[ Module Hierarchy
| Class Hierarchy ]
Class Hierarchy
- csb.bio.io.procheck.ProcheckParser:
Simple Prochceck Summary parser
- StringIO.StringIO:
class StringIO([buffer])
- 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.alignment.AbstractAlignmentAlgorithm:
Base class for all sequence alignment algorithms.
- csb.core.AbstractContainer:
Defines the behavior of a high-level object, which can hold an
array of elements.
- csb.statistics.pdf.AbstractDensity:
Defines the interface and common operations for all probability
density functions.
- csb.bio.structure.AbstractEntity:
Base class for all protein structure entities.
- csb.statistics.pdf.AbstractEstimator:
Density parameter estimation strategy.
- csb.numeric.integrators.AbstractGradient:
Abstract gradient class.
- 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.core.AbstractIndexer
- csb.numeric.integrators.AbstractIntegrator:
Abstract integrator class.
- csb.statistics.pdf.parameterized.AbstractParameter:
Abstract parameterization, which can exist independently or be
coupled to other parameters upon request.
- csb.statistics.samplers.mc.neqsteppropagator.AbstractPerturbation:
Describes an abstract system perturbation
- 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.AbstractPropagationParam:
Subclasses hold informations required for different kinds of system
propagation
- 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.propagators.AbstractPropagator:
Abstract propagator class.
- 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.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.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.AbstractSequence:
Base abstract class for all Sequence objects.
- csb.statistics.samplers.AbstractState:
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.bio.io.wwpdb.AbstractStructureParser:
A base PDB structure format-aware 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.AbstractSwapParameterInfo:
Subclass instances hold all parameters necessary for performing a
swap between two given samplers.
- 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.neqsteppropagator.AbstractSystemInfo:
Subclasses hold all information describing a current system setup
(Hamiltonian, boundaries, ...)
- csb.test.AbstractTestBuilder:
This is a base class, defining a test loader which exposes the
loadTests method.
- 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.Application:
Base CSB application class.
- 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.bio.io.noe.BasePeakListReader
- csb.bio.io.fasta.BaseSequenceParser:
FASTA parser template.
- 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.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.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.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.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.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.EnumItem
- csb.statistics.ars.Envelope:
Envelope function for adaptive rejection sampling.
- csb.apps.ExitCodes:
Exit code constants.
- 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.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.FragmentTypes
- csb.statistics.mixtures.GaussianMixture:
Gaussian mixture model for multi-dimensional data.
- 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.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.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.io.fasta.OutputBuilder:
Base sequence/alignment string format builder.
- 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.apps.hhfrag.PredictionBuilder
- csb.apps.buildhmm.ProfileBuilder
- csb.bio.hmm.ProfileHMM:
Describes a protein profile Hidden Markov Model.
- 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.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.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.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.io.fasta.SequenceAlignmentReader:
Sequence alignment parser.
- csb.bio.sequence.SequenceAlphabets:
Sequence alphabet enumerations.
- csb.bio.sequence.SequenceIndexer
- 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.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.io.tsv.Step
- 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.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.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.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.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.
- 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
- list:
list() -> new empty list list(iterable) -> new list
initialized from iterable's items
- property:
property(fget=None, fset=None, fdel=None, doc=None) -> property attribute
- type:
type(object) -> the object's type type(name, bases, dict) ->
a new type
