debian/0000755000000000000000000000000012242756065007177 5ustar debian/manpages0000644000000000000000000000004211467561401010705 0ustar debian/vina.1 debian/vina_split.1 debian/source/0000755000000000000000000000000011562762321010473 5ustar debian/source/format0000644000000000000000000000001411467007150011675 0ustar 3.0 (quilt) debian/vina.10000644000000000000000000000327711531406452010217 0ustar .TH AUTODOCK "1" "November 2010" "AutoDock Vina 1.1.1 (Apr 20, 2010)" .SH NAME vina \- docking small molecules against proteins .SH DESCRIPTION .SS "Input:" .TP \fB\-\-receptor\fR arg rigid part of the receptor (PDBQT) .TP \fB\-\-flex\fR arg flexible side chains, if any (PDBQT) .TP \fB\-\-ligand\fR arg ligand (PDBQT) .SS "Search space (required):" .TP \fB\-\-center_x\fR arg X coordinate of the center .TP \fB\-\-center_y\fR arg Y coordinate of the center .TP \fB\-\-center_z\fR arg Z coordinate of the center .TP \fB\-\-size_x\fR arg size in the X dimension (Angstroms) .TP \fB\-\-size_y\fR arg size in the Y dimension (Angstroms) .TP \fB\-\-size_z\fR arg size in the Z dimension (Angstroms) .SS "Output (optional):" .TP \fB\-\-out\fR arg output models (PDBQT), the default is chosen based on the ligand file name .TP \fB\-\-log\fR arg optionally, write log file .SS "Misc (optional):" .TP \fB\-\-cpu\fR arg the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1) .TP \fB\-\-seed\fR arg explicit random seed .TP \fB\-\-exhaustiveness\fR arg (=8) exhaustiveness of the global search (roughly proportional to time): 1+ .TP \fB\-\-num_modes\fR arg (=9) maximum number of binding modes to generate .TP \fB\-\-energy_range\fR arg (=3) maximum energy difference between the best binding mode and the worst one displayed (kcal/mol) .SS "Configuration file (optional):" .TP \fB\-\-config\fR arg the above options can be put here .SS "Information (optional):" .TP \fB\-\-help\fR display usage summary .TP \fB\-\-help_advanced\fR display usage summary with advanced options .TP \fB\-\-version\fR display program version .SH "SEE ALSO" AutoDock Vina home page on http://vina.scripps.edu. debian/README.source0000644000000000000000000000070611467561401011355 0ustar autodock-vina for Debian ------------------------ No changes were done to upstream's source code, just the name of the base directory adjusted to the Debian policy. The build process was adjusted according to http://vina.scripps.edu/manual.html#build and an otherwise missing Makefile added to allow the direct application of cdbs. The man pages were created with help2man (also available as a Debian package) and are overdue to be manually improved. debian/copyright0000644000000000000000000000242412214301166011117 0ustar Format: http://dep.debian.net/deps/dep5/ Upstream-Name: AutoDock Vina Upstream-Contact: Oleg Trott , Ruth Huey Source: http://vina.scripps.edu/download.html Files: * Copyright: © 2006-2011, The Scripps Research Institute Oleg Trott , Ruth Huey License: Apache License, Version 2.0 Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at . http://www.apache.org/licenses/LICENSE-2.0 . Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. . On Debian systems, the complete text of the Apache version 2.0 license can be found in `/usr/share/common-licenses/Apache-2.0'. Files: debian/* Copyright: © 2010 Yask Gupta © 2010-2011 Steffen Moeller © 2011 Andreas Tille License: Apache License, Version 2.0 Same license as program itself. debian/upstream0000644000000000000000000000105312214301166010744 0ustar Contact: Oleg Trott Homepage: http://vina.scripps.edu Name: AutoDock Vina Reference: author: Oleg Trott and Arthur J. Olson title: > AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading journal: Journal of Computational Chemistry volume: 31 number: 2 pages: 455-461 year: 2010 DOI: 10.1002/jcc.21334 URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.21334/abstract eprint: http://onlinelibrary.wiley.com/doi/10.1002/jcc.21334/full debian/rules0000755000000000000000000000123312242754704010254 0ustar #!