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

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