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Project: OSPREY3 (GitHub Link)
  • OSPREY3-master
    • src
      • edu
        • duke
          • cs
            • osprey
              • externalMemory
                • EnergiedConfFIFOSerializer.java
                • EMConfAStarNode.java
                • Queue.java
                • EnergiedConfPrioritySerializer.java
                • AssignmentsSerializer.java
                • EMConfAStarFactory.java
                • ScoredConfFIFOSerializer.java
                • ExternalMemory.java
              • plug
                • LPChecks.java
                • ISAtomsIterable.java
                • RCTuplePolytope.java
                • VoxelVDWListChecker.java
                • RCPairVDWChecker.java
                • PolytopeMatrix.java
                • Res2AtomsIterable.java
                • VoxConstrCache.java
                • VoxelVDWDistExplorer.java
              • astar
                • AStarTree.java
                • seq
                  • RTs.java
                  • scoring
                    • NOPSeqAStarScorer.java
                    • SeqAStarScorer.java
                  • order
                    • SeqAStarOrder.java
                    • SequentialSeqAStarOrder.java
                  • SeqAStarTree.java
                  • nodes
                    • SeqAStarNode.java
                    • LinkedSeqAStarNode.java
                • OptimizableAStarNode.java
                • AStarNode.java
                • AStarProgress.java
                • comets
                  • COMETSNode.java
                  • LME.java
                  • COMETSTree.java
                  • UpdatedPruningMatrix.java
                  • NewCOMETSTree.java
                  • NewCOMETSDoer.java
                • GMECMutSpace.java
                • ConfTree.java
                • FullAStarNode.java
                • conf
                  • ConfAStarNode.java
                  • scoring
                    • TraditionalPairwiseHScorer.java
                    • NOPAStarScorer.java
                    • NaiveTraditionalPairwiseHScorer.java
                    • PairwiseGScorer.java
                    • AStarScorer.java
                    • MPLPPairwiseHScorer.java
                    • mplp
                      • MessageVars.java
                      • NodeUpdater.java
                      • EdgeUpdater.java
                      • MPLPUpdater.java
                  • smastar
                    • ConfSMAStarQueue.java
                    • ConfSMAStarNode.java
                  • ConfSearchCache.java
                  • RCs.java
                  • order
                    • DynamicHMeanAStarOrder.java
                    • StaticEnergyHMeanAStarOrder.java
                    • SequentialAStarOrder.java
                    • AStarOrder.java
                    • UpperLowerAStarOrder.java
                    • StaticScoreHMeanAStarOrder.java
                  • ConfAStarTree.java
                  • pruning
                    • AStarPruner.java
                    • AStarSequencePruner.java
                  • linked
                    • LinkedConfAStarNode.java
                    • LinkedConfAStarFactory.java
                  • ConfAStarFactory.java
                  • ConfRanker.java
                  • ConfIndex.java
                • SlimAStarNode.java
              • lute
                • UniformConfSampler.java
                • LUTE.java
                • ConfSampler.java
                • LUTEGScorer.java
                • LUTEState.java
                • LUTEHScorer.java
                • LowEnergyConfSampler.java
                • LUTEConfEnergyCalculator.java
                • RandomizedDFSConfSampler.java
                • LUTEIO.java
                • LUTEPfunc.java
                • LUTEGMECFinder.java
              • voxq
                • VoxelsDeltaG.java
                • VoxelGCalculator.java
                • QuadraticQFunction.java
                • IntraVoxelSampler.java
                • BoltzmannIntegrator1D.java
              • sofea
                • FringeDB.java
                • StepCount.java
                • ZMatrix.java
                • BigDecimalIO.java
                • MinLMFE.java
                • RCDB.java
                • SeqDB.java
                • Sofea.java
                • SequenceLMFE.java
                • BoltzmannLute.java
              • gmec
                • MinimizingConfEnergyCalculator.java
                • Comets.java
                • EnergyRange.java
                • GMECFinder.java
                • ConfPrinters.java
                • LoggingConfPrinter.java
                • ConfSearchFactory.java
                • ConsoleConfPrinter.java
                • PruningSettings.java
                • SimpleGMECFinder.java
                • ConfPrinter.java
                • SeqGMECFinder.java
                • PrecomputedMatrices.java
                • ConfAnalyzer.java
                • DEEGMECFinder.java
                • GMECConfEnergyCalculator.java
              • partcr
                • RCSplits.java
                • PartCRConfPruner.java
                • scorers
                  • VolumeRCScorer.java
                  • SplitsRCScorer.java
                  • NopRCScorer.java
                  • RCScorer.java
                • splitters
                  • NAryRCSplitter.java
                  • RCSplitter.java
                  • SmartRCSplitter.java
                  • BinaryRCSplitter.java
                • SplitWorld.java
                • pickers
                  • WalkingConfPicker.java
                  • FirstConfPicker.java
                  • ConfPicker.java
                • PartCR.java
              • kstar
                • impl
                  • KSImplKAStar.java
                  • KSImplLinear.java
                • KStarScoreWriter.java
                • KAStarConfTree.java
                • SequenceAnalyzer.java
                • RCEnergyContribs.java
                • KSSearchProblem.java
                • pfunc
                  • impl
                    • PFParallel2.java
                    • PFAdapter.java
                    • PFParallel0.java
                    • PFUB.java
                    • PFTraditional.java
                    • PFParallel1.java
                  • PFFactory.java
                  • SimplePartitionFunction.java
                  • ParallelConfPartitionFunction.java
                  • PFAbstract.java
                  • GradientDescentPfunc.java
                  • LowerBoundCalculator.java
                  • PartitionFunction.java
