[med-svn] r2699 - in trunk/packages/theseus/trunk: . debian debian/patches
mok0-guest at alioth.debian.org
mok0-guest at alioth.debian.org
Sun Nov 16 22:30:33 UTC 2008
Author: mok0-guest
Date: 2008-11-16 22:30:33 +0000 (Sun, 16 Nov 2008)
New Revision: 2699
Added:
trunk/packages/theseus/trunk/debian/
trunk/packages/theseus/trunk/debian/changelog
trunk/packages/theseus/trunk/debian/citation.bib
trunk/packages/theseus/trunk/debian/compat
trunk/packages/theseus/trunk/debian/control
trunk/packages/theseus/trunk/debian/copyright
trunk/packages/theseus/trunk/debian/getexamples
trunk/packages/theseus/trunk/debian/patches/
trunk/packages/theseus/trunk/debian/patches/00list
trunk/packages/theseus/trunk/debian/patches/100-theseus.1.dpatch
trunk/packages/theseus/trunk/debian/patches/200-make.inc.dpatch
trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.dpatch
trunk/packages/theseus/trunk/debian/rules
trunk/packages/theseus/trunk/debian/theseus.install
Log:
[svn-inject] Applying Debian modifications to trunk
Property changes on: trunk/packages/theseus/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/theseus/trunk/debian/changelog
===================================================================
--- trunk/packages/theseus/trunk/debian/changelog (rev 0)
+++ trunk/packages/theseus/trunk/debian/changelog 2008-11-16 22:30:33 UTC (rev 2699)
@@ -0,0 +1,38 @@
+theseus (1.3.4-1) unstable; urgency=low
+
+ * New upstream release, first upload to Debian.
+
+ -- Morten Kjeldgaard <mok0 at ubuntu.com> Sun, 16 Nov 2008 22:36:36 +0100
+
+theseus (1.1.5-0ubuntu3) intrepid; urgency=low
+
+ * gfortran transition for intrepid, atlas3-base -> libatlas3-base.
+
+ -- Morten Kjeldgaard <mok0 at ubuntu.com> Thu, 04 Sep 2008 23:20:52 +0200
+
+theseus (1.1.5-0ubuntu2) hardy; urgency=low
+
+ * debian/rules: FTBFS on all archs but i386, due to missing
+ binary-arch target (LP: #181359)
+ * Removed redundant libraries.
+
+ -- Morten Kjeldgaard <mok at bioxray.dk> Tue, 08 Jan 2008 22:35:42 +0100
+
+theseus (1.1.5-0ubuntu1) hardy; urgency=low
+
+ * Initial release (LP: #173506)
+ * The upstream tarball has been versioned as 1.1.5 (not versioned upstream)
+ The get-orig-source target in debian/rules can be used for this purpose
+ once the changelog has been edited to contain the right version
+ * Patch to theseus.1 and theseus_align.1
+ - fix incorrect .TH line in theseus.1
+ - fix multiple instances of hyphen (-) to minus (\-)
+ * Patch on thesus_align.sh. The script is patched to find
+ programs in /usr/bin. The script makes use of the
+ multiple sequence alignment program muscle, which is available
+ from universe.
+ * Patch make.inc to provide correct compiler switches.
