Index
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form
A
- a - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Description
- a - Variable in class edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger.Coords
- a - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.BondAngle
- a - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.BondLength
- a - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DeltaDihedralAngle
- a - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DihedralAngle
- a - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DihedralAnglesMinDist
- a - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralSystem
- a - Variable in class edu.duke.cs.osprey.structure.Probe.AtomPair
- A() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.HBond10_12PotentialParameter
-
Returns the value of the
Arecord component. - A() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.Six12PotentialCoefficient
-
Returns the value of the
Arecord component. - aaCTPath - Variable in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.Forcefield
- aaNTPath - Variable in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.Forcefield
- aaPath - Variable in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.Forcefield
- AAScore(int, int, double) - Constructor for class edu.duke.cs.osprey.multistatekstar.ResidueOrder.AAScore
- AAType - Variable in class edu.duke.cs.osprey.confspace.RC
- AATypeOptions - Variable in class edu.duke.cs.osprey.multistatekstar.MSSearchSettings
- AATypePos - Variable in class edu.duke.cs.osprey.multistatekstar.ResidueOrder.AAScore
- abort(boolean) - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- abort(boolean) - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- Aborted - Enum constant in enum class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Status
- Aborted - Enum constant in enum class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Status
- Aborted - Enum constant in enum class edu.duke.cs.osprey.paste.PastePartitionFunction.Status
- abortPFs() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- abs() - Method in class edu.duke.cs.osprey.tools.BigExp
- absolutePos - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- AbstractPosMatrix<T> - Class in edu.duke.cs.osprey.confspace
- AbstractPosMatrix(int) - Constructor for class edu.duke.cs.osprey.confspace.AbstractPosMatrix
- AbstractPosMatrix(SimpleConfSpace) - Constructor for class edu.duke.cs.osprey.confspace.AbstractPosMatrix
- AbstractStreamSerializer(int) - Constructor for class edu.duke.cs.osprey.coffee.Serializers.AbstractStreamSerializer
- AbstractTupleMatrix<T> - Class in edu.duke.cs.osprey.confspace
- AbstractTupleMatrix() - Constructor for class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- AbstractTupleMatrix(int, int[], double, T) - Constructor for class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- AbstractTupleMatrix(AbstractTupleMatrix<T>) - Constructor for class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- AbstractTupleMatrix(ConfSpaceIteration) - Constructor for class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- AbstractTupleMatrix(ConfSpace, double, T) - Constructor for class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- AbstractTupleMatrix(SimpleConfSpace, double, T) - Constructor for class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- Acceptor - Enum constant in enum class edu.duke.cs.osprey.structure.Probe.AtomFlag
- accumulate(KSConf) - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel0
- accumulate(KSConf) - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- accumulate(KSConf) - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFTraditional
- accumulate(KSConf) - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFUB
- accumulate(ArrayList<KSConf>, boolean) - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel2
- Adapter(GMECConfEnergyCalculator) - Constructor for class edu.duke.cs.osprey.gmec.GMECConfEnergyCalculator.Async.Adapter
-
Deprecated.
- add(double) - Method in class edu.duke.cs.osprey.structure.analysis.ClusterR1
- add(double) - Method in class edu.duke.cs.osprey.structure.analysis.ClusterS1
- add(double) - Method in class edu.duke.cs.osprey.tools.BigMath
- add(double[]) - Method in class edu.duke.cs.osprey.structure.analysis.DegreesHistogram
- add(double[], double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- add(double, double) - Method in class edu.duke.cs.osprey.coffee.EnergyBoundStats
- add(int[]) - Method in class edu.duke.cs.osprey.confspace.Conf.Set
- add(int, int) - Method in class edu.duke.cs.osprey.confspace.RCIndexMap
- add(int, Residue) - Method in class edu.duke.cs.osprey.structure.Residues
- add(int, List<NodeIndex.Node>) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
-
Adds nodes to the cluster.
- add(int, List<NodeIndex.Node>) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices
- add(long) - Method in class edu.duke.cs.osprey.tools.BigMath
- add(ConfSMAStarNode) - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarQueue
- add(SeqAStarNode) - Method in class edu.duke.cs.osprey.astar.seq.SeqAStarTree
-
adds an already-enumerated node back to the tree useful for continual refinement of scores on leaf nodes
- add(NodeIndex.Node) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
-
Conveience method to add a single node.
- add(NodeIndex.Node) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex
- add(ConfSearch.EnergiedConf) - Method in class edu.duke.cs.osprey.design.analysis.EnergiedConfQueue
- add(ConfSpaceIteration, File) - Method in class edu.duke.cs.osprey.confspace.ConfDB.DBs
- add(ConfSpaceIteration, File) - Method in class edu.duke.cs.osprey.confspace.ConfDB.DBs.Adder
- add(MultiStateConfSpace.State, double) - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFEBuilder
- add(MultiStateConfSpace.State, MathTools.DoubleBounds) - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFECalculator
- add(Sequence) - Method in class edu.duke.cs.osprey.astar.conf.pruning.AStarSequencePruner
- add(ApproximatedObjectiveFunction.Approximator.Addable, double, double) - Method in interface edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction.Approximator.Addable
- add(ApproximatedObjectiveFunction.Approximator.Addable, double, double) - Method in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- add(QuadraticApproximator, QuadraticApproximator, double, double) - Static method in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- add(ResidueInteractions.Pair) - Method in class edu.duke.cs.osprey.energy.ResidueInteractions
- add(KAStarNode) - Method in class edu.duke.cs.osprey.kstar.KAStarTree
- add(Sofea.SeqResult) - Method in class edu.duke.cs.osprey.sofea.MinLMFE.TopSequences
- add(Residue) - Method in class edu.duke.cs.osprey.structure.Residues
- add(BigExp) - Method in class edu.duke.cs.osprey.tools.BigExp
- add(BigExp) - Method in class edu.duke.cs.osprey.tools.BigMath
- add(Number, String) - Method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.Tics
- add(String, double) - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFEBuilder
- add(String, MeasurementLibrary.Measurement) - Method in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary
- add(BigDecimal) - Method in class edu.duke.cs.osprey.tools.BigMath
- add(BigDecimal) - Method in class edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal
- add(BigDecimal, MathContext) - Method in class edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal
- add(BigInteger) - Method in class edu.duke.cs.osprey.tools.BigMath
- add(ArrayList<KAStarNode>) - Method in class edu.duke.cs.osprey.kstar.KAStarTree
- add(List<T>) - Method in class edu.duke.cs.osprey.tools.PrefixTreeSet
- add(T) - Method in class edu.duke.cs.osprey.coffee.directors.BestSet
- add(T) - Method in interface edu.duke.cs.osprey.coffee.nodedb.FixedIndex
-
Adds an item to the index.
- add(T) - Method in class edu.duke.cs.osprey.coffee.nodedb.PriorityDequeFixedIndex
- addAll(int, Collection<? extends Residue>) - Method in class edu.duke.cs.osprey.structure.Residues
- addAll(RCTuple) - Method in class edu.duke.cs.osprey.energy.ResInterGen
-
adds all possible residue interactions
- addAll(ResidueInteractions) - Method in class edu.duke.cs.osprey.energy.ResidueInteractions
- addAll(MeasurementLibrary) - Method in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary
- addAll(MathTools.DoubleBounds[]) - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFECalculator
- addAll(Iterable<T>, BiConsumer<T, ConfDB.DBs.Adder>) - Method in class edu.duke.cs.osprey.confspace.ConfDB.DBs
- addAll(Collection<? extends Residue>) - Method in class edu.duke.cs.osprey.structure.Residues
- addAll(Collection<double[]>) - Method in class edu.duke.cs.osprey.structure.analysis.DegreesHistogram
- addAlternate(int, Residue) - Method in class edu.duke.cs.osprey.structure.Molecule
- addAtom(Atom, double[]) - Method in class edu.duke.cs.osprey.structure.Residue
- addAtomPair(Atom, Atom) - Method in class edu.duke.cs.osprey.plug.VoxelVDWListChecker
- addBackboneDependentRotamers(String) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary.Builder
-
Backbone-dependent rotamers to add to the library
- addBond(Atom) - Method in class edu.duke.cs.osprey.structure.Atom
- addBox(double, double, double, double) - Method in class edu.duke.cs.osprey.tools.SVGPlot.Boxes
- addChild(KStarTreeNode) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- addComplete(Residues) - Method in class edu.duke.cs.osprey.energy.ResidueInteractions
- addComplete(Residues, double, double) - Method in class edu.duke.cs.osprey.energy.ResidueInteractions
- addConf(int[]) - Method in class edu.duke.cs.osprey.lute.ConfSampler.Samples
- addConfPostProcessor(MinimizingConfEnergyCalculator.ConfPostProcessor) - Method in class edu.duke.cs.osprey.gmec.MinimizingConfEnergyCalculator
-
Deprecated.
- addConstraint(Comets.LME) - Method in class edu.duke.cs.osprey.gmec.Comets.Builder
- addConstraint(MSKStar.LMFE) - Method in class edu.duke.cs.osprey.kstar.MSKStar.Builder
- addDOFInterval(DegreeOfFreedom, double, double) - Method in class edu.duke.cs.osprey.plug.VoxelVDWListChecker
- addEnergyTerms(boolean, int...) - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrixCalculator
- Adder() - Constructor for class edu.duke.cs.osprey.confspace.ConfDB.DBs.Adder
- addInPlace(double[], double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- addInter(int, int) - Method in class edu.duke.cs.osprey.energy.ResInterGen
-
energy += E(pos1, pos2)
- addInter(int, int, double, double) - Method in class edu.duke.cs.osprey.energy.ResInterGen
-
energy += [E(pos1, pos2) + offset]*weight
- addInteractionCoords(ForcefieldDebugger.AtomPair, String, ForcefieldDebugger.Coords) - Method in class edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger
- addInteractionEnergy(ForcefieldDebugger.AtomPair, String, double) - Method in class edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger
- addInternal(String, String, String, double) - Method in class edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger
- addInters(RCTuple) - Method in class edu.duke.cs.osprey.energy.ResInterGen
-
energy += E(pos1, pos2) for all pos2 < pos1 in frag
- addInters(RCTuple, double, ResInterGen.InterOffsetter) - Method in class edu.duke.cs.osprey.energy.ResInterGen
-
energy += [E(pos1, pos2) + offset(pos1, pos2)]*weight for all pos2 < pos1 in frag
- addInterval(double, double) - Method in class edu.duke.cs.osprey.tools.SVGPlot.Intervals
- addIntra(int) - Method in class edu.duke.cs.osprey.energy.ResInterGen
-
energy += E(pos)
- addIntra(int, double, double) - Method in class edu.duke.cs.osprey.energy.ResInterGen
-
energy += [E(pos) + offset]*weight
- addIntras(RCTuple) - Method in class edu.duke.cs.osprey.energy.ResInterGen
-
energy += E(pos) for all pos in frag
- addIntras(RCTuple, double, ResInterGen.IntraOffsetter) - Method in class edu.duke.cs.osprey.energy.ResInterGen
-
energy += [E(pos) + offset(pos)]*weight for all pos in frag
- additionalRotamers - Variable in class edu.duke.cs.osprey.design.models.MoleculeDto
- addLocal(int, List<NodeIndex.Node>) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
-
Add nodes to the local store
- addLocal(NodeIndex.Node) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
-
Conveience method to add a single node to the local store.
- addLovellRotamers() - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary.Builder
-
Adds rotamers from the pentiultimate rotamer library is used.
- addMoleculeForWildTypeRotamers(Molecule) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary.Builder
-
Deprecated.
- addMutableState(String, ConfSpaceIteration) - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.Builder
- addMutFile(File) - Method in class edu.duke.cs.osprey.paste.Paste.Settings.Builder
- addNegative(MultiStateConfSpace.State) - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFEBuilder
- addNegative(String) - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFEBuilder
- addNode(String, Map<Integer, BigDecimal>) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode.Builder
- addNodes(Address, int, List<NodeIndex.Node>) - Method in class edu.duke.cs.osprey.coffee.nodedb.Neighbors
- AddNodesOperation - Class in edu.duke.cs.osprey.coffee.nodedb
-
Adds nodes to the cluster member.
- AddNodesOperation() - Constructor for class edu.duke.cs.osprey.coffee.nodedb.AddNodesOperation
- AddNodesOperation(int, List<NodeIndex.Node>) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.AddNodesOperation
- addOrAssert(ConfSMAStarNode) - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarQueue
- addOrSet(double) - Method in class edu.duke.cs.osprey.tools.BigMath
- addOrSet(long) - Method in class edu.duke.cs.osprey.tools.BigMath
- addOrSet(BigExp) - Method in class edu.duke.cs.osprey.tools.BigMath
- addOrSet(BigDecimal) - Method in class edu.duke.cs.osprey.tools.BigMath
- addOrSet(BigInteger) - Method in class edu.duke.cs.osprey.tools.BigMath
- addPair(String, String) - Method in class edu.duke.cs.osprey.energy.ResidueInteractions
- addPair(String, String, double, double) - Method in class edu.duke.cs.osprey.energy.ResidueInteractions
- addParams(FileTools.PathRoot, String) - Method in class edu.duke.cs.osprey.control.ParamSet
- addParamsFromFile(File) - Method in class edu.duke.cs.osprey.control.ParamSet
- addParamsFromFile(String) - Method in class edu.duke.cs.osprey.control.ParamSet
- addParamsFromResource(String) - Method in class edu.duke.cs.osprey.control.ParamSet
- addPos(SimpleConfSpace.Position, SimpleConfSpace.ResidueConf, int) - Method in class edu.duke.cs.osprey.dof.DofInfo
- addPositive(MultiStateConfSpace.State) - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFEBuilder
- addPositive(String) - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFEBuilder
- addPosToAllowedAAs(ArrayList<ArrayList<String>>, ArrayList<String>) - Static method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- addPosToSeq(ArrayList<String>, ArrayList<String>) - Static method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- addr - Variable in class edu.duke.cs.osprey.coffee.nodedb.Neighbors.NeighborInfo
- addRC(int, int) - Method in class edu.duke.cs.osprey.confspace.RCTuple
- addResEntropy - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- addResEntropy - Variable in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- addResEntropy(boolean) - Method in class edu.duke.cs.osprey.ematrix.SimpleReferenceEnergies.Builder
- addResEntropy(boolean) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator.Builder
- addResidue(Residue) - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions
-
Deprecated.
- addResidueEntropies(String) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary.Builder
-
Residue entropies to add to the library
- addResiduePair(Residue, Residue) - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions
-
Deprecated.
- address() - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- addRotamers(String) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary.Builder
-
Rotamers to add to the library
- addScoreConsoleWriter() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings.Builder
- addScoreConsoleWriter() - Method in class edu.duke.cs.osprey.kstar.KStar.Settings.Builder
- addScoreConsoleWriter() - Method in class edu.duke.cs.osprey.markstar.MARKStar.Settings.Builder
- addScoreConsoleWriter() - Method in class edu.duke.cs.osprey.paste.Paste.Settings.Builder
- addScoreConsoleWriter(EWAKStarScoreWriter.Formatter) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings.Builder
- addScoreConsoleWriter(KStarScoreWriter.Formatter) - Method in class edu.duke.cs.osprey.kstar.KStar.Settings.Builder
- addScoreConsoleWriter(KStarScoreWriter.Formatter) - Method in class edu.duke.cs.osprey.markstar.MARKStar.Settings.Builder
- addScoreConsoleWriter(PasteScoreWriter.Formatter) - Method in class edu.duke.cs.osprey.paste.Paste.Settings.Builder
- addScoreFileWriter(File) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings.Builder
- addScoreFileWriter(File) - Method in class edu.duke.cs.osprey.kstar.KStar.Settings.Builder
- addScoreFileWriter(File) - Method in class edu.duke.cs.osprey.markstar.MARKStar.Settings.Builder
- addScoreFileWriter(File) - Method in class edu.duke.cs.osprey.paste.Paste.Settings.Builder
- addScoreFileWriter(File, EWAKStarScoreWriter.Formatter) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings.Builder
- addScoreFileWriter(File, KStarScoreWriter.Formatter) - Method in class edu.duke.cs.osprey.kstar.KStar.Settings.Builder
- addScoreFileWriter(File, KStarScoreWriter.Formatter) - Method in class edu.duke.cs.osprey.markstar.MARKStar.Settings.Builder
- addScoreFileWriter(File, PasteScoreWriter.Formatter) - Method in class edu.duke.cs.osprey.paste.Paste.Settings.Builder
- addScoreWriter(EWAKStarScoreWriter) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings.Builder
- addScoreWriter(KStarScoreWriter) - Method in class edu.duke.cs.osprey.kstar.KStar.Settings.Builder
- addScoreWriter(KStarScoreWriter) - Method in class edu.duke.cs.osprey.markstar.MARKStar.Settings.Builder
- addScoreWriter(PasteScoreWriter) - Method in class edu.duke.cs.osprey.paste.Paste.Settings.Builder
- addSeq(String) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarLimitedSequenceTrie
- addSequence(Sequence) - Method in class edu.duke.cs.osprey.coffee.directors.PfuncsDirector.Builder
- addSequences(Collection<Sequence>) - Method in class edu.duke.cs.osprey.coffee.directors.PfuncsDirector.Builder
- addShell(int) - Method in class edu.duke.cs.osprey.energy.ResInterGen
-
energy += E(pos, s) for all s in shell
- addShell(int, double, double) - Method in class edu.duke.cs.osprey.energy.ResInterGen
-
energy += [E(pos, s) + offset]*weight for all s in shell
- addShell(RCTuple) - Method in class edu.duke.cs.osprey.energy.ResInterGen
-
energy += E(pos, s) for all pos in frag, s in shell
- addShell(RCTuple, double, ResInterGen.ShellOffsetter) - Method in class edu.duke.cs.osprey.energy.ResInterGen
-
energy += [E(pos, s) + offset(pos, s)]*weight for all pos in frag, s in shell
- addShellInters - Variable in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- addShellInters() - Method in class edu.duke.cs.osprey.energy.ResInterGen
-
energy += E(s, s) for all pairs of s in shell
- addShellIntras() - Method in class edu.duke.cs.osprey.energy.ResInterGen
-
energy += E(s) for all s in shell
- addSingle(String) - Method in class edu.duke.cs.osprey.energy.ResidueInteractions
- addSingle(String, double, double) - Method in class edu.duke.cs.osprey.energy.ResidueInteractions
- addState(EwakstarDoer.State) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- addState(Comets.State, double) - Method in class edu.duke.cs.osprey.gmec.Comets.LME.Builder
- addState(MSKStar.State, double) - Method in class edu.duke.cs.osprey.kstar.MSKStar.LMFE.Builder
- addStrand(Strand, int) - Method in class edu.duke.cs.osprey.dof.DofInfo
- addStrand(Strand, StrandFlex...) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Builder
- addStrand(Strand, List<StrandFlex>) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Builder
- addStrands(Strand...) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Builder
- addStrands(Iterable<Strand>) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Builder
- addTemplateCoords(String) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary.Builder
-
Template coordinates to add to the library.
- addTemplates(String) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary.Builder
-
Templates to add to the library.
- addTemplates(Consumer<AtomConnectivity.Builder>) - Method in class edu.duke.cs.osprey.energy.EnergyCalculator.Builder
-
Deprecated.
- addTerm(EnergyFunction) - Method in class edu.duke.cs.osprey.energy.MultiTermEnergyFunction
- addTermWithCoeff(EnergyFunction, double) - Method in class edu.duke.cs.osprey.energy.MultiTermEnergyFunction
- addTicksOn(double) - Method in class edu.duke.cs.osprey.tools.SVGPlot.Axis
- addTo(NodeStats.Values) - Method in class edu.duke.cs.osprey.coffee.NodeStats.Values
- addTuple(RCTuple) - Method in class edu.duke.cs.osprey.lute.ConfSampler.Samples
- addTuple(RCTuple) - Method in class edu.duke.cs.osprey.lute.LUTE
- addTuples(Iterable<RCTuple>) - Method in class edu.duke.cs.osprey.lute.LUTE
- addUniqueTuples(Iterable<RCTuple>) - Method in class edu.duke.cs.osprey.lute.LUTE
- addUnmutableState(String, ConfSpaceIteration) - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.Builder
- addVoxLinConstr(ArrayList<LinearConstraint>) - Method in class edu.duke.cs.osprey.plug.VoxelVDWListChecker
- addWildTypeRotamers - Variable in class edu.duke.cs.osprey.confspace.Strand.ResidueFlex
- addWildTypeRotamers() - Method in class edu.duke.cs.osprey.confspace.Strand.ResidueFlex
-
Add the wild type conformation as a rotamer, including any alternate conformations.
- addWT - Variable in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- addZConf(MultiStateConfSpace.State, Sequence, BigDecimal, BigExp, ConfSearch.EnergiedConf) - Method in class edu.duke.cs.osprey.coffee.seqdb.Batch
- addZPath(int[], int, BigDecimal, BigDecimal) - Method in class edu.duke.cs.osprey.sofea.RCDB.Table
- addZPath(MultiStateConfSpace.State, Sequence, int[], int, BigDecimal, BigDecimal) - Method in class edu.duke.cs.osprey.sofea.RCDB
- addZPath(MultiStateConfSpace.State, Sequence, BigExp, BigExp) - Method in class edu.duke.cs.osprey.sofea.SeqDB.Transaction
- addZSumUpper(int, int, BigDecimal) - Method in class edu.duke.cs.osprey.sofea.RCDB.Table
- addZSumUpper(MultiStateConfSpace.State, Sequence, int[], int, BigDecimal) - Method in class edu.duke.cs.osprey.sofea.RCDB
- addZSumUpper(MultiStateConfSpace.State, Sequence, BigExp) - Method in class edu.duke.cs.osprey.coffee.seqdb.Batch
- addZSumUpper(MultiStateConfSpace.State, Sequence, BigExp) - Method in class edu.duke.cs.osprey.sofea.SeqDB.Transaction
- adjustQStar() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- advance() - Method in class edu.duke.cs.osprey.tools.ConfigFileReader
-
set the current line to the next line
- advanceToNonEmptyLine() - Method in class edu.duke.cs.osprey.tools.ConfigFileReader
-
set the current line to the next non-empty line
- AffinityDesign - Class in edu.duke.cs.osprey.design.models
- AffinityDesign() - Constructor for class edu.duke.cs.osprey.design.models.AffinityDesign
- AffinityDirector - Class in edu.duke.cs.osprey.coffee.directors
-
Directs COFFEE to find the K best sequences by binding affinity The complex and design should be mutable, the target should not.
- AffinityDirector.Builder - Class in edu.duke.cs.osprey.coffee.directors
- ai - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle
- Aij - Variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.VdwParams
- Aij14Factor - Variable in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.Forcefield
- algOption - Variable in class edu.duke.cs.osprey.gmec.PruningSettings
- all(ConfSpace, int[]) - Static method in enum class edu.duke.cs.osprey.confspace.compiled.PosInterDist
- all(ConfSpace, int[]) - Method in class edu.duke.cs.osprey.energy.compiled.PosInterGen
- all(ConfSpace, int[], boolean) - Method in class edu.duke.cs.osprey.energy.compiled.PosInterGen
- all(ConfSpace, SimpleReferenceEnergies, int[]) - Static method in enum class edu.duke.cs.osprey.confspace.compiled.PosInterDist
-
Include all interactions, except ones between unassigned positions.
- All - Enum constant in enum class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.Type
- allocate(int) - Method in class edu.duke.cs.osprey.confspace.AbstractPosMatrix
- allocate(int) - Method in class edu.duke.cs.osprey.confspace.PosMatrixGeneric
- allocate(int) - Method in class edu.duke.cs.osprey.tools.ObjectPool
- allocate(int, int) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- allocate(int, int) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixBoolean
- allocate(int, int) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- allocate(int, int) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixGeneric
- allocate(int, int) - Method in class edu.duke.cs.osprey.ematrix.ProxyEnergyMatrix
- allocateBlock() - Method in class edu.duke.cs.osprey.coffee.nodedb.BlockStore
-
If there's space, allocates a block and returns its block id.
- allocatedBytes - Variable in class edu.duke.cs.osprey.tools.JvmMem.MemInfo
-
number of bytes allocated by the JVM from the OS
- allocatedPercent - Variable in class edu.duke.cs.osprey.tools.JvmMem.MemInfo
- AllOnPairs - Enum constant in enum class edu.duke.cs.osprey.energy.EnergyPartition
-
inters on pairs, intras and shell distributed evenly among pairs
- allowedAAs - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- allowedAAs - Variable in class edu.duke.cs.osprey.kstar.KSSearchProblem
- allowedRCsAtLevel(int, int[], ArrayList<Integer>) - Method in class edu.duke.cs.osprey.kstar.KAStarConfTree
- allowedSeqs - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.Settings
- allPositionTuples(int) - Method in class edu.duke.cs.osprey.confspace.TupleEnumerator
- allStrands - Variable in class edu.duke.cs.osprey.design.commands.CommandBindingAffinity.ForceFieldParamsAndStrands
- allTermValues() - Method in class edu.duke.cs.osprey.ematrix.epic.EPICEnergyFunction
- AlmostFrozen - Static variable in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator.Conditions
-
Almost frozen temperatures: 275 K, or about 35 F
- Alphabetic - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.DominantBaseline
- altProtStateDNames - Static variable in class edu.duke.cs.osprey.restypes.DAminoAcidHandler
- altProtStateLNames - Static variable in class edu.duke.cs.osprey.restypes.DAminoAcidHandler
- alwaysIdealizeSidechainsAfterMutation - Static variable in class edu.duke.cs.osprey.control.EnvironmentVars
-
Deprecated.
- alwaysResolveClashesEnergy - Variable in class edu.duke.cs.osprey.energy.EnergyCalculator
- AMASS() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.AtomSymbolAndMass
-
Returns the value of the
AMASSrecord component. - amat - Variable in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- Amber - Enum constant in enum class edu.duke.cs.osprey.energy.compiled.EnergyCalculator.Type
- AMBER - Enum constant in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.Forcefield
- AmberEnergyCalculator - Class in edu.duke.cs.osprey.energy.compiled
-
Calculate energies from a compiled ConfSpace.AssignedCoords according to the Amber forcefield.
- AmberEnergyCalculator(String, int) - Constructor for class edu.duke.cs.osprey.energy.compiled.AmberEnergyCalculator
- AmberEnergyCalculator.Settings - Class in edu.duke.cs.osprey.energy.compiled
- aminoAcidType - Variable in class edu.duke.cs.osprey.design.models.Residue
- Amult - Variable in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.ParamInfo
- analyses - Variable in class edu.duke.cs.osprey.gmec.ConfAnalyzer.EnsembleAnalysis
- Analysis(SequenceAnalyzer.ConfSpaceInfo, Sequence, ConfAnalyzer.EnsembleAnalysis) - Constructor for class edu.duke.cs.osprey.kstar.SequenceAnalyzer.Analysis
- analyze(int[]) - Method in class edu.duke.cs.osprey.gmec.ConfAnalyzer
- analyze(int[], AStarScorer) - Method in class edu.duke.cs.osprey.gmec.ConfAnalyzer
- analyze(int[], EnergyMatrix) - Method in class edu.duke.cs.osprey.gmec.ConfAnalyzer
- analyze(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.gmec.ConfAnalyzer
- analyze(Sequence, int) - Method in class edu.duke.cs.osprey.kstar.SequenceAnalyzer
-
Analyzes the sequence by getting the ensemble purely from the conformation database.
- analyze(Sequence, int, ConfEnergyCalculator) - Method in class edu.duke.cs.osprey.kstar.SequenceAnalyzer
-
Analyzes the sequence with the given energy calculator.
- analyzeEnsemble(Queue.FIFO<? extends ConfSearch.ScoredConf>, int) - Method in class edu.duke.cs.osprey.gmec.ConfAnalyzer
- analyzeEnsemble(HashMap<Double, ConfSearch.ScoredConf>, Iterator<? extends EnergyCalculator.EnergiedParametricMolecule>, int) - Method in class edu.duke.cs.osprey.gmec.ConfAnalyzer
- analyzeEnsemble(Iterator<? extends ConfSearch.ScoredConf>, int) - Method in class edu.duke.cs.osprey.gmec.ConfAnalyzer
- analyzeEnsembleFromConfDB(File, String, int) - Method in class edu.duke.cs.osprey.gmec.ConfAnalyzer
- analyzeGMECEnsembleFromConfDB(File, int) - Method in class edu.duke.cs.osprey.gmec.ConfAnalyzer
- analyzeGMECEnsembleFromConfDB(String, int) - Method in class edu.duke.cs.osprey.gmec.ConfAnalyzer
- AngleClustering - Class in edu.duke.cs.osprey.structure.analysis
- AngleClustering() - Constructor for class edu.duke.cs.osprey.structure.analysis.AngleClustering
- AngleLadder - Static variable in class edu.duke.cs.osprey.structure.analysis.DegreesHistogram
- Angles(double, double) - Constructor for class edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry.Angles
- Any - Enum constant in enum class edu.duke.cs.osprey.confspace.SimpleConfSpace.DofTypes
- appendDofs(List<DegreeOfFreedom>) - Method in interface edu.duke.cs.osprey.confspace.compiled.ContinuousMotion
-
Create degrees of freedom from the motion and add them to the list.
- appendDofs(List<DegreeOfFreedom>) - Method in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle
- appendDofs(List<DegreeOfFreedom>) - Method in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation
- appendResidue(Residue) - Method in class edu.duke.cs.osprey.structure.Molecule
- appendSPs(ArrayList<KSSearchProblem>, KSSearchProblem, int) - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel2
- appendTuple(RCTuple) - Method in class edu.duke.cs.osprey.confspace.TuplesIndex
- apply(double) - Method in class edu.duke.cs.osprey.bbfree.BBFreeDOF
- apply(double) - Method in class edu.duke.cs.osprey.dof.deeper.perts.Perturbation
- apply(double) - Method in class edu.duke.cs.osprey.dof.DegreeOfFreedom
- apply(double) - Method in class edu.duke.cs.osprey.dof.EllipseCoordDOF
- apply(double) - Method in class edu.duke.cs.osprey.dof.FreeDihedral
- apply(double) - Method in class edu.duke.cs.osprey.dof.ProlinePucker
- apply(double) - Method in class edu.duke.cs.osprey.dof.ResidueTypeDOF
- apply(double) - Method in class edu.duke.cs.osprey.dof.StrandRotation
- apply(double) - Method in class edu.duke.cs.osprey.dof.StrandTranslation
- apply(int, int) - Method in interface edu.duke.cs.osprey.pruning.PruningMatrix.SingleConsumer
- apply(int, int, int, int) - Method in interface edu.duke.cs.osprey.pruning.PruningMatrix.PairConsumer
- apply(int, int, int, int, int, int) - Method in interface edu.duke.cs.osprey.pruning.PruningMatrix.TripleConsumer
- apply(ProlinePucker.Direction) - Method in class edu.duke.cs.osprey.dof.ProlinePucker
- applyEnergyMatrixCachePattern(String) - Method in class edu.duke.cs.osprey.markstar.MARKStar.Settings
- applyRotation(double[], int) - Method in class edu.duke.cs.osprey.tools.RotationMatrix
- approximate(ResidueInteractions.Pair, ApproximatedObjectiveFunction.Approximator.Addable) - Method in class edu.duke.cs.osprey.energy.approximation.ResidueInteractionsApproximator.Builder
- ApproximatedObjectiveFunction - Class in edu.duke.cs.osprey.energy.approximation
- ApproximatedObjectiveFunction(ObjectiveFunction, ApproximatedObjectiveFunction.Approximator) - Constructor for class edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction
- ApproximatedObjectiveFunction.Approximator - Interface in edu.duke.cs.osprey.energy.approximation
- ApproximatedObjectiveFunction.Approximator.Addable - Interface in edu.duke.cs.osprey.energy.approximation
- approximationErrorBudget - Variable in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- approximator - Variable in class edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction
- approximator - Variable in class edu.duke.cs.osprey.energy.approximation.ResidueInteractionsApproximator
- ApproximatorMatrix - Class in edu.duke.cs.osprey.energy.approximation
-
Forcefield approximators for RC,residue pairs in a conf space
- ApproximatorMatrix(SimpleConfSpace) - Constructor for class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrix
- ApproximatorMatrixCalculator - Class in edu.duke.cs.osprey.energy.approximation
- ApproximatorMatrixCalculator(ConfEnergyCalculator) - Constructor for class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrixCalculator
- ApproximatorMatrixCalculator.ApproximatorType - Enum Class in edu.duke.cs.osprey.energy.approximation
- approxInters - Variable in class edu.duke.cs.osprey.energy.approximation.ResidueInteractionsApproximator
- approxMinimizedEnergy(int[]) - Method in class edu.duke.cs.osprey.confspace.SearchProblem
- APrioriPruningProver - Class in edu.duke.cs.osprey.kstar.pruning
-
This class selects an I0 and Ew for pruning so we can know ahead of time that the error in partition functions due to skipping pruned conformations is < epsilon.
- APrioriPruningProver(KSAbstract, KSConfigFileParser, HashMap<Integer, KSAllowedSeqs>) - Constructor for class edu.duke.cs.osprey.kstar.pruning.APrioriPruningProver
- arePertStatesIncompatible(ArrayList<int[]>, ArrayList<int[]>) - Method in class edu.duke.cs.osprey.dof.deeper.PerturbationSelector
- Array() - Constructor for class edu.duke.cs.osprey.gpu.Structs.Char8.Array
- Array() - Constructor for class edu.duke.cs.osprey.gpu.Structs.Float32.Array
- Array() - Constructor for class edu.duke.cs.osprey.gpu.Structs.Float64.Array
- Array() - Constructor for class edu.duke.cs.osprey.gpu.Structs.Int32.Array
- Array() - Constructor for class edu.duke.cs.osprey.gpu.Structs.Int64.Array
- Array(long) - Constructor for class edu.duke.cs.osprey.gpu.Structs.Array
- Array(Structs.Precision) - Constructor for class edu.duke.cs.osprey.gpu.Structs.Real.Array
- array2List(int[]) - Static method in class edu.duke.cs.osprey.kstar.KSConf
- asByteBuffer() - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- askToStop() - Method in class edu.duke.cs.osprey.parallelism.WorkCrew
- askToStop() - Method in class edu.duke.cs.osprey.parallelism.WorkThread
- askToStopAndWait() - Method in class edu.duke.cs.osprey.parallelism.WorkThread
- assembleTree() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode.Builder
- assertAlignment(long, int) - Method in class edu.duke.cs.osprey.gpu.Structs.Field
- assertSplitPositions() - Method in class edu.duke.cs.osprey.astar.ConfTree
- assign() - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
-
Makes assignments with no assigned positions.
- assign() - Method in class edu.duke.cs.osprey.restypes.ResTemplateMatching
- assign(int[]) - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- assign(int[]) - Method in class edu.duke.cs.osprey.energy.compiled.NativeConfEnergyCalculator
- assign(int, int) - Method in interface edu.duke.cs.osprey.astar.conf.ConfAStarNode
- assign(int, int) - Method in class edu.duke.cs.osprey.astar.conf.ConfIndex
- assign(int, int) - Method in class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode
- assign(int, int) - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- assign(int, int) - Method in class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode
- assign(int, int) - Method in interface edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode
- assign(int, int) - Method in class edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode.Assignments
-
Assigns the residue type to the position
- assign(int, int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
-
Makes assignments with one assigned position
- assign(int, int) - Method in class edu.duke.cs.osprey.externalMemory.EMConfAStarNode
- assign(int, int) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- assign(int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
-
Makes assignments with two assigned positions
- assign(int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
-
Makes assignments with three assigned positions
- assign(int, int, String, BigDecimal, BigDecimal, double, double) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- assign(RCTuple) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- AssignedCoords - Class in edu.duke.cs.osprey.confspace.compiled
-
A copy of the conf space atom coords with the desired assignments.
- AssignedCoords(ConfSpace, int[]) - Constructor for class edu.duke.cs.osprey.confspace.compiled.AssignedCoords
- AssignedCoords.AtomInfo - Class in edu.duke.cs.osprey.confspace.compiled
- assignedPos - Variable in class edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode.Assignments
- assignedRTs - Variable in class edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode.Assignments
- assignInPlace(int, int) - Method in class edu.duke.cs.osprey.astar.conf.ConfIndex
- Assignment - Enum constant in enum class edu.duke.cs.osprey.confspace.ConfDB.SortOrder
- Assignment - Enum constant in enum class edu.duke.cs.osprey.confspace.Sequence.Renderer
-
Render "R=T" where R is the residue number, and T is the residue type.
- AssignmentMutations - Enum constant in enum class edu.duke.cs.osprey.confspace.Sequence.Renderer
-
Render "R=T" where R is the residue number, and T is the residue type, but use UPPERCASE for mutations, and lowercase for wild-type.
- assignments - Variable in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords
-
conf indices for the design positions, in order
- assignments - Variable in class edu.duke.cs.osprey.confspace.ConfDB.Conf
- assignments - Variable in class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.ByPosition
- assignments - Variable in class edu.duke.cs.osprey.gmec.ConfAnalyzer.ConfAnalysis
- assignments - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- assignments() - Method in class edu.duke.cs.osprey.confspace.Sequence
- assignments(Iterable<String>) - Method in class edu.duke.cs.osprey.confspace.Sequence
- Assignments(int) - Constructor for class edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode.Assignments
- AssignmentsSerializer - Class in edu.duke.cs.osprey.externalMemory
- AssignmentsSerializer(RCs, int) - Constructor for class edu.duke.cs.osprey.externalMemory.AssignmentsSerializer
- AssignmentsSerializer.Encoding - Enum Class in edu.duke.cs.osprey.externalMemory
- AssignmentsSerializer.WrongEncodingException - Exception in edu.duke.cs.osprey.externalMemory
- AssignmentsSerializer.WrongNumberOfAssignmentsException - Exception in edu.duke.cs.osprey.externalMemory
- assignSharedMolecule(Molecule) - Method in class edu.duke.cs.osprey.ematrix.epic.SAPE
- assignTemplate(ResidueTemplateLibrary) - Method in class edu.duke.cs.osprey.structure.Residue
- assignTemplate(ResidueTemplateLibrary, Residue.TemplateMatchingMethod) - Method in class edu.duke.cs.osprey.structure.Residue
- assignTemplate(List<ResidueTemplate>, ForcefieldParams) - Method in class edu.duke.cs.osprey.structure.Residue
- assignTemplateSimple(ResidueTemplateLibrary) - Method in class edu.duke.cs.osprey.structure.Residue
- assignTemplateSimple(ResidueTemplateLibrary, String) - Method in class edu.duke.cs.osprey.structure.Residue
-
A much simpler template assigner that works only with atom names.
- assignTemplatesToStruct - Static variable in class edu.duke.cs.osprey.control.EnvironmentVars
-
Deprecated.
- astarFactory - Variable in class edu.duke.cs.osprey.lute.LowEnergyConfSampler
- AStarNode - Interface in edu.duke.cs.osprey.astar
- AStarNode.Factory<T extends AStarNode> - Interface in edu.duke.cs.osprey.astar
- AStarOrder - Interface in edu.duke.cs.osprey.astar.conf.order
- AStarProgress - Class in edu.duke.cs.osprey.astar
- AStarProgress(int) - Constructor for class edu.duke.cs.osprey.astar.AStarProgress
- AStarPruner - Interface in edu.duke.cs.osprey.astar.conf.pruning
- AStarScorer - Interface in edu.duke.cs.osprey.astar.conf.scoring
- AStarSequencePruner - Class in edu.duke.cs.osprey.astar.conf.pruning
- AStarSequencePruner(SimpleConfSpace) - Constructor for class edu.duke.cs.osprey.astar.conf.pruning.AStarSequencePruner
- AStarTree<T extends AStarNode> - Class in edu.duke.cs.osprey.astar
- AStarTree() - Constructor for class edu.duke.cs.osprey.astar.AStarTree
- Async(Factory<? extends EnergyFunction, Molecule>, ConfSpace, TaskExecutor, Factory<? extends Minimizer, MoleculeModifierAndScorer>) - Constructor for class edu.duke.cs.osprey.minimization.ConfMinimizer.Async
- atBoundary() - Method in class edu.duke.cs.osprey.pruning.PLUG.BoundaryPoint
- atLeast(double) - Method in class edu.duke.cs.osprey.tools.BigMath
- atLeast(long) - Method in class edu.duke.cs.osprey.tools.BigMath
- atLeast(BigExp) - Method in class edu.duke.cs.osprey.tools.BigMath
- atLeast(BigDecimal) - Method in class edu.duke.cs.osprey.tools.BigMath
- atLeast(BigInteger) - Method in class edu.duke.cs.osprey.tools.BigMath
- atMost(double) - Method in class edu.duke.cs.osprey.tools.BigMath
- atMost(long) - Method in class edu.duke.cs.osprey.tools.BigMath
- atMost(BigExp) - Method in class edu.duke.cs.osprey.tools.BigMath
- atMost(BigDecimal) - Method in class edu.duke.cs.osprey.tools.BigMath
- atMost(BigInteger) - Method in class edu.duke.cs.osprey.tools.BigMath
- Atom - Class in edu.duke.cs.osprey.structure
- Atom(String) - Constructor for class edu.duke.cs.osprey.structure.Atom
- Atom(String, String) - Constructor for class edu.duke.cs.osprey.structure.Atom
- atomCanBondOtherRes(Atom) - Method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate
- atomCanBondOtherRes(Atom) - Method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate.CysteineBondingTemplate
- atomCanBondOtherRes(Atom) - Method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate.NoBondingTemplate
- atomCanBondOtherRes(Atom) - Method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate.NucleotideBondingTemplate
- atomCanBondOtherRes(Atom) - Method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate.PeptideBondingTemplate
- atomCanBondOtherRes(Atom) - Method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate.SpecifiedBondingAtomsTemplate
- AtomConnectivity - Class in edu.duke.cs.osprey.structure
-
High-performance lookups of atom pairs by bond chain length
- AtomConnectivity.AtomPairs - Class in edu.duke.cs.osprey.structure
- AtomConnectivity.Builder - Class in edu.duke.cs.osprey.structure
- atomDistanceMatrix() - Method in class edu.duke.cs.osprey.structure.Residue
- atomi - Variable in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords.AtomInfo
- atomics() - Static method in enum class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.Type
- atomIndices - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation
- AtomInfo(int, int, int) - Constructor for class edu.duke.cs.osprey.confspace.compiled.AssignedCoords.AtomInfo
- AtomInfo(String, double, List<Probe.AtomFlag>) - Constructor for class edu.duke.cs.osprey.structure.Probe.AtomInfo
- atomMolInfoIndices - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Conf
- atomNames - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Conf
- AtomNames - Enum constant in enum class edu.duke.cs.osprey.structure.Residue.TemplateMatchingMethod
-
Matches a template iff only all the atom names match exactly.
- AtomNeighbors - Class in edu.duke.cs.osprey.structure
- AtomNeighbors(Atom) - Constructor for class edu.duke.cs.osprey.structure.AtomNeighbors
- AtomNeighbors.Type - Enum Class in edu.duke.cs.osprey.structure
- atomPair - Variable in class edu.duke.cs.osprey.structure.Probe.AtomPair.Interaction
- AtomPair(Atom, Atom) - Constructor for class edu.duke.cs.osprey.structure.Probe.AtomPair
- AtomPair(Atom, Atom, Probe.AtomInfo, Probe.AtomInfo) - Constructor for class edu.duke.cs.osprey.structure.Probe.AtomPair
- AtomPair(String, String) - Constructor for class edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger.AtomPair
- AtomPairElectrostaticContribution - Class in edu.duke.cs.osprey.energy.forcefield
- AtomPairElectrostaticContribution(ResPairCache.ResPair, int, int, double, double, double, boolean, boolean, boolean) - Constructor for class edu.duke.cs.osprey.energy.forcefield.AtomPairElectrostaticContribution
- AtomPairEnergyContribution - Class in edu.duke.cs.osprey.energy.forcefield
- AtomPairEnergyContribution(ResPairCache.ResPair, int, int, double) - Constructor for class edu.duke.cs.osprey.energy.forcefield.AtomPairEnergyContribution
- AtomPairInfo(Residue, Residue, ForcefieldParams, AtomConnectivity.AtomPairs, ForcefieldParams.SolvationForcefield.ResiduesInfo) - Constructor for class edu.duke.cs.osprey.energy.forcefield.ResPairCache.AtomPairInfo
- AtomPairs(ResidueTemplate, ResidueTemplate) - Constructor for class edu.duke.cs.osprey.structure.AtomConnectivity.AtomPairs
- AtomPairSolvationContribution - Class in edu.duke.cs.osprey.energy.forcefield
- AtomPairSolvationContribution(ResPairCache.ResPair, int, int, double) - Constructor for class edu.duke.cs.osprey.energy.forcefield.AtomPairSolvationContribution
- AtomPairVanDerWaalsContribution - Class in edu.duke.cs.osprey.energy.forcefield
- AtomPairVanDerWaalsContribution(ResPairCache.ResPair, int, int, double, double, double, double) - Constructor for class edu.duke.cs.osprey.energy.forcefield.AtomPairVanDerWaalsContribution
- atomResInfoIndices - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Conf
- atoms - Variable in class edu.duke.cs.osprey.structure.Probe.Template
- atoms - Variable in class edu.duke.cs.osprey.structure.Residue
-
Information about the individual atoms.
- atoms() - Method in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords
-
returns information about the atom coords that are actually populated for this conformation
- atoms() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.BondAngleParameter
- atoms() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.BondLengthParameter
- atoms() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.DihederalParameter
- atoms() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.EquivalencingAtom
- atoms() - Method in interface edu.duke.cs.osprey.energy.forcefield.amber.HasAtoms
- atoms() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.HBond10_12PotentialParameter
- atoms() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.ImproperDihederalParameter
- atoms() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.Six12PotentialCoefficient
- atoms() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.SlaterKirkwoodParameter
- atoms() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.VanDerWaalsRadius
- AtomSymbolAndMass - Record Class in edu.duke.cs.osprey.energy.forcefield.amber
- AtomSymbolAndMass(String, float) - Constructor for record class edu.duke.cs.osprey.energy.forcefield.amber.AtomSymbolAndMass
-
Creates an instance of a
AtomSymbolAndMassrecord class. - atomSymbolsAndMasses() - Method in class edu.duke.cs.osprey.energy.forcefield.amber.ForcefieldFileParser
- atomTypeToInt(String) - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- attachCurrentThread() - Method in class edu.duke.cs.osprey.gpu.cuda.Context
- attraction - Variable in class edu.duke.cs.osprey.structure.Probe.AtomPair
- Auto - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.DominantBaseline
- autoCheckout() - Method in class edu.duke.cs.osprey.tools.ObjectPool
- AutoCleanable - Interface in edu.duke.cs.osprey.tools
- AutoCloseableNoEx - Interface in edu.duke.cs.osprey.tools
- autoExpand(double) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- autoExpand(double, int) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- autoIterate() - Method in class edu.duke.cs.osprey.partcr.PartCR
- autoIterate(int) - Method in class edu.duke.cs.osprey.partcr.PartCR
- available() - Method in class edu.duke.cs.osprey.tools.ObjectPool
- average(double[], double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- avg - Variable in class edu.duke.cs.osprey.lute.LUTE.Errors
- avgAtomPairs(int, PosInter) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- avgAtomPairs(List<PosInter>) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
-
Returns the average the number of atoms pairs for the given position interactions, over all conformations.
- await(long, TimeUnit) - Method in class edu.duke.cs.osprey.parallelism.WorkLatch
- axis - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Intervals
- Axis() - Constructor for class edu.duke.cs.osprey.tools.SVGPlot.Axis
- axisInfos - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot.Series
- axisTicksOn - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Boxes
- axisTicksOn - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Intervals
B
- b - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Description
- b - Variable in class edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger.Coords
- b - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.BondAngle
- b - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.BondLength
- b - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DeltaDihedralAngle
- b - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DihedralAngle
- b - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DihedralAnglesMinDist
- b - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralSystem
- b - Variable in class edu.duke.cs.osprey.structure.Probe.AtomPair
- B() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.HBond10_12PotentialParameter
-
Returns the value of the
Brecord component. - ba - Variable in class edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry
- BackboneDependentRotamerLibrary - Class in edu.duke.cs.osprey.restypes
- BackboneDependentRotamerLibrary() - Constructor for class edu.duke.cs.osprey.restypes.BackboneDependentRotamerLibrary
- Backrub - Class in edu.duke.cs.osprey.dof.deeper.perts
-
A backrub perturbation
- Backrub(ArrayList<Residue>) - Constructor for class edu.duke.cs.osprey.dof.deeper.perts.Backrub
- backup(ConfSMAStarQueue) - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
-
ie, the "backup" operation described by the SMA* paper
- BadClash - Enum constant in enum class edu.duke.cs.osprey.structure.Probe.Contact
- BadFileException(File, String) - Constructor for exception edu.duke.cs.osprey.tools.ObjectIO.BadFileException
- BadFileException(File, String, Throwable) - Constructor for exception edu.duke.cs.osprey.tools.ObjectIO.BadFileException
- baflat - Variable in class edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry
- barheight - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot.IntervalsX
- barrier(long, TimeUnit) - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- barwidth - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot.IntervalsY
- baseTuple - Variable in class edu.duke.cs.osprey.confspace.TupleTree
-
a common tuple prefix shared by all tuples in this tree useful for implementing a pairwise matrix of tuple trees, for e.g.
- BasicEPICTupleExpander - Class in edu.duke.cs.osprey.tupexp
- BasicEPICTupleExpander(SimpleConfSpace, double, LUTESettings, NewEPICMatrix, PruningMatrix) - Constructor for class edu.duke.cs.osprey.tupexp.BasicEPICTupleExpander
- BasicPruningTupleExpander - Class in edu.duke.cs.osprey.tupexp
- BasicPruningTupleExpander(PruningMatrix, PolytopeMatrix) - Constructor for class edu.duke.cs.osprey.tupexp.BasicPruningTupleExpander
- batch() - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqDB
- Batch - Class in edu.duke.cs.osprey.coffee.seqdb
- BBFreeBlock - Class in edu.duke.cs.osprey.bbfree
-
This is a set of consecutive residues whose backbones can move freely, subject to distance, angle, and omega constraints The freely moving zone is anchored fix CA's at either end
- BBFreeBlock() - Constructor for class edu.duke.cs.osprey.bbfree.BBFreeBlock
- BBFreeBlock(List<Residue>) - Constructor for class edu.duke.cs.osprey.bbfree.BBFreeBlock
- BBFreeDOF - Class in edu.duke.cs.osprey.bbfree
-
This is a DOF that's part of a BBFreeBlock
- BBFreeDOF(DoubleMatrix1D, BBFreeBlock, int) - Constructor for class edu.duke.cs.osprey.bbfree.BBFreeDOF
- BBKStar - Class in edu.duke.cs.osprey.kstar
-
Implementation of the BBK* algorithm to predict protein sequence mutations that improve binding affinity by computing provably accurate Boltzmann-weighted ensembles .
- BBKStar(ConfSpaceIteration, ConfSpaceIteration, ConfSpaceIteration, KStar.Settings, BBKStar.Settings) - Constructor for class edu.duke.cs.osprey.kstar.BBKStar
- BBKStar.ConfSearchFactory - Interface in edu.duke.cs.osprey.kstar
- BBKStar.ConfSpaceInfo - Class in edu.duke.cs.osprey.kstar
- BBKStar.MultiSequenceNode - Class in edu.duke.cs.osprey.kstar
- BBKStar.PfuncsStatus - Enum Class in edu.duke.cs.osprey.kstar
- BBKStar.Settings - Class in edu.duke.cs.osprey.kstar
- BBKStar.Settings.Builder - Class in edu.duke.cs.osprey.kstar
- BBKStar.SingleSequenceNode - Class in edu.duke.cs.osprey.kstar
- bbkstarSettings - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar
- bbkstarSettings - Variable in class edu.duke.cs.osprey.kstar.BBKStar
-
Optional and overridable settings for BBK*
- bc - Variable in class edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry
- bcalc - Variable in class edu.duke.cs.osprey.coffee.Coffee
- bcalc - Variable in class edu.duke.cs.osprey.coffee.FreeEnergyCalculator
- bcalc - Variable in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- bcalc - Variable in class edu.duke.cs.osprey.sofea.Sofea
- bcflat - Variable in class edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry
- bd - Variable in class edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry
- bdflat - Variable in class edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry
- bestBatchSize() - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuInfo
-
Returns the best batch size for saturating the device with work
- bestConfs - Variable in class edu.duke.cs.osprey.coffee.seqdb.StateZ
- bestNumStreams() - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuInfo
-
Returns the best number of streams/threads for saturating the device with work
- bestSeqs - Variable in class edu.duke.cs.osprey.coffee.directors.AffinityDirector
- BestSet<T> - Class in edu.duke.cs.osprey.coffee.directors
-
Track the K best things by lowest value, allowing ties.
- BestSet(int, Function<T, Double>) - Constructor for class edu.duke.cs.osprey.coffee.directors.BestSet
- BFactor - Variable in class edu.duke.cs.osprey.structure.Atom
- bi - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle
- bigAdd(BigDecimal, BigDecimal, MathContext) - Static method in class edu.duke.cs.osprey.tools.MathTools
-
return a + b, correctly handling -Inf, +Inf, and NaN
- BigDecimalBounds() - Constructor for class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- BigDecimalBounds(double, double) - Constructor for class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- BigDecimalBounds(MathTools.BigDecimalBounds) - Constructor for class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- BigDecimalBounds(String, String) - Constructor for class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- BigDecimalBounds(BigDecimal) - Constructor for class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- BigDecimalBounds(BigDecimal, BigDecimal) - Constructor for class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- BigDecimalBoundsSerializer() - Constructor for class edu.duke.cs.osprey.tools.MapDBTools.BigDecimalBoundsSerializer
- BigDecimalIO - Interface in edu.duke.cs.osprey.sofea
-
serializes BigDecimal instances to as fixed-length byte arrays based on the MathContext precision supports MathTools pseudo-values for BigDecimal like -/+inf, NaN
- BigDecimalIO.Fixed - Class in edu.duke.cs.osprey.sofea
- BigDecimalIO.Type - Enum Class in edu.duke.cs.osprey.sofea
- BigDecimalIO.Variable - Class in edu.duke.cs.osprey.sofea
- BigDecimalSerializer() - Constructor for class edu.duke.cs.osprey.tools.MapDBTools.BigDecimalSerializer
- bigDivide(BigDecimal, BigDecimal, MathContext) - Static method in class edu.duke.cs.osprey.tools.MathTools
-
return a/b, correctly handling -Inf, +Inf, and NaN
- bigDivideDivide(BigDecimal, BigDecimal, BigDecimal, MathContext) - Static method in class edu.duke.cs.osprey.tools.MathTools
-
return a/b/c, correctly handling -Inf, +Inf, and NaN
- BigExp - Class in edu.duke.cs.osprey.tools
-
A ridiculously simplistic and naive way to have floating point values with larger exponents than +-300 ish but also have fast performance for multiply and max (BigDecimal is relatively slow) The BigExp number type consists of a floating point component (fp), and an exponent component (exp).
- BigExp - Static variable in class edu.duke.cs.osprey.coffee.Serializers
- BigExp(double) - Constructor for class edu.duke.cs.osprey.tools.BigExp
- BigExp(double, int) - Constructor for class edu.duke.cs.osprey.tools.BigExp
- BigExp(BigExp) - Constructor for class edu.duke.cs.osprey.tools.BigExp
- BigExp(BigDecimal) - Constructor for class edu.duke.cs.osprey.tools.BigExp
- BigExp(BigInteger) - Constructor for class edu.duke.cs.osprey.tools.BigExp
- BigExp.Bounds - Class in edu.duke.cs.osprey.tools
- BigExpSerializer() - Constructor for class edu.duke.cs.osprey.tools.MapDBTools.BigExpSerializer
- BigForcefieldEnergy - Class in edu.duke.cs.osprey.energy.forcefield
- BigForcefieldEnergy(ForcefieldParams, ForcefieldInteractions) - Constructor for class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy
- BigForcefieldEnergy(ForcefieldParams, ForcefieldInteractions, BufferTools.Type) - Constructor for class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy
- BigForcefieldEnergy.ParamInfo - Class in edu.duke.cs.osprey.energy.forcefield
- BigForcefieldEnergy.Subset - Class in edu.duke.cs.osprey.energy.forcefield
- biggen(double) - Static method in class edu.duke.cs.osprey.tools.MathTools
- biggen(double, double) - Static method in class edu.duke.cs.osprey.tools.MathTools
- biggen(long) - Static method in class edu.duke.cs.osprey.tools.MathTools
- biggen(String) - Static method in class edu.duke.cs.osprey.tools.MathTools
- biggen(String, String) - Static method in class edu.duke.cs.osprey.tools.MathTools
- BiggestLowerboundDifferenceOrder - Class in edu.duke.cs.osprey.markstar.framework
- BiggestLowerboundDifferenceOrder() - Constructor for class edu.duke.cs.osprey.markstar.framework.BiggestLowerboundDifferenceOrder
- BiggestLowerboundDifferenceOrder(MathTools.Optimizer) - Constructor for class edu.duke.cs.osprey.markstar.framework.BiggestLowerboundDifferenceOrder
- BigIntegerBounds(BigInteger, BigInteger) - Constructor for class edu.duke.cs.osprey.tools.MathTools.BigIntegerBounds
- bigMath() - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqDB
- bigMath() - Method in class edu.duke.cs.osprey.sofea.RCDB
- bigMath() - Method in class edu.duke.cs.osprey.sofea.SeqDB
- bigMath() - Method in class edu.duke.cs.osprey.sofea.SeqDB.Transaction
- bigMath() - Method in class edu.duke.cs.osprey.sofea.Sofea
- BigMath - Class in edu.duke.cs.osprey.tools
- BigMath(int) - Constructor for class edu.duke.cs.osprey.tools.BigMath
- BigMath(MathContext) - Constructor for class edu.duke.cs.osprey.tools.BigMath
- bigMultiply(BigDecimal, BigDecimal, MathContext) - Static method in class edu.duke.cs.osprey.tools.MathTools
-
return a*b, correctly handling -Inf, +Inf, and NaN
- BigNaN - Static variable in class edu.duke.cs.osprey.tools.MathTools
- bigNegate(BigDecimal) - Static method in class edu.duke.cs.osprey.tools.MathTools
-
return -a, correctly handling -Inf, +Inf, and NaN
- BigNegativeInfinity - Static variable in class edu.duke.cs.osprey.tools.MathTools
-
See BigPositiveInfinity for usage instructions
- BigPositiveInfinity - Static variable in class edu.duke.cs.osprey.tools.MathTools
-
Sadly, Java's BigDecimal can't encode values of +Infinity or -Infinity =( These magic constants are a complete hack to try to work around that.
- bigSubtract(BigDecimal, BigDecimal, MathContext) - Static method in class edu.duke.cs.osprey.tools.MathTools
-
return a - b, correctly handling -Inf, +Inf, and NaN
- Bij - Variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.VdwParams
- Bij14Factor - Variable in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.Forcefield
- BinaryRCSplitter - Class in edu.duke.cs.osprey.partcr.splitters
- BinaryRCSplitter() - Constructor for class edu.duke.cs.osprey.partcr.splitters.BinaryRCSplitter
- blacklist - Variable in class edu.duke.cs.osprey.structure.analysis.PDBScanner
- blank() - Method in class edu.duke.cs.osprey.ematrix.epic.EPICFitter
- blockCapacity - Variable in class edu.duke.cs.osprey.coffee.nodedb.PriorityDequeFixedIndex
- blockCapacity() - Method in interface edu.duke.cs.osprey.coffee.nodedb.FixedIndex
-
Returns the max number of items per block.
- blockCapacity() - Method in class edu.duke.cs.osprey.coffee.nodedb.PriorityDequeFixedIndex
- Blocked - Enum constant in enum class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.PfuncsStatus
- Blocked - Enum constant in enum class edu.duke.cs.osprey.kstar.BBKStar.PfuncsStatus
- blockIndicesByResNum - Variable in class edu.duke.cs.osprey.dof.DofInfo
- blockShift - Variable in class edu.duke.cs.osprey.coffee.nodedb.BlockStore
- blockSize - Variable in class edu.duke.cs.osprey.coffee.nodedb.BlockStore
- BlockStore - Class in edu.duke.cs.osprey.coffee.nodedb
-
A fixed-size storage space divided into blocks, with a very simple memory allocator
- BlockStore(File, long) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.BlockStore
- BlockStore(File, long, int) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.BlockStore
- blockThreads - Variable in class edu.duke.cs.osprey.gpu.cuda.Kernel.Function
- Bmult - Variable in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.ParamInfo
- Body - Static variable in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator.Conditions
-
Body temperature: 310 K, or about 98 F
- boltzmann - Variable in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- BoltzmannCalculator - Class in edu.duke.cs.osprey.kstar.pfunc
- BoltzmannCalculator(MathContext) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- BoltzmannCalculator(MathContext, double, double) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- BoltzmannCalculator(MathContext, BoltzmannCalculator.Conditions) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- BoltzmannCalculator.Conditions - Class in edu.duke.cs.osprey.kstar.pfunc
-
Environmental conditions, like temperature and the gas constant.
- BoltzmannIntegrator1D - Class in edu.duke.cs.osprey.voxq
-
Evaluates \int_a^b exp(-f(x)/RT) dx by Simpson's rule
- BoltzmannIntegrator1D(double, double) - Constructor for class edu.duke.cs.osprey.voxq.BoltzmannIntegrator1D
- BoltzmannLute - Class in edu.duke.cs.osprey.sofea
- BoltzmannLute(LUTEConfEnergyCalculator, MathContext) - Constructor for class edu.duke.cs.osprey.sofea.BoltzmannLute
- BondAngle(String, String, String) - Constructor for class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.BondAngle
- BondAngleParameter - Record Class in edu.duke.cs.osprey.energy.forcefield.amber
- BondAngleParameter(AtomSymbolAndMass, AtomSymbolAndMass, AtomSymbolAndMass, float, float) - Constructor for record class edu.duke.cs.osprey.energy.forcefield.amber.BondAngleParameter
-
Creates an instance of a
BondAngleParameterrecord class. - bondAngleParameters() - Method in class edu.duke.cs.osprey.energy.forcefield.amber.ForcefieldFileParser
- BondDistances - Enum constant in enum class edu.duke.cs.osprey.structure.Residue.TemplateMatchingMethod
-
Matches the closest template based on comparing bond distances.
- Bonded - Enum constant in enum class edu.duke.cs.osprey.structure.Probe.Contact
- BONDED12 - Enum constant in enum class edu.duke.cs.osprey.structure.AtomNeighbors.Type
- BONDED13 - Enum constant in enum class edu.duke.cs.osprey.structure.AtomNeighbors.Type
- BONDED14 - Enum constant in enum class edu.duke.cs.osprey.structure.AtomNeighbors.Type
- BONDED15H - Enum constant in enum class edu.duke.cs.osprey.structure.AtomNeighbors.Type
- BondLength(String, String) - Constructor for class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.BondLength
- BondLengthParameter - Record Class in edu.duke.cs.osprey.energy.forcefield.amber
- BondLengthParameter(AtomSymbolAndMass, AtomSymbolAndMass, float, float) - Constructor for record class edu.duke.cs.osprey.energy.forcefield.amber.BondLengthParameter
-
Creates an instance of a
BondLengthParameterrecord class. - bondLengthParameters() - Method in class edu.duke.cs.osprey.energy.forcefield.amber.ForcefieldFileParser
- bondLengthUpperBound(int, int) - Static method in class edu.duke.cs.osprey.restypes.HardCodedResidueInfo
- bonds - Variable in class edu.duke.cs.osprey.structure.Atom
- bool() - Static method in class edu.duke.cs.osprey.gpu.Structs
- Bool() - Constructor for class edu.duke.cs.osprey.gpu.Structs.Bool
- BottleneckThread - Class in edu.duke.cs.osprey.parallelism
-
A worker thread that forces all work submitted from other threads to be serialized.
- BottleneckThread(String) - Constructor for class edu.duke.cs.osprey.parallelism.BottleneckThread
- BottomAxis() - Constructor for class edu.duke.cs.osprey.tools.SVGPlot.BottomAxis
- Bound(double, long) - Constructor for class edu.duke.cs.osprey.confspace.ConfDB.Conf.Bound
- boundaries - Variable in class edu.duke.cs.osprey.structure.analysis.Histogram
- BoundaryPoint(double) - Constructor for class edu.duke.cs.osprey.pruning.PLUG.BoundaryPoint
- BoundaryPoint(double[], double, double[]) - Constructor for class edu.duke.cs.osprey.pruning.PLUG.BoundaryPoint
- boundedLeaf - Enum constant in enum class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Type
- Bounder - Interface in edu.duke.cs.osprey.coffee.bounds
- BoundErrorByPos(int, double) - Constructor for class edu.duke.cs.osprey.kstar.RCEnergyContribs.BoundErrorByPos
- BoundErrorByPosComparator() - Constructor for class edu.duke.cs.osprey.kstar.RCEnergyContribs.BoundErrorByPosComparator
- boundLowestBoundConfUnderNode(MARKStarNode, List<MARKStarNode>) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- bounds - Variable in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFECalculator
- bounds - Variable in class edu.duke.cs.osprey.structure.analysis.ClusterR1.Stats
- bounds - Variable in class edu.duke.cs.osprey.structure.analysis.ClusterS1.Stats
- bounds() - Method in class edu.duke.cs.osprey.structure.analysis.ClusterR1
- bounds() - Method in class edu.duke.cs.osprey.structure.analysis.ClusterS1
- Bounds() - Constructor for class edu.duke.cs.osprey.tools.BigExp.Bounds
- Bounds(BigExp) - Constructor for class edu.duke.cs.osprey.tools.BigExp.Bounds
- Bounds(BigExp, BigExp) - Constructor for class edu.duke.cs.osprey.tools.BigExp.Bounds
- boundsThresh - Variable in class edu.duke.cs.osprey.gmec.PruningSettings
- Box(double, double, double, double) - Constructor for class edu.duke.cs.osprey.tools.SVGPlot.Boxes.Box
- Boxes() - Constructor for class edu.duke.cs.osprey.tools.SVGPlot.Boxes
- boxStyle - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Boxes
- Break - Enum constant in enum class edu.duke.cs.osprey.pruning.PruningMatrix.IteratorCommand
- breakdownEnergyByPosition(ResidueForcefieldBreakdown.Type) - Method in class edu.duke.cs.osprey.gmec.ConfAnalyzer.ConfAnalysis
- breakdownEnergyByResidue() - Method in class edu.duke.cs.osprey.gmec.ConfAnalyzer.ConfAnalysis
- breakdownForcefield(ResidueForcefieldBreakdown.Type) - Method in class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.ByPosition
- breakdownForcefield(ResidueForcefieldBreakdown.Type) - Method in class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.ByResidue
- breakdownScore(EnergyMatrix) - Method in class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.ByPosition
- breakdownScoreByPosition(EnergyMatrix) - Method in class edu.duke.cs.osprey.gmec.ConfAnalyzer.ConfAnalysis
- broadcast() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
- BroadcastInfo(int) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.NodeIndices.BroadcastInfo
- broadcastNs - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
- BroadcastOperation - Class in edu.duke.cs.osprey.coffee.nodedb
-
Informs other cluster members about a member's current state.
- BroadcastOperation() - Constructor for class edu.duke.cs.osprey.coffee.nodedb.BroadcastOperation
- BroadcastOperation(NodeIndices.BroadcastInfo, NodePerformance) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.BroadcastOperation
- BrokenConformation - Static variable in class edu.duke.cs.osprey.energy.forcefield.AtomPairEnergyContribution
- BrokenConformation - Static variable in class edu.duke.cs.osprey.energy.forcefield.ResPairEnergyContribution
- brokenList - Static variable in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- bucketName - Variable in class edu.duke.cs.osprey.design.S3Settings
- buckets - Variable in class edu.duke.cs.osprey.structure.analysis.DegreesHistogram
- buf - Variable in class edu.duke.cs.osprey.tools.ByteBufferInputStream
- buf - Variable in class edu.duke.cs.osprey.tools.ByteBufferOutputStream
- BufferPool<T extends Buffer> - Class in edu.duke.cs.osprey.gpu.cuda
- BufferPool(BufferPool.BufferFactory<T>, BufferPool.BufferExpander<T>) - Constructor for class edu.duke.cs.osprey.gpu.cuda.BufferPool
- BufferPool.BufferExpander<T extends Buffer> - Interface in edu.duke.cs.osprey.gpu.cuda
- BufferPool.BufferFactory<T extends Buffer> - Interface in edu.duke.cs.osprey.gpu.cuda
- BufferTools - Class in edu.duke.cs.osprey.gpu
- BufferTools() - Constructor for class edu.duke.cs.osprey.gpu.BufferTools
- BufferTools.OutOfDirectMemoryError - Error in edu.duke.cs.osprey.gpu
- BufferTools.Type - Enum Class in edu.duke.cs.osprey.gpu
- build() - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree.Builder
- build() - Method in class edu.duke.cs.osprey.astar.conf.ConfRanker.Builder
- build() - Method in class edu.duke.cs.osprey.astar.seq.SeqAStarTree.Builder
- build() - Method in class edu.duke.cs.osprey.coffee.Coffee.Builder
- build() - Method in class edu.duke.cs.osprey.coffee.directors.AffinityDirector.Builder
- build() - Method in class edu.duke.cs.osprey.coffee.directors.KStarDirector.Builder
- build() - Method in class edu.duke.cs.osprey.coffee.directors.PfuncDirector.Builder
- build() - Method in class edu.duke.cs.osprey.coffee.directors.PfuncsDirector.Builder
- build() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB.Builder
- build() - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqDB.Builder
- build() - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.Builder
- build() - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFEBuilder
- build() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Builder
- build() - Method in class edu.duke.cs.osprey.confspace.Strand.Builder
- build() - Method in class edu.duke.cs.osprey.ematrix.compiled.EmatCalculator.Builder
- build() - Method in class edu.duke.cs.osprey.ematrix.compiled.ErefCalculator.Builder
- build() - Method in class edu.duke.cs.osprey.ematrix.SimpleReferenceEnergies.Builder
- build() - Method in class edu.duke.cs.osprey.ematrix.SimplerEnergyMatrixCalculator.Builder
- build() - Method in class edu.duke.cs.osprey.energy.approximation.ResidueInteractionsApproximator.Builder
- build() - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter.Builder
-
Deprecated.
- build() - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator.Builder
- build() - Method in class edu.duke.cs.osprey.energy.EnergyCalculator.Builder
- build() - Method in class edu.duke.cs.osprey.energy.EnergyCalculator.SharedBuilder
- build() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings.Builder
- build() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.Settings.Builder
- build() - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- build() - Method in class edu.duke.cs.osprey.gmec.Comets.Builder
- build() - Method in class edu.duke.cs.osprey.gmec.Comets.LME.Builder
- build() - Method in class edu.duke.cs.osprey.gmec.DEEGMECFinder.Builder
- build() - Method in class edu.duke.cs.osprey.gmec.SimpleGMECFinder.Builder
- build() - Method in class edu.duke.cs.osprey.kstar.BBKStar.Settings.Builder
- build() - Method in class edu.duke.cs.osprey.kstar.KStar.Settings.Builder
- build() - Method in class edu.duke.cs.osprey.kstar.MSKStar.Builder
- build() - Method in class edu.duke.cs.osprey.kstar.MSKStar.LMFE.Builder
- build() - Method in class edu.duke.cs.osprey.lute.LUTEGMECFinder.Builder
- build() - Method in class edu.duke.cs.osprey.markstar.MARKStar.Settings.Builder
- build() - Method in class edu.duke.cs.osprey.minimization.CpuConfMinimizer.Builder
- build() - Method in class edu.duke.cs.osprey.minimization.GpuConfMinimizer.Builder
- build() - Method in class edu.duke.cs.osprey.parallelism.Parallelism.Builder
- build() - Method in class edu.duke.cs.osprey.paste.Paste.Settings.Builder
- build() - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary.Builder
- build() - Method in class edu.duke.cs.osprey.sofea.Sofea.Builder
- build() - Method in class edu.duke.cs.osprey.structure.AtomConnectivity.Builder
- build() - Method in interface edu.duke.cs.osprey.tools.UseableBuilder
- build(AssignedCoords, int) - Method in interface edu.duke.cs.osprey.confspace.compiled.ContinuousMotion.MolDescription
- build(AssignedCoords, int) - Method in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Description
- build(AssignedCoords, int) - Method in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Description
- build(AssignedCoords, ConfSpace.Pos) - Method in interface edu.duke.cs.osprey.confspace.compiled.ContinuousMotion.ConfDescription
- build(AssignedCoords, ConfSpace.Pos) - Method in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Description
- Builder() - Constructor for class edu.duke.cs.osprey.confspace.SimpleConfSpace.Builder
- Builder() - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings.Builder
- Builder() - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.Settings.Builder
- Builder() - Constructor for class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- Builder() - Constructor for class edu.duke.cs.osprey.gmec.Comets.LME.Builder
- Builder() - Constructor for class edu.duke.cs.osprey.kstar.BBKStar.Settings.Builder
- Builder() - Constructor for class edu.duke.cs.osprey.kstar.KStar.Settings.Builder
- Builder() - Constructor for class edu.duke.cs.osprey.kstar.MSKStar.LMFE.Builder
- Builder() - Constructor for class edu.duke.cs.osprey.markstar.MARKStar.Settings.Builder
- Builder() - Constructor for class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode.Builder
- Builder() - Constructor for class edu.duke.cs.osprey.parallelism.Parallelism.Builder
- Builder() - Constructor for class edu.duke.cs.osprey.paste.Paste.Settings.Builder
- Builder() - Constructor for class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary.Builder
- Builder() - Constructor for class edu.duke.cs.osprey.structure.AtomConnectivity.Builder
- Builder(RTs) - Constructor for class edu.duke.cs.osprey.astar.seq.SeqAStarTree.Builder
- Builder(ConfSpace, ConfSpace, ConfSpace) - Constructor for class edu.duke.cs.osprey.coffee.directors.KStarDirector.Builder
- Builder(ConfSearch, ConfEnergyCalculator) - Constructor for class edu.duke.cs.osprey.gmec.SimpleGMECFinder.Builder
- Builder(MultiStateConfSpace) - Constructor for class edu.duke.cs.osprey.coffee.Coffee.Builder
- Builder(MultiStateConfSpace) - Constructor for class edu.duke.cs.osprey.sofea.Sofea.Builder
- Builder(MultiStateConfSpace, ClusterMember) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.NodeDB.Builder
- Builder(MultiStateConfSpace, ClusterMember) - Constructor for class edu.duke.cs.osprey.coffee.seqdb.SeqDB.Builder
- Builder(MultiStateConfSpace, MultiStateConfSpace.State) - Constructor for class edu.duke.cs.osprey.coffee.directors.PfuncDirector.Builder
- Builder(MultiStateConfSpace, MultiStateConfSpace.State) - Constructor for class edu.duke.cs.osprey.coffee.directors.PfuncsDirector.Builder
- Builder(MultiStateConfSpace, MultiStateConfSpace.State, MultiStateConfSpace.State, MultiStateConfSpace.State) - Constructor for class edu.duke.cs.osprey.coffee.directors.AffinityDirector.Builder
- Builder(MultiStateConfSpace, MultiStateConfSpace.State, MultiStateConfSpace.State, MultiStateConfSpace.State) - Constructor for class edu.duke.cs.osprey.coffee.directors.KStarDirector.Builder
- Builder(MultiStateConfSpace, ForcefieldParams) - Constructor for class edu.duke.cs.osprey.energy.EnergyCalculator.Builder
- Builder(MultiStateConfSpace, String) - Constructor for class edu.duke.cs.osprey.coffee.directors.PfuncsDirector.Builder
- Builder(MultiStateConfSpace, String, String, String) - Constructor for class edu.duke.cs.osprey.coffee.directors.AffinityDirector.Builder
- Builder(MultiStateConfSpace, String, String, String) - Constructor for class edu.duke.cs.osprey.coffee.directors.KStarDirector.Builder
- Builder(SimpleConfSpace, EnergyMatrix) - Constructor for class edu.duke.cs.osprey.astar.conf.ConfRanker.Builder
- Builder(SimpleConfSpace, EnergyCalculator) - Constructor for class edu.duke.cs.osprey.ematrix.SimpleReferenceEnergies.Builder
- Builder(SimpleConfSpace, EnergyCalculator) - Constructor for class edu.duke.cs.osprey.ematrix.SimplerEnergyMatrixCalculator.Builder
-
Deprecated.
- Builder(SimpleConfSpace, EnergyCalculator) - Constructor for class edu.duke.cs.osprey.energy.ConfEnergyCalculator.Builder
- Builder(SimpleConfSpace, ForcefieldParams) - Constructor for class edu.duke.cs.osprey.energy.EnergyCalculator.Builder
- Builder(DofInfo) - Constructor for class edu.duke.cs.osprey.energy.approximation.ResidueInteractionsApproximator.Builder
- Builder(EnergyMatrix, RCs) - Constructor for class edu.duke.cs.osprey.astar.conf.ConfAStarTree.Builder
- Builder(EnergyMatrix, ConfSpace) - Constructor for class edu.duke.cs.osprey.astar.conf.ConfAStarTree.Builder
- Builder(EnergyMatrix, SimpleConfSpace) - Constructor for class edu.duke.cs.osprey.astar.conf.ConfAStarTree.Builder
- Builder(EnergyMatrix, SimpleConfSpace, EnergyCalculator, ConfEnergyCalculator, String) - Constructor for class edu.duke.cs.osprey.gmec.DEEGMECFinder.Builder
- Builder(EnergyMatrix, PruningMatrix) - Constructor for class edu.duke.cs.osprey.astar.conf.ConfAStarTree.Builder
- Builder(ConfEnergyCalculator) - Constructor for class edu.duke.cs.osprey.ematrix.compiled.EmatCalculator.Builder
- Builder(ConfEnergyCalculator) - Constructor for class edu.duke.cs.osprey.ematrix.compiled.ErefCalculator.Builder
- Builder(ConfEnergyCalculator, TaskExecutor) - Constructor for class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter.Builder
-
Deprecated.
- Builder(ConfEnergyCalculator) - Constructor for class edu.duke.cs.osprey.ematrix.SimplerEnergyMatrixCalculator.Builder
- Builder(ForcefieldParams) - Constructor for class edu.duke.cs.osprey.energy.EnergyCalculator.Builder
- Builder(ForcefieldParams) - Constructor for class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary.Builder
- Builder(ForcefieldParams.Forcefield) - Constructor for class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary.Builder
- Builder(ForcefieldParams, Factory<ForcefieldInteractions, Molecule>, ConfSpace) - Constructor for class edu.duke.cs.osprey.minimization.CpuConfMinimizer.Builder
- Builder(ForcefieldParams, Factory<ForcefieldInteractions, Molecule>, ConfSpace) - Constructor for class edu.duke.cs.osprey.minimization.GpuConfMinimizer.Builder
- Builder(Comets.LME) - Constructor for class edu.duke.cs.osprey.gmec.Comets.Builder
- Builder(MSKStar.LMFE) - Constructor for class edu.duke.cs.osprey.kstar.MSKStar.Builder
- Builder(PruningMatrix, LUTEConfEnergyCalculator) - Constructor for class edu.duke.cs.osprey.lute.LUTEGMECFinder.Builder
- Builder(ResidueTemplateLibrary, ForcefieldParams) - Constructor for class edu.duke.cs.osprey.energy.EnergyCalculator.Builder
-
Deprecated.
- Builder(Molecule) - Constructor for class edu.duke.cs.osprey.confspace.Strand.Builder
- Builder(Residues, ForcefieldParams) - Constructor for class edu.duke.cs.osprey.energy.EnergyCalculator.Builder
-
Deprecated.
- Builder(String, ConfSpaceIteration) - Constructor for class edu.duke.cs.osprey.confspace.MultiStateConfSpace.Builder
-
adds the inital mutable state that defines the sequence space
- Builder(List<SimpleConfSpace>, ForcefieldParams) - Constructor for class edu.duke.cs.osprey.energy.EnergyCalculator.Builder
- buildPolytope() - Method in class edu.duke.cs.osprey.plug.RCPairVDWChecker
- busId - Variable in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuInfo
- ByPosition(ConfEnergyCalculator, int[]) - Constructor for class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.ByPosition
- ByPosition(ConfEnergyCalculator, int[], EnergyCalculator.EnergiedParametricMolecule) - Constructor for class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.ByPosition
- ByResidue(ConfEnergyCalculator, int[]) - Constructor for class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.ByResidue
- ByResidue(ConfEnergyCalculator, EnergyCalculator.EnergiedParametricMolecule) - Constructor for class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.ByResidue
- ByResidue(ResidueForcefieldEnergy) - Constructor for class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.ByResidue
- Byte - Enum constant in enum class edu.duke.cs.osprey.externalMemory.AssignmentsSerializer.Encoding
- Byte - Enum constant in enum class edu.duke.cs.osprey.tools.IntEncoding
- ByteBufferInputStream - Class in edu.duke.cs.osprey.tools
- ByteBufferInputStream(ByteBuffer) - Constructor for class edu.duke.cs.osprey.tools.ByteBufferInputStream
- ByteBufferOutputStream - Class in edu.duke.cs.osprey.tools
- ByteBufferOutputStream(ByteBuffer) - Constructor for class edu.duke.cs.osprey.tools.ByteBufferOutputStream
- byteBuffers - Variable in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- bytes - Variable in class edu.duke.cs.osprey.coffee.nodedb.BlockStore
- bytes - Static variable in class edu.duke.cs.osprey.gpu.Structs.Bool
- bytes - Static variable in class edu.duke.cs.osprey.gpu.Structs.Char8
- bytes - Variable in class edu.duke.cs.osprey.gpu.Structs.Field
- bytes - Static variable in class edu.duke.cs.osprey.gpu.Structs.Float32
- bytes - Static variable in class edu.duke.cs.osprey.gpu.Structs.Float64
- bytes - Static variable in class edu.duke.cs.osprey.gpu.Structs.Int32
- bytes - Static variable in class edu.duke.cs.osprey.gpu.Structs.Int64
- bytes - Variable in enum class edu.duke.cs.osprey.gpu.Structs.Precision
- bytes() - Method in interface edu.duke.cs.osprey.coffee.nodedb.FixedIndex.Serializer
- bytes() - Method in class edu.duke.cs.osprey.gpu.Structs.Struct
-
Calculates the static size of the struct.
- bytes(long) - Method in class edu.duke.cs.osprey.gpu.Structs.Array
C
- c - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Description
- c - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.BondAngle
- c - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DeltaDihedralAngle
- c - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DihedralAngle
- c - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DihedralAnglesMinDist
- c - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralSystem
- C() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.Six12PotentialCoefficient
-
Returns the value of the
Crecord component. - cacheFile - Variable in class edu.duke.cs.osprey.ematrix.compiled.EmatCalculator
- cacheFile - Variable in class edu.duke.cs.osprey.ematrix.SimplerEnergyMatrixCalculator
- CAEquivalent - Variable in class edu.duke.cs.osprey.restypes.ResidueTemplate
- calc() - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFE
- calc() - Method in class edu.duke.cs.osprey.ematrix.compiled.EmatCalculator
- calc() - Method in class edu.duke.cs.osprey.ematrix.compiled.ErefCalculator
- calc() - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrixCalculator
- calc(double) - Method in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- calc(int[], List<PosInter>) - Method in interface edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator
-
Build the conformation and calculate its rigid (ie unminimized) energy, using the provided interactions.
- calc(int[], List<PosInter>) - Method in class edu.duke.cs.osprey.energy.compiled.CPUConfEnergyCalculator
- calc(int[], List<PosInter>) - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- calc(int[], List<PosInter>) - Method in class edu.duke.cs.osprey.energy.compiled.NativeConfEnergyCalculator
- calc(ConfIndex, RCs) - Method in interface edu.duke.cs.osprey.astar.conf.scoring.AStarScorer
- calc(ConfIndex, RCs) - Method in class edu.duke.cs.osprey.astar.conf.scoring.MPLPPairwiseHScorer
- calc(ConfIndex, RCs) - Method in class edu.duke.cs.osprey.astar.conf.scoring.NaiveTraditionalPairwiseHScorer
- calc(ConfIndex, RCs) - Method in class edu.duke.cs.osprey.astar.conf.scoring.NOPAStarScorer
- calc(ConfIndex, RCs) - Method in class edu.duke.cs.osprey.astar.conf.scoring.PairwiseGScorer
- calc(ConfIndex, RCs) - Method in class edu.duke.cs.osprey.astar.conf.scoring.TraditionalPairwiseHScorer
- calc(ConfIndex, RCs) - Method in class edu.duke.cs.osprey.lute.LUTEGScorer
- calc(ConfIndex, RCs) - Method in class edu.duke.cs.osprey.lute.LUTEHScorer
- calc(ConfIndex, RCs) - Method in class edu.duke.cs.osprey.markstar.UpperBoundScorer
- calc(SeqAStarNode.Assignments) - Method in class edu.duke.cs.osprey.astar.seq.scoring.NOPSeqAStarScorer
- calc(SeqAStarNode.Assignments) - Method in interface edu.duke.cs.osprey.astar.seq.scoring.SeqAStarScorer
-
calculate a score for the given node
- calc(RCTuple, ResidueInteractions) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrixCalculator
- calc(SimpleConfSpace.Position, SimpleConfSpace.ResidueConf) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrixCalculator
- calc(SimpleConfSpace.Position, SimpleConfSpace.ResidueConf, SimpleConfSpace.Position, SimpleConfSpace.ResidueConf) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrixCalculator
- calc(SimpleConfSpace.Position, SimpleConfSpace.ResidueConf, String) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrixCalculator
- calc(EnergyFunction, RCTuple, ParameterizedMoleculeCopy) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator.Cpu
-
Deprecated.
- calc(EnergyFunction, RCTuple, ParameterizedMoleculeCopy) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator.Cuda
-
Deprecated.
- calc(TaskExecutor) - Method in class edu.duke.cs.osprey.ematrix.compiled.EmatCalculator
- calc(TaskExecutor) - Method in class edu.duke.cs.osprey.ematrix.compiled.ErefCalculator
- calc(BigExp) - Method in class edu.duke.cs.osprey.coffee.FreeEnergyCalculator
- calc(MathTools.BigDecimalBounds) - Method in class edu.duke.cs.osprey.coffee.FreeEnergyCalculator
- calc(BigDecimal) - Method in class edu.duke.cs.osprey.coffee.FreeEnergyCalculator
- calc(Map<Comets.State, Double>) - Method in class edu.duke.cs.osprey.gmec.Comets.LME
-
calculate the exact value of the LME
- calc(Map<MSKStar.State, MathTools.DoubleBounds>) - Method in class edu.duke.cs.osprey.kstar.MSKStar.LMFE
-
calculate the LMFE bounds based on bounds on free energies
- calc_dih_ang(double[], double[], double[]) - Method in class edu.duke.cs.osprey.dof.deeper.perts.TripeptideClosure
- calcAllEnergies(List<ConfSearch.ScoredConf>) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- calcAllEnergies(List<ConfSearch.ScoredConf>, boolean) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- calcAllEnergies(List<ConfSearch.ScoredConf>, boolean, ConfDB.ConfTable) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- calcAllEnergies(List<ConfSearch.ScoredConf>, ConfDB.ConfTable) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- calcAllSeqGMECs() - Method in class edu.duke.cs.osprey.gmec.SeqGMECFinder
- calcBestSequences() - Method in class edu.duke.cs.osprey.astar.comets.NewCOMETSDoer
- calcBestSequences() - Method in class edu.duke.cs.osprey.control.COMETSDoer
- calcBestSequences() - Method in class edu.duke.cs.osprey.control.MSKStarDoer
- calcBounds() - Method in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Values
- calcBytes(int) - Method in interface edu.duke.cs.osprey.gpu.cuda.Kernel.SharedMemCalculator
- calcBytes(int) - Method in class edu.duke.cs.osprey.gpu.cuda.Kernel.SharedMemCalculator.None
- calcCellSize() - Method in class edu.duke.cs.osprey.confspace.Sequence
- calcConstantTerm - Variable in class edu.duke.cs.osprey.ematrix.SimplerEnergyMatrixCalculator
- calcDifferential(ConfIndex, RCs, int, int) - Method in interface edu.duke.cs.osprey.astar.conf.scoring.AStarScorer
- calcDifferential(ConfIndex, RCs, int, int) - Method in class edu.duke.cs.osprey.astar.conf.scoring.NOPAStarScorer
- calcDifferential(ConfIndex, RCs, int, int) - Method in class edu.duke.cs.osprey.astar.conf.scoring.PairwiseGScorer
- calcDifferential(ConfIndex, RCs, int, int) - Method in class edu.duke.cs.osprey.astar.conf.scoring.TraditionalPairwiseHScorer
- calcDifferential(SeqAStarNode.Assignments, int, int) - Method in class edu.duke.cs.osprey.astar.seq.scoring.NOPSeqAStarScorer
- calcDifferential(SeqAStarNode.Assignments, int, int) - Method in interface edu.duke.cs.osprey.astar.seq.scoring.SeqAStarScorer
-
calculate a score for a given assignment, using the parent node to optimize, if possible
- calcDofMatrix() - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyMatrixCalculator
-
Deprecated.
- calcEmats() - Method in class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceInfo
- calcEnergy(double, double, double[]) - Method in class edu.duke.cs.osprey.energy.compiled.AmberEnergyCalculator
- calcEnergy(double, double, double[]) - Method in class edu.duke.cs.osprey.energy.compiled.EEF1EnergyCalculator
- calcEnergy(double, double, double[]) - Method in interface edu.duke.cs.osprey.energy.compiled.EnergyCalculator
-
calculate position-pair energy
- calcEnergy(int[]) - Method in class edu.duke.cs.osprey.lute.LUTEConfEnergyCalculator
- calcEnergy(int[], List<PosInter>) - Method in interface edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator
-
Calculate the rigid (ie unminimized) energy of the conformation, using the provided interactions.
- calcEnergy(int[], List<PosInter>) - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- calcEnergy(int[], List<PosInter>) - Method in class edu.duke.cs.osprey.energy.compiled.NativeConfEnergyCalculator
- calcEnergy(AssignedCoords) - Method in interface edu.duke.cs.osprey.energy.compiled.EnergyCalculator
-
calculate the total energy for the conformation
- calcEnergy(AssignedCoords, PosInter) - Method in interface edu.duke.cs.osprey.energy.compiled.EnergyCalculator
-
calculate the energy of just the given position interaction
- calcEnergy(AssignedCoords, List<PosInter>) - Method in class edu.duke.cs.osprey.energy.compiled.CPUConfEnergyCalculator
- calcEnergy(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
Calculate energy of a scored conformation.
- calcEnergy(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.gmec.GMECConfEnergyCalculator.Async.Adapter
-
Deprecated.
- calcEnergy(ConfSearch.ScoredConf) - Method in interface edu.duke.cs.osprey.gmec.GMECConfEnergyCalculator
-
Deprecated.
- calcEnergy(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.gmec.MinimizingConfEnergyCalculator
-
Deprecated.
- calcEnergy(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.lute.LUTEConfEnergyCalculator
- calcEnergy(ConfSearch.ScoredConf, ConfDB.ConfTable) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
Calculate energy of a scored conformation, using the specified ConfDB table as a cache.
- calcEnergy(ConfSearch.ScoredConf, ConfDB.ConfTable, Supplier<ConfSearch.EnergiedConf>) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- calcEnergy(ConfSearch.ScoredConf, ResidueInteractions) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
Calculate energy of a scored conformation with specified residue interactions.
- calcEnergy(ConfSearch.ScoredConf, ResidueInteractions) - Method in class edu.duke.cs.osprey.lute.LUTEConfEnergyCalculator
- calcEnergy(ConfSearch.ScoredConf, ResidueInteractions, ConfDB.ConfTable) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
Calculate energy of a scored conformation with specified residue interactions, using the specified ConfDB table as a cache.
- calcEnergy(ConfSearch.ScoredConf, List<PosInter>) - Method in interface edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator
- calcEnergy(ParametricMolecule, ResidueInteractions) - Method in class edu.duke.cs.osprey.energy.EnergyCalculator
-
Calculate the energy of a molecule.
- calcEnergy(ParametricMolecule, ResidueInteractions, ResidueInteractionsApproximator) - Method in class edu.duke.cs.osprey.energy.EnergyCalculator
-
Calculate the energy of a molecule.
- calcEnergy(RCTuple) - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- calcEnergy(RCTuple) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
Calculate the energy of a molecule fragment generated from a conformation space using residue interactions generated by the energy partition.
- calcEnergy(RCTuple, ConfDB.ConfTable) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
Version of
ConfEnergyCalculator.calcEnergy(RCTuple)using the specified ConfDB table as a cache. - calcEnergy(RCTuple, ResidueInteractions) - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- calcEnergy(RCTuple, ResidueInteractions) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
Calculate the energy of a molecule fragment generated from a conformation space.
- calcEnergy(RCTuple, ResidueInteractions) - Method in class edu.duke.cs.osprey.lute.LUTEConfEnergyCalculator
- calcEnergy(RCTuple, ResidueInteractions, ConfDB.ConfTable) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
Version of
ConfEnergyCalculator.calcEnergy(RCTuple,ResidueInteractions)using the specified ConfDB table as a cache. - CalcEnergy - Enum constant in enum class edu.duke.cs.osprey.control.Main.Command
- calcEnergyAsync(ConfSearch.ScoredConf, ConfDB.ConfTable, TaskExecutor.TaskListener<ConfSearch.EnergiedConf>) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
Asynchronous version of
ConfEnergyCalculator.calcEnergy(ScoredConf), using the specified ConfDB table as a cache. - calcEnergyAsync(ConfSearch.ScoredConf, ResidueInteractions, ConfDB.ConfTable, TaskExecutor.TaskListener<ConfSearch.EnergiedConf>) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
Asynchronous version of
ConfEnergyCalculator.calcEnergy(ScoredConf), using the specified ConfDB table as a cache. - calcEnergyAsync(ConfSearch.ScoredConf, ResidueInteractions, TaskExecutor.TaskListener<ConfSearch.EnergiedConf>) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
Asynchronous version of
ConfEnergyCalculator.calcEnergy(ScoredConf). - calcEnergyAsync(ConfSearch.ScoredConf, GMECConfEnergyCalculator.Async.Listener) - Method in class edu.duke.cs.osprey.gmec.GMECConfEnergyCalculator.Async.Adapter
-
Deprecated.
- calcEnergyAsync(ConfSearch.ScoredConf, GMECConfEnergyCalculator.Async.Listener) - Method in interface edu.duke.cs.osprey.gmec.GMECConfEnergyCalculator.Async
-
Deprecated.
- calcEnergyAsync(ConfSearch.ScoredConf, GMECConfEnergyCalculator.Async.Listener) - Method in class edu.duke.cs.osprey.gmec.MinimizingConfEnergyCalculator
-
Deprecated.
- calcEnergyAsync(ConfSearch.ScoredConf, TaskExecutor.TaskListener<ConfSearch.EnergiedConf>) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
Asynchronous version of
ConfEnergyCalculator.calcEnergy(ScoredConf). - calcEnergyAsync(ParametricMolecule, ResidueInteractions, TaskExecutor.TaskListener<EnergyCalculator.EnergiedParametricMolecule>) - Method in class edu.duke.cs.osprey.energy.EnergyCalculator
-
Asynchronous version of
EnergyCalculator.calcEnergy(ParametricMolecule,ResidueInteractions). - calcEnergyAsync(RCTuple, ConfDB.ConfTable, TaskExecutor.TaskListener<Double>) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
Asynchronous version of
ConfEnergyCalculator.calcEnergy(RCTuple,ConfDB.ConfTable). - calcEnergyAsync(RCTuple, ResidueInteractions, ConfDB.ConfTable, TaskExecutor.TaskListener<Double>) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
Asynchronous version of
ConfEnergyCalculator.calcEnergy(RCTuple,ResidueInteractions,ConfDB.ConfTable). - calcEnergyAsync(RCTuple, ResidueInteractions, TaskExecutor.TaskListener<EnergyCalculator.EnergiedParametricMolecule>) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
Asynchronous version of
ConfEnergyCalculator.calcEnergy(RCTuple,ResidueInteractions). - calcEnergyAsync(RCTuple, TaskExecutor.TaskListener<EnergyCalculator.EnergiedParametricMolecule>) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
Asynchronous version of
ConfEnergyCalculator.calcEnergy(RCTuple). - calcEnergyMatrix() - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyMatrixCalculator
-
Deprecated.
- calcEnergyMatrix() - Method in class edu.duke.cs.osprey.ematrix.SimplerEnergyMatrixCalculator
-
Computes a matrix of energies between pairs of residue conformations to be used by A* search.
- calcEnergyMatrix(File) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyMatrixCalculator
-
Deprecated.
- calcEnergyPair(AssignedCoords, int, int) - Method in interface edu.duke.cs.osprey.energy.compiled.EnergyCalculator
-
calculate the pair energy between position i1 and position i2
- calcEnergySingle(AssignedCoords, int) - Method in interface edu.duke.cs.osprey.energy.compiled.EnergyCalculator
-
calculate the single energy of position i
- calcEnergyStatic(AssignedCoords) - Method in interface edu.duke.cs.osprey.energy.compiled.EnergyCalculator
-
get the internal energy of the static atoms
- calcEnergyStatic(AssignedCoords, int) - Method in interface edu.duke.cs.osprey.energy.compiled.EnergyCalculator
-
calculate the pair energy between position i and the static atoms
- calcEw() - Method in class edu.duke.cs.osprey.kstar.pruning.APrioriPruningProver
- calcExpansion(ArrayList<RCTuple>) - Method in class edu.duke.cs.osprey.tupexp.TupleExpander
- calcExpansionCliqueTriples(double) - Method in class edu.duke.cs.osprey.tupexp.TupExpChooser
- calcExpansionResTriples(int) - Method in class edu.duke.cs.osprey.tupexp.TupExpChooser
- calcFreeEnergyBounds() - Method in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Values
- calcFreeEnergyBounds(MathTools.DoubleBounds) - Method in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Values
- calcFreeEnergyBoundsPrecise() - Method in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Values
- calcFreeEnergyLowerBound() - Method in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Values
- calcFreeEnergyLowerBoundPrecise() - Method in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Values
- calcFreeEnergyUpperBound() - Method in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Values
- calcFreeEnergyUpperBoundPrecise() - Method in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Values
- calcG() - Method in class edu.duke.cs.osprey.minimization.IdealSeparableReference
- calcG(int[]) - Method in class edu.duke.cs.osprey.voxq.VoxelGCalculator
- calcGMEC() - Method in class edu.duke.cs.osprey.gmec.DEEGMECFinder
- calcGMEC() - Method in class edu.duke.cs.osprey.gmec.GMECFinder
- calcGMEC(double) - Method in class edu.duke.cs.osprey.gmec.DEEGMECFinder
- calcGMECEnergy() - Method in class edu.duke.cs.osprey.gmec.GMECFinder
- calcI0() - Method in class edu.duke.cs.osprey.kstar.pruning.APrioriPruningProver
- calcIntraEnergy(int, int) - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- calcIntraEnergy(int, int) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- CalcKStar - Enum constant in enum class edu.duke.cs.osprey.control.Main.Command
- calcKStarScores() - Method in class edu.duke.cs.osprey.control.KStarCalculator
-
Deprecated.
- calcLigandResEnergy(Residue) - Method in class edu.duke.cs.osprey.energy.LigandResEnergies
- CalcLigResE - Enum constant in enum class edu.duke.cs.osprey.control.Main.Command
- calcLowerBound() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Values
- calcLowerBound() - Method in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Values
- calcLowerBound() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound.Values
- calcLowerBound() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync.Values
- calcLowerBound() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid.Values
- calcLowerBound() - Method in class edu.duke.cs.osprey.paste.PastePartitionFunction.Values
- calcMatrices(EnergyMatrix, DofMatrix) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyMatrixCalculator
-
Deprecated.
- calcMatrix(SearchProblem.MatrixType) - Method in class edu.duke.cs.osprey.confspace.SearchProblem
- calcMatrix(PrecomputedMatrices.MatrixType) - Method in class edu.duke.cs.osprey.gmec.PrecomputedMatrices
- calcMaxBlockThreads() - Method in class edu.duke.cs.osprey.gpu.cuda.Kernel.Function
- calcMedoid(Collection<double[]>) - Static method in class edu.duke.cs.osprey.structure.analysis.AngleClustering
- calcModes(Map<String, List<TemplateChooser.MeasuredRes>>, List<String>) - Static method in class edu.duke.cs.osprey.structure.analysis.TemplateChooser
- calcNumSequences() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- calcOrMinimize(int[], List<PosInter>, boolean) - Method in interface edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator
- calcOrMinimizeEnergy(int[], List<PosInter>, boolean) - Method in interface edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator
- calcOrMinimizeEnergy(ConfSearch.ScoredConf, List<PosInter>, boolean) - Method in interface edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator
- calcOverfittingScore() - Method in class edu.duke.cs.osprey.lute.LUTE
- calcPair(int, int, int, int) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator
-
Deprecated.
- calcPair(int, int, int, int, ParameterizedMoleculeCopy) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator
-
Deprecated.
- calcPair(int, int, int, int, ParameterizedMoleculeCopy) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator.Cpu
-
Deprecated.
- calcPair(int, int, int, int, ParameterizedMoleculeCopy) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator.Cuda
-
Deprecated.
- calcPairEnergy(int, int, int, int) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- calcPairEnergy(RCTuple) - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- calcPairEnergy(RCTuple) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- calcPairwiseExpansion() - Method in class edu.duke.cs.osprey.tupexp.TupExpChooser
- calcPEM() - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrixCalculator
- calcPEM() - Method in class edu.duke.cs.osprey.ematrix.NewEPICMatrixCalculator
- calcPEMDistributed() - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrixCalculator
- calcPEMLocally() - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrixCalculator
- calcPfunc(int, BigDecimal) - Method in class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceInfo
- calcPfunc(int, BigDecimal, PastePartitionFunction.Result) - Method in class edu.duke.cs.osprey.paste.Paste.ConfSpaceInfo
- calcPfunc(TaskExecutor.ContextGroup, Sequence, BigDecimal) - Method in class edu.duke.cs.osprey.kstar.KStar.ConfSpaceInfo
- calcPolytopeConstr() - Method in class edu.duke.cs.osprey.plug.RCPairVDWChecker
- calcPolytopeConstr(ArrayList<String>) - Method in class edu.duke.cs.osprey.plug.RCPairVDWChecker
- calcPrecise(double) - Method in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- calcReferenceEnergies() - Method in class edu.duke.cs.osprey.ematrix.SimplerEnergyMatrixCalculator
-
Calculates a reference energy for each residue position and residue type based on the minimum energy of all residue conformations at that position and residue type.
- calcSampleTuples(int[]) - Method in class edu.duke.cs.osprey.tupexp.TupleIndexMatrix
- calcScore(SplitWorld, RC, double) - Method in class edu.duke.cs.osprey.partcr.scorers.NopRCScorer
- calcScore(SplitWorld, RC, double) - Method in interface edu.duke.cs.osprey.partcr.scorers.RCScorer
- calcScore(SplitWorld, RC, double) - Method in class edu.duke.cs.osprey.partcr.scorers.SplitsRCScorer
- calcScore(SplitWorld, RC, double) - Method in class edu.duke.cs.osprey.partcr.scorers.VolumeRCScorer
- calcSequences() - Method in class edu.duke.cs.osprey.gmec.GMECFinder
- calcSequences(double) - Method in class edu.duke.cs.osprey.gmec.GMECFinder
- calcShellEnergy(RCTuple) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- calcSingle(int, int) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator
-
Deprecated.
- calcSingle(int, int, ParameterizedMoleculeCopy) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator
-
Deprecated.
- calcSingle(int, int, ParameterizedMoleculeCopy) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator.Cpu
-
Deprecated.
- calcSingle(int, int, ParameterizedMoleculeCopy) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator.Cuda
-
Deprecated.
- calcSingleEnergy(int, int) - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- calcSingleEnergy(int, int) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- calcSingleEnergy(RCTuple) - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- calcSingleEnergy(RCTuple) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- calcSolns() - Method in class edu.duke.cs.osprey.dof.deeper.perts.LoopClosureAdjustment
- calcSpecialCenter() - Method in class edu.duke.cs.osprey.plug.VoxelVDWListChecker
- calcSubEnergy(AssignedCoords, List<PosInter>, Set<Integer>) - Method in class edu.duke.cs.osprey.energy.compiled.CPUConfEnergyCalculator
- calcTransRot(double) - Method in class edu.duke.cs.osprey.dof.deeper.perts.Backrub
- calcTupleEnergy(RCTuple) - Method in class edu.duke.cs.osprey.ematrix.TermECalculator
- calcTupleEnergy(RCTuple) - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- calcTupleEnergy(RCTuple) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- calcTupleEnergyLazy(RCTuple) - Method in class edu.duke.cs.osprey.ematrix.TermECalculator
- calculateTotalEnergy() - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldEnergy
- calcUnprunedConfsLowerBound() - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
-
calculates an lower bound on the number of conformations remaining in the conformation space after all singles and pairs pruning.
- calcUnprunedConfsUpperBound() - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
-
Calculates an upper bound on the number of conformations remaining in the conformation space after all singles and pairs pruning.
- calcUpperBound() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Values
- calcUpperBound() - Method in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Values
- calcUpperBound() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound.Values
- calcUpperBound() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync.Values
- calcUpperBound() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid.Values
- calcUpperBound() - Method in class edu.duke.cs.osprey.paste.PastePartitionFunction.Values
- calcVoxel(List<double[]>) - Static method in class edu.duke.cs.osprey.structure.analysis.AngleClustering
- calcWeightSumUpperBound(ConfSearch) - Method in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- calcZMat(int) - Method in class edu.duke.cs.osprey.coffee.Coffee
-
Compute a Z matrix.
- calcZSum(Sequence, MultiStateConfSpace.State) - Method in class edu.duke.cs.osprey.sofea.Sofea
-
WARNING: naive brute force method, for testing small trees only
- callback - Variable in class edu.duke.cs.osprey.coffee.NodeStats.Reporter
- canAddConstr(LinearConstraint, ArrayList<LinearConstraint>) - Static method in class edu.duke.cs.osprey.plug.LPChecks
- canContinue() - Method in enum class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Status
- canContinue() - Method in class edu.duke.cs.osprey.kstar.KSCalc
- canContinue() - Method in enum class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Status
- canContinue() - Method in enum class edu.duke.cs.osprey.paste.PastePartitionFunction.Status
- canMutateTo(ResidueTemplate) - Static method in class edu.duke.cs.osprey.restypes.HardCodedResidueInfo
- canPrune - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.SequenceInfo
- canPruneNode(COMETSNode) - Method in class edu.duke.cs.osprey.astar.comets.NewCOMETSTree
- canPruneNode(FullAStarNode) - Method in class edu.duke.cs.osprey.astar.comets.COMETSTree
- canPruneNode(T) - Method in class edu.duke.cs.osprey.astar.AStarTree
- canSatisfy(int) - Method in class edu.duke.cs.osprey.kstar.KSConfQ
- canSatisfy(int) - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- canSpawnChildren() - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
-
ie, is it possible to spawn any children in the future?
- CantWriteException(File, Throwable) - Constructor for exception edu.duke.cs.osprey.tools.ObjectIO.CantWriteException
- canUseHotByConfError() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- canUseHotByConfError(double) - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- canUseHotByManualSelection() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- capacity - Variable in class edu.duke.cs.osprey.coffee.directors.BestSet
- cartesianProduct(List<List<T>>) - Static method in class edu.duke.cs.osprey.tools.MathTools
- cast(double) - Method in enum class edu.duke.cs.osprey.gpu.Structs.Precision
- cast(PartitionFunction) - Static method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.WithConfDB
-
Try to cast the pfunc to WithConfDB, but throw a nice error if the cast fails.
- cast(TaskExecutor.Task<T>) - Static method in class edu.duke.cs.osprey.parallelism.Cluster.Task
-
Makes sure the task is a cluster task.
- CatPark - Class in edu.duke.cs.osprey.tests
-
Playground for CATS Using it to make a figure for the paper Meant to run in 2O9S_L2 directory http://www.catster.com/lifestyle/why-there-is-no-such-thing-as-a-cat-park
- CatPark() - Constructor for class edu.duke.cs.osprey.tests.CatPark
- CATSStrandFlex - Class in edu.duke.cs.osprey.confspace
-
StrandFlex representing a range of residues with all dihedral DOFs subject to loop closure //(i.e.
- CATSStrandFlex(Strand, String, String) - Constructor for class edu.duke.cs.osprey.confspace.CATSStrandFlex
- CCDKernelCuda - Class in edu.duke.cs.osprey.gpu.cuda.kernels
- CCDKernelCuda(GpuStream) - Constructor for class edu.duke.cs.osprey.gpu.cuda.kernels.CCDKernelCuda
- CCDMinimizer - Class in edu.duke.cs.osprey.minimization
- CCDMinimizer(ObjectiveFunction, boolean) - Constructor for class edu.duke.cs.osprey.minimization.CCDMinimizer
- center - Variable in class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel.Interval
- center - Variable in class edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry
- Central - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.DominantBaseline
- centroid - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Description
- cfp - Variable in class edu.duke.cs.osprey.kstar.KSAbstract
- cfp - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- cfp - Variable in class edu.duke.cs.osprey.multistatekstar.MSKStarSettings
- CGTupleFitter - Class in edu.duke.cs.osprey.tupexp
- CGTupleFitter() - Constructor for class edu.duke.cs.osprey.tupexp.CGTupleFitter
- CGTupleFitter(TupleIndexMatrix, ArrayList<int[]>, int, double[], ArrayList<Double>) - Constructor for class edu.duke.cs.osprey.tupexp.CGTupleFitter
- chain - Variable in class edu.duke.cs.osprey.design.models.Residue
- chainId - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.ResInfo
- char8() - Static method in class edu.duke.cs.osprey.gpu.Structs
- Char8() - Constructor for class edu.duke.cs.osprey.gpu.Structs.Char8
- char8array() - Static method in class edu.duke.cs.osprey.gpu.Structs
- charge - Variable in class edu.duke.cs.osprey.structure.Atom
- CHARMM19 - Enum constant in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.Forcefield
- CHARMM19NEUTRAL - Enum constant in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.Forcefield
- CHARMM22 - Enum constant in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.Forcefield
- check() - Method in class edu.duke.cs.osprey.coffee.Coffee.StateConfig
- checkAngles(double, double, int) - Method in class edu.duke.cs.osprey.dof.deeper.RamachandranChecker
- checkAPPP() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- checkBonds() - Method in class edu.duke.cs.osprey.structure.Residue
- checkByAAType(Residue) - Method in class edu.duke.cs.osprey.dof.deeper.RamachandranChecker
- checkConfig() - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.State
-
make sure the state is fully configured
- checkConfig() - Method in class edu.duke.cs.osprey.gmec.Comets.State
-
make sure the state is fully configured
- checkConfig() - Method in class edu.duke.cs.osprey.kstar.MSKStar.State
-
make sure the state is fully configured
- checkConsistency(KAStarNode) - Method in class edu.duke.cs.osprey.kstar.KAStarNode
- checkConstraints(int) - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
-
see if partition function satisfies constraints involving this state only
- checkConstraints(int, boolean) - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
-
see if partition function satisfies either lower or upper bound constraints involving this state only
- checkDOFList(ArrayList<DegreeOfFreedom>) - Method in class edu.duke.cs.osprey.plug.RCTuplePolytope
- checkException() - Method in class edu.duke.cs.osprey.parallelism.ConcurrentTaskExecutor
- checkInternalLimitSet() - Static method in class edu.duke.cs.osprey.externalMemory.ExternalMemory
-
Throw a
ExternalMemory.InternalMemoryLimitNotSetExceptionif the internal memory limit has not yet been set byExternalMemory.setInternalLimit(int). - checkout() - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStreamPool
- checkout() - Method in class edu.duke.cs.osprey.gpu.opencl.GpuQueuePool
- checkout() - Method in class edu.duke.cs.osprey.tools.ObjectPool
- checkout(int) - Method in class edu.duke.cs.osprey.gpu.cuda.BufferPool
- checkoutStream() - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
-
Check out a GPU stream.
- checkPointDir - Variable in class edu.duke.cs.osprey.kstar.KSAbstract
- checkPointExists() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- checkPointFilePath - Variable in class edu.duke.cs.osprey.kstar.KSAbstract
- checkpointInterval - Static variable in class edu.duke.cs.osprey.kstar.KSAbstract
- checkPointPath - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- checkPrePro(Residue) - Method in class edu.duke.cs.osprey.dof.deeper.RamachandranChecker
- checkRedundancy(LinearConstraint) - Method in class edu.duke.cs.osprey.plug.VoxConstrCache
- checkSocketIOThread() - Static method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
- checkSortedPositions() - Method in class edu.duke.cs.osprey.confspace.RCTuple
- checkSupported() - Static method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
-
Throws a helpful error message if this energy calculator is not supported.
- checkTemplateAtomNames() - Method in class edu.duke.cs.osprey.structure.Residue
- checkValid() - Method in class edu.duke.cs.osprey.dof.FreeDihedral
- checkVDW() - Method in class edu.duke.cs.osprey.plug.RCPairVDWChecker
- childConf - Variable in class edu.duke.cs.osprey.astar.ConfTree
- ci - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle
- Circle - Enum constant in enum class edu.duke.cs.osprey.tools.resultdoc.Plot.PointType
- CircleFilled - Enum constant in enum class edu.duke.cs.osprey.tools.resultdoc.Plot.PointType
- clamp(int, double) - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- clamp(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- clampDelta(int, double, double) - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- clampDelta(DoubleMatrix1D, DoubleMatrix1D) - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- Classic - Static variable in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator.Conditions
-
The time-tested consitions used in Osprey versions of years past, ie room temperature
- classifier - Variable in class edu.duke.cs.osprey.structure.Probe.Template
- classifyAtom(Atom) - Method in class edu.duke.cs.osprey.structure.AtomNeighbors
- classifyAtom(Atom) - Method in class edu.duke.cs.osprey.structure.ProbeAtomNeighbors
- clean() - Method in class edu.duke.cs.osprey.confspace.ConfDB
- clean() - Method in class edu.duke.cs.osprey.confspace.ConfDB.DBs
- clean() - Method in class edu.duke.cs.osprey.energy.EnergyCalculator
- clean() - Method in interface edu.duke.cs.osprey.energy.EnergyFunction
- clean() - Method in class edu.duke.cs.osprey.energy.forcefield.GpuForcefieldEnergy
- clean() - Method in class edu.duke.cs.osprey.gmec.MinimizingConfEnergyCalculator
-
Deprecated.
- clean() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ResidueCudaCCDMinimizer
- clean() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ResidueForcefieldEnergyCuda
- clean() - Method in class edu.duke.cs.osprey.minimization.CudaCCDMinimizer
- clean() - Method in interface edu.duke.cs.osprey.minimization.Minimizer
- clean() - Method in class edu.duke.cs.osprey.minimization.SimpleCCDMinimizer
- clean() - Method in class edu.duke.cs.osprey.parallelism.Cluster.Client
- clean() - Method in class edu.duke.cs.osprey.parallelism.Cluster.Member
- clean() - Method in class edu.duke.cs.osprey.parallelism.TaskExecutor
- clean() - Method in class edu.duke.cs.osprey.parallelism.ThreadPoolTaskExecutor
- clean() - Method in class edu.duke.cs.osprey.parallelism.Threads
- clean() - Method in class edu.duke.cs.osprey.parallelism.WorkThread
- cleanAndWait(int) - Method in class edu.duke.cs.osprey.parallelism.Threads
- cleanIfNeeded(EnergyFunction) - Static method in class edu.duke.cs.osprey.energy.EnergyFunction.Tools
- cleanIfNeeded(Minimizer) - Static method in class edu.duke.cs.osprey.minimization.Minimizer.Tools
- cleanup() - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyMatrixCalculator
-
Deprecated.
- cleanup() - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyMatrixCalculator.Cpu
-
Deprecated.
- cleanup() - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyMatrixCalculator.Cuda
-
Deprecated.
- cleanup() - Method in class edu.duke.cs.osprey.energy.EnergyCalculator.Type.Context
- cleanup() - Method in class edu.duke.cs.osprey.energy.GpuEnergyFunctionGenerator
- cleanup() - Static method in class edu.duke.cs.osprey.externalMemory.ExternalMemory
-
Clean up resources used by the external memory system.
- cleanup() - Method in interface edu.duke.cs.osprey.gmec.ConfPrinter
- cleanup() - Method in class edu.duke.cs.osprey.gmec.LoggingConfPrinter
- cleanup() - Method in class edu.duke.cs.osprey.gpu.cuda.BufferPool
- cleanup() - Method in class edu.duke.cs.osprey.gpu.cuda.Context
- cleanup() - Method in class edu.duke.cs.osprey.gpu.cuda.CUBuffer
- cleanup() - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- cleanup() - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStreamPool
- cleanup() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.CCDKernelCuda
- cleanup() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ForcefieldKernelCuda
- cleanup() - Method in interface edu.duke.cs.osprey.gpu.ForcefieldKernel
- cleanup() - Method in class edu.duke.cs.osprey.gpu.opencl.GpuQueue
- cleanup() - Method in class edu.duke.cs.osprey.gpu.opencl.GpuQueuePool
- cleanup() - Method in class edu.duke.cs.osprey.gpu.opencl.Kernel
- cleanup() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.ForcefieldKernelOpenCL
- cleanup() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.TestFancyKernel
- cleanup() - Method in class edu.duke.cs.osprey.gpu.opencl.ProfilingEvents
- cleanup() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel0
- cleanup() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- cleanup() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel2
- cleanup() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFTraditional
- cleanup() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- cleanup() - Method in class edu.duke.cs.osprey.minimization.ConfMinimizer.Async
- cleanup() - Method in class edu.duke.cs.osprey.minimization.ConfMinimizer
- cleanup() - Method in class edu.duke.cs.osprey.minimization.GpuConfMinimizer
- cleanup() - Method in interface edu.duke.cs.osprey.minimization.LineSearcher.NeedsCleanup
- cleanup() - Method in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized
- cleanup() - Method in class edu.duke.cs.osprey.parallelism.TimingThread
- cleanUp(boolean) - Method in class edu.duke.cs.osprey.kstar.KSConfQ
- cleanUp(boolean) - Method in class edu.duke.cs.osprey.kstar.KSPStarCalculator
- cleanupStrandInfoCache() - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFFactory
-
Deprecated.
- cleanWithoutCrashing() - Method in interface edu.duke.cs.osprey.tools.AutoCleanable
- clear() - Method in class edu.duke.cs.osprey.coffee.directors.BestSet
- clear() - Method in interface edu.duke.cs.osprey.coffee.nodedb.FixedIndex
-
Removes all items.
