Use rdkit to detect aromatic rings in protein. A (relatively) simpler case, since only 4 of 20 aa have rings.
        Since different forcefields can have different atom names, each of 4 aromatic residues is extracted as PDB file
        and the aromatic rings are detected for each. The case is trickier with TRP, since this residue has two aromatic rings -
        these are considered separately.
        Data is saved in self.rings dictionary.

def detect_aromatic_rings_in_protein(self):
        """Use rdkit to detect aromatic rings in protein. A (relatively) simpler case, since only 4 of 20 aa have rings.
        Since different forcefields can have different atom names, each of 4 aromatic residues is extracted as PDB file
        and the aromatic rings are detected for each. The case is trickier with TRP, since this residue has two aromatic rings -
        these are considered separately.
        Data is saved in self.rings dictionary."""
        self.rings = {}
        for ar_resname in ["PHE","TRP","TYR","HIS"]:
            for res in self.topology_data.universe.residues:
                if res.resname == ar_resname:
                    aromatic_aa = self.topology_data.universe.select_atoms("resname "+res.resname+" and resid "+str(res.resid)+" and segid "+ res.segid)
                    aromatic_aa.write(ar_resname+".pdb")
                    break
        for ar_resname in ["PHE","TRP","TYR","HIS"]:
            try:
                arom_aa_rdkit = Chem.MolFromPDBFile(ar_resname+".pdb")
                arom_aa_mda = MDAnalysis.Universe(ar_resname+".pdb")
                ring_info = arom_aa_rdkit.GetRingInfo()
                number_of_rings = ring_info.NumRings()
                for ring in range(number_of_rings):
                    atom_names_in_ring = []
                    for atom in ring_info.AtomRings()[ring]:
                        atom_names_in_ring.append(arom_aa_mda.atoms[atom].name)
                    self.rings[(ar_resname,ring)]=atom_names_in_ring
            except IOError:
                continue