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
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
|
# 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.
import unittest
try:
from numpy import array
from numpy import dot # missing in old PyPy's micronumpy
from numpy import around
from numpy import array_equal
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install NumPy if you want to use Bio.QCPSuperimposer.")
try:
from Bio.PDB.QCPSuperimposer import QCPSuperimposer
except ImportError:
from Bio import MissingExternalDependencyError
raise MissingExternalDependencyError(
"C module in Bio.QCPSuperimposer not compiled")
class QCPSuperimposerTest(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 = QCPSuperimposer()
self.sup.set(self.x, self.y)
# Public methods
def test_set(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.transformed_coords)
self.assertIsNone(self.sup.rot)
self.assertIsNone(self.sup.tran)
self.assertIsNone(self.sup.rms)
self.assertIsNone(self.sup.init_rms)
def test_run(self):
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)))
self.assertIsNone(self.sup.transformed_coords)
calc_rot = array([[0.68304939, -0.5227742, -0.51004967],
[0.53664482, 0.83293151, -0.13504605],
[0.49543503, -0.18147239, 0.84947743]])
self.assertTrue(
array_equal(around(self.sup.rot, decimals=3), around(calc_rot, decimals=3)))
calc_tran = array([-7.43885125, 36.51522275, 36.81135533])
self.assertTrue(
array_equal(around(self.sup.tran, decimals=3), around(calc_tran, decimals=3)))
calc_rms = 0.003
self.assertEqual(float('%.3f' % self.sup.rms), calc_rms)
self.assertIsNone(self.sup.init_rms)
def test_get_transformed(self):
self.sup.run()
transformed_coords = array([[49.05456082, -1.23928381, 50.58427566],
[50.02204971, -0.39367917, 51.42494181],
[51.47738545, -0.57287128, 51.06760944],
[52.39602307, -0.98417088, 52.03318837]])
self.assertTrue(
array_equal(around(self.sup.get_transformed(), decimals=3), around(transformed_coords, decimals=3)))
def test_get_init_rms(self):
x = array([[1.1, 1.2, 1.3],
[1.4, 1.5, 1.6],
[1.7, 1.8, 1.9]])
y = array([[1.0, 1.0, 1.0],
[1.0, 1.0, 1.0],
[1.0, 1.0, 1.0]])
self.sup.set(x, y)
self.assertIsNone(self.sup.init_rms)
init_rms = array([0.81, 0.9, 0.98])
self.assertTrue(
array_equal(around(self.sup.get_init_rms(), decimals=2), around(init_rms, decimals=2)))
def test_get_rotran(self):
self.sup.run()
calc_rot = array([[0.68304939, -0.5227742, -0.51004967],
[0.53664482, 0.83293151, -0.13504605],
[0.49543503, -0.18147239, 0.84947743]])
calc_tran = array([-7.43885125, 36.51522275, 36.81135533])
rot, tran = self.sup.get_rotran()
self.assertTrue(
array_equal(around(rot, decimals=3), around(calc_rot, decimals=3)))
self.assertTrue(
array_equal(around(tran, decimals=3), around(calc_tran, decimals=3)))
def test_get_rms(self):
self.sup.run()
calc_rms = 0.003
self.assertEqual(float('%.3f' % self.sup.get_rms()), calc_rms)
# Old test from Bio/PDB/QCPSuperimposer/__init__.py
def test_oldTest(self):
x = array([[-2.803, -15.373, 24.556],
[0.893, -16.062, 25.147],
[1.368, -12.371, 25.885],
[-1.651, -12.153, 28.177],
[-0.440, -15.218, 30.068],
[2.551, -13.273, 31.372],
[0.105, -11.330, 33.567]])
y = array([[-14.739, -18.673, 15.040],
[-12.473, -15.810, 16.074],
[-14.802, -13.307, 14.408],
[-17.782, -14.852, 16.171],
[-16.124, -14.617, 19.584],
[-15.029, -11.037, 18.902],
[-18.577, -10.001, 17.996]])
self.sup.set(x, y)
self.assertTrue(
array_equal(around(self.sup.reference_coords, decimals=3), around(x, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3), around(y, decimals=3)))
self.sup.run()
rot = array([[0.72216358, 0.69118937, -0.0271479],
[-0.52038257, 0.51700833, -0.67963547],
[-0.45572112, 0.50493528, 0.73304748]])
tran = array([11.68878393, -4.13245037, 6.05208344])
rms = 0.7191064509622271
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.assertEqual(float('%.3f' % self.sup.rms), around(rms, decimals=3))
rms_get = self.sup.get_rms()
self.assertTrue(
array_equal(around(rms_get, decimals=3), around(rms, decimals=3)))
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(y, rot) + tran
y_x_solution = array([[3.90787281, -16.37976032, 30.16808376],
[3.58322456, -12.81122728, 28.91874135],
[1.3580194, -13.96815768, 26.05958411],
[-0.79347336, -15.93647897, 28.48288439],
[-1.27379224, -12.9456459, 30.78004989],
[-2.03519089, -10.6822696, 27.81728956],
[-4.72366028, -13.05646024, 26.54536695]])
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)
|
