def test_get_labels_bond_order(self):
a = ConnectivityTree(depth=3, use_bond_order=True)
X = a.fit_transform([METHANE])
labels = a.get_labels()
self.assertEqual(X.shape[1], len(labels))
expected = ('1-C_1_H-1__2-H_1_C-3', '1-H_1_C-1__1-H_1_H-3')
self.assertEqual(labels, expected)
def test_get_labels_unknown(self):
a = ConnectivityTree(depth=2, add_unknown=True)
X = a.fit_transform([METHANE])
labels = a.get_labels()
self.assertEqual(X.shape[1], len(labels))
expected = ('0-Root-C-1__1-C-H-4', '0-Root-H-1__1-H-C-1', UNKNOWN)
self.assertEqual(labels, expected)
def test_get_labels_coordination(self):
a = ConnectivityTree(depth=1, use_coordination=True)
X = a.fit_transform([METHANE])
labels = a.get_labels()
self.assertEqual(X.shape[1], len(labels))
expected = ('0-Root-C4-1', '0-Root-H1-1')
self.assertEqual(labels, expected)
def test_fit_depth_3_preserve_paths(self):
a = ConnectivityTree(depth=3, use_parent_element=False,
preserve_paths=True)
a.fit(ALL_DATA)
expected = (
((0, -1, 'C', 1), (1, 0, 'C', 1), (1, 1, 'C', 1), (1, 4, 'C', 1),
(2, 1, 'C', 1), (2, 1, 'H', 1), (2, 4, 'H', 1), (2, 4, 'N', 1),
(2, 7, 'C', 1)),
((0, -1, 'C', 1), (1, 0, 'C', 1), (1, 1, 'C', 1), (1, 4, 'H', 1),
(2, 1, 'C', 1), (2, 1, 'H', 1), (2, 4, 'C', 1), (2, 4, 'H', 1)),
((0, -1, 'C', 1), (1, 0, 'C', 1), (1, 1, 'C', 1), (1, 4, 'O', 1),
(2, 1, 'C', 1), (2, 1, 'H', 1), (2, 4, 'C', 1), (2, 4, 'N', 1),
(2, 7, 'C', 1)),
((0, -1, 'C', 1), (1, 0, 'C', 1), (1, 1, 'N', 1), (1, 4, 'C', 1),
(2, 1, 'C', 1), (2, 1, 'O', 1), (2, 4, 'C', 1), (2, 6, 'C', 1),
(2, 6, 'O', 1)),
((0, -1, 'C', 1), (1, 0, 'C', 1), (1, 1, 'N', 1), (2, 1, 'C', 2)),
((0, -1, 'C', 1), (1, 0, 'O', 1), (1, 1, 'H', 1), (1, 3, 'H', 1),
(1, 4, 'H', 1), (2, 1, 'C', 1)),
((0, -1, 'H', 1), (1, 0, 'C', 1), (2, 1, 'H', 2), (2, 1, 'O', 1)),
((0, -1, 'N', 1), (1, 0, 'C', 1), (1, 1, 'C', 1), (2, 1, 'C', 1),
(2, 1, 'N', 1), (2, 4, 'C', 1), (2, 4, 'H', 1)),
((0, -1, 'O', 1), (1, 0, 'C', 1), (1, 1, 'C', 1), (2, 1, 'C', 2),
(2, 4, 'C', 2))
)
self.assertEqual(a._base_groups[::5], expected)
def test_unknown(self):
a = ConnectivityTree(add_unknown=True)
expected_results = numpy.array([[1, 4, 0],
[2, 3, 4],
[25, 15, 9]])
a.fit([METHANE])
self.assertTrue((a.transform(ALL_DATA) == expected_results).all())
def test_fit_depth_1_coordination(self):
a = ConnectivityTree(depth=1, use_coordination=True)
a.fit(ALL_DATA)
bases = ('C1', 'C2', 'C3', 'C4', 'H0', 'H1',
'N1', 'N2', 'N3', 'O0', 'O1', 'O2')
expected = tuple(((0, 'Root', x, 1), ) for x in bases)
self.assertEqual(a._base_groups, expected)
def test_fit_depth_1_use_bond_order(self):
