selected based on the type of the HKL_data object. \param cdata The HKL_data object into which data is to be imported. */ void CIFfile::import_hkl_data( HKL_data_base& cdata ) { if ( mode != READ ) Message::message( Message_warn( "CIFfile: import_hkl_data - no file open for read" ) ); if ( cdata.is_null() ) cdata.init( space_group, cell_, hkl_sampling_ ); if ( cdata.type() == data32::F_sigF::type() ) f_sigf_i = &cdata; else if ( cdata.type() == data32::F_phi::type() ) f_phi_i = &cdata; else Message::message( Message_warn( "CIFfile: import_hkl_data - data must be F_sigF or F_phi" ) ); } // return non-zero if we find a cell and symmetry and can set them. // int CIFfile::set_cell_symm_reso_by_cif(std::string cif_file_name) { FILE* cif = fopen( cif_file_name.c_str(), "r" ); if ( cif == NULL ) Message::message( Message_warn( "CIFfile: set_cell_symm_reso_by_cif - Could not read: "+cif_file_name ) ); CMMCIFFile ciffile; int ierr = ciffile.ReadMMCIFFile((char *)cif_file_name.c_str()); if (ierr!=CIFRC_Ok) { std::string mess = "CIFfile: set_cell_symm_reso_by_cif: Could not read: "; mess += filename.c_str(); mess += " dirty mmCIF file? "; Message::message( Message_warn( mess )); } else { for(int i=0; iGetStructure("_cell"); char *cat_name_str; std::string cat_name; if (mmCIFStruct != NULL) { cat_name_str = mmCIFStruct->GetCategoryName(); if (cat_name_str == NULL) { std::cout << "null cat_name_str" << std::endl; } else { cat_name = cat_name_str; if (cat_name == "_cell") { realtype a,b,c,alpha,beta,gamma; int ierr = 0; ierr += mmCIFStruct->GetReal (a, "length_a"); ierr += mmCIFStruct->GetReal (b, "length_b"); ierr += mmCIFStruct->GetReal (c, "length_c"); ierr += mmCIFStruct->GetReal (alpha, "angle_alpha"); ierr += mmCIFStruct->GetReal (beta, "angle_beta"); ierr += mmCIFStruct->GetReal (gamma, "angle_gamma"); if (! ierr) { // set clipper cell clipper_cell_set_flag = 1; cell_.init(clipper::Cell_descr(a,b,c,alpha,beta,gamma)); std::cout << "got cell from cif: " << cell_.format() << std::endl; } } } } // Try reading symmetry construction mmCIFStruct = data->GetStructure("_symmetry"); if (mmCIFStruct != NULL) { cat_name_str = mmCIFStruct->GetCategoryName(); if (cat_name_str != NULL) { cat_name = cat_name_str; if ( cat_name == "_symmetry") { int ierr; char *str = mmCIFStruct->GetString("space_group_name_H-M",ierr); if (! ierr) { std::string hmsymm(str); if (str) { hmsymm = str; space_group.init(clipper::Spgr_descr(str)); clipper_symm_set_flag = 1; std::cout << "INFO space_group from symmetry in cif: " << space_group.descr().symbol_hm() << std::endl; } } } } } // Have another try for symmetry: e.g. from shelx cif files: // (such files tell us the symmetry operators, so we can get // the space group from those rather than the name using a // clipper function). for (int icat=0; icatGetNumberOfCategories(); icat++) { PCMMCIFCategory cat = data->GetCategory(icat); std::string cat_name(cat->GetCategoryName()); PCMMCIFLoop mmCIFLoop = data->GetLoop( (char *) cat_name.c_str() ); if (mmCIFLoop) { if (cat_name == "_symmetry_equiv") { std::cout << "Found symmetry equivalents....." << std::endl; std::string symmetry_ops(""); for (int j=0; jGetLoopLength(); j++) { char *str = mmCIFLoop->GetString("pos_as_xyz", j, ierr); std::cout << "INFO:: Found cif symmetry operator " << str << std::endl; symmetry_ops += str; symmetry_ops += " ; "; } if (symmetry_ops != "") { clipper_symm_set_flag = 1; space_group.init(clipper::Spgr_descr(symmetry_ops)); std::cout << "INFO:: space_group from symm ops in cif: " << space_group.descr().symbol_hm() << std::endl; } } } } // Reflection meta data: // mmCIFStruct = data->GetStructure("_reflns"); if (mmCIFStruct != NULL) { cat_name_str = mmCIFStruct->GetCategoryName(); if (cat_name_str != NULL) { cat_name = cat_name_str; if ( cat_name == "_reflns") { realtype reso; int ierr = mmCIFStruct->GetReal(reso, "d_resolution_high"); if (! ierr ) { clipper_reso_set_flag = 1; resolution_.init(reso); std::cout << "got resolution from cif: " << resolution_.limit() << std::endl; } } } } } } return clipper_symm_set_flag && clipper_cell_set_flag; } // return non-zero if we find a cell and symmetry and can set them. // int CIFfile::set_cell_symm_reso(std::string cif_file_name) { // return non-zero if we find a cell and symmetry and can set them. // std::cout << "in set_cell_symm_reso " << cif_file_name << std::endl; if (set_cell_symm_reso_by_cif(cif_file_name)) { return 1; } else { return set_cell_symm_reso_by_kludge(cif_file_name); } } int CIFfile::set_cell_symm_reso_by_kludge(std::string cif_file_name) { // Cif files from the RCSB do not contain cell and symmetry // information in cif format (now how totally crap is that? - but I // won't go into that now). // // However, they do provide us with comment lines that look like a // conventional pdb file. e.g: // // #CRYST1 114.300 114.300 155.200 90.00 90.00 120.00 P 61 2 2 12 // #REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 // // So the plan is the open the file conventionally and grab the // cell and symmetry then after we have got to the "#CRYST1" field // or find "loop_", we close up. Notice how we don't grab the // space group symbol, since this is fraught with parsing // difficulties, instead we grab the symmetry operators and use // clipper cleverness to determine the space group. // // Return the success status. True is success, 0 failure. // // // std::string line; char word[80]; // cif standard, marvellous eh? short int read_symm_flag = 0; // 2 is good for read short int cell_coming_flag = 0; // 1 is good for read short int local_found_symm = 0; short int local_found_cell = 0; //short int local_found_reso = 0; std::string clipper_symm_string(""); std::vector cell_bits; std::ifstream from; float reso; short int read_reso_flag = 0; from.open(cif_file_name.c_str()); while (from >> &word[0]) { // std::cout << "word is " << word << std::endl; if (read_reso_flag == 1) { // We can do reso immediately. The others (cell and // symmetry) we set flags and do them at the end. // char **endptr = new (char *); reso = strtod(word, endptr); if (endptr != NULL && *endptr != word) { resolution_.init(reso); std::cout << " Found reso: " << resolution_.limit() << std::endl; clipper_reso_set_flag = 1; } delete endptr; read_reso_flag = 0; } if (! strncmp(word, "RESOLUTION.", 11)) { read_reso_flag = 1; } if (! strncmp(word, "NNNMMM",6)) { read_symm_flag = 1; } if (! strncmp(word, "OPERATOR",6)) { read_symm_flag++; } if (! strncmp(word, "WHERE",5)) { read_symm_flag =0; } if (read_symm_flag == 2) { if (strchr(word,'X') && strchr(word,'Y') && strchr(word,'Z') ) { clipper_symm_string += word; clipper_symm_string += ";"; local_found_symm = 1; } } // position dependent code (should be before CRYST1 comparison) if (cell_coming_flag == 1) { cell_bits.push_back(atof(word)); local_found_cell = 1; } if (! strncmp(word, "#CRYST1", 7)) { cell_coming_flag = 1; } if (cell_bits.size() == 6) break; if (! strncmp(word, "_refln.index_h",14)) break; } from.close(); if (clipper_symm_set_flag == 0) { if (local_found_symm) { space_group.init(clipper::Spgr_descr(clipper_symm_string)); clipper_symm_set_flag = 1; std::cout << " Symm: " << space_group.descr().symbol_hm() << std::endl; } } if (clipper_cell_set_flag == 0) { if (local_found_cell) { if (cell_bits.size() == 6 && clipper_symm_string != "") { if ( !clipper::Util::is_nan(cell_bits[0]) && !clipper::Util::is_nan(cell_bits[1]) && !clipper::Util::is_nan(cell_bits[2]) && !clipper::Util::is_nan(cell_bits[3]) && !clipper::Util::is_nan(cell_bits[4]) && !clipper::Util::is_nan(cell_bits[5]) ) { cell_.init(clipper::Cell_descr(cell_bits[0], cell_bits[1], cell_bits[2], cell_bits[3], cell_bits[4], cell_bits[5])); std::cout << cell_.format() << std::endl; clipper_cell_set_flag = 1; } } } } return clipper_cell_set_flag && clipper_symm_set_flag; } } // namespace clipper clipper-2.1/clipper/clipper-cns.h0000644000374100011300000000027110736662163013765 00000000000000/* Clipper header file */ /* (C) 2000-2002 Kevin Cowtan */ #ifndef CLIPPER_CNS_H #define CLIPPER_CNS_H #include "clipper/cns/cns_hkl_io.h" #include "clipper/cns/cns_map_io.h" #endif clipper-2.1/clipper/Makefile.am0000644000374100011300000000133111372264321013416 00000000000000# Makefile.am, passed: clipper, extracted subdir: clipper # in dir /home/cowtan/clipper-autoconf/clipper-2.1/clipper ## -*- mode: Makefile; mode: font-lock -*- SUBDIRS = \ core ${CLIPPER_MMDB_DIR} ${CLIPPER_MINIMOL_DIR} ${CLIPPER_CCP4_DIR} ${CLIPPER_CIF_DIR} ${CLIPPER_PHS_DIR} ${CLIPPER_CNS_DIR} ${CLIPPER_CCTBX_DIR} contrib INCLUDES=${FFTW_CXXFLAGS} library_include_HEADERS = \ clipper-ccp4.h \ clipper-cctbx.h \ clipper-cif.h \ clipper-cns.h \ clipper-contrib.h \ clipper.h \ clipper-minimol.h \ clipper-mmdb.h \ clipper-mmdbold.h \ clipper-phs.h \ minimal-clipper-hkl.h \ minimal-clipper-map.h library_includedir = $(pkgincludedir) clipper-2.1/clipper/COPYING0000644000374100011300000005750510736662163012444 00000000000000 GNU LESSER GENERAL PUBLIC LICENSE Version 2.1, February 1999 Copyright (C) 1991, 1999 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. 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END OF TERMS AND CONDITIONS clipper-2.1/clipper/clipper-mmdb.h0000644000374100011300000000023210736662163014116 00000000000000/* Clipper header file */ /* (C) 2000-2003 Kevin Cowtan */ #ifndef CLIPPER_MMDB_H #define CLIPPER_MMDB_H #include "clipper/mmdb/clipper_mmdb.h" #endif clipper-2.1/clipper/clipper-cctbx.h0000644000374100011300000000023610736662163014306 00000000000000/* Clipper header file */ /* (C) 2000-2002 Kevin Cowtan */ #ifndef CLIPPER_CCTBX_H #define CLIPPER_CCTBX_H #include "clipper/cctbx/clipper_cctbx.h" #endif clipper-2.1/clipper/minimal-clipper-map.h0000644000374100011300000000041110736662163015377 00000000000000/* Clipper header file */ /* (C) 2000-2002 Kevin Cowtan */ #ifndef CLIPPER_CORE_H #define CLIPPER_CORE_H #include "clipper/core/container_map.h" #include "clipper/core/rotation.h" #include "clipper/core/map_interp.h" #include "clipper/core/map_utils.h" #endif clipper-2.1/clipper/clipper.h0000644000374100011300000000103610736662163013204 00000000000000/* Clipper header file */ /* (C) 2000-2002 Kevin Cowtan */ #ifndef CLIPPER_CORE_H #define CLIPPER_CORE_H #include "clipper/core/container_hkl.h" #include "clipper/core/container_map.h" #include "clipper/core/rotation.h" #include "clipper/core/ramachandran.h" #include "clipper/core/hkl_compute.h" #include "clipper/core/hkl_operators.h" #include "clipper/core/resol_targetfn.h" #include "clipper/core/map_interp.h" #include "clipper/core/map_utils.h" #include "clipper/core/atomsf.h" #include "clipper/core/clipper_instance.h" #endif clipper-2.1/clipper/clipper-contrib.h0000644000374100011300000000077610736662163014654 00000000000000/* Clipper header file */ /* (C) 2000-2002 Kevin Cowtan */ #ifndef CLIPPER_CONTRIB_H #define CLIPPER_CONTRIB_H #include "clipper/contrib/sfcalc.h" #include "clipper/contrib/edcalc.h" #include "clipper/contrib/sfcalc_obs.h" #include "clipper/contrib/sfweight.h" #include "clipper/contrib/sfscale.h" #include "clipper/contrib/convolution_search.h" #include "clipper/contrib/fffear.h" #include "clipper/contrib/mapfilter.h" #include "clipper/contrib/skeleton.h" #include "clipper/contrib/originmatch.h" #endif clipper-2.1/clipper/mmdb/0000777000374100011300000000000011372264353012374 500000000000000clipper-2.1/clipper/mmdb/clipper_mmdb.cpp0000644000374100011300000002230411245171342015444 00000000000000/* clipper_mmdb.cpp: MMDB wrapper */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "clipper_mmdb.h" #include extern "C" { #include } namespace clipper { // MMDB wrapper types // atom String MMDBAtom::id() const { return String( name ); } String MMDBAtom::element() const { return String( CAtom::element ); } Coord_orth MMDBAtom::coord_orth() const { if ( !Ter && WhatIsSet & ASET_Coordinates ) return Coord_orth( x, y, z ); else return Coord_orth( Coord_orth::null() ); } ftype MMDBAtom::occupancy() const { if ( !Ter && WhatIsSet & ASET_Occupancy ) return CAtom::occupancy; else return Util::nan(); } ftype MMDBAtom::u_iso() const { if ( !Ter && WhatIsSet & ASET_tempFactor ) return Util::b2u(tempFactor); else return Util::nan(); } U_aniso_orth MMDBAtom::u_aniso_orth() const { if ( !Ter && WhatIsSet & ASET_Anis_tFac ) return U_aniso_orth( u11, u22, u33, u12, u13, u23 ); else return U_aniso_orth( U_aniso_orth::null() ); } Sig_Coord_orth MMDBAtom::sig_coord_orth() const { if ( !Ter && WhatIsSet & ASET_CoordSigma ) return Sig_Coord_orth( sigX, sigY, sigZ ); else return Sig_Coord_orth( Sig_Coord_orth::null() ); } ftype MMDBAtom::sig_occupancy() const { if ( !Ter && WhatIsSet & ASET_OccSigma ) return sigOcc; else return Util::nan(); } ftype MMDBAtom::sig_u_iso() const { if ( !Ter && WhatIsSet & ASET_tFacSigma ) return Util::b2u(sigTemp); else return Util::nan(); } Sig_U_aniso_orth MMDBAtom::sig_u_aniso_orth() const { if ( !Ter && WhatIsSet & ASET_Anis_tFSigma ) return Sig_U_aniso_orth( su11, su22, su33, su12, su13, su23 ); else return Sig_U_aniso_orth( Sig_U_aniso_orth::null() ); } void MMDBAtom::set_id( const String& n ) { SetAtomName( (char *)n.c_str() ); } void MMDBAtom::set_element( const String& n ) { SetElementName( (char *)n.c_str() ); } void MMDBAtom::set_coord_orth( const Coord_orth& v ) { WhatIsSet &= ~ASET_Coordinates; if ( !v.is_null() ) { x = v.x(); y = v.y(); z = v.z(); WhatIsSet |= ASET_Coordinates; } } void MMDBAtom::set_occupancy( const ftype& v ) { WhatIsSet &= ~ASET_Occupancy; if ( !Util::is_nan( v ) ) { CAtom::occupancy = v; WhatIsSet |= ASET_Occupancy; } } void MMDBAtom::set_u_iso( const ftype& v ) { WhatIsSet &= ~ASET_tempFactor; if ( !Util::is_nan( v ) ) { tempFactor = Util::u2b(v); WhatIsSet |= ASET_tempFactor; } } void MMDBAtom::set_u_aniso_orth( const U_aniso_orth& v ) { WhatIsSet &= ~ASET_Anis_tFac; if ( !v.is_null() ) { u11 = v(0,0); u22 = v(1,1); u33 = v(2,2); u12 = v(0,1); u13 = v(0,2); u23 = v(1,2); WhatIsSet |= ASET_Anis_tFac; } } void MMDBAtom::set_sig_coord_orth( const Sig_Coord_orth& s ) { WhatIsSet &= ~ASET_CoordSigma; if ( !s.is_null() ) { sigX = s.sigx(); sigY = s.sigy(); sigZ = s.sigz(); WhatIsSet |= ASET_CoordSigma; } } void MMDBAtom::set_sig_occupancy( const ftype& s ) { WhatIsSet &= ~ASET_OccSigma; if ( !Util::is_nan( s ) ) { sigOcc = s; WhatIsSet |= ASET_OccSigma; } } void MMDBAtom::set_sig_u_iso( const ftype& s ) { WhatIsSet &= ~ASET_tFacSigma; if ( !Util::is_nan( s ) ) { sigTemp = Util::u2b(s); WhatIsSet |= ASET_tFacSigma; } } void MMDBAtom::set_sig_u_aniso_orth( const Sig_U_aniso_orth& s ) { WhatIsSet &= ~ASET_Anis_tFSigma; if ( !s.is_null() ) { su11 = s(0,0); su22 = s(1,1); su33 = s(2,2); su12 = s(0,1); su13 = s(0,2); su23 = s(1,2); WhatIsSet |= ASET_Anis_tFSigma; } } /*! \return The atom alternate conformation code. */ String MMDBAtom::altconf() const { return String( altLoc ); } /*! \return The atom serial number. */ int MMDBAtom::serial_num() const { return serNum; } /*! \return The atomic charge. */ String MMDBAtom::charge() const { return String( CAtom::charge ); } // residue String MMDBResidue::type() const { return String( name ); } int MMDBResidue::seqnum() const { return seqNum; } String MMDBResidue::inscode() const { return String( insCode ); } void MMDBResidue::set_type( const String& n ) { SetResName( (char *)n.c_str() ); } void MMDBResidue::set_seqnum( const int& n ) { seqNum = n; } void MMDBResidue::set_inscode( const String& n ) { strncpy( insCode, n.c_str(), 10 ); } // chain String MMDBChain::id() const { return String( ((mmdb::CChain*)this)->GetChainID() ); } void MMDBChain::set_id( const String& n ) { SetChainID( (char *)n.c_str() ); } // model String MMDBModel::id() const { return String( ((mmdb::CModel*)this)->GetEntryID() ); } void MMDBModel::set_id( const String& n ) { SetEntryID( (char *)n.c_str() ); } // MMDBManager methods /*! For later initialisation: see init() */ MMDBManager::MMDBManager() { InitMatType(); Message::message( Message_ctor( " [MMDBManager: constructed>" ) ); } MMDBManager::~MMDBManager() { Message::message( Message_dtor( " (*this); Spacegroup sg; if ( mmdb.isSpaceGroup() ) { // get spacegroup from ops int nops = mmdb.GetNumberOfSymOps(); String ops = ""; for ( int i = 0; i < nops; i++ ) ops += String( mmdb.GetSymOp(i) ) + ";"; Spgr_descr sd( ops, Spacegroup::Symops ); sg = Spacegroup( sd ); } else { // otherwise get spacegroup from name const char* mmdbsg = mmdb.GetSpaceGroup(); if ( mmdbsg != NULL ) { String name = String( mmdbsg ).trim(); if ( name.find_first_of( "PABCFIR" ) != String::npos ) { if ( name.find_first_of( ":" ) != String::npos ) { Spgr_descr sd( name, Spacegroup::XHM ); sg = Spacegroup( sd ); } else { Spgr_descr sd( name, Spacegroup::HM ); sg = Spacegroup( sd ); } } } } return sg; } Cell MMDBManager::cell() const { mmdb::CMMDBManager& mmdb = const_cast(*this); if ( mmdb.isCrystInfo() ) { return Cell( Cell_descr( Cryst.a, Cryst.b, Cryst.c, Cryst.alpha, Cryst.beta, Cryst.gamma ) ); } else { return Cell(); // null } } void MMDBManager::set_spacegroup( const Spacegroup& spacegroup ) { // Hall method... (gives bad symbol in file) //String hall = "Hall:" + spacegroup.symbol_hall(); //SetSpaceGroup( (char*)hall.c_str() ); // HM method... //String s = spacegroup.symbol_hm(); //String x = spacegroup.symbol_hm_ext(); //if ( x.length() > 0 ) s = x + s.substr(1); //SetSpaceGroup( (char*)s.c_str() ); // xHM method SetSpaceGroup( (char*)spacegroup.symbol_xhm().c_str() ); } void MMDBManager::set_cell( const Cell& cell ) { SetCell( cell.a(), cell.b(), cell.c(), cell.alpha_deg(), cell.beta_deg(), cell.gamma_deg() ); } /*! The atom list is constructed from the MMDB atom pointers by copying. This should be fast compared to any task for which Clipper uses an atom list. \param ppcatom The MMDB array of atom pointers. \param natom The number of atoms. */ MMDBAtom_list::MMDBAtom_list( const mmdb::PPCAtom ppcatom, const int natom ) { for ( int i = 0; i < natom; i++ ) push_back( Atom( *( (const MMDBAtom*)ppcatom[i] ) ) ); } } // namespace clipper clipper-2.1/clipper/mmdb/clipper_mmdb.h0000644000374100011300000002372310736662163015131 00000000000000/*! \file clipper_mmdb.h Header file for MMDB wrapper */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_MMDB #define CLIPPER_MMDB #include "../core/coords.h" #include namespace clipper { namespace mmdb { typedef ::CAtom CAtom; typedef ::CResidue CResidue; typedef ::CChain CChain; typedef ::CModel CModel; typedef ::CMMDBManager CMMDBManager; typedef ::PCAtom PCAtom; typedef ::PCResidue PCResidue; typedef ::PCChain PCChain; typedef ::PCModel PCModel; typedef ::PCMMDBManager PCMMDBManager; typedef ::PPCAtom PPCAtom; typedef ::PPCResidue PPCResidue; typedef ::PPCChain PPCChain; typedef ::PPCModel PPCModel; typedef ::PPCMMDBManager PPCMMDBManager; } // PDB 'sigma' classes (should be depracated) //! Standard deviation of orthognal coordinates /*! see clipper::Coord_orth \note In my view this is a stupid definition, but its in the PDB. \ingroup g_mmdb */ class Sig_Coord_orth : public Vec3<> { public: Sig_Coord_orth() {} //!< null constructor explicit Sig_Coord_orth( const Vec3<>& v ) : Vec3<>( v ) {} //!< constructor: copy/convert Sig_Coord_orth( const ftype& sigx, const ftype& sigy, const ftype& sigz ) : Vec3<>( sigx, sigy, sigz ) {} //!< constructor: from sig(x,y,z) const ftype& sigx() const { return (*this)[0]; } //!< get sigx const ftype& sigy() const { return (*this)[1]; } //!< get sigy const ftype& sigz() const { return (*this)[2]; } //!< get sigz }; //! Standard deviation of anisotropic atomic displacement parameters /*! see clipper::U_aniso_orth \note In my view this is a stupid definition, but its in the PDB. \ingroup g_mmdb */ class Sig_U_aniso_orth : public Mat33sym<> { public: //! null constructor Sig_U_aniso_orth() {}; //! constructor: from Mat33sym explicit Sig_U_aniso_orth( const Mat33sym<>& m ) : Mat33sym<>(m) {} //! constructor: from sig_Uij Sig_U_aniso_orth( const ftype& su11, const ftype& su22, const ftype& su33, const ftype& su12, const ftype& su13, const ftype& su23 ) : Mat33sym<>( su11, su22, su33, su12, su13, su23 ) {} }; //! MMDB atom object /*! This class is a trivial derivation of the corresponding MMDB, providing access in terms of Clipper types. Thus, when you such access, simply cast you MMDB object reference to this type to access the additional functions. For full documentation see: http://www.ebi.ac.uk/~keb/ */ class MMDBAtom : public mmdb::CAtom { public: //! null constructor MMDBAtom() {} //! constructor: from MMDB atom MMDBAtom( const mmdb::CAtom& a ) : mmdb::CAtom(a) {} // standard atom properties String id() const; //!< Atom id, e.g. CA, CB, CH3 String element() const; //!< Atom element, e.g. C, H, Zn2+ Coord_orth coord_orth() const; //!< Atom coordinate (orthogonal Angstroms) ftype occupancy() const; //!< Atom occupancy (0...1) ftype u_iso() const; //!< Atom isotropic U U_aniso_orth u_aniso_orth() const; //!< Atom anisotropic U (orthogonal As) void set_id( const String& n ); //!< set id void set_element( const String& n ); //!< set element void set_coord_orth( const Coord_orth& v ); //!< set coordinate void set_occupancy( const ftype& v ); //!< set occupancy void set_u_iso( const ftype& v ); //!< set iso U void set_u_aniso_orth( const U_aniso_orth& v ); //!< set aniso U Sig_Coord_orth sig_coord_orth() const; // stupid sigmas ftype sig_occupancy() const; ftype sig_u_iso() const; Sig_U_aniso_orth sig_u_aniso_orth() const; void set_sig_coord_orth( const Sig_Coord_orth& s ); void set_sig_occupancy( const ftype& s ); void set_sig_u_iso( const ftype& s ); void set_sig_u_aniso_orth( const Sig_U_aniso_orth& s ); // other atom properties String altconf() const; //!< get atom alternate conformation code int serial_num() const; //!< get atom serial number String charge() const; //!< get atom charge }; //! MMDB residue object wrapper /*! This class is a trivial derivation of the corresponding MMDB, providing access in terms of Clipper types. Thus, when you such access, simply cast you MMDB object reference to this type to access the additional functions. For full documentation see: http://www.ebi.ac.uk/~keb/ */ class MMDBResidue : public mmdb::CResidue { public: //! null constructor MMDBResidue() {} //! constructor: from MMDB residue MMDBResidue( const mmdb::CResidue& a ) : mmdb::CResidue(a) {} // standard residue properties String type() const; int seqnum() const; String inscode() const; void set_type( const String& n ); void set_seqnum( const int& n ); void set_inscode( const String& n ); }; //! MMDB chain object wrapper /*! This class is a trivial derivation of the corresponding MMDB, providing access in terms of Clipper types. Thus, when you such access, simply cast you MMDB object reference to this type to access the additional functions. For full documentation see: http://www.ebi.ac.uk/~keb/ */ class MMDBChain : public mmdb::CChain { public: //! null constructor MMDBChain() {} //! constructor: from MMDB chain MMDBChain( const mmdb::CChain& a ) : mmdb::CChain(a) {} // chain properties String id() const; void set_id( const String& n ); }; //! MMDB model object wrapper /*! This class is a trivial derivation of the corresponding MMDB, providing access in terms of Clipper types. Thus, when you such access, simply cast you MMDB object reference to this type to access the additional functions. For full documentation see: http://www.ebi.ac.uk/~keb/ */ class MMDBModel : public mmdb::CModel { public: //! null constructor MMDBModel() {} //! constructor: from MMDB model MMDBModel( const mmdb::CModel& a ) : mmdb::CModel(a) {} // model properties String id() const; void set_id( const String& n ); }; //! MMDB manager wrapper /*! This class is a trivial derivation of the corresponding MMDB, providing access in terms of Clipper types. Thus, when you such access, simply cast you MMDB object reference to this type to access the additional functions. For full documentation see: http://www.ebi.ac.uk/~keb/ */ class MMDBManager : public mmdb::CMMDBManager { public: enum TYPE { Default=-1, PDB, CIF, Binary }; MMDBManager(); //! null constructor ~MMDBManager(); //! destructor Spacegroup spacegroup() const; //!< get spacegroup Cell cell() const; //!< get cell void set_spacegroup( const Spacegroup& spacegroup ); //!< set spacegroup void set_cell( const Cell& cell ); //!< set cell //-- int ReadCoorFile( char* name ); //!< For file i/o see http://www.ebi.ac.uk/~keb/cldoc/object/cl_obj_rdwr.html //-- void select( int hnd, int typ, char* str, int key ); //!< For selection functions see http://www.ebi.ac.uk/~keb/cldoc/object/cl_obj_selfnc.html //-- PCModel GetModel ( int modelNo ); //!< For accessor functions see http://www.ebi.ac.uk/~keb/cldoc/object/cl_obj_surf.html //-- int AddModel ( PCModel model ); //!< For editing functions see http://www.ebi.ac.uk/~keb/cldoc/object/cl_obj_edit.html }; //! MMDB atom list class /*! This class is used to convert an MMDB PPCAtom to a Clipper Atom_list. It is a trivial derivation of a clipper::Atom_list, and may be used wherever an Atom_list is required. */ class MMDBAtom_list : public Atom_list { public: //! constructor: from PPCAtom MMDBAtom_list( const mmdb::PPCAtom ppcatom, const int natom ); }; } // namespace clipper #endif clipper-2.1/clipper/mmdb/Makefile.am0000644000374100011300000000105611372264321014341 00000000000000# Makefile.am, passed: clipper/mmdb, extracted subdir: mmdb # in dir /home/cowtan/clipper-autoconf/clipper-2.1/clipper/mmdb ## -*- mode: Makefile; mode: font-lock -*- INCLUDES=${FFTW_CXXFLAGS} ${MMDB_CXXFLAGS} library_include_HEADERS = \ clipper_mmdb.h lib_LTLIBRARIES = libclipper-mmdb.la libclipper_mmdb_la_SOURCES = \ clipper_mmdb.cpp library_includedir = $(pkgincludedir)/mmdb libclipper_mmdb_la_LDFLAGS = -version-info @CLIPPER_LT_VERSION@ libclipper_mmdb_la_LIBADD = \ $(top_builddir)/clipper/core/libclipper-core.la $(MMDB_LIBS) 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install-data \ install-data-am install-dvi install-dvi-am install-exec \ install-exec-am install-html install-html-am install-info \ install-info-am install-library_includeHEADERS install-man \ install-pdf install-pdf-am install-ps install-ps-am \ install-strip installcheck installcheck-am installdirs \ installdirs-am maintainer-clean maintainer-clean-generic \ mostlyclean mostlyclean-generic mostlyclean-libtool pdf pdf-am \ ps ps-am tags tags-recursive uninstall uninstall-am \ uninstall-library_includeHEADERS # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: clipper-2.1/clipper/clipper-minimol.h0000644000374100011300000000037310736662163014651 00000000000000/* Clipper header file */ /* (C) 2000-2003 Kevin Cowtan */ #ifndef CLIPPER_MINIMOL_H #define CLIPPER_MINIMOL_H #include "clipper/minimol/minimol_utils.h" #include "clipper/minimol/minimol_io.h" #include "clipper/minimol/container_minimol.h" #endif clipper-2.1/clipper/cns/0000777000374100011300000000000011372264353012240 500000000000000clipper-2.1/clipper/cns/cns_map_io.cpp0000644000374100011300000005574111247655175015012 00000000000000/* map_io.cpp: class file for reflection data map importer */ //c Copyright (C) 2006 Jon A. Christopher, Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CNS licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CNS Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "cns_map_io.h" #include #include namespace clipper { namespace data { const char* cns_sg_data[] = { "Null","P 1","-P 1","P 2y","P 2yb","C 2y","P -2y","P -2yc","C -2y","C -2yc","-P 2y","-P 2yb","-C 2y","-P 2yc","-P 2ybc","-C 2yc","P 2 2","P 2c 2","P 2 2ab","P 2ac 2ab","C 2c 2","C 2 2","F 2 2","I 2 2","I 2b 2c","P 2 -2","P 2c -2","P 2 -2c","P 2 -2a","P 2c -2ac","P 2 -2bc","P 2ac -2","P 2 -2ab","P 2c -2n","P 2 -2n","C 2 -2","C 2c -2","C 2 -2c","A 2 -2","A 2 -2c","A 2 -2a","A 2 -2ac","F 2 -2","F 2 -2d","I 2 -2","I 2 -2c","I 2 -2a","-P 2 2","P 2 2 -1n","-P 2 2c","P 2 2 -1ab","-P 2a 2a","-P 2a 2bc","-P 2ac 2","-P 2a 2ac","-P 2 2ab","-P 2ab 2ac","-P 2c 2b","-P 2 2n","P 2 2ab -1ab","-P 2n 2ab","-P 2ac 2ab","-P 2ac 2n","-C 2c 2","-C 2bc 2","-C 2 2","-C 2 2c","-C 2b 2","C 2 2 -1bc","-F 2 2","F 2 2 -1d","-I 2 2","-I 2 2c","-I 2b 2c","-I 2b 2","P 4","P 4w","P 4c","P 4cw","I 4","I 4bw","P -4","I -4","-P 4","-P 4c","P 4ab -1ab","P 4n -1n","-I 4","I 4bw -1bw","P 4 2","P 4ab 2ab","P 4w 2c","P 4abw 2nw","P 4c 2","P 4n 2n","P 4cw 2c","P 4nw 2abw","I 4 2","I 4bw 2bw","P 4 -2","P 4 -2ab","P 4c -2c","P 4n -2n","P 4 -2c","P 4 -2n","P 4c -2","P 4c -2ab","I 4 -2","I 4 -2c","I 4bw -2","I 4bw -2c","P -4 2","P -4 2c","P -4 2ab","P -4 2n","P -4 -2","P -4 -2c","P -4 -2ab","P -4 -2n","I -4 -2","I -4 -2c","I -4 2","I -4 2bw","-P 4 2","-P 4 2c","P 4 2 -1ab","P 4 2 -1n","-P 4 2ab","-P 4 2n","P 4ab 2ab -1ab","P 4ab 2n -1ab","-P 4c 2","-P 4c 2c","P 4n 2c -1n","P 4n 2 -1n","-P 4c 2ab","-P 4n 2n","P 4n 2n -1n","P 4n 2ab -1n","-I 4 2","-I 4 2c","I 4bw 2bw -1bw","I 4bw 2aw -1bw","P 3","P 31","P 32","R 3","-P 3","-R 3","P 3 2","P 3 2\"","P 31 2c (0 0 1)","P 31 2\"","P 32 2c (0 0 -1)","P 32 2\"","R 3 2\"","P 3 -2\"","P 3 -2","P 3 -2\"c","P 3 -2c","R 3 -2\"","R 3 -2\"c","-P 3 2","-P 3 2c","-P 3 2\"","-P 3 2\"c","-R 3 2\"","-R 3 2\"c","P 6","P 61","P 65","P 62","P 64","P 6c","P -6","-P 6","-P 6c","P 6 2","P 61 2 (0 0 -1)","P 65 2 (0 0 1)","P 62 2c (0 0 1)","P 64 2c (0 0 -1)","P 6c 2c","P 6 -2","P 6 -2c","P 6c -2","P 6c -2c","P -6 2","P -6c 2","P -6 -2","P -6c -2c","-P 6 2","-P 6 2c","-P 6c 2","-P 6c 2c","P 2 2 3","F 2 2 3","I 2 2 3","P 2ac 2ab 3","I 2b 2c 3","-P 2 2 3","P 2 2 3 -1n","-F 2 2 3","F 2 2 3 -1d","-I 2 2 3","-P 2ac 2ab 3","-I 2b 2c 3","P 4 2 3","P 4n 2 3","F 4 2 3","F 4d 2 3","I 4 2 3","P 4acd 2ab 3","P 4bd 2ab 3","I 4bd 2c 3","P -4 2 3","F -4 2 3","I -4 2 3","P -4n 2 3","F -4c 2 3","I -4bd 2c 3","-P 4 2 3","-P 4 2 3","-P 4n 2 3","P 4n 2 3 -1n","-F 4 2 3","-F 4c 2 3","F 4d 2 3 -1d","F 4d 2 3 -1cd","-I 4 2 3","-I 4bd 2c 3" }; } // namespace data /*! Constructing an CNSMAPfile does nothing except set the spacegroup and flag the object as not attached to any file for either input or output. The default CNS setting is selected by spacegroup number. \param sg_num The spacegroup number of the CNS setting. */ CNSMAPfile::CNSMAPfile( unsigned int sg_num ) { mode = NONE; if ( sg_num == 0 || sg_num > 230 ) Message::message( Message_fatal( "CNSMAPfile: invalid spacegroup" ) ); Spgr_descr sd( data::cns_sg_data[sg_num], Spgr_descr::Hall ); spacegroup_ = Spacegroup( sd ); } /*! Constructing an CNSMAPfile does nothing except et the spacegroup and flag the object as not attached to any file for either input or output. \param spacegroup The spacegroup. */ CNSMAPfile::CNSMAPfile( Spacegroup spacegroup ) { mode = NONE; spacegroup_ = spacegroup; } /*! Close any files which were left open. This is particularly important since to access the MAP file efficiently, data reads and writes are deferred until the file is closed. */ CNSMAPfile::~CNSMAPfile() { switch ( mode ) { case READ: close_read(); break; case WRITE: close_write(); break; case NONE: break; } } /*! The file is opened for reading. This CNSMAPfile object will remain attached to this file until it is closed. Until that occurs, no other file may be opened with this object, however another CNSMAPfile object could be used to access another file. \param filename_in The input filename or pathname. */ void CNSMAPfile::open_read( const String filename_in ) { if ( mode != NONE ) Message::message( Message_fatal( "CNSMAPfile: open_read - File already open" ) ); filename = filename_in; mode = READ; FILE* f = fopen( filename.c_str(), "r" ); if ( f == NULL ) Message::message( Message_fatal( "CNSMAPfile: open_read - Could not read: "+filename ) ); fclose( f ); mode = READ; } /*! Close the file after reading. */ void CNSMAPfile::close_read() { if ( mode != READ ) Message::message( Message_fatal( "CNSMAPfile: no file open for read" ) ); mode = NONE; } /*! The file is opened for writing. This will be a new file, created entirely from data from within the program, rather than by extending an existing file. Similar restrictions apply as for open_read(). \param filename_out The output filename or pathname. */ void CNSMAPfile::open_write( const String filename_out ) { if ( mode != NONE ) Message::message( Message_fatal( "CNSMAPfile: open_write - File already open" ) ); filename = filename_out; mode = WRITE; } /*! Close the file after writing. */ void CNSMAPfile::close_write() { if ( mode != WRITE ) Message::message( Message_fatal( "CNSMAPfile: no file open for write" ) ); mode = NONE; } /*! When writing an NXmap, the cell for the output map must be set using set_cell(). Note that the NXmap is rather more general than the CNS map, since it can take an arbitrary rotation+skew matrix. The resulting map will only be sensible if the NXmap grid skew matrix reflects the supplied cell. This is not possible in the general case. (Alternatively, opening an equivalent map for read and then closing it again will also set the cell). \param cell The cell description for the output map file. */ void CNSMAPfile::set_cell( const Cell& cell ) { if ( mode != WRITE ) Message::message( Message_fatal( "CNSMAPfile: no file open for write" ) ); cell_ = cell; } /*! Get the spacegroup from the MTZ file. \return The spacegroup. */ const Spacegroup& CNSMAPfile::spacegroup() const { return spacegroup_; } /*! Get the base cell from the MTZ file. \return The cell. */ const Cell& CNSMAPfile::cell() const { return cell_; } /*! Get the grid sampling from the MTZ file. \return The grid sampling. */ const Grid_sampling& CNSMAPfile::grid_sampling() const { return grid_sam_; } /*! Import a complete Xmap object. The supplied Xmap object is examined, and if any of the parameters (spacegroup, cell, or grid_sampling) are unset, then they will be set using values from the file. The data is the imported from the file. If the spacegroups mismatch, the resulting map will obey its spacegroup symmetry, but no expansion will be performed if the file has a higher symmetry and only holds an asymmetric unit. \param xmap The Xmap to be imported. */ template void CNSMAPfile::import_xmap( Xmap& xmap ) { if ( mode != READ ) Message::message( Message_fatal( "CNSMAPfile: no file open for read" ) ); char buf[512]; FILE* f = fopen( filename.c_str(), "r" ); fgets(buf,512,f);; unsigned int n_header_lines; if (sscanf(buf,"%d",&n_header_lines) != 1) fgets(buf,512,f);; // could be blank line first if (sscanf(buf,"%d",&n_header_lines) != 1) Message::message( Message_fatal( "CNSMAPfile: can't get number of header lines" ) ); for (unsigned int i=0;i void CNSMAPfile::export_xmap( const Xmap& xmap ) { if ( mode != WRITE ) Message::message( Message_fatal( "CNSMAPfile: no file open for write" ) ); FILE* f = fopen( filename.c_str(), "w" ); fprintf(f,"\n 1\nFrom clipper Xmap\n"); // get dimensions Grid_sampling gs=xmap.grid_sampling(); Grid_range gr=xmap.grid_asu(); //FIXME: verify these ranges. should they be max+1? int nx=gs.nu(),ny=gs.nv(),nz=gs.nw(); int x0=gr.min().u(),y0=gr.min().v(),z0=gr.min().w(); int xf=gr.max().u(),yf=gr.max().v(),zf=gr.max().w(); fprintf(f,"%8d%8d%8d%8d%8d%8d%8d%8d%8d\n", nx,x0,xf, ny,y0,yf, nz,z0,zf); Cell cell=xmap.cell(); fprintf(f,"%12.5E%12.5E%12.5E%12.5E%12.5E%12.5E\n", cell.a(), cell.b(), cell.c(), cell.alpha_deg(), cell.beta_deg(), cell.gamma_deg()); fprintf(f,"ZYX\n"); int z,y,x; Xmap_base::Map_reference_coord ix( xmap ); for (z=z0; z <=zf; ++z) { fprintf(f,"%8d\n",z); unsigned int i=0; for (y=y0; y<= yf; ++y) { for (x=x0; x<=xf; ++x) { ix.set_coord( Coord_grid( x, y, z) ); fprintf(f,"%12.5E",float(xmap[ix])); i++; if (i==6) { fprintf(f,"\n"); i=0; } } } if ( i != 0 ) fprintf(f,"\n"); } fclose(f); } template void CNSMAPfile::import_nxmap( NXmap& nxmap ) { if ( mode != READ ) Message::message( Message_fatal( "CNSMAPfile: no file open for read" ) ); char buf[512]; FILE* f = fopen( filename.c_str(), "r" ); fgets(buf,512,f);; unsigned int n_header_lines; if (sscanf(buf,"%d",&n_header_lines) != 1) fgets(buf,512,f);; // could be blank line first if (sscanf(buf,"%d",&n_header_lines) != 1) Message::message( Message_fatal( "CNSMAPfile: can't get number of header lines" ) ); for (unsigned int i=0;i void CNSMAPfile::export_nxmap( const NXmap& nxmap ) { if ( mode != WRITE ) Message::message( Message_fatal( "CNSMAPfile: no file open for write" ) ); FILE* f = fopen( filename.c_str(), "w" ); fprintf(f,"\n 1\nFrom clipper NXmap\n"); // get dimensions Grid gs=nxmap.grid(); /* cribbed from ccp4_map_io.cpp. Hope I was smart enough */ /* Because CNS maps don't allow an arbitrary skew matrix, we have to jump through hoops to try and fit an NXmap into one. This code will work for those cases where it is possible and produce garbage otherwise. Don't even try to understand this unless you are pretty smart. */ // cell (set by user, or from previous map) float cp[6]; cp[0] = cell_.descr().a(); cp[3] = cell_.descr().alpha_deg(); cp[1] = cell_.descr().b(); cp[4] = cell_.descr().beta_deg (); cp[2] = cell_.descr().c(); cp[5] = cell_.descr().gamma_deg(); // grid (calculated to fit with cell provided - assume angles match) Coord_frac c0, c1; c0 = nxmap.coord_orth( Coord_map(0,0,0) ).coord_frac(cell_); c1 = nxmap.coord_orth( Coord_map( nxmap.grid().nu(), nxmap.grid().nv(), nxmap.grid().nw() ) ).coord_frac(cell_); grid_sam_ = Grid_sampling( Util::intr( ftype(nxmap.grid().nu())/(c1.u()-c0.u()) ), Util::intr( ftype(nxmap.grid().nv())/(c1.v()-c0.v()) ), Util::intr( ftype(nxmap.grid().nw())/(c1.w()-c0.w()) ) ); Coord_grid g0 = c0.coord_grid(grid_sam_); Coord_grid g1 = g0 + Coord_grid(nxmap.grid()) - Coord_grid(1,1,1); int x0=g0.u(), y0=g0.v(), z0=g0.w(); int xf=g1.u(), yf=g1.v(), zf=g1.w(); fprintf(f,"%8d%8d%8d%8d%8d%8d%8d%8d%8d\n", gs.nu(), g0.u(), g1.u(), gs.nv(), g0.v(), g1.v(), gs.nw(), g0.w(), g1.w()); fprintf(f,"%12.5E%12.5E%12.5E%12.5E%12.5E%12.5E\n", cell_.a(), cell_.b(), cell_.c(), cell_.alpha_deg(), cell_.beta_deg(), cell_.gamma_deg()); fprintf(f,"ZYX\n"); int z,y,x; NXmap_base::Map_reference_coord ix( nxmap ); for (z=z0; z <=zf; ++z) { fprintf(f,"%8d\n",z); unsigned int i=0; for (y=y0; y<= yf; ++y) { for (x=x0; x<=xf; ++x) { ix.set_coord( Coord_grid( x, y, z) ); fprintf(f,"%12.5E",float(nxmap[ix])); i++; if (i==6) { fprintf(f,"\n"); i=0; } } } if ( i != 0 ) fprintf(f,"\n"); } fclose(f); } /*! Import a complete Xmap object. The supplied Xmap object is examined, and if any of the parameters (spacegroup, cell, or grid_sampling) are unset, then they will be set using values from the file. The data is the imported from the file. If the spacegroups mismatch, the resulting map will obey its spacegroup symmetry, but no expansion will be performed if the file has a higher symmetry and only holds an asymmetric unit. This version performs a check on the symmatry of the inport map file. If the import map contains less than a complete ASU, or if it contains more than an ASU and symmetry related positions contain inconsistent values, then an error is returned. This function is only available for float or double maps. \param xmap The Xmap to be imported. \return The ASU check flag */ template CNSMAPfile::ASUerror CNSMAPfile::import_xmap_check_asu( Xmap& xmap, T missing ) { if ( mode != READ ) Message::message( Message_fatal( "CNSMAPfile: no file open for read" ) ); char buf[512]; FILE* f = fopen( filename.c_str(), "r" ); fgets(buf,512,f);; unsigned int n_header_lines; if (sscanf(buf,"%d",&n_header_lines) != 1) fgets(buf,512,f);; // could be blank line first if (sscanf(buf,"%d",&n_header_lines) != 1) Message::message( Message_fatal( "CNSMAPfile: can't get number of header lines" ) ); for (unsigned int i=0;i 0.5 ) s2 = sqrt( s2*s0 - s1*s1 ) / s0; if ( maxerr > 0.01*s2 ) asuerr = ASUINCONSISTENT; return asuerr; } // instantiate the template functions for all reasonable types // xmap import template void CNSMAPfile::import_xmap( Xmap& xmap ); template void CNSMAPfile::import_xmap( Xmap& xmap ); template void CNSMAPfile::import_xmap( Xmap& xmap ); template void CNSMAPfile::import_xmap( Xmap& xmap ); template void CNSMAPfile::import_xmap( Xmap& xmap ); template void CNSMAPfile::import_xmap( Xmap& xmap ); template void CNSMAPfile::import_xmap( Xmap& xmap ); template void CNSMAPfile::import_xmap( Xmap& xmap ); // xmap export template void CNSMAPfile::export_xmap( const Xmap& xmap ); template void CNSMAPfile::export_xmap( const Xmap& xmap ); template void CNSMAPfile::export_xmap( const Xmap& xmap ); template void CNSMAPfile::export_xmap( const Xmap& xmap ); template void CNSMAPfile::export_xmap( const Xmap& xmap ); template void CNSMAPfile::export_xmap( const Xmap& xmap ); template void CNSMAPfile::export_xmap( const Xmap& xmap ); template void CNSMAPfile::export_xmap( const Xmap& xmap ); // nxmap import template void CNSMAPfile::import_nxmap( NXmap& nxmap ); template void CNSMAPfile::import_nxmap( NXmap& nxmap ); template void CNSMAPfile::import_nxmap( NXmap& nxmap ); template void CNSMAPfile::import_nxmap( NXmap& nxmap ); template void CNSMAPfile::import_nxmap( NXmap& nxmap ); template void CNSMAPfile::import_nxmap( NXmap& nxmap ); template void CNSMAPfile::import_nxmap( NXmap& nxmap ); template void CNSMAPfile::import_nxmap( NXmap& nxmap ); // nxmap export template void CNSMAPfile::export_nxmap( const NXmap& nxmap ); template void CNSMAPfile::export_nxmap( const NXmap& nxmap ); template void CNSMAPfile::export_nxmap( const NXmap& nxmap ); template void CNSMAPfile::export_nxmap( const NXmap& nxmap ); template void CNSMAPfile::export_nxmap( const NXmap& nxmap ); template void CNSMAPfile::export_nxmap( const NXmap& nxmap ); template void CNSMAPfile::export_nxmap( const NXmap& nxmap ); template void CNSMAPfile::export_nxmap( const NXmap& nxmap ); // xmap import and check template CNSMAPfile::ASUerror CNSMAPfile::import_xmap_check_asu( Xmap& xmap, ftype32 missing ); template CNSMAPfile::ASUerror CNSMAPfile::import_xmap_check_asu( Xmap& xmap, ftype64 missing ); } // namespace clipper clipper-2.1/clipper/cns/cns_hkl_io.cpp0000644000374100011300000004302611347712651014776 00000000000000/* cns_hkl_io.cpp: class file for reflection data cns_hkl importer */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "cns_hkl_io.h" extern "C" { #include #include } namespace clipper { clipper::String cnstok( FILE* f ) { String s; char c = fgetc( f ); while ( c > '\0' && ! ( c > ' ' && c != '=' ) ) { c = fgetc( f ); } while ( c > '\0' && ( c > ' ' && c != '=' ) ) { s += toupper(c); c = fgetc( f ); } return s; } clipper::String cnsrmk( FILE* f ) { String s; char c = fgetc( f ); while ( c >= ' ' ) { s += toupper(c); c = fgetc( f ); } return s; } /*! Constructing an CNS_HKLfile does nothing except flag the object as not attached to any file for either input or output */ CNS_HKLfile::CNS_HKLfile() { mode = NONE; } /*! Close any files which were left open. This is particularly important since to access the CNS_HKL file efficiently, data reads and writes are deferred until the file is closed. */ CNS_HKLfile::~CNS_HKLfile() { switch ( mode ) { case READ: close_read(); break; case WRITE: close_write(); break; case NONE: break; } } /*! The file is opened for reading. This CNS_HKLfile object will remain attached to this file until it is closed. Until that occurs, no other file may be opened with this object, however another CNS_HKLfile object could be used to access another file. \param filename_in The input filename or pathname. */ void CNS_HKLfile::open_read( const String filename_in ) { if ( mode != NONE ) Message::message( Message_fatal( "CNS_HKLfile: open_read - File already open" ) ); // open the cns_hkl f_sigf_i = NULL; phi_wt_i = NULL; f_phi_i = NULL; abcd_i = NULL; flag_i = NULL; filename = filename_in; FILE* cns_hkl = fopen( filename.c_str(), "r" ); if ( cns_hkl == NULL ) Message::message( Message_fatal( "CNS_HKLfile: open_read - Could not read: "+filename ) ); mode = READ; // read the headers... up to first NREF String s, t, symops; ftype cell[6] = { 0.0, 0.0, 0.0, 90.0, 90.0, 90.0 }; while ( (s=cnstok(cns_hkl)).length() > 0 ) { t = (s+" ").substr(0,4); if ( t == "NREF" ) break; if ( t == "REMA" ) { s = cnsrmk(cns_hkl); std::vector toks = s.split( " =" ); if ( toks[0] == "SYMOP" ) { if ( toks.size() > 1 ) symops += toks[1].split(" ();")[0] + ";"; } if ( toks.size() >= 12 ) { if ( toks[0] == "A" && toks[2] == "B" && toks[4] == "C" ) { cell[0] = toks[1].f(); cell[1] = toks[3].f(); cell[2] = toks[5].f(); } } if ( toks.size() >= 12 ) { if ( toks[6] == "ALPHA" && toks[8] == "BETA" && toks[10] == "GAMMA" ) { cell[3] = toks[7].f(); cell[4] = toks[9].f(); cell[5] = toks[11].f(); } } } } if ( cell[0]*cell[1]*cell[2] > 0.0 ) { Cell_descr cd( cell[0], cell[1], cell[2], cell[3], cell[4], cell[5] ); cell_ = Cell( cd ); resolution_ = resolution( cell_ ); hkl_sampling_ = HKL_sampling( cell_, resolution_ ); std::cerr << cell_.format() << resolution_.limit() << std::endl; } if ( symops.length() > 0 ) { Spgr_descr sd( symops ); spacegroup_ = Spacegroup( sd ); std::cerr << spacegroup_.symbol_xhm() << std::endl; } fclose( cns_hkl ); } /*! Close the file after reading. This command also actually fills in the data in any HKL_data structures which have been marked for import. */ void CNS_HKLfile::close_read() { if ( mode != READ ) Message::message( Message_fatal( "CNS_HKLfile: no file open for read" ) ); // make sure the data list is sized if ( f_sigf_i != NULL ) f_sigf_i->update(); if ( phi_wt_i != NULL ) phi_wt_i->update(); if ( f_phi_i != NULL ) f_phi_i->update(); if ( abcd_i != NULL ) abcd_i->update(); if ( flag_i != NULL ) flag_i->update(); for ( int i = 0; i < fphis_i.size(); i++ ) fphis_i[i].first->update(); xtype fo[2], pw[2], fc[2], hl[4], fl[1]; xtype fphis[256][2]; // limit of 256 fphi column groups per CNS file HKL hkl; FILE* cns_hkl = fopen( filename.c_str(), "r" ); if ( cns_hkl == NULL ) Message::message( Message_fatal( "CNS_HKLfile: import_hkl_data - Could not read: "+filename ) ); // read the data from the CNS_HKL String s, t; while ( (s=cnstok(cns_hkl)).length() > 0 ) { t = (s+" ").substr(0,4); if ( t == "INDE" ) break; } while ( s.length() > 0 ) { hkl.h() = cnstok(cns_hkl).i(); hkl.k() = cnstok(cns_hkl).i(); hkl.l() = cnstok(cns_hkl).i(); fo[0]=fo[1]=pw[0]=pw[1]=fc[0]=fc[1]=hl[0]=hl[1]=hl[2]=hl[3]=fl[0]=0.0; for ( int i = 0; i < fphis_i.size(); i++ ) fphis[i][0]=fphis[i][1]=0.0; while ( 1 ) { s=cnstok(cns_hkl); t = (s+" ").substr(0,4); if ( s.length() == 0 || t == "INDE" ) { break; } else if ( t == "FOBS" ) { fo[0] = cnstok(cns_hkl).f(); pw[0] = Util::d2rad(cnstok(cns_hkl).f()); } else if ( t == "SIGM" ) { fo[1] = cnstok(cns_hkl).f(); } else if ( t == "FOM " ) { pw[1] = cnstok(cns_hkl).f(); } else if ( t == "FCAL" ) { fc[0] = cnstok(cns_hkl).f(); fc[1] = Util::d2rad(cnstok(cns_hkl).f()); } else if ( t == "ABCD" ) { hl[0] = cnstok(cns_hkl).f(); hl[1] = cnstok(cns_hkl).f(); hl[2] = cnstok(cns_hkl).f(); hl[3] = cnstok(cns_hkl).f(); } else if ( t == "TEST" ) { fl[0] = cnstok(cns_hkl).f(); } else { for ( int i = 0; i < fphis_i.size(); i++ ) if ( s == fphis_i[i].second ) { fphis[i][0] = cnstok(cns_hkl).f(); fphis[i][1] = Util::d2rad(cnstok(cns_hkl).f()); } } } if ( f_sigf_i != NULL ) f_sigf_i->data_import( hkl, fo ); if ( phi_wt_i != NULL ) phi_wt_i->data_import( hkl, pw ); if ( f_phi_i != NULL ) f_phi_i->data_import( hkl, fc ); if ( abcd_i != NULL ) abcd_i->data_import( hkl, hl ); if ( flag_i != NULL ) flag_i->data_import( hkl, fl ); for ( int i = 0; i < fphis_i.size(); i++ ) fphis_i[i].first->data_import( hkl, fphis[i] ); } fclose( cns_hkl ); mode = NONE; } /*! The file is opened for writing. This will be a new file, created entirely from data from within the program, rather than by extending an existing file. Similar restrictions apply as for open_read(). \param filename_out The output filename or pathname. */ void CNS_HKLfile::open_write( const String filename_out ) { if ( mode != NONE ) Message::message( Message_fatal( "CNS_HKLfile: open_write - File already open" ) ); // open the output cns_hkl hkl_ptr = NULL; f_sigf_o = NULL; phi_wt_o = NULL; f_phi_o = NULL; abcd_o = NULL; flag_o = NULL; filename = filename_out; FILE* cns_hkl = fopen( filename.c_str(), "w" ); if ( cns_hkl == NULL ) Message::message( Message_fatal( "CNS_HKLfile: open_write - Could not write: "+filename ) ); fclose( cns_hkl ); mode = WRITE; } /*! Close the file after writing. This command also actually writes the data reflection list from the HKL_info object and the data from any HKL_data objects which have been marked for import. */ void CNS_HKLfile::close_write() { if ( mode != WRITE ) Message::message( Message_fatal( "CNS_HKLfile: close_write - no file open for write" ) ); // export the marked list data to an cns_hkl file if ( hkl_ptr == NULL ) Message::message( Message_fatal( "CNS_HKLfile: close_write - no refln list exported" ) ); const HKL_info& hklinf = *hkl_ptr; HKL hkl; xtype x[4]; float f1, f2, f3, f4; FILE* cns_hkl = fopen( filename.c_str(), "w" ); if ( cns_hkl == NULL ) Message::message( Message_fatal( "CNS_HKLfile: close_write - Could not write: "+filename ) ); fprintf( cns_hkl, "NREF=%i\n", hklinf.num_reflections() ); HKL_info::HKL_reference_index ih; for ( ih = hklinf.first(); !ih.last(); ih.next() ) { f1 = f2 = f3 = f4 = 0.0; // default sigf to 0 in case missing hkl = ih.hkl(); fprintf( cns_hkl, "INDE %i %i %i", hkl.h(), hkl.k(), hkl.l() ); if ( f_sigf_o != NULL ) { f_sigf_o->data_export( hkl, x ); for ( int i = 0; i < 4; i++ ) if ( Util::is_nan(x[i]) ) x[i] = 0.0; f1 = float( x[0] ); f2 = float( x[1] ); } if ( phi_wt_o != NULL ) { phi_wt_o->data_export( hkl, x ); for ( int i = 0; i < 4; i++ ) if ( Util::is_nan(x[i]) ) x[i] = 0.0; x[0] = Util::rad2d(x[0]); f3 = float( x[0] ); f4 = float( x[1] ); } fprintf( cns_hkl, " FOBS=%.3f %.3f SIGM=%.3f FOM=%.3f",f1,f3,f2,f4 ); if ( f_phi_o != NULL ) { f_phi_o->data_export( hkl, x ); for ( int i = 0; i < 4; i++ ) if ( Util::is_nan(x[i]) ) x[i] = 0.0; x[1] = Util::rad2d(x[1]); fprintf( cns_hkl, " FCAL=%.3f %.3f",float(x[0]),float(x[1]) ); } if ( abcd_o != NULL ) { abcd_o->data_export( hkl, x ); for ( int i = 0; i < 4; i++ ) if ( Util::is_nan(x[i]) ) x[i] = 0.0; fprintf( cns_hkl, " HLA=%.1f HLB=%.1f HLC=%.1f HLD=%.1f",float(x[0]),float(x[1]),float(x[2]),float(x[3]) ); } if ( flag_o != NULL ) { abcd_o->data_export( hkl, x ); for ( int i = 0; i < 4; i++ ) if ( Util::is_nan(x[i]) ) x[i] = 0.0; fprintf( cns_hkl, " TEST=%i",Util::intr(x[0]) ); } fprintf( cns_hkl, "\n" ); } fclose( cns_hkl ); mode = NONE; } /*! Get the spacegroup from the MTZ file. \return The spacegroup. */ const Spacegroup& CNS_HKLfile::spacegroup() const { return spacegroup_; } /*! Get the base cell from the MTZ file. \return The cell. */ const Cell& CNS_HKLfile::cell() const { return cell_; } /*! Get the resolution limit from the MTZ file. \return The resolution. */ const Resolution& CNS_HKLfile::resolution() const { return resolution_; } /*! Get the HKL sampling from the MTZ file. \return The hkl_sampling. */ const HKL_sampling& CNS_HKLfile::hkl_sampling() const { return hkl_sampling_; } /*! Get the resolution limit from the CNS_HKL file. Since a CNS_HKL file does not contain cell information, a Cell object must be supplied, which will be used to determine the resultion. The result is the resolution determined by the most extreme reflection in the file. \return The resolution. */ Resolution CNS_HKLfile::resolution( const Cell& cell ) const { if ( mode != READ ) Message::message( Message_fatal( "CNS_HKLfile: resolution - no file open for read" ) ); FILE* cns_hkl = fopen( filename.c_str(), "r" ); if ( cns_hkl == NULL ) Message::message( Message_fatal( "CNS_HKLfile: resolution - Could not read: "+filename ) ); // read the reflections from the cns_hkl HKL hkl; ftype slim = 0.0; String s, t; while ( (s=cnstok(cns_hkl)).length() > 0 ) { t = (s+" ").substr(0,4); if ( t == "INDE" ) { hkl.h() = cnstok(cns_hkl).i(); hkl.k() = cnstok(cns_hkl).i(); hkl.l() = cnstok(cns_hkl).i(); slim = Util::max( slim, hkl.invresolsq(cell) ); } } fclose( cns_hkl ); return Resolution( 1.0/sqrt(slim) ); } /*! Import the list of reflection HKLs from an CNS_HKL file into an HKL_info object. For most CNS files, there is no cell or spacegroup information: In this case that data must already be present in the HKL_info object. If the resolution limit of the HKL_info object is lower than the limit of the file, any excess reflections will be rejected, as will any systematic absences or duplicates. For recent CNS files with the cell and symops in the remarks fields, the current state of the HKL_info object is discarded and replaced with the information from the file. \param target The HKL_info object to be initialised. */ void CNS_HKLfile::import_hkl_info( HKL_info& target ) { if ( mode != READ ) Message::message( Message_fatal( "CNS_HKLfile: import_hkl_info - no file open for read" ) ); FILE* cns_hkl = fopen( filename.c_str(), "r" ); if ( cns_hkl == NULL ) Message::message( Message_fatal( "CNS_HKLfile: import_hkl_info - Could not read: "+filename ) ); if ( !cell_.is_null() && !spacegroup_.is_null() && !resolution_.is_null() ) target.init( spacegroup_, cell_, resolution_, false ); ftype slim = target.resolution().invresolsq_limit(); // read the reflections from the cns_hkl std::vector hkls; HKL hkl; String s, t; while ( (s=cnstok(cns_hkl)).length() > 0 ) { t = (s+" ").substr(0,4); if ( t == "INDE" ) { hkl.h() = cnstok(cns_hkl).i(); hkl.k() = cnstok(cns_hkl).i(); hkl.l() = cnstok(cns_hkl).i(); if ( hkl.invresolsq(target.cell()) < slim ) hkls.push_back( hkl ); } } fclose( cns_hkl ); target.add_hkl_list( hkls ); } /*! Import data from an CNS_HKL file into an HKL_data object. This routine does not actually read any data, but rather marks the data to be read when the file is closed. The data to be read (F_sigF or Phi_fom) will be selected based on the type of the HKL_data object. \param cdata The HKL_data object into which data is to be imported. */ void CNS_HKLfile::import_hkl_data( HKL_data_base& cdata ) { if ( mode != READ ) Message::message( Message_fatal( "CNS_HKLfile: import_hkl_data - no file open for read" ) ); if ( cdata.is_null() ) cdata.init( spacegroup_, cell_, hkl_sampling_ ); if ( cdata.type() == data32::F_sigF::type() ) f_sigf_i = &cdata; else if ( cdata.type() == data32::Phi_fom::type() ) phi_wt_i = &cdata; else if ( cdata.type() == data32::F_phi::type() ) f_phi_i = &cdata; else if ( cdata.type() == data32::ABCD::type() ) abcd_i = &cdata; else if ( cdata.type() == data32::Flag::type() ) flag_i = &cdata; else Message::message( Message_fatal( "CNS_HKLfile: import_hkl_data - data must be F_sigF/Phi_fom/F_phi/ABCD/Flag" ) ); } /*! Import data from an CNS_HKL file into an HKL_data object. This routine does not actually read any data, but rather marks the data to be read when the file is closed. The data to be read must be of type F_phi. A column name is given. \param cdata The HKL_data object into which data is to be imported. \param name The column name of the data to import. */ void CNS_HKLfile::import_hkl_data( HKL_data_base& cdata, const String name ) { if ( mode != READ ) Message::message( Message_fatal( "CNS_HKLfile: import_hkl_data - no file open for read" ) ); if ( cdata.is_null() ) cdata.init( spacegroup_, cell_, hkl_sampling_ ); if ( cdata.type() == data32::F_phi::type() ) fphis_i.push_back( std::pair(&cdata,name) ); else Message::message( Message_fatal( "CNS_HKLfile: import_hkl_data - data must be F_phi" ) ); } /*! Export the list of reflection HKLs to an CNS_HKL file from an HKL_info object. */ void CNS_HKLfile::export_hkl_info( const HKL_info& target ) { if ( mode != WRITE ) Message::message( Message_fatal( "CNS_HKLfile: export_hkl_info - no file open for write" ) ); hkl_ptr = ⌖ } /*! Export data from an HKL_data object into an CNS_HKL file. This routine does not actually write any data, but rather marks the data to be written when the file is closed. The data to be read (F_sigF or Phi_fom) will be selected based on the type of the HKL_data object. \param cdata The HKL_data object from which data is to be exported. */ void CNS_HKLfile::export_hkl_data( const HKL_data_base& cdata ) { if ( mode != WRITE ) Message::message( Message_fatal( "CNS_HKLfile: export_hkl_data - no file open for write" ) ); if ( cdata.type() == data32::F_sigF::type() ) f_sigf_o = &cdata; else if ( cdata.type() == data32::Phi_fom::type() ) phi_wt_o = &cdata; else if ( cdata.type() == data32::F_phi::type() ) f_phi_o = &cdata; else if ( cdata.type() == data32::ABCD::type() ) abcd_o = &cdata; else if ( cdata.type() == data32::Flag::type() ) flag_o = &cdata; else Message::message( Message_fatal( "CNS_HKLfile: export_hkl_data - data must be F_sigF/Phi_fom/F_phi/ABCD/Flag" ) ); } } // namespace clipper clipper-2.1/clipper/cns/cns_hkl_io.h0000644000374100011300000001212411144056610014425 00000000000000/*! \file lib/cns_hkl_io.h Header file for reflection data cns_hkl importer */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_CNS_HKL_IO #define CLIPPER_CNS_HKL_IO #include "../core/hkl_datatypes.h" namespace clipper { //! CNS_HKL import/export parent class for clipper objects /*! This is the import/export class which can be linked to an cns_hkl file and be used to transfer data into or out of a Clipper data structure. */ class CNS_HKLfile { public: //! Constructor: does nothing CNS_HKLfile(); //! Destructor: close any file that was left open ~CNS_HKLfile(); //! Open a file for read access void open_read( const String filename_in ); //! Close a file after reading void close_read(); //! Open a file for write access void open_write( const String filename_out ); //! Close a file after writing void close_write(); //! get file spacegroup const Spacegroup& spacegroup() const; //! get file cell const Cell& cell() const; //! get file resolution const Resolution& resolution() const; //! get file HKL sampling const HKL_sampling& hkl_sampling() const; //! get file resolution (if no cell in file) Resolution resolution( const Cell& cell ) const; //! read the reflection list from the CNS_HKL file void import_hkl_info( HKL_info& target ); //! mark a hkl_data for import from CNS_HKL file void import_hkl_data( HKL_data_base& cdata ); //! mark a hkl_data for import from named column of a CNS_HKL file void import_hkl_data( HKL_data_base& cdata, const String name ); //! write the reflection list to the CNS_HKL file void export_hkl_info( const HKL_info& target ); //! mark a hkl_data for export to CNS_HKL file void export_hkl_data( const HKL_data_base& cdata ); private: enum CNS_HKLmode { NONE, READ, WRITE }; CNS_HKLmode mode; //!< file mode String filename; //!< input/output file HKL_data_base* f_sigf_i; //!< input HKL_data object HKL_data_base* phi_wt_i; //!< input HKL_data object HKL_data_base* f_phi_i ; //!< input HKL_data object HKL_data_base* abcd_i; //!< input HKL_data object HKL_data_base* flag_i; //!< input HKL_data object const HKL_data_base* f_sigf_o; //!< output HKL_data object const HKL_data_base* phi_wt_o; //!< output HKL_data object const HKL_data_base* f_phi_o; //!< output HKL_data object const HKL_data_base* abcd_o; //!< output HKL_data object const HKL_data_base* flag_o; //!< output HKL_data object //! object which supplies the hkl list (write mode only) const HKL_info* hkl_ptr; //! input HKL_data object std::vector > fphis_i; //! File spacegroup, cell, resolution Spacegroup spacegroup_; Cell cell_; Resolution resolution_; HKL_sampling hkl_sampling_; }; } // namespace clipper #endif clipper-2.1/clipper/cns/cns_map_io.h0000644000374100011300000001047311247463275014446 00000000000000/*! \file ccp4/ccp4_map_io.h Header file for reflection data map importer */ //c Copyright (C) 2006 Jon A. Christopher, Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_CNS_MAP_IO #define CLIPPER_CNS_MAP_IO #include "../core/container_map.h" namespace clipper { //! MAP import/export parent class for clipper objects /*! This is the import/export class which can be linked to a CNS map file and be used to transfer data into or out of a Clipper data structure. */ class CNSMAPfile { public: //! Constructor: from CNS spacegroup number CNSMAPfile(unsigned int sg_num=1); //! Constructor: from Spacegroup CNSMAPfile( Spacegroup spacegroup ); //! Destructor: close any file that was left open ~CNSMAPfile(); //! Open a file for read access void open_read( const String filename_in ); //! Close a file after reading void close_read(); //! Open a file for read access void open_write( const String filename_out ); //! Close a file after reading void close_write(); //! set cell desription (NXmap write only) void set_cell( const Cell& cell ); //! get file spacegroup const Spacegroup& spacegroup() const; //! get file cell const Cell& cell() const; //! get file grid_sampling const Grid_sampling& grid_sampling() const; //! import data to Xmap template void import_xmap( Xmap& xmap ); //! export data from Xmap template void export_xmap( const Xmap& xmap ); //! import data to NXmap template void import_nxmap( NXmap& nxmap ); //! export data from NXmap template void export_nxmap( const NXmap& nxmap ); enum ASUerror { ASUCORRECT, ASUINCOMPLETE, ASUINCONSISTENT }; //! import data to Xmap and check ASU (float/double only) template ASUerror import_xmap_check_asu( Xmap& xmap, T missing ); protected: enum MAPmode { NONE, READ, WRITE }; String filename; //!< filename MAPmode mode; //!< mode // header info Spacegroup spacegroup_; //!< map spacegroup Cell cell_; //!< map cell Grid_sampling grid_sam_; //!< cell grid sampling Grid_range grid_map_; //!< map grid extent }; } // namespace clipper #endif clipper-2.1/clipper/cns/Makefile.am0000644000374100011300000000106211372264321014202 00000000000000# Makefile.am, passed: clipper/cns, extracted subdir: cns # in dir /home/cowtan/clipper-autoconf/clipper-2.1/clipper/cns ## -*- mode: Makefile; mode: font-lock -*- INCLUDES=${FFTW_CXXFLAGS} library_include_HEADERS = \ cns_hkl_io.h \ cns_map_io.h lib_LTLIBRARIES = libclipper-cns.la libclipper_cns_la_SOURCES = \ cns_hkl_io.cpp \ cns_map_io.cpp library_includedir = $(pkgincludedir)/cns libclipper_cns_la_LDFLAGS = -version-info @CLIPPER_LT_VERSION@ libclipper_cns_la_LIBADD = \ $(top_builddir)/clipper/core/libclipper-core.la clipper-2.1/clipper/cns/Makefile.in0000644000374100011300000004456211372264333014232 00000000000000# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # 2003, 2004, 2005, 2006, 2007, 2008, 2009 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all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: clipper-2.1/clipper/clipper-mmdbold.h0000644000374100011300000000024510736662163014621 00000000000000/* Clipper header file */ /* (C) 2000-2003 Kevin Cowtan */ #ifndef CLIPPER_MMDBOLD_H #define CLIPPER_MMDBOLD_H #include "clipper/mmdbold/container_mmdb.h" #endif clipper-2.1/clipper/core/0000777000374100011300000000000011372264353012405 500000000000000clipper-2.1/clipper/core/fftmap.h0000644000374100011300000002534110736415734013760 00000000000000/*! \file lib/fftmap.h Header file for P1 fft map */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_FFTMAP #define CLIPPER_FFTMAP #include "coords.h" #include namespace clipper { // fft type typedef float ffttype; // forward definition namespace datatypes { template class F_phi; } // base class for FFT classes class FFTmap_base { public: enum FFTtype { Default, Measure, Estimate }; //!< optimisation options protected: static Mutex mutex; //!< Thread safety }; //! FFTmap_p1: low level P1 map used for calculating FFTs /*! This is a pure real P1 map, with an extra section in reciprocal space to allow generation of the full set of resiprocal space magnitudes. Access is by Coord_grid in both spaces, and indices must be non-negative and in range. The first and last sections along the half-length direction only have half the elements stored, the contents of the other half is ignored. */ class FFTmap_p1 : public FFTmap_base { public: //! Null constructor FFTmap_p1(); //! Copy constructor FFTmap_p1( const FFTmap_p1& other ) { copy(other); } //! Constructor: takes grid FFTmap_p1( const Grid_sampling& grid_sam, const FFTtype type = Default ); //! Assignment operator const FFTmap_p1& operator =(const FFTmap_p1& other) { return copy(other); } //! initialiser: takes grid void init( const Grid_sampling& grid_sam, const FFTtype type = Default ); //! Reset void reset(); //! Return real space grid. const Grid_sampling& grid_real() const { return grid_sam_; } //! Return reciprocal space grid (i.e. half real grid + 1 section). const Grid& grid_reci() const { return grid_reci_; } //! Test whether a coordinate is in the valid part of the recip. grid. bool uniq_reci( const Coord_grid& c ) const { return ( (c.w()>0 && c.w()0 && c.v() get_hkl( const HKL& hkl ) const; //! set reciprocal space data: slow form with hemisphere check void set_hkl( const HKL& hkl, const std::complex& f ); //! get reciprocal space data const std::complex& cplx_data( const Coord_grid& c ) const { return data_c[ grid_reci_.index( c ) ]; } //! set reciprocal space data std::complex& cplx_data( const Coord_grid& c ) { return data_c[ grid_reci_.index( c ) ]; } //! get real space data const ffttype& real_data( const Coord_grid& c ) const { return data_r[ grid_real_.index( c ) ]; } //! set real space data ffttype& real_data( const Coord_grid& c ) { return data_r[ grid_real_.index( c ) ]; } //! set/get default optimisation type static FFTtype& default_type() { return default_type_; } void debug() const; protected: const FFTmap_p1& copy( const FFTmap_p1& other ); //!< copy function enum FFTmode { NONE, RECI, REAL, OTHER }; //!< space enumeration FFTmode mode; //!< real or reciprocal space? FFTtype type_; //!< optimisation options Grid_sampling grid_sam_; //!< unit cell grid Grid grid_reci_; //!< reciprocal space grid Grid grid_real_; //!< real space grid Grid grid_half_; //!< half grid (for marking unique) Matrix req_kl, req_uv; //!< reci section lookup std::vector req_l, req_u; //!< real section lookup std::vector datavec; //!< vector for the data ffttype* data_r; //!< pointer to real data std::complex* data_c; //!< pointer to complex data static FFTtype default_type_; //!< default optimisation options }; //! FFTmap: P1 map with symmetry used for calculating FFTs /*! The FFTmap is represented in P1 in memory. However, it also has a spacegroup, and the contained data remains consistent with this spacegroup at all times. It has three states - unassigned, real-space, and reciprocal space. In real space it contains real map data. In reciprocal space it holds a hemisphere of complex structure factors, with the Friedels duplicated on the zero section. The user should be able to ignore all the issues of spacegroup symmetry, Friedel opposites, and storage order. */ class FFTmap : private FFTmap_p1 { public: //! Null constructor FFTmap(); //! Constructor: takes spacegroup, cell, grid FFTmap( const Spacegroup& spacegroup, const Cell& cell, const Grid_sampling grid_sam, const FFTtype type = Default ); //! initialiser void init( const Spacegroup& spacegroup, const Cell& cell, const Grid_sampling grid_sam, const FFTtype type = Default ); //! Reset void reset(); //! get the cell const Cell& cell() const { return cell_; } //! get the spacegroup const Spacegroup& spacegroup() const { return spacegroup_; } //! get the cell grid const Grid_sampling& grid_sampling() const { return FFTmap_p1::grid_real(); } //! Transform to real space void fft_h_to_x(); //! Transform to reciprocal space void fft_x_to_h(); //! get reciprocal space data template void get_recip_data( const HKL& rfl, datatypes::F_phi& fphi ) const; //! set reciprocal space data template void set_recip_data( const HKL& rfl, const datatypes::F_phi& fphi ); //! get real space data template void get_real_data( const Coord_grid& c, T& datum ) const; //! set real space data template void set_real_data( const Coord_grid& c, const T& datum ); //! get reciprocal space data (No error checking) datatypes::F_phi get_recip_data( const HKL& rfl ) const; //! get real space data (No error checking) const ffttype& get_real_data( const Coord_grid& c ) const { return real_data(c.unit(grid_real())); } //! calculate map-like object from reflection-like object template void fft_rfl_to_map( const H& h, X& x ); //! calculate reflection-like object from map-like object template void fft_map_to_rfl( const X& x, H& h ); void debug() const; protected: Cell cell_; //!< unit cell Spacegroup spacegroup_; //!< spacegroup std::vector isymop; //!< Integerised symops }; // template implementations /*! Fill this FFTmap object from a reflection object, transform it, and fill the given map object from the FFTmap. This will work for any reflection data object which implements a HKL_reference_index, and every map data object which implements a Map_reference_index. For the results to be sensible, the spacegroup, cell and grids should match. (The map will be zeroed if necessary). \param h The source reflection data object. \param x The target map object. */ template void FFTmap::fft_rfl_to_map( const H& h, X& x ) { // zero the map reset(); // copy from reflection data typename H::HKL_reference_index ih; for ( ih = h.first_data(); !ih.last(); h.next_data( ih ) ) set_recip_data( ih.hkl(), h[ih] ); // fft fft_h_to_x(); // and copy into the map typename X::Map_reference_index ix; for ( ix = x.first(); !ix.last(); ix.next() ) get_real_data( ix.coord(), x[ix] ); } /*! Fill this FFTmap object from a map object, transform it, and fill the given reflection object from the FFTmap. This will work for any reflection data object which implements a HKL_reference_index, and every map data object which implements a Map_reference_index. For the results to be sensible, the spacegroup, cell and grids should match. (The map will be zeroed if necessary). \param x The source map object. \param h The target reflection data object. */ template void FFTmap::fft_map_to_rfl( const X& x, H& h ) { // zero the map reset(); // copy into the map typename X::Map_reference_index ix; for ( ix = x.first(); !ix.last(); ix.next() ) set_real_data( ix.coord(), x[ix] ); // fft fft_x_to_h(); // now fill it typename H::HKL_reference_index ih; for ( ih = h.first(); !ih.last(); ih.next() ) get_recip_data( ih.hkl(), h[ih] ); } } // namespace clipper #endif clipper-2.1/clipper/core/clipper_test.cpp0000644000374100011300000000737410363703537015536 00000000000000/* clipper_test.cpp: implementation file for clipper self-test functions */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "clipper_test.h" namespace clipper { Test_base::Test_base() { stream_ = NULL; count = error_count = 0; } void Test_base::set_stream( std::ostream& stream ) { //stream.width(?); stream.precision(8); stream_ = &stream; } //! test that the next value matches the stored data bool Test_base::test( const String& id, const double& value ) { bool pass = false; if ( stream_ != NULL ) *stream_ << value << "\n"; if ( count < data_val.size() ) { double val( data_val[count] ); double tol( data_tol[count] ); if ( fabs( value - val ) < tol ) { pass = true; } else { std::cerr << "Self test: " << id << count << " Result: " << val-tol << " < " << value << " < " << val+tol << "\n"; } } else if ( count == data_val.size() ) { Message::message( Message_warn( "Self test: out of data." ) ); } count++; if ( !pass ) error_count++; return pass; } bool Test_base::test( const String& id, const double& value, const double& val, const double& tol ) { bool pass = false; if ( fabs( value - val ) < tol ) { pass = true; } else { std::cerr << "Self test: " << id << " Result: " << val-tol << " < " << value << " < " << val+tol << "\n"; } if ( !pass ) error_count++; return pass; } bool Test_base::test( const String& id, const int& value, const int& val ) { bool pass = false; if ( value == val ) { pass = true; } else { std::cerr << "Self test: " << id << " Result: " << value << " == " << val << "\n"; } if ( !pass ) error_count++; return pass; } } // namespace clipper clipper-2.1/clipper/core/clipper_memory.h0000644000374100011300000001775211205015646015526 00000000000000/*! \file lib/clipper_memory.h Header file for clipper memory handlers */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_MEMORY #define CLIPPER_MEMORY #include "clipper_thread.h" #include namespace clipper { //! Base class for properties of arbitrary types class Property_base { public: virtual Property_base* clone() const = 0; //!< factory copy method virtual ~Property_base() {}; //!< destructor }; //! Template for a property holding an arbitrary type template class Property : public Property_base { public: //! constructor: takes contents explicit Property( const T& val ) { val_ = val; } ~Property() {} Property_base* clone() const { return new Property( *this ); } const T& value() const { return val_; } //!< return value of contents private: T val_; }; //! Class for holding a list of labelled properties of arbitrary types /*! To add a property list to an object, derive it from this class, or include a member and mirror the methods. To add a property, simply call insert_property(label,property). Properties must be objects derived from clipper::Propert_base. Usually, you can just use the template form, clipper::Property. To read a property which you know exists and is of a particular type, use: \code const T& obj = dynamic_cast& >(list.get_property( label )).value(); \endcode If you are unsure if a property is present, use the exists_property(label) method. If you are unsure of a property's type, dynamic cast a pointer and test for null. e.g. \code if ( !list.exists_property( label ) ) { error("No such property"); } const Property_base* ptr = &list.get_property( label ); if ( dynamic_cast(ptr) == NULL ) { error("Wrong type"); } const T& obj = *(dynamic_cast(ptr)); \endcode */ class PropertyManager { public: PropertyManager() {} //!< null constructor PropertyManager( const PropertyManager& mgr ); //!< copy constructor PropertyManager& operator =( const PropertyManager& mgr ); //!< assign op ~PropertyManager(); //!< destructor PropertyManager& copy( const PropertyManager& mgr ); //!< copy manager //! add a labelled property to the list bool set_property(const std::string& label, const Property_base& property); //! get a labelled property from the list const Property_base& get_property( const std::string& label ) const; bool exists_property(const std::string& label) const; //!< test for property bool delete_property(const std::string& label); //!< delete property private: std::vector > property_; //static Mutex mutex; //!< thread safety }; //! Object Cache manager /*! The object cache is a tool for storing information which may appear several times. Examples include tables of information for spacegroups or crystallographic maps. When a new object is created, a check is first done to see if such an object already exists in the cache, in which case that copy is used. Otherwise a new copy is added to the cache. A cached object must implement: - a constructor from a type T - a method 'matches(T)' which tests if it constructed from that object - a 'format()' method, returning a string description of the contents The type T should be a compact unique description of the object. Referring to the cache returns an ObjectCache::Reference to a cache object. This object performs reference counting, which is used for garbage collection. To retrieve the actual cached data, use the ObjectCache::Reference::data() method. The data is held at a fixed memory location, therefore pointers to the data may be safely kept, as long as they are discarded as soon as the reference is discarded (at which point garbage collection may occur). Ideally this would be a class with static members only, but some compilers have trouble with static members of template classes. Garbage collection modes include: - ObjectCache::NORMAL : Remove an old object only when a new object is required and an old object is no longer in use. (default) - ObjectCache::MINMEM : Remove an old object as soon as it is no longer in use. - ObjectCache::MAXMEM : Never remove old objects. The more memory hungry modes may improve performance for some problems where a new object may be created which was already used and destroyed before. */ template class ObjectCache { public: //! ObjectCache reference class class Reference { public: Reference() : obj_(NULL) {} Reference( const Reference& other ); ~Reference(); void operator =( const Reference& other ); bool is_null() const { return obj_ == NULL; } const T& data() const { return obj_->second; } private: std::pair* obj_; //! unsafe constructor (thread must be locked) Reference( std::pair* obj ) { obj_ = obj; obj_->first++; } friend class ObjectCache; }; enum MODE { NORMAL, MINMEM, MAXMEM }; //!< garbage collection mode ObjectCache(); //!< constructor ~ObjectCache(); //!< destructor, can message on contents void set_mode( const MODE& mode ); //!< set garbage collection mode void purge(); //!< purge unreferenced objects from cache void destroy(); //!< VERY DANGEROUS, DO NOT USE void debug() const; //! cache or return data by key Reference cache( const typename T::Key& key ); private: std::vector*> cache_; //!< the cache ptrs MODE mode_; //!< the garbage collection mode }; // for template implementations, see clipper_instance.cpp } // namespace clipper #endif clipper-2.1/clipper/core/resol_targetfn.h0000644000374100011300000005014411270270267015512 00000000000000/*! \file lib/resol_targetfn.h Header file for resolution function generator */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_RESOL_TARGETFN #define CLIPPER_RESOL_TARGETFN #include "resol_basisfn.h" #include "hkl_datatypes.h" namespace clipper { //! simple mean |F|n target /*! This class implements the target function for calculating mean |F|n as a function of position in reciprocal space. It includes the appropriate multiplicity correction, and so can be applied to any type with an 'f' member with the same dimensions as an |F| or |U| (or an uncorrected |E|). \Note This function should not be used to scale F's to E's. See TargetFn_scaleEsq. */ template class TargetFn_meanFnth : public TargetFn_base { public: //! constructor: takes the datalist against which to calc target, and power TargetFn_meanFnth( const HKL_data& hkl_data_, const ftype& n ); //! return the value and derivatives of the target function Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& fh ) const; //! the type of the function: optionally used to improve convergence FNtype type() const { return QUADRATIC; } private: ftype power; const HKL_data* hkl_data; }; //! simple mean |E|n target /*! This class implements the target function for calculating mean |E|n as a function of position in reciprocal space. It includes the appropriate multiplicity correction, and so can be applied to any type with an 'E' member with the same dimensions as an |E| (or corrected |F| or |U|). \Note This function should not be used to scale F's to E's. See TargetFn_scaleEsq. */ template class TargetFn_meanEnth : public TargetFn_base { public: //! constructor: takes the datalist against which to calc target, and power TargetFn_meanEnth( const HKL_data& hkl_data_, const ftype& n ); //! return the value and derivatives of the target function Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& fh ) const; //! the type of the function: optionally used to improve convergence FNtype type() const { return QUADRATIC; } private: ftype power; const HKL_data* hkl_data; }; //! |F|2 scaling target /*! This class implements the target function for calculating the scale factor to scale one set of F's to another. The resulting scale is the square of the factor that scales the first set of data to match the second. */ template class TargetFn_scaleF1F2 : public TargetFn_base { public: //! constructor: takes the datalist against which to calc target TargetFn_scaleF1F2( const HKL_data& hkl_data1_, const HKL_data& hkl_data2_ ); //! return the value and derivatives of the target function Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& fh ) const; //! the type of the function: optionally used to improve convergence FNtype type() const { return QUADRATIC; } private: const HKL_data* hkl_data1; const HKL_data* hkl_data2; }; //! log |F|2 scaling target /*! This class implements the target function for calculating the scale factor to scale the weighted log of one set of F's to another. The resulting scale is the square of the factor that scales the first set of data to match the second. The log scaling target is used in conjunction with the log-Gaussian basis functions for a fast and robust approximation to iso/aniso Gaussian scaling. */ template class TargetFn_scaleLogF1F2 : public TargetFn_base { public: //! constructor: takes the datalist against which to calc target TargetFn_scaleLogF1F2( const HKL_data& hkl_data1_, const HKL_data& hkl_data2_ ); //! return the value and derivatives of the target function Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& fh ) const; //! the type of the function: optionally used to improve convergence FNtype type() const { return QUADRATIC; } private: const HKL_data* hkl_data1; const HKL_data* hkl_data2; }; /*! This class implements the target function for calculating the scale factor to scale one set of I's to another. The resulting scale is the square of the factor that scales the first set of data to match the second. */ template class TargetFn_scaleI1I2 : public TargetFn_base { public: //! constructor: takes the datalist against which to calc target TargetFn_scaleI1I2( const HKL_data& hkl_data1_, const HKL_data& hkl_data2_ ); //! return the value and derivatives of the target function Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& fh ) const; //! the type of the function: optionally used to improve convergence FNtype type() const { return QUADRATIC; } private: const HKL_data* hkl_data1; const HKL_data* hkl_data2; }; //! log |I| scaling target /*! This class implements the target function for calculating the scale factor to scale the weighted log of one set of I's to another. The resulting scale is the square of the factor that scales the first set of data to match the second. The log scaling target is used in conjunction with the log-Gaussian basis functions for a fast and robust approximation to iso/aniso Gaussian scaling. */ template class TargetFn_scaleLogI1I2 : public TargetFn_base { public: //! constructor: takes the datalist against which to calc target TargetFn_scaleLogI1I2( const HKL_data& hkl_data1_, const HKL_data& hkl_data2_ ); //! return the value and derivatives of the target function Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& fh ) const; //! the type of the function: optionally used to improve convergence FNtype type() const { return QUADRATIC; } private: const HKL_data* hkl_data1; const HKL_data* hkl_data2; }; //! |E|2 scaling target /*! This class implements the target function for calculating the scale factor to normalise to <|E|2> = 1. Note that this is not the same as dividing by <|E|2>, except in a few special cases, e.g. a simple resolution bins calculation. The resulting targen function is the square of the value by which |E| should be multiplied to acheive the correct normalisation. */ template class TargetFn_scaleEsq : public TargetFn_base { public: //! constructor: takes the datalist against which to calc target TargetFn_scaleEsq( const HKL_data& hkl_data_ ); //! return the value and derivatives of the target function Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& fh ) const; //! the type of the function: optionally used to improve convergence FNtype type() const { return QUADRATIC; } private: const HKL_data* hkl_data; }; //! \deprecated simple sigma_a target function /*! This class implements the target function for calculating sigma_a. Required is a datalist containing Eo, Ec. It actually refines omegaa = sigmaa/(1-sigmaa^2). This has better proerties for refinement. To get sigmaa use \code sigmaa = ( sqrt( 4*omegaa^2 + 1 ) - 1 ) / ( 2*omegaa ) \endcode This is available as a static function: \code sigmaa = targetfn.sigmaa( omegaa ) \endcode This version simplifies terms in |Eo|^2 and |Ec|^2 which should average out to 1 if the normalisation scheme is consistent with the sigmaa calc. Convergence is good for calculations using the 'binner' basis function, however the smooth basis function have convergence problems. This is still under investigation. */ template class TargetFn_sigmaa_omegaa : public TargetFn_base { public: //! constructor: takes the datalist against which to calc target TargetFn_sigmaa_omegaa( const HKL_data& eo, const HKL_data& ec ); //! return the value and derivatives of the target function Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& omegaa ) const; //! convert omegaa to sigmaa static ftype sigmaa( const ftype& omegaa ) { ftype omeg = (omegaa>0.05) ? omegaa : (0.05*exp(omegaa/0.05-1.0)); return 0.5 * ( sqrt( 4.0*omeg*omeg + 1.0 ) - 1.0 ) / omeg; } private: const HKL_data* eo_data; const HKL_data* ec_data; }; //! \deprecated simple sigma_a target function /*! \par Warning: Convergence of this basis-function can be unreliable under some circumstances. Use clipper::TargetFn_sigmaa_omegaa instead, except for development purposes. This class implements the target function for calculating sigma_a. Required is a datalist containing Eo, Ec. This version simplifies terms in |Eo|^2 and |Ec|^2 which should average out to 1 if the normalisation scheme is consistent with the sigmaa calc. */ template class TargetFn_sigmaa : public TargetFn_base { public: //! constructor: takes the datalist against which to calc target TargetFn_sigmaa( const HKL_data& eo, const HKL_data& ec ); //! return the value and derivatives of the target function Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& sigmaa0 ) const; //! convert function to sigmaa static ftype sigmaa( const ftype& sigm ) { return sigm; } private: const HKL_data* eo_data; const HKL_data* ec_data; }; // implementations for template functions // mean F^nth template TargetFn_meanFnth::TargetFn_meanFnth( const HKL_data& hkl_data_, const ftype& n ) { power = n; hkl_data = &hkl_data_; } template TargetFn_base::Rderiv TargetFn_meanFnth::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& fh ) const { Rderiv result; const HKL_data& data = *hkl_data; if ( !data[ih].missing() ) { ftype d = fh - pow( ftype(data[ih].f()) / sqrt(ih.hkl_class().epsilon()), power ); result.r = d * d; result.dr = 2.0 * d; result.dr2 = 2.0; } else { result.r = result.dr = result.dr2 = 0.0; } return result; } // mean E^nth template TargetFn_meanEnth::TargetFn_meanEnth( const HKL_data& hkl_data_, const ftype& n ) { power = n; hkl_data = &hkl_data_; } template TargetFn_base::Rderiv TargetFn_meanEnth::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& fh ) const { Rderiv result; const HKL_data& data = *hkl_data; if ( !data[ih].missing() ) { ftype d = fh - pow( ftype(data[ih].E()), power ); result.r = d * d; result.dr = 2.0 * d; result.dr2 = 2.0; } else { result.r = result.dr = result.dr2 = 0.0; } return result; } // F1-F2 scaling template TargetFn_scaleF1F2::TargetFn_scaleF1F2( const HKL_data& hkl_data1_, const HKL_data& hkl_data2_ ) { hkl_data1 = &hkl_data1_; hkl_data2 = &hkl_data2_; } template TargetFn_base::Rderiv TargetFn_scaleF1F2::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& fh ) const { Rderiv result; const T1& ft1 = (*hkl_data1)[ih]; const T2& ft2 = (*hkl_data2)[ih]; if ( !ft1.missing() && !ft2.missing() ) { const ftype eps = ih.hkl_class().epsilon(); const ftype f1 = pow( ft1.f(), 2 ) / eps; const ftype f2 = pow( ft2.f(), 2 ) / eps; const ftype d = fh*f1 - f2; result.r = d * d / f1; result.dr = 2.0 * d; result.dr2 = 2.0 * f1; } else { result.r = result.dr = result.dr2 = 0.0; } return result; } // Log F1-F2 scaling template TargetFn_scaleLogF1F2::TargetFn_scaleLogF1F2( const HKL_data& hkl_data1_, const HKL_data& hkl_data2_ ) { hkl_data1 = &hkl_data1_; hkl_data2 = &hkl_data2_; } template TargetFn_base::Rderiv TargetFn_scaleLogF1F2::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& fh ) const { Rderiv result; result.r = result.dr = result.dr2 = 0.0; const T1& ft1 = (*hkl_data1)[ih]; const T2& ft2 = (*hkl_data2)[ih]; if ( !ft1.missing() && !ft2.missing() ) if ( ft1.f() > 1.0e-6 && ft2.f() > 1.0e-6 ) { const ftype eps = ih.hkl_class().epsilon(); const ftype f1 = pow( ft1.f(), 2 ) / eps; const ftype f2 = pow( ft2.f(), 2 ) / eps; const ftype w = 1.0; // f1 * f2; const ftype d = fh + log(f1) - log(f2); result.r = w * d * d; result.dr = 2.0 * w * d; result.dr2 = 2.0 * w; } return result; } // I1-I2 scaling template TargetFn_scaleI1I2::TargetFn_scaleI1I2( const HKL_data& hkl_data1_, const HKL_data& hkl_data2_ ) { hkl_data1 = &hkl_data1_; hkl_data2 = &hkl_data2_; } template TargetFn_base::Rderiv TargetFn_scaleI1I2::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& fh ) const { Rderiv result; const T1& ft1 = (*hkl_data1)[ih]; const T2& ft2 = (*hkl_data2)[ih]; if ( !ft1.missing() && !ft2.missing() ) { const ftype eps = ih.hkl_class().epsilon(); const ftype f1 = ft1.I() / eps; const ftype f2 = ft2.I() / eps; const ftype d = fh*f1 - f2; result.r = d * d / f1; result.dr = 2.0 * d; result.dr2 = 2.0 * f1; } else { result.r = result.dr = result.dr2 = 0.0; } return result; } // Log I1-I2 scaling template TargetFn_scaleLogI1I2::TargetFn_scaleLogI1I2( const HKL_data& hkl_data1_, const HKL_data& hkl_data2_ ) { hkl_data1 = &hkl_data1_; hkl_data2 = &hkl_data2_; } template TargetFn_base::Rderiv TargetFn_scaleLogI1I2::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& fh ) const { Rderiv result; result.r = result.dr = result.dr2 = 0.0; const T1& ft1 = (*hkl_data1)[ih]; const T2& ft2 = (*hkl_data2)[ih]; if ( !ft1.missing() && !ft2.missing() ) if ( ft1.I() > 1.0e-6 && ft2.I() > 1.0e-6 ) { const ftype eps = ih.hkl_class().epsilon(); const ftype f1 = ft1.I() / eps; const ftype f2 = ft2.I() / eps; const ftype w = 1.0; // f1 * f2; const ftype d = fh + log(f1) - log(f2); result.r = w * d * d; result.dr = 2.0 * w * d; result.dr2 = 2.0 * w; } return result; } // E^2 scaling template TargetFn_scaleEsq::TargetFn_scaleEsq( const HKL_data& hkl_data_ ) { hkl_data = &hkl_data_; } template TargetFn_base::Rderiv TargetFn_scaleEsq::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& fh ) const { Rderiv result; const HKL_data& data = *hkl_data; const ftype two(2.0); if ( !data[ih].missing() ) { ftype fsq = pow( ftype(data[ih].E()), two ); ftype d = fsq * fh - 1.0; result.r = d * d / fsq; result.dr = two * d; result.dr2 = two * fsq; } else { result.r = result.dr = result.dr2 = 0.0; } return result; } // sigmaa (omegaa) template TargetFn_sigmaa_omegaa::TargetFn_sigmaa_omegaa( const HKL_data& eo, const HKL_data& ec ) { eo_data = &eo; ec_data = &ec; } template TargetFn_base::Rderiv TargetFn_sigmaa_omegaa::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& omegaa ) const { Rderiv result; const HKL_data& eodata = *eo_data; const HKL_data& ecdata = *ec_data; if ( eodata[ih].missing() || ecdata[ih].missing() ) { result.r = result.dr = result.dr2 = 0.0; } else { ftype eo = eodata[ih].E(); ftype ec = ecdata[ih].E(); ftype omeg = (omegaa>0.05) ? omegaa : (0.05*exp(omegaa/0.05-1.0)); ftype sigmaa = 0.5*(sqrt(4*omeg*omeg+1)-1)/omeg; ftype dx = 2.0 * eo * ec; ftype x = dx * omeg; ftype t0 = 1.0/(1-sigmaa*sigmaa) + 0.5*log((1-sigmaa*sigmaa)); ftype t1 = sigmaa; ftype t2 = pow(1-sigmaa*sigmaa,2)/(1+sigmaa*sigmaa); if ( ih.hkl_class().centric() ) { result.r = 1.0*t0 - log( cosh( x/2 ) ); result.dr = 1.0*t1 - dx*0.5*tanh( x/2 ); result.dr2 = 1.0*t2 - dx*dx*0.25*(1.0 - pow(tanh(x/2),2) ); } else { result.r = 2.0*t0 - Util::sim_integ( x ); result.dr = 2.0*t1 - dx*Util::sim( x ); result.dr2 = 2.0*t2 - dx*dx*Util::sim_deriv( x ); } if ( omegaa < 0.05 ) { ftype dy = exp( omegaa/0.05 ) / exp( 1.0 ); ftype dy2 = exp( omegaa/0.05 ) / ( 0.05*exp( 1.0 ) ); result.dr2 = result.dr*dy2 + result.dr2*dy*dy; result.dr = result.dr*dy; } } return result; } // sigmaa (norm) template TargetFn_sigmaa::TargetFn_sigmaa( const HKL_data& eo, const HKL_data& ec ) { eo_data = &eo; ec_data = &ec; } template TargetFn_base::Rderiv TargetFn_sigmaa::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& sigmaa0 ) const { Rderiv result; const HKL_data& eodata = *eo_data; const HKL_data& ecdata = *ec_data; if ( eodata[ih].missing() || ecdata[ih].missing() ) { result.r = result.dr = result.dr2 = 0.0; } else { ftype eo = eodata[ih].E(); ftype ec = ecdata[ih].E(); ftype sigmaa = Util::min( Util::max( sigmaa0, 0.01 ), 0.99 ); ftype dx = 2.0 * eo * ec; ftype x = dx * sigmaa/(1-sigmaa*sigmaa); ftype t0 = 1.0/(1-sigmaa*sigmaa) + 0.5*log((1-sigmaa*sigmaa)); ftype t1 = sigmaa; ftype t2 = pow(1-sigmaa*sigmaa,2)/(1+sigmaa*sigmaa); if ( ih.hkl_class().centric() ) { result.r = 1.0*t0 - log( cosh( x/2 ) ); result.dr = 1.0*t1 - dx*0.5*tanh( x/2 ); result.dr2 = 1.0*t2 - dx*dx*0.25*(1.0 - pow(tanh(x/2),2) ); } else { result.r = 2.0*t0 - Util::sim_integ( x ); result.dr = 2.0*t1 - dx*Util::sim( x ); result.dr2 = 2.0*t2 - dx*dx*Util::sim_deriv( x ); } ftype ds = (1+sigmaa*sigmaa)/pow(1-sigmaa*sigmaa,2); ftype ds2 = 2*sigmaa*(3+sigmaa*sigmaa)/pow(1-sigmaa*sigmaa,3); result.dr2 = result.dr*ds2 + result.dr2*ds*ds; result.dr = result.dr*ds; } return result; } } // namespace clipper #endif clipper-2.1/clipper/core/coords.h0000644000374100011300000011454211252436042013763 00000000000000/*! \file lib/coords.h Fundamental types for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_COORDS #define CLIPPER_COORDS #include "cell.h" #include "spacegroup.h" #include "clipper_stats.h" namespace clipper { // forward definitions class Grid; class Grid_sampling; class Grid_range; class Coord_grid; class Coord_map; class Coord_reci_frac; class Coord_reci_orth; class Coord_frac; class Coord_orth; class U_aniso_frac; class U_aniso_orth; //! Resolution in angstroms /*! This object represents a resolution limit which will be used for all aspects of a calculation. This is a base for a donor type. */ class Resolution { public: inline Resolution() : resol(0.0) {} //!< null constructor explicit Resolution( const ftype& resol_ ); //!< constructor: from ftype void init( const ftype& resol_ ); //!< initialiser: from ftype const ftype& limit() const; //!< get resolution limit ftype invresolsq_limit() const; //!< get invresolsq limit bool is_null() const; //!< test if value has been initialised private: ftype resol; }; //! reflection class /*! This describes the type of a reflection in a given spacegroup, including centricity, systematic absence, phase restriction, and multiplicity. */ class HKL_class { public: //! null constructor inline HKL_class() { epsilon_ = 0; allowed_ = 255; } //! constructor - from spacegroup and HKL HKL_class( const Spacegroup& spgr, const HKL& hkl ); //! get epsilon inline ftype epsilon() const { return ftype(epsilon_); } //! get epsilon for acentric, 2x epsilon for centric inline ftype epsilonc() const { if ( centric() ) return 2.0*ftype(epsilon_); else return ftype(epsilon_); } //! get allowed phase inline ftype allowed() const { return ftype(allowed_) * (Util::pi()/12.0); } inline bool centric() const { return allowed_ != 255; } //!< is centric? inline bool sys_abs() const { return epsilon_ == 0; } //!< is sys abs? private: unsigned char epsilon_, allowed_; }; //! Orthogonal operator class. /*! This class is used for any RT-operator which operates on orthogonal coordinates. For a full list of methods, see clipper::RTop */ class RTop_orth : public RTop<> { public: //! null constructor inline RTop_orth() {} //! constructor: copy/convert inline explicit RTop_orth( const RTop<>& o ) : RTop<>( o ) {} //! constructor: from rotation inline explicit RTop_orth( const Mat33<>& r ) : RTop<>( r ) {} //! constructor: from rotation and translation inline RTop_orth( const Mat33<>& r, const Vec3<>& t ) : RTop<>( r, t ) {} //! constructor: from two vectors of Coord_orth RTop_orth( const std::vector& src, const std::vector& tgt ); //! constructor: from two vectors of Coord_orth RTop_orth( const std::vector& src, const std::vector& tgt, const std::vector& wgt ); //! constructor: from two atom-list type objects template RTop_orth( const T& src, const T& tgt ); //! orthogonal-fractional conversion RTop_frac rtop_frac( const Cell& cell ) const; //! inverse operator RTop_orth inverse() const; //! return point on axis near the specified coordinate Coord_orth axis_coordinate_near( const Coord_orth& centre ) const; //! return screw translation Coord_orth screw_translation() const; //! return identity operator static RTop_orth identity(); //! return null (uninitialised) operator static RTop_orth null(); }; //! reflection 'Miller' index class HKL : public Vec3 { public: inline HKL() {} //!< null constructor inline explicit HKL( const Vec3& v ) : Vec3( v ) {} //!< constructor: copy/convert inline HKL( const int& h, const int& k, const int& l ) : Vec3( h, k, l ) {} //!< constructor: from H,K,L inline const int& h() const { return (*this)[0]; } //!< get h inline const int& k() const { return (*this)[1]; } //!< get k inline const int& l() const { return (*this)[2]; } //!< get l inline int& h() { return (*this)[0]; } //!< set h inline int& k() { return (*this)[1]; } //!< set k inline int& l() { return (*this)[2]; } //!< set l //! return inverse resolution squared for this reflection in given cell inline ftype invresolsq( const Cell& cell ) const; //! return fractional reciprocal coordinate (i.e. non-integer HKL) inline Coord_reci_frac coord_reci_frac() const; //! orthogonal-fractional reciprocal space coordinate conversion inline Coord_reci_orth coord_reci_orth( const Cell& cell ) const; //! return transformed hkl inline HKL transform( const Symop& op ) const; //! return transformed hkl inline HKL transform( const Isymop& op ) const; //! return symmetry phase shift for this HKL under op inline ftype sym_phase_shift( const Symop& op ) const; String format() const; //!< return formatted String representation friend inline HKL operator -(const HKL& h1) { return HKL( -h1.h(), -h1.k(), -h1.l() ); } friend inline HKL operator +(const HKL& h1, const HKL& h2) { return HKL( h1.h()+h2.h(), h1.k()+h2.k(), h1.l()+h2.l() ); } friend inline HKL operator -(const HKL& h1, const HKL& h2) { return HKL( h1.h()-h2.h(), h1.k()-h2.k(), h1.l()-h2.l() ); } friend inline HKL operator *(const int& s, const HKL& h1) { return HKL( s*h1.h(), s*h1.k(), s*h1.l() ); } friend inline HKL operator *(const Isymop& op, const HKL& h1) { return HKL( h1 * op.rot() ); } }; //! orthogonal reciprocal coordinate (length of which is invresolsq) class Coord_reci_orth : public Vec3<> { public: inline Coord_reci_orth() {} //!< null constructor inline explicit Coord_reci_orth( const Vec3<>& v ) : Vec3<>( v ) {} //!< constructor: copy/convert inline Coord_reci_orth( const ftype& xs, const ftype& ys, const ftype& zs ) : Vec3<>( xs, ys, zs ) {} //!< constructor: from x*,y*,z* inline const ftype& xs() const { return (*this)[0]; } //!< get x* inline const ftype& ys() const { return (*this)[1]; } //!< get y* inline const ftype& zs() const { return (*this)[2]; } //!< get z* //! return inverse resolution squared for this coord inline ftype invresolsq() const; //! orthogonal-fractional reciprocal space coordinate conversion inline Coord_reci_frac coord_reci_frac( const Cell& cell ) const; //! return transformed coordinate inline Coord_reci_orth transform( const RTop_orth& op ) const { return Coord_reci_orth( (*this) * op.rot() ); } String format() const; //!< return formatted String representation }; //! fractional reciprocal coordinate (i.e. non-integer hkl) class Coord_reci_frac : public Vec3<> { public: inline Coord_reci_frac() {} //!< null constructor inline explicit Coord_reci_frac( const Vec3<>& v ) : Vec3<>( v ) {} //!< constructor: copy/convert inline Coord_reci_frac( const ftype& us, const ftype& vs, const ftype& ws ) : Vec3<>( us, vs, ws ) {} //!< constructor: from u,v,w //! constructor: from HKL inline Coord_reci_frac( const HKL& hkl ) : Vec3<>( ftype(hkl[0]), ftype(hkl[1]), ftype(hkl[2]) ) {} //! round to HKL inline HKL hkl() const { return HKL( Util::intr(us()), Util::intr(vs()), Util::intr(ws()) ); } //! return inverse resolution squared for this reflection in given cell inline ftype invresolsq( const Cell& cell ) const; inline const ftype& us() const { return (*this)[0]; } //!< get u* inline const ftype& vs() const { return (*this)[1]; } //!< get v* inline const ftype& ws() const { return (*this)[2]; } //!< get w* //! fractional-orthogonal reciprocal space coordinate conversion inline Coord_reci_orth coord_reci_orth( const Cell& cell ) const; //! return transformed coordinate inline Coord_reci_frac transform( const RTop_frac& op ) const { return Coord_reci_frac( (*this) * op.rot() ); } String format() const; //!< return formatted String representation }; //! Grid coordinate class Coord_grid : public Vec3 { public: inline Coord_grid() {} //!< null constructor //! constructor: copy/convert inline explicit Coord_grid( const Vec3 v ) : Vec3( v ) {} //! constructor: from u,v,w inline Coord_grid( const int& u, const int& v, const int& w ) : Vec3(u,v,w) {} //! constructor: from a grid and an index in that grid inline Coord_grid( const Grid& g, const int& index ) { deindex( g, index ); } inline const int& u() const { return (*this)[0]; } //!< get u inline const int& v() const { return (*this)[1]; } //!< get v inline const int& w() const { return (*this)[2]; } //!< get w inline int& u() { return (*this)[0]; } //!< set u inline int& v() { return (*this)[1]; } //!< set v inline int& w() { return (*this)[2]; } //!< set w //! convert to Coord_map inline Coord_map coord_map() const; //! convert to Coord_frac using given Grid_sampling inline Coord_frac coord_frac( const Grid_sampling& g ) const; //! return transformed coordinate inline Coord_grid transform( const Isymop& op ) const { return op * (*this); } //! reduce to unit box: (0..nu-1, 0..nv-1, 0..nw-1) inline Coord_grid unit( const Grid_sampling& g ) const; //! increment in storage order (see index()) /*! guaranteed to increment index(g) by 1 */ inline const Coord_grid& next( const Grid& g ); //! increment in storage order (see index()) /*! guaranteed to increment index(g) by 1 */ inline const Coord_grid& next( const Grid_range& g ); //! test if done in storage order (see index()) inline bool last( const Grid& g ) const; //! test if done in storage order (see index()) inline bool last( const Grid_range& g ) const; //! grid indexing operator inline int index( const Grid& g ) const; //! grid deindexing operator inline void deindex( const Grid& g, const int& index ); // grid indexing operator //inline int index( const Grid_range& g ) const; // grid deindexing operator //inline void deindex( const Grid_range& g, const int& index ); String format() const; //!< return formatted String representation friend inline Coord_grid operator -(const Coord_grid& r1) { return ( Coord_grid( -r1.u(), -r1.v(), -r1.w() ) ); } friend inline Coord_grid operator +(const Coord_grid& r1, const Coord_grid& r2) { return ( Coord_grid( r1.u()+r2.u(), r1.v()+r2.v(), r1.w()+r2.w() ) ); } friend inline Coord_grid operator -(const Coord_grid& r1, const Coord_grid& r2) { return ( Coord_grid( r1.u()-r2.u(), r1.v()-r2.v(), r1.w()-r2.w() ) ); } friend inline Coord_grid operator *(const int& s, const Coord_grid& r1) { return ( Coord_grid( s*r1.u(), s*r1.v(), s*r1.w() ) ); } friend inline int operator == (const Coord_grid& r1, const Coord_grid& r2) { return (r1.u()==r2.u() && r1.v()==r2.v() && r1.w()==r2.w()); } friend inline int operator != (const Coord_grid& r1, const Coord_grid& r2) { return (r1.u()!=r2.u() || r1.v()!=r2.v() || r1.w()!=r2.w()); } friend inline Coord_grid operator *(const Isymop& op, const Coord_grid& r1) { return Coord_grid( op.rot() * r1 + op.trn() ); } }; //! orthogonal (Angstrom) coordinates class Coord_orth : public Vec3<> { public: inline Coord_orth() {} //!< null constructor inline explicit Coord_orth( const Vec3<>& v ) : Vec3<>( v ) {} //!< constructor: copy/convert inline Coord_orth( const ftype& x, const ftype& y, const ftype& z ) : Vec3<>( x, y, z ) {} //!< constructor: from x,y,z //! constructor: from 3 coords and bond length, angle, torsion Coord_orth( const Coord_orth& x1, const Coord_orth& x2, const Coord_orth& x3, const ftype& length, const ftype& angle, const ftype& torsion ); inline const ftype& x() const { return (*this)[0]; } //!< get x inline const ftype& y() const { return (*this)[1]; } //!< get y inline const ftype& z() const { return (*this)[2]; } //!< get z //! return square of length of vector in Angstroms inline ftype lengthsq() const; //! orthogonal-fractional coordinate conversion inline Coord_frac coord_frac( const Cell& cell ) const; //! return transformed coordinate inline Coord_orth transform( const RTop_orth& op ) const { return op*(*this); } String format() const; //!< return formatted String representation //! Return length of vector between two coord orths static ftype length( const Coord_orth& x1, const Coord_orth& x2); //! Return angle between three coord orths static ftype angle( const Coord_orth& x1, const Coord_orth& x2, const Coord_orth& x3); //! Return torsion between four coord orths static ftype torsion( const Coord_orth& x1, const Coord_orth& x2, const Coord_orth& x3, const Coord_orth& x4); friend inline Coord_orth operator -(const Coord_orth& x1) { return Coord_orth( -x1.x(), -x1.y(), -x1.z() ); } friend inline Coord_orth operator +(const Coord_orth& x1, const Coord_orth& x2) { return Coord_orth( x1.x()+x2.x(), x1.y()+x2.y(), x1.z()+x2.z() ); } friend inline Coord_orth operator -(const Coord_orth& x1, const Coord_orth& x2) { return Coord_orth( x1.x()-x2.x(), x1.y()-x2.y(), x1.z()-x2.z() ); } friend inline Coord_orth operator *(const ftype& s, const Coord_orth& x1) { return Coord_orth( s*x1.x(), s*x1.y(), s*x1.z() ); } friend inline Coord_orth operator *(const RTop_orth& op, const Coord_orth& x1) { return Coord_orth( op.rot() * x1 + op.trn() ); } }; //! fractional (cell) coordinates class Coord_frac : public Vec3<> { public: inline Coord_frac() {} //!< null constructor inline explicit Coord_frac( const Vec3<>& v ) : Vec3<>( v ) {} //!< constructor: copy/convert inline Coord_frac( const ftype& u, const ftype& v, const ftype& w ) : Vec3<>( u, v, w ) {} //!< constructor: from u,v,w inline const ftype& u() const { return (*this)[0]; } //!< get u inline const ftype& v() const { return (*this)[1]; } //!< get v inline const ftype& w() const { return (*this)[2]; } //!< get w //! return square of length of vector in Angstroms inline ftype lengthsq( const Cell& cell ) const; //! fractional-orthogonal coordinate conversion inline Coord_orth coord_orth( const Cell& cell ) const; //! fractional-grid coordinate conversion inline Coord_map coord_map( const Grid& g ) const; //! fractional-grid coordinate conversion inline Coord_grid coord_grid( const Grid& g ) const; //! return transformed coordinate inline Coord_frac transform( const RTop_frac& op ) const { return op*(*this); } //! return lattice copy nearest origin inline Coord_frac lattice_copy_zero() const { return Coord_frac(u()-rint(u()),v()-rint(v()),w()-rint(w())); } //! return lattice copy in unit box (0...1,0...1,0...1) inline Coord_frac lattice_copy_unit() const { return Coord_frac(u()-floor(u()),v()-floor(v()),w()-floor(w())); } //! return lattice copy near the specified coordinate inline Coord_frac lattice_copy_near(const Coord_frac& n) const { return (*this-n).lattice_copy_zero()+n; } //! return symmetry copy near the specified coordinate Coord_frac symmetry_copy_near(const Spacegroup& spgr, const Cell& cell, const Coord_frac& n) const; String format() const; //!< return formatted String representation friend inline Coord_frac operator -(const Coord_frac& u1) { return Coord_frac( -u1.u(), -u1.v(), -u1.w() ); } friend inline Coord_frac operator +(const Coord_frac& u1, const Coord_frac& u2) { return Coord_frac( u1.u()+u2.u(), u1.v()+u2.v(), u1.w()+u2.w() ); } friend inline Coord_frac operator -(const Coord_frac& u1, const Coord_frac& u2) { return Coord_frac( u1.u()-u2.u(), u1.v()-u2.v(), u1.w()-u2.w() ); } friend inline Coord_frac operator *(const ftype& s, const Coord_frac& u1) { return Coord_frac( s*u1.u(), s*u1.v(), s*u1.w() ); } friend inline Coord_frac operator *(const RTop_frac& op, const Coord_frac& x1) { return Coord_frac( op.rot() * x1 + op.trn() ); } }; //! map coordinate: this is like Coord_grid, but non-integer class Coord_map : public Vec3<> { public: inline Coord_map() {} //!< null constructor //! constructor: copy/convert inline explicit Coord_map( const Vec3<>& v ) : Vec3<>( v ) {} //! constructor: from Coord_grid inline explicit Coord_map( const Coord_grid& c ) : Vec3<>( ftype(c[0]), ftype(c[1]), ftype(c[2]) ) {} //! constructor: from u,v,w inline Coord_map( const ftype& u, const ftype& v, const ftype& w ) : Vec3<>( u, v, w ) {} //! grid-fractional coordinate conversion inline Coord_frac coord_frac( const Grid& g ) const; //! return integer Coord_grid nearest this coordinate inline Coord_grid coord_grid() const { return Coord_grid( Util::intr((*this)[0]), Util::intr((*this)[1]), Util::intr((*this)[2]) ); } //! return integer Coord_grid below this coordinate inline Coord_grid floor() const { return Coord_grid( Util::intf((*this)[0]), Util::intf((*this)[1]), Util::intf((*this)[2]) ); } //! return integer Coord_grid above this coordinate inline Coord_grid ceil() const { return Coord_grid( Util::intc((*this)[0]), Util::intc((*this)[1]), Util::intc((*this)[2]) ); } inline const ftype& u() const { return (*this)[0]; } //!< get u inline const ftype& v() const { return (*this)[1]; } //!< get v inline const ftype& w() const { return (*this)[2]; } //!< get w String format() const; //!< return formatted String representation friend inline Coord_map operator -(const Coord_map& u1) { return Coord_map( -u1.u(), -u1.v(), -u1.w() ); } friend inline Coord_map operator +(const Coord_map& u1, const Coord_map& u2) { return Coord_map( u1.u()+u2.u(), u1.v()+u2.v(), u1.w()+u2.w() ); } friend inline Coord_map operator -(const Coord_map& u1, const Coord_map& u2) { return Coord_map( u1.u()-u2.u(), u1.v()-u2.v(), u1.w()-u2.w() ); } friend inline Coord_map operator *(const ftype& s, const Coord_map& u1) { return Coord_map( s*u1.u(), s*u1.v(), s*u1.w() ); } }; //! Anisotropic orthogonal atomic displacement parameters /*! These are defined on orthogonal atomic coordinates in A-2, i.e. they are anisotropic U values. */ class U_aniso_orth : public Mat33sym<> { public: //! null constructor inline U_aniso_orth() {}; //! constructor: from Mat33sym inline explicit U_aniso_orth( const Mat33sym<>& m ) : Mat33sym<>(m) {} //! constructor: from isotropic U inline explicit U_aniso_orth( const ftype& u ) : Mat33sym<>( u, u, u, 0.0, 0.0, 0.0 ) {} //! constructor: from Uij U_aniso_orth( const ftype& u11, const ftype& u22, const ftype& u33, const ftype& u12, const ftype& u13, const ftype& u23 ) : Mat33sym<>( u11, u22, u33, u12, u13, u23 ) {} //! return nearest isotropic U ftype u_iso() const; //! orthogonal-fractional conversion U_aniso_frac u_aniso_frac( const Cell& cell ) const; //! return transformed U_aniso U_aniso_orth transform( const RTop_orth& op ) const; friend U_aniso_orth operator +(const U_aniso_orth& u1, const U_aniso_orth& u2) { return U_aniso_orth( u1.mat00()+u2.mat00(), u1.mat11()+u2.mat11(), u1.mat22()+u2.mat22(), u1.mat01()+u2.mat01(), u1.mat02()+u2.mat02(), u1.mat12()+u2.mat12() ); } friend U_aniso_orth operator -(const U_aniso_orth& u) { return U_aniso_orth( -u.mat00(), -u.mat11(), -u.mat22(), -u.mat01(), -u.mat02(), -u.mat12() ); } friend U_aniso_orth operator *(const ftype& s, const U_aniso_orth& u) { return U_aniso_orth( s*u.mat00(), s*u.mat11(), s*u.mat22(), s*u.mat01(), s*u.mat02(), s*u.mat12() ); } }; //! Anisotropic fractional atomic displacement parameters /*! These are defined on fractional atomic coordinates in A-2, i.e. they are anisotropic U values. */ class U_aniso_frac : public Mat33sym<> { public: //! null constructor inline U_aniso_frac() {}; //! constructor: from Mat33sym inline explicit U_aniso_frac( const Mat33sym<>& m ) : Mat33sym<>(m) {} //! constructor: from Uij U_aniso_frac( const ftype& u11, const ftype& u22, const ftype& u33, const ftype& u12, const ftype& u13, const ftype& u23 ) : Mat33sym<>( u11, u22, u33, u12, u13, u23 ) {} //! fractional-orthogonal conversion U_aniso_orth u_aniso_orth( const Cell& cell ) const; //! return transformed U_aniso U_aniso_frac transform( const RTop_frac& op ) const; friend U_aniso_frac operator +(const U_aniso_frac& u1, const U_aniso_frac& u2) { return U_aniso_frac( u1.mat00()+u2.mat00(), u1.mat11()+u2.mat11(), u1.mat22()+u2.mat22(), u1.mat01()+u2.mat01(), u1.mat02()+u2.mat02(), u1.mat12()+u2.mat12() ); } friend U_aniso_frac operator -(const U_aniso_frac& u) { return U_aniso_frac( -u.mat00(), -u.mat11(), -u.mat22(), -u.mat01(), -u.mat02(), -u.mat12() ); } friend U_aniso_frac operator *(const ftype& s, const U_aniso_frac& u) { return U_aniso_frac( s*u.mat00(), s*u.mat11(), s*u.mat22(), s*u.mat01(), s*u.mat02(), s*u.mat12() ); } }; //! generic grid /*! This holds the dimensions of a 3D array, indexed from 0 along each dimension. */ class Grid : public Vec3 { public: inline Grid() {} //!< null constructor inline Grid( const int& nu, const int& nv, const int& nw ) : Vec3( nu, nv, nw ) {} //!< constructor: from nu,nv,nw inline const int& nu() const { return (*this)[0]; } //!< get nu inline const int& nv() const { return (*this)[1]; } //!< get nv inline const int& nw() const { return (*this)[2]; } //!< get nw //! return size of grid array inline int size() const { return nu()*nv()*nw(); } //! determine if a point is in the grid inline bool in_grid( Coord_grid g ) const { return (g.u() >= 0 && g.u() < nu() && g.v() >= 0 && g.v() < nv() && g.w() >= 0 && g.w() < nw()); } //! grid indexing operator inline int index( const Coord_grid& c ) const { return c.index(*this); } //! grid deindexing operator inline Coord_grid deindex( const int& index ) const { return Coord_grid( *this, index ); } String format() const; //!< return formatted String representation void debug() const; }; //! Grid sampling of a unit cell /*! This class represents the grid sampling of a unit cell. It is otherwise identical to its parent, clipper::Grid_cell, but has an additional constructor which takes a spacegroup, cell and resolution and produces an appropriate grid obeying all of the symmetry constraints, and using efficient factors for the calculation of FFTs. \note The following methods are inherited from Grid and Grid_cell but are documented here for convenience: nu(), nv(), nw(), size(), index(), deindex(), format(), coord_frac(), coord_grid(), to_unit(). */ class Grid_sampling : public Grid { public: //! null constructor inline Grid_sampling() : Grid(Grid(0,0,0)) {} //! constructor: from nu, nv, nw inline Grid_sampling( const int& nu, const int& nv, const int& nw ) : Grid( nu, nv, nw ) {} //! constructor: from Spacegroup, Cell, Resolution, Shannon rate Grid_sampling( const Spacegroup& spacegroup, const Cell& cell, const Resolution& resol, const ftype rate = 1.5 ); //! initialiser: from Spacegroup, Cell, Resolution, Shannon rate void init( const Spacegroup& spacegroup, const Cell& cell, const Resolution& resol, const ftype rate = 1.5 ); //! return matrix which converts grid to fractional coordinates Mat33<> matrix_grid_frac() const; //! return matrix which converts fractional to grid coordinates Mat33<> matrix_frac_grid() const; //! test if object has been initialised bool is_null() const; // inherited functions listed for documentation purposes //-- const int& nu() const; //-- const int& nv() const; //-- const int& nw() const; //-- int size() const; //-- int index( const Coord_grid& c ) const; //-- Coord_grid deindex( const int& index ) const; //-- const String format() const; }; //! HKL sampling of reciprocal space /*! The HKL_sampling class uniquely describes a P0 reflection list bounded by some resolution limit in reciprocal space. It is described in terms of large integers, and so immune from rounding errors once the object is constructed. */ class HKL_sampling { public: //! null constructor HKL_sampling(); //!< Null constructor //! constructor: takes parameters of normal or inverse cell HKL_sampling( const Cell& cell, const Resolution& resolution ); //! return limiting values of H, K, L HKL hkl_limit() const; //! return approximate resolution given cell Resolution resolution( const Cell& cell ) const; //! test if a reflection is within the resolution limit inline bool in_resolution( const HKL& h ) const { return ( m00*itype64(h.h()*h.h()) + m11*itype64(h.k()*h.k()) + m22*itype64(h.l()*h.l()) + m01*itype64(h.h()*h.k()) + m02*itype64(h.h()*h.l()) + m12*itype64(h.k()*h.l()) ) <= ( sqrt_limit_value*sqrt_limit_value ); } //! test if object has been initialised bool is_null() const; String format() const; //!< return formatted String representation friend inline int operator == (const HKL_sampling& h1, const HKL_sampling& h2) { return ( h1.m00==h2.m00 && h1.m11==h2.m11 && h1.m22==h2.m22 && h1.m01==h2.m01 && h1.m02==h2.m02 && h1.m12==h2.m12 ); } private: static itype64 sqrt_limit_value; itype64 m00, m11, m22, m01, m02, m12; }; //! Grid range class: defines array limits for a grid /*! This class is used for describing 3D grids covering an arbitrary part of the 3D space, i.e. which do not start from (0,0,0). */ class Grid_range : public Grid { public: //! null constructor inline Grid_range() {} //! constructor: takes grid limits Grid_range( const Coord_grid& min, const Coord_grid& max ); //! constructor: takes cell grid and fractional limits Grid_range( const Grid& grid, const Coord_frac& min, const Coord_frac& max ); //! constructor: make grid to hold a sphere from cell, grid, radius Grid_range( const Cell& cell, const Grid& grid, const ftype& radius ); //! access grid limits const Coord_grid& min() const { return min_; } //! access grid limits const Coord_grid& max() const { return max_; } //! border: increase grid to include given border void add_border( const int b ); //! determine if a point is in the grid bool in_grid( Coord_grid g ) const { return (g.u() >= min_.u() && g.u() <= max_.u() && g.v() >= min_.v() && g.v() <= max_.v() && g.w() >= min_.w() && g.w() <= max_.w()); } //! grid indexing operator int index( const Coord_grid& c ) const { return (c - min_).index(*this); } //! grid deindexing operator Coord_grid deindex( const int& index ) const { return Coord_grid( *this, index ) + min_; } private: Coord_grid min_, max_; }; //! Obsolete form for Grid_range typedef Grid_range Grid_map; //! Atom class /*! This class defines a minimal atom object providing only those properties required for an electron density calculation. A template constructor allows it to be constructed from any other object with appropriate properties. */ class Atom { public: //! null constructor Atom() {} //! Constructor: from atom-like object template Atom( const T& atom ) : element_(atom.element()), coord_orth_(atom.coord_orth()), u_aniso_orth_(atom.u_aniso_orth()) , occupancy_(atom.occupancy()), u_iso_(atom.u_iso()){} //! get atom element name: e.g. "C", "N", "Zn2+" const String& element() const { return element_; } //! get atom orthogonal (Angstrom) coordinate const Coord_orth& coord_orth() const { return coord_orth_; } //! get atom occupancy const ftype& occupancy() const { return occupancy_; } //! get atom orthogonal isotropic U value const ftype& u_iso() const { return u_iso_; } //! get atom orthogonal anisotropic U value const U_aniso_orth& u_aniso_orth() const { return u_aniso_orth_; } void set_element( const String& s ); //!< set element void set_coord_orth( const Coord_orth& s ); //!< set coord_orth void set_occupancy( const ftype& s ); //!< set occupancy void set_u_iso( const ftype& s ); //!< set u_iso void set_u_aniso_orth( const U_aniso_orth& s ); //!