                  • UpperBoundCalculator.java
                  • PfuncSurface.java
                  • BoltzmannCalculator.java
                • KAStarNode.java
                • KSConfigFileParser.java
                • KSConfQ.java
                • KSInterface.java
                • MSKStar.java
                • KSCalc.java
                • KSConf.java
                • KSAbstract.java
                • KStarScore.java
                • pruning
                  • UnprunedPruningMatrix.java
                  • ReducedPruningMatrix.java
                  • InvertedPruningMatrix.java
                  • APrioriPruningProver.java
                • KSPStarCalculator.java
                • emat
                  • ReducedEnergyMatrix.java
                • KAStarTree.java
                • BBKStar.java
                • KSQPrimeCalculator.java
                • KStar.java
                • KSAllowedSeqs.java
              • multistatekstar
                • KStarScoreUpperBound.java
                • PruningMatrixNull.java
                • MSKStarSettings.java
                • ConfComparator.java
                • KStarScoreDiscrete.java
                • PartitionFunctionDiscreteUppperBound.java
                • PartitionFunctionDiscrete.java
                • MSKStarTree.java
                • InputValidation.java
                • PartitionFunctionMinimized.java
                • KStarScoreMinimized.java
                • ResidueTermini.java
                • MSKStarFactory.java
                • PruningMatrixInverted.java
                • MSKStarNode.java
                • ResidueOrder.java
                • LMB.java
                • KStarScore.java
                • MSSearchProblem.java
                • ResidueOrderFactory.java
                • MultiSequenceConfTree.java
                • MSConfigFileParser.java
                • MSSearchSettings.java
                • KStarScoreLowerBound.java
                • ResidueOrderStaticSequential.java
              • dof
                • MoveableStrand.java
                • StrandRotation.java
                • deeper
                  • PerturbationSelector.java
                  • RamachandranChecker.java
                  • GenChi1Calc.java
                  • ResBBState.java
                  • PertSet.java
                  • SidechainIdealizer.java
                  • perts
                    • TripeptideClosure.java
                    • Shear.java
                    • Backrub.java
                    • SturmSolver.java
                    • PerturbationBlock.java
                    • PartialStructureSwitch.java
                    • Perturbation.java
                    • LoopClosureAdjustment.java
                  • DEEPerSettings.java
                • MutAlignment.java
                • DofInfo.java
                • ProlinePucker.java
                • FreeDihedral.java
                • DihedralRotation.java
                • EllipseCoordDOF.java
                • DOFBlock.java
                • StrandTranslation.java
                • MutAlignmentCache.java
                • DegreeOfFreedom.java
                • ResidueTypeDOF.java
                • DOFCopier.java
              • ewakstar
                • EWAKStarScoreWriter.java
                • EWAKStarPartitionFunction.java
                • EWAKStarBBKStar.java
                • EwakstarDoer.java
                • EwakstarLimitedSequenceTrie.java
                • EWAKStarGradientDescentPfunc.java
                • EWAKStarScore.java
                • EWAKStar.java
              • minimization
                • CudaCCDMinimizer.java
                • SimpleCCDMinimizer.java
                • IntervalLineSearcher.java
                • GpuConfMinimizer.java
                • Minimizer.java
                • GenCoord.java
                • SurfingLineSearcher.java
                • MoleculeModifierAndScorer.java
                • ConfMinimizer.java
                • LineSearcher.java
                • CpuConfMinimizer.java
                • MoleculeObjectiveFunction.java
                • IdealSeparableReference.java
                • ObjectiveFunction.java
                • CCDMinimizer.java
              • ibis
                • KStarBeak.java
                • IBISKStarTupleExpander.java
              • energy
                • EnergyCalculator.java
                • compiled
                  • EnergyCalculator.java
                  • ConfEnergyCalculatorAdapter.java
                  • CPUConfEnergyCalculator.java
                  • EEF1EnergyCalculator.java
                  • ForcefieldDebugger.java
                  • ConfEnergyCalculator.java
                  • PosInterGen.java
                  • AmberEnergyCalculator.java
                • ParallelEnergyFunction.java
                • approximation
                  • ApproximatorMatrix.java
                  • NOPApproximator.java
                  • ResidueInteractionsApproximator.java
                  • ApproximatedObjectiveFunction.java
                  • QuadraticApproximator.java
                  • ApproximatorMatrixCalculator.java
                • ResidueForcefieldBreakdown.java
                • ResidueInteractions.java
                • EnergyFunction.java
                • EnergyPartition.java
                • forcefield
                  • GpuForcefieldEnergy.java
                  • SingleResEnergy.java
                  • SparseFFEnergy.java
                  • CoordsAndCharges.java
                  • ForcefieldParams.java
                  • ForcefieldEnergy.java
                  • ResPairCache.java
                  • EEF1.java
                  • ResidueForcefieldEnergy.java
                  • ResPairEnergy.java
                  • ForcefieldInteractions.java
                  • BigForcefieldEnergy.java
                • FFInterGen.java
                • ConfEnergyCalculator.java
                • LigandResEnergies.java
                • GpuEnergyFunctionGenerator.java
                • MultiTermEnergyFunction.java
                • ResInterGen.java
                • PoissonBoltzmannEnergy.java
                • ScaledEnergyFunction.java
                • EnergyFunctionGenerator.java
              • handlempi
                • MPIMaster.java
                • MPISlaveTask.java
              • structure
                • OMOLIO.java
                • Probe.java
                • Residue.java
                • Atom.java
                • AtomNeighbors.java
                • Residues.java
                • ProbeAtomNeighbors.java
                • Molecule.java
                • analysis
