(Please cc to list) How about commenting about:
##rb1=ring3.NewBond() ##rb2=ring3.NewBond() ##rb3=ring3.NewBond() ##rb1.SetBegin(ra1) ##rb1.SetEnd(ra2) ##rb2.SetBegin(ra2) ##rb2.SetEnd(ra3) ##rb3.SetBegin(ra3) ##rb3.SetEnd(ra1) ##rb1.SetBO(1) ##rb2.SetBO(1) ##rb3.SetBO(1) and replacing it with: ring3.AddBond(1, 2, 1) ring3.AddBond(2, 3, 1) ring3.AddBond(3, 1, 1) - Noel On 11 March 2010 14:28, Jason Power <[email protected]> wrote: > Here is something that causes a segfault every time: > > import openbabel > ring3 = openbabel.OBMol() > ra1=ring3.NewAtom() > ra2=ring3.NewAtom() > ra3=ring3.NewAtom() > ra1.SetAtomicNum(6) > ra2.SetAtomicNum(6) > ra3.SetAtomicNum(6) > rb1=ring3.NewBond() > rb2=ring3.NewBond() > rb3=ring3.NewBond() > rb1.SetBegin(ra1) > rb1.SetEnd(ra2) > rb2.SetBegin(ra2) > rb2.SetEnd(ra3) > rb3.SetBegin(ra3) > rb3.SetEnd(ra1) > rb1.SetBO(1) > rb2.SetBO(1) > rb3.SetBO(1) > print len(ring3.GetSSSR()) # OUTPUT: 0 > builder = openbabel.OBOp.FindType("Gen3D") > builder.Do(ring3) > print len(ring3.GetSSSR()) # OUTPUT: 1 > ra1.SetVector(1,0,0) > ra2.SetVector(0,-1,0) > ra3.SetVector(0,1,0) > > Sometimes is segfaults on ra2.SetVector(0,-1,0) and sometimes on > ra3.SetVector(0,1,0). Also, I don't understand why the first call the > GetSSSR() doesn't return the right number. > > Thanks again! > Jason > > On Thursday 11 March 2010 04:48:45 am you wrote: >> 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
