Loading deepchem/feat/__init__.py +1 −1 Original line number Diff line number Diff line Loading @@ -10,7 +10,7 @@ from deepchem.feat.base_classes import UserDefinedFeaturizer from deepchem.feat.graph_features import ConvMolFeaturizer from deepchem.feat.graph_features import WeaveFeaturizer from deepchem.feat.fingerprints import CircularFingerprint from deepchem.feat.basic import RDKitDescriptors from deepchem.feat.rdkit_descriptors import RDKitDescriptors from deepchem.feat.coulomb_matrices import CoulombMatrix from deepchem.feat.coulomb_matrices import CoulombMatrixEig from deepchem.feat.coulomb_matrices import BPSymmetryFunctionInput Loading deepchem/feat/basic.py→deepchem/feat/rdkit_descriptors.py +0 −30 Original line number Diff line number Diff line Loading @@ -6,36 +6,6 @@ import numpy as np from deepchem.feat.base_classes import MolecularFeaturizer class MolecularWeight(MolecularFeaturizer): """Molecular weight. Note ---- This class requires RDKit to be installed. """ def _featurize(self, mol): """ Calculate molecular weight. Parameters ---------- mol : RDKit Mol Molecule. Returns ------- np.ndarray of length 1 containing the molecular weight. """ try: from rdkit.Chem import Descriptors except ModuleNotFoundError: raise ValueError("This class requires RDKit to be installed.") wt = Descriptors.ExactMolWt(mol) wt = [wt] return np.asarray(wt) class RDKitDescriptors(MolecularFeaturizer): """RDKit descriptors. Loading deepchem/feat/tests/test_features.pydeleted 100644 → 0 +0 −69 Original line number Diff line number Diff line """ Test featurizer class. """ import unittest from deepchem.feat import ConvMolFeaturizer, CircularFingerprint from deepchem.feat.basic import MolecularWeight class TestFeaturizer(unittest.TestCase): """ Tests for Featurizer. """ def setUp(self): """ Set up tests. """ smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O' from rdkit import Chem self.mol = Chem.MolFromSmiles(smiles) def test_featurizer(self): """ Test basic functionality of Featurizer. """ f = MolecularWeight() rval = f([self.mol]) assert rval.shape == (1, 1) def test_flatten_conformers(self): """ Calculate molecule-level features for a multiconformer molecule. """ f = MolecularWeight() rval = f([self.mol]) assert rval.shape == (1, 1) def test_convmol_hashable(self): featurizer1 = ConvMolFeaturizer(atom_properties=['feature']) featurizer2 = ConvMolFeaturizer(atom_properties=['feature']) featurizer3 = ConvMolFeaturizer() d = set() d.add(featurizer1) d.add(featurizer2) d.add(featurizer3) self.assertEqual(2, len(d)) featurizers = [featurizer1, featurizer2, featurizer3] for featurizer in featurizers: self.assertTrue(featurizer in featurizers) def test_circularfingerprint_hashable(self): featurizer1 = CircularFingerprint() featurizer2 = CircularFingerprint() featurizer3 = CircularFingerprint(size=5) d = set() d.add(featurizer1) d.add(featurizer2) d.add(featurizer3) self.assertEqual(2, len(d)) featurizers = [featurizer1, featurizer2, featurizer3] for featurizer in featurizers: self.assertTrue(featurizer in featurizers) deepchem/feat/tests/test_basic.py→deepchem/feat/tests/test_rdkit_descriptors.py +1 −34 Original line number Diff line number Diff line Loading @@ -4,40 +4,7 @@ Test basic molecular features. import numpy as np import unittest from deepchem.feat.basic import MolecularWeight, RDKitDescriptors class TestMolecularWeight(unittest.TestCase): """ Test MolecularWeight. """ def setUp(self): """ Set up tests. """ smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O' from rdkit import Chem self.mol = Chem.MolFromSmiles(smiles) self.engine = MolecularWeight() def testMW(self): """ Test MW. """ assert np.allclose(self.engine([self.mol]), 180, atol=0.1) def test_MW_on_smiles(self): """ Test MW invocation on smiles." """ assert np.allclose(self.engine('CC(=O)OC1=CC=CC=C1C(=O)O'), 180, atol=0.1) def test_MW_on_mol(self): """ Test MW invocation on RDKit mol." """ assert np.allclose(self.engine(self.mol), 180, atol=0.1) from deepchem.feat.basic import RDKitDescriptors class TestRDKitDescriptors(unittest.TestCase): Loading Loading
