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MolToSmiles fails with rootedAtAtom for disconnected molecules (need for smiles augmentation) #44
Description
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I'm facing the same error for issue #113 in PR #115 , and the below might the reason
Description:
When performing SMILES augmentation using RDKit’sChem.MolToSmileswith therootedAtAtomargument, the function raises aRuntimeError: Range Error idxfor molecules containing disconnected fragments (e.g.,[F-].[Na+]).Steps to Reproduce:
from rdkit import Chem mol = Chem.MolFromSmiles("[F-].[Na+]") Chem.MolToSmiles(mol, rootedAtAtom=1, doRandom=True)
Observed Behavior:
Exception has occurred: RuntimeError Range Error idx Violation occurred on line 209 in file Code\GraphMol\ROMol.cpp Failed Expression: 1 < 1 RDKIT: 2024.09.6 BOOST: 1_85Cause:
RDKit’srootedAtAtomassumes the atom index belongs to a single connected component. For disconnected molecules (multiple fragments), this internal assumption fails and results in an out-of-bounds fragment index.To elaborate,
MolToSmiles’rootedAtAtomparameter expects the index of atom in a connected fragment — but the molecule[F-].[Na+]is two disconnected fragments. When you passrootedAtAtom=1(sodium atom), RDKit internally tries to traverse a single fragment, but the fragment index calculation fails due to it being a disconnected molecule.@sfluegel05, Please let me know if you have any suggestions for augmenting this type of smiles which are present in our processed dataset.
- changed the title
[-]MolToSmiles() gives RuntimeError for some molecules[/-][+]MolToSmiles fails with rootedAtAtom for disconnected molecules (need for smiles augmentation)[/+]on Aug 10, 2025 - changed the title
[-]MolToSmiles fails with rootedAtAtom for disconnected molecules (need for smiles augmentation)[/-][+]`MolToSmiles` fails with `rootedAtAtom` for disconnected molecules (need for smiles augmentation)[/+]on Aug 10, 2025 you are right. For some reason the
rootedAtAtomargument does not accept the atom id, but only takes the first fragment into account. I guess we should treat each fragment separately as well and then recombine them afterwardsmol = Chem.MolFromSmiles("[F-].[Na+]") fragments = Chem.GetMolFrags(mol, asMols=True) for i, fragment in enumerate(fragments): print(f"Fragment {i}: {Chem.MolToSmiles(fragment)}") # randomize SMILES for this fragment # stitch together fragment-SMILES (in random order)- added a commit that references this issue
on Aug 22, 2025 - linked a pull request that will close this issueData Augmentation : SMILES #115
on Aug 22, 2025
rdkit MolToSmiles() gives RuntimeError for some molecules (Eg: "[Cl-].[H]N+([H])[H]" ), with configuration of rootedAtAtom>0.