add molecule parsing functionality - #18
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This was referenced Aug 3, 2026
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As noticed in ChEB-AI/python-chebai-graph#40, the SMILES parsing across different workflows is not consistent. While chebi_utils provides a sanitation function and a molblock parser, during inference, SMILES (or InCHI) strings can be used as input.
To standardize SMILES / InChI parsing across different repositories, I added a
smiles_or_inchi_to_molfunction.The new SMILES / InChI / Molblock processing works as follows:
Chem.MolFrom*,sanitize=False, removeHs=False)update_mol_valencesandChem.SanitizeMolfunctionsUpdatePropertyCacheandFindFastRingsto get the minimum properties needed for GNN processing