All Classes

• ARCFileFilter
• ASULimit
• AdderDoubleArray
• Adiabatic
• AlchemicalOptions
• AlchemicalOptions.AlchemicalOptionGroup
• AlgorithmFunctions
• AlgorithmListener
• AlgorithmUtils
• AlgorithmsScript
• AlgorithmsTest
• AminoAcidUtils
• AminoAcidUtils.AA
• AminoAcidUtils.AIB
• AminoAcidUtils.ALA
• AminoAcidUtils.ARG
• AminoAcidUtils.ASD
• AminoAcidUtils.ASH
• AminoAcidUtils.ASN
• AminoAcidUtils.ASP
• AminoAcidUtils.AminoAcid1
• AminoAcidUtils.AminoAcid3
• AminoAcidUtils.AminoAcidBackboneAtoms
• AminoAcidUtils.CYD
• AminoAcidUtils.CYS
• AminoAcidUtils.CYX
• AminoAcidUtils.GLD
• AminoAcidUtils.GLH
• AminoAcidUtils.GLN
• AminoAcidUtils.GLU
• AminoAcidUtils.GLY
• AminoAcidUtils.GlycineBackboneAtoms
• AminoAcidUtils.HID
• AminoAcidUtils.HIE
• AminoAcidUtils.HIS
• AminoAcidUtils.ILE
• AminoAcidUtils.LEU
• AminoAcidUtils.LYD
• AminoAcidUtils.LYS
• AminoAcidUtils.MET
• AminoAcidUtils.ORN
• AminoAcidUtils.PCA
• AminoAcidUtils.PHE
• AminoAcidUtils.PRO
• AminoAcidUtils.ProlineBackboneAtoms
• AminoAcidUtils.ResiduePosition
• AminoAcidUtils.SER
• AminoAcidUtils.SideChainType
• AminoAcidUtils.THR
• AminoAcidUtils.TRP
• AminoAcidUtils.TYD
• AminoAcidUtils.TYR
• AminoAcidUtils.VAL
• Angle
• AngleTorsion
• AngleTorsionType
• AngleType
• AngleType.AngleFunction
• AngleType.AngleMode
• AnnealOptions
• AnnealingSchedule
• ArrayItemGenerator
• AssemblyState
• AtomOverlapLoop
• AtomSelectionOptions
• AtomSelectionOptions.AtomSelectionOptionGroup
• AtomType
• AtomicDoubleArray
• AtomicDoubleArray.AtomicDoubleArrayImpl
• AtomicDoubleArray3D
• BARFilter
• BackendClassLoader
• BackendFileInputStream
• BackendFileInputStream.Result
• BackendFileOutputStream
• BackendFileOutputStream.Result
• BackendFileReader
• BackendFileWriter
• BackendInfo
• BackendInfo.State
• Barostat
• BarostatOptions
• BarostatOptions.BarostatOptionGroup
• BarrierAction
• BaseType
• BellCurveSwitch
• BennettAcceptanceRatio
• Berendsen
• BetterBeeman
• BioType
• BoltzmannMC
• Bond
• BondType
• BondType.BondFunction
• BondedEnergy
• BondedTerm
• BondedTerm.BondedComparator
• BondedUtils
• BondedUtils.MissingAtomTypeException
• BondedUtils.MissingHeavyAtomException
• BooleanArrayBuf
• BooleanArrayBuf_1
• BooleanArrayReductionBuf
• BooleanArrayReductionBuf_1
• BooleanBuf
• BooleanItemBuf
• BooleanItemReductionBuf
• BooleanMatrixBuf
• BooleanMatrixBuf_1
• BooleanMatrixReductionBuf
• BooleanMatrixReductionBuf_1
• BooleanOp
• BootStrapStatistics
• BootstrappableEstimator
• BornGradRegion
• BornGradRegion.BornCRLoop
• BornRadiiRegion
• BornRadiiRegion.BornRadiiLoop
• BornTanhRescaling
• BoxOptCell
• Buf
• BulkSolventDensityRegion
• BulkSolventList
• BulkSolventRowRegion
• BulkSolventSliceRegion
• Bussi
• ByteArrayBuf
• ByteArrayBuf_1
• ByteArrayReductionBuf
• ByteArrayReductionBuf_1
• ByteBuf
• ByteItemBuf
• ByteItemReductionBuf
• ByteMatrixBuf
• ByteMatrixBuf_1
• ByteMatrixReductionBuf
• ByteMatrixReductionBuf_1
• ByteOp
• ByteSequence
• ByteSwap
• CCP4MapFilter
• CCP4MapWriter
• CIFFilter
• CIFFilter
• CIFHeader
• CNSFilter
• CNSMapWriter
• COMRestraint
• CarbonSASACRLoop
• CcmaConstraint
• CcmaConstraint.MatrixWalker
• ChandlerCavitation
• Channel
• ChannelClosedException
• ChannelGroup
• ChannelGroup.AcceptThread
• ChannelGroupClosedException
• CharacterArrayBuf
• CharacterArrayBuf_1
• CharacterArrayReductionBuf
• CharacterArrayReductionBuf_1
• CharacterBuf
• CharacterItemBuf
• CharacterItemReductionBuf
• CharacterMatrixBuf
• CharacterMatrixBuf_1
• CharacterMatrixReductionBuf
• CharacterMatrixReductionBuf_1
• CharacterOp
• ChargeType
• Clustering
• Clustering.Conformation
• Comm
• Comm.FloodReceiveIORequest
• CommPattern
