1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
|
# Copyright 2017 by Maximilian Greil. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Tests for SVDSuperimposer module."""
import unittest
try:
from numpy import array
from numpy import dot # missing in old PyPy's micronumpy
from numpy import array_equal
from numpy import around
from numpy.linalg import svd, det # Missing in PyPy 2.0 numpypy
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install NumPy if you want to use Bio.SVDSuperimposer."
) from None
from Bio.SVDSuperimposer import SVDSuperimposer
class SVDSuperimposerTest(unittest.TestCase):
def setUp(self):
self.x = array(
[
[51.65, -1.90, 50.07],
[50.40, -1.23, 50.65],
[50.68, -0.04, 51.54],
[50.22, -0.02, 52.85],
]
)
self.y = array(
[
[51.30, -2.99, 46.54],
[51.09, -1.88, 47.58],
[52.36, -1.20, 48.03],
[52.71, -1.18, 49.38],
]
)
self.sup = SVDSuperimposer()
self.sup.set(self.x, self.y)
def test_get_init_rms(self):
x = array([[1.19, 1.28, 1.37], [1.46, 1.55, 1.64], [1.73, 1.82, 1.91]])
y = array([[1.91, 1.82, 1.73], [1.64, 1.55, 1.46], [1.37, 1.28, 1.19]])
self.sup.set(x, y)
self.assertIsNone(self.sup.init_rms)
self.assertAlmostEqual(self.sup.get_init_rms(), 0.8049844719)
def test_oldTest(self):
self.assertTrue(
array_equal(
around(self.sup.reference_coords, decimals=3),
around(self.x, decimals=3),
)
)
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3), around(self.y, decimals=3))
)
self.assertIsNone(self.sup.rot)
self.assertIsNone(self.sup.tran)
self.assertIsNone(self.sup.rms)
self.assertIsNone(self.sup.init_rms)
self.sup.run()
self.assertTrue(
array_equal(
around(self.sup.reference_coords, decimals=3),
around(self.x, decimals=3),
)
)
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3), around(self.y, decimals=3))
)
rot = array(
[
[0.68304983, 0.53664371, 0.49543563],
[-0.52277295, 0.83293229, -0.18147242],
[-0.51005037, -0.13504564, 0.84947707],
]
)
tran = array([38.78608157, -20.65451334, -15.42227366])
self.assertTrue(
array_equal(around(self.sup.rot, decimals=3), around(rot, decimals=3))
)
self.assertTrue(
array_equal(around(self.sup.tran, decimals=3), around(tran, decimals=3))
)
self.assertIsNone(self.sup.rms)
self.assertIsNone(self.sup.init_rms)
self.assertAlmostEqual(self.sup.get_rms(), 0.00304266526014)
rot_get, tran_get = self.sup.get_rotran()
self.assertTrue(
array_equal(around(rot_get, decimals=3), around(rot, decimals=3))
)
self.assertTrue(
array_equal(around(tran_get, decimals=3), around(tran, decimals=3))
)
y_on_x1 = dot(self.y, rot) + tran
y_x_solution = array(
[
[5.16518846e01, -1.90018270e00, 5.00708397e01],
[5.03977138e01, -1.22877050e00, 5.06488200e01],
[5.06801788e01, -4.16095666e-02, 5.15368866e01],
[5.02202228e01, -1.94372374e-02, 5.28534537e01],
]
)
self.assertTrue(
array_equal(around(y_on_x1, decimals=3), around(y_x_solution, decimals=3))
)
y_on_x2 = self.sup.get_transformed()
self.assertTrue(
array_equal(around(y_on_x2, decimals=3), around(y_x_solution, decimals=3))
)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
