def test_Exceptions(self, universe):
match = "midplane_sel is 'None' and midplane_cutoff "
with pytest.raises(ValueError, match=match):
AssignLeaflets(
universe=universe,
lipid_sel="name L",
midplane_sel=None,
midplane_cutoff=5,
)
match = "midplane_sel is 'name C' and midplane_cutoff "
with pytest.raises(ValueError, match=match):
AssignLeaflets(
universe=universe,
lipid_sel="name L C",
midplane_sel="name C",
midplane_cutoff=None,
)
match = "To assign molecules to the midplane, midplane_cutoff must"
with pytest.raises(ValueError, match=match):
AssignLeaflets(
universe=universe,
lipid_sel="name L C",
midplane_sel="name C",
midplane_cutoff=-10,
)
match = "midplane_sel contains atoms that are not present in molecules selected "
with pytest.raises(ValueError, match=match):
AssignLeaflets(universe=universe,
lipid_sel="name L",
midplane_sel="name C",
midplane_cutoff=10)
def test_nbins4(self, universe):
leaflets = AssignLeaflets(universe, n_bins=4, **self.kwargs)
leaflets.run()
reference = {
'leaflets_present':
[-1, 1], # now (correctly) no midplane residues should be found
'midplane_resnames':
[], # list or residues incorrectly identified as midplane
}
assert_array_equal(np.unique(leaflets.leaflets),
reference['leaflets_present'])
assert_array_equal(
universe.residues[leaflets.leaflets[:, 0] == 0].resnames,
reference['midplane_resnames']) # noqa: E225
def test_nbins1(self, universe):
leaflets = AssignLeaflets(universe, n_bins=1, **self.kwargs)
leaflets.run()
reference = {
'leaflets_present': [-1, 0, 1],
'midplane_resnames': ["CHOL"] *
6, # list or residues incorrectly identified as midplane
}
assert_array_equal(np.unique(leaflets.leaflets),
reference['leaflets_present'])
assert_array_equal(
universe.residues[leaflets.leaflets[:, 0] == 0].resnames,
reference['midplane_resnames']) # noqa: E225
assert 'LIPID' not in universe.residues[leaflets.leaflets[:, 0] ==
0].resnames # noqa: E225
def test_nbins4_midplane(self, universe):
leaflets = AssignLeaflets(universe, **self.kwargs)
leaflets.run()
reference = {
'leaflets_present': [-1, 1],
'midplane_resnames':
[], # only one of two atoms in CHOL78 is in the midplane, so the molecule is not assigned to the midplane
'midplane_resids': []
}
assert_array_equal(np.unique(leaflets.leaflets),
reference['leaflets_present'])
assert_array_equal(
universe.residues[leaflets.leaflets[:, 0] == 0].resnames,
reference['midplane_resnames'])
assert_array_equal(
universe.residues[leaflets.leaflets[:, 0] == 0].resids,
reference['midplane_resids'])
def test_nbins4_midplane(self, universe):
leaflets = AssignLeaflets(universe, **self.kwargs)
leaflets.run()
reference = {
'leaflets_present': [-1, 0, 1],
'midplane_resnames':
["CHOL"
], # list of residues resnames (correctly) identified as midplane
'midplane_resids': [78] # resid of midplane molecules
}
assert_array_equal(np.unique(leaflets.leaflets),
reference['leaflets_present'])
assert_array_equal(
universe.residues[leaflets.leaflets[:, 0] == 0].resnames,
reference['midplane_resnames'])
assert_array_equal(
universe.residues[leaflets.leaflets[:, 0] == 0].resids,
reference['midplane_resids'])
def leaflets(self, universe):
leaflets = AssignLeaflets(universe, **self.kwargs)
leaflets.run()
return leaflets
def leaflets(self, universe):
leaflets = AssignLeaflets(universe, lipid_sel="name L C")
leaflets.run()
return leaflets