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_projections(self):
universe = MMTK.InfiniteUniverse()
universe.m1 = MMTK.Molecule('water', position=MMTK.Vector(0., 0., 0.))
universe.m2 = MMTK.Molecule('water', position=MMTK.Vector(1., 0., 0.))
rbs = [universe.m1, MMTK.Collection([universe.m2.H1, universe.m2.H2])]
s = RigidMotionSubspace(universe, rbs)
self.checkOrthonormality(s)
self.assertEqual(len(s), 11)
basis = s.getBasis()
self.assertEqual(len(basis), 11)
complement = s.complement()
complement_basis = complement.getBasis()
self.assertEqual(len(complement_basis),
universe.degreesOfFreedom() - 11)
for rb in rbs:
for t in [
Translation(MMTK.Vector(0.1, -0.2, 1.5)),
Rotation(MMTK.Vector(0.3, 1.2, -2.3), 0.001)
]:
d = rb.displacementUnderTransformation(t)
self.assert_((s.projectionOf(d) - d).norm() < 1.e-7)
self.assert_(s.projectionComplementOf(d).norm() < 1.e-7)
def setUp(self):
self.universe = MMTK.InfiniteUniverse(Amber99ForceField())
self.universe.peptide = Protein('bala1')
self.subspace = RigidMotionSubspace(self.universe,
self.universe.peptide.residues())
from MMTK.Minimization import ConjugateGradientMinimizer
from MMTK.Trajectory import StandardLogOutput
from Scientific import N
# Construct system
universe = InfiniteUniverse(Amber94ForceField())
universe.protein = Protein('bala1')
# Minimize
minimizer = ConjugateGradientMinimizer(universe,
actions=[StandardLogOutput(50)])
minimizer(convergence=1.e-3, steps=10000)
# Set up the subspace: rigid-body translation and rotation for each residue
subspace = RigidMotionSubspace(universe, universe.protein.residues())
# Calculate normal modes
modes = VibrationalModes(universe, subspace=subspace)
# Calculate full modes for comparison
full_modes = VibrationalModes(universe, subspace=None)
# Compare the modes. For each reduced mode, find the full mode with
# the most similar displacement vector. Print both frequencies and
# the overlap of the displacement vectors.
masses = universe.masses()
for i in range(6, len(modes)):
m1 = modes[i]
overlap = []
for m2 in full_modes:
def test_lrb(self):
universe = MMTK.InfiniteUniverse()
for p in [
MMTK.Vector(0., 0., 0.),
MMTK.Vector(1., 0., 0.),
MMTK.Vector(0., 1., 1.),
MMTK.Vector(0., 1., 0.),
MMTK.Vector(1., 0., 1.),
MMTK.Vector(0., 0., 1.),
MMTK.Vector(1., 1., 0.),
MMTK.Vector(1., 1., 1.)
]:
universe.addObject(MMTK.Atom('C', position=p))
atoms = universe.atomList()
# all atoms independent
s = RigidMotionSubspace(universe, atoms)
self.checkOrthonormality(s)
self.assertEqual(len(s.getBasis()), 3 * len(atoms))
# 1 rb, four free atoms
rbs = [MMTK.Collection(atoms[:4])] + atoms[4:]
s = RigidMotionSubspace(universe, rbs)
self.checkOrthonormality(s)
self.assertEqual(len(s.getBasis()), 6 + 4 * 3)
# 2 independent rbs with > 2 atoms
rbs = [MMTK.Collection(atoms[:4]), MMTK.Collection(atoms[4:])]
s = RigidMotionSubspace(universe, rbs)
self.checkOrthonormality(s)
self.assertEqual(len(s.getBasis()), 12)
# 2 independent rbs, one 2 atoms, one 6 atoms
rbs = [MMTK.Collection(atoms[:6]), MMTK.Collection(atoms[6:])]
s = RigidMotionSubspace(universe, rbs)
self.checkOrthonormality(s)
self.assertEqual(len(s.getBasis()), 11)
# 2 rbs > 2 atoms each, one atom in common
rbs = [MMTK.Collection(atoms[:5]), MMTK.Collection(atoms[4:])]
s = RigidMotionSubspace(universe, rbs)
self.checkOrthonormality(s)
self.assertEqual(len(s.getBasis()), 9)
