Class Hierarchy
- java.lang.Object
- java.util.AbstractCollection<E> (implements java.util.Collection<E>)
- java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
- edu.duke.cs.osprey.confspace.Conf.Map<V>
- edu.duke.cs.osprey.confspace.AbstractPosMatrix<T> (implements edu.duke.cs.osprey.confspace.PosMatrix<T>, java.io.Serializable)
- edu.duke.cs.osprey.confspace.AbstractTupleMatrix<T> (implements java.io.Serializable, edu.duke.cs.osprey.confspace.TupleMatrix<T>)
- edu.duke.cs.osprey.design.models.AffinityDesign
- edu.duke.cs.osprey.coffee.directors.AffinityDirector (implements edu.duke.cs.osprey.coffee.Coffee.Director)
- edu.duke.cs.osprey.coffee.directors.AffinityDirector.Builder
- edu.duke.cs.osprey.energy.compiled.AmberEnergyCalculator (implements edu.duke.cs.osprey.energy.compiled.EnergyCalculator)
- edu.duke.cs.osprey.energy.compiled.AmberEnergyCalculator.Settings
- edu.duke.cs.osprey.structure.analysis.AngleClustering
- javafx.application.Application
- edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction (implements edu.duke.cs.osprey.minimization.ObjectiveFunction)
- edu.duke.cs.osprey.energy.approximation.ApproximatorMatrix (implements edu.duke.cs.osprey.tools.IOable)
- edu.duke.cs.osprey.energy.approximation.ApproximatorMatrixCalculator
- edu.duke.cs.osprey.kstar.pruning.APrioriPruningProver
- edu.duke.cs.osprey.confspace.compiled.AssignedCoords
- edu.duke.cs.osprey.confspace.compiled.AssignedCoords.AtomInfo
- edu.duke.cs.osprey.externalMemory.AssignmentsSerializer
- edu.duke.cs.osprey.externalMemory.EnergiedConfFIFOSerializer (implements edu.duke.cs.tpie.serialization.SerializingFIFOQueue.Serializer<T>)
- edu.duke.cs.osprey.externalMemory.EnergiedConfPrioritySerializer (implements edu.duke.cs.tpie.serialization.SerializingDoublePriorityQueue.Serializer<T>)
- edu.duke.cs.osprey.externalMemory.ScoredConfFIFOSerializer (implements edu.duke.cs.tpie.serialization.SerializingFIFOQueue.Serializer<T>)
- edu.duke.cs.osprey.astar.AStarProgress (implements java.io.Serializable)
- edu.duke.cs.osprey.astar.conf.pruning.AStarSequencePruner (implements edu.duke.cs.osprey.astar.conf.pruning.AStarPruner)
- edu.duke.cs.osprey.astar.AStarTree<T> (implements edu.duke.cs.osprey.confspace.ConfSearch, java.io.Serializable)
- edu.duke.cs.osprey.structure.Atom (implements java.io.Serializable)
- edu.duke.cs.osprey.structure.AtomConnectivity
- edu.duke.cs.osprey.structure.AtomConnectivity.AtomPairs
- edu.duke.cs.osprey.structure.AtomConnectivity.Builder
- edu.duke.cs.osprey.structure.AtomNeighbors
- edu.duke.cs.osprey.energy.forcefield.AtomPairEnergyContribution
- edu.duke.cs.osprey.restypes.BackboneDependentRotamerLibrary
- edu.duke.cs.osprey.coffee.seqdb.Batch
- edu.duke.cs.osprey.bbfree.BBFreeBlock (implements edu.duke.cs.osprey.dof.DOFBlock, java.io.Serializable)
- edu.duke.cs.osprey.kstar.BBKStar
- edu.duke.cs.osprey.kstar.BBKStar.ConfSpaceInfo
- edu.duke.cs.osprey.kstar.BBKStar.MultiSequenceNode
- edu.duke.cs.osprey.kstar.BBKStar.Settings
- edu.duke.cs.osprey.kstar.BBKStar.Settings.Builder
- edu.duke.cs.osprey.kstar.BBKStar.SingleSequenceNode
- edu.duke.cs.osprey.coffee.directors.BestSet<T>
- edu.duke.cs.osprey.sofea.BigDecimalIO.Fixed (implements edu.duke.cs.osprey.sofea.BigDecimalIO)
- edu.duke.cs.osprey.sofea.BigDecimalIO.Variable (implements edu.duke.cs.osprey.sofea.BigDecimalIO)
- edu.duke.cs.osprey.tools.BigExp (implements java.lang.Comparable<T>, edu.duke.cs.osprey.tools.IOable, java.io.Serializable)
- edu.duke.cs.osprey.tools.BigExp.Bounds
- edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy (implements edu.duke.cs.osprey.energy.EnergyFunction.DecomposableByDof, edu.duke.cs.osprey.energy.EnergyFunction.ExplicitChemicalChanges)
- edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.ParamInfo
- edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.Subset (implements edu.duke.cs.osprey.energy.EnergyFunction.ExplicitChemicalChanges)
- edu.duke.cs.osprey.markstar.framework.BiggestLowerboundDifferenceOrder (implements edu.duke.cs.osprey.astar.conf.order.AStarOrder)
- edu.duke.cs.osprey.tools.BigMath
- edu.duke.cs.osprey.coffee.nodedb.BlockStore (implements java.lang.AutoCloseable)
- edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator.Conditions
- edu.duke.cs.osprey.voxq.BoltzmannIntegrator1D
- edu.duke.cs.osprey.sofea.BoltzmannLute
- edu.duke.cs.osprey.parallelism.BottleneckThread (implements java.lang.AutoCloseable)
- edu.duke.cs.osprey.gpu.cuda.BufferPool<T> (implements edu.duke.cs.tpie.Cleaner.GarbageDetectable)
- edu.duke.cs.osprey.gpu.BufferTools
- edu.duke.cs.osprey.tests.CatPark
- edu.duke.cs.osprey.minimization.CCDMinimizer (implements edu.duke.cs.osprey.minimization.Minimizer)
- edu.duke.cs.osprey.tupexp.CGTupleFitter
- edu.duke.cs.osprey.parallelism.Cluster
- edu.duke.cs.osprey.parallelism.Cluster.Task<T,C> (implements com.hazelcast.core.HazelcastInstanceAware, java.io.Serializable, edu.duke.cs.osprey.parallelism.TaskExecutor.Task.WithContext<T,C>)
- edu.duke.cs.osprey.coffee.ClusterMember (implements java.lang.AutoCloseable)
- edu.duke.cs.osprey.coffee.ClusterMember.DynamicPartition<T> (implements java.lang.AutoCloseable)
- edu.duke.cs.osprey.structure.analysis.ClusterR1
- edu.duke.cs.osprey.structure.analysis.ClusterR1.Stats
- edu.duke.cs.osprey.structure.analysis.ClusterS1
- edu.duke.cs.osprey.structure.analysis.ClusterS1.Stats
- edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- edu.duke.cs.osprey.coffee.Coffee
- edu.duke.cs.osprey.coffee.Coffee.Builder
- edu.duke.cs.osprey.coffee.Coffee.StateConfig
- edu.duke.cs.osprey.gmec.Comets
- edu.duke.cs.osprey.gmec.Comets.Builder
- edu.duke.cs.osprey.gmec.Comets.LME
- edu.duke.cs.osprey.gmec.Comets.LME.Builder
- edu.duke.cs.osprey.gmec.Comets.SequenceInfo
- edu.duke.cs.osprey.gmec.Comets.State
- edu.duke.cs.osprey.gmec.Comets.WeightedState
- edu.duke.cs.osprey.control.COMETSDoer
- edu.duke.cs.osprey.design.commands.CommandBindingAffinity.ForceFieldParamsAndStrands
- edu.duke.cs.osprey.tests.ComplicatedGMECFinding
- edu.duke.cs.osprey.confspace.Conf
- edu.duke.cs.osprey.gmec.ConfAnalyzer
- edu.duke.cs.osprey.gmec.ConfAnalyzer.ConfAnalysis
- edu.duke.cs.osprey.gmec.ConfAnalyzer.EnsembleAnalysis
- edu.duke.cs.osprey.astar.conf.ConfAStarTree (implements edu.duke.cs.osprey.confspace.ConfSearch)
- edu.duke.cs.osprey.astar.conf.ConfAStarTree.Builder
- edu.duke.cs.osprey.astar.conf.ConfAStarTree.MPLPBuilder
- edu.duke.cs.osprey.multistatekstar.ConfComparator (implements java.util.Comparator<T>)
