--- viewmol-2.4.1.orig/debian/README.Debian +++ viewmol-2.4.1/debian/README.Debian @@ -0,0 +1,18 @@ +viewmol for Debian +------------------ + +The default VIEWMOLPATH has been set to /etc/viewmol, rather than +/usr/local/lib/viewmol. It contains the default resource file, viewmolrc, +and the X resource files Xdefaults. for different languages. + +Note that the X11 applications default directory for Debian is +/etc/X11/app-defaults/, not /usr/lib/X11/app-defaults as suggested in the +Viewmol HTML manual. This is important when you want to change the default +language for viewmol to something other than English. + +As per Debian policy, binaries on Intel ia-32 (i386) have been optimised +for i486. If you run on i686 (e.g. Pentium-4), you may find a 5-10% speed +increase if you recompile for your own system. Do this by setting the value +of processor in source/getmachine, line 72. + + -- Drew Parsons , 1 Dec 2004 --- viewmol-2.4.1.orig/debian/README.source +++ viewmol-2.4.1/debian/README.source @@ -0,0 +1,83 @@ +Debian patches which have not yet been applied upstream are handled using quilt +via (for convenience) the Debian X Strike Force's build system xsfbs. + +Patches are placed in debian/patches. + +See http://git.debian.org/?p=pkg-xorg/xsfbs.git;a=summary and +/usr/share/doc/quilt/README.source for more details. + + +------------------------------------------------------ +Quick Guide To Patching This Package For The Impatient +------------------------------------------------------ + +1. Make sure you have quilt installed +2. Unpack the package as usual with "dpkg-source -x" +3. Run the "patch" target in debian/rules +4. Create a new patch with "quilt new" (see quilt(1)) +5. Edit all the files you want to include in the patch with "quilt edit" + (see quilt(1)). +6. Write the patch with "quilt refresh" (see quilt(1)) +7. Run the "clean" target in debian/rules + +Alternatively, instead of using quilt directly, you can drop the patch in to +debian/patches and add the name of the patch to debian/patches/series. + +------------------------------------ +Guide To The X Strike Force Packages +------------------------------------ + +The X Strike Force team maintains X packages in git repositories on +git.debian.org in the pkg-xorg subdirectory. Most upstream packages +are actually maintained in git repositories as well, so they often +just need to be pulled into git.debian.org in a "upstream-*" branch. +Otherwise, the upstream sources are manually installed in the Debian +git repository. + +The .orig.tar.gz upstream source file could be generated using this +"upstream-*" branch in the Debian git repository but it is actually +copied from upstream tarballs directly. + +Due to X.org being highly modular, packaging all X.org applications +as their own independent packages would have created too many Debian +packages. For this reason, some X.org applications have been grouped +into larger packages: xutils, xutils-dev, x11-apps, x11-session-utils, +x11-utils, x11-xfs-utils, x11-xkb-utils, x11-xserver-utils. +Most packages, including the X.org server itself and all libraries +and drivers are, however maintained independently. + +The Debian packaging is added by creating the "debian-*" git branch +which contains the aforementioned "upstream-*" branch plus the debian/ +repository files. +When a patch has to be applied to the Debian package, two solutions +are involved: +* If the patch is available in one of the upstream branches, it + may be git'cherry-picked into the Debian repository. In this + case, it appears directly in the .diff.gz. +* Otherwise, the patch is added to debian/patches/ which is managed + with quilt as documented in /usr/share/doc/quilt/README.source. + +quilt is actually invoked by the Debian X packaging through a larger +set of scripts called XSFBS. XSFBS brings some other X specific +features such as managing dependencies and conflicts due to the video +and input driver ABIs. +XSFBS itself is maintained in a separate repository at + git://git.debian.org/pkg-xorg/xsfbs.git +and it is pulled inside the other Debian X repositories when needed. + +The XSFBS patching system requires a build dependency on quilt. Also +a dependency on $(STAMP_DIR)/patch has to be added to debian/rules +so that the XSFBS patching occurs before the actual build. So the +very first target of the build (likely the one running autoreconf) +should depend on $(STAMP_DIR)/patch. It should also not depend on +anything so that parallel builds are correctly supported (nothing +should probably run while patching is being done). And finally, the +clean target should depend on the xsfclean target so that patches +are unapplied on clean. + +When the upstream sources contain some DFSG-nonfree files, they are +listed in text files in debian/prune/ in the "debian-*" branch of +the Debian repository. XSFBS' scripts then take care of removing +these listed files during the build so as to generate a modified +DFSG-free .orig.tar.gz tarball. + --- viewmol-2.4.1.orig/debian/changelog +++ viewmol-2.4.1/debian/changelog @@ -0,0 +1,352 @@ +viewmol (2.4.1-20) unstable; urgency=low + + * Use dh_quilt_patch instead of the xsfbs scripts. + * Allow viewmol to launch from the Gnome menus: + Remove Path=$HOME from viewmol.desktop, since Gnome cannot handle + environment variables ($HOME). Applied to patch 110_desktop_app.diff. + Closes: #709304. + * Build against libmotif-dev not lesstif2-dev. Closes: #714671. + * Don't need libxp-dev Build-Depends (Xprint is not actually used). + Closes: #623665. + * Lintian fixes: + - add build-arch, build-indep to debian/rules. + - leave binary hardening unhandled for now: viewmol has an + inconvenient build system in the form of source/getmachine + * Standards-Version: 3.9.4 + + -- Drew Parsons Sat, 21 Sep 2013 13:20:52 +1000 + +viewmol (2.4.1-19) unstable; urgency=low + + * Added watch file. Thanks Daniel Leidert. Closes: #675831. + + -- Drew Parsons Sat, 17 Nov 2012 17:27:44 +1100 + +viewmol (2.4.1-18) unstable; urgency=low + + * Build-depends: libpng-dev not libpng12-dev. Closes: #662535. + * Update Build-depends: libtiff5-dev not libtiff4-dev + * Standards-version: 3.9.3 + * In debian/rules: + - dh_pysupport is deprecated, use dh_python2 