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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.
#
# 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 exposure classes."""
from copy import deepcopy
import os
import sys
import tempfile
import unittest
import warnings
from io import StringIO
try:
import numpy
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install NumPy if you want to use Bio.PDB."
) from None
from Bio.PDB import PDBParser, MMCIFParser
from Bio.PDB import HSExposureCA, HSExposureCB, ExposureCN
from Bio.PDB.PDBExceptions import PDBConstructionException, PDBConstructionWarning
class Exposure(unittest.TestCase):
"""Testing Bio.PDB.HSExposure."""
def setUp(self):
pdb_filename = "PDB/a_structure.pdb"
with warnings.catch_warnings():
warnings.simplefilter("ignore", PDBConstructionWarning)
structure = PDBParser(PERMISSIVE=True).get_structure("X", pdb_filename)
structure[1].detach_child("B")
self.model = structure[1]
# Look at first chain only
a_residues = list(self.model["A"].child_list)
self.assertEqual(86, len(a_residues))
self.assertEqual(a_residues[0].get_resname(), "CYS")
self.assertEqual(a_residues[1].get_resname(), "ARG")
self.assertEqual(a_residues[2].get_resname(), "CYS")
self.assertEqual(a_residues[3].get_resname(), "GLY")
# ...
self.assertEqual(a_residues[-3].get_resname(), "TYR")
self.assertEqual(a_residues[-2].get_resname(), "ARG")
self.assertEqual(a_residues[-1].get_resname(), "CYS")
self.a_residues = a_residues
self.radius = 13.0
def test_HSExposureCA(self):
"""HSExposureCA."""
_ = HSExposureCA(self.model, self.radius)
residues = self.a_residues
self.assertEqual(0, len(residues[0].xtra))
self.assertEqual(0, len(residues[1].xtra))
self.assertEqual(3, len(residues[2].xtra))
self.assertAlmostEqual(
0.81250973133184456, residues[2].xtra["EXP_CB_PCB_ANGLE"]
)
self.assertEqual(14, residues[2].xtra["EXP_HSE_A_D"])
self.assertEqual(14, residues[2].xtra["EXP_HSE_A_U"])
self.assertEqual(3, len(residues[3].xtra))
self.assertAlmostEqual(1.3383737, residues[3].xtra["EXP_CB_PCB_ANGLE"])
self.assertEqual(13, residues[3].xtra["EXP_HSE_A_D"])
self.assertEqual(16, residues[3].xtra["EXP_HSE_A_U"])
# ...
self.assertEqual(3, len(residues[-2].xtra))
self.assertAlmostEqual(
0.77124014456278489, residues[-2].xtra["EXP_CB_PCB_ANGLE"]
)
self.assertEqual(24, residues[-2].xtra["EXP_HSE_A_D"])
self.assertEqual(24, residues[-2].xtra["EXP_HSE_A_U"])
self.assertEqual(0, len(residues[-1].xtra))
def test_HSExposureCB(self):
"""HSExposureCB."""
_ = HSExposureCB(self.model, self.radius)
residues = self.a_residues
self.assertEqual(0, len(residues[0].xtra))
self.assertEqual(2, len(residues[1].xtra))
self.assertEqual(20, residues[1].xtra["EXP_HSE_B_D"])
self.assertEqual(5, residues[1].xtra["EXP_HSE_B_U"])
self.assertEqual(2, len(residues[2].xtra))
self.assertEqual(10, residues[2].xtra["EXP_HSE_B_D"])
self.assertEqual(18, residues[2].xtra["EXP_HSE_B_U"])
self.assertEqual(2, len(residues[3].xtra))
self.assertEqual(7, residues[3].xtra["EXP_HSE_B_D"])
self.assertEqual(22, residues[3].xtra["EXP_HSE_B_U"])
# ...
self.assertEqual(2, len(residues[-2].xtra))
self.assertEqual(14, residues[-2].xtra["EXP_HSE_B_D"])
self.assertEqual(34, residues[-2].xtra["EXP_HSE_B_U"])
self.assertEqual(2, len(residues[-1].xtra))
self.assertEqual(23, residues[-1].xtra["EXP_HSE_B_D"])
self.assertEqual(15, residues[-1].xtra["EXP_HSE_B_U"])
def test_ExposureCN(self):
"""HSExposureCN."""
_ = ExposureCN(self.model, self.radius)
residues = self.a_residues
self.assertEqual(0, len(residues[0].xtra))
self.assertEqual(1, len(residues[1].xtra))
self.assertEqual(25, residues[1].xtra["EXP_CN"])
self.assertEqual(1, len(residues[2].xtra))
self.assertEqual(28, residues[2].xtra["EXP_CN"])
self.assertEqual(1, len(residues[3].xtra))
self.assertEqual(29, residues[3].xtra["EXP_CN"])
# ...
self.assertEqual(1, len(residues[-2].xtra))
self.assertEqual(48, residues[-2].xtra["EXP_CN"])
self.assertEqual(1, len(residues[-1].xtra))
self.assertEqual(38, residues[-1].xtra["EXP_CN"])
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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