Subject: [MMTK] MMTK 2.5.5 (fwd from khinsen * cea.fr)

From: Eugen Leitl <eugen * leitl.org>
Date: Mon, 21 Feb 2005 15:36:30 +0100

----- Forwarded message from khinsen * cea.fr -----

From: khinsen * cea.fr
Date: Mon, 21 Feb 2005 15:21:57 +0100
To: "mmtk * python.net list" <mmtk * python.net>
Subject: [MMTK] MMTK 2.5.5
X-Mailer: Apple Mail (2.619.2)

A new development release of MMTK, 2.5.5, is available now at the=20
standard locations. There are two new features that qualify as=20
experimental: the definition of molecules from within a Python script,=20
and the storage of molecular systems in XML files.

The new module MMTK.MoleculeFactory permits the definition of groups=20
and molecules in terms of atoms, groups, and bonds. Coordinates and=20
attributes can be defined as well. See the example=20
Miscellaneous/molecule_factory.py for an illustration of its use. This=20
approach to molecule construction is complementary to the usual one of=20
writing database definition files. Depending on the application, one or=20
the other may be more practical.

The XML file storage is a result of a discussion on an FSAtom mailing=20
list a while ago. The goal was the development of an XML interchange=20
format to be used by many molecular simulation packages. There was a=20
lively discussion about the format itself, but when the question turned=20
to actually implementing one in various programs, the list went silent.

The format now implemented in MMTK is the last proposal I made on that=20
list. It uses CML tags as much as possible, though I won't claim that=20
it actually is CML, as CML is so huge that I never looked at all the=20
details of the definition. At the moment there is no other program that=20
uses the same format so its use for exchanging data is more than=20
limited. However, it can already be used to apply XML tools to=20
molecular systems definitions. If a concensus about an XML exchange=20
format ever evolves and gets implemented, I will probably modify MMTK's=20
XML code to use that format as well.

To write any object (molecule, universe, ...) to an XML file, use the=20
method writeXML(). To read an XML file, use the module MMTK.XML and see=20
the example Miscellaneous/read_xml.py.

Note that for reading XML files you must have the cElementTree module=20
installed. You can obtain it from  =20
http://effbot.org/zone/celementtree.htm

Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Laboratoire L=E9on Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: khinsen * cea.fr
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