Hi all, I have come across an issue while embedding structures with stereochemistry configurations that presumably lead to clashes between atoms:
from rdkit import Chem from rdkit.Chem import AllChem smiles="C1N[C@@H]2CO[C@H]1C2" m = Chem.MolFromSmiles(smiles) mh = Chem.AddHs(m) print(AllChem.EmbedMolecule(mh, randomSeed=11)) smiles="C1N[C@@H]2CO[C@@H]1C2" m = Chem.MolFromSmiles(smiles) mh = Chem.AddHs(m) print(AllChem.EmbedMolecule(mh, randomSeed=11)) Produces: 0 (successful embedding) -1 (unsuccessful embedding) What is in your opinion the best way to deal with this in order to avoid failures? Thanks, -- *Gianmarco*
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