instead + - dh_clean -k is deprecated; use dh_prep instead + + -- Drew Parsons Sun, 03 Jun 2012 12:26:36 +1000 + +viewmol (2.4.1-17) unstable; urgency=low + + * Pre-apply the HURD patch 011_getmachine_HURD.diff from bug#534330 + in order to allow the HURD to be recognised during debian/rules + clean. This rule is run before patch by dpkg-buildpackage. + (Probably not safe to set the dependency clean: patch). + + -- Drew Parsons Sun, 26 Sep 2010 11:08:49 +1000 + +viewmol (2.4.1-16) unstable; urgency=low + + * Patch 011_getmachine_HURD.diff lets the getmachine build script + recognise the Hurd. Thanks Barry deFreese. Closes: #534330. + * Add debian/README.source to declare use of quilt patches via xsfbs. + * Remove dh_desktop from debian/rules (deprecated now). + * Standards-Version: 3.9.1 + + -- Drew Parsons Sun, 29 Aug 2010 21:20:24 +1000 + +viewmol (2.4.1-15) unstable; urgency=low + + * Transfer to group maintainership with Debian Science. + * Standards version: 3.8.1. + * Build-Depends: quilt. debian/xsfbs borrowed from XSF (Xorg + packaging) to handle quilt patches. Source patches from previous + debian diff split into separate diffs in debian/patches: + 010_build_scripts.diff + 100_locale_exception.diff + 110_desktop_app.diff + 120_PyObject.diff + 130_DEFAULTPATH.diff + 140_bin_awk.diff + + -- Drew Parsons Fri, 27 Mar 2009 16:46:00 +1100 + +viewmol (2.4.1-14) unstable; urgency=low + + * Add symlink from main dir /usr/lib/viewmol to docs. Closes: #478551. + * Standards-Version: 3.8.0. + * Specify that copyright is GPL v2. + * Add dh_desktop to debian/rules to register mimetypes in desktop file. + + -- Drew Parsons Mon, 23 Feb 2009 23:44:29 +1100 + +viewmol (2.4.1-13) unstable; urgency=low + + * Use PyObject_Del to deallocate PyObjects instead of PyMem_DEL. + Thanks Barry deFreese for the patch. Closes: #469008. + * Don't create separate links for KDE support files in /usr/share/applnk + anymore. These are handled generically (for all compliant Desktop + environments including Gnome) via + /usr/share/applications/viewmol.desktop. Closes: #466998. + * Update debian/viewmol.sgml and doc-base to encode Jörg-Rüdiger's + name in UTF-8. Regenerate viewmol.1 using docbook2man. + * Where pythonlib is defined in source/getmachine, add + | xargs echo | awk '{print $1}' + to ensure only one path is passed to dirname. + + -- Drew Parsons Tue, 18 Mar 2008 16:02:08 +1100 + +viewmol (2.4.1-12) unstable; urgency=low + + * What's so special about American English? Change en_US locale to + just en in /usr/lib/viewmol/locale (and /usr/share/viewmol/locale) + and use it as a fallback in setAtomColors.py. Move existing + /etc/viewmol/locale/en_US to .../en in preinst. Closes: #446755. + * Disable kde/install's copying of "uninstall" in /usr/local. + * Link 32x32/apps/viewmol.png into /usr/share/pixmaps so Gnome can + get the menu icon too. + * Standards-Version: 3.7.3. + * Updated menu section to "Applications/Science/Chemistry". + Use /usr/share/pixmaps/viewmol.png as icon. + * Delete libraries from LIBS in source/getmachine flagged by + dpkg-shlibdeps as not actually used by viewmol (-lz -lXp -lXext + -lpthread -lutil -ldl). Likewise remove -lm in source/Makefile + for tm and readgamess. + * source/getmachine: use -march instead of -mcpu for i386. + + -- Drew Parsons Mon, 14 Jan 2008 02:28:26 +1100 + +viewmol (2.4.1-11) unstable; urgency=low + + * Add build support for GNU/kFreeBSD (and probably Hurd too). + Closes: #415591. + + -- Drew Parsons Thu, 28 Jun 2007 10:58:10 +1000 + +viewmol (2.4.1-10) unstable; urgency=low + + * Update for new python policy and new default python version 2.4, + use dh_python. Closes: #380982. + * Change to Depends:, not merely Suggests: python. A debatable point + since viewmol will in fact work without python, but you do need + python in order to get the full proffered functionality. + * Use debhelper 5 (>= 5.0.37.2 to be precise, to use dh_python) + + -- Drew Parsons Sat, 19 Aug 2006 19:00:52 +1000 + +viewmol (2.4.1-9) unstable; urgency=low + + * Updated Build-Depends to reflect current mesa packages. + + -- Drew Parsons Tue, 6 Jun 2006 23:51:17 +1000 + +viewmol (2.4.1-8) unstable; urgency=low + + * Added Categories=Education;Science;Chemistry; to + /usr/share/applnk/Graphics/viewmol.desktop (adds a menu entry to + freedesktop.org compliant environments). Thanks, Daniel Leidert. + Closes: #370683. + * Add #!/usr/bin/awk to readdmol.awk (removes a lintian warning). + * Standards version 3.7.2. + + -- Drew Parsons Tue, 6 Jun 2006 22:55:28 +1000 + +viewmol (2.4.1-7) unstable; urgency=low + + * Recompile for new C++ ABI. + + -- Drew Parsons Fri, 12 Aug 2005 18:19:06 +1000 + +viewmol (2.4.1-6) unstable; urgency=medium + + * Exec should be /usr/bin/viewmol not /usr/local/bin/viewmol in + /usr/share/applnk/Graphics/viewmol.desktop. Closes: #290641. + + -- Drew Parsons Sun, 16 Jan 2005 14:11:50 +1100 + +viewmol (2.4.1-5) unstable; urgency=high + + * Remarkable. The buildds aren't reporting failure over unknown -mcpu + either. Enable -mcpu only for i386 and powerpc (in source/getmachine). + + -- Drew Parsons Wed, 22 Dec 2004 10:41:33 +1100 + +viewmol (2.4.1-4) unstable; urgency=high + + * Use `dpkg --print-architecture` to identify the processor, and only + compile with -malign-double on i386 (in source/getmachine). Why on earth + do the buildds say "maybe-successful" when they cannot compile because + the compilation flags are wrong??? + + -- Drew Parsons Tue, 21 Dec 2004 19:24:32 +1100 + +viewmol (2.4.1-3) unstable; urgency=high + + * Actually, remove the Build-Dependency on libdb4.3-dev altogether. + Viewmol 2.4 no longer compiles with -ldb. Thank goodness. + Closes: #286600. + * Split xlibs-dev again while we're at it. + * By the way, the russian fonts are working fine after all. Most likely I + hadn't restarted the X server after installing xfonts-cyrillic. + * Selecting a language and saving doesn't seem to have any effect when + viewmol is started the next time, unless you do "xrdb ~/.Xdefaults" or + login afresh. Otherwise you need to reset the language again each time. + This needs to get fixed. Logged at + http://sourceforge.net/tracker/index.php?func=detail&atid=106845&aid=1088821&group_id=6845. + * The menu