- edu.duke.cs.osprey.confspace.ConfDB (implements edu.duke.cs.osprey.tools.AutoCleanable)
- edu.duke.cs.osprey.confspace.ConfDB.Conf
- edu.duke.cs.osprey.confspace.ConfDB.Conf.Bound
- edu.duke.cs.osprey.confspace.ConfDB.ConfTable (implements java.lang.AutoCloseable, java.lang.Iterable<T>)
- edu.duke.cs.osprey.confspace.ConfDB.DBs (implements edu.duke.cs.osprey.tools.AutoCleanable)
- edu.duke.cs.osprey.confspace.ConfDB.DBs.Adder
- edu.duke.cs.osprey.confspace.ConfDB.Key (implements java.io.Serializable)
- edu.duke.cs.osprey.energy.ConfEnergyCalculator
- edu.duke.cs.osprey.energy.ConfEnergyCalculator.Builder
- edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator.EnergiedCoords
- edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator.MinimizationJob
- edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter.Builder
- edu.duke.cs.osprey.control.ConfigFileParser
- edu.duke.cs.osprey.tools.ConfigFileReader
- edu.duke.cs.osprey.astar.conf.ConfIndex
- edu.duke.cs.osprey.control.ConfInfo
- edu.duke.cs.osprey.minimization.ConfMinimizer
- edu.duke.cs.osprey.minimization.ConfMinimizer.Async
- edu.duke.cs.osprey.tupexp.ConfPair (implements java.lang.Comparable<T>)
- edu.duke.cs.osprey.control.ConfPrinter
- edu.duke.cs.osprey.gmec.ConfPrinter.Nop (implements edu.duke.cs.osprey.gmec.ConfPrinter)
- edu.duke.cs.osprey.gmec.ConfPrinters (implements edu.duke.cs.osprey.gmec.ConfPrinter)
- edu.duke.cs.osprey.structure.ConfProblem (implements java.io.Serializable)
- edu.duke.cs.osprey.astar.conf.ConfRanker
- edu.duke.cs.osprey.astar.conf.ConfRanker.Builder
- edu.duke.cs.osprey.lute.ConfSampler
- edu.duke.cs.osprey.lute.ConfSampler.Samples
- edu.duke.cs.osprey.confspace.ConfSearch.MultiSplitter
- edu.duke.cs.osprey.confspace.ConfSearch.MultiSplitter.Stream (implements edu.duke.cs.osprey.confspace.ConfSearch)
- edu.duke.cs.osprey.confspace.ConfSearch.ScoredConf (implements java.io.Serializable)
- edu.duke.cs.osprey.confspace.ConfSearch.Splitter
- edu.duke.cs.osprey.astar.conf.ConfSearchCache
- edu.duke.cs.osprey.astar.conf.ConfSearchCache.Entry (implements edu.duke.cs.osprey.confspace.ConfSearch)
- edu.duke.cs.osprey.gmec.ConfSearchFactory.Tools
- edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode (implements edu.duke.cs.osprey.astar.conf.ConfAStarNode)
- edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarQueue
- edu.duke.cs.osprey.confspace.compiled.ConfSpace (implements edu.duke.cs.osprey.confspace.ConfSpaceIteration)
- edu.duke.cs.osprey.confspace.ConfSpace (implements java.io.Serializable)
- edu.duke.cs.osprey.confspace.compiled.ConfSpace.Conf
- edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesPair
- edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesSingle
- edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesStatic
- edu.duke.cs.osprey.confspace.compiled.ConfSpace.MolInfo
- edu.duke.cs.osprey.confspace.compiled.ConfSpace.Pos
- edu.duke.cs.osprey.confspace.compiled.ConfSpace.ResInfo
- edu.duke.cs.osprey.gmec.ConsoleConfPrinter (implements edu.duke.cs.osprey.gmec.ConfPrinter)
- edu.duke.cs.osprey.Constants
- edu.duke.cs.osprey.gpu.cuda.Context
- edu.duke.cs.osprey.energy.forcefield.CoordsAndCharges (implements java.io.Serializable)
- edu.duke.cs.osprey.confspace.compiled.CoordsList
- edu.duke.cs.osprey.parallelism.CounterSignal
- edu.duke.cs.osprey.energy.compiled.CPUConfEnergyCalculator (implements edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator)
- edu.duke.cs.osprey.minimization.CpuConfMinimizer.Builder
- edu.duke.cs.osprey.gpu.cuda.CUBuffer<T>
- edu.duke.cs.osprey.minimization.CudaCCDMinimizer (implements edu.duke.cs.osprey.minimization.Minimizer.NeedsCleanup, edu.duke.cs.osprey.minimization.Minimizer.Reusable)
- edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator (implements edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator)
- edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.CheckedOutStream (implements java.lang.AutoCloseable)
- edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuInfo
- edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuStreams
- edu.duke.cs.osprey.restypes.DAminoAcidHandler
- edu.duke.cs.osprey.dof.deeper.DEEPerSettings (implements java.io.Serializable)
- edu.duke.cs.osprey.dof.DegreeOfFreedom (implements java.io.Serializable)
- edu.duke.cs.osprey.structure.analysis.DegreesHistogram
- edu.duke.cs.osprey.design.commands.DesignFileDelegate
- edu.duke.cs.osprey.gpu.cuda.Diagnostics
- edu.duke.cs.osprey.gpu.opencl.Diagnostics
- edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle (implements edu.duke.cs.osprey.confspace.compiled.ContinuousMotion)
- edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Description (implements edu.duke.cs.osprey.confspace.compiled.ContinuousMotion.ConfDescription, edu.duke.cs.osprey.confspace.compiled.ContinuousMotion.MolDescription)
- edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Dof (implements edu.duke.cs.osprey.confspace.compiled.DegreeOfFreedom)
- edu.duke.cs.osprey.coffee.directions.Directions
- edu.duke.cs.osprey.dof.DofInfo
- edu.duke.cs.osprey.astar.conf.order.DynamicHMeanAStarOrder (implements edu.duke.cs.osprey.astar.conf.order.AStarOrder)
- edu.duke.cs.osprey.astar.conf.scoring.mplp.EdgeUpdater (implements edu.duke.cs.osprey.astar.conf.scoring.mplp.MPLPUpdater)
- edu.duke.cs.osprey.energy.forcefield.EEF1 (implements java.io.Serializable)
- edu.duke.cs.osprey.energy.forcefield.EEF1.ResiduesInfo (implements edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.SolvationForcefield.ResiduesInfo)
- edu.duke.cs.osprey.energy.forcefield.EEF1.SolvParams
- edu.duke.cs.osprey.energy.compiled.EEF1EnergyCalculator (implements edu.duke.cs.osprey.energy.compiled.EnergyCalculator)
- edu.duke.cs.osprey.tools.EllipseTransform (implements java.io.Serializable)
- edu.duke.cs.osprey.ematrix.compiled.EmatCalculator
- edu.duke.cs.osprey.ematrix.compiled.EmatCalculator.Builder
- edu.duke.cs.osprey.externalMemory.EMConfAStarFactory (implements edu.duke.cs.osprey.astar.conf.ConfAStarFactory)
- edu.duke.cs.osprey.externalMemory.EMConfAStarNode (implements edu.duke.cs.osprey.astar.conf.ConfAStarNode)
- edu.duke.cs.osprey.design.analysis.EnergiedConfQueue
- edu.duke.cs.osprey.design.analysis.EnergyAnalysisConfListener (implements edu.duke.cs.osprey.design.analysis.CommandAnalysis)
- edu.duke.cs.osprey.coffee.EnergyBoundStats
- edu.duke.cs.osprey.control.EnergyCalculator
- edu.duke.cs.osprey.energy.EnergyCalculator (implements edu.duke.cs.osprey.tools.AutoCleanable)
