def test_transform_depth3(self):
# This is to test loop backs in the breadth-first search
a = Shell(depth=3)
a.fit(ALL_DATA)
expected_results = numpy.array([
[[0, 0, 0, 0], [0, 3, 0, 0], [0, 3, 0, 0], [0, 3, 0, 0],
[0, 3, 0, 0]],
[[0, 0, 0, 1], [0, 0, 0, 0], [1, 0, 0, 0], [0, 0, 0, 0],
[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0],
[0, 0, 0, 0]],
[[2, 2, 0, 0], [1, 1, 1, 1], [2, 2, 0, 0], [2, 1, 1, 0],
[4, 1, 0, 0], [3, 0, 0, 1], [2, 0, 0, 0], [2, 0, 0, 0],
[1, 0, 1, 0], [1, 0, 0, 0], [2, 0, 0, 0], [3, 1, 0, 0],
[2, 1, 2, 1], [3, 0, 0, 1], [3, 1, 1, 0], [3, 0, 0, 2],
[3, 0, 0, 1], [2, 0, 0, 0], [1, 0, 1, 0], [1, 0, 0, 0],
[2, 3, 0, 0], [1, 0, 0, 0], [0, 2, 0, 1], [0, 2, 0, 1],
[0, 2, 0, 1], [4, 0, 1, 0], [4, 0, 0, 1], [3, 0, 1, 1],
[5, 0, 0, 0], [4, 0, 0, 0], [2, 1, 0, 0], [1, 0, 0, 0],
[1, 0, 0, 0], [1, 0, 0, 0], [2, 0, 0, 0], [3, 2, 0, 0],
[2, 1, 2, 1], [4, 0, 0, 0], [2, 2, 1, 0], [3, 0, 0, 0],
[2, 1, 1, 0], [2, 0, 0, 0], [1, 0, 1, 0], [1, 0, 1, 0],
[1, 1, 0, 0], [1, 1, 0, 0], [2, 1, 0, 0], [1, 0, 0, 0],
[1, 0, 0, 0]]
])
self.assertTrue((a.transform(ALL_DATA) == expected_results).all())
def test_transform_depth3(self):
# This is to test loop backs in the breadth-first search
a = Shell(depth=3)
a.fit(ALL_DATA)
expected_results = numpy.array([
[[0, 0, 0, 0], [0, 3, 0, 0], [0, 3, 0, 0], [0, 3, 0, 0],
[0, 3, 0, 0]],
[[0, 0, 0, 1], [0, 0, 0, 0], [1, 0, 0, 0], [0, 0, 0, 0],
[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0],
[0, 0, 0, 0]],
[[2, 2, 0, 0], [1, 1, 1, 1], [2, 2, 0, 0], [2, 1, 1, 0],
[4, 1, 0, 0], [3, 0, 0, 1], [2, 0, 0, 0], [2, 0, 0, 0],
[1, 0, 1, 0], [1, 0, 0, 0], [2, 0, 0, 0], [3, 1, 0, 0],
[2, 1, 2, 1], [3, 0, 0, 1], [3, 1, 1, 0], [3, 0, 0, 2],
[3, 0, 0, 1], [2, 0, 0, 0], [1, 0, 1, 0], [1, 0, 0, 0],
[2, 3, 0, 0], [1, 0, 0, 0], [0, 2, 0, 1], [0, 2, 0, 1],
[0, 2, 0, 1], [4, 0, 1, 0], [4, 0, 0, 1], [3, 0, 1, 1],
[5, 0, 0, 0], [4, 0, 0, 0], [2, 1, 0, 0], [1, 0, 0, 0],
[1, 0, 0, 0], [1, 0, 0, 0], [2, 0, 0, 0], [3, 2, 0, 0],
[2, 1, 2, 1], [4, 0, 0, 0], [2, 2, 1, 0], [3, 0, 0, 0],
[2, 1, 1, 0], [2, 0, 0, 0], [1, 0, 1, 0], [1, 0, 1, 0],
[1, 1, 0, 0], [1, 1, 0, 0], [2, 1, 0, 0], [1, 0, 0, 0],
[1, 0, 0, 0]]
])
self.assertTrue((a.transform(ALL_DATA) == expected_results).all())
def test_fit_use_coordination(self):
a = Shell(depth=1, use_coordination=True)
a.fit(ALL_DATA)
self.assertEqual(
a._elements,
set([
'H0', 'H1', 'O2', 'C4', 'N1', 'C3', 'C2', 'N2', 'N3', 'C1',
'O1', 'O0'
]))
def test_add_unknown(self):
a = Shell(add_unknown=True)
a.fit([METHANE])
temp = []
for mol in BASE_SHELL:
inner = []
for atom in mol:
inner.append(atom[:2] + [atom[2] + atom[3]])
