Hi! I think the comments below are right on the money. I believe that a molecular modeling package powered by Python is a great idea, particularly for those who would like to teach computational chemistry. For example, many popular modeling packages allow the students to perform simulations using a black box approach. This is fine for introductory courses where the focus is on the end results relevant to the chemistry of a problem. In advanced undergraduate course, an instructor may wish to breakthrough the "black box". The scripting power of Python together with a set of modules would be the best tool for such a course. The students could program simulations using objects available through the modules. Each layer of the black box can be peeled by programming with lower level objects. Although I've been a bit away from Python (my last heavy use was with version 1.5x!), I certainly will support and even contribute to this effort. Unfortunately, the issue is one of leadership to initiate such a project. May be those who mantain MMTK, PyQuante, PyMol, etc. may be willing to take the initiative. The definition of a common object/data structure for the "molecule" is a first step. This is a critical step and a little bit of thought may go along way to make development not only easier but useful. It would be best not to rediscover the wheel. As a suggestion, let's consider the chemistry implementation of XML -- CML. Whatever the details of the object "molecule", it would be beneficial to input and output to/from CML. A specification of "molecule" based on CML would make it easier to interface with other technologies. I recognize that there are problems with CML, but this should not stop the community from considering this "standard". Gustavo Eugen Leitl <eu...@leitl.org> wrote:
-- -- Eugen* Leitl leitl ______________________________________________________________ ICBMTO: N48 04'14.8'' E11 36'41.2'' http://eugen.leitl.org 83E5CA02: EDE4 7193 0833 A96B 07A7 1A88 AA58 0E89 83E5 CA02 http://moleculardevices.org http://nanomachines.net ---------- Forwarded message ---------- Date: Thu, 12 Dec 2002 16:58:47 +1030 From: Michael Sorich 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. <cut stuff ...> 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. <cut stuff ...> -- Gustavo A. Mercier, Jr., MD,PhD Seattle Nuclear Medicine & U/S Associates 1229 Madison, Suite 1150 Seattle, WA 98104-1377 voice: 206-386-6300; fax: 206-386-6312 gamerc...@yahoo.com --------------------------------- Do you Yahoo!? New DSL Internet Access from SBC & Yahoo!
