def exercise_core(n=10, verbose=0):
from libtbx.test_utils import approx_equal
import random
# make two random sets of sites please
c = euler_angles_as_matrix([random.uniform(0, 360) for i in xrange(3)])
set_1 = flex.vec3_double(flex.random_double(n * 3) * 10 - 2)
set_2 = flex.vec3_double(flex.random_double(n * 3) * 10 - 2)
set_3 = tuple(c) * set_2
set_a = set_1.concatenate(set_2)
set_b = set_1.concatenate(set_3)
tmp = find_domain(set_a, set_b, initial_rms=0.02, match_radius=0.03, minimum_size=1)
if verbose:
tmp.show()
assert len(tmp.matches) == 2
assert approx_equal(tmp.matches[0][3], 0, eps=1e-5)
assert approx_equal(tmp.matches[0][4], n, eps=1e-5)
def exercise_planarity():
weights = flex.double([1,2,3,4])
for points,norm in [([(1,1,0), (-1,-1,0), (-1,1,0), (1,-1,0)], (0,0,1)),
([(0,1,1), (0,-1,-1), (0,-1,1), (0,1,-1)], (1,0,0)),
([(1,0,1), (-1,0,-1), (-1,0,1), (1,0,-1)], (0,1,0)),
([(1,1,-1), (-1,-1,1), (-1,1,-1), (1,-1,1)], (0,1,1))]:
norm = col(norm)
norm /= abs(norm)
for i_trial in xrange(5):
for i_pert in xrange(5):
if (i_trial == 0 and i_pert == 0):
sites = [col(v) for v in points]
rot_norm = norm
else:
shift = col([random.uniform(-10,10) for i in xrange(3)])
rot = sqr(euler_angles_as_matrix(
[random.uniform(0,360) for i in xrange(3)]))
rot_norm = rot * norm
if (i_pert == 0):
sites = [rot*col(v)+shift for v in points]
else:
sites = []
for v in points:
f = 0.1
pert = col([(random.random()-0.5)*f for i in xrange(3)])
sites.append(rot*col(v)+shift+pert)
pl = geometry_restraints.planarity(sites=sites, weights=weights)
n = col(pl.normal())
gradients_analytical = pl.gradients()
if (i_pert == 0):
assert abs(abs(n.dot(rot_norm))-1) < 1.e-5
assert approx_equal(pl.residual(), 0)
for grad in gradients_analytical:
assert approx_equal(grad, [0,0,0])
assert approx_equal(pl.residual(), pl.lambda_min())
residual_obj = residual_functor(
restraint_type=geometry_restraints.planarity,
weights=weights)
gradients_finite = finite_differences(sites, residual_obj)
assert approx_equal(gradients_finite, gradients_analytical)
def random_rotation(): import random from scitbx.math import euler_angles_as_matrix return euler_angles_as_matrix([random.uniform(0,360) for i in xrange(3)])
def random_rotation(): return euler_angles_as_matrix([random.uniform(0,360) for i in xrange(3)])
def random_rotation(angle_min=0, angle_max=360):
import random
from scitbx.math import euler_angles_as_matrix
return euler_angles_as_matrix(
[random.uniform(angle_min,angle_max) for i in xrange(3)])
def random_rotation(angle_min=0, angle_max=360):
import random
from scitbx.math import euler_angles_as_matrix
return euler_angles_as_matrix(
[random.uniform(angle_min,angle_max) for i in xrange(3)])
def random_rotation(angle_min=0, angle_max=360):
angles = [random.uniform(angle_min, angle_max) for i in range(3)]
print("Rotation: ", angles)
return euler_angles_as_matrix(angles, deg=True)
def random_rotation():
return euler_angles_as_matrix([random.uniform(0, 360) for i in range(3)])
def random_rotation():
import random
from scitbx.math import euler_angles_as_matrix
return euler_angles_as_matrix([random.uniform(0, 360) for i in xrange(3)])