debian/0000755000000000000000000000000012152161707007170 5ustar debian/runVision.10000644000000000000000000000232111203100456011232 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 VISION 1 "2009 May 14" .\" 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 vision \- workflows for cheminformatics and other applications .SH SYNOPSIS .B vision .SH DESCRIPTION Vision is a tool for establishing automated workflows. It is developed and used for cheminformatics, i.e. the in silico screening for functional compounds, but is applicable also for other applications. .SH SEE ALSO .BR http://mgltools.scripps.edu .SH AUTHOR This manual page was written for the Debian project by the Debian package's maintainer with the hope to have stimulated the developers to provide of a more substantial version. debian/manpages0000644000000000000000000000002311203100456010667 0ustar debian/runVision.1 debian/control0000644000000000000000000000253712146437726010614 0ustar Source: mgltools-vision Section: non-free/science Priority: optional Maintainer: Debian Med Packaging Team XS-Autobuild: yes Uploaders: Steffen Moeller , Sargis Dallakyan , Andreas Tille , Thorsten Alteholz Build-Depends: debhelper (>= 8), python-all (>= 2.6), python-numpy Standards-Version: 3.9.4 XS-Python-Version: >= 2.5 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/vision/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mgltools/vision/trunk/ Homepage: http://mgltools.scripps.edu/ Package: mgltools-vision XB-Python-Version: ${python:Versions} Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, mgltools-networkeditor, mgltools-mglutil, idle|idle-python2.6, mgltools-support Enhances: autodocktools Description: Python-based Visual Programming Environment 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. . Vision is a visual-programming environment in which a user can interactively build networks describing novel combinations of computational methods, and yielding new visualizations of their data without actually writing code. debian/pycompat0000644000000000000000000000000210733046640010740 0ustar 2 debian/copyright0000644000000000000000000001054312152154546011131 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: The main development is performed by the researchers and developers at the Molecular Graphics Laboratory led by Michael F. Sanner with contributions by Daniel Stoffler Michael F. Sanner Guillaume Vareille and the singular external contribution by Natalie Rubin Copyright: The respective authors and the Scripps Research Institute Copyright 2000-2013 Michael Sanner License: All files distributed or redistributed in this package are subject to the here presented license, regardless of the information that is explicitly stated or omitted in the respective files themselves. The original copyright holders have made respective agreements regarding this redistribution. 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. The Debian packaging is Copyright (C) 2007-2008, Steffen Moeller and is licensed under the GPL, see '/usr/share/common-licenses/GPL'. 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/changelog0000644000000000000000000001037112152154546011047 0ustar mgltools-vision (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-vision (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 * debian/control: python-numpy dependency added -- Thorsten Alteholz Fri, 01 Jun 2012 18:00:00 +0200 mgltools-vision (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-vision (1.5.6~rc2+cvs.20111222-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Thu, 22 Dec 2011 17:10:13 +0100 mgltools-vision (1.5.6~rc2+cvs.20110926-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Tue, 27 Sep 2011 10:58:16 +0200 mgltools-vision (1.5.6~rc1+cvs.20110625-1) unstable; urgency=low * using current source from cvs * debian/control: dependency on mgltools-support added (Closes: #532361) * debian/control: typo corrected to add dependency on idle -- Thorsten Alteholz Sat, 25 Jun 2011 14:20:32 +0200 mgltools-vision (1.5.6~rc1+cvs.20110617-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Fri, 17 Jun 2011 01:20:32 +0200 mgltools-vision (1.5.6~rc1+cvs.20110615-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Thu, 16 Jun 2011 21:50:30 +0200 mgltools-vision (1.5.4.cvs.20100912-2) unstable; urgency=low [ Thorsten Alteholz ] * Build-Depends: debhelper (>= 8) * debian/source/format: 3.0 (quilt) * debian/control: Build-Depends: python-all (>= 2.6) to enable python-support2 * debian/rules: switch to short dh syntax which makes dh_python2 easy (Closes: #616905) * Suppress lintian warning about duplicate license file [ Andreas Tille ] * debian/compat: 8 * debian/rules: Changes of permissions