entries at Annotate and below are not aligned against the + margin correctly, and some of them are being blanked out by the margin. + This is logged at + http://sourceforge.net/tracker/index.php?func=detail&atid=106845&aid=1088824&group_id=6845 + * Did you notice all the scripts are now working in 2.4.1. You can colour + your atoms various shades of green, or be mesmerised by the demo. + + -- Drew Parsons Tue, 21 Dec 2004 16:13:27 +1100 + +viewmol (2.4.1-2) unstable; urgency=medium + + * Restore lost changelog entries (2.4-2..2.4-5). + * Reinstate changes to kde/install. Closes: #285409. + * i386 optimisation is left at i486: tests indicated that i586 offers + small advantage (in fact performance degraded on my i686 test system). + As mentioned in README.Debian, recompile for yourself if you use i686. + + -- Drew Parsons Wed, 15 Dec 2004 11:01:10 +1100 + +viewmol (2.4.1-1) unstable; urgency=low + + * New upstream version. + * Upgraded Build-Depends: libtiff4-dev, libdb4.3-dev + * Altered Build-Depends: mesag-dev|libgl-dev due to conflict between + mesag-dev and libgl-dev. + * Added Suggests: xfonts-cyrillic to help make sure Russian fonts are there + when needed. Actually, they're screwed anyway. No size 14 koi8 fonts. Pity. + * Updated the description to that given in the spec file. + * Compile with -mcpu=i586 on i386. In my opinion, compiling for i486 runs + too slow. Let me know if you really need to run viewmol on a true i486. + + -- Drew Parsons Thu, 2 Dec 2004 01:11:45 +1100 + +viewmol (2.4-5) unstable; urgency=medium + + * Recompiled against libtiff4 (updated Build-Depends in debian/control). + + -- Drew Parsons Sun, 1 Aug 2004 01:04:44 +1000 + +viewmol (2.4-4) unstable; urgency=low + + * Removed use of -mcpu altogether from source/getmachine, since it's + just too much trouble when porting to all architectures. + * Altered kde/install to install KDE icons in + /usr/share/icons/crystalsvg, not .../default.kde, since default.kde is + supposed to be a symlink to crystalsvg, supplied by kdelibs-data. + Otherwise there will be a problem with viewmol's real default.kde + directory, if viewmol is installed before kdelibs-data. Installing + into crystalsvg was recommended by the KDE guys at the debian-qt-kde + mailing list. Closes: #254247. + + -- Drew Parsons Wed, 16 Jun 2004 15:06:08 +1000 + +viewmol (2.4-3) unstable; urgency=low + + * Altered source/getmachine to handle different machine + architectures under Linux. In particular, use "powerpc" rather + than "ppc", "i386" instead of "i686" and use -malign-double only + with "i386". + + -- Drew Parsons Mon, 14 Jun 2004 16:31:52 +1000 + +viewmol (2.4-2) unstable; urgency=low + + * Rationalised the mesa build-dependencies (libglu-dev, libgl-dev) in + debian/control. + * There is some python problem with setAtomColors.py, so remove it + for now out of scripts into examples. Let me know if you know how + to fix it. + + -- Drew Parsons Sun, 13 Jun 2004 18:28:32 +1000 + +viewmol (2.4-1) unstable; urgency=low + + * New upstream release. + * Use `uname -m` not `uname -p` in source/getmachine. + This means my Pentium II compiles with -mcpu=i686, but gcc docs + say the binary will nevertheless be compatible with i386, so I won't + fiddle with it further. + * KDE support files are now installed in their proper place. + * Russian font references (locale/ru/Viewmol, init.c) changed to refer to + fixed-cyrillic. But I couldn't fixed the russian display of the menu and + the background text at the same time ;( I left it in favour of the menu. + + -- Drew Parsons Wed, 7 Jan 2004 09:42:51 +1100 + +viewmol (2.3-7) unstable; urgency=low + + * Recompile for new default python version, python 2.3. + * Changed Build-Depends to libdb4.1-dev from libdb2-dev. I wonder if I can + get rid of it altogether, is it really used? + * Remove man compilation line from debian/rules, along with + Build-Dependency on docbook-to-man. Compile the man page once for all + during packaging, using docbook2man (gives better results than + docbook-to-man). Fixed some unknown entities in viewmol.sgml. Use + dh_installman not dh_installmanpages in debian/rules. + * Standards version 3.6.1. + * BTW, I've submitted a patch to convert the development version (v2.4) + to automake, but there were problems with it for non-Debian systems. + If you want to help fix it up, give me (or upstream) a buzz. + + -- Drew Parsons Tue, 9 Sep 2003 19:32:19 +1000 + +viewmol (2.3-6) unstable; urgency=low + + * Standards version 3.5.8. + * Changed menu entry to Apps/Science, hint "Chemistry". + * Suggests: openbabel (babel directory no longer needed in + /usr/share/doc/viewmol). + * Bumped Build-Depends on lesstif-dev to lesstif2-dev (seems to work fine). + * Removed debian/conffiles: debhelper now marks everything in /etc as a + conffile. + * As a side effect, automated dependency on python is updated to current + default (python2.2). Closes: #171044. + + -- Drew Parsons Thu, 12 Dec 2002 20:10:04 +1100 + +viewmol (2.3-5) unstable; urgency=low + + * Added doc-base control file. + * Standards version 3.5.6.0. + + -- Drew Parsons Sat, 8 Dec 2001 01:01:22 +1100 + +viewmol (2.3-4) unstable; urgency=low + + * Added -lXmu to default LIBS in source/getmachine. Closes: #90459 (really). + + -- Drew Parsons Tue, 3 Apr 2001 23:33:24 +1000 + +viewmol (2.3-3) unstable; urgency=low + + * Added xlibs-dev to Build-depends. Closes: #90459. + + -- Drew Parsons Mon, 26 Mar 2001 23:15:15 +1000 + +viewmol (2.3-2) unstable; urgency=low + + * Removed -malign-double from default OPT for Linux in source/getmachine. + Closes: #89898. + + -- Drew Parsons Tue, 20 Mar 2001 00:03:33 +1100 + +viewmol (2.3-1) unstable; urgency=low + + * Initial Release. Closes: #89051. + * DEFAULTPATH in getrc.c changed from /usr/local/lib/viewmol to + /etc/viewmol. This defined the default value of $VIEWMOLPATH, + where viewmolrc resides. + * Location of supplementary binaries and sources as defined in default + viewmolrc was split into /usr/lib/viewmol (C binaries) and + /usr/share/viewmol (scripts). + * -m486 option deleted from default OPT definition for Linux in + source/getmachine. + + -- Drew Parsons Mon, 12 Mar 2001 01:14:55 +1100 + +Local variables: +mode: debian-changelog +End: --- viewmol-2.4.1.orig/debian/compat +++ viewmol-2.4.1/debian/compat @@ -0,0 +1 @@ +5 --- viewmol-2.4.1.orig/debian/control +++ viewmol-2.4.1/debian/control @@ -0,0 +1,25 @@ +Source: viewmol +Section: science +Priority: optional +Maintainer: Debian Science Maintainers +Uploaders: Drew Parsons +Build-Depends: debhelper (>= 5.0.37.2), quilt, libtiff5-dev, libpng-dev, zlib1g-dev, libglu1-mesa-dev | libglu-dev, libgl1-mesa-dev | libgl-dev, libmotif-dev, libxmu-dev, libxi-dev, libxext-dev, libxt-dev, libx11-dev, python-dev, python-support (>= 0.3) +Standards-Version: 3.9.4 + +Package: viewmol +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends} +Suggests: openbabel, xfonts-cyrillic +XB-Python-Version: ${python:Versions} +Description: A graphical front end for computational chemistry programs. + Viewmol is a graphical front end for computational chemistry programs. + It is able to graphically aid in the generation of molecular structures for + computations and to visualize their results. + . + At present Viewmol includes input filters for Discover, DMol3, Gamess, + Gaussian 9x/03, Gulp, Mopac, PQS, Turbomole, and Vamp outputs as well as + for PDB files. Structures can be saved as Accelrys' car-files, MDL files, + and Turbomole coordinate files. Viewmol can generate input files for + Gaussian 9x/03. Viewmol's file format has been added to OpenBabel so that + OpenBabel can serve as an input as well as an output filter for + coordinates. --- viewmol-2.4.1.orig/debian/copyright +++ viewmol-2.4.1/debian/copyright @@ -0,0 +1,9 @@ +This package was debianized by Drew Parsons on +Sun, 11 Mar 2001 16:23:55 +1100. + +It was downloaded from http://viewmol.sourceforge.net/ + +Upstream Author: Jörg-Rüdiger Hill + +Copyright: 1996-2004. GNU General Public License, version 2. +See /usr/share/common-licenses/GPL-2. --- viewmol-2.4.1.orig/debian/dirs +++ viewmol-2.4.1/debian/dirs @@ -0,0 +1,15 @@ +usr/bin +usr/share/viewmol +usr/lib/viewmol +etc/viewmol +etc/viewmol/locale +usr/share/icons/crystalsvg/32x32/mimetypes +usr/share/icons/crystalsvg/32x32/apps +usr/share/icons/crystalsvg/48x48/mimetypes +usr/share/icons/crystalsvg/48x48/apps +usr/share/icons/crystalsvg/64x64/mimetypes +usr/share/icons/crystalsvg/64x64/apps +usr/share/icons/crystalsvg/128x128/mimetypes +usr/share/icons/crystalsvg/128x128/apps +usr/share/applications +usr/share/pixmaps --- viewmol-2.4.1.orig/debian/doc-base +++ viewmol-2.4.1/debian/doc-base @@ -0,0 +1,13 @@ +Document: viewmol +Title: Viewmol Manual +Author: Jörg-Rüdiger Hill (joehill@users.sourceforge.net) +Abstract: This manual describes the configuration and use of viewmol, + a graphical front end for computational chemistry programs. +Section: Science/Chemistry + +Format: pdf +Files: /usr/share/doc/viewmol/viewmol.pdf.gz + +Format: HTML +Index: /usr/share/doc/viewmol/viewmol.html +Files: /usr/share/doc/viewmol/html/*.html --- viewmol-2.4.1.orig/debian/docs +++ viewmol-2.4.1/debian/docs @@ -0,0 +1,2 @@ +README +viewmol-2.4.1-1.spec --- viewmol-2.4.1.orig/debian/links +++ viewmol-2.4.1/debian/links @@ -0,0 +1,3 @@ +etc/viewmol/viewmolrc usr/lib/viewmol/viewmolrc +usr/share/viewmol/tests usr/share/doc/viewmol/tests +usr/share/doc/viewmol usr/lib/viewmol/doc --- viewmol-2.4.1.orig/debian/menu +++ viewmol-2.4.1/debian/menu @@ -0,0 +1,5 @@ +?package(viewmol):needs="X11" section="Applications/Science/Chemistry"\ + title="viewmol" \ + command="/usr/bin/viewmol" \ + hints="Chemistry" \ + icon="/usr/share/pixmaps/viewmol.png" --- viewmol-2.4.1.orig/debian/patches/010_build_scripts.diff +++ viewmol-2.4.1/debian/patches/010_build_scripts.diff @@ -0,0 +1,140 @@ +--- viewmol-2.4.1.orig/source/getmachine ++++ viewmol-2.4.1/source/getmachine +@@ -1,4 +1,4 @@ +-#!/bin/sh ++#!/bin/bash + #******************************************************************************* + # * + # Viewmol * +@@ -63,11 +63,44 @@ + then + processor=`uname -m` + fi ++ ++ # for the Debian auto-build system, we identify the processor thus: ++ processor=`dpkg --print-architecture` ++ ++ if [ "$processor" = "i386" -o "$processor" = "i686" -o "$processor" = "i586" ] ++ then ++ # Debian policy says ia32 (i386) binaries should be optimised ++ # for no more than i486. ++ # But this runs noticably slower on i686 (P-4 class), so I recommend you ++ # change it for your own system and recompile. ++ # Note I am deliberately excluded i386 machines, by upgrading them to i486. ++ # This is because `dpkg --print-architecture` always returns i386 on ++ # Pentium level systems, but I want to optimise for no less than i486. ++ processor=i486 ++ ++ # need the following to flag for -malign-double, which is Intel only. ++ processor_is_i386=true ++ fi ++ ++ # or set the flag for true i486 too ++ if [ "$processor" = "i486" ] ++ then ++ processor_is_i386=true ++ fi + } + + target=$1 + os=`uname -s` + ++case $os in ++ GNU/k*BSD | GNU) ++ # GNU variants are treated like Linux ++ os=Linux ++ ;; ++ *) ++ ;; ++esac ++ + # Check, whether configuration file is up to date + if [ -f .config.$os ] + then +@@ -179,7 +212,7 @@ + echo "PYTHONINCLUDE = $pythoninclude" >> .config.$os + if [ "$version" != "" ] + then +- pythonlib=`dirname \`find /usr -name "lib${version}*.a" -print 2> /dev/null | grep "$version/"\`` ++ pythonlib=`dirname \`find /usr -name "lib${version}*.a" -print 2> /dev/null | grep "$version/" | xargs echo | awk '{print $1}'\`` + else + givehint + echo -n "Please enter the name of the directory where the Python library can be found: " +@@ -268,12 +301,26 @@ + Linux) dir="$os" + makedir + cat ../.config.