Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z _ __init__() (pyopenms.AAIndex method) (pyopenms.AASequence method) (pyopenms.AASeqWithMass method) (pyopenms.AbsoluteQuantitation method) (pyopenms.AbsoluteQuantitationMethod method) (pyopenms.AbsoluteQuantitationMethodFile method) (pyopenms.AbsoluteQuantitationStandards method) (pyopenms.AbsoluteQuantitationStandardsFile method) (pyopenms.AccurateMassSearchEngine method) (pyopenms.AccurateMassSearchResult method) (pyopenms.Acquisition method) (pyopenms.AcquisitionInfo method) (pyopenms.Adduct method) (pyopenms.AMSE_AdductInfo method) (pyopenms.AnnotatedMSRun method) (pyopenms.AnnotationState method) (pyopenms.AnnotationStatistics method) (pyopenms.AQS_featureConcentration method) (pyopenms.AQS_runConcentration method) (pyopenms.AScore method) (pyopenms.AverageLinkage method) (pyopenms.Base64 method) (pyopenms.BaseFeature method) (pyopenms.BaseGroupFinder method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.BedRModFile method) (pyopenms.BiGaussFitter1D method) (pyopenms.BiGaussModel method) (pyopenms.BilinearInterpolation method) (pyopenms.BinaryDataArray method) (pyopenms.BinnedSpectrum method) (pyopenms.Biosaur2Algorithm method) (pyopenms.BoundaryCondition method) (pyopenms.BrukerTimsFile method) (pyopenms.BSpline2d method) (pyopenms.CachedmzML method) (pyopenms.CachedMzMLHandler method) (pyopenms.CachedSwathFileConsumer method) (pyopenms.CalibrationData method) (pyopenms.ChannelInfo method) (pyopenms.ChargedIndexSet method) (pyopenms.ChargePair method) (pyopenms.ChecksumType method) (pyopenms.Chromatogram method) (pyopenms.ChromatogramExtractor method) (pyopenms.ChromatogramExtractorAlgorithm method) (pyopenms.ChromatogramPeak method) (pyopenms.ChromatogramRangeManager method) (pyopenms.ChromatogramSettings method) (pyopenms.ChromatogramTools method) (pyopenms.ChromeleonFile method) (pyopenms.ClusteringGrid method) (pyopenms.ClusterProxyKD method) (pyopenms.CoarseIsotopePatternGenerator method) (pyopenms.ColumnHeader method) (pyopenms.CombinationsLogic method) (pyopenms.Compomer method) (pyopenms.Compound method) (pyopenms.ConfidenceScoring method) (pyopenms.Configuration method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusMap method) (pyopenms.ConsensusMapArrowIO method) (pyopenms.ConsensusMapNormalizerAlgorithmMedian method) (pyopenms.ConsensusMapNormalizerAlgorithmQuantile method) (pyopenms.ConsensusMapNormalizerAlgorithmRTLocal method) (pyopenms.ConsensusMapNormalizerAlgorithmThreshold method) (pyopenms.ConsensusXMLFile method) (pyopenms.Contact method) (pyopenms.ContactPerson method) (pyopenms.ControlledVocabulary method) (pyopenms.ConversionIssue method) (pyopenms.ConvexHull2D method) (pyopenms.CrossLinksDB method) (pyopenms.CrossLinkSpectrumMatch method) (pyopenms.CsvFile method) (pyopenms.CubicSpline2d method) (pyopenms.CV method) (pyopenms.CvAccession method) (pyopenms.CVMappingFile method) (pyopenms.CVMappingRule method) (pyopenms.CVMappings method) (pyopenms.CVMappingTerm method) (pyopenms.CVReference method) (pyopenms.CVTerm method) (pyopenms.CVTermList method) (pyopenms.CVTermListInterface method) (pyopenms.DataFilter method) (pyopenms.DataFilters method) (pyopenms.DataProcessing method) (pyopenms.DataType method) (pyopenms.DataValue method) (pyopenms.Date method) (pyopenms.DateTime method) (pyopenms.DBoundingBox2 method) (pyopenms.DeconvolvedSpectrum method) (pyopenms.DecoyGenerator method) (pyopenms.DecoyTransitionType method) (pyopenms.DefaultParamHandler method) (pyopenms.Deisotoper method) (pyopenms.DeltaMassEntry method) (pyopenms.DeltaMassStatistics method) (pyopenms.DIAScoring method) (pyopenms.DigestionEnzyme method) (pyopenms.DigestionEnzymeProtein method) (pyopenms.DigestionEnzymeRNA method) (pyopenms.DimensionDescription method) (pyopenms.DistanceMatrix method) (pyopenms.DocumentIdentifier method) (pyopenms.DRange1 method) (pyopenms.DRange2 method) (pyopenms.DRangeIntersection method) (pyopenms.DriftTimeUnit method) (pyopenms.DTA2DFile method) (pyopenms.DTAFile method) (pyopenms.EDTAFile method) (pyopenms.Element method) (pyopenms.ElementDB method) (pyopenms.ElutionModelFitter method) (pyopenms.ElutionPeakDetection method) (pyopenms.EmgFitter1D method) (pyopenms.EmgGradientDescent method) (pyopenms.EmgModel method) (pyopenms.EmgScoring method) (pyopenms.EmpiricalFormula method) (pyopenms.EntrapmentEvaluation method) (pyopenms.EnzymaticDigestion method) (pyopenms.ExperimentalDesign method) (pyopenms.ExperimentalDesign_MSFileSectionEntry method) (pyopenms.ExperimentalDesign_SampleSection method) (pyopenms.ExperimentalDesignFile method) (pyopenms.ExperimentalSettings method) (pyopenms.ExtractedPeakMap method) (pyopenms.ExtractionCoordinates method) (pyopenms.FAIMSHelper method) (pyopenms.FalseDiscoveryRate method) (pyopenms.FASTAEntry method) (pyopenms.FASTAFile method) (pyopenms.Feature method) (pyopenms.FeatureDeconvolution method) (pyopenms.FeatureDistance method) (pyopenms.FeatureFileOptions method) (pyopenms.FeatureFinderAlgorithmMetaboIdent method) (pyopenms.FeatureFinderAlgorithmPicked method) (pyopenms.FeatureFinderAlgorithmPickedHelperStructs_MassTrace method) (pyopenms.FeatureFinderIdentificationAlgorithm method) (pyopenms.FeatureFinderMetaboIdentCompound method) (pyopenms.FeatureFinderMultiplexAlgorithm method) (pyopenms.FeatureFindingMetabo method) (pyopenms.FeatureGroupingAlgorithm method) (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.FeatureGroupingAlgorithmLabeled method) (pyopenms.FeatureGroupingAlgorithmQT method) (pyopenms.FeatureGroupingAlgorithmUnlabeled method) (pyopenms.FeatureHandle method) (pyopenms.FeatureMap method) (pyopenms.FeatureMapArrowIO method) (pyopenms.FeatureMapping method) (pyopenms.FeatureMapping_FeatureMappingInfo method) (pyopenms.FeatureMapping_FeatureToMs2Indices method) (pyopenms.FeatureOverlapFilter method) (pyopenms.FeatureUniqueIds method) (pyopenms.FeatureXMLFile method) (pyopenms.FIAMSDataProcessor method) (pyopenms.FIAMSScheduler method) (pyopenms.File method) (pyopenms.FileHandler method) (pyopenms.FileInfo method) (pyopenms.FileType method) (pyopenms.FileTypes method) (pyopenms.FineIsotopePatternGenerator method) (pyopenms.Fitter1D method) (pyopenms.FLASHDeconvAlgorithm method) (pyopenms.FLASHDeconvFeatureFile method) (pyopenms.FLASHDeconvSpectrumFile method) (pyopenms.FLASHHelperClasses method) (pyopenms.FloatDataArray method) (pyopenms.FormulaTag method) (pyopenms.GaussFilter method) (pyopenms.GaussFitResult method) (pyopenms.GaussFitter method) (pyopenms.GaussTraceFitter method) (pyopenms.GlycanComposition method) (pyopenms.GlycanStructure method) (pyopenms.GNPSMetaValueFile method) (pyopenms.GNPSMGFFile method) (pyopenms.GNPSQuantificationFile method) (pyopenms.Gradient method) (pyopenms.GridBasedCluster method) (pyopenms.HPLC method) (pyopenms.HydrophobicityScaleMethod method) (pyopenms.HyperScore method) (pyopenms.IBSpectraFile method) (pyopenms.IDConflictResolverAlgorithm method) (pyopenms.IDDecoyProbability method) (pyopenms.IdentificationData method) (pyopenms.IdentifierMSRunMapper method) (pyopenms.IDFilter method) (pyopenms.IDFreeMassErrorEstimator method) (pyopenms.IDMapper method) (pyopenms.IDMapper_PeptideIdentificationListState method) (pyopenms.IDRipper method) (pyopenms.IDScoreSwitcherAlgorithm method) (pyopenms.IDSwitchResult method) (pyopenms.IDType method) (pyopenms.IdXMLFile method) (pyopenms.ILPDCWrapper method) (pyopenms.IMFormat method) (pyopenms.IMPeakType method) (pyopenms.IMSAlphabet method) (pyopenms.IMSDataConsumer method) (pyopenms.IMSElement method) (pyopenms.IMSIsotopeDistribution method) (pyopenms.IMSIsotopeDistribution_Peak method) (pyopenms.IMSWeights method) (pyopenms.IMTypes method) (pyopenms.ImzMLAuxArrayIndex method) (pyopenms.ImzMLDataType method) (pyopenms.ImzMLFile method) (pyopenms.ImzMLMeta method) (pyopenms.ImzMLSpectrumIndex method) (pyopenms.IncludeExcludeTarget method) (pyopenms.IndexedMzMLDecoder method) (pyopenms.IndexedMzMLFileLoader method) (pyopenms.IndexedMzMLHandler method) (pyopenms.InfoTag method) (pyopenms.InspectInfile method) (pyopenms.InspectOutfile method) (pyopenms.Instrument method) (pyopenms.InstrumentSettings method) (pyopenms.IntegerDataArray method) (pyopenms.InternalCalibration method) (pyopenms.InternalCalibration_LockMass method) (pyopenms.InterpolationModel method) (pyopenms.IonDetector method) (pyopenms.IonIdentityMolecularNetworking method) (pyopenms.IonImage method) (pyopenms.IonSource method) (pyopenms.IsobaricChannelExtractor method) (pyopenms.IsobaricChannelInformation method) (pyopenms.IsobaricIsotopeCorrector method) (pyopenms.IsobaricNormalizer method) (pyopenms.IsobaricQuantifier method) (pyopenms.IsobaricQuantifierStatistics method) (pyopenms.IsobaricQuantitationMethod method) (pyopenms.IsobaricQuantities method) (pyopenms.IsoelectricPoint method) (pyopenms.IsotopeCluster method) (pyopenms.IsotopeDistribution method) (pyopenms.IsotopeFitter1D method) (pyopenms.IsotopeLabelingMDVs method) (pyopenms.IsotopeModel method) (pyopenms.IsotopeReplacement method) (pyopenms.ITRAQ_TYPES method) (pyopenms.ItraqConstants method) (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.JavaInfo method) (pyopenms.KroenikFile method) (pyopenms.Label method) (pyopenms.LabeledPairFinder method) (pyopenms.LabileModification method) (pyopenms.LevMarqFitter1D method) (pyopenms.LightCompound method) (pyopenms.LightModification method) (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.LightProtein method) (pyopenms.LightTargetedExperiment method) (pyopenms.LightTransition method) (pyopenms.LinearInterpolation method) (pyopenms.LinearResamplerAlign method) (pyopenms.LogConfigHandler method) (pyopenms.LogMzPeak method) (pyopenms.LogType method) (pyopenms.LowessSmoothing method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) (pyopenms.MapAlignmentEvaluationAlgorithm method) (pyopenms.MapAlignmentEvaluationAlgorithmPrecision method) (pyopenms.MapAlignmentEvaluationAlgorithmRecall method) (pyopenms.MapAlignmentTransformer method) (pyopenms.MapConversion method) (pyopenms.MascotGenericFile method) (pyopenms.MascotXMLFile method) (pyopenms.MassAnalyzer method) (pyopenms.MassDecomposition method) (pyopenms.MassDecompositionAlgorithm method) (pyopenms.MassDelta method) (pyopenms.MassExplainer method) (pyopenms.MassFeature_FDHS method) (pyopenms.MassTrace method) (pyopenms.MasstraceCorrelator method) (pyopenms.MassTraceDetection method) (pyopenms.MassTraces method) (pyopenms.Math method) (pyopenms.MatrixDouble method) (pyopenms.Measure method) (pyopenms.MetaboliteFeatureDeconvolution method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.MetaboTargetedAssay method) (pyopenms.MetaboTargetedAssay_CompoundTargetDecoyPair method) (pyopenms.MetaboTargetedTargetDecoy method) (pyopenms.MetaboTargetedTargetDecoy_MetaboTargetDecoyMassMapping method) (pyopenms.MetaInfo method) (pyopenms.MetaInfoDescription method) (pyopenms.MetaInfoInterface method) (pyopenms.MetaInfoRegistry method) (pyopenms.Method method) (pyopenms.MobilityPeak1D method) (pyopenms.Mobilogram method) (pyopenms.Modification method) (pyopenms.ModificationDefinition method) (pyopenms.ModificationDefinitionsSet method) (pyopenms.ModificationPattern method) (pyopenms.ModificationsDB method) (pyopenms.ModificationSummary method) (pyopenms.ModifiedPeptideGenerator method) (pyopenms.ModifiedPeptideGenerator_MapToResidueType method) (pyopenms.ModifiedSincSmoother method) (pyopenms.MorpheusScore method) (pyopenms.MorpheusScore_Result method) (pyopenms.MorphologicalFilter method) (pyopenms.MRMAssay method) (pyopenms.MRMBatchFeatureSelector method) (pyopenms.MRMDecoy method) (pyopenms.MRMFeature method) (pyopenms.MRMFeatureFilter method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MRMFeaturePicker method) (pyopenms.MRMFeaturePickerFile method) (pyopenms.MRMFeatureQC method) (pyopenms.MRMFeatureQCFile method) (pyopenms.MRMFeatureSelectorQMIP method) (pyopenms.MRMFeatureSelectorScore method) (pyopenms.MRMFile method) (pyopenms.MRMFP_ComponentGroupParams method) (pyopenms.MRMFP_ComponentParams method) (pyopenms.MRMFQC_ComponentGroupPairQCs method) (pyopenms.MRMFQC_ComponentGroupQCs method) (pyopenms.MRMFQC_ComponentQCs method) (pyopenms.MRMIonSeries method) (pyopenms.MRMMapping method) (pyopenms.MRMRTNormalizer method) (pyopenms.MRMScoring method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupPicker method) (pyopenms.MS2File method) (pyopenms.MSChromatogram method) (pyopenms.MSDataAggregatingConsumer method) (pyopenms.MSDataCachedConsumer method) (pyopenms.MSDataSqlConsumer method) (pyopenms.MSDataStoringConsumer method) (pyopenms.MSExperiment method) (pyopenms.MSImagingExperiment method) (pyopenms.MSImagingGeometry method) (pyopenms.MSImagingRegion method) (pyopenms.MsInspectFile method) (pyopenms.MSNumpressCoder method) (pyopenms.MSPFile method) (pyopenms.MSPGenericFile method) (pyopenms.MSSpectrum method) (pyopenms.MSstatsFile method) (pyopenms.MT_QUANTMETHOD method) (pyopenms.MultipleTesting method) (pyopenms.MultiplexDeltaMasses method) (pyopenms.MultiplexDeltaMasses_DeltaMass method) (pyopenms.MultiplexDeltaMassesGenerator method) (pyopenms.MultiplexDeltaMassesGenerator_Label method) (pyopenms.MultiplexIsotopicPeakPattern method) (pyopenms.MultiplexResolverAlgorithm method) (pyopenms.MzDataFile method) (pyopenms.MzIdentMLFile method) (pyopenms.MzMLFile method) (pyopenms.MzMLSpectrumDecoder method) (pyopenms.MzMLSqliteHandler method) (pyopenms.MzMLSwathFileConsumer method) (pyopenms.MzPAF method) (pyopenms.MzPAFAnnotation method) (pyopenms.MzPAFDeltaUnit method) (pyopenms.MzPAFErrorCode method) (pyopenms.MzPAFIonSeries method) (pyopenms.MzPAFMassDelta method) (pyopenms.MzPAFNeutralLoss method) (pyopenms.MzPAFPeakAnnotations method) (pyopenms.MzQCFile method) (pyopenms.MzTab method) (pyopenms.MzTabFile method) (pyopenms.MzTabM method) (pyopenms.MzTabMFile method) (pyopenms.MZTrafoModel method) (pyopenms.MzXMLFile method) (pyopenms.NamedMod method) (pyopenms.NaNPolicy method) (pyopenms.NASequence method) (pyopenms.NLargest method) (pyopenms.NonNegativeLeastSquaresSolver method) (pyopenms.NoopMSDataWritingConsumer method) (pyopenms.NormalizationMethod method) (pyopenms.Normalizer method) (pyopenms.NucleicAcidSpectrumGenerator method) (pyopenms.NumpressConfig method) (pyopenms.OMSFile method) (pyopenms.OMSSACSVFile method) (pyopenms.OMSSAXMLFile method) (pyopenms.OnDiscImzMLExperiment method) (pyopenms.OnDiscMSExperiment method) (pyopenms.OnDiscThermoRawExperiment method) (pyopenms.OpenMSBuildInfo method) (pyopenms.OpenMSOSInfo method) (pyopenms.OpenPepXLAlgorithm method) (pyopenms.OpenSearchAnalysisResult method) (pyopenms.OpenSearchModificationAnalysis method) (pyopenms.OpenSwath_Scores method) (pyopenms.OpenSwath_Scores_Usage method) (pyopenms.OpenSwathDataAccessHelper method) (pyopenms.OpenSwathHelper method) (pyopenms.OpenSwathOSWWriter method) (pyopenms.OpenSwathScoring method) (pyopenms.OPXLDataStructs method) (pyopenms.OPXLHelper method) (pyopenms.OPXLSpectrumProcessingAlgorithms method) (pyopenms.OriginAnnotationFormat method) (pyopenms.OSBinaryDataArray method) (pyopenms.OSChromatogram method) (pyopenms.OSChromatogramMeta method) (pyopenms.OSSpectrum method) (pyopenms.OSSpectrumMeta method) (pyopenms.OSW_ChromExtractParams method) (pyopenms.OSWData method) (pyopenms.OSWHierarchy method) (pyopenms.OSWIndexTrace method) (pyopenms.OSWPeakGroup method) (pyopenms.OSWPeptidePrecursor method) (pyopenms.OSWProtein method) (pyopenms.OSWTransition method) (pyopenms.Param method) (pyopenms.ParamCTDFile method) (pyopenms.ParamEntry method) (pyopenms.ParamNode method) (pyopenms.ParamValue method) (pyopenms.ParamXMLFile method) (pyopenms.ParquetFilter method) (pyopenms.ParquetWriteConfig method) (pyopenms.Peak1D method) (pyopenms.Peak2D method) (pyopenms.PeakBoundary method) (pyopenms.PeakFileOptions method) (pyopenms.PeakGroup method) (pyopenms.PeakIntegrator method) (pyopenms.PeakMapExtractor method) (pyopenms.PeakPickerChromatogram method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIM method) (pyopenms.PeakPickerIterative method) (pyopenms.PeakTypeEstimator method) (pyopenms.PeakWidthEstimator method) (pyopenms.PEFFCustomKeyDef method) (pyopenms.PEFFDatabaseMetadata method) (pyopenms.PEFFDisulfideBond method) (pyopenms.PEFFEntry method) (pyopenms.PEFFFile method) (pyopenms.PEFFModification method) (pyopenms.PEFFProcessedRegion method) (pyopenms.PEFFVariantComplex method) (pyopenms.PEFFVariantSimple method) (pyopenms.Peptide method) (pyopenms.PeptideAndProteinQuant method) (pyopenms.PeptideAndProteinQuant_PeptideData method) (pyopenms.PeptideAndProteinQuant_ProteinData method) (pyopenms.PeptideAndProteinQuant_Statistics method) (pyopenms.PeptideEvidence method) (pyopenms.PeptideHit method) (pyopenms.PeptideHit_AnalysisResult method) (pyopenms.PeptideHit_PeakAnnotation method) (pyopenms.PeptideIdentification method) (pyopenms.PeptideIdentificationList method) (pyopenms.PeptideIndexing method) (pyopenms.PeptideProteinResolution method) (pyopenms.PeptideProteinResolution_ConnectedComponent method) (pyopenms.Peptidoform method) (pyopenms.PeptidoformIon method) (pyopenms.PepXMLFile method) (pyopenms.PepXMLFileMascot method) (pyopenms.Percolator method) (pyopenms.PercolatorFeatureSetHelper method) (pyopenms.PercolatorInfile method) (pyopenms.PercolatorOutfile method) (pyopenms.PercolatorRescoring method) (pyopenms.Pi0Result method) (pyopenms.PI_PeakArea method) (pyopenms.PI_PeakBackground method) (pyopenms.PI_PeakShapeMetrics method) (pyopenms.PipEchoAlgorithm method) (pyopenms.PlainMSDataWritingConsumer method) (pyopenms.PosteriorErrorProbabilityModel method) (pyopenms.PrecalAveragine method) (pyopenms.Precursor method) (pyopenms.PrecursorCorrection method) (pyopenms.PrecursorPurity method) (pyopenms.Prediction method) (pyopenms.PreprocessedPairSpectra method) (pyopenms.ProbablePhosphoSites method) (pyopenms.Product method) (pyopenms.ProForma method) (pyopenms.ProgressLogger method) (pyopenms.ProSEAlgorithm method) (pyopenms.ProteaseDB method) (pyopenms.ProteaseDigestion method) (pyopenms.Protein method) (pyopenms.ProteinGroup method) (pyopenms.ProteinHit method) (pyopenms.ProteinIdentification method) (pyopenms.ProteinIdentificationArrowIO method) (pyopenms.ProteinProteinCrossLink method) (pyopenms.ProteinRunReferences method) (pyopenms.ProteomicsPkaScale method) (pyopenms.ProtXMLFile method) (pyopenms.PScore method) (pyopenms.PTMEntry method) (pyopenms.PTMStatistics method) (pyopenms.Publication method) (pyopenms.PurityScores method) (pyopenms.QPXFile method) (pyopenms.QTCluster method) (pyopenms.QTClusterFinder method) (pyopenms.QuotingMethod method) (pyopenms.RangeBase method) (pyopenms.RangeIntensity method) (pyopenms.RangeMobility method) (pyopenms.RangeMZ method) (pyopenms.RangeRT method) (pyopenms.RankData method) (pyopenms.RankScaler method) (pyopenms.RANSAC method) (pyopenms.RansacModelLinear method) (pyopenms.RansacModelQuadratic method) (pyopenms.RANSACParam method) (pyopenms.RANSACQuadratic method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RealMassDecomposer method) (pyopenms.RegularSwathFileConsumer method) (pyopenms.RequirementLevel method) (pyopenms.RescoreInput method) (pyopenms.RescoreOutput method) (pyopenms.Residue method) (pyopenms.ResidueDB method) (pyopenms.ResidueModification method) (pyopenms.RetentionTime method) (pyopenms.Ribonucleotide method) (pyopenms.RibonucleotideDB method) (pyopenms.RichPeak2D method) (pyopenms.RipFileContent method) (pyopenms.RipFileIdentifier method) (pyopenms.RNaseCleavageSensitiveModGroups method) (pyopenms.RNaseDB method) (pyopenms.RNaseDigestion method) (pyopenms.RNaseDigestionProduct method) (pyopenms.Sample method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.ScanWindow method) (pyopenms.Scores method) (pyopenms.ScoreSearchResult method) (pyopenms.SearchParameters method) (pyopenms.SearchResult method) (pyopenms.SeedListGenerator method) (pyopenms.SelectorParameters method) (pyopenms.SemanticValidator method) (pyopenms.SemanticValidator_CVTerm method) (pyopenms.SequenceCoverage method) (pyopenms.SequenceElement method) (pyopenms.SequestInfile method) (pyopenms.SequestOutfile method) (pyopenms.SIDE method) (pyopenms.SignalToNoiseEstimatorMeanIterative method) (pyopenms.SignalToNoiseEstimatorMedian method) (pyopenms.SignalToNoiseEstimatorMedianChrom method) (pyopenms.SignalToNoiseEstimatorMedianRapid method) (pyopenms.SimpleOpenMSSpectraFactory method) (pyopenms.SimplePeak method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.SimpleTSGXLMS method) (pyopenms.SiriusExportAlgorithm method) (pyopenms.SiriusFragmentAnnotation method) (pyopenms.SiriusFragmentAnnotation_SiriusTargetDecoySpectra method) (pyopenms.SiriusMSFile method) (pyopenms.SiriusMSFile_AccessionInfo method) (pyopenms.SiriusMSFile_CompoundInfo method) (pyopenms.Software method) (pyopenms.SourceFile method) (pyopenms.SpectralDeconvolution method) (pyopenms.SpectralMatch method) (pyopenms.SpectraMerger method) (pyopenms.SpectraSTSimilarityScore method) (pyopenms.Spectrum method) (pyopenms.SpectrumAccessOpenMS method) (pyopenms.SpectrumAccessOpenMSCached method) (pyopenms.SpectrumAccessOpenMSInMemory method) (pyopenms.SpectrumAccessSqMass method) (pyopenms.SpectrumAlignment method) (pyopenms.SpectrumAlignmentScore method) (pyopenms.SpectrumAnnotator method) (pyopenms.SpectrumHelper method) (pyopenms.SpectrumLookup method) (pyopenms.SpectrumMetaData method) (pyopenms.SpectrumMetaDataLookup method) (pyopenms.SpectrumNativeIDParser method) (pyopenms.SpectrumRangeManager method) (pyopenms.SpectrumRanges method) (pyopenms.SpectrumSettings method) (pyopenms.SplineInterpolatedPeaks method) (pyopenms.SplinePackage method) (pyopenms.SqMassConfig method) (pyopenms.SqMassFile method) (pyopenms.SqrtScaler method) (pyopenms.StablePairFinder method) (pyopenms.StringDataArray method) (pyopenms.SummaryStatistics method) (pyopenms.SwathFile method) (pyopenms.SwathMap method) (pyopenms.SwathMapMassCorrection method) (pyopenms.SwathWindowLoader method) (pyopenms.SysInfo method) (pyopenms.SystemSettings method) (pyopenms.Tagger method) (pyopenms.TargetedDataFileLoader method) (pyopenms.TargetedExperiment method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TargetedSpectraExtractor method) (pyopenms.TempDir method) (pyopenms.TempFiles method) (pyopenms.TextFile method) (pyopenms.TheoreticalGlycanSpectrumGenerator method) (pyopenms.TheoreticalSpectrumGenerator method) (pyopenms.TheoreticalSpectrumGeneratorXLMS method) (pyopenms.ThermoRawFile method) (pyopenms.ThermoRawFileOptions method) (pyopenms.ThresholdMower method) (pyopenms.TMTEighteenPlexQuantitationMethod method) (pyopenms.TMTElevenPlexQuantitationMethod method) (pyopenms.TMTSixPlexQuantitationMethod method) (pyopenms.TMTSixteenPlexQuantitationMethod method) (pyopenms.TMTTenPlexQuantitationMethod method) (pyopenms.ToolInfo method) (pyopenms.TraMLFile method) (pyopenms.TraMLProduct method) (pyopenms.TransformationDescription method) (pyopenms.TransformationModel_DataPoint method) (pyopenms.TransformationModelBSpline method) (pyopenms.TransformationModelInterpolated method) (pyopenms.TransformationModelLinear method) (pyopenms.TransformationModelLowess method) (pyopenms.TransformationStatistics method) (pyopenms.TransformationXMLFile method) (pyopenms.TransitionListEvidenceFilter method) (pyopenms.TransitionListEvidenceFilter_PrecursorEvidence method) (pyopenms.TransitionListEvidenceFilter_Result method) (pyopenms.TransitionPQPFile method) (pyopenms.TransitionTSVFile method) (pyopenms.TSE_Match method) (pyopenms.UnimodXMLFile method) (pyopenms.UniqueIdGenerator method) (pyopenms.UniqueIdInterface method) (pyopenms.Unit method) (pyopenms.UnitType method) (pyopenms.UnlocalisedMod method) (pyopenms.UnresolvedIdentifications method) (pyopenms.USI method) (pyopenms.ValueType method) (pyopenms.VersionDetails method) (pyopenms.VersionInfo method) (pyopenms.WindowMower method) (pyopenms.XFDRAlgorithm method) (pyopenms.XICParquetFile method) (pyopenms.XIMParquetFile method) (pyopenms.XIPMParquetFile method) (pyopenms.XLPrecursor method) (pyopenms.XMLFile method) (pyopenms.XQuestResultXMLFile method) (pyopenms.XQuestScores method) (pyopenms.XTandemInfile method) (pyopenms.XTandemXMLFile method) A A (pyopenms.GaussFitResult property) (pyopenms.MzPAFIonSeries attribute) AA (pyopenms.PEFFDatabaseMetadata.SequenceType attribute) AA_SUBSTITUTION (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.SourceClassification attribute) AAIndex (class in pyopenms) AASequence (class in pyopenms) AASeqWithMass (class in pyopenms) abs_charge (pyopenms.LogMzPeak property) absolutePath() (pyopenms.File static method) AbsoluteQuantitation (class in pyopenms) AbsoluteQuantitationMethod (class in pyopenms) AbsoluteQuantitationMethodFile (class in pyopenms) AbsoluteQuantitationStandards (class in pyopenms) AbsoluteQuantitationStandardsFile (class in pyopenms) ABSORPTION (pyopenms.InstrumentSettings.ScanMode attribute) ABSORPTION_CHROMATOGRAM (pyopenms.ChromatogramSettings.ChromatogramType attribute) abundance (pyopenms.IMSIsotopeDistribution_Peak property) abundances (pyopenms.PeptideAndProteinQuant_PeptideData property) ABUNDANCES_SUM_ERROR (pyopenms.IMSIsotopeDistribution attribute) accepted (pyopenms.EntrapmentEvaluation.Result property) accession (pyopenms.CvAccession property) (pyopenms.ImzMLAuxArrayIndex property) (pyopenms.PEFFModification property) (pyopenms.PEFFProcessedRegion property) (pyopenms.SemanticValidator_CVTerm property) (pyopenms.Unit property) accessions (pyopenms.PeptideAndProteinQuant_PeptideData property) (pyopenms.ProteinGroup property) AccurateMassSearchEngine (class in pyopenms) AccurateMassSearchResult (class in pyopenms) acidic() (pyopenms.AAIndex static method) ACQMODENULL (pyopenms.IonDetector.AcquisitionMode attribute) Acquisition (class in pyopenms) AcquisitionInfo (class in pyopenms) acquisitionModeToString() (pyopenms.IonDetector static method) actions (pyopenms.FileInfo.ProcessingStep property) activation_methods_flat() (pyopenms.FileInfo.PeakInfo method) activationMethodToShortString() (pyopenms.Precursor static method) activationMethodToString() (pyopenms.Precursor static method) active (pyopenms.ChannelInfo property) actual_concentration (pyopenms.AQS_featureConcentration property) (pyopenms.AQS_runConcentration property) AD (pyopenms.IonSource.IonizationMethod attribute) ADC (pyopenms.IonDetector.AcquisitionMode attribute) add() (pyopenms.Compomer method) (pyopenms.DataFilters method) add_b_ions (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) add_c_ions (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) add_diagnostic_ions (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) add_internal_fragments (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) add_monosaccharide() (pyopenms.GlycanStructure method) add_y_ions (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) add_z_ions (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) addAnalysisResults() (pyopenms.PeptideHit method) addBetaAccessions() (pyopenms.OPXLHelper static method) addChargeAdduct() (pyopenms.EmpiricalFormula method) addChromatogram() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.MSExperiment method) addCluster() (pyopenms.ClusteringGrid method) addCOMETFeatures() (pyopenms.PercolatorFeatureSetHelper static method) addCompound() (pyopenms.TargetedExperiment method) addConfiguration() (pyopenms.IncludeExcludeTarget method) (pyopenms.TraMLProduct method) addContact() (pyopenms.TargetedExperiment method) addCV() (pyopenms.TargetedExperiment method) addCVReference() (pyopenms.CVMappings method) addCVTerm() (pyopenms.Compound method) (pyopenms.Configuration method) (pyopenms.Contact method) (pyopenms.CVMappingRule method) (pyopenms.CVTermList method) (pyopenms.CVTermListInterface method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Peptide method) (pyopenms.Precursor method) (pyopenms.Prediction method) (pyopenms.Product method) (pyopenms.Protein method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.Software method) (pyopenms.SourceFile method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TraMLProduct method) addDataProcessing() (pyopenms.NoopMSDataWritingConsumer method) (pyopenms.PlainMSDataWritingConsumer method) addEluent() (pyopenms.Gradient method) addEnzymeInfo() (pyopenms.SequestInfile method) addExcludeTarget() (pyopenms.TargetedExperiment method) addFeature() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMFeature method) (pyopenms.MRMTransitionGroupCP method) addIncludeTarget() (pyopenms.TargetedExperiment method) addInstrument() (pyopenms.TargetedExperiment method) addIntermediateProduct() (pyopenms.ReactionMonitoringTransition method) addInterpretation() (pyopenms.IncludeExcludeTarget method) (pyopenms.TraMLProduct method) addIonMatchStatistics() (pyopenms.SpectrumAnnotator method) addLine() (pyopenms.AbsoluteQuantitationMethodFile method) (pyopenms.CsvFile method) (pyopenms.MRMFeaturePickerFile method) (pyopenms.MRMFeatureQCFile method) (pyopenms.TextFile method) addLossFormula() (pyopenms.Residue method) addLossName() (pyopenms.Residue method) addMappingRule() (pyopenms.CVMappings method) addMASCOTFeatures() (pyopenms.PercolatorFeatureSetHelper static method) addMissingIMToPeptideIDs() (pyopenms.SpectrumMetaDataLookup static method) addMissingRTsToPeptideIDs() (pyopenms.SpectrumMetaDataLookup static method) addMissingSpectrumReferences() (pyopenms.SpectrumMetaDataLookup static method) addModification() (pyopenms.CrossLinksDB method) (pyopenms.ModificationDefinitionsSet method) (pyopenms.ModificationsDB method) addMSGFFeatures() (pyopenms.PercolatorFeatureSetHelper static method) addMSLevel() (pyopenms.PeakFileOptions method) addNTermLossFormula() (pyopenms.Residue method) addNTermLossName() (pyopenms.Residue method) addPeakAnnotationsToPeptideHit() (pyopenms.SpectrumAnnotator method) addPeptide() (pyopenms.TargetedExperiment method) addPeptideEvidence() (pyopenms.PeptideHit method) addPercolatorFeatureList() (pyopenms.OPXLHelper static method) addPixel() (pyopenms.MSImagingGeometry method) addPoint() (pyopenms.ConvexHull2D method) addPoints() (pyopenms.ConvexHull2D method) addPointsNPY() (pyopenms.ConvexHull2D method) addPointXY() (pyopenms.ConvexHull2D method) addPrecursorChromatogram() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) addPrecursorCVTerm() (pyopenms.IncludeExcludeTarget method) (pyopenms.ReactionMonitoringTransition method) addPrecursorFeature() (pyopenms.MRMFeature method) addPredictionTerm() (pyopenms.IncludeExcludeTarget method) (pyopenms.ReactionMonitoringTransition method) addPrimaryMSRunPath() (pyopenms.ProteinIdentification method) addProductCVTerm() (pyopenms.IncludeExcludeTarget method) (pyopenms.ReactionMonitoringTransition method) addProtein() (pyopenms.OSWData method) (pyopenms.TargetedExperiment method) addProteinIdentificationRun() (pyopenms.MRMFeatureFinderScoring static method) addProteinPositionMetaValues() (pyopenms.OPXLHelper static method) addPublication() (pyopenms.TargetedExperiment method) addRatio() (pyopenms.ConsensusFeature method) addReferenceFormat() (pyopenms.SpectrumLookup method) (pyopenms.SpectrumMetaDataLookup method) addRegion() (pyopenms.MSImagingGeometry method) addResidueSet() (pyopenms.Residue method) addRow() (pyopenms.AbsoluteQuantitationMethodFile method) (pyopenms.CsvFile method) (pyopenms.MRMFeaturePickerFile method) (pyopenms.MRMFeatureQCFile method) addRun() (pyopenms.OpenSwathOSWWriter method) addSection() (pyopenms.Param method) addSoftware() (pyopenms.TargetedExperiment method) addSourceFile() (pyopenms.TargetedExperiment method) addSpectrum() (pyopenms.MSExperiment method) addSynonym() (pyopenms.DigestionEnzyme method) (pyopenms.DigestionEnzymeProtein method) (pyopenms.DigestionEnzymeRNA method) (pyopenms.Residue method) (pyopenms.ResidueModification method) addTag() (pyopenms.Param method) addTags() (pyopenms.Param method) addTargetCVTerm() (pyopenms.TargetedExperiment method) addTimepoint() (pyopenms.Gradient method) addToGroup() (pyopenms.FeatureGroupingAlgorithmUnlabeled method) addTransition() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.OSWData method) (pyopenms.TargetedExperiment method) Adduct (class in pyopenms) adduct (pyopenms.MzPAFAnnotation property) adducts (pyopenms.LightCompound property) addValue() (pyopenms.BilinearInterpolation method) (pyopenms.LinearInterpolation method) addXLTargetDecoyMV() (pyopenms.OPXLHelper static method) addXTANDEMFeatures() (pyopenms.PercolatorFeatureSetHelper static method) affected_channels (pyopenms.IsobaricChannelInformation property) aggregateFromMatrix() (pyopenms.MSExperiment method) AI (pyopenms.IonSource.IonizationMethod attribute) AIon (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) align() (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) ALIGNMENT (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) aliphatic() (pyopenms.AAIndex static method) all_detectors (pyopenms.ThermoRawFileOptions property) allow_structural (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) alpha (pyopenms.ProteinProteinCrossLink property) alpha_index (pyopenms.XLPrecursor property) alpha_seq (pyopenms.XLPrecursor property) alt_accessions (pyopenms.PEFFEntry property) ALTERNATIVE_MODS (pyopenms.ProForma.ConversionIssueType attribute) ambig_features (pyopenms.PeptideAndProteinQuant_Statistics property) ambiguity_counts (pyopenms.FileInfo.FastaInfo property) AMBIGUOUS_MOD (pyopenms.ProForma.ConversionIssueType attribute) AMBIGUOUS_REGION (pyopenms.ProForma.ConversionIssueType attribute) amino_acid (pyopenms.SequenceElement property) AminusB (pyopenms.NASequence.NASFragmentType attribute) AMSE_AdductInfo (class in pyopenms) ANALYSISXML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) analyte_index (pyopenms.MzPAFAnnotation property) analyzeModifications() (pyopenms.OpenSearchModificationAnalysis method) analyzeModificationsWithStatistics() (pyopenms.OpenSearchModificationAnalysis method) analyzeResidueFrequency() (pyopenms.OpenSearchModificationAnalysis method) ANALYZERNULL (pyopenms.MassAnalyzer.AnalyzerType attribute) analyzerTypeToString() (pyopenms.MassAnalyzer static method) AND (pyopenms.CombinationsLogic attribute) andNext() (pyopenms.ParquetFilter method) annotate() (pyopenms.IDMapper method) annotateConsensusMap() (pyopenms.IonIdentityMolecularNetworking static method) AnnotatedMSRun (class in pyopenms) annotateMatches() (pyopenms.SpectrumAnnotator method) annotateSpectra() (pyopenms.TargetedSpectraExtractor method) annotateSwathMapsFromFile() (pyopenms.SwathWindowLoader static method) annotateTransfers() (pyopenms.IDConflictResolverAlgorithm static method) annotateTransition() (pyopenms.MRMIonSeries method) annotateTransitionCV() (pyopenms.MRMIonSeries method) annotation (pyopenms.PeptideHit_PeakAnnotation property) annotation_id (pyopenms.PEFFDisulfideBond property) (pyopenms.PEFFModification property) (pyopenms.PEFFProcessedRegion property) (pyopenms.PEFFVariantComplex property) (pyopenms.PEFFVariantSimple property) annotations (pyopenms.MzPAFPeakAnnotations property) AnnotationState (class in pyopenms) AnnotationStatistics (class in pyopenms) ANYWHERE (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.TermSpecificity attribute) (pyopenms.Ribonucleotide attribute) (pyopenms.Ribonucleotide.TermSpecificityNuc attribute) AP_MALDI (pyopenms.IonSource.IonizationMethod attribute) APCI (pyopenms.IonSource.IonizationMethod attribute) apex_pos (pyopenms.PI_PeakArea property) API (pyopenms.IonSource.IonizationMethod attribute) append() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.PeptideIdentificationList method) appendColumns() (pyopenms.ConsensusMap method) appendRows() (pyopenms.ConsensusMap method) APPI (pyopenms.IonSource.IonizationMethod attribute) applied (pyopenms.PercolatorRescoring property) apply() (pyopenms.FalseDiscoveryRate method) (pyopenms.IDDecoyProbability method) (pyopenms.TransformationDescription method) applyBasic() (pyopenms.FalseDiscoveryRate method) applyBasicPeptideLevel() (pyopenms.FalseDiscoveryRate method) applyCalibration() (pyopenms.AbsoluteQuantitation method) applyEstimated() (pyopenms.FalseDiscoveryRate method) applyEvaluateProteinIDs() (pyopenms.FalseDiscoveryRate method) applyFixedModifications() (pyopenms.ModifiedPeptideGenerator static method) applyPickedProteinFDR() (pyopenms.FalseDiscoveryRate method) applyTransformation() (pyopenms.InternalCalibration static method) applyVariableModifications() (pyopenms.ModifiedPeptideGenerator static method) approximateFromPeptideWeight() (pyopenms.CoarseIsotopePatternGenerator static method) approximateIntensities() (pyopenms.CoarseIsotopePatternGenerator static method) AQS_featureConcentration (class in pyopenms) AQS_runConcentration (class in pyopenms) ARCH_32BIT (pyopenms.OpenMSOSInfo.OpenMS_Architecture attribute) ARCH_64BIT (pyopenms.OpenMSOSInfo.OpenMS_Architecture attribute) ARCH_UNKNOWN (pyopenms.OpenMSOSInfo.OpenMS_Architecture attribute) area (pyopenms.PI_PeakArea property) (pyopenms.PI_PeakBackground property) area() (pyopenms.MSImagingRegion method) ARRAYDETECTOR (pyopenms.IonDetector.Type attribute) arrow_columns() (pyopenms.MSExperiment method) ARTIFACT (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.SourceClassification attribute) as_integer_ratio() (pyopenms.Base64.ByteOrder method) (pyopenms.BasicProteinInferenceAlgorithm.AggregationMethod method) (pyopenms.BoundaryCondition method) (pyopenms.BSpline2d.BoundaryCondition method) (pyopenms.ChromatogramSettings.ChromatogramType method) (pyopenms.CombinationsLogic method) (pyopenms.ConsensusMapNormalizerAlgorithmMedian.NormalizationMethod method) (pyopenms.ControlledVocabulary.CVTerm.XRefType method) (pyopenms.DRangeIntersection method) (pyopenms.DriftTimeUnit method) (pyopenms.EntrapmentEvaluation.Kind method) (pyopenms.EntrapmentEvaluation.Level method) (pyopenms.EnzymaticDigestion.Specificity method) (pyopenms.FeatureDeconvolution.CHARGEMODE method) (pyopenms.FileType method) (pyopenms.FileTypes.FileType method) (pyopenms.HydrophobicityScaleMethod method) (pyopenms.IDMapper.Measure method) (pyopenms.IDRipper.OriginAnnotationFormat method) (pyopenms.IDType method) (pyopenms.IsotopeDistribution.Sorted method) (pyopenms.ITRAQ_TYPES method) (pyopenms.ItraqConstants.ITRAQ_TYPES method) (pyopenms.LogType method) (pyopenms.Measure method) (pyopenms.MetaboliteFeatureDeconvolution.CHARGEMODE method) (pyopenms.Method method) (pyopenms.MSNumpressCoder.NumpressCompression method) (pyopenms.MultipleTesting.LfdrTransform method) (pyopenms.MultipleTesting.Pi0Method method) (pyopenms.MzPAFDeltaUnit method) (pyopenms.MzPAFErrorCode method) (pyopenms.MzPAFIonSeries method) (pyopenms.NaNPolicy method) (pyopenms.NASequence.NASFragmentType method) (pyopenms.NormalizationMethod method) (pyopenms.OpenMSOSInfo.OpenMS_Architecture method) (pyopenms.OpenMSOSInfo.OpenMS_OS method) (pyopenms.OpenPepXLAlgorithm.ExitCodes method) (pyopenms.OPXLDataStructs.PeptidePosition method) (pyopenms.OPXLDataStructs.ProteinProteinCrossLinkType method) (pyopenms.OriginAnnotationFormat method) (pyopenms.ParquetWriteConfig.Compression method) (pyopenms.PeakGroup.TargetDecoyType method) (pyopenms.PEFFDatabaseMetadata.SequenceType method) (pyopenms.PEFFModification.ModificationType method) (pyopenms.PeptideIndexing.ExitCodes method) (pyopenms.PercolatorOutfile.ScoreType method) (pyopenms.ProForma.ConversionIssueType method) (pyopenms.ProForma.ConversionPolicy method) (pyopenms.ProForma.CvDatabase method) (pyopenms.ProForma.WriteMode method) (pyopenms.ProgressLogger.LogType method) (pyopenms.ProSEAlgorithm.ProSEAlgorithm_ExitCodes method) (pyopenms.ProteomicsPkaScale method) (pyopenms.QuotingMethod method) (pyopenms.RankData.Method method) (pyopenms.RankData.NaNPolicy method) (pyopenms.RequirementLevel method) (pyopenms.Residue.ResidueType method) (pyopenms.ResidueModification.Provenance method) (pyopenms.ResidueModification.SourceClassification method) (pyopenms.ResidueModification.TermSpecificity method) (pyopenms.Ribonucleotide.TermSpecificityNuc method) (pyopenms.Scores.IDType method) (pyopenms.SIDE method) (pyopenms.SimpleSearchEngineAlgorithm.ExitCodes method) (pyopenms.UnitType method) (pyopenms.USI.IndexType method) (pyopenms.ValueType method) (pyopenms.XFDRAlgorithm.ExitCodes method) (pyopenms.XTandemInfile.ErrorUnit method) (pyopenms.XTandemInfile.MassType method) AScore (class in pyopenms) (pyopenms.ProbablePhosphoSites property) asDict() (pyopenms.Param method) ASI (pyopenms.IonSource.IonizationMethod attribute) assigned_ids (pyopenms.FileInfo.FeatureInfo property) assignedMS2 (pyopenms.FeatureMapping_FeatureToMs2Indices property) assignMS2IndexToFeature() (pyopenms.FeatureMapping static method) asymmetry_factor (pyopenms.PI_PeakShapeMetrics property) at() (pyopenms.PeptideIdentificationList method) atEnd() (pyopenms.FASTAFile method) (pyopenms.PEFFFile method) attachment_position (pyopenms.TheoreticalGlycanSpectrumGenerator.Fragment property) attachment_residue (pyopenms.TheoreticalGlycanSpectrumGenerator.Fragment property) AUI (pyopenms.IonSource.IonizationMethod attribute) AUTO (pyopenms.BrukerTimsFile.Config.ExportMode attribute) (pyopenms.BrukerTimsFile.Config.TimsCalibrationStrategy attribute) aux (pyopenms.ImzMLSpectrumIndex property) Average (pyopenms.Method attribute) AVERAGE (pyopenms.ProteinIdentification.PeakMassType attribute) Average (pyopenms.RankData.Method attribute) AVERAGE (pyopenms.XTandemInfile attribute) (pyopenms.XTandemInfile.MassType attribute) average() (pyopenms.SpectraMerger method) AverageLinkage (class in pyopenms) averageMass() (pyopenms.IsotopeDistribution method) AVERAGINE_NUM (pyopenms.IsotopeModel attribute) (pyopenms.IsotopeModel.Averagines attribute) avg_mass (pyopenms.MassFeature_FDHS property) avg_mass_delta (pyopenms.TargetedExperiment_Modification property) avg_peptide_length (pyopenms.FileInfo.IdentInfo property) AVOGADRO (in module pyopenms.Constants) AXIALEJECTIONLINEARIONTRAP (pyopenms.MassAnalyzer.AnalyzerType attribute) B B (pyopenms.MzPAFIonSeries attribute) (pyopenms.TheoreticalGlycanSpectrumGenerator.IonType attribute) back() (pyopenms.IMSWeights method) (pyopenms.PeptideIdentificationList method) BAF (pyopenms.BrukerTimsFile.DataFormat attribute) bandwidthToM() (pyopenms.ModifiedSincSmoother static method) Base64 encoding Base64 (class in pyopenms) Base64.ByteOrder (class in pyopenms) BaseFeature (class in pyopenms) BaseFeature.AnnotationState (class in pyopenms) BaseGroupFinder (class in pyopenms) BASELINE (pyopenms.MassAnalyzer.ResolutionMethod attribute) baseline (pyopenms.MassTraces property) baseline_delta_2_height (pyopenms.PI_PeakShapeMetrics property) BASELINE_REDUCTION (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) basename() (pyopenms.File static method) BASEPEAK_CHROMATOGRAM (pyopenms.ChromatogramSettings.ChromatogramType attribute) basic() (pyopenms.AAIndex static method) BasicProteinInferenceAlgorithm (class in pyopenms) BasicProteinInferenceAlgorithm.AggregationMethod (class in pyopenms) BATCH (pyopenms.IonSource.InletType attribute) BayesianProteinInferenceAlgorithm (class in pyopenms) BC_ZERO_ENDPOINTS (pyopenms.BoundaryCondition attribute) (pyopenms.BSpline2d attribute) (pyopenms.BSpline2d.BoundaryCondition attribute) BC_ZERO_FIRST (pyopenms.BoundaryCondition attribute) (pyopenms.BSpline2d attribute) (pyopenms.BSpline2d.BoundaryCondition attribute) BC_ZERO_SECOND (pyopenms.BoundaryCondition attribute) (pyopenms.BSpline2d attribute) (pyopenms.BSpline2d.BoundaryCondition attribute) BEDRMOD (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) BedRModFile (class in pyopenms) begin (pyopenms.ScanWindow property) BEST (pyopenms.BasicProteinInferenceAlgorithm attribute) (pyopenms.BasicProteinInferenceAlgorithm.AggregationMethod attribute) BEST_EFFORT (pyopenms.ProForma.ConversionPolicy attribute) beta (pyopenms.ProteinProteinCrossLink property) beta_index (pyopenms.XLPrecursor property) beta_seq (pyopenms.XLPrecursor property) BiGaussFitter1D (class in pyopenms) BiGaussModel (class in pyopenms) BilinearInterpolation (class in pyopenms) Binary encoding (mzML) BinaryDataArray (class in pyopenms) BinnedSpectrum (class in pyopenms) BIon (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) BIonMinusH20 (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) BIonMinusNH3 (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) Biosaur2Algorithm (class in pyopenms) BIRD (pyopenms.Precursor.ActivationMethod attribute) bit_count() (pyopenms.Base64.ByteOrder method) (pyopenms.BasicProteinInferenceAlgorithm.AggregationMethod method) (pyopenms.BoundaryCondition method) (pyopenms.BSpline2d.BoundaryCondition method) (pyopenms.ChromatogramSettings.ChromatogramType method) (pyopenms.CombinationsLogic method) (pyopenms.ConsensusMapNormalizerAlgorithmMedian.NormalizationMethod method) (pyopenms.ControlledVocabulary.CVTerm.XRefType method) (pyopenms.DRangeIntersection method) (pyopenms.DriftTimeUnit method) (pyopenms.EntrapmentEvaluation.Kind method) (pyopenms.EntrapmentEvaluation.Level method) (pyopenms.EnzymaticDigestion.Specificity method) (pyopenms.FeatureDeconvolution.CHARGEMODE method) (pyopenms.FileType method) (pyopenms.FileTypes.FileType method) (pyopenms.HydrophobicityScaleMethod method) (pyopenms.IDMapper.Measure method) (pyopenms.IDRipper.OriginAnnotationFormat method) (pyopenms.IDType method) (pyopenms.IsotopeDistribution.Sorted method) (pyopenms.ITRAQ_TYPES method) (pyopenms.ItraqConstants.ITRAQ_TYPES method) (pyopenms.LogType method) (pyopenms.Measure method) (pyopenms.MetaboliteFeatureDeconvolution.CHARGEMODE method) (pyopenms.Method method) (pyopenms.MSNumpressCoder.NumpressCompression method) (pyopenms.MultipleTesting.LfdrTransform method) (pyopenms.MultipleTesting.Pi0Method method) (pyopenms.MzPAFDeltaUnit method) (pyopenms.MzPAFErrorCode method) (pyopenms.MzPAFIonSeries method) (pyopenms.NaNPolicy method) (pyopenms.NASequence.NASFragmentType method) (pyopenms.NormalizationMethod method) (pyopenms.OpenMSOSInfo.OpenMS_Architecture method) (pyopenms.OpenMSOSInfo.OpenMS_OS method) (pyopenms.OpenPepXLAlgorithm.ExitCodes method) (pyopenms.OPXLDataStructs.PeptidePosition method) (pyopenms.OPXLDataStructs.ProteinProteinCrossLinkType method) (pyopenms.OriginAnnotationFormat method) (pyopenms.ParquetWriteConfig.Compression method) (pyopenms.PeakGroup.TargetDecoyType method) (pyopenms.PEFFDatabaseMetadata.SequenceType method) (pyopenms.PEFFModification.ModificationType method) (pyopenms.PeptideIndexing.ExitCodes method) (pyopenms.PercolatorOutfile.ScoreType method) (pyopenms.ProForma.ConversionIssueType method) (pyopenms.ProForma.ConversionPolicy method) (pyopenms.ProForma.CvDatabase method) (pyopenms.ProForma.WriteMode method) (pyopenms.ProgressLogger.LogType method) (pyopenms.ProSEAlgorithm.ProSEAlgorithm_ExitCodes method) (pyopenms.ProteomicsPkaScale method) (pyopenms.QuotingMethod method) (pyopenms.RankData.Method method) (pyopenms.RankData.NaNPolicy method) (pyopenms.RequirementLevel method) (pyopenms.Residue.ResidueType method) (pyopenms.ResidueModification.Provenance method) (pyopenms.ResidueModification.SourceClassification method) (pyopenms.ResidueModification.TermSpecificity method) (pyopenms.Ribonucleotide.TermSpecificityNuc method) (pyopenms.Scores.IDType method) (pyopenms.SIDE method) (pyopenms.SimpleSearchEngineAlgorithm.ExitCodes method) (pyopenms.UnitType method) (pyopenms.USI.IndexType method) (pyopenms.ValueType method) (pyopenms.XFDRAlgorithm.ExitCodes method) (pyopenms.XTandemInfile.ErrorUnit method) (pyopenms.XTandemInfile.MassType method) bit_length() (pyopenms.Base64.ByteOrder method) (pyopenms.BasicProteinInferenceAlgorithm.AggregationMethod method) (pyopenms.BoundaryCondition method) (pyopenms.BSpline2d.BoundaryCondition method) (pyopenms.ChromatogramSettings.ChromatogramType method) (pyopenms.CombinationsLogic method) (pyopenms.ConsensusMapNormalizerAlgorithmMedian.NormalizationMethod method) (pyopenms.ControlledVocabulary.CVTerm.XRefType method) (pyopenms.DRangeIntersection method) (pyopenms.DriftTimeUnit method) (pyopenms.EntrapmentEvaluation.Kind method) (pyopenms.EntrapmentEvaluation.Level method) (pyopenms.EnzymaticDigestion.Specificity method) (pyopenms.FeatureDeconvolution.CHARGEMODE method) (pyopenms.FileType method) (pyopenms.FileTypes.FileType method) (pyopenms.HydrophobicityScaleMethod method) (pyopenms.IDMapper.Measure method) (pyopenms.IDRipper.OriginAnnotationFormat method) (pyopenms.IDType method) (pyopenms.IsotopeDistribution.Sorted method) (pyopenms.ITRAQ_TYPES method) (pyopenms.ItraqConstants.ITRAQ_TYPES method) (pyopenms.LogType method) (pyopenms.Measure method) (pyopenms.MetaboliteFeatureDeconvolution.CHARGEMODE method) (pyopenms.Method method) (pyopenms.MSNumpressCoder.NumpressCompression method) (pyopenms.MultipleTesting.LfdrTransform method) (pyopenms.MultipleTesting.Pi0Method method) (pyopenms.MzPAFDeltaUnit method) (pyopenms.MzPAFErrorCode method) (pyopenms.MzPAFIonSeries method) (pyopenms.NaNPolicy method) (pyopenms.NASequence.NASFragmentType method) (pyopenms.NormalizationMethod method) (pyopenms.OpenMSOSInfo.OpenMS_Architecture method) (pyopenms.OpenMSOSInfo.OpenMS_OS method) (pyopenms.OpenPepXLAlgorithm.ExitCodes method) (pyopenms.OPXLDataStructs.PeptidePosition method) (pyopenms.OPXLDataStructs.ProteinProteinCrossLinkType method) (pyopenms.OriginAnnotationFormat method) (pyopenms.ParquetWriteConfig.Compression method) (pyopenms.PeakGroup.TargetDecoyType method) (pyopenms.PEFFDatabaseMetadata.SequenceType method) (pyopenms.PEFFModification.ModificationType method) (pyopenms.PeptideIndexing.ExitCodes method) (pyopenms.PercolatorOutfile.ScoreType method) (pyopenms.ProForma.ConversionIssueType method) (pyopenms.ProForma.ConversionPolicy method) (pyopenms.ProForma.CvDatabase method) (pyopenms.ProForma.WriteMode method) (pyopenms.ProgressLogger.LogType method) (pyopenms.ProSEAlgorithm.ProSEAlgorithm_ExitCodes method) (pyopenms.ProteomicsPkaScale method) (pyopenms.QuotingMethod method) (pyopenms.RankData.Method method) (pyopenms.RankData.NaNPolicy method) (pyopenms.RequirementLevel method) (pyopenms.Residue.ResidueType method) (pyopenms.ResidueModification.Provenance method) (pyopenms.ResidueModification.SourceClassification method) (pyopenms.ResidueModification.TermSpecificity method) (pyopenms.Ribonucleotide.TermSpecificityNuc method) (pyopenms.Scores.IDType method) (pyopenms.SIDE method) (pyopenms.SimpleSearchEngineAlgorithm.ExitCodes method) (pyopenms.UnitType method) (pyopenms.USI.IndexType method) (pyopenms.ValueType method) (pyopenms.XFDRAlgorithm.ExitCodes method) (pyopenms.XTandemInfile.ErrorUnit method) (pyopenms.XTandemInfile.MassType method) BJELLQVIST (pyopenms.ProteomicsPkaScale attribute) BLACK_MOULD (pyopenms.HydrophobicityScaleMethod attribute) blank_features (pyopenms.PeptideAndProteinQuant_Statistics property) BOHR_RADIUS (in module pyopenms.Constants) BOLTZMANN (in module pyopenms.Constants) Bootstrap (pyopenms.MultipleTesting.Pi0Method attribute) BOTH (pyopenms.SIDE attribute) boundaries (pyopenms.BrukerTimsFile.DIAStreamingMetadata property) BoundaryCondition (class in pyopenms) branch_cleavages (pyopenms.TheoreticalGlycanSpectrumGenerator.Fragment property) BRUKER_SDK (pyopenms.BrukerTimsFile.Config.TimsCalibrationStrategy attribute) bruker_sdk_path (pyopenms.BrukerTimsFile.Config property) BRUKER_TDF (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) BrukerTimsFile (class in pyopenms) BrukerTimsFile.Config (class in pyopenms) BrukerTimsFile.Config.CentroidAlgo (class in pyopenms) BrukerTimsFile.Config.ExportMode (class in pyopenms) BrukerTimsFile.Config.PressureCompensation (class in pyopenms) BrukerTimsFile.Config.TimsCalibrationStrategy (class in pyopenms) BrukerTimsFile.DataFormat (class in pyopenms) BrukerTimsFile.DIAStreamingMetadata (class in pyopenms) bseries_score (pyopenms.OpenSwath_Scores property) BSpline2d (class in pyopenms) BSpline2d.BoundaryCondition (class in pyopenms) bufferram (pyopenms.SysInfo attribute) buildCandidates() (pyopenms.OPXLHelper static method) buildFragmentAnnotations() (pyopenms.OPXLHelper static method) buildGraph() (pyopenms.PeptideProteinResolution method) buildImagingGeometry() (pyopenms.ImzMLFile static method) buildPeptideIDs() (pyopenms.OPXLHelper static method) buildUSI() (pyopenms.PeptideIdentification method) BULL_BREESE (pyopenms.HydrophobicityScaleMethod attribute) byMSLevel() (pyopenms.SpectrumRangeManager method) BYTEORDER_BIGENDIAN (pyopenms.Base64 attribute) (pyopenms.Base64.ByteOrder attribute) BYTEORDER_LITTLEENDIAN (pyopenms.Base64 attribute) (pyopenms.Base64.ByteOrder attribute) BZ2 (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) C C (pyopenms.IsotopeModel attribute) (pyopenms.IsotopeModel.Averagines attribute) (pyopenms.MzPAFIonSeries attribute) (pyopenms.TheoreticalGlycanSpectrumGenerator.IonType attribute) C13C12_MASSDIFF_U (in module pyopenms.Constants) C18 C_TERM (pyopenms.OPXLDataStructs attribute) (pyopenms.OPXLDataStructs.PeptidePosition attribute) (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.TermSpecificity attribute) c_term_mods (pyopenms.Peptidoform property) CachedmzML (class in pyopenms) CACHEDMZML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) CachedMzMLHandler (class in pyopenms) CachedSwathFileConsumer (class in pyopenms) CAD (pyopenms.IonSource.IonizationMethod attribute) CAL_PER_JOULE (in module pyopenms.Constants) calcFragmentIsotopeDist() (pyopenms.CoarseIsotopePatternGenerator method) calcMIPrecursorCombinedScore() (pyopenms.MRMScoring method) calcMIPrecursorContrastScore() (pyopenms.MRMScoring method) calcMIPrecursorScore() (pyopenms.MRMScoring method) calcMIScore() (pyopenms.MRMScoring method) calcMIWeightedScore() (pyopenms.MRMScoring method) calcRTScore() (pyopenms.MRMScoring static method) calcSeparateMIContrastScore() (pyopenms.MRMScoring method) calcSeparateXcorrContrastCoelutionScore() (pyopenms.MRMScoring method) calcSeparateXcorrContrastShapeScore() (pyopenms.MRMScoring method) calculate_lda_prescore() (pyopenms.OpenSwath_Scores method) calculate_swath_lda_prescore() (pyopenms.OpenSwath_Scores method) calculateAveragine() (pyopenms.SpectralDeconvolution method) calculateBias() (pyopenms.AbsoluteQuantitation method) calculateBiasAndR() (pyopenms.AbsoluteQuantitation method) calculateGB() (pyopenms.AAIndex static method) calculateIntensityRankInMZWindow() (pyopenms.PScore static method) calculateIonRatio() (pyopenms.MRMFeatureFilter method) calculateIsotopicPurity() (pyopenms.IsotopeLabelingMDVs method) calculateMDV() (pyopenms.IsotopeLabelingMDVs method) calculateMDVAccuracies() (pyopenms.IsotopeLabelingMDVs method) calculateMDVAccuracy() (pyopenms.IsotopeLabelingMDVs method) calculateMDVs() (pyopenms.IsotopeLabelingMDVs method) calculatePeakLevelSpectra() (pyopenms.PScore static method) calculatePeakShapeMetrics() (pyopenms.PeakIntegrator method) calculateRankMap() (pyopenms.PScore static method) calculateRatio() (pyopenms.AbsoluteQuantitation method) calculateResolution() (pyopenms.MRMFeatureFilter method) calculateRTDifference() (pyopenms.MRMFeatureFilter method) calculateTheoreticalIsotopesNumber() (pyopenms.EmpiricalFormula method) calculateTheoreticalMZ() (pyopenms.MzPAF static method) calculateTIC() (pyopenms.Mobilogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) calcXcorrCoelutionScore() (pyopenms.MRMScoring method) calcXcorrCoelutionWeightedScore() (pyopenms.MRMScoring method) calcXcorrPrecursorContrastCoelutionScore() (pyopenms.MRMScoring method) calcXcorrPrecursorContrastShapeScore() (pyopenms.MRMScoring method) calcXcorrShapeScore() (pyopenms.MRMScoring method) calcXcorrShapeWeightedScore() (pyopenms.MRMScoring method) calibrate (pyopenms.BrukerTimsFile.Config property) calibrate() (pyopenms.InternalCalibration method) CALIBRATION (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) calibration_tolerance (pyopenms.BrukerTimsFile.Config property) CalibrationData (class in pyopenms) canCalculateMass() (pyopenms.Peptidoform method) (pyopenms.PeptidoformIon method) (pyopenms.ProForma static method) canCalculateMassIon() (pyopenms.ProForma static method) canGenerateSpectrum() (pyopenms.Peptidoform method) (pyopenms.PeptidoformIon method) (pyopenms.ProForma static method) canGenerateSpectrumIon() (pyopenms.ProForma static method) CANONICAL (pyopenms.ProForma.WriteMode attribute) canRun() (pyopenms.JavaInfo static method) category_ (pyopenms.ToolInfo property) CCS (pyopenms.DriftTimeUnit attribute) CEI (pyopenms.IonSource.IonizationMethod attribute) center (pyopenms.ChannelInfo property) (pyopenms.IsobaricChannelInformation property) (pyopenms.SwathMap property) CENTROID (pyopenms.SpectrumSettings.SpectrumType attribute) centroid (pyopenms.ThermoRawFileOptions property) CENTROID_BASED (pyopenms.FeatureOverlapFilter.FeatureOverlapMode attribute) centroid_max_scan_gap (pyopenms.BrukerTimsFile.Config property) centroid_valley_factor (pyopenms.BrukerTimsFile.Config property) chains (pyopenms.PeptidoformIon property) channel_count (pyopenms.IsobaricQuantifierStatistics property) channel_level_abundances (pyopenms.PeptideAndProteinQuant_ProteinData property) CHANNELELECTRONMULTIPLIER (pyopenms.IonDetector.Type attribute) ChannelInfo (class in pyopenms) CHANNELTRON (pyopenms.IonDetector.Type attribute) charge (pyopenms.ChargedIndexSet property) CHARGE (pyopenms.DataFilters attribute) (pyopenms.DataFilters.FilterType attribute) charge (pyopenms.FormulaTag property) (pyopenms.InternalCalibration_LockMass property) (pyopenms.LightCompound property) (pyopenms.MzPAFAnnotation property) (pyopenms.PeptideHit_PeakAnnotation property) (pyopenms.SimplePeak property) (pyopenms.SiriusMSFile_CompoundInfo property) (pyopenms.TheoreticalGlycanSpectrumGenerator.Fragment property) CHARGE_CALCULATION (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) charge_count (pyopenms.MassFeature_FDHS property) charge_data (pyopenms.ThermoRawFileOptions property) CHARGE_DECONVOLUTION (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) ChargedIndexSet (class in pyopenms) ChargePair (class in pyopenms) charges (pyopenms.FileInfo.FeatureInfo property) (pyopenms.SearchParameters property) charToIonSeries() (pyopenms.MzPAF static method) chauvenet() (pyopenms.MRMRTNormalizer static method) chauvenet_probability() (pyopenms.MRMRTNormalizer static method) check() (pyopenms.FeatureUniqueIds static method) (pyopenms.ProteinRunReferences static method) check_corrupt (pyopenms.FileInfo.Options property) check_index (pyopenms.FileInfo.Options property) checkDataFormat() (pyopenms.BrukerTimsFile static method) checkDatumRange() (pyopenms.TransformationModelBSpline method) (pyopenms.TransformationModelInterpolated method) (pyopenms.TransformationModelLinear method) (pyopenms.TransformationModelLowess method) checkDefaults() (pyopenms.Param method) checkExtraFeatures() (pyopenms.PercolatorFeatureSetHelper static method) checkIdentifications() (pyopenms.MultiplexResolverAlgorithm