[Biojava-l] biojava and STRAP

[Andreas Prlic]

Hi Christoph!


> Further it has a very fast PDB and DSSP parsers (30ms per PDB-file).

I contributed  a PDB parser and data model to biojava - CVS a while 
ago. The parser mainly parses the coordinate section of the PDB files, 
so it would be nice to get the header section parsed as well. - though 
I think that parsing of either header or atoms should be optional.

Is your parser event-based? That would be an improvement to the current 
one and it would allow fine tuned (and therefore fast) parsing of PDB 
files according to people/algorithm needs. E.g. It would be interesting 
to have event listeners that only parse Ca atoms - or only the 
mainchain atoms, etc. depending on the application. The current 
implementation will create an all atom representation of the PDB file.

The PDB data model is designed so it can deal with various exceptions 
that occur within protein structures  and the idea was that it should 
be possible to develop algorithms on top of it.

regarding DSSP: yes would be nice to have a parser for it.  :-)


> There is a wrapper for Rasmol and Pymol and a specialized multi-model
> 3D-wire viewer.

wrapper to rasmol ? Does this mean you pipe rasmol script commands to 
it?
Personally,  I usually recommend the Jmol viewer - also "speaks" rasmol 
:-)

Gruesze,
Andreas

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Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK