[MMTK] [PyMOL] improving interoperability between python molecule toolkits (fwd)

Eugen Leitl eugen@leitl.org
Thu, 12 Dec 2002 07:05:16 +0100 (CET)

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---------- Forwarded message ----------
Date: Thu, 12 Dec 2002 16:58:47 +1030
From: Michael Sorich <mike_sorich@hotmail.com>
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] improving interoperability between python molecule toolkits

Hello all,

I share in Warren's vision of extending PyMol into a "complete platform
for crystallography, computational chemistry, modeling, and
informatics". However, I believe this can only come about by cooperation
and integration with other python based molecule toolkits. MMTK has code
which may be expanded into a general molecular mechanics engine. Frowns
toolkit allows for detailed chemical analysis based on topology,
including useful tools such as substructure searching (required for
forcefield atom typing). PyQuante allows for Quantum Chemical

It seems to be in everyone's interest to allow easy interoperation
between the toolkits. However, in my experience it is a frustrating and
difficult task, even for relatively simple tasks. 

Does anyone else feel the same frustration? And if so, does anyone have
a solution?

I believe that a common set of core modules is required. The most
important feature is the molecule. Each toolkit uses a different
molecule, each with a different interface, holding different information
and optimised for specialised work. If a common molecule definition can
be agreed upon by the major authors of the toolkits concerned,
interoperability will be made MUCH easier. Other multipurpose molecular
modelling programs (MOE, Sybyl) seem to get by using a common molecule
definition, so I believe that it is theoretically possible. The aim
would be to define a molecule that contains all the functionality
required for the multiple toolkits and to maintain the interfaces used
by the toolkits as much as possible.

The question is whether the will exists to do this? Many of the toolkits
are relatively young. I feel that the longer the problem is ignored, the
less likely that it will be possible to combine features from various

I am interested in other people's thoughts on this matter.

Michael Sorich
PhD Student
School of Pharmaceutical, Molecular and Biomedical Sciences
University of South Australia
Email: michael.sorich@postgrads.unisa.edu.au

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