debian/0000755000000000000000000000000012154664440007174 5ustar debian/manpages0000644000000000000000000000002111603401612010667 0ustar debian/runCADD.1 debian/control0000644000000000000000000000566712146437726010623 0ustar Source: mgltools-cadd Section: non-free/science Priority: optional Maintainer: Debian Med Packaging Team 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: >= 2.5 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/cadd/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mgltools/cadd/trunk/ Homepage: http://mgltools.scripps.edu/ Package: mgltools-cadd XB-Python-Version: ${python:Versions} Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, mgltools-vision, mgltools-webservices Description: Computer Aided Drug Discovery (CADD) Pipeline 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. . The Computer Aided Drug Discovery (CADD) Pipeline is a workflow environment designed to support molecular dyanmics simulations and virtual screening experiments for in silico drug discovery, with a special focus on supporting the use of the Relaxed Complex Scheme. It includes web based access to applications such as NAMD, AutoDock, PDB2PQR, APBS, MGLToos and couples them in a flexible and scalable fashion through cloud computing. It is developed as a standalone application, using Vision (https://www.nbcr.net/pub/wiki/index.php?title=MGLTools#Vision) as the backend engine for visual programming and workflow execution. The scientific applications are made accessible through CADD using Opal Web services (https://www.nbcr.net/pub/wiki/index.php?title=Opal) for scalable and distributed computation. . The workflow components of the CADD pipeline are currently released as Vision networks packaged for specific processes in a modular fashion. These modules may be coupled at ease for more complex processes. In the future, they may also be accessible from workflow repositories such as MyExperiment.org, and from AutoDockTools. The Opal services used in the CADD workflow may be accessed using programmatic access, the Opal Server Dashboard or other workflow clients such as Kepler, VisTrails or Taverna through Opal plugins available at Opal Sourceforge website (http://opal.nbcr.net). . Features . * Automatic launching of NAMD simulation on TeraGrid and NBCR resources, including experimental support for migration of simulation between resources. * Selection of representative snapshots/conformations from MD simulations using clustering tools such as QR factorization from VMD and Ptraj from Amber. * Support of Virtual Screening using AutoDock, AutoDock Vina * Support of Relaxed Complex Scheme based Virtual Screening and Rescoring * Visualization and analysis of Virtual Screening hits debian/pycompat0000644000000000000000000000000211603131671010734 0ustar 2 debian/runCADD.10000644000000000000000000000477611603401612010500 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 CADD 1 "July 1, 2011" .\" 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 CADD \- A computer aided drug design using Vision .SH SYNOPSIS .B runCADD .RI [ options ] .RI [ filenames ] .SH DESCRIPTION This manual page is an almost literal translation of the output provided by .B runCADD -h command. .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 A summary of options is included below. For a complete description, refer to the tutorials and documentation that is available online. Files ending in "net.py" will be laoded as networks in vision. Other files will be executed as Python scripts in which "ed" refers to the VisualProgrammingEnvironment instance. .TP .B \-h, \-\-help Show summary of options. .TP .B \-e, \-\-runAndExit run the networks and exit .TP .B \-p, \-\-ipython create an ipython shell instead of a python shell .TP .B \-r, \-\-run run the networks on the command line .TP .B \-s, \-\-noSplash doesn't show the CADD splash screen (works only if registered) .TP .B \-t, \-\-NoTerminal vision provides its own shell (under menu 'Edit') instead of the terminal .TP .B \-\-resourceFolder foldername stores resource file under .name (defaults to .mgltools) .TP port values can be passed on the command line (but not to macros): Network_net.py nodeName:portName:value .