debian/0000755000000000000000000000000012012535033007160 5ustar debian/source/0000755000000000000000000000000012012535013010456 5ustar debian/source/format0000644000000000000000000000001411777062347011712 0ustar 3.0 (quilt) debian/README.source0000644000000000000000000000036511777767153011376 0ustar profbval for Debian =================== Uncompressed examples --------------------- dh_compress excludes examples that appear on the man page. This is in order to allow the example to work as it is pasted on the command like from the man page. debian/copyright0000644000000000000000000000452312010465303011117 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: profbval Upstream-Contact: A. Schlessinger Source: ftp://rostlab.org/profbval/ Files: examples/cad23-fil.rdbProf Copyright: Burkhard Rost, CUBIC NYC / LION Heidelberg License: GPL-2.0+ Comment: License is not indicated in this file, only copyright. Therefore the license here is that of the producing program 'profphd'. Files: debian/* Copyright: 2009 Guy Yachdav 2012 Laszlo Kajan 2012 Christof Angermüller License: GPL-3+ Files: * Copyright: 2005, 2006 Avner Schlessinger 2005, 2006 Burhard Rost 2006 Guy Yachdav License: GPL-3+ License: GPL-2.0+ This program 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 program. If not, see . . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". License: GPL-3+ This program 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 3 of the License, or (at your option) any later version. . This program 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 . On Debian systems, the full text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL-3'. debian/upstream0000644000000000000000000000121411777501463010762 0ustar Name: profbval Reference: - Author: Avner Schlessinger and Guy Yachdav and Burkhard Rost Title: 'PROFbval: predict flexible and rigid residues in proteins.' Journal: Bioinformatics Year: 2006 Volume: 22 Number: 7 Pages: 891-3 URL: http://www.ncbi.nlm.nih.gov/pubmed?term=PROFbval%3A%20predict%20flexible%20and%20rigid%20residues%20in%20proteins PMID: 16455751 - Author: Avner Schlessinger and Burkhard Rost Title: 'Protein flexibility and rigidity predicted from sequence.' Journal: Proteins Year: 2005 Volume: 61 Number: 1 Pages: 115-26 URL: http://www.ncbi.nlm.nih.gov/pubmed/16080156 PMID: 16080156 debian/rules0000755000000000000000000000035111777767153010272 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 .PHONY: override_dh_compress override_dh_compress: dh_compress -Xexamples/cad23.f -Xexamples/cad23-fil.rdbProf -Xexamples/cad23-fil.hssp %: dh $@ debian/watch0000644000000000000000000000011311777062347010230 0ustar version=3 opts=pasv ftp://rostlab.org/profbval/profbval-([0-9.]+)\.tar\.gz debian/changelog0000644000000000000000000000501012012535033011026 0ustar profbval (1.0.22-1) unstable; urgency=low * Initial release in Debian (Closes: #680140) -- Laszlo Kajan Tue, 14 Aug 2012 13:30:13 +0200 profbval (1.0.16) unstable; urgency=low * man page update for multiple output files and formats * moved references to PP standard section -- Laszlo Kajan Mon, 16 May 2011 13:37:18 +0200 profbval (1.0.15) unstable; urgency=low * Added ability to create multiple outputs with the intention to save output in multiple formats -- Laszlo Kajan Wed, 11 May 2011 15:39:45 +0200 profbval (1.0.14) stable; urgency=low * Made prof output regexp line recognize more prof outputs -- Laszlo Kajan Wed, 12 Jan 2011 17:41:42 +0100 profbval (1.0.13) * Input sequence now converted to upper case before processing (and so lower case sequences are now accepted) -- Laszlo Kajan Mon, 20 Sep 2010 17:19:10 +0200 profbval (1.0.12) * Now accepts `O' as a valid amino acid (for pyrrolysine) -- Laszlo Kajan Wed, 30 Jun 2010 11:07:23 +0200 profbval (1.0.11) * Now accepts `U' as a valid amino acid (for selenocysteine) -- Laszlo Kajan Tue, 29 Jun 2010 11:24:37 +0200 profbval (1.0.10) * Documented mode 5 a bit on the man page -- Laszlo Kajan Tue, 22 Jun 2010 12:44:59 +0200 profbval (1.0.9) * Made profbval completely silent when debug is off and operation is normal -- Laszlo Kajan Wed, 16 Jun 2010 11:48:10 +0200 profbval (1.0.8) * -> automake/autoconf -- Laszlo Kajan Mon, 14 Jun 2010 12:15:19 +0200 profbval (1.0.7) * Added early checking of input fasta sequence for valid sequence * Added debug command line option -- Laszlo Kajan Mon, 03 May 2010 14:39:22 +0200 profbval (1.0.6) * Documented environment variable PROFBVAL_ROOT -- Laszlo Kajan Sat, 19 Dec 2009 11:27:53 +0100 profbval (1.0.5) * snapfun(snap) output mode added -- Laszlo Kajan Fri, 11 Dec 2009 22:56:36 +0100 profbval (1.0.4) * temporary directory collision problem solved * prefix is now correctly respected -- Laszlo Kajan Fri, 11 Dec 2009 14:02:57 +0100 profbval (1.0.2) * Examples added. -- Guy Yachdav Wed, 09 Dec 2009 15:51:56 +0100 profbval (1.0.0) * Initial version. -- Guy Yachdav Tue, 01 Dec 2009 12:51:59 +0200 debian/compat0000644000000000000000000000000211777062347010402 0ustar 8 debian/control0000644000000000000000000000333412010465303010566 0ustar Source: profbval Section: science Priority: extra Maintainer: Debian Med Packaging Team Uploaders: Laszlo Kajan , Christof Angermüller Build-Depends: debhelper (>= 8), perl Standards-Version: 3.9.3 Homepage: https://www.rostlab.org/owiki/index.php/PROFbval Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/profbval/trunk/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/profbval/trunk/ DM-Upload-Allowed: yes Package: profbval Architecture: all Depends: ${perl:Depends}, ${misc:Depends}, profnet-bval Recommends: blast2, librg-utils-perl, pp-popularity-contest, profphd Description: predictor of flexible/rigid protein residues from sequence PROFbval can be useful for both protein structure and function predictions. For instance, a biologist can locate potentially antigenic determinants by identifying the most flexible residues on the protein surface. Additionally, a crystallographer can locate residues that potentially have high experimental B-values. . PROFbval takes the following input, further described on profbval(1): * a protein sequence in a FASTA file * secondary structure and solvent accessibility prediction by prof(1) * an HSSP file . Background: the mobility of a given residue on the protein surface is related to its functional role. Therefore, identification of extremely rigid or flexible residues on the protein surface is helpful for identifying functionally important residues in proteins. A common measure of atom mobility in proteins is B-value data from x-ray crystallography structures. PROFbval is the first tool to predict normalized backbone B-values from amino-acid sequence.