pyopenms

Python bindings to the OpenMS C++ library.

The pyOpenMS package contains Python bindings for a large part of the OpenMS library (http://www.open-ms.de) for mass spectrometry based proteomics. It thus provides providing facile access to a feature-rich, open-source algorithm library for mass-spectrometry based proteomics analysis. These Python bindings allow raw access to the data-structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ and SWATH analysis tools).

For further documentation, please see https://pyopenms.readthedocs.io

Please cite:

Röst HL, Schmitt U, Aebersold R, Malmström L. pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library. Proteomics. 2014 Jan;14(1):74-7. doi: 10.1002/pmic.201300246.

Functions

free_mem()

peptide_identifications_to_df(peps[, ...])

Converts a list of peptide identifications to a pandas DataFrame.

Classes

AAIndex

Cython implementation of _AAIndex

AASeqWithMass

Cython implementation of _AASeqWithMass

AASequence

Cython implementation of _AASequence

AMSE_AdductInfo

Cython implementation of _AMSE_AdductInfo

AQS_featureConcentration

Cython implementation of _AQS_featureConcentration

AQS_runConcentration

Cython implementation of _AQS_runConcentration

AScore

Cython implementation of _AScore

AbsoluteQuantitation

Cython implementation of _AbsoluteQuantitation

AbsoluteQuantitationMethod

Cython implementation of _AbsoluteQuantitationMethod

AbsoluteQuantitationMethodFile

Cython implementation of _AbsoluteQuantitationMethodFile

AbsoluteQuantitationStandards

Cython implementation of _AbsoluteQuantitationStandards

AbsoluteQuantitationStandardsFile

Cython implementation of _AbsoluteQuantitationStandardsFile

AccurateMassSearchEngine

Cython implementation of _AccurateMassSearchEngine

AccurateMassSearchResult

Cython implementation of _AccurateMassSearchResult

Acquisition

Cython implementation of _Acquisition

AcquisitionInfo

Cython implementation of _AcquisitionInfo

ActivationMethod

Adduct

Cython implementation of _Adduct

AggregationMethod

Aggregation method

AnalysisSummary

Cython implementation of _AnalysisSummary

AnnotationState

AnnotationStatistics

Cython implementation of _AnnotationStatistics

ArrayWrapperFloat

Assay

Cython implementation of _Assay

Attachment

Cython implementation of _Attachment

AverageLinkage

Cython implementation of _AverageLinkage

BSpline2d

Cython implementation of _BSpline2d

Base64

Cython implementation of _Base64

BaseFeature

Cython implementation of _BaseFeature

BasicProteinInferenceAlgorithm

Cython implementation of _BasicProteinInferenceAlgorithm

BayesianProteinInferenceAlgorithm

Cython implementation of _BayesianProteinInferenceAlgorithm

BernNorm

Cython implementation of _BernNorm

BiGaussFitter1D

Cython implementation of _BiGaussFitter1D

BiGaussModel

Cython implementation of _BiGaussModel

BilinearInterpolation

Cython implementation of _BilinearInterpolation[double,double]

