cleave_mol_from_index#

cleave_mol_from_index(mol, index, verbose=False, add_atom=None)[source]#

Given an atomic index of an RDKit molecule, cleave the attaching bonds and return the resulting molecules

The original atom index that corresponds to the output, coordinating_atoms, can be accessed with the atom int property, “__original_index”.

If an atom has a negative charge greater than one after cleavage, a dummy atom is added for each charge.

Parameters:

mol (rdkit.Chem.rdchem.Mol) – RDKit molecule
index (int) – Index of atom to cleave from neighbors
verbose (bool, optional, default=False) – If True, provide the number of resulting rdkit molecules
add_atom (str, optional, default=None) – If not None, add an atom of this type in place of the metal center

Returns:

fragments (list[rdkit.Chem.rdchem.Mol])) – List of RDKit molecules resulting from cleaved bonds
coordinating_atoms (list[int])) – List of atom indices that were connected to the central atom