[Bioperl-l] Parsing PDB entries in BioPerl

[Kris Boulez]

Quoting Sri Krishna S. (krishna@chop.swmed.edu):
> Hi kris,
> 
> > The idea is to parse every line in the entry and to have access to all
> > the data via some Bio:: object. The work on the SeqIO parser (Bio::SeqIO::pdb)
> > is progressing nicely.
>  
> Let me start with saying that I dont have much experience with perl.
> However I have seen lots of PDB files and the kind of inconsistencies in
> the format (sometimes biologically relevant). If possible I would
> recommend you to process the equivalent CIF file of the PDB. You will find
> the CIF file much easier to handle than the PDB file and ofcourse you will
> be able to get all the information that is present in the PDB file.
> 
[ explanation about some of the pecularities of the PDB format deleted ]

I completely agree with you and Jonathan Epstein (who suggested using
MMDB) that there are formats out there that are much easier to
parse/write and are much better from an IT standpoint.
But, we have (internally) a lot of data that is still in PDB format, and more
importantly most of our own software can only input/output PDB (and will
so for the forseeable future).
I also looked very quickly at some software packages (X-PLOR, dyana, swiss-pdb
viewer) and PDB seems the only/preferred format.

So I guess it not a question about which format is best, but which
format is used most.

Kris,
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