+ * A script (getexamples) is provided to show the user how (s)he can
+ download the data in examples/
+
+ -- Morten Kjeldgaard <mok at bioxray.dk> Sun, 02 Dec 2007 15:53:15 +0100
Added: trunk/packages/theseus/trunk/debian/citation.bib
===================================================================
--- trunk/packages/theseus/trunk/debian/citation.bib (rev 0)
+++ trunk/packages/theseus/trunk/debian/citation.bib 2008-11-16 22:30:33 UTC (rev 2699)
@@ -0,0 +1,48 @@
+ at article{Douglas L.Theobald12052006,
+author = {Theobald, Douglas L. and Wuttke, Deborah S.},
+title={{Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem}},
+journal = {Proceedings of the National Academy of Sciences},
+volume = {103},
+number = {49},
+pages = {18521-18527},
+doi = {10.1073/pnas.0508445103},
+year = {2006},
+abstract = {Procrustes analysis involves finding the optimal superposition of two or more “forms” via rotations, translations, and scalings. Procrustes problems arise in a wide range of scientific disciplines, especially when the geometrical shapes of objects are compared, contrasted, and analyzed. Classically, the optimal transformations are found by minimizing the sum of the squared distances between corresponding points in the forms. Despite its widespread use, the ordinary unweighted least-squares (LS) criterion can give erroneous solutions when the errors have heterogeneous variances (heteroscedasticity) or the errors are correlated, both common occurrences with real data. In contrast, maximum likelihood (ML) estimation can provide accurate and consistent statistical estimates in the presence of both heteroscedasticity and correlation. Here we provide a complete solution to the nonisotropic ML Procrustes problem assuming a matrix Gaussian distribution with factored covariances. Our analysis generalizes, simplifies, and extends results from previous discussions of the ML Procrustes problem. An iterative algorithm is presented for the simultaneous, numerical determination of the ML solutions.
+},
+URL = {http://www.pnas.org/content/103/49/18521.abstract},
+eprint = {http://www.pnas.org/content/103/49/18521.full.pdf+html}
+}
+
+ at article{DouglasL. Theobald09012006,
+author = {Theobald, Douglas L. and Wuttke, Deborah S.},
+title = {{THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures}},
+journal = {Bioinformatics},
+volume = {22},
+number = {17},
+pages = {2171-2172},
+doi = {10.1093/bioinformatics/btl332},
+year = {2006},
+abstract = {Summary: THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. Availability: ANSI C source code and selected binaries for various computing platforms are available under the GNU open source license from http://monkshood.colorado.edu/theseus/ or http://www.theseus3d.org Contact: douglas.theobald at colorado.edu Supplementary Information: Supplementary data including details of the ML superpositioning algorithm are available at Bioinformatics online.
+},
+URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/17/2171},
+eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/22/17/2171.pdf}
+}
+
+ at article{10.1371/journal.pcbi.0040043,
+ author = {Theobald, Douglas L AND Wuttke, Deborah S},
+ journal = {PLoS Comput Biol},
+ publisher = {Public Library of Science},
+ title = {Accurate Structural Correlations from Maximum Likelihood Superpositions},
+ year = {2008},
+ month = {Feb},
+ volume = {4},
+ url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.0040043},
+ pages = {e43},
+ abstract = {The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR) models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA) of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method (“PCA plots”) for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology. },
+ number = {2},
+ doi = {10.1371/journal.pcbi.0040043}
+}
+
+
+
+
Added: trunk/packages/theseus/trunk/debian/compat
===================================================================
--- trunk/packages/theseus/trunk/debian/compat (rev 0)
+++ trunk/packages/theseus/trunk/debian/compat 2008-11-16 22:30:33 UTC (rev 2699)
@@ -0,0 +1 @@
+5
Added: trunk/packages/theseus/trunk/debian/control
===================================================================
--- trunk/packages/theseus/trunk/debian/control (rev 0)
+++ trunk/packages/theseus/trunk/debian/control 2008-11-16 22:30:33 UTC (rev 2699)
@@ -0,0 +1,28 @@
+Source: theseus
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Morten Kjeldgaard <mok0 at ubuntu.com>
+DM-Upload-Allowed: yes
+Build-Depends: debhelper (>= 5), dpatch, libatlas-base-dev
+Standards-Version: 3.8.0
+Homepage: http://www.theseus3d.org
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/theseus/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/theseus/trunk/?rev=0&sc=0
+
+Package: theseus
+Architecture: any
+Depends: ${shlibs:Depends}
+Suggests: muscle
+Description: superimpose macromolecules using maximum likelihood
+ Theseus is a program that simultaneously superimposes multiple
+ macromolecular structures. Theseus finds the optimal solution to the
+ superposition problem using the method of maximum likelihood. By
+ down-weighting variable regions of the superposition and by correcting for
+ correlations among atoms, the ML superposition method produces very
+ accurate structural alignments.
