def setUp1(self, policy):
self.policy = policy
self.natoms = 11
if self.policy.can_permute():
self.permlist = [range(self.natoms)]
else:
self.permlist = None
self.measure = MeasureCartesian(self.permlist)
self.align = AlignClusterSimple(self.policy, self.measure)
self.transform_list = []
if self.policy.can_invert():
self.transform_list.append(utils.invert)
if self.policy.can_translate():
self.transform_list.append(utils.translate_randomly)
if self.policy.can_rotate():
self.transform_list.append(utils.rotate_randomly)
if self.policy.can_permute():
self.transform_list.append(self.permute_randomly)
def setUp1(self, policy):
self.policy = policy
self.natoms = 11
if self.policy.can_permute():
self.permlist = [range(self.natoms)]
else:
self.permlist = None
self.measure = MeasureCartesian(self.permlist)
self.align = AlignClusterSimple(self.policy, self.measure)
self.transform_list = []
if self.policy.can_invert():
self.transform_list.append(utils.invert)
if self.policy.can_translate():
self.transform_list.append(utils.translate_randomly)
if self.policy.can_rotate():
self.transform_list.append(utils.rotate_randomly)
if self.policy.can_permute():
self.transform_list.append(self.permute_randomly)
class TestAlignClusterSimple(unittest.TestCase):
def setUp(self):
policy = TransformPolicyAtomicCluster(can_permute=True,
can_rotate=False,
can_invert=True,
can_translate=True)
self.setUp1(policy)
def setUp1(self, policy):
self.policy = policy
self.natoms = 11
if self.policy.can_permute():
self.permlist = [range(self.natoms)]
else:
self.permlist = None
self.measure = MeasureCartesian(self.permlist)
self.align = AlignClusterSimple(self.policy, self.measure)
self.transform_list = []
if self.policy.can_invert():
self.transform_list.append(utils.invert)
if self.policy.can_translate():
self.transform_list.append(utils.translate_randomly)
if self.policy.can_rotate():
self.transform_list.append(utils.rotate_randomly)
if self.policy.can_permute():
self.transform_list.append(self.permute_randomly)
def permute_randomly(self, x):
utils.permute_randomly(x, self.permlist, self.natoms)
def basic_test(self, x0, x1):
"""find the best alignment and do some basic tests"""
x0bk = x0.copy()
x1bk = x1.copy()
tform = self.align.get_transformation(x0, x1)
# test the passed structures are not altered
self.assertTrue((x0 == x0bk).all())
self.assertTrue((x1 == x1bk).all())
# apply the transformation to x1 and test that distance is not worse
tform.apply(x1)
self.assertLessEqual(self.measure.get_dist(x0, x1),
self.measure.get_dist(x0bk, x1bk) + 1e-10)
def test1(self):
"""align two random configurations"""
x0 = utils.random_configuration(3 * self.natoms)
x1 = utils.random_configuration(3 * self.natoms)
self.basic_test(x0, x1)
def fchain(self, flist):
"""return a function which applies all of the functions in flist to the input"""
def function_chain(x):
for f in reversed(flist):
# print f.__name__
f(x)
return function_chain
def exact_match_test(self, f):
x0 = utils.random_configuration(3 * self.natoms)
x1 = x0.copy()
# apply transformations to x1
f(x1)
self.basic_test(x0, x1)
self.assertLess(self.measure.get_dist(x0, x1), 1e-3)
def test_1(self):
"""run exact_match_test() for all transformations"""
for f in self.transform_list:
self.exact_match_test(f)
def test_2(self):
"""run exact_match_test() on all combinations of length 2 of the transformations
"""
for flist in itertools.product(self.transform_list, repeat=2):
tform = self.fchain(flist)
self.exact_match_test(tform)
def test_3(self):
"""run exact_match_test() on all combinations of length 2 of the transformations
"""
for flist in itertools.product(self.transform_list, repeat=2):
tform = self.fchain(flist)
self.exact_match_test(tform)
def test_4(self):
"""run exact_match_test() on all combinations of length 2 of the transformations
"""
for flist in itertools.product(self.transform_list, repeat=4):
tform = self.fchain(flist)
self.exact_match_test(tform)
def test_10(self):
"""run do_tests() on combinations of length 10 of the transformations
"""
maxiter = 1000
i = 0
for flist in itertools.product(self.transform_list, repeat=10):
tform = self.fchain(flist)
self.exact_match_test(tform)
i += 1
if i > maxiter:
break
class TestAlignClusterSimple(unittest.TestCase):
def setUp(self):
policy = TransformPolicyAtomicCluster(can_permute=True, can_rotate=False, can_invert=True, can_translate=True)
self.setUp1(policy)
def setUp1(self, policy):
self.policy = policy
self.natoms = 11
if self.policy.can_permute():
self.permlist = [range(self.natoms)]
else:
self.permlist = None
self.measure = MeasureCartesian(self.permlist)
self.align = AlignClusterSimple(self.policy, self.measure)
self.transform_list = []
if self.policy.can_invert():
self.transform_list.append(utils.invert)
if self.policy.can_translate():
self.transform_list.append(utils.translate_randomly)
if self.policy.can_rotate():
self.transform_list.append(utils.rotate_randomly)
if self.policy.can_permute():
self.transform_list.append(self.permute_randomly)
def permute_randomly(self, x):
utils.permute_randomly(x, self.permlist, self.natoms)
def basic_test(self, x0, x1):
"""find the best alignment and do some basic tests"""
x0bk = x0.copy()
x1bk = x1.copy()
tform = self.align.get_transformation(x0, x1)
# test the passed structures are not altered
self.assertTrue((x0 == x0bk).all())
self.assertTrue((x1 == x1bk).all())
# apply the transformation to x1 and test that distance is not worse
tform.apply(x1)
self.assertLessEqual(self.measure.get_dist(x0, x1), self.measure.get_dist(x0bk, x1bk) + 1e-10)
def test1(self):
"""align two random configurations"""
x0 = utils.random_configuration(3 * self.natoms)
x1 = utils.random_configuration(3 * self.natoms)
self.basic_test(x0, x1)
def fchain(self, flist):
"""return a function which applies all of the functions in flist to the input"""
def function_chain(x):
for f in reversed(flist):
# print f.__name__
f(x)
return function_chain
def exact_match_test(self, f):
x0 = utils.random_configuration(3 * self.natoms)
x1 = x0.copy()
# apply transformations to x1
f(x1)
self.basic_test(x0, x1)
self.assertLess(self.measure.get_dist(x0, x1), 1e-3)
def test_1(self):
"""run exact_match_test() for all transformations"""
for f in self.transform_list:
self.exact_match_test(f)
def test_2(self):
"""run exact_match_test() on all combinations of length 2 of the transformations
"""
for flist in itertools.product(self.transform_list, repeat=2):
tform = self.fchain(flist)
self.exact_match_test(tform)
def test_3(self):
"""run exact_match_test() on all combinations of length 2 of the transformations
"""
for flist in itertools.product(self.transform_list, repeat=2):
tform = self.fchain(flist)
self.exact_match_test(tform)
def test_4(self):
"""run exact_match_test() on all combinations of length 2 of the transformations
"""
for flist in itertools.product(self.transform_list, repeat=4):
tform = self.fchain(flist)
self.exact_match_test(tform)
def test_10(self):
"""run do_tests() on combinations of length 10 of the transformations
"""
maxiter = 1000
i = 0
for flist in itertools.product(self.transform_list, repeat=10):
tform = self.fchain(flist)
self.exact_match_test(tform)
i += 1
if i > maxiter:
break
