finish rdkit upgrade (345b8bc9) · Commits · 钟慕尧 / deepchem

deepchem/feat/basic.py

+33 −116

Original line number	Diff line number	Diff line
		@@ -44,123 +44,41 @@ class RDKitDescriptors(Featurizer):

		# (ytz): This is done to avoid future compatibility issues like inclusion of
		# the 3D descriptors or changing the feature size.
		allowedDescriptors = set(['MaxAbsPartialCharge',
		'MinPartialCharge',
		'MinAbsPartialCharge',
		'HeavyAtomMolWt',
		'MaxAbsEStateIndex',
		'NumRadicalElectrons',
		'NumValenceElectrons',
		'MinAbsEStateIndex',
		'MaxEStateIndex',
		'MaxPartialCharge',
		'MinEStateIndex',
		'ExactMolWt',
		'MolWt',
		'BalabanJ',
		'BertzCT',
		'Chi0',
		'Chi0n',
		'Chi0v',
		'Chi1',
		'Chi1n',
		'Chi1v',
		'Chi2n',
		'Chi2v',
		'Chi3n',
		'Chi3v',
		'Chi4n',
		'Chi4v',
		'HallKierAlpha',
		'Ipc',
		'Kappa1',
		'Kappa2',
		'Kappa3',
		'LabuteASA',
		'PEOE_VSA1',
		'PEOE_VSA10',
		'PEOE_VSA11',
		'PEOE_VSA12',
		'PEOE_VSA13',
		'PEOE_VSA14',
		'PEOE_VSA2',
		'PEOE_VSA3',
		'PEOE_VSA4',
		'PEOE_VSA5',
		'PEOE_VSA6',
		'PEOE_VSA7',
		'PEOE_VSA8',
		'PEOE_VSA9',
		'SMR_VSA1',
		'SMR_VSA10',
		'SMR_VSA2',
		'SMR_VSA3',
		'SMR_VSA4',
		'SMR_VSA5',
		'SMR_VSA6',
		'SMR_VSA7',
		'SMR_VSA8',
		'SMR_VSA9',
		'SlogP_VSA1',
		'SlogP_VSA10',
		'SlogP_VSA11',
		'SlogP_VSA12',
		'SlogP_VSA2',
		'SlogP_VSA3',
		'SlogP_VSA4',
		'SlogP_VSA5',
		'SlogP_VSA6',
		'SlogP_VSA7',
		'SlogP_VSA8',
		'SlogP_VSA9',
		'TPSA',
		'EState_VSA1',
		'EState_VSA10',
		'EState_VSA11',
		'EState_VSA2',
		'EState_VSA3',
		'EState_VSA4',
		'EState_VSA5',
		'EState_VSA6',
		'EState_VSA7',
		'EState_VSA8',
		'EState_VSA9',
		'VSA_EState1',
		'VSA_EState10',
		'VSA_EState2',
		'VSA_EState3',
		'VSA_EState4',
		'VSA_EState5',
		'VSA_EState6',
		'VSA_EState7',
		'VSA_EState8',
		'VSA_EState9',
		'FractionCSP3',
		'HeavyAtomCount',
		'NHOHCount',
		'NOCount',
		'NumAliphaticCarbocycles',
		'NumAliphaticHeterocycles',
		'NumAliphaticRings',
		'NumAromaticCarbocycles',
		'NumAromaticHeterocycles',
		'NumAromaticRings',
		'NumHAcceptors',
		'NumHDonors',
		'NumHeteroatoms',
		'NumRotatableBonds',
		'NumSaturatedCarbocycles',
		'NumSaturatedHeterocycles',
		'NumSaturatedRings',
		'RingCount',
		'MolLogP',
		'MolMR'])

