class MoleculeTest(unittest.TestCase):
def setUp(self):
self.mol = molecule.Molecule()
self.atomC = Atom("C")
self.atomN = Atom("N")
self.atomN.add_connected(self.atomC)
self.atomO = Atom("O")
def test_add(self):
mol = self.mol
mol.add_atom(self.atomC)
mol.add_atom(self.atomN)
self.assertTrue(mol.atoms == [self.atomC, self.atomN]
or mol.atoms == [self.atomN, self.atomC])
mol.add_atom(
self.atomC
) #nothing should happen, since this atom is already in the molecule)
self.assertTrue(mol.atoms == [self.atomC, self.atomN]
or mol.atoms == [self.atomN, self.atomC])
# Integrity test, actually testing molecule_splitter
def test_get_groups(self):
mol = self.mol
mol.add_atom(self.atomC)
mol.add_atom(self.atomN)
result = mol.get_groups()
expected = {"CH3NH2": 1}
self.assertEqual(result, expected)
def setUp(self):
self.mol = molecule.Molecule()
self.atomC = Atom("C")
self.atomN = Atom("N")
self.atomN.add_connected(self.atomC)
self.atomO = Atom("O")
def setUp(self):
# construct propenamine
self.atomC1 = Atom("C")
self.atomC2 = Atom("C")
self.atomC3 = Atom("C")
self.atomN = Atom("N")
self.atomO = Atom("O")
class MoleculeTest(unittest.TestCase):
def setUp(self):
self.mol = molecule.Molecule()
self.atomC = Atom("C")
self.atomN = Atom("N")
self.atomN.add_connected(self.atomC)
self.atomO = Atom("O")
def test_add(self):
mol = self.mol
mol.add_atom(self.atomC)
mol.add_atom(self.atomN)
self.assertTrue(mol.atoms == [self.atomC, self.atomN] or mol.atoms == [self.atomN, self.atomC])
mol.add_atom(self.atomC) #nothing should happen, since this atom is already in the molecule)
self.assertTrue(mol.atoms == [self.atomC, self.atomN] or mol.atoms == [self.atomN, self.atomC])
# Integrity test, actually testing molecule_splitter
def test_get_groups(self):
mol = self.mol
mol.add_atom(self.atomC)
mol.add_atom(self.atomN)
result = mol.get_groups()
expected = {"CH3NH2" : 1}
self.assertEqual(result, expected)
def setUp(self):
# construct propenamine
self.atomC1 = Atom("C")
self.atomC2 = Atom("C")
self.atomC3 = Atom("C")
self.atomN = Atom("N")
self.atomO = Atom("O")
def test_match_atom_to_node(self):
result = (molecule_splitter._match_atom_to_node(
self.atomC1, ("ext-atom", ("atom", "C"), [("hydrogen", 4)])))
expected = (True, None)
self.assertEqual(result, expected)
self.atomC1.add_connected(Atom("Cl"))
self.atomC1.add_connected(Atom("Cl"))
result = (molecule_splitter._match_atom_to_node(
self.atomC1, ("ext-atom", ("atom", "C"), [("hydrogen", 2),
("halogen", "Cl", 2)])))
expected = (True, None)
self.assertEqual(result, expected)
def test_split2(self):
# construct cyclobutane
atomC = Atom("C")
atomC.add_connected(self.atomC1)
self.atomC1.add_connected(self.atomC2)
self.atomC2.add_connected(self.atomC3)
self.atomC3.add_connected(atomC)
mol = stub_mol([self.atomC1, atomC, self.atomC2, self.atomC3])
result = molecule_splitter.split(mol)
expected = {"CH2": 4}
self.assertEqual(result, expected)
def test_split2(self):
# construct cyclobutane
atomC = Atom("C")
atomC.add_connected(self.atomC1)
self.atomC1.add_connected(self.atomC2)
self.atomC2.add_connected(self.atomC3)
self.atomC3.add_connected(atomC)
mol = stub_mol([self.atomC1, atomC, self.atomC2, self.atomC3])
result = molecule_splitter.split(mol)
expected = {"CH2": 4}
self.assertEqual(result, expected)
def setUp(self):
self.mol = molecule.Molecule()
self.atomC = Atom("C")
self.atomN = Atom("N")
self.atomN.add_connected(self.atomC)
self.atomO = Atom("O")
def setUp(self):
self.atomC1 = Atom("C")
self.atomC2 = Atom("C")
self.atomC3 = Atom("C")
self.atomO = Atom("O")
self.atomN = Atom("N")
class AuxiliaryFuncTest(unittest.TestCase):
def setUp(self):
self.atomC1 = Atom("C")
