def test_radius_cut_method(self, universe):
acidic = universe.select_atoms(self.sel_acidic)
basic = universe.select_atoms(self.sel_basic)
r = contacts.distance_array(acidic.positions, basic.positions)
initial_contacts = contacts.contact_matrix(r, 6.0)
expected = []
for ts in universe.trajectory:
r = contacts.distance_array(acidic.positions, basic.positions)
expected.append(contacts.radius_cut_q(r[initial_contacts], None, radius=6.0))
ca = self._run_Contacts(universe, method='radius_cut')
assert_array_equal(ca.timeseries[:, 1], expected)
def test_radius_cut_q(r, r0, radius, expected_value):
# check some extremal points
assert contacts.radius_cut_q(r, r0, radius) == expected_value
def test_radius_cut_q():
# check some extremal points
assert_equal(contacts.radius_cut_q([1], None, 2), 1)
assert_equal(contacts.radius_cut_q([2], None, 1), 0)
assert_equal(contacts.radius_cut_q([2, 0.5], None, 1), 0.5)
def test_radius_cut_q():
# check some extremal points
assert_equal(contacts.radius_cut_q([1], None, 2), 1)
assert_equal(contacts.radius_cut_q([2], None, 1), 0)
assert_equal(contacts.radius_cut_q([2, 0.5], None, 1), 0.5)
def test_radius_cut_q(r, r0, radius, expected_value):
# check some extremal points
assert contacts.radius_cut_q(r, r0, radius) == expected_value