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.
`update_scores_from_df`(peps, df, main_score_name)	Updates the scores in PeptideIdentification objects using 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
`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 `_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
`DecoyGenerator`	Cython implementation of _DecoyGenerator
`DecoyTransitionType`
`Deisotoper`	Cython implementation of _Deisotoper
`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
`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 `_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
`IdentificationHit`	Cython implementation of _IdentificationHit
`IdentificationRuns`	Cython implementation of _IdentificationRuns
`IncludeExcludeTarget`	Cython implementation of _IncludeExcludeTarget
`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
`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
`LPWrapper`	Cython implementation of _LPWrapper
`LabeledPairFinder`	Cython implementation of _LabeledPairFinder
`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
`LogConfigHandler`	Cython implementation of _LogConfigHandler
`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 `_MSExperimentDF`
`MSNumpressCoder`	Cython implementation of _MSNumpressCoder
`MSPFile`	Cython implementation of _MSPFile
`MSPGenericFile`	Cython implementation of _MSPGenericFile
`MSQuantifications`	Cython implementation of _MSQuantifications
`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
`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
`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
`PeakMap`	alias of `_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 `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
`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`
`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
`SimpleOpenMSSpectraFactory`()
`SimplePairFinder`	Cython implementation of _SimplePairFinder
`SimplePeak`	Cython implementation of _SimplePeak
`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
`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