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 _ __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.ActivationMethod method) (pyopenms.Adduct method) (pyopenms.AggregationMethod method) (pyopenms.AMSE_AdductInfo method) (pyopenms.AnnotationState method) (pyopenms.AnnotationStatistics method) (pyopenms.AQS_featureConcentration method) (pyopenms.AQS_runConcentration method) (pyopenms.ArrayWrapperFloat method) (pyopenms.AScore method) (pyopenms.Attachment method) (pyopenms.AverageLinkage method) (pyopenms.Base64 method) (pyopenms.BaseFeature method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.BiGaussFitter1D method) (pyopenms.BiGaussModel method) (pyopenms.BilinearInterpolation method) (pyopenms.BinnedSpectrum method) (pyopenms.BoundaryCondition 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.ChromatogramExtractor method) (pyopenms.ChromatogramExtractorAlgorithm method) (pyopenms.ChromatogramPeak method) (pyopenms.ChromatogramSettings method) (pyopenms.ChromatogramTools method) (pyopenms.ChromeleonFile method) (pyopenms.ClusteringGrid method) (pyopenms.ClusterProxyKD method) (pyopenms.CoarseIsotopePatternGenerator method) (pyopenms.ColumnHeader method) (pyopenms.Compomer method) (pyopenms.Compound method) (pyopenms.ConfidenceScoring method) (pyopenms.Configuration method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusIDAlgorithm method) (pyopenms.ConsensusIDAlgorithmAverage method) (pyopenms.ConsensusIDAlgorithmBest method) (pyopenms.ConsensusIDAlgorithmIdentity method) (pyopenms.ConsensusIDAlgorithmPEPIons method) (pyopenms.ConsensusIDAlgorithmPEPMatrix method) (pyopenms.ConsensusIDAlgorithmRanks method) (pyopenms.ConsensusIDAlgorithmSimilarity method) (pyopenms.ConsensusIDAlgorithmWorst method) (pyopenms.ConsensusMap method) (pyopenms.ConsensusMapNormalizerAlgorithmMedian method) (pyopenms.ConsensusMapNormalizerAlgorithmQuantile method) (pyopenms.ConsensusMapNormalizerAlgorithmThreshold method) (pyopenms.ConsensusXMLFile method) (pyopenms.Contact method) (pyopenms.ContactPerson method) (pyopenms.ControlledVocabulary method) (pyopenms.ConvexHull2D method) (pyopenms.CrossLinksDB method) (pyopenms.CrossLinkSpectrumMatch method) (pyopenms.CsvFile method) (pyopenms.CubicSpline2d method) (pyopenms.CV method) (pyopenms.CVMappingFile method) (pyopenms.CVMappingRule method) (pyopenms.CVMappings method) (pyopenms.CVMappingTerm method) (pyopenms.CVReference method) (pyopenms.CVTerm method) (pyopenms.CVTerm_ControlledVocabulary 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.DecoyGenerator method) (pyopenms.DecoyTransitionType method) (pyopenms.Deisotoper method) (pyopenms.DIAScoring method) (pyopenms.Digestion method) (pyopenms.DigestionEnzyme method) (pyopenms.DigestionEnzymeProtein method) (pyopenms.DigestionEnzymeRNA method) (pyopenms.DimensionDescription method) (pyopenms.DistanceMatrix method) (pyopenms.DocumentIdentifier method) (pyopenms.DPosition1 method) (pyopenms.DPosition2 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.EnzymaticDigestion method) (pyopenms.ExperimentalDesign method) (pyopenms.ExperimentalDesign_MSFileSectionEntry method) (pyopenms.ExperimentalDesign_SampleSection method) (pyopenms.ExperimentalDesignFile method) (pyopenms.ExperimentalSettings method) (pyopenms.ExtractionCoordinates 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.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.FeatureMapping method) (pyopenms.FeatureMapping_FeatureMappingInfo method) (pyopenms.FeatureMapping_FeatureToMs2Indices method) (pyopenms.FeatureXMLFile method) (pyopenms.FIAMSDataProcessor method) (pyopenms.FIAMSScheduler method) (pyopenms.File method) (pyopenms.FileHandler method) (pyopenms.FileType method) (pyopenms.FileTypes method) (pyopenms.FineIsotopePatternGenerator method) (pyopenms.Fitter1D method) (pyopenms.FloatDataArray method) (pyopenms.GaussFilter method) (pyopenms.GaussFitResult method) (pyopenms.GaussFitter method) (pyopenms.GaussTraceFitter method) (pyopenms.GNPSMetaValueFile method) (pyopenms.GNPSMGFFile method) (pyopenms.GNPSQuantificationFile method) (pyopenms.Gradient method) (pyopenms.GridBasedCluster method) (pyopenms.HPLC method) (pyopenms.HyperScore method) (pyopenms.IBSpectraFile method) (pyopenms.IDConflictResolverAlgorithm method) (pyopenms.IDDecoyProbability method) (pyopenms.IdentificationRuns method) (pyopenms.IDFilter method) (pyopenms.IDMapper method) (pyopenms.IDMapper_SpectraIdentificationState method) (pyopenms.IDRipper method) (pyopenms.IdXMLFile method) (pyopenms.ILPDCWrapper method) (pyopenms.IMFormat method) (pyopenms.IMSAlphabet method) (pyopenms.IMSElement method) (pyopenms.IMSIsotopeDistribution method) (pyopenms.IMSIsotopeDistribution_Peak method) (pyopenms.IMSWeights method) (pyopenms.IMTypes method) (pyopenms.IncludeExcludeTarget method) (pyopenms.IndexedMzMLDecoder method) (pyopenms.IndexedMzMLFileLoader method) (pyopenms.IndexedMzMLHandler method) (pyopenms.InspectInfile method) (pyopenms.InspectOutfile method) (pyopenms.Instrument method) (pyopenms.InstrumentSettings method) (pyopenms.IntegerDataArray method) (pyopenms.Interfaces method) (pyopenms.Internal_MzMLValidator method) (pyopenms.InternalCalibration method) (pyopenms.InternalCalibration_LockMass method) (pyopenms.InterpolationModel method) (pyopenms.IonDetector method) (pyopenms.IonIdentityMolecularNetworking method) (pyopenms.IonOpticsType method) (pyopenms.IonSource method) (pyopenms.IsobaricChannelExtractor method) (pyopenms.IsobaricChannelInformation method) (pyopenms.IsobaricIsotopeCorrector method) (pyopenms.IsobaricNormalizer method) (pyopenms.IsobaricQuantifier method) (pyopenms.IsobaricQuantifierStatistics method) (pyopenms.IsotopeCluster method) (pyopenms.IsotopeDistribution method) (pyopenms.IsotopeFitter1D method) (pyopenms.IsotopeLabelingMDVs method) (pyopenms.IsotopeModel method) (pyopenms.IsotopePattern method) (pyopenms.IsotopeVariant method) (pyopenms.ITRAQ_TYPES method) (pyopenms.ItraqConstants method) (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.JavaInfo method) (pyopenms.KDTreeFeatureMaps method) (pyopenms.KDTreeFeatureNode method) (pyopenms.Kernel_MassTrace method) (pyopenms.KroenikFile method) (pyopenms.LabeledPairFinder method) (pyopenms.LightCompound method) (pyopenms.LightModification method) (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.LightProtein method) (pyopenms.LightTargetedExperiment method) (pyopenms.LightTransition method) (pyopenms.LinearInterpolation method) (pyopenms.LinearResampler method) (pyopenms.LinearResamplerAlign method) (pyopenms.LogConfigHandler method) (pyopenms.LogType method) (pyopenms.LowessSmoothing method) (pyopenms.LPWrapper method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmKD method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) (pyopenms.MapAlignmentEvaluationAlgorithmPrecision method) (pyopenms.MapAlignmentEvaluationAlgorithmRecall method) (pyopenms.MapAlignmentTransformer method) (pyopenms.MapConversion method) (pyopenms.MascotGenericFile method) (pyopenms.MascotInfile method) (pyopenms.MascotXMLFile method) (pyopenms.MassAnalyzer method) (pyopenms.MassDecomposition method) (pyopenms.MassDecompositionAlgorithm method) (pyopenms.MassExplainer method) (pyopenms.MassTrace method) (pyopenms.MasstraceCorrelator method) (pyopenms.MassTraceDetection method) (pyopenms.MassTraces 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.Modification method) (pyopenms.ModificationDefinition method) (pyopenms.ModificationDefinitionsSet method) (pyopenms.ModificationsDB method) (pyopenms.ModifiedPeptideGenerator method) (pyopenms.ModifiedPeptideGenerator_MapToResidueType method) (pyopenms.MorpheusScore method) (pyopenms.MorpheusScore_Result method) (pyopenms.MorphologicalFilter method) (pyopenms.MRMAssay 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.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.MsInspectFile method) (pyopenms.MSNumpressCoder method) (pyopenms.MSPFile method) (pyopenms.MSPGenericFile method) (pyopenms.MSSpectrum method) (pyopenms.MSstatsFile method) (pyopenms.MT_QUANTMETHOD method) (pyopenms.MultiplexDeltaMasses method) (pyopenms.MultiplexDeltaMasses_DeltaMass method) (pyopenms.MultiplexDeltaMassesGenerator method) (pyopenms.MultiplexDeltaMassesGenerator_Label method) (pyopenms.MultiplexIsotopicPeakPattern method) (pyopenms.MzDataFile method) (pyopenms.MzIdentMLFile method) (pyopenms.MzMLFile method) (pyopenms.MzMLSpectrumDecoder method) (pyopenms.MzMLSqliteHandler method) (pyopenms.MzMLSwathFileConsumer method) (pyopenms.MzQCFile method) (pyopenms.MzTab method) (pyopenms.MzTabFile method) (pyopenms.MzTabM method) (pyopenms.MzTabMFile method) (pyopenms.MZTrafoModel method) (pyopenms.MZTrafoModel_MODELTYPE method) (pyopenms.MzXMLFile method) (pyopenms.NASequence method) (pyopenms.NLargest method) (pyopenms.NoiseEstimator method) (pyopenms.NonNegativeLeastSquaresSolver method) (pyopenms.NoopMSDataWritingConsumer method) (pyopenms.NormalizationMethod method) (pyopenms.Normalizer method) (pyopenms.NucleicAcidSpectrumGenerator method) (pyopenms.NumpressConfig method) (pyopenms.OMSSACSVFile method) (pyopenms.OMSSAXMLFile method) (pyopenms.OnDiscMSExperiment method) (pyopenms.OpenMSBuildInfo method) (pyopenms.OpenMSOSInfo method) (pyopenms.OpenPepXLAlgorithm method) (pyopenms.OpenPepXLLFAlgorithm method) (pyopenms.OpenSwath_Scores method) (pyopenms.OpenSwath_Scores_Usage method) (pyopenms.OpenSwathDataAccessHelper method) (pyopenms.OpenSwathHelper method) (pyopenms.OpenSwathOSWWriter method) (pyopenms.OpenSwathScoring method) (pyopenms.OPXL_PreprocessedPairSpectra 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.OSWFile method) (pyopenms.Param method) (pyopenms.ParamCTDFile method) (pyopenms.ParamEntry method) (pyopenms.ParamNode method) (pyopenms.ParamValue method) (pyopenms.ParamXMLFile method) (pyopenms.Peak1D method) (pyopenms.Peak2D method) (pyopenms.PeakBoundary method) (pyopenms.PeakFileOptions method) (pyopenms.PeakIndex method) (pyopenms.PeakIntegrator method) (pyopenms.PeakPickerChromatogram method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) (pyopenms.PeakTypeEstimator