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[ Module Hierarchy | Class Hierarchy ]

# Class Hierarchy

- csb.bio.io.procheck.ProcheckParser: Simple Prochceck Summary parser
- StringIO.StringIO: class StringIO([buffer])
  - csb.io.MemoryStream: In-memory stream object.
- object: The most base type
  - csb.bio.io.fasta.A3MSequenceIterator
  - csb.statistics.ars.ARS
  - csb.bio.sequence.AbstractAlignment: Base class for all alignment objects.
    - csb.bio.sequence.A3MAlignment: A specific type of multiple alignment, which provides some operations relative to a master sequence (the first entry in the alignment).
    - csb.bio.sequence.SequenceAlignment: Multiple sequence alignment.
      - csb.bio.hmm.HHpredHitAlignment: Represents a query-template alignment in an HHpred result.
    - csb.bio.sequence.StructureAlignment: Multiple structure alignment.
  - csb.bio.sequence.alignment.AbstractAlignmentAlgorithm: Base class for all sequence alignment algorithms.
    - csb.bio.sequence.alignment.GlobalAlignmentAlgorithm: Needleman-Wunsch global sequence alignment.
      - csb.bio.io.wwpdb.RobustResidueMapper.GlobalAligner
    - csb.bio.sequence.alignment.LocalAlignmentAlgorithm: Smith-Waterman local sequence alignment.
  - csb.core.AbstractContainer: Defines the behavior of a high-level object, which can hold an array of elements.
    - csb.core.AbstractNIContainer: Same as the AbstractContainer, but provides access to the child elements through `AbstractNativeIndexer._getinternal` instead of the standard __getitem__.
      - csb.bio.structure.Chain: Represents a polymeric chain.
      - csb.bio.structure.Ensemble: Represents an ensemble of multiple Structure models.
      - csb.bio.structure.Residue: Base class representing a single residue.
        - csb.bio.structure.NucleicResidue: Represents a single nucleotide residue.
        - csb.bio.structure.ProteinResidue: Represents a single amino acid residue.
        - csb.bio.structure.UnknownResidue
      - csb.bio.structure.Structure: Represents a single model of a PDB 3-Dimensional molecular structure.
      - csb.bio.fragments.Target: Represents a protein structure prediction target.
        - csb.bio.fragments.ChemShiftTarget
    - csb.core.Container: Generic implementation of AbstractContainer.
    - csb.bio.fragments.rosetta.RosettaFragmentMap: Represents a Rosetta fragment library.
  - csb.statistics.pdf.AbstractDensity: Defines the interface and common operations for all probability density functions.
    - csb.statistics.pdf.BaseDensity: Base abstract class for all PDFs, which operate on simple float or array-of-float parameters.
      - csb.statistics.pdf.Dirichlet
      - csb.statistics.pdf.Gamma
        - csb.statistics.scalemixture.GammaPrior: Gamma prior on mixture weights including a weak gamma prior on its parameter.
      - csb.statistics.pdf.GeneralizedInverseGaussian
      - csb.statistics.pdf.GeneralizedNormal
      - csb.statistics.pdf.GumbelMinimum
        - csb.statistics.pdf.GumbelMaximum
      - csb.statistics.pdf.InverseGamma
        - csb.statistics.scalemixture.InvGammaPrior: Inverse Gamma prior on mixture weights including a weak gamma prior on its parameter.
      - csb.statistics.pdf.InverseGaussian
      - csb.statistics.pdf.Laplace
      - csb.statistics.maxent.MaxentModel: Fourier expansion of a biangular log-probability density
      - csb.statistics.pdf.Normal
        - csb.statistics.pdf.MultivariateGaussian
      - csb.statistics.scalemixture.ScaleMixture: Robust probabilistic superposition and comparison of protein structures Martin Mechelke and Michael Habeck
    - csb.statistics.pdf.parameterized.ParameterizedDensity: Base abstract class for all PDFs, which operate on simple or computed (chained) parameters.
  - csb.bio.structure.AbstractEntity: Base class for all protein structure entities.
    - csb.bio.structure.Atom: Represents a single atom in space.
      - csb.bio.structure.DisorderedAtom: A wobbling atom, which has alternative locations.
    - csb.bio.structure.Chain: Represents a polymeric chain.
    - csb.bio.structure.Ensemble: Represents an ensemble of multiple Structure models.
    - csb.bio.structure.Residue: Base class representing a single residue.
      - csb.bio.structure.NucleicResidue: Represents a single nucleotide residue.
      - csb.bio.structure.ProteinResidue: Represents a single amino acid residue.
      - csb.bio.structure.UnknownResidue
    - csb.bio.structure.Structure: Represents a single model of a PDB 3-Dimensional molecular structure.
  - csb.statistics.pdf.AbstractEstimator: Density parameter estimation strategy.
    - csb.statistics.pdf.DirichletEstimator
    - csb.statistics.pdf.GammaMLEstimator
    - csb.statistics.scalemixture.GammaScaleMAP: MAP estimator of the scales
    - csb.statistics.scalemixture.GammaScaleSampler: Sample the scalies given the data
    - csb.statistics.pdf.GaussianMLEstimator
    - csb.statistics.pdf.GenNormalBruteForceEstimator
    - csb.statistics.pdf.GumbelMaxMomentsEstimator
    - csb.statistics.pdf.GumbelMinMomentsEstimator
    - csb.statistics.scalemixture.InvGammaScaleMAP: MAP estimator of the scales
    - csb.statistics.scalemixture.InvGammaScaleSampler: Sample the scales given the data
    - csb.statistics.pdf.InverseGaussianMLEstimator
    - csb.statistics.pdf.LaplaceMLEstimator
    - csb.statistics.pdf.MultivariateGaussianMLEstimator
    - csb.statistics.pdf.NullEstimator: Does not estimate anything.
    - csb.statistics.scalemixture.ScaleMixturePriorEstimator: Prior on the scales of a ScaleMixture, which determines how the scales are estimated.
      - csb.statistics.scalemixture.GammaPosteriorMAP
      - csb.statistics.scalemixture.GammaPosteriorSampler
      - csb.statistics.scalemixture.InvGammaPosteriorMAP
      - csb.statistics.scalemixture.InvGammaPosteriorSampler
  - csb.numeric.integrators.AbstractGradient: Abstract gradient class.
