Python radius_cut_q Examples

Example #1

File: test_contacts.py Project: AmeyaHarmalkar/mdanalysis

    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)

Example #2

File: test_contacts.py Project: AmeyaHarmalkar/mdanalysis

def test_radius_cut_q(r, r0, radius, expected_value):
    # check some extremal points
    assert contacts.radius_cut_q(r, r0, radius) == expected_value

Example #3

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)

Example #4

File: test_contacts.py Project: alejob/mdanalysis

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)

Example #5

File: test_contacts.py Project: MDAnalysis/mdanalysis

def test_radius_cut_q(r, r0, radius, expected_value):
    # check some extremal points
    assert contacts.radius_cut_q(r, r0, radius) == expected_value