Search.setIndex({objects:{"":{MMTK:[34,0,1,""]},"MMTK.Subspace.Subspace":{complement:[34,1,1,""],projectionOf:[34,1,1,""],getBasis:[34,1,1,""],projectionComplementOf:[34,1,1,""]},"MMTK.Biopolymers.ResidueChain":{sequence:[34,1,1,""],residues:[34,1,1,""],residuesOfType:[34,1,1,""]},"MMTK.Proteins.Protein":{sidechains:[34,1,1,""],backbone:[34,1,1,""],phiPsi:[34,1,1,""],residues:[34,1,1,""],residuesOfType:[34,1,1,""]},"MMTK.ChargeFit":{ChargeFit:[34,3,1,""],EqualityConstraint:[34,3,1,""],TotalChargeConstraint:[34,3,1,""],evaluationPoints:[34,2,1,""]},"MMTK.Field":{AtomicScalarField:[34,3,1,""],AtomicField:[34,3,1,""],AtomicVectorField:[34,3,1,""]},"MMTK.Biopolymers":{Residue:[34,3,1,""],defineNucleicAcidResidue:[34,2,1,""],defineAminoAcidResidue:[34,2,1,""],ResidueChain:[34,3,1,""]},"MMTK.PDB.PDBMolecule":{createMolecule:[34,1,1,""]},"MMTK.ParticleProperties.ParticleProperty":{sumOverParticles:[34,1,1,""],scaleBy:[34,1,1,""],zero:[34,1,1,""],return_class:[34,4,1,""],selectAtoms:[34,1,1,""],assign:[34,1,1,""]},"MMTK.NormalModes.VibrationalModes.VibrationalModes":{rawMode:[34,1,1,""],incoherentScatteringFunction:[34,1,1,""],meanSquareDisplacement:[34,1,1,""],EISF:[34,1,1,""]},"MMTK.PDBMoleculeFactory":{PDBMoleculeFactory:[34,3,1,""]},"MMTK.ParticleProperties.ParticleVector":{totalNorm:[34,1,1,""],massWeightedNorm:[34,1,1,""],length:[34,1,1,""],return_class:[34,4,1,""],massWeightedDotProduct:[34,1,1,""],dotProduct:[34,1,1,""],dyadicProduct:[34,1,1,""],norm:[34,1,1,""]},"MMTK.ChemicalObjects.Atom":{translateTo:[34,1,1,""],centerOfMass:[34,1,1,""],bondedTo:[34,1,1,""],setMass:[34,1,1,""],position:[34,1,1,""],setPosition:[34,1,1,""]},"MMTK.FourierBasis":{FourierBasis:[34,3,1,""],countBasisVectors:[34,2,1,""],estimateCutoff:[34,2,1,""]},"MMTK.ForceFields.LennardJonesFF":{LennardJonesForceField:[34,3,1,""]},"MMTK.Bonds.Bond":{hasAtom:[34,1,1,""],otherAtom:[34,1,1,""]},"MMTK.NucleicAcids.Nucleotide":{bases:[34,1,1,""],backbone:[34,1,1,""]},"MMTK.Field.AtomicVectorField":{length:[34,1,1,""],divergence:[34,1,1,""],curl:[34,1,1,""],laplacian:[34,1,1,""]},"MMTK.Solvation":{shrinkUniverse:[34,2,1,""],numberOfSolventMolecules:[34,2,1,""],addSolvent:[34,2,1,""]},"MMTK.ChemicalObjects.Molecule":{findHydrogenPositions:[34,1,1,""]},"MMTK.Random":{randomPointInSphere:[34,2,1,""],randomDirections:[34,2,1,""],randomParticleVector:[34,2,1,""],randomVelocity:[34,2,1,""],randomDirection:[34,2,1,""],randomRotation:[34,2,1,""],randomPointInBox:[34,2,1,""]},"MMTK.Geometry.Line":{distanceFrom:[34,1,1,""],projectionOf:[34,1,1,""],perpendicularVector:[34,1,1,""]},"MMTK.ChemicalObjects":{CompositeChemicalObject:[34,3,1,""],Group:[34,3,1,""],AtomCluster:[34,3,1,""],ChemicalObject:[34,3,1,""],Molecule:[34,3,1,""],Complex:[34,3,1,""],ChainMolecule:[34,3,1,""],Atom:[34,3,1,""],isChemicalObject:[34,2,1,""]},"MMTK.ForceFields.Restraints":{HarmonicAngleRestraint:[34,3,1,""],HarmonicDistanceRestraint:[34,3,1,""],HarmonicDihedralRestraint:[34,3,1,""],HarmonicTrapForceField:[34,3,1,""]},"MMTK.ForceFields.CalphaFF":{CalphaForceField:[34,3,1,""]},"MMTK.Biopolymers.Residue":{nextResidue:[34,1,1,""],precedingResidue:[34,1,1,""]},"MMTK.DCD":{writeDCDPDB:[34,2,1,""],DCDReader:[34,3,1,""],writeVelocityDCDPDB:[34,2,1,""]},"MMTK.Collections.GroupOfAtoms":{numberOfCartesianCoordinates:[34,1,1,""],translateBy:[34,1,1,""],findTransformation:[34,1,1,""],numberOfFixedAtoms:[34,1,1,""],numberOfPoints:[34,1,1,""],atomsWithDefinedPositions:[34,1,1,""],numberOfAtoms:[34,1,1,""],applyTransformation:[34,1,1,""],displacementUnderTransformation:[34,1,1,""],translateTo:[34,1,1,""],temperature:[34,1,1,""],boundingSphere:[34,1,1,""],dipole:[34,1,1,""],writeToFile:[34,1,1,""],angularVelocity:[34,1,1,""],charge:[34,1,1,""],normalizeConfiguration:[34,1,1,""],momentum:[34,1,1,""],centerAndMomentOfInertia:[34,1,1,""],rotateAroundOrigin:[34,1,1,""],normalizePosition:[34,1,1,""],rmsDifference:[34,1,1,""],angularMomentum:[34,1,1,""],booleanMask:[34,1,1,""],centerOfMass:[34,1,1,""],atomCollection:[34,1,1,""],boundingBox:[34,1,1,""],kineticEnergy:[34,1,1,""],rotationalConstants:[34,1,1,""],rotateAroundAxis:[34,1,1,""],universe:[34,1,1,""],normalizingTransformation:[34,1,1,""],mass:[34,1,1,""],rotateAroundCenter:[34,1,1,""],position:[34,1,1,""],degreesOfFreedom:[34,1,1,""],view:[34,1,1,""]},"MMTK.Visualization.Viewable":{graphicsObjects:[34,1,1,""]},"MMTK.ChemicalObjects.ChemicalObject":{atomIterator:[34,1,1,""],universe:[34,1,1,""],removeDistanceConstraints:[34,1,1,""],setRigidBodyConstraints:[34,1,1,""],bondedUnits:[34,1,1,""],getAtomProperty:[34,1,1,""],distanceConstraintList:[34,1,1,""],topLevelChemicalObject:[34,1,1,""],degreesOfFreedom:[34,1,1,""],atomList:[34,1,1,""],numberOfDistanceConstraints:[34,1,1,""],fullName:[34,1,1,""],setBondConstraints:[34,1,1,""]},"MMTK.Proteins":{ConnectedChains:[34,3,1,""],Residue:[34,3,1,""],PeptideChain:[34,3,1,""],isProtein:[34,2,1,""],SubChain:[34,3,1,""],isPeptideChain:[34,2,1,""],Protein:[34,3,1,""]},"MMTK.Universe.CubicPeriodicUniverse":{setSize:[34,1,1,""]},"MMTK.PDB.PDBOutputFile":{write:[34,1,1,""],close:[34,1,1,""],nextModel:[34,1,1,""]},"MMTK.Environment":{AndersenBarostat:[34,3,1,""],NoseThermostat:[34,3,1,""]},"MMTK.Visualization":{Viewable:[34,3,1,""],viewSequence:[34,2,1,""],viewTrajectory:[34,2,1,""],definePDBViewer:[34,2,1,""],defineVRMLiewer:[34,2,1,""],view:[34,2,1,""]},"MMTK.ForceFields.ANMFF":{AnisotropicNetworkForceField:[34,3,1,""]},"MMTK.NormalModes.BrownianModes.BrownianModes":{EISF:[34,1,1,""],staticStructureFactor:[34,1,1,""],incoherentScatteringFunction:[34,1,1,""],meanSquareDisplacement:[34,1,1,""],coherentScatteringFunction:[34,1,1,""],rawMode:[34,1,1,""]},"MMTK.MoleculeFactory.MoleculeFactory":{retrieveMolecule:[34,1,1,""],addSubgroup:[34,1,1,""],addBond:[34,1,1,""],createGroup:[34,1,1,""],addAtom:[34,1,1,""]},"MMTK.Dynamics":{VelocityVerletIntegrator:[34,3,1,""],Heater:[34,3,1,""],TranslationRemover:[34,3,1,""],VelocityScaler:[34,3,1,""],BarostatReset:[34,3,1,""],RotationRemover:[34,3,1,""]},"MMTK.ProteinFriction":{calphaFrictionConstants:[34,2,1,""]},"MMTK.Collections.Collection":{map:[34,1,1,""],selectBox:[34,1,1,""],numberOfAtoms:[34,1,1,""],addObject:[34,1,1,""],universe:[34,1,1,""],removeDistanceConstraints:[34,1,1,""],atomList:[34,1,1,""],selectShell:[34,1,1,""],distanceConstraintList:[34,1,1,""],removeObject:[34,1,1,""],setBondConstraints:[34,1,1,""],numberOfDistanceConstraints:[34,1,1,""],objectList:[34,1,1,""]},MMTK:{Visualization:[34,0,1,""],Solvation:[34,0,1,""],NucleicAcids:[34,0,1,""],Trajectory:[34,0,1,""],ParticleProperties:[34,0,1,""],Environment:[34,0,1,""],Field:[34,0,1,""],ConfigIO:[34,0,1,""],Collections:[34,0,1,""],Units:[34,0,1,""],Biopolymers:[34,0,1,""],Deformation:[34,0,1,""],Minimization:[34,0,1,""],Bonds:[34,0,1,""],ChargeFit:[34,0,1,""],DCD:[34,0,1,""],Subspace:[34,0,1,""],NormalModes:[34,0,1,""],PDBMoleculeFactory:[34,0,1,""],XML:[34,0,1,""],MoleculeFactory:[34,0,1,""],MolecularSurface:[34,0,1,""],Geometry:[34,0,1,""],Universe:[34,0,1,""],FourierBasis:[34,0,1,""],Proteins:[34,0,1,""],PDB:[34,0,1,""],InternalCoordinates:[34,0,1,""],ProteinFriction:[34,0,1,""],Random:[34,0,1,""],ChemicalObjects:[34,0,1,""],Dynamics:[34,0,1,""]},"MMTK.NucleicAcids":{isNucleotideChain:[34,2,1,""],NucleotideChain:[34,3,1,""],Nucleotide:[34,3,1,""],NucleotideSubChain:[34,3,1,""]},"MMTK.Trajectory":{TrajectoryOutput:[34,3,1,""],trajectoryInfo:[34,2,1,""],StandardLogOutput:[34,3,1,""],TrajectoryAction:[34,3,1,""],TrajectorySetVariable:[34,3,1,""],SubVariable:[34,3,1,""],Trajectory:[34,3,1,""],SubTrajectory:[34,3,1,""],SnapshotGenerator:[34,3,1,""],LogOutput:[34,3,1,""],isTrajectory:[34,2,1,""],TrajectorySet:[34,3,1,""],TrajectoryVariable:[34,3,1,""],TrajectoryGenerator:[34,3,1,""],RigidBodyTrajectory:[34,3,1,""],RestartTrajectoryOutput:[34,3,1,""],ParticleTrajectory:[34,3,1,""