README
ProMOL (C) Copyright 2004-2014
Charlie Westin, Brett Hanson & Paul Craig
GPL, No Warranty

4.2 by Cyprian Corwin and Greg Dodge
Monday, July 25, 2011

Based on Maddy's and Mario Rosa's versions

5.3-r367 by the SBEVSL team, see the User's Guide
Thursday, 31 July 2014 -- HJB

Special Thanks to the following for their contributions to ProMOL:
Laura Grell, Chris Parkin, T.J. Esposito, C. Wischmeyer
   
/*************************** GPL NOTICES ******************************
 *                                                                    *
 * This program 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 program 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 program; if not, write to the Free Software        *
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA           *
 * 02111-1307  USA                                                    *
 *                                                                    *
 **********************************************************************/

ProMOL is a product of the Structural Biology Extensible Visualization
Language (SBEVSL) project, supported in part by Award Number
R15GM078077 from the National Institute Of General Medical Sciences. 
The content is solely the responsibility of the authors and does not
necessarily represent the official views of the National Institute Of 
General Medical Sciences or the National Institutes of Health.

The purpose of ProMOL is to assist in the visualization of protein structures
in PyMOL, as well as assist in the identification of small catalytic sites, and
the creation of catalytic site motifs.

=========================================================================

ProMOL Installation Instructions

ProMOL is a plugin for PyMOL.  PyMOL is available as an open source program
from

http://sourceforge.net/projects/pymol/

and is incorporated into many Unix releases.  PyMOL is also available in
proprietary versions from

http://www.pymol.org.  See that website for information on PyMOL licensing.

PyMOL is a program that was written by the late Warren DeLano.  PyMOL is a
trademark of Schrodinger, LLC.  ProMOL is a plugin for PyMOL, not a
derivative part of PyMOL, but depends on having a copy of PyMOL in order to
operate.

Therefore, in order to use ProMOL, you first must have a copy of PyMOL
installed.

Download PyMOL from http://pymol.sourceforge.net and install to default
location.

ProMOL can be downloaded in a compressed file format from

http://sourceforge.net/projects/sbevsl/files

You can choose to download either a .tar.gz compressed file
(ProMOL-5.1-r247.tar.gz) or a zip compressed file
(ProMOL-5.1-r247.zip). The way you expand the 
file depends on your operating system.

On Unix or Linux systems, or using MINGW under Windows you may unpack the
tarball with

gunzip < ProMOL-5.3-r367.tar.gz | tar xvf -

Windows and Macintosh systems may have a native application that will expand
your .tar.gz or .zip files; if not you may wish to consider using Stuffit
Expander or WinZip.

If you have not already done so, first install PyMOL. Under Mac OS X 
you may need to rename the MacPymol application to MacPymolX11Hybrid, in
order to get access to plugins.  You will also need to have the X window
system installed.  This is included on your Mac OS install disc, but may
not be installed by default.

To install ProMOL, copy ProMol.py and the folder ProMol into the correct
place in the directory tree used by PyMOL for plugins.  For example, for
PyMOL 1.7.1 under Microsoft Windows:

C:\Program Files\PyMol\modules\pmg_tk\startup\

On other systems you will need to find the portion of the PyMOL installation
tree that contains

pmg_tk/startup

and place ProMol.py and the folder ProMol in the startup folder.
For example in a fink PyMOL installation for python 2.4, 2.5 or 2.6 under
Mac OS X, the ProMol.py file and ProMol folder belongs under

/sw/lib/pymol-py24/modules/pmg_tk/startup or
/sw/lib/pymol-py25/modules/pmg_tk/startup or
/sw/lib/pymol-py26/modules/pmg_tk/startup

However, we believe that this version of ProMOL may use features of the Python
language that were introduced in 2.6, so it may not run with earlier versions.
Furthermore, has only been tested on Python 2.{5,6,7}.x, and will not work with Python 3.

