debian/0000755000000000000000000000000012152425160007164 5ustar debian/manpages0000644000000000000000000000004411614742512010705 0ustar debian/runAdt.1 debian/autoligand.1 debian/control0000644000000000000000000000325512146437726010612 0ustar Source: autodocktools 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 (>= 2.6) Standards-Version: 3.9.4 XS-Python-Version: >= 2.5 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/autodocktools/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mgltools/autodocktools/trunk/ Homepage: http://autodock.scripps.edu/ Package: autodocktools Architecture: all Depends: ${misc:Depends}, ${python:Depends}, mgltools-pmv, mgltools-molkit, mgltools-volume, mgltools-support, python-imaging-tk, mgltools-viewerframework Recommends: mgltools-pyautodock, mgltools-utpackages, mgltools-webservices Suggests: autodock, autodock-vina, ballview, mgltools-cadd Description: GUI to help set up, launch and analyze AutoDock dockings 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. . AutoDock is a well established package for the automated screening of libraries of formal representation of chemical compounds that putatively bind to a particular protein at hand. This package provides a graphical user interface that is helping with the preparation of the protein for such analyses. . The tool AutoLigand, which may help to constrain the location of the binding pocket for yet undescribed proteins, is accompanying the main executable 'runAdt'. debian/copyright0000644000000000000000000001104412152154546011126 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 Ruth Huey Garrett M. Morris David S. Goodsell Arthur J. Olson Sargis Dallakyan Rodney Harris William Lindstrom Konrad Hinsen John E. Grayson Sowjanya Karnati Sandro Cosconati Daniel Stoffler Michael F. Sanner 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) 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/changelog0000644000000000000000000000772712152154546011062 0ustar autodocktools (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 autodocktools (1.5.6~rc3~cvs.20120206-2) UNRELEASED; urgency=low * debian/upstream: Enhanced citation information -- Andreas Tille Sat, 31 Mar 2012 09:11:38 +0200 autodocktools (1.5.6~rc3~cvs.20120206-1) unstable; urgency=low * New upstream version. -- Thorsten Alteholz Mon, 06 Feb 2012 18:00:00 +0100 autodocktools (1.5.6~rc2+cvs.20111222-1) unstable; urgency=low * New upstream version. * Indentiation error was adopted by upstream, uncommented patch -- Steffen Moeller Thu, 22 Dec 2011 17:10:07 +0100 autodocktools (1.5.6~rc2+cvs.20110926-2) UNRELEASED; urgency=low * Fixed VCS fields in debian/control and debian/README.source -- Andreas Tille Wed, 07 Dec 2011 11:03:54 +0100 autodocktools (1.5.6~rc2+cvs.20110926-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Tue, 27 Sep 2011 10:58:09 +0200 autodocktools (1.5.6~rc1+cvs.20110617-2) UNRELEASED; urgency=low * New upload (lp: #623984) * Added suggests on mgltools-cadd. * Explicitly mentioning the tool AutoLigand. Further work needed. -- Steffen Moeller Fri, 17 Jun 2011 01:20:14 +0200 autodocktools (1.5.6~rc1+cvs.20110617-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Fri, 17 Jun 2011 01:20:14 +0200 autodocktools (1.5.4.cvs.20100912-3) unstable; urgency=low * Added myself to Uploaders * Debhelper 8 (control+compat) * debian/source/format: 3.0 (quilt) * debian/control: Build-Depends: python (>= 2.6) to enable python-support2 * debian/rules: switch to short dh syntax which makes dh_python2 easy Closes: #616740 * debian/pycompat: removed * debian/rules: - Make sure build process will not introduce unwanted versioned Python interpreter - Clean target remove copy of runAdt which is created in build process -- Andreas Tille Wed, 06 Apr 2011 23:08:06 +0200 autodocktools (1.5.4.cvs.20100912-2) unstable; urgency=low * Removed dependency on mgltools-scenario2, which will only be relevant for the upcoming 1.5.6 version. -- Steffen Moeller Sun, 26 Sep 2010 23:43:49 +0200 autodocktools (1.5.4.cvs.20100912-1) unstable; urgency=low * Added symbolic links to the default installation, i.e. autodocktools -> runAdt . * New upstream version. -- Steffen Moeller Sun, 12 Sep 2010 00:20:31 +0200 autodocktools (1.5.4.cvs.20090603-2) UNRELEASED; urgency=low * Documented informations in ‘debian/upstream-metadata.yaml’. -- Charles Plessy Sun, 03 Jan 2010 22:55:36 +0900 autodocktools (1.5.4.cvs.20090603-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Wed, 03 Jun 2009 11:48:19 +0200 autodocktools (1.5.4.cvs.20090528-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Thu, 28 May 2009 21:41:38 +0200 autodocktools (1.5.4.cvs.20090514-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Thu, 14 May 2009 21:46:30 +0200 autodocktools (1.5.4.cvs.20081126-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Wed, 26 Nov 2008 14:43:08 +0100 autodocktools (1.5.2.cvs.20081109-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Sun, 09 Nov 2008 15:02:28 +0100 autodocktools (1.5.2.cvs.20080731-1) unstable; urgency=low * Initial release (Closes: #458811). -- Steffen Moeller Thu, 31 Jul 2008 21:59:54 +0200 debian/compat0000644000000000000000000000000211547277203010374 0ustar 8 debian/autodocktools.links0000644000000000000000000000026211614742512013125 0ustar /usr/bin/runAdt /usr/bin/autodocktools /usr/share/man/man1/runAdt.1.gz /usr/share/man/man1/autodocktools.1.gz /usr/share/pyshared/AutoDockTools/AutoLigand.py /usr/bin/autoligand debian/watch0000644000000000000000000000012511041154457010217 0ustar version=3 http://mgltools.scripps.edu/downloads/.*mgltools_source_([0-9.]+)\.tar\.gz debian/upstream0000644000000000000000000000215711752274242010764 0ustar Donation: http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/ Homepage: http://autodock.scripps.edu/ Name: AutoDockTools Reference: - Author: Garrett M. Morris and Ruth Huey and William Lindstrom and Michel F. Sanner and Richard K. Belew and David S. Goodsell and Arthur J. Olson Title: > AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility Journal: Journal of Computational Chemistry Volume: 30 Number: 16 Pages: 2785-2791 Year: 2009 PMID: 19399780 DOI: 10.1002/jcc.21256 URL: http://www3.interscience.wiley.com/journal/122365050/abstract - Author: Rodney Harris and Arthur J Olson and David S Goodsell Title: > Automated prediction of ligand-binding sites in proteins. Journal: Proteins Year: 2008 Volume: 70 Number: 4 Pages: 1506-1517 PMID: 17910060 DOI: 10.1002/prot.21645 URL: http://onlinelibrary.wiley.com/doi/10.1002/prot.21645/abstract Registration: http://autodock.scripps.edu/downloads/autodock-registration Watch: http://mgltools.scripps.edu/downloads/.*mgltools_source_([0-9.]+)\.tar\.gz debian/get-orig-source/0000755000000000000000000000000012152425160012177 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/docs0000644000000000000000000000002710732553370010045 0ustar AutoDockTools/RELNOTES debian/autoligand.10000644000000000000000000000357711714542662011423 0ustar .\" PLEASE MODIFY THIS FILE! It is still somewhat ugly." .TH AUTOLIGAND "1" "July 2011" "AutoLigand" "User Commands" .SH NAME AutoLigand: \- identification of a receptor's ligand binding site .SH SYNOPSIS It is suggested to start AutoLigand through the GUI that the autodocktools provide. .BR .B autoligand \f-r FileBaseName \-p #_of_pts\fR .BR The above is a simplification provided for the Debian package. The regular command line invocation is through .BR python /usr/share/pyshared/AutoDockTools/AutoLigand.py \fB\-r\fR FileBaseName \fB\-p\fR #_of_pts .SH DESCRIPTION .I autoligand is a symbolic link to