Loading deepchem/feat/tests/test_rdkit_grid_features.py +101 −5 Original line number Diff line number Diff line Loading @@ -12,6 +12,13 @@ from rdkit.Chem import MolFromMolFile, rdchem from deepchem.feat import rdkit_grid_featurizer as rgf def random_string(length, chars=None): import string if chars is None: chars = list(string.ascii_letters + string.ascii_letters + '()[]+-.=#@/\\') return ''.join(np.random.choice(chars, length)) class TestHelperFunctions(unittest.TestCase): """ Test functions defined in rdkit_grid_featurizer module. Loading Loading @@ -105,8 +112,7 @@ class TestHelperFunctions(unittest.TestCase): def test_hash_ecfp(self): for power in (2, 16, 64): for _ in range(10): # FIXME strings generation is not controlled by random seed string = os.urandom(10).decode('latin1') string = random_string(10) string_hash = rgf.hash_ecfp(string, power) self.assertIsInstance(string_hash, int) self.assertLess(string_hash, 2**power) Loading @@ -115,9 +121,8 @@ class TestHelperFunctions(unittest.TestCase): def test_hash_ecfp_pair(self): for power in (2, 16, 64): for _ in range(10): # FIXME strings generation is not controlled by random seed string1 = os.urandom(10).decode('latin1') string2 = os.urandom(10).decode('latin1') string1 = random_string(10) string2 = random_string(10) pair_hash = rgf.hash_ecfp_pair((string1, string2), power) self.assertIsInstance(pair_hash, int) self.assertLess(pair_hash, 2**power) Loading @@ -141,3 +146,94 @@ class TestHelperFunctions(unittest.TestCase): self.assertIsInstance(ecfp_selected, dict) self.assertEqual(len(ecfp_selected), num_ind) self.assertEqual(sorted(ecfp_selected.keys()), sorted(indices)) def test_featurize_binding_pocket_ecfp(self): prot_xyz, prot_rdk = rgf.load_molecule(self.protein_file) lig_xyz, lig_rdk = rgf.load_molecule(self.ligand_file) distance = rgf.compute_pairwise_distances(protein_xyz=prot_xyz, ligand_xyz=lig_xyz) # check if results are the same if we provide precomputed distances prot_dict, lig_dict = rgf.featurize_binding_pocket_ecfp( prot_xyz, prot_rdk, lig_xyz, lig_rdk, ) prot_dict_dist, lig_dict_dist = rgf.featurize_binding_pocket_ecfp( prot_xyz, prot_rdk, lig_xyz, lig_rdk, pairwise_distances=distance ) # ...but first check if we actually got two dicts self.assertIsInstance(prot_dict, dict) self.assertIsInstance(lig_dict, dict) self.assertEqual(prot_dict, prot_dict_dist) self.assertEqual(lig_dict, lig_dict_dist) # check if we get less features with smaller distance cutoff prot_dict_d2, lig_dict_d2 = rgf.featurize_binding_pocket_ecfp( prot_xyz, prot_rdk, lig_xyz, lig_rdk, cutoff=2.0, ) prot_dict_d6, lig_dict_d6 = rgf.featurize_binding_pocket_ecfp( prot_xyz, prot_rdk, lig_xyz, lig_rdk, cutoff=6.0, ) self.assertLess(len(prot_dict_d2), len(prot_dict)) # ligands are typically small so all atoms might be present self.assertLessEqual(len(lig_dict_d2), len(lig_dict)) self.assertGreater(len(prot_dict_d6), len(prot_dict)) self.assertGreaterEqual(len(lig_dict_d6), len(lig_dict)) # check if using different ecfp_degree changes anything prot_dict_e3, lig_dict_e3 = rgf.featurize_binding_pocket_ecfp( prot_xyz, prot_rdk, lig_xyz, lig_rdk, ecfp_degree=3, ) self.assertNotEqual(prot_dict_e3, prot_dict) self.assertNotEqual(lig_dict_e3, lig_dict) def test_compute_splif_features_in_range(self): prot_xyz, prot_rdk = rgf.load_molecule(self.protein_file) lig_xyz, lig_rdk = rgf.load_molecule(self.ligand_file) prot_num_atoms = prot_rdk.GetNumAtoms() lig_num_atoms = lig_rdk.GetNumAtoms() distance = rgf.compute_pairwise_distances(protein_xyz=prot_xyz, ligand_xyz=lig_xyz) for bins in ((0, 2), (2, 3)): splif_dict = rgf.compute_splif_features_in_range( prot_rdk, lig_rdk, distance, bins, ) self.assertIsInstance(splif_dict, dict) for (prot_idx, lig_idx), ecfp_pair in splif_dict.items(): for idx in (prot_idx, lig_idx): self.assertIsInstance(idx, (int, np.int64)) self.assertGreaterEqual(prot_idx, 0) self.assertLess(prot_idx, prot_num_atoms) self.assertGreaterEqual(lig_idx, 0) self.assertLess(lig_idx, lig_num_atoms) for ecfp in ecfp_pair: ecfp_idx, ecfp_frag = ecfp.split(',') ecfp_idx = int(ecfp_idx) self.assertGreaterEqual(ecfp_idx, 0) # TODO upperbound? Loading
