mirror of
https://github.com/biopython/biopython.git
synced 2025-10-20 21:53:47 +08:00
de0bb21fb3
$ 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
60 lines
2.1 KiB
Python
60 lines
2.1 KiB
Python
# 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)
|