the Python script AutoLigand.py. That performs a an automated investigation of the likelihood of a particular part of a protein to bind to ligands. .IP Description of command... .HP \fB\-r\fR FileBaseName = just the name part from receptor map files (i.e., FileBaseName.C.map) .HP \fB\-p\fR #_of_pts = number of fill points to use (int) .IP Note: can be omitted if \fB\-a\fR option used. .IP Optional parameters: .IP [\-a #] = number of heavy atom for ligand (#_of_pts will be set to 6x atoms) .BR [\-x # \fB\-y\fR # \fB\-z\fR #] = optional x,y,z co\-ords for starting fill (float) .IP when starting point is input, only one fill will be run .IP [\-i # \fB\-j\fR # \fB\-k\fR #] = optional x,y,z co\-ords for second point (float) .IP when second point is input, the fill will connect both points NOTE: the connection path has not been optimized \- use with discretion .IP [\-f #] = number of fills to generate \- default is 10 .BR [\-e] = use the extra atom types NA, N, SA, and A .IP NOTE: these results can be problematic \- use with discretion .IP [\-m] = make a movie of output fill progress .SH "SEE ALSO" A tutorial is available online on http://autodock.scripps.edu/resources/autoligand/AutoLigand_tutorial.pdf .SH AUTHORS Rodney M. Harris and colleagues at The Scripps Institute, San Diego, California debian/menu0000644000000000000000000000017611037742532010065 0ustar ?package(autodocktools):needs="X11" section="Applications/Science/Biology"\ title="AutoDockTools" command="/usr/bin/runAdt" debian/patches/0000755000000000000000000000000012152425160010613 5ustar debian/patches/series0000644000000000000000000000010611675165765012052 0ustar fix_python_path.patch # Adopted by upstream #indentiationError.patch debian/patches/fix_python_path.patch0000644000000000000000000000135011572471434015050 0ustar Description: Use version independent python interpreter Author: Andreas Tille Last-Update: 2011-04-06 --- autodocktools-1.5.4.cvs.20100912.orig/AutoDockTools/bin/adt +++ autodocktools-1.5.4.cvs.20100912/AutoDockTools/bin/adt @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.5 +#!/usr/bin/python # import sys --- autodocktools-1.5.4.cvs.20100912.orig/AutoDockTools/bin/adt3 +++ autodocktools-1.5.4.cvs.20100912/AutoDockTools/bin/adt3 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.5 +#!/usr/bin/python # import sys, getopt --- autodocktools-1.5.4.cvs.20100912.orig/AutoDockTools/bin/adt4 +++ autodocktools-1.5.4.cvs.20100912/AutoDockTools/bin/adt4 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.5 +#!/usr/bin/python # import sys, getopt debian/patches/indentiationError.patch0000644000000000000000000000177611640327245015354 0ustar Index: AutoDockTools-1.5.6~rc2+cvs.20110926/AutoDockTools/Utilities24/prepare_dpf41.py =================================================================== --- AutoDockTools-1.5.6~rc2+cvs.20110926.orig/AutoDockTools/Utilities24/prepare_dpf41.py 2011-09-23 01:18:17.000000000 +0200 +++ AutoDockTools-1.5.6~rc2+cvs.20110926/AutoDockTools/Utilities24/prepare_dpf41.py 2011-09-27 12:45:17.422039506 +0200 @@ -220,7 +220,7 @@ if o in ('-p', '--p'): #parameter parameters.append(a) if verbose: print 'parameters =', parameters - if o in ('-e', '--e'): + if o in ('-e', '--e'): epdb_output = True if verbose: print 'output epdb file' parameter_list = epdb_list4_2 @@ -289,7 +289,7 @@ print "newvalue=", nv kw[key] = nv print "kw=", kw - elif key=='epdb_flag': + elif key=='epdb_flag': print "setting epdb_flag to", newvalue kw['epdb_flag'] = 1 elif 'flag' in key: debian/README.Debian0000644000000000000000000000265211614742512011237 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 the 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 the AutoDockToolkit is pretty close to a true Open Source solution. 