debian/0000775000000000000000000000000012257174622007200 5ustar debian/rules0000775000000000000000000000616712257174543010274 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 export DH_OPTIONS SHELL := /bin/bash CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) CXX=g++ CC=gcc #CXX=/usr/lib/gcc-snapshot/bin/g++ #CC=/usr/lib/gcc-snapshot/bin/gcc # see http://www.gentoo.org/proj/en/qa/asneeded.xml LDFLAGS+="-Wl,--as-needed" CFLAGS += -Wall -g # link time optimisation - as soon as gcc-4.5 hits the archive # 20.02.2013, ta, does not really work yet #CFLAGS += -flto #LDFLAGS += -flto ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) CFLAGS += -O0 else CFLAGS += -O2 endif CFLAGS += -Winline -finline-functions # the suggested const is not working sufficiently, for gcc-4.6 and higher #CFLAGS += -Wsuggest-attribute=const CXXFLAGS+=$(CFLAGS) configure: configure-stamp configure-stamp: $(QUILT_STAMPFN) dh_testdir dh_autotools-dev_updateconfig set -e; \ for d in autodock autogrid; do \ ( cd $$d && autoreconf -i && ./configure CC="$(CC)" CXX="$(CXX)" LDFLAGS="$(LDFLAGS)" CFLAGS="$(CFLAGS)" CXXFLAGS="$(CXXFLAGS)" CPPFLAGS="$(CPPFLAGS)" --prefix=/usr ) \ done touch configure-stamp build: build-arch build-indep build-arch: build-arch-stamp build-arch-stamp: configure-stamp set -e; \ pwd; \ for d in autodock autogrid; do $(MAKE) -C $$d; done touch $@ build-indep: build-indep-stamp build-indep-stamp: configure-stamp # Add here commands to compile the indep part of the package. touch $@ clean: dh_testdir dh_testroot rm -f build-arch-stamp build-indep-stamp configure-stamp for d in autodock autogrid; \ do \ if [ -r $$d/Makefile ]; then $(MAKE) -C $$d distclean; fi \ done dh_autotools-dev_restoreconfig dh_clean configure-stamp install: install-indep install-arch install-indep: dh_testdir dh_testroot dh_prep -i dh_installdirs -i dh_install -i rm -rf $(CURDIR)/debian/autodock-test/usr/share/autodock/Tests/AutoDockTools rm -rf $(CURDIR)/debian/autogrid-test/usr/share/autogrid/Tests/CVS/ rm -rf $(CURDIR)/debian/autodock-test/usr/share/autodock/Tests/CVS/ chmod 644 $(CURDIR)/debian/autodock-test/usr/share/autodock/Tests/* chmod 644 $(CURDIR)/debian/autogrid-test/usr/share/autogrid/Tests/* install-arch: dh_testdir dh_testroot dh_prep -s dh_installdirs -s for d in autodock autogrid; do \ $(MAKE) -C $$d DESTDIR=$(CURDIR)/debian/$$d install; \ done dh_install -s binary-common: dh_testdir dh_testroot dh_lintian dh_installchangelogs autodock/RELEASENOTES dh_installdocs dh_installexamples dh_installman dh_link dh_strip dh_compress dh_fixperms dh_makeshlibs dh_installdeb dh_shlibdeps dh_gencontrol dh_md5sums dh_builddeb binary-indep: build-indep install-indep $(MAKE) -f debian/rules DH_OPTIONS=-i binary-common binary-arch: build-arch install-arch $(MAKE) -f debian/rules DH_OPTIONS=-s binary-common binary: binary-arch binary-indep .PHONY: build clean binary-indep binary-arch binary install install-indep install-arch configure get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs debian/watch0000664000000000000000000000036112107712726010226 0ustar version=3 ## rc (release candidates) have to be lower than the final version opts="dversionmangle=s/\+rc/~rc/" \ http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/ tars/.*/autodocksuite-(.*)-src\.tar\.gz debian/autodock-test.install0000664000000000000000000000004211736257541013355 0ustar autodock/Tests usr/share/autodock debian/autogrid-test.dirs0000664000000000000000000000002311736257541012654 0ustar usr/share/autogrid debian/changelog0000664000000000000000000001322712257174614011060 0ustar autodocksuite (4.2.5.1-3ubuntu1) trusty; urgency=medium * Use autotools-dev to update config.