    - csb.statistics.samplers.mc.multichain.Gradient
  - csb.statistics.samplers.mc.neqsteppropagator.AbstractHeatWorkJacobianLogger: Abstract class defining the interface for objects keeping track of and accumulating heat, work and the Jacobian during a nonequilibrium trajectory.
    - csb.statistics.samplers.mc.neqsteppropagator.TrivialHeatWorkJacobianLogger
  - csb.core.AbstractIndexer
    - csb.core.BaseCollectionContainer: Base class which defines the behavior of a read-only collection container.
      - csb.core.CollectionContainer: Write-enabled Collection Container.
        - csb.bio.structure.ChainResiduesCollection
        - csb.bio.structure.DisorderedAtom: A wobbling atom, which has alternative locations.
        - csb.bio.structure.EnsembleModelsCollection
        - csb.bio.hmm.HMMLayersCollection: Provides consecutive, 1-based access to all of the layers in the profile.
        - csb.bio.structure.SecondaryStructure: Describes the secondary structure of a chain.
        - csb.bio.structure.TorsionAnglesCollection: Describes a collection of torsion angles.
        - csb.statistics.samplers.mc.Trajectory: Ordered collection of states, representing a phase-space trajectory.
          - csb.statistics.samplers.mc.neqsteppropagator.NonequilibriumTrajectory: Trajectory holding additional information about energy difference the Jacobian.
          - csb.statistics.samplers.mc.neqsteppropagator.PerturbationResult: Instances hold the result of a perturbation.
      - csb.statistics.samplers.EnsembleState: Defines an Ensemble Monte Carlo state; it is a read-only collection of State objects.
      - csb.statistics.samplers.mc.MCCollection: Collection of single-chain samplers.
      - csb.core.ReadOnlyCollectionContainer: This is a write-once container, which is filled with items only at object construction.
        - csb.bio.io.clans.ClansEntryCollection: Read-only container for holding (and internally managing) ClansEntry instances.
        - csb.bio.io.clans.ClansSeqgroupCollection: Read-only container for holding (and internally managing) ClansSeqgroup instances.
        - csb.bio.sequence.SequenceCollection: Represents a list of AbstractSequences.
    - csb.core.BaseDictionaryContainer: Base class which defines the behavior of a read only key-value collection container.
      - csb.bio.sequence.AlignmentRowsTable
      - csb.core.DictionaryContainer: Write-enabled Dictionary Container.
        - csb.bio.io.vasco.ChemicalShiftContainer
        - csb.bio.hmm.EmissionTable: Represents a lookup table of emission probabilities.
        - csb.bio.hmm.HMMLayer: Provides a dictionary-like catalog of the available states at this layer.
        - csb.bio.structure.ResidueAtomsTable: Represents a collection of atoms.
        - csb.bio.structure.StructureChainsTable
        - csb.bio.hmm.TransitionTable: Represents a lookup table of transitions that are possible from within a given state.
      - csb.core.ReadOnlyDictionaryContainer: This is a write-once container, which is filled with items only at object construction.
  - csb.numeric.integrators.AbstractIntegrator: Abstract integrator class.
    - csb.numeric.integrators.LeapFrog: Leap Frog integration scheme implementation that calculates position and momenta at equal times.
      - csb.numeric.integrators.FastLeapFrog: Leap Frog integration scheme implementation that calculates position and momenta at unequal times by concatenating the momentum updates of two successive integration steps.
    - csb.numeric.integrators.VelocityVerlet: Velocity Verlet integration scheme implementation.
  - csb.statistics.pdf.parameterized.AbstractParameter: Abstract parameterization, which can exist independently or be coupled to other parameters upon request.
    - csb.statistics.pdf.parameterized.Parameter: Default parameter implementation which accepts float values only.
      - csb.statistics.pdf.parameterized.NonVirtualParameter: A float Parameter that is explicitly non-computed and cannot be bound to another Parameter.
  - csb.statistics.samplers.mc.neqsteppropagator.AbstractPerturbation: Describes an abstract system perturbation
    - csb.statistics.samplers.mc.neqsteppropagator.ReducedHamiltonianPerturbation: System perturbation by changing the reduced Hamiltonian
  - csb.statistics.samplers.mc.neqsteppropagator.AbstractPerturbationParam: Subclasses hold informations required for different kinds of system perturbation
  - csb.statistics.samplers.mc.neqsteppropagator.AbstractPropagation: Describes an abstract system propagation
    - csb.statistics.samplers.mc.neqsteppropagator.AbstractMCPropagation: System propagation by some MC algorithm.
      - csb.statistics.samplers.mc.neqsteppropagator.HMCPropagation: System propagation by HMC
    - csb.statistics.samplers.mc.neqsteppropagator.AbstractMDPropagation: System propagation by some MD algorithm
      - csb.statistics.samplers.mc.neqsteppropagator.PlainMDPropagation: System propagation by plain, microcanonical MD
  - csb.statistics.samplers.mc.neqsteppropagator.AbstractPropagationParam: Subclasses hold informations required for different kinds of system propagation
    - csb.statistics.samplers.mc.neqsteppropagator.HMCPropagationParam: Holds all required information for propagating a system by HMC.
    - csb.statistics.samplers.mc.neqsteppropagator.MDPropagationParam
    - csb.statistics.samplers.mc.neqsteppropagator.PlainMDPropagationParam: Holds all required information for propagating a system by MD.
  - csb.statistics.samplers.mc.AbstractPropagationResult: Abstract class providing the interface for the result of a deterministic or stochastic propagation of a state.
    - csb.statistics.samplers.mc.PropagationResult: Describes the result of a deterministic or stochastic propagation of a state.
    - csb.statistics.samplers.mc.Trajectory: Ordered collection of states, representing a phase-space trajectory.
      - csb.statistics.samplers.mc.neqsteppropagator.NonequilibriumTrajectory: Trajectory holding additional information about energy difference the Jacobian.
      - csb.statistics.samplers.mc.neqsteppropagator.PerturbationResult: Instances hold the result of a perturbation.
  - csb.statistics.samplers.mc.propagators.AbstractPropagator: Abstract propagator class.
    - csb.statistics.samplers.mc.propagators.AbstractMCPropagator: Provides the interface for MC trajectory generators.
