[Biojava-dev] [Bug 3132] SITE records in PDBFileReader

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

http://bugzilla.open-bio.org/show_bug.cgi?id=3132





------- Comment #7 from darnells at dnastar.com  2010-09-03 15:55 EST -------
There is a defect in PDBFileParser.java regarding sites.

Line 2044: String pdbCode = groupString.substring(4, 10).trim();

This assigns pdbCode to "$CHAIN $RESNUM$INSCODE" (e.g. "H 221A"), where the
Group interface documentation states it should just be $RESNUM$INSCODE (e.g.
"221A").  Also, setParent() is never called and assigned to a chain object.

Currently, to get the chain id for a site residue, you need to use the first
character of pdbCode.  Is it possible to link the site residue groups to their
correct chain?  This is somewhat analogous to SSBond; is a similar approach
appropriate?


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