{sub,guess} for new arches. -- Logan Rosen Thu, 26 Dec 2013 22:52:16 -0500 autodocksuite (4.2.5.1-3) unstable; urgency=low * move package from experimental to unstable * debian/copntrol: set standard to 3.9.4 (no changes) * debian/autodock.lintian-overrides: added for wrong spelling error * debian/rules: add call to dh_lintian -- Thorsten Alteholz Sun, 02 Jun 2013 13:00:00 +0200 autodocksuite (4.2.5.1-2) experimental; urgency=low * debian/rules: remove lto flags again, does not really work -- Thorsten Alteholz Wed, 20 Feb 2013 18:00:00 +0100 autodocksuite (4.2.5.1-1) experimental; urgency=low * new upstream version * add make.patch * debian/copyright: point to GPL-2 instead of just GPL * debian/control: add more description to autodock-test and autogrid-test * debian/rules: add autodock/RELEASENOTES as upstream ChangeLog * debian/rules: introduce hardening flags * debian/rules: activate "link time optimisation" -- Thorsten Alteholz Mon, 18 Feb 2013 19:00:00 +0100 autodocksuite (4.2.3-3) UNRELEASED; urgency=low [ Charles Plessy ] * renamed debian/upstream-metadata.yaml to debian/upstream [ Andreas Tille ] * debian/upstream: - Move DOI+PMID to References - BibTeX conform Authors - added content of autodock-getdata.upstream-metadata.yaml * removed autodock-getdata.upstream-metadata.yaml -- Andreas Tille Mon, 02 Apr 2012 20:42:51 +0200 autodocksuite (4.2.3-2) unstable; urgency=low * Recompilation with gcc-4.6 * Yet no link time optimisation because of compiler errors * Added package with download instructions for getData * Rendering debian/rules more sensitive to build errors -- Steffen Moeller Sun, 04 Sep 2011 00:01:02 +0200 autodocksuite (4.2.3-1) unstable; urgency=low * New upstream version. * Removed series of template comment lines from debian/rules. -- Steffen Moeller Fri, 12 Feb 2010 23:41:59 +0100 autodocksuite (4.2.2.1-3) UNRELEASED; urgency=low * Introduced formal reference to accompanying scientific publication in ‘debian/upstream-metadata.yaml’. -- Charles Plessy Sun, 03 Jan 2010 22:17:29 +0900 autodocksuite (4.2.2.1-2) unstable; urgency=low [ Andreas Tille ] * debian/control: autogrid enhances autodock [ Nelson A. de Oliveira ] * Fix FTBFS (Closes: #550025) - debian/rules: removed old reference to /usr/share/quilt/quilt.make Thank you Nobuhiro Iwamatsu ! -- Nelson A. de Oliveira Tue, 20 Oct 2009 15:03:07 -0200 autodocksuite (4.2.2.1-1) unstable; urgency=low * New upstream release - patches are all accepted / independently performed - removed dependency on quilt * Compatibility with gcc-4.4 (no change required) * Added README.source, indicating now simplified structure of sources -- Steffen Moeller Wed, 07 Oct 2009 01:43:35 +0200 autodocksuite (4.2.1+rc1-3) UNRELEASED; urgency=low * Adding post-install message in favour of a request by upstream to possibly help their funding situation. -- Steffen Moeller Tue, 28 Jul 2009 17:05:26 +0200 autodocksuite (4.2.1+rc1-2) unstable; urgency=low * Fix FTBFS (Closes: #534601) - debian/control: add automake and csh in Build-Depends # Downgraded autodocktools from Recommends to Suggests (Closes: #534267) * Add watch file * Include myself in Uploaders. -- Nelson A. de Oliveira Thu, 25 Jun 2009 14:43:54 -0300 autodocksuite (4.2.1+rc1-1) unstable; urgency=low * new upstream release * added gcc flag to suppress char* conversion warnings * removed pointless DM-Maintainer-upload permission * bumped Debian policy compliance to 3.8.2 - no changes required * using new dh_prep instead of dh_clean -k, dependency on debhelper > 7 -- Steffen Moeller Sun, 21 Jun 2009 21:41:07 +0200 autodocksuite (4.0.1-5) UNRELEASED; urgency=low * debian/control: - updated conformance info to policy 3.8.0 - autogrid recommends autodocktools - autodock suggests autodocktools - autodock suggests autogrid, no longer recommends * debian/README.Debian: general updates, typos -- Steffen Moeller Thu, 04 Sep 2008 13:52:07 +0200 autodocksuite (4.0.1-4) unstable; urgency=low * debian/rules: - Using dh_installdocs instead of the cp command (Closes: #472538). - Using dh_installchangelogs to install src/auto[dock|grid]/ChangeLog. * debian/contol, debian/rules, debian/autodock-test.install, debian/autogrid-test.install: - Separated the test files from the main Arch:any packages into Arch:all packages. * Updated my email address. -- Charles Plessy Thu, 31 Jul 2008 13:19:15 +0900 autodocksuite (4.0.1-3) unstable; urgency=low [Charles] * debian/patches/build-with_gcc43.patch: adds #include to src/autogrid/check_size.cpp. (Thanks to Kumar Appaiah, Closes: #470972). [Steffen] * removed redundancy