\".SH EXAMPLE: .\"display protein as ribbon, non protein as sticks and balls .\"and color by atom type .\".TP .\"pmv \-i \-\-dmode sssb \-\-cmode cr myprot.pdb .\".TP .\"pmv \-i \-m sssb \-c cr myprot.pdb .SH SEE ALSO .BR http://mgltools.scripps.edu .SH AUTHOR runCADD was written by researchers of the Molecular Graphics Lab at the Scripps Institute . .PP This manual page was written by Thorsten Alteholz , for the Debian project (but may be used by others). debian/copyright0000644000000000000000000001117212152154546011130 0ustar This package was debianized by Thorsten Alteholz on Fri, 01 Jul 2011 18:00:00 +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 Anna Omelchenko Sowjanya Karnati Guillaume Vareille Daniel Stoffler Michael F. Sanner Sargis Dallakyan (TSRI) Stefano Forli (TSRI) Ruth Huey (TSRI) Art Olson (TSRI) Nadya Williams (UCSD) Wilfred Li (UCSD) Andy McCammon (UCSD) Jane Ren (UCSD) Rommie Amarao (UCI) Luca Clementi (alumni) Guillaume Vareille (alumni) Copyright: The respective authors and the Scripps Research Institute Copyright 1989-2013 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) 2011, Thorsten Alteholz 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/changelog0000644000000000000000000000340112154664376011054 0ustar mgltools-cadd (1.5.7~rc1~cvs.20130519-2) unstable; urgency=low * debian/rules: remove obsolete file with syntax errors (Closes: #711455) -- Thorsten Alteholz Sat, 08 Jun 2013 17:00:00 +0200 mgltools-cadd (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 * debian/rules: remove x bit from some helper scripts -- Thorsten Alteholz Sun, 19 May 2013 12:00:00 +0200 mgltools-cadd (1.5.6~rc3~cvs.20120206-1) unstable; urgency=low * New upstream version. * debian/control: vcs fields corrected * debian/patches: adapted to new version * debian/rules: adapted to new version -- Thorsten Alteholz Mon, 06 Feb 2012 18:00:00 +0100 mgltools-cadd (1.5.6~rc2+cvs.20111222-1) unstable; urgency=low * New upstream version. * Reduction of modifications in original source tree with extension of already existing override_dh_install. -- Steffen Moeller Thu, 22 Dec 2011 17:10:08 +0100 mgltools-cadd (1.5.6~rc2+cvs.20110926-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Tue, 27 Sep 2011 10:58:09 +0200 mgltools-cadd (1.5.6~rc1+cvs.20110703-1) unstable; urgency=low * New upstream release. -- Steffen Moeller Mon, 11 Jul 2011 00:12:53 +0200 mgltools-cadd (1.5.6~rc1+cvs.20110617-1) unstable; urgency=low * Initial release, contributes to closing ITP #458811. Upstream had created that new module only recently. -- Thorsten Alteholz Sun, 03 Jul 2011 02:20:15 +0200 debian/compat0000644000000000000000000000000211603131671010363 0ustar 8 debian/watch0000644000000000000000000000012511603131671010214 0ustar version=3 http://mgltools.scripps.edu/downloads/.*mgltools_source_([0-9.]