debian/0000755000000000000000000000000012176726300007172 5ustar debian/README.Debian0000644000000000000000000000367011522520153011231 0ustar README.Debian for TMalign and TMScore ------------------------------------- The homepage of TM-align (http://zhanglab.ccmb.med.umich.edu/TM-align/) says: TM-align is a computer algorithm for protein structure alignment using dynamic programming and TM-score rotation matrix. An optimal alignment between two proteins, as well as the TM-score, will be reported for each comparison. The value of TM-score lies in (0,1]. In general, a comparison of TM-score < 0.2 indicates that there is no similarity between two structures; a TM-score > 0.5 means the structures share the same fold. The homepage of TM-score (http://zhanglab.ccmb.med.umich.edu/TM-score/) says: TM-score is an algorithm to calculate the similarity of topologies of two protein structures. It can be exploited to quantitatively access the quality of protein structure predictions relative to native. Because TM-score weights the close matches stronger than the distant matches, TM-score is more sensitive than root-mean-square deviation (RMSD) (An illustative example can be found from here). A single score between (0,1] is assigned to each comparison. Based on statistics, if a template/model has a TM-score around or below 0.17, it means the prediction is nothing more than a random selection from PDB library. The difference between both programs is explained as follows: What is the difference between TM-score and TM-align? The TM-score program is to compare two models based on their given and known residue equivalency. It is usually NOT applied to compare two proteins of different sequences. The TM-align is a structural alignment program for comparing two proteins whose sequences can be different. The TM-align will first find the best equivalent residues of two proteins based on the structure similarity and then output a TM-score. The TM-score values in both programs have the same definition. -- Andreas Tille Sun, 30 Jan 2011 22:49:21 +0100 debian/manpages0000644000000000000000000000001311522076644010705 0ustar debian/*.1 debian/source/0000755000000000000000000000000011726141576010500 5ustar debian/source/format0000644000000000000000000000001411473514012011672 0ustar 3.0 (quilt) debian/install0000644000000000000000000000004211522076604010556 0ustar TMalign usr/bin TMscore usr/bin debian/copyright0000644000000000000000000000157312015521761011127 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: TM-align Upstream-Contact: Yang Zhang Source: http://zhanglab.ccmb.med.umich.edu/TM-align/ Files-Excluded: TMalign TMscore Files: * Copyright: © 2005-2012 Yang Zhang, Jeffrey Skolnick License: other Permission to use, copy, modify, and distribute this program for any purpose, with or without fee, is hereby granted, provided that the notices on the head, the reference information, and this copyright notice appear in all copies or substantial portions of the Software. It is provided "as is" without express or implied warranty. Files: debian/* Copyright: © 2011 Tim Booth , © 2011-2012 Andreas Tille License: GPL The Debian packaging is licensed under the GPL, see `/usr/share/common-licenses/GPL'. debian/TMalign.10000644000000000000000000000461412176725477010632 0ustar .\" Hey, EMACS: -*- nroff -*- .\" First parameter, NAME, should be all caps .\" Second parameter, SECTION, should be 1-8, maybe w/ subsection .\" other parameters are allowed: see man(7), man(1) .TH TMALIGN 1 "October 21, 2007" .\" Please adjust this date whenever revising the manpage. .\" .\" Some roff macros, for reference: .\" .nh disable hyphenation .\" .hy enable hyphenation .\" .ad l left justify .\" .ad b justify to both left and right margins .\" .nf disable filling .\" .fi enable filling .\" .br insert line break .\" .sp insert n+1 empty lines .