adding weave loader (87333b6f) · Commits · 钟慕尧 / deepchem

deepchem/molnet/check_availability.py

+18 −0

Original line number	Diff line number	Diff line
		@@ -7,6 +7,7 @@ CheckFeaturizer = {
		('bace_c', 'xgb'): ['ECFP', 1024],
		('bace_c', 'graphconv'): ['GraphConv', 75],
		('bace_c', 'dag'): ['GraphConv', 75],
		('bace_c', 'weave'): ['Weave', 75],
		('bbbp', 'logreg'): ['ECFP', 1024],
		('bbbp', 'tf'): ['ECFP', 1024],
		('bbbp', 'tf_robust'): ['ECFP', 1024],
		@@ -15,6 +16,7 @@ CheckFeaturizer = {
		('bbbp', 'xgb'): ['ECFP', 1024],
		('bbbp', 'graphconv'): ['GraphConv', 75],
		('bbbp', 'dag'): ['GraphConv', 75],
		('bbbp', 'weave'): ['Weave', 75],
		('clintox', 'logreg'): ['ECFP', 1024],
		('clintox', 'tf'): ['ECFP', 1024],
		('clintox', 'tf_robust'): ['ECFP', 1024],
		@@ -23,6 +25,7 @@ CheckFeaturizer = {
		('clintox', 'xgb'): ['ECFP', 1024],
		('clintox', 'graphconv'): ['GraphConv', 75],
		('clintox', 'dag'): ['GraphConv', 75],
		('clintox', 'weave'): ['Weave', 75],
		('hiv', 'logreg'): ['ECFP', 1024],
		('hiv', 'tf'): ['ECFP', 1024],
		('hiv', 'tf_robust'): ['ECFP', 1024],
		@@ -31,6 +34,7 @@ CheckFeaturizer = {
		('hiv', 'xgb'): ['ECFP', 1024],
		('hiv', 'graphconv'): ['GraphConv', 75],
		('hiv', 'dag'): ['GraphConv', 75],
		('hiv', 'weave'): ['Weave', 75],
		('muv', 'logreg'): ['ECFP', 1024],
		('muv', 'tf'): ['ECFP', 1024],
		('muv', 'tf_robust'): ['ECFP', 1024],
		@@ -41,6 +45,7 @@ CheckFeaturizer = {
		('muv', 'siamese'): ['GraphConv', 75],
		('muv', 'attn'): ['GraphConv', 75],
		('muv', 'res'): ['GraphConv', 75],
		('muv', 'weave'): ['Weave', 75],
		('pcba', 'logreg'): ['ECFP', 1024],
		('pcba', 'tf'): ['ECFP', 1024],
		('pcba', 'tf_robust'): ['ECFP', 1024],
		@@ -48,6 +53,7 @@ CheckFeaturizer = {
		('pcba', 'irv'): ['ECFP', 1024],
		('pcba', 'xgb'): ['ECFP', 1024],
		('pcba', 'graphconv'): ['GraphConv', 75],
		('pcba', 'weave'): ['Weave', 75],
		('sider', 'logreg'): ['ECFP', 1024],
		('sider', 'tf'): ['ECFP', 1024],
		('sider', 'tf_robust'): ['ECFP', 1024],
		@@ -56,6 +62,7 @@ CheckFeaturizer = {
		('sider', 'xgb'): ['ECFP', 1024],
		('sider', 'graphconv'): ['GraphConv', 75],
		('sider', 'dag'): ['GraphConv', 75],
		('sider', 'weave'): ['Weave', 75],
		('sider', 'siamese'): ['GraphConv', 75],
		('sider', 'attn'): ['GraphConv', 75],
		('sider', 'res'): ['GraphConv', 75],
		@@ -67,6 +74,7 @@ CheckFeaturizer = {
		('tox21', 'xgb'): ['ECFP', 1024],
		('tox21', 'graphconv'): ['GraphConv', 75],
		('tox21', 'dag'): ['GraphConv', 75],
		('tox21', 'weave'): ['Weave', 75],
		('tox21', 'siamese'): ['GraphConv', 75],
		('tox21', 'attn'): ['GraphConv', 75],
		('tox21', 'res'): ['GraphConv', 75],
		@@ -77,49 +85,59 @@ CheckFeaturizer = {
		('toxcast', 'irv'): ['ECFP', 1024],
		('toxcast', 'xgb'): ['ECFP', 1024],
		('toxcast', 'graphconv'): ['GraphConv', 75],
		('toxcast', 'weave'): ['Weave', 75],
		('bace_r', 'tf_regression'): ['ECFP', 1024],
		('bace_r', 'rf_regression'): ['ECFP', 1024],
		('bace_r', 'xgb_regression'): ['ECFP', 1024],
		('bace_r', 'graphconvreg'): ['GraphConv', 75],
		('bace_r', 'dag_regression'): ['GraphConv', 75],
		('bace_r', 'weave_regression'): ['Weave', 75],
		('chembl', 'tf_regression'): ['ECFP', 1024],
		('chembl', 'rf_regression'): ['ECFP', 1024],
		('chembl', 'xgb_regression'): ['ECFP', 1024],
		('chembl', 'graphconvreg'): ['GraphConv', 75],
		('chembl', 'weave_regression'): ['Weave', 75],
		('clearance', 'tf_regression'): ['ECFP', 1024],
		('clearance', 'rf_regression'): ['ECFP', 1024],
		('clearance', 'xgb_regression'): ['ECFP', 1024],
		('clearance', 'graphconvreg'): ['GraphConv', 75],
		('clearance', 'dag_regression'): ['GraphConv', 75],
		('clearance', 'weave_regression'): ['Weave', 75],
		('delaney', 'tf_regression'): ['ECFP', 1024],
		('delaney', 'rf_regression'): ['ECFP', 1024],
		('delaney', 'xgb_regression'): ['ECFP', 1024],
		('delaney', 'graphconvreg'): ['GraphConv', 75],
		('delaney', 'dag_regression'): ['GraphConv', 75],
		('delaney', 'weave_regression'): ['Weave', 75],
		('hopv', 'tf_regression'): ['ECFP', 1024],
		('hopv', 'rf_regression'): ['ECFP', 1024],
		('hopv', 'xgb_regression'): ['ECFP', 1024],
		('hopv', 'graphconvreg'): ['GraphConv', 75],
		('hopv', 'dag_regression'): ['GraphConv', 75],
		('hopv', 'weave_regression'): ['Weave', 75],
		('lipo', 'tf_regression'): ['ECFP', 1024],
		('lipo', 'rf_regression'): ['ECFP', 1024],
		('lipo', 'xgb_regression'): ['ECFP', 1024],
		('lipo', 'graphconvreg'): ['GraphConv', 75],
		('lipo', 'dag_regression'): ['GraphConv', 75],
		('lipo', 'weave_regression'): ['Weave', 75],
		('nci', 'tf_regression'): ['ECFP', 1024],
		('nci', 'rf_regression'): ['ECFP', 1024],
		('nci', 'xgb_regression'): ['ECFP', 1024],
		('nci', 'graphconvreg'): ['GraphConv', 75],
		('nci', 'weave_regression'): ['Weave', 75],
		('ppb', 'tf_regression'): ['ECFP', 1024],
		('ppb', 'rf_regression'): ['ECFP', 1024],
		('ppb', 'xgb_regression'): ['ECFP', 1024],
		('ppb', 'graphconvreg'): ['GraphConv', 75],
		('ppb', 'dag_regression'): ['GraphConv', 75],
		('ppb', 'weave_regression'): ['Weave', 75],
		('sampl', 'tf_regression'): ['ECFP', 1024],
		('sampl', 'rf_regression'): ['ECFP', 1024],
		('sampl', 'xgb_regression'): ['ECFP', 1024],
		('sampl', 'graphconvreg'): ['GraphConv', 75],
		('sampl', 'dag_regression'): ['GraphConv', 75],
		('sampl', 'weave_regression'): ['Weave', 75],
		('kaggle', 'tf_regression'): [None, 14293],
		('kaggle', 'rf_regression'): [None, 14293],
		('pdbbind', 'tf_regression'): ['grid', 2052],

