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|
from unittest import TestCase
from shelxfile.misc.dsrmath import vol_unitcell, distance, dice_coefficient, levenshtein, dice_coefficient2, \
SymmetryElement, Matrix, Array, mean, median, std_dev, nalimov_test, id_generator, atomic_distance, \
almost_equal
from shelxfile.misc.misc import flatten, frac_to_cart, cart_to_frac, determinante, subtract_vect
from shelxfile.shelx.shelx import Shelxfile
class Testdsrmath(TestCase):
def test_vol_unitcell(self):
volume = vol_unitcell(2, 2, 2, 90, 90, 90)
self.assertEqual(8.0, volume)
def test_distance_1(self):
d = distance(1, 1, 1, 2, 2, 2, 4)
self.assertEqual(1.7321, d)
def test_distance_2(self):
d = distance(1, 0, 0, 2, 0, 0, 4)
self.assertEqual(1.0, d)
def test_levenshtein(self):
l = levenshtein('hallo', 'holla')
self.assertEqual(2, l)
def test_dice(self):
d = dice_coefficient('hallo', 'holla')
self.assertEqual(0.25, d)
def test_dice2(self):
self.assertEqual(0.75, dice_coefficient2('hallo', 'holla'))
def test_dice3(self):
self.assertEqual(0.6, dice_coefficient2('Banze', 'Benzene'))
def test_dice4(self):
self.assertEqual(0.333333, dice_coefficient2('halo', 'Haaallo'))
def test_dice5(self):
self.assertEqual(0.2, dice_coefficient2('hallo', 'Haaallo'))
def test_dice6(self):
self.assertEqual(0.0, dice_coefficient2('hallo', 'Hallo'))
def test_dice_7(self):
self.assertEqual(1.0, dice_coefficient2('aaa', 'BBBBB'))
def test_dice_8(self):
self.assertEqual(1.0, dice_coefficient2('', ''))
def test_subtract_vect(self):
self.assertEqual((-2, 0, 1), subtract_vect([1, 2, 3], [3, 2, 2]))
class TestSymmetryElement(TestCase):
def setUp(self) -> None:
self.shx = Shelxfile(debug=True)
self.shx.read_file('tests/resources/p21c.res')
def test_to_shelxl(self):
self.assertEqual('[+X, +Y, +Z, -X, -Y, -Z, -X, 0.5+Y, 0.5-Z, +X, -0.5-Y, -0.5+Z]',
self.shx.symmcards._symmcards.__repr__())
def test_repr(self):
self.assertEqual(SymmetryElement(['-X', '-Y', '-Z']), self.shx.symmcards[1])
def test_string(self):
self.assertEqual("|-1 0 0| | 0.0|\n"
"| 0 1 0| + | 0.5|\n"
"| 0 0 -1| | 0.5|\n", self.shx.symmcards[2].__str__())
def test_equals_false(self):
self.assertEqual(False, self.shx.symmcards[0] == self.shx.symmcards[1])
def test_equals_True(self):
self.assertEqual(True, self.shx.symmcards[1] == self.shx.symmcards[1])
def test_s12_equals(self):
s1 = SymmetryElement(['0.5', '0.5', '0.5'])
s2 = SymmetryElement(['0.5', '0.5', '0.5'])
self.assertEqual(True, s1 == s2)
def test_s12_equals2(self):
s1 = SymmetryElement(['1.5', '1.5', '1.5'])
s2 = SymmetryElement(['0.5', '0.5', '0.5'])
self.assertEqual(True, s1 == s2)
def test_s34_not_equals(self):
s3 = SymmetryElement(['1', '0.5', '0.5'])
s4 = SymmetryElement(['0.5', '0.5', '0.5'])
self.assertEqual(False, s3 == s4)
class TestMatrix(TestCase):
def test_det(self):
m1 = Matrix([[2, 0, 0], [0, 2, 0], [0, 0, 2]])
self.assertEqual(8, m1.det)
def test_norm(self):
m = Matrix([[-4, -3, -2],[-1, 0, 1],[ 2, 3, 4]])
self.assertEqual(7.745966692414834, m.frobenius_norm())
self.assertEqual(7.745966692414834, m.norm)
def test_zero(self):
self.assertEqual("| 0.0000 0.0000 0.0000|\n"
"| 0.0000 0.0000 0.0000|\n"
"| 0.0000 0.0000 0.0000|\n"
"| 0.0000 0.0000 0.0000|\n"
"| 0.0000 0.0000 0.0000|\n", Matrix.zero(5, 3).__repr__())
def test_equal(self):
m1 = Matrix([(1., 2., 3.), (1., 2., 3.), (1., 2., 3.)])