# 2 rbs > 2 atoms each, two atoms in common
rbs = [MMTK.Collection(atoms[:5]), MMTK.Collection(atoms[3:])]
s = RigidMotionSubspace(universe, rbs)
self.checkOrthonormality(s)
self.assertEqual(len(s.getBasis()), 7)
# 2 rbs > 2 atoms each, three atoms in common
rbs = [MMTK.Collection(atoms[:5]), MMTK.Collection(atoms[2:])]
s = RigidMotionSubspace(universe, rbs)
self.checkOrthonormality(s)
self.assertEqual(len(s.getBasis()), 6)
# 2 rbs with 2 and 7 atoms, one atom in common
rbs = [MMTK.Collection(atoms[:2]), MMTK.Collection(atoms[1:])]
s = RigidMotionSubspace(universe, rbs)
self.checkOrthonormality(s)
self.assertEqual(len(s.getBasis()), 8)
# 3 rbs > 2 atoms each, one atom in common between rb[n] and rb[n+1]
rbs = [
MMTK.Collection(atoms[:3]),
MMTK.Collection(atoms[2:6]),
MMTK.Collection(atoms[5:])
]
s = RigidMotionSubspace(universe, rbs)
self.checkOrthonormality(s)
self.assertEqual(len(s.getBasis()), 12)
# 3 rbs > 2 atoms each, one atom in common for each pair
# (chain of 3 rbs)
rbs = [
MMTK.Collection(atoms[:3] + atoms[7:]),
MMTK.Collection(atoms[2:6]),
MMTK.Collection(atoms[5:])
]
s = RigidMotionSubspace(universe, rbs)
self.checkOrthonormality(s)
self.assertEqual(len(s.getBasis()), 10)
# 2 rbs > 2 atoms each, linked by a rigid bond
rbs = [
MMTK.Collection(atoms[:4]),
MMTK.Collection(atoms[3:5]),
MMTK.Collection(atoms[4:])
]
s = RigidMotionSubspace(universe, rbs)
self.checkOrthonormality(s)
self.assertEqual(len(s.getBasis()), 11)
class PeptideNormalModeTest(unittest.TestCase):
"""
Test mode projections on a subspace
"""
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_rmProjections(self):
p = self.rm.projectionOf(self.emodes.rawMode(6)).norm()
self.assertAlmostEqual(p, 0.932906130224)
p = self.rm.projectionOf(self.emodes.rawMode(7)).norm()
self.assertAlmostEqual(p, 0.946620894164)
p = self.rm.projectionOf(self.emodes.rawMode(8)).norm()
self.assertAlmostEqual(p, 0.918711763134)
p = self.rm.projectionOf(self.emodes.rawMode(9)).norm()
self.assertAlmostEqual(p, 0.914888590566)
p = self.rm.projectionOf(self.emodes.rawMode(10)).norm()
self.assertAlmostEqual(p, 0.954987614764)
p = self.rm.projectionOf(self.emodes.rawMode(11)).norm()
self.assertAlmostEqual(p, 0.490550926574)
p = self.rm.projectionOf(self.emodes.rawMode(12)).norm()
self.assertAlmostEqual(p, 0.974543149457)
p = self.rm.projectionOf(self.emodes.rawMode(13)).norm()
self.assertAlmostEqual(p, 0.902492405825)
p = self.rm.projectionOf(self.emodes.rawMode(14)).norm()
self.assertAlmostEqual(p, 0.873380594746)
p = self.rm.projectionOf(self.emodes.rawMode(15)).norm()
self.assertAlmostEqual(p, 0.772133237884)
p = self.rm.projectionOf(self.emodes.rawMode(16)).norm()
self.assertAlmostEqual(p, 0.883756751312)
p = self.rm.projectionOf(self.emodes.rawMode(17)).norm()
self.assertAlmostEqual(p, 0.577569822435)
p = self.rm.projectionOf(self.emodes.rawMode(18)).norm()
self.assertAlmostEqual(p, 0.703601140498)
p = self.rm.projectionOf(self.emodes.rawMode(19)).norm()
self.assertAlmostEqual(p, 0.341866735125)
p = self.rm.projectionOf(self.emodes.rawMode(20)).norm()
self.assertAlmostEqual(p, 0.590049489902)
p = self.rm.projectionOf(self.emodes.rawMode(21)).norm()
self.assertAlmostEqual(p, 0.432251617574)
p = self.rm.projectionOf(self.emodes.rawMode(22)).norm()
self.assertAlmostEqual(p, 0.245304052688)
p = self.rm.projectionOf(self.emodes.rawMode(23)).norm()
self.assertAlmostEqual(p, 0.211381043933)
