# 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)