from the patch * added Charles to Uploaders * allowed DM-upload -- Steffen Moeller Wed, 19 Mar 2008 09:37:58 +0100 autodocksuite (4.0.1-2) unstable; urgency=low * Removed popularity-contest from suggests (Closes: #470406). -- Steffen Moeller Mon, 17 Mar 2008 23:28:34 +0100 autodocksuite (4.0.1-1) unstable; urgency=low * Initial release (Closes: #434654) -- Steffen Moeller Mon, 23 Jul 2007 16:41:48 +0200 debian/autodock.docs0000664000000000000000000000011511736257541011663 0ustar autodock/AUTHORS autodock/README autodock/NEWS debian/note_from_upstream.txt debian/upstream0000664000000000000000000000247112017125504010754 0ustar Donation: http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/ Homepage: http://autodock.scripps.edu/ Name: AutoDock Reference: - Author: Garrett M. Morris and Ruth Huey and William Lindstrom and Michel F. Sanner and Richard K. Belew and David S. Goodsell and Arthur J. Olson Title: > AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility Journal: Journal of Computational Chemistry Volume: 30 Number: 16 Pages: 2785-2791 Year: 2009 PMID: 19399780 DOI: 10.1002/jcc.21256 URL: http://www3.interscience.wiley.com/journal/122365050/abstract - Debian-package: autodock-getdata Author: John J. Irwin and Brian K. Shoichet Title: "ZINC – A Free Database of Commercially Available Compounds for Virtual Screening" Journal: J Chem Inf Model. Volume: 45 Number: 1 Pages: 177-182 Year: 2005 DOI: 10.1021/ci049714 PMID: 15667143 URL: http://pubs.acs.org/doi/abs/10.1021/ci049714%2B eprint: http://pubs.acs.org/doi/pdf/10.1021/ci049714%2B Registration: http://autodock.scripps.edu/downloads/autodock-registration Watch: | opts="dversionmangle=s/\+rc/~rc/" \ http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/ \.\./autodock-registration/tars/.*/autodocksuite-(.*)-src\.tar\.gz debian/compat0000664000000000000000000000000211736257541010401 0ustar 5 debian/README.source0000664000000000000000000000011711736257541011361 0ustar The folder structure was simplified, i.e. /src renamed to autodock- . debian/autogrid4.10000664000000000000000000001015211736257541011166 0ustar .\" Hey, EMACS: -*- nroff -*- .TH AUTOGRID 1 "Juli 23, 2007" .\" 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 autogrid \- preparing protein and ligand for AutoDock analysis .SH SYNOPSIS .B autogrid4 .RI [ options ] \-p .RI gridparameterfile .SH DESCRIPTION .B AutoGrid prepares a 3D grid representation of the non-covalent interaction energies that various user-specified ligand atom types will experience around a user-specified target macromolecule. In addition, the electrostatic potential and desolvation free energy grid maps may also be calculated. The grid maps are stored in plain text files with the extension '.map' and are required by AutoDock 4 to perform dockings. AutoGrid also outputs a '.xyz' file which describes the spatial extents of the grid box, and an AVS field '.fld' file which describes the consistent set of atomic affinity grid maps that were calculated together for a given target macromolecule. Note: it is necessary to compute grid maps for all the atom types in the ligand or set of ligands that will be docked, as well as an electrostatic potential grid map and a desolvation free energy map. For example, if a ligand has an aliphatic carbon and a hydrogen-bond-accepting oxygen atom, it would be necessary to compute both a 'C' map and an 'OA' map. See http://autodock.scripps.edu/faqs-help/faq/where-do-i-set-the-autodock-4-force-field-parameters for more information about AutoDock 4 atom types. The input to .RI AutoGrid is best prepared with the program suite .RI AutoDockTools. There is no way to run .RI autodock4 without a grid. .PP .\" TeX users may be more comfortable with the \fB\fP and .\" \fI\fP escape sequences to invode bold face and italics, .