p = self.rm.projectionOf(self.emodes.rawMode(24)).norm()
self.assertAlmostEqual(p, 0.401154809528)
p = self.rm.projectionOf(self.emodes.rawMode(25)).norm()
self.assertAlmostEqual(p, 0.161820108479)
p = self.rm.projectionOf(self.emodes.rawMode(26)).norm()
self.assertAlmostEqual(p, 0.208594682213)
p = self.rm.projectionOf(self.emodes.rawMode(27)).norm()
self.assertAlmostEqual(p, 0.329444853782)
p = self.rm.projectionOf(self.emodes.rawMode(28)).norm()
self.assertAlmostEqual(p, 0.335842626795)
p = self.rm.projectionOf(self.emodes.rawMode(29)).norm()
self.assertAlmostEqual(p, 0.246955423968)
p = self.rm.projectionOf(self.emodes.rawMode(30)).norm()
self.assertAlmostEqual(p, 0.102801852182)
p = self.rm.projectionOf(self.emodes.rawMode(31)).norm()
self.assertAlmostEqual(p, 0.0445276342964)
p = self.rm.projectionOf(self.emodes.rawMode(32)).norm()
self.assertAlmostEqual(p, 0.0810509154227)
p = self.rm.projectionOf(self.emodes.rawMode(33)).norm()
self.assertAlmostEqual(p, 0.166723733735)
p = self.rm.projectionOf(self.emodes.rawMode(34)).norm()
self.assertAlmostEqual(p, 0.254081370404)
p = self.rm.projectionOf(self.emodes.rawMode(35)).norm()
self.assertAlmostEqual(p, 0.221723386921)
p = self.rm.projectionOf(self.emodes.rawMode(36)).norm()
self.assertAlmostEqual(p, 0.133163531911)
p = self.rm.projectionOf(self.emodes.rawMode(37)).norm()
self.assertAlmostEqual(p, 0.0662977755488)
p = self.rm.projectionOf(self.emodes.rawMode(38)).norm()
self.assertAlmostEqual(p, 0.156961937663)
p = self.rm.projectionOf(self.emodes.rawMode(39)).norm()
self.assertAlmostEqual(p, 0.310640400206)
p = self.rm.projectionOf(self.emodes.rawMode(40)).norm()
self.assertAlmostEqual(p, 0.424586976986)
p = self.rm.projectionOf(self.emodes.rawMode(41)).norm()
self.assertAlmostEqual(p, 0.439565895727)
p = self.rm.projectionOf(self.emodes.rawMode(42)).norm()
self.assertAlmostEqual(p, 0.220029858675)
p = self.rm.projectionOf(self.emodes.rawMode(43)).norm()
self.assertAlmostEqual(p, 0.26737834485)
p = self.rm.projectionOf(self.emodes.rawMode(44)).norm()
self.assertAlmostEqual(p, 0.367708993752)
p = self.rm.projectionOf(self.emodes.rawMode(45)).norm()
self.assertAlmostEqual(p, 0.40324227143)
p = self.rm.projectionOf(self.emodes.rawMode(46)).norm()
self.assertAlmostEqual(p, 0.192735085639)
p = self.rm.projectionOf(self.emodes.rawMode(47)).norm()
self.assertAlmostEqual(p, 0.0840421758091)
p = self.rm.projectionOf(self.emodes.rawMode(48)).norm()
self.assertAlmostEqual(p, 0.15035662682)
p = self.rm.projectionOf(self.emodes.rawMode(49)).norm()
self.assertAlmostEqual(p, 0.154260578723)
p = self.rm.projectionOf(self.emodes.rawMode(50)).norm()
self.assertAlmostEqual(p, 0.125542420544)
p = self.rm.projectionOf(self.emodes.rawMode(51)).norm()
self.assertAlmostEqual(p, 0.0451196639208)
p = self.rm.projectionOf(self.emodes.rawMode(52)).norm()
self.assertAlmostEqual(p, 0.0458762025086)
p = self.rm.projectionOf(self.emodes.rawMode(53)).norm()
self.assertAlmostEqual(p, 0.00887400641221)
p = self.rm.projectionOf(self.emodes.rawMode(54)).norm()
self.assertAlmostEqual(p, 0.017086967116)
p = self.rm.projectionOf(self.emodes.rawMode(55)).norm()
self.assertAlmostEqual(p, 0.0609002158356)
p = self.rm.projectionOf(self.emodes.rawMode(56)).norm()
self.assertAlmostEqual(p, 0.0343388857234)
p = self.rm.projectionOf(self.emodes.rawMode(57)).norm()
self.assertAlmostEqual(p, 0.0559503540031)