+ .
+ When macromolecules with different residue sequences are superimposed,
+ other programs and algorithms discard residues that are aligned with
+ gaps. Theseus, however, uses a novel superimposition algorithm that
+ includes all of the data.
Added: trunk/packages/theseus/trunk/debian/copyright
===================================================================
--- trunk/packages/theseus/trunk/debian/copyright (rev 0)
+++ trunk/packages/theseus/trunk/debian/copyright 2008-11-16 22:30:33 UTC (rev 2699)
@@ -0,0 +1,87 @@
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=196
+Upstream-Name: Theseus
+Upstream-Maintainer: Douglas Theobald <douglas.theobald at colorado.edu>
+Upstream-Source: http://www.theseus3d.org/src/theseus.tar.gz
+
+Files: *
+Copyright: © 2003-2007, Douglas L. Theobald
+License: GPL-2+
+
+ THESEUS 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 package 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 package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+X-Comment: On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'.
+
+
+Files: lbidltmath/ncbi_math.*
+Copyright: © 1991, Gish, Kans, Ostell and Schuler
+License: GPL-2+
+
+
+Files: libdltmath/myrandom.c
+Copyright: © 2002, Takuji Nishimura and Makoto Matsumoto
+License: GPL-2+
+
+
+Files: examples/*
+Copyright: PD
+License:
+ 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.
+ The distribution of modified PDB format data including the records: HEADER,
+ CAVEAT, REVDAT, SPRSDE, DBREF, SEQADV, and MODRES are not allowed.
+ .
+ * The user assumes all responsibility for insuring that intellectual property
+ claims associated with any data set deposited in the PDB archive are honored.
+ It should be understood that the PDB data files do not contain any information
+ on intellectual property claims with the exception in some cases of a reference
+ for a patent involving the structure.
+ .
+ * Any opinion, findings, and conclusions expressed in the PDB archive by the
+ authors/contributors do not necessarily reflect the views of the wwPDB.
+ .
+ * The data in the PDB archive are provided on an "as is" basis. The wwPDB
+ nor its comprising institutions cannot be held liable to any party for direct,
+ indirect, special, incidental, or consequential damages, including lost
+ profits, arising from the use of PDB materials.
+ .
+ * Resources on this site are provided without warranty of any kind, either
+ expressed or implied. This includes but is not limited to merchantability or
+ fitness for a particular purpose. The institutions managing this site make
+ no representation that these resources will not infringe any patent or other
+ proprietary right.
+
+X-Comment: The files in examples/ are in the public domain, and can be copied
+ and distributed with no restriction. It is scientific data from the Protein
+ Data Bank (http://www.pdb.org) and the database ASTRAL
+ (http://astral.berkeley.edu).
+
+Files: debian/*
+Copyright: © 2007-2008, Morten Kjeldgaard <mok at bioxray.au.dk>
+License: GPL-2+
Added: trunk/packages/theseus/trunk/debian/getexamples
===================================================================
--- trunk/packages/theseus/trunk/debian/getexamples (rev 0)
+++ trunk/packages/theseus/trunk/debian/getexamples 2008-11-16 22:30:33 UTC (rev 2699)
@@ -0,0 +1,47 @@
+#!/bin/sh
+# Get example input files for theseus
+# Copyright (C) 2007 Morten Kjeldgaard <mok at bioxray.dk>
+#
+# This script 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 2.1 of the License, or (at your option) any later
+# version.
