[Molecularmechanics] Recommendations for object oriented approaches / UML models

[peter murray-rust]

At 14:35 04/04/2006, Konrad Hinsen wrote:
>On Apr 4, 2006, at 14:40, peter murray-rust wrote:
>
>
>>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.

<cml:table> addresses these. It allows you to 
create tables with any numbers of columns and for 
those columns to be any <scalar> or other 
hardcoded CML value (e.g. x3, formalCharge, etc.) 
In this way it is trivial to emulate a PDB but 
with completely extensible semantics. You can 
design any new concept and add it through the 
dictionary mechanism. The primary requirement is 
that the table is rectangular and that values are 
whitespace (or other delimiter) separated . It 
can even be pretty printed For more complex data 
structures you have to resort to nested XML 
(which is at least more human friendly than relational tables).

It is implemented in JUMBO.

P.

>Konrad.
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>Konrad Hinsen
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>E-Mail: konrad.hinsen at cea.fr
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Peter Murray-Rust
Unilever Centre for Molecular Sciences Informatics
University of Cambridge,
Lensfield Road,  Cambridge CB2 1EW, UK
+44-1223-763069