< set u_aniso //! apply a rotation-translation operator (RTop) to the atom void transform( const RTop_orth rt ); //! test for null atom: atom is null is coord is null bool is_null() const { return coord_orth_.is_null(); } //! return null atom static Atom null(); private: String element_; Coord_orth coord_orth_; U_aniso_orth u_aniso_orth_; ftype occupancy_, u_iso_; }; //! Atom list class /*! This class defines a minimal atom list object providing only those properties required for an electron density calculation. It is a trivial derivation from std::vector. In addition a template constructor allows it to be constructed from any other object with appropriate properties. */ class Atom_list : public std::vector { public: //! null constructor Atom_list() {} //! constructor: from std::vector Atom_list( const std::vector& list ) : std::vector( list ) {} //! Constructor: from vector-like list of atom-like objects template Atom_list( const T& list ) { for ( int i = 0; i < list.size(); i++ ) push_back( Atom( list[i] ) ); } }; // some template function definitions /*! Construct the operator which relates one atom-list like object onto another. The lists must be the same size, and have the following properties: - a size() method. - a [int] operator, with int ranging from 0 to size()-1. - the object returned by the [] operator must have a coord_orth() method. Suitable objects include a vector of Atom, or an Atom_list. */ template RTop_orth::RTop_orth( const T& src, const T& tgt ) { std::vector vsrc( src.size() ); std::vector vtgt( tgt.size() ); for ( int i = 0; i < src.size(); i++ ) vsrc[i] = src[i].coord_orth(); for ( int i = 0; i < tgt.size(); i++ ) vtgt[i] = tgt[i].coord_orth(); (*this) = RTop_orth( vsrc, vtgt ); } // some inline function definitions /*! Requires integer->ftype->integer transformation. \param op The symmetry operator \return The transformed coordinate */ HKL HKL::transform( const Symop& op ) const { return Coord_reci_frac(*this).transform(op).hkl(); } /*! Optimal version. \param op The symmetry operator \return The transformed coordinate */ HKL HKL::transform( const Isymop& op ) const { return op*(*this); } /*! Get the symmetry phase shift incurred when transforming a reflection by this operator. \param hkl The reflection HKL to transform. \return The phase shift. */ ftype HKL::sym_phase_shift( const Symop& op ) const { return -Util::twopi()*( Coord_reci_frac(*this) * op.trn() ); } /*! The grid coordinate is incremented efficiently in a manner which is exaclty equivalent to increasing index() by 1 in a zero based grid. \param g The grid with which this increment is synchronised. */ const Coord_grid& Coord_grid::next( const Grid& g ) { w()++; if ( w() >= g.nw() ) { w() = 0; v()++; if ( v() >= g.nv() ) { v() = 0; u()++; } } return *this; } /*! The grid coordinate is incremented efficiently in a manner which is exaclty equivalent to increasing index() by 1 in a non-zero based grid. \param g The grid with which this increment is synchronised. */ const Coord_grid& Coord_grid::next( const Grid_range& g ) { w()++; if ( w() > g.max().w() ) { w() = g.min().w(); v()++; if ( v() > g.max().v() ) { v() = g.min().v(); u()++; } } return *this; } /*! Test whether this coordinate has been incremented using next() beyond the end of the specified zero based grid. \param g The grid concerned. */ bool Coord_grid::last( const Grid& g ) const { return ( u() >= g.nu() ); } /*! Test whether this coordinate has been incremented using next() beyond the end of the specified non-zero based grid. \param g The grid concerned. */ bool Coord_grid::last( const Grid_range& g ) const { return ( u() > g.max().u() ); } /*! Return the index in a 1-d array corresponding to this coordinate for a zero based grid. \param g The grid concerned. \return The corresponding index. */ int Coord_grid::index( const Grid& g ) const { return ( u()*g.nv() + v() )*g.nw() + w(); } /*! Return the coordinate corresponding to a given index in a zero based grid. \param g The grid concerned. \return The corresponding coordinate. */ void Coord_grid::deindex( const Grid& g, const int& index ) { u() = index/(g.nv()*g.nw()); v() = (index/g.nw()) % g.nv(); w() = (index) % g.nw(); } /*! \param g The grid concerned \return The transformed coordinate. */ Coord_grid Coord_grid::unit( const Grid_sampling& g ) const { return Coord_grid( Util::mod(u(), g.nu()), Util::mod(v(), g.nv()), Util::mod(w(), g.nw()) ); } /*! \return The non-integer coordinate. */ Coord_map Coord_grid::coord_map() const { return Coord_map( *this ); } /*! Fractional coordinate is not normalised onto range 0..1 \param g The grid concerned \return The fractional coordinate */ Coord_frac Coord_grid::coord_frac( const Grid_sampling& g ) const { return Coord_frac( ftype(u())/ftype(g.nu()), ftype(v())/ftype(g.nv()), ftype(w())/ftype(g.nw()) ); } /*! \note Normally you would get a value through clipper::HKL_info, unless you specifically want a value for a different cell. */ ftype HKL::invresolsq( const Cell& cell ) const { return cell.metric_reci().lengthsq( Coord_reci_frac( *this ) ); } /*! \return The non-integer coordinate. */ Coord_reci_frac HKL::coord_reci_frac() const { return Coord_reci_frac( *this ); } /*! \param cell The cell concerned \return The transformed coordinate. */ Coord_reci_orth HKL::coord_reci_orth( const Cell& cell ) const { return coord_reci_frac().coord_reci_orth( cell ); } /*! \return The inverse resolution squared. */ ftype Coord_reci_orth::invresolsq() const { return xs()*xs() + ys()*ys() + zs()*zs(); } /*! \param cell The cell concerned \return The transformed coordinate. */ Coord_reci_frac Coord_reci_orth::coord_reci_frac( const Cell& cell ) const { return Coord_reci_frac( (*this) * cell.matrix_orth() ); } /*! \param cell The cell concerned \return The inverse resolution squared. */ ftype Coord_reci_frac::invresolsq( const Cell& cell ) const { return cell.metric_reci().lengthsq( *this ); } /*! \param cell The cell concerned \return The transformed coordinate. */ Coord_reci_orth Coord_reci_frac::coord_reci_orth( const Cell& cell ) const { return Coord_reci_orth( (*this) * cell.matrix_frac() ); } /*! \return The squared length in Angstroms squared */ ftype Coord_orth::lengthsq() const { return x()*x()+y()*y()+z()*z(); } /*! \param cell The cell concerned \return The transformed coordinate. */ Coord_frac Coord_orth::coord_frac( const Cell& cell ) const { return Coord_frac( cell.matrix_frac() * (*this) ); } /*! \return The squared length in Angstroms squared */ ftype Coord_frac::lengthsq( const Cell& cell ) const { return cell.metric_real().lengthsq( *this ); } /*! \param cell The cell concerned \return The transformed coordinate. */ Coord_orth Coord_frac::coord_orth( const Cell& cell ) const { return Coord_orth( cell.matrix_orth() * (*this) ); } /*! \param g The grid concerned \return The transformed coordinate. */ Coord_map Coord_frac::coord_map( const Grid& g ) const { return Coord_map( u()*ftype(g.nu()), v()*ftype(g.nv()), w()*ftype(g.nw()) ); } /*! \param g The grid concerned \return The transformed coordinate. */ Coord_grid Coord_frac::coord_grid( const Grid& g ) const { return Coord_grid( Util::intr(u()*ftype(g.nu())), Util::intr(v()*ftype(g.nv())), Util::intr(w()*ftype(g.nw())) ); } /*! \param g The grid concerned \return The transformed coordinate. */ Coord_frac Coord_map::coord_frac( const Grid& g ) const { return Coord_frac( u()/ftype(g.nu()), v()/ftype(g.nv()), w()/ftype(g.nw()) ); } } // namespace clipper #endif clipper-2.1/clipper/core/container_hkl.cpp0000644000374100011300000001205310363703537015647 00000000000000/* container_hkl.cpp: class file for reflection data containers */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "container_hkl.h" namespace clipper { const HKL_info NullHKL_info; //is_null() ) sp = parent_of_type_ptr(); if ( cp->is_null() ) cp = parent_of_type_ptr(); if ( rp->is_null() ) rp = parent_of_type_ptr(); generate_ = generate_ | generate; // update generate flag // initialise if ( sp != NULL && cp != NULL && rp != NULL ) if ( !sp->is_null() && !cp->is_null() && !rp->is_null() ) HKL_info::init( *sp, *cp, *rp, generate_ ); Container::update(); } /*! The reflection list is sythesized to match the given spacegroup, cell, and resolution, and a hierarchical update is triggered to update the sizes of the reflection lists for all dependent HKL_data objects. */ void CHKL_info::generate_hkl_list() { HKL_info::generate_hkl_list(); Container::update(); } /*! Hierarchical update. If this object is uninitialised, an attempt is made to initialise the object using information from its parents in the hierarchy. The childen of the object are then updated. */ void CHKL_info::update() { if ( HKL_info::is_null() ) init( NullSpacegroup, NullCell, NullResolution, 0.0 ); else Container::update(); } } // namespace clipper clipper-2.1/clipper/core/container.cpp0000644000374100011300000001612210363703537015012 00000000000000/* container.cpp: implementation for base class of reflection heirarchy */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "container.h" namespace clipper { Message_fatal message_parent_of_root( "Container: attempt to access parent of root" ); Message_fatal message_child_out_of_range( "Container: child index out of range" ); Message_fatal message_duplicate_path( "Container: attempt to create duplicate path" ); void Container::add_child( Container& c ) { children.push_back( &c ); } void Container::del_child( Container& c ) { for ( int i = 0; i < children.size(); i++ ) if ( children[i] == &c ) { children.erase( children.begin() + i ); break; } } void Container::update() { // recursively update entire tree for ( int i = 0; i < children.size(); i++ ) child(i).update(); } Container::Container( const String name ) { destroyed_with_parent = false; parent_ = NULL; if ( name != "" ) name_ = name; else name_ = "unnamed"; // log object if required if ( Message::message_level() <= Message_ctor::level() ) Message::message( Message_ctor( "[Container: contructed (root)/"+name_+">" ) ); } Container::Container( Container& parent, const String& path ) { destroyed_with_parent = false; parent_ = NULL; name_ = path.tail(); // find desired parent using working root and path provided parent_ = parent.find_path_ptr( path.notail() ); if ( parent_ == NULL ) Message::message( Message_fatal( "Container: No such path- "+path ) ); // if no name given, make one up if ( name_ == "" ) for (int i = 1; i < 100; i++ ) { name_ = "unnamed" + String(i,2); if ( parent_->find_path_ptr( name_ ) == NULL ) break; } // otherwise check for dulicates if ( parent_->find_path_ptr( name_ ) != NULL ) Message::message( message_duplicate_path ); parent_->add_child(*this); // log object if required if ( Message::message_level() <= Message_ctor::level() ) Message::message( Message_ctor( "[Container: contructed "+parent_->name()+"/"+name_+">" ) ); } Container::~Container() { for ( int i = 0; i < children.size(); i++ ) { children[i]->parent_ = NULL; if ( children[i]->is_destroyed_with_parent() ) delete children[i]; } if ( parent_ != NULL ) parent_->del_child(*this); // log object if required if ( Message::message_level() <= Message_dtor::level() ) Message::message( Message_dtor( "= children.size() ) Message::message( message_child_out_of_range ); return *children[i]; } Container& Container::child( const int& i ) { if ( i < 0 || i >= children.size() ) Message::message( message_child_out_of_range ); return *children[i]; } const Container& Container::ultimate_parent() const { if ( has_parent() ) return parent().ultimate_parent(); else return *this; } Container& Container::ultimate_parent() { if ( has_parent() ) return parent().ultimate_parent(); else return *this; } Container* Container::parent_ptr() { return parent_; } Container* Container::find_path_ptr( const String& path_ ) { // find an object in the heirarchy using UNIX path semantics String path = path_; // check for this object if ( path == "" ) return this; // check for root-ed path if ( path[0] == '/' ) { if ( has_parent() ) { return parent().find_path_ptr( path ); } else { path = path.nohead(); if ( path.head() != name() ) return NULL; path = path.nohead(); } } // check for a child of this object for ( int i = 0; i < num_children(); i++ ) if ( path.head() == "*" || path.head() == child(i).name() ) return child(i).find_path_ptr( path.nohead() ); // else fail return NULL; } void Container::move( const String& path ) { // move this object in heirarchy to 'path' if ( has_parent() ) parent().del_child( *this ); parent_ = find_path_ptr( path.notail() ); if ( parent_ == NULL ) Message::message( Message_fatal( "Container: No such path- "+path ) ); parent_->add_child( *this ); name_ = path.tail(); update(); } void Container::debug() { std::cout << path() << "\n"; for ( int i = 0; i < num_children(); i++ ) child(i).debug(); } } // namespace clipper clipper-2.1/clipper/core/resol_targetfn.cpp0000644000374100011300000000671311270270145016043 00000000000000/* resol_targetfn.cpp: implementation file for resolution target functions */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA /* This code is derived from the 'dm' source code */ #include "resol_targetfn.h" namespace clipper { template class TargetFn_meanFnth; template class TargetFn_meanFnth; template class TargetFn_scaleF1F2; template class TargetFn_scaleLogF1F2; template class TargetFn_scaleI1I2; template class TargetFn_scaleLogI1I2; template class TargetFn_meanEnth; template class TargetFn_scaleEsq; template class TargetFn_sigmaa_omegaa; template class TargetFn_sigmaa; template class TargetFn_meanFnth; template class TargetFn_meanFnth; template class TargetFn_scaleF1F2; template class TargetFn_scaleLogF1F2; template class TargetFn_scaleI1I2; template class TargetFn_scaleLogI1I2; template class TargetFn_meanEnth; template class TargetFn_scaleEsq; template class TargetFn_sigmaa_omegaa; template class TargetFn_sigmaa; } // namespace clipper clipper-2.1/clipper/core/resol_fn.cpp0000644000374100011300000003175011311437407014635 00000000000000/* resol_fn.cpp: implementation file for resolution functions */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA /* This code is derived from the 'dm' source code */ #include "resol_fn.h" namespace clipper { void TargetFn_base::debug( const HKL_info& hkl_info ) const { Rderiv r0, r1, r2; ftype d = 0.0001; for ( HKL_info::HKL_reference_index ih = hkl_info.first(); !ih.last(); ih.next() ) { if ( ih.index()%100 == 0 ) for ( ftype f = 0.1; f < 10; f*=3.15 ) { r0 = rderiv( ih, f - d ); r1 = rderiv( ih, f ); r2 = rderiv( ih, f + d ); std::cout << ih.hkl().format() << " " << f << " val " << r1.r << " grad " << r1.dr << " " << (r2.r-r0.r)/(2*d) << " curv " << r1.dr2 << " " << (r2.dr-r0.dr)/(2*d) << " " << (r2.r+r0.r-2*r1.r)/(d*d) << "\n"; } } } /*! Defaults to GENERAL, which will always work. If the basis function is linearly dependent on the parameters, override this with a function returning LINEAR for improved performance. See the provided basis functions for examples. \return The function type enumeration. */ BasisFn_base::FNtype BasisFn_base::type() const { return GENERAL; } /*! Defaults to 0, which will always work. If the basis function has compact support among the parameters, i.e. the value for any HKL depends only on a few parameters, then set this to the number of non-zero diagonals in the upper triangle of the matrix, i.e. 1 for a diagonal matrix, 2 for a tri-diagonal matrix etc. \return The number of non-zero upper diagonals, or zero for full-matrix. */ int BasisFn_base::num_diagonals() const { return 0; } /*! The target and its derivatives are calculated by the chain rule and accumulated over all HKLs. \param params Current value of parameters. \param r The value of the target function. \param drdp The derivative of the target function. \param drdp2 The curvature of the target function. */ void ResolutionFn::calc_derivs( const std::vector& params, ftype& r, std::vector& drdp, Matrix<>& drdp2 ) const { HKL_class cls; HKL_info::HKL_reference_index ih; TargetFn_base::Rderiv rderiv; ftype w; int j, k; int nparams = basisfn_->num_params(); int ndiag = basisfn_->num_diagonals() - 1; // zero the results r = 0.0; for ( j = 0; j < nparams; j++ ) { drdp[j] = 0.0; for ( k = 0; k < nparams; k++ ) drdp2(j,k) = 0.0; } // calc dr/dp vector and d2r/dp2 matrix for ( ih = hkl_info_->first(); !ih.last(); ih.next() ) { cls = ih.hkl_class(); rderiv = targetfn_->rderiv( ih, f( ih ) ); const BasisFn_base::Fderiv& fderiv = basisfn_->fderiv( ih.hkl(), cell_, params ); const std::vector& dfdp = fderiv.df; const Matrix<>& dfdp2 = fderiv.df2; // weight for this term w = 2.0 / cls.epsilonc(); // residual, gradient r += w * rderiv.r; for ( j = 0; j < nparams; j++ ) drdp[j] += w * rderiv.dr * dfdp[j]; // curvature: optimised for special cases if ( ndiag < 0 ) { // general case for ( j = 0; j < nparams; j++ ) for ( k = 0; k < nparams; k++ ) drdp2(j,k) += w * ( rderiv.dr2*dfdp[j]*dfdp[k] + rderiv.dr*dfdp2(j,k) ); } else { // curvature matrix is (2n-1)-diagonal for ( j = 0; j < nparams; j++ ) for ( k = Util::max(j-ndiag,0); k <= Util::min(j+ndiag,nparams-1); k++ ) drdp2(j,k) += w*( rderiv.dr2*dfdp[j]*dfdp[k] + rderiv.dr*dfdp2(j,k) ); } } } /*! The constructor performs the full minimisation calculation. \param hkl_info HKL_info object which provides the reflection list. \param basisfn The basis function used to describe the desired property. \param targetfn The target function to be minimised. \param params Initial values for the function parameters. \param damp_ If > 0.0, shifts are fdamped during early cycles to help convergence with difficult bases/target conbinations. */ ResolutionFn::ResolutionFn( const HKL_info& hkl_info, const BasisFn_base& basisfn, const TargetFn_base& targetfn, const std::vector& params, const ftype damp, const bool debug ) { ftype r, g0, g1, scale; int i, k, n; hkl_info_ = &hkl_info; basisfn_ = &basisfn; targetfn_ = &targetfn; params_ = params; cell_ = hkl_info.cell(); int nparams = basisfn_->num_params(); Matrix<> dfdp2( nparams, nparams ); Matrix<> drdp2( nparams, nparams ); std::vector drdp( nparams ), dfdp( nparams ); std::vector shiftn( nparams ); params_.resize( nparams ); // loop for 20 cycles refining the params g0 = 1.0e25; for ( n = 0; n < 20; n++ ) { // calc target fn and derivs calc_derivs( params_, r, drdp, drdp2 ); g1 = 0.0; for ( k = 0; k < nparams; k++ ) g1 += drdp[k]*drdp[k]; g1 = sqrt(g1); // stop if gradient starts increasing if ( g1 < 1.0e-10 || g1 >= g0 ) break; g0 = g1; // solve for Newton-Raphson shift shiftn = drdp2.solve( drdp ); // apply shift scale = (1.0+ftype(n)) / (1.0+ftype(n)+damp); for ( i = 0; i< nparams; i++ ) params_[i] -= scale*shiftn[i]; if ( debug ) std::cout << " Resolution function cycle " << n << " " << g0 << " " << g1 << " " << scale << "\n"; // stop if the target is quadratic if ( basisfn.type() == BasisFn_base::LINEAR && targetfn.type() == TargetFn_base::QUADRATIC ) break; } } /*! \return The refined basis function parameters */ const std::vector& ResolutionFn::params() const { return params_; } /*! The constructor performs the full minimisation calculation. \param hkl_info HKL_info object which provides the reflection list. \param basisfn The basis function used to describe the desired property. \param targetfn The target function to be minimised. \param damp_ If > 0.0, shifts are fdamped during early cycles to help convergence with difficult bases/target conbinations */ ResolutionFn_nonlinear::ResolutionFn_nonlinear( const HKL_info& hkl_info, const BasisFn_base& basisfn, const TargetFn_base& targetfn, const std::vector& params, const ftype damp, const bool debug ) { ftype r0, r1, w, scale, g, s, dotprod; HKL_class cls; HKL_info::HKL_reference_index ih; int i, j, k, n; hkl_info_ = &hkl_info; basisfn_ = &basisfn; targetfn_ = &targetfn; params_ = params; cell_ = hkl_info.cell(); int nparams = basisfn_->num_params(); Matrix<> dfdp2( nparams, nparams ); Matrix<> drdp2( nparams, nparams ); std::vector drdp( nparams ), dfdp( nparams ); std::vector shiftn( nparams ), shiftg( nparams ); std::vector params_old( nparams ); params_.resize( nparams ); // loop for 20 cycles refining the params for ( n = 0; n < 20; n++ ) { params_old = params_; // calc target fn and derivs calc_derivs( params_, r0, drdp, drdp2 ); // solve for Newton-Raphson shift shiftn = drdp2.solve( drdp ); // get step sizes and check direction g = s = dotprod = 0.0; for ( k = 0; k < nparams; k++ ) { g += drdp[k]*drdp[k]; s += shiftn[k]*shiftn[k]; dotprod += drdp[k]*shiftn[k]; } g = sqrt(g); s = sqrt(s); // make gradient shift to match NR shift for ( k = 0; k < nparams; k++ ) shiftg[k] = drdp[k] * s / g; // if NR shift opposes gradient, then ignore the NR shift if ( dotprod < 0.0 ) shiftn = shiftg; if ( debug ) { std::cout << "\nResolution function cycle: " << n << "\n"; if ( dotprod < 0.0 ) std::cout << " Using scaled grad " << s / g << "\n"; std::cout << " Gradient " << g << "\n"; for ( j = 0; j < nparams; j++ ) { for ( k = 0; k < nparams; k++ ) std::cout << " " << drdp2(j,k); std::cout << "\n"; } for ( k = 0; k < nparams; k++ ) std::cout << " " << k << " " << params_[k] << " " << drdp[k] << " " << shiftn[k] << "\n"; } // now try the step and if necessary reduce the shift scale = (1.0+ftype(n)) / (1.0+ftype(n)+damp); for ( j = 0; j < 20; j++ ) { for ( i = 0; i< nparams; i++ ) params_[i] = params_old[i] - scale*shiftn[i]; r1 = 0.0; for ( ih = hkl_info.first(); !ih.last(); ih.next() ) { cls = ih.hkl_class(); w = 2.0 / cls.epsilonc(); r1 += w * targetfn.rderiv( ih, f( ih ) ).r; } if ( Util::is_nan(r1) ) { scale *= 0.5; } else { scale *= 0.5; if ( (r1-r0) <= 0.0 ) break; } } if ( debug ) std::cout << " Resolution function cycle " << n << " " << r0 << " " << r1 << " " << scale << "\n"; if ( fabs( r1 - r0 ) < 1.0e-10 ) break; } } /* ResolutionFn( const HKL_info& hkl_info, const BasisFn_base& basisfn, const TargetFn_base& targetfn, const std::vector& params, const std::vector& targetval, const std::vector& targetwgt, const ftype damp = 0.0, const bool debug = false ); The constructor performs the full minimisation calculation. Additional parameters allow the function parameters to be restrained. \param hkl_info HKL_info object which provides the reflection list. \param basisfn The basis function used to describe the desired property. \param targetfn The target function to be minimised. \param params Initial values for the function parameters. \param targetval Target values for the function parameters. \param targetwgt Target sigmas for the function parameters. \param damp_ If > 0.0, shifts are fdamped during early cycles to help convergence with difficult bases/target conbinations. ResolutionFn::ResolutionFn( const HKL_info& hkl_info, const BasisFn_base& basisfn, const TargetFn_base& targetfn, const std::vector& params, const std::vector& targetval, const std::vector& targetwgt, const ftype damp, const bool debug ) { ftype r, g0, g1, scale; int i, k, n; hkl_info_ = &hkl_info; basisfn_ = &basisfn; targetfn_ = &targetfn; params_ = params; cell_ = hkl_info.cell(); int nparams = basisfn_->num_params(); Matrix<> dfdp2( nparams, nparams ); Matrix<> drdp2( nparams, nparams ); std::vector drdp( nparams ), dfdp( nparams ); std::vector shiftn( nparams ); params_.resize( nparams ); // loop for 20 cycles refining the params g0 = 1.0e25; for ( n = 0; n < 20; n++ ) { // calc target fn and derivs calc_derivs( params_, r, drdp, drdp2 ); // add parameter restraint terms for ( k = 0; k < nparams; k++ ) { ftype d = params[k] - targetval[k]; r += targetwgt[k] * d * d; drdp[k] += 2.0 * targetwgt[k] * d; drdp2(k,k) += 2.0 * targetwgt[k]; } g1 = 0.0; for ( k = 0; k < nparams; k++ ) g1 += drdp[k]*drdp[k]; g1 = sqrt(g1); // stop if gradient starts increasing if ( g1 < 1.0e-10 || g1 >= g0 ) break; g0 = g1; // solve for Newton-Raphson shift shiftn = drdp2.solve( drdp ); // apply shift scale = (1.0+ftype(n)) / (1.0+ftype(n)+damp); for ( i = 0; i< nparams; i++ ) params_[i] -= scale*shiftn[i]; if ( debug ) std::cout << " Resolution function cycle " << n << " " << g0 << " " << g1 << " " << scale << "\n"; // stop if the target is quadratic if ( basisfn.type() == BasisFn_base::LINEAR && targetfn.type() == TargetFn_base::QUADRATIC ) break; } } */ } // namespace clipper clipper-2.1/clipper/core/nxmap.cpp0000644000374100011300000000755110363703537014161 00000000000000/* nxmap.cpp: implementation file for crystal maps */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "nxmap.h" namespace clipper { Message_ctor message_ctor_nxmap( " [NXmap: constructed]" ); /*! For later initialisation: see init() */ NXmap_base::NXmap_base() { rt_orth_grid = RTop_orth( RTop<>::null() ); Message::message( message_ctor_nxmap ); } /*! Initialise an NXmap to some rhomboid chosen from within a crystal coordinate space, specified by the grid and a transformation from orthogonal to grid coordinates. \param grid The grid dimensions of the desired map. \param rt The rotation translation op from orthogonal to grid coordinates. */ void NXmap_base::init( const Grid& grid, const RTop<>& rt ) { // set up grid and orth->grid operator grid_ = grid; rt_orth_grid = rt; rt_grid_orth = rt.inverse(); // set up grid steps du = grid_.index( Coord_grid(1,0,0) ); dv = grid_.index( Coord_grid(0,1,0) ); dw = grid_.index( Coord_grid(0,0,1) ); } /*! Initialise an NXmap to some rhomboid chosen from within a crystal grid coordinate space, specified by a cell, sampling and box within that grid. This is useful for creating an NXmap which exactly matches some subregion of a crystallographic map. \param cell Unit cell defining the crystal space. \param grid The grid sampling of the given unit cell. \param grid_extent The map extent within that cell. */ void NXmap_base::init( const Cell& cell, const Grid_sampling& grid, const Grid_range& grid_extent ) { // initialise init( grid_extent, RTop<>( grid.matrix_frac_grid() * cell.matrix_frac(), -Coord_map( grid_extent.min() ) ) ); } /*! \return true if the object has not been initalised. */ bool NXmap_base::is_null() const { return rt_orth_grid.is_null(); } } // namespace clipper clipper-2.1/clipper/core/resol_fn.h0000644000374100011300000002515711311437215014303 00000000000000/*! \file lib/resol_fn.h Header file for resolution function generator */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_RESOL_FN #define CLIPPER_RESOL_FN #include "hkl_data.h" namespace clipper { //! abstract base class for resolution function basis functions /*! A basis function must be able to return its value and derivatives for any given HKL. Optionally, performance can be improved by returning a flag to indicate if the value of the basis function for a given reflection is linearly dependent on the values of the parameter, and a value indicating whether the curvature matrix takes an N-diagonal form. \b NOTE: for performance reasons the derivatives are returned as a reference to an internal object, so if you store a reference to the result (which is also good for performance, it will be overwritten on the next call. If this matters, store a copy rather than a reference. */ class BasisFn_base { public: //! enumeration of function types: optionally used to improve convergence enum FNtype { GENERAL, LINEAR }; //! object holding the basis function and its first two derivatives class Fderiv { public: ftype f; //!< value of function std::vector df; //!< first derivative vector w.r.t params Matrix<> df2; //!< second derivative matrix w.r.t params Fderiv() {} //!< null constructor Fderiv(const int& np) : df(np,0.0), df2(np,np,0.0) {} //& params ) const { return fderiv( hkl, cell, params ).f; } //! the value of the resolution function and its first two derivatives virtual const Fderiv& fderiv( const HKL& hkl, const Cell& cell, const std::vector& params ) const = 0; //! the type of the function: optionally used to improve convergence virtual FNtype type() const; //! number of non-zero diagonals in the upper triangle of the curvatures virtual int num_diagonals() const; protected: //! provide write access to result for subclasses Fderiv& result() const { return result_; } virtual ~BasisFn_base() {} //!< destructor private: int np_; //!< number of params mutable Fderiv result_; //!< internal cache for result }; //! abstract base class for least-squares resolution function target functions /*! A target function must be able to return its value given the value of the basis function for all HKL, and its derivative with respect the values of the basis function for all HKL. Optionally, performance can be improved by returning a flag to indicate if the target function is quadratic. */ class TargetFn_base { public: //! object holding the residual function and first two derivatives class Rderiv { public: ftype r; //!< the value of the function ftype dr; //!< first derivative w.r.t basis fn ftype dr2; //!< second derivative w.r.t basis fn }; //! enumeration of function types: optionally used to improve convergence enum FNtype { GENERAL, QUADRATIC }; //! return the value and derivatives of the target function /*! If the value of f(h) is invalid, rderiv.r should be set to NaN */ virtual Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& fh ) const = 0; //! the type of the function: optionally used to improve convergence virtual FNtype type() const { return GENERAL; } virtual ~TargetFn_base() {} //!< destructor //! test that the residuals, gradients, and curvatures are consistent void debug( const HKL_info& hkl_info ) const; }; //! 2nd order resolution function evaluator /*! This is an automatic evaluator for arbitrary functions of HKL, most commonly used for evaluating a function of resolution (such a mean F^2 or sigmaa), although more general tasks including local scaling of reflections and anisotropic functions can also be handled. This form is for target functions which approach zero quadratically, e.g. least-squares targets. This version implements a naive Newton-Raphson minimiser, which only uses the gradient and curvature of the target function, ignoring its value. It is ideal for quadratic targets with linear basis functions. To evaluate a resolution function, this class must be provided with two objects: - The basis function (and gradients), which describes the value of the function for any reflection given a set of paramters. - The target function (and derivatives), which is used to determine the values of the basis function parameters. For example, the following code may be used to calculate a smooth scaling function to scale one set of data to another using an anisotropic Gaussian scaling function: \code // make data object clipper::HKL_info hkls; clipper::HKL_data fsig1( hkls ); clipper::HKL_data fsig2( hkls ); // INITIALISE THEM HERE! // calculate the scaling function std::vector params( 7, 0.0 ); // initial parameters clipper::BasisFn_aniso_gaussian basisfn; // aniso gaussian clipper::TargetFn_scaleF1F2targetfn( fsig1, fsig2 ); clipper::ResolutionFn_nonlinear rfn( hkls, basisfn, targetfn, params ); // now scale the data clipper::HKL_info::HKL_reference_index ih; for ( ih = hkls.first(); !ih.last(); ih.next() ) fsig1[ih].scale( sqrt( rfn.f(ih) ) ); \endcode The most useful isotropic resolution function is the BasisFn_spline, since it is linear and provides a good fit to most data. */ class ResolutionFn { public: //! constructor: need reflections, basis fn and target fn. ResolutionFn( const HKL_info& hkl_info, const BasisFn_base& basisfn, const TargetFn_base& targetfn, const std::vector& params, const ftype damp = 0.0, const bool debug = false ); //! return the value of the basis function with the current paramters inline ftype f( const HKL_info::HKL_reference_index& ih ) const { return basisfn_->f( ih.hkl(), cell_, params_ ); } //! return the values of the parameters const std::vector& params() const; //! print the target, gradient, and curvatures with respect to the params void debug() const; protected: const HKL_info* hkl_info_; //!< reflection list const TargetFn_base* targetfn_; //!< target function const BasisFn_base* basisfn_; //!< basis function std::vector params_; //!< basis function parameters Cell cell_; //!< cell //! calculate derivatives of target wrt params \internal void calc_derivs( const std::vector& params, ftype& r, std::vector& drdp, Matrix<>& drdp2 ) const; //! null constructor ResolutionFn() {} }; //! 2nd order resolution function evaluator /*! This is an automatic evaluator for arbitrary functions of HKL, most commonly used for evaluating a function of resolution (such a mean F^2 or sigmaa), although more general tasks including local scaling of reflections and anisotropic functions can also be handled. This form is for target functions which approach zero quadratically, e.g. least-squares targets. \note This version implements a minimiser which uses both Newton-Raphson and gradient steps depending on the situation. It can be used for non-quadratic targets or non-linear basis functions. To evaluate a resolution function, this class must be provided with two objects: - The basis function (and gradients), which describes the value of the function for any reflection given a set of paramters. - The target function (and derivatives), which is used to determine the values of the basis function parameters. */ class ResolutionFn_nonlinear: public ResolutionFn { public: //! constructor: need reflections, basis fn and target fn. ResolutionFn_nonlinear( const HKL_info& hkl_info, const BasisFn_base& basisfn, const TargetFn_base& targetfn, const std::vector& params, const ftype damp = 0.0, const bool debug = false ); }; } // namespace clipper #endif clipper-2.1/clipper/core/nxmap_operator.h0000644000374100011300000002230310363703537015531 00000000000000/*! \file lib/nxmap_operator.h Header file for non-crystal map operator */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_NXMAP_OPERATOR #define CLIPPER_NXMAP_OPERATOR #include "xmap.h" #include "nxmap.h" namespace clipper { //! NX_operator: non-crystal map operator /*! This class holds a reference to a non-crystal map frame from somewhere within a crystallographic map frame. In the general case, an orthogonal rotation-translation operator is provided which maps the orthogonal frame of the crystal space onto the orthogonal frame of the NXmap space. The object calculates and stores optimised transformations between the crystallgoraphic frame (described either in fractional or grid coordinates), and the NXmap grid. Fast paths are generated automatically if the grids are related. */ class NX_operator { public: //! null constructor NX_operator(); //! constructor: from Xmap, NXmap, and operator NX_operator( const Xmap_base& xmap, const NXmap_base& nxmap, const RTop_orth& rtop ); //! constructor: from cell, grid sampling, NXmap, and operator NX_operator( const Cell& cell, const Grid_sampling& grid, const NXmap_base& nxmap, const RTop_orth& rtop ); //! initialiser:: from Xmap, NXmap, and operator void init( const Xmap_base& xmap, const NXmap_base& nxmap, const RTop_orth& rtop ); //! initialiser:: from cell, grid sampling, NXmap, and operator void init( const Cell& cell, const Grid_sampling& grid, const NXmap_base& nxmap, const RTop_orth& rtop ); //! convert xtal frac coord to nxmap map coord inline Coord_map coord_map( const Coord_frac& c ) const { return Coord_map( xfrac_nxgrid * c ); } //! convert nxmap map coord to xtal frac coord inline Coord_frac coord_frac( const Coord_map& c ) const { return Coord_frac( nxgrid_xfrac * c ); } //! get value of nxmap at xmap grid coord using fastest appropriate method template T nxmap_data( const M& nxmap, const Coord_grid& c ) const; //! get value of xmap at nxmap grid coord using fastest appropriate method template T xmap_data( const M& xmap, const Coord_grid& c ) const; //! test if object has been initialised bool is_null() const; void debug() const; protected: RTop<> xfrac_nxgrid; //!< xtal_cell -> nxmap operator RTop<> nxgrid_xfrac; //!< nxmap -> xtal_cell operator RTop<> xgrid_nxgrid; //!< xtal_grid -> nxmap operator RTop<> nxgrid_xgrid; //!< nxmap -> xtal_grid operator RTop xgrid_nxgrid_int; //!< xtal_grid -> nxmap integer operator RTop nxgrid_xgrid_int; //!< nxmap -> xtal_grid integer operator bool x_nx_is_int; //!< true if int operator exists bool x_nx_is_trn; //!< true if int operator exists and is pure transln bool nx_x_is_int; //!< true if int operator exists bool nx_x_is_trn; //!< true if int operator exists and is pure transln }; //! NXmap_operator: non-crystal map operator referencing a particular NXmap /*! This class holds a reference to a non-crystal map object from somewhere within a crystallographic map frame. In the general case, an orthogonal rotation-translation operator is provided which maps the orthogonal frame of the crystal space onto the orthogonal frame of the NXmap space. The object calculates and stores optimised transformations between the crystallgoraphic frame (described either in fractional or grid coordinates), and the NXmap grid. Fast paths are generated automatically if the grids are related. \note This object differes from NX_operator in that it keeps a reference to an individual NXmap, which may be used to access that object directly. */ template class NXmap_operator : public NX_operator { public: //! null constructor NXmap_operator() {} //! constructor: from Xmap, NXmap, and operator NXmap_operator( const Xmap_base& xmap, const NXmap& nxmap, const RTop_orth& rtop ) { init( xmap, nxmap, rtop ); } //! constructor: from cell, grid sampling, NXmap, and operator NXmap_operator( const Cell& cell, const Grid_sampling& grid, const NXmap& nxmap, const RTop_orth& rtop ) { init( cell, grid, nxmap, rtop ); } //! initialiser:: from Xmap, NXmap, and operator void init( const Xmap_base& xmap, const NXmap& nxmap, const RTop_orth& rtop ) { init( xmap.cell(), xmap.grid_sampling(), nxmap, rtop ); } //! initialiser:: from cell, grid sampling, NXmap, and operator void init( const Cell& cell, const Grid_sampling& grid, const NXmap& nxmap, const RTop_orth& rtop ) { nxmap_ = &nxmap; NX_operator::init( cell, grid, nxmap, rtop ); } //! access NXmap directly from xmap grid coord using fastest method template T nxmap_data( const Coord_grid& c ) const { return NX_operator::nxmap_data( *nxmap_, c ); } //! get the target NXmap of this operator const NXmap& nxmap() const { return *nxmap_; } private: const NXmap* nxmap_; //!< pointer to the nxmap }; // template implementations /*! The density of the non-crystal map at the position corresponding to a crystallographic map grid coordinate is returned. If the grids match exactly either by pure translation or by rotation+translation, then fast paths are used to return the requested density directly. Otherwise the supplied interpolation template is used. No checking is performed for coordinates outside the NXmap. \param nxmap The non-crystal map (NXmap) to be queried. \param c The grid coordinate in the crystallographic coordinate frame. \return The value of the NXmap at the requested position. */ template T NX_operator::nxmap_data( const M& nxmap, const Coord_grid& c ) const { if ( x_nx_is_trn ) { return T( nxmap.get_data( Coord_grid( c + xgrid_nxgrid_int.trn() ) ) ); } else if ( x_nx_is_int ) { return T( nxmap.get_data( Coord_grid( xgrid_nxgrid_int * c ) ) ); } else { T val; I::interp( nxmap, Coord_map( xgrid_nxgrid * c.coord_map() ), val ); return val; } } /*! The density of the crystal map at the position corresponding to a non-crystallographic map grid coordinate is returned. If the grids match exactly either by pure translation or by rotation+translation, then fast paths are used to return the requested density directly. Otherwise the supplied interpolation template is used. \param xmap The crystal map (Xmap) to be queried. \param c The grid coordinate in the crystallographic coordinate frame. \return The value of the Xmap at the requested position. */ template T NX_operator::xmap_data( const M& xmap, const Coord_grid& c ) const { if ( nx_x_is_trn ) { return T( xmap.get_data( Coord_grid( c + nxgrid_xgrid_int.trn() ) ) ); } else if ( nx_x_is_int ) { return T( xmap.get_data( Coord_grid( nxgrid_xgrid_int * c ) ) ); } else { T val; I::interp( xmap, Coord_map( nxgrid_xgrid * c.coord_map() ), val ); return val; } } } // namespace clipper #endif clipper-2.1/clipper/core/resol_basisfn.cpp0000644000374100011300000002755511271603054015665 00000000000000/* resol_basisfn.cpp: implementation file for resolution basis functions */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA /* This code is derived from the 'dm' source code */ #include "resol_basisfn.h" namespace clipper { // resolution ordinal void Resolution_ordinal::init( const HKL_info& hklinfo, const ftype& power ) { HKL_info::HKL_reference_index ih; Range range; for ( ih = hklinfo.first(); !ih.last(); ih.next() ) range.include( ih.invresolsq() ); Generic_ordinal::init( range, 1000 ); for ( ih = hklinfo.first(); !ih.last(); ih.next() ) accumulate( ih.invresolsq() ); prep_ordinal(); for ( int i = 0; i < hist.size(); i++ ) hist[i] = pow( hist[i], 1.0/power ); } void Resolution_ordinal::init( const HKL_data_base& hkldata, const ftype& power ) { HKL_info::HKL_reference_index ih; Range range; for ( ih = hkldata.first_data(); !ih.last(); hkldata.next_data(ih) ) range.include( ih.invresolsq() ); Generic_ordinal::init( range, 1000 ); for ( ih = hkldata.first_data(); !ih.last(); hkldata.next_data(ih) ) accumulate( ih.invresolsq() ); prep_ordinal(); for ( int i = 0; i < hist.size(); i++ ) hist[i] = pow( hist[i], 1.0/power ); } void Resolution_ordinal::init( const HKL_data_base& hkldata, const Cell& cell, const ftype& power ) { HKL_info::HKL_reference_index ih; Range range; for ( ih = hkldata.first_data(); !ih.last(); hkldata.next_data(ih) ) range.include( ih.hkl().invresolsq( cell ) ); Generic_ordinal::init( range, 1000 ); for ( ih = hkldata.first_data(); !ih.last(); hkldata.next_data(ih) ) accumulate( ih.hkl().invresolsq( cell ) ); prep_ordinal(); for ( int i = 0; i < hist.size(); i++ ) hist[i] = pow( hist[i], 1.0/power ); } // binner ftype BasisFn_binner::f_s( const ftype& s, const std::vector& params ) const { const int& nbins = num_params(); // convert reso to int const int bin = Util::bound( 0, Util::intf( ftype(nbins) * s_ord.ordinal( s ) ), nbins-1 ); return params[bin]; } const BasisFn_base::Fderiv& BasisFn_binner::fderiv_s( const ftype& s, const std::vector& params ) const { const int& nbins = num_params(); for ( int i = 0; i < nbins; i++ ) result().df[i] = 0.0; // convert reso to int const int bin = Util::bound( 0, Util::intf( ftype(nbins) * s_ord.ordinal( s ) ), nbins-1 ); // make vector of derivatives result().f = params[bin]; result().df[bin] = 1.0; return result(); } // linear binner ftype BasisFn_linear::f_s( const ftype& s_, const std::vector& params ) const { const int& nbins = num_params(); const ftype s = ftype(nbins) * s_ord.ordinal( s_ ); const int i = Util::intf( s ); const ftype ds = s - ftype(i); const int i0 = Util::bound( 0, i , nbins-1 ); const int i1 = Util::bound( 0, i+1, nbins-1 ); return ( params[i0]*(1.0-ds) + params[i1]*(ds) ); } const BasisFn_base::Fderiv& BasisFn_linear::fderiv_s( const ftype& s_, const std::vector& params ) const { const int& nbins = num_params(); for ( int i = 0; i < nbins; i++ ) result().df[i] = 0.0; const ftype s = ftype(nbins) * s_ord.ordinal( s_ ); const int i = Util::intf( s ); const ftype ds = s - ftype(i); const int i0 = Util::bound( 0, i , nbins-1 ); const int i1 = Util::bound( 0, i+1, nbins-1 ); result().f = params[i0]*(1.0-ds) + params[i1]*(ds); result().df[i0] += (1.0-ds); result().df[i1] += (ds); return result(); } // smooth binner ftype BasisFn_spline::f_s( const ftype& s_, const std::vector& params ) const { const int& nbins = num_params(); const ftype s = ftype(nbins) * s_ord.ordinal( s_ ); const int i = Util::intf( s ); const ftype ds = s - ftype(i) - 0.5; const int i0 = Util::bound( 0, i-1, nbins-1 ); const int i1 = Util::bound( 0, i , nbins-1 ); const int i2 = Util::bound( 0, i+1, nbins-1 ); return ( params[i0]*0.5*(ds-0.5)*(ds-0.5) + params[i1]*(0.75-ds*ds) + params[i2]*0.5*(ds+0.5)*(ds+0.5) ); } const BasisFn_base::Fderiv& BasisFn_spline::fderiv_s( const ftype& s_, const std::vector& params ) const { const int& nbins = num_params(); for ( int i = 0; i < nbins; i++ ) result().df[i] = 0.0; const ftype s = ftype(nbins) * s_ord.ordinal( s_ ); const int i = Util::intf( s ); const ftype ds = s - ftype(i) - 0.5; const int i0 = Util::bound( 0, i-1, nbins-1 ); const int i1 = Util::bound( 0, i , nbins-1 ); const int i2 = Util::bound( 0, i+1, nbins-1 ); result().f = params[i0]*0.5*(ds-0.5)*(ds-0.5) + params[i1]*(0.75-ds*ds) + params[i2]*0.5*(ds+0.5)*(ds+0.5); result().df[i0] += 0.5*(ds-0.5)*(ds-0.5); result().df[i1] += 0.75-ds*ds; result().df[i2] += 0.5*(ds+0.5)*(ds+0.5); return result(); } // gaussian /* ftype BasisFn_gaussian::f_s( const ftype& s, const std::vector& params ) const { // generate Gaussian return exp( - params[1] * s + params[0] ); } */ const BasisFn_base::Fderiv& BasisFn_gaussian::fderiv_s( const ftype& s, const std::vector& params ) const { ftype f = exp( - params[1] * s + params[0] ); result().f = result().df[0] = result().df2(0,0) = f; result().df[1] = result().df2(0,1) = result().df2(1,0) = -s * f; result().df2(1,1) = s * s * f; return result(); } ftype BasisFn_gaussian::scale( const std::vector& params ) const { return exp( params[0] ); } ftype BasisFn_gaussian::u_iso( const std::vector& params ) const { return params[1] / Util::twopi2(); } // aniso gaussian /* ftype BasisFn_aniso_gaussian::f_coord( const Coord_reci_orth& xs, const std::vector& params ) const { // generate Gaussian return exp( params[0] - ( xs[0]*xs[0]*params[1] + xs[1]*xs[1]*params[2] + xs[2]*xs[2]*params[3] + 2.0*(xs[0]*xs[1]*params[4] + xs[0]*xs[2]*params[5] + xs[1]*xs[2]*params[6]) ) ); } */ const BasisFn_base::Fderiv& BasisFn_aniso_gaussian::fderiv_coord( const Coord_reci_orth& xs, const std::vector& params ) const { ftype c[7]; c[0] = 1.0; c[1] = -xs[0]*xs[0]; c[2] = -xs[1]*xs[1]; c[3] = -xs[2]*xs[2]; c[4] = -2.0*xs[0]*xs[1]; c[5] = -2.0*xs[0]*xs[2]; c[6] = -2.0*xs[1]*xs[2]; ftype f = exp( params[0] + c[1]*params[1] + c[2]*params[2] + c[3]*params[3] + c[4]*params[4] + c[5]*params[5] + c[6]*params[6] ); result().f = f; int i, j; for ( j = 0; j < 7; j++ ) { result().df[j] = c[j]*f; for ( i = 0; i < 7; i++ ) result().df2(i,j) = c[i]*c[j]*f; } return result(); } ftype BasisFn_aniso_gaussian::scale( const std::vector& params ) const { return exp( params[0] ); } U_aniso_orth BasisFn_aniso_gaussian::u_aniso_orth( const std::vector& params ) const { return U_aniso_orth( params[1]/Util::twopi2(), params[2]/Util::twopi2(), params[3]/Util::twopi2(), params[4]/Util::twopi2(), params[5]/Util::twopi2(), params[6]/Util::twopi2() ); } // log_gaussian /* ftype BasisFn_log_gaussian::f_s( const ftype& s, const std::vector& params ) const { // generate Gaussian return exp( - params[1] * s + params[0] ); } */ const BasisFn_base::Fderiv& BasisFn_log_gaussian::fderiv_s( const ftype& s, const std::vector& params ) const { ftype f = - params[1] * s + params[0]; result().f = f; result().df[0] = 1.0; result().df[1] = -s; return result(); } ftype BasisFn_log_gaussian::scale( const std::vector& params ) const { return exp( params[0] ); } ftype BasisFn_log_gaussian::u_iso( const std::vector& params ) const { return params[1] / Util::twopi2(); } // log_aniso gaussian /* ftype BasisFn_log_aniso_gaussian::f_coord( const Coord_reci_orth& xs, const std::vector& params ) const { // generate Gaussian return exp( params[0] - ( xs[0]*xs[0]*params[1] + xs[1]*xs[1]*params[2] + xs[2]*xs[2]*params[3] + 2.0*(xs[0]*xs[1]*params[4] + xs[0]*xs[2]*params[5] + xs[1]*xs[2]*params[6]) ) ); } */ const BasisFn_base::Fderiv& BasisFn_log_aniso_gaussian::fderiv_coord( const Coord_reci_orth& xs, const std::vector& params ) const { result().df[0] = 1.0; result().df[1] = -xs[0]*xs[0]; result().df[2] = -xs[1]*xs[1]; result().df[3] = -xs[2]*xs[2]; result().df[4] = -2.0*xs[0]*xs[1]; result().df[5] = -2.0*xs[0]*xs[2]; result().df[6] = -2.0*xs[1]*xs[2]; result().f = ( params[0] + result().df[1]*params[1] + result().df[2]*params[2] + result().df[3]*params[3] + result().df[4]*params[4] + result().df[5]*params[5] + result().df[6]*params[6] ); return result(); } ftype BasisFn_log_aniso_gaussian::scale( const std::vector& params ) const { return exp( params[0] ); } U_aniso_orth BasisFn_log_aniso_gaussian::u_aniso_orth( const std::vector& params ) const { return U_aniso_orth( params[1]/Util::twopi2(), params[2]/Util::twopi2(), params[3]/Util::twopi2(), params[4]/Util::twopi2(), params[5]/Util::twopi2(), params[6]/Util::twopi2() ); } // expcubic /* ftype BasisFn_expcubic::f_s( const ftype& s, const std::vector& params ) const { // generate Expcubic return exp( ( ( - params[3]*s + params[2] )*s - params[1] )*s + params[0] ); } */ const BasisFn_base::Fderiv& BasisFn_expcubic::fderiv_s( const ftype& s, const std::vector& params ) const { ftype f = exp( ( ( -params[3]*s + params[2] )*s - params[1] )*s + params[0] ); result().f = result().df[0] = result().df2(0,0) = f; f *= -s; result().df[1] = result().df2(0,1) = result().df2(1,0) = f; f *= -s; result().df[2] = result().df2(0,2) = result().df2(1,1) = result().df2(2,0) = f; f *= -s; result().df[3] = result().df2(0,3) = result().df2(1,2) = result().df2(2,1) = result().df2(3,0) = f; f *= -s; result().df2(1,3) = result().df2(2,2) = result().df2(3,1) = f; f *= -s; result().df2(2,3) = result().df2(3,2) = f; f *= -s; result().df2(3,3) = f; return result(); } } // namespace clipper clipper-2.1/clipper/core/hkl_datatypes.h0000644000374100011300000006054411102576702015332 00000000000000/*! \file lib/hkl_datatypes.h Fundamental data types for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_HKL_DATATYPES #define CLIPPER_HKL_DATATYPES #include #include "hkl_data.h" namespace clipper { // Now define some actual datatypes namespace datatypes { //! Reflection data type: I + sigI /*! Note that I_sigI also has methods for returning I_pl(), sigI_pl(), I_mi, sigI_mi(), so you can use this type in any template type where you would use I_sigI_ano. */ template class I_sigI : private Datatype_base { public: I_sigI() { Util::set_null(I_); Util::set_null(sigI_); } I_sigI( const dtype& I, const dtype& sigI ) : I_(I), sigI_(sigI) {} void set_null() { Util::set_null(I_); Util::set_null(sigI_); } static String type() { return "I_sigI"; } void friedel() {} void shift_phase(const ftype& dphi) {} bool missing() const { return (Util::is_nan(I_) || Util::is_nan(sigI_)); } static int data_size() { return 2; } static String data_names() { return "I sigI"; } void data_export( xtype array[] ) const { array[0] = I(); array[1] = sigI(); } void data_import( const xtype array[] ) { I() = array[0]; sigI() = array[1]; } //! this type is scalable - apply magnitude scale factor void scale(const ftype& s) { I_ *= (s*s); sigI_ *= (s*s); } // accessors const dtype& I() const { return I_; } // class I_sigI_ano : private Datatype_base { public: I_sigI_ano() { set_null(); } void set_null() { Util::set_null(I_pl_); Util::set_null(I_mi_); Util::set_null(sigI_pl_); Util::set_null(sigI_mi_); Util::set_null(cov_); } static String type() { return "I_sigI_ano"; } void friedel() { dtype I=I_pl_; I_pl_=I_mi_; I_mi_=I; I=sigI_pl_; sigI_pl_=sigI_mi_; sigI_mi_=I; } void shift_phase(const ftype& dphi) {} bool missing() const { return (Util::is_nan(I_pl_) && Util::is_nan(I_mi_)); } static int data_size() { return 5; } static String data_names() { return "I+ sigI+ I- sigI- covI+-"; } void data_export( xtype a[] ) const { a[0] = I_pl(); a[1] = sigI_pl(); a[2] = I_mi(); a[3] = sigI_mi(); a[4] = cov(); } void data_import( const xtype a[] ) { I_pl() = a[0]; sigI_pl() = a[1]; I_mi() = a[2]; sigI_mi() = a[3]; cov() = a[4]; } //! this type is scalable - apply magnitude scale factor void scale(const ftype& s) { I_pl_ *= (s*s); sigI_pl_ *= (s*s); I_mi_ *= (s*s); sigI_mi_ *= (s*s); cov_ *= (s*s); } // accessors const dtype& I_pl() const { return I_pl_; } // class F_sigF : private Datatype_base { public: F_sigF() { Util::set_null(f_); Util::set_null(sigf_); } F_sigF( const dtype& f, const dtype& sigf ) : f_(f), sigf_(sigf) {} void set_null() { Util::set_null(f_); Util::set_null(sigf_); } static String type() { return "F_sigF"; } void friedel() {} void shift_phase(const ftype& dphi) {} bool missing() const { return (Util::is_nan(f_) || Util::is_nan(sigf_)); } static int data_size() { return 2; } static String data_names() { return "F sigF"; } void data_export( xtype array[] ) const { array[0] = f(); array[1] = sigf(); } void data_import( const xtype array[] ) { f() = array[0]; sigf() = array[1]; } //! this type is scalable - apply magnitude scale factor void scale(const ftype& s) { f_ *= s; sigf_ *= s; } // accessors const dtype& f() const { return f_; } // class F_sigF_ano : private Datatype_base { public: F_sigF_ano() { set_null(); } void set_null() { Util::set_null(f_pl_); Util::set_null(f_mi_); Util::set_null(sigf_pl_); Util::set_null(sigf_mi_); Util::set_null(cov_); } static String type() { return "F_sigF_ano"; } void friedel() { dtype f=f_pl_; f_pl_=f_mi_; f_mi_=f; f=sigf_pl_; sigf_pl_=sigf_mi_; sigf_mi_=f; } void shift_phase(const ftype& dphi) {} bool missing() const { return (Util::is_nan(f_pl_) && Util::is_nan(f_mi_)); } static int data_size() { return 5; } static String data_names() { return "F+ sigF+ F- sigF- covF+-"; } void data_export( xtype a[] ) const { a[0] = f_pl(); a[1] = sigf_pl(); a[2] = f_mi(); a[3] = sigf_mi(); a[4] = cov(); } void data_import( const xtype a[] ) { f_pl() = a[0]; sigf_pl() = a[1]; f_mi() = a[2]; sigf_mi() = a[3]; cov() = a[4]; } //! this type is scalable - apply magnitude scale factor void scale(const ftype& s) { f_pl_ *= s; sigf_pl_ *= s; f_mi_ *= s; sigf_mi_ *= s; cov_ *= (s*s); } // accessors const dtype& f_pl() const { return f_pl_; } // fsigf; clipper::HKL_data esige; esige.compute( fsigf, clipper::data32::Compute_EsigE_from_FsigF() ); \endcode */ template class E_sigE : private Datatype_base { public: E_sigE() { Util::set_null(E_); Util::set_null(sigE_); } E_sigE( const dtype& E, const dtype& sigE ) : E_(E), sigE_(sigE) {} void set_null() { Util::set_null(E_); Util::set_null(sigE_); } static String type() { return "E_sigE"; } void friedel() {} void shift_phase(const ftype& dphi) {} bool missing() const { return (Util::is_nan(E_) || Util::is_nan(sigE_)); } static int data_size() { return 2; } static String data_names() { return "E sigE"; } void data_export( xtype array[] ) const { array[0] = E(); array[1] = sigE(); } void data_import( const xtype array[] ) { E() = array[0]; sigE() = array[1]; } //! this type is scalable - apply magnitude scale factor void scale(const ftype& s) { E_ *= s; sigE_ *= s; } // accessors const dtype& E() const { return E_; } // class E_sigE_ano : private Datatype_base { public: E_sigE_ano() { set_null(); } void set_null() { Util::set_null(E_pl_); Util::set_null(E_mi_); Util::set_null(sigE_pl_); Util::set_null(sigE_mi_); Util::set_null(cov_); } static String type() { return "E_sigE_ano"; } void friedel() { dtype e=E_pl_; E_pl_=E_mi_; E_mi_=e; e=sigE_pl_; sigE_pl_=sigE_mi_; sigE_mi_=e; } void shift_phase(const ftype& dphi) {} bool missing() const { return (Util::is_nan(E_pl_) && Util::is_nan(E_mi_)); } static int data_size() { return 5; } static String data_names() { return "E+ sigE+ E- sigE- covE+-"; } void data_export( xtype a[] ) const { a[0] = E_pl(); a[1] = sigE_pl(); a[2] = E_mi(); a[3] = sigE_mi(); a[4] = cov(); } void data_import( const xtype a[] ) { E_pl() = a[0]; sigE_pl() = a[1]; E_mi() = a[2]; sigE_mi() = a[3]; cov() = a[4]; } //! this type is scalable - apply magnitude scale factor void scale(const ftype& s) { E_pl_ *= s; sigE_pl_ *= s; E_mi_ *= s; sigE_mi_ *= s; cov_ *= (s*s); } // accessors const dtype& E_pl() const { return E_pl_; } // class F_phi : private Datatype_base { public: F_phi() { Util::set_null(f_); Util::set_null(phi_); } F_phi( const dtype& f, const dtype& phi ) : f_(f), phi_(phi) {} void set_null() { Util::set_null(f_); Util::set_null(phi_); } static String type() { return "F_phi"; } void friedel() { if (!Util::is_nan(phi_)) phi_=-phi_; } void shift_phase(const ftype& dphi) { if (!Util::is_nan(phi_)) phi_+=dphi; } bool missing() const { return (Util::is_nan(f_) || Util::is_nan(phi_)); } static int data_size() { return 2; } static String data_names() { return "F phi"; } void data_export( xtype array[] ) const { array[0] = f(); array[1] = phi(); } void data_import( const xtype array[] ) { f() = array[0]; phi() = array[1]; } //! this type is scalable - apply magnitude scale factor void scale(const ftype& s) { f_ *= s; } // accessors const dtype& f() const { return f_; } // c) { f_=std::abs(c); phi_=std::arg(c); } //! convert to complex operator std::complex() const { return std::polar(f_, phi_); } //! resolve along phase direction dtype resolve(const dtype phi) { return f_ * cos( phi_ - phi ); } //! tidy up so that real part is positive and phase 0...twopi const F_phi& norm() { if ( f_ < 0.0 ) { f_ = -f_; phi_ += Util::pi(); } phi_ = Util::mod( phi_, Util::twopi() ); return *this; } private: dtype f_,phi_; }; //! Reflection data type: best phi + fom template class Phi_fom : private Datatype_base { public: Phi_fom() { Util::set_null(phi_); Util::set_null(fom_); } Phi_fom( const dtype& phi, const dtype& fom ) : phi_(phi), fom_(fom) {} void set_null() { Util::set_null(phi_); Util::set_null(fom_); } static String type() { return "Phi_fom"; } void friedel() { if (!Util::is_nan(phi_)) phi_=-phi_; } void shift_phase(const ftype& dphi) { if (!Util::is_nan(phi_)) phi_+=dphi; } bool missing() const { return (Util::is_nan(phi_) || Util::is_nan(fom_)); } static int data_size() { return 2; } static String data_names() { return "phi fom"; } void data_export( xtype array[] ) const { array[0] = phi(); array[1] = fom(); } void data_import( const xtype array[] ) { phi() = array[0]; fom() = array[1]; } // accessors const dtype& phi() const { return phi_; } // class ABCD : private Datatype_base { public: ABCD() { Util::set_null(a_); Util::set_null(b_); Util::set_null(c_); Util::set_null(d_); } ABCD( const dtype& a, const dtype& b, const dtype& c, const dtype& d ) : a_(a), b_(b), c_(c), d_(d) {} void set_null() { Util::set_null(a_); Util::set_null(b_); Util::set_null(c_); Util::set_null(d_); } static String type() { return "ABCD"; } void friedel() { if ( !missing() ) { b_=-b_; d_=-d_; } } void shift_phase(const ftype& dphi) { if ( !missing() ) { ftype cosd,sind; dtype a1, b1, c1, d1; cosd = cos(dphi); sind = sin(dphi); a1 = a_*cosd - b_*sind; b1 = a_*sind + b_*cosd; cosd = cos(2.0*dphi); sind = sin(2.0*dphi); c1 = c_*cosd - d_*sind; d1 = c_*sind + d_*cosd; a_ = a1; b_ = b1; c_ = c1; d_ = d1; } } bool missing() const { return (Util::is_nan(a_) || Util::is_nan(b_) || Util::is_nan(c_) || Util::is_nan(d_)); } static int data_size() { return 4; } static String data_names() { return "A B C D"; } void data_export( xtype array[] ) const { array[0] = a(); array[1] = b(); array[2] = c(); array[3] = d(); } void data_import( const xtype array[] ) { a() = array[0]; b() = array[1]; c() = array[2]; d() = array[3]; } // accessors const dtype& a() const { return a_; } // class D_sigD : private Datatype_base { public: D_sigD() { Util::set_null(d_); Util::set_null(sigd_); } D_sigD( const dtype& d, const dtype& sigd ) : d_(d), sigd_(sigd) {} void set_null() { Util::set_null(d_); Util::set_null(sigd_); } static String type() { return "D_sigD"; } void friedel() { d_ = -d_; } void shift_phase(const ftype& dphi) {} bool missing() const { return (Util::is_nan(d_) || Util::is_nan(sigd_)); } static int data_size() { return 2; } static String data_names() { return "Dano sigDano"; } void data_export( xtype array[] ) const { array[0] = d(); array[1] = sigd(); } void data_import( const xtype array[] ) { d() = array[0]; sigd() = array[1]; } //! this type is scalable - apply magnitude scale factor void scale(const ftype& s) { d_ *= s; sigd_ *= s; } // accessors const dtype& d() const { return d_; } // I_sigI; //!< datatype typedef clipper::datatypes::I_sigI_ano I_sigI_ano; //!< datatype typedef clipper::datatypes::F_sigF F_sigF; //!< datatype typedef clipper::datatypes::F_sigF_ano F_sigF_ano; //!< datatype typedef clipper::datatypes::E_sigE E_sigE; //!< datatype typedef clipper::datatypes::F_phi F_phi; //!< datatype typedef clipper::datatypes::Phi_fom Phi_fom; //!< datatype typedef clipper::datatypes::ABCD ABCD; //!< datatype typedef clipper::datatypes::Flag Flag; //!< datatype typedef clipper::datatypes::Flag_bool Flag_bool; //!< datatype typedef clipper::datatypes::D_sigD D_sigD; //!< datatype } namespace data64 { typedef clipper::datatypes::I_sigI I_sigI; //!< datatype typedef clipper::datatypes::I_sigI_ano I_sigI_ano; //!< datatype typedef clipper::datatypes::F_sigF F_sigF; //!< datatype typedef clipper::datatypes::F_sigF_ano F_sigF_ano; //!< datatype typedef clipper::datatypes::E_sigE E_sigE; //!< datatype typedef clipper::datatypes::F_phi F_phi; //!< datatype typedef clipper::datatypes::Phi_fom Phi_fom; //!< datatype typedef clipper::datatypes::ABCD ABCD; //!< datatype typedef clipper::datatypes::Flag Flag; //!< datatype typedef clipper::datatypes::Flag_bool Flag_bool; //!< datatype typedef clipper::datatypes::D_sigD D_sigD; //!< datatype } } // namespace clipper #endif clipper-2.1/clipper/core/coords.cpp0000644000374100011300000006050311252436705014321 00000000000000/* coords.cpp: fundamental data types for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "coords.h" #include "spacegroup.h" #include "rotation.h" namespace clipper { /*! \param resol_ The resolution limit in Angstroms. */ Resolution::Resolution( const ftype& resol_ ) { init( resol_ ); } /*! \param resol_ The resolution limit in Angstroms. */ void Resolution::init( const ftype& resol_ ) { resol = resol_; } /*! \return The resolution limit in Angstroms. */ const ftype& Resolution::limit() const { return resol; } /*! \return The resolution limit in inverse squared Angstroms. */ ftype Resolution::invresolsq_limit() const { return 1.0/(resol*resol); } /*! \return true if the object has not been initalised. */ bool Resolution::is_null() const { return ( resol <= 0.0 ); } /*! Determine the class of a reflection for a give spacegroup. \param spgr The spacegroup. \param hkl The reflection HKL */ HKL_class::HKL_class( const Spacegroup& spgr, const HKL& hkl ) { HKL equiv; ftype shift; epsilon_ = 1; allowed_ = 255; for ( int i = 1; i < spgr.num_symops(); i++ ) { equiv = hkl.transform(spgr.symop(i)); shift = hkl.sym_phase_shift(spgr.symop(i)); if ( equiv == hkl ) { // if reflection is related to itself, then it is special or sysabs if ( cos(shift) > 0.999 ) { epsilon_++; // increase multiplicity } else { epsilon_ = allowed_ = 0; // flag sysabs break; } } else if ( equiv == -hkl ) { // if reflection is related to opposite, it is centric allowed_ = Util::intr( Util::mod(-0.5*shift, Util::pi()) / (Util::pi()/12.0) ); } } if ( hkl.h() == 0 && hkl.k() == 0 && hkl.l() == 0 ) allowed_ = 0; } /*! Construct the operator which give the least-squares fit of one set of coordinates onto another. The coodinates are stored as STL vectors of Coord_orth. The lists must be the same size, and each atom in the source list must correspond to the same atom in the target list. The algorithm employed is that of Kearsley, S.K. (1989) 'On the orthogonal transformation used for structural comparisons'. Acta Cryst. A45, 208-210. \param src The source list (i.e. the atoms to be transformed). \param tgt The target list (i.e. the fixed atoms). */ RTop_orth::RTop_orth( const std::vector& src, const std::vector& tgt ) { if ( src.size() != tgt.size() ) Message::message(Message_fatal("RTop_orth: coordinate list size mismatch")); // get centre of mass Coord_orth s, t, p, m; Coord_orth src_cen(0.0,0.0,0.0); Coord_orth tgt_cen(0.0,0.0,0.0); int n = src.size(); for ( int i = 0; i < n; i++ ) { src_cen = src_cen + src[i]; tgt_cen = tgt_cen + tgt[i]; } src_cen = (1.0/ftype(n)) * src_cen; tgt_cen = (1.0/ftype(n)) * tgt_cen; // prepare cross-sums Matrix<> mat( 4, 4, 0.0 ); for ( int i = 0; i < n; i++ ) { s = src[i] - src_cen; t = tgt[i] - tgt_cen; p = s + t; m = s - t; mat(0,0) = mat(0,0) + m[0]*m[0] + m[1]*m[1] + m[2]*m[2]; mat(1,1) = mat(1,1) + m[0]*m[0] + p[1]*p[1] + p[2]*p[2]; mat(2,2) = mat(2,2) + p[0]*p[0] + m[1]*m[1] + p[2]*p[2]; mat(3,3) = mat(3,3) + p[0]*p[0] + p[1]*p[1] + m[2]*m[2]; mat(0,1) = mat(0,1) + m[2]*p[1] - m[1]*p[2]; mat(0,2) = mat(0,2) + m[0]*p[2] - m[2]*p[0]; mat(0,3) = mat(0,3) + m[1]*p[0] - m[0]*p[1]; mat(1,2) = mat(1,2) + m[0]*m[1] - p[0]*p[1]; mat(1,3) = mat(1,3) + m[0]*m[2] - p[0]*p[2]; mat(2,3) = mat(2,3) + m[1]*m[2] - p[1]*p[2]; } mat(1,0) = mat(0,1); mat(2,0) = mat(0,2); mat(2,1) = mat(1,2); mat(3,0) = mat(0,3); mat(3,1) = mat(1,3); mat(3,2) = mat(2,3); // eigenvalue calc std::vector v = mat.eigen( true ); // get result Rotation r( mat(0,0), mat(1,0), mat(2,0), mat(3,0) ); Mat33<> rot = r.norm().matrix(); (*this) = RTop_orth( rot, tgt_cen - rot*src_cen ); } /*! Construct the operator which give the least-squares fit of one set of coordinates onto another. The coodinates are stored as STL vectors of Coord_orth. The lists must be the same size, and each atom in the source list must correspond to the same atom in the target list. The algorithm employed is that of Kearsley, S.K. (1989) 'On the orthogonal transformation used for structural comparisons'. Acta Cryst. A45, 208-210. \param src The source list (i.e. the atoms to be transformed). \param tgt The target list (i.e. the fixed atoms). \param wgt The weight to apply to each atom. */ RTop_orth::RTop_orth( const std::vector& src, const std::vector& tgt, const std::vector& wgt ) { if ( src.size() != wgt.size() || tgt.size() != wgt.size() ) Message::message(Message_fatal("RTop_orth: coordinate list size mismatch")); // get centre of mass Coord_orth s, t, p, m; Coord_orth src_cen(0.0,0.0,0.0); Coord_orth tgt_cen(0.0,0.0,0.0); ftype w = 0.0; int n = src.size(); for ( int i = 0; i < n; i++ ) { w += wgt[i]; src_cen += wgt[i] * src[i]; tgt_cen += wgt[i] * tgt[i]; } src_cen = (1.0/w) * src_cen; tgt_cen = (1.0/w) * tgt_cen; // prepare cross-sums Matrix<> mat( 4, 4, 0.0 ); for ( int i = 0; i < n; i++ ) { w = wgt[i]; s = src[i] - src_cen; t = tgt[i] - tgt_cen; p = s + t; m = s - t; mat(0,0) = mat(0,0) + w * ( m[0]*m[0] + m[1]*m[1] + m[2]*m[2] ); mat(1,1) = mat(1,1) + w * ( m[0]*m[0] + p[1]*p[1] + p[2]*p[2] ); mat(2,2) = mat(2,2) + w * ( p[0]*p[0] + m[1]*m[1] + p[2]*p[2] ); mat(3,3) = mat(3,3) + w * ( p[0]*p[0] + p[1]*p[1] + m[2]*m[2] ); mat(0,1) = mat(0,1) + w * ( m[2]*p[1] - m[1]*p[2] ); mat(0,2) = mat(0,2) + w * ( m[0]*p[2] - m[2]*p[0] ); mat(0,3) = mat(0,3) + w * ( m[1]*p[0] - m[0]*p[1] ); mat(1,2) = mat(1,2) + w * ( m[0]*m[1] - p[0]*p[1] ); mat(1,3) = mat(1,3) + w * ( m[0]*m[2] - p[0]*p[2] ); mat(2,3) = mat(2,3) + w * ( m[1]*m[2] - p[1]*p[2] ); } mat(1,0) = mat(0,1); mat(2,0) = mat(0,2); mat(2,1) = mat(1,2); mat(3,0) = mat(0,3); mat(3,1) = mat(1,3); mat(3,2) = mat(2,3); // eigenvalue calc std::vector v = mat.eigen( true ); // get result Rotation r( mat(0,0), mat(1,0), mat(2,0), mat(3,0) ); Mat33<> rot = r.norm().matrix(); (*this) = RTop_orth( rot, tgt_cen - rot*src_cen ); } /*! \param cell The cell concerned \return The transformed coordinate. */ RTop_frac RTop_orth::rtop_frac( const Cell& cell ) const { return RTop_frac( RTop<>(cell.matrix_frac()) * (*this) * RTop<>(cell.matrix_orth()) ); } /*! \return The inverse of the operator. */ RTop_orth RTop_orth::inverse() const { return RTop_orth( RTop<>::inverse() ); } /*! \param centre An arbitrary point. \return point on axis near the specified coordinate, 000 if rotation is zero */ Coord_orth RTop_orth::axis_coordinate_near( const Coord_orth& centre ) const { Rotation R(rot()); // Rotation part if ( R.abs_angle() < 0.001) return Coord_orth(0.0,0.0,0.0); Vec3<> t = trn(); // translation part // direction cosines of rotation axis n Vec3<> n = Vec3<>(R.x(),R.y(),R.z()).unit(); // parallel component of translation r = n (n.t) Vec3<> r = n * Vec3<>::dot(n, t); // Perpendicular component s = t - r Vec3<> s = t - r; // Rotation angle kappa double kappa = R.norm().polar_ccp4().kappa(); // Origin x0 = 0.5*[s + (n x s)/tan(kappa/2)] Vec3<> x0 = 0.5*(s + Vec3<>::cross(n, s) * (1./tan(0.5*kappa))); // Find closest position on axis to centre // projection on to axis through origin return Coord_orth( x0 + n * Vec3<>::dot((centre-x0), n) ); } /*! \return screw translation, 000 if rotation is zero */ Coord_orth RTop_orth::screw_translation() const { Rotation R(rot()); // Rotation part if ( R.abs_angle() < 0.001) return Coord_orth(0.0,0.0,0.0); Vec3<> t = trn(); // translation part // direction cosines of rotation axis n Vec3<> n = Vec3<>(R.x(),R.y(),R.z()).unit(); // parallel component of translation r = n (n.t) return Coord_orth( n * Vec3<>::dot(n, t) ); } /*! \return The identity operator. */ RTop_orth RTop_orth::identity() { return RTop_orth( RTop<>::identity() ); } /*! \return The null (uninitialised) operator. */ RTop_orth RTop_orth::null() { return RTop_orth( RTop<>::null() ); } /*! \return The formatted text string */ String HKL::format() const { return "HKL = ("+String(h())+","+String(k())+","+String(l())+")"; } /*! \return The formatted text string */ String Coord_reci_orth::format() const { return "x*y*z* = ("+String(xs())+","+String(ys())+","+String(zs())+")"; } /*! \return The formatted text string */ String Coord_reci_frac::format() const { return "u*v*w* = ("+String(us())+","+String(vs())+","+String(ws())+")"; } /*! The coordinate is calculated which extends the sequence of coordinates x1, x2, x3 with the specified distance to x3, angle to x2,x3, and torsion to x1,x2,x3. \param x1 First coordinate. \param x2 Second coordinate. \param x3 Third coordinate. \param length x3-new bond length in Angstroms. \param angle x2-x3-new opening angle in Radians. \param torsion x1-x2-x3-new torsion angle in Radians. */ Coord_orth::Coord_orth( const Coord_orth& x1, const Coord_orth& x2, const Coord_orth& x3, const ftype& length, const ftype& angle, const ftype& torsion ) { const Coord_orth xa( (x3-x2).unit() ); const Coord_orth xc( Vec3<>::cross( x2-x1, xa ).unit() ); const Coord_orth xb( Vec3<>::cross( xa, xc ) ); const ftype wa = -length*cos( angle ); const ftype wb = -length*sin( angle )*cos( -torsion ); const ftype wc = -length*sin( angle )*sin( -torsion ); (*this) = x3 + wa*xa + wb*xb + wc*xc; } /*! \return The bond length x1-x2 in Angstroms. */ ftype Coord_orth::length( const Coord_orth& x1, const Coord_orth& x2) { return sqrt( (x2-x1).lengthsq() ); } /*! \return The bond angle x1-x2-x3 in Radians. */ ftype Coord_orth::angle( const Coord_orth& x1, const Coord_orth& x2, const Coord_orth& x3) { return acos( (x3-x2).unit() * (x1-x2).unit() ); } /*! \return The bond torsion x1-x2-x3-x4 in Radians. */ ftype Coord_orth::torsion( const Coord_orth& x1, const Coord_orth& x2, const Coord_orth& x3, const Coord_orth& x4) { const Vec3<> xu( (x3-x2).unit() ); const Vec3<> xa( Vec3<>::cross( x2-x1, xu ) ); const Vec3<> xb( Vec3<>::cross( xu, x4-x3 ) ); const Vec3<> xc( Vec3<>::cross( xa, xb ) ); return atan2( xc*xu, xa*xb ); } /*! \return The formatted text string */ String Coord_orth::format() const { return "xyz = ("+String(x(),10,4)+","+String(y(),10,4)+","+String(z(),10,4)+")"; } Coord_frac Coord_frac::symmetry_copy_near(const Spacegroup& spgr, const Cell& cell, const Coord_frac& n) const { Coord_frac c, cmin(*this); double d2, d2min(1.0e12); for ( int k = 0; k < spgr.num_symops(); k++ ) { c = spgr.symop(k) * (*this); c = c.lattice_copy_near( n ); d2 = ( c - n ).lengthsq( cell ); if ( d2 < d2min ) { d2min = d2; cmin = c; } } return cmin; } /*! \return The formatted text string */ String Coord_frac::format() const { return "uvw = ("+String(u(),10,4)+","+String(v(),10,4)+","+String(w(),10,4)+")"; } /*! \return The formatted text string */ String Coord_grid::format() const { return "uvw = ("+String(u())+","+String(v())+","+String(w())+")"; } /*! \return The formatted text string */ String Coord_map::format() const { return "uvw = ("+String(u(),10,4)+","+String(v(),10,4)+","+String(w(),10,4)+")"; } /*! \return The formatted text string */ String Grid::format() const { return "Nuvw = ("+String(nu())+","+String(nv())+","+String(nw())+")"; } void Grid::debug() const { std::cout << format() << "\n"; } /*! Make a map grid with an oblong bounded by the coordinates min and max. \param min The lower bound coordinate in u,v,w. \param max The upper bound coordinate in u,v,w. */ Grid_range::Grid_range( const Coord_grid& min, const Coord_grid& max ) { min_ = min; max_ = max; (*this)[0] = max_.u()-min_.u()+1; (*this)[1] = max_.v()-min_.v()+1; (*this)[2] = max_.w()-min_.w()+1; } /*! Make a map grid with an oblong bounded by the fractional coordinates min and max, when the sampling of the cell is g \param g The grid sampling of the whole unit cell. \param min The lower bound coordinate in u,v,w. \param max The upper bound coordinate in u,v,w. */ Grid_range::Grid_range( const Grid& g, const Coord_frac& min, const Coord_frac& max ) { min_ = Coord_grid( Util::intc( g.nu() * min.u() ), Util::intc( g.nv() * min.v() ), Util::intc( g.nw() * min.w() ) ); max_ = Coord_grid( Util::intf( g.nu() * max.u() ), Util::intf( g.nv() * max.v() ), Util::intf( g.nw() * max.w() ) ); (*this)[0] = max_.u()-min_.u()+1; (*this)[1] = max_.v()-min_.v()+1; (*this)[2] = max_.w()-min_.w()+1; } /*! Make a map grid large enough to fully enclose a sphere about the origin of a given radius with a given cell and grid sampling. \param cell The cell parameters. \param grid The grid sampling of the whole cell. \param radius The radius of the sphere in Angstroms. */ Grid_range::Grid_range( const Cell& cell, const Grid& grid, const ftype& radius ) { Coord_grid lim( Util::intc( radius * cell.a_star() * ftype(grid.nu()) ), Util::intc( radius * cell.b_star() * ftype(grid.nv()) ), Util::intc( radius * cell.c_star() * ftype(grid.nw()) ) ); min_ = -lim; max_ = lim; (*this)[0] = max_.u()-min_.u()+1; (*this)[1] = max_.v()-min_.v()+1; (*this)[2] = max_.w()-min_.w()+1; } /*! Enlarge the grid by adding \c b cells in every direction. Will shrink the grid if \c b is negative. \param b The number of cells by which to enlarge/shrink. */ void Grid_range::add_border( const int b ) { min_ = min_ - Coord_grid(b,b,b); max_ = max_ + Coord_grid(b,b,b); (*this)[0] = max_.u()-min_.u()+1; (*this)[1] = max_.v()-min_.v()+1; (*this)[2] = max_.w()-min_.w()+1; } /*! A grid is chosen to represent the specified cell at the given resolution, obeying any restrictions imposed by the spacegroup. A slightly finer grid may be chosen if doing so is liable to significantly increase the speed of FFTs on that grid. \param spacegroup The spacegroup which the grid must obey. \param cell The cell which the grid must contain. \param resol The resolution to which the grid must sample. \param rate The linear Shannon rate (oversampling) required. If rate = 1, the grid spaceing will be half the resolution (the the minimum required). For a grid spaceing of resol/3, use the default rate=1.5. */ Grid_sampling::Grid_sampling( const Spacegroup& spacegroup, const Cell& cell, const Resolution& resol, const ftype rate ) { init( spacegroup, cell, resol, rate ); } /*! A grid is chosen to represent the specified cell at the given resolution, obeying any restrictions imposed by the spacegroup. A slightly finer grid may be chosen if doing so is liable to significantly increase the speed of FFTs on that grid. \param spacegroup The spacegroup which the grid must obey. \param cell The cell which the grid must contain. \param resol The resolution to which the grid must sample. \param rate The linear Shannon rate (oversampling) required. If rate = 1, the grid spaceing will be half the resolution (the the minimum required). For a grid spaceing of resol/3, use the default rate=1.5. */ void Grid_sampling::init( const Spacegroup& spacegroup, const Cell& cell, const Resolution& resol, const ftype rate ) { int i, j, l, n, m, nbest; bool eqxy, eqxz, eqyz; ftype t, tbest; // search symops to find grid factors and equalities Grid g( 48, 48, 48 ); Grid factors( 1, 1, 1 ); eqxy = eqxz = eqyz = false; for ( i = 0; i < spacegroup.num_symops(); i++ ) { Isymop isymop( spacegroup.symop(i), g ); eqxy = eqxy || ( isymop.rot()(0,1) != 0 ); eqxz = eqxz || ( isymop.rot()(0,2) != 0 ); eqyz = eqyz || ( isymop.rot()(1,2) != 0 ); for ( j = 0; j < 3; j++ ) factors[j] = Util::max( factors[j], g[j]/(Util::mod(isymop.trn()[j]-1, g[j])+1) ); } // now try a grid // first (lowest) estimate Grid_sampling nuvw( Util::intc( 2.0 * cell.descr().a() * rate / resol.limit() ), Util::intc( 2.0 * cell.descr().b() * rate / resol.limit() ), Util::intc( 2.0 * cell.descr().c() * rate / resol.limit() ) ); // now check against restrictions, speed for ( i = 0; i < 3; i++ ) { nbest = 0; tbest = 1.0e12; for ( n = nuvw[i]; n < 2*nuvw[i]+16; n++ ) { if ( n % (2*factors[i]) == 0 ) { l = 0; // sum of factors (approx. log n) m = n; // what is left in factorisation for ( j = 2; j <= n; j++ ) while ( m%j == 0 ) { m /= j; l += j; } // FFT time O( n * l ) - introduce an extra n^2 for 3D. t = pow( ftype(n), 3 ) * ftype(l); if ( t < tbest ) { nbest = n; tbest = t; } } } nuvw[i] = nbest; } // now check symmetry relationships if ( eqxy ) { n = Util::max( nuvw[0], nuvw[1] ); nuvw[0] = nuvw[1] = n; } if ( eqxz ) { n = Util::max( nuvw[0], nuvw[2] ); nuvw[0] = nuvw[2] = n; } if ( eqyz ) { n = Util::max( nuvw[1], nuvw[2] ); nuvw[1] = nuvw[2] = n; } (*this) = nuvw; } /*! The result is an RT operator. This is a redudent representation, but is handy for assembling compound operators. \return The operator */ Mat33<> Grid_sampling::matrix_grid_frac() const { Mat33<> m( Mat33<>::identity() ); m(0,0) = 1.0/ftype(nu()); m(1,1) = 1.0/ftype(nv()); m(2,2) = 1.0/ftype(nw()); return m; } /*! The result is an RT operator. This is a redudent representation, but is handy for assembling compound operators. \return The operator */ Mat33<> Grid_sampling::matrix_frac_grid() const { Mat33<> m( Mat33<>::identity() ); m(0,0) = ftype(nu()); m(1,1) = ftype(nv()); m(2,2) = ftype(nw()); return m; } /*! \return true if the object has not been initalised. */ bool Grid_sampling::is_null() const { return ( size() <= 0 ); } /*! Threshold value for scaling HKL-sampling coefficients */ itype64 HKL_sampling::sqrt_limit_value = 0x100000; /*! Initialise to 'null' */ HKL_sampling::HKL_sampling() { m00 = -1; } /*! Initialise using cell and resolution. */ HKL_sampling::HKL_sampling( const Cell& cell, const Resolution& resolution ) { itype64 limit_value = sqrt_limit_value*sqrt_limit_value; ftype s = ftype( limit_value ) / resolution.invresolsq_limit(); m00 = itype64( s * cell.a_star()*cell.a_star() ); m11 = itype64( s * cell.b_star()*cell.b_star() ); m22 = itype64( s * cell.c_star()*cell.c_star() ); m01 = itype64( s * 2.0*cell.a_star()*cell.b_star()*cos(cell.gamma_star()) ); m02 = itype64( s * 2.0*cell.a_star()*cell.c_star()*cos(cell.beta_star() ) ); m12 = itype64( s * 2.0*cell.b_star()*cell.c_star()*cos(cell.alpha_star()) ); } /*! Returned HKL contains maximum possible values of H, K, L respectively. \return Limiting h,k,l. */ HKL HKL_sampling::hkl_limit() const { itype64 s00(m00/sqrt_limit_value), s11(m11/sqrt_limit_value), s22(m22/sqrt_limit_value), s01(m01/sqrt_limit_value), s02(m02/sqrt_limit_value), s12(m12/sqrt_limit_value); s01 /= 2; s02 /= 2; s12 /= 2; itype64 det = s00*s11*s22 + s01*s12*s02 + s02*s12*s01 - s00*s12*s12 - s11*s02*s02 - s22*s01*s01; itype64 n00 = ( sqrt_limit_value * ( s11*s22 - s12*s12 + 1 ) ) / ( det - 3 ); itype64 n11 = ( sqrt_limit_value * ( s00*s22 - s02*s02 + 1 ) ) / ( det - 3 ); itype64 n22 = ( sqrt_limit_value * ( s00*s11 - s01*s01 + 1 ) ) / ( det - 3 ); return HKL( Util::isqrt(n00), Util::isqrt(n11), Util::isqrt(n22) ); } /*! Returned resolution is an estimate based on highest reflection in list. \return The resolution. */ Resolution HKL_sampling::resolution( const Cell& cell ) const { HKL lim = hkl_limit(); HKL rfl; // make a list of valid reflections ftype slim(0.0); for (rfl.h()= 0; rfl.h()<=lim.h(); rfl.h()++) for (rfl.k()=-lim.k(); rfl.k()<=lim.k(); rfl.k()++) for (rfl.l()=-lim.l(); rfl.l()<=lim.l(); rfl.l()++) if ( in_resolution( rfl ) ) slim = Util::max( slim, rfl.invresolsq( cell ) ); return Resolution( 0.999999 / sqrt( slim ) ); } bool HKL_sampling::is_null() const { return m00 < 0; } String HKL_sampling::format() const { return "CANNOT FORMAT HKL_sampling"; //return "m00=" + String(m00,12) + " m11=" + String(m11,12) + " m22=" + String(m22,12) + " m01=" + String(m01,12) + " m02=" + String(m02,12) + " m12=" + String(m12,12); } /*! The best isotropic U is the cube root of the determinant of the matrix of anisotropic coefficients. NOTE: This is not the conventional definition, but the mathematically correct one, and gives a better approximation to the anisotropic U (i.e. lower R-factors). \return The nearest isotropic U. */ ftype U_aniso_orth::u_iso() const { return pow( det(), 0.3333333333 ); } /*! \param cell The cell concerned \return The transformed coordinate. */ U_aniso_frac U_aniso_orth::u_aniso_frac( const Cell& cell ) const { return U_aniso_frac( Mat33sym<>( cell.matrix_frac() * Mat33<>(*this) * cell.matrix_frac().transpose() ) ); } /*! The aniso U is transformed by the given RT op. \param u The aniso U. */ U_aniso_orth U_aniso_orth::transform( const RTop_orth& op ) const { Mat33<> r = op.rot().inverse(); return U_aniso_orth( Mat33sym<> ( r.transpose() * Mat33<>( *this ) * r ) ); } /*! \param cell The cell concerned \return The transformed coordinate. */ U_aniso_orth U_aniso_frac::u_aniso_orth( const Cell& cell ) const { return U_aniso_orth( Mat33sym<>( cell.matrix_orth() * Mat33<>(*this) * cell.matrix_orth().transpose() ) ); } /*! The aniso U is transformed by the given RT op. \param u The aniso U. */ U_aniso_frac U_aniso_frac::transform( const RTop_frac& op ) const { Mat33<> r = op.rot().inverse(); return U_aniso_frac( Mat33sym<> ( r.transpose() * Mat33<>( *this ) * r ) ); } void Atom::set_element( const String& s ) { element_ = s; } void Atom::set_coord_orth( const Coord_orth& s ) { coord_orth_ = s; } void Atom::set_occupancy( const ftype& s ) { occupancy_ = s; } void Atom::set_u_iso( const ftype& s ) { u_iso_ = s; } void Atom::set_u_aniso_orth( const U_aniso_orth& s ) { u_aniso_orth_ = s; } /*! The coordinates and U_aniso_orth are transformed. The sigmas are not, since without the full variance-covariance matrix this transformation is impossible. \param rt The operator to apply. */ void Atom::transform( const RTop_orth rt ) { set_coord_orth( coord_orth().transform( rt ) ); set_u_aniso_orth( u_aniso_orth().transform( rt ) ); } Atom Atom::null() { Atom atom; atom.set_element( "" ); atom.set_coord_orth( Coord_orth( Coord_orth::null() ) ); atom.set_u_aniso_orth( U_aniso_orth( U_aniso_orth::null() ) ); atom.set_occupancy( Util::nan() ); atom.set_u_iso( Util::nan() ); return atom; } } // namespace clipper clipper-2.1/clipper/core/hkl_operators.h0000644000374100011300000001364010363703537015353 00000000000000/*! \file lib/hkl_operators.h HKL_data operators for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_HKL_OPERATORS #define CLIPPER_HKL_OPERATORS #include "hkl_datatypes.h" namespace clipper { namespace datatypes { // logical operators HKL_data operator &( const HKL_data_base& d1, const HKL_data_base& d2 ); HKL_data operator |( const HKL_data_base& d1, const HKL_data_base& d2 ); HKL_data operator ^( const HKL_data_base& d1, const HKL_data_base& d2 ); HKL_data operator !( const HKL_data_base& d1 ); HKL_data operator ==( const HKL_data& d1, const int& n ); HKL_data operator !=( const HKL_data& d1, const int& n ); HKL_data operator >=( const HKL_data& d1, const int& n ); HKL_data operator <=( const HKL_data& d1, const int& n ); HKL_data operator >( const HKL_data& d1, const int& n ); HKL_data operator <( const HKL_data& d1, const int& n ); // individual data operators template F_phi operator +( const F_phi& d1, const F_phi& d2 ); template F_phi operator -( const F_phi& d1, const F_phi& d2 ); template F_phi operator -( const F_phi& d1 ); template ABCD operator +( const ABCD& d1, const ABCD& d2 ); // data list operators template HKL_data > operator +( const HKL_data >& d1, const HKL_data >& d2 ); template HKL_data > operator -( const HKL_data >& d1, const HKL_data >& d2 ); template HKL_data > operator *( const HKL_data >& d1, const ftype& s ); template HKL_data > operator -( const HKL_data >& d1 ); template HKL_data > operator +( const HKL_data >& d1, const HKL_data >& d2 ); template HKL_data > operator *( const ftype& s, const HKL_data >& d1 ) { return d1*s; } } // namespace datatypes //! Log phase probability distribution object /*! This object is used to store and manipulate phase log-probability distributions. Centrics are handled by two values on the phase circle, acentrics by a list of values. The values can be indexed like and array. The phase() function returns the phase corresponding to the given array index. Conversion to and from Hendrickson-Lattman coefficients is provided. The object is templatised on the sampling of the phase circle. */ template class LogPhaseProb { public: //! constructor: from HKL class LogPhaseProb( const HKL_class& hkl_class ); //! set HL coeffs template void set_abcd( const datatypes::ABCD& abcd ); //! get HL coeffs template void get_abcd( datatypes::ABCD& abcd ) const; //! set phi/fom template void set_phi_fom( const datatypes::Phi_fom& phifom ); //! get phi/fom template void get_phi_fom( datatypes::Phi_fom& phifom ) const; //! get log probability const ftype& operator[] ( const int& p ) const { return q[p]; } //! set log probability ftype& operator[] ( const int& p ) { return q[p]; } //! return phase associated with index ftype phase( const int& p ) const { return Util::twopi()*ftype(p*pinc+pmin)/ftype(N); } int size() const { return q.size(); } //!< return num. of phases static int sampling() { return N; } //!< return phase sampling private: int pmin, pinc; std::vector q; }; } // namespace clipper #endif clipper-2.1/clipper/core/map_interp.cpp0000644000374100011300000000443010363703537015165 00000000000000/* map_interp.cpp: fundamental conversion ops for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "map_interp.h" namespace clipper { } // namespace clipper clipper-2.1/clipper/core/xmap.cpp0000644000374100011300000002072310776420536014002 00000000000000/* xmap.cpp: implementation file for crystal maps */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "xmap.h" #include "clipper_instance.h" namespace clipper { Message_ctor message_ctor_xmap( " [Xmap: constructed]" ); Mutex Xmap_cacheobj::mutex = Mutex(); Xmap_cacheobj::Xmap_cacheobj( const Key& xmap_cachekey ) : key( xmap_cachekey ) { Spacegroup spacegroup_( xmap_cachekey.spgr_descr() ); xtl_grid = xmap_cachekey.grid_sampling(); // Get the map grid - must contain ASU map_grid = asu_grid = Grid_range( xtl_grid, spacegroup_.asu_min(), spacegroup_.asu_max() ); map_grid.add_border(1); // Create the intergised symops (assumes legal grid) & // Precalculate shifts to index due to symmetry transformed grid steps int sym; nsym = spacegroup_.num_symops(); isymop.resize( nsym ); du.resize( nsym ); dv.resize( nsym ); dw.resize( nsym ); for ( sym = 0; sym < nsym; sym++ ) { Isymop op = Isymop( spacegroup_.symop(sym), xtl_grid ); isymop[sym] = op; du[sym] = map_grid.Grid::index( Coord_grid( op.rot()*Coord_grid(1,0,0) ) ); dv[sym] = map_grid.Grid::index( Coord_grid( op.rot()*Coord_grid(0,1,0) ) ); dw[sym] = map_grid.Grid::index( Coord_grid( op.rot()*Coord_grid(0,0,1) ) ); } // now store the symmetry permutations symperm.resize( nsym, nsym ); for ( int s1 = 0; s1 < nsym; s1++ ) for ( int s2 = 0; s2 < nsym; s2++ ) symperm( s1, s2 ) = spacegroup_.product_op( s1, s2 ); // Flag all non-ASU points in the grid with sym number + 1 Coord_grid base, rot; asu.clear(); asu.resize( map_grid.size(), 255 ); // set all non-asu flags to 255 for ( base = asu_grid.min(); !base.last(asu_grid); base.next(asu_grid) ) { for ( sym = 1; sym < nsym; sym++ ) { rot = base.transform(isymop[sym]).unit(xtl_grid); if ( asu_grid.in_grid( rot ) ) if ( asu[ map_grid.index( rot ) ] == 0 ) break; } if ( sym == nsym ) asu[ map_grid.index( base ) ] = 0; } for ( base = map_grid.min(); !base.last(map_grid); base.next(map_grid) ) if ( asu[ map_grid.index( base ) ] == 255 ) { for ( sym = 0; sym < nsym; sym++ ) { rot = base.transform(isymop[sym]).unit(xtl_grid); if ( asu_grid.in_grid( rot ) ) if ( asu[ map_grid.index( rot ) ] == 0 ) break; } asu[ map_grid.index( base ) ] = sym + 1; } } bool Xmap_cacheobj::matches( const Key& xmap_cachekey ) const { return key.spgr_descr().hash() == xmap_cachekey.spgr_descr().hash() && key.grid_sampling().nu() == xmap_cachekey.grid_sampling().nu() && key.grid_sampling().nv() == xmap_cachekey.grid_sampling().nv() && key.grid_sampling().nw() == xmap_cachekey.grid_sampling().nw(); } String Xmap_cacheobj::format() const { return key.spgr_descr().symbol_hall() + " " + key.grid_sampling().format(); } Xmap_base::FFTtype Xmap_base::default_type_ = Xmap_base::Sparse; /*! For later initialisation: see init() */ Xmap_base::Xmap_base() { Message::message( message_ctor_xmap ); } Xmap_base::Map_reference_coord& Xmap_base::Map_reference_coord::set_coord( const Coord_grid& pos ) { // use pos_ as a temporary variable to try out the current symop pos_ = map_->to_map_unit( pos.transform(map_->isymop[sym_]) ); if ( map_->asu_grid.in_grid( pos_ ) ) { index_ = map_->map_grid.index( pos_ ); if ( map_->asu[ index_ ] == 0 ) { pos_ = pos; return *this; } } map_->find_sym( pos, index_, sym_ ); // general case pos_ = pos; // store the unmodified coord return *this; } void Xmap_base::Map_reference_coord::edge() { int newsym = map_->asu[index_]-1; index_ = map_->map_grid.index( map_->to_map_unit( map_->map_grid.deindex(index_).transform( map_->isymop[newsym] ) ) ); sym_ = map_->cacheref.data().symperm( newsym, sym_ ); } /*! The Xmap is initialised with a given cell, spacegroup, and grid sampling. A unique assymetric unit (ASU) of grid cells is selected and will be used to store a unique set of data. If any of the parameters have null values, the existing values will be unchanged. The object will only be fully initialised once all parameters are available. \param spacegroup The spacegroup for the map \param cell The cell for the map \param grid_sam The grid sampling for the map, i.e. the sampling along each axis for one whole cell */ void Xmap_base::init( const Spacegroup& spacegroup, const Cell& cell, const Grid_sampling& grid_sam ) { // set parameters spacegroup_ = spacegroup; cell_ = cell; grid_sam_ = grid_sam; // check parameters if ( is_null() ) return; // get cache ref and fast access copies Xmap_cacheobj::Key key( spacegroup, grid_sam ); cacheref = ClipperInstantiator::instance().xmap_cache().cache( key ); asu = &(cacheref.data().asu[0]); isymop = &(cacheref.data().isymop[0]); du = &(cacheref.data().du[0]); dv = &(cacheref.data().dv[0]); dw = &(cacheref.data().dw[0]); asu_grid = cacheref.data().asu_grid; map_grid = cacheref.data().map_grid; nsym = cacheref.data().nsym; // store orthogonal conversions rt_grid_orth = RTop<>( cell_.matrix_orth()*grid_sam_.matrix_grid_frac() ); rt_orth_grid = rt_grid_orth.inverse(); } /*! \return true if the object has not been initalised. */ bool Xmap_base::is_null() const { return ( spacegroup_.is_null() || cell_.is_null() || grid_sam_.is_null() ); } /*! The multiplicity is the number of times the spacegroup operators map a particular grid point onto itself. This is required in order to properly weight map statistics so as to get the same result from just an ASU as using the whole cell. \param pos The coordinate of the grid point. \return The multiplicty of the point. */ int Xmap_base::multiplicity( const Coord_grid& pos ) const { int mult = 1; Coord_grid base = pos.unit(grid_sam_); for ( int sym = 1; sym < cacheref.data().nsym; sym++ ) if ( base.transform(isymop[sym]).unit(grid_sam_) == base ) mult++; return mult; } void Xmap_base::asu_error( const Coord_grid& pos ) const { std::cerr << "Failure to find grid coordinate " << pos.format() << std::endl; Message::message( Message_fatal( "Xmap: Internal map ASU error - " + cacheref.data().format() ) ); } // compile templates template class Xmap; template class Xmap; template class Xmap; template class Xmap; template class Xmap; template class Xmap; template class Xmap; template class Xmap; } // namespace clipper clipper-2.1/clipper/core/clipper_types.cpp0000644000374100011300000001242411350422676015712 00000000000000/* clipper_types.cpp: implementation file for clipper helper functions */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "clipper_types.h" #include namespace clipper { String::String( const char* str, const int l ) { std::ostringstream s; for ( int i = 0; i < l; i++ ) s << str[i]; *this = s.str(); } String::String( const int i, const int w ) { std::ostringstream s; s.width(w); s << i; *this = s.str(); } String::String( const long i, const int w ) { std::ostringstream s; s.width(w); s << i; *this = s.str(); } String::String( const float f, const int w, const int p ) { std::ostringstream s; s.width(w); s.precision(p); s << f; *this = s.str(); } String::String( const double f, const int w, const int p ) { std::ostringstream s; s.width(w); s.precision(p); s << f; *this = s.str(); } std::vector String::split(const String sep) const { std::vector splitstr; size_t tokbeg = 0, tokend = 0; while (1) { tokbeg = find_first_not_of(sep, tokend); if (tokbeg == String::npos) return splitstr; tokend = find_first_of(sep, tokbeg); if (tokend == String::npos) break; splitstr.push_back( substr(tokbeg, tokend-tokbeg) ); } splitstr.push_back( substr(tokbeg) ); return splitstr; } String String::trim() const { String trimmed; int i, j; for ( i = 0; i < length(); i++ ) if ( !isspace( (*this)[i] ) ) break; for ( j = length()-1; j >= 0; j-- ) if ( !isspace( (*this)[j] ) ) break; return substr( i, j-i+1 ); } String String::tail() const { return substr( rfind( '/' ) + 1 ); } String String::head() const { return substr( 0, find( '/' ) ); } String String::nohead() const { size_t p = find( '/' ); return ( p == String::npos ) ? "" : substr( p + 1 ); } String String::notail() const { size_t p = rfind( '/' ); return ( p == String::npos ) ? "" : substr( 0, p ); } String String::rational( const double f, const int b, const bool sign ) { std::ostringstream s; int n = Util::intr( fabs( b * f ) ); int d = b; if (sign) s << ( ( f > 0 ) ? "+" : "-" ); else s << ( ( f > 0 ) ? "" : "-" ); for ( int i = 5; i > 1; i-- ) { if ( ( n % i == 0 ) && ( d % i == 0 ) ) { n /= i; d /= i; } } s << n; if ( d != 1 ) s << "/" << d; return s.str();; } int String::i() const { std::istringstream s(*this); int i; s >> i; return i; } long String::l() const { std::istringstream s(*this); long i; s >> i; return i; } ftype32 String::f32() const { std::istringstream s(*this); float f; s >> f; return f; } ftype64 String::f64() const { std::istringstream s(*this); double f; s >> f; return f; } ftype String::f() const { std::istringstream s(*this); ftype f; s >> f; return f; } ftype String::rational() const { const String& s = (*this); int i; for ( i = 0; i < s.length(); i++ ) if ( s[i] == '/' ) break; if ( i == s.length() ) return ( s.f() ); return ( String(s.substr(0,i)).f() / String(s.substr(i+1)).f() ); } // template compilations template class Vec3; template class Mat33; template class Mat33sym; template class Matrix; template class Vec3; template class Mat33; template class Mat33sym; template class Matrix; } // namespace clipper clipper-2.1/clipper/core/spacegroup.h0000644000374100011300000002442411244731657014654 00000000000000/*! \file lib/spacegroup.h Header file for spacegroup symmetry class */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA /* some code & data converted from CCP4 library symlib.f (various authors) */ #ifndef CLIPPER_SPACEGROUP #define CLIPPER_SPACEGROUP #include "symop.h" #include "spacegroup_data.h" namespace clipper { // forward definitions class HKL; class HKL_class; class Coord_frac; //! spacegroup description /*! The spacegroup description is a compact description of a spacegroup. It may be initialised from Hall or H-M symbols, a string of symops or a number. Internally a hash code is used to refer to the spacegroup, so this object is only 32 bits in size. For more details of spacegroup symbols, see Sydney R. Hall & Ralf W. Grosse-Kunstleve 'Concise Space-Group Symbols', http://www.kristall.ethz.ch/LFK/software/sginfo/hall_symbols.html */ class Spgr_descr { public: enum TYPE { Hall, HM, XHM, Symops, Number, Unknown }; //! null constructor Spgr_descr(); //! constructor: from symbol or operators. explicit Spgr_descr( const String& symb, TYPE type = Unknown ); //! constructor: from number. explicit Spgr_descr( const int& num ); //! return the spacegroup number int spacegroup_number() const; //! return the Hall symbol String symbol_hall() const; //! return the H-M symbol String symbol_hm() const; //! return the extended H-M symbol String symbol_xhm() const; //! return the extension H-M symbol String symbol_hm_ext() const; //! set preferred default spacegroup choice static void set_preferred( const char& c ); //! Vector of symop codes and associated methods class Symop_codes : public std::vector { public: //! initialise from Hall symbol void init_hall( const String& symb ); //! initialise from symops void init_symops( const String& symb ); //! expand (incomplete) list of symops Symop_codes expand() const; //! return primitive non-inversion ops (by computation) Symop_codes primitive_noninversion_ops() const; //! return inversion ops (by computation) Symop_codes inversion_ops() const; //! return primitive incl inversion ops (by computation) Symop_codes primitive_ops() const; //! return lattice centering ops (by computation) Symop_codes centering_ops() const; //! return Laue ops Symop_codes laue_ops() const; //! return point group ops Symop_codes pgrp_ops() const; //! return Patterson ops Symop_codes patterson_ops() const; //! return minimal list of generator ops Symop_codes generator_ops() const; //! return product of this (expanded) list by another (expanded) list Symop_codes product( const Symop_codes& ops2 ) const; //! return hash code of symop list unsigned int hash() const; }; //! constructor: from symop list. explicit Spgr_descr( const Symop_codes& ops ); //! return the generators for the spacegroup const Symop_codes& generator_ops() const { return generators_; } //! return the hash code for the spacegroup \internal const unsigned int& hash() const { return hash_; } protected: unsigned int hash_; //!< hash code of spacegroup Symop_codes generators_; //!< codes for symop generators static char pref_12, pref_hr; //!< preferred origin and hex/romb symbols }; // ObjectCache data type class Spgr_cacheobj { public: typedef Spgr_descr Key; Spgr_cacheobj( const Key& spgr_cachekey ); //!< construct entry bool matches( const Key& spgr_cachekey ) const; //!< compare entry String format() const; //!< string description // data Key spgr_cachekey_; //!< spacegroup cachekey int nsym, nsymn, nsymi, nsymc, nsymp; //!< number of syms: total, primitive int lgrp; //!< Laue group number std::vector symops; //!< symmetry operators std::vector isymops; //!< symmetry operators Vec3<> asu_min_, asu_max_; //!< real space ASU static Mutex mutex; //!< thread safety }; //! Spacegroup object /*! The spacegroup object is a full description of a spacegroup, including all the most regularly used information in an efficient form. It may be initialised from a clipper::Spgr_descr. This object. For more details of spacegroup symbols, see Sydney R. Hall & Ralf W. Grosse-Kunstleve 'Concise Space-Group Symbols', http://www.kristall.ethz.ch/LFK/software/sginfo/hall_symbols.html */ class Spacegroup : public Spgr_descr { public: //! enumeration for fast construction of Null or P1 spacegroup enum TYPE { Null, P1 }; //! enumeration for cell axes enum AXIS { A=0, B=1, C=2 }; //! null constructor Spacegroup() {}; //! constructor: fast constructor for Null or P1 spacegroup explicit Spacegroup( TYPE type ); //! constructor: from spacegroup description explicit Spacegroup( const Spgr_descr& spgr_descr ); //! initialiser: from spacegroup description void init( const Spgr_descr& spgr_descr ); //! test if object has been initialised bool is_null() const; // methods //! get spacegroup description inline const Spgr_descr& descr() const { return (*this); } //! get number of symops inline const int& num_symops() const { return nsym; } //! get number of primitive symops (identical to num_primitive_symops()) inline const int& num_primops() const { return num_primitive_symops(); } //! get number of primitive symops (inc identity and inversion) inline const int& num_primitive_symops() const { return nsymp; } //! get number of centering symops (inc identity) inline const int& num_centering_symops() const { return nsymc; } //! get number of inversion symops (inc identity) inline const int& num_inversion_symops() const { return nsymi; } //! get number of primitive non-inversion symops (inc identity) inline const int& num_primitive_noninversion_symops() const { return nsymn;} //! get n'th symop inline const Symop& symop( const int& sym_no ) const { return symops[sym_no]; } //! get n'th primitive symop (identical to symop(sym_no)) inline const Symop& primitive_symop( const int& sym_no ) const { return symops[sym_no]; } //! get n'th inversion symop (0...1 max) inline const Symop& inversion_symop( const int& sym_no ) const { return symops[nsymn*sym_no]; } //! get n'th centering symop (0...3 max) inline const Symop& centering_symop( const int& sym_no ) const { return symops[nsymp*sym_no]; } //! get the order of rotational symmetry about a given axis int order_of_symmetry_about_axis( const AXIS axis ) const; //! get 'class' of reflection: multiplicity, allowed phase, absence HKL_class hkl_class( const HKL& hkl ) const; //! test if hkl is in default reciprocal ASU bool recip_asu( const HKL& hkl ) const; //! get symop number corresponding to the product of two symops int product_op( const int& s1, int& s2 ) const; //! get symop number corresponding to the inverse of a symop int inverse_op( const int& s ) const; //! get map ASU, upper bound Coord_frac asu_max() const; //! get map ASU, lower bound Coord_frac asu_min() const; //! test if change of hand preserves spacegroup bool invariant_under_change_of_hand() const; // inherited functions listed for documentation purposes //-- int spacegroup_number() const; //-- String symbol_hall() const; //-- String symbol_hm() const; //! return the Laue group symbol String symbol_laue() const; //! Return P1 spacegroup static Spacegroup p1() { return Spacegroup( P1 ); } //! Return null spacegroup static Spacegroup null() { return Spacegroup( Null ); } void debug() const; private: ObjectCache::Reference cacheref; //!< object cache reference const Symop* symops; //!< fast access ptr const Isymop* isymops; //!< fast access ptr data::ASUfn asufn; //!< fast access ptr int nsym, nsymn, nsymi, nsymc, nsymp; //!< fast access copies }; } // namespace clipper #endif clipper-2.1/clipper/core/container_map.cpp0000644000374100011300000000440610363703537015651 00000000000000/* container_map.cpp: class file for map containers */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "container_map.h" namespace clipper { } // namespace clipper clipper-2.1/clipper/core/clipper_stats.h0000644000374100011300000002067710777707715015376 00000000000000/*! \file lib/clipper_stats.h Header file for clipper helper functions */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_STATS #define CLIPPER_STATS #include "clipper_types.h" namespace clipper { //! Range - upper and lower bounds of some type template class Range { public: //! null constructor inline Range() { lmin = 999999999; lmax = -999999999; } //! constructor inline Range( const T& min, const T& max ) { lmin = min; lmax = max; } inline const T& min() const { return lmin; } //!< minimum value inline const T& max() const { return lmax; } //!< maximum value inline T range() const { return lmax-lmin; } //!< range = max - min //! update limits to include a new datum inline void include( const T& datum ) { lmin = Util::min( lmin, datum ); lmax = Util::max( lmax, datum ); } //! test if data is within limits ( min <= datum <= max ) inline bool contains( const T& datum ) const { return ( datum >= lmin && datum <= lmax ); } //! truncate data to be within range inline T truncate( const T& datum ) const { return Util::bound( lmin, datum, lmax ); } private: T lmin, lmax; }; //! Range sampling: discrete sampling of a real range. class Range_sampling : public Range { public: //! null constructor inline Range_sampling() : n_(0) {} //! constructor: from number of samplings inline Range_sampling( const int& n ) : n_(n) {} //! constructor: from range and number of samplings inline Range_sampling( const Range& range, const int& n ) : Range( range ), n_(n) {} //! return fractional posn in counting range from x-value (0..n) inline ftype indexf( const ftype& x ) const { return ftype(size())*(x-min())/range(); } //! return x-value (0..n) from fractional posn in counting range inline ftype x( const ftype& i ) const { return range()*i/ftype(size())+min(); } //! return nearest index to particular x-value inline int index( const ftype& x ) const { return Util::intf( indexf(x) ); } //! return nearest index to particular x-value (bounded 0...n-1) inline int index_bounded( const ftype& x ) const { return Util::bound( 0, Util::intf( indexf(x) ), size()-1 ); } //! return x-value corresponding to centre of i'th range inline ftype x( const int& i ) const { return x( ftype(i)+0.5 ); } //! return x-value corresponding to bottom of i'th range inline ftype x_min( const int& i ) const { return x( ftype(i) ); } //! return x-value corresponding to top of i'th range inline ftype x_max( const int& i ) const { return x( ftype(i)+1.0 ); } //! return number of samplings in range inline int size() const { return n_; } private: int n_; }; //! General histogram class /*! This class is used to accumulate and access a histogram of values spread over a specified range. On storing data or retrieving by interpolation the range is checked. */ class Histogram : public Range_sampling { public: //! null constructor Histogram() {} //! constructor: from range and sampling Histogram( const Range& range, const int& n ) : Range_sampling( range, n ), data( n, 0.0 ) {} //! add value to histogram (if it is in range) void accumulate( const ftype& x ) { if ( contains(x) ) data[ index_bounded(x) ] += 1.0; } //! add specified value to histogram (if it is in range) void accumulate( const ftype& x, const ftype& w ) { if ( contains(x) ) data[ index_bounded(x) ] += w; } //! return sum of whole histogram ftype sum() const; //! return value at index in histogram (Note: no bound check on i) inline const ftype& y( const int& i ) const { return data[i]; } //! return value at interpolated position in histogram ftype y( const ftype& x ) const; //! add the contents of two histograms (size must match) const Histogram& operator += ( const Histogram& h ); // inherited functions listed for documentation purposes //-- inline ftype x( const int& i ) const; //-- inline ftype x_min( const int& i ) const; //-- inline ftype x_max( const int& i ) const; //-- inline int size() const; private: std::vector data; }; //! Generic ordinal gernerator /*! This is a generic fast ordinal calculator. It is supplied with a list of values, from which it prepares a cumulative distribution function. This may the used to return the approximate fracitonal ordinal (in the range 0...1) for any given value from the distibution. The distibution may be initialised by providing a vector of values from the distribution, or by adding the values and calling prep_ordinal(). This distribution may also be inverted. Generation of a value from an ordinal may be used for generating random values from a given distribution, or for histogram matching. */ class Generic_ordinal { public: //! null constructor Generic_ordinal() {} //! constructor: from range and sampling Generic_ordinal( const Range& range, const int& n ) { init( range, n ); } //! initialiser: takes the source range and sampling void init( const Range& range, const int num_ranges = 1000 ); //! initialiser: takes the source distibution and a number of bins void init( const std::vector& values, const int num_ranges = 1000 ); //! return reflection ordinal ftype ordinal( const ftype& value ) const; //! accumulate values to build the distribution void accumulate( const ftype& value ); //! accumulate values to build the distribution void accumulate( const ftype& value, const ftype& weight ); //! generate the ordinal histogram void prep_ordinal(); //! invert distribution to get value from ordinal void invert(); //! DEPRECATED: initialiser: takes a number of bins for histogram void init( const int num_ranges = 1000 ); //! DEPRECATED: add a value to the distribution (pass 1 of 2) void add_pass_1( const ftype& value ); //! DEPRECATED: add a value to the distribution (pass 2 of 2) void add_pass_2( const ftype& value ); protected: ftype nranges; //!< number of ranges Range range_; //!< resolution range of data std::vector hist; //!< histogram of reflections vs resolution }; } // namespace clipper #endif clipper-2.1/clipper/core/container_types.cpp0000644000374100011300000001353610363703537016244 00000000000000/* container_types.cpp: class file for basic containers */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "container_types.h" namespace clipper { const Resolution NullResolution; //(*this) = resolution_; Container::update(); } /*! The object is initialised, and children are updated. \param spacegroup_ The value to give to the contained object. */ void CSpacegroup::init( const Spacegroup& spacegroup_ ) { dynamic_cast(*this) = spacegroup_; Container::update(); } /*! The object is initialised, and children are updated. \param cell_ The value to give to the contained object. */ void CCell::init( const Cell& cell_ ) { dynamic_cast(*this) = cell_; Container::update(); } /*! The top object in a tree is initialised from a known grid. \param name The object name. \param grid The grid sampling. */ CGrid_sampling::CGrid_sampling( const String name, const Grid_sampling& grid ) : Container( name ), Grid_sampling( grid ), rate_( 1.5 ) {} /*! The normal form for a child object - spacegroup and cell inherited. \param parent The objects parent. \param name The object name. \param rate The Shannon rate (default 1.5). */ CGrid_sampling::CGrid_sampling( Container& parent, const String name, const ftype rate ) : Container( parent, name ), rate_( rate ) { init( NullSpacegroup, NullCell, NullResolution, 0.0 ); } /*! This is still a child object but is initialised directly. \param parent The objects parent. \param name The object name. \param grid The grid sampling. */ CGrid_sampling::CGrid_sampling( Container& parent, const String name, const Grid_sampling& grid ) : Container( parent, name ), Grid_sampling( grid ), rate_( 1.5 ) {} /*! The object is initialised if the appropriate parent objects are available, and children are updated. \param spacegroup The spacegroup. \param cell The cell. \param resolution The resolution. \param rate_ The Shannon rate (If <1 previous value is used, default 1.5). */ void CGrid_sampling::init( const Spacegroup& spacegroup, const Cell& cell, const Resolution& resolution, const ftype rate ) { // use supplied values by default const Spacegroup* sp = &spacegroup; // use pointers so we can reassign const Cell* cp = &cell; const Resolution* rp = &resolution; // otherwise get them from the tree if ( sp->is_null() ) sp = parent_of_type_ptr(); if ( cp->is_null() ) cp = parent_of_type_ptr(); if ( rp->is_null() ) rp = parent_of_type_ptr(); if ( rate >= 1.0 ) rate_ = rate; // use rate if given // initialise if ( sp != NULL && cp != NULL && rp != NULL ) if ( !sp->is_null() && !cp->is_null() && !rp->is_null() ) Grid_sampling::init( *sp, *cp, *rp, rate_ ); Container::update(); } /*! The object is initialised, and children are updated. \param grid_sampling_ The value to give to the contained object. */ void CGrid_sampling::init( const Grid_sampling& grid_sampling_ ) { dynamic_cast(*this) = grid_sampling_; Container::update(); } /*! Hierarchical update. If this object is uninitialised, an attempt is made to initialise the object using information from its parents in the hierarchy. The childen of the object are then updated. */ void CGrid_sampling::update() { if ( Grid_sampling::is_null() ) init( NullSpacegroup, NullCell, NullResolution, 0.0 ); else Container::update(); } } // namespace clipper clipper-2.1/clipper/core/hkl_data.cpp0000644000374100011300000001514111205462346014573 00000000000000/* hkl_data.cpp: class file for reflection data class + children */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "hkl_data.h" #include "clipper_instance.h" namespace clipper { Message_ctor message_ctor_hkl_data( " [HKL_data: constructed]" ); Mutex HKL_data_cacheobj::mutex = Mutex(); HKL_data_cacheobj::HKL_data_cacheobj( const Key& hkl_data_cachekey ) : key( hkl_data_cachekey ) { init( Spacegroup( hkl_data_cachekey.spgr_descr() ), Cell( hkl_data_cachekey.cell_descr() ), hkl_data_cachekey.hkl_sampling(), true ); } bool HKL_data_cacheobj::matches( const Key& hkl_data_cachekey ) const { return ( key.spgr_descr().hash() == hkl_data_cachekey.spgr_descr().hash() && key.hkl_sampling() == hkl_data_cachekey.hkl_sampling() ); } String HKL_data_cacheobj::format() const { return key.spgr_descr().symbol_hall() + " " + key.hkl_sampling().format(); } /*! For later initialisation: see init() */ HKL_data_base::HKL_data_base() { parent_hkl_info = NULL; parent_cell = NULL; Message::message( message_ctor_hkl_data ); } /*! Initialise the object using a given reflection list and cell. \param hkl_info The reflection list object. \param cell The unit cell for this datalist. */ void HKL_data_base::init( const HKL_info& hkl_info, const Cell& cell ) { parent_hkl_info = &hkl_info; parent_cell = &cell; cell_matches_parent = cell.equals( hkl_info.cell(), 0.5 ); } /*! Initialise the object using a given reflection list and cell. \param hkl_data Object from which to inherit spacegrpoup, cell, sampling. */ void HKL_data_base::init( const HKL_data_base& hkl_data ) { (*this) = hkl_data; } /*! Initialise the object using a given spacegroup, cell, and sampling. \param spacegroup The spacegroup for this datalist. \param cell The unit cell for this datalist. \param hkl_sampling The reflection list description. */ void HKL_data_base::init( const Spacegroup& spacegroup, const Cell& cell, const HKL_sampling& hkl_sampling ) { // set parameters spacegroup_ = spacegroup; cell_ = cell; hkl_sampling_ = hkl_sampling; // check parameters if ( spacegroup_.is_null() || cell_.is_null() || hkl_sampling_.is_null() ) return; // estimate resolution resolution_ = hkl_sampling.resolution( cell ); // get cache ref HKL_data_cacheobj::Key key( spacegroup, cell, hkl_sampling ); cacheref = ClipperInstantiator::instance().hkl_data_cache().cache( key ); // store legacy and fast access pointers init( cacheref.data(), cell_ ); } /*! \return true if the object has not been initalised. */ bool HKL_data_base::is_null() const { if ( parent_hkl_info != NULL && parent_cell != NULL ) return ( parent_hkl_info->is_null() || parent_cell->is_null() ); else return true; } /*! Return the resolution of a particular reflection. If the cell of this list closely matches (to within 0.5A) the cell of the parent list, this is a simple lookup, otherwise a metric calculation is required. */ ftype HKL_data_base::invresolsq( const int& index ) const { if ( cell_matches_parent ) return base_hkl_info().invresolsq(index); else return base_hkl_info().hkl_of(index).invresolsq(base_cell()); } /*! \return The high and low resolution limits of the non-missing data. */ Range HKL_data_base::invresolsq_range() const { Range slim; HKL_info::HKL_reference_index ih; for ( ih = first_data(); !ih.last(); next_data(ih) ) slim.include( invresolsq( ih.index() ) ); return slim; } /*! \return The number of non-missing data in the object. */ int HKL_data_base::num_obs() const { int num = 0; HKL_info::HKL_reference_index ih; for ( ih = first_data(); !ih.last(); next_data(ih) ) num++; return num; } /*! \return HKL reference to the first data in this object. */ HKL_info::HKL_reference_index HKL_data_base::first() const { return HKL_reference_index( *parent_hkl_info, 0 ); } /*! \return HKL reference to the first non-missing data in this object. */ HKL_info::HKL_reference_index HKL_data_base::first_data() const { HKL_reference_index it( *parent_hkl_info, -1 ); return next_data(it); } /*! \param ih The HKL reference to increment. \return HKL reference to the next non-missing data in this object. */ HKL_info::HKL_reference_index& HKL_data_base::next_data( HKL_info::HKL_reference_index& ih ) const { do { ih.next(); if ( ih.last() ) break; } while ( missing( ih.index() ) ); return ih; } void HKL_data_base::debug() const { base_hkl_info().debug(); base_hkl_info().spacegroup().debug(); base_hkl_info().cell().debug(); base_cell().debug(); } } // namespace clipper clipper-2.1/clipper/core/atomsf.cpp0000644000374100011300000014241110721250650014311 00000000000000/* atomsf.cpp: implementation file for atomic scattering factors */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "atomsf.h" namespace clipper { namespace data { /* This implementation uses the coefficients from Waasmaier & Kirfel (1995), Acta Cryst. A51, 416-431. The source data can be found at: ftp://wrzx02.rz.uni-wuerzburg.de/pub/local/Crystallography/sfac.dat */ struct SFdata { char name[8]; ftype64 a[6]; ftype64 b[6]; }; SFdata sfdata[] = { {"H" ,{ 0.413048, 0.294953, 0.187491, 0.080701, 0.023736, 0.000049}, { 15.569946, 32.398468, 5.711404, 61.889874, 1.334118, 0.000000}}, {"He" ,{ 0.732354, 0.753896, 0.283819, 0.190003, 0.039139, 0.000487}, { 11.553918, 4.595831, 1.546299, 26.463964, 0.377523, 0.000000}}, {"Li" ,{ 0.974637, 0.158472, 0.811855, 0.262416, 0.790108, 0.002542}, { 4.334946, 0.342451, 97.102966,201.363831, 1.409234, 0.000000}}, {"Be" ,{ 1.533712, 0.638283, 0.601052, 0.106139, 1.118414, 0.002511}, { 42.662079, 0.595420, 99.106499, 0.151340, 1.843093, 0.000000}}, {"B" ,{ 2.085185, 1.064580, 1.062788, 0.140515, 0.641784, 0.003823}, { 23.494068, 1.137894, 61.238976, 0.114886, 0.399036, 0.000000}}, {"C" ,{ 2.657506, 1.078079, 1.490909, -4.241070, 0.713791, 4.297983}, { 14.780758, 0.776775, 42.086842, -0.000294, 0.239535, 0.000000}}, {"N" ,{ 11.893780, 3.277479, 1.858092, 0.858927, 0.912985,-11.804902}, { 0.000158, 10.232723, 30.344690, 0.656065, 0.217287, 0.000000}}, {"O" ,{ 2.960427, 2.508818, 0.637853, 0.722838, 1.142756, 0.027014}, { 14.182259, 5.936858, 0.112726, 34.958481, 0.390240, 0.000000}}, {"F" ,{ 3.511943, 2.772244, 0.678385, 0.915159, 1.089261, 0.032557}, { 10.687859, 4.380466, 0.093982, 27.255203, 0.313066, 0.000000}}, {"Ne" ,{ 4.183749, 2.905726, 0.520513, 1.135641, 1.228065, 0.025576}, { 8.175457, 3.252536, 0.063295, 21.813910, 0.224952, 0.000000}}, {"Na" ,{ 4.910127, 3.081783, 1.262067, 1.098938, 0.560991, 0.079712}, { 3.281434, 9.119178, 0.102763,132.013947, 0.405878, 0.000000}}, {"Mg" ,{ 4.708971, 1.194814, 1.558157, 1.170413, 3.239403, 0.126842}, { 4.875207,108.506081, 0.111516, 48.292408, 1.928171, 0.000000}}, {"Al" ,{ 4.730796, 2.313951, 1.541980, 1.117564, 3.154754, 0.139509}, { 3.628931, 43.051167, 0.095960,108.932388, 1.555918, 0.000000}}, {"Si" ,{ 5.275329, 3.191038, 1.511514, 1.356849, 2.519114, 0.145073}, { 2.631338, 33.730728, 0.081119, 86.288643, 1.170087, 0.000000}}, {"P" ,{ 1.950541, 4.146930, 1.494560, 1.522042, 5.729711, 0.155233}, { 0.908139, 27.044952, 0.071280, 67.520187, 1.981173, 0.000000}}, {"S" ,{ 6.372157, 5.154568, 1.473732, 1.635073, 1.209372, 0.154722}, { 1.514347, 22.092527, 0.061373, 55.445175, 0.646925, 0.000000}}, {"Cl" ,{ 1.446071, 6.870609, 6.151801, 1.750347, 0.634168, 0.146773}, { 0.052357, 1.193165, 18.343416, 46.398396, 0.401005, 0.000000}}, {"Ar" ,{ 7.188004, 6.638454, 0.454180, 1.929593, 1.523654, 0.265954}, { 0.956221, 15.339877, 15.339862, 39.043823, 0.062409, 0.000000}}, {"K" ,{ 8.163991, 7.146945, 1.070140, 0.877316, 1.486434, 0.253614}, { 12.816323, 0.808945,210.327011, 39.597652, 0.052821, 0.000000}}, {"Ca" ,{ 8.593655, 1.477324, 1.436254, 1.182839, 7.113258, 0.196255}, { 10.460644, 0.041891, 81.390381,169.847839, 0.688098, 0.000000}}, {"Sc" ,{ 1.476566, 1.487278, 1.600187, 9.177463, 7.099750, 0.157765}, { 53.131023, 0.035325,137.319489, 9.098031, 0.602102, 0.000000}}, {"Ti" ,{ 9.818524, 1.522646, 1.703101, 1.768774, 7.082555, 0.102473}, { 8.001879, 0.029763, 39.885422,120.157997, 0.532405, 0.000000}}, {"V" ,{ 10.473575, 1.547881, 1.986381, 1.865616, 7.056250, 0.067744}, { 7.081940, 0.026040, 31.909672,108.022842, 0.474882, 0.000000}}, {"Cr" ,{ 11.007069, 1.555477, 2.985293, 1.347855, 7.034779, 0.065510}, { 6.366281, 0.023987, 23.244839,105.774498, 0.429369, 0.000000}}, {"Mn" ,{ 11.709542, 1.733414, 2.673141, 2.023368, 7.003180, -0.147293}, { 5.597120, 0.017800, 21.788420, 89.517914, 0.383054, 0.000000}}, {"Fe" ,{ 12.311098, 1.876623, 3.066177, 2.070451, 6.975185, -0.304931}, { 5.009415, 0.014461, 18.743040, 82.767876, 0.346506, 0.000000}}, {"Co" ,{ 12.914510, 2.481908, 3.466894, 2.106351, 6.960892, -0.936572}, { 4.507138, 0.009126, 16.438129, 76.987320, 0.314418, 0.000000}}, {"Ni" ,{ 13.521865, 6.947285, 3.866028, 2.135900, 4.284731, -2.762697}, { 4.077277, 0.286763, 14.622634, 71.966080, 0.004437, 0.000000}}, {"Cu" ,{ 14.014192, 4.784577, 5.056806, 1.457971, 6.932996, -3.254477}, { 3.738280, 0.003744, 13.034982, 72.554794, 0.265666, 0.000000}}, {"Zn" ,{ 14.741002, 6.907748, 4.642337, 2.191766, 38.424042,-36.915829}, { 3.388232, 0.243315, 11.903689, 63.312130, 0.000397, 0.000000}}, {"Ga" ,{ 15.758946, 6.841123, 4.121016, 2.714681, 2.395246, -0.847395}, { 3.121754, 0.226057, 12.482196, 66.203621, 0.007238, 0.000000}}, {"Ge" ,{ 16.540613, 1.567900, 3.727829, 3.345098, 6.785079, 0.018726}, { 2.866618, 0.012198, 13.432163, 58.866047, 0.210974, 0.000000}}, {"As" ,{ 17.025642, 4.503441, 3.715904, 3.937200, 6.790175, -2.984117}, { 2.597739, 0.003012, 14.272119, 50.437996, 0.193015, 0.000000}}, {"Se" ,{ 17.354071, 4.653248, 4.259489, 4.136455, 6.749163, -3.160982}, { 2.349787, 0.002550, 15.579460, 45.181202, 0.177432, 0.000000}}, {"Br" ,{ 17.550570, 5.411882, 3.937180, 3.880645, 6.707793, -2.492088}, { 2.119226, 16.557184, 0.002481, 42.164009, 0.162121, 0.000000}}, {"Kr" ,{ 17.655279, 6.848105, 4.171004, 3.446760, 6.685200, -2.810592}, { 1.908231, 16.606236, 0.001598, 39.917473, 0.146896, 0.000000}}, {"Rb" ,{ 8.123134, 2.138042, 6.761702, 1.156051, 17.679546, 1.139548}, { 15.142385, 33.542667, 0.129372,224.132507, 1.713368, 0.000000}}, {"Sr" ,{ 17.730219, 9.795867, 6.099763, 2.620025, 0.600053, 1.140251}, { 1.563060, 14.310868, 0.120574,135.771317, 0.120574, 0.000000}}, {"Y" ,{ 17.792040, 10.253252, 5.714949, 3.170516, 0.918251, 1.131787}, { 1.429691, 13.132816, 0.112173,108.197029, 0.112173, 0.000000}}, {"Zr" ,{ 17.859772, 10.911038, 5.821115, 3.512513, 0.746965, 1.124859}, { 1.310692, 12.319285, 0.104353, 91.777542, 0.104353, 0.000000}}, {"Nb" ,{ 17.958399, 12.063054, 5.007015, 3.287667, 1.531019, 1.123452}, { 1.211590, 12.246687, 0.098615, 75.011948, 0.098615, 0.000000}}, {"Mo" ,{ 6.236218, 17.987711, 12.973127, 3.451426, 0.210899, 1.108770}, { 0.090780, 1.108310, 11.468720, 66.684151, 0.090780, 0.000000}}, {"Tc" ,{ 17.840963, 3.428236, 1.373012, 12.947364, 6.335469, 1.074784}, { 1.005729, 41.901382,119.320541, 9.781542, 0.083391, 0.000000}}, {"Ru" ,{ 6.271624, 17.906738, 14.123269, 3.746008, 0.908235, 1.043992}, { 0.077040, 0.928222, 9.555345, 35.860680,123.552246, 0.000000}}, {"Rh" ,{ 6.216648, 17.919739, 3.854252, 0.840326, 15.173498, 0.995452}, { 0.070789, 0.856121, 33.889484,121.686691, 9.029517, 0.000000}}, {"Pd" ,{ 6.121511, 4.784063, 16.631683, 4.318258, 13.246773, 0.883099}, { 0.062549, 0.784031, 8.751391, 34.489983, 0.784031, 0.000000}}, {"Ag" ,{ 6.073874, 17.155437, 4.173344, 0.852238, 17.988686, 0.756603}, { 0.055333, 7.896512, 28.443739,110.376106, 0.716809, 0.000000}}, {"Cd" ,{ 6.080986, 18.019468, 4.018197, 1.303510, 17.974669, 0.603504}, { 0.048990, 7.273646, 29.119284, 95.831207, 0.661231, 0.000000}}, {"In" ,{ 6.196477, 18.816183, 4.050479, 1.638929, 17.962912, 0.333097}, { 0.042072, 6.695665, 31.009790,103.284348, 0.610714, 0.000000}}, {"Sn" ,{ 19.325171, 6.281571, 4.498866, 1.856934, 17.917318, 0.119024}, { 6.118104, 0.036915, 32.529045, 95.037186, 0.565651, 0.000000}}, {"Sb" ,{ 5.394956, 6.549570, 19.650681, 1.827820, 17.867832, -0.290506}, { 33.326523, 0.030974, 5.564929, 87.130966, 0.523992, 0.000000}}, {"Te" ,{ 6.660302, 6.940756, 19.847015, 1.557175, 17.802427, -0.806668}, { 33.031654, 0.025750, 5.065547, 84.101616, 0.487660, 0.000000}}, {"I" ,{ 19.884502, 6.736593, 8.110516, 1.170953, 17.548716, -0.448811}, { 4.628591, 0.027754, 31.849096, 84.406387, 0.463550, 0.000000}}, {"Xe" ,{ 19.978920, 11.774945, 9.332182, 1.244749, 17.737501, -6.065902}, { 4.143356, 0.010142, 28.796200, 75.280685, 0.413616, 0.000000}}, {"Cs" ,{ 17.418674, 8.314444, 10.323193, 1.383834, 19.876251, -2.322802}, { 0.399828, 0.016872, 25.605827,233.339676, 3.826915, 0.000000}}, {"Ba" ,{ 19.747343, 17.368477, 10.465718, 2.592602, 11.003653, -5.183497}, { 3.481823, 0.371224, 21.226641,173.834274, 0.010719, 0.000000}}, {"La" ,{ 19.966019, 27.329655, 11.018425, 3.086696, 17.335455,-21.745489}, { 3.197408, 0.003446, 19.955492,141.381973, 0.341817, 0.000000}}, {"Ce" ,{ 17.355122, 43.988499, 20.546650, 3.130670, 11.353665,-38.386017}, { 0.328369, 0.002047, 3.088196,134.907654, 18.832960, 0.000000}}, {"Pr" ,{ 21.551311, 17.161730, 11.903859, 2.679103, 9.564197, -3.871068}, { 2.995675, 0.312491, 17.716705,152.192825, 0.010468, 0.000000}}, {"Nd" ,{ 17.331244, 62.783924, 12.160097, 2.663483, 22.239950,-57.189842}, { 0.300269, 0.001320, 17.026001,148.748993, 2.910268, 0.000000}}, {"Pm" ,{ 17.286388, 51.560162, 12.478557, 2.675515, 22.960947,-45.973682}, { 0.286620, 0.001550, 16.223755,143.984512, 2.796480, 0.000000}}, {"Sm" ,{ 23.700363, 23.072214, 12.777782, 2.684217, 17.204367,-17.452166}, { 2.689539, 0.003491, 15.495437,139.862473, 0.274536, 0.000000}}, {"Eu" ,{ 17.186195, 37.156837, 13.103387, 2.707246, 24.419271,-31.586687}, { 0.261678, 0.001995, 14.787360,134.816299, 2.581883, 0.000000}}, {"Gd" ,{ 24.898117, 17.104952, 13.222581, 3.266152, 48.995213,-43.505684}, { 2.435028, 0.246961, 13.996325,110.863091, 0.001383, 0.000000}}, {"Tb" ,{ 25.910013, 32.344139, 13.765117, 2.751404, 17.064405,-26.851971}, { 2.373912, 0.002034, 13.481969,125.836510, 0.236916, 0.000000}}, {"Dy" ,{ 26.671785, 88.687576, 14.065445, 2.768497, 17.067781,-83.279831}, { 2.282593, 0.000665, 12.920230,121.937187, 0.225531, 0.000000}}, {"Ho" ,{ 27.150190, 16.999819, 14.059334, 3.386979, 46.546471,-41.165253}, { 2.169660, 0.215414, 12.213148,100.506783, 0.001211, 0.000000}}, {"Er" ,{ 28.174887, 82.493271, 14.624002, 2.802756, 17.018515,-77.135223}, { 2.120995, 0.000640, 11.915256,114.529938, 0.207519, 0.000000}}, {"Tm" ,{ 28.925894, 76.173798, 14.904704, 2.814812, 16.998117,-70.839813}, { 2.046203, 0.000656, 11.465375,111.411980, 0.199376, 0.000000}}, {"Yb" ,{ 29.676760, 65.624069, 15.160854, 2.830288, 16.997850,-60.313812}, { 1.977630, 0.000720, 11.044622,108.139153, 0.192110, 0.000000}}, {"Lu" ,{ 30.122866, 15.099346, 56.314899, 3.540980, 16.943729,-51.049416}, { 1.883090, 10.342764, 0.000780, 89.559250, 0.183849, 0.000000}}, {"Hf" ,{ 30.617033, 15.145351, 54.933548, 4.096253, 16.896156,-49.719837}, { 1.795613, 9.934469, 0.000739, 76.189705, 0.175914, 0.000000}}, {"Ta" ,{ 31.066359, 15.341823, 49.278297, 4.577665, 16.828321,-44.119026}, { 1.708732, 9.618455, 0.000760, 66.346199, 0.168002, 0.000000}}, {"W" ,{ 31.507900, 15.682498, 37.960129, 4.885509, 16.792112,-32.864574}, { 1.629485, 9.446448, 0.000898, 59.980675, 0.160798, 0.000000}}, {"Re" ,{ 31.888456, 16.117104, 42.390297, 5.211669, 16.767591,-37.412682}, { 1.549238, 9.233474, 0.000689, 54.516373, 0.152815, 0.000000}}, {"Os" ,{ 32.210297, 16.678440, 48.559906, 5.455839, 16.735533,-43.677956}, { 1.473531, 9.049695, 0.000519, 50.210201, 0.145771, 0.000000}}, {"Ir" ,{ 32.004436, 1.975454, 17.070105, 15.939454, 5.990003, 4.018893}, { 1.353767, 81.014175, 0.128093, 7.661196, 26.659403, 0.000000}}, {"Pt" ,{ 31.273891, 18.445440, 17.063745, 5.555933, 1.575270, 4.050394}, { 1.316992, 8.797154, 0.124741, 40.177994, 1.316997, 0.000000}}, {"Au" ,{ 16.777390, 19.317156, 32.979683, 5.595453, 10.576854, -6.279078}, { 0.122737, 8.621570, 1.256902, 38.008820, 0.000601, 0.000000}}, {"Hg" ,{ 16.839890, 20.023823, 28.428564, 5.881564, 4.714706, 4.076478}, { 0.115905, 8.256927, 1.195250, 39.247227, 1.195250, 0.000000}}, {"Tl" ,{ 16.630795, 19.386616, 32.808571, 1.747191, 6.356862, 4.066939}, { 0.110704, 7.181401, 1.119730, 90.660263, 26.014978, 0.000000}}, {"Pb" ,{ 16.419567, 32.738590, 6.530247, 2.342742, 19.916475, 4.049824}, { 0.105499, 1.055049, 25.025890, 80.906593, 6.664449, 0.000000}}, {"Bi" ,{ 16.282274, 32.725136, 6.678302, 2.694750, 20.576559, 4.040914}, { 0.101180, 1.002287, 25.714146, 77.057549, 6.291882, 0.000000}}, {"Po" ,{ 16.289164, 32.807171, 21.095163, 2.505901, 7.254589, 4.046556}, { 0.098121, 0.966265, 6.046622, 76.598068, 28.096128, 0.000000}}, {"At" ,{ 16.011461, 32.615547, 8.113899, 2.884082, 21.377867, 3.995684}, { 0.092639, 0.904416, 26.543257, 68.372963, 5.499512, 0.000000}}, {"Rn" ,{ 16.070229, 32.641106, 21.489658, 2.299218, 9.480184, 4.020977}, { 0.090437, 0.876409, 5.239687, 69.188477, 27.632641, 0.000000}}, {"Fr" ,{ 16.007385, 32.663830, 21.594351, 1.598497, 11.121192, 4.003472}, { 0.087031, 0.840187, 4.954467,199.805801, 26.905106, 0.000000}}, {"Ra" ,{ 32.563690, 21.396671, 11.298093, 2.834688, 15.914965, 3.981773}, { 0.801980, 4.590666, 22.758972,160.404388, 0.083544, 0.000000}}, {"Ac" ,{ 15.914053, 32.535042, 21.553976, 11.433394, 3.612409, 3.939212}, { 0.080511, 0.770669, 4.352206, 21.381622,130.500748, 0.000000}}, {"Th" ,{ 15.784024, 32.454899, 21.849222, 4.239077, 11.736191, 3.922533}, { 0.077067, 0.735137, 4.097976,109.464111, 20.512138, 0.000000}}, {"Pa" ,{ 32.740208, 21.973675, 12.957398, 3.683832, 15.744058, 3.886066}, { 0.709545, 4.050881, 19.231543,117.255005, 0.074040, 0.000000}}, {"U" ,{ 15.679275, 32.824306, 13.660459, 3.687261, 22.279434, 3.854444}, { 0.071206, 0.681177, 18.236156,112.500038, 3.930325, 0.000000}}, {"Np" ,{ 32.999901, 22.638077, 14.219973, 3.672950, 15.683245, 3.769391}, { 0.657086, 3.854918, 17.435474,109.464485, 0.068033, 0.000000}}, {"Pu" ,{ 33.281178, 23.148544, 15.153755, 3.031492, 15.704215, 3.664200}, { 0.634999, 3.856168, 16.849735,121.292038, 0.064857, 0.000000}}, {"Am" ,{ 33.435162, 23.657259, 15.576339, 3.027023, 15.746100, 3.541160}, { 0.612785, 3.792942, 16.195778,117.757004, 0.061755, 0.000000}}, {"Cm" ,{ 15.804837, 33.480801, 24.150198, 3.655563, 15.499866, 3.390840}, { 0.058619, 0.590160, 3.674720,100.736191, 15.408296, 0.000000}}, {"Bk" ,{ 15.889072, 33.625286, 24.710381, 3.707139, 15.839268, 3.213169}, { 0.055503, 0.569571, 3.615472, 97.694786, 14.754303, 0.000000}}, {"Cf" ,{ 33.794075, 25.467693, 16.048487, 3.657525, 16.008982, 3.005326}, { 0.550447, 3.581973, 14.357388, 96.064972, 0.052450, 0.000000}}, {"H1-" ,{ 0.702260, 0.763666, 0.248678, 0.261323, 0.023017, 0.000425}, { 23.945604, 74.897919, 6.773289,233.583450, 1.337531, 0.000000}}, {"Li1+",{ 0.432724, 0.549257, 0.376575, -0.336481, 0.976060, 0.001764}, { 0.260367, 1.042836, 7.885294, 0.260368, 3.042539, 0.000000}}, {"Be2+",{ 3.055430, -2.372617, 1.044914, 0.544233, 0.381737, -0.653773}, { 0.001226, 0.001227, 1.542106, 0.456279, 4.047479, 0.000000}}, {"Cval",{ 1.258489, 0.728215, 1.119856, 2.168133, 0.705239, 0.019722}, { 10.683769, 0.208177, 0.836097, 24.603704, 58.954273, 0.000000}}, {"O1-" ,{ 3.106934, 3.235142, 1.148886, 0.783981, 0.676953, 0.046136}, { 19.868080, 6.960252, 0.170043, 65.693512, 0.630757, 0.000000}}, {"O2-" ,{ 3.990247, 2.300563, 0.607200, 1.907882, 1.167080, 0.025429}, { 16.639956, 5.636819, 0.108493, 47.299709, 0.379984, 0.000000}}, {"F1-" ,{ 0.457649, 3.841561, 1.432771, 0.801876, 3.395041, 0.069525}, { 0.917243, 5.507803, 0.164955, 51.076206, 15.821679, 0.000000}}, {"Na1+",{ 3.148690, 4.073989, 0.767888, 0.995612, 0.968249, 0.045300}, { 2.594987, 6.046925, 0.070139, 14.122657, 0.217037, 0.000000}}, {"Mg2+",{ 3.062918, 4.135106, 0.853742, 1.036792, 0.852520, 0.058851}, { 2.015803, 4.417941, 0.065307, 9.669710, 0.187818, 0.000000}}, {"Al3+",{ 4.132015, 0.912049, 1.102425, 0.614876, 3.219136, 0.019397}, { 3.528641, 7.378344, 0.133708, 0.039065, 1.644728, 0.000000}}, {"Siva",{ 2.879033, 3.072960, 1.515981, 1.390030, 4.995051, 0.146030}, { 1.239713, 38.706276, 0.081481, 93.616333, 2.770293, 0.000000}}, {"Si4+",{ 3.676722, 3.828496, 1.258033, 0.419024, 0.720421, 0.097266}, { 1.446851, 3.013144, 0.064397, 0.206254, 5.970222, 0.000000}}, {"Cl1-",{ 1.061802, 7.139886, 6.524271, 2.355626, 35.829403,-34.916603}, { 0.144727, 1.171795, 19.467655, 60.320301, 0.000436, 0.000000}}, {"K1+" ,{-17.609339, 1.494873, 7.150305, 10.899569, 15.808228, 0.257164}, { 18.840979, 0.053453, 0.812940, 22.264105, 14.351593, 0.000000}}, {"Ca2+",{ 8.501441, 12.880483, 9.765095, 7.156669, 0.711160,-21.013187}, { 10.525848, -0.004033, 0.010692, 0.684443, 27.231771, 0.000000}}, {"Sc3+",{ 7.104348, 1.511488,-53.669773, 38.404816, 24.532240, 0.118642}, { 0.601957, 0.033386, 12.572138, 10.859736, 14.125230, 0.000000}}, {"Ti2+",{ 7.040119, 1.496285, 9.657304, 0.006534, 1.649561, 0.150362}, { 0.537072, 0.031914, 8.009958,201.800293, 24.039482, 0.000000}}, {"Ti3+",{ 36.587933, 7.230255, -9.086077, 2.084594, 17.294008,-35.111282}, { 0.000681, 0.522262, 5.262317, 15.881716, 6.149805, 0.000000}}, {"Ti4+",{ 45.355537, 7.092900, 7.483858,-43.498817, 1.678915, -0.110628}, { 9.252186, 0.523046, 13.082852, 10.193876, 0.023064, 0.000000}}, {"V2+" ,{ 7.754356, 2.064100, 2.576998, 2.011404, 7.126177, -0.533379}, { 7.066315, 0.014993, 7.066308, 22.055786, 0.467568, 0.000000}}, {"V3+" ,{ 9.958480, 1.596350, 1.483442,-10.846044, 17.332867, 0.474921}, { 6.763041, 0.056895, 17.750029, 0.328826, 0.388013, 0.000000}}, {"V5+" ,{ 15.575018, 8.448095, 1.612040, -9.721855, 1.534029, 0.552676}, { 0.682708, 5.566640, 10.527077, 0.907961, 0.066667, 0.000000}}, {"Cr2+",{ 10.598877, 1.565858, 2.728280, 0.098064, 6.959321, 0.049870}, { 6.151846, 0.023519, 17.432816, 54.002388, 0.426301, 0.000000}}, {"Cr3+",{ 7.989310, 1.765079, 2.627125, 1.829380, 6.980908, -0.192123}, { 6.068867, 0.018342, 6.068887, 16.309284, 0.420864, 0.000000}}, {"Mn2+",{ 11.287712, 26.042414, 3.058096, 0.090258, 7.088306,-24.566132}, { 5.506225, 0.000774, 16.158575, 54.766354, 0.375580, 0.000000}}, {"Mn3+",{ 6.926972, 2.081342, 11.128379, 2.375107, -0.419287, -0.093713}, { 0.378315, 0.015054, 5.379957, 14.429586, 0.004939, 0.000000}}, {"Mn4+",{ 12.409131, 7.466993, 1.809947,-12.138477, 10.780248, 0.672146}, { 0.300400, 0.112814, 12.520756, 0.168653, 5.173237, 0.000000}}, {"Fe2+",{ 11.776765, 11.165097, 3.533495, 0.165345, 7.036932, -9.676919}, { 4.912232, 0.001748, 14.166556, 42.381958, 0.341324, 0.000000}}, {"Fe3+",{ 9.721638, 63.403847, 2.141347, 2.629274, 7.033846,-61.930725}, { 4.869297, 0.000293, 4.867602, 13.539076, 0.338520, 0.000000}}, {"Co2+",{ 6.993840, 26.285812, 12.254289, 0.246114, 4.017407,-24.796852}, { 0.310779, 0.000684, 4.400528, 35.741447, 12.536393, 0.000000}}, {"Co3+",{ 6.861739, 2.678570, 12.281889, 3.501741, -0.179384, -1.147345}, { 0.309794, 0.008142, 4.331703, 11.914167, 11.914167, 0.000000}}, {"Ni2+",{ 12.519017, 37.832058, 4.387257, 0.661552, 6.949072,-36.344471}, { 3.933053, 0.000442, 10.449184, 23.860998, 0.283723, 0.000000}}, {"Ni3+",{ 13.579366, 1.902844, 12.859268, 3.811005, -6.838595, -0.317618}, { 0.313140, 0.012621, 3.906407, 10.894311, 0.344379, 0.000000}}, {"Cu1+",{ 12.960763, 16.342150, 1.110102, 5.520682, 6.915452,-14.849320}, { 3.576010, 0.000975, 29.523218, 10.114283, 0.261326, 0.000000}}, {"Cu2+",{ 11.895569, 16.344978, 5.799817, 1.048804, 6.789088,-14.878383}, { 3.378519, 0.000924, 8.133653, 20.526524, 0.254741, 0.000000}}, {"Zn2+",{ 13.340772, 10.428857, 5.544489, 0.762295, 6.869172, -8.945248}, { 3.215913, 0.001413, 8.542680, 21.891756, 0.239215, 0.000000}}, {"Ga3+",{ 13.123875, 35.288189, 6.126979, 0.611551, 6.724807,-33.875122}, { 2.809960, 0.000323, 6.831534, 16.784311, 0.212002, 0.000000}}, {"Ge4+",{ 6.876636, 6.779091, 9.969591, 3.135857, 0.152389, 1.086542}, { 2.025174, 0.176650, 3.573822, 7.685848, 16.677574, 0.000000}}, {"Br1-",{ 17.714310, 6.466926, 6.947385, 4.402674, -0.697279, 1.152674}, { 2.122554, 19.050768, 0.152708, 58.690361, 58.690372, 0.000000}}, {"Rb1+",{ 17.684320, 7.761588, 6.680874, 2.668883, 0.070974, 1.133263}, { 1.710209, 14.919863, 0.128542, 31.654478, 0.128543, 0.000000}}, {"Sr2+",{ 17.694973, 1.275762, 6.154252, 9.234786, 0.515995, 1.125309}, { 1.550888, 30.133041, 0.118774, 13.821799, 0.118774, 0.000000}}, {"Y3+" ,{ 46.660366, 10.369686, 4.623042,-62.170834, 17.471146, 19.023842}, { -0.019971, 13.180257, 0.176398, -0.016727, 1.467348, 0.000000}}, {"Zr4+",{ 6.802956, 17.699253, 10.650647, -0.248108, 0.250338, 0.827902}, { 0.096228, 1.296127, 11.240715, -0.219259, -0.219021, 0.000000}}, {"Nb3+",{ 17.714323, 1.675213, 7.483963, 8.322464, 11.143573, -8.339573}, { 1.172419, 30.102791, 0.080255, -0.002983, 10.456687, 0.000000}}, {"Nb5+",{ 17.580206, 7.633277, 10.793497, 0.180884, 67.837921,-68.024780}, { 1.165852, 0.078558, 9.507652, 31.621656, -0.000438, 0.000000}}, {"Mo3+",{ 7.447050, 17.778122, 11.886068, 1.997905, 1.789626, -1.898764}, { 0.072000, 1.073145, 9.834720, 28.221746, -0.011674, 0.000000}}, {"Mo5+",{ 7.929879, 17.667669, 11.515987, 0.500402, 77.444084,-78.056595}, { 0.068856, 1.068064, 9.046229, 26.558945, -0.000473, 0.000000}}, {"Mo6+",{ 34.757683, 9.653037, 6.584769,-18.628115, 2.490594, 1.141916}, { 1.301770, 7.123843, 0.094097, 1.617443, 12.335434, 0.000000}}, {"Ru3+",{ 17.894758, 13.579529, 10.729251, 2.474095, 48.227997,-51.905243}, { 0.902827, 8.740579, 0.045125, 24.764954, -0.001699, 0.000000}}, {"Ru4+",{ 17.845776, 13.455084, 10.229087, 1.653524, 14.059795,-17.241762}, { 0.901070, 8.482392, 0.045972, 23.015272, -0.004889, 0.000000}}, {"Rh3+",{ 17.758621, 14.569813, 5.298320, 2.533579, 0.879753, 0.960843}, { 0.841779, 8.319533, 0.069050, 23.709131, 0.069050, 0.000000}}, {"Rh4+",{ 17.716188, 14.446654, 5.185801, 1.703448, 0.989992, 0.959941}, { 0.840572, 8.100647, 0.068995, 22.357307, 0.068995, 0.000000}}, {"Pd2+",{ 6.122282, 15.651012, 3.513508, 9.060790, 8.771199, 0.879336}, { 0.062424, 8.018296, 24.784275, 0.776457, 0.776457, 0.000000}}, {"Pd4+",{ 6.152421,-96.069023, 31.622141, 81.578255, 17.801403, 0.915874}, { 0.063951, 11.090354, 13.466152, 9.758302, 0.783014, 0.000000}}, {"Ag1+",{ 6.091192, 4.019526, 16.948174, 4.258638, 13.889437, 0.785127}, { 0.056305, 0.719340, 7.758938, 27.368349, 0.719340, 0.000000}}, {"Ag2+",{ 6.401808, 48.699802, 4.799859,-32.332523, 16.356710, 1.068247}, { 0.068167, 0.942270, 20.639496, 1.100365, 6.883131, 0.000000}}, {"Cd2+",{ 6.093711, 43.909691, 17.041306,-39.675117, 17.958918, 0.664795}, { 0.050624, 8.654143, 15.621396, 11.082067, 0.667591, 0.000000}}, {"In3+",{ 6.206277, 18.497746, 3.078131, 10.524613, 7.401234, 0.293677}, { 0.041357, 6.605563, 18.792250, 0.608082, 0.608082, 0.000000}}, {"Sn2+",{ 6.353672, 4.770377, 14.672025, 4.235959, 18.002131, -0.042519}, { 0.034720, 6.167891, 6.167879, 29.006456, 0.561774, 0.000000}}, {"Sn4+",{ 15.445732, 6.420892, 4.562980, 1.713385, 18.033537, -0.172219}, { 6.280898, 0.033144, 6.280899, 17.983601, 0.557980, 0.000000}}, {"Sb3+",{ 10.189171, 57.461918, 19.356573, 4.862206,-45.394096, 1.516108}, { 0.089485, 0.375256, 5.357987, 22.153736, 0.297768, 0.000000}}, {"Sb5+",{ 17.920622, 6.647932, 12.724075, 1.555545, 7.600591, -0.445371}, { 0.522315, 0.029487, 5.718210, 16.433775, 5.718204, 0.000000}}, {"I1-" ,{ 20.010330, 17.835524, 8.104130, 2.231118, 9.158548, -3.341004}, { 4.565931, 0.444266, 32.430672, 95.149040, 0.014906, 0.000000}}, {"Cs1+",{ 19.939056, 24.967621, 10.375884, 0.454243, 17.660248,-19.394306}, { 3.770511, 0.004040, 25.311275, 76.537766, 0.384730, 0.000000}}, {"Ba2+",{ 19.750200, 17.513683, 10.884892, 0.321585, 65.149834,-59.618172}, { 3.430748, 0.361590, 21.358307, 70.309402, 0.001418, 0.000000}}, {"La3+",{ 19.688887, 17.345703, 11.356296, 0.099418, 82.358124,-76.846909}, { 3.146211, 0.339586, 18.753832, 90.345459, 0.001072, 0.000000}}, {"Ce3+",{ 26.593231, 85.866432, -6.677695, 12.111847, 17.401903,-80.313423}, { 3.280381, 0.001012, 4.313575, 17.868504, 0.326962, 0.000000}}, {"Ce4+",{ 17.457533, 25.659941, 11.691037, 19.695251,-16.994749, -3.515096}, { 0.311812, -0.003793, 16.568687, 2.886395, -0.008931, 0.000000}}, {"Pr3+",{ 20.879841, 36.035797, 12.135341, 0.283103, 17.167803,-30.500784}, { 2.870897, 0.002364, 16.615236, 53.909359, 0.306993, 0.000000}}, {"Pr4+",{ 17.496082, 21.538509, 20.403114, 12.062211, -7.492043, -9.016722}, { 0.294457, -0.002742, 2.772886, 15.804613, -0.013556, 0.000000}}, {"Nd3+",{ 17.120077, 56.038139, 21.468307, 10.000671, 2.905866,-50.541992}, { 0.291295, 0.001421, 2.743681, 14.581367, 22.485098, 0.000000}}, {"Pm3+",{ 22.221066, 17.068142, 12.805423, 0.435687, 52.238770,-46.767181}, { 2.635767, 0.277039, 14.927315, 45.768017, 0.001455, 0.000000}}, {"Sm3+",{ 15.618565, 19.538092, 13.398946, -4.358811, 24.490461, -9.714854}, { 0.006001, 0.306379, 14.979594, 0.748825, 2.454492, 0.000000}}, {"Eu2+",{ 23.899035, 31.657497, 12.955752, 1.700576, 16.992199,-26.204315}, { 2.467332, 0.002230, 13.625002, 35.089481, 0.253136, 0.000000}}, {"Eu3+",{ 17.758327, 33.498665, 24.067188, 13.436883, -9.019134,-19.768026}, { 0.244474, -0.003901, 2.487526, 14.568011, -0.015628, 0.000000}}, {"Gd3+",{ 24.344999, 16.945311, 13.866931, 0.481674, 93.506378,-88.147179}, { 2.333971, 0.239215, 12.982995, 43.876347, 0.000673, 0.000000}}, {"Tb3+",{ 24.878252, 16.856016, 13.663937, 1.279671, 39.271294,-33.950317}, { 2.223301, 0.227290, 11.812528, 29.910065, 0.001527, 0.000000}}, {"Dy3+",{ 16.864344, 90.383461, 13.675473, 1.687078, 25.540651,-85.150650}, { 0.216275, 0.000593, 11.121207, 26.250975, 2.135930, 0.000000}}, {"Ho3+",{ 16.837524, 63.221336, 13.703766, 2.061602, 26.202621,-58.026505}, { 0.206873, 0.000796, 10.500283, 24.031883, 2.055060, 0.000000}}, {"Er3+",{ 16.810127, 22.681061, 13.864114, 2.294506, 26.864477,-17.513460}, { 0.198293, 0.002126, 9.973341, 22.836388, 1.979442, 0.000000}}, {"Tm3+",{ 16.787500, 15.350905, 14.182357, 2.299111, 27.573771,-10.192087}, { 0.190852, 0.003036, 9.602934, 22.526880, 1.912862, 0.000000}}, {"Yb2+",{ 28.443794, 16.849527, 14.165081, 3.445311, 28.308853,-23.214935}, { 1.863896, 0.183811, 9.225469, 23.691355, 0.001463, 0.000000}}, {"Yb3+",{ 28.191629, 16.828087, 14.167848, 2.744962, 23.171774,-18.103676}, { 1.842889, 0.182788, 9.045957, 20.799847, 0.001759, 0.000000}}, {"Lu3+",{ 28.828693, 16.823227, 14.247617, 3.079559, 25.647667,-20.626528}, { 1.776641, 0.175560, 8.575531, 19.693701, 0.001453, 0.000000}}, {"Hf4+",{ 29.267378, 16.792543, 14.785310, 2.184128, 23.791996,-18.820383}, { 1.697911, 0.168313, 8.190025, 18.277578, 0.001431, 0.000000}}, {"Ta5+",{ 29.539469, 16.741854, 15.182070, 1.642916, 16.437447,-11.542459}, { 1.612934, 0.160460, 7.654408, 17.070732, 0.001858, 0.000000}}, {"W6+" ,{ 29.729357, 17.247808, 15.184488, 1.154652, 0.739335, 3.945157}, { 1.501648, 0.140803, 6.880573, 14.299601, 14.299618, 0.000000}}, {"Os4+",{ 17.113485, 15.792370, 23.342392, 4.090271, 7.671292, 3.988390}, { 0.131850, 7.288542, 1.389307, 19.629425, 1.389307, 0.000000}}, {"Ir3+",{ 31.537575, 16.363338, 15.597141, 5.051404, 1.436935, 4.009459}, { 1.334144, 7.451918, 0.127514, 21.705648, 0.127515, 0.000000}}, {"Ir4+",{ 30.391249, 16.146996, 17.019068, 4.458904, 0.975372, 4.006865}, { 1.328519, 7.181766, 0.127337, 19.060146, 1.328519, 0.000000}}, {"Pt2+",{ 31.986849, 17.249048, 15.269374, 5.760234, 1.694079, 4.032512}, { 1.281143, 7.625512, 0.123571, 24.190826, 0.123571, 0.000000}}, {"Pt4+",{ 41.932713, 16.339224, 17.653894, 6.012420,-12.036877, 4.094551}, { 1.111409, 6.466086, 0.128917, 16.954155, 0.778721, 0.000000}}, {"Au1+",{ 32.124306, 16.716476, 16.814100, 7.311565, 0.993064, 4.040792}, { 1.216073, 7.165378, 0.118715, 20.442486, 53.095985, 0.000000}}, {"Au3+",{ 31.704271, 17.545767, 16.819551, 5.522640, 0.361725, 4.042679}, { 1.215561, 7.220506, 0.118812, 20.050970, 1.215562, 0.000000}}, {"Hg1+",{ 28.866837, 19.277540, 16.776051, 6.281459, 3.710289, 4.068430}, { 1.173967, 7.583842, 0.115351, 29.055994, 1.173968, 0.000000}}, {"Hg2+",{ 32.411079, 18.690371, 16.711773, 9.974835, -3.847611, 4.052869}, { 1.162980, 7.329806, 0.114518, 22.009489, 22.009493, 0.000000}}, {"Tl1+",{ 32.295044, 16.570049, 17.991013, 1.535355, 7.554591, 4.054030}, { 1.101544, 0.110020, 6.528559, 52.495068, 20.338634, 0.000000}}, {"Tl3+",{ 32.525639, 19.139185, 17.100321, 5.891115, 12.599463, -9.256075}, { 1.094966, 6.900992, 0.103667, 18.489614, -0.001401, 0.000000}}, {"Pb2+",{ 27.392647, 16.496822, 19.984501, 6.813923, 5.233910, 4.065623}, { 1.058874, 0.106305, 6.708123, 24.395554, 1.058874, 0.000000}}, {"Pb4+",{ 32.505657, 20.014240, 14.645661, 5.029499, 1.760138, 4.044678}, { 1.047035, 6.670321, 0.105279, 16.525040, 0.105279, 0.000000}}, {"Bi3+",{ 32.461437, 19.438683, 16.302486, 7.322662, 0.431704, 4.043703}, { 0.997930, 6.038867, 0.101338, 18.371586, 46.361046, 0.000000}}, {"Bi5+",{ 16.734028, 20.580494, 9.452623, 61.155834,-34.041023, 4.113663}, { 0.105076, 4.773282, 11.762162, 1.211775, 1.619408, 0.000000}}, {"Ra2+",{ 4.986228, 32.474945, 21.947443, 11.800013, 10.807292, 3.956572}, { 0.082597, 0.791468, 4.608034, 24.792431, 0.082597, 0.000000}}, {"Ac3+",{ 15.584983, 32.022125, 21.456327, 0.757593, 12.341252, 3.838984}, { 0.077438, 0.739963, 4.040735, 47.525002, 19.406845, 0.000000}}, {"Th4+",{ 15.515445, 32.090691, 13.996399, 12.918157, 7.635514, 3.831122}, { 0.074499, 0.711663, 3.871044, 18.596891, 3.871044, 0.000000}}, {"U3+" ,{ 15.360309, 32.395657, 21.961290, 1.325894, 14.251453, 3.706622}, { 0.067815, 0.654643, 3.643409, 39.604965, 16.330570, 0.000000}}, {"U4+" ,{ 15.355091, 32.235306, 0.557745, 14.396367, 21.751173, 3.705863}, { 0.067789, 0.652613, 42.354237, 15.908239, 3.553231, 0.000000}}, {"U6+" ,{ 15.333844, 31.770849, 21.274414, 13.872636, 0.048519, 3.700591}, { 0.067644, 0.646384, 3.317894, 14.650250, 75.339699, 0.000000}}, {"Np3+",{ 15.378152, 32.572132, 22.206125, 1.413295, 14.828381, 3.603370}, { 0.064613, 0.631420, 3.561936, 37.875511, 15.546129, 0.000000}}, {"Np4+",{ 15.373926, 32.423019, 21.969994, 0.662078, 14.969350, 3.603039}, { 0.064597, 0.629658, 3.476389, 39.438942, 15.135764, 0.000000}}, {"Np6+",{ 15.359986, 31.992825, 21.412458, 0.066574, 14.568174, 3.600942}, { 0.064528, 0.624505, 3.253441, 67.658318, 13.980832, 0.000000}}, {"Pu3+",{ 15.356004, 32.769127, 22.680210, 1.351055, 15.416232, 3.428895}, { 0.060590, 0.604663, 3.491509, 37.260635, 14.981921, 0.000000}}, {"Pu4+",{ 15.416219, 32.610569, 22.256662, 0.719495, 15.518152, 3.480408}, { 0.061456, 0.607938, 3.411848, 37.628792, 14.464360, 0.000000}}, {"Pu6+",{ 15.436506, 32.289719, 14.726737, 15.012391, 7.024677, 3.502325}, { 0.061815, 0.606541, 3.245363, 13.616438, 3.245364, 0.000000}} }; } // namespace data /*! If the atom has an anisotropic U (even if the values are isotropic), then it is initialised as anisotropic, otherwise it is isotropic. \param atom The atom object. */ AtomShapeFn::AtomShapeFn( const Atom& atom ) { init( atom ); } /*! The atom is initialised as isotropic. \param xyz The atom coordinate. \param element The atom element. \param u_iso The isotropic U-value. \param occ The occupancy. */ AtomShapeFn::AtomShapeFn( const Coord_orth& xyz, const String& element, const ftype u_iso, const ftype occ ) { init( xyz, element, u_iso, occ ); } /*! The atom is initialised as anisotropic. \param xyz The atom coordinate. \param element The atom element. \param u_aniso The anisotropic U-value. \param occ The occupancy. */ AtomShapeFn::AtomShapeFn( const Coord_orth& xyz, const String& element, const U_aniso_orth& u_aniso, const ftype occ ) { init( xyz, element, u_aniso, occ ); } /*! If the atom has an anisotropic U (even if the values are isotropic), then it is initialised as anisotropic, otherwise it is isotropic. \param atom The atom object. */ void AtomShapeFn::init( const Atom& atom ) { ftype occ = atom.occupancy(); if ( Util::is_nan( occ ) ) occ = 1.0; if ( atom.u_aniso_orth().is_null() ) { ftype u_iso = atom.u_iso(); if ( Util::is_nan( u_iso ) ) u_iso = 0.001; init( atom.coord_orth(), atom.element(), u_iso, occ ); } else { init( atom.coord_orth(), atom.element(), atom.u_aniso_orth(), occ ); } } /*! The atom is initialised as isotropic. \param xyz The atom coordinate. \param element The atom element. \param u_iso The isotropic U-value. \param occ The occupancy. */ void AtomShapeFn::init( const Coord_orth& xyz, const String& element, const ftype u_iso, const ftype occ ) { is_iso = true; coord_ = xyz; occ_ = occ; init( element, u_iso ); } /*! The atom is initialised as anisotropic. \param xyz The atom coordinate. \param element The atom element. \param u_aniso The anisotropic U-value. \param occ The occupancy. */ void AtomShapeFn::init( const Coord_orth& xyz, const String& element, const U_aniso_orth& u_aniso, const ftype occ ) { is_iso = false; coord_ = xyz; occ_ = occ; u_aniso_ = u_aniso; while ( u_aniso_.det() < 1.0e-20 ) // fix non-positive definites (crude) u_aniso_ = u_aniso_ + U_aniso_orth( 0.01, 0.01, 0.01, 0.0, 0.0, 0.0 ); init( element, u_aniso_.u_iso() ); // intialise aniso matrices for real space uaninv.resize(6); const ftype fourpi2 = Util::twopi() * Util::twopi(); const ftype pi3 = Util::pi() * Util::pi()* Util::pi(); for ( int i = 0; i < 6; i++ ) { uaninv[i] = Mat33sym<>( -2.0*u_aniso_.mat00()-b[i]/fourpi2, -2.0*u_aniso_.mat11()-b[i]/fourpi2, -2.0*u_aniso_.mat22()-b[i]/fourpi2, -2.0*u_aniso_.mat01(), -2.0*u_aniso_.mat02(), -2.0*u_aniso_.mat12() ).inverse(); double det = -uaninv[i].det(); //std::cout << aw[i] << "\t" << bw[i] << "\t"; aw[i] = a[i] * sqrt( det / pi3 ); bw[i] = -pow( det, 0.3333333333 ); //std::cout << aw[i] << "\t" << bw[i] << "\n"; } } /*! Return the scattering factor as a function of position in reciprocal space in electrons. \param rfl Position in reciprocal space. \return The scattering factor in electrons. */ ftype AtomShapeFn::f( const Coord_reci_orth& rfl ) const { // iso if ( is_iso ) return f( rfl.invresolsq() ); // aniso ftype s4 = 0.25 * rfl.invresolsq(); return occ_ * exp( -Util::twopi2() * u_aniso_.quad_form( rfl ) ) * ( a[0]*exp( -b[0]*s4 ) + a[1]*exp( -b[1]*s4 ) + a[2]*exp( -b[2]*s4 ) + a[3]*exp( -b[3]*s4 ) + a[4]*exp( -b[4]*s4 ) + a[5] ); } /*! Return the density as a function of position in real space in electrons. \param xyz Position in real space. \param The density in electrons. */ ftype AtomShapeFn::rho( const Coord_orth& xyz ) const { // iso const Coord_orth dxyz( xyz - coord_ ); if ( is_iso ) return rho( dxyz.lengthsq() ); // aniso return occ_ * ( aw[0]*exp( uaninv[0].quad_form( dxyz ) ) + aw[1]*exp( uaninv[1].quad_form( dxyz ) ) + aw[2]*exp( uaninv[2].quad_form( dxyz ) ) + aw[3]*exp( uaninv[3].quad_form( dxyz ) ) + aw[4]*exp( uaninv[4].quad_form( dxyz ) ) + aw[5]*exp( uaninv[5].quad_form( dxyz ) ) ); } /*! Return the scattering factor as a function of position in reciprocal space in electrons. \param invresolsq Inverse resolution squared in inverse Angstroms squared. \return The scattering factor in electrons. */ ftype AtomShapeFn::f( const ftype& invresolsq ) const { ftype s4 = 0.25 * invresolsq; return occ_ * exp( -Util::u2b(u_iso_)*s4 ) * ( a[0]*exp( -b[0]*s4 ) + a[1]*exp( -b[1]*s4 ) + a[2]*exp( -b[2]*s4 ) + a[3]*exp( -b[3]*s4 ) + a[4]*exp( -b[4]*s4 ) + a[5] ); } /*! Return the density as a function of position in real space in electrons. \param invresolsq Radius squared in Angstroms squared. \param The density in electrons. */ ftype AtomShapeFn::rho( const ftype& rsq ) const { return occ_ * ( aw[0]*exp(bw[0]*rsq) + aw[1]*exp(bw[1]*rsq) + aw[2]*exp(bw[2]*rsq) + aw[3]*exp(bw[3]*rsq) + aw[4]*exp(bw[4]*rsq) + aw[5]*exp(bw[5]*rsq) ); } /*! Return the Agarwal gradients of the density with respect to tha atomic parameters as a function of position in real space in electrons. The parameter list is defined by assignment to agarwal_params(). \param xyz Position in real space. \patam rho The density in electrons. \param grad Vector gradient in electrons (pre-size for best performance). */ bool AtomShapeFn::rho_grad( const Coord_orth& xyz, ftype& rho, std::vector& grad ) const { if ( is_iso ) { if ( grad.size() < params.size() ) grad.resize( params.size() ); const Coord_orth dxyz( xyz - coord_ ); const ftype rsq = dxyz.lengthsq(); const ftype r0 = aw[0]*exp(bw[0]*rsq); const ftype r1 = aw[1]*exp(bw[1]*rsq); const ftype r2 = aw[2]*exp(bw[2]*rsq); const ftype r3 = aw[3]*exp(bw[3]*rsq); const ftype r4 = aw[4]*exp(bw[4]*rsq); const ftype r5 = aw[5]*exp(bw[5]*rsq); const ftype r = r0 + r1 + r2 + r3 + r4 + r5; ftype g[5]; // temp array for gradients ftype gxyz = (r0*bw[0]+r1*bw[1]+r2*bw[2]+r3*bw[3]+r4*bw[4]+r5*bw[5]); rho = occ_ * r; g[X] = -2.0 * occ_ * gxyz * dxyz.x(); g[Y] = -2.0 * occ_ * gxyz * dxyz.y(); g[Z] = -2.0 * occ_ * gxyz * dxyz.z(); g[Occ] = r; g[Uiso] = 2.0 * occ_ * ( r0*bw[0]*(1.5+bw[0]*rsq) + r1*bw[1]*(1.5+bw[1]*rsq) + r2*bw[2]*(1.5+bw[2]*rsq) + r3*bw[3]*(1.5+bw[3]*rsq) + r4*bw[4]*(1.5+bw[4]*rsq) + r5*bw[5]*(1.5+bw[5]*rsq) ); for ( int i = 0; i < params.size(); i++ ) if ( params[i] < 5 ) grad[i] = g[params[i]]; return true; } else { if ( grad.size() < params.size() ) grad.resize( params.size() ); const Coord_orth dxyz( xyz - coord_ ); double ex[6]; for ( int i = 0; i < 6; i++ ) ex[i] = exp( uaninv[i].quad_form( dxyz ) ); const ftype r0 = aw[0]*ex[0]; const ftype r1 = aw[1]*ex[1]; const ftype r2 = aw[2]*ex[2]; const ftype r3 = aw[3]*ex[3]; const ftype r4 = aw[4]*ex[4]; const ftype r5 = aw[5]*ex[5]; const ftype r = r0 + r1 + r2 + r3 + r4 + r5; ftype g[11]; // temp array for gradients Vec3<> gxyz = r0*(uaninv[0]*dxyz) + r1*(uaninv[1]*dxyz) + r2*(uaninv[2]*dxyz) + r3*(uaninv[3]*dxyz) + r4*(uaninv[4]*dxyz) + r5*(uaninv[5]*dxyz); rho = occ_ * r; g[X] = -2.0 * occ_ * gxyz[0]; g[Y] = -2.0 * occ_ * gxyz[1]; g[Z] = -2.0 * occ_ * gxyz[2]; g[Occ] = r; // gradients wrt U_aniso double gradu[6] = { 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 }; double aexp; Vec3<> v; for ( int i = 0; i < 6; i++ ) { // loop over Gaussian params v = uaninv[i] * dxyz; aexp = aw[i] * ex[i]; gradu[0] += ( v[0]*v[0] + 0.5*uaninv[i].mat00() ) * aexp; gradu[1] += ( v[1]*v[1] + 0.5*uaninv[i].mat11() ) * aexp; gradu[2] += ( v[2]*v[2] + 0.5*uaninv[i].mat22() ) * aexp; gradu[3] += ( v[0]*v[1] + 0.5*uaninv[i].mat01() ) * aexp; gradu[4] += ( v[0]*v[2] + 0.5*uaninv[i].mat02() ) * aexp; gradu[5] += ( v[1]*v[2] + 0.5*uaninv[i].mat12() ) * aexp; } g[U11] = 2.0 * occ_ * gradu[0]; g[U22] = 2.0 * occ_ * gradu[1]; g[U33] = 2.0 * occ_ * gradu[2]; g[U12] = 4.0 * occ_ * gradu[3]; g[U13] = 4.0 * occ_ * gradu[4]; g[U23] = 4.0 * occ_ * gradu[5]; // assemble result array for ( int i = 0; i < params.size(); i++ ) grad[i] = g[params[i]]; return true; } } /*! Return the Agarwal gradients of the density with respect to tha atomic parameters as a function of position in real space in electrons. The parameter list is defined by assignment to agarwal_params(). \param xyz Position in real space. \patam rho The density in electrons. \param grad Vector gradient in electrons (pre-size for best performance). \param curv Matrix curvature in electrons (pre-size for best performance).