def test_dihedral_sign(self):
p0 = np.array([0, 0, 1], dtype=np.float)
p1 = np.array([0, 0, 0], dtype=np.float)
p2 = np.array([0, 1, 0], dtype=np.float)
p3_1 = np.array([1, 0, 0], dtype=np.float)
dihedral = get_dihedral(p0, p1, p2, p3_1)
self.assertEqual(dihedral, np.pi / 2)
p3_2 = np.array([-1, 0, 0], dtype=np.float)
dihedral = get_dihedral(p0, p1, p2, p3_2)
self.assertEqual(dihedral, -np.pi / 2)
def test_dihedral(self):
p1 = np.array([0, 0, 1.5], dtype=np.float)
p2 = np.array([0, 0, 0], dtype=np.float)
p3 = np.array([0, 0.5, 0], dtype=np.float)
for psi in np.arange(start=-np.pi, stop=np.pi, step=np.pi / 17):
p4 = np.array([np.sin(psi), 0.5, np.cos(psi)], dtype=np.float)
dihedral = get_dihedral(p1, p2, p3, p4)
self.assertAlmostEqual(psi, dihedral)
def test_dihedral_2(self):
p1 = np.array([0, 0, 1.5], dtype=np.float)
p2 = np.array([0, 0, 0], dtype=np.float)
p3 = np.array([0, 0.5, 0], dtype=np.float)
# Add delta so that the corner case of -180, 180 goes away
delta = 1E-4
for psi in np.arange(start=-np.pi + delta,
stop=np.pi - delta,
step=np.pi / 17):
p4 = np.array(
[np.sin(2 * np.pi + psi), 0.5,
np.cos(2 * np.pi + psi)],
dtype=np.float)
dihedral = get_dihedral(p1, p2, p3, p4)
self.assertAlmostEqual(psi, dihedral)
def test_positioning(self):
p0 = np.array([0, 0, 1], dtype=np.float)
p1 = np.array([0, 0, 0], dtype=np.float)
p2 = np.array([0, 1, 0], dtype=np.float)
distance = 2.5
angle = 2 * np.pi / 3
# Add delta so that the corner case of -180, 180 goes away
delta = 1E-4
for psi in np.arange(start=-np.pi + delta,
stop=np.pi - delta,
step=np.pi / 17):
p_new = position_point(p0=p0,
p1=p1,
p2=p2,
distance=distance,
angle=angle,
dihedral=psi)
self.assertAlmostEqual(get_distance(p2, p_new), distance)
self.assertAlmostEqual(get_angle(p1, p2, p_new), angle)
self.assertAlmostEqual(get_dihedral(p0, p1, p2, p_new), psi)
def test_dihedral_nan(self):
string = '4\n\nC 0.5995394918 0.0 1.0\nC -0.5995394918 0.0 1.0\nH -1.6616385861 0.0 1.0\nH 1.6616385861 0.0 1.0'
atoms = ase.io.read(io.StringIO(string), format='xyz')
dihedral = get_dihedral(*(a.position for a in atoms))
self.assertTrue(np.isnan(dihedral))