self.atomC2 = Atom("C")
self.atomC3 = Atom("C")
self.atomO = Atom("O")
self.atomN = Atom("N")
def test_match_atom_to_node(self):
result = (molecule_splitter._match_atom_to_node(
self.atomC1, ("ext-atom", ("atom", "C"), [("hydrogen", 4)])))
expected = (True, None)
self.assertEqual(result, expected)
self.atomC1.add_connected(Atom("Cl"))
self.atomC1.add_connected(Atom("Cl"))
result = (molecule_splitter._match_atom_to_node(
self.atomC1, ("ext-atom", ("atom", "C"), [("hydrogen", 2),
("halogen", "Cl", 2)])))
expected = (True, None)
self.assertEqual(result, expected)
def test_crawl(self):
self.atomC1.add_connected(self.atomC2, 2)
result = molecule_splitter._crawl(
self.atomC1,
("node", ("ext-atom", ("atom", "C"), [("hydrogen", 2)]),
("next", 2, ("node", ("ext-atom",
("atom", "C"), [("hydrogen", 2)]), None))),
[])
expected = [self.atomC1, self.atomC2]
expected_alt = [self.atomC2, self.atomC1]
self.assertTrue(result == expected or result == expected_alt)
def test_crawl_2(self):
self.atomC1.add_connected(self.atomO, 2)
self.atomC1.add_connected(self.atomN)
result = molecule_splitter._crawl(
self.atomC1,
("node", ("ext-atom", ("atom", "C"), [("next", 2,
("node",
("atom", "O"), None))]),
("next", 1,
("node", ("ext-atom",
("atom", "N"), [("hydrogen", 2)]), None)), None), [])
expected = list(
itertools.permutations([self.atomC1, self.atomN, self.atomO]))
self.assertIn(tuple(result), expected)
def test_look_for_group(self):
self.atomN.add_connected(self.atomC3)
self.atomC3.add_connected(self.atomC2)
self.atomC2.add_connected(self.atomC1, 2)
result = molecule_splitter._look_for_group(
"CH2=CH", [self.atomC1, self.atomC2, self.atomC3, self.atomN], {
"C": [0, 1, 2],
"N": 3
})
expected = [[0, 1]]
self.assertEqual(result, expected)
result = molecule_splitter._look_for_group(
"CH2NH2", [self.atomC1, self.atomC2, self.atomC3, self.atomN], {
"C": [0, 1, 2],
"N": 3
})
expected = [[2, 3]]
self.assertEqual(result, expected)
def test_look_for_group1(self):
self.atomC1.add_connected(self.atomC2)
self.atomC1.add_connected(self.atomC3)
self.atomC1.add_connected(self.atomN)
self.atomC1.add_connected(self.atomO)
result = molecule_splitter._look_for_group(
"CH0", [self.atomC1, self.atomC2, self.atomC3, self.atomN], {
"C": [0, 1, 2],
"N": 3
})
expected = [[0]]
self.assertEqual(result, expected)
class SplitterTest(unittest.TestCase):
def setUp(self):
# construct propenamine
self.atomC1 = Atom("C")
self.atomC2 = Atom("C")
self.atomC3 = Atom("C")
self.atomN = Atom("N")
self.atomO = Atom("O")
def test_split(self):
self.atomN.add_connected(self.atomC3)
self.atomC3.add_connected(self.atomC2)
self.atomC2.add_connected(self.atomC1, 2)
mol = stub_mol([self.atomC1, self.atomC2, self.atomC3, self.atomN])
result = molecule_splitter.split(mol)
expected = {"CH2=CH": 1, "CH2NH2": 1}
self.assertEqual(result, expected)
def test_split1(self):
# construct propan-2-ole
self.atomC1.add_connected(self.atomO)
self.atomC1.add_connected(self.atomC2)
self.atomC1.add_connected(self.atomC3)
mol = stub_mol([self.atomC1, self.atomC2, self.atomC3, self.atomO])
result = molecule_splitter.split(mol)
expected = {"CH3": 2, "CH": 1, "OH": 1}
self.assertEqual(result, expected)
def test_split2(self):
# construct cyclobutane
atomC = Atom("C")
atomC.add_connected(self.atomC1)
self.atomC1.add_connected(self.atomC2)
self.atomC2.add_connected(self.atomC3)
self.atomC3.add_connected(atomC)
mol = stub_mol([self.atomC1, atomC, self.atomC2, self.atomC3])
result = molecule_splitter.split(mol)
expected = {"CH2": 4}
self.assertEqual(result, expected)
def setUp(self):
self.atomC1 = Atom("C")
self.atomC2 = Atom("C")
self.atomC3 = Atom("C")
self.atomO = Atom("O")
