--- autodocksuite-4.2.3.orig/debian/changelog
+++ autodocksuite-4.2.3/debian/changelog
@@ -0,0 +1,116 @@
+autodocksuite (4.2.3-1) unstable; urgency=low
+
+ * New upstream version.
+ * Removed series of template comment lines from debian/rules.
+
+ -- Steffen Moeller <moeller@debian.org> Fri, 12 Feb 2010 23:41:59 +0100
+
+autodocksuite (4.2.2.1-3) UNRELEASED; urgency=low
+
+ * Introduced formal reference to accompanying scientific
+ publication in ‘debian/upstream-metadata.yaml’.
+
+ -- Charles Plessy <plessy@debian.org> Sun, 03 Jan 2010 22:17:29 +0900
+
+autodocksuite (4.2.2.1-2) unstable; urgency=low
+
+ [ Andreas Tille ]
+ * debian/control: autogrid enhances autodock
+
+ [ Nelson A. de Oliveira ]
+ * Fix FTBFS (Closes: #550025)
+ - debian/rules: removed old reference to /usr/share/quilt/quilt.make
+ Thank you Nobuhiro Iwamatsu <iwamatsu@nigauri.org>!
+
+ -- Nelson A. de Oliveira <naoliv@debian.org> Tue, 20 Oct 2009 15:03:07 -0200
+
+autodocksuite (4.2.2.1-1) unstable; urgency=low
+
+ * New upstream release
+ - patches are all accepted / independently performed
+ - removed dependency on quilt
+ * Compatibility with gcc-4.4 (no change required)
+ * Added README.source, indicating now simplified
+ structure of sources
+
+ -- Steffen Moeller <moeller@debian.org> Wed, 07 Oct 2009 01:43:35 +0200
+
+autodocksuite (4.2.1+rc1-3) UNRELEASED; urgency=low
+
+ * Adding post-install message in favour of a request
+ by upstream to possibly help their funding situation.
+
+ -- Steffen Moeller <moeller@debian.org> Tue, 28 Jul 2009 17:05:26 +0200
+
+autodocksuite (4.2.1+rc1-2) unstable; urgency=low
+
+ * Fix FTBFS (Closes: #534601)
+ - debian/control: add automake and csh in Build-Depends
+ # Downgraded autodocktools from Recommends to Suggests (Closes: #534267)
+ * Add watch file
+ * Include myself in Uploaders.
+
+ -- Nelson A. de Oliveira <naoliv@debian.org> Thu, 25 Jun 2009 14:43:54 -0300
+
+autodocksuite (4.2.1+rc1-1) unstable; urgency=low
+
+ * new upstream release
+ * added gcc flag to suppress char* conversion warnings
+ * removed pointless DM-Maintainer-upload permission
+ * bumped Debian policy compliance to 3.8.2 - no changes required
+ * using new dh_prep instead of dh_clean -k, dependency on debhelper > 7
+
+ -- Steffen Moeller <moeller@debian.org> Sun, 21 Jun 2009 21:41:07 +0200
+
+autodocksuite (4.0.1-5) UNRELEASED; urgency=low
+
+ * debian/control:
+ - updated conformance info to policy 3.8.0
+ - autogrid recommends autodocktools
+ - autodock suggests autodocktools
+ - autodock suggests autogrid, no longer recommends
+ * debian/README.Debian: general updates, typos
+
+ -- Steffen Moeller <moeller@debian.org> Thu, 04 Sep 2008 13:52:07 +0200
+
+autodocksuite (4.0.1-4) unstable; urgency=low
+
+ * debian/rules:
+ - Using dh_installdocs instead of the cp command (Closes: #472538).
+ - Using dh_installchangelogs to install src/auto[dock|grid]/ChangeLog.
+ * debian/contol, debian/rules, debian/autodock-test.install,
+ debian/autogrid-test.install:
+ - Separated the test files from the main Arch:any packages into Arch:all
+ packages.