For PyMOL installed from the Ubuntu Software Center (it may be the same
from source), ProMol.py and the ProMol folder can be placed under:

/usr/lib/pymodules/python2.7/pmg_tk/startup

When all files are in place, the ProMOL interface can be run by choosing
ProMOL from the PyMOL plug-in menu.

=========================================================================

WARNING: While running a search with the Motif Finder, PLEASE DO NOT
double-click in the results list of a previous search, or load, modify,
manipulate, or clear any structures or named selections present in PyMOL.
Doing so will likely lead to erroneous results!

Other important notes and tips:

- Motifs generated using the Motif Maker tab are stored the subfolder
UserMotifs in the ProMOL application data directory.  This folder is usually
located in the following places:

Windows: %AppData%/SBEVSL/ProMol/
(On Windows 7, %AppData% may be located at C:\Users\[User Name]\AppData\Roaming)
Mac OS X/Darwin: ~/Library/Application Support/SBEVSL/ProMol
Other platforms, including Ubuntu: ~/.sbevsl/ProMol

- Do not install motifs obtained from any source except SBEVSL or your Motif Maker
tab inside either ProMOL's Motifs folder or your UserMotifs folder.  You have been
warned!

- Motif finder searches tend to run significantly faster if, once the search is
started, the user selects the PyMOL Viewer window and presses Escape to switch
into text mode.  To switch back, simply press Escape again.

- Exporting CSV files via the user interface button for a search with no results
will cause ProMOL to hang.  As a workaround, check the CSV file generated for each
search located in your application data directory (see above).

=========================================================================

Work done in part with support from NIH and Nation Institute of General Medical
Sciences (NIGMS) under Grant number 1R15GM078077-01.

ASBMB Annual Meeting
April 28 -- May 3, 2007
Washington, DC

Using PyMOL's Selection Algebra for Enzyme Catalytic Site Prediction
B. R. Hanson, C. Westin, P. A Craig

<>

American Crystallographic Association Meeting
21 -- 26 July 2007
Salt Lake City, Utah

ProMOL, Simplification and Increased Functionality of PyMOL
B. Hanson, C. Westin, L. Slatest, P. Craig

<>

American Crystallographic Association Meeting
31 May -- 5 June 2008
Knoxville, TN

Homology Exploration with ProMOL
C. Wischmeyer, P. Craig, H. Bernstein
The ProMOL plugin for PyMOL is an intuitive user interface that gives users
access to many of the complex tools that exist within PyMOL, without requiring
that the user learn to program in Python. Among its many tools, ProMOL features
a motif­matching interface that can compare enzyme active sites based on the
relative positions of the catalytic residues. Tools found in ProMOL can be used
to compare any structure with more than 30 known calalytic active site motifs,
which were drawn from the Catalytic Site Atlas
(http://www.ebi.ac.uk/thornton­srv/databases/CSA/). The motif analysis tool can
be fine tuned to narrow or expand the three dimensional search space for active
site alignment. Alignment results for enzyme classes across different taxonomic
categories will be presented and compared, along with suggestions for
implementing more effective alignment strategies with the motif tool in ProMOL.

=========================================================================
[Update by current developers: there are now several sets of motifs that
may be individually selected as of 24 July 2014:  The P-set of hand
generated motifs, the A-set of automatically generated motifs,
the M-set of motifs with metal ions and amino acids, and the R-set
of other metal ion motifs.] 
=========================================================================

The previous developers of ProMOL had incorporated a modified version of the
PDB Loader Service plugin into promolglobals.py.  We have removed that code
from ProMOL in favor of launching the existing copy on the user's machine
that is distributed with PyMol, and using PyMOL's built-in functionality.
The following notice was included with older versions of ProMOL, and may no
longer be required, but we have included it for the sake of completeness.
We believe it no longer applies to anything in ProMOL.