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 be much appreciated. The packaging is organised via the Debian-Med alioth project that has its own portal on http://debian-med.alioth.debian.org and a mailing list that listens. -- Steffen Moeller Sun, 20 Jul 2008 00:33:11 +0200 debian/runAdt.10000644000000000000000000000635711572471434010530 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 ADT 1 "Januar 2, 2008" .\" 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 adt \- AutoDockTools, a graphical front-end for AutoDock .SH SYNOPSIS .B runAdt .RI [ options ] .SH DESCRIPTION This manual page is an almost literal translation of the output provided by .B runAdt -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. .TP .B \-h, \-\-help Show summary of options. .TP .B \-a or \-\-again play back lastlog file .TP .B \-\-overwriteLog overwrite log file .TP .B \-\-uniqueLog create a log file with a unique name .TP .B \-\-noLog turn off logging .TP .B \-\-noSplash turn off Splash Screen .TP .B \-\-die do not start GUI event loop .TP .B \-\-customizer file run the user specified file .TP .B \-\-lib packageName add a libraries of commands .TP .B \-v r, \-\-vision run run vision networks on the command line .TP .B \-v o, \-\-vision once run vision networks and exit ADT .TP .B \-d or \-\-dmode modes specify a display mode modes can be any a combination of display mode 'cpk' : cpk 'lines': lines 'ss' : secondary structure ribbon 'sb' : sticks and balls 'lic' : licorice 'ms' : molecular surface 'ca' : C-alpha trace 'bt' : backbone trace 'sp' : CA-spline 'sssb' : secondary structure for proteins, sticks and balls for other residues with bonds lines for other residues without bonds .TP .B \-c or \-\-cmode modes specify a dispaly mode color scheme: 'ca' : color by atom 'cr' : color by residue (RASMOL scheme) 'cc' : color by chain 'cm' : color by molecule 'cdg': color using David Goodsell's scheme 'cs' : color residues using Shapely scheme 'css': color by secondary structure element .SH EXAMPLE: display protein as ribbon, non protein as sticks and balls and color by atom type .TP adt \-i \-\-dmode sssb \-\-cmode cr myprot.pdb .TP adt \-i \-m sssb \-c cr myprot.pdb .SH SEE ALSO .BR http://mgltools.scripps.edu, .BR http://autodock.scripps.edu .SH AUTHOR AutoDockTools was written by researchers of the Molecular Graphics Lab at the Scripps Institute . .PP This manual page was written by Steffen Moeller , for the Debian project (but may be used by others). debian/README.source0000644000000000000000000000155011667635271011364 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://anonscm.debian.org/viewvc/debian-med/trunk/packages/mgltools/BUILD?view=markup -- Steffen Moeller debian/dirs0000644000000000000000000000001011014774462010047 0ustar usr/bin debian/rules0000755000000000000000000000167111714542662010263 0ustar #!/usr/bin/make -f # -*- makefile -*- # 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=AutoDockToolsDIST %: dh $@ --with python2 override_dh_install: dh_install find debian -name runAdt -exec chmod +x \{\} \; find debian -name adt -exec chmod +x \{\} \; # remove extra interpreter line ... the / in debian/ is important for the expression to work with symbolic links find debian/ \( -name runAdt -o -name AutoLigand.py -o -name VS_net.py \) -a -type f -exec sed -i '1s?#!.*?#!/usr/bin/python?' \{\} \; find debian/ -name LICENSE -delete find debian/ -name runAdt -o -name adt | xargs -r chmod +x override_dh_clean: dh_clean find . -name CVS -a -type d | xargs -r rm -r rm -f AutoDockTools/bin/runAdt rm -rf build build-stamp get-orig-source: ./debian/get-orig-source/get-orig-source $(SRC) $(BRANCH) $(RCVERSION) debian/source/0000755000000000000000000000000012152425160010464 5ustar debian/source/format0000644000000000000000000000001411547277203011704 0ustar 3.0 (quilt)