/usr/bin/make -f # debian/rules for autodoc_vinna # Authors: Yask Gupta , Andreas Tille # License: GPL # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 CFLAGS+=-fpermissive -DBOOST_FILESYSTEM_VERSION=3 --lto CXXFLAGS+=-fpermissive -DBOOST_FILESYSTEM_VERSION=3 --lto LDFLAGS+=--lto %: dh $@ override_dh_auto_build: $(MAKE) BASE=/usr -C build/linux/release CLFAGS="$(CFLAGS)" CXXFLAGS="$(CXXFLAGS)" LDFLAGS="$(LDFLAGS)" override_dh_clean: dh_clean rm -f build/linux/release/*.o build/linux/release/vina* get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs debian/patches/0000755000000000000000000000000012242756050010620 5ustar debian/patches/annoying_static_removed_was_in_for_a_reason_questionmark.patch0000644000000000000000000000103311567121431025425 0ustar Index: autodock-vina-1.1.2/build/linux/debug/Makefile =================================================================== --- autodock-vina-1.1.2.orig/build/linux/debug/Makefile 2011-05-12 13:03:59.108034987 +0200 +++ autodock-vina-1.1.2/build/linux/debug/Makefile 2011-05-12 13:04:34.736211653 +0200 @@ -1,8 +1,8 @@ -BASE=/usr/local -BOOST_VERSION=1_41 +BASE=/usr +BOOST_VERSION=1_46 BOOST_INCLUDE = $(BASE)/include -C_PLATFORM=-static -pthread -GPP=/usr/local/bin/g++ +C_PLATFORM= -pthread +GPP=g++ C_OPTIONS= -g BOOST_LIB_VERSION= debian/patches/fix_boost.patch0000644000000000000000000000567112214301166013637 0ustar Author: Sebastian Ramacher , Andreas Tille Date: Mon, 28 Nov 2011 13:52:29 +0100 Forewarded-Upstream: Oleg Trott , Ruth Huey Closes: #642697 --- autodock-vina-1.1.2.orig/build/makefile_common +++ autodock-vina-1.1.2/build/makefile_common @@ -10,7 +10,7 @@ LDFLAGS = -L$(BASE)/lib -L. -LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread +LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION} -lboost_filesystem${BOOST_LIB_VERSION} #-l pthread .SUFFIXES: .cpp .o --- autodock-vina-1.1.2.orig/src/main/main.cpp +++ autodock-vina-1.1.2/src/main/main.cpp @@ -47,7 +47,7 @@ using boost::filesystem::path; path make_path(const std::string& str) { - return path(str, boost::filesystem::native); + return path(str); } void doing(int verbosity, const std::string& str, tee& log) { @@ -661,7 +661,7 @@ cpu, seed, verbosity, max_modes_sz, energy_range, log); } catch(file_error& e) { - std::cerr << "\n\nError: could not open \"" << e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") << ".\n"; + std::cerr << "\n\nError: could not open \"" << e.name.string() << "\" for " << (e.in ? "reading" : "writing") << ".\n"; return 1; } catch(boost::filesystem::filesystem_error& e) { @@ -673,7 +673,7 @@ return 1; } catch(parse_error& e) { - std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.native_file_string() << "\": " << e.reason << '\n'; + std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.string() << "\": " << e.reason << '\n'; return 1; } catch(std::bad_alloc&) { --- autodock-vina-1.1.2.orig/src/split/split.cpp +++ autodock-vina-1.1.2/src/split/split.cpp @@ -38,7 +38,7 @@ using boost::filesystem::path; path make_path(const std::string& str) { - return path(str, boost::filesystem::native); + return path(str); } std::string default_prefix(const std::string& input_name, const std::string& add) { @@ -208,7 +208,7 @@ write_multimodel_pdbqt(tmp, ligand_prefix, flex_prefix); } catch(file_error& e) { - std::cerr << "\n\nError: could not open \"" << e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") << ".\n"; + std::cerr << "\n\nError: could not open \"" << e.name.string() << "\" for " << (e.in ? "reading" : "writing") << ".\n"; return 1; } catch(boost::filesystem::filesystem_error& e) { @@ -220,7 +220,7 @@ return 1; } catch(parse_error& e) { - std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.native_file_string() << "\": " << e.reason << '\n'; + std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.string() << "\": " << e.reason << '\n'; return 1; } catch(std::bad_alloc&) { debian/patches/do_not_link_against_unneeded_libs.patch0000644000000000000000000000154311567121431020527 0ustar Description: Avoid linking against libraries which are not used at all Author: Andreas Tille Date: Thu, 24 Feb 2011 08:14:04 +0100 Index: autodock-vina-1.1.2/build/makefile_common =================================================================== --- autodock-vina-1.1.2.orig/build/makefile_common 2011-05-11 22:35:13.000000000 +0200 +++ autodock-vina-1.1.2/build/makefile_common 2011-05-12 13:04:32.960202842 +0200 @@ -10,7 +10,7 @@ LDFLAGS = -L$(BASE)/lib -L. -LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${BOOST_LIB_VERSION} -l boost_serialization${BOOST_LIB_VERSION} -l boost_filesystem${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread +LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread .SUFFIXES: .cpp .o debian/patches/remove_static.patch0000644000000000000000000000105311567121431014502 0ustar Index: autodock-vina-1.1.2/build/linux/release/Makefile =================================================================== --- autodock-vina-1.1.2.orig/build/linux/release/Makefile 2011-05-12 15:45:29.468086887 +0200 +++ autodock-vina-1.1.2/build/linux/release/Makefile 2011-05-12 15:45:54.876212739 +0200 @@ -1,8 +1,8 @@ -BASE=/usr/local -BOOST_VERSION=1_41 +BASE=/usr +BOOST_VERSION=1_46 BOOST_INCLUDE = $(BASE)/include -C_PLATFORM=-static -pthread -GPP=/usr/local/bin/g++ +C_PLATFORM= -pthread +GPP=g++ C_OPTIONS= -O3 -DNDEBUG BOOST_LIB_VERSION= debian/patches/series0000644000000000000000000000021312242756045012035 0ustar remove_static.patch do_not_link_against_unneeded_libs.patch annoying_static_removed_was_in_for_a_reason_questionmark.patch fix_boost.patch debian/watch0000644000000000000000000000017211531402336010215 0ustar version=3 opts="uversionmangle=s/_/./g" \ http://vina.scripps.edu/download.html download/autodock_vina_([\d._]+)\.tgz debian/changelog0000644000000000000000000000450212242756065011052 0ustar autodock-vina (1.1.2-3) unstable; urgency=low [ Andreas Tille ] * debian/upstream: - Separate authors by ' and ' rather by ',' - Moved DOI to references * debian/copyright: Upstream-Contact changed and DEP5 * debian/patches/fix_boost.patch: Description of patch incl. forewarded upstream * debian/control: - cme fix dpkg-control - Priority: optional - canonical Vcs URLs - debhelper 9 [ Thorsten Alteholz ] * debian/rules: target get-orig-source added -- Andreas Tille Tue, 19 Nov 2013 17:57:26 +0100 autodock-vina (1.1.2-2) unstable; urgency=low * Fix boost compatibility error (thanks for the patch to Sebastian Ramacher ) Closes: #642697 * debian/control: Fixed Vcs fields * Debhelper 8 (control+compat) -- Andreas Tille Mon, 28 Nov 2011 10:58:42 +0100 autodock-vina (1.1.2-1) unstable; urgency=low * New upstream version * Demoted autodock and autogrid to "suggested" * Adjusted policy to 3.9.2 -- Steffen Moeller Thu, 12 May 2011 00:42:19 +0200 autodock-vina (1.1.1-3) unstable; urgency=low * Fixed debian/watch * debian/control - Team maintenance in Debian Med team - Added myself to uploaders - Recommends: autodock, autogrid * Remove debian/README.Debian (which just asks the user to install those recommended packages) * Remove debian/docs which is just empty * debian/patches/do_not_link_against_unneeded_libs.patch: Avoid linking against libraries which are not used at all * debian/rules: - Replace dh-make template by somewhat useful comment - Remove missleading get-orig-source target - there is no need at all to repack upstream source and the next version should be obtained simply by uscan * debian/*.1: Fixed name section * Added upstream-metadata.yaml -- Andreas Tille Thu, 24 Feb 2011 08:14:04 +0100 autodock-vina (1.1.1-2) unstable; urgency=low * Move from experimtenal to unstable. * Fixed two lintian warnings with respect to the man pages we contributed. -- Steffen Moeller Sat, 19 Feb 2011 15:09:51 +0100 autodock-vina (1.1.1-1) experimental; urgency=low * Initial release (Closes: #580905). -- Yask Gupta Thu, 11 Nov 2010 15:52:17 +0100 debian/vina_split.10000644000000000000000000000111611531406531011416 0ustar .TH AUTODOCK "1" "November 2010" "AutoDock Vina PDBQT Split 1.1.1 (Apr 20, 2010)" .SH NAME vina_split \- manual page for AutoDock Vina PDBQT Split 1.1.1 (Apr 20, 2010) .SH DESCRIPTION .SS "Input:" .TP \fB\-\-input\fR arg input to split (PDBQT) .SS "Output (optional) - defaults are chosen based on the input file name:" .TP \fB\-\-ligand\fR arg prefix for ligands .TP \fB\-\-flex\fR arg prefix for side chains .SS "Information (optional):" .TP \fB\-\-help\fR print this message .TP \fB\-\-version\fR print program version. .SH "SEE ALSO" AutoDock Vina home page on http://vina.scripps.edu. debian/compat0000644000000000000000000000000212242714074010367 0ustar 9 debian/control0000644000000000000000000000243312242714311010570 0ustar Source: autodock-vina Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Yask Gupta , Michael Banck , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), libboost-all-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/autodock-vina/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/autodock-vina/trunk/ Homepage: http://vina.scripps.edu Package: autodock-vina Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: autodock, autogrid Description: docking of small molecules to proteins AutoDock Vina is a program to support drug discovery, molecular docking and virtual screening of compound libraries. It offers multi-core capability, high performance and enhanced accuracy and ease of use. . The same institute also developed autodock, which is widely used. . O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461 debian/autodock-vina.install0000644000000000000000000000011011467561401013317 0ustar build/linux/release/vina usr/bin build/linux/release/vina_split usr/bin