[Biopython-dev] [Bug 2780] New: PDB file HETATMs cannot be alternative location of a residue that is an ATOM

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2780

           Summary: PDB file HETATMs cannot be alternative location of a
                    residue that is an ATOM
           Product: Biopython
           Version: 1.49
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: klaus.kopec at tuebingen.mpg.de


In PDB files where HETATMs and ATOMs are altlocs of each other (e.g. 1RR2,
residue 184), they are treated as two separate residues.

A obvious solution is to add an "else" case to the "if" in StructureBuilder.py
line 115 (method init_residue(...)) that introduces some kind of mixed (HETATM
as well as ATOM) DisorderedResidue.

The Main problem with that: the hetero field of the residue ids will differ
between the residues, therefore the whole access-over-ids mechanism will most
likely not work with these MixedDisorderedResidues as straight forward as it
does so far.

Sadly, I could not come up with a good solution for this. Maybe some
__getattr__ magic that alters the way Chains access their residues might work
by allowing access to residues by only using the second and third component of
the id 3-tuple?!


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