                  • ClusterR1.java
                  • SmallAngleVoxel.java
                  • TemplateChooser.java
                  • AngleClustering.java
                  • PDBScanner.java
                  • MeasurementLibrary.java
                  • Histogram.java
                  • DegreesHistogram.java
                  • VisIt.java
                  • ClusterS1.java
                • AtomConnectivity.java
                • PDBIO.java
                • ConfProblem.java
              • restypes
                • HardCodedResidueInfo.java
                • ResidueEntropies.java
                • BackboneDependentRotamerLibrary.java
                • DAminoAcidHandler.java
                • TemplateCoordsParser.java
                • InterResBondingTemplate.java
                • TemplateParser.java
                • ResTemplateMatching.java
                • RotamerLibraryReader.java
                • ResidueTemplateLibrary.java
                • ResidueEntropyParser.java
                • ResidueTemplate.java
              • markstar
                • MARKStar.java
                • UpperBoundScorer.java
                • framework
                  • GradientDescentMARKStarPfunc.java
                  • MARKStarNode.java
                  • StaticBiggesUpperboundDifferenceOrder.java
                  • StaticBiggestLowerboundDifferenceOrder.java
                  • MARKStarBound.java
                  • MARKStarBoundFastQueues.java
                  • MARKStarBoundAsync.java
                  • StaticLowestEntropyOrder.java
                  • MARKStarBoundRigid.java
                  • BiggestLowerboundDifferenceOrder.java
                • MARKStarProgress.java
                • visualizer
                  • Visualizer.java
                  • KStarTreeNode.java
                  • KStarTreeSplitter.java
                  • KStarTreeRenderer.java
                  • KStarTreeManipulator.java
              • paste
                • PasteGradientDescentPfunc.java
                • PasteScore.java
                • Paste.java
                • PastePartitionFunction.java
                • PasteScoreWriter.java
              • bbfree
                • BBFreeDOF.java
                • LoopVoxelSampler.java
                • BBFreeBlock.java
                • PepPlaneLinModel.java
                • VoxelSeriesChecker.java
              • pruning
                • PruningMethod.java
                • NewPruner.java
                • SimpleDEE.java
                • NewPruningControl.java
                • InvertedPruningMatrix.java
                • Pruner.java
                • PruningControl.java
                • PLUG.java
                • TransitivePruner.java
                • PruningMatrix.java
              • tests
                • ComplicatedGMECFinding.java
                • MinimizationPlayground.java
                • VoxDeltaGPlayground.java
                • PruningPlayground.java
                • OneEPICFit.java
                • NewCOMETS.java
                • CatPark.java
                • TestEWAKStar.java
              • parallelism
                • WorkThread.java
                • CounterSignal.java
                • ConcurrentTaskExecutor.java
                • Signal.java
                • TimingThread.java
                • Threads.java
                • WorkQueueThread.java
                • ThreadPoolTaskExecutor.java
                • Cluster.java
                • ThreadParallelism.java
                • Worker.java
                • Parallelism.java
                • WorkCrew.java
                • TaskExecutor.java
              • tools
                • IOable.java
                • ExpFunction.java
                • TimeTools.java
                • UseableBuilder.java
                • JvmMem.java
                • TimeFormatter.java
                • MinVolEllipse.java
                • resultdoc
                  • GNUPlot.java
                  • ResultDoc.java
                  • Plot.java
                • ByteBufferOutputStream.java
                • VectorAlgebra.java
                • MathTools.java
                • PrefixTreeSet.java
                • IntEncoding.java
                • Stopwatch.java
                • LZMA2.java
                • Profiler.java
                • AutoCloseableNoEx.java
                • MapDBTools.java
                • ByteBufferInputStream.java
                • Log.java
                • BigExp.java
                • FileTools.java
                • PeriodicTable.java
                • SVG.java
                • TomlTools.java
                • InfiniteIterator.java
                • ConfigFileReader.java
                • Protractor.java
                • Factory.java
                • TomlParseException.java
                • RigidBodyMotion.java
                • UnpossibleError.java
                • ObjectIO.java
                • ObjectPool.java
                • HashCalculator.java
                • SVGPlot.java
                • Progress.java
                • RotationMatrix.java
                • AutoCleanable.java
                • EllipseTransform.java
                • BigMath.java
                • StringParsing.java
                • Streams.java
              • confspace
                • RCTuple.java
                • Sequence.java
                • HigherTupleFinder.java
                • MultiStateConfSpace.java
                • ConfDB.java
                • compiled
                  • ContinuousMotion.java
                  • AssignedCoords.java
                  • CoordsList.java
                  • PosInter.java
                  • PosInterDist.java
                  • DegreeOfFreedom.java
                  • motions
                    • DihedralAngle.java
                    • TranslationRotation.java
                  • ConfSpace.java
                • PosMatrixGeneric.java
                • ParametricMolecule.java
                • CATSStrandFlex.java
                • SimpleConfSpace.java
                • TupleTree.java
                • TupleEnumerator.java
                • ConfSearch.java
                • Strand.java
                • Conf.java
                • TuplesIndex.java
                • PositionConfSpace.java
                • RCIndexMap.java
                • StrandFlex.java
                • ParameterizedMoleculeCopy.java
                • ConfSpaceIteration.java
                • TupleMatrixDouble.java
                • SearchProblem.java
                • SeqSpace.java
                • TupleMatrix.java
                • RC.java
                • AbstractPosMatrix.java
                • PosMatrix.java
