[MMTK] MMTK 2.5.5

david.evans at ulsop.ac.uk david.evans at ulsop.ac.uk
Tue Feb 22 11:12:24 CET 2005


Hi,

I've been working in my spare time on writing a crude docking program
using MMTK, (it'll
probably never do anything useful, but never mind)
so I'm interested in ways to define new small molecules.
Would it be sensible to use the ModuleFactory code to write a parser
to create a molecule
from a mol2 file (since this contains atom types, charges and bond
information)?

Thanks

Dave


---- Message from khinsen at cea.fr at 2005-02-21 15:21:57 ------
>A new development release of MMTK, 2.5.5, is available now at the 
>standard locations. There are two new features that qualify as 
>experimental: the definition of molecules from within a Python
script, 
>and the storage of molecular systems in XML files.
>
>The new module MMTK.MoleculeFactory permits the definition of groups 
>and molecules in terms of atoms, groups, and bonds. Coordinates and 
>attributes can be defined as well. See the example 
>Miscellaneous/molecule_factory.py for an illustration of its use.
This 
>approach to molecule construction is complementary to the usual one
of 
>writing database definition files. Depending on the application, one
or 
>the other may be more practical.
>
>The XML file storage is a result of a discussion on an FSAtom
mailing 
>list a while ago. The goal was the development of an XML interchange 
>format to be used by many molecular simulation packages. There was a 
>lively discussion about the format itself, but when the question
turned 
>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 
>list. It uses CML tags as much as possible, though I won't claim
that 
>it actually is CML, as CML is so huge that I never looked at all the 
>details of the definition. At the moment there is no other program
that 
>uses the same format so its use for exchanging data is more than 
>limited. However, it can already be used to apply XML tools to 
>molecular systems definitions. If a concensus about an XML exchange 
>format ever evolves and gets implemented, I will probably modify
MMTK's 
>XML code to use that format as well.
>
>To write any object (molecule, universe, ...) to an XML file, use
the 
>method writeXML(). To read an XML file, use the module MMTK.XML and
see 
>the example Miscellaneous/read_xml.py.
>
>Note that for reading XML files you must have the cElementTree
module 
>installed. You can obtain it from   
>http://effbot.org/zone/celementtree.htm
>
>Konrad.
>--
>---------------------------------------------------------------------
>Konrad Hinsen
>Laboratoire Léon 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 at cea.fr
>---------------------------------------------------------------------
>
>
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