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0b41684f14
Addresses a bug in the code that caused the Newton-Raphson optimization to quit earlier than it should, resulting in poorer alignments.
112 lines
3.5 KiB
Python
112 lines
3.5 KiB
Python
# Copyright 2022 by Joao Rodrigues. All rights reserved.
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#
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# This file is part of the Biopython distribution and governed by your
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# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
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# Please see the LICENSE file that should have been included as part of this
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# package.
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"""Unit tests for the Bio.PDB.CEAligner 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.PDB."
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) from None
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from Bio.PDB import CEAligner
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from Bio.PDB import MMCIFParser
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class CEAlignerTests(unittest.TestCase):
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"""Test CEAligner class."""
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@staticmethod
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def _get_ca_coords_as_array(structure):
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xyz_list = [a.coord for a in structure.get_atoms() if a.name == "CA"]
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return np.asarray(xyz_list, dtype=np.float64)
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def test_cealigner(self):
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"""Test aligning 7CFN on 6WQA."""
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ref = "PDB/6WQA.cif"
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mob = "PDB/7CFN.cif"
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result = "PDB/7CFN_aligned.cif"
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parser = MMCIFParser(QUIET=1)
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s1 = parser.get_structure("6wqa", ref)
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s2 = parser.get_structure("7cfn", mob)
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aligner = CEAligner()
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aligner.set_reference(s1)
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aligner.align(s2, final_optimization=False)
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self.assertAlmostEqual(aligner.rms, 3.83, places=2)
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# Assert the transformation was done right by comparing
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# the moved coordinates to a 'ground truth' reference.
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# Reference obtained with Pymol's CEAlign code.
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refe = parser.get_structure("7cfn_aligned", result)
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refe_coords = self._get_ca_coords_as_array(refe)
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s2_f_coords = self._get_ca_coords_as_array(s2)
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diff = refe_coords - s2_f_coords
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rmsd = np.sqrt((diff * diff).sum() / len(refe_coords))
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self.assertAlmostEqual(rmsd, 0.0, places=2)
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def test_cealigner_no_transform(self):
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"""Test aligning 7CFN on 6WQA without transforming 7CFN."""
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ref = "PDB/6WQA.cif"
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mob = "PDB/7CFN.cif"
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parser = MMCIFParser(QUIET=1)
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s1 = parser.get_structure("6wqa", ref)
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s2 = parser.get_structure("7cfn", mob)
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s2_original_coords = [list(a.coord) for a in s2.get_atoms()]
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aligner = CEAligner()
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aligner.set_reference(s1)
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aligner.align(s2, transform=False, final_optimization=False)
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s2_coords_final = [list(a.coord) for a in s2.get_atoms()]
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self.assertAlmostEqual(aligner.rms, 3.83, places=2)
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self.assertEqual(s2_original_coords, s2_coords_final)
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def test_ce_aligner_final_optimization(self):
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"""Test aligning 7CFN on 6WQA with the final optimization."""
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ref = "PDB/6WQA.cif"
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mob = "PDB/7CFN.cif"
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parser = MMCIFParser(QUIET=1)
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s1 = parser.get_structure("6wqa", ref)
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s2 = parser.get_structure("7cfn", mob)
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aligner = CEAligner()
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aligner.set_reference(s1)
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aligner.align(s2)
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self.assertAlmostEqual(aligner.rms, 3.75, places=2)
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def test_cealigner_nucleic(self):
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"""Test aligning 1LCD on 1LCD."""
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ref = "PDB/1LCD.cif"
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mob = "PDB/1LCD.cif"
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parser = MMCIFParser(QUIET=1)
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s1 = parser.get_structure("1lcd_ref", ref)
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s2 = parser.get_structure("1lcd_mob", mob)
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aligner = CEAligner()
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aligner.set_reference(s1)
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aligner.align(s2)
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self.assertAlmostEqual(aligner.rms, 0.0, places=3)
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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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