• CommRequest
• CommStatus
• Complex
• Complex3D
• Complex3DParallel
• ComplexNumber
• CompositeCurve
• CompositeSwitch
• Configuration
• ConnectListener
• ConnollyRegion
• ConnollyRegion.VolumeLoop
• ConstantSwitch
• Constants
• Constants
• Constants
• Constraint
• ConvexHullOps
• ConvolutionRegion
• CoordRestraint
• CoordShakeMove
• CoordinateFileFilter
• CosineWave
• CoulombTensorGlobal
• CoulombTensorQI
• Crystal
• CrystalMinimize
• CrystalPotential
• CrystalReciprocalSpace
• CrystalStats
• CrystalSystem
• DTDResolver
• DYNFileFilter
• DYNFilter
• DataContainer
• DataFilter
• DataInputStream
• DataOutputStream
• DataRefinementOptions
• DataSet
• DefaultRandom
• DiffractionData
• DiffractionFile
• DiffractionFileFilter
• DiffractionRefinementData
• DirectRegion
• DirectRegion.DirectLoop
• DirectoryUtils
• DispersionRegion
• DispersionRegion.DispersionLoop
• DistanceMatrix
• DistanceMatrixFileFilter
• DistanceMatrixFilter
• DistanceRegion
• DistanceRegion.DistanceLoop
• Double3
• DoubleArrayBuf
• DoubleArrayBuf_1
• DoubleArrayReductionBuf
• DoubleArrayReductionBuf_1
• DoubleBuf
• DoubleIndexPair
• DoubleItemBuf
• DoubleItemReductionBuf
• DoubleMath
• DoubleMatrixBuf
• DoubleMatrixBuf_1
• DoubleMatrixFile
• DoubleMatrixFile.Reader
• DoubleMatrixFile.Writer
• DoubleMatrixReductionBuf
• DoubleMatrixReductionBuf_1
• DoubleOp
• DoublesDataSet
• DualTopologyEnergy
• DynamicIntegerSchedule
• DynamicLongSchedule
• DynamicsOptions
• DynamicsOptions.DynamicsOptionGroup
• ESVFileFilter
• ESVFilter
• EliminatedRotamers
• EmptyBooleanBuf
• EmptyByteBuf
• EmptyCharacterBuf
• EmptyDoubleBuf
• EmptyFloatBuf
• EmptyIntegerBuf
• EmptyLongBuf
• EmptyObjectBuf
• EmptyShortBuf
• EmptySigned16BitIntegerBuf
• EmptySigned8BitIntegerBuf
• EmptyUnsigned16BitIntegerBuf
• EmptyUnsigned8BitIntegerBuf
• EnergyException
• EnergyExpansion
• EnergyRegion
• EnergyRegion.EnergyLoop
• Erf
• EstimateBootstrapper
• EwaldTensorGlobal
• EwaldTensorQI
• ExpAnnealSchedule
• ExpandInducedDipolesRegion
• ExpandInducedDipolesRegion.ExpandInducedDipoleLoop
• ExtendedSystem
• FFTRegion
• FFTXYLoop
• FFTZIZLoop
• FFTZLoop
• FFXClient
• FFXExec
• FFXFileFilter
• FFXLocale
• FFXScript
• FFXServer
• FFXSystem
• FFXTest
• FFXTornado
• FileCloser
• FileOpener
• FileUtils
• Files
• FixedIntegerSchedule
• FixedLongSchedule
• FlatEndAnnealSchedule
• Float3
• FloatArrayBuf
• FloatArrayBuf_1
• FloatArrayReductionBuf
• FloatArrayReductionBuf_1
• FloatBuf
• FloatItemBuf
• FloatItemReductionBuf
• FloatMath
• FloatMatrixBuf
• FloatMatrixBuf_1
• FloatMatrixReductionBuf
• FloatMatrixReductionBuf_1
• FloatOp
• ForceField
• ForceField.ConstraintTypes
• ForceField.ELEC_FORM
• ForceField.ForceFieldName
• ForceField.ForceFieldType
• ForceFieldEnergy
• ForceFieldEnergy.BondedRegion
• ForceFieldEnergy.BondedRegion.BondedTermLoop
• ForceFieldEnergy.BondedRegion.GradInitLoop
• ForceFieldEnergy.BondedRegion.GradReduceLoop
• ForceFieldEnergy.Platform
• ForceFieldEnergyOpenMM
• ForceFieldEnergyOpenMM.Context
• ForceFieldEnergyOpenMM.Integrator
• ForceFieldEnergyOpenMM.System
• ForceFieldFileFilter
• ForceFieldFilter
• FormFactor
• FourBodyEnergyRegion
• FourBodyEnergyRegion.QuadsEnergyLoop
• FrontendFileReader
• FrontendFileReader.FileHandler
• FrontendFileReader.FileHandler.InputFileCloseInvocation
• FrontendFileReader.FileHandler.InputFileOpenInvocation
• FrontendFileReader.FileHandler.InputFileReadInvocation
• FrontendFileReader.FileHandler.InputFileSkipInvocation
• FrontendFileReader.FileHandler.Invocation
• FrontendFileWriter
• FrontendFileWriter.FileHandler
• FrontendFileWriter.FileHandler.Invocation
• FrontendFileWriter.FileHandler.OutputFileCloseInvocation
