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

From: Konrad Hinsen <[email-masked]>
Date: 13 Dec 2002 10:41:30 +0100

Gustavo Mercier <[email-masked]> writes:

> to the chemistry of a problem. In advanced undergraduate course, an
> instructor may wish to breakthrough the "black box". The scripting

*Should* wish to do so. Understanding what one is doing is the
difference between a scientist and a lab technician.

> 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.

This issue has been addressed at a meeting on OpenSource software for
atomistic simulations (which includes physics and chemistry) this
year. The result is the formation of an informal organization called
"FSAtom": http://www.fsatom.org/ Among the goals of this organizations
is the design of common interfaces to ensure the interoperability of
OpenSource codes. There will be more meetings (not committee style,
but scientific workshops) as well as mailing list discussions.
Everybody is welcome to join.

> may go along way to make development not only easier but useful. It
> would be best not to rediscover the wheel.

And come up with a hexagon ;-)

> 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

I don't agree. I looked at CML a while ago, thought about implementing
it in MMTK, but quickly found out that almost none of the information
I needed to store about molecules could be represented in CML, except
by adding "conventions" of my own - but then I could just as well
define my own XML format. CML is based on the right intentions, but is
too weak as an implementation.

BTW, common file formats are another goal of the FSAtom organization.

Konrad.
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From: Richard Muller <[email-masked]>
Date: Fri, 13 Dec 2002 09:20:41 -0800

> BTW, common file formats are another goal of the FSAtom organization.

Konrad,

Thanks for the reminder about FSAtom. Maybe we should start a 
discussion somewhere about what needs to be included in either a common 
file format or a common interface.

R.

Rick Muller
[email-masked]
http://wag.caltech.edu/home/rpm