method) (pyopenms.PeakWidthEstimator 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.PeptideIndexing method) (pyopenms.PeptideProteinResolution method) (pyopenms.PeptideProteinResolution_ConnectedComponent method) (pyopenms.PepXMLFile method) (pyopenms.PepXMLFileMascot method) (pyopenms.PercolatorFeatureSetHelper method) (pyopenms.PercolatorInfile method) (pyopenms.PercolatorOutfile method) (pyopenms.PI_PeakArea method) (pyopenms.PI_PeakBackground method) (pyopenms.PI_PeakShapeMetrics method) (pyopenms.PlainMSDataWritingConsumer method) (pyopenms.PosteriorErrorProbabilityModel method) (pyopenms.Precursor method) (pyopenms.PrecursorCorrection method) (pyopenms.PrecursorPurity method) (pyopenms.Prediction method) (pyopenms.ProbablePhosphoSites method) (pyopenms.Product method) (pyopenms.ProgressLogger method) (pyopenms.ProteaseDB method) (pyopenms.ProteaseDigestion method) (pyopenms.Protein method) (pyopenms.ProteinGroup method) (pyopenms.ProteinHit method) (pyopenms.ProteinIdentification method) (pyopenms.ProteinInference method) (pyopenms.ProteinProteinCrossLink method) (pyopenms.ProtXMLFile method) (pyopenms.PScore method) (pyopenms.Publication method) (pyopenms.PurityScores method) (pyopenms.QcMLFile method) (pyopenms.QTCluster method) (pyopenms.QTClusterFinder method) (pyopenms.QualityParameter method) (pyopenms.QuotingMethod method) (pyopenms.RangeIntensity method) (pyopenms.RangeMobility method) (pyopenms.RangeMZ method) (pyopenms.RankScaler method) (pyopenms.RANSAC method) (pyopenms.RansacModelLinear method) (pyopenms.RansacModelQuadratic method) (pyopenms.RANSACParam method) (pyopenms.RANSACQuadratic method) (pyopenms.Ratio method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RealMassDecomposer method) (pyopenms.RegularSwathFileConsumer 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.RNaseDB method) (pyopenms.RNaseDigestion method) (pyopenms.Sample method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.ScanMode method) (pyopenms.ScanWindow method) (pyopenms.SearchParameters method) (pyopenms.Seed method) (pyopenms.SeedListGenerator method) (pyopenms.SemanticValidator method) (pyopenms.SemanticValidator_CVTerm 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.SolverParam method) (pyopenms.SourceFile method) (pyopenms.SpectralMatch method) (pyopenms.SpectraMerger method) (pyopenms.SpectraSTSimilarityScore method) (pyopenms.SpectrumAccessOpenMS method) (pyopenms.SpectrumAccessOpenMSCached method) (pyopenms.SpectrumAccessOpenMSInMemory method) (pyopenms.SpectrumAccessQuadMZTransforming method) (pyopenms.SpectrumAccessSqMass method) (pyopenms.SpectrumAccessTransforming method) (pyopenms.SpectrumAlignment method) (pyopenms.SpectrumAlignmentScore method) (pyopenms.SpectrumAnnotator method) (pyopenms.SpectrumHelper method) (pyopenms.SpectrumLookup method) (pyopenms.SpectrumMetaData method) (pyopenms.SpectrumMetaDataLookup method) (pyopenms.SpectrumSettings method) (pyopenms.SplineInterpolatedPeaks method) (pyopenms.SplinePackage method) (pyopenms.SplineSpectrum_Navigator method) (pyopenms.SqMassConfig method) (pyopenms.SqMassFile method) (pyopenms.SqrtScaler method) (pyopenms.StablePairFinder method) (pyopenms.streampos method) (pyopenms.String method) (pyopenms.StringDataArray method) (pyopenms.StringView method) (pyopenms.SwathFile method) (pyopenms.SwathMap method) (pyopenms.SwathMapMassCorrection method) (pyopenms.SwathWindowLoader method) (pyopenms.SysInfo method) (pyopenms.Tagger method) (pyopenms.Tagging method) (pyopenms.TargetedExperiment method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TargetedExperiment_Modification method) (pyopenms.TargetedSpectraExtractor method) (pyopenms.TermSpecificityNuc method) (pyopenms.TextFile method) (pyopenms.TheoreticalIsotopePattern method) (pyopenms.TheoreticalSpectrumGenerator method) (pyopenms.TheoreticalSpectrumGeneratorXLMS method) (pyopenms.ThresholdMower method) (pyopenms.TM_DataPoint method) (pyopenms.TMTEighteenPlexQuantitationMethod method) (pyopenms.TMTElevenPlexQuantitationMethod method) (pyopenms.TMTSixPlexQuantitationMethod method) (pyopenms.TMTSixteenPlexQuantitationMethod method) (pyopenms.TMTTenPlexQuantitationMethod method) (pyopenms.ToolInfo method) (pyopenms.TraceInfo method) (pyopenms.TraMLFile method) (pyopenms.TraMLProduct method) (pyopenms.TransformationDescription method) (pyopenms.TransformationModelBSpline method) (pyopenms.TransformationModelInterpolated method) (pyopenms.TransformationModelLinear method) (pyopenms.TransformationModelLowess method) (pyopenms.TransformationStatistics method) (pyopenms.TransformationXMLFile method) (pyopenms.TransitionPQPFile method) (pyopenms.TransitionTSVFile method) (pyopenms.TSE_Match method) (pyopenms.UnimodXMLFile method) (pyopenms.UniqueIdGenerator method) (pyopenms.Unit method) (pyopenms.UnitType method) (pyopenms.ValueType method) (pyopenms.VersionDetails method) (pyopenms.VersionInfo method) (pyopenms.WindowMower method) (pyopenms.XFDRAlgorithm method) (pyopenms.XLPrecursor method) (pyopenms.XMLFile method) (pyopenms.XMLHandler method) (pyopenms.XQuestResultXMLFile method) (pyopenms.XQuestScores method) (pyopenms.XRefType_CVTerm_ControlledVocabulary method) (pyopenms.XTandemInfile method) (pyopenms.XTandemXMLFile method) A A (pyopenms.GaussFitResult attribute) AAIndex (class in pyopenms) AASequence (class in pyopenms) AASeqWithMass (class in pyopenms) absolutePath() (pyopenms.File method) AbsoluteQuantitation (class in pyopenms) AbsoluteQuantitationMethod (class in pyopenms) AbsoluteQuantitationMethodFile (class in pyopenms) AbsoluteQuantitationStandards (class in pyopenms) AbsoluteQuantitationStandardsFile (class in pyopenms) ABSORPTION (pyopenms.ScanMode attribute) abundance (pyopenms.IMSIsotopeDistribution_Peak attribute) ABUNDANCES_SUM_ERROR (pyopenms.IMSIsotopeDistribution attribute) accession (pyopenms.SemanticValidator_CVTerm attribute) (pyopenms.Unit attribute) accessions (pyopenms.PeptideAndProteinQuant_PeptideData attribute) (pyopenms.ProteinGroup attribute) AccurateMassSearchEngine (class in pyopenms) AccurateMassSearchResult (class in pyopenms) acidic() (pyopenms.AAIndex method) Acquisition (class in pyopenms) AcquisitionInfo (class in pyopenms) AcquisitionMode (pyopenms.IonDetector attribute) ActionMode (pyopenms.XMLHandler attribute) ActivationMethod (class in pyopenms) active (pyopenms.ChannelInfo attribute) actual_concentration (pyopenms.AQS_featureConcentration attribute) (pyopenms.AQS_runConcentration attribute) add() (pyopenms.Compomer method) (pyopenms.DataFilters method) addAnalysisResults() (pyopenms.PeptideHit method) addBetaAccessions() (pyopenms.OPXLHelper method) addChromatogram() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.MSExperiment method) addCluster() (pyopenms.ClusteringGrid method) addColumn() (pyopenms.LPWrapper method) addCOMETFeatures() (pyopenms.PercolatorFeatureSetHelper method) addCompound() (pyopenms.TargetedExperiment method) addCONCATSEFeatures() (pyopenms.PercolatorFeatureSetHelper 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.Protein method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TraMLProduct method) addDataProcessing() (pyopenms.NoopMSDataWritingConsumer method) (pyopenms.PlainMSDataWritingConsumer method) addElement() (pyopenms.ElementDB 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.TextFile method) addLossFormula() (pyopenms.Residue method) addLossName() (pyopenms.Residue method) addMappingRule() (pyopenms.CVMappings method) addMaps() (pyopenms.KDTreeFeatureMaps method) addMASCOTFeatures() (pyopenms.PercolatorFeatureSetHelper method) addMissingRTsToPeptideIDs() (pyopenms.SpectrumMetaDataLookup method) addMissingSpectrumReferences() (pyopenms.SpectrumMetaDataLookup method) addModification() (pyopenms.ModificationDefinitionsSet method) (pyopenms.ModificationsDB method) addMSGFFeatures() (pyopenms.PercolatorFeatureSetHelper method) addMSLevel() (pyopenms.PeakFileOptions method) addMULTISEFeatures() (pyopenms.PercolatorFeatureSetHelper method) addNTermLossFormula() (pyopenms.Residue method) addNTermLossName() (pyopenms.Residue method) addPeptide() (pyopenms.TargetedExperiment method) addPeptideEvidence() (pyopenms.PeptideHit method) addPercolatorFeatureList() (pyopenms.OPXLHelper 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.TargetedExperiment method) addProteinPositionMetaValues() (pyopenms.OPXLHelper method) addPublication() (pyopenms.TargetedExperiment method) addRatio() (pyopenms.ConsensusFeature method) addReferenceFormat() (pyopenms.SpectrumLookup method) (pyopenms.SpectrumMetaDataLookup method) addResidueSet() (pyopenms.Residue method) addRow() (pyopenms.CsvFile method) (pyopenms.LPWrapper method) addRTFitData() (pyopenms.MapAlignmentAlgorithmKD method) addRunAttachment() (pyopenms.QcMLFile method) addRunQualityParameter() (pyopenms.QcMLFile method) addSection() (pyopenms.Param method) addSetAttachment() (pyopenms.QcMLFile method) addSetQualityParameter() (pyopenms.QcMLFile 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.TargetedExperiment method) Adduct (class in pyopenms) addValue() (pyopenms.BilinearInterpolation method) (pyopenms.LinearInterpolation method) addXLTargetDecoyMV() (pyopenms.OPXLHelper method) addXTANDEMFeatures() (pyopenms.PercolatorFeatureSetHelper method) affected_channels (pyopenms.IsobaricChannelInformation attribute) AggregationMethod (class in pyopenms) align() (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) align_4() (pyopenms.MapAlignmentAlgorithmIdentification method) aliphatic() (pyopenms.AAIndex method) alpha (pyopenms.ProteinProteinCrossLink attribute) alpha_index (pyopenms.XLPrecursor attribute) ambig_features (pyopenms.PeptideAndProteinQuant_Statistics attribute) AMSE_AdductInfo (class in pyopenms) ANALYSISXML (pyopenms.FileType attribute) AnalyzerType (pyopenms.MassAnalyzer attribute) annotate() (pyopenms.IDMapper method) annotateConsensusMap() (pyopenms.IonIdentityMolecularNetworking method) annotateMatches() (pyopenms.SpectrumAnnotator method) annotateSpectra() (pyopenms.TargetedSpectraExtractor