def setUp(self):
self.test_transformations = []
for i in xrange(20):
test_transformation = Complete()
test_transformation.set_rotation_properties(random.random()*math.pi*2, numpy.random.uniform(-3, 3, 3), random.sample([True, False], 1)[0])
test_transformation.t = numpy.random.uniform(-3, 3, 3)
self.test_transformations.append(test_transformation)
def setUp(self):
self.test_transformations = []
for i in xrange(20):
test_transformation = Complete()
test_transformation.set_rotation_properties(
random.random() * math.pi * 2, numpy.random.uniform(-3, 3, 3),
random.sample([True, False], 1)[0])
test_transformation.t = numpy.random.uniform(-3, 3, 3)
self.test_transformations.append(test_transformation)
def do_test(self, coordinates, masses, expected_is):
reference = MolecularDescriptorTV1(coordinates, masses)
self.assert_(reference.inversion_symmetric == expected_is)
for counter in xrange(3):
transformation = Complete()
transformation.set_rotation_properties(
random.uniform(0, 2 * math.pi),
numpy.random.uniform(-1, 1, (3, )),
False,
)
transformation.t = numpy.random.uniform(-5, 5, (3, ))
new_coordinates = numpy.array([
transformation.vector_apply(coordinate)
for coordinate in coordinates
], float)
new_descriptor = MolecularDescriptorTV1(new_coordinates, masses)
self.assert_(reference.compare_structure(new_descriptor))
self.assert_(not reference.compare_global_rotation(new_descriptor))
self.assert_(
not reference.compare_global_translation(new_descriptor))
def do_test(self, coordinates, masses, expected_is):
reference = MolecularDescriptorTV1(coordinates, masses)
self.assert_(reference.inversion_symmetric == expected_is)
for counter in xrange(3):
transformation = Complete()
transformation.set_rotation_properties(
random.uniform(0, 2*math.pi),
numpy.random.uniform(-1, 1, (3,)),
False,
)
transformation.t = numpy.random.uniform(-5, 5, (3,))
new_coordinates = numpy.array([
transformation.vector_apply(coordinate)
for coordinate
in coordinates
], float)
new_descriptor = MolecularDescriptorTV1(new_coordinates, masses)
self.assert_(reference.compare_structure(new_descriptor))
self.assert_(not reference.compare_global_rotation(new_descriptor))
self.assert_(not reference.compare_global_translation(new_descriptor))
def do(self):
cache = context.application.cache
for node in cache.nodes:
transformation = Complete()
translated_children = []
for child in node.children:
if isinstance(child, GLTransformationMixin) and isinstance(child.transformation, Translation):
if child.get_fixed():
translated_children = []
break
translated_children.append(child)
if len(translated_children) == 0:
continue
mass, com = compute_center_of_mass(yield_particles(node))
if mass == 0.0:
continue
transformation.t = com
tensor = compute_inertia_tensor(yield_particles(node), com)
transformation.r = default_rotation_matrix(tensor)
CenterAlignBase.do(self, node, translated_children, transformation)