Re: [Rdkit-discuss] isotopic SMILES

On Feb 7, 2017, at 22:26, Curt Fischer wrote: > def same_implicit_valence(mol_1, mol_2, atom_idx=1): > """Returns True if mol_1 and mol_2 have the same implicit valence for the > indexed atom""" > mol_1_implicitH =

Re: [Rdkit-discuss] isotopic SMILES

I think you've persuaded me that .SetIsotope() is the way to go... I don't understand how that avoids any problem. How do you specify the > target atom for that case? > In any case, won't the InChI normalization affect some of your structures > (e.g., detaching metals) and make it even harder to

Re: [Rdkit-discuss] isotopic SMILES

On Feb 7, 2017, at 19:02, Curt Fischer wrote: > My ultimate goal is an easy way to create rdkit molecules that have isotopic > substitutions but which are otherwise exactly the same as non-substituted > variants. What's the best approach? Is it to directly call

Re: [Rdkit-discuss] isotopic SMILES

I replied to Andrew's very nice discussion of implicit hydrogens in SMILES but forgot to include the whole list. Wow, thank you, that was very useful. I didn't realize those nuances of > SMILES. > > On the rdkit "side", the distinction made in Smiles between implicit and > explicit hydrogens

Re: [Rdkit-discuss] isotopic SMILES

On Feb 7, 2017, at 01:17, Curt Fischer wrote: > I am confused by this behavior: > > >>> labeled_etoh = Chem.MolFromSmiles('C[13C]O') > >>> print(Chem.MolToSmiles(labeled_etoh)) > > C[C]O > > >>> print(Chem.MolToSmiles(labeled_etoh, isomericSmiles=True)) > > C[13C]O >

[Rdkit-discuss] isotopic SMILES

Hellow rdkit users, What behavior should we expect for Chem.MolToSmiles() when dealing with isotopically substituted molecules? I am confused by this behavior: >>> labeled_etoh = Chem.MolFromSmiles('C[13C]O') >>> print(Chem.MolToSmiles(labeled_etoh)) C[C]O >>>