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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.
"""Tests for QCPSuperimposer module."""
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."
) from None
try:
from Bio.PDB.QCPSuperimposer import QCPSuperimposer
except ImportError:
from Bio import MissingExternalDependencyError
raise MissingExternalDependencyError(
"C module in Bio.PDB.QCPSuperimposer not compiled"
) from None
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)
|
