:rotating_light: fix lint error (865c19c9) · Commits · 钟慕尧 / deepchem

deepchem/feat/rdkit_grid_featurizer.py

+11 −9

Original line number	Diff line number	Diff line
		@@ -10,7 +10,6 @@ from scipy.spatial.distance import cdist
		from copy import deepcopy
		from deepchem.feat import ComplexFeaturizer


		logger = logging.getLogger(__name__)


		@@ -1031,7 +1030,8 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
		self.feature_types.append((True, feature_type))
		if self.flatten is False:
		if self.verbose:
		logger.warn('%s feature is used, output will be flattened' % feature_type)
		logger.warn(
		'%s feature is used, output will be flattened' % feature_type)
		self.flatten = True

		elif feature_type in self.VOXEL_FEATURES:
		@@ -1232,7 +1232,8 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
		protein_pdb_file, calc_charges=True, sanitize=self.sanitize)
		############################################################## TIMING
		time2 = time.time()
		logger.info("TIMING: Loading protein coordinates took %0.3f s" % (time2 - time1),
		logger.info(
		"TIMING: Loading protein coordinates took %0.3f s" % (time2 - time1),
		self.verbose)
		############################################################## TIMING
		############################################################## TIMING
		@@ -1242,7 +1243,8 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
		mol_pdb_file, calc_charges=True, sanitize=self.sanitize)
		############################################################## TIMING
		time2 = time.time()
		logger.info("TIMING: Loading ligand coordinates took %0.3f s" % (time2 - time1),
		logger.info(
		"TIMING: Loading ligand coordinates took %0.3f s" % (time2 - time1),
		self.verbose)
		############################################################## TIMING
		except MoleculeLoadException:

deepchem/feat/tests/test_rdkit_descriptors.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -4,7 +4,7 @@ Test basic molecular features.
		import numpy as np
		import unittest

		from deepchem.feat.basic import RDKitDescriptors
		from deepchem.feat.rdkit_descriptors import RDKitDescriptors


		class TestRDKitDescriptors(unittest.TestCase):

deepchem/feat/tests/test_rdkit_grid_features.py

+11 −11

Original line number	Diff line number	Diff line
		@@ -26,8 +26,8 @@ class TestHelperFunctions(unittest.TestCase):
		def setUp(self):
		# TODO test more formats for ligand
		current_dir = os.path.dirname(os.path.realpath(__file__))
		self.protein_file = os.path.join(current_dir,
		'data', '3ws9_protein_fixer_rdkit.pdb')
		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')

		def test_load_molecule(self):
		@@ -319,8 +319,8 @@ class TestFeaturizationFunctions(unittest.TestCase):

		def setUp(self):
		current_dir = os.path.dirname(os.path.realpath(__file__))
		self.protein_file = os.path.join(current_dir,
		'data', '3ws9_protein_fixer_rdkit.pdb')
		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')

		def test_compute_all_ecfp(self):

deepchem/models/tests/test_atomic_conv.py

+1 −2

Original line number	Diff line number	Diff line
		@@ -123,8 +123,7 @@ class TestAtomicConv(unittest.TestCase):
		neighbor_cutoff)
		# arbitrary label
		labels = np.array([0])
		features, _ = complex_featurizer.featurize([ligand_file],
		[protein_file])
		features, _ = complex_featurizer.featurize([ligand_file], [protein_file])
		dataset = deepchem.data.DiskDataset.from_numpy(features, labels)

		batch_size = 1

deepchem/molnet/load_function/pdbbind_datasets.py

+2 −4

Original line number	Diff line number	Diff line
		@@ -308,8 +308,7 @@ def load_pdbbind(reload=True,

		print("\nFeaturizing Complexes for \"%s\" ...\n" % data_folder)
		feat_t1 = time.time()
		features, failures = featurizer.featurize(ligand_files,
		protein_files)
		features, failures = featurizer.featurize(ligand_files, protein_files)
		feat_t2 = time.time()
		print("\nFeaturization finished, took %0.3f s." % (feat_t2 - feat_t1))

		@@ -437,8 +436,7 @@ def load_pdbbind_from_dir(data_folder,
		else:
		raise ValueError("Featurizer not supported")
		print("Featurizing Complexes")
		features, failures = featurizer.featurize(ligand_files,
		protein_files)
		features, failures = featurizer.featurize(ligand_files, protein_files)
		# Delete labels for failing elements
		labels = np.delete(labels, failures)
		dataset = deepchem.data.DiskDataset.from_numpy(features, labels)

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