debian/0000755000000000000000000000000011745032405007167 5ustar debian/mustang.manpages0000644000000000000000000000001611263031217012352 0ustar man/mustang.1 debian/watch0000644000000000000000000000020511736652004010220 0ustar version=3 http://www.csse.monash.edu.au/~karun/Site/mustang.html http://www.csse.unimelb.edu.au/~arun/mustang/mustang_v([.\d]*)\.tgz debian/copyright0000644000000000000000000001037111745032274011130 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: MUSTANG Upstream-Contact: Arun S Konagurthu Source: http://www.csse.monash.edu.au/~karun/Site/mustang.html Files: Makefile src/* data/test/test_zf-CCHH Copyright: 2005-2009 Arun S Konagurthu The University of Melbourne. License: BSD-like Files: debian/* Copyright: 2007-2009 Morten Kjeldgaard 2008 Steffen Möller 2010 Charles Plessy 2008-2012 Andreas Tille License: BSD-like Files: data/test/pdbs: Copyright: PD License: PD ADVISORY NOTICE FOR USE OF THE PDB ARCHIVE . By using the materials available in this archive, the user agrees to abide by the following conditions: . * The archival data files in the PDB archive are made freely available to all users. Data files within the archive may be redistributed in original form without restriction. Redistribution of modified data files using the same file name as is on the FTP server is prohibited. The rules for file names are detailed at http://www.wwpdb.org/wwpdb_charter.html. . * Data files containing PDB content may incorporate the PDB 4-letter entry name (e.g. 1ABC) in standard PDB records only if they are exactly the same as what is residing in the PDB archive. This does not prevent databases from including PDB entry_id's as cross-references where it is clear that they refer to the PDB archive. PDB records refer to the standard PDB format. 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License: BSD-like Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . * Neither the name of the University of Melbourne nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. debian/mustang.examples0000644000000000000000000000005111272113130012367 0ustar debian/runtest debian/test_zf-CCHH-small debian/changelog0000644000000000000000000001031711745032341011042 0ustar mustang (3.2.1-3) unstable; urgency=low * debian/upstream: - Use BibTeX friendly formating of authors * debian/patches/gcc-4.7.patch: Fix build issue with gcc-4.7 Closes: #667293 -- Andreas Tille Sun, 22 Apr 2012 18:18:34 +0200 mustang (3.2.1-2) unstable; urgency=low [ Charles Plessy ] * Documented information in ‘debian/upstream’. * Removed mention of the bibliographic reference in ‘debian/control’. [ Andreas Tille ] * debian/watch: Fixed homepage for download * debian/upstream: Moved DOI+PMID to references * debian/citation.bib: Removed because duplication of information * debian/mustang.docs: Removed because nothing to install any more * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Fixed Vcs fields - FIxed homepage * debian/source/format: 3.0 (quilt) * debian/{control,rules}: removed explicite quilt dependency * debian/README.source: Removed because outdated with source format 3.0 (quilt) * debian/copyright: Rewritten to match DEP5 and verified using cme fix dpkg-copyright * debian/{compat,control}: debhelper 9 -- Andreas Tille Tue, 03 Apr 2012 22:17:32 +0200 mustang (3.2.1-1) unstable; urgency=low * New upstream version * Morten Kjeldgaard lost interest in this package because of agressive upstream so I removed him from uploaders and added myself * debhelper 7 * prefer single debhelper files in debian/ instead of using arguments do debhelper scripts in the rules file which simplifies transition to short rules file * debian/watch: no uversionmangle which leads to wrong version number -- Andreas Tille Wed, 28 Oct 2009 19:59:33 +0100 mustang (3.2.0-1) unstable; urgency=low * New upstream version. * Patches 02-main.cpp.patch and 04-gcc-4.3-exit.patch