def test_find_seq(self):
"""
find_seqのテスト
"""
expected = [[0, 1, 0], [0, 2, 0], [0, 3, 0], [0, 1, 4],
[0, 2, 5], [0, 3, 6], [0, 1, 4, 7], [0, 2, 5, 7],
[1, 0, 1], [1, 0, 2], [1, 0, 3], [1, 4, 1],
[1, 0, 2, 5], [1, 4, 7, 5], [1, 0, 3, 6], [1, 4, 7],
[1, 4, 7, 8], [2, 0, 2], [2, 0, 1], [2, 0, 3],
[2, 0, 1, 4], [2, 5, 7, 4], [2, 5, 2], [2, 0, 3, 6],
[2, 5, 7], [2, 5, 7, 8], [3, 0, 3], [3, 0, 1],
[3, 0, 2], [3, 0, 1, 4], [3, 0, 2, 5], [3, 6, 3],
[4, 1, 0], [4, 1, 4], [4, 1, 0, 2], [4, 7, 5, 2],
[4, 1, 0, 3], [4, 7, 5], [4, 7, 4], [4, 7, 8],
[5, 2, 0], [5, 2, 0, 1], [5, 7, 4, 1], [5, 2, 5],
[5, 2, 0, 3], [5, 7, 4], [5, 7, 5], [5, 7, 8],
[6, 3, 0], [6, 3, 0, 1], [6, 3, 0, 2], [6, 3, 6],
[7, 4, 1, 0], [7, 5, 2, 0], [7, 4, 1], [7, 5, 2],
[7, 4, 7], [7, 5, 7], [7, 8, 7], [8, 7, 4, 1],
[8, 7, 5, 2], [8, 7, 4], [8, 7, 5], [8, 7, 8]]
c = Compound()
c.input_molfile(PATH)
actual = [i for i in c.find_seq(4)]
self.assertEqual(actual, expected)
def test_get_symbol(self):
"""
get_symbolのテスト
"""
expected = ["C", "C", "C", "C", "C", "C", "O", "C", "O"]
c = Compound()
c.input_molfile(PATH)
actual = [c.get_symbol(i) for i in range(c.n_atoms)]
self.assertEqual(actual, expected)
def test_input_molfile(self):
"""
input_molfileのテスト
"""
expected = [(0, 1), (0, 2), (0, 3), (1, 4), (2, 5), (3, 6), (4, 7),
(5, 7), (7, 8)]
c = Compound()
c.input_molfile(PATH)
actual = list(c.graph.edges())
self.assertEqual(actual, expected)
def test_has_bond(self):
"""
has_bondのテスト
assertをループにかけるので時間がかかるようなら要修正
"""
expected = [(0, 1), (0, 2), (0, 3), (1, 4), (2, 5), (3, 6), (4, 7),
(5, 7), (7, 8)]
c = Compound()
c.input_molfile(PATH)
for atom_1, atom_2 in expected:
self.assertTrue(c.has_bond(atom_1, atom_2))
def test_input_rdkmol(self):
"""
input_rdkmolのテスト
"""
rdkmol = Chem.MolFromMolBlock(MOLBLOCK)
expected = [(0, 1), (0, 2), (0, 3), (1, 4), (2, 5), (3, 6), (4, 7),
(5, 7), (7, 8)]
c = Compound()
c.input_rdkmol(rdkmol)
actual = list(c.graph.edges())
self.assertEqual(actual, expected)
def test_input_from_knapsack(self):
"""
input_from_knapsackのテスト
内部でinput_molfileを使用
"""
cid = "C00037855"
expected = [(0, 1), (0, 5), (0, 6), (1, 2), (2, 3), (3, 4), (4, 5),
(6, 7)]
c = Compound()
c.input_from_knapsack(cid)
actual = list(c.graph.edges())
self.assertEqual(actual, expected)
def test_get_vicinities(self):
"""
get_vicinitiesのテスト
"""
rdkmol = Chem.MolFromMolBlock(MOLBLOCK)
expected = [(0, [1, 2, 3]), (1, [0, 4]), (2, [0, 5]), (3, [0, 6]),
(4, [1, 7]), (5, [2, 7]), (6, [3]), (7, [4, 8, 5]),
(8, [7])]
c = Compound()
c.input_rdkmol(rdkmol)
actual = c.get_vicinities()
self.assertEqual(actual, expected)
def test_get_triplets(self):
"""
get_tripletsのテスト
内部でfind_seqを使用
"""
expected = [[0, 1, 4], [0, 2, 5], [0, 3, 6], [1, 0, 2], [1, 0, 3],
[1, 4, 7], [2, 0, 3], [2, 5, 7], [4, 7, 5], [4, 7, 8],
[5, 7, 8]]
c = Compound()
c.input_molfile(PATH)
actual = [i for i in c.get_triplets()]
self.assertEqual(actual, expected)
def test_input_smiles(self):
"""
input_smilesのテスト
内部でinput_rdkmolを使用
"""
smiles = 'O=Cc1ccc(O)cc1'
expected = [(0, 1), (1, 2), (2, 3), (2, 8), (3, 4), (4, 5), (5, 6),
(5, 7), (7, 8)]
c = Compound()
c.input_smiles(smiles)
actual = list(c.graph.edges())
self.assertEqual(actual, expected)
def test_input_inchi(self):
"""
input_inchiのテスト
内部でinput_rdkmolを使用
"""
inchi = ("InChI=1S/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h2,"
"5,7-8,10-11H,1H2/t2-,5+/m0/s1")
expected = [(0, 1), (0, 6), (1, 4), (1, 7), (2, 3), (2, 4), (2, 8),
(3, 5), (3, 9), (4, 11), (5, 10), (5, 11)]
c = Compound()
c.input_inchi(inchi)
actual = list(c.graph.edges())
self.assertEqual(actual, expected)
def test_input_from_kegg(self):
"""
input_from_keggのテスト
内部でinput_molfileを使用
"""
cid = "C00002"
expected = [(0, 1), (0, 2), (0, 3), (1, 4), (1, 5), (2, 6), (2, 7),
(3, 8), (4, 9), (4, 8), (5, 10), (6, 11), (7, 12), (7, 13),
(9, 14), (9, 15), (10, 14), (11, 16), (11, 12), (12, 17),
(16, 18), (18, 19), (19, 20), (19, 21), (19, 22), (20, 23),
(23, 24), (23, 25), (23, 26), (24, 27), (27, 28), (27, 29),
(27, 30)]
c = Compound()
c.input_from_kegg(cid)
actual = list(c.graph.edges())
self.assertEqual(actual, expected)
def test_draw_cpd_with_labels(self):
"""
draw_cpd_with_labelsのテスト
これは実行時にエラーが出るかのチェックしかしてない
"""
c = Compound()
c.input_molfile(PATH)
c.draw_cpd_with_labels()
def test_draw_cpd(self):
"""
draw_cpdのテスト
"""
c = Compound()
c.input_molfile(PATH)
c.draw_cpd("test.png")
self.assertTrue(os.path.exists("./test.png"))
os.remove("./test.png")