- clear() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex
- clear() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodePerformance
- clear() - Method in class edu.duke.cs.osprey.coffee.nodedb.PriorityDequeFixedIndex
- clear() - Method in class edu.duke.cs.osprey.coffee.NodeStats.Values
- clear() - Method in class edu.duke.cs.osprey.confspace.Conf.Map
- clear() - Method in class edu.duke.cs.osprey.confspace.Conf.Set
- clear() - Method in class edu.duke.cs.osprey.confspace.TupleTree
- clear() - Method in class edu.duke.cs.osprey.ematrix.LazyEnergyMatrix
- clear() - Method in class edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger
- clear() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.ConfSpaceInfo
- clear() - Method in class edu.duke.cs.osprey.kstar.KStar.ConfSpaceInfo
- clear() - Method in class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceInfo
- clear() - Method in class edu.duke.cs.osprey.restypes.ResidueEntropies
- clear() - Method in class edu.duke.cs.osprey.structure.Residues
- clear() - Method in class edu.duke.cs.osprey.tools.BigMath
- clear() - Method in class edu.duke.cs.osprey.tools.ObjectPool
- clear(int) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
-
Remove all the nodes from the given state
- clear(int) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices
- clear(int[]) - Static method in class edu.duke.cs.osprey.confspace.Conf
- clearLocal(int) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
- clearOneBody(int, int) - Method in class edu.duke.cs.osprey.ematrix.LazyEnergyMatrix
- ClearOperation - Class in edu.duke.cs.osprey.coffee.nodedb
-
Deletes all nodes for a state
- ClearOperation() - Constructor for class edu.duke.cs.osprey.coffee.nodedb.ClearOperation
- ClearOperation(int) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.ClearOperation
- clearPairwise(int, int, int, int) - Method in class edu.duke.cs.osprey.ematrix.LazyEnergyMatrix
- clearRefs() - Method in class edu.duke.cs.osprey.astar.conf.ConfSearchCache.Entry
- clearResidueEntropies() - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary.Builder
-
By default, residue entropies are added for natual amio acids
- clearRotamers() - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary.Builder
-
By default, the Lovell rotamer library is added.
- clearSomeResults() - Method in class edu.duke.cs.osprey.paste.PastePartitionFunction.Result
- clearTemplateCoords() - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary.Builder
-
By default, template coordinates for natual amino acids are added.
- clearTemplates() - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary.Builder
-
By default, templates for natual amino acids are added.
- Client(Parallelism) - Constructor for class edu.duke.cs.osprey.parallelism.Cluster.Client
- clientIsMember - Variable in class edu.duke.cs.osprey.parallelism.Cluster
- clique2PairTriples(int) - Method in class edu.duke.cs.osprey.confspace.TupleEnumerator
- clone() - Method in class edu.duke.cs.osprey.structure.Residues
- close() - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- close() - Method in class edu.duke.cs.osprey.coffee.ClusterMember.DynamicPartition
- close() - Method in class edu.duke.cs.osprey.coffee.nodedb.BlockStore
- close() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
- close() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices
- close() - Method in class edu.duke.cs.osprey.coffee.NodeProcessor
- close() - Method in class edu.duke.cs.osprey.coffee.NodeStats.Reporter
- close() - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqDB
- close() - Method in class edu.duke.cs.osprey.confspace.ConfDB
- close() - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- close() - Method in class edu.duke.cs.osprey.confspace.ConfSearch.MultiSplitter.Stream
- close() - Method in class edu.duke.cs.osprey.control.SpecialWarningLog
- close() - Method in interface edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator
- close() - Method in class edu.duke.cs.osprey.energy.compiled.CPUConfEnergyCalculator
- close() - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.CheckedOutStream
- close() - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- close() - Method in class edu.duke.cs.osprey.energy.compiled.NativeConfEnergyCalculator
- close() - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- close() - Method in class edu.duke.cs.osprey.parallelism.BottleneckThread
- close() - Method in class edu.duke.cs.osprey.parallelism.Generator
- close() - Method in class edu.duke.cs.osprey.parallelism.RateLimitedThread
- close() - Method in class edu.duke.cs.osprey.parallelism.TaskExecutor.ContextGroup
- close() - Method in class edu.duke.cs.osprey.sofea.FringeDB
- close() - Method in class edu.duke.cs.osprey.sofea.RCDB
- close() - Method in class edu.duke.cs.osprey.sofea.SeqDB
- close() - Method in interface edu.duke.cs.osprey.tools.AutoCleanable
- close() - Method in interface edu.duke.cs.osprey.tools.AutoCloseableNoEx
- close() - Method in class edu.duke.cs.osprey.tools.ObjectPool.Checkout
- close() - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- CloseContact - Enum constant in enum class edu.duke.cs.osprey.structure.Probe.Contact
- cluster - Variable in class edu.duke.cs.osprey.coffee.ClusterMember
- cluster - Variable in class edu.duke.cs.osprey.coffee.Coffee
- cluster - Variable in class edu.duke.cs.osprey.energy.EnergyCalculator
- cluster - Variable in class edu.duke.cs.osprey.structure.analysis.ClusterR1.Stats
- cluster - Variable in class edu.duke.cs.osprey.structure.analysis.ClusterS1.Stats
- cluster(Collection<double[]>, int, double) - Static method in class edu.duke.cs.osprey.structure.analysis.AngleClustering
-
cluster points in a toroidal space
- Cluster - Class in edu.duke.cs.osprey.parallelism
-
Provides parallelism across a compute cluster using Hazelcast.
- Cluster(String, String, int, int) - Constructor for class edu.duke.cs.osprey.parallelism.Cluster
- Cluster(String, String, int, int, boolean) - Constructor for class edu.duke.cs.osprey.parallelism.Cluster
- Cluster.Client - Class in edu.duke.cs.osprey.parallelism
- Cluster.Member - Class in edu.duke.cs.osprey.parallelism
- Cluster.Task<T,
C> - Class in edu.duke.cs.osprey.parallelism - ClusterMember - Class in edu.duke.cs.osprey.coffee
- ClusterMember(Cluster) - Constructor for class edu.duke.cs.osprey.coffee.ClusterMember
- ClusterMember.DynamicPartition<T> - Class in edu.duke.cs.osprey.coffee
- ClusterMember.TimeoutException - Exception in edu.duke.cs.osprey.coffee
- ClusterR1 - Class in edu.duke.cs.osprey.structure.analysis
-
a cluster of data points in R^1
- ClusterR1() - Constructor for class edu.duke.cs.osprey.structure.analysis.ClusterR1
- ClusterR1.Stats - Class in edu.duke.cs.osprey.structure.analysis
- ClusterS1 - Class in edu.duke.cs.osprey.structure.analysis
-
a cluster of data points in S^1
- ClusterS1() - Constructor for class edu.duke.cs.osprey.structure.analysis.ClusterS1
- ClusterS1.Stats - Class in edu.duke.cs.osprey.structure.analysis
- ClusterZMatrix - Class in edu.duke.cs.osprey.coffee.zmat
-
A boltzmann-weighted energy matrix that can be computed in parallel on a cluster.
- ClusterZMatrix(ConfSpace, PosInterGen, BoltzmannCalculator) - Constructor for class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- cm - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.LengthUnit
- coefficients - Variable in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- Coffee - Class in edu.duke.cs.osprey.coffee
-
A clusterized successor to SOFEA that uses compiled conformation spaces.
- Coffee.Builder - Class in edu.duke.cs.osprey.coffee
- Coffee.Director - Interface in edu.duke.cs.osprey.coffee
-
Tells COFFEE what nodes to look for and when to stop looking
- Coffee.StateConfig - Class in edu.duke.cs.osprey.coffee
- collectFreeEnergies(Function<MultiStateConfSpace.State, MathTools.DoubleBounds>) - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFE
- color - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot.Series
- Color(String) - Constructor for class edu.duke.cs.osprey.tools.resultdoc.Plot.Color
- colors - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot
- combine(SimpleConfSpace.DofTypes, SimpleConfSpace.DofTypes) - Static method in enum class edu.duke.cs.osprey.confspace.SimpleConfSpace.DofTypes
- combine(Iterable<SimpleConfSpace.DofTypes>) - Static method in enum class edu.duke.cs.osprey.confspace.SimpleConfSpace.DofTypes
- combineHashes(byte...) - Static method in class edu.duke.cs.osprey.tools.HashCalculator
- combineHashes(int...) - Static method in class edu.duke.cs.osprey.tools.HashCalculator
- combineHashes(long...) - Static method in class edu.duke.cs.osprey.tools.HashCalculator
- combineHashes(short...) - Static method in class edu.duke.cs.osprey.tools.HashCalculator
- combineHashesCommutative(int...) - Static method in class edu.duke.cs.osprey.tools.HashCalculator
- combineObjHashes(T...) - Static method in class edu.duke.cs.osprey.tools.HashCalculator
- combineResidues(int[]) - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFTraditional
- combineResidues(KSConf, double, double, int[]) - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- combineResidues(KSConf, double, double, int[]) - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFTraditional
- combineSeqs(Set<Sequence>, Set<Sequence>, Set<String>) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- Comets - Class in edu.duke.cs.osprey.gmec
-
Implementation of the COMETS multi-state algorithm to predict protein sequence mutations that improve binding affinity.
- Comets.Builder - Class in edu.duke.cs.osprey.gmec
- Comets.LME - Class in edu.duke.cs.osprey.gmec
-
A Linear Multi-state Energy (i.e., a weighted combination of state energies)
- Comets.LME.Builder - Class in edu.duke.cs.osprey.gmec
- Comets.SequenceInfo - Class in edu.duke.cs.osprey.gmec
- Comets.State - Class in edu.duke.cs.osprey.gmec
-
A state for a multi-state design (e.g., an unbound state, or a complex state) For COMETS, all states must share the same sequence space.
- Comets.State.InitException - Exception in edu.duke.cs.osprey.gmec
- Comets.WeightedState - Class in edu.duke.cs.osprey.gmec
- COMETSDoer - Class in edu.duke.cs.osprey.control
- COMETSDoer(ConfigFileParser) - Constructor for class edu.duke.cs.osprey.control.COMETSDoer
- COMETSNode - Class in edu.duke.cs.osprey.astar.comets
-
Node for sequence-based A* (COMETS) tree Has to deal with conformational search, so significantly more complex than standard A* node
- COMETSNode(int[], PruningMatrix[]) - Constructor for class edu.duke.cs.osprey.astar.comets.COMETSNode
- COMETSNode(COMETSNode) - Constructor for class edu.duke.cs.osprey.astar.comets.COMETSNode
- COMETSTree - Class in edu.duke.cs.osprey.astar.comets
-
Tree for constrained optimization of multistate energies by tree search
- COMETSTree(int, LME, LME[], ArrayList<ArrayList<String>>, int, String[], int, SearchProblem[], ArrayList<ArrayList<Integer>>, boolean) - Constructor for class edu.duke.cs.osprey.astar.comets.COMETSTree
- command(String) - Method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd
- command(String, Object...) - Method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd
- CommandAnalysis - Interface in edu.duke.cs.osprey.design.analysis
- CommandBindingAffinity - Class in edu.duke.cs.osprey.design.commands
- CommandBindingAffinity() - Constructor for class edu.duke.cs.osprey.design.commands.CommandBindingAffinity
- CommandBindingAffinity.ForceFieldParamsAndStrands - Class in edu.duke.cs.osprey.design.commands
- CommandDescription - Static variable in class edu.duke.cs.osprey.design.commands.CommandBindingAffinity
- CommandDescription - Static variable in class edu.duke.cs.osprey.design.commands.CommandMakeFlexShell
- CommandGMEC - Class in edu.duke.cs.osprey.design.commands
- CommandGMEC() - Constructor for class edu.duke.cs.osprey.design.commands.CommandGMEC
- CommandMakeFlexShell - Class in edu.duke.cs.osprey.design.commands
- CommandMakeFlexShell() - Constructor for class edu.duke.cs.osprey.design.commands.CommandMakeFlexShell
- CommandName - Static variable in class edu.duke.cs.osprey.design.commands.CommandBindingAffinity
- CommandName - Static variable in class edu.duke.cs.osprey.design.commands.CommandGMEC
- CommandName - Static variable in class edu.duke.cs.osprey.design.commands.CommandMakeFlexShell
- CommandName - Static variable in class edu.duke.cs.osprey.design.commands.CommandPartitionFunction
- CommandName - Static variable in class edu.duke.cs.osprey.design.commands.CommandTopNConfs
- CommandPartitionFunction - Class in edu.duke.cs.osprey.design.commands
- CommandPartitionFunction() - Constructor for class edu.duke.cs.osprey.design.commands.CommandPartitionFunction
- CommandTopNConfs - Class in edu.duke.cs.osprey.design.commands
- CommandTopNConfs() - Constructor for class edu.duke.cs.osprey.design.commands.CommandTopNConfs
- commit() - Method in class edu.duke.cs.osprey.sofea.FringeDB.Transaction
-
Flushes all pending writes to the database file.
- commit() - Method in class edu.duke.cs.osprey.sofea.RCDB
- commit() - Method in class edu.duke.cs.osprey.sofea.SeqDB.Transaction
- compare(int[], int[]) - Method in class edu.duke.cs.osprey.tools.MapDBTools.IntArraySerializer
- compare(ConfSearch.ScoredConf, ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.multistatekstar.ConfComparator
- compare(Sequence, Sequence) - Method in class edu.duke.cs.osprey.tools.MapDBTools.SequenceSerializer
- compare(KSConf, KSConf) - Method in class edu.duke.cs.osprey.kstar.KSConf.KSConfMinEComparator
- compare(RCEnergyContribs.BoundErrorByPos, RCEnergyContribs.BoundErrorByPos) - Method in class edu.duke.cs.osprey.kstar.RCEnergyContribs.BoundErrorByPosComparator
- compare(BigExp, BigExp) - Method in class edu.duke.cs.osprey.tools.MapDBTools.BigExpSerializer
- compare(MathTools.BigDecimalBounds, MathTools.BigDecimalBounds) - Method in class edu.duke.cs.osprey.tools.MapDBTools.BigDecimalBoundsSerializer
- compare(BigDecimal, BigDecimal) - Method in class edu.duke.cs.osprey.tools.MapDBTools.BigDecimalSerializer
- compare(BigDecimal, BigDecimal) - Static method in class edu.duke.cs.osprey.tools.MathTools
- compareResNums(String, String) - Static method in class edu.duke.cs.osprey.multistatekstar.ResidueTermini
- compareTo(AStarNode) - Method in class edu.duke.cs.osprey.astar.FullAStarNode
- compareTo(AStarNode) - Method in class edu.duke.cs.osprey.astar.SlimAStarNode
- compareTo(ConfAStarNode) - Method in interface edu.duke.cs.osprey.astar.conf.ConfAStarNode
- compareTo(LinkedConfAStarNode.Link) - Method in class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode.Link
- compareTo(LinkedSeqAStarNode.Link) - Method in class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode.Link
- compareTo(SeqAStarNode) - Method in interface edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode
- compareTo(SlimAStarNode.Link) - Method in class edu.duke.cs.osprey.astar.SlimAStarNode.Link
- compareTo(SeqSpace.Position) - Method in class edu.duke.cs.osprey.confspace.SeqSpace.Position
- compareTo(SeqSpace.ResType) - Method in class edu.duke.cs.osprey.confspace.SeqSpace.ResType
- compareTo(TupE) - Method in class edu.duke.cs.osprey.confspace.TupE
- compareTo(FitParams) - Method in class edu.duke.cs.osprey.ematrix.epic.FitParams
- compareTo(ForcefieldDebugger.AtomPair) - Method in class edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger.AtomPair
- compareTo(EWAKStarBBKStar.Node) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.SingleSequenceNode
- compareTo(BBKStar.Node) - Method in class edu.duke.cs.osprey.kstar.BBKStar.SingleSequenceNode
- compareTo(MARKStarNode) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- compareTo(KStarTreeNode) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- compareTo(BigExp) - Method in class edu.duke.cs.osprey.tools.BigExp
- compareTo(Object) - Method in class edu.duke.cs.osprey.kstar.KSConf
- compareTo(Object) - Method in class edu.duke.cs.osprey.tupexp.ConfPair
- competitorPruneMat - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- competitors - Variable in class edu.duke.cs.osprey.pruning.SimpleDEE
- compileProgram(String) - Method in class edu.duke.cs.osprey.gpu.opencl.Gpu
- compInitVals() - Method in class edu.duke.cs.osprey.minimization.CCDMinimizer
- compInitValsCorners() - Method in class edu.duke.cs.osprey.minimization.CCDMinimizer
- compInitValsMiddle() - Method in class edu.duke.cs.osprey.minimization.CCDMinimizer
- complex - Variable in class edu.duke.cs.osprey.coffee.directors.AffinityDirector
- complex - Variable in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- complex - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar
-
A configuration space containing both the protein and ligand strands
- complex - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar
-
A configuration space containing both the protein and ligand strands
- complex - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.SingleSequenceNode
- complex - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- complex - Variable in class edu.duke.cs.osprey.kstar.BBKStar
-
A configuration space containing both the protein and ligand strands
- complex - Variable in class edu.duke.cs.osprey.kstar.BBKStar.SingleSequenceNode
- complex - Variable in class edu.duke.cs.osprey.kstar.KStar
-
A configuration space containing both the protein and ligand strands
- complex - Variable in class edu.duke.cs.osprey.kstar.KStarScore
- complex - Variable in class edu.duke.cs.osprey.markstar.MARKStar
-
A configuration space containing both the protein and ligand strands
- Complex - Enum constant in enum class edu.duke.cs.osprey.ewakstar.EWAKStar.ConfSpaceType
- Complex - Enum constant in enum class edu.duke.cs.osprey.kstar.KStar.ConfSpaceType
- Complex - Enum constant in enum class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceType
- Complex - Enum constant in enum class edu.duke.cs.osprey.paste.Paste.ConfSpaceType
- complexConfSpace - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.ScoreInfo
- ComplicatedGMECFinding - Class in edu.duke.cs.osprey.tests
-
Based on test/GMEC/TestSimpleGMECFinder, but with added complications like DEEPer and LUTE
- ComplicatedGMECFinding() - Constructor for class edu.duke.cs.osprey.tests.ComplicatedGMECFinding
- compNonBoxConstrAffectingDOF() - Method in class edu.duke.cs.osprey.minimization.CCDMinimizer
- compress(byte[]) - Static method in class edu.duke.cs.osprey.tools.LZMA2
- compress(String) - Static method in class edu.duke.cs.osprey.tools.LZMA2
- compute() - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction
- compute() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFAdapter
- compute() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- compute() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFTraditional
- compute() - Method in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- compute() - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction
- compute() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- compute() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- compute() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- compute() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- compute() - Method in interface edu.duke.cs.osprey.paste.PastePartitionFunction
- compute(int) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarGradientDescentPfunc
- compute(int) - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction
- compute(int) - Method in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- compute(int) - Method in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- compute(int) - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction
- compute(int) - Method in class edu.duke.cs.osprey.kstar.pfunc.SimplePartitionFunction
- compute(int) - Method in class edu.duke.cs.osprey.lute.LUTEPfunc
- compute(int) - Method in class edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc
- compute(int) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- compute(int) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- compute(int) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- compute(int) - Method in interface edu.duke.cs.osprey.multistatekstar.KStarScore
- compute(int) - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
-
compute until maxNumConfs conformations have been processed
- compute(int) - Method in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionDiscrete
- compute(int) - Method in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionDiscreteUppperBound
- compute(int) - Method in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized
- compute(int, int) - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreDiscrete
- compute(int, int) - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreLowerBound
- compute(int, int) - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- compute(int, int) - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreUpperBound
- compute(int, int) - Method in class edu.duke.cs.osprey.paste.PasteGradientDescentPfunc
- compute(int, int) - Method in interface edu.duke.cs.osprey.paste.PastePartitionFunction
- compute(ClusterMember, TaskExecutor, boolean, Double, ConfEnergyCalculator) - Method in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- compute(BigDecimal) - Method in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionDiscrete
- compute(BigDecimal) - Method in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionDiscreteUppperBound
- compute(BigDecimal) - Method in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized
- compute(Duration) - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction
-
Compute the partition function to the given epsilon, but stop earaly if the timeout was reached.
- computeDihedralMovingAtoms() - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
- computeEContrib(MultiTermEnergyFunction, int[]) - Method in class edu.duke.cs.osprey.kstar.RCEnergyContribs
- computeEffectiveEpsilon() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFUB
- computeEffectiveEpsilon() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- computeEnergyErrorWithinEnergyRange(double) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- computeEnergyMap(int) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- computeEnthalpy() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- computeEnthalpy(int) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- computeEnthalpyWithEnergiesFrom(Map<String, Double>, int) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- computeEntropy() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- computeEntropy(int) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- computeEpsilonErrorBounds() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- computeExhaustivePartitionFunction(int[], int[], int, boolean) - Method in class edu.duke.cs.osprey.ibis.KStarBeak
- computeLevelMaxOccupancies() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- computeNumConformations(RCs) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- computePucker(Residue) - Static method in class edu.duke.cs.osprey.dof.ProlinePucker
- computeScore() - Method in class edu.duke.cs.osprey.kstar.BBKStar.SingleSequenceNode
- computeScoresComplexParallel(ArrayList<KAStarNode>) - Method in class edu.duke.cs.osprey.kstar.KAStarNode
- computeScoresSerial(ArrayList<KAStarNode>) - Method in class edu.duke.cs.osprey.kstar.KAStarNode
- computeScoresSimpleParallel(ArrayList<KAStarNode>) - Method in class edu.duke.cs.osprey.kstar.KAStarNode
- computeSlice() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFAdapter
- computeSlice() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- computeSlice() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFTraditional
- computeSlice() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
-
computes partition function for an interval of time then yields
- computeWTCalc() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- concatenate(ObjectiveFunction.DofBounds...) - Static method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- concatenate(List<ObjectiveFunction.DofBounds>) - Static method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- conclusion(int, int, int, long) - Method in enum class edu.duke.cs.osprey.pruning.NewPruningControl.ReportMode
- conclusion(int, int, int, long) - Method in enum class edu.duke.cs.osprey.pruning.PruningControl.ReportMode
- concurrentKernels - Variable in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuInfo
- ConcurrentTaskExecutor - Class in edu.duke.cs.osprey.parallelism
- ConcurrentTaskExecutor() - Constructor for class edu.duke.cs.osprey.parallelism.ConcurrentTaskExecutor
- conditions - Variable in class edu.duke.cs.osprey.coffee.Coffee
- Conditions(double) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator.Conditions
- Conditions(double, double) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator.Conditions
- conf - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex.Node
- conf - Variable in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator.MinimizationJob
- conf() - Method in class edu.duke.cs.osprey.sofea.FringeDB.Transaction
- Conf - Class in edu.duke.cs.osprey.confspace
- Conf() - Constructor for class edu.duke.cs.osprey.confspace.Conf
- Conf(int[], ConfDB.Conf.Bound, ConfDB.Conf.Bound) - Constructor for class edu.duke.cs.osprey.confspace.ConfDB.Conf
- Conf(int, String, String, int, int, CoordsList, String[], int[], int[], ContinuousMotion.ConfDescription[], double[]) - Constructor for class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Conf
- Conf.Map<V> - Class in edu.duke.cs.osprey.confspace
- Conf.Set - Class in edu.duke.cs.osprey.confspace
- ConfAnalysis(int[], double, EnergyCalculator.EnergiedParametricMolecule) - Constructor for class edu.duke.cs.osprey.gmec.ConfAnalyzer.ConfAnalysis
- ConfAnalyzer - Class in edu.duke.cs.osprey.gmec
-
Shows information about a single conformation.
- ConfAnalyzer(ConfEnergyCalculator) - Constructor for class edu.duke.cs.osprey.gmec.ConfAnalyzer
- ConfAnalyzer.ConfAnalysis - Class in edu.duke.cs.osprey.gmec
- ConfAnalyzer.EnsembleAnalysis - Class in edu.duke.cs.osprey.gmec
- ConfAStarFactory - Interface in edu.duke.cs.osprey.astar.conf
- ConfAStarNode - Interface in edu.duke.cs.osprey.astar.conf
- ConfAStarTree - Class in edu.duke.cs.osprey.astar.conf
- ConfAStarTree.Builder - Class in edu.duke.cs.osprey.astar.conf
- ConfAStarTree.MPLPBuilder - Class in edu.duke.cs.osprey.astar.conf
- confAtomOffsetsByPos - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- ConfComparator - Class in edu.duke.cs.osprey.multistatekstar
- ConfComparator() - Constructor for class edu.duke.cs.osprey.multistatekstar.ConfComparator
- confDB - Variable in class edu.duke.cs.osprey.gmec.SimpleGMECFinder.Builder
-
If a design experiences an unexpected abort, the conformation database can allow you to restore the design state and resume the calculation close to where it was aborted.
- confDB - Variable in class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator
- ConfDB - Class in edu.duke.cs.osprey.confspace
- ConfDB(ConfSpaceIteration) - Constructor for class edu.duke.cs.osprey.confspace.ConfDB
- ConfDB(ConfSpaceIteration, File) - Constructor for class edu.duke.cs.osprey.confspace.ConfDB
- ConfDB.Conf - Class in edu.duke.cs.osprey.confspace
- ConfDB.Conf.Bound - Class in edu.duke.cs.osprey.confspace
- ConfDB.ConfTable - Class in edu.duke.cs.osprey.confspace
- ConfDB.DBs - Class in edu.duke.cs.osprey.confspace
- ConfDB.DBs.Adder - Class in edu.duke.cs.osprey.confspace
- ConfDB.Key - Class in edu.duke.cs.osprey.confspace
-
Tracks all the info needed to create a ConfTable or SequenceDB, but can be serialized and sent over a network.
- ConfDB.SequenceDB - Class in edu.duke.cs.osprey.confspace
- ConfDB.SortOrder - Enum Class in edu.duke.cs.osprey.confspace
- confDBFile - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.ConfSpaceInfo
- confDBFile - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.ConfSpaceInfo
- confDBFile - Variable in class edu.duke.cs.osprey.gmec.Comets.State
-
set this to a File if you want to use ConfDB with COMETS
- confDBFile - Variable in class edu.duke.cs.osprey.kstar.BBKStar.ConfSpaceInfo
- confDBFile - Variable in class edu.duke.cs.osprey.kstar.KStar.ConfSpaceInfo
- confDBFile - Variable in class edu.duke.cs.osprey.kstar.MSKStar.State
-
set this to a File if you want to use ConfDB with MSK*
- confDBFile - Variable in class edu.duke.cs.osprey.kstar.SequenceAnalyzer.ConfSpaceInfo
- confDBFile - Variable in class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceInfo
- confDBFile - Variable in class edu.duke.cs.osprey.paste.Paste.ConfSpaceInfo
- confDBFile - Variable in class edu.duke.cs.osprey.sofea.Sofea.StateConfig
-
File to cache conformation energies.
- confDBPattern - Variable in class edu.duke.cs.osprey.kstar.KStar.Settings
- confDBs - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.SingleSequenceNode
- ConfDBTableName - Static variable in class edu.duke.cs.osprey.gmec.SimpleGMECFinder
- confDOFs - Variable in class edu.duke.cs.osprey.confspace.ConfSpace
- confE(int[]) - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrix
- confEcalc - Variable in class edu.duke.cs.osprey.ematrix.compiled.EmatCalculator.Builder
- confEcalc - Variable in class edu.duke.cs.osprey.ematrix.compiled.EmatCalculator
- confEcalc - Variable in class edu.duke.cs.osprey.ematrix.compiled.ErefCalculator.Builder
- confEcalc - Variable in class edu.duke.cs.osprey.ematrix.compiled.ErefCalculator
- confEcalc - Variable in class edu.duke.cs.osprey.ematrix.SimplerEnergyMatrixCalculator
- confEcalc - Variable in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrixCalculator
- confEcalc - Variable in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter.Builder
-
Deprecated.
- confEcalc - Variable in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- confEcalc - Variable in class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.ByPosition
- confEcalc - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.ConfSpaceInfo
- confEcalc - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.State
- confEcalc - Variable in class edu.duke.cs.osprey.gmec.Comets.State
- confEcalc - Variable in class edu.duke.cs.osprey.gmec.ConfAnalyzer
- confEcalc - Variable in class edu.duke.cs.osprey.gmec.SimpleGMECFinder.Builder
-
Calculates the energy for a conformation.
- confEcalc - Variable in class edu.duke.cs.osprey.gmec.SimpleGMECFinder
- confEcalc - Variable in class edu.duke.cs.osprey.kstar.KStar.ConfSpaceInfo
- confEcalc - Variable in class edu.duke.cs.osprey.kstar.MSKStar.State
- confEcalc - Variable in class edu.duke.cs.osprey.kstar.SequenceAnalyzer.ConfSpaceInfo
- confEcalc - Variable in class edu.duke.cs.osprey.lute.LUTEGMECFinder
- confEcalc - Variable in class edu.duke.cs.osprey.paste.Paste.ConfSpaceInfo
- confEcalc - Variable in class edu.duke.cs.osprey.sofea.Sofea.StateConfig
-
A tool to compute energies for conformations.
- confEcalcFactory - Variable in class edu.duke.cs.osprey.markstar.MARKStar
-
A function that makes a ConfEnergyCalculator with the desired options
- confEcalcMinimized - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.ConfSpaceInfo
-
A ConfEnergyCalculator that computes minimized energies
- confEcalcMinimized - Variable in class edu.duke.cs.osprey.kstar.BBKStar.ConfSpaceInfo
-
A ConfEnergyCalculator that computes minimized energies
- confEnergies - Variable in class edu.duke.cs.osprey.lute.LUTE.LinearSystem
- confEnergyBound(int[]) - Method in class edu.duke.cs.osprey.kstar.KAStarConfTree
- ConfEnergyCalculator - Class in edu.duke.cs.osprey.energy
-
Calculate energy for molecules created from conformation spaces.
- ConfEnergyCalculator - Interface in edu.duke.cs.osprey.energy.compiled
-
The energy calculator interface for molecules created from compiled conformation spaces.
- ConfEnergyCalculator(SimpleConfSpace, EnergyCalculator, EnergyPartition, SimpleReferenceEnergies, boolean, ApproximatorMatrix, double, boolean) - Constructor for class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- ConfEnergyCalculator(SimpleConfSpace, TaskExecutor) - Constructor for class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- ConfEnergyCalculator(ConfEnergyCalculator) - Constructor for class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- ConfEnergyCalculator(ConfEnergyCalculator, EnergyCalculator) - Constructor for class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- ConfEnergyCalculator(TaskExecutor, boolean) - Constructor for class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
This constructor is intended for the ConfEnergyCalculatorAdapter.
- ConfEnergyCalculator.Builder - Class in edu.duke.cs.osprey.energy
- ConfEnergyCalculator.EnergiedCoords - Class in edu.duke.cs.osprey.energy.compiled
- ConfEnergyCalculator.MinimizationJob - Class in edu.duke.cs.osprey.energy.compiled
- ConfEnergyCalculatorAdapter - Class in edu.duke.cs.osprey.energy.compiled
-
Deprecated.
- ConfEnergyCalculatorAdapter.Builder - Class in edu.duke.cs.osprey.energy.compiled
-
Deprecated.
- confERef(int[]) - Method in class edu.duke.cs.osprey.ematrix.ReferenceEnergies
- ConfETupleExpander - Class in edu.duke.cs.osprey.tupexp
-
Implementation of a tuple expander that expands conformational energies-- including continuous flexibility, non-pairwise terms, etc.
- ConfETupleExpander(SearchProblem) - Constructor for class edu.duke.cs.osprey.tupexp.ConfETupleExpander
- confi1 - Variable in class edu.duke.cs.osprey.coffee.zmat.Pair
- confi1 - Variable in class edu.duke.cs.osprey.coffee.zmat.Single
- confi1 - Variable in class edu.duke.cs.osprey.coffee.zmat.Triple
- confi2 - Variable in class edu.duke.cs.osprey.coffee.zmat.Pair
- confi2 - Variable in class edu.duke.cs.osprey.coffee.zmat.Triple
- confi3 - Variable in class edu.duke.cs.osprey.coffee.zmat.Triple
- confId(int, int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- confId(int, int) - Method in interface edu.duke.cs.osprey.confspace.ConfSpaceIteration
-
returns the identifier (unique at this position) of the conformation
- confId(int, int) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- config - Variable in class edu.duke.cs.osprey.coffee.StateInfo
- configEachState(Consumer<Coffee.StateConfig>) - Method in class edu.duke.cs.osprey.coffee.Coffee.Builder
- configEachState(Function<MultiStateConfSpace.State, Sofea.StateConfig>) - Method in class edu.duke.cs.osprey.sofea.Sofea.Builder
- ConfigFileParser - Class in edu.duke.cs.osprey.control
- ConfigFileParser() - Constructor for class edu.duke.cs.osprey.control.ConfigFileParser
- ConfigFileParser(ConfigFileParser) - Constructor for class edu.duke.cs.osprey.control.ConfigFileParser
- ConfigFileReader - Class in edu.duke.cs.osprey.tools
-
tool for reading text files that have sections section headers are lines that look like: [section name]
- ConfigFileReader(String) - Constructor for class edu.duke.cs.osprey.tools.ConfigFileReader
- configState(Coffee.StateConfig) - Method in class edu.duke.cs.osprey.coffee.Coffee.Builder
- configState(MultiStateConfSpace.State, Sofea.StateConfig) - Method in class edu.duke.cs.osprey.sofea.Sofea.Builder
- configState(MultiStateConfSpace.State, Consumer<Coffee.StateConfig>) - Method in class edu.duke.cs.osprey.coffee.Coffee.Builder
- configState(String, Consumer<Coffee.StateConfig>) - Method in class edu.duke.cs.osprey.coffee.Coffee.Builder
- ConfIndex - Class in edu.duke.cs.osprey.astar.conf
- ConfIndex(int) - Constructor for class edu.duke.cs.osprey.astar.conf.ConfIndex
- ConfIndex(ConfIndex) - Constructor for class edu.duke.cs.osprey.astar.conf.ConfIndex
- ConfInfo - Class in edu.duke.cs.osprey.control
-
This class outputs info (structures, energies) on specified conformations in a conformation file
- ConfInfo - Enum constant in enum class edu.duke.cs.osprey.control.Main.Command
- ConfInfo(ConfigFileParser) - Constructor for class edu.duke.cs.osprey.control.ConfInfo
- ConfLimitReached - Enum constant in enum class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Status
- ConfLimitReached - Enum constant in enum class edu.duke.cs.osprey.paste.PastePartitionFunction.Status
- confListener - Variable in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- ConfMinimizer - Class in edu.duke.cs.osprey.minimization
- ConfMinimizer() - Constructor for class edu.duke.cs.osprey.minimization.ConfMinimizer
- ConfMinimizer.Async - Class in edu.duke.cs.osprey.minimization
- ConfMinimizer.Async.Listener - Interface in edu.duke.cs.osprey.minimization
- ConfPair - Class in edu.duke.cs.osprey.tupexp
- ConfPair(int[], double[]) - Constructor for class edu.duke.cs.osprey.tupexp.ConfPair
- ConfPicker - Interface in edu.duke.cs.osprey.partcr.pickers
- ConfPrinter - Class in edu.duke.cs.osprey.control
-
Deprecated.
- ConfPrinter - Interface in edu.duke.cs.osprey.gmec
- ConfPrinter(SearchProblem, String, boolean) - Constructor for class edu.duke.cs.osprey.control.ConfPrinter
-
Deprecated.
- ConfPrinter.Nop - Class in edu.duke.cs.osprey.gmec
- ConfPrinters - Class in edu.duke.cs.osprey.gmec
- ConfPrinters(ConfPrinter...) - Constructor for class edu.duke.cs.osprey.gmec.ConfPrinters
- ConfProblem - Class in edu.duke.cs.osprey.structure
-
Some conformational degrees of freedom (loop closure adjustment, proline pucker) have parameter values that, for certain starting conformations, are geometrically impossible.
- ConfProblem(DegreeOfFreedom, Residue) - Constructor for class edu.duke.cs.osprey.structure.ConfProblem
- confProblems - Variable in class edu.duke.cs.osprey.structure.Residue
- ConfRanker - Class in edu.duke.cs.osprey.astar.conf
- ConfRanker.Builder - Class in edu.duke.cs.osprey.astar.conf
- ConfRanker.ScorerFactory - Interface in edu.duke.cs.osprey.astar.conf
- confRigidEcalc - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.State
- confs - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Pos
- confs - Variable in class edu.duke.cs.osprey.confspace.ConfSearch.Splitter
- confs - Variable in class edu.duke.cs.osprey.lute.LUTE.LinearSystem
- ConfSampler - Class in edu.duke.cs.osprey.lute
- ConfSampler(SimpleConfSpace, PruningMatrix, int) - Constructor for class edu.duke.cs.osprey.lute.ConfSampler
- ConfSampler.NoMoreSamplesException - Exception in edu.duke.cs.osprey.lute
- ConfSampler.Samples - Class in edu.duke.cs.osprey.lute
- confSearch - Variable in class edu.duke.cs.osprey.kstar.KSPStarCalculator
- confSearch - Variable in class edu.duke.cs.osprey.kstar.pfunc.impl.PFTraditional
- ConfSearch - Interface in edu.duke.cs.osprey.confspace
-
A generic interface for A* searches over a conformatio space.
- ConfSearch.EnergiedConf - Class in edu.duke.cs.osprey.confspace
-
A conformation from a conformation space with an associated score, and an associated energy.
- ConfSearch.MultiSplitter - Class in edu.duke.cs.osprey.confspace
-
Lets multiple consumers read confs from the stream regardless of order of reads.
- ConfSearch.MultiSplitter.Stream - Class in edu.duke.cs.osprey.confspace
- ConfSearch.ScoredConf - Class in edu.duke.cs.osprey.confspace
-
A conformation from a conformation space with an associated score.
- ConfSearch.Splitter - Class in edu.duke.cs.osprey.confspace
-
Lets exactly two consumers read confs from the stream, where one consumer always reads before the other.
- ConfSearch.Splitter.OutOfOrderException - Exception in edu.duke.cs.osprey.confspace
- ConfSearchCache - Class in edu.duke.cs.osprey.astar.conf
-
A cache for ConfSearch instances where the most N recently used instances are protected by strong references and cannot be garbage collected.
- ConfSearchCache(Integer) - Constructor for class edu.duke.cs.osprey.astar.conf.ConfSearchCache
- ConfSearchCache.Entry - Class in edu.duke.cs.osprey.astar.conf
- confSearchFactory - Variable in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- confSearchFactory - Variable in class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceInfo
- confSearchFactory - Variable in class edu.duke.cs.osprey.paste.Paste.ConfSpaceInfo
- ConfSearchFactory - Interface in edu.duke.cs.osprey.gmec
- ConfSearchFactory.Tools - Class in edu.duke.cs.osprey.gmec
- confSearchFactoryMinimized - Variable in class edu.duke.cs.osprey.kstar.BBKStar.ConfSpaceInfo
- confSearchFactoryRigid - Variable in class edu.duke.cs.osprey.kstar.BBKStar.ConfSpaceInfo
- confsExhausted - Variable in class edu.duke.cs.osprey.kstar.KSPStarCalculator
- ConfSMAStarNode - Class in edu.duke.cs.osprey.astar.conf.smastar
- ConfSMAStarNode() - Constructor for class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
-
make the root node
- ConfSMAStarNode.State - Enum Class in edu.duke.cs.osprey.astar.conf.smastar
- ConfSMAStarQueue - Class in edu.duke.cs.osprey.astar.conf.smastar
- ConfSMAStarQueue() - Constructor for class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarQueue
- confSpace - Variable in class edu.duke.cs.osprey.astar.conf.ConfRanker
- confSpace - Variable in class edu.duke.cs.osprey.astar.conf.pruning.AStarSequencePruner
- confSpace - Variable in class edu.duke.cs.osprey.coffee.Coffee.Builder
- confSpace - Variable in class edu.duke.cs.osprey.coffee.Coffee
- confSpace - Variable in class edu.duke.cs.osprey.coffee.Coffee.StateConfig
- confSpace - Variable in class edu.duke.cs.osprey.coffee.directions.Directions
- confSpace - Variable in class edu.duke.cs.osprey.coffee.directors.AffinityDirector
- confSpace - Variable in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- confSpace - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncDirector.Builder
- confSpace - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncDirector
- confSpace - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncsDirector.Builder
- confSpace - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncsDirector
- confSpace - Variable in class edu.duke.cs.osprey.coffee.directors.SequenceDirector
- confSpace - Variable in class edu.duke.cs.osprey.coffee.nodedb.Neighbors
- confSpace - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeDB.Builder
- confSpace - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
- confSpace - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices
- confSpace - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodePerformance
- confSpace - Variable in class edu.duke.cs.osprey.coffee.seqdb.SeqDB.Builder
- confSpace - Variable in class edu.duke.cs.osprey.coffee.seqdb.SeqDB
- confSpace - Variable in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- confSpace - Variable in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords
- confSpace - Variable in class edu.duke.cs.osprey.confspace.ConfDB
- confSpace - Variable in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFE
- confSpace - Variable in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.State
- confSpace - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- confSpace - Variable in class edu.duke.cs.osprey.confspace.TuplesIndex
- confSpace - Variable in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator
-
Deprecated.
- confSpace - Variable in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrix
- confSpace - Variable in class edu.duke.cs.osprey.energy.compiled.CPUConfEnergyCalculator
- confSpace - Variable in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- confSpace - Variable in class edu.duke.cs.osprey.energy.compiled.NativeConfEnergyCalculator
- confSpace - Variable in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- confSpace - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.ConfSpaceInfo
- confSpace - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.ConfSpaceInfo
- confSpace - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.State
-
The conformation space for the state that describes the flexibility
- confSpace - Variable in class edu.duke.cs.osprey.gmec.Comets.State
-
The conformation space for the state that describes the flexibility
- confSpace - Variable in class edu.duke.cs.osprey.gmec.DEEGMECFinder
- confSpace - Variable in class edu.duke.cs.osprey.kstar.BBKStar.ConfSpaceInfo
- confSpace - Variable in class edu.duke.cs.osprey.kstar.KStar.ConfSpaceInfo
- confSpace - Variable in class edu.duke.cs.osprey.kstar.MSKStar.State
-
The conformation space for the state that describes the flexibility
- confSpace - Variable in class edu.duke.cs.osprey.kstar.SequenceAnalyzer.ConfSpaceInfo
- confSpace - Variable in class edu.duke.cs.osprey.lute.ConfSampler
- confSpace - Variable in class edu.duke.cs.osprey.lute.LUTE
- confSpace - Variable in class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceInfo
- confSpace - Variable in class edu.duke.cs.osprey.minimization.CpuConfMinimizer.Builder
- confSpace - Variable in class edu.duke.cs.osprey.minimization.GpuConfMinimizer.Builder
- confSpace - Variable in class edu.duke.cs.osprey.paste.Paste.ConfSpaceInfo
- confSpace - Variable in class edu.duke.cs.osprey.pruning.PLUG
- confSpace - Variable in class edu.duke.cs.osprey.pruning.SimpleDEE
- confSpace - Variable in class edu.duke.cs.osprey.pruning.TransitivePruner
- confSpace - Variable in class edu.duke.cs.osprey.sofea.FringeDB
- confSpace - Variable in class edu.duke.cs.osprey.sofea.RCDB
- confSpace - Variable in class edu.duke.cs.osprey.sofea.SeqDB
- confSpace - Variable in class edu.duke.cs.osprey.sofea.Sofea.Builder
- confSpace - Variable in class edu.duke.cs.osprey.sofea.Sofea
- confSpace() - Method in interface edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator
- confSpace() - Method in class edu.duke.cs.osprey.energy.compiled.CPUConfEnergyCalculator
- confSpace() - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- confSpace() - Method in class edu.duke.cs.osprey.energy.compiled.NativeConfEnergyCalculator
- ConfSpace - Class in edu.duke.cs.osprey.confspace.compiled
-
A conformation space that reads the output produced by the ConfSpaceCompiler in the GUI.
- ConfSpace - Class in edu.duke.cs.osprey.confspace
- ConfSpace(ConfSpace) - Constructor for class edu.duke.cs.osprey.confspace.ConfSpace
- ConfSpace(String, ArrayList<String>, ArrayList<ArrayList<String>>, boolean, ArrayList<String>, boolean, DEEPerSettings, ArrayList<String[]>, ArrayList<String[]>, boolean, boolean, ResidueTermini) - Constructor for class edu.duke.cs.osprey.confspace.ConfSpace
-
initialize a new conformational space, defining all its flexibility we use one residue per position here
- ConfSpace.Conf - Class in edu.duke.cs.osprey.confspace.compiled
-
a conformation at a design position
- ConfSpace.IndicesPair - Class in edu.duke.cs.osprey.confspace.compiled
- ConfSpace.IndicesSingle - Class in edu.duke.cs.osprey.confspace.compiled
- ConfSpace.IndicesStatic - Class in edu.duke.cs.osprey.confspace.compiled
- ConfSpace.MolInfo - Class in edu.duke.cs.osprey.confspace.compiled
- ConfSpace.Pos - Class in edu.duke.cs.osprey.confspace.compiled
-
a design position
- ConfSpace.ResInfo - Class in edu.duke.cs.osprey.confspace.compiled
- ConfSpaceInfo() - Constructor for class edu.duke.cs.osprey.kstar.SequenceAnalyzer.ConfSpaceInfo
- ConfSpaceInfo(ConfSpaceIteration, KStar.ConfSpaceType) - Constructor for class edu.duke.cs.osprey.kstar.BBKStar.ConfSpaceInfo
- ConfSpaceInfo(ConfSpaceIteration, KStar.ConfSpaceType) - Constructor for class edu.duke.cs.osprey.kstar.KStar.ConfSpaceInfo
- ConfSpaceInfo(SimpleConfSpace, EWAKStar.ConfSpaceType) - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStar.ConfSpaceInfo
- ConfSpaceInfo(SimpleConfSpace, EWAKStar.ConfSpaceType) - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.ConfSpaceInfo
- ConfSpaceInfo(SimpleConfSpace, Paste.ConfSpaceType) - Constructor for class edu.duke.cs.osprey.paste.Paste.ConfSpaceInfo
- ConfSpaceInfo(MARKStar.ConfSpaceType, SimpleConfSpace, ConfEnergyCalculator, ConfEnergyCalculator) - Constructor for class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceInfo
- confSpaceInfos() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar
- confSpaceInfos() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar
- confSpaceInfos() - Method in class edu.duke.cs.osprey.kstar.BBKStar
- confSpaceInfos() - Method in class edu.duke.cs.osprey.kstar.KStar
- confSpaceInfos() - Method in class edu.duke.cs.osprey.markstar.MARKStar
- confSpaceInfos() - Method in class edu.duke.cs.osprey.paste.Paste
- confSpaceIteration() - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- confSpaceIteration() - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- ConfSpaceIteration - Interface in edu.duke.cs.osprey.confspace
-
An interface to a conformation space that only exposes enough information to iterate over design positions and conformations.
- confsQ - Variable in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- confTable - Variable in class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator
- ConfTable(String) - Constructor for class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- confToString() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- ConfTree<T extends AStarNode> - Class in edu.duke.cs.osprey.astar
- ConfTree(AStarNode.Factory<T>, boolean, EnergyMatrix, EPICMatrix, NewEPICMatrix, EnergyMatrix, PruningMatrix, boolean, EPICSettings, GMECMutSpace) - Constructor for class edu.duke.cs.osprey.astar.ConfTree
- ConfTree(AStarNode.Factory<T>, SearchProblem) - Constructor for class edu.duke.cs.osprey.astar.ConfTree
- ConfTree(AStarNode.Factory<T>, SearchProblem, PruningMatrix) - Constructor for class edu.duke.cs.osprey.astar.ConfTree
- ConfTree(AStarNode.Factory<T>, SearchProblem, PruningMatrix, boolean, GMECMutSpace) - Constructor for class edu.duke.cs.osprey.astar.ConfTree
- confTreeFactory - Variable in class edu.duke.cs.osprey.gmec.Comets.State
- confTreeFactory - Variable in class edu.duke.cs.osprey.kstar.MSKStar.State
- confTreeFactoryMin - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.State
- confTreeFactoryMinimized - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.ConfSpaceInfo
-
A ConfSearch that minimizes over conformation scores from minimized tuples
- confTreeFactoryRigid - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.ConfSpaceInfo
-
A ConfSearch that maximizes over conformation scores from rigid tuples
- confTreeFactoryRigid - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.State
- confType(int, int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- confType(int, int) - Method in interface edu.duke.cs.osprey.confspace.ConfSpaceIteration
-
returns the type of the conformation at the position
- confType(int, int) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- connectInterResBonds(Residue, boolean) - Method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate
- connectInterResBonds(Residue, boolean) - Method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate.CysteineBondingTemplate
- connectInterResBonds(Residue, boolean) - Method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate.NoBondingTemplate
- connectInterResBonds(Residue, boolean) - Method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate.NucleotideBondingTemplate
- connectInterResBonds(Residue, boolean) - Method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate.PeptideBondingTemplate
- connectInterResBonds(Residue, boolean) - Method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate.SpecifiedBondingAtomsTemplate
- connectionString - Variable in class edu.duke.cs.osprey.design.PostgresConnectionInfo
- connectivity - Variable in class edu.duke.cs.osprey.energy.forcefield.ResPairCache
- ConsoleConfPrinter - Class in edu.duke.cs.osprey.gmec
- ConsoleConfPrinter() - Constructor for class edu.duke.cs.osprey.gmec.ConsoleConfPrinter
- consolePrinter - Variable in class edu.duke.cs.osprey.gmec.SimpleGMECFinder.Builder
- consolePrinter - Variable in class edu.duke.cs.osprey.gmec.SimpleGMECFinder
- consolePrinter - Variable in class edu.duke.cs.osprey.lute.LUTEGMECFinder
- consolidateTree(KStarTreeNode, Collection<String>) - Static method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeManipulator
- Constants - Class in edu.duke.cs.osprey
- Constants() - Constructor for class edu.duke.cs.osprey.Constants
- constrainLessThan(double) - Method in class edu.duke.cs.osprey.gmec.Comets.LME.Builder
-
Specify an upper bound constraint for this LME (i.e.
- constrainLessThan(double) - Method in class edu.duke.cs.osprey.kstar.MSKStar.LMFE.Builder
-
Specify an upper bound constraint for this LMFE (i.e.
- constraints - Variable in class edu.duke.cs.osprey.gmec.Comets
- constraints - Variable in class edu.duke.cs.osprey.gmec.Comets.SequenceInfo
- constraints - Variable in class edu.duke.cs.osprey.kstar.MSKStar
- constraints - Variable in class edu.duke.cs.osprey.kstar.MSKStar.SequenceInfo
- constraints - Variable in class edu.duke.cs.osprey.multistatekstar.MSKStarSettings
- constrAsFunction(LinearConstraint) - Static method in class edu.duke.cs.osprey.plug.LPChecks
- constrOpt(DoubleMatrix1D[], int[], boolean) - Method in class edu.duke.cs.osprey.minimization.GenCoord
- constrSatisfied - Variable in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- constrSatisfied() - Method in interface edu.duke.cs.osprey.multistatekstar.KStarScore
- constrSatisfied() - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- constrSatisfied() - Method in class edu.duke.cs.osprey.multistatekstar.MSKStarNode
- constRT - Static variable in class edu.duke.cs.osprey.energy.PoissonBoltzmannEnergy
- constRT - Static variable in class edu.duke.cs.osprey.paste.PasteScore
- contact - Variable in class edu.duke.cs.osprey.structure.Probe.AtomPair.Interaction
- contains(double) - Method in class edu.duke.cs.osprey.gmec.EnergyRange
- contains(double) - Method in class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel.Interval
- contains(double) - Method in class edu.duke.cs.osprey.tools.MathTools.DoubleBounds
- contains(double[]) - Method in class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel
- contains(int) - Method in class edu.duke.cs.osprey.tools.IntRange
- contains(int[]) - Method in class edu.duke.cs.osprey.confspace.Conf.Set
- contains(int, int) - Method in class edu.duke.cs.osprey.astar.conf.RCs
- contains(int, int) - Method in class edu.duke.cs.osprey.confspace.TuplesIndex
- contains(int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.TuplesIndex
- contains(int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.TuplesIndex
- contains(RCTuple) - Method in class edu.duke.cs.osprey.confspace.TuplesIndex
- contains(RCTuple) - Method in class edu.duke.cs.osprey.ematrix.UpdatingEnergyMatrix.TupleTrie
- contains(ResidueInteractions.Pair) - Method in class edu.duke.cs.osprey.energy.ResidueInteractions
- contains(Residue) - Method in class edu.duke.cs.osprey.multistatekstar.ResidueTermini
- contains(BigExp) - Method in class edu.duke.cs.osprey.tools.BigExp.Bounds
- contains(BigExp.Bounds) - Method in class edu.duke.cs.osprey.tools.BigExp.Bounds
- contains(MathTools.BigDecimalBounds) - Method in class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- contains(MathTools.DoubleBounds) - Method in class edu.duke.cs.osprey.tools.MathTools.DoubleBounds
- contains(Object) - Method in class edu.duke.cs.osprey.confspace.Conf.Set
- contains(Object) - Method in class edu.duke.cs.osprey.structure.Residues
- contains(String) - Method in class edu.duke.cs.osprey.multistatekstar.ResidueTermini
- contains(String) - Method in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary
- contains(String) - Method in class edu.duke.cs.osprey.structure.Residues
- contains(BigDecimal) - Method in class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- contains(Collection<int[]>, int[]) - Static method in class edu.duke.cs.osprey.confspace.Conf
- contains(List<T>) - Method in class edu.duke.cs.osprey.tools.PrefixTreeSet
- contains(T) - Method in class edu.duke.cs.osprey.coffee.directors.BestSet
- containsIgnoreCase(ArrayList<String>, String) - Static method in class edu.duke.cs.osprey.tools.StringParsing
- containsKey(int[]) - Method in class edu.duke.cs.osprey.confspace.Conf.Map
- containsKey(Object) - Method in class edu.duke.cs.osprey.confspace.Conf.Map
- containsName(String) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
- containsOrBelow(double) - Method in class edu.duke.cs.osprey.gmec.EnergyRange
- containsPoint(double[]) - Method in class edu.duke.cs.osprey.plug.RCTuplePolytope
- containsSeq(String) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarLimitedSequenceTrie
- containsTuple(int[], RCTuple) - Static method in class edu.duke.cs.osprey.confspace.Conf
- containsValue(Object) - Method in class edu.duke.cs.osprey.confspace.Conf.Map
- containsWildTypeSequence() - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- containsWTSeq() - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- context - Variable in class edu.duke.cs.osprey.energy.EnergyCalculator
- context - Variable in class edu.duke.cs.osprey.tools.BigMath
- Context - Class in edu.duke.cs.osprey.gpu.cuda
- Context() - Constructor for class edu.duke.cs.osprey.energy.EnergyCalculator.Type.Context
- Context(Gpu) - Constructor for class edu.duke.cs.osprey.gpu.cuda.Context
- contextGroup() - Method in class edu.duke.cs.osprey.parallelism.Cluster.Client
- contextGroup() - Method in class edu.duke.cs.osprey.parallelism.Cluster.Member
- contextGroup() - Method in class edu.duke.cs.osprey.parallelism.TaskExecutor
- ContextGroup() - Constructor for class edu.duke.cs.osprey.parallelism.TaskExecutor.ContextGroup
- contextId() - Method in interface edu.duke.cs.osprey.parallelism.TaskExecutor.Task.WithContext
- ContextId(int, Class<?>) - Constructor for class edu.duke.cs.osprey.parallelism.TaskExecutor.ContextId
- Continue - Enum constant in enum class edu.duke.cs.osprey.pruning.PruningMatrix.IteratorCommand
- ContinuousMotion - Interface in edu.duke.cs.osprey.confspace.compiled
-
Manipulates atom positions in an AssignedCoords by varying continuous parameters.
- ContinuousMotion.ConfDescription - Interface in edu.duke.cs.osprey.confspace.compiled
-
A description of a continuous motion affecting a conformation.
- ContinuousMotion.MolDescription - Interface in edu.duke.cs.osprey.confspace.compiled
-
A description of a continuous motion affecting a molecule.
- contSCFlex - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- coordinates - Variable in class edu.duke.cs.osprey.design.models.MoleculeDto
- coords - Variable in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords
-
atom coords for the static atoms and the conformation atoms
- coords - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Conf
- coords - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle
- coords - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation
- coords - Variable in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator.EnergiedCoords
- coords - Variable in class edu.duke.cs.osprey.structure.Residue
-
coordinates of all the atoms: x1, y1, z1, x2, ...
- Coords(double, double, double, double, double, double, double) - Constructor for class edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger.Coords
- Coords(Vector3d, Vector3d, double) - Constructor for class edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger.Coords
- CoordsAndCharges - Class in edu.duke.cs.osprey.energy.forcefield
- CoordsAndCharges(Residue, Residue) - Constructor for class edu.duke.cs.osprey.energy.forcefield.CoordsAndCharges
- coordsi - Variable in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords.AtomInfo
- CoordsList - Class in edu.duke.cs.osprey.confspace.compiled
-
A supremely efficient representation for atomic coordinates.
- CoordsList(int) - Constructor for class edu.duke.cs.osprey.confspace.compiled.CoordsList
- CoordsList(CoordsList) - Constructor for class edu.duke.cs.osprey.confspace.compiled.CoordsList
- copy() - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Makes an identical copy of this sequence.
- copy() - Method in class edu.duke.cs.osprey.design.models.AffinityDesign
- copy() - Method in class edu.duke.cs.osprey.dof.DegreeOfFreedom
- copy() - Method in class edu.duke.cs.osprey.dof.FreeDihedral
- copy() - Method in class edu.duke.cs.osprey.dof.ProlinePucker
- copy() - Method in class edu.duke.cs.osprey.dof.ResidueTypeDOF
- copy() - Method in class edu.duke.cs.osprey.structure.Atom
- copy() - Method in class edu.duke.cs.osprey.tools.RotationMatrix
- copy(double[], double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- copy(double[], double[], int) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- copy(double[], int, double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- copy(double[], int, DoubleBuffer, int) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- copy(double[], DoubleBuffer, int) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- copy(DoubleBuffer, int, double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- copy(DoubleBuffer, int, double[], int) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- copyAtoms(ArrayList<Atom>) - Static method in class edu.duke.cs.osprey.structure.Residue
- copyCoords() - Method in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords
- copyForNewMolecule(Molecule, PerturbationBlock) - Method in class edu.duke.cs.osprey.dof.deeper.perts.Backrub
- copyForNewMolecule(Molecule, PerturbationBlock) - Method in class edu.duke.cs.osprey.dof.deeper.perts.LoopClosureAdjustment
- copyForNewMolecule(Molecule, PerturbationBlock) - Method in class edu.duke.cs.osprey.dof.deeper.perts.PartialStructureSwitch
- copyForNewMolecule(Molecule, PerturbationBlock) - Method in class edu.duke.cs.osprey.dof.deeper.perts.Perturbation
- copyForNewMolecule(Molecule, PerturbationBlock) - Method in class edu.duke.cs.osprey.dof.deeper.perts.Shear
- copyForNewMolecule(Molecule, LinkedHashMap<DegreeOfFreedom, DegreeOfFreedom>) - Method in class edu.duke.cs.osprey.bbfree.BBFreeBlock
- copyForNewMolecule(Molecule, LinkedHashMap<DegreeOfFreedom, DegreeOfFreedom>) - Method in class edu.duke.cs.osprey.dof.deeper.perts.PerturbationBlock
- copyForNewMolecule(Molecule, LinkedHashMap<DegreeOfFreedom, DegreeOfFreedom>) - Method in interface edu.duke.cs.osprey.dof.DOFBlock
- copyForNewMolecule(Molecule, LinkedHashMap<DegreeOfFreedom, DegreeOfFreedom>) - Method in class edu.duke.cs.osprey.dof.MoveableStrand
- copyFrom(CoordsList, int) - Method in class edu.duke.cs.osprey.confspace.compiled.CoordsList
- copyIntraBondsFrom(Residue) - Method in class edu.duke.cs.osprey.structure.Residue
- copyTo(NodeStats.Values) - Method in class edu.duke.cs.osprey.coffee.NodeStats.Values
- copyToMol(Molecule, boolean) - Method in class edu.duke.cs.osprey.structure.Residue
-
An optimized copy method (profiling shows the usual constructors are a bit slow)
- copyToRes(Residue) - Method in class edu.duke.cs.osprey.structure.Atom
-
An optimized copy method (profiling shows the usual constructors are a bit slow) but doesn't copy the bonds
- correctedNode(List<MARKStarNode>, MARKStarNode, MARKStarNode.Node) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- correctionEmat - Variable in class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceInfo
- coulombConstant - Static variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- coulombFactor - Variable in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.ParamInfo
- coulombScaling - Variable in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.Forcefield
- count() - Method in class edu.duke.cs.osprey.coffee.EnergyBoundStats
- count() - Method in class edu.duke.cs.osprey.confspace.TripleMatrix
- count() - Method in class edu.duke.cs.osprey.structure.analysis.DegreesHistogram
-
return the sum of all the buckets
- countAssignments() - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Count the number of assigned residues.
- countAssignments(int[]) - Static method in class edu.duke.cs.osprey.confspace.Conf
- countDihedralDOFs(ResidueTemplate) - Method in class edu.duke.cs.osprey.confspace.VoxelShape
- countDihedralDOFs(ResidueTemplate) - Method in class edu.duke.cs.osprey.confspace.VoxelShape.Point
- countDihedralDOFs(ResidueTemplate) - Method in class edu.duke.cs.osprey.confspace.VoxelShape.Rect
- countDofs(Strand) - Method in class edu.duke.cs.osprey.confspace.StrandFlex
- CounterSignal - Class in edu.duke.cs.osprey.parallelism
- CounterSignal(int, CounterSignal.SignalCondition) - Constructor for class edu.duke.cs.osprey.parallelism.CounterSignal
- CounterSignal.SignalCondition - Interface in edu.duke.cs.osprey.parallelism
- countMutations() - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Count the number of residues whose residue types are different from the wild-type.
- countNodesToProcess() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- countPairs() - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- countPairs() - Method in interface edu.duke.cs.osprey.confspace.ConfSpaceIteration
-
counts all the unique pos:conf - pos:conf pairs in the conf space
- countPairs() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- countProcessedConfs() - Method in class edu.duke.cs.osprey.kstar.impl.KSImplKAStar
- countProcessedConfs() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- countPrunedPairs() - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- countPrunedPairs() - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- countPrunedPairs() - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- countPrunedRCs() - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- countPrunedRCs() - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- countPrunedRCs() - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- countPrunedTriples() - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- counts - Variable in class edu.duke.cs.osprey.dof.DofInfo
- counts - Variable in class edu.duke.cs.osprey.structure.analysis.Histogram
- countSingles() - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- countSingles() - Method in interface edu.duke.cs.osprey.confspace.ConfSpaceIteration
-
counts all the unique pos:conf entries in the conf space
- countSingles() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- countTotNumConfs() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- countTuplesWithAtLeast(int) - Method in class edu.duke.cs.osprey.lute.ConfSampler.Samples
- countTuplesWithLessThan(int) - Method in class edu.duke.cs.osprey.lute.ConfSampler.Samples
- countUnprunedSingles(int) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- countUpdates() - Method in class edu.duke.cs.osprey.astar.comets.UpdatedPruningMatrix
- countUpdates() - Method in class edu.duke.cs.osprey.kstar.pruning.ReducedPruningMatrix
- Cpu - Enum constant in enum class edu.duke.cs.osprey.energy.EnergyCalculator.Type
- Cpu - Enum constant in enum class edu.duke.cs.osprey.parallelism.Parallelism.Type
- Cpu(int, ForcefieldParams, ConfSpace, List<Residue>) - Constructor for class edu.duke.cs.osprey.ematrix.SimpleEnergyMatrixCalculator.Cpu
-
Deprecated.
- Cpu(ForcefieldParams, ConfSpace, List<Residue>) - Constructor for class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator.Cpu
-
Deprecated.
- CPUConfEnergyCalculator - Class in edu.duke.cs.osprey.energy.compiled
-
A basic conformation energy calculator implementation, written in pure Java.
- CPUConfEnergyCalculator(ConfSpace) - Constructor for class edu.duke.cs.osprey.energy.compiled.CPUConfEnergyCalculator
- CpuConfMinimizer - Class in edu.duke.cs.osprey.minimization
- CpuConfMinimizer(int, ForcefieldParams, Factory<ForcefieldInteractions, Molecule>, ConfSpace, Factory<? extends Minimizer, MoleculeModifierAndScorer>) - Constructor for class edu.duke.cs.osprey.minimization.CpuConfMinimizer
- CpuConfMinimizer.Builder - Class in edu.duke.cs.osprey.minimization
- cpuEcalcs - Variable in class edu.duke.cs.osprey.coffee.NodeProcessor
- CpuOriginalCCD - Enum constant in enum class edu.duke.cs.osprey.energy.EnergyCalculator.Type
- cpuTasks - Variable in class edu.duke.cs.osprey.coffee.NodeProcessor
- create(MultiStateConfSpace, File, long) - Static method in class edu.duke.cs.osprey.sofea.FringeDB
-
create a new fringe node database, reserving the desired spase on the filesystem
- createCheckPointDir() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- createEmatDir() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- createEmats(ArrayList<Boolean>) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- createEmats(ArrayList<Boolean>) - Method in interface edu.duke.cs.osprey.kstar.KSInterface
- createHotsFromCFG() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFTraditional
- createOutputDir() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- createPanSeqSP(boolean, int) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- createPF4Seq(boolean, int, ArrayList<String>, String) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- createPFs4Seqs(ArrayList<ArrayList<String>>, ArrayList<Boolean>, ArrayList<String>) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- createReducedSP(boolean, int, ArrayList<String>, ArrayList<Integer>) - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- cross(double[], double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- crossValidateSeries(EPoly, FitParams) - Method in class edu.duke.cs.osprey.ematrix.epic.EPICFitter
- cSpace - Variable in class edu.duke.cs.osprey.plug.PolytopeMatrix
- csv(String, String) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc.File
- CUBuffer<T extends Buffer> - Class in edu.duke.cs.osprey.gpu.cuda
- CUBuffer(GpuStream, T) - Constructor for class edu.duke.cs.osprey.gpu.cuda.CUBuffer
- Cuda - Enum constant in enum class edu.duke.cs.osprey.energy.EnergyCalculator.Type
- Cuda - Enum constant in enum class edu.duke.cs.osprey.minimization.GpuConfMinimizer.Type
- Cuda(int, int, ForcefieldParams, ConfSpace, List<Residue>) - Constructor for class edu.duke.cs.osprey.ematrix.SimpleEnergyMatrixCalculator.Cuda
-
Deprecated.
- Cuda(GpuStreamPool, ForcefieldParams, ConfSpace, List<Residue>) - Constructor for class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator.Cuda
-
Deprecated.
- CudaCCD - Enum constant in enum class edu.duke.cs.osprey.energy.EnergyCalculator.Type
- CudaCCD - Enum constant in enum class edu.duke.cs.osprey.minimization.GpuConfMinimizer.Type
- CudaCCDMinimizer - Class in edu.duke.cs.osprey.minimization
- CudaCCDMinimizer(GpuStreamPool) - Constructor for class edu.duke.cs.osprey.minimization.CudaCCDMinimizer
- CudaCCDMinimizer(GpuStreamPool, ObjectiveFunction) - Constructor for class edu.duke.cs.osprey.minimization.CudaCCDMinimizer
- CudaConfEnergyCalculator - Class in edu.duke.cs.osprey.energy.compiled
-
An energy calculator that uses CUDA GPUs to accelerate the computation.
- CudaConfEnergyCalculator(ConfSpace, Structs.Precision) - Constructor for class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
-
use all the GPUs by default
- CudaConfEnergyCalculator(ConfSpace, Structs.Precision, Parallelism) - Constructor for class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
-
get GPU info from the Parallelism instance
- CudaConfEnergyCalculator(ConfSpace, Structs.Precision, List<CudaConfEnergyCalculator.GpuInfo>) - Constructor for class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
-
use just the given GPUs
- CudaConfEnergyCalculator(ConfSpace, Structs.Precision, List<CudaConfEnergyCalculator.GpuStreams>, long) - Constructor for class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- CudaConfEnergyCalculator.CheckedOutStream - Class in edu.duke.cs.osprey.energy.compiled
- CudaConfEnergyCalculator.GpuInfo - Class in edu.duke.cs.osprey.energy.compiled
- CudaConfEnergyCalculator.GpuStreams - Class in edu.duke.cs.osprey.energy.compiled
- curBestScore() - Method in class edu.duke.cs.osprey.astar.AStarTree
- curDOFVals - Variable in class edu.duke.cs.osprey.minimization.MoleculeObjectiveFunction
- curEFcnGenerator - Static variable in class edu.duke.cs.osprey.control.EnvironmentVars
-
Deprecated.
- curr - Variable in class edu.duke.cs.osprey.tools.GLibC.RLimit
- CysteineBondingTemplate() - Constructor for class edu.duke.cs.osprey.restypes.InterResBondingTemplate.CysteineBondingTemplate
D
- d - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Description
- d - Variable in class edu.duke.cs.osprey.energy.approximation.NOPApproximator
- d - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DeltaDihedralAngle
- d - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DihedralAngle
- d - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DihedralAnglesMinDist
- d - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralSystem
- DAminoAcidHandler - Class in edu.duke.cs.osprey.restypes
-
This class deals with D-amino-acid specific operations D amino acids are named as "DX" + one-letter code, e.g.
- DAminoAcidHandler() - Constructor for class edu.duke.cs.osprey.restypes.DAminoAcidHandler
- data - Variable in class edu.duke.cs.osprey.energy.forcefield.CoordsAndCharges
- data - Variable in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.Style
- data - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot.Intervals
- data - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot.LinesX
- data - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot.LinesY
- data - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot.PointsX
- data - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot.PointsY
- datablock(String, String) - Method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd
- dbFile - Variable in class edu.duke.cs.osprey.coffee.Coffee
- dbFileBytes - Variable in class edu.duke.cs.osprey.coffee.Coffee
- dbHasRoomFor(int) - Method in class edu.duke.cs.osprey.sofea.FringeDB.Transaction
-
Is there enough room in the database to add more nodes?
- dbHasRoomForCommit() - Method in class edu.duke.cs.osprey.sofea.FringeDB.Transaction
-
Is there enough room in the database to add the nodes in this transaction?
- dbMemBytes - Variable in class edu.duke.cs.osprey.coffee.Coffee
- DBs() - Constructor for class edu.duke.cs.osprey.confspace.ConfDB.DBs
- debug - Static variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldEnergy
- debug - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- debug - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- debug - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- debug - Static variable in class edu.duke.cs.osprey.restypes.RotamerLibraryReader
- debugHeap(Queue<MARKStarNode>) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- debugPrint(String) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- decimalPrecision - Static variable in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction
- decimalPrecision - Static variable in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction
- decimalPrecision - Static variable in interface edu.duke.cs.osprey.paste.PastePartitionFunction
- decompMinimizedEnergy(int[]) - Method in class edu.duke.cs.osprey.kstar.KSSearchProblem
- decomposeByDof(Molecule, List<DegreeOfFreedom>) - Method in class edu.duke.cs.osprey.ematrix.epic.EPICEnergyFunction
- decomposeByDof(Molecule, List<DegreeOfFreedom>) - Method in interface edu.duke.cs.osprey.energy.EnergyFunction.DecomposableByDof
- decomposeByDof(Molecule, List<DegreeOfFreedom>) - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy
- decomposeByDof(Molecule, List<DegreeOfFreedom>) - Method in class edu.duke.cs.osprey.energy.forcefield.GpuForcefieldEnergy
- decomposeByDof(Molecule, List<DegreeOfFreedom>) - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- decomposeByDof(Molecule, List<DegreeOfFreedom>) - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy.Vdw
- decomposeByDof(Molecule, List<DegreeOfFreedom>) - Method in class edu.duke.cs.osprey.energy.MultiTermEnergyFunction
- decomposeByDof(Molecule, List<DegreeOfFreedom>) - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ResidueForcefieldEnergyCuda
- decompressBytes(byte[]) - Static method in class edu.duke.cs.osprey.tools.LZMA2
- decompressString(byte[]) - Static method in class edu.duke.cs.osprey.tools.LZMA2
- DEEGMECFinder - Class in edu.duke.cs.osprey.gmec
-
A more complicated version of the SimpleGMECFinder, supporting DEE and related algorithms (EPIC, LUTE, etc.)
- DEEGMECFinder.Builder - Class in edu.duke.cs.osprey.gmec
- deepCopy(Object) - Static method in class edu.duke.cs.osprey.tools.ObjectIO
- deeperSettings - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- DEEPerSettings - Class in edu.duke.cs.osprey.dof.deeper
-
Holds parameters that control a DEEPer run
- DEEPerSettings() - Constructor for class edu.duke.cs.osprey.dof.deeper.DEEPerSettings
- DEEPerSettings(boolean, String, boolean, String, boolean, double, double, boolean, ArrayList<String>, String, boolean, ResidueTemplateLibrary) - Constructor for class edu.duke.cs.osprey.dof.deeper.DEEPerSettings
- DEEPerStrandFlex - Class in edu.duke.cs.osprey.confspace
-
StrandFlex representing a perturbation block
- DEEPerStrandFlex(Strand, DEEPerSettings) - Constructor for class edu.duke.cs.osprey.confspace.DEEPerStrandFlex
- defaultBackboneVoxel(Strand) - Method in class edu.duke.cs.osprey.confspace.StrandFlex
- DefaultClientIsMember - Static variable in class edu.duke.cs.osprey.parallelism.Cluster
- defaultColors - Static variable in class edu.duke.cs.osprey.tools.resultdoc.Plot
- defaultEPIC() - Static method in class edu.duke.cs.osprey.ematrix.epic.EPICSettings
- DefaultHalfWidthDegrees - Static variable in class edu.duke.cs.osprey.confspace.VoxelShape
- defaultLUTE() - Static method in class edu.duke.cs.osprey.tupexp.LUTESettings
- DefaultMaxRotDegrees - Static variable in class edu.duke.cs.osprey.confspace.StrandFlex.TranslateRotate
- DefaultMaxTranslation - Static variable in class edu.duke.cs.osprey.confspace.StrandFlex.TranslateRotate
- defaultPlotType - Variable in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- DefaultTimeoutS - Static variable in class edu.duke.cs.osprey.parallelism.Cluster.Member
- definedPos - Variable in class edu.duke.cs.osprey.astar.conf.ConfIndex
- definedPos - Variable in class edu.duke.cs.osprey.astar.ConfTree
- definedRCs - Variable in class edu.duke.cs.osprey.astar.conf.ConfIndex
- definedRCs - Variable in class edu.duke.cs.osprey.astar.ConfTree
- DegreeOfFreedom - Class in edu.duke.cs.osprey.dof
- DegreeOfFreedom - Interface in edu.duke.cs.osprey.confspace.compiled
-
A single dimension over which a minimizer can explore the energy landscape of a continuous motion.
- DegreeOfFreedom() - Constructor for class edu.duke.cs.osprey.dof.DegreeOfFreedom
- DegreesHistogram - Class in edu.duke.cs.osprey.structure.analysis
- DegreesHistogram(int) - Constructor for class edu.duke.cs.osprey.structure.analysis.DegreesHistogram
- DegreesHistogram(Collection<double[]>) - Constructor for class edu.duke.cs.osprey.structure.analysis.DegreesHistogram
- delegate - Variable in class edu.duke.cs.osprey.design.commands.RunnableCommand
- delete(String) - Static method in class edu.duke.cs.osprey.tools.ObjectIO
- deleteCheckPointFile(int) - Method in class edu.duke.cs.osprey.kstar.KSCalc
- deleteCheckPointFiles() - Method in class edu.duke.cs.osprey.kstar.KSCalc
- deletedResWarningLog - Static variable in class edu.duke.cs.osprey.control.EnvironmentVars
-
Deprecated.
- deleteFromSet(ArrayList<String>, HashSet<ArrayList<String>>) - Static method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- deleteHydrogens() - Method in class edu.duke.cs.osprey.structure.Residue
- deleteMOFStandalone() - Method in class edu.duke.cs.osprey.ematrix.epic.EPoly
- deleteNonTemplateResidues - Static variable in class edu.duke.cs.osprey.control.EnvironmentVars
-
Deprecated.
- deleteResidue(int) - Method in class edu.duke.cs.osprey.structure.Molecule
- deleteResidues(Collection<String>) - Method in class edu.duke.cs.osprey.structure.Molecule
- deleteSeqFromFile(ArrayList<String>, String) - Method in class edu.duke.cs.osprey.kstar.KSCalc
- delta - Variable in class edu.duke.cs.osprey.kstar.pfunc.UpperBoundCalculator
- DeltaDihedralAngle(String, String, String, String, String) - Constructor for class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DeltaDihedralAngle
- depth - Variable in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- deQueue() - Method in class edu.duke.cs.osprey.kstar.KSConfQ
- desc - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle
- desc - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation
- Description(double, double, int, int, int, int, int[]) - Constructor for class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Description
- Description(double, double, Vector3d) - Constructor for class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Description
- deserialize(double, ByteBuffer) - Method in class edu.duke.cs.osprey.externalMemory.EnergiedConfPrioritySerializer
- deserialize(ByteBuffer) - Method in interface edu.duke.cs.osprey.coffee.nodedb.FixedIndex.Serializer
- deserialize(ByteBuffer) - Method in class edu.duke.cs.osprey.externalMemory.EnergiedConfFIFOSerializer
- deserialize(ByteBuffer) - Method in class edu.duke.cs.osprey.externalMemory.ScoredConfFIFOSerializer
- deserialize(DataInput2, int) - Method in class edu.duke.cs.osprey.tools.MapDBTools.BigDecimalBoundsSerializer
- deserialize(DataInput2, int) - Method in class edu.duke.cs.osprey.tools.MapDBTools.BigDecimalSerializer
- deserialize(DataInput2, int) - Method in class edu.duke.cs.osprey.tools.MapDBTools.BigExpSerializer
- deserialize(DataInput2, int) - Method in class edu.duke.cs.osprey.tools.MapDBTools.IntArraySerializer
- deserialize(DataInput2, int) - Method in class edu.duke.cs.osprey.tools.MapDBTools.SequenceSerializer
- deserialize(DataInput2, int) - Method in class edu.duke.cs.osprey.tools.MapDBTools.ValuesSerializer
- deSerializePF(String, String, boolean) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- design - Variable in class edu.duke.cs.osprey.coffee.directors.AffinityDirector
- design - Variable in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- design - Variable in class edu.duke.cs.osprey.design.commands.DesignFileDelegate
- DesignFileDelegate - Class in edu.duke.cs.osprey.design.commands
- DesignFileDelegate() - Constructor for class edu.duke.cs.osprey.design.commands.DesignFileDelegate
- designIndex - Variable in class edu.duke.cs.osprey.confspace.PositionConfSpace
- designName - Variable in class edu.duke.cs.osprey.design.models.AffinityDesign
- designName - Variable in class edu.duke.cs.osprey.design.models.MoleculeDesign
- DesmetEtAl1992 - Enum constant in enum class edu.duke.cs.osprey.confspace.compiled.PosInterDist
-
Uses the traditional distribution introduced in the original DEE paper: Namely, pos-static and pos interactions are placed on "single" conf fragments.
- destroy() - Method in class edu.duke.cs.osprey.coffee.Serializers.AbstractStreamSerializer
- dGfree - Variable in class edu.duke.cs.osprey.energy.forcefield.EEF1.SolvParams
- dGref - Variable in class edu.duke.cs.osprey.energy.forcefield.EEF1.SolvParams
- di - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle
- Diagnostics - Class in edu.duke.cs.osprey.gpu.cuda
- Diagnostics - Class in edu.duke.cs.osprey.gpu.opencl
- Diagnostics() - Constructor for class edu.duke.cs.osprey.gpu.cuda.Diagnostics
- Diagnostics() - Constructor for class edu.duke.cs.osprey.gpu.opencl.Diagnostics
- Diamond - Enum constant in enum class edu.duke.cs.osprey.tools.resultdoc.Plot.PointType
- DiamondFilled - Enum constant in enum class edu.duke.cs.osprey.tools.resultdoc.Plot.PointType
- dielectric - Variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- diff(EnergyMatrix) - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrix
- differenceFromEnergy - Enum constant in enum class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode.ColorStyle
- DihederalParameter - Record Class in edu.duke.cs.osprey.energy.forcefield.amber
- DihederalParameter(AtomSymbolAndMass, AtomSymbolAndMass, AtomSymbolAndMass, AtomSymbolAndMass, int, float, float, float) - Constructor for record class edu.duke.cs.osprey.energy.forcefield.amber.DihederalParameter
-
Creates an instance of a
DihederalParameterrecord class. - dihederalParameters() - Method in class edu.duke.cs.osprey.energy.forcefield.amber.ForcefieldFileParser
- dihedFlexInterval - Static variable in class edu.duke.cs.osprey.confspace.PositionConfSpace
- dihedral - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Dof
- dihedral4Atoms - Variable in class edu.duke.cs.osprey.restypes.ResidueTemplate
- DihedralAngle - Class in edu.duke.cs.osprey.confspace.compiled.motions
- DihedralAngle(DihedralAngle.Description, AssignedCoords, int, int) - Constructor for class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle
- DihedralAngle(String, String, String, String) - Constructor for class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DihedralAngle
- DihedralAngle(String, String, String, String, String) - Constructor for class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DihedralAngle
- DihedralAngle.Description - Class in edu.duke.cs.osprey.confspace.compiled.motions
- DihedralAngle.Dof - Class in edu.duke.cs.osprey.confspace.compiled.motions
-
a dihedral angle only has one degree of freedom
- DihedralAnglesMinDist(String, double, String, String, String, String...) - Constructor for class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DihedralAnglesMinDist
- dihedralMovingAtoms - Variable in class edu.duke.cs.osprey.restypes.ResidueTemplate
- DihedralRotation - Class in edu.duke.cs.osprey.dof
-
This is a RigidBodyMotion that changes the dihedral defined by some specified atoms
- DihedralRotation(double[], double[], double) - Constructor for class edu.duke.cs.osprey.dof.DihedralRotation
- DihedralRotation(double[], double[], double, double) - Constructor for class edu.duke.cs.osprey.dof.DihedralRotation
- dimensions - Variable in class edu.duke.cs.osprey.tools.MathTools.GridIterable
- dindex - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralInPlaneAngles2
- dindex - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralOutOfPlaneAngles2
- dir - Variable in class edu.duke.cs.osprey.structure.analysis.PDBScanner
- direct(Directions, NodeProcessor) - Method in interface edu.duke.cs.osprey.coffee.Coffee.Director
-
Start the computation, manage the cluster members, and finish the computation.
- direct(Directions, NodeProcessor) - Method in class edu.duke.cs.osprey.coffee.directors.AffinityDirector
- direct(Directions, NodeProcessor) - Method in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- direct(Directions, NodeProcessor) - Method in class edu.duke.cs.osprey.coffee.directors.PfuncDirector
- direct(Directions, NodeProcessor) - Method in class edu.duke.cs.osprey.coffee.directors.PfuncsDirector
- direct(Directions, NodeProcessor) - Method in class edu.duke.cs.osprey.coffee.directors.SequenceDirector
- Direct - Enum constant in enum class edu.duke.cs.osprey.gpu.BufferTools.Type
- Directions - Class in edu.duke.cs.osprey.coffee.directions
- Directions(MultiStateConfSpace, ClusterMember) - Constructor for class edu.duke.cs.osprey.coffee.directions.Directions
- directorAddress() - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- Discrete - Enum constant in enum class edu.duke.cs.osprey.multistatekstar.KStarScore.KStarScoreType
- Discrete - Enum constant in enum class edu.duke.cs.osprey.multistatekstar.KStarScore.PartitionFunctionType
- DiscreteLowerBound - Enum constant in enum class edu.duke.cs.osprey.multistatekstar.KStarScore.KStarScoreType
- DiscreteUpperBound - Enum constant in enum class edu.duke.cs.osprey.multistatekstar.KStarScore.KStarScoreType
- dist - Variable in class edu.duke.cs.osprey.energy.compiled.PosInterGen
- dist - Variable in class edu.duke.cs.osprey.structure.Probe.AtomPair.Interaction
- distance(double[], double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- distance(double[], int, double[], int) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- distanceTo(Residue) - Method in class edu.duke.cs.osprey.structure.Residue
- distDepDielect - Variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- div(double) - Method in class edu.duke.cs.osprey.tools.BigExp
- div(double) - Method in class edu.duke.cs.osprey.tools.BigMath
- div(int) - Method in class edu.duke.cs.osprey.tools.BigExp
- div(long) - Method in class edu.duke.cs.osprey.tools.BigExp
- div(long) - Method in class edu.duke.cs.osprey.tools.BigMath
- div(BigExp) - Method in class edu.duke.cs.osprey.tools.BigExp
- div(BigExp) - Method in class edu.duke.cs.osprey.tools.BigMath
- div(BigDecimal) - Method in class edu.duke.cs.osprey.tools.BigMath
- div(BigInteger) - Method in class edu.duke.cs.osprey.tools.BigMath
- divide(BigDecimal) - Method in class edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal
- divide(BigDecimal, int, int) - Method in class edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal
- divide(BigDecimal, MathContext) - Method in class edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal
- divUp(int, int) - Static method in class edu.duke.cs.osprey.tools.MathTools
- doCalculation() - Method in class edu.duke.cs.osprey.ematrix.TermECalculator
- doCalculation() - Method in interface edu.duke.cs.osprey.handlempi.MPISlaveTask
- doCheckPoint - Static variable in class edu.duke.cs.osprey.kstar.KSAbstract
- DoCOMETS - Enum constant in enum class edu.duke.cs.osprey.control.Main.Command
- dof - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle
- Dof() - Constructor for class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Dof
- Dof(String, double, double) - Constructor for class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Dof
- DOFBlock - Interface in edu.duke.cs.osprey.dof
-
A block of degrees of freedom that are applied together
- dofBlockIds - Variable in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- dofBlockIds() - Method in interface edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction.Approximator.Addable
- dofBlockIds() - Method in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- dofBounds - Variable in class edu.duke.cs.osprey.confspace.ParametricMolecule
-
Bounds on the degrees of freedom
- dofBounds - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf
- DofBounds(int) - Constructor for class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- DofBounds(DoubleMatrix1D[]) - Constructor for class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- DofBounds(ObjectiveFunction.DofBounds) - Constructor for class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- dofCounts - Variable in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- dofCounts() - Method in interface edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction.Approximator.Addable
- dofCounts() - Method in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- dofInfo - Variable in class edu.duke.cs.osprey.energy.approximation.ResidueInteractionsApproximator.Builder
- DofInfo - Class in edu.duke.cs.osprey.dof
- DofInfo(RCTuple) - Constructor for class edu.duke.cs.osprey.dof.DofInfo
- DOFInterval(DegreeOfFreedom, double, double) - Constructor for class edu.duke.cs.osprey.plug.VoxelVDWListChecker.DOFInterval
- doFit(FitParams) - Method in class edu.duke.cs.osprey.ematrix.epic.EPICFitter
- DofMatrix - Class in edu.duke.cs.osprey.ematrix
- DofMatrix(ConfSpace) - Constructor for class edu.duke.cs.osprey.ematrix.DofMatrix
- DOFmax - Variable in class edu.duke.cs.osprey.confspace.RC
- DOFmin - Variable in class edu.duke.cs.osprey.confspace.RC
- dofPhi - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation
- dofPsi - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation
- dofs - Variable in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords
-
degrees of freedom that modify the atom coords
- dofs - Variable in class edu.duke.cs.osprey.confspace.ParametricMolecule
-
Degrees of freedom.
- DOFs - Variable in class edu.duke.cs.osprey.confspace.RC
- dofTheta - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation
- dofValues - Variable in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator.EnergiedCoords
-
non-null only when the conformation was minimized
- dofValues - Variable in class edu.duke.cs.osprey.minimization.Minimizer.Result
- dofX - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation
- dofY - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation
- dofZ - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation
- doIMinDEE - Variable in class edu.duke.cs.osprey.gmec.DEEGMECFinder
- doingKAStar() - Method in class edu.duke.cs.osprey.kstar.KSCalc
- doingPhase2 - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- doIntegral() - Method in class edu.duke.cs.osprey.voxq.BoltzmannIntegrator1D
- doMultiTermPruning(PruningMatrix, boolean) - Method in class edu.duke.cs.osprey.plug.PolytopeMatrix
- doneSignal - Variable in class edu.duke.cs.osprey.parallelism.TimingThread
- Donor - Enum constant in enum class edu.duke.cs.osprey.structure.Probe.AtomFlag
- dontApproximate(ResidueInteractions.Pair) - Method in class edu.duke.cs.osprey.energy.approximation.ResidueInteractionsApproximator.Builder
- DontDoRawMathWithMagicException() - Constructor for exception edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal.DontDoRawMathWithMagicException
- doPerturbationMotion(double) - Method in class edu.duke.cs.osprey.dof.deeper.perts.Backrub
- doPerturbationMotion(double) - Method in class edu.duke.cs.osprey.dof.deeper.perts.LoopClosureAdjustment
- doPerturbationMotion(double) - Method in class edu.duke.cs.osprey.dof.deeper.perts.PartialStructureSwitch
- doPerturbationMotion(double) - Method in class edu.duke.cs.osprey.dof.deeper.perts.Perturbation
- doPerturbationMotion(double) - Method in class edu.duke.cs.osprey.dof.deeper.perts.Shear
- doPerturbations() - Method in class edu.duke.cs.osprey.dof.deeper.DEEPerSettings
- doScan - Variable in class edu.duke.cs.osprey.design.commands.CommandBindingAffinity
- dot(double[], double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- Dot - Enum constant in enum class edu.duke.cs.osprey.tools.resultdoc.Plot.PointType
- DoubleBounds() - Constructor for class edu.duke.cs.osprey.tools.MathTools.DoubleBounds
- DoubleBounds(double, double) - Constructor for class edu.duke.cs.osprey.tools.MathTools.DoubleBounds
- doubleBuffers - Variable in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- doubleValue - Variable in class edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal
- doubleValue() - Method in class edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal
- DOWN - Enum constant in enum class edu.duke.cs.osprey.dof.ProlinePucker.Direction
- downloadAsync() - Method in class edu.duke.cs.osprey.gpu.cuda.CUBuffer
- downloadAsync(Pointer, CUdeviceptr, long, GpuStream) - Method in class edu.duke.cs.osprey.gpu.cuda.Context
- downloadBufferAsync(CLBuffer<?>) - Method in class edu.duke.cs.osprey.gpu.opencl.Kernel
- downloadBufferSync(CLBuffer<?>) - Method in class edu.duke.cs.osprey.gpu.opencl.Kernel
- downloadCoordsSync() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.ForcefieldKernelOpenCL
- downloadEnergySync() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ForcefieldKernelCuda
- downloadEnergySync() - Method in interface edu.duke.cs.osprey.gpu.ForcefieldKernel
- downloadEnergySync() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.ForcefieldKernelOpenCL
- downloadResultSync() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.CCDKernelCuda
- downloadSync() - Method in class edu.duke.cs.osprey.gpu.cuda.CUBuffer
- downloadSync() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.TestFancyKernel
- doWork() - Method in class edu.duke.cs.osprey.parallelism.Worker
- doWork() - Method in class edu.duke.cs.osprey.parallelism.WorkQueueThread
- doWork() - Method in class edu.duke.cs.osprey.parallelism.WorkThread
- doWork(T) - Method in class edu.duke.cs.osprey.parallelism.WorkQueueThread
- doWTCalc - Variable in class edu.duke.cs.osprey.kstar.KSAbstract
- draw() - Method in class edu.duke.cs.osprey.tools.SVG.Drawable
- draw(SVG) - Method in class edu.duke.cs.osprey.tools.SVGPlot.BottomAxis
- draw(SVG) - Method in class edu.duke.cs.osprey.tools.SVGPlot.Boxes
- draw(SVG) - Method in class edu.duke.cs.osprey.tools.SVGPlot.Intervals
- draw(SVG) - Method in class edu.duke.cs.osprey.tools.SVGPlot.LeftAxis
- Drawable() - Constructor for class edu.duke.cs.osprey.tools.SVG.Drawable
- drop(MultiStateConfSpace.State, Sequence, BigExp) - Method in class edu.duke.cs.osprey.coffee.seqdb.Batch
- dropHandler - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices
- dropped - Variable in class edu.duke.cs.osprey.coffee.nodedb.PriorityDequeFixedIndex
- dropped() - Method in interface edu.duke.cs.osprey.coffee.nodedb.FixedIndex
-
Returns the queue of dropped items.
- dropped() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex
- dropped() - Method in class edu.duke.cs.osprey.coffee.nodedb.PriorityDequeFixedIndex
- dump() - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqDB
- dump() - Method in class edu.duke.cs.osprey.sofea.SeqDB
- dump() - Method in class edu.duke.cs.osprey.structure.analysis.DegreesHistogram
- dump(int) - Method in class edu.duke.cs.osprey.structure.analysis.DegreesHistogram
- dump(File) - Method in class edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger
- dumpJobsTo(File) - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
-
Write minimization jobs to the file and throw an error instead of actually minimizing them.
- dumpPairs(AtomNeighbors.Type) - Method in class edu.duke.cs.osprey.structure.AtomConnectivity.AtomPairs
- DUNBRACK_PROBABILTY_CUTOFF - Static variable in class edu.duke.cs.osprey.control.EnvironmentVars
-
Deprecated.
- dynamic(ConfSpace, int[]) - Static method in enum class edu.duke.cs.osprey.confspace.compiled.PosInterDist
- dynamic(ConfSpace, int[]) - Method in class edu.duke.cs.osprey.energy.compiled.PosInterGen
- dynamic(ConfSpace, SimpleReferenceEnergies, int[]) - Static method in enum class edu.duke.cs.osprey.confspace.compiled.PosInterDist
-
Include all dynamic interactions, except ones between unassigned positions.
- DynamicHMeanAStarOrder - Class in edu.duke.cs.osprey.astar.conf.order
- DynamicHMeanAStarOrder() - Constructor for class edu.duke.cs.osprey.astar.conf.order.DynamicHMeanAStarOrder
- DynamicHMeanAStarOrder(MathTools.Optimizer) - Constructor for class edu.duke.cs.osprey.astar.conf.order.DynamicHMeanAStarOrder
- dynamicPartition(Iterator<T>) - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- DynamicSize - Static variable in class edu.duke.cs.osprey.tools.MapDBTools.SimpleSerializer
){kind=link}
){kind=link}
){kind=link}
){kind=link}
E
- e - Variable in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- e - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- E - Variable in class edu.duke.cs.osprey.confspace.TupE
- E0 - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- eAppx - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- ecalc - Variable in class edu.duke.cs.osprey.ematrix.SimpleEnergyMatrixCalculator
-
Deprecated.
- ecalc - Variable in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- ecalc - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarGradientDescentPfunc
- ecalc - Variable in class edu.duke.cs.osprey.gmec.DEEGMECFinder
- ecalc - Variable in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- ecalc - Variable in class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator
- ecalc - Variable in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- ecalc - Variable in class edu.duke.cs.osprey.kstar.pfunc.SimplePartitionFunction
- ecalc - Variable in class edu.duke.cs.osprey.lute.LUTEGScorer
- ecalc - Variable in class edu.duke.cs.osprey.lute.LUTEHScorer
- ecalc - Variable in class edu.duke.cs.osprey.lute.LUTEPfunc
- ecalc - Variable in class edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc
- ecalc - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound.ScoreContext
- ecalc - Variable in class edu.duke.cs.osprey.paste.PasteGradientDescentPfunc
- ecalcs - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- ecalcs - Variable in class edu.duke.cs.osprey.multistatekstar.MSKStarSettings
- EConvTol - Static variable in class edu.duke.cs.osprey.minimization.CCDMinimizer
- EDEP() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.VanDerWaalsRadius
-
Returns the value of the
EDEPrecord component. - EdgeUpdater - Class in edu.duke.cs.osprey.astar.conf.scoring.mplp
- EdgeUpdater() - Constructor for class edu.duke.cs.osprey.astar.conf.scoring.mplp.EdgeUpdater
- edu.duke.cs.osprey - package edu.duke.cs.osprey
- edu.duke.cs.osprey.astar - package edu.duke.cs.osprey.astar
- edu.duke.cs.osprey.astar.comets - package edu.duke.cs.osprey.astar.comets
- edu.duke.cs.osprey.astar.conf - package edu.duke.cs.osprey.astar.conf
- edu.duke.cs.osprey.astar.conf.linked - package edu.duke.cs.osprey.astar.conf.linked
- edu.duke.cs.osprey.astar.conf.order - package edu.duke.cs.osprey.astar.conf.order
- edu.duke.cs.osprey.astar.conf.pruning - package edu.duke.cs.osprey.astar.conf.pruning
- edu.duke.cs.osprey.astar.conf.scoring - package edu.duke.cs.osprey.astar.conf.scoring
- edu.duke.cs.osprey.astar.conf.scoring.mplp - package edu.duke.cs.osprey.astar.conf.scoring.mplp
- edu.duke.cs.osprey.astar.conf.smastar - package edu.duke.cs.osprey.astar.conf.smastar
- edu.duke.cs.osprey.astar.seq - package edu.duke.cs.osprey.astar.seq
- edu.duke.cs.osprey.astar.seq.nodes - package edu.duke.cs.osprey.astar.seq.nodes
- edu.duke.cs.osprey.astar.seq.order - package edu.duke.cs.osprey.astar.seq.order
- edu.duke.cs.osprey.astar.seq.scoring - package edu.duke.cs.osprey.astar.seq.scoring
- edu.duke.cs.osprey.bbfree - package edu.duke.cs.osprey.bbfree
- edu.duke.cs.osprey.coffee - package edu.duke.cs.osprey.coffee
- edu.duke.cs.osprey.coffee.bounds - package edu.duke.cs.osprey.coffee.bounds
- edu.duke.cs.osprey.coffee.directions - package edu.duke.cs.osprey.coffee.directions
- edu.duke.cs.osprey.coffee.directors - package edu.duke.cs.osprey.coffee.directors
- edu.duke.cs.osprey.coffee.nodedb - package edu.duke.cs.osprey.coffee.nodedb
- edu.duke.cs.osprey.coffee.seqdb - package edu.duke.cs.osprey.coffee.seqdb
- edu.duke.cs.osprey.coffee.zmat - package edu.duke.cs.osprey.coffee.zmat
- edu.duke.cs.osprey.confspace - package edu.duke.cs.osprey.confspace
- edu.duke.cs.osprey.confspace.compiled - package edu.duke.cs.osprey.confspace.compiled
- edu.duke.cs.osprey.confspace.compiled.motions - package edu.duke.cs.osprey.confspace.compiled.motions
- edu.duke.cs.osprey.control - package edu.duke.cs.osprey.control
- edu.duke.cs.osprey.design - package edu.duke.cs.osprey.design
- edu.duke.cs.osprey.design.analysis - package edu.duke.cs.osprey.design.analysis
- edu.duke.cs.osprey.design.commands - package edu.duke.cs.osprey.design.commands
- edu.duke.cs.osprey.design.models - package edu.duke.cs.osprey.design.models
- edu.duke.cs.osprey.dof - package edu.duke.cs.osprey.dof
- edu.duke.cs.osprey.dof.deeper - package edu.duke.cs.osprey.dof.deeper
- edu.duke.cs.osprey.dof.deeper.perts - package edu.duke.cs.osprey.dof.deeper.perts
- edu.duke.cs.osprey.ematrix - package edu.duke.cs.osprey.ematrix
- edu.duke.cs.osprey.ematrix.compiled - package edu.duke.cs.osprey.ematrix.compiled
- edu.duke.cs.osprey.ematrix.epic - package edu.duke.cs.osprey.ematrix.epic
- edu.duke.cs.osprey.energy - package edu.duke.cs.osprey.energy
- edu.duke.cs.osprey.energy.approximation - package edu.duke.cs.osprey.energy.approximation
- edu.duke.cs.osprey.energy.compiled - package edu.duke.cs.osprey.energy.compiled
- edu.duke.cs.osprey.energy.forcefield - package edu.duke.cs.osprey.energy.forcefield
- edu.duke.cs.osprey.energy.forcefield.amber - package edu.duke.cs.osprey.energy.forcefield.amber
- edu.duke.cs.osprey.ewakstar - package edu.duke.cs.osprey.ewakstar
- edu.duke.cs.osprey.externalMemory - package edu.duke.cs.osprey.externalMemory
- edu.duke.cs.osprey.gmec - package edu.duke.cs.osprey.gmec
- edu.duke.cs.osprey.gpu - package edu.duke.cs.osprey.gpu
- edu.duke.cs.osprey.gpu.cuda - package edu.duke.cs.osprey.gpu.cuda
- edu.duke.cs.osprey.gpu.cuda.kernels - package edu.duke.cs.osprey.gpu.cuda.kernels
- edu.duke.cs.osprey.gpu.opencl - package edu.duke.cs.osprey.gpu.opencl
- edu.duke.cs.osprey.gpu.opencl.kernels - package edu.duke.cs.osprey.gpu.opencl.kernels
- edu.duke.cs.osprey.handlempi - package edu.duke.cs.osprey.handlempi
- edu.duke.cs.osprey.ibis - package edu.duke.cs.osprey.ibis
- edu.duke.cs.osprey.kstar - package edu.duke.cs.osprey.kstar
- edu.duke.cs.osprey.kstar.emat - package edu.duke.cs.osprey.kstar.emat
- edu.duke.cs.osprey.kstar.impl - package edu.duke.cs.osprey.kstar.impl
- edu.duke.cs.osprey.kstar.pfunc - package edu.duke.cs.osprey.kstar.pfunc
- edu.duke.cs.osprey.kstar.pfunc.impl - package edu.duke.cs.osprey.kstar.pfunc.impl
- edu.duke.cs.osprey.kstar.pruning - package edu.duke.cs.osprey.kstar.pruning
- edu.duke.cs.osprey.lute - package edu.duke.cs.osprey.lute
- edu.duke.cs.osprey.markstar - package edu.duke.cs.osprey.markstar
- edu.duke.cs.osprey.markstar.framework - package edu.duke.cs.osprey.markstar.framework
- edu.duke.cs.osprey.markstar.visualizer - package edu.duke.cs.osprey.markstar.visualizer
- edu.duke.cs.osprey.minimization - package edu.duke.cs.osprey.minimization
- edu.duke.cs.osprey.multistatekstar - package edu.duke.cs.osprey.multistatekstar
- edu.duke.cs.osprey.parallelism - package edu.duke.cs.osprey.parallelism
- edu.duke.cs.osprey.partcr - package edu.duke.cs.osprey.partcr
- edu.duke.cs.osprey.partcr.pickers - package edu.duke.cs.osprey.partcr.pickers
- edu.duke.cs.osprey.partcr.scorers - package edu.duke.cs.osprey.partcr.scorers
- edu.duke.cs.osprey.partcr.splitters - package edu.duke.cs.osprey.partcr.splitters
- edu.duke.cs.osprey.paste - package edu.duke.cs.osprey.paste
- edu.duke.cs.osprey.plug - package edu.duke.cs.osprey.plug
- edu.duke.cs.osprey.pruning - package edu.duke.cs.osprey.pruning
- edu.duke.cs.osprey.restypes - package edu.duke.cs.osprey.restypes
- edu.duke.cs.osprey.sofea - package edu.duke.cs.osprey.sofea
- edu.duke.cs.osprey.structure - package edu.duke.cs.osprey.structure
- edu.duke.cs.osprey.structure.analysis - package edu.duke.cs.osprey.structure.analysis
- edu.duke.cs.osprey.tests - package edu.duke.cs.osprey.tests
- edu.duke.cs.osprey.tools - package edu.duke.cs.osprey.tools
- edu.duke.cs.osprey.tools.resultdoc - package edu.duke.cs.osprey.tools.resultdoc
- edu.duke.cs.osprey.tupexp - package edu.duke.cs.osprey.tupexp
- edu.duke.cs.osprey.voxq - package edu.duke.cs.osprey.voxq
- EEF1 - Class in edu.duke.cs.osprey.energy.forcefield
-
Manages the EEF1 solvation parameters; EEF1 handles only natural amino acids, so solvation energies are computed for proteins and ligands (natural amino acids) only, and not cofactors; Some important notes about assumptions of the EEF1 model are given in the comments to getSolvationParameters()
- EEF1 - Enum constant in enum class edu.duke.cs.osprey.energy.compiled.EnergyCalculator.Type
- EEF1 - Enum constant in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.SolvationForcefield
- EEF1() - Constructor for class edu.duke.cs.osprey.energy.forcefield.EEF1
- EEF1.ResiduesInfo - Class in edu.duke.cs.osprey.energy.forcefield
- EEF1.SolvParams - Class in edu.duke.cs.osprey.energy.forcefield
- EEF1EnergyCalculator - Class in edu.duke.cs.osprey.energy.compiled
-
Calculate energies from a compiled ConfSpace.AssignedCoords according to the EEF1 forcefield.
- EEF1EnergyCalculator(String, int) - Constructor for class edu.duke.cs.osprey.energy.compiled.EEF1EnergyCalculator
- eef1parms - Variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- effectiveEpsilon - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- Efficient - Enum constant in enum class edu.duke.cs.osprey.coffee.directors.Timing
-
Within the first 5 minutes of computation, use quicker batches, but gradually grow to 1 min batches.
- EFullConfOnly - Variable in class edu.duke.cs.osprey.gmec.GMECFinder
- efunc - Variable in class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.ByPosition
- efunc - Variable in class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.ByResidue
- efunc - Variable in class edu.duke.cs.osprey.minimization.MoleculeObjectiveFunction
- efuncs - Variable in class edu.duke.cs.osprey.energy.EnergyCalculator.Type.Context
- efuncsByDof - Variable in class edu.duke.cs.osprey.minimization.MoleculeObjectiveFunction
- Electrostatics - Enum constant in enum class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.Type
- elementNumber - Variable in class edu.duke.cs.osprey.structure.Atom
- elementType - Variable in class edu.duke.cs.osprey.structure.Atom
- EllipseCoordDOF - Class in edu.duke.cs.osprey.dof
- EllipseCoordDOF(boolean, int, double, DoubleMatrix2D, ArrayList<DegreeOfFreedom>, double[]) - Constructor for class edu.duke.cs.osprey.dof.EllipseCoordDOF
- EllipseTransform - Class in edu.duke.cs.osprey.tools
- EllipseTransform(DoubleMatrix2D, DoubleMatrix1D) - Constructor for class edu.duke.cs.osprey.tools.EllipseTransform
- elst - Variable in class edu.duke.cs.osprey.astar.seq.SeqAStarTree
- em - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.LengthUnit
- emat - Variable in class edu.duke.cs.osprey.astar.conf.ConfRanker
- emat - Variable in class edu.duke.cs.osprey.astar.conf.scoring.PairwiseGScorer
- emat - Variable in class edu.duke.cs.osprey.astar.conf.scoring.TraditionalPairwiseHScorer
- emat - Variable in class edu.duke.cs.osprey.astar.ConfTree
- emat - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- emat - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.State
- emat - Variable in class edu.duke.cs.osprey.gmec.DEEGMECFinder
- emat - Variable in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- emat - Variable in class edu.duke.cs.osprey.pruning.SimpleDEE
- emat - Variable in class edu.duke.cs.osprey.sofea.Sofea.StateConfig
-
An energy matrix of lower energy bounds on RC tuples.
- EMAT - Enum constant in enum class edu.duke.cs.osprey.confspace.SearchProblem.MatrixType
- EMAT - Enum constant in enum class edu.duke.cs.osprey.gmec.PrecomputedMatrices.MatrixType
- EMAT - Enum constant in enum class edu.duke.cs.osprey.kstar.KSSearchProblem.MatrixType
- EmatCalculator - Class in edu.duke.cs.osprey.ematrix.compiled
-
Calculates energy matrices for a conformation space.
- EmatCalculator.Builder - Class in edu.duke.cs.osprey.ematrix.compiled
- ematDir - Variable in class edu.duke.cs.osprey.kstar.KSAbstract
- ematRigid - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.State
- embed(byte[], String) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc.Image
-
binary image
- embed(byte[], String, String) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc.File
-
binary file
- embed(String, String) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc.Image
-
text image
- embed(String, String, String) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc.File
-
text file
- EMConfAStarFactory - Class in edu.duke.cs.osprey.externalMemory
- EMConfAStarFactory() - Constructor for class edu.duke.cs.osprey.externalMemory.EMConfAStarFactory
- EMConfAStarNode - Class in edu.duke.cs.osprey.externalMemory
- EMConfAStarNode(int) - Constructor for class edu.duke.cs.osprey.externalMemory.EMConfAStarNode
- EMConfAStarNode(EMConfAStarNode) - Constructor for class edu.duke.cs.osprey.externalMemory.EMConfAStarNode
- encoding - Variable in class edu.duke.cs.osprey.externalMemory.AssignmentsSerializer
- End - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.TextAnchor
- EnergiedConf(int[], double, double) - Constructor for class edu.duke.cs.osprey.confspace.ConfSearch.EnergiedConf
- EnergiedConf(ConfSearch.ScoredConf, double) - Constructor for class edu.duke.cs.osprey.confspace.ConfSearch.EnergiedConf
- EnergiedConfFIFOSerializer - Class in edu.duke.cs.osprey.externalMemory
- EnergiedConfFIFOSerializer(RCs) - Constructor for class edu.duke.cs.osprey.externalMemory.EnergiedConfFIFOSerializer
- EnergiedConfPrioritySerializer - Class in edu.duke.cs.osprey.externalMemory
- EnergiedConfPrioritySerializer(RCs) - Constructor for class edu.duke.cs.osprey.externalMemory.EnergiedConfPrioritySerializer
- EnergiedConfQueue - Class in edu.duke.cs.osprey.design.analysis
- EnergiedConfQueue(int) - Constructor for class edu.duke.cs.osprey.design.analysis.EnergiedConfQueue
- energiedConfs(ConfDB.SortOrder) - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- EnergiedCoords(AssignedCoords, double) - Constructor for class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator.EnergiedCoords
- EnergiedCoords(AssignedCoords, double, DoubleMatrix1D) - Constructor for class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator.EnergiedCoords
- EnergiedParametricMolecule(ParametricMolecule, ResidueInteractions, double) - Constructor for class edu.duke.cs.osprey.energy.EnergyCalculator.EnergiedParametricMolecule
- EnergiedParametricMolecule(ParametricMolecule, ResidueInteractions, DoubleMatrix1D, double) - Constructor for class edu.duke.cs.osprey.energy.EnergyCalculator.EnergiedParametricMolecule
- energies - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Conf
-
indexed by ffi
- energy - Variable in class edu.duke.cs.osprey.confspace.ConfDB.Conf.Bound
- energy - Variable in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator.EnergiedCoords
- energy - Variable in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator.MinimizationJob
- energy - Variable in class edu.duke.cs.osprey.energy.EnergyCalculator.EnergiedParametricMolecule
- energy - Variable in class edu.duke.cs.osprey.minimization.Minimizer.Result
- Energy - Enum constant in enum class edu.duke.cs.osprey.confspace.ConfDB.SortOrder
- EnergyAnalysisConfListener - Class in edu.duke.cs.osprey.design.analysis
- EnergyAnalysisConfListener(ConfEnergyCalculator, List<Integer>) - Constructor for class edu.duke.cs.osprey.design.analysis.EnergyAnalysisConfListener
- energyBoundStats - Variable in class edu.duke.cs.osprey.coffee.StateInfo
- EnergyBoundStats - Class in edu.duke.cs.osprey.coffee
-
Essentially a histogram of gaps in the energy bounds.
- EnergyBoundStats() - Constructor for class edu.duke.cs.osprey.coffee.EnergyBoundStats
- EnergyCalculator - Class in edu.duke.cs.osprey.control
- EnergyCalculator - Class in edu.duke.cs.osprey.energy
-
Computes the energy of a molecule fragment from a conformation space using the desired forcefield parameters and residue interactions.
- EnergyCalculator - Interface in edu.duke.cs.osprey.energy.compiled
-
Calculates the energy of atomic coordinates according to a forcefield definition.
- EnergyCalculator() - Constructor for class edu.duke.cs.osprey.control.EnergyCalculator
- EnergyCalculator.Builder - Class in edu.duke.cs.osprey.energy
- EnergyCalculator.EnergiedParametricMolecule - Class in edu.duke.cs.osprey.energy
- EnergyCalculator.SharedBuilder - Class in edu.duke.cs.osprey.energy
-
Create an energy calculator that shares resources with an existing energy calculator, (including thread pools, GPUs, atom connectivity cache, forcefield), but can have different configuration.
- EnergyCalculator.Type - Enum Class in edu.duke.cs.osprey.energy.compiled
- EnergyCalculator.Type - Enum Class in edu.duke.cs.osprey.energy
- EnergyCalculator.Type.Context - Class in edu.duke.cs.osprey.energy
- EnergyCalculator.Type.EfuncFactory - Interface in edu.duke.cs.osprey.energy
- energyConfs - Variable in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- EnergyFunction - Interface in edu.duke.cs.osprey.energy
- EnergyFunction.DecomposableByDof - Interface in edu.duke.cs.osprey.energy
- EnergyFunction.ExplicitChemicalChanges - Interface in edu.duke.cs.osprey.energy
- EnergyFunction.NeedsCleanup - Interface in edu.duke.cs.osprey.energy
- EnergyFunction.NeedsInit - Interface in edu.duke.cs.osprey.energy
- EnergyFunction.Tools - Class in edu.duke.cs.osprey.energy
- EnergyFunctionGenerator - Class in edu.duke.cs.osprey.energy
- EnergyFunctionGenerator(ForcefieldParams) - Constructor for class edu.duke.cs.osprey.energy.EnergyFunctionGenerator
- energyLB - Variable in class edu.duke.cs.osprey.kstar.KAStarConfTree
- energyLBs - Variable in class edu.duke.cs.osprey.multistatekstar.MSSearchSettings
- energyLBs - Variable in class edu.duke.cs.osprey.multistatekstar.MultiSequenceConfTree
- EnergyMatrix - Class in edu.duke.cs.osprey.ematrix
-
Matrix of energies between pairs of residue conformations.
- EnergyMatrix(int, int[], double) - Constructor for class edu.duke.cs.osprey.ematrix.EnergyMatrix
- EnergyMatrix(ConfSpaceIteration) - Constructor for class edu.duke.cs.osprey.ematrix.EnergyMatrix
- EnergyMatrix(ConfSpace, double) - Constructor for class edu.duke.cs.osprey.ematrix.EnergyMatrix
- EnergyMatrix(SimpleConfSpace) - Constructor for class edu.duke.cs.osprey.ematrix.EnergyMatrix
- EnergyMatrix(EnergyMatrix) - Constructor for class edu.duke.cs.osprey.ematrix.EnergyMatrix
- energyMatrixCachePattern - Variable in class edu.duke.cs.osprey.markstar.MARKStar.Settings
- EnergyMatrixCalculator - Class in edu.duke.cs.osprey.ematrix
- EnergyMatrixCalculator(ConfSpace, ArrayList<Residue>, boolean, boolean) - Constructor for class edu.duke.cs.osprey.ematrix.EnergyMatrixCalculator
- EnergyMatrixCalculator(ConfSpace, ArrayList<Residue>, boolean, PruningMatrix, EPICSettings, boolean, EnergyMatrix) - Constructor for class edu.duke.cs.osprey.ematrix.EnergyMatrixCalculator
- EnergyMatrixCalculator(ConfSpace, ArrayList<Residue>, PruningMatrix, EPICSettings) - Constructor for class edu.duke.cs.osprey.ematrix.EnergyMatrixCalculator
- energyNextConfAsync() - Method in class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator
- energyNextConfAsync(TaskExecutor.TaskListener<ConfSearch.EnergiedConf>) - Method in class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator
- EnergyPartition - Enum Class in edu.duke.cs.osprey.energy
- EnergyRange - Class in edu.duke.cs.osprey.gmec
- EnergyRange(double, double) - Constructor for class edu.duke.cs.osprey.gmec.EnergyRange
- EnergyReached - Enum constant in enum class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Status
- EnergyReached - Enum constant in enum class edu.duke.cs.osprey.paste.PastePartitionFunction.Status
- enQueue(int[]) - Method in class edu.duke.cs.osprey.kstar.KSConfQ
- ensemble - Variable in class edu.duke.cs.osprey.kstar.SequenceAnalyzer.Analysis
- EnsembleAnalysis() - Constructor for class edu.duke.cs.osprey.gmec.ConfAnalyzer.EnsembleAnalysis
- EnsembleAnalysisListener - Class in edu.duke.cs.osprey.design.analysis
- EnsembleAnalysisListener(ConfEnergyCalculator, int, String) - Constructor for class edu.duke.cs.osprey.design.analysis.EnsembleAnalysisListener
- ensembleDir - Variable in class edu.duke.cs.osprey.coffee.directors.AffinityDirector
- ensembleDir - Variable in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- ensembleFile - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncDirector
- ensembleSize - Variable in class edu.duke.cs.osprey.coffee.directors.AffinityDirector
- ensembleSize - Variable in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- ensembleSize - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncDirector
- ensembleUpdate - Variable in class edu.duke.cs.osprey.coffee.directors.AffinityDirector
- ensembleUpdate - Variable in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- ensembleUpdate - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncDirector
- ensembleUpdateUnit - Variable in class edu.duke.cs.osprey.coffee.directors.AffinityDirector
- ensembleUpdateUnit - Variable in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- ensembleUpdateUnit - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncDirector
- entrySet() - Method in class edu.duke.cs.osprey.confspace.Conf.Map
- entrySize - Variable in class edu.duke.cs.osprey.externalMemory.AssignmentsSerializer
- enumerateCandidates(PruningMethod) - Method in class edu.duke.cs.osprey.pruning.NewPruner
- enumerateCandidates(PruningMethod) - Method in class edu.duke.cs.osprey.pruning.Pruner
- enumerated - Variable in class edu.duke.cs.osprey.kstar.KSPStarCalculator
- enumeratedConfs - Variable in class edu.duke.cs.osprey.kstar.pfunc.impl.PFUB
- enumerateUnprunedTuples(int) - Method in class edu.duke.cs.osprey.confspace.TupleEnumerator
- enumerateUnprunedTuples(ArrayList<ArrayList<Integer>>) - Method in class edu.duke.cs.osprey.confspace.TupleEnumerator
- EnvironmentVars - Class in edu.duke.cs.osprey.control
-
Deprecated.
- EnvironmentVars() - Constructor for class edu.duke.cs.osprey.control.EnvironmentVars
-
Deprecated.
- epart - Variable in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- EPICEnergyFunction - Class in edu.duke.cs.osprey.ematrix.epic
-
An energy function representing a sum of EPIC terms it evaluates them using the DOF values in curDOFVals
- EPICEnergyFunction(ArrayList<EPoly>, boolean) - Constructor for class edu.duke.cs.osprey.ematrix.epic.EPICEnergyFunction
- EPICFitter - Class in edu.duke.cs.osprey.ematrix.epic
- EPICFitter(MoleculeModifierAndScorer, EPICSettings, DoubleMatrix1D, double) - Constructor for class edu.duke.cs.osprey.ematrix.epic.EPICFitter
- EPICGoalResid - Variable in class edu.duke.cs.osprey.ematrix.epic.EPICSettings
- epicMat - Variable in class edu.duke.cs.osprey.astar.ConfTree
- epicMat - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- EPICMAT - Enum constant in enum class edu.duke.cs.osprey.confspace.SearchProblem.MatrixType
- EPICMAT - Enum constant in enum class edu.duke.cs.osprey.gmec.PrecomputedMatrices.MatrixType
- EPICMAT - Enum constant in enum class edu.duke.cs.osprey.kstar.KSSearchProblem.MatrixType
- EPICMatrix - Class in edu.duke.cs.osprey.ematrix.epic
-
A matrix of 1-body, pairwise, etc.
