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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