method) checkLOD() (pyopenms.AbsoluteQuantitationMethod method) checkLOQ() (pyopenms.AbsoluteQuantitationMethod method) checkMaximalRTSpan() (pyopenms.GaussTraceFitter method) checkMinimalRTSpan() (pyopenms.GaussTraceFitter method) checkProteinAccessions() (pyopenms.ProteinRunReferences static method) checksum (pyopenms.ThermoRawFileOptions property) ChecksumType (class in pyopenms) checkSwathMapAndSelectTransitions() (pyopenms.OpenSwathHelper static method) checkValidWeight() (pyopenms.TransformationModelBSpline method) (pyopenms.TransformationModelInterpolated method) (pyopenms.TransformationModelLinear method) (pyopenms.TransformationModelLowess method) CHEMI (pyopenms.IonSource.IonizationMethod attribute) CHEMICAL_DERIVATIVE (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.SourceClassification attribute) children (pyopenms.ControlledVocabulary.CVTerm property) Chromatogram (class in pyopenms) chromatogram_df_columns() (pyopenms.MRMTransitionGroupCP method) chromatogram_types (pyopenms.FileInfo.PeakInfo property) chromatogram_view() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.MSExperiment method) chromatogram_views() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.MSExperiment method) ChromatogramExtractor (class in pyopenms) ChromatogramExtractorAlgorithm (class in pyopenms) chromatogramIdsMatch() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) ChromatogramPeak (class in pyopenms) ChromatogramRangeManager (class in pyopenms) chromatogramRanges() (pyopenms.MSExperiment method) chromatograms (pyopenms.FileInfo.Ranges property) ChromatogramSettings (class in pyopenms) ChromatogramSettings.ChromatogramType (class in pyopenms) ChromatogramTools (class in pyopenms) CHROMATOGRAPHY (pyopenms.IonSource.InletType attribute) ChromeleonFile (class in pyopenms) CHROMPARQUET (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) CI (pyopenms.IonSource.IonizationMethod attribute) CID (pyopenms.IonSource.IonizationMethod attribute) (pyopenms.Precursor.ActivationMethod attribute) CIon (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) citations_ (pyopenms.ToolInfo property) classify() (pyopenms.EntrapmentEvaluation static method) clear() (pyopenms.AbsoluteQuantitationMethodFile method) (pyopenms.CalibrationData method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusMap method) (pyopenms.ConvexHull2D method) (pyopenms.CsvFile method) (pyopenms.DataFilters method) (pyopenms.Date method) (pyopenms.DateTime method) (pyopenms.DeconvolvedSpectrum method) (pyopenms.DistanceMatrix method) (pyopenms.FeatureMap method) (pyopenms.FloatDataArray method) (pyopenms.IdentificationData method) (pyopenms.IMSAlphabet method) (pyopenms.IntegerDataArray method) (pyopenms.IsotopeDistribution method) (pyopenms.MetaInfo method) (pyopenms.Mobilogram method) (pyopenms.MRMFeaturePickerFile method) (pyopenms.MRMFeatureQCFile method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSImagingGeometry method) (pyopenms.MSSpectrum method) (pyopenms.OSWData method) (pyopenms.Param method) (pyopenms.PeptideIdentificationList method) (pyopenms.StringDataArray method) (pyopenms.TargetedExperiment method) clearEluents() (pyopenms.Gradient method) clearMetaDataArrays() (pyopenms.MSExperiment method) clearMetaInfo() (pyopenms.Acquisition method) (pyopenms.AcquisitionInfo method) (pyopenms.BaseFeature method) (pyopenms.ChromatogramSettings method) (pyopenms.ColumnHeader method) (pyopenms.Compound method) (pyopenms.Configuration method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusMap method) (pyopenms.Contact method) (pyopenms.ContactPerson method) (pyopenms.CVTermList method) (pyopenms.CVTermListInterface method) (pyopenms.DataProcessing method) (pyopenms.ExperimentalSettings method) (pyopenms.Feature method) (pyopenms.FeatureMap method) (pyopenms.FloatDataArray method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Instrument method) (pyopenms.InstrumentSettings method) (pyopenms.IntegerDataArray method) (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) (pyopenms.MetaInfoDescription method) (pyopenms.MetaInfoInterface method) (pyopenms.MRMFeature method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.Peptide method) (pyopenms.PeptideHit method) (pyopenms.PeptideIdentification method) (pyopenms.Precursor method) (pyopenms.Prediction method) (pyopenms.Product method) (pyopenms.Protein method) (pyopenms.ProteinHit method) (pyopenms.ProteinIdentification method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.RichPeak2D method) (pyopenms.Sample method) (pyopenms.ScanWindow method) (pyopenms.SearchParameters method) (pyopenms.Software method) (pyopenms.SourceFile method) (pyopenms.SpectrumSettings method) (pyopenms.StringDataArray method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TraMLProduct method) clearMSLevels() (pyopenms.PeakFileOptions method) clearPercentages() (pyopenms.Gradient method) clearProteins() (pyopenms.OSWData method) clearRanges() (pyopenms.ChromatogramRangeManager method) (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.SpectrumRangeManager method) clearRegions() (pyopenms.MSImagingGeometry method) clearTags() (pyopenms.Param method) clearTimepoints() (pyopenms.Gradient method) clearUniqueId() (pyopenms.BaseFeature method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusMap method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.FeatureMap method) (pyopenms.MRMFeature method) (pyopenms.RichPeak2D method) (pyopenms.UniqueIdInterface method) close() (pyopenms.OnDiscImzMLExperiment method) ClusteringGrid (class in pyopenms) ClusterProxyKD (class in pyopenms) CMD (pyopenms.AverageLinkage attribute) (pyopenms.CachedMzMLHandler attribute) (pyopenms.ChromatogramExtractor attribute) (pyopenms.ChromatogramExtractorAlgorithm attribute) (pyopenms.ConfidenceScoring attribute) (pyopenms.DTA2DFile attribute) (pyopenms.FASTAFile attribute) (pyopenms.GaussFilter attribute) (pyopenms.InternalCalibration attribute) (pyopenms.LogType attribute) (pyopenms.MascotGenericFile attribute) (pyopenms.ModifiedSincSmoother attribute) (pyopenms.MorphologicalFilter attribute) (pyopenms.MRMAssay attribute) (pyopenms.MS2File attribute) (pyopenms.MSDataCachedConsumer attribute) (pyopenms.PeakMapExtractor attribute) (pyopenms.PEFFFile attribute) (pyopenms.ProgressLogger attribute) (pyopenms.ProgressLogger.LogType attribute) (pyopenms.SavitzkyGolayFilter attribute) (pyopenms.SwathFile attribute) (pyopenms.TransitionPQPFile attribute) (pyopenms.TransitionTSVFile attribute) cmp (pyopenms.SiriusMSFile_CompoundInfo property) CNG (pyopenms.InstrumentSettings.ScanMode attribute) CNL (pyopenms.InstrumentSettings.ScanMode attribute) CoarseIsotopePatternGenerator (class in pyopenms) collectPrecursorCandidates() (pyopenms.OPXLHelper static method) collision-induced dissociation COLLISION_QUADRUPOLE (pyopenms.Instrument.IonOpticsType attribute) cols() (pyopenms.MatrixDouble method) ColumnHeader (class in pyopenms) CombinationsLogic (class in pyopenms) combined (pyopenms.FileInfo.Ranges property) combined() (pyopenms.RNaseCleavageSensitiveModGroups method) combinedFDP() (pyopenms.EntrapmentEvaluation.Result method) combineTopRanksFromPairs() (pyopenms.OPXLHelper static method) comment (pyopenms.MSSpectrum property) compatible() (pyopenms.MassDecomposition method) completion_time (pyopenms.FileInfo.ProcessingStep property) complex_variants (pyopenms.PEFFEntry property) Compomer (class in pyopenms) component_group_name (pyopenms.MRMFP_ComponentGroupParams property) (pyopenms.MRMFP_ComponentParams property) (pyopenms.MRMFQC_ComponentGroupPairQCs property) (pyopenms.MRMFQC_ComponentGroupQCs property) component_group_pair_qcs (pyopenms.MRMFeatureQC property) component_group_qcs (pyopenms.MRMFeatureQC property) component_name (pyopenms.AQS_runConcentration property) (pyopenms.MRMFP_ComponentParams property) (pyopenms.MRMFQC_ComponentQCs property) component_qcs (pyopenms.MRMFeatureQC property) components (pyopenms.GlycanComposition property) composition (pyopenms.TheoreticalGlycanSpectrumGenerator.Fragment property) Compound (class in pyopenms) compound_adduct (pyopenms.MetaboTargetedAssay property) compound_file (pyopenms.MetaboTargetedAssay property) compound_id (pyopenms.TransitionListEvidenceFilter_PrecursorEvidence property) compound_info (pyopenms.MetaboTargetedAssay_CompoundTargetDecoyPair property) compound_name (pyopenms.LightCompound property) (pyopenms.MetaboTargetedAssay property) compound_rt (pyopenms.MetaboTargetedAssay property) compounds (pyopenms.LightTargetedExperiment property) compounds_from_df() (pyopenms.FeatureFinderAlgorithmMetaboIdent static method) compounds_to_df() (pyopenms.FeatureFinderAlgorithmMetaboIdent static method) compress() (pyopenms.ConvexHull2D method) compressed (pyopenms.ImzMLAuxArrayIndex property) compression (pyopenms.ParquetWriteConfig property) compression_level (pyopenms.ParquetWriteConfig property) compressTrieDB() (pyopenms.InspectOutfile method) compute() (pyopenms.AScore method) (pyopenms.FeatureDeconvolution method) (pyopenms.HyperScore static method) (pyopenms.IDFreeMassErrorEstimator method) (pyopenms.ILPDCWrapper method) (pyopenms.MassExplainer method) (pyopenms.MetaboliteFeatureDeconvolution method) (pyopenms.MorpheusScore static method) compute_F() (pyopenms.SpectraSTSimilarityScore method) computeApexSNR() (pyopenms.ElutionPeakDetection method) computeBinnedCoverage() (pyopenms.MRMRTNormalizer static method) computeCharge() (pyopenms.IsoelectricPoint static method) computeConsensus() (pyopenms.ConsensusFeature method) computeCorrelation() (pyopenms.ConsensusMapNormalizerAlgorithmThreshold static method) computeCoverage() (pyopenms.ProteinIdentification method) computeDechargeConsensus() (pyopenms.ConsensusFeature method) computeDecoyProbability() (pyopenms.PosteriorErrorProbabilityModel method) computeDeltaScores() (pyopenms.OPXLHelper static method) computeFileHash() (pyopenms.FileHandler static method) computeFwhmArea() (pyopenms.MassTrace method) computeFwhmAreaSmooth() (pyopenms.MassTrace method) computeHyperScore() (pyopenms.MetaboliteSpectralMatching static method) computeHyperScoreWithAnnotations() (pyopenms.MetaboliteSpectralMatching static method) computeIntensitySum() (pyopenms.MassTrace method) computeLogLikelihood() (pyopenms.PosteriorErrorProbabilityModel method) computeMassTraceNoise() (pyopenms.ElutionPeakDetection method) computeMassTraceSNR() (pyopenms.ElutionPeakDetection method) computeMedians() (pyopenms.ConsensusMapNormalizerAlgorithmMedian static method) computeMonoisotopicConsensus() (pyopenms.ConsensusFeature method) computeMVHScore() (pyopenms.MetaboliteSpectralMatching static method) computeMVHScoreWithAnnotations() (pyopenms.MetaboliteSpectralMatching static method) computeOffsets() (pyopenms.ConsensusMapNormalizerAlgorithmRTLocal static method) computePeakArea() (pyopenms.MassTrace method) computePI() (pyopenms.IsoelectricPoint static method) computePrecursorError() (pyopenms.OPXLHelper static method) computePrecursorId() (pyopenms.OpenSwathHelper static method) computePrecursorPurity() (pyopenms.PrecursorPurity static method) computeProbability() (pyopenms.PosteriorErrorProbabilityModel method) computePScore() (pyopenms.PScore static method) computeSmoothedPeakArea() (pyopenms.MassTrace method) computeTheoretical() (pyopenms.GaussTraceFitter method) concentration_units (pyopenms.AQS_featureConcentration property) (pyopenms.AQS_runConcentration property) concept_curie (pyopenms.PEFFCustomKeyDef property) confidence (pyopenms.IDFreeMassErrorEstimator.ToleranceSuggestion property) (pyopenms.MzPAFAnnotation property) ConfidenceScoring (class in pyopenms) Configuration (class in pyopenms) configure() (pyopenms.LogConfigHandler method) conjugate() (pyopenms.Base64.ByteOrder method) (pyopenms.BasicProteinInferenceAlgorithm.AggregationMethod method) (pyopenms.BoundaryCondition method) (pyopenms.BSpline2d.BoundaryCondition method) (pyopenms.ChromatogramSettings.ChromatogramType method) (pyopenms.CombinationsLogic method) (pyopenms.ConsensusMapNormalizerAlgorithmMedian.NormalizationMethod method) (pyopenms.ControlledVocabulary.CVTerm.XRefType method) (pyopenms.DRangeIntersection method) (pyopenms.DriftTimeUnit method) (pyopenms.EntrapmentEvaluation.Kind method) (pyopenms.EntrapmentEvaluation.Level method) (pyopenms.EnzymaticDigestion.Specificity method) (pyopenms.FeatureDeconvolution.CHARGEMODE method) (pyopenms.FileType method) (pyopenms.FileTypes.FileType method) (pyopenms.HydrophobicityScaleMethod method) (pyopenms.IDMapper.Measure method) (pyopenms.IDRipper.OriginAnnotationFormat method) (pyopenms.IDType method) (pyopenms.IsotopeDistribution.Sorted method) (pyopenms.ITRAQ_TYPES method) (pyopenms.ItraqConstants.ITRAQ_TYPES method) (pyopenms.LogType method) (pyopenms.Measure method) (pyopenms.MetaboliteFeatureDeconvolution.CHARGEMODE method) (pyopenms.Method method) (pyopenms.MSNumpressCoder.NumpressCompression method) (pyopenms.MultipleTesting.LfdrTransform method) (pyopenms.MultipleTesting.Pi0Method method) (pyopenms.MzPAFDeltaUnit method) (pyopenms.MzPAFErrorCode method) (pyopenms.MzPAFIonSeries method) (pyopenms.NaNPolicy method) (pyopenms.NASequence.NASFragmentType method) (pyopenms.NormalizationMethod method) (pyopenms.OpenMSOSInfo.OpenMS_Architecture method) (pyopenms.OpenMSOSInfo.OpenMS_OS method) (pyopenms.OpenPepXLAlgorithm.ExitCodes method) (pyopenms.OPXLDataStructs.PeptidePosition method) (pyopenms.OPXLDataStructs.ProteinProteinCrossLinkType method) (pyopenms.OriginAnnotationFormat method) (pyopenms.ParquetWriteConfig.Compression method) (pyopenms.PeakGroup.TargetDecoyType method) (pyopenms.PEFFDatabaseMetadata.SequenceType method) (pyopenms.PEFFModification.ModificationType method) (pyopenms.PeptideIndexing.ExitCodes method) (pyopenms.PercolatorOutfile.ScoreType method) (pyopenms.ProForma.ConversionIssueType method) (pyopenms.ProForma.ConversionPolicy method) (pyopenms.ProForma.CvDatabase method) (pyopenms.ProForma.WriteMode method) (pyopenms.ProgressLogger.LogType method) (pyopenms.ProSEAlgorithm.ProSEAlgorithm_ExitCodes method) (pyopenms.ProteomicsPkaScale method) (pyopenms.QuotingMethod method) (pyopenms.RankData.Method method) (pyopenms.RankData.NaNPolicy method) (pyopenms.RequirementLevel method) (pyopenms.Residue.ResidueType method) (pyopenms.ResidueModification.Provenance method) (pyopenms.ResidueModification.SourceClassification method) (pyopenms.ResidueModification.TermSpecificity method) (pyopenms.Ribonucleotide.TermSpecificityNuc method) (pyopenms.Scores.IDType method) (pyopenms.SIDE method) (pyopenms.SimpleSearchEngineAlgorithm.ExitCodes method) (pyopenms.UnitType method) (pyopenms.USI.IndexType method) (pyopenms.ValueType method) (pyopenms.XFDRAlgorithm.ExitCodes method) (pyopenms.XTandemInfile.ErrorUnit method) (pyopenms.XTandemInfile.MassType method) consensus feature consensus features consensus map consensus maps consensus_feature_view() (pyopenms.ConsensusMap method) consensus_feature_views() (pyopenms.ConsensusMap method) ConsensusFeature (class in pyopenms) ConsensusFeature.Ratio (class in pyopenms) ConsensusMap (class in pyopenms) ConsensusMapArrowIO (class in pyopenms) ConsensusMapNormalizerAlgorithmMedian (class in pyopenms) ConsensusMapNormalizerAlgorithmMedian.NormalizationMethod (class in pyopenms) ConsensusMapNormalizerAlgorithmQuantile (class in pyopenms) ConsensusMapNormalizerAlgorithmRTLocal (class in pyopenms) ConsensusMapNormalizerAlgorithmRTLocal.Settings (class in pyopenms) ConsensusMapNormalizerAlgorithmThreshold (class in pyopenms) CONSENSUSPARQUET (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) CONSENSUSXML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) ConsensusXMLFile (class in pyopenms) CONSTANT (pyopenms.MassAnalyzer.ResolutionType attribute) constructTargetDecoyMassMapping() (pyopenms.MetaboTargetedTargetDecoy static method) constructTransitionsList() (pyopenms.TargetedSpectraExtractor method) consumeChromatogram() (pyopenms.CachedSwathFileConsumer method) (pyopenms.IMSDataConsumer method) (pyopenms.MSDataAggregatingConsumer method) (pyopenms.MSDataCachedConsumer method) (pyopenms.MSDataSqlConsumer method) (pyopenms.MSDataStoringConsumer method) (pyopenms.MzMLSwathFileConsumer method) (pyopenms.NoopMSDataWritingConsumer method) (pyopenms.PlainMSDataWritingConsumer method) (pyopenms.RegularSwathFileConsumer method) consumeCVTerms() (pyopenms.Compound method) (pyopenms.Configuration method) (pyopenms.Contact method) (pyopenms.CVTermList method) (pyopenms.CVTermListInterface method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Peptide method) (pyopenms.Precursor method) (pyopenms.Prediction method) (pyopenms.Product method) (pyopenms.Protein method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.Software method) (pyopenms.SourceFile method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TraMLProduct method) consumeSpectrum() (pyopenms.CachedSwathFileConsumer method) (pyopenms.IDFreeMassErrorEstimator method) (pyopenms.IMSDataConsumer method) (pyopenms.MSDataAggregatingConsumer method) (pyopenms.MSDataCachedConsumer method) (pyopenms.MSDataSqlConsumer method) (pyopenms.MSDataStoringConsumer method) (pyopenms.MzMLSwathFileConsumer method) (pyopenms.NoopMSDataWritingConsumer method) (pyopenms.PlainMSDataWritingConsumer method) (pyopenms.RegularSwathFileConsumer method) Contact (class in pyopenms) contact_ref (pyopenms.Configuration property) (pyopenms.Prediction property) ContactPerson (class in pyopenms) contacts (pyopenms.FileInfo.ExperimentMeta property) contains() (pyopenms.EmpiricalFormula method) (pyopenms.MSImagingRegion method) (pyopenms.RangeBase method) (pyopenms.RangeIntensity method) (pyopenms.RangeMobility method) (pyopenms.RangeMZ method) (pyopenms.RangeRT method) containsIMData() (pyopenms.MSSpectrum method) containsIntensity() (pyopenms.RangeIntensity method) containsInvalidReferences() (pyopenms.TargetedExperiment method) containsMobility() (pyopenms.RangeMobility method) containsMSLevel() (pyopenms.PeakFileOptions method) containsMZ() (pyopenms.RangeMZ method) containsRT() (pyopenms.RangeRT method) containsTag() (pyopenms.MassDecomposition method) CONTINUOUSFLOWFASTATOMBOMBARDMENT (pyopenms.IonSource.InletType attribute) ControlledVocabulary (class in pyopenms) ControlledVocabulary.CVTerm (class in pyopenms) ControlledVocabulary.CVTerm.XRefType (class in pyopenms) conversion (pyopenms.PEFFDatabaseMetadata property) CONVERSION_DTA (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) CONVERSION_MZDATA (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) CONVERSION_MZML (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) CONVERSION_MZXML (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) CONVERSIONDYNODE (pyopenms.IonDetector.Type attribute) CONVERSIONDYNODEELECTRONMULTIPLIER (pyopenms.IonDetector.Type attribute) CONVERSIONDYNODEPHOTOMULTIPLIER (pyopenms.IonDetector.Type attribute) ConversionIssue (class in pyopenms) convert() (pyopenms.MapConversion static method) convertChromatogramsToSpectra() (pyopenms.ChromatogramTools method) convertPeptideToAASequence() (pyopenms.OpenSwathDataAccessHelper static method) convertPQPToTargetedExperiment() (pyopenms.TransitionPQPFile method) convertSeedList() (pyopenms.SeedListGenerator method) convertSpectraToChromatograms() (pyopenms.ChromatogramTools method) convertTargetedCompound() (pyopenms.OpenSwathDataAccessHelper static method) convertTargetedExp() (pyopenms.OpenSwathDataAccessHelper static method) convertTargetedExperimentToPQP() (pyopenms.TransitionPQPFile method) convertTargetedExperimentToTSV() (pyopenms.TransitionPQPFile method) (pyopenms.TransitionTSVFile method) convertToChromatogramPtr() (pyopenms.OpenSwathDataAccessHelper static method) convertToFeatureMap() (pyopenms.FIAMSDataProcessor method) convertToOpenMSChromatogram() (pyopenms.OpenSwathDataAccessHelper static method) convertToOpenMSChromatogramFilter() (pyopenms.OpenSwathDataAccessHelper static method) convertToOpenMSSpectrum() (pyopenms.OpenSwathDataAccessHelper static method) convertToSpectrumPtr() (pyopenms.OpenSwathDataAccessHelper static method) convertTSVToTargetedExperiment() (pyopenms.TransitionPQPFile method) (pyopenms.TransitionTSVFile method) CONVEX_HULL (pyopenms.FeatureOverlapFilter.FeatureOverlapMode attribute) ConvexHull2D (class in pyopenms) copy() (pyopenms.Param method) correctIsotopicImpurities() (pyopenms.IsobaricIsotopeCorrector static method) correctToHighestIntensityMS1Peak() (pyopenms.PrecursorCorrection static method) correctToNearestFeature() (pyopenms.PrecursorCorrection static method) correctToNearestMS1Peak() (pyopenms.PrecursorCorrection static method) corruption (pyopenms.FileInfo.Result property) COTRANSLATIONAL (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.SourceClassification attribute) count (pyopenms.DeltaMassEntry property) (pyopenms.ModificationPattern property) (pyopenms.ModificationSummary property) (pyopenms.PTMEntry property) (pyopenms.SummaryStatistics property) countHits() (pyopenms.IDFilter static method) countInternalCleavageSites() (pyopenms.EnzymaticDigestion method) (pyopenms.ProteaseDigestion method) (pyopenms.RNaseDigestion method) create() (pyopenms.IdentifierMSRunMapper method) (pyopenms.VersionDetails static method) createMemdumpIndex() (pyopenms.CachedMzMLHandler method) (pyopenms.MSDataCachedConsumer method) createMRMFeature() (pyopenms.MRMTransitionGroupPicker method) createPseudoSpectra() (pyopenms.MasstraceCorrelator method) createTables() (pyopenms.MzMLSqliteHandler method) CRM (pyopenms.InstrumentSettings.ScanMode attribute) CROSS (pyopenms.OPXLDataStructs attribute) (pyopenms.OPXLDataStructs.ProteinProteinCrossLinkType attribute) cross_link (pyopenms.CrossLinkSpectrumMatch property) CROSS_LINK (pyopenms.ProForma.ConversionIssueType attribute) cross_link_position (pyopenms.ProteinProteinCrossLink property) cross_linker_mass (pyopenms.ProteinProteinCrossLink property) cross_linker_name (pyopenms.ProteinProteinCrossLink property) CrossLinksDB (class in pyopenms) CrossLinkSpectrumMatch (class in pyopenms) CSV (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) CsvFile (class in pyopenms) CTerminal (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) CubicSpline2d (class in pyopenms) custom_annotations (pyopenms.PEFFEntry property) custom_key_defs (pyopenms.PEFFDatabaseMetadata property) cuts_after_sensitive (pyopenms.RNaseCleavageSensitiveModGroups property) cuts_before_sensitive (pyopenms.RNaseCleavageSensitiveModGroups property) CV (class in pyopenms) (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.Provenance attribute) cv_group_keys (pyopenms.RescoreInput property) cv_ref (pyopenms.Unit property) CvAccession (class in pyopenms) CVMappingFile (class in pyopenms) CVMappingRule (class in pyopenms) CVMappings (class in pyopenms) CVMappingTerm (class in pyopenms) CVReference (class in pyopenms) CVTerm (class in pyopenms) CVTermList (class in pyopenms) CVTermListInterface (class in pyopenms) CYCLOTRON (pyopenms.MassAnalyzer.AnalyzerType attribute) D D (pyopenms.MzPAFIonSeries attribute) d (pyopenms.RANSACParam property) DALTON (pyopenms.MzPAFDeltaUnit attribute) DALTONS (pyopenms.XTandemInfile attribute) (pyopenms.XTandemInfile.ErrorUnit attribute) DALYDETECTOR (pyopenms.IonDetector.Type attribute) data (pyopenms.BinaryDataArray property) (pyopenms.OSBinaryDataArray property) data_page_size (pyopenms.ParquetWriteConfig property) DATA_PROCESSING (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) data_view() (pyopenms.FloatDataArray method) (pyopenms.IntegerDataArray method) (pyopenms.OSBinaryDataArray method) database (pyopenms.CvAccession property) DATABASE_EMPTY (pyopenms.PeptideIndexing.ExitCodes attribute) DataFilter (class in pyopenms) DataFilters (class in pyopenms) DataFilters.FilterOperation (class in pyopenms) DataFilters.FilterType (class in pyopenms) DataProcessing (class in pyopenms) DataProcessing.ProcessingAction (class in pyopenms) DataType (class in pyopenms) DataValue (class in pyopenms) Date (class in pyopenms) date (pyopenms.FileInfo.ExperimentMeta property) DateTime (class in pyopenms) day() (pyopenms.Date method) db (pyopenms.SearchParameters property) db_description (pyopenms.PEFFDatabaseMetadata property) db_name (pyopenms.FileInfo.IdentInfo property) (pyopenms.PEFFDatabaseMetadata property) db_sources (pyopenms.PEFFDatabaseMetadata property) db_unique_id (pyopenms.PEFFEntry property) db_version (pyopenms.FileInfo.IdentInfo property) (pyopenms.PEFFDatabaseMetadata property) (pyopenms.SearchParameters property) DBoundingBox2 (class in pyopenms) de novo de novo peptide sequencing debug() (pyopenms.BSpline2d static method) decode32() (pyopenms.Base64 static method) decode64() (pyopenms.Base64 static method) decodeIntegers() (pyopenms.Base64 static method) decodeNP() (pyopenms.MSNumpressCoder method) decodeNPRaw() (pyopenms.MSNumpressCoder method) decodeStrings() (pyopenms.Base64 static method) DeconvolvedSpectrum (class in pyopenms) DECOY (pyopenms.DecoyTransitionType attribute) (pyopenms.EntrapmentEvaluation.Kind attribute) decoy (pyopenms.LightTransition property) DECOY (pyopenms.ReactionMonitoringTransition attribute) (pyopenms.ReactionMonitoringTransition.DecoyTransitionType attribute) decoy (pyopenms.SiriusFragmentAnnotation_SiriusTargetDecoySpectra property) decoy_compound_ref (pyopenms.MetaboTargetedTargetDecoy_MetaboTargetDecoyMassMapping property) decoy_product_masses (pyopenms.MetaboTargetedTargetDecoy_MetaboTargetDecoyMassMapping property) DecoyGenerator (class in pyopenms) DecoyTransitionType (class in pyopenms) defaultArrayLength (pyopenms.Chromatogram property) (pyopenms.Spectrum property) DefaultParamHandler (class in pyopenms) DEFINED (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.Provenance attribute) DEG_PER_RAD (in module pyopenms.Constants) deisotopeAndSingleCharge() (pyopenms.Deisotoper static method) deisotopeAndSingleChargeDefault() (pyopenms.Deisotoper static method) Deisotoper (class in pyopenms) deisotopeWithAveragineModel() (pyopenms.Deisotoper static method) DEISOTOPING (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) DELAYED_EXTRACTION (pyopenms.Instrument.IonOpticsType attribute) delta_D() (pyopenms.SpectraSTSimilarityScore method) delta_mass (pyopenms.DeltaMassEntry property) (pyopenms.MultiplexDeltaMasses_DeltaMass property) (pyopenms.MultiplexDeltaMassesGenerator_Label property) delta_mass_stats (pyopenms.OpenSearchAnalysisResult property) DeltaMassEntry (class in pyopenms) DeltaMassStatistics (class in pyopenms) denominator (pyopenms.Base64.ByteOrder attribute) (pyopenms.BasicProteinInferenceAlgorithm.AggregationMethod attribute) (pyopenms.BoundaryCondition attribute) (pyopenms.BSpline2d.BoundaryCondition attribute) (pyopenms.ChromatogramSettings.ChromatogramType attribute) (pyopenms.CombinationsLogic attribute) (pyopenms.ConsensusMapNormalizerAlgorithmMedian.NormalizationMethod attribute) (pyopenms.ControlledVocabulary.CVTerm.XRefType attribute) (pyopenms.DRangeIntersection attribute) (pyopenms.DriftTimeUnit attribute) (pyopenms.EntrapmentEvaluation.Kind attribute) (pyopenms.EntrapmentEvaluation.Level attribute) (pyopenms.EnzymaticDigestion.Specificity attribute) (pyopenms.FeatureDeconvolution.CHARGEMODE attribute) (pyopenms.FileType attribute) (pyopenms.FileTypes.FileType attribute) (pyopenms.HydrophobicityScaleMethod attribute) (pyopenms.IDMapper.Measure attribute) (pyopenms.IDRipper.OriginAnnotationFormat attribute) (pyopenms.IDType attribute) (pyopenms.IsotopeDistribution.Sorted attribute) (pyopenms.ITRAQ_TYPES attribute) (pyopenms.ItraqConstants.ITRAQ_TYPES attribute) (pyopenms.LogType attribute) (pyopenms.Measure attribute) (pyopenms.MetaboliteFeatureDeconvolution.CHARGEMODE attribute) (pyopenms.Method attribute) (pyopenms.MSNumpressCoder.NumpressCompression attribute) (pyopenms.MultipleTesting.LfdrTransform attribute) (pyopenms.MultipleTesting.Pi0Method attribute) (pyopenms.MzPAFDeltaUnit attribute) (pyopenms.MzPAFErrorCode attribute) (pyopenms.MzPAFIonSeries attribute) (pyopenms.NaNPolicy attribute) (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.NormalizationMethod attribute) (pyopenms.OpenMSOSInfo.OpenMS_Architecture attribute) (pyopenms.OpenMSOSInfo.OpenMS_OS attribute) (pyopenms.OpenPepXLAlgorithm.ExitCodes attribute) (pyopenms.OPXLDataStructs.PeptidePosition attribute) (pyopenms.OPXLDataStructs.ProteinProteinCrossLinkType attribute) (pyopenms.OriginAnnotationFormat attribute) (pyopenms.ParquetWriteConfig.Compression attribute) (pyopenms.PeakGroup.TargetDecoyType attribute) (pyopenms.PEFFDatabaseMetadata.SequenceType attribute) (pyopenms.PEFFModification.ModificationType attribute) (pyopenms.PeptideIndexing.ExitCodes attribute) (pyopenms.PercolatorOutfile.ScoreType attribute) (pyopenms.ProForma.ConversionIssueType attribute) (pyopenms.ProForma.ConversionPolicy attribute) (pyopenms.ProForma.CvDatabase attribute) (pyopenms.ProForma.WriteMode attribute) (pyopenms.ProgressLogger.LogType attribute) (pyopenms.ProSEAlgorithm.ProSEAlgorithm_ExitCodes attribute) (pyopenms.ProteomicsPkaScale attribute) (pyopenms.QuotingMethod attribute) (pyopenms.RankData.Method attribute) (pyopenms.RankData.NaNPolicy attribute) (pyopenms.RequirementLevel attribute) (pyopenms.Residue.ResidueType attribute) (pyopenms.ResidueModification.Provenance attribute) (pyopenms.ResidueModification.SourceClassification attribute) (pyopenms.ResidueModification.TermSpecificity attribute) (pyopenms.Ribonucleotide.TermSpecificityNuc attribute) (pyopenms.Scores.IDType attribute) (pyopenms.SIDE attribute) (pyopenms.SimpleSearchEngineAlgorithm.ExitCodes attribute) (pyopenms.UnitType attribute) (pyopenms.USI.IndexType attribute) (pyopenms.ValueType attribute) (pyopenms.XFDRAlgorithm.ExitCodes attribute) (pyopenms.XTandemInfile.ErrorUnit attribute) (pyopenms.XTandemInfile.MassType attribute) denominator_ref_ (pyopenms.ConsensusFeature.Ratio property) Dense (pyopenms.Method attribute) (pyopenms.RankData.Method attribute) derivative() (pyopenms.BSpline2d method) (pyopenms.LinearInterpolation method) derivatives() (pyopenms.CubicSpline2d method) des (pyopenms.SiriusMSFile_CompoundInfo property) description (pyopenms.ChannelInfo property) (pyopenms.ControlledVocabulary.CVTerm property) (pyopenms.ConversionIssue property) (pyopenms.FASTAEntry property) (pyopenms.IsobaricChannelInformation property) (pyopenms.MultiplexDeltaMassesGenerator_Label property) (pyopenms.OSBinaryDataArray property) (pyopenms.ParamEntry property) (pyopenms.ParamNode property) (pyopenms.PEFFCustomKeyDef property) description_ (pyopenms.ConsensusFeature.Ratio property) (pyopenms.ToolInfo property) detail (pyopenms.FileInfo.Result property) (pyopenms.FileInfo.ValidationInfo property) detailed (pyopenms.FileInfo.Options property) detectFormat() (pyopenms.BrukerTimsFile static method) detecting_transition (pyopenms.LightTransition property) detectingTransitions() (pyopenms.MRMAssay method) detectors (pyopenms.FileInfo.ExperimentMeta property) detectPeaks() (pyopenms.ElutionPeakDetection method) determineIMFormat() (pyopenms.IMTypes static method) df_columns() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.PeptideIdentificationList method) (pyopenms.XICParquetFile method) (pyopenms.XIMParquetFile method) (pyopenms.XIPMParquetFile method) DI (pyopenms.IonSource.IonizationMethod attribute) dia_by_ion_score() (pyopenms.DIAScoring method) dia_ms1_isotope_scores() (pyopenms.DIAScoring method) dia_ms1_isotope_scores_averagine() (pyopenms.DIAScoring method) dia_ms1_massdiff_score() (pyopenms.DIAScoring method) dia_ms2_centroid (pyopenms.BrukerTimsFile.Config property) dia_ms2_min_support (pyopenms.BrukerTimsFile.Config property) dia_ms2_n_neighbors (pyopenms.BrukerTimsFile.Config property) DIAGNOSTIC (pyopenms.TheoreticalGlycanSpectrumGenerator.IonType attribute) diagnostics (pyopenms.IDFreeMassErrorEstimator.Result property) DIAScoring (class in pyopenms) digest() (pyopenms.ProteaseDigestion method) (pyopenms.RNaseDigestion method) digestDatabase() (pyopenms.OPXLHelper static method) digestion_enzyme (pyopenms.SearchParameters property) DigestionEnzyme (class in pyopenms) DigestionEnzymeProtein (class in pyopenms) DigestionEnzymeRNA (class in pyopenms) digestProducts() (pyopenms.RNaseDigestion method) digestUnmodified() (pyopenms.EnzymaticDigestion method) (pyopenms.ProteaseDigestion method) (pyopenms.RNaseDigestion method) digestWithCleavageSensitiveMods() (pyopenms.RNaseDigestion method) digestWithVariants() (pyopenms.PEFFEntry method) dilution_factor (pyopenms.AQS_featureConcentration property) (pyopenms.AQS_runConcentration property) DIMENSION (pyopenms.DimensionDescription attribute) (pyopenms.Peak2D attribute) (pyopenms.Peak2D.DimensionDescription attribute) DimensionDescription (class in pyopenms) dimensionsize() (pyopenms.DistanceMatrix method) DIon (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) DIRECT (pyopenms.IonSource.InletType attribute) Disjoint (pyopenms.DRangeIntersection attribute) DISSI (pyopenms.IonSource.IonizationMethod attribute) DistanceMatrix (class in pyopenms) disulfide_bonds (pyopenms.PEFFEntry property) divideByGCD() (pyopenms.IMSWeights method) document_id (pyopenms.FileInfo.ExperimentMeta property) DocumentIdentifier (class in pyopenms) docurl_ (pyopenms.ToolInfo property) domParseChromatogram() (pyopenms.MzMLSpectrumDecoder method) domParseSpectrum() (pyopenms.MzMLSpectrumDecoder method) dot_bias() (pyopenms.SpectraSTSimilarityScore method) dotprod_score_dia (pyopenms.OpenSwath_Scores property) DOUBLE (pyopenms.QuotingMethod attribute) DOUBLE_LIST (pyopenms.DataType attribute) (pyopenms.DataValue attribute) (pyopenms.ParamValue attribute) (pyopenms.ValueType attribute) DOUBLE_VALUE (pyopenms.DataType attribute) (pyopenms.DataValue attribute) (pyopenms.ParamValue attribute) (pyopenms.ValueType attribute) DOWN (pyopenms.MassAnalyzer.ScanDirection attribute) DRange1 (class in pyopenms) DRange2 (class in pyopenms) DRangeIntersection (class in pyopenms) drift_time (pyopenms.LightCompound property) (pyopenms.MSSpectrum property) drift_time_array_view() (pyopenms.MSSpectrum method) (pyopenms.OSSpectrum method) drift_time_unit (pyopenms.MSSpectrum property) DriftTimeUnit (class in pyopenms) driftTimeUnitToString() (pyopenms.IMTypes static method) DROP_UNLOCALISED (pyopenms.ProForma.ConversionPolicy attribute) DTA (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) DTA2D (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) DTA2DFile (class in pyopenms) DTAFile (class in pyopenms) dup_headers (pyopenms.FileInfo.FastaInfo property) dup_sequences (pyopenms.FileInfo.FastaInfo property) DYNODE (pyopenms.IonDetector.Type attribute) E E (in module pyopenms.Constants) ECD (pyopenms.Precursor.ActivationMethod attribute) EDTA (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) EDTAFile (class in pyopenms) EI (pyopenms.IonSource.IonizationMethod attribute) EIGHTPLEX (pyopenms.ITRAQ_TYPES attribute) (pyopenms.ItraqConstants attribute) (pyopenms.ItraqConstants.ITRAQ_TYPES attribute) EINZEL_LENS (pyopenms.Instrument.IonOpticsType attribute) EISENBERG (pyopenms.HydrophobicityScaleMethod attribute) EISENBERG_CONSENSUS (pyopenms.HydrophobicityScaleMethod attribute) ELECTROMAGNETIC_RADIATION_CHROMATOGRAM (pyopenms.ChromatogramSettings.ChromatogramType attribute) ELECTRON_MASS (in module pyopenms.Constants) ELECTRON_MASS_U (in module pyopenms.Constants) ELECTRONMULTIPLIER (pyopenms.IonDetector.Type attribute) ELECTRONMULTIPLIERTUBE (pyopenms.IonDetector.Type attribute) electrospray ionization ELECTROSPRAYINLET (pyopenms.IonSource.InletType attribute) Element (class in pyopenms) ELEMENTARY_CHARGE (in module pyopenms.Constants) ElementDB (class in pyopenms) elution_model_fit_score (pyopenms.OpenSwath_Scores property) elutionModelFit() (pyopenms.EmgScoring method) ElutionModelFitter (class in pyopenms) ElutionPeakDetection (class in pyopenms) email (pyopenms.FileInfo.Contact property) embedded_sequence (pyopenms.MzPAFAnnotation property) EMBOSS (pyopenms.ProteomicsPkaScale attribute) EMC (pyopenms.InstrumentSettings.ScanMode attribute) EmgFitter1D (class in pyopenms) EmgGradientDescent (class in pyopenms) EmgModel (class in pyopenms) EmgScoring (class in pyopenms) EMISSION (pyopenms.InstrumentSettings.ScanMode attribute) EMISSION_CHROMATOGRAM (pyopenms.ChromatogramSettings.ChromatogramType attribute) EmpiricalFormula (class in pyopenms) empty() (pyopenms.AASequence method) (pyopenms.BilinearInterpolation method) (pyopenms.CalibrationData method) (pyopenms.Compound method) (pyopenms.Configuration method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusMap method) (pyopenms.Contact method) (pyopenms.CVTermList method) (pyopenms.CVTermListInterface method) (pyopenms.DeconvolvedSpectrum method) (pyopenms.File static method) (pyopenms.IdentificationData method) (pyopenms.IdentifierMSRunMapper method) (pyopenms.IMSIsotopeDistribution method) (pyopenms.IncludeExcludeTarget method) (pyopenms.IsobaricQuantities method) (pyopenms.LinearInterpolation method) (pyopenms.MetaInfo method) (pyopenms.MSExperiment method) (pyopenms.MzPAFPeakAnnotations method) (pyopenms.NASequence method) (pyopenms.OnDiscMSExperiment method) (pyopenms.Param method) (pyopenms.ParquetFilter method) (pyopenms.PeakGroup method) (pyopenms.Peptide method) (pyopenms.PeptideIdentification method) (pyopenms.PeptideIdentificationList method) (pyopenms.Precursor method) (pyopenms.Prediction method) (pyopenms.Product method) (pyopenms.Protein method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.Software method) (pyopenms.SourceFile method) (pyopenms.SpectrumLookup method) (pyopenms.SpectrumMetaDataLookup method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TraMLProduct method) empty_channels (pyopenms.IsobaricQuantifierStatistics property) EMPTY_INPUT (pyopenms.MzPAFErrorCode attribute) EMPTY_VALUE (pyopenms.DataType attribute) (pyopenms.DataValue attribute) (pyopenms.ParamValue attribute) (pyopenms.ValueType attribute) EMR (pyopenms.InstrumentSettings.ScanMode attribute) EMULSION (pyopenms.Sample.SampleState attribute) encloses() (pyopenms.ConvexHull2D method) (pyopenms.DRange1 method) (pyopenms.DRange2 method) (pyopenms.Feature method) (pyopenms.MRMFeature method) enclosesXY() (pyopenms.ConvexHull2D method) encode32() (pyopenms.Base64 static method) encode64() (pyopenms.Base64 static method) encoded_bytes (pyopenms.ImzMLAuxArrayIndex property) encodeIntegers() (pyopenms.Base64 static method) encodeNP() (pyopenms.MSNumpressCoder method) encodeNPRaw() (pyopenms.MSNumpressCoder method) encodeStrings() (pyopenms.Base64 static method) end (pyopenms.ScanWindow property) end_position (pyopenms.PEFFProcessedRegion property) (pyopenms.PEFFVariantComplex property) end_position_at_10 (pyopenms.PI_PeakShapeMetrics property) end_position_at_5 (pyopenms.PI_PeakShapeMetrics property) end_position_at_50 (pyopenms.PI_PeakShapeMetrics property) endProgress() (pyopenms.AccurateMassSearchEngine method) (pyopenms.AverageLinkage method) (pyopenms.BaseGroupFinder method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.BrukerTimsFile method) (pyopenms.CachedMzMLHandler method) (pyopenms.ChromatogramExtractor method) (pyopenms.ChromatogramExtractorAlgorithm method) (pyopenms.ConfidenceScoring method) (pyopenms.DTA2DFile method) (pyopenms.ElutionPeakDetection method) (pyopenms.FASTAFile method) (pyopenms.FeatureFindingMetabo method) (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.FLASHDeconvAlgorithm method) (pyopenms.GaussFilter method) (pyopenms.ImzMLFile method) (pyopenms.InternalCalibration method) (pyopenms.LabeledPairFinder method) (pyopenms.LinearResamplerAlign method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) (pyopenms.MascotGenericFile method) (pyopenms.MasstraceCorrelator method) (pyopenms.MassTraceDetection method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.ModifiedSincSmoother method) (pyopenms.MorphologicalFilter method) (pyopenms.MRMAssay method) (pyopenms.MRMDecoy method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MS2File method) (pyopenms.MSDataCachedConsumer method) (pyopenms.MzDataFile method) (pyopenms.MzIdentMLFile method) (pyopenms.MzMLFile method) (pyopenms.MzXMLFile method) (pyopenms.PeakMapExtractor method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) (pyopenms.PEFFFile method) (pyopenms.ProgressLogger method) (pyopenms.ProSEAlgorithm method) (pyopenms.QTClusterFinder method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.StablePairFinder method) (pyopenms.SwathFile method) (pyopenms.ThermoRawFile method) (pyopenms.TransitionPQPFile method) (pyopenms.TransitionTSVFile method) ensureUniqueId() (pyopenms.BaseFeature method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusMap method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.FeatureMap method) (pyopenms.MRMFeature method) (pyopenms.RichPeak2D method) (pyopenms.UniqueIdInterface method) ENTRAPMENT (pyopenms.EntrapmentEvaluation.Kind attribute) entrapment (pyopenms.EntrapmentEvaluation.Result property) entrapment_above_target (pyopenms.EntrapmentEvaluation.Result property) entrapment_target_not_accepted (pyopenms.EntrapmentEvaluation.Result property) EntrapmentEvaluation (class in pyopenms) EntrapmentEvaluation.Kind (class in pyopenms) EntrapmentEvaluation.Level (class in pyopenms) EntrapmentEvaluation.Result (class in pyopenms) entries (pyopenms.DeltaMassStatistics property) (pyopenms.ParamNode property) (pyopenms.PTMStatistics property) entry_id (pyopenms.PEFFEntry property) entry_version (pyopenms.PEFFEntry property) enumerateCrossLinksAndMasses() (pyopenms.OPXLHelper static method) enumToName() (pyopenms.MZTrafoModel static method) EnzymaticDigestion (class in pyopenms) EnzymaticDigestion.Specificity (class in pyopenms) EPSILON (in module pyopenms.Constants) eq() (pyopenms.ParquetFilter method) EQUAL (pyopenms.DataFilters attribute) (pyopenms.DataFilters.FilterOperation attribute) erase() (pyopenms.IMSAlphabet method) err (pyopenms.MorpheusScore_Result property) err_ppm (pyopenms.MorpheusScore_Result property) errors (pyopenms.FileInfo.CorruptionInfo property) (pyopenms.FileInfo.ValidationInfo property) ESA (pyopenms.MassAnalyzer.AnalyzerType attribute) ESCAPE (pyopenms.QuotingMethod attribute) ESI (pyopenms.IonSource.IonizationMethod attribute) estimate_fixed_point (pyopenms.NumpressConfig property) estimateBackground() (pyopenms.PeakIntegrator method) EstimateBackgroundInterferences() (pyopenms.MRMFeatureFilter method) EstimateDefaultMRMFeatureQCValues() (pyopenms.MRMFeatureFilter method) estimateForFragmentFromDNAWeight() (pyopenms.CoarseIsotopePatternGenerator method) estimateForFragmentFromPeptideWeight() (pyopenms.CoarseIsotopePatternGenerator method) estimateForFragmentFromPeptideWeightAndS() (pyopenms.CoarseIsotopePatternGenerator method) estimateForFragmentFromRNAWeight() (pyopenms.CoarseIsotopePatternGenerator method) estimateForFragmentFromWeightAndComp() (pyopenms.CoarseIsotopePatternGenerator method) estimateFromDNAWeight() (pyopenms.CoarseIsotopePatternGenerator method) estimateFromPeptideWeight() (pyopenms.CoarseIsotopePatternGenerator method) estimateFromPeptideWeightAndS() (pyopenms.CoarseIsotopePatternGenerator method) estimateFromRNAWeight() (pyopenms.CoarseIsotopePatternGenerator method) estimateFromWeightAndComp() (pyopenms.CoarseIsotopePatternGenerator method) (pyopenms.EmpiricalFormula method) estimateFromWeightAndCompAndS() (pyopenms.CoarseIsotopePatternGenerator method) (pyopenms.EmpiricalFormula method) estimateFWHM() (pyopenms.MassTrace method) estimateNoise() (pyopenms.SignalToNoiseEstimatorMedianRapid method) EstimatePercRSD() (pyopenms.MRMFeatureFilter method) estimateRTRange() (pyopenms.OpenSwathHelper static method) estimateTERatio() (pyopenms.EntrapmentEvaluation static method) estimateType() (pyopenms.PeakTypeEstimator method) ETciD (pyopenms.Precursor.ActivationMethod attribute) ETD (pyopenms.Precursor.ActivationMethod attribute) (pyopenms.TheoreticalGlycanSpectrumGenerator.FragmentationMethod attribute) EThcD (pyopenms.Precursor.ActivationMethod attribute) ETHCD (pyopenms.TheoreticalGlycanSpectrumGenerator.FragmentationMethod attribute) eval() (pyopenms.BSpline2d method) (pyopenms.CubicSpline2d method) (pyopenms.GaussFitResult method) (pyopenms.SplineInterpolatedPeaks.Navigator method) (pyopenms.SplinePackage method) evaluate() (pyopenms.EntrapmentEvaluation static method) (pyopenms.TransformationModelBSpline method) (pyopenms.TransformationModelInterpolated method) (pyopenms.TransformationModelLinear method) (pyopenms.TransformationModelLowess method) evidence (pyopenms.Peptide property) (pyopenms.TransitionListEvidenceFilter_Result property) example (pyopenms.UnresolvedIdentifications property) excluded_fragment_profile_or_unknown (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) excluded_fragment_unknown (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) excluded_low_fragment_peaks (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) excluded_missing_precursor (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) excluded_profile_peak_pick_failure (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) EXE (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) EXECUTION_OK (pyopenms.OpenPepXLAlgorithm.ExitCodes attribute) (pyopenms.PeptideIndexing.ExitCodes attribute) (pyopenms.ProSEAlgorithm attribute) (pyopenms.ProSEAlgorithm.ProSEAlgorithm_ExitCodes attribute) (pyopenms.SimpleSearchEngineAlgorithm.ExitCodes attribute) (pyopenms.XFDRAlgorithm.ExitCodes attribute) EXISTS (pyopenms.DataFilters attribute) (pyopenms.DataFilters.FilterOperation attribute) exists() (pyopenms.ControlledVocabulary method) (pyopenms.File static method) (pyopenms.MetaInfo method) (pyopenms.Param method) exit_code (pyopenms.SearchResult property) expandToBoundingBox() (pyopenms.ConvexHull2D method) expectedChannelMZs() (pyopenms.MultiplexResolverAlgorithm method) experiment_meta (pyopenms.FileInfo.Result property) ExperimentalDesign (class in pyopenms) ExperimentalDesign_MSFileSectionEntry (class in pyopenms) ExperimentalDesign_SampleSection (class in pyopenms) ExperimentalDesignFile (class in pyopenms) ExperimentalSettings (class in pyopenms) EXPONENTIAL (pyopenms.MassAnalyzer.ScanLaw attribute) export_mode (pyopenms.BrukerTimsFile.Config property) exportFeatureMapToMzTabM() (pyopenms.MzTabM static method) exportProteinGroupsToParquet() (pyopenms.ProteinIdentificationArrowIO static method) exportProteinsToParquet() (pyopenms.ProteinIdentificationArrowIO static method) exportSearchParamsToParquet() (pyopenms.ProteinIdentificationArrowIO static method) exportToParquet() (pyopenms.ConsensusMapArrowIO static method) (pyopenms.FeatureMapArrowIO static method) (pyopenms.QPXFile static method) expose_hill_bounds (pyopenms.BrukerTimsFile.Config property) extend() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.PeptideIdentificationList method) (pyopenms.RangeBase method) (pyopenms.RangeIntensity method) (pyopenms.RangeMobility method) (pyopenms.RangeMZ method) (pyopenms.RangeRT method) extendIntensity() (pyopenms.RangeIntensity method) extendMobility() (pyopenms.RangeMobility method) extendMZ() (pyopenms.RangeMZ method) (pyopenms.SpectrumRangeManager method) extendRT() (pyopenms.RangeRT method) (pyopenms.SpectrumRangeManager method) extendUnsafe() (pyopenms.SpectrumRangeManager method) extra_rt_extract (pyopenms.OSW_ChromExtractParams property) extract_columnname_to_columnindex() (pyopenms.SiriusFragmentAnnotation static method) extractAndResolveSiriusAnnotations() (pyopenms.SiriusFragmentAnnotation static method) extractAnnotationsFromSiriusFile() (pyopenms.SiriusFragmentAnnotation static method) extractBasename() (pyopenms.USI static method) extractChannels() (pyopenms.IsobaricChannelExtractor method) extractChromatograms() (pyopenms.ChromatogramExtractor method) (pyopenms.ChromatogramExtractorAlgorithm method) ExtractedPeakMap (class in pyopenms) extractIntensityVectors() (pyopenms.ConsensusMapNormalizerAlgorithmQuantile static method) extraction_function (pyopenms.OSW_ChromExtractParams property) ExtractionCoordinates (class in pyopenms) extractIonImage() (pyopenms.MSImagingExperiment method) (pyopenms.OnDiscImzMLExperiment method) extractMetaboTargetedAssay() (pyopenms.MetaboTargetedAssay static method) extractMetaboTargetedAssayFragmentAnnotation() (pyopenms.MetaboTargetedAssay static method) extractPeakMaps() (pyopenms.PeakMapExtractor method) extractPeaks() (pyopenms.FIAMSDataProcessor method) extractPeptideSequences() (pyopenms.IDFilter static method) extractProteinAccessionsSet() (pyopenms.PeptideHit method) extractScanNumber() (in module pyopenms) (pyopenms.SpectrumLookup static method) (pyopenms.SpectrumMetaDataLookup static method) (pyopenms.SpectrumNativeIDParser static method) extractSpectra() (pyopenms.TargetedSpectraExtractor method) extractXICsFromMatrix() (pyopenms.MSExperiment method) F FA (pyopenms.IonSource.IonizationMethod attribute) FAB (pyopenms.IonSource.IonizationMethod attribute) FAIL_ON_LOSS (pyopenms.ProForma.ConversionPolicy attribute) FAIMS_COMPENSATION_VOLTAGE (pyopenms.DriftTimeUnit attribute) faims_cvs (pyopenms.FileInfo.PeakInfo property) FAIMSHelper (class in pyopenms) FalseDiscoveryRate (class in pyopenms) FARADAY (in module pyopenms.Constants) FARADAYCUP (pyopenms.IonDetector.Type attribute) FASTA fasta (pyopenms.FileInfo.Result property) FASTA (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) FASTAEntry (class in pyopenms) FASTAFile (class in pyopenms) FD (pyopenms.IonSource.IonizationMethod attribute) FDR (pyopenms.IDType attribute) (pyopenms.Scores.IDType attribute) feature Feature (class in pyopenms) feature (pyopenms.AQS_featureConcentration property) (pyopenms.FileInfo.Result property) FEATURE (pyopenms.OSWHierarchy attribute) (pyopenms.OSWHierarchy.Level attribute) feature finder feature map feature maps feature_columns() (pyopenms.ConsensusMap method) feature_df_columns() (pyopenms.MRMTransitionGroupCP method) FEATURE_GROUPING (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) FEATURE_ID_MULTIPLE_DIVERGENT (pyopenms.AnnotationState attribute) (pyopenms.BaseFeature attribute) (pyopenms.BaseFeature.AnnotationState attribute) (pyopenms.ConsensusFeature attribute) (pyopenms.Feature attribute) (pyopenms.MRMFeature attribute) FEATURE_ID_MULTIPLE_SAME (pyopenms.AnnotationState attribute) (pyopenms.BaseFeature attribute) (pyopenms.BaseFeature.AnnotationState attribute) (pyopenms.ConsensusFeature attribute) (pyopenms.Feature attribute) (pyopenms.MRMFeature attribute) FEATURE_ID_NONE (pyopenms.AnnotationState attribute) (pyopenms.BaseFeature attribute) (pyopenms.BaseFeature.AnnotationState attribute) (pyopenms.ConsensusFeature attribute) (pyopenms.Feature attribute) (pyopenms.MRMFeature attribute) FEATURE_ID_SINGLE (pyopenms.AnnotationState attribute) (pyopenms.BaseFeature attribute) (pyopenms.BaseFeature.AnnotationState attribute) (pyopenms.ConsensusFeature attribute) (pyopenms.Feature attribute) (pyopenms.MRMFeature attribute) feature_maps (pyopenms.FeatureMapping_FeatureMappingInfo property) feature_matrix (pyopenms.RescoreInput property) feature_names (pyopenms.RescoreInput property) feature_view() (pyopenms.FeatureMap method) (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) feature_views() (pyopenms.FeatureMap method) (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) FeatureDeconvolution (class in pyopenms) FeatureDeconvolution.CHARGEMODE (class in pyopenms) FeatureDistance (class in pyopenms) FeatureFileOptions (class in pyopenms) FeatureFinder FeatureFinderAlgorithmMetaboIdent (class in pyopenms) FeatureFinderAlgorithmPicked (class in pyopenms) FeatureFinderAlgorithmPickedHelperStructs_MassTrace (class in pyopenms) FeatureFinderIdentificationAlgorithm (class in pyopenms) FeatureFinderMetaboIdentCompound (class in pyopenms) FeatureFinderMultiplexAlgorithm (class in pyopenms) FeatureFindingMetabo (class in pyopenms) FeatureGroupingAlgorithm (class in pyopenms) FeatureGroupingAlgorithmKD (class in pyopenms) FeatureGroupingAlgorithmLabeled (class in pyopenms) FeatureGroupingAlgorithmQT (class in pyopenms) FeatureGroupingAlgorithmUnlabeled (class in pyopenms) FeatureHandle (class in pyopenms) FeatureMap (class in pyopenms) FeatureMapArrowIO (class in pyopenms) FeatureMapping (class in pyopenms) FeatureMapping_FeatureMappingInfo (class in pyopenms) FeatureMapping_FeatureToMs2Indices (class in pyopenms) FeatureOverlapFilter (class in pyopenms) FeatureOverlapFilter.FeatureOverlapMode (class in pyopenms) FeatureOverlapFilter.MergeIntensityMode (class in pyopenms) FEATUREPARQUET (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) features (pyopenms.RescoreInput property) FeatureUniqueIds (class in pyopenms) FEATUREXML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) FeatureXMLFile (class in pyopenms) FI (pyopenms.IonSource.IonizationMethod attribute) FIAMSDataProcessor (class in pyopenms) FIAMSScheduler (class in pyopenms) FIB (pyopenms.IonSource.IonizationMethod attribute) fid (pyopenms.SiriusMSFile_CompoundInfo property) field (pyopenms.DataFilter property) field_names (pyopenms.PEFFCustomKeyDef property) field_types (pyopenms.PEFFCustomKeyDef property) FII (pyopenms.IonSource.IonizationMethod attribute) File (class in pyopenms) file_index (pyopenms.SiriusMSFile_CompoundInfo property) file_level_psm_counts (pyopenms.PeptideAndProteinQuant_ProteinData property) file_name (pyopenms.FileInfo.FileMeta property) FILE_ORIGIN (pyopenms.IDRipper attribute) (pyopenms.IDRipper.OriginAnnotationFormat attribute) (pyopenms.OriginAnnotationFormat attribute) file_type (pyopenms.FileInfo.FileMeta property) file_type_name (pyopenms.FileInfo.FileMeta property) FileHandler (class in pyopenms) FileInfo (class in pyopenms) FileInfo.Contact (class in pyopenms) FileInfo.CorruptionInfo (class in pyopenms) FileInfo.DetailInfo (class in pyopenms) FileInfo.ExperimentMeta (class in pyopenms) FileInfo.FastaInfo (class in pyopenms) FileInfo.FeatureInfo (class in pyopenms) FileInfo.FileMeta (class in pyopenms) FileInfo.IdentInfo (class in pyopenms) FileInfo.MapColumn (class in pyopenms) FileInfo.MzTabInfo (class in pyopenms) FileInfo.NamedStats (class in pyopenms) FileInfo.Options (class in pyopenms) FileInfo.PeakInfo (class in pyopenms) FileInfo.ProcessingStep (class in pyopenms) FileInfo.Range (class in pyopenms) FileInfo.Ranges (class in pyopenms) FileInfo.RangeSet (class in pyopenms) FileInfo.Result (class in pyopenms) FileInfo.ValidationInfo (class in pyopenms) fileList() (pyopenms.File static method) filename (pyopenms.ColumnHeader property) (pyopenms.FileInfo.MapColumn property) FileType (class in pyopenms) FileTypes (class in pyopenms) FileTypes.FileType (class in pyopenms) fillCalibrants() (pyopenms.InternalCalibration method) fillDensities() (pyopenms.PosteriorErrorProbabilityModel method) fillLogDensities() (pyopenms.PosteriorErrorProbabilityModel method) filter() (pyopenms.GaussFilter method) (pyopenms.ModifiedSincSmoother method) (pyopenms.MorphologicalFilter method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.TransitionListEvidenceFilter method) filterByPeakWidth() (pyopenms.ElutionPeakDetection method) filtered_targets (pyopenms.TransitionListEvidenceFilter_Result property) filterExperiment() (pyopenms.GaussFilter method) (pyopenms.ModifiedSincSmoother method) (pyopenms.MorphologicalFilter method) (pyopenms.SavitzkyGolayFilter method) FilterFeatureMap() (pyopenms.MRMFeatureFilter method) FilterFeatureMapBackgroundInterference() (pyopenms.MRMFeatureFilter method) FilterFeatureMapPercRSD() (pyopenms.MRMFeatureFilter method) filterHitsByRank() (pyopenms.IDFilter static method) filterHitsByScore() (pyopenms.IDFilter static method) FILTERING (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) filterMinMaxTransitionsCompound() (pyopenms.MRMAssay method) filterPeakMap() (pyopenms.NLargest method) (pyopenms.Normalizer method) (pyopenms.RankScaler method) (pyopenms.SqrtScaler method) (pyopenms.ThresholdMower method) (pyopenms.WindowMower method) filterPeakSpectrum() (pyopenms.NLargest method) (pyopenms.Normalizer method) (pyopenms.RankScaler method) (pyopenms.SqrtScaler method) (pyopenms.ThresholdMower method) (pyopenms.WindowMower method) filterPeakSpectrumForTopNInJumpingWindow() (pyopenms.WindowMower method) filterPeakSpectrumForTopNInSlidingWindow() (pyopenms.WindowMower method) filterPeptidesByCharge() (pyopenms.IDFilter static method) filterPeptidesByFAIMSCV() (pyopenms.FAIMSHelper static method) filterPeptidesByLength() (pyopenms.IDFilter static method) filterPeptidesByMZ() (pyopenms.IDFilter static method) filterPeptidesByMZError() (pyopenms.IDFilter static method) filterPeptidesByRT() (pyopenms.IDFilter static method) filterPeptidesByRTPredictPValue() (pyopenms.IDFilter static method) filterSpectrum() (pyopenms.GaussFilter method) (pyopenms.LowessSmoothing method) (pyopenms.MorphologicalFilter method) (pyopenms.NLargest method) (pyopenms.Normalizer method) (pyopenms.RankScaler method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SqrtScaler method) (pyopenms.ThresholdMower method) (pyopenms.WindowMower method) filterUnreferencedDecoysCompound() (pyopenms.MRMAssay method) finalizeCluster() (pyopenms.QTCluster method) find() (pyopenms.File static method) findByIndex() (pyopenms.SpectrumLookup method) (pyopenms.SpectrumMetaDataLookup method) findByNativeID() (pyopenms.SpectrumLookup method) (pyopenms.SpectrumMetaDataLookup method) findByReference() (pyopenms.SpectrumLookup method) (pyopenms.SpectrumMetaDataLookup method) findByRT() (pyopenms.SpectrumLookup method) (pyopenms.SpectrumMetaDataLookup method) findByScanNumber() (pyopenms.SpectrumLookup method) (pyopenms.SpectrumMetaDataLookup method) findConnectedComponent() (pyopenms.PeptideProteinResolution method) findDatabase() (pyopenms.File static method) (pyopenms.SystemSettings static method) findDoc() (pyopenms.File static method) findEntryRecursive() (pyopenms.ParamNode method) findExecutable() (pyopenms.File static method) findFirstRT() (pyopenms.OnDiscMSExperiment method) (pyopenms.OnDiscThermoRawExperiment method) findFixedResidues() (pyopenms.MRMDecoy static method) findHighestInWindow() (pyopenms.MSSpectrum method) findIndexListOffset() (pyopenms.IndexedMzMLDecoder method) findLargestPeak() (pyopenms.MRMTransitionGroupPicker method) findLocalExtrema() (pyopenms.ElutionPeakDetection method) findMaxByIntPeak() (pyopenms.MassTrace method) findModificationIndex() (pyopenms.CrossLinksDB method) (pyopenms.ModificationsDB method) findNearest() (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) (pyopenms.MZTrafoModel static method) findParentOf() (pyopenms.ParamNode method) findScoreType() (pyopenms.IDScoreSwitcherAlgorithm method) findWidestPeakIndices() (pyopenms.MRMTransitionGroupPicker method) FINE_STRUCTURE_CONSTANT (in module pyopenms.Constants) FineIsotopePatternGenerator (class in pyopenms) first (pyopenms.ProbablePhosphoSites property) (pyopenms.TransformationModel_DataPoint