- AdderDoubleArray
- Adiabatic
- AlchemicalOptions
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- AlgorithmFunctions
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- AlgorithmsScript
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- AlgorithmUtils
- AminoAcidUtils
- AminoAcidUtils.AA
- AminoAcidUtils.AIB
- AminoAcidUtils.ALA
- AminoAcidUtils.AminoAcid1
- AminoAcidUtils.AminoAcid3
- AminoAcidUtils.AminoAcidBackboneAtoms
- AminoAcidUtils.ARG
- AminoAcidUtils.ASD
- AminoAcidUtils.ASH
- AminoAcidUtils.ASN
- AminoAcidUtils.ASP
- 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
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- ANIEnergy
- AnnealingSchedule
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- ARCFileFilter
- Arrays
- AssemblyState
- ASULimit
- Atom
- Atom.Descriptions
- Atom.ElementSymbol
- Atom.Indexing
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- AtomicDoubleArray
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- AtomicDoubleArray3D
- AtomSelectionOptions
- AtomType
- BackendClassLoader
- BackendFileInputStream
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- BackendFileReader
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- BackendInfo
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- BARFilter
- Barostat
- BarostatOptions
- BarrierAction
- BaseType
- BellCurveSwitch
- BennettAcceptanceRatio
- Berendsen
- BetterBeeman
- BioType
- BoltzmannMC
- Bond
- BondedEnergy
- BondedTerm
- BondedTerm.BondedComparator
- BondedUtils
- BondedUtils.MissingAtomTypeException
- BondedUtils.MissingHeavyAtomException
- BondType
- BondType.BondFunction
- BooleanArrayBuf
- BooleanArrayBuf_1
- BooleanBuf
- BooleanItemBuf
- BooleanMatrixBuf
- BooleanMatrixBuf_1
- BooleanOp
- BootstrappableEstimator
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- BornGradRegion
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- BoxOptCell
- Buf
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- Bussi
- ByteArrayBuf
- ByteArrayBuf_1
- ByteBuf
- ByteItemBuf
- ByteMatrixBuf
- ByteMatrixBuf_1
- ByteOp
- ByteSequence
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- CcmaConstraint
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- ChandlerCavitation
- Channel
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- CharacterArrayBuf
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- CharacterBuf
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- CharacterMatrixBuf
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- CharacterOp
- ChargeType
- CIFFilter
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- Clustering
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- CNSFilter
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- Comm
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- Complex
- Complex3D
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- CosineWave
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- CrystalStats
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- DataContainer
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- DirectoryUtils
- DirectRegion
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- DistanceMatrix
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- DistanceRegion
- Double3
- DoubleArrayBuf
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- DoubleBuf
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- Energy
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- EnergyRegion
- Erf
- EstimateBootstrapper
- ESVFileFilter
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- EwaldParameters
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- ExpandInducedDipolesRegion
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- ExtendedSystem
- FFXClient
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- FFXFileFilter
- FFXKeyword
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- FFXLocale
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- FFXTornado
- FileCloser
- FileOpener
- Files
- FileUtils
- FlatEndAnnealSchedule
- Float3
- FloatArrayBuf
- FloatArrayBuf_1
- FloatBuf
- FloatItemBuf
- FloatMath
- FloatMatrixBuf
- FloatMatrixBuf_1
- FloatOp
- ForceField
- ForceField.ConstraintTypes
- ForceField.ELEC_FORM
- ForceField.ForceFieldName
- ForceField.ForceFieldType