*/ bool AtomShapeFn::rho_curv( const Coord_orth& xyz, ftype& rho, std::vector& grad, Matrix& curv ) const { if ( is_iso ) { if ( grad.size() < params.size() ) grad.resize( params.size() ); const Coord_orth dxyz( xyz - coord_ ); const ftype rsq = dxyz.lengthsq(); const ftype rsq2 = rsq*rsq; const ftype r0 = aw[0]*exp(bw[0]*rsq); const ftype r1 = aw[1]*exp(bw[1]*rsq); const ftype r2 = aw[2]*exp(bw[2]*rsq); const ftype r3 = aw[3]*exp(bw[3]*rsq); const ftype r4 = aw[4]*exp(bw[4]*rsq); const ftype r5 = aw[5]*exp(bw[5]*rsq); const ftype r = r0 + r1 + r2 + r3 + r4 + r5; ftype bw2[6]; bw2[0] = bw[0]*bw[0]; bw2[1] = bw[1]*bw[1]; bw2[2] = bw[2]*bw[2]; bw2[3] = bw[3]*bw[3]; bw2[4] = bw[4]*bw[4]; bw2[5] = bw[5]*bw[5]; ftype g[5], c[5][5]; // temp array for gradients and curvatures ftype gxyz = (r0*bw[0] +r1*bw[1] +r2*bw[2] + r3*bw[3] +r4*bw[4] +r5*bw[5] ); ftype cxyz = (r0*bw2[0]+r1*bw2[1]+r2*bw2[2]+ r3*bw2[3]+r4*bw2[4]+r5*bw2[5]); g[X] = -2.0 * occ_ * gxyz * dxyz.x(); g[Y] = -2.0 * occ_ * gxyz * dxyz.y(); g[Z] = -2.0 * occ_ * gxyz * dxyz.z(); g[Occ] = r; g[Uiso] = 2.0 * occ_ * ( r0*bw[0]*(1.5+bw[0]*rsq) + r1*bw[1]*(1.5+bw[1]*rsq) + r2*bw[2]*(1.5+bw[2]*rsq) + r3*bw[3]*(1.5+bw[3]*rsq) + r4*bw[4]*(1.5+bw[4]*rsq) + r5*bw[5]*(1.5+bw[5]*rsq) ); c[X][X] = 2.0 * occ_ * ( gxyz + 2.0 * cxyz * dxyz.x() * dxyz.x() ); c[Y][Y] = 2.0 * occ_ * ( gxyz + 2.0 * cxyz * dxyz.y() * dxyz.y() ); c[Z][Z] = 2.0 * occ_ * ( gxyz + 2.0 * cxyz * dxyz.z() * dxyz.z() ); c[X][Y] = c[Y][X] = 4.0 * occ_ * cxyz * dxyz.x() * dxyz.y(); c[Y][Z] = c[Z][Y] = 4.0 * occ_ * cxyz * dxyz.y() * dxyz.z(); c[Z][X] = c[X][Z] = 4.0 * occ_ * cxyz * dxyz.z() * dxyz.x(); c[Occ][Occ] = 0.0; c[Occ][X] = c[X][Occ] = -2.0 * gxyz * dxyz.x(); c[Occ][Y] = c[Y][Occ] = -2.0 * gxyz * dxyz.y(); c[Occ][Z] = c[Z][Occ] = -2.0 * gxyz * dxyz.z(); c[Uiso][Uiso] = 4.0 * occ_ * ( r0*bw2[0]*(3.75 + 5.0*bw[0]*rsq + bw2[0]*rsq2) + r1*bw2[1]*(3.75 + 5.0*bw[1]*rsq + bw2[1]*rsq2) + r2*bw2[2]*(3.75 + 5.0*bw[2]*rsq + bw2[2]*rsq2) + r3*bw2[3]*(3.75 + 5.0*bw[3]*rsq + bw2[3]*rsq2) + r4*bw2[4]*(3.75 + 5.0*bw[4]*rsq + bw2[4]*rsq2) + r5*bw2[5]*(3.75 + 5.0*bw[5]*rsq + bw2[5]*rsq2) ); c[Uiso][X] = c[Uiso][Y] = c[Uiso][Z] = c[Uiso][Occ] = Util::nan(); c[X][Uiso] = c[Y][Uiso] = c[Z][Uiso] = c[Occ][Uiso] = Util::nan(); rho = occ_ * r; for ( int i = 0; i < params.size(); i++ ) if ( params[i] < 5 ) grad[i] = g[params[i]]; for ( int i = 0; i < params.size(); i++ ) if ( params[i] < 5 ) for ( int j = 0; j < params.size(); j++ ) if ( params[j] < 5 ) curv(i,j) = c[params[i]][params[j]]; return true; } else { Message::message( Message_fatal( "AtomShapeFn: missing method" ) ); return false; } } /* OBSOLETE FORM */ bool AtomShapeFn::rho_grad( const Coord_orth& xyz, std::vector& grad ) const { if ( is_iso ) { if ( grad.size() < params.size() ) grad.resize( params.size() ); const Coord_orth dxyz( xyz - coord_ ); const ftype rsq = dxyz.lengthsq(); const ftype r0 = aw[0]*exp(bw[0]*rsq); const ftype r1 = aw[1]*exp(bw[1]*rsq); const ftype r2 = aw[2]*exp(bw[2]*rsq); const ftype r3 = aw[3]*exp(bw[3]*rsq); const ftype r4 = aw[4]*exp(bw[4]*rsq); const ftype r5 = aw[5]*exp(bw[5]*rsq); ftype g[5]; // temp array for gradients ftype gxyz = -(r0*bw[0]+r1*bw[1]+r2*bw[2]+r3*bw[3]+r4*bw[4]+r5*bw[5]); g[X] = 2.0 * occ_ * gxyz * dxyz.x(); g[Y] = 2.0 * occ_ * gxyz * dxyz.y(); g[Z] = 2.0 * occ_ * gxyz * dxyz.z(); g[Occ] = r0+r1+r2+r3+r4+r5; g[Uiso] = 2.0 * occ_ * ( r0*bw[0]*(1.5+bw[0]*rsq) + r1*bw[1]*(1.5+bw[1]*rsq) + r2*bw[2]*(1.5+bw[2]*rsq) + r3*bw[3]*(1.5+bw[3]*rsq) + r4*bw[4]*(1.5+bw[4]*rsq) + r5*bw[5]*(1.5+bw[5]*rsq) ); for ( int i = 0; i < params.size(); i++ ) grad[i] = g[params[i]]; return true; } else { Message::message( Message_fatal( "AtomShapeFn: missing method" ) ); return false; } } /*! \internal */ void AtomShapeFn::init( const String& element, const ftype& u_iso ) { // standardise the atom name int nalpha = 0; String atyp; for ( int i = 0; i < element.length(); i++ ) { if ( isalpha( element[i] ) ) { nalpha++; if ( nalpha == 1 ) atyp += toupper( element[i] ); else atyp += tolower( element[i] ); } else if ( !isspace( element[i] ) ) { atyp += element[i]; } } int ntyp = sizeof(data::sfdata) / sizeof(data::sfdata[0]); int ityp = 0; for ( ityp = 0; ityp < ntyp; ityp++ ) if ( atyp == String( data::sfdata[ityp].name ) ) break; if ( ityp == ntyp ) Message::message( Message_fatal("Unknown atom type: <"+atyp+">") ); // store coeffs and derived info for ( int i = 0; i < 6; i++ ) { a[i] = data::sfdata[ityp].a[i]; b[i] = data::sfdata[ityp].b[i]; bw[i] = -4.0*Util::pi()*Util::pi() / ( b[i] + Util::u2b(u_iso) ); aw[i] = a[i] * pow( -bw[i]/Util::pi(), 1.5 ); } u_iso_ = u_iso; } // legacy AtomSF interface AtomSF::AtomSF( const String& type, const ftype u_iso, const ftype occ ) { init( type, u_iso, occ ); } AtomSF::AtomSF( const String& type, const U_aniso_orth& u_aniso, const ftype occ ) { init( type, u_aniso, occ ); } void AtomSF::init( const String& type, const ftype u_iso, const ftype occ ) { AtomShapeFn::init( clipper::Coord_orth(0.0,0.0,0.0), type, u_iso, occ ); } void AtomSF::init( const String& type, const U_aniso_orth& u_aniso, const ftype occ ) { AtomShapeFn::init( clipper::Coord_orth(0.0,0.0,0.0), type, u_aniso, occ ); } ftype AtomSF::f_iso( const ftype& s ) const { return AtomShapeFn::f( s ); } ftype AtomSF::f_aniso( const Coord_reci_orth& rfl ) const { return AtomShapeFn::f( rfl ); } ftype AtomSF::rho_iso( const ftype& d2 ) const { return AtomShapeFn::rho( d2 ); } ftype AtomSF::rho_aniso( const Coord_orth& uvw ) const { return AtomShapeFn::rho( uvw ); } } // namespace clipper clipper-2.1/clipper/core/map_utils.h0000644000374100011300000001226111001075364014460 00000000000000/*! \file lib/map_utils.h Header file for map statistics type */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_MAP_UTILS #define CLIPPER_MAP_UTILS #include "derivs.h" namespace clipper { //! Generic map statistics class /*! This class is used to calculate and store the mean and standard deviation of a generic map object of scalar types (e.g. Xmap, NXmap). If the map contains NaN values, those points are excluded for the calculation. In the case of an Xmap, the proper multiplicty corrections are applied to give statistics for a whole unit cell */ class Map_stats { public: Map_stats() {} //!< null constructor template Map_stats( const M& map ); //!< Constructor: from Xmap const ftype& mean() const { return mean_; } //!< Mean of map const ftype& std_dev() const { return std_dev_; } //!< Std deviation of map const ftype& min() const { return min_; } //!< Minimum of map const ftype& max() const { return max_; } //!< Maximum of map const Range<> range() const { return Range<>( min_, max_ ); } //!< Range private: ftype mean_, std_dev_, min_, max_; }; //! Generic map sorting class /*! This class is used to sort a vector of integer indices into a map. This includes sorting the whole map to get highest or lowest density first, or sorting some subset, e.g. a list of peak indices. Integer indices are used because they are the most compact way of referencing a unique map location. e.g. \code clipper::Xmap::Map_reference_index ix; std::vector index; for ( ix = xmap.first(); !ix.last(); ix.next() ) index.push_back( ix.index() ); Map_index_sort::sort_decreasing( xmap, index ); \endcode */ class Map_index_sort { public: //! Sort a list into increasing order template static void sort_increasing( const M& map, std::vector& index ); //! Sort a list into decreasing order template static void sort_decreasing( const M& map, std::vector& index ); //! Internal helper class used for sorting private: template class Compare_density { public: Compare_density( const M& m ) { p = &m; } bool operator() ( const int& i1, const int& i2 ) const { return p->get_data(i1) < p->get_data(i2); } private: const M* p; }; }; // template implementations /*! For float and double maps \params map The map for which moments are to be calculated. */ template Map_stats::Map_stats( const M& map ) { ftype64 w, x, s, sx, sxx; s = sx = sxx = 0.0; min_ = 1.0e12; max_ = -1.0e12; for ( typename M::Map_reference_index im = map.first(); !im.last(); im.next() ) { w = 1.0 / ftype64( map.multiplicity( im.coord() ) ); x = ftype64( map[im] ); if ( !Util::is_nan(x) ) { s += w; sx += w*x; sxx += w*x*x; if ( x < min_ ) min_ = x; if ( x > max_ ) max_ = x; } } sx /= s; sxx /= s; mean_ = sx; std_dev_ = sqrt( sxx - sx*sx ); } } // namespace clipper #endif clipper-2.1/clipper/core/test_core.cpp0000644000374100011300000003612710717057106015023 00000000000000/* test_core.cpp: implementation file for clipper core self-test */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "test_core.h" #include "test_data.h" #include "hkl_compute.h" #include "hkl_operators.h" #include "resol_targetfn.h" #include "atomsf.h" #include "xmap.h" #include namespace clipper { bool Test_core::operator() () { typedef HKL_info::HKL_reference_index HRI; data::Test_data data; const HKL_data& fsig = data.hkl_data_f_sigf(); const HKL_data& abcd = data.hkl_data_abcd(); const Spacegroup spgr = fsig.hkl_info().spacegroup(); const Cell cell = fsig.hkl_info().cell(); const Resolution reso = fsig.hkl_info().resolution(); // test data sizes { test( "FTYPE32", sizeof(clipper::ftype32), 4 ); test( "ITYPE32", sizeof(clipper::itype32), 4 ); test( "FTYPE64", sizeof(clipper::ftype64), 8 ); test( "ITYPE64", sizeof(clipper::itype64), 8 ); } // test NaN functions { ftype64 nandd = Util::nand(); ftype64 nandf = Util::nanf(); ftype32 nanfd = Util::nand(); ftype32 nanff = Util::nanf(); test( "ISNANDD", Util::isnan( nandd )?1:0, 1 ); test( "ISNANDF", Util::isnan( nandf )?1:0, 1 ); test( "ISNANFD", Util::isnan( nanfd )?1:0, 1 ); test( "ISNANFF", Util::isnan( nanff )?1:0, 1 ); test( "IS_NANDD", Util::is_nan( nandd )?1:0, 1 ); test( "IS_NANDF", Util::is_nan( nandf )?1:0, 1 ); test( "IS_NANFD", Util::is_nan( nanfd )?1:0, 1 ); test( "IS_NANFF", Util::is_nan( nanff )?1:0, 1 ); for ( double x = -30.0; x < 30.5; x += 1.0 ) { test( "ISNANX", Util::isnan(exp(x))?1:0, 0 ); test( "IS_NANX", Util::is_nan(exp(x))?1:0, 0 ); } } // test Sim functions for consistency for ( double x=0.1; x<50.0; x*=1.5 ) { test( "SIMINV", x, Util::invsim(Util::sim(x)), 0.001*x ); test( "SIMNEG", Util::sim(x), -Util::sim(-x), 0.001 ); test( "SIMINT", Util::sim(x), (Util::sim_integ(x+0.0001)-Util::sim_integ(x))/0.0001, 0.001 ); test( "SIMDRV", Util::sim_deriv(x), (Util::sim(x+0.0001)-Util::sim(x))/0.0001, 0.001 ); if ( x < 2.0 ) test( "SIM_I0", Util::sim(x), (Util::bessel_i0(x+0.0001)/Util::bessel_i0(x)-1.0)/0.0001, 0.001 ); } // test HL<->abcd conversion for ( HRI ih = abcd.first(); !ih.last(); ih.next() ) { data32::Compute_phifom_from_abcd cap; data32::Compute_abcd_from_phifom cpa; data32::Phi_fom phiw1, phiw2; data32::ABCD abcd1, abcd2; LogPhaseProb<24> q(ih.hkl_class()); q.set_abcd( abcd[ih] ); // 1st route q.get_phi_fom( phiw1 ); abcd1 = cpa( ih, phiw1 ); phiw1 = cap( ih, abcd1 ); phiw2 = cap( ih, abcd[ih] ); // 2nd route q.set_phi_fom( phiw2 ); q.get_abcd( abcd2 ); phiw2 = cap( ih, abcd2 ); test( "HLW", phiw1.fom(), phiw2.fom(), 0.003 ); } // test map calculation { HKL_data pw( fsig.hkl_info() ); HKL_data fp1( fsig.hkl_info() ), fp2( fsig.hkl_info() ); pw.compute( abcd, data32::Compute_phifom_from_abcd() ); fp1.compute( fsig, pw, data32::Compute_fphi_from_fsigf_phifom() ); Grid_sampling grid( spgr, cell, reso ); Xmap xmap( spgr, cell, grid ); xmap.fft_from( fp1 ); xmap.fft_to( fp2 ); for ( HRI ih = fp1.first(); !ih.last(); ih.next() ) { std::complex ab1(0.0,0.0), ab2(0.0,0.0); if ( !fp1[ih].missing() ) ab1 = fp1[ih]; if ( !fp2[ih].missing() ) ab2 = fp2[ih]; test( "FFT-A", ab1.real(), ab2.real(), 0.01 ); test( "FFT-B", ab1.imag(), ab2.imag(), 0.01 ); } } // test resolution ordinals { std::vector resols; for ( HRI ih = fsig.first(); !ih.last(); ih.next() ) resols.push_back( ih.invresolsq() ); clipper::Generic_ordinal ordinal; ordinal.init(resols); clipper::Generic_ordinal ordinv = ordinal; ordinv.invert(); clipper::Resolution_ordinal resord; resord.init( fsig.hkl_info(), 1.0 ); std::sort( resols.begin(), resols.end() ); for ( int i = 0; i < resols.size(); i++ ) test( "RESORD", resols[i], ordinv.ordinal(resord.ordinal(resols[i])), 0.001 ); } // test resolution functions { std::vector param( 10, 1.0 ); BasisFn_spline basisfn( fsig, 10 ); TargetFn_meanFnth targetfn( fsig, 2.0 ); ResolutionFn rfn( fsig.hkl_info(), basisfn, targetfn, param ); test( "RESFN0", rfn.params()[0], 229690.9746, 0.1 ); test( "RESFN1", rfn.params()[1], 216481.7609, 0.1 ); test( "RESFN2", rfn.params()[2], 78484.9498, 0.1 ); test( "RESFN3", rfn.params()[3], 148774.2654, 0.1 ); test( "RESFN4", rfn.params()[4], 69255.6000, 0.1 ); test( "RESFN5", rfn.params()[5], 143032.5088, 0.1 ); test( "RESFN6", rfn.params()[6], 110371.3524, 0.1 ); test( "RESFN7", rfn.params()[7], 108711.3487, 0.1 ); test( "RESFN8", rfn.params()[8], 150487.5496, 0.1 ); test( "RESFN9", rfn.params()[9], 141713.7420, 0.1 ); } // test atom shape function derivatives { ftype d = 0.001; Coord_orth co( 1.0, 2.0, 3.0 ); AtomShapeFn sf( co, "N", 0.25, 1.0 ); AtomShapeFn sfx( co+Coord_orth(d,0.0,0.0), "N", 0.25, 1.0 ); AtomShapeFn sfy( co+Coord_orth(0.0,d,0.0), "N", 0.25, 1.0 ); AtomShapeFn sfz( co+Coord_orth(0.0,0.0,d), "N", 0.25, 1.0 ); AtomShapeFn sfo( co, "N", 0.25, 1.0+d ); AtomShapeFn sfu( co, "N", 0.251, 1.0 ); AtomShapeFn sfx2( co+Coord_orth(2.0*d,0.0,0.0), "N", 0.25, 1.0 ); AtomShapeFn sfy2( co+Coord_orth(0.0,2.0*d,0.0), "N", 0.25, 1.0 ); AtomShapeFn sfz2( co+Coord_orth(0.0,0.0,2.0*d), "N", 0.25, 1.0 ); AtomShapeFn sfo2( co, "N", 0.25, 1.0+d+d ); AtomShapeFn sfu2( co, "N", 0.252, 1.0 ); AtomShapeFn sfxy( co+Coord_orth(d,d,0.0), "N", 0.25, 1.0 ); AtomShapeFn sfyz( co+Coord_orth(0.0,d,d), "N", 0.25, 1.0 ); AtomShapeFn sfzx( co+Coord_orth(d,0.0,d), "N", 0.25, 1.0 ); U_aniso_orth uai( 0.25, 0.25, 0.25, 0.0, 0.0, 0.0 ); AtomShapeFn sfuai( co, "N", uai, 1.0 ); std::vector params; params.push_back( AtomShapeFn::X ); params.push_back( AtomShapeFn::Y ); params.push_back( AtomShapeFn::Z ); params.push_back( AtomShapeFn::Occ ); params.push_back( AtomShapeFn::Uiso ); params.push_back( AtomShapeFn::U11 ); params.push_back( AtomShapeFn::U22 ); params.push_back( AtomShapeFn::U33 ); params.push_back( AtomShapeFn::U12 ); params.push_back( AtomShapeFn::U13 ); params.push_back( AtomShapeFn::U23 ); sf.agarwal_params() = params; for ( int i = 0; i < 100; i++ ) { Coord_orth c2 = co + Coord_orth( 0.11*(i%5-1.9), 0.13*(i%7-2.8), 0.15*(i%9-3.7) ); double f; std::vector g(11); Matrix c(11,11); test( "ATOMSF-A", sfuai.rho(c2), sf.rho(c2), 1.0e-8 ); sf.rho_curv( c2, f, g, c ); test( "ATOMSF-G", (sfx.rho(c2)-sf.rho(c2))/d, g[0], 0.01 ); test( "ATOMSF-G", (sfy.rho(c2)-sf.rho(c2))/d, g[1], 0.01 ); test( "ATOMSF-G", (sfz.rho(c2)-sf.rho(c2))/d, g[2], 0.01 ); test( "ATOMSF-G", (sfo.rho(c2)-sf.rho(c2))/d, g[3], 0.01 ); test( "ATOMSF-G", (sfu.rho(c2)-sf.rho(c2))/d, g[4], 0.05 ); test( "ATOMSF-C", (sfx2.rho(c2)-2*sfx.rho(c2)+sf.rho(c2))/(d*d), c(0,0), 0.1 ); test( "ATOMSF-C", (sfy2.rho(c2)-2*sfy.rho(c2)+sf.rho(c2))/(d*d), c(1,1), 0.1 ); test( "ATOMSF-C", (sfz2.rho(c2)-2*sfz.rho(c2)+sf.rho(c2))/(d*d), c(2,2), 0.1 ); test( "ATOMSF-C", (sfxy.rho(c2)-sfx.rho(c2)-sfy.rho(c2)+sf.rho(c2))/(d*d), c(0,1), 0.1 ); test( "ATOMSF-C", (sfyz.rho(c2)-sfy.rho(c2)-sfz.rho(c2)+sf.rho(c2))/(d*d), c(1,2), 0.1 ); test( "ATOMSF-C", (sfzx.rho(c2)-sfz.rho(c2)-sfx.rho(c2)+sf.rho(c2))/(d*d), c(2,0), 0.1 ); } for ( int j = 0; j < 20; j++ ) { ftype x = 0.19*(j%5-1.9); ftype y = 0.15*(j%7-2.8); ftype z = 0.13*(j%9-3.7); U_aniso_orth ua ( x*x+0.2, y*y+0.2, z*z+0.2, y*z, z*x, x*y ); U_aniso_orth ua00( ua.mat00()+d, ua.mat11(), ua.mat22(), ua.mat01(), ua.mat02(), ua.mat12() ); U_aniso_orth ua11( ua.mat00(), ua.mat11()+d, ua.mat22(), ua.mat01(), ua.mat02(), ua.mat12() ); U_aniso_orth ua22( ua.mat00(), ua.mat11(), ua.mat22()+d, ua.mat01(), ua.mat02(), ua.mat12() ); U_aniso_orth ua01( ua.mat00(), ua.mat11(), ua.mat22(), ua.mat01()+d, ua.mat02(), ua.mat12() ); U_aniso_orth ua02( ua.mat00(), ua.mat11(), ua.mat22(), ua.mat01(), ua.mat02()+d, ua.mat12() ); U_aniso_orth ua12( ua.mat00(), ua.mat11(), ua.mat22(), ua.mat01(), ua.mat02(), ua.mat12()+d ); AtomShapeFn sfua ( co, "N", ua, 1.0 ); AtomShapeFn sfuax( co+Coord_orth(d,0.0,0.0), "N", ua, 1.0 ); AtomShapeFn sfuay( co+Coord_orth(0.0,d,0.0), "N", ua, 1.0 ); AtomShapeFn sfuaz( co+Coord_orth(0.0,0.0,d), "N", ua, 1.0 ); AtomShapeFn sfuao( co, "N", ua, 1.0+d ); AtomShapeFn sfua00( co, "N", ua00, 1.0 ); AtomShapeFn sfua11( co, "N", ua11, 1.0 ); AtomShapeFn sfua22( co, "N", ua22, 1.0 ); AtomShapeFn sfua01( co, "N", ua01, 1.0 ); AtomShapeFn sfua02( co, "N", ua02, 1.0 ); AtomShapeFn sfua12( co, "N", ua12, 1.0 ); sfua.agarwal_params() = params; for ( int i = 0; i < 50; i++ ) { Coord_orth c2 = co + Coord_orth( 0.11*(i%5-1.9), 0.13*(i%7-2.8), 0.15*(i%9-3.7) ); double f; std::vector g(11); Matrix c(11,11); sfua.rho_grad( c2, f, g ); test( "ATOMSF-AG", ( sfuax.rho(c2)-sfua.rho(c2))/d, g[0], 0.01 ); test( "ATOMSF-AG", ( sfuay.rho(c2)-sfua.rho(c2))/d, g[1], 0.01 ); test( "ATOMSF-AG", ( sfuaz.rho(c2)-sfua.rho(c2))/d, g[2], 0.01 ); test( "ATOMSF-AG", ( sfuao.rho(c2)-sfua.rho(c2))/d, g[3], 0.01 ); test( "ATOMSF-AG", (sfua00.rho(c2)-sfua.rho(c2))/d, g[5], 0.05 ); test( "ATOMSF-AG", (sfua11.rho(c2)-sfua.rho(c2))/d, g[6], 0.05 ); test( "ATOMSF-AG", (sfua22.rho(c2)-sfua.rho(c2))/d, g[7], 0.05 ); test( "ATOMSF-AG", (sfua01.rho(c2)-sfua.rho(c2))/d, g[8], 0.05 ); test( "ATOMSF-AG", (sfua02.rho(c2)-sfua.rho(c2))/d, g[9], 0.05 ); test( "ATOMSF-AG", (sfua12.rho(c2)-sfua.rho(c2))/d, g[10], 0.05 ); } } } // test spacegroups { const char *pgs[] = {"-P 1", "-P 2", "-P 2y", "-P 2x", "-P 2\"", "-P 2y\"", "-P 2x\"", "-P 2'", "-P2y'", "-P 2x'", "-P 2 2", "-P 2 2\"", "-P 2 2\"(y,z,x)", "-P 2 2\"(z,x,y)", "-P3", "-P 3 (y,z,x)", "-P 3 (z,x,y)", "-P 3 (-x,y,z)", "-P 3 (y,z,-x)", "-P 3 (z,-x,y)", "-P 3*", "-P 3* (-x,y,z)", "-P 3* (x,-y,z)", "-P 3* (x,y,-z)", "-P 3 2", "-P 3 2 (y,z,x)", "-P 3 2 (z,x,y)", "-P 3* 2", "-P 3* 2 (-x,y,z)", "-P 3* 2 (x,-y,z)", "-P 3* 2 (-x,-y,z)", "-P 3 2\"", "-P 3 2\"(z,x,y)", "-P 3 2\"(y,z,x)", "-P 3 2\"(-x,y,z)", "-P 3 2\"(z,-x,y)", "-P 3 2\"(y,z,-x)", "-P 4", "-P 4 (y,z,x)", "-P 4 (z,x,y)", "-P 4 2", "-P 4 2 (y,z,x)", "-P 4 2 (z,x,y)", "-P 6", "-P 6 (y,z,x)", "-P 6 (z,x,y)", "-P 6 2", "-P 6 2 (y,z,x)", "-P 6 2 (z,x,y)", "-P 2 2 3", "-P 4 2 3" }; std::vector hallsymbols; for ( int i = 0; i < data::sgdata_size; i++ ) hallsymbols.push_back( data::sgdata[i].hall ); for ( int i = 0; i < sizeof(pgs)/sizeof(pgs[0]); i++ ) hallsymbols.push_back( pgs[i] ); Cell cellc( Cell_descr( 37, 37, 37 ) ); Cell cellha( Cell_descr( 37, 37, 37, 120, 90, 90 ) ); Cell cellhb( Cell_descr( 37, 37, 37, 90, 120, 90 ) ); Cell cellhc( Cell_descr( 37, 37, 37, 90, 90, 120 ) ); Cell cellha1( Cell_descr( 37, 37, 37, 60, 90, 90 ) ); Cell cellhb1( Cell_descr( 37, 37, 37, 90, 60, 90 ) ); Cell cellhc1( Cell_descr( 37, 37, 37, 90, 90, 60 ) ); Cell cell; String symbol; Spacegroup sg; for ( int s = 0; s < hallsymbols.size(); s++ ) { try { symbol = hallsymbols[s]; sg = Spacegroup( Spgr_descr( symbol, Spgr_descr::Hall ) ); // identify trigonal/hexagonal groups cell = cellc; for ( int sym = 1; sym < sg.num_symops(); sym++ ) { if ( ( sg.symop(sym).rot()(1,1) * sg.symop(sym).rot()(1,2) == -1 ) || ( sg.symop(sym).rot()(2,1) * sg.symop(sym).rot()(2,2) == -1 ) ) cell = cellha; if ( ( sg.symop(sym).rot()(0,0) * sg.symop(sym).rot()(0,2) == -1 ) || ( sg.symop(sym).rot()(2,0) * sg.symop(sym).rot()(2,2) == -1 ) ) cell = cellhb; if ( ( sg.symop(sym).rot()(0,0) * sg.symop(sym).rot()(0,1) == -1 ) || ( sg.symop(sym).rot()(1,0) * sg.symop(sym).rot()(1,1) == -1 ) ) cell = cellhc; if ( ( sg.symop(sym).rot()(1,1) * sg.symop(sym).rot()(1,2) == 1 ) || ( sg.symop(sym).rot()(2,1) * sg.symop(sym).rot()(2,2) == 1 ) ) cell = cellha1; if ( ( sg.symop(sym).rot()(0,0) * sg.symop(sym).rot()(0,2) == 1 ) || ( sg.symop(sym).rot()(2,0) * sg.symop(sym).rot()(2,2) == 1 ) ) cell = cellhb1; if ( ( sg.symop(sym).rot()(0,0) * sg.symop(sym).rot()(0,1) == 1 ) || ( sg.symop(sym).rot()(1,0) * sg.symop(sym).rot()(1,1) == 1 ) ) cell = cellhc1; } for ( int i = 0; i < 100; i++ ) { HKL rfl( i%5-2, i%7-3, i%9-4 ); ftype s0 = rfl.invresolsq(cell); for ( int sym = 1; sym < sg.num_symops(); sym++ ) { ftype s1 = rfl.transform(sg.symop(sym)).invresolsq(cell); test( "SG "+symbol, s0, s1, 1.0e-12 ); } } Grid_sampling grid( sg, cell, Resolution( 4.0 ) ); Xmap xmap( sg, cell, grid ); } catch ( Message_base ) { test( "SG "+symbol, sg.spacegroup_number(), -1 ); } } } return ( error_count == 0 ); } } // namespace clipper clipper-2.1/clipper/core/hkl_compute.cpp0000644000374100011300000003317311071154260015335 00000000000000/* hkl_compute.cpp: fundamental conversion ops for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "hkl_compute.h" namespace clipper { namespace datatypes { template Compute_phifom_from_abcd::Compute_phifom_from_abcd() { for ( int i = 0; i < 144; i++ ) { costab[i] = cos( Util::d2rad(ftype(5*i)) ); sintab[i] = sin( Util::d2rad(ftype(5*i)) ); } } template const Phi_fom Compute_phifom_from_abcd::operator()( const HKL_info::HKL_reference_index& ih, const ABCD& abcd ) const { clipper::datatypes::Phi_fom phifom; if ( !abcd.missing() ) { const HKL_class& cls = ih.hkl_class(); Range qrange( -50.0, 50.0 ); ftype64 q, pq, scos, ssin, ssum; if ( cls.centric() ) { // centric case: integrate over 2 allowed phases int i = Util::mod( Util::intr( Util::rad2d( cls.allowed() ) / 5 ), 36 ); q = abcd.a()*costab[i] + abcd.b()*sintab[i]; pq = exp( qrange.truncate(q) ); scos = ( pq - 1.0/pq ) * costab[i]; ssin = ( pq - 1.0/pq ) * sintab[i]; ssum = ( pq + 1.0/pq ); } else { // acentric case: integrate over phase circle in 5 degree steps scos = ssin = ssum = 0.0; for ( int i = 0; i < 72; i++ ) { q = abcd.a()*costab[i] + abcd.b()*sintab[i] + abcd.c()*costab[2*i] + abcd.d()*sintab[2*i]; pq = exp( qrange.truncate(q) ); scos += pq * costab[i]; ssin += pq * sintab[i]; ssum += pq; } } std::complex c( scos/ssum, ssin/ssum ); phifom.phi() = std::arg(c); phifom.fom() = std::abs(c); } return phifom; } template const ABCD Compute_abcd_from_phifom::operator()( const HKL_info::HKL_reference_index& ih, const Phi_fom& phifom ) const { clipper::datatypes::ABCD abcd; if ( !phifom.missing() ) { const HKL_class& cls = ih.hkl_class(); dtype x = Util::min( phifom.fom(), dtype(0.9999) ); if ( cls.centric() ) x = Util::atanh( x ); else x = Util::invsim( x ); abcd.a() = x * cos( phifom.phi() ); abcd.b() = x * sin( phifom.phi() ); abcd.c() = abcd.d() = 0.0; } return abcd; } template const F_phi Compute_fphi_from_fsigf_phifom::operator()( const HKL_info::HKL_reference_index& ih, const F_sigF& fsigf, const Phi_fom& phifom ) const { clipper::datatypes::F_phi fphi; if ( !fsigf.missing() && !phifom.missing() ) { fphi.f() = fsigf.f() * phifom.fom(); fphi.phi() = phifom.phi(); } return fphi; } template const E_sigE Compute_EsigE_from_FsigF::operator()( const HKL_info::HKL_reference_index& ih, const F_sigF& fsigf ) const { clipper::datatypes::E_sigE esige; if ( !fsigf.missing() ) { ftype sqrteps = sqrt( ih.hkl_class().epsilon() ); esige.E() = fsigf.f()/sqrteps; esige.sigE() = fsigf.sigf()/sqrteps; } return esige; } template const F_sigF Compute_mean_fsigf_from_fsigfano::operator()( const HKL_info::HKL_reference_index& ih, const F_sigF_ano& fsigfano ) const { clipper::datatypes::F_sigF fsigf; if ( Util::is_nan( fsigfano.f_pl() ) ) { fsigf.f() = fsigfano.f_mi(); fsigf.sigf() = fsigfano.sigf_mi(); } else if ( Util::is_nan( fsigfano.f_mi() ) ) { fsigf.f() = fsigfano.f_pl(); fsigf.sigf() = fsigfano.sigf_pl(); } else { fsigf.f() = 0.5 * ( fsigfano.f_pl() + fsigfano.f_mi() ); if ( Util::is_nan(fsigfano.cov()) ) fsigf.sigf() = 0.5 * sqrt( fsigfano.sigf_pl()*fsigfano.sigf_pl() + fsigfano.sigf_mi()*fsigfano.sigf_mi() ); else fsigf.sigf() = 0.5 * sqrt( fsigfano.sigf_pl()*fsigfano.sigf_pl() + fsigfano.sigf_mi()*fsigfano.sigf_mi() + 2.0 * fsigfano.cov() ); } return fsigf; } template const F_sigF Compute_diff_fsigf_from_fsigfano::operator()( const HKL_info::HKL_reference_index& ih, const F_sigF_ano& fsigfano ) const { clipper::datatypes::F_sigF fsigf; if ( Util::is_nan( fsigfano.f_pl() ) || Util::is_nan( fsigfano.f_mi() ) ) { fsigf.f() = fsigf.sigf() = Util::nan(); } else { fsigf.f() = 1.0 * ( fsigfano.f_pl() - fsigfano.f_mi() ); if ( Util::is_nan(fsigfano.cov()) ) fsigf.sigf() = 1.0 * sqrt( fsigfano.sigf_pl()*fsigfano.sigf_pl() + fsigfano.sigf_mi()*fsigfano.sigf_mi() ); else fsigf.sigf() = 1.0 * sqrt( fsigfano.sigf_pl()*fsigfano.sigf_pl() + fsigfano.sigf_mi()*fsigfano.sigf_mi() - 2.0 * fsigfano.cov() ); } return fsigf; } template const F_phi Compute_neg_fphi::operator()( const HKL_info::HKL_reference_index& ih, const F_phi& fphi1 ) const { clipper::datatypes::F_phi fphi; if ( !fphi.missing() ) fphi = clipper::datatypes::F_phi( -std::complex(fphi1) ); return fphi; } template const F_phi Compute_add_fphi::operator()( const HKL_info::HKL_reference_index& ih, const F_phi& fphi1, const F_phi& fphi2 ) const { clipper::datatypes::F_phi fphi; if ( !fphi1.missing() && !fphi2.missing() ) fphi = clipper::datatypes::F_phi( std::complex(fphi1) + std::complex(fphi2) ); return fphi; } template const F_phi Compute_sub_fphi::operator()( const HKL_info::HKL_reference_index& ih, const F_phi& fphi1, const F_phi& fphi2 ) const { clipper::datatypes::F_phi fphi; if ( !fphi1.missing() && !fphi2.missing() ) fphi = clipper::datatypes::F_phi( std::complex(fphi1) - std::complex(fphi2) ); return fphi; } template const ABCD Compute_add_abcd::operator()( const HKL_info::HKL_reference_index& ih, const ABCD& abcd1, const ABCD& abcd2 ) const { clipper::datatypes::ABCD abcd; if ( !abcd1.missing() && !abcd2.missing() ) { abcd.a() = abcd1.a() + abcd2.a(); abcd.b() = abcd1.b() + abcd2.b(); abcd.c() = abcd1.c() + abcd2.c(); abcd.d() = abcd1.d() + abcd2.d(); } return abcd; } /*! DEPRECATED: This operator applies the scale factor against intensities and the U value against magnitudes, which is counterintuitive. Compute_scale_u_iso is more intutive. Construct conversion operator to scale list according to the formula I_new = s.exp( b.|h|^2/2 ) I_old or F_new^2 = s.exp( b.|h|^2/2 ) F_old^2 where |h| = invresolsq. \param s The intensity scale factor. \param u The temperature factor (U-value). */ template Compute_scale_u::Compute_scale_u( const ftype& s, const ftype& u ) { s_ = sqrt(s); u_ = Util::twopi2()*u; } template const T Compute_scale_u::operator()( const HKL_info::HKL_reference_index& ih, T data ) const { if ( !data.missing() ) data.scale( s_ * exp( u_ * ih.invresolsq() ) ); return data; } /*! Construct conversion operator to scale list according to the formula I_new = s^2 .exp( 4 π^2 u.|h|^2 ) I_old or F_new = s.exp( 2 π^2 u.|h|^2 ) F_old where |h|^2 = invresolsq. \param s The scale factor. \param u The temperature factor (U-value). */ template Compute_scale_u_iso::Compute_scale_u_iso( const ftype& s, const ftype& u ) { s_ = s; u_ = Util::twopi2()*u; } template const T Compute_scale_u_iso::operator()( const HKL_info::HKL_reference_index& ih, T data ) const { if ( !data.missing() ) data.scale( s_ * exp( u_ * ih.invresolsq() ) ); return data; } /*! Construct conversion operator to scale list according to the formula I_new = s^2 .exp( 4 π^2 h^T U h ) I_old or F_new = s.exp( 2 π^2 h^T U h ) F_old \param s The scale factor. \param u The temperature factor (U-value). */ template Compute_scale_u_aniso::Compute_scale_u_aniso( const ftype& s, const U_aniso_orth& u ) { s_ = s; u_ = Util::twopi2()*u; } template const T Compute_scale_u_aniso::operator()( const HKL_info::HKL_reference_index& ih, T data ) const { if ( !data.missing() ) data.scale( s_ * exp( u_.quad_form( ih.hkl().coord_reci_orth( ih.base_hkl_info().cell() ) ) ) ); return data; } template const F_sigF Compute_FsigF::operator()( const HKL_info::HKL_reference_index& ih, const T& fsigf ) const { clipper::datatypes::F_sigF fsigfnew; if ( !fsigf.missing() ) { fsigfnew.f() = fsigf.f(); fsigfnew.sigf() = fsigf.sigf(); } return fsigfnew; } // compile template types template class Compute_phifom_from_abcd; template class Compute_abcd_from_phifom; template class Compute_fphi_from_fsigf_phifom; template class Compute_EsigE_from_FsigF; template class Compute_mean_fsigf_from_fsigfano; template class Compute_diff_fsigf_from_fsigfano; template class Compute_neg_fphi; template class Compute_add_fphi; template class Compute_sub_fphi; template class Compute_add_abcd; template class Compute_scale_u_iso >; template class Compute_scale_u_iso >; template class Compute_scale_u_iso >; template class Compute_scale_u_iso >; template class Compute_scale_u_iso >; template class Compute_scale_u_aniso >; template class Compute_scale_u_aniso >; template class Compute_scale_u_aniso >; template class Compute_scale_u_aniso >; template class Compute_scale_u_aniso >; template class Compute_FsigF >; template class Compute_FsigF >; template class Compute_phifom_from_abcd; template class Compute_abcd_from_phifom; template class Compute_fphi_from_fsigf_phifom; template class Compute_EsigE_from_FsigF; template class Compute_mean_fsigf_from_fsigfano; template class Compute_diff_fsigf_from_fsigfano; template class Compute_neg_fphi; template class Compute_add_fphi; template class Compute_sub_fphi; template class Compute_add_abcd; template class Compute_scale_u_iso >; template class Compute_scale_u_iso >; template class Compute_scale_u_iso >; template class Compute_scale_u_iso >; template class Compute_scale_u_iso >; template class Compute_scale_u_aniso >; template class Compute_scale_u_aniso >; template class Compute_scale_u_aniso >; template class Compute_scale_u_aniso >; template class Compute_scale_u_aniso >; template class Compute_FsigF >; template class Compute_FsigF >; // DEPRECATED template class Compute_scale_u >; template class Compute_scale_u >; template class Compute_scale_u >; template class Compute_scale_u >; template class Compute_scale_u >; template class Compute_scale_u >; template class Compute_scale_u >; template class Compute_scale_u >; template class Compute_scale_u >; template class Compute_scale_u >; } // namespace datatypes } // namespace clipper clipper-2.1/clipper/core/symop.h0000644000374100011300000001335510363703537013651 00000000000000/*! \file lib/symop.h Fundamental types for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_SYMOP #define CLIPPER_SYMOP #include "clipper_types.h" namespace clipper { // forward definitions class Cell; class Grid; class RTop_orth; //! Fractional operator class. /*! This class is used for any RT-operator which operates on fractional coordinates. For a full list of methods, see clipper::RTop */ class RTop_frac : public RTop<> { public: //! null constructor inline RTop_frac() {} //! constructor: copy/convert inline explicit RTop_frac( const RTop<>& o ) : RTop<>( o ) {} //! constructor: from rotation inline explicit RTop_frac( const Mat33<>& r ) : RTop<>( r ) {} //! constructor: from string description explicit RTop_frac( const String& strop ); //! constructor: from rotation and translation inline RTop_frac( const Mat33<>& r, const Vec3<>& t ) : RTop<>( r, t ) {} //! fractional-orthogonal conversion RTop_orth rtop_orth( const Cell& cell ) const; //! inverse operator RTop_frac inverse() const; //! return identity operator static RTop_frac identity(); //! return null (uninitialised) operator static RTop_frac null(); }; //! Crystallographic symmetry operator /*! This is identical to a fractional RTop, but has its own class since not all fractional RTops are symops. For a full list of methods, see clipper::RTop and clipper::RTop_frac */ class Symop : public RTop_frac { public: //! null constructor inline Symop() {} //! constructor: RTop explicit Symop( const RTop<>& rt ); //! constructor: from 4x4 matrix explicit Symop( const ftype mat[4][4] ); //! return formatted String representation String format() const; }; //! Integerised symmetry matrix /*! This is used for optimised calculations in real and reciprocal space */ class Isymop : public RTop { public: //! null constructor inline Isymop() {} //! constructor: RTop inline explicit Isymop( const RTop& rt ) : RTop(rt) {} //! constructor Isymop( const Symop& symop, const Grid& grid ); }; //! Compressed encoded symmetry operator /*! This is a compresses representation of a crystallographic symmetry operator, stored as a single 32-bit integer. It may be converted to or from a symop or an int and compared, sorted, etc. The following guarantees are made concerning the code: - The identity operator has a code of zero. - Operators with non-identity rotations will have higher codes than operators with identity rotations, for the same translation. - Operators with non-zero translations will have higher codes than operators with zero translations, for the same rotation. */ class Symop_code { public: //! null constructor inline Symop_code() {} //! constructor: from int inline explicit Symop_code( const int& code ) : code_(code) {} //! constructor: from Symop explicit Symop_code( const Symop& op ); //! constructor: from Isymop explicit Symop_code( const Isymop& op ); //! initialiser: from Isymop void init( const Isymop& op ); Symop_code code_rot() const; //!< return code for rotation part Symop_code code_trn() const; //!< return code for translation part Symop symop() const; //!< convert to symop Isymop isymop() const; //!< convert to integerised symop static Symop_code identity() { return Symop_code(0); } //!< identity code //! convert to integer inline operator int() const { return code_; } private: int code_; }; } // namespace clipper #endif clipper-2.1/clipper/core/derivs.cpp0000644000374100011300000000441410363703537014325 00000000000000/* derivs.cpp: fundamental data types for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "derivs.h" namespace clipper { } // namespace clipper clipper-2.1/clipper/core/spacegroup.cpp0000644000374100011300000010067011252053545015175 00000000000000/* spacegroup.cpp: methods for spacegroup symmetry class */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "spacegroup.h" #include "coords.h" #include "clipper_instance.h" #include #include namespace clipper { namespace data { // matrices Mat33<> mat_i ( 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0 ); Mat33<> mat_inv (-1.0, 0.0, 0.0, 0.0,-1.0, 0.0, 0.0, 0.0,-1.0 ); Mat33<> mat_2z (-1.0, 0.0, 0.0, 0.0,-1.0, 0.0, 0.0, 0.0, 1.0 ); Mat33<> mat_3z ( 0.0,-1.0, 0.0, 1.0,-1.0, 0.0, 0.0, 0.0, 1.0 ); Mat33<> mat_4z ( 0.0,-1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0 ); Mat33<> mat_6z ( 1.0,-1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0 ); Mat33<> mat_2q ( 0.0,-1.0, 0.0,-1.0, 0.0, 0.0, 0.0, 0.0,-1.0 ); Mat33<> mat_2qq ( 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0,-1.0 ); Mat33<> mat_3abc( 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0 ); Vec3<> vec_0( 0.0, 0.0, 0.0 ); Vec3<> vec_a( 0.5, 0.0, 0.0 ); Vec3<> vec_b( 0.0, 0.5, 0.0 ); Vec3<> vec_c( 0.0, 0.0, 0.5 ); Vec3<> vec_n( 0.5, 0.5, 0.5 ); Vec3<> vec_u( 0.25, 0.0, 0.0 ); Vec3<> vec_v( 0.0, 0.25, 0.0 ); Vec3<> vec_w( 0.0, 0.0, 0.25 ); Vec3<> vec_d( 0.25, 0.25, 0.25 ); Vec3<> vec_A( 0.0, 0.5, 0.5 ); Vec3<> vec_B( 0.5, 0.0, 0.5 ); Vec3<> vec_C( 0.5, 0.5, 0.0 ); Vec3<> vec_I( 0.5, 0.5, 0.5 ); Vec3<> vec_R( 0.666667, 0.333333, 0.333333 ); Vec3<> vec_S( 0.333333, 0.666667, 0.333333 ); Vec3<> vec_T( 0.333333, 0.333333, 0.666667 ); Vec3<> vec_H( 0.666667, 0.333333, 0.0 ); Vec3<> vec_F1( 0.0, 0.5, 0.5 ); Vec3<> vec_F2( 0.5, 0.0, 0.5 ); } // namespace data // spacegroup description object void Spgr_descr::Symop_codes::init_hall( const String& symb ) { // interpret Hall symbol using namespace data; Symop_codes& ops = (*this); std::vector tokens; String token, sym, chb; char c, inv, lat; int i, j, k, l; // separate the Hall symbol from the change of basis tokens = symb.split("()"); if ( tokens.size() > 0 ) sym = tokens[0].trim(); if ( tokens.size() > 1 ) chb = tokens[1].trim(); // now separate the parts of the Hall symbol tokens = sym.split(" \t"); // first part: lattice and inversion inv = lat = ' '; token = tokens[0]; for ( j = 0; j < token.length(); j++ ) { c = toupper( token[j] ); if ( c == '-' ) inv = c; else lat = c; } // next 1-3 parts: generating matrices int nmat = tokens.size()-1; std::vector invop(nmat,' '), order(nmat,' '), screw(nmat,' '), axis1(nmat,' '), axis2(nmat,' '); std::vector trans(nmat); for ( i = 0; i < nmat; i++ ) { token = tokens[i+1]; for ( j = 0; j < token.length(); j++ ) { c = tolower( token[j] ); if ( c == '-' ) invop[i] = c; else if ( c >= '1' && c <= '6' ) if ( order[i] == ' ' ) order[i] = c; else screw[i] = c; else if ( c >= 'x' && c <= 'z' ) axis1[i] = c; else if ( c >= '"' && c <= '*' ) axis2[i] = c; else if ( c >= 'a' && c <= 'w' ) trans[i] += c; } } // now interpret all the default conventions // default first axis to z if ( nmat >= 1 ) { if ( axis1[0] == ' ' ) axis1[0] = 'z'; } // default second axis on basis of first if ( nmat >= 2 ) { if ( axis1[1] == ' ' ) { if ( order[1] == '2' ) { if ( order[0] == '2' || order[0] == '4' ) { if ( axis2[1] == ' ' ) axis1[1] = 'x'; } else if ( order[0] == '3' || order[0] == '6' ) { axis1[1] = axis1[0]; if ( axis2[1] == ' ' ) axis2[1] = '\''; } } else if ( order[1] == '3' ) { if ( order[0] == '2' || order[0] == '4' ) { if ( axis2[1] == ' ' ) axis2[1] = '*'; } } } } // default third axis (not much choice here) if ( nmat >= 3 ) { if ( axis1[2] == ' ' ) { if ( order[2] == '3' ) { if ( axis2[2] == ' ' ) axis2[2] = '*'; } } } // now check we have everything for ( i = 0; i < nmat; i++ ) { // add fake z axes for non-axis ops if ( axis1[i] == ' ' ) { if ( order[i] == '1' ) axis1[i] = 'z'; // fake axis if ( axis2[i] != ' ' ) axis1[i] = 'z'; // fake axis } // error messages if ( axis1[i] == ' ' ) Message::message( Message_fatal("Spacegroup: Missing x/y/z in Hall symb:"+tokens[i+1]) ); if ( order[i] == ' ' ) Message::message( Message_fatal("Spacegroup: Missing order in Hall symb:"+tokens[i+1]) ); } // add identity and inversion ops.clear(); ops.push_back( Symop_code::identity() ); if ( inv == '-' ) ops.push_back(Symop_code(Symop(RTop<>(mat_inv)))); // now make the generator matrices Mat33<> mat, matperm; Vec3<> vec; for ( i = 0; i < nmat; i++ ) { // make matrix part mat = mat_i; if ( order[i] == '2' && axis2[i] == ' ' ) mat = mat_2z; if ( order[i] == '2' && axis2[i] == '\'') mat = mat_2q; if ( order[i] == '2' && axis2[i] == '"' ) mat = mat_2qq; if ( order[i] == '3' && axis2[i] == ' ' ) mat = mat_3z; if ( order[i] == '3' && axis2[i] == '*' ) mat = mat_3abc; if ( order[i] == '4' && axis2[i] == ' ' ) mat = mat_4z; if ( order[i] == '6' && axis2[i] == ' ' ) mat = mat_6z; // inverse (improper) if ( invop[i] == '-' ) mat = mat_inv * mat; // axis permutation if ( axis1[i] == 'x' ) j = 0; else if ( axis1[i] == 'y' ) j = 1; else j = 2; for ( k = 0; k < 3; k++ ) for ( l = 0; l < 3; l++ ) matperm( k, l ) = mat( (k+2-j)%3, (l+2-j)%3 ); // make translation part vec = vec_0; for ( k = 0; k < trans[i].length(); k++ ) { if ( trans[i][k] == 'a' ) vec = vec + vec_a; else if ( trans[i][k] == 'b' ) vec = vec + vec_b; else if ( trans[i][k] == 'c' ) vec = vec + vec_c; else if ( trans[i][k] == 'n' ) vec = vec + vec_n; else if ( trans[i][k] == 'u' ) vec = vec + vec_u; else if ( trans[i][k] == 'v' ) vec = vec + vec_v; else if ( trans[i][k] == 'w' ) vec = vec + vec_w; else if ( trans[i][k] == 'd' ) vec = vec + vec_d; } // screw translation if ( screw[i] != ' ' ) vec[j] += ftype( screw[i] - '0' ) / ftype( order[i] - '0' ); // store the matrix ops.push_back( Symop_code( Symop( RTop<>( matperm, vec ) ) ) ); } // add lattice centering if (lat=='A') ops.push_back(Symop_code(Symop(RTop<>(mat_i,vec_A)))); if (lat=='B') ops.push_back(Symop_code(Symop(RTop<>(mat_i,vec_B)))); if (lat=='C') ops.push_back(Symop_code(Symop(RTop<>(mat_i,vec_C)))); if (lat=='I') ops.push_back(Symop_code(Symop(RTop<>(mat_i,vec_I)))); if (lat=='R') ops.push_back(Symop_code(Symop(RTop<>(mat_i,vec_R)))); if (lat=='S') ops.push_back(Symop_code(Symop(RTop<>(mat_i,vec_S)))); if (lat=='T') ops.push_back(Symop_code(Symop(RTop<>(mat_i,vec_T)))); if (lat=='H') ops.push_back(Symop_code(Symop(RTop<>(mat_i,vec_H)))); if (lat=='Q') ops.push_back(Symop_code(Symop(RTop<>(mat_i,vec_S)))); if (lat=='F') { ops.push_back(Symop_code(Symop(RTop<>(mat_i,vec_F1)))); ops.push_back(Symop_code(Symop(RTop<>(mat_i,vec_F2)))); } // apply the change of basis operator RTop_frac cbop( RTop_frac::identity() ); if ( chb.find( ',' ) != String::npos ) { cbop = RTop_frac( chb ); } else { std::vector t = chb.split(" "); for ( i = 0; i < Util::min( int(t.size()), 3 ); i++ ) cbop.trn()[i] = ftype( t[i].i() ) / 12.0; } RTop_frac cbopi( cbop.inverse() ); for ( i = 0; i < ops.size(); i++ ) ops[i] = Symop_code( Symop( cbop*ops[i].symop()*cbopi ) ); } void Spgr_descr::Symop_codes::init_symops( const String& symb ) { Symop_codes& ops = (*this); std::vector symops = symb.split(";"); for ( int i = 0; i < symops.size(); i++ ) ops.push_back( Symop_code( Symop( RTop_frac( symops[i] ) ) ) ); } Spgr_descr::Symop_codes Spgr_descr::Symop_codes::expand() const { int i, j, l, size; Symop_code k; const Symop_codes& generators = (*this); Symop_codes ops; ops.push_back( Symop_code::identity() ); // identity is compulsory // generate all the symops do { size = ops.size(); for ( i = 0; i < generators.size(); i++ ) if ( generators[i] != Symop_code::identity() ) { for ( j = 0; j < size; j++ ) { k = Symop_code( Isymop( generators[i].isymop() * ops[j].isymop() ) ); for ( l = 0; l < ops.size(); l++ ) if ( ops[l] == k ) break; if ( l == ops.size() ) ops.push_back( k ); } } } while ( ops.size() > size ); return ops; } Spgr_descr::Symop_codes Spgr_descr::Symop_codes::primitive_noninversion_ops() const { Symop_codes pops = primitive_ops(); if ( inversion_ops().size() > 1 ) { Symop_codes nops; for ( int i = 0; i < pops.size(); i++ ) if ( pops[i].symop().rot().det() > 0.0 ) nops.push_back( pops[i] ); pops = nops; } return pops; } Spgr_descr::Symop_codes Spgr_descr::Symop_codes::inversion_ops() const { const Symop_codes& ops = (*this); Symop_codes pops; Symop_code invop = Symop_code( Symop( RTop<>( data::mat_inv ) ) ); pops.push_back( Symop_code::identity() ); int i; for ( i = 0; i < ops.size(); i++ ) if ( ops[i].code_rot() == invop ) { pops.push_back( ops[i] ); break; } return pops; } Spgr_descr::Symop_codes Spgr_descr::Symop_codes::primitive_ops() const { const Symop_codes& ops = (*this); Symop_codes pops; int i, j; pops.push_back( Symop_code::identity() ); for ( i = 0; i < ops.size(); i++ ) { for ( j = 0; j < pops.size(); j++ ) if ( ops[i].code_rot() == pops[j].code_rot() ) break; if ( j == pops.size() ) pops.push_back( ops[i] ); } return pops; } Spgr_descr::Symop_codes Spgr_descr::Symop_codes::centering_ops() const { const Symop_codes& ops = (*this); Symop_codes cops; for ( int i = 0; i < ops.size(); i++ ) if ( ops[i].code_rot() == Symop_code::identity() ) cops.push_back( ops[i] ); return cops; } Spgr_descr::Symop_codes Spgr_descr::Symop_codes::laue_ops() const { const Symop_codes& ops = (*this); Symop_codes lops; lops.push_back( Symop_code( Symop( RTop<>( data::mat_inv ) ) ) ); for ( int i = 0; i < ops.size(); i++ ) lops.push_back( ops[i].code_rot() ); return lops.expand(); } Spgr_descr::Symop_codes Spgr_descr::Symop_codes::pgrp_ops() const { const Symop_codes& ops = (*this); Symop_codes lops; for ( int i = 0; i < ops.size(); i++ ) lops.push_back( ops[i].code_rot() ); return lops.expand(); } Spgr_descr::Symop_codes Spgr_descr::Symop_codes::patterson_ops() const { const Symop_codes& ops = (*this); Symop_codes lops; lops.push_back( Symop_code( Symop( RTop<>( data::mat_inv ) ) ) ); for ( int i = 0; i < ops.size(); i++ ) if ( ops[i].code_rot() == Symop_code::identity() ) lops.push_back( ops[i] ); else lops.push_back( ops[i].code_rot() ); return lops.expand(); } Spgr_descr::Symop_codes Spgr_descr::Symop_codes::generator_ops() const { Symop_codes ops = expand(); std::sort( ops.begin(), ops.end() ); Symop_codes cens = ops.centering_ops(); Symop_codes prms = ops.primitive_ops(); Symop_codes gens; Symop_codes gend = gens.expand(); // first make the centering generators for ( int i = 1; i < cens.size(); i++ ) { for ( int j = 0; j < gend.size(); j++ ) if ( cens[i] == gend[j] ) goto skip1; gens.push_back( cens[i] ); gend = gens.expand(); if ( gend.size() == cens.size() ) break; // optional optimisation skip1:; } int ncen = gens.size(); // now add the rest of the generators for ( int i = 1; i < prms.size(); i++ ) { for ( int j = 0; j < gend.size(); j++ ) if ( prms[i] == gend[j] ) goto skip2; gens.push_back( prms[i] ); gend = gens.expand(); if ( gend.size() == ops.size() ) break; // optional optimisation skip2:; } back: // finally remove any redundent ops for ( int i = ncen; i < gens.size(); i++ ) { Symop_codes genp = gens; genp.erase( genp.begin() + i ); if ( genp.expand().size() == ops.size() ) { gens = genp; goto back; } } return gens; // return result } Spgr_descr::Symop_codes Spgr_descr::Symop_codes::product( const Symop_codes& ops2 ) const { Symop_codes ops1 = (*this); // copy first list, implying identity int i, j, n1, n2; n1 = ops1.size(); n2 = ops2.size(); for ( j = 0; j < n2; j++ ) if ( ops2[j] != Symop_code::identity() ) // skip identity, if present for ( i = 0; i < n1; i++ ) ops1.push_back(Symop_code(Isymop(ops1[i].isymop()*ops2[j].isymop()))); return ops1; } unsigned int Spgr_descr::Symop_codes::hash() const { Symop_codes data = expand(); std::sort( data.begin(), data.end() ); unsigned int polynomial = 0x04c11db7; unsigned int remainder = 0xffffffff; unsigned int datum; for ( int word = 0; word < data.size(); word++ ) { datum = data[word]; remainder ^= datum; for ( int bit = 0; bit < 32; bit++ ) { if ( remainder & 0x80000000 ) remainder = (remainder << 1) ^ polynomial; else remainder = (remainder << 1); } } return remainder; } // Spacegroup desciption object char Spgr_descr::pref_12 = '1'; char Spgr_descr::pref_hr = 'H'; /*! Construct a null description spacegroup. The result is initialised to an invalid spacegroup code. */ Spgr_descr::Spgr_descr() { hash_ = 0; } /*! Construct a spacegroup description from a text description, i.e. a symbol or operators. This may be one of the following: - Hall symbol, e.g. " P 2ac 2ab" - H-M symbol, e.g. "P 21 21 21" - Number, e.g. "19" - List of symmetry operators separated by semicolons, e.g. "x,y,z;-x+1/2,-y,z+1/2;x+1/2,-y+1/2,-z;-x,y+1/2,-z+1/2" It is best to specify the type of symbol being used, however if this parameter is omitted a guess will be made. Unfortunately, Hall and H-M symbols may be ambiguous. Any ambiguity may be removed by appending parentheses "()" to the end of the Hall symbol, otherwise the symbol will be interpreted as an H-M symbol, and a Hall symbol if that fails. H-M symbols and spacegroup numbers may correspond to 2 different entries in international tables. The choice between 2 origin settings or hexagonal/rhomohedral settings is made using the set_preferred() method. \param name The spacegroup symbol or operators. \param type The type of symbol: Spacegroup::Symops, Spacegroup::Hall, Spacegroup::HM, Spacegroup::XHM, Spacegroup::Number */ Spgr_descr::Spgr_descr( const String& symb, TYPE type ) { using clipper::data::sgdata; String symbx = symb.trim(); // try and guess symbol type (don't do this!) if ( type == Unknown ) { if ( symbx.find_first_of( "()" ) != String::npos ) type = Hall; else if ( symbx.find_first_of( ":" ) != String::npos ) type = XHM; else if ( symbx.find_first_of( "," ) != String::npos ) type = Symops; else if ( symbx.find_first_of( "ABCFHIPRSTQ" ) == String::npos ) type = Number; // otherwise still unknown: try HM then Hall. } // now make the ops int i; Symop_codes ops; if ( type == Symops ) { ops.init_symops( symbx ); } else if ( type == Hall ) { ops.init_hall( symbx ); } else if ( type == XHM ) { char ext = ' '; int c = symbx.find_first_of( ":" ); if ( c != String::npos ) { if ( c+1 < symbx.length() ) ext = symbx[c+1]; symbx = symbx.substr(0,c); symbx = symbx.trim(); } for ( i = 0; i < data::sgdata_size; i++ ) if ( symbx == String( sgdata[i].hm ) && sgdata[i].ext == ext ) break; if ( i == data::sgdata_size ) Message::message( Message_fatal( "Spgr_descr: No such HM symbol" ) ); ops.init_hall( String( sgdata[i].hall ) ); } else if ( type == HM ) { for ( i = 0; i < data::sgdata_size; i++ ) if ( symbx == String( sgdata[i].hm ) && ( sgdata[i].ext == pref_12 || sgdata[i].ext == pref_hr || sgdata[i].ext == ' ' ) ) break; if ( i == data::sgdata_size ) Message::message( Message_fatal( "Spgr_descr: No such HM symbol" ) ); ops.init_hall( String( sgdata[i].hall ) ); } else if ( type == Number ) { int num = symbx.i(); for ( i = 0; i < data::sgdata_size; i++ ) if ( num == sgdata[i].num && ( sgdata[i].ext == pref_12 || sgdata[i].ext == pref_hr || sgdata[i].ext == ' ' ) ) break; if ( i == data::sgdata_size ) Message::message( Message_fatal( "Spgr_descr: No such SG number" ) ); ops.init_hall( String( sgdata[i].hall ) ); } else { for ( i = 0; i < data::sgdata_size; i++ ) // try H-M then Hall. if ( symbx == String( sgdata[i].hm ) && ( sgdata[i].ext == pref_12 || sgdata[i].ext == pref_hr || sgdata[i].ext == ' ' ) ) break; if ( i != data::sgdata_size ) ops.init_hall( String( sgdata[i].hall ) ); else ops.init_hall( symbx ); } // store the hash and generators hash_ = ops.hash(); generators_ = ops.generator_ops(); } /*! See previous constuctor. \param num The spacegroup number. */ Spgr_descr::Spgr_descr( const int& num ) { using data::sgdata; Symop_codes ops; int i; for ( i = 0; i < data::sgdata_size; i++ ) if ( num == sgdata[i].num && ( sgdata[i].ext == pref_12 || sgdata[i].ext == pref_hr || sgdata[i].ext == ' ' ) ) break; if ( i == data::sgdata_size ) Message::message( Message_fatal( "Spgr_descr: No such SG number" ) ); ops.init_hall( String( sgdata[i].hall ) ); ops = ops.expand(); // store the hash and generators hash_ = ops.hash(); generators_ = ops.generator_ops(); } /*! This is not normally used, except in conjunction with Spgr_desc::generator_ops() to derive one group from another. */ Spgr_descr::Spgr_descr( const Symop_codes& ops ) { // store the hash and generators hash_ = ops.hash(); generators_ = ops.generator_ops(); } /*! The spacegroup number is only available if the spacegroup exists in the internal table, see Hall & Grosse-Kunstleve. \return The spacegroup number, or 0 if unavailable. */ int Spgr_descr::spacegroup_number() const { for ( int i = 0; i < data::sgdata_size; i++ ) if ( data::sgdata[i].sghash == hash_ ) return data::sgdata[i].num; return 0; } /*! The Hall symbol is only available if the spacegroup exists in the internal table, see Hall & Grosse-Kunstleve. \return The Hall symbol, or "Unknown" if unavailable. */ String Spgr_descr::symbol_hall() const { for ( int i = 0; i < data::sgdata_size; i++ ) if ( data::sgdata[i].sghash == hash_ ) return String(data::sgdata[i].hall); return "Unknown"; } /*! The H-M symbol is only available if the spacegroup exists in the internal table, see Hall & Grosse-Kunstleve. \return The H-M symbol, or "Unknown" if unavailable. */ String Spgr_descr::symbol_hm() const { for ( int i = 0; i < data::sgdata_size; i++ ) if ( data::sgdata[i].sghash == hash_ ) return String(data::sgdata[i].hm); return "Unknown"; } /*! The extended H-M symbol is only available if the spacegroup exists in the internal table, see Hall & Grosse-Kunstleve. \return The extended H-M symbol, or "Unknown" if unavailable. */ String Spgr_descr::symbol_xhm() const { for ( int i = 0; i < data::sgdata_size; i++ ) if ( data::sgdata[i].sghash == hash_ ) { String xhm( data::sgdata[i].hm ); if ( data::sgdata[i].ext != ' ' ) xhm = xhm + " :" + data::sgdata[i].ext; return xhm; } return "Unknown"; } /*! The extension H-M symbol is only available if the spacegroup exists in the internal table, see Hall & Grosse-Kunstleve. \return The extension H-M symbol, or "" */ String Spgr_descr::symbol_hm_ext() const { String ext = ""; for ( int i = 0; i < data::sgdata_size; i++ ) if ( data::sgdata[i].sghash == hash_ ) if ( data::sgdata[i].ext != ' ' ) return ext + data::sgdata[i].ext; return ext; } /*! Sets the preferred origin or setting for initialising all Spgr_descr objects using H-M symbols or Spacegroup numbers. cctbx uses origin choice '1' by default, CCP4 uses '2'. Both packages use 'H' in preference to 'R'. Preferred values are stored for both. Defaults are '1' and 'H'. CCP4 users may wish to add the following before using H-M codes or numbers. \code Spgr_descr::set_preferred('2'); \endcode \param c Either '1' or '2', 'H' or 'R'. */ void Spgr_descr::set_preferred( const char& c ) { if ( c == '1' || c == '2' ) pref_12 = c; if ( c == 'H' || c == 'R' ) pref_hr = c; } // Spacegroup cache object Mutex Spgr_cacheobj::mutex = Mutex(); struct Compare_grid{ bool operator() ( const Vec3<>& c1, const Vec3<>& c2 ) const { return (c1[0]*c1[1]*c1[2]+0.001*c1[1]+0.00001*c1[0]) <= (c2[0]*c2[1]*c2[ 2]+0.001*c2[1]+0.00001*c2[0]); } }; bool reci_asu( const Spgr_descr::Symop_codes& ops, data::ASUfn asufn ) { HKL hkl, equ; int i; // make integerised symops std::vector symops( ops.size() ); for ( i = 0; i < ops.size(); i++ ) symops[i] = ops[i].isymop(); // now test asu for uniqueness and completeness for ( hkl.h() = -2; hkl.h() <= 2; hkl.h()++ ) for ( hkl.k() = -2; hkl.k() <= 2; hkl.k()++ ) for ( hkl.l() = -2; hkl.l() <= 2; hkl.l()++ ) { if ( asufn( hkl.h(), hkl.k(), hkl.l() ) ) { for ( i = 0; i < symops.size(); i++ ) { equ = hkl.transform( symops[i] ); if ( equ != hkl && asufn(equ.h(),equ.k(),equ.l()) ) break; equ = -equ; if ( equ != hkl && asufn(equ.h(),equ.k(),equ.l()) ) break; } if ( i != symops.size() ) return false; } else { for ( i = 0; i < symops.size(); i++ ) { equ = hkl.transform( symops[i] ); if ( asufn(equ.h(),equ.k(),equ.l()) ) break; equ = -equ; if ( asufn(equ.h(),equ.k(),equ.l()) ) break; } if ( i == symops.size() ) return false; } } return true; } Vec3<> real_asu( const Spgr_descr::Symop_codes& ops ) { int i, j, sym, nasu; // make integerised symops std::vector symops( ops.size() ); for ( i = 0; i < ops.size(); i++ ) symops[i] = ops[i].isymop(); // classify each grid point by a unique 'ASU number' Coord_grid c; Grid_sampling cgrid(24,24,24); int symmap[13824], tstmap[13824]; for ( i = 0; i < cgrid.size(); i++ ) symmap[i] = -1; nasu = 0; for ( c = Coord_grid(0,0,0); !c.last(cgrid); c.next(cgrid) ) { i = c.index(cgrid); if ( symmap[i] == -1 ) { for ( sym = 0; sym < symops.size(); sym++ ) symmap[ c.transform(symops[sym]).unit(cgrid).index(cgrid) ] = nasu; nasu++; } } // identify trigonal/hexagonal groups bool trighex = false; for ( sym = 0; sym < symops.size(); sym++ ) for ( i = 0; i < 3; i++ ) { int c = 0, r = 0; // trigonal if any row/col adds to 2 for ( j = 0; j < 3; j++ ) { c += abs( symops[sym].rot()(i,j) ); r += abs( symops[sym].rot()(j,i) ); trighex = trighex || ( c == 2 ) || ( r == 2 ); } } // now set search ASU search grid, dependent on symmetry std::vector gridlim; const ftype d = 0.0001; if ( trighex ) { ftype lim[] = { 1./12-d, 1./6-d, 1./6+d, 1./3-d, 1./3+d, 1./2-d, 1./2+d, 2./3+d, 1.-d }; gridlim = std::vector( &lim[0], &lim[ sizeof(lim)/sizeof(ftype) ] ); } else { ftype lim[] = { 1./8+d, 1./4-d, 1./4+d, 1./2-d, 1./2+d, 1.-d }; gridlim = std::vector( &lim[0], &lim[ sizeof(lim)/sizeof(ftype) ] ); } // make a sorted list of grids std::vector > grids; for ( int gui = 0; gui < gridlim.size(); gui++ ) for ( int gvi = 0; gvi < gridlim.size(); gvi++ ) for ( int gwi = 0; gwi < gridlim.size(); gwi++ ) grids.push_back( Vec3<>(gridlim[gui],gridlim[gvi],gridlim[gwi]) ); std::sort( grids.begin(), grids.end(), Compare_grid() ); // now find smallest viable grid for ( j = 0; j < grids.size(); j++ ) { Grid mgrid = Grid( Util::intc(grids[j][0]*cgrid.nu()), Util::intc(grids[j][1]*cgrid.nv()), Util::intc(grids[j][2]*cgrid.nw()) ); if ( mgrid.size() >= nasu ) { // is grid big enough to be ASU? for ( i = 0; i < nasu; i++ ) tstmap[i] = 0; // if so, check for all pts for ( c = Coord_grid(0,0,0); !c.last(mgrid); c.next(mgrid) ) tstmap[ symmap[ c.index(cgrid) ] ] = 1; for ( i = 0; i < nasu; i++ ) if ( tstmap[i] == 0 ) break; if ( i == nasu ) break; // found a full asu, so we're done } } return grids[j]; } Spgr_cacheobj::Spgr_cacheobj( const Key& spgr_cachekey ) { spgr_cachekey_ = spgr_cachekey; // tidy the ops Spgr_descr::Symop_codes ops = spgr_cachekey.generator_ops().expand(); std::sort( ops.begin(), ops.end() ); Spgr_descr::Symop_codes pops = ops.primitive_noninversion_ops(); Spgr_descr::Symop_codes iops = ops.inversion_ops(); Spgr_descr::Symop_codes cops = ops.centering_ops(); std::sort( pops.begin(), pops.end() ); std::sort( iops.begin(), iops.end() ); std::sort( cops.begin(), cops.end() ); ops = pops; ops = ops.product( iops ); ops = ops.product( cops ); nsym = ops.size(); nsymn = pops.size(); nsymi = iops.size(); nsymc = cops.size(); nsymp = nsymn*nsymi; // consistency check (redundent) if ( ops.hash() != spgr_cachekey.hash() ) Message::message( Message_fatal( "Spgr_cacheobj: symops fail" ) ); // Laue group unsigned int lghash = ops.laue_ops().hash(); // first guess from the hash for ( lgrp = 0; lgrp < data::lgdata_size; lgrp++ ) if ( data::lgdata[lgrp].lghash == lghash ) break; if ( lgrp == data::lgdata_size ) lgrp = 0; // if that fails, try all the ASU functions if ( !reci_asu( pops, data::lgdata[lgrp].asufn ) ) { std::ostringstream s; s << "Spacegroup_registry: ASU warning, LGhash=0x"; s.width( 8 ); s.fill( '0' ); s.flags( s.hex | s.right ); s << lghash; Message::message( Message_warn( s.str() ) ); for ( lgrp = 0; lgrp < data::lgdata_size; lgrp++ ) if ( reci_asu( pops, data::lgdata[lgrp].asufn ) ) break; if ( lgrp == data::lgdata_size ) Message::message( Message_fatal( "Spacegroup_registry: ASU fail" ) ); } // real ASU asu_min_ = Vec3<>( -0.0001, -0.0001, -0.0001 ); asu_max_ = real_asu( ops ); // now make real symop lists for ( int i = 0; i < ops.size(); i++ ) { symops.push_back( ops[i].symop() ); isymops.push_back( ops[i].isymop() ); } } bool Spgr_cacheobj::matches( const Key& spgr_cachekey ) const { return spgr_cachekey_.hash() == spgr_cachekey.hash(); } String Spgr_cacheobj::format() const { return spgr_cachekey_.symbol_hall(); } // spacegroup object /*! Construct null or P1 spacegroup. This is faster than the normal constructor. \param type Spacegroup::Null or Spacegroup::P1 */ Spacegroup::Spacegroup( TYPE type ) { if ( type == P1 ) init( Spgr_descr( "x,y,z", Spgr_descr::Symops ) ); } /*! Construct a spacegroup and initialise with a spacegroup description. \param spgr_descr The spacegroup description. */ Spacegroup::Spacegroup( const Spgr_descr& spgr_descr ) { init( spgr_descr ); } /*! Initialise the spacegroup. \param spgr_descr The spacegroup description. */ void Spacegroup::init( const Spgr_descr& spgr_descr ) { // init spgr descr hash_ = spgr_descr.hash(); generators_ = spgr_descr.generator_ops(); // init cache entry cacheref = ClipperInstantiator::instance().spacegroup_cache().cache( spgr_descr ); symops = &(cacheref.data().symops[0]); isymops = &(cacheref.data().isymops[0]); nsym = cacheref.data().nsym; nsymn = cacheref.data().nsymn; nsymi = cacheref.data().nsymi; nsymc = cacheref.data().nsymc; nsymp = cacheref.data().nsymp; asufn = data::lgdata[cacheref.data().lgrp].asufn; } /*! \return true if the object has not been initalised. */ bool Spacegroup::is_null() const { return cacheref.is_null(); } /*! The number of rotational operators parallel to the specified axis is returned. \param axis The axis, A, B or C. \return The order of the axis. */ int Spacegroup::order_of_symmetry_about_axis( const AXIS axis ) const { int n = 0; int a0 = int( axis ); int a1 = (a0+1)%3; int a2 = (a0+2)%3; for ( int i = 0; i < nsymp; i++ ) if ( symops[i].rot().det() > 0.0 ) if ( fabs( symops[i].rot()(a0,a1) ) + fabs( symops[i].rot()(a1,a0) ) + fabs( symops[i].rot()(a0,a2) ) + fabs( symops[i].rot()(a2,a0) ) + fabs( symops[i].rot()(a0,a0) - 1.0 ) < 1.0e-6 ) n++; return n; } /*! The reflection class describes the type of a reflection in a given spacegroup, including centricity, systematic absence, phase restriction, and multiplicity. This is a shortcut to constructing an HKL_class from the spacegroup and HKL. \param hkl The reflection HKL */ HKL_class Spacegroup::hkl_class( const HKL& hkl ) const { return HKL_class( *this, hkl ); } /*! The reciprocal ASU is chosen from one of 47 optimised functions. \param hkl The HKL to test. \return true if the HKL is in the ASU. */ bool Spacegroup::recip_asu( const HKL& hkl ) const { return asufn( hkl.h(), hkl.k(), hkl.l() ); } int Spacegroup::product_op( const int& s1, int& s2 ) const { Symop mat( symops[s1] * symops[s2] ); for ( int s3 = 0; s3 < nsym; s3++ ) if ( mat.equals( symops[s3], 0.001 ) ) return s3; Message::message( Message_fatal("Spacegroup: Internal spacegroup error - missing product") ); return -1; } int Spacegroup::inverse_op( const int& s1 ) const { for ( int s2 = 0; s2 < nsym; s2++ ) if ( symops[0].equals( symops[s1] * symops[s2], 0.001 ) ) return s2; Message::message( Message_fatal("Spacegroup: Internal spacegroup error - missing inverse") ); return -1; } /*! The map ASU is an oblong which contains at least one assymetric unit. It is guaranteed to be contained withing the unit box. The lower limit is always 0,0,0. \return Fractional coordinate of the upper bound of the ASU. */ Coord_frac Spacegroup::asu_max() const { return Coord_frac( cacheref.data().asu_max_ ); } /*! The map ASU is an oblong which contains at least one assymetric unit. It is guaranteed to be contained withing the unit box. The lower limit is always 0,0,0. \return Fractional coordinate of the lower bound of the ASU. */ Coord_frac Spacegroup::asu_min() const { return Coord_frac( cacheref.data().asu_min_ ); } /*! Test if hand-change is possible. \return true if a change of hand preserves the spacegroup. */ bool Spacegroup::invariant_under_change_of_hand() const { for ( int k=0; k(); for ( int i = 0; i < num_reflections(); i++ ) { hkl_class_lookup[i] = spacegroup_.hkl_class( hkl_of( i ) ); invresolsq_lookup[i] = hkl_of( i ).invresolsq( cell_ ); invresolsq_range_.include( invresolsq_lookup[i] ); } } // public methods: // constructors/destructor HKL_info::HKL_info() { Message::message( message_ctor_hkl_info ); } /*! Construct and initialise HKL_info object. This updates the spacegroup and cell and clears the reflection list. The resolution is used as a rejection criterion for reflections - no HKL will be stored beyond the given limit. Initially there are no reflections in the reflection list: see generate_hkl_list(). If any of the parameters have null values, the existing values will be unchanged. The object will only be fully initialised once all parameters are available. \param spacegroup The spacegroup. \param cell The unit cell. \param resolution The resolution limit. */ HKL_info::HKL_info( const Spacegroup& spacegroup, const Cell& cell, const Resolution& resolution, const bool& generate ) { init( spacegroup, cell, resolution, generate ); Message::message( message_ctor_hkl_info ); } /*! Initialise the HKL_info object. This updates the spacegroup and cell and clears the reflection list. The resolution is used as a rejection criterion for reflections - no HKL will be stored beyond the given limit. Initially there are no reflections in the reflection list: see generate_hkl_list(). If any of the parameters have null values, the existing values will be unchanged. The object will only be fully initialised once all parameters are available. \param spacegroup The spacegroup. \param cell The unit cell. \param resolution The resolution limit. \param generate If true, a reflection list will be generated for an ASU. */ void HKL_info::init( const Spacegroup& spacegroup, const Cell& cell, const Resolution& resolution, const bool& generate ) { // set spacegroup and cell spacegroup_ = spacegroup; cell_ = cell; resolution_ = resolution; // check parameters if ( is_null() ) return; // Create the intergised symops (grid irrelevent) Grid g( 24, 24, 24 ); isymop.resize( spacegroup_.num_symops() ); for ( int sym = 0; sym < spacegroup_.num_symops(); sym++ ) isymop[sym] = Isymop( spacegroup_.symop(sym), g ); // reflection lists hkl.clear(); if ( generate ) generate_hkl_list(); update_hkl_list(); } /*! Initialise the HKL_info object. This updates the spacegroup and cell and clears the reflection list. The HKL_sampling determines the reflection list. If any of the parameters have null values, the existing values will be unchanged. The object will only be fully initialised once all parameters are available. \param spacegroup The spacegroup. \param cell The unit cell. \param hkl_sampling The resolution limit. \param generate If true, a reflection list will be generated for an ASU. */ void HKL_info::init( const Spacegroup& spacegroup, const Cell& cell, const HKL_sampling& hkl_sampling, const bool& generate ) { // set spacegroup and cell spacegroup_ = spacegroup; cell_ = cell; hkl_sampling_ = hkl_sampling; // check parameters if ( spacegroup_.is_null() || cell_.is_null() || hkl_sampling_.is_null() ) return; // estimate resolution resolution_ = hkl_sampling.resolution( cell ); // Create the intergised symops (grid irrelevent) Grid g( 24, 24, 24 ); isymop.resize( spacegroup_.num_symops() ); for ( int sym = 0; sym < spacegroup_.num_symops(); sym++ ) isymop[sym] = Isymop( spacegroup_.symop(sym), g ); // reflection lists hkl.clear(); if ( generate ) { std::vector add; // make a reflection list for the given refln sampling HKL lim = hkl_sampling.hkl_limit(); HKL rfl; // make a list of valid reflections for (rfl.h()=-lim.h(); rfl.h()<=lim.h(); rfl.h()++) for (rfl.k()=-lim.k(); rfl.k()<=lim.k(); rfl.k()++) for (rfl.l()=-lim.l(); rfl.l()<=lim.l(); rfl.l()++) if ( spacegroup_.recip_asu(rfl) && hkl_sampling.in_resolution( rfl ) && !( spacegroup_.hkl_class(rfl).sys_abs() ) ) add.push_back(rfl); // update the reflection data lists add_hkl_list( add ); } update_hkl_list(); } /*! \return true if the object has not been initalised. */ bool HKL_info::is_null() const { return ( spacegroup_.is_null() || cell_.is_null() || resolution_.is_null() ); } /*! Using current cell, spacegroup, resolution. */ void HKL_info::generate_hkl_list() { std::vector add; // make a reflection list for the given cell, symm and resolution /* TO MAKE A BOX TO HOLD A SPHERE IN REAL OR RECIPROCAL SPACE In reciprocal space, use the real space cell dimension / resolution In real space, use the recip space dimension * radius */ HKL rfl; int hmax = int(cell_.descr().a()/resolution_.limit()); int kmax = int(cell_.descr().b()/resolution_.limit()); int lmax = int(cell_.descr().c()/resolution_.limit()); ftype s_lim = resolution_.invresolsq_limit(); // make a list of valid reflections for (rfl.h()=-hmax; rfl.h()<=hmax; rfl.h()++) for (rfl.k()=-kmax; rfl.k()<=kmax; rfl.k()++) for (rfl.l()=-lmax; rfl.l()<=lmax; rfl.l()++) if ( spacegroup_.recip_asu(rfl) && rfl.invresolsq(cell_) < s_lim && !( spacegroup_.hkl_class(rfl).sys_abs() ) ) add.push_back(rfl); // update the reflection data lists hkl.clear(); add_hkl_list( add ); } /*! The new HKLs are transformed to the default reciprocal ASU, and added to the reflection list. Duplicates and reflections outside the resoluution limit are ignored. Then the fast lookup tables for HKL, invresolsq, and reflection class are rebuilt. \param add The list of new reflections to add. */ void HKL_info::add_hkl_list( const std::vector& add ) { HKL equiv; int sym; bool friedel; for ( int i = 0; i < add.size(); i++ ) { if ( add[i].invresolsq( cell_ ) <= resolution_.invresolsq_limit() ) { equiv = find_sym( add[i], sym, friedel ); if ( lookup.index_of( equiv ) < 0 ) hkl.push_back( equiv ); } } update_hkl_list(); } /*! Returns the index of the reflection, the sym no. and Friedel flag. \internal */ HKL HKL_info::find_sym( const HKL& rfl, int& sym, bool& friedel ) const { // find the symmetry operator mapping hkl into the reflection // list and determine the friedel flag HKL equiv; // now find the symop which gives a reflection from the list for (sym = 0; sym < spacegroup_.num_primops(); sym++) { equiv = rfl.transform(isymop[sym]); if ( spacegroup_.recip_asu(equiv) ) { friedel = false; return equiv; } equiv = -equiv; if ( spacegroup_.recip_asu(equiv) ) { friedel = true ; return equiv; } } Message::message( message_recip_asu_error ); return equiv; } void HKL_info::debug() const { std::cout << "Num reflns " << hkl.size() << "\n"; } } // namespace clipper clipper-2.1/clipper/core/clipper_precision.h0000644000374100011300000000526110363703537016210 00000000000000/*! \file lib/clipper_precision.h Header file for clipper precision */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_PRECISION #define CLIPPER_PRECISION namespace clipper { typedef float ftype32; typedef double ftype64; //! ftype definition for floating point representation /*! This type is used for all floating point values except data. The whole package could be templatised on ftype. However for now it is typedef'ed */ typedef ftype64 ftype; //! xtype definition for import/export of data typedef ftype64 xtype; } // namespace clipper #endif clipper-2.1/clipper/core/fftmap.cpp0000644000374100011300000004051710736415736014317 00000000000000/* fftmap.cpp: implementation file for P1 fft map */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "fftmap.h" #include "hkl_datatypes.h" #include #include namespace clipper { Message_fatal message_fftmap_get_real_space_error( "FFTmap: get_real_data in reciprocal space" ); Message_fatal message_fftmap_set_real_space_error( "FFTmap: set_real_data in reciprocal space" ); Message_fatal message_fftmap_get_reci_space_error( "FFTmap: get_recip_data in real space" ); Message_fatal message_fftmap_set_reci_space_error( "FFTmap: set_recip_data in real space" ); Message_ctor message_ctor_fftmap( " [FFTmap: constructed]" ); FFTmap_base::FFTtype FFTmap_p1::default_type_ = FFTmap_base::Estimate; Mutex FFTmap_base::mutex = Mutex(); /*! For later initialisation: see init() */ FFTmap_p1::FFTmap_p1() {} /*! Construct an FFTmap_p1 for a given spacegroup, cell, and grid. The map values are initialised to zero. The FFTmap_p1 is initially in neither real nor reciprocal spce, however as soon as one of the 'set' methods is called, it will be defined as in either real or reciprocal space until the next fft. \param grid_sam The grid sampling of the unit cell. \param type Can be FFTmap_p1::Measure, FFTmap_p1::Estimate. Measure performs slow precalculation (first time only) to get faster FFT. */ FFTmap_p1::FFTmap_p1( const Grid_sampling& grid_sam, const FFTtype type ) { init( grid_sam, type ); } /*! Initialise an FFTmap_p1 for a given spacegroup, cell, and grid. The map values are initialised to zero. The FFTmap_p1 is initially in neither real nor reciprocal spce, however as soon as one of the 'set' methods is called, it will be defined as in either real or reciprocal space until the next fft. \param grid_sam The grid sampling of the unit cell. \param type Can be FFTmap_p1::Measure, FFTmap_p1::Estimate. Measure performs slow precalculation (first time only) to get faster FFT. */ void FFTmap_p1::init( const Grid_sampling& grid_sam, const FFTtype type ) { grid_sam_ = grid_sam; type_ = type; if ( type_ == Default ) type_ = default_type(); // to start out with, we don't know which space we are in mode = NONE; // allocate data grid_reci_ = Grid( grid_sam_.nu(), grid_sam_.nv(), grid_sam_.nw()/2+1 ); grid_real_ = Grid( grid_reci_.nu(), grid_reci_.nv(), grid_reci_.nw()*2 ); grid_half_ = Grid( grid_sam_.nu()/2, grid_sam_.nv()/2, grid_sam_.nw()/2 ); datavec.resize( grid_real_.size(), 0.0 ); // set pointers to data data_r = &datavec[0]; data_c = (std::complex*)data_r; } /*! Reset the space and zero all the data, if necessary. */ void FFTmap_p1::reset() { mode = NONE; std::vector::iterator i; for ( i = datavec.begin(); i != datavec.end(); i++ ) *i = 0.0; } /*! \fn const Grid_sampling& FFTmap_p1::grid_real() const \return The grid sampling of the real space grid. */ /*! \fn const Grid& FFTmap_p1::grid_reci() const The reciprocal grid is half-length, plus one section, in the w direction. The remainder of the grid may be generated by Hermitian symmetry. When accessing data with reci_data, the coordinate should always be in this grid. Some points in this grid are redundent, see FFTmap_p1::uniq_reci(). \return The reciprocal grid. */ /*! \fn bool FFTmap_p1::uniq_reci( const Coord_grid& c ) const The w=0 and w=nw/2 sections contain some duplicated points related by a cetre of symmetry. On of these is considered to be significant, and the other redundent. This function returns 'true' for the significant point. \note For some calculations it may be quicker to set the whole grid than call this function for every coordinate. \param c The coordinate to test. Must be in grid_reci(). \return true if the coordinate is for a significant point. */ /*! The data is transformed from recirocal to real space. If the FFTmap_p1 is already in real space, no action is taken. \param Scale factor to apply (normally 1/cell_volume). */ void FFTmap_p1::fft_h_to_x( const ftype& scale ) { if ( mode == REAL ) return; // scale ffttype s = ffttype( scale ); int n = grid_reci_.size(); for ( int i = 0; i < n; i++ ) data_c[i] = std::conj( s * data_c[i] ); // fft int flags = ( type_ == Measure ) ? ( FFTW_IN_PLACE | FFTW_USE_WISDOM | FFTW_MEASURE ) : ( FFTW_IN_PLACE | FFTW_USE_WISDOM | FFTW_ESTIMATE ); mutex.lock(); fftwnd_plan plan = rfftw3d_create_plan( grid_sam_.nu(), grid_sam_.nv(), grid_sam_.nw(), FFTW_COMPLEX_TO_REAL, flags ); mutex.unlock(); rfftwnd_one_complex_to_real(plan, (fftw_complex*)data_c, NULL); mutex.lock(); rfftwnd_destroy_plan(plan); mutex.unlock(); // done mode = REAL; } /*! The data is transformed from real to recirocal space. If the FFTmap_p1 is already in reciproal space, no action is taken. \param Scale factor to apply (in addition to 1/N_grid factor) (normally cell_volume). */ void FFTmap_p1::fft_x_to_h( const ftype& scale ) { if ( mode == RECI ) return; // fft int flags = ( type_ == Measure ) ? ( FFTW_IN_PLACE | FFTW_USE_WISDOM | FFTW_MEASURE ) : ( FFTW_IN_PLACE | FFTW_USE_WISDOM | FFTW_ESTIMATE ); mutex.lock(); fftwnd_plan plan = rfftw3d_create_plan( grid_sam_.nu(), grid_sam_.nv(), grid_sam_.nw(), FFTW_REAL_TO_COMPLEX, flags ); mutex.unlock(); rfftwnd_one_real_to_complex(plan, (fftw_real*)data_r, NULL); mutex.lock(); rfftwnd_destroy_plan(plan); mutex.unlock(); // scale ffttype s = ffttype( scale ) / grid_sam_.size(); int n = grid_reci_.size(); for ( int i = 0; i < n; i++ ) data_c[i] = std::conj( s * data_c[i] ); // done mode = RECI; } /*! This form returns the data for an HKL. The HKL is converted into a grid reference, and the data, or if necessary the conjugate of the opposite, is returned. \param hkl The HKL of the data. */ std::complex FFTmap_p1::get_hkl( const HKL& hkl ) const { Coord_grid c = Coord_grid( hkl ).unit( grid_sam_ ); if ( c.w() < grid_reci_.nw() ) return cplx_data(c); else return std::conj( cplx_data( Coord_grid( (grid_sam_.nu()-c.u())%grid_sam_.nu(), (grid_sam_.nv()-c.v())%grid_sam_.nv(), (grid_sam_.nw()-c.w())%grid_sam_.nw() ) ) ); } /*! This form returns the data for an HKL. The HKL is converted into a grid reference, and the data, and if necessary the conjugate of the opposite, is set. \param hkl The HKL of the data. */ void FFTmap_p1::set_hkl( const HKL& hkl, const std::complex& f ) { Coord_grid c; c = Coord_grid( hkl ).unit( grid_sam_ ); if ( c.w() < grid_reci_.nw() ) cplx_data(c) = f; c = Coord_grid( -hkl ).unit( grid_sam_ ); if ( c.w() < grid_reci_.nw() ) cplx_data(c) = std::conj(f); } void FFTmap_p1::debug() const { Coord_grid c; int i, j, k; i = j = k = 0; for ( c.u() = 0; c.u() < grid_sam_.nu(); c.u()++ ) for ( c.v() = 0; c.v() < grid_sam_.nv(); c.v()++ ) for ( c.w() = 0; c.w() < grid_sam_.nw(); c.w()++ ) { if ( uniq_reci( c ) && uniq_reci( (-c).unit(grid_sam_) ) ) i++; if ( uniq_reci( c ) ) j++; k++; } std::cout << "FFTmap_p1 debug: " << i << "\t" << j << "\t" << k << "\n"; grid_sam_.debug(); for ( int i = 0; i < datavec.size(); i++ ) std::cout << i << " " << datavec[i] << "\n"; } const FFTmap_p1& FFTmap_p1::copy( const FFTmap_p1& other ) { mode = other.mode; type_ = other.type_; grid_sam_ = other.grid_sam_; grid_reci_ = other.grid_reci_; grid_real_ = other.grid_real_; grid_half_ = other.grid_half_; req_kl = other.req_kl; req_uv = other.req_uv; req_l = other.req_l; req_u = other.req_u; datavec = other.datavec; data_r = &datavec[0]; data_c = (std::complex*)data_r; return *this; } /*! For later initialisation: see init() */ FFTmap::FFTmap() { Message::message( message_ctor_fftmap ); } /*! Construct an FFTmap for a given spacegroup, cell, and grid. The map values are initialised to zero. The FFTmap is initially in neither real nor reciprocal spce, however as soon as one of the 'set' methods is called, it will be defined as in either real or reciprocal space until the next fft. \param spacegroup The spacegroup. \param cell The cell, used for scaling. \param grid_sam The grid sampling of the unit cell. \param precalc Perform slow precalculation to get faster FFT. (default: no) */ FFTmap::FFTmap( const Spacegroup& spacegroup, const Cell& cell, const Grid_sampling grid_sam, const FFTtype type ) { Message::message( message_ctor_fftmap ); init( spacegroup, cell, grid_sam, type ); } /*! Initialise an FFTmap for a given spacegroup, cell, and grid. The map values are initialised to zero. The FFTmap is initially in neither real nor reciprocal spce, however as soon as one of the 'set' methods is called, it will be defined as in either real or reciprocal space until the next fft. \param spacegroup The spacegroup. \param cell The cell, used for scaling. \param grid_sam The grid sampling of the unit cell. \param precalc Perform slow precalculation to get faster FFT. This adds a penalty of about 4s on Linux for the first FFT of any grid and direction. Subsequent FFTs will be faster. Set to true for programs which will use many FFTs. default: false.*/ void FFTmap::init( const Spacegroup& spacegroup, const Cell& cell, const Grid_sampling grid_sam, const FFTtype type ) { FFTmap_p1::init( grid_sam, type ); spacegroup_ = spacegroup; cell_ = cell; // Create the intergised symops (assumes legal grid) isymop.resize( spacegroup.num_symops() ); for ( int sym = 0; sym < spacegroup.num_symops(); sym++ ) isymop[sym] = Isymop( spacegroup.symop(sym), grid_sam ); } /*! Reset the space and zero all the data, if necessary. */ void FFTmap::reset() { mode = NONE; std::vector::iterator i; for ( i = datavec.begin(); i != datavec.end(); i++ ) *i = 0.0; } /*! The data is transformed from recirocal to real space. A scale factor of 1/v (where v is the cell volume) is applied. If the FFTmap is already in real space, no action is taken. */ void FFTmap::fft_h_to_x() { if ( mode != RECI ) return; FFTmap_p1::fft_h_to_x( 1.0/cell().volume() ); } /*! The data is transformed from real to recirocal space. A scale factor of v/n (where v is the cell volume and n the number of grid points) is applied. If the FFTmap is already in reciproal space, no action is taken. */ void FFTmap::fft_x_to_h() { if ( mode != REAL ) return; FFTmap_p1::fft_x_to_h( cell().volume() ); } /*! The data value for the given HKL, or the conjugate of its Friedel opposite if required, is returned. The symmetry related copies of the data are ignored. \param rfl The HKL of the data to be returned. \param fphi The value, as a magnitude and phase of type \c ffttype */ template void FFTmap::get_recip_data( const HKL& rfl, datatypes::F_phi& fphi ) const { if ( mode != RECI ) Message::message(message_fftmap_get_reci_space_error); fphi = std::complex( FFTmap_p1::get_hkl( rfl ) ); } /*! The data value for the given HKL, or the conjugate of its Friedel opposite if required, is set. All the symmetry related copies of the data, and any Friedel copies in the zero section, are also set. \param rfl The HKL of the data to be set. \param fphi The value, as a magnitude and phase of type \c ffttype */ template void FFTmap::set_recip_data( const HKL& rfl, const datatypes::F_phi& fphi ) { // check space if ( mode != RECI ) { if ( mode == NONE ) mode = RECI; else Message::message(message_fftmap_set_reci_space_error); } // store all sym copies of reflection // could use the F_phi type to do sym stuff, but this is faster T phi = fphi.phi(); FFTmap_p1::set_hkl( rfl, std::complex( fphi.f() * cos( phi ), fphi.f() * sin( phi ) ) ); for ( int sym = 1; sym < spacegroup_.num_primops(); sym++ ) { phi = fphi.phi() + rfl.sym_phase_shift( spacegroup_.symop(sym) ); FFTmap_p1::set_hkl( rfl.transform( isymop[sym] ), std::complex( fphi.f() * cos( phi ), fphi.f() * sin( phi ) ) ); } } /*! The data value for the given grid coordinate is returned. Symmetry related copies are ignored. \param c The coordinate of the data to be returned. \param datum The value of the data. */ template void FFTmap::get_real_data( const Coord_grid& c, T& datum ) const { if ( mode != REAL ) Message::message(message_fftmap_get_real_space_error); datum = real_data(c.unit(grid_real())); } /*! The data value for the given grid coordinate is set. All the symmetry related copies of the data are also set. \param c The coordinate of the data to be set. \param datum The value of the data. */ template void FFTmap::set_real_data( const Coord_grid& c, const T& datum ) { // check space if ( mode != REAL ) { if ( mode == NONE ) mode = REAL; else Message::message(message_fftmap_set_real_space_error); } // set all sym copies of map value real_data( c.unit(grid_sam_) ) = ffttype( datum ); for ( int sym = 1; sym < isymop.size(); sym++ ) real_data( c.transform(isymop[sym]).unit(grid_sam_) ) = ffttype( datum ); } /*! \fn datatypes::F_phi FFTmap::get_recip_data( const HKL& rfl ) const No error is produced if the space is wrong. \param rfl The HKL of the data to be returned. \return The value, as magnitude and phase of type \c ffttype */ datatypes::F_phi FFTmap::get_recip_data( const HKL& rfl ) const { return datatypes::F_phi( get_hkl(rfl) ); } /*! \fn const ffttype& FFTmap::get_real_data( const Coord_grid& c ) const No error is produced if the space is wrong. \param c The grid coordinate of the data to be returned. \return The value, as type \c ffttype */ // template instantiations template void FFTmap::get_recip_data( const HKL& rfl, datatypes::F_phi& fphi ) const; template void FFTmap::set_recip_data( const HKL& rfl, const datatypes::F_phi& fphi ); template void FFTmap::get_real_data( const Coord_grid& c, ftype32& datum ) const; template void FFTmap::set_real_data( const Coord_grid& c, const ftype32& datum ); template void FFTmap::get_recip_data( const HKL& rfl, datatypes::F_phi& fphi ) const; template void FFTmap::set_recip_data( const HKL& rfl, const datatypes::F_phi& fphi ); template void FFTmap::get_real_data( const Coord_grid& c, ftype64& datum ) const; template void FFTmap::set_real_data( const Coord_grid& c, const ftype64& datum ); } // namespace clipper clipper-2.1/clipper/core/clipper_test.h0000644000374100011300000000557110363703537015200 00000000000000/*! \file lib/clipper_test.h Header file for clipper self-test functions */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_TEST #define CLIPPER_TEST #include "clipper_types.h" namespace clipper { //! Base class for clipper self-test classes. /*! Override this class with test classes for each clipper package. */ class Test_base { public: Test_base(); void set_stream( std::ostream& stream ); protected: bool test( const String& id, const double& value ); bool test( const String& id, const double& value, const double& val, const double& tol ); bool test( const String& id, const int& value, const int& val ); std::ostream* stream_; std::vector data_val, data_tol; int count, error_count; }; } // namespace clipper #endif clipper-2.1/clipper/core/cell.h0000644000374100011300000001606310363703537013420 00000000000000/*! \file lib/cell.h Header file for unit cell class */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA /* This code is derived from the 'dm' source code */ #ifndef CLIPPER_CELL #define CLIPPER_CELL #include "clipper_types.h" namespace clipper { //! Metric tensor /*! The metric tensor is used to determine a distance in real or reciprocal space using fraction coordinates or Miller indices. It is symmetrical, so only the upper triangle is stored with the off-diagonal elements doubled. */ class Metric_tensor { public: //! null constructor inline Metric_tensor() {} //!< Null constructor //! constructor: takes parameters of normal or inverse cell Metric_tensor( const ftype& a, const ftype& b, const ftype& c, const ftype& alph, const ftype& beta, const ftype& gamm ); //! apply metric to vector inline ftype lengthsq( const Vec3<>& v ) const { return ( v[0]*(v[0]*m00 + v[1]*m01 + v[2]*m02) + v[1]*(v[1]*m11 + v[2]*m12) + v[2]*(v[2]*m22) ); } //! apply metric to int vector inline ftype lengthsq( const Vec3& v ) const { ftype h = ftype(v[0]); ftype k = ftype(v[1]); ftype l = ftype(v[2]); return h*(h*m00 + k*m01 + l*m02) + k*(k*m11 + l*m12) + l*(l*m22); } String format() const; //!< return formatted String representation private: ftype m00, m11, m22, m01, m02, m12; }; //! cell description (automatically converts to radians) /*! The cell description is a compact description of a cell, containing just the cell parameters. It is usually used to construct a full Cell object, which provides the expected functionality. */ class Cell_descr { public: inline Cell_descr() {} //!< null constructor //! constructor: from cell parameters Cell_descr( const ftype& a, const ftype& b, const ftype& c, const ftype& alpha=90.0f, const ftype& beta=90.0f, const ftype& gamma=90.0f ); inline const ftype& a() const { return a_; } //!< get a inline const ftype& b() const { return b_; } //!< get b inline const ftype& c() const { return c_; } //!< get c inline const ftype& alpha() const { return alpha_; } //!< get alpha inline const ftype& beta() const { return beta_; } //!< get beta inline const ftype& gamma() const { return gamma_; } //!< get gamma ftype alpha_deg() const; //!< get alpha in degrees ftype beta_deg() const; //!< get alpha in degrees ftype gamma_deg() const; //!< get gamma in degrees String format() const; //!< return formatted String representation protected: ftype a_,b_,c_,alpha_,beta_,gamma_; }; //! Cell object /*! The Cell class is the fully functional description of the unit cell. In addition to the cell parameters, it stores derived information including the cell volume, orthogonalising and fractionalising matrices, and the metric tensors. */ class Cell : public Cell_descr { public: //! null constructor: must initialise later inline Cell() { vol = 0.0; } //! constructor: takes a Cell descriptor explicit Cell( const Cell_descr& cell_ ) { init( cell_ ); } //! initialiser void init( const Cell_descr& cell_ ); //! test if object has been initialised bool is_null() const; ftype a_star() const; //!< get a* ftype b_star() const; //!< get b* ftype c_star() const; //!< get c* ftype alpha_star() const; //!< get alpha* ftype beta_star() const; //!< get beta* ftype gamma_star() const; //!< get gamma* // inherited functions listed for documentation purposes //-- const ftype& a() const; //-- const ftype& b() const; //-- const ftype& c() const; //-- const ftype& alpha() const; //-- const ftype& beta() const; //-- const ftype& gamma() const; //-- ftype alpha_deg() const; //-- ftype beta_deg() const; //-- ftype gamma_deg() const; //-- String format() const; //! return cell dimensions inline const Cell_descr& descr() const { return (*this); } //! return cell volume inline const ftype& volume() const { return vol; } //! test equality with another cell bool equals( const Cell& other, const ftype tol=1.0 ) const; //! return orthogonalisation matrix inline const Mat33<>& matrix_orth() const { return orthmat; } //! return fractionalisation matrix inline const Mat33<>& matrix_frac() const { return fracmat; } //! return real space metric tensor inline const Metric_tensor& metric_real() const { return realmetric; } //! return reciprocal space metric tensor inline const Metric_tensor& metric_reci() const { return recimetric; } void debug() const; private: Cell_descr descr_; //!< unit cell parameters ftype vol; //!< unit cell volume Mat33<> orthmat; //!< orthogonalisation matrix Mat33<> fracmat; //!< fractionalisation matrix Metric_tensor realmetric; //!< real space metric tensor Metric_tensor recimetric; //!< reciprocal space metric tensor }; } // namespace clipper #endif clipper-2.1/clipper/core/ramachandran.cpp0000644000374100011300000007423710363703537015462 00000000000000/* ramachandran.cpp: ramachandran plot class */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "ramachandran.h" namespace clipper { namespace data { int rama_data_size = 36; ftype32 rama_gly[] = { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,// 0 0, 0, 0, 0, 0, 0, 0, 7, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 7, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,// 1 0, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,// 2 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 3, 0, 0, 0, 0, 0, 0, 0, 3, 3, 0, 0,// 3 0, 0, 0, 11, 37, 21, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 15, 18, 74, 36, 3, 5, 2, 0, 0, 0, 0, 3, 3, 0, 0,// 4 1, 3, 30, 146, 193, 137, 30, 6, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 16, 60, 237, 329, 131, 25, 7, 2, 0, 3, 2, 0, 0, 0, 0, 1,// 5 42, 154, 432, 857, 603, 201, 52, 3, 0, 0, 0, 0, 3, 8, 0, 3, 8, 8, 49, 97, 204, 334, 409, 593, 320, 63, 11, 0, 0, 4, 3, 0, 0, 2, 5, 15,// 6 616, 1527, 1975, 1407, 577, 144, 51, 0, 0, 0, 0, 0, 1, 0, 0, 5, 34, 93, 178, 366, 452, 310, 236, 305, 210, 53, 22, 16, 3, 2, 0, 0, 7, 9, 26, 111,// 7 2655, 2916, 2032, 816, 205, 61, 14, 10, 5, 2, 7, 11, 13, 5, 19, 73, 171, 337, 524, 493, 460, 222, 127, 97, 57, 28, 21, 12, 4, 19, 31, 29, 24, 41, 196, 1032,// 8 2461, 1984, 840, 240, 74, 29, 16, 5, 10, 15, 15, 22, 23, 40, 75, 253, 356, 406, 464, 420, 289, 144, 53, 24, 20, 19, 15, 15, 0, 19, 26, 30, 41, 145, 798, 1998,// 9 1122, 937, 278, 55, 30, 6, 16, 6, 19, 12, 29, 39, 51, 83, 119, 216, 327, 228, 292, 250, 168, 101, 47, 32, 9, 19, 6, 9, 12, 0, 9, 30, 40, 218, 929, 1231,//10 467, 301, 148, 54, 6, 3, 3, 0, 6, 2, 26, 28, 41, 50, 66, 173, 205, 172, 190, 206, 112, 45, 17, 22, 2, 12, 11, 7, 3, 0, 5, 12, 58, 195, 402, 443,//11 190, 104, 33, 19, 24, 10, 5, 0, 1, 10, 17, 15, 29, 36, 71, 87, 127, 173, 156, 135, 68, 48, 32, 13, 7, 16, 5, 4, 7, 1, 16, 13, 16, 86, 102, 111,//12 64, 32, 12, 11, 32, 9, 0, 0, 0, 7, 8, 11, 10, 38, 43, 61, 86, 106, 112, 140, 132, 67, 40, 15, 9, 12, 1, 0, 13, 10, 2, 11, 11, 24, 68, 101,//13 15, 11, 9, 2, 3, 1, 0, 0, 0, 2, 3, 0, 14, 9, 28, 45, 101, 102, 169, 169, 162, 112, 60, 18, 2, 1, 0, 0, 5, 2, 0, 10, 16, 15, 26, 36,//14 7, 12, 5, 0, 0, 0, 0, 0, 0, 2, 5, 4, 10, 4, 31, 40, 76, 139, 259, 193, 137, 116, 51, 18, 4, 0, 0, 1, 0, 4, 6, 1, 21, 8, 11, 18,//15 4, 8, 0, 0, 0, 0, 0, 1, 12, 0, 1, 6, 0, 7, 6, 27, 93, 150, 202, 253, 211, 105, 30, 23, 6, 5, 3, 8, 1, 17, 16, 0, 0, 1, 3, 10,//16 0, 0, 0, 0, 0, 6, 1, 10, 0, 0, 1, 6, 9, 6, 9, 30, 104, 187, 324, 399, 208, 126, 48, 19, 12, 6, 3, 0, 0, 3, 1, 0, 0, 0, 0, 0,//17 0, 2, 1, 0, 0, 6, 0, 0, 0, 0, 0, 10, 10, 16, 38, 35, 153, 303, 421, 352, 184, 72, 54, 19, 21, 8, 7, 0, 0, 0, 0, 5, 4, 1, 0, 1,//18 4, 6, 3, 0, 1, 3, 1, 9, 0, 0, 0, 3, 3, 18, 38, 72, 191, 401, 430, 252, 172, 74, 40, 9, 9, 0, 11, 6, 7, 0, 0, 3, 12, 10, 2, 8,//19 18, 1, 0, 3, 12, 8, 11, 3, 0, 2, 0, 0, 1, 23, 71, 164, 338, 358, 286, 185, 125, 46, 17, 5, 1, 7, 4, 10, 2, 0, 0, 0, 0, 1, 0, 1,//20 4, 14, 12, 6, 5, 4, 0, 0, 2, 8, 0, 1, 14, 39, 97, 183, 245, 212, 178, 143, 107, 51, 36, 13, 11, 1, 4, 7, 0, 0, 0, 0, 0, 0, 0, 0,//21 7, 21, 18, 46, 23, 4, 10, 1, 0, 0, 0, 6, 25, 62, 150, 258, 187, 143, 150, 125, 62, 16, 35, 17, 14, 7, 4, 1, 3, 6, 0, 0, 0, 1, 6, 2,//22 24, 31, 34, 55, 25, 13, 9, 4, 0, 0, 1, 20, 40, 82, 144, 259, 208, 150, 148, 151, 88, 50, 33, 26, 25, 11, 7, 14, 8, 4, 14, 0, 0, 10, 19, 21,//23 24, 61, 51, 26, 24, 5, 6, 2, 0, 0, 0, 15, 42, 107, 142, 154, 151, 140, 113, 141, 96, 76, 31, 22, 9, 16, 19, 13, 7, 8, 12, 1, 0, 4, 23, 28,//24 86, 126, 147, 42, 16, 27, 25, 3, 0, 1, 3, 35, 54, 94, 145, 114, 153, 147, 180, 151, 129, 114, 86, 33, 24, 31, 22, 22, 25, 11, 24, 6, 9, 20, 24, 40,//25 244, 273, 176, 62, 6, 16, 20, 6, 1, 4, 31, 58, 80, 90, 107, 157, 181, 206, 254, 225, 269, 151, 100, 87, 41, 43, 30, 20, 18, 24, 10, 1, 10, 34, 73, 137,//26 499, 309, 145, 71, 18, 30, 21, 36, 30, 25, 22, 43, 45, 132, 180, 216, 225, 325, 436, 455, 378, 138, 72, 51, 21, 37, 28, 3, 17, 26, 5, 21, 32, 79, 158, 357,//27 463, 119, 15, 44, 15, 33, 40, 30, 24, 27, 19, 35, 53, 113, 225, 313, 425, 594, 531, 432, 223, 92, 34, 8, 0, 5, 4, 7, 8, 13, 28, 104, 249, 318, 354, 531,//28 174, 21, 1, 0, 1, 17, 10, 3, 4, 13, 20, 23, 72, 120, 275, 490, 579, 477, 271, 124, 48, 17, 2, 0, 0, 0, 8, 7, 0, 13, 91, 851, 2514, 1280, 752, 630,//29 36, 3, 7, 1, 0, 1, 0, 0, 0, 0, 1, 5, 48, 158, 339, 299, 137, 111, 57, 29, 2, 1, 0, 0, 0, 0, 0, 0, 0, 11, 179, 2348, 4535, 1658, 748, 240,//30 4, 0, 16, 1, 0, 0, 0, 0, 0, 0, 5, 12, 14, 74, 122, 40, 1, 10, 7, 2, 0, 0, 0, 0, 0, 0, 0, 0, 10, 12, 140, 626, 736, 309, 95, 15,//31 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 1, 13, 6, 4, 0, 0, 0, 11, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 10, 60, 85, 28, 8, 0, 0,//32 0, 0, 0, 0, 0, 3, 9, 0, 0, 0, 0, 0, 3, 9, 3, 6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 11, 10, 5, 6, 5, 0, 0, 0, 0,//33 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 5, 7, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 10, 4, 0, 0, 0, 0, 0, 0, 0,//34 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//35 }; ftype32 rama_pro[] = { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,// 0 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,// 1 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,// 2 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,// 3 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,// 4 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,// 5 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,// 6 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,// 7 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,// 8 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,// 9 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//10 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//11 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//12 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//13 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//14 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//15 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//16 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//17 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//18 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//19 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//20 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//21 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//22 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//23 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//24 3, 7, 8, 8, 18, 16, 7, 0, 0, 0, 0, 0, 0, 0, 3, 7, 11, 11, 6, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//25 89, 84, 65, 44, 8, 7, 10, 0, 0, 0, 0, 4, 23, 29, 25, 34, 70, 44, 34, 9, 0, 0, 0, 1, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 47,//26 245, 142, 121, 55, 11, 26, 52, 86, 22, 15, 15, 16, 45, 95, 111, 269, 327, 234, 109, 37, 3, 2, 2, 2, 6, 0, 0, 0, 0, 0, 0, 0, 0, 9, 122, 217,//27 399, 100, 43, 21, 45, 111, 203, 246, 126, 59, 69, 61, 149, 349, 658, 1240, 1354, 828, 239, 58, 16, 12, 7, 6, 1, 4, 2, 0, 0, 0, 0, 0, 28, 138, 434, 704,//28 309, 35, 10, 3, 10, 67, 101, 68, 42, 34, 26, 75, 280, 912, 2196, 3282, 2681, 1103, 162, 21, 3, 1, 1, 2, 11, 4, 2, 4, 2, 1, 7, 45, 400, 1155, 1852, 1359,//29 62, 9, 2, 5, 4, 3, 8, 0, 0, 9, 36, 37, 404, 1893, 3871, 3571, 1491, 290, 38, 11, 0, 0, 0, 0, 0, 0, 0, 4, 2, 14, 48, 615, 2889, 4269, 2608, 601,//30 0, 4, 3, 0, 0, 0, 0, 0, 0, 4, 14, 19, 366, 1302, 1543, 683, 130, 8, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 93, 961, 2346, 1684, 400, 18,//31 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 20, 82, 119, 85, 14, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 81, 230, 242, 85, 11, 0,//32 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 10, 11, 8, 2, 5, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 0, 5, 33, 31, 4, 1, 0, 0,//33 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 8, 0, 0, 0, 2, 3, 0, 0, 0, 0,//34 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//35 }; ftype32 rama_ngp[] = { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 0, 2, 3, 0, 0, 0, 0,// 0 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 7, 5, 2, 0, 0, 0, 0, 0, 0,// 1 0, 0, 0, 0, 0, 3, 4, 0, 0, 0, 0, 0, 0, 5, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 1, 3, 8, 0, 0, 0, 0,// 2 0, 0, 0, 0, 1, 26, 46, 23, 2, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,// 3 0, 0, 1, 14, 170, 518, 444, 135, 18, 3, 4, 5, 0, 0, 0, 0, 0, 0, 0, 0, 1, 7, 10, 29, 22, 6, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0,// 4 0, 7, 164, 821, 2467, 2335, 972, 229, 38, 7, 10, 8, 0, 0, 0, 0, 0, 0, 0, 1, 4, 29, 51, 157, 87, 29, 22, 0, 0, 0, 0, 0, 0, 5, 2, 0,// 5 46, 354, 1203, 2297, 2859, 1352, 417, 140, 36, 3, 19, 19, 3, 0, 0, 1, 2, 7, 29, 9, 36, 49, 58, 85, 90, 45, 22, 1, 3, 14, 22, 11, 18, 16, 15, 10,// 6 276, 752, 962, 848, 373, 77, 42, 30, 15, 5, 10, 10, 9, 3, 6, 8, 14, 16, 42, 15, 9, 13, 11, 10, 16, 14, 8, 0, 2, 26, 99, 65, 35, 12, 32, 65,// 7 166, 207, 109, 52, 7, 10, 9, 15, 17, 5, 5, 7, 3, 6, 18, 22, 16, 7, 3, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 7, 33, 39, 17, 6, 21, 111,// 8 18, 15, 0, 0, 0, 3, 6, 1, 12, 0, 10, 1, 9, 11, 5, 8, 1, 0, 0, 0, 2, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 2, 14,// 9 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,//10 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 1,//11 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 5, 2,//12 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 4, 0, 0, 0,//13 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 5, 14, 3, 1, 0,//14 0, 0, 0, 0, 0, 5, 3, 0, 0, 0, 0, 3, 8, 9, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 7, 2, 0,//15 0, 0, 0, 0, 0, 3, 2, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 4, 6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 1, 0, 0,//16 0, 0, 0, 0, 0, 0, 0, 0, 3, 3, 0, 0, 0, 0, 6, 16, 12, 16, 3, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0, 5, 2, 0, 5, 2, 0, 0,//17 0, 0, 0, 0, 0, 0, 0, 4, 5, 7, 8, 5, 4, 11, 36, 74, 164, 192, 69, 20, 4, 7, 0, 0, 0, 0, 0, 0, 0, 7, 3, 0, 0, 0, 0, 0,//18 2, 2, 3, 1, 3, 7, 9, 23, 37, 57, 40, 35, 62, 161, 397, 884, 1539, 1299, 524, 153, 31, 8, 0, 0, 0, 1, 6, 0, 0, 5, 3, 0, 0, 0, 0, 0,//19 16, 22, 24, 18, 31, 41, 55, 135, 119, 122, 187, 269, 365, 760, 1462, 2646, 4068, 2973, 1140, 323, 91, 27, 2, 0, 1, 2, 16, 2, 20, 13, 11, 2, 8, 9, 5, 2,//20 65, 105, 141, 97, 107, 112, 206, 297, 260, 302, 376, 583, 976, 1843, 3301, 4919, 5142, 3134, 1234, 421, 112, 36, 12, 2, 5, 15, 9, 9, 13, 42, 22, 11, 15, 40, 34, 36,//21 215, 326, 337, 260, 286, 224, 427, 636, 531, 416, 627, 1304, 2420, 4039, 5543, 6810, 6445, 3344, 1056, 322, 109, 11, 10, 11, 15, 17, 3, 19, 33, 92, 76, 61, 39, 78, 103, 174,//22 807, 852, 845, 653, 539, 340, 574, 1144, 1005, 652, 999, 2377, 5342, 8103, 7864, 7454, 6508, 3025, 893, 281, 109, 29, 13, 17, 29, 18, 15, 42, 72, 91, 122, 192, 213, 318, 367, 670,//23 1774, 1897, 1793, 1122, 556, 188, 227, 471, 600, 823, 1461, 3182, 7185,10522, 7989, 5999, 4607, 1941, 688, 286, 147, 58, 60, 21, 49, 29, 27, 68, 76, 128, 222, 341, 383, 670, 1032, 1362,//24 2961, 3726, 2711, 1208, 435, 157, 106, 90, 221, 646, 1795, 4095, 8039, 9609, 6837, 4629, 3183, 1428, 604, 199, 87, 32, 29, 7, 19, 30, 48, 55, 93, 136, 278, 545, 710, 1067, 1726, 2191,//25 5516, 5175, 2490, 769, 268, 141, 209, 303, 458, 875, 2273, 4174, 6766, 7542, 5419, 3686, 2828, 1522, 709, 257, 65, 18, 29, 8, 15, 30, 19, 34, 83, 147, 324, 1002, 1361, 1833, 2523, 3674,//26 7319, 4002, 1093, 251, 193, 284, 568, 878, 1058, 1420, 2200, 3704, 5133, 6007, 4894, 3567, 3106, 1918, 926, 405, 72, 4, 4, 6, 4, 31, 3, 7, 51, 130, 424, 1324, 2216, 3224, 4255, 6717,//27 4905, 1403, 224, 68, 80, 205, 495, 811, 922, 945, 1401, 2495, 4199, 6009, 5594, 5039, 4551, 2869, 990, 337, 49, 5, 0, 0, 0, 2, 0, 2, 39, 113, 547, 2674, 6560, 7703, 7839, 8289,//28 1646, 228, 24, 16, 11, 52, 44, 93, 153, 115, 312, 1043, 2929, 6120, 7732, 6801, 4734, 1953, 396, 36, 4, 1, 0, 0, 0, 0, 5, 3, 12, 65, 1086,21027,57767,28567,15321, 8073,//29 188, 23, 3, 0, 5, 3, 0, 2, 15, 23, 40, 295, 1803, 5781, 7356, 4257, 1641, 351, 28, 4, 0, 0, 0, 0, 6, 5, 2, 3, 14, 74, 2655,49493,86255,29323,10531, 2193,//30 5, 4, 3, 0, 0, 0, 0, 0, 0, 6, 6, 85, 795, 2705, 2139, 709, 97, 7, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 14, 85, 1433,10936,11859, 4044, 687, 60,//31 0, 0, 0, 0, 0, 0, 0, 0, 0, 5, 4, 39, 187, 346, 118, 18, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 17, 48, 323, 729, 469, 110, 5, 2,//32 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 17, 36, 15, 1, 4, 7, 0, 0, 0, 0, 0, 0, 0, 4, 3, 0, 2, 12, 25, 26, 41, 8, 4, 15, 1,//33 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, 6, 18, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 2, 0, 0, 0, 7, 3, 13, 0, 0, 2, 0,//34 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 12, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 2, 6, 0, 0, 0, 0,//35 }; } void Prob_phi_2d::init( const int& size ) { n = size; data_.clear(); data_.resize( n*n, 0.0 ); } void Prob_phi_2d::accumulate( const ftype32 table[] ) { for ( int i = 0; i < data_.size(); i++ ) data_[i] += table[i]; } /*! linear interpolation onto grid */ void Prob_phi_2d::accumulate( const ftype& phi1, const ftype& phi2, ftype wgt ) { int i1_0, i2_0, i1_1, i2_1; ftype w1_0, w2_0, w1_1, w2_1; w1_1 = ftype(n) * phi1 / Util::twopi(); w2_1 = ftype(n) * phi2 / Util::twopi(); i1_0 = Util::intf( w1_1 ); i2_0 = Util::intf( w2_1 ); w1_1 -= ftype( i1_0 ); w2_1 -= ftype( i2_0 ); w1_0 = 1.0 - w1_1; w2_0 = 1.0 - w2_1; i1_0 = Util::mod( i1_0 , n ); i2_0 = Util::mod( i2_0 , n ); i1_1 = Util::mod( i1_0+1, n ); i2_1 = Util::mod( i2_0+1, n ); data( i1_0, i2_0 ) += wgt * w1_0 * w2_0; data( i1_0, i2_1 ) += wgt * w1_0 * w2_1; data( i1_1, i2_0 ) += wgt * w1_1 * w2_0; data( i1_1, i2_1 ) += wgt * w1_1 * w2_1; } /*! normalise mean value to 1/(2pi)^2 */ void Prob_phi_2d::normalise() { ftype s = 0.0; for ( int i = 0; i < data_.size(); i++ ) s += data_[i]; s = ftype( data_.size() ) / ( Util::twopi() * Util::twopi() * s ); for ( int i = 0; i < data_.size(); i++ ) data_[i] *= s; } /*! linear interpolation off of grid */ ftype Prob_phi_2d::probability( const ftype& phi1, const ftype& phi2 ) const { int i1_0, i2_0, i1_1, i2_1; ftype w1_0, w2_0, w1_1, w2_1; w1_1 = ftype(n) * phi1 / Util::twopi(); w2_1 = ftype(n) * phi2 / Util::twopi(); i1_0 = Util::intf( w1_1 ); i2_0 = Util::intf( w2_1 ); w1_1 -= ftype( i1_0 ); w2_1 -= ftype( i2_0 ); w1_0 = 1.0 - w1_1; w2_0 = 1.0 - w2_1; i1_0 = Util::mod( i1_0 , n ); i2_0 = Util::mod( i2_0 , n ); i1_1 = Util::mod( i1_0+1, n ); i2_1 = Util::mod( i2_0+1, n ); return w1_0 * ( w2_0 * data( i1_0, i2_0 ) + w2_1 * data( i1_0, i2_1 ) ) + w1_1 * ( w2_0 * data( i1_1, i2_0 ) + w2_1 * data( i1_1, i2_1 ) ); } String Prob_phi_2d::format() const { String s; for ( int i = 0; i < n; i++ ) { for ( int j = 0; j < n; j++ ) { if ( j % 12 == 0 ) s += "\n "; int k = Util::intr( data(i,j) ); s += String( k, 5 ) + ","; } s += "//" + String( i, 2 ); } return s; } /*! Construct a Ramachandran plot of a given type. \param type The residue type of the plot. Options include: Ramachandran::Gly, Ramachandran::Pro, Ramachandran::NonGlyPro, Ramachandran::NonGly, Ramachandran::All */ Ramachandran::Ramachandran( TYPE type ) { init( type ); } /*! Construct a Ramachandran plot of a given type. \param type The residue type of the plot. Options include: Ramachandran::Gly, Ramachandran::Pro, Ramachandran::NonGlyPro, Ramachandran::NonGly, Ramachandran::All */ void Ramachandran::init( TYPE type ) { switch (type) { case Gly: Prob_phi_2d::init( data::rama_data_size ); Prob_phi_2d::accumulate( data::rama_gly ); break; case Pro: Prob_phi_2d::init( data::rama_data_size ); Prob_phi_2d::accumulate( data::rama_pro ); break; case NonGlyPro: Prob_phi_2d::init( data::rama_data_size ); Prob_phi_2d::accumulate( data::rama_ngp ); break; case NonGly: Prob_phi_2d::init( data::rama_data_size ); Prob_phi_2d::accumulate( data::rama_ngp ); Prob_phi_2d::accumulate( data::rama_pro ); break; default: Prob_phi_2d::init( data::rama_data_size ); Prob_phi_2d::accumulate( data::rama_ngp ); Prob_phi_2d::accumulate( data::rama_pro ); Prob_phi_2d::accumulate( data::rama_gly ); break; } Prob_phi_2d::normalise(); set_thresholds(); } /*! Set thresholds for favorable and allowed regions of the Ramachandran plot. The US spelling is used because it is the same length as 'allowed'. I should get out more. Sorry. \param prob_favored The probability threshold for the favored region. \param prob_allowed The probability threshold for the allowed region. */ void Ramachandran::set_thresholds( ftype prob_favored, ftype prob_allowed ) { p_favored = prob_favored; p_allowed = prob_allowed; } } // namespace clipper clipper-2.1/clipper/core/hkl_data.h0000644000374100011300000005425511205463740014250 00000000000000/*! \file lib/hkl_data.h Header file for reflection data class */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_HKL_DATA #define CLIPPER_HKL_DATA #include "hkl_info.h" namespace clipper { class HKL_data_cacheobj : public HKL_info { public: class Key { public: Key( const Spgr_descr& spgr_descr, const Cell& cell_descr, const HKL_sampling& hkl_sam ) : spgr_descr_(spgr_descr), cell_descr_(cell_descr), hkl_sampling_(hkl_sam) {} const Spgr_descr& spgr_descr() const { return spgr_descr_; } const Cell_descr& cell_descr() const { return cell_descr_; } const HKL_sampling& hkl_sampling() const { return hkl_sampling_; } private: Spgr_descr spgr_descr_; Cell_descr cell_descr_; HKL_sampling hkl_sampling_; }; HKL_data_cacheobj( const Key& hkl_data_cachekey ); bool matches( const Key& hkl_data_cachekey ) const; String format() const; static Mutex mutex; //!< thread safety private: Key key; }; //! Reflection data type objects. /*! A class from which data type objects are usually derived To define a new type for use in an HKL_data structure, subclass this class and override the following methods: - constructor - initialises to NAN - type() - returns type name, which is a list of the contained data - friedel() - applies Fridel transformation - shift_phase() - applies phase shift transformation - missing() - checks if data is present - data_size() - number of data elements in this type - data_names() - names of data elements in this type - data_export() - conversion to array (for I/O) - data_import() - conversion from array (for I/O) - scale() - (OPTIONAL) apply magnitude scale factor to data \note polymorphism is NOT used here because virtual tables would be to expensive for every individual reflection, both in terms of space and cpu cycles. */ class Datatype_base { protected: //! initialise to 'missing' //-- Datatype_base(); //! initialise to 'missing' (all elements are set to null) void set_null(); //! return the name of this data type static String type(); //! apply Friedel transformation to the data void friedel(); //! apply phase shift to the data void shift_phase(const ftype& dphi); //! return true if data is missing bool missing() const; //! return number of data elements in this type static int data_size(); //! return names of data elements in this type static String data_names(); //! conversion to array (for I/O) void data_export( xtype array[] ) const; //! conversion from array (for I/O) void data_import( const xtype array[] ); }; //! HKL_data_base /*! This is the virtual base for the typed hkl_data objects. It exists to guarantee and interface by which data can be managed without knowledge of the specific data type. */ class HKL_data_base { public: // Coordinate reference types //! Basic HKL_reference_index: see HKL_info typedef HKL_info::HKL_reference_index HKL_reference_index; //! HKL HKL_reference_index: see HKL_info typedef HKL_info::HKL_reference_coord HKL_reference_coord; //! initialiser: from parent hkl_info and cell virtual void init( const HKL_info& hkl_info, const Cell& cell ); //! initialiser: from another hkl_data virtual void init( const HKL_data_base& hkl_data ); //! [CLIPPER2] initialiser: from spacegroup, cell, and HKL_sampling virtual void init( const Spacegroup& spacegroup, const Cell& cell, const HKL_sampling& hkl_sampling ); // generic methods //! test if object has been initialised bool is_null() const; //! get the parent HKL_info object const HKL_info& base_hkl_info() const { return *parent_hkl_info; } //! get the parent cell const Cell& base_cell() const { return *parent_cell; } //! [CLIPPER2] get spacegroup const Spacegroup& spacegroup() const { return spacegroup_; } //! [CLIPPER2] get cell const Cell& cell() const { return cell_; } //! [CLIPPER2] get resolution const Resolution& resolution() const { return resolution_; } //! [CLIPPER2] get HKL_sampling const HKL_sampling& hkl_sampling() const { return hkl_sampling_; } //! [CLIPPER2] get HKL_info object const HKL_info& hkl_info() const { return *parent_hkl_info; } //! get resolution by reflection index (based on true cell) ftype invresolsq( const int& index ) const; //! get resolution limits of the list (based on true cell and missing data) Range invresolsq_range() const; //! get number of observations in this list (based on missing data) int num_obs() const; //! update: synchornize info with parent HKL_info virtual void update() = 0; //! get data type (a list of names corresponding to the im/export values) virtual String type() const = 0; //! check if a data entry in the list is marked as 'missing' virtual bool missing(const int& index) const = 0; //! set data entry in the list to its null value virtual void set_null(const int& index) = 0; //! return number of data elements in this type virtual int data_size() const = 0; //! return names of data elements in this type virtual String data_names() const = 0; //! conversion to array (for I/O) virtual void data_export( const HKL& hkl, xtype array[] ) const = 0; //! conversion from array (for I/O) virtual void data_import( const HKL& hkl, const xtype array[] ) = 0; //! mask the data by marking any data missing in 'mask' as missing virtual void mask(const HKL_data_base& mask) = 0; //! return HKL_reference_index pointing to first reflection HKL_reference_index first() const; //! return HKL_reference_index pointing to first non-missing data HKL_reference_index first_data() const; //! increment HKL_reference_index to next non-missing data HKL_reference_index& next_data( HKL_reference_index& ih ) const; void debug() const; protected: const HKL_info* parent_hkl_info; const Cell* parent_cell; bool cell_matches_parent; // clipper2 members ObjectCache::Reference cacheref; //!