mpass complexes as datapoints (06744bcc) · Commits · 钟慕尧 / deepchem

deepchem/feat/init.py

+2 −1

Original line number	Diff line number	Diff line
		@@ -34,7 +34,6 @@ from deepchem.feat.molecule_featurizers import RawFeaturizer
		from deepchem.feat.molecule_featurizers import RDKitDescriptors
		from deepchem.feat.molecule_featurizers import SmilesToImage
		from deepchem.feat.molecule_featurizers import SmilesToSeq, create_char_to_idx
		from deepchem.feat.molecule_featurizers import RobertaFeaturizer
		from deepchem.feat.molecule_featurizers import MATFeaturizer

		# complex featurizers
		@@ -74,5 +73,7 @@ try:
		except ModuleNotFoundError:
		pass

		from deepchem.feat.roberta_tokenizer import RobertaFeaturizer

		# support classes
		from deepchem.feat.molecule_featurizers import GraphMatrix

+8 −5

Original line number	Diff line number	Diff line
		@@ -156,14 +156,14 @@ class ComplexFeaturizer(Featurizer):
		"""

		def featurize(self,
		complexes: Iterable[Tuple[str, str]],
		datapoints: Iterable[Tuple[str, str]] = None,
		log_every_n: int = 100, **kwargs) -> np.ndarray:
		"""
		Calculate features for mol/protein complexes.

		Parameters
		----------
		complexes: Iterable[Tuple[str, str]]
		datapoints: Iterable[Tuple[str, str]]
		List of filenames (PDB, SDF, etc.) for ligand molecules and proteins.
		Each element should be a tuple of the form (ligand_filename,
		protein_filename).
		@@ -174,10 +174,13 @@ class ComplexFeaturizer(Featurizer):
		Array of features
		"""

		if not isinstance(complexes, Iterable):
		complexes = [cast(Tuple[str, str], complexes)]
		if 'complexes' in kwargs:
		datapoints = kwargs.get("complexes")
		raise DeprecationWarning('Complexes is being phased out as a parameter, please pass "datapoints" instead.')
		if not isinstance(datapoints, Iterable):
		datapoints = [cast(Tuple[str, str], datapoints)]
		features, failures, successes = [], [], []
		for idx, point in enumerate(complexes):
		for idx, point in enumerate(datapoints):
		if idx % log_every_n == 0:
		logger.info("Featurizing datapoint %i" % idx)
		try: