Re: [Rdkit-discuss] Iterate through atoms in molecule including hydrogens in Python

[Jeremy M. <je...@gm...>]

Thanks, Diogo and Fio. That solved that problem.

Jeremy

On Sun, Oct 8, 2023 at 1:23 AM Diogo Martins <dio...@gm...> wrote:

> 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 <je...@gm...> 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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