Hi,
I suspect that you don't modify the data structure you are iterating over but
rather the iterating object. For instance when you iterate over a list and try
to change the element, the following will not work (you probably know this):
Input:
l=[1,2,3]
for i in l:
i=5
print l
Output:
[1,
thanks Torsten, that was a good idea.
but i've done some more testing, and it seems to have
nothing to do with my modifications, but with pbmol.write():
if i simply echo back the same pybel Molecule:
> pbmol = pybel.readfile('pdbqt', pdbqf).next()
>
> pathName,basename = os.path.split(p
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
It seems I can reproduce the segfault on OS X Yosemite, but not on Ubuntu 14.04.
-David
> On Aug 4, 2015, at 8:02 PM, R. K. Belew wrote:
>
> update, if anyone is interested: it seems quite clear the
> bug is in the PDBQT output filter:
>
>>> obabel file1.pdbqt -O file2.pdbqt
>>> Segmentation
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