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?


> On Sep 16, 2016, at 6:28 PM, Sam Tonddast-Navaei <> 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> 
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