[Biopython-dev] [Biopython (old issues only) - Bug #3146] DSSP ungraceful failure

[redmine at redmine.open-bio.org]

Issue #3146 has been updated by Peter Cock.

Description updated

It would appear the PDB parser is more noisy about warnings, but were you able to run the DSSP part as well Vincent?

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Bug #3146: DSSP ungraceful failure
https://redmine.open-bio.org/issues/3146#change-15344

* Author: Patrick empty
* Status: New
* Priority: Low
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: 1.53
* URL: 
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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, ' ')

---Files--------------------------------
pdb2p0i.ent (2.24 MB)


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