                • ParameterizedMoleculePool.java
                • TupleMatrixGeneric.java
                • AbstractTupleMatrix.java
                • VoxelShape.java
                • FragmentEnergies.java
                • DEEPerStrandFlex.java
                • TupE.java
                • ConfSpace.java
                • TupleMatrixBoolean.java
              • tupexp
                • CGTupleFitter.java
                • IterativeCGTupleFitter.java
                • BasicEPICTupleExpander.java
                • TupExpChooser.java
                • TupleExpander.java
                • BasicPruningTupleExpander.java
                • FittingObjFcn.java
                • ConfPair.java
                • LUTESettings.java
                • TupleIndexMatrix.java
                • TESampleSet.java
                • ConfETupleExpander.java
                • NewConfETupleExpander.java
              • gpu
                • cuda
                  • GpuStream.java
                  • kernels
                    • ResidueCudaCCDMinimizer.java
                    • ForcefieldKernelCuda.java
                    • ResidueForcefieldEnergyCuda.java
                    • CCDKernelCuda.java
                  • Gpu.java
                  • Kernel.java
                  • Context.java
                  • Diagnostics.java
                  • GpuStreamPool.java
                  • CUBuffer.java
                  • BufferPool.java
                  • Gpus.java
                • ForcefieldKernel.java
                • opencl
                  • kernels
                    • TestFancyKernel.java
                    • ForcefieldKernelOpenCL.java
                  • Gpu.java
                  • Kernel.java
                  • Diagnostics.java
                  • GpuInitException.java
                  • ProfilingEvents.java
                  • GpuQueuePool.java
                  • Gpus.java
                  • GpuQueue.java
                • BufferTools.java
              • ematrix
                • DofMatrix.java
                • EnergyMatrix.java
                • compiled
                  • ErefCalculator.java
                  • EmatCalculator.java
                • ReferenceEnergies.java
                • TermECalculator.java
                • NegatedEnergyMatrix.java
                • EnergyMatrixCalculator.java
                • LazyEnergyMatrix.java
                • SimpleReferenceEnergies.java
                • epic
                  • FitParams.java
                  • EPoly.java
                  • EPICMatrix.java
                  • GaussianLowEnergySampler.java
                  • EPICFitter.java
                  • NewEPICMatrix.java
                  • EPICSettings.java
                  • SAPE.java
                  • SeriesFitter.java
                  • EPolyPC.java
                  • EPICEnergyFunction.java
                  • SubThreshSampler.java
                • ProxyEnergyMatrix.java
                • SimpleEnergyMatrixCalculator.java
                • SimpleEnergyCalculator.java
                • UpdatingEnergyMatrix.java
                • SimplerEnergyMatrixCalculator.java
                • NewEPICMatrixCalculator.java
              • control
                • EnergyCalculator.java
                • ConfigFileParser.java
                • SpecialWarningLog.java
                • MSKStarDoer.java
                • ConfInfo.java
                • KStarCalculator.java
                • Main.java
                • ConfPrinter.java
                • COMETSDoer.java
                • ParamSet.java
                • EnvironmentVars.java
    • resources
      • logback.xml
      • gpuKernels
        • cuda
          • forcefield.bin
          • residueForcefield.bin
          • residueForcefield.cu
          • residueCcd.cu
          • forcefield.cu
          • ccd.cu
        • opencl
          • test.cl
          • forcefield.cl
      • config
        • all_amino_charmm19_neutral_ct.in
        • all_aminoct94.in
        • all_amino_charmm19_neutral.in
        • LovellRotamer.dat.bak
        • all_amino_charmm19_nt.in
        • all_aminont94.in
        • LovellRotamer.dat
        • all_nuc_and_gr_charmm.in
        • version
        • all_damino_coords.in
        • eef1parm.dat
        • all_nuc94_and_gr.in
        • all_amino_charmm19_ct.in
        • GenericRotamers.dat.vol
        • ResEntropy.dat
        • all_amino_charmm19_neutral_nt.in
        • parm96a.dat
        • all_amino94.in
        • probe.cfg
        • template_coords_v2.txt
        • all_amino_charmm19.in
        • parmcharmm19.dat
        • defaults.cfg
        • GenericRotamers.dat
        • all_amino_coords.in
    • gradle
      • wrapper
        • gradle-wrapper.properties
        • gradle-wrapper.jar
    • examples
      • 1GUA
        • 1gua_adj.min.pdb
      • python.ccs
        • F98Y
          • 4tu5.pdb
          • kstar.py
          • 4tu5.NADPH.06W.ccsx
          • .gitignore
      • python.KStar
        • bbkstar.py
        • LUTE.train.py
        • LUTE.kstar.py
        • kstar.py
        • LUTE.bbkstar.py
        • markstar.bbkstar.py
        • markstar.kstar.py
        • LUTE.confSpaces.py
        • .gitignore
        • 2RL0.min.reduce.pdb
      • 1CC8.deeper
        • 1CC8.ss.pdb
        • 1CC8.pert
        • System.cfg
        • .gitignore
        • KStar.cfg
        • DEE.cfg
      • python.GMEC
        • findGMEC.LUTE.train.py
        • 1CC8.ss.pdb
        • findGMEC.LUTE.design.py
        • findGMEC.multipleStrands.py
        • findGMEC.resEntropy.py
        • comets.py
        • plug.py
        • findGMEC.confDB.py
        • comets.boundedMemory.py
        • findGMEC.referenceEnergies.py
        • findGMEC.energyPartitions.py
        • templateLibrary.py
        • findGMEC.DEE.py
        • findGMEC.advanced.py
        • findGMEC.py
        • analyzeConf.py
        • .gitignore
        • findGMEC.DEEPer.py
        • 2RL0.min.reduce.pdb
        • findGMEC.externalMemory.py
        • findGMEC.cats.py
      • adi.1AHO
        • 1AHO.GMEC.pdb
        • 1AHO_cleaned.pdb
        • 1AHO.EMAT.dat
        • System.cfg
        • KStar.cfg
        • DEE.cfg
      • 2RL0.kstar
        • correct.txt
        • 2RL0-output.mhall44s-MacBook-Pro.local.linear.parallelConf.txt
        • cfgSystem.txt
        • 2RL0.min.reduce.numoverlap.pdb
        • 2RL0-output.mhall44s-MacBook-Pro.local.linear.parallel0.txt
        • emat
          • 2RL0-output.min.Strand0.EMAT.dat
          • 2RL0-output.min.protein.EMAT.dat
        • 2RL0.min.reduce.pdb
        • cfgMutSearch.txt
        • cfgKStar.txt
      • python.EWAKStar
        • 1A0R
          • 1A0R.b.shell.pdb
