dump the molecule into pdb file with custom residue name and number.

def write_pdb(self, mol, filename, name=None, num=None):
        """
        dump the molecule into pdb file with custom residue name and number.
        """

        # ugly hack to get around the openbabel issues with inconsistent
        # residue labelling.
        scratch = tempfile.gettempdir()
        with ScratchDir(scratch, copy_to_current_on_exit=False) as _:
            mol.to(fmt="pdb", filename="tmp.pdb")
            bma = BabelMolAdaptor.from_file("tmp.pdb", "pdb")

        num = num or 1
        name = name or "ml{}".format(num)

        # bma = BabelMolAdaptor(mol)
        pbm = pb.Molecule(bma._obmol)
        for i, x in enumerate(pbm.residues):
            x.OBResidue.SetName(name)
            x.OBResidue.SetNum(num)

        pbm.write(format="pdb", filename=filename, overwrite=True)