docs: 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 ")