property) first_name (pyopenms.FileInfo.Contact property) first_scan (pyopenms.ThermoRawFileOptions property) FIRST_STABILITY_REGION (pyopenms.Instrument.IonOpticsType attribute) fit() (pyopenms.GaussFitter method) (pyopenms.GaussTraceFitter method) (pyopenms.PosteriorErrorProbabilityModel method) fitCalibration() (pyopenms.AbsoluteQuantitation method) fitElutionModels() (pyopenms.ElutionModelFitter method) fitEMGPeakModel() (pyopenms.EmgGradientDescent method) fitModel() (pyopenms.TransformationDescription method) fitTargetDecoy() (pyopenms.PosteriorErrorProbabilityModel method) Fitter1D (class in pyopenms) FIVE_PRIME (pyopenms.Ribonucleotide attribute) (pyopenms.Ribonucleotide.TermSpecificityNuc attribute) FivePrime (pyopenms.NASequence.NASFragmentType attribute) fixed_modifications (pyopenms.SearchParameters property) FLASHDeconvAlgorithm (class in pyopenms) FLASHDeconvFeatureFile (class in pyopenms) FLASHDeconvSpectrumFile (class in pyopenms) FLASHHelperClasses (class in pyopenms) FLOAT32 (pyopenms.ImzMLDataType attribute) FLOAT64 (pyopenms.ImzMLDataType attribute) float_arrays (pyopenms.FileInfo.PeakInfo property) float_data_array_view() (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) float_data_array_views() (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) FloatDataArray (class in pyopenms) FLOWINJECTIONANALYSIS (pyopenms.IonSource.InletType attribute) flush() (pyopenms.MSDataSqlConsumer method) fmz (pyopenms.SiriusMSFile_CompoundInfo property) FOCALPLANEARRAY (pyopenms.IonDetector.Type attribute) FOCALPLANECOLLECTOR (pyopenms.IonDetector.Type attribute) forced_type (pyopenms.FileInfo.Options property) FORMAT_CONVERSION (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) formula (pyopenms.MzPAFAnnotation property) FORMULA (pyopenms.MzPAFIonSeries attribute) formula (pyopenms.MzPAFNeutralLoss property) (pyopenms.SiriusMSFile_CompoundInfo property) formula_string (pyopenms.FormulaTag property) FormulaTag (class in pyopenms) FOURIERTRANSFORM (pyopenms.MassAnalyzer.AnalyzerType attribute) FOURPLEX (pyopenms.ITRAQ_TYPES attribute) (pyopenms.ItraqConstants attribute) (pyopenms.ItraqConstants.ITRAQ_TYPES attribute) fraction (pyopenms.ExperimentalDesign_MSFileSectionEntry property) fraction_group (pyopenms.ExperimentalDesign_MSFileSectionEntry property) fraction_group_abundances (pyopenms.PeptideAndProteinQuant_PeptideData property) (pyopenms.PeptideAndProteinQuant_ProteinData property) frag_annotations (pyopenms.CrossLinkSpectrumMatch property) fragment (pyopenms.RNaseDigestionProduct property) FRAGMENT_ANNOTATION_USERPARAM (in module pyopenms.Constants) fragment_centroid_spectra (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_charge (pyopenms.LightTransition property) fragment_da (pyopenms.IDFreeMassErrorEstimator.Result property) fragment_eligible_ms2 (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_high_intensity_fallback_used (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_high_intensity_mixture_converged (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_high_intensity_pairs (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_high_intensity_quantile (pyopenms.IDFreeMassErrorEstimator.Parameters property) fragment_high_intensity_signal_fraction (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_high_intensity_signal_pairs (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_high_intensity_threshold (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_high_res_max_sigma_da (pyopenms.IDFreeMassErrorEstimator.Parameters property) fragment_high_res_max_sigma_ppm (pyopenms.IDFreeMassErrorEstimator.Parameters property) fragment_low_res_match_da (pyopenms.IDFreeMassErrorEstimator.Parameters property) fragment_low_res_min_sigma_da (pyopenms.IDFreeMassErrorEstimator.Parameters property) fragment_low_res_min_sigma_ppm (pyopenms.IDFreeMassErrorEstimator.Parameters property) fragment_low_res_pairs (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_mass_tolerance (pyopenms.SearchParameters property) fragment_mass_tolerance_ppm (pyopenms.SearchParameters property) fragment_match_da (pyopenms.IDFreeMassErrorEstimator.Parameters property) fragment_match_window_da (pyopenms.IDFreeMassErrorEstimator.Result property) fragment_mixture_converged (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_mixture_iterations (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_mixture_mean_ppm (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_mixture_pairs (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_mixture_reference_mz (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_mixture_rejected_zero_quantization (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_mixture_signal_fraction (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_mixture_signal_pairs (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_nr (pyopenms.LightTransition property) fragment_paired_spectra (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_pairs (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_ppm (pyopenms.IDFreeMassErrorEstimator.Result property) fragment_profile_centroids (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_profile_spectra (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_resolution_regime (pyopenms.IDFreeMassErrorEstimator.Result property) fragment_tolerance_da (pyopenms.IDFreeMassErrorEstimator.Result property) fragment_tolerance_ppm (pyopenms.IDFreeMassErrorEstimator.Result property) fragment_tolerance_sigma_multiplier (pyopenms.IDFreeMassErrorEstimator.Parameters property) fragment_very_low_res_match_da (pyopenms.IDFreeMassErrorEstimator.Parameters property) fragment_very_low_res_pairs (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_window_censored (pyopenms.IDFreeMassErrorEstimator.Result property) fragment_zero_delta_fraction (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) fragment_zero_delta_pairs (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) FRAME (pyopenms.BrukerTimsFile.Config.ExportMode attribute) frame_id_max (pyopenms.BrukerTimsFile.Config property) frame_id_min (pyopenms.BrukerTimsFile.Config property) free_mem() (in module pyopenms) freehigh (pyopenms.SysInfo attribute) freeram (pyopenms.SysInfo attribute) freeswap (pyopenms.SysInfo attribute) FRINGING_FIELD (pyopenms.Instrument.IonOpticsType attribute) from_bytes() (pyopenms.Base64.ByteOrder class method) (pyopenms.BasicProteinInferenceAlgorithm.AggregationMethod class method) (pyopenms.BoundaryCondition class method) (pyopenms.BSpline2d.BoundaryCondition class method) (pyopenms.ChromatogramSettings.ChromatogramType class method) (pyopenms.CombinationsLogic class method) (pyopenms.ConsensusMapNormalizerAlgorithmMedian.NormalizationMethod class method) (pyopenms.ControlledVocabulary.CVTerm.XRefType class method) (pyopenms.DRangeIntersection class method) (pyopenms.DriftTimeUnit class method) (pyopenms.EntrapmentEvaluation.Kind class method) (pyopenms.EntrapmentEvaluation.Level class method) (pyopenms.EnzymaticDigestion.Specificity class method) (pyopenms.FeatureDeconvolution.CHARGEMODE class method) (pyopenms.FileType class method) (pyopenms.FileTypes.FileType class method) (pyopenms.HydrophobicityScaleMethod class method) (pyopenms.IDMapper.Measure class method) (pyopenms.IDRipper.OriginAnnotationFormat class method) (pyopenms.IDType class method) (pyopenms.IsotopeDistribution.Sorted class method) (pyopenms.ITRAQ_TYPES class method) (pyopenms.ItraqConstants.ITRAQ_TYPES class method) (pyopenms.LogType class method) (pyopenms.Measure class method) (pyopenms.MetaboliteFeatureDeconvolution.CHARGEMODE class method) (pyopenms.Method class method) (pyopenms.MSNumpressCoder.NumpressCompression class method) (pyopenms.MultipleTesting.LfdrTransform class method) (pyopenms.MultipleTesting.Pi0Method class method) (pyopenms.MzPAFDeltaUnit class method) (pyopenms.MzPAFErrorCode class method) (pyopenms.MzPAFIonSeries class method) (pyopenms.NaNPolicy class method) (pyopenms.NASequence.NASFragmentType class method) (pyopenms.NormalizationMethod class method) (pyopenms.OpenMSOSInfo.OpenMS_Architecture class method) (pyopenms.OpenMSOSInfo.OpenMS_OS class method) (pyopenms.OpenPepXLAlgorithm.ExitCodes class method) (pyopenms.OPXLDataStructs.PeptidePosition class method) (pyopenms.OPXLDataStructs.ProteinProteinCrossLinkType class method) (pyopenms.OriginAnnotationFormat class method) (pyopenms.ParquetWriteConfig.Compression class method) (pyopenms.PeakGroup.TargetDecoyType class method) (pyopenms.PEFFDatabaseMetadata.SequenceType class method) (pyopenms.PEFFModification.ModificationType class method) (pyopenms.PeptideIndexing.ExitCodes class method) (pyopenms.PercolatorOutfile.ScoreType class method) (pyopenms.ProForma.ConversionIssueType class method) (pyopenms.ProForma.ConversionPolicy class method) (pyopenms.ProForma.CvDatabase class method) (pyopenms.ProForma.WriteMode class method) (pyopenms.ProgressLogger.LogType class method) (pyopenms.ProSEAlgorithm.ProSEAlgorithm_ExitCodes class method) (pyopenms.ProteomicsPkaScale class method) (pyopenms.QuotingMethod class method) (pyopenms.RankData.Method class method) (pyopenms.RankData.NaNPolicy class method) (pyopenms.RequirementLevel class method) (pyopenms.Residue.ResidueType class method) (pyopenms.ResidueModification.Provenance class method) (pyopenms.ResidueModification.SourceClassification class method) (pyopenms.ResidueModification.TermSpecificity class method) (pyopenms.Ribonucleotide.TermSpecificityNuc class method) (pyopenms.Scores.IDType class method) (pyopenms.SIDE class method) (pyopenms.SimpleSearchEngineAlgorithm.ExitCodes class method) (pyopenms.UnitType class method) (pyopenms.USI.IndexType class method) (pyopenms.ValueType class method) (pyopenms.XFDRAlgorithm.ExitCodes class method) (pyopenms.XTandemInfile.ErrorUnit class method) (pyopenms.XTandemInfile.MassType class method) from_dict() (pyopenms.Param static method) fromAASequence() (pyopenms.Peptidoform class method) (pyopenms.ProForma static method) fromConsensusMap() (pyopenms.ExperimentalDesign static method) fromFASTAEntry() (in module pyopenms) (pyopenms.PEFFEntry static method) fromFeatureMap() (pyopenms.ExperimentalDesign static method) fromIdentifications() (pyopenms.ExperimentalDesign static method) fromJSON() (pyopenms.Peptidoform class method) (pyopenms.PeptidoformIon class method) fromMask() (pyopenms.MSImagingRegion static method) fromNativeID() (pyopenms.OSWData method) fromNdArray() (pyopenms.MatrixDouble static method) fromPeakAnnotation() (pyopenms.MzPAF static method) fromString() (pyopenms.AASequence static method) (pyopenms.DataFilter method) (pyopenms.NASequence static method) (pyopenms.Peptidoform class method) (pyopenms.PeptidoformIon class method) (pyopenms.USI method) fromStringPermissive() (pyopenms.AASequence static method) front() (pyopenms.PeptideIdentificationList method) Full (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) fullname (pyopenms.CV property) FWHM (pyopenms.MassAnalyzer.ResolutionMethod attribute) fwhm_im_avg (pyopenms.MassTrace property) fwhm_mz_avg (pyopenms.MassTrace property) G GAS (pyopenms.Sample.SampleState attribute) GAS_CONSTANT (in module pyopenms.Constants) GaussFilter (class in pyopenms) GaussFitResult (class in pyopenms) GaussFitter (class in pyopenms) GaussTraceFitter (class in pyopenms) GD_MS (pyopenms.IonSource.IonizationMethod attribute) ge() (pyopenms.ParquetFilter method) GELML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) gene_name (pyopenms.LightCompound property) (pyopenms.PEFFEntry property) general_comments (pyopenms.PEFFDatabaseMetadata property) generateDecoys() (pyopenms.MRMDecoy method) generateKnockoutDeltaMasses() (pyopenms.MultiplexDeltaMassesGenerator method) generateMissingDecoysByMassShift() (pyopenms.MetaboTargetedTargetDecoy static method) generatePeptides() (pyopenms.PEFFEntry method) generatePTMStatistics() (pyopenms.OpenSearchModificationAnalysis method) generateSeedList() (pyopenms.SeedListGenerator method) generateSeedLists() (pyopenms.SeedListGenerator method) generateSpectrum() (pyopenms.Peptidoform method) (pyopenms.PeptidoformIon method) (pyopenms.ProForma static method) generateSpectrumIon() (pyopenms.ProForma static method) generateTrieDB() (pyopenms.InspectOutfile method) GENERIC (pyopenms.PEFFModification.ModificationType attribute) get() (pyopenms.Date method) (pyopenms.DateTime method) (pyopenms.NASequence method) (pyopenms.Param method) (pyopenms.PrecalAveragine method) get2DPeakData() (pyopenms.MSExperiment method) get2DPeakDataIM() (pyopenms.MSExperiment method) get2DPeakDataLong() (pyopenms.MSExperiment method) get2DPeakDataSemiWide() (pyopenms.MSExperiment method) get_analyte_df() (pyopenms.XICParquetFile method) (pyopenms.XIMParquetFile method) (pyopenms.XIPMParquetFile method) get_analyte_dict() (pyopenms.XICParquetFile method) (pyopenms.XIMParquetFile method) (pyopenms.XIPMParquetFile method) get_annotation() (pyopenms.TheoreticalGlycanSpectrumGenerator.Fragment method) get_assigned_peptide_identifications() (pyopenms.FeatureMap method) get_base_peak() (pyopenms.MSSpectrum method) get_chromatogram_df() (pyopenms.MRMTransitionGroupCP method) get_chromatogram_df_columns() (pyopenms.MRMTransitionGroupCP method) get_composition() (pyopenms.GlycanStructure method) get_data() (pyopenms.FloatDataArray method) (pyopenms.IntegerDataArray method) (pyopenms.IonImage method) (pyopenms.OSBinaryDataArray method) (pyopenms.StringDataArray method) get_data_arrays() (pyopenms.OSChromatogram method) (pyopenms.OSSpectrum method) get_data_dict() (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) (pyopenms.XICParquetFile method) (pyopenms.XIMParquetFile method) (pyopenms.XIPMParquetFile method) get_data_mv() (pyopenms.FloatDataArray method) (pyopenms.IntegerDataArray method) (pyopenms.OSBinaryDataArray method) get_df() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.PeptideIdentificationList method) get_df_columns() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) get_drift_time_array() (pyopenms.MSSpectrum method) (pyopenms.OSSpectrum method) get_drift_time_array_mv() (pyopenms.MSSpectrum method) (pyopenms.OSSpectrum method) get_drift_time_array_unit() (pyopenms.MSSpectrum method) get_drift_time_unit() (pyopenms.MSSpectrum method) get_feature_df() (pyopenms.MRMTransitionGroupCP method) get_feature_df_columns() (pyopenms.MRMTransitionGroupCP method) get_fragments() (pyopenms.TheoreticalGlycanSpectrumGenerator method) get_glycopeptide_fragments() (pyopenms.TheoreticalGlycanSpectrumGenerator method) get_intensity_array() (pyopenms.MSSpectrum method) (pyopenms.OSChromatogram method) (pyopenms.OSSpectrum method) get_intensity_array_mv() (pyopenms.OSChromatogram method) (pyopenms.OSSpectrum method) get_intensity_df() (pyopenms.ConsensusMap method) get_ion_df() (pyopenms.MSExperiment method) get_mask() (pyopenms.IonImage method) (pyopenms.MSImagingRegion method) get_massql_df() (pyopenms.MSExperiment method) get_matrix() (pyopenms.MatrixDouble method) get_matrix_as_view() (pyopenms.MatrixDouble method) get_matrix_mv() (pyopenms.MatrixDouble method) get_metadata_df() (pyopenms.ConsensusMap method) get_mz() (pyopenms.TheoreticalGlycanSpectrumGenerator.Fragment method) get_mz_array() (pyopenms.MSSpectrum method) (pyopenms.OSSpectrum method) get_mz_array_mv() (pyopenms.OSSpectrum method) get_nodes() (pyopenms.GlycanStructure method) get_noise_even() (pyopenms.SignalToNoiseEstimatorMedianRapid.NoiseEstimator method) get_noise_odd() (pyopenms.SignalToNoiseEstimatorMedianRapid.NoiseEstimator method) get_noise_value() (pyopenms.SignalToNoiseEstimatorMedianRapid.NoiseEstimator method) get_options() (pyopenms.TheoreticalGlycanSpectrumGenerator method) get_peaks() (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) get_psm_columns() (pyopenms.PeptideIdentificationList method) get_psm_df() (pyopenms.PeptideIdentificationList method) get_quick_lda_score() (pyopenms.OpenSwath_Scores method) get_run_df() (pyopenms.XICParquetFile method) (pyopenms.XIMParquetFile method) (pyopenms.XIPMParquetFile method) get_run_dict() (pyopenms.XICParquetFile method) (pyopenms.XIMParquetFile method) (pyopenms.XIPMParquetFile method) get_tic() (pyopenms.MSSpectrum method) get_time_array() (pyopenms.OSChromatogram method) get_time_array_mv() (pyopenms.OSChromatogram method) getAAAfter() (pyopenms.PeptideEvidence method) getAABefore() (pyopenms.PeptideEvidence method) getAAFrequencies() (pyopenms.AASequence method) getAASequenceConversionIssues() (pyopenms.Peptidoform method) (pyopenms.ProForma static method) getAbsolute() (pyopenms.FineIsotopePatternGenerator method) getAbundance() (pyopenms.IMSIsotopeDistribution method) getAbundances() (pyopenms.IMSIsotopeDistribution method) getACAndACType() (pyopenms.InspectOutfile method) (pyopenms.SequestOutfile method) getAccession() (pyopenms.CVMappingTerm method) (pyopenms.CVTerm method) (pyopenms.OSWProtein method) (pyopenms.ProteinHit method) getAccuracy() (pyopenms.MassAnalyzer method) getAcquisitionInfo() (pyopenms.ChromatogramSettings method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) (pyopenms.SpectrumSettings method) getAcquisitionMode() (pyopenms.IonDetector method) getActivationEnergy() (pyopenms.Precursor method) getActivationMethods() (pyopenms.Precursor method) getActivationMethodsAsShortString() (pyopenms.Precursor method) getActivationMethodsAsString() (pyopenms.Precursor method) getADCSamplingFrequency() (pyopenms.IonDetector method) getAddress() (pyopenms.ContactPerson method) getAdduct() (pyopenms.FeatureFinderMetaboIdentCompound method) getAdductBase() (pyopenms.MassExplainer method) getAdductsAsString() (pyopenms.Compomer method) getAllChildTerms() (pyopenms.ControlledVocabulary method) getAllCometNames() (pyopenms.ProteaseDB method) getAllIDScoreNames() (pyopenms.Scores static method) getAllMSGFNames() (pyopenms.ProteaseDB method) getAllNames() (pyopenms.ProteaseDB method) (pyopenms.RNaseDB method) getAllNamesOfAcquisitionMode() (pyopenms.IonDetector static method) getAllNamesOfActivationMethods() (pyopenms.Precursor static method) getAllNamesOfAnalyzerType() (pyopenms.MassAnalyzer static method) getAllNamesOfChecksumType() (pyopenms.SourceFile static method) getAllNamesOfInletType() (pyopenms.IonSource static method) getAllNamesOfIonizationMethod() (pyopenms.IonSource static method) getAllNamesOfIonOpticsType() (pyopenms.Instrument static method) getAllNamesOfPeakMassType() (pyopenms.ProteinIdentification static method) getAllNamesOfPolarity() (pyopenms.IonSource static method) getAllNamesOfProcessingAction() (pyopenms.DataProcessing static method) getAllNamesOfReflectronState() (pyopenms.MassAnalyzer static method) getAllNamesOfResolutionMethod() (pyopenms.MassAnalyzer static method) getAllNamesOfResolutionType() (pyopenms.MassAnalyzer static method) getAllNamesOfSampleState() (pyopenms.Sample static method) getAllNamesOfScanDirection() (pyopenms.MassAnalyzer static method) getAllNamesOfScanLaw() (pyopenms.MassAnalyzer static method) getAllNamesOfScanMode() (pyopenms.InstrumentSettings static method) getAllNamesOfSpectrumType() (pyopenms.MSSpectrum static method) (pyopenms.SpectrumSettings static method) getAllNamesOfType() (pyopenms.IonDetector static method) getAllOMSSANames() (pyopenms.ProteaseDB method) getAllowChildren() (pyopenms.CVMappingTerm method) getAllSearchModifications() (pyopenms.CrossLinksDB method) (pyopenms.ModificationsDB method) getAllShortNamesOfActivationMethods() (pyopenms.Precursor static method) getAllXTandemNames() (pyopenms.ProteaseDB method) getAlphabetMass() (pyopenms.IMSWeights method) getAmount() (pyopenms.Adduct method) getAnalysisResults() (pyopenms.PeptideHit method) getAnalytes() (pyopenms.XICParquetFile method) (pyopenms.XIMParquetFile method) getAnnotation() (pyopenms.LightTransition method) (pyopenms.OSWTransition method) getAnnotations() (pyopenms.QTCluster method) getAnnotationState() (pyopenms.BaseFeature method) (pyopenms.ConsensusFeature method) (pyopenms.Feature method) (pyopenms.MRMFeature method) getApexIndex() (pyopenms.PrecalAveragine method) getArchAsString() (pyopenms.OpenMSOSInfo method) getArea() (pyopenms.GaussTraceFitter method) getARGP820102() (pyopenms.AAIndex static method) getAtomicNumber() (pyopenms.Element method) getAverageMass() (pyopenms.IMSElement method) (pyopenms.IMSIsotopeDistribution method) (pyopenms.ResidueModification method) getAverageMassDelta() (pyopenms.PrecalAveragine method) getAverageMasses() (pyopenms.IMSAlphabet method) getAverageMS1CycleTime() (pyopenms.MassTrace method) getAverageWeight() (pyopenms.AASequence method) (pyopenms.Element method) (pyopenms.EmpiricalFormula method) (pyopenms.NASequence method) (pyopenms.Residue method) getAveragine() (pyopenms.FLASHDeconvAlgorithm method) (pyopenms.SpectralDeconvolution method) getAvgDaError() (pyopenms.PeakGroup method) getAvgDistance() (pyopenms.ClusterProxyKD method) getAvgMass() (pyopenms.Ribonucleotide method) getAvgMZ() (pyopenms.FeatureFinderAlgorithmPickedHelperStructs_MassTrace method) (pyopenms.MassTrace method) getAvgPPMError() (pyopenms.PeakGroup method) getBackboneBasicityLeft() (pyopenms.Residue method) getBackboneBasicityRight() (pyopenms.Residue method) getBaseDir() (pyopenms.FIAMSScheduler method) getBaselossFormula() (pyopenms.Ribonucleotide method) getBBoxHeight() (pyopenms.MSImagingRegion method) getBBoxWidth() (pyopenms.MSImagingRegion method) getBestFeature() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) getBestHit() (pyopenms.IDFilter static method) getBestModificationByDiffMonoMass() (pyopenms.CrossLinksDB method) (pyopenms.ModificationsDB method) getBinaryArchitecture() (pyopenms.OpenMSOSInfo static method) getBinIndex() (pyopenms.BinnedSpectrum method) getBinIntensity() (pyopenms.BinnedSpectrum method) getBinLowerMZ() (pyopenms.BinnedSpectrum method) getBinSize() (pyopenms.BinnedSpectrum method) getBinSpread() (pyopenms.BinnedSpectrum method) getBlacklist() (pyopenms.FeatureFinderMultiplexAlgorithm method) getBlind() (pyopenms.InspectInfile method) getBothGnuplotFormula() (pyopenms.PosteriorErrorProbabilityModel method) getBoundingBox() (pyopenms.ConvexHull2D method) (pyopenms.GridBasedCluster method) getBoundingBox2D() (pyopenms.ConvexHull2D method) getBranch() (pyopenms.VersionInfo static method) getBuildType() (pyopenms.OpenMSBuildInfo static method) getCalculatedMZ() (pyopenms.AccurateMassSearchResult method) getCalibrationPoints() (pyopenms.InternalCalibration method) getCellCount() (pyopenms.ClusteringGrid method) getCenter() (pyopenms.BiGaussModel method) (pyopenms.EmgModel method) (pyopenms.GaussTraceFitter method) (pyopenms.InterpolationModel method) (pyopenms.IsotopeModel method) getCenterIndex() (pyopenms.ClusterProxyKD method) getCenterMZ() (pyopenms.QTCluster method) getCenterRT() (pyopenms.QTCluster method) getCentre() (pyopenms.GridBasedCluster method) getCentroidedExperiment() (pyopenms.FeatureFinderMultiplexAlgorithm method) getCentroidMZ() (pyopenms.MassTrace method) getCentroidRT() (pyopenms.MassTrace method) getCentroidSD() (pyopenms.MassTrace method) getChannelInformation() (pyopenms.IsobaricQuantitationMethod method) (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.TMTEighteenPlexQuantitationMethod method) (pyopenms.TMTElevenPlexQuantitationMethod method) (pyopenms.TMTSixPlexQuantitationMethod method) (pyopenms.TMTSixteenPlexQuantitationMethod method) (pyopenms.TMTTenPlexQuantitationMethod method) getCharge() (pyopenms.AccurateMassSearchResult method) (pyopenms.Adduct method) (pyopenms.AMSE_AdductInfo method) (pyopenms.BaseFeature method) (pyopenms.ChargePair method) (pyopenms.ConsensusFeature method) (pyopenms.EmpiricalFormula method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.IsotopeModel method) (pyopenms.MRMFeature method) (pyopenms.MultiplexIsotopicPeakPattern method) (pyopenms.OSWPeptidePrecursor method) (pyopenms.PeptideHit method) (pyopenms.Precursor method) getChargeIntensity() (pyopenms.PeakGroup method) getChargeIsotopeCosine() (pyopenms.PeakGroup method) getChargeMass() (pyopenms.FLASHHelperClasses static method) getCharges() (pyopenms.FeatureFinderMetaboIdentCompound method) getChargeScore() (pyopenms.PeakGroup method) getChargeSNR() (pyopenms.PeakGroup method) getChargeState() (pyopenms.Compound method) (pyopenms.LightCompound method) (pyopenms.Peptide method) (pyopenms.TraMLProduct method) getChecksum() (pyopenms.SourceFile method) getChecksumType() (pyopenms.SourceFile method) getChromatogram() (pyopenms.CachedmzML method) (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.MSExperiment method) (pyopenms.OnDiscMSExperiment method) (pyopenms.OnDiscThermoRawExperiment method) getChromatogramById() (pyopenms.IndexedMzMLHandler method) (pyopenms.OnDiscMSExperiment method) (pyopenms.SpectrumAccessOpenMS method) (pyopenms.SpectrumAccessOpenMSCached method) (pyopenms.SpectrumAccessOpenMSInMemory method) (pyopenms.SpectrumAccessSqMass method) getChromatogramByNativeId() (pyopenms.OnDiscMSExperiment method) getChromatogramIndex() (pyopenms.CachedMzMLHandler method) (pyopenms.MSDataCachedConsumer method) getChromatogramNativeID() (pyopenms.SpectrumAccessOpenMS method) (pyopenms.SpectrumAccessOpenMSCached method) (pyopenms.SpectrumAccessOpenMSInMemory method) (pyopenms.SpectrumAccessSqMass method) getChromatograms() (pyopenms.FeatureFinderAlgorithmMetaboIdent method) (pyopenms.FeatureFinderIdentificationAlgorithm method) (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.MSExperiment method) (pyopenms.XICParquetFile method) getChromatogramType() (pyopenms.ChromatogramSettings method) (pyopenms.MSChromatogram method) getCleavageSite() (pyopenms.XTandemInfile method) getCode() (pyopenms.Ribonucleotide method) getCoefficients() (pyopenms.MZTrafoModel method) getCollection() (pyopenms.USI method) getColumn() (pyopenms.HPLC method) getColumnHeaders() (pyopenms.ConsensusMap method) getColumns() (pyopenms.SequestOutfile method) (pyopenms.XICParquetFile method) (pyopenms.XIMParquetFile method) (pyopenms.XIPMParquetFile method) getCombinationsLogic() (pyopenms.CVMappingRule method) getCometID() (pyopenms.DigestionEnzymeProtein method) getComment() (pyopenms.ChromatogramSettings method) (pyopenms.ExperimentalSettings method) (pyopenms.HPLC method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.Sample method) (pyopenms.SpectrumSettings method) getCommonName() (pyopenms.SpectralMatch method) getCompensationVoltages() (pyopenms.FAIMSHelper static method) getCompletionTime() (pyopenms.DataProcessing method) getCompomer() (pyopenms.ChargePair method) getCompomerById() (pyopenms.MassExplainer method) getComponentFeatureConcentrations() (pyopenms.AbsoluteQuantitationStandards method) getComponentName() (pyopenms.AbsoluteQuantitationMethod method) getCompoundByRef() (pyopenms.LightTargetedExperiment method) (pyopenms.TargetedExperiment method) getCompoundRef() (pyopenms.IncludeExcludeTarget method) (pyopenms.LightTransition method) (pyopenms.ReactionMonitoringTransition method) getCompounds() (pyopenms.LightTargetedExperiment method) (pyopenms.TargetedExperiment method) getCompression() (pyopenms.PeakFileOptions method) getConcentration() (pyopenms.Sample method) getConcentrationUnits() (pyopenms.AbsoluteQuantitationMethod method) getConditionalFragmentIsotopeDist() (pyopenms.EmpiricalFormula method) getConfigurationList() (pyopenms.TraMLProduct method) getConfigurations() (pyopenms.IncludeExcludeTarget method) getConsensusMap() (pyopenms.FeatureFinderMultiplexAlgorithm method) getConsistentOutputfileType() (pyopenms.FileHandler static method) getContactInfo() (pyopenms.ContactPerson method) getContacts() (pyopenms.ExperimentalSettings method) (pyopenms.MSExperiment method) (pyopenms.TargetedExperiment method) getContainer() (pyopenms.IsotopeDistribution method) getConvexHull() (pyopenms.Feature method) getConvexhull() (pyopenms.FeatureFinderAlgorithmPickedHelperStructs_MassTrace method) (pyopenms.MassTrace method) getConvexHull() (pyopenms.MRMFeature method) getConvexHulls() (pyopenms.Feature method) (pyopenms.MRMFeature method) getCorrectlyAssignedFitResult() (pyopenms.PosteriorErrorProbabilityModel method) getCorrelationCoefficient() (pyopenms.AbsoluteQuantitationMethod method) getCosine() (pyopenms.SpectralDeconvolution static method) getCoverage() (pyopenms.ProteinHit method) (pyopenms.SequenceCoverage static method) getCTermGain() (pyopenms.DigestionEnzymeProtein method) getCTerminalModification() (pyopenms.AASequence method) getCTerminalModificationName() (pyopenms.AASequence method) getCurrentMaxAbsCharge() (pyopenms.DeconvolvedSpectrum method) getCurrentMaxMass() (pyopenms.DeconvolvedSpectrum method) getCurrentMinMass() (pyopenms.DeconvolvedSpectrum method) getCustomizations() (pyopenms.Instrument method) getCutsAfterRegEx() (pyopenms.DigestionEnzymeRNA method) getCutsBeforeRegEx() (pyopenms.DigestionEnzymeRNA method) getCVAccession() (pyopenms.USI static method) getCVIdentifierRef() (pyopenms.CVMappingTerm method) (pyopenms.CVTerm method) getCVName() (pyopenms.USI static method) getCVReferences() (pyopenms.CVMappings method) getCVs() (pyopenms.TargetedExperiment method) getCVTerms() (pyopenms.Compound method) (pyopenms.Configuration method) (pyopenms.Contact method) (pyopenms.CVMappingRule method) (pyopenms.CVTermList method) (pyopenms.CVTermListInterface method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Peptide method) (pyopenms.Precursor method) (pyopenms.Prediction method) (pyopenms.Product method) (pyopenms.Protein method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.Software method) (pyopenms.SourceFile method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TraMLProduct method) getData() (pyopenms.BilinearInterpolation method) (pyopenms.LinearInterpolation method) (pyopenms.MSDataStoringConsumer method) getDatabase() (pyopenms.SequestInfile method) getDataPoints() (pyopenms.TransformationDescription method) getDataProcessing() (pyopenms.ChromatogramSettings method) (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.FloatDataArray method) (pyopenms.IntegerDataArray method) (pyopenms.MetaInfoDescription method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) (pyopenms.SpectrumSettings method) (pyopenms.StringDataArray method) getDate() (pyopenms.DateTime method) getDateAndTime() (pyopenms.DateTime method) getDateComponents() (pyopenms.DateTime method) getDateTime() (pyopenms.ExperimentalSettings method) (pyopenms.MSExperiment method) (pyopenms.ProteinIdentification method) getDb() (pyopenms.InspectInfile method) getDecompositions() (pyopenms.MassDecompositionAlgorithm method) getDeconvolvedSpectrum() (pyopenms.SpectralDeconvolution method) getDecoy() (pyopenms.LightTransition method) getDecoyAveragine() (pyopenms.FLASHDeconvAlgorithm method) getDecoyString() (pyopenms.PeptideIndexing method) getDecoyTransitionType() (pyopenms.ReactionMonitoringTransition method) getDefaultParameters() (pyopenms.EmgGradientDescent method) (pyopenms.MSPGenericFile method) (pyopenms.PeakIntegrator method) (pyopenms.TargetedSpectraExtractor method) (pyopenms.TransformationModelBSpline static method) (pyopenms.TransformationModelInterpolated static method) (pyopenms.TransformationModelLinear static method) (pyopenms.TransformationModelLowess static method) getDefaultParametersFilename() (pyopenms.XTandemInfile method) getDefaults() (pyopenms.AbsoluteQuantitation method) (pyopenms.AccurateMassSearchEngine method) (pyopenms.AScore method) (pyopenms.BaseGroupFinder method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.Biosaur2Algorithm method) (pyopenms.DefaultParamHandler method) (pyopenms.DIAScoring method) (pyopenms.ElutionModelFitter method) (pyopenms.ElutionPeakDetection method) (pyopenms.EmgFitter1D method) (pyopenms.EmgGradientDescent method) (pyopenms.EmgScoring method) (pyopenms.FalseDiscoveryRate method) (pyopenms.FeatureDeconvolution method) (pyopenms.FeatureDistance method) (pyopenms.FeatureFinderAlgorithmMetaboIdent method) (pyopenms.FeatureFinderAlgorithmPicked method) (pyopenms.FeatureFinderIdentificationAlgorithm method) (pyopenms.FeatureFinderMultiplexAlgorithm method) (pyopenms.FeatureFindingMetabo method) (pyopenms.FeatureGroupingAlgorithm method) (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.FeatureGroupingAlgorithmLabeled method) (pyopenms.FeatureGroupingAlgorithmQT method) (pyopenms.FeatureGroupingAlgorithmUnlabeled method) (pyopenms.FIAMSDataProcessor method) (pyopenms.Fitter1D method) (pyopenms.FLASHDeconvAlgorithm method) (pyopenms.GaussFilter method) (pyopenms.GNPSMGFFile method) (pyopenms.IDDecoyProbability method) (pyopenms.IDMapper method) (pyopenms.IDRipper method) (pyopenms.IDScoreSwitcherAlgorithm method) (pyopenms.IsobaricChannelExtractor method) (pyopenms.IsobaricQuantifier method) (pyopenms.IsobaricQuantitationMethod method) (pyopenms.IsotopeLabelingMDVs method) (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.LabeledPairFinder method) (pyopenms.LevMarqFitter1D method) (pyopenms.LinearResamplerAlign method) (pyopenms.LowessSmoothing method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) (pyopenms.MascotGenericFile method) (pyopenms.MassDecompositionAlgorithm method) (pyopenms.MasstraceCorrelator method) (pyopenms.MassTraceDetection method) (pyopenms.MetaboliteFeatureDeconvolution method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.ModifiedSincSmoother method) (pyopenms.MorphologicalFilter method) (pyopenms.MRMDecoy method) (pyopenms.MRMFeatureFilter method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MRMMapping method) (pyopenms.MRMTransitionGroupPicker method) (pyopenms.MSPFile method) (pyopenms.MSPGenericFile method) (pyopenms.MultiplexDeltaMassesGenerator method) (pyopenms.MultiplexResolverAlgorithm method) (pyopenms.NLargest method) (pyopenms.Normalizer method) (pyopenms.NucleicAcidSpectrumGenerator method) (pyopenms.OpenPepXLAlgorithm method) (pyopenms.PeakIntegrator method) (pyopenms.PeakPickerChromatogram method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIM method) (pyopenms.PeakPickerIterative method) (pyopenms.PeptideAndProteinQuant method) (pyopenms.PeptideIndexing method) (pyopenms.Percolator method) (pyopenms.PipEchoAlgorithm method) (pyopenms.PosteriorErrorProbabilityModel method) (pyopenms.ProSEAlgorithm method) (pyopenms.QTClusterFinder method) (pyopenms.RankScaler method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SignalToNoiseEstimatorMeanIterative method) (pyopenms.SignalToNoiseEstimatorMedian method) (pyopenms.SignalToNoiseEstimatorMedianChrom method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.SimpleTSGXLMS method) (pyopenms.SiriusExportAlgorithm method) (pyopenms.SpectralDeconvolution method) (pyopenms.SpectraMerger method) (pyopenms.SpectrumAlignment method) (pyopenms.SpectrumAlignmentScore method) (pyopenms.SpectrumAnnotator method) (pyopenms.SqrtScaler method) (pyopenms.StablePairFinder method) (pyopenms.SwathMapMassCorrection method) (pyopenms.TargetedSpectraExtractor method) (pyopenms.TheoreticalSpectrumGenerator method) (pyopenms.TheoreticalSpectrumGeneratorXLMS method) (pyopenms.ThresholdMower method) (pyopenms.TMTEighteenPlexQuantitationMethod method) (pyopenms.TMTElevenPlexQuantitationMethod method) (pyopenms.TMTSixPlexQuantitationMethod method) (pyopenms.TMTSixteenPlexQuantitationMethod method) (pyopenms.TMTTenPlexQuantitationMethod method) (pyopenms.TransitionListEvidenceFilter method) (pyopenms.WindowMower method) (pyopenms.XFDRAlgorithm method) getDeltaMasses() (pyopenms.MultiplexDeltaMasses method) getDeltaMassesList() (pyopenms.MultiplexDeltaMassesGenerator method) getDescription() (pyopenms.MetaInfoRegistry method) (pyopenms.Param method) (pyopenms.ProteinHit method) getDeviations() (pyopenms.TransformationDescription method) getDiffAverageMass() (pyopenms.ResidueModification method) getDiffFormula() (pyopenms.ResidueModification method) getDiffMonoMass() (pyopenms.ResidueModification method) getDriftTime() (pyopenms.LightCompound method) (pyopenms.MSSpectrum method) (pyopenms.Precursor method) getDriftTimeArray() (pyopenms.OSSpectrum method) getDriftTimeUnit() (pyopenms.Mobilogram method) (pyopenms.MSSpectrum method) getDriftTimeUnitAsString() (pyopenms.Mobilogram method) (pyopenms.MSSpectrum method) getDriftTimeWindowLowerOffset() (pyopenms.Precursor method) getDriftTimeWindowUpperOffset() (pyopenms.Precursor method) getEdgeScore() (pyopenms.ChargePair method) getElement() (pyopenms.ElementDB method) (pyopenms.IMSAlphabet method) getElementalComposition() (pyopenms.EmpiricalFormula method) getElementIndex() (pyopenms.ChargePair method) getElementPath() (pyopenms.CVMappingRule method) getEluents() (pyopenms.Gradient method) getEmail() (pyopenms.ContactPerson method) getEmpiricalFormula() (pyopenms.AMSE_AdductInfo method) getEnd() (pyopenms.PeptideEvidence method) getEntry() (pyopenms.Param method) getEnzyme() (pyopenms.InspectInfile method) (pyopenms.ProteaseDB method) (pyopenms.RNaseDB method) getEnzymeByRegEx() (pyopenms.ProteaseDB method) (pyopenms.RNaseDB method) getEnzymeInfoAsString() (pyopenms.SequestInfile method) getEnzymeName() (pyopenms.EnzymaticDigestion method) (pyopenms.ProteaseDigestion method) (pyopenms.RNaseDigestion method) (pyopenms.SequestInfile method) getEnzymeNumber() (pyopenms.SequestInfile method) getError() (pyopenms.CalibrationData method) getExcludeTargets() (pyopenms.TargetedExperiment method) getExecutablePath() (pyopenms.File static method) getExperiment() (pyopenms.InspectOutfile method) getExperimentalSettings() (pyopenms.MSExperiment method) (pyopenms.OnDiscImzMLExperiment method) (pyopenms.OnDiscMSExperiment method) (pyopenms.OnDiscThermoRawExperiment method) getExperimentLabel() (pyopenms.PeptideIdentification method) getExperimentType() (pyopenms.ConsensusMap method) getFactors() (pyopenms.ExperimentalDesign_SampleSection method) getFactorValue() (pyopenms.ExperimentalDesign_SampleSection method) getFAUJ880111() (pyopenms.AAIndex static method) getFeatOptions() (pyopenms.FileHandler method) getFeature() (pyopenms.MRMFeature method) getFeatureIDs() (pyopenms.MRMFeature method) getFeatureIndex() (pyopenms.PeakGroup method) getFeatureList() (pyopenms.ConsensusFeature method) getFeatureMap() (pyopenms.FeatureFinderMultiplexAlgorithm method) getFeatureName() (pyopenms.AbsoluteQuantitationMethod method) getFeatures() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMFeature method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.OSWPeptidePrecursor method) getFeatureSet() (pyopenms.PercolatorInfile static method) getFeaturesMuteable() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) getFilename() (pyopenms.OnDiscThermoRawExperiment method) (pyopenms.XICParquetFile method) (pyopenms.XIMParquetFile method) (pyopenms.XIPMParquetFile method) getFilenames() (pyopenms.XICParquetFile method) (pyopenms.XIMParquetFile method) (pyopenms.XIPMParquetFile method) getFileOriginIdx() (pyopenms.RipFileIdentifier method) getFileSize() (pyopenms.SourceFile method) getFileType() (pyopenms.SourceFile method) getFillData() (pyopenms.PeakFileOptions method) getFilterByNumMassTraces() (pyopenms.SiriusExportAlgorithm method) getFINA770101() (pyopenms.AAIndex static method) getFinalMSExponent() (pyopenms.MassAnalyzer method) getFirstName() (pyopenms.ContactPerson method) getFivePrimeGain() (pyopenms.DigestionEnzymeRNA method) getFivePrimeMod() (pyopenms.NASequence method) getFixedAndVariableModificationNames() (pyopenms.ModificationDefinitionsSet method) getFixedModificationNames() (pyopenms.ModificationDefinitionsSet method) getFixedModifications() (pyopenms.ModificationDefinitionsSet method) getFloatDataArrays() (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) getFlux() (pyopenms.HPLC method) getForceMQCompatability() (pyopenms.PeakFileOptions method) getForceTPPCompatability() (pyopenms.PeakFileOptions method) getFormula() (pyopenms.AASequence method) (pyopenms.Adduct method) (pyopenms.FeatureFinderMetaboIdentCompound method) (pyopenms.IsotopeModel method) (pyopenms.NASequence method) (pyopenms.Residue method) (pyopenms.ResidueModification method) (pyopenms.Ribonucleotide method) getFormulaString() (pyopenms.AccurateMassSearchResult method) getFoundAdduct() (pyopenms.AccurateMassSearchResult method) getFoundCCS() (pyopenms.SpectralMatch method) getFoundMass() (pyopenms.AccurateMassSearchResult method) getFoundPrecursorCharge() (pyopenms.SpectralMatch method) getFoundPrecursorMass() (pyopenms.SpectralMatch method) getFractionIdentifier() (pyopenms.ExperimentalSettings method) (pyopenms.MSExperiment method) getFragmentMassErrorUnit() (pyopenms.XTandemInfile method) getFragmentMassTolerance() (pyopenms.XTandemInfile method) getFragmentPositions() (pyopenms.RNaseDigestion method) getFragmentType() (pyopenms.LightTransition method) getFullId() (pyopenms.ResidueModification method) getFullName() (pyopenms.ResidueModification method) getFWHM() (pyopenms.GaussTraceFitter method) (pyopenms.MassTrace method) getFWHMborders() (pyopenms.MassTrace method) getGaussGnuplotFormula() (pyopenms.PosteriorErrorProbabilityModel method) getGeometry() (pyopenms.MSImagingExperiment method) (pyopenms.OnDiscImzMLExperiment method) getGnuplotFormula() (pyopenms.GaussTraceFitter method) getGradient() (pyopenms.HPLC method) getGridSpacingX() (pyopenms.ClusteringGrid method) getGridSpacingY() (pyopenms.ClusteringGrid method) getGroup() (pyopenms.CalibrationData method) getGumbelGnuplotFormula() (pyopenms.PosteriorErrorProbabilityModel method) getHeaders() (pyopenms.PEFFFile method) getHeight() (pyopenms.GaussTraceFitter method) (pyopenms.IonImage method) (pyopenms.MSImagingGeometry method) getHistogramRightmostPercent() (pyopenms.SignalToNoiseEstimatorMedian method) getHits() (pyopenms.PeptideIdentification method) (pyopenms.ProteinIdentification method) getHPLC() (pyopenms.ExperimentalSettings method) (pyopenms.MSExperiment method) getHTMLCode() (pyopenms.Ribonucleotide method) getHTTPPeakListEnclosure() (pyopenms.MascotGenericFile method) getHullPoints() (pyopenms.ConvexHull2D method) getHullPointsNPY() (pyopenms.ConvexHull2D method) getHydrophobicity() (pyopenms.Residue method) getID() (pyopenms.Compomer method) getId() (pyopenms.MSImagingRegion method) getID() (pyopenms.OSWProtein method) (pyopenms.OSWTransition method) getId() (pyopenms.ResidueModification method) getIdentifier() (pyopenms.Acquisition method) (pyopenms.ConsensusMap method) (pyopenms.CVMappingRule method) (pyopenms.CVReference method) (pyopenms.DocumentIdentifier method) (pyopenms.ExperimentalSettings method) (pyopenms.FeatureMap method) (pyopenms.MSExperiment method) (pyopenms.PeptideIdentification method) (pyopenms.ProteinIdentification method) getIdentRunIdx() (pyopenms.RipFileIdentifier method) getIMData() (pyopenms.MSSpectrum method) getIMFormat() (pyopenms.MSSpectrum method) getIMPeakType() (pyopenms.MSSpectrum method) getIMRange() (pyopenms.PeakFileOptions method) getImzMLMeta() (pyopenms.OnDiscImzMLExperiment method) getInchiString() (pyopenms.SpectralMatch method) getIncludeTargets() (pyopenms.TargetedExperiment method) getIncorrectlyAssignedFitResult() (pyopenms.PosteriorErrorProbabilityModel method) getIncorrectlyAssignedGumbelFitResult() (pyopenms.PosteriorErrorProbabilityModel method) getIndex() (pyopenms.ClusteringGrid method) (pyopenms.MetaInfoRegistry method) (pyopenms.OnDiscImzMLExperiment method) (pyopenms.PeakGroup method) (pyopenms.USI method) getIndexType() (pyopenms.USI method) getIndistinguishableProteins() (pyopenms.ProteinIdentification method) getIndividualIntensities() (pyopenms.AccurateMassSearchResult method) getInletType() (pyopenms.IonSource method) getInputFilename() (pyopenms.XTandemInfile method) getInsideReferencePoint() (pyopenms.LinearInterpolation method) getInsideReferencePoint_0() (pyopenms.BilinearInterpolation method) getInsideReferencePoint_1() (pyopenms.BilinearInterpolation method) getInstance() (pyopenms.CrossLinksDB static method) (pyopenms.ElementDB static method) (pyopenms.LogConfigHandler static method) (pyopenms.ModificationsDB static method) (pyopenms.ProteaseDB static method) (pyopenms.ResidueDB static method) (pyopenms.RibonucleotideDB static method) (pyopenms.RNaseDB static method) getInstitution() (pyopenms.ContactPerson method) getInstrument() (pyopenms.ExperimentalSettings method) (pyopenms.HPLC method) (pyopenms.InspectInfile method) (pyopenms.MSExperiment method) getInstrumentConfigurations() (pyopenms.ExperimentalSettings method) (pyopenms.MSExperiment method) getInstruments() (pyopenms.TargetedExperiment method) getInstrumentSettings() (pyopenms.ChromatogramSettings method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) (pyopenms.SpectrumSettings method) getIntegerDataArrays() (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) getIntensity() (pyopenms.BaseFeature method) (pyopenms.BiGaussModel method) (pyopenms.CalibrationData method) (pyopenms.ChromatogramPeak method) (pyopenms.ConsensusFeature method) (pyopenms.EmgModel method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.InterpolationModel method) (pyopenms.IonImage method) (pyopenms.IsotopeModel method) (pyopenms.MassTrace method) (pyopenms.MobilityPeak1D method) (pyopenms.MRMFeature method) (pyopenms.Peak1D method) (pyopenms.Peak2D method) (pyopenms.PeakGroup method) (pyopenms.Precursor method) (pyopenms.RichPeak2D method) getIntensity32Bit() (pyopenms.PeakFileOptions method) getIntensityArray() (pyopenms.Chromatogram method) (pyopenms.OSChromatogram method) (pyopenms.OSSpectrum method) (pyopenms.Spectrum method) getIntensityRange() (pyopenms.FeatureFileOptions method) (pyopenms.PeakFileOptions method) getIntermediateProducts() (pyopenms.ReactionMonitoringTransition method) getInternalToAIon() (pyopenms.Residue static method) getInternalToBIon() (pyopenms.Residue static method) getInternalToCIon() (pyopenms.Residue static method) getInternalToCTerm() (pyopenms.Residue static method) getInternalToFull() (pyopenms.Residue static method) getInternalToNTerm() (pyopenms.Residue static method) getInternalToXIon() (pyopenms.Residue static method) getInternalToYIon() (pyopenms.Residue static method) getInternalToZIon() (pyopenms.Residue static method) getInterpolation() (pyopenms.BiGaussModel method) (pyopenms.EmgModel method) (pyopenms.InterpolationModel method) (pyopenms.IsotopeModel method) getInterpretation() (pyopenms.USI method) getInterpretationList() (pyopenms.TraMLProduct method) getInterpretations() (pyopenms.IncludeExcludeTarget method) getIonCutoffPercentage() (pyopenms.SequestInfile method) getIonDetectors() (pyopenms.Instrument method) getIonizationMethod() (pyopenms.IonSource method) getIonMass() (pyopenms.IMSElement method) getIonMobilities() (pyopenms.FeatureFinderMetaboIdentCompound method) getIonOptics() (pyopenms.Instrument method) getIonSeriesWeights() (pyopenms.SequestInfile method) getIonSources() (pyopenms.Instrument method) getISName() (pyopenms.AbsoluteQuantitationMethod method) getIsolationWidth() (pyopenms.MassAnalyzer method) getIsolationWindowLowerOffset() (pyopenms.Precursor method) (pyopenms.Product method) getIsolationWindowUpperOffset() (pyopenms.Precursor method) (pyopenms.Product method) getIsotonicPEPCurve() (pyopenms.PosteriorErrorProbabilityModel method) getIsotopeCorrectionMatrix() (pyopenms.IsobaricQuantitationMethod method) (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.TMTEighteenPlexQuantitationMethod method) (pyopenms.TMTElevenPlexQuantitationMethod method) (pyopenms.TMTSixPlexQuantitationMethod method) (pyopenms.TMTSixteenPlexQuantitationMethod method) (pyopenms.TMTTenPlexQuantitationMethod method) getIsotopeCosine() (pyopenms.PeakGroup method) getIsotopeCosineAndIsoOffset() (pyopenms.SpectralDeconvolution static method) getIsotopeDaDistance() (pyopenms.PeakGroup method) getIsotopeDistribution() (pyopenms.Element method) (pyopenms.EmpiricalFormula method) (pyopenms.FeatureFinderMetaboIdentCompound method) (pyopenms.IMSElement method) (pyopenms.IsotopeModel method) getIsotopeIntensities() (pyopenms.PeakGroup method) getIsotopeMatrixAsStringList() (pyopenms.ItraqConstants static method) getIsotopePatternIterations() (pyopenms.SiriusExportAlgorithm method) getIsotopesSimScore() (pyopenms.AccurateMassSearchResult method) getIsRepeatable() (pyopenms.CVMappingTerm method) getKeys() (pyopenms.Acquisition method) (pyopenms.AcquisitionInfo method) (pyopenms.BaseFeature method) (pyopenms.ChromatogramSettings method) (pyopenms.ColumnHeader method) (pyopenms.Compound method) (pyopenms.Configuration method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusMap method) (pyopenms.Contact method) (pyopenms.ContactPerson method) (pyopenms.CVTermList method) (pyopenms.CVTermListInterface method) (pyopenms.DataProcessing method) (pyopenms.ExperimentalSettings method) (pyopenms.Feature method) (pyopenms.FeatureMap method) (pyopenms.FloatDataArray method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Instrument method) (pyopenms.InstrumentSettings method) (pyopenms.IntegerDataArray method) (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) (pyopenms.MetaInfo method) (pyopenms.MetaInfoDescription method) (pyopenms.MetaInfoInterface method) (pyopenms.MRMFeature method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.Peptide method) (pyopenms.PeptideHit method) (pyopenms.PeptideIdentification method) (pyopenms.Precursor method) (pyopenms.Prediction method) (pyopenms.Product method) (pyopenms.Protein method) (pyopenms.ProteinHit method) (pyopenms.ProteinIdentification method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.RichPeak2D method) (pyopenms.Sample method) (pyopenms.ScanWindow method) (pyopenms.SearchParameters method) (pyopenms.Software method) (pyopenms.SourceFile method) (pyopenms.SpectrumSettings method) (pyopenms.StringDataArray method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TraMLProduct method) getKeysAsIntegers() (pyopenms.MetaInfo method) getKHAG800101() (pyopenms.AAIndex static method) getLabel() (pyopenms.Adduct method) (pyopenms.MassTrace method) getLabelLong() (pyopenms.MultiplexDeltaMassesGenerator method) getLabels() (pyopenms.Compomer method) (pyopenms.InspectOutfile method) getLabelShort() (pyopenms.MultiplexDeltaMassesGenerator method) getLastIndex() (pyopenms.PrecalAveragine method) getLastName() (pyopenms.ContactPerson method) getLeftCountFromApex() (pyopenms.PrecalAveragine method) getLibrary() (pyopenms.FeatureFinderAlgorithmMetaboIdent method) (pyopenms.FeatureFinderIdentificationAlgorithm method) getLibraryIntensity() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.LightTransition method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.ReactionMonitoringTransition method) getLightestIsotopeWeight() (pyopenms.EmpiricalFormula method) getLinearIonSpectrum() (pyopenms.SimpleTSGXLMS method) (pyopenms.TheoreticalSpectrumGeneratorXLMS method) getLLOD() (pyopenms.AbsoluteQuantitationMethod method) getLLOQ() (pyopenms.AbsoluteQuantitationMethod method) getLoadConvexHull() (pyopenms.FeatureFileOptions method) getLoadedFilePath() (pyopenms.ConsensusMap method) (pyopenms.DocumentIdentifier method) (pyopenms.ExperimentalSettings method) (pyopenms.FeatureMap method) (pyopenms.MSExperiment method) getLoadedFileType() (pyopenms.ConsensusMap method) (pyopenms.DocumentIdentifier method) (pyopenms.ExperimentalSettings method) (pyopenms.FeatureMap method) (pyopenms.MSExperiment method) getLoadSubordinates() (pyopenms.FeatureFileOptions method) getLogMz() (pyopenms.FLASHHelperClasses static method) getLogP() (pyopenms.Compomer method) getLogProb() (pyopenms.Adduct method) getLogType() (pyopenms.AccurateMassSearchEngine method) (pyopenms.AverageLinkage method) (pyopenms.BaseGroupFinder method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.BrukerTimsFile method) (pyopenms.CachedMzMLHandler method) (pyopenms.ChromatogramExtractor method) (pyopenms.ChromatogramExtractorAlgorithm method) (pyopenms.ConfidenceScoring method) (pyopenms.DTA2DFile method) (pyopenms.ElutionPeakDetection method) (pyopenms.FASTAFile method) (pyopenms.FeatureFindingMetabo method) (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.FLASHDeconvAlgorithm method) (pyopenms.GaussFilter method) (pyopenms.ImzMLFile method) (pyopenms.InternalCalibration method) (pyopenms.LabeledPairFinder method) (pyopenms.LinearResamplerAlign method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) (pyopenms.MascotGenericFile method) (pyopenms.MasstraceCorrelator method) (pyopenms.MassTraceDetection method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.ModifiedSincSmoother method) (pyopenms.MorphologicalFilter method) (pyopenms.MRMAssay method) (pyopenms.MRMDecoy method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MS2File method) (pyopenms.MSDataCachedConsumer method) (pyopenms.MzDataFile method) (pyopenms.MzIdentMLFile method) (pyopenms.MzMLFile method) (pyopenms.MzXMLFile method) (pyopenms.PeakMapExtractor method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) (pyopenms.PEFFFile method) (pyopenms.ProgressLogger method) (pyopenms.ProSEAlgorithm method) (pyopenms.QTClusterFinder method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.StablePairFinder method) (pyopenms.SwathFile method) (pyopenms.ThermoRawFile method) (pyopenms.TransitionPQPFile method) (pyopenms.TransitionTSVFile method) getLossFormulas() (pyopenms.Residue method) getLossNames() (pyopenms.Residue method) getLowerRTBound() (pyopenms.GaussTraceFitter method) getLowMassIons() (pyopenms.Residue method) getMagneticFieldStrength() (pyopenms.MassAnalyzer method) getMapIndex() (pyopenms.FeatureHandle method) getMapping() (pyopenms.AnnotationState method) (pyopenms.Base64.ByteOrder method) (pyopenms.BaseFeature.AnnotationState method) (pyopenms.BasicProteinInferenceAlgorithm.AggregationMethod method) (pyopenms.BoundaryCondition method) (pyopenms.BrukerTimsFile.DataFormat method) (pyopenms.BSpline2d.BoundaryCondition method) (pyopenms.ChecksumType method) (pyopenms.ChromatogramSettings.ChromatogramType method) (pyopenms.CombinationsLogic method) (pyopenms.ConsensusMapNormalizerAlgorithmMedian.NormalizationMethod method) (pyopenms.DataFilters.FilterOperation method) (pyopenms.DataFilters.FilterType method) (pyopenms.DataProcessing.ProcessingAction method) (pyopenms.DecoyTransitionType method) (pyopenms.DimensionDescription method) (pyopenms.DRangeIntersection method) (pyopenms.DriftTimeUnit method) (pyopenms.EntrapmentEvaluation.Kind method) (pyopenms.EntrapmentEvaluation.Level method) (pyopenms.EnzymaticDigestion.Specificity method) (pyopenms.FeatureDeconvolution.CHARGEMODE method) (pyopenms.FeatureOverlapFilter.FeatureOverlapMode method) (pyopenms.FeatureOverlapFilter.MergeIntensityMode method) (pyopenms.FileType method) (pyopenms.FileTypes.FileType method) (pyopenms.HydrophobicityScaleMethod method) (pyopenms.IDFreeMassErrorEstimator.FragmentResolutionRegime method) (pyopenms.IDMapper.Measure method) (pyopenms.IDRipper.OriginAnnotationFormat method) (pyopenms.IDType method) (pyopenms.IMFormat method) (pyopenms.IMPeakType method) (pyopenms.ImzMLDataType method) (pyopenms.Instrument.IonOpticsType method) (pyopenms.InstrumentSettings.ScanMode method) (pyopenms.IonDetector.AcquisitionMode method) (pyopenms.IonDetector.Type method) (pyopenms.IonSource.InletType method) (pyopenms.IonSource.IonizationMethod method) (pyopenms.IonSource.Polarity method) (pyopenms.IsotopeDistribution.Sorted method) (pyopenms.IsotopeLabelingMDVs.DerivatizationAgent method) (pyopenms.IsotopeLabelingMDVs.MassIntensityType method) (pyopenms.IsotopeModel.Averagines method) (pyopenms.ITRAQ_TYPES method) (pyopenms.ItraqConstants.ITRAQ_TYPES method) (pyopenms.LogType method) (pyopenms.MassAnalyzer.AnalyzerType method) (pyopenms.MassAnalyzer.ReflectronState method) (pyopenms.MassAnalyzer.ResolutionMethod method) (pyopenms.MassAnalyzer.ResolutionType method) (pyopenms.MassAnalyzer.ScanDirection method) (pyopenms.MassAnalyzer.ScanLaw method) (pyopenms.Measure method) (pyopenms.MetaboliteFeatureDeconvolution.CHARGEMODE method) (pyopenms.Method method) (pyopenms.MSExperiment.MSExperimentRasterAggregation method) (pyopenms.MSImagingRegion.Shape method) (pyopenms.MSNumpressCoder.NumpressCompression method) (pyopenms.MSSpectrum.MSSpectrumRasterAggregation method) (pyopenms.MT_QUANTMETHOD method) (pyopenms.MultipleTesting.LfdrTransform method) (pyopenms.MultipleTesting.Pi0Method method) (pyopenms.MzPAFDeltaUnit method) (pyopenms.MzPAFErrorCode method) (pyopenms.MzPAFIonSeries method) (pyopenms.MZTrafoModel.MODELTYPE method) (pyopenms.NaNPolicy method) (pyopenms.NASequence.NASFragmentType method) (pyopenms.NonNegativeLeastSquaresSolver.RETURN_STATUS method) (pyopenms.NormalizationMethod method) (pyopenms.OpenMSOSInfo.OpenMS_Architecture method) (pyopenms.OpenMSOSInfo.OpenMS_OS method) (pyopenms.OpenPepXLAlgorithm.ExitCodes method) (pyopenms.OPXLDataStructs.PeptidePosition method) (pyopenms.OPXLDataStructs.ProteinProteinCrossLinkType method) (pyopenms.OriginAnnotationFormat method) (pyopenms.OSWHierarchy.Level method) (pyopenms.ParquetWriteConfig.Compression method) (pyopenms.Peak2D.DimensionDescription method) (pyopenms.PeakGroup.TargetDecoyType method) (pyopenms.PEFFDatabaseMetadata.SequenceType method) (pyopenms.PEFFModification.ModificationType method) (pyopenms.PeptideIndexing.ExitCodes method) (pyopenms.PercolatorOutfile.ScoreType method) (pyopenms.PosteriorErrorProbabilityModel.ModelType method) (pyopenms.Precursor.ActivationMethod method) (pyopenms.ProForma.ConversionIssueType method) (pyopenms.ProForma.ConversionPolicy method) (pyopenms.ProForma.CvDatabase method) (pyopenms.ProForma.WriteMode method) (pyopenms.ProgressLogger.LogType method) (pyopenms.ProSEAlgorithm.ProSEAlgorithm_ExitCodes method) (pyopenms.ProteinIdentification.PeakMassType method) (pyopenms.ProteomicsPkaScale method) (pyopenms.QuotingMethod method) (pyopenms.RankData.Method method) (pyopenms.RankData.NaNPolicy method) (pyopenms.ReactionMonitoringTransition.DecoyTransitionType method) (pyopenms.RequirementLevel method) (pyopenms.Residue.ResidueType method) (pyopenms.ResidueModification.Provenance method) (pyopenms.ResidueModification.SourceClassification method) (pyopenms.ResidueModification.TermSpecificity method) (pyopenms.RetentionTime.RTType method) (pyopenms.RetentionTime.RTUnit method) (pyopenms.Ribonucleotide.TermSpecificityNuc method) (pyopenms.Sample.SampleState method) (pyopenms.Scores.IDType method) (pyopenms.SIDE method) (pyopenms.SimpleSearchEngineAlgorithm.ExitCodes method) (pyopenms.SourceFile.ChecksumType method) (pyopenms.SpectrumSettings.SpectrumType method) (pyopenms.TheoreticalGlycanSpectrumGenerator.FragmentationMethod method) (pyopenms.TheoreticalGlycanSpectrumGenerator.IonType method) (pyopenms.UnitType method) (pyopenms.USI.IndexType method) (pyopenms.ValueType method) (pyopenms.XFDRAlgorithm.ExitCodes method) (pyopenms.XTandemInfile.ErrorUnit method) (pyopenms.XTandemInfile.MassType method) getMappingRules() (pyopenms.CVMappings method) getMass() (pyopenms.Compomer