• FrontendFileWriter.FileHandler.OutputFileFlushInvocation
• FrontendFileWriter.FileHandler.OutputFileOpenInvocation
• FrontendFileWriter.FileHandler.OutputFileWriteInvocation
• FunctionDataCurve
• GKEnergyGlobal
• GKEnergyQI
• GKEnergyRegion
• GKEnergyRegion.GKEnergyLoop
• GKEnergyRegion.GKEnergyLoopQI
• GKSource
• GKSource.GK_MULTIPOLE_ORDER
• GKSource.GK_TENSOR_MODE
• GKTensorGlobal
• GKTensorQI
• GaussVol
• GaussVol.GAUSSVOL_MODE
• GeneralizedKirkwood
• GeneralizedKirkwood.NonPolar
• GenerateRotamers
• GetProteinFeatures
• GlobalBehavior
• GoldsteinPairRegion
• GoldsteinPairRegion.GoldsteinRotamerPairLoop
• GradientOptions
• GradientOptions.GradientOptionGroup
• GradientSchedule
• GraphicsAxis
• GraphicsCanvas
• GraphicsCanvas.ImageFormat
• GraphicsCanvas.LeftButtonMode
• GraphicsCanvas.MouseMode
• GraphicsEvents
• GraphicsFullScreen
• GraphicsPanel
• GraphicsPicking
• GraphicsPicking.PickLevel
• GraphicsPrefs
• GraphicsSplitPane
• GuidedIntegerSchedule
• GuidedLongSchedule
• HKL
• HeadlessMain
• Hex
• Hierarchy
• HistogramReader
• HistogramSettings
• HistogramWriter
• HttpRequest
• HttpResponse
• HttpResponse.Status
• HttpServer
• HttpServer.AcceptorThread
• Hybrid36
• HybridTeam
• HydrophobicPMFLoop
• HydrophobicPMFRegion
• HydrophobicPMFRegion.CarbonSASALoop
• IFFTRegion
• IFFTXYLoop
• IFFTZLoop
• INTFileFilter
• INTFilter
• IORequest
• IORequestList
• ImproperTorsion
• ImproperTorsionType
• IndexIndexPair
• InducedDipoleFieldReduceRegion
• InducedDipoleFieldReduceRegion.InducedDipoleFieldReduceLoop
• InducedDipoleFieldRegion
• InducedDipoleFieldRegion.InducedDipoleRealSpaceFieldRegion
• InducedDipoleFieldRegion.InducedDipoleRealSpaceFieldRegion.InducedRealSpaceFieldLoop
• InducedDipoleFieldRegion.InducedDipoleRealSpaceFieldSection
• InducedDipoleFieldRegion.InducedDipoleReciprocalFieldSection
• InducedFileFilter
• InducedFilter
• InducedGKFieldRegion
• InducedGKFieldRegion.InducedGKFieldLoop
• InitializationRegion
• InitializationRegion
• InitializationRegion.InitializationLoop
• InitializationRegion.InitializationLoop
• InitializationRegion.RotateMultipolesLoop
• Instance
• Instance.null
• Instance.null.null
• IntegerArrayBuf
• IntegerArrayBuf_1
• IntegerArrayReductionBuf
• IntegerArrayReductionBuf_1
• IntegerBuf
• IntegerForLoop
• IntegerItemBuf
• IntegerItemReductionBuf
• IntegerMatrixBuf
• IntegerMatrixBuf_1
• IntegerMatrixReductionBuf
• IntegerMatrixReductionBuf_1
• IntegerOp
• IntegerSchedule
• IntegerSchedule.null
• IntegerStrideForLoop
• Integrate1DNumeric
• Integrate1DNumeric.IntegrateWindow
• Integrate1DNumeric.IntegrationSide
• Integrate1DNumeric.IntegrationType
• Integration
• Integrator
• IntegratorEnum
• InvalidMatrixFileException
• ItemGenerator
• ItemHolder
• IteratorItemGenerator
• Job
• Job.null
• JobBackend
• JobBackend.State
• JobBackend.null
• JobBackendMessage
• JobBackendMessage.CancelJobMessage
• JobBackendMessage.CommenceJobMessage
• JobBackendMessage.InputFileCloseResultMessage
• JobBackendMessage.InputFileOpenResultMessage
• JobBackendMessage.InputFileReadResultMessage
• JobBackendMessage.InputFileSkipResultMessage
• JobBackendMessage.JobFinishedMessage
• JobBackendMessage.OutputFileCloseResultMessage
• JobBackendMessage.OutputFileFlushResultMessage
• JobBackendMessage.OutputFileOpenResultMessage
• JobBackendMessage.OutputFileWriteResultMessage
• JobBackendMessage.RenewLeaseMessage
• JobBackendMessage.ReportResourceMessage
• JobBackendProxy
• JobBackendRef
• JobFrontend
• JobFrontend.State
• JobFrontendMessage
• JobFrontendMessage.AssignBackendMessage
• JobFrontendMessage.AssignJobNumberMessage
• JobFrontendMessage.BackendFinishedMessage
