debian/0000755000000000000000000000000012214376436007176 5ustar debian/control0000644000000000000000000000330612214376361010600 0ustar Source: dssp Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Maarten L. Hekkelman , Laszlo Kajan , Andreas Tille Build-Depends: debhelper (>= 7.0.50~), libboost-filesystem-dev (>= 1.46.0), libboost-iostreams-dev (>= 1.42.0), libboost-program-options-dev (>= 1.42.0), libboost-system-dev (>= 1.42.0), libboost-thread-dev (>= 1.42.0) Standards-Version: 3.9.4 Section: science Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/dssp/trunk/ Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/dssp/trunk/ Homepage: http://www.cmbi.ru.nl/dssp.html Package: dssp Architecture: any Depends: ${misc:Depends}, ${shlibs:Depends} Description: protein secondary structure assignment based on 3D structure DSSP is an application you use to assign the secondary structure of a protein based on its solved three dimensional (3D) structure. . This version (2) of DSSP is a rewrite that produces the same output as the original DSSP, but deals better with exceptions in PDB files and is much faster. Package: dssp-dbg Architecture: any Section: debug Priority: extra Depends: dssp (= ${binary:Version}), ${misc:Depends} Description: debugging symbols for dssp DSSP is an application to assign the secondary structure of a protein based on its three dimensional (3D) structure. . This version (2) of DSSP is a rewrite that produces the same output as the original DSSP, but deals better with exceptions in PDB files and is much faster. . This package provides the detached debug symbols for dssp. debian/copyright0000644000000000000000000000337112125621004011116 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: dssp Upstream-Contact: Maarten L. Hekkelman Source: http://www.cmbi.ru.nl/dssp/ Files: debian/* Copyright: © 2012, Maarten L. Hekkelman License: Boost-1.0 Files: * Copyright: © 2009-2012, Maarten L. Hekkelman License: Boost-1.0 License: Boost-1.0 Boost Software License - Version 1.0 - August 17th, 2003 . Permission is hereby granted, free of charge, to any person or organization obtaining a copy of the software and accompanying documentation covered by this license (the "Software") to use, reproduce, display, distribute, execute, and transmit the Software, and to prepare derivative works of the Software, and to permit third-parties to whom the Software is furnished to do so, all subject to the following: . The copyright notices in the Software and this entire statement, including the above license grant, this restriction and the following disclaimer, must be included in all copies of the Software, in whole or in part, and all derivative works of the Software, unless such copies or derivative works are solely in the form of machine-executable object code generated by a source language processor. . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. debian/changelog0000644000000000000000000000262712214022020011030 0ustar dssp (2.2.1-1) unstable; urgency=low * Bug fix in mmCIF import code. * New upstream release. -- Maarten L. Hekkelman Wed, 11 Sep 2013 10:00:00 +0200 dssp (2.1.0-1) unstable; urgency=low * New upstream release. * Boost got fixed, bug was 'FTBFS: xtime.hpp:23:5: error: expected identifier before numeric constant' (no changes to dssp were required to solve bug) (Closes: #708446) -- Laszlo Kajan Wed, 08 May 2013 18:20:06 +0200 dssp (2.0.4-2) unstable; urgency=low [ Laszlo Kajan ] * Stick to debhelper compatibility level 7 to enable flawless build on Ubuntu Lucid (documented in debian/README.source) [ Maarten L. Hekkelman ] * Fix for compiling with gcc 4.7, std::min (Closes: #673434) * Added the use of dpkg-buildflags to include hardening flags since debhelper is still maintained at version 7. -- Maarten L. Hekkelman Mon, 21 May 2012 10:00:00 +0200 dssp (2.0.4-1) unstable; urgency=low * Initial release. (Closes: #669259) * Added description to dssp; added upstream (reference); parallel building now enabled; fixed spelling error in man page; added debug package; fixed debian/watch; added get-orig-source target to rules. * Changed libboost build dependency to version >= 1.42.0.1 to allow building on stable. -- Laszlo Kajan Wed, 18 Apr 2012 11:09:02 +0200 debian/compat0000644000000000000000000000000212125621004010355 0ustar 7 debian/watch0000644000000000000000000000014712125621004010212 0ustar version=3 opts="pasv" \ ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-([0-9.]