      - csb.statistics.samplers.mc.propagators.AbstractNCMCPropagator: Draws a number of samples from a PDF using the AbstractNCMCSampler.
      - csb.statistics.samplers.mc.propagators.HMCPropagator: Draws a number of samples from a PDF using the HMCSampler and returns them as a Trajectory.
      - csb.statistics.samplers.mc.propagators.RWMCPropagator: Draws a number of samples from a PDF using the RWMCSampler and returns them as a Trajectory.
    - csb.statistics.samplers.mc.propagators.MDPropagator: Molecular Dynamics propagator.
      - csb.statistics.samplers.mc.propagators.ThermostattedMDPropagator: Thermostatted Molecular Dynamics propagator.
    - csb.statistics.samplers.mc.neqsteppropagator.NonequilibriumStepPropagator: Propagator class which propagates a system using NCMC-like stepwise trajectories
  - csb.bio.io.wwpdb.AbstractResidueMapper: Defines the base interface of all residue mappers, used to align PDB ATOM records to the real (SEQRES) sequence of a chain.
    - csb.bio.io.wwpdb.CombinedResidueMapper: The best of both worlds: attempts to map the residues using FastResidueMapper, but upon failure secures success by switching to RobustResidueMapper.
    - csb.bio.io.wwpdb.FastResidueMapper: RegExp-based residue mapper.
    - csb.bio.io.wwpdb.RobustResidueMapper: Exhaustive residue mapper, which uses Needleman-Wunsch global alignment.
  - csb.statistics.samplers.AbstractSampler: Abstract interface for sampling algorithms.
    - csb.statistics.samplers.mc.AbstractMC: Abstract Monte Carlo sampler class.
      - csb.statistics.samplers.mc.multichain.AbstractEnsembleMC: Abstract class for Monte Carlo sampling algorithms simulating several ensembles.
        - csb.statistics.samplers.mc.multichain.AbstractExchangeMC: Abstract class for Monte Carlo sampling algorithms employing some replica exchange method.
          - csb.statistics.samplers.mc.multichain.AbstractRENS: Abstract Replica Exchange with Nonequilibrium Switches (RENS, Ballard & Jarzynski 2009) class.
            - csb.statistics.samplers.mc.multichain.AbstractStepRENS: Replica Exchange with Nonequilibrium Switches (RENS, Ballard & Jarzynski 2009) with stepwise trajectories as described in Nilmeier et al., "Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation", PNAS 2011.
              - csb.statistics.samplers.mc.multichain.HMCStepRENS: Replica Exchange with Nonequilibrium Switches (RENS, Ballard & Jarzynski 2009) with stepwise trajectories as described in Nilmeier et al., "Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation", PNAS 2011.
            - csb.statistics.samplers.mc.multichain.MDRENS: Replica Exchange with Nonequilibrium Switches (RENS, Ballard & Jarzynski 2009) with Molecular Dynamics (MD) trajectories.
              - csb.statistics.samplers.mc.multichain.ThermostattedMDRENS: Replica Exchange with Nonequilibrium Switches (RENS, Ballard & Jarzynski, 2009) with Andersen-thermostatted Molecular Dynamics (MD) trajectories.
          - csb.statistics.samplers.mc.multichain.ReplicaExchangeMC: Replica Exchange (RE, Swendsen & Yang 1986) implementation.
      - csb.statistics.samplers.mc.singlechain.AbstractSingleChainMC: Abstract class for Monte Carlo sampling algorithms simulating only one ensemble.
        - csb.statistics.samplers.mc.singlechain.AbstractNCMCSampler: Implementation of the NCMC sampling algorithm (Nilmeier et al., "Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation", PNAS 2011) for sampling from one ensemble only.
        - csb.statistics.samplers.mc.singlechain.HMCSampler: Hamilton Monte Carlo (HMC, also called Hybrid Monte Carlo by the inventors, Duane, Kennedy, Pendleton, Duncan 1987).
        - csb.statistics.samplers.mc.singlechain.RWMCSampler: Random Walk Metropolis Monte Carlo implementation (Metropolis, Rosenbluth, Teller, Teller 1953; Hastings, 1970).
  - csb.bio.sequence.alignment.AbstractScoringMatrix: Defines a pairwise sequence alignment scoring function.
    - csb.bio.sequence.alignment.IdentityMatrix: Simple identity-based scoring matrix.
    - csb.bio.sequence.alignment.SimilarityMatrix: Similarity scoring matrix.
  - csb.bio.sequence.AbstractSequence: Base abstract class for all Sequence objects.
    - csb.bio.sequence.ChainSequence: Sequence view for csb.bio.structure.Chain objects.
      - csb.bio.io.wwpdb.SparseChainSequence: Sequence view for reference (SEQRES) or sparse (ATOM) PDB chains.
    - csb.bio.sequence.RichSequence: Sequence implementation, which converts the sequence into a list of ResidueInfo objects.
    - csb.bio.sequence.Sequence: High-performance sequence object.
  - csb.statistics.samplers.AbstractState: Represents a point in phase-space.
    - csb.statistics.samplers.EnsembleState: Defines an Ensemble Monte Carlo state; it is a read-only collection of State objects.
    - csb.statistics.samplers.State: Represents a point in phase-space.
  - csb.statistics.samplers.mc.neqsteppropagator.AbstractStepStatistics: Abstract class defining a minimal interface for objects allowing to store statistics of what happens in Step instances.
    - csb.statistics.samplers.mc.neqsteppropagator.DummyStepStatistics
  - csb.bio.io.wwpdb.AbstractStructureParser: A base PDB structure format-aware parser.
    - csb.bio.io.wwpdb.LegacyStructureParser: This is a customized PDB parser, which is designed to read both sequence and atom data from the ATOM section.
    - csb.bio.io.wwpdb.RegularStructureParser: This is the de facto PDB parser, which is designed to read SEQRES and ATOM sections separately, and them map them.
      - csb.bio.io.wwpdb.PDBHeaderParser: Ultra fast PDB HEADER parser.
  - csb.statistics.samplers.mc.multichain.AbstractSwapCommunicator: Holds all the information which needs to be communicated between distinct swap substeps.
    - csb.statistics.samplers.mc.multichain.RENSSwapCommunicator: Holds all the information which needs to be communicated between distinct RENS swap substeps.
