pyopenms ======== .. automodule:: pyopenms .. rubric:: Functions .. autosummary:: :toctree: free_mem peptide_identifications_to_df update_scores_from_df .. rubric:: Classes .. autosummary:: :toctree: :template: custom-class-template.rst AAIndex AASeqWithMass AASequence AMSE_AdductInfo AQS_featureConcentration AQS_runConcentration AScore AbsoluteQuantitation AbsoluteQuantitationMethod AbsoluteQuantitationMethodFile AbsoluteQuantitationStandards AbsoluteQuantitationStandardsFile AccurateMassSearchEngine AccurateMassSearchResult Acquisition AcquisitionInfo ActivationMethod Adduct AggregationMethod AnalysisSummary AnnotationState AnnotationStatistics ArrayWrapperFloat Assay Attachment AverageLinkage BSpline2d Base64 BaseFeature BasicProteinInferenceAlgorithm BayesianProteinInferenceAlgorithm BernNorm BiGaussFitter1D BiGaussModel BilinearInterpolation BinnedSpectrum BoundaryCondition BoxElement CV CVMappingFile CVMappingRule CVMappingTerm CVMappings CVReference CVTerm CVTermList CVTermListInterface CVTerm_ControlledVocabulary CachedMzMLHandler CachedSwathFileConsumer CachedmzML CalibrationData ChannelInfo ChargePair ChargedIndexSet ChecksumType ChromatogramExtractor ChromatogramExtractorAlgorithm ChromatogramPeak ChromatogramSettings ChromatogramTools ChromeleonFile ClusterProxyKD ClusteringGrid CoarseIsotopePatternGenerator ColumnHeader ComplementFilter ComplementMarker Compomer Compound ConfidenceScoring Configuration ConsensusFeature ConsensusIDAlgorithm ConsensusIDAlgorithmAverage ConsensusIDAlgorithmBest ConsensusIDAlgorithmIdentity ConsensusIDAlgorithmPEPIons ConsensusIDAlgorithmPEPMatrix ConsensusIDAlgorithmRanks ConsensusIDAlgorithmSimilarity ConsensusIDAlgorithmWorst ConsensusMap ConsensusMapNormalizerAlgorithmMedian ConsensusMapNormalizerAlgorithmQuantile ConsensusMapNormalizerAlgorithmThreshold ConsensusXMLFile Contact ContactPerson ContinuousWaveletTransform ContinuousWaveletTransformNumIntegration ControlledVocabulary ConvexHull2D CrossLinkSpectrumMatch CrossLinksDB CsiAdapterHit CsiAdapterIdentification CsiAdapterRun CsiFingerIdMzTabWriter CsvFile CubicSpline2d DBoundingBox2 DIAScoring DPosition1 DPosition2 DRange1 DRange2 DRangeIntersection DTA2DFile DTAFile DataFilter DataFilters DataProcessing DataType DataValue Date DateTime DecoyGenerator DecoyTransitionType Deisotoper Digestion DigestionEnzyme DigestionEnzymeProtein DigestionEnzymeRNA DimensionDescription DistanceMatrix DocumentIdentifier DriftTimeUnit EDTAFile Element ElementDB ElutionModelFitter ElutionPeakDetection EmgFitter1D EmgGradientDescent EmgModel EmgScoring EmpiricalFormula EnzymaticDigestion ExperimentalDesign ExperimentalDesignFile ExperimentalDesign_MSFileSectionEntry ExperimentalDesign_SampleSection ExperimentalSettings ExtractionCoordinates FASTAEntry FASTAFile FIAMSDataProcessor FIAMSScheduler FalseDiscoveryRate Feature FeatureDeconvolution FeatureDistance FeatureFileOptions FeatureFinder FeatureFinderAlgorithmIsotopeWavelet FeatureFinderAlgorithmMetaboIdent