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# Copyright 2009-2010 by Eric Talevich. All rights reserved.
# Revisions copyright 2010 by Peter Cock. All rights reserved.
#
# Converted by Eric Talevich from an older unit test copyright 2002
# by Thomas Hamelryck.
#
# 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 tests for those parts of the Bio.PDB module using Bio.KDTree."""
import unittest
try:
from numpy import array
from numpy.random import random
except ImportError:
from Bio import MissingExternalDependencyError
raise MissingExternalDependencyError(
"Install NumPy if you want to use Bio.PDB.")
try:
from Bio.KDTree import _CKDTree
except ImportError:
from Bio import MissingExternalDependencyError
raise MissingExternalDependencyError(
"C module in Bio.KDTree not compiled")
from Bio.PDB.NeighborSearch import NeighborSearch
class NeighborTest(unittest.TestCase):
def test_neighbor_search(self):
"""NeighborSearch: Find nearby randomly generated coordinates.
Based on the self test in Bio.PDB.NeighborSearch.
"""
class RandomAtom(object):
def __init__(self):
self.coord = 100 * random(3)
def get_coord(self):
return self.coord
for i in range(0, 20):
atoms = [RandomAtom() for j in range(100)]
ns = NeighborSearch(atoms)
hits = ns.search_all(5.0)
self.assertTrue(isinstance(hits, list), hits)
self.assertTrue(len(hits) >= 0, hits)
x = array([250, 250, 250]) # Far away from our random atoms
self.assertEqual([], ns.search(x, 5.0, "A"))
self.assertEqual([], ns.search(x, 5.0, "R"))
self.assertEqual([], ns.search(x, 5.0, "C"))
self.assertEqual([], ns.search(x, 5.0, "M"))
self.assertEqual([], ns.search(x, 5.0, "S"))
if __name__ == '__main__':
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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