+)\.tar\.gz debian/get-orig-source/0000755000000000000000000000000012154664440012207 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/0000755000000000000000000000000012154664440010623 5ustar debian/patches/series0000644000000000000000000000004411716247415012040 0ustar fix_shebangs.patch remove_ksh.patch debian/patches/remove_ksh.patch0000644000000000000000000002155711716247415014022 0ustar Description: replace ksh by python Author: Thorsten Alteholz Last-Update: 2012-02-13 Index: mgltools-cadd-1.5.6.org/CADD/workflows/visualization/visualization_0.1.1_pmvnet.py =================================================================== --- mgltools-cadd-1.5.6.org/CADD/workflows/visualization/visualization_0.1.1_pmvnet.py 2012-02-13 18:55:53.000000000 +0200 +++ mgltools-cadd-1.5.6.org/CADD/workflows/visualization/visualization_0.1.1_pmvnet.py 2012-02-13 18:56:35.000000000 +0200 @@ -1,4 +1,4 @@ -#!/bin/ksh ~/.mgltools/pythonsh +#!/usr/bin/python ######################################################################## # # Vision Network - Python source code - file generated by vision Index: mgltools-cadd-1.5.6.org/CADD/workflows/MDanalysis/NAMDNBCR_0.1_net.py =================================================================== --- mgltools-cadd-1.5.6.org/CADD/workflows/MDanalysis/NAMDNBCR_0.1_net.py 2011-07-06 18:55:53.000000000 +0200 +++ mgltools-cadd-1.5.6.org/CADD/workflows/MDanalysis/NAMDNBCR_0.1_net.py 2011-07-06 18:56:35.000000000 +0200 @@ -1,4 +1,4 @@ -#!/bin/ksh ~/.mgltools/pythonsh +#!/usr/bin/python ######################################################################## # # Vision Network - Python source code - file generated by vision Index: mgltools-cadd-1.5.6.org/CADD/workflows/MDanalysis/GROMOSClustering_0.1_net.py =================================================================== --- mgltools-cadd-1.5.6.org/CADD/workflows/MDanalysis/GROMOSClustering_0.1_net.py 2011-07-06 18:55:53.000000000 +0200 +++ mgltools-cadd-1.5.6.org/CADD/workflows/MDanalysis/GROMOSClustering_0.1_net.py 2011-07-06 18:56:35.000000000 +0200 @@ -1,4 +1,4 @@ -#!/bin/ksh ~/.mgltools/pythonsh +#!/usr/bin/python ######################################################################## # # Vision Network - Python source code - file generated by vision Index: mgltools-cadd-1.5.6.org/CADD/workflows/MDanalysis/NAMDTeragrid_0.1_net.py =================================================================== --- mgltools-cadd-1.5.6.org/CADD/workflows/MDanalysis/NAMDTeragrid_0.1_net.py 2011-07-06 18:55:53.000000000 +0200 +++ mgltools-cadd-1.5.6.org/CADD/workflows/MDanalysis/NAMDTeragrid_0.1_net.py 2011-07-06 18:56:35.000000000 +0200 @@ -1,4 +1,4 @@ -#!/bin/ksh ~/.mgltools/pythonsh +#!/usr/bin/python ######################################################################## # # Vision Network - Python source code - file generated by vision Index: mgltools-cadd-1.5.6.org/CADD/workflows/MDanalysis/TrajQRClustering_0.1_net.py =================================================================== --- mgltools-cadd-1.5.6.org/CADD/workflows/MDanalysis/TrajQRClustering_0.1_net.py 2011-07-06 18:55:53.000000000 +0200 +++ mgltools-cadd-1.5.6.org/CADD/workflows/MDanalysis/TrajQRClustering_0.1_net.py 2011-07-06 18:56:35.000000000 +0200 @@ -1,4 +1,4 @@ -#!/bin/ksh ~/.mgltools/pythonsh +#!/usr/bin/python ######################################################################## # # Vision Network - Python source code - file generated by vision Index: mgltools-cadd-1.5.6.org/CADD/workflows/MDanalysis/AMDNBCR_0.2_net.py =================================================================== --- mgltools-cadd-1.5.6.org/CADD/workflows/MDanalysis/AMDNBCR_0.2_net.py 2011-07-06 18:55:53.000000000 +0200 +++ mgltools-cadd-1.5.6.org/CADD/workflows/MDanalysis/AMDNBCR_0.2_net.py 2011-07-06 18:56:35.000000000 +0200 @@ -1,4 +1,4 @@ -#!/bin/ksh ~/.mgltools/pythonsh +#!/usr/bin/python ######################################################################## # # Vision Network - Python source code - file generated by vision Index: mgltools-cadd-1.5.6.org/CADD/workflows/docking/AutoDockSL_0.1_net.py =================================================================== --- mgltools-cadd-1.5.6.org/CADD/workflows/docking/AutoDockSL_0.1_net.py 2011-07-06 18:55:53.000000000 +0200 +++ mgltools-cadd-1.5.6.org/CADD/workflows/docking/AutoDockSL_0.1_net.py 2011-07-06 18:56:35.000000000 +0200 @@ -1,4 +1,4 @@ -#!