- edu.duke.cs.osprey.energy.EnergyCalculator.Builder (implements edu.duke.cs.osprey.tools.UseableBuilder<T>)
- edu.duke.cs.osprey.energy.EnergyCalculator.EnergiedParametricMolecule
- edu.duke.cs.osprey.energy.EnergyCalculator.SharedBuilder
- edu.duke.cs.osprey.energy.EnergyCalculator.Type.Context
- edu.duke.cs.osprey.energy.EnergyFunction.Tools
- edu.duke.cs.osprey.energy.EnergyFunctionGenerator
- edu.duke.cs.osprey.ematrix.EnergyMatrixCalculator
- edu.duke.cs.osprey.gmec.EnergyRange
- edu.duke.cs.osprey.design.analysis.EnsembleAnalysisListener (implements edu.duke.cs.osprey.design.analysis.CommandAnalysis)
- edu.duke.cs.osprey.control.EnvironmentVars
- edu.duke.cs.osprey.ematrix.epic.EPICEnergyFunction (implements edu.duke.cs.osprey.energy.EnergyFunction.DecomposableByDof, edu.duke.cs.osprey.energy.EnergyFunction.NeedsInit)
- edu.duke.cs.osprey.ematrix.epic.EPICFitter
- edu.duke.cs.osprey.ematrix.epic.EPICSettings (implements java.io.Serializable)
- edu.duke.cs.osprey.ematrix.epic.EPoly (implements java.io.Serializable)
- edu.duke.cs.osprey.ematrix.epic.EPolyPC
- edu.duke.cs.osprey.ematrix.compiled.ErefCalculator
- edu.duke.cs.osprey.ematrix.compiled.ErefCalculator.Builder
- edu.duke.cs.osprey.ewakstar.EWAKStar
- edu.duke.cs.osprey.ewakstar.EWAKStar.ConfSpaceInfo
- edu.duke.cs.osprey.ewakstar.EWAKStar.ScoredSequence
- edu.duke.cs.osprey.ewakstar.EWAKStar.Settings
- edu.duke.cs.osprey.ewakstar.EWAKStar.Settings.Builder
- edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar
- edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.ConfSpaceInfo
- edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.MultiSequenceNode
- edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.Settings
- edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.Settings.Builder
- edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.SingleSequenceNode
- edu.duke.cs.osprey.ewakstar.EwakstarDoer
- edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- edu.duke.cs.osprey.ewakstar.EwakstarDoer.Results
- edu.duke.cs.osprey.ewakstar.EwakstarDoer.SequenceInfo
- edu.duke.cs.osprey.ewakstar.EwakstarDoer.State
- edu.duke.cs.osprey.ewakstar.EWAKStarGradientDescentPfunc (implements edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.WithConfTable, edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.WithExternalMemory)
- edu.duke.cs.osprey.ewakstar.EwakstarLimitedSequenceTrie
- edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Result
- edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Values
- edu.duke.cs.osprey.ewakstar.EWAKStarScore
- edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Formatted (implements edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter)
- edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Formatter.Log (implements edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Formatter)
- edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Formatter.SequenceKStarPfuncs (implements edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Formatter)
- edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Nop (implements edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter)
- edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.ScoreInfo
- edu.duke.cs.osprey.tools.ExpFunction (implements java.io.Serializable)
- edu.duke.cs.osprey.externalMemory.ExternalMemory
- edu.duke.cs.osprey.energy.FFInterGen
- edu.duke.cs.osprey.design.commands.FileExistsValidation (implements com.beust.jcommander.IParameterValidator)
- edu.duke.cs.osprey.tools.FileTools
- edu.duke.cs.osprey.tools.FileTools.LineIterator (implements java.lang.Iterable<T>, java.util.Iterator<E>)
- edu.duke.cs.osprey.tools.FileTools.Path
- edu.duke.cs.osprey.tools.FileTools.PathRoot (implements java.io.Serializable)
- edu.duke.cs.osprey.partcr.pickers.FirstConfPicker (implements edu.duke.cs.osprey.partcr.pickers.ConfPicker)
- edu.duke.cs.osprey.ematrix.epic.FitParams (implements java.io.Serializable)
- edu.duke.cs.osprey.design.models.Flexibility
- edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger
- edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger.AtomPair (implements java.lang.Comparable<T>)
- edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger.Coords
- edu.duke.cs.osprey.energy.forcefield.ForcefieldEnergy (implements java.io.Serializable)
- edu.duke.cs.osprey.energy.forcefield.amber.ForcefieldFileParser
- edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions.ResidueAtomGroup (implements edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions.AtomGroup)
- edu.duke.cs.osprey.energy.forcefield.ForcefieldParams (implements java.io.Serializable)
- edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.NBParams
- edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.VdwParams
- edu.duke.cs.osprey.coffee.FreeEnergyCalculator
- edu.duke.cs.osprey.sofea.FringeDB (implements java.lang.AutoCloseable)
- edu.duke.cs.osprey.sofea.FringeDB.Transaction
- edu.duke.cs.osprey.astar.FullAStarNode (implements edu.duke.cs.osprey.astar.AStarNode, java.io.Serializable)
- edu.duke.cs.osprey.astar.FullAStarNode.Factory (implements edu.duke.cs.osprey.astar.AStarNode.Factory<T>, java.io.Serializable)
- edu.duke.cs.osprey.ematrix.epic.GaussianLowEnergySampler
- edu.duke.cs.osprey.dof.deeper.GenChi1Calc
- edu.duke.cs.osprey.minimization.GenCoord (implements java.io.Serializable)
- edu.duke.cs.osprey.parallelism.Generator<T> (implements java.lang.AutoCloseable, java.lang.Iterable<T>)
- edu.duke.cs.osprey.tools.GLibC
- edu.duke.cs.osprey.tools.GLibC.RLimit
- edu.duke.cs.osprey.gmec.GMECConfEnergyCalculator.Async.Adapter (implements edu.duke.cs.osprey.gmec.GMECConfEnergyCalculator.Async)
- edu.duke.cs.osprey.gmec.GMECFinder
- edu.duke.cs.osprey.astar.GMECMutSpace
- edu.duke.cs.osprey.tools.resultdoc.GNUPlot
- edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd
- edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.LiteralProp
- edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.NumberProp
- edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.Style
- edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.TextProp
- edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.Tics
- edu.duke.cs.osprey.gpu.cuda.Gpu
- edu.duke.cs.osprey.gpu.opencl.Gpu
- edu.duke.cs.osprey.minimization.GpuConfMinimizer.Builder
- edu.duke.cs.osprey.energy.forcefield.GpuForcefieldEnergy (implements edu.duke.cs.osprey.energy.EnergyFunction.DecomposableByDof, edu.duke.cs.osprey.energy.EnergyFunction.ExplicitChemicalChanges, edu.duke.cs.osprey.energy.EnergyFunction.NeedsCleanup)
