Merge pull request #2252 from nd-02110114/fix-ci-rdkit (72659d83) · Commits · 钟慕尧 / deepchem

deepchem/feat/molecule_featurizers/rdkit_descriptors.py

+24 −5

Original line number	Diff line number	Diff line
		@@ -23,15 +23,29 @@ class RDKitDescriptors(MolecularFeaturizer):
		This class requires RDKit to be installed.
		"""

		def __init__(self):
		def __init__(self, use_fragment=True, ipc_avg=True):
		"""Initialize this featurizer.

		Parameters
		----------
		use_fragment: bool, optional (default True)
		If True, the return value includes the fragment binary descriptors like 'fr_XXX'.
		ipc_avg: bool, optional (default True)
		If True, the IPC descriptor calculates with avg=True option.
		Please see this issue: https://github.com/rdkit/rdkit/issues/1527.
		"""
		try:
		from rdkit.Chem import Descriptors
		except ModuleNotFoundError:
		raise ValueError("This class requires RDKit to be installed.")

		self.use_fragment = use_fragment
		self.ipc_avg = ipc_avg
		self.descriptors = []
		self.descList = []
		for descriptor, function in Descriptors.descList:
		if self.use_fragment is False and descriptor.startswith('fr_'):
		continue
		self.descriptors.append(descriptor)
		self.descList.append((descriptor, function))

		@@ -47,9 +61,14 @@ class RDKitDescriptors(MolecularFeaturizer):
		Returns
		-------
		np.ndarray
		1D array of RDKit descriptors for `mol`. The length is 200.
		1D array of RDKit descriptors for `mol`.
		The length is `len(self.descriptors)`.
		"""
		rval = []
		features = []
		for desc_name, function in self.descList:
		rval.append(function(mol))
		return np.asarray(rval)
		if desc_name == 'Ipc' and self.ipc_avg:
		feature = function(mol, avg=True)
		else:
		feature = function(mol)
		features.append(feature)
		return np.asarray(features)

deepchem/feat/tests/test_rdkit_descriptors.py

+17 −11

Original line number	Diff line number	Diff line
		@@ -25,10 +25,11 @@ class TestRDKitDescriptors(unittest.TestCase):
		"""
		Test simple descriptors.
		"""
		descriptors = self.featurizer([self.mol])
		assert descriptors.shape == (1, 200)
		featurizer = RDKitDescriptors()
		descriptors = featurizer([self.mol])
		assert descriptors.shape == (1, len(featurizer.descriptors))
		assert np.allclose(
		descriptors[0, self.featurizer.descriptors.index('ExactMolWt')],
		descriptors[0, featurizer.descriptors.index('ExactMolWt')],
		180,
		atol=0.1)

		@@ -36,20 +37,25 @@ class TestRDKitDescriptors(unittest.TestCase):
		"""
		Test invocation on raw smiles.
		"""
		descriptors = self.featurizer('CC(=O)OC1=CC=CC=C1C(=O)O')
		assert descriptors.shape == (1, 200)
		featurizer = RDKitDescriptors()
		descriptors = featurizer('CC(=O)OC1=CC=CC=C1C(=O)O')
		assert descriptors.shape == (1, len(featurizer.descriptors))
		assert np.allclose(
		descriptors[0, self.featurizer.descriptors.index('ExactMolWt')],
		descriptors[0, featurizer.descriptors.index('ExactMolWt')],
		180,
		atol=0.1)

		def test_rdkit_descriptors_on_mol(self):
		def test_rdkit_descriptors_with_use_fragment(self):
		"""
		Test invocation on RDKit mol.
		Test with use_fragment
		"""
		descriptors = self.featurizer(self.mol)
		assert descriptors.shape == (1, 200)
		from rdkit.Chem import Descriptors
		featurizer = RDKitDescriptors(use_fragment=False)
		descriptors = featurizer(self.mol)
		assert descriptors.shape == (1, len(featurizer.descriptors))
		all_descriptors = Descriptors.descList
		assert len(featurizer.descriptors) < len(all_descriptors)
		assert np.allclose(
		descriptors[0, self.featurizer.descriptors.index('ExactMolWt')],
		descriptors[0, featurizer.descriptors.index('ExactMolWt')],
		180,
		atol=0.1)

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