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# Copyright 2019 by Sergio Valqui. All rights reserved.
# 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.Dice Module."""
import unittest
import tempfile
import os
from Bio.PDB import Dice
from Bio.PDB import PDBParser
class DiceTests(unittest.TestCase):
"""Tests for PDB.Dice module."""
def test_dice(self):
"""Self test for PDB.Dice module."""
# Load and dice 2BEG.pdb
parser = PDBParser()
pdb_file = "PDB/2BEG.pdb"
structure = parser.get_structure("scr", pdb_file)
file_number, file_pdb_diced = tempfile.mkstemp()
os.close(file_number)
# dice 2BEG.pdb, chain "B" from residue 18 to 20"
Dice.extract(structure, "B", 18, 20, file_pdb_diced)
try:
# Load the diced file
diced_str = parser.get_structure("2beg_diced", file_pdb_diced)
l_diced_cha = list(diced_str.get_chains())
l_diced_res = list(diced_str.get_residues())
l_diced_ato = list(diced_str.get_atoms())
# Chain checks
self.assertEqual(len(l_diced_cha), 1)
self.assertEqual(l_diced_cha[0].id, "B")
# Residue Checks
self.assertEqual(len(l_diced_res), 3)
self.assertEqual(l_diced_res[0].id[1], 18)
self.assertEqual(l_diced_res[2].id[1], 20)
# Atom checks
self.assertEqual(len(l_diced_ato), 29)
self.assertEqual(l_diced_ato[0].name, "N")
self.assertEqual(l_diced_ato[0].parent.resname, "VAL")
self.assertEqual(l_diced_ato[0].parent.parent.id, "B")
self.assertEqual(l_diced_ato[28].name, "CZ")
self.assertEqual(l_diced_ato[28].parent.resname, "PHE")
self.assertEqual(l_diced_ato[28].parent.parent.id, "B")
finally:
os.remove(file_pdb_diced)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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