debian/0000755000000000000000000000000012200760644007167 5ustar debian/menu0000644000000000000000000000016511604526522010062 0ustar ?package(raccoon):needs="X11" section="Applications/Science/Chemistry"\ title="raccoon" command="/usr/bin/raccoon" debian/README.Debian0000644000000000000000000000072311604526522011234 0ustar raccoon for Debian ------------------ This package interlinks chemical ligand databases protein structure databases and the tools for ligand docking autodock, autodock-vina their preparation environment MGLTools so that a complete project can be performed that investigates many thousands of ligands against a single or multiple structures, demanding compute times of many years. -- Steffen Moeller Sun, 19 Jun 2011 13:20:27 +0200 debian/manpages0000644000000000000000000000002111604526522010700 0ustar debian/raccoon.1 debian/source/0000755000000000000000000000000012200755170010465 5ustar debian/source/format0000644000000000000000000000001411604526522011677 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000000224112200755072011120 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: raccoon Source: http://autodock.scripps.edu/resources/raccoon Files: * Copyright: 2009 Stefano Forli Molecular Graphics Lab The Scripps Research Institute License: GPL-3.0+ Files: debian/* Copyright: 2011 Steffen Moeller License: GPL-3.0+ License: GPL-3.0+ 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 3 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 3 can be found in "/usr/share/common-licenses/GPL-3". debian/upstream0000644000000000000000000000077011757362030010761 0ustar Reference: Author: Sandro Cosconati and Stefano Forli and Alex L Perryman and Rodney Harris and David S Goodsell and Arthur J Olson Title: "Virtual screening with AutoDock: theory and practice" Journal: Expert Opinion on Drug Discovery Year: 2010 Volume: 5 Number: 6 Pages: 597–607 DOI: 10.1517/17460441.2010.484460 PMID: 21532931 URL: http://informahealthcare.com/doi/abs/10.1517/17460441.2010.484460 eprint: http://informahealthcare.com/doi/pdfplus/10.1517/17460441.2010.484460 debian/rules0000755000000000000000000000033312200755243010245 0ustar #!/usr/bin/make -f # -*- makefile -*- # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 %: dh $@ override_dh_autobuild: override_dh_install: cp -a raccoon.py $(CURDIR)/debian/raccoon/usr/bin/raccoon debian/patches/0000755000000000000000000000000012200757672010625 5ustar debian/patches/python_path.patch0000644000000000000000000000036112200757672014203 0ustar Author: Steffen Moeller LastChanged: Sun, 19 Jun 2011 13:20:27 +0200 Description: Use normalised Python PATH --- a/raccoon.py +++ b/raccoon.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python # # Raccoon # debian/patches/syntaxError_columnspan.patch0000644000000000000000000000172412200757547016452 0ustar Author: Steffen Moeller LastChanged: Thu, 08 Aug 2013 19:42:32 +0200 Description: This patch is deactivated because upstream seems to have actively commented out what Steffen considered a fix for a syntax problem. Andreas Tille --- a/raccoon.py +++ b/raccoon.py @@ -5610,7 +5610,7 @@ DockSummaryLabel.grid(row = 4, column = OutputDirLabel = Label(Summary_group.interior(), textvariable = JobDirectory, justify = LEFT) OutputDirLabel.grid(row = 5, column = 2, padx = 5, sticky = W) OutputDirLabelInfo = Label(Summary_group.interior(), textvariable = JobDirectoryInfo) -OutputDirLabelInfo.grid(row = 6, column = 1, columnspan = 3, padx = 5, sticky = S) #, columnspan = 2) +OutputDirLabelInfo.grid(row = 6, column = 1, columnspan = 3, padx = 5, sticky = S, columnspan = 2) JobsSummaryLabel = Label(Summary_group.interior(), textvariable = JobsSummary) JobsSummaryLabel.grid(row = 7, column = 1, columnspan = 2, padx = 5, sticky = S) debian/patches/series0000644000000000000000000000002212200757563012033 0ustar python_path.patch debian/watch0000644000000000000000000000016312200756416010222 0ustar version=3 http://autodock.scripps.edu/resources/raccoon .*mgldev.scripps.edu/raccoon/raccoon-([0-9.a-z]+)\.tar\.gz debian/raccoon.10000644000000000000000000000254011604526522010700 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 RACCOON 1 "June 19, 2011" .\" 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 raccoon \- preparation of ligand screening projects .SH SYNOPSIS .B raccoon .SH DESCRIPTION \fBraccoon\fP takes a ligand library and the crystal structure of a protein, forms many small jobs to investigate the energy gained by bringing the two together, and allows the submission of such jobs to a job queuing engine. .SH SEE ALSO .BR autodock (1), .BR autogrid (1). .br The programs are documented fully on the home page .IR "http://autodock.scripps.edu/resources/raccoon" , .SH AUTHOR raccoon was written by Stefano Forli from The Scripps Institute. .PP This manual page was written by Steffen Moeller , for the Debian project (and may be used by others). debian/changelog0000644000000000000000000000106312200760644011041 0ustar raccoon (1.0b-1) unstable; urgency=low * new upstream version * debian/watch: fixed * debian/upstream: Added citation information * debian/control: - cme fix dpkg-control - debhelper 9 - use anonscm in Vcs fields * debian/rules: preserve timestamp of executable * debian/README.source: removed because unneeded -- Andreas Tille Thu, 08 Aug 2013 19:42:32 +0200 raccoon (1.0-1) unstable; urgency=low * Initial release (Closes: #630977) -- Steffen Moeller Sun, 19 Jun 2011 13:20:27 +0200 debian/compat0000644000000000000000000000000212200754714010366 0ustar 9 debian/raccoon.dirs0000644000000000000000000000001011604526522011467 0ustar usr/bin debian/control0000644000000000000000000000315412200755715010600 0ustar Source: raccoon Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Section: contrib/science Priority: optional Build-Depends: debhelper (>= 9) Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/raccoon/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/raccoon/trunk/ Homepage: http://autodock.scripps.edu/resources/raccoon Package: raccoon Architecture: all Depends: ${misc:Depends}, python, autodocktools Suggests: autodock, autodock-vina, torque Description: preparation of in silico drug screening projects The field of computational biology is all about modeling physiochemical entities. Structural biology is about how those entities look in 3D and behave. And we have a drug when we can change that behaviour in a way that we want it to be changed - and only that behaviour. . Some good part of the characterisation of promising drug-like compounds for their interaction with a larger protein can be done on computers. This package helps with getting collections of small ligands prepared to be fitted against a particular protein of known structure. That docking itself is then to be performed by autodock or autodock-vina. . Raccoon may not find the drug, but it may well find a lead to it. To have this package with Debian shall help smaller biochemistry labs and grants an opportunity for the general public to educate itself and/or actively join in to help the world .... just a bit.