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# Copyright 2013 Lenna X. Peterson. 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.DSSP which need the binary tool.
See also test_PDB.py for dependency free DSSP tests.
"""
from distutils.version import StrictVersion
import re
import subprocess
import unittest
from Bio import MissingExternalDependencyError
from Bio.PDB import PDBParser, MMCIFParser
from Bio.PDB import DSSP
# DSSP version, if known, as DSSP <2.2.0 does not support mmcif files
dssp_version = '0.0.0'
# Check if DSSP is installed
quiet_kwargs = dict(stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
try:
try:
# Newer versions of DSSP
version_string = subprocess.check_output(["dssp", "--version"],
universal_newlines=True)
dssp_version = re.search(r'\s*([\d.]+)', version_string).group(1)
except subprocess.CalledProcessError:
# Older versions of DSSP
subprocess.check_call(["dssp", "-h"], **quiet_kwargs)
except OSError:
try:
version_string = subprocess.check_output(["mkdssp", "--version"],
universal_newlines=True)
dssp_version = re.search(r'\s*([\d.]+)', version_string).group(1)
except OSError:
raise MissingExternalDependencyError(
"Install dssp if you want to use it from Biopython.")
class DSSP_test(unittest.TestCase):
"""Test DSSP module"""
def test_dssp(self):
"""Test DSSP generation from PDB"""
p = PDBParser()
pdbfile = "PDB/2BEG.pdb"
model = p.get_structure("2BEG", pdbfile)[0]
dssp = DSSP(model, pdbfile)
self.assertEqual(len(dssp), 130)
# Only run mmCIF tests if DSSP version installed supports mmcif
if StrictVersion(dssp_version) >= StrictVersion('2.2.0'):
def test_dssp_with_mmcif_file(self):
"""Test DSSP generation from MMCIF"""
p = MMCIFParser()
pdbfile = "PDB/2BEG.cif"
model = p.get_structure("2BEG", pdbfile)[0]
dssp = DSSP(model, pdbfile)
self.assertEqual(len(dssp), 130)
def test_dssp_with_mmcif_file_and_nonstandard_residues(self):
"""Test DSSP generation from MMCIF with non-standard residues"""
p = MMCIFParser()
pdbfile = "PDB/1AS5.cif"
model = p.get_structure("1AS5", pdbfile)[0]
dssp = DSSP(model, pdbfile)
self.assertEqual(len(dssp), 24)
if __name__ == '__main__':
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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