FeatureFinderAlgorithmPicked FeatureFinderIdentificationAlgorithm FeatureFinderMetaboIdentCompound FeatureFinderMultiplexAlgorithm FeatureFindingMetabo FeatureGroupingAlgorithm FeatureGroupingAlgorithmKD FeatureGroupingAlgorithmLabeled FeatureGroupingAlgorithmQT FeatureGroupingAlgorithmUnlabeled FeatureHandle FeatureMap FeatureMapping FeatureMapping_FeatureMappingInfo FeatureMapping_FeatureToMs2Indices FeatureXMLFile File FileHandler FileType FileTypes FilterFunctor FineIsotopePatternGenerator Fitter1D FloatDataArray GNPSMGFFile GNPSMetaValueFile GNPSQuantificationFile GaussFilter GaussFitResult GaussFitter GaussTraceFitter GoodDiffFilter Gradient GridBasedCluster HMMState HPLC HiddenMarkovModel HyperScore IBSpectraFile IDConflictResolverAlgorithm IDDecoyProbability IDFilter IDMapper IDMapper_SpectraIdentificationState IDRipper ILPDCWrapper IMFormat IMSAlphabet IMSElement IMSIsotopeDistribution IMSIsotopeDistribution_Peak IMSWeights IMTypes ISDGroup ITRAQ_TYPES IdXMLFile Identification IdentificationHit IdentificationRuns IncludeExcludeTarget IndexedMzMLDecoder IndexedMzMLFileLoader IndexedMzMLHandler InspectInfile InspectOutfile Instrument InstrumentSettings IntegerDataArray IntensityBalanceFilter Interfaces InternalCalibration InternalCalibration_LockMass Internal_MzMLValidator InterpolationModel IonDetector IonIdentityMolecularNetworking IonOpticsType IonSource IsobaricChannelExtractor IsobaricChannelInformation IsobaricIsotopeCorrector IsobaricNormalizer IsobaricQuantifier IsobaricQuantifierStatistics IsotopeCluster IsotopeDiffFilter IsotopeDistribution IsotopeDistributionCache IsotopeFitter1D IsotopeLabelingMDVs IsotopeMarker IsotopeModel IsotopePattern IsotopeVariant IsotopeWavelet IsotopeWaveletTransform ItraqConstants ItraqEightPlexQuantitationMethod ItraqFourPlexQuantitationMethod JavaInfo KDTreeFeatureMaps KDTreeFeatureNode Kernel_MassTrace KroenikFile LPWrapper LabeledPairFinder LightCompound LightMRMTransitionGroupCP LightModification LightProtein LightTargetedExperiment LightTransition LinearInterpolation LinearResampler LinearResamplerAlign LogConfigHandler LogType LowessSmoothing MRMAssay MRMDecoy MRMFP_ComponentGroupParams MRMFP_ComponentParams MRMFQC_ComponentGroupPairQCs MRMFQC_ComponentGroupQCs MRMFQC_ComponentQCs MRMFeature MRMFeatureFilter MRMFeatureFinderScoring MRMFeaturePicker MRMFeaturePickerFile MRMFeatureQC MRMFeatureQCFile MRMFragmentSelection MRMIonSeries MRMMapping MRMRTNormalizer MRMScoring MRMTransitionGroupCP MRMTransitionGroupPicker MS2File MSChromatogram MSDGroup MSDataAggregatingConsumer MSDataCachedConsumer MSDataSqlConsumer MSDataStoringConsumer MSExperiment MSNumpressCoder MSPFile MSPGenericFile MSQuantifications MSSpectrum MSstatsFile MT_QUANTMETHOD MZTrafoModel MZTrafoModel_MODELTYPE MapAlignmentAlgorithmIdentification MapAlignmentAlgorithmKD MapAlignmentAlgorithmPoseClustering MapAlignmentAlgorithmSpectrumAlignment MapAlignmentEvaluationAlgorithmPrecision MapAlignmentEvaluationAlgorithmRecall