]},"MMTK.ConfigIO.ZMatrix":{applyTo:[34,1,1,""]},"MMTK.Deformation":{NormalizedDeformationFunction:[34,3,1,""],FiniteDeformationFunction:[34,3,1,""],NormalizedDeformationEnergyFunction:[34,3,1,""],DeformationFunction:[34,3,1,""],DeformationEnergyFunction:[34,3,1,""],DeformationReducer:[34,3,1,""],FiniteDeformationEnergyFunction:[34,3,1,""],FiniteDeformationReducer:[34,3,1,""]},"MMTK.ForceFields.BondFF":{HarmonicForceField:[34,3,1,""]},"MMTK.InternalCoordinates.BondAngle":{setValue:[34,1,1,""],getValue:[34,1,1,""]},"MMTK.NucleicAcids.NucleotideChain":{bases:[34,1,1,""],backbone:[34,1,1,""]},"MMTK.PDB":{PDBOutputFile:[34,3,1,""],PDBPeptideChain:[34,3,1,""],PDBNucleotideChain:[34,3,1,""],PDBFile:[34,4,1,""],PDBConfiguration:[34,3,1,""],PDBMolecule:[34,3,1,""]},"MMTK.PDBMoleculeFactory.PDBMoleculeFactory":{retrieveAsymmetricUnit:[34,1,1,""],retrieveUniverse:[34,1,1,""],retrieveUnitCell:[34,1,1,""],retrieveMolecules:[34,1,1,""]},"MMTK.ConfigIO.Cartesian":{applyTo:[34,1,1,""]},"MMTK.Field.AtomicScalarField":{gradient:[34,1,1,""],laplacian:[34,1,1,""]},"MMTK.NormalModes":{BrownianModes:[34,0,1,""],EnergeticModes:[34,0,1,""],VibrationalModes:[34,0,1,""]},"MMTK.ForceFields.ForceFieldTest":{gradientTest:[34,2,1,""],forceConstantTest:[34,2,1,""],virialTest:[34,2,1,""]},"MMTK.NormalModes.VibrationalModes":{VibrationalModes:[34,3,1,""],VibrationalMode:[34,3,1,""]},"MMTK.Proteins.Residue":{psiAngle:[34,1,1,""],backbone:[34,1,1,""],chiAngle:[34,1,1,""],phiPsi:[34,1,1,""],sidechains:[34,1,1,""],phiAngle:[34,1,1,""]},"MMTK.InternalCoordinates.DihedralAngle":{setValue:[34,1,1,""],getValue:[34,1,1,""]},"MMTK.MolecularSurface":{findContacts:[34,2,1,""],surfacePointsAndGradients:[34,2,1,""],surfaceAndVolume:[34,2,1,""],surfaceAtoms:[34,2,1,""]},"MMTK.ForceFields.Amber":{Amber94ForceField:[34,3,1,""],OPLSForceField:[34,3,1,""],AmberForceField:[34,0,1,""],Amber99ForceField:[34,3,1,""]},"MMTK.Proteins.PeptideChain":{phiPsi:[34,1,1,""],sidechains:[34,1,1,""],backbone:[34,1,1,""],replaceResidue:[34,1,1,""],sequence:[34,1,1,""]},"MMTK.ForceFields.SPCEFF":{SPCEForceField:[34,3,1,""]},"MMTK.NormalModes.EnergeticModes.EnergeticModes":{rawMode:[34,1,1,""]},"MMTK.InternalCoordinates":{BondLength:[34,3,1,""],BondAngle:[34,3,1,""],DihedralAngle:[34,3,1,""]},"MMTK.Universe.ParallelepipedicPeriodicUniverse":{scaleSize:[34,1,1,""]},"MMTK.ParticleProperties":{ParticleScalar:[34,3,1,""],isConfiguration:[34,2,1,""],Configuration:[34,3,1,""],ParticleProperty:[34,3,1,""],ParticleVector:[34,3,1,""],ParticleTensor:[34,3,1,""],isParticleProperty:[34,2,1,""]},"MMTK.ParticleProperties.ParticleTensor":{return_class:[34,4,1,""]},"MMTK.InternalCoordinates.BondLength":{setValue:[34,1,1,""],getValue:[34,1,1,""]},"MMTK.Collections":{isCollection:[34,2,1,""],PartitionedCollection:[34,3,1,""],PartitionedAtomCollection:[34,3,1,""],GroupOfAtoms:[34,3,1,""],Collection:[34,3,1,""]},"MMTK.ForceFields":{Restraints:[34,0,1,""],ForceFieldTest:[34,0,1,""]},"MMTK.Bonds.BondAngle":{otherBond:[34,1,1,""]},"MMTK.Universe.Universe":{contiguousObjectConfiguration:[34,1,1,""],getAtomScalarArray:[34,1,1,""],environmentObjectList:[34,1,1,""],adjustVelocitiesToConstraints:[34,1,1,""],energyTerms:[34,1,1,""],addObject:[34,1,1,""],energy:[34,1,1,""],atomList:[34,1,1,""],contiguousObjectOffset:[34,1,1,""],realToBoxCoordinates:[34,1,1,""],configurationDifference:[34,1,1,""],acquireReadStateLock:[34,1,1,""],acquireWriteStateLock:[34,1,1,""],fractionalToCartesian:[34,1,1,""],removeObject:[34,1,1,""],energyAndGradients:[34,1,1,""],distanceVector:[34,1,1,""],removeDistanceConstraints:[34,1,1,""],releaseWriteStateLock:[34,1,1,""],cartesianToFractional:[34,1,1,""],addToConfiguration:[34,1,1,""],getAtomBooleanArray:[34,1,1,""],setForceField:[34,1,1,""],forcefield:[34,1,1,""],largestDistance:[34,1,1,""],releaseConfigurationChangeLock:[34,1,1,""],scaleVelocitiesToTemperature:[34,1,1,""],numberOfDistanceConstraints:[34,1,1,""],map:[34,1,1,""],basisVectors:[34,1,1,""],masses:[34,1,1,""],dihedral:[34,1,1,""],energyGradientsAndForceConstants:[34,1,1,""],setVelocities:[34,1,1,""],getParticleBoolean:[34,1,1,""],getParticleScalar:[34,1,1,""],enforceConstraints:[34,1,1,""],distanceConstraintList:[34,1,1,""],releaseReadStateLock:[34,1,1,""],angle:[34,1,1,""],configuration:[34,1,1,""],randomPoint:[34,1,1,""],objectList:[34,1,1,""],distance:[34,1,1,""],selectBox:[34,1,1,""],setConfiguration:[34,1,1,""],initializeVelocitiesToTemperature:[34,1,1,""],charges:[34,1,1,""],universe:[34,1,1,""],velocities:[34,1,1,""],setFromTrajectory:[34,1,1,""],reciprocalBasisVectors:[34,1,1,""],cellVolume:[34,1,1,""],energyAndForceConstants:[34,1,1,""],selectShell:[34,1,1,""],acquireConfigurationChangeLock:[34,1,1,""],copyConfiguration:[34,1,1,""],boxToRealCoordinates:[34,1,1,""],setBondConstraints:[34,1,1,""]},"MMTK.ParticleProperties.ParticleScalar":{applyFunction:[34,1,1,""],return_class:[34,4,1,""],minimum:[34,1,1,""],maximum:[34,1,1,""]},"MMTK.ConfigIO":{Cartesian:[34,3,1,""],ZMatrix:[34,3,1,""]},"MMTK.PDB.PDBConfiguration":{createMolecules:[34,1,1,""],peptide_chain_constructor:[34,4,1,""],applyTo:[34,1,1,""],createAll:[34,1,1,""],molecule_constructor:[34,4,1,""],asuToUnitCell:[34,1,1,""],createUnitCellUniverse:[34,1,1,""],createNucleotideChains:[34,1,1,""],nucleotide_chain_constructor:[34,4,1,""],createPeptideChains:[34,1,1,""]},"MMTK.PDB.PDBNucleotideChain":{createNucleotideChain:[34,1,1,""]},"MMTK.Universe.OrthorhombicPeriodicUniverse":{scaleSize:[34,1,1,""]},"MMTK.ForceFields.DeformationFF":{DeformationForceField:[34,3,1,""]},"MMTK.MoleculeFactory":{MoleculeFactory:[34,3,1,""]},"MMTK.Bonds":{BondAngleList:[34,3,1,""],DihedralAngle:[34,3,1,""],DihedralAngleList:[34,3,1,""],BondAngle:[34,3,1,""],Bond:[34,3,1,""]},"MMTK.Minimization":{ConjugateGradientMinimizer:[34,3,1,""],SteepestDescentMinimizer:[34,3,1,""]},"MMTK.Collections.PartitionedCollection":{pairsWithinCutoff:[34,1,1,""],partitions:[34,1,1,""]},"MMTK.Trajectory.ParticleTrajectory":{translateBy:[34,1,1,""]},"MMTK.Field.AtomicField":{view:[34,1,1,""],particleValues:[34,1,1,""],writeToFile:[34,1,1,""]},"MMTK.XML":{XMLMoleculeFactory:[34,3,1,""]},"MMTK.NormalModes.BrownianModes":{BrownianModes:[34,3,1,""],BrownianMode:[34,3,1,""]},"MMTK.Bonds.BondAngleList":{dihedralAngles:[34,1,1,""]},"MMTK.Universe":{InfiniteUniverse:[34,3,1,""],isUniverse:[34,2,1,""],Universe:[34,3,1,""],OrthorhombicPeriodicUniverse:[34,3,1,""],ParallelepipedicPeriodicUniverse:[34,3,1,""],CubicPeriodicUniverse:[34,3,1,""]},"MMTK.Geometry":{Box:[34,3,1,""],Cylinder:[34,3,1,""],RhombicLattice:[34,3,1,""],Lattice:[34,3,1,""],FCCLattice:[34,3,1,""],BravaisLattice:[34,3,1,""],BCCLattice:[34,3,1,""],Sphere:[34,3,1,""],Plane:[34,3,1,""],Cone:[34,3,1,""],Line:[34,3,1,""],SCLattice:[34,3,1,""],Circle:[34,3,1,""],superpositionFit:[34,2,1,""],GeometricalObject3D:[34,3,1,""]},"MMTK.NormalModes.EnergeticModes":{EnergeticMode:[34,3,1,""],EnergeticModes:[34,3,1,""]},"MMTK.Geometry.GeometricalObject3D":{volume:[34,1,1,""],hasPoint:[34,1,1,""],enclosesPoint:[34,1,1,""],intersectWith:[34,1,1,""]},"MMTK.Trajectory.Trajectory":{readRigidBodyTrajectory:[34,1,1,""],variables:[34,1,1,""],readParticleTrajectory:[34,1,1,""],flush:[34,1,1,""],close:[34,1,1,""],view:[34,1,1,""]},"MMTK.PDB.PDBPeptideChain":{createPeptideChain:[34,1,1,""]},"MMTK.Subspace":{RigidMotionSubspace:[34,3,1,""],PairDistanceSubspace:[34,3,1,""],LinkedRigidBodyMotionSubspace:[34,3,1,""],Subspace:[34,3,1,""]}},terms:{orthogon:34,all:[0,1,3,39,6,7,8,10,11,16,17,19,20,24,27,29,30,31,32,33,34,37,36],yellow:[12,14,38],interchang:20,four:34,prefix:34,netcdf:20,module_dict:43,forget:7,finitedeformationreduc:34,whose:[20,32,9,3,34],accur:[20,34],distancevector:34,time_rang:34,sorri:[29,19],mmtk_forcefield:[16,24,11,1],cevalu:1,deviat:34,forcefield:[2,4,5,6,7,11,12,13,14,15,16,17,19,20,21,23,24,26,27,29,34,35,38,39,40