debian/0000755000000000000000000000000012152157203007164 5ustar debian/control0000644000000000000000000000240012146437726010601 0ustar Source: mgltools-mglutil 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) Standards-Version: 3.9.4 XS-Python-Version: >= 2.6 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/mglutil/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mgltools/mglutil/trunk/ Homepage: http://mgltools.scripps.edu/ Package: mgltools-mglutil XB-Python-Version: ${python:Versions} Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, mgltools-sff, python-pmw, python-zsi (>= 2.0), idle|idle-python2.6 Recommends: qhull-bin Suggests: tcsh Description: Molecular Graphics Laboratory utility collection 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 is needed by mgltools-autodocktools at runtime, providing a series of utility functions on from parallel programming to statistics. debian/pycompat0000644000000000000000000000000210732553645010747 0ustar 2 debian/copyright0000644000000000000000000002007612152154546011133 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 Guillaume Vareille Michel Sanner Sophie I. Coon William Lindstrom Daniel Stoffler Sowjanya Karnati Yong Zhao mglutil/process.py Peter Astrand mglutil/math/TensorModule.py and mglutil/math/VectorModule.py Konrad Hinsen /mglutil/regression/testplus*.py Frederic Giacometti Copyright: The respective authors and the Scripps Research Institute Copyright 2000-2013 Michael Sanner mglutil/process.py is Copyright (c) 2003-2004 by Peter Astrand mglutil/math/TensorModule.py and mglutil/math/VectorModule.py are Copyright 1997-1999 by Konrad Hinsen /mglutil/regression/testplus*.py Copyright (C) 2002 Frederic Bruno Giacometti . All Rights Reserved. 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. An exceptional license was given for mglutil/process.py: By obtaining, using, and/or copying this software and/or its associated documentation, you agree that you have read, understood, and will comply with the following terms and conditions: Permission to use, copy, modify, and distribute this software and its associated documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appears in all copies, and that both that copyright notice and this permission notice appear in supporting documentation, and that the name of the author not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. mglutil/math/{Tensor,Vector}Module.py have a special license Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation. THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. and for mglutil/regression/testplus.py mglutil/regression/testplus_before_2_1.py the license is The contents of this file are subject to the Mozilla Publics License Version 1.1 (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.mozilla.org/MPL/ Software distributed under the License is distributed on an "AS IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for the specific language governing rights and limitations under the License. The Initial Developer of the Original Code is Frederic Bruno Giacometti. Portions created by Frederic Bruno Giacometti are Copyright (C) 2002 Frederic Bruno Giacometti. All Rights Reserved. Contributor: Frederic Giacometti, frederic.giacometti@arakne.com 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/changelog0000644000000000000000000000610312152154546011045 0ustar mgltools-mglutil (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-mglutil (1.5.6~rc3~cvs.20120206-2) UNRELEASED; urgency=low * debian/control: Fix Vcs fields -- Andreas Tille Thu, 14 Jun 2012 22:14:49 +0200 mgltools-mglutil (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-mglutil (1.5.6~rc2+cvs.20111222-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Thu, 22 Dec 2011 17:10:09 +0100 mgltools-mglutil (1.5.6~rc2+cvs.20110926-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Tue, 27 Sep 2011 10:58:11 +0200 mgltools-mglutil (1.5.6~rc1+cvs.20110617-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Fri, 17 Jun 2011 01:22:38 +0200 mgltools-mglutil (1.5.4.cvs.20100912-2) unstable; urgency=low * Debhelper 8 (control+compat) * debian/control: - Build-Depends: python-all (>= 2.6) to enable python-support2 Closes: 616891 * debian/rules: switch to short dh syntax which makes dh_python2 easy -- Andreas Tille Tue, 03 May 2011 14:07:16 +0200 mgltools-mglutil (1.5.4.cvs.20100912-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Sun, 12 Sep 2010 00:20:31 +0200 mgltools-mglutil (1.5.4.cvs.20090603-1.1) unstable; urgency=low * Non-maintainer upload. * Add fix_shebangs.patch to drop hardcoded pythoh2.5 dependency * Add fix_assertion.patch to fix compatibility with Python 2.6 * Allow