def test_operators():
import numpy as np
def as_np(xyz):
return np.array([xyz.x, xyz.y, xyz.z])
a = XYZ(5, 8, 1)
a.x, a.y, a.z = 9, 8, 7
assert a.x == 9
assert a.y == 8
assert a.z == 7
b = XYZ(1, 2, 3)
npa = as_np(a)
npb = as_np(b)
assert np.allclose(as_np(a + b), npa + npb)
assert np.allclose(as_np(-a), -npa)
assert np.allclose(as_np(a - b), npa - npb)
assert np.allclose(as_np(a * 7), npa * 7)
assert np.allclose(as_np(a / 7), npa / 7)
assert np.allclose(as_np(7 * a), 7 * npa)
assert np.allclose((a.dot(b)), np.dot(npa, npb))
assert np.allclose(a.len(), np.linalg.norm(npa))
assert np.allclose(a.len2(), np.linalg.norm(npa)**2)
assert np.allclose(as_np(a.cross(b)), np.cross(npa, npb))
def test_sasa_three_spheres():
for samples, precision in [
(10, 5e0), # 5% accuracy
(50, 1e0), # 1% accuracy
(250, 1e-1), # 0.1% accuracy
(1000, 1e-2), # 0.01% accuracy
(5000, 1e-3), # 0.001% accuracy
]:
for _ in range(100):
r1, r2, r3 = np.random.random(3) * 2 + 0.01
a = XYZ(*(np.random.random(3) * 2 - 1))
b = XYZ(*(np.random.random(3) * 2 - 1))
v = XYZ(*np.random.random(3))
v /= v.len()
c = a + v * (r1 + r3)
S1 = 4 * np.pi * r1 ** 2
S2 = 4 * np.pi * r2 ** 2
S3 = 4 * np.pi * r3 ** 2
S1_loss = first_sphere_hidden_area(a, b, r1, r2) + first_sphere_hidden_area(a, c, r1, r3)
S2_loss = first_sphere_hidden_area(b, a, r2, r1) + first_sphere_hidden_area(b, c, r2, r3)
S3_loss = first_sphere_hidden_area(c, a, r3, r1) + first_sphere_hidden_area(c, b, r3, r2)
total_area = S1 + S2 + S3
exposed_area_exact = total_area - S1_loss - S2_loss - S3_loss
sasa = calc_sasa(VectorXYZ([a, b, c]), np.array([r1, r2, r3]), 0, n_samples=samples)
exposed_area_approx = sum(sasa)
exposed_area_percent_exact = exposed_area_exact / total_area * 100
exposed_area_percent_approx = exposed_area_approx / total_area * 100
assert np.isclose(exposed_area_percent_exact,
exposed_area_percent_approx,
atol=precision), (exposed_area_percent_exact,
exposed_area_percent_approx,)