    - csb.statistics.samplers.mc.multichain.RESwapCommunicator: Holds all the information which needs to be communicated between distinct RE swap substeps.
  - csb.statistics.samplers.mc.multichain.AbstractSwapParameterInfo: Subclass instances hold all parameters necessary for performing a swap between two given samplers.
    - csb.statistics.samplers.mc.multichain.RESwapParameterInfo: Holds parameters for a standard Replica Exchange swap.
      - csb.statistics.samplers.mc.multichain.AbstractRENSSwapParameterInfo: Holds parameters for a RENS swap.
        - csb.statistics.samplers.mc.multichain.HMCStepRENSSwapParameterInfo: Holds all required information for performing HMCStepRENS swaps.
      - csb.statistics.samplers.mc.multichain.MDRENSSwapParameterInfo: Holds parameters for a MDRENS swap.
        - csb.statistics.samplers.mc.multichain.ThermostattedMDRENSSwapParameterInfo
  - csb.statistics.samplers.mc.multichain.AbstractSwapScheme: Provides the interface for classes defining schemes according to which swaps in Replica Exchange-like simulations are performed.
    - csb.statistics.samplers.mc.multichain.AlternatingAdjacentSwapScheme: Provides a swapping scheme in which tries exchanges between neighbours only following the scheme 1 <-> 2, 3 <-> 4, ...
  - csb.statistics.samplers.mc.neqsteppropagator.AbstractSystemInfo: Subclasses hold all information describing a current system setup (Hamiltonian, boundaries, ...)
    - csb.statistics.samplers.mc.neqsteppropagator.HamiltonianSysInfo: Holds information describing a system by its Hamiltonian only.
  - csb.test.AbstractTestBuilder: This is a base class, defining a test loader which exposes the `loadTests` method.
    - csb.test.AnyTestBuilder: Build a test suite of cases, marked as either unit, functional or regression tests.
    - csb.test.CustomTestBuilder: Build a test suite of cases, marked as custom tests.
    - csb.test.FunctionalTestBuilder: Build a test suite of cases, marked as functional tests.
    - csb.test.RegressionTestBuilder: Build a test suite of cases, marked as regression tests.
    - csb.test.UnitTestBuilder: Build a test suite of cases, marked as unit tests.
  - csb.statmech.wham.AbstractWHAM: Abstract base class
    - csb.statmech.wham.NonparametricWHAM: Implementation of the nonparametric WHAM outlined in Habeck 2012, in which histograms are reduced to delta peaks, this allows to use energies samples at different orders of magnitude, improving the accuracy of the DOS estimates.
    - csb.statmech.wham.WHAM: Implementation of the original WHAM methods based on histograms.
  - csb.bio.sequence.alignment.AlignmentResult: Represents a pairwise sequence alignment result.
  - csb.apps.AppRunner: A base abstract class for all application runners.
    - csb.apps.helloworld.AppRunner
    - csb.apps.csfrag.AppRunner
    - csb.apps.bfite.AppRunner
    - csb.apps.buildhmm.AppRunner
    - csb.apps.precision.AppRunner
    - csb.apps.embd.AppRunner
    - csb.apps.hhfrag.AppRunner
    - csb.apps.hhsearch.AppRunner
    - csb.apps.bfit.AppRunner
    - csb.apps.promix.AppRunner
  - csb.apps.Application: Base CSB application class.
    - csb.apps.bfit.BFitApp: Python application for robust structure superposition of two protein structures
    - csb.apps.bfite.BFitApp: Python application for robust structure superposition of two protein structures
    - csb.apps.buildhmm.BuildProfileApp
    - csb.apps.csfrag.CSfragApp
    - csb.apps.embd.DeconvolutionApp
    - csb.apps.hhfrag.HHfragApp
    - csb.apps.hhsearch.HHsearchApp
    - csb.apps.helloworld.HelloWorldApp
    - csb.apps.precision.PrecisionApp
    - csb.apps.promix.ProMixApp
  - csb.apps.ArgHandler: Command line argument handler.
  - csb.bio.fragments.AssignmentFactory
  - csb.bio.io.wwpdb.AsyncParseResult
  - csb.bio.io.wwpdb.AsyncStructureParser: Wraps StructureParser in an asynchronous call.
  - csb.bio.nmr.AtomConnectivity
  - csb.test.Attributes
  - csb.io.plots.Backends: Enumeration of chart backends.
  - exceptions.BaseException: Common base class for all exceptions
    - exceptions.Exception: Common base class for all non-exit exceptions.
      - csb.apps.AppExit: Used to signal an immediate application exit condition (e.g.
      - csb.apps.buildhmm.BuildError
        - csb.apps.buildhmm.BuildArgError
        - csb.apps.buildhmm.BuildIOError
        - csb.apps.buildhmm.NoOutputError
      - csb.bio.io.clans.DuplicateEntryError: Raised during Clans._update_index if two entries are identical in name, sequence, and coordinates.
      - csb.bio.io.clans.DuplicateEntryNameError: Raised during Clans.get_entry if two entries have identical names.
      - csb.bio.structure.InvalidOperation
      - csb.numeric.MatrixInitError
      - csb.bio.io.clans.MissingBlockError: Raised if an expected tag is not found during parsing of a CLANS file.
      - csb.io.ProcessError: Raised on Shell.run() failures.
        - csb.io.TimeoutError: Raised on Shell.run() timeouts.
      - exceptions.StandardError: Base class for all standard Python exceptions that do not represent interpreter exiting.
        - exceptions.AssertionError: Assertion failed.
        - exceptions.AttributeError: Attribute not found.
          - csb.core.EnumMemberError
          - csb.statistics.pdf.ParameterNotFoundError
          - csb.bio.hmm.UnobservableStateError
        - exceptions.ImportError: Import can't find module, or can't find name in module.
          - csb.test.InvalidNamespaceError
        - exceptions.LookupError: Base class for lookup errors.
          - exceptions.IndexError: Sequence index out of range.
            - csb.core.CollectionIndexError
              - csb.bio.structure.EntityIndexError
              - csb.bio.hmm.LayerIndexError
            - csb.bio.sequence.PositionError
              - csb.bio.sequence.ColumnPositionError
              - csb.bio.sequence.SequencePositionError
          - exceptions.KeyError: Mapping key not found.
