add **kwargs to subclasses (510b3780) · Commits · 钟慕尧 / deepchem

deepchem/feat/atomic_conformation.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -149,7 +149,7 @@ class AtomicConformationFeaturizer(Featurizer):

		"""

		def _featurize(self, datapoint: str) -> AtomicConformation:
		def _featurize(self, datapoint: str, **kwargs) -> AtomicConformation:
		"""Calculate features for a single datapoint.

		Parameters

deepchem/feat/base_classes.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -286,7 +286,7 @@ class MolecularFeaturizer(Featurizer):
		new_order = rdmolfiles.CanonicalRankAtoms(mol)
		mol = rdmolops.RenumberAtoms(mol, new_order)

		features.append(self._featurize(mol), **kwargs)
		features.append(self._featurize(mol, **kwargs))
		except Exception as e:
		if isinstance(mol, Chem.rdchem.Mol):
		mol = Chem.MolToSmiles(mol)
		@@ -456,7 +456,7 @@ class DummyFeaturizer(Featurizer):
		"""

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

		Parameters

deepchem/feat/complex_featurizers/complex_atomic_coordinates.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -118,7 +118,7 @@ class NeighborListComplexAtomicCoordinates(ComplexFeaturizer):
		# Type of data created by this featurizer
		self.dtype = object

		def _featurize(self, complex: Tuple[str, str]):
		def _featurize(self, complex: Tuple[str, str], **kwargs):
		"""
		Compute neighbor list for complex.

deepchem/feat/complex_featurizers/contact_fingerprints.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -93,7 +93,7 @@ class ContactCircularFingerprint(ComplexFeaturizer):
		self.radius = radius
		self.size = size

		def _featurize(self, complex: Tuple[str, str]):
		def _featurize(self, complex: Tuple[str, str], **kwargs):
		"""
		Compute featurization for a molecular complex

deepchem/feat/complex_featurizers/grid_featurizers.py

+6 −6

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

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

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

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

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

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

		@@ -343,7 +343,7 @@ class PiStackVoxelizer(ComplexFeaturizer):
		self.box_width = box_width
		self.voxel_width = voxel_width

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

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

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

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

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

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