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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