deepchem/feat/__init__.py +1 −1 Original line number Diff line number Diff line Loading @@ -10,7 +10,7 @@ from deepchem.feat.base_classes import UserDefinedFeaturizer from deepchem.feat.graph_features import ConvMolFeaturizer from deepchem.feat.graph_features import WeaveFeaturizer from deepchem.feat.fingerprints import CircularFingerprint from deepchem.feat.basic import RDKitDescriptors from deepchem.feat.rdkit_descriptors import RDKitDescriptors from deepchem.feat.coulomb_matrices import CoulombMatrix from deepchem.feat.coulomb_matrices import CoulombMatrixEig from deepchem.feat.coulomb_matrices import BPSymmetryFunctionInput Loading
deepchem/feat/basic.py→deepchem/feat/rdkit_descriptors.py +0 −30 Original line number Diff line number Diff line Loading @@ -6,36 +6,6 @@ import numpy as np from deepchem.feat.base_classes import MolecularFeaturizer class MolecularWeight(MolecularFeaturizer): """Molecular weight. Note ---- This class requires RDKit to be installed. """ def _featurize(self, mol): """ Calculate molecular weight. Parameters ---------- mol : RDKit Mol Molecule. Returns ------- np.ndarray of length 1 containing the molecular weight. """ try: from rdkit.Chem import Descriptors except ModuleNotFoundError: raise ValueError("This class requires RDKit to be installed.") wt = Descriptors.ExactMolWt(mol) wt = [wt] return np.asarray(wt) class RDKitDescriptors(MolecularFeaturizer): """RDKit descriptors. Loading
deepchem/feat/tests/test_features.pydeleted 100644 → 0 +0 −69 Original line number Diff line number Diff line """ Test featurizer class. """ import unittest from deepchem.feat import ConvMolFeaturizer, CircularFingerprint from deepchem.feat.basic import MolecularWeight class TestFeaturizer(unittest.TestCase): """ Tests for Featurizer. """ def setUp(self): """ Set up tests. """ smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O' from rdkit import Chem self.mol = Chem.MolFromSmiles(smiles) def test_featurizer(self): """ Test basic functionality of Featurizer. """ f = MolecularWeight() rval = f([self.mol]) assert rval.shape == (1, 1) def test_flatten_conformers(self): """ Calculate molecule-level features for a multiconformer molecule. """ f = MolecularWeight() rval = f([self.mol]) assert rval.shape == (1, 1) def test_convmol_hashable(self): featurizer1 = ConvMolFeaturizer(atom_properties=['feature']) featurizer2 = ConvMolFeaturizer(atom_properties=['feature']) featurizer3 = ConvMolFeaturizer() d = set() d.add(featurizer1) d.add(featurizer2) d.add(featurizer3) self.assertEqual(2, len(d)) featurizers = [featurizer1, featurizer2, featurizer3] for featurizer in featurizers: self.assertTrue(featurizer in featurizers) def test_circularfingerprint_hashable(self): featurizer1 = CircularFingerprint() featurizer2 = CircularFingerprint() featurizer3 = CircularFingerprint(size=5) d = set() d.add(featurizer1) d.add(featurizer2) d.add(featurizer3) self.assertEqual(2, len(d)) featurizers = [featurizer1, featurizer2, featurizer3] for featurizer in featurizers: self.assertTrue(featurizer in featurizers)
deepchem/feat/tests/test_basic.py→deepchem/feat/tests/test_rdkit_descriptors.py +1 −34 Original line number Diff line number Diff line Loading @@ -4,40 +4,7 @@ Test basic molecular features. import numpy as np import unittest from deepchem.feat.basic import MolecularWeight, RDKitDescriptors class TestMolecularWeight(unittest.TestCase): """ Test MolecularWeight. """ def setUp(self): """ Set up tests. """ smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O' from rdkit import Chem self.mol = Chem.MolFromSmiles(smiles) self.engine = MolecularWeight() def testMW(self): """ Test MW. """ assert np.allclose(self.engine([self.mol]), 180, atol=0.1) def test_MW_on_smiles(self): """ Test MW invocation on smiles." """ assert np.allclose(self.engine('CC(=O)OC1=CC=CC=C1C(=O)O'), 180, atol=0.1) def test_MW_on_mol(self): """ Test MW invocation on RDKit mol." """ assert np.allclose(self.engine(self.mol), 180, atol=0.1) from deepchem.feat.basic import RDKitDescriptors class TestRDKitDescriptors(unittest.TestCase): Loading