            - csb.bio.sequence.DuplicateSequenceError
            - csb.bio.hmm.EmissionExistsError
            - csb.bio.nmr.EntityNotSupportedError
            - csb.io.tsv.InvalidColumnError
            - csb.core.InvalidKeyError
              - csb.core.DuplicateKeyError
                - csb.bio.structure.DuplicateAtomIDError
                - csb.bio.structure.DuplicateChainIDError
                - csb.bio.structure.DuplicateModelIDError
                - csb.bio.structure.DuplicateResidueIDError
            - csb.core.ItemNotFoundError
              - csb.bio.structure.EntityNotFoundError
                - csb.bio.structure.AtomNotFoundError
                - csb.bio.structure.ChainNotFoundError
              - csb.bio.hmm.StateNotFoundError
                - csb.bio.hmm.TransitionNotFoundError
            - csb.bio.sequence.alignment.ResidueNotFoundError
            - csb.bio.sequence.SequenceNotFoundError
            - csb.bio.hmm.StateExistsError
            - csb.bio.io.wwpdb.StructureNotFoundError
            - csb.bio.hmm.TransitionExistsError
        - exceptions.NameError: Name not found globally.
          - csb.test.InvalidNamespaceError
        - exceptions.RuntimeError: Unspecified run-time error.
          - csb.bio.fragments.ClusterDivergingError
          - csb.build.RevisionError
        - exceptions.TypeError: Inappropriate argument type.
          - csb.statistics.samplers.DimensionError
          - csb.statistics.pdf.IncompatibleEstimatorError
        - exceptions.ValueError: Inappropriate argument value (of correct type).
          - csb.bio.structure.AlignmentArgumentLengthError
          - csb.apps.precision.ArgumentError
            - csb.apps.precision.ArgumentIOError
          - csb.apps.hhfrag.ArgumentError
            - csb.apps.hhfrag.ArgumentIOError
          - csb.apps.csfrag.ArgumentError
            - csb.apps.csfrag.ArgumentIOError
          - csb.bio.structure.Broken3DStructureError
            - csb.bio.structure.Missing3DStructureError
          - csb.bio.structure.BrokenSecStructureError
            - csb.bio.structure.UnknownSecStructureError
          - csb.bio.io.cs.ChemShiftFormatError
          - csb.bio.fragments.ClusterExhaustedError
            - csb.bio.fragments.ClusterEmptyError
          - csb.bio.io.dssp.DSSPParseError
          - csb.bio.io.mrc.DensityMapFormatError
          - csb.core.EnumValueError
          - csb.bio.io.hhpred.HHProfileFormatError
            - csb.bio.io.hhpred.HHOutputFormatError
            - csb.bio.io.hhpred.StructureFormatError
          - csb.bio.hmm.HMMArgumentError
          - csb.io.InvalidCommandError: Raised when Shell.run() encounters an OSError.
          - csb.apps.hhfrag.InvalidOperationError
          - csb.apps.csfrag.InvalidOperationError
          - csb.bio.nmr.InvalidResidueError
          - csb.bio.io.wwpdb.PDBParseError
            - csb.bio.io.wwpdb.HeaderFormatError
            - csb.bio.io.wwpdb.SecStructureFormatError
            - csb.bio.io.wwpdb.StructureFormatError
              - csb.bio.io.wwpdb.InvalidEntryIDError
              - csb.bio.io.wwpdb.ResidueMappingError
            - csb.bio.io.wwpdb.UnknownPDBResidueError
          - csb.bio.io.psipred.PSIPredParseError
          - csb.statistics.pdf.ParameterValueError
            - csb.statistics.pdf.EstimationFailureError
            - csb.statistics.pdf.parameterized.ParameterValueError
          - csb.statistics.pdf.parameterized.ParameterizationError
          - csb.bio.io.noe.PeakListFormatError
          - csb.bio.sequence.SequenceError
          - csb.bio.io.fasta.SequenceFormatError
          - csb.bio.io.clans.UnknownTagError: Raised if an unknown tag is encountered while parsing a CLANS file.
          - csb.io.tsv.UnsupportedTypeError
  - csb.bio.io.noe.BasePeakListReader
    - csb.bio.io.noe.SparkyPeakListReader: Sparky NOE peak list parser.
    - csb.bio.io.noe.XeasyPeakListReader: XEASY NOE peak list parser.
  - csb.bio.io.fasta.BaseSequenceParser: FASTA parser template.
    - csb.bio.io.fasta.SequenceParser: Standard FASTA parser.
      - csb.bio.io.fasta.PDBSequenceParser: PDB FASTA parser.
  - csb.bio.fragments.BenchmarkAdapter
  - csb.build.BuildTypes: Enumeration of build types.
  - csb.bio.io.mrc.ByteOrder
  - csb.apps.csfrag.CSfrag
  - csb.io.plots.Chart: Simple and clean facade to Matplotlib's plotting API.
  - csb.bio.fragments.ChemShiftAssignmentFactory
  - csb.bio.nmr.ChemShiftInfo: Chemical shift struct.
  - csb.bio.io.cs.ChemShiftReader: Simple NMR STAR v2 chemical shift reader.
    - csb.bio.io.cs.ChemShift3Reader: Simple NMR STAR v3 chemical shift reader.
  - csb.bio.nmr.ChemShiftScoringModel: Chemical shift similarity scoring model.
  - csb.bio.nmr.ChemicalShiftNetwork: Describes a network of covalently connected, chemical shift visible nuclei.
  - csb.io.tsv.SQLiteRepository.ChunkedReader
  - csb.bio.io.clans.Clans: Class for holding and manipulating data from one CLANS file.
  - csb.bio.io.clans.ClansEntry: Class holding the data of one CLANS sequence entry.
  - csb.bio.io.clans.ClansFileBuilder: Base abstract files for building a file in CLANS format.
    - csb.bio.io.clans.ClansFileWriter: Class for serializing a Clans instance to a file in CLANS format.
  - csb.bio.io.clans.ClansParams: Class for handling Clans parameters.
  - csb.bio.io.clans.ClansParser: CLANS file format aware parser.
  - csb.bio.io.clans.ClansSeqgroup: Class holding the data of one CLANS group (seqgroup).
  - csb.bio.fragments.ClusterNode: Cluster node.
