Hi Jeremy,
Chem.AddHs returns a new molecule, you could reassign the variable:
mol = Chem.AddHs(mol)
Best regards,
Diogo
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
> Portfolio: https://bertiewooster.github.io
> GitHub: https://github.com/bertiewooster
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