deal with py2/py3 integers + change formatting in tests (77ece2a4) · Commits · 钟慕尧 / deepchem

deepchem/feat/tests/test_rdkit_grid_features.py

+42 −50

Original line number	Diff line number	Diff line
		@@ -2,6 +2,7 @@
		Test rdkit_grid_featurizer module.
		"""
		import os
		from six import integer_types
		import unittest

		import numpy as np
		@@ -91,6 +92,7 @@ class TestHelperFunctions(unittest.TestCase):
		coords2 = np.random.rand(n2, 3)

		distance = rgf.compute_pairwise_distances(coords1, coords2)
		self.assertEqual(distance.shape, (n1, n2))
		self.assertTrue((distance >= 0).all())
		# random coords between 0 and 1, so the max possible distance in sqrt(2)
		self.assertTrue((distance <= 2.0**0.5).all())
		@@ -114,7 +116,7 @@ class TestHelperFunctions(unittest.TestCase):
		for _ in range(10):
		string = random_string(10)
		string_hash = rgf.hash_ecfp(string, power)
		self.assertIsInstance(string_hash, int)
		self.assertIsInstance(string_hash, integer_types)
		self.assertLess(string_hash, 2**power)
		self.assertGreaterEqual(string_hash, 0)

		@@ -124,7 +126,7 @@ class TestHelperFunctions(unittest.TestCase):
		string1 = random_string(10)
		string2 = random_string(10)
		pair_hash = rgf.hash_ecfp_pair((string1, string2), power)
		self.assertIsInstance(pair_hash, int)
		self.assertIsInstance(pair_hash, integer_types)
		self.assertLess(pair_hash, 2**power)
		self.assertGreaterEqual(pair_hash, 0)

		@@ -150,23 +152,17 @@ class TestHelperFunctions(unittest.TestCase):
		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)
		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,
		)
		lig_rdk,)
		prot_dict_dist, lig_dict_dist = rgf.featurize_binding_pocket_ecfp(
		prot_xyz,
		prot_rdk,
		lig_xyz,
		lig_rdk,
		pairwise_distances=distance
		)
		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)
		@@ -180,15 +176,13 @@ class TestHelperFunctions(unittest.TestCase):
		prot_rdk,
		lig_xyz,
		lig_rdk,
		cutoff=2.0,
		)
		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,
		)
		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))
		@@ -201,8 +195,7 @@ class TestHelperFunctions(unittest.TestCase):
		prot_rdk,
		lig_xyz,
		lig_rdk,
		ecfp_degree=3,
		)
		ecfp_degree=3,)
		self.assertNotEqual(prot_dict_e3, prot_dict)
		self.assertNotEqual(lig_dict_e3, lig_dict)

		@@ -211,16 +204,15 @@ class TestHelperFunctions(unittest.TestCase):
		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)
		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,
		)
		bins,)

		self.assertIsInstance(splif_dict, dict)
		for (prot_idx, lig_idx), ecfp_pair in splif_dict.items():

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