  - csb.bio.fragments.ClusterRep: Cluster's representative (centroid) node.
  - csb.bio.io.clans.Color: RGB color handling class.
  - csb.bio.sequence.ColumnInfo
  - csb.io.tsv.ColumnInfo: Holder object for column metadata.
  - csb.bio.structure.CompositeEntityIterator: Iterates over composite AbstractEntity hierarchies.
    - csb.bio.structure.ConfinedEntityIterator: Iterates over composite AbstractEntity hierarchies, but terminates the traversal of a branch once a specific node type is encountered.
  - csb.test.Config: General CSB Test Config.
  - csb.bio.fragments.BenchmarkAdapter.Connection
  - csb.build.Console: CSB Build Bot.
  - csb.test.Console: Build and run all tests of the specified namespace and kind.
  - csb.bio.nmr.ContactMap: Describes a protein contact map.
  - csb.bio.nmr.ContactMapComparisonInfo
  - csb.apps.hhsearch.Context
    - csb.apps.hhsearch.HHTask
    - csb.apps.hhfrag.SliceContext
  - csb.statistics.Cumulative
  - csb.bio.io.dssp.DSSPParser: Simple DSSP Secondary Structure Parser.
  - csb.io.tsv.DataRow: Represents a table data row.
  - csb.apps.embd.Deconvolution: Blind deconvolution for n-dimensional images.
  - csb.bio.io.mrc.DensityInfo
  - csb.bio.io.mrc.DensityMapReader: Binary MRC density map reader.
  - csb.bio.io.mrc.DensityMapWriter: Binary MRC density map writer.
  - csb.bio.hmm.EVDParameters
  - csb.bio.io.wwpdb.EntryID: Represents a PDB Chain identifier.
    - csb.bio.io.wwpdb.DegenerateID: Looks like a StandardID, except that the accession number may have arbitrary length.
    - csb.bio.io.wwpdb.SeqResID: Same as a StandardID, but contains an additional underscore between te accession number and the chain identifier.
    - csb.bio.io.wwpdb.StandardID: Standard PDB ID in the following form: xxxxY, where xxxx is the accession number (lower case) and Y is an optional chain identifier.
  - csb.io.EntryReader: Generic flatfile reader.
  - csb.io.EntryWriter: A simple stream writer.
  - csb.core.Enum: A collection of efficient static methods for working with enum classes.
  - csb.core.EnumBase
    - csb.core.enum: Base class for all enumeration types.
      - csb.bio.sequence.AlignmentFormats: Enumeration of multiple sequence alignment formats
      - csb.bio.sequence.AlignmentTypes: Enumeration of alignment strategies
      - csb.bio.structure.AngleUnits: Torsion angle unit types
      - csb.bio.structure.ChemElements: Periodic table elements
      - csb.bio.sequence.NucleicAlphabet: Nucleic sequence alphabet
      - csb.bio.sequence.ProteinAlphabet: Protein sequence alphabet
      - csb.bio.hmm.ScoreUnits: Enumeration of HMM emission and transition score units
      - csb.bio.structure.SecStructures: Secondary structure types
      - csb.bio.sequence.SequenceTypes: Enumeration of sequence types
      - csb.bio.hmm.States: Enumeration of HMM state types
      - csb.bio.sequence.StdProteinAlphabet: Standard protein sequence alphabet
      - csb.bio.sequence.UnknownAlphabet: Unknown sequence alphabet
  - csb.core.EnumItem
  - csb.statistics.ars.Envelope: Envelope function for adaptive rejection sampling.
  - csb.apps.ExitCodes: Exit code constants.
    - csb.apps.helloworld.ExitCodes
    - csb.apps.hhfrag.ExitCodes
    - csb.apps.embd.ExitCodes
    - csb.apps.bfite.ExitCodes
    - csb.apps.promix.ExitCodes
    - csb.apps.csfrag.ExitCodes
    - csb.apps.bfit.ExitCodes
    - csb.apps.hhsearch.ExitCodes
    - csb.apps.precision.ExitCodes
    - csb.apps.buildhmm.ExitCodes
  - csb.io.tsv.Expression: Metadata container: represents a table select or update expression.
  - csb.bio.io.wwpdb.FileBuilder: Base abstract files for all structure file formatters.
    - csb.bio.io.wwpdb.PDBFileBuilder: PDB file format builder.
      - csb.bio.io.wwpdb.PDBEnsembleFileBuilder: Supports serialization of NMR ensembles.
  - csb.bio.nmr.Filters: Pre-built atom filters for ContactMaps.
  - csb.bio.fragments.FragmentCluster: Provides clustering/filtering of the fragments, covering a common residue in the target.
  - csb.bio.fragments.FragmentMatch: Base class, representing a match between a fragment and its target.
    - csb.bio.fragments.Assignment: Represents a match between a fragment and its target.
      - csb.bio.fragments.ChemShiftAssignment
  - csb.bio.fragments.FragmentTypes
  - csb.statistics.mixtures.GaussianMixture: Gaussian mixture model for multi-dimensional data.
    - csb.statistics.mixtures.AbstractStructureMixture: Abstract mixture model for protein structure ensembles.
      - csb.statistics.mixtures.ConformerMixture: Gaussian mixture model for protein structure ensembles using a set of conformers
      - csb.statistics.mixtures.SegmentMixture: Gaussian mixture model for protein structure ensembles using a set of segments
  - csb.apps.precision.GlobalInfo
  - csb.bio.io.hhpred.HHMFileBuilder: Builder for HHpred's hhm files.
  - csb.bio.io.hhpred.HHOutputParser: Parser for HHsearch result (*.hhr) files.
  - csb.bio.io.hhpred.HHProfileParser: A class that is HHpred HMM format aware.
  - csb.apps.hhfrag.HHfrag: The HHfrag dynamic fragment detection protocol.
  - csb.bio.hmm.HHpredHit: Represents a single HHsearch hit.
  - csb.bio.hmm.HHpredHitList: Represents a collection of HHpredHits.
  - csb.apps.hhsearch.HHsearch
  - csb.bio.io.mrc.HeaderInfo
  - csb.statistics.samplers.mc.multichain.InterpolationFactory: Produces interpolations for functions changed during non-equilibrium trajectories.