,43],under:[20,34,8],slowest:[12,14,38],numberofatom:[16,37,34,35],cm2:34,cm1:34,box_coordin:34,eisenhaber1995:20,everi:[24,17,34,39,20,21,37,29,23,11],risk:20,interpolatingfunct:34,"void":[16,24,43,11],hinsen1998:20,hinsen1999:20,"6q21":42,polypeptid:20,affect:20,hinsen1997:20,hinsen1995:20,kbar:34,factori:34,translationremov:[26,34,39,4,20,21,23],vector:[0,12,14,26,27,2,17,34,19,4,5,20,28,29,7,30,38,10],vrml97:20,brownianmod:[13,34,20],philpot:20,atom4:34,seper:20,direct:[0,12,34,7,16],atom2:34,atom3:34,consequ:[20,17,29,34,23],second:[24,16,34,20,21,8,41,43,42,23,11],bondangl:34,chem:[40,34,35],even:[20,34],initializevelocitiestotemperatur:[20,21,34,39,26],randomparticlevector:34,neg:[16,34],vdw_and_stick:34,nonetyp:34,"new":[32,3,34,20,7,8],net:20,ever:20,topolog:[20,34],elimin:[20,32,34],transcarbamylas:[12,14,38],selectatom:34,never:[20,34],here:[24,27,2,17,3,19,39,20,29,8,42,11],readrigidbodytrajectori:34,path:[20,34],normalizeposit:34,superpositionfit:34,interpret:[20,31,22,34],error2:43,cdef:[16,24,11],rotation_matrix:20,prognam:34,precis:[20,34],pdbchain:34,permit:[20,34],studi:[12,20,14,38],fourier:[34,35],pairswithincutoff:34,nanomet:42,tertiari:[12,14,38],brought:20,unix:[20,34],total:[20,28,9,34],unit:[13,14,26,1,16,34,28,4,35,20,21,6,39,38,9,10,42,23,43],highli:2,bookkeep:7,plot:35,compositechemicalobject:34,dna:[41,20,34,7],pyarg_parsetupl:43,would:[20,28,22,23],plor:[20,34,7],prescript:20,call:[24,27,16,17,34,19,20,29,11],trajectoryvari:34,lennard:[20,34,26],type:[20,16,17,34,3,19,27,29,42,43],until:34,length_scal:34,relax:[20,34,4],relat:[20,34],warn:34,moleculefactori:[13,34],exce:34,harmonic_oscil:[29,19,11],loss:34,hold:34,r_new:34,must:[24,18,34,39,4,20,30,31,22,42,11],permitt:34,accid:[29,19],word:20,restor:20,setup:[20,39],work:[16,14,34,7,20],numberofcartesiancoordin:34,conceptu:20,root:[20,34],real_cutoff:34,overrid:34,environmentobjectlist:34,kinet:[16,21,43,34,20],give:[20,2,17,34,19,27,29],indic:[0,12,13,16,17,34,20,29,25,42],want:[34,3,20,6,8,42],eisenhaber1993:20,keep:[16,34,3,20,1],fractionaltocartesian:34,end:[20,34,39,43],attributefix:20,cylind:[2,34],ordinari:[20,23],iiir:34,classifi:20,how:[2,34,35,36,20,28,7,42],vel_list:34,avaiabl:34,pdbpath:14,"_memo":34,updat:[20,34],spceff:34,mess:42,earlier:20,befor:[20,34,8],wrong:20,nucleicacid:[41,13,34,20],nucleotid:[41,13,34,20],law:34,barostatreset:[20,34,26,4],parallel:[13,24,34,39,4,20,7,43,11],demonstr:[20,28,7,42],descent:[20,34],pairdistancesubspac:34,attempt:[16,20],third:[24,34,8,11],rmsdiffer:34,exclud:[20,34],view_trajectori:7,environ:[13,26,1,34,4,20],frequent:[20,34],exclus:20,harmonicoscil:29,lambda:[0,42],order:[18,34,4,36,20,6,7,30,41,31,22,42,23],pylist_typ:43,belong:34,composit:[20,34],deform:[13,34,42,20],over:[32,34,3,20,37,30,40],becaus:[14,33,34,20,8,22,42],keyboard:20,flexibl:[20,42],vari:34,pyarrayobject:[43,24,11],"\u00e5ngstr\u00f6m":20,atomclust:[33,34,36],relaxation_tim:34,ligand:[41,34,7],fit:[13,34,20,28,7,42],del:[20,32,34],fix:[13,34,19,20,29,23],selectshel:34,viewabl:[20,34],better:4,py_incref:43,easier:[32,3],them:[20,3,34,8],anim:[13,15,40,34,35,20,7,25,42],createnucleotidechain:[41,34],thei:[33,34,20,28,7,23],safe:[16,34,20],randomrot:34,nextresidu:34,"break":26,fc_length:34,haspoint:34,normalizeconfigur:[34,4],interrupt:20,setvalu:34,bank:20,choic:34,oxygen:20,getvalu:34,langevindynam:7,arrow:[0,14,2,34,20,38],each:[16,17,34,4,5,20,6,7,29,42],electrostat:[20,28,34,7],definenucleicacidresidu:34,side:34,bond:[13,34,20],energy_term:[24,11],macromolecul:[20,34],monolith:20,trajectoryact:[16,34],pyerr_occur:43,energy_data:[16,24,43,11],unbound:34,trajectoryinfo:[20,21,34,39,23],gradient:[24,16,17,34,20,29,43,11],newli:[20,34],pyffevaluatorobject:[43,11],angular:[20,21,34],content:[20,34],first_step:[16,34],adapt:7,reader:[31,34],size:[26,16,34,35,4,20,6,7,9,42,43],particlevalu:34,linear:[20,34],barrier:39,situat:20,free:[20,43],ineffici:20,orthorhombicperiodicunivers:[20,9,34,26,4],angl:[20,34,42],ato:34,atm:[34,26,4],filter:34,acquirewritestatechangelock:20,rais:[16,34,29,19,1],confus:[20,34],rang:[12,14,2,34,32,5,20,6,16,40,38,10,35],ranf:43,render:20,pyobject_getattrstr:43,independ:34,atomcollect:34,rank:[20,34,39],neglect:34,restrict:[20,14,38],alreadi:[20,34],kinetic_energi:[16,21,43],primari:34,trajectoryoutput:[32,26,34,3,39,4,20,21,6,31,10,23],cartesian:[20,34],top:[20,34],sometim:20,eisf:34,too:[20,39],similarli:20,boundingbox:[34,42,4],inv_relaxation_tim:34,consol:[20,39],tool:[20,7],lower:20,atom1:34,phipsi:34,acquirewritelock:16,somewhat:20,conserv:20,setbondconstraint:[20,34],addobject:[14,9,26,34,3,32,36,37,38,41,31,42],conveni:[20,34,43],keyword:[16,34,20,1],provid:[33,17,34,20,29,7,43],zero:[12,14,27,1,2,17,30,34,35,20,28,38,16],project:[20,34],ktm:43,temperature_factor:34,calphaff:[20,34],design:20,pdbconfigur:[34,36,20,8,41,31,42],"10th":20,rad:34,mind:20,gaussian_bivari:43,increment:34,pdbmolecul:34,seen:34,seem:42,incompat:20,retrievemolecul:34,strength:[27,17,24],recreat:[27,17,34,29,19],chargefit:[13,28,34,20],latter:34,point1:[2,34],point2:[2,34],client:34,partitionedatomcollect:34,thoma:[12,14,34,20,38,42],pydict_getitemstr:43,simplifi:[20,6,34,40],centrer:34,though:20,object:[0,1,2,3,7,8,11,12,13,14,16,17,19,20,24,27,29,30,31,32,34,38,41,36],rigidbodytransform:34,boltzmann:34,regular:[34,26],letter:[20,34],dyadicproduct:34,harmonictrapforcefield:34,doi:20,don:[42,6,7,8,23],construct_from_pdb:7,flow:20,doe:[34,39,19,20,29,7],dummi:43,do_gradi:[17,29],sum:[28,34,30],dot:[20,34,43],explan:[20,34,43],opposit:34,random:[13,34,39,4,20,6,43],radiu:[2,34,20],syntax:20,radii:[20,34],protocol:[20,34],involv:[20,34],nucleotidesubchain:34,evaluationpoint:[28,34],layout:[20,34],acquir:[16,34],ba1:34,explain:[20,6],configur:[1,3,4,6,7,8,10,11,13,22,16,17,18,39,20,21,25,23,24,26,29,30,31,32,34,36,37,41,42,43],rigidbodytrajectori:34,sugar:[20,34],"__call__":1,small_chang:34,serv:34,pylab:35,pytrajectory_veloc:[16,43],stop:[20,34,8],tetramer_1:42,report:20,symmetr:34,xmlmoleculefactori:34,bar:34,twice:[20,34],bad:20,countbasisvector:34,multipol:[20,34],datatyp:34,result:[24,17,34,20,29,7,11],fail:34,best:[7,5],subject:[20,34],peta:34,tensor:[0,20,34],colorbynam:2,databas:[13,14,20,17,34,27,8,41],psiangl:34,drawn:[20,34],approach:[20,34],attribut:[2,34,20,1],accord:[20,34],vrmlviewer:34,extend:[16,34,20],extens:34,add:[0,26,34,4,20,30,9,43],toler:[34,7],groupofatom:[33,20,34],expos:[20,34],howev:[20,34],kineticenergi:34,crystallograph:[34,8],vector_field_chimera:7,character:34,ref_i:11,pyffevaluator_typ:43,graphics_data:7,dens:20,totalchargeconstraint:[28,34],ref_z:11,ref_x:11,assum:[20,34],mpi_commun:[34,39],numpi:[16,43],three:[0,34,35,4,20,8,42],been:[16,34,4,20],trajectory_extract:7,much:[17,34,19,4,39,20,29,7,42,23],interest:[20,32,3,34,42],basic:20,life:[7,39],suppress:34,xxx:8,argument:[24,27,1,17,34,19,20,29,25,41,43,11],multithread:20,mmtk_trajectory_gener:16,ident:[20,34,42],properti:[13,20,33,17,34,27,43],commerci:20,step10:21,calcul:[2,4,5,6,7,12,14,15,16,17,19,20,27,28,29,30,34,35,37,38,40,42,43],cystein:[20,34],aid:[20,34],seven:34,have:[32,24,16,3,34,4,20,42,23,11],rotatearoundorigin:34,tabl:[13,34],toolkit:[20,34],kwarg:34,cone:[2,34],conf:[32,26,18,34,20,6,31],tediou:20,sever:[33,20,24,34,11],optionel:34,dilut:4,calpha_mod:7,perform:[20,28,10,34],make:[0,32,16,17,34,3,19,20,29,7,8,42],acquirereadstatechangelock:20,virial_index:[24,11],complex:[33,13,34,7,20],acetylaceton:[20,34],split:[34,26],group_spec:34,complet:[20,34,36],evid:20,blue:[0,34],action:[13,32,26,15,16,3,34,4,5,20,21,6,39,31,10,42,23,43],glu63:42,glu62:42,ewald:[20,34,4],atom_nam:34,squar:[20,34],kept:[20,34],thz:20,thu:[20,34],inherit:[33,24,11],particletrajectori:34,contact:[20,34],thi:[1,2,3,39,7,8,9,22,11,12,14,16,17,18,19,20,25,24,27,28,29,30,31,32,34,35,36,37,38,41,