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