+ * Updated my email address.
+
+ -- Charles Plessy <plessy@debian.org> Thu, 31 Jul 2008 13:19:15 +0900
+
+autodocksuite (4.0.1-3) unstable; urgency=low
+
+ [Charles]
+
+ * debian/patches/build-with_gcc43.patch: adds #include <cstdlib>
+ to src/autogrid/check_size.cpp.
+ (Thanks to Kumar Appaiah, Closes: #470972).
+
+ [Steffen]
+
+ * removed redundancy from the patch
+ * added Charles to Uploaders
+ * allowed DM-upload
+
+ -- Steffen Moeller <moeller@debian.org> Wed, 19 Mar 2008 09:37:58 +0100
+
+autodocksuite (4.0.1-2) unstable; urgency=low
+
+ * Removed popularity-contest from suggests (Closes: #470406).
+
+ -- Steffen Moeller <moeller@debian.org> Mon, 17 Mar 2008 23:28:34 +0100
+
+autodocksuite (4.0.1-1) unstable; urgency=low
+
+ * Initial release (Closes: #434654)
+
+ -- Steffen Moeller <moeller@debian.org> Mon, 23 Jul 2007 16:41:48 +0200
+
--- autodocksuite-4.2.3.orig/debian/control
+++ autodocksuite-4.2.3/debian/control
@@ -0,0 +1,56 @@
+Source: autodocksuite
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller@debian.org>,
+ Charles Plessy <plessy@debian.org>, Nelson A. de Oliveira <naoliv@debian.org>,
+ Andreas Tille <tille@debian.org>
+Build-Depends: debhelper (>= 7), automake, csh
+Standards-Version: 3.8.4
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/autodocksuite/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/autodocksuite/trunk/
+Homepage: http://autodock.scripps.edu/
+
+Package: autodock
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: autogrid, autodocktools
+Description: analysis of ligand binding to protein structure
+ AutoDock is a prime representative of the programs addressing the
+ simulation of the docking of fairly small chemical ligands to rather big
+ protein receptors. Earlier versions had all flexibility in the ligands
+ while the protein was kept rather ridgid. This latest version 4 also
+ allows for a flexibility of selected sidechains of surface residues,
+ i.e., takes the rotamers into account.
+ .
+ The AutoDock program performs the docking of the ligand to a set of
+ grids describing the target protein. AutoGrid pre-calculates these grids.
+
+Package: autogrid
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: autodock, autodocktools
+Enhances: autodock
+Description: pre-calculate binding of ligands to their receptor
+ The AutoDockSuite addresses the molecular analysis of the docking of
+ a smaller chemical compounds to their receptors of known three-dimensional
+ structure.
+ .
+ The AutoGrid program performs pre-calculations for the docking of a
+ ligand to a set of grids that describe the effect that the protein has
+ on point charges. The effect of these forces on the ligand is then
+ analysed by the AutoDock program.
+
+Package: autodock-test
+Architecture: all
+Suggests: autodock
+Depends: ${misc:Depends}
+Description: test files for AutoDock
+ This package contain the test files for the AutoDock program.
+
+Package: autogrid-test
+Architecture: all
+Suggests: autogrid
+Depends: ${misc:Depends}
+Description: test files for AutoGrid
+ This package contain the test files for the AutoGrid program.