< object cache ref Spacegroup spacegroup_; Cell cell_; HKL_sampling hkl_sampling_; Resolution resolution_; //! null constructor HKL_data_base(); //! destructor virtual ~HKL_data_base() {} }; //! HKL_data<> /*! An actual hkl_data object, containing actual data of type T. This implements the generic interface, and in addition provides type-specific access functions. \note The following methods are inherited from HKL_data_base but are documented here for convenience: base_hkl_info(), base_cell(), invresolsq(), invresolsq_range(), num_obs(), first(), first_data(), next_data(). */ template class HKL_data : public HKL_data_base { public: //! null constructor HKL_data() {} //! constructor: from parent hkl_info explicit HKL_data( const HKL_info& hkl_info ); //! constructor: from parent hkl_info and cell HKL_data( const HKL_info& hkl_info, const Cell& cell ); //! [CLIPPER2] constructor: from spacegroup, cell and hkl_sampling HKL_data( const Spacegroup& spacegroup, const Cell& cell, const HKL_sampling& hkl_sampling ); //! [CLIPPER2] constructor: from another HKL_data object explicit HKL_data( const HKL_data_base& hkl_data ); //! initialiser: from parent hkl_info and cell void init( const HKL_info& hkl_info, const Cell& cell ); //! [CLIPPER2] initialiser: from spacegroup, cell, and HKL_sampling void init( const Spacegroup& spacegroup, const Cell& cell, const HKL_sampling& hkl_sampling ); //! [CLIPPER2] initialiser: from another HKL_data object void init( const HKL_data_base& hkl_data ); //! update: synchornize info with parent HKL_info void update(); // type specific methods String type() const { return T::type(); } bool missing(const int& index) const { return list[index].missing(); } void set_null(const int& index) { list[index].set_null(); } int data_size() const { return T::data_size(); } String data_names() const { return T::data_names(); } void data_export( const HKL& hkl, xtype array[] ) const { T datum; get_data( hkl, datum ); datum.data_export( array ); } void data_import( const HKL& hkl, const xtype array[] ) { T datum; datum.data_import( array ); set_data( hkl, datum ); } void mask(const HKL_data_base& mask); // data access methods: by HKL_reference_index //! get data by reflection HKL_reference_index const T& operator[] (const HKL_info::HKL_reference_index& i) const { return list[i.index()]; } //! set data by reflection HKL_reference_index T& operator[] (const HKL_info::HKL_reference_index& i) { return list[i.index()]; } // data access methods: by HKL_reference_coord //! get data by HKL_reference_coord T operator[] (const HKL_info::HKL_reference_coord& ih) const; //! get data by HKL_reference_coord (returns false if no equivalent hkl) bool get_data(const HKL_info::HKL_reference_coord& ih, T& data) const; //! set data by HKL_reference_coord (returns false if no equivalent hkl) bool set_data(const HKL_info::HKL_reference_coord& ih, const T& data); // data access methods: by index //! get data by reflection index const T& operator[] (const int& index) const { return list[index]; } //! set data by reflection index T& operator[] (const int& index) { return list[index]; } // data access methods: by hkl //! get data by hkl (returns missing if no equivalent hkl) T operator[] (const HKL& hkl) const; //! get data by hkl (returns false if no equivalent hkl) bool get_data(const HKL& hkl, T& data) const; //! set data by hkl (returns false if no equivalent hkl) bool set_data(const HKL& hkl, const T& data); // COMPUTATION OPERATORS //! Basic computation: fill this data list by function call template void compute( const C& op ) { for (HKL_info::HKL_reference_index ih=parent_hkl_info->first(); !ih.last(); ih.next()) list[ih.index()] = op( ih ); } //! Unary computation: fill this data list by computation from another template void compute( const HKL_data& src, const C& op ) { for (HKL_info::HKL_reference_index ih=parent_hkl_info->first(); !ih.last(); ih.next()) list[ih.index()] = op( ih, src[ih] ); } //! Binary computation: fill this data list by computation from another template void compute( const HKL_data& src1, const HKL_data& src2, const C& op ) { for (HKL_info::HKL_reference_index ih=parent_hkl_info->first(); !ih.last(); ih.next()) list[ih.index()] = op( ih, src1[ih], src2[ih] ); } // inherited functions lists for documentation purposes //-- const HKL_info& base_hkl_info() const; //-- const Cell& base_cell() const; //-- const ftype invresolsq(const int& index) const; //-- const Range invresolsq_range() const; //-- const int num_obs() const; //-- HKL_reference_index first() const; //-- HKL_reference_index first_data() const; //-- HKL_reference_index& next_data( HKL_reference_index& ih ) const; //! assignment operator: copies the data from another list HKL_data& operator =( const HKL_data& other ); //! assignment operator: assigns a single value to the whole list HKL_data& operator =( const T& value ); void debug() const; protected: // members std::vector list; }; // Template implementations ftype HKL_info::HKL_reference_base::invresolsq( const HKL_data_base& hkldata ) const { return hkldata.invresolsq( index_ ); } /*! Construct the object using a given reflection list and cell. \param hkl_info The reflection list object. */ template HKL_data::HKL_data( const HKL_info& hkl_info ) { init( hkl_info, hkl_info.cell() ); } /*! Construct the object using a given reflection list and cell. \param hkl_info The reflection list object. \param cell The unit cell for this datalist. */ template HKL_data::HKL_data( const HKL_info& hkl_info, const Cell& cell ) { init( hkl_info, cell ); } /*! Construct the object using a given spacegroup, cell, and sampling. \param spacegroup The spacegroup for this datalist. \param cell The unit cell for this datalist. \param hkl_sampling The reflection list description. */ template HKL_data::HKL_data( const Spacegroup& spacegroup, const Cell& cell, const HKL_sampling& hkl_sampling ) { init( spacegroup, cell, hkl_sampling ); } /*! Construct the object using a given HKL_data object. The properties of the object (spacegroup, cell, sampling) are the copied, but the actual data is not. \param hkl_data The HKL_data object to provide the data. */ template HKL_data::HKL_data( const HKL_data_base& hkl_data ) { init( hkl_data ); } /*! Initialise the object using a given reflection list and cell. \param hkl_info The reflection list object. \param cell The unit cell for this datalist. */ template void HKL_data::init( const HKL_info& hkl_info, const Cell& cell ) { HKL_data_base::init( hkl_info, cell ); update(); } /*! Initialise the object using a given spacegroup, cell, and sampling. \param spacegroup The spacegroup for this datalist. \param cell The unit cell for this datalist. \param hkl_sampling The reflection list description. */ template void HKL_data::init( const Spacegroup& spacegroup, const Cell& cell, const HKL_sampling& hkl_sampling ) { HKL_data_base::init( spacegroup, cell, hkl_sampling ); update(); } /*! Initialise the object using a given HKL_data object. The properties of the object (spacegroup, cell, sampling) are the copied, but the actual data is not. \param hkl_data The HKL_data object to provide the data. */ template void HKL_data::init( const HKL_data_base& hkl_data ) { HKL_data_base::init( hkl_data ); update(); } /*! The datalist is resized if necessary to match the parent. */ template void HKL_data::update() { if ( parent_hkl_info != NULL ) { T null; null.set_null(); list.resize( parent_hkl_info->num_reflections(), null ); } } /*! For each data element, if the corresponding element in \c mask is missing, then that element in this list is also set to missing. \param mask The list to provide the mask. */ template void HKL_data::mask(const HKL_data_base& mask) { T null; null.set_null(); for ( int i = 0; i < list.size(); i++ ) if ( mask.missing(i) ) list[i] = null; } /*! If a symmetry mate of the requested HKL exists in the list, then the correct symmetry transformations are applied and the data is returned, otherwise the value of 'missing' for the datatype is returned. \param ih The reference to the HKL. \return The data, or 'missing'. */ template T HKL_data::operator[] (const HKL_info::HKL_reference_coord& ih) const { if ( ih.index() < 0 ) { T null; null.set_null(); return null; } T data = list[ih.index()]; if ( ih.friedel() ) data.friedel(); data.shift_phase( -ih.hkl().sym_phase_shift( parent_hkl_info->spacegroup().symop(ih.sym()) ) ); return data; } /*! If a symmetry mate of the requested HKL exists in the list, then the correct symmetry transformations are applied and the data is returned, otherwise the value of 'missing' for the datatype is returned. \param ih The reference to the HKL. \param data Returned with the value of the data. \return true if the data was returned. */ template bool HKL_data::get_data(const HKL_info::HKL_reference_coord& ih, T& data) const { if ( ih.index() < 0 ) { data.set_null(); return false; } data = list[ih.index()]; if ( ih.friedel() ) data.friedel(); data.shift_phase( -ih.hkl().sym_phase_shift( parent_hkl_info->spacegroup().symop(ih.sym()) ) ); return true; } /*! If a symmetry mate of the requested HKL exists in the list, then the correct symmetry transformations are applied and data is set to the supplied values, otherwise the function returns false. \param ih The reference to the HKL. \param data Value of the data to set. \return true if the data was set. */ template bool HKL_data::set_data(const HKL_info::HKL_reference_coord& ih, const T& data) { if ( ih.index() < 0 ) return false; T& ldata = list[ih.index()]; ldata = data; ldata.shift_phase( ih.hkl().sym_phase_shift( parent_hkl_info->spacegroup().symop(ih.sym()) ) ); if ( ih.friedel() ) ldata.friedel(); return true; } /*! If a symmetry mate of the requested HKL exists in the list, then the correct symmetry transformations are applied and the data is returned, otherwise the value of 'missing' for the datatype is returned. \param hkl The reflection HKL. \return The data, or 'missing'. */ template T HKL_data::operator[] (const HKL& hkl) const { int index, sym; bool friedel; index = parent_hkl_info->index_of( parent_hkl_info-> find_sym(hkl, sym, friedel) ); if ( index < 0 ) { T null; null.set_null(); return null; } T data = list[index]; if (friedel) data.friedel(); data.shift_phase( -hkl.sym_phase_shift( parent_hkl_info->spacegroup().symop(sym) ) ); return data; } /*! If a symmetry mate of the requested HKL exists in the list, then the correct symmetry transformations are applied and the supplied datatype is set, otherwise the function returns false. \param hkl The reflection HKL. \param data Returned with the value of the data. \return true if the data was returned. */ template bool HKL_data::get_data(const HKL& hkl, T& data) const { int index, sym; bool friedel; index = parent_hkl_info->index_of( parent_hkl_info-> find_sym(hkl, sym, friedel) ); if ( index < 0 ) { data.set_null(); return false; } data = list[index]; if (friedel) data.friedel(); data.shift_phase( -hkl.sym_phase_shift(parent_hkl_info->spacegroup().symop(sym)) ); return true; } /*! If a symmetry mate of the requested HKL exists in the list, then the correct symmetry transformations are applied and data is set to the supplied values, otherwise the function returns false. \param hkl The reflection HKL. \param data Value of the data to set. \return true if the data was set. */ template bool HKL_data::set_data(const HKL& hkl, const T& data_) { int index, sym; bool friedel; index = parent_hkl_info->index_of( parent_hkl_info-> find_sym(hkl, sym, friedel) ); if ( index < 0 ) { return false; } T& ldata = list[index]; ldata = data_; ldata.shift_phase( hkl.sym_phase_shift(parent_hkl_info->spacegroup().symop(sym)) ); if (friedel) ldata.friedel(); return true; } /*! The data list is copied from the assignment source to the target. If the target does not have a defined HKL_info, then that and the Cell are copied as well. If however the target does have a defined HKL_info the HKL_info objects are compared, and if they do not match an exception is thrown. \param other The datalist to copy. \return This list. */ template HKL_data& HKL_data::operator =( const HKL_data& other ) { if ( parent_hkl_info == NULL ) { init( other ); } else { if ( parent_hkl_info != other.parent_hkl_info ) Message::message( Message_fatal( "HKL_data: mismatched parent HKL_info is assignment" ) ); } list = other.list; return *this; } /*! All values, including missing values, are overwritten by the value. \param value The value to which the list is to be set. */ template HKL_data& HKL_data::operator =( const T& value ) { for ( int i = 0; i < list.size(); i++ ) list[i] = value; return *this; } template void HKL_data::debug() const { HKL_data_base::debug(); std::cout << "Size " << list.size() << "\n"; } } // namespace clipper #endif clipper-2.1/clipper/core/test_data.cpp0000644000374100011300000026415110363703537015007 00000000000000/* test_data.cpp: implementation file for clipper test data */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "test_data.h" namespace clipper { namespace data { double rnasecell[] = {64.8970,78.3230,38.7920,90.0000,90.0000,90.0000}; char rnasespgr[] = "P 2ac 2ab"; double rnasereso = 5.0; struct TESThkldata { int h,k,l; float f,s,a,b,c,d; }; TESThkldata rnasehkldata[] = { {0,0,2,29.2,87.7,0.01,-0,0,0}, {0,0,4,455.7,12.2,-65.09,-0,0,0}, {0,0,6,714.2,8.5,5.31,-0,0,0}, {0,1,1,1368.6,12.2,0,5.56,0,0}, {0,1,2,523.7,8.5,-0,-0.13,0,0}, {0,1,3,191,2.4,-0,-11.65,0,0}, {0,1,4,292.9,6.1,0,11.53,0,0}, {0,1,5,374.8,10.9,-0,-8.1,0,0}, {0,1,6,323.2,8.5,0,0.21,0,0}, {0,1,7,336.9,7.2,-0,-5.57,0,0}, {0,2,0,1485.6,17.1,-12.38,-0,0,0}, {0,2,1,1139.3,8.5,-9.22,-0,0,0}, {0,2,2,146.1,20.7,-0.77,-0,0,0}, {0,2,3,350.4,7.3,-0.09,-0,0,0}, {0,2,4,476.3,12.1,1.74,-0,0,0}, {0,2,5,103.1,2.4,-1.69,-0,0,0}, {0,2,6,243.3,4.8,6.89,-0,0,0}, {0,2,7,417.7,13.3,-16.66,-0,0,0}, {0,3,1,227.8,12.2,-0,-1.6,0,0}, {0,3,2,747.5,8.5,0,0.07,0,0}, {0,3,3,20.7,1.2,-0,-0.08,0,0}, {0,3,4,10.9,1.2,0,-0.32,0,0}, {0,3,5,397.7,8.5,-0,-1.59,0,0}, {0,3,6,670.4,10.9,-0,-0.26,0,0}, {0,3,7,534.7,10.9,0,2.3,0,0}, {0,4,0,471.4,6.1,-0.84,-0,0,0}, {0,4,1,248.4,12.2,0.38,-0,0,0}, {0,4,2,210.6,3.7,-8.84,-0,0,0}, {0,4,3,110.7,1.2,0.26,-0,0,0}, {0,4,4,216.1,3.6,0.72,-0,0,0}, {0,4,5,369.7,8.5,0.52,-0,0,0}, {0,4,6,241.9,3.6,-1.06,-0,0,0}, {0,4,7,182.2,2.4,-3.62,-0,0,0}, {0,5,1,415.1,8.5,-0,-29.92,0,0}, {0,5,2,197.1,2.4,-0,-0.55,0,0}, {0,5,3,111.8,2.4,0,5.59,0,0}, {0,5,4,140.8,2.4,0,-0.29,0,0}, {0,5,5,471.4,9.7,-0,-3.02,0,0}, {0,5,6,603.4,16.9,0,0.87,0,0}, {0,5,7,158,2.4,0,8.01,0,0}, {0,6,0,1390.9,12.2,-22.22,-0,0,0}, {0,6,1,132.6,2.4,-1.62,-0,0,0}, {0,6,2,193.3,2.4,-2.16,-0,0,0}, {0,6,3,223.5,4.9,1.36,-0,0,0}, {0,6,4,135.9,2.4,-7.14,-0,0,0}, {0,6,5,142.9,2.4,0.28,-0,0,0}, {0,6,6,15.7,2.4,0.31,-0,0,0}, {0,6,7,171.2,2.4,-5.76,-0,0,0}, {0,7,1,625,12.2,0,0.08,0,0}, {0,7,2,207.8,2.4,-0,-0.02,0,0}, {0,7,3,325.4,6.1,-0,-3.12,0,0}, {0,7,4,628,8.5,-0,-16.81,0,0}, {0,7,5,472,13.3,-0,-9.2,0,0}, {0,7,6,88.2,1.2,0,0.05,0,0}, {0,8,0,385.2,7.3,-18.35,-0,0,0}, {0,8,1,377.9,4.9,-2.97,-0,0,0}, {0,8,2,886.5,12.1,62.91,-0,0,0}, {0,8,3,287.5,6.1,0.19,-0,0,0}, {0,8,4,395,8.5,-5.48,-0,0,0}, {0,8,5,433,7.3,9.3,-0,0,0}, {0,8,6,292.1,4.8,-37.35,-0,0,0}, {0,9,1,108.1,1.2,0,2.84,0,0}, {0,9,2,525.4,12.1,0,0.23,0,0}, {0,9,3,293.4,6.1,0,0.19,0,0}, {0,9,4,173.1,3.6,0,0.57,0,0}, {0,9,5,436.3,7.3,-0,-2.15,0,0}, {0,9,6,410,7.2,-0,-0.54,0,0}, {0,10,0,10.9,6.1,0.15,-0,0,0}, {0,10,1,14.6,3.6,-0.22,-0,0,0}, {0,10,2,452.2,8.5,-11.34,-0,0,0}, {0,10,3,142.9,2.4,-6.06,-0,0,0}, {0,10,4,381,7.3,-0.81,-0,0,0}, {0,10,5,642.4,10.9,4.87,-0,0,0}, {0,11,1,77.6,2.4,0,0.21,0,0}, {0,11,2,93.3,2.4,0,-0.14,0,0}, {0,11,3,542.1,10.9,-0,-0.26,0,0}, {0,11,4,445.9,9.7,0,10.42,0,0}, {0,11,5,223.2,4.8,0,0.17,0,0}, {0,12,0,238.5,7.3,24.05,-0,0,0}, {0,12,1,130.7,2.4,2.01,-0,0,0}, {0,12,2,65.3,2.4,-0.08,-0,0,0}, {0,12,4,348.8,7.2,26.57,-0,0,0}, {0,13,1,72.5,2.4,0,2.07,0,0}, {0,13,2,235.6,4.8,0,0.08,0,0}, {0,13,3,414.1,8.5,-0,-49.34,0,0}, {0,13,4,517.2,10.9,0,0.73,0,0}, {0,14,0,588.2,16.9,2.04,-0,0,0}, {0,14,1,429.9,9.7,0.24,-0,0,0}, {0,14,2,26.6,3.6,0.78,-0,0,0}, {0,14,3,125.4,2.4,-6.07,-0,0,0}, {0,15,1,161.6,3.6,0,0.05,0,0}, {0,15,2,97.6,2.4,0,-0.06,0,0}, {1,0,1,129.2,6.1,0,1.42,0,0}, {1,0,2,406.8,6.1,-1.33,-0,0,0}, {1,0,3,9.7,2.4,-0,-0.06,0,0}, {1,0,4,295.3,6.1,-0.28,-0,0,0}, {1,0,5,346.9,7.3,0,1.6,0,0}, {1,0,6,283.3,6.1,-11.31,-0,0,0}, {1,0,7,170.3,3.6,0,0.79,0,0}, {1,1,1,386.3,6.1,2.57,-0.11,-0.45,0.23}, {1,1,2,339.8,6.1,-1.33,-3.81,3.49,-1.3}, {1,1,3,582.8,6.1,-10.31,-4.05,-3.72,-3.74}, {1,1,4,467.8,9.7,1.29,-0.24,-0.55,0.38}, {1,1,5,139.5,2.4,-2.02,-2.01,-0.46,-1.74}, {1,1,6,541.1,10.9,8.64,11.11,0.53,-3.76}, {1,1,7,422.6,6,1.41,3.07,0.15,-0.32}, {1,2,0,214.5,6.1,0,0.11,0,0}, {1,2,1,433.8,6.1,0.07,-0.11,-0.03,0.02}, {1,2,2,93.8,17,-0.27,-0.04,0.12,0.22}, {1,2,3,222.6,2.4,0.4,-1.61,1.38,0.36}, {1,2,4,432.5,6.1,-0.32,0.8,0.12,0.12}, {1,2,5,213.5,2.4,-0.08,-0.1,-0.01,-0.06}, {1,2,6,290.5,3.6,-21.13,10.63,-5.07,6.49}, {1,2,7,525.2,8.5,0.06,-8.51,2.34,0.66}, {1,3,0,342.4,6.1,-0,-5.24,0,0}, {1,3,1,430,6.1,-2.11,0.27,-0.53,-0.51}, {1,3,2,361.6,4.9,0.1,-1.42,0.55,0.15}, {1,3,3,841.7,8.5,-4.25,5.17,0.29,1.37}, {1,3,4,471.3,6.1,0.23,-1.35,0.77,2.63}, {1,3,5,605.1,8.5,16.61,-8.61,-3.84,4.99}, {1,3,6,280.7,2.4,-0.32,-0.92,0.38,-0.31}, {1,4,0,321.5,8.5,-0,-10.67,0,0}, {1,4,1,116.9,17,1.34,-0.3,-0.4,0.34}, {1,4,2,647.5,6.1,5.42,35.2,2.95,-0.92}, {1,4,3,235.9,2.4,7.29,7.79,0.47,-4.84}, {1,4,4,262.3,2.4,1.72,-17.01,5.54,1.13}, {1,4,5,50.9,1.2,-0.96,0.43,-0.23,0.1}, {1,4,6,205.6,2.4,1.69,1.42,2.13,-1.33}, {1,5,0,674.5,6.1,-0,-2.15,0,0}, {1,5,1,472.3,6.1,-3.35,1.06,-1.49,0.89}, {1,5,2,643.5,8.5,-6.1,13.27,1.33,1.54}, {1,5,3,223.6,2.4,-2.6,-2.64,0.08,-1.37}, {1,5,4,400.5,4.9,1.2,-1.52,-0.25,2.67}, {1,5,5,401,4.8,10.95,7.49,-0.28,-1.33}, {1,5,6,116.1,1.2,3.03,-4.71,0.73,1.69}, {1,5,7,190.6,2.4,0.91,0.96,-0.01,-0.09}, {1,6,0,53.5,1.2,-0,-0.42,0,0}, {1,6,1,166.7,2.4,5.09,-2.35,-1.56,2.06}, {1,6,2,155.6,2.4,-0.73,0.23,-0.19,0.33}, {1,6,3,402.1,10.9,0.02,-0.05,0.42,0.35}, {1,6,4,562.9,8.5,-1.87,-0.65,-0.33,-0.29}, {1,6,5,122.3,1.2,3.09,-3.26,0.12,2.49}, {1,6,6,161.9,1.2,-1.23,0.27,-0.12,0.77}, {1,6,7,136.2,1.2,-0.58,-3.86,1.91,-0.55}, {1,7,0,402.5,10.9,-0,-10.69,0,0}, {1,7,1,396.4,4.9,0.07,-0.46,0.16,0.14}, {1,7,2,534.7,12.2,0.64,0.67,0.02,-0.31}, {1,7,3,188.2,2.4,-4.2,4.86,0.04,1.55}, {1,7,4,173.4,1.2,-0.85,1.92,1.66,3.43}, {1,7,5,325.6,3.6,-2.92,-2.44,-0.79,-2.31}, {1,7,6,324.9,2.4,-8.48,-8.39,-0.01,-3.9}, {1,8,0,238.2,3.6,-0,-0.13,0,0}, {1,8,1,132.4,1.2,-0.13,-1.96,1.44,-0.27}, {1,8,2,365.5,4.9,5.76,14.55,3.92,-3.57}, {1,8,3,293.6,3.6,0.4,-0.92,0.43,0.29}, {1,8,4,77.5,1.2,0.34,0.44,0.08,-0.3}, {1,8,5,250.3,2.4,-0.33,-0.28,-0.01,-0.03}, {1,8,6,179.8,2.4,-1.45,-1.34,0.16,-0.6}, {1,9,0,78.9,1.2,-0,-3.32,0,0}, {1,9,1,103.2,1.2,0.08,0.17,-1.18,-0.57}, {1,9,2,252.4,2.4,0.22,-1.06,1.49,0.27}, {1,9,3,217,2.4,-20.15,2.6,-0.93,0.24}, {1,9,4,204.6,2.4,-3.65,-13.99,1.69,-1.03}, {1,9,5,761.3,10.9,-5.49,-2.47,-0.56,-0.84}, {1,9,6,109.7,1.2,0.29,0.96,0.02,-0.02}, {1,10,0,230.5,3.6,0,3.19,0,0}, {1,10,1,361.5,4.9,-2.24,14.11,2.49,0.22}, {1,10,2,337,3.6,-4.77,15.35,1.86,1.17}, {1,10,3,254.3,2.4,2.32,4.47,1.25,-1.53}, {1,10,4,327.8,3.6,-0.28,0.15,0.35,0.78}, {1,10,5,431,4.8,0.66,-2.6,1.05,0.33}, {1,11,0,37.6,2.4,-0,-0.68,0,0}, {1,11,1,315.1,3.6,-4.61,0.39,-1.27,0.12}, {1,11,2,444.5,4.8,0.68,-2.26,0.45,0.3}, {1,11,3,113.7,1.2,0.85,-1.34,0.02,0.09}, {1,11,4,211.4,2.4,4.86,6.04,0.49,-2.82}, {1,11,5,405.3,4.8,1.2,-0.64,0.41,1.54}, {1,12,0,323.2,4.8,0,42.78,0,0}, {1,12,1,256.6,2.4,6.63,1.87,-1.41,-1.3}, {1,12,2,414.9,4.8,1.6,0.38,-0.18,-0.1}, {1,12,3,461.7,4.8,-0.06,-0.31,-0.35,-0.52}, {1,12,4,143.6,1.2,-0.74,-3.67,0.42,-0.64}, {1,13,0,786,10.9,-0,-6.73,0,0}, {1,13,1,993.8,14.5,0.17,-0.33,0.01,0.01}, {1,13,4,442.4,4.8,-0.05,0.93,0.95,-1.03}, {1,14,0,22.9,3.6,0,0.38,0,0}, {1,14,1,601.3,7.2,-3.48,-0.29,-1.94,0.96}, {1,14,3,490.7,6,-1.95,1.03,-0.35,0.54}, {1,15,0,341.3,6,-0,-1.93,0,0}, {1,15,1,869.4,14.5,0.44,0.23,-0.42,-0.76}, {1,15,2,284.4,3.6,-0.46,-6.92,1.85,-0.32}, {2,0,0,615.4,6.1,-0.26,-0,0,0}, {2,0,1,350.9,6.1,-0,-10.85,0,0}, {2,0,2,93.8,14.6,-0.2,-0,0,0}, {2,0,3,305.3,4.9,-0,-20.16,0,0}, {2,0,4,82.6,1.2,-0.32,-0,0,0}, {2,0,5,282.6,3.6,-0,-24.07,0,0}, {2,0,6,107.7,1.2,12.98,-0,0,0}, {2,0,7,453.9,9.7,0,4.35,0,0}, {2,1,0,782.3,6.1,0.16,-0,0,0}, {2,1,1,166.9,8.5,-0.35,0.35,0.49,0}, {2,1,2,485.8,9.7,-0.14,-0.18,0.01,-0.05}, {2,1,3,172.7,1.2,-0.71,1.98,1.65,-0.03}, {2,1,4,302.5,3.6,-5.88,-5.46,-0.34,-0.9}, {2,1,5,160.1,2.4,11.63,-4.93,-3.56,3.8}, {2,1,6,367.9,4.8,3.85,2.07,-0.53,-0.98}, {2,2,0,64.6,20.7,-0.39,-0,0,0}, {2,2,1,269.2,6.1,0.09,0.38,-0.08,-0.27}, {2,2,2,411.5,6.1,-0.11,-0.18,0.27,0.02}, {2,2,3,467.1,9.7,-0.99,-0.91,-0.02,-0.38}, {2,2,4,253.9,2.4,-18.53,7.1,-6.63,5.64}, {2,2,5,403.8,4.9,0.57,0.03,-0.16,-0.56}, {2,2,6,210.5,2.4,4.5,14.42,4.52,-3.19}, {2,2,7,111,1.2,-0.35,0.48,0.03,0.05}, {2,3,0,248.5,6.1,0.59,-0,0,0}, {2,3,1,649.1,6.1,0.15,-0.06,-0.57,0.42}, {2,3,2,438.2,6.1,6.73,-1.03,-3.25,-0.35}, {2,3,3,520.5,6.1,-0.54,-0.17,-0.11,-0.15}, {2,3,4,188.2,2.4,4.63,2.45,-0.21,-0.48}, {2,3,5,66.7,1.2,3.55,-0.14,-0.77,0.13}, {2,3,6,398,4.8,0.06,0.59,0.05,-0.01}, {2,4,0,256.9,8.5,-6.68,-0,0,0}, {2,4,1,375,6.1,0.12,-0.02,-0.07,-0.11}, {2,4,2,856.6,8.5,-9.29,-9.01,-0.04,-1.4}, {2,4,3,367.1,3.6,-0.24,-0.33,0.04,-0.29}, {2,4,4,161.5,1.2,0.48,-0.06,-2.28,-1.77}, {2,4,5,391.4,3.6,7.89,0.56,-2.19,-0.77}, {2,4,6,240.7,2.4,3.24,4.64,0.84,-2.23}, 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{9,7,2,168,2.4,-1.71,-3.44,0.24,-0.98}, {9,7,3,282.5,3.6,0.09,-0.19,0.05,0.06}, {9,7,4,303.8,3.6,-0.1,0.08,-0.06,0.24}, {9,8,0,49.6,4.8,-0,-0.07,0,0}, {9,8,1,180,2.4,1.39,-0.6,-0.4,0.58}, {9,8,2,301.9,4.8,0.15,-1.13,0.67,0.37}, {9,8,3,518.8,8.4,3,1.15,-0.64,-0.67}, {9,9,0,213.7,4.8,0,4.26,0,0}, {9,9,1,575.9,8.5,-14.09,-1.71,-6.77,-0.83}, {9,9,2,623.9,8.4,-0.15,0.04,0.5,0.1}, {9,9,3,699.2,9.6,-2.1,-0.04,-1.17,0.08}, {9,10,0,63.9,3.6,0,0.61,0,0}, {9,10,1,265.4,3.6,3.63,-1.92,-0.41,0.29}, {9,10,2,689.6,9.6,-0.01,-0.13,0.34,-0.06}, {9,11,0,49.4,3.6,0,0.19,0,0}, {9,11,1,174.7,2.4,-0.05,-0.22,0.08,-0.02}, {10,0,0,38.7,6.1,0.38,-0,0,0}, {10,0,1,121,2.4,-0,-2.3,0,0}, {10,0,2,225,3.6,-15.35,-0,0,0}, {10,0,3,350.5,4.8,-0,-11.28,0,0}, {10,0,4,135.2,2.4,1.4,-0,0,0}, {10,1,0,393.4,7.3,-1.63,-0,0,0}, {10,1,1,142.8,1.2,-3.74,0.6,-1.67,0.52}, {10,1,2,323,3.6,7.9,-7.23,0.11,0.61}, {10,1,3,336,3.6,0.44,1.24,0.29,-0.98}, {10,1,4,630,8.4,-2.32,-1.62,-0.31,-0.81}, {10,2,0,447.9,8.5,-7.57,-0,0,0}, {10,2,1,544.6,8.5,-0.28,0.47,0.11,0.29}, {10,2,2,344.7,4.8,-4.45,-0.11,-3.85,-1.14}, {10,2,3,234.4,2.4,0.3,-0.07,-0.09,0.05}, {10,2,4,342.7,4.8,4.64,-3.87,-0.24,1.67}, {10,3,0,265,4.8,-2.94,-0,0,0}, {10,3,1,359.3,4.8,1.74,3.13,1.35,-3.08}, {10,3,2,443.8,6,0.95,1.11,0.1,-0.5}, {10,3,3,212.6,2.4,-0.08,0.28,0.02,0.01}, {10,3,4,242.5,2.4,1.03,0.78,-0.1,-0.55}, {10,4,0,428.2,8.5,-9.69,-0,0,0}, {10,4,1,506.8,7.3,3,1.22,-1.09,-0.99}, {10,4,3,253.6,2.4,-6.01,1.3,-1.72,0.73}, {10,4,4,422.1,4.8,-7.34,0.26,-0.99,0.15}, {10,5,0,91.9,3.6,0.84,-0,0,0}, {10,5,1,50.8,4.8,0.16,0.57,0.05,-0.03}, {10,5,2,238,2.4,3.84,-1.35,-1.93,0.89}, {10,5,3,503.4,7.2,3.2,-3.87,0.12,1.95}, {10,5,4,184.4,2.4,4.83,-1.26,-1.87,1.12}, {10,6,1,122,2.4,-1.68,1.59,0.11,0.53}, {10,6,2,26.6,6,-0.03,-0.05,-0.01,-0.04}, {10,6,3,346.3,3.6,-3.76,-2.93,-0.79,-2.33}, {10,7,0,273,6,-0.06,-0,0,0}, {10,7,1,233.1,3.6,-0.58,-0.12,-0.2,-0.13}, {10,7,2,211.2,3.6,1.86,1.39,-0.54,-0.67}, {10,7,3,406.3,4.8,-1.18,-0.82,-0.41,-0.91}, {10,8,0,251.1,4.8,-5.96,-0,0,0}, {10,8,1,644.4,9.7,-0.27,-1.71,1.44,0.82}, {10,8,2,221.9,3.6,-5.17,1.27,-0.48,0.1}, {10,9,0,37.4,4.8,-0.14,-0,0,0}, {10,9,1,393.1,6,-0.27,-0.13,-0.14,-0.18}, {10,9,2,139.8,2.4,0.28,0.13,0.45,0.3}, {11,0,1,375.9,7.3,-0,-3.57,0,0}, {11,0,2,152.2,2.4,-1.14,-0,0,0}, {11,0,4,662.9,13.3,-1.78,-0,0,0}, {11,1,0,265.9,4.8,-0,-13.97,0,0}, {11,1,1,72.5,2.4,0.05,0.01,-0.04,-0.22}, {11,1,2,163.1,2.4,0.12,0.28,0.46,-0.47}, {11,1,3,359.6,3.6,0.9,-1.28,0.25,0.23}, {11,1,4,184.4,2.4,0.69,-6.04,0.95,0.52}, {11,2,0,117.2,3.6,0,0.02,0,0}, {11,2,1,357.7,4.8,0.31,-0.35,-0.14,0.47}, {11,2,2,159.4,2.4,-0.11,0.22,0.12,0.12}, {11,2,3,503.2,9.7,-0.02,0.1,0.22,-0.02}, {11,3,0,870,25.4,0,0.27,0,0}, {11,3,1,196.9,2.4,-0.24,1.42,0.54,0.26}, {11,3,2,285,3.6,2.54,-11.95,4.22,1.97}, {11,3,3,19.3,3.6,0.1,0.42,0.08,-0.03}, {11,4,0,126.8,4.8,0,0.64,0,0}, {11,4,1,144.9,2.4,-0.36,0.54,-1.55,-0.45}, {11,4,2,317.5,3.6,0.18,1.05,0.77,-0.2}, {11,4,3,125.4,1.2,0.33,0.23,-1.07,0.42}, {11,5,0,206.5,4.8,0,5.32,0,0}, {11,5,1,280.1,3.6,0.09,-2.61,0.41,-0.02}, {11,5,2,290.8,4.8,0.18,0.18,-0,-0.07}, {11,5,3,512.3,7.2,-0.3,0.1,-0.08,0.06}, {11,6,0,414,8.4,-0,-0.32,0,0}, {11,6,1,433.2,6,-2.74,-9.78,3.07,-2.06}, {11,6,2,305.1,3.6,0.06,0.04,0.05,0.3}, {11,7,0,208.7,4.8,0,1.77,0,0}, {11,7,1,432.9,6,0.83,-2.2,0.27,0.14}, {11,7,2,499,7.2,-1.09,1.91,0.26,0.28}, {11,8,0,165.1,3.6,0,4.09,0,0}, {11,8,1,343.4,4.8,1.93,-4.61,1.8,1.9}, {12,0,0,457.5,12.1,-1.25,-0,0,0}, {12,0,1,505.6,9.7,0,3.34,0,0}, {12,0,2,253.3,3.6,-8.27,-0,0,0}, {12,1,0,755.6,14.5,0.33,-0,0,0}, {12,1,1,260.7,3.6,-0.74,0.15,-0.19,0.08}, {12,1,2,513.8,7.2,-1.17,-0.08,-0.65,-0.28}, {12,2,0,47.1,12.1,1.32,-0,0,0}, {12,2,1,451.3,6,-0.46,0.51,0.03,0.19}, {12,2,2,162.8,2.4,-0.11,0.18,-0.18,-0.03}, {12,3,0,774.6,15.7,7.24,-0,0,0}, {12,3,1,308.8,3.6,-1.33,-3.83,0.28,-0.19}, {12,3,2,531.7,8.4,0.21,-0.31,-0.02,0.31}, {12,4,0,518.6,10.9,-0.12,-0,0,0}, {12,4,1,259.3,3.6,-0.64,-0.22,-0.1,-0.24}, {12,4,2,653.2,10.8,-0.37,1.13,0.18,0.13}, {12,5,0,350.8,7.2,-16.35,-0,0,0}, {12,5,1,242.3,3.6,-6.99,-5.89,-0.02,-0.96}}; int rnasehkldata_size = sizeof( rnasehkldata ) / sizeof( rnasehkldata[0] ); struct TESTxyzdata { const char* element; float x,y,z,u_iso,occ; }; TESTxyzdata rnasexyzdata[] = { {"N",45.187,12.906,9.095,0.381,1}, {"O",42.435,14.184,8.265,0.725,1}, {"O",41.943,12.878,6.527,0.751,1}, {"C",42.812,13.495,7.237,0.716,1}, {"C",44.299,13.384,6.812,0.628,1}, {"C",45.241,12.515,7.674,0.452,1}, {"C",46.685,12.547,7.1,0.394,1}, {"O",47.612,13.255,7.476,0.323,1}, {"N",46.794,11.672,6.084,0.444,1}, {"C",48.093,9.185,6.279,0.39,1}, {"C",49.528,9.785,4.235,0.345,1}, {"C",48.253,10.056,5.021,0.423,1}, {"C",48.103,11.539,5.403,0.324,1}, {"C",48.199,12.621,4.353,0.371,1}, {"O",47.298,12.969,3.578,0.295,1}, {"N",49.407,13.203,4.322,0.314,1}, {"O",50.307,15.798,5.009,0.443,1}, {"C",50.798,15.174,3.823,0.309,1}, {"C",49.686,14.243,3.321,0.376,1}, {"C",50.037,13.673,1.946,0.372,1}, {"O",50.494,14.518,1.133,0.501,1}, {"N",49.876,12.516,1.386,0.289,1}, {"C",50.385,12.329,0.007,0.272,1}, {"C",51.491,11.238,0.211,0.245,1}, {"O",51.73,10.839,1.388,0.254,1}, {"N",51.932,10.774,-0.938,0.238,1}, {"C",53.4,7.466,-2.602,0.287,1}, {"O",51.293,8.136,-1.674,0.358,1}, {"C",52.564,8.674,-2.263,0.272,1}, {"C",52.967,9.734,-1.184,0.234,1}, {"C",54.232,10.484,-1.596,0.252,1}, {"O",54.092,11.564,-2.247,0.28,1}, {"N",55.4,10.028,-1.188,0.181,1}, {"C",58.59,12.293,-1.009,0.178,1}, {"C",57.502,10.963,0.829,0.174,1}, {"C",57.258,11.659,-0.505,0.178,1}, {"C",56.661,10.729,-1.577,0.143,1}, {"C",57.59,9.542,-1.997,0.126,1}, {"O",57.577,8.495,-1.285,0.134,1}, {"N",58.281,9.749,-3.068,0.119,1}, {"S",58.644,8.782,-6.092,0.165,1}, {"C",59.837,9.043,-4.746,0.142,1}, {"C",59.21,8.649,-3.442,0.103,1}, {"C",60.312,8.596,-2.377,0.112,1}, {"O",60.651,9.647,-1.84,0.16,1}, {"N",60.815,7.431,-2.09,0.132,1}, {"C",63.607,3.83,-0.269,0.105,1}, {"C",63.176,5.877,1.191,0.169,1}, {"C",63.43,5.308,-0.221,0.135,1}, {"C",62.261,5.661,-1.211,0.08,1}, {"C",61.937,7.18,-1.195,0.111,1}, {"C",63.176,8.04,-1.631,0.155,1}, {"O",63.948,8.686,-0.861,0.154,1}, {"N",63.363,8.068,-2.943,0.13,1}, {"O",63.713,9.243,-5.759,0.259,1}, {"C",64.674,8.507,-4.981,0.169,1}, {"C",64.514,8.842,-3.5,0.19,1}, {"C",64.317,10.294,-3.22,0.228,1}, {"O",65.387,10.965,-3.269,0.218,1}, {"N",63.169,10.881,-2.921,0.193,1}, {"C",61.602,12.757,-3.133,0.14,1}, {"C",62.995,12.289,-2.639,0.167,1}, {"C",63.211,12.599,-1.169,0.174,1}, {"O",63.29,13.785,-0.811,0.211,1}, {"N",63.302,11.641,-0.262,0.184,1}, {"C",60.774,11.852,2.374,0.187,1}, {"C",60.818,9.342,2.603,0.211,1}, {"C",61.313,10.545,1.786,0.189,1}, {"C",62.84,10.645,1.861,0.171,1}, {"C",63.485,11.896,1.176,0.195,1}, {"C",64.985,11.912,1.559,0.255,1}, {"O",65.787,11.418,0.738,0.244,1}, {"N",65.377,12.383,2.734,0.253,1}, {"C",65.547,13.634,4.727,0.287,1}, {"C",64.532,12.983,3.787,0.28,1}, {"C",66.753,12.736,4.607,0.245,1}, {"C",66.795,12.343,3.105,0.222,1}, {"C",67.258,10.934,2.971,0.167,1}, {"O",66.54,9.911,3.213,0.179,1}, {"N",68.557,10.718,2.673,0.205,1}, {"C",70.894,11.037,2.558,0.226,1}, {"C",69.548,11.794,2.401,0.245,1}, {"C",70.647,9.595,2.216,0.213,1}, {"C",69.137,9.388,2.567,0.172,1}, {"C",69.04,8.569,3.87,0.101,1}, {"O",69.036,7.364,3.707,0.129,1}, {"N",68.997,9.29,5.003,0.116,1}, {"O",71.736,11.345,6.212,0.266,1}, {"O",69.702,11.868,5.944,0.205,1}, {"C",70.522,11.17,6.519,0.263,1}, {"C",70.384,10.104,7.552,0.193,1}, {"C",69.09,9.366,7.421,0.169,1}, {"C",68.941,8.492,6.225,0.116,1}, {"C",67.573,7.764,6.267,0.132,1}, {"O",67.484,6.777,6.963,0.122,1}, {"N",66.525,8.231,5.537,0.14,1}, {"C",64.198,8.213,4.637,0.173,1}, {"C",65.261,7.483,5.499,0.138,1}, {"C",65.517,6.142,4.891,0.115,1}, {"O",64.95,5.016,5.254,0.131,1}, {"N",66.337,6.042,3.828,0.112,1}, {"C",68.026,3.62,1.336,0.151,1}, {"O",66.803,5.646,1.081,0.2,1}, {"C",67.634,4.924,1.96,0.117,1}, {"C",66.683,4.779,3.206,0.105,1}, 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{"C",24.804,17.954,12.548,0.125,1}, {"C",24.332,18.645,11.234,0.134,1}, {"C",25.413,19.476,10.479,0.189,1}, {"C",23.221,19.712,11.651,0.202,1}, {"C",22.702,20.412,10.39,0.208,1}, {"O",21.991,19.879,9.561,0.198,1}, {"N",23.142,21.664,10.295,0.2,1}, {"O",22.559,24.494,7.235,0.232,1}, {"O",21.711,25.889,8.598,0.295,1}, {"C",22.301,24.792,8.392,0.239,1}, {"C",22.564,23.886,9.594,0.155,1}, {"C",22.932,22.517,9.148,0.16,1}, {"C",24.27,22.598,8.362,0.146,1}, {"O",25.219,23.303,8.742,0.178,1}, {"N",24.237,21.884,7.297,0.159,1}, {"N",25.99,17.688,4.954,0.481,1}, {"O",24.286,17.229,6.406,0.378,1}, {"C",25.241,18.008,5.895,0.424,1}, {"C",25.365,19.351,6.575,0.306,1}, {"C",25.294,20.537,5.598,0.198,1}, {"C",25.445,21.8,6.41,0.179,1}, {"C",25.686,22.999,5.529,0.205,1}, {"O",26.633,22.939,4.741,0.248,1}, {"N",24.865,24.035,5.624,0.213,1}, {"C",22.994,24.497,3.511,0.26,1}, {"O",22.801,26.346,5.25,0.246,1}, {"C",23.61,25.693,4.237,0.197,1}, {"C",25.013,25.2,4.796,0.194,1}, {"C",25.702,26.348,5.483,0.175,1}, {"O",25.844,27.382,4.856,0.181,1}, {"N",26.087,26.129,6.699,0.177,1}, {"S",24.83,27.111,9.609,0.216,1}, {"C",25.787,28.063,8.333,0.181,1}, {"C",26.73,27.242,7.436,0.154,1}, {"C",27.914,26.73,8.276,0.182,1}, {"O",28.065,25.496,8.349,0.197,1}, {"O",28.487,27.688,8.839,0.213,1}, {"O",38.115,8.296,25.493,0.545,1}, {"O",40.251,8.969,26.756,0.589,1}, {"O",38.054,8.459,27.913,0.634,1}, {"O",38.578,10.575,26.544,0.637,1}, {"S",38.722,9.032,26.659,0.619,1}}; int rnasexyzdata_size = sizeof( rnasexyzdata ) / sizeof( rnasexyzdata[0] ); Test_data::Test_data() { Spacegroup spgr = Spacegroup( Spgr_descr( rnasespgr ) ); Cell cell = Cell( Cell_descr( rnasecell[0], rnasecell[1], rnasecell[2], rnasecell[3], rnasecell[4], rnasecell[5] ) ); Resolution reso( rnasereso - 1.0e-3 ); std::vector hkl; hklinfo.init( spgr, cell, reso, true ); fsig.init( hklinfo, hklinfo.cell() ); abcd.init( hklinfo, hklinfo.cell() ); datatypes::F_sigF fs; datatypes::ABCD hl; bool flag = true; for ( int i = 0; i < rnasehkldata_size; i++ ) { HKL hkl( rnasehkldata[i].h, rnasehkldata[i].k, rnasehkldata[i].l ); fs.f() = rnasehkldata[i].f; fs.sigf() = rnasehkldata[i].s; hl.a() = rnasehkldata[i].a; hl.b() = rnasehkldata[i].b; hl.c() = rnasehkldata[i].c; hl.d() = rnasehkldata[i].d; flag = flag && fsig.set_data( hkl, fs ); flag = flag && abcd.set_data( hkl, hl ); } std::vector v; for ( int i = 0; i < rnasexyzdata_size; i++ ) { Atom a = Atom::null(); a.set_element( rnasexyzdata[i].element ); a.set_coord_orth( Coord_orth( rnasexyzdata[i].x, rnasexyzdata[i].y, rnasexyzdata[i].z ) ); a.set_u_iso( rnasexyzdata[i].u_iso ); a.set_occupancy( rnasexyzdata[i].occ ); v.push_back(a); } atoms = Atom_list( v ); if ( flag == false ) Message::message( Message_warn( "Self test: error filling data." ) ); } } // namespace data } // namespace clipper clipper-2.1/clipper/core/clipper_message.cpp0000644000374100011300000000604110363703537016171 00000000000000/* clipper_message.cpp: implementation file for clipper helper functions */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "clipper_message.h" namespace clipper { int Message::message_level_ = 5; int Message::fatal_level_ = 9; std::ostream* Message::stream_ = &std::cerr; Message message; Message::Message() { message_level_ = 5; fatal_level_ = 9; set_stream( std::cerr ); } void Message::set_stream( std::ostream& stream ) { stream_ = &stream; } void Message::set_message_level( const int& level ) { if ( level < 1 ) message_level_ = 1; else if ( level > fatal_level_ ) message_level_ = fatal_level_; else message_level_ = level; } void Message::set_fatal_level( const int& level ) { if ( level < message_level_ ) fatal_level_ = message_level_; else if ( level > 9 ) fatal_level_ = 9; else fatal_level_ = level; } } // namespace clipper clipper-2.1/clipper/core/clipper_util.h0000644000374100011300000002171310363703537015172 00000000000000/*! \file lib/clipper_util.h Header file for clipper helper functions */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_UTIL #define CLIPPER_UTIL #include "clipper_precision.h" #include "clipper_sysdep.h" namespace clipper { //! Utility class /*! This class holds a set of useful static functions and values. You should never need to instantiate this class: Refer to members using Util:: */ class Util { public: Util(); //!< null constructor //! fast Util::nan() value static const ftype& nan() { return nan_; } //! fast Util::nan() value static const float& nanf() { return nanf_; } //! fast Util::nan() value static const double& nand() { return nand_; } //! set null floating value - a specific value of NaN used for missings inline static void set_null( ftype32& f ) { *((uitype32*)&f) = *((const uitype32*)&nanf_); } //! set null floating value - a specific value of NaN used for missings inline static void set_null( ftype64& f ) { *((uitype64*)&f) = *((const uitype64*)&nand_); } //! fast test for null floating value - only works if set from Util::null() inline static bool is_null( const ftype32& f ) { return ( *((const uitype32*)&f) == *((const uitype32*)&nanf_) ); } //! fast test for null floating value - only works if set from Util::null() inline static bool is_null( const ftype64& f ) { return ( *((const uitype64*)&f) == *((const uitype64*)&nand_) ); } //! fast Util::nan() test /*! Used for missing entries: THIS DOES NOT DISTINGUISH BETWEEN NAN & INF */ inline static bool is_nan( const ftype32 f ) { return ((*((const uitype32*)&f)&CLIPPER_NAN_MASK_A_32)==CLIPPER_NAN_MASK_A_32); } //! fast Util::nan() test /*! Used for missing entries: THIS DOES NOT DISTINGUISH BETWEEN NAN & INF */ inline static bool is_nan( const ftype64 f ) { return ((*((const uitype64*)&f)&CLIPPER_NAN_MASK_A_64)==CLIPPER_NAN_MASK_A_64); } //! slow general NaN test for compatibility /*! Works for all architectures with IEEE arithmetic only */ inline static bool isnan(const ftype32 f) { return ((*((const uitype32*)&f)&CLIPPER_NAN_MASK_A_32)==CLIPPER_NAN_MASK_A_32)&&((*((const uitype32*)&f)&CLIPPER_NAN_MASK_B_32)!=0U); } //! slow general NaN test for compatibility /*! Works for all architectures with IEEE arithmetic only */ inline static bool isnan(const ftype64 f) { return ((*((const uitype64*)&f)&CLIPPER_NAN_MASK_A_64)==CLIPPER_NAN_MASK_A_64)&&((*((const uitype64*)&f)&CLIPPER_NAN_MASK_B_64)!=0U); } //! Sim function: I1(X)/I0(X) static ftype sim( const ftype& x ); //! Inverse Sim function: I1(X)/I0(X) static ftype invsim( const ftype& x ); //! Integral of Sim function: log(I0(X)) static ftype sim_integ( const ftype& x ); //! Derivative of Sim function: d/dx( I1(X)/I0(x) ) static ftype sim_deriv( const ftype& x ); //! Derivative of Sim function using recurrance: -sim(x)/x + (1 - sim(x)^2) static ftype sim_deriv_recur( const ftype& x ); //! Arc hyperbolic tangent static ftype atanh( const ftype& x ) { return log((1.0+x)/(1.0-x))/2.0; } //! Modified Bessel function of the first kind static ftype bessel_i0( const ftype& x ); //! Convert isotropic U-value to B-factor static ftype u2b( const ftype& x ) { return x * eightpi2_; } //! Convert isotropic B-factor to U-value static ftype b2u( const ftype& x ) { return x / eightpi2_; } //! Convert F+/F- to mean F, with NaN checks template inline static T mean( const T& pl, const T& mi ) { if ( Util::is_nan(pl) ) return mi; else if (Util::is_nan(mi) ) return pl; else return 0.5*(pl+mi); } //! Convert sigF+/sigF-/cov to sig F, with NaN checks template inline static T sig_mean( const T& pl, const T& mi, const T& cov ) { if ( Util::is_nan(pl) ) return mi; else if (Util::is_nan(mi) ) return pl; else if (Util::is_nan(cov) ) return 0.5*sqrt(pl*pl+mi*mi); else return 0.5*sqrt(pl*pl+mi*mi+2*cov); } //! Truncate-to-integer: int(floor(a)) inline static int intf( const ftype& a ) { return int( floor( a ) ); } //! Truncate-to-integer above: int(ceil(a)) inline static int intc( const ftype& a ) { return int( ceil( a ) ); } //! Round-to-integer: int(round(a)) inline static int intr( const ftype& a ) { return int( rint( a ) ); } //! Corrected mod inline static ftype mod( const ftype& a, const ftype& b ) { ftype c = fmod(a, b); if (c < 0) c+=b; return c;} //! Corrected mod inline static int mod( const int& a, const int& b ) { int c = a%b; if (c < 0) c+=b; return c; } //! max template inline static T max(const T& a, const T& b) { return (a > b) ? a : b; } //! min template inline static T min(const T& a, const T& b) { return (a < b) ? a : b; } //! bound a value by limits template inline static T bound( const T& min, const T& val, const T& max ) { return ( (val < max) ? ( (val > min ) ? val : min ) : max ); } //! swap the contents of two objects template inline static void swap( T& a, T& b ) { T c = a; a = b; b = c; } //! swap the contents of two objects, using third as store (for speed) template inline static void swap( T& a, T& b, T& c ) { c = a; a = b; b = c; } //! square template inline static T sqr( const T& a ) { return a*a; } //! Integer square root (returns floor of sqrt) template inline static T isqrt( const T& n ) { return T(floor(sqrt(ftype(n)))); } //! pi inline static const ftype& pi() { return onepi_; } //! 2 pi inline static const ftype& twopi() { return twopi_; } //! 2 pi squared inline static const ftype& twopi2() { return twopi2_; } //! 8 pi squared inline static const ftype& eightpi2() { return eightpi2_; } //! degree-to-radian conversion static ftype d2rad( const ftype& x ); //! degree-to-radian conversion static ftype rad2d( const ftype& x ); private: static float nanf_; //!< float NaN static double nand_; //!< double NaN static ftype nan_; //!< ftype nan static ftype onepi_; //!< one*pi static ftype twopi_; //!< two*pi static ftype twopi2_; //!< two*pi*pi static ftype eightpi2_; //!< eight*pi*pi static ftype d2rad_; //!< degree-radian conversion static ftype sim_a; //!< sim fn param static ftype sim_b; //!< sim fn param static ftype sim_c; //!< sim fn param static ftype sim_d; //!< sim fn param static ftype sim_e; //!< sim fn param static ftype sim_A; //!< invsim fn param static ftype sim_B; //!< invsim fn param static ftype sim_C; //!< invsim fn param static ftype sim_g; //!< invsim fn param static ftype sim_p; //!< invsim fn param static ftype sim_q; //!< invsim fn param static ftype sim_r; //!< invsim fn param }; } // namespace clipper #endif clipper-2.1/clipper/core/test_core.h0000644000374100011300000000470710363703537014472 00000000000000/*! \file lib/test_core.h Header file for clipper core self-test functions */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_TEST_CORE #define CLIPPER_TEST_CORE #include "clipper_test.h" namespace clipper { class Test_core : public Test_base { public: //! do the self-tests bool operator() (); }; } // namespace clipper #endif clipper-2.1/clipper/core/hkl_lookup.h0000644000374100011300000000621610363703537014647 00000000000000/*! \file lib/hkl_lookup.h Header file for reflection lookup class */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_HKL_LOOKUP #define CLIPPER_HKL_LOOKUP #include "coords.h" namespace clipper { //! Fast reflection lookup object /*! This version uses a ragged array index to get reflection indices from Miller indices. */ class HKL_lookup { public: //! initialise: make a reflection index for a list of HKLs void init(const std::vector& hkl); //! lookup function int index_of(const HKL& rfl) const; void debug(); struct llookup { int min, max; std::vector p; llookup() {min=32000;max=-32000;} }; //!< lookup on l struct klookup { int min, max; std::vector p; klookup() {min=32000;max=-32000;} }; //!< lookup on k struct hlookup { int min, max; std::vector p; hlookup() {min=32000;max=-32000;} }; //!< lookup on h private: //! pointer to first list hlookup h_ptr; }; } // namespace clipper #endif clipper-2.1/clipper/core/nxmap_operator.cpp0000644000374100011300000001516510363703537016074 00000000000000/* nxmap_operator.cpp: implementation file for non-crystal map operator */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "nxmap_operator.h" namespace clipper { /*! The object is not initialised, and will return is_null(). */ NX_operator::NX_operator() { xfrac_nxgrid = RTop<>::null(); } /*! The operator and inverse operator, together with any possible optimisations, are constructed to relate the give crystallographic and non-crystallographic grid frames, using the supplied orthogonal operator. \param xmap An Xmap defining the crystal grid frame. \param nxmap An NXmap defining the non-crystal grid frame. \param rtop The operator relating the orthogonal frame of the NXmap onto the orthogonal frame of the Xmap. */ NX_operator::NX_operator( const Xmap_base& xmap, const NXmap_base& nxmap, const RTop_orth& rtop ) { init( xmap, nxmap, rtop ); } /*! The operator and inverse operator, together with any possible optimisations, are constructed to relate the give crystallographic and non-crystallographic grid frames, using the supplied orthogonal operator. \param cell The cell defining the crystal grid frame. \param grid The grid defining the crystal grid frame. \param nxmap An NXmap defining the non-crystal grid frame. \param rtop The operator relating the orthogonal frame of the NXmap onto the orthogonal frame of the Xmap. */ NX_operator::NX_operator( const Cell& cell, const Grid_sampling& grid, const NXmap_base& nxmap, const RTop_orth& rtop ) { init( cell, grid, nxmap, rtop ); } /*! The operator and inverse operator, together with any possible optimisations, are constructed to relate the give crystallographic and non-crystallographic grid frames, using the supplied orthogonal operator. \param xmap An Xmap defining the crystal grid frame. \param nxmap An NXmap defining the non-crystal grid frame. \param rtop The operator relating the orthogonal frame of the NXmap onto the orthogonal frame of the Xmap. */ void NX_operator::init( const Xmap_base& xmap, const NXmap_base& nxmap, const RTop_orth& rtop ) { init( xmap.cell(), xmap.grid_sampling(), nxmap, rtop ); } /*! The operator and inverse operator, together with any possible optimisations, are constructed to relate the give crystallographic and non-crystallographic grid frames, using the supplied orthogonal operator. \param cell The cell defining the crystal grid frame. \param grid The grid defining the crystal grid frame. \param nxmap An NXmap defining the non-crystal grid frame. \param rtop The operator relating the orthogonal frame of the NXmap onto the orthogonal frame of the Xmap. */ void NX_operator::init( const Cell& cell, const Grid_sampling& grid, const NXmap_base& nxmap, const RTop_orth& rtop ) { // make op to map nxmap grid -> cell frac coords nxgrid_xfrac = RTop_orth(cell.matrix_frac()) * rtop * nxmap.operator_grid_orth(); // make op for grid coords nxgrid_xgrid = RTop_orth(grid.matrix_frac_grid()) * nxgrid_xfrac; // make inverse op xfrac_nxgrid = nxgrid_xfrac.inverse(); xgrid_nxgrid = nxgrid_xgrid.inverse(); // now make nearest int op to cell -> nxmap op RTop_orth xgrid_nxgrid_rnd, nxgrid_xgrid_rnd; for ( int j = 0; j < 3; j++ ) { xgrid_nxgrid_rnd.trn()[j] = rint( xgrid_nxgrid.trn()[j] ); nxgrid_xgrid_rnd.trn()[j] = rint( nxgrid_xgrid.trn()[j] ); xgrid_nxgrid_int.trn()[j] = int( xgrid_nxgrid_rnd.trn()[j] ); nxgrid_xgrid_int.trn()[j] = int( nxgrid_xgrid_rnd.trn()[j] ); for ( int i = 0; i < 3; i++ ) { xgrid_nxgrid_rnd.rot()(i,j) = rint( xgrid_nxgrid.rot()(i,j) ); nxgrid_xgrid_rnd.rot()(i,j) = rint( nxgrid_xgrid.rot()(i,j) ); xgrid_nxgrid_int.rot()(i,j) = int( xgrid_nxgrid_rnd.rot()(i,j) ); nxgrid_xgrid_int.rot()(i,j) = int( nxgrid_xgrid_rnd.rot()(i,j) ); } } // check for integer mapping x_nx_is_int = xgrid_nxgrid_rnd.equals( xgrid_nxgrid, 0.01 ); x_nx_is_trn = x_nx_is_int && xgrid_nxgrid_rnd.rot().equals( Mat33<>::identity(), 0.01 ); nx_x_is_int = nxgrid_xgrid_rnd.equals( nxgrid_xgrid, 0.01 ); nx_x_is_trn = nx_x_is_int && nxgrid_xgrid_rnd.rot().equals( Mat33<>::identity(), 0.01 ); } bool NX_operator::is_null() const { return xfrac_nxgrid.is_null(); } void NX_operator::debug() const { std::cout << " X->NX is int? " << x_nx_is_int << "\n"; std::cout << " X->NX is trn? " << x_nx_is_trn << "\n"; std::cout << xgrid_nxgrid.format() << "\n"; std::cout << " NX->X is int? " << x_nx_is_int << "\n"; std::cout << " NX->X is trn? " << x_nx_is_trn << "\n"; std::cout << nxgrid_xgrid.format() << "\n"; } } // namespace clipper clipper-2.1/clipper/core/clipper_thread.cpp0000644000374100011300000000540210776417005016014 00000000000000/* clipper_thread.cpp: implementation file for threading handlers */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "clipper_thread.h" #ifndef CLIPPER_DISABLE_THREADS namespace clipper { Mutex Thread_base::mutex_global = Mutex(); int Thread_base::next_id = 0; Thread_base::Thread_base() { lock(); id_ = next_id++; unlock(); } bool Thread_base::run() { return CLIPPER_THREAD_EXEC( thread, Thread_base::Entry, this ); } bool Thread_base::join() { return CLIPPER_THREAD_JOIN( thread ); } CLIPPER_THREAD_RETTYPE Thread_base::Entry( CLIPPER_THREAD_ARGTYPE thisptr ) { ((Thread_base*)thisptr)->Run(); return NULL; } } // namespace clipper #endif clipper-2.1/clipper/core/Makefile.am0000644000374100011300000000445111372264321014354 00000000000000# Makefile.am, passed: clipper/core, extracted subdir: core # in dir /home/cowtan/clipper-autoconf/clipper-2.1/clipper/core ## -*- mode: Makefile; mode: font-lock -*- INCLUDES=${FFTW_CXXFLAGS} library_include_HEADERS = \ atomsf.h \ cell.h \ clipper_instance.h \ clipper_memory.h \ clipper_message.h \ clipper_precision.h \ clipper_stats.h \ clipper_sysdep.h \ clipper_test.h \ clipper_thread.h \ clipper_types.h \ clipper_util.h \ container.h \ container_hkl.h \ container_map.h \ container_types.h \ coords.h \ derivs.h \ fftmap.h \ fftmap_sparse.h \ hkl_compute.h \ hkl_data.h \ hkl_datatypes.h \ hkl_info.h \ hkl_lookup.h \ hkl_operators.h \ map_interp.h \ map_utils.h \ nxmap.h \ nxmap_operator.h \ ramachandran.h \ resol_basisfn.h \ resol_fn.h \ resol_targetfn.h \ rotation.h \ spacegroup_data.h \ spacegroup.h \ symop.h \ test_core.h \ test_data.h \ xmap.h lib_LTLIBRARIES = libclipper-core.la libclipper_core_la_SOURCES = \ atomsf.cpp \ cell.cpp \ clipper_instance.cpp \ clipper_memory.cpp \ clipper_message.cpp \ clipper_stats.cpp \ clipper_test.cpp \ clipper_thread.cpp \ clipper_types.cpp \ clipper_util.cpp \ container.cpp \ container_hkl.cpp \ container_map.cpp \ container_types.cpp \ coords.cpp \ derivs.cpp \ fftmap.cpp \ fftmap_sparse.cpp \ hkl_compute.cpp \ hkl_data.cpp \ hkl_datatypes.cpp \ hkl_info.cpp \ hkl_lookup.cpp \ hkl_operators.cpp \ map_interp.cpp \ map_utils.cpp \ nxmap.cpp \ nxmap_operator.cpp \ ramachandran.cpp \ resol_basisfn.cpp \ resol_fn.cpp \ resol_targetfn.cpp \ rotation.cpp \ spacegroup.cpp \ spacegroup_data.cpp \ symop.cpp \ test_core.cpp \ test_data.cpp \ xmap.cpp library_includedir = $(pkgincludedir)/core libclipper_core_la_LDFLAGS = -version-info @CLIPPER_LT_VERSION@ libclipper_core_la_LIBADD = \ $(FFTW_LIBS) \ -lpthread clipper-2.1/clipper/core/clipper_message.h0000644000374100011300000001415410363703537015642 00000000000000/*! \file lib/clipper_message.h Header file for clipper message handler */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_MESSAGE #define CLIPPER_MESSAGE #include #include namespace clipper { //! Message handler class /*! The message handler is a static class which handles messages and errors. It has 3 properties: - the output stream: to which messages will be directed (default stderr) - message level: messages with a level >= this will be output (default 5) - fatal level: messages with a level >= this will be fatal (default 9) Levels may be in the range 1-9. They are priorotised as follows: - 1-4 messages, never fatal - 5-8 warning, may be fatal - 9: always fatal. The fatal level must be greater than or equal to the message level, and greater than or equal to 5. A message is any object which implements the following methods: \code const std::string& text() const; int level() const; \endcode The level method may be static. Messages are usually derived from Message_base. */ class Message { public: Message(); //!< null constuctor //! return the current stream static std::ostream& stream() { return *stream_; } //! return the current message level static const int& message_level() { return message_level_; } //! return the current fatal error level static const int& fatal_level() { return fatal_level_; } //! set the output stream static void set_stream( std::ostream& stream ); //! set the current message level static void set_message_level( const int& level ); //! set the current fatal error level static void set_fatal_level( const int& level ); //! pass a message template inline static void message( const T& message ) { if ( message.level() >= Message::message_level() ) { Message::stream() << message.text() << "\n"; if ( message.level() >= Message::fatal_level() ) throw message; } } private: static int message_level_; static int fatal_level_; static std::ostream* stream_; }; //! Base type for messages class Message_base { public: const std::string& text() const; int level() const; protected: Message_base() {} }; //! Generic message class Message_generic : public Message_base { public: Message_generic( const int& level, const std::string& text ) : text_( text ), level_( level ) {} const std::string& text() const { return text_; } const int& level() const { return level_; } private: std::string text_; int level_; }; //! Fatal message (level = 9) class Message_fatal : public Message_base { public: Message_fatal( const std::string& text ) : text_( text ) {} const std::string& text() const { return text_; } static int level() { return 9; } private: std::string text_; }; //! Warning message (level = 5) class Message_warn : public Message_base { public: Message_warn( const std::string& text ) : text_( text ) {} const std::string& text() const { return text_; } static int level() { return 5; } private: std::string text_; }; //! Info message (level = 1) class Message_info : public Message_base { public: Message_info( const std::string& text ) : text_( text ) {} const std::string& text() const { return text_; } static int level() { return 1; } private: std::string text_; }; //! Constructor message (level = 2) class Message_ctor : public Message_base { public: Message_ctor( const std::string& text ) : text_( "+"+text ) {} const std::string& text() const { return text_; } static int level() { return 2; } private: std::string text_; }; //! Destructor message (level = 2) class Message_dtor : public Message_base { public: Message_dtor( const std::string& text ) : text_( "-"+text ) {} const std::string& text() const { return text_; } static int level() { return 2; } private: std::string text_; }; } // namespace clipper #endif clipper-2.1/clipper/core/container_map.h0000644000374100011300000002133110363703537015312 00000000000000/*! \file lib/container_map.h Header file for Container versions of various objects */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_CONTAINER_MAP #define CLIPPER_CONTAINER_MAP #include "container_types.h" #include "nxmap_operator.h" namespace clipper { //! Crystallographic map container /*! CXmap: This is a crystallographic map. */ template class CXmap : public Container, public Xmap { public: //! null constructor CXmap() {} //! constructor: inherit spacegroup, cell and grid CXmap( Container& parent, const String name = "" ); //! initialiser: supply or inherit spacegroup, cell and grid void init( const Spacegroup& spacegroup, const Cell& cell, const Grid_sampling& grid_sampling ); //! hierarchical update void update(); }; //! Non-Crystallographic map container /*! CNXmap: This is a non-crystallographic map. Since it does not exist in a crystallographic frame, it does not inherit anything. */ template class CNXmap : public Container, public NXmap { public: //! null constructor CNXmap() {} //! constructor: CNXmap( Container& parent, const String name = "" ) : Container( parent, name ) {} }; //! Non-Crystallographic map operator container /*! CNXmap: This is an operator relating a non-crystallographic map into a crystallgraphic frame. It can inherit the crystallographic cell and grid sampling. */ template class CNXmap_operator : public Container, public NXmap_operator { public: //! null constructor CNXmap_operator() {} //! constructor: do not initialise CNXmap_operator( Container& parent, const String name = "" ); //! constructor: inherit cell and grid CNXmap_operator( Container& parent, const String name, const NXmap& nxmap, const RTop_orth& nxop = RTop_orth(RTop<>::null()) ); //! initialier: supply or inherit cell, grid, NXmap, RTop_orth void init( const Cell& cell, const Grid_sampling& grid, const NXmap& nxmap, const RTop_orth& nxop ); //! hierarchical update void update(); private: const NXmap* nxmap_; //!< Store for later initialisation RTop_orth nxop_; //!< Store for later initialisation }; // template implementations /*! The object is constructed at the given location in the hierarchy. An attempt is made to initialise the object using information from its parents in the hierarchy. \param parent An object in the hierarchy (usually the parent of the new object). \param name The path from \c parent to the new object (usually just the name of the new object). */ template CXmap::CXmap( Container& parent, const String name ) : Container( parent, name ) { init( NullSpacegroup, NullCell, NullGrid_sampling ); } /*! An attempt is made to initialise the object using information from the supplied parameters, or if they are Null, from its parents in the hierarchy. \param spacegroup The spacegroup for the map. \param name The cell for the map. \param grid The grid for the map. */ template void CXmap::init( const Spacegroup& spacegroup, const Cell& cell, const Grid_sampling& grid_sampling ) { // use supplied values by default const Spacegroup* sp = &spacegroup; // use pointers so we can reassign const Cell* cp = &cell; const Grid_sampling* gp = &grid_sampling; // otherwise get them from the tree if ( sp->is_null() ) sp = parent_of_type_ptr(); if ( cp->is_null() ) cp = parent_of_type_ptr(); if ( gp->is_null() ) gp = parent_of_type_ptr(); // initialise if ( sp != NULL && cp != NULL && gp != NULL ) if ( !sp->is_null() && !cp->is_null() && !gp->is_null() ) Xmap::init( *sp, *cp, *gp ); Container::update(); } /*! Hierarchical update. If this object is uninitialised, an attempt is made to initialise the object using information from its parents in the hierarchy. The childen of the object are then updated. */ template void CXmap::update() { if ( Xmap_base::is_null() ) init( NullSpacegroup, NullCell, NullGrid_sampling ); else Container::update(); } /*! The object is not initialised. \param parent The objects parent. \param name The object name. */ template CNXmap_operator::CNXmap_operator( Container& parent, const String name ) : Container( parent, name ), nxmap_( NULL ), nxop_( RTop_orth::null() ) {} /*! The object is initialised if the appropriate parent objects are available, and children are updated. \param parent The objects parent. \param name The object name. \param nxmap The non-crystal map object. \param nxop The orth. operator mapping the NXmap into the crystal frame. */ template CNXmap_operator::CNXmap_operator( Container& parent, const String name, const NXmap& nxmap, const RTop_orth& nxop ) : Container( parent, name ), nxmap_( &nxmap ), nxop_( nxop ) { init( NullCell, NullGrid_sampling, NXmap(), RTop_orth::null() ); } /*! An attempt is made to initialise the object using information from the supplied parameters, or if they are Null, from its parents in the hierarchy. \param cell The unit cell for the crystallographic frame. \param grid The grid sampling for the crystallographic frame. \param nxmap The non-crystal map object. \param nxop The orth. operator mapping the NXmap into the crystal frame. */ template void CNXmap_operator::init( const Cell& cell, const Grid_sampling& grid_sampling, const NXmap& nxmap, const RTop_orth& nxop ) { // use supplied values by default const Cell* cp = &cell; const Grid_sampling* gp = &grid_sampling; // otherwise get them from the tree if ( cp->is_null() ) cp = parent_of_type_ptr(); if ( gp->is_null() ) gp = parent_of_type_ptr(); if ( !nxmap.is_null() ) nxmap_ = &nxmap; if ( !nxop.is_null() ) nxop_ = nxop; // initialise if ( cp != NULL && gp != NULL & nxmap_ != NULL ) if ( !cp->is_null() && !gp->is_null() && !nxmap_->is_null() ) NXmap_operator::init( *cp, *gp, *nxmap_, nxop_ ); Container::update(); } /*! Hierarchical update. If this object is uninitialised, an attempt is made to initialise the object using information from its parents in the hierarchy. The childen of the object are then updated. */ template void CNXmap_operator::update() { if ( NX_operator::is_null() ) init( NullCell, NullGrid_sampling, NXmap(), RTop_orth::null() ); else Container::update(); } } // namespace clipper #endif clipper-2.1/clipper/core/hkl_lookup.cpp0000644000374100011300000001153410363703537015201 00000000000000/* hkl_lookup.cpp: class file for reflection data lookup */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "hkl_lookup.h" namespace clipper { void HKL_lookup::init(const std::vector& hkl) { // generate an efficient 3-d lookup table for finding a reflection // given its index. We could use hash_map, but this approach is // more efficient and uses far less memory int i, h, k; if ( hkl.size() == 0 ) return; // make h lookup table for (i=0; i= h_ptr.min ) h_ptr.p.resize( h_ptr.max - h_ptr.min + 1 ); // now add k lists // make k lookup tables for (i=0; i= k_ptr.min ) k_ptr.p.resize( k_ptr.max - k_ptr.min + 1 ); // now add l lists } // make l lookup tables for (i=0; i= l_ptr.min ) l_ptr.p.resize( l_ptr.max - l_ptr.min + 1, -1 ); } } // now fill in the data for (i=0; i= h_ptr.min && h <= h_ptr.max ) { const klookup& k_ptr = h_ptr.p[h - h_ptr.min]; if ( k >= k_ptr.min && k <= k_ptr.max ) { const llookup& l_ptr = k_ptr.p[k - k_ptr.min]; if ( l >= l_ptr.min && l <= l_ptr.max ) { return l_ptr.p[ l - l_ptr.min ]; } } } // if not found, return -1 return -1; } void HKL_lookup::debug() { int size=0, h, k; for (h=h_ptr.min; h<=h_ptr.max; h++) { klookup& k_ptr = h_ptr.p[h - h_ptr.min]; for (k=k_ptr.min; k<=k_ptr.max; k++) { llookup& l_ptr = k_ptr.p[k - k_ptr.min]; size+=l_ptr.p.size(); } } std::cout << "lookup: size " << size << "\n"; } } // namespace clipper clipper-2.1/clipper/core/map_interp.h0000644000374100011300000004201710363703537014635 00000000000000/*! \file lib/map_interp.h Generic interpolation methods for crystal and non-crystal maps. */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_MAP_INTERP #define CLIPPER_MAP_INTERP #include "derivs.h" namespace clipper { //! Wrapper class for zeroth-order (nearest neighbour) interpolation fns /*! These can be used through the built-in methods in Xmap/NXmap, or passed to methods to allow a choice of interpolation methods, or directly by providing the map as an argument. For example: \code NXmap nxmap; Coord_map c; ... x1 = Interp_nearest::interp( nxmap, c ); x2 = nxmap.interp( c ); \endcode */ class Interp_nearest { public: template static bool can_interp( const M& map, const Coord_map& pos ); //!< Test if we can interpolate in map M at coord template static void interp( const M& map, const Coord_map& pos, T& val ); //!< Interpolate map M using type T at coord inline static int order() { return 0; } //!< Order of interpolant }; //! Wrapper class for first-order (linear) interpolation fns /*! These can be used through the built-in methods in Xmap/NXmap, or passed to methods to allow a choice of interpolation methods, or directly by providing the map as an argument. For example: \code NXmap nxmap; Coord_map c; float x1, x2; ... Interp_linear::interp( nxmap, c, x1 ); x2 = nxmap.interp( c ); \endcode */ class Interp_linear { public: template static bool can_interp( const M& map, const Coord_map& pos ); //!< Test if we can interpolate in map M at coord template static void interp( const M& map, const Coord_map& pos, T& val ); //!< Interpolate map M using type T at coord inline static int order() { return 1; } //!< Order of interpolant }; //! Wrapper class for third-order (cubic) interpolation fns /*! These can be used through the built-in methods in Xmap/NXmap, or passed to methods to allow a choice of interpolation methods, or directly by providing the map as an argument. For example: \code NXmap nxmap; Coord_map c; float x1, x2; ... Interp_cubic::interp( nxmap, c, x1 ); x2 = nxmap.interp( c ); \endcode */ class Interp_cubic { public: template static bool can_interp( const M& map, const Coord_map& pos ); //!< Test if we can interpolate in map M at coord template static void interp( const M& map, const Coord_map& pos, T& val ); //!< Interpolate map M using type T at coord template static void interp_grad( const M& map, const Coord_map& pos, T& val, Grad_map& grad ); template static void interp_curv( const M& map, const Coord_map& pos, T& val, Grad_map& grad, Curv_map& curv ); inline static int order() { return 3; } //!< Order of interpolant }; // template implementations /*! The map is queried to see if interpolation is possible at the given coord. For a crystallographic map, this is always true. For a non-crystallographic map, this depends if the point and enough neighbours are in the grid. \param map The map on which to perform the calculation. \param pos The map coord at which the density is to be calcuated. */ template bool Interp_nearest::can_interp( const M& map, const Coord_map& pos ) { return map.in_map( pos.coord_grid() ); } /*! The value of the map at the supplied map coordinate is calculated by zeroth order (nearest neighbour) interpolation based on 1 point. \param map The map on which to perform the calculation. \param pos The map coord at which the density is to be calcuated. \return The value of the density at that point. */ template void Interp_nearest::interp( const M& map, const Coord_map& pos, T& val ) { val = map.get_data( pos.coord_grid() ); } /*! The map is queried to see if interpolation is possible at the given coord. For a crystallographic map, this is always true. For a non-crystallographic map, this depends if the point and enough neighbours are in the grid. \param map The map on which to perform the calculation. \param pos The map coord at which the density is to be calcuated. */ template bool Interp_linear::can_interp( const M& map, const Coord_map& pos ) { Coord_grid c( pos.floor() ); // for even order change floor to coord_grid c.u() -= order()/2; c.v() -= order()/2; c.w() -= order()/2; if ( map.in_map( c ) ) { c.u() += order(); c.v() += order(); c.w() += order(); return map.in_map( c ); } return false; } /*! The value of the map at the supplied map coordinate is calculated by first order (linear) interpolation based on 8 neighbouring points. \param map The map on which to perform the calculation. \param pos The map coord at which the density is to be calcuated. \return The value of the density at that point. */ template void Interp_linear::interp( const M& map, const Coord_map& pos, T& val ) { ftype u0 = floor( pos.u() ); ftype v0 = floor( pos.v() ); ftype w0 = floor( pos.w() ); typename M::Map_reference_coord r( map, Coord_grid( int(u0), int(v0), int(w0) ) ); T cu1( pos.u() - u0 ); T cv1( pos.v() - v0 ); T cw1( pos.w() - w0 ); T cu0( 1.0 - cu1 ); T cv0( 1.0 - cv1 ); T cw0( 1.0 - cw1 ); T r00 = cw0 * map[ r ]; // careful with evaluation order r00 += cw1 * map[ r.next_w() ]; T r01 = cw1 * map[ r.next_v() ]; r01 += cw0 * map[ r.prev_w() ]; T r11 = cw0 * map[ r.next_u() ]; r11 += cw1 * map[ r.next_w() ]; T r10 = cw1 * map[ r.prev_v() ]; r10 += cw0 * map[ r.prev_w() ]; val = ( cu0*( cv0*r00 + cv1*r01 ) + cu1*( cv0*r10 + cv1*r11 ) ); } /*! The map is queried to see if interpolation is possible at the given coord. For a crystallographic map, this is always true. For a non-crystallographic map, this depends if the point and enough neighbours are in the grid. \param map The map on which to perform the calculation. \param pos The map coord at which the density is to be calcuated. */ template bool Interp_cubic::can_interp( const M& map, const Coord_map& pos ) { Coord_grid c( pos.floor() ); // for even order change floor to coord_grid c.u() -= order()/2; c.v() -= order()/2; c.w() -= order()/2; if ( map.in_map( c ) ) { c.u() += order(); c.v() += order(); c.w() += order(); return map.in_map( c ); } return false; } /*! The value of the map at the supplied map coordinate is calculated by third order (cubic) interpolation based on the surrounding 64 points. \param pos The fractional coord at which the density is to be calcuated. \return The value of the density at that point. */ template void Interp_cubic::interp( const M& map, const Coord_map& pos, T& val ) { ftype u0 = floor( pos.u() ); ftype v0 = floor( pos.v() ); ftype w0 = floor( pos.w() ); typename M::Map_reference_coord iw, iv, iu( map, Coord_grid( int(u0)-1, int(v0)-1, int(w0)-1 ) ); T su, sv, sw, cu[4], cv[4], cw[4]; T cu1( pos.u() - u0 ); T cv1( pos.v() - v0 ); T cw1( pos.w() - w0 ); T cu0( 1.0 - cu1 ); T cv0( 1.0 - cv1 ); T cw0( 1.0 - cw1 ); cu[0] = -0.5*cu1*cu0*cu0; // cubic spline coeffs: u cu[1] = cu0*( -1.5*cu1*cu1 + cu1 + 1.0 ); cu[2] = cu1*( -1.5*cu0*cu0 + cu0 + 1.0 ); cu[3] = -0.5*cu1*cu1*cu0; cv[0] = -0.5*cv1*cv0*cv0; // cubic spline coeffs: v cv[1] = cv0*( -1.5*cv1*cv1 + cv1 + 1.0 ); cv[2] = cv1*( -1.5*cv0*cv0 + cv0 + 1.0 ); cv[3] = -0.5*cv1*cv1*cv0; cw[0] = -0.5*cw1*cw0*cw0; // cubic spline coeffs: w cw[1] = cw0*( -1.5*cw1*cw1 + cw1 + 1.0 ); cw[2] = cw1*( -1.5*cw0*cw0 + cw0 + 1.0 ); cw[3] = -0.5*cw1*cw1*cw0; su = 0.0; int i, j; for ( j = 0; j < 4; j++ ) { iv = iu; sv = 0.0; for ( i = 0; i < 4; i++ ) { iw = iv; sw = cw[0] * T( map[ iw ] ); sw += cw[1] * T( map[ iw.next_w() ] ); sw += cw[2] * T( map[ iw.next_w() ] ); sw += cw[3] * T( map[ iw.next_w() ] ); sv += cv[i] * sw; iv.next_v(); } su += cu[j] * sv; iu.next_u(); } val = su; } /*! The value of the map at the supplied map coordinate and its gradient are calculated by third order (cubic) interpolation based on the surrounding 64 points. \param pos The fractional coord at which the density is to be calcuated. \param val The value of the density at that point. \param grad The interpolated value as a gradient vector with respect to the fractional coordinates (see Cell::coord_orth). */ template void Interp_cubic::interp_grad( const M& map, const Coord_map& pos, T& val, Grad_map& grad ) { ftype u0 = floor( pos.u() ); ftype v0 = floor( pos.v() ); ftype w0 = floor( pos.w() ); typename M::Map_reference_coord iw, iv, iu( map, Coord_grid( int(u0)-1, int(v0)-1, int(w0)-1 ) ); T s1, s2, s3, du1, dv1, dv2, dw1, dw2, dw3; T cu[4], cv[4], cw[4], gu[4], gv[4], gw[4]; T cu1( pos.u() - u0 ); T cv1( pos.v() - v0 ); T cw1( pos.w() - w0 ); T cu0( 1.0 - cu1 ); T cv0( 1.0 - cv1 ); T cw0( 1.0 - cw1 ); cu[0] = -0.5*cu1*cu0*cu0; // cubic spline coeffs: u cu[1] = cu0*( -1.5*cu1*cu1 + cu1 + 1.0 ); cu[2] = cu1*( -1.5*cu0*cu0 + cu0 + 1.0 ); cu[3] = -0.5*cu1*cu1*cu0; cv[0] = -0.5*cv1*cv0*cv0; // cubic spline coeffs: v cv[1] = cv0*( -1.5*cv1*cv1 + cv1 + 1.0 ); cv[2] = cv1*( -1.5*cv0*cv0 + cv0 + 1.0 ); cv[3] = -0.5*cv1*cv1*cv0; cw[0] = -0.5*cw1*cw0*cw0; // cubic spline coeffs: w cw[1] = cw0*( -1.5*cw1*cw1 + cw1 + 1.0 ); cw[2] = cw1*( -1.5*cw0*cw0 + cw0 + 1.0 ); cw[3] = -0.5*cw1*cw1*cw0; gu[0] = cu0*( 1.5*cu1 - 0.5 ); // cubic spline grad coeffs: u gu[1] = cu1*( 4.5*cu1 - 5.0 ); gu[2] = -cu0*( 4.5*cu0 - 5.0 ); gu[3] = -cu1*( 1.5*cu0 - 0.5 ); gv[0] = cv0*( 1.5*cv1 - 0.5 ); // cubic spline grad coeffs: v gv[1] = cv1*( 4.5*cv1 - 5.0 ); gv[2] = -cv0*( 4.5*cv0 - 5.0 ); gv[3] = -cv1*( 1.5*cv0 - 0.5 ); gw[0] = cw0*( 1.5*cw1 - 0.5 ); // cubic spline grad coeffs: w gw[1] = cw1*( 4.5*cw1 - 5.0 ); gw[2] = -cw0*( 4.5*cw0 - 5.0 ); gw[3] = -cw1*( 1.5*cw0 - 0.5 ); s1 = du1 = dv1 = dw1 = 0.0; int i, j; for ( j = 0; j < 4; j++ ) { iv = iu; s2 = dv2 = dw2 = 0.0; for ( i = 0; i < 4; i++ ) { iw = iv; s3 = cw[0] * T( map[ iw ] ); dw3 = gw[0] * T( map[ iw ] ); iw.next_w(); s3 += cw[1] * T( map[ iw ] ); dw3 += gw[1] * T( map[ iw ] ); iw.next_w(); s3 += cw[2] * T( map[ iw ] ); dw3 += gw[2] * T( map[ iw ] ); iw.next_w(); s3 += cw[3] * T( map[ iw ] ); dw3 += gw[3] * T( map[ iw ] ); s2 += cv[i] * s3; dv2 += gv[i] * s3; dw2 += cv[i] * dw3; iv.next_v(); } s1 += cu[j] * s2; du1 += gu[j] * s2; dv1 += cu[j] * dv2; dw1 += cu[j] * dw2; iu.next_u(); } val = s1; grad = Grad_map( du1, dv1, dw1 ); } /*! The value of the map at the supplied map coordinate and its gradient are calculated by third order (cubic) interpolation based on the surrounding 64 points. \param pos The fractional coord at which the density is to be calcuated. \param val The value of the density at that point. \param grad The interpolated value as a gradient vector with respect to the fractional coordinates (see Cell::coord_orth). */ template void Interp_cubic::interp_curv( const M& map, const Coord_map& pos, T& val, Grad_map& grad, Curv_map& curv ) { ftype u0 = floor( pos.u() ); ftype v0 = floor( pos.v() ); ftype w0 = floor( pos.w() ); typename M::Map_reference_coord iw, iv, iu( map, Coord_grid( int(u0)-1, int(v0)-1, int(w0)-1 ) ); T s1, s2, s3, du1, dv1, dv2, dw1, dw2, dw3; T duv1, duw1, dvw1, dvw2, duu1, dvv1, dvv2, dww1, dww2, dww3; T cu[4], cv[4], cw[4], gu[4], gv[4], gw[4], ggu[4], ggv[4], ggw[4]; T cu1( pos.u() - u0 ); T cv1( pos.v() - v0 ); T cw1( pos.w() - w0 ); T cu0( 1.0 - cu1 ); T cv0( 1.0 - cv1 ); T cw0( 1.0 - cw1 ); cu[0] = -0.5*cu1*cu0*cu0; // cubic spline coeffs: u cu[1] = cu0*( -1.5*cu1*cu1 + cu1 + 1.0 ); cu[2] = cu1*( -1.5*cu0*cu0 + cu0 + 1.0 ); cu[3] = -0.5*cu1*cu1*cu0; cv[0] = -0.5*cv1*cv0*cv0; // cubic spline coeffs: v cv[1] = cv0*( -1.5*cv1*cv1 + cv1 + 1.0 ); cv[2] = cv1*( -1.5*cv0*cv0 + cv0 + 1.0 ); cv[3] = -0.5*cv1*cv1*cv0; cw[0] = -0.5*cw1*cw0*cw0; // cubic spline coeffs: w cw[1] = cw0*( -1.5*cw1*cw1 + cw1 + 1.0 ); cw[2] = cw1*( -1.5*cw0*cw0 + cw0 + 1.0 ); cw[3] = -0.5*cw1*cw1*cw0; gu[0] = cu0*( 1.5*cu1 - 0.5 ); // cubic spline grad coeffs: u gu[1] = cu1*( 4.5*cu1 - 5.0 ); gu[2] = -cu0*( 4.5*cu0 - 5.0 ); gu[3] = -cu1*( 1.5*cu0 - 0.5 ); gv[0] = cv0*( 1.5*cv1 - 0.5 ); // cubic spline grad coeffs: v gv[1] = cv1*( 4.5*cv1 - 5.0 ); gv[2] = -cv0*( 4.5*cv0 - 5.0 ); gv[3] = -cv1*( 1.5*cv0 - 0.5 ); gw[0] = cw0*( 1.5*cw1 - 0.5 ); // cubic spline grad coeffs: w gw[1] = cw1*( 4.5*cw1 - 5.0 ); gw[2] = -cw0*( 4.5*cw0 - 5.0 ); gw[3] = -cw1*( 1.5*cw0 - 0.5 ); ggu[0] = 2.0 - 3.0*cu1; // cubic spline curv coeffs: u ggu[1] = 9.0*cu1 - 5.0; ggu[2] = 9.0*cu0 - 5.0; ggu[3] = 2.0 - 3.0*cu0; ggv[0] = 2.0 - 3.0*cv1; // cubic spline curv coeffs: v ggv[1] = 9.0*cv1 - 5.0; ggv[2] = 9.0*cv0 - 5.0; ggv[3] = 2.0 - 3.0*cv0; ggw[0] = 2.0 - 3.0*cw1; // cubic spline curv coeffs: w ggw[1] = 9.0*cw1 - 5.0; ggw[2] = 9.0*cw0 - 5.0; ggw[3] = 2.0 - 3.0*cw0; s1 = du1 = dv1 = dw1 = duv1 = duw1 = dvw1 = duu1 = dvv1 = dww1 = 0.0; int i, j; for ( j = 0; j < 4; j++ ) { iv = iu; s2 = dv2 = dw2 = dvw2 = dvv2 = dww2 = 0.0; for ( i = 0; i < 4; i++ ) { iw = iv; s3 = cw[0] * T( map[ iw ] ); dw3 = gw[0] * T( map[ iw ] ); dww3 = ggw[0] * T( map[ iw ] ); iw.next_w(); s3 += cw[1] * T( map[ iw ] ); dw3 += gw[1] * T( map[ iw ] ); dww3 += ggw[1] * T( map[ iw ] ); iw.next_w(); s3 += cw[2] * T( map[ iw ] ); dw3 += gw[2] * T( map[ iw ] ); dww3 += ggw[2] * T( map[ iw ] ); iw.next_w(); s3 += cw[3] * T( map[ iw ] ); dw3 += gw[3] * T( map[ iw ] ); dww3 += ggw[3] * T( map[ iw ] ); s2 += cv[i] * s3; dv2 += gv[i] * s3; dw2 += cv[i] * dw3; dvw2 += gv[i] * dw3; dvv2 += ggv[i] * s3; dww2 += cv[i] * dww3; iv.next_v(); } s1 += cu[j] * s2; du1 += gu[j] * s2; dv1 += cu[j] * dv2; dw1 += cu[j] * dw2; duv1 += gu[j] * dv2; duw1 += gu[j] * dw2; dvw1 += cu[j] * dvw2; duu1 += ggu[j] * s2; dvv1 += cu[j] * dvv2; dww1 += cu[j] * dww2; iu.next_u(); } val = s1; grad = Grad_map( du1, dv1, dw1 ); curv = Curv_map( Mat33( duu1, duv1, duw1, duv1, dvv1, dvw1, duw1, dvw1, dww1 ) ); } } // namespace clipper #endif clipper-2.1/clipper/core/container.h0000644000374100011300000001301210363703537014452 00000000000000/*! \file lib/container.h Header for generic container object */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_CONTAINER #define CLIPPER_CONTAINER #include "coords.h" namespace clipper { //! Definition for a generic container Object /*! Container is a definition for a generic container object with a name, parents, and children. Any object that wants to be part of the tree simply subclasses this class. The class also implements search and move objects. The tree is navigate using unix-like pathnames. A recursive update method can be overridden to update content after altering the hierarchy. The top container in a tree is created by passing Container() as its parent. */ class Container { public: //! constructor: make null object or top object in a tree Container( const String name = "" ); //! constructor: from any other member and a relative path Container( Container& parent, const String& path ); //! update: hierarchical content update function virtual void update(); //! get the path of this tree object String path() const; //! get the name of this tree object String name() const; //! set the name of this tree object void set_name( const String& name ); //! is this object to be destroyed when parent is destroyed? bool is_destroyed_with_parent() const; //! set this object to be destroyed when parent is destroyed void set_destroyed_with_parent( const bool d=true ); //! 'move' method moves this object to somewhere else in the hierarchy void move( const String& path ); //! test if this object has a parent bool has_parent() const; //! get the parent of this object const Container& parent() const; //! get the parent of this object Container& parent(); //! return number of children int num_children() const; //! get the i'th child of this object const Container& child( const int& i ) const; //! get the i'th child of this object Container& child( const int& i ); //! get the ultimate parent of this object - the top of the tree const Container& ultimate_parent() const; //! get the ultimate parent of this object - the top of the tree Container& ultimate_parent(); //! get the parent of this object (NULL on fail) Container* parent_ptr(); //! search up the tree for a parent of the specified type (NULL on fail) template T* parent_of_type_ptr(); //! find an object using a directory-like path (NULL on fail) Container* find_path_ptr( const String& path ); //! destructor: virtual virtual ~Container(); void debug(); private: // members String name_; Container* parent_; std::vector children; bool destroyed_with_parent; //! add a child: called by a child on construction void add_child( Container& c ); //! delete a child: called by a child on destruction void del_child( Container& c ); //! override copy constructor to prevent its use Container( const Container& c ) {} }; // template function definitions template T* Container::parent_of_type_ptr() { // this can be done recursively with references, but gcc won't compile it. Container* p = this; while ( p->has_parent() ) { p = &(p->parent()); T* pt = dynamic_cast(p); if ( pt != NULL ) return pt; } return NULL; } } // namespace clipper #endif clipper-2.1/clipper/core/rotation.h0000644000374100011300000002047710654070346014342 00000000000000/*! \file lib/rotation.h Fundamental types for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_ROTATION #define CLIPPER_ROTATION #include "clipper_types.h" namespace clipper { // forward definition class Rotation; //! Euler angle class /* Rotations are generally handled through the clipper::Rotation class. This class only exists for conversion purposes. This particular class represents generic Euler angles. The convention is selected from the 24 possible conventions according to the template parameter. The integer convention code is enumerated in the Rotation::EULERtype enumation in the form Rotation::EulerZYZr, Rotation::EulerXYZs etc., where the X/Y/Z indicates the axes of rotation in order, and the r/s indicates static or rotating axes. The type of an Euler class is also given as a prefix to the result of format(). */ template class Euler { public: //! constructor: null Euler() {} //! constructor: from specified angles Euler( const ftype& alpha, const ftype& beta, const ftype& gamma ) : alpha_(alpha), beta_(beta), gamma_(gamma) {} //! constructor: from rotation Euler( const Rotation& rot ); //! return rotation Rotation rotation() const; const ftype& alpha() const { return alpha_; } //!< return alpha const ftype& beta() const { return beta_; } //!< return beta const ftype& gamma() const { return gamma_; } //!< return gamma String format() const; //!< return formatted String representation private: static void params( int& r1, int& r2, int& r3, int& s ); ftype alpha_, beta_, gamma_; }; //! Euler_ccp4 angle class /* Rotations are generally handled through the clipper::Rotation class. This class only exists for conversion purposes. This particular class represents Euler_ccp4 angles according to the CCP4 standard, i.e. - Rotation 1 (alpha) about K, - Rotation 2 (beta) about the new J, - Rotation 3 (gamma) about the new K. */ class Euler_ccp4 { public: //! constructor: null Euler_ccp4() {} //! constructor: from specified angles Euler_ccp4( const ftype& alpha, const ftype& beta, const ftype& gamma ) : alpha_(alpha), beta_(beta), gamma_(gamma) {} const ftype& alpha() const { return alpha_; } //!< return alpha const ftype& beta() const { return beta_; } //!< return beta const ftype& gamma() const { return gamma_; } //!< return gamma String format() const; //!< return formatted String representation private: ftype alpha_, beta_, gamma_; }; //! Polar_ccp4 angle class /* Rotations are generally handled through the clipper::Rotation class. This class only exists for conversion purposes. This particular class represents Polar_ccp4 angles according to the CCP4 standard, i.e. - omega gives inclination of rotation axis to K axis, - phi gives anticlockwise rotation from I to projection of rotation axis onto I-J plane, - kappa is the rotation about the rotation axis. */ class Polar_ccp4 { public: //! null constructor Polar_ccp4() {} //! constructor: from specified angles Polar_ccp4( const ftype& omega, const ftype& phi, const ftype& kappa ) : omega_(omega), phi_(phi), kappa_(kappa) {} const ftype& psi() const { return omega_; } //!< return omega const ftype& omega() const { return omega_; } //!< return omega const ftype& phi() const { return phi_; } //!< return phi const ftype& kappa() const { return kappa_; } //!< return kappa String format() const; //!< return formatted String representation private: ftype omega_, phi_, kappa_; }; //! Rotation class /*! This class represents a rotation. The internal representation is as a unit quaternion, which is easily combined, inverted, or converted to or from other commonly used forms. */ class Rotation { public: //! null constructor Rotation() {} //! constructor: from generic Euler template explicit Rotation( const Euler& euler ) { (*this) = euler.rotation(); } //! constructor: from Euler_ccp4 explicit Rotation( const Euler_ccp4& euler ); //! constructor: from Polar_ccp4 explicit Rotation( const Polar_ccp4& polar ); //! constructor: from Matrix explicit Rotation( const Mat33<>& matrix ); //! constructor: from components Rotation( const ftype& w, const ftype& x, const ftype& y, const ftype& z ) : w_(w), x_(x), y_(y), z_(z) {} const ftype& w() const { return w_; } //!< return w component const ftype& x() const { return x_; } //!< return x component const ftype& y() const { return y_; } //!< return y component const ftype& z() const { return z_; } //!< return z component template Euler euler() const //!< return Euler angles { return Euler( *this ); } Euler_ccp4 euler_ccp4() const; //!< return Euler_ccp4 angles Polar_ccp4 polar_ccp4() const; //!< return Polar_ccp4 angles Mat33<> matrix() const; //!< return 3x3 matrix //! normalise this quaternion const Rotation& norm(); //! return absolute rotation angle ftype abs_angle() const { return acos(Util::min(2.0*(w_*w_)/(w_*w_+x_*x_+y_*y_+z_*z_)-1.0,1.0)); } //! return inverse rotation Rotation inverse() const { return Rotation( w_, -x_, -y_, -z_ ); } //! return zero rotation static Rotation zero() { return Rotation( 1.0, 0.0, 0.0, 0.0 ); } //! return null rotation static Rotation null() { return Rotation( Util::nan(), 0.0, 0.0, 0.0 ); } //! test for null (uninitialised) rotation bool is_null() const { return Util::is_nan( w_ ); } //! combine two rotations friend Rotation operator* ( const Rotation& r1, const Rotation& r2 ); String format() const; //!< return formatted String representation //! Enumeration of Euler conventions enum EULERtype { EulerXYZr,EulerXYZs,EulerXYXr,EulerXYXs, EulerXZXr,EulerXZXs,EulerXZYr,EulerXZYs, EulerYZXr,EulerYZXs,EulerYZYr,EulerYZYs, EulerYXYr,EulerYXYs,EulerYXZr,EulerYXZs, EulerZXYr,EulerZXYs,EulerZXZr,EulerZXZs, EulerZYZr,EulerZYZs,EulerZYXr,EulerZYXs }; protected: ftype w_, x_, y_, z_; }; } // namespace clipper #endif clipper-2.1/clipper/core/cell.cpp0000644000374100011300000001705210363703537013752 00000000000000/* cell.cpp: class file for unit cell class */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA /* This code is derived from the 'dm' source code */ #include "cell.h" namespace clipper { /*! \param a A axis in Angstroms. \param b B axis in Angstroms. \param c C axis in Angstroms. \param alpha Angle between B and C axes in radians or degrees, default=90 \param beta Angle between A and C axes in radians or degrees, default=90 \param gamma Angle between A and C axes in radians or degrees, default=90 */ Cell_descr::Cell_descr( const ftype& a, const ftype& b, const ftype& c, const ftype& alpha, const ftype& beta, const ftype& gamma ) { a_=a; b_=b; c_=c; alpha_=alpha; beta_=beta; gamma_=gamma; if (alpha_>M_PI) alpha_=Util::d2rad(alpha_); if (beta_ >M_PI) beta_ =Util::d2rad(beta_ ); if (gamma_>M_PI) gamma_=Util::d2rad(gamma_); } /*! \return The cell angle in degrees */ ftype Cell_descr::alpha_deg() const { return Util::rad2d(alpha_); } /*! \return The cell angle in degrees */ ftype Cell_descr::beta_deg() const { return Util::rad2d(beta_ ); } /*! \return The cell angle in degrees */ ftype Cell_descr::gamma_deg() const { return Util::rad2d(gamma_); } /*! \return A string describing the cell */ String Cell_descr::format() const { return " Cell ("+String(a())+","+String(b())+","+String(c())+","+String(alpha_deg())+","+String(beta_deg())+","+String(gamma_deg())+")"; } /*! Construct and initialise a metric tensor, given a set of real or reciprocal cell parameters. \param a Length of \b a axis in Angstroms or reciprocal Angstroms. \param b Length of \b b axis in Angstroms or reciprocal Angstroms. \param c Length of \b c axis in Angstroms or reciprocal Angstroms. \param alph Angle between \b b and \b c in radians. \param beta Angle between \b a and \b c in radians. \param gamm Angle between \b a and \b b in radians. */ Metric_tensor::Metric_tensor( const ftype& a, const ftype& b, const ftype& c, const ftype& alph, const ftype& beta, const ftype& gamm ) { m00 = a*a; m11 = b*b; m22 = c*c; m01 = 2.0*a*b*cos(gamm); m02 = 2.0*a*c*cos(beta); m12 = 2.0*b*c*cos(alph); } String Metric_tensor::format() const { return "m00=" + String(m00) + " m11=" + String(m11) + " m22=" + String(m22) + " m01=" + String(m01) + " m02=" + String(m02) + " m12=" + String(m12); } // Cell object /*! Initialise the Cell object from a cell description. \param cell_ The cell descirption. */ void Cell::init(const Cell_descr& cell_) { // store cell (allows a/b/c/alpha/beta/gamma methods) a_ = cell_.a(); b_ = cell_.b(); c_ = cell_.c(); alpha_ = cell_.alpha(); beta_ = cell_.beta(); gamma_ = cell_.gamma(); // calculate cell volume (allows a_star../alpha_star.. methods) vol = a() * b() * c() * sqrt( 2.0*cos(alpha())*cos(beta())*cos(gamma()) - cos(alpha())*cos(alpha()) - cos( beta())*cos( beta()) - cos(gamma())*cos(gamma()) + 1.0 ); // deal with null cell if ( is_null() ) return; // othogonalisation+fractionisation matrices orthmat = Mat33<>::identity(); orthmat(0,0) = a(); orthmat(0,1) = b()*cos(gamma()); orthmat(0,2) = c()*cos( beta()); orthmat(1,1) = b()*sin(gamma()); orthmat(1,2) = -c()*sin( beta())*cos(alpha_star()); orthmat(2,2) = c()*sin( beta())*sin(alpha_star()); //std::cout << sin( beta()) << " " << sin(alpha_star()) << " " << alpha_star() << "\n"; fracmat = orthmat.inverse(); // metric tensors realmetric = Metric_tensor( a(), b(), c(), alpha(), beta(), gamma() ); recimetric = Metric_tensor( a_star(), b_star(), c_star(), alpha_star(), beta_star(), gamma_star() ); } /*! \return true if the object has not been initalised. */ bool Cell::is_null() const { return ( vol <= 0.0 ); } ftype Cell::a_star() const { return b()*c()*sin(alpha())/vol; } ftype Cell::b_star() const { return c()*a()*sin(beta())/vol; } ftype Cell::c_star() const { return a()*b()*sin(gamma())/vol; } ftype Cell::alpha_star() const { return acos( (cos(gamma())*cos(beta())-cos(alpha())) / (sin(beta())*sin(gamma())) ); } ftype Cell::beta_star() const { return acos( (cos(alpha())*cos(gamma())-cos(beta())) / (sin(gamma())*sin(alpha())) ); } ftype Cell::gamma_star() const { return acos( (cos(beta())*cos(alpha())-cos(gamma())) / (sin(alpha())*sin(beta())) ); } /*! Two cells disagree if the difference in their orthogonalisation matrices is sufficient to map a reflection from one cell onto a different reflection in the other cell at the given tolerance, which is the resolution of the reflection in Angstroms. \param other The other cell to compare. \param tol The tolerance, in Angstroms. */ bool Cell::equals( const Cell& other, const ftype tol ) const { if ( is_null() || other.is_null() ) return false; ftype s = 0.0; for ( int i = 0; i < 3; i++ ) for ( int j = 0; j < 3; j++ ) s += pow( fracmat(i,j) - other.fracmat(i,j), 2.0 ); return s < ( pow( tol, 2.0 ) / pow( vol, 1.333 ) ); } void Cell::debug() const { std::cout << descr().format() << "\n"; std::cout << "Vol" << vol << "\n"; std::cout << "Orth mat\n" << orthmat.format() << "\n"; std::cout << "Frac mat\n" << fracmat.format() << "\n"; std::cout << "Prod mat\n" << (orthmat*fracmat).format() << "\n"; std::cout << "Real metric " << realmetric.format() << "\n"; std::cout << "Reci metric " << recimetric.format() << "\n"; //std::cout << "Real metric\n"+(orthmat.transpose()*orthmat).format()+"\n"; //std::cout << "Reci metric\n"+(fracmat*fracmat.transpose()).format()+"\n"; } } // namespace clipper clipper-2.1/clipper/core/atomsf.h0000644000374100011300000001455110363703537013772 00000000000000/*! \file atomsf.h Header file for atomic scattering factors \ingroup g_fftmapbspl */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_ATOMSF #define CLIPPER_ATOMSF #include "coords.h" namespace clipper { //! Atomic shape function object /*! The atomic scattering factor object is instantiated for each atom in turn, giving the atom parameters: position, element, occupancy and the isotropic or anisotropic U-value. (See clipper::Util for conversion from B-factors.). The methods of the class may then be called to return the scattering in reciprocal space or density in real space using either isotropic or anistropic models as required. If the atom only has an isotropic U, the faster isotropic methods will be used where available. This implementation uses the coefficients from Waasmaier & Kirfel (1995), Acta Cryst. A51, 416-431. The source data can be found at: ftp://wrzx02.rz.uni-wuerzburg.de/pub/local/Crystallography/sfac.dat */ class AtomShapeFn { public: enum TYPE { X, Y, Z, Uiso, Occ, U11, U22, U33, U12, U13, U23 }; //! null constructor AtomShapeFn() {} //! constructor: from atom object AtomShapeFn( const Atom& atom ); //! constructor: from coord, element, isotropic U, occupancy AtomShapeFn( const Coord_orth& xyz, const String& element, const ftype u_iso = 0.0, const ftype occ = 1.0 ); //! constructor: from coord, element, anisotropic U, occupancy AtomShapeFn( const Coord_orth& xyz, const String& element, const U_aniso_orth& u_aniso, const ftype occ = 1.0 ); //! initialiser: from atom object void init( const Atom& atom ); //! initialiser: from coord, element, isotropic U, occupancy void init( const Coord_orth& xyz, const String& element, const ftype u_iso = 0.0, const ftype occ = 1.0 ); //! initialiser: from coord, element, anisotropic U, occupancy void init( const Coord_orth& xyz, const String& element, const U_aniso_orth& u_aniso, const ftype occ = 1.0 ); //! return scattering factor as a function of reflection posn ftype f( const Coord_reci_orth& rfl ) const; //! return electron density as a function of coordinate ftype rho( const Coord_orth& xyz ) const; //! return Agarwal density gradients as a function of coordinate bool rho_grad( const Coord_orth& xyz, ftype& rho, std::vector& grad ) const; //! return Agarwal density gradient/curvature as a function of coordinate bool rho_curv( const Coord_orth& xyz, ftype& rho, std::vector& grad, Matrix& curv ) const; //! \deprecated return Agarwal density gradients as a function of coordinate bool rho_grad( const Coord_orth& xyz, std::vector& grad ) const; //! return (isotropic) scattering factor as a function of resolution ftype f( const ftype& invresolsq ) const; //! return (isotropic) electron density as a function of radius ftype rho( const ftype& rsq ) const; //! define parameters for Agarwal gradient/curvature calcs std::vector& agarwal_params() { return params; } private: //! look up atom coeffs void init( const String& element, const ftype& u_iso ); // members Coord_orth coord_; U_aniso_orth u_aniso_; ftype u_iso_, occ_; ftype a[6], b[6]; //!< atom coeffs ftype aw[6], bw[6]; //!< intermediate results (iso) std::vector > uaninv; //!< intermediate results (aniso) bool is_iso; std::vector params; }; //! Atomic scattering factor object /*! \deprecated This class has been replaced by AtomShapeFn, which is smaller, faster, and more capable. This class is now a wrapper for that class. */ class AtomSF : private AtomShapeFn { public: AtomSF( const String& type, const ftype u_iso = 0.0, const ftype occ = 1.0 ); AtomSF( const String& type, const U_aniso_orth& u_aniso, const ftype occ = 1.0 ); void init( const String& type, const ftype u_iso = 0.0, const ftype occ = 1.0 ); void init( const String& type, const U_aniso_orth& u_aniso, const ftype occ = 1.0 ); ftype f_iso( const ftype& s ) const; ftype f_aniso( const Coord_reci_orth& rfl ) const; ftype rho_iso( const ftype& d2 ) const; ftype rho_aniso( const Coord_orth& uvw ) const; }; } // namespace clipper #endif clipper-2.1/clipper/core/map_utils.cpp0000644000374100011300000001015010363703537015020 00000000000000/* map_utils.cpp: implementation file for crystal maps */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "map_utils.h" #include "xmap.h" #include "nxmap.h" #include namespace clipper { /*! The index is sorted in place \params map The map to be sorted. \params index The list of indices to sort. */ template void Map_index_sort::sort_increasing( const M& map, std::vector& index ) { std::sort( index.begin(), index.end(), Compare_density( map ) ); } /*! The index is sorted in place \params map The map to be sorted. \params index The list of indices to sort. */ template void Map_index_sort::sort_decreasing( const M& map, std::vector& index ) { std::sort( index.begin(), index.end(), Compare_density( map ) ); std::reverse( index.begin(), index.end() ); } // compile templates //template Map_stats::Map_stats( const Xmap& map ); //template Map_stats::Map_stats( const Xmap& map ); //template Map_stats::Map_stats( const NXmap& map ); //template Map_stats::Map_stats( const NXmap& map ); template void Map_index_sort::sort_increasing >( const Xmap& map, std::vector& index ); template void Map_index_sort::sort_decreasing >( const Xmap& map, std::vector& index ); template void Map_index_sort::sort_increasing >( const Xmap& map, std::vector& index ); template void Map_index_sort::sort_decreasing >( const Xmap& map, std::vector& index ); template void Map_index_sort::sort_increasing >( const Xmap& map, std::vector& index ); template void Map_index_sort::sort_decreasing >( const Xmap& map, std::vector& index ); template void Map_index_sort::sort_increasing >( const Xmap& map, std::vector& index ); template void Map_index_sort::sort_decreasing >( const Xmap& map, std::vector& index ); } // namespace clipper clipper-2.1/clipper/core/spacegroup_data.h0000644000374100011300000000562110363703537015640 00000000000000/* file lib/spacegroup_data.h Header file for spacegroup data tables */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA /* some code & data converted from CCP4 library symlib.f (various authors) */ #ifndef CLIPPER_SPACEGROUP_DATA #define CLIPPER_SPACEGROUP_DATA namespace clipper { // data namespace namespace data { // ASU function pointer typedef bool (*ASUfn)( const int&, const int&, const int& ); // Spacegroup data record struct SGdata { int sghash; const char* hall; const char* hm; char ext; int num; }; // Laue group data record struct LGdata { int lghash; ASUfn asufn; const char* lgname; }; // data tables extern LGdata lgdata[]; extern int lgdata_size; extern SGdata sgdata[]; extern int sgdata_size; } // namespace data } // namespace clipper #endif clipper-2.1/clipper/core/rotation.cpp0000644000374100011300000002624610463653243014676 00000000000000/* rotation.cpp: fundamental data types for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "rotation.h" namespace clipper { template Euler::Euler( const Rotation& rot ) { int r1, r2, r3, s; params( r1, r2, r3, s ); ftype ca, cb, cg, sa, sb, sg; if ( r1 == r3 ) { ftype w, x, y, z; w = rot.w(); x = y = z = 0.0; if ( r1==2 && r2==1 && r3==2 ) { x= rot.x(); y= rot.y(); z= rot.z(); } else if ( r1==1 && r2==0 && r3==1 ) { x= rot.z(); y= rot.x(); z= rot.y(); } else if ( r1==0 && r2==2 && r3==0 ) { x= rot.y(); y= rot.z(); z= rot.x(); } else if ( r1==2 && r2==0 && r3==2 ) { x=-rot.y(); y= rot.x(); z= rot.z(); } else if ( r1==1 && r2==2 && r3==1 ) { x=-rot.x(); y= rot.z(); z= rot.y(); } else if ( r1==0 && r2==1 && r3==0 ) { x=-rot.z(); y= rot.y(); z= rot.x(); } else Message::message( Message_fatal( "Rotation::euler() type invalid" ) ); cb = 1.0 - 2.0 * (x*x + y*y); sb = 2.0 * sqrt( (x*x + y*y) * (w*w + z*z) ); if ( sb > 0.0001 ) { ca = 2.0 * (x*z + w*y); sa = 2.0 * (y*z - w*x); cg = 2.0 * (w*y - x*z); sg = 2.0 * (y*z + w*x); } else { ca = 1.0; sa = 0.0; cg = cb; sg = 2.0*(y*z + w*x); } if ( s==1 ) (*this) = Euler( atan2(sg,cg), atan2(sb,cb), atan2(sa,ca) ); else (*this) = Euler( atan2(sa,ca), atan2(sb,cb), atan2(sg,cg) ); } else { ftype w, x, y, z; w = rot.w(); x = y = z = 0.0; if ( r1==0 && r2==1 && r3==2 ) { x= rot.x(); y= rot.y(); z= rot.z(); } else if ( r1==2 && r2==0 && r3==1 ) { x= rot.z(); y= rot.x(); z= rot.y(); } else if ( r1==1 && r2==2 && r3==0 ) { x= rot.y(); y= rot.z(); z= rot.x(); } else if ( r1==1 && r2==0 && r3==2 ) { x=-rot.y(); y= rot.x(); z= rot.z(); } else if ( r1==0 && r2==2 && r3==1 ) { x=-rot.x(); y= rot.z(); z= rot.y(); } else if ( r1==2 && r2==1 && r3==0 ) { x=-rot.z(); y= rot.y(); z= rot.x(); } else Message::message( Message_fatal( "Rotation::euler() type invalid" ) ); if ( s == 0 ) x = -x; sa = 2.0 * ( x*y + z*w ); ca = x*x - y*y - z*z + w*w; sb = 2.0 * ( y*w - x*z ); cb = sqrt( 1.0 - sb*sb ); sg = 2.0 * ( z*y + x*w ); cg = z*z - x*x - y*y + w*w; if ( ( 1 + r1 - r2 + s ) % 3 == 0 ) sg = -sg; (*this) = Euler( atan2(sg,cg), atan2(sb,cb), atan2(sa,ca) ); } } template Rotation Euler::rotation() const { int r1, r2, r3, s; params( r1, r2, r3, s ); ftype x[3]; x[0] = x[1] = x[2] = 0.0; x[r1] = sin(0.5*alpha()); Rotation rot1( cos(0.5*alpha()), x[0], x[1], x[2] ); x[0] = x[1] = x[2] = 0.0; x[r2] = sin(0.5*beta() ); Rotation rot2( cos(0.5*beta() ), x[0], x[1], x[2] ); x[0] = x[1] = x[2] = 0.0; x[r3] = sin(0.5*gamma()); Rotation rot3( cos(0.5*gamma()), x[0], x[1], x[2] ); if ( s == 1 ) return rot1*(rot2*rot3); else return rot3*(rot2*rot1); } template String Euler::format() const { char xyz[] = {'X','Y','Z'}; char rs[] = {'r','s'}; int r1, r2, r3, s; params( r1, r2, r3, s ); return String("Euler") + xyz[r1] + xyz[r2] + xyz[r3] + rs[s] + " = ("+String(Util::rad2d(alpha()))+","+String(Util::rad2d(beta()))+","+String(Util::rad2d(gamma()))+")"; } template void Euler::params( int& r1, int& r2, int& r3, int& s ) { r1 = ( ((T>>3)&3) ) % 3; r2 = ( r1 + ((T>>2)&1) + 1 ) % 3; r3 = ( r2 + ((T>>1)&1) + 1 ) % 3; s = ( T&1 ); } String Euler_ccp4::format() const { return "Euler = ("+String(Util::rad2d(alpha()))+","+String(Util::rad2d(beta()))+","+String(Util::rad2d(gamma()))+")"; } String Polar_ccp4::format() const { return "Polar = ("+String(Util::rad2d(omega()))+","+String(Util::rad2d(phi()))+","+String(Util::rad2d(kappa()))+")"; } Rotation::Rotation( const Euler_ccp4& euler ) { // not optimised ftype a1 = 0.5 * euler.alpha(); ftype a2 = 0.5 * euler.beta(); ftype a3 = 0.5 * euler.gamma(); Rotation r1( cos(a1), 0.0, 0.0, sin(a1) ); Rotation r2( cos(a2), 0.0, sin(a2), 0.0 ); Rotation r3( cos(a3), 0.0, 0.0, sin(a3) ); *this = r3*(r2*r1); } Rotation::Rotation( const Polar_ccp4& polar ) { w_ = cos( 0.5 * polar.kappa() ); x_ = sin( 0.5 * polar.kappa() ) * cos( polar.phi() ) * sin( polar.omega() ); y_ = sin( 0.5 * polar.kappa() ) * sin( polar.phi() ) * sin( polar.omega() ); z_ = sin( 0.5 * polar.kappa() ) * cos( polar.omega() ); } Rotation::Rotation( const Mat33<>& m ) { ftype tr = m(0,0) + m(1,1) + m(2,2) + 1.0; // check the diagonal if ( tr > 1.0e-8 ) { ftype s( sqrt(tr) ); w_ = s * 0.5; s = 0.5 / s; x_ = s * ( m(2,1) - m(1,2) ); y_ = s * ( m(0,2) - m(2,0) ); z_ = s * ( m(1,0) - m(0,1) ); } else { if ( m(0,0) > m(1,1) && m(0,0) > m(2,2) ) { ftype s( sqrt(1.0 + m(0,0) - m(1,1) - m(2,2) ) ); x_ = 0.5 * s; if ( s != 0.0 ) s = 0.5 / s; w_ = s * ( m(2,1) - m(1,2) ); y_ = s * ( m(0,1) + m(1,0) ); z_ = s * ( m(0,2) + m(2,0) ); } else if ( m(1,1) > m(2,2) ) { ftype s( sqrt(1.0 + m(1,1) - m(2,2) - m(0,0) ) ); y_ = 0.5 * s; if ( s != 0.0 ) s = 0.5 / s; w_ = s * ( m(0,2) - m(2,0) ); z_ = s * ( m(1,2) + m(2,1) ); x_ = s * ( m(1,0) + m(0,1) ); } else { ftype s( sqrt(1.0 + m(2,2) - m(0,0) - m(1,1) ) ); z_ = 0.5 * s; if ( s != 0.0 ) s = 0.5 / s; w_ = s * ( m(1,0) - m(0,1) ); x_ = s * ( m(2,0) + m(0,2) ); y_ = s * ( m(2,1) + m(1,2) ); } } } /*! The normalisation is performed in-place. If a rotation becomes significantly denormalised, the conversion methods will fail. Therefore it may be safer to call this before a conversion. */ const Rotation& Rotation::norm() { ftype s = w_*w_+x_*x_+y_*y_+z_*z_; if ( s < 1.0e-12 ) { w_ = 1.0; x_ = y_ = z_ = 0.0; } else { s = 1.0/sqrt(s); w_ *= s; x_ *= s; y_ *= s; z_ *= s; } return *this; } /*! If beta ~= 0, then alpha is set to zero. \return The Euler_ccp4 angles. */ Euler_ccp4 Rotation::euler_ccp4() const { ftype ca, cb, cg, sa, sb, sg; cb = 1.0 - 2.0 * (x_*x_ + y_*y_); sb = 2.0 * sqrt( (x_*x_ + y_*y_) * (w_*w_ + z_*z_) ); if ( sb > 0.0001 ) { ca = 2.0 * (x_*z_ + w_*y_); sa = 2.0 * (y_*z_ - w_*x_); cg = 2.0 * (w_*y_ - x_*z_); sg = 2.0 * (y_*z_ + w_*x_); } else { ca = 1.0; sa = 0.0; cg = cb; sg = 2.0*(y_*z_ + w_*x_); } return Euler_ccp4( atan2(sa,ca), atan2(sb,cb), atan2(sg,cg) ); } /*! If omega ~= 0, then phi is set to zero. \return The Polar_ccp4 angles. */ Polar_ccp4 Rotation::polar_ccp4() const { ftype om, ph, ka; om = ph = ka = 0.0; if ( fabs(w_) < 0.999999 ) { ftype r = sqrt( x_*x_ + y_*y_ ); om = atan2( r, z_ ); if ( r > 0.000001 ) ph = atan2( y_, x_ ); ka = 2.0*acos( w_ ); } return Polar_ccp4( om, ph, ka ); } /*! The resulting rotation matrix would commonly be used to construct a clipper::RTop_orth. \return The rotation matrix. */ Mat33<> Rotation::matrix() const { ftype xx( 2.0*x_*x_ ); ftype yy( 2.0*y_*y_ ); ftype zz( 2.0*z_*z_ ); ftype xy( 2.0*x_*y_ ); ftype yz( 2.0*y_*z_ ); ftype xz( 2.0*z_*x_ ); ftype wx( 2.0*w_*x_ ); ftype wy( 2.0*w_*y_ ); ftype wz( 2.0*w_*z_ ); return Mat33<>( 1.0-yy-zz, xy-wz, xz+wy, xy+wz, 1.0-xx-zz, yz-wx, xz-wy, yz+wx, 1.0-xx-yy ); } /*! Note: This multiplication operator combines rotations in left-to-right order, rather than the right-to-left order used for matrices. Thus, the rotation which arises from applying rotation r1 followed by rotation r2 is given by r1*r2. Similarly, the rotation which arises from applying rotation r1 followed by rotation r2 and rotation r3 is given by (r1*r2)*r3. */ /* THE FOLLOWING DOCUMENTATION IS WRONG! IT DESCRIBES THE INTENDED BEHAVIOUR, NOT THE IMPLEMENTED BEHAVIOUR. Note: This multiplication operator combines rotations in reverse order, as if they were matrices. Thus, the rotation which arises from applying rotation r1 followed by rotation r2 is given by r2*r1. Similarly, the rotation which arises from applying rotation r1 followed by rotation r2 and rotation r3 is given by r3*(r2*r1). */ Rotation operator* ( const Rotation& r1, const Rotation& r2 ) { return Rotation( r1.w_*r2.w_ - r1.x_*r2.x_ - r1.y_*r2.y_ - r1.z_*r2.z_, r1.w_*r2.x_ + r1.x_*r2.w_ + r1.z_*r2.y_ - r1.y_*r2.z_, r1.w_*r2.y_ + r1.y_*r2.w_ + r1.x_*r2.z_ - r1.z_*r2.x_, r1.w_*r2.z_ + r1.z_*r2.w_ + r1.y_*r2.x_ - r1.x_*r2.y_ ); } String Rotation::format() const { return "Quaternion wxyz = ("+String(w_)+","+String(x_)+","+String(y_)+","+String(z_)+")"; } template class Euler< 0>; template class Euler< 1>; template class Euler< 2>; template class Euler< 3>; template class Euler< 4>; template class Euler< 5>; template class Euler< 6>; template class Euler< 7>; template class Euler< 8>; template class Euler< 9>; template class Euler<10>; template class Euler<11>; template class Euler<12>; template class Euler<13>; template class Euler<14>; template class Euler<15>; template class Euler<16>; template class Euler<17>; template class Euler<18>; template class Euler<19>; template class Euler<20>; template class Euler<21>; template class Euler<22>; template class Euler<23>; } // namespace clipper clipper-2.1/clipper/core/clipper_stats.cpp0000644000374100011300000001245010777707757015725 00000000000000/* clipper_stats.cpp: implementation file for clipper helper functions */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "clipper_stats.h" namespace clipper { ftype Histogram::sum() const { ftype s = 0.0; for ( int i = 0; i < data.size(); i++ ) s += data[i]; return s; } ftype Histogram::y( const ftype& x ) const { ftype xi = indexf( truncate( x ) ) - 0.5; int i = Util::intf( xi ); ftype xf = xi - ftype( i ); ftype y0 = ( i >= 0 ) ? data[i ] : -data.front(); ftype y1 = ( i+1 < size() ) ? data[i+1] : -data.back(); return ( (1.0-xf)*y0 + xf*y1 ); } const Histogram& Histogram::operator += ( const Histogram& h ) { if ( data.size() != h.data.size() ) Message::message( Message_fatal("Histogram: sum of unequal histograms") ); for ( int i = 0; i < data.size(); i++ ) data[i] += h.data[i]; return (*this); } // generic ordinal void Generic_ordinal::init( const Range& range, const int num_ranges ) { nranges = ftype( num_ranges ); hist.clear(); hist.resize( num_ranges + 1, 0.0 ); range_ = range; } void Generic_ordinal::init( const std::vector& values, const int num_ranges ) { Range range; for ( int i = 0; i < values.size(); i++ ) range.include( values[i] ); init( range, num_ranges ); for ( int i = 0; i < values.size(); i++ ) accumulate( values[i] ); prep_ordinal(); } ftype Generic_ordinal::ordinal( const ftype& value ) const { ftype r = ( value - range_.min() ) / ( range_.max() - range_.min() ); r = Util::bound( 0.0, r, 0.99999 ) * nranges; int i = int( r ); r -= floor( r ); return (1.0-r)*hist[i] + r*hist[i+1]; } void Generic_ordinal::accumulate( const ftype& value ) { ftype r = ( value - range_.min() ) / ( range_.max() - range_.min() ); r = Util::bound( 0.0, r, 0.99999 ) * nranges; int i = int( r ); hist[i+1] += 1.0; } void Generic_ordinal::accumulate( const ftype& value, const ftype& weight ) { ftype r = ( value - range_.min() ) / ( range_.max() - range_.min() ); r = Util::bound( 0.0, r, 0.99999 ) * nranges; int i = int( r ); hist[i+1] += weight; } void Generic_ordinal::prep_ordinal() { for ( int i = 1; i < hist.size(); i++ ) hist[i] += hist[i-1]; for ( int i = 0; i < hist.size(); i++ ) hist[i] = hist[i] / hist.back(); } void Generic_ordinal::invert() { std::vector hinv( hist.size() ); hinv[0] = range_.min(); hinv[hist.size()-1] = range_.max(); for ( int i = 1; i < hist.size()-1; i++ ) { ftype target = ftype(i)/nranges; ftype guess = 0.5 * ( range_.max() + range_.min() ); ftype step = 0.5 * ( range_.max() - range_.min() ); for ( int j = 0; j < 10; j++ ) { if ( ordinal( guess ) > target ) guess -= step; else guess += step; step *= 0.5; } hinv[i] = Util::bound( range_.min(), guess, range_.max() ); } range_ = Range( 0.0, 1.0 ); hist = hinv; } // deprecated fns void Generic_ordinal::init( const int num_ranges ) { nranges = ftype( num_ranges ); hist.clear(); hist.resize( num_ranges + 1, 0.0 ); } void Generic_ordinal::add_pass_1( const ftype& value ) { range_.include( value ); } void Generic_ordinal::add_pass_2( const ftype& value ) { accumulate( value ); } } // namespace clipper clipper-2.1/clipper/core/xmap.h0000644000374100011300000007611510776420424013451 00000000000000/*! \file lib/xmap.h Header file for crystal maps */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_XMAP #define CLIPPER_XMAP #include "fftmap.h" #include "fftmap_sparse.h" #include "derivs.h" namespace clipper { class Xmap_cacheobj { public: class Key { public: Key( const Spgr_descr& spgr_descr, const Grid_sampling& grid ) : spgr_descr_(spgr_descr), grid_sampling_(grid) {} const Spgr_descr& spgr_descr() const { return spgr_descr_; } const Grid_sampling& grid_sampling() const { return grid_sampling_; } private: Spgr_descr spgr_descr_; Grid_sampling grid_sampling_; }; Xmap_cacheobj( const Key& xmap_cachekey ); //!< construct entry bool matches( const Key& xmap_cachekey ) const; //!< compare entry String format() const; //!< string description // data Key key; //!< key Grid_sampling xtl_grid; //!< grid for the cell Grid_range asu_grid; //!< grid for the ASU Grid_range map_grid; //!< grid for the ASU, plus border int nsym; // number of symops std::vector asu; //!< ASU flag array std::vector isymop; //!< Integerised symops std::vector du, dv, dw; //!< symmetry grid shifts to index Array2d symperm; //!< Perumtation matrix of symops Mat33<> mat_grid_orth; //!< for backward compatibility static Mutex mutex; //!< thread safety }; //! Xmap_base: base for crystallographic map class /*! The crystallographic map class stores a map of arbitrary data type. Its main difference from a 3-d array is that the data extent appears to be infinite, and yet internally only a unique ASU is stored. Iterators provide efficient access to data. This base contains everything except the data, which is templated in the derived type Xmap */ class Xmap_base { public: enum FFTtype { Default, Normal, Sparse }; //!< FFT backend selection //! test if object has been initialised bool is_null() const; //! get the cell const Cell& cell() const { return cell_; } //! get the spacegroup const Spacegroup& spacegroup() const { return spacegroup_; } //! get the cell grid const Grid_sampling& grid_sampling() const { return grid_sam_; } //! get the ASU grid const Grid_range& grid_asu() const { return cacheref.data().asu_grid; } //! map coordinate from index /*! \param index The index. \return The corresponding grid coordinate. */ inline Coord_grid coord_of( const int& index ) const { return cacheref.data().map_grid.deindex( index ); } //! map index from coordinate /*! This does not check symmetry equivalents. \param coord The coordinate. \return The index, or -1 if it does not exist. */ inline int index_of( const Coord_grid& coord ) const { if ( cacheref.data().asu_grid.in_grid( coord ) ) { const int i = cacheref.data().map_grid.index( coord ); if ( asu[ i ] == 0 ) return i; } return -1; } //! function to pick right cell repeat for any grid coord Coord_grid to_map_unit( const Coord_grid& pos ) const { return pos.unit( grid_sam_ ); } //! return the orthogonal-to-grid coordinate operator (translation is zero) const RTop<>& operator_orth_grid() const { return rt_orth_grid; } //! return the grid-to-orthogonal coordinate operator (translation is zero) const RTop<>& operator_grid_orth() const { return rt_grid_orth; } //! convert map coordinate to orthogonal /*! \param cm The grid coordinate to be converted. \return The equivalent orthogonal coordinate. */ inline Coord_orth coord_orth( const Coord_map& cm ) const { return Coord_orth( rt_grid_orth.rot()*cm ); } //! convert orthogonal coordinate to map /*! \param co The orthogonal coordinate to be converted. \return The equivalent grid coordinate. */ inline Coord_map coord_map( const Coord_orth& co ) const { return Coord_map ( rt_orth_grid.rot()*co ); } //! (This method is for compatibility with NXmap - it always returns true) bool in_map( const Coord_grid& pos ) const { return true; } //! (This method is for compatibility with NXmap - it always returns true) template bool in_map( const Coord_map& cm ) const { return true; } //! get multiplicity of a map grid point int multiplicity( const Coord_grid& pos ) const; //! Map reference base class /*! This is a reference to an Map. It forms a base class for index-like and coordinate-like Map references. If you write a method which will work with either, then specify this instead of either of the derived classed. \internal */ class Map_reference_base { public: //! return the parent Xmap inline const Xmap_base& base_xmap() const { return *map_; } //! Get the index into the map data array inline const int& index() const { return index_; } //! Check for end of map bool last() const { return ( index_ >= map_->map_grid.size() ); } protected: //! pointer to map for which this Map_reference_index is defined const Xmap_base* map_; //! integer index_ into map data array int index_; }; //! Map reference with index-like behaviour /*! This is a reference to a map coordinate. It behaves like a simple index into the map, but can be easily converted into a coordinate as and when required. It also implements methods for iterating through the unique portion of a map. It is very compact, but coord() involves some overhead and loses any information concerning symmetry equivelents. \note The following methods are inherited from Map_reference_base but are documented here for convenience: base_xmap(), index(), last(). */ class Map_reference_index : public Map_reference_base { public: //! Null constructor Map_reference_index() {} //! Constructor: takes parent map explicit Map_reference_index( const Xmap_base& map ) { map_ = ↦ index_=0; next(); } //! Constructor: takes parent map and coord Map_reference_index( const Xmap_base& map, const Coord_grid& pos ) { map_ = ↦ int sym; map_->find_sym( pos, index_, sym ); } //! Get current grid coordinate inline Coord_grid coord() const { return map_->map_grid.deindex(index_); } //! Get current value of orthogonal coordinate inline const Coord_orth coord_orth() const { return Coord_orth( map_->rt_grid_orth.rot() * coord().coord_map() ); } //! Set current value of coordinate - optimised for nearby coords inline Map_reference_index& set_coord( const Coord_grid& pos ) { int sym; map_->find_sym( pos, index_, sym ); return *this; } //! Simple increment inline Map_reference_index& next() { do { index_++; if ( last() ) break; } while ( map_->asu[index_] != 0 ); return *this; } //! Index of neighbouring point /* Use for e.g. peak search. Valid for -1 <= du/dv/dw <= 1 only. \param du/dv/dw Coordinate offset. \return Map index. */ inline int index_offset(const int& du,const int& dv,const int& dw) const { int i = index_ + du*map_->du[0] + dv*map_->dv[0] + dw*map_->dw[0]; if ( map_->asu[i] != 0 ) { i = map_->map_grid.index( map_->to_map_unit( map_->map_grid.deindex(i).transform( map_->isymop[map_->asu[i]-1] ) ) ); } return i; } // inherited functions listed for documentation purposes //-- const Xmap_base& base_xmap() const; //-- const int& index() const; //-- bool last() const; }; //! Map reference with coordinate-like behaviour /*! This is a reference to a map coordinate. It behaves like a coordinate, but also stores the index of the corresponding point in the map, and the symmetry operator required to get there. It also implements methods for iterating through the a map. Since the current coordinate and symmetry are stored, coord() is fast. However, it requires 1 pointer and 5 words of storage. \note The following methods are inherited from Map_reference_base but are documented here for convenience: base_xmap(), index(), last(). */ class Map_reference_coord : public Map_reference_base { public: //! Null constructor Map_reference_coord() {} //! Constructor: takes parent map explicit Map_reference_coord( const Xmap_base& map ) { map_ = ↦ index_ = 0; next(); } //! Constructor: takes parent map and coord Map_reference_coord( const Xmap_base& map, const Coord_grid& pos ) { map_ = ↦ pos_ = pos; map_->find_sym( pos_, index_, sym_ ); } //! Get current value of coordinate inline const Coord_grid& coord() const { return pos_; } //! Get current value of orthogonal coordinate inline const Coord_orth coord_orth() const { return Coord_orth( map_->rt_grid_orth.rot() * coord().coord_map() ); } //! Get current symmetry operator inline const int& sym() const { return sym_; } //! Set current value of coordinate - optimised for nearby coords Map_reference_coord& set_coord( const Coord_grid& pos ); //! Simple increment /*! Use of this function resets the stored coordinate and sym */ inline Map_reference_coord& next() { sym_ = 0; do { index_++; if ( last() ) break; } while ( map_->asu[index_] != 0 ); pos_ = map_->map_grid.deindex(index_); return *this; } // Increment u,v,w inline Map_reference_coord& next_u() { pos_.u()++; index_ += map_->du[sym_]; if (map_->asu[index_] != 0) edge(); return *this; } //!< increment u inline Map_reference_coord& next_v() { pos_.v()++; index_ += map_->dv[sym_]; if (map_->asu[index_] != 0) edge(); return *this; } //!< increment v inline Map_reference_coord& next_w() { pos_.w()++; index_ += map_->dw[sym_]; if (map_->asu[index_] != 0) edge(); return *this; } //!< increment w inline Map_reference_coord& prev_u() { pos_.u()--; index_ -= map_->du[sym_]; if (map_->asu[index_] != 0) edge(); return *this; } //!< increment u inline Map_reference_coord& prev_v() { pos_.v()--; index_ -= map_->dv[sym_]; if (map_->asu[index_] != 0) edge(); return *this; } //!< decrement v inline Map_reference_coord& prev_w() { pos_.w()--; index_ -= map_->dw[sym_]; if (map_->asu[index_] != 0) edge(); return *this; } //!< decrement w //! Assignment operator from a coord inline Map_reference_coord& operator =( const Coord_grid& pos ) { return set_coord( pos ); } // inherited functions listed for documentation purposes //-- const Xmap_base& base_xmap() const; //-- const int& index() const; //-- bool last() const; protected: //! Current symop int sym_; //! Current coord Coord_grid pos_; //! Reset index for a different symop when we hit the map border void edge(); }; //! return a Map_reference_index for this map Map_reference_index first() const { return Map_reference_index( *this ); } //! return a Map_reference_coord for this map Map_reference_coord first_coord() const { return Map_reference_coord( *this ); } //! set/get default backend type static FFTtype& default_type() { return default_type_; } protected: ObjectCache::Reference cacheref; //!< object cache reference const unsigned char* asu; //!< fast access ptr const Isymop* isymop; //!< fast access ptr const int* du; //!< fast access ptr const int* dv; //!< fast access ptr const int* dw; //!< fast access ptr Grid_range asu_grid; //!< fast access copy Grid_range map_grid; //!< fast access copy int nsym; //!< fast access copy Cell cell_; //!< unit cell Spacegroup spacegroup_; //!< spacegroup Grid_sampling grid_sam_; //!< grid for the whole cell RTop<> rt_orth_grid; //!< orth->grid operator RTop<> rt_grid_orth; //!< grid->orth operator //! Null constructor, for later initialisation Xmap_base(); //! initialiser void init( const Spacegroup& spacegroup, const Cell& cell, const Grid_sampling& grid_sam ); inline void find_sym( const Coord_grid& base, int& index, int& sym ) const; void asu_error( const Coord_grid& pos ) const; static FFTtype default_type_; //!< default backend type friend class Xmap_base::Map_reference_base; friend class Xmap_base::Map_reference_index; friend class Xmap_base::Map_reference_coord; }; //! Xmap: actual crystallographic map class /*! The crystallographic map class stores a map of arbitrary data type. Its main difference from a 3-d array is that the data extent appears to be infinite, and yet internally only a unique ASU is stored. Iterators provide efficient access to data. This is derived from Xmap_base, and adds the templatised data itself and the methods which deal with it. \note The following methods are inherited from Xmap_base but are documented here for convenience: cell(), spacegroup(), grid_sampling(), grid_asu(), in_asu(), multiplicity(), to_map_unit(), first(), first_coord(). */ template class Xmap : public Xmap_base { public: //! Null constructor, for later initialisation Xmap() {} //! constructor: from spacegroup, cell, and grid Xmap( const Spacegroup& spacegroup, const Cell& cell, const Grid_sampling& grid_sam ) { init( spacegroup, cell, grid_sam ); } //! initialiser: from spacegroup, cell, and grid void init( const Spacegroup& spacegroup, const Cell& cell, const Grid_sampling& grid_sam ) { Xmap_base::init( spacegroup, cell, grid_sam ); list.resize( cacheref.data().asu.size() ); } //! get data by Map_reference_index inline const T& operator[] (const Xmap_base::Map_reference_index& ix) const { return list[ix.index()]; } //! set data by Map_reference_index inline T& operator[] (const Xmap_base::Map_reference_index& ix) { return list[ix.index()]; } //! get data by Map_reference_coord inline const T& operator[] (const Xmap_base::Map_reference_coord& ix) const { return list[ix.index()]; } //! set data by Map_reference_coord inline T& operator[] (const Xmap_base::Map_reference_coord& ix) { return list[ix.index()]; } //! get a density value for an arbitrary position const T& get_data( const Coord_grid& pos ) const; //! set a density value for an arbitrary position void set_data( const Coord_grid& pos, const T& val ); //! get data by index (not recommended) inline const T& get_data( const int& index ) const; //! set data by index (not recommended) bool set_data( const int& index, const T& val ); //! get map value for fractional coord using supplied interpolator template T interp( const Coord_frac& pos ) const; //! get map value and grad for fractional coord using supplied interpolator template void interp_grad( const Coord_frac& pos, T& val, Grad_frac& grad ) const; //! get map value and curv for fractional coord using supplied interpolator template void interp_curv( const Coord_frac& pos, T& val, Grad_frac& grad, Curv_frac& curv ) const; //! get map value for map coord using supplied interpolator template T interp( const Coord_map& pos ) const; //! get map value and grad for map coord using supplied interpolator template void interp_grad( const Coord_map& pos, T& val, Grad_map& grad ) const; //! get map value and curv for map coord using supplied interpolator template void interp_curv( const Coord_map& pos, T& val, Grad_map& grad, Curv_map& curv ) const; //! FFT from reflection list to map template void fft_from( const H& fphidata, const FFTtype type = Default ); //! FFT from map to reflection list template void fft_to ( H& fphidata, const FFTtype type = Default ) const; // inherited functions listed for documentation purposes //-- const Cell& cell() const; //-- const Spacegroup& spacegroup() const; //-- const Grid_sampling& grid_sampling() const; //-- const Grid_range& grid_asu() const; //-- inline Coord_grid coord_of( const int& index ) const; //-- inline int index_of( const Coord_grid& coord ) const; //-- const int multiplicity( const Coord_grid& pos ) const; //-- const Coord_grid to_map_unit( const Coord_grid& pos ) const; //-- const Map_reference_index first() const; //-- const Map_reference_coord first_coord() const; //! assignment operator: assigns a single value to the whole map const T& operator =( const T& value ); //! add another map to this one const Xmap& operator +=( const Xmap& other ); //! subtract another map from this one const Xmap& operator -=( const Xmap& other ); private: std::vector list; }; // implementations void Xmap_base::find_sym( const Coord_grid& base, int& index, int& sym ) const { // first deal with first symop, and cache for highest performance Coord_grid rot = to_map_unit( base ); if ( asu_grid.in_grid( rot ) ) { index = map_grid.index( rot ); if ( asu[ index ] == 0 ) { sym = 0; } else { sym = asu[ index ] - 1; index = map_grid.index( to_map_unit( base.transform(isymop[sym]) ) ); } } else { // now deal with other symops for ( sym = 1; sym < nsym; sym++ ) { rot = to_map_unit( base.transform( isymop[sym] ) ); if ( asu_grid.in_grid( rot ) ) { index = map_grid.index( rot ); if ( asu[ index ] == 0 ) return; } } index = 0; // redundent, to avoid compiler warnings asu_error( base ); } return; } /*! Accessing the data by coordinate, rather than by Map_reference_index or Map_reference_coord, involves a symmetry lookup and is therefore slow. Avoid using these methods when you can. */ template const T& Xmap::get_data( const Coord_grid& pos ) const { int index, sym; find_sym( pos, index, sym ); return list[ index ]; } /*! Accessing the data by coordinate, rather than by Map_reference_index or Map_reference_coord, involves a symmetry lookup and is therefore slow. Avoid using these methods when you can. */ template void Xmap::set_data( const Coord_grid& pos, const T& val ) { int index, sym; find_sym( pos, index, sym ); list[ index ] = val; } /*! Accessing the data by index, rather than by Map_reference_index or Map_reference_coord, is generally to be avoided since the indices do not start at zero and do not increase contiguously. These methods are only useful when a large number of references into a map must be stored, e.g. for sorting into density order. */ template const T& Xmap::get_data( const int& index ) const { return list[index]; } /*! Accessing the data by index, rather than by Map_reference_index or Map_reference_coord, is generally to be avoided since the indices do not start at zero and do not increase contiguously. These methods are only useful when a large number of references into a map must be stored, e.g. for sorting into density order. \return true if data was set, i.e. index is valid. */ template bool Xmap::set_data( const int& index, const T& val ) { if ( index >= 0 && index < list.size() ) if ( asu[index] == 0 ) { list[index] = val; return true; } return false; } /*! The value of the map at the desired non-grid fractional coordinate are calculated using the supplied interpolator template. \code Coord_frac f( u, v, w ); y = xmap.interp( f ); \endcode \param pos The fractional coord at which the density is to be calcuated. \return The value of the density at that point. */ template template T Xmap::interp( const Coord_frac& pos ) const { T val; I::interp( *this, pos.coord_map( grid_sam_ ), val ); return val; } /*! The value of the map at the desired non-grid fractional coordinate and its gradient are calculated using the supplied interpolator template. \param pos The fractional coord at which the density is to be calcuated. \param val The value of the density at that point. \param grad The interpolated gradient vector with respect to the fractional coordinates (see Cell::coord_orth). */ template template void Xmap::interp_grad( const Coord_frac& pos, T& val, Grad_frac& grad ) const { Grad_map g; I::interp_grad( *this, pos.coord_map( grid_sam_ ), val, g ); grad = g.grad_frac( grid_sam_ ); } /*! The value of the map at the desired non-grid fractional coordinate and its gradient and curvature are calculated using the supplied interpolator template. e.g. \param pos The fractional coord at which the density is to be calcuated. \param val The value of the density at that point. \param grad The interpolated gradient vector with respect to the fractional coordinates (see Cell::coord_orth). \param curv The interpolated curvature matrix with respect to the fractional coordinates (see Cell::coord_orth). */ template template void Xmap::interp_curv( const Coord_frac& pos, T& val, Grad_frac& grad, Curv_frac& curv ) const { Grad_map g; Curv_map c; I::interp_curv( *this, pos.coord_map( grid_sam_ ), val, g, c ); grad = g.grad_frac( grid_sam_ ); curv = c.curv_frac( grid_sam_ ); } /*! The value of the map at the desired non-grid map coordinate are calculated using the supplied interpolator template. \code Coord_map m( u, v, w ); y = xmap.interp( m ); \endcode \param pos The map coord at which the density is to be calcuated. \return The value of the density at that point. */ template template T Xmap::interp( const Coord_map& pos ) const { T val; I::interp( *this, pos, val ); return val; } /*! The value of the map at the desired non-grid map coordinate and its gradient are calculated using the supplied interpolator template. \param pos The map coord at which the density is to be calcuated. \param val The value of the density at that point. \param grad The interpolated gradient vector with respect to the map coordinates (see Cell::coord_orth). */ template template void Xmap::interp_grad( const Coord_map& pos, T& val, Grad_map& grad ) const { I::interp_grad( *this, pos, val, grad ); } /*! The value of the map at the desired non-grid map coordinate and its gradient and curvature are calculated using the supplied interpolator template. e.g. \param pos The map coord at which the density is to be calcuated. \param val The value of the density at that point. \param grad The interpolated gradient vector with respect to the map coordinates (see Cell::coord_orth). \param curv The interpolated curvature matrix with respect to the map coordinates (see Cell::coord_orth). */ template template void Xmap::interp_curv( const Coord_map& pos, T& val, Grad_map& grad, Curv_map& curv ) const { I::interp_curv( *this, pos, val, grad, curv ); } /*! An FFT is calculated using the provided reflection list of F_phi, and used to fill this map. The reflection list is unchanged. \param fphidata The reflection data list to use */ template template void Xmap::fft_from( const H& fphidata, const FFTtype type ) { if ( type == Sparse || ( type == Default && default_type() == Sparse ) ) { // make a sparse fftmap FFTmap_sparse_p1_hx fftmap( grid_sampling() ); // copy from reflection data typename H::HKL_reference_index ih; ffttype f, phi0, phi1; int sym; for ( ih = fphidata.first_data(); !ih.last(); fphidata.next_data( ih ) ) { f = fphidata[ih].f(); if ( f != 0.0 ) { phi0 = fphidata[ih].phi(); const HKL& hkl = ih.hkl(); fftmap.set_hkl( hkl, std::complex( f*cos(phi0), f*sin(phi0) ) ); for ( sym = 1; sym < spacegroup_.num_primops(); sym++ ) { phi1 = phi0 + hkl.sym_phase_shift( spacegroup_.symop(sym) ); fftmap.set_hkl( hkl.transform( isymop[sym] ), std::complex( f*cos(phi1), f*sin(phi1) ) ); } } } // require output ASU coords for ( Map_reference_index ix = first(); !ix.last(); ix.next() ) fftmap.require_real_data( ix.coord() ); // do fft fftmap.fft_h_to_x(1.0/cell().volume()); // fill map ASU for ( Map_reference_index ix = first(); !ix.last(); ix.next() ) (*this)[ix] = fftmap.real_data( ix.coord() ); } else { // make a normal fftmap FFTmap_p1 fftmap( grid_sampling() ); // copy from reflection data typename H::HKL_reference_index ih; ffttype f, phi0, phi1; int sym; for ( ih = fphidata.first_data(); !ih.last(); fphidata.next_data( ih ) ) { f = fphidata[ih].f(); if ( f != 0.0 ) { phi0 = fphidata[ih].phi(); const HKL& hkl = ih.hkl(); fftmap.set_hkl( hkl, std::complex( f*cos(phi0), f*sin(phi0) ) ); for ( sym = 1; sym < spacegroup_.num_primops(); sym++ ) { phi1 = phi0 + hkl.sym_phase_shift( spacegroup_.symop(sym) ); fftmap.set_hkl( hkl.transform( isymop[sym] ), std::complex( f*cos(phi1), f*sin(phi1) ) ); } } } // do fft fftmap.fft_h_to_x(1.0/cell().volume()); // fill map ASU for ( Map_reference_index ix = first(); !ix.last(); ix.next() ) (*this)[ix] = fftmap.real_data( ix.coord() ); } } /*! The Fourier transform of this map is calculated and used to fill a reflection list of F_phi. The map is unchanged. Arguably this should be part of hkl_data>. But that requires writing a specialisation of hkl_data for F_phi. This is simpler and imposes less demands on the compiler. \param fphidata The reflection data list to set. */ template template void Xmap::fft_to ( H& fphidata, const FFTtype type ) const { if ( type == Sparse || ( type == Default && default_type() == Sparse ) ) { // make a sparse fftmap FFTmap_sparse_p1_xh fftmap( grid_sampling() ); // copy from map data ffttype f; int sym; for ( Map_reference_index ix = first(); !ix.last(); ix.next() ) { f = (*this)[ix]; if ( f != 0.0 ) { fftmap.real_data( ix.coord() ) = f; for ( sym = 1; sym < cacheref.data().nsym; sym++ ) fftmap.real_data( ix.coord().transform( isymop[sym] ).unit( grid_sam_ ) ) = f; } } // require output ASU coords typename H::HKL_reference_index ih; for ( ih = fphidata.first(); !ih.last(); ih.next() ) fftmap.require_hkl( ih.hkl() ); // do fft fftmap.fft_x_to_h(cell().volume()); // fill data ASU for ( ih = fphidata.first(); !ih.last(); ih.next() ) { std::complex c = fftmap.get_hkl( ih.hkl() ); fphidata[ih].f() = std::abs(c); fphidata[ih].phi() = std::arg(c); } } else { // make a normal fftmap FFTmap_p1 fftmap( grid_sampling() ); // copy from map data ffttype f; int sym; for ( Map_reference_index ix = first(); !ix.last(); ix.next() ) { f = (*this)[ix]; if ( f != 0.0 ) { fftmap.real_data( ix.coord() ) = f; for ( sym = 1; sym < cacheref.data().nsym; sym++ ) fftmap.real_data( ix.coord().transform( isymop[sym] ).unit( grid_sam_ ) ) = f; } } // do fft fftmap.fft_x_to_h(cell().volume()); // fill data ASU typename H::HKL_reference_index ih; for ( ih = fphidata.first(); !ih.last(); ih.next() ) { std::complex c = fftmap.get_hkl( ih.hkl() ); fphidata[ih].f() = std::abs(c); fphidata[ih].phi() = std::arg(c); } } } /*! All values, including missing values, are overwritten by the value. \param value The value to which the map is to be set. */ template const T& Xmap::operator =( const T& value ) { // copy value into map for ( Map_reference_index im = first(); !im.last(); im.next() ) list[im.index()] = value; return value; } /*! The map grids and spacegroups must match. */ template const Xmap& Xmap::operator +=( const Xmap& other ) { if ( spacegroup().hash() != other.spacegroup().hash() || grid_sampling() != other.grid_sampling() ) Message::message( Message_fatal( "Xmap: map mismatch in +=" ) ); for ( Map_reference_index im = first(); !im.last(); im.next() ) list[im.index()] += other[im]; return (*this); } /*! The map grids and spacegroups must match. */ template const Xmap& Xmap::operator -=( const Xmap& other ) { if ( spacegroup().hash() != other.spacegroup().hash() || grid_sampling() != other.grid_sampling() ) Message::message( Message_fatal( "Xmap: map mismatch in -=" ) ); for ( Map_reference_index im = first(); !im.last(); im.next() ) list[im.index()] -= other[im]; return (*this); } } // namespace clipper #endif clipper-2.1/clipper/core/clipper_sysdep.h0000644000374100011300000001235711347710616015527 00000000000000/*! \file lib/clipper_sysdep.h Header file for clipper system dependencies */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_SYSDEP #define CLIPPER_SYSDEP /* cmath is so variable, that we ignore it and use the C version: - include the math library - mirror into the 'std' namespace as below: */ #if defined(sun) || defined(sgi) || defined(__osf__) || defined(_MSC_VER) #include #include #include #include #ifndef M_PI #define M_PI 3.14159265358979 #endif #define rint(x) (floor((x)+0.5)) namespace std { using ::floor; using ::ceil; using ::fabs; using ::fmod; using ::sqrt; using ::sin; using ::cos; using ::tan; using ::asin; using ::acos; using ::atan; using ::sinh; using ::cosh; using ::tanh; using ::atan2; using ::exp; using ::log; using ::pow; } #else #include #endif /* fixes for unexpected macros */ #if defined(isnan) #undef isnan #endif #ifdef __WIN32__ #undef min #undef max #endif /* numeric types, for where they are critical */ namespace clipper { typedef float ftype32; typedef double ftype64; typedef int itype32; typedef unsigned int uitype32; # define CLIPPER_NAN_MASK_A_32 0x7f800000U # define CLIPPER_NAN_MASK_B_32 0x007fffffU # define CLIPPER_NULL_MASK_32 0x7fc00000U #if defined(__osf__) || defined(__amd64__) typedef long itype64; typedef unsigned long uitype64; # define CLIPPER_NAN_MASK_A_64 0x7ff0000000000000UL # define CLIPPER_NAN_MASK_B_64 0x000fffffffffffffUL # define CLIPPER_NULL_MASK_64 0x7ff8000000000000UL #else typedef long long itype64; typedef unsigned long long uitype64; # define CLIPPER_NAN_MASK_A_64 0x7ff0000000000000ULL # define CLIPPER_NAN_MASK_B_64 0x000fffffffffffffULL # define CLIPPER_NULL_MASK_64 0x7ff8000000000000ULL #endif } /* threading libraries and definitions */ #ifndef CLIPPER_DISABLE_THREADS #ifdef __WIN32__ #include #undef AddAtom #define CLIPPER_MUTEX_INIT(MUTEX) InitializeCriticalSection(MUTEX) #define CLIPPER_MUTEX_FREE(MUTEX) DeleteCriticalSection(MUTEX) #define CLIPPER_MUTEX_LOCK(MUTEX) EnterCriticalSection(MUTEX) #define CLIPPER_MUTEX_UNLK(MUTEX) LeaveCriticalSection(MUTEX) #define CLIPPER_MUTEX_TYPE CRITICAL_SECTION #define CLIPPER_THREAD_EXEC(THREAD,ENTRY,ARG) (THREAD=CreateThread(0,0,(LPTHREAD_START_ROUTINE)ENTRY,(void*)ARG,0,NULL),THREAD!