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$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
155 lines
4.8 KiB
Python
155 lines
4.8 KiB
Python
# Copyright 2017 by Maximilian Greil. All rights reserved.
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Tests for QCPSuperimposer module."""
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import unittest
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try:
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import numpy as np
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except ImportError:
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from Bio import MissingPythonDependencyError
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raise MissingPythonDependencyError(
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"Install NumPy if you want to use Bio.QCPSuperimposer."
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) from None
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from Bio.PDB import PDBParser
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from Bio.PDB import Selection
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from Bio.PDB.qcprot import QCPSuperimposer
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from Bio.SVDSuperimposer import SVDSuperimposer
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class QCPSuperimposerTest(unittest.TestCase):
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def setUp(self):
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self.x = np.array(
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[
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[51.65, -1.90, 50.07],
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[50.40, -1.23, 50.65],
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[50.68, -0.04, 51.54],
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[50.22, -0.02, 52.85],
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]
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)
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self.y = np.array(
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[
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[51.30, -2.99, 46.54],
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[51.09, -1.88, 47.58],
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[52.36, -1.20, 48.03],
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[52.71, -1.18, 49.38],
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]
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)
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# Public methods
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def test_set(self):
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"""Test setting of initial parameters."""
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sup = QCPSuperimposer()
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sup.set(self.x, self.y)
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self.assertTrue(np.allclose(sup.reference_coords, self.x, atol=1e-6))
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self.assertTrue(np.allclose(sup.coords, self.y, atol=1e-6))
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self.assertIsNone(sup.transformed_coords)
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self.assertIsNone(sup.rot)
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self.assertIsNone(sup.tran)
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self.assertIsNone(sup.rms)
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self.assertIsNone(sup.init_rms)
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def test_run(self):
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"""Test QCP on dummy data."""
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sup = QCPSuperimposer()
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sup.set(self.x, self.y)
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sup.run()
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self.assertTrue(np.allclose(sup.reference_coords, self.x, atol=1e-6))
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self.assertTrue(np.allclose(sup.coords, self.y, atol=1e-6))
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self.assertIsNone(sup.transformed_coords)
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calc_rot = [
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[0.683, 0.537, 0.495],
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[-0.523, 0.833, -0.181],
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[-0.510, -0.135, 0.849],
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]
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calc_tran = [38.786, -20.655, -15.422]
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self.assertTrue(np.allclose(np.array(calc_rot), sup.rot, atol=1e-3))
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self.assertTrue(np.allclose(np.array(calc_tran), sup.tran, atol=1e-3))
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# We can reduce precision here since we do a similar calculation
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# for a full structure down below.
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self.assertAlmostEqual(sup.rms, 0.003, places=3)
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self.assertIsNone(sup.init_rms)
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def test_compare_to_svd(self):
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"""Compare results of QCP to SVD."""
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sup = QCPSuperimposer()
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sup.set(self.x, self.y)
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sup.run()
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svd_sup = SVDSuperimposer()
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svd_sup.set(self.x, self.y)
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svd_sup.run()
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self.assertAlmostEqual(svd_sup.get_rms(), sup.rms, places=3)
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self.assertTrue(np.allclose(svd_sup.rot, sup.rot, atol=1e-3))
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self.assertTrue(np.allclose(svd_sup.tran, sup.tran, atol=1e-3))
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self.assertTrue(
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np.allclose(svd_sup.get_transformed(), sup.get_transformed(), atol=1e-3)
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)
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def test_get_transformed(self):
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"""Test transformation of coordinates after QCP."""
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sup = QCPSuperimposer()
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sup.set(self.x, self.y)
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sup.run()
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transformed_coords = [
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[51.652, -1.900, 50.071],
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[50.398, -1.229, 50.649],
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[50.680, -0.042, 51.537],
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[50.220, -0.019, 52.853],
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]
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self.assertTrue(
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np.allclose(sup.get_transformed(), np.array(transformed_coords), atol=1e-3)
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)
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def test_get_init_rms(self):
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"""Test initial RMS calculation."""
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x = np.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]])
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y = np.array([[2.0, 0.0, 0.0], [1.0, 1.0, 0.0], [1.0, 0.0, 1.0]])
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sup = QCPSuperimposer()
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sup.set(x, y)
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self.assertIsNone(sup.init_rms)
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expected_init_rms = 1.0
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self.assertAlmostEqual(sup.get_init_rms(), expected_init_rms, places=6)
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def test_on_pdb(self):
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"""Align a PDB to itself."""
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pdb1 = "PDB/1A8O.pdb"
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p = PDBParser()
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s1 = p.get_structure("FIXED", pdb1)
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fixed = Selection.unfold_entities(s1, "A")
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s2 = p.get_structure("MOVING", pdb1)
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moving = Selection.unfold_entities(s2, "A")
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rot = np.eye(3, dtype=np.float64)
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tran = np.array([1.0, 2.0, 3.0], dtype=np.float64)
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for atom in moving:
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atom.transform(rot, tran)
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sup = QCPSuperimposer()
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sup.set_atoms(fixed, moving)
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self.assertTrue(np.allclose(sup.rotran[0], rot, atol=1e-3))
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self.assertTrue(np.allclose(sup.rotran[1], -tran, atol=1e-3))
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self.assertAlmostEqual(sup.rms, 0.0, places=6)
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if __name__ == "__main__":
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runner = unittest.TextTestRunner(verbosity=2)
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unittest.main(testRunner=runner)
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