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
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