+#
+# This script 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 script; if not, write to the Free
+# Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+# Boston, MA 02110-1301 USA
+set -e
+
+pdbs="1s40"
+
+astrals="d1cih__ d1cih__2 d1crj__ d1csu__ d1csx__ d1kyow_ d1lfma_ d1m60a_ d1u74d_ d1yeb__ d2pcbb_"
+
+# function to fetch entries from the pdb
+pdb_fetch () {
+ for f in $* ; do
+ wget -nv http://www.pdb.org/pdb/files/$f.pdb.gz
+ gzip -dc $f.pdb.gz > $f.pdb
+ done
+}
+
+# function to fetch entries from astral
+astral_fetch() {
+ for f in $* ; do
+ wget -nv http://astral.berkeley.edu/pdbstyle.cgi?id=${f}.pdb&output=text
+ done
+}
+
+savedir=$PWD
+cd /tmp
+
+pdb_fetch $pdbs
+astral_fetch $astrals
+
+cd $savedir
Added: trunk/packages/theseus/trunk/debian/patches/00list
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/00list (rev 0)
+++ trunk/packages/theseus/trunk/debian/patches/00list 2008-11-16 22:30:33 UTC (rev 2699)
@@ -0,0 +1,3 @@
+100-theseus.1.dpatch
+200-make.inc.dpatch
+99-theseus_align.sh.dpatch
Added: trunk/packages/theseus/trunk/debian/patches/100-theseus.1.dpatch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/100-theseus.1.dpatch (rev 0)
+++ trunk/packages/theseus/trunk/debian/patches/100-theseus.1.dpatch 2008-11-16 22:30:33 UTC (rev 2699)
@@ -0,0 +1,408 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 100-theseus.1.dpatch by <mok at bioxray.dk>
+##
+## DP: Fix error in the .TH line. The manpage section must go here,
+## DP: not the program version.
+
+ at DPATCH@
+diff -urNad theseus-1.1.5~/theseus.1 theseus-1.1.5/theseus.1
+--- theseus-1.1.5~/theseus.1 2007-12-02 16:08:26.000000000 +0100
++++ theseus-1.1.5/theseus.1 2007-12-02 16:18:20.000000000 +0100
+@@ -1,31 +1,31 @@
+ .\" use 'man groff_man' to see the man page format macros
+ .\" ----------------------------------------------------------------------------
+-.TH THESEUS 1.1.5 "2 October 2007" "Brandeis University" "Likelihood Rocks"
++.TH THESEUS 1 "2 October 2007" "Brandeis University" "Likelihood Rocks"
+ .\" ----------------------------------------------------------------------------
+ .SH NAME
+ .\" ----
+ .\"
+ .B theseus
+-v. 1.1.5 \- Maximum likelihood, multiple simultaneous superpositions
++\- Maximum likelihood, multiple simultaneous superpositions
+ with statistical analysis
+ .\" ----------------------------------------------------------------------------
+ .SH SYNOPSIS
+ .\" --------
+ .\"
+ .B theseus
+-[-aAbBcCdDeEfFgGhHiIjklLmMnNoOpPqQrRsStTuvVwWxXyYZ]
++[\-aAbBcCdDeEfFgGhHiIjklLmMnNoOpPqQrRsStTuvVwWxXyYZ]
+ .I pdbfile1 [pdbfile2 ...]
+ .P
+ and
+ .P
+ .B theseus_align
+-[-aAbBcCdDeEfFgGhHiIjklLmMnNoOpPqQrRsStTuvVwWxXyYZ] -f
++[\-aAbBcCdDeEfFgGhHiIjklLmMnNoOpPqQrRsStTuvVwWxXyYZ] \-f
+ .I pdbfile1 [pdbfile2 ...]
+ .P
+ Default usage is equivalent to:
+ .P
+ .B theseus
+--a0 -e2 -g1 -i200 -k-1 -p1e-7 -r theseus -v -P0
++\-a0 \-e2 \-g1 \-i200 \-k\-1 \-p1e\-7 \-r theseus \-v \-P0
+ .I your.pdb
+ .\" ----------------------------------------------------------------------------
+ .SH DESCRIPTION
+@@ -70,13 +70,13 @@
+ different species or multiple mutated structures of hen egg white lysozyme.
+ This mode requires the user to supply a sequence alignment file of the
+ structures being superpositioned (see option
+-.B "-A"
++.B "\-A"
+ and "FILE FORMATS" below).
