docs: def analyse_hydrogen_bonds_traj(self,distance=3):
          """
          MDAnalysis.analysis.hbonds module is used to analyse hydrogen bonds formed between protein
          and ligand for each submitted trajectory. The hydrogen bonds are then counted by total value
          per frame (count_by_time), as well as obtaining the frequency of each individual hydrogen
          bond (count_by_type).
  
          Takes:
              * distance * - distance between hydrogen bond donor and acceptor in angstroms
          Output:
              * self.hbonds * - array with information about all detected hydrogen bonds
              * self.hbonds_by_time * - total hbond number by frame
              * self.hbonds_by_type * - frequency of each hydrogen bond
  
          """
          i=0
          for traj in self.trajectory:
              self.topology_data.load_trajectory(traj)
              start = timer()
              h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(self.topology_data.universe,'(segid '+str(self.topology_data.universe.ligand.segids[0])+' and resid '+str(self.topology_data.universe.ligand.resids[0])+')',"protein",distance=3,acceptors=self.acceptors,donors=self.donors,start=self.start_frame_num[i],stop=self.end_frame_num[i],step=self.skip[i])
              h.run()
              h.generate_table()
              end = timer()
              print "HBonds: " + str(end-start)
              self.hbonds[i]=h.table
              self.hbonds_timesteps[i] =h.timesteps
              self.hbonds_by_time[i] = h.count_by_time()
              self.hbonds_by_type[i] = self.count_by_type(h.table,h.timesteps)
              i+=1