Index

A

Abstract base class acquireConfigurationChangeLock() (MMTK.Universe.Universe method) acquireReadStateLock() (MMTK.Universe.Universe method) acquireWriteStateLock() (MMTK.Universe.Universe method) addAtom() (MMTK.MoleculeFactory.MoleculeFactory method) addBond() (MMTK.MoleculeFactory.MoleculeFactory method) addObject() (MMTK.Collections.Collection method) (MMTK.Universe.Universe method) addSolvent() (in module MMTK.Solvation) addSubgroup() (MMTK.MoleculeFactory.MoleculeFactory method) addToConfiguration() (MMTK.Universe.Universe method) adjustVelocitiesToConstraints() (MMTK.Universe.Universe method) Amber94ForceField (class in MMTK.ForceFields.Amber) Amber99ForceField (class in MMTK.ForceFields.Amber) AndersenBarostat (class in MMTK.Environment) angle() (MMTK.Universe.Universe method) angularMomentum() (MMTK.Collections.GroupOfAtoms method)

angularVelocity() (MMTK.Collections.GroupOfAtoms method) AnisotropicNetworkForceField (class in MMTK.ForceFields.ANMFF) applyFunction() (MMTK.ParticleProperties.ParticleScalar method) applyTo() (MMTK.ConfigIO.Cartesian method) (MMTK.ConfigIO.ZMatrix method) (MMTK.PDB.PDBConfiguration method) applyTransformation() (MMTK.Collections.GroupOfAtoms method) assign() (MMTK.ParticleProperties.ParticleProperty method) asuToUnitCell() (MMTK.PDB.PDBConfiguration method) Atom (class in MMTK.ChemicalObjects) AtomCluster (class in MMTK.ChemicalObjects) atomCollection() (MMTK.Collections.GroupOfAtoms method) AtomicField (class in MMTK.Field) AtomicScalarField (class in MMTK.Field) AtomicVectorField (class in MMTK.Field) atomIterator() (MMTK.ChemicalObjects.ChemicalObject method) atomList() (MMTK.ChemicalObjects.ChemicalObject method) (MMTK.Collections.Collection method) (MMTK.Universe.Universe method) atomsWithDefinedPositions() (MMTK.Collections.GroupOfAtoms method)

B

backbone() (MMTK.NucleicAcids.Nucleotide method) (MMTK.NucleicAcids.NucleotideChain method) (MMTK.Proteins.PeptideChain method) (MMTK.Proteins.Protein method) (MMTK.Proteins.Residue method) BarostatReset (class in MMTK.Dynamics) Base class bases() (MMTK.NucleicAcids.Nucleotide method) (MMTK.NucleicAcids.NucleotideChain method) basisVectors() (MMTK.Universe.Universe method) BCCLattice (class in MMTK.Geometry) Bond (class in MMTK.Bonds) BondAngle (class in MMTK.Bonds) (class in MMTK.InternalCoordinates) BondAngleList (class in MMTK.Bonds) bondedTo() (MMTK.ChemicalObjects.Atom method)

bondedUnits() (MMTK.ChemicalObjects.ChemicalObject method) BondLength (class in MMTK.InternalCoordinates) booleanMask() (MMTK.Collections.GroupOfAtoms method) boundingBox() (MMTK.Collections.GroupOfAtoms method) boundingSphere() (MMTK.Collections.GroupOfAtoms method) Box (class in MMTK.Geometry) boxToRealCoordinates() (MMTK.Universe.Universe method) BravaisLattice (class in MMTK.Geometry) BrownianMode (class in MMTK.NormalModes.BrownianModes) BrownianModes (class in MMTK.NormalModes.BrownianModes)

