In case user wants to analyse only a single topology file, this process will determine the residues
        that should be plotted and find the ligand atoms closest to these residues.

def analyse_topology(self,topology, cutoff=3.5):
        """
        In case user wants to analyse only a single topology file, this process will determine the residues
        that should be plotted and find the ligand atoms closest to these residues.
        """

        self.define_residues_for_plotting_topology(cutoff)
        self.find_the_closest_atoms(topology)