Segmentation Fault with basic commands

[bkmi]

mol2 = Chem.MolFromSmiles("O")
atoms2 = rdkit2ase(mol2)

atoms = smiles2atoms("O")

These commands yield a Segmentation Fault (core dumped) in 0.2.2 installed from pip with Python 3.11.13

specifically this line

atoms = ase.Atoms(
    positions=mol.GetConformer().GetPositions(),
    numbers=[atom.GetAtomicNum() for atom in mol.GetAtoms()],
)

with rdkit==2025.9.1

even more specifically

mol.GetConformer().GetPositions()

[PythonFZ]

Thanks for raising this issue. Unfortunately, this seems to be an rdkit issue. You could try installing a different rdkit version. molify does not ship any code that is likely to raise such errors.

One possibility could be the input, but you are using water smiles which I would be very surprised to cause a failure.