+ Additionally, it may be necessary to supply a mapfile that tells
+ .B theseus
+ which PDB structure files correspond to which sequences in the alignment (see
+ option
+-.B "-M"
++.B "\-M"
+ and "FILE FORMATS" below). When superpositioning based on a seqeunce
+ alignment,
+ .B theseus
+@@ -95,7 +95,7 @@
+ Example 1:
+ .IP
+ .B theseus
+--A cytc.aln -M cytc.filemap d1cih__.pdb d1csu__.pdb d1kyow_.pdb
++\-A cytc.aln \-M cytc.filemap d1cih__.pdb d1csu__.pdb d1kyow_.pdb
+ .IP
+ In the above example,
+ d1cih__.pdb, d1csu__.pdb, and d1kyow_.pdb
+@@ -104,7 +104,7 @@
+ Example 2:
+ .IP
+ .B theseus_align
+--f d1cih__.pdb d1csu__.pdb d1kyow_.pdb
++\-f d1cih__.pdb d1csu__.pdb d1kyow_.pdb
+ .IP
+ In this example, the
+ .B theseus_align
+@@ -129,7 +129,7 @@
+
+ .TP
+ .PD
+-.BI "-a [" selection ]
++.BI "\-a [" selection ]
+ Atoms to include in the superposition.
+ This option takes two types of arguments, either (1) a number specifying a
+ preselected set of atom types, or (2) an explict PDB-style, colon-delimited list
+@@ -154,7 +154,7 @@
+ .PD
+ .IP
+ Note, only the
+-.B "-a0"
++.B "\-a0"
+ option is available when superpositioning structures with
+ different sequences.
+ .IP
+@@ -164,13 +164,13 @@
+ Multiple atom types must be delimited by a colon.
+ For example,
+ .IP
+-.B "-a' N : CA : C : O '
++.B "\-a' N : CA : C : O '"
+ .IP
+ would specify the atom types in the peptide backbone.
+
+
+ .TP
+-.B "-c"
++.B "\-c"
+ Use ML atomic covariance weighting (fit correlations, much slower)
+ .IP
+ Unless you have many different structures with few residues, fitting the
+@@ -178,7 +178,7 @@
+ parameters and a paucity of data.
+
+ .TP
+-.BI "-e [" n ]
++.BI "\-e [" n ]
+ Embedding algorithm for initializing the average structure
+ .PD 0
+ .RS 8
+@@ -190,11 +190,11 @@
+ .PD
+
+ .TP
+-.BI "-f"
++.BI "\-f"
+ Only read the first model of a multi-model PDB file
+
+ .TP
+-.BI "-g [" n ]
++.BI "\-g [" n ]
+ Hierarchical model for variances
+ .PD 0
+ .RS 8
+@@ -206,33 +206,33 @@
+ .PD
+
+ .TP
+-.B "-h"
++.B "\-h"
+ Help/usage
+
+ .TP
+-.BI "-i [" nnn ]
++.BI "\-i [" nnn ]
+ Maximum iterations, {200}
+
+ .TP
+-.BI "-k [" n ]
+-constant minimum variance {-1}
++.BI "\-k [" n ]
++constant minimum variance {\-1}
+ {if set to negative value, the minimum variance is determined empirically}
+
+ .TP
+-.BI "-p [" precision ]
+-Requested relative precision for convergence, {1e-7}
++.BI "\-p [" precision ]
++Requested relative precision for convergence, {1e\-7}
+
+ .TP
+-.BI "-r [" "root name" ]
++.BI "\-r [" "root name" ]
+ Root name to be used in naming the output files, {theseus}
+
+ .TP
+-.BI "-s [" n-n:... ]
+-Residue selection (e.g. -s15-45:50-55), {all}
++.BI "\-s [" n\-n:... ]
++Residue selection (e.g. \-s15\-45:50\-55), {all}
+
+ .TP
+-.BI "-S [" n-n:... ]
+-Residues to exclude (e.g. -S15-45:50-55) {none}
++.BI "\-S [" n\-n:... ]
++Residues to exclude (e.g. \-S15\-45:50\-55) {none}
+ .IP
+ The previous two options have the same format. Residue (or alignment column)
+ ranges are indicated by beginning and end separated by a dash.
