add yapf (a49e6ca2) · Commits · 钟慕尧 / deepchem

deepchem/feat/init.py

+0 −5

Original line number	Diff line number	Diff line
		@@ -77,11 +77,6 @@ try:
		from transformers import RobertaTokenizerFast
		from deepchem.feat.roberta_tokenizer import RobertaFeaturizer
		except ModuleNotFoundError:
		# raise ImportError('This class requires transformers.')
		""" raise ImportWarning(
		'This class requires transformers. Please use "pip install transformers" to continue.'
		)
		"""
		pass

		# support classes

deepchem/feat/base_classes.py

+4 −2

Original line number	Diff line number	Diff line
		@@ -455,8 +455,10 @@ class DummyFeaturizer(Featurizer):
		'FCC(c1cccc(Br)n1)N1CCOCC1']], dtype='<U55')
		"""

		def featurize(self, datapoints: Iterable[Any],
		log_every_n: int = 1000, **kwargs) -> np.ndarray:
		def featurize(self,
		datapoints: Iterable[Any],
		log_every_n: int = 1000,
		**kwargs) -> np.ndarray:
		"""Passes through dataset, and returns the datapoint.

		Parameters

deepchem/feat/complex_featurizers/grid_featurizers.py

+10 −5

Original line number	Diff line number	Diff line
		@@ -81,7 +81,8 @@ class ChargeVoxelizer(ComplexFeaturizer):
		self.voxel_width = voxel_width
		self.reduce_to_contacts = reduce_to_contacts

		def _featurize(self, complex: Tuple[str, str], **kwargs) -> Optional[np.ndarray]:
		def _featurize(self, complex: Tuple[str, str],
		**kwargs) -> Optional[np.ndarray]:
		"""
		Compute featurization for a single mol/protein complex

		@@ -167,7 +168,8 @@ class SaltBridgeVoxelizer(ComplexFeaturizer):
		self.voxel_width = voxel_width
		self.reduce_to_contacts = reduce_to_contacts

		def _featurize(self, complex: Tuple[str, str], **kwargs) -> Optional[np.ndarray]:
		def _featurize(self, complex: Tuple[str, str],
		**kwargs) -> Optional[np.ndarray]:
		"""
		Compute featurization for a single mol/protein complex

		@@ -252,7 +254,8 @@ class CationPiVoxelizer(ComplexFeaturizer):
		self.box_width = box_width
		self.voxel_width = voxel_width

		def _featurize(self, complex: Tuple[str, str], **kwargs) -> Optional[np.ndarray]:
		def _featurize(self, complex: Tuple[str, str],
		**kwargs) -> Optional[np.ndarray]:
		"""
		Compute featurization for a single mol/protein complex

		@@ -455,7 +458,8 @@ class HydrogenBondCounter(ComplexFeaturizer):
		self.angle_cutoffs = angle_cutoffs
		self.reduce_to_contacts = reduce_to_contacts

		def _featurize(self, complex: Tuple[str, str], **kwargs) -> Optional[np.ndarray]:
		def _featurize(self, complex: Tuple[str, str],
		**kwargs) -> Optional[np.ndarray]:
		"""
		Compute featurization for a single mol/protein complex

		@@ -560,7 +564,8 @@ class HydrogenBondVoxelizer(ComplexFeaturizer):
		self.voxel_width = voxel_width
		self.reduce_to_contacts = reduce_to_contacts

		def _featurize(self, complex: Tuple[str, str], **kwargs) -> Optional[np.ndarray]:
		def _featurize(self, complex: Tuple[str, str],
		**kwargs) -> Optional[np.ndarray]:
		"""
		Compute featurization for a single mol/protein complex

deepchem/feat/graph_features.py

+2 −1

Original line number	Diff line number	Diff line
		@@ -758,7 +758,8 @@ class ConvMolFeaturizer(MolecularFeaturizer):
		def featurize(
		self,
		molecules: Union[RDKitMol, str, Iterable[RDKitMol], Iterable[str]],
		log_every_n: int = 1000, **kwargs) -> np.ndarray:
		log_every_n: int = 1000,
		**kwargs) -> np.ndarray:
		"""
		Override parent: aim is to add handling atom-depleted molecules featurization

deepchem/feat/material_featurizers/element_property_fingerprint.py

+2 −1

Original line number	Diff line number	Diff line
		@@ -59,7 +59,8 @@ class ElementPropertyFingerprint(MaterialCompositionFeaturizer):
		self.data_source = data_source
		self.ep_featurizer: Any = None

		def _featurize(self, composition: PymatgenComposition, **kwargs) -> np.ndarray:
		def _featurize(self, composition: PymatgenComposition,
		**kwargs) -> np.ndarray:
		"""
		Calculate chemical fingerprint from crystal composition.

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