def test_subset_lipids(self, universe):
neighbours = Neighbours(universe, lipid_sel="name C", cutoff=10)
neighbours.run()
# it's a hexagonal lattice, but each hexagon is irregular (two sides longer than the other 4)
# with cutoff=10, every lipid should have 2 neighbours
reference = {
'n_frames':
1,
'n_residues':
50,
'n_neighbours':
np.array([
0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0,
0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 0,
1, 0, 1, 0, 0, 1, 0, 1
])
}
assert neighbours.neighbours.shape[0] == (reference['n_frames'])
assert neighbours.neighbours[0].shape == (reference['n_residues'],
reference['n_residues'])
assert_array_equal(np.sum(neighbours.neighbours[0].toarray(), axis=0),
reference['n_neighbours'])
def test_run_method_not_called(self, universe):
neighbours = Neighbours(universe=universe,
lipid_sel='name L C',
cutoff=12.0)
match = ".neighbours attribute is None: use .run\(\) before calling .largest_cluster\(\)" # noqa:W605
with pytest.raises(NoDataError, match=match):
neighbours.largest_cluster()
def test_neighbours_cutoff10(self, universe):
neighbours = Neighbours(universe, **self.kwargs, cutoff=10)
neighbours.run()
# it's a hexagonal lattice, but each hexagon is irregular (two sides longer than the other 4)
# with cutoff=10, every lipid should have 2 neighbours
reference = {
'n_residues': 100, # there are 200 atoms but 100 lipids in total
'n_neighbours': 2,
}
assert neighbours.neighbours.shape == (reference['n_residues'],
reference['n_residues'])
assert (np.sum(neighbours.neighbours.toarray(),
axis=0) == reference['n_neighbours']).all()
def test_neighbours_cutoff12(self, universe):
neighbours = Neighbours(universe, **self.kwargs, cutoff=12)
neighbours.run()
# it's a hexagonal lattice
# with cutoff=12, every lipid should have 6 neighbours
reference = {
'n_residues': 100, # there are 200 atoms but 100 lipids in total
'n_neighbours': 6,
}
assert neighbours.neighbours.shape == (reference['n_residues'],
reference['n_residues'])
assert (np.sum(neighbours.neighbours.toarray(),
axis=0) == reference['n_neighbours']).all()
def test_Exceptions(self, universe):
match = "'cutoff' must be greater than 0"
with pytest.raises(ValueError, match=match):
Neighbours(universe=universe, lipid_sel="name L C", cutoff=-1)
def neighbours(self, universe):
neighbours = Neighbours(universe, **self.kwargs)
neighbours.run()
return neighbours