--- autodocksuite-4.2.3.orig/debian/upstream-metadata.yaml
+++ autodocksuite-4.2.3/debian/upstream-metadata.yaml
@@ -0,0 +1,18 @@
+Donation: http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/
+DOI: 10.1002/jcc.21256
+Homepage: http://autodock.scripps.edu/
+Name: AutoDock
+PMID: 19399780
+Reference:
+ Author: Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, 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
+ URL: http://www3.interscience.wiley.com/journal/122365050/abstract
+Registration: http://autodock.scripps.edu/downloads/autodock-registration
+Watch: |
+ opts="dversionmangle=s/\+rc/~rc/" \
+ http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/ \.\./autodock-registration/tars/.*/autodocksuite-(.*)-src\.tar\.gz
--- autodocksuite-4.2.3.orig/debian/compat
+++ autodocksuite-4.2.3/debian/compat
@@ -0,0 +1 @@
+5
--- autodocksuite-4.2.3.orig/debian/note_from_upstream.txt
+++ autodocksuite-4.2.3/debian/note_from_upstream.txt
@@ -0,0 +1,36 @@
+----------------------------------------------------------------------
+ ______
+ / \
+ / \
+ / \
+ \ /\ /
+ \ / \ /
+ \/ /\ \/
+ / \
+ /____\
+
+AutoDock and AutoGrid are free software, distributed under the terms of
+the GNU General Public License 2 or later. This allows us to share the
+code and to be open for improvement from the whole scientific community.
+
+The development of the AutoDock suite is entirely funded by research
+grants. For that reason, we ask you to register at the AutoDock
+Registration page
+
+ http://autodock.scripps.edu/downloads/autodock-registration
+
+in order to keep track of number of unique downloads, which we use to
+support the grant applications. Installing the Debian popularity-contest
+package is also encouraged.
+
+ Thank you, and happy docking!
+
+ The AutoDock Development Team
+
+If you plan to use AutoDock for commercial purposes we encourage
+donations to the Olson laboratory to help support further development
+of the AutoDock 4 suite of programs. Donation information provided on
+the download page.
+
+----------------------------------------------------------------------
+
--- autodocksuite-4.2.3.orig/debian/autodock-test.dirs
+++ autodocksuite-4.2.3/debian/autodock-test.dirs
@@ -0,0 +1 @@
+usr/share/autodock
--- autodocksuite-4.2.3.orig/debian/autodock4.1
+++ autodocksuite-4.2.3/debian/autodock4.1
@@ -0,0 +1,91 @@
+.\" 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 AUTODOCK 1 "Juli 23, 2007"
+.\" 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 <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+autodock \- docking of chemical ligands to protein receptors
+.SH SYNOPSIS
+.B autodock4
+.RI [ options ]
+.SH DESCRIPTION
+AutoDock perfoms the automated docking of chemical compounds to proteins, i.e. it
+predicts how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
+
+The AutoDockSuite consists of two main programs of which AutoDock performs the
+docking of the ligand to a set of grids describing the target protein and
+AutoGrid pre-calculates these grids.
+.PP
+.\" TeX users may be more comfortable with the \fB<whatever>\fP and
+.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
+.\" respectively.
+.SH OPTIONS
+.TP
+.B \-p
+.RI parameter_filename
+.TP
+.B \-l
+.RI log_filename
+.TP
+.B \-o
+Use old PDBQ format, charge q in columns 55-61
+.TP
+.B \-k
+Keep original residue numbers
+.TP
+.B \-i
+Ignore header-checking
+.TP
+.B \-t
+Parse the PDBQ file to check torsions, then stop.
+.TP
+.B \-c <
+.RI command_file
+Command mode, by file
+.TP
+.B \-c |
+.RI control_program
+Command mode, by control_program
+.SH EXAMPLE
+
+On Debian, the directory /usr/share/doc/autodock offers examples to run. Change to that directory and unpack (as root) the gzipped map files, then execute AutoDock as shown below:
+.br
+gunzip *.map.gz
+.br
+autodock4 \-p 1pgp.dpf \-l /tmp/1pgp.dlg
+
+The interpretation of results is aided by the AutoDockTools suite. Please also inspect the tutorials offered online.
+
+.SH SEE ALSO
+.BR autogrid (1),
+.BR runAdt (1).
