def setUp(self):
"""Initialize test data."""
parser = PDBParser()
struc = parser.get_structure('riboses',FCCD_EXAMPLE)
resi5 = struc[0]['A'][(' ',5,' ')]
resi5a = struc[0]['A'][(' ',5,'A')]
resi6 = struc[0]['A'][(' ',6,' ')]
self.fixed = [resi6["C4'"], resi6["C3'"], resi6["C2'"]]
self.moving = [resi5["O4'"], resi5["C4'"], \
resi5["C3'"], resi5["O3'"], \
resi5a["P"], resi5a["O5'"], resi5a["C5'"], \
resi5a["C4'"], resi5a["C3'"], resi5a["C2'"]
]
self.fccd = FCCDLoopCloser(self.moving, self.fixed)
class FCCDLoopCloserTests(TestCase):
"""
Tests the FCCD loop closing algorithm to model gaps between two riboses.
"""
def setUp(self):
"""Initialize test data."""
parser = PDBParser()
struc = parser.get_structure('riboses',FCCD_EXAMPLE)
resi5 = struc[0]['A'][(' ',5,' ')]
resi5a = struc[0]['A'][(' ',5,'A')]
resi6 = struc[0]['A'][(' ',6,' ')]
self.fixed = [resi6["C4'"], resi6["C3'"], resi6["C2'"]]
self.moving = [resi5["O4'"], resi5["C4'"], \
resi5["C3'"], resi5["O3'"], \
resi5a["P"], resi5a["O5'"], resi5a["C5'"], \
resi5a["C4'"], resi5a["C3'"], resi5a["C2'"]
]
self.fccd = FCCDLoopCloser(self.moving, self.fixed)
def tearDown(self):
"""Cleans up test data."""
self.rna = None
self.fixed = None
self.moving = None
self.fccd = None
def test_small_rmsd(self):
"""After running FCCD, the example should have a small RMSD."""
msg, rmsd, n_it = self.fccd.run_fccd(threshold=0.1)
self.fccd.copy_vectors_to_atoms()
self.assertTrue(msg.startswith('RMSD threshold reached'))
self.assertTrue(rmsd < 0.1)
self.assertTrue(n_it > 0)
def test_close_loop(self):
"""After running RMSD, the gap in the riboses should be closed."""
#TODO: uncomment after contributing RNA structure code.
#self.assertFalse(self.rna.are_residues_connected(\
# self.rna['5'], self.rna['6']))
self.fccd.run_fccd(threshold=0.1)
self.fccd.copy_vectors_to_atoms()
#self.assertTrue(self.rna.are_residues_connected(\
# self.rna['5'], self.rna['6']))
def test_get_moving_coords(self):
"""Method for moving coordinates should pass."""
center = Vector([100.0, 0.0, 0.0])
self.fccd.get_moving_coords(center)
self.assertTrue(True)
self.assertTrue(True)
def test_get_fixed_coords(self):
"""Method for fixed coordinates should pass."""
center = Vector([100.0, 0.0, 0.0])
self.fccd.get_fixed_coords(center)
self.assertTrue(True)
def test_copy_vectors(self):
"""Should modify the atom coordinates."""
self.fccd.moving[0] = Vector([1.23, 4.56, 7.89])
self.fccd.copy_vectors_to_atoms()
self.assertEqual(self.moving[0].coord[0], 1.23)
self.assertEqual(self.moving[0].coord[1], 4.56)
self.assertEqual(self.moving[0].coord[2], 7.89)