\" for manpage-specific macros, see man(7) .SH NAME TMalign \- protein structure alignment .SH SYNOPSIS .B TMalign .RI structure.pdb target.pdb [ options ] .SH DESCRIPTION TMalign performs a structural alignment of proteins. The alignment is scored by the TM-score algorithm. .PP .\" TeX users may be more comfortable with the \fB\fP and .\" \fI\fP escape sequences to invode bold face and italics, .\" respectively. .SH OPTIONS When started with no options, a summary of commands is given. With two protein structures presented as arguments, the TM-score uses the length of the second protein to be normalised. The final structural alignment is invariant to any of the options below. .TP .B -L .IR number normalises TM-score by an assigned length (in aa) .TP .B -a normalises TM-score by the average length of the two structures .TP .B -b normalises TM-score by the length of the shorter of the two structures .TP .BR -c normalises TM-score by the length of the longer of the two structures .TP .BR -o .IR filename Run TM-align and output the superposition to 'filename.sup' and 'filename.sup_all'. The output files serve as scripts to the program .IR rasmol. To view the superimposed structures of the aligned regions call 'rasmol \-script TM.sup' To view the superimposed structures of all regions 'rasmol \-script TM.sup_all'. .SH SEE ALSO .BR http://zhang.bioinformatics.ku.edu/TM-align/, .BR rasmol(1) .br When using this proram and for more detailed information, please refer to the publication in .IR Nucleic Acids Res. (2005) Volume 33 page 2303ff. by Zhang and Skolnick. .SH AUTHOR tm-align was written by Zhang and Skolnick. .PP This manual page was written by Steffen Moeller , for the Debian project (but may be used by others). debian/upstream0000644000000000000000000000100111752430261010742 0ustar Contact: Yang Zhang Homepage: http://zhanglab.ccmb.med.umich.edu/TM-align/ Name: TM-align & TM-score Reference: AUTHOR: Yang Zhang and Jeffrey Skolnick TITLE: > TM-align: A protein structure alignment algorithm based on TM-score JOURNAL: Nucleic Acids Research YEAR: 2005 PAGES: 2302-2309 VOLUME: 33 NUMBER: 7 URL: http://nar.oxfordjournals.org/content/33/7/2302 eprint: http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.pdf ISSN: 1362-4962 DOI: 10.1093/nar/gki524 PMID: 15849316 debian/rules0000755000000000000000000000103711773355243010261 0ustar #!/usr/bin/make -f # debian/rules for tm-align # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 PROGNAME=TMalign CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) %: dh $@ override_dh_auto_build: for src in `ls *.f` ; do \ gfortran -O3 -ffast-math $(CPPFLAGS) $(LDFLAGS) -lm -o `basename $${src} .f` $${src} ; \ done override_dh_auto_clean: for src in `ls *.f` ; do \ rm -f `basename $${src} .f` ; \ done dh_clean get-orig-source: . debian/get-orig-source debian/get-orig-source0000644000000000000000000000225412176724227012141 0ustar #!/bin/sh # bail out with the first problem set -e # Remark: A new uscan that enables easier handling of removing files can be # obtained via # git clone git://tille@git.debian.org/git/users/tille/devscripts.git # and then copy scripts/uscan.pl as uscan at the beginning of your PATH if uscan --help | grep -q -- --repack-compression ; then echo "Use new enhanced uscan" uscan --verbose --force-download --repack-compression xz exit fi # script to download and repack source package of TMalign which strips the binaries from upstream tarball PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` VERSION=`uscan --verbose --force-download | \ grep "Newest version on remote site is .* local version is .*" | \ head -n 1 | \ sed "s/Newest version on remote site is \([-0-9.]\+\),.