Hi Michal, You can use rdkit.Chem.rdmolfiles.MolFragmentToSmiles (or related MolFragmentToSmarts) and specify an atom id list with "atomsToUse":
e.g. rdkit.Chem.rdmolfiles.MolFragmentToSmiles(mol, atomsToUse=[11,13,22,15]) Kangway ________________________________ From: Michal Krompiec <michal.kromp...@gmail.com> Sent: Thursday, June 4, 2020 10:45 AM To: RDKit Discuss <rdkit-discuss@lists.sourceforge.net> Subject: [Rdkit-discuss] PathToSubmol on atom indices? Hello, I noticed this was discussed before and I'm wondering if anything's changed. Is it possible to extract a substructure from a molecule, based on atom indices? I understand that Chem.PathToSubmol does something similar, but takes bond indices. Best, Michal
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