debian/0000755000000000000000000000000012152372661007173 5ustar debian/control0000644000000000000000000000220512146437726010604 0ustar Source: mgltools-gle Section: non-free/libs Priority: optional Maintainer: Debian Med Packaging Team XS-Autobuild: yes Uploaders: Steffen Moeller , Sargis Dallakyan , Andreas Tille , Thorsten Alteholz Build-Depends: debhelper (>= 8), swig (>= 1.3.20), python-all-dev (>= 2.6), python-numpy, libglu1-mesa-dev, mesa-common-dev Standards-Version: 3.9.4 XS-Python-Version: >= 2.6 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/gle/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mgltools/gle/trunk/ Homepage: http://mgltools.scripps.edu/ Package: mgltools-gle XB-Python-Version: ${python:Versions} Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, python-numpy, libglu1-mesa Description: GLE library Python extension This package is part of the mgltools set of Python libraries which provide an infrastructure for the analysis of protein structures and their docking of chemical compounds. . It provides a swig-generated interface to the GLE library. debian/pycompat0000644000000000000000000000000210733045234010736 0ustar 2 debian/copyright0000644000000000000000000001576012152154546011137 0ustar This package was debianized by Steffen Moeller on Thu, 10 Jul 2008 00:03:24 +0200 It was downloaded from http://mgltools.scripps.edu Upstream Authors: Linas Vepstas Copyright: Copyright 1990-2003 Linas Vepstas and his employer IBM under the license stated below. License: From LICENSE This software is copyrighted by Michel F. Sanner (sanner@scripps.edu) and TSRI. The following terms apply to all files associated with the software unless explicitly disclaimed in individual files. MGLTOOLS SOFTWARE LICENSE AGREEMENT. 1. Grant Of Limited License; Software Use Restrictions. The programs received by you will be used only for NON COMMERCIAL purposes. This license is issued to you as an individual. For COMMERCIAL use done with the software please contact Michel F. Sanner for details about commercial usage license agreements. For any question regarding license agreements, please contact Michel Sanner: TSRI, Molecular Biology Department, TCP 26, 10550 North Torrey Pines Road, La Jolla, CA 92037 sanner@scripps.edu tel (858) 784-7742 fax (858) 784-2341 2. COMMERCIAL USAGE is defined as revenues generating activities. These include using this software for consulting activities and selling applications built on top of, or using this software. Scientific research in an academic environment and teaching are considered NON COMMERCIAL. 3. Copying Restrictions. You will not sell or otherwise distribute commercially these programs or derivatives to any other party, whether with or without consideration. 4. Ownership of Software. You will not obtain, and will not attempt to obtain copyright coverage thereon without the express purpose written consent of The Scripps Research Institute and Dr. Sanner. 5. IN NO EVENT SHALL THE AUTHORS OR DISTRIBUTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF THIS SOFTWARE, ITS DOCUMENTATION, OR ANY DERIVATIVES THEREOF, EVEN IF THE AUTHORS HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 6. THE AUTHORS AND DISTRIBUTORS SPECIFICALLY DISCLAIM ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT. THIS SOFTWARE IS PROVIDED ON AN "AS IS" BASIS, AND THE AUTHORS AND DISTRIBUTORS HAVE NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. From src/COPYING.src The following agreement applies to the source code in this directory only! It does *NOT* apply to the HTML documentation or to the demo programs, or to other items distributed with this package! --------------------------------------------------------------------- SOFTWARE AGREEMENT PLEASE READ THIS AGREEMENT CAREFULLY BEFORE INSTALLING OR USING THIS SOFTWARE. IF YOU INSTALL OR USE THIS SOFTWARE, YOU AGREE TO THESE TERMS. This software is owned by International Business Machines Corporation ("IBM"), or its subsidiaries or IBM's suppliers, and is copyrighted and licensed, not sold. IBM retains title to the software, and grants you a nonexclusive license for the software. Under this license, you may: 1) use the software on one or more machines at a time; 2) make copies of the software for use or backup purposes within your enterprise; 3) modify this software and merge it with another program; and 4) make copies of the original file