def test_get_add_sums(self):
sum_list = []
for dummy in range(100):
overfit_obj = overfit.Overfit()
overfit_obj1 = overfit.Overfit()
part_list = []
for point1, point2 in zip(self.points1, self.points2):
if random.choice([True, False]):
sums = overfit_obj.get_sums()
overfit_obj = overfit.Overfit()
overfit_obj.add_sums(sums)
part_list.append(overfit_obj1.get_sums())
overfit_obj1 = overfit.Overfit()
overfit_obj.add_point(point1, point2)
overfit_obj1.add_point(point1, point2)
part_list.append(overfit_obj1.get_sums())
sum_list.append(overfit_obj.get_sums())
assert_sums_equal(self, sum_list[-1],
functools.reduce(operator.add, part_list))
for sums1, sums2 in zip(sum_list, sum_list[1:]):
assert_sums_equal(self, sums1, sums2)
def test_add_mer(self):
for dummy in range(10):
overfit_obj1 = overfit.Overfit()
overfit_obj2 = overfit.Overfit()
for dummy in range(100):
struct = random.choice(self.structs)
mer = random.choice(list(struct))
overfit_obj1.add_mer(mer, mer)
for point in mer.representation:
overfit_obj2.add_point(point, point)
sums1 = overfit_obj1.get_sums()
sums2 = overfit_obj2.get_sums()
assert_sums_equal(self, sums1, sums2)
def test_add_struct(self):
for dummy in range(10):
overfit_obj1 = overfit.Overfit()
overfit_obj2 = overfit.Overfit()
for dummy in range(100):
struct1, struct2 = random.sample(self.structs, 2)
seg_len = random.randint(5, 20)
try:
start1 = random.choice(list(struct1[0:-seg_len]))
start2 = random.choice(list(struct2[0:-seg_len]))
sub1 = struct1[start1.ind:start1.ind + seg_len]
sub2 = struct2[start2.ind:start2.ind + seg_len]
except:
continue
will_fail = False
for mer1, mer2 in zip(*map(list, [sub1, sub2])):
if len(mer1.indicators) == len(mer2.indicators):
overfit_obj2.add_mer(mer1, mer2)
else:
self.assertRaises(TypeError, overfit_obj2.add_mer,
mer1, mer2)
will_fail = True
if will_fail:
self.assertRaises(TypeError, overfit_obj1.add_structure,
sub1, sub2)
break
overfit_obj1.add_structure(sub1, sub2)
sums1 = overfit_obj1.get_sums()
sums2 = overfit_obj2.get_sums()
assert_sums_equal(self, sums1, sums2)
def test_geom_center(self):
for dummy in range(10):
n_points = random.randint(3, 50)
point_list1 = [
self.points1[n] for n in random.sample(range(100), n_points)
]
point_list2 = [
self.points2[n] for n in random.sample(range(100), n_points)
]
overfit_obj = overfit.Overfit()
overfit_obj.add(point_list1, point_list2)
dummy_rmsd, mat = overfit_obj.overfit()
center1, center2 = [[
sum(map(operator.itemgetter(pos), plist)) / n_points
for pos in range(3)
] for plist in (point_list1, point_list2)]
map(functools.partial(self.assertAlmostEqual, places=4), center1,
mat.transform(*center2))
def test_identity(self):
for dummy in range(10):
point_list = [
self.points1[n]
for n in random.sample(range(100), random.randint(3, 50))
]
overfit_obj = overfit.Overfit()
overfit_obj.add(point_list, point_list)
rmsd, mat = overfit_obj.overfit()
self.assertAlmostEqual(rmsd, 0, places=3)
one = geometry.TRTMatrix()
map(self.assertAlmostEqual,
itertools.chain(*mat.rotation_matrix.tolist()),
itertools.chain(*one.rotation_matrix.tolist()))
map(self.assertAlmostEqual,
mat.prerotational_translation_vector.tolist(),
one.prerotational_translation_vector.tolist())
map(self.assertAlmostEqual, mat.translation_vector.tolist(),
one.translation_vector.tolist())
def test_rmsd(self):
for dummy in range(10):
n_points = random.randint(3, 50)
point_list1 = [
self.points1[n] for n in random.sample(range(100), n_points)
]
point_list2 = [
self.points2[n] for n in random.sample(range(100), n_points)
]
overfit_obj = overfit.Overfit()
overfit_obj.add(point_list1, point_list2)
rmsd, mat = overfit_obj.overfit()
rmsd1, mat1 = overfit.overfit(point_list1, point_list2)
self.assertAlmostEqual(rmsd, rmsd1)
map(self.assertAlmostEqual,
itertools.chain(*mat.rotation_matrix.tolist()),
itertools.chain(*mat1.rotation_matrix.tolist()))
map(self.assertAlmostEqual, mat.prerotational_translation_vector,
mat1.prerotational_translation_vector)
map(self.assertAlmostEqual, mat.translation_vector,
mat1.translation_vector)
sqr = lambda x: x**2
dist2 = lambda point1, point2: sum(
[sqr(c1 - c2) for c1, c2 in zip(point1, point2)])
myrmsd = math.sqrt(
sum(
map(dist2, point_list1,
[mat.transform(*p) for p in point_list2])) / n_points)
self.assertAlmostEqual(rmsd, myrmsd, places=3)
def test_zero(self):
overfit_obj = overfit.Overfit()
sums = overfit_obj.get_sums()
assert_sums_equal(self, sums, overfit.t_overfit_sums())
def test_init(self):
overfit.Overfit()