/bin/ksh ~/.mgltools/pythonsh +#!/usr/bin/python ######################################################################## # # Vision Network - Python source code - file generated by vision Index: mgltools-cadd-1.5.6.org/CADD/workflows/docking/AutoGrid_0.1_net.py =================================================================== --- mgltools-cadd-1.5.6.org/CADD/workflows/docking/AutoGrid_0.1_net.py 2011-07-06 18:55:53.000000000 +0200 +++ mgltools-cadd-1.5.6.org/CADD/workflows/docking/AutoGrid_0.1_net.py 2011-07-06 18:56:35.000000000 +0200 @@ -1,4 +1,4 @@ -#!/bin/ksh ~/.mgltools/pythonsh +#!/usr/bin/python ######################################################################## # # Vision Network - Python source code - file generated by vision Index: mgltools-cadd-1.5.6.org/CADD/workflows/docking/PrepareReceptor_0.1_net.py =================================================================== --- mgltools-cadd-1.5.6.org/CADD/workflows/docking/PrepareReceptor_0.1_net.py 2011-07-06 18:55:53.000000000 +0200 +++ mgltools-cadd-1.5.6.org/CADD/workflows/docking/PrepareReceptor_0.1_net.py 2011-07-06 18:56:35.000000000 +0200 @@ -1,4 +1,4 @@ -#!/bin/ksh ~/.mgltools/pythonsh +#!/usr/bin/python ######################################################################## # # Vision Network - Python source code - file generated by vision Index: mgltools-cadd-1.5.6.org/CADD/workflows/virtualScreening/AutoDockML_0.1_net.py =================================================================== --- mgltools-cadd-1.5.6.org/CADD/workflows/virtualScreening/AutoDockML_0.1_net.py 2011-07-06 18:55:53.000000000 +0200 +++ mgltools-cadd-1.5.6.org/CADD/workflows/virtualScreening/AutoDockML_0.1_net.py 2011-07-06 18:56:35.000000000 +0200 @@ -1,4 +1,4 @@ -#!/bin/ksh ~/.mgltools/pythonsh +#!/usr/bin/python ######################################################################## # # Vision Network - Python source code - file generated by vision Index: mgltools-cadd-1.5.6.org/CADD/workflows/virtualScreening/AutoDockVSpublic_0.1_net.py =================================================================== --- mgltools-cadd-1.5.6.org/CADD/workflows/virtualScreening/AutoDockVSpublic_0.1_net.py 2011-07-06 18:55:53.000000000 +0200 +++ mgltools-cadd-1.5.6.org/CADD/workflows/virtualScreening/AutoDockVSpublic_0.1_net.py 2011-07-06 18:56:35.000000000 +0200 @@ -1,4 +1,4 @@ -#!/bin/ksh ~/.mgltools/pythonsh +#!/usr/bin/python ######################################################################## # # Vision Network - Python source code - file generated by vision Index: mgltools-cadd-1.5.6.org/CADD/workflows/virtualScreening/VinaVSlocal_0.1_net.py =================================================================== --- mgltools-cadd-1.5.6.org/CADD/workflows/virtualScreening/VinaVSlocal_0.1_net.py 2011-07-06 18:55:53.000000000 +0200 +++ mgltools-cadd-1.5.6.org/CADD/workflows/virtualScreening/VinaVSlocal_0.1_net.py 2011-07-06 18:56:35.000000000 +0200 @@ -1,4 +1,4 @@ -#!/bin/ksh ~/.mgltools/pythonsh +#!/usr/bin/python ######################################################################## # # Vision Network - Python source code - file generated by vision Index: mgltools-cadd-1.5.6.org/CADD/workflows/virtualScreening/VinaVSpublic_0.1_net.py =================================================================== --- mgltools-cadd-1.5.6.org/CADD/workflows/virtualScreening/VinaVSpublic_0.1_net.py 2011-07-06 18:55:53.000000000 +0200 +++ mgltools-cadd-1.5.6.org/CADD/workflows/virtualScreening/VinaVSpublic_0.1_net.py 2011-07-06 18:56:35.000000000 +0200 @@ -1,4 +1,4 @@ -#!