[Biopython-dev] [Bug 3171] New: inconsistent representation of missing elements PDB.PDBIO.PDBIO and PDB.Atom.Atom

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

http://bugzilla.open-bio.org/show_bug.cgi?id=3171

           Summary: inconsistent representation of missing elements
                    PDB.PDBIO.PDBIO and PDB.Atom.Atom
           Product: Biopython
           Version: 1.56
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: edvin.fuglebakk at gmail.com


There seems to be an inconsistency in the way missing elements are represented
in PDB.PDBIO.PDBIO and PDB.Atom.Atom.

The constructor of Atom sets the attribute element to '?' if this is unkown,
while PDBIO raises a value error if it encouters atoms with the element set to
'?'. PDBIO._get_atom_line checks if Atom.element is falsish (None, False, 0
...) and chanhes the value of Atom.element to " " if it is.

So it seems Atom represents missing elements by "?", while PDBIO represents
them by falsish values, presumably None.


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