=NULL) #define CLIPPER_THREAD_JOIN(THREAD) (WaitForSingleObject(THREAD,INFINITE)>=0) #define CLIPPER_THREAD_TYPE HANDLE #define CLIPPER_THREAD_ARGTYPE LPVOID #define CLIPPER_THREAD_RETTYPE DWORD #else #include #define CLIPPER_MUTEX_INIT(MUTEX) pthread_mutex_init(MUTEX,NULL) #define CLIPPER_MUTEX_FREE(MUTEX) pthread_mutex_destroy(MUTEX) #define CLIPPER_MUTEX_LOCK(MUTEX) pthread_mutex_lock(MUTEX) #define CLIPPER_MUTEX_UNLK(MUTEX) pthread_mutex_unlock(MUTEX) #define CLIPPER_MUTEX_TYPE pthread_mutex_t #define CLIPPER_THREAD_EXEC(THREAD,ENTRY,ARG) (pthread_create(&THREAD,NULL,ENTRY,(void*)ARG)==0) #define CLIPPER_THREAD_JOIN(THREAD) (pthread_join(THREAD,NULL)==0) #define CLIPPER_THREAD_TYPE pthread_t #define CLIPPER_THREAD_ARGTYPE void* #define CLIPPER_THREAD_RETTYPE void* #endif #endif #endif clipper-2.1/clipper/core/fftmap_sparse.cpp0000644000374100011300000003250510736415744015671 00000000000000/* fftmap_sparse.cpp: implementation file for P1 fft map */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "fftmap_sparse.h" #include "hkl_datatypes.h" #include #include namespace clipper { FFTmap_base::FFTtype FFTmap_sparse_p1_base::default_type_ = FFTmap_base::Estimate; /*! Initialise an FFTmap_sparse_p1_base for a grid. \param grid_sam The grid sampling of the unit cell. \param type Can be FFTmap_sparse_base::Measure, ::Estimate. Measure performs slow precalculation (first time only) to get faster FFT. */ void FFTmap_sparse_p1_base::init( const Grid_sampling& grid_sam, const FFTtype type ) { type_ = type; if ( type_ == Default ) type_ = default_type(); // allocate data grid_real_ = grid_sam; grid_reci_ = Grid( grid_real_.nu(), grid_real_.nv(), grid_real_.nw()/2+1 ); // make section maps std::complex* fillptr = NULL; row_kl.resize( grid_reci_.nv(), grid_reci_.nw(), fillptr ); ffttype* rfillptr = NULL; row_uv.resize( grid_real_.nu(), grid_real_.nv(), rfillptr ); } FFTmap_sparse_p1_base::~FFTmap_sparse_p1_base() { int u, v, w; for ( w = 0; w < grid_reci_.nw(); w++ ) for ( v = 0; v < grid_reci_.nv(); v++ ) if ( row_kl( v, w ) != NULL ) delete[] row_kl( v, w ); for ( v = 0; v < grid_real_.nv(); v++ ) for ( u = 0; u < grid_real_.nu(); u++ ) if ( row_uv( u, v ) != NULL ) delete[] row_uv( u, v ); } ffttype* FFTmap_sparse_p1_base::map_uv( const int& u, const int& v ) { ffttype* ptr = row_uv( u, v ); if ( ptr == NULL ) { ptr = new ffttype[ grid_real_.nw() ]; const ffttype zero( 0.0 ); for ( int w = 0; w < grid_real_.nw(); w++ ) ptr[w] = zero; row_uv( u, v ) = ptr; } return ptr; } std::complex* FFTmap_sparse_p1_base::map_kl( const int& k, const int& l ) { std::complex* ptr = row_kl( k, l ); if ( ptr == NULL ) { ptr = new std::complex[ grid_reci_.nu() ]; const std::complex zero( 0.0, 0.0 ); for ( int u = 0; u < grid_reci_.nu(); u++ ) ptr[u] = zero; row_kl( k, l ) = ptr; } return ptr; } /*! For later initialisation: see init() */ FFTmap_sparse_p1_hx::FFTmap_sparse_p1_hx() {} /*! Construct an FFTmap_sparse_p1_hx for a given grid. \param grid_sam The grid sampling of the unit cell. \param type Can be FFTmap_sparse_base::Measure, ::Estimate. Measure performs slow precalculation (first time only) to get faster FFT. */ FFTmap_sparse_p1_hx::FFTmap_sparse_p1_hx( const Grid_sampling& grid_sam, const FFTtype type ) { init( grid_sam, type ); } /*! \fn void FFTmap_sparse_p1_hx::require_real_data( const Coord_grid& uvw ) The given Coord_grid will be required in the final map. ( uvw must be in grid_sampling() ) \param uvw The coordinate to require. */ /*! \fn const ffttype& FFTmap_sparse_p1_hx::real_data( const Coord_grid& uvw ) const ( uvw must be in grid_sampling(), and have been requested ) \param uvw The coordinate to get. \return The real value at that coordinate. */ /*! Friedel opposites are handled correctly \param hkl The HKL to set. \param f The complex value to set. */ void FFTmap_sparse_p1_hx::set_hkl( const HKL& hkl, const std::complex& f ) { Coord_grid c; c = Coord_grid(hkl).unit( grid_real_ ); if ( c.w() < grid_reci_.nw() ) cplx_data(c) = f; c = Coord_grid(-hkl).unit( grid_real_ ); if ( c.w() < grid_reci_.nw() ) cplx_data(c) = std::conj(f); } /*! The 'require' functions must have been called first to mark the required data in the target space. (Source space requirements are inferred automatically). */ void FFTmap_sparse_p1_hx::fft_h_to_x( const ftype& scale ) { // prep fftw std::vector > in, out; ffttype zero_real = 0.0; std::complex zero( zero_real, zero_real ); fftw_plan planu, planv; rfftw_plan planw; std::complex* ptr; ffttype* rptr; int u, v, w; int hw = grid_real_.nw()/2; ffttype s = ffttype( scale ); int flags = ( type_ == Measure ) ? ( FFTW_USE_WISDOM | FFTW_MEASURE ) : ( FFTW_USE_WISDOM | FFTW_ESTIMATE ); // make ul map std::vector map_l( grid_reci_.nw(), false ); std::vector row_u( grid_real_.nu(), false ); for ( w = 0; w < grid_reci_.nw(); w++ ) for ( v = 0; v < grid_reci_.nv(); v++ ) if ( row_kl( v, w ) != NULL ) map_l[w] = true; for ( v = 0; v < grid_real_.nv(); v++ ) for ( u = 0; u < grid_real_.nu(); u++ ) if ( row_uv( u, v ) != NULL ) row_u[u] = true; mutex.lock(); planu = fftw_create_plan_specific( grid_real_.nu(), FFTW_FORWARD, flags | FFTW_IN_PLACE, (fftw_complex*)&in[0], 1, (fftw_complex*)&out[0], 1 ); planv = fftw_create_plan_specific( grid_real_.nv(), FFTW_FORWARD, flags | FFTW_OUT_OF_PLACE, (fftw_complex*)&in[0], 1, (fftw_complex*)&out[0], 1 ); planw = rfftw_create_plan_specific( grid_real_.nw(), FFTW_COMPLEX_TO_REAL, flags | FFTW_IN_PLACE, (fftw_real*)&in[0], 1, (fftw_real*)&out[0], 1 ); mutex.unlock(); // transform along h->u in.resize( grid_reci_.nu() ); out.resize( grid_real_.nu() ); for ( w = 0; w < grid_reci_.nw(); w++ ) for ( v = 0; v < grid_reci_.nv(); v++ ) { ptr = row_kl( v, w ); if ( ptr != NULL ) fftw_one( planu, (fftw_complex*)ptr, (fftw_complex*)&out[0] ); } // copy, transform along k->v, and copy in.resize( grid_reci_.nv() ); out.resize( grid_real_.nv() ); for ( w = 0; w < grid_reci_.nw(); w++ ) if ( map_l[w] ) for ( u = 0; u < grid_real_.nu(); u++ ) if ( row_u[u] ) { for ( v = 0; v < grid_real_.nv(); v++ ) { ptr = row_kl( v, w ); if ( ptr != NULL ) in[v] = s * ptr[u]; else in[v] = zero; } fftw_one( planv, (fftw_complex*)&in[0], (fftw_complex*)&out[0] ); for ( v = 0; v < grid_real_.nv(); v++ ) { rptr = row_uv( u, v ); if ( rptr != NULL ) { rptr[w] = out[v].real(); if ( w != 0 && w != hw ) rptr[grid_real_.nw()-w] = -out[v].imag(); } } } // transform along l->w in.resize( grid_real_.nw() ); out.resize( grid_real_.nw() ); for ( v = 0; v < grid_real_.nv(); v++ ) for ( u = 0; u < grid_real_.nu(); u++ ) { rptr = row_uv( u, v ); if ( rptr != NULL ) rfftw_one( planw, (fftw_real*)rptr, (fftw_real*)&out[0] ); } mutex.lock(); fftw_destroy_plan( planu ); fftw_destroy_plan( planv ); rfftw_destroy_plan( planw ); mutex.unlock(); } /*! For later initialisation: see init() */ FFTmap_sparse_p1_xh::FFTmap_sparse_p1_xh() {} /*! Construct an FFTmap_sparse_p1_xh for a given grid. \param grid_sam The grid sampling of the unit cell. \param type Can be FFTmap_sparse_base::Measure, ::Estimate. Measure performs slow precalculation (first time only) to get faster FFT. */ FFTmap_sparse_p1_xh::FFTmap_sparse_p1_xh( const Grid_sampling& grid_sam, const FFTtype type ) { init( grid_sam, type ); } /*! Friedel opposites are handled correctly \param hkl The HKL required. */ void FFTmap_sparse_p1_xh::require_hkl( const HKL& hkl ) { Coord_grid c = Coord_grid(hkl).unit( grid_real_ ); if ( c.w() < grid_reci_.nw() ) map_kl( c.v(), c.w() ); else map_kl( ( grid_real_.nv() - c.v() ) % grid_real_.nv(), ( grid_real_.nw() - c.w() ) % grid_real_.nw() ); } /*! Friedel opposites are handled correctly \param hkl The required. */ const std::complex FFTmap_sparse_p1_xh::get_hkl( const HKL& hkl ) const { Coord_grid c = Coord_grid(hkl).unit( grid_real_ ); if ( c.w() < grid_reci_.nw() ) return row_kl( c.v(), c.w() )[ c.u() ]; else return std::conj( row_kl( ( grid_real_.nv() - c.v() ) % grid_real_.nv(), ( grid_real_.nw() - c.w() ) % grid_real_.nw() ) [ ( grid_real_.nu() - c.u() ) % grid_real_.nu() ] ); } /*! \fn void FFTmap_sparse_p1_xh::require_cplx_data( const Coord_grid& hkl ) The given Coord_grid will be required in the final reflections. ( uvw must be in grid_reci() ) \param uvw The coordinate to require. */ /*! \fn const std::complex& FFTmap_sparse_p1_xh::cplx_data( const Coord_grid& hkl ) const ( hkl must be in grid_reci(), and have been requested ) \param uvw The coordinate to get. \return The complex value at that coordinate. */ /*! \fn ffttype& FFTmap_sparse_p1_xh::real_data( const Coord_grid& uvw ) ( uvw must be in grid_real() ) */ /*! The 'require' functions must have been called first to mark the required data in the target space. (Source space requirements are inferred automatically). */ void FFTmap_sparse_p1_xh::fft_x_to_h( const ftype& scale ) { // prep fftw std::vector > in, out; ffttype zero_real = 0.0; std::complex zero( zero_real, zero_real ); fftw_plan planu, planv; rfftw_plan planw; std::complex* ptr; ffttype* rptr; int u, v, w; int hw = grid_real_.nw()/2; ffttype s = ffttype( scale ) / grid_real_.size(); int flags = ( type_ == Measure ) ? ( FFTW_USE_WISDOM | FFTW_MEASURE ) : ( FFTW_USE_WISDOM | FFTW_ESTIMATE ); // make ul map std::vector map_l( grid_reci_.nw(), false ); std::vector row_u( grid_real_.nu(), false ); for ( w = 0; w < grid_reci_.nw(); w++ ) for ( v = 0; v < grid_reci_.nv(); v++ ) if ( row_kl( v, w ) != NULL ) map_l[w] = true; for ( v = 0; v < grid_real_.nv(); v++ ) for ( u = 0; u < grid_real_.nu(); u++ ) if ( row_uv( u, v ) != NULL ) row_u[u] = true; mutex.lock(); planu = fftw_create_plan_specific( grid_real_.nu(), FFTW_BACKWARD, flags | FFTW_IN_PLACE, (fftw_complex*)&in[0], 1, (fftw_complex*)&out[0], 1 ); planv = fftw_create_plan_specific( grid_real_.nv(), FFTW_BACKWARD, flags | FFTW_OUT_OF_PLACE, (fftw_complex*)&in[0], 1, (fftw_complex*)&out[0], 1 ); planw = rfftw_create_plan_specific( grid_real_.nw(), FFTW_REAL_TO_COMPLEX, flags | FFTW_IN_PLACE, (fftw_real*)&in[0], 1, (fftw_real*)&out[0], 1 ); mutex.unlock(); // transform along l->w in.resize( grid_real_.nw() ); out.resize( grid_real_.nw() ); for ( v = 0; v < grid_real_.nv(); v++ ) for ( u = 0; u < grid_real_.nu(); u++ ) { rptr = row_uv( u, v ); if ( rptr != NULL ) rfftw_one( planw, (fftw_real*)rptr, (fftw_real*)&out[0] ); } // copy, transform along k->v, and copy in.resize( grid_reci_.nv() ); out.resize( grid_real_.nv() ); for ( w = 0; w < grid_reci_.nw(); w++ ) if ( map_l[w] ) for ( u = 0; u < grid_real_.nu(); u++ ) if ( row_u[u] ) { for ( v = 0; v < grid_real_.nv(); v++ ) { rptr = row_uv( u, v ); if ( rptr != NULL ) { if ( w != 0 && w != hw ) in[v] = std::complex( rptr[w], -rptr[grid_real_.nw()-w] ); else in[v] = std::complex( rptr[w], zero_real ); } else { in[v] = zero; } } fftw_one( planv, (fftw_complex*)&in[0], (fftw_complex*)&out[0] ); for ( v = 0; v < grid_real_.nv(); v++ ) { ptr = row_kl( v, w ); if ( ptr != NULL ) ptr[u] = s * out[v]; } } // transform along h->u in.resize( grid_reci_.nu() ); out.resize( grid_real_.nu() ); for ( w = 0; w < grid_reci_.nw(); w++ ) for ( v = 0; v < grid_reci_.nv(); v++ ) { ptr = row_kl( v, w ); if ( ptr != NULL ) fftw_one( planu, (fftw_complex*)ptr, (fftw_complex*)&out[0] ); } mutex.lock(); fftw_destroy_plan( planu ); fftw_destroy_plan( planv ); fftw_destroy_plan( planw ); mutex.unlock(); } } // namespace clipper clipper-2.1/clipper/core/test_data.h0000644000374100011300000000601610363703537014446 00000000000000/*! \file lib/test_data.h Header file for clipper test data functions */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_TEST_DATA #define CLIPPER_TEST_DATA #include "hkl_datatypes.h" namespace clipper { // data namespace namespace data { //! Class to return test data class Test_data { public: //! Null constructor: fills the arrays Test_data(); //! Return HKL_data class const HKL_data >& hkl_data_f_sigf() const { return fsig; } //! Return HKL_data class const HKL_data >& hkl_data_abcd() const { return abcd; } //! Return atom list const Atom_list& atom_list() const { return atoms; } private: HKL_info hklinfo; HKL_data > fsig; HKL_data > abcd; Atom_list atoms; }; } // namespace data } // namespace clipper #endif clipper-2.1/clipper/core/clipper_memory.cpp0000644000374100011300000001224511052517541016052 00000000000000/* clipper_memory.cpp: implementation file for clipper helper functions */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "clipper_memory.h" namespace clipper { //Mutex PropertyManager::mutex = Mutex(); /*! Makes copies of all property objects. */ PropertyManager::PropertyManager( const PropertyManager& mgr ) { copy( mgr ); } /*! Clears manager then makes copies of all property objects. */ PropertyManager& PropertyManager::operator =( const PropertyManager& mgr ) { return copy( mgr ); } /*! Deletes all stored properties. */ PropertyManager::~PropertyManager() { //mutex.lock(); for ( int i = 0; i < property_.size(); i++ ) delete property_[i].second; property_.clear(); //mutex.unlock(); } /*! This function is used by the copy constructor and assignement operator and is also useful for derived classes. */ PropertyManager& PropertyManager::copy( const PropertyManager& mgr ) { //mutex.lock(); for ( int i = 0; i < property_.size(); i++ ) delete property_[i].second; property_.clear(); for ( int i = 0; i < mgr.property_.size(); i++ ) property_.push_back( std::pair( mgr.property_[i].first, mgr.property_[i].second->clone() ) ); //mutex.unlock(); return *this; } /* \param label The label of the property to be returned. \param property The property object. \return true on success. */ bool PropertyManager::set_property( const std::string& label, const Property_base& property ) { //mutex.lock(); property_.push_back( std::pair( label, property.clone() ) ); //mutex.unlock(); return true; } /*! \param label The label of the property to be returned. \return the property object. */ const Property_base& PropertyManager::get_property( const std::string& label ) const { //mutex.lock(); const Property_base* result = NULL; for ( int i = 0; i < property_.size(); i++ ) if ( label == property_[i].first ) { result = property_[i].second; break; } //mutex.unlock(); if ( result == NULL ) Message::message( Message_fatal( "PropertyManager: label not found.\n" ) ); return *result; } /*! \param label The label of the property to be tested. \return true on success. */ bool PropertyManager::exists_property( const std::string& label ) const { //mutex.lock(); bool result = false; for ( int i = 0; i < property_.size(); i++ ) if ( label == property_[i].first ) { result = true; break; } //mutex.unlock(); return result; } /* \param label The label of the property to be deleted. \return true on success. */ bool PropertyManager::delete_property( const std::string& label ) { //mutex.lock(); bool result = false; for ( int i = 0; i < property_.size(); i++ ) if ( label == property_[i].first ) { delete property_[i].second; property_.erase( property_.begin() + i ); result = true; break; } //mutex.unlock(); return result; } // template compilations template class Property; template class Property; template class Property; template class Property; } // namespace clipper clipper-2.1/clipper/core/derivs.h0000644000374100011300000002312410363703537013771 00000000000000/*! \file lib/derivs.h Fundamental types for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_DERIVS #define CLIPPER_DERIVS #include "coords.h" namespace clipper { template class Grad_orth; template class Grad_frac; template class Grad_map; template class Curv_orth; template class Curv_frac; template class Curv_map; //! orthogonal (Angstom) gradient, with respect to orthogonal x,y,z template class Grad_orth : public Vec3 { public: Grad_orth() {} //!< null constructor explicit Grad_orth( const Vec3& v ) : Vec3( v ) {} //!< constructor: copy/convert Grad_orth( const T& dx, const T& dy, const T& dz ) : Vec3( dx, dy, dz ) {} //!< constructor: from d/dx,d/dy,d/dz const T& dx() const { return (*this)[0]; } //!< get d/dx const T& dy() const { return (*this)[1]; } //!< get d/dy const T& dz() const { return (*this)[2]; } //!< get d/dz //! orthogonal-fractional derivative conversion Grad_frac grad_frac( const Cell& cell ) const; String format() const; //!< return formatted String representation }; //! fractional (cell) gradient, with respect to fractional u,v,w template class Grad_frac : public Vec3 { public: Grad_frac() {} //!< null constructor explicit Grad_frac( const Vec3& v ) : Vec3( v ) {} //!< constructor: copy/convert Grad_frac( const T& du, const T& dv, const T& dw ) : Vec3( du, dv, dw ) {} //!< constructor: from d/du,d/dv,d/dw const T& du() const { return (*this)[0]; } //!< get d/du const T& dv() const { return (*this)[1]; } //!< get d/dv const T& dw() const { return (*this)[2]; } //!< get d/dw //! fractional-orthogonal derivative conversion Grad_orth grad_orth( const Cell& cell ) const; //! fractional-grid derivative conversion Grad_map grad_map( const Grid& g ) const; String format() const; //!< return formatted String representation }; //! map coordinate gradient, with respect to grid u,v,w template class Grad_map : public Vec3 { public: Grad_map() {} //!< null constructor explicit Grad_map( const Vec3& v ) : Vec3( v ) {} //!< constructor: copy/convert Grad_map( const T& du, const T& dv, const T& dw ) : Vec3( du, dv, dw ) {} //!< constructor: from d/du,d/dv,d/dw const T& du() const { return (*this)[0]; } //!< get d/du const T& dv() const { return (*this)[1]; } //!< get d/dv const T& dw() const { return (*this)[2]; } //!< get d/dw //! grid-fractional derivative conversion Grad_frac grad_frac( const Grid& g ) const; String format() const; //!< return formatted String representation }; //! orthogonal (Angstom) curvatures, with respect to orthogonal x,y,z template class Curv_orth : public Mat33 { public: Curv_orth() {} //!< null constructor explicit Curv_orth( const Mat33& m ) : Mat33( m ) {} //!< constructor: copy/convert //! orthogonal-fractional derivative conversion Curv_frac curv_frac( const Cell& cell ) const; }; //! fractional (cell) curvatures, with respect to fractional u,v,w template class Curv_frac : public Mat33 { public: Curv_frac() {} //!< null constructor explicit Curv_frac( const Mat33& m ) : Mat33( m ) {} //!< constructor: copy/convert //! fractional-orthogonal derivative conversion Curv_orth curv_orth( const Cell& cell ) const; //! fractional-grid derivative conversion Curv_map curv_map( const Grid& g ) const; }; //! map coordinate curvatures, with respect to grid u,v,w template class Curv_map : public Mat33 { public: Curv_map() {} //!< null constructor explicit Curv_map( const Mat33& m ) : Mat33( m ) {} //!< constructor: copy/convert //! grid-fractional derivative conversion Curv_frac curv_frac( const Grid& g ) const; }; // template implementations /*! The result is an RT operator. This is a redudent representation, but is handy for assembling compound operators. \return The operator */ /*! \return The formatted text string */ template String Grad_orth::format() const { return "d/dx,d/dy,d/dz = ("+String(dx())+","+String(dy())+","+String(dz())+")"; } /*! \param cell The cell concerned \return The transformed derivative. */ template inline Grad_frac Grad_orth::grad_frac( const Cell& cell ) const { return Grad_frac( (*this) * Mat33( cell.matrix_orth() ) ); } /*! \return The formatted text string */ template String Grad_frac::format() const { return "d/du,d/dv,d/dw = ("+String(du())+","+String(dv())+","+String(dw())+")"; } /*! \param cell The cell concerned \return The transformed derivative. */ template inline Grad_orth Grad_frac::grad_orth( const Cell& cell ) const { return Grad_orth( (*this) * Mat33( cell.matrix_frac() ) ); } /*! \param g The grid concerned \return The transformed derivative. */ template inline Grad_map Grad_frac::grad_map( const Grid& g ) const { return Grad_map( du()/g.nu(), dv()/g.nv(), dw()/g.nw() ); } /*! \return The formatted text string */ template String Grad_map::format() const { return "d/du,d/dv,d/dw = ("+String(du())+","+String(dv())+","+String(dw())+")"; } /*! \param g The grid concerned \return The transformed derivative. */ template inline Grad_frac Grad_map::grad_frac( const Grid& g ) const { return Grad_frac( du()*g.nu(), dv()*g.nv(), dw()*g.nw() ); } /*! \param cell The cell concerned \return The transformed derivative. */ template Curv_frac Curv_orth::curv_frac( const Cell& cell ) const { Mat33 m( cell.matrix_orth() ); return Curv_frac( m.transpose() * (*this) * m ); } /*! \param cell The cell concerned \return The transformed derivative. */ template Curv_orth Curv_frac::curv_orth( const Cell& cell ) const { Mat33 m( cell.matrix_frac() ); return Curv_orth( m.transpose() * (*this) * m ); } /*! \param g The grid concerned \return The transformed derivative. */ template Curv_map Curv_frac::curv_map( const Grid& g ) const { Curv_map c; c(0,0) = (*this)(0,0) / T(g.nu()*g.nu()); c(0,1) = (*this)(0,1) / T(g.nu()*g.nv()); c(0,2) = (*this)(0,2) / T(g.nu()*g.nw()); c(1,0) = (*this)(1,0) / T(g.nv()*g.nu()); c(1,1) = (*this)(1,1) / T(g.nv()*g.nv()); c(1,2) = (*this)(1,2) / T(g.nv()*g.nw()); c(2,0) = (*this)(2,0) / T(g.nw()*g.nu()); c(2,1) = (*this)(2,1) / T(g.nw()*g.nv()); c(2,2) = (*this)(2,2) / T(g.nw()*g.nw()); return c; } /*! \param g The grid concerned \return The transformed derivative. */ template Curv_frac Curv_map::curv_frac( const Grid& g ) const { Curv_frac c; c(0,0) = (*this)(0,0) * T(g.nu()*g.nu()); c(0,1) = (*this)(0,1) * T(g.nu()*g.nv()); c(0,2) = (*this)(0,2) * T(g.nu()*g.nw()); c(1,0) = (*this)(1,0) * T(g.nv()*g.nu()); c(1,1) = (*this)(1,1) * T(g.nv()*g.nv()); c(1,2) = (*this)(1,2) * T(g.nv()*g.nw()); c(2,0) = (*this)(2,0) * T(g.nw()*g.nu()); c(2,1) = (*this)(2,1) * T(g.nw()*g.nv()); c(2,2) = (*this)(2,2) * T(g.nw()*g.nw()); return c; } } // namespace clipper #endif clipper-2.1/clipper/core/symop.cpp0000644000374100011300000002110211223146616014164 00000000000000/* symop.cpp: fundamental data types for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "symop.h" #include "coords.h" namespace clipper { /*! Construct an RT operator from a string description, e.g. 1/2x,z-y+2/3,x '*' is optional for multiplication, commas are compulsory. */ RTop_frac::RTop_frac( const String& strop ) { std::vector rows = strop.split(","); if ( rows.size() != 3 ) Message::message(Message_fatal("RTop_frac: invalid string:"+strop)); rot() = Mat33<>(0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0); trn() = Vec3<> (0.0,0.0,0.0); std::vector cols; String num; ftype val; int nrow, ncol, nchr, npart; for ( nrow = 0; nrow < 3; nrow++ ) { const String& row = rows[nrow]; cols.clear(); cols.push_back(""); for ( nchr = 0; nchr < row.length(); nchr++ ) { const char& c = row[nchr]; if ( c == '+' || c == '-' ) cols.push_back( "" ); cols.back() += c; } for ( npart = 0; npart < cols.size(); npart++ ) { const String& col = cols[npart]; ncol = 3; num = ""; for ( nchr = 0; nchr < col.length(); nchr++ ) { const char& c = col[nchr]; if ( c == 'x' || c == 'X' ) ncol = 0; else if ( c == 'y' || c == 'Y' ) ncol = 1; else if ( c == 'z' || c == 'Z' ) ncol = 2; else if ( c == '-' || c == '/' || isdigit(c) ) num += c; } if ( ncol < 3 ) { if ( num == "" || num == "+" || num == "-" ) num += "1"; val = num.rational(); rot()( nrow, ncol ) = val; } else { if ( num == "" || num == "+" || num == "-" ) num += "0"; val = num.rational(); trn()[ nrow ] = val; } } } } /*! \param cell The cell concerned \return The transformed coordinate. */ RTop_orth RTop_frac::rtop_orth( const Cell& cell ) const { return RTop_orth( RTop<>(cell.matrix_orth()) * (*this) * RTop<>(cell.matrix_frac()) ); } /*! \return The inverse of the operator. */ RTop_frac RTop_frac::inverse() const { return RTop_frac( RTop<>::inverse() ); } /*! \return The identity operator. */ RTop_frac RTop_frac::identity() { return RTop_frac( RTop<>::identity() ); } /*! \return The null (uninitialised) operator. */ RTop_frac RTop_frac::null() { return RTop_frac( RTop<>::null() ); } /*! Construct a symmetry operator and initialise it to the supplied RTop. Translations are rounded to a basis of 48, and put on the range 0..1 \param mat The RTop to use. */ Symop::Symop( const RTop<>& rt ) { // initialise to the supplied matrix int i, j; for ( i=0; i<3; i++) for ( j=0; j<3; j++) rot()(i,j) = rint( rt.rot()(i,j) ); for ( i=0; i<3; i++) trn()[i] = ftype( Util::mod( Util::intr(48.*rt.trn()[i]), 48 ) ) / 48.; } /*! Construct a symmetry operator and initialise it to the supplied matrix. Translations are rounded to a basis of 48, and put on the range 0..1 \param mat The 4x4 matrix to use. The [i][3] elements contain the translation. */ Symop::Symop( const ftype mat[4][4] ) { // initialise to the supplied matrix int i, j; for ( i=0; i<3; i++) for ( j=0; j<3; j++) rot()(i,j) = mat[i][j]; for ( i=0; i<3; i++) trn()[i] = ftype( Util::mod( Util::intr(48.*mat[i][3]), 48 ) ) / 48.; } /*! Return formatted representation of the symmetry operator. \return The formatted text string, e.g. -x, -y+1/2, z. */ String Symop::format() const { String s, t, xyz="xyz"; for ( int i = 0; i < 3; i++ ) { t = ""; for ( int j = 0; j < 3; j++ ) if ( rot()(i,j) != 0.0 ) { t += ( rot()(i,j) > 0.0 ) ? "+" : "-"; if ( Util::intr( fabs( rot()(i,j) ) ) != 1 ) t += String::rational( fabs( rot()(i,j) ), 24 ); t += xyz[j]; } if ( trn()[i] != 0.0 ) t += String::rational( trn()[i], 24, true ); s += t.substr( ( t[0] == '+' ) ? 1 : 0 ); if ( i < 2 ) s+= ", "; } return s; } /*! Integerised symops are more efficient when handling integer coordinate types, e.g. HKL, Coord_grid. The rotation parts of the integerised symop are general and can be used for any recirpocal space data. The translation part is specific to an individual grid. \param symop The conventional symop. \param grid The specific grid. */ Isymop::Isymop( const Symop& symop, const Grid& grid ) { for ( int i = 0; i < 3; i++ ) for ( int j = 0; j < 3; j++ ) rot()(i,j) = Util::intr( symop.rot()(i,j) ); trn()[0] = Util::intr( grid.nu() * symop.trn()[0] ); trn()[1] = Util::intr( grid.nv() * symop.trn()[1] ); trn()[2] = Util::intr( grid.nw() * symop.trn()[2] ); } /* Construct the encoded form of the symop. */ Symop_code::Symop_code( const Symop& op ) { init( Isymop( op, Grid(24,24,24) ) ); } /* Construct the encoded form of the symop from integerised symop with a grid (base) of (24,24,24).*/ Symop_code::Symop_code( const Isymop& op ) { init( op ); } /* Initialise the encoded form of the symop from integerised symop with a grid (base) of (24,24,24).*/ void Symop_code::init( const Isymop& op ) { // initialise to the supplied code int i, j, fac, code_r, code_t; code_r = code_t = 0; fac = 1; for ( i = 0; i < 3; i++ ) { code_t += ( Util::mod( op.trn()[i], 24 ) ) * fac; fac *= 24; } fac = 1; for ( i = 0; i < 3; i++ ) for ( j = 0; j < 3; j++ ) { code_r += ( Util::mod( op.rot()(i,j) + 1, 3 ) ) * fac; fac *= 3; } // xor to make identity zero code_ = ( ( code_r ^ 0x4064 ) << 16 ) + code_t; } /*! Construct a symmetry operator and initialise it to the matrix encoded in the given int. \param code The integer code. */ Symop Symop_code::symop() const { Isymop iop = isymop(); Symop op; for ( int i = 0; i < 3; i++ ) { op.rot()(i,0) = ftype( iop.rot()(i,0) ); op.rot()(i,1) = ftype( iop.rot()(i,1) ); op.rot()(i,2) = ftype( iop.rot()(i,2) ); op.trn()[i] = ftype( iop.trn()[i] ) / 24.0; } return op; } /*! Construct an integerised symmetry operator and initialise it to the matrix encoded in the given int, with a grid (base) of (24,24,24). \param code The integer code. */ Isymop Symop_code::isymop() const { Isymop op; // initialise rotation and translation int i, j, fac, code_r, code_t; code_t = code_trn(); fac = 1; for ( i = 0; i < 3; i++ ) { op.trn()[i] = Util::mod( code_t/fac, 24 ); fac *= 24; } code_r = ( code_rot() >> 16 ) ^ 0x4064; fac = 1; for ( i = 0; i < 3; i++ ) for ( j = 0; j < 3; j++ ) { op.rot()(i,j) = Util::mod( code_r/fac, 3 ) - 1; fac *= 3; } return op; } Symop_code Symop_code::code_rot() const { return Symop_code( code_ & 0xffff0000 ); } Symop_code Symop_code::code_trn() const { return Symop_code( code_ & 0x0000ffff ); } } // namespace clipper clipper-2.1/clipper/core/clipper_thread.h0000644000374100011300000001160110776416673015471 00000000000000/*! \file lib/clipper_thread.h Header file for clipper threading handlers */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_THREAD #define CLIPPER_THREAD #include "clipper_message.h" #include "clipper_sysdep.h" namespace clipper { #ifndef CLIPPER_DISABLE_THREADS //! Mutex class: used for locking and unlocking shared resources. /*! Create a mutex for any sharted resource, i.e. non-stack object used by a multi-threaded program. The lock and unlock methods lock that resource. Recursive locks are not allowed. */ class Mutex { public: //! constructor: create the mutex Mutex() { CLIPPER_MUTEX_INIT( &mutex ); } //! destructor: destroy the mutex ~Mutex() { CLIPPER_MUTEX_FREE( &mutex ); } //! lock the mutex inline void lock() { CLIPPER_MUTEX_LOCK( &mutex ); } //! unlock the mutex inline void unlock() { CLIPPER_MUTEX_UNLK( &mutex ); } protected: CLIPPER_MUTEX_TYPE mutex; }; //! Thread base class: Override this to create new threads /*! To create a thread, override this class. Store data as members with accessors to set input and read output. Override the Run() method to do the actual work. e.g. the following class implements a thread which can sum a list of numbers. \code class Thread_test : public Thread_base { public: class Data : public std::vector { public: Data() {} Data( std::vector v ) : std::vector(v) {} }; void Run() { sum = 0; while ( 1 ) { lock(); int c = current++; unlock(); if ( c >= data_.size() ) break; sum += data_[c]; } } static void set_data( Data d ) { data_ = d; } static Data data_; static int current; int sum; }; \endcode */ class Thread_base { public: Thread_base(); virtual ~Thread_base() {} bool run(); bool join(); static void lock() { mutex_global.lock(); } static void unlock() { mutex_global.unlock(); } int id() const { return id_; } protected: virtual void Run() = 0; private: static CLIPPER_THREAD_RETTYPE Entry( CLIPPER_THREAD_ARGTYPE thisptr ); static Mutex mutex_global; static int next_id; CLIPPER_THREAD_TYPE thread; int id_; }; #else class Mutex { public: Mutex() {} ~Mutex() {} inline void lock() {} inline void unlock() {} }; class Thread_base { public: Thread_base() {} virtual ~Thread_base() {} bool run() { Run(); return true; } bool join() { return true; } static void lock() {} static void unlock() {} int id() const { return -1; } protected: virtual void Run() { clipper::Message::message( clipper::Message_fatal( "No Run method defined" ) ); } }; #endif } // namespace clipper #endif clipper-2.1/clipper/core/clipper_util.cpp0000644000374100011300000001644310363703537015531 00000000000000/* clipper_util.cpp: implementation file for clipper helper functions */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "clipper_util.h" namespace clipper { float Util::nanf_; //!< declare static double Util::nand_; //!< declare static ftype Util::nan_ ; //!< declare static ftype Util::onepi_ = M_PI; //!< one*pi ftype Util::twopi_ = 2.0*M_PI; //!< two*pi ftype Util::twopi2_ = 2.0*M_PI*M_PI; //!< two*pi*pi ftype Util::eightpi2_ = 8.0*M_PI*M_PI; //!< two*pi*pi ftype Util::d2rad_ = M_PI/180.0; //!< degree-radian conversion ftype Util::sim_a = 1.639294; //!< sim fn param ftype Util::sim_b = 3.553967; //!< sim fn param ftype Util::sim_c = 2.228716; //!< sim fn param ftype Util::sim_d = 3.524142; //!< sim fn param ftype Util::sim_e = 7.107935; //!< sim fn param ftype Util::sim_A = -1.28173889903; //!< invsim fn param ftype Util::sim_B = 0.69231689903; //!< invsim fn param ftype Util::sim_C = -1.33099462667; //!< invsim fn param ftype Util::sim_g = 2.13643992379; //!< invsim fn param ftype Util::sim_p = 0.04613803811; //!< invsim fn param ftype Util::sim_q = 1.82167089029; //!< invsim fn param ftype Util::sim_r = -0.74817947490; //!< invsim fn param Util::Util() { *((uitype32*)&nanf_) = CLIPPER_NULL_MASK_32; *((uitype64*)&nand_) = CLIPPER_NULL_MASK_64; if ( sizeof(ftype) == 4 ) *((uitype32*)&nan_) = CLIPPER_NULL_MASK_32; else if ( sizeof(ftype) == 8 ) *((uitype64*)&nan_) = CLIPPER_NULL_MASK_64; else /* fail on build */; } /*! \param x The argument \return I1(x)/I0(x) */ ftype Util::sim( const ftype& x ) { if (x >= 0.0) return (((x + sim_a)*x + sim_b)*x) / (((x + sim_c)*x + sim_d)*x + sim_e); else return -(-(-(-x + sim_a)*x + sim_b)*x) / (-(-(-x + sim_c)*x + sim_d)*x + sim_e); } /*! \param x I1(y)/I0(y) \return y */ ftype Util::invsim( const ftype& x ) { ftype x0 = fabs(x); ftype a0 = -7.107935*x0; ftype a1 = 3.553967-3.524142*x0; ftype a2 = 1.639294-2.228716*x0; ftype a3 = 1.0-x0; ftype w = a2/(3.0*a3); ftype p = a1/(3.0*a3)-w*w; ftype q = -w*w*w+0.5*(a1*w-a0)/a3; ftype d = sqrt(q*q+p*p*p); ftype q1 = q + d; ftype q2 = q - d; ftype r1 = pow(fabs(q1), 1.0/3.0); ftype r2 = pow(fabs(q2), 1.0/3.0); if (x >= 0.0) return (((q1>0.0)? r1 : -r1) + ((q2>0.0)? r2 : -r2) - w); else return -(((q1>0.0)? r1 : -r1) + ((q2>0.0)? r2 : -r2) - w); } ftype Util::sim_integ( const ftype& x0 ) { const ftype x = fabs(x0); const ftype z = (x+sim_p)/sim_q; return sim_A*log(x+sim_g) + 0.5*sim_B*log(z*z+1.0) + sim_r*atan(z) + x + 1.0; } ftype Util::sim_deriv( const ftype& x ) { if (x >= 0.0) return (((((sim_c-sim_a)*x+(2.0*sim_d-2.0*sim_b))*x+(3.0*sim_e+sim_a*sim_d-sim_b*sim_c))*x+(2.0*sim_a*sim_e))*x+(sim_b*sim_e)) / pow( (((x + sim_c)*x + sim_d)*x + sim_e), 2.0 ); else return (-(-(-(-(sim_c-sim_a)*x+(2.0*sim_d-2.0*sim_b))*x+(3.0*sim_e+sim_a*sim_d-sim_b*sim_c))*x+(2.0*sim_a*sim_e))*x+(sim_b*sim_e)) / pow( (-(-(-x + sim_c)*x + sim_d)*x + sim_e), 2.0 ); } ftype Util::sim_deriv_recur( const ftype& x0 ) { const ftype x = fabs(x0); const ftype m = sim(x); if ( x > 1.0e-4 ) return ( -m/x + ( 1.0 - m*m ) ); else return ( 0.5 - m*m ); } ftype Util::bessel_i0( const ftype& x0 ) { ftype i0 = 0.0, t, x; x = fabs(x0); t=x/3.75; if (t < 1.0) { t=t*t; i0= ((((((t*0.0045813+0.0360768)*t+0.2659732)*t+ 1.2067492)*t+3.0899424)*t+3.5156229)*t+1.0); } else { i0= (1.0/sqrt(x))*((((((((t*0.00392377-0.01647633)*t+ 0.02635537)*t-0.02057706)*t+0.00916281)*t- 0.00157565)*t+0.00225319)*t+0.01328592)*t+0.39894228)*exp(x); } return i0; } /*! \param x Angle in degrees \return Angle in radians */ ftype Util::d2rad( const ftype& x ) { return x*d2rad_; } /*! \param x Angle in radians \return Angle in degrees */ ftype Util::rad2d( const ftype& x ) { return x/d2rad_; } // template instantiations template ftype32 Util::max( const ftype32& a, const ftype32& b ); template ftype32 Util::min( const ftype32& a, const ftype32& b ); template ftype32 Util::bound( const ftype32& a, const ftype32& b, const ftype32& c ); template void Util::swap( ftype32& a, ftype32& b ); template void Util::swap( ftype32& a, ftype32& b, ftype32& c ); template ftype32 Util::sqr( const ftype32& a ); template ftype32 Util::isqrt( const ftype32& a ); template ftype64 Util::max( const ftype64& a, const ftype64& b ); template ftype64 Util::min( const ftype64& a, const ftype64& b ); template ftype64 Util::bound( const ftype64& a, const ftype64& b, const ftype64& c ); template void Util::swap( ftype64& a, ftype64& b ); template void Util::swap( ftype64& a, ftype64& b, ftype64& c ); template ftype64 Util::sqr( const ftype64& a ); template ftype64 Util::isqrt( const ftype64& a ); template int Util::max( const int& a, const int& b ); template int Util::min( const int& a, const int& b ); template int Util::bound( const int& a, const int& b, const int& c ); template void Util::swap( int& a, int& b ); template void Util::swap( int& a, int& b, int& c ); template int Util::sqr( const int& a ); template int Util::isqrt( const int& a ); } // namespace clipper clipper-2.1/clipper/core/Makefile.in0000644000374100011300000005662011372264333014375 00000000000000# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, # Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY, to the extent permitted by law; without # even the implied warranty of MERCHANTABILITY or 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mostlyclean mostlyclean-compile mostlyclean-generic \ mostlyclean-libtool pdf pdf-am ps ps-am tags uninstall \ uninstall-am uninstall-libLTLIBRARIES \ uninstall-library_includeHEADERS # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: clipper-2.1/clipper/core/clipper_types.h0000644000374100011300000006737311350422641015364 00000000000000/*! \file lib/clipper_types.h Header file for clipper basic types */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_TYPES #define CLIPPER_TYPES #include "clipper_util.h" #include "clipper_memory.h" namespace clipper { // forward definitions template class Mat33sym; //! String extension with simple parsing methods /*! String extension with primitive 'split' operation for parsing and pathname processing operations. */ class String : public std::string { public: inline String() : std::string() {} //!< null constructor inline String( const std::string str ) : std::string( str ) {} //!< constructor: from string inline String( const char* str ) : std::string( str ) {} //!< constructor: from char* String( const char* str, const int l ); //!< constructor: from char* String( const int i, const int w = 4 ); //!< constructor: from int String( const long i, const int w = 4 ); //!< constructor: from long //! constructor: from float String( const float f, const int w = 6, const int p = 6 ); //! constructor: from double String( const double f, const int w = 6, const int p = 6 ); //! String splitter - a very simple parser component std::vector split(const String sep) const; //! Return copy of string without leading and trailing blanks String trim() const; //! get trailing path element String tail() const; //! remove trailing path element String head() const; //! get leading path element String nohead() const; //! remove leading path element String notail() const; //! construct string from rational f using base b static String rational( const double f, const int b, const bool sign=false ); int i() const; //!< convert to int long l() const; //!< convert to long ftype32 f32() const; //!< convert to float ftype64 f64() const; //!< convert to double ftype f() const; //!< convert to ftype ftype rational() const; //!< convert from rational to ftype }; //! 3-vector class template class Vec3 { public: //! null constructor inline Vec3() {} //! constructor: from individual values inline Vec3( const T& v0, const T& v1, const T& v2 ) { vec[0] = v0; vec[1] = v1; vec[2] = v2; } //! constructor: copy/convert template explicit Vec3( const Vec3& v ) { vec[0] = TT(v[0]); vec[1] = TT(v[1]); vec[2] = TT(v[2]); } //! test equality bool equals( const Vec3& v, const T& tol ) const; //! get element inline const T& operator []( const int& i ) const { return vec[i]; } //! set element inline T& operator []( const int& i ) { return vec[i]; } //! return unit vector with same direction as this vector inline Vec3 unit() const { return (*this)*T(1.0/sqrt(ftype(vec[0]*vec[0]+vec[1]*vec[1]+vec[2]*vec[2]))); } //! return zero vector inline static Vec3 zero() { return Vec3( 0, 0, 0 ); } //! return null vector (only valid for floating point types) inline static Vec3 null() { return Vec3( T(Util::nan()), 0, 0 ); } //! test for null vector inline bool is_null() const { return Util::is_nan( vec[0] ); } //! Vector dot product (equivalent to *) inline static T dot( const Vec3& v1, const Vec3& v2 ) { return (v1[0]*v2[0] + v1[1]*v2[1] + v1[2]*v2[2]); } //! Vector cross product inline static Vec3 cross( const Vec3& v1, const Vec3& v2 ) { return Vec3(v1[1]*v2[2]-v2[1]*v1[2], v1[2]*v2[0]-v2[2]*v1[0], v1[0]*v2[1]-v2[0]*v1[1]); } //! return formatted String representation String format() const { return "("+String(vec[0],10,4)+","+String(vec[1],10,4)+","+String(vec[2],10,4)+")"; } //! add another vector to this one inline const Vec3& operator += ( const Vec3& v ) { vec[0] += v[0]; vec[1] += v[1]; vec[2] += v[2]; return (*this); } //! subtract another vector from this one inline const Vec3& operator -= ( const Vec3& v ) { vec[0] -= v[0]; vec[1] -= v[1]; vec[2] -= v[2]; return (*this); } //! Vector equality (for floating point types see equals()) //-- friend int operator == ( const Vec3& v1, const Vec3& v2 ); //! Vector inequality (for floating point types see equals()) //-- friend int operator != ( const Vec3& v1, const Vec3& v2 ); //! Vector negation operator //-- friend Vec3 operator -( const Vec3& v ); //! Vector addition operator //-- friend Vec3 operator +( const Vec3& v1, const Vec3 &v2 ); //! Vector subtraction operator //-- friend Vec3 operator -( const Vec3& v1, const Vec3& v2 ); //! Vector scaling operator //-- friend Vec3 operator *( const T& s, const Vec3& v1 ); //! Vector scaling operator //-- friend Vec3 operator *( const Vec3& v1, const T& s ); //! Vector dot product //-- friend T operator *( const Vec3& v1, const Vec3& v2 ); private: T vec[3]; }; template inline int operator == ( const Vec3& v1, const Vec3& v2 ) { return (v1[0]==v2[0] && v1[1]==v2[1] && v1[2]==v2[2]); } template inline int operator != ( const Vec3& v1, const Vec3& v2 ) { return (v1[0]!=v2[0] || v1[1]!=v2[1] || v1[2]!=v2[2]); } template inline Vec3 operator -( const Vec3& v ) { return Vec3( -v[0], -v[1], -v[2] ); } template inline Vec3 operator +( const Vec3& v1, const Vec3 &v2 ) { return Vec3( v1[0]+v2[0], v1[1]+v2[1], v1[2]+v2[2]); } template inline Vec3 operator -( const Vec3& v1, const Vec3& v2 ) { return Vec3( v1[0]-v2[0], v1[1]-v2[1], v1[2]-v2[2]); } template inline Vec3 operator *( const T& s, const Vec3& v1 ) { return Vec3( s*v1[0], s*v1[1], s*v1[2]); } template inline Vec3 operator *( const Vec3& v1, const T& s ) { return Vec3( s*v1[0], s*v1[1], s*v1[2]); } template inline T operator *( const Vec3& v1, const Vec3& v2 ) { return Vec3::dot(v1,v2); } //! 3x3-matrix class template class Mat33 { public: //! null constructor inline Mat33() {} //! constructor inline Mat33( const T& m00, const T& m01, const T& m02, const T& m10, const T& m11, const T& m12, const T& m20, const T& m21, const T& m22 ) { mat[0][0] = m00; mat[0][1] = m01; mat[0][2] = m02; mat[1][0] = m10; mat[1][1] = m11; mat[1][2] = m12; mat[2][0] = m20; mat[2][1] = m21; mat[2][2] = m22; } //! constructor: copy/convert template explicit Mat33( const Mat33& m ); //! constructor: copy/convert from symmetric matrix template explicit Mat33( const Mat33sym& m ); T det() const; //!< determinant Mat33 inverse() const; //!< inverse Mat33 transpose() const; //!< transpose bool equals( const Mat33& m, const T& tol ) const; //!< test equality inline const T& operator ()( const int& i, const int& j ) const { return mat[i][j]; } //!< get element inline T& operator ()( const int& i, const int& j ) { return mat[i][j]; } //!< set element //! return formatted String representation String format() const { return "|"+String(mat[0][0],10,4)+","+String(mat[0][1],10,4)+","+String(mat[0][2],10,4)+"|\n|"+String(mat[1][0],10,4)+","+String(mat[1][1],10,4)+","+String(mat[1][2],10,4)+"|\n|"+String(mat[2][0],10,4)+","+String(mat[2][1],10,4)+","+String(mat[2][2],10,4)+"|"; } //! return identity matrix inline static Mat33 identity() { Mat33 m; m.mat[0][0] = m.mat[1][1] = m.mat[2][2] = 1; m.mat[0][1] = m.mat[0][2] = m.mat[1][0] = m.mat[1][2] = m.mat[2][0] = m.mat[2][1] = 0; return m; } //! return null matrix (only valid for floating point types) inline static Mat33 null() { Mat33 m; m.mat[0][0] = Util::nan(); return m; } //! test for null matrix (only valid for floating point types) bool inline is_null() const { return Util::is_nan( mat[0][0] ); } //! Matrix-vector product /*! Assumes a column vector */ //-- friend Vec3 operator *( const Mat33& m, const Vec3& v ); //! Vector-matrix product /*! Assumes a row vector, i.e. equivalent to the matrix-vector product with the matrix trasposed */ //-- friend Vec3 operator *( const Vec3& v, const Mat33& m ); //! Matrix-matrix product //-- friend Mat33 operator *(const Mat33& m1, const Mat33& m2); //! Matrix sum //-- friend Mat33 operator +(const Mat33& m1, const Mat33& m2); //! Unary minus //-- friend Mat33 operator -(const Mat33& m); private: T mat[3][3]; }; template inline Vec3 operator *( const Mat33& m, const Vec3& v ) { return Vec3( m(0,0)*v[0]+m(0,1)*v[1]+m(0,2)*v[2], m(1,0)*v[0]+m(1,1)*v[1]+m(1,2)*v[2], m(2,0)*v[0]+m(2,1)*v[1]+m(2,2)*v[2] ); } template inline Vec3 operator *( const Vec3& v, const Mat33& m ) { return Vec3( v[0]*m(0,0)+v[1]*m(1,0)+v[2]*m(2,0), v[0]*m(0,1)+v[1]*m(1,1)+v[2]*m(2,1), v[0]*m(0,2)+v[1]*m(1,2)+v[2]*m(2,2) ); } template inline Mat33 operator *( const Mat33& m1, const Mat33& m2 ) { return Mat33 ( m1(0,0)*m2(0,0) + m1(0,1)*m2(1,0) + m1(0,2)*m2(2,0), m1(0,0)*m2(0,1) + m1(0,1)*m2(1,1) + m1(0,2)*m2(2,1), m1(0,0)*m2(0,2) + m1(0,1)*m2(1,2) + m1(0,2)*m2(2,2), m1(1,0)*m2(0,0) + m1(1,1)*m2(1,0) + m1(1,2)*m2(2,0), m1(1,0)*m2(0,1) + m1(1,1)*m2(1,1) + m1(1,2)*m2(2,1), m1(1,0)*m2(0,2) + m1(1,1)*m2(1,2) + m1(1,2)*m2(2,2), m1(2,0)*m2(0,0) + m1(2,1)*m2(1,0) + m1(2,2)*m2(2,0), m1(2,0)*m2(0,1) + m1(2,1)*m2(1,1) + m1(2,2)*m2(2,1), m1(2,0)*m2(0,2) + m1(2,1)*m2(1,2) + m1(2,2)*m2(2,2) ); } template inline Mat33 operator +( const Mat33& m1, const Mat33& m2 ) { return Mat33( m1(0,0)+m2(0,0), m1(0,1)+m2(0,1), m1(0,2)+m2(0,2), m1(1,0)+m2(1,0), m1(1,1)+m2(1,1), m1(1,2)+m2(1,2), m1(2,0)+m2(2,0), m1(2,1)+m2(2,1), m1(2,2)+m2(2,2) ); } template inline Mat33 operator -( const Mat33& m ) { return Mat33( -m(0,0), -m(0,1), -m(0,2), -m(1,0), -m(1,1), -m(1,2), -m(2,0), -m(2,1), -m(2,2) ); } //! Compressed form for 3x3 symmetric matrix class template class Mat33sym { public: //! null constructor inline Mat33sym() {} //! constructor: from Mat33 (does not check for symmetry) template explicit Mat33sym( const Mat33& m ) : m00(m(0,0)), m11(m(1,1)), m22(m(2,2)), m01(m(0,1)), m02(m(0,2)), m12(m(1,2)) {} //! constructor: from Mat33sym template explicit Mat33sym( const Mat33sym& m ) : m00(m.mat00()), m11(m.mat11()), m22(m.mat22()), m01(m.mat01()), m02(m.mat02()), m12(m.mat12()) {} //! constructor: from coefficients inline Mat33sym( const T& c00, const T& c11, const T& c22, const T& c01, const T& c02, const T& c12 ) : m00(c00), m11(c11), m22(c22), m01(c01), m02(c02), m12(c12) {} //! return formatted String representation String format() const { return "|"+String(m00,10,4)+","+String(m01,10,4)+","+String(m02,10,4)+"|\n|"+String(m01,10,4)+","+String(m11,10,4)+","+String(m12,10,4)+"|\n|"+String(m02,10,4)+","+String(m12,10,4)+","+String(m22,10,4)+"|"; } //! return identity matrix inline static Mat33sym identity() { return Mat33sym( 1, 1, 1, 0, 0, 0 ); } //! return null matrix (only valid for floating point types) inline static Mat33sym null() { return Mat33sym(Util::nan(),0,0,0,0,0); } //! test for null matrix (only valid for floating point types) inline bool is_null() const { return Util::is_nan( m00 ); } //! return quadratic form with vector T quad_form( const Vec3& v ) const; T det() const; //!< determinant Mat33 sqrt() const; //!< square root Mat33sym inverse() const; //!< inverse inline const T& mat00() const { return m00; } //!< element (0,0) inline const T& mat11() const { return m11; } //!< element (1,1) inline const T& mat22() const { return m22; } //!< element (2,2) inline const T& mat01() const { return m01; } //!< element (0,1) inline const T& mat02() const { return m02; } //!< element (0,2) inline const T& mat12() const { return m12; } //!< element (1,2) //! access elements as 3x3 matrix (inefficient) const T& operator ()( const int& i, const int& j ) const; //! Matrix-vector product //-- friend Vec3 operator *( const Mat33sym& m, const Vec3& v ); //! Matrix sum //-- friend Mat33sym operator +( const Mat33sym& m1, const Mat33sym& m2 ); //! Unary minus //-- friend Mat33sym operator -( const Mat33sym& m ); private: T m00, m11, m22, m01, m02, m12; }; template inline Vec3 operator *( const Mat33sym& m, const Vec3& v ) { return Vec3( m.mat00()*v[0]+m.mat01()*v[1]+m.mat02()*v[2], m.mat01()*v[0]+m.mat11()*v[1]+m.mat12()*v[2], m.mat02()*v[0]+m.mat12()*v[1]+m.mat22()*v[2] ); } template inline Mat33sym operator +( const Mat33sym& m1, const Mat33sym& m2 ) { return Mat33sym( m1.mat00()+m2.mat00(), m1.mat11()+m2.mat11(), m1.mat22()+m2.mat22(), m1.mat01()+m2.mat01(), m1.mat02()+m2.mat02(), m1.mat12()+m2.mat12() ); } template inline Mat33sym operator -( const Mat33sym& m ) { return Mat33sym( -m.mat00(), -m.mat11(), -m.mat22(), -m.mat01(), -m.mat02(), -m.mat12() ); } //! Rotation-translation operator template class RTop { public: //! null constructor inline RTop() {} //! constructor: from rotation inline explicit RTop( const Mat33& r ) : rot_( r ), trn_( Vec3::zero() ) {} //! constructor: from rotation and translation inline RTop( const Mat33& r, const Vec3& t ) : rot_( r ), trn_( t ) {} //! inverse RTop inverse() const { Mat33 minv = rot().inverse(); return RTop(minv, -(minv*trn())); } //! test equality with some tolerance inline bool equals( const RTop& m, const T& tol ) const { return ( rot().equals(m.rot(),tol) && trn().equals(m.trn(),tol) ); } inline const Mat33& rot() const { return rot_; } //!< get rotation inline const Vec3& trn() const { return trn_; } //!< get translation inline Mat33& rot() { return rot_; } //!< set rotation inline Vec3& trn() { return trn_; } //!< set translation //! return identity operator inline static RTop identity() { return RTop( Mat33::identity(), Vec3::zero() ); } //! return identity operator inline static RTop null() { return RTop( Mat33::null(), Vec3::null() ); } //! test for null operator inline bool is_null() const { return rot_.is_null() || trn_.is_null(); } //! return formatted String representation String format() const { return rot_.format() + "\n" + trn_.format(); } //! apply RTop to vector //-- friend Vec3 operator *( const RTop& r, const Vec3& v ); //! RTop product //-- friend RTop operator *( const RTop& r1, const RTop& r2 ); private: Mat33 rot_; Vec3 trn_; }; template inline Vec3 operator *( const RTop& r, const Vec3& v ) { return r.rot()*v + r.trn(); } template inline RTop operator *( const RTop& r1, const RTop& r2 ) { return RTop( r1.rot()*r2.rot(), r1.rot()*r2.trn()+r1.trn() ); } //! Simple 2-d array class template class Array2d { public: //! null constructor inline Array2d() { d1_ = d2_ = 0; } //! constructor inline Array2d( const int& d1, const int& d2 ) { resize( d1, d2 ); } //! constructor inline Array2d( const int& d1, const int& d2, T val ) { resize( d1, d2, val ); } //! resize void inline resize( const int& d1, const int& d2 ) { d1_ = d1; d2_ = d2; data.resize( size() ); } //! resize void inline resize( const int& d1, const int& d2, const T& val ) { d1_ = d1; d2_ = d2; data.resize( size(), val ); } inline int size() const { return d1_ * d2_; } //!< size inline const int& rows() const { return d1_; } //!< number of rows inline const int& cols() const { return d2_; } //!< number of cols //! read accessor inline const T& operator () ( const int& i1, const int& i2 ) const { return data[ i1*d2_ + i2 ]; } //! write accessor inline T& operator () ( const int& i1, const int& i2 ) { return data[ i1*d2_ + i2 ]; } protected: std::vector data; int d1_, d2_; }; //! General matrix class: like Array2d but with numerical methods template class Matrix : public Array2d { public: //! null constructor inline Matrix() {} //! constructor inline Matrix( const int& d1, const int& d2 ) { Array2d::resize( d1, d2 ); } //! constructor inline Matrix( const int& d1, const int& d2, T val ) { Array2d::resize( d1, d2, val ); } //! equation solver (square matrices only) std::vector solve( const std::vector& b ) const; //! eigenvalue calculation (square symmetric matrices only) std::vector eigen( const bool sort = true ); //! Matrix-vector product /*! Assumes a column vector */ //-- friend std::vector operator *( const Matrix& m, const std::vector& v ); }; template std::vector operator *( const Matrix& m, const std::vector& v ) { if ( m.cols() != v.size() ) Message::message( Message_fatal( "Matrix*vector dimension mismatch" ) ); std::vector r( m.rows() ); int i, j; T s; for ( i = 0; i < m.rows(); i++ ) { s = T(0); for ( j = 0; j < m.cols(); j++ ) s += m(i,j) * v[j]; r[i] = s; } return r; } // template implementations template bool Vec3::equals( const Vec3& v, const T& tol ) const { return ( pow(vec[0]-v[0],T(2)) + pow(vec[1]-v[1],T(2)) + pow(vec[2]-v[2],T(2)) <= pow(tol,T(2)) ); } template template Mat33::Mat33( const Mat33& m ) { mat[0][0]=T(m(0,0)); mat[0][1]=T(m(0,1)); mat[0][2]=T(m(0,2)); mat[1][0]=T(m(1,0)); mat[1][1]=T(m(1,1)); mat[1][2]=T(m(1,2)); mat[2][0]=T(m(2,0)); mat[2][1]=T(m(2,1)); mat[2][2]=T(m(2,2)); } template template Mat33::Mat33( const Mat33sym& m ) { mat[0][0]=T(m.mat00()); mat[1][1]=T(m.mat11()); mat[2][2]=T(m.mat22()); mat[0][1]=mat[1][0]=T(m.mat01()); mat[0][2]=mat[2][0]=T(m.mat02()); mat[1][2]=mat[2][1]=T(m.mat12()); } template bool Mat33::equals( const Mat33& m, const T& tol ) const { return ( pow(mat[0][0]-m(0,0),T(2)) + pow(mat[0][1]-m(0,1),T(2)) + pow(mat[0][2]-m(0,2),T(2)) + pow(mat[1][0]-m(1,0),T(2)) + pow(mat[1][1]-m(1,1),T(2)) + pow(mat[1][2]-m(1,2),T(2)) + pow(mat[2][0]-m(2,0),T(2)) + pow(mat[2][1]-m(2,1),T(2)) + pow(mat[2][2]-m(2,2),T(2)) <= pow(tol,T(2)) ); } template T Mat33::det() const { return ( mat[0][0]*(mat[1][1]*mat[2][2] - mat[1][2]*mat[2][1]) + mat[0][1]*(mat[1][2]*mat[2][0] - mat[1][0]*mat[2][2]) + mat[0][2]*(mat[1][0]*mat[2][1] - mat[1][1]*mat[2][0]) ); } template Mat33 Mat33::inverse() const { T d = det(); Mat33 inv; inv(0,0) = ( mat[1][1]*mat[2][2] - mat[1][2]*mat[2][1] ) / d; inv(1,0) = ( mat[1][2]*mat[2][0] - mat[1][0]*mat[2][2] ) / d; inv(2,0) = ( mat[1][0]*mat[2][1] - mat[1][1]*mat[2][0] ) / d; inv(0,1) = ( mat[2][1]*mat[0][2] - mat[2][2]*mat[0][1] ) / d; inv(1,1) = ( mat[2][2]*mat[0][0] - mat[2][0]*mat[0][2] ) / d; inv(2,1) = ( mat[2][0]*mat[0][1] - mat[2][1]*mat[0][0] ) / d; inv(0,2) = ( mat[0][1]*mat[1][2] - mat[0][2]*mat[1][1] ) / d; inv(1,2) = ( mat[0][2]*mat[1][0] - mat[0][0]*mat[1][2] ) / d; inv(2,2) = ( mat[0][0]*mat[1][1] - mat[0][1]*mat[1][0] ) / d; return inv; } template Mat33 Mat33::transpose() const { Mat33 t; t(0,0) = mat[0][0]; t(0,1) = mat[1][0]; t(0,2) = mat[2][0]; t(1,0) = mat[0][1]; t(1,1) = mat[1][1]; t(1,2) = mat[2][1]; t(2,0) = mat[0][2]; t(2,1) = mat[1][2]; t(2,2) = mat[2][2]; return t; } template T Mat33sym::det() const { return ( m00*(m11*m22 - m12*m12) + m01*(m12*m02 - m01*m22) + m02*(m01*m12 - m11*m02) ); } template Mat33 Mat33sym::sqrt() const { Mat33 half( Mat33sym( 0.5, 0.5, 0.5, 0.0, 0.0, 0.0 ) ); Mat33 target( *this ); Mat33 result( target ); result(1,0) = result(2,0) = result(2,1) = 0.0; for ( int i = 0; i < 10; i++ ) result = half * ( result.inverse() * target + result ); return result; } template Mat33sym Mat33sym::inverse() const { T d = det(); return Mat33sym ( ( m11*m22 - m12*m12 ) / d, ( m22*m00 - m02*m02 ) / d, ( m00*m11 - m01*m01 ) / d, ( m12*m02 - m22*m01 ) / d, ( m01*m12 - m02*m11 ) / d, ( m02*m01 - m00*m12 ) / d ); } template T Mat33sym::quad_form( const Vec3& v ) const { return ( v[0]*( v[0]*m00 + 2*(v[1]*m01+v[2]*m02) ) + v[1]*( v[1]*m11 + 2*(v[2]*m12) ) + v[2]*v[2]*m22 ); } template const T& Mat33sym::operator ()( const int& i, const int& j ) const { switch (i) { case 0: switch (j) { case 0: return m00; case 1: return m01; default: return m02; } case 1: switch (j) { case 0: return m01; case 1: return m11; default: return m12; } default: switch (j) { case 0: return m02; case 1: return m12; default: return m22; } } } // complex matrix methods /*! Solve the system of linear equations Ax=b for x Uses elimination. Only suitable for small systems. */ template std::vector Matrix::solve( const std::vector& b ) const { if ( Array2d::rows() != Array2d::cols() ) Message::message( Message_fatal("Matrix.solve() matrix not square") ); if ( Array2d::rows() != b.size() ) Message::message( Message_fatal("Matrix.solve() matrix/vector mismatch") ); const int n = Array2d::rows(); // solve for X by Gaussian elimination T s, pivot; int i, j, k; Matrix a = *this; std::vector x = b; for ( i = 0; i < n; i++ ) { // pick largest pivot j = i; for ( k = i+1; k < n; k++ ) if ( fabs(a(k,i)) > fabs(a(j,i)) ) j = k; // swap rows for ( k = 0; k < n; k++ ) Util::swap( a(i,k), a(j,k) ); Util::swap( x[i], x[j] ); // perform elimination pivot = a(i,i); for ( j = 0; j < n; j++ ) { if ( j != i ) { s = a(j,i) / pivot; for ( k = i+1; k < n; k++ ) a(j,k) = a(j,k) - s*a(i,k); x[j] = x[j] - s*x[i]; } } } for ( i = 0; i < n; i++ ) x[i] /= a(i,i); return x; } /*! Find the Eigenvalues and Eigenvectors of the matrix. Uses the Jacobi method. Only suitable for small systems (dimension<20). The matrix is replaced by the matrix of eigenvectors (as columns). \param sort Sort the eigenvalues and vectors, smallest first. (default=true) \return Vector of eigenvalues. */ template std::vector Matrix::eigen( const bool sort ) { if ( Array2d::rows() != Array2d::cols() ) Message::message( Message_fatal( "Matrix.eigen() matrix not square" ) ); const int n = Array2d::rows(); int cyc, j, q, p; T spp, spq, t, s, c, theta, tau, h, ap, aq, a_pq; Matrix& mat = *this; Matrix evec( n, n, 0.0 ); std::vector eval( n ); std::vector b( n ); std::vector z( n ); // Set evec to identity, eval & b to diagonal, z to 0. for( p = 0; p < n; p++ ) { evec(p,p) = 1.0; eval[p] = b[p] = mat(p,p); } for ( cyc = 1; cyc <= 50; cyc++ ) { // calc sum of diagonal, off-diagonal spp = spq = 0.0; for ( p=0; p 1.0e-12*fabs(h) ) { theta = 0.5*h/a_pq; t = 1.0/(fabs(theta) + sqrt(1.0 + theta*theta)); if ( theta < 0.0 ) t = -t; } else { t = a_pq/h; } // calc trig properties c = 1.0/sqrt(1.0+t*t); s = t*c; tau = s/(1.0+c); h = t * a_pq; // update eigenvalues z[p] -= h; z[q] += h; eval[p] -= h; eval[q] += h; // rotate the upper diagonal of the matrix mat( p, q ) = 0.0; for ( j = 0; j < p; j++ ) { ap = mat( j, p ); aq = mat( j, q ); mat( j, p ) = ap - s * ( aq + ap * tau ); mat( j, q ) = aq + s * ( ap - aq * tau ); } for ( j = p+1; j < q; j++ ) { ap = mat( p, j ); aq = mat( j, q ); mat( p, j ) = ap - s * ( aq + ap * tau ); mat( j, q ) = aq + s * ( ap - aq * tau ); } for ( j = q+1; j < n; j++ ) { ap = mat( p, j ); aq = mat( q, j ); mat( p, j ) = ap - s * ( aq + ap * tau ); mat( q, j ) = aq + s * ( ap - aq * tau ); } // apply corresponding rotation to result for ( j = 0; j < n; j++ ) { ap = evec( j, p ); aq = evec( j, q ); evec( j, p ) = ap - s * ( aq + ap * tau ); evec( j, q ) = aq + s * ( ap - aq * tau ); } } } for ( p = 0; p < n; p++ ) { b[p] += z[p]; eval[p] = b[p]; } } // sort the eigenvalues if ( sort ) { for ( p = 0; p < n; p++ ) { j = p; // set j to index of largest remaining eval for ( q = p+1; q < n; q++ ) if ( eval[q] < eval[j] ) j = q; Util::swap( eval[p], eval[j] ); // now swap evals, evecs for ( q = 0; q < n; q++ ) Util::swap( evec( q, p ), evec( q, j ) ); } } // return eigenvalues mat = evec; return eval; } } // namespace clipper #endif clipper-2.1/clipper/core/clipper_instance.h0000644000374100011300000000627111205016247016012 00000000000000/*! \file lib/clipper_instance.h Header file for clipper helper functions */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_INSTANCE #define CLIPPER_INSTANCE #include "hkl_data.h" #include "xmap.h" namespace clipper { // \internal Class used to instantiate cache objects class ClipperInstance { public: ClipperInstance(); ~ClipperInstance(); const Util& util() const { return util_; } ObjectCache& spacegroup_cache() { return sgcache_; } ObjectCache& xmap_cache() { return xmcache_; } ObjectCache& hkl_data_cache() { return hdcache_; } void destroy(); //!< VERY DANGEROUS, DO NOT USE private: Util util_; ObjectCache sgcache_; ObjectCache xmcache_; ObjectCache hdcache_; }; // \internal Class used to instantiate cache objects class ClipperInstantiator { public: ClipperInstantiator() {} ~ClipperInstantiator() {} static ClipperInstance& instance() { return inst; } private: static ClipperInstance inst; }; } // namespace clipper #endif clipper-2.1/clipper/core/fftmap_sparse.h0000644000374100011300000001437010736415747015341 00000000000000/*! \file lib/fftmap_sparse.h Header file for P1 fft map */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_FFTMAP_SPARSE #define CLIPPER_FFTMAP_SPARSE #include "fftmap.h" namespace clipper { //! base type for sparse P1 fft maps class FFTmap_sparse_p1_base : public FFTmap_base { public: //! initialiser: takes grid void init( const Grid_sampling& grid_sam, const FFTtype type = Default ); //! Destructor ~FFTmap_sparse_p1_base(); //! get real grid sampling const Grid_sampling& grid_real() const { return grid_real_; } //! get reciprocal grid const Grid& grid_reci() const { return grid_reci_; } //! set/get default optimisation type static FFTtype& default_type() { return default_type_; } protected: //! return/create row ffttype* map_uv( const int& u, const int& v ); //! return/create row std::complex* map_kl( const int& k, const int& l ); Grid_sampling grid_real_; //!< real space grid Grid grid_reci_; //!< reciprocal space grid FFTtype type_; //!< optimisation options Array2d*> row_kl; //!< section map Array2d row_uv; //!< section map static FFTtype default_type_; //!< default optimisation options }; //! FFTmap_sparse_p1_hx: low level sparse P1 map used for calculating FFTs /*! This version computes sparse Hermititan...real FFTs. By specifying what parts of the map are needed in advance, it is possible to perform highly optimised FFTs, including some of the benefits of symmetry. */ class FFTmap_sparse_p1_hx : public FFTmap_sparse_p1_base { public: //! Null constuctor FFTmap_sparse_p1_hx(); //! Constructor: takes grid FFTmap_sparse_p1_hx( const Grid_sampling& grid_sam, const FFTtype type = Default ); //-- void init( const Grid_sampling& grid_sam, const FFTtype type = Default ); //-- const Grid_sampling& grid_real() const; //-- const Grid& grid_reci() const; //! set reciprocal space data by hkl void set_hkl( const HKL& hkl, const std::complex& f ); //! set reciprocal space data (internal use) std::complex& cplx_data( const Coord_grid& uvw ) { return map_kl( uvw.v(), uvw.w() )[ uvw.u() ]; } //! express need for real space data void require_real_data( const Coord_grid& uvw ) { map_uv( uvw.u(), uvw.v() ); } //! get real space data ( uvw must be in grid_real() ) const ffttype& real_data( const Coord_grid& uvw ) const { return row_uv( uvw.u(), uvw.v() )[ uvw.w() ]; } //! Transform to real space void fft_h_to_x( const ftype& scale ); }; //! FFTmap_sparse_p1_xh: low level sparse P1 map used for calculating FFTs /*! This version computes sparse real...Hermititan FFTs. By specifying what parts of the map are needed in advance, it is possible to perform highly optimised FFTs, including some of the benefits of symmetry. */ class FFTmap_sparse_p1_xh : public FFTmap_sparse_p1_base { public: //! Null constuctor FFTmap_sparse_p1_xh(); //! Constructor: takes grid FFTmap_sparse_p1_xh( const Grid_sampling& grid_sam, const FFTtype type = Default ); //-- void init( const Grid_sampling& grid_sam, const FFTtype type = Default ); //-- const Grid_sampling& grid_real() const; //-- const Grid& grid_reci() const; //! set real space data ( uvw must be in grid_real() ) ffttype& real_data( const Coord_grid& uvw ) { return map_uv( uvw.u(), uvw.v() )[ uvw.w() ]; } //! express need for reciprocal space data by hkl void require_hkl( const HKL& hkl ); //! get reciprocal space data by hkl const std::complex get_hkl( const HKL& hkl ) const; //! express need for reciprocal space data (internal use) void require_cplx_data( const Coord_grid& hkl ) { map_kl( hkl.v(), hkl.w() ); } //! get reciprocal space data (internal use) const std::complex& cplx_data( const Coord_grid& hkl ) const { return row_kl( hkl.v(), hkl.w() )[ hkl.u() ]; } //! Transform to real space void fft_x_to_h( const ftype& scale ); }; } // namespace clipper #endif clipper-2.1/clipper/core/resol_basisfn.h0000644000374100011300000003463411271550377015337 00000000000000/*! \file lib/resol_basisfn.h Header file for resolution basis function */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_RESOL_BASISFN #define CLIPPER_RESOL_BASISFN #include "resol_fn.h" namespace clipper { //! Resolution ordinal gernerator /*! This class is a helper class for functions which need to divide reflections up by resolution whilst guaranteeing a certain distribution of number of reflections per range. It takes a list of reflections, one at a time, and calculates a function to get the approximate ordinal number of a reflection in a list sorted by resolution. */ class Resolution_ordinal : public Generic_ordinal { public: //! initialiser: takes an HKL_info and uses all reflections. void init( const HKL_info& hklinfo, const ftype& power ); //! initialiser: takes an HKL_data & uses non-missing reflections. void init( const HKL_data_base& hkldata, const ftype& power ); //! initialiser: takes an HKL_data + Cell & uses non-missing reflections. void init( const HKL_data_base& hkldata, const Cell& cell, const ftype& power ); }; //! simple binning basis function /*! This class bins reflections on the basis of resolution, i.e. it generates a resolution function from spherical shells. */ class BasisFn_binner : public BasisFn_base { public: //! constructor: include whole reflection list in histogram BasisFn_binner( const HKL_info& hklinfo, const int& nbins_, const ftype power = 1.0 ) : BasisFn_base( nbins_ ) { s_ord.init( hklinfo, power ); } //! constructor: include only non-missing reflections in histogram BasisFn_binner( const HKL_data_base& hkldata, const int& nbins_, const ftype power = 1.0 ) : BasisFn_base( nbins_ ) { s_ord.init( hkldata, hkldata.base_cell(), power ); } //! the value of the resolution function (override for speed) ftype f_s( const ftype& s, const std::vector& params ) const; //! the derivative of the resolution function w.r.t. the parameters const BasisFn_base::Fderiv& fderiv_s( const ftype& s, const std::vector& params ) const; //! the type of the function: optionally used to improve convergence FNtype type() const { return LINEAR; } //! number of non-zero diagonals in the upper triangle of the curvatures int num_diagonals() const { return 1; } //! the value of the resolution function (override for speed) ftype f( const HKL& hkl, const Cell& cell, const std::vector& params ) const { return f_s( hkl.invresolsq( cell ), params ); } //! the derivatives of the resolution function w.r.t. the parameters const BasisFn_base::Fderiv& fderiv( const HKL& hkl, const Cell& cell, const std::vector& params ) const { return fderiv_s( hkl.invresolsq( cell ), params ); } private: Resolution_ordinal s_ord; //& params ) const; //! the derivative of the resolution function w.r.t. the parameters const BasisFn_base::Fderiv& fderiv_s( const ftype& s, const std::vector& params ) const; //! the type of the function: optionally used to improve convergence FNtype type() const { return LINEAR; } //! number of non-zero diagonals in the upper triangle of the curvatures int num_diagonals() const { return 2; } //! the value of the resolution function (override for speed) ftype f( const HKL& hkl, const Cell& cell, const std::vector& params ) const { return f_s( hkl.invresolsq( cell ), params ); } //! the derivatives of the resolution function w.r.t. the parameters const BasisFn_base::Fderiv& fderiv( const HKL& hkl, const Cell& cell, const std::vector& params ) const { return fderiv_s( hkl.invresolsq( cell ), params ); } private: Resolution_ordinal s_ord; //& params ) const; //! the derivative of the resolution function w.r.t. the parameters const BasisFn_base::Fderiv& fderiv_s( const ftype& s, const std::vector& params ) const; //! the type of the function: optionally used to improve convergence FNtype type() const { return LINEAR; } //! number of non-zero diagonals in the upper triangle of the curvatures int num_diagonals() const { return 3; } //! the value of the resolution function (override for speed) ftype f( const HKL& hkl, const Cell& cell, const std::vector& params ) const { return f_s( hkl.invresolsq( cell ), params ); } //! the derivatives of the resolution function w.r.t. the parameters const BasisFn_base::Fderiv& fderiv( const HKL& hkl, const Cell& cell, const std::vector& params ) const { return fderiv_s( hkl.invresolsq( cell ), params ); } private: Resolution_ordinal s_ord; //& params ) const; //! the derivatives of the resolution function w.r.t. the parameters const BasisFn_base::Fderiv& fderiv_s( const ftype& s, const std::vector& params ) const; //! the value of the resolution function (override for speed) //ftype f( const HKL& hkl, const Cell& cell, const std::vector& params ) const { return f_s( hkl.invresolsq( cell ), params ); } //! the derivatives of the resolution function w.r.t. the parameters const BasisFn_base::Fderiv& fderiv( const HKL& hkl, const Cell& cell, const std::vector& params ) const { return fderiv_s( hkl.invresolsq( cell ), params ); } //! return the scale factor corresponding to the Gaussian parameters ftype scale( const std::vector& params ) const; //! return the isotropic U corresponding to the Gaussian parameters ftype u_iso( const std::vector& params ) const; }; //! simple anisotropic Gaussian basis function /*! This class provides a anisotropic Gaussian basis function. */ class BasisFn_aniso_gaussian : public BasisFn_base { public: //! constructor: BasisFn_aniso_gaussian() : BasisFn_base( 7 ) {} //! the derivatives of the resolution function w.r.t. the parameters const BasisFn_base::Fderiv& fderiv_coord( const Coord_reci_orth& xs, const std::vector& params ) const; //! the value of the resolution function (override for speed) //ftype f( const HKL& hkl, const Cell& cell, const std::vector& params ) const { return f_coord( hkl.coord_reci_orth( cell ), params ); } //! the derivatives of the resolution function w.r.t. the parameters const BasisFn_base::Fderiv& fderiv( const HKL& hkl, const Cell& cell, const std::vector& params ) const { return fderiv_coord( hkl.coord_reci_orth( cell ), params ); } //! return the scale factor corresponding to the Gaussian parameters ftype scale( const std::vector& params ) const; //! return the anisotropic U corresponding to the Gaussian parameters U_aniso_orth u_aniso_orth( const std::vector& params ) const; }; //! simple log Gaussian basis function /*! This class provides a Log Gaussian basis function. i.e. a quadratic function of resolution. Use this in conjunction with a Log-target function to get a fast estimate to a Gaussian fit. */ class BasisFn_log_gaussian : public BasisFn_base { public: //! constructor: BasisFn_log_gaussian() : BasisFn_base( 2 ) {} //! the value of the resolution function //ftype f_s( const ftype& s, const std::vector& params ) const; //! the derivatives of the resolution function w.r.t. the parameters const BasisFn_base::Fderiv& fderiv_s( const ftype& s, const std::vector& params ) const; //! the value of the resolution function (override for speed) //ftype f( const HKL& hkl, const Cell& cell, const std::vector& params ) const { return f_s( hkl.invresolsq( cell ), params ); } //! the derivatives of the resolution function w.r.t. the parameters const BasisFn_base::Fderiv& fderiv( const HKL& hkl, const Cell& cell, const std::vector& params ) const { return fderiv_s( hkl.invresolsq( cell ), params ); } //! the type of the function: optionally used to improve convergence FNtype type() const { return LINEAR; } //! return the scale factor corresponding to the Gaussian parameters ftype scale( const std::vector& params ) const; //! return the isotropic U corresponding to the Gaussian parameters ftype u_iso( const std::vector& params ) const; }; //! simple anisotropic Gaussian basis function /*! This class provides a anisotropic Gaussian basis function. i.e. a general quadratic function of resolution. Use this in conjunction with a Log-target function to get a fast estimate to a Gaussian fit. */ class BasisFn_log_aniso_gaussian : public BasisFn_base { public: //! constructor: BasisFn_log_aniso_gaussian() : BasisFn_base( 7 ) {} //! the derivatives of the resolution function w.r.t. the parameters const BasisFn_base::Fderiv& fderiv_coord( const Coord_reci_orth& xs, const std::vector& params ) const; //! the value of the resolution function (override for speed) //ftype f( const HKL& hkl, const Cell& cell, const std::vector& params ) const { return f_coord( hkl.coord_reci_orth( cell ), params ); } //! the derivatives of the resolution function w.r.t. the parameters const BasisFn_base::Fderiv& fderiv( const HKL& hkl, const Cell& cell, const std::vector& params ) const { return fderiv_coord( hkl.coord_reci_orth( cell ), params ); } //! the type of the function: optionally used to improve convergence FNtype type() const { return LINEAR; } //! return the scale factor corresponding to the Gaussian parameters ftype scale( const std::vector& params ) const; //! return the anisotropic U corresponding to the Gaussian parameters U_aniso_orth u_aniso_orth( const std::vector& params ) const; }; //! simple Expcubic basis function /*! This class provides a Expcubic basis function. */ class BasisFn_expcubic : public BasisFn_base { public: //! constructor BasisFn_expcubic() : BasisFn_base( 4 ) {} //! the derivatives of the resolution function w.r.t. the parameters const BasisFn_base::Fderiv& fderiv_s( const ftype& s, const std::vector& params ) const; //! the value of the resolution function (override for speed) //ftype f( const HKL& hkl, const Cell& cell, const std::vector& params ) const { return f_s( hkl.invresolsq( cell ), params ); } //! the derivatives of the resolution function w.r.t. the parameters const BasisFn_base::Fderiv& fderiv( const HKL& hkl, const Cell& cell, const std::vector& params ) const { return fderiv_s( hkl.invresolsq( cell ), params ); } }; } // namespace clipper #endif clipper-2.1/clipper/core/hkl_datatypes.cpp0000644000374100011300000000556310363703537015673 00000000000000/* hkl_datatypes.cpp: fundamental data types for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "hkl_datatypes.h" namespace clipper { namespace datatypes { // compile template types template class I_sigI; template class I_sigI_ano; template class F_sigF; template class F_sigF_ano; template class E_sigE; template class F_phi; template class Phi_fom; template class ABCD; template class I_sigI; template class I_sigI_ano; template class F_sigF; template class F_sigF_ano; template class E_sigE; template class F_phi; template class Phi_fom; template class ABCD; } // namespace datatypes } // namespace clipper clipper-2.1/clipper/core/spacegroup_data.cpp0000644000374100011300000011655210365657772016214 00000000000000/* spacegroup_data.cpp: spacegroup data tables */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA /* Some code coverted from the paper of Hall & Grosse-Kunstleve */ #include "spacegroup_data.h" namespace clipper { namespace data { // ASU fns bool ASU_111( const int& h, const int& k, const int& l ) { return (l>0 || (l==0 && (h>0 || (h==0 && k>=0)))); } bool ASU_112( const int& h, const int& k, const int& l ) { return (l>=0 && (h>0 || (h==0 && k>=0))); } bool ASU_121( const int& h, const int& k, const int& l ) { return (k>=0 && (l>0 || (l==0 && h>=0))); } bool ASU_211( const int& h, const int& k, const int& l ) { return (h>=0 && (k>0 || (k==0 && l>=0))); } bool ASU_21U( const int& h, const int& k, const int& l ) { return (h+k>=0 && (l>0 || (l==0 && h-k>=0))); } bool ASU_21V( const int& h, const int& k, const int& l ) { return (l+h>=0 && (k>0 || (k==0 && l-h>=0))); } bool ASU_21W( const int& h, const int& k, const int& l ) { return (k+l>=0 && (h>0 || (h==0 && k-l>=0))); } bool ASU_21X( const int& h, const int& k, const int& l ) { return (h-k>=0 && (l>0 || (l==0 && h+k>=0))); } bool ASU_21Y( const int& h, const int& k, const int& l ) { return (l-h>=0 && (k>0 || (k==0 && l+h>=0))); } bool ASU_21Z( const int& h, const int& k, const int& l ) { return (k-l>=0 && (h>0 || (h==0 && k+l>=0))); } bool ASU_222( const int& h, const int& k, const int& l ) { return (h>=0 && k>=0 && l>=0); } bool ASU_22U( const int& h, const int& k, const int& l ) { return (h<=k && h>=-k && l>=0); } bool ASU_22V( const int& h, const int& k, const int& l ) { return (l<=h && l>=-h && k>=0); } bool ASU_22W( const int& h, const int& k, const int& l ) { return (k<=l && k>=-l && h>=0); } bool ASU_114( const int& h, const int& k, const int& l ) { return (l>=0 && ((h>=0 && k>0) || (h==0 && k==0))); } bool ASU_141( const int& h, const int& k, const int& l ) { return (k>=0 && ((l>=0 && h>0) || (l==0 && h==0))); } bool ASU_411( const int& h, const int& k, const int& l ) { return (h>=0 && ((k>=0 && l>0) || (k==0 && l==0))); } bool ASU_224( const int& h, const int& k, const int& l ) { return (h>=k && k>=0 && l>=0); } bool ASU_242( const int& h, const int& k, const int& l ) { return (l>=h && h>=0 && k>=0); } bool ASU_422( const int& h, const int& k, const int& l ) { return (k>=l && l>=0 && h>=0); } bool ASU_113( const int& h, const int& k, const int& l ) { return (h>=0 && k>0) || (h==0 && k==0 && l >= 0); } bool ASU_131( const int& h, const int& k, const int& l ) { return (l>=0 && h>0) || (l==0 && h==0 && k >= 0); } bool ASU_311( const int& h, const int& k, const int& l ) { return (k>=0 && l>0) || (k==0 && l==0 && h >= 0); } bool ASU_11T( const int& h, const int& k, const int& l ) { return (h<=0 && k>0) || (h==0 && k==0 && l >= 0); } bool ASU_1T1( const int& h, const int& k, const int& l ) { return (l<=0 && h>0) || (l==0 && h==0 && k >= 0); } bool ASU_T11( const int& h, const int& k, const int& l ) { return (k<=0 && l>0) || (k==0 && l==0 && h >= 0); } bool ASU_31A( const int& h, const int& k, const int& l ) { return (k-l>=0 && l-h>0) || (h==l && k==l && h+k+l>=0); } bool ASU_31B( const int& h, const int& k, const int& l ) { return (k-l>=0 && l+h>0) || (-h==l && k==l && -h+k+l>=0); } bool ASU_31C( const int& h, const int& k, const int& l ) { return (-k-l>=0 && l-h>0) || (h==l && -k==l && h-k+l>=0); } bool ASU_31D( const int& h, const int& k, const int& l ) { return (k+l>=0 && -l-h>0) || (h==-l && k==-l && h+k-l>=0); } bool ASU_223( const int& h, const int& k, const int& l ) { return (h>=k && k>=0 && (k>0 || l>=0)); } bool ASU_232( const int& h, const int& k, const int& l ) { return (l>=h && h>=0 && (h>0 || k>=0)); } bool ASU_322( const int& h, const int& k, const int& l ) { return (k>=l && l>=0 && (l>0 || h>=0)); } bool ASU_32A( const int& h, const int& k, const int& l ) { return (h>=k && k+l>=h+h && (k+l>h+h || h+k+l>=0)); } bool ASU_32B( const int& h, const int& k, const int& l ) { return (-h>=k && k+l>=-h-h && (k+l>-h-h || -h+k+l>=0)); } bool ASU_32C( const int& h, const int& k, const int& l ) { return (h>=-k && -k+l>=h+h && (-k+l>h+h || h-k+l>=0)); } bool ASU_32D( const int& h, const int& k, const int& l ) { return (h>=k && k-l>=h+h && (k-l>h+h || h+k-l>=0)); } bool ASU_32U( const int& h, const int& k, const int& l ) { return (h>=k && k>=0 && (h>k || l>=0)); } bool ASU_32V( const int& h, const int& k, const int& l ) { return (k>=l && l>=0 && (k>l || h>=0)); } bool ASU_32W( const int& h, const int& k, const int& l ) { return (l>=h && h>=0 && (l>h || k>=0)); } bool ASU_32X( const int& h, const int& k, const int& l ) { return (-h>=k && k>=0 && (-h>k || l>=0)); } bool ASU_32Y( const int& h, const int& k, const int& l ) { return (-k>=l && l>=0 && (-k>l || h>=0)); } bool ASU_32Z( const int& h, const int& k, const int& l ) { return (-l>=h && h>=0 && (-l>h || k>=0)); } bool ASU_M3B( const int& h, const int& k, const int& l ) { return (h>=0 && ((l>=h && k>h) || (l==h && k==h))); } bool ASU_M3M( const int& h, const int& k, const int& l ) { return (k>=l && l>=h && h>=0); } // ABCD are 4 dirns for body diagonal, UVWXYZ are 6 dirns for face diagonal LGdata lgdata[] = { { 0x2df60a45, &ASU_111, "-1" }, // -P 1 { 0x9b92779f, &ASU_112, "2/m" }, // -P 2 { 0x068dfeb3, &ASU_121, "2/m" }, // -P 2y { 0xb08d46cf, &ASU_211, "2/m" }, // -P 2x { 0x12339040, &ASU_21U, "2/m" }, // -P 2" { 0x44aa9a14, &ASU_21V, "2/m" }, // -P 2y" { 0x53e4b366, &ASU_21W, "2/m" }, // -P 2x" { 0x4321a07d, &ASU_21X, "2/m" }, // -P 2' { 0x1c1b5411, &ASU_21Y, "2/m" }, // -P 2y' { 0xe34a99ed, &ASU_21Z, "2/m" }, // -P 2x' { 0xe7243bbc, &ASU_222, "mmm" }, // -P 2 2 { 0x885920bf, &ASU_22U, "mmm" }, // -P 2 2" { 0xe980f874, &ASU_22V, "mmm" }, // -P 2 2" (y,z,x) { 0x05c7f86e, &ASU_22W, "mmm" }, // -P 2 2" (z,x,y) { 0xfdd759b5, &ASU_113, "-3" }, // -P 3 { 0xf2769c28, &ASU_131, "-3" }, // -P 3 (y,z,x) { 0xcd4b8428, &ASU_311, "-3" }, // -P 3 (z,x,y) { 0x07fa5ca1, &ASU_11T, "-3" }, // -P 3 (-x,y,z) { 0x0f070468, &ASU_1T1, "-3" }, // -P 3 (y,z,-x) { 0x9bd3dcf4, &ASU_T11, "-3" }, // -P 3 (z,-x,y) { 0xd9a29bac, &ASU_31A, "-3" }, // -P 3* { 0x627a2f8c, &ASU_31B, "-3" }, // -P 3* (-x,y,z) { 0xcfb71d71, &ASU_31C, "-3" }, // -P 3* (x,-y,z) { 0x8a86426e, &ASU_31D, "-3" }, // -P 3* (x,y,-z) { 0xf74c7f83, &ASU_223, "-3m" }, // -P 3 2 { 0x573b981c, &ASU_232, "-3m" }, // -P 3 2 (y,z,x) { 0x1799544d, &ASU_322, "-3m" }, // -P 3 2 (z,x,y) { 0x1c80e47a, &ASU_32A, "-3m" }, // -P 3* 2 { 0xea7284da, &ASU_32B, "-3m" }, // -P 3* 2 (-x,y,z) { 0xb193db73, &ASU_32C, "-3m" }, // -P 3* 2 (x,-y,z) { 0x04fecdf9, &ASU_32D, "-3m" }, // -P 3* 2 (-x,-y,z) { 0xfc3edafb, &ASU_32U, "-3m" }, // -P 3 2" { 0xd60d11a0, &ASU_32V, "-3m" }, // -P 3 2" (z,x,y) { 0xf7d5112f, &ASU_32W, "-3m" }, // -P 3 2" (y,z,x) { 0xfbb8f18b, &ASU_32X, "-3m" }, // -P 3 2" (-x,y,z) { 0x530fcba9, &ASU_32Y, "-3m" }, // -P 3 2" (z,-x,y) { 0xa3d49592, &ASU_32Z, "-3m" }, // -P 3 2" (y,z,-x) { 0x7f473453, &ASU_114, "4/m" }, // -P 4 { 0x081d78e5, &ASU_141, "4/m" }, // -P 4 (y,z,x) { 0x6a9fa6e5, &ASU_411, "4/m" }, // -P 4 (z,x,y) { 0xb8f2113e, &ASU_224, "4/mmm" }, // -P 4 2 { 0xb9ce4369, &ASU_242, "4/mmm" }, // -P 4 2 (y,z,x) { 0xc39787b7, &ASU_422, "4/mmm" }, // -P 4 2 (z,x,y) { 0x32dacfb6, &ASU_114, "6/m" }, // -P 6 { 0xe7987b0c, &ASU_141, "6/m" }, // -P 6 (y,z,x) { 0xb5b69658, &ASU_411, "6/m" }, // -P 6 (z,x,y) { 0xf1fc7952, &ASU_224, "6/mmm" }, // -P 6 2 { 0x386f0ab4, &ASU_242, "6/mmm" }, // -P 6 2 (y,z,x) { 0xcd531b66, &ASU_422, "6/mmm" }, // -P 6 2 (z,x,y) { 0x72e55913, &ASU_M3B, "m-3" }, // -P 2 2 3 { 0x74c407d3, &ASU_M3M, "m-3m" } // -P 4 2 3 }; int lgdata_size = sizeof( lgdata ) / sizeof( lgdata[0] ); // From Hall & Grosse-Kunstleve, 'Concise Space group symbols' SGdata sgdata[] = { {0xc704dd7b,"P 1" ,"P 1" ,' ', 1}, {0x2df60a45,"-P 1" ,"P -1" ,' ', 2}, {0x902cf668,"P 2y" ,"P 1 2 1" ,' ', 3}, {0x90a34743,"P 2" ,"P 1 1 2" ,' ', 3}, {0x9b02bfbf,"P 2x" ,"P 2 1 1" ,' ', 3}, {0xda168154,"P 2yb" ,"P 1 21 1" ,' ', 4}, {0x7851c0d1,"P 2c" ,"P 1 1 21" ,' ', 4}, {0xae0e24db,"P 2xa" ,"P 21 1 1" ,' ', 4}, {0xdeb5173b,"C 2y" ,"C 1 2 1" ,' ', 5}, {0x1e4dbca6,"A 2y" ,"A 1 2 1" ,' ', 5}, {0x6042abb6,"I 2y" ,"I 1 2 1" ,' ', 5}, {0x2a55a450,"A 2" ,"A 1 1 2" ,' ', 5}, {0x458c0b8c,"B 2" ,"B 1 1 2" ,' ', 5}, {0x545ab340,"I 2" ,"I 1 1 2" ,' ', 5}, {0xc4ef9a2d,"B 2x" ,"B 2 1 1" ,' ', 5}, {0x6bce9e6c,"C 2x" ,"C 2 1 1" ,' ', 5}, {0xd53922e1,"I 2x" ,"I 2 1 1" ,' ', 5}, {0x93121e4d,"P -2y" ,"P 1 m 1" ,' ', 6}, {0x939daf66,"P -2" ,"P 1 1 m" ,' ', 6}, {0x6dd7504b,"P -2x" ,"P m 1 1" ,' ', 6}, {0x7be099df,"P -2yc" ,"P 1 c 1" ,' ', 7}, {0x4eec02bb,"P -2yac" ,"P 1 n 1" ,' ', 7}, {0xa61e8529,"P -2ya" ,"P 1 a 1" ,' ', 7}, {0xa6913402,"P -2a" ,"P 1 1 a" ,' ', 7}, {0xecab433e,"P -2ab" ,"P 1 1 n" ,' ', 7}, {0xd9a7d85a,"P -2b" ,"P 1 1 b" ,' ', 7}, {0x27ed2777,"P -2xb" ,"P b 1 1" ,' ', 7}, {0x2ac91f43,"P -2xbc" ,"P n 1 1" ,' ', 7}, {0x8525d7d9,"P -2xc" ,"P c 1 1" ,' ', 7}, {0x77b286e1,"C -2y" ,"C 1 m 1" ,' ', 8}, {0xb74a2d7c,"A -2y" ,"A 1 m 1" ,' ', 8}, {0xc9453a6c,"I -2y" ,"I 1 m 1" ,' ', 8}, {0x8352358a,"A -2" ,"A 1 1 m" ,' ', 8}, {0xec8b9a56,"B -2" ,"B 1 1 m" ,' ', 8}, {0xfd5d229a,"I -2" ,"I 1 1 m" ,' ', 8}, {0xddc257bb,"B -2x" ,"B m 1 1" ,' ', 8}, {0x72e353fa,"C -2x" ,"C m 1 1" ,' ', 8}, {0xcc14ef77,"I -2x" ,"I m 1 1" ,' ', 8}, {0x38ef08aa,"C -2yc" ,"C 1 c 1" ,' ', 9}, {0x54faf6d0,"A -2yac" ,"A 1 n 1" ,' ', 9}, {0x9d54258d,"I -2ya" ,"I 1 a 1" ,' ', 9}, {0xe35b329d,"A -2ya" ,"A 1 a 1" ,' ', 9}, {0x6cfe174b,"C -2ybc" ,"C 1 n 1" ,' ', 9}, {0x2af5e1c0,"I -2yc" ,"I 1 c 1" ,' ', 9}, {0xd7432a6b,"A -2a" ,"A 1 1 a" ,' ', 9}, {0x0f3b41fa,"B -2bc" ,"B 1 1 n" ,' ', 9}, {0x4afce6d7,"I -2b" ,"I 1 1 b" ,' ', 9}, {0x5b2a5e1b,"B -2b" ,"B 1 1 b" ,' ', 9}, {0x60e2ee26,"A -2ac" ,"A 1 1 n" ,' ', 9}, {0xa94c3d7b,"I -2a" ,"I 1 1 a" ,' ', 9}, {0x6a6393f6,"B -2xb" ,"B b 1 1" ,' ', 9}, {0x69afc250,"C -2xbc" ,"C n 1 1" ,' ', 9}, {0x2fa434db,"I -2xc" ,"I c 1 1" ,' ', 9}, {0x3dbeddb1,"C -2xc" ,"C c 1 1" ,' ', 9}, {0x3e728c17,"B -2xbc" ,"B n 1 1" ,' ', 9}, {0x7bb52b3a,"I -2xb" ,"I b 1 1" ,' ', 9}, {0x068dfeb3,"-P 2y" ,"P 1 2/m 1" ,' ', 10}, {0x9b92779f,"-P 2" ,"P 1 1 2/m" ,' ', 10}, {0xb08d46cf,"-P 2x" ,"P 2/m 1 1" ,' ', 10}, {0x54fa8558,"-P 2yb" ,"P 1 21/m 1",' ', 11}, {0x31194672,"-P 2c" ,"P 1 1 21/m",' ', 11}, {0xce8251df,"-P 2xa" ,"P 21/m 1 1",' ', 11}, {0x09efdd05,"-C 2y" ,"C 1 2/m 1" ,' ', 12}, {0x8e118804,"-A 2y" ,"A 1 2/m 1" ,' ', 12}, {0x5c5d4c9f,"-I 2y" ,"I 1 2/m 1" ,' ', 12}, {0x5a48cc10,"-A 2" ,"A 1 1 2/m" ,' ', 12}, {0x97e84b5c,"-B 2" ,"B 1 1 2/m" ,' ', 12}, {0x8804088b,"-I 2" ,"I 1 1 2/m" ,' ', 12}, {0x05a3ecad,"-B 2x" ,"B 2/m 1 1" ,' ', 12}, {0x4ffd3ee0,"-C 2x" ,"C 2/m 1 1" ,' ', 12}, {0x1a4faf7a,"-I 2x" ,"I 2/m 1 1" ,' ', 12}, {0xac06cf5e,"-P 2yc" ,"P 1 2/c 1" ,' ', 13}, {0xf817d0bf,"-P 2yac" ,"P 1 2/n 1" ,' ', 13}, {0x529ce152,"-P 2ya" ,"P 1 2/a 1" ,' ', 13}, {0xcf83687e,"-P 2a" ,"P 1 1 2/a" ,' ', 13}, {0x9df41395,"-P 2ab" ,"P 1 1 2/n" ,' ', 13}, {0xc9e50c74,"-P 2b" ,"P 1 1 2/b" ,' ', 13}, {0x4aada62e,"-P 2xb" ,"P 2/b 1 1" ,' ', 13}, {0xf45a1aa3,"-P 2xbc" ,"P 2/n 1 1" ,' ', 13}, {0xe58ca26f,"-P 2xc" ,"P 2/c 1 1" ,' ', 13}, {0x41572403,"-P 2ybc" ,"P 1 21/c 1",' ', 14}, {0x15463be2,"-P 2yn" ,"P 1 21/n 1",' ', 14}, {0x00eb9ab9,"-P 2yab" ,"P 1 21/a 1",' ', 14}, {0x65085993,"-P 2ac" ,"P 1 1 21/a",' ', 14}, {0x8859b2ce,"-P 2n" ,"P 1 1 21/n",' ', 14}, {0xdc48ad2f,"-P 2bc" ,"P 1 1 21/b",' ', 14}, {0x34a2b13e,"-P 2xab" ,"P 21/b 1 1",' ', 14}, {0x8a550db3,"-P 2xn" ,"P 21/n 1 1",' ', 14}, {0x9b83b57f,"-P 2xac" ,"P 21/c 1 1",' ', 14}, {0x673d531e,"-C 2yc" ,"C 1 2/c 1" ,' ', 15}, {0x428e62a8,"-A 2yac" ,"A 1 2/n 1" ,' ', 15}, {0xb7f841ea,"-I 2ya" ,"I 1 2/a 1" ,' ', 15}, {0x65b48571,"-A 2ya" ,"A 1 2/a 1" ,' ', 15}, {0x8c985e6b,"-C 2ybc" ,"C 1 2/n 1" ,' ', 15}, {0x90c2a633,"-I 2yc" ,"I 1 2/c 1" ,' ', 15}, {0xb1edc165,"-A 2a" ,"A 1 1 2/a" ,' ', 15}, {0x5b77a1f0,"-B 2bc" ,"B 1 1 2/n" ,' ', 15}, {0xaf3eef52,"-I 2b" ,"I 1 1 2/b" ,' ', 15}, {0xb0d2ac85,"-B 2b" ,"B 1 1 2/b" ,' ', 15}, {0x96d726bc,"-A 2ac" ,"A 1 1 2/n" ,' ', 15}, {0x63a105fe,"-I 2a" ,"I 1 1 2/a" ,' ', 15}, {0xe4301506,"-B 2xb" ,"B 2/b 1 1" ,' ', 15}, {0xaecdc717,"-C 2xbc" ,"C 2/n 1 1" ,' ', 15}, {0x62f43297,"-I 2xc" ,"I 2/c 1 1" ,' ', 15}, {0x37e5a351,"-C 2xc" ,"C 2/c 1 1" ,' ', 15}, {0x7d187140,"-B 2xbc" ,"B 2/n 1 1" ,' ', 15}, {0xfbdc56d1,"-I 2xb" ,"I 2/b 1 1" ,' ', 15}, {0xa959fc0b,"P 2 2" ,"P 2 2 2" ,' ', 16}, {0x03d2cde6,"P 2c 2" ,"P 2 2 21" ,' ', 17}, {0xd756eb1b,"P 2a 2a" ,"P 21 2 2" ,' ', 17}, {0x010e6701,"P 2 2b" ,"P 2 21 2" ,' ', 17}, {0x2b106ff0,"P 2 2ab" ,"P 21 21 2" ,' ', 18}, {0xee8326bb,"P 2bc 2" ,"P 2 21 21" ,' ', 18}, {0x82570fbb,"P 2ac 2ac" ,"P 21 2 21" ,' ', 18}, {0x8f7a6eec,"P 2ac 2ab" ,"P 21 21 21",' ', 19}, {0xd3dceae0,"C 2c 2" ,"C 2 2 21" ,' ', 20}, {0xa3d855bc,"A 2a 2a" ,"A 21 2 2" ,' ', 20}, {0x31f9a8c4,"B 2 2b" ,"B 2 21 2" ,' ', 20}, {0xbd0e64fb,"C 2 2" ,"C 2 2 2" ,' ', 21}, {0x3af031fa,"A 2 2" ,"A 2 2 2" ,' ', 21}, {0xf750b6b6,"B 2 2" ,"B 2 2 2" ,' ', 21}, {0x8a25cd68,"F 2 2" ,"F 2 2 2" ,' ', 22}, {0xe8bcf561,"I 2 2" ,"I 2 2 2" ,' ', 23}, {0x7ba265f9,"I 2b 2c" ,"I 21 21 21",' ', 24}, {0x715a8a38,"P 2 -2" ,"P m m 2" ,' ', 25}, {0x34467527,"P -2 2" ,"P 2 m m" ,' ', 25}, {0x454292ce,"P -2 -2" ,"P m 2 m" ,' ', 25}, {0xdbd1bbd5,"P 2c -2" ,"P m c 21" ,' ', 26}, {0x8ed05f75,"P 2c -2c" ,"P c m 21" ,' ', 26}, {0x1e587dd6,"P -2a 2a" ,"P 21 m a" ,' ', 26}, {0x4a496237,"P -2 2a" ,"P 21 a m" ,' ', 26}, {0xed1509c4,"P -2 -2b" ,"P b 21 m" ,' ', 26}, {0x1735e925,"P -2b -2" ,"P m 21 b" ,' ', 26}, {0x245b6e98,"P 2 -2c" ,"P c c 2" ,' ', 27}, {0x60576ac6,"P -2a 2" ,"P 2 a a" ,' ', 27}, {0xbf62722f,"P -2b -2b" ,"P b 2 b" ,' ', 27}, {0x0f559d28,"P 2 -2a" ,"P m a 2" ,' ', 28}, {0x8b7a6ad9,"P 2 -2b" ,"P b m 2" ,' ', 28}, {0x66310ecc,"P -2b 2" ,"P 2 m b" ,' ', 28}, {0x9ecd44ca,"P -2c 2" ,"P 2 c m" ,' ', 28}, {0x1043766e,"P -2c -2c" ,"P c 2 m" ,' ', 28}, {0x3b4d85de,"P -2a -2a" ,"P m 2 a" ,' ', 28}, {0xf0df4865,"P 2c -2ac" ,"P c a 21" ,' ', 29}, {0xc427e492,"P 2c -2b" ,"P b c 21" ,' ', 29}, {0x183e19dc,"P -2b 2a" ,"P 21 a b" ,' ', 29}, {0xb4d34c3b,"P -2ac 2a" ,"P 21 c a" ,' ', 29}, {0xa7e2b223,"P -2bc -2c" ,"P c 21 b" ,' ', 29}, {0x931a1ed4,"P -2a -2ab" ,"P b 21 a" ,' ', 29}, {0x358dd654,"P 2 -2bc" ,"P n c 2" ,' ', 30}, {0x5a547988,"P 2 -2ac" ,"P c n 2" ,' ', 30}, {0xcadc5b2b,"P -2ac 2" ,"P 2 n a" ,' ', 30}, {0x3220112d,"P -2ab 2" ,"P 2 a n" ,' ', 30}, {0xc16d653f,"P -2ab -2ab" ,"P b 2 n" ,' ', 30}, {0x0195cea2,"P -2bc -2bc" ,"P n 2 b" ,' ', 30}, {0x8fc0a434,"P 2ac -2" ,"P m n 21" ,' ', 31}, {0x72570ce4,"P 2bc -2bc" ,"P n m 21" ,' ', 31}, {0xb60fe6dc,"P -2ab 2ab" ,"P 21 m n" ,' ', 31}, {0x1f488697,"P -2 2ac" ,"P 21 n m" ,' ', 31}, {0x464f1412,"P -2 -2bc" ,"P n 21 m" ,' ', 31}, {0x4324f6c4,"P -2ab -2" ,"P m 21 n" ,' ', 31}, {0xf5757dc9,"P 2 -2ab" ,"P b a 2" ,' ', 32}, {0x739caf97,"P -2bc 2" ,"P 2 c b" ,' ', 32}, {0x6e4c617e,"P -2ac -2ac" ,"P c 2 a" ,' ', 32}, {0x04df4f0f,"P 2c -2n" ,"P n a 21" ,' ', 33}, {0xba28f382,"P 2c -2ab" ,"P b n 21" ,' ', 33}, {0x0d93b887,"P -2bc 2a" ,"P 21 n b" ,' ', 33}, {0x5982a766,"P -2n 2a" ,"P 21 c n" ,' ', 33}, {0xd9eda533,"P -2n -2ac" ,"P c 21 n" ,' ', 33}, {0xc83b1dff,"P -2ac -2n" ,"P n 21 a" ,' ', 33}, {0x4b82c144,"P 2 -2n" ,"P n n 2" ,' ', 34}, {0x278db076,"P -2n 2" ,"P 2 n n" ,' ', 34}, {0x7f9ad9b2,"P -2n -2n" ,"P n 2 n" ,' ', 34}, {0x93d6f19f,"C 2 -2" ,"C m m 2" ,' ', 35}, {0xeea975ee,"A -2 2" ,"A 2 m m" ,' ', 35}, {0xb633cb54,"B -2 -2" ,"B m 2 m" ,' ', 35}, {0xfd047f84,"C 2c -2" ,"C m c 21" ,' ', 36}, {0x851ce235,"C 2c -2c" ,"C c m 21" ,' ', 36}, {0x9c241cdd,"A -2a 2a" ,"A 21 m a" ,' ', 36}, {0x778111a8,"A -2 2a" ,"A 21 a m" ,' ', 36}, {0x709ad526,"B -2 -2b" ,"B b 21 m" ,' ', 36}, {0x91092c8d,"B -2b -2" ,"B m 21 b" ,' ', 36}, {0xebce6c2e,"C 2 -2c" ,"C c c 2" ,' ', 37}, {0x050c789b,"A -2a 2" ,"A 2 a a" ,' ', 37}, {0x57a032ff,"B -2b -2b" ,"B b 2 b" ,' ', 37}, {0x1428a49e,"A 2 -2" ,"A m m 2" ,' ', 38}, {0xd98823d2,"B 2 -2" ,"B m m 2" ,' ', 38}, {0x2309f2a2,"B -2 2" ,"B 2 m m" ,' ', 38}, {0x695720ef,"C -2 2" ,"C 2 m m" ,' ', 38}, {0xfc6d1919,"C -2 -2" ,"C m 2 m" ,' ', 38}, {0x7b934c18,"A -2 -2" ,"A m 2 m" ,' ', 38}, {0xf5bb5d35,"A 2 -2c" ,"A b m 2" ,' ', 39}, {0x40a04794,"B 2 -2c" ,"B m a 2" ,' ', 39}, {0xc8acffd7,"B -2c 2" ,"B 2 c m" ,' ', 39}, {0x82f22d9a,"C -2b 2" ,"C 2 m b" ,' ', 39}, {0x65457d5f,"C -2b -2b" ,"C m 2 a" ,' ', 39}, {0x9a00b5b3,"A -2c -2c" ,"A c 2 m" ,' ', 39}, {0x8d00c0d8,"A 2 -2a" ,"A m a 2" ,' ', 40}, {0x381bda79,"B 2 -2b" ,"B b m 2" ,' ', 40}, {0x0433157b,"B -2b 2" ,"B 2 m b" ,' ', 40}, {0x0785aef4,"C -2c 2" ,"C 2 c m" ,' ', 40}, {0x847584a8,"C -2c -2c" ,"C c 2 m" ,' ', 40}, {0xe2bb285e,"A -2a -2a" ,"A m 2 a" ,' ', 40}, {0x6c933973,"A 2 -2ac" ,"A b a 2" ,' ', 41}, {0xa133be3f,"B 2 -2bc" ,"B b a 2" ,' ', 41}, {0xef96180e,"B -2bc 2" ,"B 2 c b" ,' ', 41}, {0xec20a381,"C -2bc 2" ,"C 2 c b" ,' ', 41}, {0x1d5de0ee,"C -2bc -2bc" ,"C c 2 a" ,' ', 41}, {0x0328d1f5,"A -2ac -2ac" ,"A c 2 a" ,' ', 41}, {0x18172b53,"F 2 -2" ,"F m m 2" ,' ', 42}, {0xad1a17db,"F -2 2" ,"F 2 m m" ,' ', 42}, {0xa88fc3e9,"F -2 -2" ,"F m 2 m" ,' ', 42}, {0x921865a5,"F 2 -2d" ,"F d d 2" ,' ', 43}, {0x1b59dbd3,"F -2d 2" ,"F 2 d d" ,' ', 43}, {0x22808d1f,"F -2d -2d" ,"F d 2 d" ,' ', 43}, {0xc6646005,"I 2 -2" ,"I m m 2" ,' ', 44}, {0x3ce5b175,"I -2 2" ,"I 2 m m" ,' ', 44}, {0xa9df8883,"I -2 -2" ,"I m 2 m" ,' ', 44}, {0xbedffde8,"I 2 -2c" ,"I b a 2" ,' ', 45}, {0xd740bc00,"I -2a 2" ,"I 2 c b" ,' ', 45}, {0x484c7128,"I -2b -2b" ,"I c 2 a" ,' ', 45}, {0x5f4c0443,"I 2 -2a" ,"I m a 2" ,' ', 46}, {0x27f799ae,"I 2 -2b" ,"I b m 2" ,' ', 46}, {0x1bdf56ac,"I -2b 2" ,"I 2 m b" ,' ', 46}, {0xf07a5bd9,"I -2c 2" ,"I 2 c m" ,' ', 46}, {0xd164156e,"I -2c -2c" ,"I c 2 m" ,' ', 46}, {0x30f7ecc5,"I -2a -2a" ,"I m 2 a" ,' ', 46}, {0xe7243bbc,"-P 2 2" ,"P m m m" ,' ', 47}, {0x51e85b6c,"P 2 2 -1n" ,"P n n n" ,'1', 48}, {0x78ff5b81,"-P 2ab 2bc" ,"P n n n" ,'2', 48}, {0x353736e5,"-P 2 2c" ,"P c c m" ,' ', 49}, {0x0c8136c9,"-P 2a 2" ,"P m a a" ,' ', 49}, {0x02b17898,"-P 2b 2b" ,"P b m b" ,' ', 49}, {0x1392524e,"P 2 2 -1ab" ,"P b a n" ,'1', 50}, {0xe91475ed,"-P 2ab 2b" ,"P b a n" ,'2', 50}, {0x4e9de450,"P 2 2 -1bc" ,"P n c b" ,'1', 50}, {0x935a56f4,"-P 2b 2bc" ,"P n c b" ,'2', 50}, {0x38bbae1f,"P 2 2 -1ac" ,"P c n a" ,'1', 50}, {0xde923b90,"-P 2a 2c" ,"P c n a" ,'2', 50}, {0x6179e0c6,"-P 2a 2a" ,"P m m a" ,' ', 51}, {0x2be88448,"-P 2b 2" ,"P m m b" ,' ', 51}, {0xce7dc76c,"-P 2 2b" ,"P b m m" ,' ', 51}, {0xb013e0d3,"-P 2c 2c" ,"P c m m" ,' ', 51}, {0x6200ed8a,"-P 2c 2" ,"P m c m" ,' ', 51}, {0x8adcedb3,"-P 2 2a" ,"P m a m" ,' ', 51}, {0xc514e0e2,"-P 2a 2bc" ,"P n n a" ,' ', 52}, {0xfea280fb,"-P 2b 2n" ,"P n n b" ,' ', 52}, {0x38e06b40,"-P 2n 2b" ,"P b n n" ,' ', 52}, {0x637980f3,"-P 2ab 2c" ,"P c n n" ,' ', 52}, {0x15078d8e,"-P 2ab 2n" ,"P n c n" ,' ', 52}, {0xa90b452c,"-P 2n 2bc" ,"P n a n" ,' ', 52}, {0x89a5e0ff,"-P 2ac 2" ,"P m n a" ,' ', 53}, {0x42ae4859,"-P 2bc 2bc" ,"P n m b" ,' ', 53}, {0x84eca3e2,"-P 2ab 2ab" ,"P b m n" ,' ', 53}, {0x58cfe0ea,"-P 2 2ac" ,"P c n m" ,' ', 53}, {0x2eb1ed97,"-P 2 2bc" ,"P n c m" ,' ', 53}, {0xc04d893d,"-P 2ab 2" ,"P m a n" ,' ', 53}, {0xb36aed9f,"-P 2a 2ac" ,"P c c a" ,' ', 54}, {0x88dc8d86,"-P 2b 2c" ,"P c c b" ,' ', 54}, {0x25d8ca19,"-P 2a 2b" ,"P b a a" ,' ', 54}, {0x5bb6eda6,"-P 2ac 2c" ,"P c a a" ,' ', 54}, {0xd3456635,"-P 2bc 2b" ,"P b c b" ,' ', 54}, {0x6f49ae97,"-P 2b 2ab" ,"P b a b" ,' ', 54}, {0xa3851163,"-P 2 2ab" ,"P b a m" ,' ', 55}, {0x8b3b9e72,"-P 2bc 2" ,"P m c b" ,' ', 55}, {0x364e3ba9,"-P 2ac 2ac" ,"P c m a" ,' ', 55}, {0x0e8156fc,"-P 2ab 2ac" ,"P c c n" ,' ', 56}, {0x31173243,"-P 2ac 2bc" ,"P n a a" ,' ', 56}, {0xbebdb03a,"-P 2bc 2ab" ,"P b n b" ,' ', 56}, {0x3a7e15cd,"-P 2c 2b" ,"P b c m" ,' ', 57}, {0xddeb36dc,"-P 2c 2ac" ,"P c a m" ,' ', 57}, {0xe45d36f0,"-P 2ac 2a" ,"P m c a" ,' ', 57}, {0x46105247,"-P 2b 2a" ,"P m a b" ,' ', 57}, {0x48201c16,"-P 2a 2ab" ,"P b m a" ,' ', 57}, {0x280f97bc,"-P 2bc 2c" ,"P c m b" ,' ', 57}, {0x43493b98,"-P 2 2n" ,"P n n m" ,' ', 58}, {0x609e9307,"-P 2n 2" ,"P m n n" ,' ', 58}, {0xc4f39323,"-P 2n 2n" ,"P n m n" ,' ', 58}, {0x57337891,"P 2 2ab -1ab" ,"P m m n" ,'1', 59}, {0xadb55f32,"-P 2ab 2a" ,"P m m n" ,'2', 59}, {0x2282419e,"P 2bc 2 -1bc" ,"P n m m" ,'1', 59}, {0xdab23f36,"-P 2c 2bc" ,"P n m m" ,'2', 59}, {0xe9d1ae0a,"P 2ac 2ac -1ac" ,"P m n m" ,'1', 59}, {0x0ff83b85,"-P 2c 2a" ,"P m n m" ,'2', 59}, {0x5518bd4f,"-P 2n 2ab" ,"P b c n" ,' ', 60}, {0xc3aa9ac9,"-P 2n 2c" ,"P c a n" ,' ', 60}, {0xa8ec36ed,"-P 2a 2n" ,"P n c a" ,' ', 60}, {0x2f569e56,"-P 2bc 2n" ,"P n a b" ,' ', 60}, {0xd1db18b8,"-P 2ac 2b" ,"P b n a" ,' ', 60}, {0xe5245b89,"-P 2b 2ac" ,"P c n b" ,' ', 60}, {0xbc23ceb7,"-P 2ac 2ab" ,"P b c a" ,' ', 61}, {0x45f741b3,"-P 2bc 2ac" ,"P c a b" ,' ', 61}, {0x5cefe44c,"-P 2ac 2n" ,"P n m a" ,' ', 62}, {0xe6c3487d,"-P 2bc 2a" ,"P m n b" ,' ', 62}, {0x5786c3c2,"-P 2c 2ab" ,"P b n m" ,' ', 62}, {0xae524cc6,"-P 2n 2ac" ,"P c m n" ,' ', 62}, {0x0d664508,"-P 2n 2a" ,"P m c n" ,' ', 62}, {0xb74ae939,"-P 2c 2n" ,"P n a m" ,' ', 62}, {0xc0dd6737,"-C 2c 2" ,"C m c m" ,' ', 63}, {0xa4e78801,"-C 2c 2c" ,"C c m m" ,' ', 63}, {0x637ac153,"-A 2a 2a" ,"A m m a" ,' ', 63}, {0x7af93f9c,"-A 2 2a" ,"A m a m" ,' ', 63}, {0x5ea5920d,"-B 2 2b" ,"B b m m" ,' ', 63}, {0xdf056b84,"-B 2b 2" ,"B m m b" ,' ', 63}, {0xd95e99f8,"-C 2bc 2" ,"C m c a" ,' ', 64}, {0x014f7f4e,"-C 2bc 2bc" ,"C c m b" ,' ', 64}, {0xe2da38da,"-A 2ac 2ac" ,"A b m a" ,' ', 64}, {0x3e8a450b,"-A 2 2ac" ,"A c a m" ,' ', 64}, {0xe28e9b8d,"-B 2 2bc" ,"B b c m" ,' ', 64}, {0xc686954b,"-B 2bc 2" ,"B m a b" ,' ', 64}, {0xcc263714,"-C 2 2" ,"C m m m" ,' ', 65}, {0xc6d2361c,"-A 2 2" ,"A m m m" ,' ', 65}, {0x1ad6e89a,"-B 2 2" ,"B m m m" ,' ', 65}, {0xa81cd822,"-C 2 2c" ,"C c c m" ,' ', 66}, {0xdf51c8d3,"-A 2a 2" ,"A m a a" ,' ', 66}, {0x9b761113,"-B 2b 2b" ,"B b m b" ,' ', 66}, {0xd5a5c9db,"-C 2b 2" ,"C m m a" ,' ', 67}, {0x698ec05b,"-C 2b 2b" ,"C m m b" ,' ', 67}, {0x4772cf95,"-A 2c 2c" ,"A b m m" ,' ', 67}, {0x82a14c8b,"-A 2 2c" ,"A c m m" ,' ', 67}, {0xa6fde11a,"-B 2 2c" ,"B m c m" ,' ', 67}, {0x03551655,"-B 2c 2" ,"B m a m" ,' ', 67}, {0xd12ab103,"C 2 2 -1bc" ,"C c c a" ,'1', 68}, {0x0db42f6d,"-C 2b 2bc" ,"C c c a" ,'2', 68}, {0xd12ab103,"C 2 2 -1bc" ,"C c c b" ,'1', 68}, {0xb19f26ed,"-C 2b 2c" ,"C c c b" ,'2', 68}, {0x6a64cf1d,"A 2 2 -1ac" ,"A b a a" ,'1', 68}, {0x9b22b244,"-A 2a 2c" ,"A b a a" ,'2', 68}, {0x6a64cf1d,"A 2 2 -1ac" ,"A c a a" ,'1', 68}, {0x5ef1315a,"-A 2ac 2c" ,"A c a a" ,'2', 68}, {0xb660119b,"B 2 2 -1bc" ,"B b c b" ,'1', 68}, {0x82f5efdc,"-B 2bc 2b" ,"B b c b" ,'2', 68}, {0xb660119b,"B 2 2 -1bc" ,"B b a b" ,'1', 68}, {0x275d1893,"-B 2b 2bc" ,"B b a b" ,'2', 68}, {0xcd91580e,"-F 2 2" ,"F m m m" ,' ', 69}, {0xd31c4512,"F 2 2 -1d" ,"F d d d" ,'1', 70}, {0xc3fdc94f,"-F 2uv 2vw" ,"F d d d" ,'2', 70}, {0x4a8ca5fc,"-I 2 2" ,"I m m m" ,' ', 71}, {0xb2d4d6eb,"-I 2 2c" ,"I b a m" ,' ', 72}, {0x530f5b33,"-I 2a 2" ,"I m c b" ,' ', 72}, {0xcb2c5c75,"-I 2b 2b" ,"I c m a" ,' ', 72}, {0x770755f5,"-I 2b 2c" ,"I b c a" ,' ', 73}, {0x177c21a4,"-I 2a 2b" ,"I c a b" ,' ', 73}, {0x8f5f26e2,"-I 2b 2" ,"I m m a" ,' ', 74}, {0xef2452b3,"-I 2a 2a" ,"I m m b" ,' ', 74}, {0x6e84ab3a,"-I 2c 2c" ,"I b m m" ,' ', 74}, {0x0effdf6b,"-I 2 2b" ,"I c m m" ,' ', 74}, {0xf6a7ac7c,"-I 2 2a" ,"I m c m" ,' ', 74}, {0x96dcd82d,"-I 2c 2" ,"I m a m" ,' ', 74}, {0xe194247e,"P 4" ,"P 4" ,' ', 75}, {0xeb09f6d0,"P 4w" ,"P 41" ,' ', 76}, {0x1e1ef133,"P 4c" ,"P 42" ,' ', 77}, {0x21968a94,"P 4cw" ,"P 43" ,' ', 78}, {0x8d2db265,"I 4" ,"I 4" ,' ', 79}, {0x04c2f7b9,"I 4bw" ,"I 41" ,' ', 80}, {0x5b1380ec,"P -4" ,"P -4" ,' ', 81}, {0x429018fc,"I -4" ,"I -4" ,' ', 82}, {0x7f473453,"-P 4" ,"P 4/m" ,' ', 83}, {0x07df08e7,"-P 4c" ,"P 42/m" ,' ', 84}, {0x8d9739ab,"P 4ab -1ab" ,"P 4/n" ,'1', 85}, {0x28870b39,"-P 4a" ,"P 4/n" ,'2', 85}, {0xda4091d2,"P 4n -1n" ,"P 42/n" ,'1', 86}, {0xcfc232bb,"-P 4bc" ,"P 42/n" ,'2', 86}, {0xe426791e,"-I 4" ,"I 4/m" ,' ', 87}, {0xdd05fe66,"I 4bw -1bw" ,"I 41/a" ,'1', 88}, {0xf5a09fa3,"-I 4ad" ,"I 41/a" ,'2', 88}, {0x781566a5,"P 4 2" ,"P 4 2 2" ,' ', 89}, {0x529dbafe,"P 4ab 2ab" ,"P 4 21 2" ,' ', 90}, {0x1129373c,"P 4w 2c" ,"P 41 2 2" ,' ', 91}, {0x7abbc4b0,"P 4abw 2nw" ,"P 41 21 2" ,' ', 92}, {0x00a13651,"P 4c 2" ,"P 42 2 2" ,' ', 93}, {0xb11a4eb4,"P 4n 2n" ,"P 42 21 2" ,' ', 94}, {0xc507cd54,"P 4cw 2c" ,"P 43 2 2" ,' ', 95}, {0x5af2c5d9,"P 4nw 2abw" ,"P 43 21 2" ,' ', 96}, {0xcc0e6dad,"I 4 2" ,"I 4 2 2" ,' ', 97}, {0xac45c901,"I 4bw 2bw" ,"I 41 2 2" ,' ', 98}, {0x93373957,"P 4 -2" ,"P 4 m m" ,' ', 99}, {0xd7961388,"P 4 -2ab" ,"P 4 b m" ,' ',100}, {0x53dd13c8,"P 4c -2c" ,"P 42 c m" ,' ',101}, {0x25fb5987,"P 4n -2n" ,"P 42 n m" ,' ',102}, {0x4124340e,"P 4 -2c" ,"P 4 c c" ,' ',103}, {0x375a3973,"P 4 -2n" ,"P 4 n c" ,' ',104}, {0x81ce1e91,"P 4c -2" ,"P 42 m c" ,' ',105}, {0x5b8d5c98,"P 4c -2ab" ,"P 42 b c" ,' ',106}, {0xd27b6f7f,"I 4 -2" ,"I 4 m m" ,' ',107}, {0x2a231c68,"I 4 -2c" ,"I 4 c m" ,' ',108}, {0x6ee4a2b9,"I 4bw -2" ,"I 41 m d" ,' ',109}, {0xf0719502,"I 4bw -2c" ,"I 41 c d" ,' ',110}, {0xae367c74,"P -4 2" ,"P -4 2 m" ,' ',111}, {0xc47b0b46,"P -4 2c" ,"P -4 2 c" ,' ',112}, {0x84bea02f,"P -4 2ab" ,"P -4 21 m" ,' ',113}, {0x67395465,"P -4 2n" ,"P -4 21 c" ,' ',114}, {0xd50d13d5,"P -4 -2" ,"P -4 m 2" ,' ',115}, {0x3a48de91,"P -4 -2c" ,"P -4 c 2" ,' ',116}, {0x00b4acac,"P -4 -2ab" ,"P -4 b 2" ,' ',117}, {0xf7b01eef,"P -4 -2n" ,"P -4 n 2" ,' ',118}, {0x7a127a20,"I -4 -2" ,"I -4 m 2" ,' ',119}, {0xc66b145c,"I -4 -2c" ,"I -4 c 2" ,' ',120}, {0x93e9bb9a,"I -4 2" ,"I -4 2 m" ,' ',121}, {0xf3a21f36,"I -4 2bw" ,"I -4 2 d" ,' ',122}, {0xb8f2113e,"-P 4 2" ,"P 4/m m m" ,' ',123}, {0x2de869d5,"-P 4 2c" ,"P 4/m c c" ,' ',124}, {0xb7fa689e,"P 4 2 -1ab" ,"P 4/n b m" ,'1',125}, {0x026e1f11,"-P 4a 2b" ,"P 4/n b m" ,'2',125}, {0x08a4eb7f,"P 4 2 -1n" ,"P 4/n n c" ,'1',126}, {0x51368ca3,"-P 4a 2bc" ,"P 4/n n c" ,'2',126}, {0xd5a84150,"-P 4 2ab" ,"P 4/m b m" ,' ',127}, {0xf1b4f061,"-P 4 2n" ,"P 4/m n c" ,' ',128}, {0x81d6f60a,"P 4ab 2ab -1ab" ,"P 4/n m m" ,'1',129}, {0x6f344f7f,"-P 4a 2a" ,"P 4/n m m" ,'2',129}, {0x9aee9967,"P 4ab 2n -1ab" ,"P 4/n c c" ,'1',130}, {0x8d6a1517,"-P 4a 2ac" ,"P 4/n c c" ,'2',130}, {0x5a9858b3,"-P 4c 2" ,"P 42/m m c",' ',131}, {0xcf822058,"-P 4c 2c" ,"P 42/m c m",' ',132}, {0x00e9903a,"P 4n 2c -1n" ,"P 42/n b c",'1',133}, {0xf9df795b,"-P 4ac 2b" ,"P 42/n b c",'2',133}, {0xaad7368d,"P 4n 2 -1n" ,"P 42/n n m",'1',134}, {0xaa87eae9,"-P 4ac 2bc" ,"P 42/n n m",'2',134}, {0xa5c2e426,"-P 4c 2ab" ,"P 42/m b c",' ',135}, {0x53c72d93,"-P 4n 2n" ,"P 42/m n m",' ',136}, {0xe391d7d2,"P 4n 2n -1n" ,"P 42/n m c",'1',137}, {0x0685c5ce,"-P 4ac 2a" ,"P 42/n m c",'2',137}, {0xf8a9b8bf,"P 4n 2ab -1n" ,"P 42/n c m",'1',138}, {0xe4db9fa6,"-P 4ac 2ac" ,"P 42/n c m",'2',138}, {0x7a639eef,"-I 4 2" ,"I 4/m m m" ,' ',139}, {0xd7e16f02,"-I 4 2c" ,"I 4/m c m" ,' ',140}, {0xe12277ea,"I 4bw 2bw -1bw" ,"I 41/a m d",'1',141}, {0xb96409e0,"-I 4bd 2" ,"I 41/a m d",'2',141}, {0x8bdd8359,"I 4bw 2aw -1bw" ,"I 41/a c d",'1',142}, {0x08d64e97,"-I 4bd 2c" ,"I 41/a c d",'2',142}, {0x329c980e,"P 3" ,"P 3" ,' ',143}, {0x86dd212b,"P 31" ,"P 31" ,' ',144}, {0xd70a5f46,"P 32" ,"P 32" ,' ',145}, {0x8e4e25f8,"R 3" ,"R 3" ,'H',146}, {0xd5a0aa2d,"P 3*" ,"R 3" ,'R',146}, {0xfdd759b5,"-P 3" ,"P -3" ,' ',147}, {0xbe8d0d7f,"-R 3" ,"R -3" ,'H',148}, {0xd9a29bac,"-P 3*" ,"R -3" ,'R',148}, {0x65b7a72b,"P 3 2" ,"P 3 1 2" ,' ',149}, {0xc1840a7a,"P 3 2\"" ,"P 3 2 1" ,' ',150}, {0x97e2dfd5,"P 31 2c (0 0 1)" ,"P 31 1 2" ,' ',151}, {0x33d17284,"P 31 2\"" ,"P 31 2 1" ,' ',152}, {0xe39f36b4,"P 32 2c (0 0 -1)","P 32 1 2" ,' ',153}, {0x47ac9be5,"P 32 2\"" ,"P 32 2 1" ,' ',154}, {0x46ebee09,"R 3 2\"" ,"R 3 2" ,'H',155}, {0xa20b8591,"P 3* 2" ,"R 3 2" ,'R',155}, {0x9f4cffaa,"P 3 -2\"" ,"P 3 m 1" ,' ',156}, {0x39859b12,"P 3 -2" ,"P 3 1 m" ,' ',157}, {0xe04fe588,"P 3 -2\"c" ,"P 3 c 1" ,' ',158}, {0xec0db0dd,"P 3 -2c" ,"P 3 1 c" ,' ',159}, {0x6e32558c,"R 3 -2\"" ,"R 3 m" ,'H',160}, {0xb951b4f7,"P 3* -2" ,"R 3 m" ,'R',160}, {0xf7d1a830,"R 3 -2\"c" ,"R 3 c" ,'H',161}, {0x219be015,"P 3* -2n" ,"R 3 c" ,'R',161}, {0xf74c7f83,"-P 3 2" ,"P -3 1 m" ,' ',162}, {0x69dc2f41,"-P 3 2c" ,"P -3 1 c" ,' ',163}, {0xfc3edafb,"-P 3 2\"" ,"P -3 m 1" ,' ',164}, {0xe9d82a99,"-P 3 2\"c" ,"P -3 c 1" ,' ',165}, {0x6df507a9,"-R 3 2\"" ,"R -3 m" ,'H',166}, {0x1c80e47a,"-P 3* 2" ,"R -3 m" ,'R',166}, {0x9a7d09d3,"-R 3 2\"c" ,"R -3 c" ,'H',167}, {0xbb691c91,"-P 3* 2n" ,"R -3 c" ,'R',167}, {0xa2ddaf47,"P 6" ,"P 6" ,' ',168}, {0x81a2968a,"P 61" ,"P 61" ,' ',169}, {0x84b83b8b,"P 65" ,"P 65" ,' ',170}, {0x62d97e5d,"P 62" ,"P 62" ,' ',171}, {0xb22fefa7,"P 64" ,"P 64" ,' ',172}, {0xdddeb565,"P 6c" ,"P 63" ,' ',173}, {0x35eb6ccb,"P -6" ,"P -6" ,' ',174}, {0x32dacfb6,"-P 6" ,"P 6/m" ,' ',175}, {0x06c1ae99,"-P 6c" ,"P 63/m" ,' ',176}, {0x90230e5f,"P 6 2" ,"P 6 2 2" ,' ',177}, {0xeed642a2,"P 61 2 (0 0 -1)" ,"P 61 2 2" ,' ',178}, {0x891aeb21,"P 65 2 (0 0 1)" ,"P 65 2 2" ,' ',179}, {0x6f55448f,"P 62 2c (0 0 1)" ,"P 62 2 2" ,' ',180}, {0x655e4cd9,"P 64 2c (0 0 -1)","P 64 2 2" ,' ',181}, {0xa4386f70,"P 6c 2c" ,"P 63 2 2" ,' ',182}, {0x3b0a2d17,"P 6 -2" ,"P 6 m m" ,' ',183}, {0xb74f3653,"P 6 -2c" ,"P 6 c c" ,' ',184}, {0xf4d8e94d,"P 6c -2" ,"P 63 c m" ,' ',185}, {0x789df209,"P 6c -2c" ,"P 63 m c" ,' ',186}, {0xeeacb736,"P -6 2" ,"P -6 m 2" ,' ',187}, {0xfb4a4754,"P -6c 2" ,"P -6 c 2" ,' ',188}, {0x55b5be6a,"P -6 -2" ,"P -6 2 m" ,' ',189}, {0xcb25eea8,"P -6c -2c" ,"P -6 2 c" ,' ',190}, {0xf1fc7952,"-P 6 2" ,"P 6/m m m" ,' ',191}, {0x87f9e8ca,"-P 6 2c" ,"P 6/m c c" ,' ',192}, {0x1eb41bd9,"-P 6c 2" ,"P 63/m c m",' ',193}, {0x68b18a41,"-P 6c 2c" ,"P 63/m m c",' ',194}, {0x5843870d,"P 2 2 3" ,"P 2 3" ,' ',195}, {0x93e38c71,"F 2 2 3" ,"F 2 3" ,' ',196}, {0xdc4003c1,"I 2 2 3" ,"I 2 3" ,' ',197}, {0xf9e6a645,"P 2ac 2ab 3" ,"P 21 3" ,' ',198}, {0x7ec4457b,"I 2b 2c 3" ,"I 21 3" ,' ',199}, {0x72e55913,"-P 2 2 3" ,"P m -3" ,' ',200}, {0x265ce726,"P 2 2 3 -1n" ,"P n -3" ,'1',201}, {0xd419d8a3,"-P 2ab 2bc 3" ,"P n -3" ,'2',201}, {0x58320b8d,"-F 2 2 3" ,"F m -3" ,' ',202}, {0x7de7c89b,"F 2 2 3 -1d" ,"F d -3" ,'1',203}, {0x159ca8d3,"-F 2uv 2vw 3" ,"F d -3" ,'2',203}, {0xe23893df,"-I 2 2 3" ,"I m -3" ,' ',204}, {0x1d5f4d3f,"-P 2ac 2ab 3" ,"P a -3" ,' ',205}, {0x7ce42b66,"-I 2b 2c 3" ,"I a -3" ,' ',206}, {0x93a6edeb,"P 4 2 3" ,"P 4 3 2" ,' ',207}, {0xc55ae72a,"P 4n 2 3" ,"P 42 3 2" ,' ',208}, {0x25d65cf1,"F 4 2 3" ,"F 4 3 2" ,' ',209}, {0xddc15ef3,"F 4d 2 3" ,"F 41 3 2" ,' ',210}, {0x014b7ed2,"I 4 2 3" ,"I 4 3 2" ,' ',211}, {0x4bca2b34,"P 4acd 2ab 3" ,"P 43 3 2" ,' ',212}, {0x0e761d2d,"P 4bd 2ab 3" ,"P 41 3 2" ,' ',213}, {0xbb92b652,"I 4bd 2c 3" ,"I 41 3 2" ,' ',214}, {0x6fc31c7b,"P -4 2 3" ,"P -4 3 m" ,' ',215}, {0x09abdebe,"F -4 2 3" ,"F -4 3 m" ,' ',216}, {0x75d77c69,"I -4 2 3" ,"I -4 3 m" ,' ',217}, {0x393f16ba,"P -4n 2 3" ,"P -4 3 n" ,' ',218}, {0x0968710f,"F -4c 2 3" ,"F -4 3 c" ,' ',219}, {0xe2ed982e,"I -4bd 2c 3" ,"I -4 3 d" ,' ',220}, {0x74c407d3,"-P 4 2 3" ,"P m -3 m" ,' ',221}, {0xc5e3dd9f,"P 4 2 3 -1n" ,"P n -3 n" ,'1',222}, {0xc7e69ab6,"-P 4a 2bc 3" ,"P n -3 n" ,'2',222}, {0xbabd71c4,"-P 4n 2 3" ,"P m -3 n" ,' ',223}, {0x0b9aab88,"P 4n 2 3 -1n" ,"P n -3 m" ,'1',224}, {0xdbdb6bfc,"-P 4bc 2bc 3" ,"P n -3 m" ,'2',224}, {0x5225b614,"-F 4 2 3" ,"F m -3 m" ,' ',225}, {0x481e9f10,"-F 4c 2 3" ,"F m -3 c" ,' ',226}, {0x023a8184,"F 4d 2 3 -1d" ,"F d -3 m" ,'1',227}, {0x38f5e458,"-F 4vw 2vw 3" ,"F d -3 m" ,'2',227}, {0x82b6e512,"F 4d 2 3 -1cd" ,"F d -3 c" ,'1',228}, {0x4d325ad3,"-F 4cvw 2vw 3" ,"F d -3 c" ,'2',228}, {0x52045e84,"-I 4 2 3" ,"I m -3 m" ,' ',229}, {0x407de7c1,"-I 4bd 2c 3" ,"I a -3 d" ,' ',230} }; int sgdata_size = sizeof( sgdata ) / sizeof( sgdata[0] ); } // namespace data } // namespace clipper clipper-2.1/clipper/core/container_hkl.h0000644000374100011300000001515110363703537015316 00000000000000/*! \file lib/container_hkl.h Header file for Container versions of various objects */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_CONTAINER_HKL #define CLIPPER_CONTAINER_HKL #include "container_types.h" #include "hkl_data.h" namespace clipper { extern const HKL_info NullHKL_info; // class CHKL_data : public Container, public HKL_data { public: //! null constructor CHKL_data() {} //! constructor: inherit datalist and cell CHKL_data( Container& parent, const String name = "" ); //! initialiser: supply or inherit hkl list, and cell void init( const HKL_info& hkl_info, const Cell& cell ); //! initialiser: from spacegroup, cell, and HKL_sampling void init( const Spacegroup& spacegroup, const Cell& cell, const HKL_sampling& hkl_sampling ) { clipper::Message::message( clipper::Message_fatal("CHKL_data deprecated") ); } //! hierarchical update void update(); //! assignment operator: copies the data from another list HKL_data& operator =( const HKL_data& other ) { return ( dynamic_cast&>(*this) = other ); } //! assignment operator: assigns a single value to the whole list HKL_data& operator =( const T& value ) { return ( dynamic_cast&>(*this) = value ); } }; // template implementations /*! The object is constructed at the given location in the hierarchy. An attempt is made to initialise the object using information from its parents in the hierarchy. \param parent An object in the hierarchy (usually the parent of the new object). \param name The path from \c parent to the new object (usually just the name of the new object). */ template CHKL_data::CHKL_data( Container& parent, const String name ) : Container( parent, name ) { init( NullHKL_info, NullCell ); } /*! An attempt is made to initialise the object using information from the supplied parameters, or if they are Null, from its parents in the hierarchy. \param hkl_info The reflection list object for this datalist. \param cell The cell object for this datalist. */ template void CHKL_data::init( const HKL_info& hkl_info, const Cell& cell ) { // use supplied values by default const HKL_info* hp = &hkl_info; const Cell* cp = &cell; // otherwise get them from the tree if ( hp->is_null() ) hp = parent_of_type_ptr(); if ( cp->is_null() ) cp = parent_of_type_ptr(); // if we have an hkl_info, try and init if ( hp != NULL ) { // if no cell then inherit if ( cp == NULL ) cp = &(hp->cell()); // now initialise if ( !hp->is_null() && !cp->is_null() ) HKL_data::init( *hp, *cp ); } Container::update(); } /*! Hierarchical update. If this object is uninitialised, an attempt is made to initialise the object using information from its parents in the hierarchy. The childen of the object are then updated. The data list is also synchronized with the parent reflection list. */ template void CHKL_data::update() { if ( HKL_data_base::is_null() ) init( NullHKL_info, NullCell ); else Container::update(); HKL_data::update(); } } // namespace clipper #endif clipper-2.1/clipper/core/container_types.h0000644000374100011300000001316310363703537015705 00000000000000/*! \file lib/container_types.h Header file for Container versions of various objects */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_CONTAINER_TYPES #define CLIPPER_CONTAINER_TYPES #include "container.h" namespace clipper { extern const Resolution NullResolution; //. */ class NXmap_base { public: //! test if object has been initialised bool is_null() const; //! return the grid dimensions for this map const Grid& grid() const { return grid_; } //! return the orthogonal-to-grid coordinate operator const RTop<>& operator_orth_grid() const { return rt_orth_grid; } //! return the grid-to-orthogonal coordinate operator const RTop<>& operator_grid_orth() const { return rt_grid_orth; } //! convert map coordinate to orthogonal /*! \param cm The grid coordinate to be converted. \return The equivalent orthogonal coordinate. */ inline Coord_orth coord_orth( const Coord_map& cm ) const { return Coord_orth( rt_grid_orth*cm ); } //! convert orthogonal coordinate to map /*! \param co The orthogonal coordinate to be converted. \return The equivalent grid coordinate. */ inline Coord_map coord_map( const Coord_orth& co ) const { return Coord_map ( rt_orth_grid*co ); } //! is the given coord available in the map? bool in_map( const Coord_grid& pos ) const { return grid_.in_grid( pos ); } //! is the given coord available in the map using the given interpolant? template bool in_map( const Coord_map& cm ) const; //! get multiplicity of a map grid point (always 1 for NXmap) int multiplicity( const Coord_grid& pos ) const { return 1; } //! Map reference base class /*! This is a reference to an Map. It forms a base class for index-like and coordinate-like Map references. If you write a method which will work with either, then specify this instead of either of the derived classed. \internal */ class Map_reference_base { public: //! return the parent NXmap inline const NXmap_base& base_nxmap() const { return *map_; } //! Get the index into the map data array inline const int& index() const { return index_; } //! Check for end of map inline bool last() const { return ( index_ >= map_->grid_.size() ); } protected: //! pointer to map for which this Map_reference_index is defined const NXmap_base* map_; //! integer index into map data array int index_; }; //! Map reference with index-like behaviour /*! This is a reference to a map coordinate. It behaves like a simple index into the map, but can be easily converted into a coordinate as and when required. It also implements methods for iterating through the map. It is very compact, but coord() involves some overhead. \note The following methods are inherited from Map_reference_base but are documented here for convenience: base_nxmap(), index(), last(). */ class Map_reference_index : public Map_reference_base { public: //! Null constructor Map_reference_index() {} //! Constructor: need parent map explicit Map_reference_index( const NXmap_base& map ) { map_ = ↦ index_ = 0; } //! Constructor: need parent map and coord Map_reference_index( const NXmap_base& map, const Coord_grid& pos ) { map_ = ↦ index_ = map_->grid_.index( pos ); } //! Get current grid coordinate inline Coord_grid coord() const { return map_->grid_.deindex(index_); } //! Get current value of orthogonal coordinate inline const Coord_orth coord_orth() const { return map_->coord_orth( coord().coord_map() ); } //! Set current value of coordinate - optimised for nearby coords inline Map_reference_index& set_coord( const Coord_grid& pos ) { index_ = map_->grid_.index( pos ); return *this; } //! Simple increment inline Map_reference_index& next() { index_++; return *this; } //! Index of neighbouring point /* Use for e.g. peak search. Valid for -1 <= du/dv/dw <= 1 only. \param du/dv/dw Coordinate offset. \return Map index. */ inline int index_offset(const int& du,const int& dv,const int& dw) const { return index_ + du*map_->du + dv*map_->dv + dw*map_->dw; } // inherited functions listed for documentation purposes //-- const NXmap_base& base_nxmap() const; //-- const int& index() const; //-- bool last() const; }; //! Map reference with coordinate-like behaviour /*! This is a reference to a map coordinate. It behaves like a coordinate, but also stores the index of the corresponding point in the map. It also implements methods for iterating through the a map. Since the current coordinate is stored, coord() is fast. However it required 5 words of storage. \note The following methods are inherited from Map_reference_base but are documented here for convenience: base_nxmap(), index(), last(). */ class Map_reference_coord : public NXmap_base::Map_reference_base { public: //! Null constructor Map_reference_coord() {} //! Constructor: need parent map explicit Map_reference_coord( const NXmap_base& map ) { map_ = ↦ } //! Constructor: need parent map and coord Map_reference_coord( const NXmap_base& map, const Coord_grid& pos ) { map_ = ↦ set_coord( pos ); } //! Get current value of coordinate inline Coord_grid coord() const { return pos_; } //! Get current value of orthogonal coordinate inline const Coord_orth coord_orth() const { return map_->coord_orth( coord().coord_map() ); } //! Set current value of coordinate - optimised for nearby coords inline Map_reference_coord& set_coord( const Coord_grid& pos ) { pos_ = pos; index_ = map_->grid_.index( pos_ ); return *this; } //! Simple increment /*! Use of this function resets the stored coordinate and sym */ inline Map_reference_coord& next() { index_++; pos_ = map_->grid_.deindex(index_); return *this; } // Increment u,v,w inline Map_reference_coord& next_u() { pos_.u()++; index_ += map_->du; return *this; } //!< increment u inline Map_reference_coord& next_v() { pos_.v()++; index_ += map_->dv; return *this; } //!< increment v inline Map_reference_coord& next_w() { pos_.w()++; index_ += map_->dw; return *this; } //!< increment w inline Map_reference_coord& prev_u() { pos_.u()--; index_ -= map_->du; return *this; } //!< decrement u inline Map_reference_coord& prev_v() { pos_.v()--; index_ -= map_->dv; return *this; } //!< decrement v inline Map_reference_coord& prev_w() { pos_.w()--; index_ -= map_->dw; return *this; } //!< decrement w //! Assignment operator from a coord inline Map_reference_coord& operator =( const Coord_grid& pos ) { return set_coord( pos ); } // inherited functions listed for documentation purposes //-- const NXmap_base& base_nxmap() const; //-- const int& index() const; //-- bool last() const; protected: //! Current coord Coord_grid pos_; }; //! return a basic Map_reference_index for this map Map_reference_index first() const { return Map_reference_index( *this ); } //! return a coord Map_reference_index for this map Map_reference_coord first_coord() const { return Map_reference_coord( *this ); } protected: Grid grid_; //!< grid for the map RTop<> rt_orth_grid; //!< orth->grid operator RTop<> rt_grid_orth; //!< grid->orth operator int du, dv, dw; //!< steps for shifts along u,v,w //! Null constructor, for later initialisation NXmap_base(); //! initialiser: takes grid and orthogonal->grid coordinate operator void init( const Grid& grid, const RTop<>& rt ); //! initialiser: takes grid, cell, and fraction limits void init( const Cell& cell, const Grid_sampling& grid, const Grid_range& grid_extent ); friend class NXmap_base::Map_reference_base; friend class NXmap_base::Map_reference_index; friend class NXmap_base::Map_reference_coord; }; //! NXmap: actual non-crystallographic map class /*! The non-crystallographic map class stores a map of arbitrary data type. Unlike an Xmap it is finite in extent and has no symmetry. An RT operator provides mapping onto an arbitrary orthogonal coordinate frame. Iterators provide efficient access to data. This is derived from NXmap_base, and adds the templatised data itself and the methods which deal with it. \note The following methods are inherited from NXmap_base but are documented here for convenience: grid(), coord_orth(), coord_grid(), first(), first_coord(). */ template class NXmap : public NXmap_base { public: //! Null constructor, for later initialisation NXmap() {} //! Constructor: takes grid and orthogonal->grid coordinate operator NXmap( const Grid& grid, const RTop<>& rt ); //! Constructor: takes grid, cell, and extent NXmap( const Cell& cell, const Grid_sampling& grid, const Grid_range& grid_extent ); //! initialiser: takes grid and orthogonal->grid coordinate operator void init( const Grid& grid, const RTop<>& rt ); //! initialiser: takes grid, cell, and fraction limits void init( const Cell& cell, const Grid_sampling& grid, const Grid_range& grid_extent ); //! get data by Map_reference_index inline const T& operator[] (const NXmap_base::Map_reference_index i) const { return list[i.index()]; } //! set data by Map_reference_index inline T& operator[] (const NXmap_base::Map_reference_index i) { return list[i.index()]; } //! get data by Map_reference_coord inline const T& operator[] (const NXmap_base::Map_reference_coord i) const { return list[i.index()]; } //! set data by Map_reference_coord inline T& operator[] (const NXmap_base::Map_reference_coord i) { return list[i.index()]; } //! get a density value for an arbitrary position inline const T& get_data( const Coord_grid& pos ) const { return list[ grid_.index( pos ) ]; } //! set a density value for an arbitrary position inline void set_data( const Coord_grid& pos, const T& val ) { list[ grid_.index( pos ) ] = val; } //! get map value for map coord using supplied interpolator template T interp( const Coord_map& pos ) const; //! get map value and grad for map coord using supplied interpolator template void interp_grad( const Coord_map& pos, T& val, Grad_map& grad ) const; //! get map value and curv for map coord using supplied interpolator template void interp_curv( const Coord_map& pos, T& val, Grad_map& grad, Curv_map& curv ) const; // inherited functions listed for documentation purposes //-- const Grid& grid() const; //-- const RTop<> operator_orth_grid() const; //-- const RTop<> operator_grid_orth() const; //-- const Coord_orth coord_orth( const Coord_map& cg ) const; //-- const Coord_map coord_map ( const Coord_orth& co ) const; //-- const Map_reference_index first(); //-- const Map_reference_coord first_coord(); //! assignment operator: assigns a single value to the whole map const T& operator =( const T& value ); //! add another map to this one const NXmap& operator +=( const NXmap& other ); //! subtract another map from this one const NXmap& operator -=( const NXmap& other ); private: std::vector list; }; // template fucntion definitions /*! Note that the higher the order of the interpolant, the more of the boundary of the map becomes inaccessible. \param cm The coord_map to test. \return true if interpolation can be performed at that coordinate. */ template bool NXmap_base::in_map( const Coord_map& cm ) const { return I::can_interp( *this, cm ); } /*! Initialise an NXmap to some rhomboid chosen from within a crystal coordinate space, specified by the grid and a transformation from orthogonal to grid coordinates. \param grid The grid dimensions of the desired map. \param rt The rotation/transln op from orthogonal to grid coordinates. */ template NXmap::NXmap( const Grid& grid, const RTop<>& rt ) { init( grid, rt ); } /*! Initialise an NXmap to some rhomboid chosen from within a crystal grid coordinate space, specified by a cell, sampling and box within that grid. This is useful for creating an NXmap which exactly matches some subregion of a crystallographic map. \param cell Unit cell defining the crystal space. \param grid The grid sampling of the given unit cell. \param grid_extent The map extent within that cell. */ template NXmap::NXmap( const Cell& cell, const Grid_sampling& grid, const Grid_range& grid_extent ) { init( cell, grid, grid_extent ); } /*! Initialise an NXmap to some rhomboid chosen from within a crystal coordinate space, specified by the grid and a transformation from orthogonal to grid coordinates. \param grid The grid dimensions of the desired map. \param rt The rotation/transln op from orthogonal to grid coordinates. */ template void NXmap::init( const Grid& grid, const RTop<>& rt ) { NXmap_base::init( grid, rt ); list.resize( grid.size() ); } /*! Initialise an NXmap to some rhomboid chosen from within a crystal grid coordinate space, specified by a cell, sampling and box within that grid. This is useful for creating an NXmap which exactly matches some subregion of a crystallographic map. \param cell Unit cell defining the crystal space. \param grid The grid sampling of the given unit cell. \param grid_extent The map extent within that cell. */ template void NXmap::init( const Cell& cell, const Grid_sampling& grid, const Grid_range& grid_extent ) { NXmap_base::init( cell, grid, grid_extent ); list.resize( grid_extent.size() ); } /*! The value of the map at the desired non-grid map coordinate are calculated using the supplied interpolator template. \param pos The map coord at which the density is to be calcuated. \return The value of the density at that point. map coordinates (see Cell::coord_orth). */ template template T NXmap::interp( const Coord_map& pos ) const { T val; I::interp( *this, pos, val ); return val; } /*! The value of the map at the desired non-grid map coordinate and its gradient are calculated using the supplied interpolator template. \param pos The map coord at which the density is to be calcuated. \param val The value of the density at that point. \param grad The interpolated gradient vector with respect to the map coordinates (see Cell::coord_orth). \param curv The interpolated curvature matrix with respect to the map coordinates (see Cell::coord_orth). */ template template void NXmap::interp_grad( const Coord_map& pos, T& val, Grad_map& grad ) const { I::interp_grad( *this, pos, val, grad ); } /*! The value of the map at the desired non-grid map coordinate and its gradient and curvature are calculated using the supplied interpolator template. \param pos The map coord at which the density is to be calcuated. \param val The value of the density at that point. \param grad The interpolated gradient vector with respect to the map coordinates (see Cell::coord_orth). \param curv The interpolated curvature matrix with respect to the map coordinates (see Cell::coord_orth). */ template template void NXmap::interp_curv( const Coord_map& pos, T& val, Grad_map& grad, Curv_map& curv ) const { I::interp_curv( *this, pos, val, grad, curv ); } /*! All values, including missing values, are overwritten by the value. \param value The value to which the map is to be set. */ template const T& NXmap::operator =( const T& value ) { // copy value into map Map_reference_index im; for ( im = first(); !im.last(); im.next() ) list[im.index()] = value; return value; } /*! The map grids must match. */ template const NXmap& NXmap::operator +=( const NXmap& other ) { if ( grid() != other.grid() ) Message::message( Message_fatal( "NXmap: map mismatch in +=" ) ); Map_reference_index im; for ( im = first(); !im.last(); im.next() ) list[im.index()] += other[im]; return (*this); } /*! The map grids must match. */ template const NXmap& NXmap::operator -=( const NXmap& other ) { if ( grid() != other.grid() ) Message::message( Message_fatal( "NXmap: map mismatch in -=" ) ); Map_reference_index im; for ( im = first(); !im.last(); im.next() ) list[im.index()] -= other[im]; return (*this); } } // namespace clipper #endif clipper-2.1/clipper/core/hkl_compute.h0000644000374100011300000002722511070156710015004 00000000000000/*! \file lib/hkl_compute.h Data conversion operators for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_HKL_COMPUTE #define CLIPPER_HKL_COMPUTE #include "hkl_datatypes.h" namespace clipper { namespace datatypes { // Define conversion operators //! Compute from ABCD to Phi_fom by phase integration (loses bimodality) template class Compute_phifom_from_abcd { public: // constructor: sets up integration tables Compute_phifom_from_abcd(); const Phi_fom operator()( const HKL_info::HKL_reference_index& ih, const ABCD& abcd ) const; //! class Compute_abcd_from_phifom { public: const ABCD operator()( const HKL_info::HKL_reference_index& ih, const Phi_fom& phifom ) const; //! class Compute_fphi_from_fsigf_phifom { public: const F_phi operator()( const HKL_info::HKL_reference_index& ih, const F_sigF& fsigf, const Phi_fom& phifom ) const; //! class Compute_EsigE_from_FsigF { public: const E_sigE operator()( const HKL_info::HKL_reference_index& ih, const F_sigF& fsigf ) const; //! class Compute_mean_fsigf_from_fsigfano { public: const F_sigF operator()( const HKL_info::HKL_reference_index& ih, const F_sigF_ano& fsigfano ) const; //! class Compute_diff_fsigf_from_fsigfano { public: const F_sigF operator()( const HKL_info::HKL_reference_index& ih, const F_sigF_ano& fsigfano ) const; //! class Compute_neg_fphi { public: const F_phi operator()( const HKL_info::HKL_reference_index& ih, const F_phi& fphi1 ) const; //! class Compute_add_fphi { public: const F_phi operator()( const HKL_info::HKL_reference_index& ih, const F_phi& fphi1, const F_phi& fphi2 ) const; //! class Compute_sub_fphi { public: const F_phi operator()( const HKL_info::HKL_reference_index& ih, const F_phi& fphi1, const F_phi& fphi2 ) const; //! class Compute_add_abcd { public: const ABCD operator()( const HKL_info::HKL_reference_index& ih, const ABCD& abcd1, const ABCD& abcd2 ) const; //! class Compute_scale_u { public: //! constructor: takes scale, U value Compute_scale_u( const ftype& s, const ftype& u ); const T operator()( const HKL_info::HKL_reference_index& ih, T data ) const; //! class Compute_scale_u_iso { public: //! constructor: takes scale, U value Compute_scale_u_iso( const ftype& s, const ftype& u ); const T operator()( const HKL_info::HKL_reference_index& ih, T data ) const; //! class Compute_scale_u_aniso { public: //! constructor: takes scale, U value Compute_scale_u_aniso( const ftype& s, const U_aniso_orth& u ); const T operator()( const HKL_info::HKL_reference_index& ih, T data ) const; //! class Compute_FsigF { public: const F_sigF operator()( const HKL_info::HKL_reference_index& ih, const T& fsigf ) const; //! Compute_phifom_from_abcd; //!< operator typedef datatypes::Compute_abcd_from_phifom Compute_abcd_from_phifom; //!< operator typedef datatypes::Compute_fphi_from_fsigf_phifom Compute_fphi_from_fsigf_phifom; //!< operator typedef datatypes::Compute_EsigE_from_FsigF Compute_EsigE_from_FsigF; //!< operator typedef datatypes::Compute_mean_fsigf_from_fsigfano Compute_mean_fsigf_from_fsigfano; //!< operator typedef datatypes::Compute_diff_fsigf_from_fsigfano Compute_diff_fsigf_from_fsigfano; //!< operator typedef datatypes::Compute_neg_fphi Compute_neg_fphi; //!< operator typedef datatypes::Compute_add_fphi Compute_add_fphi; //!< operator typedef datatypes::Compute_sub_fphi Compute_sub_fphi; //!< operator typedef datatypes::Compute_add_abcd Compute_add_abcd; //!< operator typedef datatypes::Compute_scale_u_iso > Compute_scale_u_iso_isigi; //!< operator typedef datatypes::Compute_scale_u_iso > Compute_scale_u_iso_fsigf; //!< operator typedef datatypes::Compute_scale_u_iso > Compute_scale_u_iso_fsigfano; //!< operator typedef datatypes::Compute_scale_u_iso > Compute_scale_u_iso_fphi; //!< operator typedef datatypes::Compute_scale_u_aniso > Compute_scale_u_aniso_isigi; //!< operator typedef datatypes::Compute_scale_u_aniso > Compute_scale_u_aniso_fsigf; //!< operator typedef datatypes::Compute_scale_u_aniso > Compute_scale_u_aniso_fsigfano; //!< operator typedef datatypes::Compute_scale_u_aniso > Compute_scale_u_aniso_fphi; //!< operator typedef datatypes::Compute_FsigF > Compute_FsigF; //!< operator typedef datatypes::Compute_FsigF > Compute_FsigF_from_ano; //!< operator typedef datatypes::Compute_scale_u > Compute_scale_u_isigi; // DEPRECATED typedef datatypes::Compute_scale_u > Compute_scale_u_fsigf; // DEPRECATED typedef datatypes::Compute_scale_u > Compute_scale_u_fsigfano; // DEPRECATED typedef datatypes::Compute_scale_u > Compute_scale_u_fphi; // DEPRECATED } namespace data64 { typedef datatypes::Compute_phifom_from_abcd Compute_phifom_from_abcd; //!< operator typedef datatypes::Compute_abcd_from_phifom Compute_abcd_from_phifom; //!< operator typedef datatypes::Compute_fphi_from_fsigf_phifom Compute_fphi_from_fsigf_phifom; //!< operator typedef datatypes::Compute_EsigE_from_FsigF Compute_EsigE_from_FsigF; //!< operator typedef datatypes::Compute_mean_fsigf_from_fsigfano Compute_mean_fsigf_from_fsigfano; //!< operator typedef datatypes::Compute_diff_fsigf_from_fsigfano Compute_diff_fsigf_from_fsigfano; //!< operator typedef datatypes::Compute_neg_fphi Compute_neg_fphi; //!< operator typedef datatypes::Compute_add_fphi Compute_add_fphi; //!< operator typedef datatypes::Compute_sub_fphi Compute_sub_fphi; //!< operator typedef datatypes::Compute_add_abcd Compute_add_abcd; //!< operator typedef datatypes::Compute_scale_u_iso > Compute_scale_u_iso_isigi; //!< operator typedef datatypes::Compute_scale_u_iso > Compute_scale_u_iso_fsigf; //!< operator typedef datatypes::Compute_scale_u_iso > Compute_scale_u_iso_fsigfano; //!< operator typedef datatypes::Compute_scale_u_iso > Compute_scale_u_iso_fphi; //!< operator typedef datatypes::Compute_scale_u_aniso > Compute_scale_u_aniso_isigi; //!< operator typedef datatypes::Compute_scale_u_aniso > Compute_scale_u_aniso_fsigf; //!< operator typedef datatypes::Compute_scale_u_aniso > Compute_scale_u_aniso_fsigfano; //!< operator typedef datatypes::Compute_scale_u_aniso > Compute_scale_u_aniso_fphi; //!< operator typedef datatypes::Compute_FsigF > Compute_FsigF; //!< operator typedef datatypes::Compute_FsigF > Compute_FsigF_from_ano; //!< operator typedef datatypes::Compute_scale_u > Compute_scale_u_isigi; // DEPRECATED typedef datatypes::Compute_scale_u > Compute_scale_u_fsigf; // DEPRECATED typedef datatypes::Compute_scale_u > Compute_scale_u_fsigfano; // DEPRECATED typedef datatypes::Compute_scale_u > Compute_scale_u_fphi; // DEPRECATED } } // namespace clipper #endif clipper-2.1/clipper/core/clipper_instance.cpp0000644000374100011300000001270411205016260016336 00000000000000/* clipper_instance.cpp: implementation file for clipper helper functions */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "clipper_instance.h" namespace clipper { // template function definitions for object cache template ObjectCache::Reference::Reference( const Reference& other ) { T::mutex.lock(); obj_ = other.obj_; if ( !is_null() ) obj_->first++; T::mutex.unlock(); } template ObjectCache::Reference::~Reference() { T::mutex.lock(); if ( !is_null() ) obj_->first--; T::mutex.unlock(); } template void ObjectCache::Reference::operator =( const Reference& other ) { T::mutex.lock(); if ( !is_null() ) obj_->first--; obj_ = other.obj_; if ( !is_null() ) obj_->first++; T::mutex.unlock(); } template ObjectCache::ObjectCache() { mode_ = NORMAL; } template ObjectCache::~ObjectCache() { for ( int i = 0; i < cache_.size(); i++ ) { if ( cache_[i]->first != 0 ) { std::string num( "0000" ); num[3] += cache_[i]->first % 10; num[2] += cache_[i]->first / 10 % 10; num[1] += cache_[i]->first / 100 % 10; num[0] += cache_[i]->first / 1000; Message::message( Message_warn( "ObjectCache: Leaked "+num+" refs to <"+cache_[i]->second.format()+">" ) ); } } } template typename ObjectCache::Reference ObjectCache::cache( const typename T::Key& key ) { T::mutex.lock(); std::pair* ptr = NULL; // find existing data for ( int i = 0; i < cache_.size(); i++ ) if ( cache_[i]->second.matches(key) ) ptr = cache_[i]; // none found, make new data if ( ptr == NULL ) { // pick an appropriate place if ( mode_ == MINMEM ) // MINMEM: remove unreferenced purge(); if ( mode_ == NORMAL ) // NORMAL: replace unreferenced for ( int i = 0; i < cache_.size(); i++ ) if ( cache_[i]->first == 0 ) { ptr = cache_[i]; ptr->second = T(key); break; } // otherwise add new if ( ptr == NULL ) { ptr = new std::pair( 0, T(key) ); cache_.push_back( ptr ); } } Reference result( ptr ); T::mutex.unlock(); return result; // we have a ref to the new obj, so it is thread safe } template void ObjectCache::set_mode( const MODE& mode ) { mode_ = mode; } template void ObjectCache::purge() { for ( int i = cache_.size() - 1; i >= 0; i-- ) if ( cache_[i]->first == 0 ) { delete cache_[i]; cache_.erase( cache_.begin() + i ); } } template void ObjectCache::destroy() { cache_.clear(); } template void ObjectCache::debug() const { for ( int i = 0; i < cache_.size(); i++ ) std::cout << "Cache pos: " << i << "\t Refs: " << cache_[i]->first << "\t" << cache_[i]->second.format() << "\n"; } template class ObjectCache; template class ObjectCache; template class ObjectCache; // clipper instance ClipperInstance ClipperInstantiator::inst; ClipperInstance::ClipperInstance() { } ClipperInstance::~ClipperInstance() { xmcache_.purge(); hdcache_.purge(); sgcache_.purge(); } void ClipperInstance::destroy() { xmcache_.destroy(); hdcache_.destroy(); sgcache_.destroy(); } } // namespace clipper clipper-2.1/clipper/core/ramachandran.h0000644000374100011300000001156710363703537015124 00000000000000/*! \file ramachandran.h Ramachandran Plot class */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_RAMACHANDRAN #define CLIPPER_RAMACHANDRAN #include "clipper_types.h" namespace clipper { //! 