          • runTest.py
        • ewakstar.L.ematRigid
        • ewakstar.sequences.tsv
        • 1GWC
          • 1GWC.shell.pdb
          • runTest.1.py
        • ewakstar.2hnv.py
        • pdbs
          • G649=LEU
            • conf.01.pdb
            • conf.02.pdb
            • conf.05.pdb
            • conf.06.pdb
            • conf.07.pdb
            • conf.04.pdb
            • conf.10.pdb
            • conf.08.pdb
            • conf.09.pdb
            • conf.03.pdb
          • G649=VAL
            • conf.01.pdb
            • conf.02.pdb
            • conf.05.pdb
            • conf.06.pdb
            • conf.07.pdb
            • conf.04.pdb
            • conf.10.pdb
            • conf.08.pdb
            • conf.09.pdb
            • conf.03.pdb
          • G649=ALA
            • conf.01.pdb
            • conf.02.pdb
            • conf.05.pdb
            • conf.06.pdb
            • conf.07.pdb
            • conf.04.pdb
            • conf.10.pdb
            • conf.08.pdb
            • conf.09.pdb
            • conf.03.pdb
          • G649=ILE
            • conf.01.pdb
            • conf.02.pdb
            • conf.05.pdb
            • conf.06.pdb
            • conf.07.pdb
            • conf.04.pdb
            • conf.10.pdb
            • conf.08.pdb
            • conf.09.pdb
            • conf.03.pdb
          • A25=ser
            • conf.01.pdb
            • conf.8.pdb
            • conf.6.pdb
            • conf.02.pdb
            • conf.2.pdb
            • conf.05.pdb
            • conf.4.pdb
            • conf.5.pdb
            • conf.9.pdb
            • conf.3.pdb
            • conf.06.pdb
            • conf.7.pdb
            • conf.1.pdb
            • conf.07.pdb
            • conf.04.pdb
            • conf.10.pdb
            • conf.08.pdb
            • conf.09.pdb
            • conf.03.pdb
          • A25=ASN
            • conf.8.pdb
            • conf.6.pdb
            • conf.2.pdb
            • conf.4.pdb
            • conf.5.pdb
            • conf.9.pdb
            • conf.3.pdb
            • conf.7.pdb
            • conf.1.pdb
          • G649=phe
            • conf.01.pdb
            • conf.02.pdb
            • conf.05.pdb
            • conf.06.pdb
            • conf.07.pdb
            • conf.04.pdb
            • conf.10.pdb
            • conf.08.pdb
            • conf.09.pdb
            • conf.03.pdb
        • ewakStar.results.txt
        • ewakstar.PL.emat
        • ewakstar.py
        • ewakstar.PL.ematRigid
        • ewakstar.P.emat
        • ewakstar.P.ematRigid
        • ewakstar.L.emat
        • 2RL0.min.reduce.pdb
      • comets.junit
        • 3LQC.ub.shell.pdb
        • multistate.spec0.cfg
        • System.3LQC.ub.cfg
        • 3K75.b.shell.pdb
        • System.3LQC.b.cfg
        • System.3K75.b.cfg
        • DEE.3K75.b.cfg
        • DEE.3K75.ub.cfg
        • DEE.3LQC.ub.cfg
        • System.3K75.ub.cfg
        • 3K75.ub.shell.pdb
        • DEE.3LQC.b.cfg
        • .gitignore
        • 3LQC.b.shell.pdb
        • KStar.cfg
      • 1CC8
        • 1CC8.pert.confs.txt
        • 1CC8.ss.pdb
        • deleted_res.txt
        • 1CC8.EMAT.dat
        • 1CC8.pert.EMAT.dat
        • 1CC8.copy.pdb
        • 1CC8.GMEC.pdb
        • run.sh
        • DEE.pert.cfg
        • pdbs
          • 1CC8.STRUCT0.pdb
        • System.cfg
        • 1CC8.pert.GMEC.pdb
        • 1CC8.confs.txt
        • 1CC8.TUPEXPEMAT.dat
        • 1CC8.outputconfs.txt
        • 1CC8.GMEC.eref.pdb
        • 1CC8.pert.pert
        • testResults
          • CONFSEARCHTEST6.EMAT.dat
          • 1CC8.S39A.pdb
          • 1CC8.copy2.pdb
          • 1CC8.dih.pdb
        • KStar.cfg
        • DEE.cfg
      • 1CC8.junit
        • 1CC8.ss.pdb
        • README
        • System.cfg
        • .gitignore
        • KStar.cfg
        • DEE.cfg
      • 4NPD
        • System.cfg
        • KStar.cfg
        • DEE.cfg
      • 1FSV
        • 1FSV.confs.txt
        • System.cfg
        • 1FSV.pdb
        • KStar.cfg
        • 1FSV_fixed.pdb
        • 1FSV.EMAT.dat
        • DEE.cfg
        • 1FSV.GMEC.pdb
      • 1CC8.13
        • 1CC8.ss.pdb
        • DEE13.cfg
        • System13.cfg
        • 1CC8.13.GMEC.pdb
        • KStar.cfg
      • DAGK
        • KStar.cfg
      • 3K75.3LQC
        • 3LQC.ub.shell.pdb
        • multistate.spec0.cfg
        • System.3LQC.ub.cfg
        • 3K75.b.shell.pdb
        • System.3LQC.b.cfg
        • System.3K75.b.cfg
        • DEE.3K75.b.cfg
        • DEE.3K75.ub.cfg
        • DEE.3LQC.ub.cfg
        • System.3K75.ub.cfg
        • 3K75.ub.shell.pdb
        • DEE.3LQC.b.cfg
        • 3LQC.b.shell.pdb
        • KStar.cfg
      • python.SOFEA
        • residueEntropy.py
        • sofea.py
        • residueEntropy.multi-state.py
        • freeEnergy.py
        • .gitignore
        • 2RL0.min.reduce.pdb
      • 2O9S_L2
        • 2O9S_A_H_cleaned.pdb
        • System.cfg
        • KStar.cfg
        • DEE.cfg
      • gpu
        • diagnostics.py
      • 4HEM
        • System.cfg.full
        • System.cfg
        • KStar.cfg
        • DEE.cfg
      • python.PAStE
        • emat.protein.dat
        • mut.txt
        • paste.py
        • pdbs
          • A42=ala
            • conf.01.pdb
            • conf.13.pdb
            • conf.11.pdb
            • conf.14.pdb
            • conf.02.pdb
            • conf.05.pdb
            • conf.06.pdb
            • conf.12.pdb
            • conf.07.pdb
            • conf.04.pdb
            • conf.10.pdb
            • conf.08.pdb
            • conf.15.pdb
            • conf.09.pdb
            • conf.03.pdb
          • A42=THR
            • conf.01.pdb
            • conf.13.pdb
            • conf.11.pdb
            • conf.14.pdb
            • conf.02.pdb
            • conf.05.pdb
            • conf.06.pdb
            • conf.12.pdb
            • conf.07.pdb
            • conf.04.pdb
            • conf.10.pdb
            • conf.08.pdb
            • conf.15.pdb
            • conf.09.pdb
            • conf.03.pdb
        • paste.results.tsv
    • mut.txt
    • CITING_OSPREY.txt
    • gradlew.bat
    • test
      • edu
        • duke
          • cs
            • osprey
              • externalMemory
                • TestAStarSerialization.java
              • TestGenerateRotamerLibrary.java
              • MinimizationComparison.java
              • TestAmberEnergy.java
              • astar
                • TestConfRanker.java
                • TestConfSearchCache.java
                • TestSMAStar.java
                • TestSequencePruner.java
                • SMAStarLab.java
                • BenchmarkAStar.java
                • TestConfIndex.java
                • Matchers.java
                • BenchmarkConfRanker.java
