[Molecularmechanics] Recommendations for object oriented approaches / UML models

[peter murray-rust]

At 09:08 04/04/2006, Marc Baaden wrote:

>Hi,
>
>I hope that this message is not off-topic and that this list is not dead (last
>message from February 2005?).
>
>I was wondering whether there is any kind of standard for treating 
>molecular systems
>and molecules when it comes to object oriented approaches. I was 
>thinking along the
>lines of a generic UML model which would be applicable to any kind 
>of object oriented
>language.
>As I am new to these approaches (object oriented in general and UML 
>in particular),
>I wonder whether it is better to use (if it exists) such a model
>or alternatively to develop a new one more specifically tailored to 
>a given application.
>
>The aim of the application(s) I have in mind is to manipulate 
>molecular data as well
>as simulation output (trajectories) in various phases of 
>preparation&setup, production and
>post-production/analysis, which is why I am looking for a rather 
>general model.

I don't believe that anyone has managed to address all the points you 
mention - it is much more ambitious than it appears.

We have developed an OO approach to many of the static aspects of 
small molecular systems with CML and by translating the XSD schema 
automatically to Java. There are ca 100 significant object classes. 
See cml.sf.net including the Wiki and www.sf.net/projects/cml for the 
CVS repository

My personal feeling is that extending OO to dynamics and trajectories 
may be more effort than it is worth unless we can standardise our 
communal representation of the systems - I don't know whether this is 
possible. There are many hidden semantics in these systems.

P.



Peter Murray-Rust
Unilever Centre for Molecular Sciences Informatics
University of Cambridge,
Lensfield Road,  Cambridge CB2 1EW, UK
+44-1223-763069