- EPICMatrix(ConfSpace, double) - Constructor for class edu.duke.cs.osprey.ematrix.epic.EPICMatrix
- EPICMinimizedEnergy(int[]) - Method in class edu.duke.cs.osprey.confspace.SearchProblem
- epicSettings - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- epicSettings - Variable in class edu.duke.cs.osprey.gmec.DEEGMECFinder
- EPICSettings - Class in edu.duke.cs.osprey.ematrix.epic
- EPICSettings() - Constructor for class edu.duke.cs.osprey.ematrix.epic.EPICSettings
- EPICSettings(ParamSet) - Constructor for class edu.duke.cs.osprey.ematrix.epic.EPICSettings
- EPICThresh2 - Variable in class edu.duke.cs.osprey.ematrix.epic.EPICSettings
- epmol - Variable in class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.ByPosition
- epmol - Variable in class edu.duke.cs.osprey.gmec.ConfAnalyzer.ConfAnalysis
- epMols - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Result
- epMols - Variable in class edu.duke.cs.osprey.paste.PastePartitionFunction.Result
- EPoly - Class in edu.duke.cs.osprey.ematrix.epic
- EPoly(int, DoubleMatrix1D, DoubleMatrix1D, DoubleMatrix1D, double, double[], int, ArrayList<String>) - Constructor for class edu.duke.cs.osprey.ematrix.epic.EPoly
- EPoly(int, ArrayList<DegreeOfFreedom>, DoubleMatrix1D, DoubleMatrix1D, DoubleMatrix1D, double, double[], int) - Constructor for class edu.duke.cs.osprey.ematrix.epic.EPoly
- EPolyPC - Class in edu.duke.cs.osprey.ematrix.epic
- EPolyPC(EPoly, int, int, double) - Constructor for class edu.duke.cs.osprey.ematrix.epic.EPolyPC
- epsilon - Variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.NBParams
- epsilon - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings
- epsilon - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- epsilon - Variable in class edu.duke.cs.osprey.kstar.KStar.Settings
- epsilon - Variable in class edu.duke.cs.osprey.kstar.MSKStar
- epsilon - Variable in class edu.duke.cs.osprey.markstar.MARKStar.Settings
- epsilon - Variable in class edu.duke.cs.osprey.paste.Paste.Settings
- EPSILON_NEVER_POSSIBLE - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- EPSILON_PHASE_2 - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- epsilonBound - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- epsilonPossible() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- EpsilonReached - Enum constant in enum class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Status
- EpsilonReached - Enum constant in enum class edu.duke.cs.osprey.paste.PastePartitionFunction.Status
- equals(int[], int[]) - Static method in class edu.duke.cs.osprey.confspace.Conf
- equals(int[], int[]) - Method in class edu.duke.cs.osprey.tools.MapDBTools.IntArraySerializer
- equals(NodeIndex.Node) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex.Node
- equals(SeqFreeEnergies) - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqFreeEnergies
- equals(SeqInfo) - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqInfo
- equals(AbstractTupleMatrix<?>) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- equals(CoordsList) - Method in class edu.duke.cs.osprey.confspace.compiled.CoordsList
- equals(Conf.Map) - Method in class edu.duke.cs.osprey.confspace.Conf.Map
- equals(Conf.Set) - Method in class edu.duke.cs.osprey.confspace.Conf.Set
- equals(ConfSearch.EnergiedConf) - Method in class edu.duke.cs.osprey.confspace.ConfSearch.EnergiedConf
- equals(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.confspace.ConfSearch.ScoredConf
- equals(MultiStateConfSpace.State) - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.State
- equals(RCTuple) - Method in class edu.duke.cs.osprey.confspace.RCTuple
- equals(SeqSpace) - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- equals(SeqSpace.Position) - Method in class edu.duke.cs.osprey.confspace.SeqSpace.Position
- equals(SeqSpace.ResType) - Method in class edu.duke.cs.osprey.confspace.SeqSpace.ResType
- equals(Sequence) - Method in class edu.duke.cs.osprey.confspace.Sequence
- equals(SimpleReferenceEnergies) - Method in class edu.duke.cs.osprey.ematrix.SimpleReferenceEnergies
- equals(QuadraticApproximator) - Method in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- equals(CudaConfEnergyCalculator.GpuInfo) - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuInfo
- equals(ForcefieldDebugger.AtomPair) - Method in class edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger.AtomPair
- equals(ResidueInteractions.Pair) - Method in class edu.duke.cs.osprey.energy.ResidueInteractions.Pair
- equals(EWAKStarScore) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- equals(KStarScore) - Method in class edu.duke.cs.osprey.kstar.KStarScore
- equals(LUTEState) - Method in class edu.duke.cs.osprey.lute.LUTEState
- equals(TaskExecutor.ContextId) - Method in class edu.duke.cs.osprey.parallelism.TaskExecutor.ContextId
- equals(PasteScore) - Method in class edu.duke.cs.osprey.paste.PasteScore
- equals(SeqDB.SeqInfo) - Method in class edu.duke.cs.osprey.sofea.SeqDB.SeqInfo
- equals(BigExp) - Method in class edu.duke.cs.osprey.tools.BigExp
- equals(BigExp, BigExp) - Method in class edu.duke.cs.osprey.tools.MapDBTools.BigExpSerializer
- equals(MathTools.BigDecimalBounds) - Method in class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- equals(MathTools.BigDecimalBounds, MathTools.BigDecimalBounds) - Method in class edu.duke.cs.osprey.tools.MapDBTools.BigDecimalBoundsSerializer
- equals(MathTools.DoubleBounds) - Method in class edu.duke.cs.osprey.tools.MathTools.DoubleBounds
- equals(Object) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex.Node
- equals(Object) - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqFreeEnergies
- equals(Object) - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqInfo
- equals(Object) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- equals(Object) - Method in class edu.duke.cs.osprey.confspace.compiled.CoordsList
- equals(Object) - Method in class edu.duke.cs.osprey.confspace.Conf.Map
- equals(Object) - Method in class edu.duke.cs.osprey.confspace.Conf.Set
- equals(Object) - Method in class edu.duke.cs.osprey.confspace.ConfSearch.EnergiedConf
- equals(Object) - Method in class edu.duke.cs.osprey.confspace.ConfSearch.ScoredConf
- equals(Object) - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.State
- equals(Object) - Method in class edu.duke.cs.osprey.confspace.RCTuple
- equals(Object) - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- equals(Object) - Method in class edu.duke.cs.osprey.confspace.SeqSpace.Position
- equals(Object) - Method in class edu.duke.cs.osprey.confspace.SeqSpace.ResType
- equals(Object) - Method in class edu.duke.cs.osprey.confspace.Sequence
- equals(Object) - Method in class edu.duke.cs.osprey.design.models.Flexibility
- equals(Object) - Method in class edu.duke.cs.osprey.design.models.Residue
- equals(Object) - Method in class edu.duke.cs.osprey.design.models.ResidueModifier
- equals(Object) - Method in class edu.duke.cs.osprey.ematrix.SimpleReferenceEnergies
- equals(Object) - Method in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- equals(Object) - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuInfo
- equals(Object) - Method in class edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger.AtomPair
- equals(Object) - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.AtomSymbolAndMass
-
Indicates whether some other object is "equal to" this one.
- equals(Object) - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.BondAngleParameter
-
Indicates whether some other object is "equal to" this one.
- equals(Object) - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.BondLengthParameter
-
Indicates whether some other object is "equal to" this one.
- equals(Object) - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.DihederalParameter
-
Indicates whether some other object is "equal to" this one.
- equals(Object) - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.EquivalencingAtom
-
Indicates whether some other object is "equal to" this one.
- equals(Object) - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.HBond10_12PotentialParameter
-
Indicates whether some other object is "equal to" this one.
- equals(Object) - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.ImproperDihederalParameter
-
Indicates whether some other object is "equal to" this one.
- equals(Object) - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.Six12PotentialCoefficient
-
Indicates whether some other object is "equal to" this one.
- equals(Object) - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.Six12PotentialParameter
-
Indicates whether some other object is "equal to" this one.
- equals(Object) - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.SlaterKirkwoodParameter
-
Indicates whether some other object is "equal to" this one.
- equals(Object) - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.VanDerWaalsRadius
-
Indicates whether some other object is "equal to" this one.
- equals(Object) - Method in class edu.duke.cs.osprey.energy.ResidueInteractions.Pair
- equals(Object) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- equals(Object) - Method in class edu.duke.cs.osprey.kstar.KStarScore
- equals(Object) - Method in class edu.duke.cs.osprey.lute.LUTEState
- equals(Object) - Method in class edu.duke.cs.osprey.parallelism.TaskExecutor.ContextId
- equals(Object) - Method in class edu.duke.cs.osprey.paste.PasteScore
- equals(Object) - Method in class edu.duke.cs.osprey.sofea.SeqDB.SeqInfo
- equals(Object) - Method in class edu.duke.cs.osprey.tools.BigExp
- equals(Object) - Method in class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- equals(Object) - Method in class edu.duke.cs.osprey.tools.MathTools.DoubleBounds
- equals(Object) - Method in class edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal
- equals(BigDecimal, BigDecimal) - Method in class edu.duke.cs.osprey.tools.MapDBTools.BigDecimalSerializer
- EquivalencingAtom - Record Class in edu.duke.cs.osprey.energy.forcefield.amber
- EquivalencingAtom(AtomSymbolAndMass, AtomSymbolAndMass) - Constructor for record class edu.duke.cs.osprey.energy.forcefield.amber.EquivalencingAtom
-
Creates an instance of a
EquivalencingAtomrecord class. - equivalencingAtomsForNonBonded6_12PotentialParameters() - Method in class edu.duke.cs.osprey.energy.forcefield.amber.ForcefieldFileParser
- equivalentInMolec(Molecule) - Method in class edu.duke.cs.osprey.structure.Residue
- equivalentInMolec(ArrayList<Residue>, Molecule) - Static method in class edu.duke.cs.osprey.structure.Residue
- eref - Variable in class edu.duke.cs.osprey.energy.compiled.PosInterGen
- eref - Variable in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- ErefCalculator - Class in edu.duke.cs.osprey.ematrix.compiled
-
Calculate reference energies for a conformation space.
- ErefCalculator.Builder - Class in edu.duke.cs.osprey.ematrix.compiled
- error() - Method in interface edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction.Approximator
- error() - Method in class edu.duke.cs.osprey.energy.approximation.NOPApproximator
- error() - Method in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- error() - Method in class edu.duke.cs.osprey.energy.approximation.ResidueInteractionsApproximator.Builder
- errors - Variable in class edu.duke.cs.osprey.lute.LUTE.LinearSystem
- Errors(double[]) - Constructor for class edu.duke.cs.osprey.lute.LUTE.Errors
- estBondDistanceMatrix(ForcefieldParams) - Method in class edu.duke.cs.osprey.structure.Residue
- estBondEBL(Atom, Atom) - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- estDeltaG(double) - Method in class edu.duke.cs.osprey.voxq.VoxelsDeltaG
- Estimated - Enum constant in enum class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.PfuncsStatus
- Estimated - Enum constant in enum class edu.duke.cs.osprey.kstar.BBKStar.PfuncsStatus
- Estimated - Enum constant in enum class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Status
- estimateScore() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.MultiSequenceNode
- estimateScore() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.SingleSequenceNode
- estimateScore() - Method in class edu.duke.cs.osprey.kstar.BBKStar.MultiSequenceNode
- estimateScore() - Method in class edu.duke.cs.osprey.kstar.BBKStar.SingleSequenceNode
- Estimating - Enum constant in enum class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.PfuncsStatus
- Estimating - Enum constant in enum class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Status
- Estimating - Enum constant in enum class edu.duke.cs.osprey.kstar.BBKStar.PfuncsStatus
- Estimating - Enum constant in enum class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Status
- Estimating - Enum constant in enum class edu.duke.cs.osprey.paste.PastePartitionFunction.Status
- Et - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- eval(double[]) - Method in class edu.duke.cs.osprey.astar.comets.LME
- eval(DoubleMatrix1D, int[]) - Method in class edu.duke.cs.osprey.minimization.GenCoord
- evalAtFullDOFs(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.bbfree.BBFreeDOF
- evalSeries(double[], DoubleMatrix1D, int, boolean, int) - Static method in class edu.duke.cs.osprey.ematrix.epic.SeriesFitter
- evaluate(DoubleMatrix1D, boolean, boolean) - Method in class edu.duke.cs.osprey.ematrix.epic.EPoly
- eW - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings
- eW - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- eW - Variable in class edu.duke.cs.osprey.paste.Paste.Settings
- Ew - Variable in class edu.duke.cs.osprey.gmec.DEEGMECFinder
- EW - Variable in class edu.duke.cs.osprey.kstar.KSAbstract
- EWAKStar - Class in edu.duke.cs.osprey.ewakstar
- EWAKStar(SimpleConfSpace, SimpleConfSpace, SimpleConfSpace, EWAKStar.Settings) - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStar
- EWAKStar.ConfSpaceInfo - Class in edu.duke.cs.osprey.ewakstar
- EWAKStar.ConfSpaceType - Enum Class in edu.duke.cs.osprey.ewakstar
- EWAKStar.InitException - Exception in edu.duke.cs.osprey.ewakstar
- EWAKStar.ScoredSequence - Class in edu.duke.cs.osprey.ewakstar
- EWAKStar.Settings - Class in edu.duke.cs.osprey.ewakstar
- EWAKStar.Settings.Builder - Class in edu.duke.cs.osprey.ewakstar
- EWAKStarBBKStar - Class in edu.duke.cs.osprey.ewakstar
-
Adapted from BBKStar.java by lowegard
- EWAKStarBBKStar(EwakstarDoer.State, EwakstarDoer.State, EwakstarDoer.State, EWAKStar.Settings, EWAKStarBBKStar.Settings, Integer) - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar
- EWAKStarBBKStar.ConfSpaceInfo - Class in edu.duke.cs.osprey.ewakstar
- EWAKStarBBKStar.MultiSequenceNode - Class in edu.duke.cs.osprey.ewakstar
- EWAKStarBBKStar.PfuncsStatus - Enum Class in edu.duke.cs.osprey.ewakstar
- EWAKStarBBKStar.Settings - Class in edu.duke.cs.osprey.ewakstar
- EWAKStarBBKStar.Settings.Builder - Class in edu.duke.cs.osprey.ewakstar
- EWAKStarBBKStar.SingleSequenceNode - Class in edu.duke.cs.osprey.ewakstar
- EwakstarDoer - Class in edu.duke.cs.osprey.ewakstar
-
Implementation of the COMETS multi-state algorithm to predict protein sequence mutations that improve binding affinity.
- EwakstarDoer.Builder - Class in edu.duke.cs.osprey.ewakstar
- EwakstarDoer.Builder.InitException - Exception in edu.duke.cs.osprey.ewakstar
- EwakstarDoer.Results - Class in edu.duke.cs.osprey.ewakstar
- EwakstarDoer.SequenceInfo - Class in edu.duke.cs.osprey.ewakstar
- EwakstarDoer.State - Class in edu.duke.cs.osprey.ewakstar
-
A state for a multi-state design (e.g., an unbound state, or a complex state) For COMETS, all states must share the same sequence space.
- EwakstarDoer.State.InitException - Exception in edu.duke.cs.osprey.ewakstar
- ewakstarDoerL - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- ewakstarDoerP - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- ewakstarDoerPL - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- EWAKStarGradientDescentPfunc - Class in edu.duke.cs.osprey.ewakstar
-
This partition function calculator estimates the partition function value by alternating between two operations: 1.
- EWAKStarGradientDescentPfunc(ConfEnergyCalculator) - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarGradientDescentPfunc
- EwakstarLimitedSequenceTrie - Class in edu.duke.cs.osprey.ewakstar
- EwakstarLimitedSequenceTrie(SeqSpace) - Constructor for class edu.duke.cs.osprey.ewakstar.EwakstarLimitedSequenceTrie
- EWAKStarPartitionFunction - Interface in edu.duke.cs.osprey.ewakstar
-
based on PartitionFunction.java, author: lowegard
- EWAKStarPartitionFunction.ConfListener - Interface in edu.duke.cs.osprey.ewakstar
- EWAKStarPartitionFunction.Result - Class in edu.duke.cs.osprey.ewakstar
- EWAKStarPartitionFunction.Status - Enum Class in edu.duke.cs.osprey.ewakstar
- EWAKStarPartitionFunction.Values - Class in edu.duke.cs.osprey.ewakstar
- EWAKStarPartitionFunction.WithConfTable - Interface in edu.duke.cs.osprey.ewakstar
- EWAKStarPartitionFunction.WithConfTable.UnsupportedException - Exception in edu.duke.cs.osprey.ewakstar
- EWAKStarPartitionFunction.WithExternalMemory - Interface in edu.duke.cs.osprey.ewakstar
- EWAKStarPartitionFunction.WithExternalMemory.UnsupportedException - Exception in edu.duke.cs.osprey.ewakstar
- EWAKStarScore - Class in edu.duke.cs.osprey.ewakstar
- EWAKStarScore(EWAKStarPartitionFunction.Result, EWAKStarPartitionFunction.Result, EWAKStarPartitionFunction.Result) - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- EWAKStarScore(BigDecimal, BigDecimal, BigDecimal) - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- EWAKStarScoreWriter - Interface in edu.duke.cs.osprey.ewakstar
- EWAKStarScoreWriter.Formatted - Class in edu.duke.cs.osprey.ewakstar
- EWAKStarScoreWriter.Formatter - Interface in edu.duke.cs.osprey.ewakstar
- EWAKStarScoreWriter.Formatter.Log - Class in edu.duke.cs.osprey.ewakstar
- EWAKStarScoreWriter.Formatter.SequenceKStarPfuncs - Class in edu.duke.cs.osprey.ewakstar
- EWAKStarScoreWriter.Nop - Class in edu.duke.cs.osprey.ewakstar
- EWAKStarScoreWriter.ScoreInfo - Class in edu.duke.cs.osprey.ewakstar
- EWAKStarScoreWriter.ToConsole - Class in edu.duke.cs.osprey.ewakstar
- EWAKStarScoreWriter.ToFile - Class in edu.duke.cs.osprey.ewakstar
- EWAKStarScoreWriter.Writers - Class in edu.duke.cs.osprey.ewakstar
- ex - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.LengthUnit
- excluding - Variable in class edu.duke.cs.osprey.design.models.ScanDto
- exec(Runnable) - Method in class edu.duke.cs.osprey.parallelism.BottleneckThread
-
Run the task on the thread, and wait for it to finish.
- exitIfTimeOut() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- exp - Variable in class edu.duke.cs.osprey.tools.BigExp
- exp - Static variable in class edu.duke.cs.osprey.tools.ExpFunction
- exp(double) - Method in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- exp(double) - Static method in class edu.duke.cs.osprey.tools.BigExp
-
Return e^val
- exp(double) - Method in class edu.duke.cs.osprey.tools.ExpFunction
- expand - Variable in class edu.duke.cs.osprey.gpu.cuda.BufferPool
- expand() - Method in class edu.duke.cs.osprey.kstar.KAStarNode
- expand(double) - Method in class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel.Interval
- expand(double) - Method in class edu.duke.cs.osprey.tools.MathTools.DoubleBounds
- expand(double[]) - Method in class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel
- expand(NodeIndex.Node, NodeTree, List<NodeIndex.Node>) - Method in class edu.duke.cs.osprey.coffee.NodeProcessor
- expand(CUBuffer<T>, int) - Method in interface edu.duke.cs.osprey.gpu.cuda.BufferPool.BufferExpander
- expand(T) - Method in class edu.duke.cs.osprey.gpu.cuda.CUBuffer
- expanded - Variable in class edu.duke.cs.osprey.coffee.NodeStats.Values
- expanded() - Method in class edu.duke.cs.osprey.coffee.NodeStats.ForThread
- ExpFunction - Class in edu.duke.cs.osprey.tools
-
Manages the computation of exp(x) for large values of x, using BigDecimal; For large values of x, the standard Math.exp(x) cannot be used, since it only has double precision; Implements pow() for integer powers of a BigDecimal number and an approximation to the natural logarithm of a BigDecimal number
- ExpFunction() - Constructor for class edu.duke.cs.osprey.tools.ExpFunction
- ExpFunction(MathContext) - Constructor for class edu.duke.cs.osprey.tools.ExpFunction
- ExternalFIFOFactory(SerializingFIFOQueue.Serializer<T>) - Constructor for class edu.duke.cs.osprey.externalMemory.Queue.ExternalFIFOFactory
- ExternalMemory - Class in edu.duke.cs.osprey.externalMemory
- ExternalMemory() - Constructor for class edu.duke.cs.osprey.externalMemory.ExternalMemory
- ExternalMemory.InternalMemoryLimitNotSetException - Exception in edu.duke.cs.osprey.externalMemory
- ExternalPriorityFactory(SerializingDoublePriorityQueue.Serializer<T>) - Constructor for class edu.duke.cs.osprey.externalMemory.Queue.ExternalPriorityFactory
- extractPLSeqsByLB(double, int, EwakstarDoer.State) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- extractToTempFile(String) - Method in class edu.duke.cs.osprey.tools.FileTools.ResourcePathRoot
- extractUnboundSeqsByLB(int, Set<Sequence>, EwakstarLimitedSequenceTrie) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- extraStyle - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Boxes.Box
- extraStyle - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Intervals.Interval
- extraTemplates - Variable in class edu.duke.cs.osprey.design.models.MoleculeDto
- extraTemplatesCoordinates - Variable in class edu.duke.cs.osprey.design.models.MoleculeDto
F
- f - Variable in class edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction
- f(double) - Method in class edu.duke.cs.osprey.voxq.BoltzmannIntegrator1D
- factor - Variable in class edu.duke.cs.osprey.sofea.BoltzmannLute
- factory - Variable in class edu.duke.cs.osprey.astar.conf.ConfAStarTree
- factory - Variable in class edu.duke.cs.osprey.gpu.cuda.BufferPool
- Factory<VT,
CT> - Interface in edu.duke.cs.osprey.tools - Factory(int) - Constructor for class edu.duke.cs.osprey.astar.FullAStarNode.Factory
- Factory(int) - Constructor for class edu.duke.cs.osprey.astar.SlimAStarNode.Factory
- Failure - Static variable in class edu.duke.cs.osprey.design.Main
- FALSE - Enum constant in enum class edu.duke.cs.osprey.kstar.pfunc.PFAbstract.EApproxReached
- ffi - Variable in class edu.duke.cs.osprey.energy.compiled.AmberEnergyCalculator
- ffi - Variable in class edu.duke.cs.osprey.energy.compiled.EEF1EnergyCalculator
- ffi() - Method in class edu.duke.cs.osprey.energy.compiled.AmberEnergyCalculator
- ffi() - Method in class edu.duke.cs.osprey.energy.compiled.EEF1EnergyCalculator
- ffi() - Method in interface edu.duke.cs.osprey.energy.compiled.EnergyCalculator
-
get the index of this forcefield in the conf space
- FFInterGen - Class in edu.duke.cs.osprey.energy
-
Deprecated.
- FFInterGen() - Constructor for class edu.duke.cs.osprey.energy.FFInterGen
-
Deprecated.
- ffInters - Variable in class edu.duke.cs.osprey.energy.approximation.ResidueInteractionsApproximator
- ffparams - Variable in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator
-
Deprecated.
- ffparams - Variable in class edu.duke.cs.osprey.energy.forcefield.ResPairCache
- ffparams - Variable in class edu.duke.cs.osprey.gpu.cuda.kernels.ResidueForcefieldEnergyCuda
- ffparams - Variable in class edu.duke.cs.osprey.minimization.CpuConfMinimizer.Builder
- ffparams - Variable in class edu.duke.cs.osprey.minimization.GpuConfMinimizer.Builder
- ffparams - Variable in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
- ffparams - Variable in class edu.duke.cs.osprey.restypes.TemplateParser
- ffparams(int, int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- ffParams - Variable in class edu.duke.cs.osprey.energy.EnergyFunctionGenerator
- Field(long) - Constructor for class edu.duke.cs.osprey.gpu.Structs.Field
- FIFOFactory() - Constructor for class edu.duke.cs.osprey.externalMemory.Queue.FIFOFactory
- file - Variable in class edu.duke.cs.osprey.coffee.nodedb.BlockStore
- file - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
- file - Variable in class edu.duke.cs.osprey.coffee.seqdb.SeqDB
- file - Variable in class edu.duke.cs.osprey.confspace.ConfDB
- file - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.ToFile
- file - Variable in class edu.duke.cs.osprey.kstar.KStarScoreWriter.ToFile
- file - Variable in class edu.duke.cs.osprey.paste.PasteScoreWriter.ToFile
- file - Variable in class edu.duke.cs.osprey.sofea.FringeDB
- file - Variable in class edu.duke.cs.osprey.sofea.RCDB
- file - Variable in class edu.duke.cs.osprey.sofea.SeqDB
- file - Variable in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- File() - Constructor for class edu.duke.cs.osprey.tools.resultdoc.ResultDoc.File
- file2List(String) - Static method in class edu.duke.cs.osprey.kstar.KSAbstract
- fileBytes - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
- FileExistsValidation - Class in edu.duke.cs.osprey.design.commands
- FileExistsValidation() - Constructor for class edu.duke.cs.osprey.design.commands.FileExistsValidation
- filename - Variable in class edu.duke.cs.osprey.structure.analysis.TemplateChooser.MeasuredRes
- FilePathRoot() - Constructor for class edu.duke.cs.osprey.tools.FileTools.FilePathRoot
- FilePathRoot(File) - Constructor for class edu.duke.cs.osprey.tools.FileTools.FilePathRoot
- FilePathRoot(String) - Constructor for class edu.duke.cs.osprey.tools.FileTools.FilePathRoot
- files - Variable in class edu.duke.cs.osprey.structure.analysis.PDBScanner
- FileTools - Class in edu.duke.cs.osprey.tools
- FileTools() - Constructor for class edu.duke.cs.osprey.tools.FileTools
- FileTools.FilePathRoot - Class in edu.duke.cs.osprey.tools
- FileTools.LineIterator - Class in edu.duke.cs.osprey.tools
-
A fairly efficient line iterator for parsing text files.
- FileTools.Path - Class in edu.duke.cs.osprey.tools
- FileTools.PathRoot - Class in edu.duke.cs.osprey.tools
- FileTools.ResourcePathRoot - Class in edu.duke.cs.osprey.tools
- fill(double[]) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- fill(Boolean) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixInverted
- fill(Boolean) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- fill(Boolean) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- fill(Iterator<Boolean>) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixInverted
- fill(Iterator<Boolean>) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- fill(Iterator<Boolean>) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- fill(Iterator<T>) - Method in class edu.duke.cs.osprey.confspace.AbstractPosMatrix
- fill(Iterator<T>) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- fill(Iterator<T>) - Method in interface edu.duke.cs.osprey.confspace.PosMatrix
- fill(Iterator<T>) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- fill(T) - Method in class edu.duke.cs.osprey.confspace.AbstractPosMatrix
- fill(T) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- fill(T) - Method in interface edu.duke.cs.osprey.confspace.PosMatrix
- fill(T) - Method in class edu.duke.cs.osprey.confspace.TripleMatrix
- fill(T) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- FilledSquare - Enum constant in enum class edu.duke.cs.osprey.tools.resultdoc.Plot.PointType
- fillWildType() - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Set all unassigned residues to the wild-type residue type, when the wild-type is part of the sequence space
- filter(RTs.Filter) - Method in class edu.duke.cs.osprey.astar.seq.RTs
- filter(SeqSpace) - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Returns a new sequence containing the subset of mutable positions belonging to the smaller sequence space.
- filter(Residues) - Method in class edu.duke.cs.osprey.energy.ResidueInteractions
- filter(Collection<double[]>) - Method in class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel
- filter(Predicate<T>) - Method in interface edu.duke.cs.osprey.externalMemory.Queue.FIFO
- filterDensityWindow(int, int) - Method in class edu.duke.cs.osprey.structure.analysis.DegreesHistogram
-
remove buckets whose local neighborhood contains fewer than the threshold count
- filterHOTListByStrand(ResidueTermini, ArrayList<ArrayList<String>>) - Method in class edu.duke.cs.osprey.kstar.KSConfigFileParser
- filterNode(MultiStateConfSpace.State, int[], BoltzmannCalculator) - Method in class edu.duke.cs.osprey.sofea.MinLMFE
- filterNode(MultiStateConfSpace.State, int[], BoltzmannCalculator) - Method in class edu.duke.cs.osprey.sofea.SequenceLMFE
- filterNode(MultiStateConfSpace.State, int[], BoltzmannCalculator) - Method in interface edu.duke.cs.osprey.sofea.Sofea.Criterion
- filterTo(Q, Predicate<T>) - Method in interface edu.duke.cs.osprey.externalMemory.Queue
- finalize() - Method in class edu.duke.cs.osprey.energy.EnergyCalculator.Type.Context
- finalize() - Method in class edu.duke.cs.osprey.energy.forcefield.GpuForcefieldEnergy
- finalize() - Method in class edu.duke.cs.osprey.gpu.cuda.CUBuffer
- finalize() - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- finalize() - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStreamPool
- finalize() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.CCDKernelCuda
- finalize() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ForcefieldKernelCuda
- finalize() - Method in class edu.duke.cs.osprey.gpu.opencl.GpuQueue
- finalize() - Method in class edu.duke.cs.osprey.gpu.opencl.GpuQueuePool
- finalize() - Method in class edu.duke.cs.osprey.gpu.opencl.Kernel
- finalize() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.ForcefieldKernelOpenCL
- find() - Method in class edu.duke.cs.osprey.gmec.SimpleGMECFinder
- find() - Method in class edu.duke.cs.osprey.lute.LUTEGMECFinder
- find(double) - Method in class edu.duke.cs.osprey.gmec.SimpleGMECFinder
- find(double) - Method in class edu.duke.cs.osprey.lute.LUTEGMECFinder
- findAtomIndex(String) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Conf
- findAtomIndexOrThrow(String) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Conf
- findBestSequences(int) - Method in class edu.duke.cs.osprey.gmec.Comets
-
find the best sequences as ranked by the objective function searches all sequences within the objective window
- findBestSequences(int) - Method in class edu.duke.cs.osprey.kstar.MSKStar
-
find the best sequences as ranked by the objective function searches all sequences within the objective window
- findBoundaryNewton(PLUG.AtomPairVoxel, double) - Method in class edu.duke.cs.osprey.pruning.PLUG
-
find a point in the voxel where the atom pair overlap is close to 0 using a generalization of Newton's method starting at the voxel center
- findConf(String) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Pos
- findConfOrThrow(String) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Pos
- findDefined(int) - Method in class edu.duke.cs.osprey.astar.conf.ConfIndex
- FindGMEC - Enum constant in enum class edu.duke.cs.osprey.control.Main.Command
- findHighestNodes(int) - Method in class edu.duke.cs.osprey.coffee.nodedb.Neighbors
-
Returns the neighbor having the highest nodes, or null if no neighbors have nodes.
- findHighZNodes(int, ClusterZMatrix, NodeTree, int) - Method in class edu.duke.cs.osprey.coffee.Coffee
-
Quickly get a few nodes with high Z values.
- findIndex(Residue) - Method in class edu.duke.cs.osprey.structure.Residues
- findIndex(String) - Method in class edu.duke.cs.osprey.structure.Residues
- findIndexOrThrow(Residue) - Method in class edu.duke.cs.osprey.structure.Residues
- findIndexOrThrow(String) - Method in class edu.duke.cs.osprey.structure.Residues
- findMostFreeSpace(int) - Method in class edu.duke.cs.osprey.coffee.nodedb.Neighbors
-
Returns the neighbor having the most free space, or null if no neighbors have any free space.
- findMutAlignmentAtoms(ResidueTemplate, ResidueTemplate) - Static method in class edu.duke.cs.osprey.restypes.HardCodedResidueInfo
- findPos(String) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
-
Finds the first position with the given name, or null if no positions match.
- findPosIndex(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- FindSeqGMECs - Enum constant in enum class edu.duke.cs.osprey.control.Main.Command
- FindSequences - Enum constant in enum class edu.duke.cs.osprey.control.Main.Command
- findStaticAtomIndex(String) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
-
Finds the first static atom with the given name and returns its index, or null if no static atom names match.
- findUndefined(int) - Method in class edu.duke.cs.osprey.astar.conf.ConfIndex
- finish() - Method in class edu.duke.cs.osprey.tools.SVG
- finishChild(ConfSMAStarNode, ConfSMAStarQueue) - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- finished - Variable in class edu.duke.cs.osprey.coffee.NodeStats.Values
- finished() - Method in class edu.duke.cs.osprey.coffee.NodeStats.ForThread
- finished(long) - Method in class edu.duke.cs.osprey.parallelism.WorkLatch
- Finished - Enum constant in enum class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode.State
-
not spawned now, never need to spawn again
- finishedOperations() - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- FinishedSequencesOperation - Class in edu.duke.cs.osprey.coffee.directions
- FinishedSequencesOperation() - Constructor for class edu.duke.cs.osprey.coffee.directions.FinishedSequencesOperation
- FinishedSequencesOperation(int, Collection<Sequence>) - Constructor for class edu.duke.cs.osprey.coffee.directions.FinishedSequencesOperation
- finishedTask() - Method in class edu.duke.cs.osprey.parallelism.ConcurrentTaskExecutor
- finishedWork() - Method in class edu.duke.cs.osprey.parallelism.WorkCrew
- finishSequence(int, Sequence) - Method in class edu.duke.cs.osprey.coffee.directions.Directions
- finishSequences(int, Set<Sequence>, Set<Sequence>) - Method in class edu.duke.cs.osprey.coffee.directions.Directions
-
Adds the sequences to the finished set for the given state.
- finishStep() - Method in class edu.duke.cs.osprey.sofea.FringeDB
-
Finishes this step and prepares for the next step.
- finiteMax() - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.Interval
-
return the largest finite endpoint, or null
- finiteMin() - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.Interval
-
return the smallest finite endpoint, or null
- first - Variable in class edu.duke.cs.osprey.confspace.ConfSearch.Splitter
- FirstConfPicker - Class in edu.duke.cs.osprey.partcr.pickers
- FirstConfPicker() - Constructor for class edu.duke.cs.osprey.partcr.pickers.FirstConfPicker
- fit(ConfEnergyCalculator, ConfDB.ConfTable, ConfSampler, LUTE.Fitter, double, double) - Method in class edu.duke.cs.osprey.lute.LUTE
- fit(LUTE.Fitter, double[], TaskExecutor) - Method in class edu.duke.cs.osprey.lute.LUTE.LinearSystem
- fit(LUTE.LinearSystem, LUTE.LinearSystem.BInfo, double[], TaskExecutor) - Method in enum class edu.duke.cs.osprey.lute.LUTE.Fitter
- fitFixedVoxel(Collection<double[]>, SmallAngleVoxel, double) - Static method in class edu.duke.cs.osprey.structure.analysis.AngleClustering
- FitParams - Class in edu.duke.cs.osprey.ematrix.epic
- FitParams() - Constructor for class edu.duke.cs.osprey.ematrix.epic.FitParams
- FitParams(int, int, double, int, boolean, double) - Constructor for class edu.duke.cs.osprey.ematrix.epic.FitParams
- fitSeries(DoubleMatrix1D[], double[], double[], double, boolean, int) - Static method in class edu.duke.cs.osprey.ematrix.epic.SeriesFitter
- Fixed(int) - Constructor for class edu.duke.cs.osprey.sofea.BigDecimalIO.Fixed
- Fixed(MathContext) - Constructor for class edu.duke.cs.osprey.sofea.BigDecimalIO.Fixed
- FixedIndex<S extends Comparable<S>,
T extends FixedIndex.Indexable<S>> - Interface in edu.duke.cs.osprey.coffee.nodedb -
An index that allows queries for items with high scores, but drops items with low scores to make extra space.
- FixedIndex.Indexable<S> - Interface in edu.duke.cs.osprey.coffee.nodedb
- FixedIndex.Serializer<T> - Interface in edu.duke.cs.osprey.coffee.nodedb
- fixedSize - Variable in class edu.duke.cs.osprey.tools.MapDBTools.SimpleSerializer
- fixedSize() - Method in class edu.duke.cs.osprey.tools.MapDBTools.SimpleSerializer
- fixHazelcastLogging() - Static method in class edu.duke.cs.osprey.parallelism.Cluster
-
The default logging settings for Hazelcast are completely obnoxious! So much log spam!! Try to get it under control by installing our own logging settings.
- flags - Variable in class edu.duke.cs.osprey.energy.forcefield.ResPairCache.AtomPairInfo
- flags - Variable in class edu.duke.cs.osprey.structure.Probe.AtomInfo
- flexDistance - Variable in class edu.duke.cs.osprey.design.commands.CommandMakeFlexShell
- flexibility - Variable in class edu.duke.cs.osprey.confspace.Strand
-
Flexibility parameters for this strand
- flexibility - Variable in class edu.duke.cs.osprey.design.models.ResidueModifier
- Flexibility - Class in edu.duke.cs.osprey.design.models
- Flexibility() - Constructor for class edu.duke.cs.osprey.design.models.Flexibility
- Flexibility(List<Residue>) - Constructor for class edu.duke.cs.osprey.confspace.Strand.Flexibility
- flexibleRes - Variable in class edu.duke.cs.osprey.confspace.ConfSpace
- flexibleRes - Variable in class edu.duke.cs.osprey.kstar.KSSearchProblem
- flexRes - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- flip() - Method in enum class edu.duke.cs.osprey.dof.ProlinePucker.Direction
- float32() - Static method in class edu.duke.cs.osprey.gpu.Structs
- float32(float) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- float32(long, float) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- Float32 - Enum constant in enum class edu.duke.cs.osprey.gpu.Structs.Precision
- Float32() - Constructor for class edu.duke.cs.osprey.gpu.Structs.Float32
- float32array() - Static method in class edu.duke.cs.osprey.gpu.Structs
- float32skip() - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- float64() - Static method in class edu.duke.cs.osprey.gpu.Structs
- float64(double) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- float64(long, double) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- Float64 - Enum constant in enum class edu.duke.cs.osprey.gpu.Structs.Precision
- Float64() - Constructor for class edu.duke.cs.osprey.gpu.Structs.Float64
- float64array() - Static method in class edu.duke.cs.osprey.gpu.Structs
- float64skip() - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- flush() - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- flush() - Method in class edu.duke.cs.osprey.confspace.ConfDB
- flush() - Method in class edu.duke.cs.osprey.gpu.opencl.GpuQueue
- flush() - Method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd
- focus(int) - Method in class edu.duke.cs.osprey.coffee.directions.Directions
-
Tell all cluster members to process nodes in the specified state.
- FocusOperation - Class in edu.duke.cs.osprey.coffee.directions
- FocusOperation() - Constructor for class edu.duke.cs.osprey.coffee.directions.FocusOperation
- FocusOperation(int) - Constructor for class edu.duke.cs.osprey.coffee.directions.FocusOperation
- ForcefieldDebugger - Class in edu.duke.cs.osprey.energy.compiled
- ForcefieldDebugger() - Constructor for class edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger
- ForcefieldDebugger.AtomPair - Class in edu.duke.cs.osprey.energy.compiled
- ForcefieldDebugger.Coords - Class in edu.duke.cs.osprey.energy.compiled
- ForcefieldEnergy - Class in edu.duke.cs.osprey.energy.forcefield
- ForcefieldEnergy(boolean, List<Atom>, List<Atom>, ForcefieldParams) - Constructor for class edu.duke.cs.osprey.energy.forcefield.ForcefieldEnergy
- ForcefieldEnergy(List<Atom[]>, ForcefieldParams) - Constructor for class edu.duke.cs.osprey.energy.forcefield.ForcefieldEnergy
- ForcefieldFileParser - Class in edu.duke.cs.osprey.energy.forcefield.amber
- ForcefieldFileParser(InputStream) - Constructor for class edu.duke.cs.osprey.energy.forcefield.amber.ForcefieldFileParser
- ForcefieldFileParser(InputStream, Path) - Constructor for class edu.duke.cs.osprey.energy.forcefield.amber.ForcefieldFileParser
- forcefieldIds - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- ForcefieldInteractions - Class in edu.duke.cs.osprey.energy.forcefield
-
Deprecated.
- ForcefieldInteractions() - Constructor for class edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions
-
Deprecated.
- ForcefieldInteractions(ResidueInteractions, Molecule) - Constructor for class edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions
-
Deprecated.
- ForcefieldInteractions.AtomGroup - Interface in edu.duke.cs.osprey.energy.forcefield
-
Deprecated.
- ForcefieldInteractions.ResidueAtomGroup - Class in edu.duke.cs.osprey.energy.forcefield
-
Deprecated.
- ForcefieldKernel - Interface in edu.duke.cs.osprey.gpu
- ForcefieldKernelCuda - Class in edu.duke.cs.osprey.gpu.cuda.kernels
- ForcefieldKernelCuda(GpuStream, BigForcefieldEnergy) - Constructor for class edu.duke.cs.osprey.gpu.cuda.kernels.ForcefieldKernelCuda
- ForcefieldKernelOpenCL - Class in edu.duke.cs.osprey.gpu.opencl.kernels
- ForcefieldKernelOpenCL(GpuQueue, BigForcefieldEnergy) - Constructor for class edu.duke.cs.osprey.gpu.opencl.kernels.ForcefieldKernelOpenCL
- forcefieldParams - Variable in class edu.duke.cs.osprey.design.commands.CommandBindingAffinity.ForceFieldParamsAndStrands
- ForcefieldParams - Class in edu.duke.cs.osprey.energy.forcefield
-
Contains forcefield parameters for a variety of different published forcefields.
- ForcefieldParams() - Constructor for class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
-
creates an Amber 96 forcefield
- ForcefieldParams(ForcefieldParams) - Constructor for class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- ForcefieldParams(ForcefieldParams.Forcefield) - Constructor for class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- ForcefieldParams(ForcefieldParams.Forcefield, ForcefieldFileParser) - Constructor for class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- ForcefieldParams(String) - Constructor for class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- ForcefieldParams.Forcefield - Enum Class in edu.duke.cs.osprey.energy.forcefield
- ForcefieldParams.NBParams - Class in edu.duke.cs.osprey.energy.forcefield
- ForcefieldParams.SolvationForcefield - Enum Class in edu.duke.cs.osprey.energy.forcefield
- ForcefieldParams.SolvationForcefield.ResiduesInfo - Interface in edu.duke.cs.osprey.energy.forcefield
- ForcefieldParams.VdwParams - Class in edu.duke.cs.osprey.energy.forcefield
- ForceFieldParamsAndStrands(DesignFileDelegate, AffinityDesign) - Constructor for class edu.duke.cs.osprey.design.commands.CommandBindingAffinity.ForceFieldParamsAndStrands
- forcefieldsImpl - Variable in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- forcefieldsImpl - Variable in class edu.duke.cs.osprey.energy.compiled.NativeConfEnergyCalculator
- forceFieldType - Variable in class edu.duke.cs.osprey.structure.Atom
- forcefld - Variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- forEachHigherOrderTupleIn(int[], int, int, BiConsumer<RCTuple, T>) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
-
iterate over all higher-order (n>2) tuples matching the conformation but containing the given positions
- forEachHigherOrderTupleIn(int[], int, BiConsumer<RCTuple, T>) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
-
iterate over all higher-order (n>2) tuples matching the conformation but containing the given position
- forEachHigherOrderTupleIn(int[], BiConsumer<RCTuple, T>) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
-
iterate over all higher-order (n>2) tuples matching the conformation
- forEachIn(int[], boolean, boolean, Consumer<Integer>) - Method in class edu.duke.cs.osprey.confspace.TuplesIndex
- forEachIn(int[], int, int, BiConsumer<RCTuple, T>) - Method in class edu.duke.cs.osprey.confspace.TupleTree
- forEachIn(int[], int, BiConsumer<RCTuple, T>) - Method in class edu.duke.cs.osprey.confspace.TupleTree
- forEachIn(int[], BiConsumer<RCTuple, T>) - Method in class edu.duke.cs.osprey.confspace.TupleTree
- forEachUnprunedPair(PruningMatrix.PairConsumer) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- forEachUnprunedPairAt(int, int, PruningMatrix.PairConsumer) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- forEachUnprunedSingle(PruningMatrix.SingleConsumer) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- forEachUnprunedSingleAt(int, PruningMatrix.SingleConsumer) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- forEachUnprunedTriple(PruningMatrix.TripleConsumer) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- forEachUnprunedTripleAt(int, int, int, PruningMatrix.TripleConsumer) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- forgetChild(ConfSMAStarNode) - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- Forgotten - Enum constant in enum class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode.State
-
not spawned now, might need to spawn again
- format - Variable in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.Tics
- format(long) - Static method in class edu.duke.cs.osprey.tools.TimeFormatter
- format(long, int) - Static method in class edu.duke.cs.osprey.tools.TimeFormatter
- format(long, TimeUnit) - Static method in class edu.duke.cs.osprey.tools.TimeFormatter
- format(long, TimeUnit, int) - Static method in class edu.duke.cs.osprey.tools.TimeFormatter
- format(EWAKStarScoreWriter.ScoreInfo) - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Formatter
- format(EWAKStarScoreWriter.ScoreInfo) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Formatter.Log
- format(EWAKStarScoreWriter.ScoreInfo) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Formatter.SequenceKStarPfuncs
- format(KStarScoreWriter.ScoreInfo) - Method in interface edu.duke.cs.osprey.kstar.KStarScoreWriter.Formatter
- format(KStarScoreWriter.ScoreInfo) - Method in class edu.duke.cs.osprey.kstar.KStarScoreWriter.Formatter.Log
- format(KStarScoreWriter.ScoreInfo) - Method in class edu.duke.cs.osprey.kstar.KStarScoreWriter.Formatter.SequenceKStarPfuncs
- format(PasteScoreWriter.ScoreInfo) - Method in interface edu.duke.cs.osprey.paste.PasteScoreWriter.Formatter
- format(PasteScoreWriter.ScoreInfo) - Method in class edu.duke.cs.osprey.paste.PasteScoreWriter.Formatter.Log
- format(PasteScoreWriter.ScoreInfo) - Method in class edu.duke.cs.osprey.paste.PasteScoreWriter.Formatter.SequenceKStarPfuncs
- formatBig(BigDecimal) - Static method in class edu.duke.cs.osprey.tools.Log
- formatBig(BigInteger) - Static method in class edu.duke.cs.osprey.tools.Log
- formatBigDecimal(BigDecimal, int) - Static method in class edu.duke.cs.osprey.tools.ObjectIO
- formatBigEngineering(MathTools.BigDecimalBounds) - Static method in class edu.duke.cs.osprey.tools.Log
- formatBigEngineering(BigDecimal) - Static method in class edu.duke.cs.osprey.tools.Log
- formatBigLn(MathTools.BigDecimalBounds) - Static method in class edu.duke.cs.osprey.tools.Log
- formatBigLn(BigDecimal) - Static method in class edu.duke.cs.osprey.tools.Log
- formatBytes(long) - Static method in class edu.duke.cs.osprey.tools.MathTools
- formatConf(int[]) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- formatConf(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- formatConfPos(int[]) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Position
- formatConfPos(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Position
- formatConfRCs(int[]) - Static method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- formatConfRCs(ConfSearch.ScoredConf) - Static method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- formatConfRotamers(int[]) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- formatConfRotamers(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- formatConfRotamersWithResidueNumbers(int[]) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- formatConfSequence(int[]) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- formatConfSequence(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- formatCorrections(List<TupE>) - Method in class edu.duke.cs.osprey.ematrix.UpdatingEnergyMatrix
- formatResidueNumbers() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- Formatted(EWAKStarScoreWriter.Formatter) - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Formatted
- Formatted(KStarScoreWriter.Formatter) - Constructor for class edu.duke.cs.osprey.kstar.KStarScoreWriter.Formatted
- Formatted(PasteScoreWriter.Formatter) - Constructor for class edu.duke.cs.osprey.paste.PasteScoreWriter.Formatted
- formatter - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Formatted
- formatter - Variable in class edu.duke.cs.osprey.kstar.KStarScoreWriter.Formatted
- formatter - Variable in class edu.duke.cs.osprey.paste.PasteScoreWriter.Formatted
- ForThread() - Constructor for class edu.duke.cs.osprey.coffee.NodeStats.ForThread
- fp - Variable in class edu.duke.cs.osprey.tools.BigExp
- fragIndex - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Conf
- fragmentEnergies - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.State
- fragmentEnergies - Variable in class edu.duke.cs.osprey.gmec.Comets.State
- fragmentEnergies - Variable in class edu.duke.cs.osprey.kstar.MSKStar.State
- FragmentEnergies - Interface in edu.duke.cs.osprey.confspace
- frcmodPath - Variable in class edu.duke.cs.osprey.design.commands.DesignFileDelegate
- free(CUdeviceptr) - Method in class edu.duke.cs.osprey.gpu.cuda.Context
- freeBBZoneTermini(int) - Method in class edu.duke.cs.osprey.multistatekstar.MSConfigFileParser
- freeBlock(long) - Method in class edu.duke.cs.osprey.coffee.nodedb.BlockStore
-
Frees the block described by the given block id so someone else can use it.
- FreeDihedral - Class in edu.duke.cs.osprey.dof
- FreeDihedral(Residue, int) - Constructor for class edu.duke.cs.osprey.dof.FreeDihedral
- freeEnergies - Variable in class edu.duke.cs.osprey.coffee.seqdb.SeqFreeEnergies
- freeEnergy(BigDecimal) - Method in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- FreeEnergyCalculator - Class in edu.duke.cs.osprey.coffee
- FreeEnergyCalculator() - Constructor for class edu.duke.cs.osprey.coffee.FreeEnergyCalculator
- freeEnergyPrecise(BigExp) - Method in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- freeEnergyPrecise(BigExp.Bounds) - Method in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- freeEnergyPrecise(MathTools.BigDecimalBounds) - Method in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- freeEnergyPrecise(BigDecimal) - Method in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- freeSpace() - Method in interface edu.duke.cs.osprey.coffee.nodedb.FixedIndex
-
Returns the number of items that can be added without freeing up space.
- freeSpace() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex
- freeSpace() - Method in class edu.duke.cs.osprey.coffee.nodedb.PriorityDequeFixedIndex
- freeSpace(int) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices
- freeSpaceLocal(int) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
- freeSpaces - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices.BroadcastInfo
- freeUpSpace() - Method in interface edu.duke.cs.osprey.coffee.nodedb.FixedIndex
-
Drops low-scoring items to make more free space, and adds them to the dropped queue.
- freeUpSpace() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex
- freeUpSpace() - Method in class edu.duke.cs.osprey.coffee.nodedb.PriorityDequeFixedIndex
- FringeDB - Class in edu.duke.cs.osprey.sofea
-
An efficient and resilient database for storing fringe nodes in bounded space.
- FringeDB.Transaction - Class in edu.duke.cs.osprey.sofea
- fringedbLowerBytes - Variable in class edu.duke.cs.osprey.sofea.Sofea
- fringedbLowerFile - Variable in class edu.duke.cs.osprey.sofea.Sofea
- fringedbUpperBytes - Variable in class edu.duke.cs.osprey.sofea.Sofea
- fringedbUpperFile - Variable in class edu.duke.cs.osprey.sofea.Sofea
- fromBytes(byte[]) - Static method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
-
Loads a compiled conformation space.
- fromDouble(double) - Method in enum class edu.duke.cs.osprey.gpu.Structs.Precision
- fromSLURM() - Static method in class edu.duke.cs.osprey.parallelism.Cluster
- fromSLURM(boolean) - Static method in class edu.duke.cs.osprey.parallelism.Cluster
-
Read environment variables to determine cluster properties
- FullAStarNode - Class in edu.duke.cs.osprey.astar
- FullAStarNode(int[]) - Constructor for class edu.duke.cs.osprey.astar.FullAStarNode
- FullAStarNode(FullAStarNode) - Constructor for class edu.duke.cs.osprey.astar.FullAStarNode
- FullAStarNode.Factory - Class in edu.duke.cs.osprey.astar
- fullConfE - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- fullConfEnergy(ConfSpace, List<Residue>) - Method in class edu.duke.cs.osprey.energy.EnergyFunctionGenerator
- fullConfEnergy(ConfSpace, List<Residue>) - Method in class edu.duke.cs.osprey.energy.GpuEnergyFunctionGenerator
- fullConfEnergy(ConfSpace, List<Residue>, Molecule) - Method in class edu.duke.cs.osprey.energy.EnergyFunctionGenerator
- fullConfEnergy(ConfSpace, List<Residue>, Molecule) - Method in class edu.duke.cs.osprey.energy.GpuEnergyFunctionGenerator
- fullMolecEnergy(Molecule) - Method in class edu.duke.cs.osprey.energy.EnergyFunctionGenerator
- fullMolecEnergy(Molecule) - Method in class edu.duke.cs.osprey.energy.GpuEnergyFunctionGenerator
- fullName - Variable in class edu.duke.cs.osprey.structure.Residue
- Function(String) - Constructor for class edu.duke.cs.osprey.gpu.cuda.Kernel.Function
G
- g(ConfIndex) - Method in interface edu.duke.cs.osprey.coffee.bounds.Bounder
-
Compute the g-score of a (possibly partial) conformation.
- g(ConfIndex) - Method in class edu.duke.cs.osprey.coffee.bounds.PairwiseBounder
- g(ConfIndex) - Method in class edu.duke.cs.osprey.coffee.bounds.TriplewiseBounder
- GaussianLowEnergySampler - Class in edu.duke.cs.osprey.ematrix.epic
-
This sampler samples preferentially from the low-energy region about the center Used when this region is too small to be efficiently reached for this purpose It samples Gaussianly about the center, with variance determined by initial explorations
- GaussianLowEnergySampler(double, ObjectiveFunction, DoubleMatrix1D, DoubleMatrix1D, DoubleMatrix1D) - Constructor for class edu.duke.cs.osprey.ematrix.epic.GaussianLowEnergySampler
- GenChi1Calc - Class in edu.duke.cs.osprey.dof.deeper
-
This class handles the calculation of the generalized chi1 When we're moving around sidechains as a rigid body, idealization tells us where to place the CB but this still leaves one degree of freedom (chi1, when defined; else a generalized chi1) to determine the sidechain pose
- GenChi1Calc() - Constructor for class edu.duke.cs.osprey.dof.deeper.GenChi1Calc
- GenCoord - Class in edu.duke.cs.osprey.minimization
- GenCoord() - Constructor for class edu.duke.cs.osprey.minimization.GenCoord
- GenCoord(double[]) - Constructor for class edu.duke.cs.osprey.minimization.GenCoord
- Generator<T> - Class in edu.duke.cs.osprey.parallelism
-
Uses a thread to emulate a continuation-powered generator function.
- Generator(Consumer<Generator.Yielder<T>>) - Constructor for class edu.duke.cs.osprey.parallelism.Generator
- Generator.GeneratorFailedException - Exception in edu.duke.cs.osprey.parallelism
- Generator.Yielder<T> - Interface in edu.duke.cs.osprey.parallelism
- GeneratorFailedException(String) - Constructor for exception edu.duke.cs.osprey.parallelism.Generator.GeneratorFailedException
- get() - Method in class edu.duke.cs.osprey.coffee.NodeStats
- get() - Method in interface edu.duke.cs.osprey.confspace.compiled.DegreeOfFreedom
- get() - Method in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Dof
- get() - Method in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Dof
- get() - Static method in class edu.duke.cs.osprey.gpu.cuda.Gpus
- get() - Static method in class edu.duke.cs.osprey.gpu.opencl.Gpus
- get() - Static method in class edu.duke.cs.osprey.parallelism.Hostname
- get() - Method in class edu.duke.cs.osprey.tools.BigMath
- get() - Method in class edu.duke.cs.osprey.tools.ObjectPool.Checkout
- get() - Method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.LiteralProp
- get() - Method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.NumberProp
- get() - Method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.TextProp
- get(byte) - Static method in enum class edu.duke.cs.osprey.sofea.BigDecimalIO.Type
- get(int) - Method in class edu.duke.cs.osprey.astar.conf.RCs
- get(int) - Method in class edu.duke.cs.osprey.confspace.Strand.Flexibility
-
Deprecated.
- get(int) - Method in class edu.duke.cs.osprey.confspace.TuplesIndex
- get(int) - Static method in enum class edu.duke.cs.osprey.tools.IntEncoding
- get(int[]) - Method in class edu.duke.cs.osprey.confspace.Conf.Map
- get(int[]) - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- get(int, int) - Method in class edu.duke.cs.osprey.astar.conf.RCs
- get(int, int) - Method in interface edu.duke.cs.osprey.confspace.PosMatrix
- get(int, int) - Method in class edu.duke.cs.osprey.confspace.PosMatrixGeneric
- get(int, int) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrix
- get(int, int) - Method in class edu.duke.cs.osprey.sofea.BoltzmannLute
- get(int, int, int) - Method in class edu.duke.cs.osprey.astar.conf.scoring.mplp.MessageVars
- get(int, int, int, int) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrix
- get(int, int, int, int) - Method in class edu.duke.cs.osprey.sofea.BoltzmannLute
- get(int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.TripleMatrix
- get(int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.sofea.BoltzmannLute
- get(int, int, String) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrix
- get(int, String) - Method in class edu.duke.cs.osprey.ematrix.SimpleReferenceEnergies
- get(int, Vector3d) - Method in class edu.duke.cs.osprey.confspace.compiled.CoordsList
- get(long) - Method in class edu.duke.cs.osprey.coffee.nodedb.BlockStore
- get(ConfDB.Key) - Method in class edu.duke.cs.osprey.confspace.ConfDB
- get(ConfSpaceIteration) - Method in class edu.duke.cs.osprey.confspace.ConfDB.DBs
- get(MultiStateConfSpace.State) - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqInfo
- get(MultiStateConfSpace.State) - Method in class edu.duke.cs.osprey.sofea.SeqDB.SeqInfo
- get(MultiStateConfSpace.State, Sequence) - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqDB
-
Returns the current Z bounds and dropped Z for the state and sequence.
- get(RCTuple) - Method in class edu.duke.cs.osprey.confspace.TupleTree
- get(RCTuple) - Method in class edu.duke.cs.osprey.sofea.BoltzmannLute
- get(RCTuple, ResidueInteractions, double) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrix
- get(SeqSpace.Position) - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Get the residue type at the specified residue by sequence position
- get(Sequence) - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqDB
-
Returns the current sequenced state Z bounds for the fully-assigned sequence.
- get(SimpleConfSpace.Position, SimpleConfSpace.ResidueConf) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrix
- get(SimpleConfSpace.Position, SimpleConfSpace.ResidueConf, SimpleConfSpace.Position, SimpleConfSpace.ResidueConf) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrix
- get(SimpleConfSpace.Position, SimpleConfSpace.ResidueConf, String) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrix
- get(MemoryBuffer) - Method in class edu.duke.cs.osprey.gpu.Structs.Bool
- get(MemoryBuffer) - Method in class edu.duke.cs.osprey.gpu.Structs.Char8
- get(MemoryBuffer) - Method in class edu.duke.cs.osprey.gpu.Structs.Float32
- get(MemoryBuffer) - Method in class edu.duke.cs.osprey.gpu.Structs.Float64
- get(MemoryBuffer) - Method in class edu.duke.cs.osprey.gpu.Structs.Int32
- get(MemoryBuffer) - Method in class edu.duke.cs.osprey.gpu.Structs.Int64
- get(MemoryBuffer) - Method in class edu.duke.cs.osprey.gpu.Structs.Real
- get(MemoryBuffer, long) - Method in class edu.duke.cs.osprey.gpu.Structs.Char8.Array
- get(MemoryBuffer, long) - Method in class edu.duke.cs.osprey.gpu.Structs.Float32.Array
- get(MemoryBuffer, long) - Method in class edu.duke.cs.osprey.gpu.Structs.Float64.Array
- get(MemoryBuffer, long) - Method in class edu.duke.cs.osprey.gpu.Structs.Int32.Array
- get(MemoryBuffer, long) - Method in class edu.duke.cs.osprey.gpu.Structs.Int64.Array
- get(MemoryBuffer, long) - Method in class edu.duke.cs.osprey.gpu.Structs.Real.Array
- get(ResidueTemplate, ResidueTemplate) - Method in class edu.duke.cs.osprey.dof.MutAlignmentCache
- get(Residues, ResidueInteractions.Pair, ForcefieldParams.SolvationForcefield.ResiduesInfo) - Method in class edu.duke.cs.osprey.energy.forcefield.ResPairCache
- get(Object) - Method in class edu.duke.cs.osprey.confspace.Conf.Map
- get(String) - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Get the residue type at the specified residue by residue number
- get(String) - Method in class edu.duke.cs.osprey.confspace.Strand.Flexibility
- get(String) - Static method in enum class edu.duke.cs.osprey.control.Main.Command
- get(String) - Static method in enum class edu.duke.cs.osprey.energy.compiled.EnergyCalculator.Type
- get(String) - Static method in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.Forcefield
- get(String) - Method in class edu.duke.cs.osprey.restypes.ResidueEntropies
- get(String) - Method in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary
- get(String, String) - Method in class edu.duke.cs.osprey.energy.ResidueInteractions
- get(String, String) - Method in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary
- get(BigDecimal) - Static method in enum class edu.duke.cs.osprey.sofea.BigDecimalIO.Type
- get(Supplier<T>) - Method in class edu.duke.cs.osprey.parallelism.BottleneckThread
-
Run the task on the thread, wait for it to finish, and return the result.
- get_input_angles(double[], double[], double[], double[]) - Method in class edu.duke.cs.osprey.dof.deeper.perts.TripeptideClosure
- get_poly_coeff(double[]) - Method in class edu.duke.cs.osprey.dof.deeper.perts.TripeptideClosure
- get2DLinCoeffs(double[][]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- get4thPoint(double[], double[], double[], double, double, double) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
-
From KiNG's driftwood.r3.Builder: Given three points A, B, and C, construct a line segment from C to D of length len at angle ang to BC (in degrees, 0 to 180) and with a dihedral angle dihe to ABC (in degrees) return D Used in sidechain idealization
- getA() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.TestFancyKernel
- getA() - Method in class edu.duke.cs.osprey.tools.MinVolEllipse
- getAAsAtPos(PruningMatrix, int) - Method in class edu.duke.cs.osprey.kstar.KSSearchProblem
- getAAsFromSeq(ArrayList<String>) - Static method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getAbsolutePos() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getAffinityDesignFromFile(File) - Static method in class edu.duke.cs.osprey.design.commands.CommandBindingAffinity
- getAij() - Method in class edu.duke.cs.osprey.energy.forcefield.AtomPairVanDerWaalsContribution
- getAllConfs() - Method in class edu.duke.cs.osprey.lute.ConfSampler.Samples
- getAllowedAAs() - Method in class edu.duke.cs.osprey.control.ConfigFileParser
- getAllowedAAs() - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getAllowedAAs(ArrayList<Integer>) - Method in class edu.duke.cs.osprey.multistatekstar.MSConfigFileParser
- getAllowedSequences(int, KSAllowedSeqs) - Method in class edu.duke.cs.osprey.kstar.KSConfigFileParser
- getAllResTypes() - Method in class edu.duke.cs.osprey.confspace.Strand.ResidueFlex
-
for both library and wild-type rotamers
- getAlternates(int) - Method in class edu.duke.cs.osprey.structure.Molecule
- getAngleDegrees(double[], double[]) - Static method in class edu.duke.cs.osprey.tools.Protractor
- getAngleDegrees(double[], double[], double[]) - Static method in class edu.duke.cs.osprey.tools.Protractor
- getAngleRadians(double[], double[]) - Static method in class edu.duke.cs.osprey.tools.Protractor
- getAngleRadians(double[], double[], double[]) - Static method in class edu.duke.cs.osprey.tools.Protractor
- getAngles() - Method in class edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry
- getArgs() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ForcefieldKernelCuda
- getArgs() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.ForcefieldKernelOpenCL
- getArrayOrThrow(TomlArray, int) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getArrayOrThrow(TomlArray, int, TomlPosition) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getArrayOrThrow(TomlTable, String) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getArrayOrThrow(TomlTable, String, TomlPosition) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getAssignedAAs() - Method in class edu.duke.cs.osprey.multistatekstar.MSSearchProblem
- getAssignment(int) - Method in class edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode.Assignments
- getAssignment(BiConsumer<String, String>) - Method in class edu.duke.cs.osprey.tools.ConfigFileReader
-
parses a line like Name=Value and returns Name and Value in a callback
- getAssignmentIndex() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- getAssignments() - Method in class edu.duke.cs.osprey.confspace.ConfSearch.ScoredConf
-
Get the design position assignments of the conformation.
- getAssignments() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- getAssignments(SeqAStarNode.Assignments) - Method in class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode
- getAssignments(SeqAStarNode.Assignments) - Method in interface edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode
- getAsync() - Method in class edu.duke.cs.osprey.minimization.ConfMinimizer
- getAtom1() - Method in class edu.duke.cs.osprey.energy.forcefield.AtomPairEnergyContribution
- getAtom2() - Method in class edu.duke.cs.osprey.energy.forcefield.AtomPairEnergyContribution
- getAtomByName(String) - Method in class edu.duke.cs.osprey.structure.Residue
- getAtomByNameOrThrow(String) - Method in class edu.duke.cs.osprey.structure.Residue
- getAtomFlags() - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy
- getAtomFlags() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ForcefieldKernelCuda
- getAtomIndex(ConfSpace, int, int) - Method in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Description
- getAtomIndexByName(String) - Method in class edu.duke.cs.osprey.structure.Residue
- getAtomInfo(Atom) - Method in class edu.duke.cs.osprey.structure.Probe
- getAtomName(int) - Method in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords
- getAtomOffset(ForcefieldInteractions.AtomGroup) - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy
- getAtomOffset(Residue) - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy
- getAtomPairEnergyContributions() - Method in class edu.duke.cs.osprey.energy.forcefield.ResPairEnergyContribution
- getAtomPairNames() - Method in class edu.duke.cs.osprey.plug.RCTuplePolytope
- getAtomPairs(Residue, Residue) - Method in class edu.duke.cs.osprey.structure.AtomConnectivity
- getAtoms() - Method in interface edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions.AtomGroup
-
Deprecated.
- getAtoms() - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions.ResidueAtomGroup
-
Deprecated.
- getAttraction(Probe.AtomInfo, Probe.AtomInfo) - Method in class edu.duke.cs.osprey.structure.Probe
- getAttribute(int) - Method in class edu.duke.cs.osprey.gpu.cuda.Gpu
- getAvgIterationTimeNs() - Method in class edu.duke.cs.osprey.partcr.PartCR
- getAvgMinimizationTimeNs() - Method in class edu.duke.cs.osprey.partcr.PartCR
- getB() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.TestFancyKernel
- getBasePucker() - Method in class edu.duke.cs.osprey.dof.ProlinePucker
- getBestBlockThreads(AtomicInteger) - Method in class edu.duke.cs.osprey.gpu.cuda.Kernel.Function
- getBestConfs(MultiStateConfSpace.State) - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqDB
- getBestConfs(MultiStateConfSpace.State, Sequence) - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqDB
- getBij() - Method in class edu.duke.cs.osprey.energy.forcefield.AtomPairVanDerWaalsContribution
- getBlock() - Method in class edu.duke.cs.osprey.bbfree.BBFreeDOF
- getBlock() - Method in class edu.duke.cs.osprey.dof.deeper.perts.Perturbation
- getBlock() - Method in class edu.duke.cs.osprey.dof.DegreeOfFreedom
- getBlock() - Method in class edu.duke.cs.osprey.dof.EllipseCoordDOF
- getBlock() - Method in class edu.duke.cs.osprey.dof.FreeDihedral
- getBlock() - Method in class edu.duke.cs.osprey.dof.ProlinePucker
- getBlock() - Method in class edu.duke.cs.osprey.dof.ResidueTypeDOF
- getBlock() - Method in class edu.duke.cs.osprey.dof.StrandRotation
- getBlock() - Method in class edu.duke.cs.osprey.dof.StrandTranslation
- getBlockIndex(String) - Method in class edu.duke.cs.osprey.dof.DofInfo
- getBoltzmannWeight(double) - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getBondEquilibriumLength(Atom, Atom) - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- getBondingAtomNames() - Method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate.SpecifiedBondingAtomsTemplate
- getBool(String) - Method in class edu.duke.cs.osprey.control.ParamSet
- getBool(String, boolean) - Method in class edu.duke.cs.osprey.control.ParamSet
- getBoolean(Structs.Array, long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- getBoolean(Structs.Field) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- getBooleanOrThrow(TomlArray, int) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getBooleanOrThrow(TomlArray, int, TomlPosition) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getBooleanOrThrow(TomlTable, String) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getBooleanOrThrow(TomlTable, String, TomlPosition) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getBoundError() - Method in class edu.duke.cs.osprey.kstar.RCEnergyContribs
- getBoundErrorByPos() - Method in class edu.duke.cs.osprey.kstar.RCEnergyContribs
- getBounds() - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- getBroadcastInfo() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices
- getBrokenResidue() - Method in class edu.duke.cs.osprey.structure.ConfProblem
- getBufferSize() - Method in class edu.duke.cs.osprey.confspace.ConfSearch.MultiSplitter
- getByte(Structs.Array, long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- getByte(Structs.Field) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- getC() - Method in class edu.duke.cs.osprey.tools.MinVolEllipse
- getCapacity() - Method in class edu.duke.cs.osprey.sofea.FringeDB
-
Returns the maximum number of fringe nodes that can fit in the database.
- getCartesianCoords(double[]) - Method in class edu.duke.cs.osprey.tools.EllipseTransform
- getCenter(int) - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- getCenter(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- getCFGImpl() - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getChainId() - Method in class edu.duke.cs.osprey.structure.Residue
- getChar(Structs.Array, long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- getChar(Structs.Field) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- getCharge() - Method in class edu.duke.cs.osprey.energy.forcefield.AtomPairElectrostaticContribution
- getCheckPointDir() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getCheckPointFilePath() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getCheckPointName(boolean, int, String, ArrayList<String>) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getCheckPointPath() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getChildren() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- getChildren(COMETSNode) - Method in class edu.duke.cs.osprey.astar.comets.NewCOMETSTree
- getChildren(FullAStarNode) - Method in class edu.duke.cs.osprey.astar.comets.COMETSTree
- getChildren(T) - Method in class edu.duke.cs.osprey.astar.AStarTree
- getChildren(T) - Method in class edu.duke.cs.osprey.astar.ConfTree
- getCLEvents() - Method in class edu.duke.cs.osprey.gpu.opencl.ProfilingEvents
- getCLIds() - Method in class edu.duke.cs.osprey.gpu.opencl.ProfilingEvents
- getCLKernel() - Method in class edu.duke.cs.osprey.gpu.opencl.Kernel
- getClosestPoint(double[], double[], double[]) - Method in class edu.duke.cs.osprey.dof.deeper.perts.Backrub
- getCLQueue() - Method in class edu.duke.cs.osprey.gpu.opencl.GpuQueue
- getCoeffs() - Method in class edu.duke.cs.osprey.astar.comets.LME
- getCoeffs() - Method in class edu.duke.cs.osprey.energy.MultiTermEnergyFunction
- getCoeffs() - Method in class edu.duke.cs.osprey.energy.ParallelEnergyFunction
- getCommandDescription() - Method in class edu.duke.cs.osprey.design.commands.CommandBindingAffinity
- getCommandDescription() - Method in class edu.duke.cs.osprey.design.commands.CommandGMEC
- getCommandDescription() - Method in class edu.duke.cs.osprey.design.commands.CommandMakeFlexShell
- getCommandDescription() - Method in class edu.duke.cs.osprey.design.commands.CommandPartitionFunction
- getCommandDescription() - Method in class edu.duke.cs.osprey.design.commands.CommandTopNConfs
- getCommandDescription() - Method in class edu.duke.cs.osprey.design.commands.RunnableCommand
- getCommandName() - Method in class edu.duke.cs.osprey.design.commands.CommandBindingAffinity
- getCommandName() - Method in class edu.duke.cs.osprey.design.commands.CommandGMEC
- getCommandName() - Method in class edu.duke.cs.osprey.design.commands.CommandMakeFlexShell
- getCommandName() - Method in class edu.duke.cs.osprey.design.commands.CommandPartitionFunction
- getCommandName() - Method in class edu.duke.cs.osprey.design.commands.CommandTopNConfs
- getCommandName() - Method in class edu.duke.cs.osprey.design.commands.RunnableCommand
- getCompetitorPruneMat() - Method in class edu.duke.cs.osprey.gmec.PrecomputedMatrices
- getComputeVersion() - Method in class edu.duke.cs.osprey.gpu.cuda.Gpu
- getConf() - Method in class edu.duke.cs.osprey.externalMemory.EMConfAStarNode
- getConf() - Method in class edu.duke.cs.osprey.kstar.KSConf
- getConf(int[]) - Method in interface edu.duke.cs.osprey.astar.conf.ConfAStarNode
- getConf(int[]) - Method in class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode
- getConf(int[]) - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- getConf(int[]) - Method in class edu.duke.cs.osprey.externalMemory.EMConfAStarNode
- getConf(int[]) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- getConfArray() - Method in class edu.duke.cs.osprey.kstar.KSConf
- getConfAssignments() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- getConfAtom1Index(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesPair
- getConfAtom2Index(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesPair
- getConfAtomIndex(int, int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- getConfBound(int[]) - Method in class edu.duke.cs.osprey.kstar.KSConfQ
- getConfBound(ConfSearch, int[]) - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getConfig(MultiStateConfSpace.State) - Method in class edu.duke.cs.osprey.sofea.Sofea
- getConfIndex() - Method in class edu.duke.cs.osprey.astar.conf.scoring.mplp.MessageVars
- getConfIndex(int, int) - Method in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords
- getConfLowerBound() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- getConfLowerBound() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- getConfReport(int[]) - Method in class edu.duke.cs.osprey.control.ConfPrinter
-
Deprecated.
- getConfReport(ConfSearch.EnergiedConf) - Method in class edu.duke.cs.osprey.control.ConfPrinter
-
Deprecated.
- getConfReport(ConfSearch.EnergiedConf, EnergyRange) - Method in class edu.duke.cs.osprey.control.ConfPrinter
-
Deprecated.
- getConfReport(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.control.ConfPrinter
-
Deprecated.
- getConfReport(ConfSearch.ScoredConf, EnergyRange) - Method in class edu.duke.cs.osprey.control.ConfPrinter
-
Deprecated.
- getConfResEntropy(int[]) - Method in class edu.duke.cs.osprey.confspace.ConfSpace
- getConfs() - Method in class edu.duke.cs.osprey.partcr.PartCR
- getConfs(RCTuple) - Method in class edu.duke.cs.osprey.lute.ConfSampler.Samples
- getConfsByLowerBound(double) - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- getConfsByUpperBound(double) - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- getConfSearch() - Method in class edu.duke.cs.osprey.kstar.KSConfQ
- getConfSearchNode() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- getConfSpace() - Method in class edu.duke.cs.osprey.ematrix.epic.EPICMatrix
- getConfSpace() - Method in class edu.duke.cs.osprey.ematrix.epic.NewEPICMatrix
- getConfSpace() - Method in class edu.duke.cs.osprey.gmec.PrecomputedMatrices
- getConfSpace() - Method in class edu.duke.cs.osprey.kstar.SequenceAnalyzer.Analysis
- getConfSpaceInfo(ConfSpaceIteration) - Method in class edu.duke.cs.osprey.kstar.KStar
- getConfSpaceInfo(SimpleConfSpace) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar
- getConfSpaceInfo(SimpleConfSpace) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar
- getConfSpaceInfo(SimpleConfSpace) - Method in class edu.duke.cs.osprey.kstar.BBKStar
- getConfsThreadBuffer() - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getConfTree(boolean) - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getConfUpperBound() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- getConfUpperBound() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- getConstr() - Method in class edu.duke.cs.osprey.plug.RCTuplePolytope
- getConstraints() - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction
- getConstraints() - Method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- getConstraints() - Method in class edu.duke.cs.osprey.minimization.MoleculeObjectiveFunction
- getConstraints() - Method in interface edu.duke.cs.osprey.minimization.ObjectiveFunction
- getConstraintsResid(double[][]) - Method in class edu.duke.cs.osprey.bbfree.VoxelSeriesChecker
- getConstTerm() - Method in class edu.duke.cs.osprey.astar.comets.LME
- getConstTerm() - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrix
- getConstTerm() - Method in class edu.duke.cs.osprey.ematrix.NegatedEnergyMatrix
- getContact(double) - Method in class edu.duke.cs.osprey.structure.Probe.AtomPair
- getContact(double, double, Probe.Attraction) - Method in class edu.duke.cs.osprey.structure.Probe
- getContext() - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- getContext() - Method in class edu.duke.cs.osprey.gpu.cuda.Kernel
- getContext(int, Class<?>) - Method in class edu.duke.cs.osprey.parallelism.TaskExecutor.ContextGroup
- getContext(TaskExecutor.ContextId) - Method in class edu.duke.cs.osprey.parallelism.TaskExecutor.ContextGroup
- getContext(TaskExecutor.Task.WithContext<T, C>) - Method in class edu.duke.cs.osprey.parallelism.TaskExecutor.ContextGroup
- getCoords() - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy
- getCoords() - Method in interface edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions.AtomGroup
-
Deprecated.
- getCoords() - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions.ResidueAtomGroup
-
Deprecated.
- getCoords() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ForcefieldKernelCuda
- getCoords() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.ForcefieldKernelOpenCL
- getCoords() - Method in class edu.duke.cs.osprey.structure.Atom
- getCoordsByAtomName(String) - Method in class edu.duke.cs.osprey.structure.Residue
- getCopiedDOF(DegreeOfFreedom) - Method in class edu.duke.cs.osprey.confspace.ParameterizedMoleculeCopy
- getCopiedMolecule() - Method in class edu.duke.cs.osprey.confspace.ParameterizedMoleculeCopy
- getCorrections() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- getCorrections(RCTuple) - Method in class edu.duke.cs.osprey.ematrix.UpdatingEnergyMatrix.TupleTrie
- getCounts(int) - Method in class edu.duke.cs.osprey.structure.analysis.DegreesHistogram
-
get all buckets along angle d in [-180,179] order
- getCudaContexts() - Method in class edu.duke.cs.osprey.energy.GpuEnergyFunctionGenerator
- getCurPucker() - Method in class edu.duke.cs.osprey.dof.ProlinePucker
- getCurResType() - Method in class edu.duke.cs.osprey.dof.ResidueTypeDOF
- getCurVal() - Method in class edu.duke.cs.osprey.dof.DegreeOfFreedom
- getCurVal() - Method in class edu.duke.cs.osprey.dof.EllipseCoordDOF
- getCurVal() - Method in class edu.duke.cs.osprey.dof.FreeDihedral
- getCurValueOfDOF(int) - Method in class edu.duke.cs.osprey.minimization.IdealSeparableReference
- getCurValueOfDOF(int) - Method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- getData() - Method in class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode
- getData() - Method in interface edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode
- getDataDir() - Static method in class edu.duke.cs.osprey.control.EnvironmentVars
-
Deprecated.
- getDecomposedMinimizedEnergy(int[], EnergyFunction, String) - Method in class edu.duke.cs.osprey.confspace.ConfSpace
- getDEEPerSettings() - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getDefaultHigherInteraction() - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- getDeltaDegrees(double, double) - Static method in class edu.duke.cs.osprey.tools.Protractor
-
returns the smallest directed distance from a to b
- getDenom() - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- getDescription() - Method in class edu.duke.cs.osprey.ematrix.epic.FitParams
- getDescription() - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
- getDevice() - Method in class edu.duke.cs.osprey.gpu.cuda.Gpu
- getDevice() - Method in class edu.duke.cs.osprey.gpu.opencl.Gpu
- getDevicePointer() - Method in class edu.duke.cs.osprey.gpu.cuda.CUBuffer
- getDihedralAngle(int) - Method in class edu.duke.cs.osprey.structure.Residue
- getDihedralAngles() - Method in class edu.duke.cs.osprey.structure.Residue
- getDihedralDefiningAtoms(int) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
- getDihedralForRotamer(int, String, double, double, int, int) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
-
PGC 2015: get ideal dihedral value for a particular rotamer of a particular residue type, for backbone dependent or backbone independent rotamers.
- getDihedralForRotamer(int, String, int, int) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
- getDihedralForRotamer(String, int, int) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
- getDihedralNumber() - Method in class edu.duke.cs.osprey.dof.FreeDihedral
- getDihedralRotatedAtoms(int) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
- getDimension() - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.OneDof
- getDist() - Method in class edu.duke.cs.osprey.structure.Probe.AtomPair
- getDist(Atom, Atom) - Method in class edu.duke.cs.osprey.structure.Probe
- getDistDegrees(double, double) - Static method in class edu.duke.cs.osprey.tools.Protractor
-
returns the smallest distance between a and b
- getDistFromWT(ArrayList<String>) - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getDistSq(Atom, Atom) - Method in class edu.duke.cs.osprey.structure.Probe
- getDOFs() - Method in class edu.duke.cs.osprey.bbfree.BBFreeBlock
- getDOFs() - Method in class edu.duke.cs.osprey.dof.MoveableStrand
- getDOFs() - Method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- getDOFs() - Method in class edu.duke.cs.osprey.plug.RCTuplePolytope
- getDOFsCenter() - Method in interface edu.duke.cs.osprey.minimization.ObjectiveFunction
- getDOFTol(int, int) - Method in class edu.duke.cs.osprey.minimization.CCDMinimizer
- getDofTypes() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- getDofTypes() - Method in class edu.duke.cs.osprey.confspace.StrandFlex
- getDofTypes() - Method in class edu.duke.cs.osprey.confspace.VoxelShape
- getDofTypes() - Method in class edu.duke.cs.osprey.confspace.VoxelShape.Point
- getDofTypes() - Method in class edu.duke.cs.osprey.confspace.VoxelShape.Rect
- getDouble(Structs.Array, long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- getDouble(Structs.Field) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- getDouble(String) - Method in class edu.duke.cs.osprey.control.ParamSet
- getDouble(String, double) - Method in class edu.duke.cs.osprey.control.ParamSet
- getDoubleOrThrow(TomlArray, int) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getDoubleOrThrow(TomlArray, int, TomlPosition) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getDoubleOrThrow(TomlTable, String) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getDoubleOrThrow(TomlTable, String, TomlPosition) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getDX() - Method in class edu.duke.cs.osprey.tools.SVGPlot.Boxes.Box
- getDY() - Method in class edu.duke.cs.osprey.tools.SVGPlot.Boxes.Box
- getEdenPool() - Static method in class edu.duke.cs.osprey.tools.JvmMem
- getEffectiveEpsilon() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Values
- getEffectiveEpsilon() - Method in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Values
- getEffectiveEpsilon() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getEffectiveEpsilon() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound.Values
- getEffectiveEpsilon() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync.Values
- getEffectiveEpsilon() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid.Values
- getEffectiveEpsilon() - Method in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionDiscrete
- getEffectiveEpsilon() - Method in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionDiscreteUppperBound
- getEffectiveEpsilon() - Method in class edu.duke.cs.osprey.paste.PastePartitionFunction.Values
- getEfunc() - Method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- getEfunc(int) - Method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- getEfunc(int) - Method in class edu.duke.cs.osprey.minimization.MoleculeObjectiveFunction
- getElectrostaticsEnergy() - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- getElectrostaticsEnergy(ResPairCache.ResPair[]) - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- getElectrostaticsEnergyContributions(ResPairCache.ResPair[]) - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- getEllipsoidalArray() - Method in class edu.duke.cs.osprey.confspace.PositionConfSpace
- getEllipsoidalCoords(double[]) - Method in class edu.duke.cs.osprey.confspace.PositionConfSpace
- getEllipsoidalCoords(double[]) - Method in class edu.duke.cs.osprey.tools.EllipseTransform
- getEmat() - Method in class edu.duke.cs.osprey.confspace.TupleEnumerator
- getEmat() - Method in class edu.duke.cs.osprey.gmec.PrecomputedMatrices
- getEMATdir() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getEMatrix() - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrixCalculator
- getEnergied(int[]) - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- getEnergied(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- getEnergies() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ForcefieldKernelCuda
- getEnergies() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.ForcefieldKernelOpenCL
- getEnergy() - Method in class edu.duke.cs.osprey.confspace.ConfSearch.EnergiedConf
-
Get the energy for this conformation
- getEnergy() - Method in class edu.duke.cs.osprey.ematrix.epic.EPICEnergyFunction
- getEnergy() - Method in interface edu.duke.cs.osprey.energy.EnergyFunction
- getEnergy() - Method in class edu.duke.cs.osprey.energy.forcefield.AtomPairEnergyContribution
- getEnergy() - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy
- getEnergy() - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.Subset
- getEnergy() - Method in class edu.duke.cs.osprey.energy.forcefield.GpuForcefieldEnergy
- getEnergy() - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- getEnergy() - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy.Vdw
- getEnergy() - Method in class edu.duke.cs.osprey.energy.forcefield.ResPairEnergy
- getEnergy() - Method in class edu.duke.cs.osprey.energy.forcefield.ResPairEnergyContribution
- getEnergy() - Method in class edu.duke.cs.osprey.energy.forcefield.SingleResEnergy
- getEnergy() - Method in class edu.duke.cs.osprey.energy.forcefield.SparseFFEnergy
- getEnergy() - Method in class edu.duke.cs.osprey.energy.MultiTermEnergyFunction
- getEnergy() - Method in class edu.duke.cs.osprey.energy.ParallelEnergyFunction
- getEnergy() - Method in class edu.duke.cs.osprey.energy.PoissonBoltzmannEnergy
- getEnergy() - Method in class edu.duke.cs.osprey.energy.ScaledEnergyFunction
- getEnergy() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ResidueForcefieldEnergyCuda
- getEnergy() - Method in class edu.duke.cs.osprey.kstar.KSConf
- getEnergy(int, int) - Method in class edu.duke.cs.osprey.astar.conf.scoring.mplp.MessageVars
- getEnergy(int, int) - Method in interface edu.duke.cs.osprey.confspace.FragmentEnergies
- getEnergy(int, int) - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrix
- getEnergy(int, int) - Method in class edu.duke.cs.osprey.lute.LUTEConfEnergyCalculator
- getEnergy(int, int, int, int) - Method in interface edu.duke.cs.osprey.confspace.FragmentEnergies
- getEnergy(int, int, int, int) - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrix
- getEnergy(int, int, int, int) - Method in class edu.duke.cs.osprey.lute.LUTEConfEnergyCalculator
- getEnergy(int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.lute.LUTEConfEnergyCalculator
- getEnergy(SimpleConfSpace.Position, SimpleConfSpace.ResidueConf) - Method in interface edu.duke.cs.osprey.confspace.FragmentEnergies
- getEnergy(SimpleConfSpace.Position, SimpleConfSpace.ResidueConf, SimpleConfSpace.Position, SimpleConfSpace.ResidueConf) - Method in interface edu.duke.cs.osprey.confspace.FragmentEnergies
- getEnergy(ResidueForcefieldEnergy) - Method in enum class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.Type
- getEnergyBound() - Method in class edu.duke.cs.osprey.kstar.KSConf
- getEnergyContributions(ResPairCache.ResPair[]) - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- getEnergyFunctionGenerator() - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator.Cpu
-
Deprecated.
- getEnergyFunctionGenerator() - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator.Cuda
-
Deprecated.
- getEnergyFunctionGenerator() - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator
-
Deprecated.
- getEnergyMatrix() - Method in class edu.duke.cs.osprey.kstar.KSSearchProblem
- getEnergyMatrix() - Method in class edu.duke.cs.osprey.tupexp.TupleExpander
- getEnergyMatrixFileName() - Method in class edu.duke.cs.osprey.kstar.KSSearchProblem
- getEnergySharedMolec() - Method in class edu.duke.cs.osprey.ematrix.epic.SAPE
- getEnergySize() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.ForcefieldKernelOpenCL
- getEnergySize(BigForcefieldEnergy.Subset) - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.ForcefieldKernelOpenCL
- getEnergyStandalone(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.ematrix.epic.SAPE
- getEnergyWithout(int, int, int) - Method in class edu.duke.cs.osprey.astar.conf.scoring.mplp.MessageVars
- getEnsemblePDBName() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- getEntrySize() - Method in class edu.duke.cs.osprey.externalMemory.AssignmentsSerializer
- getEpicMat() - Method in class edu.duke.cs.osprey.gmec.PrecomputedMatrices
- getEPICMatrix() - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrixCalculator
- getEPICMatrix() - Method in class edu.duke.cs.osprey.ematrix.NewEPICMatrixCalculator
- getEpMols() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarGradientDescentPfunc
- getEpMols() - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction
- getEpMols() - Method in class edu.duke.cs.osprey.paste.PasteGradientDescentPfunc
- getEpMols() - Method in interface edu.duke.cs.osprey.paste.PastePartitionFunction
- getEpsilonStatus() - Method in class edu.duke.cs.osprey.kstar.KSCalc
- getEpsilonStatus() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- geteRefMat() - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrix
- getErrorBound() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- getEtaMs(Deque<Long>, Deque<Long>, long) - Method in enum class edu.duke.cs.osprey.tools.Progress.Model
- getExternalBytes() - Static method in class edu.duke.cs.osprey.externalMemory.ExternalMemory
-
Return the number of bytes currently used in external memory.
- getFeasiblePt(ArrayList<LinearConstraint>) - Static method in class edu.duke.cs.osprey.plug.LPChecks
- getFFEnergy() - Method in class edu.duke.cs.osprey.energy.forcefield.ResPairEnergy
- getFFEnergy() - Method in class edu.duke.cs.osprey.energy.forcefield.SingleResEnergy
- getFFParams() - Method in class edu.duke.cs.osprey.energy.forcefield.ResPairEnergy
- getFFParams() - Method in class edu.duke.cs.osprey.energy.forcefield.SingleResEnergy
- getFile(String) - Method in class edu.duke.cs.osprey.control.ParamSet
- getFilesInDir(String) - Static method in class edu.duke.cs.osprey.tools.ObjectIO
- getFirstPos() - Method in class edu.duke.cs.osprey.ewakstar.EwakstarLimitedSequenceTrie
- getFlexibility() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getFlexibleResidueNumbers() - Method in class edu.duke.cs.osprey.confspace.Strand.Flexibility
- getFlexPosIndex(String) - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getFlexRes() - Method in class edu.duke.cs.osprey.control.ConfigFileParser
- getFlexRes() - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getFlexResFromSeq(ArrayList<String>) - Static method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getFlexResIndexesFromSeq(ArrayList<String>) - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getFlexResMinE(MultiTermEnergyFunction, boolean) - Method in class edu.duke.cs.osprey.kstar.RCEnergyContribs
- getFlexResPWLB(int[], boolean) - Method in class edu.duke.cs.osprey.kstar.RCEnergyContribs
- getFloat(Structs.Array, long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- getFloat(Structs.Field) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- getFocusedStatei() - Method in class edu.duke.cs.osprey.coffee.directions.Directions
- getForcefield() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ForcefieldKernelCuda
- getForcefield() - Method in interface edu.duke.cs.osprey.gpu.ForcefieldKernel
- getForcefield() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.ForcefieldKernelOpenCL
- getFormattedSequence() - Method in class edu.duke.cs.osprey.multistatekstar.MSSearchSettings
- getFrameDegrees(double[], double[], double[]) - Static method in class edu.duke.cs.osprey.tools.Protractor
-
returns the degrees (relative to 0) in a frame defined by the axis and zero vectors the axis and zero vectors are assumed to be perpendicular v is the query vector, assumed to be perpendicular to axis angles are positive in the ccw direction when looking against the axis
- getFreeBBZoneTermini() - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getFreeDOFVoxel() - Method in class edu.duke.cs.osprey.bbfree.BBFreeBlock
- getFreeEnergy() - Method in class edu.duke.cs.osprey.coffee.directors.PfuncDirector
- getFreeEnergy(MultiStateConfSpace.State) - Method in class edu.duke.cs.osprey.coffee.directors.SequenceDirector
- getFreeMemory() - Method in class edu.duke.cs.osprey.gpu.cuda.Gpu
- getFromLetter(char) - Static method in enum class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf.Type
- getFullPolytope(RCTuple) - Method in class edu.duke.cs.osprey.plug.PolytopeMatrix
- getFullStericPolytope(RCTuple, ArrayList<DegreeOfFreedom>) - Method in class edu.duke.cs.osprey.plug.PolytopeMatrix
- getFullSubset() - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy
- getGBounds(MultiStateConfSpace.State, Sequence, SimpleConfSpace.Position, SimpleConfSpace.ResidueConf, MathContext) - Method in class edu.duke.cs.osprey.sofea.RCDB
- getGBounds(SeqDB, MultiStateConfSpace.State) - Method in class edu.duke.cs.osprey.sofea.SequenceLMFE
- getGBounds(SeqDB, MultiStateConfSpace.State, MathContext) - Method in class edu.duke.cs.osprey.sofea.SequenceLMFE
- getGenChi1(Residue) - Static method in class edu.duke.cs.osprey.dof.deeper.GenChi1Calc
- getGenChi1LastAtom(String) - Static method in class edu.duke.cs.osprey.dof.deeper.GenChi1Calc
- getGpu() - Method in class edu.duke.cs.osprey.gpu.cuda.Context
- getGpu() - Method in class edu.duke.cs.osprey.gpu.opencl.GpuQueue
- getGpuBytesNeeded() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.ForcefieldKernelOpenCL
- getGpus() - Method in class edu.duke.cs.osprey.gpu.cuda.Gpus
- getGpus() - Method in class edu.duke.cs.osprey.gpu.opencl.Gpus
- getGpusInfos() - Static method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- getGScore() - Method in class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode
- getGScore() - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- getGScore() - Method in class edu.duke.cs.osprey.astar.FullAStarNode
- getGScore() - Method in interface edu.duke.cs.osprey.astar.OptimizableAStarNode
- getGScore() - Method in class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode
- getGScore() - Method in class edu.duke.cs.osprey.astar.SlimAStarNode
- getGScore() - Method in class edu.duke.cs.osprey.externalMemory.EMConfAStarNode
- getGScore() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- getGScore(MathTools.Optimizer) - Method in interface edu.duke.cs.osprey.astar.OptimizableAStarNode
- getHalfAngleSinCos(double, double) - Static method in class edu.duke.cs.osprey.tools.Protractor
-
Deprecated.
- getHigherInteractions(int, int) - Method in class edu.duke.cs.osprey.confspace.HigherTupleFinder
- getHigherOrderEnergy(RCTuple, int, int) - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrix
- getHigherOrderTerms(int, int, int, int) - Method in class edu.duke.cs.osprey.astar.comets.UpdatedPruningMatrix
- getHigherOrderTerms(int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- getHigherOrderTerms(int, int, int, int) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- getHigherOrderTerms(int, int, int, int) - Method in class edu.duke.cs.osprey.kstar.emat.ReducedEnergyMatrix
- getHigherOrderTerms(int, int, int, int) - Method in class edu.duke.cs.osprey.kstar.pruning.InvertedPruningMatrix
- getHigherOrderTerms(int, int, int, int) - Method in class edu.duke.cs.osprey.kstar.pruning.ReducedPruningMatrix
- getHigherOrderTerms(int, int, int, int) - Method in class edu.duke.cs.osprey.kstar.pruning.UnprunedPruningMatrix
- getHigherOrderTerms(int, int, int, int) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixInverted
- getHigherOrderTerms(int, int, int, int) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- getHigherOrderTerms(int, int, int, int) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- getHigherOrderTuples(int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- getHigherOrderTuples(int, int, int, int) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
-
returns the TupleTree containing the higher order tuples, or null if none use this for reading tuples from the matrix pos1 < pos2 must be the lowest-order positions in the tuple
- GetHighestNodeOperation - Class in edu.duke.cs.osprey.coffee.nodedb
-
Returns the highest-scoring node from a cluster member.
- GetHighestNodeOperation() - Constructor for class edu.duke.cs.osprey.coffee.nodedb.GetHighestNodeOperation
- GetHighestNodeOperation(int) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.GetHighestNodeOperation
- GetHighestNodesOperation - Class in edu.duke.cs.osprey.coffee.nodedb
-
Returns the highest-scoring node from a cluster member.
- GetHighestNodesOperation() - Constructor for class edu.duke.cs.osprey.coffee.nodedb.GetHighestNodesOperation
- GetHighestNodesOperation(int, int) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.GetHighestNodesOperation
- getHighOrderTuplesByPDBResNum() - Method in class edu.duke.cs.osprey.kstar.KSConfigFileParser
- getHighOrderTuplesByStrand(int) - Method in class edu.duke.cs.osprey.kstar.KSConfigFileParser
- getHostBuffer() - Method in class edu.duke.cs.osprey.gpu.cuda.CUBuffer
- getHotBoundPct() - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getHotMethod() - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getHotNumRes() - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getHotTopRotsPct() - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getHScore() - Method in class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode
- getHScore() - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- getHScore() - Method in class edu.duke.cs.osprey.astar.FullAStarNode
- getHScore() - Method in interface edu.duke.cs.osprey.astar.OptimizableAStarNode
- getHScore() - Method in class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode
- getHScore() - Method in class edu.duke.cs.osprey.astar.SlimAStarNode
- getHScore() - Method in class edu.duke.cs.osprey.externalMemory.EMConfAStarNode
- getHScore() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- getHScore(MathTools.Optimizer) - Method in interface edu.duke.cs.osprey.astar.OptimizableAStarNode
- getId() - Method in interface edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions.AtomGroup
-
Deprecated.
- getId() - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions.ResidueAtomGroup
-
Deprecated.
- getId(Residue) - Static method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions.ResidueAtomGroup
-
Deprecated.
- getImpl() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFAdapter
- getImpl() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel0
- getImpl() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- getImpl() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel2
- getImpl() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFTraditional
- getImpl() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFUB
- getImpl() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getIndex() - Method in class edu.duke.cs.osprey.dof.EllipseCoordDOF
- getIndex(double[]) - Method in class edu.duke.cs.osprey.structure.analysis.DegreesHistogram
- getIndex(int, int) - Method in class edu.duke.cs.osprey.confspace.AbstractPosMatrix
- getIndex(int, int) - Method in class edu.duke.cs.osprey.confspace.TuplesIndex
- getIndex(int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.TuplesIndex
- getIndex(int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.TuplesIndex
- getIndex(RCTuple) - Method in class edu.duke.cs.osprey.confspace.TuplesIndex
- getIndexDelta(int) - Method in class edu.duke.cs.osprey.structure.analysis.DegreesHistogram
- getIndices(int) - Method in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords
- getIndices(int, int) - Method in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords
- getIndices(int, int, int) - Method in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords
- getInitFixableDOFs() - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction
- getInitFixableDOFs() - Method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- getInitFixableDOFs() - Method in class edu.duke.cs.osprey.minimization.MoleculeObjectiveFunction
- getInitFixableDOFs() - Method in interface edu.duke.cs.osprey.minimization.ObjectiveFunction
- getInitialStepSize() - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.OneDof
- getInitStepSize(int) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction
- getInitStepSize(int) - Method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- getInitStepSize(int) - Method in class edu.duke.cs.osprey.minimization.MoleculeObjectiveFunction
- getInitStepSize(int) - Method in interface edu.duke.cs.osprey.minimization.ObjectiveFunction
- getInitStepSize(DegreeOfFreedom) - Static method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- getInstance() - Static method in class edu.duke.cs.osprey.dof.deeper.RamachandranChecker
- getInstance() - Static method in class edu.duke.cs.osprey.handlempi.MPIMaster
- getInt(Structs.Array, long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- getInt(Structs.Field) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- getInt(String) - Method in class edu.duke.cs.osprey.control.ParamSet
- getInt(String, int) - Method in class edu.duke.cs.osprey.control.ParamSet
- getInteractingPos() - Method in class edu.duke.cs.osprey.confspace.HigherTupleFinder
- getInteraction() - Method in class edu.duke.cs.osprey.structure.Probe.AtomPair
- getInteraction(int, int) - Method in class edu.duke.cs.osprey.confspace.HigherTupleFinder
- getInteractions() - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy
- getInteractions(Residue, AtomConnectivity) - Method in class edu.duke.cs.osprey.structure.Probe
-
gets probe interactions between all atom pairs within the residue atom connectivity must have set15HasNonBonded(false) to match real probe reults
- getInteractions(Residues, ResidueInteractions, AtomConnectivity) - Method in class edu.duke.cs.osprey.structure.Probe
-
gets probe interactions between all atom pairs defined by the residue pairs atom connectivity must have set15HasNonBonded(false) to match real probe reults
- getInteriorPt(LinearMultivariateRealFunction[]) - Static method in class edu.duke.cs.osprey.plug.LPChecks
- getInteriorPt(ArrayList<LinearConstraint>) - Static method in class edu.duke.cs.osprey.plug.LPChecks
- getInternalConfAtom1Index(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesSingle
- getInternalConfAtom2Index(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesSingle
- getInternalEnergy(int, int) - Method in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords
- getInternalEnergy(RCTuple) - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrix
- getInternalEnergy(RCTuple) - Method in class edu.duke.cs.osprey.ematrix.UpdatingEnergyMatrix
- getInternalEnergyAtPos(int, RCTuple, int) - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrix
- getInternalParamsIndex(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesSingle
- getInternalSolvationEnergy() - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.Subset
- getInterval(double, double) - Method in class edu.duke.cs.osprey.structure.analysis.ClusterR1.Stats
- getInterval(double, double) - Method in class edu.duke.cs.osprey.structure.analysis.ClusterS1.Stats
- getIntervalMid(Plot.Interval) - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.Intervals
- getIntOrThrow(TomlArray, int) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getIntOrThrow(TomlArray, int, TomlPosition) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getIntOrThrow(TomlTable, String) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getIntOrThrow(TomlTable, String, TomlPosition) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getIntraResBondMatrix() - Method in class edu.duke.cs.osprey.structure.Residue
- getInvertedFromReducedPruningMatrix(KSSearchProblem) - Method in class edu.duke.cs.osprey.kstar.KSSearchProblem
- getInvertedFromUnreducedPruningMatrix(KSSearchProblem) - Method in class edu.duke.cs.osprey.kstar.KSSearchProblem
- getJoptPolytope(RCTuple, ArrayList<DegreeOfFreedom>, double) - Method in class edu.duke.cs.osprey.plug.PolytopeMatrix
- getKernel() - Method in class edu.duke.cs.osprey.energy.forcefield.GpuForcefieldEnergy
- getKernel(String) - Method in class edu.duke.cs.osprey.gpu.cuda.Context
- getKSMethod() - Method in class edu.duke.cs.osprey.kstar.impl.KSImplKAStar
- getKSMethod() - Method in class edu.duke.cs.osprey.kstar.impl.KSImplLinear
- getKSMethod() - Method in interface edu.duke.cs.osprey.kstar.KSInterface
- getKStarScore(boolean) - Method in class edu.duke.cs.osprey.kstar.KSCalc
- getKStarScoreLog10(boolean) - Method in class edu.duke.cs.osprey.kstar.KSCalc
- getKStarScoreLog10(int, boolean) - Method in class edu.duke.cs.osprey.kstar.impl.KSImplLinear
- getKStarScoreLog10(PFAbstract, PFAbstract, PFAbstract, boolean) - Static method in class edu.duke.cs.osprey.kstar.KSCalc
- getKStarScoreLog10(BigDecimal, BigDecimal, BigDecimal) - Static method in class edu.duke.cs.osprey.kstar.KSCalc
- getLBScore() - Method in class edu.duke.cs.osprey.kstar.KAStarNode
- getLeastSampledTuple(Set<RCTuple>) - Method in class edu.duke.cs.osprey.lute.ConfSampler.Samples
- getLEquivalent(String) - Static method in class edu.duke.cs.osprey.restypes.DAminoAcidHandler
- getLevel() - Method in interface edu.duke.cs.osprey.astar.AStarNode
- getLevel() - Method in class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode
- getLevel() - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- getLevel() - Method in class edu.duke.cs.osprey.astar.FullAStarNode
- getLevel() - Method in interface edu.duke.cs.osprey.astar.OptimizableAStarNode
- getLevel() - Method in class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode
- getLevel() - Method in class edu.duke.cs.osprey.astar.SlimAStarNode
- getLevel() - Method in class edu.duke.cs.osprey.externalMemory.EMConfAStarNode
- getLevel() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- getLevelNodes(int) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- getLibraryTemplate(String) - Method in class edu.duke.cs.osprey.dof.ResidueTypeDOF
- getLine() - Method in class edu.duke.cs.osprey.tools.ConfigFileReader
-
returns the current line, or null if end of file
- getLinearConstraint(PLUG.AtomPairVoxel, double) - Method in class edu.duke.cs.osprey.pruning.PLUG
- getLinearConstraints(PLUG.Voxel, ResidueInteractions, double) - Method in class edu.duke.cs.osprey.pruning.PLUG
- getLink() - Method in class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode
- getLink() - Method in class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode
- getLink() - Method in class edu.duke.cs.osprey.astar.SlimAStarNode
- getLMBsForState(int) - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
-
returns constraints that ONLY involve the spacified state
- getLMBsForState(int, boolean) - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- getLong(long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- getLong(Structs.Array, long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- getLong(Structs.Field) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- getLongitudeRadians(double[], double[], double[]) - Static method in class edu.duke.cs.osprey.tools.Protractor
- getLongOrThrow(TomlArray, int) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getLongOrThrow(TomlArray, int, TomlPosition) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getLongOrThrow(TomlTable, String) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getLongOrThrow(TomlTable, String, TomlPosition) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getLowerBound() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- getLowerBound() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- getLowerBoundScore() - Method in interface edu.duke.cs.osprey.multistatekstar.KStarScore
- getLowerBoundScore() - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreDiscrete
- getLowerBoundScore() - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- getLowerEnergyOfUnsampledConfs() - Method in class edu.duke.cs.osprey.confspace.ConfDB.SequenceDB
- getLowestBound() - Method in class edu.duke.cs.osprey.gmec.GMECFinder
- getLowestDeepest() - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarQueue
- getLuteMat() - Method in class edu.duke.cs.osprey.gmec.PrecomputedMatrices
- getMatrixFileName(KSSearchProblem.MatrixType) - Method in class edu.duke.cs.osprey.kstar.KSSearchProblem
- getMatrixType() - Method in class edu.duke.cs.osprey.kstar.KSSearchProblem
- getMax() - Method in class edu.duke.cs.osprey.gmec.EnergyRange
- getMax(int) - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- getMaxBlockThreads() - Method in class edu.duke.cs.osprey.gpu.cuda.Gpu
- getMaxGroupSize() - Method in class edu.duke.cs.osprey.gpu.opencl.Kernel
- getMaxHOTSize(boolean) - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getMaxInterval() - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getMaxNumCPUs() - Static method in class edu.duke.cs.osprey.parallelism.Parallelism
- getMaxOverlap(Probe.Attraction) - Method in class edu.duke.cs.osprey.structure.Probe
- getMaxPosNums() - Method in class edu.duke.cs.osprey.kstar.KSSearchProblem
- getMaxs() - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- getMaxScore() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- getMeshWidth(double[]) - Method in class edu.duke.cs.osprey.minimization.GenCoord
- getMethod(String) - Static method in class edu.duke.cs.osprey.pruning.PruningMethod
- getMin() - Method in class edu.duke.cs.osprey.gmec.EnergyRange
- getMin(int) - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- getMinE() - Method in class edu.duke.cs.osprey.ematrix.epic.EPoly
- getMins() - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- getMinScore() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- getMolec() - Method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- getMoveableStrand() - Method in class edu.duke.cs.osprey.dof.StrandRotation
- getMoveableStrand() - Method in class edu.duke.cs.osprey.dof.StrandTranslation
- getMoveableStrandTermini() - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getMutAlignmentAtoms() - Method in class edu.duke.cs.osprey.dof.MutAlignment
- getMutants() - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- getMutants(int) - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- getMutants(int, boolean) - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- getMutants(File) - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- getMutationsFromFile(String) - Method in class edu.duke.cs.osprey.control.KStarCalculator
-
Deprecated.
- getName() - Method in class edu.duke.cs.osprey.bbfree.BBFreeDOF
- getName() - Method in class edu.duke.cs.osprey.dof.deeper.perts.Perturbation
- getName() - Method in class edu.duke.cs.osprey.dof.DegreeOfFreedom
- getName() - Method in class edu.duke.cs.osprey.dof.EllipseCoordDOF
- getName() - Method in class edu.duke.cs.osprey.dof.FreeDihedral
- getName() - Method in class edu.duke.cs.osprey.dof.ProlinePucker
- getName() - Method in class edu.duke.cs.osprey.dof.ResidueTypeDOF
- getName() - Method in class edu.duke.cs.osprey.dof.StrandRotation
- getName() - Method in class edu.duke.cs.osprey.dof.StrandTranslation
- getName() - Method in class edu.duke.cs.osprey.gpu.cuda.Gpu
- getName() - Method in class edu.duke.cs.osprey.parallelism.WorkCrew
- getNC() - Method in class edu.duke.cs.osprey.tools.MinVolEllipse
- getNearestInRangeDOFVal(double, double, double, DoubleMatrix1D, int, int[]) - Method in class edu.duke.cs.osprey.minimization.GenCoord
- getNextAssignments(MSSearchProblem[][], int) - Method in interface edu.duke.cs.osprey.multistatekstar.ResidueOrder
- getNextAssignments(MSSearchProblem[][], int) - Method in class edu.duke.cs.osprey.multistatekstar.ResidueOrderStaticSequential
- getNextChildIndex(int) - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- getNextConfBound() - Method in class edu.duke.cs.osprey.kstar.KSConfQ
- getNextPos(ConfIndex, RCs) - Method in interface edu.duke.cs.osprey.astar.conf.order.AStarOrder
- getNextPos(ConfIndex, RCs) - Method in class edu.duke.cs.osprey.astar.conf.order.DynamicHMeanAStarOrder
- getNextPos(ConfIndex, RCs) - Method in class edu.duke.cs.osprey.astar.conf.order.SequentialAStarOrder
- getNextPos(ConfIndex, RCs) - Method in class edu.duke.cs.osprey.astar.conf.order.StaticEnergyHMeanAStarOrder
- getNextPos(ConfIndex, RCs) - Method in class edu.duke.cs.osprey.astar.conf.order.StaticScoreHMeanAStarOrder
- getNextPos(ConfIndex, RCs) - Method in class edu.duke.cs.osprey.astar.conf.order.UpperLowerAStarOrder
- getNextPos(ConfIndex, RCs) - Method in class edu.duke.cs.osprey.markstar.framework.BiggestLowerboundDifferenceOrder
- getNextPos(ConfIndex, RCs) - Method in class edu.duke.cs.osprey.markstar.framework.StaticBiggestLowerboundDifferenceOrder
- getNextPos(ConfIndex, RCs) - Method in class edu.duke.cs.osprey.markstar.framework.StaticBiggesUpperboundDifferenceOrder
- getNextPos(ConfIndex, RCs) - Method in class edu.duke.cs.osprey.markstar.framework.StaticLowestEntropyOrder
- getNextPos(SeqAStarNode.Assignments, RTs) - Method in interface edu.duke.cs.osprey.astar.seq.order.SeqAStarOrder
- getNextPos(SeqAStarNode.Assignments, RTs) - Method in class edu.duke.cs.osprey.astar.seq.order.SequentialSeqAStarOrder
- getNodeAssignments() - Method in interface edu.duke.cs.osprey.astar.AStarNode
- getNodeAssignments() - Method in class edu.duke.cs.osprey.astar.FullAStarNode
- getNodeAssignments() - Method in class edu.duke.cs.osprey.astar.SlimAStarNode
- getNonBondedParameters(Atom, ForcefieldParams.NBParams) - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- getNonBondedParameters(Atom, AtomNeighbors.Type, ForcefieldParams.NBParams) - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- getNonBondedParametersOrThrow(Atom, AtomNeighbors.Type, ForcefieldParams.NBParams) - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- getNonmovingAtomNames() - Method in class edu.duke.cs.osprey.dof.MutAlignment
- getNullTerminated(MemoryBuffer, int) - Method in class edu.duke.cs.osprey.gpu.Structs.Char8.Array
- getNum(int) - Method in class edu.duke.cs.osprey.astar.conf.RCs
- getNum14AtomPairs() - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.Subset
- getNumAssignedPos() - Method in class edu.duke.cs.osprey.multistatekstar.MSSearchProblem
- getNumAtomPairs() - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.Subset
- getNumBytes() - Method in class edu.duke.cs.osprey.gpu.cuda.CUBuffer
- getNumCalculations() - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
returns the number of energy calculations performed, excluding values cached in a conf DB
- getNumConfAtPos() - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- getNumConfAtPos(int) - Method in class edu.duke.cs.osprey.astar.comets.UpdatedPruningMatrix
- getNumConfAtPos(int) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- getNumConfAtPos(int) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- getNumConfAtPos(int) - Method in class edu.duke.cs.osprey.kstar.emat.ReducedEnergyMatrix
- getNumConfAtPos(int) - Method in class edu.duke.cs.osprey.kstar.pruning.ReducedPruningMatrix
- getNumConfAtPos(int) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixInverted
- getNumConfAtPos(int) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- getNumConfAtPos(int) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- getNumConfDBReads() - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
returns the number of energies served from a conf DB
- getNumConformations() - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree
- getNumConformations() - Method in class edu.duke.cs.osprey.astar.conf.ConfSearchCache.Entry
- getNumConformations() - Method in class edu.duke.cs.osprey.astar.conf.RCs
-
Counts the number of full conformations in the conformation space.
- getNumConformations() - Method in class edu.duke.cs.osprey.astar.ConfTree
- getNumConformations() - Method in interface edu.duke.cs.osprey.confspace.ConfSearch
-
Get the total number of conformations in the conformation space.
- getNumConformations() - Method in class edu.duke.cs.osprey.confspace.ConfSearch.MultiSplitter.Stream
- getNumConformations() - Method in class edu.duke.cs.osprey.confspace.ConfSpace
- getNumConformations() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- getNumConformations() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- getNumConformations() - Method in class edu.duke.cs.osprey.multistatekstar.MultiSequenceConfTree
- getNumConfs() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- getNumConfsAtMost(double) - Method in class edu.duke.cs.osprey.astar.conf.ConfRanker
- getNumConfsEvaluated() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarGradientDescentPfunc
- getNumConfsEvaluated() - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction
- getNumConfsEvaluated() - Method in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- getNumConfsEvaluated() - Method in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- getNumConfsEvaluated() - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction
- getNumConfsEvaluated() - Method in class edu.duke.cs.osprey.kstar.pfunc.SimplePartitionFunction
- getNumConfsEvaluated() - Method in class edu.duke.cs.osprey.lute.LUTEPfunc
- getNumConfsEvaluated() - Method in class edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc
- getNumConfsEvaluated() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- getNumConfsEvaluated() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- getNumConfsEvaluated() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- getNumConfsEvaluated() - Method in class edu.duke.cs.osprey.paste.PasteGradientDescentPfunc
- getNumConfsEvaluated() - Method in interface edu.duke.cs.osprey.paste.PastePartitionFunction
- getNumConfsForSeq(Sequence, SimpleConfSpace) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- getNumConfsScored() - Method in class edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc
- getNumConfsScored() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- getNumConfsScored() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- getNumConfsScored() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- getNumConfsUpperBound(RCTuple, TuplesIndex) - Method in class edu.duke.cs.osprey.lute.UniformConfSampler
-
Deprecated.working with a tuple set (which may not completely cover the conf space) makes getting an exact count hard, but we can at least get an upper bound somewhat efficiently
- getNumCreated() - Static method in class edu.duke.cs.osprey.kstar.KAStarNode
- getNumDihedrals() - Method in class edu.duke.cs.osprey.structure.Residue
- getNumDOFs() - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction
- getNumDOFs() - Method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- getNumDOFs() - Method in class edu.duke.cs.osprey.minimization.MoleculeObjectiveFunction
- getNumDOFs() - Method in interface edu.duke.cs.osprey.minimization.ObjectiveFunction
- getNumEnumerated() - Method in class edu.duke.cs.osprey.kstar.KSPStarCalculator
- getNumExpanded() - Static method in class edu.duke.cs.osprey.kstar.KAStarNode
- getNumGpus() - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStreamPool
- getNumGpus() - Method in class edu.duke.cs.osprey.gpu.opencl.GpuQueuePool
- getNumLeavesCompleted() - Static method in class edu.duke.cs.osprey.kstar.KAStarNode
- getNumLeavesCreated() - Static method in class edu.duke.cs.osprey.kstar.KAStarNode
- getNumMutations(SeqAStarNode.Assignments) - Method in class edu.duke.cs.osprey.astar.seq.RTs
- getNumNodes() - Method in class edu.duke.cs.osprey.sofea.FringeDB
-
Returns the total number of nodes in the database
- getNumOneBody() - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- getNumPairs() - Method in class edu.duke.cs.osprey.confspace.AbstractPosMatrix
- getNumPairs() - Method in interface edu.duke.cs.osprey.confspace.PosMatrix
- getNumPairs(AtomNeighbors.Type) - Method in class edu.duke.cs.osprey.structure.AtomConnectivity.AtomPairs
- getNumPairwise() - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- getNumParams(int, boolean, int) - Static method in class edu.duke.cs.osprey.ematrix.epic.SeriesFitter
- getNumParamsForOrder(int, int) - Static method in class edu.duke.cs.osprey.ematrix.epic.SeriesFitter
- getNumPos() - Method in class edu.duke.cs.osprey.astar.comets.UpdatedPruningMatrix
- getNumPos() - Method in class edu.duke.cs.osprey.astar.conf.RCs
- getNumPos() - Method in class edu.duke.cs.osprey.confspace.AbstractPosMatrix
- getNumPos() - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- getNumPos() - Method in interface edu.duke.cs.osprey.confspace.PosMatrix
- getNumPos() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- getNumPos() - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- getNumPos() - Method in class edu.duke.cs.osprey.kstar.emat.ReducedEnergyMatrix
- getNumPos() - Method in class edu.duke.cs.osprey.kstar.pruning.ReducedPruningMatrix
- getNumPos() - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixInverted
- getNumPos() - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- getNumPos() - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- getNumPosInHOTs() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getNumPrecomputedPerAtomPair() - Method in class edu.duke.cs.osprey.energy.forcefield.EEF1.ResiduesInfo
- getNumPrecomputedPerAtomPair() - Method in interface edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.SolvationForcefield.ResiduesInfo
- getNumProcessed() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getNumPruned() - Static method in class edu.duke.cs.osprey.kstar.KAStarNode
- getNumPruned() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getNumQueues() - Method in class edu.duke.cs.osprey.gpu.opencl.GpuQueuePool
- getNumQueuesPerGpu() - Method in class edu.duke.cs.osprey.gpu.opencl.GpuQueuePool
- getNumRCsAtPos() - Method in class edu.duke.cs.osprey.confspace.ConfSpace
- getNumRequests() - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
-
returns the number of requested energy calculations, including ones cached in a conf DB
- getNumResConfPairs() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
Gets the total number of residue conf pairs for all positions
- getNumResConfQuads() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
Gets the total number of residue conf quads for all positions
- getNumResConfs() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
Gets the total number of residue confs for all positions
- getNumResConfs(int) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
Gets the number of residue confs for a position
- getNumResConfsByPos() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
Gets the number of residue confs per position
- getNumResConfTriples() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
Gets the total number of residue conf triples for all positions
- getNumRotamers() - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
- getNumRotamers(double, double) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
-
Returns the number of rotamers for a backbone-dependent or backbone independent rotamer library.
