def test_energeticModes(self):
emodes = NormalModes.EnergeticModes(self.universe)
fc = emodes.force_constants[6:]
self.assertAlmostEqual(fc[0], 757849.3957485439, 5)
self.assertAlmostEqual(fc[1], 1041551.2240706938, 5)
self.assertAlmostEqual(fc[2], 1388251.2, 5)
for i in range(len(emodes)):
mi = emodes.rawMode(i)
norm_sq = mi.dotProduct(mi)
self.assertAlmostEqual(norm_sq, 1.)
for j in range(i + 1, len(emodes)):
overlap = mi.dotProduct(emodes.rawMode(j))
self.assert_(overlap < 1.e-15)
self.assertAlmostEqual(emodes[6].norm(), 0.0025656740328985168)
self.assertAlmostEqual(emodes[7].norm(), 0.0021885627126988836)
self.assertAlmostEqual(emodes[8].norm(), 0.0018956532696964624)
f = emodes.fluctuations()
self.assertAlmostEqual(f[self.universe.water.O], 3.359215370401356e-06)
self.assertAlmostEqual(f[self.universe.water.H1],
2.061890142153454e-06)
self.assertAlmostEqual(f[self.universe.water.H2],
2.061890142153454e-06)
af = emodes.anisotropicFluctuations()
self.assertAlmostEqual(f[self.universe.water.O],
af[self.universe.water.O].trace())
self.assertAlmostEqual(f[self.universe.water.H1],
af[self.universe.water.H1].trace())
self.assertAlmostEqual(f[self.universe.water.H2],
af[self.universe.water.H2].trace())
def setUp(self):
self.universe = MMTK.InfiniteUniverse(HarmonicForceField())
self.universe.peptide = Protein('bala1')
self.emodes = NormalModes.EnergeticModes(self.universe)
self.rm = RigidMotionSubspace(self.universe,
self.universe.peptide.residues())
self.pd = PairDistanceSubspace(self.universe, [
(self.universe.peptide[0][0].O, self.universe.peptide[0][-1].CH3)
])
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)