Test fixes (90ede031) · Commits · 钟慕尧 / deepchem

deepchem/feat/base_classes.py

+5 −4

Original line number	Diff line number	Diff line
		@@ -155,7 +155,8 @@ class ComplexFeaturizer(Featurizer):
		Abstract class for calculating features for mol/protein complexes.
		"""

		def featurize(self, complexes: Iterable[Tuple[str, str]],
		def featurize(self,
		complexes: Iterable[Tuple[str, str]],
		log_every_n: int = 100) -> np.ndarray:
		"""
		Calculate features for mol/protein complexes.
		@@ -164,13 +165,13 @@ class ComplexFeaturizer(Featurizer):
		----------
		complexes: Iterable[Tuple[str, str]]
		List of filenames (PDB, SDF, etc.) for ligand molecules and proteins.
		Each element should be a tuple of the form (ligand_filename,
		protein_filename).

		Returns
		-------
		features: np.ndarray
		Array of features
		failures: List
		Indices of complexes that failed to featurize.
		"""

		if not isinstance(complexes, Iterable):

deepchem/feat/tests/test_grid_featurizers.py

+4 −4

Original line number	Diff line number	Diff line
		@@ -13,7 +13,7 @@ def test_charge_voxelizer():
		voxel_width = 1.0
		voxelizer = dc.feat.ChargeVoxelizer(
		cutoff=cutoff, box_width=box_width, voxel_width=voxel_width)
		features = voxelizer.featurize((ligand_file, protein_file))
		features = voxelizer.featurize([(ligand_file, protein_file)])
		assert features.shape == (1, box_width, box_width, box_width, 1)


		@@ -28,7 +28,7 @@ def test_salt_bridge_voxelizer():
		voxel_width = 1.0
		voxelizer = dc.feat.SaltBridgeVoxelizer(
		cutoff=cutoff, box_width=box_width, voxel_width=voxel_width)
		features = voxelizer.featurize((ligand_file, protein_file))
		features = voxelizer.featurize([(ligand_file, protein_file)])
		assert features.shape == (1, box_width, box_width, box_width, 1)


		@@ -43,7 +43,7 @@ def test_cation_pi_voxelizer():
		voxel_width = 1.0
		voxelizer = dc.feat.CationPiVoxelizer(
		cutoff=cutoff, box_width=box_width, voxel_width=voxel_width)
		features = voxelizer.featurize((ligand_file, protein_file))
		features = voxelizer.featurize([(ligand_file, protein_file)])
		assert features.shape == (1, box_width, box_width, box_width, 1)


		@@ -58,7 +58,7 @@ def test_pi_stack_voxelizer():
		voxel_width = 1.0
		voxelizer = dc.feat.PiStackVoxelizer(
		cutoff=cutoff, box_width=box_width, voxel_width=voxel_width)
		features = voxelizer.featurize((ligand_file, protein_file))
		features = voxelizer.featurize([(ligand_file, protein_file)])
		assert features.shape == (1, box_width, box_width, box_width, 2)

deepchem/feat/tests/test_rdkit_grid_features.py

+14 −8

Original line number	Diff line number	Diff line
		@@ -471,7 +471,8 @@ class TestRdkitGridFeaturizer(unittest.TestCase):
		# test if default parameters work
		featurizer = rgf.RdkitGridFeaturizer()
		self.assertIsInstance(featurizer, rgf.RdkitGridFeaturizer)
		feature_tensor = featurizer.featurize((self.ligand_file, self.protein_file))
		feature_tensor = featurizer.featurize([(self.ligand_file,
		self.protein_file)])
		self.assertIsInstance(feature_tensor, np.ndarray)

		def test_example_featurizer(self):
		@@ -482,7 +483,8 @@ class TestRdkitGridFeaturizer(unittest.TestCase):
		ecfp_power=9,
		splif_power=9,
		flatten=True)
		feature_tensor = featurizer.featurize((self.ligand_file, self.protein_file))
		feature_tensor = featurizer.featurize([(self.ligand_file,
		self.protein_file)])
		self.assertIsInstance(feature_tensor, np.ndarray)

		def test_force_flatten(self):
		@@ -490,7 +492,8 @@ class TestRdkitGridFeaturizer(unittest.TestCase):
		featurizer = rgf.RdkitGridFeaturizer(
		feature_types=['ecfp_hashed'], flatten=False)
		featurizer.flatten = True # False should be ignored with ecfp_hashed
		feature_tensor = featurizer.featurize((self.ligand_file, self.protein_file))
		feature_tensor = featurizer.featurize([(self.ligand_file,
		self.protein_file)])
		self.assertIsInstance(feature_tensor, np.ndarray)
		self.assertEqual(feature_tensor.shape, (1, 2 * 2**featurizer.ecfp_power))

		@@ -506,7 +509,8 @@ class TestRdkitGridFeaturizer(unittest.TestCase):
		splif_power=splif_power,
		flatten=False,
		sanitize=True)
		feature_tensor = featurizer.featurize((self.ligand_file, self.protein_file))
		feature_tensor = featurizer.featurize([(self.ligand_file,
		self.protein_file)])
		self.assertIsInstance(feature_tensor, np.ndarray)
		voxel_total_len = (
		2**ecfp_power +
		@@ -521,7 +525,8 @@ class TestRdkitGridFeaturizer(unittest.TestCase):
		ecfp_power=ecfp_power,
		splif_power=splif_power,
		sanitize=True)
		feature_tensor = featurizer.featurize((self.ligand_file, self.protein_file))
		feature_tensor = featurizer.featurize([(self.ligand_file,
		self.protein_file)])
		self.assertIsInstance(feature_tensor, np.ndarray)
		flat_total_len = (
		3 * 2**ecfp_power +
		@@ -540,7 +545,8 @@ class TestRdkitGridFeaturizer(unittest.TestCase):

		self.assertTrue('pi_stack' not in featurizer.feature_types)
		self.assertTrue('cation_pi' not in featurizer.feature_types)
		feature_tensor = featurizer.featurize((self.ligand_file, self.protein_file))
		feature_tensor = featurizer.featurize([(self.ligand_file,
		self.protein_file)])
		self.assertIsInstance(feature_tensor, np.ndarray)
		total_len = voxel_total_len + flat_total_len - 3 - 2**ecfp_power
		self.assertEqual(feature_tensor.shape, (1, total_len))
		@@ -567,8 +573,8 @@ class TestRdkitGridFeaturizer(unittest.TestCase):
		feature_types=['voxel_combined'],
		flatten=False,
		sanitize=True)
		feature_tensors = featurizer.featurize((self.ligand_file,
		self.protein_file))
		feature_tensors = featurizer.featurize([(self.ligand_file,
		self.protein_file)])
		self.assertEqual(feature_tensors.shape, (1, 4, 16, 16, 16, 40))

		def test_voxelize(self):

deepchem/feat/tests/test_splif_fingerprints.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -12,7 +12,7 @@ class TestSplifFingerprints(unittest.TestCase):
		self.protein_file = os.path.join(current_dir, 'data',
		'3ws9_protein_fixer_rdkit.pdb')
		self.ligand_file = os.path.join(current_dir, 'data', '3ws9_ligand.sdf')
		self.complex_files = (self.ligand_file, self.protein_file)
		self.complex_files = [(self.ligand_file, self.protein_file)]

		def test_splif_shape(self):
		size = 8

Admin message