deepchem/molnet/load_function/bace_datasets.py

+4 −0

Original line number	Diff line number	Diff line
		@@ -40,6 +40,8 @@ def load_bace_regression(featurizer=None, split='random', reload=True):
		featurizer = deepchem.feat.CircularFingerprint(size=1024)
		elif featurizer == 'GraphConv':
		featurizer = deepchem.feat.ConvMolFeaturizer()
		elif featurizer == 'Weave':
		featurizer = deepchem.feat.WeaveFeaturizer()
		elif featurizer == 'Raw':
		featurizer = deepchem.feat.RawFeaturizer()
		elif featurizer == None:
		@@ -104,6 +106,8 @@ def load_bace_classification(featurizer=None, split='random', reload=True):
		featurizer = deepchem.feat.CircularFingerprint(size=1024)
		elif featurizer == 'GraphConv':
		featurizer = deepchem.feat.ConvMolFeaturizer()
		elif featurizer == 'Weave':
		featurizer = deepchem.feat.WeaveFeaturizer()
		elif featurizer == 'Raw':
		featurizer = deepchem.feat.RawFeaturizer()
		elif featurizer == None:

deepchem/molnet/load_function/bbbp_datasets.py

+2 −0

Original line number	Diff line number	Diff line
		@@ -39,6 +39,8 @@ def load_bbbp(featurizer='ECFP', split='index', reload=True):
		featurizer = deepchem.feat.CircularFingerprint(size=1024)
		elif featurizer == 'GraphConv':
		featurizer = deepchem.feat.ConvMolFeaturizer()
		elif featurizer == 'Weave':
		featurizer = deepchem.feat.WeaveFeaturizer()
		elif featurizer == 'Raw':
		featurizer = deepchem.feat.RawFeaturizer()

deepchem/molnet/load_function/chembl_datasets.py

+2 −0

Original line number	Diff line number	Diff line
		@@ -79,6 +79,8 @@ def load_chembl(shard_size=2000,
		featurizer = deepchem.feat.CircularFingerprint(size=1024)
		elif featurizer == 'GraphConv':
		featurizer = deepchem.feat.ConvMolFeaturizer()
		elif featurizer == 'Weave':
		featurizer = deepchem.feat.WeaveFeaturizer()
		elif featurizer == 'Raw':
		featurizer = deepchem.feat.RawFeaturizer()

deepchem/molnet/load_function/clearance_datasets.py

+2 −0

Original line number	Diff line number	Diff line
		@@ -40,6 +40,8 @@ def load_clearance(featurizer='ECFP', split='random', reload=True):
		featurizer = deepchem.feat.CircularFingerprint(size=1024)
		elif featurizer == 'GraphConv':
		featurizer = deepchem.feat.ConvMolFeaturizer()
		elif featurizer == 'Weave':
		featurizer = deepchem.feat.WeaveFeaturizer()
		elif featurizer == 'Raw':
		featurizer = deepchem.feat.RawFeaturizer()

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