2-d angular probability distibution class /*! Base for Ramachandran class (and other similar classes, such as a pseudo-ramachandran plot or the JPD of two phases ). */ class Prob_phi_2d { public: //! initialise: with sampling void init( const int& size ); //! accumulate new table of samples to probability void accumulate( const ftype32 table[] ); //! accumulate new sample to probability void accumulate( const ftype& phi1, const ftype& phi2, ftype wgt = 1.0 ); //! normalise to integrate to 1/(2pi)^2 void normalise(); //! get probability for a particular pair of angles ftype probability( const ftype& phi1, const ftype& phi2 ) const; //! formatted string representation (as C++ code) String format() const; //! 2d read access const ftype& data( const int& i, const int& j ) const { return data_[n*i+j]; } //! 2d write access ftype& data( const int& i, const int& j ) { return data_[n*i+j]; } private: int n; //!< sampling std::vector data_; }; //! Ramachandran plot class /*! This class provides a reference Ramachandran plot for Gly, Pro, other, and combinations of those types of residues. The source data comes from the best residues from the 'top500' best-determined structures list of D. C. and J. S. Richardson, http://kinemage.biochem.duke.edu/index.html The Ramachandran plot is normalised in inverse radians squared, so the mean value of a probability is 1/(2 pi)2. */ class Ramachandran : private Prob_phi_2d { public: //! enumeration of built-in Ramachandran tables enum TYPE { Gly, Pro, NonGlyPro, NonGly, All }; //! null constructor Ramachandran() {} //! constructor: from standard plot Ramachandran( TYPE type ); //! initialise: from standard plot void init( TYPE type ); //! change threshholds to different values void set_thresholds( ftype prob_favored = 0.01, ftype prob_allowed = 0.0005 ); //! get probability for a particular pair of angles ftype probability( const ftype& phi, const ftype& psi ) const { return Prob_phi_2d::probability( phi, psi ); } //! test if a pair of angles are in the favored region bool favored( const ftype& phi, const ftype& psi ) const { return ( probability( phi, psi ) > p_favored ); } //! test if a pair of angles are in the allowed region bool allowed( const ftype& phi, const ftype& psi ) const { return ( probability( phi, psi ) > p_allowed ); } private: ftype p_favored, p_allowed; }; } // namespace clipper #endif clipper-2.1/clipper/core/hkl_info.h0000644000374100011300000002646210363703537014276 00000000000000/*! \file lib/hkl_info.h Header file for hkl list class */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_HKL_INFO #define CLIPPER_HKL_INFO #include "hkl_lookup.h" namespace clipper { class HKL_data_base; //! HKL list container and tree root /*! This object contains contains a reflection list, and all the properties on which such a list depends, i.e. spacegroup, cell, resolution. It also keeps a fast reflection lookup list and lookup lists for resolutions and reflection classes. */ class HKL_info { public: //! null constructor HKL_info(); //! constructor: Takes spacegroup, cell, and resolution HKL_info( const Spacegroup& spacegroup, const Cell& cell, const Resolution& resolution, const bool& generate = false ); //! initialiser: Takes spacegroup, cell, and resolution void init( const Spacegroup& spacegroup, const Cell& cell, const Resolution& resolution, const bool& generate = false ); //! initialiser: Takes spacegroup, cell, and HKL_sampling void init( const Spacegroup& spacegroup, const Cell& cell, const HKL_sampling& hkl_sampling, const bool& generate = true ); //! test if object has been initialised bool is_null() const; //! get the cell const Cell& cell() const { return cell_; } //! get the spacegroup const Spacegroup& spacegroup() const { return spacegroup_; } //! [CLIPPER2] get HKL_sampling const HKL_sampling& hkl_sampling() const { return hkl_sampling_; } //! get the resolution const Resolution& resolution() const { return resolution_; } //! synthesize hkl list void generate_hkl_list(); //! add new reflections to the list void add_hkl_list( const std::vector& add ); //! get number of reflections in the object inline int num_reflections() const { return hkl.size(); } //! reflection hkl from index /*! \param index The index. \return The corresponding HKL. */ inline const HKL& hkl_of( const int& index ) const { return hkl[index]; } //! reflection index from hkl /*! This does not check symmetry equivalents (see find_sym). \param rfl The HKL. \return The index, or -1 if it does not exist. */ inline int index_of( const HKL& rfl ) const { return lookup.index_of( rfl ); } //! get reflection resolution using lookup inline const ftype32& invresolsq( const int& index ) const { return invresolsq_lookup[index]; } //! get resolution limits of the list inline const Range& invresolsq_range() const { return invresolsq_range_; } //! get reflection class using lookup const HKL_class& hkl_class( const int& index ) const { return hkl_class_lookup[index]; } //! find symop no and friedel to bring an HKL into ASU HKL find_sym( const HKL& rfl, int& sym, bool& friedel ) const; //! HKL reference base class /*! This is a reference to an HKL. It forms a base class for index-like and coordinate-like HKL references. If you write a method which will work with either, then specify this instead of either of the derived classed. \internal */ class HKL_reference_base { public: //! return the parent HKL_info inline const HKL_info& base_hkl_info() const { return *hklinfo; } //! return the current index (-1 if invalid) inline const int& index() const { return index_; } //! return the inv resol sq for the reflection (assumes index valid) inline ftype invresolsq( const HKL_data_base& hkldata ) const; //! return the inv resol sq for the reflection (assumes index valid) inline ftype invresolsq() const { return hklinfo->invresolsq( index_ ); } //! test if index has gone past last reflection inline bool last() const { return ( index_ >= hklinfo->num_reflections() ); } protected: const HKL_info* hklinfo; int index_; }; //! HKL reference with index-like behaviour /*! This is a reference to an HKL. It behaves like a simple index into the reflection list, but can be easily converted into an HKL as and when required. It also implements methods for iterating through a reflection list. \note The following methods are inherited from HKL_reference_base but are documented here for convenience: base_hkl_info(), index(), invresolsq(), last(). */ class HKL_reference_index : public HKL_reference_base { public: //! Null constructor HKL_reference_index() {} //! Constructor: takes parent HKL_info and initial index HKL_reference_index( const HKL_info& hklinfo_, const int& index ) { hklinfo = &hklinfo_; index_ = index; } //! return the current HKL inline const HKL& hkl() const { return hklinfo->hkl_of( index_ ); } //! return the reflection class for the reflection inline const HKL_class& hkl_class() const { return hklinfo->hkl_class( index_ ); } //! increment to next reflection inline HKL_reference_index& next() { index_++; return *this; } // inherited functions listed for documentation purposes //-- const HKL_info& base_hkl_info() const; //-- const int& index() const; //-- const ftype invresolsq() const; //-- bool last() const; }; //! HKL reference with coord-like behaviour /*! This is a reference to an HKL. It behaves like an HKL, but also stores the index of the corresponding reflection in the reflection list, if it exists, and the symmetry and friedel operators required to get there. \note The following methods are inherited from HKL_reference_base but are documented here for convenience: base_hkl_info(), index(), invresolsq(), last(). */ class HKL_reference_coord : public HKL_reference_base { public: //! Null constructor HKL_reference_coord() {} //! Constructor: takes parent HKL_info and initial HKL HKL_reference_coord( const HKL_info& hklinfo_, const HKL& hkl ) { hklinfo = &hklinfo_; hkl_ = hkl; index_ = hklinfo->index_of( hklinfo->find_sym( hkl_, sym_, friedel_ ) ); if ( index_ < 0 ) Message::message( Message_fatal( "HKL_reference_coord: hkl not found" ) ); } //! return the current HKL inline const HKL& hkl() const { return hkl_; } //! get current symop number inline const int& sym() const { return sym_; } //! get current friedel flag inline const bool& friedel() const { return friedel_; } //! assign from HKL /*! The new HKL must exist in the reflection list. The calculation is optimised for the case when the new HKL is near the old one. */ inline HKL_reference_coord& set_hkl( const HKL& hkl__ ) { hkl_ = hkl__; HKL equiv = hkl__.transform(hklinfo->isymop[sym_]); if ( friedel_ ) equiv = -equiv; index_ = hklinfo->index_of( equiv ); if ( index_ < 0 ) index_ = hklinfo->index_of( hklinfo->find_sym( hkl_, sym_, friedel_ ) ); return *this; } //! increment to next reflection inline HKL_reference_coord& next() { sym_ = 0; friedel_ = false; index_++; if ( !last() ) hkl_ = hklinfo->hkl_of( index_ ); return *this; } // increment h,k,l inline HKL_reference_coord& next_h() { hkl_.h()++; set_hkl( hkl_ ); return *this; } //!< increment h inline HKL_reference_coord& next_k() { hkl_.k()++; set_hkl( hkl_ ); return *this; } //!< increment k inline HKL_reference_coord& next_l() { hkl_.l()++; set_hkl( hkl_ ); return *this; } //!< increment l inline HKL_reference_coord& prev_h() { hkl_.h()--; set_hkl( hkl_ ); return *this; } //!< decrement h inline HKL_reference_coord& prev_k() { hkl_.k()--; set_hkl( hkl_ ); return *this; } //!< decrement k inline HKL_reference_coord& prev_l() { hkl_.l()--; set_hkl( hkl_ ); return *this; } //!< decrement l //! operator assign from HKL inline HKL_reference_coord& operator =( const HKL& hkl__ ) { return set_hkl( hkl__ ); } // inherited functions listed for documentation purposes //-- const HKL_info& base_hkl_info() const; //-- const int& index() const; //-- const ftype invresolsq() const; //-- bool last() const; protected: HKL hkl_; int sym_; bool friedel_; }; //! return HKL_reference_index pointing to first reflection HKL_reference_index first() const { return HKL_reference_index( *this, 0 ); } void debug() const; protected: Spacegroup spacegroup_; //!< spacegroup Cell cell_; //!< unit cell HKL_sampling hkl_sampling_; //!< hkl sampling Resolution resolution_; //!< resolution limit std::vector isymop; //!< integer symops //! the reflection list std::vector hkl; //! fast epsilon/centricity lookup table std::vector hkl_class_lookup; //! fast resolution lookup table std::vector invresolsq_lookup; //! fast reflection lookup table HKL_lookup lookup; //! resolution limit of the current reflection list Range invresolsq_range_; // internal methods: //! finalise reflection list \internal void update_hkl_list(); friend class HKL_info::HKL_reference_base; friend class HKL_info::HKL_reference_index; friend class HKL_info::HKL_reference_coord; }; } // namespace clipper #endif clipper-2.1/clipper/core/hkl_operators.cpp0000644000374100011300000003630610363703537015712 00000000000000/* hkl_operators.cpp: HKL_data operators for the clipper libraries */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "hkl_operators.h" namespace clipper { namespace datatypes { HKL_data operator &( const HKL_data_base& d1, const HKL_data_base& d2 ) { HKL_data result( d1.base_hkl_info(), d1.base_cell() ); for ( int i = 0; i < d1.base_hkl_info().num_reflections(); i++ ) result[i].flag() = ( !d1.missing(i) ) && ( !d2.missing(i) ); return result; } HKL_data operator |( const HKL_data_base& d1, const HKL_data_base& d2 ) { HKL_data result( d1.base_hkl_info(), d1.base_cell() ); for ( int i = 0; i < d1.base_hkl_info().num_reflections(); i++ ) result[i].flag() = ( !d1.missing(i) ) || ( !d2.missing(i) ); return result; } HKL_data operator ^( const HKL_data_base& d1, const HKL_data_base& d2 ) { HKL_data result( d1.base_hkl_info(), d1.base_cell() ); for ( int i = 0; i < d1.base_hkl_info().num_reflections(); i++ ) result[i].flag() = ( !d1.missing(i) ) ^ ( !d2.missing(i) ); return result; } HKL_data operator !( const HKL_data_base& d1 ) { HKL_data result( d1.base_hkl_info(), d1.base_cell() ); for ( int i = 0; i < d1.base_hkl_info().num_reflections(); i++ ) result[i].flag() = d1.missing(i); return result; } HKL_data operator ==( const HKL_data& d1, const int& n ) { HKL_data result( d1.base_hkl_info(), d1.base_cell() ); for ( int i = 0; i < d1.base_hkl_info().num_reflections(); i++ ) result[i].flag() = ( d1[i].flag() == n ); return result; } HKL_data operator !=( const HKL_data& d1, const int& n ) { HKL_data result( d1.base_hkl_info(), d1.base_cell() ); for ( int i = 0; i < d1.base_hkl_info().num_reflections(); i++ ) result[i].flag() = ( d1[i].flag() != n ); return result; } HKL_data operator >=( const HKL_data& d1, const int& n ) { HKL_data result( d1.base_hkl_info(), d1.base_cell() ); for ( int i = 0; i < d1.base_hkl_info().num_reflections(); i++ ) result[i].flag() = ( d1[i].flag() >= n ); return result; } HKL_data operator <=( const HKL_data& d1, const int& n ) { HKL_data result( d1.base_hkl_info(), d1.base_cell() ); for ( int i = 0; i < d1.base_hkl_info().num_reflections(); i++ ) result[i].flag() = ( d1[i].flag() <= n ); return result; } HKL_data operator >( const HKL_data& d1, const int& n ) { HKL_data result( d1.base_hkl_info(), d1.base_cell() ); for ( int i = 0; i < d1.base_hkl_info().num_reflections(); i++ ) result[i].flag() = ( d1[i].flag() > n ); return result; } HKL_data operator <( const HKL_data& d1, const int& n ) { HKL_data result( d1.base_hkl_info(), d1.base_cell() ); for ( int i = 0; i < d1.base_hkl_info().num_reflections(); i++ ) result[i].flag() = ( d1[i].flag() < n ); return result; } template F_phi operator +( const F_phi& d1, const F_phi& d2 ) { return clipper::datatypes::F_phi( std::complex(d1) + std::complex(d2) ); } template F_phi operator -( const F_phi& d1, const F_phi& d2 ) { return clipper::datatypes::F_phi( std::complex(d1) - std::complex(d2) ); } template F_phi operator -( const F_phi& d1 ) { return clipper::datatypes::F_phi( -std::complex(d1) ); } template ABCD operator +( const ABCD& d1, const ABCD& d2 ) { ABCD result; result.a() = d1.a() + d2.a(); result.b() = d1.b() + d2.b(); result.c() = d1.c() + d2.c(); result.d() = d1.d() + d2.d(); return result; } template HKL_data > operator +( const HKL_data >& d1, const HKL_data >& d2 ) { HKL_data > result( d1.base_hkl_info(), d1.base_cell() ); for ( int i = 0; i < d1.base_hkl_info().num_reflections(); i++ ) if ( !d1.missing(i) && !d2.missing(i) ) result[i] = clipper::datatypes::F_phi( std::complex(d1[i]) + std::complex(d2[i]) ); return result; } template HKL_data > operator -( const HKL_data >& d1, const HKL_data >& d2 ) { HKL_data > result( d1.base_hkl_info(), d1.base_cell() ); for ( int i = 0; i < d1.base_hkl_info().num_reflections(); i++ ) if ( !d1.missing(i) && !d2.missing(i) ) result[i] = clipper::datatypes::F_phi( std::complex(d1[i]) - std::complex(d2[i]) ); return result; } template HKL_data > operator *( const HKL_data >& d1, const ftype& s ) { HKL_data > result( d1.base_hkl_info(), d1.base_cell() ); for ( int i = 0; i < d1.base_hkl_info().num_reflections(); i++ ) if ( !d1.missing(i) ) { result[i] = d1[i]; result[i].scale(s); } return result; } template HKL_data > operator -( const HKL_data >& d1 ) { HKL_data > result( d1.base_hkl_info(), d1.base_cell() ); for ( int i = 0; i < d1.base_hkl_info().num_reflections(); i++ ) if ( !d1.missing(i) ) result[i] = clipper::datatypes::F_phi( -std::complex(d1[i]) ); return result; } template HKL_data > operator +( const HKL_data >& d1, const HKL_data >& d2 ) { HKL_data > result( d1.base_hkl_info(), d1.base_cell() ); for ( int i = 0; i < d1.base_hkl_info().num_reflections(); i++ ) if ( !d1.missing(i) && !d2.missing(i) ) { result[i].a() = d1[i].a() + d2[i].a(); result[i].b() = d1[i].b() + d2[i].b(); result[i].c() = d1[i].c() + d2[i].c(); result[i].d() = d1[i].d() + d2[i].d(); } return result; } // compile template types template F_phi operator +( const F_phi& d1, const F_phi& d2 ); template F_phi operator -( const F_phi& d1, const F_phi& d2 ); template F_phi operator -( const F_phi& d1 ); template ABCD operator +( const ABCD& d1, const ABCD& d2 ); template F_phi operator +( const F_phi& d1, const F_phi& d2 ); template F_phi operator -( const F_phi& d1, const F_phi& d2 ); template F_phi operator -( const F_phi& d1 ); template ABCD operator +( const ABCD& d1, const ABCD& d2 ); template HKL_data > operator +( const HKL_data >& d1, const HKL_data >& d2 ); template HKL_data > operator -( const HKL_data >& d1, const HKL_data >& d2 ); template HKL_data > operator *( const HKL_data >& d1, const ftype& s ); template HKL_data > operator *( const ftype& s, const HKL_data >& d1 ); template HKL_data > operator -( const HKL_data >& d1 ); template HKL_data > operator +( const HKL_data >& d1, const HKL_data >& d2 ); template HKL_data > operator +( const HKL_data >& d1, const HKL_data >& d2 ); template HKL_data > operator -( const HKL_data >& d1, const HKL_data >& d2 ); template HKL_data > operator *( const HKL_data >& d1, const ftype& s ); template HKL_data > operator *( const ftype& s, const HKL_data >& d1 ); template HKL_data > operator -( const HKL_data >& d1 ); template HKL_data > operator +( const HKL_data >& d1, const HKL_data >& d2 ); } // namespace datatypes template LogPhaseProb::LogPhaseProb( const HKL_class& hkl_class ) { if ( hkl_class.centric() ) { pmin = Util::mod( Util::intr( N*hkl_class.allowed()/Util::twopi() ), N/2 ); pinc = N/2; q.resize( 2, 0.0 ); } else { pmin = 0; pinc = 1; q.resize( N, 0.0 ); } } template template void LogPhaseProb::set_abcd( const datatypes::ABCD& abcd ) { if ( !abcd.missing() ) { ftype c, s; for ( int p = 0; p < q.size(); p++ ) { c = cos( phase(p) ); s = sin( phase(p) ); q[p] = abcd.a()*c + abcd.b()*s + abcd.c()*(c*c-s*s) + abcd.d()*(2.0*c*s); } } else { for ( int p = 0; p < q.size(); p++ ) q[p] = 0.0; } } template template void LogPhaseProb::get_abcd( datatypes::ABCD& abcd ) const { ftype q0, q1, c, s; q0 = 0.0; for ( int p = 0; p < q.size(); p++ ) q0 += q[p]; q0 /= double( q.size() ); abcd.a() = abcd.b() = abcd.c() = abcd.d() = 0.0; for ( int p = 0; p < q.size(); p++ ) { q1 = ( q[p] - q0 ) / double( (pinc==1) ? (N/2) : 2 ); c = cos( phase(p) ); s = sin( phase(p) ); abcd.a() += q1 * c; abcd.b() += q1 * s; abcd.c() += q1 * (c*c-s*s); abcd.d() += q1 * (2.0*c*s); } } template template void LogPhaseProb::set_phi_fom( const datatypes::Phi_fom& phifom ) { if ( !phifom.missing() ) { dtype x = Util::min( phifom.fom(), dtype(0.999999) ); if ( pinc != 1 ) x = Util::atanh( x ); else x = Util::invsim( x ); for ( int p = 0; p < q.size(); p++ ) q[p] = x*cos( phase(p) - phifom.phi() ); } else { for ( int p = 0; p < q.size(); p++ ) q[p] = 0.0; } } template template void LogPhaseProb::get_phi_fom( datatypes::Phi_fom& phifom ) const { Range qrange( -700.0, 700.0 ); ftype s, a, b, q0, pq; s = a = b = q0 = 0.0; for ( int p = 0; p < q.size(); p++ ) q0 += q[p]; q0 /= double( q.size() ); for ( int p = 0; p < q.size(); p++ ) { pq = exp( qrange.truncate(q[p] - q0) ); s += pq; a += pq * cos( phase(p) ); b += pq * sin( phase(p) ); } std::complex pw( a/s, b/s ); phifom.phi() = std::arg( pw ); phifom.fom() = std::abs( pw ); } template class LogPhaseProb<24>; template void LogPhaseProb<24>::set_abcd(const datatypes::ABCD& abcd); template void LogPhaseProb<24>::get_abcd(datatypes::ABCD& abcd) const; template void LogPhaseProb<24>::set_phi_fom( const datatypes::Phi_fom& phifom ); template void LogPhaseProb<24>::get_phi_fom( datatypes::Phi_fom& phifom ) const; template void LogPhaseProb<24>::set_abcd(const datatypes::ABCD& abcd); template void LogPhaseProb<24>::get_abcd(datatypes::ABCD& abcd) const; template void LogPhaseProb<24>::set_phi_fom( const datatypes::Phi_fom& phifom ); template void LogPhaseProb<24>::get_phi_fom( datatypes::Phi_fom& phifom ) const; template class LogPhaseProb<72>; template void LogPhaseProb<72>::set_abcd(const datatypes::ABCD& abcd); template void LogPhaseProb<72>::get_abcd(datatypes::ABCD& abcd) const; template void LogPhaseProb<72>::set_phi_fom( const datatypes::Phi_fom& phifom ); template void LogPhaseProb<72>::get_phi_fom( datatypes::Phi_fom& phifom ) const; template void LogPhaseProb<72>::set_abcd(const datatypes::ABCD& abcd); template void LogPhaseProb<72>::get_abcd(datatypes::ABCD& abcd) const; template void LogPhaseProb<72>::set_phi_fom( const datatypes::Phi_fom& phifom ); template void LogPhaseProb<72>::get_phi_fom( datatypes::Phi_fom& phifom ) const; template class LogPhaseProb<180>; template void LogPhaseProb<180>::set_abcd(const datatypes::ABCD& abcd); template void LogPhaseProb<180>::get_abcd(datatypes::ABCD& abcd) const; template void LogPhaseProb<180>::set_phi_fom( const datatypes::Phi_fom& phifom ); template void LogPhaseProb<180>::get_phi_fom( datatypes::Phi_fom& phifom ) const; template void LogPhaseProb<180>::set_abcd(const datatypes::ABCD& abcd); template void LogPhaseProb<180>::get_abcd(datatypes::ABCD& abcd) const; template void LogPhaseProb<180>::set_phi_fom( const datatypes::Phi_fom& phifom ); template void LogPhaseProb<180>::get_phi_fom( datatypes::Phi_fom& phifom ) const; template class LogPhaseProb<360>; template void LogPhaseProb<360>::set_abcd(const datatypes::ABCD& abcd); template void LogPhaseProb<360>::get_abcd(datatypes::ABCD& abcd) const; template void LogPhaseProb<360>::set_phi_fom( const datatypes::Phi_fom& phifom ); template void LogPhaseProb<360>::get_phi_fom( datatypes::Phi_fom& phifom ) const; template void LogPhaseProb<360>::set_abcd(const datatypes::ABCD& abcd); template void LogPhaseProb<360>::get_abcd(datatypes::ABCD& abcd) const; template void LogPhaseProb<360>::set_phi_fom( const datatypes::Phi_fom& phifom ); template void LogPhaseProb<360>::get_phi_fom( datatypes::Phi_fom& phifom ) const; } // namespace clipper clipper-2.1/clipper/contrib/0000777000374100011300000000000011372264353013115 500000000000000clipper-2.1/clipper/contrib/originmatch.cpp0000644000374100011300000001103311144026530016025 00000000000000/* originmatch.cpp: Origin matching implementation */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "originmatch.h" namespace clipper { template bool OriginMatch::operator() ( bool& invert, clipper::Coord_frac& shift, const HKL_data >& fphi1, const HKL_data >& fphi2 ) const { const Spacegroup& oldspgr = fphi1.base_hkl_info().spacegroup(); const Cell& oldcell = fphi1.base_hkl_info().cell(); const Resolution& oldreso = fphi1.base_hkl_info().resolution(); // calc point group const Spgr_descr spgrdscr( oldspgr.generator_ops().pgrp_ops() ); const Spacegroup newspgr( spgrdscr ); // new cell and resolution const Cell newcell( oldcell ); const Resolution newreso( Util::max( limit, oldreso.limit() ) ); // new reflection list HKL_info hkls( newspgr, newcell, newreso, true ); HKL_data > fphi(hkls), fphiinv(hkls); HKL_info::HKL_reference_index ih; HKL hkl; datatypes::F_phi fp1, fp2; for ( ih = hkls.first(); !ih.last(); ih.next() ) { hkl = ih.hkl(); fp1 = fphi1[hkl]; fp2 = fphi2[hkl]; if ( !fp1.missing() && !fp2.missing() ) { fphi[ih].f() = fphiinv[ih].f() = fp1.f() * fp2.f(); fphi[ih].phi() = fp1.phi() - fp2.phi(); fphiinv[ih].phi() = fp1.phi() + fp2.phi(); } else { fphi[ih].f() = fphiinv[ih].f() = fphi[ih].phi() = fphiinv[ih].phi() = 0.0; } } // new map Grid_sampling oldgrid( newspgr, newcell, newreso ); Grid_sampling newgrid( ((oldgrid.nu()+11)/12)*12, ((oldgrid.nv()+11)/12)*12, ((oldgrid.nw()+11)/12)*12 ); Xmap xmap( newspgr, newcell, newgrid ); Xmap::Map_reference_index ix; // search for highest peak T mapmax = 0.0; invert = false; shift = Coord_frac( 0.0, 0.0, 0.0 ); { xmap.fft_from( fphi ); for ( ix = xmap.first(); !ix.last(); ix.next() ) if ( xmap[ix] > mapmax ) { mapmax = xmap[ix]; shift = ix.coord().coord_frac( newgrid ); invert = false; } } if ( oldspgr.invariant_under_change_of_hand() ) { xmap.fft_from( fphiinv ); for ( ix = xmap.first(); !ix.last(); ix.next() ) if ( xmap[ix] > mapmax ) { mapmax = xmap[ix]; shift = ix.coord().coord_frac( newgrid ); invert = true; } } // check against symmetry restrictions // return the shift return true; } // compile templates template class OriginMatch; template class OriginMatch; } // namespace clipper clipper-2.1/clipper/contrib/mapfilter.h0000644000374100011300000001523210736662165015176 00000000000000/*! \file mapfilter.h Header file for sample map filtering impelementation \ingroup g_mapf */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_MAPFILTER #define CLIPPER_MAPFILTER #include "function_object_bases.h" namespace clipper { //! Base class for radial map filters class MapFilterFn_base { public: virtual ~MapFilterFn_base() {}; virtual ftype operator() ( const ftype& radius ) const = 0; }; //! Simple slow convolution-based radial mapfiltering implementation /*! This version is of course very slow, and is mainly provided so you can test the repcision of the fft version. \ingroup g_mapf */ template class MapFilter_slow : public MapFilter_base { public: //! Scaling modes enum TYPE { NONE, Absolute, Relative }; //! constructor MapFilter_slow( const MapFilterFn_base& fltr, const ftype scale = 1.0, const TYPE type = NONE ); //! constructor: shorthand for constructor+operator MapFilter_slow( clipper::Xmap& result, const clipper::Xmap& xmap, MapFilterFn_base& fltr, const ftype scale = 1.0, const TYPE type = NONE ); bool operator() ( clipper::Xmap& result, const clipper::Xmap& xmap ) const; private: const MapFilterFn_base* fltr_; ftype scale_; TYPE type_; }; //! Simple fft-based radial mapfiltering implementation /*! The FFT method is fast, and also gives good precision. The following example demonstrates how to use the MapFilter to calculate the local mean and local deviation of an electron density map, in 'xmap': \code // make squared map clipper::Xmap xmap2( xmap ); clipper::Xmap::Map_reference_index ix; for ( ix = xmap2.first(); !ix.last(); ix.next() ) xmap2[ix] = pow( xmap2[ix], 2.0 ); // now calculate local mean, local mean squared clipper::MapFilterFn_step fn( filter_radius ); clipper::MapFilter_fft fltr( fn, 1.0, clipper::MapFilter_fft::Relative ); clipper::Xmap lmean, lsigm; fltr( lmean, xmap ); fltr( lsigm, xmap2 ); // calculate std deviation for ( ix = lmean.first(); !ix.last(); ix.next() ) lsigm[ix] = sqrt( lsigm[ix] - pow( lmean[ix], 2.0 ) ); \endcode This would be a useful step in solvent mask determination, for example. \ingroup g_mapf */ template class MapFilter_fft : public MapFilter_base { public: //! Scaling modes enum TYPE { NONE, Absolute, Relative }; //! constructor MapFilter_fft( const MapFilterFn_base& fltr, const ftype scale = 1.0, const TYPE type = NONE ); //! constructor: shorthand for constructor+operator MapFilter_fft( clipper::Xmap& result, const clipper::Xmap& xmap, MapFilterFn_base& fltr, const ftype scale = 1.0, const TYPE type = NONE ); bool operator() ( clipper::Xmap& result, const clipper::Xmap& xmap ) const; bool operator() ( clipper::NXmap& result, const clipper::NXmap& nxmap ) const; private: const MapFilterFn_base* fltr_; ftype scale_; TYPE type_; }; //! Step-function radial map filter /*! \ingroup g_mapf */ class MapFilterFn_step : public MapFilterFn_base { public: //! constructor: takes radius for step function cutoff MapFilterFn_step( const ftype& radius ) : radius_( radius ) {} //! destructor MapFilterFn_step() {} //! evaluate radial step function: 1.0 if inside or 0.0 outside ftype operator() ( const ftype& radius ) const { return (radius bool SFscale_aniso::operator() ( HKL_data >& fo, const HKL_data >& fc ) { typedef HKL_info::HKL_reference_index HRI; // expand to P1 in order to preserve symmetry const HKL_info& hkls = fo.hkl_info(); Spacegroup spgrp1( Spacegroup::P1 ); HKL_info hkl1( spgrp1, hkls.cell(), hkls.resolution(), true ); HKL_data > fo1( hkl1 ); HKL_data > fc1( hkl1 ); for ( HRI ih = hkl1.first(); !ih.last(); ih.next() ) { datatypes::F_sigF f = fo[ih.hkl()]; if ( f.f() >= nsig_ * f.sigf() ) { fo1[ih] = f; fc1[ih] = fc[ih.hkl()]; } } // do the aniso scaling std::vector param( 7, 0.0 ); BasisFn_log_aniso_gaussian bfn; TargetFn_scaleLogF1F2,datatypes::F_phi > tfn( fo1, fc1 ); ResolutionFn rfn( hkl1, bfn, tfn, param ); for ( HRI ih = hkls.first(); !ih.last(); ih.next() ) if ( !fo[ih].missing() ) fo[ih].scale( exp( 0.5*bfn.f(ih.hkl(),hkls.cell(),rfn.params()) ) ); u_i = bfn.u_aniso_orth( rfn.params() ); u_f = 0.5 * u_i; return true; } template bool SFscale_aniso::operator() ( HKL_data >& fc, const HKL_data >& fo ) { typedef HKL_info::HKL_reference_index HRI; // expand to P1 in order to preserve symmetry const HKL_info& hkls = fo.hkl_info(); Spacegroup spgrp1( Spacegroup::P1 ); HKL_info hkl1( spgrp1, hkls.cell(), hkls.resolution(), true ); HKL_data > fo1( hkl1 ); HKL_data > fc1( hkl1 ); for ( HRI ih = hkl1.first(); !ih.last(); ih.next() ) { datatypes::F_sigF f = fo[ih.hkl()]; if ( f.f() >= nsig_ * f.sigf() ) { fo1[ih] = f; fc1[ih] = fc[ih.hkl()]; } } // do the aniso scaling std::vector param( 7, 0.0 ); BasisFn_log_aniso_gaussian bfn; TargetFn_scaleLogF1F2,datatypes::F_sigF > tfn( fc1, fo1 ); ResolutionFn rfn( hkl1, bfn, tfn, param ); for ( HRI ih = hkls.first(); !ih.last(); ih.next() ) if ( !fc[ih].missing() ) fc[ih].scale( exp( 0.5*bfn.f(ih.hkl(),hkls.cell(),rfn.params()) ) ); u_i = bfn.u_aniso_orth( rfn.params() ); u_f = 0.5 * u_i; return true; } template bool SFscale_aniso::operator() ( HKL_data >& fo ) { typedef datatypes::F_sigF DATA; typedef TargetFn_scaleF1F2 TGT1; typedef TargetFn_scaleLogF1F2 TGT2; typedef BasisFn_spline SCALETYPE; return scale( fo, -1.0, 12 ); } template bool SFscale_aniso::operator() ( HKL_data >& fo, ftype resfilter, const int npar_scl ) { typedef datatypes::F_sigF DATA; typedef TargetFn_scaleF1F2 TGT1; typedef TargetFn_scaleLogF1F2 TGT2; typedef BasisFn_spline SCALETYPE; return scale( fo, resfilter, npar_scl ); } template bool SFscale_aniso::operator() ( HKL_data >& Io, ftype resfilter, const int npar_scl ) { typedef datatypes::I_sigI DATA; typedef TargetFn_scaleI1I2 TGT1; typedef TargetFn_scaleLogI1I2 TGT2; typedef BasisFn_spline SCALETYPE; return scale( Io, resfilter, npar_scl ); } template template bool SFscale_aniso::scale( HKL_data& fo, const ftype resfilter, const int npar_scl ) { typedef HKL_info::HKL_reference_index HRI; // expand to P1 in order to preserve symmetry const HKL_info& hkls = fo.hkl_info(); Spacegroup spgrp1( Spacegroup::P1 ); HKL_info hkl1( spgrp1, hkls.cell(), hkls.resolution(), true ); HKL_data fo1( hkl1 ), fs1( hkl1 ), fc1( hkl1 ); for ( HRI ih = hkl1.first(); !ih.last(); ih.next() ) { D f = fo[ih.hkl()]; if ( obs(f) >= nsig_ * sigobs(f) ) fo1[ih] = f; } // calc target values fc1 = D( 1.0, 1.0 ); for ( HRI ih = fc1.first(); !ih.last(); ih.next() ) fc1[ih].scale( sqrt( ih.hkl_class().epsilon() ) ); // do correction u_i = u_f = U_aniso_orth( 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 ); std::vector param( 7, 0.0 ); BasisFn_log_aniso_gaussian bfn; ftype dp; for ( int c = 0; c < 2; c++ ) { // remove current anistropy estimate datatypes::Compute_scale_u_aniso compute_s(1.0,-u_f); fs1.compute( fo1, compute_s ); /*{ T2 tfn( fs1, fc1 ); param = std::vector( 7, 0.0 ); ResolutionFn rfn( hkl1, bfn, tfn, param ); param = rfn.params(); dp = (param[1]+param[2]+param[3])/3.0; param[1] -= dp; param[2] -= dp; param[3] -= dp; std::cout << "#" << param[1] << " " << param[2] << " " << param[3] << " " << param[4] << " " << param[5] << " " << param[6] << "\n"; std::cout << "\n"; }*/ // and calc E scale S basissc( fs1, npar_scl, 1.0 ); std::vector param_fo( basissc.num_params(), 1.0 ); T1 tfn_fo( fs1, fc1 ); ResolutionFn rfn_fo( hkl1, basissc, tfn_fo, param_fo ); param_fo = rfn_fo.params(); // prescale F to E-like scale for ( HRI ih = fs1.first(); !ih.last(); ih.next() ) { fs1[ih] = fo1[ih]; fs1[ih].scale( sqrt( basissc.f_s( ih.invresolsq(), param_fo ) ) ); } /*for ( int i = 0; i < param_fo.size(); i++ ) std::cout << param_fo[i] << " "; std::cout << std::endl; { S basissc( fs1, npar_scl, 1.0 ); std::vector param_fo( basissc.num_params(), 1.0 ); T1 tfn_fo( fs1, fc1 ); ResolutionFn rfn_fo( hkl1, basissc, tfn_fo, param_fo ); param_fo = rfn_fo.params(); for ( int i = 0; i < param_fo.size(); i++ ) std::cout << param_fo[i] << " "; std::cout << std::endl; }*/ // if required, weight low res terms towards isotropic if ( resfilter > 0.0 ) { ftype ssq = clipper::Resolution( resfilter ).invresolsq_limit(); for ( HRI ih = fs1.first(); !ih.last(); ih.next() ) if ( !fs1[ih].missing() ) { ftype w = exp( -0.5 * ih.invresolsq() / ssq ); fs1[ih] = D( exp( (1.0-w)*log(obs(fs1[ih]))+(w)*log(obs(fc1[ih])) ), sigobs(fs1[ih]) ); } } // do the aniso scaling T2 tfn( fs1, fc1 ); param = std::vector( 7, 0.0 ); ResolutionFn rfn( hkl1, bfn, tfn, param ); param = rfn.params(); // set trace to zero (i.e. no isotropic correction) dp = (param[1]+param[2]+param[3])/3.0; param[1] -= dp; param[2] -= dp; param[3] -= dp; u_i = bfn.u_aniso_orth( param ); u_f = 0.5 * u_i; //std::cout << c << " | " << param[1] << " " << param[2] << " " << param[3] << " " << param[4] << " " << param[5] << " " << param[6] << "\n"; std::cout << " DP " << dp << "\n"; } // sharpen or smooth as required Matrix m(3,3); m(0,0)= param[1]; m(1,1)= param[2]; m(2,2)= param[3]; m(0,1)=m(1,0)=param[4]; m(0,2)=m(2,0)=param[5]; m(1,2)=m(2,1)=param[6]; std::vector ev = m.eigen(); //std::cout << "EIGEN " << param[1] << " " << param[2] << " " << param[3] << " " << ev[0] << " " << ev[1] << " " << ev[2] << std::endl; dp = 0.0; if ( mode_ == SHARPEN ) dp = ev[2]; if ( mode_ == UNSHARPEN ) dp = ev[0]; param[1] -= dp; param[2] -= dp; param[3] -= dp; u_i = bfn.u_aniso_orth( param ); u_f = 0.5 * u_i; // store the results datatypes::Compute_scale_u_aniso compute_s(1.0,-u_f); fo.compute( fo, compute_s ); return true; } template const U_aniso_orth& SFscale_aniso::u_aniso_orth( TYPE t ) const { if ( t == I ) return u_i; else return u_f; } // compile templates template class SFscale_aniso; template bool SFscale_aniso::scale,TargetFn_scaleF1F2,datatypes::F_sigF >,TargetFn_scaleLogF1F2,datatypes::F_sigF >,BasisFn_binner>( HKL_data >& fo, const ftype resfilter, const int npar_scl ); template bool SFscale_aniso::scale,TargetFn_scaleF1F2,datatypes::F_sigF >,TargetFn_scaleLogF1F2,datatypes::F_sigF >,BasisFn_linear>( HKL_data >& fo, const ftype resfilter, const int npar_scl ); template bool SFscale_aniso::scale,TargetFn_scaleF1F2,datatypes::F_sigF >,TargetFn_scaleLogF1F2,datatypes::F_sigF >,BasisFn_spline>( HKL_data >& fo, const ftype resfilter, const int npar_scl ); template bool SFscale_aniso::scale,TargetFn_scaleI1I2,datatypes::I_sigI >,TargetFn_scaleLogI1I2,datatypes::I_sigI >,BasisFn_binner>( HKL_data >& fo, const ftype resfilter, const int npar_scl ); template bool SFscale_aniso::scale,TargetFn_scaleI1I2,datatypes::I_sigI >,TargetFn_scaleLogI1I2,datatypes::I_sigI >,BasisFn_linear>( HKL_data >& fo, const ftype resfilter, const int npar_scl ); template bool SFscale_aniso::scale,TargetFn_scaleI1I2,datatypes::I_sigI >,TargetFn_scaleLogI1I2,datatypes::I_sigI >,BasisFn_spline>( HKL_data >& fo, const ftype resfilter, const int npar_scl ); template class SFscale_aniso; template bool SFscale_aniso::scale,TargetFn_scaleF1F2,datatypes::F_sigF >,TargetFn_scaleLogF1F2,datatypes::F_sigF >,BasisFn_binner>( HKL_data >& fo, const ftype resfilter, const int npar_scl ); template bool SFscale_aniso::scale,TargetFn_scaleF1F2,datatypes::F_sigF >,TargetFn_scaleLogF1F2,datatypes::F_sigF >,BasisFn_linear>( HKL_data >& fo, const ftype resfilter, const int npar_scl ); template bool SFscale_aniso::scale,TargetFn_scaleF1F2,datatypes::F_sigF >,TargetFn_scaleLogF1F2,datatypes::F_sigF >,BasisFn_spline>( HKL_data >& fo, const ftype resfilter, const int npar_scl ); template bool SFscale_aniso::scale,TargetFn_scaleI1I2,datatypes::I_sigI >,TargetFn_scaleLogI1I2,datatypes::I_sigI >,BasisFn_binner>( HKL_data >& fo, const ftype resfilter, const int npar_scl ); template bool SFscale_aniso::scale,TargetFn_scaleI1I2,datatypes::I_sigI >,TargetFn_scaleLogI1I2,datatypes::I_sigI >,BasisFn_linear>( HKL_data >& fo, const ftype resfilter, const int npar_scl ); template bool SFscale_aniso::scale,TargetFn_scaleI1I2,datatypes::I_sigI >,TargetFn_scaleLogI1I2,datatypes::I_sigI >,BasisFn_spline>( HKL_data >& fo, const ftype resfilter, const int npar_scl ); } // namespace clipper clipper-2.1/clipper/contrib/sfcalc.cpp0000644000374100011300000001734210736662165015005 00000000000000/* sfcalc.cpp: Structure factor calculation implementation */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "sfcalc.h" #include "../core/atomsf.h" namespace clipper { template bool SFcalc_iso_sum::operator() ( HKL_data >& fphidata, const Atom_list& atoms ) const { const HKL_info& hkls = fphidata.base_hkl_info(); const Cell& cell = fphidata.base_cell(); const Spacegroup& spgr = hkls.spacegroup(); fphidata = datatypes::F_phi( std::complex( 0.0, 0.0 ) ); HKL_info::HKL_reference_index ih; for ( int i = 0; i < atoms.size(); i++ ) if ( !atoms[i].is_null() ) { AtomShapeFn sf( atoms[i].coord_orth(), atoms[i].element(), atoms[i].u_iso(), atoms[i].occupancy() ); for ( int j = 0; j < spgr.num_symops(); j++ ) { Coord_frac uvw = atoms[i].coord_orth().coord_frac( cell ).transform( spgr.symop(j) ); for ( ih = hkls.first(); !ih.last(); ih.next() ) { T phi = Util::twopi() * (ih.hkl().coord_reci_frac()*uvw); fphidata[ih] = std::complex(fphidata[ih]) + T( sf.f(ih.invresolsq()) ) * std::complex( cos(phi), sin(phi) ); } } } return true; } template bool SFcalc_aniso_sum::operator() ( HKL_data >& fphidata, const Atom_list& atoms ) const { const HKL_info& hkls = fphidata.base_hkl_info(); const Cell& cell = fphidata.base_cell(); const Spacegroup& spgr = hkls.spacegroup(); fphidata = datatypes::F_phi( std::complex( 0.0, 0.0 ) ); HKL_info::HKL_reference_index ih; for ( int i = 0; i < atoms.size(); i++ ) if ( !atoms[i].is_null() ) { for ( int j = 0; j < spgr.num_symops(); j++ ) { Atom atom( atoms[i] ); atom.transform( spgr.symop(j).rtop_orth( cell ) ); AtomShapeFn sf( atom ); Coord_frac uvw = atom.coord_orth().coord_frac( cell ); for ( ih = hkls.first(); !ih.last(); ih.next() ) { T phi = Util::twopi() * (ih.hkl().coord_reci_frac()*uvw); fphidata[ih] = std::complex(fphidata[ih]) + T(sf.f(ih.hkl().coord_reci_orth(cell))) * std::complex( cos(phi), sin(phi) ); } } } return true; } template bool SFcalc_iso_fft::operator() ( HKL_data >& fphidata, const Atom_list& atoms ) const { const HKL_info& hkls = fphidata.base_hkl_info(); const Cell& cell = fphidata.base_cell(); const Spacegroup& spgr = hkls.spacegroup(); const Grid_sampling grid( spgr, cell, hkls.resolution(), rate_ ); Xmap xmap( spgr, cell, grid ); Coord_frac uvw, duvw; Coord_grid g0, g1; Grid_range gd( cell, grid, radius_ ); Xmap::Map_reference_coord i0, iu, iv, iw; for ( int i = 0; i < atoms.size(); i++ ) if ( !atoms[i].is_null() ) { AtomShapeFn sf( atoms[i].coord_orth(), atoms[i].element(), atoms[i].u_iso() + uadd_, atoms[i].occupancy() ); uvw = atoms[i].coord_orth().coord_frac( cell ); g0 = uvw.coord_grid( grid ) + gd.min(); g1 = uvw.coord_grid( grid ) + gd.max(); i0 = Xmap::Map_reference_coord( xmap, g0 ); for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) xmap[iw] += sf.rho( iw.coord_orth() ); } for ( Xmap::Map_reference_index ix = xmap.first(); !ix.last(); ix.next() ) xmap[ix] *= xmap.multiplicity( ix.coord() ); xmap.fft_to( fphidata ); if ( uadd_ != 0.0 ) { ftype u = Util::twopi2()*uadd_; for ( HKL_info::HKL_reference_index ih = fphidata.first_data(); !ih.last(); fphidata.next_data( ih ) ) fphidata[ih].scale( exp( u * ih.invresolsq() ) ); } return true; } template bool SFcalc_aniso_fft::operator() ( HKL_data >& fphidata, const Atom_list& atoms ) const { const HKL_info& hkls = fphidata.base_hkl_info(); const Cell& cell = fphidata.base_cell(); const Spacegroup& spgr = hkls.spacegroup(); const Grid_sampling grid( spgr, cell, hkls.resolution(), rate_ ); Xmap xmap( spgr, cell, grid ); U_aniso_orth uadd( uadd_ ); Coord_frac uvw, duvw; Coord_grid g0, g1; Grid_range gd( cell, grid, radius_ ); Xmap::Map_reference_coord i0, iu, iv, iw; for ( int i = 0; i < atoms.size(); i++ ) if ( !atoms[i].is_null() ) { U_aniso_orth u( atoms[i].u_aniso_orth() ); if ( u.is_null() ) u = U_aniso_orth( atoms[i].u_iso() ); AtomShapeFn sf( atoms[i].coord_orth(), atoms[i].element(), u + uadd, atoms[i].occupancy() ); uvw = atoms[i].coord_orth().coord_frac( cell ); g0 = uvw.coord_grid( grid ) + gd.min(); g1 = uvw.coord_grid( grid ) + gd.max(); i0 = Xmap::Map_reference_coord( xmap, g0 ); for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) xmap[iw] += sf.rho( iw.coord_orth() ); } for ( Xmap::Map_reference_index ix = xmap.first(); !ix.last(); ix.next() ) xmap[ix] *= xmap.multiplicity( ix.coord() ); xmap.fft_to( fphidata ); if ( uadd_ != 0.0 ) { ftype u = Util::twopi2()*uadd_; for ( HKL_info::HKL_reference_index ih = fphidata.first_data(); !ih.last(); fphidata.next_data( ih ) ) fphidata[ih].scale( exp( u * ih.invresolsq() ) ); } return true; } // compile templates template class SFcalc_iso_sum; template class SFcalc_aniso_sum; template class SFcalc_iso_fft; template class SFcalc_aniso_fft; template class SFcalc_iso_sum; template class SFcalc_aniso_sum; template class SFcalc_iso_fft; template class SFcalc_aniso_fft; } // namespace clipper clipper-2.1/clipper/contrib/edcalc.h0000644000374100011300000000717510736662165014435 00000000000000/*! \file edcalc.h Header file for sample Electron density calculation impelementation \ingroup g_edcalc */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_EDCALC #define CLIPPER_EDCALC #include "function_object_bases.h" namespace clipper { //! Atom mask calculation /*! \ingroup g_edcalc All points within the specified radius of an atom will be set to 1.0, all others will be set to 0.0. */ template class EDcalc_mask : public EDcalc_base { public: EDcalc_mask( const ftype radius = 2.5 ) : radius_(radius) {} bool operator() ( Xmap& xmap, const Atom_list& atoms ) const; bool operator() ( NXmap& nxmap, const Atom_list& atoms ) const; private: const ftype radius_; }; //! Isotropic electron density calculation /*! \ingroup g_edcalc */ template class EDcalc_iso : public EDcalc_base { public: EDcalc_iso( const ftype radius = 2.5 ) : radius_(radius) {} bool operator() ( Xmap& xmap, const Atom_list& atoms ) const; bool operator() ( NXmap& nxmap, const Atom_list& atoms ) const; private: const ftype radius_; }; //! Anisotropic electron density calculation /*! \ingroup g_edcalc */ template class EDcalc_aniso : public EDcalc_base { public: EDcalc_aniso( const ftype radius = 2.5 ) : radius_(radius) {} bool operator() ( Xmap& xmap, const Atom_list& atoms ) const; bool operator() ( NXmap& nxmap, const Atom_list& atoms ) const; private: const ftype radius_; }; } // namespace clipper #endif clipper-2.1/clipper/contrib/fffear.cpp0000644000374100011300000004663211021447637015000 00000000000000/* fffear.cpp: FFFear implementation */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "fffear.h" #include "../core/map_interp.h" namespace clipper { // deprecated forms bool FFFear_slow_basic::operator() ( Xmap& result, const NXmap& srchval, const NXmap& srchwgt ) const { const Xmap& xmap = *xmp; Xmap::Map_reference_index pos; Xmap::Map_reference_coord i0, iu, iv, iw; NXmap::Map_reference_index in( srchval ); Coord_grid g0, g1, off0, off1, nx; float s; off0 = Coord_grid( srchval.grid().nu()/2, srchval.grid().nv()/2, srchval.grid().nw()/2 ); off1 = Coord_grid( srchval.grid().nu() - off0.u() - 1, srchval.grid().nv() - off0.w() - 1, srchval.grid().nw() - off0.w() - 1 ); for ( pos = result.first(); !pos.last(); pos.next() ) { g0 = pos.coord() - off0; g1 = pos.coord() + off1; i0 = Xmap_base::Map_reference_coord( *xmp, g0 ); s = 0.0; for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) { in.set_coord( iw.coord() - g0 ); s += srchwgt[in] * pow( xmap[iw] - srchval[in], 2 ); } result[pos] = s; } return true; } void FFFear_fft_basic::init( const Xmap& xmap ) { vol = xmap.cell().volume(); rho1.init( xmap.grid_sampling() ); rho2.init( xmap.grid_sampling() ); const Grid_sampling& g = xmap.grid_sampling(); float r; Xmap::Map_reference_coord i0( xmap, Coord_grid(0,0,0) ); Xmap::Map_reference_coord iu, iv, iw; for ( iu = i0; iu.coord().u() < g.nu(); iu.next_u() ) for ( iv = iu; iv.coord().v() < g.nv(); iv.next_v() ) for ( iw = iv; iw.coord().w() < g.nw(); iw.next_w() ) { r = xmap[iw]; rho1.real_data( iw.coord() ) = r; rho2.real_data( iw.coord() ) = r*r; } rho1.fft_x_to_h( vol ); rho2.fft_x_to_h( vol ); } bool FFFear_fft_basic::operator() ( Xmap& result, const NXmap& srchval, const NXmap& srchwgt ) const { const Grid_sampling& g = rho1.grid_real(); FFTmap_p1 map1( g ); FFTmap_p1 map2( g ); // copy mask into grid, with offset Coord_grid c0, c1, c; c0 = Coord_grid( srchval.grid().nu()/2, srchval.grid().nv()/2, srchval.grid().nw()/2 ); ftype f, w; ftype swff = 0.0; const Grid& gx = srchval.grid(); for ( c.u() = 0; c.u() < gx.nu(); c.u()++ ) for ( c.v() = 0; c.v() < gx.nv(); c.v()++ ) for ( c.w() = 0; c.w() < gx.nw(); c.w()++ ) { c1 = (c - c0).unit(g); f = srchval.get_data(c); w = srchwgt.get_data(c); map1.real_data( c1 ) = w; map2.real_data( c1 ) = w*f; swff += w*f*f; } // fft map1.fft_x_to_h( vol ); map2.fft_x_to_h( vol ); // calculate const Grid& gh = map1.grid_reci(); const ftype32 two = 2.0; std::complex ww, wf, r1, r2; for ( c.u() = 0; c.u() < gh.nu(); c.u()++ ) for ( c.v() = 0; c.v() < gh.nv(); c.v()++ ) for ( c.w() = 0; c.w() < gh.nw(); c.w()++ ) { r1 = rho1.cplx_data( c ); r2 = rho2.cplx_data( c ); ww = map1.cplx_data( c ); wf = map2.cplx_data( c ); map1.cplx_data( c ) = std::conj(ww)*r2 - two*std::conj(wf)*r1; } // invert map1.fft_h_to_x( 1.0 / vol ); // store ftype s = map1.grid_real().size() / vol; for ( Xmap::Map_reference_index ix = result.first(); !ix.last(); ix.next() ) result[ix] = swff + s * map1.real_data( ix.coord() ); return true; } // general forms // slow fffear template bool FFFear_slow::operator() ( Xmap& result, const NXmap& srchval, const NXmap& srchwgt ) const { NX_operator nxop( result, srchval, RTop_orth::identity() ); return (*this)( result, srchval, srchwgt, nxop ); } template bool FFFear_slow::operator() ( Xmap& result, const NXmap& srchval, const NXmap& srchwgt, const NX_operator& nxop ) const { const Grid_sampling& g = result.grid_sampling(); // calculate extent of mask function in Xmap space Coord_frac cf; Range urange, vrange, wrange; typename NXmap::Map_reference_index inx; for ( inx = srchwgt.first(); !inx.last(); inx.next() ) if ( srchwgt[inx] > 0.0 ) { cf = nxop.coord_frac( inx.coord().coord_map() ); urange.include( cf.u() ); vrange.include( cf.v() ); wrange.include( cf.w() ); } cf = Coord_frac( urange.min(), vrange.min(), wrange.min() ); Coord_grid g0 = cf.coord_map( g ).coord_grid() - Coord_grid(1,1,1); cf = Coord_frac( urange.max(), vrange.max(), wrange.max() ); Coord_grid g1 = cf.coord_map( g ).coord_grid() + Coord_grid(1,1,1); Grid_range gm( g0, g1 ); // copy provided NXmap in new NXmap shadowing the xtal grid NXmap target( result.cell(), g, gm ); NXmap weight( result.cell(), g, gm ); target = weight = 0.0; typename NXmap::Map_reference_index in; Coord_map cm; for ( in = target.first(); !in.last(); in.next() ) { cm = nxop.coord_map( in.coord_orth().coord_frac( result.cell() ) ); if ( Interp_linear::can_interp( srchval, cm ) && Interp_linear::can_interp( srchwgt, cm ) ) { Interp_linear::interp( srchval, cm, target[in] ); Interp_linear::interp( srchwgt, cm, weight[in] ); } } // now calculate the search function const Xmap& xmap = *xmp; typename Xmap::Map_reference_index pos; typename Xmap::Map_reference_coord i0, iu, iv, iw; T s; for ( pos = result.first(); !pos.last(); pos.next() ) { g0 = pos.coord() + gm.min(); g1 = pos.coord() + gm.max(); i0 = Xmap_base::Map_reference_coord( xmap, g0 ); s = 0.0; for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) { in.set_coord( iw.coord() - g0 ); s += weight[in] * pow( xmap[iw] - target[in], 2 ); } result[pos] = s; } return true; } // fast fffear template void FFFear_fft::init( const Xmap& xmap ) { cell = xmap.cell(); rho1.init( xmap.grid_sampling() ); rho2.init( xmap.grid_sampling() ); const Grid_sampling& g = xmap.grid_sampling(); T r; typename Xmap::Map_reference_coord i0( xmap, Coord_grid(0,0,0) ); typename Xmap::Map_reference_coord iu, iv, iw; for ( iu = i0; iu.coord().u() < g.nu(); iu.next_u() ) for ( iv = iu; iv.coord().v() < g.nv(); iv.next_v() ) for ( iw = iv; iw.coord().w() < g.nw(); iw.next_w() ) { r = xmap[iw]; rho1.real_data( iw.coord() ) = r; rho2.real_data( iw.coord() ) = r*r; } rho1.fft_x_to_h( cell.volume() ); rho2.fft_x_to_h( cell.volume() ); ffttype = Default; } template void FFFear_fft::set_fft_type( FFTtype type ) { ffttype = type; } template void FFFear_fft::set_resolution( Resolution reso ) { const Grid_sampling& g = rho1.grid_real(); const Grid& gr = rho1.grid_reci(); const ftype slim = reso.invresolsq_limit(); std::complex zero( 0.0, 0.0 ); Coord_grid ch( g.nu()/2, g.nv()/2, g.nw()/2 ); Coord_grid c; HKL hkl; for ( c.u() = 0; c.u() < gr.nu(); c.u()++ ) for ( c.v() = 0; c.v() < gr.nv(); c.v()++ ) for ( c.w() = 0; c.w() < gr.nw(); c.w()++ ) { hkl = HKL( ( c + ch ).unit( g ) - ch ); if ( hkl.invresolsq( cell ) > slim ) { rho1.cplx_data(c) = zero; rho2.cplx_data(c) = zero; } } } template bool FFFear_fft::operator() ( Xmap& result, const NXmap& srchval, const NXmap& srchwgt ) const { NX_operator nxop( result, srchval, RTop_orth::identity() ); return (*this)( result, srchval, srchwgt, nxop ); } template bool FFFear_fft::operator() ( Xmap& result, const NXmap& srchval, const NXmap& srchwgt, const RTop_orth& rtop ) const { NX_operator nxop( result, srchval, rtop ); return (*this)( result, srchval, srchwgt, nxop ); } template bool FFFear_fft::operator() ( Xmap& result, const NXmap& srchval, const NXmap& srchwgt, const NX_operator& nxop ) const { if ( cell.is_null() ) Message::message( Message_fatal( "FFFear_fft uninitialised" ) ); const double vol = cell.volume(); // calculate extent of mask function in Xmap space const Grid_sampling& g = rho1.grid_real(); Coord_frac cf; Range urange, vrange, wrange; typename NXmap::Map_reference_index inx; for ( inx = srchwgt.first(); !inx.last(); inx.next() ) if ( srchwgt[inx] > 0.0 ) { cf = nxop.coord_frac( inx.coord().coord_map() ); urange.include( cf.u() ); vrange.include( cf.v() ); wrange.include( cf.w() ); } cf = Coord_frac( urange.min(), vrange.min(), wrange.min() ); Coord_grid g0 = cf.coord_map( g ).coord_grid() - Coord_grid(1,1,1); cf = Coord_frac( urange.max(), vrange.max(), wrange.max() ); Coord_grid g1 = cf.coord_map( g ).coord_grid() + Coord_grid(1,1,1); if ( ffttype == Normal || ffttype == Default ) { // NORMAL MAP CALCULATION FFTmap_p1 map1( g ), map2( g ); // copy mask into grid, with offset Coord_grid c, cu; Coord_map cm; T f, w; ftype64 swff = 0.0; for ( c.u() = g0.u(); c.u() <= g1.u(); c.u()++ ) for ( c.v() = g0.v(); c.v() <= g1.v(); c.v()++ ) for ( c.w() = g0.w(); c.w() <= g1.w(); c.w()++ ) { cm = nxop.coord_map( c.coord_frac( g ) ); if ( Interp_linear::can_interp( srchval, cm ) && Interp_linear::can_interp( srchwgt, cm ) ) { Interp_linear::interp( srchval, cm, f ); Interp_linear::interp( srchwgt, cm, w ); cu = c.unit(g); map1.real_data( cu ) = w; map2.real_data( cu ) = w*f; swff += w*f*f; } } // fft map1.fft_x_to_h( vol ); map2.fft_x_to_h( vol ); // calculate const Grid& gh = map1.grid_reci(); const ftype32 two = 2.0; std::complex ww, wf, r1, r2; for ( c.u() = 0; c.u() < gh.nu(); c.u()++ ) for ( c.v() = 0; c.v() < gh.nv(); c.v()++ ) for ( c.w() = 0; c.w() < gh.nw(); c.w()++ ) { r1 = rho1.cplx_data( c ); r2 = rho2.cplx_data( c ); ww = map1.cplx_data( c ); wf = map2.cplx_data( c ); map1.cplx_data( c ) = std::conj(ww)*r2 - two*std::conj(wf)*r1; } // invert map1.fft_h_to_x( map1.grid_real().size() / pow( vol, 2 ) ); // store for ( typename Xmap::Map_reference_index ix = result.first(); !ix.last(); ix.next() ) result[ix] = swff + map1.real_data( ix.coord() ); } else { // if ffttype // SPARSE MAP CALCULATION FFTmap_sparse_p1_xh smap1( g ), smap2( g ); FFTmap_p1 map1( g ); // copy mask into grid, with offset Coord_grid c, cu; Coord_map cm; T f, w; ftype64 swff = 0.0; for ( c.u() = g0.u(); c.u() <= g1.u(); c.u()++ ) for ( c.v() = g0.v(); c.v() <= g1.v(); c.v()++ ) for ( c.w() = g0.w(); c.w() <= g1.w(); c.w()++ ) { cm = nxop.coord_map( c.coord_frac( g ) ); if ( Interp_linear::can_interp( srchval, cm ) && Interp_linear::can_interp( srchwgt, cm ) ) { Interp_linear::interp( srchval, cm, f ); Interp_linear::interp( srchwgt, cm, w ); if ( w > 0.0 ) { cu = c.unit(g); smap1.real_data( cu ) = w; smap2.real_data( cu ) = w*f; swff += w*f*f; } } } // require hkls const Grid& gh = map1.grid_reci(); Coord_grid ch( g.nu()/2, g.nv()/2, g.nw()/2 ); HKL hkl; for ( c.u() = 0; c.u() < gh.nu(); c.u()++ ) for ( c.v() = 0; c.v() < gh.nv(); c.v()++ ) for ( c.w() = 0; c.w() < gh.nw(); c.w()++ ) { const std::complex& r1 = rho1.cplx_data(c); const std::complex& r2 = rho2.cplx_data(c); if ( r1.real() != 0.0 || r1.imag() != 0.0 || r2.real() != 0.0 || r2.imag() != 0.0 ) { hkl = HKL( ( c + ch ).unit( g ) - ch ); smap1.require_hkl( hkl ); smap2.require_hkl( hkl ); } } // fft smap1.fft_x_to_h( vol ); smap2.fft_x_to_h( vol ); // calculate const ftype32 two( 2.0 ); std::complex ww, wf; for ( c.u() = 0; c.u() < gh.nu(); c.u()++ ) for ( c.v() = 0; c.v() < gh.nv(); c.v()++ ) for ( c.w() = 0; c.w() < gh.nw(); c.w()++ ) { const std::complex& r1 = rho1.cplx_data(c); const std::complex& r2 = rho2.cplx_data(c); if ( r1.real() != 0.0 || r1.imag() != 0.0 || r2.real() != 0.0 || r2.imag() != 0.0 ) { ww = smap1.cplx_data( c ); wf = smap2.cplx_data( c ); map1.cplx_data( c ) = std::conj(ww)*r2 - two*std::conj(wf)*r1; } else { map1.cplx_data( c ) = std::complex(0.0,0.0); } } // invert map1.fft_h_to_x( map1.grid_real().size() / pow( vol, 2 ) ); // store for ( typename Xmap::Map_reference_index ix = result.first(); !ix.last(); ix.next() ) result[ix] = swff + map1.real_data( ix.coord() ); } // if ffttype return true; } // compile templates template class FFFear_slow; template class FFFear_slow; template class FFFear_fft; template class FFFear_fft; } // namespace clipper /* template void FFFear_fft::init( const Xmap& xmap, const NXmap& srchval, const NXmap& srchwgt ) { // initialise map init( xmap ); // initialise search function int n = 64; int n2 = n / 2; const Grid_sampling gfft(n,n,n); const Grid_sampling grcp(n+1,n+1,n+1); Coord_orth c0 = srchval.coord_orth( Coord_map(0.0,0.0,0.0) ); Coord_orth c1 = srchval.coord_orth( Coord_map(1.0,0.0,0.0) ); Coord_orth c2 = srchval.coord_orth( Coord_map(0.0,1.0,0.0) ); Coord_orth c3 = srchval.coord_orth( Coord_map(0.0,0.0,1.0) ); ftype d1 = c1.x() - c0.x(); ftype d2 = c2.y() - c0.y(); ftype d3 = c3.z() - c0.z(); ftype dr = ( fabs(c1.y()-c0.y())+fabs(c2.z()-c0.z())+fabs(c3.x()-c0.x()) + fabs(c1.z()-c0.z())+fabs(c2.x()-c0.x())+fabs(c3.y()-c0.y()) ); if ( d2 - d1 > 1.0e-6 || d3 - d1 > 1.0e-6 || dr > 1.0e-6 ) clipper::Message::message( clipper::Message_fatal( "FFFear_fft: NXmap noncubic" ) ); ftype d = ( d1 + d2 + d3 ) / 3.0; slim = 0.5 / d; sumwff = 0.0; ftype cx = ftype( n2 ); ftype sx = cx / slim; double volfft = gfft.size() * d * d * d; RTop<> rtnull = RTop<>::identity(); recip1.init( grcp, rtnull ); recip2.init( grcp, rtnull ); FFTmap_p1 wrk1( gfft ), wrk2( gfft ); int ni = srchval.grid().nu(); int ni2 = (ni-1)/2; for ( int u = 0; u < ni; u++ ) for ( int v = 0; v < ni; v++ ) for ( int w = 0; w < ni; w++ ) { Coord_grid ci( u, v, w ); Coord_grid cf( u-ni2, v-ni2, w-ni2 ); cf = cf.unit( gfft ); double f = srchval.get_data( ci ); double w = srchwgt.get_data( ci ); wrk1.real_data( cf ) = w; wrk2.real_data( cf ) = w*f; } wrk1.fft_x_to_h( volfft ); wrk2.fft_x_to_h( volfft ); for ( int h = -n2; h <= n2; h++ ) for ( int k = -n2; k <= n2; k++ ) for ( int l = -n2; l <= n2; l++ ) { HKL hkl( h, k, l ); Coord_grid cg( h+n2, k+n2, l+n2 ); recip1.set_data( cg, wrk1.get_hkl( hkl ) ); recip2.set_data( cg, wrk2.get_hkl( hkl ) ); } } template bool FFFear_fft::operator() ( Xmap& result, const RTop_orth& rtop ) const { if ( cell.is_null() ) Message::message( Message_fatal( "FFFear_fft uninitialised" ) ); const double vol = cell.volume(); const Grid_sampling& g = rho1.grid_real(); FFTmap_p1 map1( g ); // calculate int n = recip1.grid().nu()-1; int n2 = n / 2; ftype cx = ftype( n2 ); ftype sx = cx / slim; int gu0, gv0, gw0, gu1, gv1, gw1; T wu0, wv0, ww0, wu1, wv1, ww1; const Grid& gh = map1.grid_reci(); const Grid& gx = map1.grid_real(); const ftype32 two = 2.0; std::complex ww, wf, r1, r2; Coord_reci_orth cro; Coord_grid c; Coord_map cm; HKL hkl; ftype slim2 = slim*slim; for ( c.u() = 0; c.u() < gh.nu(); c.u()++ ) for ( c.v() = 0; c.v() < gh.nv(); c.v()++ ) for ( c.w() = 0; c.w() < gh.nw(); c.w()++ ) { hkl.h() = Util::mod( c.u() + gx.nu()/2, gx.nu() ) - gx.nu()/2; hkl.k() = Util::mod( c.v() + gx.nv()/2, gx.nv() ) - gx.nv()/2; hkl.l() = Util::mod( c.w() + gx.nw()/2, gx.nw() ) - gx.nw()/2; cro = hkl.coord_reci_orth( cell ); if ( Vec3<>::dot( cro, cro ) < slim2 ) { cm = ( Coord_map( sx * ( rtop.rot() * cro ) ) + Coord_map( cx, cx, cx ) ); gu0 = Util::intf( cm.u() ); gv0 = Util::intf( cm.v() ); gw0 = Util::intf( cm.w() ); gu1 = gu0 + 1; gv1 = gv0 + 1; gw1 = gw0 + 1; wu1 = cm.u() - floor( cm.u() ); wv1 = cm.v() - floor( cm.v() ); ww1 = cm.w() - floor( cm.w() ); wu0 = 1.0 - wu1; wv0 = 1.0 - wv1; ww0 = 1.0 - ww1; ww = (wu0*(wv0*(ww0*recip1.get_data(Coord_grid(gu0,gv0,gw0))+ ww1*recip1.get_data(Coord_grid(gu0,gv0,gw1)))+ wv1*(ww0*recip1.get_data(Coord_grid(gu0,gv1,gw0))+ ww1*recip1.get_data(Coord_grid(gu0,gv1,gw1))))+ wu1*(wv0*(ww0*recip1.get_data(Coord_grid(gu1,gv0,gw0))+ ww1*recip1.get_data(Coord_grid(gu1,gv0,gw1)))+ wv1*(ww0*recip1.get_data(Coord_grid(gu1,gv1,gw0))+ ww1*recip1.get_data(Coord_grid(gu1,gv1,gw1))))); wf = (wu0*(wv0*(ww0*recip2.get_data(Coord_grid(gu0,gv0,gw0))+ ww1*recip2.get_data(Coord_grid(gu0,gv0,gw1)))+ wv1*(ww0*recip2.get_data(Coord_grid(gu0,gv1,gw0))+ ww1*recip2.get_data(Coord_grid(gu0,gv1,gw1))))+ wu1*(wv0*(ww0*recip2.get_data(Coord_grid(gu1,gv0,gw0))+ ww1*recip2.get_data(Coord_grid(gu1,gv0,gw1)))+ wv1*(ww0*recip2.get_data(Coord_grid(gu1,gv1,gw0))+ ww1*recip2.get_data(Coord_grid(gu1,gv1,gw1))))); r1 = rho1.cplx_data( c ); r2 = rho2.cplx_data( c ); map1.cplx_data( c ) = std::conj(ww)*r2 - two*std::conj(wf)*r1; } } // invert map1.fft_h_to_x( map1.grid_real().size() / pow( vol, 2 ) ); // store for ( typename Xmap::Map_reference_index ix = result.first(); !ix.last(); ix.next() ) result[ix] = sumwff + map1.real_data( ix.coord() ); return true; } */ clipper-2.1/clipper/contrib/skeleton.cpp0000644000374100011300000003175510736662166015403 00000000000000/* skeleton.cpp: Skeletonisation implementation */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "skeleton.h" #include "../core/map_utils.h" namespace clipper { // Skeleton_basic Skeleton_basic::Neighbours::Neighbours( const clipper::Xmap_base &map, const float min_distsq, const float max_distsq ) { /* note that thisd2 is a mesure of distance in real space So here we look around an arbitary current point and take note if the distance between the centre point and points one unit away from it (all directions) is less than a certain cuttoff distance. We are left with a list of ndn neighbouring cells that are sufficicently close to be considered neighbours. Typically, ndn will be 18-20 at then end of this block. Note that body diagonals have length sqrt(3) ~= 1.73, but we passed squared limits. */ clipper::Cell_descr rcd( map.cell().descr() ); clipper::Cell_descr vcd( 1.0,1.0,1.0, rcd.alpha(), rcd.beta(), rcd.gamma() ); clipper::Cell vcell( vcd ); clipper::Coord_grid g0(-1,-1,-1); clipper::Coord_grid g1( 1, 1, 1); clipper::Grid_sampling vgrid( 1, 1, 1 ); clipper::Coord_grid iu, iv, iw; float thisd2; for ( iu = g0; iu.u() <= g1.u(); iu.u()++ ) { for ( iv = iu; iv.v() <= g1.v(); iv.v()++ ) { for ( iw = iv; iw.w() <= g1.w(); iw.w()++ ) { thisd2 = iw.coord_frac( vgrid ).lengthsq( vcell ); if (thisd2 > min_distsq && thisd2 < max_distsq) nlist.push_back( iw ); } } } } Skeleton_basic::NCube::NCube( const int& n ) { m = clipper::Grid_range( clipper::Coord_grid( -n, -n, -n ), clipper::Coord_grid( n, n, n ) ); data.resize( m.size() ); } bool Skeleton_basic::operator() ( clipper::Xmap& xskl, const clipper::Xmap& xmap ) const { std::vector index; clipper::Xmap::Map_reference_index ix; /* now get the map in sorted order. We only sort those points which are to be considered, i.e. non-zero */ for ( ix = xmap.first(); !ix.last(); ix.next() ) if ( xskl[ix] > 0 ) index.push_back( ix.index() ); Map_index_sort::sort_increasing( xmap, index ); /* make neighbours The neighbours of a point are the other grid points which are 'near' it. The exact choice depends on the grid geometry. The cutoff is chosen to give 18-20 neighbours. For a cubic grid, these are a 3x3x3 cube without the vertices, for a hex grid they are a hexagonal cylinder. */ Skeleton_basic::Neighbours neigh( xmap ); /* make the skeleton map. This will contain: 0 for non-skeleton grids (inter ridge spaces) 1 for untested grids 1 for skeleton grids (ridges) (The untested and skeleton grids can have the same value, because the untested ones are still in the index). We loop through point in order, starting with the lowest and decide whether each one is part of the skeleton. */ for ( int i = 0; i < index.size(); i++ ) if ( !isInSkel( xskl, xskl.coord_of(index[i]), neigh, box_ ) ) xskl.set_data( index[ i ], 0 ); return true; } bool Skeleton_basic::isInSkel( const clipper::Xmap& xskl, const clipper::Coord_grid& c, const Skeleton_basic::Neighbours& neigh, const int& box ) { Skeleton_basic::NCube cube( box ); // 1 or 2? Look at the results to decide. /* Fill the cube with flags Each non-rejected grid point is given its own number. We will the reduce these to 'region numbers', so that each connected region takes the value of one of its neighbours. (A performace benefit is gaine from allocating these in decreasing order). */ clipper::Coord_grid g0 = c + cube.grid().min(); clipper::Coord_grid g1 = c + cube.grid().max(); clipper::Xmap_base::Map_reference_coord i0, iu, iv, iw; i0 = clipper::Xmap::Map_reference_coord( xskl, g0 ); int i = cube.grid().size(); for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) cube[ iw.coord() - c ] = ( xskl[iw] > 0 ) ? i-- : 0; // the centre cannot be a link - set to zero cube[ clipper::Coord_grid(0,0,0) ] = 0; /* The following is a simple optimisation which could be omitted. We count the number of neightbours or the centre point which are not yet eliminated from the skeleton. If this is more than 14 or less than 1, then this pint cannot be part of the skeleton. */ int nneigh = 0; for ( i = 0; i < neigh.size(); i++ ) if ( cube[neigh[i]] > 0 ) nneigh++; if ( nneigh > 14 ) return false; if ( nneigh < 1 ) return false; /* Now reduce the flags to connected regions. We consider each point in turn, and replace it with the highest value of any of its neighbours. This is repeated until no points change. When this occurs, each connected region will be set to the largest value of any of its initial members. */ int val, nchg; do { nchg = 0; clipper::Coord_grid u, v, w, x; for ( u = cube.grid().min(); u.u() <= cube.grid().max().u(); u.u()++ ) for ( v = u; v.v() <= cube.grid().max().v(); v.v()++ ) for ( w = v; w.w() <= cube.grid().max().w(); w.w()++ ) { val = cube[w]; if ( val != 0 ) { for ( i = 0; i < neigh.size(); i++ ) { x = w + neigh[i]; if ( cube.grid().in_grid( x ) ) if ( cube[x] > val ) val = cube[x]; } if ( val > cube[w] ) { cube[w] = val; nchg++; } } } } while ( nchg > 0 ); /* The following code uses an STL set to count the number of different, non-zero numbers in the region bordering the centre of the cube */ std::set uniqnbrs; for ( i = 0; i < neigh.size(); i++ ) { const int& val = cube[neigh[i]]; if ( val > 0 ) uniqnbrs.insert( val ); } return (uniqnbrs.size() > 1); } // Skeleton_fast template Skeleton_fast::Neighbours::Neighbours( const clipper::Xmap_base &map, const float min_distsq, const float max_distsq ) { /* note that thisd2 is a mesure of distance in real space So here we look around an arbitary current point and take note if the distance between the centre point and points one unit away from it (all directions) is less than a certain cuttoff distance. We are left with a list of ndn neighbouring cells that are sufficicently close to be considered neighbours. Typically, ndn will be 18-20 at then end of this block. Note that body diagonals have length sqrt(3) ~= 1.73, but we passed squared limits. */ clipper::Cell_descr rcd( map.cell().descr() ); clipper::Cell_descr vcd( 1.0,1.0,1.0, rcd.alpha(), rcd.beta(), rcd.gamma() ); clipper::Cell vcell( vcd ); clipper::Coord_grid g0(-1,-1,-1); clipper::Coord_grid g1( 1, 1, 1); clipper::Grid_sampling vgrid( 1, 1, 1 ); clipper::Coord_grid iu, iv, iw; float thisd2; for ( iu = g0; iu.u() <= g1.u(); iu.u()++ ) { for ( iv = iu; iv.v() <= g1.v(); iv.v()++ ) { for ( iw = iv; iw.w() <= g1.w(); iw.w()++ ) { thisd2 = iw.coord_frac( vgrid ).lengthsq( vcell ); if (thisd2 > min_distsq && thisd2 < max_distsq) nlist.push_back( iw ); } } } } template bool Skeleton_fast::operator() ( clipper::Xmap& xskl, const clipper::Xmap& xmap ) const { std::vector index; Xmap_base::Map_reference_index ix; /* now get the map in sorted order. We only sort those points which are to be considered, i.e. non-zero */ for ( ix = xmap.first(); !ix.last(); ix.next() ) if ( xskl[ix] > 0 ) index.push_back( ix.index() ); Map_index_sort::sort_increasing( xmap, index ); /* make neighbours The neighbours of a point are the other grid points which are 'near' it. The exact choice depends on the grid geometry. The cutoff is chosen to give 18-20 neighbours. For a cubic grid, these are a 3x3x3 cube without the vertices, for a hex grid they are a hexagonal cylinder. */ neigh = Neighbours( xmap ); /* make the skeleton map. This will contain: 0 for non-skeleton grids (inter ridge spaces) 1 for untested grids 1 for skeleton grids (ridges) (The untested and skeleton grids can have the same value, because the untested ones are still in the index). We loop through point in order, starting with the lowest and decide whether each one is part of the skeleton. */ for ( int i = 0; i < index.size(); i++ ) if ( !isInSkel( xskl, xskl.coord_of(index[i]) ) ) xskl.set_data( index[ i ], 0 ); return true; } template bool Skeleton_fast::isInSkel( const clipper::Xmap& xskl, const clipper::Coord_grid& c ) const { int dx, dy, dz; /* Fill the cube with flags Each non-rejected grid point is given its own number. We will the reduce these to 'region numbers', so that each connected region takes the value of one of its neighbours. (A performace benefit is gaine from allocating these in decreasing order). */ clipper::Xmap_base::Map_reference_index ix( xskl, c ); for ( dz = 0; dz < 3; dz++ ) for ( dy = 0; dy < 3; dy++ ) for ( dx = 0; dx < 3; dx++ ) cube[dx][dy][dz] = xskl.get_data( ix.index_offset( dx-1, dy-1, dz-1 ) ); // the centre cannot be a link - set to zero cube[1][1][1] = 0; /* The following is a simple optimisation which could be omitted. We count the number of neightbours or the centre point which are not yet eliminated from the skeleton. If this is more than 14 or less than 1, then this pint cannot be part of the skeleton. */ int nneigh = 0; for ( int i = 0; i < neigh.size(); i++ ) { dx = neigh[i].u()+1; dy = neigh[i].v()+1; dz = neigh[i].w()+1; if ( cube[dx][dy][dz] > 0 ) nneigh++; } if ( nneigh > 14 ) return false; if ( nneigh < 1 ) return false; /* Now alter flags for one connected region. If all flags are altered, then this point is not part of the skeleton. */ for ( int i = 0; i < neigh.size(); i++ ) { dx = neigh[i].u()+1; dy = neigh[i].v()+1; dz = neigh[i].w()+1; if ( cube[dx][dy][dz] > 0 ) break; } flood_cube( dx, dy, dz ); for ( int i = 0; i < neigh.size(); i++ ) { dx = neigh[i].u()+1; dy = neigh[i].v()+1; dz = neigh[i].w()+1; if ( cube[dx][dy][dz] > 0 ) return true; } return false; } template void Skeleton_fast::flood_cube( const int x, const int y, const int z ) const { cube[x][y][z] = -1; for ( int i = 0; i < neigh.size(); i++ ) { int dx = x + neigh[i].u(); if ( dx >= 0 && dx < 3 ) { int dy = y + neigh[i].v(); if ( dy >= 0 && dy < 3 ) { int dz = z + neigh[i].w(); if ( dz >= 0 && dz < 3 ) if ( cube[dx][dy][dz] > 0 ) flood_cube( dx, dy, dz ); } } } } // template instantiations template class Skeleton_fast; template class Skeleton_fast; template class Skeleton_fast; template class Skeleton_fast; template class Skeleton_fast; template class Skeleton_fast; } // namespace clipper clipper-2.1/clipper/contrib/sfweight.h0000644000374100011300000001503611005574251015021 00000000000000/*! \file sfweight.h Header file for structure factor weighting object */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_SFWEIGHT #define CLIPPER_SFWEIGHT #include "function_object_bases.h" #include "../core/resol_basisfn.h" namespace clipper { //! Structure factor weighting by sigmaa-related spline method. /*! Perform structure factor weighting to obtain likelihood weights for structure factors. This implementation uses a single list of reflections for both scaling and sigmaa, thus the only relevent usage flags are NONE/BOTH. The number of spline parameters or the number of reflections per parameter may be specified. If either is zero, the other takes priority. If both are non-zero, a compromise value is used. \ingroup g_funcobj */ template class SFweight_spline : public SFweight_base { public: //! constructor SFweight_spline( const int n_reflns = 1000, const int n_params = 20, const int n_phases = 24 ) { init( n_reflns, n_params, n_phases ); } //! constructor: shorthand for constructor+operator SFweight_spline( HKL_data >& fb, HKL_data >& fd, HKL_data >& phiw, const HKL_data >& fo, const HKL_data >& fc, const HKL_data& usage, const int n_reflns = 1000, const int n_params = 20 ); //! initialise: from parameters void init( const int n_reflns = 1000, const int n_params = 20, const int n_phases = 24 ); bool operator() ( HKL_data >& fb, HKL_data >& fd, HKL_data >& phiw, const HKL_data >& fo0, const HKL_data >& fc0, const HKL_data& usage ); bool operator() ( HKL_data >& fb, HKL_data >& fd, HKL_data >& phiw, HKL_data >& hl, const HKL_data >& fo0, const HKL_data >& hl0, const HKL_data >& fc0, const HKL_data& usage ); template bool evaluate( HKL_data >& fb, HKL_data >& fd, HKL_data >& phiw, HKL_data >& hl, const HKL_data >& fo0, const HKL_data >& hl0, const HKL_data >& fc0, const HKL_data& usage, F tgt ); template bool reevaluate( HKL_data >& fb, HKL_data >& fd, HKL_data >& phiw, HKL_data >& hl, const HKL_data >& fo0, const HKL_data >& hl0, const HKL_data >& fc0, const HKL_data& usage, F tgt ); const std::vector& params_scale() { return param_s; } const std::vector& params_error() { return param_w; } const double& log_likelihood_work() { return llw; } const double& log_likelihood_free() { return llf; } void debug() const; struct TargetResult { ftype r, ds, dw, dss, dww, dsw; }; TargetResult targetfn( const HKL_class cls, const datatypes::F_sigF& fo0, const datatypes::F_phi& fc0, const ftype& s, const ftype& w ) const; TargetResult targethl( const HKL_class cls, const datatypes::F_sigF& fo0, const datatypes::ABCD& hl0, const datatypes::F_phi& fc0, const ftype& s, const ftype& w ) const; private: struct HLterms { ftype cosa, sina, cos2a, sin2a; }; class TargetFo { public: TargetResult operator() ( const HKL_class cls, const datatypes::F_sigF& fo0, const datatypes::ABCD& hl0, const datatypes::F_phi& fc0, const ftype& s, const ftype& w, const std::vector& hlterms ); datatypes::ABCD abcd; datatypes::Phi_fom phiw; }; class TargetHL { public: TargetResult operator() ( const HKL_class cls, const datatypes::F_sigF& fo0, const datatypes::ABCD& hl0, const datatypes::F_phi& fc0, const ftype& s, const ftype& w, const std::vector& hlterms ); datatypes::ABCD abcd; datatypes::Phi_fom phiw; }; int num_params( const HKL_data& flag ) const; int nparams, nreflns; std::vector param_s, param_w; std::vector scale_fo, scale_fc, value_s, value_w; std::vector hlterms; double llw, llf; }; } // namespace clipper #endif clipper-2.1/clipper/contrib/sfcalc_obs.cpp0000644000374100011300000001336311070157657015644 00000000000000/* sfweight.cpp: structure factor calculation vs observed implementation */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "sfcalc_obs.h" #include "edcalc.h" #include "../core/hkl_compute.h" #include "../core/resol_targetfn.h" namespace clipper { template bool SFcalc_obs_bulk::operator() ( HKL_data >& fphi, const HKL_data >& fsig, const Atom_list& atoms ) { // set U value constants double u_atom = Util::b2u( 20.0 ); double u_mask = Util::b2u( 50.0 ); // increase the U values Atom_list atomu = atoms; U_aniso_orth uadd( u_atom ), u; for ( int i = 0; i < atomu.size(); i++ ) if ( !atomu[i].is_null() ) { u = atomu[i].u_aniso_orth(); if ( u.is_null() ) u = U_aniso_orth( atomu[i].u_iso() ); atomu[i].set_u_aniso_orth( u + uadd ); } // now make the map for ed calcs const HKL_info& hkls = fsig.base_hkl_info(); const Spacegroup& spgr = hkls.spacegroup(); const Cell& cell = fsig.base_cell(); HKL_data > fphi_atom( hkls, cell ), fphi_mask( hkls, cell ); const Grid_sampling grid( spgr, cell, hkls.resolution() ); Xmap xmap( spgr, cell, grid ); // do ed calc from atomu EDcalc_aniso edcalc; edcalc( xmap, atomu ); xmap.fft_to( fphi_atom ); fphi_atom.compute( fphi_atom, datatypes::Compute_scale_u_iso >( 1.0, u_atom ) ); // do density calc from mask EDcalc_mask emcalc; emcalc( xmap, atomu ); for ( Xmap::Map_reference_index ix = xmap.first(); !ix.last(); ix.next() ) xmap[ix] = 1.0 - xmap[ix]; xmap.fft_to( fphi_mask ); fphi_mask.compute( fphi_mask, datatypes::Compute_scale_u_iso >( 1.0, -u_mask ) ); // try some different scale factors std::vector params( nparams, 1.0 ); BasisFn_spline basisfn( hkls, nparams, 1.0 ); TargetFn_scaleF1F2,datatypes::F_sigF > targetfn( fphi, fsig ); T x1 = 0.35, dx = 0.35, x; ftype y[3] = { 0.0, 0.0, 0.0 }; for ( int i = 0; i < 8; i++ ) { // take 3 samples of function for ( int d = -1; d <= 1; d++ ) if ( y[d+1] == 0.0 ) { HKL_data::HKL_reference_index ih; x = x1 + T(d)*dx; for ( ih = fphi.first(); !ih.last(); ih.next() ) fphi[ih] = std::complex(fphi_atom[ih]) + x * std::complex(fphi_mask[ih]); ResolutionFn rfn( hkls, basisfn, targetfn, params ); double r = 0.0; for ( ih = fsig.first(); !ih.last(); ih.next() ) if ( !fsig[ih].missing() ) { double eps = ih.hkl_class().epsilon(); r += (2.0/eps) * fabs( sqrt(rfn.f(ih))*fphi[ih].f() - fsig[ih].f() ); // r += ( 2.0/eps ) * pow( rfn.f(ih) * pow(fphi[ih].f(),2)/eps - pow(fsig[ih].f(),2)/eps, 2 ); } y[d+1] = r; //std::cout << d << "\t" << x << "\t" << r << "\n"; } // find minimum of current 3 samples if ( y[0] < y[1] && y[0] < y[2] ) { y[1] = y[0]; x1 -= dx; } else if ( y[2] < y[1] && y[2] < y[0] ) { y[1] = y[2]; x1 += dx; } // reduce step and search again y[0] = y[2] = 0.0; dx /= 2.0; } // adopt final scale for ( HKL_data::HKL_reference_index ih = fphi.first(); !ih.last(); ih.next() ) fphi[ih] = std::complex(fphi_atom[ih]) + x1 * std::complex(fphi_mask[ih]); // store stats ftype64 w, s0 = 0.0, s1 = 0.0; for ( Xmap::Map_reference_index ix = xmap.first(); !ix.last(); ix.next() ) { w = 1.0/ftype64( xmap.multiplicity( ix.coord() ) ); s0 += w; s1 += w*xmap[ix]; } bulkfrc = s1/s0; bulkscl = x1; return true; } // compile templates template class SFcalc_obs_bulk; template class SFcalc_obs_bulk; } // namespace clipper clipper-2.1/clipper/contrib/Makefile.am0000644000374100011300000000206311372264321015061 00000000000000# Makefile.am, passed: clipper/contrib, extracted subdir: contrib # in dir /home/cowtan/clipper-autoconf/clipper-2.1/clipper/contrib ## -*- mode: Makefile; mode: font-lock -*- INCLUDES=${FFTW_CXXFLAGS} ${MMDB_CXXFLAGS} library_include_HEADERS = \ convolution_search.h \ edcalc.h \ fffear.h \ function_object_bases.h \ mapfilter.h \ originmatch.h \ sfcalc.h \ sfcalc_obs.h \ sfscale.h \ sfweight.h \ skeleton.h \ test_contrib.h lib_LTLIBRARIES = libclipper-contrib.la libclipper_contrib_la_SOURCES = \ convolution_search.cpp \ edcalc.cpp \ fffear.cpp \ function_object_bases.cpp \ mapfilter.cpp \ originmatch.cpp \ sfcalc.cpp \ sfcalc_obs.cpp \ sfscale.cpp \ sfweight.cpp \ skeleton.cpp \ test_contrib.cpp library_includedir = $(pkgincludedir)/contrib libclipper_contrib_la_LDFLAGS = -version-info @CLIPPER_LT_VERSION@ libclipper_contrib_la_LIBADD = \ $(top_builddir)/clipper/core/libclipper-core.la clipper-2.1/clipper/contrib/convolution_search.cpp0000644000374100011300000001666510736662166017466 00000000000000/* convolution_search.cpp: convolution search implementation */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "convolution_search.h" #include "../core/map_interp.h" namespace clipper { // general forms // slow Convolution_search template bool Convolution_search_slow::operator() ( Xmap& result, const NXmap& srchval ) const { NX_operator nxop( result, srchval, RTop_orth::identity() ); return (*this)( result, srchval, nxop ); } template bool Convolution_search_slow::operator() ( Xmap& result, const NXmap& srchval, const NX_operator& nxop ) const { const Grid_sampling& g = result.grid_sampling(); // calculate extent of mask function in Xmap space Coord_frac cf; Range urange, vrange, wrange; typename NXmap::Map_reference_index inx; for ( inx = srchval.first(); !inx.last(); inx.next() ) if ( srchval[inx] != 0.0 ) { cf = nxop.coord_frac( inx.coord().coord_map() ); urange.include( cf.u() ); vrange.include( cf.v() ); wrange.include( cf.w() ); } cf = Coord_frac( urange.min(), vrange.min(), wrange.min() ); Coord_grid g0 = cf.coord_map( g ).coord_grid() - Coord_grid(1,1,1); cf = Coord_frac( urange.max(), vrange.max(), wrange.max() ); Coord_grid g1 = cf.coord_map( g ).coord_grid() + Coord_grid(1,1,1); Grid_range gm( g0, g1 ); // copy provided NXmap in new NXmap shadowing the xtal grid NXmap target( result.cell(), g, gm ); target = 0.0; typename NXmap::Map_reference_index in; Coord_map cm; for ( in = target.first(); !in.last(); in.next() ) { cm = nxop.coord_map( in.coord_orth().coord_frac( result.cell() ) ); if ( Interp_linear::can_interp( srchval, cm ) ) { Interp_linear::interp( srchval, cm, target[in] ); } } // now calculate the search function const Xmap& xmap = *xmp; typename Xmap::Map_reference_index pos; typename Xmap::Map_reference_coord i0, iu, iv, iw; T s; for ( pos = result.first(); !pos.last(); pos.next() ) { g0 = pos.coord() + gm.min(); g1 = pos.coord() + gm.max(); i0 = Xmap_base::Map_reference_coord( xmap, g0 ); s = 0.0; for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) { in.set_coord( iw.coord() - g0 ); s += xmap[iw] * target[in]; } result[pos] = s; } return true; } // fast Convolution_search template void Convolution_search_fft::init( const Xmap& xmap ) { vol = xmap.cell().volume(); rho1.init( xmap.grid_sampling() ); const Grid_sampling& g = xmap.grid_sampling(); T r; typename Xmap::Map_reference_coord i0( xmap, Coord_grid(0,0,0) ); typename Xmap::Map_reference_coord iu, iv, iw; for ( iu = i0; iu.coord().u() < g.nu(); iu.next_u() ) for ( iv = iu; iv.coord().v() < g.nv(); iv.next_v() ) for ( iw = iv; iw.coord().w() < g.nw(); iw.next_w() ) { r = xmap[iw]; rho1.real_data( iw.coord() ) = r; } rho1.fft_x_to_h( vol ); } template bool Convolution_search_fft::operator() ( Xmap& result, const NXmap& srchval ) const { NX_operator nxop( result, srchval, RTop_orth::identity() ); return (*this)( result, srchval, nxop ); } template bool Convolution_search_fft::operator() ( Xmap& result, const NXmap& srchval, const NX_operator& nxop ) const { const Grid_sampling& g = rho1.grid_real(); FFTmap_p1 map1( g ); // calculate extent of mask function in Xmap space Coord_frac cf; Range urange, vrange, wrange; typename NXmap::Map_reference_index inx; for ( inx = srchval.first(); !inx.last(); inx.next() ) if ( srchval[inx] != 0.0 ) { cf = nxop.coord_frac( inx.coord().coord_map() ); urange.include( cf.u() ); vrange.include( cf.v() ); wrange.include( cf.w() ); } cf = Coord_frac( urange.min(), vrange.min(), wrange.min() ); Coord_grid g0 = cf.coord_map( g ).coord_grid() - Coord_grid(1,1,1); cf = Coord_frac( urange.max(), vrange.max(), wrange.max() ); Coord_grid g1 = cf.coord_map( g ).coord_grid() + Coord_grid(1,1,1); // copy mask into grid, with offset Coord_grid c, cu; Coord_map cm; T f; for ( c.u() = g0.u(); c.u() <= g1.u(); c.u()++ ) for ( c.v() = g0.v(); c.v() <= g1.v(); c.v()++ ) for ( c.w() = g0.w(); c.w() <= g1.w(); c.w()++ ) { cm = nxop.coord_map( c.coord_frac( g ) ); if ( Interp_linear::can_interp( srchval, cm ) ) { Interp_linear::interp( srchval, cm, f ); cu = c.unit(g); map1.real_data( cu ) = f; } } // fft map1.fft_x_to_h( vol ); // calculate const Grid& gh = map1.grid_reci(); std::complex r1, f1; for ( c.u() = 0; c.u() < gh.nu(); c.u()++ ) for ( c.v() = 0; c.v() < gh.nv(); c.v()++ ) for ( c.w() = 0; c.w() < gh.nw(); c.w()++ ) { r1 = rho1.cplx_data( c ); f1 = map1.cplx_data( c ); map1.cplx_data( c ) = std::conj(f1)*r1; } // invert map1.fft_h_to_x( map1.grid_real().size() / pow( vol, 2 ) ); // store for ( typename Xmap::Map_reference_index ix = result.first(); !ix.last(); ix.next() ) result[ix] = map1.real_data( ix.coord() ); return true; } // compile templates template class Convolution_search_slow; template class Convolution_search_slow; template class Convolution_search_fft; template class Convolution_search_fft; } // namespace clipper clipper-2.1/clipper/contrib/test_contrib.h0000644000374100011300000000473610736662166015722 00000000000000/*! \file lib/test_contrib.h Header file for clipper contrib self-test functions */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_TEST_CONTRIB #define CLIPPER_TEST_CONTRIB #include "../core/clipper_test.h" namespace clipper { class Test_contrib : public Test_base { public: //! do the self-tests bool operator() (); }; } // namespace clipper #endif clipper-2.1/clipper/contrib/fffear.h0000644000374100011300000001475011021232614014424 00000000000000/*! \file fffear.h Header file for sample fffear impelementation \ingroup g_fffear */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_FFFEAR #define CLIPPER_FFFEAR #include "function_object_bases.h" namespace clipper { //! Simple fffear implementation /*! \deprecated This is for testing purposes only, as it is very slow. The search target and weights are not handled generally in this implementation: The NXmaps are assumed to have a grid matching the map grid with the origin at the centre. */ class FFFear_slow_basic { public: //! constructor FFFear_slow_basic( const Xmap& xmap ) : xmp( &xmap ) {} //! constructor: shorthand for constructor+operator FFFear_slow_basic( Xmap& result, const NXmap& srchval, const NXmap& srchwgt, const Xmap& xmap ) : xmp( &xmap ) { (*this)( result, srchval, srchwgt ); } bool operator() ( Xmap& result, const NXmap& srchval, const NXmap& srchwgt ) const; private: const Xmap* xmp; }; //! FFT-based fffear implementation /*! \deprecated This implementation is currently unoptimised, but much faster then the simple implementation. The search target and weights are not handled generally in this implementation: The NXmaps are assumed to have a grid matching the map grid with the origin at the centre. */ class FFFear_fft_basic { public: //! constructor FFFear_fft_basic( const Xmap& xmap ) { init( xmap ); } //! constructor: shorthand for constructor+operator FFFear_fft_basic( Xmap& result, const NXmap& srchval, const NXmap& srchwgt, const Xmap& xmap ) { init( xmap ); (*this)( result, srchval, srchwgt ); } //! initialiser: initialise with the given target Xmap void init( const Xmap& xmap ); bool operator() ( Xmap& result, const NXmap& srchval, const NXmap& srchwgt ) const; private: ftype vol; FFTmap_p1 rho1; FFTmap_p1 rho2; }; //! FFT-based fffear implementation /*! \ingroup g_fffear This implementation is currently unoptimised, but much faster then the simple implementation. */ template class FFFear_slow : public FFFear_base { public: //! constructor FFFear_slow() {} //! constructor FFFear_slow( const Xmap& xmap ) { init( xmap ); } //! constructor: shorthand for constructor+operator FFFear_slow( Xmap& result, const NXmap& srchval, const NXmap& srchwgt, const Xmap& xmap, const NX_operator& nxop ) { init( xmap ); (*this)( result, srchval, srchwgt, nxop ); } //! initialiser: initialise with the given target Xmap void init( const Xmap& xmap ) { xmp = ⟼ } bool operator() ( Xmap& result, const NXmap& srchval, const NXmap& srchwgt, const NX_operator& nxop ) const; bool operator() ( Xmap& result, const NXmap& srchval, const NXmap& srchwgt ) const; //!< \deprecated private: const Xmap* xmp; }; //! FFT-based fffear implementation /*! \ingroup g_fffear This implementation is currently unoptimised, but much faster then the simple implementation. */ template class FFFear_fft : public FFFear_base { public: enum FFTtype { Default, Normal, Sparse }; //!< FFT backend selection //! constructor FFFear_fft() {} //! constructor FFFear_fft( const Xmap& xmap ) { init( xmap ); } //! constructor: shorthand for constructor+operator FFFear_fft( Xmap& result, const NXmap& srchval, const NXmap& srchwgt, const Xmap& xmap, const NX_operator& nxop ) { init( xmap ); (*this)( result, srchval, srchwgt, nxop ); } //! initialiser: initialise with the given target Xmap void init( const Xmap& xmap ); void set_fft_type( FFTtype type ); //! option: fft backend void set_resolution( Resolution reso ); //! option: resolution cutoff bool operator() ( Xmap& result, const NXmap& srchval, const NXmap& srchwgt, const NX_operator& nxop ) const; //!< search for given target bool operator() ( Xmap& result, const NXmap& srchval, const NXmap& srchwgt, const RTop_orth& rtop ) const; //!< search for given target bool operator() ( Xmap& result, const NXmap& srchval, const NXmap& srchwgt ) const; //!< \deprecated private: Cell cell; FFTmap_p1 rho1, rho2; FFTtype ffttype; }; } // namespace clipper #endif clipper-2.1/clipper/contrib/sfscale.h0000644000374100011300000001043511311732432014614 00000000000000/*! \file sfscale.h Header file for structure factor anisotropic scaling object */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_SFSCALE #define CLIPPER_SFSCALE #include "function_object_bases.h" #include "../core/resol_targetfn.h" namespace clipper { //! Structure factor anisotropic scaling /*! Perform structure factor anisotropic scaling, observed to calculated, calculated to observed, or observed against itself. \ingroup g_funcobj */ template class SFscale_aniso : public SFscale_base { public: enum TYPE { F, I }; //!< type for returning U_aniso_orth enum MODE { NORMAL, SHARPEN, UNSHARPEN }; //!< mode for scaling //! constructor: takes rejection criterion for F/sigF SFscale_aniso( ftype nsig = 0.0, MODE mode = NORMAL ) : nsig_(nsig), mode_(mode) {} //! Scale Fo to Fc bool operator() ( HKL_data >& fo, const HKL_data >& fc ); //! Scale Fc to Fo bool operator() ( HKL_data >& fc, const HKL_data >& fo ); //! Scale Fo to isotropic (approximate) bool operator() ( HKL_data >& fo ); //! Scale Fo to isotropic (approximate) bool operator() ( HKL_data >& fo, const ftype resfilter, const int npar_scl ); //! Scale Io to isotropic (approximate) bool operator() ( HKL_data >& Io, const ftype resfilter, const int npar_scl ); //! Primitive scaling functions for F and I template bool scale( HKL_data& fo, const ftype resfilter, const int npar_scl ); //! return aniso correction on F or I const U_aniso_orth& u_aniso_orth( TYPE t ) const; const U_aniso_orth& u_aniso_orth() const { return u_i; } //!< \deprecated private: const T& obs( const datatypes::F_sigF& f ) { return f.f(); } const T& obs( const datatypes::I_sigI& f ) { return f.I(); } const T& sigobs( const datatypes::F_sigF& f ) { return f.sigf(); } const T& sigobs( const datatypes::I_sigI& f ) { return f.sigI(); } U_aniso_orth u_i, u_f; ftype nsig_; MODE mode_; }; } // namespace clipper #endif clipper-2.1/clipper/contrib/sfcalc.h0000644000374100011300000001214110736737607014446 00000000000000/*! \file sfcalc.h Header file for sample structure factor calculation impelementation \ingroup g_sfcalc */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_SFCALC #define CLIPPER_SFCALC #include "function_object_bases.h" namespace clipper { //! Isotropic structure factor calculation by slow summation /*! \ingroup g_sfcalc */ template class SFcalc_iso_sum : public SFcalc_base { public: //! constructor SFcalc_iso_sum() {} //! constructor: shorthand for constructor+operator SFcalc_iso_sum( HKL_data >& fphidata, const Atom_list& atoms ) { (*this)( fphidata, atoms ); } bool operator() ( HKL_data >& fphidata, const Atom_list& atoms ) const; }; //! Anisotropic structure factor calculation by slow summation /*! \ingroup g_sfcalc */ template class SFcalc_aniso_sum : public SFcalc_base { public: //! constructor SFcalc_aniso_sum() {} //! constructor: shorthand for constructor+operator SFcalc_aniso_sum( HKL_data >& fphidata, const Atom_list& atoms ) { (*this)( fphidata, atoms ); } bool operator() ( HKL_data >& fphidata, const Atom_list& atoms ) const; }; //! Isotropic structure factor calculation by fast Fourier /*! \ingroup g_sfcalc */ template class SFcalc_iso_fft : public SFcalc_base { public: //! constructor /*! \param rate Shannon rate (oversampling) of the FFT grid. \param uadd Additional U for smoothing atoms. */ SFcalc_iso_fft( const ftype radius = 2.5, const ftype rate = 1.5, const ftype uadd = 0.0 ) : radius_(radius), rate_(rate), uadd_(uadd) {} //! constructor: shorthand for constructor+operator SFcalc_iso_fft( HKL_data >& fphidata, const Atom_list& atoms, const ftype radius = 2.5, const ftype rate = 1.5, const ftype uadd = 0.0 ) : radius_(radius), rate_(rate), uadd_(uadd) { (*this)( fphidata, atoms ); } bool operator() ( HKL_data >& fphidata, const Atom_list& atoms ) const; private: const ftype radius_, rate_, uadd_; }; //! Anisotropic structure factor calculation by fast Fourier /*! \ingroup g_sfcalc */ template class SFcalc_aniso_fft : public SFcalc_base { public: //! constructor /*! \param rate Shannon rate (oversampling) of the FFT grid. \param uadd Additional U for smoothing atoms. */ SFcalc_aniso_fft( const ftype radius = 2.5, const ftype rate = 1.5, const ftype uadd = 0.0 ) : radius_(radius), rate_(rate), uadd_(uadd) {} //! constructor: shorthand for constructor+operator SFcalc_aniso_fft( HKL_data >& fphidata, const Atom_list& atoms, const ftype radius = 2.5, const ftype rate = 1.5, const ftype uadd = 0.0 ) : radius_(radius), rate_(rate), uadd_(uadd) { (*this)( fphidata, atoms ); } bool operator() ( HKL_data >& fphidata, const Atom_list& atoms ) const; private: const ftype radius_, rate_, uadd_; }; } // namespace clipper #endif clipper-2.1/clipper/contrib/mapfilter.cpp0000644000374100011300000003041510736662166015532 00000000000000/* mapfilter.cpp: Electron density calculation implementation */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "mapfilter.h" namespace clipper { /*! The filter function is constructed with the given filter. Scaling may also be optionally applied. This may be absolute, which just applies a scale factor to the result, or relative, which scales the filter relative to its own integral. Therefore, relative scaling with a scale factor of 1.0 gives an output map on the same scale as the input map. Note that the filter is not stored internally, and so must persist as long as the MapFilter is required. \param fltr The radial filter to apply. \param scale The scale factor to apply (default = 1.0). \param type The type of scaling to apply: NONE, Absolute, Relative. */ template MapFilter_slow::MapFilter_slow( const MapFilterFn_base& fltr, const ftype scale, const TYPE type ) : fltr_( &fltr ), scale_( scale ), type_( type ) {} template MapFilter_slow::MapFilter_slow( clipper::Xmap& result, const clipper::Xmap& xmap, MapFilterFn_base& fltr, const ftype scale, const TYPE type ) : fltr_( &fltr ), scale_( scale ), type_( type ) { (*this)( result, xmap ); } /*! Apply the filter to a given map. \param result The filtered map. \param xmap The map to be filtered. */ template bool MapFilter_slow::operator() ( clipper::Xmap& result, const clipper::Xmap& xmap ) const { const MapFilterFn_base& fltr = *fltr_; const Grid_sampling& g = xmap.grid_sampling(); result.init( xmap.spacegroup(), xmap.cell(), g ); // first determine the effective radius of the radial function const int nrad = 1000; const ftype drad = 0.25; int i; ftype r, sum[nrad]; for ( i = 0; i < nrad; i++ ) { r = drad * ( ftype(i) + 0.5 ); sum[i] = r*r*fabs(fltr(r)); } for ( i = 1; i < nrad; i++ ) sum[i] += sum[i-1]; for ( i = 0; i < nrad; i++ ) if ( sum[i] > 0.99*sum[nrad-1] ) break; ftype rad = drad * ( ftype(i) + 1.0 ); // now prepare a map from the filter Grid_range gm( xmap.cell(), g, rad ); NXmap flt( xmap.cell(), g, gm ); // calculate the filter typename NXmap::Map_reference_index in; ftype64 f000 = 0.0; for ( in = flt.first(); !in.last(); in.next() ) { r = fltr( sqrt( in.coord_orth().lengthsq() ) ); f000 += r; flt[in] = r; } // calc scale factor ftype scale = 1.0; if ( type_ == Absolute ) scale = scale_; if ( type_ == Relative ) scale = scale_ / f000; // now calculate the search function Coord_grid g0, g1; typename Xmap::Map_reference_index pos; typename Xmap::Map_reference_coord i0, iu, iv, iw; ftype s; for ( pos = result.first(); !pos.last(); pos.next() ) { g0 = pos.coord() + gm.min(); g1 = pos.coord() + gm.max(); i0 = Xmap_base::Map_reference_coord( xmap, g0 ); s = 0.0; for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) { in.set_coord( iw.coord() - g0 ); s += flt[in] * xmap[iw]; } result[pos] = scale * s; } return true; } /*! The filter function is constructed with the given filter. Scaling may also be optionally applied. This may be absolute, which just applies a scale factor to the result, or relative, which scales the filter relative to its own integral. Therefore, relative scaling with a scale factor of 1.0 gives an output map on the same scale as the input map. Note that the filter is not stored internally, and so must persist as long as the MapFilter is required. \param fltr The radial filter to apply. \param scale The scale factor to apply (default = 1.0). \param type The type of scaling to apply: NONE, Absolute, Relative. */ template MapFilter_fft::MapFilter_fft( const MapFilterFn_base& fltr, const ftype scale, const TYPE type ) : fltr_( &fltr ), scale_( scale ), type_( type ) {} template MapFilter_fft::MapFilter_fft( clipper::Xmap& result, const clipper::Xmap& xmap, MapFilterFn_base& fltr, const ftype scale, const TYPE type ) : fltr_( &fltr ), scale_( scale ), type_( type ) { (*this)( result, xmap ); } /*! Apply the filter to a given map. \param result The filtered map. \param xmap The map to be filtered. */ template bool MapFilter_fft::operator() ( clipper::Xmap& result, const clipper::Xmap& xmap ) const { const MapFilterFn_base& fltr = *fltr_; const Grid_sampling& g = xmap.grid_sampling(); // first determine the effective radius of the radial function const int nrad = 1000; const ftype drad = 0.25; int i; ftype r, sum[nrad]; for ( i = 0; i < nrad; i++ ) { r = drad * ( ftype(i) + 0.5 ); sum[i] = r*r*fabs(fltr(r)); } for ( i = 1; i < nrad; i++ ) sum[i] += sum[i-1]; for ( i = 0; i < nrad; i++ ) if ( sum[i] > 0.99*sum[nrad-1] ) break; ftype rad = drad * ( ftype(i) + 1.0 ); // make the fft maps FFTmap_p1 map( g ); FFTmap_p1 flt( g ); // fill the fft maps Coord_grid c, half( g.nu()/2, g.nv()/2, g.nw()/2 ); typename Xmap::Map_reference_coord i0( xmap, Coord_grid(0,0,0) ); typename Xmap::Map_reference_coord iu, iv, iw; ftype64 f000 = 0.0; for ( iu = i0; iu.coord().u() < g.nu(); iu.next_u() ) for ( iv = iu; iv.coord().v() < g.nv(); iv.next_v() ) for ( iw = iv; iw.coord().w() < g.nw(); iw.next_w() ) { c = (iw.coord() + half).unit(g) - half; r = sqrt( c.coord_frac(g).lengthsq(xmap.cell()) ); map.real_data( iw.coord() ) = xmap[iw]; if ( r < rad ) { r = fltr(r); f000 += r; flt.real_data( iw.coord() ) = r; } } // calc scale factor ftype32 scale = 1.0; if ( type_ == Absolute ) scale = scale_; if ( type_ == Relative ) scale = scale_ / f000; // fft flt.fft_x_to_h( xmap.cell().volume() ); map.fft_x_to_h( xmap.cell().volume() ); // do filter const Grid& gh = map.grid_reci(); for ( c.u() = 0; c.u() < gh.nu(); c.u()++ ) for ( c.v() = 0; c.v() < gh.nv(); c.v()++ ) for ( c.w() = 0; c.w() < gh.nw(); c.w()++ ) map.cplx_data( c ) = scale * map.cplx_data(c) * flt.cplx_data(c); // invert map.fft_h_to_x( map.grid_real().size() / pow( xmap.cell().volume(), 2 ) ); // store result.init( xmap.spacegroup(), xmap.cell(), g ); for ( typename Xmap::Map_reference_index ix = result.first(); !ix.last(); ix.next() ) result[ix] = map.real_data( ix.coord() ); return true; } /*! Apply the filter to a given map. \param result The filtered map. \param nxmap The map to be filtered. */ template bool MapFilter_fft::operator() ( clipper::NXmap& result, const clipper::NXmap& nxmap ) const { const MapFilterFn_base& fltr = *fltr_; const Grid& gnx = nxmap.grid(); // Now make fft grid compatible with this NXmap grid Grid_sampling nuvw( gnx.nu()+2, gnx.nv()+2, gnx.nw()+2 ); for ( int i = 0; i < 3; i++ ) { // find most efficient sampling int j, l, m, n, nbest = 0; ftype t, tbest = 1.0e12; for ( n = nuvw[i]; n < 2*nuvw[i]; n++ ) { if ( n % 2 == 0 ) { l = 0; // sum of factors (approx. log n) m = n; // what is left in factorisation for ( j = 2; j <= n; j++ ) while ( m%j == 0 ) { m /= j; l += j; } // FFT time O( n * l ) - introduce an extra n^2 for 3D. t = pow( ftype(n), 3 ) * ftype(l); if ( t < tbest ) { nbest = n; tbest = t; } } } nuvw[i] = nbest; } const Grid_sampling& g = nuvw; // Get grid skew matrix nxmap.operator_grid_orth().rot(); Coord_orth::zero(); RTop<> rtop( nxmap.operator_grid_orth().rot(), Coord_orth::zero() ); // make the fft maps FFTmap_p1 map( g ); FFTmap_p1 flt( g ); // fill fft map from nx map Coord_grid l( (g.nu()-gnx.nu())/2,(g.nv()-gnx.nv())/2,(g.nw()-gnx.nw())/2 ); Coord_grid h( l + gnx - Coord_grid(1,1,1) ); typedef NXmap::Map_reference_index MRI; for ( MRI ix = nxmap.first(); !ix.last(); ix.next() ) map.real_data( ix.coord()+l ) = nxmap[ix]; // mirror the remaining points Coord_grid iw, im; for ( iw.u() = 0; iw.u() < g.nu(); iw.u()++ ) for ( iw.v() = 0; iw.v() < g.nv(); iw.v()++ ) for ( iw.w() = 0; iw.w() < g.nw(); iw.w()++ ) { im = iw; if ( im.u() < l.u() ) im.u() = l.u() + ( l.u() - im.u() ); if ( im.v() < l.v() ) im.v() = l.v() + ( l.v() - im.v() ); if ( im.w() < l.w() ) im.w() = l.w() + ( l.w() - im.w() ); if ( im.u() > h.u() ) im.u() = h.u() + ( h.u() - im.u() ); if ( im.v() > h.v() ) im.v() = h.v() + ( h.v() - im.v() ); if ( im.w() > h.w() ) im.w() = h.w() + ( h.w() - im.w() ); map.real_data( iw ) = map.real_data( im ); } // first determine the effective radius of the radial function const int nrad = 1000; const ftype drad = 0.25; int i; ftype r, sum[nrad]; for ( i = 0; i < nrad; i++ ) { r = drad * ( ftype(i) + 0.5 ); sum[i] = r*r*fabs(fltr(r)); } for ( i = 1; i < nrad; i++ ) sum[i] += sum[i-1]; for ( i = 0; i < nrad; i++ ) if ( sum[i] > 0.99*sum[nrad-1] ) break; ftype rad = drad * ( ftype(i) + 1.0 ); // fill the radial function map Coord_grid c, half( g.nu()/2, g.nv()/2, g.nw()/2 ); ftype64 f000 = 0.0; for ( iw.u() = 0; iw.u() < g.nu(); iw.u()++ ) for ( iw.v() = 0; iw.v() < g.nv(); iw.v()++ ) for ( iw.w() = 0; iw.w() < g.nw(); iw.w()++ ) { c = (iw + half).unit(g) - half; r = sqrt( Coord_orth(rtop*c.coord_map()).lengthsq() ); if ( r < rad ) { r = fltr(r); f000 += r; flt.real_data( iw ) = r; } } // calc scale factor ftype32 scale = 1.0; if ( type_ == Absolute ) scale = scale_; if ( type_ == Relative ) scale = scale_ / f000; // fft flt.fft_x_to_h( 1.0 ); map.fft_x_to_h( 1.0 ); // do filter const Grid& gh = map.grid_reci(); for ( c.u() = 0; c.u() < gh.nu(); c.u()++ ) for ( c.v() = 0; c.v() < gh.nv(); c.v()++ ) for ( c.w() = 0; c.w() < gh.nw(); c.w()++ ) map.cplx_data( c ) = scale * map.cplx_data(c) * flt.cplx_data(c); // invert map.fft_h_to_x( map.grid_real().size() ); // store result.init( gnx, nxmap.operator_orth_grid() ); for ( MRI ix = nxmap.first(); !ix.last(); ix.next() ) result[ix] = map.real_data( ix.coord()+l ); return true; } // compile templates template class MapFilter_slow; template class MapFilter_slow; template class MapFilter_fft; template class MapFilter_fft; } // namespace clipper clipper-2.1/clipper/contrib/test_contrib.cpp0000644000374100011300000004705711144270164016243 00000000000000/* test_contrib.cpp: implementation file for clipper contrib self-test */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "test_contrib.h" #include "mapfilter.h" #include "convolution_search.h" #include "fffear.h" #include "sfcalc.h" #include "sfcalc_obs.h" #include "sfweight.h" #include "sfscale.h" #include "../core/test_data.h" #include "../core/hkl_compute.h" namespace clipper { namespace data { float contrib_vals[] = {62085,0,-2.35103e-05,-537.853,2.04953e-05,271.468,313.756,-1.14655e-05,88.939,-1.97969e-06,-1.41777e-05,137.227,-1020.36,-230.467,258.784,19.4909,-21.0352,168.158,82.8908,82.9012,-3.63488e-05,-106.365,-4.12642,311.855,-182.047,291.716,-473.216,24.3527,58.3351,-90.6147,-72.7842,46.5314,123.021,-21.1225,-156.35,110.062,-277.139,-442.304,-142.18,89.8283,1.87174e-05,-73.6002,271.811,-64.1525,-270.657,-265.162,273.196,779.432,256.913,276.635,226.079,544.524,644.946,-244.673,8.01921e-06,-504.567,4.02743,-451.095,27.369,95.8539,-1049.43,0,332.786,-326.619,-120.613,-233.546,374.933,-125.7,-1.43747e-05,328.855,67.4085,-117.594,-579.966,-250.85,-286.214,421.978,-407.023,-3.5e-12,379.259,20.3695,-546.954,33.0029,638.675,-649.005,70.5812,-146.142,224.169,43.466,302.437,49.827,390.892,-184.531,215.482,-101.874,545.265,474.695,-3.76247e-05,364.171,-5.44969e-05,-1246.74,-2.18374e-05,-499.581,0.99955,5.34325e-06,70.7734,-3.57623e-06,-81.8145,0.965747,629.401,-2.29999e-05,196.403,-7.17707e-06,0.999995,56.9272,-1.26714e-06,-5.00108,5.96175e-07,0.47382,-1.68563e-05,163.153,-2.71878e-06,26.3152,0.803509,-636.356,-143.732,169.765,38.3443,0.981854,110.28,8.30599,-57.1612,-4.30521,0.880984,6.49867,-51.951,11.3566,-90.7857,0.504998,187.239,187.262,61.0691,61.0767,0.844098,-3.9956e-05,-116.921,-1.60269e-05,-46.8987,0.19955,-6.80942,514.623,-1.80122,136.128,0.937416,-158.815,254.487,-13.0074,20.8433,0.826057,-459.028,23.6226,-46.6823,2.40237,0.964024,64.2033,-99.7301,9.28487,-14.4226,0.621669,-25.9256,4.45139,-35.6622,6.12313,0.102692,34.3516,-24.1816,77.2152,-54.3552,0.601134,-203.365,-324.564,11.8764,18.9543,0.961987,-104.664,66.1263,3.25264,-2.055,0.706816,9.51035e-05,-373.964,3.97517e-05,-156.311,0.736061,186.115,-43.9266,-23.964,5.65595,0.917733,-149.75,-146.71,34.3991,33.7007,0.918732,216.55,617.822,-2.34832,-6.6998,0.983464,103.747,111.711,-47.8103,-51.4805,0.933024,138.133,332.702,-27.9613,-67.3465,0.978446,600.51,-227.816,37.9841,-14.4101,0.978923,5.68373e-06,-357.619,-7.21378e-07,16.5032,0.999258,3.50463,-392.538,0.0360139,-4.03376,0.967671,12.9659,45.4102,-3.82199,-13.3857,0.486054,-687.716,5e-12,71.8843,4.5e-12,1,231.469,-227.18,-9.31488,9.14227,0.965045,-76.4861,-148.101,8.49971,16.4581,0.864654,333.513,-111.814,11.3842,-3.81669,0.96192,-3.95762e-06,90.5398,6.19183e-06,-82.0133,0.961299,-29.0476,50.6733,-40.9055,71.3594,0.333013,-455.874,-197.177,-2.65068,-1.14648,0.974159,-180.118,265.555,21.9202,-32.3179,0.979928,-5.86636,-3.24e-12,152.988,1.5e-12,0.987289,81.058,4.35351,-100.564,-5.40116,0.932738,-457.759,27.6209,5.42575,-0.327387,0.976693,586.908,-596.401,17.798,-18.0858,0.990935,199.589,-413.259,72.816,-150.769,0.873015,530.378,102.839,175.409,34.0114,0.946546,235.809,38.8499,-10.2464,-1.68811,0.939609,323.264,-152.605,12.3157,-5.81392,0.957015,165.082,-78.0461,-6.46434,3.05617,0.898444,298.646,259.994,-75.8603,-66.0422,0.98677,-3.71094e-06,35.9183,9.71826e-06,-128.722,0.997217}; float contrib_tols[] = {3.1,1e-09,0.00038,0.027,9.7e-05,0.014,0.016,6.1e-05,0.0045,8.5e-05,0.00012,0.007,0.051,0.012,0.013,0.001,0.0011,0.0085,0.0042,0.0042,0.00025,0.0058,0.00032,0.016,0.0093,0.015,0.024,0.0016,0.0031,0.0046,0.0038,0.0024,0.0063,0.0012,0.008,0.0056,0.014,0.022,0.0073,0.0047,0.00012,0.0038,0.014,0.0033,0.014,0.013,0.014,0.039,0.013,0.014,0.012,0.027,0.032,0.012,9e-05,0.025,0.00036,0.023,0.0014,0.0049,0.053,0.00048,0.017,0.016,0.0062,0.012,0.019,0.0064,0.00012,0.017,0.0035,0.006,0.029,0.013,0.014,0.021,0.021,0.00018,0.019,0.0012,0.028,0.002,0.032,0.033,0.0036,0.0074,0.011,0.0022,0.015,0.0026,0.02,0.0093,0.011,0.0052,0.027,0.024,0.0002,0.018,0.00089,0.063,0.00036,0.025,5e-05,2.5e-05,0.0036,2.9e-05,0.0042,4.8e-05,0.032,0.00012,0.0099,3.8e-05,5e-05,0.0029,5.4e-05,0.00027,4.1e-06,2.4e-05,0.00015,0.0082,2.4e-05,0.0014,4.1e-05,0.032,0.0076,0.0088,0.0021,4.9e-05,0.0056,0.00044,0.0029,0.00024,4.4e-05,0.00036,0.0027,0.00063,0.0046,2.6e-05,0.0095,0.0096,0.0031,0.0031,4.2e-05,0.00027,0.0063,0.00011,0.0025,1.1e-05,0.00052,0.026,0.00014,0.0069,4.7e-05,0.0082,0.013,0.0007,0.0011,4.1e-05,0.023,0.0015,0.0025,0.00015,4.8e-05,0.0033,0.0051,0.00048,0.00075,3.1e-05,0.0013,0.00026,0.0018,0.00036,5.2e-06,0.0018,0.0012,0.004,0.0028,3e-05,0.01,0.016,0.00073,0.0012,4.8e-05,0.0053,0.0035,0.00019,0.00013,3.6e-05,0.0006,0.019,0.00025,0.008,3.8e-05,0.0094,0.0023,0.0013,0.00031,4.6e-05,0.0077,0.0075,0.0018,0.0018,4.6e-05,0.011,0.031,0.00015,0.00038,4.9e-05,0.0053,0.0058,0.0026,0.0028,4.7e-05,0.007,0.017,0.0015,0.0036,4.9e-05,0.03,0.011,0.0022,0.00082,4.9e-05,6.4e-05,0.018,5.9e-06,0.001,5e-05,0.00032,0.02,4.5e-06,0.00035,4.8e-05,0.00067,0.0023,0.0002,0.00069,2.5e-05,0.035,0.00031,0.0038,3.3e-05,5e-05,0.012,0.012,0.00056,0.00053,4.8e-05,0.0039,0.0075,0.00048,0.00093,4.3e-05,0.017,0.0057,0.00067,0.00024,4.8e-05,3.2e-05,0.0045,2.9e-05,0.0041,4.8e-05,0.0015,0.0026,0.0021,0.0037,1.7e-05,0.023,0.01,0.00021,0.00012,4.9e-05,0.0093,0.013,0.0012,0.0017,4.9e-05,0.00042,2.7e-06,0.0078,6.9e-05,4.9e-05,0.0042,0.00025,0.0052,0.00032,4.7e-05,0.023,0.0017,0.00036,2.7e-05,4.9e-05,0.03,0.03,0.001,0.0011,5e-05,0.01,0.021,0.0037,0.0076,4.4e-05,0.027,0.0053,0.0089,0.0017,4.7e-05,0.012,0.002,0.00066,0.00011,4.7e-05,0.016,0.0077,0.00065,0.00031,4.8e-05,0.0084,0.004,0.00042,0.00019,4.5e-05,0.015,0.013,0.004,0.0034,4.9e-05,1.9e-05,0.0019,4.6e-05,0.0065,5e-05}; int contrib_size = sizeof(contrib_vals)/sizeof(contrib_vals[0]); } bool Test_contrib::operator() () { data_val = std::vector( data::contrib_vals, data::contrib_vals+data::contrib_size ); data_tol = std::vector( data::contrib_tols, data::contrib_tols+data::contrib_size ); typedef HKL_info::HKL_reference_index HRI; data::Test_data data; const HKL_data& fsig = data.hkl_data_f_sigf(); const HKL_data& abcd = data.hkl_data_abcd(); const clipper::Atom_list& xyzb = data.atom_list(); const Spacegroup spgr = fsig.hkl_info().spacegroup(); const Cell cell = fsig.hkl_info().cell(); const Resolution reso = fsig.hkl_info().resolution(); typedef HKL_info::HKL_reference_index HRI; typedef Xmap::Map_reference_index MRI; // test sfcalc objects { // select spacegroup std::vector hallsymbols; for ( int i = 0; i < data::sgdata_size; i += 10 ) hallsymbols.push_back( data::sgdata[i].hall ); // build model Atom_list atoms; Atom atom = Atom::null(); atom.set_occupancy( 1.0 ); atom.set_u_iso( 0.5 ); atom.set_element( "C" ); atom.set_coord_orth( Coord_orth( 12, 8, 5 ) ); atoms.push_back( atom ); atom.set_element( "N" ); atom.set_coord_orth( Coord_orth( 11, 6, 4 ) ); atoms.push_back( atom ); atom.set_element( "O" ); atom.set_coord_orth( Coord_orth( 13, 5, 4 ) ); atoms.push_back( atom ); // calc cell Cell cellc( Cell_descr( 37, 37, 37 ) ); Cell cellha( Cell_descr( 37, 37, 37, 120, 90, 90 ) ); Cell cellhb( Cell_descr( 37, 37, 37, 90, 120, 90 ) ); Cell cellhc( Cell_descr( 37, 37, 37, 90, 90, 120 ) ); Cell cg; String symbol; Spacegroup sg; for ( int s = 0; s < hallsymbols.size(); s++ ) { try { symbol = hallsymbols[s]; sg = Spacegroup( Spgr_descr( symbol, Spgr_descr::Hall ) ); // identify trigonal/hexagonal groups cg = cellc; for ( int sym = 1; sym < sg.num_symops(); sym++ ) { if ( ( sg.symop(sym).rot()(1,1) * sg.symop(sym).rot()(1,2) == -1 ) || ( sg.symop(sym).rot()(2,1) * sg.symop(sym).rot()(2,2) == -1 ) ) cg = cellha; if ( ( sg.symop(sym).rot()(0,0) * sg.symop(sym).rot()(0,2) == -1 ) || ( sg.symop(sym).rot()(2,0) * sg.symop(sym).rot()(2,2) == -1 ) ) cg = cellhb; if ( ( sg.symop(sym).rot()(0,0) * sg.symop(sym).rot()(0,1) == -1 ) || ( sg.symop(sym).rot()(1,0) * sg.symop(sym).rot()(1,1) == -1 ) ) cg = cellhc; } HKL_info hkl_info( sg, cg, Resolution( 5.0 ), true ); HKL_data fp1( hkl_info ); HKL_data fp2( hkl_info ); SFcalc_iso_sum( fp1, atoms ); SFcalc_iso_fft( fp2, atoms, 2.5, 2.5, 0.25 ); // begin extra fft tests Grid_sampling gg( sg, cg, hkl_info.resolution() ); Xmap xg( sg, cg, gg ); FFTmap fftmap( sg, cg, gg ); xg.fft_from( fp2, Xmap_base::Normal ); xg.fft_to( fp2, Xmap_base::Sparse ); fftmap.fft_rfl_to_map( fp2, xg ); xg.fft_to( fp2, Xmap_base::Normal ); xg.fft_from( fp2, Xmap_base::Sparse ); fftmap.fft_map_to_rfl( xg, fp2 ); // end extra fft tests float tol = 0.005 * fp1[ HKL( 0, 0, 0 ) ].f(); for ( HRI ih = fp1.first(); !ih.last(); ih.next() ) { std::complex ab1(0.0,0.0), ab2(0.0,0.0); if ( !fp1[ih].missing() ) ab1 = fp1[ih]; if ( !fp2[ih].missing() ) ab2 = fp2[ih]; test( "SF-A", ab1.real(), ab2.real(), tol ); test( "SF-B", ab1.imag(), ab2.imag(), tol ); } } catch ( Message_base ) { test( "SFSG "+symbol, sg.spacegroup_number(), -1 ); } } } // test sfcalc_obs and sfweight { // sfcalc_obs HKL_data fcal( fsig.hkl_info() ); SFcalc_obs_bulk sfcb; sfcb( fcal, fsig, xyzb ); // sfcalc_obs results for ( HRI ih = fcal.first(); !ih.last(); ih.next() ) if ( ih.index() % 20 == 0 ) { std::complex ab( fcal[ih] ); test( "SFO-A", ab.real() ); test( "SFO-B", ab.imag() ); } // sfweight //SFcalc_iso_fft sfc; //sfc( fcal, xyzb ); HKL_data fb1( fsig.hkl_info() ), fb2( fsig.hkl_info() ); HKL_data fd1( fsig.hkl_info() ), fd2( fsig.hkl_info() ); HKL_data phiw1(fsig.hkl_info()), phiw2(fsig.hkl_info()); HKL_data flag( fsig.hkl_info() ); HKL_data abcd( fsig.hkl_info() ), abcd2( fsig.hkl_info() ); abcd = data32::ABCD( 0.0, 0.0, 0.0, 0.0 ); for ( HRI ih = flag.first(); !ih.last(); ih.next() ) if ( !fsig[ih].missing() ) flag[ih].flag() = SFweight_spline::BOTH; else flag[ih].flag() = SFweight_spline::NONE; clipper::SFweight_spline sfw( 600, 12 ); bool fl = sfw( fb1, fd1, phiw1, fsig, fcal, flag ); if ( !fl ) test( "SFW-FAIL", 1, 0 ); // sfweight results for ( HRI ih = phiw1.first(); !ih.last(); ih.next() ) if ( !fsig[ih].missing() ) if ( ih.index() % 20 == 0 ) { std::complex ab_b( fb1[ih] ); std::complex ab_d( fd1[ih] ); test( "SFWB-A", ab_b.real() ); test( "SFWB-B", ab_b.imag() ); test( "SFWD-A", ab_d.real() ); test( "SFWD-B", ab_d.imag() ); test( "SFW-W", phiw1[ih].fom() ); } // sfweight-hl results HKL_data fsig0( fsig.hkl_info() ); for ( HRI ih = fsig.first(); !ih.last(); ih.next() ) if ( !fsig[ih].missing() ) fsig0[ih] = data32::F_sigF( fsig[ih].f(), 0.0 ); clipper::SFweight_spline sfw1( 600, 12 ), sfw2( 600, 12 ); bool fl1 = sfw1( fb1, fd1, phiw1, fsig0, fcal, flag ); if ( !fl1 ) test( "SFW-FAIL1", 1, 0 ); bool fl2 = sfw2( fb2, fd2, phiw2, abcd2, fsig0, abcd, fcal, flag ); if ( !fl2 ) test( "SFW-FAIL2", 1, 0 ); std::vector params_e1 = sfw1.params_error(); std::vector params_s1 = sfw1.params_scale(); std::vector params_e2 = sfw2.params_error(); std::vector params_s2 = sfw2.params_scale(); for ( int i = 0; i < params_e1.size(); i++ ) { test( "SFWHL-E", params_e1[i], params_e2[i], 0.025 ); test( "SFWHL-S", params_s1[i], params_s2[i], 0.025 ); } for ( HRI ih = fsig0.first(); !ih.last(); ih.next() ) if ( !fsig0[ih].missing() ) { clipper::SFweight_spline::TargetResult r00, r01, r10, r11, rhl; for ( double s = 0.20; s <= 1.01; s += 0.2 ) { for ( double p = 0.20; p <= 1.01; p += 0.2 ) { double w = p * fsig0[ih].f(); w = w * w; const double d = 0.000001; r00 = sfw1.targetfn( ih.hkl_class(), fsig0[ih], fcal[ih], s, w ); rhl = sfw1.targethl( ih.hkl_class(), fsig0[ih], abcd[ih], fcal[ih], s, w ); //std::cout << fsig0[ih].f() << " " << fcal[ih].f() << " " << s << " " << w << " " << r00.r << " " << rhl.r << std::endl; test( "SFW-TGT-CMP", r00.r, rhl.r, 1.0 ); r00 = sfw1.targetfn( ih.hkl_class(), fsig0[ih], fcal[ih], s, w ); r01 = sfw1.targetfn( ih.hkl_class(), fsig0[ih], fcal[ih], s, w+d ); r10 = sfw1.targetfn( ih.hkl_class(), fsig0[ih], fcal[ih], s+d, w ); r11 = sfw1.targetfn( ih.hkl_class(), fsig0[ih], fcal[ih], s+d, w+d ); test( "SFW-FN-DW ", (r01.r-r00.r)/d, r00.dw, 0.02 ); test( "SFW-FN-DS ", (r10.r-r00.r)/d, r00.ds, 0.02 ); test( "SFW-FN-DWW", (r01.dw-r00.dw)/d, r00.dww, 0.02 ); test( "SFW-FN-DSS", (r10.ds-r00.ds)/d, r00.dss, 0.02 ); r00 = sfw1.targethl( ih.hkl_class(), fsig0[ih], abcd[ih], fcal[ih], s, w ); r01 = sfw1.targethl( ih.hkl_class(), fsig0[ih], abcd[ih], fcal[ih], s, w+d ); r10 = sfw1.targethl( ih.hkl_class(), fsig0[ih], abcd[ih], fcal[ih], s+d, w ); r11 = sfw1.targethl( ih.hkl_class(), fsig0[ih], abcd[ih], fcal[ih], s+d, w+d ); test( "SFW-HL-DW ", (r01.r-r00.r)/d, r00.dw, 0.02 ); test( "SFW-HL-DS ", (r10.r-r00.r)/d, r00.ds, 0.02 ); test( "SFW-HL-DWW", (r01.dw-r00.dw)/d, r00.dww, 0.02 ); test( "SFW-HL-DSS", (r10.ds-r00.ds)/d, r00.dss, 0.02 ); } } } } // test map filter objects { HKL_data pw( fsig.hkl_info() ); HKL_data fp( fsig.hkl_info() ); pw.compute( abcd, data32::Compute_phifom_from_abcd() ); fp.compute( fsig, pw, data32::Compute_fphi_from_fsigf_phifom() ); Grid_sampling grid( spgr, cell, reso, 2.5 ); Xmap xmap( spgr, cell, grid ); xmap.fft_from( fp ); MapFilterFn_step step( 2.5 ); MapFilter_slow fltr1( step, 1.0, MapFilter_slow::Relative ); MapFilter_fft fltr2( step, 1.0, MapFilter_fft::Relative ); Xmap f1, f2; fltr1( f1, xmap ); fltr2( f2, xmap ); for ( MRI ix = xmap.first(); !ix.last(); ix.next() ) test( "MAPFILTER", f1[ix], f2[ix], 0.0001 ); } // test the convolution and fffear objects { HKL_data pw( fsig.hkl_info() ); HKL_data fp( fsig.hkl_info() ); pw.compute( abcd, data32::Compute_phifom_from_abcd() ); fp.compute( fsig, pw, data32::Compute_fphi_from_fsigf_phifom() ); Grid_sampling grid( spgr, cell, reso, 2.5 ); Xmap xmap( spgr, cell, grid ); xmap.fft_from( fp ); Xmap r1( Spacegroup::p1(), xmap.cell(), xmap.grid_sampling() ); Xmap r2( Spacegroup::p1(), xmap.cell(), xmap.grid_sampling() ); int irad = 3; clipper::Grid_range tg( clipper::Coord_grid(-irad,-irad,-irad), clipper::Coord_grid( irad, irad, irad) ); NXmap target( xmap.cell(), xmap.grid_sampling(), tg ); NXmap weight( xmap.cell(), xmap.grid_sampling(), tg ); target = weight = 0.0; for ( Coord_grid c = tg.min(); !c.last(tg); c.next(tg) ) { if ( c*c <= 5 ) { target.set_data(c-tg.min(),xmap.get_data(c)); weight.set_data(c-tg.min(),1.0); } } Convolution_search_slow conv1( xmap ); Convolution_search_fft conv2( xmap ); conv1( r1, target ); conv2( r2, target ); for ( MRI ix = r1.first(); !ix.last(); ix.next() ) test( "CONVOL", r1[ix], r2[ix], 0.0001 ); FFFear_slow srch1( xmap ); FFFear_fft srch2( xmap ); srch1( r1, target, weight ); srch2( r2, target, weight ); for ( MRI ix = r1.first(); !ix.last(); ix.next() ) test( "FFFEAR", r1[ix], r2[ix], 0.0001 ); } // test anisotropic scaling { // expand to P1 Spacegroup spgrp1( Spacegroup::P1 ); HKL_info hkl1( spgrp1, cell, fsig.hkl_info().resolution(), true ); HKL_data fs( hkl1 ); for ( HRI ih = hkl1.first(); !ih.last(); ih.next() ) fs[ih] = fsig[ih.hkl()]; // make data objects HKL_data fp( fs.hkl_info() ); HKL_data fs1 = fs; HKL_data fs2 = fs; U_aniso_orth u_ref( 0.10, 0.13, 0.17, -0.02, 0.03, -0.04 ); // simulate aniso data for ( HRI ih = fs.first(); !ih.last(); ih.next() ) if ( !fs[ih].missing() ) { Coord_reci_orth c = ih.hkl().coord_reci_orth(cell); double s = exp( Util::twopi2() * u_ref.quad_form( c ) ); fs1[ih].scale(s); fs2[ih].scale(1.0/s); fp[ih] = data32::F_phi( fs[ih].f(), 0.0 ); } // now attempt scaling SFscale_aniso::TYPE F = SFscale_aniso::F; SFscale_aniso sfscl; sfscl( fs1, fp ); U_aniso_orth u_wrk1 = sfscl.u_aniso_orth(F); sfscl( fp, fs2 ); U_aniso_orth u_wrk2 = sfscl.u_aniso_orth(F); test( "ANISO-O-00", u_ref.mat00(), u_wrk1.mat00(), 1.0e-6 ); test( "ANISO-O-11", u_ref.mat11(), u_wrk1.mat11(), 1.0e-6 ); test( "ANISO-O-22", u_ref.mat22(), u_wrk1.mat22(), 1.0e-6 ); test( "ANISO-O-01", u_ref.mat01(), u_wrk1.mat01(), 1.0e-6 ); test( "ANISO-O-02", u_ref.mat02(), u_wrk1.mat02(), 1.0e-6 ); test( "ANISO-O-12", u_ref.mat12(), u_wrk1.mat12(), 1.0e-6 ); test( "ANISO-C-00", u_ref.mat00(), u_wrk2.mat00(), 1.0e-6 ); test( "ANISO-C-11", u_ref.mat11(), u_wrk2.mat11(), 1.0e-6 ); test( "ANISO-C-22", u_ref.mat22(), u_wrk2.mat22(), 1.0e-6 ); test( "ANISO-C-01", u_ref.mat01(), u_wrk2.mat01(), 1.0e-6 ); test( "ANISO-C-02", u_ref.mat02(), u_wrk2.mat02(), 1.0e-6 ); test( "ANISO-C-12", u_ref.mat12(), u_wrk2.mat12(), 1.0e-6 ); } return ( error_count == 0 ); } } // namespace clipper clipper-2.1/clipper/contrib/sfcalc_obs.h0000644000374100011300000000654610736662166015322 00000000000000/*! \file sfcalc_obs.h Header file for structure factor calculation vs observed object */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_SFCALC_OBS #define CLIPPER_SFCALC_OBS #include "function_object_bases.h" namespace clipper { //! Structure factor calculation vs observed using bulk solvent. /*! Perform structure factor calculation, adding an additional bulk solvent/missing correction to give best fit to observed data. A scaling is used internally, but not output. \ingroup g_funcobj */ template class SFcalc_obs_bulk : public SFcalc_obs_base { public: //! constructor SFcalc_obs_bulk( const int n_params = 12 ) : nparams(n_params) {} //! constructor: shorthand for constructor+operator SFcalc_obs_bulk( HKL_data >& fphi, const HKL_data >& fsig, const Atom_list& atoms, const int n_params = 12 ) : nparams(n_params) { (*this)( fphi, fsig, atoms ); } bool operator() ( HKL_data >& fphi, const HKL_data >& fsig, const Atom_list& atoms ); const ftype& bulk_frac() { return bulkfrc; } const ftype& bulk_scale() { return bulkscl; } private: int nparams; double bulkfrc, bulkscl; }; } // namespace clipper #endif clipper-2.1/clipper/contrib/skeleton.h0000644000374100011300000001163610736662166015044 00000000000000/*! \file skeleton.h Header file for sample skeletonisation impelementation \ingroup g_skel */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_SKELETON #define CLIPPER_SKELETON #include #include #include "function_object_bases.h" namespace clipper { //! Simple skeletonisation implementation /*! \ingroup g_skel */ class Skeleton_basic : public Skeleton_base { public: // helper classes class Neighbours { public: Neighbours( const clipper::Xmap_base &map, const float min_dist = 0.5, const float max_dist = 2.5 ); clipper::Coord_grid operator[] (int i) const { return nlist[i]; } int size() const { return nlist.size(); } private: std::vector nlist; }; class NCube { public: NCube( const int& n ); const int& operator[] ( const clipper::Coord_grid& c ) const { return data[m.index(c)]; } int& operator[] ( const clipper::Coord_grid& c ) { return data[m.index(c)]; } const clipper::Grid_range& grid() const { return m; } private: clipper::Grid_range m; std::vector data; }; // methods //! constructor Skeleton_basic( const int box = 1 ) : box_(box) {} //! constructor: shorthand for constructor+operator Skeleton_basic( clipper::Xmap& xskl, const clipper::Xmap& xmap, const int box = 1 ) : box_(box) { (*this)( xskl, xmap ); } //! Skeletonise a map bool operator() ( clipper::Xmap& xskl, const clipper::Xmap& xmap ) const; private: static bool isInSkel( const clipper::Xmap& xskl, const clipper::Coord_grid& c, const Skeleton_basic::Neighbours& neigh, const int& box ); int box_; }; //! Fast template skeletonisation implementation /*! \ingroup g_skel */ template class Skeleton_fast : public Skeleton_base { public: // helper classes class Neighbours { public: Neighbours() {} Neighbours( const clipper::Xmap_base &map, const float min_dist = 0.5, const float max_dist = 2.5 ); clipper::Coord_grid operator[] (int i) const { return nlist[i]; } int size() const { return nlist.size(); } private: std::vector nlist; }; // methods //! constructor Skeleton_fast() {} //! constructor: shorthand for constructor+operator Skeleton_fast( clipper::Xmap& xskl, const clipper::Xmap& xmap ) { (*this)( xskl, xmap ); } //! Skeletonise a map bool operator() ( clipper::Xmap& xskl, const clipper::Xmap& xmap ) const; private: mutable int cube[3][3][3]; mutable Neighbours neigh; bool isInSkel( const clipper::Xmap& xskl, const clipper::Coord_grid& c ) const; void flood_cube( const int x, const int y, const int z ) const; }; } // namespace clipper #endif clipper-2.1/clipper/contrib/function_object_bases.h0000644000374100011300000002754410736662166017555 00000000000000/*! \file function_object_bases.h Header file for specifying interfaces to function objects \ingroup g_funcobj */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_FUNCTION_OBJECT_BASES #define CLIPPER_FUNCTION_OBJECT_BASES #include "../core/hkl_datatypes.h" #include "../core/xmap.h" #include "../core/nxmap_operator.h" namespace clipper { //! Base class for structure factor calculation methods /*! \ingroup g_funcobj */ template class SFcalc_base { public: //! Structure factor calculation function definition /*! In the implementations, this function will do the actual structure factor calculation. \param fphidata Fourier coefficients to be calculated. On output this holds the Fourier coefficients corresponding to the atomic model. \param atoms The atom selection from which the density is to be calculated. \return true on success. */ virtual bool operator() ( HKL_data >& fphidata, const Atom_list& atoms ) const = 0; virtual ~SFcalc_base() {} //!< destructor }; //! Base class for electron density calculation methods /*! \ingroup g_funcobj */ template class EDcalc_base { public: //! Electron density calculation function definition /*! In the implementations, this function will do the actual electron density calculation. \param xmap Electron density map to be calculated. On output this holds the electron density map corresponding to the atomic model. \param atoms The atom selection from which the density is to be calculated. \return true on success. */ virtual bool operator() ( Xmap& xmap, const Atom_list& atoms ) const = 0; virtual bool operator() ( NXmap& nxmap, const Atom_list& atoms ) const = 0; virtual ~EDcalc_base() {} //!< destructor }; //! Base class for structure factor calculation vs observed methods /*! \ingroup g_funcobj */ template class SFcalc_obs_base { public: //! Structure factor calculation function definition /*! In the implementations, this function will do the actual structure factor calculation. \param fphidata Fourier coefficients to be calculated. On output this holds the Fourier coefficients corresponding to the atomic model. \param fo Observed data against which to reference the Fcalc, e.g. to fit scale and/or bulk solvent. \param atoms The atom selection from which the density is to be calculated. \return true on success. */ virtual bool operator() ( HKL_data >& fphi, const HKL_data >& fsig, const Atom_list& atoms ) = 0; virtual ~SFcalc_obs_base() {} //!< destructor }; //! Base class for structure factor weighting (sigmaa) methods /*! \ingroup g_funcobj */ template class SFweight_base { public: //! Flag values for different reflection purposes enum TYPE { NONE, SIGMAA, SCALE, BOTH }; //! Structure factor weighting (sigmaa) definition /*! In the implementations, this function will do the actual structure factor weighting calculation \param fb Output best map coefficients. \param fd Output difference map coefficients. \param phiw Output phase and figure-of-merit. \param fo Input observed structure factors. \param fc Input calculated map coefficients. \param flag Input flag indicating what to use this reflection for. \return true on success. */ virtual bool operator() ( HKL_data >& fb, HKL_data >& fd, HKL_data >& phiw, const HKL_data >& fo, const HKL_data >& fc, const HKL_data& usage ) = 0; virtual ~SFweight_base() {} //!< destructor }; //! Base class for structure factor scaling methods /*! \ingroup g_funcobj */ template class SFscale_base { public: //! Structure factor scaling definition /*! In the implementations, this function will do the actual structure factor scaling calculation. \param fo Observed structure factors to be scaled. \param fc Calculated structure factors to scale against. \return true on success. */ virtual bool operator() ( HKL_data >& fo, const HKL_data >& fc ) = 0; //! Structure factor scaling definition /*! In the implementations, this function will do the actual structure factor scaling calculation. \param fc Calculated structure factors to be scaled. \param fo Observed structure factors to scale against. \return true on success. */ virtual bool operator() ( HKL_data >& fc, const HKL_data >& fo ) = 0; //! Structure factor scaling definition /*! In the implementations, this function will do the actual structure factor scaling calculation. \param fo Observed structure factors to be scaled. \return true on success. */ virtual bool operator() ( HKL_data >& fo ) = 0; virtual ~SFscale_base() {} //!< destructor }; //! Base class for map filtering calculation methods /*! \ingroup g_funcobj */ template class MapFilter_base { public: //! Map filtering function definition /*! In the implementations, this function will do the actual map filtering calculation. \param result On output this holds the filtered electron density. \param xmap Electron density map to be filtered. \return true on success. */ virtual bool operator() ( Xmap& result, const Xmap& xmap ) const = 0; virtual ~MapFilter_base() {} //!< destructor }; //! Base class for convolution search methods /*! \ingroup g_funcobj Note: that target map must be supplied in the constructor or initialiser. This allows precalculation of some of the coefficients required. The () operator performs an actual search in that map for a given target. */ template class Convolution_search_base { public: /*! In the implementations, this function will do the actual convolution search calculation. \param result The convolution search residual map, containing the value of the search function for each offset of the search model. The search function is a least squares residual, or may be a negative log likelihood, therefore it is positive and low values represent better fits. \param srchval Map of the target density for which to search. \param nxop Operator relating the coordinate frames of the search target and the crystallographic map, used to rotate the search target. \return true on success. */ virtual bool operator() ( Xmap& result, const NXmap& srchval, const NX_operator& nxop ) const = 0; virtual ~Convolution_search_base() {} //!< destructor }; //! Base class for Fast Fourier Feature recongition (FFFEAR) methods /*! \ingroup g_funcobj Note: that target map must be supplied in the constructor or initialiser. This allows precalculation of some of the coefficients required. The () operator performs an actual search in that map for a given target. */ template class FFFear_base { public: /*! In the implementations, this function will do the actual fffear calculation. \param result The fffear residual map, containing the value of the search function for each offset of the search model. The search function is a least squares residual, or may be a negative log likelihood, therefore it is positive and low values represent better fits. \param srchval Map of the target density for which to search. \param srchwgt Map of the target weights for each density point. \param nxop Operator relating the coordinate frames of the search target and the crystallographic map, used to rotate the search target. \return true on success. */ virtual bool operator() ( Xmap& result, const NXmap& srchval, const NXmap& srchwgt, const NX_operator& nxop ) const = 0; virtual ~FFFear_base() {} //!< destructor }; //! Base class for skeleton calculation methods /*! \ingroup g_funcobj */ template class Skeleton_base { public: //! Skeletonisation function definition /*! In the implementations, this function will do the actual skeletonisation. \param xskl int/short/char map. On input this may hold 1 for any grid point which is to be considered for skeletonisation, and 0 for any other point (e.g. low density, solvent) [This feaure may not be present in all implementations]. On output this map holds 1 for any grid point which is part of a skeleton ridge, and 0 for any point which is not. \param xmap float/double map. This map holds the actual electron density values for the map. \return true on success. */ virtual bool operator() ( Xmap& xskl, const Xmap& xmap ) const = 0; virtual ~Skeleton_base() {} //!< destructor }; //! Base class for origin matching calculation methods /*! \ingroup g_funcobj */ template class OriginMatch_base { public: //! Origin matching function definition /*! In the implementations, this function will do the actual origin matching. \param invert True if the phases must be inverted. \param shift The coordinate shift required to match the phases. \patam fphi1 The first set of map coefficients. \patam fphi2 The second set of map coefficients. \return true on success. */ virtual bool operator() ( bool& invert, Coord_frac& shift, const HKL_data >& fphi1, const HKL_data >& fphi2 ) const = 0; virtual ~OriginMatch_base() {} //!