C

CalphaForceField (class in MMTK.ForceFields.CalphaFF) calphaFrictionConstants() (in module MMTK.ProteinFriction) Cartesian (class in MMTK.ConfigIO) cartesianToFractional() (MMTK.Universe.Universe method) cellVolume() (MMTK.Universe.Universe method) centerAndMomentOfInertia() (MMTK.Collections.GroupOfAtoms method) centerOfMass() (MMTK.ChemicalObjects.Atom method) (MMTK.Collections.GroupOfAtoms method) ChainMolecule (class in MMTK.ChemicalObjects) charge() (MMTK.Collections.GroupOfAtoms method) ChargeFit (class in MMTK.ChargeFit) charges() (MMTK.Universe.Universe method) ChemicalObject (class in MMTK.ChemicalObjects) chiAngle() (MMTK.Proteins.Residue method) Circle (class in MMTK.Geometry) close() (MMTK.PDB.PDBOutputFile method) (MMTK.Trajectory.Trajectory method) coherentScatteringFunction() (MMTK.NormalModes.BrownianModes.BrownianModes method) Collection (class in MMTK.Collections) complement() (MMTK.Subspace.Subspace method) Complex (class in MMTK.ChemicalObjects) CompositeChemicalObject (class in MMTK.ChemicalObjects) Cone (class in MMTK.Geometry)

Configuration (class in MMTK.ParticleProperties) configuration() (MMTK.Universe.Universe method) configurationDifference() (MMTK.Universe.Universe method) ConjugateGradientMinimizer (class in MMTK.Minimization) ConnectedChains (class in MMTK.Proteins) contiguousObjectConfiguration() (MMTK.Universe.Universe method) contiguousObjectOffset() (MMTK.Universe.Universe method) copyConfiguration() (MMTK.Universe.Universe method) countBasisVectors() (in module MMTK.FourierBasis) createAll() (MMTK.PDB.PDBConfiguration method) createGroup() (MMTK.MoleculeFactory.MoleculeFactory method) createMolecule() (MMTK.PDB.PDBMolecule method) createMolecules() (MMTK.PDB.PDBConfiguration method) createNucleotideChain() (MMTK.PDB.PDBNucleotideChain method) createNucleotideChains() (MMTK.PDB.PDBConfiguration method) createPeptideChain() (MMTK.PDB.PDBPeptideChain method) createPeptideChains() (MMTK.PDB.PDBConfiguration method) createUnitCellUniverse() (MMTK.PDB.PDBConfiguration method) CubicPeriodicUniverse (class in MMTK.Universe) curl() (MMTK.Field.AtomicVectorField method) Cylinder (class in MMTK.Geometry)

D

DCDReader (class in MMTK.DCD) defineAminoAcidResidue() (in module MMTK.Biopolymers) defineNucleicAcidResidue() (in module MMTK.Biopolymers) definePDBViewer() (in module MMTK.Visualization) defineVRMLiewer() (in module MMTK.Visualization) DeformationEnergyFunction (class in MMTK.Deformation) DeformationForceField (class in MMTK.ForceFields.DeformationFF) DeformationFunction (class in MMTK.Deformation) DeformationReducer (class in MMTK.Deformation) degreesOfFreedom() (MMTK.ChemicalObjects.ChemicalObject method) (MMTK.Collections.GroupOfAtoms method) dihedral() (MMTK.Universe.Universe method) DihedralAngle (class in MMTK.Bonds) (class in MMTK.InternalCoordinates)

DihedralAngleList (class in MMTK.Bonds) dihedralAngles() (MMTK.Bonds.BondAngleList method) dipole() (MMTK.Collections.GroupOfAtoms method) displacementUnderTransformation() (MMTK.Collections.GroupOfAtoms method) distance() (MMTK.Universe.Universe method) distanceConstraintList() (MMTK.ChemicalObjects.ChemicalObject method) (MMTK.Collections.Collection method) (MMTK.Universe.Universe method) distanceFrom() (MMTK.Geometry.Line method) distanceVector() (MMTK.Universe.Universe method) divergence() (MMTK.Field.AtomicVectorField method) dotProduct() (MMTK.ParticleProperties.ParticleVector method) dyadicProduct() (MMTK.ParticleProperties.ParticleVector method)