+@@ -240,31 +240,31 @@
+ Chains may also be selected by giving the chain ID immediately preceding the
+ residue range.
+ For example,
+-.B -sA1-20:A40-71
++.B \-sA1-20:A40-71
+ will only include residues 1 through 20
+ and 40 through 70 in chain A. Chains cannot be specified when superpositioning
+ structures with different sequences.
+
+ .TP
+-.B "-v"
++.B "\-v"
+ use ML variance weighting (no correlations) {default}
+
+ .PD
+ .SS Input/output options:
+
+ .TP
+-.BI "-A [" "sequence alignment file" ]
++.BI "\-A [" "sequence alignment file" ]
+ Sequence alignment file to use as a guide (CLUSTAL or A2M format)
+ .IP
+ For use when superpositioning structures with different sequences.
+ See "FILE FORMATS" below.
+
+ .TP
+-.B "-E"
++.B "\-E"
+ Print expert options
+
+ .TP
+-.B "-F"
++.B "\-F"
+ Print FASTA files of the sequences in PDB files and quit
+ .IP
+ A useful option when superpositioning structures with different sequences.
+@@ -273,39 +273,39 @@
+ alignment file used as
+ .B theseus
+ input with the
+-.B "-A"
++.B "\-A"
+ option.
+
+ .TP
+-.B "-h"
++.B "\-h"
+ Help/usage
+
+ .TP
+-.B "-I"
++.B "\-I"
+ Just calculate statistics for input file; don't superposition
+
+ .TP
+-.BI "-M [" mapfile ]
++.BI "\-M [" mapfile ]
+ File that maps sequences in the alignment file to PDB files
+ .IP
+ A simple two-column formatted file; see "FILE FORMATS" below. Used with mode 2.
+
+ .TP
+-.B "-n"
++.B "\-n"
+ Don't write transformed pdb file
+
+ .TP
+-.BI "-o [" "reference structure" ]
++.BI "\-o [" "reference structure" ]
+ Reference file to superposition on, all rotations are relative to the first
+ model in this file
+ .IP
+-For example, 'theseus -o cytc1.pdb cytc1.pdb cytc2.pdb cytc3.pdb' will
++For example, 'theseus \-o cytc1.pdb cytc1.pdb cytc2.pdb cytc3.pdb' will
+ superposition the structures and rotate the entire final superposition so that
+ the structure from cytc1.pdb is in the same orientation as the structure in the
+ original cytc1.pdb PDB file.
+
+ .TP
+-.B "-O"
++.B "\-O"
+ Olve's segID file
+ .IP
+ Useful output when superpositioning structures with different sequences (mode 2).
+@@ -321,26 +321,26 @@
+ the very atoms that were included in the ML superposition calculation.
+ That is, it will only contain alpha carbons or phosphorous atoms, and it will
+ only contain atoms from the columns selected with the
+-.B "-s"
++.B "\-s"
+ or
+ .B
+-"-S"
++"\-S"
+ options.
+ Requested by Olve Peersen of Colorado State University.
+
+ .TP
+-.B "-V"
++.B "\-V"
+ Version
+
+ .PD
+ .SS Principal components analysis:
+
+ .TP
+-.B "-C"
++.B "\-C"
+ Use covariance matrix for PCA (correlation matrix is default)
+
+ .TP
+-.BI "-P [" nnn ]
++.BI "\-P [" nnn ]
+ Number of principal components to calculate {0}
+
+ .IP
+@@ -358,23 +358,23 @@
+
+ .P
+ .B theseus
+--l -r new2sdf
++\-l \-r new2sdf
+ .I 2sdf.pdb
+
+ .P
+ .B theseus
+--s15-45 -P3
++\-s15-45 \-P3
+ .I 2sdf.pdb
+
+ .P
+ .B theseus
+--A
++\-A
+ .I cytc.aln
+--M
++\-M
+ .I cytc.mapfile
+--o
++\-o
+ .I cytc1.pdb
+--s1-40
++\-s1\-40
+ .I cytc1.pdb cytc2.pdb cytc3.pdb cytc4.pdb
+ .\" ----------------------------------------------------------------------------
+ .SH ENVIRONMENT
+@@ -408,7 +408,7 @@
+ equal), a sequence alignment file must be included for
+ .B theseus
+ to use as a guide (specified by the
+-.B "-A"
++.B "\-A"
+ option).