only in install target -- Andreas Tille Fri, 10 Jun 2011 11:50:06 +0200 mgltools-vision (1.5.4.cvs.20100912-1.1) unstable; urgency=low * Non-maintainer upload. * debian/patches/unversioned_shebang.patch: - Do not use versioned shebangs (Closes: #602243). -- Luca Falavigna Mon, 09 May 2011 21:30:41 +0200 mgltools-vision (1.5.4.cvs.20100912-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Sun, 12 Sep 2010 00:20:31 +0200 mgltools-vision (1.5.4.cvs.20090603-2) UNRELEASED; urgency=low * debian/control: - Enhances: autodocktools - debhelper 7 - Standards-Version: 3.8.3 (no changes needed) -- Andreas Tille Fri, 16 Oct 2009 22:31:10 +0200 mgltools-vision (1.5.4.cvs.20090603-1.1) unstable; urgency=low * Non-maintainer upload. * Allow byte-compilation for Python >= 2.5 (closes: 586851) -- Piotr Ożarowski Fri, 09 Jul 2010 23:55:58 +0200 mgltools-vision (1.5.4.cvs.20090603-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Wed, 03 Jun 2009 11:48:26 +0200 mgltools-vision (1.5.4.cvs.20090528-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Sat, 16 May 2009 00:51:34 +0200 mgltools-vision (1.5.4.cvs.20090514-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Thu, 14 May 2009 21:46:48 +0200 mgltools-vision (1.5.4.cvs.20081126-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Wed, 26 Nov 2008 14:43:22 +0100 mgltools-vision (1.5.2.cvs.20081109-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Sun, 09 Nov 2008 15:02:42 +0100 mgltools-vision (1.5.2.cvs.20080731-1) unstable; urgency=low * Initial release, contributes to closing ITP #458811. -- Steffen Moeller Thu, 31 Jul 2008 22:00:08 +0200 debian/compat0000644000000000000000000000000211574370451010373 0ustar 8 debian/watch0000644000000000000000000000012511041154457010217 0ustar version=3 http://mgltools.scripps.edu/downloads/.*mgltools_source_([0-9.]+)\.tar\.gz debian/mgltools-vision.lintian-overrides0000644000000000000000000000016511573211757015726 0ustar # the license is in debian/copyright but upstream wants to have it there as well mgltools-vision: extra-license-file debian/get-orig-source/0000755000000000000000000000000012152161707012203 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/patches/0000755000000000000000000000000012152161707010617 5ustar debian/patches/series0000644000000000000000000000003211573211757012036 0ustar unversioned_shebang.patch debian/patches/unversioned_shebang.patch0000644000000000000000000000217511573211757015704 0ustar Description: remove version from path to python interpreter Author: Luca Falavigna Last-Update: 2011-05-09 Index: mgltools-vision-1.5.4.cvs.20100912/setup.py =================================================================== --- mgltools-vision-1.5.4.cvs.20100912//setup.py 2007-09-28 19:55:27.000000000 +0200 +++ mgltools-vision-1.5.4.cvs.20100912.new//setup.py 2011-05-09 21:29:52.563352863 +0200 @@ -43,7 +43,7 @@ forig = open(script+".py", "r") txt = forig.readlines() forig.close() - fnew.write("#!/usr/bin/env python2.4\n") + fnew.write("#!/usr/bin/python\n") fnew.writelines(txt) fnew.close() build_scripts.copy_scripts(self) Index: mgltools-vision-1.5.4.cvs.20100912/Vision/bin/vision =================================================================== --- mgltools-vision-1.5.4.cvs.20100912/Vision/bin/vision 2007-10-30 22:22:10.000000000 +0100 +++ mgltools-vision-1.5.4.cvs.20100912.new/Vision/bin/vision 2011-05-09 21:29:35.735352874 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.5 +#!/usr/bin/python # import sys debian/README.Debian0000644000000000000000000000330711572471434011242 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. This MolKit package has a few issues with the pdb2pqr conversion tool that it ships with it. That tool however is currently being packaged for Debian independently from this effort and the expectation is that the sources for this package will be simplified respectively once that this other package hits the mirrors. -- 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/dirs0000644000000000000000000000002210733046640010047 0ustar usr/bin usr/share debian/rules0000755000000000000000000000105411762226702010253 0ustar #!/usr/bin/make -f # -*- makefile -*- # debian/rules for mgltools-vision # 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=VisionDIST %: dh $@ --with python2 override_dh_install: dh_install dh_numpy find debian -name "runVision" | xargs -r chmod +x find debian -name *.jpg -o -name *.png -o -name *.pdb -o -name *.gif | xargs -r chmod 644 get-orig-source: ./debian/get-orig-source/get-orig-source $(SRC) $(BRANCH) $(RCVERSION) debian/source/0000755000000000000000000000000012152161707010470 5ustar debian/source/format0000644000000000000000000000001411572471434011704 0ustar 3.0 (quilt)