$os > makefile +- use_icc=`type icc 2> /dev/null` ++# use_icc=`type icc 2> /dev/null` ++ use_icc="" ++ echo "using Linux and use_icc=\"${use_icc}\"" + if [ "$use_icc" = "" ] + then + findProcessor ++ if [ "$processor_is_i386" ] ++ then ++ # -malign-double applies only to intel systems ++ machine_opts="-malign-double" ++ processor_opt="-march=$processor" ++ elif [ "$processor" == "powerpc" ] ++ then ++ # there is no -mcpu option for the more obscure ++ # architectures like arm, ia64, so we have to be selective. ++ # In fact, it only applies to i386 and powerpc. ++ processor_opt="-mcpu=$processor" ++ fi + echo 'COMPILER=gcc' >> makefile +- echo "OPT=-O6 -mcpu=$processor -fomit-frame-pointer -ffast-math -malign-double" >> makefile ++ echo "OPT=-O6 $processor_opt -fomit-frame-pointer -ffast-math $machine_opts" >> makefile + echo 'CFLAGS=-Wall -I/usr/X11R6/include -DLINUX -Wno-strict-aliasing' >> makefile + echo "LDFLAGS=$LINKFORSHARED" >> makefile + else +@@ -285,7 +332,7 @@ + echo 'SCANDIR=' >> makefile + echo 'INCLUDE=$(TIFFINCLUDE) -I$(PNGINCLUDE) -I$(PYTHONINCLUDE)' >> makefile + echo 'LIBRARY=$(LIBTIFF) $(LIBPNG) -L$(LIBPYTHON)' >> makefile +- echo 'LIBS=-L/usr/local/lib -l${PYTHONVERSION} -ltiff -lpng -lz -lGLU -lGL -L/usr/X11R6/lib -lXm -lXmu -lXp -lXi -lXext -lXt -lX11 -lpthread -lutil -ldl -lm' >> makefile ++ echo 'LIBS=-L/usr/local/lib -l${PYTHONVERSION} -ltiff -lpng -lGLU -lGL -L/usr/X11R6/lib -lXm -lXmu -lXi -lXt -lX11 -lm' >> makefile + ;; + # + # This is FreeBSD +--- viewmol-2.4.1.orig/source/Makefile ++++ viewmol-2.4.1/source/Makefile +@@ -144,11 +144,11 @@ + viewmol : ; /bin/sh getmachine viewmol + viewmol_: $(OBJ) ; $(COMPILER) -o viewmol $(BAGGER) $(LDFLAGS) $(OBJ) $(LIBRARY) $(LIBS) + tm : ; /bin/sh getmachine tm +-tm_ : tm.o readframe.o getmem.o ; $(COMPILER) -o tm $(LDFLAGS) tm.o readframe.o getmem.o -lm ++tm_ : tm.o readframe.o getmem.o ; $(COMPILER) -o tm $(LDFLAGS) tm.o readframe.o getmem.o + bio : ; /bin/sh getmachine bio + bio_ : bio.o readframe.o getmem.o ; $(COMPILER) -o bio $(LDFLAGS) bio.o readframe.o getmem.o + readgamess: ; /bin/sh getmachine readgamess +-readgamess_: readgamess.o eof.o getmem.o ; $(COMPILER) -o readgamess $(LDFLAGS) readgamess.o eof.o getmem.o -lm ++readgamess_: readgamess.o eof.o getmem.o ; $(COMPILER) -o readgamess $(LDFLAGS) readgamess.o eof.o getmem.o + readgauss: ; /bin/sh getmachine readgauss + readgauss_: readgauss.o eof.o getmem.o ; $(COMPILER) -o readgauss $(LDFLAGS) readgauss.o eof.o getmem.o + readmopac: ; /bin/sh getmachine readmopac +--- viewmol-2.4.1.orig/source/install ++++ viewmol-2.4.1/source/install +@@ -40,6 +40,10 @@ + IRIX*) dir="${os}_`hinv | awk '/CPU:/ {print $3}' | cut -d/ -f2`" + dirorig="IRIX_R5000" + ;; ++ GNU/k*BSD | GNU*) ++ dir=Linux ++ dirorig=Linux ++ ;; + *) dir="$os" + dirorig="$os" + ;; +@@ -71,7 +75,9 @@ + find $ROOT/lib/viewmol -type d -exec chmod a+rx {} \; + sed 's/\/source//g' viewmolrc > $ROOT/lib/viewmol/viewmolrc + chmod -R 644 $ROOT/lib/viewmol/viewmolrc +-if [ -d /usr/X11R6/lib/X11/app-defaults ] ++# We do not want the code below to run for Debian; ++# the $ROOT/... reference keeps it from proceeding. ++if [ -d $ROOT/X11R6/lib/X11/app-defaults ] + then + locale=`echo $LANG | cut -c1-2` + if [ "$locale" = "en" ] --- viewmol-2.4.1.orig/debian/patches/011_getmachine_HURD.diff +++ viewmol-2.4.1/debian/patches/011_getmachine_HURD.diff @@ -0,0 +1,35 @@ +--- viewmol-2.4.1.orig/source/getmachine ++++ viewmol-2.4.1/source/getmachine +@@ -388,6 +435,32 @@ + echo 'LIBRARY=$(LIBTIFF) $(LIBPNG) -L$(LIBPYTHON)' >> makefile + echo 'LIBS=-L/usr/local/BerkeleyDB.4.0/lib -L/usr/local/lib -l${PYTHONVERSION} -ltiff -lpng12 -lz -lGLU -lGL -L/usr/X11R6/lib -lXmu -lXm -lXp -lXi -lXext -lXt -lX11 -lpthread -lm -lSM -lICE' >> makefile + ;; ++ ++# ++# This is GNU. ++# ++ GNU) dir="$os" ++ makedir ++ cat ../.config.$os > makefile ++ use_icc=`type icc 2> /dev/null` ++ if [ "$use_icc" = "" ] ++ then ++ findProcessor ++ echo 'COMPILER=gcc' >> makefile ++ echo "OPT=-O6 -mcpu=$processor -fomit-frame-pointer -ffast-math -malign-double" >> makefile ++ echo 'CFLAGS=-Wall -I/usr/X11R6/include -DLINUX -Wno-strict-aliasing' >> makefile ++ echo "LDFLAGS=$LINKFORSHARED" >> makefile ++ else ++ echo 'COMPILER=icc' >> makefile ++ echo 'OPT=-O2 -ipo' >> makefile ++ echo 'CFLAGS=-I/opt/intel/compiler50/ia32/include -I/usr/X11R6/include -DLINUX' >> makefile ++ echo "LDFLAGS=$LINKFORSHARED -ipo" >> makefile ++ fi ++ echo 'SCANDIR=' >> makefile ++ echo 'INCLUDE=$(TIFFINCLUDE) -I$(PNGINCLUDE) -I$(PYTHONINCLUDE)' >> makefile ++ echo 'LIBRARY=$(LIBTIFF) $(LIBPNG) -L$(LIBPYTHON)' >> makefile ++ echo 'LIBS=-L/usr/local/lib -l${PYTHONVERSION} -ltiff -lpng -lz -lGLU -lGL -L/usr/X11R6/lib -lXm -lXmu -lXp -lXi -lXext -lXt -lX11 -lpthread -lutil -ldl -lm' >> makefile ++ ;; + # + # This is a (not yet) known operating system. + # --- viewmol-2.4.1.orig/debian/patches/100_locale_exception.diff +++ viewmol-2.4.1/debian/patches/100_locale_exception.diff @@ -0,0 +1,16 @@ +--- viewmol-2.4.1.orig/scripts/setAtomColors.py ++++ viewmol-2.4.1/scripts/setAtomColors.py +@@ -39,7 +39,12 @@ + dir='/usr/local/viewmol' + + #catalog=gettext.translation('Viewmol', localedir=dir + '/locale', languages=['en_US']) +-catalog=gettext.translation('Viewmol', localedir=dir + '/locale') ++try: ++ catalog=gettext.translation('Viewmol', localedir=dir + '/locale') ++except IOError: ++ # gettext.translation will fail if the user's locale is not one that viewmol knows ++ # in which case fallback to en ++ catalog=gettext.translation('Viewmol', localedir=dir + '/locale', languages=['en']) + _ = catalog.gettext + def N_(message): return message + --- viewmol-2.4.1.orig/debian/patches/110_desktop_app.diff +++ viewmol-2.4.1/debian/patches/110_desktop_app.diff @@ -0,0 +1,82 @@ +Index: viewmol/kde/install +=================================================================== +--- viewmol.orig/kde/install 2013-09-21 14:08:57.432936468 +1000 ++++ viewmol/kde/install 2013-09-21 14:08:57.428936585 +1000 +@@ -1,6 +1,6 @@ + #!