Merge branch 'walid/pass_featurizer_kwargs' into walid/roberta-tokenizer (1244af3a) · Commits · 钟慕尧 / deepchem

deepchem/feat/base_classes.py

+14 −10

Original line number	Diff line number	Diff line
		@@ -161,7 +161,8 @@ class ComplexFeaturizer(Featurizer):

		def featurize(self,
		complexes: Iterable[Tuple[str, str]],
		log_every_n: int = 100) -> np.ndarray:
		log_every_n: int = 100,
		**kwargs) -> np.ndarray:
		"""
		Calculate features for mol/protein complexes.

		@@ -185,7 +186,7 @@ class ComplexFeaturizer(Featurizer):
		if idx % log_every_n == 0:
		logger.info("Featurizing datapoint %i" % idx)
		try:
		features.append(self._featurize(point))
		features.append(self._featurize(point, **kwargs))
		successes.append(idx)
		except:
		logger.warning(
		@@ -208,7 +209,7 @@ class ComplexFeaturizer(Featurizer):

		return np.asarray(features)

		def _featurize(self, complex: Tuple[str, str]):
		def _featurize(self, complex: Tuple[str, str], **kwargs):
		"""
		Calculate features for single mol/protein complex.

		@@ -238,7 +239,7 @@ class MolecularFeaturizer(Featurizer):
		The subclasses of this class require RDKit to be installed.
		"""

		def featurize(self, molecules, log_every_n=1000) -> np.ndarray:
		def featurize(self, molecules, log_every_n=1000, **kwargs) -> np.ndarray:
		"""Calculate features for molecules.

		Parameters
		@@ -282,7 +283,7 @@ class MolecularFeaturizer(Featurizer):
		new_order = rdmolfiles.CanonicalRankAtoms(mol)
		mol = rdmolops.RenumberAtoms(mol, new_order)

		features.append(self._featurize(mol))
		features.append(self._featurize(mol, **kwargs))
		except Exception as e:
		if isinstance(mol, Chem.rdchem.Mol):
		mol = Chem.MolToSmiles(mol)
		@@ -320,7 +321,8 @@ class MaterialStructureFeaturizer(Featurizer):

		def featurize(self,
		structures: Iterable[Union[Dict[str, Any], PymatgenStructure]],
		log_every_n: int = 1000) -> np.ndarray:
		log_every_n: int = 1000,
		**kwargs) -> np.ndarray:
		"""Calculate features for crystal structures.

		Parameters
		@@ -351,7 +353,7 @@ class MaterialStructureFeaturizer(Featurizer):
		try:
		if isinstance(structure, Dict):
		structure = Structure.from_dict(structure)
		features.append(self._featurize(structure))
		features.append(self._featurize(structure, **kwargs))
		except:
		logger.warning(
		"Failed to featurize datapoint %i. Appending empty array" % idx)
		@@ -383,8 +385,10 @@ class MaterialCompositionFeaturizer(Featurizer):
		installed.
		"""

		def featurize(self, compositions: Iterable[str],
		log_every_n: int = 1000) -> np.ndarray:
		def featurize(self,
		compositions: Iterable[str],
		log_every_n: int = 1000,
		**kwargs) -> np.ndarray:
		"""Calculate features for crystal compositions.

		Parameters
		@@ -412,7 +416,7 @@ class MaterialCompositionFeaturizer(Featurizer):
		logger.info("Featurizing datapoint %i" % idx)
		try:
		c = Composition(composition)
		features.append(self._featurize(c))
		features.append(self._featurize(c, **kwargs))
		except:
		logger.warning(
		"Failed to featurize datapoint %i. Appending empty array" % idx)

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