thanks very much David and Torsten. i can also make
this work on (ubuntu 14.04) linux.
that's the good news. the bad news (for my purposes) is that
the output PDBQT file is considerably perturbed from the original:
user/remark lines dropped, torsion tree traversal order, and
esp. atom numbering.
Hi all,
I can confirm that writing the pdbqt file works without problems on several
Linux distributions (including some CentOS, RedHat and Debian Systems and
derivates). Hence, unfortunately, I cannot try to find the location of the bug
as I don't have a MacOS-system available.
It should not be t
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
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
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
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,
