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__abstractmethods__ (in AppRunner)	__init__() (in HHProfileParser)	__package__ (in csb.test)
__abstractmethods__ (in Application)	__init__() (in DensityInfo)	__package__ (in csb.test.app)
__abstractmethods__ (in AppRunner)	__init__() (in DensityMapReader)	__reduce__() (in EnumItem)
__abstractmethods__ (in BFitApp)	__init__() (in HeaderInfo)	__repr__() (in Version)
__abstractmethods__ (in AppRunner)	__init__() (in SparkyPeakListReader)	__repr__() (in HHpredHit)
__abstractmethods__ (in BFitApp)	__init__() (in XeasyFileBuilder)	__repr__() (in HHpredHitList)
__abstractmethods__ (in AppRunner)	__init__() (in XeasyPeakListReader)	__repr__() (in State)
__abstractmethods__ (in BuildProfileApp)	__init__() (in ProcheckParser)	__repr__() (in TransitionType)
__abstractmethods__ (in FASTAProfileBuilder)	__init__() (in PSIPredResidueInfo)	__repr__() (in ClansEntry)
__abstractmethods__ (in PDBProfileBuilder)	__init__() (in SSCartoonBuilder)	__repr__() (in ClansSeqgroup)
__abstractmethods__ (in ProfileBuilder)	__init__() (in ChemicalShiftContainer)	__repr__() (in HHOutputParser)
__abstractmethods__ (in AppRunner)	__init__() (in ShiftInfo)	__repr__() (in AsyncParseResult)
__abstractmethods__ (in CSfragApp)	__init__() (in VascoStructureParser)	__repr__() (in AbstractSequence)
__abstractmethods__ (in AppRunner)	__init__() (in WhatCheckParser)	__repr__() (in ColumnInfo)
__abstractmethods__ (in DeconvolutionApp)	__init__() (in AbstractStructureParser)	__repr__() (in ResidueInfo)
__abstractmethods__ (in AppRunner)	__init__() (in AsyncParseResult)	__repr__() (in SequenceAdapter)
__abstractmethods__ (in HelloWorldApp)	__init__() (in AsyncStructureParser)	__repr__() (in Atom)
__abstractmethods__ (in AppRunner)	__init__() (in CustomStructureProvider)	__repr__() (in Chain)
__abstractmethods__ (in HHfragApp)	__init__() (in EntryID)	__repr__() (in ChainResiduesCollection)
__abstractmethods__ (in AppRunner)	__init__() (in FastResidueMapper)	__repr__() (in DisorderedAtom)
__abstractmethods__ (in HHsearchApp)	__init__() (in FileBuilder)	__repr__() (in Ensemble)
__abstractmethods__ (in AppRunner)	__init__() (in FileSystemStructureProvider)	__repr__() (in Residue)
__abstractmethods__ (in PrecisionApp)	__init__() (in RemoteStructureProvider)	__repr__() (in ResidueAtomsTable)
__abstractmethods__ (in AppRunner)	__init__() (in ResidueInfo)	__repr__() (in SecondaryStructureElement)
__abstractmethods__ (in ProMixApp)	__init__() (in RobustResidueMapper)	__repr__() (in Structure)
__abstractmethods__ (in Target)	__init__() (in AtomConnectivity)	__repr__() (in StructureChainsTable)
__abstractmethods__ (in RosettaFragmentMap)	__init__() (in ChemShiftInfo)	__repr__() (in TorsionAngles)
__abstractmethods__ (in ClansFileBuilder)	__init__() (in ChemShiftScoringModel)	__repr__() (in TorsionAnglesCollection)
__abstractmethods__ (in ClansFileWriter)	__init__() (in ChemicalShiftNetwork)	__repr__() (in BaseCollectionContainer)
__abstractmethods__ (in A3MOutputBuilder)	__init__() (in ContactMap)	__repr__() (in BaseDictionaryContainer)
__abstractmethods__ (in BaseSequenceParser)	__init__() (in ContactMapComparisonInfo)	__repr__() (in EnumItem)
__abstractmethods__ (in FASTAOutputBuilder)	__init__() (in Label)	__repr__() (in EnumMeta)
__abstractmethods__ (in OutputBuilder)	__init__() (in NOEPeak)	__repr__() (in DataRow)
__abstractmethods__ (in PIROutputBuilder)	__init__() (in NOESpectrum)	__rmul__() (in InvertibleMatrix)
__abstractmethods__ (in SequenceParser)	__init__() (in RandomCoil)	__set__() (in typedproperty)
__abstractmethods__ (in BasePeakListReader)	__init__() (in A3MAlignment)	__set__() (in validatedproperty)
__abstractmethods__ (in SparkyPeakListReader)	__init__() (in AbstractAlignment)	__setattr__() (in EnumMeta)
__abstractmethods__ (in XeasyPeakListReader)	__init__() (in AbstractSequence)	__setitem__() (in Clans)
__abstractmethods__ (in AbstractResidueMapper)	__init__() (in AlignedSequenceAdapter)	__setitem__() (in Table)
__abstractmethods__ (in AbstractStructureParser)	__init__() (in AlignmentRowsTable)	__setitem__() (in InvertibleMatrix)
__abstractmethods__ (in CombinedResidueMapper)	__init__() (in ColumnInfo)	__setitem__() (in AbstractDensity)
__abstractmethods__ (in CustomStructureProvider)	__init__() (in PositionError)	__setstate__() (in Table)
__abstractmethods__ (in DegenerateID)	__init__() (in ResidueInfo)	__str__() (in Version)
__abstractmethods__ (in EntryID)	__init__() (in Sequence)	__str__() (in MatchInfo)
__abstractmethods__ (in FastResidueMapper)	__init__() (in SequenceAdapter)	__str__() (in GlobalInfo)
__abstractmethods__ (in FileBuilder)	__init__() (in SequenceCollection)	__str__() (in TorsionPredictionInfo)
__abstractmethods__ (in FileSystemStructureProvider)	__init__() (in SequenceIndexer)	__str__() (in RosettaFragment)
__abstractmethods__ (in LegacyStructureParser)	__init__() (in SliceHelper)	__str__() (in HHpredHit)
__abstractmethods__ (in PDBFileBuilder)	__init__() (in AbstractAlignmentAlgorithm)	__str__() (in HHpredHitList)
__abstractmethods__ (in RegularStructureParser)	__init__() (in AlignmentResult)	__str__() (in Transition)
__abstractmethods__ (in RemoteStructureProvider)	__init__() (in GlobalAlignmentAlgorithm)	__str__() (in Clans)
__abstractmethods__ (in RobustResidueMapper)	__init__() (in IdentityMatrix)	__str__() (in ClansParser)
__abstractmethods__ (in SeqResID)	__init__() (in LocalAlignmentAlgorithm)	__str__() (in Color)
__abstractmethods__ (in StandardID)	__init__() (in SimilarityMatrix)	__str__() (in ShiftInfo)
__abstractmethods__ (in StructureProvider)	__init__() (in Atom)	__str__() (in EntryID)
__abstractmethods__ (in A3MAlignment)	__init__() (in Chain)	__str__() (in ChemShiftInfo)
__abstractmethods__ (in AbstractAlignment)	__init__() (in ChainResiduesCollection)	__str__() (in Label)
__abstractmethods__ (in AbstractSequence)	__init__() (in CompositeEntityIterator)	__str__() (in NOEPeak)
__abstractmethods__ (in ChainSequence)	__init__() (in ConfinedEntityIterator)	__str__() (in NOESpectrum)
__abstractmethods__ (in RichSequence)	__init__() (in DisorderedAtom)	__str__() (in AbstractSequence)
__abstractmethods__ (in Sequence)	__init__() (in Ensemble)	__str__() (in PositionError)
__abstractmethods__ (in SequenceAlignment)	__init__() (in EnsembleModelsCollection)	__str__() (in SequenceAdapter)
__abstractmethods__ (in StructureAlignment)	__init__() (in NucleicResidue)	__str__() (in AlignmentResult)
__abstractmethods__ (in AbstractAlignmentAlgorithm)	__init__() (in ProteinResidue)	__str__() (in SecondaryStructure)
__abstractmethods__ (in AbstractScoringMatrix)	__init__() (in Residue)	__str__() (in SecondaryStructureElement)
__abstractmethods__ (in GlobalAlignmentAlgorithm)	__init__() (in ResidueAtomsTable)	__str__() (in EnumItem)
__abstractmethods__ (in IdentityMatrix)	__init__() (in SecondaryStructure)	__str__() (in EnumMeta)
__abstractmethods__ (in LocalAlignmentAlgorithm)	__init__() (in SecondaryStructureElement)	__str__() (in InvalidCommandError)
__abstractmethods__ (in SimilarityMatrix)	__init__() (in Structure)	__str__() (in ProcessError)
__abstractmethods__ (in AbstractEntity)	__init__() (in StructureChainsTable)	__str__() (in TimeoutError)
__abstractmethods__ (in Atom)	__init__() (in SuperimposeInfo)	__str__() (in ColumnInfo)
__abstractmethods__ (in Chain)	__init__() (in TorsionAngles)	__str__() (in DataRow)
__abstractmethods__ (in Ensemble)	__init__() (in TorsionAnglesCollection)	__str__() (in Predicate)
__abstractmethods__ (in Residue)	__init__() (in UnknownResidue)	__str__() (in InvertibleMatrix)
__abstractmethods__ (in Structure)	__init__() (in Console)	__str__() (in AbstractDensity)
__abstractmethods__ (in AbstractContainer)	__init__() (in GitHandler)	__str__() (in ParameterValueError)
__abstractmethods__ (in Container)	__init__() (in MercurialHandler)	__sub__() (in GlobalInfo)
__abstractmethods__ (in Backend)	__init__() (in RevisionError)	__truediv__() (in InvertibleMatrix)
__abstractmethods__ (in WxBackendImpl)	__init__() (in RevisionHandler)	_abc_cache (in AppRunner)
__abstractmethods__ (in Between)	__init__() (in RevisionInfo)	_abc_cache (in Application)
__abstractmethods__ (in Equals)	__init__() (in SubversionHandler)	_abc_cache (in ProfileBuilder)
__abstractmethods__ (in Greater)	__init__() (in BaseCollectionContainer)	_abc_cache (in ClansFileBuilder)
__abstractmethods__ (in GreaterOrEquals)	__init__() (in BaseDictionaryContainer)	_abc_cache (in A3MOutputBuilder)
__abstractmethods__ (in In)	__init__() (in CollectionContainer)	_abc_cache (in BaseSequenceParser)
__abstractmethods__ (in Lower)	__init__() (in Container)	_abc_cache (in FASTAOutputBuilder)
__abstractmethods__ (in LowerOrEquals)	__init__() (in DictionaryContainer)	_abc_cache (in OutputBuilder)
__abstractmethods__ (in NotEquals)	__init__() (in EnumItem)	_abc_cache (in PIROutputBuilder)
