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# Copyright 2013 Gokcen Eraslan. 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.
"""Unit test for Bio.PDB.NACCESS which needs NACCESS tool.
See also test_PDB.py for dependency free NACCESS tests.
"""
import subprocess
import unittest
from Bio import MissingExternalDependencyError
from Bio.PDB import PDBParser
from Bio.PDB.NACCESS import NACCESS
# Check if NACCESS is installed
try:
subprocess.check_call(["naccess", "-q"],
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
except OSError:
raise MissingExternalDependencyError(
"Install naccess if you want to use it from Biopython.")
class NACCESS_test(unittest.TestCase):
"""Test NACCESS module"""
def test_NACCESS(self):
"""Test NACCESS generation from PDB"""
p = PDBParser()
pdbfile = "PDB/1A8O.pdb"
model = p.get_structure("1A8O", pdbfile)[0]
naccess = NACCESS(model, pdbfile)
self.assertEqual(len(naccess), 66)
if __name__ == '__main__':
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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