[Molecularmechanics] Recommendations for object oriented approaches / UML models

[Konrad Hinsen]

On Apr 4, 2006, at 14:40, peter murray-rust wrote:

> * it is important to have running code. Designs without code are of  
> limited value. They are usually overcomplex.

I think this is a very important point. Experience has shown that  
people are much more willing to debate (and thus complexify)  
specifications than to implement them. That has also been a major  
weakness of this list: in spite of lengthy discussions about a common  
format, no proposal has ever been implemented in more than one  
program, and therefore no test of usability in data exchange has ever  
been made.

> * Complicated systems will only be adopted if they can be shown to  
> produce real value and involved little effort. This is very hard to  
> achieve.

Indeed!

> CML - which describes a trajectory. And it should be done fairly  
> succinctly - people are frightened by data structures that do not  
> look like FORTRAN tables. For that

There is also the argument of human readability, a weak spot of many  
XML-based formats. For an illustration, try to find some specific  
information in a PDBML file. Good old PDB is much more user-friendly  
there - though it remains very deficient in many other respects.

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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