method) annotateSwathMapsFromFile() (pyopenms.SwathWindowLoader method) annotateTransition() (pyopenms.MRMIonSeries method) annotateTransitionCV() (pyopenms.MRMIonSeries method) annotation (pyopenms.PeptideHit_PeakAnnotation attribute) AnnotationState (class in pyopenms) AnnotationStatistics (class in pyopenms) ANYWHERE (pyopenms.TermSpecificityNuc attribute) apex_pos (pyopenms.PI_PeakArea attribute) appendColumns() (pyopenms.ConsensusMap method) appendRows() (pyopenms.ConsensusMap method) apply() (pyopenms.ConsensusIDAlgorithm method) (pyopenms.ConsensusIDAlgorithmAverage method) (pyopenms.ConsensusIDAlgorithmBest method) (pyopenms.ConsensusIDAlgorithmIdentity method) (pyopenms.ConsensusIDAlgorithmPEPIons method) (pyopenms.ConsensusIDAlgorithmPEPMatrix method) (pyopenms.ConsensusIDAlgorithmRanks method) (pyopenms.ConsensusIDAlgorithmSimilarity method) (pyopenms.ConsensusIDAlgorithmWorst method) (pyopenms.FalseDiscoveryRate method) (pyopenms.IDDecoyProbability method) (pyopenms.TransformationDescription method) applyBasic() (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 method) applyVariableModifications() (pyopenms.ModifiedPeptideGenerator static method) approximateFromPeptideWeight() (pyopenms.CoarseIsotopePatternGenerator method) approximateIntensities() (pyopenms.CoarseIsotopePatternGenerator method) AQS_featureConcentration (class in pyopenms) AQS_runConcentration (class in pyopenms) area (pyopenms.PI_PeakArea attribute) (pyopenms.PI_PeakBackground attribute) ArrayWrapperFloat (class in pyopenms) AScore (class in pyopenms) (pyopenms.ProbablePhosphoSites attribute) asDict() (pyopenms.Param method) assignMS2IndexToFeature() (pyopenms.FeatureMapping method) assignRanks() (pyopenms.PeptideIdentification method) (pyopenms.ProteinIdentification method) asymmetry_factor (pyopenms.PI_PeakShapeMetrics attribute) atEnd() (pyopenms.FASTAFile method) Attachment (class in pyopenms) average() (pyopenms.SpectraMerger method) AverageLinkage (class in pyopenms) averageMass() (pyopenms.IsotopeDistribution method) Averagines (pyopenms.IsotopeModel attribute) avg_mass_delta (pyopenms.TargetedExperiment_Modification attribute) AVOGADRO (in module pyopenms.Constants) B back() (pyopenms.IMSWeights method) backtrack_tech (pyopenms.SolverParam attribute) Base64 encoding Base64 (class in pyopenms) BaseFeature (class in pyopenms) baseline (pyopenms.MassTraces attribute) baseline_delta_2_height (pyopenms.PI_PeakShapeMetrics attribute) basename() (pyopenms.File method) basic() (pyopenms.AAIndex method) BasicProteinInferenceAlgorithm (class in pyopenms) BayesianProteinInferenceAlgorithm (class in pyopenms) BC_ZERO_ENDPOINTS (pyopenms.BoundaryCondition attribute) BC_ZERO_FIRST (pyopenms.BoundaryCondition attribute) BC_ZERO_SECOND (pyopenms.BoundaryCondition attribute) begin (pyopenms.ScanWindow attribute) BEST (pyopenms.AggregationMethod attribute) beta (pyopenms.ProteinProteinCrossLink attribute) beta_index (pyopenms.XLPrecursor attribute) BiGaussFitter1D (class in pyopenms) BiGaussModel (class in pyopenms) BilinearInterpolation (class in pyopenms) binary (pyopenms.Attachment attribute) Binary encoding (mzML) BinaryDataArray (pyopenms.Interfaces attribute) BinnedSpectrum (class in pyopenms) BIRD (pyopenms.ActivationMethod attribute) blank_features (pyopenms.PeptideAndProteinQuant_Statistics attribute) BOHR_RADIUS (in module pyopenms.Constants) BOLTZMANN (in module pyopenms.Constants) BOTH (pyopenms.SIDE attribute) BoundaryCondition (class in pyopenms) branching_tech (pyopenms.SolverParam attribute) bseries_score (pyopenms.OpenSwath_Scores attribute) BSpline2d (class in pyopenms) bufferram (pyopenms.SysInfo attribute) buildCandidates() (pyopenms.OPXLHelper method) buildFragmentAnnotations() (pyopenms.OPXLHelper method) buildGraph() (pyopenms.PeptideProteinResolution method) buildPeptideIDs() (pyopenms.OPXLHelper method) ByteOrder (pyopenms.Base64 attribute) C C13C12_MASSDIFF_U (in module pyopenms.Constants) C18 c_str() (pyopenms.String method) CachedmzML (class in pyopenms) CACHEDMZML (pyopenms.FileType attribute) CachedMzMLHandler (class in pyopenms) CachedSwathFileConsumer (class in pyopenms) 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 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) calculateBias() (pyopenms.AbsoluteQuantitation method) calculateBiasAndR() (pyopenms.AbsoluteQuantitation method) calculateGB() (pyopenms.AAIndex method) calculateIntensityRankInMZWindow() (pyopenms.PScore method) calculateIsotopicPurity() (pyopenms.IsotopeLabelingMDVs method) calculateMDV() (pyopenms.IsotopeLabelingMDVs method) calculateMDVAccuracies() (pyopenms.IsotopeLabelingMDVs method) calculateMDVAccuracy() (pyopenms.IsotopeLabelingMDVs method) calculateMDVs() (pyopenms.IsotopeLabelingMDVs method) calculatePeakLevelSpectra() (pyopenms.PScore method) calculatePeakShapeMetrics() (pyopenms.PeakIntegrator method) calculateRankMap() (pyopenms.PScore method) calculateRatio() (pyopenms.AbsoluteQuantitation method) calculateTheoreticalIsotopesNumber() (pyopenms.EmpiricalFormula method) calculateTIC() (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.InternalCalibration method) CalibrationData (class in pyopenms) canRun() (pyopenms.JavaInfo method) center (pyopenms.ChannelInfo attribute) (pyopenms.IsobaricChannelInformation attribute) (pyopenms.SwathMap attribute) channel_count (pyopenms.IsobaricQuantifierStatistics attribute) ChannelInfo (class in pyopenms) charge (pyopenms.ChargedIndexSet attribute) (pyopenms.InternalCalibration_LockMass attribute) (pyopenms.LightCompound attribute) (pyopenms.PeptideHit_PeakAnnotation attribute) (pyopenms.SimplePeak attribute) charge() (pyopenms.KDTreeFeatureMaps method) ChargedIndexSet (class in pyopenms) CHARGEMODE_FD (pyopenms.FeatureDeconvolution attribute) CHARGEMODE_MFD (pyopenms.MetaboliteFeatureDeconvolution attribute) ChargePair (class in pyopenms) charges (pyopenms.SearchParameters attribute) chauvenet() (pyopenms.MRMRTNormalizer method) chauvenet_probability() (pyopenms.MRMRTNormalizer method) checkDatumRange() (pyopenms.TransformationModelBSpline method) (pyopenms.TransformationModelInterpolated method) (pyopenms.TransformationModelLinear method) (pyopenms.TransformationModelLowess method) checkDefaults() (pyopenms.Param method) checkExtraFeatures() (pyopenms.PercolatorFeatureSetHelper method) checkLOD() (pyopenms.AbsoluteQuantitationMethod method) checkLOQ() (pyopenms.AbsoluteQuantitationMethod method) checkMaximalRTSpan() (pyopenms.GaussTraceFitter method) checkMinimalRTSpan() (pyopenms.GaussTraceFitter method) ChecksumType (class in pyopenms) checkSwathMapAndSelectTransitions() (pyopenms.OpenSwathHelper method) checkValidWeight() (pyopenms.TransformationModelBSpline method) (pyopenms.TransformationModelInterpolated method) (pyopenms.TransformationModelLinear method) (pyopenms.TransformationModelLowess method) children (pyopenms.CVTerm_ControlledVocabulary attribute) Chromatogram (pyopenms.Interfaces attribute) ChromatogramExtractor (class in pyopenms) ChromatogramExtractorAlgorithm (class in pyopenms) chromatogramIdsMatch() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) ChromatogramPeak (class in pyopenms) ChromatogramSettings (class in pyopenms) ChromatogramTools (class in pyopenms) ChromatogramType (pyopenms.ChromatogramSettings attribute) ChromeleonFile (class in pyopenms) CID (pyopenms.ActivationMethod attribute) clear() (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.DistanceMatrix method) (pyopenms.FeatureMap method) (pyopenms.FloatDataArray method) (pyopenms.IMSAlphabet method) (pyopenms.IntegerDataArray method) (pyopenms.IsotopeDistribution method) (pyopenms.KDTreeFeatureMaps method) (pyopenms.MetaInfo method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.Param method) (pyopenms.PeakIndex 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.Instrument method) (pyopenms.InstrumentSettings method) (pyopenms.IntegerDataArray method) (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) (pyopenms.MetaInfoDescription method) (pyopenms.MetaInfoInterface method) (pyopenms.Modification 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.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.SpectrumSettings method) (pyopenms.StringDataArray method) (pyopenms.TraMLProduct method) clearMSLevels() (pyopenms.PeakFileOptions method) clearPercentages() (pyopenms.Gradient method) clearRanges() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum 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) ClusteringGrid (class in pyopenms) ClusterProxyKD (class in pyopenms) CMD (pyopenms.LogType attribute) CNG (pyopenms.ScanMode attribute) CNL (pyopenms.ScanMode attribute) CoarseIsotopePatternGenerator (class in pyopenms) collectPrecursorCandidates() (pyopenms.OPXLHelper method) collectSetParameter() (pyopenms.QcMLFile method) collision-induced dissociation COLLISION_QUADRUPOLE (pyopenms.IonOpticsType attribute) cols() (pyopenms.MatrixDouble method) colTypes (pyopenms.Attachment attribute) ColumnHeader (class in pyopenms) CombinationsLogic (pyopenms.CVMappingRule attribute) combineTopRanksFromPairs() (pyopenms.OPXLHelper method) compatible() (pyopenms.MassDecomposition method) Compomer (class in pyopenms) component_group_name (pyopenms.MRMFP_ComponentGroupParams attribute) (pyopenms.MRMFP_ComponentParams attribute) (pyopenms.MRMFQC_ComponentGroupPairQCs attribute) (pyopenms.MRMFQC_ComponentGroupQCs attribute) component_group_pair_qcs (pyopenms.MRMFeatureQC attribute) component_group_qcs (pyopenms.MRMFeatureQC attribute) component_name (pyopenms.AQS_runConcentration attribute) (pyopenms.MRMFP_ComponentParams attribute) (pyopenms.MRMFQC_ComponentQCs attribute) component_qcs (pyopenms.MRMFeatureQC attribute) Compound (class in pyopenms) compound_name (pyopenms.LightCompound attribute) compounds (pyopenms.LightTargetedExperiment attribute) compress() (pyopenms.ConvexHull2D method) compressTrieDB() (pyopenms.InspectOutfile method) compute() (pyopenms.AScore method) (pyopenms.FeatureDeconvolution method) (pyopenms.HyperScore method) (pyopenms.ILPDCWrapper method) (pyopenms.MassExplainer