Loading .travis.yml +1 −0 Original line number Diff line number Diff line language: python python: - '2.7' - '3.5' sudo: required dist: trusty install: Loading deepchem/datasets/__init__.py +4 −4 Original line number Diff line number Diff line Loading @@ -257,7 +257,7 @@ class Dataset(object): """ if not len(self.metadata_df): raise ValueError("No data in dataset.") return self.metadata_df.iterrows().next()[1]['task_names'] return next(self.metadata_df.iterrows())[1]['task_names'] def get_data_shape(self): """ Loading @@ -268,7 +268,7 @@ class Dataset(object): sample_X = load_from_disk( os.path.join( self.data_dir, self.metadata_df.iterrows().next()[1]['X-transformed']))[0] next(self.metadata_df.iterrows())[1]['X-transformed']))[0] return np.shape(sample_X) def get_shard_size(self): Loading @@ -278,7 +278,7 @@ class Dataset(object): sample_y = load_from_disk( os.path.join( self.data_dir, self.metadata_df.iterrows().next()[1]['y-transformed'])) next(self.metadata_df.iterrows())[1]['y-transformed'])) return len(sample_y) def _get_metadata_filename(self): Loading Loading @@ -891,7 +891,7 @@ class Dataset(object): energy = y[:,0] grad = y[:,1:] for i in xrange(energy.size): for i in range(energy.size): grad[i] *= energy[i] ydely_means = np.sum(grad, axis=0)/y_n[1:] Loading deepchem/datasets/pdbbind_datasets.py +1 −1 Original line number Diff line number Diff line Loading @@ -39,7 +39,7 @@ def compute_pdbbind_grid_feature(compound_featurizers, complex_featurizers, """Compute features for a given complex""" protein_file = os.path.join(pdb_subdir, "%s_protein.pdb" % pdb_code) ligand_file = os.path.join(pdb_subdir, "%s_ligand.sdf" % pdb_code) rdkit_mol = Chem.SDMolSupplier(str(ligand_file)).next() rdkit_mol = next(Chem.SDMolSupplier(str(ligand_file))) all_features = [] for complex_featurizer in complex_featurizers: Loading deepchem/datasets/tests/test_load.py +1 −1 Original line number Diff line number Diff line Loading @@ -47,7 +47,7 @@ class TestLoad(TestAPI): shutil.move(data_dir, moved_data_dir) moved_dataset = Dataset( moved_data_dir, reload=reload) moved_data_dir, reload=True) X_moved, y_moved, w_moved, ids_moved = moved_dataset.to_numpy() Loading deepchem/featurizers/__init__.py +3 −3 Original line number Diff line number Diff line Loading @@ -212,8 +212,8 @@ class Featurizer(object): # - second axis = max # conformers # - remaining axes = determined by feature shape features_shape = None for i in xrange(len(features)): for j in xrange(len(features[i])): for i in range(len(features)): for j in range(len(features[i])): if features[i][j] is not None: features_shape = features[i][0].shape break Loading @@ -230,7 +230,7 @@ class Featurizer(object): try: x[i, :n_confs] = mol_features except ValueError: # handle None conformer values for j in xrange(n_confs): for j in range(n_confs): x[i, j] = mol_features[j] return x Loading Loading
.travis.yml +1 −0 Original line number Diff line number Diff line language: python python: - '2.7' - '3.5' sudo: required dist: trusty install: Loading
deepchem/datasets/__init__.py +4 −4 Original line number Diff line number Diff line Loading @@ -257,7 +257,7 @@ class Dataset(object): """ if not len(self.metadata_df): raise ValueError("No data in dataset.") return self.metadata_df.iterrows().next()[1]['task_names'] return next(self.metadata_df.iterrows())[1]['task_names'] def get_data_shape(self): """ Loading @@ -268,7 +268,7 @@ class Dataset(object): sample_X = load_from_disk( os.path.join( self.data_dir, self.metadata_df.iterrows().next()[1]['X-transformed']))[0] next(self.metadata_df.iterrows())[1]['X-transformed']))[0] return np.shape(sample_X) def get_shard_size(self): Loading @@ -278,7 +278,7 @@ class Dataset(object): sample_y = load_from_disk( os.path.join( self.data_dir, self.metadata_df.iterrows().next()[1]['y-transformed'])) next(self.metadata_df.iterrows())[1]['y-transformed'])) return len(sample_y) def _get_metadata_filename(self): Loading Loading @@ -891,7 +891,7 @@ class Dataset(object): energy = y[:,0] grad = y[:,1:] for i in xrange(energy.size): for i in range(energy.size): grad[i] *= energy[i] ydely_means = np.sum(grad, axis=0)/y_n[1:] Loading
deepchem/datasets/pdbbind_datasets.py +1 −1 Original line number Diff line number Diff line Loading @@ -39,7 +39,7 @@ def compute_pdbbind_grid_feature(compound_featurizers, complex_featurizers, """Compute features for a given complex""" protein_file = os.path.join(pdb_subdir, "%s_protein.pdb" % pdb_code) ligand_file = os.path.join(pdb_subdir, "%s_ligand.sdf" % pdb_code) rdkit_mol = Chem.SDMolSupplier(str(ligand_file)).next() rdkit_mol = next(Chem.SDMolSupplier(str(ligand_file))) all_features = [] for complex_featurizer in complex_featurizers: Loading
deepchem/datasets/tests/test_load.py +1 −1 Original line number Diff line number Diff line Loading @@ -47,7 +47,7 @@ class TestLoad(TestAPI): shutil.move(data_dir, moved_data_dir) moved_dataset = Dataset( moved_data_dir, reload=reload) moved_data_dir, reload=True) X_moved, y_moved, w_moved, ids_moved = moved_dataset.to_numpy() Loading
deepchem/featurizers/__init__.py +3 −3 Original line number Diff line number Diff line Loading @@ -212,8 +212,8 @@ class Featurizer(object): # - second axis = max # conformers # - remaining axes = determined by feature shape features_shape = None for i in xrange(len(features)): for j in xrange(len(features[i])): for i in range(len(features)): for j in range(len(features[i])): if features[i][j] is not None: features_shape = features[i][0].shape break Loading @@ -230,7 +230,7 @@ class Featurizer(object): try: x[i, :n_confs] = mol_features except ValueError: # handle None conformer values for j in xrange(n_confs): for j in range(n_confs): x[i, j] = mol_features[j] return x Loading