                • TestLinkedConfAStarNode.java
              • ConfTreeProfiling.java
              • FlexLab.java
              • BenchmarkEnergies.java
              • TestConfSearch.java
              • lute
                • LUTELab.java
                • TestRandomizedDFSSampler.java
                • TestLute.java
                • TestLUTEIO.java
                • BenchmarkTupleIndex.java
              • sofea
                • SofeaLab.java
                • TestSeqDB.java
                • MathLab.java
                • TestBigDecimalIO.java
                • TestSofea.java
                • BenchmarkSofea.java
                • TestFringeDB.java
              • EnergyMatrixProfiling.java
              • TestWorkCrew.java
              • gmec
                • TestDEEGMECFinder.java
                • TestSimpleGMECFinder.java
                • BenchmarkGMECFinder.java
                • TestFindGMEC.java
                • CometsLab.java
                • TestComets.java
              • partcr
                • TestPartCR.java
                • TestRCSplits.java
              • kstar
                • KStarRunner.java
                • PfuncPlayground.java
                • compiled
                  • TestKStar.java
                  • TestConfEnergyCalculatorAdapter.java
                  • TestBBKStar.java
                • TestKStarScore.java
                • TestSequenceAnalyzer.java
                • TestKStar.java
                • TestBBKStar.java
                • BenchmarkPartitionFunction.java
                • NewMethPlayground.java
                • TestSimplePartitionFunction.java
                • TestMSKStar.java
              • dof
                • TestFreeDihedral.java
                • TestDOFs.java
              • PruningProfiling.java
              • minimization
                • BenchmarkMinimization.java
                • TestMinimization.java
                • ExampleParallelMinimization.java
                • TestAmberWells.java
                • TestMinimizationStability.java
              • energy
                • TestMinimizingEnergyCalculators.java
                • TestResidueForcefieldBreakdown.java
                • MisBoundPlayground.java
                • TestUpdatingEnergyMatrix.java
                • forcefield
                  • TestForcefieldEnergy.java
                  • TestResidueForcefieldEnergyVdw.java
                  • BenchmarkForcefields.java
                  • TestResidueForcefieldSubEnergies.java
                  • BenchmarkApproximatedForcefield.java
                  • TestApproximatedForcefields.java
                • TestRigidEMatVsNBodyMinimization.java
              • Benchmark.java
              • structure
                • TestOMOLIO.java
                • TestAtomConnectivity.java
                • TestProbe.java
                • TestAtom.java
                • TestPDBIO.java
                • TestStrand.java
              • ClusterLab.java
              • python
                • TestPythonScripts.java
              • markstar
                • TestMARKStar.java
                • TestMARKStarDesignProblems.java
              • paste
                • PasteRunner.java
              • TestTools.java
              • TestCOMETS.java
              • TestConfSpace.java
              • pruning
                • BenchmarkSimpleDEE.java
                • TestSimpleDEE.java
                • TestUnprunedConfBounding.java
                • TestPLUG.java
                • TestTransitivePruning.java
                • PLUGLab.java
              • mplp
                • TestMessageVars.java
              • TestAStar.java
              • parallelism
                • BenchmarkMulticore.java
                • BenchmarkTaskExecutor.java
                • TestThreadPoolTaskExecutor.java
              • newEwakstar
                • EwakstarLab.java
              • MPLPPLayground.java
              • tools
                • resultdoc
                  • TestGNUPlot.java
                  • TestResultDoc.java
                • TestJvmMem.java
                • TestBigExp.java
                • TestPrefixTree.java
                • TestDihedrals.java
                • TestTimeTools.java
                • TestExpFunction.java
                • TestMathTools.java
              • confspace
                • TestConfSearchMultiSplitter.java
                • compiled
                  • TestConfSpace.java
                • TestTupleTree.java
                • TestSequence.java
                • TestConf.java
                • TestSimpleConfSpace.java
                • TestConfSearchSplitter.java
                • TestRCIndexMap.java
                • TestConfDB.java
              • ConfSpaceTests.java
              • gpu
                • BenchmarkForcefieldKernel.java
                • TestEnergyFunctionGenerator.java
                • opencl
                  • TestGpu.java
              • ematrix
                • TestSimpleEnergyMatrixCalculator.java
                • compiled
                  • TestConfEnergyCalculatorAdapter.java
                • TestSimplerEnergyMatrixCalculator.java
                • BenchmarkEmat.java
                • ExampleParallelEmat.java
                • TestSimpleEnergyCalculator.java
                • EnergyPartitionsPlayground.java
                • TestEmatCorrections.java
                • TestEnergyPartitions.java
              • EnergyProfiling.java
              • TestBase.java
    • gradlew
    • azure-pipelines.yml
    • lib
      • kdtree.jar
    • pdbs
      • G649=LEU
        • conf.01.pdb
        • conf.02.pdb
        • conf.05.pdb
        • conf.06.pdb
        • conf.07.pdb
        • conf.04.pdb
        • conf.10.pdb
        • conf.08.pdb
        • conf.09.pdb
        • conf.03.pdb
      • A42=LYS
        • conf.01.pdb
        • conf.02.pdb
        • conf.05.pdb
        • conf.06.pdb
        • conf.1.pdb
        • conf.07.pdb
        • conf.04.pdb
        • conf.10.pdb
        • conf.08.pdb
        • conf.09.pdb
        • conf.03.pdb
      • G649=VAL
        • conf.01.pdb
        • conf.02.pdb
        • conf.05.pdb
        • conf.06.pdb
        • conf.07.pdb
        • conf.04.pdb
        • conf.10.pdb
        • conf.08.pdb
        • conf.09.pdb
        • conf.03.pdb
      • A42=ala
        • conf.01.pdb
        • conf.02.pdb
        • conf.05.pdb
        • conf.06.pdb
        • conf.07.pdb
        • conf.04.pdb
        • conf.10.pdb
        • conf.08.pdb
        • conf.09.pdb
        • conf.03.pdb
      • A42=THR
        • conf.01.pdb
        • conf.02.pdb
        • conf.05.pdb
        • conf.06.pdb
