Geoff, I will complies a list of SMILES and will post it to the issue tracker.
Thanks, Sam On Sat, Sep 17, 2016 at 12:33 PM, Geoffrey Hutchison < geoff.hutchi...@gmail.com> wrote: > 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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