Error Handling in pdbbind grid (03e32f17) · Commits · 钟慕尧 / deepchem

deepchem/utils/rdkit_util.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -63,7 +63,7 @@ def add_hydrogens_to_mol(mol):
		return Chem.MolFromPDBBlock(
		hydrogenated_io.read(), sanitize=False, removeHs=False)
		except ValueError as e:
		logging.warning("Unable to add hydrogens", e)
		logging.warning("Unable to add hydrogens %s", e)
		raise MoleculeLoadException(e)
		finally:
		try:

+7 −10

Original line number	Diff line number	Diff line
		@@ -84,8 +84,8 @@ def featurize_pdbbind(data_dir=None, feat="grid", subset="core"):
		elif feat == "coord":
		neighbor_cutoff = 4
		max_num_neighbors = 10
		featurizer = dc.feat.NeighborListComplexAtomicCoordinates(max_num_neighbors,
		neighbor_cutoff)
		featurizer = dc.feat.NeighborListComplexAtomicCoordinates(
		max_num_neighbors, neighbor_cutoff)
		elif feat == 'atomic_conv':
		dataset = compute_atomic_conv_features(tasks, data_dir, pdbbind_dir, y, ids)
		return dataset, tasks
		@@ -161,19 +161,16 @@ def compute_atomic_conv_features(tasks, data_dir, pdbbind_dir, y, ids):


		def compute_single_pdbbind_feature(x):
		try:
		ind, pdb_code, pdbbind_dir, featurizer = x[0], x[1], x[2], x[3]
		print("Processing complex %d, %s" % (ind, str(pdb_code)))
		pdb_subdir = os.path.join(pdbbind_dir, pdb_code)
		try:
		computed_feature = compute_pdbbind_features(featurizer, pdb_subdir,
		pdb_code)
		except MoleculeLoadException as e:
		logging.warning("Unable to compute features for %s" % x)
		return None
		return ind, computed_feature
		except Exception as e:
		logging.warning("Unable to compute features for %s" % x)
		logging.warning("Unable to compute features for %s" % str(x))
		return None
		return ind, computed_feature


		def compute_pdbbind_features(grid_featurizer, pdb_subdir, pdb_code):