+.br
+http://autodock.scripps.edu
+.br
+http://autodock.scripps.edu/faqs-help/faq/what-is-the-command-line-to-start-autodock-4
+.SH LICENSE
+This software is made available under the terms of the GNU Public
+License version 2 or later. This implies that this software may be
+redistributed if the source is made available. It would however help
+the future development of the AutoDockSuite if you register yourself
+at http://autodock.scripps.edu/downloads.
+.SH AUTHOR
+The most prominent author of the version 4 of autodock is G. Morris
+<garrett@scripps.edu>. See the AUTHORS file in /usr/share/doc/autodock
+for details.
+.PP
+This manual page was written by Steffen Moeller <moeller@debian.org>,
+for the Debian project (but may be used by others and is hopefully
+adopted by the upstream developers).
--- autodocksuite-4.2.3.orig/debian/rules
+++ autodocksuite-4.2.3/debian/rules
@@ -0,0 +1,97 @@
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+export DH_OPTIONS
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+configure: configure-stamp
+configure-stamp: $(QUILT_STAMPFN)
+ dh_testdir
+ for d in autogrid autodock; do \
+ ( cd $$d && autoreconf -i && ./configure CFLAGS="$(CFLAGS)" --prefix=/usr ) \
+ done
+
+ touch configure-stamp
+
+build: build-arch build-indep
+
+build-arch: build-arch-stamp
+build-arch-stamp: configure-stamp
+ for d in autogrid autodock; do $(MAKE) -C $$d; done
+ touch $@
+
+build-indep: build-indep-stamp
+build-indep-stamp: configure-stamp
+ # Add here commands to compile the indep part of the package.
+ touch $@
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-arch-stamp build-indep-stamp configure-stamp
+
+ for d in autodock autogrid; \
+ do \
+ if [ -r $$d/Makefile ]; then $(MAKE) -C $$d distclean; fi \
+ done
+ dh_clean configure-stamp
+
+install: install-indep install-arch
+install-indep:
+ dh_testdir
+ dh_testroot
+ dh_prep -i
+ dh_installdirs -i
+ dh_install -i
+ rm -rf $(CURDIR)/debian/autodock-test/usr/share/autodock/Tests/AutoDockTools
+ rm -rf $(CURDIR)/debian/autogrid-test/usr/share/autogrid/Tests/CVS/
+ rm -rf $(CURDIR)/debian/autodock-test/usr/share/autodock/Tests/CVS/
+ chmod 644 $(CURDIR)/debian/autodock-test/usr/share/autodock/Tests/*
+ chmod 644 $(CURDIR)/debian/autogrid-test/usr/share/autogrid/Tests/*
+
+install-arch:
+ dh_testdir
+ dh_testroot
+ dh_prep -s
+ dh_installdirs -s
+
+ for d in autodock autogrid; do \
+ $(MAKE) -C $$d DESTDIR=$(CURDIR)/debian/$$d install; \
+ done
+ dh_install -s
+
+binary-common:
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installexamples
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_makeshlibs
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary-indep: build-indep install-indep
+ $(MAKE) -f debian/rules DH_OPTIONS=-i binary-common
+
+binary-arch: build-arch install-arch
+ $(MAKE) -f debian/rules DH_OPTIONS=-s binary-common
+
+binary: binary-arch binary-indep
+
+.PHONY: build clean binary-indep binary-arch binary install install-indep install-arch configure
--- autodocksuite-4.2.3.orig/debian/autodock-test.install
+++ autodocksuite-4.2.3/debian/autodock-test.install
@@ -0,0 +1 @@
+autodock/Tests usr/share/autodock
--- autodocksuite-4.2.3.orig/debian/autogrid-test.dirs
+++ autodocksuite-4.2.3/debian/autogrid-test.dirs
@@ -0,0 +1 @@
+usr/share/autogrid
--- autodocksuite-4.2.3.orig/debian/autodock.postinst