E

EISF() (MMTK.NormalModes.BrownianModes.BrownianModes method) (MMTK.NormalModes.VibrationalModes.VibrationalModes method) enclosesPoint() (MMTK.Geometry.GeometricalObject3D method) EnergeticMode (class in MMTK.NormalModes.EnergeticModes) EnergeticModes (class in MMTK.NormalModes.EnergeticModes) energy() (MMTK.Universe.Universe method) energyAndForceConstants() (MMTK.Universe.Universe method) energyAndGradients() (MMTK.Universe.Universe method)

energyGradientsAndForceConstants() (MMTK.Universe.Universe method) energyTerms() (MMTK.Universe.Universe method) enforceConstraints() (MMTK.Universe.Universe method) environmentObjectList() (MMTK.Universe.Universe method) EqualityConstraint (class in MMTK.ChargeFit) estimateCutoff() (in module MMTK.FourierBasis) evaluationPoints() (in module MMTK.ChargeFit)

F

FCCLattice (class in MMTK.Geometry) findContacts() (in module MMTK.MolecularSurface) findHydrogenPositions() (MMTK.ChemicalObjects.Molecule method) findTransformation() (MMTK.Collections.GroupOfAtoms method) FiniteDeformationEnergyFunction (class in MMTK.Deformation) FiniteDeformationFunction (class in MMTK.Deformation) FiniteDeformationReducer (class in MMTK.Deformation)

flush() (MMTK.Trajectory.Trajectory method) forceConstantTest() (in module MMTK.ForceFields.ForceFieldTest) forcefield() (MMTK.Universe.Universe method) FourierBasis (class in MMTK.FourierBasis) fractionalToCartesian() (MMTK.Universe.Universe method) fullName() (MMTK.ChemicalObjects.ChemicalObject method)

G

GeometricalObject3D (class in MMTK.Geometry) getAtomBooleanArray() (MMTK.Universe.Universe method) getAtomProperty() (MMTK.ChemicalObjects.ChemicalObject method) getAtomScalarArray() (MMTK.Universe.Universe method) getBasis() (MMTK.Subspace.Subspace method) getParticleBoolean() (MMTK.Universe.Universe method) getParticleScalar() (MMTK.Universe.Universe method)

getValue() (MMTK.InternalCoordinates.BondAngle method) (MMTK.InternalCoordinates.BondLength method) (MMTK.InternalCoordinates.DihedralAngle method) gradient() (MMTK.Field.AtomicScalarField method) gradientTest() (in module MMTK.ForceFields.ForceFieldTest) graphicsObjects() (MMTK.Visualization.Viewable method) Group (class in MMTK.ChemicalObjects) GroupOfAtoms (class in MMTK.Collections)

H

HarmonicAngleRestraint (class in MMTK.ForceFields.Restraints) HarmonicDihedralRestraint (class in MMTK.ForceFields.Restraints) HarmonicDistanceRestraint (class in MMTK.ForceFields.Restraints) HarmonicForceField (class in MMTK.ForceFields.BondFF)

HarmonicTrapForceField (class in MMTK.ForceFields.Restraints) hasAtom() (MMTK.Bonds.Bond method) hasPoint() (MMTK.Geometry.GeometricalObject3D method) Heater (class in MMTK.Dynamics)

I

incoherentScatteringFunction() (MMTK.NormalModes.BrownianModes.BrownianModes method) (MMTK.NormalModes.VibrationalModes.VibrationalModes method) InfiniteUniverse (class in MMTK.Universe) initializeVelocitiesToTemperature() (MMTK.Universe.Universe method) intersectWith() (MMTK.Geometry.GeometricalObject3D method) isChemicalObject() (in module MMTK.ChemicalObjects) isCollection() (in module MMTK.Collections) isConfiguration() (in module MMTK.ParticleProperties)

isNucleotideChain() (in module MMTK.NucleicAcids) isParticleProperty() (in module MMTK.ParticleProperties) isPeptideChain() (in module MMTK.Proteins) isProtein() (in module MMTK.Proteins) isTrajectory() (in module MMTK.Trajectory) isUniverse() (in module MMTK.Universe)