# Copyright Notice
# ================
# 
# The PyMOL Plugin source code [below this point] is copyrighted, but you can
# freely use and copy it as long as you don't change or remove any of
# the copyright notices.
# 
# ----------------------------------------------------------------------
# This PyMOL Plugin is Copyright (C) 2004 by Charles Moad <[email protected]>
# 
#                        All Rights Reserved
# 
# 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(s) of the author(s) not be used in advertising or publicity
# pertaining to distribution of the software without specific, written
# prior permission.
# 
# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS.  IN
# NO EVENT SHALL THE AUTHOR(S) 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.
# ----------------------------------------------------------------------

=========================================================================

Change log:

Revision 367
Modified Thursday, July 31, 2014 by Herbert J. Bernstein

Make state of EC number entry boxes consistent with their content.
If there is a number is it enabled.  If there is a bank or zero
and we are below the top level it is disabled.  This fixes a bug
report by Talia McKay.

Revision 364
Modified Thursday, July 24, 2014 by Herbert J. Bernstein

Change background color to white on alignment

Revision 363
Modified Thursday, July 24, 2014 by Herbert J. Bernstein

Update readme.txt, version.py, and installer to r363

Revision 362
Modified Thursday, July 24, 2014 by Herbert J. Bernstein.

Update to algorithm 1.2, changing Levenshtein distance
filter to be based on the minimum distance relative to
the length os the motif rather than the maximum.
Change the background for alignment images to white.
Update the Users Guide as editied by T. McKay.

Revision 347
Modified Sunday, July 13, 2014 by Herbert J. Bernstein

Remove pre-installed U set motifs
Add latest metal ion motifs
Add buttons to select Metal Amino and
Metal Other to select M set and R set.
Add a draft 5.3 windows installer
  HJB merging KVAS r346 branch into trunk

Revision 305
Modified Tuesday, June 24, 2014 by Herbert J. Bernstein

Correct index error in RMSD reporting in EC coce changes
in motif.py

Revision 241
Modified Wednesday, Novembe 20, 2013

Cameron Baker's updated proutils

Revision 228
Modified Monday, October 28, 2013 by Herbert J. Bernstein

Temporary patches
  1.  Display non-bonded atoms as small balls -- HJB
  2.  Cut off Lev. dist. at 1 -- KB

Revision 224
Modified Friday, June 21, 2013 by Herbert J. Bernstein

Release 224 fix -- require at least 2 residues in a match
Fix by MK and HJB

Revision 219
Modified Sunday, April 21, 2013 by Herbert J. Bernstein

Update installer for A_ motifs, version and readme to r219

Revision 218
Modified Sunday, April 21, 2013 by Herbert J. Bernstein

Update installer and readme for r218

Revision 217
Modified Sunday, April 21, 2013 by Herbert J. Bernstein

Add A_ set and related commands -- MO

Revision 214
Modified Friday, April 19, 2013 by Herbert J. Bernstein

Make tagged ProMOL-5.0 release 

Revision 213
Modified Friday, April 19, 2013 by Herbert J. Bernstein

Post release fixes to allow NSIS installer to build and
to make the revisio visible. -- HJB

Revision 212
Modified Friday, April 19, 2013 by Herbert J. Bernstein

Update to r212 for release -- HJB

Revision 211
Modified Friday, April 19, 2013 by Herbert J. Bernstein

Update User Guide pdf -- HJB

Revision 210
Modified Friday, April 19, 2013 by Herbert J. Bernstein

Update NSIS installer to r210
Update users guide as per MK changes
Remove materials that may be a GPL issue.
  -- HJB

Revision 209
Modified Thursday, April 11, 2013 by Herbert J. Bernstein

Updated version of MK fix for Jess motifs being used in all
Put 5.0-r209 version information everywhere
Update some comments -- HJB

Revision 208
Modified Friday. February 22, 2013 by Herbert J. Bernstein

Fix bug in blank chain handling for fetch PDB
Update version to 5.0-r208 -- HJB

Revision 207
Modified Friday. February 15, 2013 by Herbert J. Bernstein

Remove old nsi -- HJB

Revision 206
Modified Friday. February 15, 2013 by Herbert J. Bernstein

Update trunk to rev 203 from MO branch -- HJB

Revision 205
Modified Friday. February 15, 2013 by Herbert J. Bernstein

Bring trunk up to rev 202 from HJB branch -- HJB

Revision 202
Modified Thursday, November 15, 2012

Suppress use of Jess motifs unless environment variable PROMOL_JESS is 
defined -- HJB