+ .B Theseus
+ accepts both CLUSTAL and A2M (FASTA) formatted multiple sequence alignment
+@@ -422,14 +422,14 @@
+ PDB file. An easy way to ensure that your sequences exactly match the PDB
+ files is to generate the sequences using
+ .B theseus'
+-.B "-F"
++.B "\-F"
+ option, which writes out a FASTA formatted sequence file of the chain(s)
+ in the PDB files. The files output with this option can then be aligned with
+ a multiple sequence alignment program such as CLUSTAL or MUSCLE, and the
+ resulting output alignment file used as
+ .B theseus
+ input with the
+-.B "-A"
++.B "\-A"
+ option.
+
+ .PD
+@@ -439,7 +439,7 @@
+ PDB file. That is, there can be extra sequences in the alignment that are
+ not used for guiding the superposition.
+
+-.SS PDB -> Sequence mapfile
++.SS PDB \-> Sequence mapfile
+
+ If the names of the PDB files and the names of the corresponding sequences
+ in the alignemnt are identical, the mapfile may be omitted. Otherwise,
+@@ -447,7 +447,7 @@
+ needs to know which sequences in the alignment file correspond to which
+ PDB structure files. This information is included in a mapfile with a very
+ simple format (specified with the
+-.B "-M"
++.B "\-M"
+ option). There are only two columns separated by whitespace: the first column
+ lists the names of the PDB structure files, while the second column lists the
+ corresponding sequence names exactly as given in the multiple sequence
+@@ -526,10 +526,10 @@
+ model is a matrix Gaussian distribution of the structures with equal
+ variances and no correlations. For the ML fits, the assumed models can
+ either be (1) unequal variances and no correlations, as calculated with the
+-.B "-v"
++.B "\-v"
+ option [default] or (2) unequal variances and correlations, as calculated
+ with the
+-.B "-c"
++.B "\-c"
+ option. This statistic is for the superposition only, and does
+ not include the fit of the covariance matrix eigenvalues to an inverse gamma
+ distribution. See 'Omnibus chi^2' below.
+@@ -641,7 +641,7 @@
+ .PD
+ .P
+ When Principal Components are calculated (with the
+-.B "-P"
++.B "\-P"
+ option), the following
+ files are also produced:
+
+diff -urNad theseus-1.1.5~/theseus_align.1 theseus-1.1.5/theseus_align.1
+--- theseus-1.1.5~/theseus_align.1 2007-09-25 22:56:26.000000000 +0200
++++ theseus-1.1.5/theseus_align.1 2007-12-02 16:19:23.000000000 +0100
+@@ -20,7 +20,7 @@
+ .SH SYNOPSIS
+ .B theseus_align
+ .RI [ "theseus options" ]
+--f \fIpdbfile1.pdb\fR \fIpdbfile2.pdb\fR ...
++\-f \fIpdbfile1.pdb\fR \fIpdbfile2.pdb\fR ...
+ .SH OPTIONS
+ The options given to the script will be passed on to \fBtheseus\fR. For a
+ complete description, see the man page for \fBtheseus\fR (1).
