:bug: warn -> warning (2ddfd44e) · Commits · 钟慕尧 / deepchem

deepchem/feat/rdkit_grid_featurizer.py

+14 −14

Original line number	Diff line number	Diff line
		@@ -685,7 +685,7 @@ def get_partial_charge(atom):


		def get_formal_charge(atom):
		logger.warn(
		logger.warning(
		'get_formal_charge function is deprecated and will be removed'
		' in version 1.4, use get_partial_charge instead', DeprecationWarning)
		return get_partial_charge(atom)
		@@ -818,7 +818,7 @@ def convert_atom_to_voxel(molecule_xyz,
		(molecule_xyz[atom_index] + box_width / 2.0) / voxel_width).astype(int)
		if ((indices < 0) \| (indices >= box_width / voxel_width)).any():
		if verbose:
		logger.warn('Coordinates are outside of the box (atom id = %s,'
		logger.warning('Coordinates are outside of the box (atom id = %s,'
		' coords xyz = %s, coords in box = %s' %
		(atom_index, molecule_xyz[atom_index], indices))

		@@ -946,7 +946,7 @@ class RdkitGridFeaturizer(ComplexFeaturizer):

		for arg in deprecated_args:
		if arg in kwargs and verbose:
		logger.warn(
		logger.warning(
		'%s argument was removed and it is ignored,'
		' using it will result in error in version 1.4' % arg,
		DeprecationWarning)
		@@ -1017,20 +1017,20 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
		for feature_type in feature_types:
		if self.sanitize is False and feature_type in require_sanitized:
		if self.verbose:
		logger.warn('sanitize is set to False, %s feature will be ignored' %
		feature_type)
		logger.warning('sanitize is set to False, %s feature will be ignored'
		% feature_type)
		continue
		if feature_type in not_implemented:
		if self.verbose:
		logger.warn('%s feature is not implemented yet and will be ignored' %
		feature_type)
		logger.warning('%s feature is not implemented yet and will be ignored'
		% feature_type)
		continue

		if feature_type in self.FLAT_FEATURES:
		self.feature_types.append((True, feature_type))
		if self.flatten is False:
		if self.verbose:
		logger.warn(
		logger.warning(
		'%s feature is used, output will be flattened' % feature_type)
		self.flatten = True

		@@ -1043,7 +1043,7 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
		if ftype not in ignored_features]
		if self.flatten is False:
		if self.verbose:
		logger.warn('Flat features are used, output will be flattened')
		logger.warning('Flat features are used, output will be flattened')
		self.flatten = True

		elif feature_type == 'voxel_combined':
		@@ -1059,10 +1059,10 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
		if ftype not in ignored_features]
		if self.flatten is False:
		if self.verbose:
		logger.warn('Flat feature are used, output will be flattened')
		logger.warning('Flat feature are used, output will be flattened')
		self.flatten = True
		elif self.verbose:
		logger.warn('Ignoring unknown feature %s' % feature_type)
		logger.warning('Ignoring unknown feature %s' % feature_type)

		def _compute_feature(self, feature_name, prot_xyz, prot_rdk, lig_xyz, lig_rdk,
		distances):
		@@ -1248,7 +1248,7 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
		self.verbose)
		############################################################## TIMING
		except MoleculeLoadException:
		logger.warn("Some molecules cannot be loaded by Rdkit. Skipping")
		logger.warning("Some molecules cannot be loaded by Rdkit. Skipping")
		return None

		############################################################## TIMING

deepchem/utils/rdkit_util.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -289,7 +289,7 @@ def load_molecule(molecule_file,
		Chem.SanitizeMol(my_mol)
		# Ideally we should catch AtomValenceException but Travis seems to choke on it for some reason.
		except:
		logger.warn("Mol %s failed sanitization" % Chem.MolToSmiles(my_mol))
		logger.warning("Mol %s failed sanitization" % Chem.MolToSmiles(my_mol))
		if calc_charges:
		# This updates in place
		compute_charges(my_mol)

Admin message