K

kineticEnergy() (MMTK.Collections.GroupOfAtoms method)

L

laplacian() (MMTK.Field.AtomicScalarField method) (MMTK.Field.AtomicVectorField method) largestDistance() (MMTK.Universe.Universe method) Lattice (class in MMTK.Geometry) length() (MMTK.Field.AtomicVectorField method) (MMTK.ParticleProperties.ParticleVector method)

LennardJonesForceField (class in MMTK.ForceFields.LennardJonesFF) Line (class in MMTK.Geometry) LinkedRigidBodyMotionSubspace (class in MMTK.Subspace) LogOutput (class in MMTK.Trajectory)

M

map() (MMTK.Collections.Collection method) (MMTK.Universe.Universe method) mass() (MMTK.Collections.GroupOfAtoms method) masses() (MMTK.Universe.Universe method) massWeightedDotProduct() (MMTK.ParticleProperties.ParticleVector method) massWeightedNorm() (MMTK.ParticleProperties.ParticleVector method) maximum() (MMTK.ParticleProperties.ParticleScalar method) meanSquareDisplacement() (MMTK.NormalModes.BrownianModes.BrownianModes method) (MMTK.NormalModes.VibrationalModes.VibrationalModes method) minimum() (MMTK.ParticleProperties.ParticleScalar method) Mix-in class MMTK (module) MMTK.Biopolymers (module) MMTK.Bonds (module) MMTK.ChargeFit (module) MMTK.ChemicalObjects (module) MMTK.Collections (module) MMTK.ConfigIO (module) MMTK.DCD (module) MMTK.Deformation (module) MMTK.Dynamics (module) MMTK.Environment (module) MMTK.Field (module) MMTK.ForceFields.Amber.AmberForceField (module) MMTK.ForceFields.ForceFieldTest (module) MMTK.ForceFields.Restraints (module) MMTK.FourierBasis (module) MMTK.Geometry (module)

MMTK.InternalCoordinates (module) MMTK.Minimization (module) MMTK.MolecularSurface (module) MMTK.MoleculeFactory (module) MMTK.NormalModes (module) MMTK.NormalModes.BrownianModes (module) MMTK.NormalModes.EnergeticModes (module) MMTK.NormalModes.VibrationalModes (module) MMTK.NucleicAcids (module) MMTK.ParticleProperties (module) MMTK.PDB (module) MMTK.PDBMoleculeFactory (module) MMTK.ProteinFriction (module) MMTK.Proteins (module) MMTK.Random (module) MMTK.Solvation (module) MMTK.Subspace (module) MMTK.Trajectory (module) MMTK.Units (module) MMTK.Universe (module) MMTK.Visualization (module) MMTK.XML (module) Molecule (class in MMTK.ChemicalObjects) molecule_constructor (MMTK.PDB.PDBConfiguration attribute) MoleculeFactory (class in MMTK.MoleculeFactory) momentum() (MMTK.Collections.GroupOfAtoms method)

