add move_mean argument (c5e8cc45) · Commits · 钟慕尧 / deepchem

deepchem/molnet/load_function/bace_datasets.py

+5 −2

Original line number	Diff line number	Diff line
		@@ -12,7 +12,10 @@ from deepchem.molnet.load_function.bace_features import bace_user_specified_feat
		logger = logging.getLogger(__name__)


		def load_bace_regression(featurizer='ECFP', split='random', reload=True):
		def load_bace_regression(featurizer='ECFP',
		split='random',
		reload=True,
		move_mean=True):
		"""Load bace datasets."""
		# Featurize bace dataset
		logger.info("About to featurize bace dataset.")
		@@ -53,7 +56,7 @@ def load_bace_regression(featurizer='ECFP', split='random', reload=True):
		# Initialize transformers
		transformers = [
		deepchem.trans.NormalizationTransformer(
		transform_y=True, dataset=dataset)
		transform_y=True, dataset=dataset, move_mean=move_mean)
		]

		logger.info("About to transform data")

deepchem/molnet/load_function/delaney_datasets.py

+2 −2

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


		def load_delaney(featurizer='ECFP', split='index', reload=True):
		def load_delaney(featurizer='ECFP', split='index', reload=True, move_mean=True):
		"""Load delaney datasets."""
		# Featurize Delaney dataset
		logger.info("About to featurize Delaney dataset.")
		@@ -50,7 +50,7 @@ def load_delaney(featurizer='ECFP', split='index', reload=True):
		# Initialize transformers
		transformers = [
		deepchem.trans.NormalizationTransformer(
		transform_y=True, dataset=dataset)
		transform_y=True, dataset=dataset, move_mean=move_mean)
		]

		logger.info("About to transform data")

deepchem/molnet/load_function/lipo_datasets.py

+2 −2

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


		def load_lipo(featurizer='ECFP', split='index', reload=True):
		def load_lipo(featurizer='ECFP', split='index', reload=True, move_mean=True):
		"""Load Lipophilicity datasets."""
		# Featurize Lipophilicity dataset
		logger.info("About to featurize Lipophilicity dataset.")
		@@ -50,7 +50,7 @@ def load_lipo(featurizer='ECFP', split='index', reload=True):
		# Initialize transformers
		transformers = [
		deepchem.trans.NormalizationTransformer(
		transform_y=True, dataset=dataset)
		transform_y=True, dataset=dataset, move_mean=move_mean)
		]

		logger.info("About to transform data")

deepchem/molnet/load_function/qm7_datasets.py

+11 −6

Original line number	Diff line number	Diff line
		@@ -12,7 +12,8 @@ import scipy.io

		def load_qm7_from_mat(featurizer='CoulombMatrix',
		split='stratified',
		reload=True):
		reload=True,
		move_mean=True):
		data_dir = deepchem.utils.get_data_dir()
		if reload:
		save_dir = os.path.join(data_dir, "qm7/" + featurizer + "/" + str(split))
		@@ -83,7 +84,7 @@ def load_qm7_from_mat(featurizer='CoulombMatrix',

		transformers = [
		deepchem.trans.NormalizationTransformer(
		transform_y=True, dataset=train_dataset)
		transform_y=True, dataset=train_dataset, move_mean=move_mean)
		]

		for transformer in transformers:
		@@ -99,7 +100,8 @@ def load_qm7_from_mat(featurizer='CoulombMatrix',

		def load_qm7b_from_mat(featurizer='CoulombMatrix',
		split='stratified',
		reload=True):
		reload=True,
		move_mean=True):
		data_dir = deepchem.utils.get_data_dir()
		dataset_file = os.path.join(data_dir, "qm7b.mat")

		@@ -129,7 +131,7 @@ def load_qm7b_from_mat(featurizer='CoulombMatrix',

		transformers = [
		deepchem.trans.NormalizationTransformer(
		transform_y=True, dataset=train_dataset)
		transform_y=True, dataset=train_dataset, move_mean=move_mean)
		]

		for transformer in transformers:
		@@ -141,7 +143,10 @@ def load_qm7b_from_mat(featurizer='CoulombMatrix',
		return qm7_tasks, (train_dataset, valid_dataset, test_dataset), transformers


		def load_qm7(featurizer='CoulombMatrix', split='random', reload=True):
		def load_qm7(featurizer='CoulombMatrix',
		split='random',
		reload=True,
		move_mean=True):
		"""Load qm7 datasets."""
		# Featurize qm7 dataset
		print("About to featurize qm7 dataset.")
		@@ -178,7 +183,7 @@ def load_qm7(featurizer='CoulombMatrix', split='random', reload=True):

		transformers = [
		deepchem.trans.NormalizationTransformer(
		transform_y=True, dataset=train_dataset)
		transform_y=True, dataset=train_dataset, move_mean=move_mean)
		]

		for transformer in transformers:

deepchem/molnet/load_function/qm8_datasets.py

+5 −2

Original line number	Diff line number	Diff line
		@@ -8,7 +8,10 @@ import os
		import deepchem


		def load_qm8(featurizer='CoulombMatrix', split='random', reload=True):
		def load_qm8(featurizer='CoulombMatrix',
		split='random',
		reload=True,
		move_mean=True):
		data_dir = deepchem.utils.get_data_dir()
		if reload:
		save_dir = os.path.join(data_dir, "qm8/" + featurizer + "/" + str(split))
		@@ -80,7 +83,7 @@ def load_qm8(featurizer='CoulombMatrix', split='random', reload=True):
		dataset)
		transformers = [
		deepchem.trans.NormalizationTransformer(
		transform_y=True, dataset=train_dataset)
		transform_y=True, dataset=train_dataset, move_mean=move_mean)
		]
		for transformer in transformers:
		train_dataset = transformer.transform(train_dataset)

Admin message