There are some bugs in the stereo perception, and this looks like one. Was the molecule read in from SMILES?
It might be worth compiling a list of all problematic molecules you come across (well, one example of each type) so that a future developer can fix this. Regards, - Noel On 27 April 2016 at 01:29, Stefano Forli <fo...@scripps.edu> wrote: > Hi all, > > I'm trying to enumerate all enantiomers for chiral centers in a given > molecule, and I'm > using the following Python code: > > org = self.facade.GetTetrahedralStereo(idx).GetConfig().refs > new = ( org[1], org[0], org[2] ) > self.chiralSet.append((org, new)) > > This code works well most of the times. Problems arise with molecules like > "CC1CCCC[NH+]1C", in which nitrogen has as a tetrahedral configuration > defined, but the > carbon (C1) doesn't. > > Is there a better way to deal with chirality and avoid this issue? > > Thanks, > > S > > > -- > > Stefano Forli, PhD > > Assistant Professor of Integrative > Structural and Computational Biology, > Molecular Graphics Laboratory > > Dept. of Integrative Structural > and Computational Biology, MB-112A > 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/ > > ------------------------------------------------------------------------------ > Find and fix application performance issues faster with Applications Manager > Applications Manager provides deep performance insights into multiple tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
