[Molecularmechanics] CML info on the Wiki

[Konrad Hinsen]

On Tuesday 02 December 2003 19:39, Peter Murray-Rust wrote:

> CML is therefore designed to be used as a series of components rather than
> a "one fits all" chemical system. We are developing an approach to create
> schemas tailored to specific applications. Thus - in principle - GROMACS

OK, so we could have our sub-schema as well, I suppose. That sounds like a 
good project.

> The approach depends on being able to make components independent and to
> create an API automatically from the schema. So far this looks feasible.

The automatic API generation looks interesting. That should help a lot with 
tool development.

> scripting and glueware and not in compute-intensive regions. We expect that
> applications will read from CML, convert to internal data structure,
> compute, reconvert to CML and output.

Yes, of course. Some might want to use it internally for communication between 
components, but that wouldn't change much in this picture.

> The Wiki and the Java have already been automatically generated. We intend
> to extend this to C++, F90 and python. The code would provide means to read
> CML generically, with validation, and an API for accessing the data read
> in. Output is the reverse. A typical sequence (in pseudocode) is:

That sounds interesting. But is it possible to define internal data structures 
that are both sufficiently flexible to handle all of CML and sufficiently 
simple to use in a particular project that needs only a fraction of all that? 
The experience with DOM is rather disappointing in that respect. At least in 
the Python world, many programmers prefer to use the SAX interface and 
generate their own internal data structures, because the DOM trees are just 
too cumbersome to use, in addition to eating up memory for unused data.

If you would like some help with the Python implementation, just let me know.

Konrad.
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