deepchem/feat/tests/test_rdkit_grid_features.py +101 −5 Original line number Diff line number Diff line Loading @@ -12,6 +12,13 @@ from rdkit.Chem import MolFromMolFile, rdchem from deepchem.feat import rdkit_grid_featurizer as rgf def random_string(length, chars=None): import string if chars is None: chars = list(string.ascii_letters + string.ascii_letters + '()[]+-.=#@/\\') return ''.join(np.random.choice(chars, length)) class TestHelperFunctions(unittest.TestCase): """ Test functions defined in rdkit_grid_featurizer module. Loading Loading @@ -105,8 +112,7 @@ class TestHelperFunctions(unittest.TestCase): def test_hash_ecfp(self): for power in (2, 16, 64): for _ in range(10): # FIXME strings generation is not controlled by random seed string = os.urandom(10).decode('latin1') string = random_string(10) string_hash = rgf.hash_ecfp(string, power) self.assertIsInstance(string_hash, int) self.assertLess(string_hash, 2**power) Loading @@ -115,9 +121,8 @@ class TestHelperFunctions(unittest.TestCase): def test_hash_ecfp_pair(self): for power in (2, 16, 64): for _ in range(10): # FIXME strings generation is not controlled by random seed string1 = os.urandom(10).decode('latin1') string2 = os.urandom(10).decode('latin1') string1 = random_string(10) string2 = random_string(10) pair_hash = rgf.hash_ecfp_pair((string1, string2), power) self.assertIsInstance(pair_hash, int) self.assertLess(pair_hash, 2**power) Loading @@ -141,3 +146,94 @@ class TestHelperFunctions(unittest.TestCase): self.assertIsInstance(ecfp_selected, dict) self.assertEqual(len(ecfp_selected), num_ind) self.assertEqual(sorted(ecfp_selected.keys()), sorted(indices)) def test_featurize_binding_pocket_ecfp(self): prot_xyz, prot_rdk = rgf.load_molecule(self.protein_file) lig_xyz, lig_rdk = rgf.load_molecule(self.ligand_file) distance = rgf.compute_pairwise_distances(protein_xyz=prot_xyz, ligand_xyz=lig_xyz) # check if results are the same if we provide precomputed distances prot_dict, lig_dict = rgf.featurize_binding_pocket_ecfp( prot_xyz, prot_rdk, lig_xyz, lig_rdk, ) prot_dict_dist, lig_dict_dist = rgf.featurize_binding_pocket_ecfp( prot_xyz, prot_rdk, lig_xyz, lig_rdk, pairwise_distances=distance ) # ...but first check if we actually got two dicts self.assertIsInstance(prot_dict, dict) self.assertIsInstance(lig_dict, dict) self.assertEqual(prot_dict, prot_dict_dist) self.assertEqual(lig_dict, lig_dict_dist) # check if we get less features with smaller distance cutoff prot_dict_d2, lig_dict_d2 = rgf.featurize_binding_pocket_ecfp( prot_xyz, prot_rdk, lig_xyz, lig_rdk, cutoff=2.0, ) prot_dict_d6, lig_dict_d6 = rgf.featurize_binding_pocket_ecfp( prot_xyz, prot_rdk, lig_xyz, lig_rdk, cutoff=6.0, ) self.assertLess(len(prot_dict_d2), len(prot_dict)) # ligands are typically small so all atoms might be present self.assertLessEqual(len(lig_dict_d2), len(lig_dict)) self.assertGreater(len(prot_dict_d6), len(prot_dict)) self.assertGreaterEqual(len(lig_dict_d6), len(lig_dict)) # check if using different ecfp_degree changes anything prot_dict_e3, lig_dict_e3 = rgf.featurize_binding_pocket_ecfp( prot_xyz, prot_rdk, lig_xyz, lig_rdk, ecfp_degree=3, ) self.assertNotEqual(prot_dict_e3, prot_dict) self.assertNotEqual(lig_dict_e3, lig_dict) def test_compute_splif_features_in_range(self): prot_xyz, prot_rdk = rgf.load_molecule(self.protein_file) lig_xyz, lig_rdk = rgf.load_molecule(self.ligand_file) prot_num_atoms = prot_rdk.GetNumAtoms() lig_num_atoms = lig_rdk.GetNumAtoms() distance = rgf.compute_pairwise_distances(protein_xyz=prot_xyz, ligand_xyz=lig_xyz) for bins in ((0, 2), (2, 3)): splif_dict = rgf.compute_splif_features_in_range( prot_rdk, lig_rdk, distance, bins, ) self.assertIsInstance(splif_dict, dict) for (prot_idx, lig_idx), ecfp_pair in splif_dict.items(): for idx in (prot_idx, lig_idx): self.assertIsInstance(idx, (int, np.int64)) self.assertGreaterEqual(prot_idx, 0) self.assertLess(prot_idx, prot_num_atoms) self.assertGreaterEqual(lig_idx, 0) self.assertLess(lig_idx, lig_num_atoms) for ecfp in ecfp_pair: ecfp_idx, ecfp_frag = ecfp.split(',') ecfp_idx = int(ecfp_idx) self.assertGreaterEqual(ecfp_idx, 0) # TODO upperbound?
