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

Peter Murray-Rust pm286@cam.ac.uk
Thu, 19 Dec 2002 16:32:28 +0000


At 10:41 13/12/2002 +0100, Konrad Hinsen wrote:

>Gustavo Mercier <gamercier@yahoo.com> writes:

 >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

> > 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.

CML is designed to be extensible by a variety of mechanisms such as 
external ontologies and we would be delighted to hear from those who find 
it "too weak". We are currently developing a computational chemistry 
implementation (CCML) as previously mentioned on this list. The feature of 
XML languages is that XML requires semantics to be well designed and 
interoperable, *and* to have communally available software tools for 
reading, validating and writing and linking to ontologies.  CML is designed 
for collaborative working and  we shall shortly announce the mailing list.

P.

Unilever Centre for Molecular Informatics
Cambridge University, UK