method) (pyopenms.MetaboliteFeatureDeconvolution method) (pyopenms.MorpheusScore method) compute_F() (pyopenms.SpectraSTSimilarityScore method) computeApexSNR() (pyopenms.ElutionPeakDetection method) computeBinnedCoverage() (pyopenms.MRMRTNormalizer method) computeConsensus() (pyopenms.ConsensusFeature method) computeCorrelation() (pyopenms.ConsensusMapNormalizerAlgorithmThreshold method) computeCoverage() (pyopenms.ProteinIdentification method) computeDechargeConsensus() (pyopenms.ConsensusFeature method) computeDeltaScores() (pyopenms.OPXLHelper method) computeFileHash() (pyopenms.FileHandler method) computeFwhmArea() (pyopenms.Kernel_MassTrace method) computeFwhmAreaSmooth() (pyopenms.Kernel_MassTrace method) computeHyperScore() (pyopenms.MetaboliteSpectralMatching method) computeLogLikelihood() (pyopenms.PosteriorErrorProbabilityModel method) computeMassTraceNoise() (pyopenms.ElutionPeakDetection method) computeMassTraceSNR() (pyopenms.ElutionPeakDetection method) computeMedians() (pyopenms.ConsensusMapNormalizerAlgorithmMedian method) computeMonoisotopicConsensus() (pyopenms.ConsensusFeature method) computePeakArea() (pyopenms.Kernel_MassTrace method) computePrecursorError() (pyopenms.OPXLHelper method) computePrecursorId() (pyopenms.OpenSwathHelper method) computePrecursorPurity() (pyopenms.PrecursorPurity method) computeProbability() (pyopenms.PosteriorErrorProbabilityModel method) computePScore() (pyopenms.PScore method) computeSmoothedPeakArea() (pyopenms.Kernel_MassTrace method) computeTheoretical() (pyopenms.GaussTraceFitter method) CONCATENATED (pyopenms.IMFormat attribute) concatMULTISEPeptideIds() (pyopenms.PercolatorFeatureSetHelper method) concentration_units (pyopenms.AQS_featureConcentration attribute) (pyopenms.AQS_runConcentration attribute) ConfidenceScoring (class in pyopenms) Configuration (class in pyopenms) configure() (pyopenms.LogConfigHandler method) consensus feature consensus features consensus map consensus maps ConsensusFeature (class in pyopenms) ConsensusIDAlgorithm (class in pyopenms) ConsensusIDAlgorithmAverage (class in pyopenms) ConsensusIDAlgorithmBest (class in pyopenms) ConsensusIDAlgorithmIdentity (class in pyopenms) ConsensusIDAlgorithmPEPIons (class in pyopenms) ConsensusIDAlgorithmPEPMatrix (class in pyopenms) ConsensusIDAlgorithmRanks (class in pyopenms) ConsensusIDAlgorithmSimilarity (class in pyopenms) ConsensusIDAlgorithmWorst (class in pyopenms) ConsensusMap (class in pyopenms) ConsensusMapNormalizerAlgorithmMedian (class in pyopenms) ConsensusMapNormalizerAlgorithmQuantile (class in pyopenms) ConsensusMapNormalizerAlgorithmThreshold (class in pyopenms) CONSENSUSXML (pyopenms.FileType attribute) ConsensusXMLFile (class in pyopenms) constructTargetDecoyMassMapping() (pyopenms.MetaboTargetedTargetDecoy method) constructTransitionsList() (pyopenms.TargetedSpectraExtractor method) consumeChromatogram() (pyopenms.CachedSwathFileConsumer 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.Peptide method) (pyopenms.Precursor method) (pyopenms.Prediction method) (pyopenms.Protein method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TraMLProduct method) consumeSpectrum() (pyopenms.CachedSwathFileConsumer 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 attribute) (pyopenms.Prediction attribute) ContactPerson (class in pyopenms) contains() (pyopenms.EmpiricalFormula method) containsIMData() (pyopenms.MSSpectrum method) containsInvalidReferences() (pyopenms.TargetedExperiment method) containsMSLevel() (pyopenms.PeakFileOptions method) containsTag() (pyopenms.MassDecomposition method) ControlledVocabulary (class in pyopenms) convert() (pyopenms.MapConversion method) convertChromatogramsToSpectra() (pyopenms.ChromatogramTools method) convertPeptideToAASequence() (pyopenms.OpenSwathDataAccessHelper method) convertPQPToTargetedExperiment() (pyopenms.TransitionPQPFile method) convertSeedList() (pyopenms.SeedListGenerator method) convertSpectraToChromatograms() (pyopenms.ChromatogramTools method) convertTargetedCompound() (pyopenms.OpenSwathDataAccessHelper method) convertTargetedExp() (pyopenms.OpenSwathDataAccessHelper method) convertTargetedExperimentToPQP() (pyopenms.TransitionPQPFile method) convertTargetedExperimentToTSV() (pyopenms.TransitionPQPFile method) (pyopenms.TransitionTSVFile method) convertToChromatogramPtr() (pyopenms.OpenSwathDataAccessHelper method) convertToFeatureMap() (pyopenms.FIAMSDataProcessor method) convertToOpenMSChromatogram() (pyopenms.OpenSwathDataAccessHelper method) convertToOpenMSChromatogramFilter() (pyopenms.OpenSwathDataAccessHelper method) convertToOpenMSSpectrum() (pyopenms.OpenSwathDataAccessHelper method) convertToSpectrumPtr() (pyopenms.OpenSwathDataAccessHelper method) convertTSVToTargetedExperiment() (pyopenms.TransitionPQPFile method) (pyopenms.TransitionTSVFile method) ConvexHull2D (class in pyopenms) copy() (pyopenms.Param method) correctIsotopicImpurities() (pyopenms.IsobaricIsotopeCorrector method) correctToHighestIntensityMS1Peak() (pyopenms.PrecursorCorrection method) correctToNearestFeature() (pyopenms.PrecursorCorrection method) correctToNearestMS1Peak() (pyopenms.PrecursorCorrection method) countHits() (pyopenms.IDFilter method) countInternalCleavageSites() (pyopenms.EnzymaticDigestion method) (pyopenms.ProteaseDigestion method) (pyopenms.RNaseDigestion method) countTreatments() (pyopenms.Sample method) create() (pyopenms.VersionDetails method) createMemdumpIndex() (pyopenms.CachedMzMLHandler method) createMRMFeature() (pyopenms.MRMTransitionGroupPicker method) createPseudoSpectra() (pyopenms.MasstraceCorrelator method) createTables() (pyopenms.MzMLSqliteHandler method) CRM (pyopenms.ScanMode attribute) cross_link (pyopenms.CrossLinkSpectrumMatch attribute) cross_link_position (pyopenms.ProteinProteinCrossLink attribute) cross_linker_mass (pyopenms.ProteinProteinCrossLink attribute) cross_linker_name (pyopenms.ProteinProteinCrossLink attribute) CrossLinksDB (class in pyopenms) CrossLinkSpectrumMatch (class in pyopenms) CSV (pyopenms.FileType attribute) CsvFile (class in pyopenms) CubicSpline2d (class in pyopenms) CV (class in pyopenms) cv_ref (pyopenms.Unit attribute) cvAcc (pyopenms.Attachment attribute) (pyopenms.QualityParameter attribute) CVMappingFile (class in pyopenms) CVMappingRule (class in pyopenms) CVMappings (class in pyopenms) CVMappingTerm (class in pyopenms) cvRef (pyopenms.Attachment attribute) (pyopenms.QualityParameter attribute) CVReference (class in pyopenms) CVTerm (class in pyopenms) CVTerm_ControlledVocabulary (class in pyopenms) CVTermList (class in pyopenms) CVTermListInterface (class in pyopenms) D d (pyopenms.RANSACParam attribute) data (pyopenms.OSBinaryDataArray attribute) DataFilter (class in pyopenms) DataFilters (class in pyopenms) DataProcessing (class in pyopenms) DataType (class in pyopenms) DataValue (class in pyopenms) Date (class in pyopenms) DateTime (class in pyopenms) db (pyopenms.SearchParameters attribute) db_version (pyopenms.SearchParameters attribute) DBoundingBox2 (class in pyopenms) de novo peptide sequencing debug() (pyopenms.BSpline2d method) decode32() (pyopenms.Base64 method) decode64() (pyopenms.Base64 method) decodeIntegers() (pyopenms.Base64 method) decodeNP() (pyopenms.MSNumpressCoder method) decodeNPRaw() (pyopenms.MSNumpressCoder method) decodeStrings() (pyopenms.Base64 method) DECOY (pyopenms.DecoyTransitionType attribute) decoy (pyopenms.LightTransition attribute) DecoyGenerator (class in pyopenms) DecoyTransitionType (class in pyopenms) DEG_PER_RAD (in module pyopenms.Constants) deisotopeAndSingleCharge() (pyopenms.Deisotoper method) deisotopeAndSingleChargeDefault() (pyopenms.Deisotoper method) Deisotoper (class in pyopenms) deisotopeWithAveragineModel() (pyopenms.Deisotoper method) DELAYED_EXTRACTION (pyopenms.IonOpticsType attribute) deleteRow() (pyopenms.LPWrapper method) delta_D() (pyopenms.SpectraSTSimilarityScore method) delta_mass (pyopenms.MultiplexDeltaMasses_DeltaMass attribute) (pyopenms.MultiplexDeltaMassesGenerator_Label attribute) denominator_ref_ (pyopenms.Ratio attribute) derivative() (pyopenms.BSpline2d method) (pyopenms.LinearInterpolation method) derivatives() (pyopenms.CubicSpline2d method) DerivatizationAgent (pyopenms.XQuestResultXMLFile attribute) description (pyopenms.ChannelInfo attribute) (pyopenms.CVTerm_ControlledVocabulary attribute) (pyopenms.FASTAEntry attribute) (pyopenms.IsobaricChannelInformation attribute) (pyopenms.MultiplexDeltaMassesGenerator_Label attribute) (pyopenms.OSBinaryDataArray attribute) (pyopenms.ParamEntry attribute) (pyopenms.ParamNode attribute) (pyopenms.TraceInfo attribute) description_ (pyopenms.Ratio attribute) descriptions() (pyopenms.Param method) detecting_transition (pyopenms.LightTransition attribute) detectingTransitions() (pyopenms.MRMAssay method) detectPeaks() (pyopenms.ElutionPeakDetection method) determineIMFormat() (pyopenms.IMTypes method) 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) DIAScoring (class in pyopenms) digest() (pyopenms.ProteaseDigestion method) (pyopenms.RNaseDigestion method) digestDatabase() (pyopenms.OPXLHelper method) Digestion (class in pyopenms) digestion_enzyme (pyopenms.SearchParameters attribute) DigestionEnzyme (class in pyopenms) DigestionEnzymeProtein (class in pyopenms) DigestionEnzymeRNA (class in pyopenms) DigestionFilter (pyopenms.IDFilter attribute) digestUnmodified() (pyopenms.EnzymaticDigestion method) (pyopenms.ProteaseDigestion method) (pyopenms.RNaseDigestion method) dilution_factor (pyopenms.AQS_featureConcentration attribute) (pyopenms.AQS_runConcentration attribute) DIMENSION (pyopenms.DimensionDescription attribute) DimensionDescription (class in pyopenms) dimensionsize() (pyopenms.DistanceMatrix method) Disjoint (pyopenms.DRangeIntersection attribute) DistanceMatrix (class in pyopenms) divideByGCD() (pyopenms.IMSWeights method) DocumentIdentifier (class in pyopenms) domParseChromatogram() (pyopenms.MzMLSpectrumDecoder method) domParseSpectrum() (pyopenms.MzMLSpectrumDecoder method) dot_bias() (pyopenms.SpectraSTSimilarityScore