+++ autodocksuite-4.2.3/debian/autodock.postinst
@@ -0,0 +1,42 @@
+#!/bin/sh
+# postinst script for autodock
+#
+# see: dh_installdeb(1)
+
+set -e
+
+# summary of how this script can be called:
+# * <postinst> `configure' <most-recently-configured-version>
+# * <old-postinst> `abort-upgrade' <new version>
+# * <conflictor's-postinst> `abort-remove' `in-favour' <package>
+# <new-version>
+# * <postinst> `abort-remove'
+# * <deconfigured's-postinst> `abort-deconfigure' `in-favour'
+# <failed-install-package> <version> `removing'
+# <conflicting-package> <version>
+# for details, see http://www.debian.org/doc/debian-policy/ or
+# the debian-policy package
+
+
+case "$1" in
+ configure)
+ if [ -r /usr/share/doc/autodock/note_from_upstream.txt ]; then
+ cat /usr/share/doc/autodock/note_from_upstream.txt
+ fi
+ ;;
+
+ abort-upgrade|abort-remove|abort-deconfigure)
+ ;;
+
+ *)
+ echo "postinst called with unknown argument \`$1'" >&2
+ exit 1
+ ;;
+esac
+
+# dh_installdeb will replace this with shell code automatically
+# generated by other debhelper scripts.
+
+#DEBHELPER#
+
+exit 0
--- autodocksuite-4.2.3.orig/debian/autodock.manpages
+++ autodocksuite-4.2.3/debian/autodock.manpages
@@ -0,0 +1 @@
+debian/autodock4.1
--- autodocksuite-4.2.3.orig/debian/README.source
+++ autodocksuite-4.2.3/debian/README.source
@@ -0,0 +1 @@
+The folder structure was simplified, i.e. /src renamed to autodock-<version> .
--- autodocksuite-4.2.3.orig/debian/autodock.docs
+++ autodocksuite-4.2.3/debian/autodock.docs
@@ -0,0 +1,4 @@
+autodock/AUTHORS
+autodock/README
+autodock/NEWS
+debian/note_from_upstream.txt
--- autodocksuite-4.2.3.orig/debian/autogrid-test.install
+++ autodocksuite-4.2.3/debian/autogrid-test.install
@@ -0,0 +1 @@
+autogrid/Tests usr/share/autogrid/
--- autodocksuite-4.2.3.orig/debian/autogrid4.1
+++ autodocksuite-4.2.3/debian/autogrid4.1
@@ -0,0 +1,106 @@
+.\" Hey, EMACS: -*- nroff -*-
+.TH AUTOGRID 1 "Juli 23, 2007"
+.\" 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 <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+autogrid \- preparing protein and ligand for AutoDock analysis
+.SH SYNOPSIS
+.B autogrid4
+.RI [ options ]
+\-p
+.RI gridparameterfile
+.SH DESCRIPTION
+.B AutoGrid
+prepares a 3D grid representation of the non-covalent interaction
+energies that various user-specified ligand atom types will experience
+around a user-specified target macromolecule. In addition, the
+electrostatic potential and desolvation free energy grid maps may also
+be calculated. The grid maps are stored in plain text files with the
+extension '.map' and are required by AutoDock 4 to perform dockings.
+AutoGrid also outputs a '.xyz' file which describes the spatial
+extents of the grid box, and an AVS field '.fld' file which describes
+the consistent set of atomic affinity grid maps that were calculated
+together for a given target macromolecule. Note: it is necessary
+to compute grid maps for all the atom types in the ligand or set of
+ligands that will be docked, as well as an electrostatic potential
+grid map and a desolvation free energy map. For example, if a ligand
+has an aliphatic carbon and a hydrogen-bond-accepting oxygen atom,
+it would be necessary to compute both a 'C' map and an 'OA' map. See
+http://autodock.scripps.edu/faqs-help/faq/where-do-i-set-the-autodock-4-force-field-parameters
+for more information about AutoDock 4 atom types.
