def test_get_labels_eigen(self):
a = CoulombMatrix(eigen=True)
X = a.fit_transform([METHANE])
labels = a.get_labels()
self.assertEqual(X.shape[1], len(labels))
expected = ('coul-0', 'coul-1', 'coul-2', 'coul-3', 'coul-4')
self.assertEqual(labels, expected)
def test_get_labels(self):
a = CoulombMatrix()
X = a.fit_transform([METHANE])
labels = a.get_labels()
self.assertEqual(X.shape[1], len(labels))
expected = (
'coul-0-0',
'coul-0-1',
'coul-0-2',
'coul-0-3',
'coul-0-4',
'coul-1-0',
'coul-1-1',
'coul-1-2',
'coul-1-3',
'coul-1-4',
'coul-2-0',
'coul-2-1',
'coul-2-2',
'coul-2-3',
'coul-2-4',
'coul-3-0',
'coul-3-1',
'coul-3-2',
'coul-3-3',
'coul-3-4',
'coul-4-0',
'coul-4-1',
'coul-4-2',
'coul-4-3',
'coul-4-4',
)
self.assertEqual(labels, expected)
def test_eigen(self):
a = CoulombMatrix(eigen=True)
expected_results = numpy.array(
[40.04619974, -1.00605888, -0.06059994, -0.06071616, -0.06071957])
try:
numpy.testing.assert_array_almost_equal(
a.fit_transform([METHANE])[0], expected_results)
except AssertionError as e:
self.fail(e)
def test_only_lower_triangle(self):
a = CoulombMatrix(only_lower_triangle=True)
expected_results = numpy.array([36.858105, 5.49459, 0.5, 5.494629,
0.560719, 0.5, 5.4945, 0.560717,
0.560718, 0.5, 5.490313, 0.56064,
0.560641, 0.560638, 0.5])
try:
numpy.testing.assert_array_almost_equal(
a.fit_transform([METHANE])[0],
expected_results)
except AssertionError as e:
self.fail(e)
def test_fit_transform(self):
a = CoulombMatrix()
expected_results = numpy.array([[
36.8581052, 5.49459021, 5.49462885, 5.4945, 5.49031286, 5.49459021,
0.5, 0.56071947, 0.56071656, 0.56064037, 5.49462885, 0.56071947,
0.5, 0.56071752, 0.56064089, 5.4945, 0.56071656, 0.56071752, 0.5,
0.56063783, 5.49031286, 0.56064037, 0.56064089, 0.56063783, 0.5
]])
try:
numpy.testing.assert_array_almost_equal(a.fit_transform([METHANE]),
expected_results)
except AssertionError as e:
self.fail(e)
def test_sort(self):
a = CoulombMatrix(sort=True)
b = CoulombMatrix()
res_a = a.fit_transform([MID])
res_b = b.fit_transform([MID])
self.assertFalse(numpy.allclose(res_a, res_b))
expected_results = numpy.array([
73.51669472, 45.84796673, 20.4393443, 18.51709592, 34.38200956,
19.92342035, 1.71317156, 1.39374152, 1.20676731
])
try:
numpy.testing.assert_array_almost_equal(res_a[0, :9],
expected_results)
except AssertionError as e:
self.fail(e)
def test_transform_before_fit(self):
a = CoulombMatrix()
with self.assertRaises(ValueError):
a.transform(ALL_DATA)
def test_small_to_large_transform_drop_values(self):
a = CoulombMatrix(drop_values=True)
a.fit([METHANE])
a.transform(ALL_DATA)
self.assertEqual(a.transform(ALL_DATA).shape, (3, 25))
def test_small_to_large_transform(self):
a = CoulombMatrix()
a.fit([METHANE])
with self.assertRaises(ValueError):
a.transform(ALL_DATA)
def test_fit(self):
a = CoulombMatrix()
a.fit(ALL_DATA)
self.assertEqual(a._max_size, 49)