• JobFrontendMessage.BackendReadyMessage
• JobFrontendMessage.CancelJobMessage
• JobFrontendMessage.InputFileCloseMessage
• JobFrontendMessage.InputFileOpenMessage
• JobFrontendMessage.InputFileReadMessage
• JobFrontendMessage.InputFileSkipMessage
• JobFrontendMessage.OutputFileCloseMessage
• JobFrontendMessage.OutputFileFlushMessage
• JobFrontendMessage.OutputFileOpenMessage
• JobFrontendMessage.OutputFileWriteMessage
• JobFrontendMessage.RenewLeaseMessage
• JobFrontendMessage.ReportCommentMessage
• JobFrontendMessage.RequestResourceMessage
• JobFrontendProxy
• JobFrontendRef
• JobGenerator
• JobInfo
• JobInfo.State
• JobScheduler
• JobSchedulerException
• JobSchedulerMessage
• JobSchedulerMessage.BackendFailedMessage
• JobSchedulerMessage.CancelJobMessage
• JobSchedulerMessage.JobFinishedMessage
• JobSchedulerMessage.RenewLeaseMessage
• JobSchedulerMessage.ReportCommentMessage
• JobSchedulerMessage.RequestJobMessage
• JobSchedulerProxy
• JobSchedulerRef
• Joint
• KeyFileEditor
• KeyFileFilter
• KeyFilter
• Keyword
• KeywordComponent
• KeywordComponent.SwingRepresentation
• KeywordPanel
• KillRegion
• LBFGS
• LambdaInterface
• LambdaMove
• LambdaParticleOptions
• LambdaParticleOptions.LambdaParticleOptionGroup
• LambdaReader
• LambdaWriter
• LatticeSystem
• LaueSystem
• LineBufferedOutputStream
• LineSearch
• LineSearchResult
• LinearAnnealSchedule
• LinearDerivativeSwitch
• Lock
• Lock.Synchronizer
• LogFormatter
• LogHandler
• LogPanel
• Logger
• LoggerSevereError
• LongArrayBuf
• LongArrayBuf_1
• LongArrayReductionBuf
• LongArrayReductionBuf_1
• LongBuf
• LongForLoop
• LongItemBuf
• LongItemReductionBuf
• LongMatrixBuf
• LongMatrixBuf_1
• LongMatrixReductionBuf
• LongMatrixReductionBuf_1
• LongOp
• LongRange
• LongSchedule
• LongSchedule.null
• LongStrideForLoop
• Loop
• LoopClosure
• LoopbackChannel
• MCLoop
• MCLoop.MCOverride
• MCMove
• MDMove
• MPObjectInputStream
• MSNode
• MSRoot
• MTZFileFilter
• MTZFilter
• MTZWriter
• MTZWriter.MTZType
• Main
• MainMenu
• MainPanel
• ManyBodyOptions
• ManyBodyOptions.BoxOptionGroup
• ManyBodyOptions.EnergyOptionGroup
• ManyBodyOptions.ManyBodyOptionGroup
• ManyBodyOptions.ResidueOptionGroup
• ManyBodyOptions.WindowOptionGroup
• MaskingInterface
• Mathe
• MatrixMath
• Mcg1Random
• MergeFilter
• Message
• MetropolisMC
• Minimize
• Minimize.MinimizationEngine
• MinimizeOpenMM
• MinimizeOptions
• MinimizeOptions.MinimizeOptionGroup
• ModelingPanel
• ModelingPanel.FFXLauncher
• ModelingShell
• ModifiedBessel
• MolecularAssembly
• MolecularAssembly.FractionalMode
• MolecularDynamics
• MolecularDynamics.AssemblyInfo
• MolecularDynamics.CoordinateSnapshot
• MolecularDynamics.DynamicsEngine
• MolecularDynamics.DynamicsState
• MolecularDynamics.MonteCarloNotification
• MolecularDynamics.VerbosityLevel
• MolecularDynamics.WriteActions
• MolecularDynamicsOpenMM
• MolecularMC
• Molecule
• MonteCarloListener
• MonteCarloOST
• MouseBehavior
• MouseBehaviorCallback
• MouseOrbit
• MouseProperties
• MouseRotate
• MouseSelection
• MouseTranslate
• MouseZoom
• MultiDoubleArray
• MultiDynamicsOptions
• MultiDynamicsOptions.MultiDynamicsOptionGroup
• MultiResidue
• MultiTerminus
• MultipleParallelException
• MultiplicativeSwitch
• MultipoleTensor
• MultipoleTensor.COORDINATES
• MultipoleTensor.OPERATOR
• MultipoleType
• MultipoleType.MultipoleFrameDefinition
• NCSCrystal
• NCSRestraint
• NamingUtils
• NamingUtils.HetAtoms
• NeckIntegral
• NeighborList
• NetworkChannel
• NetworkChannelReceiveThread
• NetworkChannelSendThread
• NeutronFormFactor
• NonPjJobFrontend
• NonPjJobFrontend.State
• NonbondedCutoff
• NucleicAcidUtils