/bin/ksh ~/.mgltools/pythonsh +#!/usr/bin/python ######################################################################## # # Vision Network - Python source code - file generated by vision Index: mgltools-cadd-1.5.6.org/CADD/workflows/virtualScreening/AutoDockVSlocal_0.1_net.py =================================================================== --- mgltools-cadd-1.5.6.org/CADD/workflows/virtualScreening/AutoDockVSlocal_0.1_net.py 2011-07-06 18:55:53.000000000 +0200 +++ mgltools-cadd-1.5.6.org/CADD/workflows/virtualScreening/AutoDockVSlocal_0.1_net.py 2011-07-06 18:56:35.000000000 +0200 @@ -1,4 +1,4 @@ -#!/bin/ksh ~/.mgltools/pythonsh +#!/usr/bin/python ######################################################################## # # Vision Network - Python source code - file generated by vision Index: mgltools-cadd-1.5.6.org/CADD/workflows/visualization/VSResults_0.1_pmvnet.py =================================================================== --- mgltools-cadd-1.5.6.org/CADD/workflows/visualization/VSResults_0.1_pmvnet.py 2011-07-06 18:55:53.000000000 +0200 +++ mgltools-cadd-1.5.6.org/CADD/workflows/visualization/VSResults_0.1_pmvnet.py 2011-07-06 18:56:35.000000000 +0200 @@ -1,4 +1,4 @@ -#!/bin/ksh ~/.mgltools/pythonsh +#!/usr/bin/python ######################################################################## # # Vision Network - Python source code - file generated by vision debian/patches/fix_shebangs.patch0000644000000000000000000000222211716247415014304 0ustar Description: drop hardcoded python2.x dependency Author: Thorsten Alteholz Last-Update: 2012-02-13 Index: mgltools-cadd-1.5.6/CADD/bin/CADD =================================================================== --- mgltools-cadd-1.5.6.org/CADD/bin/CADD 2011-07-01 18:08:38.000000000 +0200 +++ mgltools-cadd-1.5.6/CADD/bin/CADD 2011-07-01 18:09:47.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.5 +#!/usr/bin/env python # # $Header: /opt/cvs/CADD/bin/CADD,v 1.2 2011/01/18 00:56:07 nadya Exp $ # $Id: CADD,v 1.2 2011/01/18 00:56:07 nadya Exp $ Index: mgltools-cadd-1.5.6/setup.py =================================================================== --- mgltools-cadd-1.5.6.org/setup.py 2011-07-01 18:24:45.000000000 +0200 +++ mgltools-cadd-1.5.6/setup.py 2011-07-01 18:25:10.000000000 +0200 @@ -43,7 +43,7 @@ forig = open(script+".py", "r") txt = forig.readlines() forig.close() - fnew.write("#!/usr/bin/env python2.5\n") + fnew.write("#!/usr/bin/env python\n") fnew.writelines(txt) fnew.close() build_scripts.copy_scripts(self) debian/README.Debian0000644000000000000000000000261111603131671011226 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.source0000644000000000000000000000155211603131671011347 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/rules0000755000000000000000000000154312154664376010267 0ustar #!/usr/bin/make -f # -*- makefile -*- # debian/rules for mgltools-volume # 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=CADDDIST %: dh $@ --with python2 override_dh_install: dh_install # remove some obsolete file, change if file vanishes upstream rm $(CURDIR)/debian/mgltools-cadd/usr/lib/python2.7/dist-packages/CADD/Raccoon2/RaccoonTools.py find $(CURDIR)/debian/mgltools-cadd -name runCADD | xargs -r chmod 755 find $(CURDIR)/debian/mgltools-cadd -name *.prm -o -name *.res | xargs -r chmod -x find $(CURDIR)/debian/mgltools-cadd -name raccoonLauncher | xargs -r chmod -x find $(CURDIR)/debian/mgltools-cadd -name *.bat | xargs -r chmod -x get-orig-source: ./debian/get-orig-source/get-orig-source $(SRC) $(BRANCH) $(RCVERSION) debian/source/0000755000000000000000000000000012154664440010474 5ustar debian/source/format0000644000000000000000000000001411603401612011666 0ustar 3.0 (quilt)