method) dotprod_score_dia (pyopenms.OpenSwath_Scores attribute) DOUBLE (pyopenms.QuotingMethod attribute) DOUBLE_LIST (pyopenms.DataType attribute) (pyopenms.ValueType attribute) DOUBLE_VALUE (pyopenms.DataType attribute) (pyopenms.ValueType attribute) DPosition1 (class in pyopenms) DPosition2 (class in pyopenms) DRange1 (class in pyopenms) DRange2 (class in pyopenms) DRangeIntersection (class in pyopenms) drift_time (pyopenms.LightCompound attribute) DriftTimeUnit (class in pyopenms) DTA (pyopenms.FileType attribute) DTA2D (pyopenms.FileType attribute) DTA2DFile (class in pyopenms) DTAFile (class in pyopenms) E E (in module pyopenms.Constants) ECD (pyopenms.ActivationMethod attribute) EDTA (pyopenms.FileType attribute) EDTAFile (class in pyopenms) EIGHTPLEX (pyopenms.ITRAQ_TYPES attribute) EINZEL_LENS (pyopenms.IonOpticsType attribute) ELECTRON_MASS (in module pyopenms.Constants) ELECTRON_MASS_U (in module pyopenms.Constants) electrospray ionization Element (class in pyopenms) ELEMENTARY_CHARGE (in module pyopenms.Constants) ElementDB (class in pyopenms) elution_model_fit_score (pyopenms.OpenSwath_Scores attribute) elutionModelFit() (pyopenms.EmgScoring method) ElutionModelFitter (class in pyopenms) ElutionPeakDetection (class in pyopenms) EMC (pyopenms.ScanMode attribute) EmgFitter1D (class in pyopenms) EmgGradientDescent (class in pyopenms) EmgModel (class in pyopenms) EmgScoring (class in pyopenms) EMISSION (pyopenms.ScanMode 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.File method) (pyopenms.IMSIsotopeDistribution method) (pyopenms.IncludeExcludeTarget method) (pyopenms.LinearInterpolation method) (pyopenms.MetaInfo method) (pyopenms.MSExperiment method) (pyopenms.NASequence method) (pyopenms.Param method) (pyopenms.Peptide method) (pyopenms.PeptideIdentification method) (pyopenms.Precursor method) (pyopenms.Prediction method) (pyopenms.Protein method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.SpectrumLookup method) (pyopenms.SpectrumMetaDataLookup method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TraMLProduct method) EMPTY_VALUE (pyopenms.DataType attribute) (pyopenms.ValueType attribute) EMR (pyopenms.ScanMode attribute) enable_binarization (pyopenms.SolverParam attribute) enable_clq_cuts (pyopenms.SolverParam attribute) enable_cov_cuts (pyopenms.SolverParam attribute) enable_feas_pump_heuristic (pyopenms.SolverParam attribute) enable_gmi_cuts (pyopenms.SolverParam attribute) enable_mir_cuts (pyopenms.SolverParam attribute) enable_presolve (pyopenms.SolverParam attribute) encloses() (pyopenms.ConvexHull2D method) (pyopenms.DRange1 method) (pyopenms.Feature method) (pyopenms.MRMFeature method) enclosesXY() (pyopenms.ConvexHull2D method) encode32() (pyopenms.Base64 method) encode64() (pyopenms.Base64 method) encodeIntegers() (pyopenms.Base64 method) encodeNP() (pyopenms.MSNumpressCoder method) encodeNPRaw() (pyopenms.MSNumpressCoder method) encodeStrings() (pyopenms.Base64 method) end (pyopenms.ScanWindow attribute) end_position_at_10 (pyopenms.PI_PeakShapeMetrics attribute) end_position_at_5 (pyopenms.PI_PeakShapeMetrics attribute) end_position_at_50 (pyopenms.PI_PeakShapeMetrics attribute) endProgress() (pyopenms.AccurateMassSearchEngine method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.CachedMzMLHandler method) (pyopenms.ChromatogramExtractor method) (pyopenms.ChromatogramExtractorAlgorithm method) (pyopenms.DTA2DFile method) (pyopenms.ElutionPeakDetection method) (pyopenms.FeatureFindingMetabo method) (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.GaussFilter method) (pyopenms.InternalCalibration method) (pyopenms.LabeledPairFinder method) (pyopenms.LinearResampler method) (pyopenms.LinearResamplerAlign method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) (pyopenms.MascotGenericFile method) (pyopenms.MascotInfile method) (pyopenms.MasstraceCorrelator method) (pyopenms.MassTraceDetection method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.MorphologicalFilter method) (pyopenms.MRMAssay method) (pyopenms.MRMDecoy method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MS2File method) (pyopenms.MzDataFile method) (pyopenms.MzIdentMLFile method) (pyopenms.MzMLFile method) (pyopenms.MzXMLFile method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) (pyopenms.ProgressLogger method) (pyopenms.QcMLFile method) (pyopenms.QTClusterFinder method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.StablePairFinder method) (pyopenms.SwathFile 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) entries (pyopenms.ParamNode attribute) enumerateCrossLinksAndMasses() (pyopenms.OPXLHelper method) enumToName() (pyopenms.MZTrafoModel method) EnzymaticDigestion (class in pyopenms) EPSILON (in module pyopenms.Constants) erase() (pyopenms.IMSAlphabet method) err (pyopenms.MorpheusScore_Result attribute) error() (pyopenms.QcMLFile method) (pyopenms.XMLHandler method) ErrorUnit (pyopenms.XTandemInfile attribute) ESCAPE (pyopenms.QuotingMethod attribute) ESI estimate_fixed_point (pyopenms.NumpressConfig attribute) estimateBackground() (pyopenms.PeakIntegrator 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.Kernel_MassTrace method) estimateNoise() (pyopenms.SignalToNoiseEstimatorMedianRapid method) estimateRTRange() (pyopenms.OpenSwathHelper method) estimateType() (pyopenms.PeakTypeEstimator method) ETD (pyopenms.ActivationMethod attribute) eval() (pyopenms.BSpline2d method) (pyopenms.CubicSpline2d method) (pyopenms.GaussFitResult method) (pyopenms.SplinePackage method) (pyopenms.SplineSpectrum_Navigator method) evaluate() (pyopenms.TransformationModelBSpline method) (pyopenms.TransformationModelInterpolated method) (pyopenms.TransformationModelLinear method) (pyopenms.TransformationModelLowess method) evidence (pyopenms.Peptide attribute) exists() (pyopenms.ControlledVocabulary method) (pyopenms.File method) (pyopenms.MetaInfo method) (pyopenms.Param method) existsRun() (pyopenms.QcMLFile method) existsRunQualityParameter() (pyopenms.QcMLFile method) existsSet() (pyopenms.QcMLFile method) existsSetQualityParameter() (pyopenms.QcMLFile method) expandToBoundingBox() (pyopenms.ConvexHull2D method) ExperimentalDesign (class in pyopenms) ExperimentalDesign_MSFileSectionEntry (class in pyopenms) ExperimentalDesign_SampleSection (class in pyopenms) ExperimentalDesignFile (class in pyopenms) ExperimentalSettings (class in pyopenms) exportAttachment() (pyopenms.QcMLFile method) exportFeatureMapToMzTabM() (pyopenms.MzTabM method) exportIDstats() (pyopenms.QcMLFile method) exportQP() (pyopenms.QcMLFile method) exportQPs() (pyopenms.QcMLFile method) extra_rt_extract (pyopenms.OSW_ChromExtractParams attribute) extract_columnname_to_columnindex() (pyopenms.SiriusFragmentAnnotation method) extractAndResolveSiriusAnnotations() (pyopenms.SiriusFragmentAnnotation method) extractAnnotationsFromSiriusFile() (pyopenms.SiriusFragmentAnnotation method) extractChannels() (pyopenms.IsobaricChannelExtractor method) extractChromatograms() (pyopenms.ChromatogramExtractor method) (pyopenms.ChromatogramExtractorAlgorithm method) extractIntensityVectors() (pyopenms.ConsensusMapNormalizerAlgorithmQuantile method) extraction_function (pyopenms.OSW_ChromExtractParams attribute) ExtractionCoordinates (class in pyopenms) extractMetaboTargetedAssay() (pyopenms.MetaboTargetedAssay method) extractMetaboTargetedAssayFragmentAnnotation() (pyopenms.MetaboTargetedAssay method) extractPeaks() (pyopenms.FIAMSDataProcessor method) extractPeptideSequences() (pyopenms.IDFilter method) extractProteinAccessionsSet() (pyopenms.PeptideHit method) extractScanNumber() (pyopenms.SpectrumLookup method) (pyopenms.SpectrumMetaDataLookup method) extractSpectra() (pyopenms.TargetedSpectraExtractor method) F FAIMS_COMPENSATION_VOLTAGE (pyopenms.DriftTimeUnit attribute) FalseDiscoveryRate (class in pyopenms) FARADAY (in module pyopenms.Constants) FASTA (pyopenms.FileType attribute) FASTAEntry (class in pyopenms) FASTAFile (class in pyopenms) feature Feature (class in pyopenms) feature (pyopenms.AQS_featureConcentration attribute) feature map feature maps FEATURE_ID_MULTIPLE_DIVERGENT (pyopenms.AnnotationState attribute) FEATURE_ID_MULTIPLE_SAME (pyopenms.AnnotationState attribute) FEATURE_ID_NONE (pyopenms.AnnotationState attribute) FEATURE_ID_SINGLE (pyopenms.AnnotationState attribute) FeatureDeconvolution (class in pyopenms) FeatureDistance (class in pyopenms) FeatureFileOptions (class in pyopenms) FeatureFinderAlgorithmMetaboIdent (class in pyopenms) FeatureFinderAlgorithmPicked (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) FeatureMapping (class in pyopenms) FeatureMapping_FeatureMappingInfo (class in pyopenms) FeatureMapping_FeatureToMs2Indices (class in pyopenms) features FEATUREXML (pyopenms.FileType attribute) FeatureXMLFile (class in pyopenms) FIAMSDataProcessor (class in pyopenms) FIAMSScheduler (class in pyopenms) field (pyopenms.DataFilter attribute) File (class in pyopenms) FILE_ORIGIN (pyopenms.OriginAnnotationFormat attribute) FileHandler (class in pyopenms) fileList() (pyopenms.File method) filename (pyopenms.ColumnHeader attribute) FileType (class in pyopenms) FileTypes (class in pyopenms) fillCalibrants() (pyopenms.InternalCalibration method) fillDensities() (pyopenms.PosteriorErrorProbabilityModel method) fillLogDensities() (pyopenms.PosteriorErrorProbabilityModel method) filter() (pyopenms.GaussFilter method) (pyopenms.MorphologicalFilter method) (pyopenms.SavitzkyGolayFilter method) filterByPeakWidth() (pyopenms.ElutionPeakDetection method) filterExperiment() (pyopenms.GaussFilter method) (pyopenms.MorphologicalFilter method) (pyopenms.SavitzkyGolayFilter method) FilterFeatureMap() (pyopenms.MRMFeatureFilter method) filterHitsByRank() (pyopenms.IDFilter method) filterHitsByScore() (pyopenms.IDFilter method) filterMinMaxTransitionsCompound() (pyopenms.MRMAssay method) FilterOperation (pyopenms.DataFilters attribute) 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 method) filterPeptidesByLength() (pyopenms.IDFilter method) filterPeptidesByMZ() (pyopenms.IDFilter