BinnedSpectrum

Cython implementation of _BinnedSpectrum

BoundaryCondition

BoxElement

Cython implementation of _BoxElement

CV

Cython implementation of _CV

CVMappingFile

Cython implementation of _CVMappingFile

CVMappingRule

Cython implementation of _CVMappingRule

CVMappingTerm

Cython implementation of _CVMappingTerm

CVMappings

Cython implementation of _CVMappings

CVReference

Cython implementation of _CVReference

CVTerm

Cython implementation of _CVTerm

CVTermList

Cython implementation of _CVTermList

CVTermListInterface

Cython implementation of _CVTermListInterface

CVTerm_ControlledVocabulary

Cython implementation of _CVTerm_ControlledVocabulary

CachedMzMLHandler

Cython implementation of _CachedMzMLHandler

CachedSwathFileConsumer

Cython implementation of _CachedSwathFileConsumer

CachedmzML

Cython implementation of _CachedmzML

CalibrationData

Cython implementation of _CalibrationData

ChannelInfo

Cython implementation of _ChannelInfo

ChargePair

Cython implementation of _ChargePair

ChargedIndexSet

Cython implementation of _ChargedIndexSet

ChecksumType

ChromatogramExtractor

Cython implementation of _ChromatogramExtractor

ChromatogramExtractorAlgorithm

Cython implementation of _ChromatogramExtractorAlgorithm

ChromatogramPeak

Cython implementation of _ChromatogramPeak

ChromatogramSettings

Cython implementation of _ChromatogramSettings

ChromatogramTools

Cython implementation of _ChromatogramTools

ChromeleonFile

Cython implementation of _ChromeleonFile

ClusterProxyKD

Cython implementation of _ClusterProxyKD

ClusteringGrid

Cython implementation of _ClusteringGrid

CoarseIsotopePatternGenerator

Cython implementation of _CoarseIsotopePatternGenerator

ColumnHeader

Cython implementation of _ColumnHeader

CompNovoIdentification

Cython implementation of _CompNovoIdentification

CompNovoIdentificationCID

Cython implementation of _CompNovoIdentificationCID

CompNovoIonScoring

Cython implementation of _CompNovoIonScoring

CompNovoIonScoringCID

Cython implementation of _CompNovoIonScoringCID

ComplementFilter

Cython implementation of _ComplementFilter

ComplementMarker

Cython implementation of _ComplementMarker

Compomer

Cython implementation of _Compomer

Compound

Cython implementation of _Compound

ConfidenceScoring

Cython implementation of _ConfidenceScoring

Configuration

Cython implementation of _Configuration

ConsensusFeature

Cython implementation of _ConsensusFeature

ConsensusIDAlgorithm

Cython implementation of _ConsensusIDAlgorithm

ConsensusIDAlgorithmAverage

Cython implementation of _ConsensusIDAlgorithmAverage

ConsensusIDAlgorithmBest

Cython implementation of _ConsensusIDAlgorithmBest

ConsensusIDAlgorithmIdentity

Cython implementation of _ConsensusIDAlgorithmIdentity

ConsensusIDAlgorithmPEPIons

Cython implementation of _ConsensusIDAlgorithmPEPIons

ConsensusIDAlgorithmPEPMatrix

Cython implementation of _ConsensusIDAlgorithmPEPMatrix

ConsensusIDAlgorithmRanks

Cython implementation of _ConsensusIDAlgorithmRanks

ConsensusIDAlgorithmSimilarity

Cython implementation of _ConsensusIDAlgorithmSimilarity

ConsensusIDAlgorithmWorst

Cython implementation of _ConsensusIDAlgorithmWorst

ConsensusMap

alias of pyopenms._dataframes._ConsensusMapDF

ConsensusMapNormalizerAlgorithmMedian

Cython implementation of _ConsensusMapNormalizerAlgorithmMedian

ConsensusMapNormalizerAlgorithmQuantile

Cython implementation of _ConsensusMapNormalizerAlgorithmQuantile

ConsensusMapNormalizerAlgorithmThreshold

Cython implementation of _ConsensusMapNormalizerAlgorithmThreshold

ConsensusXMLFile

Cython implementation of _ConsensusXMLFile

Contact

Cython implementation of _Contact

ContactPerson

Cython implementation of _ContactPerson

ContinuousWaveletTransform

Cython implementation of _ContinuousWaveletTransform

ContinuousWaveletTransformNumIntegration

Cython implementation of _ContinuousWaveletTransformNumIntegration

ControlledVocabulary

Cython implementation of _ControlledVocabulary

ConvexHull2D

Cython implementation of _ConvexHull2D

CrossLinkSpectrumMatch

Cython implementation of _CrossLinkSpectrumMatch

CrossLinksDB

Cython implementation of _CrossLinksDB

CsiAdapterHit

Cython implementation of _CsiAdapterHit

CsiAdapterIdentification

Cython implementation of _CsiAdapterIdentification

CsiAdapterRun

Cython implementation of _CsiAdapterRun

CsiFingerIdMzTabWriter

Cython implementation of _CsiFingerIdMzTabWriter

CsvFile

Cython implementation of _CsvFile

CubicSpline2d

Cython implementation of _CubicSpline2d

DBoundingBox2

Cython implementation of _DBoundingBox2

DIAScoring

Cython implementation of _DIAScoring

DPosition1

DPosition2

DRange1

Cython implementation of _DRange1

DRange2

Cython implementation of _DRange2

DRangeIntersection

DTA2DFile

Cython implementation of _DTA2DFile

DTAFile

Cython implementation of _DTAFile

DataFilter

Cython implementation of _DataFilter

DataFilters

Cython implementation of _DataFilters

DataProcessing

Cython implementation of _DataProcessing

DataType

DataValue

Cython implementation of _DataValue

Date

Cython implementation of _Date

DateTime

Cython implementation of _DateTime

DeNovoIonScore

Cython implementation of _DeNovoIonScore

DecoyGenerator

Cython implementation of _DecoyGenerator

DecoyTransitionType

Deisotoper

Cython implementation of _Deisotoper

DigestSimulation

Cython implementation of _DigestSimulation

Digestion

Cython implementation of _Digestion

DigestionEnzyme

Cython implementation of _DigestionEnzyme

DigestionEnzymeProtein

Cython implementation of _DigestionEnzymeProtein

DigestionEnzymeRNA

Cython implementation of _DigestionEnzymeRNA

DimensionDescription

DistanceMatrix

Cython implementation of _DistanceMatrix[float]