N

nextModel() (MMTK.PDB.PDBOutputFile method) nextResidue() (MMTK.Biopolymers.Residue method) norm() (MMTK.ParticleProperties.ParticleVector method) normalizeConfiguration() (MMTK.Collections.GroupOfAtoms method) NormalizedDeformationEnergyFunction (class in MMTK.Deformation) NormalizedDeformationFunction (class in MMTK.Deformation) normalizePosition() (MMTK.Collections.GroupOfAtoms method) normalizingTransformation() (MMTK.Collections.GroupOfAtoms method) NoseThermostat (class in MMTK.Environment) Nucleotide (class in MMTK.NucleicAcids)

nucleotide_chain_constructor (MMTK.PDB.PDBConfiguration attribute) NucleotideChain (class in MMTK.NucleicAcids) NucleotideSubChain (class in MMTK.NucleicAcids) numberOfAtoms() (MMTK.Collections.Collection method) (MMTK.Collections.GroupOfAtoms method) numberOfCartesianCoordinates() (MMTK.Collections.GroupOfAtoms method) numberOfDistanceConstraints() (MMTK.ChemicalObjects.ChemicalObject method) (MMTK.Collections.Collection method) (MMTK.Universe.Universe method) numberOfFixedAtoms() (MMTK.Collections.GroupOfAtoms method) numberOfPoints() (MMTK.Collections.GroupOfAtoms method) numberOfSolventMolecules() (in module MMTK.Solvation)

O

objectList() (MMTK.Collections.Collection method) (MMTK.Universe.Universe method) OPLSForceField (class in MMTK.ForceFields.Amber) OrthorhombicPeriodicUniverse (class in MMTK.Universe)

otherAtom() (MMTK.Bonds.Bond method) otherBond() (MMTK.Bonds.BondAngle method)

P

PairDistanceSubspace (class in MMTK.Subspace) pairsWithinCutoff() (MMTK.Collections.PartitionedCollection method) ParallelepipedicPeriodicUniverse (class in MMTK.Universe) ParticleProperty (class in MMTK.ParticleProperties) ParticleScalar (class in MMTK.ParticleProperties) ParticleTensor (class in MMTK.ParticleProperties) ParticleTrajectory (class in MMTK.Trajectory) particleValues() (MMTK.Field.AtomicField method) ParticleVector (class in MMTK.ParticleProperties) PartitionedAtomCollection (class in MMTK.Collections) PartitionedCollection (class in MMTK.Collections) partitions() (MMTK.Collections.PartitionedCollection method) PDBConfiguration (class in MMTK.PDB) PDBFile (in module MMTK.PDB) PDBMolecule (class in MMTK.PDB) PDBMoleculeFactory (class in MMTK.PDBMoleculeFactory)

PDBNucleotideChain (class in MMTK.PDB) PDBOutputFile (class in MMTK.PDB) PDBPeptideChain (class in MMTK.PDB) peptide_chain_constructor (MMTK.PDB.PDBConfiguration attribute) PeptideChain (class in MMTK.Proteins) perpendicularVector() (MMTK.Geometry.Line method) phiAngle() (MMTK.Proteins.Residue method) phiPsi() (MMTK.Proteins.PeptideChain method) (MMTK.Proteins.Protein method) (MMTK.Proteins.Residue method) Plane (class in MMTK.Geometry) position() (MMTK.ChemicalObjects.Atom method) (MMTK.Collections.GroupOfAtoms method) precedingResidue() (MMTK.Biopolymers.Residue method) projectionComplementOf() (MMTK.Subspace.Subspace method) projectionOf() (MMTK.Geometry.Line method) (MMTK.Subspace.Subspace method) Protein (class in MMTK.Proteins) psiAngle() (MMTK.Proteins.Residue method)