< destructor }; } // namespace clipper #endif clipper-2.1/clipper/contrib/Makefile.in0000644000374100011300000004747611372264333015116 00000000000000# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, # Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, 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mostlyclean-generic \ mostlyclean-libtool pdf pdf-am ps ps-am tags uninstall \ uninstall-am uninstall-libLTLIBRARIES \ uninstall-library_includeHEADERS # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: clipper-2.1/clipper/contrib/edcalc.cpp0000644000374100011300000002171410736662166014764 00000000000000/* edcalc.cpp: Electron density calculation implementation */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "edcalc.h" #include "../core/atomsf.h" namespace clipper { template bool EDcalc_mask::operator() ( Xmap& xmap, const Atom_list& atoms ) const { xmap = 0.0; const Cell& cell = xmap.cell(); const Grid_sampling& grid = xmap.grid_sampling(); Coord_orth xyz; Coord_grid g0, g1; Grid_range gd( cell, grid, radius_ ); typename Xmap::Map_reference_coord i0, iu, iv, iw; for ( int i = 0; i < atoms.size(); i++ ) if ( !atoms[i].is_null() ) { xyz = atoms[i].coord_orth(); g0 = xmap.coord_map( xyz ).coord_grid() + gd.min(); g1 = xmap.coord_map( xyz ).coord_grid() + gd.max(); i0 = typename Xmap::Map_reference_coord( xmap, g0 ); for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) if ( ( xyz - iw.coord_orth() ).lengthsq() < radius_*radius_ ) xmap[iw] = 1.0; } return true; } template bool EDcalc_mask::operator() ( NXmap& nxmap, const Atom_list& atoms ) const { nxmap = 0.0; Coord_orth xyz; Coord_grid g0, g1; g0 = Coord_map( nxmap.operator_orth_grid().rot() * Vec3<>(radius_,radius_,radius_) ).coord_grid(); Grid_range gd( -g0, g0 ); Grid_range box( Coord_grid(0,0,0), Coord_grid(nxmap.grid())-Coord_grid(1,1,1) ); typename NXmap::Map_reference_coord i0, iu, iv, iw; for ( int i = 0; i < atoms.size(); i++ ) if ( !atoms[i].is_null() ) { xyz = atoms[i].coord_orth(); g0 = nxmap.coord_map( xyz ).coord_grid() + gd.min(); g1 = nxmap.coord_map( xyz ).coord_grid() + gd.max(); i0 = typename NXmap::Map_reference_coord( nxmap, g0 ); for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) if ( box.in_grid( iw.coord() ) ) if ( ( xyz - iw.coord_orth() ).lengthsq() < radius_*radius_ ) nxmap[iw] = 1.0; } return true; } template bool EDcalc_iso::operator() ( Xmap& xmap, const Atom_list& atoms ) const { xmap = 0.0; const Cell& cell = xmap.cell(); const Grid_sampling& grid = xmap.grid_sampling(); Coord_orth xyz; Coord_grid g0, g1; Grid_range gd( cell, grid, radius_ ); typename Xmap::Map_reference_coord i0, iu, iv, iw; for ( int i = 0; i < atoms.size(); i++ ) if ( !atoms[i].is_null() ) { AtomShapeFn sf( atoms[i].coord_orth(), atoms[i].element(), atoms[i].u_iso(), atoms[i].occupancy() ); g0 = xmap.coord_map( atoms[i].coord_orth() ).coord_grid() + gd.min(); g1 = xmap.coord_map( atoms[i].coord_orth() ).coord_grid() + gd.max(); i0 = typename Xmap::Map_reference_coord( xmap, g0 ); for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) xmap[iw] += sf.rho( iw.coord_orth() ); } for ( typename Xmap::Map_reference_index ix = xmap.first(); !ix.last(); ix.next() ) xmap[ix] *= xmap.multiplicity( ix.coord() ); return true; } template bool EDcalc_iso::operator() ( NXmap& nxmap, const Atom_list& atoms ) const { nxmap = 0.0; Coord_orth xyz; Coord_grid g0, g1; g0 = Coord_map( nxmap.operator_orth_grid().rot() * Vec3<>(radius_,radius_,radius_) ).coord_grid(); Grid_range gd( -g0, g0 ); Grid_range box( Coord_grid(0,0,0), Coord_grid(nxmap.grid())-Coord_grid(1,1,1) ); typename NXmap::Map_reference_coord i0, iu, iv, iw; for ( int i = 0; i < atoms.size(); i++ ) if ( !atoms[i].is_null() ) { AtomShapeFn sf( atoms[i].coord_orth(), atoms[i].element(), atoms[i].u_iso(), atoms[i].occupancy() ); g0 = nxmap.coord_map( atoms[i].coord_orth() ).coord_grid() + gd.min(); g1 = nxmap.coord_map( atoms[i].coord_orth() ).coord_grid() + gd.max(); i0 = typename NXmap::Map_reference_coord( nxmap, g0 ); for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) if ( box.in_grid( iw.coord() ) ) nxmap[iw] += sf.rho( iw.coord_orth() ); } return true; } template bool EDcalc_aniso::operator() ( Xmap& xmap, const Atom_list& atoms ) const { xmap = 0.0; const Cell& cell = xmap.cell(); const Grid_sampling& grid = xmap.grid_sampling(); Coord_orth xyz; Coord_grid g0, g1; Grid_range gd( cell, grid, radius_ ); typename Xmap::Map_reference_coord i0, iu, iv, iw; for ( int i = 0; i < atoms.size(); i++ ) if ( !atoms[i].is_null() ) { U_aniso_orth u( atoms[i].u_aniso_orth() ); if ( u.is_null() ) u = U_aniso_orth( atoms[i].u_iso() ); AtomShapeFn sf( atoms[i].coord_orth(), atoms[i].element(), u, atoms[i].occupancy() ); g0 = xmap.coord_map( atoms[i].coord_orth() ).coord_grid() + gd.min(); g1 = xmap.coord_map( atoms[i].coord_orth() ).coord_grid() + gd.max(); i0 = typename Xmap::Map_reference_coord( xmap, g0 ); for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) xmap[iw] += sf.rho( iw.coord_orth() ); } for ( typename Xmap::Map_reference_index ix = xmap.first(); !ix.last(); ix.next() ) xmap[ix] *= xmap.multiplicity( ix.coord() ); return true; } template bool EDcalc_aniso::operator() ( NXmap& nxmap, const Atom_list& atoms ) const { nxmap = 0.0; Coord_orth xyz; Coord_grid g0, g1; g0 = Coord_map( nxmap.operator_orth_grid().rot() * Vec3<>(radius_,radius_,radius_) ).coord_grid(); Grid_range gd( -g0, g0 ); Grid_range box( Coord_grid(0,0,0), Coord_grid(nxmap.grid())-Coord_grid(1,1,1) ); typename NXmap::Map_reference_coord i0, iu, iv, iw; for ( int i = 0; i < atoms.size(); i++ ) if ( !atoms[i].is_null() ) { U_aniso_orth u( atoms[i].u_aniso_orth() ); if ( u.is_null() ) u = U_aniso_orth( atoms[i].u_iso() ); AtomShapeFn sf( atoms[i].coord_orth(), atoms[i].element(), u, atoms[i].occupancy() ); g0 = nxmap.coord_map( atoms[i].coord_orth() ).coord_grid() + gd.min(); g1 = nxmap.coord_map( atoms[i].coord_orth() ).coord_grid() + gd.max(); i0 = typename NXmap::Map_reference_coord( nxmap, g0 ); for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) if ( box.in_grid( iw.coord() ) ) nxmap[iw] += sf.rho( iw.coord_orth() ); } return true; } // compile templates template class EDcalc_mask; template class EDcalc_mask; template class EDcalc_iso; template class EDcalc_iso; template class EDcalc_aniso; template class EDcalc_aniso; } // namespace clipper clipper-2.1/clipper/contrib/convolution_search.h0000644000374100011300000001040310736662166017113 00000000000000/*! \file convolution_search.h Header file for sample Convolution_search impelementation \ingroup g_convolution_search */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_CONVOLUTION_SEARCH #define CLIPPER_CONVOLUTION_SEARCH #include "function_object_bases.h" namespace clipper { //! FFT-based Convolution_search implementation /*! \ingroup g_convolution_search This implementation is currently unoptimised, but much faster then the simple implementation. */ template class Convolution_search_slow : public Convolution_search_base { public: //! constructor Convolution_search_slow( const Xmap& xmap ) { init( xmap ); } //! constructor: shorthand for constructor+operator Convolution_search_slow( Xmap& result, const NXmap& srchval, const Xmap& xmap, const NX_operator& nxop ) { init( xmap ); (*this)( result, srchval, nxop ); } //! initialiser: initialise with the given target Xmap void init( const Xmap& xmap ) { xmp = ⟼ } bool operator() ( Xmap& result, const NXmap& srchval, const NX_operator& nxop ) const; bool operator() ( Xmap& result, const NXmap& srchval ) const; //!< \deprecated private: const Xmap* xmp; }; //! FFT-based Convolution_search implementation /*! \ingroup g_convolution_search This implementation is currently unoptimised, but much faster then the simple implementation. */ template class Convolution_search_fft : public Convolution_search_base { public: //! constructor Convolution_search_fft( const Xmap& xmap ) { init( xmap ); } //! constructor: shorthand for constructor+operator Convolution_search_fft( Xmap& result, const NXmap& srchval, const Xmap& xmap, const NX_operator& nxop ) { init( xmap ); (*this)( result, srchval, nxop ); } //! initialiser: initialise with the given target Xmap void init( const Xmap& xmap ); bool operator() ( Xmap& result, const NXmap& srchval, const NX_operator& nxop ) const; bool operator() ( Xmap& result, const NXmap& srchval ) const; //!< \deprecated private: ftype vol; FFTmap_p1 rho1; }; } // namespace clipper #endif clipper-2.1/clipper/contrib/function_object_bases.cpp0000644000374100011300000000440710736662166020101 00000000000000/* function_object_bases.cpp: implementation */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "function_object_bases.h" namespace clipper { } // namespace clipper clipper-2.1/clipper/contrib/sfweight.cpp0000644000374100011300000004657411144270113015361 00000000000000/* sfweight.cpp: structure factor weighting implementation */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #include "sfweight.h" #include "../core/hkl_operators.h" #include "../core/resol_targetfn.h" namespace clipper { template typename SFweight_spline::TargetResult SFweight_spline::TargetFo::operator() ( const HKL_class cls, const datatypes::F_sigF& fo0, const datatypes::ABCD& hl0, const datatypes::F_phi& fc0, const ftype& s, const ftype& w, const std::vector& hlterms ) { ftype fo(0.0), fc(0.0), phic(0.0), sfo(1.0); if ( !fo0.missing() ) { fo = fo0.f(); sfo = fo0.sigf(); } if ( !fc0.missing() ) { fc = fc0.f(); phic = fc0.phi(); } const ftype epc = cls.epsilonc(); const ftype s2 = s*s; const ftype fo2 = fo*fo; const ftype fc2 = fc*fc; const ftype d = 2.0*sfo*sfo + epc*w; const ftype d2 = d*d; const ftype d3 = d*d2; const ftype d4 = d*d3; const ftype x = 2.0*fo*fc*s/d; ftype i0, di0, ddi0, cf; TargetResult r; if ( cls.centric() ) { i0 = (fabs(x)<10.0) ? log(cosh(x)) : fabs(x)+log(0.5); di0 = tanh(x); ddi0 = 1.0-pow(tanh(x),2); cf = 0.5; } else { i0 = Util::sim_integ(x); di0 = Util::sim(x); ddi0 = Util::sim_deriv(x); cf = 1.0; } r.r = cf*log(d) + (fo2+s2*fc2)/d - i0; r.ds = 2.0*s*fc2/d - (2.0*fo*fc/d)*di0; r.dw = epc*( cf/d - (fo2+s2*fc2)/d2 + (2.0*fo*fc*s/d2)*di0 ); r.dss = 2.0*fc2/d - (4.0*fo2*fc2/d2)*ddi0; r.dww = epc*epc*( -cf/d2 + 2.0*(fo2+s2*fc2)/d3 - (4.0*fo*fc*s/d3)*di0 - (4.0*fo2*fc2*s2/d4)*ddi0 ); r.dsw = epc*( -2.0*s*fc2/d2 + (2.0*fo*fc/d2)*di0 + (4.0*fo2*fc2*s/d3)*ddi0 ); abcd = datatypes::ABCD( x*cos(phic), x*sin(phic), 0.0, 0.0 ); phiw = datatypes::Phi_fom( phic, di0 ); return r; } template typename SFweight_spline::TargetResult SFweight_spline::TargetHL::operator() ( const HKL_class cls, const datatypes::F_sigF& fo0, const datatypes::ABCD& hl0, const datatypes::F_phi& fc0, const ftype& s, const ftype& w, const std::vector& hlterms ) { ftype fo(0.0), fc(0.0), phic(0.0), sfo(1.0); ftype a0(0.0), b0(0.0), c0(0.0), d0(0.0); if ( !fo0.missing() ) { fo = fo0.f(); sfo = fo0.sigf(); } if ( !fc0.missing() ) { fc = fc0.f(); phic = fc0.phi(); } if ( !hl0.missing() ) { a0=hl0.a(); b0=hl0.b(); c0=hl0.c(); d0=hl0.d(); } const ftype epc = cls.epsilonc(); const ftype s2 = s*s; const ftype fo2 = fo*fo; const ftype fc2 = fc*fc; const ftype d = 2.0*sfo*sfo + epc*w; const ftype d2 = d*d; const ftype d3 = d*d2; //const ftype d4 = d*d3; const ftype epcd = epc/d; const ftype sf2 = fo2 + s2*fc2; const ftype xs = 2.0*fo*fc/d; const ftype cosc = cos(phic); const ftype sinc = sin(phic); const ftype hl_a = a0 + xs*s*cosc; const ftype hl_b = b0 + xs*s*sinc; const ftype hl_c = c0; const ftype hl_d = d0; ftype cf = 1.0; int a_zero = 0; int a_step = 1; if ( cls.centric() ) { a_step = hlterms.size()/2; a_zero = Util::intr( ftype(hlterms.size())*cls.allowed()/Util::twopi() ); a_zero = Util::mod( a_zero, a_step ); cf = 0.5; } ftype an, asum, asum_ds, asum_dss, asum_dw, asum_dww, asum_dsw, asum_a, asum_b; an = asum = asum_ds = asum_dss = asum_dw = asum_dww = asum_dsw = asum_a = asum_b = 0.0; ftype q, q1, q2, e; ftype qmax = sqrt( hl_a*hl_a + hl_b*hl_b ); for ( int a = a_zero; a < hlterms.size(); a += a_step ) { const HLterms& trig = hlterms[a]; q = hl_a*trig.cosa + hl_b*trig.sina + hl_c*trig.cos2a + hl_d*trig.sin2a; q1 = xs * ( cosc*trig.cosa + sinc*trig.sina ); q2 = s * q1; e = exp( q - qmax ); an += 1.0; asum += e; asum_ds += e * q1; asum_dss += e * q1*q1; asum_dw += e * ( -q2 )*epcd; asum_dww += e * ( 2.0 + q2 )*q2*epcd*epcd; asum_a += e * trig.cosa; asum_b += e * trig.sina; // asum_dsw += ?; } asum_a /= asum; asum_b /= asum; asum /= an; asum_ds /= an; asum_dss /= an; asum_dw /= an; asum_dww /= an; abcd = datatypes::ABCD( hl_a, hl_b, hl_c, hl_d ); phiw = datatypes::Phi_fom( atan2( asum_b, asum_a ), sqrt( asum_a*asum_a + asum_b*asum_b ) ); TargetResult r; r.r = cf*log(d) + sf2/d - log( asum ) - qmax; r.ds = (2.0*s*fc2)/d - asum_ds/asum; r.dw = epc*(cf/d-sf2/d2) - asum_dw/asum; r.dss = (2.0*fc2)/d - asum_dss/asum + Util::sqr(asum_ds/asum); r.dww = epc*epc*(-cf/d2+2.0*sf2/d3) - asum_dww/asum + Util::sqr(asum_dw/asum); r.dsw = Util::nan(); return r; } template SFweight_spline::SFweight_spline( HKL_data >& fb, HKL_data >& fd, HKL_data >& phiw, const HKL_data >& fo, const HKL_data >& fc, const HKL_data& usage, const int n_reflns, const int n_params ) { init( n_reflns, n_params ); (*this)( fb, fd, phiw, fo, fc, usage ); } template void SFweight_spline::init( const int n_reflns, const int n_params, const int n_phases ) { nreflns = n_reflns; nparams = n_params; hlterms.resize( n_phases ); for ( int a = 0; a < hlterms.size(); a++ ) { ftype phi = ( Util::twopi() * ftype(a)/ftype(hlterms.size()) ); hlterms[a].cosa = cos(phi); hlterms[a].sina = sin(phi); hlterms[a].cos2a = cos(2.0*phi); hlterms[a].sin2a = sin(2.0*phi); } } template bool SFweight_spline::operator() ( HKL_data >& fb, HKL_data >& fd, HKL_data >& phiw, const HKL_data >& fo0, const HKL_data >& fc0, const HKL_data& usage ) { TargetFo tgt; HKL_data > hl0( fo0.hkl_info() ), hl( fo0.hkl_info() ); return evaluate( fb, fd, phiw, hl, fo0, hl0, fc0, usage, tgt ); } template bool SFweight_spline::operator() ( HKL_data >& fb, HKL_data >& fd, HKL_data >& phiw, HKL_data >& hl, const HKL_data >& fo0, const HKL_data >& hl0, const HKL_data >& fc0, const HKL_data& usage ) { TargetHL tgt; return evaluate( fb, fd, phiw, hl, fo0, hl0, fc0, usage, tgt ); } template template bool SFweight_spline::evaluate( HKL_data >& fb, HKL_data >& fd, HKL_data >& phiw, HKL_data >& hl, const HKL_data >& fo0, const HKL_data >& hl0, const HKL_data >& fc0, const HKL_data& usage, F tgt ) { const HKL_info& hkls = fo0.base_hkl_info(); typedef clipper::HKL_info::HKL_reference_index HRI; bool status = false; // count reflections and determine number of params HKL_data flag(hkls); for ( HRI ih = flag.first(); !ih.last(); ih.next() ) flag[ih].flag() = (!fo0[ih].missing()) && (!fc0[ih].missing()) && (usage[ih].flag()!=SFweight_base::NONE); int npar_sig = num_params( flag ); int npar_scl = npar_sig; while ( npar_scl < 12 ) npar_scl *= 2; // prepare function BasisFn_spline basisfn( flag, npar_sig, 1.0 ); BasisFn_spline basissc( flag, npar_scl, 1.0 ); BasisFn_base::Fderiv dsdp, dwdp; TargetResult fn; scale_fo.resize( hkls.num_reflections() ); scale_fc.resize( hkls.num_reflections() ); value_s.resize( hkls.num_reflections() ); value_w.resize( hkls.num_reflections() ); // create E's for scaling HKL_data > eo( hkls ), ec( hkls ); for ( HRI ih = fo0.first(); !ih.last(); ih.next() ) { eo[ih].E() = fo0[ih].f() / sqrt( ih.hkl_class().epsilon() ); ec[ih].E() = fc0[ih].f() / sqrt( ih.hkl_class().epsilon() ); eo[ih].sigE() = ec[ih].sigE() = 1.0; } // calc scale std::vector param_fo( basissc.num_params(), 1.0 ); TargetFn_scaleEsq > tfn_fo( eo ); ResolutionFn rfn_fo( hkls, basissc, tfn_fo, param_fo ); param_fo = rfn_fo.params(); std::vector param_fc( basissc.num_params(), 1.0 ); TargetFn_scaleEsq > tfn_fc( ec ); ResolutionFn rfn_fc( hkls, basissc, tfn_fc, param_fc ); param_fc = rfn_fc.params(); // prescale Fo, Fc HKL_data > fo = fo0; HKL_data > fc = fc0; for ( HRI ih = fo0.first(); !ih.last(); ih.next() ) { scale_fo[ ih.index() ] = sqrt( basissc.f_s( ih.invresolsq(), param_fo ) ); scale_fc[ ih.index() ] = sqrt( basissc.f_s( ih.invresolsq(), param_fc ) ); fo[ih].scale( scale_fo[ ih.index() ] ); fc[ih].scale( scale_fc[ ih.index() ] ); } // make first estimate of s param_s = std::vector( npar_sig, 1.0 ); // make first estimate of w HKL_data > ftmp( hkls ); for ( HRI ih = flag.first(); !ih.last(); ih.next() ) if ( flag[ih].flag() ) ftmp[ih].f() = ftmp[ih].sigf() = pow( fo[ih].f() - sqrt(basisfn.f_s(ih.invresolsq(),param_s))*fc[ih].f(), 2.0 ) / ih.hkl_class().epsilonc(); TargetFn_meanFnth > target_w( ftmp, 1.0 ); ResolutionFn rfn2( hkls, basisfn, target_w, param_w ); param_w = rfn2.params(); //for ( int i = 0; i < npar_sig; i++ ) std::cout << i << " " << param_s[i] << " \t" << param_w[i] << "\n"; // smooth the error term for ( int i = 0; i < npar_sig-1; i++ ) param_w[i] = Util::max( param_w[i], 0.5*param_w[i+1] ); //for ( int i = 0; i < npar_sig; i++ ) std::cout << i << " " << param_s[i] << " \t" << param_w[i] << "\n"; ftype ll, ll_old = 1.0e30; // now 25 cycles to refine s and w int c = 0, clim = 25; for ( c = 0; c < clim; c++ ) { std::vector grad_s( npar_sig, 0.0 ), shft_s( npar_sig, 0.0 ); std::vector grad_w( npar_sig, 0.0 ), shft_w( npar_sig, 0.0 ); Matrix curv_s( npar_sig, npar_sig, 0.0 ); Matrix curv_w( npar_sig, npar_sig, 0.0 ); ll = 0.0; // build matrices for ( HRI ih = flag.first(); !ih.last(); ih.next() ) if ( flag[ih].flag() ) { dsdp = basisfn.fderiv_s( ih.invresolsq(), param_s ); dwdp = basisfn.fderiv_s( ih.invresolsq(), param_w ); fn = tgt( ih.hkl_class(), fo[ih], hl0[ih], fc[ih], dsdp.f, dwdp.f, hlterms ); //if ( Util::isnan(fn.r) ) std::cout << ih.hkl().format() << fo[ih].f() << " " << fo[ih].sigf() << " " << fc[ih].f() << " " << fc[ih].missing() << flag[ih].missing() << " " << hl0[ih].a() << " " << hl0[ih].b() << " " << hl0[ih].c() << " " << hl0[ih].d() << " " << dsdp.f << " " << dwdp.f << " \tFo,SIGo,Fc,missing\n"; ll += fn.r; for ( int i = 0; i < npar_sig; i++ ) { grad_s[i] += fn.ds * dsdp.df[i]; grad_w[i] += fn.dw * dwdp.df[i]; //for ( int j = 0; j < npar_sig; j++ ) { for ( int j = Util::max(i-1,0); j <= Util::min(i+1,npar_sig-1); j++ ) { curv_s(i,j) += dsdp.df2(i,j)*fn.ds + dsdp.df[i]*dsdp.df[j]*fn.dss; curv_w(i,j) += dwdp.df2(i,j)*fn.dw + dwdp.df[i]*dwdp.df[j]*fn.dww; } } } //std::cout << c << "\t" << ll << "\n"; if ( ll > ll_old ) break; // break on divergence shft_s = curv_s.solve( grad_s ); shft_w = curv_w.solve( grad_w ); for ( int i = 0; i < npar_sig; i++ ) { //std::cout << i << " \t" << param_s[i] << " \t" << param_w[i] << " \t" << shft_s[i] << " \t" << shft_w[i] << "\n"; // soft buffers to prevent negatives param_s[i] -= Util::min( shft_s[i], 0.25*param_s[i] ); param_w[i] -= Util::min( shft_w[i], 0.25*param_w[i] ); } if ( ll / ll_old > 0.999999 ) { status=true; break; } // break on convergence ll_old = ll; } // store s,w for ( HRI ih = fo0.first(); !ih.last(); ih.next() ) { value_s[ih.index()] = basisfn.f_s( ih.invresolsq(), param_s ); value_w[ih.index()] = basisfn.f_s( ih.invresolsq(), param_w ); } // calculate map coeffs and FOM reevaluate( fb, fd, phiw, hl, fo0, hl0, fc0, usage, tgt ); return status; } template template bool SFweight_spline::reevaluate( HKL_data >& fb, HKL_data >& fd, HKL_data >& phiw, HKL_data >& hl, const HKL_data >& fo0, const HKL_data >& hl0, const HKL_data >& fc0, const HKL_data& usage, F tgt ) { typedef clipper::HKL_info::HKL_reference_index HRI; // prepare function TargetResult fn; datatypes::F_sigF fo; datatypes::F_phi fc, twomfo, mfo, dfc, fzero(0.0,0.0); // calculate map coeffs and FOM llw = llf = 0.0; for ( HRI ih = fo0.first(); !ih.last(); ih.next() ) { // prescale Fo, Fc fo = fo0[ih]; fc = fc0[ih]; fo.scale( scale_fo[ih.index()] ); fc.scale( scale_fc[ih.index()] ); // get params an llk const ftype s = value_s[ih.index()]; const ftype w = value_w[ih.index()]; fn = tgt( ih.hkl_class(), fo, hl0[ih], fc, s, w, hlterms ); hl[ih] = tgt.abcd; phiw[ih] = tgt.phiw; mfo = datatypes::F_phi( tgt.phiw.fom() * fo.f(), tgt.phiw.phi() ); twomfo = datatypes::F_phi( 2.0 * mfo.f(), mfo.phi() ); dfc = datatypes::F_phi( s * fc.f(), fc.phi() ); if ( (!fo.missing()) && (!fc.missing()) ) { if ( usage[ih].flag()==SFweight_base::NONE ) llw += fn.r; else llf += fn.r; } // deal with all possibilities of missing and non-missing if ( !fc.missing() ) { if ( !fo.missing() ) { fb[ih] = twomfo - dfc; fd[ih] = mfo - dfc; } else { fb[ih] = dfc; fd[ih] = fzero; } } else { if ( !fo.missing() ) { fb[ih] = mfo; fd[ih] = fzero; } else { fb[ih] = fzero; fd[ih] = fzero; } } // undo scaling on fb, fd fb[ih].scale( 1.0/scale_fo[ih.index()] ); fd[ih].scale( 1.0/scale_fo[ih.index()] ); } return true; } template typename SFweight_spline::TargetResult SFweight_spline::targetfn( const HKL_class cls, const datatypes::F_sigF& fo0, const datatypes::F_phi& fc0, const ftype& s, const ftype& w ) const { const datatypes::ABCD hl0; TargetFo tgt; return tgt( cls, fo0, hl0, fc0, s, w, hlterms ); } template typename SFweight_spline::TargetResult SFweight_spline::targethl( const HKL_class cls, const datatypes::F_sigF& fo0, const datatypes::ABCD& hl0, const datatypes::F_phi& fc0, const ftype& s, const ftype& w ) const { TargetHL tgt; return tgt( cls, fo0, hl0, fc0, s, w, hlterms ); } template int SFweight_spline::num_params( const HKL_data& flag ) const { int npar; int n_use = flag.num_obs(); if ( nparams == 0 ) { npar = Util::max( n_use / nreflns, 2 ); } else if ( nreflns == 0 ) { npar = nparams; } else { ftype np1 = ftype(nparams+0.499); ftype np2 = ftype(n_use) / ftype(nreflns); ftype np = sqrt( np1*np1*np2*np2 / ( np1*np1+np2*np2 ) ); npar = Util::max( int(np), 2 ); } return npar; } template void SFweight_spline::debug() const { TargetResult r00, r01, r10, r11, rxx; Spacegroup p1( Spacegroup::P1 ); HKL_class cls; datatypes::F_sigF fo; datatypes::F_phi fc; fo.f() = 10.0; fo.sigf() = 2.0; fc.f() = 15.0; fc.phi() = 0.0; fo.sigf() = 0.0; //!!!!! ftype ds = 0.000001; ftype dw = 0.000001; datatypes::ABCD hl( 0.0, 0.0, 0.0, 0.0 ); for ( int h = 0; h < 2; h++ ) { cls = HKL_class( p1, HKL( h, 0, 0 ) ); std::cout << "\nCentric? " << cls.centric() << " epsc " << cls.epsilonc() << "\n"; for ( ftype w = 10.0; w < 1000.0; w *= 3.0 ) for ( ftype s = 0.4; s < 2.0; s *= 2.0 ) { rxx = targethl( cls, fo, hl, fc, s, w ); r00 = targetfn( cls, fo, fc, s, w ); r01 = targetfn( cls, fo, fc, s, w+dw ); r10 = targetfn( cls, fo, fc, s+ds, w ); r11 = targetfn( cls, fo, fc, s+ds, w+dw ); std::cout << w << " " << s << "\t" << r00.r << " " << r01.r << " " << r10.r << " " << r11.r << " " << rxx.r << "\n"; std::cout << (r10.r-r00.r)/ds << "\t" << r00.ds << "\n"; std::cout << (r01.r-r00.r)/dw << "\t" << r00.dw << "\n"; std::cout << (r10.ds-r00.ds)/ds << "\t" << r00.dss << "\n"; std::cout << (r01.dw-r00.dw)/dw << "\t" << r00.dww << "\n"; std::cout << (r01.ds-r00.ds)/dw << "\t" << r00.dsw << "\n"; std::cout << (r10.dw-r00.dw)/ds << "\t" << r00.dsw << "\n"; } } for ( int h = 0; h < 2; h++ ) { cls = HKL_class( p1, HKL( h, 0, 0 ) ); std::cout << "\nCentric? " << cls.centric() << " epsc " << cls.epsilonc() << "\n"; for ( ftype w = 10.0; w < 1000.0; w *= 3.0 ) for ( ftype s = 0.4; s < 2.0; s *= 2.0 ) { rxx = targetfn( cls, fo, fc, s, w ); r00 = targethl( cls, fo, hl, fc, s, w ); r01 = targethl( cls, fo, hl, fc, s, w+dw ); r10 = targethl( cls, fo, hl, fc, s+ds, w ); r11 = targethl( cls, fo, hl, fc, s+ds, w+dw ); std::cout << w << " " << s << "\t" << r00.r << " " << r01.r << " " << r10.r << " " << r11.r << " " << rxx.r << "\n"; std::cout << (r10.r-r00.r)/ds << "\t" << r00.ds << "\n"; std::cout << (r01.r-r00.r)/dw << "\t" << r00.dw << "\n"; std::cout << (r10.ds-r00.ds)/ds << "\t" << r00.dss << "\n"; std::cout << (r01.dw-r00.dw)/dw << "\t" << r00.dww << "\n"; std::cout << (r01.ds-r00.ds)/dw << "\t" << r00.dsw << "\n"; std::cout << (r10.dw-r00.dw)/ds << "\t" << r00.dsw << "\n"; } } } // compile templates template class SFweight_spline; template class SFweight_spline; } // namespace clipper clipper-2.1/clipper/contrib/originmatch.h0000644000374100011300000000627510736662166015527 00000000000000/*! \file originmatch.h Header file for origin matching function object */ //C Copyright (C) 2000-2006 Kevin Cowtan and University of York //L //L This library is free software and is distributed under the terms //L and conditions of version 2.1 of the GNU Lesser General Public //L Licence (LGPL) with the following additional clause: //L //L `You may also combine or link a "work that uses the Library" to //L produce a work containing portions of the Library, and distribute //L that work under terms of your choice, provided that you give //L prominent notice with each copy of the work that the specified //L version of the Library is used in it, and that you include or //L provide public access to the complete corresponding //L machine-readable source code for the Library including whatever //L changes were used in the work. (i.e. If you make changes to the //L Library you must distribute those, but you do not need to //L distribute source or object code to those portions of the work //L not covered by this licence.)' //L //L Note that this clause grants an additional right and does not impose //L any additional restriction, and so does not affect compatibility //L with the GNU General Public Licence (GPL). If you wish to negotiate //L other terms, please contact the maintainer. //L //L You can redistribute it and/or modify the library under the terms of //L the GNU Lesser General Public License as published by the Free Software //L Foundation; either version 2.1 of the License, or (at your option) any //L later version. //L //L This library is distributed in the hope that it will be useful, but //L WITHOUT ANY WARRANTY; without even the implied warranty of //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU //L Lesser General Public License for more details. //L //L You should have received a copy of the CCP4 licence and/or GNU //L Lesser General Public License along with this library; if not, write //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. //L The GNU Lesser General Public can also be obtained by writing to the //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, //L MA 02111-1307 USA #ifndef CLIPPER_ORIGINMATCH #define CLIPPER_ORIGINMATCH #include "function_object_bases.h" namespace clipper { //! Origin matching method using fast translation function. /*! Perform origin matching by performing a fast translation function. Both hands are tested if possible. \ingroup g_funcobj */ template class OriginMatch : public OriginMatch_base { public: //! constructor OriginMatch( const ftype resol_limit = 0.1 ) : limit(resol_limit) {} //! constructor: shorthand for constructor+operator OriginMatch( bool& invert, Coord_frac& shift, const HKL_data >& fphi1, const HKL_data >& fphi2, const ftype resol_limit = 0.1 ) : limit(resol_limit) { (*this)( invert, shift, fphi1, fphi2 ); } bool operator() ( bool& invert, Coord_frac& shift, const HKL_data >& fphi1, const HKL_data >& fphi2 ) const; private: ftype limit; }; } // namespace clipper #endif clipper-2.1/clipper/clipper-ccp4.h0000644000374100011300000000034410736662166014037 00000000000000/* Clipper header file */ /* (C) 2000-2002 Kevin Cowtan */ #ifndef CLIPPER_CCP4_H #define CLIPPER_CCP4_H #include "clipper/ccp4/ccp4_utils.h" #include "clipper/ccp4/ccp4_mtz_io.h" #include "clipper/ccp4/ccp4_map_io.h" #endif clipper-2.1/README0000644000374100011300000000105610736662166010624 00000000000000The aim of the project is to produce a set of object-oriented libraries for the organisation of crystallographic data and the performance of crystallographic computation. The libraries are designed as a framework for new crystallographic software, which will allow the full power of modern programming techniques to be exploited by the developer. This will lead to greater functionality from simpler code which will be easier to develop and debug. For installation instructions and documentation see: http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html clipper-2.1/INSTALL0000644000374100011300000002243211372264321010762 00000000000000Installation Instructions ************************* Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005 Free Software Foundation, Inc. This file is free documentation; the Free Software Foundation gives unlimited permission to copy, distribute and modify it. Basic Installation ================== These are generic installation instructions. The `configure' shell script attempts to guess correct values for various system-dependent variables used during compilation. It uses those values to create a `Makefile' in each directory of the package. It may also create one or more `.h' files containing system-dependent definitions. Finally, it creates a shell script `config.status' that you can run in the future to recreate the current configuration, and a file `config.log' containing compiler output (useful mainly for debugging `configure'). It can also use an optional file (typically called `config.cache' and enabled with `--cache-file=config.cache' or simply `-C') that saves the results of its tests to speed up reconfiguring. (Caching is disabled by default to prevent problems with accidental use of stale cache files.) If you need to do unusual things to compile the package, please try to figure out how `configure' could check whether to do them, and mail diffs or instructions to the address given in the `README' so they can be considered for the next release. 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Run `configure --help' for more details. clipper-2.1/examples/0000777000374100011300000000000011372264353011635 500000000000000clipper-2.1/examples/csymmatch.cpp0000644000374100011300000002215311226615230014240 00000000000000// Clipper app to move one model to match another using xtal symmetry /* Copyright 2007 Kevin Cowtan & University of York all rights reserved */ #include #include #include #include class MapFilterFn_g5 : public clipper::MapFilterFn_base { public: clipper::ftype operator() ( const clipper::ftype& radius ) const { return exp(-radius*radius/50.0); } }; int main( int argc, char** argv ) { CCP4Program prog( "csymmatch", "0.3", "$Date: 2009/07/13" ); // defaults clipper::String title; clipper::String ippdbref = "NONE"; clipper::String ippdb = "NONE"; clipper::String oppdb = "symmatch.pdb"; double crad = 2.0; bool omatch = false; // command input CCP4CommandInput args( argc, argv, true ); int arg = 0; while ( ++arg < args.size() ) { if ( args[arg] == "-title" ) { if ( ++arg < args.size() ) title = args[arg]; } else if ( args[arg] == "-pdbin-ref" ) { if ( ++arg < args.size() ) ippdbref = args[arg]; } else if ( args[arg] == "-pdbin" ) { if ( ++arg < args.size() ) ippdb = args[arg]; } else if ( args[arg] == "-pdbout" ) { if ( ++arg < args.size() ) oppdb = args[arg]; } else if ( args[arg] == "-connectivity-radius" ) { if ( ++arg < args.size() ) crad = clipper::String(args[arg]).f(); } else if ( args[arg] == "-origin-hand" ) { omatch = true; } else { std::cout << "Unrecognized:\t" << args[arg] << "\n"; args.clear(); } } if ( args.size() <= 1 ) { std::cout << "Usage: csymmatch\n\t-pdbin-ref \n\t-pdbin \n\t-pdbout \n\t-connectivity-radius \n\t-origin-hand\nApply symmetry and cell shifts to each chain in 'pdbin' to obtain the best match to 'pdbin-ref'.\n"; exit(1); } // atomic models const int mmdbflags = MMDBF_IgnoreBlankLines | MMDBF_IgnoreDuplSeqNum | MMDBF_IgnoreNonCoorPDBErrors | MMDBF_IgnoreRemarks; clipper::MMDBfile mmdbref, mmdbwrk; clipper::MiniMol molref, molwrk; mmdbref.SetFlag( mmdbflags ); mmdbwrk.SetFlag( mmdbflags ); mmdbref.read_file( ippdbref ); mmdbwrk.read_file( ippdb ); mmdbref.import_minimol( molref ); mmdbwrk.import_minimol( molwrk ); clipper::Spacegroup spg1 = clipper::Spacegroup(clipper::Spacegroup::P1); clipper::Spacegroup spgr = mmdbwrk.spacegroup(); clipper::Cell cell = mmdbwrk.cell(); if ( spgr.is_null() ) { std::cerr << "Cannot get spacegroup, check PDB file and CCP4 setup" << std::endl; exit(1); } // user output std::cout << std::endl << "Reference molecule:" << std::endl; if ( !mmdbref.spacegroup().is_null() ) std::cout << " Spacegroup: " << mmdbref.spacegroup().symbol_hm() << std::endl; if ( !mmdbref.cell().is_null() ) std::cout << " Unit cell: " << mmdbref.cell().format() << std::endl; std::cout << "Moving molecule:" << std::endl; if ( !mmdbwrk.spacegroup().is_null() ) std::cout << " Spacegroup: " << mmdbwrk.spacegroup().symbol_hm() << std::endl; if ( !mmdbwrk.cell().is_null() ) std::cout << " Unit cell: " << mmdbwrk.cell().format() << std::endl; std::cout << std::endl; // do origin matching if required if ( omatch ) { // calculate structure factors clipper::Spacegroup rspgr = molref.spacegroup(); clipper::Cell rcell = molref.cell(); clipper::Resolution rreso( 3.0 ); clipper::HKL_sampling hkls( rcell, rreso ); clipper::HKL_data fphi1( rspgr, rcell, hkls ); clipper::HKL_data fphi2( rspgr, rcell, hkls ); clipper::SFcalc_iso_fft sfc; clipper::Atom_list atoms1 = molref.atom_list(); clipper::Atom_list atoms2 = molwrk.atom_list(); sfc( fphi1, atoms1 ); sfc( fphi2, atoms2 ); // get origin shift bool invert = false; clipper::Coord_frac x( 0.0, 0.0, 0.0 ); clipper::OriginMatch( invert, x, fphi1, fphi2 ); if ( invert ) std::cout << std::endl << " Change of hand : YES" << std::endl; else std::cout << std::endl << " Change of hand : NO" << std::endl; std::cout << " Change of origin: " << x.format() << std::endl << std::endl; // now move the atoms clipper::Mat33<> rot = clipper::Mat33<>::identity(); clipper::Coord_orth trn = x.coord_orth( rcell ); if ( invert ) rot = clipper::Mat33<>(-1.0,0.0,0.0,0.0,-1.0,0.0,0.0,0.0,-1.0); clipper::RTop_orth rt( rot, trn ); molwrk.transform( rt ); } // calculate extent of model clipper::Atom_list atomr = molref.atom_list(); clipper::Range urange, vrange, wrange; clipper::Coord_frac cfr( 0.0, 0.0, 0.0 ); for ( int i = 0; i < atomr.size(); i++ ) { clipper::Coord_frac cf = atomr[i].coord_orth().coord_frac( cell ); cfr += cf; urange.include( cf.u() ); vrange.include( cf.v() ); wrange.include( cf.w() ); } clipper::Coord_frac cf0( urange.min(), vrange.min(), wrange.min() ); clipper::Coord_frac cf1( urange.max(), vrange.max(), wrange.max() ); cfr = (1.0/double(atomr.size())) * cfr; // calculate mask using wrk cell and ref atoms clipper::Resolution reso( 5.0 ); clipper::Grid_sampling grid( spg1, cell, reso ); clipper::Grid_range grng( grid, cf0, cf1 ); grng.add_border(4); clipper::NXmap nxmap( cell, grid, grng ), nxflt( cell, grid, grng ); clipper::EDcalc_mask maskcalc( 2.0 ); nxmap = 0.0; maskcalc( nxmap, atomr ); MapFilterFn_g5 fn; clipper::MapFilter_fft fltr( fn, 1.0, clipper::MapFilter_fft::Relative ); fltr( nxflt, nxmap ); // make a list of work atom groups std::vector > groups; for ( int c = 0; c < molwrk.size(); c++ ) { std::vector group; for ( int r0 = 0; r0 < molwrk[c].size(); r0++ ) { // add this monomer for ( int a0 = 0; a0 < molwrk[c][r0].size(); a0++ ) group.push_back( clipper::MAtomIndex(c,r0,a0) ); // check if next monomer is connected to this bool iscon = false; int r1 = r0 + 1; if ( r1 < molwrk[c].size() ) { for ( int a0 = 0; a0 < molwrk[c][r0].size(); a0++ ) for ( int a1 = 0; a1 < molwrk[c][r1].size(); a1++ ) if ( ( molwrk[c][r0][a0].coord_orth() - molwrk[c][r1][a1].coord_orth() ).lengthsq() < crad*crad ) iscon = true; } // if not, add this group if ( !iscon ) { groups.push_back( group ); group.clear(); } } } // now score each chain, symmetry and offset in turn for ( int g = 0; g < groups.size(); g++ ) { const std::vector& group = groups[g]; clipper::Atom_list atoms; for ( int i = 0; i < group.size(); i++ ) atoms.push_back( molwrk[group[i].polymer()][group[i].monomer()] [group[i].atom()] ); double bestscr = 0.0; int bestsym = 0; clipper::Coord_frac bestoff( 0.0, 0.0, 0.0 ); const clipper::Coord_frac cfh( 0.5, 0.5, 0.5 ); for ( int sym = 0; sym < spgr.num_symops(); sym++ ) { clipper::Atom_list atomw = atoms; clipper::RTop_orth rtop = spgr.symop(sym).rtop_orth( cell ); clipper::Coord_orth cow( 0.0, 0.0, 0.0 ); for ( int a = 0; a < atomw.size(); a++ ) { atomw[a].transform( rtop ); cow += atomw[a].coord_orth(); } if ( atomw.size() > 0 ) cow = (1.0/double(atomw.size())) * cow; clipper::Coord_frac cfw = cow.coord_frac( cell ); clipper::Coord_frac cfwt = cfw.lattice_copy_near( cfr - cfh ); clipper::Coord_frac off0 = cfwt - cfw; // try offsets for ( double du = 0.0; du <= 1.01; du += 1.0 ) for ( double dv = 0.0; dv < 1.01; dv += 1.0 ) for ( double dw = 0.0; dw < 1.01; dw += 1.0 ) { clipper::Coord_frac off( rint( off0.u() ) + du, rint( off0.v() ) + dv, rint( off0.w() ) + dw ); clipper::Coord_orth ofo = off.coord_orth( cell ); double scr = 0.0; for ( int a = 0; a < atomw.size(); a++ ) { clipper::Coord_orth coa = atomw[a].coord_orth() + ofo; clipper::Coord_grid cga = nxflt.coord_map( coa ).coord_grid(); if ( nxflt.in_map( cga ) ) scr += nxflt.get_data( cga ); } if ( scr > bestscr ) { bestscr = scr; bestsym = sym; bestoff = off; } } } // now transform using the best operator clipper::Coord_orth cot = bestoff.coord_orth( cell ); clipper::RTop_orth rtop = spgr.symop(bestsym).rtop_orth( cell ); rtop = clipper::RTop_orth( rtop.rot(), rtop.trn()+cot ); for ( int i = 0; i < group.size(); i++ ) molwrk[group[i].polymer()][group[i].monomer()] [group[i].atom()].transform( rtop ); // user output clipper::MAtomIndex g0 = group.front(); clipper::MAtomIndex g1 = group.back(); std::cout << "Chain: " << molwrk[g0.polymer()].id() << " " << molwrk[g0.polymer()][g0.monomer()].id() << "-" << molwrk[g1.polymer()][g1.monomer()].id() << " will be transformed as follows:" << std::endl << " Symmetry operator: " << spgr.symop(bestsym).format() << std::endl << " Lattice shift: " << bestoff.format() << std::endl; } // write file mmdbwrk.export_minimol( molwrk ); mmdbwrk.write_file( oppdb ); } clipper-2.1/examples/clipper_test.cpp0000644000374100011300000000132711110525543014744 00000000000000// Clipper app to run self-tests /* Copyright 2003-2004 Kevin Cowtan & University of York all rights reserved */ #include #include #include #include extern "C" { #include } int main( int argc, char** argv ) { // do self tests std::cout << "Test core:\n"; clipper::Test_core test_core; bool result_core = test_core(); if ( result_core ) std::cout << "OK\n"; std::cout << "Test contrib:\n"; clipper::Test_contrib test_contrib; bool result_contrib = test_contrib(); if ( result_contrib ) std::cout << "OK\n"; // done self tests // error exit code if ( !( result_core && result_contrib ) ) exit(1); } clipper-2.1/examples/cinvfft.cpp0000644000374100011300000000414211362102650013703 00000000000000// Clipper app to perform inverse ffts /* Copyright 2003-2004 Kevin Cowtan & University of York all rights reserved */ #include #include extern "C" { #include } int main( int argc, char** argv ) { CCP4Program prog( "cinvfft", "0.1", "$Date: 2004/06/01" ); // defaults clipper::String title; clipper::String ipmap = "NONE"; clipper::String ipfile = "NONE"; clipper::String opfile = "NONE"; clipper::String opcol = "invfft"; // command input CCP4CommandInput args( argc, argv, true ); int arg = 0; while ( ++arg < args.size() ) { if ( args[arg] == "-title" ) { if ( ++arg < args.size() ) title = args[arg]; } else if ( args[arg] == "-mapin" ) { if ( ++arg < args.size() ) ipmap = args[arg]; } else if ( args[arg] == "-mtzin" ) { if ( ++arg < args.size() ) ipfile = args[arg]; } else if ( args[arg] == "-mtzout" ) { if ( ++arg < args.size() ) opfile = args[arg]; } else if ( args[arg] == "-colout" ) { if ( ++arg < args.size() ) opcol = args[arg]; } else { std::cout << "Unrecognized:\t" << args[arg] << "\n"; args.clear(); } } if ( args.size() <= 1 ) { std::cout << "Usage: cinvfft\n\t-mapin \n\t-mtzin \n\t-mtzout \n\t-colout \nInverse FFT\n"; exit(1); } // make data objects clipper::CCP4MTZfile mtzin, mtzout; clipper::MTZcrystal cxtl; clipper::Xmap xmap; clipper::HKL_info hkls; mtzin.set_column_label_mode( clipper::CCP4MTZfile::Legacy ); // open file mtzin.open_read( ipfile ); if ( opcol[0] != '/' ) opcol = mtzin.assigned_paths().back().notail()+"/"+opcol; mtzin.import_hkl_info( hkls ); mtzin.import_crystal( cxtl, opcol ); clipper::HKL_data fphi( hkls, cxtl ); mtzin.close_read(); // import xmap clipper::CCP4MAPfile mapin; mapin.open_read( ipmap ); mapin.import_xmap( xmap ); mapin.close_read(); // calc fft xmap.fft_to( fphi ); // output data mtzout.open_append( ipfile, opfile ); mtzout.export_hkl_data( fphi, opcol ); mtzout.close_append(); } clipper-2.1/examples/ftplib.c0000644000374100011300000006610010736662167013210 00000000000000/***************************************************************************/ /* */ /* ftplib.c - callable ftp access routines */ /* Copyright (C) 1996-2000 Thomas Pfau, pfau@cnj.digex.net */ /* 73 Catherine Street, South Bound Brook, NJ, 08880 */ /* */ /* This library is free software; you can redistribute it and/or */ /* modify it under the terms of the GNU Library General Public */ /* License as published by the Free Software Foundation; either */ /* version 2 of the License, or (at your option) any later version. */ /* */ /* This library is distributed in the hope that it will be useful, */ /* but WITHOUT ANY WARRANTY; without even the implied warranty of */ /* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU */ /* Library General Public License for more details. */ /* */ /* You should have received a copy of the GNU Library General Public */ /* License along with this progam; if not, write to the */ /* Free Software Foundation, Inc., 59 Temple Place - Suite 330, */ /* Boston, MA 02111-1307, USA. */ /* */ /***************************************************************************/ #if defined(__unix__) || defined(__VMS) || defined (__APPLE__) || defined (unix) #include #endif #if defined(_WIN32) #include #include #endif #include #include #include #include #include #if defined(__unix__) || defined (__APPLE__) || defined (unix) #include #include #include #include #include #include #elif defined(VMS) #include #include #include #include #include #elif defined(_WIN32) #include #endif #define BUILDING_LIBRARY #include "ftplib.h" #if defined(_WIN32) #define SETSOCKOPT_OPTVAL_TYPE (const char *) #else #define SETSOCKOPT_OPTVAL_TYPE (void *) #endif #if defined(__osf__) #define SOCKLEN_TYPE int #else #define SOCKLEN_TYPE socklen_t #endif #define FTPLIB_BUFSIZ 8192 #define ACCEPT_TIMEOUT 30 #define FTPLIB_CONTROL 0 #define FTPLIB_READ 1 #define FTPLIB_WRITE 2 #if !defined FTPLIB_DEFMODE #define FTPLIB_DEFMODE FTPLIB_PASSIVE #endif struct NetBuf { char *cput,*cget; int handle; int cavail,cleft; char *buf; int dir; netbuf *ctrl; netbuf *data; int cmode; struct timeval idletime; FtpCallback idlecb; void *idlearg; int xfered; int cbbytes; int xfered1; char response[256]; }; static char *version = "ftplib Release 3.1-1 9/16/00, copyright 1996-2000 Thomas Pfau"; int ftplib_debug = 0; #if defined(__unix__) || defined(VMS) || defined (__APPLE__) || defined (unix) #define net_read read #define net_write write #define net_close close #elif defined(_WIN32) #define net_read(x,y,z) recv(x,y,z,0) #define net_write(x,y,z) send(x,y,z,0) #define net_close closesocket #endif #if defined(NEED_MEMCCPY) /* * VAX C does not supply a memccpy routine so I provide my own */ void *memccpy(void *dest, const void *src, int c, size_t n) { int i=0; const unsigned char *ip=src; unsigned char *op=dest; while (i < n) { if ((*op++ = *ip++) == c) break; i++; } if (i == n) return NULL; return op; } #endif #if defined(NEED_STRDUP) /* * strdup - return a malloc'ed copy of a string */ char *strdup(const char *src) { int l = strlen(src) + 1; char *dst = malloc(l); if (dst) strcpy(dst,src); return dst; } #endif /* * socket_wait - wait for socket to receive or flush data * * return 1 if no user callback, otherwise, return value returned by * user callback */ static int socket_wait(netbuf *ctl) { fd_set fd,*rfd = NULL,*wfd = NULL; struct timeval tv; int rv = 0; if ((ctl->dir == FTPLIB_CONTROL) || (ctl->idlecb == NULL)) return 1; if (ctl->dir == FTPLIB_WRITE) wfd = &fd; else rfd = &fd; FD_ZERO(&fd); do { FD_SET(ctl->handle,&fd); tv = ctl->idletime; rv = select(ctl->handle+1, rfd, wfd, NULL, &tv); if (rv == -1) { rv = 0; strncpy(ctl->ctrl->response, strerror(errno), sizeof(ctl->ctrl->response)); break; } else if (rv > 0) { rv = 1; break; } } while ((rv = ctl->idlecb(ctl, ctl->xfered, ctl->idlearg))); return rv; } /* * read a line of text * * return -1 on error or bytecount */ static int readline(char *buf,int max,netbuf *ctl) { int x,retval = 0; char *end,*bp=buf; int eof = 0; if ((ctl->dir != FTPLIB_CONTROL) && (ctl->dir != FTPLIB_READ)) return -1; if (max == 0) return 0; do { if (ctl->cavail > 0) { x = (max >= ctl->cavail) ? ctl->cavail : max-1; end = (char *)memccpy(bp,ctl->cget,'\n',x); if (end != NULL) x = end - bp; retval += x; bp += x; *bp = '\0'; max -= x; ctl->cget += x; ctl->cavail -= x; if (end != NULL) { bp -= 2; if (strcmp(bp,"\r\n") == 0) { *bp++ = '\n'; *bp++ = '\0'; --retval; } break; } } if (max == 1) { *buf = '\0'; break; } if (ctl->cput == ctl->cget) { ctl->cput = ctl->cget = ctl->buf; ctl->cavail = 0; ctl->cleft = FTPLIB_BUFSIZ; } if (eof) { if (retval == 0) retval = -1; break; } if (!socket_wait(ctl)) return retval; if ((x = net_read(ctl->handle,ctl->cput,ctl->cleft)) == -1) { perror("read"); retval = -1; break; } if (x == 0) eof = 1; ctl->cleft -= x; ctl->cavail += x; ctl->cput += x; } while (1); return retval; } /* * write lines of text * * return -1 on error or bytecount */ static int writeline(char *buf, int len, netbuf *nData) { int x, nb=0, w; char *ubp = buf, *nbp; char lc=0; if (nData->dir != FTPLIB_WRITE) return -1; nbp = nData->buf; for (x=0; x < len; x++) { if ((*ubp == '\n') && (lc != '\r')) { if (nb == FTPLIB_BUFSIZ) { if (!socket_wait(nData)) return x; w = net_write(nData->handle, nbp, FTPLIB_BUFSIZ); if (w != FTPLIB_BUFSIZ) { printf("net_write(1) returned %d, errno = %d\n", w, errno); return(-1); } nb = 0; } nbp[nb++] = '\r'; } if (nb == FTPLIB_BUFSIZ) { if (!socket_wait(nData)) return x; w = net_write(nData->handle, nbp, FTPLIB_BUFSIZ); if (w != FTPLIB_BUFSIZ) { printf("net_write(2) returned %d, errno = %d\n", w, errno); return(-1); } nb = 0; } nbp[nb++] = lc = *ubp++; } if (nb) { if (!socket_wait(nData)) return x; w = net_write(nData->handle, nbp, nb); if (w != nb) { printf("net_write(3) returned %d, errno = %d\n", w, errno); return(-1); } } return len; } /* * read a response from the server * * return 0 if first char doesn't match * return 1 if first char matches */ static int readresp(char c, netbuf *nControl) { char match[5]; if (readline(nControl->response,256,nControl) == -1) { perror("Control socket read failed"); return 0; } if (ftplib_debug > 1) fprintf(stderr,"%s",nControl->response); if (nControl->response[3] == '-') { strncpy(match,nControl->response,3); match[3] = ' '; match[4] = '\0'; do { if (readline(nControl->response,256,nControl) == -1) { perror("Control socket read failed"); return 0; } if (ftplib_debug > 1) fprintf(stderr,"%s",nControl->response); } while (strncmp(nControl->response,match,4)); } if (nControl->response[0] == c) return 1; return 0; } /* * FtpInit for stupid operating systems that require it (Windows NT) */ void FtpInit(void) { #if defined(_WIN32) WORD wVersionRequested; WSADATA wsadata; int err; wVersionRequested = MAKEWORD(1,1); if ((err = WSAStartup(wVersionRequested,&wsadata)) != 0) fprintf(stderr,"Network failed to start: %d\n",err); #endif } /* * FtpLastResponse - return a pointer to the last response received */ char *FtpLastResponse(netbuf *nControl) { if ((nControl) && (nControl->dir == FTPLIB_CONTROL)) return nControl->response; return NULL; } /* * FtpConnect - connect to remote server * * return 1 if connected, 0 if not */ int FtpConnect(const char *host, netbuf **nControl) { int sControl; struct sockaddr_in sin; struct hostent *phe; struct servent *pse; int on=1; netbuf *ctrl; char *lhost; char *pnum; memset(&sin,0,sizeof(sin)); sin.sin_family = AF_INET; lhost = strdup(host); pnum = strchr(lhost,':'); if (pnum == NULL) { #if defined(VMS) sin.sin_port = htons(21); #else if ((pse = getservbyname("ftp","tcp")) == NULL) { perror("getservbyname"); return 0; } sin.sin_port = pse->s_port; #endif } else { *pnum++ = '\0'; if (isdigit(*pnum)) sin.sin_port = htons(atoi(pnum)); else { pse = getservbyname(pnum,"tcp"); sin.sin_port = pse->s_port; } } if ((sin.sin_addr.s_addr = inet_addr(lhost)) == -1) { if ((phe = gethostbyname(lhost)) == NULL) { perror("gethostbyname"); return 0; } memcpy((char *)&sin.sin_addr, phe->h_addr, phe->h_length); } free(lhost); sControl = socket(PF_INET, SOCK_STREAM, IPPROTO_TCP); if (sControl == -1) { perror("socket"); return 0; } if (setsockopt(sControl,SOL_SOCKET,SO_REUSEADDR, SETSOCKOPT_OPTVAL_TYPE &on, sizeof(on)) == -1) { perror("setsockopt"); net_close(sControl); return 0; } if (connect(sControl, (struct sockaddr *)&sin, sizeof(sin)) == -1) { perror("connect"); net_close(sControl); return 0; } ctrl = (netbuf *)calloc(1,sizeof(netbuf)); if (ctrl == NULL) { perror("calloc"); net_close(sControl); return 0; } ctrl->buf = (char *)malloc(FTPLIB_BUFSIZ); if (ctrl->buf == NULL) { perror("calloc"); net_close(sControl); free(ctrl); return 0; } ctrl->handle = sControl; ctrl->dir = FTPLIB_CONTROL; ctrl->ctrl = NULL; ctrl->cmode = FTPLIB_DEFMODE; ctrl->idlecb = NULL; ctrl->idletime.tv_sec = ctrl->idletime.tv_usec = 0; ctrl->idlearg = NULL; ctrl->xfered = 0; ctrl->xfered1 = 0; ctrl->cbbytes = 0; if (readresp('2', ctrl) == 0) { net_close(sControl); free(ctrl->buf); free(ctrl); return 0; } *nControl = ctrl; return 1; } /* * FtpOptions - change connection options * * returns 1 if successful, 0 on error */ int FtpOptions(int opt, long val, netbuf *nControl) { int v,rv=0; switch (opt) { case FTPLIB_CONNMODE: v = (int) val; if ((v == FTPLIB_PASSIVE) || (v == FTPLIB_PORT)) { nControl->cmode = v; rv = 1; } break; case FTPLIB_CALLBACK: nControl->idlecb = (FtpCallback) val; rv = 1; break; case FTPLIB_IDLETIME: v = (int) val; rv = 1; nControl->idletime.tv_sec = v / 1000; nControl->idletime.tv_usec = (v % 1000) * 1000; break; case FTPLIB_CALLBACKARG: rv = 1; nControl->idlearg = (void *) val; break; case FTPLIB_CALLBACKBYTES: rv = 1; nControl->cbbytes = (int) val; break; } return rv; } /* * FtpSendCmd - send a command and wait for expected response * * return 1 if proper response received, 0 otherwise */ static int FtpSendCmd(const char *cmd, char expresp, netbuf *nControl) { char buf[256]; if (nControl->dir != FTPLIB_CONTROL) return 0; if (ftplib_debug > 2) fprintf(stderr,"%s\n",cmd); if ((strlen(cmd) + 3) > sizeof(buf)) return 0; sprintf(buf,"%s\r\n",cmd); if (net_write(nControl->handle,buf,strlen(buf)) <= 0) { perror("write"); return 0; } return readresp(expresp, nControl); } /* * FtpLogin - log in to remote server * * return 1 if logged in, 0 otherwise */ int FtpLogin(const char *user, const char *pass, netbuf *nControl) { char tempbuf[64]; if (((strlen(user) + 7) > sizeof(tempbuf)) || ((strlen(pass) + 7) > sizeof(tempbuf))) return 0; sprintf(tempbuf,"USER %s",user); if (!FtpSendCmd(tempbuf,'3',nControl)) { if (nControl->response[0] == '2') return 1; return 0; } sprintf(tempbuf,"PASS %s",pass); return FtpSendCmd(tempbuf,'2',nControl); } /* * FtpOpenPort - set up data connection * * return 1 if successful, 0 otherwise */ static int FtpOpenPort(netbuf *nControl, netbuf **nData, int mode, int dir) { int sData; union { struct sockaddr sa; struct sockaddr_in in; } sin; struct linger lng = { 0, 0 }; SOCKLEN_TYPE l; int on=1; netbuf *ctrl; char *cp; unsigned int v[6]; char buf[256]; if (nControl->dir != FTPLIB_CONTROL) return -1; if ((dir != FTPLIB_READ) && (dir != FTPLIB_WRITE)) { sprintf(nControl->response, "Invalid direction %d\n", dir); return -1; } if ((mode != FTPLIB_ASCII) && (mode != FTPLIB_IMAGE)) { sprintf(nControl->response, "Invalid mode %c\n", mode); return -1; } l = sizeof(sin); if (nControl->cmode == FTPLIB_PASSIVE) { memset(&sin, 0, l); sin.in.sin_family = AF_INET; if (!FtpSendCmd("PASV",'2',nControl)) return -1; cp = strchr(nControl->response,'('); if (cp == NULL) return -1; cp++; sscanf(cp,"%u,%u,%u,%u,%u,%u",&v[2],&v[3],&v[4],&v[5],&v[0],&v[1]); sin.sa.sa_data[2] = v[2]; sin.sa.sa_data[3] = v[3]; sin.sa.sa_data[4] = v[4]; sin.sa.sa_data[5] = v[5]; sin.sa.sa_data[0] = v[0]; sin.sa.sa_data[1] = v[1]; } else { if (getsockname(nControl->handle, &sin.sa, &l) < 0) { perror("getsockname"); return 0; } } sData = socket(PF_INET,SOCK_STREAM,IPPROTO_TCP); if (sData == -1) { perror("socket"); return -1; } if (setsockopt(sData,SOL_SOCKET,SO_REUSEADDR, SETSOCKOPT_OPTVAL_TYPE &on,sizeof(on)) == -1) { perror("setsockopt"); net_close(sData); return -1; } if (setsockopt(sData,SOL_SOCKET,SO_LINGER, SETSOCKOPT_OPTVAL_TYPE &lng,sizeof(lng)) == -1) { perror("setsockopt"); net_close(sData); return -1; } if (nControl->cmode == FTPLIB_PASSIVE) { if (connect(sData, &sin.sa, sizeof(sin.sa)) == -1) { perror("connect"); net_close(sData); return -1; } } else { sin.in.sin_port = 0; if (bind(sData, &sin.sa, sizeof(sin)) == -1) { perror("bind"); net_close(sData); return 0; } if (listen(sData, 1) < 0) { perror("listen"); net_close(sData); return 0; } if (getsockname(sData, &sin.sa, &l) < 0) return 0; sprintf(buf, "PORT %d,%d,%d,%d,%d,%d", (unsigned char) sin.sa.sa_data[2], (unsigned char) sin.sa.sa_data[3], (unsigned char) sin.sa.sa_data[4], (unsigned char) sin.sa.sa_data[5], (unsigned char) sin.sa.sa_data[0], (unsigned char) sin.sa.sa_data[1]); if (!FtpSendCmd(buf,'2',nControl)) { net_close(sData); return 0; } } ctrl = (netbuf *)calloc(1,sizeof(netbuf)); if (ctrl == NULL) { perror("calloc"); net_close(sData); return -1; } if ((mode == 'A') && ((ctrl->buf = (char *)malloc(FTPLIB_BUFSIZ)) == NULL)) { perror("calloc"); net_close(sData); free(ctrl); return -1; } ctrl->handle = sData; ctrl->dir = dir; ctrl->idletime = nControl->idletime; ctrl->idlearg = nControl->idlearg; ctrl->xfered = 0; ctrl->xfered1 = 0; ctrl->cbbytes = nControl->cbbytes; if (ctrl->idletime.tv_sec || ctrl->idletime.tv_usec || ctrl->cbbytes) ctrl->idlecb = nControl->idlecb; else ctrl->idlecb = NULL; *nData = ctrl; return 1; } /* * FtpAcceptConnection - accept connection from server * * return 1 if successful, 0 otherwise */ static int FtpAcceptConnection(netbuf *nData, netbuf *nControl) { int sData; struct sockaddr addr; SOCKLEN_TYPE l; int i; struct timeval tv; fd_set mask; int rv; FD_ZERO(&mask); FD_SET(nControl->handle, &mask); FD_SET(nData->handle, &mask); tv.tv_usec = 0; tv.tv_sec = ACCEPT_TIMEOUT; i = nControl->handle; if (i < nData->handle) i = nData->handle; i = select(i+1, &mask, NULL, NULL, &tv); if (i == -1) { strncpy(nControl->response, strerror(errno), sizeof(nControl->response)); net_close(nData->handle); nData->handle = 0; rv = 0; } else if (i == 0) { strcpy(nControl->response, "timed out waiting for connection"); net_close(nData->handle); nData->handle = 0; rv = 0; } else { if (FD_ISSET(nData->handle, &mask)) { l = sizeof(addr); sData = accept(nData->handle, &addr, &l); i = errno; net_close(nData->handle); if (sData > 0) { rv = 1; nData->handle = sData; } else { strncpy(nControl->response, strerror(i), sizeof(nControl->response)); nData->handle = 0; rv = 0; } } else if (FD_ISSET(nControl->handle, &mask)) { net_close(nData->handle); nData->handle = 0; readresp('2', nControl); rv = 0; } } return rv; } /* * FtpAccess - return a handle for a data stream * * return 1 if successful, 0 otherwise */ int FtpAccess(const char *path, int typ, int mode, netbuf *nControl, netbuf **nData) { char buf[256]; int dir; if ((path == NULL) && ((typ == FTPLIB_FILE_WRITE) || (typ == FTPLIB_FILE_READ))) { sprintf(nControl->response, "Missing path argument for file transfer\n"); return 0; } sprintf(buf, "TYPE %c", mode); if (!FtpSendCmd(buf, '2', nControl)) return 0; switch (typ) { case FTPLIB_DIR: strcpy(buf,"NLST"); dir = FTPLIB_READ; break; case FTPLIB_DIR_VERBOSE: strcpy(buf,"LIST"); dir = FTPLIB_READ; break; case FTPLIB_FILE_READ: strcpy(buf,"RETR"); dir = FTPLIB_READ; break; case FTPLIB_FILE_WRITE: strcpy(buf,"STOR"); dir = FTPLIB_WRITE; break; default: sprintf(nControl->response, "Invalid open type %d\n", typ); return 0; } if (path != NULL) { int i = strlen(buf); buf[i++] = ' '; if ((strlen(path) + i) >= sizeof(buf)) return 0; strcpy(&buf[i],path); } if (FtpOpenPort(nControl, nData, mode, dir) == -1) return 0; if (!FtpSendCmd(buf, '1', nControl)) { FtpClose(*nData); *nData = NULL; return 0; } (*nData)->ctrl = nControl; nControl->data = *nData; if (nControl->cmode == FTPLIB_PORT) { if (!FtpAcceptConnection(*nData,nControl)) { FtpClose(*nData); *nData = NULL; nControl->data = NULL; return 0; } } return 1; } /* * FtpRead - read from a data connection */ int FtpRead(void *buf, int max, netbuf *nData) { int i; if (nData->dir != FTPLIB_READ) return 0; if (nData->buf) i = readline((char *)buf, max, nData); else { i = socket_wait(nData); if (i != 1) return 0; i = net_read(nData->handle, buf, max); } if (i == -1) return 0; nData->xfered += i; if (nData->idlecb && nData->cbbytes) { nData->xfered1 += i; if (nData->xfered1 > nData->cbbytes) { if (nData->idlecb(nData, nData->xfered, nData->idlearg) == 0) return 0; nData->xfered1 = 0; } } return i; } /* * FtpWrite - write to a data connection */ int FtpWrite(void *buf, int len, netbuf *nData) { int i; if (nData->dir != FTPLIB_WRITE) return 0; if (nData->buf) i = writeline((char *)buf, len, nData); else { socket_wait(nData); i = net_write(nData->handle, buf, len); } if (i == -1) return 0; nData->xfered += i; if (nData->idlecb && nData->cbbytes) { nData->xfered1 += i; if (nData->xfered1 > nData->cbbytes) { nData->idlecb(nData, nData->xfered, nData->idlearg); nData->xfered1 = 0; } } return i; } /* * FtpClose - close a data connection */ int FtpClose(netbuf *nData) { netbuf *ctrl; switch (nData->dir) { case FTPLIB_WRITE: /* potential problem - if buffer flush fails, how to notify user? */ if (nData->buf != NULL) writeline(NULL, 0, nData); case FTPLIB_READ: if (nData->buf) free(nData->buf); shutdown(nData->handle,2); net_close(nData->handle); ctrl = nData->ctrl; free(nData); if (ctrl) { ctrl->data = NULL; return(readresp('2', ctrl)); } return 1; case FTPLIB_CONTROL: if (nData->data) { nData->ctrl = NULL; FtpClose(nData); } net_close(nData->handle); free(nData); return 0; } return 1; } /* * FtpSite - send a SITE command * * return 1 if command successful, 0 otherwise */ int FtpSite(const char *cmd, netbuf *nControl) { char buf[256]; if ((strlen(cmd) + 7) > sizeof(buf)) return 0; sprintf(buf,"SITE %s",cmd); if (!FtpSendCmd(buf,'2',nControl)) return 0; return 1; } /* * FtpSysType - send a SYST command * * Fills in the user buffer with the remote system type. If more * information from the response is required, the user can parse * it out of the response buffer returned by FtpLastResponse(). * * return 1 if command successful, 0 otherwise */ int FtpSysType(char *buf, int max, netbuf *nControl) { int l = max; char *b = buf; char *s; if (!FtpSendCmd("SYST",'2',nControl)) return 0; s = &nControl->response[4]; while ((--l) && (*s != ' ')) *b++ = *s++; *b++ = '\0'; return 1; } /* * FtpMkdir - create a directory at server * * return 1 if successful, 0 otherwise */ int FtpMkdir(const char *path, netbuf *nControl) { char buf[256]; if ((strlen(path) + 6) > sizeof(buf)) return 0; sprintf(buf,"MKD %s",path); if (!FtpSendCmd(buf,'2', nControl)) return 0; return 1; } /* * FtpChdir - change path at remote * * return 1 if successful, 0 otherwise */ int FtpChdir(const char *path, netbuf *nControl) { char buf[256]; if ((strlen(path) + 6) > sizeof(buf)) return 0; sprintf(buf,"CWD %s",path); if (!FtpSendCmd(buf,'2',nControl)) return 0; return 1; } /* * FtpCDUp - move to parent directory at remote * * return 1 if successful, 0 otherwise */ int FtpCDUp(netbuf *nControl) { if (!FtpSendCmd("CDUP",'2',nControl)) return 0; return 1; } /* * FtpRmdir - remove directory at remote * * return 1 if successful, 0 otherwise */ int FtpRmdir(const char *path, netbuf *nControl) { char buf[256]; if ((strlen(path) + 6) > sizeof(buf)) return 0; sprintf(buf,"RMD %s",path); if (!FtpSendCmd(buf,'2',nControl)) return 0; return 1; } /* * FtpPwd - get working directory at remote * * return 1 if successful, 0 otherwise */ int FtpPwd(char *path, int max, netbuf *nControl) { int l = max; char *b = path; char *s; if (!FtpSendCmd("PWD",'2',nControl)) return 0; s = strchr(nControl->response, '"'); if (s == NULL) return 0; s++; while ((--l) && (*s) && (*s != '"')) *b++ = *s++; *b++ = '\0'; return 1; } /* * FtpXfer - issue a command and transfer data * * return 1 if successful, 0 otherwise */ static int FtpXfer(const char *localfile, const char *path, netbuf *nControl, int typ, int mode) { int l,c; char *dbuf; FILE *local = NULL; netbuf *nData; int rv=1; if (localfile != NULL) { char ac[4] = "w"; if (typ == FTPLIB_FILE_WRITE) ac[0] = 'r'; if (mode == FTPLIB_IMAGE) ac[1] = 'b'; local = fopen(localfile, ac); if (local == NULL) { strncpy(nControl->response, strerror(errno), sizeof(nControl->response)); return 0; } } if (local == NULL) local = (typ == FTPLIB_FILE_WRITE) ? stdin : stdout; if (!FtpAccess(path, typ, mode, nControl, &nData)) return 0; dbuf = (char *)malloc(FTPLIB_BUFSIZ); if (typ == FTPLIB_FILE_WRITE) { while ((l = fread(dbuf, 1, FTPLIB_BUFSIZ, local)) > 0) if ((c = FtpWrite(dbuf, l, nData)) < l) { printf("short write: passed %d, wrote %d\n", l, c); rv = 0; break; } } else { while ((l = FtpRead(dbuf, FTPLIB_BUFSIZ, nData)) > 0) if (fwrite(dbuf, 1, l, local) <= 0) { perror("localfile write"); rv = 0; break; } } free(dbuf); fflush(local); if (localfile != NULL) fclose(local); FtpClose(nData); return rv; } /* * FtpNlst - issue an NLST command and write response to output * * return 1 if successful, 0 otherwise */ int FtpNlst(const char *outputfile, const char *path, netbuf *nControl) { return FtpXfer(outputfile, path, nControl, FTPLIB_DIR, FTPLIB_ASCII); } /* * FtpDir - issue a LIST command and write response to output * * return 1 if successful, 0 otherwise */ int FtpDir(const char *outputfile, const char *path, netbuf *nControl) { return FtpXfer(outputfile, path, nControl, FTPLIB_DIR_VERBOSE, FTPLIB_ASCII); } /* * FtpSize - determine the size of a remote file * * return 1 if successful, 0 otherwise */ int FtpSize(const char *path, int *size, char mode, netbuf *nControl) { char cmd[256]; int resp,sz,rv=1; if ((strlen(path) + 7) > sizeof(cmd)) return 0; sprintf(cmd, "TYPE %c", mode); if (!FtpSendCmd(cmd, '2', nControl)) return 0; sprintf(cmd,"SIZE %s",path); if (!FtpSendCmd(cmd,'2',nControl)) rv = 0; else { if (sscanf(nControl->response, "%d %d", &resp, &sz) == 2) *size = sz; else rv = 0; } return rv; } /* * FtpModDate - determine the modification date of a remote file * * return 1 if successful, 0 otherwise */ int FtpModDate(const char *path, char *dt, int max, netbuf *nControl) { char buf[256]; int rv = 1; if ((strlen(path) + 7) > sizeof(buf)) return 0; sprintf(buf,"MDTM %s",path); if (!FtpSendCmd(buf,'2',nControl)) rv = 0; else strncpy(dt, &nControl->response[4], max); return rv; } /* * FtpGet - issue a GET command and write received data to output * * return 1 if successful, 0 otherwise */ int FtpGet(const char *outputfile, const char *path, char mode, netbuf *nControl) { return FtpXfer(outputfile, path, nControl, FTPLIB_FILE_READ, mode); } /* * FtpPut - issue a PUT command and send data from input * * return 1 if successful, 0 otherwise */ int FtpPut(const char *inputfile, const char *path, char mode, netbuf *nControl) { return FtpXfer(inputfile, path, nControl, FTPLIB_FILE_WRITE, mode); } /* * FtpRename - rename a file at remote * * return 1 if successful, 0 otherwise */ int FtpRename(const char *src, const char *dst, netbuf *nControl) { char cmd[256]; if (((strlen(src) + 7) > sizeof(cmd)) || ((strlen(dst) + 7) > sizeof(cmd))) return 0; sprintf(cmd,"RNFR %s",src); if (!FtpSendCmd(cmd,'3',nControl)) return 0; sprintf(cmd,"RNTO %s",dst); if (!FtpSendCmd(cmd,'2',nControl)) return 0; return 1; } /* * FtpDelete - delete a file at remote * * return 1 if successful, 0 otherwise */ int FtpDelete(const char *fnm, netbuf *nControl) { char cmd[256]; if ((strlen(fnm) + 7) > sizeof(cmd)) return 0; sprintf(cmd,"DELE %s",fnm); if (!FtpSendCmd(cmd,'2', nControl)) return 0; return 1; } /* * FtpQuit - disconnect from remote * * return 1 if successful, 0 otherwise */ void FtpQuit(netbuf *nControl) { if (nControl->dir != FTPLIB_CONTROL) return; FtpSendCmd("QUIT",'2',nControl); net_close(nControl->handle); free(nControl->buf); free(nControl); } clipper-2.1/examples/ftplib.h0000644000374100011300000000662610736662167013224 00000000000000/***************************************************************************/ /* */ /* ftplib.h - header file for callable ftp access routines */ /* Copyright (C) 1996, 1997 Thomas Pfau, pfau@cnj.digex.net */ /* 73 Catherine Street, South Bound Brook, NJ, 08880 */ /* Modified Kevin Cowtan cowtan@ysbl.york.ac.uk 12/10/2004 */ /* */ /* This library is free software; you can redistribute it and/or */ /* modify it under the terms of the GNU Library General Public */ /* License as published by the Free Software Foundation; either */ /* version 2 of the License, or (at your option) any later version. */ /* */ /* This library is distributed in the hope that it will be useful, */ /* but WITHOUT ANY WARRANTY; without even the implied warranty of */ /* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU */ /* Library General Public License for more details. */ /* */ /* You should have received a copy of the GNU Library General Public */ /* License along with this progam; if not, write to the */ /* Free Software Foundation, Inc., 59 Temple Place - Suite 330, */ /* Boston, MA 02111-1307, USA. */ /* */ /***************************************************************************/ #if !defined(__FTPLIB_H) #define __FTPLIB_H /* FtpAccess() type codes */ #define FTPLIB_DIR 1 #define FTPLIB_DIR_VERBOSE 2 #define FTPLIB_FILE_READ 3 #define FTPLIB_FILE_WRITE 4 /* FtpAccess() mode codes */ #define FTPLIB_ASCII 'A' #define FTPLIB_IMAGE 'I' #define FTPLIB_TEXT FTPLIB_ASCII #define FTPLIB_BINARY FTPLIB_IMAGE /* connection modes */ #define FTPLIB_PASSIVE 1 #define FTPLIB_PORT 2 /* connection option names */ #define FTPLIB_CONNMODE 1 #define FTPLIB_CALLBACK 2 #define FTPLIB_IDLETIME 3 #define FTPLIB_CALLBACKARG 4 #define FTPLIB_CALLBACKBYTES 5 #ifdef __cplusplus extern "C" { #endif typedef struct NetBuf netbuf; typedef int (*FtpCallback)(netbuf *nControl, int xfered, void *arg); void FtpInit(void); char *FtpLastResponse(netbuf *nControl); int FtpConnect(const char *host, netbuf **nControl); int FtpOptions(int opt, long val, netbuf *nControl); int FtpLogin(const char *user, const char *pass, netbuf *nControl); int FtpAccess(const char *path, int typ, int mode, netbuf *nControl, netbuf **nData); int FtpRead(void *buf, int max, netbuf *nData); int FtpWrite(void *buf, int len, netbuf *nData); int FtpClose(netbuf *nData); int FtpSite(const char *cmd, netbuf *nControl); int FtpSysType(char *buf, int max, netbuf *nControl); int FtpMkdir(const char *path, netbuf *nControl); int FtpChdir(const char *path, netbuf *nControl); int FtpCDUp(netbuf *nControl); int FtpRmdir(const char *path, netbuf *nControl); int FtpPwd(char *path, int max, netbuf *nControl); int FtpNlst(const char *output, const char *path, netbuf *nControl); int FtpDir(const char *output, const char *path, netbuf *nControl); int FtpSize(const char *path, int *size, char mode, netbuf *nControl); int FtpModDate(const char *path, char *dt, int max, netbuf *nControl); int FtpGet(const char *output, const char *path, char mode, netbuf *nControl); int FtpPut(const char *input, const char *path, char mode, netbuf *nControl); int FtpRename(const char *src, const char *dst, netbuf *nControl); int FtpDelete(const char *fnm, netbuf *nControl); void FtpQuit(netbuf *nControl); #ifdef __cplusplus } #endif #endif /* __FTPLIB_H */ clipper-2.1/examples/cfft.cpp0000644000374100011300000002322311221530047013166 00000000000000// Clipper app to perform ffts and map stats /* Copyright 2003-2004 Kevin Cowtan & University of York all rights reserved */ #include #include #include double sfunc( double q, int i, int j ); double pfunc( double t, int nt ); int main( int argc, char** argv ) { CCP4Program prog( "cfft", "0.1", "$Date: 2004/05/01" ); // defaults clipper::String title; clipper::String ipfile = "NONE"; clipper::String ipcolf = "NONE"; clipper::String ipcold = "NONE"; clipper::String ipcola = "NONE"; clipper::String ipcolh = "NONE"; clipper::String ipcolm = "NONE"; clipper::String opfile = "NONE"; bool stats = false; bool adiff = false; double statsrad = -1.0; double uvalue = 0.0; clipper::Resolution reso; clipper::Grid_sampling grid; // command input CCP4CommandInput args( argc, argv, true ); int arg = 0; while ( ++arg < args.size() ) { if ( args[arg] == "-title" ) { if ( ++arg < args.size() ) title = args[arg]; } else if ( args[arg] == "-mtzin" ) { if ( ++arg < args.size() ) ipfile = args[arg]; } else if ( args[arg] == "-mapout" ) { if ( ++arg < args.size() ) opfile = args[arg]; } else if ( args[arg] == "-colin-fo" ) { if ( ++arg < args.size() ) ipcolf = args[arg]; } else if ( args[arg] == "-colin-fano" ) { if ( ++arg < args.size() ) ipcola = args[arg]; } else if ( args[arg] == "-colin-fdiff" ) { if ( ++arg < args.size() ) ipcold = args[arg]; } else if ( args[arg] == "-colin-hl" ) { if ( ++arg < args.size() ) ipcolh = args[arg]; } else if ( args[arg] == "-colin-fc" ) { if ( ++arg < args.size() ) ipcolm = args[arg]; } else if ( args[arg] == "-u-value" ) { if ( ++arg < args.size() ) uvalue = clipper::String(args[arg]).f(); } else if ( args[arg] == "-b-value" ) { if ( ++arg < args.size() ) uvalue = clipper::Util::b2u(clipper::String(args[arg]).f()); } else if ( args[arg] == "-resolution" ) { if ( ++arg < args.size() ) { reso = clipper::Resolution( clipper::String(args[arg]).f() ); } } else if ( args[arg] == "-grid" ) { if ( ++arg < args.size() ) { std::vector g = clipper::String(args[arg]).split(", "); grid = clipper::Grid_sampling( g[0].i(), g[1].i(), g[2].i() ); } } else if ( args[arg] == "-anomalous" ) { adiff = true; } else if ( args[arg] == "-stats" ) { stats = true; } else if ( args[arg] == "-stats-radius" ) { if ( ++arg < args.size() ) statsrad = clipper::String(args[arg]).f(); } else { std::cout << "Unrecognized:\t" << args[arg] << "\n"; args.clear(); } } if ( args.size() <= 1 ) { std::cout << "Usage: cfft\n\t-mtzin \n\t-mapout \n\t-colin-fo \n\t-colin-fano \n\t-colin-fdiff \n\t-colin-hl \n\t-colin-fc \n\t-u-value \n\t-b-value \n\t-resolution \n\t-grid ,,\n\t-anomalous\n\t-stats\n\t-stats-radius \nIf -colin-hl is specified, conversion is ABCD->phi/fom.\nIf -colin-fo and -colin-hl are specified, they are used to calculate\nmap coefficient. Otherwise the map coefficient may be provided using\n-colin-fc.\n"; exit(1); } // make data objects clipper::CCP4MTZfile mtzin; clipper::MTZcrystal cxtl; clipper::HKL_info hkls; typedef clipper::HKL_data_base::HKL_reference_index HRI; mtzin.set_column_label_mode( clipper::CCP4MTZfile::Legacy ); // open file mtzin.open_read( ipfile ); clipper::Spacegroup spgr = mtzin.spacegroup(); clipper::Cell cell = mtzin.cell(); if ( ipcolf != "NONE" ) mtzin.import_crystal( cxtl, ipcolf+".F_sigF.F" ); if ( ipcola != "NONE" ) mtzin.import_crystal( cxtl, ipcola+".F_sigF_ano.F+"); if ( ipcolm != "NONE" ) mtzin.import_crystal( cxtl, ipcolm+".F_phi.F" ); if ( !cxtl.is_null() ) cell = cxtl; if ( reso.is_null() ) reso = mtzin.resolution(); hkls.init( spgr, cell, reso, true ); clipper::HKL_data abcd( hkls ); clipper::HKL_data fsig( hkls ); clipper::HKL_data dsig( hkls ); clipper::HKL_data fano( hkls ); clipper::HKL_data fphi( hkls ); if ( ipcolf != "NONE" ) mtzin.import_hkl_data( fsig, ipcolf ); if ( ipcola != "NONE" ) mtzin.import_hkl_data( fano, ipcola ); if ( ipcold != "NONE" ) mtzin.import_hkl_data( dsig, ipcolf ); if ( ipcolh != "NONE" ) mtzin.import_hkl_data( abcd, ipcolh ); if ( ipcolm != "NONE" ) mtzin.import_hkl_data( fphi, ipcolm ); mtzin.close_read(); // make anomalous F if necessary if ( ipcola != "NONE" ) { if ( adiff ) fsig.compute( fano, clipper::data32::Compute_diff_fsigf_from_fsigfano() ); else fsig.compute( fano, clipper::data32::Compute_mean_fsigf_from_fsigfano() ); } // subtract difference F if necessary if ( ipcold != "NONE" ) for ( HRI ih = fsig.first(); !ih.last(); ih.next() ) if ( !fsig[ih].missing() && !dsig[ih].missing() ) fsig[ih].f() -= dsig[ih].f(); else fsig[ih].f() = 0.0; // make map coeffs if necessary if ( ipcolm == "NONE" ) { clipper::HKL_data phiw( hkls ); phiw.compute( abcd, clipper::data32::Compute_phifom_from_abcd() ); fphi.compute( fsig, phiw,clipper::data32::Compute_fphi_from_fsigf_phifom()); } // shift phase for anomalous differences is necessary if ( adiff ) for ( HRI ih = fphi.first(); !ih.last(); ih.next() ) fphi[ih].shift_phase( 0.5*clipper::Util::pi() ); // apply U value fphi.compute( fphi, clipper::data32::Compute_scale_u_iso_fphi(1.0,-uvalue) ); // make grid if necessary if ( grid.is_null() ) grid.init( spgr, cell, reso ); // make xmap clipper::Xmap xmap( spgr, cell, grid ); xmap.fft_from( fphi ); // write map if ( opfile != "NONE" ) { clipper::CCP4MAPfile mapout; mapout.open_write( opfile ); mapout.export_xmap( xmap ); mapout.close_write(); } /* ------------------------------------------------------------------------ Calculation is done. Now calculate some stats. ------------------------------------------------------------------------ */ // calculate stats if ( stats ) { double m1z, m1m, m2z, m2m, m3z, m3m, mn, mi, ma, w, r; m1z = m1m = m2z = m2m = m3z = m3m = mn = 0.0; mi = 1.0e20; ma = -1.0e20; clipper::data32::F_phi f000 = fphi[clipper::HKL(0,0,0)]; if ( !f000.missing() ) m1z = f000.f() / cell.volume(); clipper::Xmap::Map_reference_index ix( xmap ); for ( ix = xmap.first(); !ix.last(); ix.next() ) { w = xmap.spacegroup().num_symops() / xmap.multiplicity( ix.coord() ); r = xmap[ix]; mn += w; m2z += w*r*r; m3z += w*r*r*r; r -= m1z; m1m += w*r; m2m += w*r*r; m3m += w*r*r*r; if ( r < mi ) mi = r; if ( r > ma ) ma = r; } m2z = pow( m2z/mn, 0.50000000 ); m3z = pow( m3z/mn, 0.33333333 ); m1m = m1m / mn; m2m = pow( m2m/mn, 0.50000000 ); m3m = pow( m3m/mn, 0.33333333 ); std::cout << "\nMap statistics:\n Number of points in cell: " << clipper::String(mn,20,12) << "\n 1st moment about zero (mean): " << clipper::String(m1z,12,6) << " About mean : " << clipper::String(m1m,12,6) << "\n 2nd moment about zero : " << clipper::String(m2z,12,6) << " About mean (rmsd): " << clipper::String(m2m,12,6) << "\n 3rd moment about zero : " << clipper::String(m3z,12,6) << " About mean (skew): " << clipper::String(m3m,12,6) << "\n Range: Min " << clipper::String(mi,12,6) << " Max " << clipper::String(ma,12,6) << "\n"; if ( statsrad > 0.0 ) { // make squared map clipper::Xmap lmom1( xmap ); clipper::Xmap lmom2( xmap ); for ( ix = lmom2.first(); !ix.last(); ix.next() ) lmom2[ix] = clipper::Util::sqr( lmom2[ix] ); // now calculate local mom1, local mom1 squared clipper::MapFilterFn_step fn( statsrad ); clipper::MapFilter_fft fltr( fn, 1.0, clipper::MapFilter_fft::Relative ); fltr( lmom1, lmom1 ); fltr( lmom2, lmom2 ); // calculate std deviation for ( ix = lmom1.first(); !ix.last(); ix.next() ) lmom2[ix] = sqrt( lmom2[ix] - clipper::Util::sqr( lmom1[ix] ) ); // now get stats of local standard deviation clipper::Map_stats m( lmom2 ); std::cout << "\nLocal map statistics:\n Mean of local RMSD : " << clipper::String( m.mean(), 12, 6 ) << " RMSD of local RMSD: " << clipper::String( m.std_dev(), 12, 6 ) << "\n"; // next do some handidness checks double s, sx, sy, sxx, syy, sxy; s = sx = sy = sxx = syy = sxy = 0.0; for ( ix = lmom1.first(); !ix.last(); ix.next() ) { s += 1.0; sx += lmom1[ix]; sy += lmom2[ix]; sxx += lmom1[ix]*lmom1[ix]; syy += lmom2[ix]*lmom2[ix]; sxy += lmom1[ix]*lmom2[ix]; } int n = fphi.num_obs() - 2; double r = (s*sxy-sx*sy)/sqrt((s*sxx-sx*sx)*(s*syy-sy*sy)); double t = r * sqrt( double(n) / ( 1.0 - r*r ) ); double p = 1.0 - pfunc( t, n ); std::cout << "\n Local mean/variance correlation : " << r << "\n"; std::cout << "\n Local mean/variance significance: " << t << " " << n << " " << p << "\n"; } } } double sfunc( double q, int i, int j ) { double s, t; s = t = 1.0; for ( int k = i; k <= j; k+= 2 ) { t *= q*double(k)/double(k+1); s += t; } return s; } double pfunc( double t, int nt ) { double w = t / sqrt(double(nt)); double th = atan( w ); double c = cos(th); double s = sin(th); if ( nt%2 == 1 ) return 1.0-0.63662*(th+s*c*sfunc(c*c,2,nt-3)); else return 1.0-(s*sfunc(c*c,1,nt-3)); } clipper-2.1/examples/csfcalc.cpp0000644000374100011300000001640211223373653013655 00000000000000// Clipper app to perform structure factor calculation /* Copyright 2003-2004 Kevin Cowtan & University of York all rights reserved */ #include #include #include #include extern "C" { #include } int main( int argc, char** argv ) { CCP4Program prog( "csfcalc", "0.1", "$Date: 2004/06/01" ); // defaults enum ANISO { NONE, FOBS, FCAL }; clipper::String title; clipper::String ippdb = "NONE"; clipper::String ipfile = "NONE"; clipper::String ipcolfo = "NONE"; clipper::String ipcolfree = "NONE"; clipper::String opfile = "sfcalc.mtz"; clipper::String opcol = "sfcalc"; bool bulk = true; ANISO aniso = NONE; int freeflag = 0; int n_refln = 1000; int n_param = 20; int verbose = 0; // command input CCP4CommandInput args( argc, argv, true ); int arg = 0; while ( ++arg < args.size() ) { if ( args[arg] == "-title" ) { if ( ++arg < args.size() ) title = args[arg]; } else if ( args[arg] == "-pdbin" ) { if ( ++arg < args.size() ) ippdb = args[arg]; } else if ( args[arg] == "-mtzin" ) { if ( ++arg < args.size() ) ipfile = args[arg]; } else if ( args[arg] == "-colin-fo" ) { if ( ++arg < args.size() ) ipcolfo = args[arg]; } else if ( args[arg] == "-colin-free" ) { if ( ++arg < args.size() ) ipcolfree = args[arg]; } else if ( args[arg] == "-mtzout" ) { if ( ++arg < args.size() ) opfile = args[arg]; } else if ( args[arg] == "-colout" ) { if ( ++arg < args.size() ) opcol = args[arg]; } else if ( args[arg] == "-free-flag" ) { if ( ++arg < args.size() ) freeflag = clipper::String(args[arg]).i(); } else if ( args[arg] == "-num-reflns" ) { if ( ++arg < args.size() ) n_refln = clipper::String(args[arg]).i(); } else if ( args[arg] == "-num-params" ) { if ( ++arg < args.size() ) n_param = clipper::String(args[arg]).i(); } else if ( args[arg] == "-no-bulk" ) { bulk = false; } else if ( args[arg] == "-aniso-obs" ) { aniso = FOBS; } else if ( args[arg] == "-aniso-cal" ) { aniso = FCAL; } else if ( args[arg] == "-verbose" ) { if ( ++arg < args.size() ) verbose = clipper::String(args[arg]).i(); } else { std::cout << "Unrecognized:\t" << args[arg] << "\n"; args.clear(); } } if ( args.size() <= 1 ) { std::cout << "Usage: csfcalc\n\t-pdbin \n\t-mtzin \n\t-colin-fo \n\t-colin-free \n\t-mtzout \n\t-colout \n\t-free-flag \n\t-num-reflns \n\t-num-params \n\t-no-bulk\n\t-aniso-obs\n\t-aniso-cal\nStructure factor calculation with bulk solvent correction.\n"; exit(1); } // make data objects clipper::CCP4MTZfile mtzin, mtzout; clipper::MTZcrystal cxtl; clipper::HKL_info hkls; double bulkfrc, bulkscl; typedef clipper::HKL_data_base::HKL_reference_index HRI; using clipper::data32::F_sigF; using clipper::data32::F_phi; using clipper::data32::Phi_fom; using clipper::data32::Flag; mtzin.set_column_label_mode( clipper::CCP4MTZfile::Legacy ); // open file mtzin.open_read( ipfile ); mtzin.import_hkl_info( hkls ); mtzin.import_crystal( cxtl, ipcolfo+".F_sigF.F" ); clipper::HKL_data fo( hkls, cxtl ); clipper::HKL_data free( hkls, cxtl ); mtzin.import_hkl_data( fo, ipcolfo ); if ( ipcolfree != "NONE" ) mtzin.import_hkl_data( free, ipcolfree ); if ( opcol[0] != '/' ) opcol = mtzin.assigned_paths()[0].notail()+"/"+opcol; mtzin.close_read(); // atomic model clipper::MMDBManager mmdb; const int mmdbflags = MMDBF_IgnoreBlankLines | MMDBF_IgnoreDuplSeqNum | MMDBF_IgnoreNonCoorPDBErrors | MMDBF_IgnoreRemarks; mmdb.SetFlag( mmdbflags ); mmdb.ReadPDBASCII( (char*)ippdb.c_str() ); // get a list of all the atoms clipper::mmdb::PPCAtom psel; int hndl, nsel; hndl = mmdb.NewSelection(); mmdb.SelectAtoms( hndl, 0, 0, SKEY_NEW ); mmdb.GetSelIndex( hndl, psel, nsel ); clipper::MMDBAtom_list atoms( psel, nsel ); mmdb.DeleteSelection( hndl ); // calculate structure factors clipper::HKL_data fc( hkls, cxtl ); if ( bulk ) { clipper::SFcalc_obs_bulk sfcb; sfcb( fc, fo, atoms ); bulkfrc = sfcb.bulk_frac(); bulkscl = sfcb.bulk_scale(); } else { clipper::SFcalc_aniso_fft sfc; sfc( fc, atoms ); bulkfrc = bulkscl = 0.0; } // do anisotropic scaling if ( aniso != NONE ) { clipper::SFscale_aniso::TYPE F = clipper::SFscale_aniso::F; clipper::SFscale_aniso sfscl; if ( aniso == FOBS ) sfscl( fo, fc ); // scale Fobs if ( aniso == FCAL ) sfscl( fc, fo ); // scale Fcal std::cout << "\nAnisotropic scaling:\n" << sfscl.u_aniso_orth(F).format() << "\n"; } // now do sigmaa calc clipper::HKL_data fb( hkls, cxtl ), fd( hkls, cxtl ); clipper::HKL_data phiw( hkls, cxtl ); clipper::HKL_data flag( hkls, cxtl ); for ( HRI ih = flag.first(); !ih.last(); ih.next() ) if ( !fo[ih].missing() && (free[ih].missing()||free[ih].flag()==freeflag) ) flag[ih].flag() = clipper::SFweight_spline::BOTH; else flag[ih].flag() = clipper::SFweight_spline::NONE; // do sigmaa calc clipper::SFweight_spline sfw( n_refln, n_param ); sfw( fb, fd, phiw, fo, fc, flag ); // calc abcd clipper::HKL_data abcd( hkls ); abcd.compute( phiw, clipper::data32::Compute_abcd_from_phifom() ); // output data mtzout.open_append( ipfile, opfile ); mtzout.export_hkl_data( abcd, opcol ); mtzout.export_hkl_data( fc, opcol ); mtzout.export_hkl_data( fb, opcol+"_BEST" ); mtzout.export_hkl_data( fd, opcol+"_DIFF" ); mtzout.close_append(); // now calc R and R-free std::vector params( n_param, 1.0 ); clipper::BasisFn_spline basisfn( fo, n_param, 1.0 ); clipper::TargetFn_scaleF1F2 targetfn( fc, fo ); clipper::ResolutionFn rfn( hkls, basisfn, targetfn, params ); double r1w, f1w, r1f, f1f, Fo, Fc; r1w = f1w = r1f = f1f = 0.0; for ( HRI ih = fo.first(); !ih.last(); ih.next() ) if ( !fo[ih].missing() ) { Fo = fo[ih].f(); Fc = sqrt( rfn.f(ih) ) * fc[ih].f(); if ( free[ih].flag() == freeflag ) { r1f += fabs( Fo - Fc ); f1f += Fo; } else { r1w += fabs( Fo - Fc ); f1w += Fo; } } r1f /= clipper::Util::max( f1f, 0.1 ); r1w /= clipper::Util::max( f1w, 0.1 ); std::cout << "\n R-factor : " << r1w << "\n Free R-factor : " << r1f << "\n"; // DIAGNOSTIC OUTPUT if ( verbose > 1 ) { std::cout << "\n Bulk Correction Volume: " << bulkfrc; std::cout << "\n Bulk Correction Factor: " << bulkscl << "\n"; std::cout << "\nNumber of spline params: " << sfw.params_scale().size() << "\n"; clipper::BasisFn_spline basisfn( hkls, sfw.params_scale().size(), 1.0 ); printf("\n $TABLE: Sigmaa statistics :\n $GRAPHS:scale vs resolution:N:1,2:\n :lack of closure vs resolution:N:1,3:\n $$\n 1/resol^2 scale lack_of_closure $$\n $$\n"); for ( int i = 0; i <= 20.0; i++ ) { double s = hkls.resolution().invresolsq_limit()*double(i)/20.0; printf( "%6.3f %12.3f %12.3f\n", s, basisfn.f_s(s,sfw.params_scale()), basisfn.f_s(s,sfw.params_error()) ); } printf(" $$\n"); } } clipper-2.1/examples/chltofom.cpp0000644000374100011300000000724611221530224014063 00000000000000// Clipper app to convert HL coeffs to phi/fom or back /* Copyright 2003-2004 Kevin Cowtan & University of York all rights reserved */ #include #include extern "C" { #include } int main( int argc, char** argv ) { CCP4Program prog( "chltofom", "0.1", "$Date: 2004/05/01" ); // defaults clipper::String title; clipper::String ipfile = "NONE"; clipper::String ipcolf = "NONE"; clipper::String ipcolh = "NONE"; clipper::String ipcolp = "NONE"; clipper::String opfile = "hltofom.mtz"; clipper::String opcol = "hltofom"; // command input CCP4CommandInput args( argc, argv, true ); int arg = 0; while ( ++arg < args.size() ) { if ( args[arg] == "-title" ) { if ( ++arg < args.size() ) title = args[arg]; } else if ( args[arg] == "-mtzin" ) { if ( ++arg < args.size() ) ipfile = args[arg]; } else if ( args[arg] == "-mtzout" ) { if ( ++arg < args.size() ) opfile = args[arg]; } else if ( args[arg] == "-colin-hl" ) { if ( ++arg < args.size() ) ipcolh = args[arg]; } else if ( args[arg] == "-colin-phifom" ) { if ( ++arg < args.size() ) ipcolp = args[arg]; } else if ( args[arg] == "-colin-fo" ) { if ( ++arg < args.size() ) ipcolf = args[arg]; } else if ( args[arg] == "-colout" ) { if ( ++arg < args.size() ) opcol = args[arg]; } else { std::cout << "Unrecognized:\t" << args[arg] << "\n"; args.clear(); } } if ( args.size() <= 1 ) { std::cout << "Usage: chltofom\n\t-mtzin \n\t-mtzout \n\t-colin-fo \n\t-colin-hl \n\t-colin-phifom \n\t-colout \nIf -colin-hl is specified, conversion is ABCD->phi/fom.\nIf -colin-phifom is specified, conversion is phi/fom->ABCD.\nIf -colin-fo is specified, weighted map coefficients are calculated in addition.\nIf no FOM is present, it is set to 0.99.\n"; exit(1); } // make data objects clipper::CCP4MTZfile mtzin, mtzout; clipper::HKL_info hkls; mtzin.set_column_label_mode( clipper::CCP4MTZfile::Legacy ); // actual work mtzin.open_read( ipfile ); mtzin.import_hkl_info( hkls ); clipper::HKL_data phiw( hkls ); clipper::HKL_data abcd( hkls ); clipper::HKL_data fsig( hkls ); clipper::HKL_data fphi( hkls ); if ( ipcolh != "NONE" ) mtzin.import_hkl_data( abcd, ipcolh ); if ( ipcolp != "NONE" ) mtzin.import_hkl_data( phiw, ipcolp ); if ( ipcolf != "NONE" ) mtzin.import_hkl_data( fsig, ipcolf ); clipper::String opbase = mtzin.assigned_paths()[0]; if ( opcol == "" ) opcol = opbase.substr( 0, opbase.find(".") ); else if ( opcol[0] != '/' ) opcol = opbase.notail()+"/"+opcol; mtzin.close_read(); mtzout.open_append( ipfile, opfile ); // compute phi+fom from abcd if ( ipcolh != "NONE" ) { phiw.compute( abcd, clipper::data32::Compute_phifom_from_abcd() ); mtzout.export_hkl_data( phiw, opcol ); } // compute abcd from phi+fom if ( ipcolp != "NONE" ) { // if weights absent, then set to 0.99 clipper::HKL_data_base::HKL_reference_index ih; for ( ih = phiw.first(); !ih.last(); ih.next() ) if ( !clipper::Util::is_nan( phiw[ih].fom() ) ) break; if ( ih.last() ) for ( ih = phiw.first(); !ih.last(); ih.next() ) phiw[ih].fom() = 0.99; abcd.compute( phiw, clipper::data32::Compute_abcd_from_phifom() ); mtzout.export_hkl_data( abcd, opcol ); } // compute weighted F from F + phi if ( ipcolf != "NONE" ) { fphi.compute( fsig, phiw, clipper::data32::Compute_fphi_from_fsigf_phifom() ); mtzout.export_hkl_data( fphi, opcol ); } mtzout.close_append(); } clipper-2.1/examples/csfcreate.cpp0000644000374100011300000000754211145025637014222 00000000000000// Clipper app to perform inverse ffts /* Copyright 2003-2004 Kevin Cowtan & University of York all rights reserved */ #include #include #include #include extern "C" { #include } int main( int argc, char** argv ) { CCP4Program prog( "csfcreate.cpp", "0.1", "$Date: 2004/06/01" ); // defaults clipper::String title; clipper::String ipmap = "NONE"; clipper::String ippdb = "NONE"; clipper::String opfile = "sfcreate.mtz"; clipper::String opcol = "sfcreate"; clipper::Resolution reso( 2.0 ); // command input CCP4CommandInput args( argc, argv, true ); int arg = 0; while ( ++arg < args.size() ) { if ( args[arg] == "-title" ) { if ( ++arg < args.size() ) title = args[arg]; } else if ( args[arg] == "-mapin" ) { if ( ++arg < args.size() ) ipmap = args[arg]; } else if ( args[arg] == "-pdbin" ) { if ( ++arg < args.size() ) ippdb = args[arg]; } else if ( args[arg] == "-mtzout" ) { if ( ++arg < args.size() ) opfile = args[arg]; } else if ( args[arg] == "-colout" ) { if ( ++arg < args.size() ) opcol = args[arg]; } else if ( args[arg] == "-resolution" ) { if ( ++arg < args.size() ) { reso = clipper::Resolution( clipper::String(args[arg]).f() ); } } else { std::cout << "Unrecognized:\t" << args[arg] << "\n"; args.clear(); } } if ( args.size() <= 1 ) { std::cout << "Usage: csfcreate.cpp\n\t-mapin \n\t-pdbin \n\t-resolution \n\t-mtzout \n\t-colout \nCreate structure factor file from map or pdb.\n"; exit(1); } // get crystal and dataset names clipper::String colnm = ""; clipper::String prjnm = "project"; clipper::String xtlnm = "xtal"; clipper::String setnm = "dset"; std::vector oppath = opcol.split("/"); colnm = oppath[oppath.size()-1]; if ( oppath.size() >= 2 ) setnm = oppath[oppath.size()-2]; if ( oppath.size() >= 3 ) xtlnm = oppath[oppath.size()-3]; // make data objects clipper::CCP4MTZfile mtzout; clipper::Spacegroup spgr; clipper::Cell cell; clipper::HKL_info hkls; clipper::HKL_data< clipper::data32::F_phi> fphi( hkls ); if ( ipmap != "NONE" ) { // import xmap clipper::Xmap xmap; clipper::CCP4MAPfile mapin; mapin.open_read( ipmap ); mapin.import_xmap( xmap ); mapin.close_read(); // calc structure factors hkls = clipper::HKL_info( xmap.spacegroup(), xmap.cell(), reso, true ); fphi = clipper::HKL_data< clipper::data32::F_phi>( hkls ); xmap.fft_to( fphi ); } else if ( ippdb != "NONE" ) { // import pdb clipper::MMDBManager mmdb; const int mmdbflags = MMDBF_IgnoreBlankLines | MMDBF_IgnoreDuplSeqNum | MMDBF_IgnoreNonCoorPDBErrors | MMDBF_IgnoreRemarks; mmdb.SetFlag( mmdbflags ); mmdb.ReadPDBASCII( (char*)ippdb.c_str() ); // get a list of all the atoms clipper::mmdb::PPCAtom psel; int hndl, nsel; hndl = mmdb.NewSelection(); mmdb.SelectAtoms( hndl, 0, 0, SKEY_NEW ); mmdb.GetSelIndex( hndl, psel, nsel ); clipper::MMDBAtom_list atoms( psel, nsel ); mmdb.DeleteSelection( hndl ); // calc structure factors hkls = clipper::HKL_info( mmdb.spacegroup(), mmdb.cell(), reso, true ); fphi = clipper::HKL_data< clipper::data32::F_phi>( hkls ); clipper::SFcalc_aniso_fft sfc; sfc( fphi, atoms ); } else { std::cerr << "ERROR: Neither map nor pdb given" << std::endl; } // output data clipper::MTZcrystal mxtl( xtlnm, prjnm, hkls.cell()); clipper::MTZdataset mset( setnm, 1.0 ); mtzout.open_write( opfile ); mtzout.export_hkl_info( hkls ); mtzout.export_crystal( mxtl, "/"+xtlnm ); mtzout.export_dataset( mset, "/"+xtlnm+"/"+setnm ); mtzout.export_hkl_data( fphi, "/"+xtlnm+"/"+setnm+"/"+colnm ); mtzout.close_write(); } clipper-2.1/examples/cmakereference.cpp0000644000374100011300000002503010736662170015216 00000000000000// Clipper app to prepare reference structure /* Copyright 2003-2004 Kevin Cowtan & University of York all rights reserved */ #include #include #include #include #include extern "C" { #if defined _MSC_VER #include #define MY_RDONLY O_RDONLY|O_BINARY #else #include #define MY_RDONLY O_RDONLY #endif #include #include #include #include "ftplib.h" // ftp client lib extern void decompress(int,int); // decompress lib } int main( int argc, char** argv ) { CCP4Program prog( "cmakereference", "0.2", "$Date: 2005/04/15" ); std::cout << "\n This program includes a modified version of ftplib\n by Thomas Pfau (see http://nbpfaus.net/~pfau/ftplib/),\n and a portion of the public domain 'ncompress' code.\n It is distributed under CCP4 part 0 or LGPL.\n\n"; // defaults clipper::String pdbid = "NONE"; clipper::String pdbfilez = "NONE"; clipper::String rflfilez = "NONE"; clipper::String ipcolf = "NONE"; clipper::String mtzout = "NONE"; clipper::String pdbout = "NONE"; clipper::Resolution reso; bool bulk = true; int n_refln = 1000; int n_param = 20; int verbose = 0; // command input CCP4CommandInput args( argc, argv, true ); int arg = 0; while ( ++arg < args.size() ) { if ( args[arg] == "-pdbid" ) { if ( ++arg < args.size() ) pdbid = args[arg]; } else if ( args[arg] == "-pdbin" ) { if ( ++arg < args.size() ) pdbfilez = args[arg]; } else if ( args[arg] == "-cifin" ) { if ( ++arg < args.size() ) rflfilez = args[arg]; } else if ( args[arg] == "-mtzout" ) { if ( ++arg < args.size() ) mtzout = args[arg]; } else if ( args[arg] == "-pdbout" ) { if ( ++arg < args.size() ) pdbout = args[arg]; } else if ( args[arg] == "-colin-fo" ) { if ( ++arg < args.size() ) ipcolf = args[arg]; } else if ( args[arg] == "-resolution" ) { if ( ++arg < args.size() ) reso = clipper::Resolution( clipper::String(args[arg]).f() ); } else if ( args[arg] == "-num-reflns" ) { if ( ++arg < args.size() ) n_refln = clipper::String(args[arg]).i(); } else if ( args[arg] == "-num-params" ) { if ( ++arg < args.size() ) n_param = clipper::String(args[arg]).i(); } else if ( args[arg] == "-no-bulk" ) { bulk = false; } else if ( args[arg] == "-verbose" ) { if ( ++arg < args.size() ) verbose = clipper::String(args[arg]).i(); } else { std::cout << "Unrecognized:\t" << args[arg] << "\n"; args.clear(); } } if ( args.size() <= 1 ) { std::cout << "Usage: cmakereference\n\t-pdbid \t\tCOMPULSORY\n\t-pdbin <.ent.Z-file>\n\t-cifin <.ent.Z-file>\n\t-mtzout \n\t-pdbout \n\t-resolution \nGenerate reference structure for pirate/buccaneer.\nIf no .ent.Z files are given, they are fetched by ftp if possible.\n"; exit(1); } // post input if ( mtzout == "NONE" ) mtzout = "reference-"+pdbid+".mtz"; if ( pdbout == "NONE" ) pdbout = "reference-"+pdbid+".pdb"; // ftp settings // db specific std::string host = "ftp.ebi.ac.uk"; std::string pdbdir = "/pub/databases/rcsb/pdb/data/structures/all/pdb/"; std::string rfldir = "/pub/databases/rcsb/pdb/data/structures/all/structure_factors/"; // generic clipper::String user = "anonymous"; clipper::String pass = "user@host"; clipper::String tmpdir = "/tmp"; // from environment const char *ptrusr = getenv("USER"); const char *ptrhst = getenv("HOST"); const char *ptrscr = getenv("CCP4_SCR"); if ( ptrusr != NULL && ptrhst != NULL ) pass = std::string(ptrusr) + "@" + std::string(ptrhst); if ( ptrscr != NULL ) tmpdir = std::string(ptrscr); // messages clipper::Message_fatal noserver( "Unable to connect to server. Try manual ftp and give filenames." ); clipper::Message_fatal nologin( "Unable to login to server. Try manual ftp and give filenames." ); clipper::Message_fatal nopdb( "Unable to fetch coordinate file.\nCheck coordinates are available. Try manual ftp and give filenames." ); clipper::Message_fatal norfl( "Unable to fetch reflection file.\nCheck reflections are available. Try manual ftp and give filenames." ); clipper::Message_fatal nordc( "Unable to read compressed file." ); clipper::Message_fatal nowrc( "Unable to write uncompressed file." ); // ftp the files, if required if ( pdbfilez == "NONE" || rflfilez == "NONE" ) { // provide instructions std::cout << "\nAttempting to connect to EBI/MSD for file download. If this step fails, use \nyour preferred ftp client to fetch the files, then re-run giving the \nfilenames as arguments, or use the EBI/MSD website.\n\nftp " << host << "\n" << user << "\n" << pass << "\nbinary\ncd " << pdbdir << "\nget pdb" << pdbid << ".ent.Z\ncd " << rfldir << "\nget r" << pdbid << "sf.ent.Z\nquit\n\n"; netbuf *pbuf; int err; FtpInit(); std::cout << "Connecting...\n\n"; err = FtpConnect( host.c_str(), &pbuf ); if ( err != 1 ) clipper::Message::message( noserver ); err = FtpLogin( user.c_str(), pass.c_str(), pbuf ); if ( err != 1 ) clipper::Message::message( nologin ); if ( pdbfilez == "NONE" ) { std::cout << "Fetching coordinates...\n\n"; pdbfilez = tmpdir + "/pdb" + pdbid + ".ent.Z"; err = FtpChdir( pdbdir.c_str(), pbuf ); if ( err != 1 ) clipper::Message::message( nopdb ); err = FtpGet(pdbfilez.c_str(),pdbfilez.tail().c_str(),FTPLIB_IMAGE,pbuf); if ( err != 1 ) clipper::Message::message( nopdb ); } if ( rflfilez == "NONE" ) { std::cout << "Fetching reflections...\n\n"; rflfilez = tmpdir + "/r" + pdbid + "sf.ent.Z"; err = FtpChdir( rfldir.c_str(), pbuf ); if ( err != 1 ) clipper::Message::message( norfl ); err = FtpGet(rflfilez.c_str(),rflfilez.tail().c_str(),FTPLIB_IMAGE,pbuf); if ( err != 1 ) clipper::Message::message( norfl ); } FtpQuit( pbuf ); } // now uncompress the files int fdip, fdop; clipper::String pdbfile( pdbfilez ), rflfile( rflfilez ); if ( pdbfilez.substr( pdbfilez.length() - 2 ) == ".Z" ) { std::cout << "Decompressing coordinates...\n\n"; pdbfile = pdbfilez.substr( 0, pdbfilez.length() - 2 ); fdip = open( pdbfilez.c_str(), MY_RDONLY ); if ( fdip < 0 ) clipper::Message::message( nordc ); fdop = open( pdbfile.c_str(), O_CREAT|O_WRONLY|O_TRUNC, S_IREAD|S_IWRITE ); if ( fdop < 0 ) clipper::Message::message( nowrc ); decompress( fdip, fdop ); close( fdip ); close( fdop ); } if ( rflfilez.substr( rflfilez.length() - 2 ) == ".Z" ) { std::cout << "Decompressing reflections...\n\n"; rflfile = rflfilez.substr( 0, rflfilez.length() - 2 ); fdip = open( rflfilez.c_str(), MY_RDONLY ); if ( fdip < 0 ) clipper::Message::message( nordc ); fdop = open( rflfile.c_str(), O_CREAT|O_WRONLY|O_TRUNC, S_IREAD|S_IWRITE ); if ( fdop < 0 ) clipper::Message::message( nowrc ); decompress( fdip, fdop ); close( fdip ); close( fdop ); } // make data objects clipper::CIFfile cifin; clipper::CCP4MTZfile mtzfile; clipper::HKL_info hkls_in; double bulkfrc, bulkscl; typedef clipper::HKL_data_base::HKL_reference_index HRI; // atomic model clipper::MMDBManager mmdb; const int mmdbflags = MMDBF_IgnoreBlankLines | MMDBF_IgnoreDuplSeqNum | MMDBF_IgnoreNonCoorPDBErrors | MMDBF_IgnoreRemarks; mmdb.SetFlag( mmdbflags ); mmdb.ReadPDBASCII( (char*)pdbfile.c_str() ); // read reflection info clipper::Spacegroup spgr = mmdb.spacegroup(); clipper::Cell cell = mmdb.cell(); clipper::HKL_info hkls; clipper::HKL_data fo(hkls); if ( rflfile.substr( rflfile.length() - 4 ) == ".ent" ) { // cif format cifin.open_read( rflfile ); if ( reso.is_null() ) reso = cifin.resolution( cell ); hkls.init( spgr, cell, reso, true ); cifin.import_hkl_data( fo ); cifin.close_read(); } else { // mtz format mtzfile.open_read( rflfile ); if ( reso.is_null() ) reso = mtzfile.resolution(); hkls.init( spgr, cell, reso, true ); mtzfile.import_hkl_data( fo, ipcolf ); mtzfile.close_read(); } std::cout << "Number of reflections: " << hkls.num_reflections() << "\n"; // get a list of all the atoms clipper::mmdb::PPCAtom psel; int hndl, nsel; hndl = mmdb.NewSelection(); mmdb.SelectAtoms( hndl, 0, 0, SKEY_NEW ); mmdb.GetSelIndex( hndl, psel, nsel ); clipper::MMDBAtom_list atoms( psel, nsel ); mmdb.DeleteSelection( hndl ); // calculate structure factors clipper::HKL_data fc( hkls ); if ( bulk ) { clipper::SFcalc_obs_bulk sfcb; sfcb( fc, fo, atoms ); bulkfrc = sfcb.bulk_frac(); bulkscl = sfcb.bulk_scale(); } else { clipper::SFcalc_aniso_fft sfc; sfc( fc, atoms ); bulkfrc = bulkscl = 0.0; } // now do sigmaa calc clipper::HKL_data fb( hkls ), fd( hkls ); clipper::HKL_data phiw( hkls ); clipper::HKL_data flag( hkls ); for ( HRI ih = flag.first(); !ih.last(); ih.next() ) if ( !fo[ih].missing() ) flag[ih].flag() = clipper::SFweight_spline::BOTH; else flag[ih].flag() = clipper::SFweight_spline::NONE; // do sigmaa calc clipper::SFweight_spline sfw( n_refln, n_param ); sfw( fb, fd, phiw, fo, fc, flag ); // calc abcd clipper::HKL_data abcd( hkls ); abcd.compute( phiw, clipper::data32::Compute_abcd_from_phifom() ); // output data mtzfile.open_write( mtzout ); mtzfile.export_hkl_info( hkls ); mtzfile.export_hkl_data( fo, "/*/*/FP" ); mtzfile.export_hkl_data( abcd, "/*/*/FC" ); mtzfile.export_hkl_data( fb, "/*/*/FC_BEST" ); mtzfile.export_hkl_data( fd, "/*/*/FC_DIFF" ); mtzfile.close_write(); mmdb.WritePDBASCII( (char*)pdbout.c_str() ); // now calc R and R-free std::vector params( n_param, 1.0 ); clipper::BasisFn_spline basisfn( fo, n_param, 1.0 ); clipper::TargetFn_scaleF1F2 targetfn( fc, fo ); clipper::ResolutionFn rfn( hkls, basisfn, targetfn, params ); double r1w, f1w, r1f, f1f, Fo, Fc; r1w = f1w = r1f = f1f = 0.0; for ( HRI ih = fo.first(); !ih.last(); ih.next() ) if ( !fo[ih].missing() ) { Fo = fo[ih].f(); Fc = sqrt( rfn.f(ih) ) * fc[ih].f(); r1w += fabs( Fo - Fc ); f1w += Fo; } r1f /= clipper::Util::max( f1f, 0.1 ); r1w /= clipper::Util::max( f1w, 0.1 ); std::cout << "\n R-factor : " << r1w << "\n"; } clipper-2.1/examples/cncsfrommodel.cpp0000644000374100011300000001352411114746706015116 00000000000000// Clipper app to get NCS from model /* Copyright 2008 Kevin Cowtan & University of York all rights reserved */ #include #include #include #include extern "C" { #include #include } clipper::String chain_sequence( const clipper::MPolymer& mp ) { const int NTYPE = 27; const char rtype1[NTYPE] = { 'A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V', 'M', 'a', 'c', 'g', 't', 'u', '?'}; const char rtype3[NTYPE][4] = {"ALA","ARG","ASN","ASP","CYS","GLN","GLU","GLY","HIS","ILE", "LEU","LYS","MET","PHE","PRO","SER","THR","TRP","TYR","VAL", "MSE"," A"," C"," G"," T"," U","UNK"}; clipper::String seq = ""; for ( int res = 0; res < mp.size(); res++ ) { char c = ' '; for ( int t = 0; t < NTYPE; t++ ) if ( strncmp( mp[res].type().c_str(), rtype3[t], 3 ) == 0 ) c = rtype1[t]; if ( c == ' ' ) c = char( (mp[res].type()[0] + mp[res].type()[1] + mp[res].type()[2]) % 128 + 128 ); // use dummy sequence symbols for unknown types seq += c; } return seq; } clipper::RTop_orth superpose( const clipper::MPolymer& mp1, const clipper::MPolymer& mp2, const double& rmsd, const int& nmin ) { clipper::RTop_orth result = clipper::RTop_orth::null(); clipper::String seq1 = chain_sequence( mp1 ); clipper::String seq2 = chain_sequence( mp2 ); // ensure that '?'s don't match for ( int i = 0; i < seq1.size(); i++ ) if ( seq1[i] == '?' ) seq1[i] = '1'; for ( int i = 0; i < seq2.size(); i++ ) if ( seq2[i] == '?' ) seq2[i] = '2'; // get the sequence alignment clipper::MSequenceAlign align( clipper::MSequenceAlign::LOCAL, 1.0, 0.001, -1.0 ); std::pair,std::vector > valign = align( seq1, seq2 ); const std::vector& v1( valign.first ), v2( valign.second ); // reject any bad matches int nmat, nmis; nmat = nmis = 0; for ( int i1 = 0; i1 < seq1.size(); i1++ ) { int i2 = v1[i1]; if ( i2 >= 0 && i2 < seq2.size() ) if ( isalpha(seq1[i1]) && isalpha(seq2[i2]) ) { if ( seq1[i1] == seq2[i2] ) nmat++; else nmis++; } } if ( nmat < nmin ) return result; // now get the coordinates std::vector c1, c2; for ( int i1 = 0; i1 < seq1.size(); i1++ ) { int i2 = v1[i1]; if ( i2 >= 0 && i2 < seq2.size() ) if ( seq1[i1] == seq2[i2] ) if ( isalpha(seq1[i1]) ) { int a1 = mp1[i1].lookup( " CA ", clipper::MM::ANY ); int a2 = mp2[i2].lookup( " CA ", clipper::MM::ANY ); if ( a1 < 0 && a2 < 0 ) { a1 = mp1[i1].lookup( " C1*", clipper::MM::ANY ); a2 = mp2[i2].lookup( " C1*", clipper::MM::ANY ); } if ( a1 >= 0 && a2 >= 0 ) { c1.push_back( mp1[i1][a1].coord_orth() ); c2.push_back( mp2[i2][a2].coord_orth() ); } } } // refine the alignment clipper::RTop_orth rtop_tmp; double r2; for ( int c = 0; c < 5; c++ ) { int nc = c1.size(); // get transformation rtop_tmp = clipper::RTop_orth( c1, c2 ); // get rmsd std::vector > r2index( nc ); r2 = 0.0; for ( int i = 0; i < nc; i++ ) { double d2 = ( rtop_tmp * c1[i] - c2[i] ).lengthsq(); r2 += d2; r2index[i] = std::pair( d2, i ); } r2 /= double( nc ); // prune the list to improve it std::sort( r2index.begin(), r2index.end() ); std::vector t1, t2; for ( int i = 0; i < (9*r2index.size())/10; i++ ) { t1.push_back( c1[r2index[i].second] ); t2.push_back( c2[r2index[i].second] ); } c1 = t1; c2 = t2; } // if a close match has been found, return it if ( r2 < rmsd*rmsd ) result = rtop_tmp; return result; } int main( int argc, char** argv ) { CCP4Program prog( "cncsfrommodel", "0.1", "$Date: 2008/03/31" ); // defaults clipper::String title; clipper::String ippdb = "NONE"; double rmsd = 1.0; int over = 12; // command input CCP4CommandInput args( argc, argv, true ); int arg = 0; while ( ++arg < args.size() ) { if ( args[arg] == "-title" ) { if ( ++arg < args.size() ) title = args[arg]; } else if ( args[arg] == "-pdbin" ) { if ( ++arg < args.size() ) ippdb = args[arg]; } else if ( args[arg] == "-max-rmsd" ) { if ( ++arg < args.size() ) rmsd = clipper::String(args[arg]).f(); } else if ( args[arg] == "-min-overlap" ) { if ( ++arg < args.size() ) over = clipper::String(args[arg]).i(); } else { std::cout << "Unrecognized:\t" << args[arg] << "\n"; args.clear(); } } if ( args.size() <= 1 ) { std::cout << "Usage: cncsfrompdb\n\t-pdbin \n\t-max-rmsd \n\t-min-overlap \nDetermine NCS from a protein model.\n"; exit(1); } // atomic models const int mmdbflags = MMDBF_IgnoreBlankLines | MMDBF_IgnoreDuplSeqNum | MMDBF_IgnoreNonCoorPDBErrors | MMDBF_IgnoreRemarks; clipper::MMDBfile mmdb; clipper::MiniMol mol; mmdb.SetFlag( mmdbflags ); mmdb.read_file( ippdb ); mmdb.import_minimol( mol ); for ( int c1 = 0; c1 < mol.size(); c1++ ) for ( int c2 = 0; c2 < mol.size(); c2++ ) if ( c1 != c2 ) { clipper::RTop_orth rtop = superpose( mol[c1], mol[c2], rmsd, over ); if ( !rtop.is_null() ) { clipper::Rotation rot( rtop.rot() ); clipper::Euler_ccp4 euler = rot.euler_ccp4(); clipper::Coord_orth coord( rtop.trn() ); std::cout << std::endl << "NCS operator found relating chains " << mol[c1].id() << " and " << mol[c2].id() << std::endl; std::cout << "Euler rotation/deg: " << clipper::Util::rad2d(euler.alpha()) << "," << clipper::Util::rad2d(euler.beta()) << "," << clipper::Util::rad2d(euler.gamma()) << std::endl; std::cout << "Orth translation/A: " << coord.x() << "," << coord.y() << "," << coord.z() << std::endl; } } } clipper-2.1/examples/Makefile.am0000644000374100011300000000326011372264322013602 00000000000000# Makefile.am, passed: examples, extracted subdir: examples # in dir /home/cowtan/clipper-autoconf/clipper-2.1/examples ## -*- mode: Makefile; mode: font-lock -*- bin_PROGRAMS = caniso cecalc cfft chltofom cinvfft clipper_test cmakereference cmaplocal cmodeltoseq cncsfrommodel convert2mtz cpatterson cphasecombine cphasematch csfcalc csfcreate csigmaa csymmatch maketestdata caniso_SOURCES = caniso.cpp cecalc_SOURCES = cecalc.cpp cfft_SOURCES = cfft.cpp chltofom_SOURCES = chltofom.cpp cinvfft_SOURCES = cinvfft.cpp clipper_test_SOURCES = clipper_test.cpp cmakereference_SOURCES = cmakereference.cpp ftplib.h ftplib.c compress42.c cmaplocal_SOURCES = cmaplocal.cpp cmodeltoseq_SOURCES = cmodeltoseq.cpp cncsfrommodel_SOURCES = cncsfrommodel.cpp convert2mtz_SOURCES = convert2mtz.cpp convert2mtz.h cpatterson_SOURCES = cpatterson.cpp cphasecombine_SOURCES = cphasecombine.cpp cphasematch_SOURCES = cphasematch.cpp csfcalc_SOURCES = csfcalc.cpp csfcreate_SOURCES = csfcreate.cpp csigmaa_SOURCES = csigmaa.cpp csymmatch_SOURCES = csymmatch.cpp # no ftndemo maketestdata_SOURCES = maketestdata.cpp TESTS = maketestdata INCLUDES = -I.. $(FFTW_CXXFLAGS) $(MMDB_CXXFLAGS) $(CCP4_CXXFLAGS) $(CCTBX_CXXFLAGS) $(BOOST_CXXFLAGS) LIBS = $(FFTW_LIBS) $(CCP4_LIBS) $(MMDB_LIBS) $(CCTBX_LIBS) LDADD = \ $(top_builddir)/clipper/contrib/libclipper-contrib.la \ $(top_builddir)/clipper/ccp4/libclipper-ccp4.la \ $(top_builddir)/clipper/phs/libclipper-phs.la \ $(top_builddir)/clipper/cns/libclipper-cns.la \ $(top_builddir)/clipper/cif/libclipper-cif.la \ $(top_builddir)/clipper/minimol/libclipper-minimol.la \ $(top_builddir)/clipper/core/libclipper-core.la \ -lpthread clipper-2.1/examples/cphasecombine.cpp0000644000374100011300000000663011221530357015053 00000000000000// Clipper app to combine HL coeffs /* Copyright 2003-2004 Kevin Cowtan & University of York all rights reserved */ #include #include extern "C" { #include } int main( int argc, char** argv ) { CCP4Program prog( "cphasecombine", "0.1", "$Date: 2004/06/01" ); // defaults clipper::String title; clipper::String ipfile = "NONE"; clipper::String ipcolh1 = "NONE"; clipper::String ipcolh2 = "NONE"; clipper::String opfile = "phasecombine.mtz"; clipper::String opcol = "hlcomb"; float hlwt1 = 1.0; float hlwt2 = 1.0; // command input CCP4CommandInput args( argc, argv, true ); int arg = 0; while ( ++arg < args.size() ) { if ( args[arg] == "-title" ) { if ( ++arg < args.size() ) title = args[arg]; } else if ( args[arg] == "-mtzin" ) { if ( ++arg < args.size() ) ipfile = args[arg]; } else if ( args[arg] == "-mtzout" ) { if ( ++arg < args.size() ) opfile = args[arg]; } else if ( args[arg] == "-colin-hl-1" ) { if ( ++arg < args.size() ) ipcolh1 = args[arg]; } else if ( args[arg] == "-colin-hl-2" ) { if ( ++arg < args.size() ) ipcolh2 = args[arg]; } else if ( args[arg] == "-weight-hl-1" ) { if ( ++arg < args.size() ) hlwt1 = clipper::String(args[arg]).f(); } else if ( args[arg] == "-weight-hl-2" ) { if ( ++arg < args.size() ) hlwt2 = clipper::String(args[arg]).f(); } else if ( args[arg] == "-colout" ) { if ( ++arg < args.size() ) opcol = args[arg]; } else { std::cout << "Unrecognized:\t" << args[arg] << "\n"; args.clear(); } } if ( args.size() <= 1 ) { std::cout << "Usage: cphasecombine\n\t-mtzin \n\t-mtzout \n\t-colin-hl-1 \n\t-colin-hl-2 \n\t-colout \n\t-weight-hl-1 \n\t-weight-hl-2 \nThe specified phase probabilities, given by HL coefficients, are combined.\nIf weights are supplied, these are applied.\nIf the second set of coefficients are omitted, scaling alone occurs.\n"; exit(1); } // make data objects clipper::CCP4MTZfile mtzin, mtzout; clipper::HKL_info hkls; mtzin.set_column_label_mode( clipper::CCP4MTZfile::Legacy ); // input mtzin.open_read( ipfile ); mtzin.import_hkl_info( hkls ); clipper::HKL_data abcd1( hkls ); clipper::HKL_data abcd2( hkls ); if ( ipcolh1 != "NONE" ) mtzin.import_hkl_data( abcd1, ipcolh1 ); if ( ipcolh2 != "NONE" ) mtzin.import_hkl_data( abcd2, ipcolh2 ); if ( opcol[0] != '/' ) opcol = mtzin.assigned_paths()[0].notail()+"/"+opcol; mtzin.close_read(); // actual work clipper::HKL_data abcd( hkls ); for ( clipper::HKL_data::HKL_reference_index ih = abcd.first(); !ih.last(); ih.next() ) { abcd[ih].a() = abcd[ih].b() = abcd[ih].c() = abcd[ih].d() = 0.0; if ( !abcd1[ih].missing() ) { abcd[ih].a() += hlwt1 * abcd1[ih].a(); abcd[ih].b() += hlwt1 * abcd1[ih].b(); abcd[ih].c() += hlwt1 * abcd1[ih].c(); abcd[ih].d() += hlwt1 * abcd1[ih].d(); } if ( !abcd2[ih].missing() ) { abcd[ih].a() += hlwt2 * abcd2[ih].a(); abcd[ih].b() += hlwt2 * abcd2[ih].b(); abcd[ih].c() += hlwt2 * abcd2[ih].c(); abcd[ih].d() += hlwt2 * abcd2[ih].d(); } } // output mtzout.open_append( ipfile, opfile ); mtzout.export_hkl_data( abcd, opcol ); mtzout.close_append(); } clipper-2.1/examples/compress42.c0000644000374100011300000004430411077601630013716 00000000000000/* (N)compress42.c - File compression ala IEEE Computer, Mar 1992. * * Authors: * Spencer W. Thomas (decvax!harpo!utah-cs!utah-gr!thomas) * Jim McKie (decvax!mcvax!jim) * Steve Davies (decvax!vax135!petsd!peora!srd) * Ken Turkowski (decvax!decwrl!turtlevax!ken) * James A. Woods (decvax!ihnp4!ames!jaw) * Joe Orost (decvax!vax135!petsd!joe) * Dave Mack (csu@alembic.acs.com) * Peter Jannesen, Network Communication Systems * (peter@ncs.nl) * * Revision unlabelled: 08/10/22 cowtan@ysbl.york.ac.uk * Include stdlib.h and string.h * * Revision unlabelled: 04/10/12 cowtan@ysbl.york.ac.uk * Reduce to minimal subset for slow decompression. * * Revision 4.2.3 92/03/14 peter@ncs.nl * Optimise compress and decompress function and a lot of cleanups. * New fast hash algoritme added (if more than 800Kb available). * * Revision 4.1 91/05/26 csu@alembic.acs.com * Modified to recursively compress directories ('r' flag). As a side * effect, compress will no longer attempt to compress things that * aren't "regular" files. See Changes. * * Revision 4.0 85/07/30 12:50:00 joe * Removed ferror() calls in output routine on every output except first. * Prepared for release to the world. * * Revision 3.6 85/07/04 01:22:21 joe * Remove much wasted storage by overlaying hash table with the tables * used by decompress: tab_suffix[1<putc] and * added signal catcher [plus beef in write_error()] to delete effluvia. * * Revision 2.0 84/08/28 22:00:00 petsd!joe * Add check for foreground before prompting user. Insert maxbits into * compressed file. Force file being uncompressed to end with ".Z". * Added "-c" flag and "zcat". Prepared for release. * * Revision 1.10 84/08/24 18:28:00 turtlevax!ken * Will only compress regular files (no directories), added a magic number * header (plus an undocumented -n flag to handle old files without headers), * added -f flag to force overwriting of possibly existing destination file, * otherwise the user is prompted for a response. Will tack on a .Z to a * filename if it doesn't have one when decompressing. Will only replace * file if it was compressed. * * Revision 1.9 84/08/16 17:28:00 turtlevax!ken * Removed scanargs(), getopt(), added .Z extension and unlimited number of * filenames to compress. Flags may be clustered (-Ddvb12) or separated * (-D -d -v -b 12), or combination thereof. Modes and other status is * copied with copystat(). -O bug for 4.2 seems to have disappeared with * 1.8. * * Revision 1.8 84/08/09 23:15:00 joe * Made it compatible with vax version, installed jim's fixes/enhancements * * Revision 1.6 84/08/01 22:08:00 joe * Sped up algorithm significantly by sorting the compress chain. * * Revision 1.5 84/07/13 13:11:00 srd * Added C version of vax asm routines. Changed structure to arrays to * save much memory. Do unsigned compares where possible (faster on * Perkin-Elmer) * * Revision 1.4 84/07/05 03:11:11 thomas * Clean up the code a little and lint it. (Lint complains about all * the regs used in the asm, but I'm not going to "fix" this.) * * Revision 1.3 84/07/05 02:06:54 thomas * Minor fixes. * * Revision 1.2 84/07/05 00:27:27 thomas * Add variable bit length output. * */ #include #include #include #include #include #include #include #include #include #ifdef DIRENT # include # define RECURSIVE 1 # undef SYSDIR #endif #ifdef SYSDIR # include # define RECURSIVE 1 #endif #ifdef UTIME_H # include #else struct utimbuf { time_t actime; time_t modtime; }; #endif #ifdef __STDC__ # define ARGS(a) a #else # define ARGS(a) () #endif #define LARGS(a) () /* Relay on include files for libary func defs. */ #ifndef SIG_TYPE # define SIG_TYPE void (*)() #endif #define MARK(a) { asm(" .globl M.a"); asm("M.a:"); } #ifdef DEF_ERRNO extern int errno; #endif #undef min #define min(a,b) ((a>b) ? b : a) #ifndef IBUFSIZ # define IBUFSIZ BUFSIZ /* Defailt input buffer size */ #endif #ifndef OBUFSIZ # define OBUFSIZ BUFSIZ /* Default output buffer size */ #endif #define MAXPATHLEN 1024 /* MAXPATHLEN - maximum length of a pathname we allow */ #define SIZE_INNER_LOOP 256 /* Size of the inter (fast) compress loop */ /* Defines for third byte of header */ #define MAGIC_1 (char_type)'\037'/* First byte of compressed file */ #define MAGIC_2 (char_type)'\235'/* Second byte of compressed file */ #define BIT_MASK 0x1f /* Mask for 'number of compresssion bits' */ /* Masks 0x20 and 0x40 are free. */ /* I think 0x20 should mean that there is */ /* a fourth header byte (for expansion). */ #define BLOCK_MODE 0x80 /* Block compresssion if table is full and */ /* compression rate is dropping flush tables */ /* the next two codes should not be changed lightly, as they must not */ /* lie within the contiguous general code space. */ #define FIRST 257 /* first free entry */ #define CLEAR 256 /* table clear output code */ #define INIT_BITS 9 /* initial number of bits/code */ #ifndef SACREDMEM /* * SACREDMEM is the amount of physical memory saved for others; compress * will hog the rest. */ # define SACREDMEM 0 #endif #ifndef USERMEM /* * Set USERMEM to the maximum amount of physical user memory available * in bytes. USERMEM is used to determine the maximum BITS that can be used * for compression. */ # define USERMEM 450000 /* default user memory */ #endif #ifndef BYTEORDER # define BYTEORDER 0000 #endif #ifndef NOALLIGN # define NOALLIGN 0 #endif /* * machine variants which require cc -Dmachine: pdp11, z8000, DOS */ #ifndef O_BINARY # define O_BINARY 0 /* System has no binary mode */ #endif #ifndef BITS /* General processor calculate BITS */ # if USERMEM >= (800000+SACREDMEM) # define FAST # else # if USERMEM >= (433484+SACREDMEM) # define BITS 16 # else # if USERMEM >= (229600+SACREDMEM) # define BITS 15 # else # if USERMEM >= (127536+SACREDMEM) # define BITS 14 # else # if USERMEM >= (73464+SACREDMEM) # define BITS 13 # else # define BITS 12 # endif # endif # endif # endif # endif #endif /* BITS */ #ifdef FAST # define HBITS 17 /* 50% occupancy */ # define HSIZE (1<>3]) |= ((long)(c))<<((o)&0x7);\ (o) += (n); \ } #else #ifdef BYTEORDER #define output(b,o,c,n) { char_type *p = &(b)[(o)>>3]; \ union bytes i; \ i.word = ((long)(c))<<((o)&0x7); \ p[0] |= i.bytes.b1; \ p[1] |= i.bytes.b2; \ p[2] |= i.bytes.b3; \ (o) += (n); \ } #else #define output(b,o,c,n) { char_type *p = &(b)[(o)>>3]; \ long i = ((long)(c))<<((o)&0x7); \ p[0] |= (char_type)(i); \ p[1] |= (char_type)(i>>8); \ p[2] |= (char_type)(i>>16); \ (o) += (n); \ } #endif #endif #if BYTEORDER == 4321 && NOALLIGN == 1 #define input(b,o,c,n,m){ \ (c) = (*(long *)(&(b)[(o)>>3])>>((o)&0x7))&(m); \ (o) += (n); \ } #else #define input(b,o,c,n,m){ char_type *p = &(b)[(o)>>3]; \ (c) = ((((long)(p[0]))|((long)(p[1])<<8)| \ ((long)(p[2])<<16))>>((o)&0x7))&(m); \ (o) += (n); \ } #endif char *progname; /* Program name */ int silent = 0; /* don't tell me about errors */ int quiet = 1; /* don't tell me about compression */ int do_decomp = 0; /* Decompress mode */ int force = 0; /* Force overwrite of files and links */ int nomagic = 0; /* Use a 3-byte magic number header, */ /* unless old file */ int block_mode = BLOCK_MODE;/* Block compress mode -C compatible with 2.0*/ int maxbits = BITS; /* user settable max # bits/code */ int zcat_flg = 0; /* Write output on stdout, suppress messages */ int recursive = 0; /* compress directories */ int exit_code = -1; /* Exitcode of compress (-1 no file compressed) */ char_type inbuf[IBUFSIZ+64]; /* Input buffer */ char_type outbuf[OBUFSIZ+2048];/* Output buffer */ struct stat infstat; /* Input file status */ char *ifname; /* Input filename */ int remove_ofname = 0; /* Remove output file on a error */ char ofname[MAXPATHLEN]; /* Output filename */ int fgnd_flag = 0; /* Running in background (SIGINT=SIGIGN) */ long bytes_in; /* Total number of byte from input */ long bytes_out; /* Total number of byte to output */ /* Normal machine */ count_int htab[HSIZE]; unsigned short codetab[HSIZE]; # define htabof(i) htab[i] # define codetabof(i) codetab[i] # define tab_prefixof(i) codetabof(i) # define tab_suffixof(i) ((char_type *)(htab))[i] # define de_stack ((char_type *)&(htab[HSIZE-1])) # define clear_htab() memset(htab, -1, sizeof(htab)) # define clear_tab_prefixof() memset(codetab, 0, 256); void decompress ARGS((int,int)); void read_error ARGS((void)); void write_error ARGS((void)); void abort_compress ARGS((void)); /* * Decompress stdin to stdout. This routine adapts to the codes in the * file building the "string" table on-the-fly; requiring no table to * be stored in the compressed file. The tables used herein are shared * with those of the compress() routine. See the definitions above. */ void decompress(int fdin, int fdout) { char_type *stackp; code_int code; int finchar; code_int oldcode; code_int incode; int inbits; int posbits; int outpos; int insize; int bitmask; code_int free_ent; code_int maxcode; code_int maxmaxcode; int n_bits; int rsize; bytes_in = 0; bytes_out = 0; insize = 0; while (insize < 3 && (rsize = read(fdin, inbuf+insize, IBUFSIZ)) > 0) insize += rsize; if (insize < 3 || inbuf[0] != MAGIC_1 || inbuf[1] != MAGIC_2) { if (rsize < 0) read_error(); if (insize > 0) { fprintf(stderr, "%s: not in compressed format\n", (ifname[0] != '\0'? ifname : "stdin")); exit_code = 1; } return ; } maxbits = inbuf[2] & BIT_MASK; block_mode = inbuf[2] & BLOCK_MODE; maxmaxcode = MAXCODE(maxbits); if (maxbits > BITS) { fprintf(stderr, "%s: compressed with %d bits, can only handle %d bits\n", (*ifname != '\0' ? ifname : "stdin"), maxbits, BITS); exit_code = 4; return; } bytes_in = insize; maxcode = MAXCODE(n_bits = INIT_BITS)-1; bitmask = (1<= 0 ; --code) tab_suffixof(code) = (char_type)code; do { resetbuf: ; { int i; int e; int o; e = insize-(o = (posbits>>3)); for (i = 0 ; i < e ; ++i) inbuf[i] = inbuf[i+o]; insize = e; posbits = 0; } if (insize < sizeof(inbuf)-IBUFSIZ) { if ((rsize = read(fdin, inbuf+insize, IBUFSIZ)) < 0) read_error(); insize += rsize; } inbits = ((rsize > 0) ? (insize - insize%n_bits)<<3 : (insize<<3)-(n_bits-1)); while (inbits > posbits) { if (free_ent > maxcode) { posbits = ((posbits-1) + ((n_bits<<3) - (posbits-1+(n_bits<<3))%(n_bits<<3))); ++n_bits; if (n_bits == maxbits) maxcode = maxmaxcode; else maxcode = MAXCODE(n_bits)-1; bitmask = (1<= free_ent) /* Special case for KwKwK string. */ { if (code > free_ent) { char_type *p; posbits -= n_bits; p = &inbuf[posbits>>3]; fprintf(stderr, "insize:%d posbits:%d inbuf:%02X %02X %02X %02X %02X (%d)\n", insize, posbits, p[-1],p[0],p[1],p[2],p[3], (posbits&07)); fprintf(stderr, "uncompress: corrupt input\n"); abort_compress(); } *--stackp = (char_type)finchar; code = oldcode; } while ((cmp_code_int)code >= (cmp_code_int)256) { /* Generate output characters in reverse order */ *--stackp = tab_suffixof(code); code = tab_prefixof(code); } *--stackp = (char_type)(finchar = tab_suffixof(code)); /* And put them out in forward order */ { int i; if (outpos+(i = (de_stack-stackp)) >= OBUFSIZ) { do { if (i > OBUFSIZ-outpos) i = OBUFSIZ-outpos; if (i > 0) { memcpy(outbuf+outpos, stackp, i); outpos += i; } if (outpos >= OBUFSIZ) { if (write(fdout, outbuf, outpos) != outpos) write_error(); outpos = 0; } stackp+= i; } while ((i = (de_stack-stackp)) > 0); } else { memcpy(outbuf+outpos, stackp, i); outpos += i; } } if ((code = free_ent) < maxmaxcode) /* Generate the new entry. */ { tab_prefixof(code) = (unsigned short)oldcode; tab_suffixof(code) = (char_type)finchar; free_ent = code+1; } oldcode = incode; /* Remember previous code. */ } bytes_in += rsize; } while (rsize > 0); if (outpos > 0 && write(fdout, outbuf, outpos) != outpos) write_error(); } void read_error() { fprintf(stderr, "\nread error on"); perror((ifname[0] != '\0') ? ifname : "stdin"); abort_compress(); } void write_error() { fprintf(stderr, "\nwrite error on"); perror((ofname[0] != '\0') ? ofname : "stdout"); abort_compress(); } void abort_compress() { if (remove_ofname) unlink(ofname); exit(1); } clipper-2.1/examples/cmaplocal.cpp0000644000374100011300000000431411041401234014172 00000000000000// Clipper app to calc local map moments /* Copyright 2003-2004 Kevin Cowtan & University of York all rights reserved */ #include #include #include int main( int argc, char** argv ) { CCP4Program prog( "cmaplocal", "0.1", "$Date: 2004/05/01" ); // defaults clipper::String ipfile = "NONE"; clipper::String opfile1 = "NONE"; clipper::String opfile2 = "NONE"; double statsrad = -1.0; // command input CCP4CommandInput args( argc, argv, true ); int arg = 0; while ( ++arg < args.size() ) { if ( args[arg] == "-mapin" ) { if ( ++arg < args.size() ) ipfile = args[arg]; } else if ( args[arg] == "-mapout-1" ) { if ( ++arg < args.size() ) opfile1 = args[arg]; } else if ( args[arg] == "-mapout-2" ) { if ( ++arg < args.size() ) opfile2 = args[arg]; } else if ( args[arg] == "-radius" ) { if ( ++arg < args.size() ) statsrad = clipper::String(args[arg]).f(); } else { std::cout << "Unrecognized:\t" << args[arg] << "\n"; args.clear(); } } if ( args.size() <= 1 ) { std::cout << "Usage: cmaplocal\n\t-mapin \n\t-mapout-1 \n\t-mapout-2 \n\t-radius \n"; exit(1); } clipper::CCP4MAPfile file; clipper::Xmap xmap; file.open_read( ipfile ); file.import_xmap( xmap ); file.close_read(); // make squared map clipper::Xmap lmom1( xmap ); clipper::Xmap lmom2( xmap ); for ( clipper::Xmap::Map_reference_index ix = lmom2.first(); !ix.last(); ix.next() ) lmom2[ix] = clipper::Util::sqr( lmom2[ix] ); // now calculate local mom1, local mom1 squared clipper::MapFilterFn_step fn( statsrad ); clipper::MapFilter_fft fltr( fn, 1.0, clipper::MapFilter_fft::Relative ); fltr( lmom1, lmom1 ); fltr( lmom2, lmom2 ); // calculate std deviation for ( clipper::Xmap::Map_reference_index ix = lmom1.first(); !ix.last(); ix.next() ) lmom2[ix] = sqrt( lmom2[ix] - clipper::Util::sqr( lmom1[ix] ) ); // output map file.open_write( opfile1 ); file.export_xmap( lmom1 ); file.close_write(); file.open_write( opfile2 ); file.export_xmap( lmom2 ); file.close_write(); } clipper-2.1/examples/COPYING0000644000374100011300000005750510736662170012622 00000000000000 GNU LESSER GENERAL PUBLIC LICENSE Version 2.1, February 1999 Copyright (C) 1991, 1999 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. 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END OF TERMS AND CONDITIONS clipper-2.1/examples/csigmaa.cpp0000644000374100011300000001116611223373666013671 00000000000000// Clipper app to do sigmaa calc /* Copyright 2003-2004 Kevin Cowtan & University of York all rights reserved */ #include #include #include extern "C" { #include } int main( int argc, char** argv ) { CCP4Program prog( "csigmaa", "0.1", "$Date: 2004/06/01" ); // defaults clipper::String title; clipper::String ipfile = "NONE"; clipper::String ipcolfo = "NONE"; clipper::String ipcolfc = "NONE"; clipper::String ipcolfree = "NONE"; clipper::String opfile = "sigmaa.mtz"; clipper::String opcol = "sigmaa"; int freeflag = 0; int n_refln = 1000; int n_param = 20; int verbose = 0; // command input CCP4CommandInput args( argc, argv, true ); int arg = 0; while ( ++arg < args.size() ) { if ( args[arg] == "-title" ) { if ( ++arg < args.size() ) title = args[arg]; } else if ( args[arg] == "-mtzin" ) { if ( ++arg < args.size() ) ipfile = args[arg]; } else if ( args[arg] == "-mtzout" ) { if ( ++arg < args.size() ) opfile = args[arg]; } else if ( args[arg] == "-colin-fo" ) { if ( ++arg < args.size() ) ipcolfo = args[arg]; } else if ( args[arg] == "-colin-fc" ) { if ( ++arg < args.size() ) ipcolfc = args[arg]; } else if ( args[arg] == "-colin-free" ) { if ( ++arg < args.size() ) ipcolfree = args[arg]; } else if ( args[arg] == "-colout" ) { if ( ++arg < args.size() ) opcol = args[arg]; } else if ( args[arg] == "-free-flag" ) { if ( ++arg < args.size() ) freeflag = clipper::String(args[arg]).i(); } else if ( args[arg] == "-num-reflns" ) { if ( ++arg < args.size() ) n_refln = clipper::String(args[arg]).i(); } else if ( args[arg] == "-num-params" ) { if ( ++arg < args.size() ) n_param = clipper::String(args[arg]).i(); } else if ( args[arg] == "-verbose" ) { if ( ++arg < args.size() ) verbose = clipper::String(args[arg]).i(); } else { std::cout << "Unrecognized:\t" << args[arg] << "\n"; args.clear(); } } if ( args.size() <= 1 ) { std::cout << "Usage: csigmaa\n\t-mtzin \n\t-mtzout \n\t-colin-fo \n\t-colin-fc \n\t-colin-free \n\t-colout \n\t-free-flag \n\t-num-reflns \n\t-num-params \nCalculate HL coeffs from Fo and Fc.\n"; exit(1); } // make data objects clipper::CCP4MTZfile mtzin, mtzout; clipper::HKL_info hkls; typedef clipper::HKL_data_base::HKL_reference_index HRI; mtzin.set_column_label_mode( clipper::CCP4MTZfile::Legacy ); mtzin.open_read( ipfile ); mtzin.import_hkl_info( hkls ); clipper::HKL_data fo( hkls ); clipper::HKL_data fc( hkls ); clipper::HKL_data free( hkls ); mtzin.import_hkl_data( fo, ipcolfo ); mtzin.import_hkl_data( fc, ipcolfc ); if ( ipcolfree != "NONE" ) mtzin.import_hkl_data( free, ipcolfree ); if ( opcol[0] != '/' ) opcol = mtzin.assigned_paths()[0].notail()+"/"+opcol; mtzin.close_read(); // flag reflections clipper::HKL_data fb( hkls ), fd( hkls ); clipper::HKL_data phiw( hkls ); clipper::HKL_data flag( hkls ); for ( HRI ih = flag.first(); !ih.last(); ih.next() ) if ( !fo[ih].missing() && (free[ih].missing()||free[ih].flag()==freeflag) ) flag[ih].flag() = clipper::SFweight_spline::BOTH; else flag[ih].flag() = clipper::SFweight_spline::NONE; // do sigmaa calc clipper::SFweight_spline sfw( n_refln, n_param ); sfw( fb, fd, phiw, fo, fc, flag ); // calc abcd clipper::HKL_data abcd( hkls ); abcd.compute( phiw, clipper::data32::Compute_abcd_from_phifom() ); // output data mtzout.open_append( ipfile, opfile ); mtzout.export_hkl_data( abcd, opcol ); mtzout.export_hkl_data( fb, opcol+"_BEST" ); mtzout.export_hkl_data( fd, opcol+"_DIFF" ); mtzout.close_append(); // DIAGNOSTIC OUTPUT if ( verbose > 1 ) { std::cout << "\nNumber of spline params: " << sfw.params_scale().size() << "\n"; clipper::BasisFn_spline basisfn( hkls, sfw.params_scale().size(), 1.0 ); printf("\n $TABLE: Sigmaa statistics :\n $GRAPHS:scale vs resolution:N:1,2:\n :lack of closure vs resolution:N:1,3:\n $$\n 1/resol^2 scale lack_of_closure $$\n $$\n"); for ( int i = 0; i <= 20.0; i++ ) { double s = hkls.resolution().invresolsq_limit()*double(i)/20.0; printf( "%6.3f %12.3f %12.3f\n", s, basisfn.f_s(s,sfw.params_scale()), basisfn.f_s(s,sfw.params_error()) ); } printf(" $$\n"); } } clipper-2.1/examples/convert2mtz.cpp0000644000374100011300000004776211050270035014555 00000000000000// clipper CNS->MTZ utility /* (C) 2007 Kevin Cowtan */ #include #include #include #include #include "convert2mtz.h" int main( int argc, char** argv ) { CCP4Program prog( "convert2mtz", "0.4", "$Date: 2007/03/30" ); // defaults clipper::String title; clipper::String ipfile = "NONE"; clipper::String opfile = "NONE"; clipper::String ccell = "NONE"; clipper::String cspgr = "NONE"; clipper::String ipfilepdb = "NONE"; clipper::String colin = "NONE"; bool complete = true; bool anom = false; int seed = 54321; int verbose = 0; // command input CCP4CommandInput args( argc, argv, true ); int arg = 0; while ( ++arg < args.size() ) { if ( args[arg] == "-title" ) { if ( ++arg < args.size() ) title = args[arg]; } else if ( args[arg] == "-hklin" || args[arg] == "-cnsin" ) { if ( ++arg < args.size() ) ipfile = args[arg]; } else if ( args[arg] == "-mtzout" ) { if ( ++arg < args.size() ) opfile = args[arg]; } else if ( args[arg] == "-cell" ) { if ( ++arg < args.size() ) ccell = args[arg]; } else if ( args[arg] == "-spacegroup" ) { if ( ++arg < args.size() ) cspgr = args[arg]; } else if ( args[arg] == "-pdbin" ) { if ( ++arg < args.size() ) ipfilepdb = args[arg]; } else if ( args[arg] == "-colin" ) { if ( ++arg < args.size() ) colin = args[arg]; } else if ( args[arg] == "-anomalous" ) { anom = true; } else if ( args[arg] == "-no-complete" ) { complete = false; } else if ( args[arg] == "-seed" ) { if ( ++arg < args.size() ) seed = clipper::String(args[arg]).i(); } else if ( args[arg] == "-verbose" ) { if ( ++arg < args.size() ) verbose = clipper::String(args[arg]).i(); } else { std::cout << "Unrecognized:\t" << args[arg] << "\n"; args.clear(); } } if ( args.size() <= 1 ) { std::cout << "Usage: convert2mtz\n\t-hklin [COMPULSORY]\n\t-mtzout \n\t-cell a,b,c,a,b,g\n\t-spacegroup \n\t-pdbin \n\t-anomalous\n\t-no-complete\n\t-colin \n\t-seed \nConvert formatted reflection file to MTZ.\nCell and spacegroup may be specified directly or by providing a PDB file.\nFor CNS files, column labels and anomalous are detected automatically.\nFor other files (e.g. Shelx/XtalView), give -colin.\n"; exit(1); } if ( ipfilepdb == "NONE" && ccell == "NONE" ) { std::cout << "Missing cell."; exit(1); } if ( ipfilepdb == "NONE" && cspgr == "NONE" ) { std::cout << "Missing spacegroup."; exit(1); } // set defaults srand( seed ); if ( opfile == "NONE" ) { opfile = ipfile; int ldot = int(opfile.rfind(".")); if ( ldot != int(std::string::npos) ) opfile = opfile.substr(0,ldot); opfile = opfile + ".mtz"; } // set crystal info clipper::Cell cell; clipper::Spacegroup spgr; clipper::Resolution reso; if ( ipfilepdb != "NONE" ) { clipper::MMDBManager mmdb; mmdb.ReadCoorFile( (char*)ipfilepdb.c_str() ); spgr = mmdb.spacegroup(); cell = mmdb.cell(); } else { double cd[] = { 100.0, 100.0, 100.0, 90.0, 90.0, 90.0 }; std::vector cellx = ccell.split( ", " ); for ( int i = 0; i < cellx.size(); i++ ) cd[i] = cellx[i].f(); clipper::Cell_descr celld( cd[0], cd[1], cd[2], cd[3], cd[4], cd[5] ); clipper::Spgr_descr spgrd( cspgr ); cell = clipper::Cell( celld ); spgr = clipper::Spacegroup( spgrd ); } // read input file std::vector words; std::ifstream file( ipfile.c_str() ); int lvl = 0; std::string word; while ( file.good() ) { char c; file.get( c ); if ( c == '{' ) lvl++; if ( lvl == 0 ) { if ( isspace(c) || c == '=' ) { if ( word.length() != 0 ) { words.push_back( word ); word = ""; } } else { word = word + c; } } if ( c == '}' ) lvl--; } file.close(); // file info int nref = 0; std::vector cols, typs; std::vector > > grps; cols.push_back( "H" ); cols.push_back( "K" ); cols.push_back( "L" ); typs.push_back( "H" ); typs.push_back( "H" ); typs.push_back( "H" ); std::vector vals; // loop over words and read all info from file int pos = 0; // header section while ( pos < words.size() ) { // CNS headers (irrelevent for non-CNS files) if ( words[pos].substr(0,4) == "NREF" ) { if ( ++pos < words.size() ) nref = clipper::String(words[pos]).i(); } else if ( words[pos].substr(0,4) == "ANOM" ) { if ( ++pos < words.size() ) anom = ( words[pos][0] == 'T' ); } else if ( words[pos].substr(0,4) == "HERM" ) { if ( ++pos < words.size() ) anom = ( words[pos][0] == 'F' ); } else if ( words[pos].substr(0,4) == "DECL" ) { // COLUMN DECLARATIONS ++pos; std::string col, dom, typ; while ( pos < words.size() ) { if ( words[pos] == "END" ) { if ( dom.substr(0,4) == "RECI" ) { if ( typ.substr(0,4) == "INTE" ) { cols.push_back( col ); typs.push_back( "I" ); } else if ( typ.substr(0,4) == "REAL" ) { cols.push_back( col ); typs.push_back( "R" ); } else if ( typ.substr(0,4) == "COMP" ) { cols.push_back( col ); typs.push_back( "F" ); cols.push_back( col+".phase" ); typs.push_back( "P" ); } } break; } else if ( words[pos].substr(0,4) == "NAME" ) { if ( ++pos < words.size() ) col = words[pos]; } else if ( words[pos].substr(0,4) == "DOMA" ) { if ( ++pos < words.size() ) dom = words[pos]; } else if ( words[pos].substr(0,4) == "TYPE" ) { if ( ++pos < words.size() ) typ = words[pos]; } ++pos; } } else if ( words[pos].substr(0,4) == "GROU" ) { // GROUP DECLARATIONS ++pos; std::string gtyp; std::vector gcol; while ( pos < words.size() ) { if ( words[pos] == "END" ) { grps.push_back( std::pair >( gtyp, gcol ) ); break; } else if ( words[pos].substr(0,4) == "TYPE" ) { if ( ++pos < words.size() ) gtyp = words[pos]; } else if ( words[pos].substr(0,4) == "OBJE" ) { if ( ++pos < words.size() ) gcol.push_back( words[pos] ); } ++pos; } } else { if ( words[pos].find_first_not_of("0123456789.