  - csb.numeric.InvertibleMatrix: Matrix object which is intended to save time in MCMC sampling algorithms involving repeated integration of Hamiltonian equations of motion and frequent draws from multivariate normal distributions involving mass matrices as covariance matrices.
  - csb.bio.nmr.Label: Utility class for working with chemical shift labels.
  - csb.apps.precision.LibrarySuperimposer
  - csb.statistics.ars.LogProb
    - csb.statistics.scalemixture.ARSPosteriorAlpha: This class represents the posterior distribution of the alpha parameter of the Gamma and Inverse Gamma prior, and allows sampling using adaptive rejection sampling ARS.
    - csb.statistics.ars.Gauss
  - csb.statistics.samplers.mc.propagators.Looper: Implements an iterable list with a ring-like topology, that is, if the iterator points on the last element, next() returns the first element.
  - csb.statistics.samplers.mc.neqsteppropagator.MDParam: Holds all required information for calculating a MD trajectory.
    - csb.statistics.samplers.mc.neqsteppropagator.HMCPropagationParam: Holds all required information for propagating a system by HMC.
    - csb.statistics.samplers.mc.neqsteppropagator.MDPropagationParam
    - csb.statistics.samplers.mc.neqsteppropagator.PlainMDPropagationParam: Holds all required information for propagating a system by MD.
  - csb.apps.csfrag.MatchInfo
  - csb.apps.csfrag.MatchTable
  - csb.statistics.maxent.MaxentPosterior: Object to hold and calculate the posterior (log)probability given an exponential family model and corresponding data.
  - csb.bio.fragments.Metrics
  - csb.bio.nmr.NOEPeak: Describes a single NOE peak.
  - csb.bio.nmr.NOESpectrum: Describes an NOE spectrum.
  - csb.apps.hhsearch.HHsearch.Options
  - csb.bio.fragments.rosetta.OutputBuilder: Rosetta fragment file formatter.
    - csb.bio.fragments.rosetta.ExtendedOutputBuilder: Builds non-standard fragment files, which contain the CA coordinates of each residue at the end of each line.
  - csb.bio.io.fasta.OutputBuilder: Base sequence/alignment string format builder.
    - csb.bio.io.fasta.A3MOutputBuilder: Formats sequences as A3M strings.
    - csb.bio.io.fasta.FASTAOutputBuilder: Formats sequences as standard FASTA strings.
    - csb.bio.io.fasta.PIROutputBuilder: Formats sequences as PIR FASTA strings, recognized by Modeller.
  - csb.apps.embd.OutputPathBuilder
  - csb.bio.io.psipred.PSIPredParser: Simple PSI-PRED Secondary Structure Parser.
  - csb.bio.io.psipred.PSIPredResidueInfo
  - csb.io.plots.PlotsCollection: A list-like collection of all plots in the chart (0-based).
  - csb.io.tsv.Predicate
    - csb.io.tsv.Between
    - csb.io.tsv.Equals
    - csb.io.tsv.Greater
    - csb.io.tsv.GreaterOrEquals
    - csb.io.tsv.In
    - csb.io.tsv.Lower
    - csb.io.tsv.LowerOrEquals
    - csb.io.tsv.NotEquals
    - csb.io.tsv.NotIn
  - csb.apps.hhfrag.PredictionBuilder
  - csb.apps.buildhmm.ProfileBuilder
    - csb.apps.buildhmm.FASTAProfileBuilder
    - csb.apps.buildhmm.PDBProfileBuilder
  - csb.bio.hmm.ProfileHMM: Describes a protein profile Hidden Markov Model.
    - csb.bio.hmm.ProfileHMMRegion: A shallow proxy referring to a sub-region of a given Profile HMM.
    - csb.bio.hmm.ProfileHMMSegment: Represents a segment (fragment) of a ProfileHMM.
      - csb.bio.hmm.EmissionProfileSegment: Represents a segment of the Match state emission probabilities of a ProfileHMM.
  - csb.bio.hmm.ProfileLength
  - csb.statistics.samplers.mc.neqsteppropagator.Protocol: Describes a stepwise protocol as in Nilmeier et al.
  - csb.core.Proxy: Base class implementing the proxy pattern.
    - csb.io.AutoFlushStream: Wrapper around a buffered stream which automatically calls flush() after each write().
    - csb.io.TempFile: Create a temporary file and take care of deleting it upon object destruction.
  - csb.bio.hmm.pseudocounts.PseudocountBuilder: Constructs profile HMMs with pseudocounts.
  - csb.core.REMatchProxy
  - csb.statistics.samplers.mc.multichain.RENSTrajInfo: Holds information necessary for calculating a RENS trajectory.
  - csb.bio.nmr.RandomCoil: Utility class containing all necessary data and methods for computing secondary chemical shifts.
  - csb.statistics.samplers.mc.neqsteppropagator.ReducedHamiltonian: Describes a reduced Hamiltonian (Hamiltonian, its position gradient and the system temperature)
  - csb.statistics.samplers.mc.multichain.ReplicaHistory: Replica history object, works with both RE and RENS for the AlternatingAdjacentSwapScheme.
  - csb.io.tsv.RepositoryImp: Abstract SQL backend interface.
    - csb.io.tsv.SQLiteRepository: SQLite-based concrete repository implementor.
  - csb.bio.io.dssp.ResidueAssignmentInfo
  - csb.bio.fragments.ResidueAssignmentInfo
  - csb.bio.fragments.ResidueEventInfo
  - csb.bio.fragments.rosetta.ResidueInfo: Container struct for a single rosetta fragment residue.
  - csb.bio.io.wwpdb.ResidueInfo: High-performance struct, which functions as a container for unmapped Atoms.
  - csb.bio.sequence.ResidueInfo
  - csb.build.RevisionHandler: Determines the current repository revision number of a working copy.
    - csb.build.GitHandler
    - csb.build.MercurialHandler
    - csb.build.SubversionHandler
  - csb.build.RevisionInfo
  - csb.bio.fragments.rosetta.RosettaFragment: Represents a single Rosetta fragment match.
  - csb.bio.fragments.RosettaFragsetFactory: Simplifies the construction of fragment libraries.
  - csb.bio.io.svg.SSCartoonBuilder: Creates 2D vector diagrams from SecondaryStructure objects.