p = self.rm.projectionOf(self.emodes.rawMode(58)).norm()
self.assertAlmostEqual(p, 0.0332620617319)
p = self.rm.projectionOf(self.emodes.rawMode(59)).norm()
self.assertAlmostEqual(p, 0.0583023511826)
p = self.rm.projectionOf(self.emodes.rawMode(60)).norm()
self.assertAlmostEqual(p, 0.0663342593349)
p = self.rm.projectionOf(self.emodes.rawMode(61)).norm()
self.assertAlmostEqual(p, 0.0568833304731)
p = self.rm.projectionOf(self.emodes.rawMode(62)).norm()
self.assertAlmostEqual(p, 0.161627264195)
p = self.rm.projectionOf(self.emodes.rawMode(63)).norm()
self.assertAlmostEqual(p, 0.1722951381)
p = self.rm.projectionOf(self.emodes.rawMode(64)).norm()
self.assertAlmostEqual(p, 0.239075225836)
p = self.rm.projectionOf(self.emodes.rawMode(65)).norm()
self.assertAlmostEqual(p, 0.241338995808)
def test_pdProjections(self):
p = self.pd.projectionOf(self.emodes.rawMode(6)).norm()
self.assertAlmostEqual(p, 0.0283570029711)
p = self.pd.projectionOf(self.emodes.rawMode(7)).norm()
self.assertAlmostEqual(p, 0.00570349238657)
p = self.pd.projectionOf(self.emodes.rawMode(8)).norm()
self.assertAlmostEqual(p, 0.132182279933)
p = self.pd.projectionOf(self.emodes.rawMode(9)).norm()
self.assertAlmostEqual(p, 0.372076699964)
p = self.pd.projectionOf(self.emodes.rawMode(10)).norm()
self.assertAlmostEqual(p, 0.294163776112)
p = self.pd.projectionOf(self.emodes.rawMode(11)).norm()
self.assertAlmostEqual(p, 0.183147528471)
p = self.pd.projectionOf(self.emodes.rawMode(12)).norm()
self.assertAlmostEqual(p, 0.0271240228062)
p = self.pd.projectionOf(self.emodes.rawMode(13)).norm()
self.assertAlmostEqual(p, 0.178665480086)
p = self.pd.projectionOf(self.emodes.rawMode(14)).norm()
self.assertAlmostEqual(p, 0.128834250691)
p = self.pd.projectionOf(self.emodes.rawMode(15)).norm()
self.assertAlmostEqual(p, 0.0591397692555)
p = self.pd.projectionOf(self.emodes.rawMode(16)).norm()
self.assertAlmostEqual(p, 0.198830357382)
p = self.pd.projectionOf(self.emodes.rawMode(17)).norm()
self.assertAlmostEqual(p, 0.0421877341135)
p = self.pd.projectionOf(self.emodes.rawMode(18)).norm()
self.assertAlmostEqual(p, 0.00971216016261)
p = self.pd.projectionOf(self.emodes.rawMode(19)).norm()
self.assertAlmostEqual(p, 0.0736856356204)
p = self.pd.projectionOf(self.emodes.rawMode(20)).norm()
self.assertAlmostEqual(p, 0.114536706027)
p = self.pd.projectionOf(self.emodes.rawMode(21)).norm()
self.assertAlmostEqual(p, 0.274928559325)
p = self.pd.projectionOf(self.emodes.rawMode(22)).norm()
self.assertAlmostEqual(p, 0.0686378784385)
p = self.pd.projectionOf(self.emodes.rawMode(23)).norm()
self.assertAlmostEqual(p, 0.0130940520067)
p = self.pd.projectionOf(self.emodes.rawMode(24)).norm()
self.assertAlmostEqual(p, 0.0281201750134)
p = self.pd.projectionOf(self.emodes.rawMode(25)).norm()
self.assertAlmostEqual(p, 0.196135377387)
p = self.pd.projectionOf(self.emodes.rawMode(26)).norm()
self.assertAlmostEqual(p, 0.0194536676741)
p = self.pd.projectionOf(self.emodes.rawMode(27)).norm()
self.assertAlmostEqual(p, 0.0120311581935)
p = self.pd.projectionOf(self.emodes.rawMode(28)).norm()
self.assertAlmostEqual(p, 0.0479444837967)
p = self.pd.projectionOf(self.emodes.rawMode(29)).norm()
self.assertAlmostEqual(p, 0.113826710408)
p = self.pd.projectionOf(self.emodes.rawMode(30)).norm()
self.assertAlmostEqual(p, 0.0346732822148)
p = self.pd.projectionOf(self.emodes.rawMode(31)).norm()
self.assertAlmostEqual(p, 0.0693022722289)
