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