[BioPython] PDBConstructionException message
Gad Abraham
g.abraham at ms.unimelb.edu.au
Sat Jul 8 09:12:34 UTC 2006
Hi,
I apologise in advance if this question is trivial, but I'm a Python and
BioPython novice, and the mailing list search facility isn't working :)
I'm using Bio.PDB to parse the PDB file 1LUC, and write output to stdout
(running python inside a script, not shown here).
PDBParser seems to be throwing an exception, and its message goes to
stdout, even though I'm trying to catch it:
Python 2.4.3 (#2, Apr 27 2006, 14:43:58)
[GCC 4.0.3 (Ubuntu 4.0.3-1ubuntu5)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio.PDB import *
>>> parser = PDBParser()
>>> try:
... s = parser.get_structure('1LUC', 'pdb1luc')
... except:
... print "Caught exception"
...
PDBConstructionException: Atom O defined twice in residue <Residue GLN
het= resseq=355 icode= > at line 2930.
Exception ignored.
Some atoms or residues will be missing in the data structure.
>>>
(biopython 1.41)
How can I either catch this exception or prevent the message from being
printed to stdout?
Thanks,
Gad
--
Gad Abraham
Department of Mathematics and Statistics
University of Melbourne
Victoria 3010, Australia
email: g.abraham at ms.unimelb.edu.au
web: http://www.ms.unimelb.edu.au/~gabraham
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