MapAlignmentTransformer MapConversion MarkerMower MascotGenericFile MascotInfile MascotXMLFile MassAnalyzer MassDecomposition MassDecompositionAlgorithm MassExplainer MassTrace MassTraceDetection MassTraces MasstraceCorrelator MatrixDouble Measure MetaInfo MetaInfoDescription MetaInfoInterface MetaInfoRegistry MetaboTargetedAssay MetaboTargetedAssay_CompoundTargetDecoyPair MetaboTargetedTargetDecoy MetaboTargetedTargetDecoy_MetaboTargetDecoyMassMapping MetaboliteFeatureDeconvolution MetaboliteSpectralMatching Modification ModificationDefinition ModificationDefinitionsSet ModificationsDB ModifiedPeptideGenerator ModifiedPeptideGenerator_MapToResidueType MorpheusScore MorpheusScore_Result MorphologicalFilter MsInspectFile MultiplexDeltaMasses MultiplexDeltaMassesGenerator MultiplexDeltaMassesGenerator_Label MultiplexDeltaMasses_DeltaMass MultiplexIsotopicPeakPattern MzDataFile MzIdentMLFile MzMLFile MzMLSpectrumDecoder MzMLSqliteHandler MzMLSwathFileConsumer MzQCFile MzQuantMLFile MzTab MzTabFile MzTabM MzTabMFile MzXMLFile NASequence NLargest NeutralLossDiffFilter NeutralLossMarker NoiseEstimator NonNegativeLeastSquaresSolver NoopMSDataWritingConsumer NormalizationMethod Normalizer NucleicAcidSpectrumGenerator NumpressConfig OMSSACSVFile OMSSAXMLFile OPXLDataStructs OPXLHelper OPXLSpectrumProcessingAlgorithms OPXL_PreprocessedPairSpectra OSBinaryDataArray OSChromatogram OSChromatogramMeta OSSpectrum OSSpectrumMeta OSWFile OSW_ChromExtractParams OnDiscMSExperiment OpenMSBuildInfo OpenMSOSInfo OpenPepXLAlgorithm OpenPepXLLFAlgorithm OpenSwathDataAccessHelper OpenSwathHelper OpenSwathOSWWriter OpenSwathScoring OpenSwath_Scores OpenSwath_Scores_Usage OptimizationFunctions_PenaltyFactors OptimizePeakDeconvolution OptimizePeakDeconvolution_Data OptimizePick OptimizePick_Data OriginAnnotationFormat PI_PeakArea PI_PeakBackground PI_PeakShapeMetrics PSProteinInference PScore Param ParamCTDFile ParamEntry ParamNode ParamValue ParamXMLFile ParentPeakMower Peak1D Peak2D PeakBoundary PeakCandidate PeakFileOptions PeakIndex PeakIntegrator PeakMap PeakMarker PeakPickerCWT PeakPickerHiRes PeakPickerIterative PeakPickerMRM PeakPickerMaxima PeakPickerSH PeakShape PeakSpectrum PeakTypeEstimator PeakWidthEstimator PenaltyFactorsIntensity PepXMLFile PepXMLFileMascot Peptide PeptideAndProteinQuant PeptideAndProteinQuant_PeptideData PeptideAndProteinQuant_ProteinData PeptideAndProteinQuant_Statistics PeptideEntry PeptideEvidence PeptideHit PeptideHit_AnalysisResult PeptideHit_PeakAnnotation PeptideIdentification PeptideIndexing PeptideProteinResolution PeptideProteinResolution_ConnectedComponent PercolatorFeatureSetHelper PercolatorInfile PercolatorOutfile PlainMSDataWritingConsumer PosteriorErrorProbabilityModel Precursor PrecursorCorrection PrecursorPurity Prediction ProbablePhosphoSites Product ProgressLogger ProtXMLFile ProteaseDB ProteaseDigestion Protein ProteinEntry ProteinGroup ProteinHit ProteinIdentification ProteinInference ProteinProteinCrossLink