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 = mol_1.GetAtomWithIdx(atom_idx).GetImplicitValence()
> mol_2_implicitH
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 s
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 .SetIsotope()
> like I do above
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 see
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
>
> 1. Why are there any br
5 matches
Mail list logo