def test_gen_frag_has_no_empty_molecules(self):
cs = chem_structure(inchi=inchi1)
cg = chem_graph(cs.mol)
for level in range(0, 4):
frag = cg.gen_frag(level)
nonempty_frag = [f for f in frag if len(f.chem_formula()) > 0]
self.assertEqual(frag, nonempty_frag)
def test_graph_from_OBMol(self):
cs = chem_structure(inchi=inchi1)
graph = chem_graph.graph_from_OBMol(cs.mol)
self.assertStringEqual(graph.number_of_nodes(), 16)
self.assertStringEqual(graph.node[1]['atom'], ELEMENTS['C'])
self.assertStringEqual(graph.node[2]['atom'], ELEMENTS['C'])
self.assertStringEqual(graph.node[3]['atom'], ELEMENTS['C'])
self.assertStringEqual(graph.node[4]['atom'], ELEMENTS['C'])
self.assertStringEqual(graph.node[5]['atom'], ELEMENTS['C'])
self.assertStringEqual(graph.node[6]['atom'], ELEMENTS['N'])
self.assertStringEqual(graph.node[7]['atom'], ELEMENTS['N'])
self.assertStringEqual(graph.node[8]['atom'], ELEMENTS['N'])
self.assertStringEqual(graph.node[9]['atom'], ELEMENTS['N'])
self.assertStringEqual(graph.node[10]['atom'], ELEMENTS['N'])
self.assertStringEqual(graph.node[11]['atom'], ELEMENTS['O'])
self.assertStringEqual(graph.node[12]['atom'], ELEMENTS['H'])
self.assertStringEqual(graph.node[13]['atom'], ELEMENTS['H'])
self.assertStringEqual(graph.node[14]['atom'], ELEMENTS['H'])
self.assertStringEqual(graph.node[15]['atom'], ELEMENTS['H'])
self.assertStringEqual(graph.node[16]['atom'], ELEMENTS['H'])
for n in range(1, 17):
self.assertTrue('X' in graph.node[n])
self.assertTrue('Y' in graph.node[n])
for edge in graph.edges():
self.assertTrue('order' in graph[edge[0]][edge[1]])
self.assertEqual(graph.number_of_edges(), 17)
edge_set = [(1, 12), (12, 1),
(1, 7), (7, 1),
(1, 8), (8, 1),
(2, 7), (7, 2),
(3, 8), (8, 3),
(2, 3), (3, 2),
(2, 4), (4, 2),
(4, 11), (11, 4),
(4, 10), (10, 4),
(10, 16), (16, 10),
(5, 10), (10, 5),
(5, 6), (6, 5),
(5, 9), (9, 5),
(3, 9), (9, 3),
(8, 15), (15, 8),
(6, 13), (13, 6),
(6, 14), (14, 6)]
for edge in graph.edges():
self.assertIn(edge, edge_set)
edge_set.remove(edge)
edge_set.remove((edge[1], edge[0]))
self.assertEqual(edge_set, [])
def test_chem_formula(self): cs = chem_structure(inchi=inchi1) cg = chem_graph(cs.mol) self.assertEqual(cg.chem_formula(), cs.chem_formula())
def test_chem_graph_from_OBMol(self): cs = chem_structure(inchi=inchi1) cg = chem_graph(cs.mol) self.assertEqual(cg.G.number_of_nodes(), 16) self.assertEqual(cg.G.number_of_edges(), 17)
def test_chem_structure_with_inchi_input(self): cs = chem_structure(inchi=inchi1) self.assertEqual(cs.inchi, inchi1) self.assertEqual(cs.mol.NumAtoms(), 16) self.assertEqual(cs.mol.NumBonds(), 17)
def test_chem_structure_without_input(self): cs = chem_structure() self.assertEqual(cs.inchi, None)
def test_gen_frag_with_additional_steps_uniqueness(self):
cs = chem_structure(inchi=inchi1)
cg = chem_graph(cs.mol)
for level in range(1, 4):
frag = cg.gen_frag(level)
self.assertEqual(len(frag), len(set(frag)))
def test_gen_frag_with_no_additional_steps(self): cs = chem_structure(inchi=inchi1) cg = chem_graph(cs.mol) self.assertEqual(cg.gen_frag(0), [cg])
def test_mass(self): cs = chem_structure(inchi=inchi1) cg = chem_graph(cs.mol) self.assertTrue(abs(cg.mass() - cs.mass()) / cg.mass() < 0.001)