The problem seems to be related to the internal coordinate pointers not being initialized correctly. I suggest forcing a manual update after changing the molecule:
import openbabel as ob obmol = ob.OBMol() obmol.BeginModify() obatom = obmol.NewAtom() obatom.SetAtomicNum(6) obatom.SetVector(1.0, 1.0, 1.0) obmol.EndModify() obmol.AddHydrogens() obatom2 = obmol.GetAtom(2) print obatom2.GetX() -------- Original-Nachricht -------- Betreff: [Open Babel] AddHydrogens() and subsequent GetX() causes segmentation fault Von: Peng Bai <peng...@umn.edu> An: openbabel-discuss@lists.sourceforge.net Datum: 07.04.2016 18:30 > Dear OpenBabel users, > > I wanted to use the AddHydrogens() method from Python, and things work > fine if I create an OBMol object by reading in a file, but it crashes > with a segmentation fault if I used it as in the example below. I > tried it on different machines: > > (1) Python 2.7.9 > OpenBabel git:d56a5d compiled with gcc 5.1.0 > or OpenBabel 2.3.2 compiled with gcc 4.9.2 > (2) Python 2.7.10 > OpenBabel git:d56a5d compiled with gcc 4.8 > > An example interactive session: > > ~~~ > In [1]: import openbabel as ob > In [2]: obmol = ob.OBMol() > In [3]: obatom = obmol.NewAtom() > In [4]: obatom.SetAtomicNum(6) > In [5]: obatom.SetVector(1.0, 1.0, 1.0) > In [6]: obmol.NumAtoms() > Out[6]: 1 > In [7]: obmol.AddHydrogens() > Out[7]: True > In [8]: obmol.NumAtoms() > Out[8]: 5 > In [9]: obatom2 = obmol.GetAtom(2) > In [10]: obatom2.GetAtomicNum() > Out[10]: 1 > In [11]: obatom2.GetAtomicMass() > Out[11]: 1.00794 > In [12]: obatom2.GetX() > Segmentation fault > ~~~ > > Any suggestions why this may happen? Thanks very much in advance! > > Best regards, > > Peng > > ------------------------------------------------------------------------------ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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