[Molecularmechanics] Recommendations for object oriented approaches / UML models

[Konrad Hinsen]

On Apr 4, 2006, at 10:08, Marc Baaden wrote:

> I hope that this message is not off-topic and that this list is not  
> dead (last
> message from February 2005?).

You just started a revival!

> 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.

I am not aware of any such standard. The closest attempt was probably  
the workshop "Computational Representation of Biomolecules" held in  
2003. Its goal was to work towards a common object-oriented API for  
working with biomolecules. Although UML was not mentioned, it would  
be one way to defined a specification for such an API. For more  
information, look at the workshop report:

	https://mgldev.scripps.edu/CRBM/report

Unfortunately, there has been no follow-up until now. A second  
workshop was planned for March 2006, but apparently hasn't taken place.

> 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.

What exactly is your goal? Do you want to write software, find  
software ready to use, glue together different software, define an  
interchange standard, or yet something else?

I agree with Peter that a full formal description of molecular  
simulation would be a very ambitious project, considering the many  
different approaches already published and the even more numerous  
techniques and models still under development. I am not sure that  
formal approaches such as UML, which were developed for big software  
projects, are well adapted to scientific computing, which is  
characterized by fast change and small development groups.

If you are new to OO techniques, you might want to start by looking  
at existing OO approaches to molecular simulation. The ones I am  
aware of are (in alphabetical order):

- Adun: http://diana.imim.es/Adun
- mmLib: http://pymmlib.sourceforge.net/
- NAMD: http://www.ks.uiuc.edu/Research/namd/
- OOMPAA: http://mccammon.ucsd.edu/~oompaa/
- OOPSE: http://oopse.org/

and my very own one:

- MMTK: http://dirac.cnrs-orleans.fr/MMTK/

Konrad.
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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: konrad.hinsen at cea.fr
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