update, if anyone is interested: it seems quite clear the
bug is in the PDBQT output filter:
>> obabel file1.pdbqt -O file2.pdbqt
>> Segmentation fault: 11
>> obabel file1.pdbqt -O file2.pdb
>> 1 molecule converted
and has nothing particular to do with pybel; pybel is
silently eating this fault and generating only partial
output before it dies.
Rik
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