def scc(self, universe):
scc = SCC(
universe=universe,
tail_sel="not name ROH"
)
scc.run()
return scc
def test_SCC(self, universe):
scc = SCC(universe, **self.kwargs)
scc.run()
reference = {
'n_residues': 100,
'n_frames': 1,
'scc': np.full((100, 1), fill_value=-0.5) # all bonds are perpendicular to the z-axis
}
assert scc.SCC.shape == (reference['n_residues'], reference['n_frames'])
assert_array_almost_equal(scc.SCC, reference['scc'])
def test_SCC_weighted_average_different_tails(self, universe, sn1_scc):
sn2_scc = SCC(universe, "name L")
sn2_scc.run()
scc = SCC.weighted_average(sn1_scc, sn2_scc)
reference = {
'n_residues': 100,
'n_frames': 1,
'scc': np.full(
(100, 1),
fill_value=-0.5) # all bonds are perpendicular to the z-axis
}
assert scc.SCC.shape == (reference['n_residues'],
reference['n_frames'])
assert_array_almost_equal(scc.SCC, reference['scc'])
def test_SCC_normals_3D(self, universe):
# The Scc should be the same whether the normal is the positive or negative z-axis
normals = np.zeros((100, 1, 3))
normals[:, :50, 2] = 1.0
normals[:, 50:, 2] = -1.0
scc = SCC(universe, **self.kwargs, normals=normals)
scc.run()
reference = {
'n_residues': 100,
'n_frames': 1,
'scc': np.full(
(100, 1),
fill_value=-0.5) # all bonds are perpendicular to the z-axis
}
assert scc.SCC.shape == (reference['n_residues'],
reference['n_frames'])
assert_array_almost_equal(scc.SCC, reference['scc'])
def test_SCC_weighted_average(self, sn1_scc):
scc = SCC.weighted_average(sn1_scc, sn1_scc)
reference = {
'n_residues': 50,
'n_frames': 1,
'scc': np.full((50, 1), fill_value=-0.5) # all bonds are perpendicular to the z-axis
}
assert scc.SCC.shape == (reference['n_residues'], reference['n_frames'])
assert_array_almost_equal(scc.SCC, reference['scc'])
def test_Exceptions(self, universe):
match = "'normals' must be a 3D array containing local membrane normals of each lipi at each frame."
with pytest.raises(ValueError, match=match):
SCC(
universe=universe,
**self.kwargs,
normals=np.ones(100) # Wrong dimension
)
match = "The shape of 'normals' must be \\(n_residues, n_frames, 3\\)"
with pytest.raises(ValueError, match=match):
SCC(
universe=universe,
**self.kwargs,
normals=np.ones((99, 1, 3)) # Too few molecules
)
match = "The frames to analyse must be identical to those used "
with pytest.raises(ValueError, match=match):
scc = SCC(
universe=universe,
**self.kwargs,
normals=np.ones((100, 2, 3)) # Too many frames
)
scc.run()
def test_Exceptions(self, universe):
match = "'normals' must either be a 2D array containing leaflet ids "
with pytest.raises(ValueError, match=match):
SCC(
universe=universe,
**self.kwargs,
normals=np.ones(100)
)
match = "The shape of 'normals' must be \\(n_residues,\\)"
with pytest.raises(ValueError, match=match):
SCC(
universe=universe,
**self.kwargs,
normals=np.ones((99, 1))
)
match = "The frames to analyse must be identical to those used "
with pytest.raises(ValueError, match=match):
scc = SCC(
universe=universe,
**self.kwargs,
normals=np.ones((100, 2))
)
scc.run()
def sn1_scc(self, universe):
sn1_scc = SCC(universe, "name C")
sn1_scc.run()
return sn1_scc
def test_Exceptions(self, universe, sn1_scc):
match = "sn1_scc and sn2_scc must have been run with the same frames"
with pytest.raises(ValueError, match=match):
sn2_scc = SCC(
universe=universe,
**self.kwargs,
)
sn2_scc.run(stop=0)
SCC.weighted_average(sn1_scc, sn2_scc)
with pytest.raises(ValueError, match=match):
sn2_scc = SCC(
universe=universe,
**self.kwargs,
)
sn2_scc.run(stop=1)
sn2_scc.frames = np.array([10])
SCC.weighted_average(sn1_scc, sn2_scc)
def sn1_scc(self, universe):
sn1_scc = SCC(universe, **self.kwargs)
sn1_scc.run()
return sn1_scc