:bug: fix build (63fdcc7b) · Commits · 钟慕尧 / deepchem

deepchem/molnet/init.py

+0 −4

Original line number	Diff line number	Diff line
		@@ -43,7 +43,3 @@ from deepchem.molnet.dnasim import simulate_motif_counting
		from deepchem.molnet.dnasim import simple_motif_embedding
		from deepchem.molnet.dnasim import motif_density
		from deepchem.molnet.dnasim import simulate_single_motif_detection

		from deepchem.molnet.run_benchmark import run_benchmark
		#from deepchem.molnet.run_benchmark_low_data import run_benchmark_low_data
		from deepchem.molnet import run_benchmark_models

+8 −24

Original line number	Diff line number	Diff line
		@@ -47,31 +47,15 @@ class TransformerGenerator(object):


		featurizers = {
		'graphconv': dc.feat.ConvMolFeaturizer(),
		'weave': dc.feat.WeaveFeaturizer(),
		'coulombmatrix': lambda: dc.feat.CoulombMatrix(29),
		'ecfp': lambda: dc.feat.CircularFingerprint(size=1024),
		'graphconv': lambda: dc.feat.ConvMolFeaturizer(),
		'raw': lambda: dc.feat.RawFeaturizer(),
		'onehot': lambda: dc.feat.OneHotFeaturizer(),
		'smiles2img': lambda: dc.feat.SmilesToImage(img_size=80, img_spec='std'),
		'weave': lambda: dc.feat.WeaveFeaturizer(),
		}

		# some featurizers require soft dependencies to instantiate
		try:
		featurizers['ecfp'] = dc.feat.CircularFingerprint(size=1024)
		except ImportError:
		pass

		try:
		featurizers['raw'] = dc.feat.RawFeaturizer()
		except ImportError:
		pass

		try:
		featurizers['smiles2img'] = dc.feat.SmilesToImage(img_size=80, img_spec='std')
		except ImportError:
		pass

		try:
		featurizers['onehot'] = dc.feat.OneHotFeaturizer()
		except ImportError:
		pass

		splitters = {
		'index': dc.splits.IndexSplitter(),
		'random': dc.splits.RandomSplitter(),
		@@ -132,7 +116,7 @@ class _MolnetLoader(object):
		splitter = kwargs['split']
		logger.warning("'split' is deprecated. Use 'splitter' instead.")
		if isinstance(featurizer, str):
		featurizer = featurizers[featurizer.lower()]
		featurizer = featurizers[featurizer.lower()]()
		if isinstance(splitter, str):
		splitter = splitters[splitter.lower()]
		if data_dir is None:

+1 −1

Original line number	Diff line number	Diff line
		@@ -27,7 +27,7 @@ class _QM7Loader(_MolnetLoader):


		def load_qm7(
		featurizer: Union[dc.feat.Featurizer, str] = dc.feat.CoulombMatrix(23),
		featurizer: Union[dc.feat.Featurizer, str] = 'CoulombMatrix',
		splitter: Union[dc.splits.Splitter, str, None] = 'random',
		transformers: List[Union[TransformerGenerator, str]] = ['normalization'],
		reload: bool = True,

+1 −1

Original line number	Diff line number	Diff line
		@@ -29,7 +29,7 @@ class _QM8Loader(_MolnetLoader):


		def load_qm8(
		featurizer: Union[dc.feat.Featurizer, str] = dc.feat.CoulombMatrix(26),
		featurizer: Union[dc.feat.Featurizer, str] = 'CoulombMatrix',
		splitter: Union[dc.splits.Splitter, str, None] = 'random',
		transformers: List[Union[TransformerGenerator, str]] = ['normalization'],
		reload: bool = True,

+1 −1

Original line number	Diff line number	Diff line
		@@ -28,7 +28,7 @@ class _QM9Loader(_MolnetLoader):


		def load_qm9(
		featurizer: Union[dc.feat.Featurizer, str] = dc.feat.CoulombMatrix(29),
		featurizer: Union[dc.feat.Featurizer, str] = 'ColumbMatrix',
		splitter: Union[dc.splits.Splitter, str, None] = 'random',
		transformers: List[Union[TransformerGenerator, str]] = ['normalization'],
		reload: bool = True,