method) (pyopenms.FeatureFinderMetaboIdentCompound method) (pyopenms.IMSAlphabet method) (pyopenms.IMSElement method) (pyopenms.IMSIsotopeDistribution method) (pyopenms.Sample method) getMassAnalyzers() (pyopenms.Instrument method) getMassCalculationIssues() (pyopenms.Peptidoform method) (pyopenms.PeptidoformIon method) (pyopenms.ProForma static method) getMassCalculationIssuesIon() (pyopenms.ProForma static method) getMassDiff() (pyopenms.ChargePair method) getMassErrors() (pyopenms.PeakGroup method) getMasses() (pyopenms.IMSAlphabet method) (pyopenms.IMSIsotopeDistribution method) getMassShift() (pyopenms.AMSE_AdductInfo method) getMassShiftAt() (pyopenms.MultiplexIsotopicPeakPattern method) getMassShiftCount() (pyopenms.MultiplexIsotopicPeakPattern method) getMassShiftIndex() (pyopenms.MultiplexIsotopicPeakPattern method) getMassShifts() (pyopenms.MultiplexIsotopicPeakPattern method) getMasstraceIntensities() (pyopenms.AccurateMassSearchResult method) getMassTypeFragment() (pyopenms.SequestInfile method) getMassTypeParent() (pyopenms.SequestInfile method) getMatchingHMDBids() (pyopenms.AccurateMassSearchResult method) getMatchingIndex() (pyopenms.AccurateMassSearchResult method) getMatchingScore() (pyopenms.SpectralMatch method) getMatchingSpectrumIndex() (pyopenms.SpectralMatch method) getMatchPeakAllowedError() (pyopenms.SequestInfile method) getMatchPeakCount() (pyopenms.SequestInfile method) getMatchPeakTolerance() (pyopenms.SequestInfile method) getMax() (pyopenms.IsotopeDistribution method) (pyopenms.RangeBase method) (pyopenms.RangeIntensity method) (pyopenms.RangeMobility method) (pyopenms.RangeMZ method) (pyopenms.RangeRT method) getMaxAAPerModPerPeptide() (pyopenms.SequestInfile method) getMaxDataPoolSize() (pyopenms.PeakFileOptions method) getMaxIntensity() (pyopenms.ChromatogramRangeManager method) (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.MassTrace method) (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.RangeIntensity method) (pyopenms.SpectrumRangeManager method) (pyopenms.SpectrumRanges method) getMaxInternalCleavageSites() (pyopenms.SequestInfile method) getMaxIsotope() (pyopenms.CoarseIsotopePatternGenerator method) getMaxIsotopeIndex() (pyopenms.PrecalAveragine method) getMaxMobility() (pyopenms.Mobilogram method) (pyopenms.MSExperiment method) (pyopenms.RangeMobility method) (pyopenms.SpectrumRangeManager method) (pyopenms.SpectrumRanges method) getMaxModifications() (pyopenms.ModificationDefinitionsSet method) getMaxModsPerPeptide() (pyopenms.SequestInfile method) getMaxMZ() (pyopenms.ChromatogramRangeManager method) (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.RangeMZ method) (pyopenms.SpectrumRangeManager method) (pyopenms.SpectrumRanges method) getMaxOccurrences() (pyopenms.ModificationDefinition method) getMaxPrecursorCharge() (pyopenms.XTandemInfile method) getMaxPTMsize() (pyopenms.InspectInfile method) getMaxRoundingError() (pyopenms.IMSWeights method) getMaxRT() (pyopenms.ChromatogramRangeManager method) (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.RangeRT method) (pyopenms.SpectrumRangeManager method) (pyopenms.SpectrumRanges method) getMaxScore() (pyopenms.XQuestResultXMLFile method) getMaxValidEValue() (pyopenms.XTandemInfile method) getMaxX() (pyopenms.MSImagingRegion method) getMaxY() (pyopenms.MSImagingRegion method) getMetaData() (pyopenms.CachedmzML method) (pyopenms.OnDiscMSExperiment method) getMetadataOnly() (pyopenms.FeatureFileOptions method) (pyopenms.PeakFileOptions method) getMetaValue() (pyopenms.Acquisition method) (pyopenms.AcquisitionInfo method) (pyopenms.BaseFeature method) (pyopenms.ChromatogramSettings method) (pyopenms.ColumnHeader method) (pyopenms.Compound method) (pyopenms.Configuration method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusMap method) (pyopenms.Contact method) (pyopenms.ContactPerson method) (pyopenms.CVTermList method) (pyopenms.CVTermListInterface method) (pyopenms.DataProcessing method) (pyopenms.ExperimentalSettings method) (pyopenms.Feature method) (pyopenms.FeatureMap method) (pyopenms.FloatDataArray method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Instrument method) (pyopenms.InstrumentSettings method) (pyopenms.IntegerDataArray method) (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) (pyopenms.MetaInfoDescription method) (pyopenms.MetaInfoInterface method) (pyopenms.MRMFeature method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.Peptide method) (pyopenms.PeptideHit method) (pyopenms.PeptideIdentification method) (pyopenms.Precursor method) (pyopenms.Prediction method) (pyopenms.Product method) (pyopenms.Protein method) (pyopenms.ProteinHit method) (pyopenms.ProteinIdentification method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.RichPeak2D method) (pyopenms.Sample method) (pyopenms.ScanWindow method) (pyopenms.SearchParameters method) (pyopenms.Software method) (pyopenms.SourceFile method) (pyopenms.SpectrumSettings method) (pyopenms.StringDataArray method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TraMLProduct method) getMetaValues() (pyopenms.Acquisition method) (pyopenms.CalibrationData static method) (pyopenms.ColumnHeader method) (pyopenms.ContactPerson method) (pyopenms.CVTermListInterface method) (pyopenms.DataProcessing method) (pyopenms.Instrument method) (pyopenms.InstrumentSettings method) (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) (pyopenms.MetaInfoDescription method) (pyopenms.MetaInfoInterface method) (pyopenms.ProteinHit method) (pyopenms.RetentionTime method) (pyopenms.Sample method) (pyopenms.ScanWindow method) (pyopenms.SearchParameters method) (pyopenms.SpectrumSettings method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TraMLProduct method) getMethodOfCombination() (pyopenms.AcquisitionInfo method) getMIMatrix() (pyopenms.MRMScoring method) getMin() (pyopenms.IsotopeDistribution method) (pyopenms.RangeBase method) (pyopenms.RangeIntensity method) (pyopenms.RangeMobility method) (pyopenms.RangeMZ method) (pyopenms.RangeRT method) getMinElementCoordinates() (pyopenms.DistanceMatrix method) getMinIntensity() (pyopenms.ChromatogramRangeManager method) (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.RangeIntensity method) (pyopenms.SpectrumRangeManager method) (pyopenms.SpectrumRanges method) getMinMobility() (pyopenms.Mobilogram method) (pyopenms.MSExperiment method) (pyopenms.RangeMobility method) (pyopenms.SpectrumRangeManager method) (pyopenms.SpectrumRanges method) getMinMZ() (pyopenms.ChromatogramRangeManager method) (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.RangeMZ method) (pyopenms.SpectrumRangeManager method) (pyopenms.SpectrumRanges method) getMinNegativeIsotopeIndex() (pyopenms.PeakGroup method) getMinRoundingError() (pyopenms.IMSWeights method) getMinRT() (pyopenms.ChromatogramRangeManager method) (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.RangeRT method) (pyopenms.SpectrumRangeManager method) (pyopenms.SpectrumRanges method) getMinScore() (pyopenms.XQuestResultXMLFile method) getMinX() (pyopenms.MSImagingRegion method) getMinY() (pyopenms.MSImagingRegion method) getMissedCleavages() (pyopenms.EnzymaticDigestion method) (pyopenms.ProteaseDigestion method) (pyopenms.RNaseDigestion method) getMobility() (pyopenms.MobilityPeak1D method) getMobilograms() (pyopenms.XIMParquetFile method) getModel() (pyopenms.Instrument method) getModelParameters() (pyopenms.TransformationDescription method) getModelType() (pyopenms.PosteriorErrorProbabilityModel method) (pyopenms.TransformationDescription method) getModelTypes() (pyopenms.TransformationDescription static method) getModification() (pyopenms.CrossLinksDB method) (pyopenms.ModificationDefinition method) (pyopenms.ModificationsDB method) (pyopenms.Residue method) getModificationName() (pyopenms.ModificationDefinition method) (pyopenms.Residue method) getModificationNames() (pyopenms.ModificationDefinitionsSet method) getModifications() (pyopenms.InspectInfile method) (pyopenms.ModificationDefinitionsSet method) (pyopenms.ModifiedPeptideGenerator static method) (pyopenms.SequestInfile method) (pyopenms.XTandemInfile method) getModificationsPerPeptide() (pyopenms.InspectInfile method) getModifiedResidue() (pyopenms.ResidueDB method) getModifiedSequence() (pyopenms.PEFFEntry method) getMolMultiplier() (pyopenms.AMSE_AdductInfo method) getMonoMass() (pyopenms.PeakGroup method) (pyopenms.ResidueModification method) (pyopenms.Ribonucleotide method) getMonoWeight() (pyopenms.AASequence method) (pyopenms.Element method) (pyopenms.EmpiricalFormula method) (pyopenms.NASequence method) (pyopenms.Peptidoform method) (pyopenms.PeptidoformIon method) (pyopenms.ProForma static method) (pyopenms.Residue method) getMonoWeightIon() (pyopenms.ProForma static method) getMostAbundant() (pyopenms.IsotopeDistribution method) getMostAbundantMassDelta() (pyopenms.PrecalAveragine method) getMSChromatogramById() (pyopenms.IndexedMzMLHandler method) getMSChromatogramByNativeId() (pyopenms.IndexedMzMLHandler method) getMSData() (pyopenms.Biosaur2Algorithm method) (pyopenms.FeatureFinderAlgorithmMetaboIdent method) (pyopenms.FeatureFinderIdentificationAlgorithm method) getMSExperiment() (pyopenms.AnnotatedMSRun method) (pyopenms.MSImagingExperiment method) getMSFileSection() (pyopenms.ExperimentalDesign method) getMSGFID() (pyopenms.DigestionEnzymeProtein method) getMSLevel() (pyopenms.MSSpectrum method) getMSLevels() (pyopenms.MSExperiment method) (pyopenms.PeakFileOptions method) (pyopenms.SpectrumRangeManager method) getMSRun() (pyopenms.USI method) getMSRunPaths() (pyopenms.IdentifierMSRunMapper method) getMSSpectrumById() (pyopenms.IndexedMzMLHandler method) getMSSpectrumByNativeId() (pyopenms.IndexedMzMLHandler method) getMulticharge() (pyopenms.InspectInfile method) getMZ() (pyopenms.AASequence method) (pyopenms.AMSE_AdductInfo method) (pyopenms.BaseFeature method) (pyopenms.CalibrationData method) (pyopenms.ConsensusFeature method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.MRMFeature method) (pyopenms.MSChromatogram method) (pyopenms.Peak1D method) (pyopenms.Peak2D method) (pyopenms.PeptideIdentification method) (pyopenms.Peptidoform method) (pyopenms.PeptidoformIon method) (pyopenms.Precursor method) (pyopenms.Product method) (pyopenms.ProForma static method) (pyopenms.RichPeak2D method) (pyopenms.TraMLProduct method) getMz32Bit() (pyopenms.PeakFileOptions method) getMZArray() (pyopenms.OSSpectrum method) (pyopenms.Spectrum method) getMZCharge() (pyopenms.ProForma static method) getMZErrorPPM() (pyopenms.AccurateMassSearchResult method) getMZRange() (pyopenms.FeatureFileOptions method) getMzRange() (pyopenms.IonImage method) getMZRange() (pyopenms.PeakFileOptions method) getMZShiftAt() (pyopenms.MultiplexIsotopicPeakPattern method) getMZShiftCount() (pyopenms.MultiplexIsotopicPeakPattern method) getNADH010106() (pyopenms.AAIndex static method) getNADH010107() (pyopenms.AAIndex static method) getName() (pyopenms.AbsoluteQuantitation method) (pyopenms.AccurateMassSearchEngine method) (pyopenms.AMSE_AdductInfo method) (pyopenms.AScore method) (pyopenms.BaseGroupFinder method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.Biosaur2Algorithm method) (pyopenms.CVReference method) (pyopenms.CVTerm method) (pyopenms.DefaultParamHandler method) (pyopenms.DIAScoring method) (pyopenms.DigestionEnzyme method) (pyopenms.DigestionEnzymeProtein method) (pyopenms.DigestionEnzymeRNA method) (pyopenms.Element method) (pyopenms.ElutionModelFitter method) (pyopenms.ElutionPeakDetection method) (pyopenms.EmgFitter1D method) (pyopenms.EmgGradientDescent method) (pyopenms.FalseDiscoveryRate method) (pyopenms.FeatureDeconvolution method) (pyopenms.FeatureDistance method) (pyopenms.FeatureFinderAlgorithmMetaboIdent method) (pyopenms.FeatureFinderAlgorithmPicked method) (pyopenms.FeatureFinderIdentificationAlgorithm method) (pyopenms.FeatureFinderMetaboIdentCompound method) (pyopenms.FeatureFinderMultiplexAlgorithm method) (pyopenms.FeatureFindingMetabo method) (pyopenms.FeatureGroupingAlgorithm method) (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.FeatureGroupingAlgorithmLabeled method) (pyopenms.FeatureGroupingAlgorithmQT method) (pyopenms.FeatureGroupingAlgorithmUnlabeled method) (pyopenms.FIAMSDataProcessor method) (pyopenms.Fitter1D method) (pyopenms.FLASHDeconvAlgorithm method) (pyopenms.FloatDataArray method) (pyopenms.GaussFilter method) (pyopenms.GNPSMGFFile method) (pyopenms.IDDecoyProbability method) (pyopenms.IDMapper method) (pyopenms.IDRipper method) (pyopenms.IDScoreSwitcherAlgorithm method) (pyopenms.IMSAlphabet method) (pyopenms.IMSElement method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Instrument method) (pyopenms.IntegerDataArray method) (pyopenms.IsobaricChannelExtractor method) (pyopenms.IsobaricQuantifier method) (pyopenms.IsobaricQuantitationMethod method) (pyopenms.IsotopeLabelingMDVs method) (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.LabeledPairFinder method) (pyopenms.LevMarqFitter1D method) (pyopenms.LinearResamplerAlign method) (pyopenms.LowessSmoothing method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) (pyopenms.MascotGenericFile method) (pyopenms.MassDecompositionAlgorithm method) (pyopenms.MasstraceCorrelator method) (pyopenms.MassTraceDetection method) (pyopenms.MetaboliteFeatureDeconvolution method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.MetaInfoDescription method) (pyopenms.MetaInfoRegistry method) (pyopenms.ModifiedSincSmoother method) (pyopenms.MorphologicalFilter method) (pyopenms.MRMDecoy method) (pyopenms.MRMFeatureFilter method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MRMMapping method) (pyopenms.MRMTransitionGroupPicker method) (pyopenms.MSChromatogram method) (pyopenms.MSImagingRegion method) (pyopenms.MSPFile method) (pyopenms.MSPGenericFile method) (pyopenms.MSSpectrum method) (pyopenms.MultiplexDeltaMassesGenerator method) (pyopenms.MultiplexResolverAlgorithm method) (pyopenms.NLargest method) (pyopenms.Normalizer method) (pyopenms.NucleicAcidSpectrumGenerator method) (pyopenms.OpenPepXLAlgorithm method) (pyopenms.PeakIntegrator method) (pyopenms.PeakPickerChromatogram method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIM method) (pyopenms.PeakPickerIterative method) (pyopenms.PeptideAndProteinQuant method) (pyopenms.PeptideIndexing method) (pyopenms.Percolator method) (pyopenms.PipEchoAlgorithm method) (pyopenms.PosteriorErrorProbabilityModel method) (pyopenms.ProSEAlgorithm method) (pyopenms.QTClusterFinder method) (pyopenms.RankScaler method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.Residue method) (pyopenms.ResidueModification method) (pyopenms.Ribonucleotide method) (pyopenms.Sample method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SignalToNoiseEstimatorMeanIterative method) (pyopenms.SignalToNoiseEstimatorMedian method) (pyopenms.SignalToNoiseEstimatorMedianChrom method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.SimpleTSGXLMS method) (pyopenms.SiriusExportAlgorithm method) (pyopenms.Software method) (pyopenms.SpectralDeconvolution method) (pyopenms.SpectraMerger method) (pyopenms.SpectrumAlignment method) (pyopenms.SpectrumAlignmentScore method) (pyopenms.SpectrumAnnotator method) (pyopenms.SqrtScaler method) (pyopenms.StablePairFinder method) (pyopenms.StringDataArray method) (pyopenms.SwathMapMassCorrection method) (pyopenms.TargetedSpectraExtractor method) (pyopenms.TheoreticalSpectrumGenerator method) (pyopenms.TheoreticalSpectrumGeneratorXLMS method) (pyopenms.ThresholdMower method) (pyopenms.TMTEighteenPlexQuantitationMethod method) (pyopenms.TMTElevenPlexQuantitationMethod method) (pyopenms.TMTSixPlexQuantitationMethod method) (pyopenms.TMTSixteenPlexQuantitationMethod method) (pyopenms.TMTTenPlexQuantitationMethod method) (pyopenms.TransitionListEvidenceFilter method) (pyopenms.WindowMower method) (pyopenms.XFDRAlgorithm method) getNameOfFile() (pyopenms.SourceFile method) getNativeID() (pyopenms.ChromatogramSettings method) (pyopenms.LightTransition method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.SpectrumSettings method) getNativeIDType() (pyopenms.SourceFile method) getNativeIDTypeAccession() (pyopenms.SourceFile method) getNavigator() (pyopenms.SplineInterpolatedPeaks method) getNegativeCharges() (pyopenms.Compomer method) getNegativePrior() (pyopenms.PosteriorErrorProbabilityModel method) getNetCharge() (pyopenms.Compomer method) getNeutralLossAverageMasses() (pyopenms.ResidueModification method) getNeutralLossDiffFormulas() (pyopenms.ResidueModification method) getNeutralLossesForIons() (pyopenms.SequestInfile method) getNeutralLossMonoMasses() (pyopenms.ResidueModification method) getNeutralMass() (pyopenms.AMSE_AdductInfo method) getNewCode() (pyopenms.Ribonucleotide method) getNextPos() (pyopenms.SplineInterpolatedPeaks.Navigator method) getNoiseDecoyWeight() (pyopenms.FLASHDeconvAlgorithm method) getNominalMass() (pyopenms.IMSElement method) (pyopenms.IMSIsotopeDistribution method) (pyopenms.SpectralDeconvolution static method) getNormalizeXcorr() (pyopenms.SequestInfile method) getNPoints() (pyopenms.AbsoluteQuantitationMethod method) getNrChromatograms() (pyopenms.CachedmzML method) (pyopenms.IndexedMzMLHandler method) (pyopenms.MSExperiment method) (pyopenms.MzMLSqliteHandler method) (pyopenms.OnDiscMSExperiment method) (pyopenms.OnDiscThermoRawExperiment method) (pyopenms.SpectrumAccessOpenMS method) (pyopenms.SpectrumAccessOpenMSCached method) (pyopenms.SpectrumAccessOpenMSInMemory method) (pyopenms.SpectrumAccessSqMass method) getNrChromatogramsWritten() (pyopenms.NoopMSDataWritingConsumer method) (pyopenms.PlainMSDataWritingConsumer method) getNrOfGroups() (pyopenms.CalibrationData method) getNrSpectra() (pyopenms.CachedmzML method) (pyopenms.IndexedMzMLHandler method) (pyopenms.MSExperiment method) (pyopenms.MzMLSqliteHandler method) (pyopenms.OnDiscImzMLExperiment method) (pyopenms.OnDiscMSExperiment method) (pyopenms.OnDiscThermoRawExperiment method) (pyopenms.SpectrumAccessOpenMS method) (pyopenms.SpectrumAccessOpenMSCached method) (pyopenms.SpectrumAccessOpenMSInMemory method) (pyopenms.SpectrumAccessSqMass method) getNrSpectraWritten() (pyopenms.NoopMSDataWritingConsumer method) (pyopenms.PlainMSDataWritingConsumer method) getNShared() (pyopenms.FeatureFinderAlgorithmMetaboIdent method) getNTermGain() (pyopenms.DigestionEnzymeProtein method) getNTerminalModification() (pyopenms.AASequence method) getNTerminalModificationName() (pyopenms.AASequence method) getNTermLossFormulas() (pyopenms.Residue method) getNTermLossNames() (pyopenms.Residue method) getNucleotideReadingFrame() (pyopenms.SequestInfile method) getNumber() (pyopenms.Sample method) getNumberOf() (pyopenms.EmpiricalFormula method) getNumberOfAtoms() (pyopenms.EmpiricalFormula method) getNumberOfChannels() (pyopenms.IsobaricQuantitationMethod method) (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.TMTEighteenPlexQuantitationMethod method) (pyopenms.TMTElevenPlexQuantitationMethod method) (pyopenms.TMTSixPlexQuantitationMethod method) (pyopenms.TMTSixteenPlexQuantitationMethod method) (pyopenms.TMTTenPlexQuantitationMethod method) getNumberOfDecompositions() (pyopenms.RealMassDecomposer method) getNumberOfFixedModifications() (pyopenms.ModificationDefinitionsSet method) getNumberOfFractionGroups() (pyopenms.ExperimentalDesign method) getNumberOfFractions() (pyopenms.ExperimentalDesign method) getNumberOfHits() (pyopenms.XQuestResultXMLFile method) getNumberOfLabels() (pyopenms.ExperimentalDesign method) getNumberOfMaxAA() (pyopenms.MassDecomposition method) getNumberOfMissedCleavages() (pyopenms.XTandemInfile method) getNumberOfModifications() (pyopenms.CrossLinksDB method) (pyopenms.ModificationDefinitionsSet method) (pyopenms.ModificationsDB method) getNumberOfModifiedResidues() (pyopenms.ResidueDB method) getNumberOfMSFiles() (pyopenms.ExperimentalDesign method) getNumberOfPixels() (pyopenms.MSImagingExperiment method) (pyopenms.MSImagingGeometry method) getNumberOfRegions() (pyopenms.MSImagingGeometry method) getNumberOfResidues() (pyopenms.ResidueDB method) getNumberOfSamples() (pyopenms.ExperimentalDesign method) getNumberOfSpectra() (pyopenms.MSImagingExperiment method) getNumberOfThreads() (pyopenms.XTandemInfile method) getNumberOfVariableModifications() (pyopenms.ModificationDefinitionsSet method) getNumpressConfigurationFloatDataArray() (pyopenms.PeakFileOptions method) getNumpressConfigurationIntensity() (pyopenms.PeakFileOptions method) getNumpressConfigurationMassTime() (pyopenms.PeakFileOptions method) getObservedCCS() (pyopenms.SpectralMatch method) getObservedIntensity() (pyopenms.AccurateMassSearchResult method) getObservedMZ() (pyopenms.AccurateMassSearchResult method) getObservedPrecursorMass() (pyopenms.SpectralMatch method) getObservedPrecursorRT() (pyopenms.SpectralMatch method) getObservedRT() (pyopenms.AccurateMassSearchResult method) getObservedSpectrumIndex() (pyopenms.SpectralMatch method) getOffset() (pyopenms.BinnedSpectrum method) (pyopenms.IsotopeModel method) (pyopenms.LinearInterpolation method) getOffset_0() (pyopenms.BilinearInterpolation method) getOffset_1() (pyopenms.BilinearInterpolation method) getOMSSAID() (pyopenms.DigestionEnzymeProtein method) getOneLetterCode() (pyopenms.Residue method) getOOBM850104() (pyopenms.AAIndex static method) getOpenMPMaxNumThreads() (pyopenms.OpenMSBuildInfo static method) getOpenMSConfigDir() (pyopenms.SystemSettings static method) getOpenMSDataPath() (pyopenms.File static method) getOpenMSHomePath() (pyopenms.File static method) (pyopenms.SystemSettings static method) getOptions() (pyopenms.ConsensusXMLFile method) (pyopenms.DTA2DFile method) (pyopenms.FeatureXMLFile method) (pyopenms.FileHandler method) (pyopenms.ImzMLFile method) (pyopenms.IndexedMzMLFileLoader method) (pyopenms.MzDataFile method) (pyopenms.MzMLFile method) (pyopenms.MzXMLFile method) (pyopenms.OnDiscMSExperiment method) (pyopenms.OnDiscThermoRawExperiment method) (pyopenms.PlainMSDataWritingConsumer method) (pyopenms.ThermoRawFile method) getOrder() (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) getOrganism() (pyopenms.Sample method) getOrigin() (pyopenms.ResidueModification method) (pyopenms.Ribonucleotide method) getOriginalSpectrum() (pyopenms.DeconvolvedSpectrum method) getOriginFullname() (pyopenms.RipFileIdentifier method) getOSAsString() (pyopenms.OpenMSOSInfo method) getOSInfo() (pyopenms.OpenMSOSInfo static method) getOSVersionAsString() (pyopenms.OpenMSOSInfo method) getOutputBasename() (pyopenms.RipFileIdentifier method) getOutputFilename() (pyopenms.XTandemInfile method) getOutputLines() (pyopenms.SequestInfile method) getOutputResults() (pyopenms.XTandemInfile method) getOutsideReferencePoint() (pyopenms.LinearInterpolation method) getOutsideReferencePoint_0() (pyopenms.BilinearInterpolation method) getOutsideReferencePoint_1() (pyopenms.BilinearInterpolation method) getOverallQuality() (pyopenms.Feature method) (pyopenms.MRMFeature method) getParameters() (pyopenms.AbsoluteQuantitation method) (pyopenms.AccurateMassSearchEngine method) (pyopenms.AScore method) (pyopenms.BaseGroupFinder method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.Biosaur2Algorithm method) (pyopenms.DefaultParamHandler method) (pyopenms.DIAScoring method) (pyopenms.ElutionModelFitter method) (pyopenms.ElutionPeakDetection method) (pyopenms.EmgFitter1D method) (pyopenms.EmgGradientDescent method) (pyopenms.FalseDiscoveryRate method) (pyopenms.FeatureDeconvolution method) (pyopenms.FeatureDistance method) (pyopenms.FeatureFinderAlgorithmMetaboIdent method) (pyopenms.FeatureFinderAlgorithmPicked method) (pyopenms.FeatureFinderIdentificationAlgorithm method) (pyopenms.FeatureFinderMultiplexAlgorithm method) (pyopenms.FeatureFindingMetabo method) (pyopenms.FeatureGroupingAlgorithm method) (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.FeatureGroupingAlgorithmLabeled method) (pyopenms.FeatureGroupingAlgorithmQT method) (pyopenms.FeatureGroupingAlgorithmUnlabeled method) (pyopenms.FIAMSDataProcessor method) (pyopenms.Fitter1D method) (pyopenms.FLASHDeconvAlgorithm method) (pyopenms.GaussFilter method) (pyopenms.GNPSMGFFile method) (pyopenms.IDDecoyProbability method) (pyopenms.IDFreeMassErrorEstimator method) (pyopenms.IDMapper method) (pyopenms.IDRipper method) (pyopenms.IDScoreSwitcherAlgorithm method) (pyopenms.IsobaricChannelExtractor method) (pyopenms.IsobaricQuantifier method) (pyopenms.IsobaricQuantitationMethod method) (pyopenms.IsotopeLabelingMDVs method) (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.LabeledPairFinder method) (pyopenms.LevMarqFitter1D method) (pyopenms.LinearResamplerAlign method) (pyopenms.LowessSmoothing method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) (pyopenms.MascotGenericFile method) (pyopenms.MassDecompositionAlgorithm method) (pyopenms.MasstraceCorrelator method) (pyopenms.MassTraceDetection method) (pyopenms.MetaboliteFeatureDeconvolution method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.ModifiedSincSmoother method) (pyopenms.MorphologicalFilter method) (pyopenms.MRMDecoy method) (pyopenms.MRMFeatureFilter method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MRMMapping method) (pyopenms.MRMTransitionGroupPicker method) (pyopenms.MSPFile method) (pyopenms.MSPGenericFile method) (pyopenms.MultiplexDeltaMassesGenerator method) (pyopenms.MultiplexResolverAlgorithm method) (pyopenms.NLargest method) (pyopenms.Normalizer method) (pyopenms.NucleicAcidSpectrumGenerator method) (pyopenms.OpenPepXLAlgorithm method) (pyopenms.PeakIntegrator method) (pyopenms.PeakPickerChromatogram method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIM method) (pyopenms.PeakPickerIterative method) (pyopenms.PeptideAndProteinQuant method) (pyopenms.PeptideIndexing method) (pyopenms.Percolator method) (pyopenms.PipEchoAlgorithm method) (pyopenms.PosteriorErrorProbabilityModel method) (pyopenms.ProSEAlgorithm method) (pyopenms.QTClusterFinder method) (pyopenms.RankScaler method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SignalToNoiseEstimatorMeanIterative method) (pyopenms.SignalToNoiseEstimatorMedian method) (pyopenms.SignalToNoiseEstimatorMedianChrom method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.SimpleTSGXLMS method) (pyopenms.SiriusExportAlgorithm method) (pyopenms.SpectralDeconvolution method) (pyopenms.SpectraMerger method) (pyopenms.SpectrumAlignment method) (pyopenms.SpectrumAlignmentScore method) (pyopenms.SpectrumAnnotator method) (pyopenms.SqrtScaler method) (pyopenms.StablePairFinder method) (pyopenms.SwathMapMassCorrection method) (pyopenms.TargetedSpectraExtractor method) (pyopenms.TheoreticalSpectrumGenerator method) (pyopenms.TheoreticalSpectrumGeneratorXLMS method) (pyopenms.ThresholdMower method) (pyopenms.TMTEighteenPlexQuantitationMethod method) (pyopenms.TMTElevenPlexQuantitationMethod method) (pyopenms.TMTSixPlexQuantitationMethod method) (pyopenms.TMTSixteenPlexQuantitationMethod method) (pyopenms.TMTTenPlexQuantitationMethod method) (pyopenms.TransformationModelBSpline method) (pyopenms.TransformationModelInterpolated method) (pyopenms.TransformationModelLinear method) (pyopenms.TransformationModelLowess method) (pyopenms.TransitionListEvidenceFilter method) (pyopenms.WindowMower method) (pyopenms.XFDRAlgorithm method) getParentMass() (pyopenms.IMSWeights method) getParsingSuccess() (pyopenms.IndexedMzMLHandler method) getPartialSequence() (pyopenms.SequestInfile method) getPath() (pyopenms.TempDir method) getPathToFile() (pyopenms.SourceFile method) getPCMz() (pyopenms.OSWPeptidePrecursor method) getPeakAnnotations() (pyopenms.PeptideHit method) getPeakCount() (pyopenms.MassTraces method) getPeakMaps() (pyopenms.XIPMParquetFile method) getPeakMassTolerance() (pyopenms.InspectInfile method) (pyopenms.SequestInfile method) getPeakOccupancy() (pyopenms.PeakGroup method) getPeaksPerPeptide() (pyopenms.MultiplexIsotopicPeakPattern method) getPeakWidth() (pyopenms.PeakWidthEstimator method) getPeptideByRef() (pyopenms.LightTargetedExperiment method) (pyopenms.TargetedExperiment method) getPeptideEvidences() (pyopenms.PeptideHit method) getPeptideGroupLabel() (pyopenms.Peptide method) getPeptideIdentifications() (pyopenms.AnnotatedMSRun method) (pyopenms.BaseFeature method) (pyopenms.ConsensusFeature method) (pyopenms.Feature method) (pyopenms.MRMFeature method) (pyopenms.RipFileContent method) getPeptideMassUnit() (pyopenms.SequestInfile method) getPeptidePrecursors() (pyopenms.OSWProtein method) getPeptideRef() (pyopenms.IncludeExcludeTarget method) (pyopenms.LightTransition method) (pyopenms.ReactionMonitoringTransition method) getPeptideResults() (pyopenms.PeptideAndProteinQuant method) getPeptides() (pyopenms.TargetedExperiment method) getPercentage() (pyopenms.Gradient method) getPiValue() (pyopenms.Residue method) getPixelSizeUnit() (pyopenms.MSImagingGeometry method) getPixelSizeX() (pyopenms.MSImagingGeometry method) getPixelSizeY() (pyopenms.MSImagingGeometry method) getPka() (pyopenms.Residue method) getPkb() (pyopenms.Residue method) getPkc() (pyopenms.Residue method) getPoints() (pyopenms.GridBasedCluster method) getPolarity() (pyopenms.InstrumentSettings method) (pyopenms.IonSource method) getPos() (pyopenms.ChromatogramPeak method) (pyopenms.MobilityPeak1D method) (pyopenms.Peak1D method) (pyopenms.Precursor method) getPosition() (pyopenms.ChromatogramPeak method) getPositiveCharges() (pyopenms.Compomer method) getPosMax() (pyopenms.SplineInterpolatedPeaks method) (pyopenms.SplinePackage method) getPosMin() (pyopenms.SplineInterpolatedPeaks method) (pyopenms.SplinePackage method) getPossibleChargeStates() (pyopenms.Precursor method) getPosStepWidth() (pyopenms.SplinePackage method) getPPM() (in module pyopenms) (pyopenms.Math static method) getPPMAbs() (in module pyopenms) (pyopenms.Math static method) getPrecision() (pyopenms.IMSWeights method) getPrecursor() (pyopenms.ChromatogramSettings method) (pyopenms.DeconvolvedSpectrum method) (pyopenms.MSChromatogram method) getPrecursorAdduct() (pyopenms.SpectralMatch method) getPrecursorCharge() (pyopenms.DeconvolvedSpectrum method) getPrecursorChromatogram() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) getPrecursorChromatograms() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) getPrecursorCVTermList() (pyopenms.IncludeExcludeTarget method) (pyopenms.ReactionMonitoringTransition method) getPrecursorErrorType() (pyopenms.XTandemInfile method) getPrecursorFeature() (pyopenms.MRMFeature method) getPrecursorFeatureIDs() (pyopenms.MRMFeature method) getPrecursorIM() (pyopenms.LightTransition method) getPrecursorMassErrorUnit() (pyopenms.XTandemInfile method) getPrecursorMassTolerance() (pyopenms.InspectInfile method) (pyopenms.SequestInfile method) getPrecursorMassToleranceMinus() (pyopenms.XTandemInfile method) getPrecursorMassTolerancePlus() (pyopenms.XTandemInfile method) getPrecursorMZ() (pyopenms.IncludeExcludeTarget method) (pyopenms.LightTransition method) (pyopenms.ReactionMonitoringTransition method) getPrecursorMZRange() (pyopenms.PeakFileOptions method) getPrecursorMzTolerance() (pyopenms.SiriusExportAlgorithm method) getPrecursorPeakGroup() (pyopenms.DeconvolvedSpectrum method) getPrecursorPrecisionPPM() (pyopenms.IDFreeMassErrorEstimator method) getPrecursorRtTolerance() (pyopenms.SiriusExportAlgorithm method) getPrecursors() (pyopenms.BinnedSpectrum method) (pyopenms.MSSpectrum method) (pyopenms.PrecursorCorrection static method) (pyopenms.SpectrumSettings method) getPrecursorScanNumber() (pyopenms.DeconvolvedSpectrum method) getPrecursorSpectrum() (pyopenms.MSExperiment method) getPrediction() (pyopenms.IncludeExcludeTarget method) (pyopenms.ReactionMonitoringTransition method) getPrefix() (pyopenms.AASequence method) (pyopenms.NASequence method) getPrefixAndSuffixIonsMZ() (pyopenms.TheoreticalSpectrumGenerator method) getPressure() (pyopenms.HPLC method) getPrimaryIdentifier() (pyopenms.SpectralMatch method) getPrimaryMSRunPath() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.MSExperiment method) (pyopenms.ProteinIdentification method) getPrintDuplicateReferences() (pyopenms.SequestInfile method) getProcessedSequence() (pyopenms.PEFFEntry method) getProcessingActions() (pyopenms.DataProcessing method) getProduct() (pyopenms.ChromatogramSettings method) (pyopenms.MSChromatogram method) (pyopenms.ReactionMonitoringTransition method) getProductChargeState() (pyopenms.LightTransition method) (pyopenms.ReactionMonitoringTransition method) getProductCVTermList() (pyopenms.IncludeExcludeTarget method) getProductMZ() (pyopenms.IncludeExcludeTarget method) (pyopenms.LightTransition method) (pyopenms.OSWTransition method) (pyopenms.ReactionMonitoringTransition method) getProducts() (pyopenms.MSSpectrum method) (pyopenms.SpectrumSettings method) getPropertiesB() (pyopenms.GridBasedCluster method) getPropertyA() (pyopenms.GridBasedCluster method) getProteinAccession() (pyopenms.PeptideEvidence method) getProteinByRef() (pyopenms.TargetedExperiment method) getProteinGroups() (pyopenms.ProteinIdentification method) getProteinIdentifications() (pyopenms.AnnotatedMSRun method) (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.RipFileContent method) getProteinMassFilter() (pyopenms.SequestInfile method) getProteinResults() (pyopenms.PeptideAndProteinQuant method) getProteins() (pyopenms.LightTargetedExperiment method) (pyopenms.OSWData method) (pyopenms.TargetedExperiment method) getProvenance() (pyopenms.ResidueModification method) getPSIID() (pyopenms.DigestionEnzymeProtein method) getPSIMODAccession() (pyopenms.ResidueModification method) getPublications() (pyopenms.TargetedExperiment method) getQscore() (pyopenms.PeakGroup method) getQscore2D() (pyopenms.PeakGroup method) getQuality() (pyopenms.BaseFeature method) (pyopenms.ConsensusFeature method) (pyopenms.Feature method) (pyopenms.MRMFeature method) (pyopenms.QTCluster method) getQuantities() (pyopenms.DeconvolvedSpectrum method) getQuantMethod() (pyopenms.MassTrace method) getQuantMethods() (pyopenms.AbsoluteQuantitation method) getQueryMass() (pyopenms.AccurateMassSearchResult method) getQValue() (pyopenms.OSWPeakGroup method) getQvalue() (pyopenms.PeakGroup method) getRank() (pyopenms.PeptideHit method) (pyopenms.ProteinHit method) getRatios() (pyopenms.ConsensusFeature method) getReferenceChannel() (pyopenms.IsobaricQuantitationMethod method) (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.TMTEighteenPlexQuantitationMethod method) (pyopenms.TMTElevenPlexQuantitationMethod method) (pyopenms.TMTSixPlexQuantitationMethod method) (pyopenms.TMTSixteenPlexQuantitationMethod method) (pyopenms.TMTTenPlexQuantitationMethod method) getReferencingHits() (pyopenms.PeptideIdentification static method) getReflectronState() (pyopenms.MassAnalyzer method) getRefMZ() (pyopenms.CalibrationData method) getRegEx() (pyopenms.DigestionEnzyme method) (pyopenms.DigestionEnzymeProtein method) (pyopenms.DigestionEnzymeRNA method) getRegExDescription() (pyopenms.DigestionEnzyme method) (pyopenms.DigestionEnzymeProtein method) (pyopenms.DigestionEnzymeRNA method) getRegExFromNativeID() (in module pyopenms) (pyopenms.SpectrumNativeIDParser static method) getRegion() (pyopenms.MSImagingGeometry method) getRegionPixels() (pyopenms.MSImagingGeometry method) getRegions() (pyopenms.MSImagingGeometry method) getRegionSpectrumIndices() (pyopenms.MSImagingExperiment method) (pyopenms.MSImagingGeometry method) getRemovePrecursorNearPeaks() (pyopenms.SequestInfile method) getRepAbsCharge() (pyopenms.PeakGroup method) getRequirementLevel() (pyopenms.CVMappingRule method) getResidue() (pyopenms.AASequence method) (pyopenms.ResidueDB method) getResidues() (pyopenms.ResidueDB method) getResidueSets() (pyopenms.Residue method) (pyopenms.ResidueDB method) getResiduesInUpperCase() (pyopenms.SequestInfile method) getResidueTypeName() (pyopenms.Residue static method) getResolution() (pyopenms.IonDetector method) (pyopenms.MassAnalyzer method) getResolutionMethod() (pyopenms.MassAnalyzer method) getResolutionType() (pyopenms.MassAnalyzer method) getResult() (pyopenms.IDFreeMassErrorEstimator method) getResultMap() (pyopenms.FeatureGroupingAlgorithmUnlabeled method) getRetentionTime() (pyopenms.Compound method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Peptide method) (pyopenms.ReactionMonitoringTransition method) getRetentionTimeType() (pyopenms.Compound method) (pyopenms.Peptide method) getRetentionTimeUnit() (pyopenms.Compound method) (pyopenms.Peptide method) getRevision() (pyopenms.VersionInfo static method) getRibonucleotide() (pyopenms.RibonucleotideDB method) getRibonucleotideAlternatives() (pyopenms.RibonucleotideDB method) getRibonucleotidePrefix() (pyopenms.RibonucleotideDB method) getRightCountFromApex() (pyopenms.PrecalAveragine method) getROBB760107() (pyopenms.AAIndex static method) getRoundMasses() (pyopenms.CoarseIsotopePatternGenerator method) getRow() (pyopenms.AbsoluteQuantitationMethodFile method) (pyopenms.CsvFile method) (pyopenms.MRMFeaturePickerFile method) (pyopenms.MRMFeatureQCFile method) getRT() (pyopenms.BaseFeature method) (pyopenms.CalibrationData method) (pyopenms.ChromatogramPeak method) (pyopenms.ConsensusFeature method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.Mobilogram method) (pyopenms.MRMFeature method) (pyopenms.MSSpectrum method) (pyopenms.MZTrafoModel method) (pyopenms.Peak2D method) (pyopenms.PeptideIdentification method) (pyopenms.RetentionTime method) (pyopenms.RichPeak2D method) getRTBounds() (pyopenms.MassTraces method) getRTDelta() (pyopenms.OSWPeakGroup method) getRTExperimental() (pyopenms.OSWPeakGroup method) getRTLeftWidth() (pyopenms.OSWPeakGroup method) getRTRange() (pyopenms.FeatureFileOptions method) (pyopenms.PeakFileOptions method) getRTRanges() (pyopenms.FeatureFinderMetaboIdentCompound method) getRTRightWidth() (pyopenms.OSWPeakGroup method) getRTs() (pyopenms.FeatureFinderMetaboIdentCompound method) getRTShift() (pyopenms.Adduct method) (pyopenms.Compomer method) getRunID() (pyopenms.MzMLSqliteHandler method) (pyopenms.OSWData method) getRuns() (pyopenms.XICParquetFile method) (pyopenms.XIMParquetFile method) (pyopenms.XIPMParquetFile method) getSample() (pyopenms.ExperimentalDesign method) (pyopenms.ExperimentalSettings method) (pyopenms.MSExperiment method) getSamples() (pyopenms.ExperimentalDesign_SampleSection method) getSampleSection() (pyopenms.ExperimentalDesign method) getSatelliteLossFormula() (pyopenms.Residue method) getScale() (pyopenms.LinearInterpolation method) getScale_0() (pyopenms.BilinearInterpolation method) getScale_1() (pyopenms.BilinearInterpolation method) getScalingFactor() (pyopenms.BiGaussModel method) (pyopenms.EmgModel method) (pyopenms.InterpolationModel method) (pyopenms.IsotopeModel method) getScanDirection() (pyopenms.MassAnalyzer method) getScanLaw() (pyopenms.MassAnalyzer method) getScanMode() (pyopenms.InstrumentSettings method) getScanNumber() (pyopenms.DeconvolvedSpectrum method) (pyopenms.FLASHDeconvAlgorithm static method) (pyopenms.OnDiscThermoRawExperiment method) (pyopenms.PeakGroup method) getScanRate() (pyopenms.MassAnalyzer method) getScanTime() (pyopenms.MassAnalyzer method) getScanWindows() (pyopenms.InstrumentSettings method) getScopePath() (pyopenms.CVMappingRule method) getScore() (pyopenms.PeptideHit method) (pyopenms.ProteinHit method) getScoreNames() (pyopenms.IDScoreSwitcherAlgorithm method) getScores() (pyopenms.MRMFeature method) getScoreType() (pyopenms.PeptideIdentification method) (pyopenms.PercolatorOutfile static method) (pyopenms.ProteinIdentification method) getSearchEngine() (pyopenms.ProteinIdentification method) getSearchEngineAndVersion() (pyopenms.InspectOutfile method) getSearchEngineVersion() (pyopenms.ProteinIdentification method) getSearchParameters() (pyopenms.ProteinIdentification method) getSecondaryIdentifier() (pyopenms.SpectralMatch method) getSectionDescription() (pyopenms.Param method) getSeed() (pyopenms.UniqueIdGenerator static method) getSequence() (pyopenms.IMSElement method) (pyopenms.NASequence method) (pyopenms.OSWPeptidePrecursor method) (pyopenms.PEFFEntry method) (pyopenms.PeptideHit method) (pyopenms.ProteinHit method) getSequenceHeaderFilter() (pyopenms.SequestInfile method) getSequences() (pyopenms.InspectOutfile method) (pyopenms.SequestOutfile method) getShape() (pyopenms.MSImagingRegion method) getShowFragmentIons() (pyopenms.SequestInfile method) getSideChainBasicity() (pyopenms.Residue method) getSigma() (pyopenms.GaussTraceFitter method) getSignalToNoise() (pyopenms.SignalToNoiseEstimatorMeanIterative method) (pyopenms.SignalToNoiseEstimatorMedian method) (pyopenms.SignalToNoiseEstimatorMedianChrom method) getSignificanceThreshold() (pyopenms.PeptideIdentification method) (pyopenms.ProteinIdentification method) getSingleMass() (pyopenms.Adduct method) getSize() (pyopenms.ClusterProxyKD method) (pyopenms.MassTrace method) (pyopenms.MSExperiment method) getSizeOnly() (pyopenms.FeatureFileOptions method) getSkipXMLChecks() (pyopenms.PeakFileOptions method) getSmallestScore() (pyopenms.PosteriorErrorProbabilityModel method) getSMILESString() (pyopenms.SpectralMatch method) getSmoothedIntensities() (pyopenms.MassTrace method) getSNR() (pyopenms.PeakGroup method) getSNRMultiplicationFactor() (pyopenms.PrecalAveragine method) getSoftware() (pyopenms.DataProcessing method) (pyopenms.Instrument method) (pyopenms.TargetedExperiment method) getSortChromatogramsByRT() (pyopenms.PeakFileOptions method) getSortSpectraByMZ() (pyopenms.PeakFileOptions method) getSourceClassification() (pyopenms.ResidueModification method) getSourceClassificationName() (pyopenms.ResidueModification method) getSourceFeatureIndex() (pyopenms.AccurateMassSearchResult method) getSourceFile() (pyopenms.ChromatogramSettings method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) (pyopenms.SpectrumSettings method) getSourceFiles() (pyopenms.ExperimentalSettings method) (pyopenms.MSExperiment method) (pyopenms.TargetedExperiment method) getSparseWindowPercent() (pyopenms.SignalToNoiseEstimatorMedian method) getSpecificity() (pyopenms.EnzymaticDigestion method) (pyopenms.ProteaseDigestion method) (pyopenms.RNaseDigestion method) getSpecificityByName() (pyopenms.EnzymaticDigestion static method) (pyopenms.ProteaseDigestion static method) (pyopenms.RNaseDigestion static method) getSpectra() (pyopenms.InspectInfile method) (pyopenms.MSExperiment method) getSpectraByRT() (pyopenms.SpectrumAccessOpenMS method) (pyopenms.SpectrumAccessOpenMSCached method) (pyopenms.SpectrumAccessOpenMSInMemory method) (pyopenms.SpectrumAccessSqMass method) getSpectraIndex() (pyopenms.CachedMzMLHandler method) (pyopenms.MSDataCachedConsumer method) getSpectraIndicesbyRT() (pyopenms.MzMLSqliteHandler method) getSpectrum() (pyopenms.CachedmzML method) (pyopenms.MSExperiment method) (pyopenms.MSImagingExperiment method) (pyopenms.NucleicAcidSpectrumGenerator method) (pyopenms.OnDiscImzMLExperiment method) (pyopenms.OnDiscMSExperiment method) (pyopenms.OnDiscThermoRawExperiment method) (pyopenms.TheoreticalSpectrumGenerator method) getSpectrumAccessOpenMSPtr() (pyopenms.SimpleOpenMSSpectraFactory static method) getSpectrumAlignment() (pyopenms.SpectrumAlignment method) getSpectrumAlignmentFastCharge() (pyopenms.OPXLSpectrumProcessingAlgorithms static method) getSpectrumAlignmentSimple() (pyopenms.OPXLSpectrumProcessingAlgorithms static method) getSpectrumAtCoord() (pyopenms.OnDiscImzMLExperiment method) getSpectrumById() (pyopenms.IndexedMzMLHandler method) (pyopenms.OnDiscMSExperiment method) (pyopenms.SpectrumAccessOpenMS method) (pyopenms.SpectrumAccessOpenMSCached method) (pyopenms.SpectrumAccessOpenMSInMemory method) (pyopenms.SpectrumAccessSqMass method) getSpectrumByNativeId() (pyopenms.OnDiscMSExperiment method) (pyopenms.OnDiscThermoRawExperiment method) getSpectrumGenerationIssues() (pyopenms.Peptidoform method) (pyopenms.PeptidoformIon method) (pyopenms.ProForma static method) getSpectrumGenerationIssuesIon() (pyopenms.ProForma static method) getSpectrumIndex() (pyopenms.MSImagingGeometry method) getSpectrumIndexByScanNumber() (pyopenms.OnDiscThermoRawExperiment method) getSpectrumMetadata() (pyopenms.OnDiscMSExperiment method) (pyopenms.OnDiscThermoRawExperiment method) getSpectrumMetaData() (pyopenms.SpectrumMetaDataLookup static method) getSpectrumMSLevel() (pyopenms.OnDiscMSExperiment method) (pyopenms.OnDiscThermoRawExperiment method) getSpectrumNativeID() (pyopenms.OnDiscThermoRawExperiment method) getSpectrumPeaks() (pyopenms.OnDiscThermoRawExperiment method) getSpectrumPtr() (pyopenms.SwathMap method) getSpectrumReference() (pyopenms.PeptideIdentification method) getSpectrumRT() (pyopenms.OnDiscMSExperiment method) (pyopenms.OnDiscThermoRawExperiment method) getSqlSourceFile() (pyopenms.OSWData method) getStandardFeatureSet() (pyopenms.PercolatorInfile static method) getStart() (pyopenms.PeptideEvidence method) getState() (pyopenms.Sample method) getStatistics() (pyopenms.PeptideAndProteinQuant method) (pyopenms.TransformationDescription method) getStringDataArrays() (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) getSubordinates() (pyopenms.Feature method) (pyopenms.MRMFeature method) getSubsamples() (pyopenms.Sample method) getSubsections() (pyopenms.AbsoluteQuantitation method) (pyopenms.AccurateMassSearchEngine method) (pyopenms.AScore method) (pyopenms.BaseGroupFinder method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.Biosaur2Algorithm method) (pyopenms.DefaultParamHandler method) (pyopenms.DIAScoring method) (pyopenms.ElutionModelFitter method) (pyopenms.ElutionPeakDetection method) (pyopenms.EmgFitter1D method) (pyopenms.EmgGradientDescent method) (pyopenms.FalseDiscoveryRate method) (pyopenms.FeatureDeconvolution method) (pyopenms.FeatureDistance method) (pyopenms.FeatureFinderAlgorithmMetaboIdent method) (pyopenms.FeatureFinderAlgorithmPicked method) (pyopenms.FeatureFinderIdentificationAlgorithm method) (pyopenms.FeatureFinderMultiplexAlgorithm method) (pyopenms.FeatureFindingMetabo method) (pyopenms.FeatureGroupingAlgorithm method) (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.FeatureGroupingAlgorithmLabeled method) (pyopenms.FeatureGroupingAlgorithmQT method) (pyopenms.FeatureGroupingAlgorithmUnlabeled method) (pyopenms.FIAMSDataProcessor method) (pyopenms.Fitter1D method) (pyopenms.FLASHDeconvAlgorithm method) (pyopenms.GaussFilter method) (pyopenms.GNPSMGFFile method) (pyopenms.IDDecoyProbability method) (pyopenms.IDMapper method) (pyopenms.IDRipper method) (pyopenms.IDScoreSwitcherAlgorithm method) (pyopenms.IsobaricChannelExtractor method) (pyopenms.IsobaricQuantifier method) (pyopenms.IsobaricQuantitationMethod method) (pyopenms.IsotopeLabelingMDVs method) (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.LabeledPairFinder method) (pyopenms.LevMarqFitter1D method) (pyopenms.LinearResamplerAlign method) (pyopenms.LowessSmoothing method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) (pyopenms.MascotGenericFile method) (pyopenms.MassDecompositionAlgorithm method) (pyopenms.MasstraceCorrelator method) (pyopenms.MassTraceDetection method) (pyopenms.MetaboliteFeatureDeconvolution method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.ModifiedSincSmoother method) (pyopenms.MorphologicalFilter method) (pyopenms.MRMDecoy method) (pyopenms.MRMFeatureFilter method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MRMMapping method) (pyopenms.MRMTransitionGroupPicker method) (pyopenms.MSPFile method) (pyopenms.MSPGenericFile method) (pyopenms.MultiplexDeltaMassesGenerator method) (pyopenms.MultiplexResolverAlgorithm method) (pyopenms.NLargest method) (pyopenms.Normalizer method) (pyopenms.NucleicAcidSpectrumGenerator method) (pyopenms.OpenPepXLAlgorithm method) (pyopenms.PeakIntegrator method) (pyopenms.PeakPickerChromatogram method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIM method) (pyopenms.PeakPickerIterative method) (pyopenms.PeptideAndProteinQuant method) (pyopenms.PeptideIndexing method) (pyopenms.Percolator method) (pyopenms.PipEchoAlgorithm method) (pyopenms.PosteriorErrorProbabilityModel method) (pyopenms.ProSEAlgorithm method) (pyopenms.QTClusterFinder method) (pyopenms.RankScaler method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SignalToNoiseEstimatorMeanIterative method) (pyopenms.SignalToNoiseEstimatorMedian method) (pyopenms.SignalToNoiseEstimatorMedianChrom method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.SimpleTSGXLMS method) (pyopenms.SiriusExportAlgorithm method) (pyopenms.SpectralDeconvolution method) (pyopenms.SpectraMerger method) (pyopenms.SpectrumAlignment method) (pyopenms.SpectrumAlignmentScore method) (pyopenms.SpectrumAnnotator method) (pyopenms.SqrtScaler method) (pyopenms.StablePairFinder method) (pyopenms.SwathMapMassCorrection method) (pyopenms.TargetedSpectraExtractor method) (pyopenms.TheoreticalSpectrumGenerator method) (pyopenms.TheoreticalSpectrumGeneratorXLMS method) (pyopenms.ThresholdMower method) (pyopenms.TMTEighteenPlexQuantitationMethod method) (pyopenms.TMTElevenPlexQuantitationMethod method) (pyopenms.TMTSixPlexQuantitationMethod method) (pyopenms.TMTSixteenPlexQuantitationMethod method) (pyopenms.TMTTenPlexQuantitationMethod method) (pyopenms.TransitionListEvidenceFilter method) (pyopenms.WindowMower method) (pyopenms.XFDRAlgorithm method) getSubsequence() (pyopenms.AASequence method) (pyopenms.NASequence method) getSuffix() (pyopenms.AASequence method) (pyopenms.NASequence method) getSumFormula() (pyopenms.SpectralMatch method) getSymbol() (pyopenms.Element method) getSynonyms() (pyopenms.DigestionEnzyme method) (pyopenms.DigestionEnzymeProtein method) (pyopenms.DigestionEnzymeRNA method) (pyopenms.Residue method) (pyopenms.ResidueModification method) getSystemParameters() (pyopenms.File static method) (pyopenms.SystemSettings static method) getTag() (pyopenms.Tagger method) getTagCount() (pyopenms.InspectInfile method) getTags() (pyopenms.Param method) getTargetCVTerms() (pyopenms.TargetedExperiment method) getTargetDecoyAUC() (pyopenms.PosteriorErrorProbabilityModel method) getTargetDecoyIncorrectFraction() (pyopenms.PosteriorErrorProbabilityModel method) getTargetDecoyType() (pyopenms.PeakGroup method) getTaxon() (pyopenms.XTandemInfile method) getTaxonomyFilename() (pyopenms.XTandemInfile method) getTempDirectory() (pyopenms.File static method) (pyopenms.SystemSettings static method) getTemperature() (pyopenms.HPLC method) getTemporaryFile() (pyopenms.File static method) (pyopenms.TempFiles static method) getTerm() (pyopenms.ControlledVocabulary method) getTermByName() (pyopenms.ControlledVocabulary method) getTermName() (pyopenms.CVMappingTerm method) getTermSpecificity() (pyopenms.ResidueModification method) (pyopenms.Ribonucleotide method) getTermSpecificityName() (pyopenms.ResidueModification method) getTheoreticalmaxPosition() (pyopenms.MassTraces method) getThreeLetterCode() (pyopenms.Residue method) getThreePrimeGain() (pyopenms.DigestionEnzymeRNA method) getThreePrimeMod() (pyopenms.NASequence method) getThreshold() (pyopenms.FineIsotopePatternGenerator method) getTime() (pyopenms.DateTime method) (pyopenms.VersionInfo static method) getTimeArray() (pyopenms.Chromatogram method) (pyopenms.OSChromatogram method) getTimeComponents() (pyopenms.DateTime method) getTimepoints() (pyopenms.Gradient method) getTOFTotalPathLength() (pyopenms.MassAnalyzer method) getTolerances() (pyopenms.FLASHDeconvAlgorithm method) getTotalProbability() (pyopenms.FineIsotopePatternGenerator method) getTraceLength() (pyopenms.MassTrace method) getTransformationModel() (pyopenms.AbsoluteQuantitationMethod method) getTransformationModelParams() (pyopenms.AbsoluteQuantitationMethod method) getTransformations() (pyopenms.FeatureFinderAlgorithmMetaboIdent method) getTransition() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.OSWData method) getTransitionGroupID() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) getTransitionIDs() (pyopenms.OSWPeakGroup method) getTransitions() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.LightTargetedExperiment method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.TargetedExperiment method) getTransitionsMuteable() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) getType() (pyopenms.FileHandler static method) (pyopenms.IonDetector method) (pyopenms.MassAnalyzer method) (pyopenms.MSSpectrum method) (pyopenms.OSWTransition method) (pyopenms.ProteinProteinCrossLink method) (pyopenms.SpectrumSettings method) getTypeByContent() (pyopenms.FileHandler static method) getTypeByFileName() (pyopenms.FileHandler static method) getULOD() (pyopenms.AbsoluteQuantitationMethod method) getULOQ() (pyopenms.AbsoluteQuantitationMethod method) getUnassignedPeptideIdentifications() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) getUnchargedMass() (pyopenms.LogMzPeak method) (pyopenms.Precursor method) getUniModAccession() (pyopenms.ResidueModification method) getUniModRecordId() (pyopenms.ResidueModification method) getUniqueId() (pyopenms.BaseFeature method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusMap method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.FeatureMap method) (pyopenms.MRMFeature method) (pyopenms.RichPeak2D method) (pyopenms.UniqueIdGenerator static method) (pyopenms.UniqueIdInterface method) getUniqueName() (pyopenms.File static method) getUnit() (pyopenms.CVTerm method) (pyopenms.MetaInfoRegistry method) getUpperRTBound() (pyopenms.GaussTraceFitter method) getURL() (pyopenms.ContactPerson method) getUserDirectory() (pyopenms.File static method) (pyopenms.SystemSettings static method) getUseTerm() (pyopenms.CVMappingTerm method) getUseTermName() (pyopenms.CVMappingTerm method) getValidStrings() (pyopenms.Param method) getValidXWeights() (pyopenms.TransformationModelBSpline method) (pyopenms.TransformationModelInterpolated method) (pyopenms.TransformationModelLinear method) (pyopenms.TransformationModelLowess method) getValidYWeights() (pyopenms.TransformationModelBSpline method) (pyopenms.TransformationModelInterpolated method) (pyopenms.TransformationModelLinear method) (pyopenms.TransformationModelLowess method) getValue() (pyopenms.CVTerm method) (pyopenms.DistanceMatrix method) (pyopenms.GaussTraceFitter method) (pyopenms.MatrixDouble method) (pyopenms.MetaInfo method) (pyopenms.Param method) getValueType() (pyopenms.Param method) getVariableModificationNames() (pyopenms.ModificationDefinitionsSet method) getVariableModifications() (pyopenms.ModificationDefinitionsSet method) getVariantSequences() (pyopenms.PEFFEntry method) getVASM830103() (pyopenms.AAIndex static method) getVendor() (pyopenms.Instrument method) getVersion() (pyopenms.ConsensusXMLFile method) (pyopenms.FeatureXMLFile method) (pyopenms.IdXMLFile method) (pyopenms.MascotXMLFile method) (pyopenms.MzDataFile method) (pyopenms.MzIdentMLFile method) (pyopenms.MzMLFile method) (pyopenms.MzXMLFile method) (pyopenms.OMSSAXMLFile method) (pyopenms.ParamXMLFile method) (pyopenms.PepXMLFile method) (pyopenms.PepXMLFileMascot method) (pyopenms.ProtXMLFile method) (pyopenms.Software method) (pyopenms.TraMLFile method) (pyopenms.TransformationXMLFile method) (pyopenms.UnimodXMLFile method) (pyopenms.VersionInfo static method) (pyopenms.XMLFile method) (pyopenms.XQuestResultXMLFile method) (pyopenms.XTandemInfile method) (pyopenms.XTandemXMLFile method) getVersionStruct() (pyopenms.VersionInfo static method) getVLossFormula() (pyopenms.Residue method) getVolume() (pyopenms.Sample method) getWantedRecords() (pyopenms.InspectOutfile method) getWeight() (pyopenms.CalibrationData method) (pyopenms.IMSWeights method) getWidth() (pyopenms.BaseFeature method) (pyopenms.ConsensusFeature method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.IonImage method) (pyopenms.MRMFeature method) (pyopenms.MSImagingGeometry method) getWILM950102() (pyopenms.AAIndex static method) getWriteIndex() (pyopenms.PeakFileOptions method) getWriteSupplementalData() (pyopenms.PeakFileOptions method) getXCoord() (pyopenms.QTCluster method) getXLinkIonSpectrum() (pyopenms.SimpleTSGXLMS method) (pyopenms.TheoreticalSpectrumGeneratorXLMS method) getXRefTypeName() (pyopenms.ControlledVocabulary.CVTerm static method) getXTandemID() (pyopenms.DigestionEnzymeProtein method) getYCoord() (pyopenms.QTCluster method) getZoomScan() (pyopenms.InstrumentSettings method) getZstdCompression() (pyopenms.PeakFileOptions method) GLOBAL (pyopenms.BrukerTimsFile.Config.PressureCompensation attribute) GLOBAL_MOD (pyopenms.ProForma.ConversionIssueType attribute) GlycanComposition (class in pyopenms) GlycanStructure (class in pyopenms) GlycanStructure.Node (class in pyopenms) GNO (pyopenms.ProForma.CvDatabase attribute) GNPSMetaValueFile (class in pyopenms) GNPSMGFFile (class in pyopenms) GNPSQuantificationFile (class in pyopenms) Gradient (class in pyopenms) GRAVITATIONAL_CONSTANT (in module pyopenms.Constants) GREATER_EQUAL (pyopenms.DataFilters attribute) (pyopenms.DataFilters.FilterOperation attribute) GREEDY2D (pyopenms.BrukerTimsFile.Config.CentroidAlgo attribute) GridBasedCluster (class in pyopenms) gridHeight() (pyopenms.OnDiscImzMLExperiment method) gridWidth() (pyopenms.OnDiscImzMLExperiment method) group() (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.FeatureGroupingAlgorithmLabeled method) (pyopenms.FeatureGroupingAlgorithmQT method) (pyopenms.FeatureGroupingAlgorithmUnlabeled method) (pyopenms.PipEchoAlgorithm method) gt() (pyopenms.ParquetFilter method) GUI (pyopenms.AverageLinkage attribute) (pyopenms.CachedMzMLHandler attribute) (pyopenms.ChromatogramExtractor attribute) (pyopenms.ChromatogramExtractorAlgorithm attribute) (pyopenms.ConfidenceScoring attribute) (pyopenms.DTA2DFile attribute) (pyopenms.FASTAFile attribute) (pyopenms.GaussFilter attribute) (pyopenms.InternalCalibration attribute) (pyopenms.LogType attribute) (pyopenms.MascotGenericFile attribute) (pyopenms.ModifiedSincSmoother attribute) (pyopenms.MorphologicalFilter attribute) (pyopenms.MRMAssay attribute) (pyopenms.MS2File attribute) (pyopenms.MSDataCachedConsumer attribute) (pyopenms.PeakMapExtractor attribute) (pyopenms.PEFFFile attribute) (pyopenms.ProgressLogger attribute) (pyopenms.ProgressLogger.LogType attribute) (pyopenms.SavitzkyGolayFilter attribute) (pyopenms.SwathFile attribute) (pyopenms.TransitionPQPFile attribute) (pyopenms.TransitionTSVFile attribute) GUY (pyopenms.HydrophobicityScaleMethod attribute) GZ (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) GZIP (pyopenms.ParquetWriteConfig attribute) (pyopenms.ParquetWriteConfig.Compression attribute) H H (pyopenms.IsotopeModel attribute) (pyopenms.IsotopeModel.Averagines attribute) handlePTMs() (pyopenms.InspectInfile method) (pyopenms.SequestInfile method) HARDKLOER (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) has() (pyopenms.AASequence method) (pyopenms.CrossLinksDB method) (pyopenms.ModificationsDB