  - csb.statistics.scalemixture.ScaleMixturePrior: Prior on the scales of a ScaleMixture, which determines how the scales are estimated.
    - csb.statistics.scalemixture.GammaPrior: Gamma prior on mixture weights including a weak gamma prior on its parameter.
    - csb.statistics.scalemixture.InvGammaPrior: Inverse Gamma prior on mixture weights including a weak gamma prior on its parameter.
  - csb.apps.csfrag.ScoringHelper
  - csb.apps.hhsearch.SecStructureScoring
  - csb.apps.csfrag.SecondaryShiftConverter: Helper, which reads assigned shifts from NMR STAR files and calculates corrected secondary shifts.
  - csb.apps.csfrag.SecondaryShiftReader: Reads secondary shifts from files in CSfrag format.
  - csb.bio.structure.SecondaryStructureElement: Describes a Secondary Structure Element.
  - csb.bio.sequence.SequenceAdapter: Base wrapper class for AbstractSequence objects.
    - csb.bio.sequence.AlignedSequenceAdapter: Adapter, which wraps a gapped AbstractSequence object and makes it compatible with the MSA row/entry interface, expected by AbstractAlignment.
  - csb.bio.io.fasta.SequenceAlignmentReader: Sequence alignment parser.
  - csb.bio.sequence.SequenceAlphabets: Sequence alphabet enumerations.
  - csb.bio.sequence.SequenceIndexer
    - csb.bio.sequence.ColumnIndexer
    - csb.bio.sequence.UngappedSequenceIndexer
  - csb.io.Shell
  - csb.io.ShellInfo: Shell command execution info
  - csb.bio.io.vasco.ShiftInfo
  - csb.statistics.samplers.mc.singlechain.SimpleProposalCommunicator: This holds all the information needed to calculate the acceptance probability in both the RWMCSampler and HMCSampler classes, that is, only the proposal state.
    - csb.statistics.samplers.mc.singlechain.NCMCProposalCommunicator: Holds all information (that is, the trajectory with heat, work, Hamiltonian difference and jacbian) needed to calculate the acceptance probability in the AbstractNCMCSampler class.
  - csb.statistics.samplers.mc.multichain.SingleSwapStatistics: Tracks swap statistics of a single sampler pair.
  - csb.bio.sequence.SliceHelper
  - csb.bio.hmm.State: Describes a Hidden Markov Model state.
  - csb.bio.hmm.StateFactory: Simplifies the construction of protein profile HMM states.
  - csb.statmech.ensembles.StatisticalEnsemble
    - csb.statmech.ensembles.BoltzmannEnsemble
      - csb.statmech.ensembles.FermiEnsemble
    - csb.statmech.ensembles.CompositeEnsemble
    - csb.statmech.ensembles.TsallisEnsemble
  - csb.io.tsv.Step
    - csb.io.tsv.Operator
    - csb.io.tsv.Where
  - csb.statistics.samplers.mc.neqsteppropagator.Step: Defines a step in an NCMC-like stepwise protocol.
  - csb.bio.io.dssp.StrideParser: Simple STRIDE Secondary Structure Parser.
  - csb.bio.io.fasta.StructureAlignmentFactory: Protein structure alignment parser.
  - csb.bio.io.wwpdb.StructureProvider: Base class for all PDB data source providers.
    - csb.bio.io.wwpdb.CustomStructureProvider: A custom PDB data source.
    - csb.bio.io.wwpdb.FileSystemStructureProvider: Simple file system based PDB data source.
    - csb.bio.io.wwpdb.RemoteStructureProvider: Retrieves PDB structures from a specified remote URL.
  - csb.bio.structure.SuperimposeInfo: Describes a structural alignment result.
  - csb.statistics.samplers.mc.multichain.SwapStatistics: Tracks swap statistics for an AbstractExchangeMC subclass instance.
  - csb.io.tsv.Table: Build and query a TSV Table.
  - csb.bio.fragments.TargetResidue: Wrapper around Target's native residues.
    - csb.bio.fragments.ChemShiftTargetResidue
  - csb.io.TempFolder: Create a temporary directory which is automatically wiped when the object is closed.
  - unittest.case.TestCase: A class whose instances are single test cases.
    - csb.test.Case: Base class, defining a CSB Test Case.
  - csb.bio.fragments.TorsionAnglePredictor: Fragment-based phi/psi angles predictor.
  - csb.bio.structure.TorsionAngles: Describes a collection of phi, psi and omega backbone torsion angles.
  - csb.bio.fragments.TorsionPredictionInfo: Struct container for a single torsion angle prediction.
  - csb.statistics.samplers.mc.TrajectoryBuilder: Allows to build a Trajectory object step by step.
    - csb.statistics.samplers.mc.ShortTrajectoryBuilder
  - csb.bio.hmm.Transition: Describes a Hidden Markov Model transition between two states.
  - csb.bio.hmm.TransitionType
  - csb.apps.ArgHandler.Type
  - csb.apps.embd.Util
  - csb.bio.io.vasco.VascoStructureParser: Simple Vasco Parser
  - csb.Version: CSB version number.
  - csb.bio.io.whatif.WhatCheckParser: Simple WhatIf/WhatCheck Summary parser
  - csb.bio.io.noe.XeasyFileBuilder: XEASY output format builder.
  - threading._Verbose
    - threading.Thread: A class that represents a thread of control.
      - csb.io.plots.Backend: Abstract class defining the behavior of all Chart GUI backends.
        - csb.io.plots.WxBackendImpl: WxPython Backend implementor.
      - csb.core.InterruptibleThread
  - dict: dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object's (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = {} for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list.
    - collections.OrderedDict: Dictionary that remembers insertion order
      - csb.core.OrderedDict
  - list: list() -> new empty list list(iterable) -> new list initialized from iterable's items
    - csb.core.Stack
  - property: property(fget=None, fset=None, fdel=None, doc=None) -> property attribute
    - csb.core.typedproperty: Property decorator for convenient creation of typed, encapsulated fields.
    - csb.core.validatedproperty: Property decorator with predefined getter/setter and value checking or casting in the setter.
  - type: type(object) -> the object's type type(name, bases, dict) -> a new type
    - abc.ABCMeta: Metaclass for defining Abstract Base Classes (ABCs).
    - csb.core.EnumMeta: Metaclass for enum types.