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# Pickle tests
#
# Written by Konrad Hinsen
#
import unittest
import MMTK
from MMTK.Proteins import Protein
from MMTK.ForceFields import Amber99ForceField
from MMTK import NormalModes
from Scientific import N
import os
class PeptideTest(unittest.TestCase):
"""
Test pickling a small protein
"""
def setUp(self):
self.universe = MMTK.InfiniteUniverse(Amber99ForceField())
self.universe.peptide = Protein('bala1')
def test_energy(self):
# Check that the energy terms after pickling and reloading
# are the same.
energy_terms = self.universe.energyTerms()
MMTK.save(self.universe, 'test.pickle')
restored_universe = MMTK.load('test.pickle')
r_energy_terms = restored_universe.energyTerms()
self.assertEqual(energy_terms.keys(), r_energy_terms.keys())
def test_normal_modes(self):
emodes = NormalModes.EnergeticModes(self.universe)
MMTK.save(emodes, 'test.pickle')
restored_modes = MMTK.load('test.pickle')
for i in range(len(emodes)):
self.assertEqual(emodes[i].force_constant,
restored_modes[i].force_constant)
err = N.minimum.reduce(N.fabs(N.ravel(emodes[i].array
-restored_modes[i].array)))
self.assert_(err < 1.e-15)
class WaterTest(unittest.TestCase):
"""
Test pickling a water molecule
"""
def setUp(self):
self.universe = MMTK.InfiniteUniverse(Amber99ForceField())
self.universe.water1 = MMTK.Molecule('water',
position=MMTK.Vector(0.,0.,0.))
self.universe.water2 = MMTK.Molecule('water',
position=MMTK.Vector(0.5,0.,0.))
def tearDown(self):
try:
os.remove('test.pickle')
except OSError:
pass
def test_energy(self):
# Check that the energy terms after pickling and reloading
# are the same.
energy_terms = self.universe.energyTerms()
MMTK.save(self.universe, 'test.pickle')
restored_universe = MMTK.load('test.pickle')
self.assertEqual(energy_terms, restored_universe.energyTerms())
def test_parent(self):
# Check that pickling an object from a universe sets that
# objects's parent to None, rather than pickling the whole universe.
MMTK.save(self.universe.water1, 'test.pickle')
restored_molecule = MMTK.load('test.pickle')
self.assertEqual(restored_molecule.parent, None)
def test_type(self):
# Check that the MoleculeType object is not pickled, but
# always taken from the database.
MMTK.save(self.universe.water1, 'test.pickle')
restored_molecule = MMTK.load('test.pickle')
self.assertEqual(restored_molecule.type, self.universe.water1.type)
def suite():
loader = unittest.TestLoader()
s = unittest.TestSuite()
s.addTest(loader.loadTestsFromTestCase(PeptideTest))
s.addTest(loader.loadTestsFromTestCase(WaterTest))
return s
if __name__ == '__main__':
unittest.main()
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