method) has_annotation_identifiers (pyopenms.PEFFDatabaseMetadata property) has_mobility (pyopenms.FileInfo.RangeSet property) has_unit_accession (pyopenms.SemanticValidator_CVTerm property) has_unit_name (pyopenms.SemanticValidator_CVTerm property) has_value (pyopenms.SemanticValidator_CVTerm property) hasCalibrationWarning() (pyopenms.PosteriorErrorProbabilityModel method) hasCharge() (pyopenms.Compound method) (pyopenms.Peptide method) (pyopenms.TraMLProduct method) hasChromatogram() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) hasCompound() (pyopenms.TargetedExperiment method) hasCTerminalModification() (pyopenms.AASequence method) hasCVReference() (pyopenms.CVMappings method) hasCVTerm() (pyopenms.Compound method) (pyopenms.Configuration method) (pyopenms.Contact method) (pyopenms.CVTermList method) (pyopenms.CVTermListInterface method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Peptide method) (pyopenms.Precursor method) (pyopenms.Prediction method) (pyopenms.Product method) (pyopenms.Protein method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.Software method) (pyopenms.SourceFile method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TraMLProduct method) hasElement() (pyopenms.ElementDB method) (pyopenms.EmpiricalFormula method) hasEnzyme() (pyopenms.ProteaseDB method) (pyopenms.RNaseDB method) hasFactor() (pyopenms.ExperimentalDesign_SampleSection method) hasFilters() (pyopenms.PeakFileOptions method) hasFivePrimeMod() (pyopenms.NASequence method) hasIdentifier() (pyopenms.IdentifierMSRunMapper method) hasIMRange() (pyopenms.PeakFileOptions method) hasIntensityRange() (pyopenms.FeatureFileOptions method) (pyopenms.PeakFileOptions method) hasInterpretation() (pyopenms.USI method) hasInvalidUniqueId() (pyopenms.BaseFeature method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusMap method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.FeatureMap method) (pyopenms.MRMFeature method) (pyopenms.RichPeak2D method) (pyopenms.UniqueIdInterface method) hasMSLevels() (pyopenms.PeakFileOptions method) hasMZ() (pyopenms.PeptideIdentification method) hasMZRange() (pyopenms.FeatureFileOptions method) (pyopenms.PeakFileOptions method) hasName() (pyopenms.IMSAlphabet method) hasNeutralLoss() (pyopenms.Residue method) (pyopenms.ResidueModification method) hasNTerminalModification() (pyopenms.AASequence method) hasNTermNeutralLosses() (pyopenms.Residue method) hasPeptide() (pyopenms.TargetedExperiment method) hasPixel() (pyopenms.IonImage method) (pyopenms.MSImagingExperiment method) (pyopenms.MSImagingGeometry method) hasPrecursorChromatogram() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) hasPrecursorCVTerms() (pyopenms.ReactionMonitoringTransition method) hasPrecursorMZRange() (pyopenms.PeakFileOptions method) hasPrediction() (pyopenms.ReactionMonitoringTransition method) hasPrefix() (pyopenms.AASequence method) hasProtein() (pyopenms.TargetedExperiment method) hasRegEx() (pyopenms.ProteaseDB method) hasResidue() (pyopenms.ResidueDB method) hasRetentionTime() (pyopenms.Compound method) (pyopenms.Peptide method) hasRT() (pyopenms.PeptideIdentification method) hasRTRange() (pyopenms.FeatureFileOptions method) (pyopenms.PeakFileOptions method) hasSample() (pyopenms.ExperimentalDesign_SampleSection method) hasSatelliteLoss() (pyopenms.Residue method) hasSubsequence() (pyopenms.AASequence method) hasSuffix() (pyopenms.AASequence method) hasTag() (pyopenms.Param method) hasTermWithName() (pyopenms.ControlledVocabulary method) hasThreePrimeMod() (pyopenms.NASequence method) hasTransition() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) hasUnit() (pyopenms.CVTerm method) hasValidExtension() (pyopenms.FileHandler static method) hasValidLimits() (pyopenms.PeptideEvidence method) hasValidUniqueId() (pyopenms.BaseFeature method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusMap method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.FeatureMap method) (pyopenms.MRMFeature method) (pyopenms.RichPeak2D method) (pyopenms.UniqueIdInterface method) hasValue() (pyopenms.CVTerm method) hasVLoss() (pyopenms.Residue method) HCD (pyopenms.Precursor.ActivationMethod attribute) (pyopenms.TheoreticalGlycanSpectrumGenerator.FragmentationMethod attribute) HCID (pyopenms.Precursor.ActivationMethod attribute) headerMatches() (pyopenms.FASTAEntry method) height (pyopenms.PI_PeakArea property) (pyopenms.PI_PeakBackground property) high performance liquid chromatography HIGH_RESOLUTION (pyopenms.IDFreeMassErrorEstimator.FragmentResolutionRegime attribute) higher_is_better (pyopenms.PeptideHit_AnalysisResult property) HILL_BASED (pyopenms.BrukerTimsFile.Config.CentroidAlgo attribute) HN (pyopenms.IonSource.IonizationMethod attribute) HOPP_WOODS (pyopenms.HydrophobicityScaleMethod attribute) HPINS (pyopenms.RetentionTime attribute) (pyopenms.RetentionTime.RTType attribute) HPLC (class in pyopenms) HTML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) hull_points (pyopenms.PI_PeakArea property) hybrid_supported (pyopenms.TransitionListEvidenceFilter_Result property) HydrophobicityScaleMethod (class in pyopenms) HyperScore (class in pyopenms) HYPOTHETICAL (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.SourceClassification attribute) I ibd_file_path (pyopenms.ImzMLMeta property) ibd_md5 (pyopenms.ImzMLMeta property) ibd_sha1 (pyopenms.ImzMLMeta property) IBSpectraFile (class in pyopenms) ICP (pyopenms.IonSource.IonizationMethod attribute) id (pyopenms.ChannelInfo property) (pyopenms.Compound property) (pyopenms.Contact property) (pyopenms.ControlledVocabulary.CVTerm property) (pyopenms.CV property) (pyopenms.ExtractionCoordinates property) (pyopenms.IsobaricChannelInformation property) (pyopenms.LightCompound property) (pyopenms.LightProtein property) (pyopenms.OSChromatogramMeta property) (pyopenms.OSSpectrumMeta property) (pyopenms.Peptide property) (pyopenms.Protein property) (pyopenms.Publication property) (pyopenms.TargetedExperiment_Instrument property) id1 (pyopenms.PEFFDisulfideBond property) id2 (pyopenms.PEFFDisulfideBond property) ID_MERGE_INDEX (pyopenms.IDRipper attribute) (pyopenms.IDRipper.OriginAnnotationFormat attribute) (pyopenms.OriginAnnotationFormat attribute) IDConflictResolverAlgorithm (class in pyopenms) IDDecoyProbability (class in pyopenms) ident (pyopenms.FileInfo.Result property) IDENTIFICATION (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) IDENTIFICATION_MAPPING (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) IdentificationData (class in pyopenms) identified (pyopenms.IDMapper_PeptideIdentificationListState property) identifier (pyopenms.FASTAEntry property) (pyopenms.FileInfo.MapColumn property) (pyopenms.Label property) (pyopenms.MetaboTargetedTargetDecoy_MetaboTargetDecoyMassMapping property) (pyopenms.PEFFEntry property) IdentifierMSRunMapper (class in pyopenms) identifying_transition (pyopenms.LightTransition property) IDFilter (class in pyopenms) IDFreeMassErrorEstimator (class in pyopenms) IDFreeMassErrorEstimator.Diagnostics (class in pyopenms) IDFreeMassErrorEstimator.FragmentResolutionRegime (class in pyopenms) IDFreeMassErrorEstimator.Parameters (class in pyopenms) IDFreeMassErrorEstimator.Result (class in pyopenms) IDFreeMassErrorEstimator.RobustError (class in pyopenms) IDFreeMassErrorEstimator.ToleranceSuggestion (class in pyopenms) IDMapper (class in pyopenms) IDMapper.Measure (class in pyopenms) IDMapper_PeptideIdentificationListState (class in pyopenms) IDPARQUET (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) IDRipper (class in pyopenms) IDRipper.OriginAnnotationFormat (class in pyopenms) ids_per_element (pyopenms.FileInfo.FeatureInfo property) IDScoreSwitcherAlgorithm (class in pyopenms) IDSwitchResult (class in pyopenms) IDType (class in pyopenms) idx_feat (pyopenms.OSWIndexTrace property) idx_pep (pyopenms.OSWIndexTrace property) idx_prot (pyopenms.OSWIndexTrace property) idx_trans (pyopenms.OSWIndexTrace property) IDXML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) IdXMLFile (class in pyopenms) ILLEGAL_PARAMETERS (pyopenms.OpenPepXLAlgorithm.ExitCodes attribute) (pyopenms.PeptideIndexing.ExitCodes attribute) (pyopenms.ProSEAlgorithm attribute) (pyopenms.ProSEAlgorithm.ProSEAlgorithm_ExitCodes attribute) (pyopenms.SimpleSearchEngineAlgorithm.ExitCodes attribute) (pyopenms.XFDRAlgorithm.ExitCodes attribute) ILPDCWrapper (class in pyopenms) IM_CENTROIDED (pyopenms.IMPeakType attribute) im_delta (pyopenms.OpenSwath_Scores property) im_delta_score (pyopenms.OpenSwath_Scores property) im_drift (pyopenms.OpenSwath_Scores property) im_drift_left (pyopenms.OpenSwath_Scores property) im_drift_right (pyopenms.OpenSwath_Scores property) im_drift_weighted (pyopenms.OpenSwath_Scores property) im_extraction_window (pyopenms.OSW_ChromExtractParams property) im_ind_contrast_coelution (pyopenms.OpenSwath_Scores property) im_ind_contrast_shape (pyopenms.OpenSwath_Scores property) im_ind_sum_contrast_coelution (pyopenms.OpenSwath_Scores property) im_ind_sum_contrast_shape (pyopenms.OpenSwath_Scores property) im_log_intensity (pyopenms.OpenSwath_Scores property) im_max (pyopenms.BrukerTimsFile.Config property) im_min (pyopenms.BrukerTimsFile.Config property) im_ms1_contrast_coelution (pyopenms.OpenSwath_Scores property) im_ms1_contrast_shape (pyopenms.OpenSwath_Scores property) im_ms1_delta (pyopenms.OpenSwath_Scores property) im_ms1_delta_score (pyopenms.OpenSwath_Scores property) im_ms1_drift (pyopenms.OpenSwath_Scores property) im_ms1_sum_contrast_coelution (pyopenms.OpenSwath_Scores property) im_ms1_sum_contrast_shape (pyopenms.OpenSwath_Scores property) IM_PEAK (pyopenms.IMFormat attribute) IM_PROFILE (pyopenms.IMPeakType attribute) IM_SPECTRUM (pyopenms.IMFormat attribute) im_xcorr_coelution_score (pyopenms.OpenSwath_Scores property) im_xcorr_shape_score (pyopenms.OpenSwath_Scores property) imag (pyopenms.Base64.ByteOrder attribute) (pyopenms.BasicProteinInferenceAlgorithm.AggregationMethod attribute) (pyopenms.BoundaryCondition attribute) (pyopenms.BSpline2d.BoundaryCondition attribute) (pyopenms.ChromatogramSettings.ChromatogramType attribute) (pyopenms.CombinationsLogic attribute) (pyopenms.ConsensusMapNormalizerAlgorithmMedian.NormalizationMethod attribute) (pyopenms.ControlledVocabulary.CVTerm.XRefType attribute) (pyopenms.DRangeIntersection attribute) (pyopenms.DriftTimeUnit attribute) (pyopenms.EntrapmentEvaluation.Kind attribute) (pyopenms.EntrapmentEvaluation.Level attribute) (pyopenms.EnzymaticDigestion.Specificity attribute) (pyopenms.FeatureDeconvolution.CHARGEMODE attribute) (pyopenms.FileType attribute) (pyopenms.FileTypes.FileType attribute) (pyopenms.HydrophobicityScaleMethod attribute) (pyopenms.IDMapper.Measure attribute) (pyopenms.IDRipper.OriginAnnotationFormat attribute) (pyopenms.IDType attribute) (pyopenms.IsotopeDistribution.Sorted attribute) (pyopenms.ITRAQ_TYPES attribute) (pyopenms.ItraqConstants.ITRAQ_TYPES attribute) (pyopenms.LogType attribute) (pyopenms.Measure attribute) (pyopenms.MetaboliteFeatureDeconvolution.CHARGEMODE attribute) (pyopenms.Method attribute) (pyopenms.MSNumpressCoder.NumpressCompression attribute) (pyopenms.MultipleTesting.LfdrTransform attribute) (pyopenms.MultipleTesting.Pi0Method attribute) (pyopenms.MzPAFDeltaUnit attribute) (pyopenms.MzPAFErrorCode attribute) (pyopenms.MzPAFIonSeries attribute) (pyopenms.NaNPolicy attribute) (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.NormalizationMethod attribute) (pyopenms.OpenMSOSInfo.OpenMS_Architecture attribute) (pyopenms.OpenMSOSInfo.OpenMS_OS attribute) (pyopenms.OpenPepXLAlgorithm.ExitCodes attribute) (pyopenms.OPXLDataStructs.PeptidePosition attribute) (pyopenms.OPXLDataStructs.ProteinProteinCrossLinkType attribute) (pyopenms.OriginAnnotationFormat attribute) (pyopenms.ParquetWriteConfig.Compression attribute) (pyopenms.PeakGroup.TargetDecoyType attribute) (pyopenms.PEFFDatabaseMetadata.SequenceType attribute) (pyopenms.PEFFModification.ModificationType attribute) (pyopenms.PeptideIndexing.ExitCodes attribute) (pyopenms.PercolatorOutfile.ScoreType attribute) (pyopenms.ProForma.ConversionIssueType attribute) (pyopenms.ProForma.ConversionPolicy attribute) (pyopenms.ProForma.CvDatabase attribute) (pyopenms.ProForma.WriteMode attribute) (pyopenms.ProgressLogger.LogType attribute) (pyopenms.ProSEAlgorithm.ProSEAlgorithm_ExitCodes attribute) (pyopenms.ProteomicsPkaScale attribute) (pyopenms.QuotingMethod attribute) (pyopenms.RankData.Method attribute) (pyopenms.RankData.NaNPolicy attribute) (pyopenms.RequirementLevel attribute) (pyopenms.Residue.ResidueType attribute) (pyopenms.ResidueModification.Provenance attribute) (pyopenms.ResidueModification.SourceClassification attribute) (pyopenms.ResidueModification.TermSpecificity attribute) (pyopenms.Ribonucleotide.TermSpecificityNuc attribute) (pyopenms.Scores.IDType attribute) (pyopenms.SIDE attribute) (pyopenms.SimpleSearchEngineAlgorithm.ExitCodes attribute) (pyopenms.UnitType attribute) (pyopenms.USI.IndexType attribute) (pyopenms.ValueType attribute) (pyopenms.XFDRAlgorithm.ExitCodes attribute) (pyopenms.XTandemInfile.ErrorUnit attribute) (pyopenms.XTandemInfile.MassType attribute) imaging_mode (pyopenms.ImzMLMeta property) IMD (pyopenms.Precursor.ActivationMethod attribute) IMFormat (class in pyopenms) imFormatToString() (pyopenms.IMTypes static method) IMMONIUM (pyopenms.MzPAFIonSeries attribute) immonium_residue (pyopenms.MzPAFAnnotation property) IMPeakType (class in pyopenms) imPeakTypeToString() (pyopenms.IMTypes static method) importFromParquet() (pyopenms.ConsensusMapArrowIO static method) (pyopenms.FeatureMapArrowIO static method) (pyopenms.ProteinIdentificationArrowIO static method) importProteinGroupsFromParquet() (pyopenms.ProteinIdentificationArrowIO static method) importProteinsFromParquet() (pyopenms.ProteinIdentificationArrowIO static method) importSearchParamsFromParquet() (pyopenms.ProteinIdentificationArrowIO static method) IMSAlphabet (class in pyopenms) IMSDataConsumer (class in pyopenms) IMSElement (class in pyopenms) IMSIsotopeDistribution (class in pyopenms) IMSIsotopeDistribution_Peak (class in pyopenms) IMSWeights (class in pyopenms) IMTypes (class in pyopenms) IMZML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) ImzMLAuxArrayIndex (class in pyopenms) ImzMLDataType (class in pyopenms) ImzMLFile (class in pyopenms) ImzMLMeta (class in pyopenms) ImzMLSpectrumIndex (class in pyopenms) in_() (pyopenms.ParquetFilter method) IncludeExcludeTarget (class in pyopenms) INCOMPATIBLE_INPUT_DATA (pyopenms.OpenPepXLAlgorithm.ExitCodes attribute) inconsistent_score_direction (pyopenms.UnresolvedIdentifications property) index (pyopenms.ImzMLSpectrumIndex property) (pyopenms.MassFeature_FDHS property) (pyopenms.OSChromatogramMeta property) (pyopenms.OSSpectrumMeta property) INDEX (pyopenms.USI.IndexType attribute) index2key() (pyopenms.LinearInterpolation method) index2key_0() (pyopenms.BilinearInterpolation method) index2key_1() (pyopenms.BilinearInterpolation method) index_checked (pyopenms.FileInfo.ValidationInfo property) index_valid (pyopenms.FileInfo.ValidationInfo property) indexed_chromatograms (pyopenms.FileInfo.ValidationInfo property) indexed_spectra (pyopenms.FileInfo.ValidationInfo property) IndexedMzMLDecoder (class in pyopenms) IndexedMzMLFileLoader (class in pyopenms) IndexedMzMLHandler (class in pyopenms) indexTypeFromString() (pyopenms.USI static method) indexTypeToString() (pyopenms.USI static method) INDUCTIVEDETECTOR (pyopenms.IonDetector.Type attribute) INDUCTIVELYCOUPLEDPLASMA (pyopenms.IonSource.InletType attribute) inferCleavageSensitiveMods() (pyopenms.RNaseDigestion method) inferFromPeptides() (pyopenms.ModificationDefinitionsSet method) inferPosteriorProbabilities() (pyopenms.BayesianProteinInferenceAlgorithm method) InfoTag (class in pyopenms) INFUSION (pyopenms.IonSource.InletType attribute) INI (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) init() (pyopenms.AccurateMassSearchEngine method) (pyopenms.SignalToNoiseEstimatorMeanIterative method) (pyopenms.SignalToNoiseEstimatorMedian method) (pyopenms.SignalToNoiseEstimatorMedianChrom method) initialize() (pyopenms.ConfidenceScoring method) (pyopenms.OpenSwathScoring method) initializeCluster() (pyopenms.QTCluster method) initializeGlm() (pyopenms.ConfidenceScoring method) initializeLookup() (pyopenms.MascotXMLFile static method) initPlots() (pyopenms.PosteriorErrorProbabilityModel method) INLETNULL (pyopenms.IonSource.InletType attribute) inletTypeToString() (pyopenms.IonSource static method) INPUT_FILE_EMPTY (pyopenms.ProSEAlgorithm attribute) (pyopenms.ProSEAlgorithm.ProSEAlgorithm_ExitCodes attribute) (pyopenms.SimpleSearchEngineAlgorithm.ExitCodes attribute) insert() (pyopenms.ConsensusFeature method) (pyopenms.IsotopeDistribution method) (pyopenms.Param method) (pyopenms.ParamNode method) insertCalibrationPoint() (pyopenms.CalibrationData method) insertHit() (pyopenms.PeptideIdentification method) (pyopenms.ProteinIdentification method) insertIndistinguishableProteins() (pyopenms.ProteinIdentification method) insertProteinGroup() (pyopenms.ProteinIdentification method) Inside (pyopenms.DRangeIntersection attribute) INSOURCE (pyopenms.Precursor.ActivationMethod attribute) InspectInfile (class in pyopenms) InspectOutfile (class in pyopenms) install Instrument (class in pyopenms) Instrument.IonOpticsType (class in pyopenms) instrument_methods (pyopenms.ThermoRawFileOptions property) instrument_model (pyopenms.FileInfo.ExperimentMeta property) instrument_name (pyopenms.FileInfo.ExperimentMeta property) (pyopenms.FileInfo.PeakInfo property) instrument_ref (pyopenms.Configuration property) instrument_vendor (pyopenms.FileInfo.ExperimentMeta property) InstrumentSettings (class in pyopenms) InstrumentSettings.ScanMode (class in pyopenms) INT32 (pyopenms.ImzMLDataType attribute) INT64 (pyopenms.ImzMLDataType attribute) int_arrays (pyopenms.FileInfo.PeakInfo property) int_compressed (pyopenms.ImzMLSpectrumIndex property) int_data_type (pyopenms.ImzMLMeta property) int_length (pyopenms.ImzMLSpectrumIndex property) INT_LIST (pyopenms.DataType attribute) (pyopenms.DataValue attribute) (pyopenms.ParamValue attribute) (pyopenms.ValueType attribute) int_offset (pyopenms.ImzMLSpectrumIndex property) int_sum (pyopenms.CrossLinkSpectrumMatch property) int_type (pyopenms.ImzMLSpectrumIndex property) INT_VALUE (pyopenms.DataType attribute) (pyopenms.DataValue attribute) (pyopenms.ParamValue attribute) (pyopenms.ValueType attribute) intact (pyopenms.TheoreticalGlycanSpectrumGenerator.PeptideRetention property) integer_data_array_view() (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) integer_data_array_views() (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) IntegerDataArray (class in pyopenms) integratePeak() (pyopenms.PeakIntegrator method) INTENSITY (pyopenms.DataFilters attribute) (pyopenms.DataFilters.FilterType attribute) intensity (pyopenms.ExtractedPeakMap property) (pyopenms.FileInfo.RangeSet property) INTENSITY (pyopenms.IsotopeDistribution attribute) (pyopenms.IsotopeDistribution.Sorted attribute) intensity (pyopenms.LogMzPeak property) (pyopenms.OpenSwath_Scores property) (pyopenms.Peak1D property) (pyopenms.PeptideHit_PeakAnnotation property) intensity_array_view() (pyopenms.OSChromatogram method) (pyopenms.OSSpectrum method) intensity_l (pyopenms.MRMFQC_ComponentGroupQCs property) (pyopenms.MRMFQC_ComponentQCs property) intensity_u (pyopenms.MRMFQC_ComponentGroupQCs property) (pyopenms.MRMFQC_ComponentQCs property) intensityInRange() (pyopenms.MSSpectrum method) interfering_peak_count (pyopenms.PurityScores property) interfering_peaks (pyopenms.PurityScores property) INTERNAL (pyopenms.MzPAFIonSeries attribute) Internal (pyopenms.NASequence.NASFragmentType attribute) INTERNAL (pyopenms.OPXLDataStructs attribute) (pyopenms.OPXLDataStructs.PeptidePosition attribute) Internal (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) INTERNAL_ERROR (pyopenms.MzPAFErrorCode attribute) internal_range (pyopenms.MzPAFAnnotation property) InternalCalibration (class in pyopenms) InternalCalibration_LockMass (class in pyopenms) InterpolationModel (class in pyopenms) Intersects (pyopenms.DRangeIntersection attribute) intersects() (pyopenms.MSImagingRegion method) intsum_alpha (pyopenms.CrossLinkSpectrumMatch property) intsum_beta (pyopenms.CrossLinkSpectrumMatch property) INVALID_CHARGE (pyopenms.MzPAFErrorCode attribute) INVALID_CONFIDENCE (pyopenms.MzPAFErrorCode attribute) INVALID_DELTA (pyopenms.MzPAFErrorCode attribute) INVALID_FORMULA (pyopenms.MzPAFErrorCode attribute) INVALID_ION_SERIES (pyopenms.MzPAFErrorCode attribute) INVALID_NUMBER (pyopenms.MzPAFErrorCode attribute) invert() (pyopenms.TransformationDescription method) (pyopenms.TransformationModelLinear method) ion_mobility (pyopenms.ExtractedPeakMap property) (pyopenms.ExtractionCoordinates property) ION_MOBILITY_BINNING (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) ion_ratio_feature_name (pyopenms.MRMFQC_ComponentGroupQCs property) ion_ratio_l (pyopenms.MRMFQC_ComponentGroupQCs property) ion_ratio_pair_name_1 (pyopenms.MRMFQC_ComponentGroupQCs property) ion_ratio_pair_name_2 (pyopenms.MRMFQC_ComponentGroupQCs property) ion_ratio_u (pyopenms.MRMFQC_ComponentGroupQCs property) ion_series (pyopenms.MzPAFAnnotation property) ion_sources (pyopenms.FileInfo.ExperimentMeta property) ion_type (pyopenms.TheoreticalGlycanSpectrumGenerator.Fragment property) IonDetector (class in pyopenms) IonDetector.AcquisitionMode (class in pyopenms) IonDetector.Type (class in pyopenms) IonIdentityMolecularNetworking (class in pyopenms) IonImage (class in pyopenms) ionization (pyopenms.SiriusMSFile_CompoundInfo property) ionizationMethodToString() (pyopenms.IonSource static method) IONMETHODNULL (pyopenms.IonSource.IonizationMethod attribute) ionSeriesToChar() (pyopenms.MzPAF static method) IonSource (class in pyopenms) IonSource.InletType (class in pyopenms) IonSource.IonizationMethod (class in pyopenms) IonSource.Polarity (class in pyopenms) IONSTORAGE (pyopenms.MassAnalyzer.AnalyzerType attribute) IONTOPHOTONDETECTOR (pyopenms.IonDetector.Type attribute) iontype (pyopenms.TargetedExperiment_Interpretation property) IRT (pyopenms.RetentionTime attribute) (pyopenms.RetentionTime.RTType attribute) IS_actual_concentration (pyopenms.AQS_featureConcentration property) (pyopenms.AQS_runConcentration property) IS_component_name (pyopenms.AQS_runConcentration property) is_consensus (pyopenms.FileInfo.FeatureInfo property) is_decoy (pyopenms.MassFeature_FDHS property) (pyopenms.PEFFDatabaseMetadata property) (pyopenms.RescoreInput property) is_experiment (pyopenms.FileInfo.Ranges property) IS_feature (pyopenms.AQS_featureConcentration property) is_integer() (pyopenms.Base64.ByteOrder method) (pyopenms.BasicProteinInferenceAlgorithm.AggregationMethod method) (pyopenms.BoundaryCondition method) (pyopenms.BSpline2d.BoundaryCondition method) (pyopenms.ChromatogramSettings.ChromatogramType method) (pyopenms.CombinationsLogic method) (pyopenms.ConsensusMapNormalizerAlgorithmMedian.NormalizationMethod method) (pyopenms.ControlledVocabulary.CVTerm.XRefType method) (pyopenms.DRangeIntersection method) (pyopenms.DriftTimeUnit method) (pyopenms.EntrapmentEvaluation.Kind method) (pyopenms.EntrapmentEvaluation.Level method) (pyopenms.EnzymaticDigestion.Specificity method) (pyopenms.FeatureDeconvolution.CHARGEMODE method) (pyopenms.FileType method) (pyopenms.FileTypes.FileType method) (pyopenms.HydrophobicityScaleMethod method) (pyopenms.IDMapper.Measure method) (pyopenms.IDRipper.OriginAnnotationFormat method) (pyopenms.IDType method) (pyopenms.IsotopeDistribution.Sorted method) (pyopenms.ITRAQ_TYPES method) (pyopenms.ItraqConstants.ITRAQ_TYPES method) (pyopenms.LogType method) (pyopenms.Measure method) (pyopenms.MetaboliteFeatureDeconvolution.CHARGEMODE method) (pyopenms.Method method) (pyopenms.MSNumpressCoder.NumpressCompression method) (pyopenms.MultipleTesting.LfdrTransform method) (pyopenms.MultipleTesting.Pi0Method method) (pyopenms.MzPAFDeltaUnit method) (pyopenms.MzPAFErrorCode method) (pyopenms.MzPAFIonSeries method) (pyopenms.NaNPolicy method) (pyopenms.NASequence.NASFragmentType method) (pyopenms.NormalizationMethod method) (pyopenms.OpenMSOSInfo.OpenMS_Architecture method) (pyopenms.OpenMSOSInfo.OpenMS_OS method) (pyopenms.OpenPepXLAlgorithm.ExitCodes method) (pyopenms.OPXLDataStructs.PeptidePosition method) (pyopenms.OPXLDataStructs.ProteinProteinCrossLinkType method) (pyopenms.OriginAnnotationFormat method) (pyopenms.ParquetWriteConfig.Compression method) (pyopenms.PeakGroup.TargetDecoyType method) (pyopenms.PEFFDatabaseMetadata.SequenceType method) (pyopenms.PEFFModification.ModificationType method) (pyopenms.PeptideIndexing.ExitCodes method) (pyopenms.PercolatorOutfile.ScoreType method) (pyopenms.ProForma.ConversionIssueType method) (pyopenms.ProForma.ConversionPolicy method) (pyopenms.ProForma.CvDatabase method) (pyopenms.ProForma.WriteMode method) (pyopenms.ProgressLogger.LogType method) (pyopenms.ProSEAlgorithm.ProSEAlgorithm_ExitCodes method) (pyopenms.ProteomicsPkaScale method) (pyopenms.QuotingMethod method) (pyopenms.RankData.Method method) (pyopenms.RankData.NaNPolicy method) (pyopenms.RequirementLevel method) (pyopenms.Residue.ResidueType method) (pyopenms.ResidueModification.Provenance method) (pyopenms.ResidueModification.SourceClassification method) (pyopenms.ResidueModification.TermSpecificity method) (pyopenms.Ribonucleotide.TermSpecificityNuc method) (pyopenms.Scores.IDType method) (pyopenms.SIDE method) (pyopenms.SimpleSearchEngineAlgorithm.ExitCodes method) (pyopenms.UnitType method) (pyopenms.USI.IndexType method) (pyopenms.ValueType method) (pyopenms.XFDRAlgorithm.ExitCodes method) (pyopenms.XTandemInfile.ErrorUnit method) (pyopenms.XTandemInfile.MassType method) is_known_modification (pyopenms.DeltaMassEntry property) is_main_score_type (pyopenms.ScoreSearchResult property) is_nucleic_acid (pyopenms.FileInfo.FastaInfo property) is_open_search (pyopenms.SearchResult property) is_positive (pyopenms.LogMzPeak property) is_proteoform_db (pyopenms.PEFFDatabaseMetadata property) isActive() (pyopenms.ChargePair method) (pyopenms.DataFilters method) (pyopenms.OpenSwathOSWWriter method) isBool() (pyopenms.Param method) (pyopenms.ParamEntry method) isCharged() (pyopenms.EmpiricalFormula method) isChildOf() (pyopenms.ControlledVocabulary method) isCompatible() (pyopenms.AMSE_AdductInfo method) (pyopenms.BinnedSpectrum static method) (pyopenms.ModificationDefinitionsSet method) isConflicting() (pyopenms.Compomer method) isDecoy() (pyopenms.DeconvolvedSpectrum method) (pyopenms.OSWPeptidePrecursor method) (pyopenms.OSWTransition method) (pyopenms.PeptideHit method) (pyopenms.ProteinHit method) isDetectingTransition() (pyopenms.LightTransition method) (pyopenms.ReactionMonitoringTransition method) isDirectory() (pyopenms.File static method) isEmpty() (pyopenms.DataValue method) (pyopenms.DRange1 method) (pyopenms.DRange2 method) (pyopenms.EmpiricalFormula method) (pyopenms.ParamValue method) isFeatureOnly() (pyopenms.SiriusExportAlgorithm method) isFixedModification() (pyopenms.ModificationDefinition method) isFractionated() (pyopenms.ExperimentalDesign method) isHigherBetter() (pyopenms.Scores static method) isHigherBetterScore() (pyopenms.ControlledVocabulary.CVTerm static method) isHigherScoreBetter() (pyopenms.PeptideIdentification method) (pyopenms.ProteinIdentification method) ISI (pyopenms.IonSource.IonizationMethod attribute) isIdentifyingTransition() (pyopenms.LightTransition method) (pyopenms.ReactionMonitoringTransition method) isInPackage() (pyopenms.SplinePackage method) isInResidueSet() (pyopenms.Residue method) isInstantiated() (pyopenms.CrossLinksDB static method) (pyopenms.ModificationsDB static method) isInternallyConsistent() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) isIntersected() (pyopenms.DRange1 method) (pyopenms.DRange2 method) isInvalid() (pyopenms.QTCluster method) isKnownScoreType() (pyopenms.Scores static method) isMetaEmpty() (pyopenms.Acquisition method) (pyopenms.AcquisitionInfo method) (pyopenms.BaseFeature method) (pyopenms.ChromatogramSettings method) (pyopenms.ColumnHeader method) (pyopenms.Compound method) (pyopenms.Configuration method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusMap method) (pyopenms.Contact method) (pyopenms.ContactPerson method) (pyopenms.CVTermList method) (pyopenms.CVTermListInterface method) (pyopenms.DataProcessing method) (pyopenms.ExperimentalSettings method) (pyopenms.Feature method) (pyopenms.FeatureMap method) (pyopenms.FloatDataArray method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Instrument method) (pyopenms.InstrumentSettings method) (pyopenms.IntegerDataArray method) (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) (pyopenms.MetaInfoDescription method) (pyopenms.MetaInfoInterface method) (pyopenms.MRMFeature method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.Peptide method) (pyopenms.PeptideHit method) (pyopenms.PeptideIdentification method) (pyopenms.Precursor method) (pyopenms.Prediction method) (pyopenms.Product method) (pyopenms.Protein method) (pyopenms.ProteinHit method) (pyopenms.ProteinIdentification method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.RichPeak2D method) (pyopenms.Sample method) (pyopenms.ScanWindow method) (pyopenms.SearchParameters method) (pyopenms.Software method) (pyopenms.SourceFile method) (pyopenms.SpectrumSettings method) (pyopenms.StringDataArray method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TraMLProduct method) isModified() (pyopenms.AASequence method) (pyopenms.Residue method) (pyopenms.Ribonucleotide method) isMzPAFFormat() (pyopenms.MzPAF static method) isNativeID() (in module pyopenms) (pyopenms.SpectrumNativeIDParser static method) isNoMasstraceInfoIsotopePattern() (pyopenms.SiriusExportAlgorithm method) isNonEmptyCell() (pyopenms.ClusteringGrid method) isNull() (pyopenms.Date method) (pyopenms.DateTime method) iso_number_ms2_negative (pyopenms.IsobaricQuantifierStatistics property) iso_number_reporter_different (pyopenms.IsobaricQuantifierStatistics property) iso_number_reporter_negative (pyopenms.IsobaricQuantifierStatistics property) iso_offset (pyopenms.MassFeature_FDHS property) iso_solution_different_intensity (pyopenms.IsobaricQuantifierStatistics property) iso_total_intensity_negative (pyopenms.IsobaricQuantifierStatistics property) IsobaricChannelExtractor (class in pyopenms) IsobaricChannelInformation (class in pyopenms) IsobaricIsotopeCorrector (class in pyopenms) IsobaricNormalizer (class in pyopenms) IsobaricQuantifier (class in pyopenms) IsobaricQuantifierStatistics (class in pyopenms) IsobaricQuantitationMethod (class in pyopenms) IsobaricQuantities (class in pyopenms) IsoelectricPoint (class in pyopenms) isoPeakMeans() (pyopenms.OPXLHelper static method) isOpen() (pyopenms.OnDiscImzMLExperiment method) (pyopenms.OnDiscThermoRawExperiment method) isOpenMPEnabled() (pyopenms.OpenMSBuildInfo static method) isotope (pyopenms.IsotopeReplacement property) isotope_correlation (pyopenms.OpenSwath_Scores property) isotope_offset (pyopenms.MzPAFAnnotation property) isotope_overlap (pyopenms.OpenSwath_Scores property) isotope_score (pyopenms.MassFeature_FDHS property) IsotopeCluster (class in pyopenms) IsotopeDistribution (class in pyopenms) IsotopeDistribution.Sorted (class in pyopenms) IsotopeFitter1D (class in pyopenms) isotopeIndex (pyopenms.LogMzPeak property) IsotopeLabelingMDVs (class in pyopenms) IsotopeLabelingMDVs.DerivatizationAgent (class in pyopenms) IsotopeLabelingMDVs.MassIntensityType (class in pyopenms) IsotopeModel (class in pyopenms) IsotopeModel.Averagines (class in pyopenms) IsotopeReplacement (class in pyopenms) ISOTOPIC_LABEL (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.SourceClassification attribute) isotopic_prefilter (pyopenms.BrukerTimsFile.Config property) isotopic_prefilter_tol_ppm (pyopenms.BrukerTimsFile.Config property) isotopicCorrection() (pyopenms.IsotopeLabelingMDVs method) isotopicCorrections() (pyopenms.IsotopeLabelingMDVs method) isPEFFFile() (in module pyopenms) (pyopenms.PEFFFile static method) isPeptide() (pyopenms.LightCompound method) isPeptideFragmentIon() (pyopenms.MzPAF static method) isPositive() (pyopenms.PeakGroup method) isPrecursorImSet() (pyopenms.LightTransition method) isPrefix() (pyopenms.PeptideIndexing method) isProductChargeStateSet() (pyopenms.LightTransition method) (pyopenms.ReactionMonitoringTransition method) isQuantifyingTransition() (pyopenms.LightTransition method) (pyopenms.ReactionMonitoringTransition method) isRepresentableAsAASequence() (pyopenms.Peptidoform method) (pyopenms.ProForma static method) isRTset() (pyopenms.RetentionTime method) isScoreType() (pyopenms.IDScoreSwitcherAlgorithm method) (pyopenms.Scores static method) isScoreTypeHigherBetter() (pyopenms.IDScoreSwitcherAlgorithm method) isSemanticallyValid() (pyopenms.MzDataFile method) (pyopenms.MzIdentMLFile method) (pyopenms.MzMLFile method) (pyopenms.TraMLFile method) isSet() (pyopenms.OSWIndexTrace method) isSingleAdduct() (pyopenms.Compomer method) isSorted() (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) isSortedByRT() (pyopenms.OnDiscMSExperiment method) (pyopenms.OnDiscThermoRawExperiment method) isSupported() (pyopenms.FileHandler static method) isTargeted() (pyopenms.PeakGroup method) isTrained() (pyopenms.MZTrafoModel method) isUserDefined() (pyopenms.ResidueModification method) isValid() (pyopenms.BaseFeature static method) (pyopenms.ClusterProxyKD method) (pyopenms.ConsensusFeature static method) (pyopenms.ConsensusMap static method) (pyopenms.Date method) (pyopenms.DateTime method) (pyopenms.Feature static method) (pyopenms.FeatureFinderAlgorithmPickedHelperStructs_MassTrace method) (pyopenms.FeatureHandle static method) (pyopenms.FeatureMap static method) (pyopenms.Gradient method) (pyopenms.ImzMLFile method) (pyopenms.MassTraces method) (pyopenms.MRMFeature static method) (pyopenms.MzPAFAnnotation method) (pyopenms.ParamEntry method) (pyopenms.RichPeak2D static method) (pyopenms.UniqueIdInterface static method) (pyopenms.USI method) isValidModel() (pyopenms.MZTrafoModel static method) isValidProduct() (pyopenms.EnzymaticDigestion method) (pyopenms.ProteaseDigestion method) (pyopenms.RNaseDigestion method) isValidUSI() (pyopenms.USI static method) IT (pyopenms.MassAnalyzer.AnalyzerType attribute) items() (pyopenms.Param method) iter_chromatogram_views() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.MSExperiment method) iter_consensus_feature_views() (pyopenms.ConsensusMap method) iter_feature_views() (pyopenms.FeatureMap method) (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) iter_float_data_array_views() (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) iter_integer_data_array_views() (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) iter_peptide_identification_views() (pyopenms.PeptideIdentificationList method) iter_spectrum_views() (pyopenms.MSExperiment method) iter_string_data_array_views() (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) ITERATION_EXCEEDED (pyopenms.NonNegativeLeastSquaresSolver attribute) (pyopenms.NonNegativeLeastSquaresSolver.RETURN_STATUS attribute) iTRAQ ITRAQ_TYPES (class in pyopenms) ItraqConstants (class in pyopenms) ItraqConstants.ITRAQ_TYPES (class in pyopenms) ItraqEightPlexQuantitationMethod (class in pyopenms) ItraqFourPlexQuantitationMethod (class in pyopenms) J JavaInfo (class in pyopenms) JETSEPARATOR (pyopenms.IonSource.InletType attribute) JOULE_PER_CAL (in module pyopenms.Constants) JSON (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) K k (pyopenms.RANSACParam property) keepBestPeptideHits() (pyopenms.IDFilter static method) keepBestPerPeptide() (pyopenms.IDFilter static method) keepBestPerPeptidePerRun() (pyopenms.IDFilter static method) keepHitsMatchingProteins() (pyopenms.IDFilter static method) keepNativeSpectrumName() (pyopenms.PepXMLFile method) keepNBestHits() (pyopenms.IDFilter static method) keepNBestSpectra() (pyopenms.IDFilter static method) keepPeptidesWithMatchingModifications() (pyopenms.IDFilter static method) keepPeptidesWithMatchingSequences() (pyopenms.IDFilter static method) keepUniquePeptidesPerProtein() (pyopenms.IDFilter static method) Kernel_MassTrace (in module pyopenms) key2index() (pyopenms.LinearInterpolation method) key2index_0() (pyopenms.BilinearInterpolation method) key2index_1() (pyopenms.BilinearInterpolation method) key_name (pyopenms.PEFFCustomKeyDef property) keys() (pyopenms.Param method) KINETIC_ENERGY_ANALYZER (pyopenms.Instrument.IonOpticsType attribute) KROENIK (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) KroenikFile (class in pyopenms) KYTE_DOOLITTLE (pyopenms.HydrophobicityScaleMethod attribute) L Label (class in pyopenms) label (pyopenms.ColumnHeader property) (pyopenms.ExperimentalDesign_MSFileSectionEntry property) (pyopenms.FileInfo.MapColumn property) label_set (pyopenms.MultiplexDeltaMasses_DeltaMass property) label_type (pyopenms.LightCompound property) LabeledPairFinder (class in pyopenms) LABILE_MOD (pyopenms.ProForma.ConversionIssueType attribute) labile_mods (pyopenms.Peptidoform property) LabileModification (class in pyopenms) lambda_ (pyopenms.Pi0Result property) last_name (pyopenms.FileInfo.Contact property) last_scan (pyopenms.ThermoRawFileOptions property) LC LC-MS LC-MS/MS LCID (pyopenms.Precursor.ActivationMethod attribute) LCMS LD (pyopenms.IonSource.IonizationMethod attribute) le() (pyopenms.ParquetFilter method) LEFT (pyopenms.SIDE attribute) LEHNINGER (pyopenms.ProteomicsPkaScale attribute) length (pyopenms.ImzMLAuxArrayIndex property) length_stats (pyopenms.FileInfo.FastaInfo property) LESS_EQUAL (pyopenms.DataFilters attribute) (pyopenms.DataFilters.FilterOperation attribute) LevMarqFitter1D (class in pyopenms) lfdr() (pyopenms.MultipleTesting static method) lfdrTransformToString() (pyopenms.MultipleTesting static method) library_corr (pyopenms.OpenSwath_Scores property) library_dotprod (pyopenms.OpenSwath_Scores property) library_intensity (pyopenms.LightTransition property) library_manhattan (pyopenms.OpenSwath_Scores property) library_norm_manhattan (pyopenms.OpenSwath_Scores property) library_rootmeansquare (pyopenms.OpenSwath_Scores property) library_sangle (pyopenms.OpenSwath_Scores property) LIFT (pyopenms.Precursor.ActivationMethod attribute) LightCompound (class in pyopenms) LightModification (class in pyopenms) LightMRMTransitionGroupCP (class in pyopenms) LightProtein (class in pyopenms) LightTargetedExperiment (class in pyopenms) LightTransition (class in pyopenms) line_scan_direction (pyopenms.ImzMLMeta property) LINEAR (pyopenms.BrukerTimsFile.Config.TimsCalibrationStrategy attribute) (pyopenms.MassAnalyzer.ScanLaw attribute) (pyopenms.MSNumpressCoder attribute) (pyopenms.MSNumpressCoder.NumpressCompression attribute) (pyopenms.MZTrafoModel.MODELTYPE attribute) linear_fp_mass_acc (pyopenms.NumpressConfig property) (pyopenms.SqMassConfig property) LINEAR_WEIGHTED (pyopenms.MZTrafoModel.MODELTYPE attribute) LinearInterpolation (class in pyopenms) LinearResamplerAlign (class in pyopenms) lines (pyopenms.FileInfo.DetailInfo property) linkage (pyopenms.GlycanStructure.Node property) LIQUID (pyopenms.Sample.SampleState attribute) liquid chromatography liquid chromatography coupled tandem mass spectrometry LIT (pyopenms.MassAnalyzer.AnalyzerType attribute) load() (pyopenms.AbsoluteQuantitationMethodFile method) (pyopenms.AbsoluteQuantitationStandardsFile method) (pyopenms.BrukerTimsFile method) (pyopenms.CachedmzML static method) (pyopenms.ChromeleonFile method) (pyopenms.ConsensusXMLFile method) (pyopenms.CsvFile method) (pyopenms.CVMappingFile method) (pyopenms.DTA2DFile method) (pyopenms.DTAFile method) (pyopenms.EDTAFile method) (pyopenms.ExperimentalDesignFile static method) (pyopenms.FASTAFile method) (pyopenms.FeatureXMLFile method) (pyopenms.IdXMLFile method) (pyopenms.IMSAlphabet method) (pyopenms.ImzMLFile method) (pyopenms.IndexedMzMLFileLoader method) (pyopenms.InspectOutfile method) (pyopenms.KroenikFile method) (pyopenms.MascotGenericFile method) (pyopenms.MascotXMLFile method) (pyopenms.MRMFeaturePickerFile method) (pyopenms.MRMFeatureQCFile method) (pyopenms.MS2File method) (pyopenms.MsInspectFile method) (pyopenms.MSPFile method) (pyopenms.MSPGenericFile method) (pyopenms.MzDataFile method) (pyopenms.MzIdentMLFile method) (pyopenms.MzMLFile method) (pyopenms.MzTabFile method) (pyopenms.MzXMLFile method) (pyopenms.OMSFile method) (pyopenms.OMSSACSVFile method) (pyopenms.OMSSAXMLFile method) (pyopenms.ParamXMLFile method) (pyopenms.PEFFFile method) (pyopenms.PepXMLFile method) (pyopenms.PercolatorOutfile method) (pyopenms.ProtXMLFile method) (pyopenms.SequestOutfile method) (pyopenms.SqMassFile method) (pyopenms.TextFile method) (pyopenms.ThermoRawFile method) (pyopenms.TraMLFile method) (pyopenms.TransformationXMLFile method) (pyopenms.XQuestResultXMLFile method) (pyopenms.XTandemXMLFile method) load_ms1 (pyopenms.BrukerTimsFile.Config property) load_ms2 (pyopenms.BrukerTimsFile.Config property) loadBuffer() (pyopenms.MzMLFile method) loadConsensusFeatures() (pyopenms.FileHandler method) loadExperiment() (pyopenms.FileHandler method) loadFeatures() (pyopenms.FileHandler method) loadFile() (pyopenms.TargetedDataFileLoader static method) loadFromOBO() (pyopenms.ControlledVocabulary method) loadIdentifications() (pyopenms.FileHandler method) loadImagingExperiment() (pyopenms.FileHandler method) loadMzML() (pyopenms.MRMFile static method) (pyopenms.SwathFile method) loadMzXML() (pyopenms.SwathFile method) loads (pyopenms.SysInfo attribute) loadSize() (pyopenms.FeatureXMLFile method) loadSpectraIndex() (pyopenms.ImzMLFile method) loadSpectrum() (pyopenms.FileHandler method) loadSplit() (pyopenms.SwathFile method) loadTransformations() (pyopenms.FileHandler method) loadTransitions() (pyopenms.FileHandler method) LOCAL (pyopenms.RetentionTime attribute) (pyopenms.RetentionTime.RTType attribute) locality_weight (pyopenms.SelectorParameters property) locateTerm() (pyopenms.SemanticValidator method) location (pyopenms.LightModification property) (pyopenms.TargetedExperiment_Modification property) log_occupancy (pyopenms.CrossLinkSpectrumMatch property) log_occupancy_alpha (pyopenms.CrossLinkSpectrumMatch property) log_occupancy_beta (pyopenms.CrossLinkSpectrumMatch property) log_sn_score (pyopenms.OpenSwath_Scores property) log_type (pyopenms.FileInfo.Options property) LogConfigHandler (class in pyopenms) logFeatureSpectraNumber() (pyopenms.SiriusExportAlgorithm method) Logit (pyopenms.MultipleTesting.LfdrTransform attribute) logMz (pyopenms.LogMzPeak property) LogMzPeak (class in pyopenms) logOccupancyProb() (pyopenms.XQuestScores static method) LogType (class in pyopenms) long_name (pyopenms.MultiplexDeltaMassesGenerator_Label property) LOOP (pyopenms.OPXLDataStructs attribute) (pyopenms.OPXLDataStructs.ProteinProteinCrossLinkType attribute) LOSSLESS (pyopenms.ProForma.WriteMode attribute) LOW_RESOLUTION (pyopenms.IDFreeMassErrorEstimator.FragmentResolutionRegime attribute) lower (pyopenms.SwathMap property) lowerBoundFDP() (pyopenms.EntrapmentEvaluation.Result method) lowerq (pyopenms.SummaryStatistics property) LowessSmoothing (class in pyopenms) lowest (pyopenms.OSWIndexTrace property) LSI (pyopenms.IonSource.IonizationMethod attribute) lt() (pyopenms.ParquetFilter method) LuciphorAdapter LZ4 (pyopenms.ParquetWriteConfig attribute) (pyopenms.ParquetWriteConfig.Compression attribute) M m_ids (pyopenms.SiriusMSFile_CompoundInfo property) m_ids_id (pyopenms.SiriusMSFile_CompoundInfo property) M_PER_FOOT (in module pyopenms.Constants) MAGNETIC_DEFLECTION (pyopenms.Instrument.IonOpticsType attribute) main_score (pyopenms.PeptideHit_AnalysisResult property) MALDI (pyopenms.IonSource.IonizationMethod attribute) manhatt_score_dia (pyopenms.OpenSwath_Scores property) map_columns (pyopenms.FileInfo.FeatureInfo property) MAP_INDEX (pyopenms.IDRipper attribute) (pyopenms.IDRipper.OriginAnnotationFormat attribute) (pyopenms.OriginAnnotationFormat attribute) MapAlignmentAlgorithmIdentification (class in pyopenms) MapAlignmentAlgorithmPoseClustering (class in pyopenms) MapAlignmentEvaluationAlgorithm (class in pyopenms) MapAlignmentEvaluationAlgorithmPrecision (class in pyopenms) MapAlignmentEvaluationAlgorithmRecall (class in pyopenms) MapAlignmentTransformer (class in pyopenms) MapConversion (class in pyopenms) mapExperiment() (pyopenms.MRMMapping method) mapped_modification (pyopenms.DeltaMassEntry property) mapPrecursorsToIdentifications() (pyopenms.IDMapper static method) markRescoredRuns() (pyopenms.Percolator static method) MascotAdapterOnline MascotGenericFile (class in pyopenms) MASCOTXML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) MascotXMLFile (class in pyopenms) Mask (pyopenms.MSImagingRegion.Shape attribute) mass (pyopenms.IMSIsotopeDistribution_Peak property) MASS (pyopenms.IsotopeDistribution attribute) (pyopenms.IsotopeDistribution.Sorted attribute) mass (pyopenms.LogMzPeak property) (pyopenms.MassDelta property) mass spectra Mass Spectrometry mass spectrum mass_analyzers (pyopenms.FileInfo.ExperimentMeta property) (pyopenms.FileInfo.PeakInfo property) MASS_CHROMATOGRAM (pyopenms.ChromatogramSettings.ChromatogramType attribute) mass_delta (pyopenms.MzPAFAnnotation property) mass_deviation (pyopenms.PTMEntry property) MASS_ONLY (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.Provenance attribute) mass_type (pyopenms.SearchParameters property) MassAnalyzer (class in pyopenms) MassAnalyzer.AnalyzerType (class in pyopenms) MassAnalyzer.ReflectronState (class in pyopenms) MassAnalyzer.ResolutionMethod (class in pyopenms) MassAnalyzer.ResolutionType (class in pyopenms) MassAnalyzer.ScanDirection (class in pyopenms) MassAnalyzer.ScanLaw (class in pyopenms) MassDecomposition (class in pyopenms) MassDecompositionAlgorithm (class in pyopenms) MassDelta (class in pyopenms) massdev_score (pyopenms.OpenSwath_Scores property) masses (pyopenms.ModificationPattern property) (pyopenms.ModificationSummary property) MassExplainer (class in pyopenms) MassFeature_FDHS (class in pyopenms) MASSSPECTRUM (pyopenms.InstrumentSettings.ScanMode attribute) MassTrace (class in pyopenms) MasstraceCorrelator (class in pyopenms) MassTraceDetection (class in pyopenms) MassTraces (class in pyopenms) match_odds (pyopenms.CrossLinkSpectrumMatch property) match_odds_alpha (pyopenms.CrossLinkSpectrumMatch property) match_odds_beta (pyopenms.CrossLinkSpectrumMatch property) matched_linear_alpha (pyopenms.CrossLinkSpectrumMatch property) matched_linear_beta (pyopenms.CrossLinkSpectrumMatch property) matched_spectra (pyopenms.FileInfo.IdentInfo property) matched_xlink_alpha (pyopenms.CrossLinkSpectrumMatch property) matched_xlink_beta (pyopenms.CrossLinkSpectrumMatch property) matchedCurrentChain() (pyopenms.XQuestScores static method) matches (pyopenms.MorpheusScore_Result property) matchOddsScore() (pyopenms.XQuestScores static method) Math (class in pyopenms) matrix_view() (pyopenms.MatrixDouble method) MatrixDouble (class in pyopenms) MAX (pyopenms.FeatureOverlapFilter.MergeIntensityMode attribute) max (pyopenms.FileInfo.Range property) Max (pyopenms.Method attribute) MAX (pyopenms.MSExperiment.MSExperimentRasterAggregation attribute) (pyopenms.MSSpectrum.MSSpectrumRasterAggregation attribute) Max (pyopenms.RankData.Method attribute) max (pyopenms.SummaryStatistics property) max_candidates_per_bin (pyopenms.IDFreeMassErrorEstimator.Parameters property) max_charge (pyopenms.MassFeature_FDHS property) (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) max_cleavages (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) max_composition_size (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) max_count_x (pyopenms.ImzMLMeta property) max_count_y (pyopenms.ImzMLMeta property) max_count_z (pyopenms.ImzMLMeta property) max_dim_x (pyopenms.ImzMLMeta property) max_dim_y (pyopenms.ImzMLMeta property) max_float (pyopenms.ParamEntry property) max_fragments (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) max_int (pyopenms.ParamEntry property) max_oxonium_charge (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) max_rt (pyopenms.FeatureFinderAlgorithmPickedHelperStructs_MassTrace property) max_scan_number (pyopenms.MassFeature_FDHS property) max_states (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) max_trace (pyopenms.MassTraces property) maxPosition() (pyopenms.DBoundingBox2 method) maxX() (pyopenms.DRange1 method) (pyopenms.DRange2 method) maxY() (pyopenms.DRange2 method) MAY (pyopenms.RequirementLevel attribute) MD5 (pyopenms.ChecksumType attribute) (pyopenms.SourceFile.ChecksumType attribute) mean (pyopenms.SummaryStatistics property) mean_delta_mass (pyopenms.DeltaMassStatistics property) Measure (class in pyopenms) MEASURE_DA (pyopenms.IDMapper attribute) (pyopenms.IDMapper.Measure attribute) (pyopenms.Measure attribute) MEASURE_PPM (pyopenms.IDMapper attribute) (pyopenms.IDMapper.Measure attribute) (pyopenms.Measure attribute) median (pyopenms.SummaryStatistics property) median() (pyopenms.CalibrationData method) median_delta_mass (pyopenms.DeltaMassStatistics property) mem_unit (pyopenms.SysInfo attribute) MEMBRANE (pyopenms.IonSource.InletType attribute) MEMBRANESEPARATOR (pyopenms.IonSource.InletType attribute) merge() (pyopenms.IsotopeDistribution method) (pyopenms.Param method) mergeAnnotatedSpectra() (pyopenms.OPXLSpectrumProcessingAlgorithms static method) mergeCoincidentFeatures() (pyopenms.FeatureOverlapFilter static method) merged_quantities (pyopenms.IsobaricQuantities property) mergeFAIMSFeatures() (in module pyopenms) (pyopenms.FeatureOverlapFilter static method) mergeFeatures() (pyopenms.TargetedSpectraExtractor method) mergeMULTISEProteinIds() (pyopenms.PercolatorFeatureSetHelper static method) mergeOverlappingFeatures() (in module pyopenms) (pyopenms.FeatureOverlapFilter static method) mergeSpectraBlockWise() (pyopenms.SpectraMerger method) mergeSpectraPrecursors() (pyopenms.SpectraMerger method) MESI (pyopenms.IonSource.IonizationMethod attribute) meta (pyopenms.FileInfo.Options property) (pyopenms.FileInfo.Result property) META_DATA (pyopenms.DataFilters attribute) (pyopenms.DataFilters.FilterType attribute) meta_name (pyopenms.DataFilter property) MetaboliteFeatureDeconvolution (class in pyopenms) MetaboliteFeatureDeconvolution.CHARGEMODE (class in pyopenms) MetaboliteSpectralMatching (class in pyopenms) MetaboTargetedAssay (class in pyopenms) MetaboTargetedAssay_CompoundTargetDecoyPair (class in pyopenms) MetaboTargetedTargetDecoy (class in pyopenms) MetaboTargetedTargetDecoy_MetaboTargetDecoyMassMapping (class in pyopenms) metadata_only (pyopenms.ThermoRawFileOptions property) MetaInfo (class in pyopenms) MetaInfoDescription (class in pyopenms) MetaInfoInterface (class in pyopenms) MetaInfoRegistry (class in pyopenms) metaRegistry() (pyopenms.Acquisition static method) (pyopenms.AcquisitionInfo static method) (pyopenms.BaseFeature static method) (pyopenms.ChromatogramSettings static method) (pyopenms.ColumnHeader static method) (pyopenms.Compound static method) (pyopenms.Configuration static method) (pyopenms.ConsensusFeature static method) (pyopenms.ConsensusMap static method) (pyopenms.Contact static method) (pyopenms.ContactPerson static method) (pyopenms.CVTermList static method) (pyopenms.CVTermListInterface static method) (pyopenms.DataProcessing static method) (pyopenms.ExperimentalSettings static method) (pyopenms.Feature static method) (pyopenms.FeatureMap static method) (pyopenms.FloatDataArray static method) (pyopenms.IncludeExcludeTarget static method) (pyopenms.Instrument static method) (pyopenms.InstrumentSettings static method) (pyopenms.IntegerDataArray static method) (pyopenms.IonDetector static method) (pyopenms.IonSource static method) (pyopenms.MassAnalyzer static method) (pyopenms.MetaInfoDescription static method) (pyopenms.MetaInfoInterface static method) (pyopenms.MRMFeature static method) (pyopenms.MSChromatogram static method) (pyopenms.MSExperiment static method) (pyopenms.MSSpectrum static method) (pyopenms.Peptide static method) (pyopenms.PeptideHit static method) (pyopenms.PeptideIdentification static method) (pyopenms.Precursor static method) (pyopenms.Prediction static method) (pyopenms.Product static method) (pyopenms.Protein static method) (pyopenms.ProteinHit static method) (pyopenms.ProteinIdentification static method) (pyopenms.Publication static method) (pyopenms.ReactionMonitoringTransition static method) (pyopenms.RetentionTime static method) (pyopenms.RichPeak2D static method) (pyopenms.Sample static method) (pyopenms.ScanWindow static method) (pyopenms.SearchParameters static method) (pyopenms.Software static method) (pyopenms.SourceFile static method) (pyopenms.SpectrumSettings static method) (pyopenms.StringDataArray static method) (pyopenms.TargetedExperiment_Instrument static method) (pyopenms.TargetedExperiment_Interpretation static method) (pyopenms.TargetedExperiment_Modification static method) (pyopenms.TraMLProduct static method) metaValueExists() (pyopenms.Acquisition method) (pyopenms.AcquisitionInfo method) (pyopenms.BaseFeature method) (pyopenms.ChromatogramSettings method) (pyopenms.ColumnHeader method) (pyopenms.Compound method) (pyopenms.Configuration method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusMap method) (pyopenms.Contact method) (pyopenms.ContactPerson method) (pyopenms.CVTermList method) (pyopenms.CVTermListInterface method) (pyopenms.DataProcessing method) (pyopenms.ExperimentalSettings method) (pyopenms.Feature method) (pyopenms.FeatureMap method) (pyopenms.FloatDataArray method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Instrument method) (pyopenms.InstrumentSettings method) (pyopenms.IntegerDataArray method) (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) (pyopenms.MetaInfoDescription method) (pyopenms.MetaInfoInterface method) (pyopenms.MRMFeature method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.Peptide method) (pyopenms.PeptideHit method) (pyopenms.PeptideIdentification method) (pyopenms.Precursor method) (pyopenms.Prediction method) (pyopenms.Product method) (pyopenms.Protein method) (pyopenms.ProteinHit method) (pyopenms.ProteinIdentification method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.RichPeak2D method) (pyopenms.Sample method) (pyopenms.ScanWindow method) (pyopenms.SearchParameters method) (pyopenms.Software method) (pyopenms.SourceFile method) (pyopenms.SpectrumSettings method) (pyopenms.StringDataArray method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TraMLProduct method) Method (class in pyopenms) MGF (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) mi_score (pyopenms.OpenSwath_Scores property) MIC (pyopenms.MorpheusScore_Result property) MICROCHANNELPLATEDETECTOR (pyopenms.IonDetector.Type attribute) MILLISECOND (pyopenms.DriftTimeUnit attribute) min (pyopenms.FileInfo.Range property) Min (pyopenms.Method attribute) (pyopenms.RankData.Method attribute) min (pyopenms.SummaryStatistics property) min_charge (pyopenms.MassFeature_FDHS property) (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) min_composition_size (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) min_float (pyopenms.ParamEntry property) min_fragment_pairs (pyopenms.IDFreeMassErrorEstimator.Parameters property) min_fragment_tolerance_pairs (pyopenms.IDFreeMassErrorEstimator.Parameters property) min_fragment_tolerance_spectra (pyopenms.IDFreeMassErrorEstimator.Parameters property) min_int (pyopenms.ParamEntry property) min_maps (pyopenms.ConsensusMapNormalizerAlgorithmRTLocal.Settings property) min_matched_peaks (pyopenms.IDFreeMassErrorEstimator.Parameters property) min_overlap_fraction (pyopenms.IDFreeMassErrorEstimator.Parameters property) min_oxonium_charge (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) min_precursor_cluster_size (pyopenms.IDFreeMassErrorEstimator.Parameters property) min_precursor_clusters (pyopenms.IDFreeMassErrorEstimator.Parameters property) min_reference (pyopenms.ConsensusMapNormalizerAlgorithmRTLocal.Settings property) min_scan_number (pyopenms.MassFeature_FDHS property) min_spectrum_pairs (pyopenms.IDFreeMassErrorEstimator.Parameters property) min_tolerance_clusters (pyopenms.IDFreeMassErrorEstimator.Parameters property) min_tolerance_pairs (pyopenms.IDFreeMassErrorEstimator.Parameters property) min_upper_edge_dist (pyopenms.OSW_ChromExtractParams property) minPosition() (pyopenms.DBoundingBox2 method) MINUTE (pyopenms.RetentionTime attribute) (pyopenms.RetentionTime.RTUnit attribute) minX() (pyopenms.DRange1 method) (pyopenms.DRange2 method) minY() (pyopenms.DRange2 method) mirror_plot_spectrum() (in module pyopenms.plotting) missed_cleavages (pyopenms.SearchParameters property) missingRunMessage() (pyopenms.ProteinRunReferences static method) MIXTURE (pyopenms.PosteriorErrorProbabilityModel.ModelType attribute) MM_PER_INCH (in module pyopenms.Constants) mobility (pyopenms.FileInfo.RangeSet property) MobilityPeak1D (class in pyopenms) Mobilogram (class in pyopenms) MOBILPARQUET (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) MOD (pyopenms.ProForma.CvDatabase attribute) mode (pyopenms.FileInfo.MzTabInfo property) modelTypeToString() (pyopenms.PosteriorErrorProbabilityModel static method) Modification (class in pyopenms) modification (pyopenms.LabileModification property) modification_analysis (pyopenms.SearchResult property) modification_counts (pyopenms.FileInfo.IdentInfo property) ModificationDefinition (class in pyopenms) ModificationDefinitionsSet (class in pyopenms) ModificationPattern (class in pyopenms) modifications (pyopenms.LightCompound property) (pyopenms.PEFFEntry property) (pyopenms.SequenceElement property) (pyopenms.UnlocalisedMod property) ModificationsDB (class in pyopenms) ModificationSummary (class in pyopenms) modified_psms (pyopenms.DeltaMassStatistics property) MODIFIED_RANGE (pyopenms.ProForma.ConversionIssueType attribute) modified_tophits (pyopenms.FileInfo.IdentInfo property) ModifiedPeptideGenerator (class in pyopenms) ModifiedPeptideGenerator_MapToResidueType (class in pyopenms) ModifiedSincSmoother (class in pyopenms) mods (pyopenms.Peptide property) module pyopenms pyopenms.Constants pyopenms.plotting molecular_formula (pyopenms.Compound property) (pyopenms.MetaboTargetedAssay property) MONO (pyopenms.OPXLDataStructs attribute) (pyopenms.OPXLDataStructs.ProteinProteinCrossLinkType attribute) mono_mass_delta (pyopenms.TargetedExperiment_Modification property) MONOISOTOPIC (pyopenms.ProteinIdentification.PeakMassType attribute) (pyopenms.XTandemInfile attribute) (pyopenms.XTandemInfile.MassType attribute) monosaccharide (pyopenms.GlycanStructure.Node property) month() (pyopenms.Date method) MorpheusScore (class in pyopenms) MorpheusScore_Result (class in pyopenms) MorphologicalFilter (class in pyopenms) MOVINGBELT (pyopenms.IonSource.InletType attribute) MOVINGWIRE (pyopenms.IonSource.InletType attribute) MPI (pyopenms.IonSource.IonizationMethod attribute) MRM (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) MRMAssay (class in pyopenms) MRMBatchFeatureSelector (class in pyopenms) MRMDecoy (class in pyopenms) MRMFeature (class in pyopenms) MRMFeatureFilter (class in pyopenms) MRMFeatureFinderScoring (class in pyopenms) MRMFeaturePicker (class in pyopenms) MRMFeaturePickerFile (class in pyopenms) MRMFeatureQC (class in pyopenms) MRMFeatureQCFile (class in pyopenms) MRMFeatureSelectorQMIP (class in pyopenms) MRMFeatureSelectorScore (class in pyopenms) MRMFile (class in pyopenms) MRMFP_ComponentGroupParams (class in pyopenms) MRMFP_ComponentParams (class in pyopenms) MRMFQC_ComponentGroupPairQCs (class in pyopenms) MRMFQC_ComponentGroupQCs (class in pyopenms) MRMFQC_ComponentQCs (class in pyopenms) MRMIonSeries (class in pyopenms) MRMMapping (class in pyopenms) MRMRTNormalizer (class in pyopenms) MRMScoring (class in pyopenms) MRMTransitionGroupCP (class in pyopenms) MRMTransitionGroupPicker (class in pyopenms) MS (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) MS/MS MS1 ms1 (pyopenms.SwathMap property) ms1_best_rt (pyopenms.TransitionListEvidenceFilter_PrecursorEvidence property) ms1_centroid_algo (pyopenms.BrukerTimsFile.Config property) ms1_centroid_im_pct (pyopenms.BrukerTimsFile.Config property) ms1_centroid_max_peaks (pyopenms.BrukerTimsFile.Config property) ms1_centroid_min_hill_length (pyopenms.BrukerTimsFile.Config property) ms1_centroid_mz_ppm (pyopenms.BrukerTimsFile.Config property) ms1_hit_count (pyopenms.TransitionListEvidenceFilter_PrecursorEvidence property) ms1_isotope_correlation (pyopenms.OpenSwath_Scores property) ms1_isotope_overlap (pyopenms.OpenSwath_Scores property) ms1_max_intensity (pyopenms.TransitionListEvidenceFilter_PrecursorEvidence property) ms1_max_rt_distance_sec (pyopenms.BrukerTimsFile.Config property) ms1_mi_combined_score (pyopenms.OpenSwath_Scores property) ms1_mi_contrast_score (pyopenms.OpenSwath_Scores property) ms1_mi_score (pyopenms.OpenSwath_Scores property) ms1_min_support (pyopenms.BrukerTimsFile.Config property) ms1_n_neighbors (pyopenms.BrukerTimsFile.Config property) ms1_ppm_score (pyopenms.OpenSwath_Scores property) ms1_sum_intensity (pyopenms.TransitionListEvidenceFilter_PrecursorEvidence property) ms1_supported (pyopenms.TransitionListEvidenceFilter_Result property) ms1_xcorr_coelution_combined_score (pyopenms.OpenSwath_Scores property) ms1_xcorr_coelution_contrast_score (pyopenms.OpenSwath_Scores property) ms1_xcorr_coelution_score (pyopenms.OpenSwath_Scores property) ms1_xcorr_shape_combined_score (pyopenms.OpenSwath_Scores property) ms1_xcorr_shape_contrast_score (pyopenms.OpenSwath_Scores property) ms1_xcorr_shape_score (pyopenms.OpenSwath_Scores property) MS1SPECTRUM (pyopenms.InstrumentSettings.ScanMode attribute) MS2 (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) ms2_best_fragment_hits (pyopenms.TransitionListEvidenceFilter_PrecursorEvidence property) ms2_best_rt (pyopenms.TransitionListEvidenceFilter_PrecursorEvidence property) ms2_centroid_algo (pyopenms.BrukerTimsFile.Config property) ms2_centroid_min_hill_length (pyopenms.BrukerTimsFile.Config property) ms2_centroid_mz_ppm (pyopenms.BrukerTimsFile.Config property) ms2_hit_count (pyopenms.TransitionListEvidenceFilter_PrecursorEvidence property) ms2_max_intensity (pyopenms.TransitionListEvidenceFilter_PrecursorEvidence property) ms2_sum_intensity (pyopenms.TransitionListEvidenceFilter_PrecursorEvidence property) ms2_supported (pyopenms.TransitionListEvidenceFilter_Result property) MS2File (class in pyopenms) MS3 ms_level (pyopenms.InternalCalibration_LockMass property) (pyopenms.MassFeature_FDHS property) (pyopenms.MSSpectrum property) (pyopenms.OSSpectrumMeta property) (pyopenms.SpectrumMetaData property) ms_levels (pyopenms.FileInfo.PeakInfo property) (pyopenms.ThermoRawFileOptions property) MS_ONTOLOGY (pyopenms.UnitType attribute) MSChromatogram (class in pyopenms) MSDataAggregatingConsumer (class in pyopenms) MSDataCachedConsumer (class in pyopenms) MSDataSqlConsumer (class in pyopenms) MSDataStoringConsumer (class in pyopenms) MSExperiment (class in pyopenms) MSExperiment.MSExperimentRasterAggregation (class in pyopenms) MSGFPlusAdapter MSImagingExperiment (class in pyopenms) MSImagingGeometry (class in pyopenms) MSImagingRegion (class in pyopenms) MSImagingRegion.Shape (class in pyopenms) MsInspectFile (class in pyopenms) MSNSPECTRUM (pyopenms.InstrumentSettings.ScanMode attribute) MSNumpressCoder (class in pyopenms) MSNumpressCoder.NumpressCompression (class in pyopenms) MSP (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) MSPFile (class in pyopenms) MSPGenericFile (class in pyopenms) MSSpectrum (class in pyopenms) MSSpectrum.MSSpectrumRasterAggregation (class in pyopenms) MSstatsFile (class in pyopenms) mt (pyopenms.MassFeature_FDHS property) MT_QUANT_AREA (pyopenms.MT_QUANTMETHOD attribute) MT_QUANT_HEIGHT (pyopenms.MT_QUANTMETHOD attribute) MT_QUANT_MEDIAN (pyopenms.MT_QUANTMETHOD attribute) MT_QUANTMETHOD (class in pyopenms) MULTICOLLECTOR (pyopenms.IonDetector.Type attribute) MULTIPLE (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.SourceClassification attribute) MULTIPLE_CHAINS (pyopenms.ProForma.ConversionIssueType attribute) MultipleTesting (class in pyopenms) MultipleTesting.LfdrTransform (class in pyopenms) MultipleTesting.Pi0Method (class in pyopenms) MultiplexDeltaMasses (class in pyopenms) MultiplexDeltaMasses_DeltaMass (class in pyopenms) MultiplexDeltaMassesGenerator (class in pyopenms) MultiplexDeltaMassesGenerator_Label (class in pyopenms) MultiplexIsotopicPeakPattern (class in pyopenms) MultiplexResolverAlgorithm (class in pyopenms) multiply_identified_spectra (pyopenms.UnresolvedIdentifications property) MUST (pyopenms.RequirementLevel attribute) MZ (pyopenms.DimensionDescription attribute) mz (pyopenms.ExtractedPeakMap property) (pyopenms.ExtractionCoordinates property) (pyopenms.FileInfo.RangeSet property) (pyopenms.InternalCalibration_LockMass property) (pyopenms.LogMzPeak property) (pyopenms.Peak1D property) MZ (pyopenms.Peak2D attribute) (pyopenms.Peak2D.DimensionDescription attribute) mz (pyopenms.PeptideHit_PeakAnnotation property) (pyopenms.SimplePeak property) mz_array_view() (pyopenms.OSSpectrum method) mz_compressed (pyopenms.ImzMLSpectrumIndex property) mz_data_type (pyopenms.ImzMLMeta property) mz_extraction_window (pyopenms.OSW_ChromExtractParams property) mz_length (pyopenms.ImzMLSpectrumIndex property) mz_max (pyopenms.PeakBoundary property) mz_min (pyopenms.PeakBoundary property) mz_offset (pyopenms.ImzMLSpectrumIndex property) mz_precursor (pyopenms.ExtractionCoordinates property) mz_start (pyopenms.SignalToNoiseEstimatorMedianRapid.NoiseEstimator property) mz_type (pyopenms.ImzMLSpectrumIndex property) mzData mzdata MZDATA (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) MzDataFile (class in pyopenms) MZIDENTML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) MzIdentMLFile (class in pyopenms) mzML mzml MZML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) MzMLFile (class in pyopenms) MzMLSpectrumDecoder (class in pyopenms) MzMLSqliteHandler (class in pyopenms) MzMLSwathFileConsumer (class in pyopenms) MzPAF (class in pyopenms) MzPAFAnnotation (class in pyopenms) MzPAFDeltaUnit (class in pyopenms) MzPAFErrorCode (class in pyopenms) MzPAFIonSeries (class in pyopenms) MzPAFMassDelta (class in pyopenms) MzPAFNeutralLoss (class in pyopenms) MzPAFPeakAnnotations (class in pyopenms) MZPEAK (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) MZQC (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) MzQCFile (class in pyopenms) MzTab (class in pyopenms) mztab (pyopenms.FileInfo.Result property) MZTAB (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) MzTabFile (class in pyopenms) MzTabM (class in pyopenms) MzTabMFile (class in pyopenms) MZTrafoModel (class in pyopenms) MZTrafoModel.MODELTYPE (class in pyopenms) MZTrafoModel_MODELTYPE (in module pyopenms) mzXML mzxml MZXML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) MzXMLFile (class in pyopenms) N N (pyopenms.IsotopeModel attribute) (pyopenms.IsotopeModel.Averagines attribute) n (pyopenms.RANSACParam property) n_detecting_l (pyopenms.MRMFQC_ComponentGroupQCs property) n_detecting_u (pyopenms.MRMFQC_ComponentGroupQCs property) n_fractions (pyopenms.PeptideAndProteinQuant_Statistics property) n_heavy_l (pyopenms.MRMFQC_ComponentGroupQCs property) n_heavy_u (pyopenms.MRMFQC_ComponentGroupQCs property) n_identifying_l (pyopenms.MRMFQC_ComponentGroupQCs property) n_identifying_u (pyopenms.MRMFQC_ComponentGroupQCs property) n_light_l (pyopenms.MRMFQC_ComponentGroupQCs property) n_light_u (pyopenms.MRMFQC_ComponentGroupQCs property) n_ms_files (pyopenms.PeptideAndProteinQuant_Statistics property) n_peaks (pyopenms.MorpheusScore_Result property) n_quantifying_l (pyopenms.MRMFQC_ComponentGroupQCs property) n_quantifying_u (pyopenms.MRMFQC_ComponentGroupQCs property) n_samples (pyopenms.PeptideAndProteinQuant_Statistics property) N_TERM (pyopenms.OPXLDataStructs attribute) (pyopenms.OPXLDataStructs.PeptidePosition attribute) (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.TermSpecificity attribute) n_term_mods (pyopenms.Peptidoform property) n_transitions_l (pyopenms.MRMFQC_ComponentGroupQCs property) n_transitions_u (pyopenms.MRMFQC_ComponentGroupQCs property) NA (pyopenms.PEFFDatabaseMetadata.SequenceType attribute) name (pyopenms.ChannelInfo property) (pyopenms.ControlledVocabulary.CVTerm property) (pyopenms.ImzMLAuxArrayIndex property) (pyopenms.IsobaricChannelInformation property) (pyopenms.ModificationSummary property) (pyopenms.MSSpectrum property) (pyopenms.NamedMod property) (pyopenms.ParamEntry property) (pyopenms.ParamNode property) (pyopenms.PEFFModification property) (pyopenms.PEFFProcessedRegion property) (pyopenms.PTMEntry property) (pyopenms.SemanticValidator_CVTerm property) (pyopenms.TheoreticalGlycanSpectrumGenerator.Fragment property) (pyopenms.Unit property) name() (pyopenms.ControlledVocabulary method) name_ (pyopenms.ToolInfo property) NAMED (pyopenms.MzPAFIonSeries attribute) named_compound (pyopenms.MzPAFAnnotation property) NamedMod (class in pyopenms) nameToEnum() (pyopenms.MZTrafoModel static method) nameToType() (pyopenms.FileTypes static method) NANOSPRAY (pyopenms.IonSource.InletType attribute) NaNPolicy (class in pyopenms) NASequence (class in pyopenms) NASequence.NASFragmentType (class in pyopenms) native_id (pyopenms.ExtractedPeakMap property) (pyopenms.MSSpectrum property) (pyopenms.SpectrumMetaData property) native_id_accession (pyopenms.SiriusMSFile_AccessionInfo property) native_id_type (pyopenms.SiriusMSFile_AccessionInfo property) native_ids (pyopenms.SiriusMSFile_CompoundInfo property) native_ids_id (pyopenms.SiriusMSFile_CompoundInfo property) NATIVEID (pyopenms.USI.IndexType attribute) nativeIdToUSIIndex() (pyopenms.USI static method) NATURAL (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.SourceClassification attribute) ncbi_tax_id (pyopenms.PEFFEntry property) ne() (pyopenms.ParquetFilter method) NEGATIVE (pyopenms.IonSource.Polarity attribute) neighbors (pyopenms.ConsensusMapNormalizerAlgorithmRTLocal.Settings property) NESI (pyopenms.IonSource.IonizationMethod attribute) neutral_losses (pyopenms.MzPAFAnnotation property) (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) neutral_mass (pyopenms.TheoreticalGlycanSpectrumGenerator.Fragment property) NEUTRON_MASS (in module pyopenms.Constants) NEUTRON_MASS_U (in module pyopenms.Constants) nextProgress() (pyopenms.AccurateMassSearchEngine method) (pyopenms.AverageLinkage method) (pyopenms.BaseGroupFinder method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.BrukerTimsFile method) (pyopenms.CachedMzMLHandler method) (pyopenms.ChromatogramExtractor method) (pyopenms.ChromatogramExtractorAlgorithm method) (pyopenms.ConfidenceScoring method) (pyopenms.DTA2DFile method) (pyopenms.ElutionPeakDetection method) (pyopenms.FASTAFile method) (pyopenms.FeatureFindingMetabo method) (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.FLASHDeconvAlgorithm method) (pyopenms.GaussFilter method) (pyopenms.ImzMLFile method) (pyopenms.InternalCalibration method) (pyopenms.LabeledPairFinder method) (pyopenms.LinearResamplerAlign method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) (pyopenms.MascotGenericFile method) (pyopenms.MasstraceCorrelator method) (pyopenms.MassTraceDetection method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.ModifiedSincSmoother method) (pyopenms.MorphologicalFilter method) (pyopenms.MRMAssay method) (pyopenms.MRMDecoy method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MS2File method) (pyopenms.MSDataCachedConsumer method) (pyopenms.MzDataFile method) (pyopenms.MzIdentMLFile method) (pyopenms.MzMLFile method) (pyopenms.MzXMLFile method) (pyopenms.PeakMapExtractor method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) (pyopenms.PEFFFile method) (pyopenms.ProgressLogger method) (pyopenms.ProSEAlgorithm method) (pyopenms.QTClusterFinder method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.StablePairFinder method) (pyopenms.SwathFile method) (pyopenms.ThermoRawFile method) (pyopenms.TransitionPQPFile method) (pyopenms.TransitionTSVFile method) NICI (pyopenms.IonSource.IonizationMethod attribute) nightly snapshot NLargest (class in pyopenms) NLINKED_GLYCOSYLATION (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.SourceClassification attribute) NM_SCALE (pyopenms.ConsensusMapNormalizerAlgorithmMedian attribute) (pyopenms.ConsensusMapNormalizerAlgorithmMedian.NormalizationMethod attribute) (pyopenms.NormalizationMethod attribute) NM_SHIFT (pyopenms.ConsensusMapNormalizerAlgorithmMedian attribute) (pyopenms.ConsensusMapNormalizerAlgorithmMedian.NormalizationMethod attribute) (pyopenms.NormalizationMethod attribute) nn_threshold (pyopenms.SelectorParameters property) no_precursors (pyopenms.IDMapper_PeptideIdentificationListState property) NO_REGION (pyopenms.MSImagingGeometry attribute) nodes (pyopenms.ParamNode property) noise_data (pyopenms.ThermoRawFileOptions property) noise_decoy (pyopenms.PeakGroup attribute) (pyopenms.PeakGroup.TargetDecoyType attribute) noiseGainToM() (pyopenms.ModifiedSincSmoother static method) non_redundant_peptides (pyopenms.FileInfo.IdentInfo property) non_redundant_protein_hits (pyopenms.FileInfo.IdentInfo property) NONE (pyopenms.AverageLinkage attribute) (pyopenms.BrukerTimsFile.Config.PressureCompensation attribute) (pyopenms.BrukerTimsFile.DataFormat attribute) (pyopenms.CachedMzMLHandler attribute) (pyopenms.ChromatogramExtractor attribute) (pyopenms.ChromatogramExtractorAlgorithm attribute) (pyopenms.ConfidenceScoring attribute) (pyopenms.ControlledVocabulary.CVTerm.XRefType attribute) (pyopenms.DriftTimeUnit attribute) (pyopenms.DTA2DFile attribute) (pyopenms.FASTAFile attribute) (pyopenms.GaussFilter attribute) (pyopenms.IMFormat attribute) (pyopenms.InternalCalibration attribute) (pyopenms.LogType attribute) (pyopenms.MascotGenericFile attribute) (pyopenms.MassAnalyzer.ReflectronState attribute) (pyopenms.ModifiedSincSmoother attribute) (pyopenms.MorphologicalFilter attribute) (pyopenms.MRMAssay attribute) (pyopenms.MS2File attribute) (pyopenms.MSDataCachedConsumer attribute) (pyopenms.MSNumpressCoder attribute) (pyopenms.MSNumpressCoder.NumpressCompression attribute) (pyopenms.ParquetWriteConfig attribute) (pyopenms.ParquetWriteConfig.Compression attribute) (pyopenms.PeakMapExtractor attribute) (pyopenms.PEFFFile attribute) (pyopenms.PosteriorErrorProbabilityModel.ModelType attribute) (pyopenms.ProgressLogger attribute) (pyopenms.ProgressLogger.LogType attribute) (pyopenms.QuotingMethod attribute) (pyopenms.SavitzkyGolayFilter attribute) (pyopenms.SwathFile attribute) (pyopenms.TransitionPQPFile attribute) (pyopenms.TransitionTSVFile attribute) NonIdentified (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) NonNegativeLeastSquaresSolver (class in pyopenms) NonNegativeLeastSquaresSolver.RETURN_STATUS (class in pyopenms) NONSTANDARD_RESIDUE (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.SourceClassification attribute) NoopMSDataWritingConsumer (class in pyopenms) NORM_MAX (pyopenms.IsotopeLabelingMDVs.MassIntensityType attribute) norm_rt_score (pyopenms.OpenSwath_Scores property) NORM_SUM (pyopenms.IsotopeLabelingMDVs.MassIntensityType attribute) NORMALIZATION (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) NormalizationMethod (class in pyopenms) normalize() (pyopenms.IMSIsotopeDistribution method) (pyopenms.IsobaricNormalizer method) NORMALIZED (pyopenms.RetentionTime attribute) (pyopenms.RetentionTime.RTType attribute) normalized_experimental_rt (pyopenms.OpenSwath_Scores property) normalizeMaps() (pyopenms.ConsensusMapNormalizerAlgorithmMedian static method) (pyopenms.ConsensusMapNormalizerAlgorithmQuantile static method) (pyopenms.ConsensusMapNormalizerAlgorithmRTLocal static method) (pyopenms.ConsensusMapNormalizerAlgorithmThreshold static method) Normalizer (class in pyopenms) normalizeScoreName() (pyopenms.Scores static method) NOT_SELECTED (pyopenms.IsotopeLabelingMDVs.DerivatizationAgent attribute) note (pyopenms.TransformationModel_DataPoint property) NOVOR (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) now() (pyopenms.DateTime static method) np_compression (pyopenms.NumpressConfig property) nr_ms1_spectra (pyopenms.BrukerTimsFile.DIAStreamingMetadata property) nr_ms2_spectra (pyopenms.BrukerTimsFile.DIAStreamingMetadata property) nr_peaks (pyopenms.OpenSwath_Scores property) nr_windows (pyopenms.SignalToNoiseEstimatorMedianRapid.NoiseEstimator property) NRMS (pyopenms.IonSource.IonizationMethod attribute) NTerminal (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) nucleic_acids (pyopenms.FileInfo.MzTabInfo property) NucleicAcidSpectrumGenerator (class in pyopenms) num_charge_states (pyopenms.DeltaMassEntry property) (pyopenms.ModificationPattern property) (pyopenms.ModificationSummary property) (pyopenms.PTMEntry property) num_chrom_peaks (pyopenms.FileInfo.PeakInfo property) num_chromatograms (pyopenms.FileInfo.PeakInfo property) num_features (pyopenms.FileInfo.FeatureInfo property) num_iso_peaks_mean (pyopenms.CrossLinkSpectrumMatch property) num_iso_peaks_mean_linear_alpha (pyopenms.CrossLinkSpectrumMatch property) num_iso_peaks_mean_linear_beta (pyopenms.CrossLinkSpectrumMatch property) num_iso_peaks_mean_xlinks_alpha (pyopenms.CrossLinkSpectrumMatch property) num_iso_peaks_mean_xlinks_beta (pyopenms.CrossLinkSpectrumMatch property) num_runs (pyopenms.FileInfo.IdentInfo property) num_sequences (pyopenms.FileInfo.FastaInfo property) num_spectra (pyopenms.FileInfo.PeakInfo property) num_unique_modifications (pyopenms.PTMStatistics property) number_ms2_empty (pyopenms.IsobaricQuantifierStatistics property) number_ms2_total (pyopenms.IsobaricQuantifierStatistics property) NUMBER_OF_CROSS_LINK_TYPES (pyopenms.OPXLDataStructs attribute) (pyopenms.OPXLDataStructs.ProteinProteinCrossLinkType attribute) number_of_entries (pyopenms.PEFFDatabaseMetadata property) NUMBER_OF_PROVENANCE (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.Provenance attribute) NUMBER_OF_SOURCE_CLASSIFICATIONS (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.SourceClassification attribute) NUMBER_OF_TERM_SPECIFICITY (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.TermSpecificity attribute) (pyopenms.Ribonucleotide attribute) (pyopenms.Ribonucleotide.TermSpecificityNuc attribute) numerator (pyopenms.Base64.ByteOrder attribute) (pyopenms.BasicProteinInferenceAlgorithm.AggregationMethod attribute) (pyopenms.BoundaryCondition attribute) (pyopenms.BSpline2d.BoundaryCondition attribute) (pyopenms.ChromatogramSettings.ChromatogramType attribute) (pyopenms.CombinationsLogic attribute) (pyopenms.ConsensusMapNormalizerAlgorithmMedian.NormalizationMethod attribute) (pyopenms.ControlledVocabulary.CVTerm.XRefType attribute) (pyopenms.DRangeIntersection attribute) (pyopenms.DriftTimeUnit attribute) (pyopenms.EntrapmentEvaluation.Kind attribute) (pyopenms.EntrapmentEvaluation.Level attribute) (pyopenms.EnzymaticDigestion.Specificity attribute) (pyopenms.FeatureDeconvolution.CHARGEMODE attribute) (pyopenms.FileType attribute) (pyopenms.FileTypes.FileType attribute) (pyopenms.HydrophobicityScaleMethod attribute) (pyopenms.IDMapper.Measure attribute) (pyopenms.IDRipper.OriginAnnotationFormat attribute) (pyopenms.IDType attribute) (pyopenms.IsotopeDistribution.Sorted attribute) (pyopenms.ITRAQ_TYPES attribute) (pyopenms.ItraqConstants.ITRAQ_TYPES attribute) (pyopenms.LogType attribute) (pyopenms.Measure attribute) (pyopenms.MetaboliteFeatureDeconvolution.CHARGEMODE attribute) (pyopenms.Method attribute) (pyopenms.MSNumpressCoder.NumpressCompression attribute) (pyopenms.MultipleTesting.LfdrTransform attribute) (pyopenms.MultipleTesting.Pi0Method attribute) (pyopenms.MzPAFDeltaUnit attribute) (pyopenms.MzPAFErrorCode attribute) (pyopenms.MzPAFIonSeries attribute) (pyopenms.NaNPolicy attribute) (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.NormalizationMethod attribute) (pyopenms.OpenMSOSInfo.OpenMS_Architecture attribute) (pyopenms.OpenMSOSInfo.OpenMS_OS attribute) (pyopenms.OpenPepXLAlgorithm.ExitCodes attribute) (pyopenms.OPXLDataStructs.PeptidePosition attribute) (pyopenms.OPXLDataStructs.ProteinProteinCrossLinkType attribute) (pyopenms.OriginAnnotationFormat attribute) (pyopenms.ParquetWriteConfig.Compression attribute) (pyopenms.PeakGroup.TargetDecoyType attribute) (pyopenms.PEFFDatabaseMetadata.SequenceType attribute) (pyopenms.PEFFModification.ModificationType attribute) (pyopenms.PeptideIndexing.ExitCodes attribute) (pyopenms.PercolatorOutfile.ScoreType attribute) (pyopenms.ProForma.ConversionIssueType attribute) (pyopenms.ProForma.ConversionPolicy attribute) (pyopenms.ProForma.CvDatabase attribute) (pyopenms.ProForma.WriteMode attribute) (pyopenms.ProgressLogger.LogType attribute) (pyopenms.ProSEAlgorithm.ProSEAlgorithm_ExitCodes attribute) (pyopenms.ProteomicsPkaScale attribute) (pyopenms.QuotingMethod attribute) (pyopenms.RankData.Method attribute) (pyopenms.RankData.NaNPolicy attribute) (pyopenms.RequirementLevel attribute) (pyopenms.Residue.ResidueType attribute) (pyopenms.ResidueModification.Provenance attribute) (pyopenms.ResidueModification.SourceClassification attribute) (pyopenms.ResidueModification.TermSpecificity attribute) (pyopenms.Ribonucleotide.TermSpecificityNuc attribute) (pyopenms.Scores.IDType attribute) (pyopenms.SIDE attribute) (pyopenms.SimpleSearchEngineAlgorithm.ExitCodes attribute) (pyopenms.UnitType attribute) (pyopenms.USI.IndexType attribute) (pyopenms.ValueType attribute) (pyopenms.XFDRAlgorithm.ExitCodes attribute) (pyopenms.XTandemInfile.ErrorUnit attribute) (pyopenms.XTandemInfile.MassType attribute) numerator_ref_ (pyopenms.ConsensusFeature.Ratio property) numpress NumpressConfig (class in pyopenms) numpressErrorTolerance (pyopenms.NumpressConfig property) numpressFixedPoint (pyopenms.NumpressConfig property) O O (pyopenms.IsotopeModel attribute) (pyopenms.IsotopeModel.Averagines attribute) OBO (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) observed_mass (pyopenms.PTMEntry property) obsolete (pyopenms.ControlledVocabulary.CVTerm property) octadecyl OFF (pyopenms.BrukerTimsFile.Config.CentroidAlgo attribute) (pyopenms.MassAnalyzer.ReflectronState attribute) offset (pyopenms.ImzMLAuxArrayIndex property) ok() (pyopenms.BSpline2d method) oligonucleotides (pyopenms.FileInfo.MzTabInfo property) OLINKED_GLYCOSYLATION (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.SourceClassification attribute) Omit (pyopenms.NaNPolicy attribute) (pyopenms.RankData.NaNPolicy attribute) OMS (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) OMSFile (class in pyopenms) OMSSACSVFile (class in pyopenms) OMSSAXML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) OMSSAXMLFile (class in pyopenms) ON (pyopenms.MassAnalyzer.ReflectronState attribute) OnDiscImzMLExperiment (class in pyopenms) OnDiscMSExperiment (class in pyopenms) OnDiscThermoRawExperiment (class in pyopenms) op (pyopenms.DataFilter property) open() (pyopenms.OnDiscImzMLExperiment method) openFile() (pyopenms.IndexedMzMLHandler method) (pyopenms.OnDiscMSExperiment method) (pyopenms.OnDiscThermoRawExperiment method) OpenMS API OpenMSBuildInfo (class in pyopenms) OpenMSOSInfo (class in pyopenms) OpenMSOSInfo.OpenMS_Architecture (class in pyopenms) OpenMSOSInfo.OpenMS_OS (class in pyopenms) OpenPepXLAlgorithm (class in pyopenms) OpenPepXLAlgorithm.ExitCodes (class in pyopenms) OpenSearchAnalysisResult (class in pyopenms) OpenSearchModificationAnalysis (class in pyopenms) OPENSPLIT (pyopenms.IonSource.InletType attribute) OpenSwath_Scores (class in pyopenms) OpenSwath_Scores_Usage (class in pyopenms) OpenSwathDataAccessHelper (class in pyopenms) OpenSwathHelper (class in pyopenms) OpenSwathOSWWriter (class in pyopenms) OpenSwathScoring (class in pyopenms) optimal_threshold (pyopenms.SelectorParameters property) optimizeCalibrationCurveIterative() (pyopenms.AbsoluteQuantitation method) optimizeSingleCalibrationCurve() (pyopenms.AbsoluteQuantitation method) optional_tag (pyopenms.PEFFDisulfideBond property) (pyopenms.PEFFModification property) (pyopenms.PEFFProcessedRegion property) (pyopenms.PEFFVariantComplex property) (pyopenms.PEFFVariantSimple property) optional_tag_defs (pyopenms.PEFFDatabaseMetadata property) OPXLDataStructs (class in pyopenms) OPXLDataStructs.PeptidePosition (class in pyopenms) OPXLDataStructs.ProteinProteinCrossLinkType (class in pyopenms) OPXLHelper (class in pyopenms) OPXLSpectrumProcessingAlgorithms (class in pyopenms) OR (pyopenms.CombinationsLogic attribute) Orbitrap orbitrap ORBITRAP (pyopenms.MassAnalyzer.AnalyzerType attribute) Ordinal (pyopenms.Method attribute) ordinal (pyopenms.MzPAFAnnotation property) Ordinal (pyopenms.RankData.Method attribute) ordinal (pyopenms.TargetedExperiment_Interpretation property) original_score_higher_better (pyopenms.IDSwitchResult property) original_score_name (pyopenms.IDSwitchResult property) original_score_type (pyopenms.IDSwitchResult property) original_text (pyopenms.MassDelta property) OriginAnnotationFormat (class in pyopenms) orNext() (pyopenms.ParquetFilter method) OS_LINUX (pyopenms.OpenMSOSInfo.OpenMS_OS attribute) OS_MACOS (pyopenms.OpenMSOSInfo.OpenMS_OS attribute) OS_UNKNOWN (pyopenms.OpenMSOSInfo.OpenMS_OS attribute) OS_WINDOWS (pyopenms.OpenMSOSInfo.OpenMS_OS attribute) OSBinaryDataArray (class in pyopenms) OSChromatogram (class in pyopenms) OSChromatogramMeta (class in pyopenms) osms (pyopenms.FileInfo.MzTabInfo property) OSSpectrum (class in pyopenms) OSSpectrumMeta (class in pyopenms) OSW (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) OSW_ChromExtractParams (class in pyopenms) OSWData (class in pyopenms) OSWHierarchy (class in pyopenms) OSWHierarchy.Level (class in pyopenms) OSWIndexTrace (class in pyopenms) OSWPeakGroup (class in pyopenms) OSWPeptidePrecursor (class in pyopenms) OSWPQ (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) OSWProtein (class in pyopenms) OSWTransition (class in pyopenms) OTHER (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.SourceClassification attribute) (pyopenms.UnitType attribute) OTHER_GLYCOSYLATION (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.SourceClassification attribute) overall_quality_l (pyopenms.MRMFQC_ComponentGroupQCs property) (pyopenms.MRMFQC_ComponentQCs property) overall_quality_u (pyopenms.MRMFQC_ComponentGroupQCs property) (pyopenms.MRMFQC_ComponentQCs property) P padding (pyopenms.SysInfo attribute) pairCompoundWithAnnotatedTDSpectraPairs() (pyopenms.MetaboTargetedAssay static method) paired (pyopenms.EntrapmentEvaluation.Result property) pairedFDP() (pyopenms.EntrapmentEvaluation.Result method) pairPeptides() (pyopenms.EntrapmentEvaluation static method) pairwise_median (pyopenms.IDFreeMassErrorEstimator.RobustError property) pairwise_p95_abs (pyopenms.IDFreeMassErrorEstimator.RobustError property) pairwise_sigma (pyopenms.IDFreeMassErrorEstimator.RobustError property) Param (class in pyopenms) ParamCTDFile (class in pyopenms) ParamEntry (class in pyopenms) ParamNode (class in pyopenms) params (pyopenms.MRMFP_ComponentGroupParams property) (pyopenms.MRMFP_ComponentParams property) ParamValue (class in pyopenms) PARAMXML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) ParamXMLFile (class in pyopenms) parent (pyopenms.GlycanStructure.Node property) parents (pyopenms.ControlledVocabulary.CVTerm property) PARQUET (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) ParquetFilter (class in pyopenms) ParquetWriteConfig (class in pyopenms) ParquetWriteConfig.Compression (class in pyopenms) parse() (pyopenms.LogConfigHandler method) (pyopenms.MzPAF static method) (pyopenms.ProForma static method) parseAdductString() (pyopenms.AMSE_AdductInfo static method) parseIDType() (pyopenms.Scores static method) parseIon() (pyopenms.ProForma static method) parseMultiple() (pyopenms.MzPAF static method) PARTICLEBEAM (pyopenms.IonSource.InletType attribute) passes() (pyopenms.DataFilters method) path (pyopenms.ExperimentalDesign_MSFileSectionEntry property) path() (pyopenms.File static method) PAULIONTRAP (pyopenms.MassAnalyzer.AnalyzerType attribute) PD (pyopenms.IonSource.IonizationMethod attribute) (pyopenms.Precursor.ActivationMethod attribute) peak (pyopenms.FileInfo.Result property) peak map peak maps Peak1D (class in pyopenms) Peak2D (class in pyopenms) Peak2D.DimensionDescription (class in pyopenms) peak_depth (pyopenms.ProbablePhosphoSites property) PEAK_PICKING (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) peak_type_per_ms_level (pyopenms.FileInfo.PeakInfo property) PeakBoundary (class in pyopenms) PeakFileOptions (class in pyopenms) PeakGroup (class in pyopenms) PeakGroup.TargetDecoyType (class in pyopenms) PeakIntegrator (class in pyopenms) PeakMap (in module pyopenms) PeakMapExtractor (class in pyopenms) PEAKMAPPARQUET (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) PeakPickerChromatogram (class in pyopenms) PeakPickerHiRes (class in pyopenms) PeakPickerIM (class in pyopenms) PeakPickerIterative (class in pyopenms) peaks (pyopenms.IsotopeCluster property) peaks_struct() (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) PeakSpectrum (in module pyopenms) PeakTypeEstimator (class in pyopenms) PeakWidthEstimator (class in pyopenms) PEFF (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) PEFFCustomKeyDef (class in pyopenms) PEFFDatabaseMetadata (class in pyopenms) PEFFDatabaseMetadata.SequenceType (class in pyopenms) PEFFDisulfideBond (class in pyopenms) PEFFEntry (class in pyopenms) PEFFFile (class in pyopenms) PEFFModification (class in pyopenms) PEFFModification.ModificationType (class in pyopenms) PEFFProcessedRegion (class in pyopenms) PEFFVariantComplex (class in pyopenms) PEFFVariantSimple (class in pyopenms) PEI (pyopenms.IonSource.IonizationMethod attribute) PEP (pyopenms.IDType attribute) (pyopenms.Scores.IDType attribute) pep_indices (pyopenms.PeptideProteinResolution_ConnectedComponent property) PEPLIST (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) PepNovo peps (pyopenms.RescoreOutput property) peps_np() (pyopenms.RescoreOutput method) Peptide (class in pyopenms) PEPTIDE (pyopenms.EntrapmentEvaluation.Level attribute) (pyopenms.OSWHierarchy attribute) (pyopenms.OSWHierarchy.Level attribute) (pyopenms.TheoreticalGlycanSpectrumGenerator.IonType attribute) peptide-spectrum match peptide_df_columns() (pyopenms.FeatureMap method) peptide_fraction_group_abundances (pyopenms.PeptideAndProteinQuant_ProteinData property) peptide_group_label (pyopenms.LightCompound property) peptide_hits (pyopenms.FileInfo.IdentInfo property) peptide_id_index (pyopenms.CrossLinkSpectrumMatch property) peptide_identification_view() (pyopenms.PeptideIdentificationList method) peptide_identification_views() (pyopenms.PeptideIdentificationList method) peptide_identifications_to_df() (in module pyopenms) peptide_ids (pyopenms.SearchResult property) PEPTIDE_IDS_EMPTY (pyopenms.PeptideIndexing.ExitCodes attribute) peptide_keys (pyopenms.RescoreInput property) peptide_mass (pyopenms.AASeqWithMass property) peptide_peps (pyopenms.RescoreOutput property) peptide_psm_counts (pyopenms.PeptideAndProteinQuant_ProteinData property) peptide_q_values (pyopenms.RescoreOutput property) peptide_ref (pyopenms.LightTransition property) peptide_retention (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) peptide_seq (pyopenms.AASeqWithMass property) PeptideAndProteinQuant (class in pyopenms) PeptideAndProteinQuant_PeptideData (class in pyopenms) PeptideAndProteinQuant_ProteinData (class in pyopenms) PeptideAndProteinQuant_Statistics (class in pyopenms) peptideCount() (pyopenms.ProteaseDigestion method) PeptideEvidence (class in pyopenms) PeptideHit (class in pyopenms) PeptideHit_AnalysisResult (class in pyopenms) PeptideHit_PeakAnnotation (class in pyopenms) PeptideIdentification (class in pyopenms) PeptideIdentificationList (class in pyopenms) PeptideIndexing (class in pyopenms) PeptideIndexing.ExitCodes (class in pyopenms) PeptideProteinResolution (class in pyopenms) PeptideProteinResolution_ConnectedComponent (class in pyopenms) peptides (pyopenms.FileInfo.MzTabInfo property) Peptidoform (class in pyopenms) peptidoformFromJSON() (pyopenms.ProForma static method) PeptidoformIon (class in pyopenms) peptidoformIonFromJSON() (pyopenms.ProForma static method) peptidoformIonToJSON() (pyopenms.ProForma static method) peptidoforms (pyopenms.LightTransition property) peptidoformToJSON() (pyopenms.ProForma static method) PEPXML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) PepXMLFile (class in pyopenms) PepXMLFileMascot (class in pyopenms) per_charge_intensity (pyopenms.MassFeature_FDHS property) PER_FRAME (pyopenms.BrukerTimsFile.Config.PressureCompensation attribute) per_isotope_intensity (pyopenms.MassFeature_FDHS property) per_ms_level (pyopenms.FileInfo.Ranges property) percentage (pyopenms.DeltaMassEntry property) (pyopenms.PTMEntry property) percentiles_after (pyopenms.TransformationStatistics property) percentiles_before (pyopenms.TransformationStatistics property) percents (pyopenms.TransformationStatistics property) Percolator (class in pyopenms) percolator (pyopenms.SearchResult property) PercolatorFeatureSetHelper (class in pyopenms) PercolatorInfile (class in pyopenms) PercolatorOutfile (class in pyopenms) PercolatorOutfile.ScoreType (class in pyopenms) PercolatorRescoring (class in pyopenms) percTIC (pyopenms.CrossLinkSpectrumMatch property) performed (pyopenms.FileInfo.CorruptionInfo property) (pyopenms.FileInfo.DetailInfo property) (pyopenms.FileInfo.ValidationInfo property) performSpectrumDeconvolution() (pyopenms.SpectralDeconvolution method) PHD (pyopenms.Precursor.ActivationMethod attribute) PHOTODIODEARRAYDETECTOR (pyopenms.IonDetector.Type attribute) PHOTOMULTIPLIER (pyopenms.IonDetector.Type attribute) PI (in module pyopenms.Constants) (pyopenms.IonSource.IonizationMethod attribute) pi0 (pyopenms.Pi0Result property) pi0_lambda (pyopenms.Pi0Result property) pi0_smooth (pyopenms.Pi0Result property) pi0Est() (pyopenms.MultipleTesting static method) pi0MethodToString() (pyopenms.MultipleTesting static method) Pi0Result (class in pyopenms) PI_PeakArea (class in pyopenms) PI_PeakBackground (class in pyopenms) PI_PeakShapeMetrics (class in pyopenms) PIC (pyopenms.MSNumpressCoder attribute) (pyopenms.MSNumpressCoder.NumpressCompression attribute) pick() (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) pickChromatogram() (pyopenms.PeakPickerChromatogram method) pickExperiment() (pyopenms.MRMFeatureFinderScoring method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) pickIMCluster() (pyopenms.PeakPickerIM method) pickIMElutionProfiles() (pyopenms.PeakPickerIM method) pickIMTraces() (pyopenms.PeakPickerIM method) pickSpectrum() (pyopenms.TargetedSpectraExtractor method) pickTransitionGroup() (pyopenms.MRMTransitionGroupPicker method) PIN (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) pint_mono (pyopenms.SiriusMSFile_CompoundInfo property) PipEchoAlgorithm (class in pyopenms) pixel_size_unit (pyopenms.ImzMLMeta property) pixel_size_x (pyopenms.ImzMLMeta property) pixel_size_y (pyopenms.ImzMLMeta property) pixels_struct() (pyopenms.MSImagingGeometry method) PlainMSDataWritingConsumer (class in pyopenms) PLANCK (in module pyopenms.Constants) plot_chromatogram() (in module pyopenms.plotting) plot_spectrum() (in module pyopenms.plotting) plotTargetDecoyEstimation() (pyopenms.PosteriorErrorProbabilityModel method) pmass (pyopenms.SiriusMSFile_CompoundInfo property) PNG (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) pNorm() (pyopenms.MultipleTesting static method) POINTCOLLECTOR (pyopenms.IonDetector.Type attribute) points_across_baseline (pyopenms.PI_PeakShapeMetrics property) points_across_half_height (pyopenms.PI_PeakShapeMetrics property) polar() (pyopenms.AAIndex static method) polarity (pyopenms.ImzMLMeta property) polarityToString() (pyopenms.IonSource static method) POLNULL (pyopenms.IonSource.Polarity attribute) pop_back() (pyopenms.DeconvolvedSpectrum method) pos_neg_mean_weighted_posteriors() (pyopenms.PosteriorErrorProbabilityModel method) position (pyopenms.AASeqWithMass property) (pyopenms.ConversionIssue property) (pyopenms.PEFFModification property) (pyopenms.PEFFVariantSimple property) (pyopenms.RNaseDigestionProduct property) POSITIVE (pyopenms.IonSource.Polarity attribute) POSTACCELERATIONDETECTOR (pyopenms.IonDetector.Type attribute) PosteriorErrorProbabilityModel (class in pyopenms) PosteriorErrorProbabilityModel.ModelType (class in pyopenms) POSTERRPROB (pyopenms.PercolatorOutfile.ScoreType attribute) POSTTRANSLATIONAL (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.SourceClassification attribute) potential_cmp (pyopenms.MetaboTargetedAssay property) potential_rmts (pyopenms.MetaboTargetedAssay property) PP (pyopenms.IDType attribute) (pyopenms.Scores.IDType attribute) PPM (pyopenms.MzPAFDeltaUnit attribute) ppm (pyopenms.OSW_ChromExtractParams property) PPM (pyopenms.XTandemInfile attribute) (pyopenms.XTandemInfile.ErrorUnit attribute) ppm_error_abs_sum (pyopenms.CrossLinkSpectrumMatch property) ppm_error_abs_sum_alpha (pyopenms.CrossLinkSpectrumMatch property) ppm_error_abs_sum_beta (pyopenms.CrossLinkSpectrumMatch property) ppm_error_abs_sum_linear (pyopenms.CrossLinkSpectrumMatch property) ppm_error_abs_sum_linear_alpha (pyopenms.CrossLinkSpectrumMatch property) ppm_error_abs_sum_linear_beta (pyopenms.CrossLinkSpectrumMatch property) ppm_error_abs_sum_xlinks (pyopenms.CrossLinkSpectrumMatch property) ppm_error_abs_sum_xlinks_alpha (pyopenms.CrossLinkSpectrumMatch property) ppm_error_abs_sum_xlinks_beta (pyopenms.CrossLinkSpectrumMatch property) ppmToMass() (in module pyopenms) (pyopenms.Math static method) ppmToMassAbs() (in module pyopenms) (pyopenms.Math static method) PQD (pyopenms.Precursor.ActivationMethod attribute) PQP (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) pre_release_identifier (pyopenms.VersionDetails property) pre_score (pyopenms.CrossLinkSpectrumMatch property) PrecalAveragine (class in pyopenms) Precursor (class in pyopenms) PRECURSOR (pyopenms.InstrumentSettings.ScanMode attribute) (pyopenms.MzPAFIonSeries attribute) Precursor (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) Precursor.ActivationMethod (class in pyopenms) precursor_candidate_ppm (pyopenms.IDFreeMassErrorEstimator.Parameters property) precursor_charge (pyopenms.SpectrumMetaData property) precursor_charges (pyopenms.FileInfo.PeakInfo property) precursor_clusters_used (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) precursor_correction (pyopenms.CrossLinkSpectrumMatch property) (pyopenms.ProteinProteinCrossLink property) precursor_da (pyopenms.IDFreeMassErrorEstimator.Result property) precursor_eligible_ms2 (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) precursor_error_ppm (pyopenms.CrossLinkSpectrumMatch property) PRECURSOR_ERROR_PPM_USERPARAM (in module pyopenms.Constants) precursor_im (pyopenms.LightTransition property) (pyopenms.TransitionListEvidenceFilter_PrecursorEvidence property) precursor_im_scale (pyopenms.TransitionListEvidenceFilter_Result property) precursor_im_scaled_by_charge (pyopenms.TransitionListEvidenceFilter_Result property) precursor_int (pyopenms.MetaboTargetedAssay property) precursor_mass (pyopenms.IsobaricQuantities property) (pyopenms.XLPrecursor property) precursor_mass_tolerance (pyopenms.SearchParameters property) precursor_mass_tolerance_ppm (pyopenms.SearchParameters property) precursor_mz (pyopenms.IsobaricQuantities property) (pyopenms.LightTransition property) (pyopenms.MetaboTargetedAssay property) (pyopenms.SpectrumMetaData property) (pyopenms.TransitionListEvidenceFilter_PrecursorEvidence property) precursor_mz_max (pyopenms.ThermoRawFileOptions property) precursor_mz_min (pyopenms.ThermoRawFileOptions property) precursor_paired_spectra (pyopenms.IDFreeMassErrorEstimator.Diagnostics property) precursor_ppm (pyopenms.IDFreeMassErrorEstimator.Result property) PRECURSOR_RECALCULATION (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) precursor_residual_peak_count (pyopenms.CrossLinkSpectrumMatch property) precursor_rt (pyopenms.SpectrumMetaData property) precursor_signal_proportion (pyopenms.CrossLinkSpectrumMatch property) precursor_target_intensity (pyopenms.CrossLinkSpectrumMatch property) precursor_target_peak_count (pyopenms.CrossLinkSpectrumMatch property) precursor_tolerance_ppm (pyopenms.IDFreeMassErrorEstimator.Result property) precursor_total_intensity (pyopenms.CrossLinkSpectrumMatch property) PrecursorCorrection (class in pyopenms) precursorMzToleranceUnitIsPPM() (pyopenms.SiriusExportAlgorithm method) PrecursorPurity (class in pyopenms) predict() (pyopenms.MZTrafoModel method) PREDICTED (pyopenms.RetentionTime attribute) (pyopenms.RetentionTime.RTType attribute) Prediction (class in pyopenms) prefix (pyopenms.PEFFDatabaseMetadata property) (pyopenms.PEFFEntry property) prepare_coordinates() (pyopenms.ChromatogramExtractor static method) prepareLine() (pyopenms.OpenSwathOSWWriter method) prepareProteinPeptideMaps_() (pyopenms.MRMFeatureFinderScoring method) preprocess() (pyopenms.SpectraSTSimilarityScore method) PreprocessedPairSpectra (class in pyopenms) preprocessing() (pyopenms.SiriusExportAlgorithm method) preprocessSpectra() (pyopenms.OPXLSpectrumProcessingAlgorithms static method) preScore() (pyopenms.XQuestScores static method) present (pyopenms.FileInfo.ExperimentMeta property) (pyopenms.FileInfo.Range property) preserve_trailers (pyopenms.ThermoRawFileOptions property) pressure_compensation (pyopenms.BrukerTimsFile.Config property) PRETRANSLATIONAL (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.SourceClassification attribute) probability (pyopenms.ProteinGroup property) ProbablePhosphoSites (class in pyopenms) Probit (pyopenms.MultipleTesting.LfdrTransform attribute) processed_regions (pyopenms.PEFFEntry property) processing (pyopenms.FileInfo.Options property) (pyopenms.FileInfo.Result property) processingActionToString() (pyopenms.DataProcessing static method) procs (pyopenms.SysInfo attribute) PROD (pyopenms.BasicProteinInferenceAlgorithm attribute) (pyopenms.BasicProteinInferenceAlgorithm.AggregationMethod attribute) Product (class in pyopenms) product_mz (pyopenms.LightTransition property) PROFILE (pyopenms.SpectrumSettings.SpectrumType attribute) ProForma (class in pyopenms) ProForma.ConversionIssueType (class in pyopenms) ProForma.ConversionPolicy (class in pyopenms) ProForma.CvDatabase (class in pyopenms) ProForma.WriteMode (class in pyopenms) ProgressLogger (class in pyopenms) ProgressLogger.LogType (class in pyopenms) Propagate (pyopenms.NaNPolicy attribute) (pyopenms.RankData.NaNPolicy attribute) PROPORTIONAL (pyopenms.MassAnalyzer.ResolutionType attribute) ProSEAlgorithm (class in pyopenms) ProSEAlgorithm.ProSEAlgorithm_ExitCodes (class in pyopenms) prot_grp_indices (pyopenms.PeptideProteinResolution_ConnectedComponent property) ProteaseDB (class in pyopenms) ProteaseDigestion (class in pyopenms) Protein (class in pyopenms) PROTEIN (pyopenms.OSWHierarchy attribute) (pyopenms.OSWHierarchy.Level attribute) PROTEIN_C_TERM (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.TermSpecificity attribute) protein_existence (pyopenms.PEFFEntry property) protein_hits (pyopenms.FileInfo.IdentInfo property) protein_ids (pyopenms.SearchResult property) PROTEIN_N_TERM (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.TermSpecificity attribute) protein_names (pyopenms.PEFFEntry property) protein_refs (pyopenms.LightCompound property) (pyopenms.Peptide property) ProteinGroup (class in pyopenms) ProteinHit (class in pyopenms) ProteinIdentification (class in pyopenms) ProteinIdentification.PeakMassType (class in pyopenms) ProteinIdentificationArrowIO (class in pyopenms) ProteinProteinCrossLink (class in pyopenms) ProteinRunReferences (class in pyopenms) proteins (pyopenms.FileInfo.MzTabInfo property) (pyopenms.LightTargetedExperiment property) proteoforms (pyopenms.PEFFEntry property) ProteomicsPkaScale (class in pyopenms) ProteoWizard PROTON_MASS (in module pyopenms.Constants) PROTON_MASS_U (in module pyopenms.Constants) PROTXML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) ProtXMLFile (class in pyopenms) PScore (class in pyopenms) PSD (pyopenms.Precursor.ActivationMethod attribute) PSI_MOD (pyopenms.PEFFModification.ModificationType attribute) PSM (pyopenms.EntrapmentEvaluation.Level attribute) psm_columns() (pyopenms.PeptideIdentificationList method) psm_count (pyopenms.PeptideAndProteinQuant_PeptideData property) (pyopenms.PeptideAndProteinQuant_ProteinData property) psm_counts (pyopenms.PeptideAndProteinQuant_PeptideData property) PSMs psms (pyopenms.FileInfo.MzTabInfo property) PSMS (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) psms_per_spectrum (pyopenms.FileInfo.IdentInfo property) PSQ (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) ptm_stats (pyopenms.OpenSearchAnalysisResult property) PTMEntry (class in pyopenms) PTMStatistics (class in pyopenms) Publication (class in pyopenms) PULSECOUNTING (pyopenms.IonDetector.AcquisitionMode attribute) PurityScores (class in pyopenms) push_back() (pyopenms.AcquisitionInfo method) (pyopenms.ConsensusMap method) (pyopenms.DeconvolvedSpectrum method) (pyopenms.FeatureMap method) (pyopenms.FloatDataArray method) (pyopenms.IMSAlphabet method) (pyopenms.IntegerDataArray method) (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) (pyopenms.PeakGroup method) (pyopenms.PeptideIdentificationList method) (pyopenms.StringDataArray method) PYMS (pyopenms.IonSource.IonizationMethod attribute) pyopenms module pyopenms.Constants module pyopenms.plotting module Python Enhancement Proposals PEP 561 Q q_values (pyopenms.RescoreOutput property) q_values_np() (pyopenms.RescoreOutput method) QALL (pyopenms.FeatureDeconvolution.CHARGEMODE attribute) (pyopenms.MetaboliteFeatureDeconvolution.CHARGEMODE attribute) QFROMFEATURE (pyopenms.FeatureDeconvolution.CHARGEMODE attribute) (pyopenms.MetaboliteFeatureDeconvolution.CHARGEMODE attribute) QHEURISTIC (pyopenms.FeatureDeconvolution.CHARGEMODE attribute) (pyopenms.MetaboliteFeatureDeconvolution.CHARGEMODE attribute) QPXFile (class in pyopenms) qscore (pyopenms.MassFeature_FDHS property) QTCluster (class in pyopenms) QTClusterFinder (class in pyopenms) QUADRATIC (pyopenms.MassAnalyzer.ScanLaw attribute) (pyopenms.MZTrafoModel.MODELTYPE attribute) QUADRATIC_WEIGHTED (pyopenms.MZTrafoModel.MODELTYPE attribute) quadrupole QUADRUPOLE (pyopenms.MassAnalyzer.AnalyzerType attribute) QUALITY (pyopenms.DataFilters attribute) (pyopenms.DataFilters.FilterType attribute) quant_features (pyopenms.PeptideAndProteinQuant_Statistics property) quant_peptides (pyopenms.PeptideAndProteinQuant_Statistics property) quant_proteins (pyopenms.PeptideAndProteinQuant_Statistics property) quantify() (pyopenms.IsobaricQuantifier method) quantifyComponents() (pyopenms.AbsoluteQuantitation method) quantifying_transition (pyopenms.LightTransition property) quantifyPeptides() (pyopenms.PeptideAndProteinQuant method) quantifyProteins() (pyopenms.PeptideAndProteinQuant method) QUANTITATION (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) quantities (pyopenms.IsobaricQuantities property) query() (pyopenms.MassExplainer method) query_chromatograms() (pyopenms.XICParquetFile method) query_mobilograms() (pyopenms.XIMParquetFile method) query_peak_maps() (pyopenms.XIPMParquetFile method) queryByConsensusFeature() (pyopenms.AccurateMassSearchEngine method) queryByFeature() (pyopenms.AccurateMassSearchEngine method) queryByMZ() (pyopenms.AccurateMassSearchEngine method) QuotingMethod (class in pyopenms) QVAL (pyopenms.IDType attribute) (pyopenms.Scores.IDType attribute) QVALUE (pyopenms.PercolatorOutfile.ScoreType attribute) qValue() (pyopenms.EntrapmentEvaluation static method) (pyopenms.MultipleTesting static method) R RAD_PER_DEG (in module pyopenms.Constants) RADIALEJECTIONLINEARIONTRAP (pyopenms.MassAnalyzer.AnalyzerType attribute) Raise (pyopenms.NaNPolicy attribute) (pyopenms.RankData.NaNPolicy attribute) RangeBase (class in pyopenms) RangeIntensity (class in pyopenms) RangeMobility (class in pyopenms) RangeMZ (class in pyopenms) RangeRT (class in pyopenms) ranges (pyopenms.FileInfo.Result property) rank (pyopenms.CrossLinkSpectrumMatch property) (pyopenms.TargetedExperiment_Interpretation property) RankData (class in pyopenms) RankData.Method (class in pyopenms) RankData.NaNPolicy (class in pyopenms) rankdata_double() (pyopenms.RankData static method) rankdata_float() (pyopenms.RankData static method) rankdata_int() (pyopenms.RankData static method) RankScaler (class in pyopenms) RANSAC (class in pyopenms) ransac() (pyopenms.RANSAC method) (pyopenms.RANSACQuadratic method) RansacModelLinear (class in pyopenms) RansacModelQuadratic (class in pyopenms) RANSACParam (class in pyopenms) RANSACQuadratic (class in pyopenms) raster() (pyopenms.LinearResamplerAlign method) raster_align() (pyopenms.LinearResamplerAlign method) rasterExperiment() (pyopenms.LinearResamplerAlign method) rasterizeIMFrame() (pyopenms.MSSpectrum method) rasterizeRTMZ() (pyopenms.MSExperiment method) ratio_value_ (pyopenms.ConsensusFeature.Ratio property) RATIONAL (pyopenms.BrukerTimsFile.Config.TimsCalibrationStrategy attribute) RAW (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) (pyopenms.IDType attribute) (pyopenms.Scores.IDType attribute) RAW_EVAL (pyopenms.IDType attribute) (pyopenms.Scores.IDType attribute) raw_rt_score (pyopenms.OpenSwath_Scores property) ReactionMonitoringTransition (class in pyopenms) ReactionMonitoringTransition.DecoyTransitionType (class in pyopenms) readable() (pyopenms.File static method) readChromatograms() (pyopenms.MzMLSqliteHandler method) readDIAMetadata() (pyopenms.BrukerTimsFile method) readExperiment() (pyopenms.MzMLSqliteHandler method) readMemdump() (pyopenms.CachedMzMLHandler method) (pyopenms.MSDataCachedConsumer method) readNext() (pyopenms.FASTAFile method) (pyopenms.PEFFFile method) readOutHeader() (pyopenms.InspectOutfile method) readQuantData() (pyopenms.PeptideAndProteinQuant method) readSpectra() (pyopenms.MzMLSqliteHandler method) (pyopenms.SpectrumLookup method) (pyopenms.SpectrumMetaDataLookup method) readStart() (pyopenms.FASTAFile method) (pyopenms.PEFFFile method) readSwathWindows() (pyopenms.SwathWindowLoader static method) real (pyopenms.Base64.ByteOrder attribute) (pyopenms.BasicProteinInferenceAlgorithm.AggregationMethod attribute) (pyopenms.BoundaryCondition attribute) (pyopenms.BSpline2d.BoundaryCondition attribute) (pyopenms.ChromatogramSettings.ChromatogramType attribute) (pyopenms.CombinationsLogic attribute) (pyopenms.ConsensusMapNormalizerAlgorithmMedian.NormalizationMethod attribute) (pyopenms.ControlledVocabulary.CVTerm.XRefType attribute) (pyopenms.DRangeIntersection attribute) (pyopenms.DriftTimeUnit attribute) (pyopenms.EntrapmentEvaluation.Kind attribute) (pyopenms.EntrapmentEvaluation.Level attribute) (pyopenms.EnzymaticDigestion.Specificity attribute) (pyopenms.FeatureDeconvolution.CHARGEMODE attribute) (pyopenms.FileType attribute) (pyopenms.FileTypes.FileType attribute) (pyopenms.HydrophobicityScaleMethod attribute) (pyopenms.IDMapper.Measure attribute) (pyopenms.IDRipper.OriginAnnotationFormat attribute) (pyopenms.IDType attribute) (pyopenms.IsotopeDistribution.Sorted attribute) (pyopenms.ITRAQ_TYPES attribute) (pyopenms.ItraqConstants.ITRAQ_TYPES attribute) (pyopenms.LogType attribute) (pyopenms.Measure attribute) (pyopenms.MetaboliteFeatureDeconvolution.CHARGEMODE attribute) (pyopenms.Method attribute) (pyopenms.MSNumpressCoder.NumpressCompression attribute) (pyopenms.MultipleTesting.LfdrTransform attribute) (pyopenms.MultipleTesting.Pi0Method attribute) (pyopenms.MzPAFDeltaUnit attribute) (pyopenms.MzPAFErrorCode attribute) (pyopenms.MzPAFIonSeries attribute) (pyopenms.NaNPolicy attribute) (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.NormalizationMethod attribute) (pyopenms.OpenMSOSInfo.OpenMS_Architecture attribute) (pyopenms.OpenMSOSInfo.OpenMS_OS attribute) (pyopenms.OpenPepXLAlgorithm.ExitCodes attribute) (pyopenms.OPXLDataStructs.PeptidePosition attribute) (pyopenms.OPXLDataStructs.ProteinProteinCrossLinkType attribute) (pyopenms.OriginAnnotationFormat attribute) (pyopenms.ParquetWriteConfig.Compression attribute) (pyopenms.PeakGroup.TargetDecoyType attribute) (pyopenms.PEFFDatabaseMetadata.SequenceType attribute) (pyopenms.PEFFModification.ModificationType attribute) (pyopenms.PeptideIndexing.ExitCodes attribute) (pyopenms.PercolatorOutfile.ScoreType attribute) (pyopenms.ProForma.ConversionIssueType attribute) (pyopenms.ProForma.ConversionPolicy attribute) (pyopenms.ProForma.CvDatabase attribute) (pyopenms.ProForma.WriteMode attribute) (pyopenms.ProgressLogger.LogType attribute) (pyopenms.ProSEAlgorithm.ProSEAlgorithm_ExitCodes attribute) (pyopenms.ProteomicsPkaScale attribute) (pyopenms.QuotingMethod attribute) (pyopenms.RankData.Method attribute) (pyopenms.RankData.NaNPolicy attribute) (pyopenms.RequirementLevel attribute) (pyopenms.Residue.ResidueType attribute) (pyopenms.ResidueModification.Provenance attribute) (pyopenms.ResidueModification.SourceClassification attribute) (pyopenms.ResidueModification.TermSpecificity attribute) (pyopenms.Ribonucleotide.TermSpecificityNuc attribute) (pyopenms.Scores.IDType attribute) (pyopenms.SIDE attribute) (pyopenms.SimpleSearchEngineAlgorithm.ExitCodes attribute) (pyopenms.UnitType attribute) (pyopenms.USI.IndexType attribute) (pyopenms.ValueType attribute) (pyopenms.XFDRAlgorithm.ExitCodes attribute) (pyopenms.XTandemInfile.ErrorUnit attribute) (pyopenms.XTandemInfile.MassType attribute) RealMassDecomposer (class in pyopenms) reannotateTransitions() (pyopenms.MRMAssay method) Rectangle (pyopenms.MSImagingRegion.Shape attribute) rectangle() (pyopenms.MSImagingRegion static method) reduce() (pyopenms.DistanceMatrix method) reduceToOnePerSpectrum() (pyopenms.IDConflictResolverAlgorithm static method) REFLECTRON (pyopenms.Instrument.IonOpticsType attribute) reflectronStateToString() (pyopenms.MassAnalyzer static method) REFLSTATENULL (pyopenms.MassAnalyzer.ReflectronState attribute) regexp (pyopenms.PEFFCustomKeyDef property) regionOf() (pyopenms.MSImagingGeometry method) registerName() (pyopenms.MetaInfoRegistry method) registry() (pyopenms.MetaInfo static method) RegularSwathFileConsumer (class in pyopenms) relative_d (pyopenms.RANSACParam property) remove() (pyopenms.DataFilters method) (pyopenms.File static method) (pyopenms.Param method) remove_overlapping_features() (pyopenms.MRMTransitionGroupPicker method) removeAdduct() (pyopenms.Compomer method) removeAll() (pyopenms.Param method) removeAllClusters() (pyopenms.ClusteringGrid method) removeBetaPeptideHits() (pyopenms.OPXLHelper static method) removeCluster() (pyopenms.ClusteringGrid method) removed (pyopenms.UnresolvedIdentifications property) removeDanglingProteinReferences() (pyopenms.IDFilter static method) removeDecoyHits() (pyopenms.IDFilter static method) removeDirRecursively() (pyopenms.File static method) removeDuplicatePeptideHits() (pyopenms.IDFilter static method) removeEmptyIdentifications() (pyopenms.IDFilter static method) removeEmptyPrimaryMSRunPaths() (pyopenms.ProteinIdentification method) removeHitsMatchingProteins() (pyopenms.IDFilter static method) removeMetaValue() (pyopenms.Acquisition method) (pyopenms.AcquisitionInfo method) (pyopenms.BaseFeature method) (pyopenms.ChromatogramSettings method) (pyopenms.ColumnHeader method) (pyopenms.Compound method) (pyopenms.Configuration method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusMap method) (pyopenms.Contact method) (pyopenms.ContactPerson method) (pyopenms.CVTermList method) (pyopenms.CVTermListInterface method) (pyopenms.DataProcessing method) (pyopenms.ExperimentalSettings method) (pyopenms.Feature method) (pyopenms.FeatureMap method) (pyopenms.FloatDataArray method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Instrument method) (pyopenms.InstrumentSettings method) (pyopenms.IntegerDataArray method) (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) (pyopenms.MetaInfoDescription method) (pyopenms.MetaInfoInterface method) (pyopenms.MRMFeature method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.Peptide method) (pyopenms.PeptideHit method) (pyopenms.PeptideIdentification method) (pyopenms.Precursor method) (pyopenms.Prediction method) (pyopenms.Product method) (pyopenms.Protein method) (pyopenms.ProteinHit method) (pyopenms.ProteinIdentification method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.RichPeak2D method) (pyopenms.Sample method) (pyopenms.ScanWindow method) (pyopenms.SearchParameters method) (pyopenms.Software method) (pyopenms.SourceFile method) (pyopenms.SpectrumSettings method) (pyopenms.StringDataArray method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TraMLProduct method) removeOutliersIterative() (pyopenms.MRMRTNormalizer static method) removeOutliersRANSAC() (pyopenms.MRMRTNormalizer static method) removePeaks() (pyopenms.SpectrumHelper static method) removePeptidesWithMatchingModifications() (pyopenms.IDFilter static method) removePeptidesWithMatchingSequences() (pyopenms.IDFilter static method) removeRegion() (pyopenms.MSImagingGeometry method) removeUnreferencedProteins() (pyopenms.IDFilter static method) removeValue() (pyopenms.MetaInfo method) REMPI (pyopenms.IonSource.IonizationMethod attribute) rename() (pyopenms.File static method) renormalize() (pyopenms.IsotopeDistribution method) rep_charge (pyopenms.MassFeature_FDHS property) rep_mz (pyopenms.MassFeature_FDHS property) replace() (pyopenms.DataFilters method) replaceCVTerm() (pyopenms.Compound method) (pyopenms.Configuration method) (pyopenms.Contact method) (pyopenms.CVTermList method) (pyopenms.CVTermListInterface method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Peptide method) (pyopenms.Precursor method) (pyopenms.Prediction method) (pyopenms.Product method) (pyopenms.Protein method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.Software method) (pyopenms.SourceFile method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TraMLProduct method) replaceCVTerms() (pyopenms.Compound method) (pyopenms.Configuration method) (pyopenms.Contact method) (pyopenms.CVTermList method) (pyopenms.CVTermListInterface method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Peptide method) (pyopenms.Precursor method) (pyopenms.Prediction method) (pyopenms.Product method) (pyopenms.Protein method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.Software method) (pyopenms.SourceFile method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TraMLProduct method) replacement (pyopenms.PEFFVariantComplex property) REPORTER (pyopenms.MzPAFIonSeries attribute) reporter_name (pyopenms.MzPAFAnnotation property) requested_score_higher_better (pyopenms.IDSwitchResult property) requested_score_name (pyopenms.IDSwitchResult property) requested_score_type (pyopenms.IDSwitchResult property) RequirementLevel (class in pyopenms) resample() (pyopenms.ConsensusMapNormalizerAlgorithmQuantile static method) rescore() (pyopenms.Percolator method) RescoreInput (class in pyopenms) RescoreOutput (class in pyopenms) rescorePSMs() (pyopenms.Percolator method) reserve() (pyopenms.ConsensusMap method) (pyopenms.DeconvolvedSpectrum method) (pyopenms.FloatDataArray method) (pyopenms.IntegerDataArray method) (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.PeakGroup method) reserveSpaceChromatograms() (pyopenms.MSExperiment method) reserveSpaceSpectra() (pyopenms.MSExperiment method) RESERVOIR (pyopenms.IonSource.InletType attribute) reset() (pyopenms.IDFreeMassErrorEstimator method) (pyopenms.IsobaricQuantifierStatistics method) (pyopenms.MSExperiment method) resetInterpretations() (pyopenms.TraMLProduct method) RESID (pyopenms.ProForma.CvDatabase attribute) Residue (class in pyopenms) Residue.ResidueType (class in pyopenms) residue_counts (pyopenms.PTMEntry property) ResidueDB (class in pyopenms) ResidueModification (class in pyopenms) ResidueModification.Provenance (class in pyopenms) ResidueModification.SourceClassification (class in pyopenms) ResidueModification.TermSpecificity (class in pyopenms) residueTypeToIonLetter() (pyopenms.Residue static method) resize() (pyopenms.AcquisitionInfo method) (pyopenms.DistanceMatrix method) (pyopenms.FloatDataArray method) (pyopenms.IntegerDataArray method) (pyopenms.IonImage method) (pyopenms.IsotopeDistribution method) (pyopenms.MatrixDouble method) (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.StringDataArray method) RESMETHNULL (pyopenms.MassAnalyzer.ResolutionMethod attribute) resolution_l (pyopenms.MRMFQC_ComponentGroupPairQCs property) resolution_pair_name (pyopenms.MRMFQC_ComponentGroupPairQCs property) resolution_u (pyopenms.MRMFQC_ComponentGroupPairQCs property) resolutionMethodToString() (pyopenms.MassAnalyzer static method) resolutionTypeToString() (pyopenms.MassAnalyzer static method) resolve() (pyopenms.IDConflictResolverAlgorithm static method) (pyopenms.MultiplexResolverAlgorithm method) resolveAllHitRankAggregation() (pyopenms.IDConflictResolverAlgorithm static method) resolveBetweenFeatures() (pyopenms.IDConflictResolverAlgorithm static method) resolveConnectedComponent() (pyopenms.PeptideProteinResolution method) resolveGraph() (pyopenms.PeptideProteinResolution method) resolveModifications() (pyopenms.ProForma static method) resolveOverlappingTargetDecoyMassesByDecoyMassShift() (pyopenms.MetaboTargetedTargetDecoy static method) restrictTransitions() (pyopenms.MRMAssay method) RESTYPENULL (pyopenms.MassAnalyzer.ResolutionType attribute) result_windows_even (pyopenms.SignalToNoiseEstimatorMedianRapid.NoiseEstimator property) result_windows_odd (pyopenms.SignalToNoiseEstimatorMedianRapid.NoiseEstimator property) retention_time_l (pyopenms.MRMFQC_ComponentGroupQCs property) (pyopenms.MRMFQC_ComponentQCs property) retention_time_type (pyopenms.RetentionTime property) retention_time_u (pyopenms.MRMFQC_ComponentGroupQCs property) (pyopenms.MRMFQC_ComponentQCs property) retention_time_unit (pyopenms.RetentionTime property) RetentionTime (class in pyopenms) RetentionTime.RTType (class in pyopenms) RetentionTime.RTUnit (class in pyopenms) retrieveSwathMaps() (pyopenms.CachedSwathFileConsumer method) (pyopenms.MzMLSwathFileConsumer method) (pyopenms.RegularSwathFileConsumer method) reversePeptides() (pyopenms.DecoyGenerator method) reverseProtein() (pyopenms.DecoyGenerator method) Ribonucleotide (class in pyopenms) Ribonucleotide.TermSpecificityNuc (class in pyopenms) RibonucleotideDB (class in pyopenms) RichPeak2D (class in pyopenms) RIGHT (pyopenms.SIDE attribute) rip() (pyopenms.IDRipper method) RipFileContent (class in pyopenms) RipFileIdentifier (class in pyopenms) RNaseCleavageSensitiveModGroups (class in pyopenms) RNaseDB (class in pyopenms) RNaseDigestion (class in pyopenms) RNaseDigestionProduct (class in pyopenms) robust_inlier_count (pyopenms.IDFreeMassErrorEstimator.RobustError property) robust_inlier_fraction (pyopenms.IDFreeMassErrorEstimator.RobustError property) robust_inlier_p95_abs_centered (pyopenms.IDFreeMassErrorEstimator.RobustError property) robust_inlier_threshold_3sigma (pyopenms.IDFreeMassErrorEstimator.RobustError property) robust_outlier_count (pyopenms.IDFreeMassErrorEstimator.RobustError property) rocN() (pyopenms.FalseDiscoveryRate method) root_cleavage (pyopenms.TheoreticalGlycanSpectrumGenerator.Fragment property) rounds (pyopenms.ConsensusMapNormalizerAlgorithmRTLocal.Settings property) row_group_size (pyopenms.ParquetWriteConfig property) rows() (pyopenms.MatrixDouble method) RT (pyopenms.DimensionDescription attribute) rt (pyopenms.ExtractedPeakMap property) (pyopenms.FileInfo.RangeSet property) (pyopenms.IsobaricQuantities property) (pyopenms.LightCompound property) (pyopenms.MSSpectrum property) RT (pyopenms.OSSpectrumMeta property) (pyopenms.Peak2D attribute) (pyopenms.Peak2D.DimensionDescription attribute) rt (pyopenms.SiriusMSFile_CompoundInfo property) (pyopenms.SpectrumMetaData property) rt_diff_l (pyopenms.MRMFQC_ComponentGroupPairQCs property) rt_diff_u (pyopenms.MRMFQC_ComponentGroupPairQCs property) rt_difference (pyopenms.OpenSwath_Scores property) rt_end (pyopenms.ExtractedPeakMap property) (pyopenms.ExtractionCoordinates property) rt_extraction_window (pyopenms.OSW_ChromExtractParams property) rt_max (pyopenms.ThermoRawFileOptions property) rt_max_sec (pyopenms.BrukerTimsFile.Config property) rt_min (pyopenms.ThermoRawFileOptions property) rt_min_sec (pyopenms.BrukerTimsFile.Config property) rt_selects_spectra (pyopenms.BrukerTimsFile.Config property) rt_start (pyopenms.ExtractedPeakMap property) (pyopenms.ExtractionCoordinates property) rt_tolerance (pyopenms.SpectrumLookup property) (pyopenms.SpectrumMetaDataLookup property) rt_window_seconds (pyopenms.IDFreeMassErrorEstimator.Parameters property) rts (pyopenms.Compound property) (pyopenms.Peptide property) run() (pyopenms.AccurateMassSearchEngine method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.Biosaur2Algorithm method) (pyopenms.CoarseIsotopePatternGenerator method) (pyopenms.FeatureFinderAlgorithmMetaboIdent method) (pyopenms.FeatureFinderAlgorithmPicked method) (pyopenms.FeatureFinderIdentificationAlgorithm method) (pyopenms.FeatureFinderMultiplexAlgorithm method) (pyopenms.FeatureFindingMetabo method) (pyopenms.FIAMSDataProcessor method) (pyopenms.FIAMSScheduler method) (pyopenms.FileInfo method) (pyopenms.FineIsotopePatternGenerator method) (pyopenms.FLASHDeconvAlgorithm method) (pyopenms.LabeledPairFinder method) (pyopenms.MassTraceDetection method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.OpenPepXLAlgorithm method) (pyopenms.PeptideIndexing method) (pyopenms.PeptideProteinResolution static method) (pyopenms.QTClusterFinder method) (pyopenms.SiriusExportAlgorithm method) (pyopenms.StablePairFinder method) (pyopenms.XFDRAlgorithm method) run_all() (pyopenms.FileInfo method) run_from_df() (pyopenms.FeatureFinderAlgorithmMetaboIdent method) runOnCandidates() (pyopenms.FeatureFinderIdentificationAlgorithm method) S S (pyopenms.IsotopeModel attribute) (pyopenms.IsotopeModel.Averagines attribute) SALDI (pyopenms.IonSource.IonizationMethod attribute) sameNrOfMSFilesPerFraction() (pyopenms.ExperimentalDesign method) Sample (class in pyopenms) sample (pyopenms.ExperimentalDesign_MSFileSectionEntry property) Sample.SampleState (class in pyopenms) sample_comment (pyopenms.FileInfo.ExperimentMeta property) sample_name (pyopenms.AQS_runConcentration property) (pyopenms.ExperimentalDesign_MSFileSectionEntry property) (pyopenms.FileInfo.ExperimentMeta property) sample_organism (pyopenms.FileInfo.ExperimentMeta property) SAMPLENULL (pyopenms.Sample.SampleState attribute) sampleStateToString() (pyopenms.Sample static method) satellite_subtype (pyopenms.MzPAFAnnotation property) savitzkyGolayBandwidth() (pyopenms.ModifiedSincSmoother static method) SavitzkyGolayFilter (class in pyopenms) scan (pyopenms.IsobaricQuantities property) SCAN (pyopenms.USI.IndexType attribute) scan_direction (pyopenms.ImzMLMeta property) scan_index_heavy (pyopenms.CrossLinkSpectrumMatch property) scan_index_light (pyopenms.CrossLinkSpectrumMatch property) scan_indices (pyopenms.SiriusMSFile_CompoundInfo property) scan_number (pyopenms.MassFeature_FDHS property) (pyopenms.SpectrumMetaData property) scan_pattern (pyopenms.ImzMLMeta property) scanDirectionToString() (pyopenms.MassAnalyzer static method) SCANDIRNULL (pyopenms.MassAnalyzer.ScanDirection attribute) SCANLAWNULL (pyopenms.MassAnalyzer.ScanLaw attribute) scanLawToString() (pyopenms.MassAnalyzer static method) scanModeToString() (pyopenms.InstrumentSettings static method) scans (pyopenms.IsotopeCluster property) ScanWindow (class in pyopenms) schema_version (pyopenms.FileInfo.ValidationInfo property) score (pyopenms.CrossLinkSpectrumMatch property) (pyopenms.MorpheusScore_Result property) SCORE (pyopenms.PercolatorOutfile.ScoreType attribute) score (pyopenms.TSE_Match property) score_name (pyopenms.ScoreSearchResult property) score_switched (pyopenms.IDSwitchResult property) score_type (pyopenms.PeptideHit_AnalysisResult property) score_with_isotopes() (pyopenms.DIAScoring method) scoreMap() (pyopenms.ConfidenceScoring method) scorePeakgroups() (pyopenms.MRMFeatureFinderScoring method) Scores (class in pyopenms) scores (pyopenms.RescoreOutput property) Scores.IDType (class in pyopenms) scores_np() (pyopenms.RescoreOutput method) ScoreSearchResult (class in pyopenms) scoreSpectra() (pyopenms.TargetedSpectraExtractor method) search() (pyopenms.ProSEAlgorithm method) (pyopenms.SimpleSearchEngineAlgorithm method) search_engines (pyopenms.FileInfo.IdentInfo property) searchModifications() (pyopenms.CrossLinksDB method) (pyopenms.ModificationsDB method) searchModificationsByDiffMonoMass() (pyopenms.CrossLinksDB method) (pyopenms.ModificationsDB method) SearchParameters (class in pyopenms) SearchResult (class in pyopenms) searchSpectrum() (pyopenms.TargetedSpectraExtractor method) searchWithModificationAnalysis() (pyopenms.ProSEAlgorithm method) second (pyopenms.ProbablePhosphoSites property) SECOND (pyopenms.RetentionTime attribute) (pyopenms.RetentionTime.RTUnit attribute) second (pyopenms.TransformationModel_DataPoint property) SECTOR (pyopenms.MassAnalyzer.AnalyzerType attribute) SeedListGenerator (class in pyopenms) segment_step_length (pyopenms.SelectorParameters property) segment_window_length (pyopenms.SelectorParameters property) SELDI (pyopenms.IonSource.IonizationMethod attribute) select() (pyopenms.MSSpectrum method) select_transition_group (pyopenms.SelectorParameters property) SELECTED_ION_CURRENT_CHROMATOGRAM (pyopenms.ChromatogramSettings.ChromatogramType attribute) SELECTED_ION_FLOW_TUBE (pyopenms.Instrument.IonOpticsType attribute) SELECTED_ION_MONITORING_CHROMATOGRAM (pyopenms.ChromatogramSettings.ChromatogramType attribute) SELECTED_REACTION_MONITORING_CHROMATOGRAM (pyopenms.ChromatogramSettings.ChromatogramType attribute) selectMRMFeature() (pyopenms.MRMFeatureSelectorQMIP method) (pyopenms.MRMFeatureSelectorScore method) SelectorParameters (class in pyopenms) selectSpectra() (pyopenms.TargetedSpectraExtractor method) SemanticValidator (class in pyopenms) SemanticValidator_CVTerm (class in pyopenms) SEND (pyopenms.IonSource.IonizationMethod attribute) SEPTUM (pyopenms.IonSource.InletType attribute) seq_1 (pyopenms.ProbablePhosphoSites property) seq_2 (pyopenms.ProbablePhosphoSites property) seq_with_ambiguous (pyopenms.FileInfo.FastaInfo property) sequence (pyopenms.FASTAEntry property) (pyopenms.LightCompound property) (pyopenms.LightProtein property) (pyopenms.PEFFEntry property) (pyopenms.Peptide property) (pyopenms.Protein property) (pyopenms.TransitionListEvidenceFilter_PrecursorEvidence property) sequence_length (pyopenms.PEFFEntry property) sequence_type (pyopenms.PEFFDatabaseMetadata property) sequence_version (pyopenms.PEFFEntry property) SequenceCoverage (class in pyopenms) SequenceElement (class in pyopenms) sequenceMatches() (pyopenms.FASTAEntry method) SequestInfile (class in pyopenms) SequestOutfile (class in pyopenms) set() (pyopenms.Date method) (pyopenms.DateTime method) (pyopenms.IsotopeDistribution method) (pyopenms.NASequence method) set_data() (pyopenms.FloatDataArray method) (pyopenms.IntegerDataArray method) (pyopenms.StringDataArray method) set_data_arrays() (pyopenms.OSChromatogram method) (pyopenms.OSSpectrum method) set_drift_time_array() (pyopenms.MSSpectrum method) set_features_np() (pyopenms.RescoreInput method) set_intensity_array() (pyopenms.OSChromatogram method) (pyopenms.OSSpectrum method) set_is_decoy_np() (pyopenms.RescoreInput method) set_matrix() (pyopenms.MatrixDouble method) set_mz_array() (pyopenms.OSSpectrum method) set_options() (pyopenms.TheoreticalGlycanSpectrumGenerator method) set_peaks() (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) set_time_array() (pyopenms.OSChromatogram method) setAAAfter() (pyopenms.PeptideEvidence method) setAABefore() (pyopenms.PeptideEvidence method) setAbsolute() (pyopenms.FineIsotopePatternGenerator method) setAccession() (pyopenms.CVMappingTerm method) (pyopenms.CVTerm method) (pyopenms.ProteinHit method) setAccessionAttribute() (pyopenms.SemanticValidator method) setAccuracy() (pyopenms.MassAnalyzer method) setAcquisitionInfo() (pyopenms.ChromatogramSettings method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) (pyopenms.SpectrumSettings method) setAcquisitionMode() (pyopenms.IonDetector method) setActivationEnergy() (pyopenms.Precursor method) setActivationMethods() (pyopenms.Precursor method) setActive() (pyopenms.ChargePair method) (pyopenms.DataFilters method) setADCSamplingFrequency() (pyopenms.IonDetector method) setAddress() (pyopenms.ContactPerson method) setAdductBase() (pyopenms.MassExplainer method) setAllowChildren() (pyopenms.CVMappingTerm method) setAllowIsotopeError() (pyopenms.XTandemInfile method) setAmount() (pyopenms.Adduct method) setAnalysisResults() (pyopenms.PeptideHit method) setAverageMass() (pyopenms.ResidueModification method) setAverageWeight() (pyopenms.Residue method) setAveragine() (pyopenms.SpectralDeconvolution method) setAvgMass() (pyopenms.Ribonucleotide method) setAvgPPMError() (pyopenms.PeakGroup method) setBackboneBasicityLeft() (pyopenms.Residue method) setBackboneBasicityRight() (pyopenms.Residue method) setBaselossFormula() (pyopenms.Ribonucleotide method) setBlind() (pyopenms.InspectInfile method) setCalculatedMZ() (pyopenms.AccurateMassSearchResult method) setCentroidSD() (pyopenms.MassTrace method) setCharge() (pyopenms.AccurateMassSearchResult method) (pyopenms.Adduct method) (pyopenms.BaseFeature method) (pyopenms.ChargePair method) (pyopenms.ConsensusFeature method) (pyopenms.EmpiricalFormula method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.MRMFeature method) (pyopenms.PeptideHit method) (pyopenms.Precursor method) setChargeIsotopeCosine() (pyopenms.PeakGroup method) setChargeScore() (pyopenms.PeakGroup method) setChargeSNR() (pyopenms.PeakGroup method) setChargeState() (pyopenms.Compound method) (pyopenms.LightCompound method) (pyopenms.Peptide method) (pyopenms.TraMLProduct method) setChecksum() (pyopenms.SourceFile method) setCheckTermValueTypes() (pyopenms.SemanticValidator method) setCheckUnits() (pyopenms.SemanticValidator method) setChromatograms() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.MSExperiment method) setChromatogramType() (pyopenms.ChromatogramSettings method) (pyopenms.MSChromatogram method) setCleavageSite() (pyopenms.XTandemInfile method) setCode() (pyopenms.Ribonucleotide method) setCoefficientLimits() (pyopenms.MZTrafoModel static method) setCoefficients() (pyopenms.MZTrafoModel method) setCollection() (pyopenms.USI method) setColumn() (pyopenms.HPLC method) setColumnHeaders() (pyopenms.ConsensusMap method) setCombinationsLogic() (pyopenms.CVMappingRule method) setCometID() (pyopenms.DigestionEnzymeProtein method) setComment() (pyopenms.ChromatogramSettings method) (pyopenms.ExperimentalSettings method) (pyopenms.HPLC method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.Sample method) (pyopenms.SpectrumSettings method) setCommonName() (pyopenms.SpectralMatch method) setCompletionTime() (pyopenms.DataProcessing method) setCompomer() (pyopenms.ChargePair method) setComponentName() (pyopenms.AbsoluteQuantitationMethod method) setCompoundRef() (pyopenms.IncludeExcludeTarget method) (pyopenms.ReactionMonitoringTransition method) setCompounds() (pyopenms.TargetedExperiment method) setCompression() (pyopenms.NumpressConfig method) (pyopenms.PeakFileOptions method) setConcentration() (pyopenms.Sample method) setConcentrationUnits() (pyopenms.AbsoluteQuantitationMethod method) setConfig() (pyopenms.MzMLSqliteHandler method) (pyopenms.SqMassFile method) setConfigurations() (pyopenms.IncludeExcludeTarget method) setContactInfo() (pyopenms.ContactPerson method) setContacts() (pyopenms.ExperimentalSettings method) (pyopenms.MSExperiment method) (pyopenms.TargetedExperiment method) setConvexHulls() (pyopenms.Feature method) (pyopenms.MRMFeature method) setCorrelationCoefficient() (pyopenms.AbsoluteQuantitationMethod method) setCoverage() (pyopenms.ProteinHit method) setCTermGain() (pyopenms.DigestionEnzymeProtein method) setCTerminalModification() (pyopenms.AASequence method) setCTerminalModificationByDiffMonoMass() (pyopenms.AASequence method) setCustomizations() (pyopenms.Instrument method) setCutsAfterRegEx() (pyopenms.DigestionEnzymeRNA method) setCutsBeforeRegEx() (pyopenms.DigestionEnzymeRNA method) setCVIdentifierRef() (pyopenms.CVMappingTerm method) (pyopenms.CVTerm method) setCVReferences() (pyopenms.CVMappings method) setCVs() (pyopenms.TargetedExperiment method) setCVTerms() (pyopenms.Compound method) (pyopenms.Configuration method) (pyopenms.Contact method) (pyopenms.CVMappingRule method) (pyopenms.CVTermList method) (pyopenms.CVTermListInterface method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Peptide method) (pyopenms.Precursor method) (pyopenms.Prediction method) (pyopenms.Product method) (pyopenms.Protein method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.Software method) (pyopenms.SourceFile method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TraMLProduct method) setData() (pyopenms.BilinearInterpolation method) (pyopenms.LinearInterpolation method) setDatabase() (pyopenms.SequestInfile method) setDataPoints() (pyopenms.TransformationDescription method) setDataProcessing() (pyopenms.ChromatogramSettings method) (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.FloatDataArray method) (pyopenms.IntegerDataArray method) (pyopenms.MetaInfoDescription method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) (pyopenms.SpectrumSettings method) (pyopenms.StringDataArray method) setDate() (pyopenms.DateTime method) setDateTime() (pyopenms.ExperimentalSettings method) (pyopenms.MSExperiment method) (pyopenms.ProteinIdentification method) setDb() (pyopenms.InspectInfile method) setDecoy() (pyopenms.LightTransition method) setDecoyTransitionType() (pyopenms.ReactionMonitoringTransition method) setDefaultParametersFilename() (pyopenms.XTandemInfile method) setDefaults() (pyopenms.Param method) setDescription() (pyopenms.MetaInfoRegistry method) (pyopenms.ProteinHit method) setDetectingTransition() (pyopenms.LightTransition method) (pyopenms.ReactionMonitoringTransition method) setDiffAverageMass() (pyopenms.ResidueModification method) setDiffFormula() (pyopenms.ResidueModification method) setDiffMonoMass() (pyopenms.ResidueModification method) setDimensions() (pyopenms.MSImagingGeometry method) setDriftTime() (pyopenms.LightCompound method) (pyopenms.MSSpectrum method) (pyopenms.Precursor method) setDriftTimeArray() (pyopenms.OSSpectrum method) setDriftTimeUnit() (pyopenms.Mobilogram method) (pyopenms.MSSpectrum method) setDriftTimeWindowLowerOffset() (pyopenms.Precursor method) setDriftTimeWindowUpperOffset() (pyopenms.Precursor method) setEdgeScore() (pyopenms.ChargePair method) setElement() (pyopenms.IMSAlphabet method) setElementIndex() (pyopenms.ChargePair method) setElementPath() (pyopenms.CVMappingRule method) setEmail() (pyopenms.ContactPerson method) setEmpiricalFormula() (pyopenms.AccurateMassSearchResult method) setEnd() (pyopenms.PeptideEvidence method) setEnzyme() (pyopenms.EnzymaticDigestion method) (pyopenms.InspectInfile method) (pyopenms.ProteaseDigestion method) (pyopenms.RNaseDigestion method) (pyopenms.SequestInfile method) setExcludeTargets() (pyopenms.TargetedExperiment method) setExpectedSize() (pyopenms.CachedSwathFileConsumer method) (pyopenms.IMSDataConsumer method) (pyopenms.MSDataAggregatingConsumer method) (pyopenms.MSDataCachedConsumer method) (pyopenms.MSDataSqlConsumer method) (pyopenms.MSDataStoringConsumer method) (pyopenms.MzMLSwathFileConsumer method) (pyopenms.NoopMSDataWritingConsumer method) (pyopenms.PlainMSDataWritingConsumer method) (pyopenms.RegularSwathFileConsumer method) setExperimentalSettings() (pyopenms.CachedSwathFileConsumer method) (pyopenms.IMSDataConsumer method) (pyopenms.MSDataAggregatingConsumer method) (pyopenms.MSDataCachedConsumer method) (pyopenms.MSDataSqlConsumer method) (pyopenms.MSDataStoringConsumer method) (pyopenms.MzMLSwathFileConsumer method) (pyopenms.NoopMSDataWritingConsumer method) (pyopenms.PlainMSDataWritingConsumer method) (pyopenms.RegularSwathFileConsumer method) setExperimentLabel() (pyopenms.PeptideIdentification method) setExperimentType() (pyopenms.ConsensusMap method) setFeatOptions() (pyopenms.FileHandler method) setFeatureIndex() (pyopenms.PeakGroup method) setFeatureName() (pyopenms.AbsoluteQuantitationMethod method) setFeatures() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) setFileSize() (pyopenms.SourceFile method) setFileType() (pyopenms.SourceFile method) setFillData() (pyopenms.PeakFileOptions method) setFinalMSExponent() (pyopenms.MassAnalyzer method) setFirstName() (pyopenms.ContactPerson method) setFitterParam() (pyopenms.EmgScoring method) setFivePrimeGain() (pyopenms.DigestionEnzymeRNA method) setFivePrimeMod() (pyopenms.NASequence method) setFixedModification() (pyopenms.ModificationDefinition method) setFloatDataArrays() (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) setFlux() (pyopenms.HPLC method) setForceMQCompatability() (pyopenms.PeakFileOptions method) setForceTPPCompatability() (pyopenms.PeakFileOptions method) setFormula() (pyopenms.Adduct method) (pyopenms.Residue method) (pyopenms.ResidueModification method) (pyopenms.Ribonucleotide method) setFoundAdduct() (pyopenms.AccurateMassSearchResult method) setFoundCCS() (pyopenms.SpectralMatch method) setFoundMass() (pyopenms.AccurateMassSearchResult method) setFoundPrecursorCharge() (pyopenms.SpectralMatch method) setFoundPrecursorMass() (pyopenms.SpectralMatch method) setFractionIdentifier() (pyopenms.ExperimentalSettings method) (pyopenms.MSExperiment method) setFragmentMassErrorUnit() (pyopenms.XTandemInfile method) setFragmentMassTolerance() (pyopenms.XTandemInfile method) setFragmentType() (pyopenms.LightTransition method) setFullId() (pyopenms.ResidueModification method) setFullName() (pyopenms.ResidueModification method) setGeometry() (pyopenms.MSImagingExperiment method) setGradient() (pyopenms.HPLC method) setHigherScoreBetter() (pyopenms.PeptideIdentification method) (pyopenms.ProteinIdentification method) setHits() (pyopenms.PeptideIdentification method) (pyopenms.ProteinIdentification method) setHPLC() (pyopenms.ExperimentalSettings method) (pyopenms.MSExperiment method) setHTMLCode() (pyopenms.Ribonucleotide method) setHullPoints() (pyopenms.ConvexHull2D method) setHullPointsNPY() (pyopenms.ConvexHull2D method) setID() (pyopenms.Compomer method) setId() (pyopenms.ResidueModification method) setIdentifier() (pyopenms.Acquisition method) (pyopenms.ConsensusMap method) (pyopenms.CVMappingRule method) (pyopenms.CVReference method) (pyopenms.DocumentIdentifier method) (pyopenms.ExperimentalSettings method) (pyopenms.FeatureMap method) (pyopenms.MSExperiment method) (pyopenms.PeptideIdentification method) (pyopenms.ProteinIdentification method) setIdentifyingTransition() (pyopenms.LightTransition method) (pyopenms.ReactionMonitoringTransition method) setIMFormat() (pyopenms.MSSpectrum method) setIMPeakType() (pyopenms.MSSpectrum method) setIMRange() (pyopenms.PeakFileOptions method) setInchiString() (pyopenms.SpectralMatch method) setIncludeTargets() (pyopenms.TargetedExperiment method) setIndex() (pyopenms.PeakGroup method) (pyopenms.USI method) setIndexType() (pyopenms.USI method) setIndividualIntensities() (pyopenms.AccurateMassSearchResult method) setInitialParameters() (pyopenms.GaussFitter method) setInletType() (pyopenms.IonSource method) setInputFilename() (pyopenms.XTandemInfile method) setInstitution() (pyopenms.ContactPerson method) setInstrument() (pyopenms.ExperimentalSettings method) (pyopenms.HPLC method) (pyopenms.InspectInfile method) (pyopenms.MSExperiment method) setInstrumentConfigurations() (pyopenms.ExperimentalSettings method) (pyopenms.MSExperiment method) setInstruments() (pyopenms.TargetedExperiment method) setInstrumentSettings() (pyopenms.ChromatogramSettings method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) (pyopenms.SpectrumSettings method) setIntegerDataArrays() (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) setIntensity() (pyopenms.BaseFeature method) (pyopenms.ChromatogramPeak method) (pyopenms.ConsensusFeature method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.IonImage method) (pyopenms.MobilityPeak1D method) (pyopenms.MRMFeature method) (pyopenms.Peak1D method) (pyopenms.Peak2D method) (pyopenms.Precursor method) (pyopenms.RichPeak2D method) setIntensity32Bit() (pyopenms.PeakFileOptions method) setIntensityArray() (pyopenms.Chromatogram method) (pyopenms.OSChromatogram method) (pyopenms.OSSpectrum method) (pyopenms.Spectrum method) setIntensityRange() (pyopenms.FeatureFileOptions method) (pyopenms.PeakFileOptions method) setIntermediateProducts() (pyopenms.ReactionMonitoringTransition method) setInterpolationStep() (pyopenms.BiGaussModel method) (pyopenms.EmgModel method) (pyopenms.InterpolationModel method) (pyopenms.IsotopeModel method) setInterpretation() (pyopenms.USI method) setInterpretations() (pyopenms.IncludeExcludeTarget method) setInvalid() (pyopenms.QTCluster method) setIonCutoffPercentage() (pyopenms.SequestInfile method) setIonDetectors() (pyopenms.Instrument method) setIonizationMethod() (pyopenms.IonSource method) setIonOptics() (pyopenms.Instrument method) setIonSeriesWeights() (pyopenms.SequestInfile method) setIonSources() (pyopenms.Instrument method) setISName() (pyopenms.AbsoluteQuantitationMethod method) setIsolationWidth() (pyopenms.MassAnalyzer method) setIsolationWindowLowerOffset() (pyopenms.Precursor method) (pyopenms.Product method) setIsolationWindowUpperOffset() (pyopenms.Precursor method) (pyopenms.Product method) setIsotopeCosine() (pyopenms.PeakGroup method) setIsotopeDaDistance() (pyopenms.PeakGroup method) setIsotopeDistribution() (pyopenms.IMSElement method) setIsotopesSimScore() (pyopenms.AccurateMassSearchResult method) setIsRepeatable() (pyopenms.CVMappingTerm method) setLabel() (pyopenms.MassTrace method) setLastName() (pyopenms.ContactPerson method) setLibraryIntensity() (pyopenms.LightTransition method) (pyopenms.ReactionMonitoringTransition method) setLLOD() (pyopenms.AbsoluteQuantitationMethod method) setLLOQ() (pyopenms.AbsoluteQuantitationMethod method) setLoadConvexHull() (pyopenms.FeatureFileOptions method) setLoadedFilePath() (pyopenms.ConsensusMap method) (pyopenms.DocumentIdentifier method) (pyopenms.ExperimentalSettings method) (pyopenms.FeatureMap method) (pyopenms.MSExperiment method) setLoadedFileType() (pyopenms.ConsensusMap method) (pyopenms.DocumentIdentifier method) (pyopenms.ExperimentalSettings method) (pyopenms.FeatureMap method) (pyopenms.MSExperiment method) setLoadSubordinates() (pyopenms.FeatureFileOptions method) setLogLevel() (pyopenms.LogConfigHandler method) setLogProb() (pyopenms.Adduct method) setLogType() (pyopenms.AccurateMassSearchEngine method) (pyopenms.AverageLinkage method) (pyopenms.BaseGroupFinder method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.BrukerTimsFile method) (pyopenms.CachedMzMLHandler method) (pyopenms.ChromatogramExtractor method) (pyopenms.ChromatogramExtractorAlgorithm method) (pyopenms.ConfidenceScoring method) (pyopenms.DTA2DFile method) (pyopenms.ElutionPeakDetection method) (pyopenms.FASTAFile method) (pyopenms.FeatureFindingMetabo method) (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.FLASHDeconvAlgorithm method) (pyopenms.GaussFilter method) (pyopenms.ImzMLFile method) (pyopenms.InternalCalibration method) (pyopenms.LabeledPairFinder method) (pyopenms.LinearResamplerAlign method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) (pyopenms.MascotGenericFile method) (pyopenms.MasstraceCorrelator method) (pyopenms.MassTraceDetection method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.ModifiedSincSmoother method) (pyopenms.MorphologicalFilter method) (pyopenms.MRMAssay method) (pyopenms.MRMDecoy method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MS2File method) (pyopenms.MSDataCachedConsumer method) (pyopenms.MzDataFile method) (pyopenms.MzIdentMLFile method) (pyopenms.MzMLFile method) (pyopenms.MzXMLFile method) (pyopenms.PeakMapExtractor method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) (pyopenms.PEFFFile method) (pyopenms.ProgressLogger method) (pyopenms.ProSEAlgorithm method) (pyopenms.QTClusterFinder method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.StablePairFinder method) (pyopenms.SwathFile method) (pyopenms.ThermoRawFile method) (pyopenms.TransitionPQPFile method) (pyopenms.TransitionTSVFile method) setLossFormulas() (pyopenms.Residue method) setLossNames() (pyopenms.Residue method) setLowMassIons() (pyopenms.Residue method) setMagneticFieldStrength() (pyopenms.MassAnalyzer method) setMapIndex() (pyopenms.FeatureHandle method) setMapping() (pyopenms.LinearInterpolation method) setMapping_0() (pyopenms.BilinearInterpolation method) setMapping_1() (pyopenms.BilinearInterpolation method) setMappingRules() (pyopenms.CVMappings method) setMass() (pyopenms.Sample method) setMassAnalyzers() (pyopenms.Instrument method) setMassDiff() (pyopenms.ChargePair method) setMasstraceIntensities() (pyopenms.AccurateMassSearchResult method) setMassTypeFragment() (pyopenms.SequestInfile method) setMassTypeParent() (pyopenms.SequestInfile method) setMatchingHMDBids() (pyopenms.AccurateMassSearchResult method) setMatchingIndex() (pyopenms.AccurateMassSearchResult method) setMatchingScore() (pyopenms.SpectralMatch method) setMatchingSpectrumIndex() (pyopenms.SpectralMatch method) setMatchPeakAllowedError() (pyopenms.SequestInfile method) setMatchPeakCount() (pyopenms.SequestInfile method) setMatchPeakTolerance() (pyopenms.SequestInfile method) setMax() (pyopenms.RangeBase method) (pyopenms.RangeIntensity method) (pyopenms.RangeMobility method) (pyopenms.RangeMZ method) (pyopenms.RangeRT method) setMaxAAPerModPerPeptide() (pyopenms.SequestInfile method) setMaxCharge() (pyopenms.Tagger method) setMaxDataPoolSize() (pyopenms.PeakFileOptions method) setMaxFloat() (pyopenms.Param method) setMaxInt() (pyopenms.Param method) setMaxIntensity() (pyopenms.RangeIntensity method) setMaxInternalCleavageSites() (pyopenms.SequestInfile method) setMaxIsotope() (pyopenms.CoarseIsotopePatternGenerator method) setMaxIsotopeIndex() (pyopenms.PrecalAveragine method) setMaxMobility() (pyopenms.RangeMobility method) setMaxModifications() (pyopenms.ModificationDefinitionsSet method) setMaxModsPerPeptide() (pyopenms.SequestInfile method) setMaxMZ() (pyopenms.RangeMZ method) setMaxOccurrences() (pyopenms.ModificationDefinition method) setMaxPrecursorCharge() (pyopenms.XTandemInfile method) setMaxPTMsize() (pyopenms.InspectInfile method) setMaxRT() (pyopenms.RangeRT method) setMaxValidEValue() (pyopenms.XTandemInfile method) setMaxX() (pyopenms.DRange1 method) (pyopenms.DRange2 method) setMaxY() (pyopenms.DRange2 method) setMetadataOnly() (pyopenms.FeatureFileOptions method) (pyopenms.PeakFileOptions method) setMetaValue() (pyopenms.Acquisition method) (pyopenms.AcquisitionInfo method) (pyopenms.BaseFeature method) (pyopenms.ChromatogramSettings method) (pyopenms.ColumnHeader method) (pyopenms.Compound method) (pyopenms.Configuration method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusMap method) (pyopenms.Contact method) (pyopenms.ContactPerson method) (pyopenms.CVTermList method) (pyopenms.CVTermListInterface method) (pyopenms.DataProcessing method) (pyopenms.ExperimentalSettings method) (pyopenms.Feature method) (pyopenms.FeatureMap method) (pyopenms.FloatDataArray method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Instrument method) (pyopenms.InstrumentSettings method) (pyopenms.IntegerDataArray method) (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) (pyopenms.MetaInfoDescription method) (pyopenms.MetaInfoInterface method) (pyopenms.MRMFeature method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.Peptide method) (pyopenms.PeptideHit method) (pyopenms.PeptideIdentification method) (pyopenms.Precursor method) (pyopenms.Prediction method) (pyopenms.Product method) (pyopenms.Protein method) (pyopenms.ProteinHit method) (pyopenms.ProteinIdentification method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.RichPeak2D method) (pyopenms.Sample method) (pyopenms.ScanWindow method) (pyopenms.SearchParameters method) (pyopenms.Software method) (pyopenms.SourceFile method) (pyopenms.SpectrumSettings method) (pyopenms.StringDataArray method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TraMLProduct method) setMetaValues() (pyopenms.Acquisition method) (pyopenms.ColumnHeader method) (pyopenms.ContactPerson method) (pyopenms.CVTermListInterface method) (pyopenms.DataProcessing method) (pyopenms.Instrument method) (pyopenms.InstrumentSettings method) (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) (pyopenms.MetaInfoDescription method) (pyopenms.MetaInfoInterface method) (pyopenms.ProteinHit method) (pyopenms.RetentionTime method) (pyopenms.Sample method) (pyopenms.ScanWindow method) (pyopenms.SearchParameters method) (pyopenms.SpectrumSettings method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TraMLProduct method) setMethodOfCombination() (pyopenms.AcquisitionInfo method) setMin() (pyopenms.RangeBase method) (pyopenms.RangeIntensity method) (pyopenms.RangeMobility method) (pyopenms.RangeMZ method) (pyopenms.RangeRT method) setMinFloat() (pyopenms.Param method) setMinInt() (pyopenms.Param method) setMinIntensity() (pyopenms.RangeIntensity method) setMinMobility() (pyopenms.RangeMobility method) setMinMZ() (pyopenms.RangeMZ method) setMinRT() (pyopenms.RangeRT method) setMinX() (pyopenms.DRange1 method) (pyopenms.DRange2 method) setMinY() (pyopenms.DRange2 method) setMissedCleavages() (pyopenms.EnzymaticDigestion method) (pyopenms.ProteaseDigestion method) (pyopenms.RNaseDigestion method) setMobility() (pyopenms.MobilityPeak1D method) setModel() (pyopenms.Instrument method) setModification() (pyopenms.AASequence method) (pyopenms.ModificationDefinition method) (pyopenms.Residue method) setModificationByDiffMonoMass() (pyopenms.AASequence method) (pyopenms.Residue method) setModificationDefinitionsSet() (pyopenms.OMSSAXMLFile method) setModifications() (pyopenms.ModificationDefinitionsSet method) (pyopenms.XTandemInfile method) setModificationsPerPeptide() (pyopenms.InspectInfile method) setMonoisotopicMass() (pyopenms.PeakGroup method) setMonoMass() (pyopenms.ResidueModification method) (pyopenms.Ribonucleotide method) setMonoWeight() (pyopenms.Residue method) setMS1Map() (pyopenms.MRMFeatureFinderScoring method) setMSData() (pyopenms.Biosaur2Algorithm method) (pyopenms.FeatureFinderAlgorithmMetaboIdent method) (pyopenms.FeatureFinderIdentificationAlgorithm method) setMSExperiment() (pyopenms.AnnotatedMSRun method) (pyopenms.MSImagingExperiment method) setMSFileSection() (pyopenms.ExperimentalDesign method) setMSGFID() (pyopenms.DigestionEnzymeProtein method) setMSLevel() (pyopenms.MSSpectrum method) setMSLevels() (pyopenms.PeakFileOptions method) setMSRun() (pyopenms.USI method) setMulticharge() (pyopenms.InspectInfile method) setMZ() (pyopenms.BaseFeature method) (pyopenms.ConsensusFeature method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.MRMFeature method) (pyopenms.Peak1D method) (pyopenms.Peak2D method) (pyopenms.PeptideIdentification method) (pyopenms.Precursor method) (pyopenms.Product method) (pyopenms.RichPeak2D method) (pyopenms.TraMLProduct method) setMz32Bit() (pyopenms.PeakFileOptions method) setMZArray() (pyopenms.OSSpectrum method) (pyopenms.Spectrum method) setMZErrorPPM() (pyopenms.AccurateMassSearchResult method) setMZRange() (pyopenms.FeatureFileOptions method) setMzRange() (pyopenms.IonImage method) setMZRange() (pyopenms.PeakFileOptions method) setName() (pyopenms.AbsoluteQuantitation method) (pyopenms.AccurateMassSearchEngine method) (pyopenms.AScore method) (pyopenms.BaseGroupFinder method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.Biosaur2Algorithm method) (pyopenms.ContactPerson method) (pyopenms.CVReference method) (pyopenms.CVTerm method) (pyopenms.DefaultParamHandler method) (pyopenms.DIAScoring method) (pyopenms.DigestionEnzyme method) (pyopenms.DigestionEnzymeProtein method) (pyopenms.DigestionEnzymeRNA method) (pyopenms.ElutionModelFitter method) (pyopenms.ElutionPeakDetection method) (pyopenms.EmgFitter1D method) (pyopenms.EmgGradientDescent method) (pyopenms.FalseDiscoveryRate method) (pyopenms.FeatureDeconvolution method) (pyopenms.FeatureDistance method) (pyopenms.FeatureFinderAlgorithmMetaboIdent method) (pyopenms.FeatureFinderAlgorithmPicked method) (pyopenms.FeatureFinderIdentificationAlgorithm method) (pyopenms.FeatureFinderMultiplexAlgorithm method) (pyopenms.FeatureFindingMetabo method) (pyopenms.FeatureGroupingAlgorithm method) (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.FeatureGroupingAlgorithmLabeled method) (pyopenms.FeatureGroupingAlgorithmQT method) (pyopenms.FeatureGroupingAlgorithmUnlabeled method) (pyopenms.FIAMSDataProcessor method) (pyopenms.Fitter1D method) (pyopenms.FLASHDeconvAlgorithm method) (pyopenms.FloatDataArray method) (pyopenms.GaussFilter method) (pyopenms.GNPSMGFFile method) (pyopenms.IDDecoyProbability method) (pyopenms.IDMapper method) (pyopenms.IDRipper method) (pyopenms.IDScoreSwitcherAlgorithm method) (pyopenms.IMSElement method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Instrument method) (pyopenms.IntegerDataArray method) (pyopenms.IsobaricChannelExtractor method) (pyopenms.IsobaricQuantifier method) (pyopenms.IsobaricQuantitationMethod method) (pyopenms.IsotopeLabelingMDVs method) (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.LabeledPairFinder method) (pyopenms.LevMarqFitter1D method) (pyopenms.LinearResamplerAlign method) (pyopenms.LowessSmoothing method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) (pyopenms.MascotGenericFile method) (pyopenms.MassDecompositionAlgorithm method) (pyopenms.MasstraceCorrelator method) (pyopenms.MassTraceDetection method) (pyopenms.MetaboliteFeatureDeconvolution method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.MetaInfoDescription method) (pyopenms.ModifiedSincSmoother method) (pyopenms.MorphologicalFilter method) (pyopenms.MRMDecoy method) (pyopenms.MRMFeatureFilter method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MRMMapping method) (pyopenms.MRMTransitionGroupPicker method) (pyopenms.MSChromatogram method) (pyopenms.MSPFile method) (pyopenms.MSPGenericFile method) (pyopenms.MSSpectrum method) (pyopenms.MultiplexDeltaMassesGenerator method) (pyopenms.MultiplexResolverAlgorithm method) (pyopenms.NLargest method) (pyopenms.Normalizer method) (pyopenms.NucleicAcidSpectrumGenerator method) (pyopenms.OpenPepXLAlgorithm method) (pyopenms.PeakIntegrator method) (pyopenms.PeakPickerChromatogram method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIM method) (pyopenms.PeakPickerIterative method) (pyopenms.PeptideAndProteinQuant method) (pyopenms.PeptideIndexing method) (pyopenms.Percolator method) (pyopenms.PipEchoAlgorithm method) (pyopenms.PosteriorErrorProbabilityModel method) (pyopenms.ProSEAlgorithm method) (pyopenms.QTClusterFinder method) (pyopenms.RankScaler method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.Residue method) (pyopenms.ResidueModification method) (pyopenms.Ribonucleotide method) (pyopenms.Sample method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SignalToNoiseEstimatorMeanIterative method) (pyopenms.SignalToNoiseEstimatorMedian method) (pyopenms.SignalToNoiseEstimatorMedianChrom method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.SimpleTSGXLMS method) (pyopenms.SiriusExportAlgorithm method) (pyopenms.Software method) (pyopenms.SpectralDeconvolution method) (pyopenms.SpectraMerger method) (pyopenms.SpectrumAlignment method) (pyopenms.SpectrumAlignmentScore method) (pyopenms.SpectrumAnnotator method) (pyopenms.SqrtScaler method) (pyopenms.StablePairFinder method) (pyopenms.StringDataArray method) (pyopenms.SwathMapMassCorrection method) (pyopenms.TargetedSpectraExtractor method) (pyopenms.TheoreticalSpectrumGenerator method) (pyopenms.TheoreticalSpectrumGeneratorXLMS method) (pyopenms.ThresholdMower method) (pyopenms.TMTEighteenPlexQuantitationMethod method) (pyopenms.TMTElevenPlexQuantitationMethod method) (pyopenms.TMTSixPlexQuantitationMethod method) (pyopenms.TMTSixteenPlexQuantitationMethod method) (pyopenms.TMTTenPlexQuantitationMethod method) (pyopenms.TransitionListEvidenceFilter method) (pyopenms.WindowMower method) (pyopenms.XFDRAlgorithm method) setNameAttribute() (pyopenms.SemanticValidator method) setNameOfFile() (pyopenms.SourceFile method) setNativeID() (pyopenms.ChromatogramSettings method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.SpectrumSettings method) setNativeIDType() (pyopenms.SourceFile method) setNativeIDTypeAccession() (pyopenms.SourceFile method) setNeutralLossAverageMasses() (pyopenms.ResidueModification method) setNeutralLossDiffFormulas() (pyopenms.ResidueModification method) setNeutralLossesForIons() (pyopenms.SequestInfile method) setNeutralLossMonoMasses() (pyopenms.ResidueModification method) setNewCode() (pyopenms.Ribonucleotide method) setNominalMass() (pyopenms.IMSIsotopeDistribution method) setNormalizedIntensityValues() (pyopenms.ConsensusMapNormalizerAlgorithmQuantile static method) setNormalizeXcorr() (pyopenms.SequestInfile method) setNPoints() (pyopenms.AbsoluteQuantitationMethod method) setNTermGain() (pyopenms.DigestionEnzymeProtein method) setNTerminalModification() (pyopenms.AASequence method) setNTerminalModificationByDiffMonoMass() (pyopenms.AASequence method) setNTermLossFormulas() (pyopenms.Residue method) setNTermLossNames() (pyopenms.Residue method) setNucleotideReadingFrame() (pyopenms.SequestInfile method) setNumber() (pyopenms.Sample method) setNumberOfMissedCleavages() (pyopenms.XTandemInfile method) setNumberOfThreads() (pyopenms.XTandemInfile method) setNumpressConfigurationFloatDataArray() (pyopenms.PeakFileOptions method) setNumpressConfigurationIntensity() (pyopenms.PeakFileOptions method) setNumpressConfigurationMassTime() (pyopenms.PeakFileOptions method) setObservedCCS() (pyopenms.SpectralMatch method) setObservedIntensity() (pyopenms.AccurateMassSearchResult method) setObservedMZ() (pyopenms.AccurateMassSearchResult method) setObservedPrecursorMass() (pyopenms.SpectralMatch method) setObservedPrecursorRT() (pyopenms.SpectralMatch method) setObservedRT() (pyopenms.AccurateMassSearchResult method) setObservedSpectrumIndex() (pyopenms.SpectralMatch method) setOffset() (pyopenms.BiGaussModel method) (pyopenms.EmgModel method) (pyopenms.InterpolationModel method) (pyopenms.IsotopeModel method) (pyopenms.LinearInterpolation method) setOffset_0() (pyopenms.BilinearInterpolation method) setOffset_1() (pyopenms.BilinearInterpolation method) setOMSSAID() (pyopenms.DigestionEnzymeProtein method) setOneLetterCode() (pyopenms.Residue method) setOpenMPNumThreads() (pyopenms.OpenMSBuildInfo static method) setOptions() (pyopenms.ConsensusXMLFile method) (pyopenms.DTA2DFile method) (pyopenms.FeatureXMLFile method) (pyopenms.FileHandler method) (pyopenms.ImzMLFile method) (pyopenms.IndexedMzMLFileLoader method) (pyopenms.MzDataFile method) (pyopenms.MzMLFile method) (pyopenms.MzXMLFile method) (pyopenms.OnDiscMSExperiment method) (pyopenms.PlainMSDataWritingConsumer method) (pyopenms.ThermoRawFile method) setOrder() (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) setOrganism() (pyopenms.Sample method) setOrigin() (pyopenms.ResidueModification method) (pyopenms.Ribonucleotide method) setOriginalSpectrum() (pyopenms.DeconvolvedSpectrum method) setOutputFilename() (pyopenms.XTandemInfile method) setOutputLines() (pyopenms.SequestInfile method) setOutputResults() (pyopenms.XTandemInfile method) setOverallQuality() (pyopenms.Feature method) (pyopenms.MRMFeature method) setParameters() (pyopenms.AbsoluteQuantitation method) (pyopenms.AccurateMassSearchEngine method) (pyopenms.AScore method) (pyopenms.BaseGroupFinder method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.Biosaur2Algorithm method) (pyopenms.DefaultParamHandler method) (pyopenms.DIAScoring method) (pyopenms.ElutionModelFitter method) (pyopenms.ElutionPeakDetection method) (pyopenms.EmgFitter1D method) (pyopenms.EmgGradientDescent method) (pyopenms.FalseDiscoveryRate method) (pyopenms.FeatureDeconvolution method) (pyopenms.FeatureDistance method) (pyopenms.FeatureFinderAlgorithmMetaboIdent method) (pyopenms.FeatureFinderAlgorithmPicked method) (pyopenms.FeatureFinderIdentificationAlgorithm method) (pyopenms.FeatureFinderMultiplexAlgorithm method) (pyopenms.FeatureFindingMetabo method) (pyopenms.FeatureGroupingAlgorithm method) (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.FeatureGroupingAlgorithmLabeled method) (pyopenms.FeatureGroupingAlgorithmQT method) (pyopenms.FeatureGroupingAlgorithmUnlabeled method) (pyopenms.FIAMSDataProcessor method) (pyopenms.Fitter1D method) (pyopenms.FLASHDeconvAlgorithm method) (pyopenms.GaussFilter method) (pyopenms.GNPSMGFFile method) (pyopenms.IDDecoyProbability method) (pyopenms.IDFreeMassErrorEstimator method) (pyopenms.IDMapper method) (pyopenms.IDRipper method) (pyopenms.IDScoreSwitcherAlgorithm method) (pyopenms.IsobaricChannelExtractor method) (pyopenms.IsobaricQuantifier method) (pyopenms.IsobaricQuantitationMethod method) (pyopenms.IsotopeLabelingMDVs method) (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.LabeledPairFinder method) (pyopenms.LevMarqFitter1D method) (pyopenms.LinearResamplerAlign method) (pyopenms.LowessSmoothing method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) (pyopenms.MascotGenericFile method) (pyopenms.MassDecompositionAlgorithm method) (pyopenms.MasstraceCorrelator method) (pyopenms.MassTraceDetection method) (pyopenms.MetaboliteFeatureDeconvolution method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.ModifiedSincSmoother method) (pyopenms.MorphologicalFilter method) (pyopenms.MRMDecoy method) (pyopenms.MRMFeatureFilter method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MRMMapping method) (pyopenms.MRMTransitionGroupPicker method) (pyopenms.MSPFile method) (pyopenms.MSPGenericFile method) (pyopenms.MultiplexDeltaMassesGenerator method) (pyopenms.MultiplexResolverAlgorithm method) (pyopenms.NLargest method) (pyopenms.Normalizer method) (pyopenms.NucleicAcidSpectrumGenerator method) (pyopenms.OpenPepXLAlgorithm method) (pyopenms.PeakIntegrator method) (pyopenms.PeakPickerChromatogram method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIM method) (pyopenms.PeakPickerIterative method) (pyopenms.PeptideAndProteinQuant method) (pyopenms.PeptideIndexing method) (pyopenms.Percolator method) (pyopenms.PipEchoAlgorithm method) (pyopenms.PosteriorErrorProbabilityModel method) (pyopenms.ProSEAlgorithm method) (pyopenms.QTClusterFinder method) (pyopenms.RankScaler method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SignalToNoiseEstimatorMeanIterative method) (pyopenms.SignalToNoiseEstimatorMedian method) (pyopenms.SignalToNoiseEstimatorMedianChrom method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.SimpleTSGXLMS method) (pyopenms.SiriusExportAlgorithm method) (pyopenms.SpectralDeconvolution method) (pyopenms.SpectraMerger method) (pyopenms.SpectrumAlignment method) (pyopenms.SpectrumAlignmentScore method) (pyopenms.SpectrumAnnotator method) (pyopenms.SqrtScaler method) (pyopenms.StablePairFinder method) (pyopenms.SwathMapMassCorrection method) (pyopenms.TargetedSpectraExtractor method) (pyopenms.TheoreticalSpectrumGenerator method) (pyopenms.TheoreticalSpectrumGeneratorXLMS method) (pyopenms.ThresholdMower method) (pyopenms.TMTEighteenPlexQuantitationMethod method) (pyopenms.TMTElevenPlexQuantitationMethod method) (pyopenms.TMTSixPlexQuantitationMethod method) (pyopenms.TMTSixteenPlexQuantitationMethod method) (pyopenms.TMTTenPlexQuantitationMethod method) (pyopenms.TransitionListEvidenceFilter method) (pyopenms.WindowMower method) (pyopenms.XFDRAlgorithm method) setParseUnknownScores() (pyopenms.PepXMLFile method) setPartialSequence() (pyopenms.SequestInfile method) setPathToFile() (pyopenms.SourceFile method) setPeakAnnotations() (pyopenms.PeptideHit method) setPeakGroups() (pyopenms.DeconvolvedSpectrum method) setPeakMassTolerance() (pyopenms.InspectInfile method) (pyopenms.SequestInfile method) setPeptideEvidences() (pyopenms.PeptideHit method) setPeptideGroupLabel() (pyopenms.Peptide method) setPeptideIdentifications() (pyopenms.AnnotatedMSRun method) (pyopenms.BaseFeature method) (pyopenms.ConsensusFeature method) (pyopenms.Feature method) (pyopenms.MRMFeature method) setPeptideMassUnit() (pyopenms.SequestInfile method) setPeptideRef() (pyopenms.IncludeExcludeTarget method) (pyopenms.ReactionMonitoringTransition method) setPeptides() (pyopenms.TargetedExperiment method) setPercentage() (pyopenms.Gradient method) setPixelSize() (pyopenms.MSImagingGeometry method) setPka() (pyopenms.Residue method) setPkb() (pyopenms.Residue method) setPkc() (pyopenms.Residue method) setPolarity() (pyopenms.InstrumentSettings method) (pyopenms.IonSource method) setPos() (pyopenms.ChromatogramPeak method) (pyopenms.MobilityPeak1D method) (pyopenms.Peak1D method) (pyopenms.Precursor method) setPosition() (pyopenms.ChromatogramPeak method) setPossibleChargeStates() (pyopenms.Precursor method) setPrecision() (pyopenms.IMSWeights method) setPrecursor() (pyopenms.ChromatogramSettings method) (pyopenms.DeconvolvedSpectrum method) (pyopenms.MSChromatogram method) setPrecursorAdduct() (pyopenms.SpectralMatch method) setPrecursorChromatograms() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) setPrecursorCVTermList() (pyopenms.IncludeExcludeTarget method) (pyopenms.ReactionMonitoringTransition method) setPrecursorErrorType() (pyopenms.XTandemInfile method) setPrecursorMassErrorUnit() (pyopenms.XTandemInfile method) setPrecursorMassTolerance() (pyopenms.InspectInfile method) (pyopenms.SequestInfile method) setPrecursorMassToleranceMinus() (pyopenms.XTandemInfile method) setPrecursorMassTolerancePlus() (pyopenms.XTandemInfile method) setPrecursorMZ() (pyopenms.IncludeExcludeTarget method) (pyopenms.ReactionMonitoringTransition method) setPrecursorMZRange() (pyopenms.PeakFileOptions method) setPrecursorPeakGroup() (pyopenms.DeconvolvedSpectrum method) setPrecursors() (pyopenms.MSSpectrum method) (pyopenms.SpectrumSettings method) setPrecursorScanNumber() (pyopenms.DeconvolvedSpectrum method) setPrediction() (pyopenms.IncludeExcludeTarget method) (pyopenms.ReactionMonitoringTransition method) setPressure() (pyopenms.HPLC method) setPrimaryIdentifier() (pyopenms.SpectralMatch method) setPrimaryMSRunPath() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.ProteinIdentification method) setPrintDuplicateReferences() (pyopenms.SequestInfile method) setProcessingActions() (pyopenms.DataProcessing method) setProduct() (pyopenms.ChromatogramSettings method) (pyopenms.MSChromatogram method) (pyopenms.ReactionMonitoringTransition method) setProductCVTermList() (pyopenms.IncludeExcludeTarget method) setProductMZ() (pyopenms.IncludeExcludeTarget method) (pyopenms.ReactionMonitoringTransition method) setProducts() (pyopenms.MSSpectrum method) (pyopenms.SpectrumSettings method) setProgress() (pyopenms.AccurateMassSearchEngine method) (pyopenms.AverageLinkage method) (pyopenms.BaseGroupFinder method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.BrukerTimsFile method) (pyopenms.CachedMzMLHandler method) (pyopenms.ChromatogramExtractor method) (pyopenms.ChromatogramExtractorAlgorithm method) (pyopenms.ConfidenceScoring method) (pyopenms.DTA2DFile method) (pyopenms.ElutionPeakDetection method) (pyopenms.FASTAFile method) (pyopenms.FeatureFindingMetabo method) (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.FLASHDeconvAlgorithm method) (pyopenms.GaussFilter method) (pyopenms.ImzMLFile method) (pyopenms.InternalCalibration method) (pyopenms.LabeledPairFinder method) (pyopenms.LinearResamplerAlign method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) (pyopenms.MascotGenericFile method) (pyopenms.MasstraceCorrelator method) (pyopenms.MassTraceDetection method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.ModifiedSincSmoother method) (pyopenms.MorphologicalFilter method) (pyopenms.MRMAssay method) (pyopenms.MRMDecoy method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MS2File method) (pyopenms.MSDataCachedConsumer method) (pyopenms.MzDataFile method) (pyopenms.MzIdentMLFile method) (pyopenms.MzMLFile method) (pyopenms.MzXMLFile method) (pyopenms.PeakMapExtractor method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) (pyopenms.PEFFFile method) (pyopenms.ProgressLogger method) (pyopenms.ProSEAlgorithm method) (pyopenms.QTClusterFinder method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.StablePairFinder method) (pyopenms.SwathFile method) (pyopenms.ThermoRawFile method) (pyopenms.TransitionPQPFile method) (pyopenms.TransitionTSVFile method) setProteinAccession() (pyopenms.PeptideEvidence method) setProteinIdentifications() (pyopenms.AnnotatedMSRun method) (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) setProteinMassFilter() (pyopenms.SequestInfile method) setProteins() (pyopenms.TargetedExperiment method) setProvenance() (pyopenms.ResidueModification method) setPSIID() (pyopenms.DigestionEnzymeProtein method) setPSIMODAccession() (pyopenms.ResidueModification method) setPublications() (pyopenms.TargetedExperiment method) setQscore() (pyopenms.PeakGroup method) setQscore2D() (pyopenms.PeakGroup method) setQuality() (pyopenms.BaseFeature method) (pyopenms.ConsensusFeature method) (pyopenms.Feature method) (pyopenms.MRMFeature method) setQuantifyingTransition() (pyopenms.LightTransition method) (pyopenms.ReactionMonitoringTransition method) setQuantities() (pyopenms.DeconvolvedSpectrum method) setQuantMethod() (pyopenms.MassTrace method) setQuantMethods() (pyopenms.AbsoluteQuantitation method) setQueryMass() (pyopenms.AccurateMassSearchResult method) setQvalue() (pyopenms.PeakGroup method) setRank() (pyopenms.PeptideHit method) (pyopenms.ProteinHit method) setRANSACParams() (pyopenms.MZTrafoModel static method) setRANSACSeed() (pyopenms.MZTrafoModel static method) setRatios() (pyopenms.ConsensusFeature method) setReference() (pyopenms.FeatureGroupingAlgorithmUnlabeled method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) setReflectronState() (pyopenms.MassAnalyzer method) setRegEx() (pyopenms.DigestionEnzyme method) (pyopenms.DigestionEnzymeProtein method) (pyopenms.DigestionEnzymeRNA method) setRegExDescription() (pyopenms.DigestionEnzyme method) (pyopenms.DigestionEnzymeProtein method) (pyopenms.DigestionEnzymeRNA method) setRemovePrecursorNearPeaks() (pyopenms.SequestInfile method) setRepAbsCharge() (pyopenms.PeakGroup method) setRequirementLevel() (pyopenms.CVMappingRule method) setResidueSets() (pyopenms.Residue method) setResiduesInUpperCase() (pyopenms.SequestInfile method) setResolution() (pyopenms.IonDetector method) (pyopenms.MassAnalyzer method) setResolutionMethod() (pyopenms.MassAnalyzer method) setResolutionType() (pyopenms.MassAnalyzer method) setRetentionTime() (pyopenms.IncludeExcludeTarget method) (pyopenms.ReactionMonitoringTransition method) setRoundMasses() (pyopenms.CoarseIsotopePatternGenerator method) setRT() (pyopenms.BaseFeature method) (pyopenms.ChromatogramPeak method) (pyopenms.ConsensusFeature method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.Mobilogram method) (pyopenms.MRMFeature method) (pyopenms.MSSpectrum method) (pyopenms.Peak2D method) (pyopenms.PeptideIdentification method) (pyopenms.RetentionTime method) (pyopenms.RichPeak2D method) setRTRange() (pyopenms.FeatureFileOptions method) (pyopenms.PeakFileOptions method) setRunId() (pyopenms.OpenSwathOSWWriter method) setRunID() (pyopenms.OSWData method) setSample() (pyopenms.ExperimentalSettings method) (pyopenms.MSExperiment method) setSamples() (pyopenms.BiGaussModel method) (pyopenms.EmgModel method) (pyopenms.InterpolationModel method) (pyopenms.IsotopeModel method) setSampleSection() (pyopenms.ExperimentalDesign method) setScale() (pyopenms.LinearInterpolation method) setScale_0() (pyopenms.BilinearInterpolation method) setScale_1() (pyopenms.BilinearInterpolation method) setScalingFactor() (pyopenms.BiGaussModel