ProteinResolver ProteinResolverResult_Type ProtonDistributionModel Publication PurityScores QTCluster QTClusterFinder QcMLFile QualityParameter QuantitativeExperimentalDesign QuotingMethod RANSAC RANSACParam RANSACQuadratic RNPxlMarkerIonExtractor RNPxlModificationMassesResult RNPxlModificationsGenerator RNPxlReport RNPxlReportRow RNPxlReportRowHeader RNaseDB RNaseDigestion RansacModelLinear RansacModelQuadratic Ratio ReactionMonitoringTransition RealMassDecomposer RegularSwathFileConsumer Residue ResidueDB ResidueModification ResolverResult RetentionTime Ribonucleotide RibonucleotideDB RichPeak2D RipFileContent RipFileIdentifier SIDE Sample SavitzkyGolayFilter Scaler ScanMode ScanWindow SearchParameters Seed SeedListGenerator SemanticValidator SemanticValidator_CVTerm SequestInfile SequestOutfile SignalToNoiseEstimatorMeanIterative SignalToNoiseEstimatorMedian SignalToNoiseEstimatorMedianChrom SignalToNoiseEstimatorMedianRapid SimpleOpenMSSpectraFactory SimplePairFinder SimplePeak SimpleSearchEngineAlgorithm SimpleTSGXLMS SiriusAdapterAlgorithm SiriusAdapterHit SiriusAdapterIdentification SiriusAdapterRun SiriusFragmentAnnotation SiriusFragmentAnnotation_SiriusTargetDecoySpectra SiriusMSFile SiriusMSFile_AccessionInfo SiriusMSFile_CompoundInfo SiriusMzTabWriter SiriusMzTabWriter_SiriusSpectrumMSInfo SiriusTemporaryFileSystemObjects Software SolverParam SourceFile SpectraMerger SpectraSTSimilarityScore SpectralMatch SpectrumAccessOpenMS SpectrumAccessOpenMSCached SpectrumAccessOpenMSInMemory SpectrumAccessQuadMZTransforming SpectrumAccessSqMass SpectrumAccessTransforming SpectrumAlignment SpectrumAlignmentScore SpectrumAnnotator SpectrumHelper SpectrumIdentification SpectrumLookup SpectrumMetaData SpectrumMetaDataLookup SpectrumSettings SplineInterpolatedPeaks SplinePackage SplineSpectrum_Navigator SqMassConfig SqMassFile SqrtMower StablePairFinder String StringDataArray StringView SwathFile SwathMap SwathMapMassCorrection SwathWindowLoader SysInfo TICFilter TMTEighteenPlexQuantitationMethod TMTElevenPlexQuantitationMethod TMTSixPlexQuantitationMethod TMTSixteenPlexQuantitationMethod TMTTenPlexQuantitationMethod TM_DataPoint TOFCalibration TSE_Match Tagger Tagging TargetedExperiment TargetedExperiment_Instrument TargetedExperiment_Interpretation TargetedExperiment_Modification TargetedSpectraExtractor TermSpecificityNuc TextFile TheoreticalIsotopePattern TheoreticalSpectrumGenerator TheoreticalSpectrumGeneratorXLMS ThresholdMower ToolInfo TraMLFile TraMLProduct TraceInfo TransformationDescription TransformationModelBSpline TransformationModelInterpolated TransformationModelLinear TransformationModelLowess TransformationStatistics TransformationXMLFile TransitionPQPFile TransitionTSVFile TwoDOptimization UnimodXMLFile UniqueIdGenerator Unit UnitType ValueType VersionDetails VersionInfo WindowMower XFDRAlgorithm XLPrecursor XMLFile XMLHandler XQuestResultXMLFile XQuestScores XRefType_CVTerm_ControlledVocabulary XTandemInfile XTandemXMLFile streampos