m2 = Matrix([(1, 2, 3), (1, 2, 3), (1, 2, 3)])
self.assertEqual(True, m1 == m2)
def test_equal2(self):
m1 = Matrix([(1, 2, 3), (1, 2, 3), (1, 2, 3)])
m2 = Matrix([(1, 2, 3), (3, 2, 3), (1, 2, 3)])
self.assertEqual(False, m1 == m2)
def test_subtract_matrix_from_matrix(self):
self.assertEqual([[2, 0, -2], [2, 0, -2], [2, 0, 0]],
Matrix([[3, 2, 1], [3, 2, 1], [3, 2, 3]]) - Matrix([[1, 2, 3], [1, 2, 3], [1, 2, 3]]))
def test_transposed(self):
m = Matrix([[1, 2, 3], [1, 2, 3], [1, 2, 3]])
self.assertEqual([(1, 1, 1), (2, 2, 2), (3, 3, 3)], m.transposed.values)
def test_transpose_alt(self):
m = Matrix([[1, 2, 3], [1, 2, 3], [1, 2, 3]])
self.assertEqual([[1, 1, 1], [2, 2, 2], [3, 3, 3]], m.transposed_alt.values)
def test_cholesky(self):
m = Matrix([[25, 15, -5], [15, 18, 0], [-5, 0, 11]])
self.assertEqual(
"| 5.0000 0.0000 0.0000|\n"
"| 3.0000 3.0000 0.0000|\n"
"|-1.0000 1.0000 3.0000|\n", m.cholesky().__repr__())
def test_inversed(self):
self.assertEqual("|-0.8125 0.1250 0.1875|\n"
"| 0.1250 -0.2500 0.1250|\n"
"| 0.5208 0.1250 -0.1458|\n",
Matrix([[1, 2, 3], [4, 1, 6], [7, 8, 9]]).inversed.__repr__())
def test_foo(self):
m = Matrix([[1, 2, 300], [4.1, 4.2, 4.3], [5, 6, 7]])
x = m + m
self.assertEqual("| 2.0000 4.0000 600.0000|\n"
"| 8.2000 8.4000 8.6000|\n"
"|10.0000 12.0000 14.0000|\n", x.__repr__())
m *= 3
self.assertEqual("| 3.0000 6.0000 900.0000|\n"
"|12.3000 12.6000 12.9000|\n"
"|15.0000 18.0000 21.0000|\n", m.__repr__())
def test_getitem(self):
m = Matrix([[2., 2., 3.], [1., 2.2, 3.], [1., 2., 3.]])