__abstractmethods__ (in NotIn)	__init__() (in InterruptibleThread)	_abc_cache (in BasePeakListReader)
__abstractmethods__ (in Predicate)	__init__() (in Proxy)	_abc_cache (in AbstractResidueMapper)
__abstractmethods__ (in RepositoryImp)	__init__() (in REMatchProxy)	_abc_cache (in AbstractStructureParser)
__abstractmethods__ (in SQLiteRepository)	__init__() (in enum)	_abc_cache (in EntryID)
__abstractmethods__ (in AbstractGradient)	__init__() (in typedproperty)	_abc_cache (in FileBuilder)
__abstractmethods__ (in AbstractIntegrator)	__init__() (in validatedproperty)	_abc_cache (in StructureProvider)
__abstractmethods__ (in LeapFrog)	__init__() (in AutoFlushStream)	_abc_cache (in AbstractAlignment)
__abstractmethods__ (in VelocityVerlet)	__init__() (in EntryReader)	_abc_cache (in AbstractSequence)
__abstractmethods__ (in MaxentModel)	__init__() (in EntryWriter)	_abc_cache (in AbstractAlignmentAlgorithm)
__abstractmethods__ (in AbstractStructureMixture)	__init__() (in InvalidCommandError)	_abc_cache (in AbstractScoringMatrix)
__abstractmethods__ (in ConformerMixture)	__init__() (in ProcessError)	_abc_cache (in IdentityMatrix)
__abstractmethods__ (in SegmentMixture)	__init__() (in ShellInfo)	_abc_cache (in SimilarityMatrix)
__abstractmethods__ (in AbstractDensity)	__init__() (in TempFile)	_abc_cache (in AbstractEntity)
__abstractmethods__ (in AbstractEstimator)	__init__() (in TempFolder)	_abc_cache (in AbstractContainer)
__abstractmethods__ (in Dirichlet)	__init__() (in TimeoutError)	_abc_cache (in Backend)
__abstractmethods__ (in DirichletEstimator)	__init__() (in Backend)	_abc_cache (in Predicate)
__abstractmethods__ (in Gamma)	__init__() (in Chart)	_abc_cache (in RepositoryImp)
__abstractmethods__ (in GammaMLEstimator)	__init__() (in PlotsCollection)	_abc_cache (in AbstractGradient)
__abstractmethods__ (in GaussianMLEstimator)	__init__() (in WxBackendImpl)	_abc_cache (in AbstractIntegrator)
__abstractmethods__ (in GenNormalBruteForceEstimator)	__init__() (in Between)	_abc_cache (in AbstractStructureMixture)
__abstractmethods__ (in GeneralizedInverseGaussian)	__init__() (in ColumnInfo)	_abc_cache (in AbstractDensity)
__abstractmethods__ (in GeneralizedNormal)	__init__() (in DataRow)	_abc_cache (in AbstractEstimator)
__abstractmethods__ (in GumbelMaxMomentsEstimator)	__init__() (in Expression)	_abc_cache (in AbstractSampler)
__abstractmethods__ (in GumbelMinMomentsEstimator)	__init__() (in Operator)	_abc_cache (in AbstractState)
__abstractmethods__ (in GumbelMinimum)	__init__() (in Predicate)	_abc_cache (in AbstractPropagationResult)
__abstractmethods__ (in InverseGamma)	__init__() (in RepositoryImp)	_abc_cache (in AbstractSwapCommunicator)
__abstractmethods__ (in InverseGaussian)	__init__() (in ChunkedReader)	_abc_cache (in AbstractSwapParameterInfo)
__abstractmethods__ (in InverseGaussianMLEstimator)	__init__() (in SQLiteRepository)	_abc_cache (in AbstractSwapScheme)
__abstractmethods__ (in Laplace)	__init__() (in Step)	_abc_cache (in AbstractPerturbation)
__abstractmethods__ (in LaplaceMLEstimator)	__init__() (in Table)	_abc_cache (in AbstractPropagation)
__abstractmethods__ (in MultivariateGaussianMLEstimator)	__init__() (in Where)	_abc_cache (in AbstractPropagator)
__abstractmethods__ (in Normal)	__init__() (in InvertibleMatrix)	_abc_cache (in SimpleProposalCommunicator)
__abstractmethods__ (in NullEstimator)	__init__() (in AbstractIntegrator)	_abc_cache (in StatisticalEnsemble)
__abstractmethods__ (in AbstractSampler)	__init__() (in Cumulative)	_abc_cache (in AbstractWHAM)
__abstractmethods__ (in AbstractState)	__init__() (in ARS)	_abc_cache (in AbstractTestBuilder)
__abstractmethods__ (in EnsembleState)	__init__() (in Envelope)	_abc_invalidation_counter (in ABCMeta)
__abstractmethods__ (in State)	__init__() (in Gauss)	_abc_negative_cache (in AppRunner)
__abstractmethods__ (in AbstractMC)	__init__() (in MaxentModel)	_abc_negative_cache (in Application)
__abstractmethods__ (in AbstractPropagationResult)	__init__() (in MaxentPosterior)	_abc_negative_cache (in ProfileBuilder)
__abstractmethods__ (in PropagationResult)	__init__() (in AbstractStructureMixture)	_abc_negative_cache (in ClansFileBuilder)
__abstractmethods__ (in Trajectory)	__init__() (in GaussianMixture)	_abc_negative_cache (in BaseSequenceParser)
__abstractmethods__ (in AbstractEnsembleMC)	__init__() (in AbstractDensity)	_abc_negative_cache (in OutputBuilder)
__abstractmethods__ (in AbstractExchangeMC)	