rxn.chemutils.smiles_standardization.standardize_smiles

rxn.chemutils.smiles_standardization.standardize_smiles(smiles, canonicalize=True, sanitize=True, find_radicals=True, inchify=False)[source]

Ensure that a SMILES follows a desired standard.

It allows canonicalization, sanitization and inchification keeping stereochemistry with isomericSmile=True. It can process multiple molecules separated by “.”. Note that inchify set to True will also canonicalize the molecule.

Parameters

  • smiles (str) – SMILES representation of a molecule.

  • canonicalize (bool, default: True) – canonicalize SMILES. Defaults to True.

  • sanitize (bool, default: True) – sanitize SMILES. Defaults to True.

  • inchify (bool, default: False) – inchify the SMILES. Defaults to False.

  • find_radicals (bool, default: True) –

Return type

str

Returns

a SMILES following the desired standard.