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 TestAATransform(unittest.TestCase):
def setUp(self):
self.nrigid = 10
self.topology = RBTopology()
self.topology.add_sites([create_water() for _ in range(self.nrigid)])
self.topology.finalize_setup()
self.transform = TransformAngleAxisCluster(self.topology)
def test_cpp_rotate(self):
x0 = np.array([random_aa() for _ in range(2*self.nrigid)]).ravel()
aa = random_aa()
mx = aa2mx(aa)
x0_rotated = x0.copy()
self.transform.rotate(x0_rotated, mx)
x0_rotated_python = x0.copy()
self.transform._rotate_python(x0_rotated_python, mx)
assert_arrays_almost_equal(self, x0_rotated, x0_rotated_python)
mx_reverse = aa2mx(-aa)
self.transform.rotate(x0_rotated, mx_reverse)
assert_arrays_almost_equal(self, x0, x0_rotated)
class TestAATransform(unittest.TestCase):
def setUp(self):
self.nrigid = 10
self.topology = RBTopology()
self.topology.add_sites([create_water() for _ in range(self.nrigid)])
self.topology.finalize_setup()
self.transform = TransformAngleAxisCluster(self.topology)
def test_cpp_rotate(self):
x0 = np.array([random_aa() for _ in range(2 * self.nrigid)]).ravel()
aa = random_aa()
mx = aa2mx(aa)
x0_rotated = x0.copy()
self.transform.rotate(x0_rotated, mx)
x0_rotated_python = x0.copy()
self.transform._rotate_python(x0_rotated_python, mx)
assert_arrays_almost_equal(self, x0_rotated, x0_rotated_python)
mx_reverse = aa2mx(-aa)
self.transform.rotate(x0_rotated, mx_reverse)
assert_arrays_almost_equal(self, x0, x0_rotated)
def setUp(self):
self.nrigid = 10
self.topology = RBTopology()
self.topology.add_sites([create_water() for _ in range(self.nrigid)])
self.topology.finalize_setup()
self.transform = TransformAngleAxisCluster(self.topology)
def setUp(self):
self.nrigid = 10
self.topology = RBTopology()
self.topology.add_sites([create_water() for _ in range(self.nrigid)])
self.topology.finalize_setup()
self.transform = TransformAngleAxisCluster(self.topology)