- getNumRunningTasks() - Method in class edu.duke.cs.osprey.parallelism.ConcurrentTaskExecutor
- getNumSeqs() - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getNumSeqsCompleted(int) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getNumSeqsCreated(int) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getNumSequences() - Method in class edu.duke.cs.osprey.astar.seq.RTs
-
returns the number of full (not partial) sequences selected by this instance
- getNumSequences() - Method in class edu.duke.cs.osprey.astar.seq.SeqAStarTree
- getNumSequences() - Method in class edu.duke.cs.osprey.confspace.ConfDB
- getNumSequences() - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- getNumStreams() - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStreamPool
- getNumStreamsAvailable() - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStreamPool
- getNumStreamsPerGpu() - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStreamPool
- getNumSubSeqs() - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getNumTerms() - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldEnergy
- getNumThreads() - Static method in class edu.duke.cs.osprey.energy.MultiTermEnergyFunction
- getNumThreads() - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getNumThreads() - Static method in class edu.duke.cs.osprey.parallelism.ThreadParallelism
- getNumTopConfsToSave() - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getNumTopSavedConfs() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getNumTrivialPos() - Method in class edu.duke.cs.osprey.astar.conf.RCs
- getNumTrivialPos() - Method in class edu.duke.cs.osprey.astar.seq.RTs
-
counts the number of positions with exactly one residue type
- getNumUnAssignedPos() - Method in class edu.duke.cs.osprey.multistatekstar.MSSearchProblem
- getNumUnEnumerated() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel0
- getNumUnEnumerated() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- getNumUnEnumerated() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFUB
- getNumUnEnumerated() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getNumUnPruned() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getNumVoxels() - Method in class edu.duke.cs.osprey.partcr.RCSplits.RCInfo
- getNumWorkDone() - Method in class edu.duke.cs.osprey.tools.Progress
- getOffset(int, String) - Method in class edu.duke.cs.osprey.ematrix.SimpleReferenceEnergies
- getOffset(SimpleConfSpace, int, int) - Method in class edu.duke.cs.osprey.ematrix.SimpleReferenceEnergies
- getOffsetsEnergy() - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- getOffsetsEnergy(ResPairCache.ResPair[]) - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- getOldPool() - Static method in class edu.duke.cs.osprey.tools.JvmMem
- getOneBody(int, int) - Method in class edu.duke.cs.osprey.astar.comets.UpdatedPruningMatrix
- getOneBody(int, int) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- getOneBody(int, int) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixBoolean
- getOneBody(int, int) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- getOneBody(int, int) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixGeneric
- getOneBody(int, int) - Method in class edu.duke.cs.osprey.ematrix.LazyEnergyMatrix
- getOneBody(int, int) - Method in class edu.duke.cs.osprey.ematrix.NegatedEnergyMatrix
- getOneBody(int, int) - Method in class edu.duke.cs.osprey.ematrix.ProxyEnergyMatrix
- getOneBody(int, int) - Method in class edu.duke.cs.osprey.kstar.emat.ReducedEnergyMatrix
- getOneBody(int, int) - Method in class edu.duke.cs.osprey.kstar.pruning.InvertedPruningMatrix
- getOneBody(int, int) - Method in class edu.duke.cs.osprey.kstar.pruning.ReducedPruningMatrix
- getOneBody(int, int) - Method in class edu.duke.cs.osprey.kstar.pruning.UnprunedPruningMatrix
- getOneBody(int, int) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixInverted
- getOneBody(int, int) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- getOneBody(int, int) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- getOneBody(SimpleConfSpace.Position, SimpleConfSpace.ResidueConf) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- getOneBodyIndex(int, int) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- getOneLet(String) - Static method in class edu.duke.cs.osprey.restypes.HardCodedResidueInfo
- getOpenclQueuePool() - Method in class edu.duke.cs.osprey.energy.GpuEnergyFunctionGenerator
- getOputputFilePath() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getOrMake(String) - Method in class edu.duke.cs.osprey.tools.Profiler
- getOrMakeHigherOrderTuples(int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- getOrMakeHigherOrderTuples(int, int, int, int) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
-
returns the TupleTree containing the higher order tuples if a tuple tree doesn't exist for this pair yet, a new one is created pos1 < pos2 must be the lowest-order positions in the tuple
- getOrMakeWildTypeTemplate(Residue) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
- getOrNull(String) - Method in class edu.duke.cs.osprey.structure.Residues
- getOrthogVectors(DoubleMatrix2D) - Static method in class edu.duke.cs.osprey.plug.VoxelVDWListChecker
- getOrThrow(String) - Method in class edu.duke.cs.osprey.structure.Residues
- getOrThrow(TomlArray, int) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getOrThrow(TomlArray, int, TomlPosition) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getOrThrow(TomlTable, String) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getOrThrow(TomlTable, String, TomlPosition) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getOtherResNum(String) - Method in class edu.duke.cs.osprey.energy.ResidueInteractions.Pair
- getOut() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.TestFancyKernel
- getOutputDir() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getOverheadPool() - Static method in class edu.duke.cs.osprey.tools.JvmMem
- getOverlap(Probe.AtomInfo, Probe.AtomInfo, double) - Method in class edu.duke.cs.osprey.structure.Probe
- getPairEnergy(int, int, int, int) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.State
- getPairEnergy(int, int, int, int) - Method in class edu.duke.cs.osprey.gmec.Comets.WeightedState
- getPairEnergy(int, int, int, int) - Method in class edu.duke.cs.osprey.kstar.MSKStar.WeightedState
- getPairIndicesByType(List<Atom>, List<Atom>, boolean, AtomNeighbors.Type) - Static method in class edu.duke.cs.osprey.structure.AtomNeighbors
- getPairs(int[]) - Static method in class edu.duke.cs.osprey.confspace.Conf
- getPairs(AtomNeighbors.Type) - Method in class edu.duke.cs.osprey.structure.AtomConnectivity.AtomPairs
- getPairs14(List<Atom[]>) - Static method in class edu.duke.cs.osprey.structure.AtomNeighbors
- getPairs14(List<Atom>, List<Atom>, boolean) - Static method in class edu.duke.cs.osprey.structure.AtomNeighbors
- getPairsByType(List<Atom[]>, AtomNeighbors.Type) - Static method in class edu.duke.cs.osprey.structure.AtomNeighbors
- getPairsByType(List<Atom>, List<Atom>, boolean, AtomNeighbors.Type) - Static method in class edu.duke.cs.osprey.structure.AtomNeighbors
- getPairsNonBonded(List<Atom[]>) - Static method in class edu.duke.cs.osprey.structure.AtomNeighbors
- getPairsNonBonded(List<Atom>, List<Atom>, boolean) - Static method in class edu.duke.cs.osprey.structure.AtomNeighbors
- getPairwise(int, int, int, int) - Method in class edu.duke.cs.osprey.astar.comets.UpdatedPruningMatrix
- getPairwise(int, int, int, int) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- getPairwise(int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixBoolean
- getPairwise(int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- getPairwise(int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixGeneric
- getPairwise(int, int, int, int) - Method in class edu.duke.cs.osprey.ematrix.LazyEnergyMatrix
- getPairwise(int, int, int, int) - Method in class edu.duke.cs.osprey.ematrix.NegatedEnergyMatrix
- getPairwise(int, int, int, int) - Method in class edu.duke.cs.osprey.ematrix.ProxyEnergyMatrix
- getPairwise(int, int, int, int) - Method in class edu.duke.cs.osprey.kstar.emat.ReducedEnergyMatrix
- getPairwise(int, int, int, int) - Method in class edu.duke.cs.osprey.kstar.pruning.InvertedPruningMatrix
- getPairwise(int, int, int, int) - Method in class edu.duke.cs.osprey.kstar.pruning.ReducedPruningMatrix
- getPairwise(int, int, int, int) - Method in class edu.duke.cs.osprey.kstar.pruning.UnprunedPruningMatrix
- getPairwise(int, int, int, int) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixInverted
- getPairwise(int, int, int, int) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- getPairwise(int, int, int, int) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- getPairwise(SimpleConfSpace.Position, SimpleConfSpace.ResidueConf, SimpleConfSpace.Position, SimpleConfSpace.ResidueConf) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- getPairwiseIndex(int, int) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- getPairwiseIndex(int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- getPanInversePruningMatrix() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getPanPruningMatrix() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getPanSeqSearchProblem() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getParallelism() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarGradientDescentPfunc
- getParallelism() - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction
- getParallelism() - Method in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- getParallelism() - Method in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- getParallelism() - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction
- getParallelism() - Method in class edu.duke.cs.osprey.kstar.pfunc.SimplePartitionFunction
- getParallelism() - Method in class edu.duke.cs.osprey.lute.LUTEPfunc
- getParallelism() - Method in class edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc
- getParallelism() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- getParallelism() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- getParallelism() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- getParallelism() - Method in class edu.duke.cs.osprey.parallelism.Cluster.Client
- getParallelism() - Method in class edu.duke.cs.osprey.parallelism.Cluster.Member
- getParallelism() - Method in class edu.duke.cs.osprey.parallelism.ConcurrentTaskExecutor
- getParallelism() - Method in class edu.duke.cs.osprey.parallelism.Parallelism
-
get the maximum number of tasks to be be executed in parallel, on a single node
- getParallelism() - Method in class edu.duke.cs.osprey.parallelism.TaskExecutor
- getParallelism() - Method in class edu.duke.cs.osprey.parallelism.ThreadPoolTaskExecutor
- getParallelism() - Method in class edu.duke.cs.osprey.paste.PasteGradientDescentPfunc
- getParallelism() - Method in interface edu.duke.cs.osprey.paste.PastePartitionFunction
- getParallelism(Parallelism) - Method in enum class edu.duke.cs.osprey.parallelism.Parallelism.Type
- getParams() - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy
- getParams(int, int) - Method in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords
- getParamsIndex(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesPair
- getParamsIndex(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesStatic
- getParent() - Method in class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode.Link
- getParent() - Method in class edu.duke.cs.osprey.astar.SlimAStarNode.Link
- getParent() - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.OneDof
- getParent() - Method in class edu.duke.cs.osprey.partcr.RCSplits.RCInfo
- getParentLBScore() - Method in class edu.duke.cs.osprey.kstar.KAStarNode
- getPartitionFunction() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFAdapter
- getPartitionFunction(boolean, int, String, ArrayList<String>) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getPartitionFunction(int, ArrayList<String>) - Method in class edu.duke.cs.osprey.kstar.impl.KSImplLinear
- getPartitionFunction(String, int, ArrayList<String>, ArrayList<Integer>, String, String, KSConfigFileParser, KSSearchProblem) - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFFactory
-
Deprecated.
- getPath() - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- getPDBResNumber() - Method in class edu.duke.cs.osprey.structure.Residue
- getPercentBoundError() - Method in class edu.duke.cs.osprey.kstar.RCEnergyContribs
- getPercentErrorForTopPos(int) - Method in class edu.duke.cs.osprey.kstar.RCEnergyContribs
- getPercentQPrime() - Method in class edu.duke.cs.osprey.kstar.KSQPrimeCalculator
- getPerpendicular(double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- getPertIntervals() - Method in class edu.duke.cs.osprey.dof.deeper.DEEPerSettings
- getPerts() - Method in class edu.duke.cs.osprey.dof.deeper.perts.PerturbationBlock
- getPertStates(int) - Method in class edu.duke.cs.osprey.dof.deeper.DEEPerSettings
- getPF(int) - Method in class edu.duke.cs.osprey.kstar.KSCalc
- getPhase2Method() - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getPhiPsi(Residue) - Static method in class edu.duke.cs.osprey.dof.deeper.RamachandranChecker
- getPhiPsi(Residue) - Static method in class edu.duke.cs.osprey.tools.Protractor
-
Returns {phi,psi} for the residue.
- getPos() - Method in class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode.Link
- getPos() - Method in class edu.duke.cs.osprey.astar.SlimAStarNode.Link
- getPos() - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- getPosition(String) - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- getPositionOrNull(String) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
Gets a design position by residue number, or returns null
- getPositionOrThrow(String) - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- getPositionOrThrow(String) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
Gets a design position by residue number, or throws an exception
- getPosNums(boolean) - Method in class edu.duke.cs.osprey.multistatekstar.MSSearchProblem
- getPosNums(boolean) - Method in class edu.duke.cs.osprey.multistatekstar.MultiSequenceConfTree
- getPosOfSeq(ArrayList<String>) - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getPreCompE() - Method in class edu.duke.cs.osprey.energy.MultiTermEnergyFunction
- getPrecomputed() - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy
- getPrecomputed() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ForcefieldKernelCuda
- getProcess() - Static method in class edu.duke.cs.osprey.tools.JvmMem
- getProcessedConfsSet() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getProcessedDuringInterval() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getProfilingEvents() - Method in class edu.duke.cs.osprey.gpu.opencl.Kernel
- getProgram(String) - Method in class edu.duke.cs.osprey.gpu.opencl.Gpu
- getProgress() - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree
- getProjCAtomCoeffs() - Method in class edu.duke.cs.osprey.bbfree.PepPlaneLinModel
- getProperties(SimpleConfSpace) - Method in class edu.duke.cs.osprey.confspace.ConfSearch.EnergiedConf
- getPruneMat() - Method in class edu.duke.cs.osprey.astar.conf.RCs
- getPruneMat() - Method in class edu.duke.cs.osprey.gmec.PrecomputedMatrices
- getPruningInterval() - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- getPruningInterval() - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- getPStar() - Method in class edu.duke.cs.osprey.kstar.KSPStarCalculator
- getPStar() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getQCapacity() - Method in class edu.duke.cs.osprey.kstar.KSConfQ
- getQDagger() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getQPrime() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getQPrime(BigDecimal) - Method in class edu.duke.cs.osprey.kstar.KSQPrimeCalculator
- getQStar() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getQStarLowerBound() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getQStarUpperBound() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getQueue() - Method in class edu.duke.cs.osprey.astar.AStarTree
- getQueue() - Method in class edu.duke.cs.osprey.gpu.opencl.Kernel
- getR2() - Method in class edu.duke.cs.osprey.energy.forcefield.AtomPairVanDerWaalsContribution
- getRadius() - Method in class edu.duke.cs.osprey.energy.forcefield.AtomPairElectrostaticContribution
- getRC() - Method in class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode.Link
- getRC() - Method in class edu.duke.cs.osprey.astar.SlimAStarNode.Link
- getRC(int) - Method in class edu.duke.cs.osprey.confspace.RCTuple
- getRC(int, int) - Method in class edu.duke.cs.osprey.partcr.SplitWorld
- getRCInfo(int, int) - Method in class edu.duke.cs.osprey.partcr.RCSplits
- getRCInfo(RC) - Method in class edu.duke.cs.osprey.partcr.RCSplits
- getRcMap(int) - Method in class edu.duke.cs.osprey.partcr.SplitWorld
- getRCResEntropy(int, int) - Method in class edu.duke.cs.osprey.confspace.ConfSpace
- getRCs() - Method in class edu.duke.cs.osprey.astar.conf.scoring.mplp.MessageVars
- getRCs() - Method in class edu.duke.cs.osprey.partcr.RCSplits.RCInfo
- getReComputedBoundError() - Method in class edu.duke.cs.osprey.kstar.RCEnergyContribs
- getReducedEnergyMatrix() - Method in class edu.duke.cs.osprey.kstar.KSSearchProblem
- getReducedInversePruningMatrix() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getReducedPruningMatrix() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getReducedPruningMatrix(SearchProblem) - Method in class edu.duke.cs.osprey.kstar.KSSearchProblem
- getReducedSearchProblem() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getReducedSearchProblem(String, ArrayList<ArrayList<String>>, ArrayList<String>, ArrayList<Integer>) - Method in class edu.duke.cs.osprey.kstar.KSSearchProblem
- getReducedSearchProblemName() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getRes() - Method in class edu.duke.cs.osprey.energy.forcefield.SingleResEnergy
- getRes1() - Method in class edu.duke.cs.osprey.energy.forcefield.ResPairEnergy
- getRes2() - Method in class edu.duke.cs.osprey.energy.forcefield.ResPairEnergy
- getResByFullName(String) - Method in class edu.duke.cs.osprey.structure.Molecule
- getResByPDBResNumber(String) - Method in class edu.duke.cs.osprey.structure.Molecule
- getResByPDBResNumberOrNull(String) - Method in class edu.duke.cs.osprey.structure.Molecule
- getResEntropy(SimpleConfSpace, int, int) - Static method in enum class edu.duke.cs.osprey.energy.EnergyPartition
- getResEntropy(String) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
- getResidue() - Method in class edu.duke.cs.osprey.dof.DegreeOfFreedom
- getResidue() - Method in class edu.duke.cs.osprey.dof.FreeDihedral
- getResidue() - Method in class edu.duke.cs.osprey.dof.ProlinePucker
- getResidue() - Method in class edu.duke.cs.osprey.dof.ResidueTypeDOF
- getResidue() - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions.ResidueAtomGroup
-
Deprecated.
- getResidueAtomGroup(Residue) - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions
-
Deprecated.
- getResidueConfs(int[]) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- getResidueConfs(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- getResidueNumbers() - Method in class edu.duke.cs.osprey.energy.ResidueInteractions
- getResidueOrder(ParamSet, MSSearchProblem[][]) - Static method in class edu.duke.cs.osprey.multistatekstar.ResidueOrderFactory
- getResidues() - Method in class edu.duke.cs.osprey.bbfree.BBFreeBlock
- getResidues() - Method in class edu.duke.cs.osprey.dof.MoveableStrand
- getResiduesByPDBResNumbers(Iterable<String>) - Method in class edu.duke.cs.osprey.structure.Molecule
- getResiduesByPDBResNumbers(Set<String>) - Method in class edu.duke.cs.osprey.structure.Molecule
- getResNum() - Method in class edu.duke.cs.osprey.confspace.Sequence.Assignment
-
Get the residue number to which this assignment refers
- getResNum(int) - Method in class edu.duke.cs.osprey.energy.ResInterGen
- getResNums() - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- getResPair() - Method in class edu.duke.cs.osprey.energy.forcefield.ResPairEnergyContribution
- getResPairEnergy(Residue, Residue) - Method in class edu.duke.cs.osprey.energy.forcefield.EEF1.ResiduesInfo
- getResPairEnergy(Residue, Residue) - Method in interface edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.SolvationForcefield.ResiduesInfo
- getResponse() - Method in class edu.duke.cs.osprey.coffee.nodedb.GetHighestNodeOperation
- getResponse() - Method in class edu.duke.cs.osprey.coffee.nodedb.GetHighestNodesOperation
- getResRangeByPDBResNumber(String, String) - Method in class edu.duke.cs.osprey.structure.Molecule
- getResType() - Method in class edu.duke.cs.osprey.confspace.Sequence.Assignment
-
Get the residue type of this assignment, or null if none
- getResType(String) - Method in class edu.duke.cs.osprey.confspace.SeqSpace.Position
- getResTypeOrThrow(String) - Method in class edu.duke.cs.osprey.confspace.SeqSpace.Position
- getrlimit(GLibC.RLimitResource) - Static method in class edu.duke.cs.osprey.tools.GLibC
- getrlimits() - Static method in class edu.duke.cs.osprey.tools.GLibC
- getRoot(String) - Method in class edu.duke.cs.osprey.control.ParamSet
- getRotamerCode() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf
- getRotamericDihedrals(double, double, int) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
- getRotamericDihedrals(double, double, int, int) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
-
Returns the dihedral angle dihedralNum, for rotamer rotNum, for the backbone closest to the values phi and psi.
- getRotamericDihedrals(int) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
- getRotamericDihedrals(int, int) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
- getRunName() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getRunSpecificFileName(String, String) - Method in class edu.duke.cs.osprey.control.ParamSet
- getRunState() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getSConfs() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarGradientDescentPfunc
- getSConfs() - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction
- getSConfs() - Method in class edu.duke.cs.osprey.paste.PasteGradientDescentPfunc
- getSConfs() - Method in interface edu.duke.cs.osprey.paste.PastePartitionFunction
- getScore() - Method in interface edu.duke.cs.osprey.astar.AStarNode
- getScore() - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- getScore() - Method in class edu.duke.cs.osprey.astar.FullAStarNode
- getScore() - Method in interface edu.duke.cs.osprey.astar.OptimizableAStarNode
- getScore() - Method in class edu.duke.cs.osprey.astar.SlimAStarNode
- getScore() - Method in class edu.duke.cs.osprey.confspace.ConfSearch.ScoredConf
-
Get the score for the conformation
- getScore() - Method in interface edu.duke.cs.osprey.multistatekstar.KStarScore
- getScore() - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- getScore() - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreUpperBound
- getScore() - Method in class edu.duke.cs.osprey.multistatekstar.MSKStarNode
- getScore(MathTools.Optimizer) - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- getScore(MathTools.Optimizer) - Method in interface edu.duke.cs.osprey.astar.OptimizableAStarNode
- getScored(int[]) - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- getSearchProblem() - Method in class edu.duke.cs.osprey.control.ConfigFileParser
- getSearchProblem() - Method in class edu.duke.cs.osprey.partcr.SplitWorld
- getSearchProblem(int, int, ArrayList<Integer>, boolean) - Method in class edu.duke.cs.osprey.multistatekstar.MSConfigFileParser
- getSearchProblem(int, KSAllowedSeqs) - Method in class edu.duke.cs.osprey.kstar.KSConfigFileParser
- getSearchProblemName(boolean, int) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getSearchProblemName(boolean, int, String, ArrayList<String>) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getSectionName() - Method in class edu.duke.cs.osprey.tools.ConfigFileReader
-
returns the section name of the current line, if any
- getSeq(String) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarLimitedSequenceTrie
- getSeqsFromFile(String) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getSequence() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getSequence(Sequence) - Method in class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode
- getSequence(Sequence) - Method in interface edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode
- getSequence(Sequence) - Method in class edu.duke.cs.osprey.confspace.ConfDB
- getSequenced() - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqDB
-
returns Z bounds for all sequences returns bounds for both full and partial sequences
- getSequencedSums() - Method in class edu.duke.cs.osprey.sofea.SeqDB
-
returns accumulated state Z values for all sequences
- getSequencedSums(Sequence) - Method in class edu.duke.cs.osprey.sofea.SeqDB
-
returns accumulated state Z values for the queried sequence does not include Z uncertainty from ancestral partial sequences (you probably don't want this unless you're debugging)
- getSequencedZSumBounds() - Method in class edu.duke.cs.osprey.sofea.SeqDB
-
returns Z bounds for all sequences returns bounds for both full and partial sequences
- getSequencedZSumBounds(Sequence) - Method in class edu.duke.cs.osprey.sofea.SeqDB
-
returns the current state Z bounds for the queried sequence bounds for partial sequences only describe *unexplored* subtrees as more subtrees get explored, those Z values will be transfered to more fully-assigned sequences bounds for fully-explored partial sequences will be zero
- getSequenceId(Sequence) - Method in class edu.duke.cs.osprey.tools.MapDBTools.SequenceSerializer
- getSequenceLength() - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getSequenceNumber() - Method in interface edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions.AtomGroup
-
Deprecated.
- getSequenceNumber() - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions.ResidueAtomGroup
-
Deprecated.
- getSequences() - Method in class edu.duke.cs.osprey.confspace.ConfDB
- getSequences() - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- getSequences(int) - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- getSequences(int) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getServiceName() - Method in class edu.duke.cs.osprey.coffee.directions.FinishedSequencesOperation
- getServiceName() - Method in class edu.duke.cs.osprey.coffee.directions.FocusOperation
- getServiceName() - Method in class edu.duke.cs.osprey.coffee.directions.StopOperation
- getServiceName() - Method in class edu.duke.cs.osprey.coffee.directions.TreeOperation
- getServiceName() - Method in class edu.duke.cs.osprey.coffee.nodedb.AddNodesOperation
- getServiceName() - Method in class edu.duke.cs.osprey.coffee.nodedb.BroadcastOperation
- getServiceName() - Method in class edu.duke.cs.osprey.coffee.nodedb.ClearOperation
- getServiceName() - Method in class edu.duke.cs.osprey.coffee.nodedb.GetHighestNodeOperation
- getServiceName() - Method in class edu.duke.cs.osprey.coffee.nodedb.GetHighestNodesOperation
- getServiceName() - Method in class edu.duke.cs.osprey.coffee.seqdb.SaveOperation
- getServiceName() - Method in class edu.duke.cs.osprey.coffee.zmat.TuplesOperation
- getSettings() - Method in interface edu.duke.cs.osprey.multistatekstar.KStarScore
- getSettings() - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- getSingleEnergy(int, int) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.State
- getSingleEnergy(int, int) - Method in class edu.duke.cs.osprey.gmec.Comets.WeightedState
- getSingleEnergy(int, int) - Method in class edu.duke.cs.osprey.kstar.MSKStar.WeightedState
- getSolvationEnergy() - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- getSolvationEnergy(ResPairCache.ResPair[]) - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- getSolvationEnergyContributions(ResPairCache.ResPair[]) - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- getSolvationParameters(Atom, EEF1.SolvParams) - Method in class edu.duke.cs.osprey.energy.forcefield.EEF1
- getSolvationParametersOrDefaults(Atom, EEF1.SolvParams) - Method in class edu.duke.cs.osprey.energy.forcefield.EEF1
- getSource() - Method in class edu.duke.cs.osprey.confspace.ConfSearch.MultiSplitter.Stream
- getSplits() - Method in class edu.duke.cs.osprey.partcr.SplitWorld
- getSPs() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel2
- getStabilityThresh() - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getStartTime() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getState(String) - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace
- getStateInfo(MultiStateConfSpace.State) - Method in class edu.duke.cs.osprey.sofea.Sofea
- getStateKStarObjects(LMB) - Method in class edu.duke.cs.osprey.multistatekstar.MSKStarNode
- getStateKStarScores(LMB) - Method in class edu.duke.cs.osprey.multistatekstar.MSKStarNode
- getStaticAtom1Index(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesStatic
- getStaticAtom2Index(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesStatic
- getStaticAtomIndex(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- getStaticConfAtomIndex(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesSingle
- getStaticEnergy(int) - Method in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords
- getStaticIndex(int) - Method in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords
- getStaticParamsIndex(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesSingle
- getStaticResidueNumbers() - Method in class edu.duke.cs.osprey.confspace.Strand.Flexibility
- getStaticStaticAtomIndex(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesSingle
- getStatus() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.SingleSequenceNode
- getStatus() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarGradientDescentPfunc
- getStatus() - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction
- getStatus() - Method in class edu.duke.cs.osprey.kstar.BBKStar.SingleSequenceNode
- getStatus() - Method in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- getStatus() - Method in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- getStatus() - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction
- getStatus() - Method in class edu.duke.cs.osprey.kstar.pfunc.SimplePartitionFunction
- getStatus() - Method in class edu.duke.cs.osprey.lute.LUTEPfunc
- getStatus() - Method in class edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc
- getStatus() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- getStatus() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- getStatus() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- getStatus() - Method in class edu.duke.cs.osprey.paste.PasteGradientDescentPfunc
- getStatus() - Method in interface edu.duke.cs.osprey.paste.PastePartitionFunction
- getStepSize(int, int) - Method in class edu.duke.cs.osprey.minimization.CCDMinimizer
- getStrand() - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getStrand() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- getStrandDOFBounds(DegreeOfFreedom) - Static method in class edu.duke.cs.osprey.dof.MoveableStrand
- getStrandLimits() - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getStrandLimits(int) - Method in class edu.duke.cs.osprey.kstar.KSConfigFileParser
- getStrandSeqAtPos(int) - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getStrandSeqList() - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getStrandStringsAtPos(int) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getStrandSubSeq(int, int, int) - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getStrandSubSeqList() - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getStrandSubSeqList2(KSAllowedSeqs, KSAllowedSeqs) - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getStrandSubSeqsAtDepth(int) - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getStrandSubSeqsAtDepth(int, KSAllowedSeqs, KSAllowedSeqs) - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getStrandSubSeqsMaxDepth() - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getStream() - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- getStream() - Method in class edu.duke.cs.osprey.gpu.cuda.Kernel
- getStringOrThrow(TomlArray, int) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getStringOrThrow(TomlArray, int, TomlPosition) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getStringOrThrow(TomlTable, String) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getStringOrThrow(TomlTable, String, TomlPosition) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getSubset() - Method in class edu.duke.cs.osprey.energy.forcefield.GpuForcefieldEnergy
- getSubset() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ForcefieldKernelCuda
- getSubset() - Method in interface edu.duke.cs.osprey.gpu.ForcefieldKernel
- getSubset() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.ForcefieldKernelOpenCL
- getSubsetTable() - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.Subset
- getSubsetTable() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ForcefieldKernelCuda
- getSubtreeLowerBound() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- getSubtreeUpperBound() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- getSummaryFileExtension() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getSuperposingRotMatrix(double[], double[], double[], double[]) - Static method in class edu.duke.cs.osprey.tools.RotationMatrix
- getSurvivorPool() - Static method in class edu.duke.cs.osprey.tools.JvmMem
- getTableOrThrow(TomlArray, int) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getTableOrThrow(TomlArray, int, TomlPosition) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getTableOrThrow(TomlTable, String) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getTableOrThrow(TomlTable, String, TomlPosition) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- getTargetDist(Atom, Atom) - Static method in class edu.duke.cs.osprey.plug.VoxelVDWListChecker
- getTasks() - Method in class edu.duke.cs.osprey.gmec.GMECConfEnergyCalculator.Async.Adapter
-
Deprecated.
- getTasks() - Method in interface edu.duke.cs.osprey.gmec.GMECConfEnergyCalculator.Async
-
Deprecated.
- getTasks() - Method in class edu.duke.cs.osprey.gmec.MinimizingConfEnergyCalculator
-
Deprecated.
- getTasks() - Method in class edu.duke.cs.osprey.minimization.ConfMinimizer.Async
- getTemplate(Residue) - Method in class edu.duke.cs.osprey.structure.Probe
- getTemplate(String) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
- getTemplate(String, boolean) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
- getTemplateForMutation(String, Residue) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
- getTemplateName(Residue) - Static method in class edu.duke.cs.osprey.restypes.HardCodedResidueInfo
- getTemplateOrThrow(String) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
- getTemplateOrThrow(String, boolean) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
- getTerms() - Method in class edu.duke.cs.osprey.energy.MultiTermEnergyFunction
- getTerms() - Method in class edu.duke.cs.osprey.energy.ParallelEnergyFunction
- getTestSystem() - Method in class edu.duke.cs.osprey.lute.LUTE
- getTime() - Method in class edu.duke.cs.osprey.tools.Stopwatch
- getTime(int) - Method in class edu.duke.cs.osprey.tools.Stopwatch
- getTime(TimeUnit) - Method in class edu.duke.cs.osprey.tools.Stopwatch
- getTime(TimeUnit, int) - Method in class edu.duke.cs.osprey.tools.Stopwatch
- getTimeH() - Method in class edu.duke.cs.osprey.tools.Stopwatch
- getTimeH(long) - Static method in class edu.duke.cs.osprey.tools.TimeFormatter
- getTimeM() - Method in class edu.duke.cs.osprey.tools.Stopwatch
- getTimeM(long) - Static method in class edu.duke.cs.osprey.tools.TimeFormatter
- getTimeMs() - Method in class edu.duke.cs.osprey.tools.Stopwatch
- getTimeMs(long) - Static method in class edu.duke.cs.osprey.tools.TimeFormatter
- getTimeNs() - Method in class edu.duke.cs.osprey.tools.Progress
- getTimeNs() - Method in class edu.duke.cs.osprey.tools.Stopwatch
- getTimeS() - Method in class edu.duke.cs.osprey.tools.Stopwatch
- getTimeS(long) - Static method in class edu.duke.cs.osprey.tools.TimeFormatter
- getTimestampMs() - Static method in class edu.duke.cs.osprey.tools.TimeTools
-
Returns the number of milliseconds elapsed since midnight, January 1, 1970 UTC.
- getTimestampNs() - Static method in class edu.duke.cs.osprey.tools.TimeTools
-
Returns approximately the number of nanoseconds elapsed since midnight, January 1, 1970 UTC.
- getTimestampUs() - Static method in class edu.duke.cs.osprey.tools.TimeTools
-
Returns approximately the number of microseconds elapsed since midnight, January 1, 1970 UTC.
- getTimeUs() - Method in class edu.duke.cs.osprey.tools.Stopwatch
- getTimeUs(long) - Static method in class edu.duke.cs.osprey.tools.TimeFormatter
- getToken(String, int) - Static method in class edu.duke.cs.osprey.tools.StringParsing
- getTopEnergyContributions(int) - Method in class edu.duke.cs.osprey.energy.forcefield.ResPairEnergyContribution
- getTopPosCausingError(int) - Method in class edu.duke.cs.osprey.kstar.RCEnergyContribs
- getTopSamples(int, int) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- getTopSamples(int, int, Map<KStarTreeNode, List<KStarTreeNode>>) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- getTopSamplesInSubtree(int) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- getTopSequences(SeqDB, BoltzmannCalculator) - Method in class edu.duke.cs.osprey.sofea.MinLMFE
- getTopSequences(SeqDB, MathContext) - Method in class edu.duke.cs.osprey.sofea.MinLMFE
- getTotalEnergy() - Method in class edu.duke.cs.osprey.astar.conf.scoring.mplp.MessageVars
- getTotalMemory() - Method in class edu.duke.cs.osprey.gpu.cuda.Gpu
- getTotalNs() - Method in class edu.duke.cs.osprey.gpu.opencl.ProfilingEvents
- getTotalPF() - Method in class edu.duke.cs.osprey.kstar.KSPStarCalculator
- getTotalWork() - Method in class edu.duke.cs.osprey.tools.Progress
- getTrainingSystem() - Method in class edu.duke.cs.osprey.lute.LUTE
- getTree(int) - Method in class edu.duke.cs.osprey.coffee.directions.Directions
- getTuple(RCTuple) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- getTuple(RCTuple) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- getTupleIndexMatrix() - Method in class edu.duke.cs.osprey.tupexp.TupleExpander
- getType() - Method in class edu.duke.cs.osprey.energy.EnergyCalculator.Builder
- getType() - Method in class edu.duke.cs.osprey.structure.Residue
- getTypeId() - Method in class edu.duke.cs.osprey.coffee.Serializers.AbstractStreamSerializer
- getUBScore() - Method in class edu.duke.cs.osprey.kstar.KAStarNode
- getUndefinedPos(RCTuple) - Method in class edu.duke.cs.osprey.kstar.KAStarConfTree
- getUnexplored(Sequence) - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqDB
-
Returns the current state Z bounds for unexplored subtrees of the partially-assigned sequence.
- getUniqueSequences(int) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getUnprunedPairTuples(PruningMatrix) - Method in class edu.duke.cs.osprey.lute.LUTE
- getUnprunedPruningMatrix(KSSearchProblem, double) - Method in class edu.duke.cs.osprey.kstar.KSSearchProblem
- getUnprunedSingleTuples(PruningMatrix) - Method in class edu.duke.cs.osprey.lute.LUTE
- getUnprunedTripleTuples(PruningMatrix) - Method in class edu.duke.cs.osprey.lute.LUTE
- getUnsequenced(MultiStateConfSpace.State) - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqDB
-
Returns the current Z bounds and dropped Z for the unsequenced state.
- getUnsequencedGBounds(SeqDB, MathContext) - Method in class edu.duke.cs.osprey.sofea.MinLMFE
- getUnsequencedSum(MultiStateConfSpace.State) - Method in class edu.duke.cs.osprey.sofea.SeqDB
-
returns accumulated Z values for the queried state (you probably don't want this unless you're debugging)
- getUnsequencedZSumBounds(MultiStateConfSpace.State) - Method in class edu.duke.cs.osprey.sofea.SeqDB
-
returns the current Z bounds for the queried state
- getUpdatedPruningMatrix() - Method in class edu.duke.cs.osprey.kstar.pruning.ReducedPruningMatrix
- getUpperBound() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- getUpperBound() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- getUpperBoundScore() - Method in interface edu.duke.cs.osprey.multistatekstar.KStarScore
- getUpperBoundScore() - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreDiscrete
- getUpperBoundScore() - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- getUpperBoundScore() - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreUpperBound
- getUsageReport() - Static method in class edu.duke.cs.osprey.externalMemory.ExternalMemory
- getValForDOF(int, double) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction
- getValForDOF(int, double) - Method in class edu.duke.cs.osprey.minimization.IdealSeparableReference
- getValForDOF(int, double) - Method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- getValForDOF(int, double) - Method in class edu.duke.cs.osprey.minimization.MoleculeObjectiveFunction
- getValForDOF(int, double) - Method in interface edu.duke.cs.osprey.minimization.ObjectiveFunction
- getValForDOF(int, double, DoubleMatrix1D) - Method in interface edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction.Approximator
- getValForDOF(int, double, DoubleMatrix1D) - Method in class edu.duke.cs.osprey.energy.approximation.NOPApproximator
- getValForDOF(int, double, DoubleMatrix1D) - Method in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- getValue(double) - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.OneDof
- getValue(DoubleMatrix1D) - Method in interface edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction.Approximator
- getValue(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction
- getValue(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.energy.approximation.NOPApproximator
- getValue(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- getValue(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.minimization.IdealSeparableReference
- getValue(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- getValue(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.minimization.MoleculeObjectiveFunction
- getValue(DoubleMatrix1D) - Method in interface edu.duke.cs.osprey.minimization.ObjectiveFunction
- getValue(String) - Method in class edu.duke.cs.osprey.control.ParamSet
- getValue(String, String) - Method in class edu.duke.cs.osprey.control.ParamSet
- getValues() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarGradientDescentPfunc
- getValues() - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction
- getValues() - Method in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- getValues() - Method in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- getValues() - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction
- getValues() - Method in class edu.duke.cs.osprey.kstar.pfunc.SimplePartitionFunction
- getValues() - Method in class edu.duke.cs.osprey.lute.LUTEPfunc
- getValues() - Method in class edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc
- getValues() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- getValues() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- getValues() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- getValues() - Method in class edu.duke.cs.osprey.paste.PasteGradientDescentPfunc
- getValues() - Method in interface edu.duke.cs.osprey.paste.PastePartitionFunction
- getVanDerWaalsEnergy() - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- getVanDerWaalsEnergy(ResPairCache.ResPair[]) - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- getVanDerWaalsEnergyContributions(ResPairCache.ResPair[]) - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- getVdwParams(Atom, Atom, AtomNeighbors.Type) - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- getVDWRadius(Atom) - Static method in class edu.duke.cs.osprey.plug.VoxelVDWDistExplorer
- getViolation(double) - Method in class edu.duke.cs.osprey.structure.Probe.AtomPair
-
return the overlap of the two atoms beyond the max allowed overlap, and beyond any extra tolerance
- getViolation(double) - Method in class edu.duke.cs.osprey.structure.Probe.AtomPair.Interaction
- getViolation(double, double, double) - Method in class edu.duke.cs.osprey.structure.Probe
- getWarpThreads() - Method in class edu.duke.cs.osprey.gpu.cuda.Gpu
- getWeight(MultiStateConfSpace.State) - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFE
- getWidth(int) - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- getWildType() - Method in class edu.duke.cs.osprey.confspace.Sequence.Assignment
-
Get the residue type of the wild-type at the residue of this assignment.
- getWildType(String) - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Returns the residue type of the wild-type at the specified residue
- getWorkers() - Method in class edu.duke.cs.osprey.parallelism.WorkCrew
- getWTKSCalc() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getWtRotOnlyRes() - Method in class edu.duke.cs.osprey.control.ConfigFileParser
- getWtSeq(ArrayList<Integer>) - Method in class edu.duke.cs.osprey.multistatekstar.MSConfigFileParser
- getWTSeq() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- getWTSeq() - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- getWTSequence() - Method in class edu.duke.cs.osprey.control.KStarCalculator
-
Deprecated.
- getWTSequence() - Method in class edu.duke.cs.osprey.kstar.KSConfigFileParser
- getXMax() - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.OneDof
- getXMin() - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.OneDof
- getYoungPool() - Static method in class edu.duke.cs.osprey.tools.JvmMem
- getZBounds(SeqDB, MultiStateConfSpace.State) - Method in class edu.duke.cs.osprey.sofea.SequenceLMFE
- getZSumBounds(int, int) - Method in class edu.duke.cs.osprey.sofea.RCDB.Table
- getZSumBounds(MultiStateConfSpace.State, Sequence, int, int) - Method in class edu.duke.cs.osprey.sofea.RCDB
- getZSumBounds(MultiStateConfSpace.State, Sequence, SimpleConfSpace.Position, SimpleConfSpace.ResidueConf) - Method in class edu.duke.cs.osprey.sofea.RCDB
- getZSumMax(MultiStateConfSpace.State) - Method in class edu.duke.cs.osprey.sofea.FringeDB
-
Returns the largest Z value for the nodes to read.
- GLibC - Class in edu.duke.cs.osprey.tools
-
Access GLibC functions from Java
- GLibC() - Constructor for class edu.duke.cs.osprey.tools.GLibC
- GLibC.RLimit - Class in edu.duke.cs.osprey.tools
- gMax - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncDirector
- GMECConfEnergyCalculator - Interface in edu.duke.cs.osprey.gmec
-
Deprecated.
- GMECConfEnergyCalculator.Async - Interface in edu.duke.cs.osprey.gmec
-
Deprecated.
- GMECConfEnergyCalculator.Async.Adapter - Class in edu.duke.cs.osprey.gmec
-
Deprecated.
- GMECConfEnergyCalculator.Async.Listener - Interface in edu.duke.cs.osprey.gmec
-
Deprecated.
- GMECFinder - Class in edu.duke.cs.osprey.gmec
- GMECFinder() - Constructor for class edu.duke.cs.osprey.gmec.GMECFinder
- GMECFinder.ConfPruner - Interface in edu.duke.cs.osprey.gmec
- GMECMutSpace - Class in edu.duke.cs.osprey.astar
-
A space of sequences that we want to limit a GMEC search to Defined by a mut file
- GMECMutSpace(String, ConfSpace) - Constructor for class edu.duke.cs.osprey.astar.GMECMutSpace
- GMECMutSpace(String, SimpleConfSpace) - Constructor for class edu.duke.cs.osprey.astar.GMECMutSpace
- GMECs - Variable in class edu.duke.cs.osprey.gmec.Comets.SequenceInfo
- GNUPlot - Class in edu.duke.cs.osprey.tools.resultdoc
- GNUPlot() - Constructor for class edu.duke.cs.osprey.tools.resultdoc.GNUPlot
- GNUPlot.Cmd - Class in edu.duke.cs.osprey.tools.resultdoc
- GNUPlot.Cmd.LiteralProp - Class in edu.duke.cs.osprey.tools.resultdoc
- GNUPlot.Cmd.NumberProp - Class in edu.duke.cs.osprey.tools.resultdoc
- GNUPlot.Cmd.Style - Class in edu.duke.cs.osprey.tools.resultdoc
- GNUPlot.Cmd.TextProp - Class in edu.duke.cs.osprey.tools.resultdoc
- GNUPlot.Cmd.Tics - Class in edu.duke.cs.osprey.tools.resultdoc
- GNUPlot.Plotter - Interface in edu.duke.cs.osprey.tools.resultdoc
- goalResid - Variable in class edu.duke.cs.osprey.tupexp.LUTESettings
- goSignal - Variable in class edu.duke.cs.osprey.parallelism.TimingThread
- Gpu - Class in edu.duke.cs.osprey.gpu.cuda
- Gpu - Class in edu.duke.cs.osprey.gpu.opencl
- Gpu - Enum constant in enum class edu.duke.cs.osprey.parallelism.Parallelism.Type
- Gpu(CLDevice) - Constructor for class edu.duke.cs.osprey.gpu.opencl.Gpu
- Gpu(CUdevice) - Constructor for class edu.duke.cs.osprey.gpu.cuda.Gpu
- GpuConfMinimizer - Class in edu.duke.cs.osprey.minimization
- GpuConfMinimizer(GpuConfMinimizer.Type, int, int, ForcefieldParams, Factory<ForcefieldInteractions, Molecule>, ConfSpace) - Constructor for class edu.duke.cs.osprey.minimization.GpuConfMinimizer
- GpuConfMinimizer.Builder - Class in edu.duke.cs.osprey.minimization
- GpuConfMinimizer.Type - Enum Class in edu.duke.cs.osprey.minimization
- gpuEcalcs - Variable in class edu.duke.cs.osprey.coffee.NodeProcessor
- GpuEnergyFunctionGenerator - Class in edu.duke.cs.osprey.energy
- GpuEnergyFunctionGenerator(ForcefieldParams, GpuStreamPool) - Constructor for class edu.duke.cs.osprey.energy.GpuEnergyFunctionGenerator
- GpuEnergyFunctionGenerator(ForcefieldParams, GpuQueuePool) - Constructor for class edu.duke.cs.osprey.energy.GpuEnergyFunctionGenerator
- GpuForcefieldEnergy - Class in edu.duke.cs.osprey.energy.forcefield
- GpuForcefieldEnergy(ForcefieldParams, ForcefieldInteractions, GpuStreamPool) - Constructor for class edu.duke.cs.osprey.energy.forcefield.GpuForcefieldEnergy
- GpuForcefieldEnergy(ForcefieldParams, ForcefieldInteractions, GpuQueuePool) - Constructor for class edu.duke.cs.osprey.energy.forcefield.GpuForcefieldEnergy
- GpuForcefieldEnergy(GpuForcefieldEnergy, ForcefieldInteractions) - Constructor for class edu.duke.cs.osprey.energy.forcefield.GpuForcefieldEnergy
- gpuInfo - Variable in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuStreams
- GpuInfo - Enum constant in enum class edu.duke.cs.osprey.control.Main.Command
- GpuInfo(int, String, String, boolean, boolean, int, int, long, long) - Constructor for class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuInfo
- GpuInitException - Exception in edu.duke.cs.osprey.gpu.opencl
- GpuInitException(String, Throwable) - Constructor for exception edu.duke.cs.osprey.gpu.opencl.GpuInitException
- GpuQueue - Class in edu.duke.cs.osprey.gpu.opencl
- GpuQueue(Gpu) - Constructor for class edu.duke.cs.osprey.gpu.opencl.GpuQueue
- GpuQueue(Gpu, boolean, boolean) - Constructor for class edu.duke.cs.osprey.gpu.opencl.GpuQueue
- GpuQueuePool - Class in edu.duke.cs.osprey.gpu.opencl
- GpuQueuePool() - Constructor for class edu.duke.cs.osprey.gpu.opencl.GpuQueuePool
- GpuQueuePool(int) - Constructor for class edu.duke.cs.osprey.gpu.opencl.GpuQueuePool
- GpuQueuePool(int, int) - Constructor for class edu.duke.cs.osprey.gpu.opencl.GpuQueuePool
- GpuQueuePool(int, int, boolean) - Constructor for class edu.duke.cs.osprey.gpu.opencl.GpuQueuePool
- Gpus - Class in edu.duke.cs.osprey.gpu.cuda
- Gpus - Class in edu.duke.cs.osprey.gpu.opencl
- GpuStream - Class in edu.duke.cs.osprey.gpu.cuda
- GpuStream(Context) - Constructor for class edu.duke.cs.osprey.gpu.cuda.GpuStream
- GpuStreamPool - Class in edu.duke.cs.osprey.gpu.cuda
- GpuStreamPool() - Constructor for class edu.duke.cs.osprey.gpu.cuda.GpuStreamPool
- GpuStreamPool(int) - Constructor for class edu.duke.cs.osprey.gpu.cuda.GpuStreamPool
- GpuStreamPool(int, int) - Constructor for class edu.duke.cs.osprey.gpu.cuda.GpuStreamPool
- GpuStreamPool(int, int, boolean) - Constructor for class edu.duke.cs.osprey.gpu.cuda.GpuStreamPool
- gpuStreams - Variable in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- GpuStreams(CudaConfEnergyCalculator.GpuInfo, int) - Constructor for class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuStreams
- gradient(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.ematrix.epic.EPoly
- GradientDescentMARKStarPfunc - Class in edu.duke.cs.osprey.markstar.framework
-
This partition function calculator estimates the partition function value by alternating between two operations: 1.
- GradientDescentMARKStarPfunc(SimpleConfSpace, EnergyMatrix, EnergyMatrix, RCs, ConfEnergyCalculator) - Constructor for class edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc
- GradientDescentPfunc - Class in edu.duke.cs.osprey.kstar.pfunc
-
This partition function calculator estimates the partition function value by alternating between two operations: 1.
- GradientDescentPfunc(ConfEnergyCalculator, ConfSearch, ConfSearch, BigInteger) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- GradientDescentPfunc(ConfEnergyCalculator, ConfSearch, BigInteger) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- gradientDxFactor - Variable in class edu.duke.cs.osprey.pruning.PLUG
-
factor of the voxel width used to approximate the gradient of the violation function
- greaterThan(BigExp) - Method in class edu.duke.cs.osprey.tools.BigExp
- greaterThan(BigExp, double) - Method in class edu.duke.cs.osprey.tools.BigExp
- greaterThanOrEqual(BigExp) - Method in class edu.duke.cs.osprey.tools.BigExp
- greaterThanOrEqual(BigExp, double) - Method in class edu.duke.cs.osprey.tools.BigExp
- GridIterable(int[]) - Constructor for class edu.duke.cs.osprey.tools.MathTools.GridIterable
- grPath - Variable in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.Forcefield
- gscore - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- gscorer - Variable in class edu.duke.cs.osprey.astar.conf.ConfAStarTree
- gscorer - Variable in class edu.duke.cs.osprey.astar.seq.SeqAStarTree
- gscorer - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound.ScoreContext
- gscorerFactory - Variable in class edu.duke.cs.osprey.astar.conf.ConfRanker
- gThresholdUpper - Variable in class edu.duke.cs.osprey.sofea.Sofea
- GVCountBigger - Variable in class edu.duke.cs.osprey.minimization.CCDMinimizer
- GVCountEdge - Variable in class edu.duke.cs.osprey.minimization.CCDMinimizer
- GVCountEstmin - Variable in class edu.duke.cs.osprey.minimization.CCDMinimizer
- GVCountSmaller - Variable in class edu.duke.cs.osprey.minimization.CCDMinimizer
- gWidthMax - Variable in class edu.duke.cs.osprey.coffee.directors.AffinityDirector
- gWidthMax - Variable in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- gWidthMax - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncDirector
- gWidthMax - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncsDirector
- gWidthMax - Variable in class edu.duke.cs.osprey.coffee.directors.SequenceDirector
H
- h(ConfIndex, NodeTree) - Method in interface edu.duke.cs.osprey.coffee.bounds.Bounder
-
Comptue the h-score of a partial conformation.
- h(ConfIndex, NodeTree) - Method in class edu.duke.cs.osprey.coffee.bounds.PairwiseBounder
- h(ConfIndex, NodeTree) - Method in class edu.duke.cs.osprey.coffee.bounds.TriplewiseBounder
- h1(String) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- h2(String) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- h3(String) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- h4(String) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- h5(String) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- h6(String) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- halfWidth - Variable in class edu.duke.cs.osprey.confspace.VoxelShape.Rect
- handleAATypeOptions(int, int, MSConfigFileParser) - Method in class edu.duke.cs.osprey.multistatekstar.InputValidation
- handleChemicalChanges() - Method in interface edu.duke.cs.osprey.energy.EnergyFunction.ExplicitChemicalChanges
- handleChemicalChanges() - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy
- handleChemicalChanges() - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.Subset
- handleChemicalChanges() - Method in class edu.duke.cs.osprey.energy.forcefield.GpuForcefieldEnergy
- handleConstraints(ParamSet, LMB[]) - Method in class edu.duke.cs.osprey.multistatekstar.InputValidation
- handleDropped() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices
- handleDrops(Stream<NodeIndex.Node>) - Method in class edu.duke.cs.osprey.coffee.NodeProcessor
- handleObjFcn(ParamSet, LMB) - Method in class edu.duke.cs.osprey.multistatekstar.InputValidation
- handleStateParams(int, ParamSet, ParamSet) - Method in class edu.duke.cs.osprey.multistatekstar.InputValidation
- handleTasks(ArrayList<MPISlaveTask>) - Method in class edu.duke.cs.osprey.handlempi.MPIMaster
- Hanging - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.DominantBaseline
- HardCodedResidueInfo - Class in edu.duke.cs.osprey.restypes
- HardCodedResidueInfo() - Constructor for class edu.duke.cs.osprey.restypes.HardCodedResidueInfo
- has(int, int) - Method in class edu.duke.cs.osprey.sofea.BoltzmannLute
- has(int, int, int, int) - Method in class edu.duke.cs.osprey.sofea.BoltzmannLute
- hasAminoAcidBB(Residue) - Static method in class edu.duke.cs.osprey.restypes.HardCodedResidueInfo
- hasAssignments(int[]) - Static method in class edu.duke.cs.osprey.confspace.Conf
- HasAtoms - Interface in edu.duke.cs.osprey.energy.forcefield.amber
- hasBucket(double[]) - Method in class edu.duke.cs.osprey.structure.analysis.DegreesHistogram
- hasConfs() - Method in class edu.duke.cs.osprey.astar.conf.RCs
- hasGMECMutFile() - Method in class edu.duke.cs.osprey.control.ConfigFileParser
- hasGPUs() - Static method in class edu.duke.cs.osprey.parallelism.Parallelism
- HashCalculator - Class in edu.duke.cs.osprey.tools
- HashCalculator() - Constructor for class edu.duke.cs.osprey.tools.HashCalculator
- hashCode() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex.Node
- hashCode() - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqInfo
- hashCode() - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- hashCode() - Method in class edu.duke.cs.osprey.confspace.Conf.Map
- hashCode() - Method in class edu.duke.cs.osprey.confspace.Conf.Set
- hashCode() - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.State
- hashCode() - Method in class edu.duke.cs.osprey.confspace.RCTuple
- hashCode() - Method in class edu.duke.cs.osprey.confspace.Sequence
- hashCode() - Method in class edu.duke.cs.osprey.design.models.Flexibility
- hashCode() - Method in class edu.duke.cs.osprey.design.models.Residue
- hashCode() - Method in class edu.duke.cs.osprey.design.models.ResidueModifier
- hashCode() - Method in class edu.duke.cs.osprey.ematrix.SimpleReferenceEnergies
- hashCode() - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuInfo
- hashCode() - Method in class edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger.AtomPair
- hashCode() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.AtomSymbolAndMass
-
Returns a hash code value for this object.
- hashCode() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.BondAngleParameter
-
Returns a hash code value for this object.
- hashCode() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.BondLengthParameter
-
Returns a hash code value for this object.
- hashCode() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.DihederalParameter
-
Returns a hash code value for this object.
- hashCode() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.EquivalencingAtom
-
Returns a hash code value for this object.
- hashCode() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.HBond10_12PotentialParameter
-
Returns a hash code value for this object.
- hashCode() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.ImproperDihederalParameter
-
Returns a hash code value for this object.
- hashCode() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.Six12PotentialCoefficient
-
Returns a hash code value for this object.
- hashCode() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.Six12PotentialParameter
-
Returns a hash code value for this object.
- hashCode() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.SlaterKirkwoodParameter
-
Returns a hash code value for this object.
- hashCode() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.VanDerWaalsRadius
-
Returns a hash code value for this object.
- hashCode() - Method in class edu.duke.cs.osprey.energy.ResidueInteractions.Pair
- hashCode() - Method in class edu.duke.cs.osprey.parallelism.TaskExecutor.ContextId
- hashCode() - Method in class edu.duke.cs.osprey.sofea.SeqDB.SeqInfo
- hashCode() - Method in class edu.duke.cs.osprey.structure.Molecule
- hashCode() - Method in class edu.duke.cs.osprey.tools.BigExp
- hashCode() - Method in class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- hashCode() - Method in class edu.duke.cs.osprey.tools.MathTools.DoubleBounds
- hashCode(int[]) - Static method in class edu.duke.cs.osprey.confspace.Conf
- hashCode(int[], int) - Method in class edu.duke.cs.osprey.tools.MapDBTools.IntArraySerializer
- hashCode(MathTools.BigDecimalBounds, int) - Method in class edu.duke.cs.osprey.tools.MapDBTools.BigDecimalBoundsSerializer
- hashCode(BigDecimal, int) - Method in class edu.duke.cs.osprey.tools.MapDBTools.BigDecimalSerializer
- hashIds(int...) - Static method in class edu.duke.cs.osprey.tools.HashCalculator
- hasHigherOrderTermFor(RCTuple) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- hasHigherOrderTermFor(RCTuple) - Method in class edu.duke.cs.osprey.ematrix.UpdatingEnergyMatrix
- hasHigherOrderTerms() - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- hasHigherOrderTerms() - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- hasHigherOrderTerms() - Method in class edu.duke.cs.osprey.ematrix.UpdatingEnergyMatrix
- hasHigherOrderTuples() - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- hasHigherOrderTuples() - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- HasLowEnergies - Enum constant in enum class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator.Status
- hasMinimizableDofs(ConfSpace, RCTuple) - Static method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- hasMutants() - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- hasMutants() - Method in class edu.duke.cs.osprey.confspace.SeqSpace.Position
- hasMutations - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Pos
- hasMutations() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Position
- hasMutations(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- hasMutations(int) - Method in interface edu.duke.cs.osprey.confspace.ConfSpaceIteration
-
returns true iff this position has conformations whose types are not the wild type
- hasMutations(int) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- hasNext() - Method in class edu.duke.cs.osprey.tools.FileTools.LineIterator
- hasNext() - Method in class edu.duke.cs.osprey.tools.InfiniteIterator
- hasNodesToRead() - Method in class edu.duke.cs.osprey.sofea.FringeDB
-
returns true if there are no remaining nodes to read in this sweep, false otherwise
- hasNodesToRead() - Method in class edu.duke.cs.osprey.sofea.FringeDB.Transaction
-
returns true if there are no remaining nodes to read in this sweep, false otherwise
- hasNonBoxConstr() - Method in class edu.duke.cs.osprey.plug.RCTuplePolytope
- hasNucleicAcidBB(Residue) - Static method in class edu.duke.cs.osprey.restypes.HardCodedResidueInfo
- hasOneBody(int, int) - Method in class edu.duke.cs.osprey.ematrix.LazyEnergyMatrix
- hasPairwise(int, int, int, int) - Method in class edu.duke.cs.osprey.ematrix.LazyEnergyMatrix
- hasSpawnedChildren() - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- hasTriples() - Method in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- hasTuple(int, int) - Method in class edu.duke.cs.osprey.lute.LUTEConfEnergyCalculator
- hasTuple(int, int, int, int) - Method in class edu.duke.cs.osprey.lute.LUTEConfEnergyCalculator
- hasTuple(int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.lute.LUTEConfEnergyCalculator
- hasWork - Variable in class edu.duke.cs.osprey.parallelism.Worker
- hazelcastNode(MultiStateConfSpace) - Static method in class edu.duke.cs.osprey.coffee.Serializers
- hazelcastNodeDeserializeDeNovo(ObjectDataInput) - Static method in class edu.duke.cs.osprey.coffee.Serializers
- hazelcastNodeSerializeDeNovo(ObjectDataOutput, MultiStateConfSpace, NodeIndex.Node) - Static method in class edu.duke.cs.osprey.coffee.Serializers
- hazelcastSeqDBDeserializeDeNovo(ObjectDataInput, SaveOperation) - Static method in class edu.duke.cs.osprey.coffee.Serializers
- hazelcastSeqDBSerializeDeNovo(ObjectDataOutput, MultiStateConfSpace, SaveOperation) - Static method in class edu.duke.cs.osprey.coffee.Serializers
- Hbond - Enum constant in enum class edu.duke.cs.osprey.structure.Probe.Attraction
- HBond10_12PotentialParameter - Record Class in edu.duke.cs.osprey.energy.forcefield.amber
- HBond10_12PotentialParameter(AtomSymbolAndMass, AtomSymbolAndMass, float, float) - Constructor for record class edu.duke.cs.osprey.energy.forcefield.amber.HBond10_12PotentialParameter
-
Creates an instance of a
HBond10_12PotentialParameterrecord class. - hbond10_12PotentialParameters() - Method in class edu.duke.cs.osprey.energy.forcefield.amber.ForcefieldFileParser
- header() - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Formatter
- header() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Formatter.Log
- header() - Method in interface edu.duke.cs.osprey.kstar.KStarScoreWriter.Formatter
- header() - Method in class edu.duke.cs.osprey.kstar.KStarScoreWriter.Formatter.Log
- header() - Method in interface edu.duke.cs.osprey.paste.PasteScoreWriter.Formatter
- header() - Method in class edu.duke.cs.osprey.paste.PasteScoreWriter.Formatter.Log
- height - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot
- hElect - Variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- HELIX - Enum constant in enum class edu.duke.cs.osprey.structure.Residue.SecondaryStructure
- hessian(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.ematrix.epic.EPoly
- hex - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot.Color
- hide() - Method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.Tics
-
hide the axis entirely
- higherOrderContrib(int, int, int, int, int[], ArrayList<Integer>) - Method in class edu.duke.cs.osprey.kstar.KAStarConfTree
- higherOrderContrib(int, int, int, int, RCTuple) - Method in class edu.duke.cs.osprey.multistatekstar.MultiSequenceConfTree
- higherOrderPrunedTuples(RCTuple) - Method in class edu.duke.cs.osprey.tupexp.BasicPruningTupleExpander
- HigherTupleFinder<T> - Class in edu.duke.cs.osprey.confspace
-
This is an object associated to a particular tuple t (pair or higher) in a TupleMatrix It lists any higher-tuples that include t and that have non-trivial values ("trivial" meaning 0 for energies, unpruned for pruning) Tuples of order size(t)+1 are held explicitly; we recursively list HigherTupleFinder objects for higher orders if there are even bigger tuples
- HigherTupleFinder(T) - Constructor for class edu.duke.cs.osprey.confspace.HigherTupleFinder
- highestScore() - Method in interface edu.duke.cs.osprey.coffee.nodedb.FixedIndex
-
Returns the highest score of any currently stored item.
- highestScore() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex
- highestScore() - Method in class edu.duke.cs.osprey.coffee.nodedb.PriorityDequeFixedIndex
- highestScore(int) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices
- histogram() - Method in class edu.duke.cs.osprey.coffee.EnergyBoundStats
- Histogram - Class in edu.duke.cs.osprey.structure.analysis
- Histogram(Collection<Double>, int) - Constructor for class edu.duke.cs.osprey.structure.analysis.Histogram
- HistorySize - Static variable in class edu.duke.cs.osprey.coffee.nodedb.NodePerformance
- Hostname - Class in edu.duke.cs.osprey.parallelism
- Hostname() - Constructor for class edu.duke.cs.osprey.parallelism.Hostname
- hotBoundPct - Static variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- hotMethod - Static variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- hotNumRes - Static variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- HOTs - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- HOTsContains(Integer) - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- hotTopRotsPct - Static variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- hr() - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
-
horizontal rule
- hscorer - Variable in class edu.duke.cs.osprey.astar.conf.ConfAStarTree
- hscorer - Variable in class edu.duke.cs.osprey.astar.seq.SeqAStarTree
- hscorer - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound.ScoreContext
- hscorerFactory - Variable in class edu.duke.cs.osprey.astar.conf.ConfRanker
- hVDW - Variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- hydrophilicAtoms() - Method in class edu.duke.cs.osprey.energy.forcefield.amber.ForcefieldFileParser
I
- I0 - Variable in class edu.duke.cs.osprey.gmec.DEEGMECFinder
- I0 - Variable in class edu.duke.cs.osprey.kstar.KSAbstract
- IBISKStarTupleExpander - Class in edu.duke.cs.osprey.ibis
-
A tuple expander wrt sequences for some residues and RC's for others
- IBISKStarTupleExpander(int, PruningMatrix, PruningMatrix, EnergyMatrix, ArrayList<ArrayList<Integer>>) - Constructor for class edu.duke.cs.osprey.ibis.IBISKStarTupleExpander
- IBT() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.BondLengthParameter
-
Returns the value of the
IBTrecord component. - id - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Conf
- id - Variable in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- id - Variable in class edu.duke.cs.osprey.energy.compiled.AmberEnergyCalculator
- id - Variable in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuInfo
- id - Variable in class edu.duke.cs.osprey.energy.compiled.EEF1EnergyCalculator
- id - Variable in enum class edu.duke.cs.osprey.energy.compiled.EnergyCalculator.Type
- id - Variable in class edu.duke.cs.osprey.energy.ResidueInteractions.Pair
- id - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.ConfSpaceInfo
- id - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.ConfSpaceInfo
- id - Variable in class edu.duke.cs.osprey.kstar.BBKStar.ConfSpaceInfo
- id - Variable in class edu.duke.cs.osprey.kstar.KStar.ConfSpaceInfo
- id - Variable in class edu.duke.cs.osprey.kstar.SequenceAnalyzer.ConfSpaceInfo
- id - Variable in class edu.duke.cs.osprey.parallelism.Cluster
- id - Variable in class edu.duke.cs.osprey.parallelism.Cluster.Task
- id - Variable in class edu.duke.cs.osprey.paste.Paste.ConfSpaceInfo
- id - Variable in class edu.duke.cs.osprey.sofea.RCDB.Table
- id - Variable in class edu.duke.cs.osprey.structure.Probe.Template
- id - Variable in enum class edu.duke.cs.osprey.tools.resultdoc.Plot.PointType
- id - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Boxes.Box
- id - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Intervals.Interval
- id() - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- id() - Method in class edu.duke.cs.osprey.energy.compiled.AmberEnergyCalculator
- id() - Method in class edu.duke.cs.osprey.energy.compiled.EEF1EnergyCalculator
- id() - Method in interface edu.duke.cs.osprey.energy.compiled.EnergyCalculator
-
get the id of this energy calculator, that matches the forcefield ids in the conf space
- idealizeProRing(ResidueTemplateLibrary, Residue) - Static method in class edu.duke.cs.osprey.dof.deeper.SidechainIdealizer
- idealizeRingHydrogens(Residue, Residue) - Static method in class edu.duke.cs.osprey.dof.deeper.SidechainIdealizer
- idealizeSidechain(ResidueTemplateLibrary, Residue) - Static method in class edu.duke.cs.osprey.dof.deeper.SidechainIdealizer
- IdealSeparableReference - Class in edu.duke.cs.osprey.minimization
-
When trying to get the free energy of a conformation, it could help to have a separable reference objective function that can be integrated 1 DOF at a time but whose delta G from the actual conf could be computed quickly by BAR this is an idealized version of that (matches true conf energy exactly along axes) to see if can get good accuracy with not too many samples
- IdealSeparableReference(EnergyFunction, ConfSpace, RCTuple, DoubleMatrix1D) - Constructor for class edu.duke.cs.osprey.minimization.IdealSeparableReference
- identity - Variable in class edu.duke.cs.osprey.design.models.ResidueModifier
- identity() - Static method in class edu.duke.cs.osprey.tools.RotationMatrix
- IdentityOffset - Static variable in class edu.duke.cs.osprey.energy.ResidueInteractions.Pair
- IdentityWeight - Static variable in class edu.duke.cs.osprey.energy.ResidueInteractions.Pair
- Ideographic - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.DominantBaseline
- IDIVF() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.DihederalParameter
-
Returns the value of the
IDIVFrecord component. - IdNode - Static variable in class edu.duke.cs.osprey.coffee.Serializers
- ids - Variable in class edu.duke.cs.osprey.dof.DofInfo
- IEQV() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.EquivalencingAtom
-
Returns the value of the
IEQVrecord component. - image - Variable in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- Image() - Constructor for class edu.duke.cs.osprey.tools.resultdoc.ResultDoc.Image
- immutablePositions - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
The subset of design positions with no mutations
- ImproperDihederalParameter - Record Class in edu.duke.cs.osprey.energy.forcefield.amber
- ImproperDihederalParameter(AtomSymbolAndMass, AtomSymbolAndMass, AtomSymbolAndMass, AtomSymbolAndMass, float, float, float) - Constructor for record class edu.duke.cs.osprey.energy.forcefield.amber.ImproperDihederalParameter
-
Creates an instance of a
ImproperDihederalParameterrecord class. - improperDihederalParameters() - Method in class edu.duke.cs.osprey.energy.forcefield.amber.ForcefieldFileParser
- in - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.LengthUnit
- includeConst - Variable in class edu.duke.cs.osprey.ematrix.epic.FitParams
- includeStaticStatic - Variable in class edu.duke.cs.osprey.coffee.Coffee
- includeStaticStatic - Variable in class edu.duke.cs.osprey.coffee.NodeProcessor
- includeStaticStatic - Variable in class edu.duke.cs.osprey.ematrix.compiled.EmatCalculator
- includeStaticStatic - Variable in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- includeStructureRotamer - Variable in class edu.duke.cs.osprey.design.models.Flexibility
- increaseOrder(boolean) - Method in class edu.duke.cs.osprey.ematrix.epic.FitParams
- incrementNumSeqsReturned() - Method in class edu.duke.cs.osprey.astar.comets.NewCOMETSTree
- incrementProgress() - Method in class edu.duke.cs.osprey.tools.Progress
- incrementProgress(long) - Method in class edu.duke.cs.osprey.tools.Progress
- index - Variable in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- index - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Conf
- index - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Pos
- index - Variable in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.State
- index - Variable in class edu.duke.cs.osprey.confspace.SeqSpace.Position
- index - Variable in class edu.duke.cs.osprey.confspace.SeqSpace.ResType
- index - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Position
-
index in the positions list
- index - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf
- index - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound.ScoreContext
- index(int[]) - Static method in class edu.duke.cs.osprey.confspace.Conf
- index(int[], ConfIndex) - Static method in class edu.duke.cs.osprey.confspace.Conf
- index(int, int, int) - Method in class edu.duke.cs.osprey.confspace.TripleMatrix
- index(int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.TripleMatrix
- index(ConfIndex) - Method in interface edu.duke.cs.osprey.astar.conf.ConfAStarNode
- index(ConfIndex) - Method in class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode
- index(ConfIndex) - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- index(ConfIndex) - Method in class edu.duke.cs.osprey.externalMemory.EMConfAStarNode
- index(ConfIndex) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- index(ConfIndex) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- indexInChain - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.ResInfo
- indexInMolecule - Variable in class edu.duke.cs.osprey.structure.Residue
-
Index of this residue in the molecule it's in
- indexInRes - Variable in class edu.duke.cs.osprey.structure.Atom
- indexNode(MultiStateConfSpace.State) - Static method in class edu.duke.cs.osprey.coffee.Serializers
- indexOf(Residue) - Method in class edu.duke.cs.osprey.structure.Residues
- indexOf(Object) - Method in class edu.duke.cs.osprey.structure.Residues
- indicesAt(int) - Method in class edu.duke.cs.osprey.astar.seq.RTs
- IndicesPair(int[][]) - Constructor for class edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesPair
- indicesPairs(int, int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- indicesPairsByFrags(int, int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- indicesSingles(int, int, int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- indicesSinglesByFrag(int, int, int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- indicesStatic(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- IndicesStatic(int[][]) - Constructor for class edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesStatic
- inferElementProperties(Atom) - Static method in class edu.duke.cs.osprey.tools.PeriodicTable
- inferInterResBonding(Residue) - Static method in class edu.duke.cs.osprey.restypes.HardCodedResidueInfo
- InfiniteIterator<T> - Class in edu.duke.cs.osprey.tools
- InfiniteIterator() - Constructor for class edu.duke.cs.osprey.tools.InfiniteIterator
- infiniteWellEnergy - Variable in class edu.duke.cs.osprey.energy.EnergyCalculator
- inFlexRes(Residue) - Method in class edu.duke.cs.osprey.kstar.RCEnergyContribs
- info - Variable in class edu.duke.cs.osprey.energy.forcefield.ResPairCache.ResPair
- info - Variable in class edu.duke.cs.osprey.kstar.SequenceAnalyzer.Analysis
- infoa - Variable in class edu.duke.cs.osprey.structure.Probe.AtomPair
- infob - Variable in class edu.duke.cs.osprey.structure.Probe.AtomPair
- infos - Variable in class edu.duke.cs.osprey.coffee.Coffee
- infos - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- Inherit - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.DominantBaseline
- init() - Method in class edu.duke.cs.osprey.multistatekstar.MultiSequenceConfTree
- init() - Method in class edu.duke.cs.osprey.parallelism.TimingThread
- init() - Method in class edu.duke.cs.osprey.sofea.Sofea
-
Start a new design using the conf space, or fail if previous results already exist.
- init(boolean) - Method in class edu.duke.cs.osprey.sofea.Sofea
-
Start a new design using the conf space, or fail unless overwrite=true.
- init(double) - Method in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- init(double) - Method in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- init(double) - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction
-
Initializes the partition function for calculation.
- init(double) - Method in class edu.duke.cs.osprey.kstar.pfunc.SimplePartitionFunction
- init(double) - Method in class edu.duke.cs.osprey.lute.LUTEPfunc
- init(double) - Method in class edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc
- init(double) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- init(double) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- init(double) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- init(double) - Method in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionDiscrete
- init(double) - Method in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized
- init(double, BigDecimal) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- init(double, BigDecimal) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- init(double, BigDecimal) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- init(int) - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- init(int, Factory<? extends EnergyFunction, Molecule>, Factory<? extends Minimizer, MoleculeModifierAndScorer>, ConfSpace) - Method in class edu.duke.cs.osprey.minimization.ConfMinimizer
- init(int, String...) - Method in class edu.duke.cs.osprey.gpu.Structs.Struct
- init(ConfSearch, ConfSearch, BigInteger, double, double, int, boolean) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarGradientDescentPfunc
- init(ConfSearch, ConfSearch, BigInteger, double, double, int, boolean) - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction
-
Initializes the partition function for calculation.
- init(ConfSearch, ConfSearch, BigInteger, double, double, PastePartitionFunction.Result, boolean) - Method in class edu.duke.cs.osprey.paste.PasteGradientDescentPfunc
- init(ConfSearch, ConfSearch, BigInteger, double, double, PastePartitionFunction.Result, boolean) - Method in interface edu.duke.cs.osprey.paste.PastePartitionFunction
-
Initializes the partition function for calculation.
- init(SearchProblem, PruningControl, ConfSearchFactory, GMECConfEnergyCalculator.Async, double, boolean, double, boolean, boolean, boolean, boolean, boolean, boolean, String, double) - Method in class edu.duke.cs.osprey.gmec.GMECFinder
- init(ConfigFileParser) - Method in class edu.duke.cs.osprey.gmec.GMECFinder
- init(ConfigFileParser, SearchProblem) - Method in class edu.duke.cs.osprey.gmec.GMECFinder
- init(KSAbstract, HashMap<Integer, KSAllowedSeqs>, KSCalc) - Static method in class edu.duke.cs.osprey.kstar.KAStarNode
- init(MoleculeModifierAndScorer) - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.CCDKernelCuda
-
Deprecated.
- init(MoleculeObjectiveFunction) - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.CCDKernelCuda
- init(ObjectiveFunction) - Method in class edu.duke.cs.osprey.minimization.CudaCCDMinimizer
- init(ObjectiveFunction) - Method in interface edu.duke.cs.osprey.minimization.Minimizer.Reusable
- init(ObjectiveFunction) - Method in class edu.duke.cs.osprey.minimization.SimpleCCDMinimizer
- init(ObjectiveFunction.OneDof) - Method in class edu.duke.cs.osprey.minimization.IntervalLineSearcher
- init(ObjectiveFunction.OneDof) - Method in interface edu.duke.cs.osprey.minimization.LineSearcher
- init(ObjectiveFunction.OneDof) - Method in class edu.duke.cs.osprey.minimization.SurfingLineSearcher
- init(MSSearchProblem[][]) - Method in class edu.duke.cs.osprey.multistatekstar.ResidueOrderStaticSequential
-
iterate through all aatypeoptions and assign an increasing numerical score
- init(Molecule, List<DegreeOfFreedom>, DoubleMatrix1D) - Method in class edu.duke.cs.osprey.ematrix.epic.EPICEnergyFunction
- init(Molecule, List<DegreeOfFreedom>, DoubleMatrix1D) - Method in interface edu.duke.cs.osprey.energy.EnergyFunction.NeedsInit
- init(HashMap<Integer, KSAllowedSeqs>) - Method in class edu.duke.cs.osprey.kstar.impl.KSImplKAStar
- init(HashMap<Integer, KSAllowedSeqs>) - Method in class edu.duke.cs.osprey.kstar.impl.KSImplLinear
- init(HashMap<Integer, KSAllowedSeqs>) - Method in interface edu.duke.cs.osprey.kstar.KSInterface
- initBigDecimal() - Method in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
- initBounder() - Method in class edu.duke.cs.osprey.coffee.StateInfo
- initDouble() - Method in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
- InitException(EWAKStar.ConfSpaceType, String) - Constructor for exception edu.duke.cs.osprey.ewakstar.EWAKStar.InitException
- InitException(EwakstarDoer.State, String) - Constructor for exception edu.duke.cs.osprey.ewakstar.EwakstarDoer.State.InitException
- InitException(Comets.State, String) - Constructor for exception edu.duke.cs.osprey.gmec.Comets.State.InitException
- InitException(KStar.ConfSpaceType, String) - Constructor for exception edu.duke.cs.osprey.kstar.KStar.InitException
- InitException(MSKStar.State, String) - Constructor for exception edu.duke.cs.osprey.kstar.MSKStar.State.InitException
- InitException(MARKStar.ConfSpaceType, String) - Constructor for exception edu.duke.cs.osprey.markstar.MARKStar.InitException
- InitException(Paste.ConfSpaceType, String) - Constructor for exception edu.duke.cs.osprey.paste.Paste.InitException
- InitException(String) - Constructor for exception edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder.InitException
- initFloat() - Method in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
- initialAngleRadians - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle
- initialize_loop_closure(double[], double[], double[]) - Method in class edu.duke.cs.osprey.dof.deeper.perts.TripeptideClosure
- initializeCalculation(List<Atom>, List<Atom>) - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldEnergy
- initialized - Variable in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- initializeRotamerArrays() - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
-
Initialize the numRotamers and rotamericDihedrals arrays to the number of bins according to each rotamer library.
- InitialNs - Static variable in class edu.duke.cs.osprey.coffee.nodedb.NodePerformance
- initialStepSize() - Method in interface edu.duke.cs.osprey.confspace.compiled.DegreeOfFreedom
- initialStepSize() - Method in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Dof
- initialStepSize() - Method in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Dof
- initInt() - Method in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
- initLong() - Method in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
- initProgress() - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree
- initQueue(T) - Method in class edu.duke.cs.osprey.astar.AStarTree
- initRootNode(int, NodeTree) - Method in class edu.duke.cs.osprey.coffee.NodeProcessor
- initSleepTime - Variable in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- initStatText() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- initStrandInfoCache() - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFFactory
-
Deprecated.
- initThree2One() - Static method in class edu.duke.cs.osprey.restypes.HardCodedResidueInfo
- initTraditionalAStar(EnergyMatrix) - Method in class edu.duke.cs.osprey.astar.conf.scoring.mplp.MessageVars
- initTradPStar() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- inPlaneAxis - Variable in class edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry
- inPlaneDegrees - Variable in class edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry.Angles
- inPlaneDegrees - Variable in class edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry
- InputValidation - Class in edu.duke.cs.osprey.multistatekstar
- InputValidation(ArrayList<ArrayList<ArrayList<ArrayList<String>>>>, ArrayList<ArrayList<ArrayList<Integer>>>) - Constructor for class edu.duke.cs.osprey.multistatekstar.InputValidation
- insert(TupE) - Method in class edu.duke.cs.osprey.ematrix.UpdatingEnergyMatrix.TupleTrie
- inst - Variable in class edu.duke.cs.osprey.coffee.ClusterMember
- inst - Variable in class edu.duke.cs.osprey.parallelism.Cluster.Task
- instance - Static variable in class edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger
- instanceId - Variable in class edu.duke.cs.osprey.parallelism.Cluster.Task
- instanceId - Variable in class edu.duke.cs.osprey.parallelism.TaskExecutor.ContextId
- instanceId() - Method in class edu.duke.cs.osprey.parallelism.Cluster.Task
- instanceId() - Method in interface edu.duke.cs.osprey.parallelism.TaskExecutor.Task.WithContext
- instanceIdOrThrow() - Method in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- Int - Enum constant in enum class edu.duke.cs.osprey.externalMemory.AssignmentsSerializer.Encoding
- Int - Enum constant in enum class edu.duke.cs.osprey.tools.IntEncoding
- int32() - Static method in class edu.duke.cs.osprey.gpu.Structs
- int32(int) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- int32(long, int) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- Int32() - Constructor for class edu.duke.cs.osprey.gpu.Structs.Int32
- int32array() - Static method in class edu.duke.cs.osprey.gpu.Structs
- int32skip() - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- int64() - Static method in class edu.duke.cs.osprey.gpu.Structs
- int64(long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- int64(long, long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- Int64() - Constructor for class edu.duke.cs.osprey.gpu.Structs.Int64
- int64array() - Static method in class edu.duke.cs.osprey.gpu.Structs
- int64skip() - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- IntArraySerializer(int, int) - Constructor for class edu.duke.cs.osprey.tools.MapDBTools.IntArraySerializer
- intBuffers - Variable in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- integrated - Variable in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuInfo
- IntEncoding - Enum Class in edu.duke.cs.osprey.tools
- Interaction(double, double, Probe.Contact) - Constructor for class edu.duke.cs.osprey.structure.Probe.AtomPair.Interaction
- interactionEnergy(ForcefieldInteractions) - Method in class edu.duke.cs.osprey.energy.EnergyFunctionGenerator
- interactions - Variable in class edu.duke.cs.osprey.minimization.CpuConfMinimizer.Builder
- interactions - Variable in class edu.duke.cs.osprey.minimization.GpuConfMinimizer.Builder
- internal - Enum constant in enum class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Type
- internalEnergyFunction(RCTuple, boolean) - Method in class edu.duke.cs.osprey.ematrix.epic.EPICMatrix
- internalEnergyFunction(RCTuple, boolean) - Method in class edu.duke.cs.osprey.ematrix.epic.NewEPICMatrix
- InternalMemoryLimitNotSetException() - Constructor for exception edu.duke.cs.osprey.externalMemory.ExternalMemory.InternalMemoryLimitNotSetException
- internalTimeAverage - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- interResBonding - Variable in class edu.duke.cs.osprey.restypes.ResidueTemplate
- InterResBondingTemplate - Class in edu.duke.cs.osprey.restypes
-
This class is meant to be part of a residue template; it specifies what inter-residue bonds the template can form Since residues may be disordered, we do not always expect these bonds to be present though
- InterResBondingTemplate() - Constructor for class edu.duke.cs.osprey.restypes.InterResBondingTemplate
- InterResBondingTemplate.CysteineBondingTemplate - Class in edu.duke.cs.osprey.restypes
- InterResBondingTemplate.NoBondingTemplate - Class in edu.duke.cs.osprey.restypes
- InterResBondingTemplate.NucleotideBondingTemplate - Class in edu.duke.cs.osprey.restypes
- InterResBondingTemplate.PeptideBondingTemplate - Class in edu.duke.cs.osprey.restypes
- InterResBondingTemplate.SpecifiedBondingAtomsTemplate - Class in edu.duke.cs.osprey.restypes
- interResBondsMarked - Variable in class edu.duke.cs.osprey.structure.Residue
- inters - Variable in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator.MinimizationJob
- inters - Variable in class edu.duke.cs.osprey.energy.EnergyCalculator.EnergiedParametricMolecule
- inters - Variable in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- inters - Variable in class edu.duke.cs.osprey.gpu.cuda.kernels.ResidueForcefieldEnergyCuda
- intersect(RCTuple) - Method in class edu.duke.cs.osprey.confspace.RCTuple
- intersect(RCTuple, RCTuple) - Static method in class edu.duke.cs.osprey.confspace.RCTuple
- intersects(MathTools.BigDecimalBounds) - Method in class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- intersects(MathTools.DoubleBounds) - Method in class edu.duke.cs.osprey.tools.MathTools.DoubleBounds
- interval - Variable in class edu.duke.cs.osprey.coffee.NodeStats.Reporter
- interval - Variable in class edu.duke.cs.osprey.parallelism.RateLimitedThread
- Interval(double) - Constructor for class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel.Interval
- Interval(double, double) - Constructor for class edu.duke.cs.osprey.tools.resultdoc.Plot.Interval
- Interval(double, double) - Constructor for class edu.duke.cs.osprey.tools.SVGPlot.Intervals.Interval
- Interval(double, double, double) - Constructor for class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel.Interval
- IntervalLineSearcher - Class in edu.duke.cs.osprey.minimization
- IntervalLineSearcher() - Constructor for class edu.duke.cs.osprey.minimization.IntervalLineSearcher
- intervals - Variable in class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel
- Intervals() - Constructor for class edu.duke.cs.osprey.tools.SVGPlot.Intervals
- Intervals(Plot.Axis) - Constructor for class edu.duke.cs.osprey.tools.resultdoc.Plot.Intervals
- intervalSpacing - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Intervals
- intervalStyle - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Intervals
- IntervalsX() - Constructor for class edu.duke.cs.osprey.tools.resultdoc.Plot.IntervalsX
- IntervalsY() - Constructor for class edu.duke.cs.osprey.tools.resultdoc.Plot.IntervalsY
- intervalWidth - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Intervals
- intraAndDistributedShellEnergy(Residue, List<Residue>, int, double) - Method in class edu.duke.cs.osprey.energy.EnergyFunctionGenerator
- intraAndDistributedShellEnergy(Residue, List<Residue>, int, double) - Method in class edu.duke.cs.osprey.energy.GpuEnergyFunctionGenerator
- intraAndShellEnergy(Residue, List<Residue>) - Method in class edu.duke.cs.osprey.energy.EnergyFunctionGenerator
- intraAndShellEnergy(Residue, List<Residue>) - Method in class edu.duke.cs.osprey.energy.GpuEnergyFunctionGenerator
- IntRange - Class in edu.duke.cs.osprey.tools
- IntRange(int, int) - Constructor for class edu.duke.cs.osprey.tools.IntRange
- intraResBondsMarked - Variable in class edu.duke.cs.osprey.structure.Residue
- IntraVoxelSampler - Class in edu.duke.cs.osprey.voxq
-
This will draw samples from a voxel
- IntraVoxelSampler(MoleculeModifierAndScorer) - Constructor for class edu.duke.cs.osprey.voxq.IntraVoxelSampler
- inverseMat - Variable in class edu.duke.cs.osprey.kstar.KSSearchProblem
- InvertedPruningMatrix - Class in edu.duke.cs.osprey.kstar.pruning
- InvertedPruningMatrix - Class in edu.duke.cs.osprey.pruning
- InvertedPruningMatrix(KSSearchProblem, UpdatedPruningMatrix) - Constructor for class edu.duke.cs.osprey.kstar.pruning.InvertedPruningMatrix
- InvertedPruningMatrix(PruningMatrix) - Constructor for class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- invmat - Variable in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized
- IOable - Interface in edu.duke.cs.osprey.tools
- IORG() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.EquivalencingAtom
-
Returns the value of the
IORGrecord component. - IPT() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.DihederalParameter
-
Returns the value of the
IPTrecord component. - IPT() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.ImproperDihederalParameter
-
Returns the value of the
IPTrecord component. - isAbsolutelySame(BigDecimal, BigDecimal, double) - Static method in class edu.duke.cs.osprey.tools.MathTools
- isAligned(long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- isAllowed(String) - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- isAllowed(ArrayList<String>) - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- isAssigned() - Method in class edu.duke.cs.osprey.confspace.Sequence.Assignment
-
Return true if this residue is assigned
- isAssigned(int) - Method in class edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode.Assignments
- isAssigned(SeqSpace.Position) - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Return true if the specified sequence position is assigned.
- isAssigned(String) - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Return true if the specified residue is assigned.
- isAssignmentCoveredByPairs(int[], int, int) - Method in class edu.duke.cs.osprey.confspace.TuplesIndex
- isAtomic - Variable in enum class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.Type
- ISAtomsIterable - Class in edu.duke.cs.osprey.plug
-
Collection of intra+shell atoms that interact with an atom at1, made to be iterable over
- ISAtomsIterable(Atom, Residue, ArrayList<Residue>) - Constructor for class edu.duke.cs.osprey.plug.ISAtomsIterable
- isBetter(double, double) - Method in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
- isBetter(float, float) - Method in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
- isBetter(int, int) - Method in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
- isBetter(long, long) - Method in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
- isBetter(BigDecimal, BigDecimal) - Method in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
- isBond - Variable in enum class edu.duke.cs.osprey.structure.Probe.Attraction
- isBond - Variable in enum class edu.duke.cs.osprey.structure.Probe.Contact
- isBondedTo(Residue) - Method in class edu.duke.cs.osprey.structure.Residue
- isBroken - Variable in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- isBroken - Variable in class edu.duke.cs.osprey.gpu.cuda.kernels.ResidueForcefieldEnergyCuda
- isBroken() - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.Subset
- isBroken() - Method in interface edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions.AtomGroup
-
Deprecated.
- isBroken() - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions.ResidueAtomGroup
-
Deprecated.
- isBusy() - Method in class edu.duke.cs.osprey.parallelism.ConcurrentTaskExecutor
- isBusy() - Method in class edu.duke.cs.osprey.parallelism.TaskExecutor
- isCarbon() - Method in class edu.duke.cs.osprey.structure.Atom
- isChildOf(KStarTreeNode) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- isClash - Variable in enum class edu.duke.cs.osprey.structure.Probe.Contact
- isClash(double) - Method in class edu.duke.cs.osprey.structure.Probe.AtomPair.Interaction
- isCompletelyAssigned(int[]) - Static method in class edu.duke.cs.osprey.confspace.Conf
- isCompletelyUnassigned(int[]) - Static method in class edu.duke.cs.osprey.confspace.Conf
- isComplexUseful(EWAKStarPartitionFunction.Result, EWAKStarPartitionFunction.Result) - Static method in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- isComplexUseful(PartitionFunction.Result, PartitionFunction.Result) - Static method in class edu.duke.cs.osprey.kstar.KStarScore
- isComputeVersionAtLeast(int, int) - Method in class edu.duke.cs.osprey.gpu.cuda.Gpu
- isContact - Variable in enum class edu.duke.cs.osprey.structure.Probe.Contact
- isContinuous() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- isContinuouslyFlexible(int[]) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- isContinuouslyFlexible(RCTuple) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
Return true if the conformation has continuous degrees of freedom, false otherwise.
- isCrewStarted() - Static method in class edu.duke.cs.osprey.energy.ParallelEnergyFunction
- isDAminoAcidName(String) - Static method in class edu.duke.cs.osprey.restypes.DAminoAcidHandler
- isDefined(int) - Method in class edu.duke.cs.osprey.astar.conf.ConfIndex
- isDirector() - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- isDoEnergy() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.ForcefieldKernelOpenCL
- isDOFAngle(int) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction
- isDOFAngle(int) - Method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- isDOFAngle(int) - Method in class edu.duke.cs.osprey.minimization.MoleculeObjectiveFunction
- isDOFAngle(int) - Method in interface edu.duke.cs.osprey.minimization.ObjectiveFunction
- isDOFAngle(DegreeOfFreedom) - Static method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- isDynamic() - Method in interface edu.duke.cs.osprey.astar.conf.order.AStarOrder
- isDynamic() - Method in class edu.duke.cs.osprey.astar.conf.order.DynamicHMeanAStarOrder
- isDynamic() - Method in class edu.duke.cs.osprey.astar.conf.order.SequentialAStarOrder
- isDynamic() - Method in class edu.duke.cs.osprey.astar.conf.order.StaticEnergyHMeanAStarOrder
- isDynamic() - Method in class edu.duke.cs.osprey.astar.conf.order.StaticScoreHMeanAStarOrder
- isDynamic() - Method in class edu.duke.cs.osprey.astar.conf.order.UpperLowerAStarOrder
- isDynamic() - Method in class edu.duke.cs.osprey.markstar.framework.BiggestLowerboundDifferenceOrder
- isDynamic() - Method in class edu.duke.cs.osprey.markstar.framework.StaticBiggestLowerboundDifferenceOrder
- isDynamic() - Method in class edu.duke.cs.osprey.markstar.framework.StaticBiggesUpperboundDifferenceOrder
- isDynamic() - Method in class edu.duke.cs.osprey.markstar.framework.StaticLowestEntropyOrder
- isEmpty() - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarQueue
- isEmpty() - Method in class edu.duke.cs.osprey.coffee.seqdb.Batch
- isEmpty() - Method in class edu.duke.cs.osprey.confspace.Conf.Map
- isEmpty() - Method in class edu.duke.cs.osprey.confspace.Conf.Set
- isEmpty() - Method in class edu.duke.cs.osprey.energy.approximation.ResidueInteractionsApproximator.Builder
- isEmpty() - Method in interface edu.duke.cs.osprey.externalMemory.Queue
- isEmpty() - Method in class edu.duke.cs.osprey.sofea.FringeDB
-
Returns true if there are no nodes in the database, false otherwise.
- isEmpty() - Method in class edu.duke.cs.osprey.sofea.SeqDB.SeqInfo
- isEmpty() - Method in class edu.duke.cs.osprey.sofea.SeqDB.Transaction
- isEmpty() - Method in class edu.duke.cs.osprey.structure.analysis.ClusterR1
- isExhausted() - Method in class edu.duke.cs.osprey.kstar.KSConfQ
- isExhausted() - Method in class edu.duke.cs.osprey.kstar.KSPStarCalculator
- isFinal - Variable in class edu.duke.cs.osprey.multistatekstar.MSKStarSettings
- isFinal() - Method in interface edu.duke.cs.osprey.multistatekstar.KStarScore
- isFinal() - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- isFinished() - Method in class edu.duke.cs.osprey.tools.Progress
- isFinished(int, Sequence) - Method in class edu.duke.cs.osprey.coffee.directions.Directions
- isFinite() - Method in class edu.duke.cs.osprey.tools.BigExp
- isFinite() - Method in class edu.duke.cs.osprey.tools.MathTools.DoubleBounds
- isFinite(BigDecimal) - Static method in class edu.duke.cs.osprey.tools.MathTools
- isFlexible - Variable in class edu.duke.cs.osprey.design.models.Flexibility
- isFlexible() - Method in class edu.duke.cs.osprey.confspace.Strand.ResidueFlex
- isFullyAssigned() - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Return true if all residues are assigned, false if not.
- isFullyAssigned() - Method in interface edu.duke.cs.osprey.multistatekstar.KStarScore
- isFullyAssigned() - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- isFullyAssigned() - Method in class edu.duke.cs.osprey.multistatekstar.MSKStarNode
- isFullyAssigned() - Method in class edu.duke.cs.osprey.multistatekstar.MSSearchProblem
- isFullyAssigned(COMETSNode) - Method in class edu.duke.cs.osprey.astar.comets.NewCOMETSTree
- isFullyAssigned(FullAStarNode) - Method in class edu.duke.cs.osprey.astar.comets.COMETSTree
- isFullyAssigned(T) - Method in class edu.duke.cs.osprey.astar.AStarTree
- isFullyAssigned(T) - Method in class edu.duke.cs.osprey.astar.ConfTree
- isFullyDefined() - Method in interface edu.duke.cs.osprey.astar.AStarNode
- isFullyDefined() - Method in class edu.duke.cs.osprey.astar.conf.ConfIndex
- isFullyDefined() - Method in class edu.duke.cs.osprey.astar.FullAStarNode
- isFullyDefined() - Method in class edu.duke.cs.osprey.astar.SlimAStarNode
- isFullyDefined() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- isFullyProcessed() - Method in class edu.duke.cs.osprey.kstar.KAStarNode
- isFullyProcessed() - Method in interface edu.duke.cs.osprey.multistatekstar.KStarScore
- isFullyProcessed() - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- isGreaterThan(BigDecimal, BigDecimal) - Static method in class edu.duke.cs.osprey.tools.MathTools
-
return a > b, correctly handling -Inf, +Inf, and NaN
- isGreaterThanOrEqual(BigDecimal, BigDecimal) - Static method in class edu.duke.cs.osprey.tools.MathTools
-
return a >= b, correctly handling -Inf, +Inf, and NaN
- isHeavyPair() - Method in class edu.duke.cs.osprey.energy.forcefield.AtomPairElectrostaticContribution
- isHydrogen() - Method in class edu.duke.cs.osprey.structure.Atom
- isInBounds(int, double) - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- isInBounds(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- isIncludedIn(Set<Integer>) - Method in class edu.duke.cs.osprey.confspace.compiled.PosInter
- isInf(BigDecimal) - Static method in class edu.duke.cs.osprey.tools.MathTools
- isInternalLimitSet() - Static method in class edu.duke.cs.osprey.externalMemory.ExternalMemory
-
Return true if the internal memory limit has been set by a call to
ExternalMemory.setInternalLimit(int). - isInterResBondedForward(Residue, Residue) - Method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate
- isInterResBondedForward(Residue, Residue) - Method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate.NoBondingTemplate
- isInterResBondedForward(Residue, Residue) - Method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate.NucleotideBondingTemplate
- isInterResBondedForward(Residue, Residue) - Method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate.PeptideBondingTemplate
- isInterResBondedForward(Residue, Residue) - Method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate.SpecifiedBondingAtomsTemplate
- isIs14Bonded() - Method in class edu.duke.cs.osprey.energy.forcefield.AtomPairElectrostaticContribution
- isLeaf() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex.Node
- isLeaf() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- isLeafNode() - Method in class edu.duke.cs.osprey.multistatekstar.MSKStarNode
- isLessThan(BigDecimal, BigDecimal) - Static method in class edu.duke.cs.osprey.tools.MathTools
-
return a < b, correctly handling -Inf, +Inf, and NaN
- isLessThanOrEqual(BigDecimal, BigDecimal) - Static method in class edu.duke.cs.osprey.tools.MathTools
-
return a <= b, correctly handling -Inf, +Inf, and NaN
- isLigandComplexUseful(EWAKStarPartitionFunction.Result) - Static method in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- isLigandComplexUseful(PartitionFunction.Result) - Static method in class edu.duke.cs.osprey.kstar.KStarScore
- isMinimized() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- isMinimizing - Variable in class edu.duke.cs.osprey.energy.EnergyCalculator
- isMutable() - Method in class edu.duke.cs.osprey.confspace.Strand.ResidueFlex
- isMutated() - Method in class edu.duke.cs.osprey.confspace.Sequence.Assignment
-
Return true if this residue is assigned and differs from the wild-type.
- isMutated(SeqSpace.Position) - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Return true if the specified seqeucence position is assigned, and the residue type differs from the wild-type.
- isMutated(String) - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Return true if the specified residue is assigned, and the residue type differs from the wild-type.
- isMutation() - Method in class edu.duke.cs.osprey.confspace.SeqSpace.ResType
- isNaN() - Method in class edu.duke.cs.osprey.tools.BigExp
- isNaN(BigDecimal) - Static method in class edu.duke.cs.osprey.tools.MathTools
- isNegative() - Method in class edu.duke.cs.osprey.tools.BigExp
- isNegative(BigDecimal) - Static method in class edu.duke.cs.osprey.tools.MathTools
- isNewRCAllowed(int[], int, int) - Method in class edu.duke.cs.osprey.astar.GMECMutSpace
- isOutOfRange(double, int) - Method in class edu.duke.cs.osprey.minimization.CCDMinimizer
- isOutOfRange(double, int, double) - Method in class edu.duke.cs.osprey.minimization.CCDMinimizer
- isOutOfRange(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- isOxygen() - Method in class edu.duke.cs.osprey.structure.Atom
- isPairPruned(int, int, int, int) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- isParametricallyIncompatibleWith(RC) - Method in class edu.duke.cs.osprey.confspace.RC
- isParametricallyIncompatibleWith(SimpleConfSpace.ResidueConf) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf
- isParentOf(KStarTreeNode) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- isPointFeasible(int[], DoubleMatrix1D, ArrayList<DegreeOfFreedom>) - Method in class edu.duke.cs.osprey.plug.PolytopeMatrix
- isPointInPolytope(ArrayList<LinearConstraint>, double[]) - Static method in class edu.duke.cs.osprey.plug.LPChecks
- isPositive() - Method in class edu.duke.cs.osprey.tools.BigExp
- isPositive(BigDecimal) - Static method in class edu.duke.cs.osprey.tools.MathTools
- isProfilingEnabled() - Method in class edu.duke.cs.osprey.gpu.opencl.GpuQueue
- isProtected() - Method in class edu.duke.cs.osprey.astar.conf.ConfSearchCache.Entry
- isPruned(ConfAStarNode) - Method in interface edu.duke.cs.osprey.astar.conf.pruning.AStarPruner
-
check to see if a node should be pruned, after it comes off the heap
- isPruned(ConfAStarNode) - Method in class edu.duke.cs.osprey.astar.conf.pruning.AStarSequencePruner
- isPruned(ConfAStarNode, int, int) - Method in interface edu.duke.cs.osprey.astar.conf.pruning.AStarPruner
-
check to see if a child node should be pruned before it's created and scored
- isPruned(ConfAStarNode, int, int) - Method in class edu.duke.cs.osprey.astar.conf.pruning.AStarSequencePruner
- isPruned(RCTuple) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- isPruned(RCTuple) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- isPruned(RCTuple) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- isPruned(RCTuple) - Method in class edu.duke.cs.osprey.tupexp.BasicPruningTupleExpander
- isPruned(RCTuple) - Method in class edu.duke.cs.osprey.tupexp.ConfETupleExpander
- isPrunedHigherOrder(RCTuple, int, HigherTupleFinder<Boolean>) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- isPrunedHigherOrder(RCTuple, int, HigherTupleFinder<Boolean>) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- isPrunedHigherOrder(RCTuple, int, HigherTupleFinder<Boolean>) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- isQuadruplePruned(int, int, int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- isQuintuplePruned(int, int, int, int, int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- isRelativelySame(BigDecimal, BigDecimal, MathContext, double) - Static method in class edu.duke.cs.osprey.tools.MathTools
- isReportingProgress - Variable in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- isReportingProgress - Variable in class edu.duke.cs.osprey.multistatekstar.MSKStarSettings
- isRes(Residue, String, String) - Method in class edu.duke.cs.osprey.kstar.RCEnergyContribs
- isRoot() - Method in class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode.Link
- isRoot() - Method in class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode.Link
- isRoot() - Method in class edu.duke.cs.osprey.astar.SlimAStarNode.Link
- isRunning() - Method in class edu.duke.cs.osprey.coffee.directions.Directions
- isRunning() - Method in class edu.duke.cs.osprey.parallelism.WorkThread
- isRunning() - Method in class edu.duke.cs.osprey.tools.Stopwatch
- isSameTuple(RCTuple) - Method in class edu.duke.cs.osprey.confspace.RCTuple
-
returns true if they are the same tuple AND if positions are in the same order
- isSameValue(BigDecimal, BigDecimal) - Static method in class edu.duke.cs.osprey.tools.MathTools
-
Tests for sameness of values, rather than BigDecimal.equals(), which tests sameness of representation (i.e., the same value can have multiple representations in BigDecimal)
- isSatisfied(SeqDB, FringeDB, FringeDB, long, long, BoltzmannCalculator) - Method in class edu.duke.cs.osprey.sofea.MinLMFE
- isSatisfied(SeqDB, FringeDB, FringeDB, long, long, BoltzmannCalculator) - Method in class edu.duke.cs.osprey.sofea.SequenceLMFE
- isSatisfied(SeqDB, FringeDB, FringeDB, long, long, BoltzmannCalculator) - Method in interface edu.duke.cs.osprey.sofea.Sofea.Criterion
- isSatisfied(SeqDB, FringeDB, FringeDB, long, long, BoltzmannCalculator) - Method in class edu.duke.cs.osprey.sofea.StepCount
- isSequenced - Variable in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.State
- isSimilarTo(EWAKStarScore, double) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- isSimilarTo(KStarScore, double) - Method in class edu.duke.cs.osprey.kstar.KStarScore
- isSinglePruned(int, int) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- isSpecifiedDist(ArrayList<String>, ArrayList<String>) - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
-
Returns true iff the two sequences (of the same length) differ by exactly inDist number of elements
- isSplit() - Method in class edu.duke.cs.osprey.partcr.RCSplits.RCInfo
- isStandardLAminoAcid(String) - Static method in class edu.duke.cs.osprey.restypes.DAminoAcidHandler
- isSubsequenceOf(Sequence) - Method in class edu.duke.cs.osprey.confspace.Sequence
- isSubsetOf(SeqSpace) - Method in class edu.duke.cs.osprey.confspace.SeqSpace
-
Returns true iff every position in this space is in the other space, with the same residue types
- isSulfur() - Method in class edu.duke.cs.osprey.structure.Atom
- isSupported() - Static method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator.Cuda
-
Deprecated.
- isSupported() - Static method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- isSupported() - Method in enum class edu.duke.cs.osprey.energy.EnergyCalculator.Type
- isSupported() - Method in enum class edu.duke.cs.osprey.minimization.GpuConfMinimizer.Type
- isTemplate(ResidueTemplate) - Method in class edu.duke.cs.osprey.dof.ResidueTypeDOF
- isTop(MathTools.DoubleBounds) - Method in class edu.duke.cs.osprey.sofea.MinLMFE.TopSequences
- isTriplePruned(int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- isTrusted() - Method in class edu.duke.cs.osprey.tools.MapDBTools.SimpleSerializer
- isTupleFeasible(RCTuple) - Method in class edu.duke.cs.osprey.plug.PolytopeMatrix
- isUnboundUnstable - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.SingleSequenceNode
-
signals whether or not partition function values are allowed the stability threshold
- isUnboundUnstable - Variable in class edu.duke.cs.osprey.kstar.BBKStar.SingleSequenceNode
-
signals whether or not partition function values are allowed the stability threshold
- isUndefined(int) - Method in class edu.duke.cs.osprey.astar.conf.ConfIndex
- isUsesDistanceDependentDialectic() - Method in class edu.duke.cs.osprey.energy.forcefield.AtomPairElectrostaticContribution
- isValid() - Method in class edu.duke.cs.osprey.dof.FreeDihedral
- isValid() - Method in class edu.duke.cs.osprey.tools.BigExp.Bounds
- isValid() - Method in class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- isValid() - Method in class edu.duke.cs.osprey.tools.MathTools.DoubleBounds
- isValid(T) - Method in interface edu.duke.cs.osprey.tools.ObjectIO.Validator
- isVerbose() - Method in class edu.duke.cs.osprey.control.ParamSet
- isVerbose() - Method in enum class edu.duke.cs.osprey.pruning.NewPruningControl.ReportMode
- isVerbose() - Method in enum class edu.duke.cs.osprey.pruning.PruningControl.ReportMode
- isWildType() - Method in class edu.duke.cs.osprey.confspace.SeqSpace.ResType
- isWildType() - Method in class edu.duke.cs.osprey.confspace.Sequence.Assignment
-
Return true if this residue is assigned and matches the wild-type.
- isWildType() - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Return true if the residue types of all residues match the wild-type.
- isWildType(SeqSpace.Position) - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Return true if the specified sequence position is assigned, and the residue type matches the wild-type.
- isWildType(String) - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Return true if the specified residue is assigned, and the residue type matches the wild-type.
- isWorking() - Method in class edu.duke.cs.osprey.parallelism.ConcurrentTaskExecutor
- isWorking() - Method in class edu.duke.cs.osprey.parallelism.TaskExecutor
- isWT - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.SequenceInfo
- isWT(KSCalc) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- isWTSeq - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.SingleSequenceNode
- isZero() - Method in class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- isZero(BigDecimal) - Static method in class edu.duke.cs.osprey.tools.MathTools
- isZero(BigInteger) - Static method in class edu.duke.cs.osprey.tools.MathTools
- item - Variable in class edu.duke.cs.osprey.coffee.nodedb.Neighbors.NeighborInfo
- itemBytes - Variable in class edu.duke.cs.osprey.gpu.Structs.Array
- iterate() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFAdapter
- iterate() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel0
- iterate() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- iterate() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel2
- iterate() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFTraditional
- iterate() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- iterate() - Method in class edu.duke.cs.osprey.partcr.PartCR
- IterativeCGTupleFitter - Class in edu.duke.cs.osprey.tupexp
-
Modified least-squares fitter for LUTE coefficients Uses iterations of conjugate gradient
- IterativeCGTupleFitter(TupleIndexMatrix, ArrayList<int[]>, int, ArrayList<double[]>) - Constructor for class edu.duke.cs.osprey.tupexp.IterativeCGTupleFitter
- iterator() - Method in class edu.duke.cs.osprey.confspace.Conf.Set
- iterator() - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- iterator() - Method in class edu.duke.cs.osprey.confspace.TuplesIndex
- iterator() - Method in class edu.duke.cs.osprey.energy.ResidueInteractions
- iterator() - Method in interface edu.duke.cs.osprey.externalMemory.Queue
- iterator() - Method in class edu.duke.cs.osprey.parallelism.Generator
- iterator() - Method in class edu.duke.cs.osprey.parallelism.WorkCrew
- iterator() - Method in class edu.duke.cs.osprey.plug.ISAtomsIterable
- iterator() - Method in class edu.duke.cs.osprey.plug.Res2AtomsIterable
- iterator() - Method in class edu.duke.cs.osprey.tools.FileTools.LineIterator
- iterator() - Method in class edu.duke.cs.osprey.tools.MathTools.GridIterable
- iterator() - Method in class edu.duke.cs.osprey.tools.ObjectPool
- ITT() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.BondAngleParameter
-
Returns the value of the
ITTrecord component.
J
- JBT() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.BondLengthParameter
-
Returns the value of the
JBTrecord component. - joinToString(double[], String, DoubleFunction<String>) - Static method in class edu.duke.cs.osprey.tools.Streams
- joinToString(int[], String, IntFunction<String>) - Static method in class edu.duke.cs.osprey.tools.Streams
- joinToString(long[], String, LongFunction<String>) - Static method in class edu.duke.cs.osprey.tools.Streams
- joinToString(Iterable<T>, String) - Static method in class edu.duke.cs.osprey.tools.Streams
- joinToString(Iterable<T>, String, Function<T, String>) - Static method in class edu.duke.cs.osprey.tools.Streams
- joinToString(Map<K, V>, String) - Static method in class edu.duke.cs.osprey.tools.Streams
- joinToString(Map<K, V>, String, BiFunction<K, V, String>) - Static method in class edu.duke.cs.osprey.tools.Streams
- joinToString(T[], String) - Static method in class edu.duke.cs.osprey.tools.Streams
- joinToString(T[], String, Function<T, String>) - Static method in class edu.duke.cs.osprey.tools.Streams
- JPT() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.DihederalParameter
-
Returns the value of the
JPTrecord component. - JPT() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.ImproperDihederalParameter
-
Returns the value of the
JPTrecord component. - JTT() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.BondAngleParameter
-
Returns the value of the
JTTrecord component. - JvmMem - Class in edu.duke.cs.osprey.tools
- JvmMem() - Constructor for class edu.duke.cs.osprey.tools.JvmMem
- JvmMem.MemInfo - Class in edu.duke.cs.osprey.tools
K
- K - Variable in class edu.duke.cs.osprey.coffee.directors.AffinityDirector
- KAStarConfTree - Class in edu.duke.cs.osprey.kstar
- KAStarConfTree(KSSearchProblem, PruningMatrix, PruningMatrix) - Constructor for class edu.duke.cs.osprey.kstar.KAStarConfTree
- KAStarNode - Class in edu.duke.cs.osprey.kstar
- KAStarNode(KSCalc, KSCalc, boolean) - Constructor for class edu.duke.cs.osprey.kstar.KAStarNode
- KAStarTree - Class in edu.duke.cs.osprey.kstar
- KAStarTree(KSAbstract, HashMap<Integer, KSAllowedSeqs>, KSCalc) - Constructor for class edu.duke.cs.osprey.kstar.KAStarTree
- keepBestConfs(ConfSearch.EnergiedConf, int) - Method in class edu.duke.cs.osprey.coffee.seqdb.StateZ
- KeepSweeping - Enum constant in enum class edu.duke.cs.osprey.sofea.Sofea.Criterion.Satisfied
- Kernel - Class in edu.duke.cs.osprey.gpu.cuda
- Kernel - Class in edu.duke.cs.osprey.gpu.opencl
- Kernel(GpuStream, String) - Constructor for class edu.duke.cs.osprey.gpu.cuda.Kernel
- Kernel(GpuQueue, String, String) - Constructor for class edu.duke.cs.osprey.gpu.opencl.Kernel
- Kernel.Function - Class in edu.duke.cs.osprey.gpu.cuda
- Kernel.SharedMemCalculator - Interface in edu.duke.cs.osprey.gpu.cuda
- Kernel.SharedMemCalculator.None - Class in edu.duke.cs.osprey.gpu.cuda
- key - Variable in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd
- key - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot
- Key(int[]) - Constructor for class edu.duke.cs.osprey.confspace.ConfDB.Key
- Key(Sequence) - Constructor for class edu.duke.cs.osprey.confspace.ConfDB.Key
- Key(String) - Constructor for class edu.duke.cs.osprey.confspace.ConfDB.Key
- keySet() - Method in class edu.duke.cs.osprey.confspace.Conf.Map
- killThreads() - Method in class edu.duke.cs.osprey.parallelism.WorkCrew
- KINDNB() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.Six12PotentialParameter
-
Returns the value of the
KINDNBrecord component. - KNDSYM() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.AtomSymbolAndMass
-
Returns the value of the
KNDSYMrecord component. - KPT() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.DihederalParameter
-
Returns the value of the
KPTrecord component. - KPT() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.ImproperDihederalParameter
-
Returns the value of the
KPTrecord component. - KSAbstract - Class in edu.duke.cs.osprey.kstar
- KSAbstract(KSConfigFileParser) - Constructor for class edu.duke.cs.osprey.kstar.KSAbstract
- KSAllowedSeqs - Class in edu.duke.cs.osprey.kstar
- KSAllowedSeqs(int, ResidueTermini, DEEPerSettings, ArrayList<String[]>, ArrayList<String[]>, ArrayList<String>, KSAllowedSeqs, ArrayList<ArrayList<String>>, int, int) - Constructor for class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- KSAllowedSeqs(int, ResidueTermini, DEEPerSettings, ArrayList<String[]>, ArrayList<String[]>, ArrayList<String>, ArrayList<ArrayList<String>>, ArrayList<String>, boolean, int, boolean) - Constructor for class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- KSCalc - Class in edu.duke.cs.osprey.kstar
- KSCalc(int, ConcurrentHashMap<Integer, PFAbstract>) - Constructor for class edu.duke.cs.osprey.kstar.KSCalc
- KSConf - Class in edu.duke.cs.osprey.kstar
- KSConf(int[], double) - Constructor for class edu.duke.cs.osprey.kstar.KSConf
- KSConf(int[], double, double) - Constructor for class edu.duke.cs.osprey.kstar.KSConf
- KSConf(ArrayList<Integer>, double) - Constructor for class edu.duke.cs.osprey.kstar.KSConf
- KSConf(ArrayList<Integer>, double, double) - Constructor for class edu.duke.cs.osprey.kstar.KSConf
- KSConf.KSConfMinEComparator - Class in edu.duke.cs.osprey.kstar
- KSConfigFileParser - Class in edu.duke.cs.osprey.kstar
- KSConfigFileParser() - Constructor for class edu.duke.cs.osprey.kstar.KSConfigFileParser
- KSConfigFileParser(ConfigFileParser) - Constructor for class edu.duke.cs.osprey.kstar.KSConfigFileParser
- KSConfMinEComparator() - Constructor for class edu.duke.cs.osprey.kstar.KSConf.KSConfMinEComparator
- KSConfQ - Class in edu.duke.cs.osprey.kstar
- KSConfQ(PFAbstract, int, BigDecimal) - Constructor for class edu.duke.cs.osprey.kstar.KSConfQ
- KSImplKAStar - Class in edu.duke.cs.osprey.kstar.impl
- KSImplKAStar(KSConfigFileParser) - Constructor for class edu.duke.cs.osprey.kstar.impl.KSImplKAStar
- KSImplLinear - Class in edu.duke.cs.osprey.kstar.impl
- KSImplLinear(KSConfigFileParser) - Constructor for class edu.duke.cs.osprey.kstar.impl.KSImplLinear
- KSInterface - Interface in edu.duke.cs.osprey.kstar
- KSPStarCalculator - Class in edu.duke.cs.osprey.kstar
- KSPStarCalculator(PFAbstract) - Constructor for class edu.duke.cs.osprey.kstar.KSPStarCalculator
- KSQPrimeCalculator - Class in edu.duke.cs.osprey.kstar
- KSQPrimeCalculator(PFAbstract) - Constructor for class edu.duke.cs.osprey.kstar.KSQPrimeCalculator
- KSSearchProblem - Class in edu.duke.cs.osprey.kstar
- KSSearchProblem(SearchProblem) - Constructor for class edu.duke.cs.osprey.kstar.KSSearchProblem
- KSSearchProblem(ParamSet, String, String, ArrayList<String>, ArrayList<ArrayList<String>>, boolean, boolean, boolean, EPICSettings, boolean, LUTESettings, DEEPerSettings, ArrayList<String[]>, ArrayList<String[]>, boolean, boolean, boolean, boolean, ResidueTermini, boolean) - Constructor for class edu.duke.cs.osprey.kstar.KSSearchProblem
- KSSearchProblem(KSSearchProblem, String, ArrayList<ArrayList<String>>, ArrayList<String>, ArrayList<Integer>) - Constructor for class edu.duke.cs.osprey.kstar.KSSearchProblem
- KSSearchProblem.MatrixType - Enum Class in edu.duke.cs.osprey.kstar
- kstar - Variable in class edu.duke.cs.osprey.kstar.KStarScoreWriter.ScoreInfo
- KStar - Class in edu.duke.cs.osprey.kstar
-
Implementation of the K* algorithm to predict protein sequence mutations that improve binding affinity by computing provably accurate Boltzmann-weighted ensembles .
- KStar(ConfSpaceIteration, ConfSpaceIteration, ConfSpaceIteration, KStar.Settings) - Constructor for class edu.duke.cs.osprey.kstar.KStar
- KStar.ConfSpaceInfo - Class in edu.duke.cs.osprey.kstar
- KStar.ConfSpaceType - Enum Class in edu.duke.cs.osprey.kstar
- KStar.InitException - Exception in edu.duke.cs.osprey.kstar
- KStar.PfuncFactory - Interface in edu.duke.cs.osprey.kstar
- KStar.ScoredSequence - Class in edu.duke.cs.osprey.kstar
- KStar.Settings - Class in edu.duke.cs.osprey.kstar
- KStar.Settings.Builder - Class in edu.duke.cs.osprey.kstar
- KStarBeak - Class in edu.duke.cs.osprey.ibis
-
Special beak for K*, relies on tuple expander machinery rather than dealing with repeated matrix entries thus easier to do higher-order terms wrt sequence
- KStarBeak(EnergyMatrix, PruningMatrix, ConfSpace) - Constructor for class edu.duke.cs.osprey.ibis.KStarBeak
- KStarCalculator - Class in edu.duke.cs.osprey.control
-
Deprecated.
- KStarCalculator(KSConfigFileParser) - Constructor for class edu.duke.cs.osprey.control.KStarCalculator
-
Deprecated.
- KStarDirector - Class in edu.duke.cs.osprey.coffee.directors
-
An implementation of the K* algorithm that uses COFFEE for partition function calculation.
