tests for bug-fixes + cosmetic changes (c78bd74b) · Commits · 钟慕尧 / deepchem

deepchem/feat/tests/test_rdkit_grid_features.py

+26 −2

Original line number	Diff line number	Diff line
		@@ -8,7 +8,8 @@ import unittest
		import numpy as np
		np.random.seed(123)

		from rdkit.Chem import MolFromMolFile, rdchem
		from rdkit.Chem import MolFromMolFile
		from rdkit.Chem.AllChem import Mol, ComputeGasteigerCharges

		from deepchem.feat import rdkit_grid_featurizer as rgf

		@@ -56,7 +57,7 @@ class TestHelperFunctions(unittest.TestCase):
		calc_charges)
		num_atoms = mol_rdk.GetNumAtoms()
		self.assertIsInstance(mol_xyz, np.ndarray)
		self.assertIsInstance(mol_rdk, rdchem.Mol)
		self.assertIsInstance(mol_rdk, Mol)
		self.assertEqual(mol_xyz.shape, (num_atoms, 3))

		def test_generate_random__unit_vector(self):
		@@ -271,6 +272,19 @@ class TestHelperFunctions(unittest.TestCase):
		# coordinates were properly translated and scaled
		self.assertTrue(
		(voxel[0] < (box_width + coords_range) / 2.0 / voxel_width).all())
		self.assertTrue(
		np.allclose(voxel[0],
		np.floor((xyz[idx] + box_width / 2.0) / voxel_width)))

		# for coordinates outside of the box function should properly transform them
		# to indices and warn the user
		for args in ((np.array([[0, 1, 6]]), 0, 10, 1.0), (np.array([[0, 4, -6]]),
		0, 10, 1.0)):
		# TODO check if function warns. There is assertWarns method in unittest,
		# but it is not implemented in 2.7 and buggy in 3.5 (issue 29620)
		voxel = rgf.convert_atom_to_voxel(*args)
		self.assertTrue(
		np.allclose(voxel[0], np.floor((args[0] + args[2] / 2.0) / args[3])))

		def test_convert_atom_pair_to_voxel(self):
		# 20 points with coords between -5 and 5, centered at 0
		@@ -288,3 +302,13 @@ class TestHelperFunctions(unittest.TestCase):
		self.assertEqual(len(v_pair), 2)
		self.assertTrue((v1 == v_pair[0]).all())
		self.assertTrue((v2 == v_pair[1]).all())

		def test_compute_charge_dictionary(self):
		for fname in (self.ligand_file, self.protein_file):
		_, mol = rgf.load_molecule(fname)
		ComputeGasteigerCharges(mol)
		charge_dict = rgf.compute_charge_dictionary(mol)
		self.assertEqual(len(charge_dict), mol.GetNumAtoms())
		for i in range(mol.GetNumAtoms()):
		self.assertIn(i, charge_dict)
		self.assertIsInstance(charge_dict[i], (float, int))

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