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

[redmine at redmine.open-bio.org]

Issue #3146 has been updated by Vincent Davis.

File pdb2p0i.ent added

I am getting very different results on current biopython.

from Bio.PDB import PDBParser
parser = PDBParser()
from Bio.PDB.DSSP import DSSP
structure=parser.get_structure("2p0i","pdb2p0i.ent")

/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 27135.
  PDBConstructionWarning)
/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 27164.
  PDBConstructionWarning)
/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain C is discontinuous at line 27180.
  PDBConstructionWarning)
/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain D is discontinuous at line 27185.
  PDBConstructionWarning)
/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain E is discontinuous at line 27207.
  PDBConstructionWarning)
/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain F is discontinuous at line 27234.
  PDBConstructionWarning)
/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain G is discontinuous at line 27263.
  PDBConstructionWarning)
/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain H is discontinuous at line 27293.
  PDBConstructionWarning)
/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 27315.
  PDBConstructionWarning)
/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 27461.
  PDBConstructionWarning)
/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain C is discontinuous at line 27612.
  PDBConstructionWarning)
/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain D is discontinuous at line 27738.
  PDBConstructionWarning)
/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain E is discontinuous at line 27866.
  PDBConstructionWarning)
/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain F is discontinuous at line 27987.
  PDBConstructionWarning)
/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain G is discontinuous at line 28094.
  PDBConstructionWarning)
/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain H is discontinuous at line 28225.
  PDBConstructionWarning)



----------------------------------------
Bug #3146: DSSP ungraceful failure
https://redmine.open-bio.org/issues/3146#change-15336

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