• NucleicAcidUtils.NA
• NucleicAcidUtils.NucleicAcid1
• NucleicAcidUtils.NucleicAcid3
• OPTRegion
• OPTRegion.OPTLoop
• OSTOptions
• OSTOptions.MCOSTOptionGroup
• OSTOptions.OSTOptionGroup
• OSXAdapter
• ObjectArrayBuf
• ObjectArrayBuf_1
• ObjectArrayReductionBuf
• ObjectArrayReductionBuf_1
• ObjectBuf
• ObjectItemBuf
• ObjectItemReductionBuf
• ObjectMatrixBuf
• ObjectMatrixBuf_1
• ObjectMatrixReductionBuf
• ObjectMatrixReductionBuf_1
• ObjectOp
• ObjectPair
• Octree
• OctreeCell
• OctreeParticle
• OctreePoint
• Op
• OptimizationListener
• OrthogonalSpaceTempering
• OrthogonalSpaceTempering.Histogram
• OrthogonalSpaceTempering.OptimizationParameters
• OutOfPlaneBend
• OutOfPlaneBendType
• PCGSolver
• PCGSolver.InducedDipolePreconditionerRegion
• PCGSolver.InducedDipolePreconditionerRegion.InducedPreconditionerFieldLoop
• PCGSolver.PCGInitRegion1
• PCGSolver.PCGInitRegion1.PCGInitLoop
• PCGSolver.PCGInitRegion2
• PCGSolver.PCGInitRegion2.PCGInitLoop
• PCGSolver.PCGIterRegion1
• PCGSolver.PCGIterRegion1.PCGIterLoop1
• PCGSolver.PCGIterRegion1.PCGIterLoop2
• PCGSolver.PCGIterRegion2
• PCGSolver.PCGIterRegion2.PCGIterLoop1
• PCGSolver.PCGIterRegion2.PCGIterLoop2
• PDBFileFilter
• PDBFilter
• PDBFilter.Mutation
• PDBFilter.PDBFileStandard
• PDBFilter.Record
• PDBMLFileFilter
• PDBMLFilter
• PJDoubleArray
• PJProperties
• Packing
• PairwiseSchedule
• ParallelConstruct
• ParallelFFT
• ParallelFFT.FFTXYLoop
• ParallelForLoop
• ParallelIteration
• ParallelRegion
• ParallelSection
• ParallelTeam
• ParallelTeamThread
• ParallelTeamThread_0
• ParticleMeshEwald
• ParticleMeshEwald.AlchemicalParameters
• ParticleMeshEwald.EwaldParameters
• ParticleMeshEwald.LambdaFactors
• ParticleMeshEwald.LambdaFactorsESV
• ParticleMeshEwald.LambdaFactorsOST
• ParticleMeshEwald.LambdaMode
• ParticleMeshEwald.PMETimings
• ParticleMeshEwald.Polarization
• ParticleMeshEwald.RealSpaceNeighborParameters
• ParticleMeshEwald.SCFAlgorithm
• ParticleMeshEwald.SCFPredictor
• ParticleMeshEwald.SCFPredictorParameters
• ParticleMeshEwald.SCFPredictorParameters.LeastSquaresPredictor
• ParticleMeshEwald.ScaleParameters
• PermanentFieldRegion
• PermanentFieldRegion.PermanentRealSpaceFieldRegion
• PermanentFieldRegion.PermanentRealSpaceFieldRegion.InitializationLoop
• PermanentFieldRegion.PermanentRealSpaceFieldRegion.PermanentRealSpaceFieldLoop
• PermanentFieldRegion.PermanentRealSpaceFieldSection
• PermanentFieldRegion.PermanentReciprocalSection
• PermanentGKFieldRegion
• PermanentGKFieldRegion.PermanentGKFieldLoop
• PiOrbitalTorsion
• PiOrbitalTorsionType
• PickMouseBehavior
• PickOrbitBehavior
• PickPropertiesBehavior
• PickRotateBehavior
• PickSelectionBehavior
• PickTranslateBehavior
• PickZoomBehavior
• PickingCallback
• PolarizableMultipole
• PolarizationEnergyRegion
• PolarizationEnergyRegion.PolarizationEnergyLoop
• PolarizeType
• Polymer
• PolymerUtils
• PolynomialCurve
• PortUtils
• Potential
• Potential.STATE
• Potential.VARIABLE_TYPE
• PotentialComponent
• PotentialScript
• PotentialTest
• PotentialsFileOpener
• PotentialsFunctions
• PotentialsUtils
• PowerSwitch
• PrintStreamLogger
• ProcessInfo
• ProcessInfo.State
• ProgressiveAlignmentOfCrystals
• Proxy
• QIFrame
• QuadTopologyEnergy
• QuadTopologyEnergy.EnergyASection
• QuadTopologyEnergy.EnergyBSection
• QuadTopologyEnergy.EnergyRegion
• QuasiLinearThetaMap
• ROLS
• ROLSP
• ROLSP.PARALLELMETHOD
• Random
• RandomSample
• RandomSubset
• RandomSubset.DenseHelper
• RandomSubset.Helper
• RandomSubset.SparseHelper
• RandomUnitCellOptions
• RandomUnitCellOptions.RandomUnitCellOptionGroup
• Range
• Rattle
• Real
• Real3D
• Real3DParallel
• RealSpaceData