\" respectively. .ad l .SH OPTIONS .B \-o Use old PDBq format (q in columns 55-61) .TP .B \-u Usage information, also \-h on Debian. .TP .B \-d Increased verbosity of messages to help debugging. .TP .B \-l .RI logfile .TP .B \-p .RI filename Specifies Grid Parameter File .SH EXAMPLE A range of tests is made available with the AutoGrid sources that can be used as follows: .br $ D=/usr/share/doc/autogrid/Tests .br $ cd /tmp .br $ ln \-s $D/AD4_parameters.dat . .br $ gunzip \-c $D/hsg1_sm.pdbqt.gz > hsg1_sm.pdbqt .br .nh $ autogrid4 \-p $D/hsg1_no_receptor_types.gpf \-l hsg1_no_receptor_types.glg .ad b .TP This command prepares grid map files for each of the AutoDock atom types specified in the grid parameter file (in this case: hsg1_sm.A.map, hsg1_sm.C.map, hsg1_sm.d.map, hsg1_sm.e.map, hsg1_sm.HD.map, hsg1_sm.NA.map, hsg1_sm.N.map, hsg1_sm.OA.map), the AVS field file (hsg1_sm.maps.fld) and hsg1_sm.maps.xyz. To perform the cocking calculation, AutoDock should be executed, though it demands a separate docking parameter file (with extension .dpf). The 'DPF' refers to the grid map files that are necessary to the docking and allows the setting of other important parameters, such as the search method and how many dockings to perform. .SH SEE ALSO .BR autodock (1), .BR runAdt (1). .br http://autodock.scripps.edu .SH LICENSE This software is made available under the terms of the GNU Public License version 2 or later. This implies that this software may be redistributed if the source is made available. It would however help the future development of the AutoDockSuite if you register yourself at http://autodock.scripps.edu/downloads. .SH AUTHOR The most prominent author of the version 4 of AutoDock is G. Morris . See the AUTHORS file in /usr/share/doc/autogrid for details. .PP This manual page was written by Steffen Moeller and much revised by upstream author Garrett Morris. It was prepared for the Debian project but may be used by others and is hopefully adopted by the upstream developers. debian/autodock-zinc.getData0000664000000000000000000000176011736257541013254 0ustar print STDERR "Reading autodock-zinc configuration file\n" if $verbose; # This file is Copyright (C) Steffen Moeller # and made availabel under the terms of the GPL version 2 or any # later version as presented in '/usr/share/common-licenses/GPL-2'. # No chemical post-processing required since all files are in pdbqt format # already. But one needs to untar the files. foreach $n (("asinex", "chembridge_buildingblocks_pdbqt_1000split", "drugbank_nutraceutics", "drugbank_smallmol", "fda_approved", "human_metabolome_pdbqt_1000split", "otava", "zinc_natural_products")) { print "$n\n"; $toBeMirrored{"zinc.pdbqt.$n"}={ "name" => "ZINC - PDBQT formatted – $n", "tags" => ["pdbqt","compounds"], "source" => "wget $sharedWgetOptions http://zinc.docking.org/pdbqt/$n.tar.gz", "post-download" => "tar --no-same-owner --exclude prepare_lig.log --exclude mol2 -xzvf $n.tar.gz && chmod -R go+r . && find . -type d -exec chmod +x {} \\; " }; } 1; debian/autodock-getdata.install0000664000000000000000000000006211736257541014011 0ustar debian/autodock-zinc.getData /etc/getData.conf.d/ debian/autodock4.10000664000000000000000000000562511736257541011172 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 AUTODOCK 1 "Juli 23, 2007" .\" 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 autodock \- docking of chemical ligands to protein receptors .SH SYNOPSIS .B autodock4 .RI [ options ] .SH DESCRIPTION AutoDock perfoms the automated docking of chemical compounds to proteins, i.e. it predicts how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. The AutoDockSuite consists of two main programs of which AutoDock performs the docking of the ligand to a set of grids describing the target protein and AutoGrid pre-calculates these grids. .PP .\" TeX users may be more comfortable with the \fB\fP and .\" \fI\fP escape sequences to invode bold face and italics, .