[Biopython-dev] [Bug 2933] New: PDBList() get_status_list bug

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2933

           Summary: PDBList() get_status_list bug
           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


Hi,

Upon testing, I believe the following code in the PDBList class get_status_list
 method is based on an older file format for added.pdb, modified.pdb, and
obsolete.pdb:

        # added by S. Lee
        list = map(lambda x: x[3:7], \
                   filter(lambda x: x[-4:] == '.ent', \
                          map(lambda x: x.split()[-1], file)))

I think the file format used to be:
-rw-r--r--   1 rcsb     rcsb      330156 Oct 14  2003 pdb1cyq.ent
-rw-r--r--   1 rcsb     rcsb      333639 Oct 14  2003 pdb1cz0.ent

Now the file format is simply:
1cyq
1cz0
etc

Therefore, I believe the correct code to be:
        list = map(lambda x: x[0:4], file)

Paul


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