+)\.t[bgx]z debian uupdate debian/upstream0000644000000000000000000000047512125621004010750 0ustar Name: dssp Reference: - Author: W. Kabsch and C. Sander Title: 'Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.' Journal: Biopolymers Volume: 22 Pages: 2577-2637 Year: 1983 URL: http://www.ncbi.nlm.nih.gov/pubmed/6667333 PMID: 6667333 debian/dssp.install0000644000000000000000000000000512125621004011513 0ustar usr/ debian/patches/0000755000000000000000000000000012214376436010625 5ustar debian/patches/series0000644000000000000000000000003012213564503012024 0ustar thread_include makefile debian/patches/thread_include0000644000000000000000000000116212213564503013513 0ustar Description: moving boost thread include out of header that does not use it Patch is not yet forwarded upstream. Author: Laszlo Kajan --- a/src/utils.h +++ b/src/utils.h @@ -10,7 +10,6 @@ #endif #include -#include #include #include #include --- a/src/structure.cpp +++ b/src/structure.cpp @@ -18,6 +18,7 @@ #define foreach BOOST_FOREACH #include #include +#include #include "align-2d.h" #include "utils.h" debian/patches/makefile0000644000000000000000000000427512214022020012306 0ustar Description: assorted fixes [Maarten L. Hekkelman ] * DEST_DIR patched to DESTDIR . [Laszlo Kajan ] * stripping is patched out so that it can be done by dh into a debug package * line echo suppression is removed * spelling errors in man page fixed . Upstream is aware of this patch. Author: Maarten L. Hekkelman Author: Laszlo Kajan --- a/makefile +++ b/makefile @@ -11,18 +11,16 @@ all: mkdssp -include make.config - VERSION = 2.2.1 DEST_DIR ?= /usr/local LIB_DIR = $(BOOST_LIB_DIR) INC_DIR = $(BOOST_INC_DIR) -BIN_DIR = $(DEST_DIR)/bin -MAN_DIR = $(DEST_DIR)/man/man1 +BIN_DIR = $(DESTDIR)$(DEST_DIR)/bin +MAN_DIR = $(DESTDIR)$(DEST_DIR)/share/man/man1 -BOOST_LIBS = thread filesystem program_options iostreams system -LIBS = $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) z bz2 +BOOST_LIBS = thread program_options iostreams system +LIBS = $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) DEFINES = USE_COMPRESSION LINUX VERSION='"$(VERSION)"' CXX = g++ @@ -49,22 +47,19 @@ OBJECTS = $(OBJ_DIR)/mkdssp.o $(OBJ_DIR)/dssp.o $(OBJ_DIR)/primitives-3d.o $(OBJ_DIR)/structure.o $(OBJ_DIR)/utils.o $(OBJ_DIR)/mas.o $(OBJ_DIR)/iocif.o mkdssp: $(OBJECTS) - @ echo linking $@ - @ $(CXX) -static -o $@ $^ $(LDOPTS) + $(CXX) -o $@ $^ $(LDOPTS) -include $(OBJECTS:%.o=%.d) +-include $(OBJECTS:%.o=%.d) $(OBJECTS:.o=.d): $(OBJ_DIR): - @ mkdir -p $(OBJ_DIR) + mkdir -p $(OBJ_DIR) $(OBJ_DIR)/%.o: %.cpp | $(OBJ_DIR) - @ echo compiling $@ - @ $(CXX) -MD -c -o $@ $< $(CFLAGS) + $(CXX) -MD -c -o $@ $< $(CPPFLAGS) $(CFLAGS) clean: - install -d $(BIN_DIR) $(MAN_DIR) rm -rf $(OBJ_DIR)/* mkdssp install: mkdssp @@ -85,11 +80,3 @@ @ cp doc/mkdssp.1 $(DIST_NAME)/doc/mkdssp.1 tar czf $(DIST_NAME).tgz $(DIST_NAME) cp $(DIST_NAME).tgz dssp_$(VERSION).orig.tar.gz - -make.config: - @echo "creating empty make.config file" - @echo "# Set local options for make here" > make.config - @echo "#BOOST_LIB_SUFFIX = -mt" >> make.config - @echo "#BOOST_LIB_DIR = $(HOME)/projects/boost/lib" >> make.config - @echo "#BOOST_INC_DIR = $(HOME)/projects/boost/include" >> make.config - debian/README.source0000644000000000000000000000023712125621004011340 0ustar [Laszlo Kajan