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# Copyright 2009-2011 by Eric Talevich. All rights reserved.
# Revisions copyright 2009-2013 by Peter Cock. All rights reserved.
# Revisions copyright 2013 Lenna X. Peterson. All rights reserved.
# Revisions copyright 2013 Gokcen Eraslan. All rights reserved.
# Revisions copyright 2020 Joao Rodrigues. All rights reserved.
#
# Converted by Eric Talevich from an older unit test copyright 2002
# by Thomas Hamelryck.
#
# Merged related test files into one, by Joao Rodrigues (2020)
#
# 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.NACCESS submodule."""
import subprocess
import unittest
import warnings
try:
import numpy
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install NumPy if you want to use Bio.PDB."
) from None
from Bio import MissingExternalDependencyError
from Bio.PDB import PDBParser
from Bio.PDB.NACCESS import NACCESS, process_asa_data, process_rsa_data
class NACCESS_test(unittest.TestCase):
"""Tests for Bio.PDB.NACCESS and output parsing."""
def test_NACCESS_rsa_file(self):
"""Test parsing of pregenerated rsa NACCESS file."""
with open("PDB/1A8O.rsa") as rsa:
naccess = process_rsa_data(rsa)
self.assertEqual(len(naccess), 66)
def test_NACCESS_asa_file(self):
"""Test parsing of pregenerated asa NACCESS file."""
with open("PDB/1A8O.asa") as asa:
naccess = process_asa_data(asa)
self.assertEqual(len(naccess), 524)
def test_NACCESS(self):
"""Test calling NACCESS from Bio.PDB."""
# Check if NACCESS is available
try:
subprocess.check_call(
["naccess", "-q"], stdout=subprocess.PIPE, stderr=subprocess.STDOUT
)
except OSError:
raise self.skipTest("Install naccess if you want to use it from Biopython.")
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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