def restore_site_properties(self, site_property="ff_map", filename=None):
        """
        Restore the site properties for the final packed molecule.

        Args:
            site_property (str):
            filename (str): path to the final packed molecule.

        Returns:
            Molecule
        """

        # only for pdb
        if not self.control_params["filetype"] == "pdb":
            raise ValueError()

        filename = filename or self.control_params["output"]
        bma = BabelMolAdaptor.from_file(filename, "pdb")
        pbm = pb.Molecule(bma._obmol)

        assert len(pbm.residues) == sum([x["number"]
                                         for x in self.param_list])

        packed_mol = self.convert_obatoms_to_molecule(
            pbm.residues[0].atoms, residue_name=pbm.residues[0].name,
            site_property=site_property)

        for resid in pbm.residues[1:]:
            mol = self.convert_obatoms_to_molecule(
                resid.atoms, residue_name=resid.name,
                site_property=site_property)
            for site in mol:
                packed_mol.append(site.species, site.coords,
                                  properties=site.properties)

        return packed_mol
def restore_site_properties ( self , site_property = "ff_map" , filename = None ) : if not self . control_params [ "filetype" ] == "pdb" : raise ValueError ( ) filename = filename or self . control_params [ "output" ] bma = BabelMolAdaptor . from_file ( filename , "pdb" ) pbm = pb . Molecule ( bma . _obmol ) assert len ( pbm . residues ) == sum ( [ x [ "number" ] for x in self . param_list ] ) packed_mol = self . convert_obatoms_to_molecule ( pbm . residues [ 0 ] . atoms , residue_name = pbm . residues [ 0 ] . name , site_property = site_property ) for resid in pbm . residues [ 1 : ] : mol = self . convert_obatoms_to_molecule ( resid . atoms , residue_name = resid . name , site_property = site_property ) for site in mol : packed_mol . append ( site . species , site . coords , properties = site . properties ) return packed_mol
Restore the site properties for the final packed molecule.

        Args:
            site_property (str):
            filename (str): path to the final packed molecule.

        Returns:
            Molecule