-") == std::string::npos ) { vals.push_back( clipper::String(words[pos]).f() ); } } ++pos; } // Now do group assignments for ( int g = 0; g < grps.size(); g++ ) { if ( grps[g].first == "HL" ) { for ( int c = 0; c < grps[g].second.size(); c++ ) { for ( int i = 0; i < cols.size(); i++ ) { if ( cols[i] == grps[g].second[c] ) typs[i] = "A"; } } } } // if columns were input, they override the headers if ( colin != "NONE" ) { cols.clear(); typs.clear(); cols.push_back( "H" ); cols.push_back( "K" ); cols.push_back( "L" ); typs.push_back( "H" ); typs.push_back( "H" ); typs.push_back( "H" ); std::vector cin = colin.split(" ,"); for ( int i = 0; i < cin.size(); i++ ) { cols.push_back( cin[i] ); typs.push_back( "R" ); } nref = vals.size() / cols.size(); } // check data length int ncol = cols.size(); if ( ncol*nref != vals.size() ) { std::cout << "Error: data length does not match number of reflections.\n"; exit(1); } // column assignment heuristics for ( int i = 3; i < ncol; i++ ) { std::string c; for ( int j = 0; j < cols[i].length(); j++ ) c += toupper( cols[i][j] ); if ( typs[i] == "R" ) { if ( cols[i].find("SIG") != std::string::npos ) typs[i] = "Q"; else if ( cols[i].find("FOM") != std::string::npos ) typs[i] = "W"; else if ( cols[i].find("HLA") != std::string::npos ) typs[i] = "A"; else if ( cols[i].find("FREE")!= std::string::npos ) typs[i] = "I"; else if ( cols[i][0] == 'F' ) typs[i] = "F"; else if ( cols[i][0] == 'E' ) typs[i] = "E"; else if ( cols[i][0] == 'I' ) typs[i] = "J"; else if ( cols[i][0] == 'P' ) typs[i] = "P"; else if ( cols[i][0] == 'S' ) typs[i] = "Q"; else if ( cols[i][0] == 'W' ) typs[i] = "W"; else if ( cols[i][0] == 'M' ) typs[i] = "W"; else if ( cols[i][0] == 'A' ) typs[i] = "A"; else if ( cols[i][0] == 'B' ) typs[i] = "A"; else if ( cols[i][0] == 'C' ) typs[i] = "A"; else if ( cols[i][0] == 'D' ) typs[i] = "A"; else if ( cols[i][0] == 'H' ) typs[i] = "A"; } } // post-assignment diagnostics std::cout << std::endl << "Columns found:" << std::endl; for ( int i = 0; i < cols.size(); i++ ) { std::cout << " " << i << " " << cols[i] << " " << typs[i] << std::endl; } std::cout << "Note: these do not represent the final MTZ column types" << std::endl << std::endl; // get reflections std::set hkl_set; const clipper::HKL zero( 0, 0, 0 ); for ( int i = 0; i < nref; i++ ) { clipper::HKL hkl( Util::intr(vals[i*ncol ]), Util::intr(vals[i*ncol+1]), Util::intr(vals[i*ncol+2]) ); clipper::HKL asu; if ( hkl != zero ) { for ( int s = 0; s < spgr.num_primops(); s++ ) { asu = hkl.transform( spgr.symop(s) ); if ( spgr.recip_asu( asu ) ) break; asu = -asu; if ( spgr.recip_asu( asu ) ) break; } hkl_set.insert( asu ); } } std::vector hkl_list( hkl_set.begin(), hkl_set.end() ); // get resolution double smax = 0.0; for ( int i = 0; i < hkl_list.size(); i++ ) { double s = hkl_list[i].invresolsq( cell ); if ( s > smax ) smax = s; } reso = clipper::Resolution( 0.999999/sqrt(smax) ); // prepare data arrays clipper::HKL_info hkls( spgr, cell, reso ); if ( complete ) { hkl_list.clear(); clipper::HKL_info hkl0( spgr, cell, reso, true ); for ( int i = 0; i < hkl0.num_reflections(); i++ ) if ( hkl0.hkl_of(i) != zero ) hkl_list.push_back( hkl0.hkl_of(i) ); } hkls.add_hkl_list( hkl_list ); std::vector opcols; std::vector > datai; std::vector > dataf; std::vector > dataiano; std::vector > datafano; std::vector > datasigiano; std::vector > datasigfano; std::vector > datae; std::vector > datasig; std::vector > dataphi; std::vector > datafom; std::vector > dataabcd; std::vector > dataflag; clipper::HKL_data datafree(hkls); // fill data arrays // loop over the columns bool friedel; int isym; for ( int col = 3; col < ncol; col++ ) { // I or Iano if ( typs[col] == "J" ) { if ( !anom ) { clipper::HKL_data data( hkls ); for ( int ref = 0; ref < nref; ref++ ) { clipper::HKL hkl( Util::intr(vals[ref*ncol ]), Util::intr(vals[ref*ncol+1]), Util::intr(vals[ref*ncol+2]) ); dataI dat( vals[ref*ncol+col] ); data.set_data( hkl, dat ); } datai.push_back( data ); opcols.push_back("i"+cols[col]); } else { clipper::HKL_data data( hkls ); for ( int ref = 0; ref < nref; ref++ ) { clipper::HKL hkl( Util::intr(vals[ref*ncol ]), Util::intr(vals[ref*ncol+1]), Util::intr(vals[ref*ncol+2]) ); clipper::HKL hkl1 = hkls.find_sym( hkl, isym, friedel ); int index = hkls.index_of( hkl1 ); float v = vals[ref*ncol+col]; if ( friedel ) data[index] = dataIano( data[index].I_pl(), v ); else data[index] = dataIano( v, data[index].I_mi() ); } dataiano.push_back( data ); opcols.push_back("I"+cols[col]+"+,"+cols[col]+"-"); } } // F or Fano if ( typs[col] == "F" ) { if ( !anom ) { clipper::HKL_data data( hkls ); for ( int ref = 0; ref < nref; ref++ ) { clipper::HKL hkl( Util::intr(vals[ref*ncol ]), Util::intr(vals[ref*ncol+1]), Util::intr(vals[ref*ncol+2]) ); dataF dat( vals[ref*ncol+col] ); data.set_data( hkl, dat ); } dataf.push_back( data ); opcols.push_back("f"+cols[col]); } else { clipper::HKL_data data( hkls ); for ( int ref = 0; ref < nref; ref++ ) { clipper::HKL hkl( Util::intr(vals[ref*ncol ]), Util::intr(vals[ref*ncol+1]), Util::intr(vals[ref*ncol+2]) ); clipper::HKL hkl1 = hkls.find_sym( hkl, isym, friedel ); int index = hkls.index_of( hkl1 ); float v = vals[ref*ncol+col]; if ( friedel ) data[index] = dataFano( data[index].F_pl(), v ); else data[index] = dataFano( v, data[index].F_mi() ); } datafano.push_back( data ); opcols.push_back("F"+cols[col]+"+,"+cols[col]+"-"); } } // sigF or sigFano or sigIano if ( typs[col] == "Q" ) { if ( !anom ) { clipper::HKL_data data( hkls ); for ( int ref = 0; ref < nref; ref++ ) { clipper::HKL hkl( Util::intr(vals[ref*ncol ]), Util::intr(vals[ref*ncol+1]), Util::intr(vals[ref*ncol+2]) ); dataSig dat( vals[ref*ncol+col] ); data.set_data( hkl, dat ); } datasig.push_back( data ); opcols.push_back("S"+cols[col]); } else { if ( typs[col-1] == "J" ) { clipper::HKL_data data( hkls ); for ( int ref = 0; ref < nref; ref++ ) { clipper::HKL hkl( Util::intr(vals[ref*ncol ]), Util::intr(vals[ref*ncol+1]), Util::intr(vals[ref*ncol+2]) ); clipper::HKL hkl1 = hkls.find_sym( hkl, isym, friedel ); int index = hkls.index_of( hkl1 ); float v = vals[ref*ncol+col]; if ( friedel ) data[index] = dataSigIano(data[index].sigI_pl(), v); else data[index] = dataSigIano(v, data[index].sigI_mi()); } datasigiano.push_back( data ); opcols.push_back("1"+cols[col]+"+,"+cols[col]+"-"); } else { clipper::HKL_data data( hkls ); for ( int ref = 0; ref < nref; ref++ ) { clipper::HKL hkl( Util::intr(vals[ref*ncol ]), Util::intr(vals[ref*ncol+1]), Util::intr(vals[ref*ncol+2]) ); clipper::HKL hkl1 = hkls.find_sym( hkl, isym, friedel ); int index = hkls.index_of( hkl1 ); float v = vals[ref*ncol+col]; if ( friedel ) data[index] = dataSigFano(data[index].sigF_pl(), v); else data[index] = dataSigFano(v, data[index].sigF_mi()); } datasigfano.push_back( data ); opcols.push_back("2"+cols[col]+"+,"+cols[col]+"-"); } } } // E if ( typs[col] == "E" ) { clipper::HKL_data data( hkls ); for ( int ref = 0; ref < nref; ref++ ) { clipper::HKL hkl( Util::intr(vals[ref*ncol ]), Util::intr(vals[ref*ncol+1]), Util::intr(vals[ref*ncol+2]) ); dataE dat( vals[ref*ncol+col] ); data.set_data( hkl, dat ); } datae.push_back( data ); opcols.push_back("E"+cols[col]); } // Phase if ( typs[col] == "P" ) { clipper::HKL_data data( hkls ); for ( int ref = 0; ref < nref; ref++ ) { clipper::HKL hkl( Util::intr(vals[ref*ncol ]), Util::intr(vals[ref*ncol+1]), Util::intr(vals[ref*ncol+2]) ); dataPhi dat( Util::d2rad(vals[ref*ncol+col]) ); data.set_data( hkl, dat ); } dataphi.push_back( data ); opcols.push_back("P"+cols[col]); } // FOM if ( typs[col] == "W" ) { clipper::HKL_data data( hkls ); for ( int ref = 0; ref < nref; ref++ ) { clipper::HKL hkl( Util::intr(vals[ref*ncol ]), Util::intr(vals[ref*ncol+1]), Util::intr(vals[ref*ncol+2]) ); dataFom dat( vals[ref*ncol+col] ); data.set_data( hkl, dat ); } datafom.push_back( data ); opcols.push_back("W"+cols[col]); } // Flag if ( typs[col] == "I" ) { clipper::HKL_data data( hkls ); for ( int ref = 0; ref < nref; ref++ ) { clipper::HKL hkl( Util::intr(vals[ref*ncol ]), Util::intr(vals[ref*ncol+1]), Util::intr(vals[ref*ncol+2]) ); dataFlag dat( Util::max(Util::intr(vals[ref*ncol+col]), 0 ) ); data.set_data( hkl, dat ); } dataflag.push_back( data ); opcols.push_back("X"+cols[col]); } // HL coeffs if ( typs[col] == "A" && col < ncol-3 ) { clipper::HKL_data data( hkls ); for ( int ref = 0; ref < nref; ref++ ) { clipper::HKL hkl( Util::intr(vals[ref*ncol ]), Util::intr(vals[ref*ncol+1]), Util::intr(vals[ref*ncol+2]) ); dataABCD dat( vals[ref*ncol+col ], vals[ref*ncol+col+1], vals[ref*ncol+col+2], vals[ref*ncol+col+3] ); data.set_data( hkl, dat ); } dataabcd.push_back( data ); opcols.push_back("A"+cols[col]+","+cols[col+1]+","+cols[col+2]+","+cols[col+3]); col += 3; } } // Check for Fano/Iano without sigFano/sigIano if ( dataiano.size() > 0 && datasigiano.size() == 0 ) { clipper::HKL_data data( hkls ); dataSigIano dat( 1.0, 1.0 ); data = dat; datasigiano.push_back( data ); opcols.push_back("1SIGI+,SIGI-"); } if ( datafano.size() > 0 && datasigfano.size() == 0 ) { clipper::HKL_data data( hkls ); dataSigFano dat( 1.0, 1.0 ); data = dat; datasigfano.push_back( data ); opcols.push_back("2SIGF+,SIGF-"); } // Free-R flag conversion typedef clipper::HKL_info::HKL_reference_index HRI; if ( dataflag.size() > 0 ) { int n, n0, n1, fl, nfl; n = n0 = n1 = 0; for ( HRI ih = dataflag[0].first(); !ih.last(); ih.next() ) { if ( dataflag[0][ih].flag() >= 0 ) n++; if ( dataflag[0][ih].flag() == 0 ) n0++; if ( dataflag[0][ih].flag() == 1 ) n1++; } fl = 1; nfl = n1; // conventional CNS flag definition if ( n0 < n1/2 ) { fl = 0; nfl = n0; } // SHELX flag definition // generate CCP4 free flags int nfree = Util::intr( double(n) / double(nfl) ); for ( HRI ih = dataflag[0].first(); !ih.last(); ih.next() ) if ( dataflag[0][ih].flag() == fl ) // free: add to free set datafree[ih] = dataFlag( 0 ); else // missing or work: pick a working set datafree[ih] = dataFlag( rand()%(nfree-1) + 1 ); } else { int nfree = nref / 1000; if ( nfree < 10 ) nfree = 10; if ( nfree > 20 ) nfree = 20; for ( HRI ih = datafree.first(); !ih.last(); ih.next() ) datafree[ih] = dataFlag( rand()%nfree ); } // tidy phases for ( int i = 0; i < dataphi.size(); i++ ) for ( HRI ih = dataphi[i].first(); !ih.last(); ih.next() ) dataphi[i][ih].phi() = clipper::Util::mod( dataphi[i][ih].phi(), clipper::Util::twopi() ); // export clipper::CCP4MTZfile mtzout; mtzout.open_write( opfile ); mtzout.export_hkl_info( hkls ); for ( int i = 0; i < opcols.size(); i++ ) { // game name clipper::String ty = opcols[i].substr(0,1); clipper::String nm = "/*/*/["+opcols[i].substr(1)+"]"; // count which column to export int pos = 0; for ( int j = 0; j < i; j++ ) if ( opcols[i][0] == opcols[j][0] ) pos++; // and export if ( ty == "I" ) mtzout.export_hkl_data( dataiano[pos], nm ); if ( ty == "1" ) mtzout.export_hkl_data( datasigiano[pos], nm ); if ( ty == "F" ) mtzout.export_hkl_data( datafano[pos], nm ); if ( ty == "2" ) mtzout.export_hkl_data( datasigfano[pos], nm ); if ( ty == "i" ) mtzout.export_hkl_data( datai[pos], nm ); if ( ty == "f" ) mtzout.export_hkl_data( dataf[pos], nm ); if ( ty == "E" ) mtzout.export_hkl_data( datae[pos], nm ); if ( ty == "S" ) mtzout.export_hkl_data( datasig[pos], nm ); if ( ty == "P" ) mtzout.export_hkl_data( dataphi[pos], nm ); if ( ty == "W" ) mtzout.export_hkl_data( datafom[pos], nm ); if ( ty == "X" ) mtzout.export_hkl_data( dataflag[pos], nm ); if ( ty == "A" ) mtzout.export_hkl_data( dataabcd[pos], nm ); } mtzout.export_hkl_data( datafree, "/*/*/[FreeF_flag]" ); mtzout.close_write(); // output std::cout << ( anom ? "Collecting HKL and -HKL" : "Not collecting HKL and -HKL - anomalous data will be lost." ) << std::endl; std::cout << ( complete ? "Inserting missing reflections" : "Not inserting missing reflections" ) << std::endl; std::cout << "Number of reflections input : " << nref << std::endl; std::cout << "Number of reflections output: " << hkls.num_reflections() << std::endl; } clipper-2.1/examples/convert2mtz.h0000644000374100011300000002622510736662171014231 00000000000000// clipper CNS->MTZ utility /* (C) 2007 Kevin Cowtan */ #include #include #include using clipper::ftype; using clipper::xtype; using clipper::String; using clipper::Datatype_base; using clipper::Util; //! Reflection data type: I class dataI : private Datatype_base { public: dataI() { Util::set_null(i_); } dataI( const float& i ) : i_(i) {} void set_null() { Util::set_null(i_); } static String type() { return ""; } void friedel() {} void shift_phase(const ftype& dphi) {} bool missing() const { return (Util::is_nan(i_)); } static int data_size() { return 1; } static String data_names() { return "I"; } void data_export( xtype array[] ) const { array[0] = I(); } void data_import( const xtype array[] ) { I() = array[0]; } void scale(const ftype& s) { i_ *= s*s; } // accessors const float& I() const { return i_; } // #include #include extern "C" { #include } int main( int argc, char** argv ) { CCP4Program prog( "caniso", "0.1", "$Date: 2007/03/01" ); // defaults enum ANISO { NONE, FOBS, FCAL }; clipper::String title; clipper::String ipfile = "NONE"; clipper::String ipcolfo = "NONE"; clipper::String opfile = "aniso.mtz"; clipper::String opcol = "aniso"; double resflt = -1.0; // command input CCP4CommandInput args( argc, argv, true ); int arg = 0; while ( ++arg < args.size() ) { if ( args[arg] == "-title" ) { if ( ++arg < args.size() ) title = args[arg]; } else if ( args[arg] == "-mtzin" ) { if ( ++arg < args.size() ) ipfile = args[arg]; } else if ( args[arg] == "-colin-fo" ) { if ( ++arg < args.size() ) ipcolfo = args[arg]; } else if ( args[arg] == "-mtzout" ) { if ( ++arg < args.size() ) opfile = args[arg]; } else if ( args[arg] == "-colout" ) { if ( ++arg < args.size() ) opcol = args[arg]; } else if ( args[arg] == "-resolution-filter" ) { if ( ++arg < args.size() ) resflt = clipper::String(args[arg]).f(); } else { std::cout << "Unrecognized:\t" << args[arg] << "\n"; args.clear(); } } if ( args.size() <= 1 ) { std::cout << "Usage: caniso\n\t-mtzin \n\t-colin-fo \n\t-mtzout \n\t-colout \nAnisotropy correction.\n"; exit(1); } // make data objects clipper::CCP4MTZfile mtzin, mtzout; clipper::MTZcrystal cxtl; clipper::HKL_info hkls; typedef clipper::HKL_data_base::HKL_reference_index HRI; using clipper::data32::F_sigF; mtzin.set_column_label_mode( clipper::CCP4MTZfile::Legacy ); // open file mtzin.open_read( ipfile ); mtzin.import_hkl_info( hkls ); mtzin.import_crystal( cxtl, ipcolfo+".F_sigF.F" ); clipper::HKL_data fo( hkls, cxtl ); mtzin.import_hkl_data( fo, ipcolfo ); if ( opcol[0] != '/' ) opcol = mtzin.assigned_paths()[0].notail()+"/"+opcol; mtzin.close_read(); // scale structure factors clipper::SFscale_aniso::TYPE F = clipper::SFscale_aniso::F; clipper::SFscale_aniso::MODE M = clipper::SFscale_aniso::NORMAL; clipper::SFscale_aniso sfscl( 3.0, M ); sfscl( fo, resflt, 12 ); std::cout << "\nAnisotropic scaling:\n" << sfscl.u_aniso_orth(F).format() << "\n"; // output data mtzout.open_append( ipfile, opfile ); mtzout.export_hkl_data( fo, opcol ); mtzout.close_append(); } clipper-2.1/examples/cecalc.cpp0000644000374100011300000000637011221530271013461 00000000000000// Clipper app to do E calc /* Copyright 2003-2004 Kevin Cowtan & University of York all rights reserved */ #include #include extern "C" { #include } int main( int argc, char** argv ) { CCP4Program prog( "cecalc", "0.1", "$Date: 2004/07/01" ); // defaults clipper::String title; clipper::String ipfile = "NONE"; clipper::String ipcolfo = "NONE"; clipper::String opfile = "ecalc.mtz"; clipper::String opcol = "ecalc"; const int nprm = 12; // command input CCP4CommandInput args( argc, argv, true ); int arg = 0; while ( ++arg < args.size() ) { if ( args[arg] == "-title" ) { if ( ++arg < args.size() ) title = args[arg]; } else if ( args[arg] == "-mtzin" ) { if ( ++arg < args.size() ) ipfile = args[arg]; } else if ( args[arg] == "-mtzout" ) { if ( ++arg < args.size() ) opfile = args[arg]; } else if ( args[arg] == "-colin-fo" ) { if ( ++arg < args.size() ) ipcolfo = args[arg]; } else if ( args[arg] == "-colout" ) { if ( ++arg < args.size() ) opcol = args[arg]; } else { std::cout << "Unrecognized:\t" << args[arg] << "\n"; args.clear(); } } if ( args.size() <= 1 ) { std::cout << "Usage: cecalc\n\t-mtzin \n\t-mtzout \n\t-colin-fo \n\t-colout \nCalculate E's from F's\n"; exit(1); } // make data objects clipper::CCP4MTZfile mtzin, mtzout; clipper::HKL_info hkls; typedef clipper::HKL_data_base::HKL_reference_index HRI; mtzin.set_column_label_mode( clipper::CCP4MTZfile::Legacy ); // open file mtzin.open_read( ipfile ); mtzin.import_hkl_info( hkls ); clipper::HKL_data fsig( hkls ); mtzin.import_hkl_data( fsig, ipcolfo ); if ( opcol[0] != '/' ) opcol = mtzin.assigned_paths()[0].notail()+"/"+opcol; mtzin.close_read(); // create initial E clipper::HKL_data esig( hkls ); esig.compute( fsig, clipper::data32::Compute_EsigE_from_FsigF() ); // calc E-scaling std::vector params_init( nprm, 1.0 ); clipper::BasisFn_spline basis_fo( esig, nprm, 2.0 ); clipper::TargetFn_scaleEsq target_fo( esig ); clipper::ResolutionFn escale( hkls, basis_fo, target_fo, params_init ); // apply E-scaling for ( HRI ih = esig.first(); !ih.last(); ih.next() ) if ( 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maintainer-clean-generic mostlyclean mostlyclean-compile \ mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \ tags uninstall uninstall-am uninstall-binPROGRAMS # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: clipper-2.1/examples/cmodeltoseq.cpp0000644000374100011300000000462011114746561014576 00000000000000// Clipper app to get sequence from model /* Copyright 2008 Kevin Cowtan & University of York all rights reserved */ #include #include #include #include extern "C" { #include } int main( int argc, char** argv ) { CCP4Program prog( "cmodeltoseq", "0.1", "$Date: 2008/06/09" ); // defaults clipper::String title; clipper::String ippdb = "NONE"; clipper::String opseq = "modeltoseq.seq"; // command input CCP4CommandInput args( argc, argv, true ); int arg = 0; while ( ++arg < args.size() ) { if ( args[arg] == "-title" ) { if ( ++arg < args.size() ) title = args[arg]; } else if ( args[arg] == "-pdbin" ) { if ( ++arg < args.size() ) ippdb = args[arg]; } else if ( args[arg] == "-seqout" ) { if ( ++arg < args.size() ) opseq = args[arg]; } else { std::cout << "Unrecognized:\t" << args[arg] << "\n"; args.clear(); } } if ( args.size() <= 1 ) { std::cout << "Usage: cmodeltoseq\n\t-pdbin \n\t-seqout \nGet sequence from model\n"; exit(1); } // atomic models const int mmdbflags = MMDBF_IgnoreBlankLines | MMDBF_IgnoreDuplSeqNum | MMDBF_IgnoreNonCoorPDBErrors | MMDBF_IgnoreRemarks; clipper::MMDBfile mmdbwrk; clipper::MiniMol molwrk; mmdbwrk.SetFlag( mmdbflags ); mmdbwrk.read_file( ippdb ); mmdbwrk.import_minimol( molwrk ); // assemble sequences const char rtype1[21] = { 'A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V', 'M'}; const char rtype3[21][4] = {"ALA","ARG","ASN","ASP","CYS","GLN","GLU","GLY","HIS","ILE", "LEU","LYS","MET","PHE","PRO","SER","THR","TRP","TYR","VAL", "MSE"}; const int ntype = sizeof( rtype1 ) / sizeof( rtype1[0] ); clipper::String seqfile = ""; for ( int c = 0; c < molwrk.size(); c++ ) { clipper::String id = molwrk[c].id(); clipper::String seq = ""; for ( int r = 0; r < molwrk[c].size(); r++ ) { char symbol = ' '; for ( int t = 0; t < ntype; t++ ) if ( molwrk[c][r].type() == rtype3[t] ) symbol = rtype1[t]; if ( symbol != ' ' ) seq = seq + symbol; } if ( seq.length() > 0 ) seqfile = seqfile + "> " + id + "\n\n" + seq + "\n\n"; } // write file std::ofstream file( opseq.c_str() ); file << seqfile; file.close(); } clipper-2.1/examples/cphasematch.cpp0000644000374100011300000003330711226573166014546 00000000000000// Clipper app to match origins and calculate phase statistics /* Copyright 2003-2004 Kevin Cowtan & University of York all rights reserved */ #include #include #include extern "C" { #include } int main( int argc, char** argv ) { CCP4Program prog( "cphasematch", "0.1", "$Date: 2004/06/01" ); // defaults clipper::String title; clipper::String ipfile = "NONE"; clipper::String ipcolfo = "NONE"; clipper::String ipcolhl1 = "NONE"; clipper::String ipcolpw1 = "NONE"; clipper::String ipcolfc1 = "NONE"; clipper::String ipcolhl2 = "NONE"; clipper::String ipcolpw2 = "NONE"; clipper::String ipcolfc2 = "NONE"; clipper::String opfile = "NONE"; clipper::String opcol = "phasematch"; int res_bins = 12; int fom_bins = 20; bool omatch = true; // command input CCP4CommandInput args( argc, argv, true ); int arg = 0; while ( ++arg < args.size() ) { if ( args[arg] == "-title" ) { if ( ++arg < args.size() ) title = args[arg]; } else if ( args[arg] == "-mtzin" ) { if ( ++arg < args.size() ) ipfile = args[arg]; } else if ( args[arg] == "-mtzout" ) { if ( ++arg < args.size() ) opfile = args[arg]; } else if ( args[arg] == "-colin-fo" ) { if ( ++arg < args.size() ) ipcolfo = args[arg]; } else if ( args[arg] == "-colin-hl-1" ) { if ( ++arg < args.size() ) ipcolhl1 = args[arg]; } else if ( args[arg] == "-colin-phifom-1" ) { if ( ++arg < args.size() ) ipcolpw1 = args[arg]; } else if ( args[arg] == "-colin-fc-1" ) { if ( ++arg < args.size() ) ipcolfc1 = args[arg]; } else if ( args[arg] == "-colin-hl-2" ) { if ( ++arg < args.size() ) ipcolhl2 = args[arg]; } else if ( args[arg] == "-colin-phifom-2" ) { if ( ++arg < args.size() ) ipcolpw2 = args[arg]; } else if ( args[arg] == "-colin-fc-2" ) { if ( ++arg < args.size() ) ipcolfc2 = args[arg]; } else if ( args[arg] == "-colout" ) { if ( ++arg < args.size() ) opcol = args[arg]; } else if ( args[arg] == "-resolution-bins" ) { if ( ++arg < args.size() ) res_bins = clipper::String(args[arg]).i(); } else if ( args[arg] == "-no-origin-hand" ) { omatch = false; } else { std::cout << "Unrecognized:\t" << args[arg] << "\n"; args.clear(); } } if ( args.size() <= 1 ) { std::cout << "Usage: cphasematch\n\t-mtzin \n\t-mtzout \n\t-colin-fo \n\t-colin-hl-1 \n\t-colin-phifom-1 \n\t-colin-fc-1 \n\t-colin-hl-2 \n\t-colin-phifom-2 \n\t-colin-fc-2 \n\t-colout \n\t-resolution-bins \n\t-no-origin-hand\nInput fo and any one of fc/phifom/abcd for each of dataset 1 and 2.\nIf mtzout is given, the second dataset is shifted to match the first.\n"; exit(1); } // make data objects clipper::CCP4MTZfile mtzin, mtzout; clipper::HKL_info hkls; clipper::HKL_info::HKL_reference_index ih; mtzin.set_column_label_mode( clipper::CCP4MTZfile::Legacy ); // actual work mtzin.open_read( ipfile ); mtzin.import_hkl_info( hkls ); clipper::HKL_data fsig( hkls ); clipper::HKL_data phiw1( hkls ); clipper::HKL_data abcd1( hkls ); clipper::HKL_data fphi1( hkls ); clipper::HKL_data phiw2( hkls ); clipper::HKL_data abcd2( hkls ); clipper::HKL_data fphi2( hkls ); mtzin.import_hkl_data( fsig, ipcolfo ); if ( ipcolhl1 != "NONE" ) mtzin.import_hkl_data( abcd1, ipcolhl1 ); if ( ipcolpw1 != "NONE" ) mtzin.import_hkl_data( phiw1, ipcolpw1 ); if ( ipcolfc1 != "NONE" ) mtzin.import_hkl_data( fphi1, ipcolfc1 ); if ( ipcolhl2 != "NONE" ) mtzin.import_hkl_data( abcd2, ipcolhl2 ); if ( ipcolpw2 != "NONE" ) mtzin.import_hkl_data( phiw2, ipcolpw2 ); if ( ipcolfc2 != "NONE" ) mtzin.import_hkl_data( fphi2, ipcolfc2 ); if ( opcol[0] != '/' ) opcol = mtzin.assigned_paths()[0].notail()+"/"+opcol; mtzin.close_read(); // fill in data for input 1 if ( ipcolhl1 != "NONE" ) { phiw1.compute( abcd1, clipper::data32::Compute_phifom_from_abcd() ); fphi1.compute( fsig, phiw1, clipper::data32::Compute_fphi_from_fsigf_phifom() ); } else if ( ipcolpw1 != "NONE" ) { abcd1.compute( phiw1, clipper::data32::Compute_abcd_from_phifom() ); fphi1.compute( fsig, phiw1, clipper::data32::Compute_fphi_from_fsigf_phifom() ); } else if ( ipcolfc1 != "NONE" ) { for ( ih = hkls.first(); !ih.last(); ih.next() ) { phiw1[ih].phi() = fphi1[ih].phi(); phiw1[ih].fom() = 0.9998; } abcd1.compute( phiw1, clipper::data32::Compute_abcd_from_phifom() ); } else { clipper::Message::message( clipper::Message_fatal( "Missing input 1" ) ); } // fill in data for input 2 if ( ipcolhl2 != "NONE" ) { phiw2.compute( abcd2, clipper::data32::Compute_phifom_from_abcd() ); fphi2.compute( fsig, phiw2, clipper::data32::Compute_fphi_from_fsigf_phifom() ); } else if ( ipcolpw2 != "NONE" ) { abcd2.compute( phiw2, clipper::data32::Compute_abcd_from_phifom() ); fphi2.compute( fsig, phiw2, clipper::data32::Compute_fphi_from_fsigf_phifom() ); } else if ( ipcolfc2 != "NONE" ) { for ( ih = hkls.first(); !ih.last(); ih.next() ) { phiw2[ih].phi() = fphi2[ih].phi(); phiw2[ih].fom() = 0.9998; } abcd2.compute( phiw2, clipper::data32::Compute_abcd_from_phifom() ); } else { clipper::Message::message( clipper::Message_fatal( "Missing input 2" ) ); } // crude mean phase error double sw1 = 0.0, sd1 = 0.0; for ( ih = hkls.first(); !ih.last(); ih.next() ) if ( !fphi1[ih].missing() && !fphi2[ih].missing() ) { double w = 1.0 / ih.hkl_class().epsilon(); sw1 += w; sd1 += w * acos( cos( fphi1[ih].phi() - fphi2[ih].phi() ) ); } // calculate phase shift bool invert( false ); clipper::Coord_frac x( 0.0, 0.0, 0.0 ); if ( omatch ) clipper::OriginMatch( invert, x, fphi1, fphi2 ); if ( invert ) std::cout << std::endl << " Change of hand : YES" << std::endl; else std::cout << std::endl << " Change of hand : NO" << std::endl; std::cout << " Change of origin: " << x.format() << std::endl << " (Shift is applied to second set of phases to match first)" << std::endl << std::endl; // shift phases for ( ih = hkls.first(); !ih.last(); ih.next() ) { clipper::Coord_reci_frac h( ih.hkl() ); const double hx = h * x; const double dphi = clipper::Util::twopi() * ( hx - floor(hx) ); if ( invert ) fphi2[ih].friedel(); if ( invert ) phiw2[ih].friedel(); if ( invert ) abcd2[ih].friedel(); fphi2[ih].shift_phase( dphi ); phiw2[ih].shift_phase( dphi ); abcd2[ih].shift_phase( dphi ); } // crude mean phase error double sw2 = 0.0, sd2 = 0.0; for ( ih = hkls.first(); !ih.last(); ih.next() ) if ( !fphi1[ih].missing() && !fphi2[ih].missing() ) { double w = 1.0 / ih.hkl_class().epsilon(); sw2 += w; sd2 += w * acos( cos( fphi1[ih].phi() - fphi2[ih].phi() ) ); } // verify the origin shift with crude stats std::cout << " Mean phase error before origin fixing: " << clipper::Util::rad2d( sd1/sw1 ) << std::endl; std::cout << " Mean phase error after origin fixing: " << clipper::Util::rad2d( sd2/sw2 ) << std::endl; // output shifted phases if required if ( opfile != "NONE" ) { mtzout.open_append( ipfile, opfile ); if ( ipcolhl2 != "NONE" ) { mtzout.export_hkl_data( abcd2, opcol ); } else if ( ipcolpw2 != "NONE" ) { mtzout.export_hkl_data( phiw2, opcol ); } else if ( ipcolfc2 != "NONE" ) { mtzout.export_hkl_data( fphi2, opcol ); } mtzout.close_append(); } // NOW DO DETAILED REFLECTION STATISTICS // calculate E scale factor const int nprm = 10; clipper::HKL_data esig( hkls ); esig.compute( fsig, clipper::data32::Compute_EsigE_from_FsigF() ); std::vector params_init( nprm, 1.0 ); clipper::BasisFn_binner basis_fo( hkls, nprm, 2.0 ); clipper::TargetFn_scaleEsq target_fo( esig ); clipper::ResolutionFn escale( hkls, basis_fo, target_fo, params_init ); // accumulate stats in bins and overall clipper::Resolution_ordinal resord; resord.init( hkls, 1.0 ); int res_binx = res_bins + 1; double res_scl = 0.9999 * double( res_bins ); std::vector snr(res_binx,0.0), swr(res_binx,0.0), sw1r(res_binx,0.0), sw2r(res_binx,0.0), sdr(res_binx,0.0), sdw1r(res_binx,0.0), sdw2r(res_binx,0.0), scr1(res_binx,0.0), scr2(res_binx,0.0), scr12(res_binx,0.0), scer1(res_binx,0.0), scer2(res_binx,0.0), scer12(res_binx,0.0), sww1(res_binx,0.0), sww2(res_binx,0.0), sdw1(res_binx,0.0), sdw2(res_binx,0.0); std::vector nrfl1(fom_bins,0.0), nrfl2(fom_bins,0.0), mcosd1(fom_bins,0.0), mcosd2(fom_bins,0.0); for ( ih = hkls.first(); !ih.last(); ih.next() ) if ( !fphi1[ih].missing() && !fphi2[ih].missing() ) { int bin = int( res_scl * resord.ordinal( ih.invresolsq() ) ); double w = 1.0 / ih.hkl_class().epsilon(); double cosd = cos( phiw1[ih].phi() - phiw2[ih].phi() ); double d = acos(cosd); snr[bin] += 1.0; swr[bin] += w; sw1r[bin] += w * phiw1[ih].fom(); sw2r[bin] += w * phiw2[ih].fom(); sdr[bin] += w * d; sdw1r[bin] += w * phiw1[ih].fom() * d; sdw2r[bin] += w * phiw2[ih].fom() * d; scr1[bin] += w * fphi1[ih].f() * fphi1[ih].f(); scr2[bin] += w * fphi2[ih].f() * fphi2[ih].f(); scr12[bin] += w * fphi1[ih].f() * fphi2[ih].f() * cosd; sww1[bin] += w * phiw1[ih].fom() * phiw1[ih].fom(); sww2[bin] += w * phiw2[ih].fom() * phiw2[ih].fom(); sdw1[bin] += w * phiw1[ih].fom() * d; sdw2[bin] += w * phiw2[ih].fom() * d; snr[res_bins] += 1.0; swr[res_bins] += w; sw1r[res_bins] += w * phiw1[ih].fom(); sw2r[res_bins] += w * phiw2[ih].fom(); sdr[res_bins] += w * d; sdw1r[res_bins] += w * phiw1[ih].fom() * d; sdw2r[res_bins] += w * phiw2[ih].fom() * d; scr1[res_bins] += w * fphi1[ih].f() * fphi1[ih].f(); scr2[res_bins] += w * fphi2[ih].f() * fphi2[ih].f(); scr12[res_bins] += w * fphi1[ih].f() * fphi2[ih].f() * cosd; sww1[res_bins] += w * phiw1[ih].fom() * phiw1[ih].fom(); sww2[res_bins] += w * phiw2[ih].fom() * phiw2[ih].fom(); sdw1[res_bins] += w * cosd * phiw1[ih].fom(); sdw2[res_bins] += w * cosd * phiw2[ih].fom(); w *= escale.f(ih); scer1[bin] += w * fphi1[ih].f() * fphi1[ih].f(); scer2[bin] += w * fphi2[ih].f() * fphi2[ih].f(); scer12[bin] += w * fphi1[ih].f() * fphi2[ih].f() * cosd; scer1[res_bins] += w * fphi1[ih].f() * fphi1[ih].f(); scer2[res_bins] += w * fphi2[ih].f() * fphi2[ih].f(); scer12[res_bins] += w * fphi1[ih].f() * fphi2[ih].f() * cosd; bin = clipper::Util::bound(0, int(double(fom_bins)*phiw1[ih].fom()), fom_bins-1); nrfl1[bin] += 1.0; mcosd1[bin] += cosd; bin = clipper::Util::bound(0, int(double(fom_bins)*phiw2[ih].fom()), fom_bins-1); nrfl2[bin] += 1.0; mcosd2[bin] += cosd; } // finalise statistics for ( int bin = 0; bin < res_binx; bin++ ) { // phase differences sdr[bin] /= clipper::Util::max( swr[bin], 1.0 ); sdw1r[bin] /= clipper::Util::max( sw1r[bin], 1.0 ); sdw2r[bin] /= clipper::Util::max( sw2r[bin], 1.0 ); // mean foms sw1r[bin] /= clipper::Util::max( swr[bin], 1.0 ); sw2r[bin] /= clipper::Util::max( swr[bin], 1.0 ); // correlation scr12[bin] /= sqrt( clipper::Util::max( scr1[bin]*scr2[bin], 1.0 ) ); scer12[bin] /= sqrt( clipper::Util::max( scer1[bin]*scer2[bin], 1.0 ) ); // Qfom sdw1[bin] /= sww1[bin]; sdw2[bin] /= sww2[bin]; } for ( int bin = 0; bin < fom_bins; bin++ ) { if ( nrfl1[bin] > 0.5 ) mcosd1[bin] /= nrfl1[bin]; if ( nrfl2[bin] > 0.5 ) mcosd2[bin] /= nrfl2[bin]; } // and display resord.invert(); printf("\n $TABLE: Phase statistics with resolution:\n $GRAPHS: vs resolution:N:1,4,5:\n :Unweighted and weighted vs resolution:N:1,6,7,8:\n :Reflection correlation vs resolution:N:1,9,10:\n $$\n 1/resol^2 hi Nrefl w1 w2 wFcorr wEcorr $$\n $$\n"); for ( int bin = 0; bin < res_bins; bin++ ) printf( "%6.3f %6.3f %7i %6.3f %6.3f %7.2f %7.2f %7.2f %6.3f %6.3f\n", resord.ordinal( double(bin)/res_scl ), resord.ordinal( double(bin+0.999)/res_scl ), int(snr[bin]), sw1r[bin], sw2r[bin], clipper::Util::rad2d(sdr[bin]), clipper::Util::rad2d(sdw1r[bin]), clipper::Util::rad2d(sdw2r[bin]), scr12[bin], scer12[bin] ); printf(" $$\n"); printf("\n $TABLE: Phase analysis with FOM:\n $GRAPHS:Histogram of FOM1:N:1,3:\n :Phase difference vs FOM1:N:1,2,4:\n :Histogram of FOM2:N:1,5:\n :Phase difference vs FOM2:N:1,2,6:\n $$\n FOM acos(FOM) N(FOM1) acos N(FOM2) acos$$\n $$\n"); for ( int bin = 0; bin < fom_bins; bin++ ) printf( "%9.3f %9.3f %9.0f %9.3f %9.0f %9.3f\n", (double(bin)+0.5)/double(fom_bins), clipper::Util::rad2d(acos((double(bin)+0.5)/double(fom_bins))), nrfl1[bin],clipper::Util::rad2d(acos(mcosd1[bin])), nrfl2[bin],clipper::Util::rad2d(acos(mcosd2[bin])) ); printf(" $$\n"); printf("\nOverall statistics:\n Nrefl w1 w2 wFcorr wEcorr Qfom1 Qfom2\n"); printf( "%7i %6.3f %6.3f %7.2f %7.2f %7.2f %6.3f %6.3f %6.3f %6.3f\n", int(snr[res_bins]), sw1r[res_bins], sw2r[res_bins], clipper::Util::rad2d(sdr[res_bins]), clipper::Util::rad2d(sdw1r[res_bins]), clipper::Util::rad2d(sdw2r[res_bins]), scr12[res_bins], scer12[res_bins], sdw1[res_bins], sdw2[res_bins] ); } clipper-2.1/examples/cpatterson.cpp0000644000374100011300000001427011221530315014426 00000000000000// Clipper app to perform ffts and map stats /* Copyright 2003-2004 Kevin Cowtan & University of York all rights reserved */ #include #include #include int main( int argc, char** argv ) { CCP4Program prog( "cpatterson", "0.1", "$Date: 2004/07/01" ); // defaults clipper::String title; clipper::String ipfile = "NONE"; clipper::String ipcolf = "NONE"; clipper::String ipcold = "NONE"; clipper::String ipcola = "NONE"; clipper::String ipcolh = "NONE"; clipper::String opfile = "patterson.map"; bool adiff = false; bool oremv = false; double limit_e = 1.0e20; double weight_e = 0.0; clipper::Resolution reso; clipper::Grid_sampling grid; const int nprm = 12; // command input CCP4CommandInput args( argc, argv, true ); int arg = 0; while ( ++arg < args.size() ) { if ( args[arg] == "-title" ) { if ( ++arg < args.size() ) title = args[arg]; } else if ( args[arg] == "-mtzin" ) { if ( ++arg < args.size() ) ipfile = args[arg]; } else if ( args[arg] == "-mapout" ) { if ( ++arg < args.size() ) opfile = args[arg]; } else if ( args[arg] == "-colin-fo" ) { if ( ++arg < args.size() ) ipcolf = args[arg]; } else if ( args[arg] == "-colin-fano" ) { if ( ++arg < args.size() ) ipcola = args[arg]; } else if ( args[arg] == "-colin-fdiff" ) { if ( ++arg < args.size() ) ipcold = args[arg]; } else if ( args[arg] == "-resolution" ) { if ( ++arg < args.size() ) { reso = clipper::Resolution( clipper::String(args[arg]).f() ); } } else if ( args[arg] == "-grid" ) { if ( ++arg < args.size() ) { std::vector g = clipper::String(args[arg]).split(", "); grid = clipper::Grid_sampling( g[0].i(), g[1].i(), g[2].i() ); } } else if ( args[arg] == "-e-limit" ) { if ( ++arg < args.size() ) limit_e = clipper::String(args[arg]).f(); } else if ( args[arg] == "-e-weight" ) { if ( ++arg < args.size() ) weight_e = clipper::String(args[arg]).f(); } else if ( args[arg] == "-anomalous" ) { adiff = true; } else if ( args[arg] == "-origin-removal" ) { oremv = true; } else { std::cout << "Unrecognized:\t" << args[arg] << "\n"; args.clear(); } } if ( args.size() <= 1 ) { std::cout << "Usage: cpatterson\n\t-mtzin \n\t-mapout \n\t-colin-fo \n\t-colin-fano \n\t-colin-fdiff \n\t-resolution \n\t-grid ,,\n\t-e-limit \n\t-e-weight \n\t-anomalous\n\t-origin-removal\nCalculate Patterson from Fobs or Fano.\nFor E-Patterson = 1, for F-Patterson = 0, and other values.\n can reject reflections or differences by E-value.\n"; exit(1); } // make data objects clipper::CCP4MTZfile mtzin; clipper::MTZcrystal cxtl; clipper::HKL_info hkls, hklp; typedef clipper::HKL_data_base::HKL_reference_index HRI; mtzin.set_column_label_mode( clipper::CCP4MTZfile::Legacy ); // open file mtzin.open_read( ipfile ); clipper::Spacegroup spgr = mtzin.spacegroup(); clipper::Cell cell = mtzin.cell(); if ( ipcolf != "NONE" ) mtzin.import_crystal( cxtl, ipcolf+".F_sigF.F" ); if ( ipcola != "NONE" ) mtzin.import_crystal( cxtl, ipcola+".F_sigF_ano.F+"); if ( !cxtl.is_null() ) cell = cxtl; if ( reso.is_null() ) reso = mtzin.resolution(); hkls.init( spgr, cell, reso, true ); clipper::HKL_data fsig( hkls ); clipper::HKL_data dsig( hkls ); clipper::HKL_data fano( hkls ); if ( ipcolf != "NONE" ) mtzin.import_hkl_data( fsig, ipcolf ); if ( ipcola != "NONE" ) mtzin.import_hkl_data( fano, ipcola ); if ( ipcold != "NONE" ) mtzin.import_hkl_data( dsig, ipcolf ); mtzin.close_read(); // make mean/difference F if necessary if ( ipcola != "NONE" ) { if ( adiff ) fsig.compute( fano, clipper::data32::Compute_diff_fsigf_from_fsigfano() ); else fsig.compute( fano, clipper::data32::Compute_mean_fsigf_from_fsigfano() ); } // subtract difference F if necessary if ( ipcold != "NONE" ) for ( HRI ih = fsig.first(); !ih.last(); ih.next() ) if ( !fsig[ih].missing() && !dsig[ih].missing() ) fsig[ih].f() -= dsig[ih].f(); else fsig[ih].f() = 0.0; // calculate E scale factor clipper::HKL_data esig( hkls ); esig.compute( fsig, clipper::data32::Compute_EsigE_from_FsigF() ); std::vector params_init( nprm, 1.0 ); clipper::BasisFn_spline basis_fo( esig, nprm, 2.0 ); clipper::TargetFn_scaleEsq target_fo( esig ); clipper::ResolutionFn escale( hkls, basis_fo, target_fo, params_init ); // reject reflections by E-value for ( HRI ih = esig.first(); !ih.last(); ih.next() ) if ( !esig[ih].missing() ) if ( esig[ih].E() / sqrt( escale.f(ih) ) > limit_e ) fsig[ih] = clipper::data32::F_sigF(); // calculate E-F combination for ( HRI ih = fsig.first(); !ih.last(); ih.next() ) if ( !fsig[ih].missing() ) fsig[ih].scale( pow( escale.f(ih), 0.5*weight_e ) ); // get Patterson spacegroup clipper::Spacegroup pspgr( clipper::Spgr_descr( spgr.generator_ops().patterson_ops() ) ); hklp.init( pspgr, cell, reso, true ); // make patterson coeffs clipper::HKL_data fphi( hklp ); for ( HRI ih = fphi.first(); !ih.last(); ih.next() ) { clipper::data32::F_sigF f = fsig[ih.hkl()]; if ( !f.missing() ) { fphi[ih].f() = f.f()*f.f(); fphi[ih].phi() = 0.0 ; } } // origin removal if ( oremv ) { clipper::BasisFn_spline basis_fp( fphi, nprm, 2.0 ); clipper::TargetFn_meanFnth target_fp( fphi, 1.0 ); clipper::ResolutionFn oscale( hklp, basis_fp, target_fp, params_init ); for ( HRI ih = fphi.first(); !ih.last(); ih.next() ) if ( !fphi[ih].missing() ) fphi[ih].f() -= oscale.f(ih); } // make grid if necessary if ( grid.is_null() ) grid.init( pspgr, cell, reso ); // make xmap clipper::Xmap xmap( pspgr, cell, grid ); xmap.fft_from( fphi ); // write map clipper::CCP4MAPfile mapout; mapout.open_write( opfile ); mapout.export_xmap( xmap ); mapout.close_write(); } clipper-2.1/examples/maketestdata.cpp0000644000374100011300000001027411062443724014725 00000000000000// Clipper app to make test data /* Copyright 2003-2004 Kevin Cowtan & University of York all rights reserved */ #include #include #include #include #include #include #include extern "C" { #include } int main( int argc, char** argv ) { if ( argc == 1 ) { // do self tests std::cout << "Test core:\n"; clipper::Test_core test_core; bool result_core = test_core(); if ( result_core ) std::cout << "OK\n"; std::cout << "Test contrib:\n"; clipper::Test_contrib test_contrib; bool result_contrib = test_contrib(); if ( result_contrib ) std::cout << "OK\n"; // done self tests // error exit code if ( !( result_core && result_contrib ) ) exit(1); } else { // make data for self-tests // make data objects for reflection data clipper::CCP4MTZfile mtzin; clipper::HKL_info hkls; clipper::HKL_data fsig( hkls ); clipper::HKL_data abcd( hkls ); typedef clipper::HKL_data_base::HKL_reference_index HRI; // open file mtzin.open_read( argv[1] ); clipper::Spacegroup spgr = mtzin.spacegroup(); clipper::Cell cell = mtzin.cell(); clipper::Resolution reso( 5.0 ); hkls.init( spgr, cell, reso, true ); mtzin.import_hkl_data( fsig, "/*/*/[FNAT,SIGFNAT]" ); mtzin.import_hkl_data( abcd, "/*/*/[HLA,HLB,HLC,HLD]" ); mtzin.close_read(); // print data for ( HRI ih = hkls.first(); !ih.last(); ih.next() ) { if ( !fsig[ih].missing() && !abcd[ih].missing() ) { int h = ih.hkl().h(); int k = ih.hkl().k(); int l = ih.hkl().l(); double f = rint(fsig[ih].f()/0.1)*0.1; double sigf = rint(fsig[ih].sigf()/0.1)*0.1; double a = rint(abcd[ih].a()/0.01)*0.01; double b = rint(abcd[ih].b()/0.01)*0.01; double c = rint(abcd[ih].c()/0.01)*0.01; double d = rint(abcd[ih].d()/0.01)*0.01; std::cout << "{" << h << "," << k << "," << l << "," << f << "," << sigf << "," << a << "," << b << "," << c << "," << d << "},\n"; } } // make data objects for model data clipper::MMDBManager mmdb; mmdb.ReadPDBASCII( argv[2] ); // get a list of all the non-solvent atoms clipper::mmdb::PPCAtom psel; int hndl, nsel; hndl = mmdb.NewSelection(); mmdb.Select( hndl, STYPE_ATOM, "(!WAT,H2O,HOH)", SKEY_NEW ); mmdb.GetSelIndex( hndl, psel, nsel ); clipper::MMDBAtom_list atoms( psel, nsel ); mmdb.DeleteSelection( hndl ); // print data for ( int i = 0; i < atoms.size(); i++ ) { atoms[i].set_element( atoms[i].element().trim() ); double x = rint(atoms[i].coord_orth().x()/0.001)*0.001; double y = rint(atoms[i].coord_orth().y()/0.001)*0.001; double z = rint(atoms[i].coord_orth().z()/0.001)*0.001; double u_iso = rint(atoms[i].u_iso()/0.001)*0.001; double occ = rint(atoms[i].occupancy()/0.001)*0.001; std::cout << "{\"" << atoms[i].element() << "\"," << x << "," << y << "," << z << "," << u_iso << "," << occ << "},\n"; } // check the existing data clipper::data::Test_data data; for ( HRI ih = hkls.first(); !ih.last(); ih.next() ) { clipper::data32::F_sigF fs = data.hkl_data_f_sigf()[ih.hkl()]; if ( !fs.missing() ) if ( fabs( fs.f() - fsig[ih].f() ) > 0.05 ) std::cerr << "Err: " << ih.hkl().format() << "\n"; } for ( int i = 0; i < data.atom_list().size(); i++ ) { if ( atoms[i].element() != data.atom_list()[i].element() || fabs(atoms[i].u_iso() -data.atom_list()[i].u_iso() ) > 0.001 || fabs(atoms[i].occupancy()-data.atom_list()[i].occupancy()) > 0.001 || ( atoms[i].coord_orth() - data.atom_list()[i].coord_orth() ).lengthsq() > 0.001 ) { std::cerr << "Err: " << data.atom_list()[i].element() << "\t" << data.atom_list()[i].coord_orth().format() << "\n"; } } // make tables for big result lists clipper::Test_contrib test_contrib; std::fstream contrib_data( "test_contrib.dat", std::fstream::out ); test_contrib.set_stream( contrib_data ); test_contrib(); contrib_data.close(); // done make test data } } clipper-2.1/ChangeLog0000644000374100011300000003414211372264167011514 00000000000000Latest changes:
16/04/10:
Minor compatibility fixes. A lot of extra searching and selection functionality added to MiniMol.
15/12/09:
Update anisotropy correction code to handle I's and low resolution data. Update autoconf and bump so version.
14/07/09:
Update mtz write to give correct symbols. Extend csymmatch to handle waters and to do optional origin and hand matching. Provide legacy mtz column label syntax. gcc 4.4 fixes.
22/05/09:
Enable MiniMol to export alternate conformation codes. Correntions to new Clipper2-stype HKL_data handling.
20/05/09:
Clipper2-stype HKL_data handling extended, including CNS, CIF import. Experimental patch to allow clean shutdown in Coot. Screw operator decomposition in RTop_orth (Phil).
10/02/09:
Support for new extended CNS file import, minor warning fixes.
01/12/08:
2.1 release. Support for threading. New MLHL weighting function. Improved anisotropy correction. gcc 4.3 fixes.
18/11/08:
2.1 release. Support for threading. New MLHL weighting function. Improved anisotropy correction. gcc 4.3 fixes.
07/09/07:
Minor bug fix in Rotation::abs_angle. Avoid crash on reading pdb file with missing CRYST1. Compiler warning fix.
25/04/07:
Work around for compiler bug in gcc 3.2/3.3. No other changes.
12/04/07:
MTZ file creation from scratch fixes. Anisotropic scaling improvements. 'caniso' anisotropic correction tool. 'convert2mtz' file conversion tool. Autoconf build system option.
16/06/06:
Rotation fixes. Backport of ccp4 utilities from 2.0 branch.
31/08/05:
Minimol fix. Additional cfft output.
15/07/05:
Fedora Core 4 NaN fix. New mapfilter method to support NCS in pirate.
17/03/05:
Minor portability fixes for CCP4 release. 'Lattman' spelling fix (sorry).
25/02/05:
Minor portability fixes for CCP4 release.
22/11/04:
Minor portability fixes for CCP4 release.
22/10/04:
Added Fortran sfcalc demo code. Fix in SF weighting 'best' coeffs (from RWGK).
12/10/04:
Fixes and testing of SF calc, SF weighting. Additional cctbx methods. cmakereference app for pirate.
16/07/04:
Add some additional spacegroup methods, extend utilities and add 2 new utilties programs.
25/06/04:
Fix for compilation -O3 on gcc 3.2, other portability fixes, add 1 new jiffy programs.
16/06/04:
Add structure factor calculation with bulk solvent method, sigmaa spline method, add 3 new jiffy programs.
25/05/04:
Add error checking on mtz/map i/o, add origin/hand matching method, add map curvature methods, add 4 new jiffy programs.
06/04/04:
Synchronize to fixes in CCP4 libs.
08/03/04:
Bugfix in MiniMol export to MMDB.
18/02/04:
Bugfix in LogPhaseProb conversion to and from HL coeffs.
03/02/04:
Bugfixes in MiniMol, license update, CCP4v5 install.
27/10/03:
Virtual destructors adjusted for gcc 3.2 bug.
23/10/03:
MTZ History now preserved. Created MTZ's now fixed for common spacegroups. Virtual destructors supplied for all virtual bases (I hope).
08/10/03:
Second attempt at update for new CCP4 v5 libraries.
06/10/03:
Update for new CCP4 v5 libraries.
31/07/03:
New classes for phase probability distributions. Lots of portability fixes.
18/07/03:
License now LGPL (or CCP4 part 0). SCONS now build non-shared libraries on alpha and sun. rpath still not implmented.
07/06/03:
Resolution function tidyup, added SCONS build system.
30/05/03:
Bug fix release for xmap crash and gcc 2.95.3.
17/05/03:
API change from previous release reversed.
14/05/03:
Port Xmap and Spacegroup to ObjectCache architecture for improved performance.
24/04/03:
More documentation. Even more documentation. Documentation tidyup. MiniMol tidyup.
17/04/03:
New MMDB lightweight interface added. New MiniMol STL model added.
10/04/03:
Separated out old MMDB interface as separate package. Started work for ObjectCache architecture. Fixes for Windows build using MinGW.
27/03/03:
Support for new CCP4 C-libraries. New fast NaN tests.
12/03/03:
Fix reflection cif build. Fix to mmdb wrapper segfault.
04/03/03:
Reflection cif import added (Paul Emsley). Preparation for new MTZ interface. Minor updates.
14/02/03:
Tiny MMDB 'is_atom()' fix. Minor updates.
07/02/03:
Ported to Sun. This version tested on gcc 3.2, SGI, Alpha, Sun. Hopefully still builds on MacOSX and gcc 2.96 too.
20/01/03:
Implemented AtomShapeFn, with Agarwal coeffs for isotropic atoms.
10/01/03:
Minor cleanups.
08/01/03:
New FFFear methods, MapFilter methods, generic Euler angles.
10/12/02:
+=, -= implemented for all maps, Vec3<>s.
28/11/02:
Heavy spacegroup testing completed: see cctbxtest.
22/11/02:
Sparse FFT map added.
23/10/02:
Ramachandran class, FFFear methods, new FFTmap backend.
10/10/02:
All files and libraries reorganised, mccp4 and cctbx optional.
07/10/02:
Stand-alone spacegroup library.
30/09/02:
MMDB associative behaviour, MMDB unsorted selections, map statistics objects, map sorting object, PHS file i/o.
30/08/02:
Generic rotation class, least squares coordinate fitting, and lots of stress testing on real calculations.
18/07/02:
Function objects for structure factor calculations, skeletonisation. Message passing library added.
25/06/02:
Slight changes for skeletonisation.
24/06/02:
Anisotropic map calculation implemented (see sftest.cpp). Anisotropic basis function added to resolution function evaluator.
22/05/02:
Audit of communication in hierarchies completed. Minor changes to i/o classes.
08/05/02:
Form factor class added. Demo structure factor calculation added, using either FFT or direct summation. Map bug fixed (for spacegroups where symops do not commute, e.g. P422).
26/04/02:
Rewrite of coordinate types. Reflection datalist operators added.
21/03/02:
More complete MMDB wrapper. New classes for Aniso U's.
16/03/02:
First attempt at MMDB wrapper object. Numerous other cleanups.
05/03/02:
NX_operator, NXmap_operator added. Pluggable interpolators added. Code style imporvements. Resolution function evaluator speedups. New mccp4 library.
12/02/02:
More documentation, cleanups.
09/02/02:
Added lots of conversion operators for structure factor arithmetic and manipulation of HL coeffs. A new mini-ccp4 library includes both mmtzlib and cmaplib. Most importantly, the SGI PORT IS WORKING. There is now a 'fake' configure script which detect the platform. You'll need up to date compilers and gmake.
30/01/02:
Cleanups, more documentation.
23/01/02:
Hopefully finished method renaming, updated fft example.
22/01/02:
Major rewrite of the container hierarchy, including new inheritables (resolution, grid sampling), updated i/o classes, more flexibility, more automation. In particular containers can now be stored in STL vectors.
13/01/02:
New classes for grid samplings (consistent with spacegroup, cell, resolution and FFT), and reciprocal space fractional and orthogonal coordinates. Documentation improvements (now 250 pages).
11/01/02:
Bspline FFTmap class added. Classes for orthogonal and fractional gradients and curvatures and their transformations added. Map I/O class now imports and exports NXmap<>s.
07/01/02:
Map I/O class now imports and exports Xmap<>s. NXmap<>s coming soon. The patched CMAP lib has now been packaged, and the auto-install script updated accordingly.
04/01/02:
Map I/O class started. Map import is working, as long as you have a hacked version of the CMAP lib. I'll tidy this up for distribution as soon as I can.
19/12/01:
More tidyups.
15/12/01:
More tidyups.
13/12/01:
More tidyups: easier MTZ import function, lose the last few pointer methods, fill in some default parameters to allow default name generation for container objects.
08/12/01:
Basic interpolation methods added to Xmap. Documentation improvements.
05/12/01:
Smooth bspline resolution basis function implemented. Lots more cleanups.
04/12/01:
'cfft' works again. Major cleanups. 'HKL_data_base' now contains a full list of virtual functions. Naive binner replaced with something rather more sensible.
03/12/01:
Implemented the strict donor/recipient model for inheriting cell and spacegroup information. Some tidying up will probably be needed. I think cfft is broken - I don't know when this happened yet.
01/12/01:
Iterators and reflection classes renamed to something clearer. Updated to use cctbx 1.0. That should make installation rather simpler.
29/11/01:
The mtz i/o layer has been abstracted from the Clipper core, i.e. Clipper is now completely independent of MTZ (and therefore CCP4). This should make it very simple to interface to other file formats, e.g. CNS, and eventually the PHENIX database.
A sigmaa-target has been implemented for the resolution function evaluator. Convergence is not very fast since it doesn't know how to pick sensible starting values, and it produces copious debugging output, but I think it is working.
01/11/01:
Conversion operators to convert between HKL_data types are implented. (Unary only for now, but binary operators are easy). A sample operator to convert phi_fom to abcd is provided. The reciprocal ASU is now mandatory, as this allows rather faster symmetry lookups.
15/10/01:
Resolution function evaluator implemented. This will evaluate an arbitrary function of HKL, by optimising the parameters of a user defined basis function to minimise a user defined target functions. This completely replaces the idea of 'resolution bins', and does a lot of other things besides. A terget for mean |F|2 is provided, a sigmaa taget shouldn't be too hard.
FFTw config has changed again: FFTw should be configured with just --enable-float
01/10/01:
Do type conversion in fft's. FFTw should be configured with --enable-float --enable-type-prefix
25/09/01:
Update to latest version of cctbx.
10/09/01:
Small tidyups and documentation improvements.
04/09/01:
Various small tidyups and documentation improvements. umtzlib extended to handle multi-record MTZ files.
01/09/01:
MTZ interface completely replaced. MTZ i/o is now handled through a new lightweight C library: umtzlib/mmtzlib (Micro/Mini mtzlib). The mtz i/o interface has also been cleaned up.
16/08/01:
Interface redesign completed. The whole package is now (at least from the outside) written in such a way that programs can be written without using new, delete, or pointers. License changed to CCP4 part (i).
09/08/01:
FFTs implemented! You'll need fftw. The interfaces have been largely redesigned to remove most of the pointers and new/delete. My current priorities are: finishing the interface cleanup, relicencing under CCP4 part (i) (to be consistent with fftw), writing a binner/optimiser, and a non-crystal map class. Long term it would be nice to implement mmdb coordinate objects and density generation (including anisotropic atoms).
26/07/01:
Two big jobs completed: Firstly, the optimised map class is working. Secondly, the package now uses the cctbx libraries for all its symmetry information. You'll need to install cctbx to compile clipper. The Makefile needs to be tweaked by hand for now.
29/06/01:
Map class working (but not optimised, and no interpolation yet). More importantly I've done another major re-architecture. Every object now comes in two forms: a non-tree and a tree variant. You can now use the maps and Datalists as stand-alone components, although for Datalists you will have to manage linking a Datalist to an HKL_list yourself. In future the map class will probably be split up in the same way, providing one object which provides organizational and fast indexing services, from which a number of Data objects can be hung.
20/06/01:
Map class started (It doesn't build yet). Spacegroup extended to include ASU calculation.
01/05/01:
MTZ io re-written to allow extension to other formats in future. Other general tidyups.
25/04/01:
Created a simple `cad' utility to combine and manipulate mtz files as clipper datalists. A few extra methods were provided for this purpose. In the light of this work the MTZ import/export framework is going to be rewritten again.
28/03/01:
Updated to latest CMTZ library.
27/03/01:
The mtz i/o has been rewritten to allow any combination of input, input-append, output, output-append. This should make it trivial to write a clipper-cad utility.
05/03/01:
Namespaces have been implemented. The data types have been templatised as `dtype' so that float or double data may be stored, and selected by a single `using' statement. (i/o to mtz must be float of course). All other values are defined as `ftype', defined in clipper_util, which will normally be double. (This could easily be templatised too).
22/02/01:
Efficient handle class for Datalists implemented. MTZ hierarchical name parsing improved. Recursive update fixed. Doxygen documentation implemented. CMTZ cell export bug fixed (my fault - thanks Martyn).
20/02/01:
Project level removed from both CMTZ and Clipper hierarchy. Minor architechture improvements.
12/02/01:
Mark 2 design now exports as well as imports MTZs.
10/02/01:
CMTZ modified to support hierarchical data naming and duplicate names. `reflection_data_mtz' now updated use the new data structure (import works, export still pending).
07/02/01:
Data structure completely rewritten. The data hierarchy is now a completely generic tree object, so any type can be insterted anywhere. Objects are addressed using UNIX-like directory references. MTZ i/o has not yet been ported to the new structure, but MTZ items will arrive in the hierarchy at '/project/crystal/dataset/datalist', and must be similarly positioned for export.

Things to do

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END OF TERMS AND CONDITIONS clipper-2.1/configure0000755000374100011300000333752611372264330011660 00000000000000#! /bin/sh # Guess values for system-dependent variables and create Makefiles. # Generated by GNU Autoconf 2.63 for clipper 2.1. # # Report bugs to . # # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001, # 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. # This configure script is free software; the Free Software Foundation # gives unlimited permission to copy, distribute and modify it. ## --------------------- ## ## M4sh Initialization. ## ## --------------------- ## # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then emulate sh NULLCMD=: # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which # is contrary to our usage. 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Likely further. if test -x /sbin/sysctl; then lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax` elif test -x /usr/sbin/sysctl; then lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax` else lt_cv_sys_max_cmd_len=65536 # usable default for all BSDs fi # And add a safety zone lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` ;; interix*) # We know the value 262144 and hardcode it with a safety zone (like BSD) lt_cv_sys_max_cmd_len=196608 ;; osf*) # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not # nice to cause kernel panics so lets avoid the loop below. # First set a reasonable default. lt_cv_sys_max_cmd_len=16384 # if test -x /sbin/sysconfig; then case `/sbin/sysconfig -q proc exec_disable_arg_limit` in *1*) lt_cv_sys_max_cmd_len=-1 ;; esac fi ;; sco3.2v5*) lt_cv_sys_max_cmd_len=102400 ;; sysv5* | sco5v6* | sysv4.2uw2*) kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null` if test -n "$kargmax"; then lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[ ]//'` else lt_cv_sys_max_cmd_len=32768 fi ;; *) lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null` if test -n "$lt_cv_sys_max_cmd_len"; then lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` else SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}} while (test "X"`$SHELL $0 --fallback-echo "X$teststring" 2>/dev/null` \ = "XX$teststring") >/dev/null 2>&1 && new_result=`expr "X$teststring" : ".*" 2>&1` && lt_cv_sys_max_cmd_len=$new_result && test $i != 17 # 1/2 MB should be enough do i=`expr $i + 1` teststring=$teststring$teststring done teststring= # Add a significant safety factor because C++ compilers can tack on massive # amounts of additional arguments before passing them to the linker. # It appears as though 1/2 is a usable value. lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2` fi ;; esac fi if test -n $lt_cv_sys_max_cmd_len ; then { $as_echo "$as_me:$LINENO: result: $lt_cv_sys_max_cmd_len" >&5 $as_echo "$lt_cv_sys_max_cmd_len" >&6; } else { $as_echo "$as_me:$LINENO: result: none" >&5 $as_echo "none" >&6; } fi # Check for command to grab the raw symbol name followed by C symbol from nm. { $as_echo "$as_me:$LINENO: checking command to parse $NM output from $compiler object" >&5 $as_echo_n "checking command to parse $NM output from $compiler object... " >&6; } if test "${lt_cv_sys_global_symbol_pipe+set}" = set; then $as_echo_n "(cached) " >&6 else # These are sane defaults that work on at least a few old systems. # [They come from Ultrix. What could be older than Ultrix?!! ;)] # Character class describing NM global symbol codes. symcode='[BCDEGRST]' # Regexp to match symbols that can be accessed directly from C. sympat='\([_A-Za-z][_A-Za-z0-9]*\)' # Transform an extracted symbol line into a proper C declaration lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^. .* \(.*\)$/extern int \1;/p'" # Transform an extracted symbol line into symbol name and symbol address lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (lt_ptr) 0},/p' -e 's/^$symcode \([^ ]*\) \([^ ]*\)$/ {\"\2\", (lt_ptr) \&\2},/p'" # Define system-specific variables. case $host_os in aix*) symcode='[BCDT]' ;; cygwin* | mingw* | pw32*) symcode='[ABCDGISTW]' ;; hpux*) # Its linker distinguishes data from code symbols if test "$host_cpu" = ia64; then symcode='[ABCDEGRST]' fi lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (lt_ptr) 0},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"\2\", (lt_ptr) \&\2},/p'" ;; linux* | k*bsd*-gnu) if test "$host_cpu" = ia64; then symcode='[ABCDGIRSTW]' lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (lt_ptr) 0},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"\2\", (lt_ptr) \&\2},/p'" fi ;; irix* | nonstopux*) symcode='[BCDEGRST]' ;; osf*) symcode='[BCDEGQRST]' ;; solaris*) symcode='[BDRT]' ;; sco3.2v5*) symcode='[DT]' ;; sysv4.2uw2*) symcode='[DT]' ;; sysv5* | sco5v6* | unixware* | OpenUNIX*) symcode='[ABDT]' ;; sysv4) symcode='[DFNSTU]' ;; esac # Handle CRLF in mingw tool chain opt_cr= case $build_os in mingw*) opt_cr=`echo 'x\{0,1\}' | tr x '\015'` # option cr in regexp ;; esac # If we're using GNU nm, then use its standard symbol codes. case `$NM -V 2>&1` in *GNU* | *'with BFD'*) symcode='[ABCDGIRSTW]' ;; esac # Try without a prefix undercore, then with it. for ac_symprfx in "" "_"; do # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol. symxfrm="\\1 $ac_symprfx\\2 \\2" # Write the raw and C identifiers. lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[ ]\($symcode$symcode*\)[ ][ ]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'" # Check to see that the pipe works correctly. pipe_works=no rm -f conftest* cat > conftest.$ac_ext <&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; then # Now try to grab the symbols. nlist=conftest.nm if { (eval echo "$as_me:$LINENO: \"$NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist\"") >&5 (eval $NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) 2>&5 ac_status=$? $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && test -s "$nlist"; then # Try sorting and uniquifying the output. if sort "$nlist" | uniq > "$nlist"T; then mv -f "$nlist"T "$nlist" else rm -f "$nlist"T fi # Make sure that we snagged all the symbols we need. if grep ' nm_test_var$' "$nlist" >/dev/null; then if grep ' nm_test_func$' "$nlist" >/dev/null; then cat < conftest.$ac_ext #ifdef __cplusplus extern "C" { #endif EOF # Now generate the symbol file. eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | grep -v main >> conftest.$ac_ext' cat <> conftest.$ac_ext #if defined (__STDC__) && __STDC__ # define lt_ptr_t void * #else # define lt_ptr_t char * # define const #endif /* The mapping between symbol names and symbols. */ const struct { const char *name; lt_ptr_t address; } lt_preloaded_symbols[] = { EOF $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (lt_ptr_t) \&\2},/" < "$nlist" | grep -v main >> conftest.$ac_ext cat <<\EOF >> conftest.$ac_ext {0, (lt_ptr_t) 0} }; #ifdef __cplusplus } #endif EOF # Now try linking the two files. mv conftest.$ac_objext conftstm.$ac_objext lt_save_LIBS="$LIBS" lt_save_CFLAGS="$CFLAGS" LIBS="conftstm.$ac_objext" CFLAGS="$CFLAGS$lt_prog_compiler_no_builtin_flag" if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>&5 ac_status=$? $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && test -s conftest${ac_exeext}; then pipe_works=yes fi LIBS="$lt_save_LIBS" CFLAGS="$lt_save_CFLAGS" else echo "cannot find nm_test_func in $nlist" >&5 fi else echo "cannot find nm_test_var in $nlist" >&5 fi else echo "cannot run $lt_cv_sys_global_symbol_pipe" >&5 fi else echo "$progname: failed program was:" >&5 cat conftest.$ac_ext >&5 fi rm -rf conftest* conftst* # Do not use the global_symbol_pipe unless it works. if test "$pipe_works" = yes; then break else lt_cv_sys_global_symbol_pipe= fi done fi if test -z "$lt_cv_sys_global_symbol_pipe"; then lt_cv_sys_global_symbol_to_cdecl= fi if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then { $as_echo "$as_me:$LINENO: result: failed" >&5 $as_echo "failed" >&6; } else { $as_echo "$as_me:$LINENO: result: ok" >&5 $as_echo "ok" >&6; } fi { $as_echo "$as_me:$LINENO: checking for objdir" >&5 $as_echo_n "checking for objdir... " >&6; } if test "${lt_cv_objdir+set}" = set; then $as_echo_n "(cached) " >&6 else rm -f .libs 2>/dev/null mkdir .libs 2>/dev/null if test -d .libs; then lt_cv_objdir=.libs else # MS-DOS does not allow filenames that begin with a dot. lt_cv_objdir=_libs fi rmdir .libs 2>/dev/null fi { $as_echo "$as_me:$LINENO: result: $lt_cv_objdir" >&5 $as_echo "$lt_cv_objdir" >&6; } objdir=$lt_cv_objdir case $host_os in aix3*) # AIX sometimes has problems with the GCC collect2 program. For some # reason, if we set the COLLECT_NAMES environment variable, the problems # vanish in a puff of smoke. if test "X${COLLECT_NAMES+set}" != Xset; then COLLECT_NAMES= export COLLECT_NAMES fi ;; esac # Sed substitution that helps us do robust quoting. It backslashifies # metacharacters that are still active within double-quoted strings. Xsed='sed -e 1s/^X//' sed_quote_subst='s/\([\\"\\`$\\\\]\)/\\\1/g' # Same as above, but do not quote variable references. double_quote_subst='s/\([\\"\\`\\\\]\)/\\\1/g' # Sed substitution to delay expansion of an escaped shell variable in a # double_quote_subst'ed string. delay_variable_subst='s/\\\\\\\\\\\$/\\\\\\$/g' # Sed substitution to avoid accidental globbing in evaled expressions no_glob_subst='s/\*/\\\*/g' # Constants: rm="rm -f" # Global variables: default_ofile=libtool can_build_shared=yes # All known linkers require a `.a' archive for static linking (except MSVC, # which needs '.lib'). libext=a ltmain="$ac_aux_dir/ltmain.sh" ofile="$default_ofile" with_gnu_ld="$lt_cv_prog_gnu_ld" if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}ar", so it can be a program name with args. set dummy ${ac_tool_prefix}ar; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_AR+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$AR"; then ac_cv_prog_AR="$AR" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_AR="${ac_tool_prefix}ar" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi AR=$ac_cv_prog_AR if test -n "$AR"; then { $as_echo "$as_me:$LINENO: result: $AR" >&5 $as_echo "$AR" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_AR"; then ac_ct_AR=$AR # Extract the first word of "ar", so it can be a program name with args. set dummy ar; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_AR+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_AR"; then ac_cv_prog_ac_ct_AR="$ac_ct_AR" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_AR="ar" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_AR=$ac_cv_prog_ac_ct_AR if test -n "$ac_ct_AR"; then { $as_echo "$as_me:$LINENO: result: $ac_ct_AR" >&5 $as_echo "$ac_ct_AR" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_AR" = x; then AR="false" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac AR=$ac_ct_AR fi else AR="$ac_cv_prog_AR" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args. set dummy ${ac_tool_prefix}ranlib; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_RANLIB+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$RANLIB"; then ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi RANLIB=$ac_cv_prog_RANLIB if test -n "$RANLIB"; then { $as_echo "$as_me:$LINENO: result: $RANLIB" >&5 $as_echo "$RANLIB" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_RANLIB"; then ac_ct_RANLIB=$RANLIB # Extract the first word of "ranlib", so it can be a program name with args. set dummy ranlib; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_RANLIB"; then ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_RANLIB="ranlib" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB if test -n "$ac_ct_RANLIB"; then { $as_echo "$as_me:$LINENO: result: $ac_ct_RANLIB" >&5 $as_echo "$ac_ct_RANLIB" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_RANLIB" = x; then RANLIB=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac RANLIB=$ac_ct_RANLIB fi else RANLIB="$ac_cv_prog_RANLIB" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args. set dummy ${ac_tool_prefix}strip; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_STRIP+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$STRIP"; then ac_cv_prog_STRIP="$STRIP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_STRIP="${ac_tool_prefix}strip" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi STRIP=$ac_cv_prog_STRIP if test -n "$STRIP"; then { $as_echo "$as_me:$LINENO: result: $STRIP" >&5 $as_echo "$STRIP" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_STRIP"; then ac_ct_STRIP=$STRIP # Extract the first word of "strip", so it can be a program name with args. set dummy strip; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_STRIP"; then ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_STRIP="strip" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP if test -n "$ac_ct_STRIP"; then { $as_echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5 $as_echo "$ac_ct_STRIP" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_STRIP" = x; then STRIP=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac STRIP=$ac_ct_STRIP fi else STRIP="$ac_cv_prog_STRIP" fi old_CC="$CC" old_CFLAGS="$CFLAGS" # Set sane defaults for various variables test -z "$AR" && AR=ar test -z "$AR_FLAGS" && AR_FLAGS=cru test -z "$AS" && AS=as test -z "$CC" && CC=cc test -z "$LTCC" && LTCC=$CC test -z "$LTCFLAGS" && LTCFLAGS=$CFLAGS test -z "$DLLTOOL" && DLLTOOL=dlltool test -z "$LD" && LD=ld test -z "$LN_S" && LN_S="ln -s" test -z "$MAGIC_CMD" && MAGIC_CMD=file test -z "$NM" && NM=nm test -z "$SED" && SED=sed test -z "$OBJDUMP" && OBJDUMP=objdump test -z "$RANLIB" && RANLIB=: test -z "$STRIP" && STRIP=: test -z "$ac_objext" && ac_objext=o # Determine commands to create old-style static archives. old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs' old_postinstall_cmds='chmod 644 $oldlib' old_postuninstall_cmds= if test -n "$RANLIB"; then case $host_os in openbsd*) old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib" ;; *) old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib" ;; esac old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib" fi for cc_temp in $compiler""; do case $cc_temp in compile | *[\\/]compile | ccache | *[\\/]ccache ) ;; distcc | *[\\/]distcc | purify | *[\\/]purify ) ;; \-*) ;; *) break;; esac done cc_basename=`$echo "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"` # Only perform the check for file, if the check method requires it case $deplibs_check_method in file_magic*) if test "$file_magic_cmd" = '$MAGIC_CMD'; then { $as_echo "$as_me:$LINENO: checking for ${ac_tool_prefix}file" >&5 $as_echo_n "checking for ${ac_tool_prefix}file... " >&6; } if test "${lt_cv_path_MAGIC_CMD+set}" = set; then $as_echo_n "(cached) " >&6 else case $MAGIC_CMD in [\\/*] | ?:[\\/]*) lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path. ;; *) lt_save_MAGIC_CMD="$MAGIC_CMD" lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR ac_dummy="/usr/bin$PATH_SEPARATOR$PATH" for ac_dir in $ac_dummy; do IFS="$lt_save_ifs" test -z "$ac_dir" && ac_dir=. if test -f $ac_dir/${ac_tool_prefix}file; then lt_cv_path_MAGIC_CMD="$ac_dir/${ac_tool_prefix}file" if test -n "$file_magic_test_file"; then case $deplibs_check_method in "file_magic "*) file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"` MAGIC_CMD="$lt_cv_path_MAGIC_CMD" if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null | $EGREP "$file_magic_regex" > /dev/null; then : else cat <&2 *** Warning: the command libtool uses to detect shared libraries, *** $file_magic_cmd, produces output that libtool cannot recognize. *** The result is that libtool may fail to recognize shared libraries *** as such. This will affect the creation of libtool libraries that *** depend on shared libraries, but programs linked with such libtool *** libraries will work regardless of this problem. Nevertheless, you *** may want to report the problem to your system manager and/or to *** bug-libtool@gnu.org EOF fi ;; esac fi break fi done IFS="$lt_save_ifs" MAGIC_CMD="$lt_save_MAGIC_CMD" ;; esac fi MAGIC_CMD="$lt_cv_path_MAGIC_CMD" if test -n "$MAGIC_CMD"; then { $as_echo "$as_me:$LINENO: result: $MAGIC_CMD" >&5 $as_echo "$MAGIC_CMD" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi if test -z "$lt_cv_path_MAGIC_CMD"; then if test -n "$ac_tool_prefix"; then { $as_echo "$as_me:$LINENO: checking for file" >&5 $as_echo_n "checking for file... " >&6; } if test "${lt_cv_path_MAGIC_CMD+set}" = set; then $as_echo_n "(cached) " >&6 else case $MAGIC_CMD in [\\/*] | ?:[\\/]*) lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path. ;; *) lt_save_MAGIC_CMD="$MAGIC_CMD" lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR ac_dummy="/usr/bin$PATH_SEPARATOR$PATH" for ac_dir in $ac_dummy; do IFS="$lt_save_ifs" test -z "$ac_dir" && ac_dir=. if test -f $ac_dir/file; then lt_cv_path_MAGIC_CMD="$ac_dir/file" if test -n "$file_magic_test_file"; then case $deplibs_check_method in "file_magic "*) file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"` MAGIC_CMD="$lt_cv_path_MAGIC_CMD" if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null | $EGREP "$file_magic_regex" > /dev/null; then : else cat <&2 *** Warning: the command libtool uses to detect shared libraries, *** $file_magic_cmd, produces output that libtool cannot recognize. *** The result is that libtool may fail to recognize shared libraries *** as such. This will affect the creation of libtool libraries that *** depend on shared libraries, but programs linked with such libtool *** libraries will work regardless of this problem. Nevertheless, you *** may want to report the problem to your system manager and/or to *** bug-libtool@gnu.org EOF fi ;; esac fi break fi done IFS="$lt_save_ifs" MAGIC_CMD="$lt_save_MAGIC_CMD" ;; esac fi MAGIC_CMD="$lt_cv_path_MAGIC_CMD" if test -n "$MAGIC_CMD"; then { $as_echo "$as_me:$LINENO: result: $MAGIC_CMD" >&5 $as_echo "$MAGIC_CMD" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi else MAGIC_CMD=: fi fi fi ;; esac case $host_os in rhapsody* | darwin*) if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}dsymutil", so it can be a program name with args. set dummy ${ac_tool_prefix}dsymutil; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_DSYMUTIL+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$DSYMUTIL"; then ac_cv_prog_DSYMUTIL="$DSYMUTIL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_DSYMUTIL="${ac_tool_prefix}dsymutil" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi DSYMUTIL=$ac_cv_prog_DSYMUTIL if test -n "$DSYMUTIL"; then { $as_echo "$as_me:$LINENO: result: $DSYMUTIL" >&5 $as_echo "$DSYMUTIL" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_DSYMUTIL"; then ac_ct_DSYMUTIL=$DSYMUTIL # Extract the first word of "dsymutil", so it can be a program name with args. set dummy dsymutil; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_DSYMUTIL+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_DSYMUTIL"; then ac_cv_prog_ac_ct_DSYMUTIL="$ac_ct_DSYMUTIL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_DSYMUTIL="dsymutil" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_DSYMUTIL=$ac_cv_prog_ac_ct_DSYMUTIL if test -n "$ac_ct_DSYMUTIL"; then { $as_echo "$as_me:$LINENO: result: $ac_ct_DSYMUTIL" >&5 $as_echo "$ac_ct_DSYMUTIL" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_DSYMUTIL" = x; then DSYMUTIL=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac DSYMUTIL=$ac_ct_DSYMUTIL fi else DSYMUTIL="$ac_cv_prog_DSYMUTIL" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}nmedit", so it can be a program name with args. set dummy ${ac_tool_prefix}nmedit; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_NMEDIT+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$NMEDIT"; then ac_cv_prog_NMEDIT="$NMEDIT" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_NMEDIT="${ac_tool_prefix}nmedit" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi NMEDIT=$ac_cv_prog_NMEDIT if test -n "$NMEDIT"; then { $as_echo "$as_me:$LINENO: result: $NMEDIT" >&5 $as_echo "$NMEDIT" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_NMEDIT"; then ac_ct_NMEDIT=$NMEDIT # Extract the first word of "nmedit", so it can be a program name with args. set dummy nmedit; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... 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amigaos*) archive_cmds='$rm $output_objdir/a2ixlibrary.data~$echo "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$echo "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$echo "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$echo "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' hardcode_libdir_flag_spec='-L$libdir' hardcode_minus_L=yes # see comment about different semantics on the GNU ld section ld_shlibs=no ;; bsdi[45]*) export_dynamic_flag_spec=-rdynamic ;; cygwin* | mingw* | pw32*) # When not using gcc, we currently assume that we are using # Microsoft Visual C++. # hardcode_libdir_flag_spec is actually meaningless, as there is # no search path for DLLs. hardcode_libdir_flag_spec=' ' allow_undefined_flag=unsupported # Tell ltmain to make .lib files, not .a files. libext=lib # Tell ltmain to make .dll files, not .so files. shrext_cmds=".dll" # FIXME: Setting linknames here is a bad hack. archive_cmds='$CC -o $lib $libobjs $compiler_flags `echo "$deplibs" | $SED -e '\''s/ -lc$//'\''` -link -dll~linknames=' # The linker will automatically build a .lib file if we build a DLL. old_archive_From_new_cmds='true' # FIXME: Should let the user specify the lib program. old_archive_cmds='lib -OUT:$oldlib$oldobjs$old_deplibs' fix_srcfile_path='`cygpath -w "$srcfile"`' enable_shared_with_static_runtimes=yes ;; darwin* | rhapsody*) case $host_os in rhapsody* | darwin1.[012]) allow_undefined_flag='${wl}-undefined ${wl}suppress' ;; *) # Darwin 1.3 on if test -z ${MACOSX_DEPLOYMENT_TARGET} ; then allow_undefined_flag='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' else case ${MACOSX_DEPLOYMENT_TARGET} in 10.[012]) allow_undefined_flag='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;; 10.*) allow_undefined_flag='${wl}-undefined ${wl}dynamic_lookup' ;; esac fi ;; esac archive_cmds_need_lc=no hardcode_direct=no hardcode_automatic=yes hardcode_shlibpath_var=unsupported whole_archive_flag_spec='' link_all_deplibs=yes if test "$GCC" = yes ; then output_verbose_link_cmd='echo' archive_cmds="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}" module_cmds="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}" archive_expsym_cmds="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}" module_expsym_cmds="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}" else case $cc_basename in xlc*) output_verbose_link_cmd='echo' archive_cmds='$CC -qmkshrobj $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-install_name ${wl}`echo $rpath/$soname` $xlcverstring' module_cmds='$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags' # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin lds archive_expsym_cmds='sed -e "s,#.*,," -e "s,^[ ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -qmkshrobj $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-install_name ${wl}$rpath/$soname $xlcverstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}' module_expsym_cmds='sed -e "s,#.*,," -e "s,^[ ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}' ;; *) ld_shlibs=no ;; esac fi ;; dgux*) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec='-L$libdir' hardcode_shlibpath_var=no ;; freebsd1*) ld_shlibs=no ;; # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor # support. Future versions do this automatically, but an explicit c++rt0.o # does not break anything, and helps significantly (at the cost of a little # extra space). freebsd2.2*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o' hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; # Unfortunately, older versions of FreeBSD 2 do not have this feature. freebsd2*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=yes hardcode_minus_L=yes hardcode_shlibpath_var=no ;; # FreeBSD 3 and greater uses gcc -shared to do shared libraries. freebsd* | dragonfly*) archive_cmds='$CC -shared -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; hpux9*) if test "$GCC" = yes; then archive_cmds='$rm $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' else archive_cmds='$rm $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' fi hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_separator=: hardcode_direct=yes # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes export_dynamic_flag_spec='${wl}-E' ;; hpux10*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' fi if test "$with_gnu_ld" = no; then hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_separator=: hardcode_direct=yes export_dynamic_flag_spec='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes fi ;; hpux11*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then case $host_cpu in hppa*64*) archive_cmds='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) archive_cmds='$CC -shared ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac else case $host_cpu in hppa*64*) archive_cmds='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac fi if test "$with_gnu_ld" = no; then hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_separator=: case $host_cpu in hppa*64*|ia64*) hardcode_libdir_flag_spec_ld='+b $libdir' hardcode_direct=no hardcode_shlibpath_var=no ;; *) hardcode_direct=yes export_dynamic_flag_spec='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes ;; esac fi ;; irix5* | irix6* | nonstopux*) if test "$GCC" = yes; then archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else archive_cmds='$LD -shared $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib' hardcode_libdir_flag_spec_ld='-rpath $libdir' fi hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: link_all_deplibs=yes ;; netbsd*) if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out else archive_cmds='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF fi hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; newsos6) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=yes hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: hardcode_shlibpath_var=no ;; openbsd*) if test -f /usr/libexec/ld.so; then hardcode_direct=yes hardcode_shlibpath_var=no if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols' hardcode_libdir_flag_spec='${wl}-rpath,$libdir' export_dynamic_flag_spec='${wl}-E' else case $host_os in openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec='-R$libdir' ;; *) archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec='${wl}-rpath,$libdir' ;; esac fi else ld_shlibs=no fi ;; os2*) hardcode_libdir_flag_spec='-L$libdir' hardcode_minus_L=yes allow_undefined_flag=unsupported archive_cmds='$echo "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$echo "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$echo DATA >> $output_objdir/$libname.def~$echo " SINGLE NONSHARED" >> $output_objdir/$libname.def~$echo EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def' old_archive_From_new_cmds='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' ;; osf3*) if test "$GCC" = yes; then allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else allow_undefined_flag=' -expect_unresolved \*' archive_cmds='$LD -shared${allow_undefined_flag} $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib' fi hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: ;; osf4* | osf5*) # as osf3* with the addition of -msym flag if test "$GCC" = yes; then allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' else allow_undefined_flag=' -expect_unresolved \*' archive_cmds='$LD -shared${allow_undefined_flag} $libobjs $deplibs $linker_flags -msym -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib' archive_expsym_cmds='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; echo "-hidden">> $lib.exp~ $LD -shared${allow_undefined_flag} -input $lib.exp $linker_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib~$rm $lib.exp' # Both c and cxx compiler support -rpath directly hardcode_libdir_flag_spec='-rpath $libdir' fi hardcode_libdir_separator=: ;; solaris*) no_undefined_flag=' -z text' if test "$GCC" = yes; then wlarc='${wl}' archive_cmds='$CC -shared ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~ $CC -shared ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$rm $lib.exp' else wlarc='' archive_cmds='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' archive_expsym_cmds='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$rm $lib.exp' fi hardcode_libdir_flag_spec='-R$libdir' hardcode_shlibpath_var=no case $host_os in solaris2.[0-5] | solaris2.[0-5].*) ;; *) # The compiler driver will combine and reorder linker options, # but understands `-z linker_flag'. GCC discards it without `$wl', # but is careful enough not to reorder. # Supported since Solaris 2.6 (maybe 2.5.1?) if test "$GCC" = yes; then whole_archive_flag_spec='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract' else whole_archive_flag_spec='-z allextract$convenience -z defaultextract' fi ;; esac link_all_deplibs=yes ;; sunos4*) if test "x$host_vendor" = xsequent; then # Use $CC to link under sequent, because it throws in some extra .o # files that make .init and .fini sections work. archive_cmds='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags' fi hardcode_libdir_flag_spec='-L$libdir' hardcode_direct=yes hardcode_minus_L=yes hardcode_shlibpath_var=no ;; sysv4) case $host_vendor in sni) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=yes # is this really true??? ;; siemens) ## LD is ld it makes a PLAMLIB ## CC just makes a GrossModule. archive_cmds='$LD -G -o $lib $libobjs $deplibs $linker_flags' reload_cmds='$CC -r -o $output$reload_objs' hardcode_direct=no ;; motorola) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=no #Motorola manual says yes, but my tests say they lie ;; esac runpath_var='LD_RUN_PATH' hardcode_shlibpath_var=no ;; sysv4.3*) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_shlibpath_var=no export_dynamic_flag_spec='-Bexport' ;; sysv4*MP*) if test -d /usr/nec; then archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_shlibpath_var=no runpath_var=LD_RUN_PATH hardcode_runpath_var=yes ld_shlibs=yes fi ;; sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7* | sco3.2v5.0.[024]*) no_undefined_flag='${wl}-z,text' archive_cmds_need_lc=no hardcode_shlibpath_var=no runpath_var='LD_RUN_PATH' if test "$GCC" = yes; then archive_cmds='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' fi ;; sysv5* | sco3.2v5* | sco5v6*) # Note: We can NOT use -z defs as we might desire, because we do not # link with -lc, and that would cause any symbols used from libc to # always be unresolved, which means just about no library would # ever link correctly. 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then echo "${wl}${allow_undefined_flag}"; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag" else if test "$host_cpu" = ia64; then hardcode_libdir_flag_spec_F77='${wl}-R $libdir:/usr/lib:/lib' allow_undefined_flag_F77="-z nodefs" archive_expsym_cmds_F77="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols" else # Determine the default libpath from the value encoded in an empty executable. cat >conftest.$ac_ext <<_ACEOF program main end _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (ac_try="$ac_link" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" $as_echo "$ac_try_echo") >&5 (eval "$ac_link") 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { test -z "$ac_f77_werror_flag" || test ! -s conftest.err } && test -s conftest$ac_exeext && { test "$cross_compiling" = yes || $as_test_x conftest$ac_exeext }; then lt_aix_libpath_sed=' /Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/ p } }' aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` # Check for a 64-bit object if we didn't find anything. if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` fi else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -rf conftest.dSYM rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ conftest$ac_exeext conftest.$ac_ext if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi hardcode_libdir_flag_spec_F77='${wl}-blibpath:$libdir:'"$aix_libpath" # Warning - without using the other run time loading flags, # -berok will link without error, but may produce a broken library. no_undefined_flag_F77=' ${wl}-bernotok' allow_undefined_flag_F77=' ${wl}-berok' # Exported symbols can be pulled into shared objects from archives whole_archive_flag_spec_F77='$convenience' archive_cmds_need_lc_F77=yes # This is similar to how AIX traditionally builds its shared libraries. archive_expsym_cmds_F77="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' fi fi ;; amigaos*) archive_cmds_F77='$rm $output_objdir/a2ixlibrary.data~$echo "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$echo "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$echo "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$echo "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' hardcode_libdir_flag_spec_F77='-L$libdir' hardcode_minus_L_F77=yes # see comment about different semantics on the GNU ld section ld_shlibs_F77=no ;; bsdi[45]*) export_dynamic_flag_spec_F77=-rdynamic ;; cygwin* | mingw* | pw32*) # When not using gcc, we currently assume that we are using # Microsoft Visual C++. # hardcode_libdir_flag_spec is actually meaningless, as there is # no search path for DLLs. hardcode_libdir_flag_spec_F77=' ' allow_undefined_flag_F77=unsupported # Tell ltmain to make .lib files, not .a files. libext=lib # Tell ltmain to make .dll files, not .so files. shrext_cmds=".dll" # FIXME: Setting linknames here is a bad hack. archive_cmds_F77='$CC -o $lib $libobjs $compiler_flags `echo "$deplibs" | $SED -e '\''s/ -lc$//'\''` -link -dll~linknames=' # The linker will automatically build a .lib file if we build a DLL. old_archive_From_new_cmds_F77='true' # FIXME: Should let the user specify the lib program. old_archive_cmds_F77='lib -OUT:$oldlib$oldobjs$old_deplibs' fix_srcfile_path_F77='`cygpath -w "$srcfile"`' enable_shared_with_static_runtimes_F77=yes ;; darwin* | rhapsody*) case $host_os in rhapsody* | darwin1.[012]) allow_undefined_flag_F77='${wl}-undefined ${wl}suppress' ;; *) # Darwin 1.3 on if test -z ${MACOSX_DEPLOYMENT_TARGET} ; then allow_undefined_flag_F77='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' else case ${MACOSX_DEPLOYMENT_TARGET} in 10.[012]) allow_undefined_flag_F77='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;; 10.*) allow_undefined_flag_F77='${wl}-undefined ${wl}dynamic_lookup' ;; esac fi ;; esac archive_cmds_need_lc_F77=no hardcode_direct_F77=no hardcode_automatic_F77=yes hardcode_shlibpath_var_F77=unsupported whole_archive_flag_spec_F77='' link_all_deplibs_F77=yes if test "$GCC" = yes ; then output_verbose_link_cmd='echo' archive_cmds_F77="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}" module_cmds_F77="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}" archive_expsym_cmds_F77="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}" module_expsym_cmds_F77="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}" else case $cc_basename in xlc*) output_verbose_link_cmd='echo' archive_cmds_F77='$CC -qmkshrobj $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-install_name ${wl}`echo $rpath/$soname` $xlcverstring' module_cmds_F77='$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags' # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin lds archive_expsym_cmds_F77='sed -e "s,#.*,," -e "s,^[ ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -qmkshrobj $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-install_name ${wl}$rpath/$soname $xlcverstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}' module_expsym_cmds_F77='sed -e "s,#.*,," -e "s,^[ ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}' ;; *) ld_shlibs_F77=no ;; esac fi ;; dgux*) archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec_F77='-L$libdir' hardcode_shlibpath_var_F77=no ;; freebsd1*) ld_shlibs_F77=no ;; # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor # support. Future versions do this automatically, but an explicit c++rt0.o # does not break anything, and helps significantly (at the cost of a little # extra space). freebsd2.2*) archive_cmds_F77='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o' hardcode_libdir_flag_spec_F77='-R$libdir' hardcode_direct_F77=yes hardcode_shlibpath_var_F77=no ;; # Unfortunately, older versions of FreeBSD 2 do not have this feature. freebsd2*) archive_cmds_F77='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_direct_F77=yes hardcode_minus_L_F77=yes hardcode_shlibpath_var_F77=no ;; # FreeBSD 3 and greater uses gcc -shared to do shared libraries. freebsd* | dragonfly*) archive_cmds_F77='$CC -shared -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec_F77='-R$libdir' hardcode_direct_F77=yes hardcode_shlibpath_var_F77=no ;; hpux9*) if test "$GCC" = yes; then archive_cmds_F77='$rm $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' else archive_cmds_F77='$rm $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' fi hardcode_libdir_flag_spec_F77='${wl}+b ${wl}$libdir' hardcode_libdir_separator_F77=: hardcode_direct_F77=yes # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L_F77=yes export_dynamic_flag_spec_F77='${wl}-E' ;; hpux10*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then archive_cmds_F77='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds_F77='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' fi if test "$with_gnu_ld" = no; then hardcode_libdir_flag_spec_F77='${wl}+b ${wl}$libdir' hardcode_libdir_separator_F77=: hardcode_direct_F77=yes export_dynamic_flag_spec_F77='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L_F77=yes fi ;; hpux11*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then case $host_cpu in hppa*64*) archive_cmds_F77='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) archive_cmds_F77='$CC -shared ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) archive_cmds_F77='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac else case $host_cpu in hppa*64*) archive_cmds_F77='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) archive_cmds_F77='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) archive_cmds_F77='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac fi if test "$with_gnu_ld" = no; then hardcode_libdir_flag_spec_F77='${wl}+b ${wl}$libdir' hardcode_libdir_separator_F77=: case $host_cpu in hppa*64*|ia64*) hardcode_libdir_flag_spec_ld_F77='+b $libdir' hardcode_direct_F77=no hardcode_shlibpath_var_F77=no ;; *) hardcode_direct_F77=yes export_dynamic_flag_spec_F77='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L_F77=yes ;; esac fi ;; irix5* | irix6* | nonstopux*) if test "$GCC" = yes; then archive_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else archive_cmds_F77='$LD -shared $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib' hardcode_libdir_flag_spec_ld_F77='-rpath $libdir' fi hardcode_libdir_flag_spec_F77='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator_F77=: link_all_deplibs_F77=yes ;; netbsd*) if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then archive_cmds_F77='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out else archive_cmds_F77='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF fi hardcode_libdir_flag_spec_F77='-R$libdir' hardcode_direct_F77=yes hardcode_shlibpath_var_F77=no ;; newsos6) archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct_F77=yes hardcode_libdir_flag_spec_F77='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator_F77=: hardcode_shlibpath_var_F77=no ;; openbsd*) if test -f /usr/libexec/ld.so; then hardcode_direct_F77=yes hardcode_shlibpath_var_F77=no if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then archive_cmds_F77='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds_F77='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols' hardcode_libdir_flag_spec_F77='${wl}-rpath,$libdir' export_dynamic_flag_spec_F77='${wl}-E' else case $host_os in openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*) archive_cmds_F77='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec_F77='-R$libdir' ;; *) archive_cmds_F77='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec_F77='${wl}-rpath,$libdir' ;; esac fi else ld_shlibs_F77=no fi ;; os2*) hardcode_libdir_flag_spec_F77='-L$libdir' hardcode_minus_L_F77=yes allow_undefined_flag_F77=unsupported archive_cmds_F77='$echo "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$echo "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$echo DATA >> $output_objdir/$libname.def~$echo " SINGLE NONSHARED" >> $output_objdir/$libname.def~$echo EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def' old_archive_From_new_cmds_F77='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' ;; osf3*) if test "$GCC" = yes; then allow_undefined_flag_F77=' ${wl}-expect_unresolved ${wl}\*' archive_cmds_F77='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else allow_undefined_flag_F77=' -expect_unresolved \*' archive_cmds_F77='$LD -shared${allow_undefined_flag} $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib' fi hardcode_libdir_flag_spec_F77='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator_F77=: ;; osf4* | osf5*) # as osf3* with the addition of -msym flag if test "$GCC" = yes; then allow_undefined_flag_F77=' ${wl}-expect_unresolved ${wl}\*' archive_cmds_F77='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' hardcode_libdir_flag_spec_F77='${wl}-rpath ${wl}$libdir' else allow_undefined_flag_F77=' -expect_unresolved \*' archive_cmds_F77='$LD -shared${allow_undefined_flag} $libobjs $deplibs $linker_flags -msym -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib' archive_expsym_cmds_F77='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; echo "-hidden">> $lib.exp~ $LD -shared${allow_undefined_flag} -input $lib.exp $linker_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib~$rm $lib.exp' # Both c and cxx compiler support -rpath directly hardcode_libdir_flag_spec_F77='-rpath $libdir' fi hardcode_libdir_separator_F77=: ;; solaris*) no_undefined_flag_F77=' -z text' if test "$GCC" = yes; then wlarc='${wl}' archive_cmds_F77='$CC -shared ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds_F77='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~ $CC -shared ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$rm $lib.exp' else wlarc='' archive_cmds_F77='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' archive_expsym_cmds_F77='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$rm $lib.exp' fi hardcode_libdir_flag_spec_F77='-R$libdir' hardcode_shlibpath_var_F77=no case $host_os in solaris2.[0-5] | solaris2.[0-5].*) ;; *) # The compiler driver will combine and reorder linker options, # but understands `-z linker_flag'. GCC discards it without `$wl', # but is careful enough not to reorder. # Supported since Solaris 2.6 (maybe 2.5.1?) if test "$GCC" = yes; then whole_archive_flag_spec_F77='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract' else whole_archive_flag_spec_F77='-z allextract$convenience -z defaultextract' fi ;; esac link_all_deplibs_F77=yes ;; sunos4*) if test "x$host_vendor" = xsequent; then # Use $CC to link under sequent, because it throws in some extra .o # files that make .init and .fini sections work. archive_cmds_F77='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds_F77='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags' fi hardcode_libdir_flag_spec_F77='-L$libdir' hardcode_direct_F77=yes hardcode_minus_L_F77=yes hardcode_shlibpath_var_F77=no ;; sysv4) case $host_vendor in sni) archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct_F77=yes # is this really true??? ;; siemens) ## LD is ld it makes a PLAMLIB ## CC just makes a GrossModule. archive_cmds_F77='$LD -G -o $lib $libobjs $deplibs $linker_flags' reload_cmds_F77='$CC -r -o $output$reload_objs' hardcode_direct_F77=no ;; motorola) archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct_F77=no #Motorola manual says yes, but my tests say they lie ;; esac runpath_var='LD_RUN_PATH' hardcode_shlibpath_var_F77=no ;; sysv4.3*) archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_shlibpath_var_F77=no export_dynamic_flag_spec_F77='-Bexport' ;; sysv4*MP*) if test -d /usr/nec; then archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_shlibpath_var_F77=no runpath_var=LD_RUN_PATH hardcode_runpath_var=yes ld_shlibs_F77=yes fi ;; sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7* | sco3.2v5.0.[024]*) no_undefined_flag_F77='${wl}-z,text' archive_cmds_need_lc_F77=no hardcode_shlibpath_var_F77=no runpath_var='LD_RUN_PATH' if test "$GCC" = yes; then archive_cmds_F77='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds_F77='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds_F77='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds_F77='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' fi ;; sysv5* | sco3.2v5* | sco5v6*) # Note: We can NOT use -z defs as we might desire, because we do not # link with -lc, and that would cause any symbols used from libc to # always be unresolved, which means just about no library would # ever link correctly. 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esac ;; gnu*) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH hardcode_into_libs=yes ;; hpux9* | hpux10* | hpux11*) # Give a soname corresponding to the major version so that dld.sl refuses to # link against other versions. version_type=sunos need_lib_prefix=no need_version=no case $host_cpu in ia64*) shrext_cmds='.so' hardcode_into_libs=yes dynamic_linker="$host_os dld.so" shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' if test "X$HPUX_IA64_MODE" = X32; then sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib" else sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64" fi sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec ;; hppa*64*) shrext_cmds='.sl' hardcode_into_libs=yes dynamic_linker="$host_os dld.sl" shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64" sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec ;; *) shrext_cmds='.sl' dynamic_linker="$host_os dld.sl" shlibpath_var=SHLIB_PATH shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' ;; esac # HP-UX runs *really* slowly unless shared libraries are mode 555. postinstall_cmds='chmod 555 $lib' ;; interix[3-9]*) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes ;; irix5* | irix6* | nonstopux*) case $host_os in nonstopux*) version_type=nonstopux ;; *) if test "$lt_cv_prog_gnu_ld" = yes; then version_type=linux else version_type=irix fi ;; esac need_lib_prefix=no need_version=no soname_spec='${libname}${release}${shared_ext}$major' library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}' case $host_os in irix5* | nonstopux*) libsuff= shlibsuff= ;; *) case $LD in # libtool.m4 will add one of these switches to LD *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ") libsuff= shlibsuff= libmagic=32-bit;; *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ") libsuff=32 shlibsuff=N32 libmagic=N32;; *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ") libsuff=64 shlibsuff=64 libmagic=64-bit;; *) libsuff= shlibsuff= libmagic=never-match;; esac ;; esac shlibpath_var=LD_LIBRARY${shlibsuff}_PATH shlibpath_overrides_runpath=no sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}" sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}" hardcode_into_libs=yes ;; # No shared lib support for Linux oldld, aout, or coff. linux*oldld* | linux*aout* | linux*coff*) dynamic_linker=no ;; # This must be Linux ELF. linux* | k*bsd*-gnu) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no # This implies no fast_install, which is unacceptable. # Some rework will be needed to allow for fast_install # before this can be enabled. hardcode_into_libs=yes sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}" sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}" # Append ld.so.conf contents to the search path if test -f /etc/ld.so.conf; then lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '` sys_lib_dlsearch_path_spec="$sys_lib_dlsearch_path_spec $lt_ld_extra" fi # We used to test for /lib/ld.so.1 and disable shared libraries on # powerpc, because MkLinux only supported shared libraries with the # GNU dynamic linker. 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FIXME archive_cmds_GCJ='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' else ld_shlibs_GCJ=no fi ;; cygwin* | mingw* | pw32*) # _LT_AC_TAGVAR(hardcode_libdir_flag_spec, GCJ) is actually meaningless, # as there is no search path for DLLs. hardcode_libdir_flag_spec_GCJ='-L$libdir' allow_undefined_flag_GCJ=unsupported always_export_symbols_GCJ=no enable_shared_with_static_runtimes_GCJ=yes export_symbols_cmds_GCJ='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1 DATA/'\'' -e '\''/^[AITW][ ]/s/.*[ ]//'\'' | sort | uniq > $export_symbols' if $LD --help 2>&1 | grep 'auto-import' > /dev/null; then archive_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' # If the export-symbols file already is a .def file (1st line # is EXPORTS), use it as is; otherwise, prepend... archive_expsym_cmds_GCJ='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then cp $export_symbols $output_objdir/$soname.def; else echo EXPORTS > $output_objdir/$soname.def; cat $export_symbols >> $output_objdir/$soname.def; fi~ $CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' else ld_shlibs_GCJ=no fi ;; interix[3-9]*) hardcode_direct_GCJ=no hardcode_shlibpath_var_GCJ=no hardcode_libdir_flag_spec_GCJ='${wl}-rpath,$libdir' export_dynamic_flag_spec_GCJ='${wl}-E' # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc. # Instead, shared libraries are loaded at an image base (0x10000000 by # default) and relocated if they conflict, which is a slow very memory # consuming and fragmenting process. To avoid this, we pick a random, # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link # time. Moving up from 0x10000000 also allows more sbrk(2) space. archive_cmds_GCJ='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib' archive_expsym_cmds_GCJ='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib' ;; gnu* | linux* | k*bsd*-gnu) if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then tmp_addflag= case $cc_basename,$host_cpu in pgcc*) # Portland Group C compiler whole_archive_flag_spec_GCJ='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}--no-whole-archive' tmp_addflag=' $pic_flag' ;; pgf77* | pgf90* | pgf95*) # Portland Group f77 and f90 compilers whole_archive_flag_spec_GCJ='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}--no-whole-archive' tmp_addflag=' $pic_flag -Mnomain' ;; ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64 tmp_addflag=' -i_dynamic' ;; efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64 tmp_addflag=' -i_dynamic -nofor_main' ;; ifc* | ifort*) # Intel Fortran compiler tmp_addflag=' -nofor_main' ;; esac case `$CC -V 2>&1 | sed 5q` in *Sun\ C*) # Sun C 5.9 whole_archive_flag_spec_GCJ='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}--no-whole-archive' tmp_sharedflag='-G' ;; *Sun\ F*) # Sun Fortran 8.3 tmp_sharedflag='-G' ;; *) tmp_sharedflag='-shared' ;; esac archive_cmds_GCJ='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' if test $supports_anon_versioning = yes; then archive_expsym_cmds_GCJ='$echo "{ global:" > $output_objdir/$libname.ver~ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~ $echo "local: *; };" >> $output_objdir/$libname.ver~ $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib' fi else ld_shlibs_GCJ=no fi ;; netbsd*) if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then archive_cmds_GCJ='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib' wlarc= else archive_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' fi ;; solaris*) if $LD -v 2>&1 | grep 'BFD 2\.8' > /dev/null; then ld_shlibs_GCJ=no cat <&2 *** Warning: The releases 2.8.* of the GNU linker cannot reliably *** create shared libraries on Solaris systems. Therefore, libtool *** is disabling shared libraries support. We urge you to upgrade GNU *** binutils to release 2.9.1 or newer. Another option is to modify *** your PATH or compiler configuration so that the native linker is *** used, and then restart. EOF elif $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then archive_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' else ld_shlibs_GCJ=no fi ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*) case `$LD -v 2>&1` in *\ [01].* | *\ 2.[0-9].* | *\ 2.1[0-5].*) ld_shlibs_GCJ=no cat <<_LT_EOF 1>&2 *** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not *** reliably create shared libraries on SCO systems. Therefore, libtool *** is disabling shared libraries support. We urge you to upgrade GNU *** binutils to release 2.16.91.0.3 or newer. Another option is to modify *** your PATH or compiler configuration so that the native linker is *** used, and then restart. _LT_EOF ;; *) if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then hardcode_libdir_flag_spec_GCJ='`test -z "$SCOABSPATH" && echo ${wl}-rpath,$libdir`' archive_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib' archive_expsym_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname,\${SCOABSPATH:+${install_libdir}/}$soname,-retain-symbols-file,$export_symbols -o $lib' else ld_shlibs_GCJ=no fi ;; esac ;; sunos4*) archive_cmds_GCJ='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags' wlarc= hardcode_direct_GCJ=yes hardcode_shlibpath_var_GCJ=no ;; *) if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then archive_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' else ld_shlibs_GCJ=no fi ;; esac if test "$ld_shlibs_GCJ" = no; then runpath_var= hardcode_libdir_flag_spec_GCJ= export_dynamic_flag_spec_GCJ= whole_archive_flag_spec_GCJ= fi else # PORTME fill in a description of your system's linker (not GNU ld) case $host_os in aix3*) allow_undefined_flag_GCJ=unsupported always_export_symbols_GCJ=yes archive_expsym_cmds_GCJ='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname' # Note: this linker hardcodes the directories in LIBPATH if there # are no directories specified by -L. hardcode_minus_L_GCJ=yes if test "$GCC" = yes && test -z "$lt_prog_compiler_static"; then # Neither direct hardcoding nor static linking is supported with a # broken collect2. hardcode_direct_GCJ=unsupported fi ;; aix[4-9]*) if test "$host_cpu" = ia64; then # On IA64, the linker does run time linking by default, so we don't # have to do anything special. aix_use_runtimelinking=no exp_sym_flag='-Bexport' no_entry_flag="" else # If we're using GNU nm, then we don't want the "-C" option. # -C means demangle to AIX nm, but means don't demangle with GNU nm if $NM -V 2>&1 | grep 'GNU' > /dev/null; then export_symbols_cmds_GCJ='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$2 == "T") || (\$2 == "D") || (\$2 == "B")) && (substr(\$3,1,1) != ".")) { print \$3 } }'\'' | sort -u > $export_symbols' else export_symbols_cmds_GCJ='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$2 == "T") || (\$2 == "D") || (\$2 == "B")) && (substr(\$3,1,1) != ".")) { print \$3 } }'\'' | sort -u > $export_symbols' fi aix_use_runtimelinking=no # Test if we are trying to use run time linking or normal # AIX style linking. If -brtl is somewhere in LDFLAGS, we # need to do runtime linking. case $host_os in aix4.[23]|aix4.[23].*|aix[5-9]*) for ld_flag in $LDFLAGS; do if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then aix_use_runtimelinking=yes break fi done ;; esac exp_sym_flag='-bexport' no_entry_flag='-bnoentry' fi # When large executables or shared objects are built, AIX ld can # have problems creating the table of contents. If linking a library # or program results in "error TOC overflow" add -mminimal-toc to # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS. archive_cmds_GCJ='' hardcode_direct_GCJ=yes hardcode_libdir_separator_GCJ=':' link_all_deplibs_GCJ=yes if test "$GCC" = yes; then case $host_os in aix4.[012]|aix4.[012].*) # We only want to do this on AIX 4.2 and lower, the check # below for broken collect2 doesn't work under 4.3+ collect2name=`${CC} -print-prog-name=collect2` if test -f "$collect2name" && \ strings "$collect2name" | grep resolve_lib_name >/dev/null then # We have reworked collect2 : else # We have old collect2 hardcode_direct_GCJ=unsupported # It fails to find uninstalled libraries when the uninstalled # path is not listed in the libpath. Setting hardcode_minus_L # to unsupported forces relinking hardcode_minus_L_GCJ=yes hardcode_libdir_flag_spec_GCJ='-L$libdir' hardcode_libdir_separator_GCJ= fi ;; esac shared_flag='-shared' if test "$aix_use_runtimelinking" = yes; then shared_flag="$shared_flag "'${wl}-G' fi else # not using gcc if test "$host_cpu" = ia64; then # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release # chokes on -Wl,-G. The following line is correct: shared_flag='-G' else if test "$aix_use_runtimelinking" = yes; then shared_flag='${wl}-G' else shared_flag='${wl}-bM:SRE' fi fi fi # It seems that -bexpall does not export symbols beginning with # underscore (_), so it is better to generate a list of symbols to export. always_export_symbols_GCJ=yes if test "$aix_use_runtimelinking" = yes; then # Warning - without using the other runtime loading flags (-brtl), # -berok will link without error, but may produce a broken library. allow_undefined_flag_GCJ='-berok' # Determine the default libpath from the value encoded in an empty executable. cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int main () { ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (ac_try="$ac_link" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" $as_echo "$ac_try_echo") >&5 (eval "$ac_link") 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { test -z "$ac_c_werror_flag" || test ! -s conftest.err } && test -s conftest$ac_exeext && { test "$cross_compiling" = yes || $as_test_x conftest$ac_exeext }; then lt_aix_libpath_sed=' /Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/ p } }' aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` # Check for a 64-bit object if we didn't find anything. if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` fi else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -rf conftest.dSYM rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ conftest$ac_exeext conftest.$ac_ext if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi hardcode_libdir_flag_spec_GCJ='${wl}-blibpath:$libdir:'"$aix_libpath" archive_expsym_cmds_GCJ="\$CC"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then echo "${wl}${allow_undefined_flag}"; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag" else if test "$host_cpu" = ia64; then hardcode_libdir_flag_spec_GCJ='${wl}-R $libdir:/usr/lib:/lib' allow_undefined_flag_GCJ="-z nodefs" archive_expsym_cmds_GCJ="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols" else # Determine the default libpath from the value encoded in an empty executable. cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int main () { ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (ac_try="$ac_link" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" $as_echo "$ac_try_echo") >&5 (eval "$ac_link") 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { test -z "$ac_c_werror_flag" || test ! -s conftest.err } && test -s conftest$ac_exeext && { test "$cross_compiling" = yes || $as_test_x conftest$ac_exeext }; then lt_aix_libpath_sed=' /Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/ p } }' aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` # Check for a 64-bit object if we didn't find anything. if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` fi else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -rf conftest.dSYM rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ conftest$ac_exeext conftest.$ac_ext if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi hardcode_libdir_flag_spec_GCJ='${wl}-blibpath:$libdir:'"$aix_libpath" # Warning - without using the other run time loading flags, # -berok will link without error, but may produce a broken library. no_undefined_flag_GCJ=' ${wl}-bernotok' allow_undefined_flag_GCJ=' ${wl}-berok' # Exported symbols can be pulled into shared objects from archives whole_archive_flag_spec_GCJ='$convenience' archive_cmds_need_lc_GCJ=yes # This is similar to how AIX traditionally builds its shared libraries. archive_expsym_cmds_GCJ="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' fi fi ;; amigaos*) archive_cmds_GCJ='$rm $output_objdir/a2ixlibrary.data~$echo "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$echo "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$echo "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$echo "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' hardcode_libdir_flag_spec_GCJ='-L$libdir' hardcode_minus_L_GCJ=yes # see comment about different semantics on the GNU ld section ld_shlibs_GCJ=no ;; bsdi[45]*) export_dynamic_flag_spec_GCJ=-rdynamic ;; cygwin* | mingw* | pw32*) # When not using gcc, we currently assume that we are using # Microsoft Visual C++. # hardcode_libdir_flag_spec is actually meaningless, as there is # no search path for DLLs. hardcode_libdir_flag_spec_GCJ=' ' allow_undefined_flag_GCJ=unsupported # Tell ltmain to make .lib files, not .a files. libext=lib # Tell ltmain to make .dll files, not .so files. shrext_cmds=".dll" # FIXME: Setting linknames here is a bad hack. archive_cmds_GCJ='$CC -o $lib $libobjs $compiler_flags `echo "$deplibs" | $SED -e '\''s/ -lc$//'\''` -link -dll~linknames=' # The linker will automatically build a .lib file if we build a DLL. old_archive_From_new_cmds_GCJ='true' # FIXME: Should let the user specify the lib program. old_archive_cmds_GCJ='lib -OUT:$oldlib$oldobjs$old_deplibs' fix_srcfile_path_GCJ='`cygpath -w "$srcfile"`' enable_shared_with_static_runtimes_GCJ=yes ;; darwin* | rhapsody*) case $host_os in rhapsody* | darwin1.[012]) allow_undefined_flag_GCJ='${wl}-undefined ${wl}suppress' ;; *) # Darwin 1.3 on if test -z ${MACOSX_DEPLOYMENT_TARGET} ; then allow_undefined_flag_GCJ='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' else case ${MACOSX_DEPLOYMENT_TARGET} in 10.[012]) allow_undefined_flag_GCJ='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;; 10.*) allow_undefined_flag_GCJ='${wl}-undefined ${wl}dynamic_lookup' ;; esac fi ;; esac archive_cmds_need_lc_GCJ=no hardcode_direct_GCJ=no hardcode_automatic_GCJ=yes hardcode_shlibpath_var_GCJ=unsupported whole_archive_flag_spec_GCJ='' link_all_deplibs_GCJ=yes if test "$GCC" = yes ; then output_verbose_link_cmd='echo' archive_cmds_GCJ="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}" module_cmds_GCJ="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}" archive_expsym_cmds_GCJ="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}" module_expsym_cmds_GCJ="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}" else case $cc_basename in xlc*) output_verbose_link_cmd='echo' archive_cmds_GCJ='$CC -qmkshrobj $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-install_name ${wl}`echo $rpath/$soname` $xlcverstring' module_cmds_GCJ='$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags' # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin lds archive_expsym_cmds_GCJ='sed -e "s,#.*,," -e "s,^[ ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -qmkshrobj $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-install_name ${wl}$rpath/$soname $xlcverstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}' module_expsym_cmds_GCJ='sed -e "s,#.*,," -e "s,^[ ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}' ;; *) ld_shlibs_GCJ=no ;; esac fi ;; dgux*) archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec_GCJ='-L$libdir' hardcode_shlibpath_var_GCJ=no ;; freebsd1*) ld_shlibs_GCJ=no ;; # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor # support. Future versions do this automatically, but an explicit c++rt0.o # does not break anything, and helps significantly (at the cost of a little # extra space). freebsd2.2*) archive_cmds_GCJ='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o' hardcode_libdir_flag_spec_GCJ='-R$libdir' hardcode_direct_GCJ=yes hardcode_shlibpath_var_GCJ=no ;; # Unfortunately, older versions of FreeBSD 2 do not have this feature. freebsd2*) archive_cmds_GCJ='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_direct_GCJ=yes hardcode_minus_L_GCJ=yes hardcode_shlibpath_var_GCJ=no ;; # FreeBSD 3 and greater uses gcc -shared to do shared libraries. freebsd* | dragonfly*) archive_cmds_GCJ='$CC -shared -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec_GCJ='-R$libdir' hardcode_direct_GCJ=yes hardcode_shlibpath_var_GCJ=no ;; hpux9*) if test "$GCC" = yes; then archive_cmds_GCJ='$rm $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' else archive_cmds_GCJ='$rm $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' fi hardcode_libdir_flag_spec_GCJ='${wl}+b ${wl}$libdir' hardcode_libdir_separator_GCJ=: hardcode_direct_GCJ=yes # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L_GCJ=yes export_dynamic_flag_spec_GCJ='${wl}-E' ;; hpux10*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then archive_cmds_GCJ='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds_GCJ='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' fi if test "$with_gnu_ld" = no; then hardcode_libdir_flag_spec_GCJ='${wl}+b ${wl}$libdir' hardcode_libdir_separator_GCJ=: hardcode_direct_GCJ=yes export_dynamic_flag_spec_GCJ='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L_GCJ=yes fi ;; hpux11*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then case $host_cpu in hppa*64*) archive_cmds_GCJ='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) archive_cmds_GCJ='$CC -shared ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) archive_cmds_GCJ='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac else case $host_cpu in hppa*64*) archive_cmds_GCJ='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) archive_cmds_GCJ='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) archive_cmds_GCJ='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac fi if test "$with_gnu_ld" = no; then hardcode_libdir_flag_spec_GCJ='${wl}+b ${wl}$libdir' hardcode_libdir_separator_GCJ=: case $host_cpu in hppa*64*|ia64*) hardcode_libdir_flag_spec_ld_GCJ='+b $libdir' hardcode_direct_GCJ=no hardcode_shlibpath_var_GCJ=no ;; *) hardcode_direct_GCJ=yes export_dynamic_flag_spec_GCJ='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L_GCJ=yes ;; esac fi ;; irix5* | irix6* | nonstopux*) if test "$GCC" = yes; then archive_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else archive_cmds_GCJ='$LD -shared $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib' hardcode_libdir_flag_spec_ld_GCJ='-rpath $libdir' fi hardcode_libdir_flag_spec_GCJ='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator_GCJ=: link_all_deplibs_GCJ=yes ;; netbsd*) if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then archive_cmds_GCJ='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out else archive_cmds_GCJ='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF fi hardcode_libdir_flag_spec_GCJ='-R$libdir' hardcode_direct_GCJ=yes hardcode_shlibpath_var_GCJ=no ;; newsos6) archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct_GCJ=yes hardcode_libdir_flag_spec_GCJ='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator_GCJ=: hardcode_shlibpath_var_GCJ=no ;; openbsd*) if test -f /usr/libexec/ld.so; then hardcode_direct_GCJ=yes hardcode_shlibpath_var_GCJ=no if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then archive_cmds_GCJ='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds_GCJ='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols' hardcode_libdir_flag_spec_GCJ='${wl}-rpath,$libdir' export_dynamic_flag_spec_GCJ='${wl}-E' else case $host_os in openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*) archive_cmds_GCJ='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec_GCJ='-R$libdir' ;; *) archive_cmds_GCJ='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec_GCJ='${wl}-rpath,$libdir' ;; esac fi else ld_shlibs_GCJ=no fi ;; os2*) hardcode_libdir_flag_spec_GCJ='-L$libdir' hardcode_minus_L_GCJ=yes allow_undefined_flag_GCJ=unsupported archive_cmds_GCJ='$echo "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$echo "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$echo DATA >> $output_objdir/$libname.def~$echo " SINGLE NONSHARED" >> $output_objdir/$libname.def~$echo EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def' old_archive_From_new_cmds_GCJ='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' ;; osf3*) if test "$GCC" = yes; then allow_undefined_flag_GCJ=' ${wl}-expect_unresolved ${wl}\*' archive_cmds_GCJ='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else allow_undefined_flag_GCJ=' -expect_unresolved \*' archive_cmds_GCJ='$LD -shared${allow_undefined_flag} $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib' fi hardcode_libdir_flag_spec_GCJ='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator_GCJ=: ;; osf4* | osf5*) # as osf3* with the addition of -msym flag if test "$GCC" = yes; then allow_undefined_flag_GCJ=' ${wl}-expect_unresolved ${wl}\*' archive_cmds_GCJ='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' hardcode_libdir_flag_spec_GCJ='${wl}-rpath ${wl}$libdir' else allow_undefined_flag_GCJ=' -expect_unresolved \*' archive_cmds_GCJ='$LD -shared${allow_undefined_flag} $libobjs $deplibs $linker_flags -msym -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib' archive_expsym_cmds_GCJ='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; echo "-hidden">> $lib.exp~ $LD -shared${allow_undefined_flag} -input $lib.exp $linker_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib~$rm $lib.exp' # Both c and cxx compiler support -rpath directly hardcode_libdir_flag_spec_GCJ='-rpath $libdir' fi hardcode_libdir_separator_GCJ=: ;; solaris*) no_undefined_flag_GCJ=' -z text' if test "$GCC" = yes; then wlarc='${wl}' archive_cmds_GCJ='$CC -shared ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds_GCJ='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~ $CC -shared ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$rm $lib.exp' else wlarc='' archive_cmds_GCJ='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' archive_expsym_cmds_GCJ='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$rm $lib.exp' fi hardcode_libdir_flag_spec_GCJ='-R$libdir' hardcode_shlibpath_var_GCJ=no case $host_os in solaris2.[0-5] | solaris2.[0-5].*) ;; *) # The compiler driver will combine and reorder linker options, # but understands `-z linker_flag'. GCC discards it without `$wl', # but is careful enough not to reorder. # Supported since Solaris 2.6 (maybe 2.5.1?) if test "$GCC" = yes; then whole_archive_flag_spec_GCJ='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract' else whole_archive_flag_spec_GCJ='-z allextract$convenience -z defaultextract' fi ;; esac link_all_deplibs_GCJ=yes ;; sunos4*) if test "x$host_vendor" = xsequent; then # Use $CC to link under sequent, because it throws in some extra .o # files that make .init and .fini sections work. archive_cmds_GCJ='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds_GCJ='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags' fi hardcode_libdir_flag_spec_GCJ='-L$libdir' hardcode_direct_GCJ=yes hardcode_minus_L_GCJ=yes hardcode_shlibpath_var_GCJ=no ;; sysv4) case $host_vendor in sni) archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct_GCJ=yes # is this really true??? ;; siemens) ## LD is ld it makes a PLAMLIB ## CC just makes a GrossModule. archive_cmds_GCJ='$LD -G -o $lib $libobjs $deplibs $linker_flags' reload_cmds_GCJ='$CC -r -o $output$reload_objs' hardcode_direct_GCJ=no ;; motorola) archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct_GCJ=no #Motorola manual says yes, but my tests say they lie ;; esac runpath_var='LD_RUN_PATH' hardcode_shlibpath_var_GCJ=no ;; sysv4.3*) archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_shlibpath_var_GCJ=no export_dynamic_flag_spec_GCJ='-Bexport' ;; sysv4*MP*) if test -d /usr/nec; then archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_shlibpath_var_GCJ=no runpath_var=LD_RUN_PATH hardcode_runpath_var=yes ld_shlibs_GCJ=yes fi ;; sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7* | sco3.2v5.0.[024]*) no_undefined_flag_GCJ='${wl}-z,text' archive_cmds_need_lc_GCJ=no hardcode_shlibpath_var_GCJ=no runpath_var='LD_RUN_PATH' if test "$GCC" = yes; then archive_cmds_GCJ='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds_GCJ='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds_GCJ='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds_GCJ='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' fi ;; sysv5* | sco3.2v5* | sco5v6*) # Note: We can NOT use -z defs as we might desire, because we do not # link with -lc, and that would cause any symbols used from libc to # always be unresolved, which means just about no library would # ever link correctly. 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The import file would start with # the line `#! .'. This would cause the generated library to # depend on `.', always an invalid library. This was fixed in # development snapshots of GCC prior to 3.0. case $host_os in aix4 | aix4.[01] | aix4.[01].*) if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)' echo ' yes ' echo '#endif'; } | ${CC} -E - | grep yes > /dev/null; then : else can_build_shared=no fi ;; esac # AIX (on Power*) has no versioning support, so currently we can not hardcode correct # soname into executable. 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However, doing the test right would require a runtime test, and that would make cross-compilation harder. Let us hope that IBM fixes the xlc bug, and also adds support for this kind of constant expression. In the meantime, this test will reject xlc, which is OK, since our stdbool.h substitute should suffice. We also test this with GCC, where it should work, to detect more quickly whether someone messes up the test in the future. */ char digs[] = "0123456789"; int xlcbug = 1 / (&(digs + 5)[-2 + (bool) 1] == &digs[4] ? 1 : -1); # endif /* Catch a bug in an HP-UX C compiler. 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