you downloaded and distribute it, provided that you transfer a copy of this license to the other party. The other party agrees to these terms by its first use of this software. You must reproduce the copyright notice and any other legend of ownership on each copy or partial copy of the software. This software, as provided by IBM, is only intended to assist in the development of a working software program. The software may not function as written: additional code is required. In addition, the software may not compile and/or bind successfully as written. IBM PROVIDES THE SOFTWARE "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS WITH YOU. SHOULD ANY PART OF THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE ENTIRE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. IN NO EVENT, UNLESS REQUIRED BY APPLICABLE LAW, SHALL IBM BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE SOFTWARE (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE SOFTWARE TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF IBM HAS BEEN ADVISED IN ADVANCE OF THE POSSIBILITY OF SUCH DAMAGES. IBM does not warrant that the contents of the software will meet your requirements, that the software is error-free or that the software does not infringe on any intellectual property rights of any third party. IBM may make improvements and/or changes in the software at any time. Changes may or may not be made periodically to the information in the software; these changes may be reported, for the software included herein, in new editions. References, if any, in the software to IBM products, programs, or services do not imply that IBM intends to make these available in all countries in which IBM operates. Any reference to an IBM licensed program in the software is not intended to state or imply that only IBM's licensed program may be used. Any functionally equivalent program may be used. The laws of New York State govern this agreement. In addition to the license above, the Debian project also got the explicit permission from the copyright owner to distribute the software: Date: Mon, 20 May 2013 10:07:13 -0700 From: Michel Sanner To: Thorsten Alteholz Cc: "annao >> Anna Omelchenko" Subject: Re: mgltools license Hello Thorsten Sorry for not following up this earlier. We are delighted to have Debian include the MGLTools in their distribution. So you need us to amend the License text or will this email suffice ? Thanks -- ----------------------------------------------------------------------- o / Michel F. Sanner Ph.D. The Scripps Research Institute o Associate Professor Department of Molecular Biology \ 10550 North Torrey Pines Road o Tel. (858) 784-7742 La Jolla, CA 92037, TPC 26 / Fax. (858) 784-2341 o sanner@scripps.edu http://www.scripps.edu/~sanner ----------------------------------------------------------------------- debian/changelog0000644000000000000000000000723612152154546011055 0ustar mgltools-gle (1.5.7~rc1~cvs.20130519-1) unstable; urgency=low * New upstream version. * debian/control: bump standard to 3.9.4 (no changes) * debian/control: remove DM-Upload-Allowed * debian/copyright: add permission for debian to distribute mgltools -- Thorsten Alteholz Sun, 19 May 2013 12:00:00 +0200 mgltools-gle (1.5.6~rc3~cvs.20120601-1) unstable; urgency=low * New upstream version. * debian/rules: add call to dh_numpy * debian/control: bump standard to 3.9.3 -- Thorsten Alteholz Fri, 01 Jun 2012 18:00:00 +0200 mgltools-gle (1.5.6~rc3~cvs.20120206-1) unstable; urgency=low * New upstream version. * debian/control: vcs fields corrected -- Thorsten Alteholz Mon, 06 Feb 2012 18:00:00 +0100 mgltools-gle (1.5.6~rc2+cvs.20111222-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Thu, 22 Dec 2011 17:10:09 +0100 mgltools-gle (1.5.6~rc2+cvs.20110926-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Tue, 27 Sep 2011 10:58:11 +0200 mgltools-gle (1.5.6~rc1+cvs.20110617-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Fri, 17 Jun 2011 01:20:18 +0200 mgltools-gle (1.5.6~rc1+cvs.20110615-1) unstable; urgency=low * New upstream version. * debian/control: added myseld to Uploaders: * debian/README.Debian: spelling corrected -- Thorsten Alteholz Wed, 15 Jun 2011 21:43:38 +0200 mgltools-gle (1.5.4.cvs.20100912-2) unstable; urgency=low * Debhelper 8 (control+compat) * debian/source/format: 3.0 (quilt) * debian/control: - Build-Depends: python-all-dev (>= 2.6) to enable