Revision 201
Modified Sunday, July 22, 2012 by Herbert J. Bernstein

Changes to increase readability of results -- HJB

Revision 194
Modified Saturday June 09, 2012 by Herbert J. Bernstein

Update installer script to check directory and set version at 194 -- HJB

Revision 193
Modified Thursday June 07, 2012 by Herbert J. Bernstein

Update JESS motifs -- extended shell to compensate for
imprecision in selection logic.  No shells. -- HJB

Revision 191
Modified Monday May 28, 2012 by Herbert J. Bernstein

Change Jess Motifs to sphere, not shell -- HJB

Revision 190
Modified Monday May 28, 2012 by Herbert J. Bernstein

Restore Help directory -- HJB

Revision 189
Modified Monday May 28, 2012 by Herbert J. Bernstein

Restore AminoPics -- HJB

Revision 188
Modified Monday May 28, 2012 by Herbert J. Bernstein

Update to Jess motifs and prepare as r188 release -- HJB

Revision 187
Modified Saturday May 26, 2012 by Herbert J. Bernstein

Fix missing line to populate CSV file. -- HJB

Revision 186
Modified Friday May 25, 2012 by Herbert J. Bernstein

Update version and nsi installer for r186 -- HJB

Revision 185
Modified Friday May 25, 2012 by Herbert J. Bernstein

Fix handling of selector errors in bad motifs -- HJB

Revision 184
Modified Thursday May 24, 2012 by Herbert J. Bernstein

Allow general code in Jab_ Jfa_ motifs -- HJB

Revision 183
Modified Thursday May 24, 2012 by Herbert J. Bernstein

Change .format to % for python 2.5 use -- HJB

Revision 182
Modified Thursday, May 24, 2012 by Herbert J. Bernstein

Pick of MM RMSD code and bring up to same level on all other code, then
back convert to Python 2.5 (changing with ... as xxx
  xxx = ...
  try:
     xxx.__enter__()
  finally:
     xxx.__exit__()
-- HJB

Revision 178
Modified Monday, April 30, 2012 by Herbert J. Bernstein

Add NSIS installer script for windows -- HJB

Revision 177
Modified Tuesday, April 24, 2012 by Herbert J. Bernstein

Revised JESS motifs, thin shell, default 0.1 Angstrom -- HJB

Revision 176
Modified Tuesday, April 03, 2012 by Herbert J. Bernstein 

Update motifs with 2.8A shell -- HJB

Revision 175
Modified Wednesday, March 28, 2012 by Herbert J. Bernstein

Updated motif for thin shells using around instead of within

Revision 174
Modified Tuesday, March 27, 2012 by Herbert J. Bernstein

Fix bad selections -- HJB

Revision 173
Modified Tuesday, March 27, 2012  by Herbert J. Bernstein

correct typo in promolglobals
change to Jess motifs using shells instead of spheres -- HJB

Revision 172
Modified Monday, March 26, 2012 by Madolyn MacDonald

RMSD implemented, a few bugs still need to be fixed

Revision 171
Modified Thursday, March 22, 2012 by Herbert J. Bernstein

Backconvert promolglobals to allow it to run with python 2.5 by replacing
with and .format with older code -- HJB

Revision 170
Modified Thursday, March 22, 2012 by Herbert J. Bernstein

Backconvert 4.2 motif.py to work with python 2.5 by replacing
with clauses by try...finally clauses, and replacing .format
with % -- HJB

Revision 167
Modified Monday, February 20, 2012 by Cyprian Corwin

Changed Random PDB selection to only download the master list once per 
program start, like it did before 4.2.  In 4.2, due to the removal of the 
persistent database class, the download began occcuring each time the 
button is clicked (my fault).  This revision introduces a trivial 
change that eliminates many of these unneccessary data downloads; 
more importantly, the code present in 4.2 appears to max out the number 
of connections to the server as well, which should be fixed here too.