- KStarDirector.Builder - Class in edu.duke.cs.osprey.coffee.directors
- kstarScore - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.ScoreInfo
- kstarScore - Variable in class edu.duke.cs.osprey.kstar.KStarScoreWriter.ScoreInfo
- KStarScore - Class in edu.duke.cs.osprey.kstar
- KStarScore - Interface in edu.duke.cs.osprey.multistatekstar
- KStarScore(PartitionFunction.Result, PartitionFunction.Result, PartitionFunction.Result) - Constructor for class edu.duke.cs.osprey.kstar.KStarScore
- KStarScore(BigDecimal, BigDecimal, BigDecimal) - Constructor for class edu.duke.cs.osprey.kstar.KStarScore
- KStarScore.KStarScoreType - Enum Class in edu.duke.cs.osprey.multistatekstar
- KStarScore.PartitionFunctionType - Enum Class in edu.duke.cs.osprey.multistatekstar
- KStarScoreDiscrete - Class in edu.duke.cs.osprey.multistatekstar
- KStarScoreDiscrete(MSKStarSettings) - Constructor for class edu.duke.cs.osprey.multistatekstar.KStarScoreDiscrete
- KStarScoreLowerBound - Class in edu.duke.cs.osprey.multistatekstar
- KStarScoreLowerBound(MSKStarSettings) - Constructor for class edu.duke.cs.osprey.multistatekstar.KStarScoreLowerBound
- KStarScoreMinimized - Class in edu.duke.cs.osprey.multistatekstar
- KStarScoreMinimized(MSKStarSettings) - Constructor for class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- KStarScoreUpperBound - Class in edu.duke.cs.osprey.multistatekstar
- KStarScoreUpperBound(MSKStarSettings) - Constructor for class edu.duke.cs.osprey.multistatekstar.KStarScoreUpperBound
- KStarScoreWriter - Interface in edu.duke.cs.osprey.kstar
- KStarScoreWriter.Formatted - Class in edu.duke.cs.osprey.kstar
- KStarScoreWriter.Formatter - Interface in edu.duke.cs.osprey.kstar
- KStarScoreWriter.Formatter.Log - Class in edu.duke.cs.osprey.kstar
- KStarScoreWriter.Formatter.SequenceKStarPfuncs - Class in edu.duke.cs.osprey.kstar
- KStarScoreWriter.Nop - Class in edu.duke.cs.osprey.kstar
- KStarScoreWriter.ScoreInfo - Class in edu.duke.cs.osprey.kstar
- KStarScoreWriter.ToConsole - Class in edu.duke.cs.osprey.kstar
- KStarScoreWriter.ToFile - Class in edu.duke.cs.osprey.kstar
- KStarScoreWriter.Writers - Class in edu.duke.cs.osprey.kstar
- kstarSettings - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar
-
Optional and overridable settings for BBK*, shared with K*
- kstarSettings - Variable in class edu.duke.cs.osprey.kstar.BBKStar
-
Optional and overridable settings for BBK*, shared with K*
- KStarTreeManipulator - Class in edu.duke.cs.osprey.markstar.visualizer
- KStarTreeManipulator() - Constructor for class edu.duke.cs.osprey.markstar.visualizer.KStarTreeManipulator
- KStarTreeNode - Class in edu.duke.cs.osprey.markstar.visualizer
- KStarTreeNode(int, String[], int[], BigDecimal, BigDecimal, double, double, double) - Constructor for class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- KStarTreeNode.Builder - Class in edu.duke.cs.osprey.markstar.visualizer
- KStarTreeNode.ColorStyle - Enum Class in edu.duke.cs.osprey.markstar.visualizer
- KStarTreeRenderer - Class in edu.duke.cs.osprey.markstar.visualizer
- KStarTreeRenderer() - Constructor for class edu.duke.cs.osprey.markstar.visualizer.KStarTreeRenderer
- KStarTreeSplitter - Class in edu.duke.cs.osprey.markstar.visualizer
-
Sorts the chosen levels of a conf tree in the desired order and pushes those levels to the top of the tree.
- KStarTreeSplitter() - Constructor for class edu.duke.cs.osprey.markstar.visualizer.KStarTreeSplitter
- KT1() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.HBond10_12PotentialParameter
-
Returns the value of the
KT1record component. - KT2() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.HBond10_12PotentialParameter
-
Returns the value of the
KT2record component. - KTT() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.BondAngleParameter
-
Returns the value of the
KTTrecord component. - KUStarNodeComparator - Static variable in class edu.duke.cs.osprey.kstar.KAStarNode
L
- LABEL() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.Six12PotentialParameter
-
Returns the value of the
LABELrecord component. - lambda - Variable in class edu.duke.cs.osprey.energy.forcefield.EEF1.SolvParams
- LASSO - Enum constant in enum class edu.duke.cs.osprey.lute.LUTE.Fitter
-
least absolute shrinkage and selection operator ie, L1 regularized linear regression not as fast as conjugate gradient, but tends to overfit less, so usually requires fewer training samples.
- lastBoltzmannWeight - Variable in class edu.duke.cs.osprey.kstar.KSPStarCalculator
- lastEnergyBound - Variable in class edu.duke.cs.osprey.kstar.KSPStarCalculator
- lastIndexOf(Residue) - Method in class edu.duke.cs.osprey.structure.Residues
- lastIndexOf(Object) - Method in class edu.duke.cs.osprey.structure.Residues
- launch(Runnable) - Method in class edu.duke.cs.osprey.parallelism.BottleneckThread
-
Run the task on the thread, and don't wait for it to finish.
- launchKernel(CUfunction, int, int, int, Pointer, GpuStream) - Method in class edu.duke.cs.osprey.gpu.cuda.Context
- launchPseudoCluster(int, Consumer<Cluster>) - Static method in class edu.duke.cs.osprey.coffee.ClusterMember
-
Launch a pseudo-cluster on different threads.
- LazyEnergyMatrix - Class in edu.duke.cs.osprey.ematrix
- LazyEnergyMatrix(ConfSpace, double, SimpleEnergyCalculator) - Constructor for class edu.duke.cs.osprey.ematrix.LazyEnergyMatrix
- LazyEnergyMatrix(ConfSpace, double, SimpleEnergyCalculator, double) - Constructor for class edu.duke.cs.osprey.ematrix.LazyEnergyMatrix
- LazyEnergyMatrix(EnergyMatrix, SimpleEnergyCalculator) - Constructor for class edu.duke.cs.osprey.ematrix.LazyEnergyMatrix
- LazyEnergyMatrix(EnergyMatrix, SimpleEnergyCalculator, double) - Constructor for class edu.duke.cs.osprey.ematrix.LazyEnergyMatrix
- LazyEnergyMatrix(LazyEnergyMatrix) - Constructor for class edu.duke.cs.osprey.ematrix.LazyEnergyMatrix
- lb - Variable in class edu.duke.cs.osprey.kstar.KAStarNode
- lBound - Variable in class edu.duke.cs.osprey.multistatekstar.ResidueTermini
- lbScore - Variable in class edu.duke.cs.osprey.kstar.KAStarNode
- leafTimeAverage - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- leavesBySequenceUpper(ConfIndex, NodeTree) - Method in class edu.duke.cs.osprey.coffee.StateInfo
- LeftAxis() - Constructor for class edu.duke.cs.osprey.tools.SVGPlot.LeftAxis
- less - Variable in class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel.Interval
- lessThan(BigExp) - Method in class edu.duke.cs.osprey.tools.BigExp
- lessThan(BigExp, double) - Method in class edu.duke.cs.osprey.tools.BigExp
- lessThanOrEqual(BigExp) - Method in class edu.duke.cs.osprey.tools.BigExp
- lessThanOrEqual(BigExp, double) - Method in class edu.duke.cs.osprey.tools.BigExp
- letter - Variable in enum class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf.Type
- level - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- level - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- Library - Enum constant in enum class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf.Type
- ligand - Variable in class edu.duke.cs.osprey.design.models.AffinityDesign
- ligand - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar
-
A configuration space containing just the ligand strand
- ligand - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar
-
A configuration space containing just the ligand strand
- ligand - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.SingleSequenceNode
- ligand - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- ligand - Variable in class edu.duke.cs.osprey.kstar.BBKStar
-
A configuration space containing just the ligand strand
- ligand - Variable in class edu.duke.cs.osprey.kstar.BBKStar.SingleSequenceNode
- ligand - Variable in class edu.duke.cs.osprey.kstar.KStar
-
A configuration space containing just the ligand strand
- ligand - Variable in class edu.duke.cs.osprey.kstar.KStarScore
- ligand - Variable in class edu.duke.cs.osprey.markstar.MARKStar
-
A configuration space containing just the ligand strand
- Ligand - Enum constant in enum class edu.duke.cs.osprey.ewakstar.EWAKStar.ConfSpaceType
- Ligand - Enum constant in enum class edu.duke.cs.osprey.kstar.KStar.ConfSpaceType
- Ligand - Enum constant in enum class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceType
- Ligand - Enum constant in enum class edu.duke.cs.osprey.paste.Paste.ConfSpaceType
- ligandConfSpace - Variable in class edu.duke.cs.osprey.design.commands.CommandBindingAffinity.ForceFieldParamsAndStrands
- LigandResEnergies - Class in edu.duke.cs.osprey.energy
-
For each residue in a ligand, calculate its interactions with the target
- LigandResEnergies(ParamSet) - Constructor for class edu.duke.cs.osprey.energy.LigandResEnergies
- Linear - Enum constant in enum class edu.duke.cs.osprey.tools.Progress.Model
- LinearSystem(TuplesIndex, ConfSampler.Samples, Map<int[], Double>) - Constructor for class edu.duke.cs.osprey.lute.LUTE.LinearSystem
- LineIterator(String) - Constructor for class edu.duke.cs.osprey.tools.FileTools.LineIterator
- lineNumber() - Method in class edu.duke.cs.osprey.tools.FileTools.LineIterator
-
human-readable, matches text editors, starts at 1
- Lines() - Constructor for class edu.duke.cs.osprey.tools.resultdoc.Plot.Lines
- LineSearcher - Interface in edu.duke.cs.osprey.minimization
- LineSearcher.NeedsCleanup - Interface in edu.duke.cs.osprey.minimization
- lineStyle - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Axis
- LinesX() - Constructor for class edu.duke.cs.osprey.tools.resultdoc.Plot.LinesX
- LinesY() - Constructor for class edu.duke.cs.osprey.tools.resultdoc.Plot.LinesY
- Link() - Constructor for class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode.Link
- Link() - Constructor for class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode.Link
- Link() - Constructor for class edu.duke.cs.osprey.astar.SlimAStarNode.Link
- Link(LinkedConfAStarNode.Link, int, int) - Constructor for class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode.Link
- Link(LinkedSeqAStarNode.Link, int, int) - Constructor for class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode.Link
- Link(SlimAStarNode.Link, int, int) - Constructor for class edu.duke.cs.osprey.astar.SlimAStarNode.Link
- LinkedConfAStarFactory - Class in edu.duke.cs.osprey.astar.conf.linked
- LinkedConfAStarFactory() - Constructor for class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarFactory
- LinkedConfAStarNode - Class in edu.duke.cs.osprey.astar.conf.linked
- LinkedConfAStarNode() - Constructor for class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode
- LinkedConfAStarNode.Link - Class in edu.duke.cs.osprey.astar.conf.linked
- LinkedSeqAStarNode - Class in edu.duke.cs.osprey.astar.seq.nodes
- LinkedSeqAStarNode() - Constructor for class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode
- LinkedSeqAStarNode.Link - Class in edu.duke.cs.osprey.astar.seq.nodes
- list1D2ListOfLists(ArrayList<String>) - Static method in class edu.duke.cs.osprey.kstar.KSAbstract
- list1D2String(ArrayList<String>, String) - Static method in class edu.duke.cs.osprey.kstar.KSAbstract
- list2Array(ArrayList<Integer>) - Static method in class edu.duke.cs.osprey.kstar.KSConf
- listAllDOFs() - Method in class edu.duke.cs.osprey.confspace.ConfSpace
- listBackboneVoxels(SimpleConfSpace.Position) - Method in class edu.duke.cs.osprey.confspace.CATSStrandFlex
- listBackboneVoxels(SimpleConfSpace.Position) - Method in class edu.duke.cs.osprey.confspace.DEEPerStrandFlex
- listBackboneVoxels(SimpleConfSpace.Position) - Method in class edu.duke.cs.osprey.confspace.StrandFlex
- listBackboneVoxels(SimpleConfSpace.Position) - Method in class edu.duke.cs.osprey.confspace.StrandFlex.None
- listBackboneVoxels(SimpleConfSpace.Position) - Method in class edu.duke.cs.osprey.confspace.StrandFlex.TranslateRotate
- listBBAtomsForMut(ResidueTemplate, ResidueTemplate) - Static method in class edu.duke.cs.osprey.restypes.HardCodedResidueInfo
- listClashes(double[]) - Method in class edu.duke.cs.osprey.plug.RCTuplePolytope
- listClashes(int[], DoubleMatrix1D, ArrayList<DegreeOfFreedom>) - Method in class edu.duke.cs.osprey.plug.PolytopeMatrix
- listener - Variable in exception edu.duke.cs.osprey.parallelism.TaskExecutor.TaskException
- listInteractionsWithValue(T) - Method in class edu.duke.cs.osprey.confspace.HigherTupleFinder
- listNames() - Static method in enum class edu.duke.cs.osprey.control.Main.Command
- LiteralProp(String) - Constructor for class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.LiteralProp
- LiteralProp(String, String) - Constructor for class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.LiteralProp
- LMB - Class in edu.duke.cs.osprey.multistatekstar
- LMB(String, int) - Constructor for class edu.duke.cs.osprey.multistatekstar.LMB
- LME - Class in edu.duke.cs.osprey.astar.comets
-
Linear multistate energy
- LME(double, List<Comets.WeightedState>) - Constructor for class edu.duke.cs.osprey.gmec.Comets.LME
- LME(String, int) - Constructor for class edu.duke.cs.osprey.astar.comets.LME
- lmfe - Variable in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFECalculator
- lmfe - Variable in class edu.duke.cs.osprey.sofea.SequenceLMFE
-
The multi-state objective function.
- lmfe() - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace
-
build a linear multi-state free energy
- LMFE(double, List<MSKStar.WeightedState>) - Constructor for class edu.duke.cs.osprey.kstar.MSKStar.LMFE
- LMFEBuilder() - Constructor for class edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFEBuilder
- LMFECalculator(MultiStateConfSpace.LMFE) - Constructor for class edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFECalculator
- lmfeFreeEnergy - Variable in class edu.duke.cs.osprey.sofea.Sofea.SeqResult
- ln() - Method in class edu.duke.cs.osprey.tools.BigExp
- ln(BigExp) - Method in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- ln(BigDecimal) - Method in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- ln1p(BigExp) - Method in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- ln1p(BigDecimal) - Method in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
-
computes the following: for z == 0: 0 for z > 0: ln(1+z) for z < 0: -ln(1-z)
- load(String) - Method in class edu.duke.cs.osprey.structure.Probe
-
loads configuration info (eg, params, templates) into this instance
- loadAndPruneMatrices(HashMap<String, Integer>) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- loadData() - Method in class edu.duke.cs.osprey.control.ConfigFileParser
-
Deprecated.
- loadEnergyMatrix() - Method in class edu.duke.cs.osprey.confspace.SearchProblem
- loadEnergyMatrix() - Method in class edu.duke.cs.osprey.gmec.PrecomputedMatrices
- loadEPICMatrix() - Method in class edu.duke.cs.osprey.confspace.SearchProblem
- loadEPICMatrix() - Method in class edu.duke.cs.osprey.gmec.PrecomputedMatrices
- loadMatrix(SearchProblem.MatrixType) - Method in class edu.duke.cs.osprey.confspace.SearchProblem
- loadMatrix(PrecomputedMatrices.MatrixType) - Method in class edu.duke.cs.osprey.gmec.PrecomputedMatrices
- loadPertFile(ResidueTermini) - Method in class edu.duke.cs.osprey.dof.deeper.DEEPerSettings
- loadPertFile(String, boolean, ResidueTermini) - Method in class edu.duke.cs.osprey.dof.deeper.PertSet
- loadPLUGMatrix() - Method in class edu.duke.cs.osprey.confspace.SearchProblem
- loadTupExpEMatrix() - Method in class edu.duke.cs.osprey.confspace.SearchProblem
- loadTupExpEMatrix() - Method in class edu.duke.cs.osprey.gmec.PrecomputedMatrices
- local() - Method in class edu.duke.cs.osprey.energy.EnergyCalculator
-
Create a copy of the energy calculator whose TaskExecutor will only run locally on this cluster node.
- lock - Variable in class edu.duke.cs.osprey.kstar.KSConfQ
- lock - Variable in class edu.duke.cs.osprey.kstar.KSPStarCalculator
- log() - Method in class edu.duke.cs.osprey.tools.BigExp
- log(StringBuilder, String, Object...) - Static method in class edu.duke.cs.osprey.tools.Log
- log(String, Object...) - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- log(String, Object...) - Method in class edu.duke.cs.osprey.sofea.Sofea
- log(String, Object...) - Static method in class edu.duke.cs.osprey.tools.Log
-
write a line to the log (a new line is appended)
- log(BigDecimal) - Method in class edu.duke.cs.osprey.tools.ExpFunction
- Log - Class in edu.duke.cs.osprey.tools
- Log() - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Formatter.Log
- Log() - Constructor for class edu.duke.cs.osprey.kstar.KStarScoreWriter.Formatter.Log
- Log() - Constructor for class edu.duke.cs.osprey.paste.PasteScoreWriter.Formatter.Log
- Log() - Constructor for class edu.duke.cs.osprey.tools.Log
- log0(String, Object...) - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- log10(BigDecimal) - Method in class edu.duke.cs.osprey.tools.ExpFunction
- log10(BigDecimal) - Static method in class edu.duke.cs.osprey.tools.MathTools
- log10p1(double) - Static method in class edu.duke.cs.osprey.tools.MathTools
- log10p1(BigDecimal) - Static method in class edu.duke.cs.osprey.tools.MathTools
-
returns log10(x+1) chosen because it maps [0,inf] to [0,inf] whereas just log10 maps [0,inf] to [-inf,inf]
- logf(String, Object...) - Method in class edu.duke.cs.osprey.sofea.Sofea
- logf(String, Object...) - Static method in class edu.duke.cs.osprey.tools.Log
-
write a fragment to the log (no newline is appended)
- logFile - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- logFile - Variable in class edu.duke.cs.osprey.gmec.Comets
- logFile - Variable in class edu.duke.cs.osprey.kstar.MSKStar
- LoggingConfPrinter - Class in edu.duke.cs.osprey.gmec
- LoggingConfPrinter(File) - Constructor for class edu.duke.cs.osprey.gmec.LoggingConfPrinter
- logOccupancy - Enum constant in enum class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode.ColorStyle
- logPrinter - Variable in class edu.duke.cs.osprey.gmec.SimpleGMECFinder.Builder
- logPrinter - Variable in class edu.duke.cs.osprey.gmec.SimpleGMECFinder
- logPrinter - Variable in class edu.duke.cs.osprey.lute.LUTEGMECFinder
- logToDouble(BigDecimal) - Method in class edu.duke.cs.osprey.tools.ExpFunction
- Long - Enum constant in enum class edu.duke.cs.osprey.pruning.NewPruningControl.ReportMode
- Long - Enum constant in enum class edu.duke.cs.osprey.pruning.PruningControl.ReportMode
- longBuffers - Variable in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- LOOP - Enum constant in enum class edu.duke.cs.osprey.structure.Residue.SecondaryStructure
- loopCleanup(List<MARKStarNode>, Stopwatch, int) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- LoopClosureAdjustment - Class in edu.duke.cs.osprey.dof.deeper.perts
-
This is a discrete perturbation that performs a backbone conformational change on just 3 residues, preserving bond lengths and angles and omegas The motion is composed of the same 3 rotations as a backrub, but for different angles
- LoopClosureAdjustment(ArrayList<Residue>) - Constructor for class edu.duke.cs.osprey.dof.deeper.perts.LoopClosureAdjustment
- loopTasks - Static variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- LoopVoxelSampler - Class in edu.duke.cs.osprey.bbfree
-
Sample conformations of a loop within a voxel, CA to CA flexible)
- LoopVoxelSampler() - Constructor for class edu.duke.cs.osprey.bbfree.LoopVoxelSampler
- LowEnergyConfSampler - Class in edu.duke.cs.osprey.lute
- LowEnergyConfSampler(SimpleConfSpace, PruningMatrix, int, Function<RCs, ConfSearch>) - Constructor for class edu.duke.cs.osprey.lute.LowEnergyConfSampler
- lower - Variable in class edu.duke.cs.osprey.confspace.ConfDB.Conf
- lower - Variable in class edu.duke.cs.osprey.tools.BigExp.Bounds
- lower - Variable in class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- lower - Variable in class edu.duke.cs.osprey.tools.MathTools.BigIntegerBounds
- lower - Variable in class edu.duke.cs.osprey.tools.MathTools.DoubleBounds
- lowerBound - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
-
lower bound on K* score
- lowerBound - Variable in class edu.duke.cs.osprey.kstar.KStarScore
-
lower bound on K* score
- lowerBound - Variable in class edu.duke.cs.osprey.paste.PasteScore
-
lower bound on K* score
- lowerBound(int[]) - Method in class edu.duke.cs.osprey.confspace.SearchProblem
- LowerBoundCalculator - Class in edu.duke.cs.osprey.kstar.pfunc
- LowerBoundCalculator(ConfSearch, ConfEnergyCalculator) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator
- LowerBoundCalculator.Status - Enum Class in edu.duke.cs.osprey.kstar.pfunc
- lowerBoundContribByRC(int, int[], int) - Method in class edu.duke.cs.osprey.kstar.KSSearchProblem
- lowerBoundLog10() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- lowerBoundLog10() - Method in class edu.duke.cs.osprey.kstar.KStarScore
- lowerBoundLog10String() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- lowerBoundLog10String() - Method in class edu.duke.cs.osprey.kstar.KStarScore
- lowerBoundLog10String() - Method in class edu.duke.cs.osprey.paste.PasteScore
- lowerBounds() - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- lowestConf - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.SequenceInfo
- lowestPairwiseBound(SearchProblem) - Method in class edu.duke.cs.osprey.gmec.GMECFinder
- LPChecks - Class in edu.duke.cs.osprey.plug
- LPChecks() - Constructor for class edu.duke.cs.osprey.plug.LPChecks
- LPT() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.DihederalParameter
-
Returns the value of the
LPTrecord component. - LPT() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.ImproperDihederalParameter
-
Returns the value of the
LPTrecord component. - LTYNB() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.Six12PotentialCoefficient
-
Returns the value of the
LTYNBrecord component. - LTYNB() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.SlaterKirkwoodParameter
-
Returns the value of the
LTYNBrecord component. - LTYNB() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.VanDerWaalsRadius
-
Returns the value of the
LTYNBrecord component. - LUTE - Class in edu.duke.cs.osprey.lute
- LUTE(SimpleConfSpace) - Constructor for class edu.duke.cs.osprey.lute.LUTE
- LUTE.Errors - Class in edu.duke.cs.osprey.lute
- LUTE.Fitter - Enum Class in edu.duke.cs.osprey.lute
- LUTE.LinearSystem - Class in edu.duke.cs.osprey.lute
- LUTEConfEnergyCalculator - Class in edu.duke.cs.osprey.lute
- LUTEConfEnergyCalculator(SimpleConfSpace, LUTEState) - Constructor for class edu.duke.cs.osprey.lute.LUTEConfEnergyCalculator
- luteEcalc - Variable in class edu.duke.cs.osprey.sofea.BoltzmannLute
- LUTEGMECFinder - Class in edu.duke.cs.osprey.lute
-
Just like SimpleGMECFinder, except it doesn't use lower bounds on conformation energies at all.
- LUTEGMECFinder.Builder - Class in edu.duke.cs.osprey.lute
- LUTEGScorer - Class in edu.duke.cs.osprey.lute
- LUTEGScorer(LUTEConfEnergyCalculator) - Constructor for class edu.duke.cs.osprey.lute.LUTEGScorer
- LUTEHScorer - Class in edu.duke.cs.osprey.lute
- LUTEHScorer(LUTEConfEnergyCalculator) - Constructor for class edu.duke.cs.osprey.lute.LUTEHScorer
- LUTEIO - Class in edu.duke.cs.osprey.lute
- LUTEIO() - Constructor for class edu.duke.cs.osprey.lute.LUTEIO
- LUTEPfunc - Class in edu.duke.cs.osprey.lute
-
Since LUTE energies are assumed to be correct, we don't have to deal with minimization and bounding, so it's vastly easier to estimate partition functions.
- LUTEPfunc(LUTEConfEnergyCalculator, ConfAStarTree, BigInteger) - Constructor for class edu.duke.cs.osprey.lute.LUTEPfunc
- luteSettings - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- luteSettings - Variable in class edu.duke.cs.osprey.gmec.DEEGMECFinder
- LUTESettings - Class in edu.duke.cs.osprey.tupexp
-
Settings for LUTE
- LUTESettings() - Constructor for class edu.duke.cs.osprey.tupexp.LUTESettings
- LUTESettings(ParamSet) - Constructor for class edu.duke.cs.osprey.tupexp.LUTESettings
- LUTEState - Class in edu.duke.cs.osprey.lute
-
a persistable form of all the state needed to compute conformation energies
- LUTEState(int) - Constructor for class edu.duke.cs.osprey.lute.LUTEState
- LUTEState(LUTE.LinearSystem) - Constructor for class edu.duke.cs.osprey.lute.LUTEState
- LZMA2 - Class in edu.duke.cs.osprey.tools
-
A utility for LZMA2 compression and decompression.
- LZMA2() - Constructor for class edu.duke.cs.osprey.tools.LZMA2
M
- m - Variable in class edu.duke.cs.osprey.confspace.ConfSpace
- MagicBigDecimal(double) - Constructor for class edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal
- main(String[]) - Static method in class edu.duke.cs.osprey.control.Main
- main(String[]) - Static method in class edu.duke.cs.osprey.design.Main
- main(String[]) - Static method in class edu.duke.cs.osprey.gpu.cuda.Diagnostics
- main(String[]) - Static method in class edu.duke.cs.osprey.gpu.opencl.Diagnostics
- main(String[]) - Static method in class edu.duke.cs.osprey.ibis.KStarBeak
- main(String[]) - Static method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeSplitter
- main(String[]) - Static method in class edu.duke.cs.osprey.markstar.visualizer.Visualizer
- main(String[]) - Static method in class edu.duke.cs.osprey.parallelism.Hostname
- main(String[]) - Static method in class edu.duke.cs.osprey.plug.VoxelVDWDistExplorer
- main(String[]) - Static method in class edu.duke.cs.osprey.structure.analysis.TemplateChooser
- main(String[]) - Static method in class edu.duke.cs.osprey.tests.CatPark
- main(String[]) - Static method in class edu.duke.cs.osprey.tests.ComplicatedGMECFinding
- main(String[]) - Static method in class edu.duke.cs.osprey.tests.MinimizationPlayground
- main(String[]) - Static method in class edu.duke.cs.osprey.tests.NewCOMETS
- main(String[]) - Static method in class edu.duke.cs.osprey.tests.OneEPICFit
- main(String[]) - Static method in class edu.duke.cs.osprey.tests.PruningPlayground
- main(String[]) - Static method in class edu.duke.cs.osprey.tests.VoxDeltaGPlayground
- Main - Class in edu.duke.cs.osprey.control
- Main - Class in edu.duke.cs.osprey.design
- Main() - Constructor for class edu.duke.cs.osprey.control.Main
- Main() - Constructor for class edu.duke.cs.osprey.design.Main
- Main.Command - Enum Class in edu.duke.cs.osprey.control
- make() - Method in interface edu.duke.cs.osprey.astar.conf.scoring.AStarScorer
- make() - Method in class edu.duke.cs.osprey.astar.conf.scoring.MPLPPairwiseHScorer
- make() - Method in class edu.duke.cs.osprey.astar.conf.scoring.NaiveTraditionalPairwiseHScorer
- make() - Method in class edu.duke.cs.osprey.astar.conf.scoring.NOPAStarScorer
- make() - Method in class edu.duke.cs.osprey.astar.conf.scoring.PairwiseGScorer
- make() - Method in class edu.duke.cs.osprey.astar.conf.scoring.TraditionalPairwiseHScorer
- make() - Method in class edu.duke.cs.osprey.energy.ResInterGen
- make() - Method in class edu.duke.cs.osprey.externalMemory.Queue.ExternalFIFOFactory
- make() - Method in class edu.duke.cs.osprey.externalMemory.Queue.ExternalPriorityFactory
- make() - Method in interface edu.duke.cs.osprey.externalMemory.Queue.Factory.FIFO
- make() - Method in interface edu.duke.cs.osprey.externalMemory.Queue.Factory
- make() - Method in class edu.duke.cs.osprey.externalMemory.Queue.FIFOFactory
- make() - Method in class edu.duke.cs.osprey.externalMemory.Queue.PriorityFactory
- make() - Method in class edu.duke.cs.osprey.lute.LUTEGScorer
- make() - Method in class edu.duke.cs.osprey.lute.LUTEHScorer
- make() - Method in class edu.duke.cs.osprey.markstar.UpperBoundScorer
- make() - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- make(double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- make(int, int) - Static method in class edu.duke.cs.osprey.parallelism.Parallelism
- make(int, int, int) - Static method in class edu.duke.cs.osprey.parallelism.Parallelism
- make(CT) - Method in interface edu.duke.cs.osprey.tools.Factory
- make(ConfIndex) - Static method in class edu.duke.cs.osprey.confspace.Conf
- make(RCs) - Method in interface edu.duke.cs.osprey.kstar.BBKStar.ConfSearchFactory
- make(RCs) - Method in interface edu.duke.cs.osprey.kstar.KStar.PfuncFactory
- make(RCs) - Method in interface edu.duke.cs.osprey.paste.Paste.ConfSearchFactory
- make(FullAStarNode, int, int) - Method in class edu.duke.cs.osprey.astar.FullAStarNode.Factory
- make(SlimAStarNode, int, int) - Method in class edu.duke.cs.osprey.astar.SlimAStarNode.Factory
- make(ConfSpaceIteration) - Static method in class edu.duke.cs.osprey.confspace.Conf
- make(SimpleConfSpace) - Static method in class edu.duke.cs.osprey.confspace.Conf
- make(SimpleConfSpace, RCTuple) - Static method in class edu.duke.cs.osprey.confspace.Conf
- make(SimpleConfSpace, EnergyCalculator) - Method in interface edu.duke.cs.osprey.markstar.MARKStar.ConfEnergyCalculatorFactory
- make(EnergyMatrix) - Method in interface edu.duke.cs.osprey.astar.conf.ConfRanker.ScorerFactory
- make(EnergyMatrix) - Method in interface edu.duke.cs.osprey.markstar.framework.MARKStarNode.ScorerFactory
- make(EnergyMatrix, RCs) - Method in interface edu.duke.cs.osprey.markstar.MARKStar.ConfSearchFactory
- make(EnergyMatrix, PruningMatrix) - Method in interface edu.duke.cs.osprey.gmec.ConfSearchFactory
- make(ForcefieldParams, SearchProblem) - Static method in class edu.duke.cs.osprey.gmec.MinimizingConfEnergyCalculator
-
Deprecated.
- make(ForcefieldParams, SearchProblem, Parallelism) - Static method in class edu.duke.cs.osprey.gmec.MinimizingConfEnergyCalculator
-
Deprecated.
- make(ResidueInteractions, Molecule) - Method in interface edu.duke.cs.osprey.energy.EnergyCalculator.Type.EfuncFactory
- make(Supplier<ConfSearch>) - Method in class edu.duke.cs.osprey.astar.conf.ConfSearchCache
- make(T, int, int) - Method in interface edu.duke.cs.osprey.astar.AStarNode.Factory
- makeAborted() - Static method in class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Result
- makeAborted() - Static method in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Result
- makeAborted() - Static method in class edu.duke.cs.osprey.paste.PastePartitionFunction.Result
- makeAll(SimpleConfSpace, SimpleReferenceEnergies, boolean, RCTuple) - Static method in enum class edu.duke.cs.osprey.energy.EnergyPartition
- makeAxis() - Method in class edu.duke.cs.osprey.tools.SVGPlot.Intervals
- makeBest(ConfSpace, Parallelism) - Static method in interface edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator
-
Builds the best conformation energy calculator based on the given resources, and using Float64 precision.
- makeBest(ConfSpace, Parallelism, Structs.Precision) - Static method in interface edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator
-
Builds the best conformation energy calculator based on the given resources.
- makeBounds(Strand) - Method in class edu.duke.cs.osprey.confspace.CATSStrandFlex
- makeBounds(Strand) - Method in class edu.duke.cs.osprey.confspace.DEEPerStrandFlex
- makeBounds(Strand) - Method in class edu.duke.cs.osprey.confspace.StrandFlex
- makeBounds(Strand) - Method in class edu.duke.cs.osprey.confspace.StrandFlex.None
- makeBounds(Strand) - Method in class edu.duke.cs.osprey.confspace.StrandFlex.TranslateRotate
- makeBuffer(T) - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- makeByte(int) - Method in enum class edu.duke.cs.osprey.gpu.BufferTools.Type
- makeByteBuffer(int) - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- makeChild(MARKStarNode.Node) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- makeChildren() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.MultiSequenceNode
- makeChildren() - Method in class edu.duke.cs.osprey.kstar.BBKStar.MultiSequenceNode
- makeConf(int) - Method in interface edu.duke.cs.osprey.astar.conf.ConfAStarNode
- makeConfIndex() - Method in class edu.duke.cs.osprey.coffee.StateInfo
- makeConfSearchFactory(MSSearchProblem, MSConfigFileParser) - Static method in class edu.duke.cs.osprey.multistatekstar.MSKStarFactory
- makeContext(int, int) - Method in enum class edu.duke.cs.osprey.minimization.GpuConfMinimizer.Type
- makeContext(Parallelism, ResPairCache) - Method in enum class edu.duke.cs.osprey.energy.EnergyCalculator.Type
- makeCoords(int[]) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
-
Makes coordinates with the given assignments
- makeCpu(int) - Static method in class edu.duke.cs.osprey.parallelism.Parallelism
- makeDefaultFFParams(ParamSet) - Static method in class edu.duke.cs.osprey.multistatekstar.MSKStarFactory
- makeDihedralBounds(ResidueTemplate, int) - Method in class edu.duke.cs.osprey.confspace.VoxelShape
-
make bounds for degrees of freedom for the residue in its current state (ie, ignore possible mutations)
- makeDihedralBounds(ResidueTemplate, int) - Method in class edu.duke.cs.osprey.confspace.VoxelShape.Point
- makeDihedralBounds(ResidueTemplate, int) - Method in class edu.duke.cs.osprey.confspace.VoxelShape.Rect
- makeDihedralDOFs(Residue) - Method in class edu.duke.cs.osprey.confspace.VoxelShape
-
make degrees of freedom for the residue in its current state (ie, ignore possible mutations)
- makeDihedralDOFs(Residue) - Method in class edu.duke.cs.osprey.confspace.VoxelShape.Point
- makeDihedralDOFs(Residue) - Method in class edu.duke.cs.osprey.confspace.VoxelShape.Rect
- makeDihedrals(long) - Method in class edu.duke.cs.osprey.structure.analysis.DegreesHistogram
- makeDir(String, boolean) - Static method in class edu.duke.cs.osprey.tools.ObjectIO
- makeDiscreteMolecule(RCTuple) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
create a new
Moleculein the specified conformation but without any continuous flexibility - makeDiscreteVersion() - Method in class edu.duke.cs.osprey.dof.deeper.DEEPerSettings
- makeDOFBounds(double) - Method in class edu.duke.cs.osprey.confspace.PositionConfSpace
- makeDofInfo(RCTuple) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- makeDofs() - Method in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords
- makeDofs(Strand, Molecule) - Method in class edu.duke.cs.osprey.confspace.CATSStrandFlex
- makeDofs(Strand, Molecule) - Method in class edu.duke.cs.osprey.confspace.DEEPerStrandFlex
- makeDofs(Strand, Molecule) - Method in class edu.duke.cs.osprey.confspace.StrandFlex
- makeDofs(Strand, Molecule) - Method in class edu.duke.cs.osprey.confspace.StrandFlex.None
- makeDofs(Strand, Molecule) - Method in class edu.duke.cs.osprey.confspace.StrandFlex.TranslateRotate
- makeDouble(int) - Method in enum class edu.duke.cs.osprey.gpu.BufferTools.Type
- makeDoubleBuffer(int) - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- makeDTemplate(ResidueTemplate) - Static method in class edu.duke.cs.osprey.restypes.DAminoAcidHandler
- makeDTemplates(List<ResidueTemplate>) - Static method in class edu.duke.cs.osprey.restypes.DAminoAcidHandler
-
Make a D-amino acid template for every standard L-amino acid template in the library This lets us do D-amino acids without having to have separate templates A D-amino acid is just an inverted L-amino acid (including Ile and Thr, which have a second chiral center)
- makeEmat() - Method in class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.ByPosition
- makeEmat() - Method in class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.ByResidue
- makeEnergyCalculator(MSConfigFileParser, SearchProblem, Parallelism) - Static method in class edu.duke.cs.osprey.multistatekstar.MSKStarFactory
- makeEnergyFunction(ParametricMolecule, ResidueInteractions) - Method in class edu.duke.cs.osprey.energy.EnergyCalculator
- makeEnergyFunction(EnergyCalculator.EnergiedParametricMolecule) - Method in class edu.duke.cs.osprey.energy.EnergyCalculator
- makeEnergyObjFcn(ParametricMolecule, ResidueInteractions) - Method in class edu.duke.cs.osprey.energy.EnergyCalculator
- makeEPoly(RCTuple) - Method in class edu.duke.cs.osprey.ematrix.NewEPICMatrixCalculator
- makeFile(File) - Static method in class edu.duke.cs.osprey.tools.FileTools.Path
- makeFile(String) - Static method in class edu.duke.cs.osprey.tools.FileTools.Path
- makeFragInters(RCTuple) - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- makeFragInters(RCTuple) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- makeFragment(SimpleConfSpace, SimpleReferenceEnergies, boolean, RCTuple) - Static method in enum class edu.duke.cs.osprey.energy.EnergyPartition
- makeFromBounds(double[]) - Static method in class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel
- makeFromConfig(SearchProblem, ConfigFileParser) - Static method in class edu.duke.cs.osprey.gmec.ConfSearchFactory.Tools
- makeFromConfig(ConfigFileParser) - Static method in class edu.duke.cs.osprey.parallelism.Parallelism
- makeFromConfSpaceInfo(BBKStar.ConfSpaceInfo, RCs) - Static method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- makeFromConfSpaceInfo(BBKStar.ConfSpaceInfo, RCs) - Static method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- makeFromConfSpaceInfo(BBKStar.ConfSpaceInfo, RCs) - Static method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- makeFromFilePaths(Iterable<String>) - Static method in class edu.duke.cs.osprey.control.ConfigFileParser
- makeFromFilePaths(String...) - Static method in class edu.duke.cs.osprey.control.ConfigFileParser
- makeFromFiles(Iterable<File>) - Static method in class edu.duke.cs.osprey.control.ConfigFileParser
- makeFromResidueConfs(Residue...) - Static method in class edu.duke.cs.osprey.restypes.ResidueTemplate
- makeFromResidueConfs(List<Residue>) - Static method in class edu.duke.cs.osprey.restypes.ResidueTemplate
- makeFull(SearchProblem) - Static method in class edu.duke.cs.osprey.astar.ConfTree
- makeFull(SearchProblem, PruningMatrix) - Static method in class edu.duke.cs.osprey.astar.ConfTree
- makeFull(SearchProblem, PruningMatrix, GMECMutSpace) - Static method in class edu.duke.cs.osprey.astar.ConfTree
- makeFull(PrecomputedMatrices, GMECMutSpace, boolean, boolean, EPICSettings, int) - Static method in class edu.duke.cs.osprey.astar.ConfTree
- makeFullConf(ConfSpace, List<Residue>) - Static method in class edu.duke.cs.osprey.energy.FFInterGen
-
Deprecated.
- makeFullConf(ConfSpace, List<Residue>, Molecule) - Static method in class edu.duke.cs.osprey.energy.FFInterGen
-
Deprecated.
- makeFullConf(SimpleConfSpace, Molecule) - Static method in class edu.duke.cs.osprey.energy.FFInterGen
-
Deprecated.
- makeFullMol(Molecule) - Static method in class edu.duke.cs.osprey.energy.FFInterGen
-
Deprecated.
- makeFullRange() - Static method in class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Values
- makeFullRange() - Static method in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Values
- makeFullRange() - Static method in class edu.duke.cs.osprey.paste.PastePartitionFunction.Values
- makeFunction(String) - Method in class edu.duke.cs.osprey.gpu.cuda.Kernel
- makeIdentity(List<Integer>, List<Integer>) - Method in interface edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction.Approximator.Addable
- makeIdentity(List<Integer>, List<Integer>) - Method in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- makeIfNeeded(ConfSpaceIteration, File) - Static method in class edu.duke.cs.osprey.confspace.ConfDB
- makeInfo(ForcefieldParams, Residues) - Method in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.SolvationForcefield
- makeInt(int) - Method in enum class edu.duke.cs.osprey.gpu.BufferTools.Type
- makeIntBuffer(int) - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- makeInters(int[], boolean) - Method in class edu.duke.cs.osprey.coffee.Coffee.StateConfig
- makeIntraAndShell(ConfSpace, int, List<Residue>, Molecule) - Static method in class edu.duke.cs.osprey.energy.FFInterGen
-
Deprecated.
- makeIntraAndShell(SimpleConfSpace, int, Molecule) - Static method in class edu.duke.cs.osprey.energy.FFInterGen
-
Deprecated.
- makeIntraAndShell(Residue, List<Residue>) - Static method in class edu.duke.cs.osprey.energy.FFInterGen
-
Deprecated.
- makeIntraShellObjFcn(int, int) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- makeIntraShellObjFcn(int, int) - Method in class edu.duke.cs.osprey.lute.LUTEConfEnergyCalculator
- makeJob(ConfSpace, PosInterGen) - Method in class edu.duke.cs.osprey.coffee.zmat.Pair
- makeJob(ConfSpace, PosInterGen) - Method in class edu.duke.cs.osprey.coffee.zmat.Single
- makeJob(ConfSpace, PosInterGen) - Method in class edu.duke.cs.osprey.coffee.zmat.Triple
- makeJob(ConfSpace, PosInterGen) - Method in interface edu.duke.cs.osprey.coffee.zmat.Tuple
- makeKStarScore() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.SingleSequenceNode
- makeKStarScore() - Method in class edu.duke.cs.osprey.kstar.BBKStar.SingleSequenceNode
- makeKStarScore(ParamSet, int, MSConfigFileParser, LMB[], MSSearchProblem[], MSSearchProblem[], GMECConfEnergyCalculator.Async[], GMECConfEnergyCalculator.Async[], KStarScore.KStarScoreType) - Static method in class edu.duke.cs.osprey.multistatekstar.MSKStarFactory
- makeLeafProgressReport() - Method in class edu.duke.cs.osprey.astar.AStarProgress
- makeLeafProgressReport() - Method in class edu.duke.cs.osprey.markstar.MARKStarProgress
- makeLigandMolecule() - Method in class edu.duke.cs.osprey.design.models.AffinityDesign
- makeLine(double, double, double, double) - Method in class edu.duke.cs.osprey.tools.SVG
- makeLong(int) - Method in enum class edu.duke.cs.osprey.gpu.BufferTools.Type
- makeLongBuffer(int) - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- makeMolecule(int[]) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- makeMolecule(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- makeMolecule(RCTuple) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
create a new
ParametricMoleculein the specified conformation for analysis (e.g., energy calculation, minimization) To increase stability of analysis, each analysis should be conducted with a new molecule instance. - makeNoCopy(ConfSpace) - Static method in class edu.duke.cs.osprey.confspace.ParameterizedMoleculeCopy
- makeOffset(int, int) - Method in interface edu.duke.cs.osprey.energy.ResInterGen.IntraOffsetter
- makeOffset(int, int, int, int) - Method in interface edu.duke.cs.osprey.energy.ResInterGen.InterOffsetter
- makeOffset(int, int, String) - Method in interface edu.duke.cs.osprey.energy.ResInterGen.ShellOffsetter
- makeOrExpandBuffer(CUBuffer<T>, T) - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- makeOrExpandByteBuffer(CUBuffer<ByteBuffer>, int) - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- makeOrExpandDoubleBuffer(CUBuffer<DoubleBuffer>, int) - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- makeOrExpandIntBuffer(CUBuffer<IntBuffer>, int) - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- makeOrExpandLongBuffer(CUBuffer<LongBuffer>, int) - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- makePair(SimpleConfSpace, SimpleReferenceEnergies, boolean, int, int, int, int) - Method in enum class edu.duke.cs.osprey.energy.EnergyPartition
- makePairEfunc(int, int) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator
-
Deprecated.
- makePairEfunc(int, int, Molecule) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator.Cpu
-
Deprecated.
- makePairEfunc(int, int, Molecule) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator.Cuda
-
Deprecated.
- makePairEfunc(int, int, Molecule) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator
-
Deprecated.
- makePairInters(int, int, int, int) - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- makePairInters(int, int, int, int) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- makePairInters(int, int, int, int) - Method in class edu.duke.cs.osprey.lute.LUTEConfEnergyCalculator
- makePairwiseObjFcn(int, int, int, int) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- makePairwiseObjFcn(int, int, int, int) - Method in class edu.duke.cs.osprey.lute.LUTEConfEnergyCalculator
- makePartitionFunction(KStarScore.PartitionFunctionType, EnergyMatrix, PruningMatrix, PruningMatrix, ConfSearchFactory, GMECConfEnergyCalculator.Async) - Static method in class edu.duke.cs.osprey.multistatekstar.MSKStarFactory
- makePerturbations(Molecule) - Method in class edu.duke.cs.osprey.dof.deeper.DEEPerSettings
- makePoint(double, double, double) - Method in class edu.duke.cs.osprey.tools.SVG
- makeProgressReport() - Method in class edu.duke.cs.osprey.astar.AStarProgress
- makeProgressReport() - Method in class edu.duke.cs.osprey.markstar.MARKStarProgress
- makeProteinMolecule() - Method in class edu.duke.cs.osprey.design.models.AffinityDesign
- makeQuadCorrection(SimpleConfSpace, SimpleReferenceEnergies, boolean, int, int, int, int, int, int, int, int) - Method in enum class edu.duke.cs.osprey.energy.EnergyPartition
- makeQuadCorrectionInters(int, int, int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- makeQuadCorrectionInters(int, int, int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- makeQueue(RCs) - Method in interface edu.duke.cs.osprey.astar.conf.ConfAStarFactory
- makeQueue(RCs) - Method in class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarFactory
- makeQueue(RCs) - Method in class edu.duke.cs.osprey.externalMemory.EMConfAStarFactory
- makeRC(RC, int, double, double) - Method in class edu.duke.cs.osprey.partcr.splitters.RCSplitter
- makeRCs(int[]) - Method in class edu.duke.cs.osprey.partcr.RCSplits
- makeRCs(ConfSpaceIteration) - Method in class edu.duke.cs.osprey.confspace.Sequence
- makeRCs(SeqSpace, SimpleConfSpace) - Method in class edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode.Assignments
- makeRect(double, double, double, double) - Method in class edu.duke.cs.osprey.tools.SVG
- makeRectWH(double, double, double, double) - Method in class edu.duke.cs.osprey.tools.SVG
- makeRelative(File) - Method in class edu.duke.cs.osprey.tools.FileTools.FilePathRoot
- makeRelative(String) - Method in class edu.duke.cs.osprey.tools.FileTools.FilePathRoot
- makeRelative(String) - Method in class edu.duke.cs.osprey.tools.FileTools.PathRoot
- makeRelative(String) - Method in class edu.duke.cs.osprey.tools.FileTools.ResourcePathRoot
- makeReport() - Method in class edu.duke.cs.osprey.gpu.opencl.ProfilingEvents
- makeReport(ConfSearch.EnergiedConf, SimpleConfSpace, EnergyRange) - Static method in class edu.duke.cs.osprey.gmec.ConsoleConfPrinter
- makeReport(TimeUnit) - Method in class edu.duke.cs.osprey.tools.Profiler
- makeReportMap(ConfSearch.EnergiedConf, SimpleConfSpace, EnergyRange) - Static method in class edu.duke.cs.osprey.gmec.ConsoleConfPrinter
- makeResource(String) - Static method in class edu.duke.cs.osprey.tools.FileTools.Path
- makeResPair(ConfSpace, int, int, Molecule) - Static method in class edu.duke.cs.osprey.energy.FFInterGen
-
Deprecated.
- makeResPair(SimpleConfSpace, int, int, Molecule) - Static method in class edu.duke.cs.osprey.energy.FFInterGen
-
Deprecated.
- makeResPair(Residue, Residue) - Static method in class edu.duke.cs.osprey.energy.FFInterGen
-
Deprecated.
- makeResPairIndicesSubset(Residue) - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- makeResPairsSubset(Residue) - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- makeResult() - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction
- makeResult() - Method in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- makeResult() - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction
- makeResult() - Method in class edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc
- makeResult() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- makeResult() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- makeResult() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- makeResult() - Method in interface edu.duke.cs.osprey.paste.PastePartitionFunction
- makeResultDoc(SeqDB, File) - Method in class edu.duke.cs.osprey.sofea.MinLMFE
- makeRoot() - Method in interface edu.duke.cs.osprey.astar.AStarNode.Factory
- makeRoot() - Method in class edu.duke.cs.osprey.astar.FullAStarNode.Factory
- makeRoot() - Method in class edu.duke.cs.osprey.astar.SlimAStarNode.Factory
- makeRoot(SimpleConfSpace, EnergyMatrix, EnergyMatrix, RCs, AStarScorer, AStarScorer, AStarScorer, AStarScorer, boolean) - Static method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- makeRootNode(int) - Method in interface edu.duke.cs.osprey.astar.conf.ConfAStarFactory
- makeRootNode(int) - Method in class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarFactory
- makeRootNode(int) - Method in class edu.duke.cs.osprey.externalMemory.EMConfAStarFactory
- makeSequence(ConfSpaceIteration, int[]) - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- makeSequence(SeqSpace) - Method in interface edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode
- makeSequence(String...) - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- makeSequence(List<String>) - Method in class edu.duke.cs.osprey.confspace.SeqSpace
-
Make a sequence with the given residue type names residue type names must be given in the same order as the positions in the sequence space
- makeSequenceFromAssignments(int[]) - Method in interface edu.duke.cs.osprey.confspace.ConfSpaceIteration
-
creates a new sequence out of assignments from this conf space
- makeSequenceFromConf(ConfSearch.ScoredConf) - Method in interface edu.duke.cs.osprey.confspace.ConfSpaceIteration
-
creates a new sequence out of conformation from this conf space
- makeSequenceFromId(String) - Method in class edu.duke.cs.osprey.tools.MapDBTools.SequenceSerializer
- makeShell(SimpleConfSpace) - Static method in enum class edu.duke.cs.osprey.energy.EnergyPartition
- makeShellInters() - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- makeShellInters() - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- makeSingle(SimpleConfSpace, SimpleReferenceEnergies, boolean, int, int) - Method in enum class edu.duke.cs.osprey.energy.EnergyPartition
- makeSingleEfunc(int) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator
-
Deprecated.
- makeSingleEfunc(int, Molecule) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator.Cpu
-
Deprecated.
- makeSingleEfunc(int, Molecule) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator.Cuda
-
Deprecated.
- makeSingleEfunc(int, Molecule) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator
-
Deprecated.
- makeSingleEfunc(int, Molecule, BufferTools.Type) - Method in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator.Cuda
-
Deprecated.
- makeSingleInters(int, int) - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- makeSingleInters(int, int) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- makeSingleInters(int, int) - Method in class edu.duke.cs.osprey.lute.LUTEConfEnergyCalculator
- makeSingleRes(ConfSpace, int, Molecule) - Static method in class edu.duke.cs.osprey.energy.FFInterGen
-
Deprecated.
- makeSingleRes(SimpleConfSpace, int, Molecule) - Static method in class edu.duke.cs.osprey.energy.FFInterGen
-
Deprecated.
- makeSingleRes(Residue) - Static method in class edu.duke.cs.osprey.energy.FFInterGen
-
Deprecated.
- makeStream() - Method in class edu.duke.cs.osprey.confspace.ConfSearch.MultiSplitter
-
Make a new stream for this conf search that starts at the current position of the search.
- makeStyleClass(String) - Method in class edu.duke.cs.osprey.tools.SVG
- makeSubset(ResidueInteractions) - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- makeSubset(ResidueInteractions.Pair) - Method in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- makeSubsetByResidue(Residue) - Method in class edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions
-
Deprecated.
- makeSubspace(Strand) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- makeTaskExecutor() - Method in class edu.duke.cs.osprey.parallelism.Parallelism
- makeTaskExecutor(Parallelism) - Method in class edu.duke.cs.osprey.parallelism.Cluster
- makeTaskExecutor(Integer) - Method in class edu.duke.cs.osprey.parallelism.Parallelism
-
Makes a TaskExecutor to process tasks, possibly in parallel
- makeText(String) - Method in class edu.duke.cs.osprey.tools.SVG
- makeTripleCorrection(SimpleConfSpace, SimpleReferenceEnergies, boolean, int, int, int, int, int, int) - Method in enum class edu.duke.cs.osprey.energy.EnergyPartition
- makeTripleCorrectionInters(int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- makeTripleCorrectionInters(int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- makeTuple(SimpleConfSpace, SimpleReferenceEnergies, boolean, RCTuple) - Method in enum class edu.duke.cs.osprey.energy.EnergyPartition
- makeTupleInters(RCTuple) - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- makeTupleInters(RCTuple) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- makeTuplesList() - Method in class edu.duke.cs.osprey.confspace.TupleTree
- makeUnassignedSequence() - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- makeUnassignedSequence() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- makeUnknown(int) - Static method in class edu.duke.cs.osprey.coffee.seqdb.StateZ
- makeUnknown(MultiStateConfSpace) - Static method in class edu.duke.cs.osprey.coffee.seqdb.SeqInfo
- makeUnprunedClusterExpansion() - Method in class edu.duke.cs.osprey.ibis.KStarBeak
- makeWildTypeSequence() - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- makeWildTypeSequence() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- makeXAxis() - Method in class edu.duke.cs.osprey.tools.SVGPlot.Boxes
- makeYAxis() - Method in class edu.duke.cs.osprey.tools.SVGPlot.Boxes
- makeZero() - Static method in class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- makeZero(int) - Static method in class edu.duke.cs.osprey.coffee.seqdb.StateZ
- makeZero(MultiStateConfSpace) - Static method in class edu.duke.cs.osprey.coffee.seqdb.SeqInfo
- malloc(long) - Method in class edu.duke.cs.osprey.gpu.cuda.Context
- map(T, T) - Method in enum class edu.duke.cs.osprey.gpu.Structs.Precision
- Map() - Constructor for class edu.duke.cs.osprey.confspace.Conf.Map
- mapdbConf(ConfSpaceIteration) - Static method in class edu.duke.cs.osprey.coffee.Serializers
- mapdbSeq(SeqSpace) - Static method in class edu.duke.cs.osprey.coffee.Serializers
- mapdbSeqInfo(MultiStateConfSpace) - Static method in class edu.duke.cs.osprey.coffee.Serializers
- mapdbStateZ(MultiStateConfSpace) - Static method in class edu.duke.cs.osprey.coffee.Serializers
- MapDBTools - Class in edu.duke.cs.osprey.tools
- MapDBTools() - Constructor for class edu.duke.cs.osprey.tools.MapDBTools
- MapDBTools.BigDecimalBoundsSerializer - Class in edu.duke.cs.osprey.tools
- MapDBTools.BigDecimalSerializer - Class in edu.duke.cs.osprey.tools
- MapDBTools.BigExpSerializer - Class in edu.duke.cs.osprey.tools
- MapDBTools.IntArraySerializer - Class in edu.duke.cs.osprey.tools
- MapDBTools.SequenceSerializer - Class in edu.duke.cs.osprey.tools
- MapDBTools.SimpleSerializer<T> - Class in edu.duke.cs.osprey.tools
- MapDBTools.ValuesSerializer<T> - Class in edu.duke.cs.osprey.tools
- mapPositionsTo(SimpleConfSpace) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- markAsPruned(RCTuple) - Method in class edu.duke.cs.osprey.astar.comets.UpdatedPruningMatrix
- markAsPruned(RCTuple) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixInverted
- markAsPruned(RCTuple) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- markAsPruned(RCTuple) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- markAsPruned(RCTuple) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- markInterResBonds() - Method in class edu.duke.cs.osprey.structure.Molecule
- markIntraResBondsByTemplate() - Method in class edu.duke.cs.osprey.structure.Residue
-
Assign all the bonds between atoms in this residue, based on the template
- MARKStar - Class in edu.duke.cs.osprey.markstar
-
Implementation of the K* algorithm to predict protein sequence mutations that improve binding affinity by computing provably accurate Boltzmann-weighted ensembles .
- MARKStar(SimpleConfSpace, SimpleConfSpace, SimpleConfSpace, EnergyCalculator, EnergyCalculator, MARKStar.ConfEnergyCalculatorFactory, MARKStar.Settings) - Constructor for class edu.duke.cs.osprey.markstar.MARKStar
- MARKStar.ConfEnergyCalculatorFactory - Interface in edu.duke.cs.osprey.markstar
- MARKStar.ConfSearchFactory - Interface in edu.duke.cs.osprey.markstar
- MARKStar.ConfSpaceInfo - Class in edu.duke.cs.osprey.markstar
- MARKStar.ConfSpaceType - Enum Class in edu.duke.cs.osprey.markstar
- MARKStar.InitException - Exception in edu.duke.cs.osprey.markstar
- MARKStar.ScoredSequence - Class in edu.duke.cs.osprey.markstar
- MARKStar.Settings - Class in edu.duke.cs.osprey.markstar
- MARKStar.Settings.Builder - Class in edu.duke.cs.osprey.markstar
- MARKStarBound - Class in edu.duke.cs.osprey.markstar.framework
- MARKStarBound(SimpleConfSpace, EnergyMatrix, EnergyMatrix, ConfEnergyCalculator, RCs, Parallelism) - Constructor for class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- MARKStarBound.ScoreContext - Class in edu.duke.cs.osprey.markstar.framework
- MARKStarBound.Values - Class in edu.duke.cs.osprey.markstar.framework
- MARKStarBoundAsync - Class in edu.duke.cs.osprey.markstar.framework
- MARKStarBoundAsync(SimpleConfSpace, EnergyMatrix, EnergyMatrix, ConfEnergyCalculator, RCs, Parallelism, BigInteger) - Constructor for class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- MARKStarBoundAsync.Values - Class in edu.duke.cs.osprey.markstar.framework
- MARKStarBoundFastQueues - Class in edu.duke.cs.osprey.markstar.framework
- MARKStarBoundFastQueues(SimpleConfSpace, EnergyMatrix, EnergyMatrix, ConfEnergyCalculator, RCs, Parallelism) - Constructor for class edu.duke.cs.osprey.markstar.framework.MARKStarBoundFastQueues
- MARKStarBoundRigid - Class in edu.duke.cs.osprey.markstar.framework
- MARKStarBoundRigid(SimpleConfSpace, EnergyMatrix, EnergyMatrix, ConfEnergyCalculator, RCs, Parallelism) - Constructor for class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- MARKStarBoundRigid.Values - Class in edu.duke.cs.osprey.markstar.framework
- MARKStarNode - Class in edu.duke.cs.osprey.markstar.framework
- MARKStarNode.Node - Class in edu.duke.cs.osprey.markstar.framework
- MARKStarNode.ScorerFactory - Interface in edu.duke.cs.osprey.markstar.framework
- MARKStarNode.Type - Enum Class in edu.duke.cs.osprey.markstar.framework
- MARKStarProgress - Class in edu.duke.cs.osprey.markstar
- MARKStarProgress(int) - Constructor for class edu.duke.cs.osprey.markstar.MARKStarProgress
- markUpdated() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- mass - Variable in class edu.duke.cs.osprey.structure.Atom
- matches(ConfSpaceIteration) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- matchTemplate(ResidueTemplate) - Method in class edu.duke.cs.osprey.structure.Probe
-
finds the templates that match the residue type, then tries to match a template to the atom names in a residue (should match eg N-terminal or C-terminal amino acids if needed)
- matchTemplates(SimpleConfSpace) - Method in class edu.duke.cs.osprey.structure.Probe
-
finds a probe template for each template in the conf space and remembers the mapping
- matchTemplates(ResidueTemplateLibrary) - Method in class edu.duke.cs.osprey.structure.Probe
-
finds a probe template for each template in the library and remembers the mapping
- matchTemplates(Residues) - Method in class edu.duke.cs.osprey.structure.Probe
-
finds a probe template for each template in the residues and remembers the mapping
- matchTemplates(Collection<ResidueTemplate>) - Method in class edu.duke.cs.osprey.structure.Probe
-
finds a probe template for each template in the library and remembers the mapping
- mathContext - Variable in class edu.duke.cs.osprey.coffee.Coffee
- mathContext - Variable in class edu.duke.cs.osprey.coffee.FreeEnergyCalculator
- mathContext - Variable in class edu.duke.cs.osprey.coffee.seqdb.SeqDB
- mathContext - Variable in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- mathContext - Variable in class edu.duke.cs.osprey.sofea.RCDB
- mathContext - Variable in class edu.duke.cs.osprey.sofea.SeqDB
- mathContext - Variable in class edu.duke.cs.osprey.sofea.Sofea
- mathContext - Static variable in class edu.duke.cs.osprey.tools.BigExp
- Mathematical - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.DominantBaseline
- MathTools - Class in edu.duke.cs.osprey.tools
- MathTools() - Constructor for class edu.duke.cs.osprey.tools.MathTools
- MathTools.BigDecimalBounds - Class in edu.duke.cs.osprey.tools
- MathTools.BigIntegerBounds - Class in edu.duke.cs.osprey.tools
- MathTools.DoubleBounds - Class in edu.duke.cs.osprey.tools
- MathTools.GridIterable - Class in edu.duke.cs.osprey.tools
- MathTools.MagicBigDecimal - Class in edu.duke.cs.osprey.tools
- MathTools.MagicBigDecimal.DontDoRawMathWithMagicException - Exception in edu.duke.cs.osprey.tools
- MathTools.Optimizer - Enum Class in edu.duke.cs.osprey.tools
- max - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Dof
- max - Variable in class edu.duke.cs.osprey.lute.LUTE.Errors
- max - Variable in class edu.duke.cs.osprey.tools.GLibC.RLimit
- max - Variable in class edu.duke.cs.osprey.tools.IntRange
-
exclusive
- max - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot.Interval
- max - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Axis
- max - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Intervals.Interval
- max() - Method in interface edu.duke.cs.osprey.confspace.compiled.DegreeOfFreedom
- max() - Method in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Dof
- max() - Method in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Dof
- max() - Method in class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel.Interval
- max(double) - Method in class edu.duke.cs.osprey.tools.BigMath
- max(long) - Method in class edu.duke.cs.osprey.tools.BigMath
- max(BigExp) - Method in class edu.duke.cs.osprey.tools.BigExp
- max(BigExp) - Method in class edu.duke.cs.osprey.tools.BigMath
- max(BigDecimal) - Method in class edu.duke.cs.osprey.tools.BigMath
- max(BigInteger) - Method in class edu.duke.cs.osprey.tools.BigMath
- MAX_CONFSPACE_FRACTION - Static variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- MAX_VALUE - Static variable in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized
- maxAngleRadians - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle
- maxBatchSize - Variable in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- maxBatchSize() - Method in interface edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator
- maxBatchSize() - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- maxBytes - Variable in class edu.duke.cs.osprey.tools.JvmMem.MemInfo
-
the limit, if any, on this memory pool
- maxConfErrorBound() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- maxCriterionCheckSeconds - Variable in class edu.duke.cs.osprey.sofea.Sofea
- maxDegrees - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Description
- maxDistance - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Description
- Maximize - Enum constant in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
- maxKSConfs - Static variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- maxKSConfsReached() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- maxMinimizations - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- maxNumAtoms - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Pos
- maxNumConfAtoms - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- maxNumConfs - Variable in class edu.duke.cs.osprey.markstar.MARKStar.Settings
- maxNumDofs - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- maxNumDofs() - Method in interface edu.duke.cs.osprey.confspace.compiled.ContinuousMotion.ConfDescription
- maxNumDofs() - Method in interface edu.duke.cs.osprey.confspace.compiled.ContinuousMotion.MolDescription
- maxNumDofs() - Method in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Description
- maxNumDofs() - Method in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Description
- maxNumIterations - Variable in class edu.duke.cs.osprey.pruning.PLUG
-
max num iterations of generalized Newton iteration to find a "boundary" point where the violation function is zero
- maxNumMinimizations - Variable in class edu.duke.cs.osprey.sofea.Sofea
- maxNumPfConfs - Variable in class edu.duke.cs.osprey.paste.Paste.Settings
- maxNumRCsPerResType() - Method in class edu.duke.cs.osprey.confspace.PositionConfSpace
- maxNumTopConfs - Variable in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized
- maxOrSet(double) - Method in class edu.duke.cs.osprey.tools.BigMath
- maxOrSet(long) - Method in class edu.duke.cs.osprey.tools.BigMath
- maxOrSet(BigExp) - Method in class edu.duke.cs.osprey.tools.BigMath
- maxOrSet(BigDecimal) - Method in class edu.duke.cs.osprey.tools.BigMath
- maxOrSet(BigInteger) - Method in class edu.duke.cs.osprey.tools.BigMath
- maxOverlap - Variable in class edu.duke.cs.osprey.structure.Probe.AtomPair
- maxOverlapHBond - Variable in class edu.duke.cs.osprey.structure.Probe
- maxOverlapSaltBridge - Variable in class edu.duke.cs.osprey.structure.Probe
- maxPass1Steps - Variable in class edu.duke.cs.osprey.sofea.StepCount
- maxPass2Steps - Variable in class edu.duke.cs.osprey.sofea.StepCount
- maxPFConfs - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings
- maxPrecision - Variable in class edu.duke.cs.osprey.tools.ExpFunction
- maxRotationRadians - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Description
- maxScore() - Method in class edu.duke.cs.osprey.coffee.directors.BestSet
- maxScores - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices.BroadcastInfo
- maxSimultaneousMutations - Variable in class edu.duke.cs.osprey.coffee.directors.AffinityDirector
- maxSimultaneousMutations - Variable in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- maxSimultaneousMutations - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeTree
- maxSimultaneousMutations - Variable in class edu.duke.cs.osprey.design.commands.DesignFileDelegate
- maxSimultaneousMutations - Variable in class edu.duke.cs.osprey.gmec.Comets
- maxSimultaneousMutations - Variable in class edu.duke.cs.osprey.kstar.KStar.Settings
- maxSimultaneousMutations - Variable in class edu.duke.cs.osprey.kstar.MSKStar
- maxSimultaneousMutations - Variable in class edu.duke.cs.osprey.markstar.MARKStar.Settings
- maxSimultaneousMutations - Variable in class edu.duke.cs.osprey.paste.Paste.Settings
- maxStrandRot - Static variable in class edu.duke.cs.osprey.dof.MoveableStrand
- maxStrandTrans - Static variable in class edu.duke.cs.osprey.dof.MoveableStrand
- maxVal - Variable in enum class edu.duke.cs.osprey.externalMemory.AssignmentsSerializer.Encoding
- maxValue - Variable in enum class edu.duke.cs.osprey.tools.IntEncoding
- maxValues() - Method in class edu.duke.cs.osprey.coffee.directors.BestSet
- maxWeightedErrorBound() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- maxWriteBufferNodes() - Method in class edu.duke.cs.osprey.sofea.FringeDB.Transaction
-
the total number of nodes that can fit in the transaction write buffer
- mc - Static variable in class edu.duke.cs.osprey.tools.ExpFunction
- mean - Variable in class edu.duke.cs.osprey.structure.analysis.ClusterR1.Stats
- mean - Variable in class edu.duke.cs.osprey.structure.analysis.ClusterS1.Stats
- mean() - Method in class edu.duke.cs.osprey.structure.analysis.ClusterR1
- mean(SmallAngleVoxel.Interval) - Method in class edu.duke.cs.osprey.structure.analysis.ClusterS1
- meanGap() - Method in class edu.duke.cs.osprey.coffee.EnergyBoundStats
- measure(Residue) - Method in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.BondAngle
- measure(Residue) - Method in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.BondLength
- measure(Residue) - Method in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DeltaDihedralAngle
- measure(Residue) - Method in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DihedralAngle
- measure(Residue) - Method in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DihedralAnglesMinDist
- measure(Residue) - Method in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.Measurement
- measure(Residue) - Method in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralInPlaneAngle
- measure(Residue) - Method in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralInPlaneAngles2
- measure(Residue) - Method in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralOutOfPlaneAngle
- measure(Residue) - Method in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralOutOfPlaneAngles2
- measure(Residue) - Method in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralSystem
- measure(Residue) - Method in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralSystems2
- measure(Residue, String) - Method in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary
- measureAngleDegrees() - Method in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle
- measureAngleRadians() - Method in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle
- measureBondAngle(double[][]) - Static method in class edu.duke.cs.osprey.tools.Protractor
- measureBondAngle(double[], int[]) - Static method in class edu.duke.cs.osprey.tools.Protractor
- measureBondAngle(double[], int, double[], int, double[], int) - Static method in class edu.duke.cs.osprey.tools.Protractor
-
measure the bond angle between three atoms, A, B, C, in degrees
- measureBondAngle(double[], int, int, int) - Static method in class edu.duke.cs.osprey.tools.Protractor
- measureBondLength(double[], int, double[], int) - Static method in class edu.duke.cs.osprey.tools.Protractor
- measureBondLength(double[], int, int) - Static method in class edu.duke.cs.osprey.tools.Protractor
- measureDihedral(double[][]) - Static method in class edu.duke.cs.osprey.tools.Protractor
- measureDihedral(double[], int[]) - Static method in class edu.duke.cs.osprey.tools.Protractor
- measureDihedral(double[], int, double[], int, double[], int, double[], int) - Static method in class edu.duke.cs.osprey.tools.Protractor
- measureDihedral(double[], int, int, int, int) - Static method in class edu.duke.cs.osprey.tools.Protractor
- measureDihedralDegrees() - Method in class edu.duke.cs.osprey.dof.FreeDihedral
- measureDihedralSinCos(double[][]) - Static method in class edu.duke.cs.osprey.tools.Protractor
- measureDihedralSinCos(double[], int, double[], int, double[], int, double[], int) - Static method in class edu.duke.cs.osprey.tools.Protractor
- measureDihedralSinCos(double[], int, int, int, int) - Static method in class edu.duke.cs.osprey.tools.Protractor
- MeasuredRes(String, String, double[], double) - Constructor for class edu.duke.cs.osprey.structure.analysis.TemplateChooser.MeasuredRes
- Measurement(String, MeasurementLibrary.Space) - Constructor for class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.Measurement
- MeasurementLibrary - Class in edu.duke.cs.osprey.structure.analysis
- MeasurementLibrary() - Constructor for class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary
- MeasurementLibrary.BondAngle - Class in edu.duke.cs.osprey.structure.analysis
- MeasurementLibrary.BondLength - Class in edu.duke.cs.osprey.structure.analysis
- MeasurementLibrary.DeltaDihedralAngle - Class in edu.duke.cs.osprey.structure.analysis
- MeasurementLibrary.DihedralAngle - Class in edu.duke.cs.osprey.structure.analysis
- MeasurementLibrary.DihedralAnglesMinDist - Class in edu.duke.cs.osprey.structure.analysis
-
returns the smallest dihedral angle distance to 180 among the d atoms
- MeasurementLibrary.Measurement - Class in edu.duke.cs.osprey.structure.analysis
- MeasurementLibrary.Space - Enum Class in edu.duke.cs.osprey.structure.analysis
- MeasurementLibrary.TetrahedralInPlaneAngle - Class in edu.duke.cs.osprey.structure.analysis
- MeasurementLibrary.TetrahedralInPlaneAngles2 - Class in edu.duke.cs.osprey.structure.analysis
-
in-plane angle of the ith d atom, sorted by out-of-plane angle distance to -90 degrees (eg CH2 groups)
- MeasurementLibrary.TetrahedralOutOfPlaneAngle - Class in edu.duke.cs.osprey.structure.analysis
- MeasurementLibrary.TetrahedralOutOfPlaneAngles2 - Class in edu.duke.cs.osprey.structure.analysis
-
out-of-plane angle of the ith d atom, sorted by out-of-plane angle distance to -90 degrees (eg CH2 groups)
- MeasurementLibrary.TetrahedralSystem - Class in edu.duke.cs.osprey.structure.analysis
- MeasurementLibrary.TetrahedralSystems2 - Class in edu.duke.cs.osprey.structure.analysis
- measurements - Variable in class edu.duke.cs.osprey.structure.analysis.TemplateChooser.MeasuredRes
- measureResidues(File, Collection<String>) - Static method in class edu.duke.cs.osprey.structure.analysis.TemplateChooser
- measureResidues(File, Collection<String>, Predicate<Residue>) - Static method in class edu.duke.cs.osprey.structure.analysis.TemplateChooser
- medoid() - Method in class edu.duke.cs.osprey.structure.analysis.ClusterS1
- member - Variable in class edu.duke.cs.osprey.coffee.directions.Directions
- member - Variable in class edu.duke.cs.osprey.coffee.nodedb.Neighbors
- member - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeDB.Builder
- member - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
- member - Variable in class edu.duke.cs.osprey.coffee.seqdb.SeqDB.Builder
- member - Variable in class edu.duke.cs.osprey.coffee.seqdb.SeqDB
- Member(Parallelism) - Constructor for class edu.duke.cs.osprey.parallelism.Cluster.Member
- memBytes - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
- memBytes - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices
- memFree - Variable in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuInfo
- MemInfo(MemoryPoolMXBean) - Constructor for class edu.duke.cs.osprey.tools.JvmMem.MemInfo
- MemInfo(String, long, long, long) - Constructor for class edu.duke.cs.osprey.tools.JvmMem.MemInfo
- MemInfo(String, List<MemoryPoolMXBean>) - Constructor for class edu.duke.cs.osprey.tools.JvmMem.MemInfo
- memoizePosInHot(int...) - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- MemoryBuffer - Class in edu.duke.cs.osprey.gpu
-
A tool to easily write primitive types to a MemorySegment, without the limitations of NIO ByteBuffers and without exposing the incubating jdk.incubator.foreign module to API clients.
- MemoryBuffer(long) - Constructor for class edu.duke.cs.osprey.gpu.MemoryBuffer
- memTotal - Variable in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuInfo
- mergeChildren(KStarTreeNode, int, int[]) - Static method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeManipulator
- mergeResiduePositions(int...) - Method in class edu.duke.cs.osprey.kstar.KSSearchProblem
- mergeSubtreeIntoOneLevel(KStarTreeNode, int, int[]) - Static method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeManipulator
- mergeSubtreeLevels(KStarTreeNode, int) - Static method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeManipulator
- MessageVars - Class in edu.duke.cs.osprey.astar.conf.scoring.mplp
- MessageVars(RCs, ConfIndex) - Constructor for class edu.duke.cs.osprey.astar.conf.scoring.mplp.MessageVars
- MessageVars(RCs, ConfIndex, boolean) - Constructor for class edu.duke.cs.osprey.astar.conf.scoring.mplp.MessageVars
- Middle - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.DominantBaseline
- Middle - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.TextAnchor
- min - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Dof
- min - Variable in class edu.duke.cs.osprey.lute.LUTE.Errors
- min - Variable in class edu.duke.cs.osprey.tools.IntRange
-
inclusive
- min - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot.Interval
- min - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Axis
- min - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Intervals.Interval
- min() - Method in interface edu.duke.cs.osprey.confspace.compiled.DegreeOfFreedom
- min() - Method in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Dof
- min() - Method in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Dof
- min() - Method in class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel.Interval
- min(double) - Method in class edu.duke.cs.osprey.tools.BigMath
- min(long) - Method in class edu.duke.cs.osprey.tools.BigMath
- min(BigExp) - Method in class edu.duke.cs.osprey.tools.BigExp
- min(BigExp) - Method in class edu.duke.cs.osprey.tools.BigMath
- min(BigDecimal) - Method in class edu.duke.cs.osprey.tools.BigMath
- min(BigInteger) - Method in class edu.duke.cs.osprey.tools.BigMath
- MIN_VALUE - Static variable in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized
- minAngleRadians - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle
- minCapacity - Variable in class edu.duke.cs.osprey.astar.conf.ConfSearchCache
- minContE(int[]) - Method in class edu.duke.cs.osprey.ematrix.epic.NewEPICMatrix
- minDegrees - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Description
- mindex - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Position
-
index in the mutable positions list, or -1 if not there
- minFreeEnergyWidth - Variable in class edu.duke.cs.osprey.sofea.MinLMFE
-
The best desired precision for a state free energy.
- minFreeEnergyWidth - Variable in class edu.duke.cs.osprey.sofea.SequenceLMFE
-
The best desired precision for a state free energy.
- MINIMIZATION_FACTOR - Static variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- MinimizationJob(int[], List<PosInter>) - Constructor for class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator.MinimizationJob
- MinimizationPlayground - Class in edu.duke.cs.osprey.tests
-
Playing with minimization
- MinimizationPlayground() - Constructor for class edu.duke.cs.osprey.tests.MinimizationPlayground
- minimize - Variable in class edu.duke.cs.osprey.ematrix.compiled.EmatCalculator
- minimize - Variable in class edu.duke.cs.osprey.ematrix.compiled.ErefCalculator
- minimize - Variable in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- minimize() - Method in interface edu.duke.cs.osprey.minimization.Minimizer
- minimize(int[], List<PosInter>) - Method in interface edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator
-
Minimize the conformation, using the provided interactions.
- minimize(int[], List<PosInter>) - Method in class edu.duke.cs.osprey.energy.compiled.CPUConfEnergyCalculator
- minimize(int[], List<PosInter>) - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- minimize(int[], List<PosInter>) - Method in class edu.duke.cs.osprey.energy.compiled.NativeConfEnergyCalculator
- minimize(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.minimization.ConfMinimizer
-
NOTE: don't call this in a loop, you'll loose all the parallelism but it's here if you need one-off minimizations
- minimize(List<ConfSearch.ScoredConf>) - Method in class edu.duke.cs.osprey.minimization.ConfMinimizer
- Minimize - Enum constant in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
- minimizeAsync(ConfSearch.ScoredConf, ConfMinimizer.Async.Listener) - Method in class edu.duke.cs.osprey.minimization.ConfMinimizer.Async
- minimizeCoords(int, List<int[]>) - Method in class edu.duke.cs.osprey.coffee.NodeProcessor
- minimized - Variable in class edu.duke.cs.osprey.coffee.NodeStats.Values
- minimized() - Method in class edu.duke.cs.osprey.coffee.NodeStats.ForThread
- Minimized - Enum constant in enum class edu.duke.cs.osprey.multistatekstar.KStarScore.KStarScoreType
- Minimized - Enum constant in enum class edu.duke.cs.osprey.multistatekstar.KStarScore.PartitionFunctionType
- minimizedEnergy(int[]) - Method in class edu.duke.cs.osprey.confspace.SearchProblem
- minimizedLeaf - Enum constant in enum class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Type
- MinimizedLowerBound - Enum constant in enum class edu.duke.cs.osprey.multistatekstar.KStarScore.KStarScoreType
- MinimizedUpperBound - Enum constant in enum class edu.duke.cs.osprey.multistatekstar.KStarScore.KStarScoreType
- minimizeEnergies(List<ConfEnergyCalculator.MinimizationJob>) - Method in interface edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator
-
Calculate the minimized enegries of a batch of conformations and interactions.
- minimizeEnergies(List<ConfEnergyCalculator.MinimizationJob>) - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- minimizeEnergies(List<ConfEnergyCalculator.MinimizationJob>, CudaConfEnergyCalculator.CheckedOutStream) - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- minimizeEnergy(int[]) - Method in class edu.duke.cs.osprey.ematrix.epic.NewEPICMatrix
- minimizeEnergy(int[], EnergyFunction, String) - Method in class edu.duke.cs.osprey.confspace.ConfSpace
- minimizeEnergy(int[], List<PosInter>) - Method in interface edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator
-
Calculate the minimized energy of the conformation, using the provided interactions.
- minimizeEnergy(int[], List<PosInter>) - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- minimizeEnergy(int[], List<PosInter>) - Method in class edu.duke.cs.osprey.energy.compiled.NativeConfEnergyCalculator
- minimizeEnergy(ConfSearch.ScoredConf, List<PosInter>) - Method in interface edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator
- minimizeEnergy(RCTuple, boolean) - Method in class edu.duke.cs.osprey.ematrix.epic.EPICMatrix
- minimizeEnergy(RCTuple, boolean) - Method in class edu.duke.cs.osprey.ematrix.epic.NewEPICMatrix
- minimizeFrom(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ResidueCudaCCDMinimizer
- minimizeFrom(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.minimization.CCDMinimizer
- minimizeFrom(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.minimization.CudaCCDMinimizer
- minimizeFrom(DoubleMatrix1D) - Method in interface edu.duke.cs.osprey.minimization.Minimizer
- minimizeFrom(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.minimization.SimpleCCDMinimizer
- minimizeFromCenter() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ResidueCudaCCDMinimizer
- minimizeFromCenter() - Method in class edu.duke.cs.osprey.minimization.CCDMinimizer
- minimizeFromCenter() - Method in class edu.duke.cs.osprey.minimization.CudaCCDMinimizer
- minimizeFromCenter() - Method in interface edu.duke.cs.osprey.minimization.Minimizer
- minimizeFromCenter() - Method in class edu.duke.cs.osprey.minimization.SimpleCCDMinimizer
- minimizeFromCurPoint() - Method in class edu.duke.cs.osprey.minimization.CCDMinimizer
- Minimizer - Interface in edu.duke.cs.osprey.minimization
- Minimizer.NeedsCleanup - Interface in edu.duke.cs.osprey.minimization
- Minimizer.Result - Class in edu.duke.cs.osprey.minimization
- Minimizer.Reusable - Interface in edu.duke.cs.osprey.minimization
- Minimizer.Tools - Class in edu.duke.cs.osprey.minimization
- minimizers - Variable in class edu.duke.cs.osprey.energy.EnergyCalculator.Type.Context
- minimizeSync(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.minimization.ConfMinimizer.Async
- minimizingConfEcalc - Variable in class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceInfo
- MinimizingConfEnergyCalculator - Class in edu.duke.cs.osprey.gmec
-
Deprecated.
- MinimizingConfEnergyCalculator(ConfMinimizer) - Constructor for class edu.duke.cs.osprey.gmec.MinimizingConfEnergyCalculator
-
Deprecated.
- MinimizingConfEnergyCalculator.ConfPostProcessor - Interface in edu.duke.cs.osprey.gmec
-
Deprecated.
- minimizingEcalc - Variable in class edu.duke.cs.osprey.markstar.MARKStar
-
Calculates the minimized energy for a molecule
- minimizingEmat - Variable in class edu.duke.cs.osprey.kstar.MSKStar.Builder
- minimizingEmat - Variable in class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceInfo
- MinLMFE - Class in edu.duke.cs.osprey.sofea
-
Finishes SOFEA computation when we've found the best K sequences that minimize an LMFE objective function.
- MinLMFE(MultiStateConfSpace.LMFE, int, double) - Constructor for class edu.duke.cs.osprey.sofea.MinLMFE
- MinLMFE.TopSequences - Class in edu.duke.cs.osprey.sofea
- minNumConfTrees - Variable in class edu.duke.cs.osprey.gmec.Comets
- minNumConfTrees - Variable in class edu.duke.cs.osprey.kstar.MSKStar
- minOrSet(double) - Method in class edu.duke.cs.osprey.tools.BigMath
- minOrSet(long) - Method in class edu.duke.cs.osprey.tools.BigMath
- minOrSet(BigExp) - Method in class edu.duke.cs.osprey.tools.BigMath
- minOrSet(BigDecimal) - Method in class edu.duke.cs.osprey.tools.BigMath
- minOrSet(BigInteger) - Method in class edu.duke.cs.osprey.tools.BigMath
- minOverlapBadClash - Variable in class edu.duke.cs.osprey.structure.Probe
- minOverlapCloseContact - Variable in class edu.duke.cs.osprey.structure.Probe
- minOverlapWideContact - Variable in class edu.duke.cs.osprey.structure.Probe
- minPartialConfs - Variable in class edu.duke.cs.osprey.astar.ConfTree
- minPartialConfs - Variable in class edu.duke.cs.osprey.ematrix.epic.EPICSettings
- minRectHeight - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Intervals
- minScore() - Method in class edu.duke.cs.osprey.coffee.directors.BestSet
- minValues() - Method in class edu.duke.cs.osprey.coffee.directors.BestSet
- MinVolEllipse - Class in edu.duke.cs.osprey.tools
- MinVolEllipse(DoubleMatrix2D, double, boolean) - Constructor for class edu.duke.cs.osprey.tools.MinVolEllipse
- MinVolEllipse(DoubleMatrix2D, double, MinVolEllipse[], MinVolEllipse) - Constructor for class edu.duke.cs.osprey.tools.MinVolEllipse
- mm - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.LengthUnit
- mode - Variable in class edu.duke.cs.osprey.structure.analysis.ClusterR1.Stats
- mode - Variable in class edu.duke.cs.osprey.structure.analysis.ClusterS1.Stats
- mode(SmallAngleVoxel.Interval, int) - Method in class edu.duke.cs.osprey.structure.analysis.ClusterS1
-
use a histogram with a certain number of buckets to find the mode
- mode(MathTools.DoubleBounds, int) - Method in class edu.duke.cs.osprey.structure.analysis.ClusterR1
-
use a histogram with a certain number of buckets to find the mode
- modelAtomNumber - Variable in class edu.duke.cs.osprey.structure.Atom
- modGet(List<T>, int) - Static method in class edu.duke.cs.osprey.tools.resultdoc.Plot
-
get the i-th item from the list, using modular arithmetic
- modifiedPosIndices - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation
- modifiedPosIndices() - Method in interface edu.duke.cs.osprey.confspace.compiled.DegreeOfFreedom
-
which design positions are modified by this DoF?
- modifiedPosIndices() - Method in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Dof
- modifiedPosIndices() - Method in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Dof
- modify(Residue) - Method in interface edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf.PostTemplateModifier
- modifyNBParams(Atom, AtomNeighbors.Type, ForcefieldParams.NBParams) - Method in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.Forcefield
- modp(SturmSolver.poly, SturmSolver.poly, SturmSolver.poly) - Method in class edu.duke.cs.osprey.dof.deeper.perts.SturmSolver
- mol - Variable in class edu.duke.cs.osprey.confspace.ParametricMolecule
-
The molecule manipulated by the degrees of freedom.
- mol - Variable in class edu.duke.cs.osprey.confspace.Strand
-
The molecule this strand represents
- molec - Variable in class edu.duke.cs.osprey.structure.Residue
-
The molecule the residue's in
- molecule - Variable in class edu.duke.cs.osprey.design.models.MoleculeDesign
- Molecule - Class in edu.duke.cs.osprey.structure
-
A molecule is a list of
Residueand their alternates - Molecule() - Constructor for class edu.duke.cs.osprey.structure.Molecule
- Molecule(Molecule) - Constructor for class edu.duke.cs.osprey.structure.Molecule
- Molecule(Molecule, boolean) - Constructor for class edu.duke.cs.osprey.structure.Molecule
- Molecule(Residues) - Constructor for class edu.duke.cs.osprey.structure.Molecule
- MoleculeDesign - Class in edu.duke.cs.osprey.design.models
- MoleculeDesign() - Constructor for class edu.duke.cs.osprey.design.models.MoleculeDesign
- MoleculeDto - Class in edu.duke.cs.osprey.design.models
- MoleculeDto() - Constructor for class edu.duke.cs.osprey.design.models.MoleculeDto
- MoleculeModifierAndScorer - Class in edu.duke.cs.osprey.minimization
- MoleculeModifierAndScorer(EnergyFunction, DoubleMatrix1D[], Molecule, ArrayList<DegreeOfFreedom>) - Constructor for class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- MoleculeModifierAndScorer(EnergyFunction, ConfSpace) - Constructor for class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- MoleculeModifierAndScorer(EnergyFunction, ConfSpace, RCTuple) - Constructor for class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- MoleculeModifierAndScorer(EnergyFunction, ConfSpace, RCTuple, ParameterizedMoleculeCopy) - Constructor for class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- MoleculeModifierAndScorer(MoleculeObjectiveFunction) - Constructor for class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
-
Deprecated.
- MoleculeObjectiveFunction - Class in edu.duke.cs.osprey.minimization
- MoleculeObjectiveFunction(ParametricMolecule, EnergyFunction) - Constructor for class edu.duke.cs.osprey.minimization.MoleculeObjectiveFunction
- MoleculeObjectiveFunction(MoleculeModifierAndScorer) - Constructor for class edu.duke.cs.osprey.minimization.MoleculeObjectiveFunction
-
Deprecated.
- moli - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle
- MolInfo(String, String, int) - Constructor for class edu.duke.cs.osprey.confspace.compiled.ConfSpace.MolInfo
- molInfos - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- monitorMemoryToStdout(Duration, boolean) - Static method in class edu.duke.cs.osprey.tools.JvmMem
-
Launches a thread that periodically reports memory usage statistics to stdout.
- more - Variable in class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel.Interval
- motions - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Conf
- motions - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.MolInfo
- MoveableStrand - Class in edu.duke.cs.osprey.dof
-
This is a subportion of the molecule that can move as a rigid body there may be other (e.g., dihedral) motions on top of that
- MoveableStrand() - Constructor for class edu.duke.cs.osprey.dof.MoveableStrand
- MoveableStrand(ArrayList<Residue>) - Constructor for class edu.duke.cs.osprey.dof.MoveableStrand
- moveableUbStateTermini(int) - Method in class edu.duke.cs.osprey.multistatekstar.MSConfigFileParser
- moveSidechain(Residue, RigidBodyMotion) - Static method in class edu.duke.cs.osprey.dof.deeper.SidechainIdealizer
- MPIMaster - Class in edu.duke.cs.osprey.handlempi
- MPISlaveTask - Interface in edu.duke.cs.osprey.handlempi
- MPLPBuilder() - Constructor for class edu.duke.cs.osprey.astar.conf.ConfAStarTree.MPLPBuilder
- MPLPBuilder() - Static method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree
- MPLPPairwiseHScorer - Class in edu.duke.cs.osprey.astar.conf.scoring
- MPLPPairwiseHScorer(MPLPUpdater, EnergyMatrix, int, double) - Constructor for class edu.duke.cs.osprey.astar.conf.scoring.MPLPPairwiseHScorer
- MPLPUpdater - Interface in edu.duke.cs.osprey.astar.conf.scoring.mplp
- MSConfigFileParser - Class in edu.duke.cs.osprey.multistatekstar
- MSConfigFileParser() - Constructor for class edu.duke.cs.osprey.multistatekstar.MSConfigFileParser
- MSConfigFileParser(String[]) - Constructor for class edu.duke.cs.osprey.multistatekstar.MSConfigFileParser
- MSConfigFileParser(String[], boolean) - Constructor for class edu.duke.cs.osprey.multistatekstar.MSConfigFileParser
- MSKStar - Class in edu.duke.cs.osprey.kstar
-
basically COMETS, but with thermodynamic ensembles at least, that's the goal
- MSKStar.Builder - Class in edu.duke.cs.osprey.kstar
- MSKStar.LMFE - Class in edu.duke.cs.osprey.kstar
-
A Linear Multi-state Free Energy (i.e., a weighted combination of state free energies)
- MSKStar.LMFE.Builder - Class in edu.duke.cs.osprey.kstar
- MSKStar.SequenceInfo - Class in edu.duke.cs.osprey.kstar
- MSKStar.State - Class in edu.duke.cs.osprey.kstar
-
A state for a multi-state design (e.g., an unbound state, or a complex state)
- MSKStar.State.InitException - Exception in edu.duke.cs.osprey.kstar
- MSKStar.WeightedState - Class in edu.duke.cs.osprey.kstar
- MSKStarDoer - Class in edu.duke.cs.osprey.control
- MSKStarDoer(ConfigFileParser) - Constructor for class edu.duke.cs.osprey.control.MSKStarDoer
- MSKStarFactory - Class in edu.duke.cs.osprey.multistatekstar
- MSKStarFactory() - Constructor for class edu.duke.cs.osprey.multistatekstar.MSKStarFactory
- MSKStarNode - Class in edu.duke.cs.osprey.multistatekstar
- MSKStarNode(KStarScore[], KStarScore[]) - Constructor for class edu.duke.cs.osprey.multistatekstar.MSKStarNode
- MSKStarSettings - Class in edu.duke.cs.osprey.multistatekstar
- MSKStarSettings() - Constructor for class edu.duke.cs.osprey.multistatekstar.MSKStarSettings
- MSKStarTree - Class in edu.duke.cs.osprey.multistatekstar
- MSKStarTree(int, int, int, int, LMB, LMB[], LMB[][], ArrayList<ArrayList<ArrayList<Integer>>>, ArrayList<ArrayList<ArrayList<ArrayList<String>>>>, ArrayList<String[]>, SearchProblem[][], SearchProblem[][], GMECConfEnergyCalculator.Async[][], GMECConfEnergyCalculator.Async[][], ParamSet, MSConfigFileParser[]) - Constructor for class edu.duke.cs.osprey.multistatekstar.MSKStarTree
- MSSearchProblem - Class in edu.duke.cs.osprey.multistatekstar
- MSSearchProblem(SearchProblem, MSSearchSettings) - Constructor for class edu.duke.cs.osprey.multistatekstar.MSSearchProblem
- MSSearchSettings - Class in edu.duke.cs.osprey.multistatekstar
- MSSearchSettings() - Constructor for class edu.duke.cs.osprey.multistatekstar.MSSearchSettings
- mult(double) - Method in class edu.duke.cs.osprey.tools.BigExp
- mult(double) - Method in class edu.duke.cs.osprey.tools.BigMath
- mult(int) - Method in class edu.duke.cs.osprey.tools.BigExp
- mult(long) - Method in class edu.duke.cs.osprey.tools.BigExp
- mult(long) - Method in class edu.duke.cs.osprey.tools.BigMath
- mult(BigExp) - Method in class edu.duke.cs.osprey.tools.BigExp
- mult(BigExp) - Method in class edu.duke.cs.osprey.tools.BigMath
- mult(BigDecimal) - Method in class edu.duke.cs.osprey.tools.BigMath
- mult(BigInteger) - Method in class edu.duke.cs.osprey.tools.BigMath
- multiply(RotationMatrix) - Method in class edu.duke.cs.osprey.tools.RotationMatrix
- multiply(BigDecimal) - Method in class edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal
- multiply(BigDecimal, MathContext) - Method in class edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal
- MultiSequenceConfTree - Class in edu.duke.cs.osprey.multistatekstar
- MultiSequenceConfTree(MSSearchProblem, EnergyMatrix, PruningMatrix) - Constructor for class edu.duke.cs.osprey.multistatekstar.MultiSequenceConfTree
- MultiSequenceNode(Sequence) - Constructor for class edu.duke.cs.osprey.kstar.BBKStar.MultiSequenceNode
- MultiSequenceNode(Sequence, ConfDB.DBs) - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.MultiSequenceNode
- MultiSplitter(ConfSearch) - Constructor for class edu.duke.cs.osprey.confspace.ConfSearch.MultiSplitter
-
Create a splitter for a conformation search
- MultiStateConfSpace - Class in edu.duke.cs.osprey.confspace
-
A composite conformation space composed of other conformation spaces.
- MultiStateConfSpace.Builder - Class in edu.duke.cs.osprey.confspace
- MultiStateConfSpace.LMFE - Class in edu.duke.cs.osprey.confspace
-
A linear multi-state free energy.
- MultiStateConfSpace.LMFEBuilder - Class in edu.duke.cs.osprey.confspace
- MultiStateConfSpace.LMFECalculator - Class in edu.duke.cs.osprey.confspace
- MultiStateConfSpace.State - Class in edu.duke.cs.osprey.confspace
- MultiStateKStar - Enum constant in enum class edu.duke.cs.osprey.control.Main.Command
- MultiTermEnergyFunction - Class in edu.duke.cs.osprey.energy
- MultiTermEnergyFunction() - Constructor for class edu.duke.cs.osprey.energy.MultiTermEnergyFunction
- multOrSet(double) - Method in class edu.duke.cs.osprey.tools.BigMath
- multOrSet(long) - Method in class edu.duke.cs.osprey.tools.BigMath
- multOrSet(BigExp) - Method in class edu.duke.cs.osprey.tools.BigMath
- multOrSet(BigDecimal) - Method in class edu.duke.cs.osprey.tools.BigMath
- multOrSet(BigInteger) - Method in class edu.duke.cs.osprey.tools.BigMath
- mutability - Variable in class edu.duke.cs.osprey.design.models.ResidueModifier
- mutableIndexOrThrow() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Position
- mutablePositions - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
The subset of design positions with allowed mutations
- mutableType - Variable in class edu.duke.cs.osprey.astar.seq.SeqAStarTree
- mutableType - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- MutAlignment - Class in edu.duke.cs.osprey.dof
- MutAlignment(ResidueTemplate, ResidueTemplate) - Constructor for class edu.duke.cs.osprey.dof.MutAlignment
- MutAlignmentCache - Class in edu.duke.cs.osprey.dof
-
A thread-safe cache for MutAlignment instances, which are relatively expensive to compute
- MutAlignmentCache() - Constructor for class edu.duke.cs.osprey.dof.MutAlignmentCache
- mutateTo(String) - Method in class edu.duke.cs.osprey.dof.ResidueTypeDOF
- mutationName() - Method in class edu.duke.cs.osprey.confspace.SeqSpace.ResType
-
Returns the residue type name in lower case if wild-type, upper case if mutation.
- mutations - Variable in class edu.duke.cs.osprey.confspace.SeqSpace.Position
- mutDOFs - Variable in class edu.duke.cs.osprey.confspace.ConfSpace
- mutFile - Variable in class edu.duke.cs.osprey.paste.Paste.Settings
- mutRes - Variable in class edu.duke.cs.osprey.multistatekstar.MSSearchSettings
N
- NaiveTraditionalPairwiseHScorer - Class in edu.duke.cs.osprey.astar.conf.scoring
- NaiveTraditionalPairwiseHScorer(EnergyMatrix) - Constructor for class edu.duke.cs.osprey.astar.conf.scoring.NaiveTraditionalPairwiseHScorer
- name - Variable in class edu.duke.cs.osprey.coffee.ClusterMember
- name - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.MolInfo
- name - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- name - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Pos
- name - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Dof
- name - Variable in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.State
- name - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- name - Variable in class edu.duke.cs.osprey.confspace.SeqSpace.ResType
- name - Variable in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuInfo
- name - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.State
-
A name for the state
- name - Variable in class edu.duke.cs.osprey.gmec.Comets.State
-
A name for the state
- name - Variable in class edu.duke.cs.osprey.gpu.Structs.Field
- name - Variable in class edu.duke.cs.osprey.kstar.MSKStar.State
-
A name for the state
- name - Variable in class edu.duke.cs.osprey.parallelism.BottleneckThread
- name - Variable in class edu.duke.cs.osprey.parallelism.Cluster
- name - Variable in class edu.duke.cs.osprey.parallelism.RateLimitedThread
- name - Variable in class edu.duke.cs.osprey.restypes.ResidueTemplate
-
The three letter code, e.g.
- name - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.Measurement
- name - Variable in class edu.duke.cs.osprey.structure.Atom
- name - Variable in class edu.duke.cs.osprey.structure.Molecule
- name - Variable in class edu.duke.cs.osprey.structure.Probe.AtomInfo
- name - Variable in class edu.duke.cs.osprey.tools.JvmMem.MemInfo
- name - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot.Series
- name - Variable in class edu.duke.cs.osprey.tools.SVG.StyleClass
- name() - Method in interface edu.duke.cs.osprey.confspace.compiled.DegreeOfFreedom
- name() - Method in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Dof
- name() - Method in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Dof
- name() - Method in class edu.duke.cs.osprey.gpu.Structs.Field
- name(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- name(int) - Method in interface edu.duke.cs.osprey.confspace.ConfSpaceIteration
-
returns the name of the position
- name(int) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- name2PF - Variable in class edu.duke.cs.osprey.kstar.KSAbstract
- name2SP - Variable in class edu.duke.cs.osprey.kstar.KSAbstract
- nameToIndexMap(List<DegreeOfFreedom>) - Static method in class edu.duke.cs.osprey.dof.DegreeOfFreedom
- NaN - Enum constant in enum class edu.duke.cs.osprey.sofea.BigDecimalIO.Type
- NAryRCSplitter - Class in edu.duke.cs.osprey.partcr.splitters
- NAryRCSplitter() - Constructor for class edu.duke.cs.osprey.partcr.splitters.NAryRCSplitter
- NativeConfEnergyCalculator - Class in edu.duke.cs.osprey.energy.compiled
-
A reference implementation of a conformation minimizer and energy calculator in C++, rather than Java.
- NativeConfEnergyCalculator(ConfSpace, Structs.Precision) - Constructor for class edu.duke.cs.osprey.energy.compiled.NativeConfEnergyCalculator
- nBodyCalc() - Method in class edu.duke.cs.osprey.ematrix.TermECalculator
- NBParams() - Constructor for class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.NBParams
- nearbyResidueModifiers(Residue, Molecule, double) - Static method in class edu.duke.cs.osprey.design.commands.CommandBindingAffinity
- nearbyResidues(Residue, Molecule, double) - Static method in class edu.duke.cs.osprey.design.commands.CommandBindingAffinity
- needsCleanup - Variable in class edu.duke.cs.osprey.energy.EnergyCalculator.Type.Context
- negate() - Method in class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- negate() - Method in class edu.duke.cs.osprey.tools.BigExp
- negate() - Method in class edu.duke.cs.osprey.tools.BigMath
- NegatedEnergyMatrix - Class in edu.duke.cs.osprey.ematrix
- NegatedEnergyMatrix(SimpleConfSpace, EnergyMatrix) - Constructor for class edu.duke.cs.osprey.ematrix.NegatedEnergyMatrix
- negatedhscorer - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound.ScoreContext
- Negative - Enum constant in enum class edu.duke.cs.osprey.structure.Probe.AtomFlag
- NegInf - Enum constant in enum class edu.duke.cs.osprey.sofea.BigDecimalIO.Type
- negligableFreeEnergy - Variable in class edu.duke.cs.osprey.sofea.Sofea
- NeighborInfo(Address, T) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.Neighbors.NeighborInfo
- Neighbors - Class in edu.duke.cs.osprey.coffee.nodedb
-
Tracks statistics about other members in the cluster.
- Neighbors(MultiStateConfSpace, ClusterMember) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.Neighbors
- Neighbors.NeighborInfo<T> - Class in edu.duke.cs.osprey.coffee.nodedb
- NewCOMETS - Class in edu.duke.cs.osprey.tests
- NewCOMETS() - Constructor for class edu.duke.cs.osprey.tests.NewCOMETS
- NewCOMETSDoer - Class in edu.duke.cs.osprey.astar.comets
-
This version of NewCOMETSDoer is intended to be usable via Python
- NewCOMETSDoer(SimpleConfSpace[], PrecomputedMatrices[], LME, LME[], ArrayList<ArrayList<Integer>>, ArrayList<ArrayList<String>>, int, String[], int, boolean, ConfEnergyCalculator[]) - Constructor for class edu.duke.cs.osprey.astar.comets.NewCOMETSDoer
- NewCOMETSTree - Class in edu.duke.cs.osprey.astar.comets
-
SimpleConfSpace/Python version of COMETSTree
- NewCOMETSTree(int, LME, LME[], ArrayList<ArrayList<String>>, int, String[], int, SimpleConfSpace[], PrecomputedMatrices[], ArrayList<ArrayList<Integer>>, boolean, ConfEnergyCalculator[]) - Constructor for class edu.duke.cs.osprey.astar.comets.NewCOMETSTree
- NewConfETupleExpander - Class in edu.duke.cs.osprey.tupexp
-
A TupleExpander that is based on minimized conformational energies like ConfETupleExpander, but uses the SimpleConfSpace/ConfEnergyCalculator framework instead of SearchProblem
- NewConfETupleExpander(SimpleConfSpace, double, LUTESettings, ConfEnergyCalculator, PruningMatrix) - Constructor for class edu.duke.cs.osprey.tupexp.NewConfETupleExpander
- newEPICMat - Variable in class edu.duke.cs.osprey.astar.ConfTree
- NewEPICMatrix - Class in edu.duke.cs.osprey.ematrix.epic
-
SimpleConfSpace/MoleculeObjectiveFunction version of EPICMatrix also made to provide full EPIC energies instead of E-mtx lower bounds + EPIC cont part, thus avoiding error if the minimizer found different minima when computing the E mtx and the EPIC mtx
- NewEPICMatrix(SimpleConfSpace, double) - Constructor for class edu.duke.cs.osprey.ematrix.epic.NewEPICMatrix
- NewEPICMatrixCalculator - Class in edu.duke.cs.osprey.ematrix
- NewEPICMatrixCalculator(SimpleConfSpace, ConfEnergyCalculator, PruningMatrix, EPICSettings) - Constructor for class edu.duke.cs.osprey.ematrix.NewEPICMatrixCalculator
- NewPruner - Class in edu.duke.cs.osprey.pruning
-
A version of Pruner that works with PrecomputedMatrices instead of SearchProblem Goes with NewPruningControl
- NewPruner(PrecomputedMatrices, boolean, double, double, boolean, boolean) - Constructor for class edu.duke.cs.osprey.pruning.NewPruner
- NewPruner(PrecomputedMatrices, PruningMatrix, boolean, double, double, boolean, boolean) - Constructor for class edu.duke.cs.osprey.pruning.NewPruner
- NewPruningControl - Class in edu.duke.cs.osprey.pruning
- NewPruningControl(PrecomputedMatrices, double, boolean, double, int, boolean, boolean, boolean, boolean, boolean, double) - Constructor for class edu.duke.cs.osprey.pruning.NewPruningControl
- NewPruningControl.ReportMode - Enum Class in edu.duke.cs.osprey.pruning
- newToOld(int) - Method in class edu.duke.cs.osprey.confspace.RCIndexMap
- next() - Method in class edu.duke.cs.osprey.tools.FileTools.LineIterator
- nextConf() - Method in class edu.duke.cs.osprey.astar.AStarTree
- nextConf() - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree
- nextConf() - Method in class edu.duke.cs.osprey.astar.conf.ConfSearchCache.Entry
- nextConf() - Method in class edu.duke.cs.osprey.confspace.ConfSearch.MultiSplitter.Stream
- nextConf() - Method in interface edu.duke.cs.osprey.confspace.ConfSearch
-
Get the conformation in the conformation space with the next lowest score.
- nextConfs(double) - Method in class edu.duke.cs.osprey.astar.AStarTree
- nextConfs(double) - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree
- nextConfs(double) - Method in interface edu.duke.cs.osprey.confspace.ConfSearch
-
Get the next conformations in the conformation space with scores up to maxEnergy.
- nextConfs(int) - Method in interface edu.duke.cs.osprey.confspace.ConfSearch
-
Get the next `num` conformations in the conformation space
- nextLeafNode() - Method in class edu.duke.cs.osprey.astar.seq.SeqAStarTree
- nextLeafNodes(double) - Method in class edu.duke.cs.osprey.astar.AStarTree
- nextLevelToExpand(T) - Method in class edu.duke.cs.osprey.astar.ConfTree
- nextLowest - Variable in class edu.duke.cs.osprey.sofea.MinLMFE.TopSequences
- nextSample() - Method in class edu.duke.cs.osprey.voxq.IntraVoxelSampler
- nextSeq() - Method in class edu.duke.cs.osprey.multistatekstar.MSKStarTree
- nextSplitPosAssignments(int) - Method in class edu.duke.cs.osprey.multistatekstar.ResidueOrderStaticSequential
- nextWorks(int) - Method in class edu.duke.cs.osprey.coffee.ClusterMember.DynamicPartition
- NoBondingTemplate() - Constructor for class edu.duke.cs.osprey.restypes.InterResBondingTemplate.NoBondingTemplate
- NoChange - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.DominantBaseline
- NoContact - Enum constant in enum class edu.duke.cs.osprey.structure.Probe.Contact
- node - Variable in class edu.duke.cs.osprey.astar.conf.ConfIndex
- Node(int) - Constructor for class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- Node(int, int) - Constructor for class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- Node(int, int[], BigExp, BigExp) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.NodeIndex.Node
- Node(NodeIndex.Node, BigExp) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.NodeIndex.Node
-
re-score a node
- nodedb - Variable in class edu.duke.cs.osprey.coffee.NodeProcessor
- NodeDB - Class in edu.duke.cs.osprey.coffee.nodedb
- NodeDB.Builder - Class in edu.duke.cs.osprey.coffee.nodedb
- nodeExpansionMethod - Static variable in class edu.duke.cs.osprey.kstar.impl.KSImplKAStar
- nodeId - Variable in class edu.duke.cs.osprey.parallelism.Cluster
- NodeIndex - Class in edu.duke.cs.osprey.coffee.nodedb
-
A specialization of FixedIndex for COFFEE nodes.
- NodeIndex(BlockStore, MultiStateConfSpace.State) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.NodeIndex
- NodeIndex.Node - Class in edu.duke.cs.osprey.coffee.nodedb
- NodeIndices - Class in edu.duke.cs.osprey.coffee.nodedb
- NodeIndices(MultiStateConfSpace, long) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.NodeIndices
- NodeIndices.BroadcastInfo - Class in edu.duke.cs.osprey.coffee.nodedb
- NodePerformance - Class in edu.duke.cs.osprey.coffee.nodedb
- NodePerformance(MultiStateConfSpace) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.NodePerformance
- NodeProcessor - Class in edu.duke.cs.osprey.coffee
- NodeProcessor(TaskExecutor, SeqDB, NodeDB, StateInfo[], boolean, Parallelism, Structs.Precision, Duration) - Constructor for class edu.duke.cs.osprey.coffee.NodeProcessor
- nodeScoringLog - Variable in class edu.duke.cs.osprey.coffee.Coffee
- nodesPerBlock() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex
- nodesPerBlock(int) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
- nodesPerBlock(int) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices
- nodeStats - Variable in class edu.duke.cs.osprey.coffee.NodeProcessor
- NodeStats - Class in edu.duke.cs.osprey.coffee
-
Collects statistics on node processing.
- NodeStats() - Constructor for class edu.duke.cs.osprey.coffee.NodeStats
- NodeStats.ForThread - Class in edu.duke.cs.osprey.coffee
-
A single thread's view of the stats.
- NodeStats.Report - Class in edu.duke.cs.osprey.coffee
- NodeStats.Reporter - Class in edu.duke.cs.osprey.coffee
-
Starts a thread to periodically report node stats
- NodeStats.Values - Class in edu.duke.cs.osprey.coffee
- nodeStatsReportingInterval - Variable in class edu.duke.cs.osprey.coffee.Coffee
- NodeTree - Class in edu.duke.cs.osprey.coffee.nodedb
- NodeTree(RCs) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.NodeTree
-
Make a node tree with no restriction on the number of simultaneous mutations.
- NodeTree(RCs, Integer) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.NodeTree
- NodeUpdater - Class in edu.duke.cs.osprey.astar.conf.scoring.mplp
- NodeUpdater() - Constructor for class edu.duke.cs.osprey.astar.conf.scoring.mplp.NodeUpdater
- NONBONDED - Enum constant in enum class edu.duke.cs.osprey.structure.AtomNeighbors.Type
- None - Enum constant in enum class edu.duke.cs.osprey.confspace.SimpleConfSpace.DofTypes
- None - Enum constant in enum class edu.duke.cs.osprey.pruning.NewPruningControl.ReportMode
- None - Enum constant in enum class edu.duke.cs.osprey.pruning.PruningControl.ReportMode
- None - Enum constant in enum class edu.duke.cs.osprey.structure.Probe.Attraction
- None() - Constructor for class edu.duke.cs.osprey.confspace.StrandFlex.None
- None() - Constructor for class edu.duke.cs.osprey.gpu.cuda.Kernel.SharedMemCalculator.None
- NonMutablePositionException(SimpleConfSpace.Position) - Constructor for exception edu.duke.cs.osprey.confspace.SimpleConfSpace.NonMutablePositionException
- nonTemplateResNames - Variable in class edu.duke.cs.osprey.confspace.Strand
-
Names of residues that couldn't be matched to templates
- Nop() - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Nop
- Nop() - Constructor for class edu.duke.cs.osprey.gmec.ConfPrinter.Nop
- Nop() - Constructor for class edu.duke.cs.osprey.kstar.KStarScoreWriter.Nop
- Nop() - Constructor for class edu.duke.cs.osprey.paste.PasteScoreWriter.Nop
- NOPApproximator - Class in edu.duke.cs.osprey.energy.approximation
- NOPApproximator(int) - Constructor for class edu.duke.cs.osprey.energy.approximation.NOPApproximator
- NOPAStarScorer - Class in edu.duke.cs.osprey.astar.conf.scoring
-
ie, a no-op
- NOPAStarScorer() - Constructor for class edu.duke.cs.osprey.astar.conf.scoring.NOPAStarScorer
- NopRCScorer - Class in edu.duke.cs.osprey.partcr.scorers
- NopRCScorer() - Constructor for class edu.duke.cs.osprey.partcr.scorers.NopRCScorer
- NOPSeqAStarScorer - Class in edu.duke.cs.osprey.astar.seq.scoring
-
ie, a no-op
- NOPSeqAStarScorer() - Constructor for class edu.duke.cs.osprey.astar.seq.scoring.NOPSeqAStarScorer
- NoResidue - Static variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- norm(double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- Normal - Enum constant in enum class edu.duke.cs.osprey.gpu.BufferTools.Type
- normalize - Variable in enum class edu.duke.cs.osprey.lute.LUTE.Fitter
- normalize(boolean) - Method in class edu.duke.cs.osprey.tools.BigExp
- normalize(double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- normalizeDegrees(double) - Static method in class edu.duke.cs.osprey.tools.Protractor
- normalizeInPlace(double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- normalizeMinusPiToPi(double) - Static method in class edu.duke.cs.osprey.tools.Protractor
- normalizeName(String) - Static method in enum class edu.duke.cs.osprey.control.Main.Command
- normalizeResNum(String) - Static method in class edu.duke.cs.osprey.structure.Residues
- normsq(double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- NoSuchConfSpaceException(Sequence) - Constructor for exception edu.duke.cs.osprey.kstar.SequenceAnalyzer.NoSuchConfSpaceException
- NoSuchTupleException(RCTuple, int[]) - Constructor for exception edu.duke.cs.osprey.confspace.TuplesIndex.NoSuchTupleException
- NOT_POSSIBLE - Enum constant in enum class edu.duke.cs.osprey.kstar.pfunc.PFAbstract.EApproxReached
- NOT_STABLE - Enum constant in enum class edu.duke.cs.osprey.kstar.pfunc.PFAbstract.EApproxReached
- NotAssigned - Static variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- NotAssigned - Static variable in class edu.duke.cs.osprey.externalMemory.EMConfAStarNode
- NOTSTARTED - Enum constant in enum class edu.duke.cs.osprey.kstar.pfunc.PFAbstract.RunState
- NoWindowOverlap - Enum constant in enum class edu.duke.cs.osprey.paste.PastePartitionFunction.Status
- NSpH - Static variable in class edu.duke.cs.osprey.tools.TimeFormatter
- NSpM - Static variable in class edu.duke.cs.osprey.tools.TimeFormatter
- NSpMS - Static variable in class edu.duke.cs.osprey.tools.TimeFormatter
- NSpS - Static variable in class edu.duke.cs.osprey.tools.TimeFormatter
- NSpUS - Static variable in class edu.duke.cs.osprey.tools.TimeFormatter
- NucleotideBondingTemplate() - Constructor for class edu.duke.cs.osprey.restypes.InterResBondingTemplate.NucleotideBondingTemplate
- Null - Enum constant in enum class edu.duke.cs.osprey.sofea.BigDecimalIO.Type
- nullify() - Method in class edu.duke.cs.osprey.kstar.KSPStarCalculator
- nullify() - Method in class edu.duke.cs.osprey.kstar.KSQPrimeCalculator
- NUM_MAX_MUT - Static variable in class edu.duke.cs.osprey.multistatekstar.MSKStarNode
- numActiveThreads - Variable in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized
- numAngles - Variable in class edu.duke.cs.osprey.structure.analysis.DegreesHistogram
- numAssigned - Variable in class edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode.Assignments
- numAsyncEngines - Variable in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuInfo
- numAtomPairs - Variable in class edu.duke.cs.osprey.energy.forcefield.ResPairCache.AtomPairInfo
- numAtoms - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Conf
- numberFormat - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- numberOfPhiPsiBins - Variable in class edu.duke.cs.osprey.restypes.ResidueTemplate
- NumberProp(String) - Constructor for class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.NumberProp
- NumberProp(String, String) - Constructor for class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.NumberProp
- numBestConfs - Variable in class edu.duke.cs.osprey.coffee.seqdb.SeqDB
- numBestConfs() - Method in interface edu.duke.cs.osprey.coffee.Coffee.Director
-
Return the number of best conformations to track for each state and sequence.