python-support2 Closes: 616890 - XS-Python-Version: >= 2.6 Closes: #623904 * debian/rules: switch to short dh syntax which makes dh_python2 easy -- Andreas Tille Tue, 26 Apr 2011 10:52:16 +0200 mgltools-gle (1.5.4.cvs.20100912-1) unstable; urgency=low * New upstream version. * Adjusted dependencies (Closes: #596319). -- Steffen Moeller Sun, 12 Sep 2010 00:20:31 +0200 mgltools-gle (1.5.4.cvs.20090603-1.2) unstable; urgency=low * Non-maintainer upload. * Build extension for all supported Python versions (closes: #586839) -- Piotr Ożarowski Wed, 30 Jun 2010 21:50:08 +0200 mgltools-gle (1.5.4.cvs.20090603-1.1) unstable; urgency=low * Non-maintainer upload. * Move package to non-free due to non DFSG-free license, fix debian/copyright accordingly. Patch from Scott Kitterman. (Closes: #545515) -- Stefano Zacchiroli Sun, 20 Dec 2009 12:19:01 +0100 mgltools-gle (1.5.4.cvs.20090603-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Wed, 03 Jun 2009 11:48:20 +0200 mgltools-gle (1.5.4.cvs.20090528-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Sat, 16 May 2009 00:51:23 +0200 mgltools-gle (1.5.4.cvs.20090514-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Thu, 14 May 2009 21:46:34 +0200 mgltools-gle (1.5.4.cvs.20081126-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Wed, 26 Nov 2008 14:43:11 +0100 mgltools-gle (1.5.2.cvs.20081109-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Sun, 09 Nov 2008 15:02:32 +0100 mgltools-gle (1.5.2.cvs.20080731-1) unstable; urgency=low * Initial release, contributes to closing ITP #458811. -- Steffen Moeller Thu, 31 Jul 2008 21:59:58 +0200 debian/compat0000644000000000000000000000000211555505004010364 0ustar 8 debian/watch0000644000000000000000000000012511041154457010217 0ustar version=3 http://mgltools.scripps.edu/downloads/.*mgltools_source_([0-9.]+)\.tar\.gz debian/get-orig-source/0000755000000000000000000000000012152372661012206 5ustar debian/get-orig-source/rc-version0000644000000000000000000000000512146202375014210 0ustar ~rc1 debian/get-orig-source/current-branch0000644000000000000000000000001112146202375015033 0ustar rc-1-5-7 debian/get-orig-source/get-orig-source0000755000000000000000000000555712145665571015172 0ustar #!/bin/bash # # usage: get-orig-source # e.g.: get-orig-source VolumeDIST rc-1-5-6 ~rc1 # package=$1 branch=$2 rcversion=$3 REMOTECVSROOT=:pserver:anonymous@mgl1.scripps.edu:2401/opt/cvs CVS=/usr/bin/cvs MGLTOOLSCVS=../../mgltools-cvs # Expected by svn-buildpackage as 'tarballs' TARDIR=../tarballs PREFIX="mgltools-" if [ "$package" == "AutoDockToolsDIST" ]; then PREFIX="" fi DEBPACKAGE=$PREFIX`echo $package|sed "s/DIST//g"| tr 'A'-'Z' 'a'-'z'` # do some stuff echo "I: get $package (-> $DEBPACKAGE) from branch $branch" loginDone=`grep "$REMOTECVSROOT" ~/.cvspass|wc -l` if [ "$loginDone" == "0" ]; then $CVS -d$REMOTECVSROOT login fi if [ -d "$MGLTOOLSCVS" ]; then echo "I: cvs directory already available" else echo "I: create directory '$MGLTOOLSCVS' to store new CVS checkout" mkdir "$MGLTOOLSCVS" fi if [ -d $MGLTOOLSCVS/$package ]; then echo "I: ... checkout already done" if [ -r "$MGLTOOLSCVS/$package/CVS/Tag" ]; then echo "W: check whether this is the correct tag: `cat $MGLTOOLSCVS/$package/CVS/Tag`" else echo "W: no tag file found. You may be working on the trunk, not on the release branch. Is that what you want?" fi sleep 3 (cd $MGLTOOLSCVS/$package && $CVS -z3 update -d) else echo "I: ... now performing checkout" (cd "$MGLTOOLSCVS" && $CVS -z3 -d$REMOTECVSROOT co -r $branch $package) fi version=`echo $branch|sed "s/rc-//g"|tr '-' '.'` DATE=`date +"%Y%m%d"` if [ -f $MGLTOOLSCVS/build-for-date ]; then DATE=`cat $MGLTOOLSCVS/build-for-date` fi if [ -z ${rcversion} ]; then echo "I: no rc but real release" origFilename=${DEBPACKAGE}_${version}${rcversion}.orig.tar.gz origDirname=${DEBPACKAGE}-${version}${rcversion} else origFilename=${DEBPACKAGE}_${version}${rcversion}~cvs.${DATE}.orig.tar.gz origDirname=${DEBPACKAGE}-${version}${rcversion}~cvs.