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_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_empty_list(self):
with self.assertRaises(ValueError):
load([], top=pdb_file)
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 test_load_traj(self):
filename = traj_files[0]
features = api.featurizer(pdb_file)
res = load(filename, features)
self.assertEqual(type(res), np.ndarray)
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 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 testUnicodeString_without_featurizer(self):
filename = unicode(traj_files[0])
with self.assertRaises(ValueError):
load(filename)
