sanitize_ligand

sanitize_ligand(mol, delete_list=[], wipe=True, tool='hybrid', charge=0, sanitize=True, verbose=False)

Delete atoms from a molecule and then redetermine bond orders.

Note:

• An empty list can be provided to just redetermine bond orders for a molecule

Parameters:

• mol (rdkit.Chem.rdchem.Mol) – RDKit molecule

• delete_list (list[rdkit.Chem.rdchem.Atom], optional, default=[]) – List of RDKit atom objects to delete.

• wipe (bool, optional, default=True) – Whether to wipe bond information from the molecule

• tool (str, optional, default=”hybrid”) – Choose the tool used to determine bond borders.

  • mdanalysis: _infer_bo_and_charges

  • rdkit: rdDetermineBonds.DetermineBondOrders

  • openbabel: PerceiveBondOrders

  • hybrid: Run openbabel, and if None, run mdanalysis

• charge (int, optional, default=0) – If using RDKit for bond orders, optionally set the charge. If set to 0, some atoms may be defined as radicals.

• sanitize (bool, optional, default=True) – If True, the resulting molecule will be sanitized

• verbose (bool, optional, default=False) – Whether RDKit failure is returned

• Returns – mol (rdkit.Chem.rdchem.Mol): RDKit molecule