I would say that it's something no-one should ever do (but that
everyone does at least once when learning!). The cost of protecting
you against this would slow down Open Babel across the board.
We welcome patches to the documentation.
- Noel
On 28 April 2015 at 22:50, Stefano Forli <fo...@scripps.edu> wrote:
> Hi,
> I found what looks like another gotcha in the Python implementation, so I'm
> reporting it because it could be useful to somebody else (also because I
> want to understand if there's something absolutely wrong about what I do).
>
> The following code will result in a segmentation fault when running on the
> attached molecule:
> -------------------------------------
> import pybel
> ob = pybel.ob
> pmol = pybel.readfile('pdb', 'taxol.pdb').next()
> mol = pmol.OBMol
> for a in ob.OBMolAtomIter(mol):
> valence = a.GetValence()
> implicit = a.GetImplicitValence()
> if not (valence == implicit):
> mol.AddHydrogens(a)
> -------------------------------------
> Basically, the code adds hydrogens *on the fly* to atoms that miss them.
> Adding Begin/EndModify() would not prevent the crash.
> I suspect it has something to do with the fact that I'm altering the
> molecule data structure while iterating, and that messes up with the
> iterator.
> In fact, the following code works without errors:
> -------------------------------------
> import pybel
> ob = pybel.ob
> pmol = pybel.readfile('pdb', 'taxol.pdb').next()
> mol = pmol.OBMol
> missing = []
> for a in ob.OBMolAtomIter(mol):
> valence = a.GetValence()
> implicit = a.GetImplicitValence()
> if not (valence == implicit):
> missing.append(a)
> for a in missing:
> mol.AddHydrogens(a)
> -------------------------------------
>
> Now, I understand that a segFault shouldn't happen, but I'm not sure what
> would be the way to prevent it. Is this a bug or something that nobody
> should ever do (and it should be added to the documentation)?
>
> Thanks!
>
> S
>
>
>
>
> --
> Stefano Forli, PhD
>
> Staff Scientist
> Molecular Graphics Laboratory
> Dept. of Integrative Structural
> and Computational Biology, MB-112F
> The Scripps Research Institute
> 10550 North Torrey Pines Road
> La Jolla, CA 92037-1000, USA.
>
> tel: +1 (858)784-2055
> fax: +1 (858)784-2860
> email: fo...@scripps.edu
> http://www.scripps.edu/~forli/
>
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