__init__() (in Dirichlet)	_abc_negative_cache (in BasePeakListReader)
__abstractmethods__ (in AbstractRENS)	__init__() (in DirichletEstimator)	_abc_negative_cache (in AbstractResidueMapper)
__abstractmethods__ (in AbstractStepRENS)	__init__() (in Gamma)	_abc_negative_cache (in AbstractStructureParser)
__abstractmethods__ (in AbstractSwapCommunicator)	__init__() (in GammaMLEstimator)	_abc_negative_cache (in EntryID)
__abstractmethods__ (in AbstractSwapParameterInfo)	__init__() (in GenNormalBruteForceEstimator)	_abc_negative_cache (in FileBuilder)
__abstractmethods__ (in AbstractSwapScheme)	__init__() (in GeneralizedInverseGaussian)	_abc_negative_cache (in StructureProvider)
__abstractmethods__ (in AlternatingAdjacentSwapScheme)	__init__() (in GeneralizedNormal)	_abc_negative_cache (in AbstractAlignment)
__abstractmethods__ (in Gradient)	__init__() (in GumbelMaximum)	_abc_negative_cache (in AbstractSequence)
__abstractmethods__ (in HMCStepRENS)	__init__() (in GumbelMinimum)	_abc_negative_cache (in AbstractAlignmentAlgorithm)
__abstractmethods__ (in MDRENS)	__init__() (in InverseGamma)	_abc_negative_cache (in AbstractScoringMatrix)
__abstractmethods__ (in ReplicaExchangeMC)	__init__() (in InverseGaussian)	_abc_negative_cache (in AbstractEntity)
__abstractmethods__ (in AbstractMCPropagation)	__init__() (in Laplace)	_abc_negative_cache (in AbstractContainer)
__abstractmethods__ (in AbstractMDPropagation)	__init__() (in MultivariateGaussian)	_abc_negative_cache (in Backend)
__abstractmethods__ (in AbstractPerturbation)	__init__() (in MultivariateGaussianMLEstimator)	_abc_negative_cache (in Predicate)
__abstractmethods__ (in AbstractPropagation)	__init__() (in Normal)	_abc_negative_cache (in RepositoryImp)
__abstractmethods__ (in HMCPropagation)	__init__() (in ParameterValueError)	_abc_negative_cache (in AbstractGradient)
__abstractmethods__ (in NonequilibriumStepPropagator)	__init__() (in AbstractParameter)	_abc_negative_cache (in AbstractIntegrator)
__abstractmethods__ (in PlainMDPropagation)	__init__() (in Parameter)	_abc_negative_cache (in AbstractStructureMixture)
__abstractmethods__ (in ReducedHamiltonianPerturbation)	__init__() (in EnsembleState)	_abc_negative_cache (in AbstractDensity)
__abstractmethods__ (in AbstractMCPropagator)	__init__() (in State)	_abc_negative_cache (in AbstractEstimator)
__abstractmethods__ (in AbstractPropagator)	__init__() (in AbstractMC)	_abc_negative_cache (in AbstractSampler)
__abstractmethods__ (in HMCPropagator)	__init__() (in MCCollection)	_abc_negative_cache (in AbstractState)
__abstractmethods__ (in MDPropagator)	__init__() (in PropagationResult)	_abc_negative_cache (in AbstractPropagationResult)
__abstractmethods__ (in RWMCPropagator)	__init__() (in Trajectory)	_abc_negative_cache (in AbstractSwapCommunicator)
__abstractmethods__ (in AbstractNCMCSampler)	__init__() (in TrajectoryBuilder)	_abc_negative_cache (in AbstractSwapParameterInfo)
__abstractmethods__ (in AbstractSingleChainMC)	__init__() (in AbstractEnsembleMC)	_abc_negative_cache (in AbstractSwapScheme)
__abstractmethods__ (in HMCSampler)	__init__() (in AbstractExchangeMC)	_abc_negative_cache (in AbstractPerturbation)
__abstractmethods__ (in RWMCSampler)	__init__() (in AbstractRENSSwapParameterInfo)	_abc_negative_cache (in AbstractPropagation)
__abstractmethods__ (in SimpleProposalCommunicator)	__init__() (in AbstractStepRENS)	_abc_negative_cache (in AbstractPropagator)
__abstractmethods__ (in GammaPosteriorMAP)	__init__() (in AbstractSwapCommunicator)	_abc_negative_cache (in SimpleProposalCommunicator)
__abstractmethods__ (in GammaPosteriorSampler)	__init__() (in AbstractSwapParameterInfo)	_abc_negative_cache (in StatisticalEnsemble)
__abstractmethods__ (in GammaScaleMAP)	__init__() (in AbstractSwapScheme)	_abc_negative_cache (in AbstractWHAM)
__abstractmethods__ (in GammaScaleSampler)	__init__() (in AlternatingAdjacentSwapScheme)	_abc_negative_cache (in AbstractTestBuilder)
__abstractmethods__ (in InvGammaPosteriorMAP)	__init__() (in Gradient)	_abc_negative_cache_version (in AppRunner)
__abstractmethods__ (in InvGammaPosteriorSampler)	__init__() (in HMCStepRENS)	_abc_negative_cache_version (in Application)
__abstractmethods__ (in InvGammaScaleMAP)	__init__() (in HMCStepRENSSwapParameterInfo)	_abc_negative_cache_version (in AppRunner)
__abstractmethods__ (in InvGammaScaleSampler)	__init__() (in InterpolationFactory)	_abc_negative_cache_version (in BFitApp)
