[Biopython-dev] [Bug 3146] New: DSSP ungraceful failure

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

http://bugzilla.open-bio.org/show_bug.cgi?id=3146

           Summary: DSSP ungraceful failure
           Product: Biopython
           Version: 1.53
          Platform: PC
        OS/Version: All
            Status: NEW
          Severity: minor
          Priority: P4
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: patrick.winters at gmail.com


The DSSP annotator should probably fail gracefully when the PDBParser and DSSP
disagree about the existence of a residue at a certain position.  Here, DSSP
reports values for residue 115 of chain A, while the PDBParser throws a key
error.

from Bio.PDB import PDBParser
parser = PDBParser()
from Bio.PDB.DSSP import DSSP
structure=parser.get_structure("2p0i","pdb2p0i.ent")
model=structure[0]
dssp=DSSP(model, "pdb2p0i.ent")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/pymodules/python2.6/Bio/PDB/DSSP.py", line 175, in __init__
    res=chain[res_id]
  File "/usr/lib/pymodules/python2.6/Bio/PDB/Chain.py", line 71, in __getitem__
    return Entity.__getitem__(self, id)
  File "/usr/lib/pymodules/python2.6/Bio/PDB/Entity.py", line 38, in
__getitem__
    return self.child_dict[id]
KeyError: (' ', 115, ' ')
>>> model['A'][114]
<Residue GLN het=  resseq=114 icode= >
>>> model['A'][116]
<Residue TYR het=  resseq=116 icode= >
>>> model['A'][115]
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/pymodules/python2.6/Bio/PDB/Chain.py", line 71, in __getitem__
    return Entity.__getitem__(self, id)
  File "/usr/lib/pymodules/python2.6/Bio/PDB/Entity.py", line 38, in
__getitem__
    return self.child_dict[id]
KeyError: (' ', 115, ' ')


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