• RealSpaceEnergy
• RealSpaceEnergyRegion
• RealSpaceEnergyRegion.RealSpaceEnergyLoop
• RealSpaceFile
• RealSpaceFileFilter
• RealSpaceOptions
• RealSpaceRefinementData
• ReciprocalEnergyRegion
• ReciprocalEnergyRegion.InducedDipoleReciprocalEnergyLoop
• ReciprocalEnergyRegion.PermanentReciprocalEnergyLoop
• ReciprocalSpace
• ReduceArrays
• ReduceRegion
• ReduceRegion.ReduceLoop
• ReduceRegion.TorqueLoop
• RefinementEnergy
• RefinementMinimize
• RefinementMinimize.RefinementMode
• RefinementModel
• ReflectionList
• ReflectionSpline
• RelativeSolvation
• RelativeSolvation.SolvationLibrary
• RelativeSolvationType
• Renderer
• RendererCache
• RendererCache.ColorModel
• RendererCache.ViewModel
• RepExOST
• RepExOST.OstType
• RepExOptions
• RepExOptions.RepExOptionGroup
• RepexOSTOptions
• ReplicaExchange
• ReplicatedBoolean
• ReplicatedBoolean.Receiver
• ReplicatedByte
• ReplicatedByte.Receiver
• ReplicatedCharacter
• ReplicatedCharacter.Receiver
• ReplicatedDouble
• ReplicatedDouble.Receiver
• ReplicatedFloat
• ReplicatedFloat.Receiver
• ReplicatedInteger
• ReplicatedInteger.Receiver
• ReplicatedLong
• ReplicatedLong.Receiver
• ReplicatedObject
• ReplicatedObject.Receiver
• ReplicatedShort
• ReplicatedShort.Receiver
• ReplicatesCrystal
• Residue
• Residue.ResidueType
• Residue.SSType
• ResidueState
• Resolution
• ResourceCache
• ResourceCache.ResourceInfo
• Resources
• Respa
• RestrainGroups
• RestraintBond
• RestraintTorsion
• RosenbluthCBMC
• RosenbluthChi0Move
• RosenbluthChiAllMove
• RosenbluthChiAllMove.BackBondedList
• RosenbluthChiAllMove.MODE
• RosenbluthChiAllMove.SnapshotWriter
• RosenbluthChiAllMove.TORSION_OFFSET_AMPRO13
• RosenbluthChiAllMove.TrialSet
• RosenbluthOBMC
• Rotamer
• RotamerLibrary
• RotamerLibrary.NonstandardRotLibrary
• RotamerLibrary.NucleicAcidLibrary
• RotamerLibrary.NucleicSugarPucker
• RotamerLibrary.ProteinLibrary
• RotamerLibrary.RotamerGuess
• RotamerMatrixMC
• RotamerMatrixMove
• RotamerOptimization
• RotamerOptimization.Algorithm
• RotamerOptimization.BoxOptimization
• RotamerOptimization.Direction
• RotamerOptimization.DistanceMethod
• RowLoop
• RowRegion
• RowRegion.GridInitLoop
• RowSchedule
• Runner
• RunningStatistics
• SORRegion
• SORRegion.SORLoop
• SSETest
• SaveOptions
• ScalarMath
• ScaleBulkEnergy
• ScaleBulkEnergy.ScaleBulkEnergyRegion
• ScaleBulkEnergy.ScaleBulkEnergyRegion.ScaleBulkEnergyLoop
• ScaleBulkMinimize
• ScfPredictor
• ScfPredictor.LeastSquaresPredictor
• ScfPredictor.PredictorMode
• Schedule
• Searching
• Searching.Byte
• Searching.Character
• Searching.Double
• Searching.Float
• Searching.Integer
• Searching.Long
• Searching.Object
• Searching.Short
• Selection
• SelfEnergyRegion
• SelfEnergyRegion.SelfEnergyLoop
• SendAsynchronous
• SendSynchronous
• SequentialEstimator
• SettleConstraint
• SharedBoolean
• SharedBooleanArray
• SharedBooleanArrayBuf
• SharedBooleanArrayBuf_1
• SharedBooleanArrayReductionBuf
• SharedBooleanArrayReductionBuf_1
• SharedBooleanBuf
• SharedBooleanReductionBuf
• SharedByte
• SharedByteArray
• SharedByteArrayBuf
• SharedByteArrayBuf_1
• SharedByteArrayReductionBuf
• SharedByteArrayReductionBuf_1
• SharedByteBuf
• SharedByteReductionBuf
• SharedCharacter
• SharedCharacterArray
• SharedCharacterArrayBuf
• SharedCharacterArrayBuf_1
• SharedCharacterArrayReductionBuf
• SharedCharacterArrayReductionBuf_1
• SharedCharacterBuf
• SharedCharacterReductionBuf
• SharedDouble
• SharedDoubleArray
• SharedDoubleArrayBuf
• SharedDoubleArrayBuf_1
• SharedDoubleArrayReductionBuf
• SharedDoubleArrayReductionBuf_1
• SharedDoubleBuf
• SharedDoubleReductionBuf
• SharedFloat
• SharedFloatArray
• SharedFloatArrayBuf
