Plotting of amino diagrams - circles with residue name and id, colored according to the
        residue type. If the protein has more than one chain, chain identity is also included in
        the plot. The plot is saved as svg file with residue id and chain id as filename for more
        certain identification.

def plot_amino_diagrams(self):
        """
        Plotting of amino diagrams - circles with residue name and id, colored according to the
        residue type. If the protein has more than one chain, chain identity is also included in
        the plot. The plot is saved as svg file with residue id and chain id as filename for more
        certain identification.
        """

        for res in self.topology_data.dict_of_plotted_res:
            try:
                color = [self.colors_amino_acids[self.amino_acids[res[0]]],'white']
            except KeyError:
                color = ["pink",'white']
            plt.figure(figsize=(2.5,2.5))
            ring1,_=plt.pie([1],  radius=1, startangle=90, colors=color, counterclock=False)
            plt.axis('equal')
            plt.setp(ring1, width=1, edgecolor=color[0])
            if len(self.topology_data.universe.protein.segments)<=1:
                #Parameters for amino diagrams without segids
                plt.text(0,-0.45,res[0]+"\n"+res[1],ha='center',size=36, fontweight="bold")
            else:
                #Parameters for amino diagrams with segids
                plt.text(0,-0.37,res[0]+"\n"+res[1]+" "+res[2],ha='center',size=30, fontweight="bold")
            #play with the dpi
            pylab.savefig(str(res[1])+res[2]+".svg", dpi=300, transparent=True)