__abstractmethods__ (in ScaleMixture)	__init__() (in MDRENS)	_abc_negative_cache_version (in AppRunner)
__abstractmethods__ (in ScaleMixturePriorEstimator)	__init__() (in MDRENSSwapParameterInfo)	_abc_negative_cache_version (in BFitApp)
__abstractmethods__ (in BoltzmannEnsemble)	__init__() (in RENSTrajInfo)	_abc_negative_cache_version (in AppRunner)
__abstractmethods__ (in CompositeEnsemble)	__init__() (in ReplicaHistory)	_abc_negative_cache_version (in BuildProfileApp)
__abstractmethods__ (in StatisticalEnsemble)	__init__() (in SingleSwapStatistics)	_abc_negative_cache_version (in ProfileBuilder)
__abstractmethods__ (in TsallisEnsemble)	__init__() (in SwapStatistics)	_abc_negative_cache_version (in AppRunner)
__abstractmethods__ (in AbstractWHAM)	__init__() (in ThermostattedMDRENS)	_abc_negative_cache_version (in CSfragApp)
__abstractmethods__ (in NonparametricWHAM)	__init__() (in ThermostattedMDRENSSwapParameterInfo)	_abc_negative_cache_version (in AppRunner)
__abstractmethods__ (in WHAM)	__init__() (in AbstractHeatWorkJacobianLogger)	_abc_negative_cache_version (in DeconvolutionApp)
__abstractmethods__ (in AbstractTestBuilder)	__init__() (in AbstractMCPropagation)	_abc_negative_cache_version (in AppRunner)
__abstractmethods__ (in AnyTestBuilder)	__init__() (in AbstractMDPropagation)	_abc_negative_cache_version (in HHfragApp)
__abstractmethods__ (in CustomTestBuilder)	__init__() (in AbstractPerturbation)	_abc_negative_cache_version (in AppRunner)
__abstractmethods__ (in FunctionalTestBuilder)	__init__() (in AbstractPropagation)	_abc_negative_cache_version (in HHsearchApp)
__abstractmethods__ (in RegressionTestBuilder)	__init__() (in HMCPropagation)	_abc_negative_cache_version (in AppRunner)
__abstractmethods__ (in UnitTestBuilder)	__init__() (in HMCPropagationParam)	_abc_negative_cache_version (in PrecisionApp)
__array__() (in Table)	__init__() (in HamiltonianSysInfo)	_abc_negative_cache_version (in AppRunner)
__array__() (in InvertibleMatrix)	__init__() (in MDParam)	_abc_negative_cache_version (in ProMixApp)
__bool__() (in EVDParameters)	__init__() (in NonequilibriumStepPropagator)	_abc_negative_cache_version (in Target)
__bool__() (in TorsionAngles)	__init__() (in NonequilibriumTrajectory)	_abc_negative_cache_version (in RosettaFragmentMap)
__bool__() (in BaseCollectionContainer)	__init__() (in PerturbationResult)	_abc_negative_cache_version (in ClansFileBuilder)
__bool__() (in BaseDictionaryContainer)	__init__() (in PlainMDPropagation)	_abc_negative_cache_version (in BaseSequenceParser)
__call__() (in typedproperty)	__init__() (in PlainMDPropagationParam)	_abc_negative_cache_version (in OutputBuilder)
__call__() (in AbstractGradient)	__init__() (in Protocol)	_abc_negative_cache_version (in BasePeakListReader)
__call__() (in Cumulative)	__init__() (in ReducedHamiltonian)	_abc_negative_cache_version (in AbstractResidueMapper)
__call__() (in Gauss)	__init__() (in ReducedHamiltonianPerturbation)	_abc_negative_cache_version (in AbstractStructureParser)
__call__() (in LogProb)	__init__() (in Step)	_abc_negative_cache_version (in EntryID)
__call__() (in MaxentPosterior)	__init__() (in AbstractMCPropagator)	_abc_negative_cache_version (in FileBuilder)
__call__() (in AbstractDensity)	__init__() (in AbstractNCMCPropagator)	_abc_negative_cache_version (in StructureProvider)
__call__() (in AbstractPerturbation)	__init__() (in HMCPropagator)	_abc_negative_cache_version (in AbstractAlignment)
__call__() (in AbstractPropagation)	__init__() (in Looper)	_abc_negative_cache_version (in AbstractSequence)
__call__() (in ReducedHamiltonian)	__init__() (in MDPropagator)	_abc_negative_cache_version (in AbstractAlignmentAlgorithm)
__call__() (in ARSPosteriorAlpha)	__init__() (in RWMCPropagator)	_abc_negative_cache_version (in AbstractScoringMatrix)
__call__() (in StatisticalEnsemble)	__init__() (in ThermostattedMDPropagator)	_abc_negative_cache_version (in AbstractEntity)
__cmp__() (in MatchInfo)	__init__() (in AbstractNCMCSampler)	_abc_negative_cache_version (in Chain)
__contains__() (in ContactMap)	__init__() (in AbstractSingleChainMC)	_abc_negative_cache_version (in Ensemble)
__contains__() (in BaseCollectionContainer)	__init__() (in HMCSampler)	_abc_negative_cache_version (in Residue)
__contains__() (in BaseDictionaryContainer)	__init__() (in NCMCProposalCommunicator)	_abc_negative_cache_version (in Structure)
__contains__() (in EnumMeta)	__init__() (in RWMCSampler)	