# This should be the exact same thing as doing it with
# use_bond_order=False
a = ConnectivityTree(depth=1, use_parent_element=False,
use_bond_order=True)
a.fit(ALL_DATA)
base = ('C', 'H', 'N', 'O')
self.assertEqual(a._base_groups, tuple(((0, x, 1), ) for x in base))
def test_fit_depth_2_use_bond_order(self):
a = ConnectivityTree(depth=2,
use_parent_element=False,
use_bond_order=True)
a.fit(ALL_DATA)
expected = (((0, 'H', 1), ), ((1, 'C_1_O', 1), (1, 'C_Ar_O', 1)),
((1, 'C_2_C', 1), (1, 'N_3_C', 1)), ((1, 'C_Ar_C', 1), ),
((1, 'C_Ar_C', 2), (1, 'H_1_C', 1)), ((1, 'H_1_C', 4), ))
self.assertEqual(a._base_groups[::5], expected)
def test_tfidf(self):
a = ConnectivityTree(do_tfidf=True)
expected = numpy.array([[0., 0., 0., 0.], [0., 0., 0., 1.62186043],
[0., 0., 5.49306144, 1.62186043]])
a.fit(ALL_DATA)
try:
m = a.transform(ALL_DATA)
numpy.testing.assert_array_almost_equal(m, expected)
except AssertionError as e:
self.fail(e)
def test_fit_depth_2(self):
a = ConnectivityTree(depth=2, use_parent_element=False)
a.fit(ALL_DATA)
expected = (
((0, 'C', 1), (1, 'C', 1)),
((0, 'C', 1), (1, 'C', 1), (1, 'H', 1), (1, 'N', 1)),
((0, 'C', 1), (1, 'C', 1), (1, 'N', 1), (1, 'O', 1)),
((0, 'C', 1), (1, 'C', 1), (1, 'O', 1)),
((0, 'C', 1), (1, 'C', 2), (1, 'H', 1)),
((0, 'C', 1), (1, 'C', 2), (1, 'O', 1)),
((0, 'C', 1), (1, 'H', 3), (1, 'O', 1)), ((0, 'H', 1),),
((0, 'H', 1), (1, 'H', 1)),
((0, 'H', 1), (1, 'O', 1)),
((0, 'N', 1), (1, 'C', 1), (1, 'H', 2)), ((0, 'O', 1),),
((0, 'O', 1), (1, 'C', 1), (1, 'H', 1)),
((0, 'O', 1), (1, 'O', 1)),
)
self.assertEqual(a._base_groups[::2], expected)
def test_fit_transform(self):
a = ConnectivityTree(depth=2)
self.assertTrue((a.fit_transform(ALL_DATA) == ALL_ATOM_TREE).all())
def test_transform_before_fit(self):
a = ConnectivityTree()
with self.assertRaises(ValueError):
a.transform(ALL_DATA)
def test_large_to_small_transform(self):
a = ConnectivityTree(depth=2)
a.fit([BIG])
idxs = numpy.where(ALL_ATOM_TREE[2] != 0)[0]
expected = ALL_ATOM_TREE[:, idxs]
self.assertTrue((a.transform(ALL_DATA) == expected).all())
def test_transform(self):
a = ConnectivityTree()
a.fit(ALL_DATA)
self.assertTrue((a.transform(ALL_DATA) == ALL_ATOM).all())
def test_fit_depth_1_separated(self):
a = ConnectivityTree(depth=1)
a.fit([METHANE2])
self.assertTrue(
(a.transform([METHANE2]) == numpy.array([[1, 4]])).all())
def test_fit_depth_1(self):
a = ConnectivityTree(depth=1, use_parent_element=False)
a.fit(ALL_DATA)
base = ('C', 'H', 'N', 'O')
self.assertEqual(a._base_groups, tuple(((0, x, 1), ) for x in base))
