# 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)