*/\1/"` # mkdir -p does not fail when directories exist already mkdir -p ../tarballs cd ../tarballs TARBALLDIR=`pwd` UPSTREAMDIR=${PKG}-${VERSION} mkdir -p ${UPSTREAMDIR} cd ${UPSTREAMDIR} tar -xzf ../../TMtools${VERSION}.tar.gz rm -rf TMscore TMalign cd .. GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz "${UPSTREAMDIR}" rm -rf "${UPSTREAMDIR}" debian/watch0000644000000000000000000000016212176723504010225 0ustar version=3 opts=dversionmangle=s/[~\+]dfsg// \ http://zhanglab.ccmb.med.umich.edu/TM-align/TMtools([\d]*)\.tar\.gz debian/TMscore.pod0000644000000000000000000000340011522720332011240 0ustar # #=============================================================================== # # FILE: TMscore.pod # # DESCRIPTION: A POD-manpage for TMscore # # AUTHOR: Y. Zhang and J. Skolnick # COMPANY: Zhang Lab University of Michigan # CREATED: 03/02/11 14:18:17 GMT # REVISION: --- #=============================================================================== =head1 NAME TM-score - an algorithm to calculate the similarity of topologies of two protein structures =head1 VERSION This documentation refers to TM-score version released on 2011/01/30 =head1 SYNOPSIS 1. Run TM-score to compare 'model' and 'native': TMscore model native 2. Run TM-score with an assigned d0, e.g. 5 Angstroms: TMscore model native -d 5 3. Run TM-score with superposition output, e.g. 'TM.sup', and view in Rasmol: TMscore model native -o TM.sup rasmol -script TM.sup =head1 DESCRIPTION This program is to compare two protein structures and identify the best superposition that has the highest TM-score. Input structures must be in the PDB format. By default, TM-score is normalized by the second protein. Users can obtain a brief instruction by simply running the program without arguments. =head1 OPTIONS =over 4 B<-o> L Outputs the superposition to the specified file, suitable for use in rasmol. B<-d> L Sets d0 to the specified number of angstroms. =back =head1 SEE ALSO L, L When using this proram and for more detailed information, please refer to the publication in NucleicAcidsRes. (2005) Volume 33 page 2303ff. by Zhang and Skolnick. =head1 AUTHOR For comments/suggestions,please contact email: zhng@umich.edu. This manpage was compiled by Tim Booth (tbooth@ceh.ac.uk) =cut debian/changelog0000644000000000000000000000741212176726165011061 0ustar tm-align (20130511+dfsg-1) unstable; urgency=low * New upstream version * debian/copyright: - Add Files-Excluded to document what was removed from original source * debian/watch: enable handling of +dfsg suffix * debian/get-orig-source: use new uscan of available * debian/upstream: more detailed information * debian/control: - cme fix dpkg-control - use anonscm in Vcs fields -- Andreas Tille Fri, 02 Aug 2013 14:55:58 +0200 tm-align (20120507-1) unstable; urgency=low * New upstream version * debian/rules: Add hardening options -- Andreas Tille Fri, 29 Jun 2012 18:30:36 +0200 tm-align (20120124-1) unstable; urgency=low [ Charles Plessy ] * debian/upstream: renamed from upstream-metadata.yaml [ Andreas Tille ] * New upstream version * debian/upstream: - Fixed typo (s/TITILE/TITLE/) - Moved DOI+PMID to references * debian/control: Standards-Version: 3.9.3 (no changes needed) * debhelper 9 (control+compat) * debian/changelog: DEP5 verified using cme fix dpkg-copyright -- Andreas Tille Thu, 08 Mar 2012 15:35:07 +0100 tm-align (20111012-1) unstable; urgency=low * New upstream release * Enhances t-coffee * Standards-Version: 3.9.2 (no changes needed) * Debhelper 8 (control + compat) * Fixed Vcs fields -- Andreas Tille Fri, 21 Oct 2011 10:00:04 +0200 tm-align (20110130-2) unstable; urgency=low * New upstream version (Closes: #447505) - 2011/01/30: An open source license is attached to the program * Reverting changelog to keep the history. -- Steffen Moeller Sat, 05 Feb 2011 12:43:32 +0100 tm-align (20110130-1) UNRELEASED; urgency=low * Initial release. -- Andreas Tille Sun, 30 Jan 2011 22:49:21 +0100 tm-align (20110124-1) UNRELEASED; urgency=low * New upstream version - 2005/06/01: A small bug of two-point superposition was fixed. - 2005/10/19: the program was reformed so that the alignment results are not dependent on the specific compilers. - 2006/06/20: select 'A' if there is altLoc when reading PDB file. - 2007/02/27: rotation matrix from Chain-1 to Chain-2 was added. - 2007/04/18: added options with TM-score normalized by average length, shorter