Revision 164
Modified Thursday, February 16, 2012 by Herbert J. Bernstein

Set up framework for installer development, starting with work
by Barry LaPierre at Dowling in Fall 2011 -- HJB

Revision 160
Modified Tuesday, December 13, 2011 by Cyprian Corwin

r160: Restored Alex's algorithm version constant and include it in 
CSV headers; automatically hide the PyMOL Viewer window when starting 
a search and restore it when finished; changed format of version 
string to a simple SVN revision number for now.

Revision 159
Modified Friday, December 9, 2011 by Cyprian Corwin

4.2.12.  Thoroughly commented promolglobals.py; removed 2 unused 
dictionaries; fixed 2 spots where in a previous revision I changed 
the name of something but missed changing it in 2 other spots; improved 
motif maker file closing code.

Revision 158
Modified Thursday, December 8, 2011 by Cyprian Corwin

ProMOL 4.2.11.  Updated funding info, restored on demand full CSV 
export, changed mode of all file operations from binary to text, 
removed help button, and replaced tabs with spaces in splitRespectingQuotes().

Revision 157
Modified Friday, December 2, 2011 by Cyprian Corwin

ProMOL 4.2.10.  The list of changes is extensive, and will be described 
in detail in a document soon to be sent out to the SBEVSL mailing list.

Revision 156
Modified Saturday, August 27, 2011 by Cyprian Corwin

Version 4.2.9.  Commented out Optimize button on Motif Maker, since 
the algorithm it uses has a problem and Greg Dodge said it was not needed.

Revision 155
Modified Saturday, August 27, 2011 by Cyprian Corwin

Version 4.2.8.  Created subfolder in OFFSITE user data folder just 
for automatically created CSVs.  Reworked CSV export user interface.  
Implemented opening of new CSV folder on demand.  Also replaced a 
tab with spaces.


Revision 154 
Modified Wednesday, August 10, 2011 by Cyprian Corwin

4.2.7: Restored order recommendation button in motif maker (now 
labeled Optimize), however it currently deletes multiple rows 
containing the same amino acid even at different locations/chains.  
Removed duplicate copy of GPL.  Moved version string into its own 
file.

Revision 153
Modified Tuesday, Aug 09 2011 by Cyprian Corwin

ProMOL 4.2.6 - added basic support for row reordering in Motif Maker.

Revision 152
Modified Friday, Aug 05, 2011 by Cyprian Corwin

These are the changes for 4.2.5, which is a development version.  
Most of the files that make up ProMOL were modified, and the 
change list is rather extensive, so PLEASE read the updated 
change log near the bottom of the readme file.  (The file promol-
changes has not been updated since 4.2.0.)  This version should be 
considered an experimental work in progress, and at least one feature 
has been temporarily disabled.  It still needs to be thoroughly tested.  
Also, please note that in at least one file, the standard diff utility, 
and tools that depend on it, does not properly match up the changes, 
so it appears to be more different than it is.

Revusuib 164
Modified Thursday, February 16, 2012 by Herbert J. Bernstein
Set up framework for installer development, starting with work
by Barry LaPierre at Dowling in Fall 2011 -- HJB

Revision 151
Modified Tuesday, July 26, 2011 by Herbert J. Bernstein

Update to Release 4.2

Revision 149
Modified Monday, July 25, 2011 by Cyprian Corwin and Greg Dodge
Version 4.2.  Many bug fixes, a few enhancements, and code cleanup
based on Maddy's Revision 142.  Major changes from 142 include a new,
larger set of 440 motifs, removal of PERSISTENT database code,
changes to the way PDB structures are fetched and the way
the PDB Loader Service dialog is launched from within ProMOL, simplification of
the way in which aligned matches are rendered and named (when double-clicking
a result in Motif Finder), a fix for the issue preventing the creation of
motifs for active sites containing alanine, and a fix for the hang that
would formerly happen when a motif search returned zero results, among others.
For the full list, please see the file promol-changes.txt.