- ForceFieldEnergy
- ForceFieldEnergy.Platform
- ForceFieldEnergyOpenMM
- ForceFieldFileFilter
- ForceFieldFilter
- FormFactor
- FourBodyEnergyRegion
- FrontendFileReader
- FrontendFileWriter
- FunctionDataCurve
- GaussVol
- GeneralizedKirkwood
- GeneralizedKirkwood.NonPolarModel
- GenerateRotamers
- GetProteinFeatures
- GKEnergyGlobal
- GKEnergyQI
- GKEnergyRegion
- GKSource
- GKSource.GK_MULTIPOLE_ORDER
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- GKTensorGlobal
- GKTensorQI
- GlobalBehavior
- GoldsteinPairRegion
- GradientOptions
- GradientSchedule
- GraphicsAxis
- GraphicsCanvas
- GraphicsCanvas.ImageFormat
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- GraphicsEvents
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- GraphicsPrefs
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- HeadlessMain
- Hex
- Hierarchy
- HistogramReader
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- HKL
- HttpRequest
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- Hybrid36
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- HydrophobicPMFRegion
- ImproperTorsion
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- IndexIndexPair
- InducedDipoleFieldReduceRegion
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- InducedFileFilter
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- InitializationRegion
- InitializationRegion
- Instance
- IntegerArrayBuf
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- IntegerBuf
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- IntegerMatrixBuf_1
- IntegerOp
- IntegerSchedule
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- Integrate1DNumeric
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- Integration
- Integrator
- IntegratorEnum
- INTFileFilter
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- InvalidMatrixFileException
- IORequest
- Job
- JobBackend
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- JobSchedulerProxy
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- Joint
- KeyFileEditor
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- KeyFilter
- Keyword
- KeywordComponent
- KeywordComponent.SwingRepresentation
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- KillRegion
- LambdaInterface
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- LambdaParticleOptions
- LambdaReader
- LatticeSystem
- LaueSystem
- LBFGS
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- LineBufferedOutputStream
- LineSearch
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- Lock
- LogFormatter
- Logger
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- LogHandler
- LogPanel
- LongArrayBuf
- LongArrayBuf_1
- LongBuf
- LongForLoop
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- LongMatrixBuf
- LongMatrixBuf_1
- LongOp
- LongRange
- LongSchedule
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- Loop
- LoopClosure
- Main
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- MainPanel
- ManyBodyOptions
- MaskingInterface
- Mathe
- MatrixMath
- Mcg1Random
- MCLoop
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- MDMove
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- ModelingPanel
- ModelingShell
- ModifiedBessel
- MolecularAssembly
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- MolecularDynamics
- MolecularDynamics.AssemblyInfo
- MolecularDynamics.DynamicsEngine
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- MolecularDynamicsOpenMM
- MolecularMC
- Molecule
- MonteCarloListener
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- MouseBehavior
- MouseBehaviorCallback
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- MSGroup
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- MultiDoubleArray
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- MultipoleTensor
- MultipoleTensor.COORDINATES
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- MultipoleType
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- MultiResidue
- MultiTerminus
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- NamingUtils
- NamingUtils.HetAtoms
- NCSCrystal
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- NeckIntegral
- NeighborList
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- NeutronFormFactor
- NonbondedCutoff
- NonPjJobFrontend
- NucleicAcidUtils
- NucleicAcidUtils.NA
