def test_rsgcn_preprocessor(mol):
preprocessor = RSGCNPreprocessor(max_atoms=4, out_size=4)
ret_atom_array, ret_adj_array = preprocessor.get_input_features(mol)
expect_atom_array = numpy.array([6, 7, 6, 8], dtype=numpy.int32)
expect_adj_array = numpy.array(
[[0.5, 0.4082, 0, 0], [0.4082, 0.3333, 0.3333, 0],
[0, 0.3333, 0.3333, 0.4082], [0, 0, 0.4082, 0.5]],
dtype=numpy.float32)
numpy.testing.assert_array_equal(ret_atom_array, expect_atom_array)
numpy.testing.assert_allclose(
ret_adj_array, expect_adj_array, rtol=1e-03, atol=1e-03)
def test_atomic_number_non_default_padding_preprocessor(mol):
preprocessor = RSGCNPreprocessor(out_size=7)
ret_atom_array, ret_adj_array = preprocessor.get_input_features(mol)
expect_atom_array = numpy.array([6, 7, 6, 8, 0, 0, 0], dtype=numpy.int32)
expect_adj_array = numpy.array(
[[0.5, 0.4082, 0, 0, 0, 0, 0], [0.4082, 0.3333, 0.3333, 0, 0, 0, 0],
[0, 0.3333, 0.3333, 0.4082, 0, 0, 0], [0, 0, 0.4082, 0.5, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0]],
dtype=numpy.float32)
numpy.testing.assert_array_equal(ret_atom_array, expect_atom_array)
numpy.testing.assert_allclose(ret_adj_array,
expect_adj_array,
rtol=1e-03,
atol=1e-03)
def test_rsgcn_preprocessor_with_tox21():
preprocessor = RSGCNPreprocessor()
# labels=None as default, and label information is not returned.
dataset = SDFFileParser(preprocessor)\
.parse(get_tox21_filepath('train'))['dataset']
index = numpy.random.choice(len(dataset), None)
atoms, adjacency = dataset[index]
assert atoms.ndim == 1 # (atom, )
assert atoms.dtype == numpy.int32
assert adjacency.ndim == 2
assert adjacency.dtype == numpy.float32
def test_rsgcn_preprocessor_default():
preprocessor = RSGCNPreprocessor()
dataset = SmilesParser(preprocessor).parse(
['C#N', 'Cc1cnc(C=O)n1C', 'c1ccccc1'])['dataset']
index = numpy.random.choice(len(dataset), None)
atoms, adjacency = dataset[index]
assert atoms.ndim == 1 # (atom, )
assert atoms.dtype == numpy.int32
assert adjacency.ndim == 2
assert adjacency.dtype == numpy.float32
def test_rsgcn_non_default_max_atoms_preprocessor(mol):
preprocessor = RSGCNPreprocessor(max_atoms=5)
ret_atom_array, ret_adj_array = preprocessor.get_input_features(mol)
expect_atom_array = numpy.array([6, 7, 6, 8], dtype=numpy.int32)
expect_adj_array = numpy.array(
[[0.5, 0.4082, 0, 0], [0.4082, 0.3333, 0.3333, 0],
[0, 0.3333, 0.3333, 0.4082], [0, 0, 0.4082, 0.5]],
dtype=numpy.float32)
numpy.testing.assert_array_equal(ret_atom_array, expect_atom_array)
numpy.testing.assert_allclose(
ret_adj_array, expect_adj_array, rtol=1e-03, atol=1e-03)
preprocessor = RSGCNPreprocessor(max_atoms=3)
with pytest.raises(MolFeatureExtractionError):
preprocessor.get_input_features(mol)
def test_rsgcn_preprocessor_assert_raises():
with pytest.raises(ValueError):
RSGCNPreprocessor(max_atoms=3, out_size=2) # NOQA