# Subspace tests # # Written by Konrad Hinsen # import unittest import MMTK from MMTK.Proteins import Protein from MMTK.ForceFields import HarmonicForceField from MMTK.Subspace import RigidMotionSubspace, PairDistanceSubspace from MMTK import NormalModes from Scientific.Geometry.Transformation import Rotation, Translation class RigidBodyTest(unittest.TestCase): """ Test rigid-body motion subspace """ 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 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) def checkOrthonormality(self, subspace): basis = subspace.getBasis() ndim = len(basis) for i in range(ndim): v = basis[i] self.assertAlmostEqual(v.dotProduct(v), 1., 10) for j in range(i+1, ndim): self.assert_(abs(v.dotProduct(basis[j])) < 1.e-10) 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) def suite(): loader = unittest.TestLoader() s = unittest.TestSuite() s.addTest(loader.loadTestsFromTestCase(RigidBodyTest)) s.addTest(loader.loadTestsFromTestCase(PeptideNormalModeTest)) return s if __name__ == '__main__': unittest.main()