def setUp(self):
self.nrigid = 10
self.topology = RBTopology()
self.topology.add_sites(
[create_tetrahedron() for _ in range(self.nrigid)])
self.topology.finalize_setup()
self.measure = MeasureAngleAxisCluster(self.topology)
def get_mindist(self, **kwargs):
from pele.angleaxis import MinPermDistAACluster
from pele.angleaxis import TransformAngleAxisCluster, MeasureAngleAxisCluster
transform = TransformAngleAxisCluster(self.aatopology)
measure = MeasureAngleAxisCluster(self.aatopology, transform=transform,
permlist=[])
return MinPermDistAACluster(self.aasystem, measure=measure, transform=transform,
accuracy=0.1, **kwargs)
class TestAAMeasure(unittest.TestCase):
def setUp(self):
self.nrigid = 10
self.topology = RBTopology()
self.topology.add_sites(
[create_tetrahedron() for _ in range(self.nrigid)])
self.topology.finalize_setup()
self.measure = MeasureAngleAxisCluster(self.topology)
def test_cpp_align(self):
x1 = np.array([random_aa() for _ in range(2 * self.nrigid)]).ravel()
x2 = np.array([random_aa() for _ in range(2 * self.nrigid)]).ravel()
x1_cpp = x1.copy()
x2_cpp = x2.copy()
x1_python = x1.copy()
x2_python = x2.copy()
ret = self.measure._align_pythonic(x1_python, x2_python)
self.assertIsNone(ret)
ret = self.measure.align(x1_cpp, x2_cpp)
self.assertIsNone(ret)
assert_arrays_almost_equal(self, x1_python, x1)
assert_arrays_almost_equal(self, x1_cpp, x1)
# assert that the center of mass coordinates didn't change
assert_arrays_almost_equal(self, x2_python[:3 * self.nrigid],
x2[:3 * self.nrigid])
assert_arrays_almost_equal(self, x2_cpp[:3 * self.nrigid],
x2[:3 * self.nrigid])
# assert that x2 actually changed
max_change = np.max(np.abs(x2_cpp - x2))
self.assertGreater(max_change, 1e-3)
assert_arrays_almost_equal(self, x2_python, x2_cpp)
def test_align_bad_input(self):
x1 = np.array([random_aa() for _ in range(2 * self.nrigid)]).ravel()
x2 = list(x1)
with self.assertRaises(TypeError):
self.measure.align(x1, x2)
def test_symmetries(self):
tet = create_tetrahedron()
print(tet.symmetries)
self.assertEqual(len(tet.symmetries), 12)
def test_align_exact(self):
x1 = np.array([random_aa() for _ in range(2 * self.nrigid)]).ravel()
x2 = x1.copy()
tet = create_tetrahedron()
mx = tet.symmetries[2].copy()
p = x2[-3:].copy()
x2[-3:] = rotations.rotate_aa(rotations.mx2aa(mx), p)
self.measure._align_pythonic(x1, x2)
assert_arrays_almost_equal(self, x1, x2)
class TestAAMeasure(unittest.TestCase):
def setUp(self):
self.nrigid = 10
self.topology = RBTopology()
self.topology.add_sites([create_tetrahedron() for _ in range(self.nrigid)])
self.topology.finalize_setup()
self.measure = MeasureAngleAxisCluster(self.topology)
def test_cpp_align(self):
x1 = np.array([random_aa() for _ in range(2*self.nrigid)]).ravel()
x2 = np.array([random_aa() for _ in range(2*self.nrigid)]).ravel()
x1_cpp = x1.copy()
x2_cpp = x2.copy()
x1_python = x1.copy()
x2_python = x2.copy()
ret = self.measure._align_pythonic(x1_python, x2_python)
self.assertIsNone(ret)
ret = self.measure.align(x1_cpp, x2_cpp)
self.assertIsNone(ret)
assert_arrays_almost_equal(self, x1_python, x1)
assert_arrays_almost_equal(self, x1_cpp, x1)
# assert that the center of mass coordinates didn't change
assert_arrays_almost_equal(self, x2_python[:3*self.nrigid], x2[:3*self.nrigid])
assert_arrays_almost_equal(self, x2_cpp[:3*self.nrigid], x2[:3*self.nrigid])
# assert that x2 actually changed
max_change = np.max(np.abs(x2_cpp - x2))
self.assertGreater(max_change, 1e-3)
assert_arrays_almost_equal(self, x2_python, x2_cpp)
def test_align_bad_input(self):
x1 = np.array([random_aa() for _ in range(2*self.nrigid)]).ravel()
x2 = list(x1)
with self.assertRaises(TypeError):
self.measure.align(x1, x2)
def test_symmetries(self):
tet = create_tetrahedron()
print(tet.symmetries)
self.assertEqual(len(tet.symmetries), 12)
def test_align_exact(self):
x1 = np.array([random_aa() for _ in range(2*self.nrigid)]).ravel()
x2 = x1.copy()
tet = create_tetrahedron()
mx = tet.symmetries[2].copy()
p = x2[-3:].copy()
x2[-3:] = rotations.rotate_aa(rotations.mx2aa(mx), p)
self.measure._align_pythonic(x1, x2)
assert_arrays_almost_equal(self, x1, x2)
def setUp(self):
self.nrigid = 10
self.topology = RBTopology()
self.topology.add_sites([create_tetrahedron() for _ in range(self.nrigid)])
self.topology.finalize_setup()
self.measure = MeasureAngleAxisCluster(self.topology)