self.atomN = Atom("N")
class AuxiliaryFuncTest(unittest.TestCase):
def setUp(self):
self.atomC1 = Atom("C")
self.atomC2 = Atom("C")
self.atomC3 = Atom("C")
self.atomO = Atom("O")
self.atomN = Atom("N")
def test_match_atom_to_node(self):
result = molecule_splitter._match_atom_to_node(self.atomC1, ("ext-atom", ("atom", "C"), [("hydrogen", 4)]))
expected = (True, None)
self.assertEqual(result, expected)
self.atomC1.add_connected(Atom("Cl"))
self.atomC1.add_connected(Atom("Cl"))
result = molecule_splitter._match_atom_to_node(
self.atomC1, ("ext-atom", ("atom", "C"), [("hydrogen", 2), ("halogen", "Cl", 2)])
)
expected = (True, None)
self.assertEqual(result, expected)
def test_crawl(self):
self.atomC1.add_connected(self.atomC2, 2)
result = molecule_splitter._crawl(
self.atomC1,
(
"node",
("ext-atom", ("atom", "C"), [("hydrogen", 2)]),
("next", 2, ("node", ("ext-atom", ("atom", "C"), [("hydrogen", 2)]), None)),
),
[],
)
expected = [self.atomC1, self.atomC2]
expected_alt = [self.atomC2, self.atomC1]
self.assertTrue(result == expected or result == expected_alt)
def test_crawl_2(self):
self.atomC1.add_connected(self.atomO, 2)
self.atomC1.add_connected(self.atomN)
result = molecule_splitter._crawl(
self.atomC1,
(
"node",
("ext-atom", ("atom", "C"), [("next", 2, ("node", ("atom", "O"), None))]),
("next", 1, ("node", ("ext-atom", ("atom", "N"), [("hydrogen", 2)]), None)),
None,
),
[],
)
expected = list(itertools.permutations([self.atomC1, self.atomN, self.atomO]))
self.assertIn(tuple(result), expected)
def test_look_for_group(self):
self.atomN.add_connected(self.atomC3)
self.atomC3.add_connected(self.atomC2)
self.atomC2.add_connected(self.atomC1, 2)
result = molecule_splitter._look_for_group(
"CH2=CH", [self.atomC1, self.atomC2, self.atomC3, self.atomN], {"C": [0, 1, 2], "N": 3}
)
expected = [[0, 1]]
self.assertEqual(result, expected)
result = molecule_splitter._look_for_group(
"CH2NH2", [self.atomC1, self.atomC2, self.atomC3, self.atomN], {"C": [0, 1, 2], "N": 3}
)
expected = [[2, 3]]
self.assertEqual(result, expected)
def test_look_for_group1(self):
self.atomC1.add_connected(self.atomC2)
self.atomC1.add_connected(self.atomC3)
self.atomC1.add_connected(self.atomN)
self.atomC1.add_connected(self.atomO)
result = molecule_splitter._look_for_group(
"CH0", [self.atomC1, self.atomC2, self.atomC3, self.atomN], {"C": [0, 1, 2], "N": 3}
)
expected = [[0]]
self.assertEqual(result, expected)
class SplitterTest(unittest.TestCase):
def setUp(self):
# construct propenamine
self.atomC1 = Atom("C")
self.atomC2 = Atom("C")
self.atomC3 = Atom("C")
self.atomN = Atom("N")
self.atomO = Atom("O")
def test_split(self):
self.atomN.add_connected(self.atomC3)
self.atomC3.add_connected(self.atomC2)
self.atomC2.add_connected(self.atomC1, 2)
mol = stub_mol([self.atomC1, self.atomC2, self.atomC3, self.atomN])
result = molecule_splitter.split(mol)
expected = {"CH2=CH": 1, "CH2NH2": 1}
self.assertEqual(result, expected)
def test_split1(self):
# construct propan-2-ole
self.atomC1.add_connected(self.atomO)
self.atomC1.add_connected(self.atomC2)
self.atomC1.add_connected(self.atomC3)
mol = stub_mol([self.atomC1, self.atomC2, self.atomC3, self.atomO])
result = molecule_splitter.split(mol)
expected = {"CH3": 2, "CH": 1, "OH": 1}
self.assertEqual(result, expected)
def test_split2(self):
# construct cyclobutane
atomC = Atom("C")
atomC.add_connected(self.atomC1)
self.atomC1.add_connected(self.atomC2)
self.atomC2.add_connected(self.atomC3)
self.atomC3.add_connected(atomC)
mol = stub_mol([self.atomC1, atomC, self.atomC2, self.atomC3])
result = molecule_splitter.split(mol)
expected = {"CH2": 4}
self.assertEqual(result, expected)
