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))