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# Copyright 2017 by Francesco Gastaldello. All rights reserved.
#
# Converted by Francesco Gastaldello from an older unit test copyright 2004
# by Thomas Hamelryck.
#
# 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.StructureAlignment module."""
import unittest
from Bio import Align
from Bio import AlignIO
from Bio.PDB import PDBParser
from Bio.PDB import StructureAlignment
class StructureAlignTests(unittest.TestCase):
"""Test module StructureAlignment."""
def test_StructAlign(self):
"""Tests on module to align two proteins according to a FASTA alignment file."""
p = PDBParser(QUIET=1)
al_file = "PDB/alignment_file.fa"
# Using Bio.AlignIO, which returns a MultipleSeqAlignment object:
with open(al_file) as handle:
records = AlignIO.read(handle, "fasta")
# Using Bio.Align, which returns an Alignment object:
with open(al_file) as handle:
alignment = Align.read(handle, "fasta")
s1 = p.get_structure("1", "PDB/2XHE.pdb")
s2 = p.get_structure("2", "PDB/1A8O.pdb")
m1 = s1[0]
m2 = s2[0]
for argument in (records, alignment):
al = StructureAlignment(argument, m1, m2)
self.assertNotEqual(al.map12, al.map21)
self.assertTrue(len(al.map12), 566)
self.assertTrue(len(al.map21), 70)
chain1_A = m1["A"]
chain2_A = m2["A"]
self.assertEqual(chain1_A[202].get_resname(), "ILE")
self.assertEqual(chain2_A[202].get_resname(), "LEU")
self.assertEqual(chain1_A[291].get_resname(), chain2_A[180].get_resname())
self.assertNotEqual(
chain1_A[291].get_resname(), chain2_A[181].get_resname()
)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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