method) filterPeptidesByMZError() (pyopenms.IDFilter method) filterPeptidesByRT() (pyopenms.IDFilter method) filterPeptidesByRTPredictPValue() (pyopenms.IDFilter method) filterSpectrum() (pyopenms.NLargest method) (pyopenms.Normalizer method) (pyopenms.RankScaler method) (pyopenms.SqrtScaler method) (pyopenms.ThresholdMower method) FilterType (pyopenms.DataFilters attribute) filterUnreferencedDecoysCompound() (pyopenms.MRMAssay method) finalizeCluster() (pyopenms.QTCluster method) find() (pyopenms.File 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 method) findDoc() (pyopenms.File method) findEntryRecursive() (pyopenms.ParamNode method) findExecutable() (pyopenms.File method) findFixedResidues() (pyopenms.MRMDecoy method) findHighestInWindow() (pyopenms.MSSpectrum method) findIndexListOffset() (pyopenms.IndexedMzMLDecoder method) findLargestPeak() (pyopenms.MRMTransitionGroupPicker method) findLocalExtrema() (pyopenms.ElutionPeakDetection method) findMaxByIntPeak() (pyopenms.Kernel_MassTrace method) findModificationIndex() (pyopenms.CrossLinksDB method) (pyopenms.ModificationsDB method) findNearest() (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) (pyopenms.MZTrafoModel method) findParentOf() (pyopenms.ParamNode method) findWidestPeakIndices() (pyopenms.MRMTransitionGroupPicker method) FINE_STRUCTURE_CONSTANT (in module pyopenms.Constants) FineIsotopePatternGenerator (class in pyopenms) first (pyopenms.ProbablePhosphoSites attribute) (pyopenms.TM_DataPoint attribute) FIRST_STABILITY_REGION (pyopenms.IonOpticsType attribute) fit() (pyopenms.GaussFitter method) (pyopenms.GaussTraceFitter method) (pyopenms.PosteriorErrorProbabilityModel method) fitCalibration() (pyopenms.AbsoluteQuantitation method) fitElutionModels() (pyopenms.ElutionModelFitter method) fitEMGPeakModel() (pyopenms.EmgGradientDescent method) fitLOWESS() (pyopenms.MapAlignmentAlgorithmKD method) fitModel() (pyopenms.TransformationDescription method) Fitter1D (class in pyopenms) FIVE_PRIME (pyopenms.TermSpecificityNuc attribute) fixed_modifications (pyopenms.SearchParameters attribute) flag (pyopenms.QualityParameter attribute) FloatDataArray (class in pyopenms) flush() (pyopenms.MSDataSqlConsumer method) FOURPLEX (pyopenms.ITRAQ_TYPES attribute) fraction (pyopenms.ExperimentalDesign_MSFileSectionEntry attribute) fraction_group (pyopenms.ExperimentalDesign_MSFileSectionEntry attribute) frag_annotations (pyopenms.CrossLinkSpectrumMatch attribute) FRAGMENT_ANNOTATION_USERPARAM (in module pyopenms.Constants) fragment_charge (pyopenms.LightTransition attribute) fragment_mass_tolerance (pyopenms.SearchParameters attribute) fragment_mass_tolerance_ppm (pyopenms.SearchParameters attribute) free_mem() (in module pyopenms) freehigh (pyopenms.SysInfo attribute) freeram (pyopenms.SysInfo attribute) freeswap (pyopenms.SysInfo attribute) FRINGING_FIELD (pyopenms.IonOpticsType attribute) fromConsensusMap() (pyopenms.ExperimentalDesign method) fromFeatureMap() (pyopenms.ExperimentalDesign method) fromIdentifications() (pyopenms.ExperimentalDesign method) fromString() (pyopenms.AASequence method) (pyopenms.DataFilter method) (pyopenms.NASequence method) fromStringPermissive() (pyopenms.AASequence method) fullname (pyopenms.CV attribute) fwhm_mz_avg (pyopenms.Kernel_MassTrace attribute) G GAS_CONSTANT (in module pyopenms.Constants) GaussFilter (class in pyopenms) GaussFitResult (class in pyopenms) GaussFitter (class in pyopenms) GaussTraceFitter (class in pyopenms) GELML (pyopenms.FileType attribute) generateDecoys() (pyopenms.MRMDecoy method) generateKnockoutDeltaMasses() (pyopenms.MultiplexDeltaMassesGenerator method) generateMissingDecoysByMassShift() (pyopenms.MetaboTargetedTargetDecoy method) generateSeedList() (pyopenms.SeedListGenerator method) generateTrieDB() (pyopenms.InspectOutfile method) get() (pyopenms.Date method) (pyopenms.DateTime method) (pyopenms.NASequence method) (pyopenms.Param method) get2DPeakDataLong() (pyopenms.MSExperiment method) get2DPeakDataLongIon() (pyopenms.MSExperiment method) get_assigned_peptide_identifications() (pyopenms.FeatureMap method) get_chromatogram_df() (pyopenms.MRMTransitionGroupCP method) get_data() (pyopenms.FloatDataArray method) (pyopenms.IntegerDataArray method) get_df() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) get_feature_df() (pyopenms.MRMTransitionGroupCP method) get_intensity_df() (pyopenms.ConsensusMap method) get_ion_df() (pyopenms.MSExperiment method) get_massql_df() (pyopenms.MSExperiment method) get_matrix() (pyopenms.MatrixDouble method) get_matrix_as_view() (pyopenms.MatrixDouble method) get_metadata_df() (pyopenms.ConsensusMap method) get_noise_even() (pyopenms.NoiseEstimator method) get_noise_odd() (pyopenms.NoiseEstimator method) get_noise_value() (pyopenms.NoiseEstimator method) get_peaks() (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) get_quick_lda_score() (pyopenms.OpenSwath_Scores method) getAAAfter() (pyopenms.PeptideEvidence method) getAABefore() (pyopenms.PeptideEvidence method) getAAFrequencies() (pyopenms.AASequence 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.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) getADCSamplingFrequency() (pyopenms.IonDetector method) getAddress() (pyopenms.ContactPerson method) getAdductBase() (pyopenms.MassExplainer method) getAdductsAsString() (pyopenms.Compomer method) getAffectedAminoAcids() (pyopenms.Modification method) getAllChildTerms() (pyopenms.ControlledVocabulary method) getAllCometNames() (pyopenms.ProteaseDB method) getAllMSGFNames() (pyopenms.ProteaseDB method) getAllNames() (pyopenms.ProteaseDB method) (pyopenms.RNaseDB method) getAllOMSSANames() (pyopenms.ProteaseDB method) getAllowChildren() (pyopenms.CVMappingTerm method) getAllSearchModifications() (pyopenms.CrossLinksDB method) (pyopenms.ModificationsDB method) getAllXTandemNames() (pyopenms.ProteaseDB method) getAlphabetMass() (pyopenms.IMSWeights method) getAmount() (pyopenms.Adduct method) getAnalysisResults() (pyopenms.PeptideHit method) getAnnotations() (pyopenms.QTCluster method) getAnnotationState() (pyopenms.BaseFeature method) (pyopenms.ConsensusFeature method) (pyopenms.Feature method) (pyopenms.MRMFeature method) getArchAsString() (pyopenms.OpenMSOSInfo method) getArea() (pyopenms.GaussTraceFitter method) getARGP820102() (pyopenms.AAIndex method) getAtomicNumber() (pyopenms.Element method) getAverageMass() (pyopenms.IMSElement method) (pyopenms.IMSIsotopeDistribution method) (pyopenms.ResidueModification method) getAverageMasses() (pyopenms.IMSAlphabet method) getAverageMS1CycleTime() (pyopenms.Kernel_MassTrace method) getAverageWeight() (pyopenms.AASequence method) (pyopenms.Element method) (pyopenms.EmpiricalFormula method) (pyopenms.NASequence method) (pyopenms.Residue method) getAvgDistance() (pyopenms.ClusterProxyKD method) getAvgMass() (pyopenms.Ribonucleotide method) getAvgMZ() (pyopenms.MassTrace method) getBackboneBasicityLeft() (pyopenms.Residue method) getBackboneBasicityRight() (pyopenms.Residue method) getBaseDir() (pyopenms.FIAMSScheduler method) getBaselossFormula() (pyopenms.Ribonucleotide method) getBaseName() (pyopenms.PeptideIdentification method) getBestFeature() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) getBestHit() (pyopenms.IDFilter method) getBestModificationByDiffMonoMass() (pyopenms.CrossLinksDB method) (pyopenms.ModificationsDB method) getBinaryArchitecture() (pyopenms.OpenMSOSInfo method) getBinIndex() (pyopenms.BinnedSpectrum method) getBinIntensity() (pyopenms.BinnedSpectrum method) getBinLowerMZ() (pyopenms.BinnedSpectrum method) getBinSize() (pyopenms.BinnedSpectrum method) getBinSpread() (pyopenms.BinnedSpectrum method) getBlind() (pyopenms.InspectInfile method) getBothGnuplotFormula() (pyopenms.PosteriorErrorProbabilityModel method) getBoundary() (pyopenms.MascotInfile method) getBoundingBox() (pyopenms.ConvexHull2D method) (pyopenms.GridBasedCluster method) getBoundingBox2D() (pyopenms.ConvexHull2D method) getBranch() (pyopenms.VersionInfo method) getBuildType() (pyopenms.OpenMSBuildInfo 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) getCentroidMZ() (pyopenms.Kernel_MassTrace method) getCentroidRT() (pyopenms.Kernel_MassTrace method) getCentroidSD() (pyopenms.Kernel_MassTrace method) getChannelInformation() (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.PeptideHit method) (pyopenms.Precursor method) getCharges() (pyopenms.FeatureFinderMetaboIdentCompound method) (pyopenms.MascotInfile 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) getChromatogramById() (pyopenms.IndexedMzMLHandler method) (pyopenms.OnDiscMSExperiment method) (pyopenms.SpectrumAccessOpenMS method) (pyopenms.SpectrumAccessOpenMSCached method) (pyopenms.SpectrumAccessOpenMSInMemory method) (pyopenms.SpectrumAccessQuadMZTransforming method) (pyopenms.SpectrumAccessSqMass method) (pyopenms.SpectrumAccessTransforming method) getChromatogramByNativeId() (pyopenms.OnDiscMSExperiment method) getChromatogramIndex() (pyopenms.CachedMzMLHandler method) getChromatogramNativeID() (pyopenms.SpectrumAccessOpenMS method) (pyopenms.SpectrumAccessOpenMSCached method) (pyopenms.SpectrumAccessOpenMSInMemory method) (pyopenms.SpectrumAccessQuadMZTransforming method) (pyopenms.SpectrumAccessSqMass method) (pyopenms.SpectrumAccessTransforming method) getChromatograms() (pyopenms.FeatureFinderAlgorithmMetaboIdent method) (pyopenms.FeatureFinderIdentificationAlgorithm method) (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.MSExperiment method) getChromatogramType() (pyopenms.ChromatogramSettings method) (pyopenms.MSChromatogram method) getCleavage() (pyopenms.MascotInfile method) getCleavageSite() (pyopenms.XTandemInfile method) getCode() (pyopenms.Ribonucleotide method) getCoefficients() (pyopenms.MZTrafoModel method) getColumn() (pyopenms.HPLC method) getColumnHeaders() (pyopenms.ConsensusMap method) getColumnIndex() (pyopenms.LPWrapper method) getColumnLowerBound() (pyopenms.LPWrapper method) getColumnName() (pyopenms.LPWrapper method) getColumns() (pyopenms.SequestOutfile method) getColumnType() (pyopenms.LPWrapper