On 19 October 2010 13:13, Noel O'Boyle <baoille...@gmail.com> wrote: > On 19 October 2010 13:04, Geoffrey Hutchison <ge...@geoffhutchison.net> wrote: >> >> On Oct 19, 2010, at 6:31 AM, Noel O'Boyle wrote: >> >>> tetrahedral center. That is, it's called from the smiles parser and it >>> finds it fine, but later on it's called again and doesn't find it :-/ >>> >>> I can't track down the problem easily but reverting r4220 appears to fix it. >> >> The revision only changed 3 files. >> http://openbabel.svn.sf.net/viewvc/openbabel?view=revision&revision=4220 >> >> Two changes were adding square planar hybridization to Cu, Pt, Pd, etc. So >> that can't be it. The other changes were in builder.cpp. >> >> The most obvious culprit would be: >> 231 // check to see if atom is a square planar in disguise >> 232 if (atom->GetHyb() == 3) { >> 233 OBStereoFacade >> stereoFacade((OBMol*)atom->GetParent()); >> 234 if >> (stereoFacade.HasSquarePlanarStereo(atom->GetId())) >> 235 atom->SetHyb(4); // force sq. planar geometry >> for sq. planar stereo >> 236 } >> >> Now, this seemed to make sense to me at the time -- look for an "SP" stereo >> designation on the atom and force it to be square planar. >> >> So I've commented out this code, but why doesn't it work? Why does your >> SMILES yield square planar stereo on that atom? > > It must be that HasSquarePlanarStereo isn't working. The facade code > is not widely exercised by existing library code. I'll track it down, > but first I need to check in this new code...
I've figured out the problem. The stereo is reperceived but unfortunately, the molecule is being built at the time, and so it can't detect the stereo very well. Once I get home, I'll try adding perceive=false in the parameters to the constructor to OBStereoFacade. >> -Geoff > ------------------------------------------------------------------------------ Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-dev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
