docs: def analysis_of_prot_lig_interactions(self):
          """
          The classes and function that deal with protein-ligand interaction analysis.
          """
          self.hbonds = HBonds(self.topol_data,self.trajectory,self.start,self.end,self.skip,self.analysis_cutoff,distance=3)
          self.pistacking = PiStacking(self.topol_data,self.trajectory,self.start,self.end,self.skip, self.analysis_cutoff)
          self.sasa = SASA(self.topol_data,self.trajectory)
          self.lig_descr = LigDescr(self.topol_data)
          if self.trajectory!=[]:
              self.rmsf = RMSF_measurements(self.topol_data,self.topology,self.trajectory,self.ligand,self.start,self.end,self.skip)
          self.salt_bridges = SaltBridges(self.topol_data,self.trajectory,self.lig_descr,self.start,self.end,self.skip,self.analysis_cutoff)