Gustavo Mercier <gamerc...@yahoo.com> 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. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hin...@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais -------------------------------------------------------------------------------
