[Biopython] Bio.PDB and Bio.SeqIO.PdbIO

[Téletchéa Stéphane]

Le 20/02/2015 15:28, Tiago Antao a écrit :
> Or, to put it another way, a generic PDB file is not completely
> accessible from inside Biopython in the sense that we cannot access
> some of the records (SHEET and HELIX being the examples here). Or is
> there a way to get to them via Bio.PDB?

To be more generic, parsing pdb files is a mess since the PDB format has
evolved a lot and is quite  "uncontrolled".

If you are looking for pdb parsers, you either have to enrich existing ones,
or rely on specific ones, like for instance:

http://bioserv.rpbs.univ-paris-diderot.fr/software/PDBpy/
http://prody.csb.pitt.edu/tutorials/structure_analysis/pdbfiles.html
https://code.google.com/p/pdbparse/

But after trying them all (and of course biopython routines), my 
experience is
that a lot of precautions must be used (nearly a try/except for each 
REMARK/HEADER
section), and even with this, you'll have to set up your own list of 
problematic
pdb files to have testable hypothesis.

Best,

Stéphane

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