- numBestConfs() - Method in class edu.duke.cs.osprey.coffee.directors.AffinityDirector
- numBestConfs() - Method in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- numBestConfs() - Method in class edu.duke.cs.osprey.coffee.directors.PfuncDirector
- numBestSequences - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.Settings
- numBestSequences - Variable in class edu.duke.cs.osprey.kstar.BBKStar.Settings
- numBlocks - Variable in class edu.duke.cs.osprey.coffee.nodedb.BlockStore
- numBlocks - Variable in class edu.duke.cs.osprey.gpu.cuda.Kernel.Function
- numBytes - Variable in enum class edu.duke.cs.osprey.externalMemory.AssignmentsSerializer.Encoding
- numBytes - Variable in class edu.duke.cs.osprey.sofea.BigDecimalIO.Fixed
- numBytes - Variable in enum class edu.duke.cs.osprey.tools.IntEncoding
- NumBytes - Static variable in class edu.duke.cs.osprey.tools.BigExp
- numCalculations - Variable in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- numConf(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- numConf(int) - Method in interface edu.duke.cs.osprey.confspace.ConfSpaceIteration
-
returns the number of conformations at the given design position
- numConf(int) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- numConfByPos - Variable in class edu.duke.cs.osprey.confspace.TripleMatrix
- numConfDBReads - Variable in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- numConfs - Variable in class edu.duke.cs.osprey.design.commands.DesignFileDelegate
- numConfs - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Result
- numConfs - Variable in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Result
- numConfs - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- numConfs - Variable in class edu.duke.cs.osprey.paste.PastePartitionFunction.Result
- numConfs(PruningMatrix) - Method in class edu.duke.cs.osprey.kstar.KSSearchProblem
- numConfsBeforePruning - Variable in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- numConfsByPos() - Method in interface edu.duke.cs.osprey.confspace.ConfSpaceIteration
- numConfsEnergied - Variable in class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator
- numConfsEvaluated - Variable in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- numConfsPerBatch - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.Settings
- numConfsPerBatch - Variable in class edu.duke.cs.osprey.kstar.BBKStar.Settings
- numConfsScored - Variable in class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator
- numConfsToScore - Variable in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- numConfsWithin(double) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- numCPUs - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- numData - Variable in class edu.duke.cs.osprey.structure.analysis.Histogram
- numDefined - Variable in class edu.duke.cs.osprey.astar.conf.ConfIndex
- numDefined - Variable in class edu.duke.cs.osprey.astar.ConfTree
- numDihedrals - Variable in class edu.duke.cs.osprey.restypes.ResidueTemplate
- numDihedralsForResType(String) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
- numDims - Variable in class edu.duke.cs.osprey.ematrix.epic.FitParams
- numDofs - Variable in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- numDofs() - Method in class edu.duke.cs.osprey.dof.DofInfo
- numDofs() - Method in interface edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction.Approximator
- numDofs() - Method in class edu.duke.cs.osprey.energy.approximation.NOPApproximator
- numDofs() - Method in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- numDOFs - Variable in class edu.duke.cs.osprey.ematrix.epic.EPICFitter
- numEmatThreads - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- numEnergies - Variable in class edu.duke.cs.osprey.kstar.pfunc.PfuncSurface
- numEWAKStarSeqs - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- numExpanded - Variable in class edu.duke.cs.osprey.astar.AStarTree
- numFrag(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- numFrags - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Pos
- numFreeBlocks() - Method in class edu.duke.cs.osprey.coffee.nodedb.BlockStore
- numGpus - Variable in class edu.duke.cs.osprey.minimization.GpuConfMinimizer.Builder
- numGpus - Variable in class edu.duke.cs.osprey.parallelism.Parallelism
- numInternalNodesProcessed - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- numIter - Static variable in class edu.duke.cs.osprey.minimization.CCDMinimizer
- numLeavesCompleted - Static variable in class edu.duke.cs.osprey.kstar.KAStarNode
- numLeavesCreated - Static variable in class edu.duke.cs.osprey.kstar.KAStarNode
- numMembers() - Method in class edu.duke.cs.osprey.parallelism.Cluster
- numMutable - Variable in class edu.duke.cs.osprey.astar.seq.SeqAStarTree
- numMutable - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- numMutations - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings
- numNodes - Variable in class edu.duke.cs.osprey.parallelism.Cluster
- numNodesToRead() - Method in class edu.duke.cs.osprey.sofea.FringeDB
-
number of unread nodes left in this sweep
- numNodesToRead() - Method in class edu.duke.cs.osprey.sofea.FringeDB.Transaction
-
number of unread nodes left in this sweep
- numPairs() - Method in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- numPairsPerSingle(int) - Static method in class edu.duke.cs.osprey.tools.MathTools
- numParams() - Method in class edu.duke.cs.osprey.ematrix.epic.FitParams
- numParams() - Method in interface edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction.Approximator.Addable
- numParams() - Method in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- numPCParams - Variable in class edu.duke.cs.osprey.ematrix.epic.FitParams
- numPfConfs - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- numPos - Variable in class edu.duke.cs.osprey.astar.conf.ConfIndex
- numPos - Variable in class edu.duke.cs.osprey.astar.ConfTree
- numPos - Variable in class edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode.Assignments
- numPos - Variable in class edu.duke.cs.osprey.astar.seq.RTs
- numPos - Variable in class edu.duke.cs.osprey.confspace.ConfSpace
- numPos - Variable in class edu.duke.cs.osprey.confspace.TripleMatrix
- numPos() - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- numPos() - Method in interface edu.duke.cs.osprey.confspace.ConfSpaceIteration
-
returns the number of design positions in the conf space
- numPos() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- numPrecomputedPerAtomPair - Variable in class edu.duke.cs.osprey.energy.forcefield.ResPairCache.AtomPairInfo
- numProcessors - Variable in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuInfo
- numPruned - Variable in class edu.duke.cs.osprey.astar.AStarTree
- numQuadsPerPair(int) - Static method in class edu.duke.cs.osprey.tools.MathTools
- numQuadsPerSingle(int) - Static method in class edu.duke.cs.osprey.tools.MathTools
- numRotamers - Variable in class edu.duke.cs.osprey.restypes.ResidueTemplate
- numRotForResType(int, String, double, double) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
-
PGC 2015: Returns the number of rotamers for the specified residue type, for backbone dependent or backbone independent rotamers.
- numSamplesNeeded() - Method in class edu.duke.cs.osprey.ematrix.epic.FitParams
- numSamplesNeeded() - Method in class edu.duke.cs.osprey.voxq.VoxelsDeltaG
- numScoreBatches - Variable in class edu.duke.cs.osprey.kstar.pfunc.PfuncSurface
- numScoredConfs - Variable in class edu.duke.cs.osprey.kstar.pfunc.UpperBoundCalculator
- numScores - Variable in class edu.duke.cs.osprey.kstar.pfunc.PfuncSurface
- numSequencedStates - Variable in class edu.duke.cs.osprey.coffee.seqdb.SaveOperation
- numSequences - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.ScoreInfo
- numSequences - Variable in class edu.duke.cs.osprey.kstar.KStarScoreWriter.ScoreInfo
- numSequences - Variable in class edu.duke.cs.osprey.paste.PasteScoreWriter.ScoreInfo
- numSequences - Variable in class edu.duke.cs.osprey.sofea.MinLMFE
-
The number of best sequences to find.
- numSingles() - Method in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- numStates - Variable in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- numStatesAtLevel(int) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- numStaticAtoms - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- numStreams - Variable in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuStreams
- numStreams - Variable in class edu.duke.cs.osprey.energy.EnergyCalculator.Type.Context
- numStreams() - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- numStreamsPerGpu - Variable in class edu.duke.cs.osprey.minimization.GpuConfMinimizer.Builder
- numStreamsPerGpu - Variable in class edu.duke.cs.osprey.parallelism.Parallelism
- numThreads - Static variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- numThreads - Variable in class edu.duke.cs.osprey.minimization.CpuConfMinimizer.Builder
- numThreads - Variable in class edu.duke.cs.osprey.parallelism.Parallelism
- numTopConfsToSave - Static variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- numTopConfsToSave - Variable in class edu.duke.cs.osprey.multistatekstar.MSKStarSettings
- numTopOverallSeqs - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings
- numTopOverallSeqs - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- numTriples() - Method in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- numTriplesPerPair(int) - Static method in class edu.duke.cs.osprey.tools.MathTools
- numTriplesPerSingle(int) - Static method in class edu.duke.cs.osprey.tools.MathTools
- numTypesAt(int) - Method in class edu.duke.cs.osprey.astar.seq.RTs
- numUnassigned - Variable in class edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode.Assignments
- numUndefined - Variable in class edu.duke.cs.osprey.astar.conf.ConfIndex
- numUndefined - Variable in class edu.duke.cs.osprey.astar.ConfTree
- numUnscoredConfs - Variable in class edu.duke.cs.osprey.kstar.pfunc.UpperBoundCalculator
- numUsedBlocks() - Method in class edu.duke.cs.osprey.coffee.nodedb.BlockStore
- numUsedBytes() - Method in class edu.duke.cs.osprey.coffee.nodedb.BlockStore
- numUsedBytes() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices
O
- OBJ_FUNC - Static variable in class edu.duke.cs.osprey.multistatekstar.MSKStarNode
- ObjectIO - Class in edu.duke.cs.osprey.tools
- ObjectIO() - Constructor for class edu.duke.cs.osprey.tools.ObjectIO
- ObjectIO.BadFileException - Exception in edu.duke.cs.osprey.tools
- ObjectIO.CantWriteException - Exception in edu.duke.cs.osprey.tools
- ObjectIO.Validator<T> - Interface in edu.duke.cs.osprey.tools
- objective - Variable in class edu.duke.cs.osprey.gmec.Comets
- objective - Variable in class edu.duke.cs.osprey.gmec.Comets.SequenceInfo
- objective - Variable in class edu.duke.cs.osprey.kstar.MSKStar
- objective - Variable in class edu.duke.cs.osprey.kstar.MSKStar.SequenceInfo
- objective - Variable in class edu.duke.cs.osprey.sofea.MinLMFE
-
The multi-state objective function to be minimized.
- ObjectiveFunction - Interface in edu.duke.cs.osprey.minimization
- ObjectiveFunction.DofBounds - Class in edu.duke.cs.osprey.minimization
- ObjectiveFunction.OneDof - Class in edu.duke.cs.osprey.minimization
- objectiveWindowMax - Variable in class edu.duke.cs.osprey.gmec.Comets
- objectiveWindowMax - Variable in class edu.duke.cs.osprey.kstar.MSKStar
- objectiveWindowSize - Variable in class edu.duke.cs.osprey.gmec.Comets
- objectiveWindowSize - Variable in class edu.duke.cs.osprey.kstar.MSKStar
- ObjectPool<T> - Class in edu.duke.cs.osprey.tools
- ObjectPool(Factory<T, Void>) - Constructor for class edu.duke.cs.osprey.tools.ObjectPool
- ObjectPool.Checkout<T> - Class in edu.duke.cs.osprey.tools
- occupancy - Enum constant in enum class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode.ColorStyle
- of(SimpleConfSpace) - Static method in class edu.duke.cs.osprey.energy.ResInterGen
- of(SerializingDoublePriorityQueue.Serializer<T>, T...) - Static method in class edu.duke.cs.osprey.externalMemory.Queue.ExternalPriorityFactory
- of(SerializingFIFOQueue.Serializer<T>, T...) - Static method in class edu.duke.cs.osprey.externalMemory.Queue.ExternalFIFOFactory
- of(Iterable<T>) - Static method in class edu.duke.cs.osprey.tools.Streams
- of(Iterable<T>, long) - Static method in class edu.duke.cs.osprey.externalMemory.Queue.FIFOFactory
- of(Object) - Static method in interface edu.duke.cs.osprey.tools.IOable
- of(Comparator<T>, T...) - Static method in class edu.duke.cs.osprey.externalMemory.Queue.PriorityFactory
- of(Iterator<T>) - Static method in class edu.duke.cs.osprey.tools.Streams
- of(Iterator<T>, long) - Static method in class edu.duke.cs.osprey.externalMemory.Queue.FIFOFactory
- of(T...) - Static method in class edu.duke.cs.osprey.externalMemory.Queue.FIFOFactory
- of(T[]) - Static method in class edu.duke.cs.osprey.tools.Streams
- ofByteBuffer(ByteBuffer) - Static method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- offset - Variable in class edu.duke.cs.osprey.confspace.compiled.PosInter
-
weight*(energy + offset)
- offset - Variable in class edu.duke.cs.osprey.energy.forcefield.ResPairCache.ResPair
- offset - Variable in class edu.duke.cs.osprey.energy.ResidueInteractions.Pair
- offset - Variable in class edu.duke.cs.osprey.gmec.Comets.LME
- offset - Variable in class edu.duke.cs.osprey.gpu.Structs.Field
- offset - Variable in class edu.duke.cs.osprey.kstar.MSKStar.LMFE
- offset() - Method in class edu.duke.cs.osprey.gpu.Structs.Field
- offset(int) - Method in class edu.duke.cs.osprey.parallelism.CounterSignal
- offsetEnergy(double) - Method in class edu.duke.cs.osprey.confspace.ConfSearch.EnergiedConf
-
Adds val to the energy for this conformation
- offsetOf(MemoryBuffer) - Method in class edu.duke.cs.osprey.gpu.Structs.StructField
- offsetQuadEnergy(int, int, int, int, int, int, int, int, EnergyMatrix) - Method in enum class edu.duke.cs.osprey.energy.EnergyPartition
- offsets - Variable in class edu.duke.cs.osprey.dof.DofInfo
- Offsets - Enum constant in enum class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.Type
- offsetScore(double) - Method in class edu.duke.cs.osprey.confspace.ConfSearch.ScoredConf
-
Adds val to the score for this conformation
- offsetTripleEnergy(int, int, int, int, int, int, EnergyMatrix) - Method in enum class edu.duke.cs.osprey.energy.EnergyPartition
- ol(String) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
-
ordered list
- oldToNew(int) - Method in class edu.duke.cs.osprey.confspace.RCIndexMap
- OLSCG - Enum constant in enum class edu.duke.cs.osprey.lute.LUTE.Fitter
-
ordinary least squares via conjugate gradient ie, plain old linear regression TL;DR - OLSCG is faster than LASSO here, use OLSCG by default fastest to compute, tends to overfit a bit more than LASSO though, so requires more samples (even with the extra sample energies, CG is still generally faster overall than LASSO though)
- OMOLIO - Class in edu.duke.cs.osprey.structure
-
Reads and writes OSPREY Molecules as TOML files
- OMOLIO() - Constructor for class edu.duke.cs.osprey.structure.OMOLIO
- onConf(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.design.analysis.EnergyAnalysisConfListener
- onConf(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.design.analysis.EnsembleAnalysisListener
- onConf(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.design.analysis.ThermodynamicsConfListener
- onConf(ConfSearch.ScoredConf) - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.ConfListener
- onConf(ConfSearch.ScoredConf) - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.ConfListener
- onConf(ConfSearch.ScoredConf) - Method in interface edu.duke.cs.osprey.paste.PastePartitionFunction.ConfListener
- One - Enum constant in enum class edu.duke.cs.osprey.sofea.BigDecimalIO.Type
- one2three - Static variable in class edu.duke.cs.osprey.restypes.HardCodedResidueInfo
- oneBodyCalc() - Method in class edu.duke.cs.osprey.ematrix.TermECalculator
- OneDof(ObjectiveFunction, int) - Constructor for class edu.duke.cs.osprey.minimization.ObjectiveFunction.OneDof
- OneEPICFit - Class in edu.duke.cs.osprey.tests
-
Fit just one EPIC term This is to improve EPIC by dealing with problem terms
- OneEPICFit() - Constructor for class edu.duke.cs.osprey.tests.OneEPICFit
- oneLineReport() - Static method in class edu.duke.cs.osprey.tools.JvmMem
-
A one line string memory report that shows usage and limits for the JVM heap and the JVM process.
- onFinished(T) - Method in interface edu.duke.cs.osprey.parallelism.TaskExecutor.TaskListener
- OnlyDihedrals - Enum constant in enum class edu.duke.cs.osprey.confspace.SimpleConfSpace.DofTypes
- onMinimized(ConfSearch.EnergiedConf) - Method in interface edu.duke.cs.osprey.minimization.ConfMinimizer.Async.Listener
- open() - Method in class edu.duke.cs.osprey.tools.FileTools.Path
- open(MultiStateConfSpace, File) - Static method in class edu.duke.cs.osprey.sofea.FringeDB
-
open an existing fringe node database
- open(File) - Method in class edu.duke.cs.osprey.tools.FileTools.FilePathRoot
- open(String) - Method in class edu.duke.cs.osprey.tools.FileTools.FilePathRoot
- open(String) - Method in class edu.duke.cs.osprey.tools.FileTools.PathRoot
- open(String) - Method in class edu.duke.cs.osprey.tools.FileTools.ResourcePathRoot
- OpenCL - Enum constant in enum class edu.duke.cs.osprey.energy.EnergyCalculator.Type
- OpenCL - Enum constant in enum class edu.duke.cs.osprey.minimization.GpuConfMinimizer.Type
- openFile(File) - Static method in class edu.duke.cs.osprey.tools.FileTools
- openFile(String) - Static method in class edu.duke.cs.osprey.tools.FileTools
- openFringeDBLower() - Method in class edu.duke.cs.osprey.sofea.Sofea
- openFringeDBUpper() - Method in class edu.duke.cs.osprey.sofea.Sofea
- openRCDB() - Method in class edu.duke.cs.osprey.sofea.Sofea
- openResource(String) - Static method in class edu.duke.cs.osprey.tools.FileTools
- openResource(String, Class<?>) - Static method in class edu.duke.cs.osprey.tools.FileTools
- openSeqDB() - Method in class edu.duke.cs.osprey.sofea.Sofea
- opt(double, double) - Method in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
- opt(float, float) - Method in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
- opt(int, int) - Method in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
- opt(long, long) - Method in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
- opt(BigDecimal, BigDecimal) - Method in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
- OptimizableAStarNode - Interface in edu.duke.cs.osprey.astar
- OptimizableAStarNode.Tools - Class in edu.duke.cs.osprey.astar
- optimizer - Variable in class edu.duke.cs.osprey.astar.conf.ConfAStarTree
- optimizer - Variable in class edu.duke.cs.osprey.astar.conf.order.DynamicHMeanAStarOrder
- optimizer - Variable in class edu.duke.cs.osprey.astar.conf.scoring.PairwiseGScorer
- optimizer - Variable in class edu.duke.cs.osprey.astar.conf.scoring.TraditionalPairwiseHScorer
- optimizer - Variable in class edu.duke.cs.osprey.astar.seq.SeqAStarTree
- optimizer - Variable in class edu.duke.cs.osprey.markstar.framework.BiggestLowerboundDifferenceOrder
- optimizer - Variable in class edu.duke.cs.osprey.markstar.framework.StaticBiggestLowerboundDifferenceOrder
- optimizer - Variable in class edu.duke.cs.osprey.markstar.framework.StaticBiggesUpperboundDifferenceOrder
- optimizer - Variable in class edu.duke.cs.osprey.markstar.framework.StaticLowestEntropyOrder
- optimizeScore(double, MathTools.Optimizer) - Static method in class edu.duke.cs.osprey.astar.OptimizableAStarNode.Tools
- order - Variable in class edu.duke.cs.osprey.astar.conf.ConfAStarTree
- order - Variable in class edu.duke.cs.osprey.astar.seq.SeqAStarTree
- order - Variable in class edu.duke.cs.osprey.ematrix.epic.FitParams
- order - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- order - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- order - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- orderOfMag - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- ordinalIndexOf(String, String, int) - Static method in class edu.duke.cs.osprey.tools.StringParsing
- ospreyVersion - Variable in class edu.duke.cs.osprey.design.models.AffinityDesign
- ospreyVersion - Variable in class edu.duke.cs.osprey.design.models.MoleculeDesign
- otherMemberAddresses() - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- outFilePath - Variable in class edu.duke.cs.osprey.kstar.KSAbstract
- OutOfConformations - Enum constant in enum class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Status
- OutOfConformations - Enum constant in enum class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Status
- OutOfConformations - Enum constant in enum class edu.duke.cs.osprey.paste.PastePartitionFunction.Status
- OutOfConfs - Enum constant in enum class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator.Status
- OutOfDirectMemoryError(int, OutOfMemoryError) - Constructor for error edu.duke.cs.osprey.gpu.BufferTools.OutOfDirectMemoryError
- OutOfLowEnergies - Enum constant in enum class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Status
- OutOfLowEnergies - Enum constant in enum class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator.Status
- OutOfLowEnergies - Enum constant in enum class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Status
- OutOfLowEnergies - Enum constant in enum class edu.duke.cs.osprey.paste.PastePartitionFunction.Status
- OutOfOrderException() - Constructor for exception edu.duke.cs.osprey.confspace.ConfSearch.Splitter.OutOfOrderException
- outOfPlaneAxis - Variable in class edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry
- outOfPlaneDegrees - Variable in class edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry.Angles
- outOfPlaneDegrees - Variable in class edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry
- outputConfInfo() - Method in class edu.duke.cs.osprey.control.ConfInfo
- outputDir - Variable in class edu.duke.cs.osprey.kstar.KSAbstract
- outputMinimizedStruct(int[], String) - Method in class edu.duke.cs.osprey.confspace.SearchProblem
- outputNode(COMETSNode) - Method in class edu.duke.cs.osprey.astar.comets.NewCOMETSTree
- outputNode(FullAStarNode) - Method in class edu.duke.cs.osprey.astar.comets.COMETSTree
- outputNode(T) - Method in class edu.duke.cs.osprey.astar.AStarTree
- overlap - Variable in class edu.duke.cs.osprey.structure.Probe.AtomPair.Interaction
P
- p - Static variable in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- pad(long) - Static method in class edu.duke.cs.osprey.gpu.Structs
- Pad(long) - Constructor for class edu.duke.cs.osprey.gpu.Structs.Pad
- padToAlignment(long, long) - Static method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- pair(int, int, int, int) - Method in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- pair(ConfSpace, int, int, int, int) - Method in class edu.duke.cs.osprey.energy.compiled.PosInterGen
- pair(ConfSpace, SimpleReferenceEnergies, int, int, int, int) - Method in enum class edu.duke.cs.osprey.confspace.compiled.PosInterDist
- Pair - Class in edu.duke.cs.osprey.coffee.zmat
- Pair(int, int, int, int) - Constructor for class edu.duke.cs.osprey.coffee.zmat.Pair
- Pair(int, int, int, int, BigExp) - Constructor for class edu.duke.cs.osprey.coffee.zmat.Pair
- Pair(String, String, double, double) - Constructor for class edu.duke.cs.osprey.energy.ResidueInteractions.Pair
- pairIndex(int, int) - Method in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- pairIndex(int, int, int, int) - Method in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- PairwiseBounder - Class in edu.duke.cs.osprey.coffee.bounds
- PairwiseBounder(ClusterZMatrix) - Constructor for class edu.duke.cs.osprey.coffee.bounds.PairwiseBounder
- pairwiseCalc() - Method in class edu.duke.cs.osprey.ematrix.TermECalculator
- PairwiseGScorer - Class in edu.duke.cs.osprey.astar.conf.scoring
- PairwiseGScorer(EnergyMatrix) - Constructor for class edu.duke.cs.osprey.astar.conf.scoring.PairwiseGScorer
- PairwiseGScorer(EnergyMatrix, MathTools.Optimizer) - Constructor for class edu.duke.cs.osprey.astar.conf.scoring.PairwiseGScorer
- PairWiseMinimized - Enum constant in enum class edu.duke.cs.osprey.multistatekstar.KStarScore.KStarScoreType
- panPmat - Variable in class edu.duke.cs.osprey.kstar.KAStarConfTree
- panSP - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- panUprunedRCsAtPos - Variable in class edu.duke.cs.osprey.kstar.KAStarConfTree
- parallelComponent(double[], double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- ParallelConfPartitionFunction - Class in edu.duke.cs.osprey.kstar.pfunc
-
Deprecated.
- ParallelConfPartitionFunction(EnergyMatrix, PruningMatrix, ConfSearchFactory, GMECConfEnergyCalculator.Async) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- parallelCreateSPs(KSSearchProblem, int) - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel2
- ParallelEnergyFunction - Class in edu.duke.cs.osprey.energy
- ParallelEnergyFunction(ArrayList<EnergyFunction>, ArrayList<Double>) - Constructor for class edu.duke.cs.osprey.energy.ParallelEnergyFunction
- parallelism - Variable in class edu.duke.cs.osprey.coffee.Coffee
- parallelism - Variable in class edu.duke.cs.osprey.coffee.NodeProcessor
- parallelism - Variable in class edu.duke.cs.osprey.energy.EnergyCalculator
- parallelism - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- parallelism - Variable in class edu.duke.cs.osprey.markstar.MARKStar.Settings
- parallelism - Variable in class edu.duke.cs.osprey.parallelism.Cluster.Client
- parallelism - Variable in class edu.duke.cs.osprey.parallelism.Cluster.Member
- Parallelism - Class in edu.duke.cs.osprey.parallelism
-
Specified how Osprey should use available hardware.
- Parallelism(int, int, int) - Constructor for class edu.duke.cs.osprey.parallelism.Parallelism
- Parallelism.Builder - Class in edu.duke.cs.osprey.parallelism
- Parallelism.Type - Enum Class in edu.duke.cs.osprey.parallelism
- ParameterizedMoleculeCopy - Class in edu.duke.cs.osprey.confspace
-
Sometimes we will want to minimize conformations in parallel, so each thread will need a copy of the molecule and its DOFs.
- ParameterizedMoleculeCopy(ConfSpace) - Constructor for class edu.duke.cs.osprey.confspace.ParameterizedMoleculeCopy
- ParameterizedMoleculePool - Class in edu.duke.cs.osprey.confspace
- ParameterizedMoleculePool(ConfSpace) - Constructor for class edu.duke.cs.osprey.confspace.ParameterizedMoleculePool
- ParametricMolecule - Class in edu.duke.cs.osprey.confspace
-
A
Moleculeinstance with associated continuous degrees of freedom. - ParametricMolecule(Molecule) - Constructor for class edu.duke.cs.osprey.confspace.ParametricMolecule
-
A parametric molecule with no degrees of freedom
- ParametricMolecule(Molecule, List<DegreeOfFreedom>, ObjectiveFunction.DofBounds) - Constructor for class edu.duke.cs.osprey.confspace.ParametricMolecule
-
A parametric molecule with bounds on its degrees of freedom SimpleConfSpace generates a ParametricMolecule for a particular conf (RC list), with the residue types and starting conformation implied by that conf It is helpful to bundle it with the conf's DOF bounds, especially for DEEPer and CATS
- ParamInfo(ForcefieldParams) - Constructor for class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.ParamInfo
- params - Variable in class edu.duke.cs.osprey.control.ConfigFileParser
- params - Variable in class edu.duke.cs.osprey.energy.EnergyCalculator.EnergiedParametricMolecule
- params - Variable in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.ParamInfo
- params - Variable in class edu.duke.cs.osprey.kstar.KSSearchProblem
- ParamSet - Class in edu.duke.cs.osprey.control
-
Handles reading in and managing parameter/value pairs from the input configuration files
- ParamSet() - Constructor for class edu.duke.cs.osprey.control.ParamSet
- ParamSet(ParamSet) - Constructor for class edu.duke.cs.osprey.control.ParamSet
- paramsPath - Variable in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.Forcefield
- parent - Variable in class edu.duke.cs.osprey.astar.comets.UpdatedPruningMatrix
- parent - Variable in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- parent - Variable in class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode.Link
- parent() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- parentlbScore - Variable in class edu.duke.cs.osprey.kstar.KAStarNode
- parentOf(String) - Static method in class edu.duke.cs.osprey.tools.FileTools.ResourcePathRoot
- parse(File) - Static method in class edu.duke.cs.osprey.design.models.AffinityDesign
- parse(String) - Method in class edu.duke.cs.osprey.restypes.ResidueEntropyParser
- parse(String) - Method in class edu.duke.cs.osprey.restypes.TemplateCoordsParser
- parse(String) - Method in class edu.duke.cs.osprey.restypes.TemplateParser
- parseDesignSpec(Class<T>) - Method in class edu.duke.cs.osprey.design.commands.RunnableCommand
- parseGMECMutFile() - Method in class edu.duke.cs.osprey.gmec.DEEGMECFinder
- parseGMECMutFile(ConfSpace) - Method in class edu.duke.cs.osprey.control.ConfigFileParser
- parseLines(String) - Static method in class edu.duke.cs.osprey.tools.FileTools
- parseLinesFast(Reader) - Static method in class edu.duke.cs.osprey.tools.FileTools
-
like parseLines(), but never returns null lines, so is functionally incompatible also empirically much faster
- parseLinesFast(String) - Static method in class edu.duke.cs.osprey.tools.FileTools
- parseOrThrow(String) - Static method in class edu.duke.cs.osprey.tools.TomlTools
- parseTree(File, boolean, Map<Integer, BigDecimal>) - Static method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- parseTree(String) - Static method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- PartCR - Class in edu.duke.cs.osprey.partcr
- PartCR(SearchProblem, ForcefieldParams, double, List<ConfSearch.ScoredConf>) - Constructor for class edu.duke.cs.osprey.partcr.PartCR
- PartCRConfPruner - Class in edu.duke.cs.osprey.partcr
- PartCRConfPruner(SearchProblem, double) - Constructor for class edu.duke.cs.osprey.partcr.PartCRConfPruner
- partialQLB - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- PartialStructureSwitch - Class in edu.duke.cs.osprey.dof.deeper.perts
-
This is a perturbation that substitutes in the backbone conformation from alternate structures
- PartialStructureSwitch(ArrayList<Residue>, double, int, PerturbationBlock, ArrayList<ArrayList<ResBBState>>) - Constructor for class edu.duke.cs.osprey.dof.deeper.perts.PartialStructureSwitch
- PartialStructureSwitch(ArrayList<Residue>, ArrayList<String>) - Constructor for class edu.duke.cs.osprey.dof.deeper.perts.PartialStructureSwitch
- PartitionFunction - Interface in edu.duke.cs.osprey.kstar.pfunc
- PartitionFunction.ConfListener - Interface in edu.duke.cs.osprey.kstar.pfunc
- PartitionFunction.Result - Class in edu.duke.cs.osprey.kstar.pfunc
- PartitionFunction.Status - Enum Class in edu.duke.cs.osprey.kstar.pfunc
- PartitionFunction.Values - Class in edu.duke.cs.osprey.kstar.pfunc
- PartitionFunction.WithConfDB - Interface in edu.duke.cs.osprey.kstar.pfunc
- PartitionFunction.WithExternalMemory - Interface in edu.duke.cs.osprey.kstar.pfunc
- PartitionFunction.WithExternalMemory.UnsupportedException - Exception in edu.duke.cs.osprey.kstar.pfunc
- PartitionFunctionDiscrete - Class in edu.duke.cs.osprey.multistatekstar
- PartitionFunctionDiscrete(EnergyMatrix, PruningMatrix, PruningMatrix, ConfSearchFactory, GMECConfEnergyCalculator.Async) - Constructor for class edu.duke.cs.osprey.multistatekstar.PartitionFunctionDiscrete
- PartitionFunctionDiscreteUppperBound - Class in edu.duke.cs.osprey.multistatekstar
- PartitionFunctionDiscreteUppperBound(EnergyMatrix, PruningMatrix, PruningMatrix, ConfSearchFactory, GMECConfEnergyCalculator.Async) - Constructor for class edu.duke.cs.osprey.multistatekstar.PartitionFunctionDiscreteUppperBound
- PartitionFunctionMinimized - Class in edu.duke.cs.osprey.multistatekstar
- PartitionFunctionMinimized(EnergyMatrix, PruningMatrix, PruningMatrix, ConfSearchFactory, GMECConfEnergyCalculator.Async) - Constructor for class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized
- partitionFunctions - Variable in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- password - Variable in class edu.duke.cs.osprey.design.PostgresConnectionInfo
- Paste - Class in edu.duke.cs.osprey.paste
-
Implementation of the K* algorithm to predict protein sequence mutations that improve binding affinity by computing provably accurate Boltzmann-weighted ensembles .
- Paste(SimpleConfSpace, Paste.Settings, int) - Constructor for class edu.duke.cs.osprey.paste.Paste
- Paste.ConfSearchFactory - Interface in edu.duke.cs.osprey.paste
- Paste.ConfSpaceInfo - Class in edu.duke.cs.osprey.paste
- Paste.ConfSpaceType - Enum Class in edu.duke.cs.osprey.paste
- Paste.InitException - Exception in edu.duke.cs.osprey.paste
- Paste.ScoredSequence - Class in edu.duke.cs.osprey.paste
- Paste.Settings - Class in edu.duke.cs.osprey.paste
- Paste.Settings.Builder - Class in edu.duke.cs.osprey.paste
- PasteGradientDescentPfunc - Class in edu.duke.cs.osprey.paste
-
This partition function calculator estimates the partition function value by alternating between two operations: 1.
- PasteGradientDescentPfunc(ConfEnergyCalculator) - Constructor for class edu.duke.cs.osprey.paste.PasteGradientDescentPfunc
- PastePartitionFunction - Interface in edu.duke.cs.osprey.paste
-
based on PartitionFunction.java, author: lowegard
- PastePartitionFunction.ConfListener - Interface in edu.duke.cs.osprey.paste
- PastePartitionFunction.Result - Class in edu.duke.cs.osprey.paste
- PastePartitionFunction.Status - Enum Class in edu.duke.cs.osprey.paste
- PastePartitionFunction.Values - Class in edu.duke.cs.osprey.paste
- PastePartitionFunction.WithConfTable - Interface in edu.duke.cs.osprey.paste
- PastePartitionFunction.WithConfTable.UnsupportedException - Exception in edu.duke.cs.osprey.paste
- PastePartitionFunction.WithExternalMemory - Interface in edu.duke.cs.osprey.paste
- PastePartitionFunction.WithExternalMemory.UnsupportedException - Exception in edu.duke.cs.osprey.paste
- pasteScore - Variable in class edu.duke.cs.osprey.paste.PasteScoreWriter.ScoreInfo
- PasteScore - Class in edu.duke.cs.osprey.paste
- PasteScore(PastePartitionFunction.Result, PastePartitionFunction.Result) - Constructor for class edu.duke.cs.osprey.paste.PasteScore
- PasteScore(Double, Double, Double) - Constructor for class edu.duke.cs.osprey.paste.PasteScore
- PasteScoreWriter - Interface in edu.duke.cs.osprey.paste
- PasteScoreWriter.Formatted - Class in edu.duke.cs.osprey.paste
- PasteScoreWriter.Formatter - Interface in edu.duke.cs.osprey.paste
- PasteScoreWriter.Formatter.Log - Class in edu.duke.cs.osprey.paste
- PasteScoreWriter.Formatter.SequenceKStarPfuncs - Class in edu.duke.cs.osprey.paste
- PasteScoreWriter.Nop - Class in edu.duke.cs.osprey.paste
- PasteScoreWriter.ScoreInfo - Class in edu.duke.cs.osprey.paste
- PasteScoreWriter.ToConsole - Class in edu.duke.cs.osprey.paste
- PasteScoreWriter.ToFile - Class in edu.duke.cs.osprey.paste
- PasteScoreWriter.Writers - Class in edu.duke.cs.osprey.paste
- path - Variable in class edu.duke.cs.osprey.tools.FileTools.Path
- Path(FileTools.PathRoot, String) - Constructor for class edu.duke.cs.osprey.tools.FileTools.Path
- PathRoot(String) - Constructor for class edu.duke.cs.osprey.tools.FileTools.PathRoot
- pc - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.LengthUnit
- PCFac - Variable in class edu.duke.cs.osprey.ematrix.epic.FitParams
- PCOrder - Variable in class edu.duke.cs.osprey.ematrix.epic.FitParams
- PCTemplate - Variable in class edu.duke.cs.osprey.ematrix.epic.EPICFitter
- PDBIO - Class in edu.duke.cs.osprey.structure
-
this is a clean PDB reader that doesn't know anything about templates or bonds its only job is to turn PDB text into a molecule representing a polymer with residues and atoms
- PDBIO() - Constructor for class edu.duke.cs.osprey.structure.PDBIO
- PDBScanner - Class in edu.duke.cs.osprey.structure.analysis
- PDBScanner(File, String...) - Constructor for class edu.duke.cs.osprey.structure.analysis.PDBScanner
- PDBScanner(File, Set<String>) - Constructor for class edu.duke.cs.osprey.structure.analysis.PDBScanner
- peek() - Method in interface edu.duke.cs.osprey.externalMemory.Queue
- peek() - Method in class edu.duke.cs.osprey.kstar.KAStarTree
- peek() - Method in class edu.duke.cs.osprey.tools.FileTools.LineIterator
- peekHead() - Method in class edu.duke.cs.osprey.kstar.KSConfQ
- peekTail() - Method in class edu.duke.cs.osprey.kstar.KSConfQ
- PepPlaneLinModel - Class in edu.duke.cs.osprey.bbfree
-
This is a linear model of a peptide plane, allowing us to get C', H, and O coordinates as a linear function of the N and CA coordinates (CA1, N, CA2) This model can be used even if the peptide plane is translated and rotated
- PepPlaneLinModel(Residue, Residue) - Constructor for class edu.duke.cs.osprey.bbfree.PepPlaneLinModel
- PeptideBondingTemplate() - Constructor for class edu.duke.cs.osprey.restypes.InterResBondingTemplate.PeptideBondingTemplate
- percent - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.LengthUnit
- perf - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
- performanceLogFile - Variable in class edu.duke.cs.osprey.sofea.Sofea
- PeriodicTable - Class in edu.duke.cs.osprey.tools
- PeriodicTable() - Constructor for class edu.duke.cs.osprey.tools.PeriodicTable
- perpendicularComponent(double[], double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- PertSet - Class in edu.duke.cs.osprey.dof.deeper
-
Description of the perturbations in our system, not set up in a molecule (describes the content of a .pert file)
- PertSet() - Constructor for class edu.duke.cs.osprey.dof.deeper.PertSet
- Perturbation - Class in edu.duke.cs.osprey.dof.deeper.perts
-
A perturbation, as in DEEPer Note: This DEEPer package, unlike the rest of the software, consists of perturbations specific to proteins and so it will make explicit reference to protein atoms outside HardCodedResidueInfo DEEPer perturbations can be used in the protein part of a mixed protein-nonprotein system
- Perturbation(ArrayList<Residue>) - Constructor for class edu.duke.cs.osprey.dof.deeper.perts.Perturbation
- PerturbationBlock - Class in edu.duke.cs.osprey.dof.deeper.perts
-
In DEEPer, perturbations don't necessarily commute We'll put them into "perturbation blocks," which do this way, when we want to apply a parameter value for a perturbation, we can appropriately handle any perturbations that come after it Note: All sidechains within a perturbation block will be idealized (in the C-beta sense) since the original sidechain conformations are no longer valid for perturbed backbones
- PerturbationBlock() - Constructor for class edu.duke.cs.osprey.dof.deeper.perts.PerturbationBlock
- PerturbationBlock(ArrayList<Perturbation>) - Constructor for class edu.duke.cs.osprey.dof.deeper.perts.PerturbationBlock
- PerturbationSelector - Class in edu.duke.cs.osprey.dof.deeper
- PerturbationSelector(String, boolean, double, double, boolean, ArrayList<String>, String, ResidueTermini, boolean, ResidueTemplateLibrary) - Constructor for class edu.duke.cs.osprey.dof.deeper.PerturbationSelector
- pf - Variable in class edu.duke.cs.osprey.kstar.KSPStarCalculator
- PFAbstract - Class in edu.duke.cs.osprey.kstar.pfunc
- PFAbstract() - Constructor for class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- PFAbstract(int, ArrayList<String>, ArrayList<Integer>, String, String, KSConfigFileParser, KSSearchProblem) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- PFAbstract.EApproxReached - Enum Class in edu.duke.cs.osprey.kstar.pfunc
- PFAbstract.RunState - Enum Class in edu.duke.cs.osprey.kstar.pfunc
- PFAdapter - Class in edu.duke.cs.osprey.kstar.pfunc.impl
- PFAdapter(String, int, ArrayList<String>, ArrayList<Integer>, String, String, KSConfigFileParser, KSSearchProblem) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.impl.PFAdapter
- pfEw - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- PFFactory - Class in edu.duke.cs.osprey.kstar.pfunc
-
Deprecated.
- PFFactory() - Constructor for class edu.duke.cs.osprey.kstar.pfunc.PFFactory
-
Deprecated.
- PFParallel0 - Class in edu.duke.cs.osprey.kstar.pfunc.impl
- PFParallel0() - Constructor for class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel0
- PFParallel0(int, ArrayList<String>, ArrayList<Integer>, String, String, KSConfigFileParser, KSSearchProblem) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel0
- PFParallel1 - Class in edu.duke.cs.osprey.kstar.pfunc.impl
- PFParallel1() - Constructor for class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- PFParallel1(int, ArrayList<String>, ArrayList<Integer>, String, String, KSConfigFileParser, KSSearchProblem) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- PFParallel2 - Class in edu.duke.cs.osprey.kstar.pfunc.impl
- PFParallel2() - Constructor for class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel2
- PFParallel2(int, ArrayList<String>, ArrayList<Integer>, String, String, KSConfigFileParser, KSSearchProblem) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel2
- PFTraditional - Class in edu.duke.cs.osprey.kstar.pfunc.impl
- PFTraditional() - Constructor for class edu.duke.cs.osprey.kstar.pfunc.impl.PFTraditional
- PFTraditional(int, ArrayList<String>, ArrayList<Integer>, String, String, KSConfigFileParser, KSSearchProblem) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.impl.PFTraditional
- pfTypes - Variable in class edu.duke.cs.osprey.multistatekstar.MSKStarSettings
- pfUB - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.SequenceInfo
- PFUB - Class in edu.duke.cs.osprey.kstar.pfunc.impl
- PFUB() - Constructor for class edu.duke.cs.osprey.kstar.pfunc.impl.PFUB
- PFUB(int, ArrayList<String>, ArrayList<Integer>, String, String, KSConfigFileParser, KSSearchProblem) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.impl.PFUB
- pFuncCFGImpl - Static variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- PfuncDirector - Class in edu.duke.cs.osprey.coffee.directors
- PfuncDirector.Builder - Class in edu.duke.cs.osprey.coffee.directors
- pfuncFactory - Variable in class edu.duke.cs.osprey.kstar.BBKStar.ConfSpaceInfo
- pfuncFactory - Variable in class edu.duke.cs.osprey.kstar.KStar.ConfSpaceInfo
- pfuncFactory - Variable in class edu.duke.cs.osprey.kstar.MSKStar.State
- pfuncResults - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.ConfSpaceInfo
- pfuncResults - Variable in class edu.duke.cs.osprey.kstar.KStar.ConfSpaceInfo
- pfuncResults - Variable in class edu.duke.cs.osprey.kstar.MSKStar.SequenceInfo
- pfuncResults - Variable in class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceInfo
- PfuncsDirector - Class in edu.duke.cs.osprey.coffee.directors
- PfuncsDirector.Builder - Class in edu.duke.cs.osprey.coffee.directors
- PfuncSurface - Class in edu.duke.cs.osprey.kstar.pfunc
-
Samples the 2D decision space of estimating a partition function (ie, refine the upper bound, or refine the lower bound) and reports the delta value of the pfunc estimation as a VTK file.
- PfuncSurface(int, int, int) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.PfuncSurface
- PfuncSurface.Trace - Class in edu.duke.cs.osprey.kstar.pfunc
- pfuncTimeout - Variable in class edu.duke.cs.osprey.kstar.KStar.Settings
- PHASE() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.DihederalParameter
-
Returns the value of the
PHASErecord component. - PHASE() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.ImproperDihederalParameter
-
Returns the value of the
PHASErecord component. - phase2() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- phase2Method - Static variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- phiPsiResolution - Variable in class edu.duke.cs.osprey.restypes.ResidueTemplate
- pick(List<ConfSearch.ScoredConf>) - Method in interface edu.duke.cs.osprey.partcr.pickers.ConfPicker
- pick(List<ConfSearch.ScoredConf>) - Method in class edu.duke.cs.osprey.partcr.pickers.FirstConfPicker
- pick(List<ConfSearch.ScoredConf>) - Method in class edu.duke.cs.osprey.partcr.pickers.WalkingConfPicker
- pickBest(int) - Static method in enum class edu.duke.cs.osprey.externalMemory.AssignmentsSerializer.Encoding
- pickBest(ConfSpace) - Static method in enum class edu.duke.cs.osprey.minimization.GpuConfMinimizer.Type
- pickBest(SimpleConfSpace.DofTypes) - Static method in enum class edu.duke.cs.osprey.energy.EnergyCalculator.Type
- pickBestOrThrow(ConfSpace) - Static method in enum class edu.duke.cs.osprey.minimization.GpuConfMinimizer.Type
- pickColor(int, List<Plot.Color>) - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.Series
- pickInitVals(ArrayList<DoubleMatrix1D>) - Method in class edu.duke.cs.osprey.minimization.CCDMinimizer
- pieChart(int) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- pieChart(int...) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- pinBuffer(Pointer, long) - Method in class edu.duke.cs.osprey.gpu.cuda.Context
- PK() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.DihederalParameter
-
Returns the value of the
PKrecord component. - PK() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.ImproperDihederalParameter
-
Returns the value of the
PKrecord component. - place(Structs.Array, long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- place(Structs.Array, long, long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- place(Structs.Struct) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
-
Returns a view of the MemoryBuffer at its current position and increments the position by the number of bytes the struct takes.
- plot(GNUPlot.Cmd) - Method in interface edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Plotter
- plot(Plot) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- plot(Plot, ResultDoc.PlotType) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- Plot - Class in edu.duke.cs.osprey.tools.resultdoc
- Plot() - Constructor for class edu.duke.cs.osprey.tools.resultdoc.Plot
- Plot.Color - Class in edu.duke.cs.osprey.tools.resultdoc
- Plot.Interval - Class in edu.duke.cs.osprey.tools.resultdoc
- Plot.Intervals - Class in edu.duke.cs.osprey.tools.resultdoc
- Plot.IntervalsX - Class in edu.duke.cs.osprey.tools.resultdoc
- Plot.IntervalsY - Class in edu.duke.cs.osprey.tools.resultdoc
- Plot.Lines - Class in edu.duke.cs.osprey.tools.resultdoc
- Plot.LinesX - Class in edu.duke.cs.osprey.tools.resultdoc
- Plot.LinesY - Class in edu.duke.cs.osprey.tools.resultdoc
- Plot.Points - Class in edu.duke.cs.osprey.tools.resultdoc
- Plot.PointsX - Class in edu.duke.cs.osprey.tools.resultdoc
- Plot.PointsY - Class in edu.duke.cs.osprey.tools.resultdoc
- Plot.PointType - Enum Class in edu.duke.cs.osprey.tools.resultdoc
- Plot.Series - Class in edu.duke.cs.osprey.tools.resultdoc
- plotPng(int, int, GNUPlot.Plotter) - Static method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot
- plotSvg(int, int, GNUPlot.Plotter) - Static method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot
- PLUG - Class in edu.duke.cs.osprey.pruning
-
Pruning of Local Unrealistic Geometries (PLUG) prunes RC tuples if probe-style clashes are unavoidable
- PLUG(SimpleConfSpace) - Constructor for class edu.duke.cs.osprey.pruning.PLUG
- PLUG.BoundaryPoint - Class in edu.duke.cs.osprey.pruning
- plugMat - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- PLUGMAT - Enum constant in enum class edu.duke.cs.osprey.confspace.SearchProblem.MatrixType
- Plus - Enum constant in enum class edu.duke.cs.osprey.tools.resultdoc.Plot.PointType
- pmat - Variable in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- pmat - Variable in class edu.duke.cs.osprey.lute.ConfSampler
- pmat - Variable in class edu.duke.cs.osprey.lute.LUTEGMECFinder
- pmat - Variable in class edu.duke.cs.osprey.pruning.SimpleDEE
- pmol - Variable in class edu.duke.cs.osprey.energy.EnergyCalculator.EnergiedParametricMolecule
- pmol - Variable in class edu.duke.cs.osprey.minimization.MoleculeObjectiveFunction
- PN() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.DihederalParameter
-
Returns the value of the
PNrecord component. - PN() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.ImproperDihederalParameter
-
Returns the value of the
PNrecord component. - png(byte[]) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc.Image
- PNG - Enum constant in enum class edu.duke.cs.osprey.tools.resultdoc.ResultDoc.PlotType
- Point() - Constructor for class edu.duke.cs.osprey.confspace.VoxelShape.Point
- points - Variable in class edu.duke.cs.osprey.kstar.pfunc.PfuncSurface.Trace
- Points() - Constructor for class edu.duke.cs.osprey.tools.resultdoc.Plot.Points
- PointsX() - Constructor for class edu.duke.cs.osprey.tools.resultdoc.Plot.PointsX
- PointsY() - Constructor for class edu.duke.cs.osprey.tools.resultdoc.Plot.PointsY
- PoissonBoltzmann - Enum constant in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.SolvationForcefield
- PoissonBoltzmannEnergy - Class in edu.duke.cs.osprey.energy
-
An energy function that evaluates the Poisson-Boltzmann solvation energy for a molecule
- PoissonBoltzmannEnergy(Molecule) - Constructor for class edu.duke.cs.osprey.energy.PoissonBoltzmannEnergy
- POL() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.SlaterKirkwoodParameter
-
Returns the value of the
POLrecord component. - poll() - Method in interface edu.duke.cs.osprey.externalMemory.Queue
- poll() - Method in class edu.duke.cs.osprey.kstar.KAStarTree
- poly_mul_sub1(double[], double[], double[], double[], int, int, int, int, double[]) - Method in class edu.duke.cs.osprey.dof.deeper.perts.TripeptideClosure
- poly_mul1(double[], double[], int, int, double[]) - Method in class edu.duke.cs.osprey.dof.deeper.perts.TripeptideClosure
- poly_sub1(double[], double[], int, int, double[]) - Method in class edu.duke.cs.osprey.dof.deeper.perts.TripeptideClosure
- polytopeHasFeasiblePt(ArrayList<LinearConstraint>) - Static method in class edu.duke.cs.osprey.plug.LPChecks
- PolytopeMatrix - Class in edu.duke.cs.osprey.plug
-
A matrix of polytopes representing the allowed area According to this matrix, confs for a given RC list will be limited to the intersection of the polytopes for all RC tuples within that list (note: DOF bounds won't be in this list bc too redundant)
- PolytopeMatrix(ConfSpace) - Constructor for class edu.duke.cs.osprey.plug.PolytopeMatrix
- PolytopeMatrix(SearchProblem, boolean) - Constructor for class edu.duke.cs.osprey.plug.PolytopeMatrix
- pop() - Method in interface edu.duke.cs.osprey.externalMemory.Queue
- populateQueues(Queue<MARKStarNode>, List<MARKStarNode>, List<MARKStarNode>, BigDecimal, BigDecimal, BigDecimal[]) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- populateQueues(Queue<MARKStarNode>, List<MARKStarNode>, List<MARKStarNode>, BigDecimal, BigDecimal, BigDecimal[]) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundFastQueues
- pos - Variable in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- pos - Variable in class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode.Link
- pos - Variable in class edu.duke.cs.osprey.confspace.RCTuple
- pos - Variable in class edu.duke.cs.osprey.confspace.SeqSpace.ResType
- pos - Variable in class edu.duke.cs.osprey.confspace.Sequence.Assignment
- pos - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- pos - Variable in exception edu.duke.cs.osprey.tools.TomlParseException
- Pos(int, String, String, int, ConfSpace.Conf[]) - Constructor for class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Pos
- posComesBefore(int, int, RCTuple) - Method in class edu.duke.cs.osprey.multistatekstar.MultiSequenceConfTree
- posComesBefore(int, int, ArrayList<Integer>) - Method in class edu.duke.cs.osprey.kstar.KAStarConfTree
- posERef(int, int) - Method in class edu.duke.cs.osprey.ematrix.ReferenceEnergies
- posFlex - Variable in class edu.duke.cs.osprey.confspace.ConfSpace
- posi - Variable in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords.AtomInfo
- posi - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle
- posi1 - Variable in class edu.duke.cs.osprey.coffee.zmat.Pair
- posi1 - Variable in class edu.duke.cs.osprey.coffee.zmat.Single
- posi1 - Variable in class edu.duke.cs.osprey.coffee.zmat.Triple
- posi1 - Variable in class edu.duke.cs.osprey.confspace.compiled.PosInter
-
Index in conf space of position 1, or `StaticPos` for the static atoms.
- posi2 - Variable in class edu.duke.cs.osprey.coffee.zmat.Pair
- posi2 - Variable in class edu.duke.cs.osprey.coffee.zmat.Triple
- posi2 - Variable in class edu.duke.cs.osprey.confspace.compiled.PosInter
-
Index in conf space of position 2, or `StaticPos` for the static atoms.
- posi3 - Variable in class edu.duke.cs.osprey.coffee.zmat.Triple
- PosInf - Enum constant in enum class edu.duke.cs.osprey.sofea.BigDecimalIO.Type
- PosInfo(PositionConfSpace) - Constructor for class edu.duke.cs.osprey.partcr.RCSplits.PosInfo
- PosInter - Class in edu.duke.cs.osprey.confspace.compiled
-
An energetic interaction between design positions in a conformation space.
- PosInter(int, int, double, double) - Constructor for class edu.duke.cs.osprey.confspace.compiled.PosInter
- PosInterDist - Enum Class in edu.duke.cs.osprey.confspace.compiled
-
Defines how position interactions should be distributed among conformation fragments.
- posInterGen - Variable in class edu.duke.cs.osprey.coffee.Coffee.StateConfig
- posInterGen - Variable in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- posInterGen - Variable in class edu.duke.cs.osprey.ematrix.compiled.EmatCalculator
- posInterGen - Variable in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter
-
Deprecated.
- PosInterGen - Class in edu.duke.cs.osprey.energy.compiled
-
Position Interaction Generator Generates position interactions for conformation energy calculators.
- PosInterGen(PosInterDist, SimpleReferenceEnergies) - Constructor for class edu.duke.cs.osprey.energy.compiled.PosInterGen
- Position(int, int, Strand, Residue, List<String>) - Constructor for class edu.duke.cs.osprey.confspace.SimpleConfSpace.Position
- PositionConfSpace - Class in edu.duke.cs.osprey.confspace
- PositionConfSpace(int, Residue, ArrayList<DegreeOfFreedom>, ArrayList<String>, boolean, ArrayList<DegreeOfFreedom>, ArrayList<Perturbation>, ArrayList<ArrayList<double[]>>, ArrayList<ArrayList<int[]>>, BBFreeBlock, boolean, ResidueTemplate, boolean) - Constructor for class edu.duke.cs.osprey.confspace.PositionConfSpace
- PositionConfSpace(PositionConfSpace) - Constructor for class edu.duke.cs.osprey.confspace.PositionConfSpace
- positionIdentifier() - Method in class edu.duke.cs.osprey.design.models.Residue
- positions - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- positions - Variable in class edu.duke.cs.osprey.confspace.SeqSpace
- positions - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
The design positions
- positions - Variable in class edu.duke.cs.osprey.dof.DofInfo
- Positive - Enum constant in enum class edu.duke.cs.osprey.structure.Probe.AtomFlag
- PosMatrix<T> - Interface in edu.duke.cs.osprey.confspace
- PosMatrixGeneric<T> - Class in edu.duke.cs.osprey.confspace
- PosMatrixGeneric(int) - Constructor for class edu.duke.cs.osprey.confspace.PosMatrixGeneric
- PosMatrixGeneric(SimpleConfSpace) - Constructor for class edu.duke.cs.osprey.confspace.PosMatrixGeneric
- posNums - Variable in class edu.duke.cs.osprey.kstar.KSSearchProblem
- posPermutation - Variable in class edu.duke.cs.osprey.coffee.StateInfo
- possibleBBAtoms - Static variable in class edu.duke.cs.osprey.restypes.HardCodedResidueInfo
- possibleBBAtomsLookup - Static variable in class edu.duke.cs.osprey.restypes.HardCodedResidueInfo
- PostgresConnectionInfo - Class in edu.duke.cs.osprey.design
- PostgresConnectionInfo(String, String, String) - Constructor for class edu.duke.cs.osprey.design.PostgresConnectionInfo
- PostgresScoreWriter - Class in edu.duke.cs.osprey.design
- PostgresScoreWriter(PostgresConnectionInfo, S3Settings, String, List<String>, int) - Constructor for class edu.duke.cs.osprey.design.PostgresScoreWriter
- postProcess(ConfSearch.EnergiedConf) - Method in interface edu.duke.cs.osprey.gmec.MinimizingConfEnergyCalculator.ConfPostProcessor
-
Deprecated.
- postRun(int, int, int) - Method in enum class edu.duke.cs.osprey.pruning.NewPruningControl.ReportMode
- postRun(int, int, int) - Method in enum class edu.duke.cs.osprey.pruning.PruningControl.ReportMode
- postTemplateModifier - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf
- pow(double) - Method in class edu.duke.cs.osprey.tools.BigExp
-
returns this^pow
- pow10(double) - Static method in class edu.duke.cs.osprey.tools.BigExp
-
Return 10^val
- powerset(List<T>) - Static method in class edu.duke.cs.osprey.tools.MathTools
- powersetUpTo(List<T>, int) - Static method in class edu.duke.cs.osprey.tools.MathTools
- preamble(double) - Method in enum class edu.duke.cs.osprey.pruning.NewPruningControl.ReportMode
- preamble(double) - Method in enum class edu.duke.cs.osprey.pruning.PruningControl.ReportMode
- precalcEmats() - Method in class edu.duke.cs.osprey.markstar.MARKStar
- Precise - Enum constant in enum class edu.duke.cs.osprey.coffee.directors.Timing
-
Uniform 1 s batches of computation.
- precision - Variable in class edu.duke.cs.osprey.coffee.Coffee
- precision - Variable in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- precision - Variable in class edu.duke.cs.osprey.energy.compiled.NativeConfEnergyCalculator
- precision - Variable in class edu.duke.cs.osprey.gpu.Structs.Real.Array
- precision - Variable in class edu.duke.cs.osprey.gpu.Structs.Real
- precision() - Method in interface edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculator
- precision() - Method in class edu.duke.cs.osprey.energy.compiled.CPUConfEnergyCalculator
- precision() - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- precision() - Method in class edu.duke.cs.osprey.energy.compiled.NativeConfEnergyCalculator
- precision() - Method in class edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal
- precomputed - Variable in class edu.duke.cs.osprey.energy.forcefield.ResPairCache.AtomPairInfo
- PrecomputedMatrices - Class in edu.duke.cs.osprey.gmec
-
Information about RC tuples in a single-state design system (possibly part of a multistate design) Stored in matrices.
- PrecomputedMatrices(double, double, String, EnergyMatrix, SimpleConfSpace, EnergyCalculator, ConfEnergyCalculator, EPICSettings, LUTESettings, PruningSettings) - Constructor for class edu.duke.cs.osprey.gmec.PrecomputedMatrices
- PrecomputedMatrices.MatrixType - Enum Class in edu.duke.cs.osprey.gmec
- precomputeMatrices(double) - Method in class edu.duke.cs.osprey.gmec.GMECFinder
- preDraw(SVG) - Method in class edu.duke.cs.osprey.tools.SVGPlot.Axis
- PrefixTreeSet<T> - Class in edu.duke.cs.osprey.tools
- PrefixTreeSet() - Constructor for class edu.duke.cs.osprey.tools.PrefixTreeSet
- preparePanSeqSPs(ArrayList<Boolean>) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- preprocess() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- preRun(int) - Method in enum class edu.duke.cs.osprey.pruning.NewPruningControl.ReportMode
- preRun(int) - Method in enum class edu.duke.cs.osprey.pruning.PruningControl.ReportMode
- print(ConfSearch.EnergiedConf) - Method in interface edu.duke.cs.osprey.gmec.ConfPrinter
- print(ConfSearch.EnergiedConf, SimpleConfSpace) - Method in interface edu.duke.cs.osprey.gmec.ConfPrinter
- print(ConfSearch.EnergiedConf, SimpleConfSpace, EnergyRange) - Method in class edu.duke.cs.osprey.gmec.ConfPrinter.Nop
- print(ConfSearch.EnergiedConf, SimpleConfSpace, EnergyRange) - Method in interface edu.duke.cs.osprey.gmec.ConfPrinter
- print(ConfSearch.EnergiedConf, SimpleConfSpace, EnergyRange) - Method in class edu.duke.cs.osprey.gmec.ConfPrinters
- print(ConfSearch.EnergiedConf, SimpleConfSpace, EnergyRange) - Method in class edu.duke.cs.osprey.gmec.ConsoleConfPrinter
- print(ConfSearch.EnergiedConf, SimpleConfSpace, EnergyRange) - Method in class edu.duke.cs.osprey.gmec.LoggingConfPrinter
- print(ConfSearch.ScoredConf) - Method in interface edu.duke.cs.osprey.gmec.ConfPrinter
- print(ConfSearch.ScoredConf, SimpleConfSpace) - Method in interface edu.duke.cs.osprey.gmec.ConfPrinter
- print(String) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- printAllSeqs() - Method in class edu.duke.cs.osprey.control.MSKStarDoer
- printAllTermValues() - Method in class edu.duke.cs.osprey.ematrix.epic.EPICEnergyFunction
- printConf(ConfSearch.EnergiedConf) - Method in class edu.duke.cs.osprey.control.ConfPrinter
-
Deprecated.
- printedHeader - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- printEnergies() - Method in class edu.duke.cs.osprey.energy.LigandResEnergies
- printers - Variable in class edu.duke.cs.osprey.gmec.ConfPrinters
- printGpuInfo - Static variable in class edu.duke.cs.osprey.gpu.cuda.Gpus
- printHeader() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFAdapter
- printHeader() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel0
- printHeader() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- printHeader() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFTraditional
- printHeader() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFUB
- printHeader() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- printIfMaster(String) - Static method in class edu.duke.cs.osprey.handlempi.MPIMaster
- printIntermediateConfsToConsole - Variable in class edu.duke.cs.osprey.gmec.SimpleGMECFinder.Builder
-
True to print all conformations found during A* search to the console
- printIntermediateConfsToConsole - Variable in class edu.duke.cs.osprey.gmec.SimpleGMECFinder
- printIntermediateConfsToConsole - Variable in class edu.duke.cs.osprey.lute.LUTEGMECFinder
- printLeafProgressReport() - Method in class edu.duke.cs.osprey.astar.AStarProgress
- println() - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- println(String) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- printNodeExpansionData() - Method in class edu.duke.cs.osprey.astar.comets.NewCOMETSTree
- printPDBs - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings
- printPDBs - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- printPoolSize - Static variable in class edu.duke.cs.osprey.gpu.cuda.GpuStreamPool
- printProgressReport() - Method in class edu.duke.cs.osprey.astar.AStarProgress
- printResults() - Method in interface edu.duke.cs.osprey.design.analysis.CommandAnalysis
- printResults() - Method in class edu.duke.cs.osprey.design.analysis.EnergyAnalysisConfListener
- printResults() - Method in class edu.duke.cs.osprey.design.analysis.EnsembleAnalysisListener
- printResults() - Method in class edu.duke.cs.osprey.design.analysis.ThermodynamicsConfListener
- printSequences() - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- printSize() - Method in class edu.duke.cs.osprey.ewakstar.EwakstarLimitedSequenceTrie
- printSummary(String, long, long, long) - Method in class edu.duke.cs.osprey.kstar.KSCalc
- printSummaryHeader(String) - Static method in class edu.duke.cs.osprey.kstar.KSCalc
- printToConsole - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- printToConsole - Variable in class edu.duke.cs.osprey.gmec.Comets
- printToConsole - Variable in class edu.duke.cs.osprey.gmec.SimpleGMECFinder.Builder
-
Print status and progress info to the console
- printToConsole - Variable in class edu.duke.cs.osprey.gmec.SimpleGMECFinder
- printToConsole - Variable in class edu.duke.cs.osprey.kstar.MSKStar
- printTree() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- printTree() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- printTree(String) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- printTree(String, SimpleConfSpace) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- printTree(String, FileWriter) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- printTree(String, FileWriter, SimpleConfSpace) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- printTreeLikeMARKStar(Writer) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
-
printTree uses a different format than MARK* apparently
- printTreeLikeMARKStar(Writer, String) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- printWarnings - Static variable in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.ParamInfo
- printWarnings - Static variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- priority - Variable in class edu.duke.cs.osprey.tools.SVG.StyleClass
- PriorityDequeFixedIndex<S extends Comparable<S>,
T extends FixedIndex.Indexable<S>> - Class in edu.duke.cs.osprey.coffee.nodedb -
A fast and correct implementation of FixedIndex.
- PriorityDequeFixedIndex(BlockStore, FixedIndex.Serializer<T>) - Constructor for class edu.duke.cs.osprey.coffee.nodedb.PriorityDequeFixedIndex
- PriorityFactory(Comparator<T>) - Constructor for class edu.duke.cs.osprey.externalMemory.Queue.PriorityFactory
- probe - Variable in class edu.duke.cs.osprey.structure.Probe.AtomPair
- Probe - Class in edu.duke.cs.osprey.structure
-
implements probe-style rules for describing non-bonded atomic interactions, eg close contacts, clashes, hydrogen bonds, salt bridges probe is software available at: http://kinemage.biochem.duke.edu/software/probe.php
- Probe() - Constructor for class edu.duke.cs.osprey.structure.Probe
- Probe(boolean) - Constructor for class edu.duke.cs.osprey.structure.Probe
- Probe.AtomFlag - Enum Class in edu.duke.cs.osprey.structure
- Probe.AtomInfo - Class in edu.duke.cs.osprey.structure
- Probe.AtomPair - Class in edu.duke.cs.osprey.structure
- Probe.AtomPair.Interaction - Class in edu.duke.cs.osprey.structure
- Probe.Attraction - Enum Class in edu.duke.cs.osprey.structure
- Probe.Contact - Enum Class in edu.duke.cs.osprey.structure
- Probe.Template - Class in edu.duke.cs.osprey.structure
- ProbeAtomNeighbors - Class in edu.duke.cs.osprey.structure
-
This version of AtomNeighbors matches the convention in Probe where atoms bonded 1,5 are only treated as non-bonded if neither is an H
- ProbeAtomNeighbors(Atom) - Constructor for class edu.duke.cs.osprey.structure.ProbeAtomNeighbors
- Process - Enum constant in enum class edu.duke.cs.osprey.sofea.Sofea.Criterion.Filter
- processedConfs - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- processedConfsDuringInterval - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- processedConfsSet - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- processFullConfNode(List<MARKStarNode>, MARKStarNode, MARKStarNode.Node) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- processingConfs - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- processPartialConfNode(List<MARKStarNode>, MARKStarNode, MARKStarNode.Node) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- productUndefinedRots() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- profileOutput - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- profileOutput - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- profileOutput - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- profilePrint(String) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- Profiler - Class in edu.duke.cs.osprey.tools
- Profiler() - Constructor for class edu.duke.cs.osprey.tools.Profiler
- Profiler(String) - Constructor for class edu.duke.cs.osprey.tools.Profiler
- ProfilingEvents - Class in edu.duke.cs.osprey.gpu.opencl
- ProfilingEvents(int) - Constructor for class edu.duke.cs.osprey.gpu.opencl.ProfilingEvents
- ProgramName - Static variable in class edu.duke.cs.osprey.design.Main
- Progress - Class in edu.duke.cs.osprey.tools
- Progress(long) - Constructor for class edu.duke.cs.osprey.tools.Progress
- Progress(long, long) - Constructor for class edu.duke.cs.osprey.tools.Progress
- Progress(long, long, Progress.Model) - Constructor for class edu.duke.cs.osprey.tools.Progress
- Progress.Model - Enum Class in edu.duke.cs.osprey.tools
- projectPointLine(double[], double[], double[]) - Method in class edu.duke.cs.osprey.dof.deeper.perts.Backrub
- projectPointPlane(double[], double[], double[], double[]) - Method in class edu.duke.cs.osprey.dof.deeper.perts.Backrub
- ProlinePucker - Class in edu.duke.cs.osprey.dof
-
This degree of freedom specifies the ring pucker of a proline 0 indicates the original pucker, and 1 the "flipped" one
- ProlinePucker(ResidueTemplateLibrary, Residue) - Constructor for class edu.duke.cs.osprey.dof.ProlinePucker
- ProlinePucker.Direction - Enum Class in edu.duke.cs.osprey.dof
- propertiesFile - Variable in class edu.duke.cs.osprey.design.commands.DesignFileDelegate
- protein - Variable in class edu.duke.cs.osprey.design.models.AffinityDesign
- protein - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar
-
A configuration space containing just the protein strand
- protein - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar
-
A configuration space containing just the protein strand
- protein - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.SingleSequenceNode
- protein - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- protein - Variable in class edu.duke.cs.osprey.kstar.BBKStar
-
A configuration space containing just the protein strand
- protein - Variable in class edu.duke.cs.osprey.kstar.BBKStar.SingleSequenceNode
- protein - Variable in class edu.duke.cs.osprey.kstar.KStar
-
A configuration space containing just the protein strand
- protein - Variable in class edu.duke.cs.osprey.kstar.KStarScore
- protein - Variable in class edu.duke.cs.osprey.markstar.MARKStar
-
A configuration space containing just the protein strand
- protein - Variable in class edu.duke.cs.osprey.paste.Paste
-
A configuration space containing just the protein strand
- protein - Variable in class edu.duke.cs.osprey.paste.PasteScore
- Protein - Enum constant in enum class edu.duke.cs.osprey.ewakstar.EWAKStar.ConfSpaceType
- Protein - Enum constant in enum class edu.duke.cs.osprey.kstar.KStar.ConfSpaceType
- Protein - Enum constant in enum class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceType
- Protein - Enum constant in enum class edu.duke.cs.osprey.paste.Paste.ConfSpaceType
- proteinConfSpace - Variable in class edu.duke.cs.osprey.design.commands.CommandBindingAffinity.ForceFieldParamsAndStrands
- Protractor - Class in edu.duke.cs.osprey.tools
- Protractor() - Constructor for class edu.duke.cs.osprey.tools.Protractor
- Protractor.TetrahedralGeometry - Class in edu.duke.cs.osprey.tools
-
eg the bond geometry around a Ca atom: a = N b = Ca c = C d = Cb center is b inPlaneAxis is halfway between ba and bc, negated and normalized outOfPlaneAxis is perpendicular to the plane of a-b-c, normalized
- Protractor.TetrahedralGeometry.Angles - Class in edu.duke.cs.osprey.tools
- ProxyEnergyMatrix - Class in edu.duke.cs.osprey.ematrix
- ProxyEnergyMatrix(SimpleConfSpace, EnergyMatrix) - Constructor for class edu.duke.cs.osprey.ematrix.ProxyEnergyMatrix
- prune() - Method in class edu.duke.cs.osprey.pruning.NewPruningControl
- prune() - Method in class edu.duke.cs.osprey.pruning.PruningControl
- prune(String) - Method in class edu.duke.cs.osprey.pruning.NewPruner
- prune(String) - Method in class edu.duke.cs.osprey.pruning.Pruner
- prune(List<ConfSearch.ScoredConf>, GMECConfEnergyCalculator) - Method in interface edu.duke.cs.osprey.gmec.GMECFinder.ConfPruner
- prune(List<ConfSearch.ScoredConf>, GMECConfEnergyCalculator) - Method in class edu.duke.cs.osprey.partcr.PartCRConfPruner
- prunedConfs - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- prunedRCsAtPos(int) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- prunedRCsAtPos(int) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- prunedRCsAtPos(int) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- prunedRCsAtPos(ArrayList<Integer>, int) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- prunedRCsAtPos(ArrayList<Integer>, int) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- prunedRCsAtPos(ArrayList<Integer>, int) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- pruneMat - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- prunePair(int, int, int, int) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- prunePairs(PruningMatrix, double) - Method in class edu.duke.cs.osprey.pruning.PLUG
- prunePairs(PruningMatrix, double, TaskExecutor) - Method in class edu.duke.cs.osprey.pruning.PLUG
- prunePairs(PruningMatrix, TaskExecutor) - Method in class edu.duke.cs.osprey.pruning.TransitivePruner
- prunePairsByThreshold(double) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE
- prunePairsFromSingle(int, int) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- prunePairsFromSingles() - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- prunePairsGoldstein(double, boolean) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE
- prunePairsGoldstein(double, boolean, Parallelism) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE
- prunePmat() - Method in class edu.duke.cs.osprey.multistatekstar.MSSearchProblem
- pruner - Variable in class edu.duke.cs.osprey.astar.conf.ConfAStarTree
- pruner - Variable in class edu.duke.cs.osprey.gmec.SimpleGMECFinder.Builder
- pruner - Variable in class edu.duke.cs.osprey.gmec.SimpleGMECFinder
- pruner - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- pruner - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- pruner - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- Pruner - Class in edu.duke.cs.osprey.pruning
- Pruner(SearchProblem, boolean, double, double, boolean, boolean) - Constructor for class edu.duke.cs.osprey.pruning.Pruner
- Pruner(SearchProblem, PruningMatrix, boolean, double, double, boolean, boolean) - Constructor for class edu.duke.cs.osprey.pruning.Pruner
- pruneSingle(int, int) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- pruneSingles(PruningMatrix, double) - Method in class edu.duke.cs.osprey.pruning.PLUG
- pruneSingles(PruningMatrix, double, TaskExecutor) - Method in class edu.duke.cs.osprey.pruning.PLUG
- pruneSingles(PruningMatrix, TaskExecutor) - Method in class edu.duke.cs.osprey.pruning.TransitivePruner
- pruneSinglesByThreshold(double) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE
- pruneSinglesGoldstein(double, boolean) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE
- pruneSteric(double) - Method in class edu.duke.cs.osprey.pruning.NewPruner
- pruneSteric(double) - Method in class edu.duke.cs.osprey.pruning.Pruner
- pruneTriple(int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- pruneTriples(PruningMatrix, double) - Method in class edu.duke.cs.osprey.pruning.PLUG
- pruneTriples(PruningMatrix, double, TaskExecutor) - Method in class edu.duke.cs.osprey.pruning.PLUG
- pruneTriples(PruningMatrix, TaskExecutor) - Method in class edu.duke.cs.osprey.pruning.TransitivePruner
- pruneTriplesGoldstein(double, boolean) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE
- pruneTriplesGoldstein(double, boolean, Parallelism) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE
- pruneTuple(RCTuple) - Method in class edu.duke.cs.osprey.tupexp.BasicPruningTupleExpander
- PruningControl - Class in edu.duke.cs.osprey.pruning
- PruningControl(SearchProblem, double, boolean, double, int, boolean, boolean, boolean, boolean, boolean, double) - Constructor for class edu.duke.cs.osprey.pruning.PruningControl
- PruningControl.ReportMode - Enum Class in edu.duke.cs.osprey.pruning
- PruningMatrix - Class in edu.duke.cs.osprey.pruning
- PruningMatrix() - Constructor for class edu.duke.cs.osprey.pruning.PruningMatrix
- PruningMatrix(int, int[], double) - Constructor for class edu.duke.cs.osprey.pruning.PruningMatrix
- PruningMatrix(ConfSpace, double) - Constructor for class edu.duke.cs.osprey.pruning.PruningMatrix
- PruningMatrix(SimpleConfSpace) - Constructor for class edu.duke.cs.osprey.pruning.PruningMatrix
- PruningMatrix(PruningMatrix) - Constructor for class edu.duke.cs.osprey.pruning.PruningMatrix
- PruningMatrix.IteratorCommand - Enum Class in edu.duke.cs.osprey.pruning
- PruningMatrix.PairConsumer - Interface in edu.duke.cs.osprey.pruning
- PruningMatrix.SingleConsumer - Interface in edu.duke.cs.osprey.pruning
- PruningMatrix.TripleConsumer - Interface in edu.duke.cs.osprey.pruning
- PruningMatrixInverted - Class in edu.duke.cs.osprey.multistatekstar
- PruningMatrixInverted(MSSearchProblem, PruningMatrix) - Constructor for class edu.duke.cs.osprey.multistatekstar.PruningMatrixInverted
- PruningMatrixNull - Class in edu.duke.cs.osprey.multistatekstar
- PruningMatrixNull(PruningMatrix) - Constructor for class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- PruningMethod - Class in edu.duke.cs.osprey.pruning
- PruningMethod(boolean, int, PruningMethod.CheckSumType) - Constructor for class edu.duke.cs.osprey.pruning.PruningMethod
- PruningPlayground - Class in edu.duke.cs.osprey.tests
-
the main game here is comparing PLUG and DEE
- PruningPlayground(String[]) - Constructor for class edu.duke.cs.osprey.tests.PruningPlayground
- pruningSettings - Variable in class edu.duke.cs.osprey.gmec.DEEGMECFinder
- PruningSettings - Class in edu.duke.cs.osprey.gmec
- PruningSettings() - Constructor for class edu.duke.cs.osprey.gmec.PruningSettings
- pruningWindow - Variable in class edu.duke.cs.osprey.multistatekstar.MSSearchSettings
- pstar - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Values
- pstar - Variable in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Values
- pstar - Variable in class edu.duke.cs.osprey.paste.PastePartitionFunction.Values
- pStar - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- pStarCalculator - Variable in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- pt - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.LengthUnit
- pucker - Variable in class edu.duke.cs.osprey.structure.Residue
- PulseSignal - Class in edu.duke.cs.osprey.parallelism
-
a cyclic signal, ie it can be reused multiple times
- PulseSignal() - Constructor for class edu.duke.cs.osprey.parallelism.PulseSignal
- PulseSignal.Result - Enum Class in edu.duke.cs.osprey.parallelism
- push(T) - Method in interface edu.duke.cs.osprey.externalMemory.Queue
- pushAll(Collection<T>) - Method in interface edu.duke.cs.osprey.externalMemory.Queue
- pushAll(T[]) - Method in interface edu.duke.cs.osprey.externalMemory.Queue
- put(int[], V) - Method in class edu.duke.cs.osprey.confspace.Conf.Map
- put(RCTuple, T) - Method in class edu.duke.cs.osprey.confspace.TupleTree
- putBoolean(Structs.Array, long, boolean) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- putBoolean(Structs.Field, boolean) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- putByte(Structs.Array, long, byte) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- putByte(Structs.Field, byte) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- putChar(Structs.Array, long, char) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- putChar(Structs.Field, char) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- putContext(int, Class<?>, Object) - Method in class edu.duke.cs.osprey.parallelism.TaskExecutor.ContextGroup
- putContext(TaskExecutor.ContextId, Object) - Method in class edu.duke.cs.osprey.parallelism.TaskExecutor.ContextGroup
- putDouble(Structs.Array, long, double) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- putDouble(Structs.Field, double) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- putFloat(Structs.Array, long, float) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- putFloat(Structs.Field, float) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- putInState(Residue) - Method in class edu.duke.cs.osprey.dof.deeper.ResBBState
- putInt(Structs.Array, long, int) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- putInt(Structs.Field, int) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- putLong(Structs.Array, long, long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- putLong(Structs.Field, long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- putPrecomputed(double[], int, Residue, int, Residue, int, double) - Method in class edu.duke.cs.osprey.energy.forcefield.EEF1.ResiduesInfo
- putPrecomputed(double[], int, Residue, int, Residue, int, double) - Method in interface edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.SolvationForcefield.ResiduesInfo
- putStyleClasses(SVG.StyleClass...) - Method in class edu.duke.cs.osprey.tools.SVG
- putTaskContexts(TaskExecutor.ContextGroup) - Method in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- putTaskContexts(TaskExecutor.ContextGroup) - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction
-
Override to support task contexts, for contextual task executors
- px - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.LengthUnit
){kind=link}
){kind=link}
Q
- qCapacity - Static variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- qprime - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Values
- qprime - Variable in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Values
- qprime - Variable in class edu.duke.cs.osprey.paste.PastePartitionFunction.Values
- qPrime - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- qPrimeCalculator - Variable in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- qprimeUnevaluated - Variable in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- qprimeUnscored - Variable in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- qstar - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Values
- qstar - Variable in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Values
- qstar - Variable in class edu.duke.cs.osprey.paste.PastePartitionFunction.Values
- qStar - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- qstarScoreWeights - Variable in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized
- quadCorrectionThreshold - Variable in class edu.duke.cs.osprey.ematrix.SimplerEnergyMatrixCalculator
- quadOnly - Variable in class edu.duke.cs.osprey.ematrix.epic.EPICSettings
- quadratic(int, boolean) - Static method in class edu.duke.cs.osprey.ematrix.epic.FitParams
- Quadratic - Enum constant in enum class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrixCalculator.ApproximatorType
- Quadratic - Enum constant in enum class edu.duke.cs.osprey.tools.Progress.Model
- QuadraticApproximator - Class in edu.duke.cs.osprey.energy.approximation
- QuadraticApproximator(List<Integer>, List<Integer>) - Constructor for class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- QuadraticQFunction - Class in edu.duke.cs.osprey.voxq
-
Q-function for Metropolis sampling in one dimension within a voxel the energy surface is likely to be roughly quadratic in each dimension (at least around the current point)
- QuadraticQFunction(MoleculeModifierAndScorer, int, double) - Constructor for class edu.duke.cs.osprey.voxq.QuadraticQFunction
- queue - Variable in class edu.duke.cs.osprey.astar.seq.SeqAStarTree
- queue - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- queue - Variable in class edu.duke.cs.osprey.parallelism.Threads
- queue - Variable in class edu.duke.cs.osprey.parallelism.WorkQueueThread
- Queue<T> - Interface in edu.duke.cs.osprey.externalMemory
-
A queue that can only be iterated once.
- Queue.ExternalFIFOFactory<T> - Class in edu.duke.cs.osprey.externalMemory
- Queue.ExternalPriorityFactory<T> - Class in edu.duke.cs.osprey.externalMemory
- Queue.Factory<T> - Interface in edu.duke.cs.osprey.externalMemory
- Queue.Factory.FIFO<T> - Interface in edu.duke.cs.osprey.externalMemory
- Queue.FIFO<T> - Interface in edu.duke.cs.osprey.externalMemory
-
A special interface for FIFO queues, since they allow more space-efficient in-place filtering.
- Queue.FIFOFactory<T> - Class in edu.duke.cs.osprey.externalMemory
- Queue.PriorityFactory<T> - Class in edu.duke.cs.osprey.externalMemory
- queueSize - Variable in class edu.duke.cs.osprey.parallelism.ThreadPoolTaskExecutor
-
Controls task queue size.
R
- r - Variable in class edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger.Coords
- r - Variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.NBParams
- R - Enum constant in enum class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.Space
- R - Static variable in class edu.duke.cs.osprey.Constants
-
The gas constant, in kcal * K^(-1) * mol^(-1)
- R - Variable in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator.Conditions
-
gas constant, in kcal/K/mol
- R - Variable in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- R() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.VanDerWaalsRadius
-
Returns the value of the
Rrecord component. - radius - Variable in class edu.duke.cs.osprey.energy.forcefield.EEF1.SolvParams
- radius - Variable in class edu.duke.cs.osprey.structure.Atom
- raiseFitOrder(FitParams) - Method in class edu.duke.cs.osprey.ematrix.epic.EPICFitter
- raiseFitOrderQuadOnly(FitParams) - Method in class edu.duke.cs.osprey.ematrix.epic.EPICFitter
- raiseFitOrderSAPEHeavy(FitParams) - Method in class edu.duke.cs.osprey.ematrix.epic.EPICFitter
- RamachandranChecker - Class in edu.duke.cs.osprey.dof.deeper
- rand - Variable in class edu.duke.cs.osprey.lute.ConfSampler
- RandomizedDFSConfSampler - Class in edu.duke.cs.osprey.lute
-
Samples confs for a tuple by doing DFS search.
- RandomizedDFSConfSampler(SimpleConfSpace, PruningMatrix, int) - Constructor for class edu.duke.cs.osprey.lute.RandomizedDFSConfSampler
- randomSeed - Variable in class edu.duke.cs.osprey.lute.ConfSampler
- RateLimitedThread - Class in edu.duke.cs.osprey.parallelism
-
Runs a task no more than once every interval.
- RateLimitedThread(String, long, TimeUnit, Runnable) - Constructor for class edu.duke.cs.osprey.parallelism.RateLimitedThread
- rc - Variable in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- rc - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- RC - Class in edu.duke.cs.osprey.confspace
- RC(RC) - Constructor for class edu.duke.cs.osprey.confspace.RC
- RC(String, ResidueTemplate, int, ArrayList<DegreeOfFreedom>, ArrayList<Double>, ArrayList<Double>, int) - Constructor for class edu.duke.cs.osprey.confspace.RC
- rcContribAtPos(int, int[], int) - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrix
- RCContribution(int, int, RCTuple) - Method in class edu.duke.cs.osprey.multistatekstar.MultiSequenceConfTree
- RCContribution(int, int, RCTuple, int[], ArrayList<Integer>) - Method in class edu.duke.cs.osprey.kstar.KAStarConfTree
- RCDB - Class in edu.duke.cs.osprey.sofea
- RCDB(MultiStateConfSpace, MathContext) - Constructor for class edu.duke.cs.osprey.sofea.RCDB
- RCDB(MultiStateConfSpace, MathContext, File) - Constructor for class edu.duke.cs.osprey.sofea.RCDB
- RCDB.Table - Class in edu.duke.cs.osprey.sofea
- rcdbFile - Variable in class edu.duke.cs.osprey.sofea.Sofea
- RCEnergyContribs - Class in edu.duke.cs.osprey.kstar
- RCEnergyContribs(PFAbstract, MultiTermEnergyFunction, int[]) - Constructor for class edu.duke.cs.osprey.kstar.RCEnergyContribs
- RCEnergyContribs.BoundErrorByPos - Class in edu.duke.cs.osprey.kstar
- RCEnergyContribs.BoundErrorByPosComparator - Class in edu.duke.cs.osprey.kstar
- RCIndex - Variable in class edu.duke.cs.osprey.confspace.RC
- RCIndexMap - Class in edu.duke.cs.osprey.confspace
- RCIndexMap(int) - Constructor for class edu.duke.cs.osprey.confspace.RCIndexMap
- RCInfo(RC) - Constructor for class edu.duke.cs.osprey.partcr.RCSplits.RCInfo
- RClassic - Static variable in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- RCPairVDWChecker - Class in edu.duke.cs.osprey.plug
-
This class looks for possible contacts between atoms in a pair of RCs or between an RC and the shell if there's just one RC It makes a polytope representing the geometrically favorable region, or determines there is none For now, assuming a polytope suffices and that pushing any of the good contacts that are possible anywhere in the voxel out of the favorable distance range will create a hole or clash Then higher-order checks on the voxels (up to full confs) can limit themselves to the intersection of pairwise polytopes, and can check the contacts in each pair to make sure each atom that should have a contact does have one
- RCPairVDWChecker(ConfSpace, RCTuple, ArrayList<Residue>) - Constructor for class edu.duke.cs.osprey.plug.RCPairVDWChecker
- RCPairVDWChecker(Residue, RC, Residue, RC, ArrayList<Residue>) - Constructor for class edu.duke.cs.osprey.plug.RCPairVDWChecker
- rcs - Variable in class edu.duke.cs.osprey.astar.conf.ConfAStarTree
- rcs - Variable in class edu.duke.cs.osprey.astar.conf.ConfRanker
- rcs - Variable in class edu.duke.cs.osprey.astar.conf.scoring.TraditionalPairwiseHScorer
- rcs - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeTree
- rcs - Variable in class edu.duke.cs.osprey.externalMemory.AssignmentsSerializer
- RCs - Class in edu.duke.cs.osprey.astar.conf
- RCs - Variable in class edu.duke.cs.osprey.confspace.PositionConfSpace
- RCs - Variable in class edu.duke.cs.osprey.confspace.RCTuple
- RCs - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- RCs(int[][]) - Constructor for class edu.duke.cs.osprey.astar.conf.RCs
- RCs(RCs) - Constructor for class edu.duke.cs.osprey.astar.conf.RCs
- RCs(RCs, PruningMatrix) - Constructor for class edu.duke.cs.osprey.astar.conf.RCs
- RCs(RCs, BiPredicate<Integer, Integer>) - Constructor for class edu.duke.cs.osprey.astar.conf.RCs
- RCs(ConfSpaceIteration) - Constructor for class edu.duke.cs.osprey.astar.conf.RCs
- RCs(ConfSpaceIteration, BiPredicate<Integer, Integer>) - Constructor for class edu.duke.cs.osprey.astar.conf.RCs
- RCs(SimpleConfSpace) - Constructor for class edu.duke.cs.osprey.astar.conf.RCs
-
Deprecated.
- RCs(SimpleConfSpace, BiPredicate<SimpleConfSpace.Position, SimpleConfSpace.ResidueConf>) - Constructor for class edu.duke.cs.osprey.astar.conf.RCs
-
Deprecated.
- RCs(PruningMatrix) - Constructor for class edu.duke.cs.osprey.astar.conf.RCs
- RCs(List<List<Integer>>) - Constructor for class edu.duke.cs.osprey.astar.conf.RCs
- rcsAtPos(PruningMatrix, int, String, boolean) - Method in class edu.duke.cs.osprey.kstar.KSSearchProblem
- RCScorer - Interface in edu.duke.cs.osprey.partcr.scorers
- RCSplits - Class in edu.duke.cs.osprey.partcr
- RCSplits(ConfSpace) - Constructor for class edu.duke.cs.osprey.partcr.RCSplits
- RCSplits.PosInfo - Class in edu.duke.cs.osprey.partcr
- RCSplits.RCInfo - Class in edu.duke.cs.osprey.partcr
- RCSplitter - Class in edu.duke.cs.osprey.partcr.splitters
- RCSplitter() - Constructor for class edu.duke.cs.osprey.partcr.splitters.RCSplitter
- rcTuple - Variable in class edu.duke.cs.osprey.astar.ConfTree
- RCTuple - Class in edu.duke.cs.osprey.confspace
-
An n-sized tuple for holding pairs of design positions with their corresponding discrete adopted conformation.
- RCTuple() - Constructor for class edu.duke.cs.osprey.confspace.RCTuple
- RCTuple(int[]) - Constructor for class edu.duke.cs.osprey.confspace.RCTuple
- RCTuple(int, int) - Constructor for class edu.duke.cs.osprey.confspace.RCTuple
- RCTuple(int, int, int, int) - Constructor for class edu.duke.cs.osprey.confspace.RCTuple
- RCTuple(int, int, int, int, int, int) - Constructor for class edu.duke.cs.osprey.confspace.RCTuple
- RCTuple(int, int, int, int, int, int, int, int) - Constructor for class edu.duke.cs.osprey.confspace.RCTuple
- RCTuple(ConfIndex) - Constructor for class edu.duke.cs.osprey.confspace.RCTuple
- RCTuple(ArrayList<Integer>, ArrayList<Integer>) - Constructor for class edu.duke.cs.osprey.confspace.RCTuple
- RCTuplePolytope - Class in edu.duke.cs.osprey.plug
-
Polytope for a particular set of DOFs, representing the feasible region for an RC tuple
- RCTuplePolytope(ArrayList<DegreeOfFreedom>, ArrayList<LinearConstraint>) - Constructor for class edu.duke.cs.osprey.plug.RCTuplePolytope
- read() - Method in class edu.duke.cs.osprey.energy.forcefield.amber.ForcefieldFileParser
-
This method reads all of the parameters from an Amber parm.dat file into the fields.
- read() - Method in class edu.duke.cs.osprey.tools.ByteBufferInputStream
- read() - Method in class edu.duke.cs.osprey.tools.FileTools.Path
- read(byte[]) - Static method in class edu.duke.cs.osprey.lute.LUTEIO
- read(byte[], int, int) - Method in class edu.duke.cs.osprey.tools.ByteBufferInputStream
- read(SimpleConfSpace, File) - Static method in class edu.duke.cs.osprey.pruning.SimpleDEE
-
Reads a saved pruning matrix from disk, or throws an exception
- read(DataInput) - Static method in class edu.duke.cs.osprey.coffee.zmat.Pair
- read(DataInput) - Static method in class edu.duke.cs.osprey.coffee.zmat.Single
- read(DataInput) - Static method in class edu.duke.cs.osprey.coffee.zmat.Triple
- read(DataInput) - Method in class edu.duke.cs.osprey.sofea.BigDecimalIO.Fixed
- read(DataInput) - Method in interface edu.duke.cs.osprey.sofea.BigDecimalIO
- read(DataInput) - Method in class edu.duke.cs.osprey.sofea.BigDecimalIO.Variable
- read(DataInput) - Static method in class edu.duke.cs.osprey.tools.BigExp
- read(DataInput) - Method in enum class edu.duke.cs.osprey.tools.IntEncoding
- read(DataInputStream) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- read(DataInputStream) - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrix
- read(File) - Static method in class edu.duke.cs.osprey.ematrix.EnergyMatrix
- read(File) - Static method in class edu.duke.cs.osprey.lute.LUTEIO
- read(File) - Method in class edu.duke.cs.osprey.tools.FileTools.FilePathRoot
- read(File, Class<T>) - Static method in class edu.duke.cs.osprey.tools.ObjectIO
- read(String) - Static method in class edu.duke.cs.osprey.structure.OMOLIO
- read(String) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- read(String) - Method in class edu.duke.cs.osprey.tools.FileTools.PathRoot
- read(String, Class<T>) - Static method in class edu.duke.cs.osprey.tools.ObjectIO
- read(ByteBuffer) - Method in enum class edu.duke.cs.osprey.tools.IntEncoding
- read(ByteBuffer, int[]) - Method in enum class edu.duke.cs.osprey.externalMemory.AssignmentsSerializer.Encoding
- readAll(String) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- readAssignments(ByteBuffer) - Method in class edu.duke.cs.osprey.externalMemory.AssignmentsSerializer
- readAssignments(ByteBuffer, int[]) - Method in class edu.duke.cs.osprey.externalMemory.AssignmentsSerializer
- readBytes(File) - Method in class edu.duke.cs.osprey.tools.FileTools.FilePathRoot
- readBytes(String) - Method in class edu.duke.cs.osprey.tools.FileTools.PathRoot
- readDunbrackRotamerLibraryForResiduePosition(String, List<ResidueTemplate>) - Static method in class edu.duke.cs.osprey.restypes.RotamerLibraryReader
-
PGC 2015: Read all the rotamer entries for the dunbrack rotamer library and add the corresponding ones to the residue templates in the template library templateLib.
- readEEF1parm() - Method in class edu.duke.cs.osprey.energy.forcefield.EEF1
- readFile(File) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- readFile(File) - Static method in class edu.duke.cs.osprey.tools.FileTools
- readFile(String) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- readFile(String) - Static method in class edu.duke.cs.osprey.tools.FileTools
- readFileBytes(File) - Static method in class edu.duke.cs.osprey.tools.FileTools
- readFileBytes(String) - Static method in class edu.duke.cs.osprey.tools.FileTools
- readFrom(DataInput) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrix
- readFrom(DataInput) - Method in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- readFrom(DataInput) - Method in class edu.duke.cs.osprey.tools.BigExp
- readFrom(DataInput) - Method in interface edu.duke.cs.osprey.tools.IOable
- readFrom(File) - Method in interface edu.duke.cs.osprey.tools.IOable
- readFromGZIP(File) - Method in interface edu.duke.cs.osprey.tools.IOable
- readInputFiles(String, String, String, String) - Method in class edu.duke.cs.osprey.dof.deeper.RamachandranChecker
- readInternal(ObjectDataInput) - Method in class edu.duke.cs.osprey.coffee.directions.FinishedSequencesOperation
- readInternal(ObjectDataInput) - Method in class edu.duke.cs.osprey.coffee.directions.FocusOperation
- readInternal(ObjectDataInput) - Method in class edu.duke.cs.osprey.coffee.directions.TreeOperation
- readInternal(ObjectDataInput) - Method in class edu.duke.cs.osprey.coffee.nodedb.AddNodesOperation
- readInternal(ObjectDataInput) - Method in class edu.duke.cs.osprey.coffee.nodedb.BroadcastOperation
- readInternal(ObjectDataInput) - Method in class edu.duke.cs.osprey.coffee.nodedb.ClearOperation
- readInternal(ObjectDataInput) - Method in class edu.duke.cs.osprey.coffee.nodedb.GetHighestNodeOperation
- readInternal(ObjectDataInput) - Method in class edu.duke.cs.osprey.coffee.nodedb.GetHighestNodesOperation
- readInternal(ObjectDataInput) - Method in class edu.duke.cs.osprey.coffee.seqdb.SaveOperation
- readInternal(ObjectDataInput) - Method in class edu.duke.cs.osprey.coffee.zmat.TuplesOperation
- readMols(File) - Static method in class edu.duke.cs.osprey.structure.PDBIO
-
faster reading method for bulk reads doesn't do secondary structure annotation
- readMols(String) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- readNode() - Method in class edu.duke.cs.osprey.sofea.FringeDB.Transaction
-
reads and removes the node at the head of the queue
- readObject(String, boolean) - Static method in class edu.duke.cs.osprey.tools.ObjectIO
- readOrMake(File, Class<T>, String, Factory<T, Void>) - Static method in class edu.duke.cs.osprey.tools.ObjectIO
- readOrMake(File, Class<T>, String, ObjectIO.Validator<T>, Factory<T, Void>) - Static method in class edu.duke.cs.osprey.tools.ObjectIO
- readOrThrow(File, Class<T>, String, ObjectIO.Validator<T>) - Static method in class edu.duke.cs.osprey.tools.ObjectIO
- readPath(String) - Method in class edu.duke.cs.osprey.control.ParamSet
- readPerts(BufferedReader) - Method in class edu.duke.cs.osprey.dof.deeper.PertSet
- readPerts(BufferedReader, ResidueTermini) - Method in class edu.duke.cs.osprey.dof.deeper.PertSet
- readResource(String) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- readResource(String) - Static method in class edu.duke.cs.osprey.tools.FileTools
- readResource(String, Class<?>) - Static method in class edu.duke.cs.osprey.tools.FileTools
- readResourceBytes(String) - Static method in class edu.duke.cs.osprey.tools.FileTools
- readResourceBytes(String, Class<?>) - Static method in class edu.duke.cs.osprey.tools.FileTools
- readRotLibrary(String, List<ResidueTemplate>) - Static method in class edu.duke.cs.osprey.restypes.RotamerLibraryReader
- readSettings(DataInput) - Method in class edu.duke.cs.osprey.energy.compiled.AmberEnergyCalculator
- readSettings(DataInput) - Method in interface edu.duke.cs.osprey.energy.compiled.EnergyCalculator
-
read runtime settings from the stream
- real(Structs.Precision) - Static method in class edu.duke.cs.osprey.gpu.Structs
- realarray(Structs.Precision) - Static method in class edu.duke.cs.osprey.gpu.Structs
- reallyDraw() - Method in class edu.duke.cs.osprey.tools.SVG.Drawable
- reallyDraw() - Method in class edu.duke.cs.osprey.tools.SVG.ShapeDrawable
- reallyDraw() - Method in class edu.duke.cs.osprey.tools.SVG.TextDrawable
- receiveBroadcast(Address, NodeIndices.BroadcastInfo) - Method in class edu.duke.cs.osprey.coffee.nodedb.Neighbors
- recenter(double, double) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- recip() - Method in class edu.duke.cs.osprey.tools.BigMath
- recomputeEpsilon() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- reComputePartialQLB(ConfSearch) - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- reconnectInterResBonds() - Method in class edu.duke.cs.osprey.structure.Residue
- recordCorrection(double, double) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- recordException(TaskExecutor.Task<?>, TaskExecutor.TaskListener<?>, Throwable) - Method in class edu.duke.cs.osprey.parallelism.ConcurrentTaskExecutor
- Rect() - Constructor for class edu.duke.cs.osprey.confspace.VoxelShape.Rect
- Rect(double) - Constructor for class edu.duke.cs.osprey.confspace.VoxelShape.Rect
- reducedAllowedAAs - Variable in class edu.duke.cs.osprey.kstar.KSSearchProblem
- ReducedEnergyMatrix - Class in edu.duke.cs.osprey.kstar.emat
- ReducedEnergyMatrix(KSSearchProblem, EnergyMatrix) - Constructor for class edu.duke.cs.osprey.kstar.emat.ReducedEnergyMatrix
- reducedMat - Variable in class edu.duke.cs.osprey.kstar.KSSearchProblem
- reducedPmat - Variable in class edu.duke.cs.osprey.kstar.KAStarConfTree
- ReducedPruningMatrix - Class in edu.duke.cs.osprey.kstar.pruning
- ReducedPruningMatrix(KSSearchProblem) - Constructor for class edu.duke.cs.osprey.kstar.pruning.ReducedPruningMatrix
- ReducedPruningMatrix(KSSearchProblem, UpdatedPruningMatrix) - Constructor for class edu.duke.cs.osprey.kstar.pruning.ReducedPruningMatrix
- reducedSP - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- reducedSPName - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- reduceMinimizations - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- reduceMinimizations - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- reduceMinimizations - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- reduceMinimizations - Variable in class edu.duke.cs.osprey.markstar.MARKStar.Settings
- refAngle - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.DihedralAnglesMinDist
- referenceEnergies(ReferenceEnergies) - Static method in interface edu.duke.cs.osprey.gmec.MinimizingConfEnergyCalculator.ConfPostProcessor
-
Deprecated.
- ReferenceEnergies - Class in edu.duke.cs.osprey.ematrix
-
This class computes a reference energy for each residue position & AA type (which is the minimum intra-RC energy at that position & AA type) and then corrects the energy matrix accordingly
- ReferenceEnergies(ConfSpace) - Constructor for class edu.duke.cs.osprey.ematrix.ReferenceEnergies
- refine(Sofea.Criterion) - Method in class edu.duke.cs.osprey.sofea.Sofea
-
Keep sweeping the threshold over the parameter space until the criterion is satisfied.
- refine(Sofea.Criterion, boolean) - Method in class edu.duke.cs.osprey.sofea.Sofea
-
Keep sweeping the threshold over the parameter space until the criterion is satisfied.
- refineScore(T) - Method in class edu.duke.cs.osprey.astar.AStarTree
- refineScore(T) - Method in class edu.duke.cs.osprey.astar.ConfTree
- region - Variable in class edu.duke.cs.osprey.design.S3Settings
- registerSerializer(Class<T>, StreamSerializer<T>) - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- registerService(String, Object) - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- release(CUBuffer<T>) - Method in class edu.duke.cs.osprey.gpu.cuda.BufferPool
- release(GpuStream) - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStreamPool
- release(GpuQueue) - Method in class edu.duke.cs.osprey.gpu.opencl.GpuQueuePool
- release(T) - Method in class edu.duke.cs.osprey.tools.ObjectPool
- remove(int) - Method in class edu.duke.cs.osprey.confspace.RCIndexMap
- remove(int) - Method in class edu.duke.cs.osprey.structure.Residues
- remove(int[]) - Method in class edu.duke.cs.osprey.confspace.Conf.Map
- remove(int[]) - Method in class edu.duke.cs.osprey.confspace.Conf.Set
- remove(int[]) - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- remove(ConfSMAStarNode) - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarQueue
- remove(Residue) - Method in class edu.duke.cs.osprey.structure.Residues
- remove(Object) - Method in class edu.duke.cs.osprey.confspace.Conf.Map
- remove(Object) - Method in class edu.duke.cs.osprey.confspace.Conf.Set
- remove(Object) - Method in class edu.duke.cs.osprey.structure.Residues
- remove(String) - Method in class edu.duke.cs.osprey.structure.Residues
- removeAll(Collection<?>) - Method in class edu.duke.cs.osprey.structure.Residues
- removeFromMap(String, boolean, boolean) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- removeFromParent() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- removeFromRes() - Method in class edu.duke.cs.osprey.structure.ConfProblem
- removeHigh(int) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
-
Conveience method to remove a single node.
- removeHigh(int, int, List<NodeIndex.Node>) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
-
Removes high-scoring nodes from the cluster.
- removeHighest() - Method in interface edu.duke.cs.osprey.coffee.nodedb.FixedIndex
-
Removes the highest-scoring item currently stored.
- removeHighest() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex
- removeHighest() - Method in class edu.duke.cs.osprey.coffee.nodedb.PriorityDequeFixedIndex
- removeHighest(int, int, List<NodeIndex.Node>) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices
- removeHighestLocal(int) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
-
Conveience method to remove a single node.
- removeHighestLocal(int, int, List<NodeIndex.Node>) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
-
Removes the highest node from the local index.
- removeHighestNodes(Address, int, int, List<NodeIndex.Node>) - Method in class edu.duke.cs.osprey.coffee.nodedb.Neighbors
- removeHighestShallowestLeaf() - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarQueue
- removeIf(Predicate<? super Residue>) - Method in class edu.duke.cs.osprey.structure.Residues
- removeInterResBonds() - Method in class edu.duke.cs.osprey.structure.Residue
- removeOrAssert(ConfSMAStarNode) - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarQueue
- removePosFromAllowedAAs(ArrayList<ArrayList<String>>) - Static method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- removeRange(int, int) - Method in class edu.duke.cs.osprey.structure.Residues
- removeStrandSeq(int) - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- render() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- render() - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.Color
- render(double) - Method in enum class edu.duke.cs.osprey.tools.SVG.LengthUnit
- render(Sequence.Assignment) - Method in enum class edu.duke.cs.osprey.confspace.Sequence.Renderer
- render(Group) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- renderCols() - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.Intervals
- renderCols() - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.LinesX
- renderCols() - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.LinesY
- renderCols() - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.PointsX
- renderCols() - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.PointsY
- renderCols() - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.Series
- renderData(Map<Plot.Axis, Double>, Map<Plot.Axis, Double>) - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.IntervalsX
- renderData(Map<Plot.Axis, Double>, Map<Plot.Axis, Double>) - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.IntervalsY
- renderData(Map<Plot.Axis, Double>, Map<Plot.Axis, Double>) - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.LinesX
- renderData(Map<Plot.Axis, Double>, Map<Plot.Axis, Double>) - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.LinesY
- renderData(Map<Plot.Axis, Double>, Map<Plot.Axis, Double>) - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.PointsX
- renderData(Map<Plot.Axis, Double>, Map<Plot.Axis, Double>) - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.PointsY
- renderData(Map<Plot.Axis, Double>, Map<Plot.Axis, Double>) - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.Series
- renderData1D(List<Double>, Double, Double) - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.Lines
- renderData1D(List<Double>, Double, Double) - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.Points
- renderNames(List<SVG.StyleClass>) - Static method in class edu.duke.cs.osprey.tools.SVG.StyleClass
- renderPng() - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot
- renderStyle(int, List<Plot.Color>) - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.Intervals
- renderStyle(int, List<Plot.Color>) - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.Lines
- renderStyle(int, List<Plot.Color>) - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.Points
- renderStyle(int, List<Plot.Color>) - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot.Series
- renderSvg() - Method in class edu.duke.cs.osprey.tools.resultdoc.Plot
- renderText(String) - Static method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd
-
escape text values and box with " chars
- renderTree(KStarTreeNode) - Static method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeRenderer
- replaceAll(UnaryOperator<Residue>) - Method in class edu.duke.cs.osprey.structure.Residues
- replaceRc(int, RC, List<RC>) - Method in class edu.duke.cs.osprey.partcr.SplitWorld
- replaceRC(RC, List<RC>) - Method in class edu.duke.cs.osprey.confspace.PositionConfSpace
- report() - Method in class edu.duke.cs.osprey.coffee.directors.AffinityDirector
- Report(long, long, NodeStats.Values) - Constructor for class edu.duke.cs.osprey.coffee.NodeStats.Report
- reportConfSpaceSize() - Method in class edu.duke.cs.osprey.lute.LUTE
- reportConfSpaceSize(PruningMatrix) - Method in class edu.duke.cs.osprey.lute.LUTE
- Reporter(Duration, Consumer<NodeStats.Report>) - Constructor for class edu.duke.cs.osprey.coffee.NodeStats.Reporter
- reportInternalNode(int, double, double, long, int) - Method in class edu.duke.cs.osprey.astar.AStarProgress
- reportInternalNode(int, double, double, long, int, double) - Method in class edu.duke.cs.osprey.markstar.MARKStarProgress
- reportLeafNode(double, long) - Method in class edu.duke.cs.osprey.astar.AStarProgress
- reportLeafNode(double, long, double) - Method in class edu.duke.cs.osprey.markstar.MARKStarProgress
- reportPartialMinimization(int, double) - Method in class edu.duke.cs.osprey.markstar.MARKStarProgress
- reportProgress - Variable in class edu.duke.cs.osprey.astar.conf.ConfRanker
- reportProgress - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncDirector
- reportProgress - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncsDirector
- reportProgress - Variable in class edu.duke.cs.osprey.coffee.directors.SequenceDirector
- reportStateProgress - Variable in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- rePruneReducedSP(double) - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- REQ() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.BondLengthParameter
-
Returns the value of the
REQrecord component. - request() - Method in class edu.duke.cs.osprey.parallelism.RateLimitedThread
- requestFrom(Operation, Address, long, TimeUnit) - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- Requeue - Enum constant in enum class edu.duke.cs.osprey.sofea.Sofea.Criterion.Filter
- res - Variable in class edu.duke.cs.osprey.confspace.PositionConfSpace
- res - Variable in class edu.duke.cs.osprey.structure.Atom
- res1 - Variable in class edu.duke.cs.osprey.energy.forcefield.CoordsAndCharges
- res1 - Variable in class edu.duke.cs.osprey.energy.forcefield.ResPairCache.ResPair
- res1Start - Variable in class edu.duke.cs.osprey.energy.forcefield.CoordsAndCharges
- res2 - Variable in class edu.duke.cs.osprey.energy.forcefield.CoordsAndCharges
- res2 - Variable in class edu.duke.cs.osprey.energy.forcefield.ResPairCache.ResPair
- Res2AtomsIterable - Class in edu.duke.cs.osprey.plug
- Res2AtomsIterable(Atom, Residue, Residue) - Constructor for class edu.duke.cs.osprey.plug.Res2AtomsIterable
- res2Start - Variable in class edu.duke.cs.osprey.energy.forcefield.CoordsAndCharges
- ResBBState - Class in edu.duke.cs.osprey.dof.deeper
-
Records backbone coordinates for a residue, so we can restore them when performing perturbations Sidechain is moved as a rigid body (including CA)
- ResBBState(ResBBState) - Constructor for class edu.duke.cs.osprey.dof.deeper.ResBBState
- ResBBState(Residue) - Constructor for class edu.duke.cs.osprey.dof.deeper.ResBBState
- resConfs - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Position
- resConfs - Variable in class edu.duke.cs.osprey.dof.DofInfo
- rescored - Variable in class edu.duke.cs.osprey.coffee.NodeStats.Values
- rescored() - Method in class edu.duke.cs.osprey.coffee.NodeStats.ForThread
- reset() - Method in class edu.duke.cs.osprey.parallelism.Signal
- reset() - Method in class edu.duke.cs.osprey.tools.Stopwatch
- resetCounters() - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- resetProcessedDuringInterval() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- ResetSize - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.DominantBaseline
- resetSPs() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel2
- resFlex - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Position
- resId - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.ResInfo
- residual - Variable in class edu.duke.cs.osprey.lute.LUTE.Errors
- Residue - Class in edu.duke.cs.osprey.design.models
- Residue - Class in edu.duke.cs.osprey.structure
-
A Residue is a piece of a molecular system that can mutate, take on RCs, etc.
- Residue() - Constructor for class edu.duke.cs.osprey.design.models.Residue
- Residue(Residue) - Constructor for class edu.duke.cs.osprey.structure.Residue
- Residue(ArrayList<Atom>, double[], String, Molecule) - Constructor for class edu.duke.cs.osprey.structure.Residue
- Residue(ArrayList<Atom>, ArrayList<double[]>, String, Molecule) - Constructor for class edu.duke.cs.osprey.structure.Residue
- Residue.SecondaryStructure - Enum Class in edu.duke.cs.osprey.structure
- Residue.TemplateMatchingMethod - Enum Class in edu.duke.cs.osprey.structure
- ResidueAtomGroup(Residue) - Constructor for class edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions.ResidueAtomGroup
-
Deprecated.
- ResidueConf(SimpleConfSpace.Position, int, ResidueTemplate, SimpleConfSpace.ResidueConf.Type, Integer, HashMap<String, double[]>) - Constructor for class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf
- ResidueConf(SimpleConfSpace.Position, int, ResidueTemplate, SimpleConfSpace.ResidueConf.Type, HashMap<String, double[]>) - Constructor for class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf
- ResidueCuda - Enum constant in enum class edu.duke.cs.osprey.energy.EnergyCalculator.Type
- ResidueCudaCCD - Enum constant in enum class edu.duke.cs.osprey.energy.EnergyCalculator.Type
- ResidueCudaCCDMinimizer - Class in edu.duke.cs.osprey.gpu.cuda.kernels
- ResidueCudaCCDMinimizer(GpuStreamPool, ObjectiveFunction) - Constructor for class edu.duke.cs.osprey.gpu.cuda.kernels.ResidueCudaCCDMinimizer
- residueEntropies - Variable in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
- ResidueEntropies - Class in edu.duke.cs.osprey.restypes
- ResidueEntropies() - Constructor for class edu.duke.cs.osprey.restypes.ResidueEntropies
- residueEntropy(ConfSpace) - Static method in interface edu.duke.cs.osprey.gmec.MinimizingConfEnergyCalculator.ConfPostProcessor
-
Deprecated.
- ResidueEntropyParser - Class in edu.duke.cs.osprey.restypes
- ResidueEntropyParser(ResidueEntropies) - Constructor for class edu.duke.cs.osprey.restypes.ResidueEntropyParser
- ResidueFlex(String) - Constructor for class edu.duke.cs.osprey.confspace.Strand.ResidueFlex
- ResidueForcefieldBreakdown - Class in edu.duke.cs.osprey.energy
- ResidueForcefieldBreakdown() - Constructor for class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown
- ResidueForcefieldBreakdown.ByPosition - Class in edu.duke.cs.osprey.energy
- ResidueForcefieldBreakdown.ByResidue - Class in edu.duke.cs.osprey.energy
- ResidueForcefieldBreakdown.Type - Enum Class in edu.duke.cs.osprey.energy
- ResidueForcefieldEnergy - Class in edu.duke.cs.osprey.energy.forcefield
- ResidueForcefieldEnergy(ResPairCache, ResidueInteractions, Molecule) - Constructor for class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- ResidueForcefieldEnergy(ResPairCache, ResidueInteractions, Residues) - Constructor for class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- ResidueForcefieldEnergy.Vdw - Class in edu.duke.cs.osprey.energy.forcefield
- ResidueForcefieldEnergyCuda - Class in edu.duke.cs.osprey.gpu.cuda.kernels
- ResidueForcefieldEnergyCuda(GpuStreamPool, ResPairCache, ResidueInteractions, Molecule) - Constructor for class edu.duke.cs.osprey.gpu.cuda.kernels.ResidueForcefieldEnergyCuda
- ResidueForcefieldEnergyCuda(GpuStreamPool, ResPairCache, ResidueInteractions, Residues) - Constructor for class edu.duke.cs.osprey.gpu.cuda.kernels.ResidueForcefieldEnergyCuda
- residueInteractionEnergy(Residues, ResidueInteractions) - Method in class edu.duke.cs.osprey.energy.EnergyFunctionGenerator
- ResidueInteractions - Class in edu.duke.cs.osprey.energy
-
Represents interactions between residues (or within single residues) based on residue numbers.
- ResidueInteractions() - Constructor for class edu.duke.cs.osprey.energy.ResidueInteractions
- ResidueInteractions(ResidueInteractions.Pair...) - Constructor for class edu.duke.cs.osprey.energy.ResidueInteractions
- ResidueInteractions.Pair - Class in edu.duke.cs.osprey.energy
- ResidueInteractionsApproximator - Class in edu.duke.cs.osprey.energy.approximation
- ResidueInteractionsApproximator(ApproximatedObjectiveFunction.Approximator, ResidueInteractions, ResidueInteractions) - Constructor for class edu.duke.cs.osprey.energy.approximation.ResidueInteractionsApproximator
- ResidueInteractionsApproximator.Builder - Class in edu.duke.cs.osprey.energy.approximation
- ResidueModifier - Class in edu.duke.cs.osprey.design.models
- ResidueModifier() - Constructor for class edu.duke.cs.osprey.design.models.ResidueModifier
- residueModifiers - Variable in class edu.duke.cs.osprey.design.models.MoleculeDto
- residueNumber - Variable in class edu.duke.cs.osprey.design.models.Residue
- ResidueOrder - Interface in edu.duke.cs.osprey.multistatekstar
- ResidueOrder.AAScore - Class in edu.duke.cs.osprey.multistatekstar
- ResidueOrderFactory - Class in edu.duke.cs.osprey.multistatekstar
- ResidueOrderFactory() - Constructor for class edu.duke.cs.osprey.multistatekstar.ResidueOrderFactory
- ResidueOrderStaticSequential - Class in edu.duke.cs.osprey.multistatekstar
- ResidueOrderStaticSequential(MSSearchProblem[][]) - Constructor for class edu.duke.cs.osprey.multistatekstar.ResidueOrderStaticSequential
- residuePos - Variable in class edu.duke.cs.osprey.multistatekstar.ResidueOrder.AAScore
- residues - Variable in class edu.duke.cs.osprey.design.models.ScanDto
- residues - Variable in class edu.duke.cs.osprey.energy.forcefield.EEF1.ResiduesInfo
- residues - Variable in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- residues - Variable in class edu.duke.cs.osprey.gpu.cuda.kernels.ResidueForcefieldEnergyCuda
- residues - Variable in class edu.duke.cs.osprey.structure.Molecule
- Residues - Class in edu.duke.cs.osprey.structure
-
This class implements a collection of Residues with fast lookups.
- Residues() - Constructor for class edu.duke.cs.osprey.structure.Residues
- Residues(Residue...) - Constructor for class edu.duke.cs.osprey.structure.Residues
- ResiduesInfo(Residues) - Constructor for class edu.duke.cs.osprey.energy.forcefield.EEF1.ResiduesInfo
- ResidueTemplate - Class in edu.duke.cs.osprey.restypes
- ResidueTemplate(Residue, String, InterResBondingTemplate, String) - Constructor for class edu.duke.cs.osprey.restypes.ResidueTemplate
- ResidueTemplateLibrary - Class in edu.duke.cs.osprey.restypes
-
Library of
ResidueTemplateinstances used byStrandinstances to define discrete flexibilty. - ResidueTemplateLibrary.Builder - Class in edu.duke.cs.osprey.restypes
- ResidueTermini - Class in edu.duke.cs.osprey.multistatekstar
- ResidueTermini(int, String, String) - Constructor for class edu.duke.cs.osprey.multistatekstar.ResidueTermini
- ResidueTypeDOF - Class in edu.duke.cs.osprey.dof
- ResidueTypeDOF(ResidueTemplateLibrary, Residue) - Constructor for class edu.duke.cs.osprey.dof.ResidueTypeDOF
-
Deprecated.
- ResidueTypeDOF(ResidueTemplateLibrary, Residue, boolean) - Constructor for class edu.duke.cs.osprey.dof.ResidueTypeDOF
-
Deprecated.
- resIndex1 - Variable in class edu.duke.cs.osprey.energy.forcefield.ResPairCache.ResPair
- resIndex2 - Variable in class edu.duke.cs.osprey.energy.forcefield.ResPairCache.ResPair
- ResInfo(String, String, String, int) - Constructor for class edu.duke.cs.osprey.confspace.compiled.ConfSpace.ResInfo
- resInfos - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- ResInterGen - Class in edu.duke.cs.osprey.energy
-
Helper class to create
ResidueInteractionsFirst call ResInterGen.of(yourConfSpace), then .addXXX() for each interactions you wish to add. - ResInterGen.InterOffsetter - Interface in edu.duke.cs.osprey.energy
- ResInterGen.IntraOffsetter - Interface in edu.duke.cs.osprey.energy
- ResInterGen.ShellOffsetter - Interface in edu.duke.cs.osprey.energy
- resizeMatrices() - Method in class edu.duke.cs.osprey.partcr.SplitWorld
- resListFromTermini(String[], ArrayList<String>) - Method in class edu.duke.cs.osprey.structure.Molecule
- resNum - Variable in class edu.duke.cs.osprey.confspace.SeqSpace.Position
- resNum - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Position
- resNum - Variable in class edu.duke.cs.osprey.structure.analysis.TemplateChooser.MeasuredRes
- ResNum - Enum constant in enum class edu.duke.cs.osprey.confspace.Sequence.Renderer
-
Render just the residue number.
- resNum1 - Variable in class edu.duke.cs.osprey.energy.ResidueInteractions.Pair
- resNum2 - Variable in class edu.duke.cs.osprey.energy.ResidueInteractions.Pair
- resNums() - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Returns the list of residue numbers for this sequence.
- resolve(File) - Method in class edu.duke.cs.osprey.tools.FileTools.FilePathRoot
- resolve(String) - Method in class edu.duke.cs.osprey.tools.FileTools.FilePathRoot
- resolve(String) - Method in class edu.duke.cs.osprey.tools.FileTools.PathRoot
- resolve(String) - Method in class edu.duke.cs.osprey.tools.FileTools.ResourcePathRoot
- ResourcePathRoot() - Constructor for class edu.duke.cs.osprey.tools.FileTools.ResourcePathRoot
- ResourcePathRoot(Class<?>) - Constructor for class edu.duke.cs.osprey.tools.FileTools.ResourcePathRoot
- ResourcePathRoot(String) - Constructor for class edu.duke.cs.osprey.tools.FileTools.ResourcePathRoot
- ResPair(int, int, Residue, Residue, double, double, ResPairCache.AtomPairInfo, ForcefieldParams.SolvationForcefield.ResiduesInfo, double) - Constructor for class edu.duke.cs.osprey.energy.forcefield.ResPairCache.ResPair
- resPairAndDistributedShellEnergy(Residue, Residue, List<Residue>, int, double) - Method in class edu.duke.cs.osprey.energy.EnergyFunctionGenerator
- resPairAndDistributedShellEnergy(Residue, Residue, List<Residue>, int, double) - Method in class edu.duke.cs.osprey.energy.GpuEnergyFunctionGenerator
- resPairCache - Variable in class edu.duke.cs.osprey.energy.EnergyCalculator
- resPairCache - Variable in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- ResPairCache - Class in edu.duke.cs.osprey.energy.forcefield
- ResPairCache(ForcefieldParams, AtomConnectivity) - Constructor for class edu.duke.cs.osprey.energy.forcefield.ResPairCache
- ResPairCache.AtomPairInfo - Class in edu.duke.cs.osprey.energy.forcefield
- ResPairCache.ResPair - Class in edu.duke.cs.osprey.energy.forcefield
- resPairEnergy(Residue, Residue) - Method in class edu.duke.cs.osprey.energy.EnergyFunctionGenerator
- resPairEnergy(Residue, Residue) - Method in class edu.duke.cs.osprey.energy.GpuEnergyFunctionGenerator
- ResPairEnergy - Class in edu.duke.cs.osprey.energy.forcefield
- ResPairEnergy(Residue, Residue, ForcefieldParams) - Constructor for class edu.duke.cs.osprey.energy.forcefield.ResPairEnergy
- ResPairEnergyContribution - Class in edu.duke.cs.osprey.energy.forcefield
- ResPairEnergyContribution(ResPairCache.ResPair, List<AtomPairEnergyContribution>) - Constructor for class edu.duke.cs.osprey.energy.forcefield.ResPairEnergyContribution
- resPairs - Variable in class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
- restart() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- ResTemplateMatching - Class in edu.duke.cs.osprey.restypes
- ResTemplateMatching(Residue, ResidueTemplate, ForcefieldParams) - Constructor for class edu.duke.cs.osprey.restypes.ResTemplateMatching
- resTemplates - Static variable in class edu.duke.cs.osprey.control.EnvironmentVars
-
Deprecated.
