[med-svn] r12304 - in trunk/packages/concavity/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Mon Oct 1 12:56:54 UTC 2012
Author: lkajan-guest
Date: 2012-10-01 12:56:54 +0000 (Mon, 01 Oct 2012)
New Revision: 12304
Added:
trunk/packages/concavity/trunk/debian/concavity.manpages
trunk/packages/concavity/trunk/debian/patches/manpage
Modified:
trunk/packages/concavity/trunk/debian/control
trunk/packages/concavity/trunk/debian/copyright
trunk/packages/concavity/trunk/debian/patches/compiler_errors
trunk/packages/concavity/trunk/debian/patches/series
trunk/packages/concavity/trunk/debian/rules
Log:
added man page; fixed missing copyright for some files in pkg/; fixed some compiler warnings
Added: trunk/packages/concavity/trunk/debian/concavity.manpages
===================================================================
--- trunk/packages/concavity/trunk/debian/concavity.manpages (rev 0)
+++ trunk/packages/concavity/trunk/debian/concavity.manpages 2012-10-01 12:56:54 UTC (rev 12304)
@@ -0,0 +1 @@
+concavity.1
Modified: trunk/packages/concavity/trunk/debian/control
===================================================================
--- trunk/packages/concavity/trunk/debian/control 2012-09-30 21:08:59 UTC (rev 12303)
+++ trunk/packages/concavity/trunk/debian/control 2012-10-01 12:56:54 UTC (rev 12304)
@@ -18,16 +18,16 @@
ConCavity predicts protein ligand binding sites by combining evolutionary
sequence conservation and 3D structure.
.
- ConCavity takes as input a PDB format protein structure and (optionally)
+ ConCavity takes as input a PDB format protein structure and optionally
files that characterize the evolutionary sequence conservation of the chains
in the structure file.
.
- The following result files are produced (by default):
- * residue ligand binding predictions for each chain (*.scores)
- * residue ligand binding predictions in a PDB format file (residue
- scores placed in the temp. factor field, *_residue.pdb
- * pocket prediction locations in a DX format file (*.dx)
- * PyMOL script to visualize the predictions (*.pml)
+ The following result files are produced by default:
+ * Residue ligand binding predictions for each chain (*.scores).
+ * Residue ligand binding predictions in a PDB format file (residue
+ scores placed in the temp. factor field, *_residue.pdb).
+ * Pocket prediction locations in a DX format file (*.dx).
+ * PyMOL script to visualize the predictions (*.pml).
.
ConCavity has many features. The default run of concavity is equivalent to
ConCavity^L in the paper:
Modified: trunk/packages/concavity/trunk/debian/copyright
===================================================================
--- trunk/packages/concavity/trunk/debian/copyright 2012-09-30 21:08:59 UTC (rev 12303)
+++ trunk/packages/concavity/trunk/debian/copyright 2012-10-01 12:56:54 UTC (rev 12304)
@@ -4,6 +4,19 @@
John A. Capra <tonyc at cs.princeton.edu>
Source: http://compbio.cs.princeton.edu/concavity/
+Files: pkgs/R3Shapes/ply.*
+Copyright: 1994 The Board of Trustees of The Leland Stanford Junior University.
+ All rights reserved.
+License:
+ Permission to use, copy, modify and distribute this software and its
+ documentation for any purpose is hereby granted without fee, provided
+ that the above copyright notice and this permission notice appear in
+ all copies of this software and that you do not sell the software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS" AND WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS, IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY
+ WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.