temp.append(inner)
expected = numpy.array(temp)
self.assertTrue((a.transform(ALL_DATA) == expected).all())
def test_add_unknown(self):
a = Shell(add_unknown=True)
a.fit([METHANE])
temp = []
for mol in BASE_SHELL:
inner = []
for atom in mol:
inner.append(atom[:2] + [atom[2] + atom[3]])
temp.append(inner)
expected = numpy.array(temp)
self.assertTrue((a.transform(ALL_DATA) == expected).all())
def test_transform_use_coordination(self):
a = Shell(depth=1, use_coordination=True)
a.fit([MID])
expected_results = numpy.array([[[1, 0, 0, 0, 0,
0], [0, 1, 0, 0, 0, 0],
[0, 0, 0, 0, 0,
1], [0, 0, 0, 0, 1, 0],
[0, 0, 0, 0, 0,
1], [0, 0, 0, 0, 0, 1],
[0, 0, 1, 0, 0,
0], [0, 0, 0, 1, 0, 0],
[0, 0, 0, 1, 0, 0]]])
self.assertTrue((a.transform([MID]) == expected_results).all())
def test_transform_use_coordination(self):
a = Shell(depth=1, use_coordination=True)
a.fit([MID])
expected_results = numpy.array([
[[1, 0, 0, 0, 0, 0],
[0, 1, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 1],
[0, 0, 0, 0, 1, 0],
[0, 0, 0, 0, 0, 1],
[0, 0, 0, 0, 0, 1],
[0, 0, 1, 0, 0, 0],
[0, 0, 0, 1, 0, 0],
[0, 0, 0, 1, 0, 0]]
])
self.assertTrue((a.transform([MID]) == expected_results).all())
def test_transform_depth2(self):
a = Shell(depth=2)
a.fit(ALL_DATA)
expected_results = numpy.array([[[0, 4, 0, 0], [1, 0, 0, 0],
[1, 0, 0, 0], [1, 0, 0, 0],
[1, 0, 0, 0]],
[[1, 0, 0, 0], [1, 0, 0, 1],
[1, 0, 0, 0], [0, 0, 0, 0],
[0, 0, 0, 1], [0, 0, 0, 1],
[0, 0, 0, 0], [0, 1, 0, 0],
[0, 1, 0, 0]],
[[1, 0, 1, 1], [2, 1, 0, 0],
[2, 1, 0, 0], [2, 1, 0, 0],
[2, 0, 1, 0], [2, 0, 0, 0],
[1, 0, 0, 0], [1, 0, 0, 0],
[1, 1, 0, 0], [0, 0, 0, 1],
[1, 0, 0, 0], [1, 0, 1, 1],
[3, 0, 0, 0], [2, 1, 0, 0],
[2, 0, 0, 1], [2, 0, 1, 0],
[2, 0, 0, 0], [1, 0, 0, 0],
[1, 1, 0, 0], [0, 0, 0, 1],
[2, 0, 0, 0], [0, 3, 0, 1],
[1, 0, 0, 0], [1, 0, 0, 0],
[1, 0, 0, 0], [2, 0, 0, 1],
[3, 0, 0, 0], [3, 0, 0, 0],
[2, 0, 0, 1], [2, 0, 0, 0],
[2, 0, 0, 0], [1, 1, 0, 0],
[1, 0, 0, 0], [1, 0, 0, 0],
[1, 0, 1, 0], [1, 0, 2, 0],
[3, 0, 0, 0], [2, 1, 0, 0],
[3, 0, 0, 0], [1, 1, 1, 0],
[2, 0, 0, 0], [1, 0, 0, 0],
[1, 0, 0, 0], [1, 2, 0, 0],
[0, 0, 1, 0], [0, 0, 1, 0],
[2, 0, 0, 0], [1, 1, 0, 0],
[1, 0, 0, 0]]])
self.assertTrue((a.transform(ALL_DATA) == expected_results).all())
def test_transform_depth2(self):
a = Shell(depth=2)
a.fit(ALL_DATA)
expected_results = numpy.array([
[[0, 4, 0, 0], [1, 0, 0, 0], [1, 0, 0, 0], [1, 0, 0, 0],
[1, 0, 0, 0]],
[[1, 0, 0, 0], [1, 0, 0, 1], [1, 0, 0, 0], [0, 0, 0, 0],
[0, 0, 0, 1], [0, 0, 0, 1], [0, 0, 0, 0], [0, 1, 0, 0],
[0, 1, 0, 0]],
[[1, 0, 1, 1], [2, 1, 0, 0], [2, 1, 0, 0], [2, 1, 0, 0],