DocumentIdentifier

Cython implementation of _DocumentIdentifier

DriftTimeUnit

EDTAFile

Cython implementation of _EDTAFile

Element

Cython implementation of _Element

ElementDB

Cython implementation of _ElementDB

ElutionModelFitter

Cython implementation of _ElutionModelFitter

ElutionPeakDetection

Cython implementation of _ElutionPeakDetection

EmgFitter1D

Cython implementation of _EmgFitter1D

EmgGradientDescent

Cython implementation of _EmgGradientDescent

EmgModel

Cython implementation of _EmgModel

EmgScoring

Cython implementation of _EmgScoring

EmpiricalFormula

Cython implementation of _EmpiricalFormula

EnzymaticDigestion

Cython implementation of _EnzymaticDigestion

EnzymaticDigestionLogModel

Cython implementation of _EnzymaticDigestionLogModel

ExperimentalDesign

Cython implementation of _ExperimentalDesign

ExperimentalDesignFile

Cython implementation of _ExperimentalDesignFile

ExperimentalDesign_MSFileSectionEntry

Cython implementation of _ExperimentalDesign_MSFileSectionEntry

ExperimentalDesign_SampleSection

Cython implementation of _ExperimentalDesign_SampleSection

ExperimentalSettings

Cython implementation of _ExperimentalSettings

ExtractionCoordinates

Cython implementation of _ExtractionCoordinates

FASTAEntry

Cython implementation of _FASTAEntry

FASTAFile

Cython implementation of _FASTAFile

FIAMSDataProcessor

Cython implementation of _FIAMSDataProcessor

FIAMSScheduler

Cython implementation of _FIAMSScheduler

FalseDiscoveryRate

Cython implementation of _FalseDiscoveryRate

Feature

Cython implementation of _Feature

FeatureDeconvolution

Cython implementation of _FeatureDeconvolution

FeatureDistance

Cython implementation of _FeatureDistance

FeatureFileOptions

Cython implementation of _FeatureFileOptions

FeatureFinder

Cython implementation of _FeatureFinder

FeatureFinderAlgorithmIsotopeWavelet

Cython implementation of _FeatureFinderAlgorithmIsotopeWavelet

FeatureFinderAlgorithmMetaboIdent

Cython implementation of _FeatureFinderAlgorithmMetaboIdent

FeatureFinderAlgorithmPicked

Cython implementation of _FeatureFinderAlgorithmPicked

FeatureFinderIdentificationAlgorithm

Cython implementation of _FeatureFinderIdentificationAlgorithm

FeatureFinderMetaboIdentCompound

Cython implementation of _FeatureFinderMetaboIdentCompound

FeatureFinderMultiplexAlgorithm

Cython implementation of _FeatureFinderMultiplexAlgorithm

FeatureFindingMetabo

Cython implementation of _FeatureFindingMetabo

FeatureGroupingAlgorithm

Cython implementation of _FeatureGroupingAlgorithm

FeatureGroupingAlgorithmKD

Cython implementation of _FeatureGroupingAlgorithmKD

FeatureGroupingAlgorithmLabeled

Cython implementation of _FeatureGroupingAlgorithmLabeled

FeatureGroupingAlgorithmQT

Cython implementation of _FeatureGroupingAlgorithmQT

FeatureGroupingAlgorithmUnlabeled

Cython implementation of _FeatureGroupingAlgorithmUnlabeled

FeatureHandle

Cython implementation of _FeatureHandle

FeatureMap

alias of pyopenms._dataframes._FeatureMapDF

FeatureMapping

Cython implementation of _FeatureMapping

FeatureMapping_FeatureMappingInfo

Cython implementation of _FeatureMapping_FeatureMappingInfo

FeatureMapping_FeatureToMs2Indices

Cython implementation of _FeatureMapping_FeatureToMs2Indices

FeatureXMLFile

Cython implementation of _FeatureXMLFile

File

Cython implementation of _File

FileHandler

Cython implementation of _FileHandler

FileType

FileTypes

Cython implementation of _FileTypes

FilterFunctor

Cython implementation of _FilterFunctor

FineIsotopePatternGenerator

Cython implementation of _FineIsotopePatternGenerator

Fitter1D

Cython implementation of _Fitter1D

FloatDataArray

Cython implementation of _FloatDataArray

GNPSMGFFile

Cython implementation of _GNPSMGFFile

GNPSMetaValueFile

Cython implementation of _GNPSMetaValueFile

GNPSQuantificationFile

Cython implementation of _GNPSQuantificationFile

GaussFilter

Cython implementation of _GaussFilter

GaussFitResult

Cython implementation of _GaussFitResult

GaussFitter

Cython implementation of _GaussFitter

GaussTraceFitter

Cython implementation of _GaussTraceFitter

GoodDiffFilter

Cython implementation of _GoodDiffFilter

Gradient

Cython implementation of _Gradient

GridBasedCluster

Cython implementation of _GridBasedCluster

HMMState

Cython implementation of _HMMState

HPLC

Cython implementation of _HPLC

HiddenMarkovModel

Cython implementation of _HiddenMarkovModel

HyperScore

Cython implementation of _HyperScore

IBSpectraFile

Cython implementation of _IBSpectraFile

IDConflictResolverAlgorithm

Cython implementation of _IDConflictResolverAlgorithm

IDDecoyProbability

Cython implementation of _IDDecoyProbability

IDFilter

Cython implementation of _IDFilter

IDMapper

Cython implementation of _IDMapper

IDMapper_SpectraIdentificationState

Cython implementation of _IDMapper_SpectraIdentificationState

IDRipper

Cython implementation of _IDRipper

ILPDCWrapper

Cython implementation of _ILPDCWrapper

IMFormat

IMSAlphabet

Cython implementation of _IMSAlphabet

IMSElement

Cython implementation of _IMSElement

IMSIsotopeDistribution

Cython implementation of _IMSIsotopeDistribution

IMSIsotopeDistribution_Peak

Cython implementation of _IMSIsotopeDistribution_Peak

IMSWeights

Cython implementation of _IMSWeights

IMTypes

Cython implementation of _IMTypes

ISDGroup

Cython implementation of _ISDGroup

ITRAQ_TYPES

IdXMLFile

Cython implementation of _IdXMLFile

Identification

Cython implementation of _Identification

IdentificationData

Cython implementation of _IdentificationData

IdentificationDataConverter

Cython implementation of _IdentificationDataConverter

IdentificationHit

Cython implementation of _IdentificationHit

IdentificationRuns

Cython implementation of _IdentificationRuns

IncludeExcludeTarget

Cython implementation of _IncludeExcludeTarget

InclusionExclusionList

Cython implementation of _InclusionExclusionList

IndexTriple

Cython implementation of _IndexTriple

IndexedMzMLDecoder

Cython implementation of _IndexedMzMLDecoder

IndexedMzMLFileLoader

Cython implementation of _IndexedMzMLFileLoader

IndexedMzMLHandler

Cython implementation of _IndexedMzMLHandler

InspectInfile

Cython implementation of _InspectInfile

InspectOutfile

Cython implementation of _InspectOutfile

Instrument

Cython implementation of _Instrument

InstrumentSettings

Cython implementation of _InstrumentSettings

IntegerDataArray

Cython implementation of _IntegerDataArray

IntensityBalanceFilter

Cython implementation of _IntensityBalanceFilter

Interfaces()

InternalCalibration

Cython implementation of _InternalCalibration

InternalCalibration_LockMass

Cython implementation of _InternalCalibration_LockMass

Internal_MzMLValidator

Cython implementation of _Internal_MzMLValidator

InterpolationModel

Cython implementation of _InterpolationModel

IonDetector

Cython implementation of _IonDetector

IonIdentityMolecularNetworking

Cython implementation of _IonIdentityMolecularNetworking

IonOpticsType

IonSource

Cython implementation of _IonSource

IonType

Cython implementation of _IonType

IsobaricChannelExtractor

Cython implementation of _IsobaricChannelExtractor

IsobaricChannelInformation

Cython implementation of _IsobaricChannelInformation

IsobaricIsotopeCorrector

Cython implementation of _IsobaricIsotopeCorrector

IsobaricNormalizer

Cython implementation of _IsobaricNormalizer

IsobaricQuantifier

Cython implementation of _IsobaricQuantifier

IsobaricQuantifierStatistics

Cython implementation of _IsobaricQuantifierStatistics

IsotopeCluster

Cython implementation of _IsotopeCluster

IsotopeDiffFilter

Cython implementation of _IsotopeDiffFilter

IsotopeDistribution

Cython implementation of _IsotopeDistribution

IsotopeDistributionCache

Cython implementation of _IsotopeDistributionCache

IsotopeFitter1D

Cython implementation of _IsotopeFitter1D

IsotopeLabelingMDVs

Cython implementation of _IsotopeLabelingMDVs

IsotopeMarker

Cython implementation of _IsotopeMarker

IsotopeModel

Cython implementation of _IsotopeModel

IsotopePattern

Cython implementation of _IsotopePattern

IsotopeVariant

IsotopeWavelet

Cython implementation of _IsotopeWavelet

IsotopeWaveletTransform

Cython implementation of _IsotopeWaveletTransform[_Peak1D]

