Hi,
I'm comparing stereo centers assigned by ChemAxon JChem and RDKit.
The code would be:
#----------------------------------------------------------------------------------------------------------------------
from rdkit import Chem
def getStereoInfo(smiles):
ret = []
mol = Chem.MolFromSmiles(smiles)
Chem.AssignStereochemistry(mol, flagPossibleStereoCenters=True, force=True)
for atom in mol.GetAtoms():
stereo = str(atom.GetChiralTag())
atomIndex = atom.GetIdx()
if str(atom.GetChiralTag()) != "CHI_UNSPECIFIED":
if stereo == "CHI_TETRAHEDRAL_CW":
chirality = "R"
elif stereo == "CHI_TETRAHEDRAL_CCW":
chirality = "S"
else:
chirality = "R/S"
ret.append({"atomIndex":atomIndex,"chirality":chirality})
return ret
#-------------------------------------------------------------------------------------------------------------------
Now for (1R,2S,3S)-1,2,3-trichlorocyclopentane
(Cl[C@H]1CC[C@@H](Cl)[C@H]1Cl), both RDKit and JChem give the same
results:
https://dl.dropboxusercontent.com/u/10967207/a.png
But for ephedrine (O[C@H](c1ccccc1)[C@@H](NC)C) stereo centers are
reversed. RDKit gives:
https://dl.dropboxusercontent.com/u/10967207/b.png
and JChem gives:
https://dl.dropboxusercontent.com/u/10967207/c.png
The same is shown by pseudo-ephedrine (O[C@@H](c1ccccc1)[C@@H](NC)C)
which returns both stereo centers as 'R'.
Is that a bug or an expected behavior? Are there any parameters in
RDKit that can be set to get results similar to JChem?
Regards,
Michał Nowotka
------------------------------------------------------------------------------
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