+
Files: debian/*
Copyright: 2012 Laszlo Kajan <lkajan at rostlab.org>
License: GPL-3.0+
Modified: trunk/packages/concavity/trunk/debian/patches/compiler_errors
===================================================================
--- trunk/packages/concavity/trunk/debian/patches/compiler_errors 2012-09-30 21:08:59 UTC (rev 12303)
+++ trunk/packages/concavity/trunk/debian/patches/compiler_errors 2012-10-01 12:56:54 UTC (rev 12304)
@@ -31,3 +31,36 @@
// Get chain jsd filename
strcpy(chain_filename, jsd_basename);
strcat(chain_filename, "_");
+--- a/pkgs/R3Shapes/R3Grid.C
++++ b/pkgs/R3Shapes/R3Grid.C
+@@ -2151,7 +2151,7 @@
+ }
+
+ // Read toplbl from file
+- char toplbl[32];
++ char toplbl[64];
+ if (fread(toplbl, sizeof(char), 60, fp) != 60) {
+ RNFail("Unable to read toplbl from delphi file: %s\n", filename);
+ return 0;
+--- a/pkgs/R3Shapes/R3Triangle.C
++++ b/pkgs/R3Shapes/R3Triangle.C
+@@ -254,7 +254,7 @@
+ RNLength length = 0.0;
+ length += R3Distance(v[0]->Position(), v[1]->Position());
+ length += R3Distance(v[1]->Position(), v[2]->Position());
+- length += R3Distance(v[2]->Position(), v[3]->Position());
++ length += R3Distance(v[2]->Position(), v[0]->Position());
+ return length;
+ }
+
+--- a/pkgs/PDB/PDBUtil.C
++++ b/pkgs/PDB/PDBUtil.C
+@@ -161,7 +161,7 @@
+ }
+ #else
+ // Count atoms on each side of axes for each element type
+- RNScalar sum[3][6] = { 0 };
++ RNScalar sum[3][6] = { { 0 } };
+ for (int a = 0; a < atoms.NEntries(); a++) {
+ PDBAtom *atom = atoms[a];
+ PDBElement *element = atom->Element();
Added: trunk/packages/concavity/trunk/debian/patches/manpage
===================================================================
--- trunk/packages/concavity/trunk/debian/patches/manpage (rev 0)
+++ trunk/packages/concavity/trunk/debian/patches/manpage 2012-10-01 12:56:54 UTC (rev 12304)
@@ -0,0 +1,237 @@
+Author: Laszlo Kajan <lkajan at rostlab.org>
+Description: man page for concavity
+Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-October/017343.html
+--- /dev/null
++++ b/concavity.1.pod
+@@ -0,0 +1,190 @@
++=pod
++
++=head1 NAME
++
++concavity - predictor of protein ligand binding sites from structure and conservation
++
++=head1 SYNOPSIS
++
++concavity [options] PDBFILE OUTPUT_NAME
++
++=head1 DESCRIPTION
++
++ConCavity predicts protein ligand binding sites by combining evolutionary
++sequence conservation and 3D structure.
++
++ConCavity takes as input a PDB format protein structure B<PDBFILE> and optionally
++files that characterize the evolutionary sequence conservation of the chains
++in the structure file.
++
++The following result files are produced by default:
++
++=over
++
++=item * Residue ligand binding predictions for each chain (*.scores).
++
++=item * Residue ligand binding predictions in a PDB format file (residue scores placed in the temp. factor field, *_residue.pdb).
++
++=item * Pocket prediction locations in a DX format file (*.dx).
++
++=item * PyMOL script to visualize the predictions (*.pml).
++
++=back
++
++To visualize the predictions in PyMol (it if is installed on your
++system), load the script by typing "pymol 1G6C_test1.pml" at the
++prompt or by loading it through the pymol interface.
++
++The PDB and DX files can be input into other molecular viewers if
++preferred. Several additional output formats are available; see
++below. Note that the residue numbering in the .scores files may not
++match that of the PDB file.
++
++The ConCavity approach proceeds in three conceptual steps: grid
++creation, pocket extraction, and residue mapping (see Methods in
++paper). First, the structural and evolutionary properties of the
++protein are used to create a regular 3D grid surrounding the protein
++in which the score associated with each grid point represents an
++estimated likelihood that it overlaps a bound ligand atom. Second,
++groups of contiguous, high-scoring grid points are clustered to
++extract pockets that adhere to given shape and size
++constraints. Finally, every protein residue is scored with an estimate
++of how likely it is to bind to a ligand based on its proximity to
++extracted pockets.
++
++Each of the algorithms described for these steps is implemented in
++concavity. See the examples.
++
++=head1 REFERENCES
++
++=over
++
++=item Capra JA, Laskowski RA, Thornton JM, Singh M, and Funkhouser TA(2009) Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure. PLoS Comput Biol, 5(12).
++
++=back
++
++=head1 OPTIONS
++
++B<PDBFILE> is a protein structure file in PDB format. B<OUTPUT_NAME> becomes part of the output file names and may not contain "/". Output is written to the current directory.
++
++=head2 Input
++
++=over
++
++=item B<-conservation> I<PATH>
++
++If the "-conservation" option is not given, then conservation
++information is not considered. Note that there are separate
++conservation files for each protein chain in the structure, and the
++input to the -conservation option is the prefix of these files.
++Pre-computed conservation files available for almost the entire PQS on
++the ConCavity web site. If you'd like to compute sequence
++conservation values for your own alignments, we recommend the JSD
++algorithm: http://compbio.cs.princeton.edu/conservation/
++
++=back
++
++=head2 Grid Creation
++
++=over
++
++=item B<-grid_method> I<ligsite|surfnet|pocketfinder|custom>
++
++=item B<-resolution> I<int> I<int> I<int>
++
++Set the grid resolution.
++
++=item B<-spacing> I<float>
++
++Set the grid spacing.
++
++=back
++
++=head2 Pocket Extraction
++
++=over
++
++=item B<-extraction_method> I<search|topn|custom>
++
++=back
++
++=head2 Residue Mapping
++
++=over
++
++=item B<-res_map_method> I<blur|dist|dist-thresh|custom>
++
++=back
++
++Each of these algorithms is described in the text, and each has a
++number of additional parameters that change their behavior. The
++"custom" option allows you to set the values of all parameters for
++each step yourself. The presets (e.g. ligsite, search, blur) may
++override values you set on the command line, so use "custom" to have
++complete control.
