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 specify isotopes?
but just to clarify, here is the admittedly hackish via-InChI conversion I
had in mind. The specification of isotopes still happens in smiles, which
I find easier for humans to grok than InChI. {{Side note: the end
application here is modeling the labeling patterns in structurally complex
natural products that are biosynthesized from simple labeled substrates
(such as ethanol). So I ultimately want to feed my labeled molecules to a
series of SMARTS reactions that will eventually lead to a complex
structure. Given the vagaries of SMARTS reaction matching, I want to be
sure that all my reactions apply equally well to labeled and unlabeled
substrates.}}
def convert_to_smiles_via_inchi(smiles):
"""Make a molecule from SMILES but via Inchi"""
temp_mol = Chem.MolFromSmiles(smiles)
inchi = Chem.MolToInchi(temp_mol)
final_mol = Chem.MolFromInchi(inchi)
return final_mol
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 = mol_2.GetAtomWithIdx(atom_idx).GetImplicitValence()
return mol_1_implicitH == mol_2_implicitH
etoh_v1 = 'C[13C]O'
etoh_v2 = 'CCO'
etoh_versions = [etoh_v1, etoh_v2]
via_inchi = [convert_to_smiles_via_inchi(mol) for mol in etoh_versions]
smiles_only = [Chem.MolFromSmiles(mol) for mol in etoh_versions]
# this works
assert same_implicit_valence(*via_inchi)
# this doesn't
assert same_implicit_valence(*smiles_only)
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