+
+The input to
+.RI AutoGrid
+is best prepared with the program suite
+.RI AutoDockTools.
+There is no way to run
+.RI autodock4
+without a grid.
+.PP
+.\" TeX users may be more comfortable with the \fB<whatever>\fP and
+.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
+.\" respectively.
+.ad l
+.SH OPTIONS
+.B \-o
+Use old PDBq format (q in columns 55-61)
+.TP
+.B \-u
+Usage information, also \-h on Debian.
+.TP
+.B \-d
+Increased verbosity of messages to help debugging.
+.TP
+.B \-l
+.RI logfile
+.TP
+.B \-p
+.RI filename
+Specifies Grid Parameter File
+.SH EXAMPLE
+A range of tests is made available with the AutoGrid sources that can be used as follows:
+.br
+$ D=/usr/share/doc/autogrid/Tests
+.br
+$ cd /tmp
+.br
+$ ln \-s $D/AD4_parameters.dat .
+.br
+$ gunzip \-c $D/hsg1_sm.pdbqt.gz > hsg1_sm.pdbqt
+.br
+.nh
+$ autogrid4 \-p $D/hsg1_no_receptor_types.gpf \-l hsg1_no_receptor_types.glg
+.ad b
+.TP
+This command prepares grid map files for each of the AutoDock atom types specified in the grid parameter file (in this case: hsg1_sm.A.map, hsg1_sm.C.map, hsg1_sm.d.map, hsg1_sm.e.map, hsg1_sm.HD.map, hsg1_sm.NA.map, hsg1_sm.N.map, hsg1_sm.OA.map), the AVS field file (hsg1_sm.maps.fld) and hsg1_sm.maps.xyz. To perform the cocking calculation, AutoDock should be executed, though it demands a separate docking parameter file (with extension .dpf). The 'DPF' refers to the grid map files that are necessary to the docking and allows the setting of other important parameters, such as the search method and how many dockings to perform.
+
+.SH SEE ALSO
+.BR autodock (1),
+.BR runAdt (1).
+.br
+http://autodock.scripps.edu
+.SH LICENSE
+This software is made available under the terms of the GNU Public
+License version 2 or later. This implies that this software may be
+redistributed if the source is made available. It would however help
+the future development of the AutoDockSuite if you register yourself
+at http://autodock.scripps.edu/downloads.
+.SH AUTHOR
+The most prominent author of the version 4 of AutoDock is G. Morris
+<garrett@scripps.edu>. See the AUTHORS file in /usr/share/doc/autogrid
+for details.
+.PP
+This manual page was written by Steffen Moeller <moeller@debian.org>
+and much revised by upstream author Garrett Morris.
+It was prepared for the Debian project but may be used by others and
+is hopefully adopted by the upstream developers.
--- autodocksuite-4.2.3.orig/debian/autogrid.manpages
+++ autodocksuite-4.2.3/debian/autogrid.manpages
@@ -0,0 +1 @@
+debian/autogrid4.1
--- autodocksuite-4.2.3.orig/debian/autogrid.docs
+++ autodocksuite-4.2.3/debian/autogrid.docs
@@ -0,0 +1,3 @@
+autogrid/AUTHORS
+autogrid/README
+autogrid/NEWS
--- autodocksuite-4.2.3.orig/debian/watch
+++ autodocksuite-4.2.3/debian/watch
@@ -0,0 +1,6 @@
+version=3
+## rc (release candidates) have to be lower than the final version
+#opts="dversionmangle=s/\+rc/~rc/" \
+#http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/ \.\./autodock-registration/tars/.*/autodocksuite-(.*)-src\.tar\.gz
+# Please help with the watch file
+http://autodock.scripps.edu/downloads/autodock-registration/tars/dist423/autodocksuite-(4.2.3)-src.tar.gz
--- autodocksuite-4.2.3.orig/debian/README.Debian
+++ autodocksuite-4.2.3/debian/README.Debian
@@ -0,0 +1,42 @@
+autodocksuite for Debian
+------------------------
+
+AutoDock is a prime representative of the programs addressing the
+simulation of the docking of fairly small chemical ligands to rather big
+protein receptors. Earlier versions had all flexibility in the ligands
+while the protein was kept rather ridgid. This latest version 4 also
+allows for a flexibility of selected sidechains of surface residues,
+i.e., takes the rotamers of selected residues into account.
