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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:
import numpy as np
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install NumPy if you want to use Bio.QCPSuperimposer."
) from None
from Bio.PDB import PDBParser
from Bio.PDB import Selection
from Bio.PDB.qcprot import QCPSuperimposer
from Bio.SVDSuperimposer import SVDSuperimposer
class QCPSuperimposerTest(unittest.TestCase):
def setUp(self):
self.x = np.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 = np.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],
]
)
# Public methods
def test_set(self):
"""Test setting of initial parameters."""
sup = QCPSuperimposer()
sup.set(self.x, self.y)
self.assertTrue(np.allclose(sup.reference_coords, self.x, atol=1e-6))
self.assertTrue(np.allclose(sup.coords, self.y, atol=1e-6))
self.assertIsNone(sup.transformed_coords)
self.assertIsNone(sup.rot)
self.assertIsNone(sup.tran)
self.assertIsNone(sup.rms)
self.assertIsNone(sup.init_rms)
def test_run(self):
"""Test QCP on dummy data."""
sup = QCPSuperimposer()
sup.set(self.x, self.y)
sup.run()
self.assertTrue(np.allclose(sup.reference_coords, self.x, atol=1e-6))
self.assertTrue(np.allclose(sup.coords, self.y, atol=1e-6))
self.assertIsNone(sup.transformed_coords)
calc_rot = [
[0.683, 0.537, 0.495],
[-0.523, 0.833, -0.181],
[-0.510, -0.135, 0.849],
]
calc_tran = [38.786, -20.655, -15.422]
self.assertTrue(np.allclose(np.array(calc_rot), sup.rot, atol=1e-3))
self.assertTrue(np.allclose(np.array(calc_tran), sup.tran, atol=1e-3))
# We can reduce precision here since we do a similar calculation
# for a full structure down below.
self.assertAlmostEqual(sup.rms, 0.003, places=3)
self.assertIsNone(sup.init_rms)
def test_compare_to_svd(self):
"""Compare results of QCP to SVD."""
sup = QCPSuperimposer()
sup.set(self.x, self.y)
sup.run()
svd_sup = SVDSuperimposer()
svd_sup.set(self.x, self.y)
svd_sup.run()
self.assertAlmostEqual(svd_sup.get_rms(), sup.rms, places=3)
self.assertTrue(np.allclose(svd_sup.rot, sup.rot, atol=1e-3))
self.assertTrue(np.allclose(svd_sup.tran, sup.tran, atol=1e-3))
self.assertTrue(
np.allclose(svd_sup.get_transformed(), sup.get_transformed(), atol=1e-3)
)
def test_get_transformed(self):
"""Test transformation of coordinates after QCP."""
sup = QCPSuperimposer()
sup.set(self.x, self.y)
sup.run()
transformed_coords = [
[51.652, -1.900, 50.071],
[50.398, -1.229, 50.649],
[50.680, -0.042, 51.537],
[50.220, -0.019, 52.853],
]
self.assertTrue(
np.allclose(sup.get_transformed(), np.array(transformed_coords), atol=1e-3)
)
def test_get_init_rms(self):
"""Test initial RMS calculation."""
x = np.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]])
y = np.array([[2.0, 0.0, 0.0], [1.0, 1.0, 0.0], [1.0, 0.0, 1.0]])
sup = QCPSuperimposer()
sup.set(x, y)
self.assertIsNone(sup.init_rms)
expected_init_rms = 1.0
self.assertAlmostEqual(sup.get_init_rms(), expected_init_rms, places=6)
def test_on_pdb(self):
"""Align a PDB to itself."""
pdb1 = "PDB/1A8O.pdb"
p = PDBParser()
s1 = p.get_structure("FIXED", pdb1)
fixed = Selection.unfold_entities(s1, "A")
s2 = p.get_structure("MOVING", pdb1)
moving = Selection.unfold_entities(s2, "A")
rot = np.eye(3, dtype=np.float64)
tran = np.array([1.0, 2.0, 3.0], dtype=np.float64)
for atom in moving:
atom.transform(rot, tran)
sup = QCPSuperimposer()
sup.set_atoms(fixed, moving)
self.assertTrue(np.allclose(sup.rotran[0], rot, atol=1e-3))
self.assertTrue(np.allclose(sup.rotran[1], -tran, atol=1e-3))
self.assertAlmostEqual(sup.rms, 0.0, places=6)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