\" respectively. .SH OPTIONS .TP .B \-p .RI parameter_filename .TP .B \-l .RI log_filename .TP .B \-o Use old PDBQ format, charge q in columns 55-61 .TP .B \-k Keep original residue numbers .TP .B \-i Ignore header-checking .TP .B \-t Parse the PDBQ file to check torsions, then stop. .TP .B \-c < .RI command_file Command mode, by file .TP .B \-c | .RI control_program Command mode, by control_program .SH EXAMPLE On Debian, the directory /usr/share/doc/autodock offers examples to run. Change to that directory and unpack (as root) the gzipped map files, then execute AutoDock as shown below: .br gunzip *.map.gz .br autodock4 \-p 1pgp.dpf \-l /tmp/1pgp.dlg The interpretation of results is aided by the AutoDockTools suite. Please also inspect the tutorials offered online. .SH SEE ALSO .BR autogrid (1), .BR runAdt (1). .br http://autodock.scripps.edu .br http://autodock.scripps.edu/faqs-help/faq/what-is-the-command-line-to-start-autodock-4 .SH LICENSE This software is made available under the terms of the GNU Public License version 2 or later. This implies that this software may be redistributed if the source is made available. It would however help the future development of the AutoDockSuite if you register yourself at http://autodock.scripps.edu/downloads. .SH AUTHOR The most prominent author of the version 4 of autodock is G. Morris . See the AUTHORS file in /usr/share/doc/autodock for details. .PP This manual page was written by Steffen Moeller , for the Debian project (but may be used by others and is hopefully adopted by the upstream developers). debian/autodock.lintian-overrides0000664000000000000000000000014212152627500014356 0ustar # In this context Ang means Angstrom autodock: spelling-error-in-binary usr/bin/autodock4 Ang And debian/copyright0000664000000000000000000000402712110354553011125 0ustar This package was debianized by Steffen Moeller on Mon, 23 Jul 2007 16:41:48 +0200. It was downloaded from http://autodock.scripps.edu/downloads Upstream Authors: Primary: Garrett M. Morris David S. Goodsell Scott Halliday Ruth Huey William E. Hart Max Chang Richard K. Belew Arthur J. Olson Contributing: Peter Reilly Scott Kurowski Copyright: Copyright © 1989-2008, All Rights Reserved. Garrett M. Morris David S. Goodsell Scott Halliday Ruth Huey William E. Hart Max Chang Richard K. Belew Arthur J. Olson Peter Reilly Scott Kurowski and The Scripps Research Institute License: AutoDock is a Trade Mark of The Scripps Research Institute. This package 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 On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL-2'. The Debian packaging is © 2007, Steffen Moeller and is licensed under the GPL, see above. debian/source/0000775000000000000000000000000012152650265010474 5ustar debian/source/format0000664000000000000000000000001412110163546011675 0ustar 3.0 (quilt) debian/autogrid.manpages0000664000000000000000000000002311736257541012531 0ustar debian/autogrid4.1 debian/README.Debian0000664000000000000000000000400611736257541011244 0ustar autodocksuite for Debian ------------------------ AutoDock is a prime representative of the programs addressing the simulation of the docking of fairly small chemical ligands to rather big protein receptors. Earlier versions had all flexibility in the ligands while the protein was kept rather ridgid. This latest version 4 also allows for a flexibility of selected sidechains of surface residues, i.e., takes the rotamers of selected residues into account. You may find other spots where to help with the packaging of AutoDock. Please give feedback. Debian-Med community is very friendly and open towards collaborative package maintenance, just say "hello". Success stories are warmely welcomed. The upstream developers at Scripps have accompanied this package with a set of programs that are more prone to be used by the user directly. These are located in a separate package, named 'autodocktools' and have very recently also been made available via Debian. Dr Garrett Morris of the upstream developers was very supportive of this packaging. The Scripps Institute asks for registrations prior to the download of the tarball or the binaries at this URL http://autodock.scripps.edu/downloads/autodock-registration which does not affect the distribution of this package under the GPL. Nevertheless, please respect upstream's genuine interest to know about the impact that their work has on the field, which is key for writing grant applications. You may decide to register on that site albeit having this package received via Debian already. Also please consider installing the