This is a revised version of autodock.py, the Autodock/Vina plugin for PyMol
by Daniel Seeliger.  See "http://wwwuser.gwdg.de/~dseelig/adplugin.html
for the original release.

The revisions made here are in an attempt to adapt this plugin, which works
well with Python 2.7.9 and PrMOL 1.7.x on Linux or Mac for use on Windows.
As of 28 March 2015, this version now appears to work reasonably well under
both OS X and Windows XP.  Further work and a proper installer will be needed.

  -- H. J. Bernstein, yayahjb@gmail.com

This copyright notice for the original code is:

# Autodock/Vina plugin  Copyright Notice
# ============================
#
# ----------------------------------------------------------------------
# Autodock/Vina plugin is Copyright (C) 2009 -- 2015 by Daniel Seeliger
#
#                        All Rights Reserved
#
# EFFECTIVE 28 MARCH 2015, YOU MAY REDISTRBUTE THE AUTODOCK/VINA PLUGIN
# UNDER THE TERMS OF THE LGPL
#
#************************* LGPL NOTICES *******************************
#                                                                    *
# This plugin is free software; you can redistribute it and/or      *
# modify it under the terms of the GNU Lesser General Public         *
# License as published by the Free Software Foundation; either       *
# version 2.1 of the License, or (at your option) any later version. *
#                                                                    *
# This plugin 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  *
# Lesser General Public License for more details.                    *
#                                                                    *
# You should have received a copy of the GNU Lesser General Public   *
# License along with this plugin; if not, write to the Free         *
# Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston,    *
# MA  02110-1301  USA                                                *
#                                                                    *
#*********************************************************************/
#
# ORIGINAL AUTODOCK/VINA NOTICES APPLICABLE TO VERSIONS PRIOR TO
# 28 MARCH 2015
#
# The Autodock/Vina plugin source code is copyrighted, but you can
# freely use and copy it as long as you don't change or remove any of
# the copyright notices.
#
# Permission to use, copy, modify, distribute, and distribute modified
# versions of 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 the copyright notice and
# this permission notice appear in supporting documentation, and that
# the name of Daniel Seeliger not be used in advertising or publicity
# pertaining to distribution of the software without specific, written
# prior permission.
#
# DANIEL SEELIGER DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS
# SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
# FITNESS.  IN NO EVENT SHALL DANIEL SEELIGER 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.
# ----------------------------------------------------------------------

The revisions here are by Herbert J. Bernstein, 6 - 28 March 2015, with the
intention of incorporating the plugin within the larger ProMOL package releases
under the GPL.  With the agreement of Daniel Seeliger, the Autodock/Vina
plugin is now under the LGPL. All warranties are also disclaimed by
Herbert J. Bernstein.

Note:  As a derived work, the copyright of _all_ plugin versions made from
Daniel Seeliger's version remain under his copyright.

See the svn change history for the revisions made.

  -- H. J. Bernstein, yayahjb@gmail.com

INSTALLATION INSTRUCTIONS

1.  Autodock 4:  Autodock 4 and AutodockTools 4 is a product of the Scripps
Research Institute.  To install this plugin, you first must install Autodock 4,
including autodock4, autogrid4, and vina.  See
http://autodock.scripps.edu/

2.  MGLTools 1.5.7:  You need MGLTools for operation of this plugin, also from
the Scripps Research Institute.  See http://http://mgltools.scripps.edu/.  The
plugin has been test both with MGLTools 1.5.6 and MGLTools 1.5.7 RC1.  1.5.7
is recommended.

3.  Python 2.7.9:  While portions of the Autodoc system come with an internal
version of python, it is helpful to have a system installation of Python 2.7.9.
See https://www.python.org/downloads/release/python-279/

4.  PyMOL 1.7:  The plugin is a plugin for the PyMOL molecular visualization
program PyMOL developed by the late Warren Delano and not maintained by
Schrodinger LLC.  See http://www.pymol.org for the Schrodinger-supported version.
See http://sourceforge.net/projects/pymol/, http://www.pymolwiki.org,
http://www.pymolwiki.org/index.php/Windows_Install,
http://www.pymolwiki.org/index.php/MAC_Install and
http://www.pymolwiki.org/index.php/Linux_Install for additional options

5.  Use the standard PyMOL Plugin manager to install autodock.py from this kit
as a plugin.

6.  Several enviroment variables may be set to simplify configuration:

    ADPLUGIN_PATH  -- the contents of this variable with be copied to PATH
before executing threads and processes from the script.  You should put
paths for the internal MGLTools version of python, as well as for autodock4,
autogrid4 and vina _before_ the other path elements appropriate for your system.
Then you can use these program names without paths in the configuration.

    ADPLUGIN_PYTHONHOME, ADPLUGIN_PYTHONPATH  -- the contents of these variables
will be copied to PYTHONHOME and PYTHONPATH before executing threads and
processes from the script.  You should set these to values appropriate for the
MGLTools version of python, which may otherwise conflict with the system version
you use to start PyMOL

    ADPLUGIN_FONT -- the contents of this variable may be used to override the
default "Courier 10" font used by the plugin

7.  In configuring AutoDockTools  Utilities24 configuration entry, you are giving
a path to various python scripts.  It is important that your system process these
scripts with the correct version of python from MGLTools.  It helps to prefix
the path with "python " and set ADPLUGIN_PATH, ADPLUGIN_PYTHONHOME,  and
ADPLUGIN_PYTHONPATH to values that with point to the MGLTools copy of python.
For example in a Mac MGLTools 1.5.7rc1 installation, appropriate lines to place
in .bashrc would be

export ADPLUGIN_PATH=/Library/MGLTools/1.5.7rc1/bin:$PATH
export ADPLUGIN_PYTHONHOME=/Library/MGLTools/1.5.7rc1
export ADPLUGIN_PYTHONPATH=/Library/MGLTools/1.5.7rc1/MGLToolsPckgs:/Library/MGLTools/1.5.7rc1/lib/python2.7