There's currently no code to test for chiral nitrogens - the stereochemical analysis assumes all nitrogens can invert and are therefore non-chiral.
Would you be willing to upload this example as a SMILES or Mol to the issue tracker for 2.4.1? http://github.com/openbabel/openbabel/issues Thanks! -Geoff > On Sep 16, 2016, at 6:28 PM, Sam Tonddast-Navaei <s.tondd...@gmail.com> wrote: > > Hello everyone, > > I was trying to filter through the SMILES with missing stereochemistry > information. So I am using the below script to loop over the atoms and check > if the atom is a chiral center and if so, is the stereochemistry information > there or not. > > mol = pybel.readstring('smi', smi) > facade = ob.OBStereoFacade(mol.OBMol) > for atom in mol: > idx = atom.OBAtom.GetIdx()-1 > if facade.HasTetrahedralStereo(idx) and not > facade.GetTetrahedralStereo(idx).GetConfig().specified: > > It works for many cases, but I have figured out that in many cases like the > attached picture, though the stereochemistry of nitrogen is presented, it > will still get marked as none > (facade.GetTetrahedralStereo(idx).GetConfig().specified returns False). I > have scanned over 700k molecules and figured out that this happens to only > nitrogens that are in the ring. Just wanted to report this and ask if anyone > had a similar issue. > > Thanks, > Sam > <example.jpg> > ------------------------------------------------------------------------------ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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