[OpenBabel-scripting] Using CML with Open Babel Python - segfault

[richard a. <ric...@ya...>]

I get a segmentation fault on exiting interactive
python after using CML:

>>> import openbabel
>>> mol=openbabel.OBMol()
>>> c=openbabel.OBConversion()
>>> c.SetInAndOutFormats('smiles', 'cml')
True
>>> c.ReadString(mol, 'c1ccccc1')
True
>>> print c.WriteString(mol)
<molecule>
 <atomArray>
  <atom id="a1" elementType="C"/>
  <atom id="a2" elementType="C"/>
  <atom id="a3" elementType="C"/>
  <atom id="a4" elementType="C"/>
  <atom id="a5" elementType="C"/>
  <atom id="a6" elementType="C"/>
 </atomArray>
 <bondArray>
  <bond atomRefs2="a1 a2" order="1"/>
  <bond atomRefs2="a2 a3" order="2"/>
  <bond atomRefs2="a3 a4" order="1"/>
  <bond atomRefs2="a4 a5" order="2"/>
  <bond atomRefs2="a5 a6" order="1"/>
  <bond atomRefs2="a1 a6" order="2"/>
 </bondArray>
</molecule>

>>>#pressed [Ctrl-d]
Segmentation fault

My system is amd64 Linux (Mandriva 2007), Python 2.4.3
and Open Babel SVN trunk rev 1578.

Running the above code with input set to 'smi' and
output set to 'inchi' causes no segfault on exiting
interactive python.

I see a similar CML-releated problem when running
OBRuby. In that case, I also don't get the segfault
until interactive Ruby exits, or the Ruby interpreter
finished executing. And there, I only see the problem
when using CML, not with other format
interconversions.

Any ideas?

thanks,
Rich

____________________________
Richard Apodaca
Blog: http://depth-first.com


 
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