self.assertEqual(2.2, m[1, 1])
self.assertEqual(2.2, m[1][1])
def test_matrix_add_matrix(self):
m1 = Matrix([[1, 1, 1], [1, 1, 1], [1, 1, 1]])
m2 = Matrix([[1, 1, 1], [1, 1, 1], [1, 1, 1]])
t1 = m1 + m2
self.assertEqual(
"| 2.0000 2.0000 2.0000|\n"
"| 2.0000 2.0000 2.0000|\n"
"| 2.0000 2.0000 2.0000|\n", t1.__repr__())
t2 = m1 + 0.5
self.assertEqual(
"| 1.5000 1.5000 1.5000|\n"
"| 1.5000 1.5000 1.5000|\n"
"| 1.5000 1.5000 1.5000|\n", t2.__repr__())
def test_matrix_multiply1(self):
m = Matrix([[1, 1, 1], [1, 1, 1], [1, 1, 1]]) * 2
self.assertEqual("| 2.0000 2.0000 2.0000|\n"
"| 2.0000 2.0000 2.0000|\n"
"| 2.0000 2.0000 2.0000|\n", m.__repr__())
def test_matrix_multiply2(self):
m = Matrix([[1, 1, 1], [1, 1, 1], [1, 1, 1]])
m2 = Matrix([[2, 2, 2], [0.5, 0.5, 0.5], [2, 2, 1]])
x = m * m2
self.assertEqual("| 6.0000 1.5000 5.0000|\n"
"| 6.0000 1.5000 5.0000|\n"
"| 6.0000 1.5000 5.0000|\n", x.__repr__())
self.assertEqual("| 1.0000 1.0000 1.0000|\n"
"| 1.0000 1.0000 1.0000|\n"
"| 1.0000 1.0000 1.0000|\n", m.__repr__())
def test_matrix_multiply_array(self):
m = Matrix([[1, 1, 1], [1, 1, 1], [1, 1, 1]])
self.assertEqual(Array([6, 6, 6]), m * Array([2, 2, 2]))
def test_matrix_multiply4(self):
m = Matrix([(0, 1, 0), (-1, -1, 0), (0, 0, 1)])
self.assertEqual(Array([-0.666667, -0.333334, 0.45191]), Array([0.333333, 0.666667, 0.45191]) * m)
class TestArray(TestCase):
def test_add_array_to_array_inplace(self):
a = Array([1, 2, 3, 4.1])
a += a
self.assertEqual(Array([2, 4, 6, 8.2]), a)
def test_add_constant_to_array(self):
a = Array([1, 2, 3, 4.1])
self.assertEqual(Array([5, 6, 7, 8.1]), a + 4)
def test_add_array_to_array(self):
a = Array([1, 2, 3, 4.1])
self.assertEqual(Array([2, 4, 6, 8.2]), a + a)
def test_getitem(self):
a = Array([2, 4, 6, 8.2])
self.assertEqual(4, a[1])
def test_get_item(self):
self.assertEqual(2, Array([1, 2, 3])[1])
def test_multiply_constant_inplace(self):
a = Array([1, 2, 3, 4.1])
a *= 3
self.assertEqual(Array([3, 6, 9, 12.299999999999999]), a)
def test_dot_multiply(self):
a = Array([1, 2, 3, 4.1])
self.assertEqual(30.81, a.dot(a))
def test_multiply_array_with_array(self):
a = Array([1, 2, 3, 4.1])
self.assertEqual(30.81, a * a)
def test_norm(self):
a = Array([1, 2, 3, 4])
self.assertEqual(30, a.norm())
def test_normalized(self):
a = Array([2, 2, 1])
self.assertEqual(3.0, a.normalized())
def test_zero(self):
self.assertEqual(Array([0.0, 0.0, 0.0, 0.0, 0.0]), Array.zero(5))
def test_floor(self):
self.assertEqual(Array([3, 2, 0]), Array([3.634, 2, 0.345]).floor)
def test_cross(self):
a = Array([1, 2, 3])
b = Array([-7, 8, 9])
self.assertEqual(Array([-6, -30, 22]), a.cross(b))
def test_angle(self):
a = Array([1, 0, 1])
b = Array([1, 0, 0])
self.assertEqual(45.0, a.angle(b))
def test_angle_2(self):
va = Array([0.03562, 0.14298, 0.24008]) - Array([0.04402, 0.16614, 0.22275])
vb = Array([0.07078, 0.17382, 0.22106]) - Array([0.04402, 0.16614, 0.22275])
self.assertEqual(120.9401, round(va.angle(vb), 4))
def test_add(self):