- restoreCoordsFromTemplate() - Method in class edu.duke.cs.osprey.dof.ResidueTypeDOF
- resType - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.ResInfo
- resType - Variable in class edu.duke.cs.osprey.structure.Probe.Template
- ResType - Enum constant in enum class edu.duke.cs.osprey.confspace.Sequence.Renderer
-
Render just the residue type.
- ResType(SeqSpace.Position, int, String) - Constructor for class edu.duke.cs.osprey.confspace.SeqSpace.ResType
- ResTypeMutations - Enum constant in enum class edu.duke.cs.osprey.confspace.Sequence.Renderer
-
Render just the residue type, but use UPPERCASE for mutations, and lowercase for wild-type.
- resTypes - Variable in class edu.duke.cs.osprey.confspace.SeqSpace.Position
- resTypes - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Position
- resTypes - Variable in class edu.duke.cs.osprey.confspace.Strand.ResidueFlex
- Result(DoubleMatrix1D, double) - Constructor for class edu.duke.cs.osprey.minimization.Minimizer.Result
- Result(EWAKStarPartitionFunction.Status, ArrayList<EnergyCalculator.EnergiedParametricMolecule>, HashMap<Double, ConfSearch.ScoredConf>, EWAKStarPartitionFunction.Values, int) - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Result
- Result(PartitionFunction.Status, PartitionFunction.Values, int) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Result
- Result(PastePartitionFunction.Status, ArrayList<EnergyCalculator.EnergiedParametricMolecule>, HashMap<Double, ConfSearch.ScoredConf>, PastePartitionFunction.Values, int) - Constructor for class edu.duke.cs.osprey.paste.PastePartitionFunction.Result
- ResultDoc - Class in edu.duke.cs.osprey.tools.resultdoc
- ResultDoc() - Constructor for class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- ResultDoc(File) - Constructor for class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- ResultDoc(OutputStream) - Constructor for class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- ResultDoc(String) - Constructor for class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- ResultDoc(Path) - Constructor for class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- ResultDoc.File - Class in edu.duke.cs.osprey.tools.resultdoc
- ResultDoc.Image - Class in edu.duke.cs.osprey.tools.resultdoc
- ResultDoc.PlotType - Enum Class in edu.duke.cs.osprey.tools.resultdoc
- Results() - Constructor for class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Results
- resume - Variable in class edu.duke.cs.osprey.kstar.KStar.Settings
- resume() - Method in class edu.duke.cs.osprey.tools.Stopwatch
- resume(boolean) - Method in class edu.duke.cs.osprey.kstar.KStar.Settings.Builder
- resume(String) - Method in class edu.duke.cs.osprey.tools.Profiler
- retainAll(Collection<?>) - Method in class edu.duke.cs.osprey.structure.Residues
- returnsResponse() - Method in class edu.duke.cs.osprey.coffee.directions.FinishedSequencesOperation
- returnsResponse() - Method in class edu.duke.cs.osprey.coffee.directions.FocusOperation
- returnsResponse() - Method in class edu.duke.cs.osprey.coffee.directions.StopOperation
- returnsResponse() - Method in class edu.duke.cs.osprey.coffee.directions.TreeOperation
- returnsResponse() - Method in class edu.duke.cs.osprey.coffee.nodedb.AddNodesOperation
- returnsResponse() - Method in class edu.duke.cs.osprey.coffee.nodedb.BroadcastOperation
- returnsResponse() - Method in class edu.duke.cs.osprey.coffee.nodedb.ClearOperation
- returnsResponse() - Method in class edu.duke.cs.osprey.coffee.nodedb.GetHighestNodeOperation
- returnsResponse() - Method in class edu.duke.cs.osprey.coffee.nodedb.GetHighestNodesOperation
- returnsResponse() - Method in class edu.duke.cs.osprey.coffee.seqdb.SaveOperation
- returnsResponse() - Method in class edu.duke.cs.osprey.coffee.zmat.TuplesOperation
- reverse() - Method in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
- ri - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle
- RigidBodyMotion - Class in edu.duke.cs.osprey.tools
- RigidBodyMotion(double[][], double[][]) - Constructor for class edu.duke.cs.osprey.tools.RigidBodyMotion
- RigidBodyMotion(double[], double[], double, boolean) - Constructor for class edu.duke.cs.osprey.tools.RigidBodyMotion
- RigidBodyMotion(double[], double[], double, double) - Constructor for class edu.duke.cs.osprey.tools.RigidBodyMotion
- RigidBodyMotion(double[], RotationMatrix, double[]) - Constructor for class edu.duke.cs.osprey.tools.RigidBodyMotion
- rigidConfEcalc - Variable in class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceInfo
- rigidEcalc - Variable in class edu.duke.cs.osprey.markstar.MARKStar
-
Calculates the rigid energy for a molecule
- rigidEmat - Variable in class edu.duke.cs.osprey.kstar.MSKStar.Builder
-
Temporary MARKStar fields because this interface doesn't cleanly support non-ConfSearch PartitionFunction implementations...
- rigidEmat - Variable in class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceInfo
- rigidScore - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- rigidscorer - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound.ScoreContext
- ringCloseable() - Method in class edu.duke.cs.osprey.dof.ProlinePucker
- RK() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.BondLengthParameter
-
Returns the value of the
RKrecord component. - RMIN() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.SlaterKirkwoodParameter
-
Returns the value of the
RMINrecord component. - rms - Variable in class edu.duke.cs.osprey.lute.LUTE.Errors
- rmsViolation - Variable in class edu.duke.cs.osprey.structure.analysis.TemplateChooser.MeasuredRes
- Room - Static variable in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator.Conditions
-
Room temperature: 25 C, or about 298.15 K, or about 77 F
- root - Variable in class edu.duke.cs.osprey.confspace.TupleTree
- root - Variable in class edu.duke.cs.osprey.tools.FileTools.Path
- rootNode - Variable in class edu.duke.cs.osprey.astar.seq.SeqAStarTree
- rootNode - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
-
TODO: 1.
- rootNode() - Method in class edu.duke.cs.osprey.astar.AStarTree
- rootNode() - Method in class edu.duke.cs.osprey.astar.comets.COMETSTree
- rootNode() - Method in class edu.duke.cs.osprey.astar.comets.NewCOMETSTree
- rootNode() - Method in class edu.duke.cs.osprey.astar.ConfTree
- rotamerIndex - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf
- RotamerLibraryReader - Class in edu.duke.cs.osprey.restypes
-
This class implements a rotamer library reader.
- RotamerLibraryReader() - Constructor for class edu.duke.cs.osprey.restypes.RotamerLibraryReader
- rotate - Variable in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.Tics
- rotate(double[], double[], double[], double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- rotated - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Description
- rotateDegrees - Variable in class edu.duke.cs.osprey.design.models.TranslateRotateDto
- rotateInverse(double[], double[], double[], double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- rotateVector(double[]) - Method in class edu.duke.cs.osprey.tools.RotationMatrix
- RotationMatrix - Class in edu.duke.cs.osprey.tools
-
x
- RotationMatrix(double[][]) - Constructor for class edu.duke.cs.osprey.tools.RotationMatrix
- RotationMatrix(double, double, double, double, boolean) - Constructor for class edu.duke.cs.osprey.tools.RotationMatrix
- RotationMatrix(double, double, double, double, double) - Constructor for class edu.duke.cs.osprey.tools.RotationMatrix
- rotNum - Variable in class edu.duke.cs.osprey.confspace.RC
- roundUpToMultiple(int, int) - Static method in class edu.duke.cs.osprey.tools.MathTools
- roundUpWorkSize(int, int) - Method in class edu.duke.cs.osprey.gpu.opencl.Kernel
- RPrecise - Static variable in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- rt - Variable in class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode.Link
- RT - Static variable in class edu.duke.cs.osprey.ibis.IBISKStarTupleExpander
- RT - Static variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- RT - Static variable in class edu.duke.cs.osprey.voxq.IntraVoxelSampler
- rtIndices - Variable in class edu.duke.cs.osprey.confspace.ConfDB.Key
- rtIndices - Variable in class edu.duke.cs.osprey.confspace.Sequence
- rts - Variable in class edu.duke.cs.osprey.astar.seq.SeqAStarTree
- RTs - Class in edu.duke.cs.osprey.astar.seq
-
ie, residue types analagous to the RCs class for residue conformations
- RTs(RTs, RTs.Filter) - Constructor for class edu.duke.cs.osprey.astar.seq.RTs
-
select a subset of RTs using an arbitrary filter
- RTs(SeqSpace) - Constructor for class edu.duke.cs.osprey.astar.seq.RTs
-
create RTs using the full sequence space
- RTs.Filter - Interface in edu.duke.cs.osprey.astar.seq
- run() - Method in class edu.duke.cs.osprey.coffee.directions.FinishedSequencesOperation
- run() - Method in class edu.duke.cs.osprey.coffee.directions.FocusOperation
- run() - Method in class edu.duke.cs.osprey.coffee.directions.StopOperation
- run() - Method in class edu.duke.cs.osprey.coffee.directions.TreeOperation
- run() - Method in class edu.duke.cs.osprey.coffee.nodedb.AddNodesOperation
- run() - Method in class edu.duke.cs.osprey.coffee.nodedb.BroadcastOperation
- run() - Method in class edu.duke.cs.osprey.coffee.nodedb.ClearOperation
- run() - Method in class edu.duke.cs.osprey.coffee.nodedb.GetHighestNodeOperation
- run() - Method in class edu.duke.cs.osprey.coffee.nodedb.GetHighestNodesOperation
- run() - Method in class edu.duke.cs.osprey.coffee.NodeStats.Reporter
- run() - Method in class edu.duke.cs.osprey.coffee.seqdb.SaveOperation
- run() - Method in class edu.duke.cs.osprey.coffee.zmat.TuplesOperation
- run() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar
- run() - Method in class edu.duke.cs.osprey.kstar.BBKStar
- run() - Method in class edu.duke.cs.osprey.kstar.impl.KSImplKAStar
- run() - Method in class edu.duke.cs.osprey.kstar.impl.KSImplLinear
- run() - Method in class edu.duke.cs.osprey.kstar.KSConfQ
- run() - Method in interface edu.duke.cs.osprey.kstar.KSInterface
- run() - Method in class edu.duke.cs.osprey.kstar.KSPStarCalculator
- run() - Method in class edu.duke.cs.osprey.kstar.KStar
- run() - Method in class edu.duke.cs.osprey.markstar.MARKStar
- run() - Method in interface edu.duke.cs.osprey.parallelism.TaskExecutor.Task
- run() - Method in interface edu.duke.cs.osprey.parallelism.TaskExecutor.Task.WithContext
- run() - Method in class edu.duke.cs.osprey.parallelism.TimingThread
- run() - Method in class edu.duke.cs.osprey.parallelism.WorkThread
- run() - Method in class edu.duke.cs.osprey.paste.Paste
- run(int) - Method in class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator
- run(int) - Method in class edu.duke.cs.osprey.kstar.pfunc.UpperBoundCalculator
- run(int, double) - Method in class edu.duke.cs.osprey.kstar.pfunc.UpperBoundCalculator
- run(int, TaskExecutor.TaskListener<ConfSearch.EnergiedConf>) - Method in class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator
- run(C) - Method in interface edu.duke.cs.osprey.parallelism.TaskExecutor.Task.WithContext
- run(JCommander, String[]) - Method in class edu.duke.cs.osprey.design.commands.CommandBindingAffinity
- run(JCommander, String[]) - Method in class edu.duke.cs.osprey.design.commands.CommandGMEC
- run(JCommander, String[]) - Method in class edu.duke.cs.osprey.design.commands.CommandMakeFlexShell
- run(JCommander, String[]) - Method in class edu.duke.cs.osprey.design.commands.CommandPartitionFunction
- run(JCommander, String[]) - Method in class edu.duke.cs.osprey.design.commands.CommandTopNConfs
- run(JCommander, String[]) - Method in class edu.duke.cs.osprey.design.commands.RunnableCommand
- run(Coffee.Director) - Method in class edu.duke.cs.osprey.coffee.Coffee
- run(SimpleConfSpace, EnergyMatrix) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- run(ConfigFileParser) - Method in class edu.duke.cs.osprey.control.EnergyCalculator
- run(Main.CommandArgs) - Method in enum class edu.duke.cs.osprey.control.Main.Command
- run(EwakstarDoer.State) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
-
find the best sequences as ranked by the objective function searches all sequences within the objective window
- run(KSCalc, boolean, boolean) - Method in class edu.duke.cs.osprey.kstar.KSCalc
- run(TaskExecutor) - Method in class edu.duke.cs.osprey.kstar.BBKStar
- run(TaskExecutor) - Method in class edu.duke.cs.osprey.kstar.KStar
- run(String[]) - Method in class edu.duke.cs.osprey.design.Main
- run(T) - Method in interface edu.duke.cs.osprey.tools.UseableBuilder.Block
- runAsync() - Method in class edu.duke.cs.osprey.gpu.cuda.Kernel.Function
- runAsync() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ForcefieldKernelCuda
- runAsync() - Method in interface edu.duke.cs.osprey.gpu.ForcefieldKernel
- runAsync() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.ForcefieldKernelOpenCL
- runAsync() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.TestFancyKernel
- runAsync(int, int) - Method in class edu.duke.cs.osprey.gpu.opencl.Kernel
- runAsync(DoubleMatrix1D, ObjectiveFunction.DofBounds) - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.CCDKernelCuda
- runFCFS() - Method in class edu.duke.cs.osprey.kstar.impl.KSImplLinear
- RunnableCommand - Class in edu.duke.cs.osprey.design.commands
- RunnableCommand() - Constructor for class edu.duke.cs.osprey.design.commands.RunnableCommand
- runName - Variable in class edu.duke.cs.osprey.kstar.KSAbstract
- Runner() - Constructor for class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- runPF(PFAbstract, PFAbstract, boolean, boolean) - Method in class edu.duke.cs.osprey.kstar.KSCalc
- runRR() - Method in class edu.duke.cs.osprey.kstar.impl.KSImplLinear
- runSlice(long) - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- runState - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- runSync(DoubleMatrix1D, ObjectiveFunction.DofBounds) - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.CCDKernelCuda
- runTask(TaskExecutor.Task<T>) - Method in class edu.duke.cs.osprey.parallelism.TaskExecutor
- runTimeout - Static variable in class edu.duke.cs.osprey.kstar.KSAbstract
- runToCompletion() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
S
- S - Enum constant in enum class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.Space
- S3Settings - Class in edu.duke.cs.osprey.design
- S3Settings(String, String) - Constructor for class edu.duke.cs.osprey.design.S3Settings
- SaltBridge - Enum constant in enum class edu.duke.cs.osprey.structure.Probe.Attraction
- sample(RCTuple, TuplesIndex) - Method in class edu.duke.cs.osprey.lute.UniformConfSampler
-
Deprecated.
- sample(RCTuple, Set<int[]>, int, TuplesIndex) - Method in class edu.duke.cs.osprey.lute.UniformConfSampler
-
Deprecated.
- sample(ConfEnergyCalculator, EnergyMatrix) - Method in class edu.duke.cs.osprey.kstar.pfunc.PfuncSurface
- sample(ConfEnergyCalculator, EnergyMatrix, RCs) - Method in class edu.duke.cs.osprey.kstar.pfunc.PfuncSurface
- sampleAllPairsAndFit(ConfEnergyCalculator, EnergyMatrix, PruningMatrix, ConfDB.ConfTable, ConfSampler, LUTE.Fitter, double, double) - Method in class edu.duke.cs.osprey.lute.LUTE
-
for when you know the fit will be difficult and just want to sample all the pairs and triples
- sampleAllPairsTriplesAndFit(ConfEnergyCalculator, EnergyMatrix, PruningMatrix, ConfDB.ConfTable, ConfSampler, LUTE.Fitter, double, double) - Method in class edu.duke.cs.osprey.lute.LUTE
-
for when you know the fit will be difficult and just want to sample all the pairs and triples
- sampleConfsForTuples(ConfSampler.Samples, int) - Method in class edu.duke.cs.osprey.lute.ConfSampler
- sampleConfsForTuples(ConfSampler.Samples, int) - Method in class edu.duke.cs.osprey.lute.LowEnergyConfSampler
- sampleConfsForTuples(ConfSampler.Samples, int) - Method in class edu.duke.cs.osprey.lute.RandomizedDFSConfSampler
- sampleConfsForTuples(ConfSampler.Samples, int) - Method in class edu.duke.cs.osprey.lute.UniformConfSampler
-
Deprecated.
- Samples(TuplesIndex) - Constructor for class edu.duke.cs.osprey.lute.ConfSampler.Samples
- sampleTripleTuplesByFitError(PruningMatrix, ConfDB.ConfTable, double) - Method in class edu.duke.cs.osprey.lute.LUTE
-
Turns out, this approach doesn't work terribly well unless you return lots of tuples I think it tends to overfit to the pairs training set, but doesn't fit well on later sampled confs for triples
- sampleTripleTuplesByStrongInteractions(EnergyMatrix, PruningMatrix, int) - Method in class edu.duke.cs.osprey.lute.LUTE
- sampleTuplesAndFit(ConfEnergyCalculator, EnergyMatrix, PruningMatrix, ConfDB.ConfTable, ConfSampler, LUTE.Fitter, double, double) - Method in class edu.duke.cs.osprey.lute.LUTE
-
general-purpose tuple sampler that tries to fit smaller tuple sets first before trying bigger ones
- SAPE - Class in edu.duke.cs.osprey.ematrix.epic
-
Sparse Atom-Pair Energies This is a listing of atom-pair energies for just a small number of the atom pairs involved in an interactions
- SAPE(MoleculeModifierAndScorer, double, DoubleMatrix1D[]) - Constructor for class edu.duke.cs.osprey.ematrix.epic.SAPE
- SAPECutoff - Variable in class edu.duke.cs.osprey.ematrix.epic.FitParams
- save() - Method in class edu.duke.cs.osprey.coffee.seqdb.Batch
- save(File) - Method in class edu.duke.cs.osprey.lute.LUTE
- saveConf(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized
- saveDir - Variable in class edu.duke.cs.osprey.design.commands.DesignFileDelegate
- saveEConfs(PriorityQueue<ConfSearch.ScoredConf>) - Method in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized
- SaveOperation - Class in edu.duke.cs.osprey.coffee.seqdb
- SaveOperation() - Constructor for class edu.duke.cs.osprey.coffee.seqdb.SaveOperation
- SaveOperation(MultiStateConfSpace, Batch) - Constructor for class edu.duke.cs.osprey.coffee.seqdb.SaveOperation
- SaveOperation.SequencedSum - Class in edu.duke.cs.osprey.coffee.seqdb
- SaveOperation.UnsequencedSum - Class in edu.duke.cs.osprey.coffee.seqdb
- saveResultsToDb - Variable in class edu.duke.cs.osprey.design.commands.DesignFileDelegate
- saveTopConf(KSConf) - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- saveTopConfsAsPDB - Static variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- scale - Variable in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.Tics
- scale() - Method in class edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal
- scale(double[], double) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- scaledCoulombFactor - Variable in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.ParamInfo
- ScaledEnergyFunction - Class in edu.duke.cs.osprey.energy
- ScaledEnergyFunction(EnergyFunction, double) - Constructor for class edu.duke.cs.osprey.energy.ScaledEnergyFunction
- scaleInPlace(double[], double) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- scan(int, BiConsumer<File, Molecule>) - Method in class edu.duke.cs.osprey.structure.analysis.PDBScanner
-
scans the first N files in the folder for molecules
- scan(String, BiConsumer<File, Molecule>) - Method in class edu.duke.cs.osprey.structure.analysis.PDBScanner
-
scan just the named file
- scan(BiConsumer<File, Molecule>) - Method in class edu.duke.cs.osprey.structure.analysis.PDBScanner
-
scans the folder for molecules
- scanDistance - Variable in class edu.duke.cs.osprey.design.commands.CommandBindingAffinity
- ScanDto - Class in edu.duke.cs.osprey.design.models
- ScanDto() - Constructor for class edu.duke.cs.osprey.design.models.ScanDto
- scanFlexDistance - Variable in class edu.duke.cs.osprey.design.commands.CommandBindingAffinity
- scanOutput - Variable in class edu.duke.cs.osprey.design.commands.CommandBindingAffinity
- scanSettings - Variable in class edu.duke.cs.osprey.design.models.AffinityDesign
- sConfs - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Result
- sConfs - Variable in class edu.duke.cs.osprey.paste.PastePartitionFunction.Result
- score - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex.Node
- score - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.ScoredSequence
- score - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.SingleSequenceNode
-
for comparing in the tree, higher is first
- score - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
-
the K* score, guaranteed to be an epsilon-approximation or null
- score - Variable in class edu.duke.cs.osprey.gmec.ConfAnalyzer.ConfAnalysis
- score - Variable in class edu.duke.cs.osprey.kstar.BBKStar.SingleSequenceNode
-
for comparing in the tree, higher is first
- score - Variable in class edu.duke.cs.osprey.kstar.KStar.ScoredSequence
- score - Variable in class edu.duke.cs.osprey.kstar.KStarScore
-
the K* score, guaranteed to be an epsilon-approximation or null
- score - Variable in class edu.duke.cs.osprey.markstar.MARKStar.ScoredSequence
- score - Variable in class edu.duke.cs.osprey.multistatekstar.ResidueOrder.AAScore
- score - Variable in class edu.duke.cs.osprey.paste.Paste.ScoredSequence
- score - Variable in class edu.duke.cs.osprey.paste.PasteScore
-
the K* score, guaranteed to be an epsilon-approximation or null
- score - Variable in class edu.duke.cs.osprey.restypes.ResTemplateMatching
- score() - Method in interface edu.duke.cs.osprey.coffee.nodedb.FixedIndex.Indexable
- score() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex.Node
- score(int, int[], BigExp) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodePerformance
- score(NodeIndex.Node) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodePerformance
- score(Sequence, TaskExecutor) - Method in class edu.duke.cs.osprey.kstar.KStar
- Score - Enum constant in enum class edu.duke.cs.osprey.confspace.ConfDB.SortOrder
- scoreAssignmentList(int[]) - Method in class edu.duke.cs.osprey.ibis.IBISKStarTupleExpander
- scoreAssignmentList(int[]) - Method in class edu.duke.cs.osprey.tupexp.BasicPruningTupleExpander
- scoreBatch - Variable in class edu.duke.cs.osprey.kstar.pfunc.PfuncSurface
- scoreConfDifferential(FullAStarNode, int, int) - Method in class edu.duke.cs.osprey.kstar.KAStarConfTree
- scoreConfDifferential(FullAStarNode, int, int) - Method in class edu.duke.cs.osprey.multistatekstar.MultiSequenceConfTree
- scoreConfDifferential(T, int, int) - Method in class edu.duke.cs.osprey.astar.ConfTree
- scoreConfs - Variable in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- scoreConfsBatchSize - Variable in class edu.duke.cs.osprey.kstar.pfunc.SimplePartitionFunction
-
number of conformations to score per batch when refining the partition function upper bound for single-threaded parallelism, this setting determines how many conformations we should score to refine the upper bound *per each* conformation that is minimized to refine the lower bound.
- ScoreContext() - Constructor for class edu.duke.cs.osprey.markstar.framework.MARKStarBound.ScoreContext
- ScoredConf(int[], double) - Constructor for class edu.duke.cs.osprey.confspace.ConfSearch.ScoredConf
-
Make a new scored conformation
- ScoredConf(ConfSearch.ScoredConf) - Constructor for class edu.duke.cs.osprey.confspace.ConfSearch.ScoredConf
-
Make a copy of an existing scored conformation
- ScoredConfFIFOSerializer - Class in edu.duke.cs.osprey.externalMemory
- ScoredConfFIFOSerializer(RCs) - Constructor for class edu.duke.cs.osprey.externalMemory.ScoredConfFIFOSerializer
- scoredConfs(ConfDB.SortOrder) - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- ScoredSequence(Sequence, EWAKStarScore) - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStar.ScoredSequence
- ScoredSequence(Sequence, KStarScore) - Constructor for class edu.duke.cs.osprey.kstar.KStar.ScoredSequence
- ScoredSequence(Sequence, KStarScore) - Constructor for class edu.duke.cs.osprey.markstar.MARKStar.ScoredSequence
- ScoredSequence(Sequence, PasteScore) - Constructor for class edu.duke.cs.osprey.paste.Paste.ScoredSequence
- ScoreInfo(int, int, Sequence, SimpleConfSpace, EWAKStarScore) - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.ScoreInfo
- ScoreInfo(int, int, Sequence, KStarScore) - Constructor for class edu.duke.cs.osprey.kstar.KStarScoreWriter.ScoreInfo
- ScoreInfo(int, int, Sequence, KStarScore, KStar) - Constructor for class edu.duke.cs.osprey.kstar.KStarScoreWriter.ScoreInfo
- ScoreInfo(int, int, Sequence, PasteScore) - Constructor for class edu.duke.cs.osprey.paste.PasteScoreWriter.ScoreInfo
- scoreLog10() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- scoreLog10() - Method in class edu.duke.cs.osprey.kstar.KStarScore
- scoreLog10String() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- scoreLog10String() - Method in class edu.duke.cs.osprey.kstar.KStarScore
- scoreNeedsRefinement - Variable in class edu.duke.cs.osprey.kstar.KAStarNode
- scoreNeedsRefinement() - Method in interface edu.duke.cs.osprey.astar.AStarNode
- scoreNeedsRefinement() - Method in class edu.duke.cs.osprey.astar.FullAStarNode
- scoreNeedsRefinement() - Method in class edu.duke.cs.osprey.astar.SlimAStarNode
- scoreNeedsRefinement() - Method in class edu.duke.cs.osprey.kstar.KAStarNode
- scoreNextConf() - Method in class edu.duke.cs.osprey.kstar.pfunc.UpperBoundCalculator
- scoreNode(int[]) - Method in class edu.duke.cs.osprey.kstar.KAStarConfTree
- scoreNode(int[]) - Method in class edu.duke.cs.osprey.multistatekstar.MultiSequenceConfTree
- scoreNode(T) - Method in class edu.duke.cs.osprey.astar.ConfTree
- scoreNodeDifferential(T, T, int, int) - Method in class edu.duke.cs.osprey.astar.ConfTree
- scorer - Variable in class edu.duke.cs.osprey.coffee.directors.BestSet
- scores - Variable in class edu.duke.cs.osprey.multistatekstar.ResidueOrderStaticSequential
- scores() - Method in class edu.duke.cs.osprey.coffee.directors.BestSet
- scoreToLog10(Double) - Static method in class edu.duke.cs.osprey.paste.PasteScore
- scoreToLog10(BigDecimal) - Static method in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- scoreToLog10(BigDecimal) - Static method in class edu.duke.cs.osprey.kstar.KStarScore
- scoreToLog10String(Double) - Static method in class edu.duke.cs.osprey.paste.PasteScore
- scoreToLog10String(BigDecimal) - Static method in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- scoreToLog10String(BigDecimal) - Static method in class edu.duke.cs.osprey.kstar.KStarScore
- scoreToString(Double) - Static method in class edu.duke.cs.osprey.paste.PasteScore
- scoreToString(BigDecimal) - Static method in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- scoreType - Variable in class edu.duke.cs.osprey.multistatekstar.MSKStarSettings
- scoreWriters - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings
- scoreWriters - Variable in class edu.duke.cs.osprey.kstar.KStar.Settings
- scoreWriters - Variable in class edu.duke.cs.osprey.markstar.MARKStar.Settings
- scoreWriters - Variable in class edu.duke.cs.osprey.paste.Paste.Settings
- scoringLog - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
- search - Variable in class edu.duke.cs.osprey.gmec.SimpleGMECFinder.Builder
-
A* implementation to sort conformations in the conformation space.
- search - Variable in class edu.duke.cs.osprey.gmec.SimpleGMECFinder
- search - Variable in class edu.duke.cs.osprey.multistatekstar.MSKStarSettings
- search(double) - Method in class edu.duke.cs.osprey.minimization.IntervalLineSearcher
- search(double) - Method in interface edu.duke.cs.osprey.minimization.LineSearcher
- search(double) - Method in class edu.duke.cs.osprey.minimization.SurfingLineSearcher
- searchNeedsHigherOrderTerms() - Method in class edu.duke.cs.osprey.confspace.SearchProblem
- searchParams(String) - Method in class edu.duke.cs.osprey.control.ParamSet
- SearchProblem - Class in edu.duke.cs.osprey.confspace
- SearchProblem(SearchProblem) - Constructor for class edu.duke.cs.osprey.confspace.SearchProblem
- SearchProblem(String, String, ArrayList<String>, ArrayList<ArrayList<String>>, boolean, boolean, boolean, EPICSettings, boolean, LUTESettings, DEEPerSettings, ArrayList<String[]>, ArrayList<String[]>, boolean, boolean, boolean, boolean, ResidueTermini, boolean, ArrayList<String>) - Constructor for class edu.duke.cs.osprey.confspace.SearchProblem
- SearchProblem.MatrixType - Enum Class in edu.duke.cs.osprey.confspace
- second - Variable in class edu.duke.cs.osprey.confspace.ConfSearch.Splitter
- secondaryStruct - Variable in class edu.duke.cs.osprey.structure.Residue
- segmentRMSD(String, String) - Static method in class edu.duke.cs.osprey.tests.CatPark
- selectPerturbations(ResidueTermini) - Method in class edu.duke.cs.osprey.dof.deeper.PerturbationSelector
- SELF - Enum constant in enum class edu.duke.cs.osprey.structure.AtomNeighbors.Type
- sendSignal() - Method in class edu.duke.cs.osprey.parallelism.Signal
- sendTo(Operation, Address) - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- sendToOthers(Supplier<Operation>) - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- sendWork() - Method in class edu.duke.cs.osprey.parallelism.WorkCrew
- seq - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncDirector
- seq - Variable in class edu.duke.cs.osprey.coffee.directors.SequenceDirector
- seq - Variable in class edu.duke.cs.osprey.coffee.seqdb.SaveOperation.SequencedSum
- seq - Variable in class edu.duke.cs.osprey.coffee.seqdb.SeqFreeEnergies
- seq - Variable in class edu.duke.cs.osprey.sofea.RCDB.Table
- seq - Variable in class edu.duke.cs.osprey.sofea.SequenceLMFE
-
The sequence.
- seqAsString(int[]) - Method in class edu.duke.cs.osprey.astar.comets.COMETSTree
- seqAsString(int[]) - Method in class edu.duke.cs.osprey.astar.comets.NewCOMETSTree
- SeqAStarNode - Interface in edu.duke.cs.osprey.astar.seq.nodes
- SeqAStarNode.Assignments - Class in edu.duke.cs.osprey.astar.seq.nodes
-
efficiently-accessible assignment info regardless of how nodes are implemented internally position orders must always be sorted in increasing order
- SeqAStarOrder - Interface in edu.duke.cs.osprey.astar.seq.order
- SeqAStarScorer - Interface in edu.duke.cs.osprey.astar.seq.scoring
- SeqAStarTree - Class in edu.duke.cs.osprey.astar.seq
- SeqAStarTree.Builder - Class in edu.duke.cs.osprey.astar.seq
- seqdb - Variable in class edu.duke.cs.osprey.coffee.NodeProcessor
- seqdb - Variable in class edu.duke.cs.osprey.coffee.seqdb.Batch
- SeqDB - Class in edu.duke.cs.osprey.coffee.seqdb
-
A database of information about sequences.
- SeqDB - Class in edu.duke.cs.osprey.sofea
- SeqDB(MultiStateConfSpace, MathContext) - Constructor for class edu.duke.cs.osprey.sofea.SeqDB
- SeqDB(MultiStateConfSpace, MathContext, File) - Constructor for class edu.duke.cs.osprey.sofea.SeqDB
- SeqDB.Builder - Class in edu.duke.cs.osprey.coffee.seqdb
- SeqDB.SeqInfo - Class in edu.duke.cs.osprey.sofea
- SeqDB.Transaction - Class in edu.duke.cs.osprey.sofea
- seqdbFile - Variable in class edu.duke.cs.osprey.coffee.Coffee
- seqdbFile - Variable in class edu.duke.cs.osprey.sofea.Sofea
- seqdbMathContext - Variable in class edu.duke.cs.osprey.coffee.Coffee
- seqdbMathContext - Variable in class edu.duke.cs.osprey.sofea.Sofea
- seqFilterOnly - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- SeqFreeEnergies - Class in edu.duke.cs.osprey.coffee.seqdb
- SeqFreeEnergies(Sequence, MathTools.DoubleBounds[]) - Constructor for class edu.duke.cs.osprey.coffee.seqdb.SeqFreeEnergies
- SeqGMECFinder - Class in edu.duke.cs.osprey.gmec
-
This is for when you have a bunch of sequences and you want the GMEC for each Commands: -c KStar.cfg findSeqGMECs System.cfg DEE.cfg sequences.mut
- SeqGMECFinder(ConfigFileParser) - Constructor for class edu.duke.cs.osprey.gmec.SeqGMECFinder
- seqgs - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncsDirector
- SeqInfo - Class in edu.duke.cs.osprey.coffee.seqdb
- SeqInfo(int) - Constructor for class edu.duke.cs.osprey.sofea.SeqDB.SeqInfo
- SeqInfo(MultiStateConfSpace) - Constructor for class edu.duke.cs.osprey.coffee.seqdb.SeqInfo
- seqPos - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Position
- SeqResult(Sequence, MathTools.DoubleBounds, MathTools.DoubleBounds[]) - Constructor for class edu.duke.cs.osprey.sofea.Sofea.SeqResult
- seqs - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncsDirector
- seqSpace - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- seqSpace - Variable in class edu.duke.cs.osprey.confspace.MultiStateConfSpace
- seqSpace - Variable in class edu.duke.cs.osprey.confspace.SeqSpace.Position
- seqSpace - Variable in class edu.duke.cs.osprey.confspace.Sequence
- seqSpace - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
The sequence space for this conformation space
- seqSpace - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- seqSpace - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarLimitedSequenceTrie
- seqSpace - Variable in class edu.duke.cs.osprey.gmec.Comets
- seqSpace - Variable in class edu.duke.cs.osprey.kstar.MSKStar
- seqSpace - Variable in class edu.duke.cs.osprey.tools.MapDBTools.SequenceSerializer
- seqSpace() - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- seqSpace() - Method in interface edu.duke.cs.osprey.confspace.ConfSpaceIteration
-
returns the sequence space for this conformation space
- seqSpace() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- SeqSpace - Class in edu.duke.cs.osprey.confspace
-
analogous to the conf space, but just for sequences
- SeqSpace(ConfSpace) - Constructor for class edu.duke.cs.osprey.confspace.SeqSpace
- SeqSpace(SimpleConfSpace) - Constructor for class edu.duke.cs.osprey.confspace.SeqSpace
- SeqSpace.Position - Class in edu.duke.cs.osprey.confspace
- SeqSpace.ResType - Class in edu.duke.cs.osprey.confspace
- sequence - Variable in class edu.duke.cs.osprey.confspace.ConfDB.SequenceDB
- sequence - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.ScoredSequence
- sequence - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.SingleSequenceNode
- sequence - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.SequenceInfo
- sequence - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.ScoreInfo
- sequence - Variable in class edu.duke.cs.osprey.gmec.Comets.SequenceInfo
- sequence - Variable in class edu.duke.cs.osprey.kstar.BBKStar.SingleSequenceNode
- sequence - Variable in class edu.duke.cs.osprey.kstar.KStar.ScoredSequence
- sequence - Variable in class edu.duke.cs.osprey.kstar.KStarScoreWriter.ScoreInfo
- sequence - Variable in class edu.duke.cs.osprey.kstar.MSKStar.SequenceInfo
- sequence - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- sequence - Variable in class edu.duke.cs.osprey.kstar.SequenceAnalyzer.Analysis
- sequence - Variable in class edu.duke.cs.osprey.markstar.MARKStar.ScoredSequence
- sequence - Variable in class edu.duke.cs.osprey.paste.Paste.ScoredSequence
- sequence - Variable in class edu.duke.cs.osprey.paste.PasteScoreWriter.ScoreInfo
- sequence - Variable in class edu.duke.cs.osprey.sofea.Sofea.SeqResult
- Sequence - Class in edu.duke.cs.osprey.confspace
- Sequence(SeqSpace) - Constructor for class edu.duke.cs.osprey.confspace.Sequence
- Sequence(SeqSpace, int[]) - Constructor for class edu.duke.cs.osprey.confspace.Sequence
- Sequence.Assignment - Class in edu.duke.cs.osprey.confspace
- Sequence.Renderer - Enum Class in edu.duke.cs.osprey.confspace
- SequenceAnalyzer - Class in edu.duke.cs.osprey.kstar
-
Shows information about a single sequence.
- SequenceAnalyzer(BBKStar) - Constructor for class edu.duke.cs.osprey.kstar.SequenceAnalyzer
-
make a SequenceAnalyzer from a BBKStar instance
- SequenceAnalyzer(KStar) - Constructor for class edu.duke.cs.osprey.kstar.SequenceAnalyzer
-
make a SequenceAnalyzer from a KStar instance
- SequenceAnalyzer.Analysis - Class in edu.duke.cs.osprey.kstar
- SequenceAnalyzer.ConfSpaceInfo - Class in edu.duke.cs.osprey.kstar
- SequenceAnalyzer.NoSuchConfSpaceException - Exception in edu.duke.cs.osprey.kstar
- SequenceDB(Sequence) - Constructor for class edu.duke.cs.osprey.confspace.ConfDB.SequenceDB
- sequencedIndex - Variable in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.State
- SequenceDirector - Class in edu.duke.cs.osprey.coffee.directors
- SequenceDirector(MultiStateConfSpace, Sequence, double, boolean) - Constructor for class edu.duke.cs.osprey.coffee.directors.SequenceDirector
- sequencedStates - Variable in class edu.duke.cs.osprey.confspace.MultiStateConfSpace
- SequencedSum(int[], StateZ[]) - Constructor for class edu.duke.cs.osprey.coffee.seqdb.SaveOperation.SequencedSum
- sequencedSums - Variable in class edu.duke.cs.osprey.coffee.seqdb.SaveOperation
- sequenceGs - Variable in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- SequenceInfo(SeqAStarNode, EwakstarDoer.SeqConfs, double) - Constructor for class edu.duke.cs.osprey.ewakstar.EwakstarDoer.SequenceInfo
- SequenceInfo(SeqAStarNode, Comets.SeqConfs) - Constructor for class edu.duke.cs.osprey.gmec.Comets.SequenceInfo
- SequenceInfo(SeqAStarNode, MSKStar.SeqConfs) - Constructor for class edu.duke.cs.osprey.kstar.MSKStar.SequenceInfo
- SequenceKStarPfuncs() - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Formatter.SequenceKStarPfuncs
- SequenceKStarPfuncs() - Constructor for class edu.duke.cs.osprey.kstar.KStarScoreWriter.Formatter.SequenceKStarPfuncs
- SequenceKStarPfuncs() - Constructor for class edu.duke.cs.osprey.paste.PasteScoreWriter.Formatter.SequenceKStarPfuncs
- SequenceLMFE - Class in edu.duke.cs.osprey.sofea
-
Finished SOFEA computation when the state free energies for a single sequence reach a desired precision.
- SequenceLMFE(Sequence, MultiStateConfSpace.LMFE, double) - Constructor for class edu.duke.cs.osprey.sofea.SequenceLMFE
- sequenceNumber - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.ScoreInfo
- sequenceNumber - Variable in class edu.duke.cs.osprey.kstar.KStarScoreWriter.ScoreInfo
- sequenceNumber - Variable in class edu.duke.cs.osprey.paste.PasteScoreWriter.ScoreInfo
- sequences - Variable in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- sequences - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Results
- sequences - Variable in class edu.duke.cs.osprey.sofea.MinLMFE.TopSequences
- SequenceSerializer(SeqSpace) - Constructor for class edu.duke.cs.osprey.tools.MapDBTools.SequenceSerializer
- SequentialAStarOrder - Class in edu.duke.cs.osprey.astar.conf.order
- SequentialAStarOrder() - Constructor for class edu.duke.cs.osprey.astar.conf.order.SequentialAStarOrder
- SequentialSeqAStarOrder - Class in edu.duke.cs.osprey.astar.seq.order
- SequentialSeqAStarOrder() - Constructor for class edu.duke.cs.osprey.astar.seq.order.SequentialSeqAStarOrder
- serialize(ConfSearch.EnergiedConf, ByteBuffer) - Method in class edu.duke.cs.osprey.externalMemory.EnergiedConfFIFOSerializer
- serialize(ConfSearch.EnergiedConf, ByteBuffer) - Method in class edu.duke.cs.osprey.externalMemory.EnergiedConfPrioritySerializer
- serialize(ConfSearch.ScoredConf, ByteBuffer) - Method in class edu.duke.cs.osprey.externalMemory.ScoredConfFIFOSerializer
- serialize(ByteBuffer, T) - Method in interface edu.duke.cs.osprey.coffee.nodedb.FixedIndex.Serializer
- serialize(DataOutput2, int[]) - Method in class edu.duke.cs.osprey.tools.MapDBTools.IntArraySerializer
- serialize(DataOutput2, Sequence) - Method in class edu.duke.cs.osprey.tools.MapDBTools.SequenceSerializer
- serialize(DataOutput2, BigExp) - Method in class edu.duke.cs.osprey.tools.MapDBTools.BigExpSerializer
- serialize(DataOutput2, MathTools.BigDecimalBounds) - Method in class edu.duke.cs.osprey.tools.MapDBTools.BigDecimalBoundsSerializer
- serialize(DataOutput2, BigDecimal) - Method in class edu.duke.cs.osprey.tools.MapDBTools.BigDecimalSerializer
- serialize(DataOutput2, List<T>) - Method in class edu.duke.cs.osprey.tools.MapDBTools.ValuesSerializer
- serializePF(int) - Method in class edu.duke.cs.osprey.kstar.KSCalc
- serializePFs() - Method in class edu.duke.cs.osprey.kstar.KSCalc
- serializer - Variable in class edu.duke.cs.osprey.coffee.nodedb.PriorityDequeFixedIndex
- Serializers - Class in edu.duke.cs.osprey.coffee
- Serializers() - Constructor for class edu.duke.cs.osprey.coffee.Serializers
- Serializers.AbstractStreamSerializer<T> - Class in edu.duke.cs.osprey.coffee
- series - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot
- Series() - Constructor for class edu.duke.cs.osprey.tools.resultdoc.Plot.Series
- SeriesFitter - Class in edu.duke.cs.osprey.ematrix.epic
- SeriesFitter() - Constructor for class edu.duke.cs.osprey.ematrix.epic.SeriesFitter
- ServiceName - Static variable in class edu.duke.cs.osprey.coffee.ClusterMember.DynamicPartition
- ServiceName - Static variable in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
- ServiceName - Static variable in class edu.duke.cs.osprey.coffee.seqdb.SeqDB
- ServiceName - Static variable in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- set(double) - Method in interface edu.duke.cs.osprey.confspace.compiled.DegreeOfFreedom
- set(double) - Method in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle.Dof
- set(double) - Method in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Dof
- set(double) - Method in class edu.duke.cs.osprey.tools.BigExp
- set(double) - Method in class edu.duke.cs.osprey.tools.BigMath
- set(double[], double, double, double) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- set(double, int) - Method in class edu.duke.cs.osprey.tools.BigExp
- set(int[]) - Method in class edu.duke.cs.osprey.confspace.RCTuple
- set(int, double, double) - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- set(int, double, double, double) - Method in class edu.duke.cs.osprey.confspace.compiled.CoordsList
- set(int, int) - Method in class edu.duke.cs.osprey.confspace.RCTuple
- set(int, int[]) - Method in class edu.duke.cs.osprey.astar.conf.RCs
- set(int, int, int, double) - Method in class edu.duke.cs.osprey.astar.conf.scoring.mplp.MessageVars
- set(int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.RCTuple
- set(int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.RCTuple
- set(int, int, int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.confspace.RCTuple
- set(int, int, int, int, int, int, BigExp) - Method in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- set(int, int, int, int, int, int, T) - Method in class edu.duke.cs.osprey.confspace.TripleMatrix
- set(int, int, int, int, ApproximatedObjectiveFunction.Approximator.Addable) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrix
- set(int, int, int, int, BigExp) - Method in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- set(int, int, ApproximatedObjectiveFunction.Approximator.Addable) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrix
- set(int, int, BigExp) - Method in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- set(int, int, String, ApproximatedObjectiveFunction.Approximator.Addable) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrix
- set(int, int, T) - Method in interface edu.duke.cs.osprey.confspace.PosMatrix
- set(int, int, T) - Method in class edu.duke.cs.osprey.confspace.PosMatrixGeneric
- set(int, Residue) - Method in class edu.duke.cs.osprey.structure.Residues
- set(int, String, double) - Method in class edu.duke.cs.osprey.ematrix.SimpleReferenceEnergies
- set(int, Vector3dc) - Method in class edu.duke.cs.osprey.confspace.compiled.CoordsList
- set(long) - Method in class edu.duke.cs.osprey.tools.BigMath
- set(ConfIndex) - Method in class edu.duke.cs.osprey.confspace.RCTuple
- set(RCTuple) - Method in class edu.duke.cs.osprey.confspace.RCTuple
- set(SeqSpace.Position, SeqSpace.ResType) - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Set the residue type at the specified sequence position.
- set(SeqSpace.Position, String) - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Set the residue type name at the specified residue number.
- set(SimpleConfSpace.Position, SimpleConfSpace.ResidueConf, SimpleConfSpace.Position, SimpleConfSpace.ResidueConf, ApproximatedObjectiveFunction.Approximator.Addable) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrix
- set(SimpleConfSpace.Position, SimpleConfSpace.ResidueConf, ApproximatedObjectiveFunction.Approximator.Addable) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrix
- set(SimpleConfSpace.Position, SimpleConfSpace.ResidueConf, String, ApproximatedObjectiveFunction.Approximator.Addable) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrix
- set(EnergyMatrix) - Method in class edu.duke.cs.osprey.sofea.ZMatrix
- set(MemoryBuffer, boolean) - Method in class edu.duke.cs.osprey.gpu.Structs.Bool
- set(MemoryBuffer, char) - Method in class edu.duke.cs.osprey.gpu.Structs.Char8
- set(MemoryBuffer, double) - Method in class edu.duke.cs.osprey.gpu.Structs.Float64
- set(MemoryBuffer, double) - Method in class edu.duke.cs.osprey.gpu.Structs.Real
- set(MemoryBuffer, float) - Method in class edu.duke.cs.osprey.gpu.Structs.Float32
- set(MemoryBuffer, int) - Method in class edu.duke.cs.osprey.gpu.Structs.Int32
- set(MemoryBuffer, long) - Method in class edu.duke.cs.osprey.gpu.Structs.Int64
- set(MemoryBuffer, long, char) - Method in class edu.duke.cs.osprey.gpu.Structs.Char8.Array
- set(MemoryBuffer, long, double) - Method in class edu.duke.cs.osprey.gpu.Structs.Float64.Array
- set(MemoryBuffer, long, double) - Method in class edu.duke.cs.osprey.gpu.Structs.Real.Array
- set(MemoryBuffer, long, float) - Method in class edu.duke.cs.osprey.gpu.Structs.Float32.Array
- set(MemoryBuffer, long, int) - Method in class edu.duke.cs.osprey.gpu.Structs.Int32.Array
- set(MemoryBuffer, long, long) - Method in class edu.duke.cs.osprey.gpu.Structs.Int64.Array
- set(LUTE.LinearSystem) - Method in class edu.duke.cs.osprey.lute.LUTEState
- set(BigExp) - Method in class edu.duke.cs.osprey.tools.BigExp
- set(BigExp) - Method in class edu.duke.cs.osprey.tools.BigMath
- set(Number) - Method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.NumberProp
- set(String) - Method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.LiteralProp
- set(String) - Method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.NumberProp
- set(String) - Method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.TextProp
- set(String, double) - Method in class edu.duke.cs.osprey.restypes.ResidueEntropies
- set(String, Object...) - Method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.LiteralProp
- set(String, Object...) - Method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.TextProp
- set(String, String) - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Set the residue type name at the specified residue number.
- set(String, String) - Method in class edu.duke.cs.osprey.tools.SVG.StyleClass
- set(BigDecimal) - Method in class edu.duke.cs.osprey.tools.BigExp
- set(BigDecimal) - Method in class edu.duke.cs.osprey.tools.BigMath
- set(BigInteger) - Method in class edu.duke.cs.osprey.tools.BigExp
- set(BigInteger) - Method in class edu.duke.cs.osprey.tools.BigMath
- set(Map<Number, String>) - Method in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.Tics
- Set() - Constructor for class edu.duke.cs.osprey.confspace.Conf.Set
- Set(int[]...) - Constructor for class edu.duke.cs.osprey.confspace.Conf.Set
- Set(Collection<int[]>) - Constructor for class edu.duke.cs.osprey.confspace.Conf.Set
- Set(Set<Conf.Wrapper>) - Constructor for class edu.duke.cs.osprey.confspace.Conf.Set
- set15HasNonBonded(boolean) - Method in class edu.duke.cs.osprey.structure.AtomConnectivity.Builder
- setAddShellInters(boolean) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator.Builder
- setAll(ResidueEntropies) - Method in class edu.duke.cs.osprey.restypes.ResidueEntropies
- setAllowedSeqs(EwakstarLimitedSequenceTrie) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.Settings.Builder
- setAlwaysResolveClashesEnergy(Double) - Method in class edu.duke.cs.osprey.energy.EnergyCalculator.Builder
- setAngle(double) - Method in class edu.duke.cs.osprey.confspace.compiled.motions.DihedralAngle
- setApproximationErrorBudget(double) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator.Builder
- setApproximatorMatrix(ApproximatorMatrix) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator.Builder
- setApproximatorType(ApproximatorMatrixCalculator.ApproximatorType) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrixCalculator
- setArgs(int) - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.TestFancyKernel
- setArgs(Pointer) - Method in class edu.duke.cs.osprey.gpu.cuda.Kernel.Function
- setBasePucker(ProlinePucker.Direction) - Method in class edu.duke.cs.osprey.dof.ProlinePucker
- setBounds(double, double, double, double) - Method in class edu.duke.cs.osprey.tools.SVG
- setBounds(int[], double, double, long) - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- setBounds(ConfSearch.EnergiedConf, long) - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- setBounds(SVG, double, double) - Method in class edu.duke.cs.osprey.tools.SVGPlot.Boxes
- setBounds(SVG, double, double) - Method in class edu.duke.cs.osprey.tools.SVGPlot.Intervals
- setBoundsFromConfLowerAndUpper(double, double) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- setBoundsFromConfLowerAndUpper(double, double) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- setBroadcastNs(long) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB.Builder
- setCacheFile(File) - Method in class edu.duke.cs.osprey.ematrix.compiled.EmatCalculator.Builder
- setCacheFile(File) - Method in class edu.duke.cs.osprey.ematrix.SimplerEnergyMatrixCalculator.Builder
- setCacheFile(File) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrixCalculator
- setCacheFile(File) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setCalcConstantTerm(boolean) - Method in class edu.duke.cs.osprey.ematrix.SimplerEnergyMatrixCalculator.Builder
- setCanPrune(boolean) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.SequenceInfo
- setCFGImpl(String) - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- setCheckPointInterval(long) - Static method in class edu.duke.cs.osprey.kstar.KSAbstract
- setCluster(Cluster) - Method in class edu.duke.cs.osprey.coffee.Coffee.Builder
- setCluster(Cluster) - Method in class edu.duke.cs.osprey.energy.EnergyCalculator.Builder
- setColorStyle(KStarTreeNode.ColorStyle) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- setConditions(BoltzmannCalculator.Conditions) - Method in class edu.duke.cs.osprey.coffee.Coffee.Builder
- setConfDB(ConfDB, ConfDB.Key) - Method in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- setConfDB(ConfDB, ConfDB.Key) - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.WithConfDB
- setConfDB(ConfDB, ConfDB.Key) - Method in class edu.duke.cs.osprey.lute.LUTEPfunc
- setConfDB(ConfDB, ConfDB.Key) - Method in class edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc
- setConfDB(ConfDB, ConfDB.Key) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- setConfDB(ConfDB, Sequence) - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.WithConfDB
- setConfDB(ConfDB, String) - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.WithConfDB
- setConfDB(File) - Method in class edu.duke.cs.osprey.gmec.SimpleGMECFinder.Builder
- setConfDBFile(String) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.ConfSpaceInfo
- setConfDBFile(String) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.ConfSpaceInfo
- setConfDBFile(String) - Method in class edu.duke.cs.osprey.kstar.BBKStar.ConfSpaceInfo
- setConfDBFile(String) - Method in class edu.duke.cs.osprey.paste.Paste.ConfSpaceInfo
- setConfDBPattern(String) - Method in class edu.duke.cs.osprey.kstar.KStar.Settings.Builder
- setConfListener(EWAKStarPartitionFunction.ConfListener) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarGradientDescentPfunc
- setConfListener(EWAKStarPartitionFunction.ConfListener) - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction
- setConfListener(PartitionFunction.ConfListener) - Method in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- setConfListener(PartitionFunction.ConfListener) - Method in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- setConfListener(PartitionFunction.ConfListener) - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction
- setConfListener(PartitionFunction.ConfListener) - Method in class edu.duke.cs.osprey.kstar.pfunc.SimplePartitionFunction
- setConfListener(PartitionFunction.ConfListener) - Method in class edu.duke.cs.osprey.lute.LUTEPfunc
- setConfListener(PartitionFunction.ConfListener) - Method in class edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc
- setConfListener(PartitionFunction.ConfListener) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- setConfListener(PartitionFunction.ConfListener) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- setConfListener(PartitionFunction.ConfListener) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- setConfListener(PastePartitionFunction.ConfListener) - Method in class edu.duke.cs.osprey.paste.PasteGradientDescentPfunc
- setConfListener(PastePartitionFunction.ConfListener) - Method in interface edu.duke.cs.osprey.paste.PastePartitionFunction
- setConfPruner(GMECFinder.ConfPruner) - Method in class edu.duke.cs.osprey.gmec.GMECFinder
- setConfsThreadBuffer(int) - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- setConfTable(ConfDB.ConfTable) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarGradientDescentPfunc
- setConfTable(ConfDB.ConfTable) - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.WithConfTable
- setConfTable(ConfDB.ConfTable) - Method in class edu.duke.cs.osprey.paste.PasteGradientDescentPfunc
- setConfTable(ConfDB.ConfTable) - Method in interface edu.duke.cs.osprey.paste.PastePartitionFunction.WithConfTable
- setConsolePrinter(ConfPrinter) - Method in class edu.duke.cs.osprey.gmec.SimpleGMECFinder.Builder
- setConsolePrinter(ConfPrinter) - Method in class edu.duke.cs.osprey.lute.LUTEGMECFinder.Builder
- setConstTerm(double) - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrix
- setConstTerm(double) - Method in class edu.duke.cs.osprey.ematrix.NegatedEnergyMatrix
- setContinuous() - Method in class edu.duke.cs.osprey.confspace.Strand.ResidueFlex
-
Uses a continuous voxel with default half width of
VoxelShape.DefaultHalfWidthDegrees - setContinuous(double) - Method in class edu.duke.cs.osprey.confspace.Strand.ResidueFlex
- setConvergenceThreshold(double) - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree.MPLPBuilder
- setCoords(double, double, double) - Method in class edu.duke.cs.osprey.structure.Atom
- setCoordsByAtomName(String, double[]) - Method in class edu.duke.cs.osprey.structure.Residue
- setCorrections(UpdatingEnergyMatrix) - Method in class edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc
- setCorrections(UpdatingEnergyMatrix) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- setCorrections(UpdatingEnergyMatrix) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- setCorrections(UpdatingEnergyMatrix) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- setCurPucker(ProlinePucker.Direction) - Method in class edu.duke.cs.osprey.dof.ProlinePucker
- setCustom(AStarOrder, AStarScorer, AStarScorer) - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree.Builder
- setData(Object) - Method in class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode
- setData(Object) - Method in interface edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode
- setDataDir(String) - Static method in class edu.duke.cs.osprey.control.EnvironmentVars
-
Deprecated.
- setDefaultNumThreads() - Static method in class edu.duke.cs.osprey.parallelism.ThreadParallelism
- setDefaultTempDir() - Static method in class edu.duke.cs.osprey.externalMemory.ExternalMemory
-
Set the temporary directory for external memory to the JVM default.
- setDiscrete() - Method in class edu.duke.cs.osprey.confspace.Strand.ResidueFlex
- setDoEnergy(boolean) - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.ForcefieldKernelOpenCL
- setDOF(int, double) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction
- setDOF(int, double) - Method in class edu.duke.cs.osprey.minimization.IdealSeparableReference
- setDOF(int, double) - Method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- setDOF(int, double) - Method in class edu.duke.cs.osprey.minimization.MoleculeObjectiveFunction
- setDOF(int, double) - Method in interface edu.duke.cs.osprey.minimization.ObjectiveFunction
- setDOFs(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.bbfree.BBFreeBlock
- setDOFs(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction
- setDOFs(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.minimization.IdealSeparableReference
- setDOFs(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- setDOFs(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.minimization.MoleculeObjectiveFunction
- setDOFs(DoubleMatrix1D) - Method in interface edu.duke.cs.osprey.minimization.ObjectiveFunction
- setDofTypes(SimpleConfSpace.DofTypes) - Method in class edu.duke.cs.osprey.energy.EnergyCalculator.Builder
- setDominantBaseline(SVG.StyleClass.DominantBaseline) - Method in class edu.duke.cs.osprey.tools.SVG.StyleClass
- setDropHandler(Consumer<Stream<NodeIndex.Node>>) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
-
Set a function to call when dropped nodes need to be processed.
- setDY(double, SVG.LengthUnit) - Method in class edu.duke.cs.osprey.tools.SVG.TextDrawable
- setEfunc(EnergyFunction) - Method in class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
- setEFunc(ParallelEnergyFunction) - Static method in class edu.duke.cs.osprey.energy.ParallelEnergyFunction
- setElementProperties(Atom, String) - Static method in class edu.duke.cs.osprey.tools.PeriodicTable
- setEmat(EnergyMatrix) - Method in class edu.duke.cs.osprey.confspace.TupleEnumerator
- setEmpty() - Method in class edu.duke.cs.osprey.sofea.SeqDB.SeqInfo
- setEnergy(double) - Method in class edu.duke.cs.osprey.confspace.ConfSearch.EnergiedConf
-
Set the energy for this conformation
- setEnergy(double) - Method in class edu.duke.cs.osprey.kstar.KSConf
- setEnergy(double) - Method in class edu.duke.cs.osprey.paste.Paste.Settings.Builder
- setEnergyBound(double) - Method in class edu.duke.cs.osprey.kstar.KSConf
- setEnergyMatrixCachePattern(String) - Method in class edu.duke.cs.osprey.markstar.MARKStar.Settings.Builder
- setEnergyPartition(EnergyPartition) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator.Builder
- setEnsembleMinUpdate(long, TimeUnit) - Method in class edu.duke.cs.osprey.coffee.directors.AffinityDirector.Builder
-
Sets the minimum interval for writing the next lowest-energy ensemble PDB files.
- setEnsembleMinUpdate(long, TimeUnit) - Method in class edu.duke.cs.osprey.coffee.directors.KStarDirector.Builder
-
Sets the minimum interval for writing the next lowest-energy ensemble PDB files.
- setEnsembleMinUpdate(long, TimeUnit) - Method in class edu.duke.cs.osprey.coffee.directors.PfuncDirector.Builder
-
Sets the minimum interval for writing the next lowest-energy ensemble PDB file.
- setEnsembleTracking(int, File) - Method in class edu.duke.cs.osprey.coffee.directors.AffinityDirector.Builder
-
Tracks the lowest-energy conformations for the best sequences and periodically writes out ensemble PDB files to the specified directory.
- setEnsembleTracking(int, File) - Method in class edu.duke.cs.osprey.coffee.directors.KStarDirector.Builder
-
Tracks the lowest-energy conformations for the best sequences and periodically writes out ensemble PDB files to the specified directory.
- setEnsembleTracking(int, File) - Method in class edu.duke.cs.osprey.coffee.directors.PfuncDirector.Builder
-
Tracks the K lowest-energy conformations and periodically writes out an ensemble PDB file.
- setEpsilon(double) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings.Builder
- setEpsilon(double) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- setEpsilon(double) - Method in class edu.duke.cs.osprey.kstar.KStar.Settings.Builder
- setEpsilon(double) - Method in class edu.duke.cs.osprey.kstar.MSKStar.Builder
- setEpsilon(double) - Method in class edu.duke.cs.osprey.markstar.MARKStar.Settings.Builder
- setEpsilon(double) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode.Builder
- setEpsilon(double) - Method in class edu.duke.cs.osprey.paste.Paste.Settings.Builder
- setEpsilonStatus(PFAbstract.EApproxReached) - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- seteRefMat(ReferenceEnergies) - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrix
- setErrorOnNonTemplateResidues(boolean) - Method in class edu.duke.cs.osprey.confspace.Strand.Builder
- setEw(double) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings.Builder
- setEw(double) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- setExternalMemory(boolean) - Method in class edu.duke.cs.osprey.kstar.KStar.Settings.Builder
- setExternalMemory(boolean) - Method in class edu.duke.cs.osprey.paste.Paste.Settings.Builder
- setFile(File) - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqDB.Builder
- setFile(File, long) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB.Builder
- setFillColor(int) - Method in class edu.duke.cs.osprey.tools.SVG.StyleClass
- setFontSize(double, SVG.LengthUnit) - Method in class edu.duke.cs.osprey.tools.SVG.StyleClass
- setFringeDBLowerBytes(long) - Method in class edu.duke.cs.osprey.sofea.Sofea.Builder
- setFringeDBLowerFile(File) - Method in class edu.duke.cs.osprey.sofea.Sofea.Builder
- setFringeDBLowerMiB(int) - Method in class edu.duke.cs.osprey.sofea.Sofea.Builder
- setFringeDBUpperBytes(long) - Method in class edu.duke.cs.osprey.sofea.Sofea.Builder
- setFringeDBUpperFile(File) - Method in class edu.duke.cs.osprey.sofea.Sofea.Builder
- setFringeDBUpperMiB(int) - Method in class edu.duke.cs.osprey.sofea.Sofea.Builder
- setGenChi1(Residue, double) - Static method in class edu.duke.cs.osprey.dof.deeper.GenChi1Calc
- setGMax(Double) - Method in class edu.duke.cs.osprey.coffee.directors.PfuncDirector.Builder
-
Sets the maximum free energy value that is useful.
- setGoalScore(double) - Method in class edu.duke.cs.osprey.astar.AStarProgress
- setGoalScore(double) - Method in class edu.duke.cs.osprey.markstar.MARKStarProgress
- setGoldsteinDiffThreshold(Double) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setGpuInfo(GpuConfMinimizer.Type, int, int) - Method in class edu.duke.cs.osprey.minimization.GpuConfMinimizer.Builder
- setGroup(Group) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- setGScore(double) - Method in class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode
- setGScore(double) - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- setGScore(double) - Method in class edu.duke.cs.osprey.astar.FullAStarNode
- setGScore(double) - Method in interface edu.duke.cs.osprey.astar.OptimizableAStarNode
- setGScore(double) - Method in class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode
- setGScore(double) - Method in class edu.duke.cs.osprey.astar.SlimAStarNode
- setGScore(double) - Method in class edu.duke.cs.osprey.externalMemory.EMConfAStarNode
- setGScore(double) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- setGScore(double, MathTools.Optimizer) - Method in interface edu.duke.cs.osprey.astar.OptimizableAStarNode
- setGScorerFactory(ConfRanker.ScorerFactory) - Method in class edu.duke.cs.osprey.astar.conf.ConfRanker.Builder
- setGWidthMax(double) - Method in class edu.duke.cs.osprey.coffee.directors.AffinityDirector.Builder
-
Sets the largest precision desired for free energy calculations.
- setGWidthMax(double) - Method in class edu.duke.cs.osprey.coffee.directors.KStarDirector.Builder
- setGWidthMax(double) - Method in class edu.duke.cs.osprey.coffee.directors.PfuncDirector.Builder
-
Sets the largest precision desired for free energy calculations.
- setGWidthMax(double) - Method in class edu.duke.cs.osprey.coffee.directors.PfuncsDirector.Builder
-
Sets the largest precision desired for free energy calculations.
- setHazelcastInstance(HazelcastInstance) - Method in class edu.duke.cs.osprey.parallelism.Cluster.Task
- setHeuristics(SeqAStarOrder, SeqAStarScorer, SeqAStarScorer) - Method in class edu.duke.cs.osprey.astar.seq.SeqAStarTree.Builder
- setHigherOrder(RCTuple, Boolean) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixInverted
- setHigherOrder(RCTuple, Boolean) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- setHigherOrder(RCTuple, Boolean) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- setHigherOrder(RCTuple, Double) - Method in class edu.duke.cs.osprey.ematrix.ProxyEnergyMatrix
- setHigherOrder(RCTuple, Double) - Method in class edu.duke.cs.osprey.ematrix.UpdatingEnergyMatrix
- setHigherOrder(RCTuple, T) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- setHigherOrderTerms(int, int, int, int, HigherTupleFinder<Boolean>) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixInverted
- setHigherOrderTerms(int, int, int, int, HigherTupleFinder<Boolean>) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- setHigherOrderTerms(int, int, int, int, HigherTupleFinder<Boolean>) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- setHigherOrderTerms(int, int, int, int, HigherTupleFinder<T>) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- setHigherOrderTerms(int, int, int, int, HigherTupleFinder<T>) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- setHotBoundPct(String, double) - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- setHotMethod(String, String) - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- setHotNumRes(String, int) - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- setHotTopRotsPct(String, double) - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- setHScore(double) - Method in class edu.duke.cs.osprey.astar.conf.linked.LinkedConfAStarNode
- setHScore(double) - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- setHScore(double) - Method in class edu.duke.cs.osprey.astar.FullAStarNode
- setHScore(double) - Method in interface edu.duke.cs.osprey.astar.OptimizableAStarNode
- setHScore(double) - Method in class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode
- setHScore(double) - Method in class edu.duke.cs.osprey.astar.SlimAStarNode
- setHScore(double) - Method in class edu.duke.cs.osprey.externalMemory.EMConfAStarNode
- setHScore(double) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- setHScore(double, MathTools.Optimizer) - Method in interface edu.duke.cs.osprey.astar.OptimizableAStarNode
- setHScorerFactory(ConfRanker.ScorerFactory) - Method in class edu.duke.cs.osprey.astar.conf.ConfRanker.Builder
- setId(String) - Method in class edu.duke.cs.osprey.tools.SVG.Drawable
- setIncludeStaticStatic(boolean) - Method in class edu.duke.cs.osprey.ematrix.compiled.EmatCalculator.Builder
- setIncludeStaticStatic(boolean) - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter.Builder
-
Deprecated.
- setInfiniteWellEnergy(Double) - Method in class edu.duke.cs.osprey.energy.EnergyCalculator.Builder
- setInitVals(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.minimization.CCDMinimizer
- setInstanceId(int) - Method in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- setInstanceId(int) - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction
-
Override to support task contexts, for contextual task executors
- setInteraction(RCTuple, T) - Method in class edu.duke.cs.osprey.confspace.HigherTupleFinder
- setInternalLimit(int) - Static method in class edu.duke.cs.osprey.externalMemory.ExternalMemory
-
Set the maximum amount of internal memory (eg, RAM) to use for large data structures.
- setIsMinimizing(boolean) - Method in class edu.duke.cs.osprey.energy.EnergyCalculator.Builder
- setIsMinimizing(boolean) - Method in class edu.duke.cs.osprey.energy.EnergyCalculator.SharedBuilder
- setK(int) - Method in class edu.duke.cs.osprey.coffee.directors.AffinityDirector.Builder
- setLevel(int) - Method in class edu.duke.cs.osprey.externalMemory.EMConfAStarNode
- setLibraryRotamers(String...) - Method in class edu.duke.cs.osprey.confspace.Strand.ResidueFlex
-
Set the mutatable residue types (e.g., amino acids) for this residue.
- setLibraryRotamers(List<String>) - Method in class edu.duke.cs.osprey.confspace.Strand.ResidueFlex
- setLog(File) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodePerformance
- setLogConfsToConsole(boolean) - Method in class edu.duke.cs.osprey.gmec.GMECFinder
- setLogFile(File) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- setLogFile(File) - Method in class edu.duke.cs.osprey.gmec.Comets.Builder
- setLogFile(File) - Method in class edu.duke.cs.osprey.kstar.MSKStar.Builder
- setLogPrinter(ConfPrinter) - Method in class edu.duke.cs.osprey.gmec.SimpleGMECFinder.Builder
- setLogPrinter(ConfPrinter) - Method in class edu.duke.cs.osprey.lute.LUTEGMECFinder.Builder
- setLowerBound(int[], double, long) - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- setLowerEnergyOfUnsampledConfs(double) - Method in class edu.duke.cs.osprey.confspace.ConfDB.SequenceDB
- setLUTE(LUTEConfEnergyCalculator) - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree.Builder
-
Uses estimation functions that are compatible with LUTE conformation energies
- setMakeDAminoAcidTemplates(boolean) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary.Builder
-
True to make D amino acid templates, false otherwise.
- setMathContext(MathContext) - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqDB.Builder
- setMaxCriterionCheckSeconds(int) - Method in class edu.duke.cs.osprey.sofea.Sofea.Builder
- setMaxKSconfs(long) - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- setMaxNumConf(int) - Method in class edu.duke.cs.osprey.kstar.KStar.Settings.Builder
- setMaxNumConfs(int) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings.Builder
- setMaxNumConfs(int) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- setMaxNumConfs(int) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- setMaxNumConfs(int) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- setMaxNumConfs(int) - Method in class edu.duke.cs.osprey.markstar.MARKStar.Settings.Builder
- setMaxNumMinimizations(long) - Method in class edu.duke.cs.osprey.sofea.Sofea.Builder
- setMaxNumNodes(int) - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree.Builder
- setMaxNumNodes(Long) - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree.Builder
- setMaxSimultaneousMutations(int) - Method in class edu.duke.cs.osprey.gmec.Comets.Builder
- setMaxSimultaneousMutations(int) - Method in class edu.duke.cs.osprey.kstar.KStar.Settings.Builder
- setMaxSimultaneousMutations(int) - Method in class edu.duke.cs.osprey.kstar.MSKStar.Builder
- setMaxSimultaneousMutations(int) - Method in class edu.duke.cs.osprey.markstar.MARKStar.Settings.Builder
- setMaxSimultaneousMutations(int) - Method in class edu.duke.cs.osprey.paste.Paste.Settings.Builder
- setMaxSimultaneousMutations(Integer) - Method in class edu.duke.cs.osprey.coffee.directors.AffinityDirector.Builder
- setMaxSimultaneousMutations(Integer) - Method in class edu.duke.cs.osprey.coffee.directors.KStarDirector.Builder
- setMem(long) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB.Builder
- setMinE(double) - Method in class edu.duke.cs.osprey.ematrix.epic.EPoly
- setMinimizationRatio(double) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- setMinimize(boolean) - Method in class edu.duke.cs.osprey.ematrix.compiled.EmatCalculator.Builder
- setMinimize(boolean) - Method in class edu.duke.cs.osprey.ematrix.compiled.ErefCalculator.Builder
- setMinimize(boolean) - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter.Builder
-
Deprecated.
- setMinimizers(Factory<Minimizer, MoleculeModifierAndScorer>) - Method in class edu.duke.cs.osprey.minimization.CpuConfMinimizer.Builder
- setMinNumConfTrees(Integer) - Method in class edu.duke.cs.osprey.gmec.Comets.Builder
- setMinNumConfTrees(Integer) - Method in class edu.duke.cs.osprey.kstar.MSKStar.Builder
- setMolecule(Molecule) - Method in class edu.duke.cs.osprey.dof.DegreeOfFreedom
- setMolecule(Molecule) - Method in class edu.duke.cs.osprey.dof.FreeDihedral
- setMolecule(Molecule) - Method in class edu.duke.cs.osprey.dof.ProlinePucker
- setMolecule(Molecule) - Method in class edu.duke.cs.osprey.dof.ResidueTypeDOF
- setMPLP() - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree.Builder
-
Creates an A* search using a newer estimation function based on Max Product Linear Programming (MPLP).
- setMPLP(ConfAStarTree.MPLPBuilder) - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree.Builder
- setMutableType(String) - Method in class edu.duke.cs.osprey.astar.seq.SeqAStarTree.Builder
- setMutableType(String) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- setNegligableFreeEnergy(double) - Method in class edu.duke.cs.osprey.sofea.Sofea.Builder
- setNodeDBFile(File, long) - Method in class edu.duke.cs.osprey.coffee.Coffee.Builder
- setNodeDBMem(long) - Method in class edu.duke.cs.osprey.coffee.Coffee.Builder
- setNodeScoringLog(File) - Method in class edu.duke.cs.osprey.coffee.Coffee.Builder
- setNodeStatsReportingInterval(Duration) - Method in class edu.duke.cs.osprey.coffee.Coffee.Builder
- setNoFill() - Method in class edu.duke.cs.osprey.tools.SVG.StyleClass
- setNoRotamers() - Method in class edu.duke.cs.osprey.confspace.Strand.ResidueFlex
- setNoStroke() - Method in class edu.duke.cs.osprey.tools.SVG.StyleClass
- setNumberOfPhiPsiBins(int) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
-
Number of "bins" for Phi/Psi angles for backbone dependent rotamer libraries.
- setNumBestConfs(int) - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqDB.Builder
- setNumBestSequences(int) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.Settings.Builder
- setNumBestSequences(int) - Method in class edu.duke.cs.osprey.kstar.BBKStar.Settings.Builder
- setNumConfsPerBatch(int) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.Settings.Builder
- setNumConfsPerBatch(int) - Method in class edu.duke.cs.osprey.kstar.BBKStar.Settings.Builder
- setNumCpus(int) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- setNumCpus(int) - Method in class edu.duke.cs.osprey.parallelism.Parallelism.Builder
- setNumDihedrals(int) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
-
PGC 2015: Set the number of dihedrals for this Residue type
- setNumEWAKStarSeqs(Double) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- setNumGpus(int) - Method in class edu.duke.cs.osprey.parallelism.Parallelism.Builder
- setNumIterations(int) - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree.MPLPBuilder
- setNumIterations(int) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setNumMaxPfConfs(int) - Method in class edu.duke.cs.osprey.paste.Paste.Settings.Builder
- setNumMutable(int) - Method in class edu.duke.cs.osprey.astar.seq.SeqAStarTree.Builder
- setNumMutable(int) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- setNumMutations(int) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings.Builder
- setNumPfConfs(int) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- setNumPruned() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- setNumRotamers(int) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
- setNumRotamers(int, int, int) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
-
PGC 2015: Sets the number of rotamers for a residue template; phi and psi are only used when using a backbone dependent rotamer library.
- setNumSamplesPerParam(int) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrixCalculator
- setNumStreamsPerGpu(int) - Method in class edu.duke.cs.osprey.parallelism.Parallelism.Builder
- setNumThreads(int) - Static method in class edu.duke.cs.osprey.energy.MultiTermEnergyFunction
- setNumThreads(int) - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- setNumThreads(int) - Method in class edu.duke.cs.osprey.minimization.CpuConfMinimizer.Builder
- setNumThreads(int) - Static method in class edu.duke.cs.osprey.parallelism.ThreadParallelism
- setNumThreadsIfPossible(int) - Static method in class edu.duke.cs.osprey.parallelism.ThreadParallelism
- setNumTopConfsToSave(int) - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- setNumTopOverallSeqs(int) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings.Builder
- setNumTopOverallSeqs(int) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- setNumUnPruned() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- setObjectiveWindowMax(double) - Method in class edu.duke.cs.osprey.gmec.Comets.Builder
- setObjectiveWindowMax(double) - Method in class edu.duke.cs.osprey.kstar.MSKStar.Builder
- setObjectiveWindowSize(double) - Method in class edu.duke.cs.osprey.gmec.Comets.Builder
- setObjectiveWindowSize(double) - Method in class edu.duke.cs.osprey.kstar.MSKStar.Builder
- setOffset(double) - Method in class edu.duke.cs.osprey.gmec.Comets.LME.Builder
- setOffset(double) - Method in class edu.duke.cs.osprey.kstar.MSKStar.LMFE.Builder
- setOneBody(int, int, Boolean) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixBoolean
- setOneBody(int, int, Boolean) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixInverted
- setOneBody(int, int, Boolean) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- setOneBody(int, int, Boolean) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- setOneBody(int, int, Double) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- setOneBody(int, int, Double) - Method in class edu.duke.cs.osprey.ematrix.NegatedEnergyMatrix
- setOneBody(int, int, Double) - Method in class edu.duke.cs.osprey.ematrix.ProxyEnergyMatrix
- setOneBody(int, int, T) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- setOneBody(int, int, T) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixGeneric
- setOneBody(int, ArrayList<Boolean>) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixBoolean
- setOneBody(int, ArrayList<Boolean>) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixInverted
- setOneBody(int, ArrayList<Boolean>) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- setOneBody(int, ArrayList<Boolean>) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- setOneBody(int, ArrayList<Double>) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- setOneBody(int, ArrayList<T>) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- setOneBody(int, ArrayList<T>) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixGeneric
- setOneBody(SimpleConfSpace.Position, SimpleConfSpace.ResidueConf, T) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- setOnlyGoldstein(boolean) - Method in class edu.duke.cs.osprey.pruning.NewPruningControl
- setOnlyGoldstein(boolean) - Method in class edu.duke.cs.osprey.pruning.PruningControl
- setOptimizer(MathTools.Optimizer) - Method in class edu.duke.cs.osprey.astar.seq.SeqAStarTree.Builder
- setOrderOfMag(int) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- setOrThrow(EWAKStarPartitionFunction, boolean, RCs) - Static method in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.WithExternalMemory
- setOrThrow(EWAKStarPartitionFunction, ConfDB.ConfTable) - Static method in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.WithConfTable
- setOrThrow(PartitionFunction, boolean, RCs) - Static method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.WithExternalMemory
- setOrThrow(PastePartitionFunction, boolean, RCs) - Static method in interface edu.duke.cs.osprey.paste.PastePartitionFunction.WithExternalMemory
- setOrThrow(PastePartitionFunction, ConfDB.ConfTable) - Static method in interface edu.duke.cs.osprey.paste.PastePartitionFunction.WithConfTable
- setPairsGoldsteinDiffThreshold(Double) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setPairsPlugThreshold(double) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setPairsThreshold(Double) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setPairsTransitivePruning(boolean) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setPairwise(int, int, int, int, Boolean) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixBoolean
- setPairwise(int, int, int, int, Boolean) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixInverted
- setPairwise(int, int, int, int, Boolean) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- setPairwise(int, int, int, int, Boolean) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- setPairwise(int, int, int, int, Double) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- setPairwise(int, int, int, int, Double) - Method in class edu.duke.cs.osprey.ematrix.NegatedEnergyMatrix
- setPairwise(int, int, int, int, Double) - Method in class edu.duke.cs.osprey.ematrix.ProxyEnergyMatrix
- setPairwise(int, int, int, int, T) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- setPairwise(int, int, int, int, T) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixGeneric
- setPairwise(int, int, ArrayList<ArrayList<Boolean>>) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixBoolean
- setPairwise(int, int, ArrayList<ArrayList<Boolean>>) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixInverted
- setPairwise(int, int, ArrayList<ArrayList<Boolean>>) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- setPairwise(int, int, ArrayList<ArrayList<Boolean>>) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- setPairwise(int, int, ArrayList<ArrayList<Double>>) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- setPairwise(int, int, ArrayList<ArrayList<T>>) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- setPairwise(int, int, ArrayList<ArrayList<T>>) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixGeneric
- setPairwise(SimpleConfSpace.Position, SimpleConfSpace.ResidueConf, SimpleConfSpace.Position, SimpleConfSpace.ResidueConf, T) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- setPanSeqSP(KSSearchProblem) - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- setParallelism(Parallelism) - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree
- setParallelism(Parallelism) - Method in class edu.duke.cs.osprey.coffee.Coffee.Builder
- setParallelism(Parallelism) - Method in class edu.duke.cs.osprey.energy.EnergyCalculator.Builder
- setParallelism(Parallelism) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- setParallelism(Parallelism) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- setParallelism(Parallelism) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- setParallelism(Parallelism) - Method in class edu.duke.cs.osprey.markstar.MARKStar.Settings.Builder
- setParallelism(Parallelism) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setPartitionFunction(PartitionFunction) - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFAdapter
- setPerformanceLogFile(File) - Method in class edu.duke.cs.osprey.sofea.Sofea.Builder
- setPfConfs(int) - Method in class edu.duke.cs.osprey.paste.Paste.Settings.Builder
- setPfEw(double) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- setPfuncTimeout(Duration) - Method in class edu.duke.cs.osprey.kstar.KStar.Settings.Builder
- setPhase2Method(String) - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- setPicker(ConfPicker) - Method in class edu.duke.cs.osprey.partcr.PartCR
- setPlugThreshold(double) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setPos(double, double) - Method in class edu.duke.cs.osprey.tools.SVG.TextDrawable
- setPosInterDist(PosInterDist) - Method in class edu.duke.cs.osprey.ematrix.compiled.EmatCalculator.Builder
- setPosInterDist(PosInterDist) - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter.Builder
-
Deprecated.
- setPreciseBcalc(boolean) - Method in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
-
If true, uses BoltzmannCalculator.calcPrecise() instead of BoltzmannCalculator.calc().
- setPrecision(Structs.Precision) - Method in class edu.duke.cs.osprey.coffee.Coffee.Builder
- setPreCompE(double) - Method in class edu.duke.cs.osprey.energy.MultiTermEnergyFunction
- setPreferUpRipple(boolean) - Method in class edu.duke.cs.osprey.minimization.CCDMinimizer
- setPrintIntermediateConfsToConsole(boolean) - Method in class edu.duke.cs.osprey.gmec.SimpleGMECFinder.Builder
- setPrintIntermediateConfsToConsole(boolean) - Method in class edu.duke.cs.osprey.lute.LUTEGMECFinder.Builder
- setPrintPDBs(boolean) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings.Builder
- setPrintPDBs(boolean) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- setPrintToConsole(boolean) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- setPrintToConsole(boolean) - Method in class edu.duke.cs.osprey.gmec.Comets.Builder
- setPrintToConsole(boolean) - Method in class edu.duke.cs.osprey.gmec.SimpleGMECFinder.Builder
- setPrintToConsole(boolean) - Method in class edu.duke.cs.osprey.kstar.MSKStar.Builder
- setProfilingEvents(ProfilingEvents) - Method in class edu.duke.cs.osprey.gpu.opencl.Kernel
- setProgress(long) - Method in class edu.duke.cs.osprey.tools.Progress
- setPruner(AStarPruner) - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree.Builder
- setPruningInterval(double) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- setPruningInterval(double) - Method in class edu.duke.cs.osprey.pruning.NewPruningControl
- setPruningInterval(double) - Method in class edu.duke.cs.osprey.pruning.PruningControl
- setPruningMatrix() - Method in class edu.duke.cs.osprey.multistatekstar.MSSearchProblem
- setPruningMatrix(PruningMatrix) - Method in class edu.duke.cs.osprey.multistatekstar.MSSearchProblem
- setQCapacity(int) - Method in class edu.duke.cs.osprey.kstar.KSConfQ
- setQuadCorrectionThreshold(Double) - Method in class edu.duke.cs.osprey.ematrix.SimplerEnergyMatrixCalculator.Builder
- setRCDBFile(File) - Method in class edu.duke.cs.osprey.sofea.Sofea.Builder
- setRCs(RCs) - Method in class edu.duke.cs.osprey.astar.conf.ConfRanker.Builder
- setRCs(RCs) - Method in class edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc
- setRCs(RCs) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- setRCs(RCs) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- setRCs(RCs) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- setReduceMinimizations(boolean) - Method in class edu.duke.cs.osprey.markstar.MARKStar.Settings.Builder
- setReferenceEnergies(SimpleReferenceEnergies) - Method in class edu.duke.cs.osprey.ematrix.compiled.EmatCalculator.Builder
- setReferenceEnergies(SimpleReferenceEnergies) - Method in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter.Builder
-
Deprecated.
- setReferenceEnergies(SimpleReferenceEnergies) - Method in class edu.duke.cs.osprey.energy.ConfEnergyCalculator.Builder
- setRender(boolean) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode.Builder
- setRender(boolean) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- setReportMemory(boolean) - Method in class edu.duke.cs.osprey.tools.Progress
- setReportMode(NewPruningControl.ReportMode) - Method in class edu.duke.cs.osprey.pruning.NewPruningControl
- setReportMode(PruningControl.ReportMode) - Method in class edu.duke.cs.osprey.pruning.PruningControl
- setReportProgress(boolean) - Method in class edu.duke.cs.osprey.astar.conf.ConfRanker.Builder
- setReportProgress(boolean) - Method in class edu.duke.cs.osprey.coffee.directors.PfuncDirector.Builder
- setReportProgress(boolean) - Method in class edu.duke.cs.osprey.coffee.directors.PfuncsDirector.Builder
- setReportProgress(boolean) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarGradientDescentPfunc
- setReportProgress(boolean) - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction
- setReportProgress(boolean) - Method in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- setReportProgress(boolean) - Method in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- setReportProgress(boolean) - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction
- setReportProgress(boolean) - Method in class edu.duke.cs.osprey.kstar.pfunc.SimplePartitionFunction
- setReportProgress(boolean) - Method in class edu.duke.cs.osprey.lute.LUTEPfunc
- setReportProgress(boolean) - Method in class edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc
- setReportProgress(boolean) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- setReportProgress(boolean) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- setReportProgress(boolean) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- setReportProgress(boolean) - Method in class edu.duke.cs.osprey.minimization.ConfMinimizer
- setReportProgress(boolean) - Method in class edu.duke.cs.osprey.paste.PasteGradientDescentPfunc
- setReportProgress(boolean) - Method in interface edu.duke.cs.osprey.paste.PastePartitionFunction
- setReportStateProgress(boolean) - Method in class edu.duke.cs.osprey.coffee.directors.KStarDirector.Builder
- setResidueMutability(String, List<String>, boolean, boolean) - Method in class edu.duke.cs.osprey.confspace.Strand.Builder
- setResidues(int, int) - Method in class edu.duke.cs.osprey.confspace.Strand.Builder
-
Deprecated.
- setResidues(ResidueTermini) - Method in class edu.duke.cs.osprey.confspace.Strand.Builder
-
Deprecated.
- setResidues(String, String) - Method in class edu.duke.cs.osprey.confspace.Strand.Builder
- setResPairCache(ResPairCache) - Method in class edu.duke.cs.osprey.energy.EnergyCalculator.Builder
- setResType(String) - Method in class edu.duke.cs.osprey.confspace.Sequence.Assignment
-
Set the residue type of this assignment.
- setRingCloseable(boolean) - Method in class edu.duke.cs.osprey.dof.ProlinePucker
- setRLphiPsiResolution(double) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
-
Resolution of backbone "bins" in the rotamer library.
- setRotamericDihedrals(double[][]) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
- setRotamericDihedrals(double[][], int, int) - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
-
PGC 2015: Sets the number of rotamers for a residue template; phi and psi are only used when using a backbone dependent rotamer library.
- setRunState(PFAbstract.RunState) - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- setScore(double) - Method in interface edu.duke.cs.osprey.astar.AStarNode
- setScore(double) - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- setScore(double) - Method in class edu.duke.cs.osprey.astar.FullAStarNode
- setScore(double) - Method in class edu.duke.cs.osprey.astar.SlimAStarNode
- setScore(double) - Method in class edu.duke.cs.osprey.confspace.ConfSearch.ScoredConf
-
Sets the score for this conformation
- setScore(double, MathTools.Optimizer) - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- setScore(LMB) - Method in class edu.duke.cs.osprey.multistatekstar.MSKStarNode
- setScoreNeedsRefinement(boolean) - Method in interface edu.duke.cs.osprey.astar.AStarNode
- setScoreNeedsRefinement(boolean) - Method in class edu.duke.cs.osprey.astar.FullAStarNode
- setScoreNeedsRefinement(boolean) - Method in class edu.duke.cs.osprey.astar.SlimAStarNode
- setScorer(RCScorer) - Method in class edu.duke.cs.osprey.partcr.PartCR
- setScorers(AStarScorer, AStarScorer) - Method in interface edu.duke.cs.osprey.astar.conf.order.AStarOrder
- setScorers(AStarScorer, AStarScorer) - Method in class edu.duke.cs.osprey.astar.conf.order.DynamicHMeanAStarOrder
- setScorers(AStarScorer, AStarScorer) - Method in class edu.duke.cs.osprey.astar.conf.order.SequentialAStarOrder
- setScorers(AStarScorer, AStarScorer) - Method in class edu.duke.cs.osprey.astar.conf.order.StaticEnergyHMeanAStarOrder
- setScorers(AStarScorer, AStarScorer) - Method in class edu.duke.cs.osprey.astar.conf.order.StaticScoreHMeanAStarOrder
- setScorers(AStarScorer, AStarScorer) - Method in class edu.duke.cs.osprey.astar.conf.order.UpperLowerAStarOrder
- setScorers(AStarScorer, AStarScorer) - Method in class edu.duke.cs.osprey.markstar.framework.BiggestLowerboundDifferenceOrder
- setScorers(AStarScorer, AStarScorer) - Method in class edu.duke.cs.osprey.markstar.framework.StaticBiggestLowerboundDifferenceOrder
- setScorers(AStarScorer, AStarScorer) - Method in class edu.duke.cs.osprey.markstar.framework.StaticBiggesUpperboundDifferenceOrder
- setScorers(AStarScorer, AStarScorer) - Method in class edu.duke.cs.osprey.markstar.framework.StaticLowestEntropyOrder
- setScoringLog(File) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB.Builder
- setSeqDBFile(File) - Method in class edu.duke.cs.osprey.coffee.Coffee.Builder
- setSeqDBFile(File) - Method in class edu.duke.cs.osprey.sofea.Sofea.Builder
- setSeqDBMathContext(MathContext) - Method in class edu.duke.cs.osprey.coffee.Coffee.Builder
- setSeqDBMathContext(MathContext) - Method in class edu.duke.cs.osprey.sofea.Sofea.Builder
- setSeqFilterOnly(boolean) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- setSeqTrie(EwakstarLimitedSequenceTrie) - Method in class edu.duke.cs.osprey.astar.seq.SeqAStarTree.Builder
- setSequence(Sequence) - Method in class edu.duke.cs.osprey.coffee.directors.PfuncDirector.Builder
- setShellDistance(double) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Builder
- setShowPfuncProgress(boolean) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings.Builder
- setShowPfuncProgress(boolean) - Method in class edu.duke.cs.osprey.kstar.KStar.Settings.Builder
- setShowPfuncProgress(boolean) - Method in class edu.duke.cs.osprey.markstar.MARKStar.Settings.Builder
- setShowPfuncProgress(boolean) - Method in class edu.duke.cs.osprey.paste.Paste.Settings.Builder
- setShowProgress(boolean) - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree.Builder
- setShowProgress(boolean) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setShowProgress(boolean) - Method in class edu.duke.cs.osprey.sofea.Sofea.Builder
- setSigFigs(BigDecimal) - Static method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- setSigFigs(BigDecimal, int) - Static method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- setSinglesGoldsteinDiffThreshold(Double) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setSinglesPlugThreshold(double) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setSinglesThreshold(Double) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setSinglesTransitivePruning(boolean) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setSplitter(RCSplitter) - Method in class edu.duke.cs.osprey.partcr.PartCR
- setStabilityThresh(double) - Static method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- setStabilityThreshold(Double) - Method in class edu.duke.cs.osprey.coffee.directors.KStarDirector.Builder
- setStabilityThreshold(Double) - Method in class edu.duke.cs.osprey.kstar.KStar.Settings.Builder
- setStabilityThreshold(Double) - Method in class edu.duke.cs.osprey.markstar.MARKStar.Settings.Builder
- setStabilityThreshold(Double) - Method in class edu.duke.cs.osprey.paste.Paste.Settings.Builder
- setStabilityThreshold(BigDecimal) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarGradientDescentPfunc
- setStabilityThreshold(BigDecimal) - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction
-
Sets the stability threshold for this PartitionFunction, if supported
- setStabilityThreshold(BigDecimal) - Method in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- setStabilityThreshold(BigDecimal) - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction
-
Sets the stability threshold for this PartitionFunction, if supported
- setStabilityThreshold(BigDecimal) - Method in class edu.duke.cs.osprey.kstar.pfunc.SimplePartitionFunction
- setStabilityThreshold(BigDecimal) - Method in class edu.duke.cs.osprey.lute.LUTEPfunc
- setStabilityThreshold(BigDecimal) - Method in class edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc
- setStabilityThreshold(BigDecimal) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- setStabilityThreshold(BigDecimal) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- setStabilityThreshold(BigDecimal) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- setStabilityThreshold(BigDecimal) - Method in class edu.duke.cs.osprey.paste.PasteGradientDescentPfunc
- setStabilityThreshold(BigDecimal) - Method in interface edu.duke.cs.osprey.paste.PastePartitionFunction
-
Sets the stability threshold for this PartitionFunction, if supported
- setStartTime(long) - Method in class edu.duke.cs.osprey.kstar.KSAbstract
- setStaticStatic(boolean) - Method in class edu.duke.cs.osprey.coffee.Coffee.Builder
- setStatus(PartitionFunction.Status) - Method in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized
- setStrokeColor(int) - Method in class edu.duke.cs.osprey.tools.SVG.StyleClass
- setStrokeDashArray(int...) - Method in class edu.duke.cs.osprey.tools.SVG.StyleClass
- setStrokeOpacity(double) - Method in class edu.duke.cs.osprey.tools.SVG.StyleClass
- setStrokeWidth(double) - Method in class edu.duke.cs.osprey.tools.SVG.StyleClass
- setStyleClasses(SVG.StyleClass...) - Method in class edu.duke.cs.osprey.tools.SVG.Drawable
- setSubset(BigForcefieldEnergy.Subset) - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ForcefieldKernelCuda
- setSubset(BigForcefieldEnergy.Subset) - Method in interface edu.duke.cs.osprey.gpu.ForcefieldKernel
- setSubset(BigForcefieldEnergy.Subset) - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.ForcefieldKernelOpenCL
- setSweepIncrement(double) - Method in class edu.duke.cs.osprey.sofea.Sofea.Builder
- setTemp(double) - Method in class edu.duke.cs.osprey.coffee.Coffee.Builder
- setTempDir(String) - Static method in class edu.duke.cs.osprey.externalMemory.ExternalMemory
-
Set temporary directory to host external memory.
- setTempDir(String, String) - Static method in class edu.duke.cs.osprey.externalMemory.ExternalMemory
-
Set temporary directory to host external memory.
- setTemplateLibrary(ResidueTemplateLibrary) - Method in class edu.duke.cs.osprey.confspace.Strand.Builder
- setTemplateMatchingMethod(Residue.TemplateMatchingMethod) - Method in class edu.duke.cs.osprey.confspace.Strand.Builder
- setTextAnchor(SVG.StyleClass.TextAnchor) - Method in class edu.duke.cs.osprey.tools.SVG.StyleClass
- setTextRoot(Group) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- setThreshold(Double) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setTiming(Timing) - Method in class edu.duke.cs.osprey.coffee.directors.AffinityDirector.Builder
- setTiming(Timing) - Method in class edu.duke.cs.osprey.coffee.directors.KStarDirector.Builder
- setTiming(Timing) - Method in class edu.duke.cs.osprey.coffee.directors.PfuncDirector.Builder
- setTiming(Timing) - Method in class edu.duke.cs.osprey.coffee.directors.PfuncsDirector.Builder
- settings - Variable in class edu.duke.cs.osprey.energy.compiled.AmberEnergyCalculator
- settings - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar
-
Optional and overridable settings for K*
- settings - Variable in class edu.duke.cs.osprey.kstar.KStar
-
Optional and overridable settings for K*
- settings - Variable in class edu.duke.cs.osprey.markstar.MARKStar
-
Optional and overridable settings for K*
- settings - Variable in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- settings - Variable in class edu.duke.cs.osprey.multistatekstar.MSSearchProblem
- settings - Variable in class edu.duke.cs.osprey.paste.Paste
-
Optional and overridable settings for K*
- Settings() - Constructor for class edu.duke.cs.osprey.energy.compiled.AmberEnergyCalculator.Settings
- Settings(boolean, boolean, boolean, int, double, double, int, int, EWAKStarScoreWriter.Writers, boolean, boolean) - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings
- Settings(double, double, int, Double, int, PasteScoreWriter.Writers, boolean, boolean, boolean, File) - Constructor for class edu.duke.cs.osprey.paste.Paste.Settings
- Settings(double, Double, int, KStarScoreWriter.Writers, boolean, boolean, String, boolean, int, Duration) - Constructor for class edu.duke.cs.osprey.kstar.KStar.Settings
- Settings(double, Double, int, KStarScoreWriter.Writers, boolean, String, Parallelism, int, boolean) - Constructor for class edu.duke.cs.osprey.markstar.MARKStar.Settings
- Settings(int, int) - Constructor for class edu.duke.cs.osprey.kstar.BBKStar.Settings
- Settings(EwakstarLimitedSequenceTrie, int, int) - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.Settings
- setTotalWork(long) - Method in class edu.duke.cs.osprey.tools.Progress
- setTraditional() - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree.Builder
-
Uses the traditional estimation function to guide the tree search.
- setTraditionalOpt(MathTools.Optimizer) - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree.Builder
-
Just like setTraditional, but allow maximization or minimization
- setTransitivePruning(boolean) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setTree(int, NodeTree) - Method in class edu.duke.cs.osprey.coffee.directions.Directions
-
Tell all cluster members the node tree topology for each state.
- setTripleCorrectionThreshold(Double) - Method in class edu.duke.cs.osprey.coffee.Coffee.Builder
- setTripleCorrectionThreshold(Double) - Method in class edu.duke.cs.osprey.ematrix.SimplerEnergyMatrixCalculator.Builder
- setTriplesGoldsteinDiffThreshold(Double) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setTriplesPlugThreshold(double) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setTriplesTransitivePruning(boolean) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setTuple(RCTuple, T) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- setTupleEnergies(double[], double, TaskExecutor) - Method in class edu.duke.cs.osprey.lute.LUTE.LinearSystem
- setTupleValue(RCTuple, Boolean) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixInverted
- setTupleValue(RCTuple, Boolean) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- setTupleValue(RCTuple, Boolean) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- setTupleValue(RCTuple, T) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- setTupleValue(RCTuple, T) - Method in interface edu.duke.cs.osprey.confspace.TupleMatrix
- setType(EnergyCalculator.Type) - Method in class edu.duke.cs.osprey.energy.EnergyCalculator.Builder
- setTypeDependent(boolean) - Method in class edu.duke.cs.osprey.pruning.SimpleDEE.Runner
- setUpdater(MPLPUpdater) - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree.MPLPBuilder
- setupDEEPer() - Method in class edu.duke.cs.osprey.control.ConfigFileParser
- setupDEEPer(int) - Method in class edu.duke.cs.osprey.kstar.KSConfigFileParser
- setupDEEPer(int, int, ArrayList<Integer>, boolean) - Method in class edu.duke.cs.osprey.multistatekstar.MSConfigFileParser
- setUpperBound(int[], double, long) - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- setupPruning(SearchProblem, double, boolean, boolean) - Method in class edu.duke.cs.osprey.control.ConfigFileParser
- setupSMA(boolean, int) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- setupUnboundStates() - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- setUseEPIC(boolean) - Method in class edu.duke.cs.osprey.pruning.NewPruningControl
- setUseEPIC(boolean) - Method in class edu.duke.cs.osprey.pruning.PruningControl
- setUseExact(boolean) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings.Builder
- setUseExternalMemory(boolean) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings.Builder
- setUseExternalMemory(boolean, RCs) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarGradientDescentPfunc
- setUseExternalMemory(boolean, RCs) - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.WithExternalMemory
- setUseExternalMemory(boolean, RCs) - Method in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- setUseExternalMemory(boolean, RCs) - Method in interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.WithExternalMemory
- setUseExternalMemory(boolean, RCs) - Method in class edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc
- setUseExternalMemory(boolean, RCs) - Method in class edu.duke.cs.osprey.paste.PasteGradientDescentPfunc
- setUseExternalMemory(boolean, RCs) - Method in interface edu.duke.cs.osprey.paste.PastePartitionFunction.WithExternalMemory
- setUseTupExp(boolean) - Method in class edu.duke.cs.osprey.pruning.NewPruningControl
- setUseTupExp(boolean) - Method in class edu.duke.cs.osprey.pruning.PruningControl
- setUseWindowCriterion(boolean) - Method in class edu.duke.cs.osprey.paste.Paste.Settings.Builder
- setUseWtBenchmark(boolean) - Method in class edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder
- setValue(String, String) - Method in class edu.duke.cs.osprey.control.ParamSet
- setValue(String, String, FileTools.PathRoot) - Method in class edu.duke.cs.osprey.control.ParamSet
- setVerbose(boolean) - Method in class edu.duke.cs.osprey.pruning.NewPruner
- setVerbose(boolean) - Method in class edu.duke.cs.osprey.pruning.Pruner
- setVerbosity(boolean) - Method in class edu.duke.cs.osprey.control.ParamSet
- setVoxelShape(VoxelShape) - Method in class edu.duke.cs.osprey.confspace.Strand.ResidueFlex
- setWildType() - Method in class edu.duke.cs.osprey.confspace.Sequence.Assignment
-
Set the residue type of this assignment to the wild-type.
- setWildType(SeqSpace.Position) - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Sets the residue type at the specified sequence position to wild-type
- setWildType(String) - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Sets the residue type at the specified residue to wild-type
- setWTBenchmark(boolean) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings.Builder
- setX(double) - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.OneDof
- setX(int, double) - Method in class edu.duke.cs.osprey.confspace.compiled.CoordsList
- setY(int, double) - Method in class edu.duke.cs.osprey.confspace.compiled.CoordsList
- setZ(int, double) - Method in class edu.duke.cs.osprey.confspace.compiled.CoordsList
- setZ(BigExp) - Method in class edu.duke.cs.osprey.coffee.zmat.Pair
- setZ(BigExp) - Method in class edu.duke.cs.osprey.coffee.zmat.Single
- setZ(BigExp) - Method in class edu.duke.cs.osprey.coffee.zmat.Triple
- setZ(BigExp) - Method in interface edu.duke.cs.osprey.coffee.zmat.Tuple
- shape - Variable in class edu.duke.cs.osprey.tools.SVG.ShapeDrawable
- ShapeDrawable(Shape) - Constructor for class edu.duke.cs.osprey.tools.SVG.ShapeDrawable
- SharedBuilder(EnergyCalculator) - Constructor for class edu.duke.cs.osprey.energy.EnergyCalculator.SharedBuilder
- sharedMemCalc - Variable in class edu.duke.cs.osprey.gpu.cuda.Kernel.Function
- Shear - Class in edu.duke.cs.osprey.dof.deeper.perts
-
Shear perturbation: small perturbation appropriate for helices
- Shear(ArrayList<Residue>) - Constructor for class edu.duke.cs.osprey.dof.deeper.perts.Shear
- SHEET - Enum constant in enum class edu.duke.cs.osprey.structure.Residue.SecondaryStructure
- shellDist - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
Distance from flexible residues (in Angstroms) within which to include shell residues
- shellDistCutoff - Variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
-
Deprecated.
- shellResidues - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- shellResidues - Variable in class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator
-
Deprecated.
- shellResNumbers - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
The residue numbers of the shell residues
- Short - Enum constant in enum class edu.duke.cs.osprey.externalMemory.AssignmentsSerializer.Encoding
- Short - Enum constant in enum class edu.duke.cs.osprey.pruning.NewPruningControl.ReportMode
- Short - Enum constant in enum class edu.duke.cs.osprey.pruning.PruningControl.ReportMode
- Short - Enum constant in enum class edu.duke.cs.osprey.tools.IntEncoding
- shouldMinimize(MARKStarNode.Node) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- shouldPruneTuple(RCTuple, double) - Method in class edu.duke.cs.osprey.pruning.PLUG
- shouldSignal(int) - Method in interface edu.duke.cs.osprey.parallelism.CounterSignal.SignalCondition
- shouldWeUseEPIC() - Method in class edu.duke.cs.osprey.ematrix.epic.EPICSettings
- shouldWeUseLUTE() - Method in class edu.duke.cs.osprey.gmec.PrecomputedMatrices
- shouldWeUseLUTE() - Method in class edu.duke.cs.osprey.tupexp.LUTESettings
- showBoundStats - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncDirector
- showPfuncProgress - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings
- showPfuncProgress - Variable in class edu.duke.cs.osprey.kstar.KStar.Settings
- showPfuncProgress - Variable in class edu.duke.cs.osprey.markstar.MARKStar.Settings
- showPfuncProgress - Variable in class edu.duke.cs.osprey.paste.Paste.Settings
- showProgress - Variable in class edu.duke.cs.osprey.sofea.Sofea
- showRoot() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- SidechainIdealizer - Class in edu.duke.cs.osprey.dof.deeper
-
This class handles idealization of sidechains; residues moved by DEEPer have idealized sidechains because orig sidechain geometry not valid for perturbed backbones
- SidechainIdealizer() - Constructor for class edu.duke.cs.osprey.dof.deeper.SidechainIdealizer
- sign() - Method in class edu.duke.cs.osprey.tools.BigExp
- signal() - Method in class edu.duke.cs.osprey.parallelism.PulseSignal
- Signal - Class in edu.duke.cs.osprey.parallelism
- Signal() - Constructor for class edu.duke.cs.osprey.parallelism.Signal
- Signaled - Enum constant in enum class edu.duke.cs.osprey.parallelism.PulseSignal.Result
- signum() - Method in class edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal
- SimpleCCDMinimizer - Class in edu.duke.cs.osprey.minimization
- SimpleCCDMinimizer() - Constructor for class edu.duke.cs.osprey.minimization.SimpleCCDMinimizer
- SimpleCCDMinimizer(ObjectiveFunction) - Constructor for class edu.duke.cs.osprey.minimization.SimpleCCDMinimizer
- SimpleCCDMinimizer(Factory<LineSearcher, Void>) - Constructor for class edu.duke.cs.osprey.minimization.SimpleCCDMinimizer
- SimpleConfSpace - Class in edu.duke.cs.osprey.confspace
-
Maintains the design positions and residue conformations for a list of strands.
- SimpleConfSpace(List<Strand>, Map<Strand, List<StrandFlex>>, double) - Constructor for class edu.duke.cs.osprey.confspace.SimpleConfSpace
- SimpleConfSpace.Builder - Class in edu.duke.cs.osprey.confspace
- SimpleConfSpace.DofTypes - Enum Class in edu.duke.cs.osprey.confspace
-
What kind of degree of freedom? Used mainly to decide if we can use GPU CCD implementations or not, which only support dihedral angles for now.
- SimpleConfSpace.NonMutablePositionException - Exception in edu.duke.cs.osprey.confspace
- SimpleConfSpace.Position - Class in edu.duke.cs.osprey.confspace
- SimpleConfSpace.ResidueConf - Class in edu.duke.cs.osprey.confspace
- SimpleConfSpace.ResidueConf.PostTemplateModifier - Interface in edu.duke.cs.osprey.confspace
- SimpleConfSpace.ResidueConf.Type - Enum Class in edu.duke.cs.osprey.confspace
- SimpleDEE - Class in edu.duke.cs.osprey.pruning
-
Simple, fast implementation of DEE.
- SimpleDEE(SimpleConfSpace, EnergyMatrix, PruningMatrix) - Constructor for class edu.duke.cs.osprey.pruning.SimpleDEE
- SimpleDEE(SimpleConfSpace, EnergyMatrix, PruningMatrix, PruningMatrix) - Constructor for class edu.duke.cs.osprey.pruning.SimpleDEE
- SimpleDEE.Runner - Class in edu.duke.cs.osprey.pruning
-
Runs various pruning algorithms including steric/threshold pruning Dead-End Elimination (DEE) Pruning of Local Unrealistic Geometries (PLUG) Transitive pruning (ie, prune tuples implied by other pruned tuples) to remove tuples of RCs that will not appear in low-energy conformations.
- SimpleEnergyCalculator - Class in edu.duke.cs.osprey.ematrix
-
Deprecated.
- SimpleEnergyCalculator(ForcefieldParams, ConfSpace, List<Residue>) - Constructor for class edu.duke.cs.osprey.ematrix.SimpleEnergyCalculator
-
Deprecated.
- SimpleEnergyCalculator.Cpu - Class in edu.duke.cs.osprey.ematrix
-
Deprecated.
- SimpleEnergyCalculator.Cuda - Class in edu.duke.cs.osprey.ematrix
-
Deprecated.
- SimpleEnergyMatrixCalculator - Class in edu.duke.cs.osprey.ematrix
-
Deprecated.
- SimpleEnergyMatrixCalculator() - Constructor for class edu.duke.cs.osprey.ematrix.SimpleEnergyMatrixCalculator
-
Deprecated.
- SimpleEnergyMatrixCalculator.Cpu - Class in edu.duke.cs.osprey.ematrix
-
Deprecated.
- SimpleEnergyMatrixCalculator.Cuda - Class in edu.duke.cs.osprey.ematrix
-
Deprecated.
- SimpleGMECFinder - Class in edu.duke.cs.osprey.gmec
-
Searches a conformation space for the single conformation that minimizes the desired energy function, ie the Global Minimum Energy Conformation, or GMEC.
- SimpleGMECFinder(ConfSearch, ConfEnergyCalculator, GMECFinder.ConfPruner, ConfPrinter, ConfPrinter, boolean, boolean, boolean, File) - Constructor for class edu.duke.cs.osprey.gmec.SimpleGMECFinder
- SimpleGMECFinder.Builder - Class in edu.duke.cs.osprey.gmec
- simplePartition(int) - Method in class edu.duke.cs.osprey.coffee.ClusterMember
-
Statically partition a simple range among the cluster members into contiguous blocks, one per memeber
- SimplePartitionFunction - Class in edu.duke.cs.osprey.kstar.pfunc
-
This partition function calculator estimates the partition function value by alternating between two operations: 1.
- SimplePartitionFunction(ConfEnergyCalculator, ConfSearch, BigInteger) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.SimplePartitionFunction
- SimpleReferenceEnergies - Class in edu.duke.cs.osprey.ematrix
-
This class stores a reference energy for each residue position & AA type (which is the minimum intra-RC energy at that position & AA type)
- SimpleReferenceEnergies() - Constructor for class edu.duke.cs.osprey.ematrix.SimpleReferenceEnergies
- SimpleReferenceEnergies.Builder - Class in edu.duke.cs.osprey.ematrix
- SimplerEnergyMatrixCalculator - Class in edu.duke.cs.osprey.ematrix
- SimplerEnergyMatrixCalculator.Builder - Class in edu.duke.cs.osprey.ematrix
- SimpleSerializer() - Constructor for class edu.duke.cs.osprey.tools.MapDBTools.SimpleSerializer
- SimpleSerializer(int) - Constructor for class edu.duke.cs.osprey.tools.MapDBTools.SimpleSerializer
- single(int, int) - Method in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- single(ConfSpace, int, int) - Method in class edu.duke.cs.osprey.energy.compiled.PosInterGen
- single(ConfSpace, SimpleReferenceEnergies, int, int) - Method in enum class edu.duke.cs.osprey.confspace.compiled.PosInterDist
- Single - Class in edu.duke.cs.osprey.coffee.zmat
- Single(int, int) - Constructor for class edu.duke.cs.osprey.coffee.zmat.Single
- Single(int, int, BigExp) - Constructor for class edu.duke.cs.osprey.coffee.zmat.Single
- singleIndex(int, int) - Method in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- singleResEnergy(Residue) - Method in class edu.duke.cs.osprey.energy.EnergyFunctionGenerator
- singleResEnergy(Residue) - Method in class edu.duke.cs.osprey.energy.GpuEnergyFunctionGenerator
- SingleResEnergy - Class in edu.duke.cs.osprey.energy.forcefield
- SingleResEnergy(Residue, ForcefieldParams) - Constructor for class edu.duke.cs.osprey.energy.forcefield.SingleResEnergy
- SingleSequenceNode(Sequence) - Constructor for class edu.duke.cs.osprey.kstar.BBKStar.SingleSequenceNode
- SingleSequenceNode(Sequence, ConfDB.DBs) - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.SingleSequenceNode
- singlesPairsToString(int, int) - Method in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- SingleThreaded - Static variable in class edu.duke.cs.osprey.parallelism.Parallelism
- Six12PotentialCoefficient - Record Class in edu.duke.cs.osprey.energy.forcefield.amber
- Six12PotentialCoefficient(AtomSymbolAndMass, float, float) - Constructor for record class edu.duke.cs.osprey.energy.forcefield.amber.Six12PotentialCoefficient
-
Creates an instance of a
Six12PotentialCoefficientrecord class. - six12PotentialCoefficients() - Method in class edu.duke.cs.osprey.energy.forcefield.amber.ForcefieldFileParser
- Six12PotentialParameter - Record Class in edu.duke.cs.osprey.energy.forcefield.amber
- Six12PotentialParameter(String, String) - Constructor for record class edu.duke.cs.osprey.energy.forcefield.amber.Six12PotentialParameter
-
Creates an instance of a
Six12PotentialParameterrecord class. - size - Variable in class edu.duke.cs.osprey.confspace.compiled.CoordsList
- size - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot.Points
- size() - Method in class edu.duke.cs.osprey.coffee.directors.BestSet
- size() - Method in interface edu.duke.cs.osprey.coffee.nodedb.FixedIndex
-
Returns the number of items currently stored.
- size() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex
- size() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices.BroadcastInfo
- size() - Method in class edu.duke.cs.osprey.coffee.nodedb.PriorityDequeFixedIndex
- size() - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesPair
- size() - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesStatic
- size() - Method in class edu.duke.cs.osprey.confspace.Conf.Map
- size() - Method in class edu.duke.cs.osprey.confspace.Conf.Set
- size() - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- size() - Method in class edu.duke.cs.osprey.confspace.RCTuple
- size() - Method in class edu.duke.cs.osprey.confspace.TripleMatrix
- size() - Method in class edu.duke.cs.osprey.confspace.TuplesIndex
- size() - Method in class edu.duke.cs.osprey.dof.DofInfo
- size() - Method in class edu.duke.cs.osprey.ematrix.UpdatingEnergyMatrix.TupleTrie
- size() - Method in class edu.duke.cs.osprey.energy.ResidueInteractions
- size() - Method in interface edu.duke.cs.osprey.externalMemory.Queue
- size() - Method in class edu.duke.cs.osprey.gpu.cuda.CUBuffer
- size() - Method in class edu.duke.cs.osprey.kstar.KAStarTree
- size() - Method in class edu.duke.cs.osprey.kstar.KSConfQ
- size() - Method in class edu.duke.cs.osprey.lute.ConfSampler.Samples
- size() - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- size() - Method in class edu.duke.cs.osprey.parallelism.Threads
- size() - Method in class edu.duke.cs.osprey.structure.analysis.ClusterR1
- size() - Method in class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel.Interval
- size() - Method in class edu.duke.cs.osprey.tools.IntRange
- size() - Method in class edu.duke.cs.osprey.tools.MathTools.DoubleBounds
- size() - Method in class edu.duke.cs.osprey.tools.ObjectPool
- size(int) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
- size(int) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices
- size(MathContext) - Method in class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- sizeInternals() - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesSingle
- sizeStatics() - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.IndicesSingle
- skip(long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
-
Skips the desired number of bytes, returns the position before skipping.
- skipToAlignment(long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- SlaterKirkwoodParameter - Record Class in edu.duke.cs.osprey.energy.forcefield.amber
- SlaterKirkwoodParameter(AtomSymbolAndMass, float, float, float) - Constructor for record class edu.duke.cs.osprey.energy.forcefield.amber.SlaterKirkwoodParameter
-
Creates an instance of a
SlaterKirkwoodParameterrecord class. - slaterKirkwoodParameters() - Method in class edu.duke.cs.osprey.energy.forcefield.amber.ForcefieldFileParser
- sleep(int) - Static method in class edu.duke.cs.osprey.parallelism.ThreadTools
- sleep(long, TimeUnit) - Static method in class edu.duke.cs.osprey.parallelism.ThreadTools
- sliceFrom(long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- SlimAStarNode - Class in edu.duke.cs.osprey.astar
- SlimAStarNode.Factory - Class in edu.duke.cs.osprey.astar
- SlimAStarNode.Link - Class in edu.duke.cs.osprey.astar
- SmallAngleVoxel - Class in edu.duke.cs.osprey.structure.analysis
-
a cartesian product of intervals in S^1 x S^1 x S^1 ...
- SmallAngleVoxel(double[]) - Constructor for class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel
- SmallAngleVoxel(SmallAngleVoxel.Interval...) - Constructor for class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel
- SmallAngleVoxel.Interval - Class in edu.duke.cs.osprey.structure.analysis
-
an interval on S^1, localized around a point
- SmallClash - Enum constant in enum class edu.duke.cs.osprey.structure.Probe.Contact
- smaNodes - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- SmartRCSplitter - Class in edu.duke.cs.osprey.partcr.splitters
- SmartRCSplitter(double[], int) - Constructor for class edu.duke.cs.osprey.partcr.splitters.SmartRCSplitter
- Sofea - Class in edu.duke.cs.osprey.sofea
-
SOFEA - Sweep Operations for Free Energy Approximation Explores a (possibly multi-sequence and multi-state) conformation space by visiting subtrees containing low-energy conformations first, in less than exponential memory.
- Sofea.Builder - Class in edu.duke.cs.osprey.sofea
- Sofea.Criterion - Interface in edu.duke.cs.osprey.sofea
-
decides if computation should continue or not, and which nodes we should process
- Sofea.Criterion.Filter - Enum Class in edu.duke.cs.osprey.sofea
- Sofea.Criterion.Satisfied - Enum Class in edu.duke.cs.osprey.sofea
- Sofea.SeqResult - Class in edu.duke.cs.osprey.sofea
- Sofea.StateConfig - Class in edu.duke.cs.osprey.sofea
-
Per-state configuration needed to run SOFEA.