method) getColumnUpperBound() (pyopenms.LPWrapper method) getColumnValue() (pyopenms.LPWrapper method) getCombinationsLogic() (pyopenms.CVMappingRule method) getCometID() (pyopenms.DigestionEnzymeProtein method) getComment() (pyopenms.ChromatogramSettings method) (pyopenms.ExperimentalSettings method) (pyopenms.HPLC method) (pyopenms.Modification method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.Sample method) (pyopenms.SpectrumSettings method) getCommonName() (pyopenms.SpectralMatch 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) getContactInfo() (pyopenms.ContactPerson method) getContacts() (pyopenms.ExperimentalSettings method) (pyopenms.MSExperiment method) (pyopenms.TargetedExperiment method) getContainer() (pyopenms.IsotopeDistribution method) getConvexHull() (pyopenms.Feature method) getConvexhull() (pyopenms.Kernel_MassTrace method) (pyopenms.MassTrace method) getConvexHull() (pyopenms.MRMFeature method) getConvexHulls() (pyopenms.Feature method) (pyopenms.MRMFeature method) getCorrectlyAssignedFitResult() (pyopenms.PosteriorErrorProbabilityModel method) getCorrelationCoefficient() (pyopenms.AbsoluteQuantitationMethod method) getCoverage() (pyopenms.ProteinHit method) getCTermGain() (pyopenms.DigestionEnzymeProtein method) getCTerminalModification() (pyopenms.AASequence method) getCTerminalModificationName() (pyopenms.AASequence method) getCustomizations() (pyopenms.Instrument method) getCutsAfterRegEx() (pyopenms.DigestionEnzymeRNA method) getCutsBeforeRegEx() (pyopenms.DigestionEnzymeRNA method) getCVIdentifierRef() (pyopenms.CVMappingTerm method) (pyopenms.CVTerm 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.Protein method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation 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) getDateTime() (pyopenms.ExperimentalSettings method) (pyopenms.MSExperiment method) (pyopenms.ProteinIdentification method) getDb() (pyopenms.InspectInfile method) getDB() (pyopenms.MascotInfile method) getDecompositions() (pyopenms.MassDecompositionAlgorithm method) getDecoyString() (pyopenms.PeptideIndexing method) getDecoyTransitionType() (pyopenms.ReactionMonitoringTransition method) getDefaultParameters() (pyopenms.EmgGradientDescent method) (pyopenms.MSPGenericFile method) (pyopenms.PeakIntegrator method) (pyopenms.TargetedSpectraExtractor method) (pyopenms.TransformationModelBSpline method) (pyopenms.TransformationModelInterpolated method) (pyopenms.TransformationModelLinear method) (pyopenms.TransformationModelLowess method) getDefaultParametersFilename() (pyopenms.XTandemInfile method) getDefaults() (pyopenms.AbsoluteQuantitation method) (pyopenms.AccurateMassSearchEngine method) (pyopenms.AScore method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.ConsensusIDAlgorithm method) (pyopenms.ConsensusIDAlgorithmAverage method) (pyopenms.ConsensusIDAlgorithmBest method) (pyopenms.ConsensusIDAlgorithmIdentity method) (pyopenms.ConsensusIDAlgorithmPEPIons method) (pyopenms.ConsensusIDAlgorithmPEPMatrix method) (pyopenms.ConsensusIDAlgorithmRanks method) (pyopenms.ConsensusIDAlgorithmSimilarity method) (pyopenms.ConsensusIDAlgorithmWorst method) (pyopenms.DIAScoring method) (pyopenms.ElutionModelFitter method) (pyopenms.ElutionPeakDetection 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.GaussFilter method) (pyopenms.GNPSMGFFile method) (pyopenms.IDDecoyProbability method) (pyopenms.IDMapper method) (pyopenms.IDRipper method) (pyopenms.IsobaricChannelExtractor method) (pyopenms.IsobaricQuantifier method) (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.KDTreeFeatureMaps method) (pyopenms.LabeledPairFinder method) (pyopenms.LinearResampler 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.MorphologicalFilter method) (pyopenms.MRMFeatureFilter method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MRMMapping method) (pyopenms.MRMTransitionGroupPicker method) (pyopenms.MSPGenericFile method) (pyopenms.MultiplexDeltaMassesGenerator method) (pyopenms.NLargest method) (pyopenms.Normalizer method) (pyopenms.NucleicAcidSpectrumGenerator method) (pyopenms.OpenPepXLAlgorithm method) (pyopenms.OpenPepXLLFAlgorithm method) (pyopenms.PeakIntegrator method) (pyopenms.PeakPickerChromatogram method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) (pyopenms.PeptideAndProteinQuant method) (pyopenms.PeptideIndexing method) (pyopenms.PosteriorErrorProbabilityModel method) (pyopenms.QTClusterFinder method) (pyopenms.RankScaler method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.SimpleTSGXLMS method) (pyopenms.SiriusExportAlgorithm method) (pyopenms.SpectraMerger method) (pyopenms.SpectrumAlignment method) (pyopenms.SpectrumAlignmentScore method) (pyopenms.SpectrumAnnotator method) (pyopenms.SqrtScaler method) (pyopenms.StablePairFinder 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.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) getDigestionTime() (pyopenms.Digestion method) getDriftTime() (pyopenms.LightCompound method) (pyopenms.MSSpectrum method) (pyopenms.Precursor method) getDriftTimeUnit() (pyopenms.MSSpectrum method) getDriftTimeUnitAsString() (pyopenms.MSSpectrum method) getDriftTimeWindowLowerOffset() (pyopenms.Precursor method) getDriftTimeWindowUpperOffset() (pyopenms.Precursor method) getEdgeScore() (pyopenms.ChargePair method) getElement() (pyopenms.ElementDB method) (pyopenms.IMSAlphabet method) (pyopenms.LPWrapper method) getElementalComposition() (pyopenms.EmpiricalFormula method) getElementIndex() (pyopenms.ChargePair method) getElementPath() (pyopenms.CVMappingRule method) getEluents() (pyopenms.Gradient method) getEmail() (pyopenms.ContactPerson method) getEnd() (pyopenms.PeptideEvidence method) getEntry() (pyopenms.Param method) getEnzyme() (pyopenms.Digestion method) (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 method) getExperiment() (pyopenms.InspectOutfile method) getExperimentalSettings() (pyopenms.MSExperiment method) (pyopenms.OnDiscMSExperiment method) getExperimentLabel() (pyopenms.PeptideIdentification method) getExperimentType() (pyopenms.ConsensusMap method) getFactors() (pyopenms.ExperimentalDesign_SampleSection method) getFactorValue() (pyopenms.ExperimentalDesign_SampleSection method) getFAUJ880111() (pyopenms.AAIndex method) getFeature() (pyopenms.MRMFeature method) (pyopenms.PeakIndex method) getFeatureIDs() (pyopenms.MRMFeature method) getFeatureList() (pyopenms.ConsensusFeature method) getFeatureMap() (pyopenms.FeatureFinderMultiplexAlgorithm method) getFeatureName() (pyopenms.AbsoluteQuantitationMethod method) getFeatures() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMFeature method) (pyopenms.MRMTransitionGroupCP method) getFeaturesMuteable() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) getFileOriginIdx() (pyopenms.RipFileIdentifier method) getFileSize() (pyopenms.SourceFile method) getFileType() (pyopenms.SourceFile method) getFillData() (pyopenms.PeakFileOptions method) getFilterByNumMassTraces() (pyopenms.SiriusExportAlgorithm method) getFINA770101() (pyopenms.AAIndex method) getFinalMSExponent() (pyopenms.MassAnalyzer method) getFirstName() (pyopenms.ContactPerson method) getFivePrimeGain() (pyopenms.DigestionEnzymeRNA method) getFivePrimeMod() (pyopenms.NASequence method) getFixedModificationNames() (pyopenms.ModificationDefinitionsSet method) getFixedModifications() (pyopenms.ModificationDefinitionsSet method) getFloatDataArrays() (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) getFormVersion() (pyopenms.MascotInfile method) getFoundAdduct() (pyopenms.AccurateMassSearchResult 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) getFullId() (pyopenms.ResidueModification method) getFullName() (pyopenms.ResidueModification method) getFWHM() (pyopenms.GaussTraceFitter method) (pyopenms.Kernel_MassTrace method) getFWHMborders() (pyopenms.Kernel_MassTrace method) getGaussGnuplotFormula() (pyopenms.PosteriorErrorProbabilityModel 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) getHeight() (pyopenms.GaussTraceFitter method) getHistogramRightmostPercent() (pyopenms.SignalToNoiseEstimatorMedian method) getHits() (pyopenms.MascotInfile method) (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) getID() (pyopenms.Compomer 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) getInchiString() (pyopenms.SpectralMatch method) getIncludeTargets() (pyopenms.TargetedExperiment method) getIncorrectlyAssignedFitResult() (pyopenms.PosteriorErrorProbabilityModel method) getIndex() (pyopenms.ClusteringGrid method) (pyopenms.KDTreeFeatureNode method) (pyopenms.MetaInfoRegistry 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) getInstitution() (pyopenms.ContactPerson method) getInstrument() (pyopenms.ExperimentalSettings method) (pyopenms.HPLC method) (pyopenms.InspectInfile method) (pyopenms.MascotInfile method) (pyopenms.MSExperiment method) getInstruments() (pyopenms.TargetedExperiment method) getInstrumentSettings() (pyopenms.ChromatogramSettings method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) (pyopenms.SpectrumSettings method) getIntegerDataArrays() (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) getIntensity() (pyopenms.BaseFeature method) (pyopenms.CalibrationData method) (pyopenms.ChromatogramPeak method) (pyopenms.ConsensusFeature method) (pyopenms.EmgModel method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.InterpolationModel method) (pyopenms.Kernel_MassTrace method) (pyopenms.MRMFeature method) (pyopenms.Peak1D method) (pyopenms.Peak2D method) (pyopenms.Precursor method) (pyopenms.RichPeak2D method) getIntensity32Bit() (pyopenms.PeakFileOptions method) getIntensityArray() (pyopenms.OSChromatogram method) (pyopenms.OSSpectrum method) getIntensityRange() (pyopenms.FeatureFileOptions method) (pyopenms.PeakFileOptions method) getIntermediateProducts() (pyopenms.ReactionMonitoringTransition method) getInternalToAIon() (pyopenms.Residue method) getInternalToBIon() (pyopenms.Residue method) getInternalToCIon() (pyopenms.Residue method) getInternalToCTerm() (pyopenms.Residue method) getInternalToFull() (pyopenms.Residue method) getInternalToNTerm() (pyopenms.Residue method) getInternalToXIon() (pyopenms.Residue method) getInternalToYIon() (pyopenms.Residue method) getInternalToZIon() (pyopenms.Residue method) getInterpolation() (pyopenms.EmgModel method) (pyopenms.InterpolationModel 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) 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) getIsotopeCorrectionMatrix() (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.TMTEighteenPlexQuantitationMethod method) (pyopenms.TMTElevenPlexQuantitationMethod method) (pyopenms.TMTSixPlexQuantitationMethod method) (pyopenms.TMTSixteenPlexQuantitationMethod method) (pyopenms.TMTTenPlexQuantitationMethod method) getIsotopeDistribution() (pyopenms.Element method) (pyopenms.EmpiricalFormula method) (pyopenms.FeatureFinderMetaboIdentCompound method) (pyopenms.IMSElement method) (pyopenms.IsotopeModel method) getIsotopeMatrixAsStringList() (pyopenms.ItraqConstants 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.