${DATE} fi echo "I: Filename of origFile: $origFilename" cd "$MGLTOOLSCVS" if [ -d "$TARDIR" ]; then echo "I: directory for orig tarballs already available" else echo "I: creating directory for irog tarballs: '$TARDIR'" mkdir "$TARDIR" fi if [ -f "$TARDIR"/"$origFilename" ]; then echo "I: delete old file '$origFilename' " rm "$TARDIR"/"$origFilename" fi if [ -n "$origDirname" -a -d "$origDirname" ]; then echo "W: Amazingly, temporary directory name '$origDirname' is already existing. Stop this script if this shall not be removed -- within 3 seconds." sleep 3 rm -r "$origDirname" fi echo "I: remove some files in '$package' " cd $package echo "I: ... *.dll " find . -name *.dll -a -type f| xargs -r rm -rf cd .. echo "I: Temporarily renaming and taring $package " echo " --> $MGLTOOLSCVS/$TARDIR/$origFilename" mv "$package" "$origDirname" echo -n "I: Number of files in package: " GZIP=-9 tar --exclude CVS -czvf "$TARDIR/$origFilename" "$origDirname" | wc -l mv "$origDirname" "$package" echo "I: done" debian/get-orig-source/README0000644000000000000000000000066611600144512013063 0ustar This directory contains all scripts/data/whatsoever to automatically build mgltools-packages. Using svn externals, this directory appears in the debian directory of each package. So in case you need to change anything (like the branch to be used), there is only one place to make the modifications. Command in trunk/debian: svn propset svn:externals \ '^/trunk/packages/mgltools/mgltools-external-get-orig-source get-orig-source' . debian/get-orig-source/rc-version.ok0000644000000000000000000000000512145647165014631 0ustar ~rc3 debian/docs0000644000000000000000000000002111040471665010036 0ustar src/README.gutil debian/README.Debian0000644000000000000000000000261111572471434011237 0ustar autodocktools and other modules of MGLtools for Debian ====================================================== This package aims at providing the complete infrastructure for ligand screening with Debian Linux. It is part of the MGL (Molecular Graphics Labs at Scripps) Python tools set for the computational and visual interaction of protein structures and their ligands. The Debian community shall thank Sargis Dallakyan for his help in easing the compatibility with Debian by accepting our patches and providing more himself. Also, the leader of the Molecular Graphics Labs, Prof. Michael Sanner, is thanked for his support. Please be continuously reminded that that closer a software gets towards identifying or further describing functional compounds in medicine, the harder it is to get access to free (as in beer) solutions. And it certainly does not get much closer than with the AutoDockToolkit. To have the AutoDockToolkit with Debian is special and good for the world as it spawns the development of new drugs. We will need to wait a bit longer for a DFSG compatible license, though. If you are a regular user of this package, your feedback to us packagers would much appreciated. The packaging is organised via the Debian-Med alioth project that has its own portal on http://debian-med.alioth.debian.org. -- Steffen Moeller Sun, 20 Jul 2008 00:33:11 +0200 debian/README.source0000644000000000000000000000155211040465741011352 0ustar Any package of the MGLtools suite ================================= The URL presented in debian/watch guides to a tar file as the source distribution of the MGLtools set. That tar file has a subdirectory MGLPACKS that comprises many tar files itself, each representing a distinguished Python module. For the packaging of the AutoDockTool kit, the maintainers have decided to package each module individually, to foster the collaboration between similar applications. The maintainers of the Debian package may decide to release interim version from the upstream CVS source repository, instead of waiting for an official release by the upstream developers. For further details on how to prepare the source for the packaging, please refer to http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/BUILD?op=file&rev=0&sc=0 -- Steffen Moeller debian/rules0000755000000000000000000000105311762226702010252 0ustar #!/usr/bin/make -f # -*- makefile -*- # debian/rules for mgltools-gle # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 BRANCH=`cat debian/get-orig-source/current-branch` RCVERSION=`cat debian/get-orig-source/rc-version` SRC=gleDIST PYVERS := $(shell pyversions -vs) %: dh $@ --with python2 override_dh_clean: dh_clean find . -name CVS -a -type d| xargs -r rm -r rm -rf build build-stamp debian/Pmv override_dh_install: dh_install dh_numpy get-orig-source: ./debian/get-orig-source/get-orig-source $(SRC) $(BRANCH) $(RCVERSION) debian/source/0000755000000000000000000000000012152372661010473 5ustar debian/source/format0000644000000000000000000000001411555505004011674 0ustar 3.0 (quilt)