ItraqConstants

Cython implementation of _ItraqConstants

ItraqEightPlexQuantitationMethod

Cython implementation of _ItraqEightPlexQuantitationMethod

ItraqFourPlexQuantitationMethod

Cython implementation of _ItraqFourPlexQuantitationMethod

JavaInfo

Cython implementation of _JavaInfo

KDTreeFeatureMaps

Cython implementation of _KDTreeFeatureMaps

KDTreeFeatureNode

Cython implementation of _KDTreeFeatureNode

Kernel_MassTrace

Cython implementation of _Kernel_MassTrace

KroenikFile

Cython implementation of _KroenikFile

LLMParam

Cython implementation of _LLMParam

LPWrapper

Cython implementation of _LPWrapper

LabeledPairFinder

Cython implementation of _LabeledPairFinder

LibSVMEncoder

Cython implementation of _LibSVMEncoder

LightCompound

Cython implementation of _LightCompound

LightMRMTransitionGroupCP

Cython implementation of _MRMTransitionGroup[_MSChromatogram,_LightTransition]

LightModification

Cython implementation of _LightModification

LightProtein

Cython implementation of _LightProtein

LightTargetedExperiment

Cython implementation of _LightTargetedExperiment

LightTransition

Cython implementation of _LightTransition

LinearInterpolation

Cython implementation of _LinearInterpolation[double,double]

LinearResampler

Cython implementation of _LinearResampler

LinearResamplerAlign

Cython implementation of _LinearResamplerAlign

LocalLinearMap

Cython implementation of _LocalLinearMap

LogType

LowessSmoothing

Cython implementation of _LowessSmoothing

MRMAssay

Cython implementation of _MRMAssay

MRMDecoy

Cython implementation of _MRMDecoy

MRMFP_ComponentGroupParams

Cython implementation of _MRMFP_ComponentGroupParams

MRMFP_ComponentParams

Cython implementation of _MRMFP_ComponentParams

MRMFQC_ComponentGroupPairQCs

Cython implementation of _MRMFQC_ComponentGroupPairQCs

MRMFQC_ComponentGroupQCs

Cython implementation of _MRMFQC_ComponentGroupQCs

MRMFQC_ComponentQCs

Cython implementation of _MRMFQC_ComponentQCs

MRMFeature

Cython implementation of _MRMFeature

MRMFeatureFilter

Cython implementation of _MRMFeatureFilter

MRMFeatureFinderScoring

Cython implementation of _MRMFeatureFinderScoring

MRMFeaturePicker

Cython implementation of _MRMFeaturePicker

MRMFeaturePickerFile

Cython implementation of _MRMFeaturePickerFile

MRMFeatureQC

Cython implementation of _MRMFeatureQC

MRMFeatureQCFile

Cython implementation of _MRMFeatureQCFile

MRMFragmentSelection

Cython implementation of _MRMFragmentSelection

MRMIonSeries

Cython implementation of _MRMIonSeries

MRMMapping

Cython implementation of _MRMMapping

MRMRTNormalizer

Cython implementation of _MRMRTNormalizer

MRMScoring

Cython implementation of _MRMScoring

MRMTransitionGroupCP

Cython implementation of _MRMTransitionGroup[_MSChromatogram,_ReactionMonitoringTransition]

MRMTransitionGroupPicker

Cython implementation of _MRMTransitionGroupPicker

MS2File

Cython implementation of _MS2File

MSChromatogram

Cython implementation of _MSChromatogram

MSDGroup

Cython implementation of _MSDGroup

MSDataAggregatingConsumer

Cython implementation of _MSDataAggregatingConsumer

MSDataCachedConsumer

Cython implementation of _MSDataCachedConsumer

MSDataSqlConsumer

Cython implementation of _MSDataSqlConsumer

MSDataStoringConsumer

Cython implementation of _MSDataStoringConsumer

MSExperiment

alias of pyopenms._dataframes._MSExperimentDF

MSNumpressCoder

Cython implementation of _MSNumpressCoder

MSPFile

Cython implementation of _MSPFile

MSPGenericFile

Cython implementation of _MSPGenericFile

MSQuantifications

Cython implementation of _MSQuantifications

MSSim

Cython implementation of _MSSim

MSSpectrum

Cython implementation of _MSSpectrum

MSstatsFile

Cython implementation of _MSstatsFile

MT_QUANTMETHOD

MZTrafoModel

Cython implementation of _MZTrafoModel

MZTrafoModel_MODELTYPE

MapAlignmentAlgorithmIdentification

Cython implementation of _MapAlignmentAlgorithmIdentification

MapAlignmentAlgorithmKD

Cython implementation of _MapAlignmentAlgorithmKD

MapAlignmentAlgorithmPoseClustering

Cython implementation of _MapAlignmentAlgorithmPoseClustering

MapAlignmentAlgorithmSpectrumAlignment

Cython implementation of _MapAlignmentAlgorithmSpectrumAlignment

MapAlignmentEvaluationAlgorithmPrecision

Cython implementation of _MapAlignmentEvaluationAlgorithmPrecision

MapAlignmentEvaluationAlgorithmRecall

Cython implementation of _MapAlignmentEvaluationAlgorithmRecall

MapAlignmentTransformer

Cython implementation of _MapAlignmentTransformer

MapConversion

Cython implementation of _MapConversion

MarkerMower

Cython implementation of _MarkerMower

MascotGenericFile

Cython implementation of _MascotGenericFile

MascotInfile

Cython implementation of _MascotInfile

MascotXMLFile

Cython implementation of _MascotXMLFile

MassAnalyzer

Cython implementation of _MassAnalyzer

MassDecomposition

Cython implementation of _MassDecomposition

MassDecompositionAlgorithm

Cython implementation of _MassDecompositionAlgorithm

MassExplainer

Cython implementation of _MassExplainer

MassTrace

Cython implementation of _MassTrace

MassTraceDetection

Cython implementation of _MassTraceDetection

MassTraces

Cython implementation of _MassTraces

MasstraceCorrelator

Cython implementation of _MasstraceCorrelator

MatrixDouble

Cython implementation of _Matrix[double]