++
++=head2 Output
++
++There are also several output format options. Pocket
++prediction grid values can be output in the following formats:
++
++=over
++
++=item B<-print_grid_dx> I<0|1>
++
++DX format. This is I<1> by default.
++
++=item B<-print_grid_pdb> I<0|1>
++
++PDB format. The residue predictions are output as a PDB file with the residue
++scores mapped to the temp. factor field and pocket numbers to the
++residue sequence field.
++
++=item B<-print_grid_txt> I<0|1>
++
++Raw text.
++
++=item B<-v>
++
++Verbose mode.
++
++=back
++
++=head1 EXAMPLES
++
++=over
++
++=item 1
++
++This will run concavity with default values (equivalent to ConCavity^L
++in the paper) on the structure 1G6C.pdb and consider the conservation
++values found in conservation_data/. This set of predictions will be
++called "test1". This produces the following default result files in the current directory:
++
++ concavity -conservation __docdir__/examples/conservation_data/1G6C __docdir__/examples/1G6C.pdb test1
++
++=item 2
++
++For example to score the structure 1G6C.pdb with
++ConCavity_Pocketfinder, Search, and Blur, you'd type:
++
++ concavity -conservation __docdir__/examples/conservation_data/1G6C -grid_method pocketfinder -extraction_method search -res_map_method blur __docdir__/examples/1G6C.pdb cc-pocketfinder_search_blur
++
++=back
++
++=head1 NOTES
++
++The authors primarily use PyMol and Chimera for visualization, but the range of
++output formats means you should be able to import the data into most
++structural analysis program. Let us know if there are other output
++formats you'd like to see.
++
++=head1 SEE ALSO
++
++=over
++
++=item Concavity Homepage L<http://compbio.cs.princeton.edu/concavity/>
++
++=back
++
++=cut
+--- a/Makefile
++++ b/Makefile
+@@ -1,9 +1,15 @@
+ #
+ # Makefile for GAPS
+ #
++PACKAGE:=concavity
++VERSION?=0.1
++prefix?=/usr
++
++datarootdir:=${prefix}/share
++docdir:=${datarootdir}/doc/${PACKAGE}
+
+ .PHONY: all opt
+-all: opt
++all: opt man
+
+ opt:
+ $(MAKE) target "TARGET=$@"
+@@ -13,6 +19,7 @@
+
+ clean:
+ $(MAKE) target "TARGET=$@"
++ rm -f concavity.1
+
+ release:
+ mkdir -p release
+@@ -26,8 +33,12 @@
+ cd pkgs && $(MAKE) $(TARGET)
+ cd apps && $(MAKE) $(TARGET)
+
++.PHONY: man
++man: concavity.1
+
+-
++%.1: %.1.pod
++ sed -e 's|__docdir__|$(docdir)|g;s|__pkgdatadir__|$(pkgdatadir)|g;s|__sysconfdir__|$(sysconfdir)|g;s|__bindir__|$(bindir)|g;s|__VERSION__|$(VERSION)|g;s|__PACKAGE_VERSION__|$(PACKAGE_VERSION)|g;' "$<" | \
++ pod2man -c 'User Commands' -r "$(VERSION)" -name $(shell echo "$(basename $@)" | tr '[:lower:]' '[:upper:]') > "$@"
+
+
+
Modified: trunk/packages/concavity/trunk/debian/patches/series
===================================================================
--- trunk/packages/concavity/trunk/debian/patches/series 2012-09-30 21:08:59 UTC (rev 12303)
+++ trunk/packages/concavity/trunk/debian/patches/series 2012-10-01 12:56:54 UTC (rev 12304)
@@ -2,6 +2,7 @@
safe_recursive_make
freeglut
CFLAGSasf
+spelling
+noopengllink
compiler_errors
-noopengllink
-spelling
+manpage
Modified: trunk/packages/concavity/trunk/debian/rules
===================================================================
--- trunk/packages/concavity/trunk/debian/rules 2012-09-30 21:08:59 UTC (rev 12303)
+++ trunk/packages/concavity/trunk/debian/rules 2012-10-01 12:56:54 UTC (rev 12304)
@@ -6,7 +6,9 @@
export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS)
export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
+export prefix:=/usr
export USER_CFLAGS:="-Wno-write-strings"
+export VERSION:=$(shell dpkg-parsechangelog --format rfc822|sed --posix -n -e 's/^Version: \([0-9.]*\).*/\1/p;')
.PHONY: get-orig-source
get-orig-source:
@@ -29,6 +31,12 @@
%:
dh $@ --parallel
+.PHONY: man
+man:
+ set
+ export
+ $(MAKE) man
+
.PHONY: override_dh_strip
override_dh_strip:
dh_strip --dbg-package=concavity-dbg
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