- edu.duke.cs.osprey.gpu.opencl.GpuQueue
- edu.duke.cs.osprey.gpu.opencl.GpuQueuePool
- edu.duke.cs.osprey.gpu.cuda.Gpus
- edu.duke.cs.osprey.gpu.opencl.Gpus
- edu.duke.cs.osprey.gpu.cuda.GpuStream
- edu.duke.cs.osprey.gpu.cuda.GpuStreamPool
- edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc (implements edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.WithConfDB, edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.WithExternalMemory)
- edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc (implements edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.WithConfDB, edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.WithExternalMemory)
- org.mapdb.serializer.GroupSerializerObjectArray<A> (implements org.mapdb.serializer.GroupSerializer<A>)
- edu.duke.cs.osprey.restypes.HardCodedResidueInfo
- edu.duke.cs.osprey.tools.HashCalculator
- edu.duke.cs.osprey.confspace.HigherTupleFinder<T> (implements java.io.Serializable)
- edu.duke.cs.osprey.structure.analysis.Histogram
- edu.duke.cs.osprey.parallelism.Hostname
- edu.duke.cs.osprey.tools.InfiniteIterator<T> (implements java.util.Iterator<E>)
- java.io.InputStream (implements java.io.Closeable)
- edu.duke.cs.osprey.multistatekstar.InputValidation
- edu.duke.cs.osprey.restypes.InterResBondingTemplate (implements java.io.Serializable)
- edu.duke.cs.osprey.minimization.IntervalLineSearcher (implements edu.duke.cs.osprey.minimization.LineSearcher)
- edu.duke.cs.osprey.tools.IntRange
- edu.duke.cs.osprey.voxq.IntraVoxelSampler
- edu.duke.cs.osprey.plug.ISAtomsIterable (implements java.lang.Iterable<T>)
- edu.duke.cs.osprey.tools.JvmMem
- edu.duke.cs.osprey.tools.JvmMem.MemInfo
- edu.duke.cs.osprey.kstar.KAStarNode
- edu.duke.cs.osprey.kstar.KAStarTree
- edu.duke.cs.osprey.gpu.cuda.Kernel
- edu.duke.cs.osprey.gpu.opencl.Kernel
- edu.duke.cs.osprey.gpu.cuda.Kernel.Function
- edu.duke.cs.osprey.gpu.cuda.Kernel.SharedMemCalculator.None (implements edu.duke.cs.osprey.gpu.cuda.Kernel.SharedMemCalculator)
- edu.duke.cs.osprey.kstar.KSAbstract (implements edu.duke.cs.osprey.kstar.KSInterface)
- edu.duke.cs.osprey.kstar.KSAllowedSeqs
- edu.duke.cs.osprey.kstar.KSCalc
- edu.duke.cs.osprey.kstar.KSConf (implements java.lang.Comparable<T>, java.io.Serializable)
- edu.duke.cs.osprey.kstar.KSConf.KSConfMinEComparator (implements java.util.Comparator<T>, java.io.Serializable)
- edu.duke.cs.osprey.kstar.KStar
- edu.duke.cs.osprey.kstar.KStar.ConfSpaceInfo
- edu.duke.cs.osprey.kstar.KStar.ScoredSequence
- edu.duke.cs.osprey.kstar.KStar.Settings
- edu.duke.cs.osprey.kstar.KStar.Settings.Builder
- edu.duke.cs.osprey.ibis.KStarBeak
- edu.duke.cs.osprey.control.KStarCalculator
- edu.duke.cs.osprey.coffee.directors.KStarDirector (implements edu.duke.cs.osprey.coffee.Coffee.Director)
- edu.duke.cs.osprey.coffee.directors.KStarDirector.Builder
- edu.duke.cs.osprey.kstar.KStarScore
- edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized (implements edu.duke.cs.osprey.multistatekstar.KStarScore)
- edu.duke.cs.osprey.kstar.KStarScoreWriter.Formatted (implements edu.duke.cs.osprey.kstar.KStarScoreWriter)
- edu.duke.cs.osprey.kstar.KStarScoreWriter.Formatter.Log (implements edu.duke.cs.osprey.kstar.KStarScoreWriter.Formatter)
- edu.duke.cs.osprey.kstar.KStarScoreWriter.Formatter.SequenceKStarPfuncs (implements edu.duke.cs.osprey.kstar.KStarScoreWriter.Formatter)
- edu.duke.cs.osprey.kstar.KStarScoreWriter.Nop (implements edu.duke.cs.osprey.kstar.KStarScoreWriter)
- edu.duke.cs.osprey.kstar.KStarScoreWriter.ScoreInfo
- edu.duke.cs.osprey.markstar.visualizer.KStarTreeManipulator
- edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode (implements java.lang.Comparable<T>)
- edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode.Builder
- edu.duke.cs.osprey.markstar.visualizer.KStarTreeRenderer
- edu.duke.cs.osprey.markstar.visualizer.KStarTreeSplitter
- edu.duke.cs.osprey.energy.LigandResEnergies
- edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarFactory (implements edu.duke.cs.osprey.astar.conf.ConfAStarFactory)
- edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode (implements edu.duke.cs.osprey.astar.conf.ConfAStarNode)
- edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode.Link (implements java.lang.Comparable<T>)
- edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode (implements edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode)
- edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode.Link (implements java.lang.Comparable<T>)
- edu.duke.cs.osprey.multistatekstar.LMB
- edu.duke.cs.osprey.astar.comets.LME (implements java.io.Serializable)
- edu.duke.cs.osprey.tools.Log
- edu.duke.cs.osprey.gmec.LoggingConfPrinter (implements edu.duke.cs.osprey.gmec.ConfPrinter)
- edu.duke.cs.osprey.bbfree.LoopVoxelSampler
- edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator
- edu.duke.cs.osprey.plug.LPChecks
- edu.duke.cs.osprey.lute.LUTE
- edu.duke.cs.osprey.lute.LUTE.Errors
- edu.duke.cs.osprey.lute.LUTE.LinearSystem
- edu.duke.cs.osprey.lute.LUTEGMECFinder
- edu.duke.cs.osprey.lute.LUTEGMECFinder.Builder
- edu.duke.cs.osprey.lute.LUTEGScorer (implements edu.duke.cs.osprey.astar.conf.scoring.AStarScorer)
- edu.duke.cs.osprey.lute.LUTEHScorer (implements edu.duke.cs.osprey.astar.conf.scoring.AStarScorer)
- edu.duke.cs.osprey.lute.LUTEIO
- edu.duke.cs.osprey.lute.LUTEPfunc (implements edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.WithConfDB)
- edu.duke.cs.osprey.tupexp.LUTESettings (implements java.io.Serializable)
- edu.duke.cs.osprey.lute.LUTEState
- edu.duke.cs.osprey.tools.LZMA2
- edu.duke.cs.osprey.control.Main
- edu.duke.cs.osprey.design.Main
- edu.duke.cs.osprey.tools.MapDBTools
- edu.duke.cs.osprey.markstar.MARKStar
- edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceInfo
- edu.duke.cs.osprey.markstar.MARKStar.ScoredSequence
- edu.duke.cs.osprey.markstar.MARKStar.Settings
- edu.duke.cs.osprey.markstar.MARKStar.Settings.Builder
- edu.duke.cs.osprey.markstar.framework.MARKStarBound (implements edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.WithConfDB)
- edu.duke.cs.osprey.markstar.framework.MARKStarBound.ScoreContext
- edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync (implements edu.duke.cs.osprey.kstar.pfunc.PartitionFunction)
- edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid (implements edu.duke.cs.osprey.kstar.pfunc.PartitionFunction)
- edu.duke.cs.osprey.markstar.framework.MARKStarNode (implements java.lang.Comparable<T>)
- edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node (implements edu.duke.cs.osprey.astar.conf.ConfAStarNode)
- edu.duke.cs.osprey.tools.MathTools
- edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- edu.duke.cs.osprey.tools.MathTools.BigIntegerBounds
- edu.duke.cs.osprey.tools.MathTools.DoubleBounds
- edu.duke.cs.osprey.tools.MathTools.GridIterable (implements java.lang.Iterable<T>)
- edu.duke.cs.osprey.structure.analysis.MeasurementLibrary
- edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.Measurement
- edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralSystem
- edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralSystems2
- edu.duke.cs.osprey.gpu.MemoryBuffer (implements java.lang.AutoCloseable)
- edu.duke.cs.osprey.astar.conf.scoring.mplp.MessageVars
- edu.duke.cs.osprey.tests.MinimizationPlayground
- edu.duke.cs.osprey.minimization.Minimizer.Result
- edu.duke.cs.osprey.minimization.Minimizer.Tools
- edu.duke.cs.osprey.gmec.MinimizingConfEnergyCalculator (implements edu.duke.cs.osprey.gmec.GMECConfEnergyCalculator.Async)
- edu.duke.cs.osprey.sofea.MinLMFE (implements edu.duke.cs.osprey.sofea.Sofea.Criterion)
- edu.duke.cs.osprey.sofea.MinLMFE.TopSequences
- edu.duke.cs.osprey.tools.MinVolEllipse (implements java.io.Serializable)
- edu.duke.cs.osprey.structure.Molecule (implements java.io.Serializable)
- edu.duke.cs.osprey.design.models.MoleculeDesign
- edu.duke.cs.osprey.design.models.MoleculeDto
- edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer (implements edu.duke.cs.osprey.minimization.ObjectiveFunction)
- edu.duke.cs.osprey.minimization.MoleculeObjectiveFunction (implements edu.duke.cs.osprey.minimization.ObjectiveFunction)
- edu.duke.cs.osprey.dof.MoveableStrand (implements edu.duke.cs.osprey.dof.DOFBlock, java.io.Serializable)
- edu.duke.cs.osprey.handlempi.MPIMaster
- edu.duke.cs.osprey.astar.conf.scoring.MPLPPairwiseHScorer (implements edu.duke.cs.osprey.astar.conf.scoring.AStarScorer)
- edu.duke.cs.osprey.kstar.MSKStar
- edu.duke.cs.osprey.kstar.MSKStar.Builder
- edu.duke.cs.osprey.kstar.MSKStar.LMFE
- edu.duke.cs.osprey.kstar.MSKStar.LMFE.Builder
- edu.duke.cs.osprey.kstar.MSKStar.SequenceInfo
- edu.duke.cs.osprey.kstar.MSKStar.State
- edu.duke.cs.osprey.kstar.MSKStar.WeightedState
- edu.duke.cs.osprey.control.MSKStarDoer
- edu.duke.cs.osprey.multistatekstar.MSKStarFactory
- edu.duke.cs.osprey.multistatekstar.MSKStarNode
- edu.duke.cs.osprey.multistatekstar.MSKStarSettings
- edu.duke.cs.osprey.multistatekstar.MSKStarTree
- edu.duke.cs.osprey.multistatekstar.MSSearchSettings (implements java.io.Serializable)
- edu.duke.cs.osprey.confspace.MultiStateConfSpace
- edu.duke.cs.osprey.confspace.MultiStateConfSpace.Builder
- edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFE
- edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFEBuilder
- edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFECalculator
- edu.duke.cs.osprey.confspace.MultiStateConfSpace.State
- edu.duke.cs.osprey.energy.MultiTermEnergyFunction (implements edu.duke.cs.osprey.energy.EnergyFunction.DecomposableByDof)
- edu.duke.cs.osprey.dof.MutAlignment
- edu.duke.cs.osprey.dof.MutAlignmentCache
- edu.duke.cs.osprey.astar.conf.scoring.NaiveTraditionalPairwiseHScorer (implements edu.duke.cs.osprey.astar.conf.scoring.AStarScorer)
- edu.duke.cs.osprey.energy.compiled.NativeConfEnergyCalculator (implements edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator)
- edu.duke.cs.osprey.coffee.nodedb.Neighbors
- edu.duke.cs.osprey.coffee.nodedb.Neighbors.NeighborInfo<T>
- edu.duke.cs.osprey.tests.NewCOMETS
- edu.duke.cs.osprey.astar.comets.NewCOMETSDoer
- edu.duke.cs.osprey.ematrix.NewEPICMatrixCalculator
- edu.duke.cs.osprey.pruning.NewPruner
- edu.duke.cs.osprey.pruning.NewPruningControl
- edu.duke.cs.osprey.coffee.nodedb.NodeDB (implements java.lang.AutoCloseable)
- edu.duke.cs.osprey.coffee.nodedb.NodeDB.Builder
- edu.duke.cs.osprey.coffee.nodedb.NodeIndex
- edu.duke.cs.osprey.coffee.nodedb.NodeIndex.Node (implements edu.duke.cs.osprey.coffee.nodedb.FixedIndex.Indexable<S>)
- edu.duke.cs.osprey.coffee.nodedb.NodeIndices (implements java.lang.AutoCloseable)
- edu.duke.cs.osprey.coffee.nodedb.NodeIndices.BroadcastInfo
- edu.duke.cs.osprey.coffee.nodedb.NodePerformance
- edu.duke.cs.osprey.coffee.NodeProcessor (implements java.lang.AutoCloseable)
- edu.duke.cs.osprey.coffee.NodeStats
- edu.duke.cs.osprey.coffee.NodeStats.ForThread
- edu.duke.cs.osprey.coffee.NodeStats.Report
- edu.duke.cs.osprey.coffee.NodeStats.Reporter (implements java.lang.AutoCloseable, java.lang.Runnable)
- edu.duke.cs.osprey.coffee.NodeStats.Values
- edu.duke.cs.osprey.coffee.nodedb.NodeTree
- edu.duke.cs.osprey.astar.conf.scoring.mplp.NodeUpdater (implements edu.duke.cs.osprey.astar.conf.scoring.mplp.MPLPUpdater)
- edu.duke.cs.osprey.energy.approximation.NOPApproximator (implements edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction.Approximator)
- edu.duke.cs.osprey.astar.conf.scoring.NOPAStarScorer (implements edu.duke.cs.osprey.astar.conf.scoring.AStarScorer)
- edu.duke.cs.osprey.partcr.scorers.NopRCScorer (implements edu.duke.cs.osprey.partcr.scorers.RCScorer)
- edu.duke.cs.osprey.astar.seq.scoring.NOPSeqAStarScorer (implements edu.duke.cs.osprey.astar.seq.scoring.SeqAStarScorer)
- java.lang.Number (implements java.io.Serializable)
- edu.duke.cs.osprey.tools.ObjectIO
- edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds (implements java.io.Serializable)
- edu.duke.cs.osprey.minimization.ObjectiveFunction.OneDof (implements java.io.Serializable)
- edu.duke.cs.osprey.tools.ObjectPool<T> (implements java.lang.Iterable<T>)
- edu.duke.cs.osprey.tools.ObjectPool.Checkout<T> (implements java.io.Closeable)
- edu.duke.cs.osprey.structure.OMOLIO
- edu.duke.cs.osprey.tests.OneEPICFit
- com.hazelcast.spi.impl.operationservice.Operation (implements com.hazelcast.nio.serialization.DataSerializable)
- edu.duke.cs.osprey.astar.OptimizableAStarNode.Tools
- java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
- edu.duke.cs.osprey.coffee.zmat.Pair (implements edu.duke.cs.osprey.coffee.zmat.Tuple)
- edu.duke.cs.osprey.coffee.bounds.PairwiseBounder (implements edu.duke.cs.osprey.coffee.bounds.Bounder)
- edu.duke.cs.osprey.astar.conf.scoring.PairwiseGScorer (implements edu.duke.cs.osprey.astar.conf.scoring.AStarScorer)
- edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction (implements edu.duke.cs.osprey.kstar.pfunc.PartitionFunction)
- edu.duke.cs.osprey.energy.ParallelEnergyFunction (implements edu.duke.cs.osprey.energy.EnergyFunction)