/bin/sh + +-prgname=`/bin/basename $0` ++prgname=`/usr/bin/basename $0` + + if [ "$KDEDIR" != "" ] + then +@@ -53,25 +53,25 @@ + echo -n "." + if [ "$prgname" = "install" ] + then +- /bin/cp icons/32x32/mimetypes/*.png $DIR/share/icons/default.kde/32x32/mimetypes +- /bin/cp icons/32x32/apps/*.png $DIR/share/icons/default.kde/32x32/apps ++ /bin/cp icons/32x32/mimetypes/*.png $DIR/share/icons/crystalsvg/32x32/mimetypes ++ /bin/cp icons/32x32/apps/*.png $DIR/share/icons/crystalsvg/32x32/apps + echo -n "." +- /bin/cp icons/48x48/mimetypes/*.png $DIR/share/icons/default.kde/48x48/mimetypes +- /bin/cp icons/48x48/apps/*.png $DIR/share/icons/default.kde/48x48/apps ++ /bin/cp icons/48x48/mimetypes/*.png $DIR/share/icons/crystalsvg/48x48/mimetypes ++ /bin/cp icons/48x48/apps/*.png $DIR/share/icons/crystalsvg/48x48/apps + echo -n "." +- /bin/cp icons/64x64/mimetypes/*.png $DIR/share/icons/default.kde/64x64/mimetypes +- /bin/cp icons/64x64/apps/*.png $DIR/share/icons/default.kde/64x64/apps ++ /bin/cp icons/64x64/mimetypes/*.png $DIR/share/icons/crystalsvg/64x64/mimetypes ++ /bin/cp icons/64x64/apps/*.png $DIR/share/icons/crystalsvg/64x64/apps + echo -n "." +- /bin/cp icons/128x128/mimetypes/*.png $DIR/share/icons/default.kde/128x128/mimetypes +- /bin/cp icons/128x128/apps/*.png $DIR/share/icons/default.kde/128x128/apps ++ /bin/cp icons/128x128/mimetypes/*.png $DIR/share/icons/crystalsvg/128x128/mimetypes ++ /bin/cp icons/128x128/apps/*.png $DIR/share/icons/crystalsvg/128x128/apps + echo -n "." + else + for i in 128x128 64x64 48x48 32x32 + do +- /bin/rm -f $DIR/share/icons/default.kde/${i}/mimetypes/solid.png \ +- $DIR/share/icons/default.kde/${i}/mimetypes/molecule.png \ +- $DIR/share/icons/default.kde/${i}/mimetypes/qc.png \ +- $DIR/share/icons/default.kde/${i}/apps/viewmol.png ++ /bin/rm -f $DIR/share/icons/crystalsvg/${i}/mimetypes/solid.png \ ++ $DIR/share/icons/crystalsvg/${i}/mimetypes/molecule.png \ ++ $DIR/share/icons/crystalsvg/${i}/mimetypes/qc.png \ ++ $DIR/share/icons/crystalsvg/${i}/apps/viewmol.png + done + fi + echo -n "." +@@ -85,10 +85,10 @@ + /bin/rm -f $DIR/share/$APPLNK/Graphics/viewmol.desktop + fi + echo -n "." +-if [ "$prgname" = "install" ] +-then +- /bin/mkdir -p /usr/local/lib/viewmol/kde/mimelnk +- /bin/cp ./install /usr/local/lib/viewmol/kde/uninstall +- /bin/cp mimelnk/magic /usr/local/lib/viewmol/kde/mimelnk +-fi ++#if [ "$prgname" = "install" ] ++#then ++# /bin/mkdir -p /usr/local/lib/viewmol/kde/mimelnk ++# /bin/cp ./install /usr/local/lib/viewmol/kde/uninstall ++# /bin/cp mimelnk/magic /usr/local/lib/viewmol/kde/mimelnk ++#fi + echo " done." +Index: viewmol/kde/applications/viewmol.desktop +=================================================================== +--- viewmol.orig/kde/applications/viewmol.desktop 2013-09-21 14:08:57.432936468 +1000 ++++ viewmol/kde/applications/viewmol.desktop 2013-09-21 14:18:36.718184554 +1000 +@@ -6,8 +6,8 @@ + MimeType=chemical/x-msi-car;chemical/x-dmol;chemical/x-mopac;chemical/x-gaussian-log;chemical/x-gulp;chemical/x-pdb;chemical/x-turbomole-control;chemical/x-turbomole-coord; + Comment=Viewmol + Type=Application +-Exec=/usr/local/bin/viewmol %f ++Exec=/usr/bin/viewmol %f + Icon=viewmol.png + MiniIcon= +-Path=$HOME + Terminal=0 ++Categories=Education;Science;Chemistry; --- viewmol-2.4.1.orig/debian/patches/120_PyObject.diff +++ viewmol-2.4.1/debian/patches/120_PyObject.diff @@ -0,0 +1,99 @@ +--- viewmol-2.4.1.orig/source/historymodule.c ++++ viewmol-2.4.1/source/historymodule.c +@@ -318,7 +318,7 @@ + static void history_dealloc(PyHistorySpecObject *self) + { + if (!self) return; +- PyMem_DEL(self); ++ PyObject_Del(self); + quitHistory((Widget)0, (caddr_t)0, (XmAnyCallbackStruct *)0); + (void)checkInterrupt(); + } +--- viewmol-2.4.1.orig/source/spectrummodule.c ++++ viewmol-2.4.1/source/spectrummodule.c +@@ -383,7 +383,7 @@ + static void spectrum_dealloc(PySpectrumSpecObject *self) + { + if (!self) return; +- PyMem_DEL(self); ++ PyObject_Del(self); + quitSpectrum((Widget)0, (caddr_t)0, (XmAnyCallbackStruct *)0); + (void)checkInterrupt(); + } +--- viewmol-2.4.1.orig/source/input.c ++++ viewmol-2.4.1/source/input.c +@@ -1603,7 +1603,7 @@ + if (mol->exponents != NULL) fremem((void **)&(mol->exponents)); + if (mol->addedBonds != NULL) fremem((void **)&(mol->addedBonds)); + if (mol->deletedBonds != NULL) fremem((void **)&(mol->deletedBonds)); +-/* PyMem_DEL(mol->pyObject);*/ ++/* PyObject_Del(mol->pyObject);*/ + + if (first != nmolecule-1) + { +--- viewmol-2.4.1.orig/source/labelmodule.c ++++ viewmol-2.4.1/source/labelmodule.c +@@ -217,7 +217,7 @@ + static void label_dealloc(PyLabelSpecObject *self) + { + /* This has to be a dummy function, since labels are handled in Viewmol +- PyMem_DEL(self); */ ++ PyObject_Del(self); */ + } + + static PyObject *label_getattr(PyLabelSpecObject *self, char *name) +--- viewmol-2.4.1.orig/source/atommodule.c ++++ viewmol-2.4.1/source/atommodule.c +@@ -374,7 +374,7 @@ + static void atom_dealloc(PyAtomSpecObject *self) + { + if (!self) return; +- PyMem_DEL(self); ++ PyObject_Del(self); + } + + static PyObject *atom_getattr(PyAtomSpecObject *self, char *name) +--- viewmol-2.4.1.orig/source/lightmodule.c ++++ viewmol-2.4.1/source/lightmodule.c +@@ -134,7 +134,7 @@ + static void light_dealloc(PyLightSpecObject *self) + { + if (!self) return; +- PyMem_DEL(self); ++ PyObject_Del(self); + } + + static PyObject *light_getattr(PyLightSpecObject *self, char *name) +--- viewmol-2.4.1.orig/source/energylevelmodule.c ++++ viewmol-2.4.1/source/energylevelmodule.c +@@ -304,7 +304,7 @@ + static void energylevels_dealloc(PyEnergyLevelSpecObject *self) + { + if (!self) return; +- PyMem_DEL(self); ++ PyObject_Del(self); + quitMODiagram((Widget)0, (caddr_t)0, (XmAnyCallbackStruct *)0); + (void)checkInterrupt(); + } +--- viewmol-2.4.1.orig/source/elementmodule.c ++++ viewmol-2.4.1/source/elementmodule.c +@@ -369,7 +369,7 @@ + static void element_dealloc(PyElementSpecObject *self) + { + if (!self) return; +- PyMem_DEL(self); ++ PyObject_Del(self); + } + + static PyObject *element_getattr(PyElementSpecObject *self, char *name) +--- viewmol-2.4.1.orig/source/moleculemodule.c ++++ viewmol-2.4.1/source/moleculemodule.c +@@ -1017,7 +1017,7 @@ + static void molecule_dealloc(PyMoleculeSpecObject *self) + { + /* A dummy function is required here to avoid crashing +- PyMem_DEL(self); */ ++ PyObject_Del(self); */ + } + + void initMoleculeModule(void) --- viewmol-2.4.1.orig/debian/patches/130_DEFAULTPATH.diff +++ viewmol-2.4.1/debian/patches/130_DEFAULTPATH.diff @@ -0,0 +1,11 @@ +--- viewmol-2.4.1.orig/source/getrc.c ++++ viewmol-2.4.1/source/getrc.c +@@ -87,7 +87,7 @@ + + static char viewmolpath[MAXLENLINE]; + +-#define DEFAULTPATH "/usr/local/lib/viewmol" ++#define DEFAULTPATH "/usr/lib/viewmol" + + int getrc(void) + { --- viewmol-2.4.1.orig/debian/patches/140_bin_awk.diff +++ viewmol-2.4.1/debian/patches/140_bin_awk.diff @@ -0,0 +1,7 @@ +--- viewmol-2.4.1.orig/readdmol.awk ++++ viewmol-2.4.1/readdmol.awk +@@ -1,3 +1,4 @@ ++#!