42],endif:43,lijnzaad:20,everyth:[0,20,3,34],left:34,identifi:[20,34],force_const:[16,17,34,19,29,43,11],just:[32,27,34,17,3,19,20,29,8,42],applyto:[34,42],yet:34,languag:20,previous:[20,34],pressure_unit_nam:43,characterist:42,easi:20,energy_unit_nam:[16,43],conjug:[20,34],ideal:[20,34],fortran:[20,34],els:[32,17,39,35,20,8,43],save:[13,32,3,39,20],anisotropicnetworkforcefield:[13,34],applic:[12,14,33,34,39,4,20,28,38,7],which:[32,24,34,18,33,2,17,30,3,19,36,20,6,7,16,29,31,22,42,11],rna:20,rotatearoundaxi:34,isconfigur:34,machin:20,linearli:34,background:[16,34],elabor:[12,14,38],opl:34,measur:20,vdw:34,specif:[13,34,19,20,29,36,43],filenam:[20,14,34],arbitrari:[20,34,7],manual:[20,34,10,7],right:[2,6,34],peptide_chain_constructor:34,deal:[20,42],interv:[34,26],eas:20,percentag:20,intern:[34,19,20,29,7,36],cubicperiodicunivers:[20,34],successfulli:34,cooper:20,bottom:34,chain_calpha:32,subclass:[33,20,34],multipli:[20,14,34,38],condit:[20,34],bcclattic:34,core:[16,24,34,11],plu:[0,16,34,4,20],subspac:[13,34,20,35,5],enclosespoint:34,quaternion:[20,34],unreason:20,emissivemateri:[0,2],elementary_cel:34,chapter:20,obj:34,eggebrecht:20,fourierbasi:[13,34,35,20],biopolym:[13,34],surround:[20,34],simul:[14,26,34,39,4,20,21,38,7,23],coars:34,natom:[16,24],runcommand:14,produc:[20,34],py_decref:43,thermostat:[13,26,16,34,4,20],"float":[16,34,29,19],bound:[16,34,42,20],bath:[20,43],down:[20,39,4],normalizeddeformationenergyfunct:34,bool:[16,34],storag:20,rotationalconst:34,akma_tim:34,suffici:[20,34],setconfigur:[6,32,3,34],support:[16,34,20,1],transform:[13,42,10,34,20],avail:[16,34,7,20],width:34,scientificpython:20,fraction:34,overhead:20,connectedchain:34,electrostatic_energi:[28,34],analysi:[12,13,14,34,35,20,38,7,8,42],form:[20,34,8],offer:20,forc:[13,24,26,1,16,17,34,27,19,4,20,29,7,8,40,43,11],some:[26,34,4,20,7,8,42,23,43],recommend:20,heat:[20,21,34,39,43],multiprocessor:20,ff99sb:21,"true":[16,17,34,19,27,29],reset:[20,34,26,4],setveloc:34,inquir:[20,17,29,19,27],maximum:[20,34],crystal:34,mth:20,largestdist:34,featur:[16,42,34,20,1],classic:20,logoutput:[20,34,26,4],"abstract":[33,34,17,29],proven:[20,34],exist:[20,34],nucleotidechain:[41,20,34],check:[1,16,19,20,29,7,43],assembl:[20,10,34],calpha:[12,14,2,34,32,35,37,6,38],symmetricpairtensor:[34,17,29],viduna:[20,34],when:[16,17,34,19,36,20,29,8,42],jone:[20,34,26],test:[20,21,34,39,26],shrink:[34,4],vrml:[0,12,13,34,20,42],objects3d:[9,34],intend:20,initio:28,sqr:43,boundscheck:16,releasereadstatechangelock:20,first_mod:34,intent:[33,20],consid:[20,34],src:20,uniformli:34,parallelepiped:34,longer:34,furthermor:20,anywher:20,surfaceandvolum:34,pseudo:34,ignor:20,time:[26,16,17,34,39,4,20,21,29,7,22,42,23,43],releasewritelock:16,centerandmomentofinertia:[0,34],chain:[13,32,33,34,35,20,37,8,41,31,42],skip:[20,34],global:[32,24,34,39,20,21,43,23,11],brownian:[20,34],no_hydrogen:[34,42,8],deformationevaluationfunct:34,last_step:34,subobject:34,hierarch:20,decid:34,depend:[20,6,34,4],color_valu:[34,42],intermedi:34,chain_id:34,subtrajectori:34,point_dens:34,giga:34,translatebi:34,sourc:[20,34],string:[20,34,26,25],fcclattic:34,mmtk_harmonic_oscil:[7,19],oplsforcefield:34,fourth:[24,34,8,11],feasibl:20,internalcoordin:[13,34],pdbmap:20,exact:20,level:[20,16,34,19,27,29,43],is_wat:3,pyeval_restorethread:43,iter:[20,34],andersenbarostat:[20,34,26,4],item:[20,3,34],array_typ:34,quick:42,round:42,prevent:[20,34],slower:[20,34],empir:[34,6],applytransform:[34,32,10,42],complex_spec:34,output_act:[26,4,39],deformation_funct:42,lys101:42,chage:34,vector3:[43,24,11],favour:20,uniform:[27,17,34],current:[20,34,42],fluctiat:37,xplor:[31,22],createpeptidechain:[20,31,34,8],deriv:[20,34],sizeof:43,gener:[0,13,32,2,3,34,20,6,7,8,10,43],coeffici:[43,34,1],lattice_s:9,water:[34,3,4,20,7,9],contiguousobjectoffset:34,explicitli:[20,34],modif:[16,34,20,7,8,23],estimatecutoff:[34,35],along:[20,21,34],wait:34,box:[26,16,34,4,20,42,43],shift:34,behav:[20,34],overriden:20,extrem:34,kcal:34,commonli:[20,34],semant:16,modul:[0,13,1,2,34,20,7,16,43],prefer:34,mmtk_electric_field:[27,7],centerofmass:34,fake:[2,7],instal:20,planck:34,market:20,myoglobin:20,documnent:[16,34],hinsen1999a:20,hinsen1999b:20,memori:[20,34],univers:[1,2,3,4,5,6,7,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,26,27,29,30,31,32,34,35,36,37,38,39,40,41,42,43],temperature_unit_nam:43,criteria:[41,8],dict:[34,43],analyz:[13,32,34,3,20,42],capit:20,share:[20,34],finit:[34,43],enhanc:20,random1:43,visual:[0,2,3,7,9,12,13,14,15,40,39,20,21,25,23,30,32,34,35,38,41,42],rigid:[32,34,5,20,7,42],accept:20,cartesiantofract:34,removeobject:34,overdamp:20,easiest:20,graphic:[0,12,14,2,34,20,38,7,41,42],linkedrigidbodymotionsubspac:34,prepar:16,uniqu:20,descriptor:43,can:[24,27,1,33,2,17,34,20,28,7,8,16,41,43,36,23,11],cal:34,purpos:[20,34],materi:[0,2],eps0:34,nearest:34,removeresidu:[42,8],trajectory_calpha:32,stream:34,pytrajectory_outputspecif:43,topic:20,vdw_radiu:20,konrad:[16,43,20,1],graphicsobject:[0,12,14,2,34,20,38,42],spc:34,hydrogen:[41,20,34,42,8],occur:[20,34],clair:20,occup:34,orthorhomb:[20,34],alwai:[20,34],differenti:34,multipl:[20,34,39],deformationff:[20,34],write:[2,34,39,20,21,7,8,16,10,23,43],anyon:20,dcdreader:[20,31,34],pure:[20,17,29,7,39],pyarray_fromdim:43,map:[0,32,26,34,20,42],product:[20,21,34,39,26],data_rank:34,polar_charmm:34,book:20,max:[34,35],frcmod:21,usabl:33,xtick:35,partition_s:34,mai:[20,34,42],numberofpoint:34,underscor:34,length_unit_nam:43,data:[32,24,16,3,34,20,21,7,2,43,22,36,23,11],harmon:[40,34,19,35,20,29,7,11],deformationfunct:34,practic:[20,34],liquid:[7,26],stdin:34,explicit:[20,34,8],dyn:34,maxwel:34,inform:[20,21,34],"switch":42,preced:34,combin:[20,34],callabl:34,residuechain:34,prefactor:34,surfaceatom:34,residue_numb:34,hoh:20,enforceconstraint:[20,34],global_data:[27,17,29,19],pointer:43,dynam:[13,26,1,16,34,35,4,39,20,21,7,40,23,43],entiti:20,protein_calpha:32,group:[33,13,34,8,20],declaretrajectoryvariable_arrai:16,corner1:34,"\u03b1":[20,34,7],platform:34,window:34,main:[16,43],permit_undefin:34,iiil:34,non:[12,13,14,15,2,34,35,20,38,8,40],initi:[32,26,27,16,17,34,19,20,21,29,23,43],cellsiz:34,conf_fil:26,therebi:4,half:[16,6,34],now:[42,4],nor:[20,34],introduct:[13,34,20],term:[24,27,16,17,34,19,20,29,7,11],namd:[34,7],name:[0,14,24,32,27,2,17,34,3,19,35,20,29,8,43,11],realist:4,addbond:34,tera:34,separ:[16,34,20],full_nam:34,attributeerror:3,compil:[16,20],domain:[20,34,35],"3x4x5":9,replac:34,individu:[20,34],writedcdpdb:[20,22,34],gaussian:[34,6,43],conf_calpha:32,mmtkdatabas:20,calphafrictionconst:34,significantli:34,operand:34,wavelength:34,his94:42,py_ssize_t:16,shown:[14,24,34,20,38,8,11],space:[14,34,19,20,38,29],profit:[20,39],atom_spec:34,formula:34,correct:[20,34,43],createmolecul:[41,34],after:[20,34],"goto":43,gase:20,argv:25,return_class:34,argo:20,org:20,argc:25,care:[16,17,34,19,20,29],wai:[20,36,34,7,42],frequenc:[15,40,34,35,5,20],correction_funct:43,synchron:[16,39,20],motion:[12,14,34,32,5,20,38,7,35],turn:34,place:[32,34,3,20,7,9],trajectoryset:34,principl:20,imposs:22,arraytyp:[24,11],first:[12,14,24,25,1,15,2,17,34,32,35,20,29,8,16,40,38,43,42,23,11],origin:[20,34,7,4,42],suspend:34,barostat:[13,26,16,34,4,20],directli:[33,20,34,7,8],onc:[20,34],arrai:[0,32,24,1,16,17,34,27,43,11],isnucleotidechain:34,yourself:20,reopen:21,pyimport_importmodul:43,symmetri:34,open:[14,26,34,3,32,20,37,30],predefin:34,getact:1,random_forc:43,given:[1,17,34,20,6,7,25,29,11],potential_energi:[16,43],convent:[20,34],lj_radiu:34,necessarili:20,averag:[20,37,34,7,30],circl:34,white:20,environmentobject:34,cite:34,editor:20,pdb_file_nam:34,writevelocitydcdpdb:34,especi:20,memo:34,copi:[13,32,34,20,6,42],specifi:[1,16,34,39,20,42],radiosensit:20,mostli:20,floppi:42,calpha_transform:42,than:[16,34,4,20],energygradientsandforceconst:34,wide:20,spceforcefield:[13,34],conglomer:20,getatomscalararrai:34,serg:20,were:[34,7],posit:[26,16,34,4,20,28,8,41,9,42,23,43],residuesoftyp:[0,34],browser:[0,12,20],sai:[27,17,29,19],ang:[14,26,34,20,38,42],anm:34,createal:[20,34,36],ani:[0,24,27,2,17,34,4,20,29,8,23,11],scale_factor:34,scharf:20,engin:[27,17,29,19],techniqu:[20,34,7,35],gunsteren:20,mmtk_langevin:[43,1],moreov:32,imol:34,note:[32,18,16,17,3,34,4,39,20,28,37,6,8,30,29,31,22,42,23],subformat:34,take:[32,17,34,19,20,29],advis:34,green:[0,34],noth:[17,34,39,36,20,29,42],incoher:34,begin:34,sure:[16,34,7,20],importantli:20,normal:[12,13,14,15,2,34,35,5,20,6,7,40,38],buffer:34,compress:[34,4],random_vector:34,t_action:20,beta:34,pair:[20,34],distancefrom:34,later:[20,2,17,19,27,29,8,42],quantiti:[20,34],bondedto:34,lj_option:34,asu_cont:34,wolf1999:20,axi:[0,12,34,42,20],translat:[34,39,5,20,21,42,23],chains_calpha:32,time_unit_nam:[16,43],show:[12,14,15,2,34,35,36,20,38,7,25,40,41,42],xmol:[20,34],atom:[0,1,6,7,8,22,13,16,17,19,20,26,27,28,29,31,32,33,34,35,36,37,41,42,43],friction:[43,34,1],partitionedcollect:[20,34],calculateenergi:16,corner:34,fifth:[20,21,23],deci:34,xml:[13,34],onli:[14,24,27,2,17,38,34,39,36,20,37,6,7,41,29,42,23,11],replaceresidu:34,state:[16,34,39,4,20,23,43],finalizetrajectoryact:16,black:20,helix:42,analyt:[20,34],analys:20,gly_34:34,mmtk_langevinmodul:7,compoundforcefield:34,variou:[20,34,42],get:[24,1,19,20,29,43,42,11],"_energi":34,kneller:[20,34,35,40],repr:34,deca:34,colorscal:[2,34],unscal:34,cannot:[33,34,32,3,39],basisvector:34,chemic:[13,34,20],requir:[24,27,17,34,19,4,20,29,8,42,11],configuraton:34,mmtk_energy_thread:[16,34,20],yield:[20,34],where:[20,34],summari:34,numberofsolventmolecul:[34,4],additional_object:7,assumpt:20,pytrajectory_particlescalar:43,electric_field:[27,17,24],chemicaobject:33,infinit:[20,34],detect:34,enumer:18,label:34,between:[14,34,4,20,38,10,42],"import":[0,1,2,3,4,5,6,7,8,9,10,12,14,22,15,16,17,18,19,20,21,25,23,26,27,28,29,30,31,32,34,35,36,37,38,39,40,41,42,43],across:34,randompointinspher:34,spars:[20,34],parent:34,comp:34,screen:[20,21,34,23],import_mmtk_trajectori:43,energyandforceconst:34,cycl:34,getparticlescalar:[34,1],virial:[17,34,43],come:[20,28],unrel:20,region:[20,42],mont:[20,6,7],tutori:20,improv:20,bonded_scale_factor:34,improp:34,pdb_altern:20,acceler:16,nbasi:35,color:[0,12,14,2,34,20,38],overview:[13,20],period:[13,26,16,34,4,20,9,43],insist:42,exagger:34,sentinel:43,deformationforcefield:[12,13,34],amino:[20,34,7],"110d":41,charge_properti:[27,17],coupl:20,"_3ter":34,invers:[20,34],booleanmask:[37,34],valueerror:[16,34,29,19,1],benoit:20,andrei:20,repres:[27,17,34,20,29,36],former:34,those:[20,34],"case":[27,33,17,34,19,39,20,21,29,8],atom_pair:34,trick:2,findhydrogenposit:34,keblinski:20,advantag:20,stdout:34,canon:34,cdivis:16,ext_temp:43,destin:34,cluster:[20,34],protein:[0,2,3,4,5,6,7,8,10,12,13,14,15,40,39,20,21,23,30,31,32,33,34,35,37,38,42],"__init__":[24,1,2,17,34,19,27,29,16,11],restarttrajectoryoutput:[20,21,34,39,23],develop:[20,34],author:20,same:[16,34,39,20,6,7,31,22,36],binari:[20,34],inconsist:34,document:[20,34],finish:34,closest:20,someon:[29,19],proteinfrict:[13,34],capabl:42,available_data:16,kneller1990:20,mani:[20,34],extern:[27,17,34,20,7,42],isotop:20,appropri:[20,34],convienc:20,iupac:20,equilibr:[20,21,26,4,39],without:[32,24,34,3,4,20,8,11],setmass:[34,6],harmonicforcefield:[13,34,40],model:[0,12,14,2,34,32,5,20,6,7,8,38,42,35],roughli:20,atomiter:34,vangunsteren1982:20,hinsen2000:20,execut:[16,34,7,20],minima:20,dihedr:[20,34],tip:[34,42],aspect:34,kilo:34,speed:[20,24,34,4,11],reciprocal_cutoff:34,miscellan:[13,34,20],except:[20,32,3,34,1],littl:[20,42],anis:34,identif:20,rescal:[20,34,26,4],treatment:20,versa:20,swope:20,momentum:[20,21,34],real:[32,34,39,4,20,28,7],psi:34,around:[20,34,42],read:[32,26,18,16,3,34,20,21,37,7,8,30,31,22,42],nobl:[20,26],temperatur:[26,1,34,39,4,20,21,6,7,43],grid:[38,14,34],mol:[20,34],world:39,amu:[20,34],"1mbd":20,stationari:34,integ:[20,34],server:20,either:[16,34,20],output:[26,16,34,39,20,21,31,23,43],manag:20,thermodynam:[26,34,39,4,20,21,23,43],nucleic:[20,34],distanceconstraintlist:34,constitut:34,slice:[20,34],easili:[20,4],tube:34,definit:[13,34,39,20,8,41],legal:20,boltzman:43,mod_fil:[21,34],complic:[20,37],refer:[13,32,34,20,42,11],process:[20,8,4,1],power:20,auxiliari:[34,26,4],bivari:43,mpi:[20,34,7,39],inspect:[20,34],broken:20,chlorin:20,fulli:[16,34,20],slowli:[34,4],comparison:[20,5],central:34,energyandgradi:34,degre:[20,34,42,43],pdbfile:[20,34],wolf:[20,34],stand:[20,34],act:[16,34,29,19,20],"nos\u00e9":20,mean:[20,34],processor:[20,39],probe_radiu:34,amber:[20,34],heater:[20,21,34,39,23],effici:[16,17,34,19,4,20,29,7,11],amplitud:[34,6],elementari:[20,34],mari:20,createunitcellunivers:34,strip:34,mark:[20,8],your:[20,7],electricfield:[27,17,7],amber94forcefield:[15,34,39,4,5,23],methyl:20,log:[26,39,4,20,21,23,43],area:[20,34],start:[16,34,4,20,7,8],interfac:[20,34],low:[27,34,19,35,20,29,43],standardlogoutput:[15,34,39,5,20,21,23],strictli:20,energyevalu:[24,1],randompoint:34,edge_length:[2,9],newtonian:20,micellan:7,tupl:[24,34,4,20,42,11],py_end_allow_thread:43,alternate_cod:34,argon_npt:26,pytrajectory_configur:43,addtoconfigur:34,scalebi:34,faster:[20,37,34,8,4],harmonicoscillatorforcefield:[29,19],particleproperti:[13,20,34,16,1],possibl:[17,34,39,4,36,20,29,7,31,42],"default":[20,16,17,1,34,27,23],spefici:20,massweighteddotproduct:[34,5],k_b:[34,43],chamic:34,eigenvector:0,getatomproperti:[27,17,34],creat:[0,18,2,4,6,7,8,9,10,12,13,14,16,17,39,20,21,22,23,26,29,30,31,33,34,38,41,43],certain:20,strongli:[20,4],residue_nam:34,file:[18,3,39,6,7,8,22,13,16,19,20,21,25,23,26,29,30,31,32,34,36,37,41,42],proport:12,nb_exclus:34,energi:[13,24,26,27,16,17,34,19,4,39,20,21,29,7,43,28,23,11],again:42,extract:[32,2,34,20,3,7],orient:[20,34,42],field:[12,13,14,24,26,1,2,17,34,27,19,4,20,29,7,8,40,38,43,42,11],cleanup:43,presenc:[20,34],valin:0,you:[32,18,34,3,20,7,8,30,31,22,42,23],constrained_mod:7,polar:[20,34],water_dens:4,sequenc:[32,18,34,20,7,42],symbol:[20,34],closebi:42,degrees_of_freedom:43,normalizeddeformationfunct:34,oh2:20,network:[20,7],reduc:[20,32,34,7,5],amberforcefield:[13,34,20],directori:[20,34,7],terminus_5:34,descript:[20,34,35,40],pyuniversespecobject:43,mass:[0,1,16,34,4,5,20,6,9,43],amber99forcefield:[20,21,34],potenti:[16,34,19,20,28,29,7,43],boundingspher:34,represent:[0,20,32,34,7],viewtrajectori:[34,25],consider:20,illustr:[14,39,20,37,38,7,8,30],fc_fn:[16,43],projectioncomplementof:34,scalar:[20,34],follow:[20,16,17,34,19,4,27,29],pdboutputfil:34,disk:20,this_thread:43,nstep:16,wavenumb:[20,34],staticstructurefactor:34,articl:34,program:[32,34,3,39,20,28,7,25,30,36],norm:[20,34],precedingresidu:34,straightforward:20,mpa:34,fals:[16,34],heme:20,util:34,mechan:[34,29,19],fall:34,veri:[20,34,7],vibrationalmod:[13,15,40,34,5,20],orthonorm:34,strand:[41,7],energybasedtrajectorygener:16,ball_radiu:34,data_arrai:34,molecularsurfac:[13,34,20],list:[24,27,16,17,34,19,20,29,43,11],universe_spec:43,adjust:[34,4],stderr:34,small:[34,39,4,20,28,7,42],desoxyribos:20,py_begin_allow_thread:43,dimens:[43,24,34,11],meansquaredisplac:34,infinitesim:34,pyobject:43,dummygraph:2,biolog:42,pressur:[26,34,4,20,7,43],releaseconfigurationchangelock:[20,34],pass:[32,20,2,17,34,19,27,29,43],further:[20,34],what:[20,34,42,39],phycocyanin:6,sub:20,nano:34,section:20,abl:20,overload:34,amber_atom_typ:20,delet:[20,8],version:[20,34,7],intersect:34,sup:20,consecut:34,method:[20,33,16,17,34,19,4,27,29],movement:[20,42],full:[20,3,34,35,5],molecule_nam:34,behaviour:20,modular:20,stick_radiu:34,excess:34,velocityscal:[20,34,26,4],boxtorealcoordin:34,standard:[15,34,4,20,7,8,23],modifi:[13,16,34,20,7,8],valu:[1,16,34,20,28,6,7,2,42,43