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
190 lines
6.7 KiB
Python
190 lines
6.7 KiB
Python
# Copyright 2017 by Francesco Gastaldello. All rights reserved.
|
|
# Revisions copyright 2020 Joao Rodrigues. 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.Polypeptide module."""
|
|
|
|
import unittest
|
|
|
|
from Bio.PDB import CaPPBuilder
|
|
from Bio.PDB import PDBParser
|
|
from Bio.PDB import PPBuilder
|
|
from Bio.Seq import Seq
|
|
|
|
|
|
class PolypeptideTests(unittest.TestCase):
|
|
"""Test Polypeptide module."""
|
|
|
|
@classmethod
|
|
def setUpClass(self):
|
|
pdb1 = "PDB/1A8O.pdb"
|
|
self.parser = PDBParser(PERMISSIVE=True)
|
|
self.structure = self.parser.get_structure("scr", pdb1)
|
|
|
|
def test_ppbuilder_real(self):
|
|
"""Test PPBuilder on real PDB file."""
|
|
ppb = PPBuilder()
|
|
pp = ppb.build_peptides(self.structure)
|
|
|
|
self.assertEqual(len(pp), 3)
|
|
|
|
# Check termini
|
|
self.assertEqual(pp[0][0].get_id()[1], 152)
|
|
self.assertEqual(pp[0][-1].get_id()[1], 184)
|
|
self.assertEqual(pp[1][0].get_id()[1], 186)
|
|
self.assertEqual(pp[1][-1].get_id()[1], 213)
|
|
self.assertEqual(pp[2][0].get_id()[1], 216)
|
|
self.assertEqual(pp[2][-1].get_id()[1], 220)
|
|
|
|
# Now check sequences
|
|
pp0_seq = pp[0].get_sequence()
|
|
pp1_seq = pp[1].get_sequence()
|
|
pp2_seq = pp[2].get_sequence()
|
|
self.assertIsInstance(pp0_seq, Seq)
|
|
self.assertEqual(pp0_seq, "DIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNW")
|
|
self.assertEqual(pp1_seq, "TETLLVQNANPDCKTILKALGPGATLEE")
|
|
self.assertEqual(pp2_seq, "TACQG")
|
|
|
|
def test_ppbuilder_real_nonstd(self):
|
|
"""Test PPBuilder on real PDB file allowing non-standard amino acids."""
|
|
ppb = PPBuilder()
|
|
pp = ppb.build_peptides(self.structure, False)
|
|
|
|
self.assertEqual(len(pp), 1)
|
|
|
|
# Check the start and end positions
|
|
self.assertEqual(pp[0][0].get_id()[1], 151)
|
|
self.assertEqual(pp[0][-1].get_id()[1], 220)
|
|
|
|
# Check the sequence
|
|
s = pp[0].get_sequence()
|
|
self.assertIsInstance(s, Seq)
|
|
# Here non-standard MSE are shown as M
|
|
self.assertEqual(
|
|
"MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQG", s
|
|
)
|
|
|
|
def test_ppbuilder_torsion(self):
|
|
"""Test phi/psi angles calculated with PPBuilder."""
|
|
ppb = PPBuilder()
|
|
pp = ppb.build_peptides(self.structure)
|
|
|
|
phi_psi = pp[0].get_phi_psi_list()
|
|
self.assertIsNone(phi_psi[0][0])
|
|
self.assertAlmostEqual(phi_psi[0][1], -0.46297171497725553, places=3)
|
|
self.assertAlmostEqual(phi_psi[1][0], -1.0873937604007962, places=3)
|
|
self.assertAlmostEqual(phi_psi[1][1], 2.1337707832637109, places=3)
|
|
self.assertAlmostEqual(phi_psi[2][0], -2.4052232743651878, places=3)
|
|
self.assertAlmostEqual(phi_psi[2][1], 2.3807316946081554, places=3)
|
|
|
|
phi_psi = pp[1].get_phi_psi_list()
|
|
self.assertIsNone(phi_psi[0][0])
|
|
self.assertAlmostEqual(phi_psi[0][1], -0.6810077089092923, places=3)
|
|
self.assertAlmostEqual(phi_psi[1][0], -1.2654003477656888, places=3)
|
|
self.assertAlmostEqual(phi_psi[1][1], -0.58689987042756309, places=3)
|
|
self.assertAlmostEqual(phi_psi[2][0], -1.7467679151684763, places=3)
|
|
self.assertAlmostEqual(phi_psi[2][1], -1.5655066256698336, places=3)
|
|
|
|
phi_psi = pp[2].get_phi_psi_list()
|
|
self.assertIsNone(phi_psi[0][0])
|
|
self.assertAlmostEqual(phi_psi[0][1], -0.73222884210889716, places=3)
|
|
self.assertAlmostEqual(phi_psi[1][0], -1.1044740234566259, places=3)
|
|
self.assertAlmostEqual(phi_psi[1][1], -0.69681334592782884, places=3)
|
|
self.assertAlmostEqual(phi_psi[2][0], -1.8497413300164958, places=3)
|
|
self.assertAlmostEqual(phi_psi[2][1], 0.34762889834809058, places=3)
|
|
|
|
def test_cappbuilder_real(self):
|
|
"""Test CaPPBuilder on real PDB file."""
