Hi Jeremy,
iirc you have to write mol = Chem.AddHs(mol).
In your code you are not keeping the object with the added Hs so there are
no explicit Hs to find when you iterate.
Cheers,
Fio
On Sat, Oct 7, 2023 at 9:36 PM Jeremy Monat <jemo...@gmail.com> wrote:
> In Python, I'd like to iterate through all the atoms in a molecule,
> including hydrogens, so I can assign an isotope to each atom. I haven't
> been able to include hydrogens in the iterable of atoms:
>
> from rdkit import Chem
>
> mol = Chem.MolFromSmiles("CCO") # Example molecule: Ethanol (C2H5OH)
>
> # Add explicit hydrogens
> Chem.AddHs(mol)
>
> for atom in mol.GetAtoms():
> print(f"Atom Symbol: {atom.GetSymbol()}")
> Output:
> Atom Symbol: C
> Atom Symbol: C
> Atom Symbol: O
>
> Similarly, mol.GetAtomWithIdx() works up to an index of only 3, giving C,
> C, and O atoms but no hydrogens.
>
> Thanks,
> Jeremy
> -- ~ -- ~ --
> Jeremy Monat, PhD
> LinkedIn: http://www.linkedin.com/in/jemonat
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> GitHub: https://github.com/bertiewooster
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