_abc_negative_cache_version (in AbstractContainer)
__copy__() (in EnumItem)	__init__() (in SimpleProposalCommunicator)	_abc_negative_cache_version (in Backend)
__deepcopy__() (in EnumItem)	__init__() (in ARSPosteriorAlpha)	_abc_negative_cache_version (in Predicate)
__del__() (in LibrarySuperimposer)	__init__() (in GammaPosteriorMAP)	_abc_negative_cache_version (in RepositoryImp)
__del__() (in AbstractStructureParser)	__init__() (in GammaPosteriorSampler)	_abc_negative_cache_version (in AbstractGradient)
__del__() (in EntryReader)	__init__() (in GammaPrior)	_abc_negative_cache_version (in AbstractIntegrator)
__del__() (in EntryWriter)	__init__() (in InvGammaPosteriorMAP)	_abc_negative_cache_version (in AbstractStructureMixture)
__del__() (in TempFile)	__init__() (in InvGammaPosteriorSampler)	_abc_negative_cache_version (in AbstractDensity)
__del__() (in TempFolder)	__init__() (in InvGammaPrior)	_abc_negative_cache_version (in AbstractEstimator)
__del__() (in Backend)	__init__() (in ScaleMixture)	_abc_negative_cache_version (in AbstractSampler)
__del__() (in Table)	__init__() (in ScaleMixturePrior)	_abc_negative_cache_version (in AbstractState)
__enter__() (in Connection)	__init__() (in BoltzmannEnsemble)	_abc_negative_cache_version (in AbstractPropagationResult)
__enter__() (in EntryWriter)	__init__() (in CompositeEnsemble)	_abc_negative_cache_version (in AbstractSwapCommunicator)
__enter__() (in MemoryStream)	__init__() (in FermiEnsemble)	_abc_negative_cache_version (in AbstractSwapParameterInfo)
__enter__() (in TempFile)	__init__() (in TsallisEnsemble)	_abc_negative_cache_version (in AbstractSwapScheme)
__enter__() (in TempFolder)	__init__() (in AbstractWHAM)	_abc_negative_cache_version (in AbstractPerturbation)
__enter__() (in Chart)	__init__() (in WHAM)	_abc_negative_cache_version (in AbstractPropagation)
__eq__() (in SecondaryStructureElement)	__init__() (in Console)	_abc_negative_cache_version (in AbstractPropagator)
__eq__() (in EnumItem)	__int__() (in EnumItem)	_abc_negative_cache_version (in SimpleProposalCommunicator)
__eq__() (in InvertibleMatrix)	__iter__() (in MatchTable)	_abc_negative_cache_version (in StatisticalEnsemble)
__eq__() (in State)	__iter__() (in RosettaFragment)	_abc_negative_cache_version (in AbstractWHAM)
__exit__() (in Connection)	__iter__() (in HHpredHitList)	_abc_negative_cache_version (in AbstractTestBuilder)
__exit__() (in EntryWriter)	__iter__() (in A3MSequenceIterator)	_abc_registry (in AppRunner)
__exit__() (in MemoryStream)	__iter__() (in HeaderInfo)	_abc_registry (in Application)
__exit__() (in TempFile)	__iter__() (in ChemicalShiftNetwork)	_abc_registry (in ProfileBuilder)
__exit__() (in TempFolder)	__iter__() (in ContactMap)	_abc_registry (in ClansFileBuilder)
__exit__() (in Chart)	__iter__() (in NOEPeak)	_abc_registry (in BaseSequenceParser)
__float__() (in EnumItem)	__iter__() (in NOESpectrum)	_abc_registry (in OutputBuilder)
__get__() (in typedproperty)	__iter__() (in AbstractAlignment)	_abc_registry (in BasePeakListReader)
__get__() (in validatedproperty)	__iter__() (in AbstractSequence)	_abc_registry (in AbstractResidueMapper)
__getattr__() (in DisorderedAtom)	__iter__() (in AlignedSequenceAdapter)	_abc_registry (in AbstractStructureParser)
__getattr__() (in Proxy)	__iter__() (in AlignmentRowsTable)	_abc_registry (in EntryID)
__getitem__() (in MatchTable)	__iter__() (in SequenceAdapter)	_abc_registry (in FileBuilder)
__getitem__() (in HHpredHitList)	__iter__() (in SequenceIndexer)	_abc_registry (in StructureProvider)
__getitem__() (in Clans)	__iter__() (in UngappedSequenceIndexer)	_abc_registry (in AbstractAlignment)
__getitem__() (in HeaderInfo)	__iter__() (in CompositeEntityIterator)	_abc_registry (in AbstractSequence)
__getitem__() (in StructureProvider)	__iter__() (in AbstractContainer)	_abc_registry (in AbstractAlignmentAlgorithm)
__getitem__() (in NOEPeak)	__iter__() (in BaseCollectionContainer)	_abc_registry (in AbstractScoringMatrix)
__getitem__() (in NOESpectrum)	__iter__() (in BaseDictionaryContainer)	_abc_registry (in AbstractEntity)
__getitem__() (in AbstractAlignment)	__iter__() (in EnumMeta)	_abc_registry (in AbstractContainer)
__getitem__() (in AbstractSequence)	__iter__() (in PlotsCollection)	_abc_registry (in Backend)
__getitem__() (in AlignedSequenceAdapter)	__iter__() (in DataRow)	_abc_registry (in Predicate)
__getitem__() (in AlignmentRowsTable)	__iter__() (in ChunkedReader)	_abc_registry (in