Measure

MetaInfo

Cython implementation of _MetaInfo

MetaInfoDescription

Cython implementation of _MetaInfoDescription

MetaInfoInterface

Cython implementation of _MetaInfoInterface

MetaInfoRegistry

Cython implementation of _MetaInfoRegistry

MetaboTargetedAssay

Cython implementation of _MetaboTargetedAssay

MetaboTargetedAssay_CompoundTargetDecoyPair

Cython implementation of _MetaboTargetedAssay_CompoundTargetDecoyPair

MetaboTargetedTargetDecoy

Cython implementation of _MetaboTargetedTargetDecoy

MetaboTargetedTargetDecoy_MetaboTargetDecoyMassMapping

Cython implementation of _MetaboTargetedTargetDecoy_MetaboTargetDecoyMassMapping

MetaboliteFeatureDeconvolution

Cython implementation of _MetaboliteFeatureDeconvolution

MetaboliteSpectralMatching

Cython implementation of _MetaboliteSpectralMatching

Modification

Cython implementation of _Modification

ModificationDefinition

Cython implementation of _ModificationDefinition

ModificationDefinitionsSet

Cython implementation of _ModificationDefinitionsSet

ModificationsDB

Cython implementation of _ModificationsDB

ModifiedPeptideGenerator

Cython implementation of _ModifiedPeptideGenerator

ModifiedPeptideGenerator_MapToResidueType

Cython implementation of _ModifiedPeptideGenerator_MapToResidueType

MorpheusScore

Cython implementation of _MorpheusScore

MorpheusScore_Result

Cython implementation of _MorpheusScore_Result

MorphologicalFilter

Cython implementation of _MorphologicalFilter

MsInspectFile

Cython implementation of _MsInspectFile

MultiplexDeltaMasses

Cython implementation of _MultiplexDeltaMasses

MultiplexDeltaMassesGenerator

Cython implementation of _MultiplexDeltaMassesGenerator

MultiplexDeltaMassesGenerator_Label

Cython implementation of _MultiplexDeltaMassesGenerator_Label

MultiplexDeltaMasses_DeltaMass

Cython implementation of _MultiplexDeltaMasses_DeltaMass

MultiplexIsotopicPeakPattern

Cython implementation of _MultiplexIsotopicPeakPattern

MzDataFile

Cython implementation of _MzDataFile

MzIdentMLFile

Cython implementation of _MzIdentMLFile

MzMLFile

Cython implementation of _MzMLFile

MzMLSpectrumDecoder

Cython implementation of _MzMLSpectrumDecoder

MzMLSqliteHandler

Cython implementation of _MzMLSqliteHandler

MzMLSwathFileConsumer

Cython implementation of _MzMLSwathFileConsumer

MzQCFile

Cython implementation of _MzQCFile

MzQuantMLFile

Cython implementation of _MzQuantMLFile

MzTab

Cython implementation of _MzTab

MzTabFile

Cython implementation of _MzTabFile

MzTabM

Cython implementation of _MzTabM

MzTabMFile

Cython implementation of _MzTabMFile

MzXMLFile

Cython implementation of _MzXMLFile

NASequence

Cython implementation of _NASequence

NLargest

Cython implementation of _NLargest

NeutralLossDiffFilter

Cython implementation of _NeutralLossDiffFilter

NeutralLossMarker

Cython implementation of _NeutralLossMarker

NoiseEstimator

Cython implementation of _NoiseEstimator

NonNegativeLeastSquaresSolver

Cython implementation of _NonNegativeLeastSquaresSolver

NoopMSDataWritingConsumer

Cython implementation of _NoopMSDataWritingConsumer

NormalizationMethod

Normalizer

Cython implementation of _Normalizer

NucleicAcidSpectrumGenerator

Cython implementation of _NucleicAcidSpectrumGenerator

NumpressConfig

Cython implementation of _NumpressConfig

OMSSACSVFile

Cython implementation of _OMSSACSVFile

OMSSAXMLFile

Cython implementation of _OMSSAXMLFile

OPXLDataStructs

Cython implementation of _OPXLDataStructs

OPXLHelper

Cython implementation of _OPXLHelper

OPXLSpectrumProcessingAlgorithms

Cython implementation of _OPXLSpectrumProcessingAlgorithms

OPXL_PreprocessedPairSpectra

Cython implementation of _OPXL_PreprocessedPairSpectra

OSBinaryDataArray

Cython implementation of _OSBinaryDataArray

OSChromatogram

Cython implementation of _OSChromatogram

OSChromatogramMeta

Cython implementation of _OSChromatogramMeta

OSSpectrum

Cython implementation of _OSSpectrum

OSSpectrumMeta

Cython implementation of _OSSpectrumMeta

OSWFile

Cython implementation of _OSWFile

OSW_ChromExtractParams

Cython implementation of _OSW_ChromExtractParams

OfflinePrecursorIonSelection

Cython implementation of _OfflinePrecursorIonSelection

OnDiscMSExperiment

Cython implementation of _OnDiscMSExperiment

OpenMSBuildInfo

Cython implementation of _OpenMSBuildInfo

OpenMSOSInfo

Cython implementation of _OpenMSOSInfo

OpenPepXLAlgorithm

Cython implementation of _OpenPepXLAlgorithm

OpenPepXLLFAlgorithm

Cython implementation of _OpenPepXLLFAlgorithm

OpenSwathDataAccessHelper

Cython implementation of _OpenSwathDataAccessHelper

OpenSwathHelper

Cython implementation of _OpenSwathHelper

OpenSwathOSWWriter

Cython implementation of _OpenSwathOSWWriter

OpenSwathScoring

Cython implementation of _OpenSwathScoring

OpenSwath_Scores

Cython implementation of _OpenSwath_Scores

OpenSwath_Scores_Usage

Cython implementation of _OpenSwath_Scores_Usage

OptimizationFunctions_PenaltyFactors

Cython implementation of _OptimizationFunctions_PenaltyFactors

OptimizePeakDeconvolution

Cython implementation of _OptimizePeakDeconvolution

OptimizePeakDeconvolution_Data

Cython implementation of _OptimizePeakDeconvolution_Data

OptimizePick

Cython implementation of _OptimizePick

OptimizePick_Data

