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 seems to live in the atom properties ImplicitValence and
> NumImplicitHs. rdkit, unlike SMILES apparently, does not require that
> isotopically labeled atoms have an implicit valence explicitly specified.
>
> # print out some key properties of all atoms in a molecule
> def print_atom_info(mol):
> for atom in mol.GetAtoms():
> print(atom.GetIdx(), atom.GetSymbol(),
> atom.GetIsotope(), atom.GetImplicitValence(),
> atom.GetNumImplicitHs())
> print('\n')
> return
>
> # make some ethanol
> ethanol_v1 = Chem.MolFromSmiles('CCO')
>
> # label carbon #1 with C13
> ethanol_v1.GetAtomWithIdx(1).SetIsotope(13)
>
> # make more ethanol, labeled as it's created
> ethanol_v2 = Chem.MolFromSmiles('C[13C]O')
>
> # implicit valence is different for the two molecules
> # so is implicit
> show_atom_info(ethanol_v1)
> show_atom_info(ethanol_v2)
>
> Draw.MolsToGridImage([ethanol_v1, ethanol_v2])
>
I also didn't finish my thought here. 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? This
requires figuring out the rdkit atom index of my target atom, which is
doable but perhaps (?) overly complicated? Converting to InChI and back
seems to avoid the problem, I guess because MolToInchi() has a removeHs
parameter that defaults to True. That also seems a bit hack-ish but I'm
not sure what the best approach is.
Curt
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
