[Molecularmechanics] Recommendations for object oriented approaches / UML models

[David van der Spoel]

peter murray-rust wrote:
> 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.
> 

We are still considering doing something like this for GROMACS, but at a 
   minimum-effort kind of way. Design criteria
- simplicity: for developers and users
- compatibility: we can not expect our users to write XSLT files so we 
have to built in compatibility with older (GROMACS) formats and other 
"Industry Standard" formats such as pdb.

Although we should be able to use some of the CML stuff, much of the MD 
trajectories etc. is too specific to add into a CML itself.

I welcome a discussion just before we start coding...

> P.
> 
> 
> 
> Peter Murray-Rust
> Unilever Centre for Molecular Sciences Informatics
> University of Cambridge,
> Lensfield Road,  Cambridge CB2 1EW, UK
> +44-1223-763069
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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