def test_load_features_pass_trajectory_as_topology(self): import mdtraj t = mdtraj.load(pdb_file) features = api.featurizer(t) traj_files = [f for f in self.bpti_mini_files if f.endswith('.netcdf')] load(traj_files, features=features)
def test_with_trajs_without_featurizer_or_top(self): with self.assertRaises(ValueError): load(traj_files) output = load(traj_files, top=pdb_file) self.assertEqual(type(output), list) self.assertEqual(len(output), len(traj_files))
def test_various_formats_load(self): chunksizes = [0, 13] X = None bpti_mini_previous = None for cs in chunksizes: for bpti_mini in self.bpti_mini_files: Y = api.load(bpti_mini, top=self.bpti_pdbfile, chunksize=cs) if X is not None: np.testing.assert_array_almost_equal( X, Y, err_msg='Comparing %s to %s failed for chunksize %s' % (bpti_mini, bpti_mini_previous, cs)) X = Y bpti_mini_previous = bpti_mini
def test_load_traj(self): filename = traj_files[0] features = api.featurizer(pdb_file) res = load(filename, features) self.assertEqual(type(res), np.ndarray)
def testUnicodeString(self): filename = text_type(traj_files[0]) features = api.featurizer(pdb_file) load(filename, features)
def testUnicodeString_without_featurizer(self): filename = text_type(traj_files[0]) with self.assertRaises(ValueError): load(filename)
def test_empty_list(self): with self.assertRaises(ValueError): load([], top=pdb_file)
def testUnicodeString(self): filename = unicode(traj_files[0]) features = api.featurizer(pdb_file) load(filename, features)
def testUnicodeString(self): filename = u''.join(traj_files[0]) features = api.featurizer(pdb_file) load(filename, features)
def test_non_existant_input(self): input_files = [traj_files[0], "does_not_exist_for_sure"] with self.assertRaises(ValueError): load(trajfiles=input_files, top=pdb_file)
def test_load_trajs(self): features = api.featurizer(pdb_file) res = load(traj_files, features) self.assertEqual(type(res), list) self.assertTrue(all(type(x) == np.ndarray for x in res))
def testUnicodeString_without_featurizer(self): filename = unicode(traj_files[0]) with self.assertRaises(ValueError): load(filename)