[med-svn] r2701 - in trunk/packages/theseus/trunk/debian: . patches
mok0-guest at alioth.debian.org
mok0-guest at alioth.debian.org
Mon Nov 17 12:35:19 UTC 2008
Author: mok0-guest
Date: 2008-11-17 12:35:19 +0000 (Mon, 17 Nov 2008)
New Revision: 2701
Added:
trunk/packages/theseus/trunk/debian/patches/00-makefile.dpatch
trunk/packages/theseus/trunk/debian/patches/01-theseus.1.dpatch
trunk/packages/theseus/trunk/debian/patches/02-thesus_align.1.dpatch
Removed:
trunk/packages/theseus/trunk/debian/patches/100-theseus.1.dpatch
Modified:
trunk/packages/theseus/trunk/debian/control
trunk/packages/theseus/trunk/debian/patches/00list
trunk/packages/theseus/trunk/debian/patches/200-make.inc.dpatch
Log:
Clean target now works. Hyphen issues in manpages resolved.
Modified: trunk/packages/theseus/trunk/debian/control
===================================================================
--- trunk/packages/theseus/trunk/debian/control 2008-11-17 00:40:25 UTC (rev 2700)
+++ trunk/packages/theseus/trunk/debian/control 2008-11-17 12:35:19 UTC (rev 2701)
@@ -4,7 +4,7 @@
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
+Build-Depends: debhelper (>= 5), dpatch, libatlas-base-dev, libgsl0-dev
Standards-Version: 3.8.0
Homepage: http://www.theseus3d.org
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/theseus/trunk/
Added: trunk/packages/theseus/trunk/debian/patches/00-makefile.dpatch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/00-makefile.dpatch (rev 0)
+++ trunk/packages/theseus/trunk/debian/patches/00-makefile.dpatch 2008-11-17 12:35:19 UTC (rev 2701)
@@ -0,0 +1,19 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 00makefile.dpatch by Morten Kjeldgaard <mok0 at ubuntu.com>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Use rm -f in clean target
+
+ at DPATCH@
+diff -urNad theseus-1.3.4~/Makefile theseus-1.3.4/Makefile
+--- theseus-1.3.4~/Makefile 2008-04-16 16:13:23.000000000 +0200
++++ theseus-1.3.4/Makefile 2008-11-17 12:32:24.000000000 +0100
+@@ -145,6 +145,6 @@
+ cp lib/*.a ${LOCALLIBDIR}
+
+ clean:
+- find . -name '*.[oa]' -exec rm {} \;
+- rm theseus &> /dev/null
++ find . -name '*.[oa]' -exec rm -f {} \;
++ rm -f theseus &> /dev/null
+
Property changes on: trunk/packages/theseus/trunk/debian/patches/00-makefile.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Modified: trunk/packages/theseus/trunk/debian/patches/00list
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/00list 2008-11-17 00:40:25 UTC (rev 2700)
+++ trunk/packages/theseus/trunk/debian/patches/00list 2008-11-17 12:35:19 UTC (rev 2701)
@@ -1,3 +1,5 @@
-100-theseus.1.dpatch
+00-makefile.dpatch
+01-theseus.1.dpatch
+02-thesus_align.1.dpatch
200-make.inc.dpatch
99-theseus_align.sh.dpatch
Added: trunk/packages/theseus/trunk/debian/patches/01-theseus.1.dpatch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/01-theseus.1.dpatch (rev 0)
+++ trunk/packages/theseus/trunk/debian/patches/01-theseus.1.dpatch 2008-11-17 12:35:19 UTC (rev 2701)
@@ -0,0 +1,405 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 01-theseus.1.dpatch by Morten Kjeldgaard <mok0 at ubuntu.com>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Correct version number in manpage, and fix some hyphen issues.
+
+ at DPATCH@
+diff -urNad theseus~/theseus.1 theseus/theseus.1
+--- theseus~/theseus.1 2008-01-22 16:52:21.000000000 +0100
++++ theseus/theseus.1 2008-11-17 13:21:36.000000000 +0100
+@@ -1,31 +1,31 @@
+ .\" use 'man groff_man' to see the man page format macros
+ .\" ----------------------------------------------------------------------------
+-.TH THESEUS 1.2.6 "22 January 2008" "Brandeis University" "Likelihood Rocks"
++.TH THESEUS 1 "22 January 2008" "Brandeis University" "Likelihood Rocks"
+ .\" ----------------------------------------------------------------------------
+ .SH NAME
+ .\" ----
+ .\"
+ .B theseus
+-v. 1.2.6 \- 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:
+
+@@ -738,7 +738,7 @@
+ PLOS Computational Biology,
+ .I in press
+
+-.\" ----------------------------------------------------------------------------
++.\" ---------------------------------------------------------------------------
+ .SH HISTORY
+ .\" -------
+ .\"
Property changes on: trunk/packages/theseus/trunk/debian/patches/01-theseus.1.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/theseus/trunk/debian/patches/02-thesus_align.1.dpatch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/02-thesus_align.1.dpatch (rev 0)
+++ trunk/packages/theseus/trunk/debian/patches/02-thesus_align.1.dpatch 2008-11-17 12:35:19 UTC (rev 2701)
@@ -0,0 +1,19 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 02-thesus_align.1.dpatch by Morten Kjeldgaard <mok0 at ubuntu.com>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Fix hyphen issue in theseus_align manpage.
+
+ at DPATCH@
+diff -urNad theseus~/theseus_align.1 theseus/theseus_align.1
+--- theseus~/theseus_align.1 2007-09-25 22:56:26.000000000 +0200
++++ theseus/theseus_align.1 2008-11-17 13:28:57.000000000 +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/02-thesus_align.1.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Deleted: trunk/packages/theseus/trunk/debian/patches/100-theseus.1.dpatch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/100-theseus.1.dpatch 2008-11-17 00:40:25 UTC (rev 2700)
+++ trunk/packages/theseus/trunk/debian/patches/100-theseus.1.dpatch 2008-11-17 12:35:19 UTC (rev 2701)
@@ -1,408 +0,0 @@
-#! /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).
Modified: trunk/packages/theseus/trunk/debian/patches/200-make.inc.dpatch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/200-make.inc.dpatch 2008-11-17 00:40:25 UTC (rev 2700)
+++ trunk/packages/theseus/trunk/debian/patches/200-make.inc.dpatch 2008-11-17 12:35:19 UTC (rev 2701)
@@ -5,17 +5,17 @@
## DP: Customize make.inc for Ubuntu building
@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 @@
+diff -urNad theseus-1.3.4~/make.inc theseus-1.3.4/make.inc
+--- theseus-1.3.4~/make.inc 2008-11-17 12:52:53.000000000 +0100
++++ theseus-1.3.4/make.inc 2008-11-17 12:53:04.000000000 +0100
+@@ -195,3 +195,16 @@
# CFLAGS = $(WARN)
# CC = cc
+
+# Ubuntu Linux x86 & amd64
+SYSLIBS = -lpthread -lm -lc
-+LIBS = -Llib -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils
++LIBS = -Llib -ldistfit -lgsl -lmsa -ldssplite -ldltmath -lDLTutils
+BLASLIB = -L/usr/lib/atlas -llapack
+BLASLIBDIR =
+LAPACKLIB =
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