def test_robustscaler_vs_sklearn():
# Compare msmbuilder.preprocessing.RobustScaler
# with sklearn.preprocessing.RobustScaler
robustscalerr = RobustScalerR()
robustscalerr.fit(np.concatenate(trajs))
robustscaler = RobustScaler()
robustscaler.fit(trajs)
y_ref1 = robustscalerr.transform(trajs[0])
y1 = robustscaler.transform(trajs)[0]
np.testing.assert_array_almost_equal(y_ref1, y1)
def test_robustscaler_vs_sklearn():
# Compare msmbuilder.preprocessing.RobustScaler
# with sklearn.preprocessing.RobustScaler
robustscalerr = RobustScalerR()
robustscalerr.fit(np.concatenate(trajs))
robustscaler = RobustScaler()
robustscaler.fit(trajs)
y_ref1 = robustscalerr.transform(trajs[0])
y1 = robustscaler.transform(trajs)[0]
np.testing.assert_array_almost_equal(y_ref1, y1)
class TestUtils:
def setUp(self):
numpy.random.seed(12)
self.top = 'data_app/runs/structure.prmtop'
self.traj_1 = 'data_app/runs/run-000.nc'
self.traj_2 = 'data_app/runs/run-001.nc'
self.feat = DihedralFeaturizer()
self.traj_dict = {
0: load(self.traj_1, top=self.top),
1: load(self.traj_2, top=self.top)
}
self.scaler = RobustScaler()
self.tica = tICA(n_components=2)
self.ftrajs = {
0: numpy.random.rand(100, 50),
1: numpy.random.rand(100, 50),
}
def test_get_ftrajs(self):
output = get_ftrajs(self.traj_dict, self.feat)
assert len(output) == 2
assert type(output) == dict
def test_get_sctrajs(self):
self.scaler.fit(list(self.ftrajs.values()))
output = get_sctrajs(self.ftrajs, self.scaler)
assert len(output) == 2
assert type(output) == dict
def test_get_ttrajs(self):
self.tica.fit(list(self.ftrajs.values()))
output = get_ttrajs(self.ftrajs, self.tica)
assert len(output) == 2
assert type(output) == dict
def test_traj_from_stateinds(self):
traj = traj_from_stateinds(spawns, meta)
assert traj.n_frames == 1
def test_write_production_file(self):
write_production_file()
assert os.path.exists('Production.in')
os.remove('Production.in')
def test_write_cpptraj_script(self):
write_cpptraj_script(self.traj_1, self.top)
assert os.path.exists('script.cpptraj')
os.remove('script.cpptraj')
def test_write_tleap_script(self):
write_tleap_script(write=True)
assert os.path.exists('script.tleap')
os.remove('script.tleap')
def test_create_folder(self):
fname = 'foo'
create_folder(fname)
assert os.path.isdir(fname)
os.removedirs(fname)
def test_create_symlinks(self):
create_folder('src_symlinks')
create_folder('dst_symlinks')
with open('src_symlinks/1.txt', 'w') as f:
f.writelines('foo')
create_symlinks(files='src_symlinks/*.txt', dst_folder='dst_symlinks')
assert os.path.exists('dst_symlinks/1.txt')
rmtree('src_symlinks')
rmtree('dst_symlinks')
def test_hmr_prmtop(self):
new_top = hmr_prmtop(self.top, save=False)
assert isinstance(new_top, AmberParm)