have been incorporated upstream and are no longer required. -- Morten Kjeldgaard Mon, 05 Oct 2009 13:10:26 +0200 mustang (3.0-2) unstable; urgency=low * Converted to quilt patch system. * New uploader email * Added citation.bib file, installed in /usr/share/doc/mustang -- Morten Kjeldgaard Sun, 14 Dec 2008 13:55:03 +0100 mustang (3.0-1) unstable; urgency=low [ Nelson A. de Oliveira ] * debian/rules: CFLAGS -> CPPFLAGS * debian/control: add ${misc:Depends} to binary package, and add Suggests: mustang-testdata * Add debian/watch [ Morten Kjeldgaard ] * Upload mustang to Debian (Closes: #459637). * debian/control: Maintainer and homepage fields set as per Debian policy. * Include test pdb files in a separate package. * debian/rules: add get-orig-source target. * Include new upstream patches. * Upstream now distributes manpage which is installed. * Include pdb files from upstream tarball in a separate package, for a more extensive test. [ Andreas Tille ] * Maintainer: Debian-Med Packaging Team Uploaders: Morten Kjeldgaard * XS-DM-Upload-Allowed: Yes * Vcs-Browser, Vcs-Svn [ Steffen Moeller ] * Policy 3.8.0 * Patch for gcc-4.3 * debian/control has less redundany and easier working, added ref to paper. * changed debian watch to reflect version mangling in debian/changelog -- Morten Kjeldgaard Mon, 04 Aug 2008 10:42:14 +0200 mustang (3.0-0ubuntu1) gutsy; urgency=low * Initial release * Manpage mustang.1 authored from information in the README.txt file. * The upstream tarball was repackaged to remove PDB files which have an undetermined copyright status and hence can not be distributed. Furthermore, the license was extracted from one of the source files and placed in the file 'LICENSE'. A note describing the repackaging in detail is placed in debian/copyright. * Instead of the PDB files included in the original tarball, a script is supplied that allows the user to fetch a few PDB files and test that mustang works. * A patch on main.cpp is supplied to beautify the output of the initial author blurb. The tabs in the output were removed to make the output easier to read in a default 80 columns wide terminal window. -- Morten Kjeldgaard Mon, 25 Jun 2007 15:55:12 +0000 debian/test_zf-CCHH-small0000644000000000000000000000320711263031217012376 0ustar ############################################################################################### ## This is a valid desciption file. ## ## ## ## Line starting with '>' symbol is treated as PATH to the directory containing structures ## ## to be aligned. ## ## ## ## Lines starting with '+' symbol are treated as file names. If PATH is specified (as in ## ## this case), then only the filenames should be provided. However, if PATH line is NOT ## ## provided, then the absolute/relative paths of the structure files should be provided. ## ## ## ## All the lines NOT starting with '>' and '+' are simply ignored. ## ## ## ## Do NOT use comments in the same lines containg PATH and FILENAMES. ## ## ## ## Whitespaces are intentionally inserted before and/or after '>' and --in some cases-- '+' ## ## symbols to show that the whitespaces are ignored ## ############################################################################################### > /tmp/mustang +1sp1.pdb +1sp2.pdb debian/source/0000755000000000000000000000000011745031207010466 5ustar debian/source/format0000644000000000000000000000001411717554366011713 0ustar 3.0 (quilt) debian/compat0000644000000000000000000000000211736654367010406 0ustar 9 debian/patches/0000755000000000000000000000000011745032030010610 5ustar debian/patches/gcc-4.7.patch0000644000000000000000000000075411745032030012701 0ustar Author: Andreas Tille Date: Sun, 22 Apr 2012 18:06:41 +0200 Bug-Closed: http://bugs.debian.org/667293 Description: Build with g++ version 4.7 Followed hint given at http://gcc.gnu.org/gcc-4.7/porting_to.html --- MUSTANG_v3.2.1.orig/src/superpose_on_core_2.cpp +++ MUSTANG_v3.2.1/src/superpose_on_core_2.cpp @@ -44,6 +44,8 @@ using std::ifstream ; using std::ofstream ; +#include + #include "macros.h" #include "globals.h" #include "alloc_routines.h" debian/patches/series0000644000000000000000000000004411745031323012027 0ustar 03-test_zf-cchh.patch gcc-4.7.patch debian/patches/03-test_zf-cchh.patch0000644000000000000000000000056411736654167014464 0ustar This patch merely changes the name of the directory storing the example pdb files. --- mustang-3.2.1.orig/data/test/test_zf-CCHH +++ mustang-3.2.1/data/test/test_zf-CCHH @@ -20,7 +20,7 @@ ################################################################################ -> ./data/test/pdbs +> /usr/share/doc/mustang-testdata/examples/pdbs +1ard.pdb +1bboN.pdb debian/mustang-testdata.install0000644000000000000000000000021111272113457014040 0ustar data/test/pdbs/[0-9]* usr/share/doc/mustang-testdata/examples/pdbs data/test/test_zf-CCHH usr/share/doc/mustang-testdata/examples debian/rules0000755000000000000000000000043411736652510010255 0ustar #!/usr/bin/make -f # -*- mode: makefile; mode: font-lock -*- %: dh $@ override_dh_compress: dh_compress -X.pdb override_dh_auto_clean: rm -f obj/*.o rm -f bin/mustang-3.2* # dh_clean override_dh_auto_install: install -D -m755 bin/mustang-3.2* debian/mustang/usr/bin/mustang debian/runtest0000644000000000000000000000107111263031217010610 0ustar #!/bin/sh # pdbget script for mustang that fetches # db entries to run test file. # set -e SERVER=www.pdb.org entries="1sp1 1sp2 3znf" pdb_fetch () { for n in $* ; do wget -nv http://${SERVER}/pdb/files/$n.pdb.gz done } # The process will run in this directory: tmpdir=/tmp/mustang savedir=$PWD rm -rf $tmpdir mkdir -p $tmpdir cd $tmpdir pdb_fetch $entries for f in $entries; do gzip -dc $f.pdb.gz > $f.pdb ; done mustang -f /usr/share/doc/mustang/examples/test_zf-CCHH-small cd $savedir echo Results are in $tmpdir/results.html and $tmpdir/results.pdb debian/control0000644000000000000000000000266411736654421010612 0ustar Source: mustang Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille DM-Upload-Allowed: yes Homepage: http://www.csse.monash.edu.au/~karun/Site/mustang.html Build-Depends: debhelper (>= 9) Standards-Version: 3.9.3 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mustang/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mustang/trunk/ Package: mustang Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: mustang-testdata Description: multiple structural alignment of proteins Mustang is an algorithm to align multiple protein structures. Given a set of PDB files, the program uses the spatial information in the Calpha atoms of the set to produce a sequence alignment. Based on a progressive pairwise heuristic the algorithm then proceeds through a number of refinement passes. Mustang reports the multiple sequence alignment and the corresponding superposition of structures. Package: mustang-testdata Architecture: all Enhances: mustang Depends: ${misc:Depends} Description: multiple structural alignment of proteins, test data This package contains a larger set of test data than what comes with the binary package. . To run the test, change to a directory where you have write access, then issue the command: mustang -f /usr/share/doc/mustang-testdata/examples/test_zf-CCHH debian/upstream0000644000000000000000000000100611745031073010747 0ustar Contact: Arun S. Konagurthu (http://www.csse.unimelb.edu.au/~arun) Homepage: http://www.cs.mu.oz.au/~arun/mustang/ Name: MUSTANG Reference: Author: Arun S. Konagurthu and James C. Whisstock and Peter J. Stuckey and Arthur M. Lesk Title: > MUSTANG: A multiple structural alignment algorithm Journal: > Proteins: Structure, Function, and Bioinformatics Volume: 64 Number: 3 Pages: 559-574 Year: 2006 DOI: 10.1002/prot.20921 PMID: 16736488 URL: http://www3.interscience.wiley.com/journal/112638073/abstract