Fixed shapes, layers work in sequence (2bf077b7) · Commits · 钟慕尧 / deepchem

deepchem/feat/molecule_featurizers/mat_featurizer.py

+4 −0

Original line number	Diff line number	Diff line
		@@ -243,4 +243,8 @@ class MATFeaturizer(MolecularFeaturizer):
		adjacency_matrix = self.pad_sequence(adjacency_matrix)
		distance_matrix = self.pad_sequence(distance_matrix)

		node_features = np.expand_dims(node_features, 0)
		adjacency_matrix = np.expand_dims(adjacency_matrix, 0)
		distance_matrix = np.expand_dims(distance_matrix, 0)

		return MATEncoding(node_features, adjacency_matrix, distance_matrix)

+10 −10

Original line number	Diff line number	Diff line
		@@ -24,10 +24,10 @@ class TestMATFeaturizer(unittest.TestCase):
		out = featurizer.featurize(self.mol)
		assert (type(out) == np.ndarray)
		assert (out.shape == (1,))
		assert (out[0].node_features.shape == (3, 36))
		assert (out[0].adjacency_matrix.shape == (3, 3))
		assert (out[0].distance_matrix.shape == (3, 3))
		expected_node_features = np.array([[
		assert (out[0].node_features.shape == (1, 3, 36))
		assert (out[0].adjacency_matrix.shape == (1, 3, 3))
		assert (out[0].distance_matrix.shape == (1, 3, 3))
		expected_node_features = np.array([[[
		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., 0., 0., 0., 0., 0., 0., 0., 0.
		], [
		@@ -36,12 +36,12 @@ class TestMATFeaturizer(unittest.TestCase):
		], [
		0., 0., 1., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 1., 0., 0., 0., 0.,
		0., 0., 0., 1., 0., 0., 0., 0., 0., 0., 1., 0., 0., 0., 0., 0., 0., 0.
		]])
		expected_adjacency_matrix = np.array([[0., 0., 0.], [0., 0., 1.],
		[0., 1., 0.]])
		expected_distance_matrix = np.array([[1.e+06, 1.e+06,
		]]])
		expected_adjacency_matrix = np.array([[[0., 0., 0.], [0., 0., 1.],
		[0., 1., 0.]]])
		expected_distance_matrix = np.array([[[1.e+06, 1.e+06,
		1.e+06], [1.e+06, 0.e+00, 1.e+00],
		[1.e+06, 1.e+00, 0.e+00]])
		[1.e+06, 1.e+00, 0.e+00]]])
		assert (np.array_equal(out[0].node_features, expected_node_features))
		assert (np.array_equal(out[0].adjacency_matrix, expected_adjacency_matrix))
		assert (np.array_equal(out[0].distance_matrix, expected_distance_matrix))