Revision 119
Modified Tue Dec 7 by vinnyrose
Version 4.1rc2. Minor backwards compatibility fix. Updated readme.

Revision 115
Modified Thu Aug 5 by vinnyrose 
Version 4.1rc1. Added and alignment option in the motif finder. [Turn alignment
on and double click on a motif in the result box to see the alignment of the
template pdb to the test pdb. The color of each may be specified by clicking on
the color boxes adjacent to "template color" and "motif color". These boxes are
only clickable if alignment is clicked on. The alignment box does not have to be
clicked on prior to starting a test, but it does need to be clicked on prior to
double clicking a result if you want the alignment to appear. You cannot align a
PDB with itself.] Many sorts have been changed to be faster and to have
backwards and forwards compatibility. All motifs have been changed to include a
LOCI attribute which includes information on where the residues were located in
the original template pdb. The motif maker has been updated to include the LOCI
attribute. The color functions have been changed to make the custom colors more
optimized and to avoid conflicting colors. global.show_as function added to
compensate for cmd.as being changed to cmd.show_as due to reservation of 'as' in
python 2.6. More reliable and faster finding of chains in global.update
function.

Revision 110
Modified Tue Jul 20 by vinnyrose 
Fetch falls back to non-compressed on zlib error. Thanks button removed.

Revision 109 
Modified Wed Jul 14 by yaya-hjb 

Add actual authors on copyright line.
Add gpl.txt
Needs a readme. -- HJB

Revision 107 
Modified Tue Jul 13 by vinnyrose 

System dependent bug fix.

Revision 105 
Modified Tue Jul 13 by vinnyrose 

ProMol
Changed persistent storage. Changed gui dictionary to a class object. Several 
small bug fixes. Promol will now advise the user to install the 'ProMol' folder
if it was not installed in the startup folder. Bug in random pdb fixed, now it 
actually is random. Version 4.0rc4.
ConSCRIPT
Some small fixes. 2.0rc4.1

Revision 98 
Modified Tue Jul 6 by yaya-hjb 

Raise rc number to 3.2 -- HJB

Revision 94 
Modified Tue Jun 29 by vinnyrose 

ConSCRIPT select function fixed. Many changes made to the structure of the code 
including making the class truly classified. Before all the functions were in 
the init of the class. The handle command now looks at token equality instead 
of command substrings. Parsing colors has been modified to a smaller code base.
Promol: some small bug fixes in the motif maker that occur when unwanted spaces
occur in the input fields, a fixed motif was added. A better way of updating
motif files is needed when this is all distributed. Version changed to 3.6.2.
Version 4.0 candidate 3.2

Revision 93 
Modified Fri Jun 25 by vinnyrose 

Some small bug fixes. Version changed to 3.6.1. Version 4.0 candidate 3.1.

Revision 92 
Modified Tue Jun 22 by vinnyrose 

Some small bug fixes. Updated the motif finder to support batch processing.
Motif maker has the capablity to change the order of the motifs being made.
Several organizational changes such as folder names and locations.
ChimeConverter is now active, and accessible with the 'c' command prefix.
Pmw has been replace by tkinter functions in many places.
Version changed to 3.06. Version 4.0 candidate 3.

Revision 88 
Modified Fri Jun 11 by vinnyrose 

Added all the motifs made so far. Created error reporting on motif loading.
Changed welcome screen. All pdb's entered into motif maker will be lowercased.
4.0 release candidate 2. (3.05)

Revision 87 
Modified Thu Jun 10 by vinnyrose 

Several changes. The motif maker has some bug fixes, as well as the ability to
check against homologs and random pdb's. The motif finder uses a levenshtein
distance calculation and reports the minimum and maximum (min/max) edit
distance found, if the min and max are the same it reports one distance.
It searches into each chain individually and the whole structure. In addition
it searches through every permutation of residues in cases where that is
applicable. Version changed to 3.04. Version 4.0 candidate.

