[Biopython-dev] [Bug 2751] PDBParser crashes on empty tempFactor fields
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Mon Feb 9 12:20:46 EST 2009
http://bugzilla.open-bio.org/show_bug.cgi?id=2751
------- Comment #7 from biopython-bugzilla at maubp.freeserve.co.uk 2009-02-09 12:20 EST -------
Hi Eric,
Could you try out Bio/PDB/PDBParser.py CVS revision 1.25 please? This allows
missing occupancy and B factor (temp factor) fields in permissive mode, and the
exception or printed error message does include the line number.
I can appreciate that getting these warnings hundreds of times from a single
file would be annoying, so perhaps if the fields are just blank a single
warning should be given? If you can find any official PDB examples which do
this, or get clarification regarding the "legality" of omitting these fields,
then I would be happy to change this code. Where are you getting your PDB
files from?
Note that I have not attempted to deal with ANISOU, SIGUIJ or SIGATM records.
Do you have any examples of this, or were these changes just defensive
programming?
Peter
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