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# Copyright 2022 by Joao Rodrigues. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Unit tests for the Bio.PDB.CEAligner module."""
import unittest
try:
import numpy as np
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install NumPy if you want to use Bio.PDB."
) from None
from Bio.PDB import CEAligner
from Bio.PDB import MMCIFParser
class CEAlignerTests(unittest.TestCase):
"""Test CEAligner class."""
@staticmethod
def _get_ca_coords_as_array(structure):
xyz_list = [a.coord for a in structure.get_atoms() if a.name == "CA"]
return np.asarray(xyz_list, dtype=np.float64)
def test_cealigner(self):
"""Test aligning 7CFN on 6WQA."""
ref = "PDB/6WQA.cif"
mob = "PDB/7CFN.cif"
result = "PDB/7CFN_aligned.cif"
parser = MMCIFParser(QUIET=1)
s1 = parser.get_structure("6wqa", ref)
s2 = parser.get_structure("7cfn", mob)
aligner = CEAligner()
aligner.set_reference(s1)
aligner.align(s2, final_optimization=False)
self.assertAlmostEqual(aligner.rms, 3.74, places=2)
# Assert the transformation was done right by comparing
# the moved coordinates to a 'ground truth' reference.
# Reference obtained with Pymol's CEAlign code.
refe = parser.get_structure("7cfn_aligned", result)
refe_coords = self._get_ca_coords_as_array(refe)
s2_f_coords = self._get_ca_coords_as_array(s2)
diff = refe_coords - s2_f_coords
rmsd = np.sqrt((diff * diff).sum() / len(refe_coords))
self.assertTrue(rmsd < 0.5)
def test_cealigner_no_transform(self):
"""Test aligning 7CFN on 6WQA without transforming 7CFN."""
ref = "PDB/6WQA.cif"
mob = "PDB/7CFN.cif"
parser = MMCIFParser(QUIET=1)
s1 = parser.get_structure("6wqa", ref)
s2 = parser.get_structure("7cfn", mob)
s2_original_coords = [list(a.coord) for a in s2.get_atoms()]
aligner = CEAligner()
aligner.set_reference(s1)
aligner.align(s2, transform=False, final_optimization=False)
s2_coords_final = [list(a.coord) for a in s2.get_atoms()]
self.assertAlmostEqual(aligner.rms, 3.74, places=2)
self.assertEqual(s2_original_coords, s2_coords_final)
def test_ce_aligner_final_optimization(self):
"""Test aligning 7CFN on 6WQA with the final optimization."""
ref = "PDB/6WQA.cif"
mob = "PDB/7CFN.cif"
parser = MMCIFParser(QUIET=1)
s1 = parser.get_structure("6wqa", ref)
s2 = parser.get_structure("7cfn", mob)
aligner = CEAligner()
aligner.set_reference(s1)
aligner.align(s2)
self.assertAlmostEqual(aligner.rms, 3.66, places=2)
def test_cealigner_nucleic(self):
"""Test aligning 1LCD on 1LCD."""
ref = "PDB/1LCD.cif"
mob = "PDB/1LCD.cif"
parser = MMCIFParser(QUIET=1)
s1 = parser.get_structure("1lcd_ref", ref)
s2 = parser.get_structure("1lcd_mob", mob)
aligner = CEAligner()
aligner.set_reference(s1)
aligner.align(s2)
self.assertAlmostEqual(aligner.rms, 0.0, places=3)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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