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# Copyright 2017 by Sourav Singh. All rights reserved.
# Revisions copyright 2017 by Peter Cock. All rights reserved.
#
# 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.
"""Tests for PDB FragmentMapper module."""
import unittest
try:
import numpy as np
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install NumPy if you want to use Bio.PDB."
) from None
from Bio.PDB import FragmentMapper
from Bio.PDB import PDBParser
from Bio.PDB import Selection
class FragmentMapperTests(unittest.TestCase):
"""Tests for FragmentMapper module."""
def test_fragment_mapper(self):
"""Self test for FragmentMapper module."""
p = PDBParser()
pdb1 = "PDB/1A8O.pdb"
s = p.get_structure("X", pdb1)
m = s[0]
fm = FragmentMapper(m, 10, 5, "PDB")
for r in Selection.unfold_entities(m, "R"):
if r in fm:
self.assertTrue(str(fm[r]).startswith("<Fragment length=5 id="))
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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