[Biopython-dev] [Bug 2751] PDBParser crashes on empty tempFactor fields

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

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


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.