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# 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 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 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)
init_rms = 0.8049844719
self.assertTrue(
float('%.3f' % self.sup.get_init_rms()), float('%.3f' % init_rms))
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)
rms = 0.00304266526014
self.assertEqual(
float('%.3f' % self.sup.get_rms()), float('%.3f' % rms))
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(
[[5.16518846e+01, -1.90018270e+00, 5.00708397e+01],
[5.03977138e+01, -1.22877050e+00, 5.06488200e+01],
[5.06801788e+01, -4.16095666e-02, 5.15368866e+01],
[5.02202228e+01, -1.94372374e-02, 5.28534537e+01]])
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)
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