/usr/bin/awk + #******************************************************************************* + # * + # Viewmol * --- viewmol-2.4.1.orig/debian/patches/series +++ viewmol-2.4.1/debian/patches/series @@ -0,0 +1,7 @@ +010_build_scripts.diff +#011_getmachine_HURD.diff # already applied pre-quilt (to allow debian/rules clean to recognise HURD) +100_locale_exception.diff +110_desktop_app.diff +120_PyObject.diff +130_DEFAULTPATH.diff +140_bin_awk.diff --- viewmol-2.4.1.orig/debian/preinst +++ viewmol-2.4.1/debian/preinst @@ -0,0 +1,14 @@ +#!/bin/sh -e + +# rename locale/en_US to en (from 2.4.1-12) +if [ "$1" = "upgrade" ]; then + if dpkg --compare-versions "$2" lt-nl 2.4.1-12; then + if [ -d /etc/viewmol/locale/en_US/ ] && [ ! -d /etc/viewmol/locale/en/ ]; then + echo "Moving /etc/viewmol/locale/en_US/ to .../en" + mv /etc/viewmol/locale/en_US /etc/viewmol/locale/en + fi + fi +fi + + +#DEBHELPER# --- viewmol-2.4.1.orig/debian/pycompat +++ viewmol-2.4.1/debian/pycompat @@ -0,0 +1 @@ +2 --- viewmol-2.4.1.orig/debian/rules +++ viewmol-2.4.1/debian/rules @@ -0,0 +1,113 @@ +#!/usr/bin/make -f +# Sample debian/rules that uses debhelper. +# GNU copyright 1997 to 1999 by Joey Hess. + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +DESTDIR=$(CURDIR)/debian/viewmol + +patch: + dh_quilt_patch + +unpatch: + dh_quilt_unpatch + +configure: patch configure-stamp +configure-stamp: + dh_testdir + # Add here commands to configure the package. + touch configure-stamp + +build: configure build-arch build-indep +build-arch: build-stamp +build-indep: build-stamp +build-stamp: + dh_testdir + + # Add here commands to compile the package. + $(MAKE) -C source + + touch build-stamp + +clean: + dh_testdir + dh_testroot + rm -f build-stamp configure-stamp + + # Add here commands to clean up after the build process. + [ ! -f source/Makefile ] || $(MAKE) -C source clean + # viewmol's make clean does not clean out the '$$(os)' directory, so do it here. + -rm -r source/Linux source/.config.Linux + dh_quilt_unpatch + dh_clean + +install: build + dh_testdir + dh_testroot + dh_prep + dh_installdirs + + # install the package into debian/viewmol. + cd source; ./install $(DESTDIR)/usr + + # put arch-independent files into /usr/share/viewmol (make FHS compliant) + mv $(DESTDIR)/usr/lib/viewmol/viewmolrc $(DESTDIR)/etc/viewmol + # why didn't this link work? Use dh_link instead ;/ + #ln -s /etc/viewmol/viewmolrc $(DESTDIR)/usr/lib/viewmol/viewmolrc + cd $(DESTDIR)/usr/lib/viewmol; mv readdmol readgulp readpqs writecar \ + writegauss.py writemol writetm readdmol.awk \ + $(DESTDIR)/usr/share/viewmol + cd $(DESTDIR)/usr/lib/viewmol; mv examples locale scripts tests \ + $(DESTDIR)/usr/share/viewmol + # viewmol has no standard English, so change en_US to en + # or else other English locales fail + cd $(DESTDIR)/usr/share/viewmol/locale; mv en_US en + + # localised Viewmol settings may be user-configurable + # (conffiles go in /etc) + for i in $(DESTDIR)/usr/share/viewmol/locale/*; do \ + mkdir $(DESTDIR)/etc/viewmol/locale/`basename $${i}` ; \ + mv $${i}/Viewmol $(DESTDIR)/etc/viewmol/locale/`basename $${i}` ; \ + ln -s /etc/viewmol/locale/`basename $${i}`/Viewmol $${i}/Viewmol ; \ + done + + + # Viewmol scripts heavily depend on VIEWMOLPATH, without + # distinguishing between ../share and ../lib, so make a symlink. + for i in $(DESTDIR)/usr/share/viewmol/*; do \ + ln -s /usr/share/viewmol/`basename $${i}` $(DESTDIR)/usr/lib/viewmol/`basename $${i}` ; \ + done + + # install KDE (and generic Desktop) support files + cd kde; KDEDIR=$(DESTDIR)/usr ./install + ln -s /usr/share/icons/crystalsvg/32x32/apps/viewmol.png $(DESTDIR)/usr/share/pixmaps + +# Build architecture-independent files here. +binary-indep: build install +# We have nothing to do by default. + +# Build architecture-dependent files here. +binary-arch: build install + dh_testdir + dh_testroot + dh_installdocs $(DESTDIR)/usr/lib/viewmol/doc/* + rm -r $(DESTDIR)/usr/lib/viewmol/doc + # don't want to compress examples, so don't use dh_installexamples + ln -s /usr/share/viewmol/examples/ $(DESTDIR)/usr/share/doc/viewmol + dh_installmenu + dh_installman debian/viewmol.1 + dh_installchangelogs + dh_link + dh_python2 + dh_strip + dh_compress + dh_fixperms + dh_installdeb + dh_shlibdeps + dh_gencontrol + dh_md5sums + dh_builddeb + +binary: binary-indep binary-arch +.PHONY: build clean binary-indep binary-arch binary install configure --- viewmol-2.4.1.orig/debian/source.lintian-overrides +++ viewmol-2.4.1/debian/source.lintian-overrides @@ -0,0 +1,5 @@ +# HURD patch 011_getmachine_HURD.diff from bug#534330 had to be pre-applied +# in order to allow the HURD to be recognised during debian/rules clean. +# This rule is run before patch by dpkg-buildpackage. +viewmol source: patch-system-but-direct-changes-in-diff source/getmachine + --- viewmol-2.4.1.orig/debian/viewmol.1 +++ viewmol-2.4.1/debian/viewmol.1 @@ -0,0 +1,102 @@ +.\" This manpage has been automatically generated by docbook2man +.\" from a DocBook document. This tool can be found at: +.\" +.\" Please send any bug reports, improvements, comments, patches, +.\" etc. to Steve Cheng . +.TH "VIEWMOL" "1" "18 March 2008" "" "" + +.SH NAME +viewmol \- a graphical front end for computational chemistry programs +.SH SYNOPSIS + +\fBviewmol\fR + +.SH "DESCRIPTION" +.PP +\fBviewmol\fR is a graphical front end for +computational chemistry programs. +It is able to graphically aid in the generation of molecular structures for +computations and to visualize their results. The program's capabilities +include: +.TP 0.2i +\(bu +Building and editing of molecules +.TP 0.2i +\(bu +Visualization of the geometry of a molecule +.TP 0.2i +\(bu +Tracing of a geometry optimization or a MD trajectory +.TP 0.2i +\(bu +Animation of normal vibrations or to show them as arrows +.TP 0.2i +\(bu +Drawing of IR, Raman, and inelastic neutron scattering spectra +.TP 0.2i +\(bu +Drawing of an MO energy level or density of states diagram +.TP 0.2i +\(bu +Drawing of basis functions, molecular orbitals, and electron densities +.TP 0.2i +\(bu +Display of forces acting on each atom in a certain configuration +.TP 0.2i +\(bu +Display of Miller planes in crystals +.TP 0.2i +\(bu +Calculation of thermodynamic properties for molecules andreactions +.TP 0.2i +\(bu +Drawings generated by \fBviewmol\fR can be saved as TIFF, HPGL, or +PostScript files +.TP 0.2i +\(bu +Animations of normal modes can be converted to a video file (MPEG), +e.