[Biopython-dev] [Bug 2605] New: test_PDB failure with Python 2.6

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2605

           Summary: test_PDB failure with Python 2.6
           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: bsouthey at gmail.com


Running 'python setup.py test --no-gui' results in failure for test_PDB on
linux x86_64 running Python 2.6 compiled with gcc 4.3.2



======================================================================
ERROR: test_PDB                                                       
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 152, in runTest
    self.runSafeTest()
  File "run_tests.py", line 165, in runSafeTest
    cur_test = __import__(self.test_name)
  File "test_PDB.py", line 68, in <module>
    run_test()
  File "test_PDB.py", line 22, in run_test
    structure=p.get_structure("example", "PDB/a_structure.pdb")
  File
"/home/bsouthey/python/biopython_cvs/biopython/build/lib.linux-x86_64-2.6/Bio/PDB/PDBParser.py",
line 69, in get_structure
    self._parse(file.readlines())
  File
"/home/bsouthey/python/biopython_cvs/biopython/build/lib.linux-x86_64-2.6/Bio/PDB/PDBParser.py",
line 89, in _parse
    self.trailer=self._parse_coordinates(coords_trailer)
  File
"/home/bsouthey/python/biopython_cvs/biopython/build/lib.linux-x86_64-2.6/Bio/PDB/PDBParser.py",
line 186, in _parse_coordinates
    structure_builder.init_atom(name, coord, bfactor, occupancy, altloc,
fullname, serial_number)
  File
"/home/bsouthey/python/biopython_cvs/biopython/build/lib.linux-x86_64-2.6/Bio/PDB/StructureBuilder.py",
line 224, in init_atom
    residue.add(atom)
  File
"/home/bsouthey/python/biopython_cvs/biopython/build/lib.linux-x86_64-2.6/Bio/PDB/Residue.py",
line 81, in add
    raise PDBConstructionException, "Atom %s defined twice in residue %s" %
(atom_id, self)
TypeError: exceptions must be classes or instances, not str

======================================================================


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