def component(self):
b_h_real = self.b_h_real.text()
b_t_real = self.b_t_real.text()
b_h_imag = self.b_h_imag.text()
b_t_imag = self.b_t_imag.text()
b_t = complex(float(b_t_real), float(b_t_imag))
b_h = complex(float(b_h_real), float(b_h_imag))
V_h = self.V_h.value()
V_t = self.V_t.value()
APM = self.APM.value()
thick_h = self.thick_h.value()
thick_t = self.thick_t.value()
head_solvent = self.head_solvent.value()
tail_solvent = self.tail_solvent.value()
leaflet = LipidLeaflet(
APM,
b_h,
V_h,
thick_h,
b_t,
V_t,
thick_t,
3,
3,
head_solvent=SLD(head_solvent, name="head solvent"),
tail_solvent=SLD(tail_solvent, name="tail solvent"),
)
leaflet.name = "leaflet"
return leaflet
def test_initialisation_with_SLD(self):
# we should be able to initialise with SLD objects
heads = SLD(6.01e-4 + 0j)
tails = SLD(-2.92e-4 + 0j)
new_leaflet = LipidLeaflet(self.APM, heads, self.V_h, self.thick_h,
tails, self.V_t, self.thick_t, 2, 3)
slabs = self.leaflet.slabs()
new_slabs = new_leaflet.slabs()
assert_allclose(new_slabs, slabs)
def setup_method(self):
self.b_h = 6.01e-4
self.V_h = 319.
self.b_t = -2.92e-4
self.V_t = 782.
self.APM = 60.
self.thick_h = 9.
self.thick_t = 14.
self.leaflet = LipidLeaflet(self.APM, self.b_h, self.V_h, self.thick_h,
self.b_t, self.V_t, self.thick_t, 2, 3)
self.rho_h = self.b_h / self.V_h / 1e-6
self.rho_t = self.b_t / self.V_t / 1e-6
self.phi_solv_h = 1 - (self.V_h / (self.APM * self.thick_h))
self.phi_solv_t = 1 - (self.V_t / (self.APM * self.thick_t))
class TestLipidLeaflet(object):
def setup_method(self):
self.b_h = 6.01e-4
self.V_h = 319.0
self.b_t = -2.92e-4
self.V_t = 782.0
self.APM = 60.0
self.thick_h = 9.0
self.thick_t = 14.0
self.leaflet = LipidLeaflet(
self.APM,
self.b_h,
self.V_h,
self.thick_h,
self.b_t,
self.V_t,
self.thick_t,
2,
3,
)
self.rho_h = self.b_h / self.V_h / 1e-6
self.rho_t = self.b_t / self.V_t / 1e-6
self.phi_solv_h = 1 - (self.V_h / (self.APM * self.thick_h))
self.phi_solv_t = 1 - (self.V_t / (self.APM * self.thick_t))
def test_slabs(self):
# check that slab calculation from parameters is correct
slabs = self.leaflet.slabs()
theoretical = np.array([
[self.thick_h, self.rho_h, 0, 3, self.phi_solv_h],
[self.thick_t, self.rho_t, 0, 2, self.phi_solv_t],
])
assert_allclose(slabs, theoretical, rtol=1e-15)
# check that we can flip the lipid leaflet
self.leaflet.reverse_monolayer = True
theoretical = np.flipud(theoretical)
theoretical[:, 3] = theoretical[::-1, 3]
assert_allclose(self.leaflet.slabs(), theoretical, rtol=1e-15)
def test_solvent_penetration(self):
# check different types of solvation for heads/tails.
self.leaflet.head_solvent = SLD(1.23)
slabs = self.leaflet.slabs()
assert_allclose(
slabs[0, 1],
1.23 * self.phi_solv_h + (1 - self.phi_solv_h) * self.rho_h,
)
assert_allclose(slabs[0, 4], 0)
self.leaflet.head_solvent = None
self.leaflet.tail_solvent = SLD(1.23)
slabs = self.leaflet.slabs()
assert_allclose(
slabs[1, 1],
1.23 * self.phi_solv_t + (1 - self.phi_solv_t) * self.rho_t,
)
assert_allclose(slabs[1, 4], 0)
def test_initialisation_with_SLD(self):
# we should be able to initialise with SLD objects
heads = SLD(6.01e-4 + 0j)
tails = SLD(-2.92e-4 + 0j)
new_leaflet = LipidLeaflet(
self.APM,
heads,
self.V_h,
self.thick_h,
tails,
self.V_t,
self.thick_t,
2,
3,
)
slabs = self.leaflet.slabs()
new_slabs = new_leaflet.slabs()
assert_allclose(new_slabs, slabs)
def test_repr(self):
# test that we can reconstruct the object from a repr
s = repr(self.leaflet)
q = eval(s)
assert_equal(q.slabs(), self.leaflet.slabs())