\~g. for inclusion into World Wide Web documents (requires additional +programs available on the Internet) +.TP 0.2i +\(bu +Interface to the freeware ray tracing program \fBRAYSHADE\fR (input +file generation and use of \fBRAYSHADE\fR from within \fBviewmol\fR) +.TP 0.2i +\(bu +Input and output in a variety of formats, new formats can be added +easily by the user +\fBviewmol\fR includes a Python interpreter for automation. +.PP +At present \fBviewmol\fR includes input filters for +\fBDISCOVER\fR, \fBDMOL\fR, +\fBGAMESS\fR, \fBGAUSSIAN 9X\fR, +\fBGULP\fR, \fBMOPAC\fR, and +\fBTURBOMOLE\fR +outputs as well as for PDB files (\fBviewmol\fR is therefore suited as a viewer +for structural data on the World Wide Web). Structures can be saved as MSI +car-files, MDL files, and \fBTURBOMOLE\fR coordinate files. \fBviewmol\fR\&'s +file format has been added to \fBBABEL\fR so that +\fBBABEL\fR can serve as an +input as well as an output filter for coordinates. +.PP +\fBviewmol\fR supports a space ball as input device. +.PP +The support programs for converting to and from the various +coordinate file types may potentially be useful as stand alone +utilities. They are split between /usr/share/viewmol (scripts) +and /usr/lib/viewmol (C binaries), but individual documentation +for them is not available. +.SH "SEE ALSO" +.PP +rasmol (1), gperiodic (1). +.PP +Complete HTML documentation may be found in +/usr/share/doc/viewmol. +.SH "AUTHOR" +.PP +\fBviewmol\fR was written by +Jörg-Rüdiger Hill +\&. +.PP +This manual page was written by Drew Parsons for +the Debian GNU/Linux system (but may be used by others). --- viewmol-2.4.1.orig/debian/viewmol.sgml +++ viewmol-2.4.1/debian/viewmol.sgml @@ -0,0 +1,156 @@ +Drew"> + Parsons"> + + March 11, 2001"> + 1"> + dparsons@debian.org"> + + VIEWMOL"> + + + Debian GNU/Linux"> + GNU"> +]> + + + +
+ &dhemail; +
+ + &dhfirstname; + &dhsurname; + + + 2001 + &dhusername; + + &dhdate; + + + &dhucpackage; + + &dhsection; + + + &dhpackage; + + a graphical front end for computational chemistry programs + + + + &dhpackage; + + + + DESCRIPTION + + &dhpackage; is a graphical front end for + computational chemistry programs. +It is able to graphically aid in the generation of molecular structures for +computations and to visualize their results. The program's capabilities +include: + + +Building and editing of molecules +Visualization of the geometry of a molecule +Tracing of a geometry optimization or a MD trajectory +Animation of normal vibrations or to show them as arrows +Drawing of IR, Raman, and inelastic neutron scattering spectra +Drawing of an MO energy level or density of states diagram +Drawing of basis functions, molecular orbitals, and electron densities +Display of forces acting on each atom in a certain configuration +Display of Miller planes in crystals +Calculation of thermodynamic properties for molecules andreactions +Drawings generated by &dhpackage; can be saved as TIFF, HPGL, or +PostScript files +Animations of normal modes can be converted to a video file (MPEG), +e. g. for inclusion into World Wide Web documents (requires additional +programs available on the Internet) + +Interface to the freeware ray tracing program RAYSHADE (input +file generation and use of RAYSHADE from within &dhpackage;) + +Input and output in a variety of formats, new formats can be added +easily by the user + + +&dhpackage; includes a Python interpreter for automation. + + + +At present &dhpackage; includes input filters for +DISCOVER, DMOL, +GAMESS, GAUSSIAN 9X, +GULP, MOPAC, and +TURBOMOLE +outputs as well as for PDB files (&dhpackage; is therefore suited as a viewer +for structural data on the World Wide Web). Structures can be saved as MSI +car-files, MDL files, and TURBOMOLE coordinate files. &dhpackage;'s +file format has been added to BABEL so that +BABEL can serve as an +input as well as an output filter for coordinates. + + + +&dhpackage; supports a space ball as input device. + + +The support programs for converting to and from the various + coordinate file types may potentially be useful as stand alone + utilities. They are split between /usr/share/viewmol (scripts) + and /usr/lib/viewmol (C binaries), but individual documentation + for them is not available. + + + + + SEE ALSO + + rasmol (1), gperiodic (1). + +Complete HTML documentation may be found in + /usr/share/doc/viewmol. + + + + AUTHOR + &dhpackage; was written by + Jörg-Rüdiger Hill + joehill@users.sourceforge.net. + + +This manual page was written by &dhusername; &dhemail; for + the &debian; system (but may be used by others). + + + + + + + + + --- viewmol-2.4.1.orig/debian/watch +++ viewmol-2.4.1/debian/watch @@ -0,0 +1,2 @@ +version=3 +http://sf.net/viewmol/viewmol-([\d.]+)\.src\.tgz --- viewmol-2.4.1.orig/source/getmachine +++ viewmol-2.4.1/source/getmachine @@ -388,6 +388,32 @@ echo 'LIBRARY=$(LIBTIFF) $(LIBPNG) -L$(LIBPYTHON)' >> makefile echo 'LIBS=-L/usr/local/BerkeleyDB.4.0/lib -L/usr/local/lib -l${PYTHONVERSION} -ltiff -lpng12 -lz -lGLU -lGL -L/usr/X11R6/lib -lXmu -lXm -lXp -lXi -lXext -lXt -lX11 -lpthread -lm -lSM -lICE' >> makefile ;; + +# +# This is GNU. +# + GNU) dir="$os" + makedir + cat ../.config.$os > makefile + use_icc=`type icc 2> /dev/null` + if [ "$use_icc" = "" ] + then + findProcessor + echo 'COMPILER=gcc' >> makefile + echo "OPT=-O6 -mcpu=$processor -fomit-frame-pointer -ffast-math -malign-double" >> makefile + echo 'CFLAGS=-Wall -I/usr/X11R6/include -DLINUX -Wno-strict-aliasing' >> makefile + echo "LDFLAGS=$LINKFORSHARED" >> makefile + else + echo 'COMPILER=icc' >> makefile + echo 'OPT=-O2 -ipo' >> makefile + echo 'CFLAGS=-I/opt/intel/compiler50/ia32/include -I/usr/X11R6/include -DLINUX' >> makefile + echo "LDFLAGS=$LINKFORSHARED -ipo" >> makefile + fi + echo 'SCANDIR=' >> makefile + echo 'INCLUDE=$(TIFFINCLUDE) -I$(PNGINCLUDE) -I$(PYTHONINCLUDE)' >> makefile + echo 'LIBRARY=$(LIBTIFF) $(LIBPNG) -L$(LIBPYTHON)' >> makefile + echo 'LIBS=-L/usr/local/lib -l${PYTHONVERSION} -ltiff -lpng -lz -lGLU -lGL -L/usr/X11R6/lib -lXm -lXmu -lXp -lXi -lXext -lXt -lX11 -lpthread -lutil -ldl -lm' >> makefile + ;; # # This is a (not yet) known operating system. #