method) (pyopenms.EmgModel method) (pyopenms.InterpolationModel method) (pyopenms.IsotopeModel method) setScanDirection() (pyopenms.MassAnalyzer method) setScanLaw() (pyopenms.MassAnalyzer method) setScanMode() (pyopenms.InstrumentSettings method) setScanNumber() (pyopenms.PeakGroup method) setScanRate() (pyopenms.MassAnalyzer method) setScanTime() (pyopenms.MassAnalyzer method) setScanWindows() (pyopenms.InstrumentSettings method) setScopePath() (pyopenms.CVMappingRule method) setScore() (pyopenms.PeptideHit method) (pyopenms.ProteinHit method) setScores() (pyopenms.MRMFeature method) setScoreType() (pyopenms.PeptideIdentification method) (pyopenms.ProteinIdentification method) setSearchEngine() (pyopenms.ProteinIdentification method) setSearchEngineVersion() (pyopenms.ProteinIdentification method) setSearchParameters() (pyopenms.ProteinIdentification method) setSecondaryIdentifier() (pyopenms.SpectralMatch method) setSectionDescription() (pyopenms.Param method) setSeed() (pyopenms.DecoyGenerator method) (pyopenms.UniqueIdGenerator static method) setSemiCleavage() (pyopenms.XTandemInfile method) setSequence() (pyopenms.IMSElement method) (pyopenms.NASequence method) (pyopenms.PeptideHit method) (pyopenms.ProteinHit method) setSequenceHeaderFilter() (pyopenms.SequestInfile method) setShowFragmentIons() (pyopenms.SequestInfile method) setSideChainBasicity() (pyopenms.Residue method) setSignificanceThreshold() (pyopenms.PeptideIdentification method) (pyopenms.ProteinIdentification method) setSingleMass() (pyopenms.Adduct method) setSizeOnly() (pyopenms.FeatureFileOptions method) setSkipXMLChecks() (pyopenms.IndexedMzMLHandler method) (pyopenms.MzMLSpectrumDecoder method) (pyopenms.OnDiscMSExperiment method) (pyopenms.PeakFileOptions method) setSMILESString() (pyopenms.SpectralMatch method) setSmoothedIntensities() (pyopenms.MassTrace method) setSNR() (pyopenms.PeakGroup method) setSoftware() (pyopenms.DataProcessing method) (pyopenms.Instrument method) (pyopenms.TargetedExperiment method) setSortChromatogramsByRT() (pyopenms.PeakFileOptions method) setSortSpectraByMZ() (pyopenms.PeakFileOptions method) setSourceClassification() (pyopenms.ResidueModification method) setSourceFeatureIndex() (pyopenms.AccurateMassSearchResult method) setSourceFile() (pyopenms.ChromatogramSettings method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) (pyopenms.SpectrumSettings method) setSourceFiles() (pyopenms.ExperimentalSettings method) (pyopenms.MSExperiment method) (pyopenms.TargetedExperiment method) setSpecificity() (pyopenms.EnzymaticDigestion method) (pyopenms.ProteaseDigestion method) (pyopenms.RNaseDigestion method) setSpectra() (pyopenms.InspectInfile method) (pyopenms.MSExperiment method) setSpectraDataRef() (pyopenms.SpectrumMetaDataLookup method) setSpectrum() (pyopenms.MSImagingExperiment method) setSpectrumPtr() (pyopenms.SwathMap method) setSpectrumReference() (pyopenms.PeptideIdentification method) setSqlSourceFile() (pyopenms.OSWData method) setStart() (pyopenms.PeptideEvidence method) setState() (pyopenms.Sample method) setStrictFlag() (pyopenms.MRMFeatureFinderScoring method) setStringDataArrays() (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) setSubordinates() (pyopenms.Feature method) (pyopenms.MRMFeature method) setSubsamples() (pyopenms.Sample method) setSumFormula() (pyopenms.SpectralMatch method) setSynonyms() (pyopenms.DigestionEnzyme method) (pyopenms.DigestionEnzymeProtein method) (pyopenms.DigestionEnzymeRNA method) (pyopenms.Residue method) (pyopenms.ResidueModification method) setTag() (pyopenms.SemanticValidator method) setTagCount() (pyopenms.InspectInfile method) setTargetCVTerms() (pyopenms.TargetedExperiment method) setTargetDecoyType() (pyopenms.PeakGroup method) (pyopenms.SpectralDeconvolution method) setTargeted() (pyopenms.PeakGroup method) setTargetMasses() (pyopenms.SpectralDeconvolution method) setTargetMetaValue() (pyopenms.TargetedExperiment method) setTaxon() (pyopenms.XTandemInfile method) setTaxonomyFilename() (pyopenms.XTandemInfile method) setTemperature() (pyopenms.HPLC method) setTermName() (pyopenms.CVMappingTerm method) setTermSpecificity() (pyopenms.ResidueModification method) (pyopenms.Ribonucleotide method) setThreeLetterCode() (pyopenms.Residue method) setThreePrimeGain() (pyopenms.DigestionEnzymeRNA method) setThreePrimeMod() (pyopenms.NASequence method) setThreshold() (pyopenms.FineIsotopePatternGenerator method) setTime() (pyopenms.DateTime method) setTimeArray() (pyopenms.Chromatogram method) (pyopenms.OSChromatogram method) setTOFTotalPathLength() (pyopenms.MassAnalyzer method) setToleranceEstimation() (pyopenms.SpectralDeconvolution method) setTotalProbability() (pyopenms.FineIsotopePatternGenerator method) setTransformationModel() (pyopenms.AbsoluteQuantitationMethod method) setTransformationModelParams() (pyopenms.AbsoluteQuantitationMethod method) setTransitionGroupID() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) setTransitions() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.TargetedExperiment method) setType() (pyopenms.IonDetector method) (pyopenms.MassAnalyzer method) (pyopenms.MSSpectrum method) (pyopenms.SpectrumSettings method) setULOD() (pyopenms.AbsoluteQuantitationMethod method) setULOQ() (pyopenms.AbsoluteQuantitationMethod method) setUnassignedPeptideIdentifications() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) setUniModRecordId() (pyopenms.ResidueModification method) setUniqueId() (pyopenms.BaseFeature method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusMap method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.FeatureMap method) (pyopenms.MRMFeature method) (pyopenms.RichPeak2D method) (pyopenms.UniqueIdInterface method) setUniqueIds() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) setUnit() (pyopenms.CVTerm method) (pyopenms.MetaInfoRegistry method) setUnitAccessionAttribute() (pyopenms.SemanticValidator method) setUnitNameAttribute() (pyopenms.SemanticValidator method) setURL() (pyopenms.ContactPerson method) setUsePPM() (pyopenms.CalibrationData method) setUseTerm() (pyopenms.CVMappingTerm method) setUseTermName() (pyopenms.CVMappingTerm method) setValidStrings() (pyopenms.Param method) setValue() (pyopenms.CVTerm method) (pyopenms.DistanceMatrix method) (pyopenms.MatrixDouble method) (pyopenms.MetaInfo method) (pyopenms.Param method) setValueAttribute() (pyopenms.SemanticValidator method) setValueFromFile() (pyopenms.DigestionEnzyme method) (pyopenms.DigestionEnzymeProtein method) (pyopenms.DigestionEnzymeRNA method) setValueQuick() (pyopenms.DistanceMatrix method) setVendor() (pyopenms.Instrument method) setVersion() (pyopenms.Software method) setVolume() (pyopenms.Sample method) setWidth() (pyopenms.BaseFeature method) (pyopenms.ConsensusFeature method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.MRMFeature method) setWriteIndex() (pyopenms.PeakFileOptions method) setWriteSupplementalData() (pyopenms.PeakFileOptions method) setXTandemID() (pyopenms.DigestionEnzymeProtein method) setZoomScan() (pyopenms.InstrumentSettings method) setZstdCompression() (pyopenms.PeakFileOptions method) sf_accession (pyopenms.SiriusMSFile_AccessionInfo property) sf_filename (pyopenms.SiriusMSFile_AccessionInfo property) sf_path (pyopenms.SiriusMSFile_AccessionInfo property) sf_type (pyopenms.SiriusMSFile_AccessionInfo property) SHA1 (pyopenms.ChecksumType attribute) (pyopenms.SourceFile.ChecksumType attribute) sharedram (pyopenms.SysInfo attribute) short_name (pyopenms.MultiplexDeltaMassesGenerator_Label property) SHOULD (pyopenms.RequirementLevel attribute) shuffle() (pyopenms.DecoyGenerator method) shufflePeptides() (pyopenms.DecoyGenerator method) SI (pyopenms.IonSource.IonizationMethod attribute) SID (pyopenms.Precursor.ActivationMethod attribute) SIDE (class in pyopenms) sigma (pyopenms.GaussFitResult property) sigma_multiplier (pyopenms.IDFreeMassErrorEstimator.ToleranceSuggestion property) signal_decoy (pyopenms.PeakGroup attribute) (pyopenms.PeakGroup.TargetDecoyType attribute) signal_proportion (pyopenms.PurityScores property) SignalToNoiseEstimatorMeanIterative (class in pyopenms) SignalToNoiseEstimatorMedian (class in pyopenms) SignalToNoiseEstimatorMedianChrom (class in pyopenms) SignalToNoiseEstimatorMedianRapid (class in pyopenms) SignalToNoiseEstimatorMedianRapid.NoiseEstimator (class in pyopenms) SILAC SILI (pyopenms.IonSource.IonizationMethod attribute) SILLERO (pyopenms.ProteomicsPkaScale attribute) SIM (pyopenms.InstrumentSettings.ScanMode attribute) simple_variants (pyopenms.PEFFEntry property) SimpleOpenMSSpectraFactory (class in pyopenms) SimplePeak (class in pyopenms) SimpleSearchEngineAlgorithm (class in pyopenms) SimpleSearchEngineAlgorithm.ExitCodes (class in pyopenms) SimpleTSGXLMS (class in pyopenms) single_measurement_sigma (pyopenms.IDFreeMassErrorEstimator.RobustError property) (pyopenms.IDFreeMassErrorEstimator.ToleranceSuggestion property) SiriusExportAlgorithm (class in pyopenms) SiriusFragmentAnnotation (class in pyopenms) SiriusFragmentAnnotation_SiriusTargetDecoySpectra (class in pyopenms) SiriusMSFile (class in pyopenms) SiriusMSFile_AccessionInfo (class in pyopenms) SiriusMSFile_CompoundInfo (class in pyopenms) size (pyopenms.ColumnHeader property) SIZE (pyopenms.DataFilters attribute) (pyopenms.DataFilters.FilterType attribute) size (pyopenms.FileInfo.MapColumn property) SIZE (pyopenms.IMSIsotopeDistribution attribute) size() (pyopenms.AASequence method) (pyopenms.AcquisitionInfo method) (pyopenms.CalibrationData method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusMap method) (pyopenms.DataFilters method) (pyopenms.DeconvolvedSpectrum method) (pyopenms.FeatureMap method) (pyopenms.FloatDataArray method) (pyopenms.IdentifierMSRunMapper method) (pyopenms.IMSAlphabet method) (pyopenms.IMSIsotopeDistribution method) (pyopenms.IMSWeights method) (pyopenms.IntegerDataArray method) (pyopenms.IsotopeDistribution method) (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MassTraces method) (pyopenms.MatrixDouble method) (pyopenms.Mobilogram method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.MzPAFPeakAnnotations method) (pyopenms.NASequence method) (pyopenms.OnDiscImzMLExperiment method) (pyopenms.OnDiscMSExperiment method) (pyopenms.OnDiscThermoRawExperiment method) (pyopenms.Param method) (pyopenms.ParamNode method) (pyopenms.PeakGroup method) (pyopenms.PeptideIdentificationList method) (pyopenms.QTCluster method) (pyopenms.SplineInterpolatedPeaks method) (pyopenms.StringDataArray method) size_distribution (pyopenms.FileInfo.FeatureInfo property) SIZE_OF_ACQUISITIONMODE (pyopenms.IonDetector.AcquisitionMode attribute) SIZE_OF_ACTIVATIONMETHOD (pyopenms.Precursor.ActivationMethod attribute) SIZE_OF_ANALYZERTYPE (pyopenms.MassAnalyzer.AnalyzerType attribute) SIZE_OF_ANNOTATIONSTATE (pyopenms.AnnotationState attribute) (pyopenms.BaseFeature attribute) (pyopenms.BaseFeature.AnnotationState attribute) (pyopenms.ConsensusFeature attribute) (pyopenms.Feature attribute) (pyopenms.MRMFeature attribute) SIZE_OF_CHECKSUMTYPE (pyopenms.ChecksumType attribute) (pyopenms.SourceFile.ChecksumType attribute) SIZE_OF_CHROMATOGRAM_TYPE (pyopenms.ChromatogramSettings.ChromatogramType attribute) SIZE_OF_DERIVATIZATIONAGENT (pyopenms.IsotopeLabelingMDVs.DerivatizationAgent attribute) SIZE_OF_DRIFTTIMEUNIT (pyopenms.DriftTimeUnit attribute) SIZE_OF_IMFORMAT (pyopenms.IMFormat attribute) SIZE_OF_IMPEAKTYPE (pyopenms.IMPeakType attribute) SIZE_OF_INLETTYPE (pyopenms.IonSource.InletType attribute) SIZE_OF_IONIZATIONMETHOD (pyopenms.IonSource.IonizationMethod attribute) SIZE_OF_IONOPTICSTYPE (pyopenms.Instrument.IonOpticsType attribute) SIZE_OF_ITRAQ_TYPES (pyopenms.ITRAQ_TYPES attribute) (pyopenms.ItraqConstants attribute) (pyopenms.ItraqConstants.ITRAQ_TYPES attribute) SIZE_OF_MASSINTENSITYTYPE (pyopenms.IsotopeLabelingMDVs.MassIntensityType attribute) SIZE_OF_MODELTYPE (pyopenms.MZTrafoModel.MODELTYPE attribute) SIZE_OF_MT_QUANTMETHOD (pyopenms.MT_QUANTMETHOD attribute) SIZE_OF_NUMPRESSCOMPRESSION (pyopenms.MSNumpressCoder attribute) (pyopenms.MSNumpressCoder.NumpressCompression attribute) SIZE_OF_OPENMS_ARCHITECTURE (pyopenms.OpenMSOSInfo.OpenMS_Architecture attribute) SIZE_OF_OPENMS_OS (pyopenms.OpenMSOSInfo.OpenMS_OS attribute) SIZE_OF_ORIGIN_ANNOTATION_FORMAT (pyopenms.IDRipper attribute) (pyopenms.IDRipper.OriginAnnotationFormat attribute) (pyopenms.OriginAnnotationFormat attribute) SIZE_OF_PEAKMASSTYPE (pyopenms.ProteinIdentification.PeakMassType attribute) SIZE_OF_POLARITY (pyopenms.IonSource.Polarity attribute) SIZE_OF_PROCESSINGACTION (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) SIZE_OF_PROTEOMICS_PKA_SCALES (pyopenms.ProteomicsPkaScale attribute) SIZE_OF_REFLECTRONSTATE (pyopenms.MassAnalyzer.ReflectronState attribute) SIZE_OF_RESOLUTIONMETHOD (pyopenms.MassAnalyzer.ResolutionMethod attribute) SIZE_OF_RESOLUTIONTYPE (pyopenms.MassAnalyzer.ResolutionType attribute) SIZE_OF_RTTYPE (pyopenms.RetentionTime attribute) (pyopenms.RetentionTime.RTType attribute) SIZE_OF_RTUNIT (pyopenms.RetentionTime attribute) (pyopenms.RetentionTime.RTUnit attribute) SIZE_OF_SAMPLESTATE (pyopenms.Sample.SampleState attribute) SIZE_OF_SCANDIRECTION (pyopenms.MassAnalyzer.ScanDirection attribute) SIZE_OF_SCANLAW (pyopenms.MassAnalyzer.ScanLaw attribute) SIZE_OF_SCANMODE (pyopenms.InstrumentSettings.ScanMode attribute) SIZE_OF_SCORETYPE (pyopenms.PercolatorOutfile.ScoreType attribute) SIZE_OF_SPECIFICITY (pyopenms.EnzymaticDigestion attribute) (pyopenms.EnzymaticDigestion.Specificity attribute) (pyopenms.ProteaseDigestion attribute) (pyopenms.RNaseDigestion attribute) SIZE_OF_SPECTRUMTYPE (pyopenms.SpectrumSettings.SpectrumType attribute) SIZE_OF_TYPE (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) (pyopenms.IonDetector.Type attribute) SIZE_OF_VALUES (pyopenms.OSWHierarchy attribute) (pyopenms.OSWHierarchy.Level attribute) SizeOfNASFragmentType (pyopenms.NASequence.NASFragmentType attribute) SizeOfResidueType (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) skip_chromatograms (pyopenms.ThermoRawFileOptions property) skipped_reason (pyopenms.PercolatorRescoring property) SLOF (pyopenms.MSNumpressCoder attribute) (pyopenms.MSNumpressCoder.NumpressCompression attribute) slope_of_baseline (pyopenms.PI_PeakShapeMetrics property) small_molecules (pyopenms.FileInfo.MzTabInfo property) smiles (pyopenms.LightCompound property) smiles_string (pyopenms.Compound property) smooth() (pyopenms.ModifiedSincSmoother method) smoothData() (pyopenms.ElutionPeakDetection method) (pyopenms.LowessSmoothing method) Smoother (pyopenms.MultipleTesting.Pi0Method attribute) SMOOTHING (pyopenms.DataProcessing attribute) (pyopenms.DataProcessing.ProcessingAction attribute) sn_ratio (pyopenms.OpenSwath_Scores property) SNAPPY (pyopenms.ParquetWriteConfig attribute) (pyopenms.ParquetWriteConfig.Compression attribute) Software (class in pyopenms) software_name (pyopenms.FileInfo.ProcessingStep property) software_ref (pyopenms.Prediction property) (pyopenms.RetentionTime property) software_version (pyopenms.FileInfo.ProcessingStep property) SOI (pyopenms.IonSource.IonizationMethod attribute) SOLID (pyopenms.Sample.SampleState attribute) SOLUTION (pyopenms.Sample.SampleState attribute) solve() (pyopenms.BSpline2d method) (pyopenms.NonNegativeLeastSquaresSolver static method) SOLVED (pyopenms.NonNegativeLeastSquaresSolver attribute) (pyopenms.NonNegativeLeastSquaresSolver.RETURN_STATUS attribute) SORI (pyopenms.Precursor.ActivationMethod attribute) sort() (pyopenms.DeconvolvedSpectrum method) (pyopenms.PeakGroup method) (pyopenms.PeptideIdentification method) (pyopenms.ProteinIdentification method) sortByIntensity() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.IsotopeDistribution method) (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) sortByMaps() (pyopenms.ConsensusMap method) sortByMass() (pyopenms.IsotopeDistribution method) sortByMZ() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) sortByNames() (pyopenms.IMSAlphabet method) sortByOverallQuality() (pyopenms.FeatureMap method) sortByPosition() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) sortByQscore() (pyopenms.DeconvolvedSpectrum method) sortByQuality() (pyopenms.ConsensusMap method) sortByRT() (pyopenms.CalibrationData method) (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) sortBySize() (pyopenms.ConsensusMap method) sortByValues() (pyopenms.IMSAlphabet method) sortChromatograms() (pyopenms.MSExperiment method) sortPeptideIdentificationsByMapIndex() (pyopenms.ConsensusMap method) sortSpectra() (pyopenms.MSExperiment method) sortTransitionsByProductMZ() (pyopenms.TargetedExperiment method) source, [1] source_file (pyopenms.SiriusMSFile_CompoundInfo property) source_format (pyopenms.SiriusMSFile_CompoundInfo property) SourceFile (class in pyopenms) SourceFile.ChecksumType (class in pyopenms) SPEC_FULL (pyopenms.EnzymaticDigestion attribute) (pyopenms.EnzymaticDigestion.Specificity attribute) (pyopenms.ProteaseDigestion attribute) (pyopenms.RNaseDigestion attribute) SPEC_NOCTERM (pyopenms.EnzymaticDigestion attribute) (pyopenms.EnzymaticDigestion.Specificity attribute) (pyopenms.ProteaseDigestion attribute) (pyopenms.RNaseDigestion attribute) SPEC_NONE (pyopenms.EnzymaticDigestion attribute) (pyopenms.EnzymaticDigestion.Specificity attribute) (pyopenms.ProteaseDigestion attribute) (pyopenms.RNaseDigestion attribute) SPEC_NONTERM (pyopenms.EnzymaticDigestion attribute) (pyopenms.EnzymaticDigestion.Specificity attribute) (pyopenms.ProteaseDigestion attribute) (pyopenms.RNaseDigestion attribute) SPEC_SEMI (pyopenms.EnzymaticDigestion attribute) (pyopenms.EnzymaticDigestion.Specificity attribute) (pyopenms.ProteaseDigestion attribute) (pyopenms.RNaseDigestion attribute) SPEC_UNKNOWN (pyopenms.EnzymaticDigestion attribute) (pyopenms.EnzymaticDigestion.Specificity attribute) (pyopenms.ProteaseDigestion attribute) (pyopenms.RNaseDigestion attribute) specific_keys (pyopenms.PEFFDatabaseMetadata property) specific_neutral_losses (pyopenms.TheoreticalGlycanSpectrumGenerator.Options property) specific_values (pyopenms.PEFFDatabaseMetadata property) specref_format (pyopenms.SiriusMSFile_CompoundInfo property) specrefs (pyopenms.SiriusMSFile_CompoundInfo property) spectra_all_peaks (pyopenms.PreprocessedPairSpectra property) spectra_linear_peaks (pyopenms.PreprocessedPairSpectra property) spectra_overall (pyopenms.FileInfo.Ranges property) spectra_per_ms_level (pyopenms.FileInfo.PeakInfo property) spectra_xlink_peaks (pyopenms.PreprocessedPairSpectra property) SpectralDeconvolution (class in pyopenms) SpectralMatch (class in pyopenms) SpectraMerger (class in pyopenms) SpectraSTSimilarityScore (class in pyopenms) Spectrum (class in pyopenms) SPECTRUM (pyopenms.BrukerTimsFile.Config.ExportMode attribute) spectrum (pyopenms.TSE_Match property) spectrum_view() (pyopenms.MSExperiment method) spectrum_views() (pyopenms.MSExperiment method) SpectrumAccessOpenMS (class in pyopenms) SpectrumAccessOpenMSCached (class in pyopenms) SpectrumAccessOpenMSInMemory (class in pyopenms) SpectrumAccessSqMass (class in pyopenms) SpectrumAlignment (class in pyopenms) SpectrumAlignmentScore (class in pyopenms) SpectrumAnnotator (class in pyopenms) SpectrumHelper (class in pyopenms) SpectrumLookup (class in pyopenms) SpectrumMetaData (class in pyopenms) SpectrumMetaDataLookup (class in pyopenms) SpectrumNativeIDParser (class in pyopenms) SpectrumRangeManager (class in pyopenms) SpectrumRanges (class in pyopenms) spectrumRanges() (pyopenms.MSExperiment method) SpectrumSettings (class in pyopenms) SpectrumSettings.SpectrumType (class in pyopenms) spectrumTypeToString() (pyopenms.MSSpectrum static method) (pyopenms.SpectrumSettings static method) SPECXML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) SPEED_OF_LIGHT (in module pyopenms.Constants) SPI (pyopenms.IonSource.IonizationMethod attribute) SPLIB (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) SplineInterpolatedPeaks (class in pyopenms) SplineInterpolatedPeaks.Navigator (class in pyopenms) SplinePackage (class in pyopenms) SQMASS (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) SqMassConfig (class in pyopenms) SqMassFile (class in pyopenms) SqrtScaler (class in pyopenms) SRM (pyopenms.InstrumentSettings.ScanMode attribute) stable isotope labeling with amino acids in cell culture StablePairFinder (class in pyopenms) start_position (pyopenms.PEFFProcessedRegion property) (pyopenms.PEFFVariantComplex property) start_position_at_10 (pyopenms.PI_PeakShapeMetrics property) start_position_at_5 (pyopenms.PI_PeakShapeMetrics property) start_position_at_50 (pyopenms.PI_PeakShapeMetrics property) startProgress() (pyopenms.AccurateMassSearchEngine method) (pyopenms.AverageLinkage method) (pyopenms.BaseGroupFinder method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.BrukerTimsFile method) (pyopenms.CachedMzMLHandler method) (pyopenms.ChromatogramExtractor method) (pyopenms.ChromatogramExtractorAlgorithm method) (pyopenms.ConfidenceScoring method) (pyopenms.DTA2DFile method) (pyopenms.ElutionPeakDetection method) (pyopenms.FASTAFile method) (pyopenms.FeatureFindingMetabo method) (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.FLASHDeconvAlgorithm method) (pyopenms.GaussFilter method) (pyopenms.ImzMLFile method) (pyopenms.InternalCalibration method) (pyopenms.LabeledPairFinder method) (pyopenms.LinearResamplerAlign method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) (pyopenms.MascotGenericFile method) (pyopenms.MasstraceCorrelator method) (pyopenms.MassTraceDetection method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.ModifiedSincSmoother method) (pyopenms.MorphologicalFilter method) (pyopenms.MRMAssay method) (pyopenms.MRMDecoy method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MS2File method) (pyopenms.MSDataCachedConsumer method) (pyopenms.MzDataFile method) (pyopenms.MzIdentMLFile method) (pyopenms.MzMLFile method) (pyopenms.MzXMLFile method) (pyopenms.PeakMapExtractor method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) (pyopenms.PEFFFile method) (pyopenms.ProgressLogger method) (pyopenms.ProSEAlgorithm method) (pyopenms.QTClusterFinder method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.StablePairFinder method) (pyopenms.SwathFile method) (pyopenms.ThermoRawFile method) (pyopenms.TransitionPQPFile method) (pyopenms.TransitionTSVFile method) states (pyopenms.AnnotationStatistics property) STATIC_FIELD (pyopenms.Instrument.IonOpticsType attribute) statistics (pyopenms.FileInfo.Options property) (pyopenms.FileInfo.Result property) stats (pyopenms.FileInfo.NamedStats property) store() (pyopenms.AbsoluteQuantitationMethodFile method) (pyopenms.BedRModFile method) (pyopenms.CachedmzML static method) (pyopenms.ConsensusXMLFile method) (pyopenms.CsvFile method) (pyopenms.DTA2DFile method) (pyopenms.DTAFile method) (pyopenms.EDTAFile method) (pyopenms.FASTAFile method) (pyopenms.FeatureXMLFile method) (pyopenms.GNPSMetaValueFile static method) (pyopenms.GNPSMGFFile method) (pyopenms.GNPSQuantificationFile static method) (pyopenms.IBSpectraFile method) (pyopenms.IdXMLFile method) (pyopenms.ImzMLFile method) (pyopenms.IndexedMzMLFileLoader method) (pyopenms.InspectInfile method) (pyopenms.KroenikFile method) (pyopenms.MascotGenericFile method) (pyopenms.MRMFeaturePickerFile method) (pyopenms.MRMFeatureQCFile method) (pyopenms.MsInspectFile method) (pyopenms.MSPFile method) (pyopenms.MSPGenericFile method) (pyopenms.MzDataFile method) (pyopenms.MzIdentMLFile method) (pyopenms.MzMLFile method) (pyopenms.MzQCFile method) (pyopenms.MzTabFile method) (pyopenms.MzTabMFile method) (pyopenms.MzXMLFile method) (pyopenms.OMSFile method) (pyopenms.ParamCTDFile method) (pyopenms.ParamXMLFile method) (pyopenms.PEFFFile method) (pyopenms.PepXMLFile method) (pyopenms.PercolatorInfile static method) (pyopenms.ProtXMLFile method) (pyopenms.SequestInfile method) (pyopenms.SqMassFile method) (pyopenms.TextFile method) (pyopenms.TraMLFile method) (pyopenms.TransformationXMLFile method) (pyopenms.XQuestResultXMLFile method) storeBuffer() (pyopenms.MzMLFile method) storeConsensusFeatures() (pyopenms.FileHandler method) storeExperiment() (pyopenms.FileHandler method) storeFeatures() (pyopenms.FileHandler method) storeIdentifications() (pyopenms.FileHandler method) storeISO() (pyopenms.MSstatsFile method) storeLFQ() (pyopenms.MSstatsFile method) storeSpectraMSP() (pyopenms.TargetedSpectraExtractor method) storeSpectrum() (pyopenms.FileHandler method) storeTIC() (pyopenms.DTA2DFile method) storeTransformations() (pyopenms.FileHandler method) storeTransitions() (pyopenms.FileHandler method) storeWeights() (pyopenms.Percolator method) string_arrays (pyopenms.FileInfo.PeakInfo property) string_data_array_view() (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) string_data_array_views() (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) STRING_LIST (pyopenms.DataType attribute) (pyopenms.DataValue attribute) (pyopenms.ParamValue attribute) (pyopenms.ValueType attribute) STRING_VALUE (pyopenms.DataType attribute) (pyopenms.DataValue attribute) (pyopenms.ParamValue attribute) (pyopenms.ValueType attribute) StringDataArray (class in pyopenms) stripExtension() (pyopenms.FileHandler static method) stripped (pyopenms.TheoreticalGlycanSpectrumGenerator.PeptideRetention property) stubs (pyopenms.TheoreticalGlycanSpectrumGenerator.PeptideRetention property) sub_scores (pyopenms.PeptideHit_AnalysisResult property) subset() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) subtractMinimumIntensity() (pyopenms.SpectrumHelper static method) suffix() (pyopenms.ParamNode method) SUI (pyopenms.IonSource.IonizationMethod attribute) SUM (pyopenms.BasicProteinInferenceAlgorithm attribute) (pyopenms.BasicProteinInferenceAlgorithm.AggregationMethod attribute) (pyopenms.FeatureOverlapFilter.MergeIntensityMode attribute) (pyopenms.MSExperiment.MSExperimentRasterAggregation attribute) (pyopenms.MSSpectrum.MSSpectrumRasterAggregation attribute) sum_formula (pyopenms.LightCompound property) summaries (pyopenms.OpenSearchAnalysisResult property) summary (pyopenms.TransitionListEvidenceFilter_Result property) SummaryStatistics (class in pyopenms) support (pyopenms.IDFreeMassErrorEstimator.ToleranceSuggestion property) supported (pyopenms.FileInfo.ValidationInfo property) supported_ms1 (pyopenms.TransitionListEvidenceFilter_PrecursorEvidence property) supported_ms2 (pyopenms.TransitionListEvidenceFilter_PrecursorEvidence property) supported_precursors (pyopenms.TransitionListEvidenceFilter_Result property) supportMax() (pyopenms.LinearInterpolation method) supportMax_0() (pyopenms.BilinearInterpolation method) supportMax_1() (pyopenms.BilinearInterpolation method) supportMin() (pyopenms.LinearInterpolation method) supportMin_0() (pyopenms.BilinearInterpolation method) supportMin_1() (pyopenms.BilinearInterpolation method) SUSPENSION (pyopenms.Sample.SampleState attribute) swap() (pyopenms.FeatureMap method) (pyopenms.IMSWeights method) (pyopenms.MSExperiment method) swapExtension() (pyopenms.FileHandler static method) swapFeaturesOnly() (pyopenms.FeatureMap method) SWATH SwathFile (class in pyopenms) SwathMap (class in pyopenms) SwathMapMassCorrection (class in pyopenms) SwathWindowLoader (class in pyopenms) SWIFT (pyopenms.MassAnalyzer.AnalyzerType attribute) switchBackScoreType() (pyopenms.IDScoreSwitcherAlgorithm static method) switchScores() (pyopenms.IDScoreSwitcherAlgorithm method) switchToGeneralScoreType() (pyopenms.IDScoreSwitcherAlgorithm method) switchToScoreType() (pyopenms.IDScoreSwitcherAlgorithm static method) synonyms (pyopenms.ControlledVocabulary.CVTerm property) SysInfo (class in pyopenms) SystemSettings (class in pyopenms) T t (pyopenms.RANSACParam property) Tagger (class in pyopenms) tags (pyopenms.ParamEntry property) tailing_factor (pyopenms.PI_PeakShapeMetrics property) tandem mass spectrometry TARGET (pyopenms.DecoyTransitionType attribute) (pyopenms.EntrapmentEvaluation.Kind attribute) target (pyopenms.PeakGroup attribute) (pyopenms.PeakGroup.TargetDecoyType attribute) TARGET (pyopenms.ReactionMonitoringTransition attribute) (pyopenms.ReactionMonitoringTransition.DecoyTransitionType attribute) target (pyopenms.SiriusFragmentAnnotation_SiriusTargetDecoySpectra property) target_compound_ref (pyopenms.MetaboTargetedTargetDecoy_MetaboTargetDecoyMassMapping property) TARGET_DECOY_ISOTONIC (pyopenms.PosteriorErrorProbabilityModel.ModelType attribute) target_decoy_spectra (pyopenms.MetaboTargetedAssay_CompoundTargetDecoyPair property) target_intensity (pyopenms.PurityScores property) target_ion_mobility (pyopenms.ExtractedPeakMap property) target_mz (pyopenms.ExtractedPeakMap property) target_peak_count (pyopenms.PurityScores property) target_product_masses (pyopenms.MetaboTargetedTargetDecoy_MetaboTargetDecoyMassMapping property) target_residues (pyopenms.PTMEntry property) target_rt (pyopenms.ExtractedPeakMap property) targeted_summary (pyopenms.FileInfo.Result property) TargetedDataFileLoader (class in pyopenms) TargetedExperiment (class in pyopenms) TargetedExperiment_Instrument (class in pyopenms) TargetedExperiment_Interpretation (class in pyopenms) TargetedExperiment_Modification (class in pyopenms) TargetedSpectraExtractor (class in pyopenms) targetPeptides() (pyopenms.EntrapmentEvaluation static method) taxonomy (pyopenms.FileInfo.IdentInfo property) (pyopenms.SearchParameters property) taxonomy_name (pyopenms.PEFFEntry property) TBDMS (pyopenms.IsotopeLabelingMDVs.DerivatizationAgent attribute) TDC (pyopenms.IonDetector.AcquisitionMode attribute) TDF (pyopenms.BrukerTimsFile.DataFormat attribute) (pyopenms.InstrumentSettings.ScanMode attribute) te_ratio (pyopenms.EntrapmentEvaluation.Result property) TempDir (class in pyopenms) TempFiles (class in pyopenms) TENPERCENTVALLEY (pyopenms.MassAnalyzer.ResolutionMethod attribute) term_spec_alpha (pyopenms.ProteinProteinCrossLink property) term_spec_beta (pyopenms.ProteinProteinCrossLink property) text (pyopenms.FileInfo.Result property) (pyopenms.InfoTag property) TextFile (class in pyopenms) theoretical_int (pyopenms.FeatureFinderAlgorithmPickedHelperStructs_MassTrace property) theoretical_mass (pyopenms.Compound property) (pyopenms.PTMEntry property) TheoreticalGlycanSpectrumGenerator (class in pyopenms) TheoreticalGlycanSpectrumGenerator.Fragment (class in pyopenms) TheoreticalGlycanSpectrumGenerator.FragmentationMethod (class in pyopenms) TheoreticalGlycanSpectrumGenerator.IonType (class in pyopenms) TheoreticalGlycanSpectrumGenerator.Options (class in pyopenms) TheoreticalGlycanSpectrumGenerator.PeptideRetention (class in pyopenms) TheoreticalSpectrumGenerator (class in pyopenms) TheoreticalSpectrumGeneratorXLMS (class in pyopenms) ThermoRawFile (class in pyopenms) ThermoRawFileOptions (class in pyopenms) THERMOSPRAYINLET (pyopenms.IonSource.InletType attribute) THREE_PRIME (pyopenms.Ribonucleotide attribute) (pyopenms.Ribonucleotide.TermSpecificityNuc attribute) ThreePrime (pyopenms.NASequence.NASFragmentType attribute) ThresholdMower (class in pyopenms) TI (pyopenms.IonSource.IonizationMethod attribute) tic (pyopenms.FileInfo.FeatureInfo property) TIC (pyopenms.MorpheusScore_Result property) time-of-flight time_array_view() (pyopenms.OSChromatogram method) TIME_LAG_FOCUSING (pyopenms.Instrument.IonOpticsType attribute) tims_calibration_strategy (pyopenms.BrukerTimsFile.Config property) title (pyopenms.FileInfo.NamedStats property) TM_DataPoint (in module pyopenms) TMT TMT_SIXPLEX (pyopenms.ITRAQ_TYPES attribute) (pyopenms.ItraqConstants attribute) (pyopenms.ItraqConstants.ITRAQ_TYPES attribute) TMTEighteenPlexQuantitationMethod (class in pyopenms) TMTElevenPlexQuantitationMethod (class in pyopenms) TMTSixPlexQuantitationMethod (class in pyopenms) TMTSixteenPlexQuantitationMethod (class in pyopenms) TMTTenPlexQuantitationMethod (class in pyopenms) to_arrow() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.Mobilogram method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.PeptideIdentificationList method) (pyopenms.XICParquetFile method) (pyopenms.XIMParquetFile method) (pyopenms.XIPMParquetFile method) to_bytes() (pyopenms.Base64.ByteOrder method) (pyopenms.BasicProteinInferenceAlgorithm.AggregationMethod method) (pyopenms.BoundaryCondition method) (pyopenms.BSpline2d.BoundaryCondition method) (pyopenms.ChromatogramSettings.ChromatogramType method) (pyopenms.CombinationsLogic method) (pyopenms.ConsensusMapNormalizerAlgorithmMedian.NormalizationMethod method) (pyopenms.ControlledVocabulary.CVTerm.XRefType method) (pyopenms.DRangeIntersection method) (pyopenms.DriftTimeUnit method) (pyopenms.EntrapmentEvaluation.Kind method) (pyopenms.EntrapmentEvaluation.Level method) (pyopenms.EnzymaticDigestion.Specificity method) (pyopenms.FeatureDeconvolution.CHARGEMODE method) (pyopenms.FileType method) (pyopenms.FileTypes.FileType method) (pyopenms.HydrophobicityScaleMethod method) (pyopenms.IDMapper.Measure method) (pyopenms.IDRipper.OriginAnnotationFormat method) (pyopenms.IDType method) (pyopenms.IsotopeDistribution.Sorted method) (pyopenms.ITRAQ_TYPES method) (pyopenms.ItraqConstants.ITRAQ_TYPES method) (pyopenms.LogType method) (pyopenms.Measure method) (pyopenms.MetaboliteFeatureDeconvolution.CHARGEMODE method) (pyopenms.Method method) (pyopenms.MSNumpressCoder.NumpressCompression method) (pyopenms.MultipleTesting.LfdrTransform method) (pyopenms.MultipleTesting.Pi0Method method) (pyopenms.MzPAFDeltaUnit method) (pyopenms.MzPAFErrorCode method) (pyopenms.MzPAFIonSeries method) (pyopenms.NaNPolicy method) (pyopenms.NASequence.NASFragmentType method) (pyopenms.NormalizationMethod method) (pyopenms.OpenMSOSInfo.OpenMS_Architecture method) (pyopenms.OpenMSOSInfo.OpenMS_OS method) (pyopenms.OpenPepXLAlgorithm.ExitCodes method) (pyopenms.OPXLDataStructs.PeptidePosition method) (pyopenms.OPXLDataStructs.ProteinProteinCrossLinkType method) (pyopenms.OriginAnnotationFormat method) (pyopenms.ParquetWriteConfig.Compression method) (pyopenms.PeakGroup.TargetDecoyType method) (pyopenms.PEFFDatabaseMetadata.SequenceType method) (pyopenms.PEFFModification.ModificationType method) (pyopenms.PeptideIndexing.ExitCodes method) (pyopenms.PercolatorOutfile.ScoreType method) (pyopenms.ProForma.ConversionIssueType method) (pyopenms.ProForma.ConversionPolicy method) (pyopenms.ProForma.CvDatabase method) (pyopenms.ProForma.WriteMode method) (pyopenms.ProgressLogger.LogType method) (pyopenms.ProSEAlgorithm.ProSEAlgorithm_ExitCodes method) (pyopenms.ProteomicsPkaScale method) (pyopenms.QuotingMethod method) (pyopenms.RankData.Method method) (pyopenms.RankData.NaNPolicy method) (pyopenms.RequirementLevel method) (pyopenms.Residue.ResidueType method) (pyopenms.ResidueModification.Provenance method) (pyopenms.ResidueModification.SourceClassification method) (pyopenms.ResidueModification.TermSpecificity method) (pyopenms.Ribonucleotide.TermSpecificityNuc method) (pyopenms.Scores.IDType method) (pyopenms.SIDE method) (pyopenms.SimpleSearchEngineAlgorithm.ExitCodes method) (pyopenms.UnitType method) (pyopenms.USI.IndexType method) (pyopenms.ValueType method) (pyopenms.XFDRAlgorithm.ExitCodes method) (pyopenms.XTandemInfile.ErrorUnit method) (pyopenms.XTandemInfile.MassType method) to_chromatogram_df() (pyopenms.MRMTransitionGroupCP method) to_df() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.PeptideIdentificationList method) (pyopenms.XICParquetFile method) (pyopenms.XIMParquetFile method) (pyopenms.XIPMParquetFile method) to_dict() (pyopenms.Param method) to_feature_arrow() (pyopenms.ConsensusMap method) to_feature_df() (pyopenms.ConsensusMap method) (pyopenms.MRMTransitionGroupCP method) to_feature_parquet() (pyopenms.ConsensusMap method) to_feature_qpx() (pyopenms.ConsensusMap method) to_parquet() (pyopenms.PeptideIdentificationList method) to_peptide_df() (pyopenms.FeatureMap method) to_psm_arrow() (pyopenms.PeptideIdentificationList method) to_psm_df() (pyopenms.PeptideIdentificationList method) to_psm_qpx() (pyopenms.PeptideIdentificationList method) to_qpx() (pyopenms.PeptideIdentificationList method) to_spectrum() (pyopenms.TheoreticalGlycanSpectrumGenerator static method) to_text() (pyopenms.FileInfo static method) to_tsv() (pyopenms.FileInfo static method) to_tuple() (pyopenms.Peak1D method) toAASequence() (pyopenms.Peptidoform method) (pyopenms.ProForma static method) toAcquisitionMode() (pyopenms.IonDetector static method) toActivationMethod() (pyopenms.Precursor static method) toAnalyzerType() (pyopenms.MassAnalyzer static method) toBool() (pyopenms.DataValue method) (pyopenms.ParamValue method) toBracketString() (pyopenms.AASequence method) today() (pyopenms.Date static method) toDouble() (pyopenms.DataValue method) (pyopenms.ParamValue method) toDoubleList() (pyopenms.DataValue method) toDoubleVector() (pyopenms.ParamValue method) toDriftTimeUnit() (pyopenms.IMTypes static method) toExpandedString() (pyopenms.MassDecomposition method) TOF (pyopenms.MassAnalyzer.AnalyzerType attribute) toFASTAEntry() (pyopenms.PEFFEntry method) toIMFormat() (pyopenms.IMTypes static method) toIMPeakType() (pyopenms.IMTypes static method) toInletType() (pyopenms.IonSource static method) toInt() (pyopenms.DataValue method) (pyopenms.ParamValue method) toIntList() (pyopenms.DataValue method) toIntVector() (pyopenms.ParamValue method) toIonizationMethod() (pyopenms.IonSource static method) toJSON() (pyopenms.ProForma static method) toJSONIon() (pyopenms.ProForma static method) tolerance (pyopenms.IDFreeMassErrorEstimator.ToleranceSuggestion property) tolerance_sigma_multiplier (pyopenms.IDFreeMassErrorEstimator.Parameters property) toLfdrTransform() (pyopenms.MultipleTesting static method) too_few_peptides (pyopenms.PeptideAndProteinQuant_Statistics property) ToolInfo (class in pyopenms) top_peaks (pyopenms.IDFreeMassErrorEstimator.Parameters property) toPeakAnnotation() (pyopenms.MzPAF static method) toPi0Method() (pyopenms.MultipleTesting static method) toPolarity() (pyopenms.IonSource static method) TOPP TOPP tools TOPPAS (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) TOPPView toProcessingAction() (pyopenms.DataProcessing static method) toProForma() (in module pyopenms) (pyopenms.PEFFFile static method) toReflectronState() (pyopenms.MassAnalyzer static method) toResolutionMethod() (pyopenms.MassAnalyzer static method) toResolutionType() (pyopenms.MassAnalyzer static method) toSampleState() (pyopenms.Sample static method) toScanDirection() (pyopenms.MassAnalyzer static method) toScanLaw() (pyopenms.MassAnalyzer static method) toScanMode() (pyopenms.InstrumentSettings static method) toScoreTypeEnum() (pyopenms.IDScoreSwitcherAlgorithm static method) toSpectrum() (pyopenms.DeconvolvedSpectrum method) toSpectrumType() (pyopenms.MSSpectrum static method) (pyopenms.SpectrumSettings static method) toString() (pyopenms.AASequence method) (pyopenms.DataFilter method) (pyopenms.DataValue method) (pyopenms.EmpiricalFormula method) (pyopenms.MassDecomposition method) (pyopenms.MzPAF static method) (pyopenms.MZTrafoModel method) (pyopenms.NASequence method) (pyopenms.ParamValue method) (pyopenms.Peptidoform method) (pyopenms.PeptidoformIon method) (pyopenms.ProForma static method) (pyopenms.RANSACParam method) (pyopenms.Residue method) (pyopenms.USI method) toStringIon() (pyopenms.ProForma static method) toStringList() (pyopenms.DataValue method) toStringMultiple() (pyopenms.MzPAF static method) toStringVector() (pyopenms.ParamValue method) total_current (pyopenms.CrossLinkSpectrumMatch property) total_distinct_peptides (pyopenms.PeptideAndProteinQuant_ProteinData property) total_features (pyopenms.PeptideAndProteinQuant_Statistics property) total_intensity (pyopenms.PurityScores property) TOTAL_ION_CURRENT_CHROMATOGRAM (pyopenms.ChromatogramSettings.ChromatogramType attribute) total_modified_psms (pyopenms.PTMStatistics property) total_peaks (pyopenms.FileInfo.PeakInfo property) total_peptides (pyopenms.PeptideAndProteinQuant_Statistics property) total_psm_counts (pyopenms.PeptideAndProteinQuant_PeptideData property) (pyopenms.PeptideAndProteinQuant_ProteinData property) total_psms (pyopenms.DeltaMassStatistics property) total_residues (pyopenms.FileInfo.FastaInfo property) total_target_precursors (pyopenms.TransitionListEvidenceFilter_Result property) total_width (pyopenms.PI_PeakShapeMetrics property) total_xic (pyopenms.OpenSwath_Scores property) totalhigh (pyopenms.SysInfo attribute) totalMatchedCurrent() (pyopenms.XQuestScores static method) totalram (pyopenms.SysInfo attribute) totalswap (pyopenms.SysInfo attribute) toType() (pyopenms.IonDetector static method) toUniModString() (pyopenms.AASequence method) toUnmodifiedString() (pyopenms.AASequence method) toXMLString() (pyopenms.ControlledVocabulary.CVTerm method) TRACE_LEVEL (pyopenms.FeatureOverlapFilter.FeatureOverlapMode attribute) trackNoise() (pyopenms.FIAMSDataProcessor method) train() (pyopenms.MZTrafoModel method) TRAML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) TraMLFile (class in pyopenms) TraMLProduct (class in pyopenms) TransferLLOQAndULOQToCalculatedConcentrationBounds() (pyopenms.MRMFeatureFilter method) transferSubelements() (pyopenms.FeatureGroupingAlgorithm method) (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.FeatureGroupingAlgorithmLabeled method) (pyopenms.FeatureGroupingAlgorithmQT method) (pyopenms.FeatureGroupingAlgorithmUnlabeled method) (pyopenms.PipEchoAlgorithm method) transform() (pyopenms.BrukerTimsFile method) (pyopenms.MzMLFile method) (pyopenms.MzXMLFile method) (pyopenms.SpectraSTSimilarityScore method) (pyopenms.ThermoRawFile method) transformation_summary (pyopenms.FileInfo.Result property) TransformationDescription (class in pyopenms) TransformationModel_DataPoint (class in pyopenms) TransformationModelBSpline (class in pyopenms) TransformationModelInterpolated (class in pyopenms) TransformationModelLinear (class in pyopenms) TransformationModelLowess (class in pyopenms) TransformationStatistics (class in pyopenms) TRANSFORMATIONXML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) TransformationXMLFile (class in pyopenms) transformRetentionTimes() (pyopenms.MapAlignmentTransformer static method) TRANSIENTRECORDER (pyopenms.IonDetector.AcquisitionMode attribute) TRANSITION (pyopenms.OSWHierarchy attribute) (pyopenms.OSWHierarchy.Level attribute) transition_name (pyopenms.LightTransition property) transition_quality_score (pyopenms.MetaboTargetedAssay property) transitionCount() (pyopenms.OSWData method) TransitionListEvidenceFilter (class in pyopenms) TransitionListEvidenceFilter_PrecursorEvidence (class in pyopenms) TransitionListEvidenceFilter_Result (class in pyopenms) TransitionPQPFile (class in pyopenms) transitions (pyopenms.LightTargetedExperiment property) TransitionTSVFile (class in pyopenms) translateIsotopeMatrix() (pyopenms.ItraqConstants static method) TRAP (pyopenms.Precursor.ActivationMethod attribute) trimIntensities() (pyopenms.IsotopeDistribution method) trimLeft() (pyopenms.IsotopeDistribution method) trimRight() (pyopenms.IsotopeDistribution method) tryGnuplot() (pyopenms.PosteriorErrorProbabilityModel method) tryParse() (pyopenms.MzPAF static method) tryParseMultiple() (pyopenms.MzPAF static method) TSE_Match (class in pyopenms) TSF (pyopenms.BrukerTimsFile.DataFormat attribute) TSP (pyopenms.IonSource.IonizationMethod attribute) tsv (pyopenms.FileInfo.Result property) TSV (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) TXT (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) type (pyopenms.ConversionIssue property) (pyopenms.FileInfo.MzTabInfo property) (pyopenms.ImzMLAuxArrayIndex property) (pyopenms.PEFFModification property) TYPENULL (pyopenms.IonDetector.Type attribute) typeToDescription() (pyopenms.FileTypes static method) typeToExtensions() (pyopenms.FileTypes static method) typeToMZML() (pyopenms.FileTypes static method) typeToName() (pyopenms.FileTypes static method) typeToString() (pyopenms.IonDetector static method) U uisTransitions() (pyopenms.MRMAssay method) Unannotated (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) unassigned_ids (pyopenms.FileInfo.FeatureInfo property) unassignedMS2 (pyopenms.FeatureMapping_FeatureToMs2Indices property) UNAVAILABLE (pyopenms.IDFreeMassErrorEstimator.FragmentResolutionRegime attribute) UNCLOSED_BRACKET (pyopenms.MzPAFErrorCode attribute) UNDEFINED (pyopenms.IsotopeDistribution attribute) (pyopenms.IsotopeDistribution.Sorted attribute) UNEXPECTED_CHARACTER (pyopenms.MzPAFErrorCode attribute) UNEXPECTED_END_OF_INPUT (pyopenms.MzPAFErrorCode attribute) UNEXPECTED_RESULT (pyopenms.OpenPepXLAlgorithm.ExitCodes attribute) (pyopenms.PeptideIndexing.ExitCodes attribute) (pyopenms.ProSEAlgorithm attribute) (pyopenms.ProSEAlgorithm.ProSEAlgorithm_ExitCodes attribute) (pyopenms.SimpleSearchEngineAlgorithm.ExitCodes attribute) (pyopenms.XFDRAlgorithm.ExitCodes attribute) unidentified (pyopenms.IDMapper_PeptideIdentificationListState property) unify() (pyopenms.MSSpectrum method) (pyopenms.SpectrumSettings method) UNIMOD (pyopenms.PEFFModification.ModificationType attribute) (pyopenms.ProForma.CvDatabase attribute) unimod_id (pyopenms.LightModification property) (pyopenms.TargetedExperiment_Modification property) UnimodXMLFile (class in pyopenms) uniprot_id (pyopenms.LightProtein property) unique_id (pyopenms.ColumnHeader property) unique_peptides (pyopenms.DeltaMassEntry property) (pyopenms.PTMEntry property) UniqueIdGenerator (class in pyopenms) UniqueIdInterface (class in pyopenms) Unit (class in pyopenms) unit (pyopenms.IDFreeMassErrorEstimator.ToleranceSuggestion property) (pyopenms.MzPAFMassDelta property) unit_accession (pyopenms.ImzMLAuxArrayIndex property) (pyopenms.SemanticValidator_CVTerm property) unit_name (pyopenms.SemanticValidator_CVTerm property) UNIT_ONTOLOGY (pyopenms.UnitType attribute) united() (pyopenms.DRange1 method) (pyopenms.DRange2 method) units (pyopenms.ControlledVocabulary.CVTerm property) UnitType (class in pyopenms) UNKNOWN (pyopenms.DecoyTransitionType attribute) (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) (pyopenms.IMFormat attribute) (pyopenms.IMPeakType attribute) (pyopenms.ImzMLDataType attribute) (pyopenms.Instrument.IonOpticsType attribute) (pyopenms.InstrumentSettings.ScanMode attribute) (pyopenms.MzPAFIonSeries attribute) (pyopenms.ReactionMonitoringTransition attribute) (pyopenms.ReactionMonitoringTransition.DecoyTransitionType attribute) (pyopenms.ResidueModification attribute) (pyopenms.ResidueModification.SourceClassification attribute) (pyopenms.RetentionTime attribute) (pyopenms.RetentionTime.RTType attribute) (pyopenms.RetentionTime.RTUnit attribute) (pyopenms.SpectrumSettings.SpectrumType attribute) UNKNOWN_CHECKSUM (pyopenms.ChecksumType attribute) (pyopenms.SourceFile.ChecksumType attribute) UNKNOWN_ERROR (pyopenms.ProSEAlgorithm attribute) (pyopenms.ProSEAlgorithm.ProSEAlgorithm_ExitCodes attribute) (pyopenms.SimpleSearchEngineAlgorithm.ExitCodes attribute) unknown_modification_psms (pyopenms.PTMStatistics property) UNKNOWN_OAF (pyopenms.IDRipper attribute) (pyopenms.IDRipper.OriginAnnotationFormat attribute) (pyopenms.OriginAnnotationFormat attribute) UNLOCALISED_MOD (pyopenms.ProForma.ConversionIssueType attribute) unlocalised_mods (pyopenms.Peptidoform property) UnlocalisedMod (class in pyopenms) unmodified_psms (pyopenms.DeltaMassStatistics property) unmodified_seq (pyopenms.AASeqWithMass property) unparsed (pyopenms.ControlledVocabulary.CVTerm property) UNREADABLE_ARCHIVE (pyopenms.BrukerTimsFile.DataFormat attribute) unrecognized_keys (pyopenms.PEFFDatabaseMetadata property) UNRESOLVED_MOD (pyopenms.ProForma.ConversionIssueType attribute) UnresolvedIdentifications (class in pyopenms) UNSUPPORTED_FEATURE (pyopenms.ProForma.ConversionIssueType attribute) unWeightData() (pyopenms.TransformationModelBSpline method) (pyopenms.TransformationModelInterpolated method) (pyopenms.TransformationModelLinear method) (pyopenms.TransformationModelLowess method) unWeightDatum() (pyopenms.TransformationModelBSpline method) (pyopenms.TransformationModelInterpolated method) (pyopenms.TransformationModelLinear method) (pyopenms.TransformationModelLowess method) UP (pyopenms.MassAnalyzer.ScanDirection attribute) update() (pyopenms.Param method) update_scores_from_df() (in module pyopenms) (pyopenms.PeptideIdentificationList method) updateBaseline() (pyopenms.MassTraces method) updateIsotopeMatrixFromStringList() (pyopenms.ItraqConstants static method) updateMaximum() (pyopenms.FeatureFinderAlgorithmPickedHelperStructs_MassTrace method) updateMeanMZ() (pyopenms.MassTrace method) updateMedianMZ() (pyopenms.MassTrace method) updateMedianRT() (pyopenms.MassTrace method) updateMinElement() (pyopenms.DistanceMatrix method) updateProteinGroups() (pyopenms.IDFilter static method) updateProteinReferences() (pyopenms.IDFilter static method) updateRanges() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.Mobilogram method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) updateSmoothedMaxRT() (pyopenms.MassTrace method) updateSmoothedWeightedMeanRT() (pyopenms.MassTrace method) updateWeightedMeanMZ() (pyopenms.MassTrace method) updateWeightedMeanRT() (pyopenms.MassTrace method) updateWeightedMZsd() (pyopenms.MassTrace method) upper (pyopenms.SwathMap property) upperq (pyopenms.SummaryStatistics property) uptime (pyopenms.SysInfo attribute) URI (pyopenms.CV property) use_coelution_score_ (pyopenms.OpenSwath_Scores_Usage property) use_dia_scores_ (pyopenms.OpenSwath_Scores_Usage property) use_elution_model_score_ (pyopenms.OpenSwath_Scores_Usage property) use_im_scores (pyopenms.OpenSwath_Scores_Usage property) use_intensity_score_ (pyopenms.OpenSwath_Scores_Usage property) use_ionseries_scores (pyopenms.OpenSwath_Scores_Usage property) use_library_score_ (pyopenms.OpenSwath_Scores_Usage property) use_lossy_numpress (pyopenms.SqMassConfig property) use_mi_score_ (pyopenms.OpenSwath_Scores_Usage property) use_ms1_correlation (pyopenms.OpenSwath_Scores_Usage property) use_ms1_fullscan (pyopenms.OpenSwath_Scores_Usage property) use_ms1_mi (pyopenms.OpenSwath_Scores_Usage property) use_ms2_isotope_scores (pyopenms.OpenSwath_Scores_Usage property) use_nr_peaks_score_ (pyopenms.OpenSwath_Scores_Usage property) use_peak_shape_metrics (pyopenms.OpenSwath_Scores_Usage property) use_rt_score_ (pyopenms.OpenSwath_Scores_Usage property) use_shape_score_ (pyopenms.OpenSwath_Scores_Usage property) use_sn_score_ (pyopenms.OpenSwath_Scores_Usage property) use_total_mi_score_ (pyopenms.OpenSwath_Scores_Usage property) use_total_xic_score_ (pyopenms.OpenSwath_Scores_Usage property) use_uis_scores (pyopenms.OpenSwath_Scores_Usage property) usePPM() (pyopenms.CalibrationData method) USI (class in pyopenms) USI.IndexType (class in pyopenms) uuid (pyopenms.ImzMLMeta property) V V (pyopenms.MzPAFIonSeries attribute) VACUUM_PERMEABILITY (in module pyopenms.Constants) VACUUM_PERMITTIVITY (in module pyopenms.Constants) valid (pyopenms.FileInfo.ValidationInfo property) valid_strings (pyopenms.ParamEntry property) validate (pyopenms.FileInfo.Options property) validate() (pyopenms.MSImagingExperiment method) (pyopenms.SemanticValidator method) validateClassArguments() (pyopenms.XFDRAlgorithm method) validateTargetedExperiment() (pyopenms.TransitionPQPFile method) (pyopenms.TransitionTSVFile method) validation (pyopenms.FileInfo.Result property) validations (pyopenms.Configuration property) value (pyopenms.DataFilter property) (pyopenms.MzPAFMassDelta property) (pyopenms.ParamEntry property) (pyopenms.SemanticValidator_CVTerm property) value() (pyopenms.BilinearInterpolation method) (pyopenms.LinearInterpolation method) value_is_numerical (pyopenms.DataFilter property) value_string (pyopenms.DataFilter property) values() (pyopenms.Param method) ValueType (class in pyopenms) valueType() (pyopenms.DataValue method) (pyopenms.ParamValue method) variable_modifications (pyopenms.SearchParameters property) variance (pyopenms.SummaryStatistics property) variant_aa (pyopenms.PEFFVariantSimple property) version (pyopenms.CV property) (pyopenms.FileInfo.MzTabInfo property) (pyopenms.PEFFDatabaseMetadata property) version_ (pyopenms.ToolInfo property) version_major (pyopenms.VersionDetails property) version_minor (pyopenms.VersionDetails property) version_patch (pyopenms.VersionDetails property) VersionDetails (class in pyopenms) VersionInfo (class in pyopenms) VI (pyopenms.IonSource.IonizationMethod attribute) VIon (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) VSSC (pyopenms.DriftTimeUnit attribute) W W (pyopenms.MzPAFIonSeries attribute) warning (pyopenms.PercolatorRescoring property) warnings (pyopenms.FileInfo.CorruptionInfo property) (pyopenms.FileInfo.ValidationInfo property) weightData() (pyopenms.TransformationModelBSpline method) (pyopenms.TransformationModelInterpolated method) (pyopenms.TransformationModelLinear method) (pyopenms.TransformationModelLowess method) weightDatum() (pyopenms.TransformationModelBSpline method) (pyopenms.TransformationModelInterpolated method) (pyopenms.TransformationModelLinear method) (pyopenms.TransformationModelLowess method) weighted_coelution_score (pyopenms.OpenSwath_Scores property) weighted_massdev_score (pyopenms.OpenSwath_Scores property) weighted_mi_score (pyopenms.OpenSwath_Scores property) weighted_xcorr_shape (pyopenms.OpenSwath_Scores property) weightedTICScore() (pyopenms.XQuestScores static method) weightedTICScoreXQuest() (pyopenms.XQuestScores static method) width_at_10 (pyopenms.PI_PeakShapeMetrics property) width_at_5 (pyopenms.PI_PeakShapeMetrics property) width_at_50 (pyopenms.PI_PeakShapeMetrics property) window_length (pyopenms.SignalToNoiseEstimatorMedianRapid.NoiseEstimator property) WindowMower (class in pyopenms) WIon (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) without_spectrum_reference (pyopenms.UnresolvedIdentifications property) writable() (pyopenms.File static method) write() (pyopenms.XTandemInfile method) write_full_meta (pyopenms.SqMassConfig property) write_statistics (pyopenms.ParquetWriteConfig property) writeChromatograms() (pyopenms.MzMLSqliteHandler method) writeDeltaMassStatistics() (pyopenms.OpenSearchModificationAnalysis method) writeEnd() (pyopenms.FASTAFile method) (pyopenms.PEFFFile method) writeExperiment() (pyopenms.MzMLSqliteHandler method) writeHeader() (pyopenms.OpenSwathOSWWriter method) writeHist() (pyopenms.PrecursorCorrection static method) writeLines() (pyopenms.OpenSwathOSWWriter method) writeMemdump() (pyopenms.CachedMzMLHandler method) (pyopenms.MSDataCachedConsumer method) writeMetadata() (pyopenms.CachedMzMLHandler method) (pyopenms.MSDataCachedConsumer method) writeMzML() (pyopenms.FLASHDeconvSpectrumFile static method) writeNext() (pyopenms.FASTAFile method) (pyopenms.PEFFFile method) writePeakAnnotationsString_() (pyopenms.PeptideHit_PeakAnnotation static method) writePTMStatistics() (pyopenms.OpenSearchModificationAnalysis method) writeRunLevelInformation() (pyopenms.MzMLSqliteHandler method) writeSpectra() (pyopenms.MzMLSqliteHandler method) writeStart() (pyopenms.FASTAFile method) (pyopenms.PEFFFile method) writeSupplementaryPairTable() (pyopenms.IonIdentityMolecularNetworking static method) writeXQuestXMLSpec() (pyopenms.XQuestResultXMLFile static method) wTIC (pyopenms.CrossLinkSpectrumMatch property) wTICold (pyopenms.CrossLinkSpectrumMatch property) X x (pyopenms.ImzMLSpectrumIndex property) X (pyopenms.MzPAFIonSeries attribute) x0 (pyopenms.GaussFitResult property) xcorr_coelution_score (pyopenms.OpenSwath_Scores property) xcorr_shape_score (pyopenms.OpenSwath_Scores property) xcorrc_max (pyopenms.CrossLinkSpectrumMatch property) xCorrelation() (pyopenms.XQuestScores static method) xCorrelationPrescore() (pyopenms.XQuestScores static method) xcorrx_max (pyopenms.CrossLinkSpectrumMatch property) XFDRAlgorithm (class in pyopenms) XFDRAlgorithm.ExitCodes (class in pyopenms) XICParquetFile (class in pyopenms) XIMParquetFile (class in pyopenms) XIon (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) XIPMParquetFile (class in pyopenms) XLMOD (pyopenms.ProForma.CvDatabase attribute) XLPrecursor (class in pyopenms) XMASS (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) xmax (pyopenms.TransformationStatistics property) xmin (pyopenms.TransformationStatistics property) XML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) XMLFile (class in pyopenms) XOR (pyopenms.CombinationsLogic attribute) xquest_score (pyopenms.CrossLinkSpectrumMatch property) XQuestResultXMLFile (class in pyopenms) XQuestScores (class in pyopenms) XQUESTXML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) xref_binary (pyopenms.ControlledVocabulary.CVTerm property) xref_type (pyopenms.ControlledVocabulary.CVTerm property) XSD (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) XSD_ANYURI (pyopenms.ControlledVocabulary.CVTerm.XRefType attribute) XSD_BOOLEAN (pyopenms.ControlledVocabulary.CVTerm.XRefType attribute) XSD_DATE (pyopenms.ControlledVocabulary.CVTerm.XRefType attribute) XSD_DECIMAL (pyopenms.ControlledVocabulary.CVTerm.XRefType attribute) XSD_INTEGER (pyopenms.ControlledVocabulary.CVTerm.XRefType attribute) XSD_NEGATIVE_INTEGER (pyopenms.ControlledVocabulary.CVTerm.XRefType attribute) XSD_NON_NEGATIVE_INTEGER (pyopenms.ControlledVocabulary.CVTerm.XRefType attribute) XSD_NON_POSITIVE_INTEGER (pyopenms.ControlledVocabulary.CVTerm.XRefType attribute) XSD_POSITIVE_INTEGER (pyopenms.ControlledVocabulary.CVTerm.XRefType attribute) XSD_STRING (pyopenms.ControlledVocabulary.CVTerm.XRefType attribute) XTandemInfile (class in pyopenms) XTandemInfile.ErrorUnit (class in pyopenms) XTandemInfile.MassType (class in pyopenms) XTandemXMLFile (class in pyopenms) Y y (pyopenms.ImzMLSpectrumIndex property) Y (pyopenms.MzPAFIonSeries attribute) (pyopenms.TheoreticalGlycanSpectrumGenerator.IonType attribute) YAML (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) year() (pyopenms.Date method) YIon (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) YIonMinusH20 (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) YIonMinusNH3 (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) ymax (pyopenms.TransformationStatistics property) ymin (pyopenms.TransformationStatistics property) yseries_score (pyopenms.OpenSwath_Scores property) Z z (pyopenms.ImzMLSpectrumIndex property) Z (pyopenms.MzPAFIonSeries attribute) (pyopenms.TheoreticalGlycanSpectrumGenerator.IonType attribute) ZIon (pyopenms.NASequence.NASFragmentType attribute) (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) ZIP (pyopenms.FileType attribute) (pyopenms.FileTypes attribute) (pyopenms.FileTypes.FileType attribute) Zp1Ion (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) Zp2Ion (pyopenms.Residue attribute) (pyopenms.Residue.ResidueType attribute) ZSTD (pyopenms.ParquetWriteConfig attribute) (pyopenms.ParquetWriteConfig.Compression attribute) zstd compression