Cython implementation of _OptimizePick_Data

OriginAnnotationFormat

PI_PeakArea

Cython implementation of _PI_PeakArea

PI_PeakBackground

Cython implementation of _PI_PeakBackground

PI_PeakShapeMetrics

Cython implementation of _PI_PeakShapeMetrics

PSLPFormulation

Cython implementation of _PSLPFormulation

PSProteinInference

Cython implementation of _PSProteinInference

PScore

Cython implementation of _PScore

Param

Cython implementation of _Param

ParamCTDFile

Cython implementation of _ParamCTDFile

ParamEntry

Cython implementation of _ParamEntry

ParamNode

Cython implementation of _ParamNode

ParamValue

Cython implementation of _ParamValue

ParamXMLFile

Cython implementation of _ParamXMLFile

ParentPeakMower

Cython implementation of _ParentPeakMower

Peak1D

Cython implementation of _Peak1D

Peak2D

Cython implementation of _Peak2D

PeakBoundary

Cython implementation of _PeakBoundary

PeakCandidate

Cython implementation of _PeakCandidate

PeakFileOptions

Cython implementation of _PeakFileOptions

PeakIndex

Cython implementation of _PeakIndex

PeakIntegrator

Cython implementation of _PeakIntegrator

PeakIntensityPredictor

Cython implementation of _PeakIntensityPredictor

PeakMap

alias of pyopenms._dataframes._MSExperimentDF

PeakMarker

Cython implementation of _PeakMarker

PeakPickerCWT

Cython implementation of _PeakPickerCWT

PeakPickerHiRes

Cython implementation of _PeakPickerHiRes

PeakPickerIterative

Cython implementation of _PeakPickerIterative

PeakPickerMRM

Cython implementation of _PeakPickerMRM

PeakPickerMaxima

Cython implementation of _PeakPickerMaxima

PeakPickerSH

Cython implementation of _PeakPickerSH

PeakShape

Cython implementation of _PeakShape

PeakSpectrum

alias of pyopenms._pyopenms_5.MSSpectrum

PeakTypeEstimator

Cython implementation of _PeakTypeEstimator

PeakWidthEstimator

Cython implementation of _PeakWidthEstimator

PenaltyFactorsIntensity

Cython implementation of _PenaltyFactorsIntensity

PepXMLFile

Cython implementation of _PepXMLFile

PepXMLFileMascot

Cython implementation of _PepXMLFileMascot

Peptide

Cython implementation of _Peptide

PeptideAndProteinQuant

Cython implementation of _PeptideAndProteinQuant

PeptideAndProteinQuant_PeptideData

Cython implementation of _PeptideAndProteinQuant_PeptideData

PeptideAndProteinQuant_ProteinData

Cython implementation of _PeptideAndProteinQuant_ProteinData

PeptideAndProteinQuant_Statistics

Cython implementation of _PeptideAndProteinQuant_Statistics

PeptideEntry

Cython implementation of _PeptideEntry

PeptideEvidence

Cython implementation of _PeptideEvidence

PeptideHit

Cython implementation of _PeptideHit

PeptideHit_AnalysisResult

Cython implementation of _PeptideHit_AnalysisResult

PeptideHit_PeakAnnotation

Cython implementation of _PeptideHit_PeakAnnotation

PeptideIdentification

Cython implementation of _PeptideIdentification

PeptideIndexing

Cython implementation of _PeptideIndexing

PeptideProteinResolution

Cython implementation of _PeptideProteinResolution

PeptideProteinResolution_ConnectedComponent

Cython implementation of _PeptideProteinResolution_ConnectedComponent

PercolatorFeatureSetHelper

Cython implementation of _PercolatorFeatureSetHelper

PercolatorInfile

Cython implementation of _PercolatorInfile

PercolatorOutfile

Cython implementation of _PercolatorOutfile

PlainMSDataWritingConsumer

Cython implementation of _PlainMSDataWritingConsumer

PosteriorErrorProbabilityModel

Cython implementation of _PosteriorErrorProbabilityModel

Precursor

Cython implementation of _Precursor

PrecursorCorrection

Cython implementation of _PrecursorCorrection

PrecursorIonSelection

Cython implementation of _PrecursorIonSelection

PrecursorIonSelectionPreprocessing

Cython implementation of _PrecursorIonSelectionPreprocessing

PrecursorPurity

Cython implementation of _PrecursorPurity

Prediction

Cython implementation of _Prediction

ProbablePhosphoSites

Cython implementation of _ProbablePhosphoSites

Product

Cython implementation of _Product

ProgressLogger

Cython implementation of _ProgressLogger

ProtXMLFile

Cython implementation of _ProtXMLFile

ProteaseDB

Cython implementation of _ProteaseDB

ProteaseDigestion

Cython implementation of _ProteaseDigestion

Protein

Cython implementation of _Protein

ProteinEntry

Cython implementation of _ProteinEntry

ProteinGroup

Cython implementation of _ProteinGroup

ProteinHit

Cython implementation of _ProteinHit

ProteinIdentification

Cython implementation of _ProteinIdentification

ProteinInference

Cython implementation of _ProteinInference

ProteinProteinCrossLink

Cython implementation of _ProteinProteinCrossLink

ProteinResolver

Cython implementation of _ProteinResolver

ProteinResolverResult_Type

ProtonDistributionModel

Cython implementation of _ProtonDistributionModel

Publication

Cython implementation of _Publication

PurityScores

Cython implementation of _PurityScores

QTCluster

Cython implementation of _QTCluster

QTClusterFinder

Cython implementation of _QTClusterFinder

QcMLFile

Cython implementation of _QcMLFile

QualityParameter

Cython implementation of _QualityParameter

QuantitativeExperimentalDesign

Cython implementation of _QuantitativeExperimentalDesign

QuotingMethod

RANSAC

Cython implementation of _RANSAC[_RansacModelLinear]