length, or longer length of two structures. - 2007/05/23: added additional output file 'TM.sup_all' for showing all atoms while 'TM.sup' is only for aligned atoms - 2007/09/19: added a new feature alignment to deal with the problem of aligning fractional structures (e.g. protein interfaces). - 2007/10/16: A bug for irregular bond-length models was fixed. - 2009/03/14: A new initial alignment was added and previous initial alignments are further enhanced. This change increased accuracy by 4% but increases CPU cost by 40%. - 2009/08/20: A bug for asymmetry alignment result was fixed. - 2010/08/02: A new RMSD matrix was used to remove obsolete statements. Staled subroutines were deleted. - 2011/01/03: The length of pdb file names were extended to 500 - 2011/01/24: Fixed a bug on output file name created on 2011/01/03 * Tweaked get-orig-source in rules to spot version in upstream file * New standards version 3.9.4 -- Tim Booth Sun, 30 Jan 2011 13:34:53 +0000 tm-align (20050601-2) UNRELEASED; urgency=low * Updated to Standards-Version 3.7.3 (no changes needed) -- David Paleino Wed, 06 Feb 2008 13:11:58 +0100 tm-align (20050601-1) UNRELEASED; urgency=low * Initial packaging. -- Steffen Moeller Sun, 21 Oct 2007 17:11:53 +0200 debian/TMscore.10000644000000000000000000001236711522720332010632 0ustar .\" Automatically generated by Pod::Man 2.22 (Pod::Simple 3.07) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. 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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" TM\-score \- an algorithm to calculate the similarity of topologies of two protein structures .SH "VERSION" .IX Header "VERSION" This documentation refers to TM-score version released on 2011/01/30 .SH "SYNOPSIS" .IX Header "SYNOPSIS" 1. Run TM-score to compare 'model' and 'native': .PP .Vb 1 \& TMscore model native .Ve .PP 2. Run TM-score with an assigned d0, e.g. 5 Angstroms: .PP .Vb 1 \& TMscore model native \-d 5 .Ve .PP 3. Run TM-score with superposition output, e.g. '\s-1TM\s0.sup', and view in Rasmol: .PP .Vb 2 \& TMscore model native \-o TM.sup \& rasmol \-script TM.sup .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" This program is to compare two protein structures and identify the best superposition that has the highest TM-score. Input structures must be in the \s-1PDB\s0 format. By default, TM-score is normalized by the second protein. Users can obtain a brief instruction by simply running the program without arguments. .SH "OPTIONS" .IX Header "OPTIONS" .RS 4 \&\fB\-o\fR filename.sup Outputs the superposition to the specified file, suitable for use in rasmol. .Sp \&\fB\-d\fR value Sets d0 to the specified number of angstroms. .RE .SH "SEE ALSO" .IX Header "SEE ALSO" TMalign, rasmol .PP When using this proram and for more detailed information, please refer to the publication in NucleicAcidsRes. (2005) Volume 33 page 2303ff. by Zhang and Skolnick. .SH "AUTHOR" .IX Header "AUTHOR" For comments/suggestions,please contact email: zhng@umich.edu. .PP This manpage was compiled by Tim Booth (tbooth@ceh.ac.uk) debian/compat0000644000000000000000000000000211726143114010364 0ustar 9 debian/control0000644000000000000000000000204612176725610010602 0ustar Source: tm-align Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Tim Booth , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), gfortran Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/tm-align/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/tm-align/trunk/ Homepage: http://zhang.bioinformatics.ku.edu/TM-align/ Package: tm-align Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: pymol, rasmol Enhances: t-coffee Description: structual alignment of proteins TM-align is a computer algorithm for protein structure alignment using dynamic programming. The scoring is performed by the TM-score rotation matrix. This is similar to the RMSD in that unaligned portions of the structure influence the scoring less than the more structurally conserved regions.