PDBInf allows you to read PDB files using RDKit and assign bond orders from .cif (PDBx) template files.

# provide a PDBx defining the TPO nonstandard residue
nonstandard_residues = gemmi.cif.read('./tpo.cif')

# load a PDB file using the built-in standard amino acid doc and providing information on the nonstandard residues
pdbinf.load_pdb_file('./tpo.pdb', templates=[pdbinf.STANDARD_AA_DOC, nonstandard_residues])