RepositoryImp)
__getitem__() (in ColumnIndexer)	__iter__() (in Table)	_abc_registry (in AbstractGradient)
__getitem__() (in SequenceAdapter)	__iter__() (in PropagationResult)	_abc_registry (in AbstractIntegrator)
__getitem__() (in SequenceIndexer)	__iter__() (in Looper)	_abc_registry (in AbstractStructureMixture)
__getitem__() (in UngappedSequenceIndexer)	__itruediv__() (in InvertibleMatrix)	_abc_registry (in AbstractDensity)
__getitem__() (in AbstractContainer)	__len__() (in RosettaFragment)	_abc_registry (in AbstractEstimator)
__getitem__() (in AbstractIndexer)	__len__() (in RosettaFragmentMap)	_abc_registry (in AbstractSampler)
__getitem__() (in AbstractNIContainer)	__len__() (in HHpredHitList)	_abc_registry (in AbstractState)
__getitem__() (in BaseCollectionContainer)	__len__() (in Clans)	_abc_registry (in AbstractPropagationResult)
__getitem__() (in BaseDictionaryContainer)	__len__() (in ClansSeqgroup)	_abc_registry (in AbstractSwapCommunicator)
__getitem__() (in Chart)	__len__() (in NOESpectrum)	_abc_registry (in AbstractSwapParameterInfo)
__getitem__() (in PlotsCollection)	__len__() (in AbstractSequence)	_abc_registry (in AbstractSwapScheme)
__getitem__() (in DataRow)	__len__() (in Chain)	_abc_registry (in AbstractPerturbation)
__getitem__() (in Table)	__len__() (in AbstractContainer)	_abc_registry (in AbstractPropagation)
__getitem__() (in InvertibleMatrix)	__len__() (in BaseCollectionContainer)	_abc_registry (in AbstractPropagator)
__getitem__() (in AbstractDensity)	__len__() (in BaseDictionaryContainer)	_abc_registry (in SimpleProposalCommunicator)
__getstate__() (in Table)	__len__() (in PlotsCollection)	_abc_registry (in StatisticalEnsemble)
__hash__() (in EnumItem)	__len__() (in DataRow)	_abc_registry (in AbstractWHAM)
__imul__() (in InvertibleMatrix)	__len__() (in Table)	_abc_registry (in AbstractTestBuilder)
__init__() (in Version)	__len__() (in InvertibleMatrix)	_axis (in ConformerMixture)
__init__() (in AppExit)	__lt__() (in SliceContext)	_axis (in GaussianMixture)
__init__() (in AppRunner)	__lt__() (in TorsionPredictionInfo)	_axis (in SegmentMixture)
__init__() (in Application)	__lt__() (in RosettaFragment)	_DEFAULTS (in ClansParams)
__init__() (in ArgHandler)	__lt__() (in HHpredHit)	_du (in BuildTypes)
__init__() (in NoOutputError)	__lt__() (in Atom)	_instance (in AtomConnectivity)
__init__() (in ProfileBuilder)	__lt__() (in SecondaryStructureElement)	_instance (in RandomCoil)
__init__() (in CSfrag)	__lt__() (in EnumItem)	_instances (in Backend)
__init__() (in MatchInfo)	__ne__() (in EnumItem)	_name (in ScoreUnits)
__init__() (in MatchTable)	__new__() (in EnumMeta)	_name (in States)
__init__() (in ScoringHelper)	__next__() (in A3MSequenceIterator)	_name (in AlignmentFormats)
__init__() (in Deconvolution)	__next__() (in CompositeEntityIterator)	_name (in AlignmentTypes)
__init__() (in OutputPathBuilder)	__nonzero__() (in EVDParameters)	_name (in NucleicAlphabet)
__init__() (in HHfrag)	__nonzero__() (in TorsionAngles)	_name (in ProteinAlphabet)
__init__() (in PredictionBuilder)	__nonzero__() (in AbstractContainer)	_name (in SequenceTypes)
__init__() (in SliceContext)	__nonzero__() (in BaseCollectionContainer)	_name (in StdProteinAlphabet)
__init__() (in Context)	__nonzero__() (in BaseDictionaryContainer)	_name (in UnknownAlphabet)
__init__() (in HHTask)	__package__ (in csb)	_name (in AngleUnits)
__init__() (in HHsearch)	__package__ (in csb.apps)	_name (in ChemElements)
__init__() (in GlobalInfo)	__package__ (in csb.apps.bfit)	_name (in SecStructures)
__init__() (in LibrarySuperimposer)	__package__ (in csb.apps.bfite)	_name (in EnumBase)
__init__() (in Assignment)	__package__ (in csb.apps.buildhmm)	_name (in enum)
__init__() (in Connection)	__package__ (in csb.apps.csfrag)	_names (in ScoreUnits)
__init__() (in BenchmarkAdapter)	__package__ (in csb.apps.embd)	_names (in States)
__init__() (in ChemShiftAssignment)	__package__ (in csb.apps.helloworld)	_names (in AlignmentFormats)
__init__() (in ChemShiftTarget)	__package__ (in csb.apps.hhfrag)	_names (in AlignmentTypes)
__init__() (in ClusterNode)	__package__ (in csb.apps.hhsearch)	_names (in NucleicAlphabet)
__init__() (in ClusterRep)	__package__ (in csb.apps.precision)	_names (in ProteinAlphabet)
__init__() (in FragmentCluster)	__package__ (in csb.apps.promix)	_names (in SequenceTypes)
__init__() (in FragmentMatch)	__package__ (in csb.bio)	_names (in StdProteinAlphabet)
__init__() (in ResidueAssignmentInfo)	__package__ (in csb.bio.fragments)	_names (in UnknownAlphabet)
__init__() (in ResidueEventInfo)	__package__ (in csb.bio.fragments.rosetta)	_names (in AngleUnits)
__init__() (in RosettaFragsetFactory)	__package__ (in csb.bio.hmm)	_names (in ChemElements)
__init__() (in Target)	__package__ (in csb.bio.hmm.pseudocounts)	_names (in SecStructures)
__init__() (in TargetResidue)	__package__ (in csb.bio.io)	_names (in EnumBase)
__init__() (in TorsionAnglePredictor)	__package__ (in csb.bio.io.clans)	_namesci (in ScoreUnits)
__init__() (in TorsionPredictionInfo)	__package__ (in csb.bio.io.cs)	_namesci (in States)
__init__() (in OutputBuilder)	__package__ (in csb.bio.io.dssp)	_namesci (in AlignmentFormats)
__init__() (in ResidueInfo)	__package__ (in csb.bio.io.fasta)	_namesci (in AlignmentTypes)
__init__() (in RosettaFragment)	__package__ (in csb.bio.io.hhpred)	_namesci (in NucleicAlphabet)
__init__() (in RosettaFragmentMap)	__package__ (in csb.bio.io.mrc)	_namesci (in ProteinAlphabet)
__init__() (in EVDParameters)	__package__ (in csb.bio.io.noe)	_namesci (in SequenceTypes)
__init__() (in EmissionTable)	__package__ (in csb.bio.io.procheck)	_namesci (in StdProteinAlphabet)
__init__() (in HHpredHit)	__package__ (in csb.bio.io.psipred)	_namesci (in UnknownAlphabet)
__init__() (in HHpredHitAlignment)	__package__ (in csb.bio.io.svg)	_namesci (in AngleUnits)
__init__() (in HHpredHitList)	__package__ (in csb.bio.io.vasco)	_namesci (in ChemElements)
__init__() (in HMMLayer)	__package__ (in csb.bio.io.whatif)	_namesci (in SecStructures)
__init__() (in HMMLayersCollection)	__package__ (in csb.bio.io.wwpdb)	_namesci (in EnumBase)
__init__() (in ProfileHMM)	__package__ (in csb.bio.nmr)	_registry (in OutputBuilder)
__init__() (in ProfileHMMRegion)	__package__ (in csb.bio.sequence)	_serial (in Chart)
__init__() (in ProfileHMMSegment)	__package__ (in csb.bio.sequence.alignment)	_values (in ScoreUnits)
__init__() (in ProfileLength)	__package__ (in csb.bio.structure)	_values (in States)
__init__() (in State)	__package__ (in csb.bio.utils)	_values (in AlignmentFormats)
__init__() (in StateFactory)	__package__ (in csb.build)	_values (in AlignmentTypes)
__init__() (in Transition)	__package__ (in csb.core)	_values (in NucleicAlphabet)
__init__() (in TransitionTable)	__package__ (in csb.io)	_values (in ProteinAlphabet)
__init__() (in TransitionType)	__package__ (in csb.io.plots)	_values (in SequenceTypes)
__init__() (in PseudocountBuilder)	__package__ (in csb.io.tsv)	_values (in StdProteinAlphabet)
__init__() (in Clans)	__package__ (in csb.numeric)	_values (in UnknownAlphabet)
__init__() (in ClansEntry)	__package__ (in csb.numeric.integrators)	_values (in AngleUnits)
__init__() (in ClansEntryCollection)	__package__ (in csb.statistics)	_values (in ChemElements)
__init__() (in ClansFileBuilder)	__package__ (in csb.statistics.ars)	_values (in SecStructures)
__init__() (in ClansFileWriter)	__package__ (in csb.statistics.maxent)	_values (in EnumBase)
__init__() (in ClansParams)	__package__ (in csb.statistics.mixtures)	_valuesci (in ScoreUnits)
__init__() (in ClansParser)	__package__ (in csb.statistics.pdf)	_valuesci (in States)
__init__() (in ClansSeqgroup)	__package__ (in csb.statistics.pdf.parameterized)	_valuesci (in AlignmentFormats)
__init__() (in ClansSeqgroupCollection)	__package__ (in csb.statistics.rand)	_valuesci (in AlignmentTypes)
__init__() (in Color)	__package__ (in csb.statistics.samplers)	_valuesci (in NucleicAlphabet)
__init__() (in ChemShiftReader)	__package__ (in csb.statistics.samplers.mc)	_valuesci (in ProteinAlphabet)
__init__() (in ResidueAssignmentInfo)	__package__ (in csb.statistics.samplers.mc.multichain)	_valuesci (in SequenceTypes)
__init__() (in A3MSequenceIterator)	__package__ (in csb.statistics.samplers.mc.neqsteppropagator)	_valuesci (in StdProteinAlphabet)
__init__() (in BaseSequenceParser)	__package__ (in csb.statistics.samplers.mc.propagators)	_valuesci (in UnknownAlphabet)
__init__() (in OutputBuilder)	__package__ (in csb.statistics.samplers.mc.singlechain)	_valuesci (in AngleUnits)
__init__() (in SequenceAlignmentReader)	__package__ (in csb.statistics.scalemixture)	_valuesci (in SecStructures)
__init__() (in StructureAlignmentFactory)	__package__ (in csb.statmech)	_valuesci (in EnumBase)
__init__() (in HHMFileBuilder)	__package__ (in csb.statmech.ensembles)	_wxapp (in WxBackendImpl)
__init__() (in HHOutputParser)	__package__ (in csb.statmech.wham)