        • conf.07.pdb
        • conf.04.pdb
        • conf.10.pdb
        • conf.08.pdb
        • conf.09.pdb
        • conf.03.pdb
      • G649=ALA
        • conf.01.pdb
        • conf.02.pdb
        • conf.05.pdb
        • conf.06.pdb
        • conf.07.pdb
        • conf.04.pdb
        • conf.10.pdb
        • conf.08.pdb
        • conf.09.pdb
        • conf.03.pdb
      • G649=ILE
        • conf.01.pdb
        • conf.02.pdb
        • conf.05.pdb
        • conf.06.pdb
        • conf.07.pdb
        • conf.04.pdb
        • conf.10.pdb
        • conf.08.pdb
        • conf.09.pdb
        • conf.03.pdb
      • G649=phe
        • conf.01.pdb
        • conf.02.pdb
        • conf.05.pdb
        • conf.06.pdb
        • conf.07.pdb
        • conf.04.pdb
        • conf.10.pdb
        • conf.08.pdb
        • conf.09.pdb
        • conf.03.pdb
    • README.rst
    • python
      • listplatforms.py
      • setup.py
      • wheelhouse
        • JPype_py2-0.5.8-cp27-cp27m-win_amd64.whl
      • doc
        • api.ematrix.epic.EPICMatrix.rst
        • api.energy.ResInterGen.ShellOffsetter.rst
        • api.sofea.SequenceLMFE.rst
        • api.sofea.MinLMFE.rst
        • api.confspace.SimpleConfSpace.ResidueConf.rst
        • api.astar.seq.nodes.SeqAStarNode.rst
        • api.kstar.pfunc.PartitionFunction.Status.rst
        • api.energy.ResInterGen.IntraOffsetter.rst
        • api.confspace.StrandFlex.rst
        • api.confspace.SearchProblem.rst
        • api.control.ConfigFileParser.rst
        • api.plug.PolytopeMatrix.rst
        • api.externalMemory.ExternalMemory.InternalMemoryLimitNotSetException.rst
        • api.gmec.ConfPrinter.rst
        • api.structure.Residue.rst
        • api.paste.Paste.ConfSearchFactory.rst
        • api.paste.PastePartitionFunction.Status.rst
        • api.dof.DOFBlock.rst
        • api.gmec.Comets.LME.rst
        • api.kstar.KStarScoreWriter.ScoreInfo.rst
        • api.confspace.compiled.PosInter.rst
        • api.kstar.BBKStar.rst
        • api.pruning.PruningMatrix.rst
        • todo.rst
        • api.energy.forcefield.ResPairCache.AtomPairInfo.rst
        • api.dof.ProlinePucker.Direction.rst
        • api.kstar.MSKStar.SeqConfs.rst
        • api.structure.AtomNeighbors.Type.rst
        • api.bbfree.BBFreeBlock.rst
        • api.externalMemory.Queue.rst
        • api.astar.seq.nodes.SeqAStarNode.Assignments.rst
        • api.confspace.ConfSearch.ScoredConf.rst
        • api.confspace.Sequence.Assignment.rst
        • api.ematrix.epic.EPoly.rst
        • api.confspace.PositionConfSpace.rst
        • api.energy.approximation.ApproximatorMatrix.Entry.rst
        • api.energy.ConfEnergyCalculator.rst
        • api.energy.ResInterGen.rst
        • api.ematrix.ReferenceEnergies.rst
        • api.energy.EnergyCalculator.Type.rst
        • api.dof.DegreeOfFreedom.rst
        • api.kstar.MSKStar.rst
        • api.gmec.ConfAnalyzer.rst
        • api.astar.AStarProgress.rst
        • api.pruning.PruningMatrix.IteratorCommand.rst
        • api.astar.conf.ConfAStarTree.MPLPBuilder.rst
        • api.dof.MutAlignment.rst
        • api.confspace.VoxelShape.rst
        • api.gmec.GMECFinder.ConfPruner.rst
        • api.sofea.Sofea.Criterion.rst
        • api.lute.ConfSampler.rst
        • api.externalMemory.ExternalMemory.rst
        • api.astar.conf.ConfAStarTree.rst
        • api.sofea.MinLMFE.TopSequences.rst
        • constructors.rst
        • api.confspace.compiled.CoordsList.rst
        • api.lute.LUTEState.rst
        • api.bbfree.BBFreeDOF.rst
        • api.confspace.compiled.ContinuousMotion.rst
        • api.pruning.PruningControl.ReportMode.rst
        • api.sofea.Sofea.rst
        • api.energy.forcefield.ForcefieldParams.VdwParams.rst
        • api.structure.AtomConnectivity.rst
        • api.control.ParamSet.rst
        • api.tools.BigExp.rst
        • api.confspace.compiled.ConfSpace.IndicesSingle.rst
        • api.confspace.Strand.rst
        • api.structure.Residues.rst
        • api.energy.approximation.ApproximatedObjectiveFunction.rst
        • api.energy.ResidueInteractions.rst
        • api.astar.conf.ConfIndex.rst
        • api.tools.MathTools.rst
        • api.confspace.compiled.ConfSpace.Conf.rst
        • api.confspace.RCIndexMap.rst
        • api.parallelism.TaskExecutor.Task.rst
        • api.energy.EnergyCalculator.rst
        • api.astar.seq.RTs.Filter.rst
        • api.confspace.MultiStateConfSpace.LMFECalculator.rst
        • api.gmec.ConfAnalyzer.ConfAnalysis.rst
        • api.confspace.ConfDB.SequenceDB.rst
        • api.lute.LUTEConfEnergyCalculator.rst
        • api.energy.forcefield.EEF1.SolvParams.rst
        • api.astar.conf.order.AStarOrder.rst
        • api.sofea.SeqDB.SeqInfo.rst
        • api.gmec.Comets.rst
        • api.tupexp.LUTESettings.rst
        • api.kstar.SequenceAnalyzer.ConfSpaceInfo.rst
        • api.astar.conf.scoring.AStarScorer.rst
        • api.minimization.MoleculeObjectiveFunction.rst
        • api.confspace.Strand.Flexibility.rst
        • api.paste.Paste.Settings.rst
        • api.confspace.compiled.AssignedCoords.rst
        • api.confspace.ConfSearch.rst
        • api.kstar.MSKStar.LMFE.rst
        • api.energy.ResidueForcefieldBreakdown.rst
        • api.energy.ResInterGen.InterOffsetter.rst
        • api.pruning.PruningMatrix.PairConsumer.rst
        • api.confspace.ConfSpaceIteration.rst
        • api.sofea.SeqDB.Transaction.rst
        • api.astar.conf.scoring.mplp.MPLPUpdater.rst
        • api.sofea.FringeDB.Transaction.rst
        • api.sofea.Sofea.Criterion.Filter.rst
        • api.minimization.MoleculeModifierAndScorer.rst
        • api.energy.approximation.ResidueInteractionsApproximator.rst
        • api.confspace.compiled.ConfSpace.rst
        • api.sofea.RCDB.Table.rst
        • api.kstar.KStar.rst
        • api.dof.ResidueTypeDOF.rst
        • api.astar.conf.scoring.mplp.MessageVars.rst
        • tutorial.rst
        • api.kstar.pfunc.PartitionFunction.Values.rst
        • api.pruning.PruningMatrix.TripleConsumer.rst
        • api.astar.seq.RTs.rst
        • api.tools.MathTools.DoubleBounds.rst
        • api.kstar.KStarScore.rst
        • api.tools.FileTools.PathRoot.rst
        • api.confspace.HigherTupleFinder.rst
        • api.confspace.Sequence.rst
        • api.confspace.SimpleConfSpace.ResidueConf.Type.rst
        • api.gmec.Comets.WeightedState.rst
        • api.confspace.compiled.ConfSpace.ResInfo.rst
        • api.lute.LUTE.Errors.rst
        • api.gmec.Comets.State.rst
        • api.kstar.KStar.ScoredSequence.rst
        • api.kstar.KStar.Settings.rst
        • api.confspace.SimpleConfSpace.Position.rst
        • api.energy.forcefield.ForcefieldParams.rst
