[Biopython-dev] Re: [BioPython] martel & mindy

Thomas Hamelryck thamelry at vub.ac.be
Thu Jul 18 06:02:16 EDT 2002

> Oooh, can I do that with PDB? Can anyone point me to documentation?

What exactly do you want to do? 

> I have the CVS version of BioPython with PDB parser but don't know much
> about its internals yet. 

It only parses the atomic data and puts this in a nice hierarchical data 
structure (Structure-Model-Chain-Residue-Atom). It doesn't look at the PDB 
header at all. I assume you want to get info from the header.

As far as I can see it does not make much sense to do the parsing of the 
atomic data with Martel. Martel would be excellent to parse the header. 

> It is also pretty slow with big records, and
> building an index on just a few fields would be really useful.

Slow? It builds a full SMCRA datastructure+sanity checking in
3s for an 11000 atom structure. That's quite OK I think! Of course that's 
completely unimpressive if you need data from the header....


Thomas Hamelryck      Vrije Universiteit Brussel (VUB)
Intitute for Molecular Biology            ULTR Department
Paardenstraat 65    1640 Sint-Gensius-Rode, Belgium

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