Property changes on: trunk/packages/theseus/trunk/debian/patches/100-theseus.1.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/theseus/trunk/debian/patches/200-make.inc.dpatch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/200-make.inc.dpatch (rev 0)
+++ trunk/packages/theseus/trunk/debian/patches/200-make.inc.dpatch 2008-11-16 22:30:33 UTC (rev 2699)
@@ -0,0 +1,27 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 200-makefile.dpatch by Morten Kjeldgaard <mok at bioxray.dk>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Customize make.inc for Ubuntu building
+
+ at DPATCH@
+diff -urNad theseus-1.1.3~/make.inc theseus-1.1.3/make.inc
+--- theseus-1.1.3~/make.inc 2007-09-27 17:07:18.000000000 +0200
++++ theseus-1.1.3/make.inc 2007-09-28 00:34:56.000000000 +0200
+@@ -146,3 +146,16 @@
+ # CFLAGS = $(WARN)
+ # CC = cc
+
++
++# Ubuntu Linux x86 & amd64
++SYSLIBS = -lpthread -lm -lc
++LIBS = -Llib -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils
++BLASLIB = -L/usr/lib/atlas -llapack
++BLASLIBDIR =
++LAPACKLIB =
++LAPACKLIBDIR =
++INSTALLDIR =
++OPT = -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize
++WARN = -Wall -pedantic -std=c99
++CFLAGS += $(WARN)
++CC = gcc
Property changes on: trunk/packages/theseus/trunk/debian/patches/200-make.inc.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.dpatch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.dpatch (rev 0)
+++ trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.dpatch 2008-11-16 22:30:33 UTC (rev 2699)
@@ -0,0 +1,26 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 99-theseus_align.sh.dpatch by <mok at bioxray.dk>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Define clustalw to be the active alignment program.
+## DP: Fix the directory where theseus is found -> /usr/bin.
+
+ at DPATCH@
+--- theseus_align.orig 2007-09-27 15:12:04.000000000 +0200
++++ foo/theseus_align 2007-09-27 15:13:14.000000000 +0200
+@@ -41,13 +41,13 @@
+ # The following six constant strings should be modified to whatever is
+ # convenient and applicable.
+
+-theseus="/usr/local/bin/theseus"; # where to find the THESEUS binary executable
++theseus="/usr/bin/theseus"; # where to find the THESEUS binary executable
+ fastafile="theseus.fasta";
+ filemapfile="theseus.filemap";
+ alignmentfile="theseus.aln";
+
+ # for MUSCLE -- http://www.drive5.com/muscle/
+-alignprog="/usr/local/bin/muscle";
++alignprog="/usr/bin/muscle";
+ align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict";
+
+ # for CLUSTALW -- ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/
Property changes on: trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/theseus/trunk/debian/rules
===================================================================
--- trunk/packages/theseus/trunk/debian/rules (rev 0)
+++ trunk/packages/theseus/trunk/debian/rules 2008-11-16 22:30:33 UTC (rev 2699)
@@ -0,0 +1,61 @@
+#!/usr/bin/make -f
+# -*- mode: makefile; mode: font-lock -*-
+
+include /usr/share/dpatch/dpatch.make
+
+# extract the upstream version from debian/changelog
+uvers := $(shell sed 's/.*(\(.*\)-.*).*/\1/;q' < debian/changelog)
+
+get-orig-source:
+ wget -q http://www.theseus3d.org/src/theseus.tar.gz \
+ -O ../theseus_$(uvers).orig.tar.gz
+
+build: patch-stamp build-stamp
+
+build-stamp:
+ dh_testdir
+
+ # compiler flags are hardwired in make.inc
+ $(MAKE)
+
+ touch $@
+
+clean: unpatch
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp
+
+ $(MAKE) clean
+ rm -f theseus distfit
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+
+binary-indep: build install
+# Nothing to build here
+
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_install
+ dh_installdocs debian/citation.bib
+ dh_installchangelogs
+ dh_installman theseus.1 theseus_align.1
+ dh_installexamples examples/* debian/getexamples
+ 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 get-orig-source
+
+####
Property changes on: trunk/packages/theseus/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/theseus/trunk/debian/theseus.install
===================================================================
--- trunk/packages/theseus/trunk/debian/theseus.install (rev 0)
+++ trunk/packages/theseus/trunk/debian/theseus.install 2008-11-16 22:30:33 UTC (rev 2699)
@@ -0,0 +1,2 @@
+theseus usr/bin
+theseus_align /usr/bin
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