[Biopython-dev] [Bug 2951] New: PDBParser assigns model 0 to first model no matter what...

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

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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