],search:[13,20],reason:[20,42,34,7,35],prior:[20,34],amount:[12,20],pico:34,rotatearoundcent:34,introductori:20,magnitud:[20,6],geometricalobject3d:34,diamet:34,via:[20,34],"_spec":43,massweightednorm:34,heurist:34,select:[20,37,34],wirefram:[0,34],etc:[16,43,34,7,20],two:[17,34,39,20,28,29,42],releasereadstatelock:34,taken:[16,34,20],step_siz:[20,34],minor:23,more:[12,14,34,32,36,20,37,38,7,42,23],desir:[20,34],grid_siz:34,gradienttest:34,flag:[34,17,29],stick:34,particular:[20,24,34,11],known:[20,28,34],none:[0,1,2,3,4,5,6,22,10,16,17,18,19,20,21,25,23,26,27,29,30,31,32,34,35,36,37,39,42],describ:[20,34,7,40],valuabl:[20,34],der:[20,34],launch:[38,34],solvat:[13,3,34,39,4,7],histori:20,remain:[20,7],realtoboxcoordin:34,learn:[20,7],trajecori:[34,32,3,30],def:[24,1,2,17,19,27,29,16,11],deg:[20,10,34,42],nosethermostat:[20,34,26,4],templat:[20,34],sphere:[2,34,20],minimum:[20,6,34],chimera:[14,7],huge:20,terminus_3:34,goal:20,divid:[20,34,30],rather:[16,34,7,4],anoth:[33,20,34,42],eval_func:[43,24,11],divis:16,calpha_mask:37,simpl:[13,1,16,34,39,20,21,7,8,9],subset_trajectori:3,resourc:20,referenc:20,variant:[20,34],plane:34,charmm:[20,31,22,7,34],inquiri:[20,34],varianc:20,associ:[20,34],"short":[20,34],onto:34,caus:[20,34],spheric:[20,34],ensembl:[20,34,6,7,4],constitu:[20,34],pylistobject:43,rotat:[12,18,22,34,39,5,20,21,31,10,42,23],soon:34,lattice_vector:34,through:[20,34],get_data_descriptor:43,angularmomentum:[21,34],hierarchi:[20,34],paramet:[24,26,27,16,17,34,19,4,20,43,29,7,25,9,11],style:20,rigidbodymotionsubspac:34,readparticletrajectori:34,gerald:20,wrl:34,some_fil:[20,36],coulomb:[20,34],might:[20,17,29,34,8],tri:20,good:[34,42],"return":[20,2,17,34,19,27,29,43],"_ct":34,scalevelocitiestotemperatur:[20,34],thereof:20,aka:20,oper:[13,30,34,20,16],projectionof:34,micro:34,radian:[34,42],special_protein:8,vector_field:[2,7,20],found:[20,34],truncat:20,selectbox:34,weight:[34,6],procedur:[20,34,36,4],ball:34,expect:[20,6,42],fist:8,beren:20,quantum:[20,34],calphaforcefield:[13,14,2,34,35,20,6,38],beyond:8,reduct:34,atomswithdefinedposit:[20,34],magnet:34,harmonicdihedralrestraint:34,dcd_file_nam:34,myst:34,setsiz:34,copyconfigur:[20,34],print:[15,2,34,28,4,5,20,21,37,40,42,35],occurr:20,particlescalar:[27,17,1,34,20,37],solvent:[20,34,4],advanc:20,special_residu:8,differ:[20,34,42,23],like:[20,34,7],amber94:[27,17],hecto:34,base:[33,20,34],put:[32,3,4,20,41,9,42],amber99:[27,17],basi:[20,34,35],lennardjonesff:[20,34],thread:[13,1,16,34,20,43],surfacepointsandgradi:34,rhombiclattic:[20,34],veloc:[13,32,26,1,16,34,39,4,20,21,23,43],perhap:20,gradient_fn:[16,43],assign:[20,24,34,39,11],major:20,polici:20,exchang:[7,36],number:[13,1,16,34,4,20,30,23,43],dihedralangl:34,contour:20,done:[20,17,29],uninterest:20,stabl:[20,34,4],miss:[41,20,42,8],electricfieldterm:[27,17,24],guess:[34,42],exponenti:34,interact:[20,17,34,7,27],unrestrict:20,gpa:34,construct:[12,13,32,26,1,15,40,34,35,39,5,20,28,6,7,8,41,9,10,36],statement:20,molecular:[0,13,16,17,34,39,4,20,21,29,7,23],store:[32,24,27,2,17,34,3,19,20,29,8,16,11],insulin_backbon:6,option:[13,1,16,34,20,25],monomer_configur:42,atom_map:34,charge_fit:[20,34,7],part:[13,24,27,1,34,19,20,37,7,43,42,11],off:[34,42,8],diffusion:20,kind:[33,20,34,8],cyclic:[20,34,23],remov:[20,21,34,39,23],reus:[20,23],block_siz:[20,34],str:[27,17,34],verlet:[16,34,20],arrang:34,toward:20,comput:[20,17,29,34,30],pytrajectory_energi:[16,43],wilfr:20,packag:20,pytrajectoryoutputspec:43,p_energi:43,dedic:20,"null":[16,24,43,11],lie:34,wilson:20,built:[20,34,7,36],lib:20,self:[24,27,1,2,17,19,20,29,16,11],also:[16,34,20,7,8,41,42],exampl:[0,18,2,3,7,8,9,22,11,12,13,14,17,39,20,24,29,30,31,32,33,34,35,36,37,38,42],build:[20,34,42,36],command:[20,34],objectlist:[32,37,34],cube:[2,34],distribut:[20,34,7,43],getatomparameterindic:[29,19],index:[13,32,24,16,34,19,20,29,11],choos:[20,32],reach:4,mixtur:20,most:[33,20,34,5],plai:34,plan:[20,7],removedistanceconstraint:[20,34],alpha:[32,37,34,7,35],sclattic:[20,9,34],charg:[13,24,20,17,34,27,28,7],clear:20,cellparamet:34,cover:[20,34],hartre:34,dimension:[20,34],energeticmod:[13,14,34,35,20,38],exp:[34,43],incur:20,acquirereadstatelock:34,latest:34,n_terminu:[34,8],carefulli:[20,7],pressure_avail:43,belliss:[20,35],particularli:[20,30],conf_list:34,find:[0,34,35,4,5,20,42],pytrajectory_gradi:[16,43],access:[2,34,20,16],copyright:20,langevinintegr:1,solut:[20,34,8,4],addsolv:[34,4],factor:[20,14,6,34,43],determinist:[34,39],express:34,value_rank:34,py_non:43,longest:34,restart:[34,39,20,21,7,23],angluar:34,whenev:[20,34],adjustvelocitiestoconstraint:34,common:[33,20,34],cimport:16,pytrajectory_intern:43,set:[16,34,35,4,5,20,6,41,43],art:20,randomveloc:34,karplu:20,see:[12,14,24,16,34,35,39,20,38,7,40,43,11],virial_avail:43,dcd_file:[31,34],arg:[34,43],close:[32,26,16,3,34,4,39,20,21,6,31,10,23],outward:34,analog:20,numberoffixedatom:34,collinear:34,reciprocalbasisvector:34,matter:34,systemat:20,deformationenergyfunct:34,particip:34,smallest:[20,34,42],nontrivi:20,atom_index:[29,19,11],altern:[20,34],atomicvectorfield:[12,2,14,34,38],numer:[24,2,34,20,7,16,11],complement:34,sole:33,isol:20,dotproduct:34,default_opt:16,minut:20,nmode:34,disclaim:42,last:[8,34,20,25,42,23],mega:34,delleru:[20,35],atomlist:[27,17,34,6,28],bondanglelist:34,degreesoffreedom:34,hbar:34,whole:[20,34,42,40],pdb:[12,13,14,18,34,35,36,20,6,7,8,41,38,31,22,42],load:[13,14,39,20,8,41,23],simpli:20,undefin:[20,34],point:[34,19,20,28,29,7,9],unrealist:28,residu:[33,34,35,5,20,37,7,8,41,42],param:[16,17,34,19,27,29],suppli:34,bridg:[20,34],ribos:20,damp:34,due:[20,28,34,42],empti:[20,17,34,27],r_old:34,newcom:20,wraparound:16,double_precis:34,strategi:20,color_scal:34,imag:[20,34],finitedeformationfunct:[34,42],coordin:[13,24,2,34,4,20,43,11],understand:20,repetit:[20,34],randompointinbox:34,look:[20,34,7],bondlength:34,straight:34,erron:20,"while":[34,7,26,43],abov:[20,34],error:[20,29,19,43],fun:42,sumoverparticl:[17,37,34],langevin_method:43,loop:[32,16,3,34,20,30,42,43],"m\u00fclder":20,malloc:43,angularveloc:34,retrieveasymmetricunit:34,readi:[27,17,29,19],sidechain:[0,20,34,42],subchain:[20,34],pdbnucleotidechain:[20,34],centi:34,itself:[33,20,34,29,19],residue_filt:34,phiangl:34,rid:42,molecule_spec:34,numberofdistanceconstraint:34,minim:[13,15,34,4,5,20,42],definepdbview:34,mpicommun:34,perdiod:34,shorter:20,funni:42,lengthi:20,elong:34,pairwis:20,ischemicalobject:34,conflict:20,higher:[20,34],optim:[20,24,34,4,11],restraint:[13,34],wherea:[20,14,34],moment:[16,34,20,1],temporari:20,user:[13,34,20],pdbviewer:34,chang:[12,14,34,39,20,21,38,42],amber_charg:[20,17,27],travers:34,task:[20,34],equival:[20,34],older:[20,34],entri:[41,20,34],chemistri:[20,34],pickl:[20,17,29,19,27],person:20,expens:34,know:[20,17,29,34,42],energyterm:[34,17,24,29,11],vacuum:[34,7],collabor:20,shape:34,move:[20,34,43],conjugategradientminim:[15,20,34,5],cut:[42,8],pytrajectory_tim:[16,43],harmonicdistancerestraint:34,rgb:2,shrinkunivers:[34,4],input:[32,24,34,3,20,28,8,30,11],subsequ:[20,34],nonbond:34,invcm:[20,34],dcd_export:[31,7],format:[13,34,20,7,31,22],big:[20,35,42],lj_energi:34,molecul:[13,14,33,34,3,4,20,38,7,9,10],macromolecular:20,bit:42,harmonicoscillatorff:7,k_energi:43,formal:42,configurationdiffer:34,segment_id:34,signal:[20,29,19],collect:[12,13,14,27,1,33,34,17,3,20,28,37,38,7,41],princip:[0,20,34,4],pytrajectory_outputfinish:43,encount:34,often:[20,34],creation:[20,10,34],displacementundertransform:34,back:[34,4],understood:20,sampl:[20,6],definevrmliew:34,scale:[0,12,14,34,39,4,21,6,38],per:[20,34],substitut:0,mathemat:[20,34],larg:[20,34,42],finitedeformationenergyfunct:34,reproduc:20,nose:34,atomicscalarfield:34,run:[32,1,16,18,3,34,4,39,20,21,7,8,30,31,22,23],delta_t:[26,1,16,34,39,4,20,21,23,43],perpendicular:34,step:[32,26,1,15,