Where do beginAtom and endAtom come from in your code snippet. The best thing would be if you can you create a simple and short self-contained script that exhibits the problem.
- Noel On 11 March 2010 03:59, Jason Power <[email protected]> wrote: > Hi all, > > I am currently developing a pure-python 2-D molecule editor for use within > another project I am currently working on. To begin with I decided to use the > OBMol object as a model, thinking it would save me time and effort. However, I > have run into a variety of issues that I'm not sure are due to my own > misunderstandings, limitations of the python bindings, or bugs. > > I am building the OBMol object slowly over time as the user adds atoms and > bonds. So I have a numerous places where I basically call > > self.mol.BeginModify() > bond = self.mol.NewBond() > bond.SetBegin(beginAtom) > bond.SetEnd(endAtom) > self.mol.EndModify() > > and > > self.mol.BeginModify() > newAtom = self.mol.NewAtom() > newAtom.SetVector(self.translateToAtomCoords(pos)) > newAtom.SetAtomicNum(atomicNum) > self.mol.EndModify() > > and similar to delete. I find that with these calls when I go on to do other > interesting things it fails, often as a segfault. Also, if I try to make a > call like self.mol.GetSSSR() even though there is a ring, (I can trace the > indices of the ends of the bonds myself), it returns a zero length list. > > I have found that if I call self.builder.Do(self.mol) before I run GetSSSR() > it will return the right numbers, but I do not want to build the full 3-D > coords, and worse, self.builder.Do(self.mol) randomly segfaults. > > Am I doing something wrong? Is there something that I am missing while > building the molecule? > > Thanks for you help! > Jason > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > OpenBabel-scripting mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ OpenBabel-scripting mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
