[Open Babel] SegFault while adding hydrogens (Python)

[Stefano Forli]

Hi,



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.

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)
-------------------------------------



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/

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). 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. 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)?

taxol.pdb
Description: application/aportisdoc

------------------------------------------------------------------------------
One dashboard for servers and applications across Physical-Virtual-Cloud 
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss