# Copyright 2022 by Valentin Vareskic (valentin.vareskic@gmail.com). # All rights reserved. This code is part of the Biopython distribution # and governed by its license. Please see the LICENSE file that should # have been included as part of this package. """Tests for PDB PSEA.""" import io import os import sys import unittest from subprocess import getoutput from Bio import MissingExternalDependencyError from Bio.PDB import PDBParser from Bio.PDB.PSEA import PSEA from Bio.PDB.PSEA import psea from Bio.PDB.PSEA import psea2HEC from Bio.PDB.PSEA import run_psea os.environ["LANG"] = "C" cmd_output = getoutput("psea -h") if not cmd_output.startswith("o---"): raise MissingExternalDependencyError( "Download and install psea from " "ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. " "Make sure that psea is on path" ) def remove_sea_files(): for file in os.listdir(): if file.endswith(".sea"): os.remove(file) class TestPDBPSEA(unittest.TestCase): def tearDown(self): remove_sea_files() def test_run_psea_verbose(self): captured_ouput = io.StringIO() sys.stdout = captured_ouput psae_run = run_psea("PDB/1A8O.pdb", verbose=True) sys.stdout = sys.__stdout__ self.assertEqual(psae_run, "1A8O.sea") self.assertTrue(captured_ouput.getvalue()) def test_run_psea_quiet(self): captured_ouput = io.StringIO() sys.stdout = captured_ouput psae_run = run_psea("PDB/1A8O.pdb", verbose=False) sys.stdout = sys.__stdout__ self.assertEqual(psae_run, "1A8O.sea") self.assertFalse(captured_ouput.getvalue()) def test_psea(self): psae_run = psea("PDB/2BEG.pdb") self.assertEqual(psae_run, "ccccbbbbbbbccccbbbbbbbbbbc") def test_psea_2HEC(self): seq = psea("PDB/2BEG.pdb") psae_run = psea2HEC(seq) self.assertEqual( psae_run, [ "C", "C", "C", "C", "E", "E", "E", "E", "E", "E", "E", "C", "C", "C", "C", "E", "E", "E", "E", "E", "E", "E", "E", "E", "E", "C", ], ) class TestPSEA(unittest.TestCase): def tearDown(self): remove_sea_files() def test_get_seq(self): p = PDBParser() s = p.get_structure("X", "PDB/2BEG.pdb") psea_class = PSEA(s[0], "PDB/2BEG.pdb") self.assertEqual( psea_class.get_seq(), [ "C", "C", "C", "C", "E", "E", "E", "E", "E", "E", "E", "C", "C", "C", "C", "E", "E", "E", "E", "E", "E", "E", "E", "E", "E", "C", ], ) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)