SmilesToImage featurizer for datasets (3199dd61) · Commits · 钟慕尧 / deepchem

deepchem/molnet/load_function/hiv_datasets.py

+5 −1

Original line number	Diff line number	Diff line
		@@ -11,7 +11,7 @@ import deepchem
		logger = logging.getLogger(__name__)


		def load_hiv(featurizer='ECFP', split='index', reload=True):
		def load_hiv(featurizer='ECFP', split='index', reload=True, **kwargs):
		"""Load hiv datasets. Does not do train/test split"""
		# Featurize hiv dataset
		logger.info("About to featurize hiv dataset.")
		@@ -41,6 +41,10 @@ def load_hiv(featurizer='ECFP', split='index', reload=True):
		featurizer = deepchem.feat.WeaveFeaturizer()
		elif featurizer == 'Raw':
		featurizer = deepchem.feat.RawFeaturizer()
		elif featurizer == "smiles2img":
		img_spec = kwargs.get("img_spec", "std")
		logger.info(img_spec)
		featurizer = deepchem.feat.SmilesToImage(img_spec=img_spec)

		loader = deepchem.data.CSVLoader(
		tasks=hiv_tasks, smiles_field="smiles", featurizer=featurizer)

+5 −1

Original line number	Diff line number	Diff line
		@@ -11,7 +11,7 @@ import deepchem
		logger = logging.getLogger(__name__)


		def load_sampl(featurizer='ECFP', split='index', reload=True, move_mean=True):
		def load_sampl(featurizer='ECFP', split='index', reload=True, move_mean=True, **kwargs):
		"""Load SAMPL datasets."""
		# Featurize SAMPL dataset
		logger.info("About to featurize SAMPL dataset.")
		@@ -46,6 +46,10 @@ def load_sampl(featurizer='ECFP', split='index', reload=True, move_mean=True):
		featurizer = deepchem.feat.WeaveFeaturizer()
		elif featurizer == 'Raw':
		featurizer = deepchem.feat.RawFeaturizer()
		elif featurizer == 'smiles2img':
		img_spec = kwargs.get("img_spec", "std")
		logger.info(img_spec)
		featurizer = deepchem.feat.SmilesToImage(img_spec=img_spec)

		loader = deepchem.data.CSVLoader(
		tasks=SAMPL_tasks, smiles_field="smiles", featurizer=featurizer)

+5 −1

Original line number	Diff line number	Diff line
		@@ -11,7 +11,7 @@ import deepchem
		logger = logging.getLogger(__name__)


		def load_tox21(featurizer='ECFP', split='index', reload=True, K=4):
		def load_tox21(featurizer='ECFP', split='index', reload=True, K=4, **kwargs):
		"""Load Tox21 datasets. Does not do train/test split"""
		# Featurize Tox21 dataset

		@@ -45,6 +45,10 @@ def load_tox21(featurizer='ECFP', split='index', reload=True, K=4):
		elif featurizer == 'AdjacencyConv':
		featurizer = deepchem.feat.AdjacencyFingerprint(
		max_n_atoms=150, max_valence=6)
		elif featurizer == "smiles2img":
		img_spec = kwargs.get("img_spec", "std")
		logger.info(img_spec)
		featurizer = deepchem.feat.SmilesToImage(img_spec=img_spec)

		loader = deepchem.data.CSVLoader(
		tasks=tox21_tasks, smiles_field="smiles", featurizer=featurizer)