Debian package popularity-contest. This counts the installations and may thus further help upstream to further develop their software. Dr Morris kindly proofread the copyright notice and the autogrid4.1 man page. This was much appreciated and I thank him for this. Thanks for improving the AutoDock/-Grid packaging for Debian also go to David Paleino and the Debian-Med community at large. -- Steffen Moeller Mon, 15 Dec 2008 01:01:37 +0100 debian/autogrid-test.install0000664000000000000000000000004311736257541013363 0ustar autogrid/Tests usr/share/autogrid/ debian/autodock.manpages0000664000000000000000000000002311736257541012524 0ustar debian/autodock4.1 debian/note_from_upstream.txt0000664000000000000000000000262711736257541013663 0ustar ---------------------------------------------------------------------- ______ / \ / \ / \ \ /\ / \ / \ / \/ /\ \/ / \ /____\ AutoDock and AutoGrid are free software, distributed under the terms of the GNU General Public License 2 or later. This allows us to share the code and to be open for improvement from the whole scientific community. The development of the AutoDock suite is entirely funded by research grants. For that reason, we ask you to register at the AutoDock Registration page http://autodock.scripps.edu/downloads/autodock-registration in order to keep track of number of unique downloads, which we use to support the grant applications. Installing the Debian popularity-contest package is also encouraged. Thank you, and happy docking! The AutoDock Development Team If you plan to use AutoDock for commercial purposes we encourage donations to the Olson laboratory to help support further development of the AutoDock 4 suite of programs. Donation information provided on the download page. ---------------------------------------------------------------------- debian/control0000664000000000000000000000753612257174616010621 0ustar Source: autodocksuite Section: science Priority: optional Maintainer: Ubuntu Developers XSBC-Original-Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Nelson A. de Oliveira , Andreas Tille , Thorsten Alteholz Build-Depends: debhelper (>= 7), automake, csh, autotools-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/autodocksuite/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/autodocksuite/trunk/ Homepage: http://autodock.scripps.edu/ Package: autodock Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: autogrid, autodocktools Description: analysis of ligand binding to protein structure AutoDock is a prime representative of the programs addressing the simulation of the docking of fairly small chemical ligands to rather big protein receptors. Earlier versions had all flexibility in the ligands while the protein was kept rather ridgid. This latest version 4 also allows for a flexibility of selected sidechains of surface residues, i.e., takes the rotamers into account. . The AutoDock program performs the docking of the ligand to a set of grids describing the target protein. AutoGrid pre-calculates these grids. Package: autogrid Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: autodock, autodocktools Enhances: autodock Description: pre-calculate binding of ligands to their receptor The AutoDockSuite addresses the molecular analysis of the docking of a smaller chemical compounds to their receptors of known three-dimensional structure. . The AutoGrid program performs pre-calculations for the docking of a ligand to a set of grids that describe the effect that the protein has on point charges. The effect of these forces on the ligand is then analysed by the AutoDock program. Package: autodock-test Architecture: all Suggests: autodock Depends: ${misc:Depends} Description: test files for AutoDock AutoDock is a prime representative of the programs addressing the simulation of the docking of fairly small chemical ligands to rather big protein receptors. Earlier versions had all flexibility in the ligands while the protein was kept rather ridgid. This latest version 4 also allows for a flexibility of selected sidechains of surface residues, i.e., takes the rotamers into account. . This