16,39,3,34,4,5,20,21,37,7,25,30,10,23,43],subdatabas:20,subtract:[20,34],graphics_modul:[0,12,14,2,34,38,42],constraint:[13,28,34,20],"4q21":42,argsort:5,mass_unit_nam:43,paralel:20,block:[20,34],cutoff:[20,34,26,4,35],within:[20,17,34,27],pytrajectory_boxs:43,pdbpeptidechain:[20,34],url:20,ensur:[20,28,34],pyarray_doubl:43,occupi:20,inclus:34,rhombic:34,span:34,fast:[20,34],custom:[0,20,7],arithmet:20,includ:[24,16,34,20,25,43,11],md_mpi:39,ref_arrai:11,blueprint:34,everyt:41,otherbond:34,namdm:20,decomposit:34,atoi:25,link:[20,34],polar_hydrogen:34,delta:[34,29],max_angl:34,line:[2,34,26,20],atof:26,forcefieldtest:[13,34],findtransform:[32,34,42],consist:[27,17,34,4,20,6,9],caller:34,configio:[13,34],highlight:34,readlin:26,similar:[20,34,5],constant:[26,16,17,34,19,4,20,29,7,43],chao:20,doesn:20,particletensor:[20,34],incomplet:[42,8],guarante:[20,34,39],peptide_chain:[31,34,42,8],curl:[12,34],periodic3dunivers:34,kneller1996:20,insulin:[0,12,14,2,35,20,6,8,38],sequenti:34,declar:[16,24,34,11],nav:34,angstrom:[14,42,26],pdb_export:7,asymmetr:34,dcd_import:7,equalityconstraint:34,clean:20,simplehttpserv:20,molecule_constructor:34,meaning:20,eval:[24,11],diffusemateri:2,setcallopt:1,trajectory_averag:7,snapshotgener:[32,34,3,20,6,10],code1:34,code3:34,algorithm:[20,34],vice:20,steepestdescentminim:[20,34],random2:43,evenli:20,velocity_unit_nam:[16,43],insulin_with_h:8,code:[13,27,16,17,34,19,20,29,7,43],partial:20,edg:[20,34],langevin:[43,7,1],pytrajectory_intscalar:43,infiniteunivers:[12,14,15,2,34,32,5,20,21,6,39,36,40,41,38,31,10,42,23,35],compact:34,cython:[24,27,16,19,20,7,11],full_trajectori:[32,3],sensit:34,elsewher:34,friendli:20,sens:[20,34,29,19],configuration1:42,configuration2:42,waitflag:34,harmonicoscillatorterm:[29,19,11],full_mod:5,wave:34,viduna2000:20,electron:34,volum:[13,43,34,4,20],bondedunit:34,center2:34,relev:20,center1:34,recip:20,alin:20,"try":[32,3,1],nucleotide_chain_constructor:34,rigid_bodi:34,energy_spec:[24,11],dimer:6,slow:[39,20,7,35],impli:20,smaller:[32,3,34,4,20,7],among:20,normalmod:[12,13,14,15,2,34,35,5,20,6,40,38],jump:34,object1:[20,34],object2:[20,34],leakag:20,fullnam:34,acid:[20,34,7],carlo:[20,6,7],append:[0,32,2,34,5,28,8],getatombooleanarrai:34,compat:[20,34,7],writetofil:[20,34,8,18],bondff:34,compar:[34,39,5,20,7,8,42],releasewritestatelock:34,bravaislattic:[20,34],tetram:42,cell:[20,9,34],experiment:[20,34],whatev:[20,34],forceconstanttest:34,vibrat:[20,6,34,40],"50th":20,len:[32,34,35,5,20,37,6,25,30],arond:34,bodi:[32,34,5],let:42,ba2:34,becom:[20,34],sinc:[20,6,34,8],convert:[18,16,34,20,7,31,22],convers:[18,34,19,20,29,31,22],larger:[20,34,42,4],foldcoordinatesintobox:16,converg:[15,20,34,5],geometry_data:43,setposit:[32,34],typic:[20,34],acquirewritestatelock:34,conf2:34,conf1:34,atom_filt:34,scales:34,appli:[17,34,39,20,21,29,10,42],approxim:[20,34,35],interdepend:[27,17,29,19],submodul:[20,34],setrigidbodyconstraint:34,daunomycin:41,pxi:[16,24,11],"boolean":34,creategroup:34,pytrajectoryvari:43,from:[0,1,2,3,4,5,6,7,8,9,10,11,12,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43],commun:[20,34,39],chi:34,doubl:[24,16,34,20,11,43],"_nt":34,next:[20,34,42,43],few:[20,7],usr:20,lock:[16,43,34,20],import_arrai:43,rotationremov:[20,21,34,39,23],sort:[20,34],iir:34,hasatom:34,trajectory_set:34,iil:34,applyfunct:34,account:[20,34],retriev:[20,17,34,27],ball_and_stick:34,alia:34,critic:20,obvious:28,freedom:[20,34,43],bondi1964:20,control:20,tau:34,mmatomparamet:34,superposit:[20,34],deepcopi:[20,34],high:20,tag:34,defineaminoacidresidu:[34,8],serial:20,everywher:20,surfac:[13,28,34,7,20],andersen:[20,34],calpha_trajectori:[32,7],findcontact:34,subdirectori:20,agglomer:34,orthrhombicperiodicunivers:34,partit:[20,34],sim:34,initmmtk_langevin:43,setfromtrajectori:[34,23],overridden:20,singular:[20,34],trajectorysetvari:34,pymodule_getdict:43,npt:[20,34,26,4],initializetrajectoryact:16,physic:[20,34],deformationreduc:34,alloc:[34,43],essenti:[20,24,34,11],light:34,correspond:[0,12,14,34,20,38],pyuniversespec_statelock:43,element:[20,34],allow:[41,20,34,43],subtyp:34,fastest:20,least:[20,6,34],aminoacid:34,routin:[20,2,34,19,27,29],vmd:[20,38,34,7,42],anmff:34,lennardjonesforcefield:[13,34,26],perfect:20,outer:34,chosen:[20,34,7,4],py_fatalerror:43,pytrajectory_scalar:43,restrain:34,ddio:43,criterion:34,therefor:[24,27,17,34,20,11],spec_list:43,crash:[24,11],file_or_filenam:34,python:[24,27,1,16,17,34,19,20,29,7,43,11],dihedralanglelist:34,mention:[20,34,23],facilit:20,instead:[20,34,29,19],pymethoddef:43,anyth:[20,34],subvari:34,mode:[12,13,14,15,2,34,35,5,20,6,7,40,38],c_alpha:[32,35,20,37,6,42],circular:34,particlevector:[16,17,34,20,37,29,30],subset:[27,34,17,3,19,20,29,7],imposit:20,energy_gradient_unit_nam:[16,43],temp1:34,"static":[34,43],fluctuat:[37,34,7,35],our:[27,17,29,19],tenth:37,volume_funct:43,special:[33,2,34,8,20],out:[20,34,42,8],variabl:[13,1,16,34,20,30,43],matrix:[20,34],contigu:[32,34],influenc:[20,34],rev:34,waal:[20,34],categori:[16,34],suitabl:[0,32,34,3,20,9],rel:[34,42],lattic:[13,9,34,7,20],red:[0,12,34],ljforcefield:34,initial_conf_calpha:32,force_field:34,insid:[20,34,42],manipul:[20,34],dictionari:[20,34],usual:[33,20,34],releas:[16,34],expft:43,afterward:34,chainmolecul:34,istrajectori:34,steal:34,could:[20,34],ask:[16,20],david:20,counterpart:32,length:[0,12,14,34,20,28,38,43],enforc:[20,34],outsid:[20,17,29],geometri:[13,20,17,34,19,27,29,9],trajectorygener:34,zmatrix:[20,34],data_descriptor:43,ndim:16,softwar:20,pdb_conf:34,suffix:34,scene:[0,12,14,20,38,42],date:20,retrieveunitcel:34,"long":[20,34],dm1:41,unknown:[41,34],licens:20,perfectli:34,system:[0,2,4,5,6,7,9,10,12,13,15,16,17,39,20,21,23,28,29,34,35,37,40],messag:20,attach:[34,29,19],eisenhab:20,termin:[34,8],"final":[16,43,34,4,20],shell:34,thermochem:34,isparticleproperti:[34,1],argon:[7,26],intersectwith:34,harmonicanglerestraint:34,declaretrajectoryvariable_doubl:16,exactli:[20,24,34,39,11],peptidechain:[32,33,34,20,8,42],harmonic_force_field:7,structur:[13,24,34,20,7,8,30,42,11],charact:[20,34],restart_data:16,viewer:[34,7,42],chemicalobject:[13,33,34,19,20,29],symmetriccolorscal:[2,34],coher:34,iscollect:34,need:[24,1,34,20,8,11],nucleotide_chain:34,roux:[20,34],min:34,diverg:34,mid:[16,6,7,43],whatsoev:20,mix:[33,20,34],milli:34,singl:[24,17,34,20,29,41,11],pyx:7,energet:[20,34],unless:20,vrml2:[0,12,20],velocityverletintegr:[26,16,34,39,4,20,21,23],oscil:[29,7,19,11],segment:34,"class":[32,24,27,1,33,2,17,34,19,20,29,16,43,11],placement:4,r_0:34,gather:16,request:[16,17,29,34,20],face:34,asutounitcel:34,snapshot:[13,32,18,22,3,20,6,7,10],determin:[20,37,6,34],constrain:[20,34],gln61:42,fact:[2,20],text:[20,34,26,43],connect:[20,34],pyeval_savethread:43,checkfeatur:1,trivial:[15,40,35],anywai:20,redirect:2,locat:20,perpendicularvector:34,forev:20,should:[32,24,34,17,3,4,20,6,29,11],pytrajectory_particlevector:43,won:34,suppos:20,getbasi:34,sulfur:[20,34],moleculardynam:[39,30],local:[12,20,34,42],equilibrium:[20,34],meant:[34,7,39],obj2:34,contribut:[27,17],serial_numb:34,perahia:[12,14,38],increas:[20,34],acquireconfigurationchangelock:[20,34],bondi:20,rotation_from_dcd:31,totalnorm:34,axis_direct:34,enabl:[20,7],quaternari:[12,14,38],upper:[20,34],displac:[14,34,5,20,38,42],isprotein:34,monom:42,addatom:34,polar_opl:34,integr:[13,26,1,16,34,39,4,20,21,7,23,43],randomdirect:34,contain:[14,24,34,32,4,20,37,38,7,8,41,42,23,11],view:[0,12,14,15,40,34,35,39,20,21,38,30,41,9,42,23],conform:[20,37,34,7,42],dcd_reader:31,knowledg:20,displai:[0,20,14,34,21],elast:[20,34,7],temporarili:16,funel:[20,35],dyadic:34,particl:[20,24,34,30,11],statu:20,still:7,correctli:20,boundari:[20,34,4],cours:[20,7],written:[1,16,34,20,6,7,43],progress:34,neither:[20,34],viewsequ:[20,34,42],vector_field_vmd:7,kei:34,coherentscatteringfunct:34,steepest:[20,34],entir:20,avogadro:34,contiguousobjectconfigur:[32,34],addit:[20,34,7],actual:[20,17,29,39],nextmodel:34,tkinter:20,incoherentscatteringfunct:34,equal:[20,28,34],corner2:34,instanc:[33,34],equat:[20,34],contact_factor:34,freeli:20,evaluatorterm:[27,17,29,19],comment:[20,34],nonbondedinteract:34,wall:34,exec_path:34,disulfid:[20,34],carbon:20,respect:[16,34,29,19,20],petrescu:[20,35],subset1:[27,17,34,29,19],subset2:[27,17,34,29,19],rigidmotionsubspac:[34,5],compos:[20,34],inertia:[0,20,34,4],compon:[20,34],swope1982:20,treat:[20,34],electr:[27,17,24,34,7],trajectori:[1,3,4,5,6,7,22,10,13,15,16,17,18,19,20,21,25,23,26,27,29,30,31,32,34,37,39,43],confrmat:[12,14,38],immedi:[27,17,34,29,19],both:[20,32,3,34,5],mmforcefield:34,protect:20,neighbour:20,c12x:43,togeth:[20,34],pyarray_typ:43,present:[20,34,42],replic:20,multi:[20,34],obj1:34,plain:[20,34,23,1],align:[34,42],rbt:34,rectangular:[34,42],defin:[31,26,27,33,17,34,28,4,39,20,21,9,42,23,43],scatter:34,glossari:[33,13],nb_excluss:34,almost:[20,42],mpipython:20,site:20,integrateld:[43,1],pytrajectory_thermodynam:43,textfil:26,deletehydrogen:8,heteregen:20,satisfi:34,isunivers:34,sqrt:[0,43,5],retrieveunivers:34,handl:[20,2,17,34,19,27,29],setforcefield:[34,4],"_5ter":34,largest:34,atomicfield:34,phi:34,overal:34,http:20,import_mmtk_univers:43,cubic:[20,9,34],effect:[20,34],beast:42,phy:[40,34,35],femto:34,expand:34,parallelepipedicperiodicunivers:[20,34],center:[0,2,34,19,4,20,29,9],lysozym:37,well:[20,34,42,4,36],bohr:34,box_siz:[32,43],q_rang:34,interpol:34,ispeptidechain:34,releasewritestatechangelock:20,c_terminu:[31,34,42],subgroup:[20,34],distanc:[13,34,42,20],less:[20,34],obtain:[27,17,34,19,20,29,7,43],simultan:[20,34],cellvolum:34,dipol:34,web:20,rapid:20,geometry_data_length:43,valid:20,bibliographi:[13,20],densiti:[34,4],c12:43,mmtk_trajectori:16,match:[31,34,42],nvt:[20,34],rememb:[17,29],universe_calpha:32,nve:20,five:[20,34],proton:[20,34],guid:[13,20],python2:20,insert:34,resid:20,backbon:[0,12,34,20,6,7,42],success:34,bravai:34,necessari:[14,27,16,17,34,19,20,29,8,38,42],martin:20,es_opt:34,page:13,therein:34,"export":[13,20],flush:34,proper:34,home:20,librari:[20,34],summat:[20,34],lead:[20,34],avoid:[20,34],do_force_const:[17,29],overlap:[20,34,4,5],mmtk:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43],estim:34,leav:[20,34],aspart:[12,14,38],encourag:20,axisandangl:[20,42],dcd:[13,34,20,7,31,22],usag:20,getparticleboolean:34,ndarrai:16,although:20,offset:[34,4,11],geometr:[41,20,34,8],simpler:[20,34],about:[2,17,34,20,21,29,42],rare:20,pyarray_copi:43,normalizingtransform:34,ndf:43,constructor:34,disabl:20,subgroup_nam:34,own:[20,7],virialtest:34,pdbmoleculefactori:[13,34],automat:[16,6,34,20],terminu:42,diagon:[0,34],chiangl:34,laplacian:34,van:[20,34],val:0,pictur:[34,42],transfer:[20,34],intention:4,hinsen:[12,14,1,16,34,35,20,38,40,42,43],inner:34,"var":[43,1],"function":[24,2,34,20,11,43],keyerror:[32,1],continu:[20,34,7,23],neutral:[20,28,34],toplevelchemicalobject:34,highest:[20,34],count:34,pyfloat_asdoubl:43,made:[20,34],temp2:34,whether:34,wish:20,redistribut:20,record:34,below:[32,3,34,8,23,43],limit:[20,34],indefinit:[20,34],nonperiod:34,otherwis:[20,31,22,34,23],problem:[20,34,8],unformat:34,reciproc:34,evalu:[13,24,27,1,16,17,34,19,39,20,29,7,43,11],"int":[16,24,34,43,11],dure:[20,34],import_mmtk_forcefield:43,implement:[24,1,16,17,34,20,7,43,11],"1nm":34,detail:[24,34,20,7,42,11],other:[0,20,33,16,17,34,39,36,27,29,7,42,43],lookup:34,futur:20,branch:[20,34],getopt:[16,1],py_initmodul:43,translateto:34,repeat:34,pytrajectory_output:43,pythreadst:43,rawmod:34,peptid:[13,32,33,34,35,20,37,8,42],scientif:[0,12,14,32,26,27,2,17,34,19,5,20,29,39,38,9,42],bala1:[15,40,34,39,4,5,21,30,10,23],otheratom:34,indirectli:34,rule:[20,24,11],addsubgroup:34,klass:34,phosphat:[20,34]},objtypes:{"0":"py:module","1":"py:method","2":"py:function","3":"py:class","4":"py:attribute"},titles:["Adding custom graphics to a molecular system visualization","An integrator for Langevin dynamics (Python part)","Extracting numerical values from graphics objects","Extract a subset from a trajectory","Solvation of a protein in water","Normal modes of a protein using a rigid-residue model","Sampling a backbone-only configuration ensemble","Code Examples","Protein construction beyond the simple cases","Place molecules on a lattice","Assembling a trajectory step by step","An efficient harmonic oscillator term (Cython part)","Vector fields for analysis and visualization of collective motions","MMTK User Guide","Vector field visualization of a normal mode (using Chimera)","Normal modes of a protein","A simple Velocity Verlet integrator","An electric field term implemented in pure Python","Converting a trajectory to a sequence of PDB files","An efficient harmonic oscillator term (Python part)","MMTK User’s Guide","Simulation of a protein","Convert a trajectory to DCD format","Restarting the protein simulation","An electric field term (Cython part)","Show an animation of a trajectory","Simulation of liquid argon","An electric field term (Python part)","Fitting point charges to an electrostatic potential surface","A harmonic oscillator term in pure Python","Compute an average structure from a trajectory","Importing a trajectory in DCD format","Extract a C-alpha trajectory from an all-atom trajectory","Glossary","Module Reference","Slow normal modes of a protein using a C-alpha model","Building a complete universe from a PDB file","Calculating atomic fluctuations from a trajectory","Vector field visualization of a normal mode (using VMD)","Protein solvation in parallel","Normal modes of a protein using a simplified force field","Constructing a DNA strand with a ligand","Comparing protein configurations","An integrator for Langevin dynamics (C part)"],objnames:{"0":["py","module","Python module"],"1":["py","method","Python method"],"2":["py","function","Python function"],"3":["py","class","Python class"],"4":["py","attribute","Python attribute"]},filenames:["Examples/Visualization/additional_objects.py","Examples/LangevinDynamics/LangevinDynamics.py","Examples/Visualization/graphics_data.py","Examples/Trajectories/trajectory_extraction.py","Examples/MolecularDynamics/solvation.py","Examples/NormalModes/constrained_modes.py","Examples/MonteCarlo/backbone.py","examples","Examples/Proteins/construction.py","Examples/Miscellaneous/lattice.py","Examples/Trajectories/snapshot.py","Examples/Forcefield/HarmonicOscillator/Cython/MMTK_harmonic_oscillator.pyx","Examples/Miscellaneous/vector_field.py","index","Examples/Visualization/vector_field_chimera.py","Examples/NormalModes/modes.py","Examples/MDIntegrator/VelocityVerlet.pyx","Examples/Forcefield/ElectricField/Python/ElectricField.py","Examples/Trajectories/pdb_export.py","Examples/Forcefield/HarmonicOscillator/Cython/HarmonicOscillatorFF.py","mmtk","Examples/MolecularDynamics/protein.py","Examples/Trajectories/dcd_export.py","Examples/MolecularDynamics/restart.py","Examples/Forcefield/ElectricField/Cython/MMTK_electric_field.pyx","Examples/Trajectories/view_trajectory.py","Examples/MolecularDynamics/argon.py","Examples/Forcefield/ElectricField/Cython/ElectricField.py","Examples/Miscellaneous/charge_fit.py","Examples/Forcefield/HarmonicOscillator/Python/HarmonicOscillatorFF.py","Examples/Trajectories/trajectory_average.py","Examples/Trajectories/dcd_import.py","Examples/Trajectories/calpha_trajectory.py","glossary","modules","Examples/NormalModes/calpha_modes.py","Examples/Miscellaneous/construct_from_pdb.py","Examples/Trajectories/fluctuations.py","Examples/Visualization/vector_field_vmd.py","Examples/MPI/md.py","Examples/NormalModes/harmonic_force_field.py","Examples/DNA/construction.py","Examples/Proteins/analysis.py","Examples/LangevinDynamics/MMTK_langevin.c"]})