byte-compilation for Python >= 2.5 (closes: 586840) -- Piotr Ożarowski Wed, 30 Jun 2010 20:35:25 +0200 mgltools-mglutil (1.5.4.cvs.20090603-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Wed, 03 Jun 2009 11:48:21 +0200 mgltools-mglutil (1.5.4.cvs.20090528-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Sat, 16 May 2009 00:51:24 +0200 mgltools-mglutil (1.5.4.cvs.20090514-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Thu, 14 May 2009 21:46:35 +0200 mgltools-mglutil (1.5.4.cvs.20081126-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Wed, 26 Nov 2008 14:43:12 +0100 mgltools-mglutil (1.5.2.cvs.20081109-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Sun, 09 Nov 2008 15:02:32 +0100 mgltools-mglutil (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/compat0000644000000000000000000000000211557774677010416 0ustar 8 debian/watch0000644000000000000000000000012511041154457010217 0ustar version=3 http://mgltools.scripps.edu/downloads/.*mgltools_source_([0-9.]+)\.tar\.gz debian/get-orig-source/0000755000000000000000000000000012152157203012177 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/0000755000000000000000000000000012152157203010613 5ustar debian/patches/fix_assertion.patch0000644000000000000000000000117311573460123014517 0ustar Description: fix compatibility with Python 2.6 Author: Piotr Ożarowski Last-Update: 2010-06-30 Index: mgltools-mglutil-1.5.4.cvs.20090603/mglutil/math/Tests/test_matToAxis.py =================================================================== --- mgltools-mglutil-1.5.4.cvs.20090603.orig/mglutil/math/Tests/test_matToAxis.py +++ mgltools-mglutil-1.5.4.cvs.20090603/mglutil/math/Tests/test_matToAxis.py @@ -33,7 +33,7 @@ def rotateObject(): for i in range(len(m1)): if fabs(m1[i]-m2[i]) > 1e-4: bSame = False - assert (bSame, True) + assert bSame, True def test_rotateObject(): debian/patches/series0000644000000000000000000000004711573460123012035 0ustar fix_assertion.patch fix_shebangs.patch debian/patches/fix_shebangs.patch0000644000000000000000000000253611573460123014306 0ustar Description: drop hardcoded pythoh2.5 dependency Author: Piotr Ożarowski Last-Update: 2010-06-30 Index: mgltools-mglutil-1.5.4.cvs.20090603/mglutil/TestUtil/bin/publish =================================================================== --- mgltools-mglutil-1.5.4.cvs.20090603.orig/mglutil/TestUtil/bin/publish +++ mgltools-mglutil-1.5.4.cvs.20090603/mglutil/TestUtil/bin/publish @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.5 +#!/usr/bin/env python # from optparse import OptionParser import time, sys, os, string Index: mgltools-mglutil-1.5.4.cvs.20090603/mglutil/TestUtil/bin/tester =================================================================== --- mgltools-mglutil-1.5.4.cvs.20090603.orig/mglutil/TestUtil/bin/tester +++ mgltools-mglutil-1.5.4.cvs.20090603/mglutil/TestUtil/bin/tester @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.5 +#!/usr/bin/env python # import sys print "running Python:", sys.executable Index: mgltools-mglutil-1.5.4.cvs.20090603/mglutil/TestUtil/publishPack.csh =================================================================== --- mgltools-mglutil-1.5.4.cvs.20090603.orig/mglutil/TestUtil/publishPack.csh +++ mgltools-mglutil-1.5.4.cvs.20090603/mglutil/TestUtil/publishPack.csh @@ -1,4 +1,4 @@ -#!/bin/tcsh +#!/usr/bin/tcsh # 1) go to the mgl version of the packages # cd /mgl/python/share/lib/python2.5/site-packages/ debian/README.Debian0000644000000000000000000000261111557774677011261 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/mgltools-mglutil.lintian-overrides0000644000000000000000000000016611573460123016066 0ustar # the license is in debian/copyright but upstream wants to have it there as well mgltools-mglutil: extra-license-file 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/rules0000755000000000000000000000142511600425310010240 0ustar #!/usr/bin/make -f # -*- makefile -*- # debian/rules for mgltools-util # 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=mglutilDIST PYVERS := $(shell pyversions -vs) %: dh $@ --with python2 override_dh_clean: dh_clean find . -name CVS -a -type d| xargs -r rm -r find . -name "*.gif" | xargs -r chmod -x find . -name "*.csh" -o -name "getlatest" | xargs -r chmod +x rm -rf build build-stamp debian/mglutil override_dh_install: dh_install # this file is not needed and gives a lintian warning, so go away find debian -name publishPack.csh -a -type f| xargs -r rm -r get-orig-source: ./debian/get-orig-source/get-orig-source $(SRC) $(BRANCH) $(RCVERSION) debian/source/0000755000000000000000000000000012152157203010464 5ustar debian/source/format0000644000000000000000000000001411443176034011677 0ustar 3.0 (quilt)