		allowedDescriptors = set([
		'MaxAbsPartialCharge', 'MinPartialCharge', 'MinAbsPartialCharge',
		'HeavyAtomMolWt', 'MaxAbsEStateIndex', 'NumRadicalElectrons',
		'NumValenceElectrons', 'MinAbsEStateIndex', 'MaxEStateIndex',
		'MaxPartialCharge', 'MinEStateIndex', 'ExactMolWt', 'MolWt', 'BalabanJ',
		'BertzCT', 'Chi0', 'Chi0n', 'Chi0v', 'Chi1', 'Chi1n', 'Chi1v', 'Chi2n',
		'Chi2v', 'Chi3n', 'Chi3v', 'Chi4n', 'Chi4v', 'HallKierAlpha', 'Ipc',
		'Kappa1', 'Kappa2', 'Kappa3', 'LabuteASA', 'PEOE_VSA1', 'PEOE_VSA10',
		'PEOE_VSA11', 'PEOE_VSA12', 'PEOE_VSA13', 'PEOE_VSA14', 'PEOE_VSA2',
		'PEOE_VSA3', 'PEOE_VSA4', 'PEOE_VSA5', 'PEOE_VSA6', 'PEOE_VSA7',
		'PEOE_VSA8', 'PEOE_VSA9', 'SMR_VSA1', 'SMR_VSA10', 'SMR_VSA2', 'SMR_VSA3',
		'SMR_VSA4', 'SMR_VSA5', 'SMR_VSA6', 'SMR_VSA7', 'SMR_VSA8', 'SMR_VSA9',
		'SlogP_VSA1', 'SlogP_VSA10', 'SlogP_VSA11', 'SlogP_VSA12', 'SlogP_VSA2',
		'SlogP_VSA3', 'SlogP_VSA4', 'SlogP_VSA5', 'SlogP_VSA6', 'SlogP_VSA7',
		'SlogP_VSA8', 'SlogP_VSA9', 'TPSA', 'EState_VSA1', 'EState_VSA10',
		'EState_VSA11', 'EState_VSA2', 'EState_VSA3', 'EState_VSA4',
		'EState_VSA5', 'EState_VSA6', 'EState_VSA7', 'EState_VSA8', 'EState_VSA9',
		'VSA_EState1', 'VSA_EState10', 'VSA_EState2', 'VSA_EState3',
		'VSA_EState4', 'VSA_EState5', 'VSA_EState6', 'VSA_EState7', 'VSA_EState8',
		'VSA_EState9', 'FractionCSP3', 'HeavyAtomCount', 'NHOHCount', 'NOCount',
		'NumAliphaticCarbocycles', 'NumAliphaticHeterocycles',
		'NumAliphaticRings', 'NumAromaticCarbocycles', 'NumAromaticHeterocycles',
		'NumAromaticRings', 'NumHAcceptors', 'NumHDonors', 'NumHeteroatoms',
		'NumRotatableBonds', 'NumSaturatedCarbocycles',
		'NumSaturatedHeterocycles', 'NumSaturatedRings', 'RingCount', 'MolLogP',
		'MolMR'
		])

		def __init__(self):
		self.descriptors = []
		self.descList = []
		for descriptor, function in Descriptors.descList:
		if descriptor in self.allowedDescriptors:
		self.descriptors.append(descriptor)
		self.descList.append((descriptor, function))

		def _featurize(self, mol):
		"""
		@@ -172,7 +90,6 @@ class RDKitDescriptors(Featurizer):
		Molecule.
		"""
		rval = []
		for desc_name, function in Descriptors.descList:
		if desc_name in self.allowedDescriptors:
		for desc_name, function in self.descList:
		rval.append(function(mol))
		return rval

deepchem/feat/tests/test_basic.py

+7 −2

Original line number	Diff line number	Diff line
		@@ -13,6 +13,7 @@ class TestMolecularWeight(unittest.TestCase):
		"""
		Test MolecularWeight.
		"""

		def setUp(self):
		"""
		Set up tests.
		@@ -32,6 +33,7 @@ class TestRDKitDescriptors(unittest.TestCase):
		"""
		Test RDKitDescriptors.
		"""

		def setUp(self):
		"""
		Set up tests.
		@@ -45,6 +47,9 @@ class TestRDKitDescriptors(unittest.TestCase):
		Test simple descriptors.
		"""
		descriptors = self.engine([self.mol])
		print(descriptors)
		print(descriptors[0, self.engine.descriptors.index('ExactMolWt')])
		assert np.allclose(
		descriptors[0, self.engine.descriptors.index('ExactMolWt')], 180,
		descriptors[0, self.engine.descriptors.index('ExactMolWt')],
		180,
		atol=0.1)

deepchem/splits/tests/test_splitter.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -292,7 +292,7 @@ class TestSplitters(unittest.TestCase):
		y[:n_positives] = 1
		w = np.ones((n_samples, n_tasks))
		# Set half the positives to have zero weight
		w[:n_positives / 2] = 0
		w[:n_positives // 2] = 0
		ids = np.arange(n_samples)

		stratified_splitter = dc.splits.RandomStratifiedSplitter()

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