RANSACParam

Cython implementation of _RANSACParam

RANSACQuadratic

Cython implementation of _RANSAC[_RansacModelQuadratic]

RNPxlMarkerIonExtractor

Cython implementation of _RNPxlMarkerIonExtractor

RNPxlModificationMassesResult

Cython implementation of _RNPxlModificationMassesResult

RNPxlModificationsGenerator

Cython implementation of _RNPxlModificationsGenerator

RNPxlReport

Cython implementation of _RNPxlReport

RNPxlReportRow

Cython implementation of _RNPxlReportRow

RNPxlReportRowHeader

Cython implementation of _RNPxlReportRowHeader

RNaseDB

Cython implementation of _RNaseDB

RNaseDigestion

Cython implementation of _RNaseDigestion

RansacModelLinear

Cython implementation of _RansacModelLinear

RansacModelQuadratic

Cython implementation of _RansacModelQuadratic

Ratio

Cython implementation of _Ratio

ReactionMonitoringTransition

Cython implementation of _ReactionMonitoringTransition

RealMassDecomposer

Cython implementation of _RealMassDecomposer

RegularSwathFileConsumer

Cython implementation of _RegularSwathFileConsumer

Residue

Cython implementation of _Residue

ResidueDB

Cython implementation of _ResidueDB

ResidueModification

Cython implementation of _ResidueModification

ResolverResult

Cython implementation of _ResolverResult

RetentionTime

Cython implementation of _RetentionTime

Ribonucleotide

Cython implementation of _Ribonucleotide

RibonucleotideDB

Cython implementation of _RibonucleotideDB

RichPeak2D

Cython implementation of _RichPeak2D

RipFileContent

Cython implementation of _RipFileContent

RipFileIdentifier

Cython implementation of _RipFileIdentifier

SIDE

SILACLabeler

Cython implementation of _SILACLabeler

SVMData

Cython implementation of _SVMData

SVMPrediction

Cython implementation of _SVMPrediction

SVMWrapper

Cython implementation of _SVMWrapper

Sample

Cython implementation of _Sample

SavitzkyGolayFilter

Cython implementation of _SavitzkyGolayFilter

Scaler

Cython implementation of _Scaler

ScanMode

ScanWindow

Cython implementation of _ScanWindow

SearchParameters

Cython implementation of _SearchParameters

Seed

Cython implementation of _Seed

SeedListGenerator

Cython implementation of _SeedListGenerator

SemanticValidator

Cython implementation of _SemanticValidator

SemanticValidator_CVTerm

Cython implementation of _SemanticValidator_CVTerm

SequestInfile

Cython implementation of _SequestInfile

SequestOutfile

Cython implementation of _SequestOutfile

SignalToNoiseEstimatorMeanIterative

Cython implementation of _SignalToNoiseEstimatorMeanIterative[_MSSpectrum]

SignalToNoiseEstimatorMedian

Cython implementation of _SignalToNoiseEstimatorMedian[_MSSpectrum]

SignalToNoiseEstimatorMedianChrom

SignalToNoiseEstimatorMedianRapid

Cython implementation of _SignalToNoiseEstimatorMedianRapid

SimProtein

Cython implementation of _SimProtein

SimRandomNumberGenerator

Cython implementation of _SimRandomNumberGenerator

SimpleOpenMSSpectraFactory()

