determine_connectivity

determine_connectivity(rdkit_mol, method='hybrid', distance_tolerance=0.1)

Determine connectivity for molecules, particularly transition metal organometallic complexes.

Parameters:

rdkit_molrdkit.Chem.Mol

RDKit molecule without bonds

methodstr, optional, default=’hybrid’

Method to use: ‘rdkit’, ‘openbabel’, or ‘hybrid’ where openbabel is attempted and rdkit is the fall back.

distance_tolerancefloat, optional, default=0.1

Additional tolerance for bond distance cutoffs (Angstroms)

Returns:

rdkit.Chem.Mol

RDKit molecule with bonds added