def setUp(self): """To be run before each test.""" molecule = Molecule().from_adjacency_list(""" 1 C u0 p0 c0 {2,B} {6,B} {7,S} 2 C u0 p0 c0 {1,B} {3,B} {8,S} 3 C u0 p0 c0 {2,B} {4,B} {9,S} 4 C u0 p0 c0 {3,B} {5,B} {10,S} 5 C u0 p0 c0 {4,B} {6,B} {11,S} 6 C u0 p0 c0 {1,B} {5,B} {12,S} 7 H u0 p0 c0 {1,S} 8 H u0 p0 c0 {2,S} 9 H u0 p0 c0 {3,S} 10 H u0 p0 c0 {4,S} 11 H u0 p0 c0 {5,S} 12 H u0 p0 c0 {6,S} """) bonds = set() for atom in molecule.atoms: bonds.update(list(atom.bonds.values())) ring_atoms, ring_bonds = molecule.get_aromatic_rings() self.aromatic_ring = AromaticRing(ring_atoms[0], set(ring_bonds[0]), bonds - set(ring_bonds[0]))