[Biopython-dev] [Bug 2931] New: Error in PDBList() code for get_all_obsolete

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2931

           Summary: Error in PDBList() code for get_all_obsolete
           Product: Biopython
           Version: 1.52
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Other
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: TallPaulInJax at yahoo.com


Hi,

I believe this code:
        # extract pdb codes
        obsolete = map(lambda x: x[21:25].lower(),
                       filter(lambda x: x[:6] == 'OBSLTE', url.readlines()))

Should instead be
        # extract pdb codes
        obsolete = map(lambda x: x[20:24].lower(),
                       filter(lambda x: x[:6] == 'OBSLTE', url.readlines()))

As-is, it is missing the first characters of the PDB code and reading one
character past it's end upon testing.

Paul


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