I have met another glitch, I would like your opinion about. I previously reported an issue about identification of chiral centres on S atoms. I now have a similar situation - on a C atom.
The following script using RDKit 2011.09.01 #!/usr/bin/env python """ Try to show incomplete stereochem @author: JP """ from rdkit import Chem from rdkit.Chem import AllChem mol_block = """1q6r_LX1_1_B_9301__F___ -ISIS- 3D Created by: Ligand Depot 13 12 0 0 0 0 0 0 0 0 0 40.7470 4.7140 13.2080 O 0 0 0 0 0 40.8090 5.1440 11.6320 P 0 0 0 0 0 41.5820 4.1140 10.7090 O 0 0 0 0 0 39.2960 5.3700 11.1140 O 0 0 0 0 0 41.5340 6.7450 11.2760 O 0 0 0 0 0 41.0300 7.8890 11.9210 C 0 0 0 0 0 41.9250 8.2720 13.0860 C 0 0 0 0 0 41.3150 9.4640 13.5990 O 0 0 0 0 0 43.4030 8.4270 12.7750 C 0 0 0 0 0 43.6880 9.3100 11.6630 O 0 0 0 0 0 44.0970 8.9680 14.0190 C 0 0 0 0 0 44.4830 10.1450 14.1600 O 0 0 0 0 0 44.2970 7.9470 15.0230 C 0 0 0 0 0 1 2 1 0 0 0 2 3 2 0 0 0 2 4 1 0 0 0 2 5 1 0 0 0 5 6 1 0 0 0 6 7 1 0 0 0 7 8 1 0 0 0 7 9 1 0 0 0 9 10 1 0 0 0 9 11 1 0 0 0 11 12 1 0 0 0 11 13 1 0 0 0 M END""" mol = Chem.MolFromMolBlock(mol_block) print mol AllChem.AssignAtomChiralTagsFromStructure(mol) print Chem.MolToSmiles(mol, isomericSmiles=True) Generates a molecule with 2 chiral centres, but the molecule actually has 3 (I think). I have attached an example of what I was expecting, and the RDKit output - because I like to make people's life easy. - Jean-Paul Ebejer Early Stage Researcher
<<attachment: stereo.png>>
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