• SharedFloatArrayBuf_1
• SharedFloatArrayReductionBuf
• SharedFloatArrayReductionBuf_1
• SharedFloatBuf
• SharedFloatReductionBuf
• SharedInteger
• SharedIntegerArray
• SharedIntegerArrayBuf
• SharedIntegerArrayBuf_1
• SharedIntegerArrayReductionBuf
• SharedIntegerArrayReductionBuf_1
• SharedIntegerBuf
• SharedIntegerMatrix
• SharedIntegerReductionBuf
• SharedLong
• SharedLongArray
• SharedLongArrayBuf
• SharedLongArrayBuf_1
• SharedLongArrayReductionBuf
• SharedLongArrayReductionBuf_1
• SharedLongBuf
• SharedLongMatrix
• SharedLongReductionBuf
• SharedObject
• SharedObjectArray
• SharedObjectArrayBuf
• SharedObjectArrayBuf_1
• SharedObjectArrayReductionBuf
• SharedObjectArrayReductionBuf_1
• SharedObjectBuf
• SharedObjectReductionBuf
• SharedShort
• SharedShortArray
• SharedShortArrayBuf
• SharedShortArrayBuf_1
• SharedShortArrayReductionBuf
• SharedShortArrayReductionBuf_1
• SharedShortBuf
• SharedShortReductionBuf
• SharedSigned16BitIntegerArrayBuf
• SharedSigned16BitIntegerArrayBuf_1
• SharedSigned16BitIntegerArrayReductionBuf
• SharedSigned16BitIntegerArrayReductionBuf_1
• SharedSigned16BitIntegerBuf
• SharedSigned16BitIntegerReductionBuf
• SharedSigned8BitIntegerArrayBuf
• SharedSigned8BitIntegerArrayBuf_1
• SharedSigned8BitIntegerArrayReductionBuf
• SharedSigned8BitIntegerArrayReductionBuf_1
• SharedSigned8BitIntegerBuf
• SharedSigned8BitIntegerReductionBuf
• SharedUnsigned16BitIntegerArrayBuf
• SharedUnsigned16BitIntegerArrayBuf_1
• SharedUnsigned16BitIntegerArrayReductionBuf
• SharedUnsigned16BitIntegerArrayReductionBuf_1
• SharedUnsigned16BitIntegerBuf
• SharedUnsigned16BitIntegerReductionBuf
• SharedUnsigned8BitIntegerArrayBuf
• SharedUnsigned8BitIntegerArrayBuf_1
• SharedUnsigned8BitIntegerArrayReductionBuf
• SharedUnsigned8BitIntegerArrayReductionBuf_1
• SharedUnsigned8BitIntegerBuf
• SharedUnsigned8BitIntegerReductionBuf
• ShortArrayBuf
• ShortArrayBuf_1
• ShortArrayReductionBuf
• ShortArrayReductionBuf_1
• ShortBuf
• ShortItemBuf
• ShortItemReductionBuf
• ShortMatrixBuf
• ShortMatrixBuf_1
• ShortMatrixReductionBuf
• ShortMatrixReductionBuf_1
• ShortOp
• SigmaAEnergy
• SigmaAMinimize
• Signed16BitIntegerArrayBuf
• Signed16BitIntegerArrayBuf_1
• Signed16BitIntegerArrayReductionBuf
• Signed16BitIntegerArrayReductionBuf_1
• Signed16BitIntegerBuf
• Signed16BitIntegerItemBuf
• Signed16BitIntegerItemReductionBuf
• Signed16BitIntegerMatrixBuf
• Signed16BitIntegerMatrixBuf_1
• Signed16BitIntegerMatrixReductionBuf
• Signed16BitIntegerMatrixReductionBuf_1
• Signed8BitIntegerArrayBuf
• Signed8BitIntegerArrayBuf_1
• Signed8BitIntegerArrayReductionBuf
• Signed8BitIntegerArrayReductionBuf_1
• Signed8BitIntegerBuf
• Signed8BitIntegerItemBuf
• Signed8BitIntegerItemReductionBuf
• Signed8BitIntegerMatrixBuf
• Signed8BitIntegerMatrixBuf_1
• Signed8BitIntegerMatrixReductionBuf
• Signed8BitIntegerMatrixReductionBuf_1
• SimulatedAnnealing
• SimulatedAnnealing.ScheduleConstructor
• SimulatedAnnealing.Schedules
• SimulationDefinition
• SimulationFilter
• SimulationLoader
• SimulationMessage
• SimulationUpdate
• SinWave
• SliceLoop
• SliceRegion
• SliceRegion.GridInitLoop
• SliceSchedule
• SoluteType
• SoluteType.SOLUTE_RADII_TYPE
• SolventBinaryFormFactor
• SolventGaussFormFactor
• SolventPolyFormFactor
• Sorting
• Sorting.Byte
• Sorting.Character
• Sorting.Double
• Sorting.Float
• Sorting.Integer
• Sorting.Long
• Sorting.Object
• Sorting.Short
• SpaceGroup
• SpaceGroupConversions
• SpaceGroupDefinitions
• SpaceGroupInfo
• SpatialDensityLoop
• SpatialDensityRegion
• SpatialDensitySchedule
• Spinner
• SplineEnergy
• SplineEnergy.Type
• SplineMinimize
• SquareRoot
• SquaredTrigSwitch