R

randomDirection() (in module MMTK.Random) randomDirections() (in module MMTK.Random) randomParticleVector() (in module MMTK.Random) randomPoint() (MMTK.Universe.Universe method) randomPointInBox() (in module MMTK.Random) randomPointInSphere() (in module MMTK.Random) randomRotation() (in module MMTK.Random) randomVelocity() (in module MMTK.Random) rawMode() (MMTK.NormalModes.BrownianModes.BrownianModes method) (MMTK.NormalModes.EnergeticModes.EnergeticModes method) (MMTK.NormalModes.VibrationalModes.VibrationalModes method) readParticleTrajectory() (MMTK.Trajectory.Trajectory method) readRigidBodyTrajectory() (MMTK.Trajectory.Trajectory method) realToBoxCoordinates() (MMTK.Universe.Universe method) reciprocalBasisVectors() (MMTK.Universe.Universe method) releaseConfigurationChangeLock() (MMTK.Universe.Universe method) releaseReadStateLock() (MMTK.Universe.Universe method) releaseWriteStateLock() (MMTK.Universe.Universe method) removeDistanceConstraints() (MMTK.ChemicalObjects.ChemicalObject method) (MMTK.Collections.Collection method) (MMTK.Universe.Universe method) removeObject() (MMTK.Collections.Collection method) (MMTK.Universe.Universe method) replaceResidue() (MMTK.Proteins.PeptideChain method) Residue (class in MMTK.Biopolymers) (class in MMTK.Proteins)

ResidueChain (class in MMTK.Biopolymers) residues() (MMTK.Biopolymers.ResidueChain method) (MMTK.Proteins.Protein method) residuesOfType() (MMTK.Biopolymers.ResidueChain method) (MMTK.Proteins.Protein method) RestartTrajectoryOutput (class in MMTK.Trajectory) retrieveAsymmetricUnit() (MMTK.PDBMoleculeFactory.PDBMoleculeFactory method) retrieveMolecule() (MMTK.MoleculeFactory.MoleculeFactory method) retrieveMolecules() (MMTK.PDBMoleculeFactory.PDBMoleculeFactory method) retrieveUnitCell() (MMTK.PDBMoleculeFactory.PDBMoleculeFactory method) retrieveUniverse() (MMTK.PDBMoleculeFactory.PDBMoleculeFactory method) return_class (MMTK.ParticleProperties.ParticleProperty attribute) (MMTK.ParticleProperties.ParticleScalar attribute) (MMTK.ParticleProperties.ParticleTensor attribute) (MMTK.ParticleProperties.ParticleVector attribute) RhombicLattice (class in MMTK.Geometry) RigidBodyTrajectory (class in MMTK.Trajectory) RigidMotionSubspace (class in MMTK.Subspace) rmsDifference() (MMTK.Collections.GroupOfAtoms method) rotateAroundAxis() (MMTK.Collections.GroupOfAtoms method) rotateAroundCenter() (MMTK.Collections.GroupOfAtoms method) rotateAroundOrigin() (MMTK.Collections.GroupOfAtoms method) rotationalConstants() (MMTK.Collections.GroupOfAtoms method) RotationRemover (class in MMTK.Dynamics)

S

scaleBy() (MMTK.ParticleProperties.ParticleProperty method) scaleSize() (MMTK.Universe.OrthorhombicPeriodicUniverse method) (MMTK.Universe.ParallelepipedicPeriodicUniverse method) scaleVelocitiesToTemperature() (MMTK.Universe.Universe method) SCLattice (class in MMTK.Geometry) selectAtoms() (MMTK.ParticleProperties.ParticleProperty method) selectBox() (MMTK.Collections.Collection method) (MMTK.Universe.Universe method) selectShell() (MMTK.Collections.Collection method) (MMTK.Universe.Universe method) sequence() (MMTK.Biopolymers.ResidueChain method) (MMTK.Proteins.PeptideChain method) setBondConstraints() (MMTK.ChemicalObjects.ChemicalObject method) (MMTK.Collections.Collection method) (MMTK.Universe.Universe method) setConfiguration() (MMTK.Universe.Universe method) setForceField() (MMTK.Universe.Universe method) setFromTrajectory() (MMTK.Universe.Universe method) setMass() (MMTK.ChemicalObjects.Atom method) setPosition() (MMTK.ChemicalObjects.Atom method) setRigidBodyConstraints() (MMTK.ChemicalObjects.ChemicalObject method) setSize() (MMTK.Universe.CubicPeriodicUniverse method) setValue() (MMTK.InternalCoordinates.BondAngle method) (MMTK.InternalCoordinates.BondLength method) (MMTK.InternalCoordinates.DihedralAngle method) setVelocities() (MMTK.Universe.Universe method)