- edu.duke.cs.osprey.parallelism.Parallelism
- edu.duke.cs.osprey.parallelism.Parallelism.Builder
- edu.duke.cs.osprey.confspace.ParameterizedMoleculeCopy
- edu.duke.cs.osprey.confspace.ParametricMolecule (implements java.io.Serializable)
- edu.duke.cs.osprey.control.ParamSet (implements java.io.Serializable)
- edu.duke.cs.osprey.partcr.PartCR
- edu.duke.cs.osprey.partcr.PartCRConfPruner (implements edu.duke.cs.osprey.gmec.GMECFinder.ConfPruner)
- edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Result
- edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Values
- edu.duke.cs.osprey.paste.Paste
- edu.duke.cs.osprey.paste.Paste.ConfSpaceInfo
- edu.duke.cs.osprey.paste.Paste.ScoredSequence
- edu.duke.cs.osprey.paste.Paste.Settings
- edu.duke.cs.osprey.paste.Paste.Settings.Builder
- edu.duke.cs.osprey.paste.PasteGradientDescentPfunc (implements edu.duke.cs.osprey.paste.PastePartitionFunction.WithConfTable, edu.duke.cs.osprey.paste.PastePartitionFunction.WithExternalMemory)
- edu.duke.cs.osprey.paste.PastePartitionFunction.Result
- edu.duke.cs.osprey.paste.PastePartitionFunction.Values
- edu.duke.cs.osprey.paste.PasteScore
- edu.duke.cs.osprey.paste.PasteScoreWriter.Formatted (implements edu.duke.cs.osprey.paste.PasteScoreWriter)
- edu.duke.cs.osprey.paste.PasteScoreWriter.Formatter.Log (implements edu.duke.cs.osprey.paste.PasteScoreWriter.Formatter)
- edu.duke.cs.osprey.paste.PasteScoreWriter.Formatter.SequenceKStarPfuncs (implements edu.duke.cs.osprey.paste.PasteScoreWriter.Formatter)
- edu.duke.cs.osprey.paste.PasteScoreWriter.Nop (implements edu.duke.cs.osprey.paste.PasteScoreWriter)
- edu.duke.cs.osprey.paste.PasteScoreWriter.ScoreInfo
- edu.duke.cs.osprey.structure.PDBIO
- edu.duke.cs.osprey.structure.analysis.PDBScanner
- edu.duke.cs.osprey.bbfree.PepPlaneLinModel (implements java.io.Serializable)
- edu.duke.cs.osprey.tools.PeriodicTable
- edu.duke.cs.osprey.dof.deeper.PertSet (implements java.io.Serializable)
- edu.duke.cs.osprey.dof.deeper.perts.PerturbationBlock (implements edu.duke.cs.osprey.dof.DOFBlock, java.io.Serializable)
- edu.duke.cs.osprey.dof.deeper.PerturbationSelector
- edu.duke.cs.osprey.kstar.pfunc.PFAbstract (implements java.io.Serializable)
- edu.duke.cs.osprey.kstar.pfunc.PFFactory
- edu.duke.cs.osprey.coffee.directors.PfuncDirector (implements edu.duke.cs.osprey.coffee.Coffee.Director)
- edu.duke.cs.osprey.coffee.directors.PfuncDirector.Builder
- edu.duke.cs.osprey.coffee.directors.PfuncsDirector (implements edu.duke.cs.osprey.coffee.Coffee.Director)
- edu.duke.cs.osprey.coffee.directors.PfuncsDirector.Builder
- edu.duke.cs.osprey.kstar.pfunc.PfuncSurface
- edu.duke.cs.osprey.kstar.pfunc.PfuncSurface.Trace
- edu.duke.cs.osprey.tools.resultdoc.Plot
- edu.duke.cs.osprey.tools.resultdoc.Plot.Color
- edu.duke.cs.osprey.tools.resultdoc.Plot.Interval
- edu.duke.cs.osprey.tools.resultdoc.Plot.Series
- edu.duke.cs.osprey.pruning.PLUG
- edu.duke.cs.osprey.pruning.PLUG.BoundaryPoint
- edu.duke.cs.osprey.energy.PoissonBoltzmannEnergy (implements edu.duke.cs.osprey.energy.EnergyFunction)
- edu.duke.cs.osprey.confspace.compiled.PosInter
- edu.duke.cs.osprey.energy.compiled.PosInterGen
- edu.duke.cs.osprey.confspace.PositionConfSpace (implements java.io.Serializable)
- edu.duke.cs.osprey.design.PostgresConnectionInfo
- edu.duke.cs.osprey.design.PostgresScoreWriter (implements edu.duke.cs.osprey.kstar.KStarScoreWriter)
- edu.duke.cs.osprey.gmec.PrecomputedMatrices
- edu.duke.cs.osprey.tools.PrefixTreeSet<T>
- edu.duke.cs.osprey.coffee.nodedb.PriorityDequeFixedIndex<S,T> (implements edu.duke.cs.osprey.coffee.nodedb.FixedIndex<S,T>)
- edu.duke.cs.osprey.structure.Probe
- edu.duke.cs.osprey.structure.Probe.AtomInfo
- edu.duke.cs.osprey.structure.Probe.AtomPair
- edu.duke.cs.osprey.structure.Probe.AtomPair.Interaction
- edu.duke.cs.osprey.structure.Probe.Template
- edu.duke.cs.osprey.tools.Profiler
- edu.duke.cs.osprey.gpu.opencl.ProfilingEvents
- edu.duke.cs.osprey.tools.Progress
- edu.duke.cs.osprey.tools.Protractor
- edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry
- edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry.Angles
- edu.duke.cs.osprey.pruning.Pruner
- edu.duke.cs.osprey.pruning.PruningControl
- edu.duke.cs.osprey.pruning.PruningMethod
- edu.duke.cs.osprey.tests.PruningPlayground
- edu.duke.cs.osprey.gmec.PruningSettings (implements java.io.Serializable)
- edu.duke.cs.osprey.parallelism.PulseSignal
- edu.duke.cs.osprey.energy.approximation.QuadraticApproximator (implements edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction.Approximator.Addable, edu.duke.cs.osprey.tools.IOable)
- edu.duke.cs.osprey.voxq.QuadraticQFunction
- edu.duke.cs.osprey.externalMemory.Queue.ExternalFIFOFactory<T> (implements edu.duke.cs.osprey.externalMemory.Queue.Factory.FIFO<T>)
- edu.duke.cs.osprey.externalMemory.Queue.ExternalPriorityFactory<T> (implements edu.duke.cs.osprey.externalMemory.Queue.Factory<T>)
- edu.duke.cs.osprey.externalMemory.Queue.FIFOFactory<T> (implements edu.duke.cs.osprey.externalMemory.Queue.Factory.FIFO<T>)
- edu.duke.cs.osprey.externalMemory.Queue.PriorityFactory<T> (implements edu.duke.cs.osprey.externalMemory.Queue.Factory<T>)
- edu.duke.cs.osprey.dof.deeper.RamachandranChecker
- edu.duke.cs.osprey.parallelism.RateLimitedThread (implements java.lang.AutoCloseable)
- edu.duke.cs.osprey.confspace.RC (implements java.io.Serializable)
- edu.duke.cs.osprey.sofea.RCDB (implements java.lang.AutoCloseable)
- edu.duke.cs.osprey.sofea.RCDB.Table
- edu.duke.cs.osprey.kstar.RCEnergyContribs
- edu.duke.cs.osprey.kstar.RCEnergyContribs.BoundErrorByPos
- edu.duke.cs.osprey.kstar.RCEnergyContribs.BoundErrorByPosComparator (implements java.util.Comparator<T>)
- edu.duke.cs.osprey.confspace.RCIndexMap
- edu.duke.cs.osprey.plug.RCPairVDWChecker
- edu.duke.cs.osprey.astar.conf.RCs
- edu.duke.cs.osprey.partcr.RCSplits
- edu.duke.cs.osprey.partcr.RCSplits.PosInfo
- edu.duke.cs.osprey.partcr.RCSplits.RCInfo
- edu.duke.cs.osprey.partcr.splitters.RCSplitter
- edu.duke.cs.osprey.confspace.RCTuple (implements java.io.Serializable)
- edu.duke.cs.osprey.plug.RCTuplePolytope (implements java.io.Serializable)
- java.lang.Record
- edu.duke.cs.osprey.ematrix.ReferenceEnergies (implements java.io.Serializable)
- edu.duke.cs.osprey.plug.Res2AtomsIterable (implements java.lang.Iterable<T>)
- edu.duke.cs.osprey.dof.deeper.ResBBState (implements java.io.Serializable)
- edu.duke.cs.osprey.design.models.Residue
- edu.duke.cs.osprey.structure.Residue (implements java.io.Serializable)
