prepare_complex

prepare_complex(mol, verbose=False, value_missing_coord=0, add_hydrogens=False)

Prepare complex removing anomalous substructs, adding additional metal connections, checking for missing coordinates, and possible addition of hydrogens.

Parameters:

• mol (rdkit.Chem.rdchem.Mol) – RDKit molecule representing the transition metal complex.

• verbose (bool, optional, default=False) – If True, print updates during processing.

• value_missing_coord (float, optional, default=0) – Value used to detect missing coordinates (e.g., 0 for (0,0,0)).

• add_hydrogens (bool, optional, default=False) – If True, add explicit hydrogens to the structure if needed.

Returns:

mol – RDKit molecule representing the transition metal complex.

Return type:

rdkit.Chem.rdchem.Mol