shrinkUniverse() (in module MMTK.Solvation) sidechains() (MMTK.Proteins.PeptideChain method) (MMTK.Proteins.Protein method) (MMTK.Proteins.Residue method) SnapshotGenerator (class in MMTK.Trajectory) SPCEForceField (class in MMTK.ForceFields.SPCEFF) Sphere (class in MMTK.Geometry) StandardLogOutput (class in MMTK.Trajectory) staticStructureFactor() (MMTK.NormalModes.BrownianModes.BrownianModes method) SteepestDescentMinimizer (class in MMTK.Minimization) SubChain (class in MMTK.Proteins) Subclass Subspace (class in MMTK.Subspace) SubTrajectory (class in MMTK.Trajectory) SubVariable (class in MMTK.Trajectory) sumOverParticles() (MMTK.ParticleProperties.ParticleProperty method) superpositionFit() (in module MMTK.Geometry) surfaceAndVolume() (in module MMTK.MolecularSurface) surfaceAtoms() (in module MMTK.MolecularSurface) surfacePointsAndGradients() (in module MMTK.MolecularSurface)

T

temperature() (MMTK.Collections.GroupOfAtoms method) topLevelChemicalObject() (MMTK.ChemicalObjects.ChemicalObject method) TotalChargeConstraint (class in MMTK.ChargeFit) totalNorm() (MMTK.ParticleProperties.ParticleVector method) Trajectory (class in MMTK.Trajectory) TrajectoryAction (class in MMTK.Trajectory) TrajectoryGenerator (class in MMTK.Trajectory) trajectoryInfo() (in module MMTK.Trajectory)

TrajectoryOutput (class in MMTK.Trajectory) TrajectorySet (class in MMTK.Trajectory) TrajectorySetVariable (class in MMTK.Trajectory) TrajectoryVariable (class in MMTK.Trajectory) translateBy() (MMTK.Collections.GroupOfAtoms method) (MMTK.Trajectory.ParticleTrajectory method) translateTo() (MMTK.ChemicalObjects.Atom method) (MMTK.Collections.GroupOfAtoms method) TranslationRemover (class in MMTK.Dynamics)

U

Universe (class in MMTK.Universe)

universe() (MMTK.ChemicalObjects.ChemicalObject method) (MMTK.Collections.Collection method) (MMTK.Collections.GroupOfAtoms method) (MMTK.Universe.Universe method)

V

variables() (MMTK.Trajectory.Trajectory method) velocities() (MMTK.Universe.Universe method) VelocityScaler (class in MMTK.Dynamics) VelocityVerletIntegrator (class in MMTK.Dynamics) VibrationalMode (class in MMTK.NormalModes.VibrationalModes) VibrationalModes (class in MMTK.NormalModes.VibrationalModes)

view() (in module MMTK.Visualization) (MMTK.Collections.GroupOfAtoms method) (MMTK.Field.AtomicField method) (MMTK.Trajectory.Trajectory method) Viewable (class in MMTK.Visualization) viewSequence() (in module MMTK.Visualization) viewTrajectory() (in module MMTK.Visualization) virialTest() (in module MMTK.ForceFields.ForceFieldTest) volume() (MMTK.Geometry.GeometricalObject3D method)

W

write() (MMTK.PDB.PDBOutputFile method) writeDCDPDB() (in module MMTK.DCD)

writeToFile() (MMTK.Collections.GroupOfAtoms method) (MMTK.Field.AtomicField method) writeVelocityDCDPDB() (in module MMTK.DCD)

X

XMLMoleculeFactory (class in MMTK.XML)

Z

zero() (MMTK.ParticleProperties.ParticleProperty method)

ZMatrix (class in MMTK.ConfigIO)