- Sofea.StateInfo - Class in edu.duke.cs.osprey.sofea
- Solvation - Enum constant in enum class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.Type
- solvationCutoff2 - Variable in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.ParamInfo
- solvationForcefield - Variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- solvCoeff - Variable in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.ParamInfo
- solvCutoff - Static variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- solvCutoff2 - Static variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- solve_3pep_poly(double[], double[], double[], double[], double[][][], double[][][], double[][][]) - Method in class edu.duke.cs.osprey.dof.deeper.perts.TripeptideClosure
- solve_sturm(int, double[], double[]) - Method in class edu.duke.cs.osprey.dof.deeper.perts.SturmSolver
- solvEnergy - Variable in class edu.duke.cs.osprey.energy.forcefield.ResPairCache.ResPair
- SolvParams() - Constructor for class edu.duke.cs.osprey.energy.forcefield.EEF1.SolvParams
- solvScale - Variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- sort(Comparator<? super Residue>) - Method in class edu.duke.cs.osprey.structure.Residues
- sortAssigned() - Method in class edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode.Assignments
-
ensures assigned and unassigned positions are sorted in increasing order
- sortDefined() - Method in class edu.duke.cs.osprey.astar.conf.ConfIndex
-
ensures assigned and unassigned positions are sorted in increasing order
- sorted() - Method in class edu.duke.cs.osprey.confspace.RCTuple
- sortPositions() - Method in class edu.duke.cs.osprey.confspace.RCTuple
- sourceECalc - Variable in class edu.duke.cs.osprey.ematrix.UpdatingEnergyMatrix
- sp - Variable in class edu.duke.cs.osprey.kstar.emat.ReducedEnergyMatrix
- sp - Variable in class edu.duke.cs.osprey.kstar.KAStarConfTree
- sp - Variable in class edu.duke.cs.osprey.kstar.pruning.ReducedPruningMatrix
- space - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.Measurement
- SparseFFEnergy - Class in edu.duke.cs.osprey.energy.forcefield
-
A forcefield energy consisting of only the electrostatics and VDW energies for a selected set of residue pairs Involves only 1 pairs of residues (pairwise interactions) or a single residue (intra-residue energies) Used for SAPE
- SparseFFEnergy(ArrayList<Atom[]>, ForcefieldParams) - Constructor for class edu.duke.cs.osprey.energy.forcefield.SparseFFEnergy
- spawnChild(int, int, int) - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- Spawned - Enum constant in enum class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode.State
-
in the child array
- SpecialWarningLog - Class in edu.duke.cs.osprey.control
-
This writes some particular kind of warning to a special file e.g., residues that are deleted because we can't find a template for them
- SpecialWarningLog(String) - Constructor for class edu.duke.cs.osprey.control.SpecialWarningLog
- SpecifiedBondingAtomsTemplate(List<String>) - Constructor for class edu.duke.cs.osprey.restypes.InterResBondingTemplate.SpecifiedBondingAtomsTemplate
- split(int, RC) - Method in class edu.duke.cs.osprey.partcr.splitters.BinaryRCSplitter
- split(int, RC) - Method in class edu.duke.cs.osprey.partcr.splitters.NAryRCSplitter
- split(int, RC) - Method in class edu.duke.cs.osprey.partcr.splitters.RCSplitter
- split(int, RC) - Method in class edu.duke.cs.osprey.partcr.splitters.SmartRCSplitter
- split(RC, List<RC>) - Method in class edu.duke.cs.osprey.partcr.RCSplits
- split(ParamSet) - Method in class edu.duke.cs.osprey.multistatekstar.MSKStarNode
- splitPositions(FullAStarNode) - Method in class edu.duke.cs.osprey.multistatekstar.MultiSequenceConfTree
- splitPositions(T) - Method in class edu.duke.cs.osprey.astar.ConfTree
- SplitsRCScorer - Class in edu.duke.cs.osprey.partcr.scorers
- SplitsRCScorer() - Constructor for class edu.duke.cs.osprey.partcr.scorers.SplitsRCScorer
- SplitsRCScorer(double) - Constructor for class edu.duke.cs.osprey.partcr.scorers.SplitsRCScorer
- Splitter(ConfSearch) - Constructor for class edu.duke.cs.osprey.confspace.ConfSearch.Splitter
- Splitter(ConfSearch, boolean, RCs) - Constructor for class edu.duke.cs.osprey.confspace.ConfSearch.Splitter
- SplitWorld - Class in edu.duke.cs.osprey.partcr
- SplitWorld(SearchProblem, ForcefieldParams) - Constructor for class edu.duke.cs.osprey.partcr.SplitWorld
- Square - Enum constant in enum class edu.duke.cs.osprey.tools.resultdoc.Plot.PointType
- stability - Variable in class edu.duke.cs.osprey.paste.PasteScore
- stabilityFunction - Variable in class edu.duke.cs.osprey.sofea.MinLMFE
-
A function to represent the stability of a sequence.
- stabilityGap - Variable in class edu.duke.cs.osprey.sofea.MinLMFE
-
A sequence is stable iff: stability(sequence) <= stability(wild-type) + gap for at least one value in the uncertainty ranges of the stability functions.
- stabilityThresh - Static variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- stabilityThreshold - Variable in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- stabilityThreshold - Variable in class edu.duke.cs.osprey.design.commands.CommandBindingAffinity
- stabilityThreshold - Variable in class edu.duke.cs.osprey.kstar.KStar.Settings
- stabilityThreshold - Variable in class edu.duke.cs.osprey.markstar.MARKStar.Settings
- stabilityThreshold - Variable in class edu.duke.cs.osprey.paste.Paste.Settings
- Star - Enum constant in enum class edu.duke.cs.osprey.tools.resultdoc.Plot.PointType
- start() - Method in class edu.duke.cs.osprey.coffee.NodeStats
- start() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFAdapter
- start() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel0
- start() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- start() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel2
- start() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFTraditional
- start() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- start() - Method in class edu.duke.cs.osprey.parallelism.WorkCrew
- start() - Method in class edu.duke.cs.osprey.tools.Stopwatch
- start(int) - Method in class edu.duke.cs.osprey.parallelism.ThreadPoolTaskExecutor
- start(int, Directions) - Method in class edu.duke.cs.osprey.coffee.NodeProcessor
- start(String) - Method in class edu.duke.cs.osprey.tools.Profiler
- start(Duration) - Method in class edu.duke.cs.osprey.coffee.NodeStats
- start(Stage) - Method in class edu.duke.cs.osprey.markstar.visualizer.Visualizer
- Start - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.TextAnchor
- startCrew(int) - Static method in class edu.duke.cs.osprey.energy.ParallelEnergyFunction
- STARTED - Enum constant in enum class edu.duke.cs.osprey.kstar.pfunc.PFAbstract.RunState
- startedTask() - Method in class edu.duke.cs.osprey.parallelism.ConcurrentTaskExecutor
- startNs - Variable in class edu.duke.cs.osprey.coffee.NodeStats.Report
- startTime - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- state - Variable in class edu.duke.cs.osprey.coffee.Coffee.StateConfig
- state - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncDirector.Builder
- state - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncDirector
- state - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncsDirector.Builder
- state - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncsDirector
- state - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex
- state - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- state - Variable in class edu.duke.cs.osprey.gmec.Comets.WeightedState
- state - Variable in class edu.duke.cs.osprey.kstar.MSKStar.WeightedState
- state - Variable in class edu.duke.cs.osprey.lute.LUTEConfEnergyCalculator
- state - Variable in class edu.duke.cs.osprey.multistatekstar.MSKStarSettings
- state - Variable in class edu.duke.cs.osprey.multistatekstar.ResidueTermini
- state - Variable in class edu.duke.cs.osprey.sofea.RCDB.Table
- state() - Method in class edu.duke.cs.osprey.sofea.FringeDB.Transaction
- State(String, SimpleConfSpace) - Constructor for class edu.duke.cs.osprey.ewakstar.EwakstarDoer.State
- State(String, SimpleConfSpace) - Constructor for class edu.duke.cs.osprey.gmec.Comets.State
- State(String, SimpleConfSpace) - Constructor for class edu.duke.cs.osprey.kstar.MSKStar.State
- StateConfig(MultiStateConfSpace.State) - Constructor for class edu.duke.cs.osprey.coffee.Coffee.StateConfig
- StateConfig(EnergyMatrix, ConfEnergyCalculator, File) - Constructor for class edu.duke.cs.osprey.sofea.Sofea.StateConfig
- stateConfigs - Variable in class edu.duke.cs.osprey.coffee.Coffee
- stateConfigs - Variable in class edu.duke.cs.osprey.sofea.Sofea
- stateFreeEnergies - Variable in class edu.duke.cs.osprey.sofea.Sofea.SeqResult
- statei - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex.Node
- statei - Variable in class edu.duke.cs.osprey.coffee.seqdb.StateZ
- StateInfo - Class in edu.duke.cs.osprey.coffee
- StateInfo(Coffee.StateConfig) - Constructor for class edu.duke.cs.osprey.coffee.StateInfo
- stateInfos - Variable in class edu.duke.cs.osprey.coffee.NodeProcessor
- stateName - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- stateName - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync
- stateName - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundFastQueues
- stateName - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid
- states - Variable in class edu.duke.cs.osprey.confspace.MultiStateConfSpace
- states - Variable in class edu.duke.cs.osprey.gmec.Comets.LME
- states - Variable in class edu.duke.cs.osprey.gmec.Comets
- states - Variable in class edu.duke.cs.osprey.kstar.MSKStar.LMFE
- states - Variable in class edu.duke.cs.osprey.kstar.MSKStar
- states() - Method in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.LMFE
- statez - Variable in class edu.duke.cs.osprey.coffee.seqdb.SaveOperation.UnsequencedSum
- StateZ - Class in edu.duke.cs.osprey.coffee.seqdb
- StateZ(int, MathTools.BigDecimalBounds, BigDecimal) - Constructor for class edu.duke.cs.osprey.coffee.seqdb.StateZ
- statezs - Variable in class edu.duke.cs.osprey.coffee.seqdb.SaveOperation.SequencedSum
- statezs - Variable in class edu.duke.cs.osprey.coffee.seqdb.SeqInfo
- StaticBiggestLowerboundDifferenceOrder - Class in edu.duke.cs.osprey.markstar.framework
- StaticBiggestLowerboundDifferenceOrder() - Constructor for class edu.duke.cs.osprey.markstar.framework.StaticBiggestLowerboundDifferenceOrder
- StaticBiggestLowerboundDifferenceOrder(MathTools.Optimizer) - Constructor for class edu.duke.cs.osprey.markstar.framework.StaticBiggestLowerboundDifferenceOrder
- StaticBiggesUpperboundDifferenceOrder - Class in edu.duke.cs.osprey.markstar.framework
- StaticBiggesUpperboundDifferenceOrder() - Constructor for class edu.duke.cs.osprey.markstar.framework.StaticBiggesUpperboundDifferenceOrder
- StaticBiggesUpperboundDifferenceOrder(MathTools.Optimizer) - Constructor for class edu.duke.cs.osprey.markstar.framework.StaticBiggesUpperboundDifferenceOrder
- staticCoords - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- staticEnergies - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- StaticEnergyHMeanAStarOrder - Class in edu.duke.cs.osprey.astar.conf.order
- StaticEnergyHMeanAStarOrder(EnergyMatrix) - Constructor for class edu.duke.cs.osprey.astar.conf.order.StaticEnergyHMeanAStarOrder
- StaticLowestEntropyOrder - Class in edu.duke.cs.osprey.markstar.framework
- StaticLowestEntropyOrder() - Constructor for class edu.duke.cs.osprey.markstar.framework.StaticLowestEntropyOrder
- StaticLowestEntropyOrder(MathTools.Optimizer) - Constructor for class edu.duke.cs.osprey.markstar.framework.StaticLowestEntropyOrder
- staticMolInfoIndices - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- staticNames - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- StaticPos - Static variable in class edu.duke.cs.osprey.confspace.compiled.PosInter
- staticResInfoIndices - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- StaticScoreHMeanAStarOrder - Class in edu.duke.cs.osprey.astar.conf.order
- StaticScoreHMeanAStarOrder() - Constructor for class edu.duke.cs.osprey.astar.conf.order.StaticScoreHMeanAStarOrder
- staticStatic() - Method in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- staticStatic() - Static method in enum class edu.duke.cs.osprey.confspace.compiled.PosInterDist
-
Include interactions between static regions (unaffected by motions and mutations) in the input molecules.
- staticStatic() - Method in class edu.duke.cs.osprey.energy.compiled.PosInterGen
- Stats(double, int) - Constructor for class edu.duke.cs.osprey.structure.analysis.ClusterR1.Stats
- Stats(double, int) - Constructor for class edu.duke.cs.osprey.structure.analysis.ClusterS1.Stats
- statsReporterInterval - Variable in class edu.duke.cs.osprey.coffee.NodeProcessor
- status - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Result
- status - Variable in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- status - Variable in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Result
- status - Variable in class edu.duke.cs.osprey.paste.PastePartitionFunction.Result
- step - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Dof
- step(long, long, double) - Method in class edu.duke.cs.osprey.kstar.pfunc.PfuncSurface.Trace
- StepCount - Class in edu.duke.cs.osprey.sofea
- StepCount(int, int) - Constructor for class edu.duke.cs.osprey.sofea.StepCount
- stericThresh - Variable in class edu.duke.cs.osprey.gmec.PruningSettings
- stericThreshold - Variable in class edu.duke.cs.osprey.multistatekstar.MSSearchSettings
- stop() - Method in class edu.duke.cs.osprey.coffee.directions.Directions
-
Tell all cluster members to stop processing.
- stop() - Method in class edu.duke.cs.osprey.parallelism.ThreadPoolTaskExecutor
- stop() - Method in class edu.duke.cs.osprey.tools.Profiler
- stop() - Method in class edu.duke.cs.osprey.tools.Stopwatch
- stopAndWait(int) - Method in class edu.duke.cs.osprey.parallelism.ThreadPoolTaskExecutor
- stopCrew() - Static method in class edu.duke.cs.osprey.energy.ParallelEnergyFunction
- stopNs - Variable in class edu.duke.cs.osprey.coffee.NodeStats.Report
- StopOperation - Class in edu.duke.cs.osprey.coffee.directions
- StopOperation() - Constructor for class edu.duke.cs.osprey.coffee.directions.StopOperation
- stopProgress() - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree
- stopwatch - Variable in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- Stopwatch - Class in edu.duke.cs.osprey.tools
- Stopwatch() - Constructor for class edu.duke.cs.osprey.tools.Stopwatch
- store - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex
- store - Variable in class edu.duke.cs.osprey.coffee.nodedb.PriorityDequeFixedIndex
- strand - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Position
- strand - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- Strand - Class in edu.duke.cs.osprey.confspace
-
A molecule with associated residue flexibility information.
- Strand.Builder - Class in edu.duke.cs.osprey.confspace
- Strand.Flexibility - Class in edu.duke.cs.osprey.confspace
- Strand.ResidueFlex - Class in edu.duke.cs.osprey.confspace
-
configured flexibility for one residue
- strand2AllowedSeqs - Variable in class edu.duke.cs.osprey.kstar.KSAbstract
- strand2SPs - Static variable in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel2
- strandFlex - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
The flexibility of each strand
- StrandFlex - Class in edu.duke.cs.osprey.confspace
- StrandFlex() - Constructor for class edu.duke.cs.osprey.confspace.StrandFlex
- StrandFlex.None - Class in edu.duke.cs.osprey.confspace
- StrandFlex.TranslateRotate - Class in edu.duke.cs.osprey.confspace
- StrandRotation - Class in edu.duke.cs.osprey.dof
- StrandRotation(MoveableStrand, int) - Constructor for class edu.duke.cs.osprey.dof.StrandRotation
- strands - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace
-
The strands
- strands - Variable in class edu.duke.cs.osprey.dof.DofInfo
- StrandTranslation - Class in edu.duke.cs.osprey.dof
- StrandTranslation(MoveableStrand, int) - Constructor for class edu.duke.cs.osprey.dof.StrandTranslation
- stream - Variable in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.CheckedOutStream
- streams - Variable in class edu.duke.cs.osprey.gpu.cuda.kernels.ResidueCudaCCDMinimizer
- streams - Variable in class edu.duke.cs.osprey.gpu.cuda.kernels.ResidueForcefieldEnergyCuda
- Streams - Class in edu.duke.cs.osprey.tools
- Streams() - Constructor for class edu.duke.cs.osprey.tools.Streams
- stringListing() - Method in class edu.duke.cs.osprey.confspace.RCTuple
- StringParsing - Class in edu.duke.cs.osprey.tools
- StringParsing() - Constructor for class edu.duke.cs.osprey.tools.StringParsing
- strongInteractingPairs(int) - Method in class edu.duke.cs.osprey.confspace.TupleEnumerator
- struct(T) - Static method in class edu.duke.cs.osprey.gpu.Structs
- Struct() - Constructor for class edu.duke.cs.osprey.gpu.Structs.Struct
- StructField(T) - Constructor for class edu.duke.cs.osprey.gpu.Structs.StructField
- Structs - Class in edu.duke.cs.osprey.gpu
-
A crude way to represent and access C structs and arrays using MemoryAddresses and MemoryHandles from the Foreign-Memory Access API.
- Structs() - Constructor for class edu.duke.cs.osprey.gpu.Structs
- Structs.Array - Class in edu.duke.cs.osprey.gpu
- Structs.Bool - Class in edu.duke.cs.osprey.gpu
- Structs.Char8 - Class in edu.duke.cs.osprey.gpu
- Structs.Char8.Array - Class in edu.duke.cs.osprey.gpu
- Structs.Field - Class in edu.duke.cs.osprey.gpu
- Structs.Float32 - Class in edu.duke.cs.osprey.gpu
- Structs.Float32.Array - Class in edu.duke.cs.osprey.gpu
- Structs.Float64 - Class in edu.duke.cs.osprey.gpu
- Structs.Float64.Array - Class in edu.duke.cs.osprey.gpu
- Structs.Int32 - Class in edu.duke.cs.osprey.gpu
- Structs.Int32.Array - Class in edu.duke.cs.osprey.gpu
- Structs.Int64 - Class in edu.duke.cs.osprey.gpu
- Structs.Int64.Array - Class in edu.duke.cs.osprey.gpu
- Structs.Pad - Class in edu.duke.cs.osprey.gpu
- Structs.Precision - Enum Class in edu.duke.cs.osprey.gpu
-
Determines the level of floating-point precision for calculations.
- Structs.Real - Class in edu.duke.cs.osprey.gpu
- Structs.Real.Array - Class in edu.duke.cs.osprey.gpu
- Structs.Struct - Class in edu.duke.cs.osprey.gpu
- Structs.StructField<T extends Structs.Struct> - Class in edu.duke.cs.osprey.gpu
- StructureFileScoreWriter - Class in edu.duke.cs.osprey.design
- StructureFileScoreWriter(String, int) - Constructor for class edu.duke.cs.osprey.design.StructureFileScoreWriter
- SturmSolver - Class in edu.duke.cs.osprey.dof.deeper.perts
- style - Variable in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd
- Style() - Constructor for class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.Style
- StyleClass(String) - Constructor for class edu.duke.cs.osprey.tools.SVG.StyleClass
- sub(double) - Method in class edu.duke.cs.osprey.tools.BigMath
- sub(long) - Method in class edu.duke.cs.osprey.tools.BigMath
- sub(BigExp) - Method in class edu.duke.cs.osprey.tools.BigExp
- sub(BigExp) - Method in class edu.duke.cs.osprey.tools.BigMath
- sub(BigDecimal) - Method in class edu.duke.cs.osprey.tools.BigMath
- sub(BigInteger) - Method in class edu.duke.cs.osprey.tools.BigMath
- subLinearMultiStateSearch() - Method in class edu.duke.cs.osprey.control.MSKStarDoer
- submit(long, TimeUnit, Runnable) - Method in class edu.duke.cs.osprey.parallelism.Threads
- submit(TaskExecutor.Task<T>, TaskExecutor.TaskListener<T>) - Method in class edu.duke.cs.osprey.parallelism.Cluster.Client
-
Submits a task to run on the cluster.
- submit(TaskExecutor.Task<T>, TaskExecutor.TaskListener<T>) - Method in class edu.duke.cs.osprey.parallelism.Cluster.Member
- submit(TaskExecutor.Task<T>, TaskExecutor.TaskListener<T>) - Method in class edu.duke.cs.osprey.parallelism.ConcurrentTaskExecutor
- submit(TaskExecutor.Task<T>, TaskExecutor.TaskListener<T>) - Method in class edu.duke.cs.osprey.parallelism.TaskExecutor
- submit(TaskExecutor.Task<T>, TaskExecutor.TaskListener<T>) - Method in class edu.duke.cs.osprey.parallelism.ThreadPoolTaskExecutor
- submitLoop(long, TimeUnit, Runnable) - Method in class edu.duke.cs.osprey.parallelism.Threads
- submitToListener(Runnable) - Method in class edu.duke.cs.osprey.parallelism.Threads
- Subset(ForcefieldInteractions) - Constructor for class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.Subset
- Subset(ForcefieldInteractions, boolean) - Constructor for class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.Subset
- SubThreshSampler - Class in edu.duke.cs.osprey.ematrix.epic
- SubThreshSampler(double, ObjectiveFunction, DoubleMatrix1D, DoubleMatrix1D) - Constructor for class edu.duke.cs.osprey.ematrix.epic.SubThreshSampler
- subtract(double[], double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- subtract(ResidueInteractions, ResidueInteractions) - Static method in class edu.duke.cs.osprey.energy.ResidueInteractions
- subtract(BigDecimal) - Method in class edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal
- subtract(BigDecimal, MathContext) - Method in class edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal
- subtractInPlace(double[], double[]) - Static method in class edu.duke.cs.osprey.tools.VectorAlgebra
- subtractMember(int) - Method in class edu.duke.cs.osprey.confspace.RCTuple
- subZSumUpper(int, int, BigDecimal) - Method in class edu.duke.cs.osprey.sofea.RCDB.Table
- subZSumUpper(MultiStateConfSpace.State, Sequence, int[], int, BigDecimal) - Method in class edu.duke.cs.osprey.sofea.RCDB
- subZSumUpper(MultiStateConfSpace.State, Sequence, BigExp) - Method in class edu.duke.cs.osprey.coffee.seqdb.Batch
- subZSumUpper(MultiStateConfSpace.State, Sequence, BigExp) - Method in class edu.duke.cs.osprey.sofea.SeqDB.Transaction
- Success - Static variable in class edu.duke.cs.osprey.design.Main
- sum() - Method in class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- sum(T[], ToLongFunction<? super T>) - Static method in class edu.duke.cs.osprey.gpu.Structs
- supportsDoubles() - Method in class edu.duke.cs.osprey.gpu.cuda.Gpu
- supportsDoubles() - Method in class edu.duke.cs.osprey.gpu.opencl.Gpu
- supportsDoubles(CLDevice) - Static method in class edu.duke.cs.osprey.gpu.opencl.Diagnostics
- supportsDynamicParallelism() - Method in class edu.duke.cs.osprey.gpu.cuda.Gpu
- suppressOutput - Static variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- SurfingLineSearcher - Class in edu.duke.cs.osprey.minimization
- SurfingLineSearcher() - Constructor for class edu.duke.cs.osprey.minimization.SurfingLineSearcher
- svg(String) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc.Image
- SVG - Class in edu.duke.cs.osprey.tools
- SVG - Enum constant in enum class edu.duke.cs.osprey.tools.resultdoc.ResultDoc.PlotType
- SVG() - Constructor for class edu.duke.cs.osprey.tools.SVG
- SVG.Drawable - Class in edu.duke.cs.osprey.tools
- SVG.Finished - Class in edu.duke.cs.osprey.tools
- SVG.LengthUnit - Enum Class in edu.duke.cs.osprey.tools
- SVG.ShapeDrawable - Class in edu.duke.cs.osprey.tools
- SVG.StyleClass - Class in edu.duke.cs.osprey.tools
- SVG.StyleClass.DominantBaseline - Enum Class in edu.duke.cs.osprey.tools
- SVG.StyleClass.TextAnchor - Enum Class in edu.duke.cs.osprey.tools
- SVG.TextDrawable - Class in edu.duke.cs.osprey.tools
- SVGPlot - Class in edu.duke.cs.osprey.tools
- SVGPlot() - Constructor for class edu.duke.cs.osprey.tools.SVGPlot
- SVGPlot.Axis - Class in edu.duke.cs.osprey.tools
- SVGPlot.BottomAxis - Class in edu.duke.cs.osprey.tools
- SVGPlot.Boxes - Class in edu.duke.cs.osprey.tools
- SVGPlot.Boxes.Box - Class in edu.duke.cs.osprey.tools
- SVGPlot.Intervals - Class in edu.duke.cs.osprey.tools
- SVGPlot.Intervals.Interval - Class in edu.duke.cs.osprey.tools
- SVGPlot.LeftAxis - Class in edu.duke.cs.osprey.tools
- sweepIncrement - Variable in class edu.duke.cs.osprey.sofea.Sofea
- switchToTemplate(ResidueTemplate) - Method in class edu.duke.cs.osprey.dof.ResidueTypeDOF
- switchToTemplate(ResidueTemplateLibrary, Residue, ResidueTemplate, boolean) - Static method in class edu.duke.cs.osprey.dof.ResidueTypeDOF
- switchToTemplate(ResidueTemplateLibrary, Residue, ResidueTemplate, boolean, MutAlignmentCache, boolean) - Static method in class edu.duke.cs.osprey.dof.ResidueTypeDOF
- sync() - Method in class edu.duke.cs.osprey.coffee.NodeStats.ForThread
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T
- T - Static variable in class edu.duke.cs.osprey.Constants
-
In degrees Kelvin
- T - Variable in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator.Conditions
-
temperature in Kelvins
- T - Variable in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- table - Variable in class edu.duke.cs.osprey.confspace.ConfDB.Key
- table(MultiStateConfSpace.State, Sequence) - Method in class edu.duke.cs.osprey.sofea.RCDB
- table(String) - Method in class edu.duke.cs.osprey.confspace.ConfDB
- Table(MultiStateConfSpace.State, Sequence, String) - Constructor for class edu.duke.cs.osprey.sofea.RCDB.Table
- tableHeader(String...) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- tableRow(String...) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
- TAlmostFrozen - Static variable in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- target - Variable in class edu.duke.cs.osprey.coffee.directors.AffinityDirector
- target - Variable in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- target - Variable in class edu.duke.cs.osprey.design.models.ScanDto
- target - Variable in class edu.duke.cs.osprey.ematrix.ProxyEnergyMatrix
- targetEpsilon - Variable in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- targetEpsilon - Static variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- targetEpsilon - Variable in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- targetEpsilon - Variable in class edu.duke.cs.osprey.multistatekstar.MSKStarSettings
- targetFreeEnergy - Variable in class edu.duke.cs.osprey.coffee.directors.AffinityDirector
- targetG - Variable in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- task - Variable in class edu.duke.cs.osprey.parallelism.RateLimitedThread
- task - Variable in exception edu.duke.cs.osprey.parallelism.TaskExecutor.TaskException
- Task(int) - Constructor for class edu.duke.cs.osprey.parallelism.Cluster.Task
- taskClass - Variable in class edu.duke.cs.osprey.parallelism.TaskExecutor.ContextId
- TaskException(TaskExecutor.Task<?>, TaskExecutor.TaskListener<?>, Throwable) - Constructor for exception edu.duke.cs.osprey.parallelism.TaskExecutor.TaskException
- TaskExecutor - Class in edu.duke.cs.osprey.parallelism
- TaskExecutor() - Constructor for class edu.duke.cs.osprey.parallelism.TaskExecutor
- TaskExecutor.ContextGroup - Class in edu.duke.cs.osprey.parallelism
- TaskExecutor.ContextId - Class in edu.duke.cs.osprey.parallelism
- TaskExecutor.Task<T> - Interface in edu.duke.cs.osprey.parallelism
- TaskExecutor.Task.WithContext<T,
C> - Interface in edu.duke.cs.osprey.parallelism - TaskExecutor.TaskException - Exception in edu.duke.cs.osprey.parallelism
- TaskExecutor.TaskListener<T> - Interface in edu.duke.cs.osprey.parallelism
- taskFailure(TaskExecutor.Task<?>, TaskExecutor.TaskListener<?>, Throwable) - Method in class edu.duke.cs.osprey.parallelism.ConcurrentTaskExecutor
- tasks - Variable in class edu.duke.cs.osprey.ematrix.SimpleEnergyMatrixCalculator
-
Deprecated.
- tasks - Variable in class edu.duke.cs.osprey.energy.compiled.ConfEnergyCalculatorAdapter.Builder
-
Deprecated.
- tasks - Variable in class edu.duke.cs.osprey.energy.ConfEnergyCalculator
- tasks - Variable in class edu.duke.cs.osprey.energy.EnergyCalculator
- taskSuccess(TaskExecutor.Task<T>, TaskExecutor.TaskListener<T>, T) - Method in class edu.duke.cs.osprey.parallelism.ConcurrentTaskExecutor
- taskSuccessCoerceTypes(TaskExecutor.Task<?>, TaskExecutor.TaskListener<?>, Object) - Method in class edu.duke.cs.osprey.parallelism.ConcurrentTaskExecutor
- TBody - Static variable in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- TClassic - Static variable in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- templ1 - Variable in class edu.duke.cs.osprey.structure.AtomConnectivity.AtomPairs
- templ2 - Variable in class edu.duke.cs.osprey.structure.AtomConnectivity.AtomPairs
- template - Variable in class edu.duke.cs.osprey.confspace.RC
- template - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf
- template - Variable in class edu.duke.cs.osprey.structure.Residue
-
Gives the name of the residue like "GLU" or "H2O" or whatever and any information about bonds, force-field, rotatable dihedrals, and rotamers Only assignment using
Residue.assignTemplate(ResidueTemplateLibrary), which will reorder atoms to match template. - Template(String, String, String, List<Probe.AtomInfo>) - Constructor for class edu.duke.cs.osprey.structure.Probe.Template
- TemplateChooser - Class in edu.duke.cs.osprey.structure.analysis
-
chooses the most ideal template for each residue type from a folder full of PDB files
- TemplateChooser() - Constructor for class edu.duke.cs.osprey.structure.analysis.TemplateChooser
- TemplateChooser.MeasuredRes - Class in edu.duke.cs.osprey.structure.analysis
- TemplateCoordsParser - Class in edu.duke.cs.osprey.restypes
- TemplateCoordsParser(List<ResidueTemplate>) - Constructor for class edu.duke.cs.osprey.restypes.TemplateCoordsParser
- templateLib - Variable in class edu.duke.cs.osprey.confspace.Strand
-
The template library used to pick templates for this strand
- templateLib - Variable in class edu.duke.cs.osprey.dof.ResidueTypeDOF
- templateNameSet() - Method in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
- TemplateParser - Class in edu.duke.cs.osprey.restypes
- TemplateParser(ForcefieldParams) - Constructor for class edu.duke.cs.osprey.restypes.TemplateParser
- templateRes - Variable in class edu.duke.cs.osprey.restypes.ResidueTemplate
- templates - Variable in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
- templates - Variable in class edu.duke.cs.osprey.restypes.TemplateCoordsParser
- TEQ() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.BondAngleParameter
-
Returns the value of the
TEQrecord component. - TermECalculator - Class in edu.duke.cs.osprey.ematrix
- TermECalculator(ConfSpace, ArrayList<Residue>, boolean, boolean, PruningMatrix, EPICSettings, boolean, int...) - Constructor for class edu.duke.cs.osprey.ematrix.TermECalculator
- terminal - Variable in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd
- Terminate - Enum constant in enum class edu.duke.cs.osprey.sofea.Sofea.Criterion.Satisfied
- TESampleSet - Class in edu.duke.cs.osprey.tupexp
- TESampleSet(TupleExpander) - Constructor for class edu.duke.cs.osprey.tupexp.TESampleSet
- test(int, int) - Method in interface edu.duke.cs.osprey.astar.seq.RTs.Filter
- test_two_cone_existence_soln(double, double, double, double, char[]) - Method in class edu.duke.cs.osprey.dof.deeper.perts.TripeptideClosure
- TestFancyKernel - Class in edu.duke.cs.osprey.gpu.opencl.kernels
- TestFancyKernel(GpuQueue) - Constructor for class edu.duke.cs.osprey.gpu.opencl.kernels.TestFancyKernel
- testSet - Variable in class edu.duke.cs.osprey.lute.LUTE
- testVsExhaustiveLUTE(boolean) - Method in class edu.duke.cs.osprey.ibis.KStarBeak
- tetra - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralInPlaneAngle
- tetra - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralOutOfPlaneAngle
- TetrahedralGeometry() - Constructor for class edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry
- TetrahedralInPlaneAngle(String, String, String, String) - Constructor for class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralInPlaneAngle
- TetrahedralInPlaneAngles2(String, String, String, String, String, int) - Constructor for class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralInPlaneAngles2
- TetrahedralOutOfPlaneAngle(String, String, String, String) - Constructor for class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralOutOfPlaneAngle
- TetrahedralOutOfPlaneAngles2(String, String, String, String, String, int) - Constructor for class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralOutOfPlaneAngles2
- TetrahedralSystem(String, String, String, String) - Constructor for class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralSystem
- TetrahedralSystems2(String, String, String, String, String) - Constructor for class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralSystems2
- tetras - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralInPlaneAngles2
- tetras - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralOutOfPlaneAngles2
- tetras - Variable in class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.TetrahedralSystems2
- text - Variable in class edu.duke.cs.osprey.tools.SVG.TextDrawable
- TextAfterEdge - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.DominantBaseline
- TextBeforeEdge - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.DominantBaseline
- TextDrawable(String) - Constructor for class edu.duke.cs.osprey.tools.SVG.TextDrawable
- TextProp(String) - Constructor for class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.TextProp
- TextProp(String, String) - Constructor for class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.TextProp
- ThermodynamicsConfListener - Class in edu.duke.cs.osprey.design.analysis
- ThermodynamicsConfListener() - Constructor for class edu.duke.cs.osprey.design.analysis.ThermodynamicsConfListener
- threadConfsBuffer - Static variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- ThreadParallelism - Class in edu.duke.cs.osprey.parallelism
- ThreadParallelism() - Constructor for class edu.duke.cs.osprey.parallelism.ThreadParallelism
- ThreadPoolTaskExecutor - Class in edu.duke.cs.osprey.parallelism
- ThreadPoolTaskExecutor() - Constructor for class edu.duke.cs.osprey.parallelism.ThreadPoolTaskExecutor
- Threads - Class in edu.duke.cs.osprey.parallelism
- Threads(int, int) - Constructor for class edu.duke.cs.osprey.parallelism.Threads
- ThreadTools - Class in edu.duke.cs.osprey.parallelism
- ThreadTools() - Constructor for class edu.duke.cs.osprey.parallelism.ThreadTools
- three2one - Static variable in class edu.duke.cs.osprey.restypes.HardCodedResidueInfo
- throwTimeout(String) - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- tickFormat - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Axis
- tickLength - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Axis
- ticks - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Axis
- tickTextDy - Variable in class edu.duke.cs.osprey.tools.SVGPlot.LeftAxis
- tickTextHeight - Variable in class edu.duke.cs.osprey.tools.SVGPlot.BottomAxis
- tickTextMargin - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Axis
- tickTextStyle - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Axis
- Tics(String) - Constructor for class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd.Tics
- tightenBoundInPhases() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- tightenBoundInPhases() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBoundFastQueues
- TighterBounds - Enum constant in enum class edu.duke.cs.osprey.confspace.compiled.PosInterDist
-
A newer distribution that yields tighter lower bounds on conformation energy.
- time() - Method in class edu.duke.cs.osprey.parallelism.TimingThread
- TimedOut - Enum constant in enum class edu.duke.cs.osprey.parallelism.PulseSignal.Result
- TimeFormatter - Class in edu.duke.cs.osprey.tools
- TimeFormatter() - Constructor for class edu.duke.cs.osprey.tools.TimeFormatter
- timeNs - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.ScoreInfo
- timeNs - Variable in class edu.duke.cs.osprey.kstar.KStarScoreWriter.ScoreInfo
- timeNs - Variable in class edu.duke.cs.osprey.paste.PasteScoreWriter.ScoreInfo
- TimeoutException(String) - Constructor for exception edu.duke.cs.osprey.coffee.ClusterMember.TimeoutException
- timeoutS - Variable in class edu.duke.cs.osprey.parallelism.Cluster.Member
- timestampNs - Variable in class edu.duke.cs.osprey.confspace.ConfDB.Conf.Bound
- timeThreads(List<TimingThread>) - Static method in class edu.duke.cs.osprey.parallelism.TimingThread
- TimeTools - Class in edu.duke.cs.osprey.tools
- TimeTools() - Constructor for class edu.duke.cs.osprey.tools.TimeTools
- timing - Variable in class edu.duke.cs.osprey.coffee.directors.AffinityDirector
- timing - Variable in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- timing - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncDirector
- timing - Variable in class edu.duke.cs.osprey.coffee.directors.PfuncsDirector
- Timing - Enum Class in edu.duke.cs.osprey.coffee.directors
- TimingThread - Class in edu.duke.cs.osprey.parallelism
- TimingThread(String) - Constructor for class edu.duke.cs.osprey.parallelism.TimingThread
- TK() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.BondAngleParameter
-
Returns the value of the
TKrecord component. - toBigDecimal() - Method in class edu.duke.cs.osprey.tools.BigExp
- toBigDecimal(MathContext) - Method in class edu.duke.cs.osprey.tools.BigExp
- ToConsole(EWAKStarScoreWriter.Formatter) - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.ToConsole
- ToConsole(KStarScoreWriter.Formatter) - Constructor for class edu.duke.cs.osprey.kstar.KStarScoreWriter.ToConsole
- ToConsole(PasteScoreWriter.Formatter) - Constructor for class edu.duke.cs.osprey.paste.PasteScoreWriter.ToConsole
- toDouble() - Method in class edu.duke.cs.osprey.tools.BigExp
- toDouble(Object) - Method in enum class edu.duke.cs.osprey.gpu.Structs.Precision
- toEnergiedConf() - Method in class edu.duke.cs.osprey.confspace.ConfDB.Conf
- ToFile(File, EWAKStarScoreWriter.Formatter) - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.ToFile
- ToFile(File, KStarScoreWriter.Formatter) - Constructor for class edu.duke.cs.osprey.kstar.KStarScoreWriter.ToFile
- ToFile(File, PasteScoreWriter.Formatter) - Constructor for class edu.duke.cs.osprey.paste.PasteScoreWriter.ToFile
- toggleCenter() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- token - Variable in enum class edu.duke.cs.osprey.tools.SVG.LengthUnit
- token - Variable in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.DominantBaseline
- toLinearConstraint(LinearMultivariateRealFunction) - Static method in class edu.duke.cs.osprey.plug.LPChecks
- toLinearMultivariateRealFunction(LinearConstraint) - Static method in class edu.duke.cs.osprey.plug.LPChecks
- toLinearMultivariateRealFunction(LinearConstraint, double) - Static method in class edu.duke.cs.osprey.plug.LPChecks
- toList() - Method in class edu.duke.cs.osprey.coffee.directors.BestSet
- TomlParseException - Exception in edu.duke.cs.osprey.tools
- TomlParseException(String) - Constructor for exception edu.duke.cs.osprey.tools.TomlParseException
- TomlParseException(String, TomlPosition) - Constructor for exception edu.duke.cs.osprey.tools.TomlParseException
- TomlTools - Class in edu.duke.cs.osprey.tools
- TomlTools() - Constructor for class edu.duke.cs.osprey.tools.TomlTools
- toMol() - Method in class edu.duke.cs.osprey.confspace.compiled.AssignedCoords
-
Converts the coordinates to a Molecule instance.
- Tools() - Constructor for class edu.duke.cs.osprey.astar.OptimizableAStarNode.Tools
- Tools() - Constructor for class edu.duke.cs.osprey.energy.EnergyFunction.Tools
- Tools() - Constructor for class edu.duke.cs.osprey.gmec.ConfSearchFactory.Tools
- Tools() - Constructor for class edu.duke.cs.osprey.minimization.Minimizer.Tools
- toOrderedList() - Method in class edu.duke.cs.osprey.design.analysis.EnergiedConfQueue
- topConfs - Variable in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized
- topConfsPQ - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- topPairwiseInteractions() - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrix
- topPositionTriples(int) - Method in class edu.duke.cs.osprey.confspace.TupleEnumerator
- TopSequences() - Constructor for class edu.duke.cs.osprey.sofea.MinLMFE.TopSequences
- toScoredConf() - Method in class edu.duke.cs.osprey.confspace.ConfDB.Conf
- toString() - Method in class edu.duke.cs.osprey.astar.conf.ConfIndex
- toString() - Method in class edu.duke.cs.osprey.astar.conf.RCs
- toString() - Method in class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode
- toString() - Method in class edu.duke.cs.osprey.astar.seq.nodes.LinkedSeqAStarNode
- toString() - Method in class edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode.Assignments
- toString() - Method in class edu.duke.cs.osprey.coffee.EnergyBoundStats
- toString() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex.Node
- toString() - Method in class edu.duke.cs.osprey.coffee.NodeStats.Report
- toString() - Method in class edu.duke.cs.osprey.coffee.seqdb.Batch
- toString() - Method in class edu.duke.cs.osprey.coffee.seqdb.SeqInfo
- toString() - Method in class edu.duke.cs.osprey.coffee.seqdb.StateZ
- toString() - Method in class edu.duke.cs.osprey.confspace.compiled.CoordsList
- toString() - Method in class edu.duke.cs.osprey.confspace.compiled.PosInter
- toString() - Method in class edu.duke.cs.osprey.confspace.Conf.Map
- toString() - Method in class edu.duke.cs.osprey.confspace.Conf.Set
- toString() - Method in class edu.duke.cs.osprey.confspace.ConfSearch.EnergiedConf
- toString() - Method in class edu.duke.cs.osprey.confspace.ConfSearch.ScoredConf
- toString() - Method in class edu.duke.cs.osprey.confspace.RCTuple
- toString() - Method in class edu.duke.cs.osprey.confspace.SeqSpace.Position
- toString() - Method in class edu.duke.cs.osprey.confspace.SeqSpace.ResType
- toString() - Method in class edu.duke.cs.osprey.confspace.SeqSpace
- toString() - Method in class edu.duke.cs.osprey.confspace.Sequence
- toString() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace.Position
- toString() - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf
- toString() - Method in class edu.duke.cs.osprey.confspace.TupleMatrixBoolean
- toString() - Method in class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- toString() - Method in class edu.duke.cs.osprey.dof.DofInfo
- toString() - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator.GpuInfo
- toString() - Method in class edu.duke.cs.osprey.energy.compiled.ForcefieldDebugger.AtomPair
- toString() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.AtomSymbolAndMass
-
Returns a string representation of this record class.
- toString() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.BondAngleParameter
-
Returns a string representation of this record class.
- toString() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.BondLengthParameter
-
Returns a string representation of this record class.
- toString() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.DihederalParameter
-
Returns a string representation of this record class.
- toString() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.EquivalencingAtom
-
Returns a string representation of this record class.
- toString() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.HBond10_12PotentialParameter
-
Returns a string representation of this record class.
- toString() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.ImproperDihederalParameter
-
Returns a string representation of this record class.
- toString() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.Six12PotentialCoefficient
-
Returns a string representation of this record class.
- toString() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.Six12PotentialParameter
-
Returns a string representation of this record class.
- toString() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.SlaterKirkwoodParameter
-
Returns a string representation of this record class.
- toString() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.VanDerWaalsRadius
-
Returns a string representation of this record class.
- toString() - Method in class edu.duke.cs.osprey.energy.forcefield.ResPairCache.ResPair
- toString() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.ScoredSequence
- toString() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.MultiSequenceNode
- toString() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.SingleSequenceNode
- toString() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Result
- toString() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- toString() - Method in class edu.duke.cs.osprey.gmec.ConfAnalyzer.ConfAnalysis
- toString() - Method in class edu.duke.cs.osprey.gmec.ConfAnalyzer.EnsembleAnalysis
- toString() - Method in class edu.duke.cs.osprey.gpu.cuda.Gpu
- toString() - Method in class edu.duke.cs.osprey.gpu.opencl.Gpu
- toString() - Method in class edu.duke.cs.osprey.kstar.BBKStar.MultiSequenceNode
- toString() - Method in class edu.duke.cs.osprey.kstar.BBKStar.SingleSequenceNode
- toString() - Method in class edu.duke.cs.osprey.kstar.KStar.ScoredSequence
- toString() - Method in class edu.duke.cs.osprey.kstar.KStarScore
- toString() - Method in class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator
- toString() - Method in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Result
- toString() - Method in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Values
- toString() - Method in class edu.duke.cs.osprey.kstar.pfunc.UpperBoundCalculator
- toString() - Method in class edu.duke.cs.osprey.kstar.SequenceAnalyzer.Analysis
- toString() - Method in class edu.duke.cs.osprey.lute.LUTE.Errors
- toString() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Node
- toString() - Method in class edu.duke.cs.osprey.markstar.MARKStar.ScoredSequence
- toString() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- toString() - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- toString() - Method in interface edu.duke.cs.osprey.multistatekstar.KStarScore
- toString() - Method in class edu.duke.cs.osprey.multistatekstar.KStarScoreMinimized
- toString() - Method in class edu.duke.cs.osprey.multistatekstar.MSKStarNode
- toString() - Method in class edu.duke.cs.osprey.paste.Paste.ScoredSequence
- toString() - Method in class edu.duke.cs.osprey.paste.PastePartitionFunction.Result
- toString() - Method in class edu.duke.cs.osprey.paste.PasteScore
- toString() - Method in class edu.duke.cs.osprey.pruning.PLUG.BoundaryPoint
- toString() - Method in class edu.duke.cs.osprey.restypes.ResidueTemplate
- toString() - Method in class edu.duke.cs.osprey.sofea.SeqDB.SeqInfo
- toString() - Method in class edu.duke.cs.osprey.structure.analysis.Histogram
- toString() - Method in class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel.Interval
- toString() - Method in class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel
- toString() - Method in class edu.duke.cs.osprey.structure.Atom
- toString() - Method in class edu.duke.cs.osprey.structure.Probe.AtomPair.Interaction
- toString() - Method in class edu.duke.cs.osprey.structure.Probe.AtomPair
- toString() - Method in class edu.duke.cs.osprey.tools.BigExp.Bounds
- toString() - Method in class edu.duke.cs.osprey.tools.BigExp
- toString() - Method in class edu.duke.cs.osprey.tools.FileTools.FilePathRoot
- toString() - Method in class edu.duke.cs.osprey.tools.FileTools.ResourcePathRoot
- toString() - Method in class edu.duke.cs.osprey.tools.JvmMem.MemInfo
- toString() - Method in class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- toString() - Method in class edu.duke.cs.osprey.tools.MathTools.BigIntegerBounds
- toString() - Method in class edu.duke.cs.osprey.tools.MathTools.DoubleBounds
- toString() - Method in class edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal
- toString(int) - Method in class edu.duke.cs.osprey.tools.BigExp
- toString(int) - Method in class edu.duke.cs.osprey.tools.MathTools.DoubleBounds
- toString(int[]) - Static method in class edu.duke.cs.osprey.confspace.Conf
- toString(int[], SimpleConfSpace) - Static method in class edu.duke.cs.osprey.confspace.Conf
- toString(int, int) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- toString(int, int) - Method in class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
- toString(int, int, int) - Method in class edu.duke.cs.osprey.structure.analysis.Histogram
- toString(int, Function<T, String>) - Method in class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
- toString(ConfSpace) - Method in class edu.duke.cs.osprey.ematrix.SimpleReferenceEnergies
- toString(SeqSpace) - Method in class edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode.Assignments
- toString(Sequence) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStar.ScoredSequence
- toString(Sequence) - Method in class edu.duke.cs.osprey.kstar.KStar.ScoredSequence
- toString(Sequence) - Method in class edu.duke.cs.osprey.markstar.MARKStar.ScoredSequence
- toString(Sequence) - Method in class edu.duke.cs.osprey.paste.Paste.ScoredSequence
- toString(Sequence.Renderer) - Method in class edu.duke.cs.osprey.confspace.Sequence
- toString(Sequence.Renderer, int) - Method in class edu.duke.cs.osprey.confspace.Sequence
- toString(Sequence.Renderer, Integer, List<String>) - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Render the sequence into a string.
- toString(SimpleConfSpace) - Method in class edu.duke.cs.osprey.confspace.ConfSearch.EnergiedConf
-
Generates a nicely formatted description of this conformation with its score and energy.
- toString(Integer, Integer) - Method in class edu.duke.cs.osprey.tools.MathTools.DoubleBounds
- toStringArray() - Method in class edu.duke.cs.osprey.multistatekstar.ResidueTermini
- toStringScientific() - Method in class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- toStringVisual() - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- totalBound - Variable in class edu.duke.cs.osprey.kstar.pfunc.UpperBoundCalculator
- totalBytes - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices.BroadcastInfo
- totalNumRotamers - Variable in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
- totalPF - Variable in class edu.duke.cs.osprey.kstar.KSPStarCalculator
- toTuple() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- Trace() - Constructor for class edu.duke.cs.osprey.kstar.pfunc.PfuncSurface.Trace
- traceTo(PfuncSurface) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarGradientDescentPfunc
- traceTo(PfuncSurface) - Method in class edu.duke.cs.osprey.kstar.pfunc.GradientDescentPfunc
- traceTo(PfuncSurface) - Method in class edu.duke.cs.osprey.markstar.framework.GradientDescentMARKStarPfunc
- traceTo(PfuncSurface) - Method in class edu.duke.cs.osprey.paste.PasteGradientDescentPfunc
- Traditional - Enum constant in enum class edu.duke.cs.osprey.energy.EnergyPartition
-
intras and shell on singles, inters on pairs
- TraditionalPairwiseHScorer - Class in edu.duke.cs.osprey.astar.conf.scoring
- TraditionalPairwiseHScorer(EnergyMatrix, RCs) - Constructor for class edu.duke.cs.osprey.astar.conf.scoring.TraditionalPairwiseHScorer
- TraditionalPairwiseHScorer(EnergyMatrix, RCs, MathTools.Optimizer) - Constructor for class edu.duke.cs.osprey.astar.conf.scoring.TraditionalPairwiseHScorer
- traditionalScore - Variable in class edu.duke.cs.osprey.astar.ConfTree
- train(double) - Method in interface edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction.Approximator.Addable
- train(double) - Method in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- train(List<Minimizer.Result>, List<Minimizer.Result>) - Method in interface edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction.Approximator.Addable
- train(List<Minimizer.Result>, List<Minimizer.Result>) - Method in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- trainingSet - Variable in class edu.duke.cs.osprey.lute.LUTE
- transaction() - Method in class edu.duke.cs.osprey.sofea.FringeDB
-
starts a new transaction in the current sweep
- transaction() - Method in class edu.duke.cs.osprey.sofea.SeqDB
- transferConstraints(ArrayList<DegreeOfFreedom>, ArrayList<? extends DegreeOfFreedom>, ArrayList<LinearConstraint>) - Static method in class edu.duke.cs.osprey.plug.RCTuplePolytope
- transform(double[]) - Method in class edu.duke.cs.osprey.tools.RigidBodyMotion
- transform(double[], int) - Method in class edu.duke.cs.osprey.tools.RigidBodyMotion
- TransitivePruner - Class in edu.duke.cs.osprey.pruning
-
Checks if each tuple can possibly be part of a full unpruned conformation.
- TransitivePruner(SimpleConfSpace) - Constructor for class edu.duke.cs.osprey.pruning.TransitivePruner
- translateAngstroms - Variable in class edu.duke.cs.osprey.design.models.TranslateRotateDto
- translateConf(ConfSearch.ScoredConf) - Method in class edu.duke.cs.osprey.partcr.SplitWorld
- translateRotate - Variable in class edu.duke.cs.osprey.design.models.MoleculeDto
- TranslateRotate() - Constructor for class edu.duke.cs.osprey.confspace.StrandFlex.TranslateRotate
- TranslateRotate(double, double) - Constructor for class edu.duke.cs.osprey.confspace.StrandFlex.TranslateRotate
- TranslateRotateDto - Class in edu.duke.cs.osprey.design.models
- TranslateRotateDto(boolean) - Constructor for class edu.duke.cs.osprey.design.models.TranslateRotateDto
- TranslateRotateDto(double, double) - Constructor for class edu.duke.cs.osprey.design.models.TranslateRotateDto
- translationRotation - Variable in class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation.Dof
- TranslationRotation - Class in edu.duke.cs.osprey.confspace.compiled.motions
- TranslationRotation(TranslationRotation.Description, AssignedCoords, int) - Constructor for class edu.duke.cs.osprey.confspace.compiled.motions.TranslationRotation
- TranslationRotation.Description - Class in edu.duke.cs.osprey.confspace.compiled.motions
- TranslationRotation.Dof - Class in edu.duke.cs.osprey.confspace.compiled.motions
- transpose() - Method in class edu.duke.cs.osprey.tools.RotationMatrix
- treat15HasNonBonded - Variable in class edu.duke.cs.osprey.structure.AtomConnectivity
- tree - Variable in class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator
- tree - Variable in class edu.duke.cs.osprey.kstar.pfunc.UpperBoundCalculator
- TreeOperation - Class in edu.duke.cs.osprey.coffee.directions
- TreeOperation() - Constructor for class edu.duke.cs.osprey.coffee.directions.TreeOperation
- TreeOperation(int, NodeTree) - Constructor for class edu.duke.cs.osprey.coffee.directions.TreeOperation
- TriangleDown - Enum constant in enum class edu.duke.cs.osprey.tools.resultdoc.Plot.PointType
- TriangleDownFilled - Enum constant in enum class edu.duke.cs.osprey.tools.resultdoc.Plot.PointType
- TriangleUp - Enum constant in enum class edu.duke.cs.osprey.tools.resultdoc.Plot.PointType
- TriangleUpFilled - Enum constant in enum class edu.duke.cs.osprey.tools.resultdoc.Plot.PointType
- trigConst - Static variable in class edu.duke.cs.osprey.energy.forcefield.EEF1
- TripeptideClosure - Class in edu.duke.cs.osprey.dof.deeper.perts
- TripeptideClosure(List<Residue>) - Constructor for class edu.duke.cs.osprey.dof.deeper.perts.TripeptideClosure
- triple(int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- Triple - Class in edu.duke.cs.osprey.coffee.zmat
- Triple(int, int, int, int, int, int) - Constructor for class edu.duke.cs.osprey.coffee.zmat.Triple
- Triple(int, int, int, int, int, int, BigExp) - Constructor for class edu.duke.cs.osprey.coffee.zmat.Triple
- tripleCorrection(ConfSpace, int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.energy.compiled.PosInterGen
- tripleCorrection(ConfSpace, SimpleReferenceEnergies, int, int, int, int, int, int) - Method in enum class edu.duke.cs.osprey.confspace.compiled.PosInterDist
-
Interactions of a tuple of three positions, but weighted to prevent over-counting when all possible triples are used simultaneously.
- tripleCorrectionThreshold - Variable in class edu.duke.cs.osprey.coffee.Coffee
- tripleCorrectionThreshold - Variable in class edu.duke.cs.osprey.ematrix.SimplerEnergyMatrixCalculator
- tripleIndex(int, int, int) - Method in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- tripleIndex(int, int, int, int, int, int) - Method in class edu.duke.cs.osprey.coffee.zmat.ClusterZMatrix
- TripleMatrix<T> - Class in edu.duke.cs.osprey.confspace
-
Uses simple flat array storing triples.
- TripleMatrix(int, int[]) - Constructor for class edu.duke.cs.osprey.confspace.TripleMatrix
- TripleMatrix(ConfSpaceIteration) - Constructor for class edu.duke.cs.osprey.confspace.TripleMatrix
- TriplewiseBounder - Class in edu.duke.cs.osprey.coffee.bounds
- TriplewiseBounder(ClusterZMatrix) - Constructor for class edu.duke.cs.osprey.coffee.bounds.TriplewiseBounder
- TRoom - Static variable in class edu.duke.cs.osprey.kstar.pfunc.BoltzmannCalculator
- TRUE - Enum constant in enum class edu.duke.cs.osprey.kstar.pfunc.PFAbstract.EApproxReached
- truncateAllowedAAs() - Method in class edu.duke.cs.osprey.kstar.KSAllowedSeqs
- truncateAllowedSequences(String) - Method in class edu.duke.cs.osprey.control.KStarCalculator
-
Deprecated.
- tryAdd(int, List<NodeIndex.Node>) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices
- tryAddingTuple(RCTuple) - Method in class edu.duke.cs.osprey.tupexp.TupleExpander
- tryAssigningTemplates(Molecule, ResidueTemplateLibrary, Residue.TemplateMatchingMethod) - Static method in class edu.duke.cs.osprey.confspace.Strand
- tryCheckoutStream() - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
-
Try to check out a GPU stream.
- tryHotForConf(KSConf, MultiTermEnergyFunction) - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- tryHotForConf(KSConf, MultiTermEnergyFunction) - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFTraditional
- tryHotForConfs(ArrayList<MultiTermEnergyFunction>) - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel2
- tryRenamingAsD(Residue) - Static method in class edu.duke.cs.osprey.restypes.DAminoAcidHandler
- tryToMakeDisulfideBond(Residue, Residue) - Static method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate
- tryToMakeNucleotideBond(Residue, Residue) - Static method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate
- tryToMakePeptideBond(Residue, Residue) - Static method in class edu.duke.cs.osprey.restypes.InterResBondingTemplate
- tsv(String, String) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc.File
- tup - Variable in class edu.duke.cs.osprey.confspace.TupE
- TupE - Class in edu.duke.cs.osprey.confspace
-
Like ConfPair but with an (RCTuple,energy) pair
- TupE(RCTuple, double) - Constructor for class edu.duke.cs.osprey.confspace.TupE
- TupExpChooser - Class in edu.duke.cs.osprey.tupexp
-
Chooses what tuple expansion to make for a particular problem (what tuples to include), uses a TupleExpander to calculate it Can use a pairwise expansion, or can look at how changes at certain positions affect other local energies, to get a comprehensive higher-order expansion
- TupExpChooser(TupleExpander, TupleEnumerator) - Constructor for class edu.duke.cs.osprey.tupexp.TupExpChooser
- tupExpEMat - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- TUPEXPEMAT - Enum constant in enum class edu.duke.cs.osprey.confspace.SearchProblem.MatrixType
- TUPEXPEMAT - Enum constant in enum class edu.duke.cs.osprey.gmec.PrecomputedMatrices.MatrixType
- tuple - Variable in class edu.duke.cs.osprey.dof.DofInfo
- Tuple - Interface in edu.duke.cs.osprey.coffee.zmat
- tupleEnergies - Variable in class edu.duke.cs.osprey.lute.LUTE.LinearSystem
- tupleEnergies - Variable in class edu.duke.cs.osprey.lute.LUTEState
- tupleEnergyOffset - Variable in class edu.duke.cs.osprey.lute.LUTE.LinearSystem
- tupleEnergyOffset - Variable in class edu.duke.cs.osprey.lute.LUTEState
- TupleEnumerator - Class in edu.duke.cs.osprey.confspace
- TupleEnumerator(PruningMatrix, EnergyMatrix, int) - Constructor for class edu.duke.cs.osprey.confspace.TupleEnumerator
- TupleExpander - Class in edu.duke.cs.osprey.tupexp
-
Create an energy matrix that approximates a function of many integers (e.g., list of RCs for all flexible residues) as a sum of terms dependent on low-order tuples (e.g., tuple of RCs at a few positions)
- TupleExpander(int, int[], double, LUTESettings) - Constructor for class edu.duke.cs.osprey.tupexp.TupleExpander
- TupleIndexMatrix - Class in edu.duke.cs.osprey.tupexp
-
This TupleMatrix gives the indices for all the tuples in a TupleExpander It is intended for fast lookup of what tuples are in a given sample (for use in fitting: in large designs, storing all tuples for each samples is taking too much memory)
- TupleIndexMatrix(int, int[], double) - Constructor for class edu.duke.cs.osprey.tupexp.TupleIndexMatrix
- TupleMatrix<T> - Interface in edu.duke.cs.osprey.confspace
- TupleMatrixBoolean - Class in edu.duke.cs.osprey.confspace
- TupleMatrixBoolean() - Constructor for class edu.duke.cs.osprey.confspace.TupleMatrixBoolean
- TupleMatrixBoolean(int, int[], double, boolean) - Constructor for class edu.duke.cs.osprey.confspace.TupleMatrixBoolean
- TupleMatrixBoolean(ConfSpace, double, boolean) - Constructor for class edu.duke.cs.osprey.confspace.TupleMatrixBoolean
- TupleMatrixBoolean(SimpleConfSpace, double, boolean) - Constructor for class edu.duke.cs.osprey.confspace.TupleMatrixBoolean
- TupleMatrixBoolean(TupleMatrixBoolean) - Constructor for class edu.duke.cs.osprey.confspace.TupleMatrixBoolean
- TupleMatrixDouble - Class in edu.duke.cs.osprey.confspace
- TupleMatrixDouble(int, int[], double, double) - Constructor for class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- TupleMatrixDouble(ConfSpaceIteration) - Constructor for class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- TupleMatrixDouble(ConfSpace, double, double) - Constructor for class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- TupleMatrixDouble(SimpleConfSpace, double, double) - Constructor for class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- TupleMatrixDouble(TupleMatrixDouble) - Constructor for class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- TupleMatrixGeneric<T> - Class in edu.duke.cs.osprey.confspace
- TupleMatrixGeneric() - Constructor for class edu.duke.cs.osprey.confspace.TupleMatrixGeneric
- TupleMatrixGeneric(int, int[], double, T) - Constructor for class edu.duke.cs.osprey.confspace.TupleMatrixGeneric
- TupleMatrixGeneric(ConfSpaceIteration) - Constructor for class edu.duke.cs.osprey.confspace.TupleMatrixGeneric
- TupleMatrixGeneric(ConfSpace, double, T) - Constructor for class edu.duke.cs.osprey.confspace.TupleMatrixGeneric
- TupleMatrixGeneric(SimpleConfSpace) - Constructor for class edu.duke.cs.osprey.confspace.TupleMatrixGeneric
- tuples - Variable in class edu.duke.cs.osprey.coffee.zmat.TuplesOperation
- tuples - Variable in class edu.duke.cs.osprey.lute.ConfSampler.Samples
- tuples - Variable in class edu.duke.cs.osprey.lute.LUTE.LinearSystem
- tuples - Variable in class edu.duke.cs.osprey.lute.LUTEConfEnergyCalculator
- tuples - Variable in class edu.duke.cs.osprey.lute.LUTEState
- tuplesIndex - Variable in class edu.duke.cs.osprey.lute.LUTE
- TuplesIndex - Class in edu.duke.cs.osprey.confspace
-
Provies efficient mapping between tuples and tuple indices.
- TuplesIndex(SimpleConfSpace) - Constructor for class edu.duke.cs.osprey.confspace.TuplesIndex
- TuplesIndex(SimpleConfSpace, RCTuple[]) - Constructor for class edu.duke.cs.osprey.confspace.TuplesIndex
- TuplesIndex.NoSuchTupleException - Exception in edu.duke.cs.osprey.confspace
- TuplesOperation - Class in edu.duke.cs.osprey.coffee.zmat
- TuplesOperation() - Constructor for class edu.duke.cs.osprey.coffee.zmat.TuplesOperation
- TuplesOperation(List<Tuple>) - Constructor for class edu.duke.cs.osprey.coffee.zmat.TuplesOperation
- TupleTree<T> - Class in edu.duke.cs.osprey.confspace
-
efficient storage for high-dimensional RC tuples based on a prefix tree (aka "trie")
- TupleTree() - Constructor for class edu.duke.cs.osprey.confspace.TupleTree
- TupleTree(RCTuple) - Constructor for class edu.duke.cs.osprey.confspace.TupleTree
- TupleTrie(List<SimpleConfSpace.Position>) - Constructor for class edu.duke.cs.osprey.ematrix.UpdatingEnergyMatrix.TupleTrie
- txHasRoomFor(int) - Method in class edu.duke.cs.osprey.sofea.FringeDB.Transaction
-
Is there enough room in the transaction write buffer to add more nodes?
- type - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Conf
- type - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.MolInfo
-
can be null
- type - Variable in class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf
- type - Static variable in class edu.duke.cs.osprey.energy.compiled.AmberEnergyCalculator
- type - Static variable in class edu.duke.cs.osprey.energy.compiled.EEF1EnergyCalculator
- type - Variable in class edu.duke.cs.osprey.energy.EnergyCalculator
- type - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.ConfSpaceInfo
- type - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.ConfSpaceInfo
- type - Variable in class edu.duke.cs.osprey.kstar.BBKStar.ConfSpaceInfo
- type - Variable in class edu.duke.cs.osprey.kstar.KStar.ConfSpaceInfo
- type - Variable in class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceInfo
- type - Variable in class edu.duke.cs.osprey.minimization.GpuConfMinimizer.Builder
- type - Variable in class edu.duke.cs.osprey.parallelism.Parallelism
- type - Variable in class edu.duke.cs.osprey.paste.Paste.ConfSpaceInfo
- type - Variable in class edu.duke.cs.osprey.structure.Atom
- type - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot.Points
- type() - Method in class edu.duke.cs.osprey.coffee.zmat.Pair
- type() - Method in class edu.duke.cs.osprey.coffee.zmat.Single
- type() - Method in class edu.duke.cs.osprey.coffee.zmat.Triple
- type() - Method in interface edu.duke.cs.osprey.coffee.zmat.Tuple
- type() - Method in class edu.duke.cs.osprey.energy.compiled.AmberEnergyCalculator
- type() - Method in class edu.duke.cs.osprey.energy.compiled.EEF1EnergyCalculator
- type() - Method in interface edu.duke.cs.osprey.energy.compiled.EnergyCalculator
-
get the type of this energy calculator
- type(RCs) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- Type - Static variable in class edu.duke.cs.osprey.coffee.zmat.Pair
- Type - Static variable in class edu.duke.cs.osprey.coffee.zmat.Single
- Type - Static variable in class edu.duke.cs.osprey.coffee.zmat.Triple
- typedep - Variable in class edu.duke.cs.osprey.gmec.PruningSettings
- typeId - Variable in class edu.duke.cs.osprey.coffee.Serializers.AbstractStreamSerializer
U
- ub - Variable in class edu.duke.cs.osprey.kstar.KAStarNode
- UB - Variable in class edu.duke.cs.osprey.astar.FullAStarNode
- UBConf - Variable in class edu.duke.cs.osprey.astar.FullAStarNode
- uBound - Variable in class edu.duke.cs.osprey.multistatekstar.ResidueTermini
- ubScore - Variable in class edu.duke.cs.osprey.kstar.KAStarNode
- uint32(int) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- uint32(long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- uint32(long, int) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- uint32(long, long) - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- uint32skip() - Method in class edu.duke.cs.osprey.gpu.MemoryBuffer
- ul(String) - Method in class edu.duke.cs.osprey.tools.resultdoc.ResultDoc
-
unordered list
- unassign(int) - Method in class edu.duke.cs.osprey.astar.conf.ConfIndex
- unassign(int) - Method in class edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode.Assignments
-
Removes the assignment from the position
- Unassigned - Static variable in class edu.duke.cs.osprey.confspace.Conf
- Unassigned - Static variable in class edu.duke.cs.osprey.confspace.Sequence
- unassignedPos - Variable in class edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode.Assignments
- unassignFor(int[], int, Runnable) - Static method in class edu.duke.cs.osprey.confspace.Conf
- unassignFor(int[], int, Supplier<T>) - Static method in class edu.duke.cs.osprey.confspace.Conf
- unassignInPlace(int) - Method in class edu.duke.cs.osprey.astar.conf.ConfIndex
- unassignSharedMolec() - Method in class edu.duke.cs.osprey.ematrix.epic.EPICEnergyFunction
- unboundIsStable(PFAbstract, PFAbstract) - Method in class edu.duke.cs.osprey.kstar.KSCalc
- undefinedPos - Variable in class edu.duke.cs.osprey.astar.conf.ConfIndex
- undefinedPos - Variable in class edu.duke.cs.osprey.astar.ConfTree
- UniformConfSampler - Class in edu.duke.cs.osprey.lute
-
Deprecated.
- UniformConfSampler(SimpleConfSpace, PruningMatrix, int) - Constructor for class edu.duke.cs.osprey.lute.UniformConfSampler
-
Deprecated.
- union(SeqSpace, SeqSpace) - Static method in class edu.duke.cs.osprey.confspace.SeqSpace
-
Combine multiple sequence spaces into a single sequence space If any residue appears in multiple spaces, it must have the same wild type and residue types in all spaces
- union(List<SeqSpace>) - Static method in class edu.duke.cs.osprey.confspace.SeqSpace
-
Combine multiple sequence spaces into a single sequence space If any position appears in multiple spaces, it must have the same residue types in all spaces
- unit - Variable in class edu.duke.cs.osprey.parallelism.RateLimitedThread
- UnitX - Static variable in class edu.duke.cs.osprey.tools.VectorAlgebra
- UnitY - Static variable in class edu.duke.cs.osprey.tools.VectorAlgebra
- UnitZ - Static variable in class edu.duke.cs.osprey.tools.VectorAlgebra
- UnmatchedAtom - Static variable in class edu.duke.cs.osprey.energy.forcefield.amber.ForcefieldFileParser
- unpinBuffer(Pointer) - Method in class edu.duke.cs.osprey.gpu.cuda.Context
- UnpossibleError - Error in edu.duke.cs.osprey.tools
- UnpossibleError() - Constructor for error edu.duke.cs.osprey.tools.UnpossibleError
- unprunedAtPos(PruningMatrix, int, String) - Method in class edu.duke.cs.osprey.multistatekstar.MSSearchProblem
- unPrunedConfs - Variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- UnprunedPruningMatrix - Class in edu.duke.cs.osprey.kstar.pruning
- UnprunedPruningMatrix(KSSearchProblem, UpdatedPruningMatrix, double) - Constructor for class edu.duke.cs.osprey.kstar.pruning.UnprunedPruningMatrix
- unprunedRCsAtPos - Variable in class edu.duke.cs.osprey.astar.ConfTree
- unprunedRCsAtPos(int) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- unprunedRCsAtPos(int) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- unprunedRCsAtPos(int) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- unprunedRCsAtPos(ArrayList<Integer>, int) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- unprunedRCsAtPos(ArrayList<Integer>, int) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- unprunedRCsAtPos(ArrayList<Integer>, int) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- unprunedRCTuplesAtPos(ArrayList<Integer>) - Method in class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
- unprunedRCTuplesAtPos(ArrayList<Integer>) - Method in class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
- unprunedRCTuplesAtPos(ArrayList<Integer>) - Method in class edu.duke.cs.osprey.pruning.PruningMatrix
- unregisterService(String) - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- unrotateVector(double[]) - Method in class edu.duke.cs.osprey.tools.RotationMatrix
- unscoredBound - Variable in class edu.duke.cs.osprey.kstar.pfunc.UpperBoundCalculator
- unsequencedIndex - Variable in class edu.duke.cs.osprey.confspace.MultiStateConfSpace.State
- unsequencedStates - Variable in class edu.duke.cs.osprey.confspace.MultiStateConfSpace
- UnsequencedSum(StateZ) - Constructor for class edu.duke.cs.osprey.coffee.seqdb.SaveOperation.UnsequencedSum
- unsequencedSums - Variable in class edu.duke.cs.osprey.coffee.seqdb.SaveOperation
- unset(SeqSpace.Position) - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Set the specified residue number to unassigned.
- unset(String) - Method in class edu.duke.cs.osprey.confspace.Sequence
-
Set the specified residue number to unassigned.
- Unspawned - Enum constant in enum class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode.State
-
never spawned yet
- Unstable - Enum constant in enum class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Status
- Unstable - Enum constant in enum class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Status
- Unstable - Enum constant in enum class edu.duke.cs.osprey.paste.PastePartitionFunction.Status
- UnsupportedException(EWAKStarPartitionFunction) - Constructor for exception edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.WithConfTable.UnsupportedException
- UnsupportedException(EWAKStarPartitionFunction) - Constructor for exception edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.WithExternalMemory.UnsupportedException
- UnsupportedException(PartitionFunction) - Constructor for exception edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.WithExternalMemory.UnsupportedException
- UnsupportedException(PastePartitionFunction) - Constructor for exception edu.duke.cs.osprey.paste.PastePartitionFunction.WithConfTable.UnsupportedException
- UnsupportedException(PastePartitionFunction) - Constructor for exception edu.duke.cs.osprey.paste.PastePartitionFunction.WithExternalMemory.UnsupportedException
- UP - Enum constant in enum class edu.duke.cs.osprey.dof.ProlinePucker.Direction
- update(double[], int, double[], int, double[], int, double[], int) - Method in class edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry
- update(double[], int, int, int, int) - Method in class edu.duke.cs.osprey.tools.Protractor.TetrahedralGeometry
- update(int, int[], long) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodePerformance
- update(int, int, Consumer<MathTools.BigDecimalBounds>) - Method in class edu.duke.cs.osprey.sofea.RCDB.Table
- update(MessageVars, EnergyMatrix) - Method in class edu.duke.cs.osprey.astar.conf.scoring.mplp.EdgeUpdater
- update(MessageVars, EnergyMatrix) - Method in interface edu.duke.cs.osprey.astar.conf.scoring.mplp.MPLPUpdater
- update(MessageVars, EnergyMatrix) - Method in class edu.duke.cs.osprey.astar.conf.scoring.mplp.NodeUpdater
- updateAndLog(int, int[], long, BigExp, BigExp, BigExp) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodePerformance
- updateAndLog(NodeIndex.Node, long, BigExp) - Method in class edu.duke.cs.osprey.coffee.nodedb.NodePerformance
- updateAndReportConfBoundChange(ConfIndex, RCs, AStarScorer, AStarScorer) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- updateBound() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarBound
- updateBoundsFromChildren(MathContext) - Method in class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
- updateConfBounds(ConfIndex, RCs, AStarScorer, AStarScorer) - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- updateCoords() - Method in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy
- updateCoords() - Method in class edu.duke.cs.osprey.energy.forcefield.CoordsAndCharges
- updateDihedralCoords() - Method in class edu.duke.cs.osprey.dof.FreeDihedral
- UpdatedPruningMatrix - Class in edu.duke.cs.osprey.astar.comets
-
Within a given state, each node in the COMETS tree can have a different set of unpruned RCs and pairs, but these will usually be small updates to the previous node This "updated" matrix will behave as a pruning matrix for purposes of storing/checking pruned RCs and pairs at a node, but without full storage
- UpdatedPruningMatrix(PruningMatrix) - Constructor for class edu.duke.cs.osprey.astar.comets.UpdatedPruningMatrix
- updateLowerEnergyOfUnsampledConfs(double) - Method in class edu.duke.cs.osprey.confspace.ConfDB.SequenceDB
- updateMin(double) - Method in class edu.duke.cs.osprey.gmec.EnergyRange
- updatePruningMatrix(int, String) - Method in class edu.duke.cs.osprey.multistatekstar.MSSearchProblem
- updatePruningMatrix(ArrayList<Integer>, ArrayList<ArrayList<String>>) - Method in class edu.duke.cs.osprey.multistatekstar.MSSearchProblem
- updatePStar() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- updateQprime(ConfSearch.EnergiedConf) - Method in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- updateQprime(ConfSearch.EnergiedConf) - Method in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized
- updateQprime(BigDecimal) - Method in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionDiscrete
- updateQPrime() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
- updateQPrime() - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFUB
- updateQPrime() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- updateQStar(KSConf) - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- updateQStarUB(KSConf) - Method in class edu.duke.cs.osprey.kstar.pfunc.impl.PFUB
- updateResidue(ResidueTemplateLibrary, Residue, MutAlignmentCache) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf
- updateSubtreeBounds() - Method in class edu.duke.cs.osprey.markstar.framework.MARKStarNode
- updateUnassigned() - Method in class edu.duke.cs.osprey.astar.seq.nodes.SeqAStarNode.Assignments
-
Populates the unassigned positions, based on what's not assigned
- updateUndefined() - Method in class edu.duke.cs.osprey.astar.conf.ConfIndex
-
Populates the unassigned positions, based on what's not assigned defined positions must be sorted
- UpdatingEnergyMatrix - Class in edu.duke.cs.osprey.ematrix
- UpdatingEnergyMatrix(SimpleConfSpace, EnergyMatrix) - Constructor for class edu.duke.cs.osprey.ematrix.UpdatingEnergyMatrix
- UpdatingEnergyMatrix(SimpleConfSpace, EnergyMatrix, ConfEnergyCalculator) - Constructor for class edu.duke.cs.osprey.ematrix.UpdatingEnergyMatrix
- UpdatingEnergyMatrix.TupleTrie - Class in edu.duke.cs.osprey.ematrix
- uploadAsync() - Method in class edu.duke.cs.osprey.gpu.cuda.CUBuffer
- uploadAsync(CUdeviceptr, Pointer, long, GpuStream) - Method in class edu.duke.cs.osprey.gpu.cuda.Context
- uploadBufferAsync(CLBuffer<?>) - Method in class edu.duke.cs.osprey.gpu.opencl.Kernel
- uploadCoordsAsync() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.CCDKernelCuda
- uploadCoordsAsync() - Method in class edu.duke.cs.osprey.gpu.cuda.kernels.ForcefieldKernelCuda
- uploadCoordsAsync() - Method in interface edu.duke.cs.osprey.gpu.ForcefieldKernel
- uploadCoordsAsync() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.ForcefieldKernelOpenCL
- uploadPartialBufferAsync(CLBuffer<?>) - Method in class edu.duke.cs.osprey.gpu.opencl.Kernel
- uploadSync() - Method in class edu.duke.cs.osprey.gpu.opencl.kernels.TestFancyKernel
- upm - Variable in class edu.duke.cs.osprey.kstar.pruning.ReducedPruningMatrix
- upper - Variable in class edu.duke.cs.osprey.confspace.ConfDB.Conf
- upper - Variable in class edu.duke.cs.osprey.tools.BigExp.Bounds
- upper - Variable in class edu.duke.cs.osprey.tools.MathTools.BigDecimalBounds
- upper - Variable in class edu.duke.cs.osprey.tools.MathTools.BigIntegerBounds
- upper - Variable in class edu.duke.cs.osprey.tools.MathTools.DoubleBounds
- upperBound - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
-
upper bound on K* score, could be singleton instance MathTools.BigPositiveInfinity
- upperBound - Variable in class edu.duke.cs.osprey.kstar.KStarScore
-
upper bound on K* score, could be singleton instance MathTools.BigPositiveInfinity
- upperBound - Variable in class edu.duke.cs.osprey.paste.PasteScore
-
upper bound on K* score, could be singleton instance MathTools.BigPositiveInfinity
- UpperBound - Enum constant in enum class edu.duke.cs.osprey.multistatekstar.KStarScore.PartitionFunctionType
- UpperBoundCalculator - Class in edu.duke.cs.osprey.kstar.pfunc
- UpperBoundCalculator(ConfSearch, BigInteger) - Constructor for class edu.duke.cs.osprey.kstar.pfunc.UpperBoundCalculator
- upperBoundLog10() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- upperBoundLog10() - Method in class edu.duke.cs.osprey.kstar.KStarScore
- upperBoundLog10String() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScore
- upperBoundLog10String() - Method in class edu.duke.cs.osprey.kstar.KStarScore
- upperBoundLog10String() - Method in class edu.duke.cs.osprey.paste.PasteScore
- upperBounds() - Method in class edu.duke.cs.osprey.confspace.ConfDB.ConfTable
- UpperBoundScorer - Class in edu.duke.cs.osprey.markstar
- UpperBoundScorer(EnergyMatrix) - Constructor for class edu.duke.cs.osprey.markstar.UpperBoundScorer
- UpperLowerAStarOrder - Class in edu.duke.cs.osprey.astar.conf.order
- UpperLowerAStarOrder() - Constructor for class edu.duke.cs.osprey.astar.conf.order.UpperLowerAStarOrder
- usage() - Method in class edu.duke.cs.osprey.coffee.nodedb.NodeDB
-
Returns the ratio of used space to total space.
- usage(long, long) - Method in class edu.duke.cs.osprey.coffee.nodedb.Neighbors
- use(int, TPIE.Block) - Static method in class edu.duke.cs.osprey.externalMemory.ExternalMemory
-
Convenience method to initialize the external memory system, run a block of code, and then make sure the external memory gets cleaned up before returning.
- use(UseableBuilder.Block<T>) - Method in interface edu.duke.cs.osprey.tools.UseableBuilder
- UseableBuilder<T extends AutoCleanable> - Interface in edu.duke.cs.osprey.tools
- UseableBuilder.Block<T> - Interface in edu.duke.cs.osprey.tools
- useContinuous - Variable in class edu.duke.cs.osprey.design.models.Flexibility
- usedBytes - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeIndices.BroadcastInfo
- usedBytes - Variable in class edu.duke.cs.osprey.tools.JvmMem.MemInfo
-
number of bytes used by the JVM
- useDistDependentDielectric - Variable in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.ParamInfo
- usedPercent - Variable in class edu.duke.cs.osprey.tools.JvmMem.MemInfo
- useDynamicAStar - Variable in class edu.duke.cs.osprey.astar.ConfTree
- useEEF1 - Variable in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.ParamInfo
- useEllipses - Variable in class edu.duke.cs.osprey.confspace.ConfSpace
- useEPIC - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- useEPICPruning - Variable in class edu.duke.cs.osprey.ematrix.epic.EPICSettings
- useERef - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- useExact - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings
- useExact - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- useExternalMemory - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings
- useExternalMemory - Variable in class edu.duke.cs.osprey.gmec.SimpleGMECFinder.Builder
-
True to use external memory (eg, disk, SSD, NAS) for when large data structures cannot fit in internal memory (eg, RAM).
- useExternalMemory - Variable in class edu.duke.cs.osprey.kstar.KStar.Settings
- useExternalMemory - Variable in class edu.duke.cs.osprey.paste.Paste.Settings
- useExternalMemory() - Method in class edu.duke.cs.osprey.astar.conf.ConfAStarTree.Builder
-
Use external memory (eg, disk, SSD, NAS) when large A* searches cannot fit in internal memory (eg, RAM).
- useExternalMemory() - Method in class edu.duke.cs.osprey.gmec.SimpleGMECFinder.Builder
- useFlags - Variable in class edu.duke.cs.osprey.gmec.PruningSettings
- useHElectrostatics - Variable in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.ParamInfo
- useHVdw - Variable in class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.ParamInfo
- useMarkstar - Variable in class edu.duke.cs.osprey.design.commands.CommandBindingAffinity
- useMaxKSConfs - Static variable in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- useMPI - Static variable in class edu.duke.cs.osprey.control.EnvironmentVars
-
Deprecated.
- useRefinement - Variable in class edu.duke.cs.osprey.astar.ConfTree
- username - Variable in class edu.duke.cs.osprey.design.PostgresConnectionInfo
- UseScript - Enum constant in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.DominantBaseline
- useSMA - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
- useTightBounds - Static variable in class edu.duke.cs.osprey.kstar.impl.KSImplKAStar
- useTriples - Variable in class edu.duke.cs.osprey.gmec.PruningSettings
- useTupExp - Variable in class edu.duke.cs.osprey.gmec.GMECFinder
- useTupExpForSearch - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- useVoxelG - Variable in class edu.duke.cs.osprey.confspace.SearchProblem
- useVoxelG - Variable in class edu.duke.cs.osprey.kstar.KSAbstract
- useWindowCriterion - Variable in class edu.duke.cs.osprey.paste.Paste.Settings
- useWtBenchmark - Variable in class edu.duke.cs.osprey.ewakstar.EwakstarDoer
V
- Val - Enum constant in enum class edu.duke.cs.osprey.sofea.BigDecimalIO.Type
- validate() - Method in class edu.duke.cs.osprey.design.models.AffinityDesign
- validate(String, String) - Method in class edu.duke.cs.osprey.design.commands.FileExistsValidation
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode.State
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.coffee.directors.Timing
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.confspace.compiled.PosInterDist
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.confspace.ConfDB.SortOrder
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.confspace.SearchProblem.MatrixType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.confspace.Sequence.Renderer
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.confspace.SimpleConfSpace.DofTypes
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.control.Main.Command
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.dof.ProlinePucker.Direction
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrixCalculator.ApproximatorType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.energy.compiled.EnergyCalculator.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.energy.EnergyCalculator.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.energy.EnergyPartition
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.Forcefield
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.SolvationForcefield
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.ewakstar.EWAKStar.ConfSpaceType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.PfuncsStatus
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Status
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.externalMemory.AssignmentsSerializer.Encoding
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.gmec.PrecomputedMatrices.MatrixType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.gpu.BufferTools.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.gpu.Structs.Precision
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.kstar.BBKStar.PfuncsStatus
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.kstar.KSSearchProblem.MatrixType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.kstar.KStar.ConfSpaceType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator.Status
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Status
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.kstar.pfunc.PFAbstract.EApproxReached
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.kstar.pfunc.PFAbstract.RunState
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.lute.LUTE.Fitter
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode.ColorStyle
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.minimization.GpuConfMinimizer.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.multistatekstar.KStarScore.KStarScoreType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.multistatekstar.KStarScore.PartitionFunctionType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.parallelism.Parallelism.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.parallelism.PulseSignal.Result
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.paste.Paste.ConfSpaceType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.paste.PastePartitionFunction.Status
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.pruning.NewPruningControl.ReportMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.pruning.PruningControl.ReportMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.pruning.PruningMatrix.IteratorCommand
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.sofea.BigDecimalIO.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.sofea.Sofea.Criterion.Filter
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.sofea.Sofea.Criterion.Satisfied
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.Space
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.structure.AtomNeighbors.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.structure.Probe.AtomFlag
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.structure.Probe.Attraction
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.structure.Probe.Contact
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.structure.Residue.SecondaryStructure
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.structure.Residue.TemplateMatchingMethod
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.tools.IntEncoding
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.tools.Progress.Model
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.tools.resultdoc.Plot.PointType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.tools.resultdoc.ResultDoc.PlotType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.tools.SVG.LengthUnit
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.DominantBaseline
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.TextAnchor
-
Returns the enum constant of this class with the specified name.
- values - Variable in class edu.duke.cs.osprey.coffee.NodeStats.Report
- values - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Result
- values - Variable in class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction
-
Deprecated.
- values - Variable in class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Result
- values - Variable in class edu.duke.cs.osprey.paste.PastePartitionFunction.Result
- values - Variable in class edu.duke.cs.osprey.tools.SVG.StyleClass
- values() - Static method in enum class edu.duke.cs.osprey.astar.conf.smastar.ConfSMAStarNode.State
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.coffee.directors.Timing
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.confspace.compiled.PosInterDist
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Method in class edu.duke.cs.osprey.confspace.Conf.Map
- values() - Static method in enum class edu.duke.cs.osprey.confspace.ConfDB.SortOrder
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.confspace.SearchProblem.MatrixType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.confspace.Sequence.Renderer
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.confspace.SimpleConfSpace.DofTypes
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.control.Main.Command
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.dof.ProlinePucker.Direction
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrixCalculator.ApproximatorType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.energy.compiled.EnergyCalculator.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.energy.EnergyCalculator.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.energy.EnergyPartition
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.Forcefield
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams.SolvationForcefield
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.ewakstar.EWAKStar.ConfSpaceType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.ewakstar.EWAKStarBBKStar.PfuncsStatus
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Status
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.externalMemory.AssignmentsSerializer.Encoding
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.gmec.PrecomputedMatrices.MatrixType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.gpu.BufferTools.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.gpu.Structs.Precision
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.kstar.BBKStar.PfuncsStatus
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.kstar.KSSearchProblem.MatrixType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.kstar.KStar.ConfSpaceType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator.Status
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Status
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.kstar.pfunc.PFAbstract.EApproxReached
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.kstar.pfunc.PFAbstract.RunState
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.lute.LUTE.Fitter
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.markstar.framework.MARKStarNode.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.markstar.MARKStar.ConfSpaceType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode.ColorStyle
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.minimization.GpuConfMinimizer.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.multistatekstar.KStarScore.KStarScoreType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.multistatekstar.KStarScore.PartitionFunctionType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.parallelism.Parallelism.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.parallelism.PulseSignal.Result
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.paste.Paste.ConfSpaceType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.paste.PastePartitionFunction.Status
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.pruning.NewPruningControl.ReportMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.pruning.PruningControl.ReportMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.pruning.PruningMatrix.IteratorCommand
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.sofea.BigDecimalIO.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.sofea.Sofea.Criterion.Filter
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.sofea.Sofea.Criterion.Satisfied
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.structure.analysis.MeasurementLibrary.Space
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.structure.AtomNeighbors.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.structure.Probe.AtomFlag
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.structure.Probe.Attraction
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.structure.Probe.Contact
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.structure.Residue.SecondaryStructure
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.structure.Residue.TemplateMatchingMethod
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.tools.IntEncoding
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.tools.MathTools.Optimizer
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.tools.Progress.Model
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.tools.resultdoc.Plot.PointType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.tools.resultdoc.ResultDoc.PlotType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.tools.SVG.LengthUnit
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.DominantBaseline
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class edu.duke.cs.osprey.tools.SVG.StyleClass.TextAnchor
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values(double) - Method in class edu.duke.cs.osprey.coffee.directors.BestSet
- Values() - Constructor for class edu.duke.cs.osprey.coffee.NodeStats.Values
- Values() - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.Values
- Values() - Constructor for class edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.Values
- Values() - Constructor for class edu.duke.cs.osprey.markstar.framework.MARKStarBound.Values
- Values() - Constructor for class edu.duke.cs.osprey.markstar.framework.MARKStarBoundAsync.Values
- Values() - Constructor for class edu.duke.cs.osprey.markstar.framework.MARKStarBoundRigid.Values
- Values() - Constructor for class edu.duke.cs.osprey.paste.PastePartitionFunction.Values
- valuesInRange(DoubleMatrix1D) - Method in class edu.duke.cs.osprey.ematrix.epic.EPoly
- ValuesSerializer(GroupSerializer<T>) - Constructor for class edu.duke.cs.osprey.tools.MapDBTools.ValuesSerializer
- VanDerWaals - Enum constant in enum class edu.duke.cs.osprey.energy.ResidueForcefieldBreakdown.Type
- vanDerWaalsRadii() - Method in class edu.duke.cs.osprey.energy.forcefield.amber.ForcefieldFileParser
- VanDerWaalsRadius - Record Class in edu.duke.cs.osprey.energy.forcefield.amber
- VanDerWaalsRadius(AtomSymbolAndMass, float, float) - Constructor for record class edu.duke.cs.osprey.energy.forcefield.amber.VanDerWaalsRadius
-
Creates an instance of a
VanDerWaalsRadiusrecord class. - Variable() - Constructor for class edu.duke.cs.osprey.sofea.BigDecimalIO.Variable
- Vdw(ResidueForcefieldEnergy) - Constructor for class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy.Vdw
- Vdw(ResPairCache, ResidueInteractions, Molecule) - Constructor for class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy.Vdw
- Vdw(ResPairCache, ResidueInteractions, Residues) - Constructor for class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy.Vdw
- vdwMultiplier - Variable in class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
- vdwRadius - Variable in class edu.duke.cs.osprey.structure.Probe.AtomInfo
- VectorAlgebra - Class in edu.duke.cs.osprey.tools
- VectorAlgebra() - Constructor for class edu.duke.cs.osprey.tools.VectorAlgebra
- verifyStrandsMutuallyExclusive() - Method in class edu.duke.cs.osprey.kstar.KSConfigFileParser
- version() - Method in class edu.duke.cs.osprey.energy.compiled.CudaConfEnergyCalculator
- version() - Method in class edu.duke.cs.osprey.energy.compiled.NativeConfEnergyCalculator
- Version - Enum constant in enum class edu.duke.cs.osprey.control.Main.Command
-
Prints the version and exits
- Version - Static variable in class edu.duke.cs.osprey.control.Main
- violationThreshold - Variable in class edu.duke.cs.osprey.pruning.PLUG
-
distance threshold to claim that a violation value is close enough to zero
- VisIt - Class in edu.duke.cs.osprey.structure.analysis
-
tool to write VisIt files for various data sets
- VisIt() - Constructor for class edu.duke.cs.osprey.structure.analysis.VisIt
- Visualizer - Class in edu.duke.cs.osprey.markstar.visualizer
- Visualizer() - Constructor for class edu.duke.cs.osprey.markstar.visualizer.Visualizer
- volume - Variable in class edu.duke.cs.osprey.energy.forcefield.EEF1.SolvParams
- volume() - Method in class edu.duke.cs.osprey.structure.analysis.SmallAngleVoxel
- VolumeRCScorer - Class in edu.duke.cs.osprey.partcr.scorers
- VolumeRCScorer() - Constructor for class edu.duke.cs.osprey.partcr.scorers.VolumeRCScorer
- VoxConstrCache - Class in edu.duke.cs.osprey.plug
-
This for checking for repeats of voxel constraints in a polytope
- VoxConstrCache() - Constructor for class edu.duke.cs.osprey.plug.VoxConstrCache
- VoxDeltaGPlayground - Class in edu.duke.cs.osprey.tests
- VoxDeltaGPlayground() - Constructor for class edu.duke.cs.osprey.tests.VoxDeltaGPlayground
- voxelFreeEnergy(int[]) - Method in class edu.duke.cs.osprey.confspace.SearchProblem
- VoxelGCalculator - Class in edu.duke.cs.osprey.voxq
-
Calculates the free energy for a voxel.
- VoxelGCalculator(SearchProblem) - Constructor for class edu.duke.cs.osprey.voxq.VoxelGCalculator
- VoxelsDeltaG - Class in edu.duke.cs.osprey.voxq
-
Calculate the energy difference between two voxels, using BAR-type method
- VoxelsDeltaG(MoleculeModifierAndScorer, MoleculeModifierAndScorer, boolean) - Constructor for class edu.duke.cs.osprey.voxq.VoxelsDeltaG
- VoxelSeriesChecker - Class in edu.duke.cs.osprey.bbfree
-
This function checks if a particular series for full DOFs as a function of free DOFs is accurate over a particular voxel in terms of constraints being nearly satisfied
- VoxelSeriesChecker(List<Residue>, int, int, double[][], PepPlaneLinModel[], DoubleMatrix2D, DoubleMatrix1D) - Constructor for class edu.duke.cs.osprey.bbfree.VoxelSeriesChecker
- voxelShape - Variable in class edu.duke.cs.osprey.confspace.Strand.ResidueFlex
- VoxelShape - Class in edu.duke.cs.osprey.confspace
- VoxelShape() - Constructor for class edu.duke.cs.osprey.confspace.VoxelShape
- VoxelShape.Point - Class in edu.duke.cs.osprey.confspace
- VoxelShape.Rect - Class in edu.duke.cs.osprey.confspace
- VoxelVDWDistExplorer - Class in edu.duke.cs.osprey.plug
-
Explore distances between atoms w/ significant VDW
- VoxelVDWDistExplorer() - Constructor for class edu.duke.cs.osprey.plug.VoxelVDWDistExplorer
- VoxelVDWListChecker - Class in edu.duke.cs.osprey.plug
-
For a specified voxel (bounds on specified dihedrals), check if VDW interactions between the specified atoms can be made to fall in range FOR NOW use linear programming, (relaxing clashes?? or linearize if need, thus cutting vox)
- VoxelVDWListChecker() - Constructor for class edu.duke.cs.osprey.plug.VoxelVDWListChecker
- VoxelVDWListChecker(ArrayList<VoxelVDWListChecker.DOFInterval>, ArrayList<Atom[]>, ArrayList<Residue>, ArrayList<Residue>, ArrayList<LinearConstraint>) - Constructor for class edu.duke.cs.osprey.plug.VoxelVDWListChecker
- VoxelVDWListChecker.DOFInterval - Class in edu.duke.cs.osprey.plug
W
- waitForFinish() - Method in class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator
- waitForFinish() - Method in class edu.duke.cs.osprey.parallelism.ConcurrentTaskExecutor
- waitForFinish() - Method in class edu.duke.cs.osprey.parallelism.TaskExecutor
- waitForFinish() - Method in class edu.duke.cs.osprey.parallelism.TimingThread
- waitForGpu() - Method in class edu.duke.cs.osprey.gpu.cuda.Context
- waitForGpu() - Method in class edu.duke.cs.osprey.gpu.cuda.GpuStream
- waitForGpu() - Method in class edu.duke.cs.osprey.gpu.cuda.Kernel
- waitForGpu() - Method in interface edu.duke.cs.osprey.gpu.ForcefieldKernel
- waitForGpu() - Method in class edu.duke.cs.osprey.gpu.opencl.GpuQueue
- waitForGpu() - Method in class edu.duke.cs.osprey.gpu.opencl.Kernel
- waitForOperation(long, long, TimeUnit) - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- waitForOperationsQuiet(long, TimeUnit, long, TimeUnit) - Method in class edu.duke.cs.osprey.coffee.ClusterMember
- waitForResults(int) - Method in class edu.duke.cs.osprey.parallelism.WorkCrew
- waitForSignal() - Method in class edu.duke.cs.osprey.parallelism.CounterSignal
- waitForSignal() - Method in class edu.duke.cs.osprey.parallelism.Signal
- waitForSignal(long) - Method in class edu.duke.cs.osprey.parallelism.CounterSignal
- waitForSignal(long) - Method in class edu.duke.cs.osprey.parallelism.Signal
- waitForSignal(long, TimeUnit) - Method in class edu.duke.cs.osprey.parallelism.PulseSignal
- waitForStop() - Method in class edu.duke.cs.osprey.coffee.directions.Directions
- waitForWork(Worker, int) - Method in class edu.duke.cs.osprey.parallelism.WorkCrew
- WalkingConfPicker - Class in edu.duke.cs.osprey.partcr.pickers
- WalkingConfPicker() - Constructor for class edu.duke.cs.osprey.partcr.pickers.WalkingConfPicker
- WalkingConfPicker(int) - Constructor for class edu.duke.cs.osprey.partcr.pickers.WalkingConfPicker
- warmup() - Method in class edu.duke.cs.osprey.parallelism.TimingThread
- warmupSignal - Variable in class edu.duke.cs.osprey.parallelism.TimingThread
- weight - Variable in class edu.duke.cs.osprey.confspace.compiled.PosInter
-
weight*(energy + offset)
- weight - Variable in class edu.duke.cs.osprey.energy.forcefield.ResPairCache.ResPair
- weight - Variable in class edu.duke.cs.osprey.energy.ResidueInteractions.Pair
- weight - Variable in class edu.duke.cs.osprey.gmec.Comets.WeightedState
- weight - Variable in class edu.duke.cs.osprey.kstar.MSKStar.WeightedState
- weightedEnergySum - Variable in class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator
- weightedScoreSum - Variable in class edu.duke.cs.osprey.kstar.pfunc.LowerBoundCalculator
- weightedScoreSum - Variable in class edu.duke.cs.osprey.kstar.pfunc.UpperBoundCalculator
- WeightedState(Comets.State, double) - Constructor for class edu.duke.cs.osprey.gmec.Comets.WeightedState
- WeightedState(MSKStar.State, double) - Constructor for class edu.duke.cs.osprey.kstar.MSKStar.WeightedState
- WideContact - Enum constant in enum class edu.duke.cs.osprey.structure.Probe.Contact
- width - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot
- WILDCARD_RC - Static variable in class edu.duke.cs.osprey.ematrix.UpdatingEnergyMatrix.TupleTrie
- WildcardAtom - Static variable in class edu.duke.cs.osprey.energy.forcefield.amber.ForcefieldFileParser
- wildType - Variable in class edu.duke.cs.osprey.confspace.compiled.ConfSpace.Pos
- wildType - Variable in class edu.duke.cs.osprey.confspace.SeqSpace.Position
- wildType - Variable in class edu.duke.cs.osprey.confspace.Strand.ResidueFlex
- wildType(int) - Method in class edu.duke.cs.osprey.confspace.compiled.ConfSpace
- wildType(int) - Method in interface edu.duke.cs.osprey.confspace.ConfSpaceIteration
-
returns the wild type for the position
- wildType(int) - Method in class edu.duke.cs.osprey.confspace.SimpleConfSpace
- WildType - Enum constant in enum class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf.Type
- WildType - Static variable in class edu.duke.cs.osprey.confspace.Strand
-
Magic value that represents the wild-type residue type.
- wildTypeAt(int) - Method in class edu.duke.cs.osprey.astar.seq.RTs
- wildTypeG - Variable in class edu.duke.cs.osprey.coffee.directors.KStarDirector
- wildTypeTemplates - Variable in class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
- WorkCrew<T extends Worker> - Class in edu.duke.cs.osprey.parallelism
- WorkCrew(String) - Constructor for class edu.duke.cs.osprey.parallelism.WorkCrew
- WorkCrew.CalledByBoss - Annotation Interface in edu.duke.cs.osprey.parallelism
- WorkCrew.CalledByWorker - Annotation Interface in edu.duke.cs.osprey.parallelism
- Worker - Class in edu.duke.cs.osprey.parallelism
- Worker(WorkCrew<? extends Worker>) - Constructor for class edu.duke.cs.osprey.parallelism.Worker
- workers - Variable in class edu.duke.cs.osprey.parallelism.WorkCrew
- workIt() - Method in class edu.duke.cs.osprey.parallelism.Worker
- WorkLatch - Class in edu.duke.cs.osprey.parallelism
-
Allows threads to wait for a large amount of work to be finished.
- WorkLatch(long) - Constructor for class edu.duke.cs.osprey.parallelism.WorkLatch
- workMs(Stopwatch) - Method in enum class edu.duke.cs.osprey.coffee.directors.Timing
- WorkQueueThread<T> - Class in edu.duke.cs.osprey.parallelism
- WorkQueueThread(String, BlockingQueue<T>) - Constructor for class edu.duke.cs.osprey.parallelism.WorkQueueThread
- WorkThread - Class in edu.duke.cs.osprey.parallelism
- WorkThread(String) - Constructor for class edu.duke.cs.osprey.parallelism.WorkThread
- write(byte[], int, int) - Method in class edu.duke.cs.osprey.tools.ByteBufferOutputStream
- write(int) - Method in class edu.duke.cs.osprey.tools.ByteBufferOutputStream
- write(int[], ByteBuffer) - Method in enum class edu.duke.cs.osprey.externalMemory.AssignmentsSerializer.Encoding
- write(TupleMatrixGeneric<BigExp>, TripleMatrix<BigExp>) - Method in class edu.duke.cs.osprey.coffee.zmat.Pair
- write(TupleMatrixGeneric<BigExp>, TripleMatrix<BigExp>) - Method in class edu.duke.cs.osprey.coffee.zmat.Single
- write(TupleMatrixGeneric<BigExp>, TripleMatrix<BigExp>) - Method in class edu.duke.cs.osprey.coffee.zmat.Triple
- write(TupleMatrixGeneric<BigExp>, TripleMatrix<BigExp>) - Method in interface edu.duke.cs.osprey.coffee.zmat.Tuple
- write(EnergyMatrix, File) - Static method in class edu.duke.cs.osprey.ematrix.EnergyMatrix
- write(EnergyCalculator.EnergiedParametricMolecule) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- write(EnergyCalculator.EnergiedParametricMolecule, String) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- write(LUTEState) - Static method in class edu.duke.cs.osprey.lute.LUTEIO
- write(LUTEState, File) - Static method in class edu.duke.cs.osprey.lute.LUTEIO
- write(Molecule) - Static method in class edu.duke.cs.osprey.structure.OMOLIO
- write(Molecule) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- write(Molecule, String, Double, boolean) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- write(Molecule, String, Double, boolean, boolean) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- write(DataOutput) - Method in class edu.duke.cs.osprey.coffee.zmat.Pair
- write(DataOutput) - Method in class edu.duke.cs.osprey.coffee.zmat.Single
- write(DataOutput) - Method in class edu.duke.cs.osprey.coffee.zmat.Triple
- write(DataOutput) - Method in interface edu.duke.cs.osprey.coffee.zmat.Tuple
- write(DataOutput, int) - Method in enum class edu.duke.cs.osprey.tools.IntEncoding
- write(DataOutput, BigDecimal) - Method in class edu.duke.cs.osprey.sofea.BigDecimalIO.Fixed
- write(DataOutput, BigDecimal) - Method in class edu.duke.cs.osprey.sofea.BigDecimalIO.Variable
- write(DataOutput, BigDecimal) - Method in interface edu.duke.cs.osprey.sofea.BigDecimalIO
- write(DataOutputStream) - Method in class edu.duke.cs.osprey.confspace.TupleMatrixDouble
- write(DataOutputStream) - Method in class edu.duke.cs.osprey.ematrix.EnergyMatrix
- write(File) - Method in class edu.duke.cs.osprey.kstar.pfunc.PfuncSurface
- write(File) - Method in class edu.duke.cs.osprey.tools.SVG.Finished
- write(OutputStream) - Method in class edu.duke.cs.osprey.design.models.AffinityDesign
- write(Writer) - Method in class edu.duke.cs.osprey.tools.SVG.Finished
- write(Object, File) - Static method in class edu.duke.cs.osprey.tools.ObjectIO
- write(Object, String) - Static method in class edu.duke.cs.osprey.tools.ObjectIO
- write(String) - Method in class edu.duke.cs.osprey.control.SpecialWarningLog
- write(String) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Formatted
- write(String) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.ToConsole
- write(String) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.ToFile
- write(String) - Method in class edu.duke.cs.osprey.kstar.KStarScoreWriter.Formatted
- write(String) - Method in class edu.duke.cs.osprey.kstar.KStarScoreWriter.ToConsole
- write(String) - Method in class edu.duke.cs.osprey.kstar.KStarScoreWriter.ToFile
- write(String) - Method in class edu.duke.cs.osprey.paste.PasteScoreWriter.Formatted
- write(String) - Method in class edu.duke.cs.osprey.paste.PasteScoreWriter.ToConsole
- write(String) - Method in class edu.duke.cs.osprey.paste.PasteScoreWriter.ToFile
- write(String, File) - Method in class edu.duke.cs.osprey.tools.FileTools.FilePathRoot
- write(String, String) - Method in class edu.duke.cs.osprey.tools.FileTools.FilePathRoot
- write(ByteBuffer, int) - Method in enum class edu.duke.cs.osprey.tools.IntEncoding
- write(Path) - Method in class edu.duke.cs.osprey.design.models.AffinityDesign
- write(List<EnergyCalculator.EnergiedParametricMolecule>, String) - Static method in class edu.duke.cs.osprey.structure.PDBIO
-
Writes an ensemble of structures into a single PDB file
- write(List<Molecule>, List<Double>, String) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- writeAngles2D(Collection<double[]>, int, int, File) - Static method in class edu.duke.cs.osprey.structure.analysis.VisIt
- writeAssignments(int[], ByteBuffer) - Method in class edu.duke.cs.osprey.externalMemory.AssignmentsSerializer
- writeBytes(byte[], File) - Method in class edu.duke.cs.osprey.tools.FileTools.FilePathRoot
- writeBytes(byte[], String) - Method in class edu.duke.cs.osprey.tools.FileTools.FilePathRoot
- writeEcoords(List<ConfEnergyCalculator.EnergiedCoords>, String) - Static method in class edu.duke.cs.osprey.structure.PDBIO
-
Writes an ensemble of structures into a single PDB file
- writeEnsemble(List<EnergyCalculator.EnergiedParametricMolecule>, String) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- writeFile(EnergyCalculator.EnergiedParametricMolecule, File) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- writeFile(EnergyCalculator.EnergiedParametricMolecule, String) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- writeFile(EnergyCalculator.EnergiedParametricMolecule, String, File) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- writeFile(EnergyCalculator.EnergiedParametricMolecule, String, String) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- writeFile(Molecule, File) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- writeFile(Molecule, String) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- writeFile(Molecule, String, Double, File) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- writeFile(Molecule, String, Double, String) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- writeFile(String, File) - Static method in class edu.duke.cs.osprey.tools.FileTools
- writeFile(String, String) - Static method in class edu.duke.cs.osprey.tools.FileTools
- writeFile(List<EnergyCalculator.EnergiedParametricMolecule>, File, String) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- writeFile(List<EnergyCalculator.EnergiedParametricMolecule>, String, String) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- writeFileBytes(byte[], File) - Static method in class edu.duke.cs.osprey.tools.FileTools
- writeFileBytes(byte[], String) - Static method in class edu.duke.cs.osprey.tools.FileTools
- writeFileEcoords(List<ConfEnergyCalculator.EnergiedCoords>, File, String) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- writeFileEcoords(List<ConfEnergyCalculator.EnergiedCoords>, String, String) - Static method in class edu.duke.cs.osprey.structure.PDBIO
- writeGrid2D(double[], double[], double[][], File) - Static method in class edu.duke.cs.osprey.structure.analysis.VisIt
-
values stored in y-major order
- writeHeader() - Method in class edu.duke.cs.osprey.design.PostgresScoreWriter
- writeHeader() - Method in class edu.duke.cs.osprey.design.StructureFileScoreWriter
- writeHeader() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Formatted
- writeHeader() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Nop
- writeHeader() - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter
- writeHeader() - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Writers
- writeHeader() - Method in class edu.duke.cs.osprey.kstar.KStarScoreWriter.Formatted
- writeHeader() - Method in class edu.duke.cs.osprey.kstar.KStarScoreWriter.Nop
- writeHeader() - Method in interface edu.duke.cs.osprey.kstar.KStarScoreWriter
- writeHeader() - Method in class edu.duke.cs.osprey.kstar.KStarScoreWriter.Writers
- writeHeader() - Method in class edu.duke.cs.osprey.paste.PasteScoreWriter.Formatted
- writeHeader() - Method in class edu.duke.cs.osprey.paste.PasteScoreWriter.Nop
- writeHeader() - Method in interface edu.duke.cs.osprey.paste.PasteScoreWriter
- writeHeader() - Method in class edu.duke.cs.osprey.paste.PasteScoreWriter.Writers
- writeInternal(ObjectDataOutput) - Method in class edu.duke.cs.osprey.coffee.directions.FinishedSequencesOperation
- writeInternal(ObjectDataOutput) - Method in class edu.duke.cs.osprey.coffee.directions.FocusOperation
- writeInternal(ObjectDataOutput) - Method in class edu.duke.cs.osprey.coffee.directions.TreeOperation
- writeInternal(ObjectDataOutput) - Method in class edu.duke.cs.osprey.coffee.nodedb.AddNodesOperation
- writeInternal(ObjectDataOutput) - Method in class edu.duke.cs.osprey.coffee.nodedb.BroadcastOperation
- writeInternal(ObjectDataOutput) - Method in class edu.duke.cs.osprey.coffee.nodedb.ClearOperation
- writeInternal(ObjectDataOutput) - Method in class edu.duke.cs.osprey.coffee.nodedb.GetHighestNodeOperation
- writeInternal(ObjectDataOutput) - Method in class edu.duke.cs.osprey.coffee.nodedb.GetHighestNodesOperation
- writeInternal(ObjectDataOutput) - Method in class edu.duke.cs.osprey.coffee.seqdb.SaveOperation
- writeInternal(ObjectDataOutput) - Method in class edu.duke.cs.osprey.coffee.zmat.TuplesOperation
- writeObject(Object, String) - Static method in class edu.duke.cs.osprey.tools.ObjectIO
- writePdb(String, String) - Method in class edu.duke.cs.osprey.gmec.ConfAnalyzer.EnsembleAnalysis
- writePdb(String, String) - Method in class edu.duke.cs.osprey.kstar.SequenceAnalyzer.Analysis
- writePdbs(String) - Method in class edu.duke.cs.osprey.gmec.ConfAnalyzer.EnsembleAnalysis
- writePdbs(String) - Method in class edu.duke.cs.osprey.kstar.SequenceAnalyzer.Analysis
- writePdbString(String) - Method in class edu.duke.cs.osprey.gmec.ConfAnalyzer.EnsembleAnalysis
- writePertFile(String) - Method in class edu.duke.cs.osprey.dof.deeper.PertSet
- writeReplacementNode(MultiStateConfSpace.State, int[], BigExp) - Method in class edu.duke.cs.osprey.sofea.FringeDB.Transaction
-
add a node to the transaction write buffer with the same state as the last-read node in the sweep
- writeRootNode(MultiStateConfSpace.State, BigExp) - Method in class edu.duke.cs.osprey.sofea.FringeDB.Transaction
-
add a node to the transaction write buffer with the same state as the last-read node in the sweep
- Writers() - Constructor for class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Writers
- Writers() - Constructor for class edu.duke.cs.osprey.kstar.KStarScoreWriter.Writers
- Writers() - Constructor for class edu.duke.cs.osprey.paste.PasteScoreWriter.Writers
- writeScore(EWAKStarScoreWriter.ScoreInfo) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Formatted
- writeScore(EWAKStarScoreWriter.ScoreInfo) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Nop
- writeScore(EWAKStarScoreWriter.ScoreInfo) - Method in class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Writers
- writeScore(EWAKStarScoreWriter.ScoreInfo) - Method in interface edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter
- writeScore(KStarScoreWriter.ScoreInfo) - Method in class edu.duke.cs.osprey.design.PostgresScoreWriter
- writeScore(KStarScoreWriter.ScoreInfo) - Method in class edu.duke.cs.osprey.design.StructureFileScoreWriter
- writeScore(KStarScoreWriter.ScoreInfo) - Method in class edu.duke.cs.osprey.kstar.KStarScoreWriter.Formatted
- writeScore(KStarScoreWriter.ScoreInfo) - Method in class edu.duke.cs.osprey.kstar.KStarScoreWriter.Nop
- writeScore(KStarScoreWriter.ScoreInfo) - Method in class edu.duke.cs.osprey.kstar.KStarScoreWriter.Writers
- writeScore(KStarScoreWriter.ScoreInfo) - Method in interface edu.duke.cs.osprey.kstar.KStarScoreWriter
- writeScore(PasteScoreWriter.ScoreInfo) - Method in class edu.duke.cs.osprey.paste.PasteScoreWriter.Formatted
- writeScore(PasteScoreWriter.ScoreInfo) - Method in class edu.duke.cs.osprey.paste.PasteScoreWriter.Nop
- writeScore(PasteScoreWriter.ScoreInfo) - Method in class edu.duke.cs.osprey.paste.PasteScoreWriter.Writers
- writeScore(PasteScoreWriter.ScoreInfo) - Method in interface edu.duke.cs.osprey.paste.PasteScoreWriter
- writeTemplateCoords(Residue, String) - Static method in class edu.duke.cs.osprey.restypes.TemplateCoordsParser
- writeTo(DataOutput) - Method in class edu.duke.cs.osprey.energy.approximation.ApproximatorMatrix
- writeTo(DataOutput) - Method in class edu.duke.cs.osprey.energy.approximation.QuadraticApproximator
- writeTo(DataOutput) - Method in class edu.duke.cs.osprey.tools.BigExp
- writeTo(DataOutput) - Method in interface edu.duke.cs.osprey.tools.IOable
- writeTo(File) - Method in interface edu.duke.cs.osprey.tools.IOable
- writeToGZIP(File) - Method in interface edu.duke.cs.osprey.tools.IOable
- writeTopConfs() - Method in class edu.duke.cs.osprey.kstar.pfunc.PFAbstract
- writeTopConfs(int, MSSearchProblem) - Method in class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized
- writeTraces(File) - Method in class edu.duke.cs.osprey.kstar.pfunc.PfuncSurface
- writeVoxels(List<SmallAngleVoxel>, int, int, File) - Static method in class edu.duke.cs.osprey.structure.analysis.VisIt
- WrongEncodingException(AssignmentsSerializer.Encoding, int) - Constructor for exception edu.duke.cs.osprey.externalMemory.AssignmentsSerializer.WrongEncodingException
- WrongNumberOfAssignmentsException(RCs, int[]) - Constructor for exception edu.duke.cs.osprey.externalMemory.AssignmentsSerializer.WrongNumberOfAssignmentsException
- wt - Variable in class edu.duke.cs.osprey.paste.PasteScore
- WT_SEQS - Static variable in class edu.duke.cs.osprey.multistatekstar.MSKStarNode
- wtBenchmark - Variable in class edu.duke.cs.osprey.ewakstar.EWAKStar.Settings
- wtKSCalc - Variable in class edu.duke.cs.osprey.kstar.KSAbstract
- wtRCs - Variable in class edu.duke.cs.osprey.confspace.PositionConfSpace
- wtSeq - Variable in class edu.duke.cs.osprey.kstar.KSAbstract
X
- x - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Axis
- x(int) - Method in class edu.duke.cs.osprey.confspace.compiled.CoordsList
- X - Enum constant in enum class edu.duke.cs.osprey.tools.resultdoc.Plot.PointType
- xaxis - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Boxes
- xlabel - Variable in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd
- xlabel - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot
- xlabelrotate - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot
- xlabels - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot
- xmax - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Boxes.Box
- xmax - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Boxes
- xmax - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Intervals
- xmin - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Boxes.Box
- xmin - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Boxes
- xmin - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Intervals
- XNEFF() - Method in record class edu.duke.cs.osprey.energy.forcefield.amber.SlaterKirkwoodParameter
-
Returns the value of the
XNEFFrecord component. - xtics - Variable in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd
Y
- y - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Axis
- y(int) - Method in class edu.duke.cs.osprey.confspace.compiled.CoordsList
- yaxis - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Boxes
- yield(T) - Method in interface edu.duke.cs.osprey.parallelism.Generator.Yielder
- ylabel - Variable in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd
- ylabel - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot
- ylabels - Variable in class edu.duke.cs.osprey.tools.resultdoc.Plot
- ymax - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Boxes.Box
- ymax - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Boxes
- ymax - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Intervals
- ymin - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Boxes.Box
- ymin - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Boxes
- ymin - Variable in class edu.duke.cs.osprey.tools.SVGPlot.Intervals
- ytics - Variable in class edu.duke.cs.osprey.tools.resultdoc.GNUPlot.Cmd
Z
- z - Variable in class edu.duke.cs.osprey.coffee.zmat.Pair
- z - Variable in class edu.duke.cs.osprey.coffee.zmat.Single
- z - Variable in class edu.duke.cs.osprey.coffee.zmat.Triple
- z(int) - Method in class edu.duke.cs.osprey.confspace.compiled.CoordsList
- Zero - Enum constant in enum class edu.duke.cs.osprey.sofea.BigDecimalIO.Type
- zmat - Variable in class edu.duke.cs.osprey.coffee.bounds.PairwiseBounder
- zmat - Variable in class edu.duke.cs.osprey.coffee.bounds.TriplewiseBounder
- zmat - Variable in class edu.duke.cs.osprey.coffee.StateInfo
- ZMatrix - Class in edu.duke.cs.osprey.sofea
-
a matrix of Boltzmann-weighted energies
- ZMatrix(ConfSpaceIteration) - Constructor for class edu.duke.cs.osprey.sofea.ZMatrix
- zPathHead(ConfIndex) - Method in class edu.duke.cs.osprey.coffee.StateInfo
- zPathTailUpper(ConfIndex, NodeTree) - Method in class edu.duke.cs.osprey.coffee.StateInfo
- zPathUpper(ConfIndex, NodeTree) - Method in class edu.duke.cs.osprey.coffee.StateInfo
- zPruneThreshold - Variable in class edu.duke.cs.osprey.sofea.Sofea
- zSumBounds - Variable in class edu.duke.cs.osprey.coffee.seqdb.StateZ
- zSumBounds - Variable in class edu.duke.cs.osprey.sofea.SeqDB.SeqInfo
- zSumDropped - Variable in class edu.duke.cs.osprey.coffee.seqdb.StateZ
- zSumUpper - Variable in class edu.duke.cs.osprey.coffee.nodedb.NodeIndex.Node
- zSumUpper() - Method in class edu.duke.cs.osprey.sofea.FringeDB.Transaction
- zSumUpper(ConfIndex, NodeTree) - Method in class edu.duke.cs.osprey.coffee.StateInfo
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form