Get an atom selection for the selected from both topology and trajectory. Rename the ligand LIG
        to help with ligand names that are not standard, e.g. contain numbers.
            Takes:
                * ligand_name * - MDAnalysis atom selection for the ligand selected by user
            Output:
                * self.ligand * - renamed ligand with resname LIG,
                * self.ligand_noH * - renamed ligand with resname LIG and without H atoms (these are not
                present in the final 2D representation and are therefore excluded from some analysis scripts.)

def rename_ligand(self,ligand_name,mol_file):
        """
        Get an atom selection for the selected from both topology and trajectory. Rename the ligand LIG
        to help with ligand names that are not standard, e.g. contain numbers.
            Takes:
                * ligand_name * - MDAnalysis atom selection for the ligand selected by user
            Output:
                * self.ligand * - renamed ligand with resname LIG,
                * self.ligand_noH * - renamed ligand with resname LIG and without H atoms (these are not
                present in the final 2D representation and are therefore excluded from some analysis scripts.)
        """

        self.universe.ligand = self.universe.select_atoms(ligand_name)
        #Both resname and resnames options need to be reset in order for complete renaming.
        self.universe.ligand.residues.resnames = "LIG"
        self.universe.ligand.resname = "LIG"
        if mol_file is None:
            self.universe.ligand.write("lig.pdb")

            os.system("babel -ipdb lig.pdb -omol lig.mol ")