SimplePairFinder

Cython implementation of _SimplePairFinder

SimplePeak

Cython implementation of _SimplePeak

SimpleSVM

Cython implementation of _SimpleSVM

SimpleSearchEngineAlgorithm

Cython implementation of _SimpleSearchEngineAlgorithm

SimpleTSGXLMS

Cython implementation of _SimpleTSGXLMS

SiriusAdapterAlgorithm

Cython implementation of _SiriusAdapterAlgorithm

SiriusAdapterHit

Cython implementation of _SiriusAdapterHit

SiriusAdapterIdentification

Cython implementation of _SiriusAdapterIdentification

SiriusAdapterRun

Cython implementation of _SiriusAdapterRun

SiriusFragmentAnnotation

Cython implementation of _SiriusFragmentAnnotation

SiriusFragmentAnnotation_SiriusTargetDecoySpectra

Cython implementation of _SiriusFragmentAnnotation_SiriusTargetDecoySpectra

SiriusMSFile

Cython implementation of _SiriusMSFile

SiriusMSFile_AccessionInfo

Cython implementation of _SiriusMSFile_AccessionInfo

SiriusMSFile_CompoundInfo

Cython implementation of _SiriusMSFile_CompoundInfo

SiriusMzTabWriter

Cython implementation of _SiriusMzTabWriter

SiriusMzTabWriter_SiriusSpectrumMSInfo

Cython implementation of _SiriusMzTabWriter_SiriusSpectrumMSInfo

SiriusTemporaryFileSystemObjects

Cython implementation of _SiriusTemporaryFileSystemObjects

Software

Cython implementation of _Software

SolverParam

Cython implementation of _SolverParam

SourceFile

Cython implementation of _SourceFile

SpectraMerger

Cython implementation of _SpectraMerger

SpectraSTSimilarityScore

Cython implementation of _SpectraSTSimilarityScore

SpectralMatch

Cython implementation of _SpectralMatch

SpectrumAccessOpenMS

Cython implementation of _SpectrumAccessOpenMS

SpectrumAccessOpenMSCached

Cython implementation of _SpectrumAccessOpenMSCached

SpectrumAccessOpenMSInMemory

Cython implementation of _SpectrumAccessOpenMSInMemory

SpectrumAccessQuadMZTransforming

Cython implementation of _SpectrumAccessQuadMZTransforming

SpectrumAccessSqMass

Cython implementation of _SpectrumAccessSqMass

SpectrumAccessTransforming

Cython implementation of _SpectrumAccessTransforming

SpectrumAlignment

Cython implementation of _SpectrumAlignment

SpectrumAlignmentScore

Cython implementation of _SpectrumAlignmentScore

SpectrumAnnotator

Cython implementation of _SpectrumAnnotator

SpectrumHelper

Cython implementation of _SpectrumHelper

SpectrumIdentification

Cython implementation of _SpectrumIdentification

SpectrumLookup

Cython implementation of _SpectrumLookup

SpectrumMetaData

Cython implementation of _SpectrumMetaData

SpectrumMetaDataLookup

Cython implementation of _SpectrumMetaDataLookup

SpectrumSettings

Cython implementation of _SpectrumSettings

SplineInterpolatedPeaks

Cython implementation of _SplineInterpolatedPeaks

SplinePackage

Cython implementation of _SplinePackage

SplineSpectrum_Navigator

Cython implementation of _SplineSpectrum_Navigator

SqMassConfig

Cython implementation of _SqMassConfig

SqMassFile

Cython implementation of _SqMassFile

SqrtMower

Cython implementation of _SqrtMower

StablePairFinder

Cython implementation of _StablePairFinder

String

Cython implementation of _String

StringDataArray

Cython implementation of _StringDataArray

StringView

Cython implementation of _StringView

SvmModelParameterSet

Cython implementation of _SvmModelParameterSet

SvmTheoreticalSpectrumGenerator

Cython implementation of _SvmTheoreticalSpectrumGenerator

SvmTheoreticalSpectrumGeneratorSet

Cython implementation of _SvmTheoreticalSpectrumGeneratorSet

SvmTheoreticalSpectrumGeneratorTrainer

Cython implementation of _SvmTheoreticalSpectrumGeneratorTrainer

SwathFile

Cython implementation of _SwathFile

SwathMap

Cython implementation of _SwathMap

SwathMapMassCorrection

Cython implementation of _SwathMapMassCorrection

SwathWindowLoader

Cython implementation of _SwathWindowLoader

SysInfo

TICFilter

Cython implementation of _TICFilter

TMTEighteenPlexQuantitationMethod

Cython implementation of _TMTEighteenPlexQuantitationMethod

TMTElevenPlexQuantitationMethod

Cython implementation of _TMTElevenPlexQuantitationMethod

TMTSixPlexQuantitationMethod

Cython implementation of _TMTSixPlexQuantitationMethod

TMTSixteenPlexQuantitationMethod

Cython implementation of _TMTSixteenPlexQuantitationMethod

TMTTenPlexQuantitationMethod

Cython implementation of _TMTTenPlexQuantitationMethod

TM_DataPoint

Cython implementation of _TM_DataPoint

TOFCalibration

Cython implementation of _TOFCalibration

TSE_Match

Cython implementation of _TSE_Match

Tagger

Cython implementation of _Tagger

Tagging

Cython implementation of _Tagging

TargetedExperiment

Cython implementation of _TargetedExperiment

TargetedExperiment_Instrument

Cython implementation of _TargetedExperiment_Instrument

TargetedExperiment_Interpretation

Cython implementation of _TargetedExperiment_Interpretation

TargetedExperiment_Modification

Cython implementation of _TargetedExperiment_Modification

TargetedSpectraExtractor

Cython implementation of _TargetedSpectraExtractor

TermSpecificityNuc

TextFile

Cython implementation of _TextFile

TheoreticalIsotopePattern

Cython implementation of _TheoreticalIsotopePattern

TheoreticalSpectrumGenerator

Cython implementation of _TheoreticalSpectrumGenerator

TheoreticalSpectrumGeneratorXLMS

Cython implementation of _TheoreticalSpectrumGeneratorXLMS

ThresholdMower

Cython implementation of _ThresholdMower

ToolInfo

Cython implementation of _ToolInfo

TraMLFile

Cython implementation of _TraMLFile

TraMLProduct

Cython implementation of _TraMLProduct

TraceInfo

Cython implementation of _TraceInfo

TransformationDescription

Cython implementation of _TransformationDescription

TransformationModelBSpline

Cython implementation of _TransformationModelBSpline

TransformationModelInterpolated

Cython implementation of _TransformationModelInterpolated

TransformationModelLinear

Cython implementation of _TransformationModelLinear

TransformationModelLowess

Cython implementation of _TransformationModelLowess

TransformationStatistics

Cython implementation of _TransformationStatistics

TransformationXMLFile

Cython implementation of _TransformationXMLFile

TransitionPQPFile

Cython implementation of _TransitionPQPFile

TransitionTSVFile

Cython implementation of _TransitionTSVFile

TwoDOptimization

Cython implementation of _TwoDOptimization

UnimodXMLFile

Cython implementation of _UnimodXMLFile

UniqueIdGenerator

Cython implementation of _UniqueIdGenerator

Unit

Cython implementation of _Unit

UnitType

ValueType

VersionDetails

Cython implementation of _VersionDetails

VersionInfo

Cython implementation of _VersionInfo

WindowMower

Cython implementation of _WindowMower

XFDRAlgorithm

Cython implementation of _XFDRAlgorithm

XLPrecursor

Cython implementation of _XLPrecursor

XMLFile

Cython implementation of _XMLFile

XMLHandler

Cython implementation of _XMLHandler

XQuestResultXMLFile

Cython implementation of _XQuestResultXMLFile

XQuestScores

Cython implementation of _XQuestScores

XRefType_CVTerm_ControlledVocabulary

XTandemInfile

Cython implementation of _XTandemInfile

XTandemXMLFile

Cython implementation of _XTandemXMLFile

streampos

Cython implementation of _streampos