[Biopython-dev] [Bug 2751] New: PDBParser crashes on empty tempFactor fields

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2751

           Summary: PDBParser crashes on empty tempFactor fields
           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: eric.talevich at gmail.com


When parsing ATOM lines, Bio.PDB.PDBParser appears to be passing the contents
of indexes 60-66 directly to the float() constructor without checking if the
string is empty (or all spaces).

The PDB spec seems to indicate that the default value for this field should be
0.0:
http://www.wwpdb.org/documentation/format23/sect9.html#ATOM

I interpret that to mean PDBParser should assume 0.0 if the string is blank, at
least in permissive mode; otherwise, perhaps a PDBException should be raised.


Here's a traceback:

  File "/usr/lib/python2.5/site-packages/Bio/PDB/PDBParser.py", line 66, in
get_structure
    self._parse(file.readlines())
  File "/usr/lib/python2.5/site-packages/Bio/PDB/PDBParser.py", line 86, in
_parse
    self.trailer=self._parse_coordinates(coords_trailer)
  File "/usr/lib/python2.5/site-packages/Bio/PDB/PDBParser.py", line 160, in
_parse_coordinates
    bfactor=float(line[60:66])
ValueError: empty string for float()


This occurs when parsing a file that looks like this:

HEADER    1ad5
ATOM   4255  N   GLU B  82      -6.363  45.622 156.936  1.00 69.02        
ATOM   4256  CA  GLU B  82      -6.235  44.414 157.713  1.00 68.26        
ATOM   4257  C   GLU B  82      -5.067  44.774 158.648  1.00 68.19        
ATOM   4258  O   GLU B  82      -5.169  45.863 159.227  1.00 67.24        
ATOM   4259  CB  GLU B  82      -5.903  43.230 156.774  1.00 68.47        
ATOM   4260  H1  GLU B  82      -6.252  46.392 157.641  1.00 0
ATOM   4261  H2  GLU B  82      -5.588  45.683 156.246  1.00 0
ATOM   4262  H3  GLU B  82      -7.267  45.667 156.437  1.00 0
ATOM   4263  N   ASP B  83      -3.979  43.981 158.770  1.00 67.44   
...


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