- NucleicAcidUtils.NucleicAcid1
- NucleicAcidUtils.NucleicAcid3
- ObjectArrayBuf
- ObjectArrayBuf_1
- ObjectBuf
- ObjectItemBuf
- ObjectMatrixBuf
- ObjectMatrixBuf_1
- ObjectOp
- ObjectPair
- Octree
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- OctreePoint
- Op
- OptimizationListener
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- OrthogonalSpaceTempering
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- OSXAdapter
- OutOfPlaneBend
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- Packing
- PairwiseSchedule
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- ParallelForLoop
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- ParallelSection
- ParallelTeam
- ParticleMeshEwald
- PCGSolver
- PDBFileFilter
- PDBFilter
- PDBFilter.Mutation
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- PDBMLFileFilter
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- PermanentFieldRegion
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- PhMinimize
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- PickingCallback
- PickMouseBehavior
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- PiOrbitalTorsion
- PiOrbitalTorsionType
- PJDoubleArray
- PJProperties
- PMETimings
- PolarizableMultipole
- Polarization
- PolarizationEnergyRegion
- PolarizeType
- Polymer
- PolymerUtils
- PolynomialCurve
- PortUtils
- Potential
- Potential.STATE
- Potential.VARIABLE_TYPE
- PotentialCommand
- PotentialScript
- PotentialsFileOpener
- PotentialsFunctions
- PotentialsUtils
- PotentialTest
- PowerSwitch
- PrintStreamLogger
- ProcessInfo
- ProcessInfo.State
- ProgressiveAlignmentOfCrystals
- Proxy
- QIFrame
- QuadTopologyEnergy
- QuasiLinearThetaMap
- Random
- RandomSample
- RandomSubset
- RandomUnitCellOptions
- Range
- Rattle
- Real
- Real3D
- Real3DParallel
- RealSpaceData
- RealSpaceEnergy
- RealSpaceEnergyRegion
- RealSpaceFile
- RealSpaceFileFilter
- RealSpaceNeighborParameters
- RealSpaceOptions
- RealSpaceRefinementData
- ReciprocalEnergyRegion
- ReciprocalSpace
- ReciprocalSpace.GridMethod
- ReduceArrays
- ReduceRegion
- RefinementEnergy
- RefinementMinimize
- RefinementMinimize.RefinementMode
- RefinementModel
- ReflectionList
- ReflectionSpline
- RelativeSolvation
- RelativeSolvation.SolvationLibrary
- RelativeSolvationType
- Renderer
- RendererCache
- RendererCache.ColorModel
- RendererCache.ViewModel
- RepExOptions
- RepExOST
- RepexOSTOptions
- ReplicaExchange
- ReplicatedBoolean
- ReplicatedByte
- ReplicatedCharacter
- ReplicatedDouble
- ReplicatedFloat
- ReplicatedInteger
- ReplicatedLong
- ReplicatedObject
- ReplicatedShort
- ReplicatesCrystal
- Residue
- Residue.ResidueType
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- ResidueState
- Resolution
- ResourceCache
- Resources
- Respa
- RestrainGroups
- RestraintBond
- RestraintTorsion
- ROLS
- ROLSP
- ROLSP.PARALLELMETHOD
- RosenbluthCBMC
- RosenbluthChi0Move
- RosenbluthChiAllMove
- RosenbluthChiAllMove.MODE
- RosenbluthOBMC
- Rotamer
- RotamerLibrary
- RotamerLibrary.NucleicAcidLibrary
- RotamerLibrary.NucleicSugarPucker
- RotamerLibrary.ProteinLibrary
- RotamerLibrary.RotamerGuess
- RotamerMatrixMC
- RotamerMatrixMove
- RotamerOptimization
- RotamerOptimization.Algorithm
- RotamerOptimization.Direction
- RotamerOptimization.DistanceMethod
- RowLoop
- RowRegion
- RowSchedule
- Runner
- RunningStatistics
- SaveOptions
- ScalarMath
- ScaleBulkEnergy
- ScaleBulkMinimize
- ScaleParameters
- SCFAlgorithm
- ScfPredictor
- SCFPredictor
- ScfPredictor.PredictorMode
- SCFPredictorParameters
- Schedule
- Searching
- Searching.Byte
- Searching.Character
- Searching.Double
- Searching.Float
- Searching.Integer
- Searching.Long
- Searching.Object
- Searching.Short
- Selection
- SelfEnergyRegion
- SendSynchronous
- SequentialEstimator
- SettleConstraint
- SharedBoolean
- SharedBooleanArray
- SharedBooleanArrayBuf
- SharedBooleanArrayBuf_1
- SharedBooleanBuf
- SharedByte
- SharedByteArray
- SharedByteArrayBuf
- SharedByteArrayBuf_1
- SharedByteBuf
- SharedCharacter
- SharedCharacterArray
- SharedCharacterArrayBuf
- SharedCharacterArrayBuf_1
- SharedCharacterBuf
- SharedDouble
- SharedDoubleArray
- SharedDoubleArrayBuf
- SharedDoubleArrayBuf_1
- SharedDoubleBuf
- SharedFloat
- SharedFloatArray
- SharedFloatArrayBuf
- SharedFloatArrayBuf_1