        • api.kstar.BBKStar.Settings.rst
        • api.paste.PasteScoreWriter.rst
        • api.paste.PastePartitionFunction.Result.rst
        • api.gmec.Comets.SeqConfs.rst
        • api.dof.EllipseCoordDOF.rst
        • api.tools.ExpFunction.rst
        • api.confspace.MultiStateConfSpace.State.rst
        • api.kstar.KStar.ConfSpaceInfo.rst
        • api.ematrix.epic.EPICEnergyFunction.rst
        • api.paste.Paste.ConfSpaceInfo.rst
        • api.tools.MathTools.BigDecimalBounds.rst
        • api.structure.Residue.SecondaryStructure.rst
        • api.lute.LUTE.Fitter.rst
        • api.confspace.compiled.ConfSpace.MolInfo.rst
        • api.energy.forcefield.ForcefieldParams.NBParams.rst
        • api.structure.Molecule.rst
        • api.confspace.Strand.ResidueFlex.rst
        • api.kstar.pfunc.PartitionFunction.Result.rst
        • api.paste.PasteScoreWriter.ScoreInfo.rst
        • api.confspace.MultiStateConfSpace.LMFEBuilder.rst
        • api.lute.LUTEGMECFinder.rst
        • api.sofea.FringeDB.rst
        • api.confspace.SimpleConfSpace.ResidueConf.PostTemplateModifier.rst
        • api.confspace.ConfSpace.rst
        • api.confspace.compiled.ConfSpace.Pos.rst
        • api.dof.deeper.perts.Perturbation.rst
        • api.paste.Paste.rst
        • api.kstar.BBKStar.ConfSpaceInfo.rst
        • api.gmec.SimpleGMECFinder.rst
        • api.astar.conf.scoring.mplp.EdgeUpdater.rst
        • api.confspace.compiled.ConfSpace.IndicesPair.rst
        • api.multistatekstar.ResidueTermini.rst
        • api.sofea.RCDB.rst
        • api.energy.forcefield.ResPairCache.ResPair.rst
        • api.ematrix.SimpleReferenceEnergies.rst
        • api.dof.MutAlignmentCache.rst
        • api.parallelism.Parallelism.rst
        • api.gmec.ConfAnalyzer.EnsembleAnalysis.rst
        • api.lute.LUTE.rst
        • api.restypes.ResidueEntropies.rst
        • api.energy.forcefield.EEF1.rst
        • api.astar.conf.ConfAStarNode.rst
        • api.energy.ResidueInteractions.Pair.rst
        • api.confspace.SeqSpace.rst
        • api.confspace.compiled.DegreeOfFreedom.rst
        • api.astar.conf.scoring.mplp.NodeUpdater.rst
        • api.confspace.TupleMatrix.rst
        • api.lute.LUTE.LinearSystem.rst
        • api.parallelism.TaskExecutor.TaskListener.rst
        • api.confspace.ConfDB.rst
        • api.gmec.Comets.ConfDBs.rst
        • api.confspace.MultiStateConfSpace.rst
        • api.astar.conf.ConfAStarFactory.rst
        • api.energy.forcefield.ForcefieldParams.SolvationForcefield.rst
        • api.astar.GMECMutSpace.rst
        • api.gmec.GMECConfEnergyCalculator.rst
        • api.confspace.TuplesIndex.rst
        • api.parallelism.TaskExecutor.rst
        • api.energy.forcefield.ForcefieldParams.Forcefield.rst
        • api.sofea.Sofea.Criterion.Satisfied.rst
        • api.paste.PasteScore.rst
        • api.astar.conf.pruning.AStarPruner.rst
        • api.structure.AtomConnectivity.AtomPairs.rst
        • api.confspace.SearchProblem.MatrixType.rst
        • api.confspace.SimpleConfSpace.Builder.rst
        • api.paste.Paste.ConfSpaceType.rst
        • api.gmec.EnergyRange.rst
        • api.confspace.Sequence.Renderer.rst
        • api.energy.EnergyPartition.rst
        • api.confspace.ParametricMolecule.rst
        • api.astar.conf.RCs.rst
        • api.dof.ProlinePucker.rst
        • api.sofea.SeqDB.rst
        • api.confspace.SeqSpace.ResType.rst
        • api.structure.AtomNeighbors.rst
        • api.confspace.ParameterizedMoleculeCopy.rst
        • api.confspace.RCTuple.rst
        • api.pruning.PruningMatrix.SingleConsumer.rst
        • api.kstar.SequenceAnalyzer.Analysis.rst
        • api.ematrix.epic.EPICSettings.rst
        • api.structure.Atom.rst
        • api.energy.compiled.EnergyCalculator.rst
        • api.kstar.KStarScoreWriter.rst
        • api.minimization.ObjectiveFunction.rst
        • index.rst
        • api.energy.forcefield.ResPairCache.rst
        • conf.py
        • api.energy.approximation.ApproximatorMatrix.rst
        • api.structure.ConfProblem.rst
        • javadoc.py
        • api.kstar.SequenceAnalyzer.rst
        • api.kstar.pfunc.BoltzmannCalculator.rst
        • api.kstar.KStar.ConfSearchFactory.rst
        • api.dof.deeper.DEEPerSettings.rst
        • api.confspace.compiled.ConfSpace.IndicesStatic.rst
        • api.energy.approximation.ApproximatedObjectiveFunction.Approximator.rst
        • api.kstar.MSKStar.State.rst
        • api.gmec.Comets.SequenceInfo.rst
        • api.paste.PastePartitionFunction.ConfListener.rst
        • api.sofea.Sofea.StateConfig.rst
        • api.confspace.RC.rst
        • api.restypes.ResidueTemplate.rst
        • api.parallelism.Parallelism.Type.rst
        • api.ematrix.EnergyMatrix.rst
        • api.paste.PastePartitionFunction.Values.rst
        • api.confspace.TupleTree.rst
        • api.paste.PastePartitionFunction.rst
        • api.dof.deeper.perts.PerturbationBlock.rst
        • api.confspace.MultiStateConfSpace.LMFE.rst
        • api.kstar.pfunc.PartitionFunction.rst
        • api.pruning.PruningControl.rst
        • api.minimization.ObjectiveFunction.DofBounds.rst
        • api.osprey.rst
        • api.kstar.MSKStar.WeightedState.rst
        • _templates
          • layout.html
        • api.kstar.MSKStar.SequenceInfo.rst
        • _static
          • style.css
        • api.confspace.ConfSearch.EnergiedConf.rst
        • api.confspace.TupleTree.Node.rst
        • api.restypes.InterResBondingTemplate.rst
        • api.energy.EnergyFunction.rst
        • api.lute.ConfSampler.Samples.rst
        • api.kstar.KStar.ConfSpaceType.rst
        • api.restypes.ResidueTemplateLibrary.rst
        • api.energy.MultiTermEnergyFunction.rst
        • api.confspace.SimpleConfSpace.rst
        • todoFix.py
        • api.confspace.SimpleConfSpace.DofTypes.rst
        • api.confspace.SeqSpace.Position.rst
        • api.kstar.pfunc.PartitionFunction.ConfListener.rst
        • api.energy.EnergyCalculator.EnergiedParametricMolecule.rst
      • osprey
        • wraps.py
        • __init__.py
        • jvm.py
    • .travis.yml
    • build.gradle.kts
    • CONTRIBUTING.rst
    • upload.sh
    • test-resources
      • 1GWC.shell.pdb
      • confSpaces
        • dipeptide.5hydrophobic.ccsx
        • 2RL0.G.ccsx
      • 1CC8.ss.pdb
      • probe
        • probe.c
      • gp120
        • all_nuc94_and_gr.in
        • GenericRotamers.dat
        • all_amino_coords.in
      • 4npd.A_DomainA_noH_trim_his_clean.min.pdb
      • 1gua_adj.min.pdb
      • 1CC8.CYX.pdb
      • 2RL0.min.reduce.pdb
    • .gitignore
    • LICENSE.txt
    • osprey3_todo.txt
    • settings.gradle.kts