OpenFF Recharge documentation

openff-recharge

openff.recharge.utilities.toolkits.match_smirks

openff.recharge.utilities.toolkits.match_smirks(smirks: str, molecule: Molecule, is_atom_aromatic: Dict[int, bool], is_bond_aromatic: Dict[Tuple[int, int], bool], unique: bool = False, kekulize: bool = False) → List[Dict[int, int]]

Attempt to find the indices (optionally unique) of all atoms which match a particular SMIRKS pattern.

Parameters

• smirks – The SMIRKS pattern to match.

• molecule – The molecule to match against.

• is_atom_aromatic – A dictionary of the form is_atom_aromatic[atom_index] = is_aromatic.

• is_bond_aromatic – A dictionary of the form is_bond_aromatic[(atom_index_a, atom_index_b)] = is_aromatic.

• unique – Whether to return only unique matches.

• kekulize – Whether to kekulize the molecule before matching.

Returns

• A list of all the matches where each match is stored as a dictionary of

• the smirks indices and their corresponding matched atom indices.