- edu.duke.cs.osprey.restypes.ResidueEntropies (implements java.io.Serializable)
- edu.duke.cs.osprey.restypes.ResidueEntropyParser
- edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown
- edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.ByPosition
- edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.ByResidue
- edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy (implements edu.duke.cs.osprey.energy.EnergyFunction.DecomposableByDof)
- edu.duke.cs.osprey.energy.ResidueInteractions (implements java.lang.Iterable<T>)
- edu.duke.cs.osprey.energy.ResidueInteractions.Pair
- edu.duke.cs.osprey.energy.approximation.ResidueInteractionsApproximator
- edu.duke.cs.osprey.energy.approximation.ResidueInteractionsApproximator.Builder
- edu.duke.cs.osprey.design.models.ResidueModifier
- edu.duke.cs.osprey.multistatekstar.ResidueOrder.AAScore
- edu.duke.cs.osprey.multistatekstar.ResidueOrderFactory
- edu.duke.cs.osprey.multistatekstar.ResidueOrderStaticSequential (implements edu.duke.cs.osprey.multistatekstar.ResidueOrder)
- edu.duke.cs.osprey.restypes.ResidueTemplate (implements java.io.Serializable)
- edu.duke.cs.osprey.restypes.ResidueTemplateLibrary (implements java.io.Serializable)
- edu.duke.cs.osprey.restypes.ResidueTemplateLibrary.Builder
- edu.duke.cs.osprey.multistatekstar.ResidueTermini (implements java.io.Serializable)
- edu.duke.cs.osprey.energy.ResInterGen
- edu.duke.cs.osprey.energy.forcefield.ResPairCache
- edu.duke.cs.osprey.energy.forcefield.ResPairCache.AtomPairInfo
- edu.duke.cs.osprey.energy.forcefield.ResPairCache.ResPair
- edu.duke.cs.osprey.energy.forcefield.ResPairEnergy (implements edu.duke.cs.osprey.energy.EnergyFunction)
- edu.duke.cs.osprey.energy.forcefield.ResPairEnergyContribution
- edu.duke.cs.osprey.restypes.ResTemplateMatching
- edu.duke.cs.osprey.tools.resultdoc.ResultDoc (implements java.lang.AutoCloseable)
- edu.duke.cs.osprey.tools.resultdoc.ResultDoc.File
- edu.duke.cs.osprey.tools.resultdoc.ResultDoc.Image
- edu.duke.cs.osprey.tools.RigidBodyMotion
- edu.duke.cs.osprey.restypes.RotamerLibraryReader (implements java.io.Serializable)
- edu.duke.cs.osprey.tools.RotationMatrix (implements java.io.Serializable)
- edu.duke.cs.osprey.astar.seq.RTs
- edu.duke.cs.osprey.design.commands.RunnableCommand
- edu.duke.cs.osprey.design.S3Settings
- edu.duke.cs.osprey.ematrix.epic.SAPE (implements java.io.Serializable)
- edu.duke.cs.osprey.coffee.seqdb.SaveOperation.SequencedSum
- edu.duke.cs.osprey.coffee.seqdb.SaveOperation.UnsequencedSum
- edu.duke.cs.osprey.energy.ScaledEnergyFunction (implements edu.duke.cs.osprey.energy.EnergyFunction)
- edu.duke.cs.osprey.design.models.ScanDto
- edu.duke.cs.osprey.confspace.SearchProblem (implements java.io.Serializable)
- edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode.Assignments
- edu.duke.cs.osprey.astar.seq.SeqAStarTree
- edu.duke.cs.osprey.astar.seq.SeqAStarTree.Builder
- edu.duke.cs.osprey.coffee.seqdb.SeqDB (implements java.lang.AutoCloseable)
- edu.duke.cs.osprey.sofea.SeqDB (implements java.lang.AutoCloseable)
- edu.duke.cs.osprey.coffee.seqdb.SeqDB.Builder
- edu.duke.cs.osprey.sofea.SeqDB.SeqInfo
- edu.duke.cs.osprey.sofea.SeqDB.Transaction
- edu.duke.cs.osprey.coffee.seqdb.SeqFreeEnergies
- edu.duke.cs.osprey.gmec.SeqGMECFinder
- edu.duke.cs.osprey.coffee.seqdb.SeqInfo
- edu.duke.cs.osprey.confspace.SeqSpace (implements java.io.Serializable)
- edu.duke.cs.osprey.confspace.SeqSpace.Position (implements java.lang.Comparable<T>, java.io.Serializable)
- edu.duke.cs.osprey.confspace.SeqSpace.ResType (implements java.lang.Comparable<T>, java.io.Serializable)
- edu.duke.cs.osprey.confspace.Sequence
- edu.duke.cs.osprey.confspace.Sequence.Assignment
- edu.duke.cs.osprey.kstar.SequenceAnalyzer
- edu.duke.cs.osprey.kstar.SequenceAnalyzer.Analysis
- edu.duke.cs.osprey.kstar.SequenceAnalyzer.ConfSpaceInfo
- edu.duke.cs.osprey.coffee.directors.SequenceDirector (implements edu.duke.cs.osprey.coffee.Coffee.Director)
- edu.duke.cs.osprey.sofea.SequenceLMFE (implements edu.duke.cs.osprey.sofea.Sofea.Criterion)
- edu.duke.cs.osprey.astar.conf.order.SequentialAStarOrder (implements edu.duke.cs.osprey.astar.conf.order.AStarOrder)
- edu.duke.cs.osprey.astar.seq.order.SequentialSeqAStarOrder (implements edu.duke.cs.osprey.astar.seq.order.SeqAStarOrder)
- edu.duke.cs.osprey.coffee.Serializers
- edu.duke.cs.osprey.coffee.Serializers.AbstractStreamSerializer<T> (implements com.hazelcast.nio.serialization.StreamSerializer<T>)
- edu.duke.cs.osprey.ematrix.epic.SeriesFitter
- edu.duke.cs.osprey.dof.deeper.SidechainIdealizer
- edu.duke.cs.osprey.parallelism.Signal
- edu.duke.cs.osprey.minimization.SimpleCCDMinimizer (implements edu.duke.cs.osprey.minimization.Minimizer.NeedsCleanup, edu.duke.cs.osprey.minimization.Minimizer.Reusable)
- edu.duke.cs.osprey.confspace.SimpleConfSpace (implements edu.duke.cs.osprey.confspace.ConfSpaceIteration, java.io.Serializable)
- edu.duke.cs.osprey.confspace.SimpleConfSpace.Builder
- edu.duke.cs.osprey.confspace.SimpleConfSpace.Position (implements java.io.Serializable)
- edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf (implements java.io.Serializable)
- edu.duke.cs.osprey.pruning.SimpleDEE
- edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator
- edu.duke.cs.osprey.ematrix.SimpleEnergyMatrixCalculator
- edu.duke.cs.osprey.gmec.SimpleGMECFinder
- edu.duke.cs.osprey.gmec.SimpleGMECFinder.Builder
- edu.duke.cs.osprey.kstar.pfunc.SimplePartitionFunction (implements edu.duke.cs.osprey.kstar.pfunc.PartitionFunction)
- edu.duke.cs.osprey.ematrix.SimpleReferenceEnergies (implements java.io.Serializable)
- edu.duke.cs.osprey.ematrix.SimpleReferenceEnergies.Builder
- edu.duke.cs.osprey.ematrix.SimplerEnergyMatrixCalculator
- edu.duke.cs.osprey.ematrix.SimplerEnergyMatrixCalculator.Builder
- edu.duke.cs.osprey.coffee.zmat.Single (implements edu.duke.cs.osprey.coffee.zmat.Tuple)
- edu.duke.cs.osprey.energy.forcefield.SingleResEnergy (implements edu.duke.cs.osprey.energy.EnergyFunction)
- edu.duke.cs.osprey.astar.SlimAStarNode (implements edu.duke.cs.osprey.astar.AStarNode, java.io.Serializable)
- edu.duke.cs.osprey.astar.SlimAStarNode.Factory (implements edu.duke.cs.osprey.astar.AStarNode.Factory<T>, java.io.Serializable)
- edu.duke.cs.osprey.astar.SlimAStarNode.Link (implements java.lang.Comparable<T>, java.io.Serializable)
- edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel
- edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel.Interval
- edu.duke.cs.osprey.sofea.Sofea