[2, 0, 1, 0], [2, 0, 0, 0], [1, 0, 0, 0], [1, 0, 0, 0],
[1, 1, 0, 0], [0, 0, 0, 1], [1, 0, 0, 0], [1, 0, 1, 1],
[3, 0, 0, 0], [2, 1, 0, 0], [2, 0, 0, 1], [2, 0, 1, 0],
[2, 0, 0, 0], [1, 0, 0, 0], [1, 1, 0, 0], [0, 0, 0, 1],
[2, 0, 0, 0], [0, 3, 0, 1], [1, 0, 0, 0], [1, 0, 0, 0],
[1, 0, 0, 0], [2, 0, 0, 1], [3, 0, 0, 0], [3, 0, 0, 0],
[2, 0, 0, 1], [2, 0, 0, 0], [2, 0, 0, 0], [1, 1, 0, 0],
[1, 0, 0, 0], [1, 0, 0, 0], [1, 0, 1, 0], [1, 0, 2, 0],
[3, 0, 0, 0], [2, 1, 0, 0], [3, 0, 0, 0], [1, 1, 1, 0],
[2, 0, 0, 0], [1, 0, 0, 0], [1, 0, 0, 0], [1, 2, 0, 0],
[0, 0, 1, 0], [0, 0, 1, 0], [2, 0, 0, 0], [1, 1, 0, 0],
[1, 0, 0, 0]]
])
self.assertTrue((a.transform(ALL_DATA) == expected_results).all())
def test_small_to_large_transform(self):
a = Shell()
a.fit([METHANE])
expected = numpy.array([numpy.array(x)[:, :2].tolist()
for x in BASE_SHELL])
self.assertTrue((a.transform(ALL_DATA) == expected).all())
def test_transform(self):
a = Shell()
a.fit(ALL_DATA)
self.assertTrue((a.transform(ALL_DATA) == BASE_SHELL).all())
def test_fit(self):
a = Shell(depth=1)
a.fit(ALL_DATA)
self.assertEqual(a._elements, ('C', 'H', 'N', 'O'))
def test_get_labels_unknown(self):
a = Shell(add_unknown=True)
a.fit(ALL_DATA)
expected = ('C', 'H', 'N', 'O', UNKNOWN)
self.assertEqual(a.get_labels(), expected)
def test_get_labels(self):
a = Shell()
a.fit(ALL_DATA)
expected = ('C', 'H', 'N', 'O')
self.assertEqual(a.get_labels(), expected)
def test_large_to_small_transform(self):
a = Shell()
a.fit([BIG])
self.assertTrue((a.transform(ALL_DATA) == BASE_SHELL).all())
def test_large_to_small_transform(self):
a = Shell()
a.fit([BIG])
self.assertTrue((a.transform(ALL_DATA) == BASE_SHELL).all())
def test_small_to_large_transform(self):
a = Shell()
a.fit([METHANE])
expected = numpy.array(
[numpy.array(x)[:, :2].tolist() for x in BASE_SHELL])
self.assertTrue((a.transform(ALL_DATA) == expected).all())
def test_get_labels(self):
a = Shell()
a.fit(ALL_DATA)
expected = ('C', 'H', 'N', 'O')
self.assertEqual(a.get_labels(), expected)
def test_transform(self):
a = Shell()
a.fit(ALL_DATA)
self.assertTrue((a.transform(ALL_DATA) == BASE_SHELL).all())
def test_fit_use_coordination(self):
a = Shell(depth=1, use_coordination=True)
a.fit(ALL_DATA)
self.assertEqual(a._elements, ('C1', 'C2', 'C3', 'C4', 'H0', 'H1',
'N1', 'N2', 'N3', 'O0', 'O1', 'O2'))
def test_fit(self):
a = Shell(depth=1)
a.fit(ALL_DATA)
self.assertEqual(a._elements, ('C', 'H', 'N', 'O'))
def test_get_labels_unknown(self):
a = Shell(add_unknown=True)
a.fit(ALL_DATA)
expected = ('C', 'H', 'N', 'O', 'UNKNOWN')
self.assertEqual(a.get_labels(), expected)