package contain the test files for the AutoDock program. Package: autogrid-test Architecture: all Suggests: autogrid Depends: ${misc:Depends} Description: test files for AutoGrid The AutoDockSuite addresses the molecular analysis of the docking of a smaller chemical compounds to their receptors of known three-dimensional structure. . This package contain the test files for the AutoGrid program. Package: autodock-getdata Architecture: all Suggests: autodock, autogrid, autodocktools Recommends: getdata Depends: ${misc:Depends} Description: instructions for getData to collect compounds This package provides instructions for getData to retrieve descriptions for sets of molecular compounds that can be used directly as input for autodock. The data is not provided direclty by this package. Only the instructions for the download are maintained here. . The FightAids@Home project of the World Community Grid publicly provides the input sets of their runs. The original structures come from the ZINC database and have been processed from the mol2 to pdbqt format by the Scripps institute: * asinex * chembridge_buildingblocks_pdbqt_1000split * drugbank_nutraceutics * drugbank_smallmol * fda_approved * human_metabolome_pdbqt_1000split * otava * zinc_natural_products . Please cite the ZINC database when using that data. debian/autogrid.docs0000664000000000000000000000005711736257541011675 0ustar autogrid/AUTHORS autogrid/README autogrid/NEWS debian/patches/0000775000000000000000000000000012152650265010623 5ustar debian/patches/series0000664000000000000000000000001312110132062012012 0ustar make.patch debian/patches/make.patch0000664000000000000000000000176612110354722012564 0ustar Description: adapt make process to Debian build environment Author: Thorsten Alteholz Last-Update: 2013-02-16 Index: src/autogrid/Makefile.am =================================================================== --- src.orig/autogrid/Makefile.am 2013-02-17 18:47:22.000000000 +0100 +++ src/autogrid/Makefile.am 2013-02-17 18:48:18.000000000 +0100 @@ -155,7 +155,8 @@ default_parameters.h : $(srcdir)/../autodock/paramdat2h.csh $(srcdir)/../autodock/AD4_parameters.dat $(srcdir)/../autodock/AD4.1_bound.dat rm -f $@ csh $(srcdir)/../autodock/paramdat2h.csh $(srcdir)/../autodock/AD4_parameters.dat $(srcdir)/../autodock/AD4.1_bound.dat > $@ - sh ../copyfilesfromAD -b # copying from build dir , not source dir +# sh ./copyfilesfromAD -b # copying from build dir , not source dir + sh ./copyfilesfromAD # copying from src dir , not build dir # 2007-04-30 MP & GMM: this line is necessary to be able to compile read_parameter_library.o read_parameter_library.o : default_parameters.h debian/autodock.postinst0000664000000000000000000000206711736257541012626 0ustar #!/bin/sh # postinst script for autodock # # see: dh_installdeb(1) set -e # summary of how this script can be called: # * `configure' # * `abort-upgrade' # * `abort-remove' `in-favour' # # * `abort-remove' # * `abort-deconfigure' `in-favour' # `removing' # # for details, see http://www.debian.org/doc/debian-policy/ or # the debian-policy package case "$1" in configure) if [ -r /usr/share/doc/autodock/note_from_upstream.txt ]; then cat /usr/share/doc/autodock/note_from_upstream.txt fi ;; abort-upgrade|abort-remove|abort-deconfigure) ;; *) echo "postinst called with unknown argument \`$1'" >&2 exit 1 ;; esac # dh_installdeb will replace this with shell code automatically # generated by other debhelper scripts. #DEBHELPER# exit 0 debian/autodock-test.dirs0000664000000000000000000000002311736257541012647 0ustar usr/share/autodock debian/autodock-getdata.README.Debian0000664000000000000000000000073711736257541014472 0ustar autodock-getdata ================ The integration of 'getData' with Debian is still in its infancy. We will be learning while we are doing it. The PDBQT-variant of mol2 files in ZINC is described in November 2, 2009 volume 8 of the FightAids@Home newletter, available online on http://fightaidsathome.scripps.edu/images/FAAHvol8.pdf Files can be retrieved manually on http://zinc.docking.org/pdbqt/ -- Steffen Moeller Sun, 04 Sep 2011 00:51:12 +0200