a = Array([1, 2, 3])
b = Array([1, 1, 1])
self.assertEqual(Array([2, 3, 4]), a + b)
def test_setitem(self):
a = Array([0, 0, 0])
a[1] = 5
self.assertEqual(Array([0, 5, 0]), a)
def test_multiply(self):
a1 = Array([1, 2, 3])
a2 = Array([1, 2, 3])
self.assertEqual(14, a1 * a2)
def test_subtract(self):
a = Array([1, 2, 3])
b = Array([1, 1, 1])
self.assertEqual(Array([0, 1, 2]), a - b)
self.assertEqual(Array([0, -1, -2]), b - a)
def test_equality(self):
a1 = Array([1, 2, 3, 4])
a2 = Array([1, 2, 3.0, 4.0])
self.assertEqual(True, a1 == a2)
def test_equality_false(self):
a1 = Array([1, 2, 3, 4])
a2 = Array([2, 2, 3.0, 4.0])
self.assertEqual(False, a1 == a2)
class TestMisc(TestCase):
def test_mean(self):
self.assertEqual(2.5, mean([1, 2, 3, 4, 1, 2, 3, 4]))
def test_median1(self):
self.assertEqual(2, median([2]))
def test_median2(self):
self.assertEqual(2.5, median([1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4]))
def test_median3(self):
self.assertEqual(3, median([1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4.1, 1000000]))
def test_median4(self):
with self.assertRaises(ValueError):
median([])
def test_std_dev1(self):
l1 = [1.334, 1.322, 1.345, 1.451, 1.000, 1.434, 1.321, 1.322]
self.assertEqual(0.13797871, round(std_dev(l1), 8))
def test_std_dev2(self):
l2 = [1.234, 1.222, 1.345, 1.451, 2.500, 1.234, 1.321, 1.222]
self.assertEqual(0.43536797, round(std_dev(l2), 8))
def test_std_dev3(self):
l1 = [1.334, 1.322, 1.345, 1.451, 1.000, 1.434, 1.321, 1.322]
self.assertEqual(1.328, median(l1))
self.assertEqual(1.316125, mean(l1))
def test_nalimov_test(self):
data = [1.120, 1.234, 1.224, 1.469, 1.145, 1.222, 1.123, 1.223, 1.2654, 1.221, 1.215]
self.assertEqual([3], nalimov_test(data))
def test_flatten_list(self):
self.assertEqual(['wer', 234, 'brdt5', 'dfg', 21, 34, 5, 'fhg', 4],
flatten([['wer', 234, 'brdt5'], ['dfg'], [[21, 34, 5], ['fhg', 4]]]))
def test_id_generator(self):
self.assertEqual('a', id_generator(1, 'a'))
def test_atomic_distance(self):
cell = [10.5086, 20.9035, 20.5072, 90, 94.13, 90]
coord1 = [-0.186843, 0.282708, 0.526803]
coord2 = [-0.155278, 0.264593, 0.600644]
self.assertEqual(1.5729229943265979, atomic_distance(coord1, coord2, cell))
def test_determinante(self):
m1 = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
self.assertEqual(8, determinante(m1))
def test_almost_equal(self):
self.assertEqual(True, almost_equal(1.0001, 1.0005))
self.assertEqual(False, almost_equal(1.1, 1.0005))
self.assertEqual(False, almost_equal(2, 1))
def test_fractional_to_cartesian(self):
cell = [10.5086, 20.9035, 20.5072, 90, 94.13, 90]
coord1 = [-0.186843, 0.282708, 0.526803]
self.assertEqual([-2.741505423999065, 5.909586678000002, 10.775200700893734], frac_to_cart(coord1, cell))
def test_cart_to_frac(self):
cell = [10.5086, 20.9035, 20.5072, 90, 94.13, 90]
coords = [-2.74150542399906, 5.909586678, 10.7752007008937]
self.assertEqual((-0.1868429999999998, 0.28270799999999996, 0.5268029999999984), cart_to_frac(coords, cell))
|
