def test_antiregistred(self, leaflets):
registration = Registration(leaflets=leaflets,
upper_sel="name L",
lower_sel="name C")
registration.run()
reference = {'n_frames': 1, 'registration': -1}
assert registration.registration.size == reference['n_frames']
assert_array_almost_equal(registration.registration,
reference['registration'])
def test_antiregistred(self, universe):
registration = Registration(universe=universe,
leaflets=self.kwargs['leaflets'],
upper_sel="name L",
lower_sel="name C")
registration.run()
reference = {'n_frames': 1, 'registration': -1}
assert registration.registration.size == reference['n_frames']
assert_array_almost_equal(registration.registration,
reference['registration'])
def test_nbins100(self, leaflets):
registration = Registration(leaflets=leaflets,
upper_sel="name L C",
lower_sel="name L C",
n_bins=100)
registration.run()
reference = {'n_frames': 1, 'registration': 1}
assert registration.registration.size == reference['n_frames']
assert_array_almost_equal(registration.registration,
reference['registration'])
def test_filter_by_registered(self, leaflets):
filter_by = np.zeros(100)
filter_by[1::2] = 1
registration = Registration(leaflets=leaflets, filter_by=filter_by)
registration.run()
reference = {'n_frames': 1, 'registration': 1}
assert registration.registration.size == reference['n_frames']
assert_array_almost_equal(registration.registration,
reference['registration'],
decimal=4)
def test_Exceptions(self, universe):
match = "'leaflets' must either be a 1D array containing non-changing "
with pytest.raises(ValueError, match=match):
Registration(universe=universe,
upper_sel="name L C",
lower_sel="name L C",
leaflets=None)
with pytest.raises(ValueError, match=match):
Registration(
universe=universe,
upper_sel="name L C",
lower_sel="name L C",
leaflets=np.array([[[], []], [[],
[]]]) # cannot pass a 3D array
)
match = (
"The shape of 'leaflets' must be \\(n_residues,\\), but 'lipid_sel' "
"generates an AtomGroup with 100 residues"
" and 'leaflets' has shape \\(99, 1\\).")
with pytest.raises(ValueError, match=match):
Registration(
universe=universe,
upper_sel="name L C",
lower_sel="name L C",
leaflets=np.array([[1]] * 50 +
[[-1]] * 49) # one residue too few
)
filter_by = np.zeros(100)
filter_by[1::2] = 1
match = "'filter_by' must either be a 1D array containing non-changing boolean"
with pytest.raises(ValueError, match=match):
Registration(universe=universe,
upper_sel="name L C",
lower_sel="name L C",
leaflets=self.kwargs['leaflets'],
filter_by=np.array(None))
match = "The shape of 'filter_by' must be \(n_residues,\)" # noqa:W605
with pytest.raises(ValueError, match=match):
Registration(universe=universe,
upper_sel="name L C",
lower_sel="name L C",
leaflets=self.kwargs['leaflets'],
filter_by=filter_by[:99])
def test_Exceptions(self, leaflets):
match = "leaflets must be of type AssignLeaflets"
with pytest.raises(ValueError, match=match):
Registration(leaflets=leaflets.leaflets # this is a NumPy array
)
filter_by = np.zeros(100)
filter_by[1::2] = 1
match = "'filter_by' must either be a 1D array containing non-changing boolean"
with pytest.raises(ValueError, match=match):
Registration(leaflets=leaflets, filter_by=np.array(None))
match = "The shape of 'filter_by' must be \(n_residues,\)" # noqa:W605
with pytest.raises(ValueError, match=match):
Registration(leaflets=leaflets, filter_by=filter_by[:99])
def test_filter_by_registered(self, universe):
filter_by = np.zeros(100)
filter_by[1::2] = 1
registration = Registration(universe=universe,
leaflets=self.kwargs['leaflets'],
upper_sel="name L C",
lower_sel="name L C",
filter_by=filter_by)
registration.run()
reference = {'n_frames': 1, 'registration': 1}
assert registration.registration.size == reference['n_frames']
assert_array_almost_equal(registration.registration,
reference['registration'],
decimal=4)
def test_nbins1000_sd0(self, leaflets):
# The bins are 0.1 Anstrom wide, and gaussian_sd=0 means there is no spead
# in density
# So, registration should be
registration = Registration(leaflets=leaflets,
upper_sel="name L",
lower_sel="name C",
n_bins=1000,
gaussian_sd=0)
registration.run()
reference = {'n_frames': 1, 'registration': 0}
assert registration.registration.size == reference['n_frames']
assert_array_almost_equal(registration.registration,
reference['registration'],
decimal=4)