[Biopython-dev] [Bug 2951] New: PDBParser assigns model 0 to first model no matter what...
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Tue Nov 17 01:11:32 EST 2009
http://bugzilla.open-bio.org/show_bug.cgi?id=2951
Summary: PDBParser assigns model 0 to first model no matter
what...
Product: Biopython
Version: 1.52
Platform: PC
OS/Version: Windows XP
Status: NEW
Severity: normal
Priority: P2
Component: Main Distribution
AssignedTo: biopython-dev at biopython.org
ReportedBy: TallPaulInJax at yahoo.com
I'm not sure if this is a bug or a feature, but PDBParser assigns the first
model it sees as model 0 then increments that. This means someone thinking they
are studying model X is actually studying X+1, and that assumes that authors
always use sequential model numbers without skips. If authors CAN skip model
number, ie, MODEL 2, then MODEL 4, then MODEL 5... then in biopython these be
models 0,1, and 2 in the structure... yuck.
If this needs to be maintained for posterity, I would suggest adding another
field to capture the TRUE model number if it exists.
See lines 106 and 122 here:
http://github.com/biopython/biopython/blob/master/Bio/PDB/PDBParser.py#106
Paul
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