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# 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.Polypetide module."""
import unittest
from Bio.PDB import PDBParser, PPBuilder, CaPPBuilder
from Bio.Seq import Seq
class PolypeptideTests(unittest.TestCase):
"""Test Polypetide 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(str(pp0_seq), "DIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNW")
self.assertEqual(str(pp1_seq), "TETLLVQNANPDCKTILKALGPGATLEE")
self.assertEqual(str(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",
str(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.assertEqual(phi_psi[0][0], None)
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.assertEqual(phi_psi[0][0], None)
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.assertEqual(phi_psi[0][0], None)
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(str(pp0_seq), "DIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNW")
self.assertEqual(str(pp1_seq), "TETLLVQNANPDCKTILKALGPGATLEE")
self.assertEqual(str(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",
str(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)
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