[Biopython-dev] [Bug 2619] Bio.PDB.MMCIFParser component MMCIFlex commented out in setup.py

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2619





------- Comment #2 from cjoldfield at gmail.com  2008-10-21 13:42 EST -------
> In the short term, a note in the documentation would help... were you refering
> to "The Biopython Structural Bioinformatics FAQ"?
> http://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf

The FAQ in part, but there is also a link from RCSB that claims BioPython can
parse mmCIF:

http://sw-tools.rcsb.org/

I've run the Bio.PDB mmCIF parser over all of PDB, and it plain fails on >10%
of files (>40,000 files, >5,000 failures, mostly spurious missing key
exceptions).  From what I've seen, it seems that an inconsistency in one table
of a mmCIF file throws a wrench in the whole parse.  

I tried the C++ mmCIF parser from ncbi (only on a few files so far) and it
doesn't suffer these parse problems (though it reports the faulty entries).  If
Bio.PDB were to be updated, this seems like a good candidate for a back end
(assuming its portable).  I have the inclination, maybe not the time ;), to do
this, unless this should fall to Thomas or others.

Chris


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