+
+You may find other spots where to help with the packaging of AutoDock.
+Please give feedback. Debian-Med community is very friendly and open
+towards collaborative package maintenance, just say "hello". Success
+stories are warmely welcomed.
+
+The upstream developers at Scripps have accompanied this package with
+a set of programs that are more prone to be used by the user directly.
+These are located in a separate package, named 'autodocktools' and have
+very recently also been made available via Debian.
+
+Dr Garrett Morris of the upstream developers was very supportive of
+this packaging. The Scripps Institute asks for registrations prior to
+the download of the tarball or the binaries at this URL
+
+ http://autodock.scripps.edu/downloads/autodock-registration
+
+which does not affect the distribution of this package under the
+GPL. Nevertheless, please respect upstream's genuine interest to know
+about the impact that their work has on the field, which is key for writing
+grant applications. You may decide to register on that site albeit having
+this package received via Debian already. Also please consider installing
+the Debian package popularity-contest. This counts the installations and
+may thus further help upstream to further develop their software.
+
+Dr Morris kindly proofread the copyright notice and the autogrid4.1 man
+page. This was much appreciated and I thank him for this. Thanks for
+improving the AutoDock/-Grid packaging for Debian also go to David
+Paleino and the Debian-Med community at large.
+
+Steffen
+
+ -- Steffen Moeller <moeller@debian.org> Mon, 15 Dec 2008 01:01:37 +0100
--- autodocksuite-4.2.3.orig/debian/copyright
+++ autodocksuite-4.2.3/debian/copyright
@@ -0,0 +1,62 @@
+This package was debianized by Steffen Moeller <moeller@debian.org> on
+Mon, 23 Jul 2007 16:41:48 +0200.
+
+It was downloaded from http://autodock.scripps.edu/downloads
+
+Upstream Authors:
+
+ Primary:
+
+ Garrett M. Morris <garrett@scripps.edu>
+ David S. Goodsell <goodsell@scripps.edu>
+ Scott Halliday
+ Ruth Huey <rhuey@scripps.edu>
+ William E. Hart <wehart@sandia.gov>
+ Max Chang <mchang@ucsd.edu>
+ Richard K. Belew <rik@cogsci@ucsd.edu>
+ Arthur J. Olson <olson@scripps.edu>
+
+ Contributing:
+
+ Peter Reilly <reilly@iastate.edu>
+ Scott Kurowski <scott@scottkurowski.com>
+
+Copyright:
+
+ Copyright © 1989-2008, All Rights Reserved.
+ Garrett M. Morris <garrett@scripps.edu>
+ David S. Goodsell <goodsell@scripps.edu>
+ Scott Halliday
+ Ruth Huey <rhuey@scripps.edu>
+ William E. Hart <wehart@sandia.gov>
+ Max Chang <mchang@ucsd.edu>
+ Richard K. Belew <rik@cogsci@ucsd.edu>
+ Arthur J. Olson <olson@scripps.edu>
+ Peter Reilly <reilly@iastate.edu>
+ Scott Kurowski <scott@scottkurowski.com>
+ and The Scripps Research Institute
+
+
+License:
+
+ AutoDock is a Trade Mark of The Scripps Research Institute.
+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL'.
+
+The Debian packaging is © 2007, Steffen Moeller <moeller@debian.org> and
+is licensed under the GPL, see above.
![[patchlogo]](http://patch-tracker.debian.org/static/img/swirlpatch.png)