p = self.pd.projectionOf(self.emodes.rawMode(32)).norm()
self.assertAlmostEqual(p, 0.0427314320652)
p = self.pd.projectionOf(self.emodes.rawMode(33)).norm()
self.assertAlmostEqual(p, 0.0145340306202)
p = self.pd.projectionOf(self.emodes.rawMode(34)).norm()
self.assertAlmostEqual(p, 0.0655196353298)
p = self.pd.projectionOf(self.emodes.rawMode(35)).norm()
self.assertAlmostEqual(p, 0.0446686455027)
p = self.pd.projectionOf(self.emodes.rawMode(36)).norm()
self.assertAlmostEqual(p, 0.0447414683339)
p = self.pd.projectionOf(self.emodes.rawMode(37)).norm()
self.assertAlmostEqual(p, 0.105694607933)
p = self.pd.projectionOf(self.emodes.rawMode(38)).norm()
self.assertAlmostEqual(p, 0.0369811368042)
p = self.pd.projectionOf(self.emodes.rawMode(39)).norm()
self.assertAlmostEqual(p, 0.099422515813)
p = self.pd.projectionOf(self.emodes.rawMode(40)).norm()
self.assertAlmostEqual(p, 0.214824447562)
p = self.pd.projectionOf(self.emodes.rawMode(41)).norm()
self.assertAlmostEqual(p, 0.0113247783174)
p = self.pd.projectionOf(self.emodes.rawMode(42)).norm()
self.assertAlmostEqual(p, 0.0428190611544)
p = self.pd.projectionOf(self.emodes.rawMode(43)).norm()
self.assertAlmostEqual(p, 0.0395942495882)
p = self.pd.projectionOf(self.emodes.rawMode(44)).norm()
self.assertAlmostEqual(p, 0.184574456157)
p = self.pd.projectionOf(self.emodes.rawMode(45)).norm()
self.assertAlmostEqual(p, 0.0389662995269)
p = self.pd.projectionOf(self.emodes.rawMode(46)).norm()
self.assertAlmostEqual(p, 0.0443754728854)
p = self.pd.projectionOf(self.emodes.rawMode(47)).norm()
self.assertAlmostEqual(p, 0.0189823224475)
p = self.pd.projectionOf(self.emodes.rawMode(48)).norm()
self.assertAlmostEqual(p, 0.106332137903)
p = self.pd.projectionOf(self.emodes.rawMode(49)).norm()
self.assertAlmostEqual(p, 0.182336029271)
p = self.pd.projectionOf(self.emodes.rawMode(50)).norm()
self.assertAlmostEqual(p, 0.222418516151)
p = self.pd.projectionOf(self.emodes.rawMode(51)).norm()
self.assertAlmostEqual(p, 0.208379764186)
p = self.pd.projectionOf(self.emodes.rawMode(52)).norm()
self.assertAlmostEqual(p, 0.161707260103)
p = self.pd.projectionOf(self.emodes.rawMode(53)).norm()
self.assertAlmostEqual(p, 0.29786008418)
p = self.pd.projectionOf(self.emodes.rawMode(54)).norm()
self.assertAlmostEqual(p, 0.00783831845487)
p = self.pd.projectionOf(self.emodes.rawMode(55)).norm()
self.assertAlmostEqual(p, 0.0265930190584)
p = self.pd.projectionOf(self.emodes.rawMode(56)).norm()
self.assertAlmostEqual(p, 0.00543966569196)
p = self.pd.projectionOf(self.emodes.rawMode(57)).norm()
self.assertAlmostEqual(p, 0.00405705977917)
p = self.pd.projectionOf(self.emodes.rawMode(58)).norm()
self.assertAlmostEqual(p, 0.0622064557348)
p = self.pd.projectionOf(self.emodes.rawMode(59)).norm()
self.assertAlmostEqual(p, 0.0489324788794)
p = self.pd.projectionOf(self.emodes.rawMode(60)).norm()
self.assertAlmostEqual(p, 0.199110460545)
p = self.pd.projectionOf(self.emodes.rawMode(61)).norm()
self.assertAlmostEqual(p, 0.148263694589)
p = self.pd.projectionOf(self.emodes.rawMode(62)).norm()
self.assertAlmostEqual(p, 0.14306616768)
p = self.pd.projectionOf(self.emodes.rawMode(63)).norm()
self.assertAlmostEqual(p, 0.0798824699709)
p = self.pd.projectionOf(self.emodes.rawMode(64)).norm()
self.assertAlmostEqual(p, 0.021465578636)
p = self.pd.projectionOf(self.emodes.rawMode(65)).norm()
self.assertAlmostEqual(p, 0.0166782530763)