yapf (b09ee6ad) · Commits · 钟慕尧 / deepchem

deepchem/models/tensorgraph/tests/test_atomic_conv.py

+9 −7

Original line number	Diff line number	Diff line
		@@ -106,8 +106,10 @@ class TestAtomicConv(unittest.TestCase):
		def test_atomic_conv_with_feat(self):
		"""A simple test for running an atomic convolution on featurized data."""
		dir_path = os.path.dirname(os.path.realpath(__file__))
		ligand_file = os.path.join(dir_path, "../../../feat/tests/data/3zso_ligand_hyd.pdb")
		protein_file = os.path.join(dir_path, "../../../feat/tests/data/3zso_protein.pdb")
		ligand_file = os.path.join(dir_path,
		"../../../feat/tests/data/3zso_ligand_hyd.pdb")
		protein_file = os.path.join(dir_path,
		"../../../feat/tests/data/3zso_protein.pdb")
		# Pulled from PDB files. For larger datasets with more PDBs, would use
		# max num atoms instead of exact.
		frag1_num_atoms = 44 # for ligand atoms
		@@ -121,8 +123,8 @@ class TestAtomicConv(unittest.TestCase):
		neighbor_cutoff)
		# arbitrary label
		labels = np.array([0])
		features, _ = complex_featurizer.featurize_complexes(
		[ligand_file], [protein_file])
		features, _ = complex_featurizer.featurize_complexes([ligand_file],
		[protein_file])
		dataset = deepchem.data.DiskDataset.from_numpy(features, labels)

		batch_size = 1

+4 −1

Original line number	Diff line number	Diff line
		@@ -211,7 +211,10 @@ def load_pdbbind(featurizer="grid", split="random", subset="core", reload=True):
		if featurizer == "grid":
		featurizer = rgf.RdkitGridFeaturizer(
		voxel_width=2.0,
		feature_types=['ecfp', 'splif', 'hbond', 'salt_bridge', 'pi_stack', 'cation_pi', 'charge'],
		feature_types=[
		'ecfp', 'splif', 'hbond', 'salt_bridge', 'pi_stack', 'cation_pi',
		'charge'
		],
		flatten=True)
		elif featurizer == "atomic":
		# Pulled from PDB files. For larger datasets with more PDBs, would use