[Biopython-dev] [Bug 2879] missing __delitem__ in Bio.PDB.Entity.Entity
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Wed Jul 22 08:17:06 UTC 2009
http://bugzilla.open-bio.org/show_bug.cgi?id=2879
------- Comment #2 from katja.luck at unistra.fr 2009-07-22 04:17 EST -------
(In reply to comment #1)
> Could you give a short but complete example showing the problem?
>
example code:
from Bio.PDB.PDBParser import PDBParser
if '__main__' == __name__:
parser = PDBParser(PERMISSIVE=1)
PDBID = '1N7T'
PDB_file = '/Network/Servers/sumba/Volumes/s/luck/pymol/1N7T.pdb'
structure = parser.get_structure(PDBID,PDB_file)
chain = structure[0]['A']
print chain[66].get_id()
chain.__delitem__(66)
command line output:
[carlit:/Users/katja] luck% python Python_scripts/PDZ_project/bug_example.py
(' ', 66, ' ')
Traceback (most recent call last):
File "Python_scripts/PDZ_project/bug_example.py", line 14, in <module>
chain.__delitem__(66)
File "/Library/Python/2.5/site-packages/Bio/PDB/Chain.py", line 79, in
__delitem__
return Entity.__delitem__(self, id)
AttributeError: class Entity has no attribute '__delitem__'
Okay, I now realised that I should rather use detach_child() than the private
method __delitem__() for deleting residues from a chain but still thought it
might be good to report this bug.
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