Revision 86 
Modified Mon Mar 22 by vinnyrose 

Residues are capital insensitive in motif maker, multiple ec numbers can be
entered separated by a comma. The motifs are going through the last steps to
transfer them to individual files.

Revision 85 
Modified Sun Mar 21 by vinnyrose 

Some small changes, and preparing the motifs to be separated into individual 
files

Revision 83 
Modified Wed Mar 17 by vinnyrose 

More changes to the motif maker.

Revision 82 
Modified Wed Mar 17 by vinnyrose 

Changes to ConSCRIPT to make it compatible with Linux.

Many changes to ProMol.
Changed motif maker to have it's own tab, and am still working on making it
compatible with motif finder.
Made changes to make it more compatible with linux and need to make more
changes in that area.
Changed the GUI in many areas.
Deleted many motifs that don't seem to have a use right now. 

Revision 81 
Modified Tue Feb 16 by vinnyrose 

Remove reference to batch motif.

Revision 74 
Modified Wed Feb 3 by vinnyrose 

Temporarily commented out some tabs.

Revision 73 
Modified Mon Feb 1 by vinnyrose 

Moved remote_pdb_load into the Promol_dir as well as make a few changes in the
code. Made the motif finder faster.

Revision 65 
Modified Tue Jan 26 by vinnyrose 

Jess templates are done. Motif finder reworked. Random PDB finder is working
again.

Revision 63 
Modified Thu Jan 7 by vinnyrose 

Hooking stuff onto the new organization. Most Motif related functions have been
hooked on.

Revision 62 
Modified Thu Dec 24 by vinnyrose 

Made lots of organizational changes. Stable but with many bugs.

Revision 60 
Modified Tue Dec 15 by vinnyrose 

Made changes to the built-in motifs. No functionality changes, just making
things prettier. Still unstable, latest stable in 57.

Revision 59 
Modified Mon Dec 14 by vinnyrose 

This revision is absolutely positively unstable, DO NOT USE IT!

Removed unnecessary files and folders.

Removed ProMOL_302. If you want the latest stable go to revision 57.

Changed amino acid pictures names so that they are not confusing.

Changes to ProMol.py include:
	separating the code into multiple files
	Optimizing the code
	standardizing the formatting
This is the first commit in several to come that will dramatically change the
code. The functionality in most cases will not be changed.

Much of the indentation is not correct due an attempt to standardize.
Indentations will be fixed in a future revision.

Revision 58 
Modified Mon Dec 14 by vinnyrose 

~/Desktop/commit.rtf

Revision 57 
Modified Thu Jul 9 by vinnyrose 

the make motif function can now handle between 2 and 10 residue motifs and is
much faster. The make motif window can now handle empty rows. Amino acid list
are in alphabetical order. Trimmed white space at the end of lines. Made global
list of amino acids three letter codes. And made global list of alphabetical
letters.

Revision 55 
Modified Fri Jun 12 by vinnyrose 

Revisions made to makemotif fuction:
This revision is able to build a motif for active sites that have repeating
amino acids. The code has been commented so that it can be followed more easily
and the motifs that are built now have a smaller file size. The while loops
were improved and variable names were changed. -MROSA

Revision 40 
Modified Tue Jul 22 by yaya-hjb 

Correct spacing garbled on last upload -- HJB

Revision 39 
Modified Wed Jul 16 by yaya-hjb 

This update allows users to use commands that were once only available
in ProMOL in the command line as well as scripts (as long as
ProMOL itself is open).  See ProMOL_README.txt.
Mod by C. Wischmeyer. -- HJB

Revision 36 
Modified Wed Jun 25 by yaya-hjb 

Mods by Corey Wischmeyer introducing commands for ProMol ops
See the sbevsl wiki on sourceforge for details.

Revision 34 
Added Wed Jun 11 by yaya-hjb 
Copied from: trunk/promol/ProMOL_302.py revision 33
Remove version from name of ProMol.py, update to 303 with
batch motifier.  Mods by Corey Wischmeyer. -- HJB