- SharedFloatBuf
- SharedInteger
- SharedIntegerArray
- SharedIntegerArrayBuf
- SharedIntegerArrayBuf_1
- SharedIntegerBuf
- SharedIntegerMatrix
- SharedLong
- SharedLongArray
- SharedLongArrayBuf
- SharedLongArrayBuf_1
- SharedLongBuf
- SharedLongMatrix
- SharedObject
- SharedObjectArray
- SharedObjectArrayBuf
- SharedObjectArrayBuf_1
- SharedObjectBuf
- SharedShort
- SharedShortArray
- SharedShortArrayBuf
- SharedShortArrayBuf_1
- SharedShortBuf
- SharedSigned16BitIntegerArrayBuf
- SharedSigned16BitIntegerArrayBuf_1
- SharedSigned16BitIntegerBuf
- SharedSigned8BitIntegerArrayBuf
- SharedSigned8BitIntegerArrayBuf_1
- SharedSigned8BitIntegerBuf
- SharedUnsigned16BitIntegerArrayBuf
- SharedUnsigned16BitIntegerArrayBuf_1
- SharedUnsigned16BitIntegerBuf
- SharedUnsigned8BitIntegerArrayBuf
- SharedUnsigned8BitIntegerArrayBuf_1
- SharedUnsigned8BitIntegerBuf
- ShortArrayBuf
- ShortArrayBuf_1
- ShortBuf
- ShortItemBuf
- ShortMatrixBuf
- ShortMatrixBuf_1
- ShortOp
- SigmaAEnergy
- SigmaAMinimize
- Signed16BitIntegerArrayBuf
- Signed16BitIntegerArrayBuf_1
- Signed16BitIntegerBuf
- Signed16BitIntegerItemBuf
- Signed16BitIntegerMatrixBuf
- Signed16BitIntegerMatrixBuf_1
- Signed8BitIntegerArrayBuf
- Signed8BitIntegerArrayBuf_1
- Signed8BitIntegerBuf
- Signed8BitIntegerItemBuf
- Signed8BitIntegerMatrixBuf
- Signed8BitIntegerMatrixBuf_1
- SimulatedAnnealing
- SimulatedAnnealing.Schedules
- SimulationDefinition
- SimulationFilter
- SimulationLoader
- SimulationMessage
- SimulationUpdate
- SinWave
- SliceLoop
- SliceRegion
- SliceSchedule
- SoluteType
- SoluteType.SOLUTE_RADII_TYPE
- SolventBinaryFormFactor
- SolventGaussFormFactor
- SolventPolyFormFactor
- SORRegion
- Sorting
- Sorting.Byte
- Sorting.Character
- Sorting.Double
- Sorting.Float
- Sorting.Integer
- Sorting.Long
- Sorting.Object
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- SpaceGroup
- SpaceGroupConversions
- SpaceGroupDefinitions
- SpaceGroupInfo
- SpatialDensityLoop
- SpatialDensityRegion
- SpatialDensitySchedule
- SplineEnergy
- SplineEnergy.Type
- SplineMinimize
- SquaredTrigSwitch
- SquareRoot
- SSETest
- StatisticalEstimator
- Status
- Stdio
- Stochastic
- StreamFile
- StretchBend
- StretchBendType
- StretchTorsion
- StretchTorsionType
- StringOutputStream
- StringUtils
- StructureMetrics
- SturmMethod
- SummaryStatistics
- Superpose
- SurfaceAreaRegion
- SwingWorker
- SymOp
- SystemFilter
- SystemFilter.Versioning
- SystemTemperatureException
- Terminatable
- ThermodynamicsOptions
- ThermodynamicsOptions.ThermodynamicsAlgorithm
- Thermostat
- ThermostatEnum
- TholeTensorGlobal
- TholeTensorQI
- ThreeBodyEnergyRegion
- Timer
- TimerOptions
- TimerTask
- TimerThread
- TinkerUtils
- TitrationManyBody
- TitrationUtils
- TitrationUtils.CysteineAtomNames
- TitrationUtils.HistidineAtomNames
- TitrationUtils.LysineAtomNames
- TitrationUtils.Titration
- TopologyOptions
- TornadoDFT
- Torque
- Torsion
- TorsionTorsion
- TorsionTorsionType
- TorsionType
- TorsionType.TorsionMode
- Trajectory
- TriCubicSpline
- TwoBodyEnergyRegion
- UIFileCloser
- UIFileOpener
- UIUtils
- UniformBSpline
- UnivariateDiffFunction
- UnivariateFunctionFactory
- UnivariateSwitchingFunction
- Unsigned16BitIntegerArrayBuf
- Unsigned16BitIntegerArrayBuf_1
- Unsigned16BitIntegerBuf
- Unsigned16BitIntegerItemBuf
- Unsigned16BitIntegerMatrixBuf
- Unsigned16BitIntegerMatrixBuf_1
- Unsigned8BitIntegerArrayBuf
- Unsigned8BitIntegerArrayBuf_1
- Unsigned8BitIntegerBuf
- Unsigned8BitIntegerItemBuf
- Unsigned8BitIntegerMatrixBuf
- Unsigned8BitIntegerMatrixBuf_1
- UreyBradley
- UreyBradleyType
- Utilities
- Utilities.FileType
- Utilities.PolymerType
- VanDerWaals
- VanDerWaalsForm
- VanDerWaalsForm.EPSILON_RULE
- VanDerWaalsForm.RADIUS_RULE
- VanDerWaalsForm.RADIUS_SIZE
- VanDerWaalsForm.RADIUS_TYPE
- VanDerWaalsForm.VDW_TYPE
- VanDerWaalsTornado
- VDWPairType
- VDWType
- VDWType.VDWMode
- VelocityVerlet
- Version
- WorkerConstruct
- WorkerForLoop
- WorkerIntegerForLoop
- WorkerIntegerStrideForLoop
- WorkerIteration
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- WorkerLongStrideForLoop
- WorkerRegion
- WorkerTeam
- WriteoutOptions
- XPHFileFilter
- XPHFilter
- XRayEnergy
- XRayFormFactor
- XrayOptions
- XtalEnergy
- XYZFileFilter
- XYZFilter
- Zwanzig
- Zwanzig.Directionality