- edu.duke.cs.osprey.sofea.Sofea.Builder
- edu.duke.cs.osprey.sofea.Sofea.SeqResult
- edu.duke.cs.osprey.sofea.Sofea.StateConfig
- edu.duke.cs.osprey.sofea.Sofea.StateInfo
- edu.duke.cs.osprey.energy.forcefield.SparseFFEnergy (implements edu.duke.cs.osprey.energy.EnergyFunction)
- edu.duke.cs.osprey.control.SpecialWarningLog
- edu.duke.cs.osprey.partcr.scorers.SplitsRCScorer (implements edu.duke.cs.osprey.partcr.scorers.RCScorer)
- edu.duke.cs.osprey.partcr.SplitWorld
- edu.duke.cs.osprey.coffee.StateInfo
- edu.duke.cs.osprey.coffee.seqdb.StateZ
- edu.duke.cs.osprey.markstar.framework.StaticBiggestLowerboundDifferenceOrder (implements edu.duke.cs.osprey.astar.conf.order.AStarOrder)
- edu.duke.cs.osprey.markstar.framework.StaticBiggesUpperboundDifferenceOrder (implements edu.duke.cs.osprey.astar.conf.order.AStarOrder)
- edu.duke.cs.osprey.astar.conf.order.StaticEnergyHMeanAStarOrder (implements edu.duke.cs.osprey.astar.conf.order.AStarOrder)
- edu.duke.cs.osprey.markstar.framework.StaticLowestEntropyOrder (implements edu.duke.cs.osprey.astar.conf.order.AStarOrder)
- edu.duke.cs.osprey.astar.conf.order.StaticScoreHMeanAStarOrder (implements edu.duke.cs.osprey.astar.conf.order.AStarOrder)
- edu.duke.cs.osprey.sofea.StepCount (implements edu.duke.cs.osprey.sofea.Sofea.Criterion)
- edu.duke.cs.osprey.tools.Stopwatch (implements java.io.Serializable)
- edu.duke.cs.osprey.confspace.Strand (implements java.io.Serializable)
- edu.duke.cs.osprey.confspace.Strand.Builder
- edu.duke.cs.osprey.confspace.Strand.Flexibility (implements java.io.Serializable)
- edu.duke.cs.osprey.confspace.Strand.ResidueFlex (implements java.io.Serializable)
- edu.duke.cs.osprey.confspace.StrandFlex (implements java.io.Serializable)
- edu.duke.cs.osprey.tools.Streams
- edu.duke.cs.osprey.tools.StringParsing
- edu.duke.cs.osprey.gpu.Structs
- edu.duke.cs.osprey.gpu.Structs.Array
- edu.duke.cs.osprey.gpu.Structs.Field
- edu.duke.cs.osprey.gpu.Structs.Struct
- edu.duke.cs.osprey.design.StructureFileScoreWriter (implements edu.duke.cs.osprey.kstar.KStarScoreWriter)
- edu.duke.cs.osprey.dof.deeper.perts.SturmSolver (implements java.io.Serializable)
- edu.duke.cs.osprey.ematrix.epic.SubThreshSampler
- edu.duke.cs.osprey.minimization.SurfingLineSearcher (implements edu.duke.cs.osprey.minimization.LineSearcher)
- edu.duke.cs.osprey.tools.SVG
- edu.duke.cs.osprey.tools.SVG.Drawable
- edu.duke.cs.osprey.tools.SVG.Finished
- edu.duke.cs.osprey.tools.SVG.StyleClass
- edu.duke.cs.osprey.tools.SVGPlot
- edu.duke.cs.osprey.tools.SVGPlot.Axis
- edu.duke.cs.osprey.tools.SVGPlot.Boxes
- edu.duke.cs.osprey.tools.SVGPlot.Boxes.Box
- edu.duke.cs.osprey.tools.SVGPlot.Intervals
- edu.duke.cs.osprey.tools.SVGPlot.Intervals.Interval
- edu.duke.cs.osprey.parallelism.TaskExecutor (implements edu.duke.cs.osprey.tools.AutoCleanable)
- edu.duke.cs.osprey.parallelism.TaskExecutor.ContextGroup (implements java.lang.AutoCloseable)
- edu.duke.cs.osprey.parallelism.TaskExecutor.ContextId
- edu.duke.cs.osprey.structure.analysis.TemplateChooser
- edu.duke.cs.osprey.structure.analysis.TemplateChooser.MeasuredRes
- edu.duke.cs.osprey.restypes.TemplateCoordsParser
- edu.duke.cs.osprey.restypes.TemplateParser
- edu.duke.cs.osprey.ematrix.TermECalculator (implements edu.duke.cs.osprey.handlempi.MPISlaveTask)
- edu.duke.cs.osprey.tupexp.TESampleSet (implements java.io.Serializable)
- edu.duke.cs.osprey.design.analysis.ThermodynamicsConfListener (implements edu.duke.cs.osprey.design.analysis.CommandAnalysis)
- java.lang.Thread (implements java.lang.Runnable)
- edu.duke.cs.osprey.parallelism.ThreadParallelism
- edu.duke.cs.osprey.parallelism.Threads (implements edu.duke.cs.osprey.tools.AutoCleanable)
- edu.duke.cs.osprey.parallelism.ThreadTools
- java.lang.Throwable (implements java.io.Serializable)
- edu.duke.cs.osprey.tools.TimeFormatter
- edu.duke.cs.osprey.tools.TimeTools
- edu.duke.cs.osprey.tools.TomlTools
- edu.duke.cs.osprey.astar.conf.scoring.TraditionalPairwiseHScorer (implements edu.duke.cs.osprey.astar.conf.scoring.AStarScorer)
- edu.duke.cs.osprey.pruning.TransitivePruner
- edu.duke.cs.osprey.design.models.TranslateRotateDto
- edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation (implements edu.duke.cs.osprey.confspace.compiled.ContinuousMotion)
- edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Description (implements edu.duke.cs.osprey.confspace.compiled.ContinuousMotion.MolDescription)
- edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Dof (implements edu.duke.cs.osprey.confspace.compiled.DegreeOfFreedom)
- edu.duke.cs.osprey.dof.deeper.perts.TripeptideClosure (implements java.io.Serializable)
- edu.duke.cs.osprey.coffee.zmat.Triple (implements edu.duke.cs.osprey.coffee.zmat.Tuple)
- edu.duke.cs.osprey.confspace.TripleMatrix<T>
- edu.duke.cs.osprey.coffee.bounds.TriplewiseBounder (implements edu.duke.cs.osprey.coffee.bounds.Bounder)
- edu.duke.cs.osprey.confspace.TupE (implements java.lang.Comparable<T>)
- edu.duke.cs.osprey.tupexp.TupExpChooser
- edu.duke.cs.osprey.confspace.TupleEnumerator
- edu.duke.cs.osprey.tupexp.TupleExpander (implements java.io.Serializable)
- edu.duke.cs.osprey.confspace.TuplesIndex (implements java.lang.Iterable<T>)
- edu.duke.cs.osprey.confspace.TupleTree<T> (implements java.io.Serializable)
- edu.duke.cs.osprey.ematrix.UpdatingEnergyMatrix.TupleTrie
- edu.duke.cs.osprey.kstar.pfunc.UpperBoundCalculator
- edu.duke.cs.osprey.markstar.UpperBoundScorer (implements edu.duke.cs.osprey.astar.conf.scoring.AStarScorer)
- edu.duke.cs.osprey.astar.conf.order.UpperLowerAStarOrder (implements edu.duke.cs.osprey.astar.conf.order.AStarOrder)
- edu.duke.cs.osprey.tools.VectorAlgebra
- edu.duke.cs.osprey.structure.analysis.VisIt
- edu.duke.cs.osprey.partcr.scorers.VolumeRCScorer (implements edu.duke.cs.osprey.partcr.scorers.RCScorer)
- edu.duke.cs.osprey.plug.VoxConstrCache
- edu.duke.cs.osprey.tests.VoxDeltaGPlayground
- edu.duke.cs.osprey.voxq.VoxelGCalculator
- edu.duke.cs.osprey.voxq.VoxelsDeltaG
- edu.duke.cs.osprey.bbfree.VoxelSeriesChecker
- edu.duke.cs.osprey.confspace.VoxelShape (implements java.io.Serializable)
- edu.duke.cs.osprey.plug.VoxelVDWDistExplorer
- edu.duke.cs.osprey.plug.VoxelVDWListChecker
- edu.duke.cs.osprey.plug.VoxelVDWListChecker.DOFInterval
- edu.duke.cs.osprey.partcr.pickers.WalkingConfPicker (implements edu.duke.cs.osprey.partcr.pickers.ConfPicker)
- edu.duke.cs.osprey.parallelism.WorkCrew<T> (implements java.lang.Iterable<T>)
- edu.duke.cs.osprey.parallelism.WorkLatch
Annotation Interface Hierarchy