[Biopython-dev] [Bug 2290] New: Not reading 1YVE.pdb

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2290

           Summary: Not reading 1YVE.pdb
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: proszek at gmail.com


biopython 1.42 fails to read 1YVE.pdb file, although it reads test.pdb created
by:
awk '{if($1=="ATOM"){print}}' 1YVE.pdb
line 8610 is a HETATM line

Traceback below (where file=sys.argv[1]=1YVE.pdb)

WARNING: Chain J is discontinuous at line 8610.
Traceback (most recent call last):
  File "./wezly.py", line 122, in ?
    b=Protein(sys.argv[1])
  File "./wezly.py", line 15, in __init__
    self.struct=self.parser.get_structure('X',file)
  File "/usr/lib/python2.4/site-packages/Bio/PDB/PDBParser.py", line 66, in
get_structure
    self._parse(file.readlines())
  File "/usr/lib/python2.4/site-packages/Bio/PDB/PDBParser.py", line 87, in
_parse
    self.trailer=self._parse_coordinates(coords_trailer)
  File "/usr/lib/python2.4/site-packages/Bio/PDB/PDBParser.py", line 179, in
_parse_coordinates
    structure_builder.init_residue(resname, hetero_flag, resseq, icode)
  File "/usr/lib/python2.4/site-packages/Bio/PDB/StructureBuilder.py", line
155, in init_residue
    self.chain.add(residue)
  File "/usr/lib/python2.4/site-packages/Bio/PDB/Entity.py", line 80, in add
    raise PDBConstructionException, "%s defined twice" % entity.get_full_id()
  File "/usr/lib/python2.4/site-packages/Bio/PDB/Entity.py", line 132, in
get_full_id
    parent=self.get_parent()
  File "/usr/lib/python2.4/site-packages/Bio/PDB/Entity.py", line 102, in
get_parent
    raise PDBException, 'No parent'
PDBException: No parent


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