|
|
ppb = CaPPBuilder()
|
|
pp = ppb.build_peptides(self.structure)
|
|
|
|
pp0_seq = pp[0].get_sequence()
|
|
pp1_seq = pp[1].get_sequence()
|
|
pp2_seq = pp[2].get_sequence()
|
|
self.assertEqual(pp0_seq, "DIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNW")
|
|
self.assertEqual(pp1_seq, "TETLLVQNANPDCKTILKALGPGATLEE")
|
|
self.assertEqual(pp2_seq, "TACQG")
|
|
self.assertEqual(
|
|
[ca.serial_number for ca in pp[0].get_ca_list()],
|
|
[
|
|
10,
|
|
18,
|
|
26,
|
|
37,
|
|
46,
|
|
50,
|
|
57,
|
|
66,
|
|
75,
|
|
82,
|
|
93,
|
|
104,
|
|
112,
|
|
124,
|
|
131,
|
|
139,
|
|
150,
|
|
161,
|
|
173,
|
|
182,
|
|
189,
|
|
197,
|
|
208,
|
|
213,
|
|
222,
|
|
231,
|
|
236,
|
|
242,
|
|
251,
|
|
260,
|
|
267,
|
|
276,
|
|
284,
|
|
],
|
|
)
|
|
|
|
def test_cappbuilder_real_nonstd(self):
|
|
"""Test CaPPBuilder on real PDB file allowing non-standard amino acids."""
|
|
ppb = CaPPBuilder()
|
|
pp = ppb.build_peptides(self.structure, False)
|
|
|
|
self.assertEqual(len(pp), 1)
|
|
|
|
# Check the start and end positions
|
|
self.assertEqual(pp[0][0].get_id()[1], 151)
|
|
self.assertEqual(pp[0][-1].get_id()[1], 220)
|
|
|
|
# Check the sequence
|
|
s = pp[0].get_sequence()
|
|
self.assertIsInstance(s, Seq)
|
|
# Here non-standard MSE are shown as M
|
|
self.assertEqual(
|
|
"MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQG", s
|
|
)
|
|
|
|
def test_cappbuilder_tau(self):
|
|
"""Test tau angles calculated with CaPPBuilder."""
|
|
ppb = CaPPBuilder()
|
|
pp = ppb.build_peptides(self.structure)
|
|
|
|
taus = pp[1].get_tau_list()
|
|
self.assertAlmostEqual(taus[0], 0.3597907225123525, places=3)
|
|
self.assertAlmostEqual(taus[1], 0.43239284636769254, places=3)
|
|
self.assertAlmostEqual(taus[2], 0.99820157492712114, places=3)
|
|
thetas = pp[2].get_theta_list()
|
|
self.assertAlmostEqual(thetas[0], 1.6610069445335354, places=3)
|
|
self.assertAlmostEqual(thetas[1], 1.7491703334817772, places=3)
|
|
self.assertAlmostEqual(thetas[2], 2.0702447422720143, places=3)
|
|
|
|
|
|
if __name__ == "__main__":
|
|
runner = unittest.TextTestRunner(verbosity=2)
|
|
unittest.main(testRunner=runner)
|