• State
• StatisticalEstimator
• Status
• Stderr
• Stdin
• Stdio
• Stdout
• Stochastic
• StreamFile
• StretchBend
• StretchBendType
• StretchTorsion
• StretchTorsionType
• StringOutputStream
• StringUtils
• StructureMetrics
• SturmMethod
• SummaryStatistics
• Superpose
• SurfaceAreaLoop
• SurfaceAreaRegion
• SurfaceAreaRegion.IndexedDouble
• SurfaceAreaRegion.InitLoop
• SwingWorker
• SwingWorker.ThreadVar
• SymOp
• SystemFilter
• SystemFilter.Versioning
• SystemTemperatureException
• Terminatable
• ThermodynamicsOptions
• ThermodynamicsOptions.ThermodynamicsAlgorithm
• ThermodynamicsOptions.ThermodynamicsOptionGroup
• Thermostat
• ThermostatEnum
• TholeTensorGlobal
• TholeTensorQI
• ThreeBodyEnergyRegion
• ThreeBodyEnergyRegion.ThreeBodyEnergyLoop
• Timer
• TimerOptions
• TimerOptions.TimerOptionGroup
• TimerTask
• TimerThread
• TimerThread.TimeoutInfo
• TinkerUtils
• TitrationManyBody
• TitrationUtils
• TitrationUtils.AspStates
• TitrationUtils.AspartateAtomNames
• TitrationUtils.CysStates
• TitrationUtils.CystineAtomNames
• TitrationUtils.GluStates
• TitrationUtils.GlutamateAtomNames
• TitrationUtils.HisStates
• TitrationUtils.HistidineAtomNames
• TitrationUtils.LysStates
• TitrationUtils.LysineAtomNames
• TitrationUtils.Titration
• TopologyOptions
• TopologyOptions.TopologyOptionGroup
• TornadoFFT
• Torque
• Torsion
• TorsionTorsion
• TorsionTorsionType
• TorsionType
• TorsionType.TorsionMode
• Trajectory
• TriCubicSpline
• TwoBodyEnergyRegion
• TwoBodyEnergyRegion.TwoBodyEnergyLoop
• UIFileCloser
• UIFileOpener
• UIUtils
• UniformBSpline
• UnivariateDiffFunction
• UnivariateFunctionFactory
• UnivariateSwitchingFunction
• Unsigned16BitIntegerArrayBuf
• Unsigned16BitIntegerArrayBuf_1
• Unsigned16BitIntegerArrayReductionBuf
• Unsigned16BitIntegerArrayReductionBuf_1
• Unsigned16BitIntegerBuf
• Unsigned16BitIntegerItemBuf
• Unsigned16BitIntegerItemReductionBuf
• Unsigned16BitIntegerMatrixBuf
• Unsigned16BitIntegerMatrixBuf_1
• Unsigned16BitIntegerMatrixReductionBuf
• Unsigned16BitIntegerMatrixReductionBuf_1
• Unsigned8BitIntegerArrayBuf
• Unsigned8BitIntegerArrayBuf_1
• Unsigned8BitIntegerArrayReductionBuf
• Unsigned8BitIntegerArrayReductionBuf_1
• Unsigned8BitIntegerBuf
• Unsigned8BitIntegerItemBuf
• Unsigned8BitIntegerItemReductionBuf
• Unsigned8BitIntegerMatrixBuf
• Unsigned8BitIntegerMatrixBuf_1
• Unsigned8BitIntegerMatrixReductionBuf
• Unsigned8BitIntegerMatrixReductionBuf_1
• UreyBradley
• UreyBradleyType
• Utilities
• Utilities.FileType
• Utilities.PolymerType
• VDWPairType
• VDWType
• VDWType.VDWMode
• VanDerWaals
• VanDerWaals.ExpandLoop
• VanDerWaals.LambdaFactors
• VanDerWaals.LambdaFactorsOST
• VanDerWaals.ReductionLoop
• VanDerWaals.VanDerWaalsLoop
• VanDerWaals.VanDerWaalsRegion
• VanDerWaals.VanDerWaalsRegion.InitializationLoop
• VanDerWaalsForm
• VanDerWaalsForm.Buffered_14_7
• VanDerWaalsForm.EPSILON_RULE
• VanDerWaalsForm.LJ_6_12
• VanDerWaalsForm.RADIUS_RULE
• VanDerWaalsForm.RADIUS_SIZE
• VanDerWaalsForm.RADIUS_TYPE
• VanDerWaalsForm.VDWPowers
• VanDerWaalsForm.VDW_TYPE
• VanDerWaalsTornado
• VelocityVerlet
• Version
• WorkerConstruct
• WorkerForLoop
• WorkerIntegerForLoop
• WorkerIntegerStrideForLoop
• WorkerIteration
• WorkerLongForLoop
• WorkerLongStrideForLoop
• WorkerRegion
• WorkerTeam
• WorkerTeamThread
• WriteoutOptions
• WriteoutOptions.Extensions
• XPHFileFilter
• XPHFilter
• XRayEnergy
• XRayFormFactor
• XYZFileFilter
• XYZFilter
• XrayOptions
• XrayOptions.BFactorGroup
• XrayOptions.BulkSolventGroup
• XrayOptions.ScatteringGroup
• XrayOptions.XrayOptionGroup
• XrayOptions.XrayReflectionsGroup
• XtalEnergy
• Zwanzig
• Zwanzig.Directionality