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.Modification 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.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.SpectrumSettings method) (pyopenms.StringDataArray method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TraMLProduct method) getKeysAsIntegers() (pyopenms.MetaInfo method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) getKHAG800101() (pyopenms.AAIndex method) getLabel() (pyopenms.Adduct method) (pyopenms.Kernel_MassTrace method) getLabelLong() (pyopenms.MultiplexDeltaMassesGenerator method) getLabels() (pyopenms.Compomer method) (pyopenms.InspectOutfile method) getLabelShort() (pyopenms.MultiplexDeltaMassesGenerator method) getLastName() (pyopenms.ContactPerson method) getLibrary() (pyopenms.FeatureFinderAlgorithmMetaboIdent method) (pyopenms.FeatureFinderIdentificationAlgorithm method) getLibraryIntensity() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.LightTransition method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.ReactionMonitoringTransition 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) getLogP() (pyopenms.Compomer method) getLogProb() (pyopenms.Adduct method) getLogType() (pyopenms.AccurateMassSearchEngine method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.CachedMzMLHandler method) (pyopenms.ChromatogramExtractor method) (pyopenms.ChromatogramExtractorAlgorithm method) (pyopenms.DTA2DFile method) (pyopenms.ElutionPeakDetection method) (pyopenms.FeatureFindingMetabo method) (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.GaussFilter method) (pyopenms.InternalCalibration method) (pyopenms.LabeledPairFinder method) (pyopenms.LinearResampler method) (pyopenms.LinearResamplerAlign method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) (pyopenms.MascotGenericFile method) (pyopenms.MascotInfile method) (pyopenms.MasstraceCorrelator method) (pyopenms.MassTraceDetection method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.MorphologicalFilter method) (pyopenms.MRMAssay method) (pyopenms.MRMDecoy method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MS2File method) (pyopenms.MzDataFile method) (pyopenms.MzIdentMLFile method) (pyopenms.MzMLFile method) (pyopenms.MzXMLFile method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) (pyopenms.ProgressLogger method) (pyopenms.QcMLFile method) (pyopenms.QTClusterFinder method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.StablePairFinder method) (pyopenms.SwathFile 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.ActivationMethod method) (pyopenms.AggregationMethod method) (pyopenms.AnnotationState method) (pyopenms.BoundaryCondition method) (pyopenms.ChecksumType method) (pyopenms.DataType method) (pyopenms.DecoyTransitionType method) (pyopenms.DimensionDescription method) (pyopenms.DRangeIntersection method) (pyopenms.DriftTimeUnit method) (pyopenms.FileType method) (pyopenms.IMFormat method) (pyopenms.IonOpticsType method) (pyopenms.IsotopeVariant method) (pyopenms.ITRAQ_TYPES method) (pyopenms.LogType method) (pyopenms.Measure method) (pyopenms.MT_QUANTMETHOD method) (pyopenms.MZTrafoModel_MODELTYPE method) (pyopenms.NormalizationMethod method) (pyopenms.OriginAnnotationFormat method) (pyopenms.QuotingMethod method) (pyopenms.ScanMode method) (pyopenms.SIDE method) (pyopenms.TermSpecificityNuc method) (pyopenms.UnitType method) (pyopenms.ValueType method) (pyopenms.XRefType_CVTerm_ControlledVocabulary method) getMappingRules() (pyopenms.CVMappings method) getMass() (pyopenms.Compomer method) (pyopenms.FeatureFinderMetaboIdentCompound method) (pyopenms.IMSAlphabet method) (pyopenms.IMSElement method) (pyopenms.IMSIsotopeDistribution method) (pyopenms.Modification method) (pyopenms.Sample method) getMassAnalyzers() (pyopenms.Instrument method) getMassDiff() (pyopenms.ChargePair method) getMasses() (pyopenms.IMSAlphabet method) (pyopenms.IMSIsotopeDistribution method) getMassShift() (pyopenms.Tagging method) getMassShiftAt() (pyopenms.MultiplexIsotopicPeakPattern method) getMassShiftCount() (pyopenms.MultiplexIsotopicPeakPattern method) getMassShiftIndex() (pyopenms.MultiplexIsotopicPeakPattern method) getMassShifts() (pyopenms.MultiplexIsotopicPeakPattern method) getMasstraceIntensities() (pyopenms.AccurateMassSearchResult method) getMassType() (pyopenms.MascotInfile 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) getMatrixRow() (pyopenms.LPWrapper method) getMax() (pyopenms.IsotopeDistribution method) getMaxAAPerModPerPeptide() (pyopenms.SequestInfile method) getMaxDataPoolSize() (pyopenms.PeakFileOptions method) getMaxIntensity() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.Kernel_MassTrace method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) getMaxInternalCleavageSites() (pyopenms.SequestInfile method) getMaxIsotope() (pyopenms.CoarseIsotopePatternGenerator method) getMaxModifications() (pyopenms.ModificationDefinitionsSet method) getMaxModsPerPeptide() (pyopenms.SequestInfile method) getMaxMZ() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) getMaxOccurrences() (pyopenms.ModificationDefinition method) getMaxPrecursorCharge() (pyopenms.XTandemInfile method) getMaxPTMsize() (pyopenms.InspectInfile method) getMaxRoundingError() (pyopenms.IMSWeights method) getMaxRT() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) getMaxScore() (pyopenms.XQuestResultXMLFile method) getMaxValidEValue() (pyopenms.XTandemInfile 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.Instrument method) (pyopenms.InstrumentSettings method) (pyopenms.IntegerDataArray method) (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) (pyopenms.MetaInfoDescription method) (pyopenms.MetaInfoInterface method) (pyopenms.Modification 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.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.SpectrumSettings method) (pyopenms.StringDataArray method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TraMLProduct method) getMetaValues() (pyopenms.CalibrationData method) (pyopenms.MetaInfoInterface method) getMethodOfCombination() (pyopenms.AcquisitionInfo method) getMIMatrix() (pyopenms.MRMScoring method) getMin() (pyopenms.IsotopeDistribution method) getMinElementCoordinates() (pyopenms.DistanceMatrix method) getMinIntensity() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) getMinMZ() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) getMinRoundingError() (pyopenms.IMSWeights method) getMinRT() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) getMinScore() (pyopenms.XQuestResultXMLFile method) getMissedCleavages() (pyopenms.EnzymaticDigestion method) (pyopenms.MascotInfile method) (pyopenms.ProteaseDigestion method) (pyopenms.RNaseDigestion method) getModel() (pyopenms.Instrument method) getModelParameters() (pyopenms.TransformationDescription method) getModelType() (pyopenms.TransformationDescription method) getModelTypes() (pyopenms.TransformationDescription 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.MascotInfile method) (pyopenms.ModificationDefinitionsSet method) (pyopenms.ModifiedPeptideGenerator static method) (pyopenms.SequestInfile method) (pyopenms.XTandemInfile method) getModificationsPerPeptide() (pyopenms.InspectInfile method) getModifiedResidue() (pyopenms.ResidueDB method) getMonoMass() (pyopenms.ResidueModification method) (pyopenms.Ribonucleotide method) getMonoWeight() (pyopenms.AASequence method) (pyopenms.Element method) (pyopenms.EmpiricalFormula method) (pyopenms.NASequence method) (pyopenms.Residue method) getMostAbundant() (pyopenms.IsotopeDistribution method) getMSChromatogramById() (pyopenms.IndexedMzMLHandler method) getMSChromatogramByNativeId() (pyopenms.IndexedMzMLHandler method) getMSData() (pyopenms.FeatureFinderAlgorithmMetaboIdent method) (pyopenms.FeatureFinderIdentificationAlgorithm method) getMSFileSection() (pyopenms.ExperimentalDesign method) getMSGFID() (pyopenms.DigestionEnzymeProtein method) getMSLevel() (pyopenms.MSSpectrum method) getMSLevels() (pyopenms.MSExperiment method) (pyopenms.PeakFileOptions 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.Precursor method) (pyopenms.Product method) (pyopenms.RichPeak2D method) (pyopenms.TraMLProduct method) getMz32Bit() (pyopenms.PeakFileOptions method) getMZArray() (pyopenms.OSSpectrum method) getMZErrorPPM() (pyopenms.AccurateMassSearchResult method) getMZRange() (pyopenms.FeatureFileOptions method) (pyopenms.PeakFileOptions method) getMZShiftAt() (pyopenms.MultiplexIsotopicPeakPattern method) getMZShiftCount() (pyopenms.MultiplexIsotopicPeakPattern method) getNADH010106() (pyopenms.AAIndex method) getNADH010107() (pyopenms.AAIndex method) getName() (pyopenms.AbsoluteQuantitation method) (pyopenms.AccurateMassSearchEngine method) (pyopenms.AMSE_AdductInfo method) (pyopenms.AScore method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.ConsensusIDAlgorithm method) (pyopenms.ConsensusIDAlgorithmAverage method) (pyopenms.ConsensusIDAlgorithmBest method) (pyopenms.ConsensusIDAlgorithmIdentity method) (pyopenms.ConsensusIDAlgorithmPEPIons method) (pyopenms.ConsensusIDAlgorithmPEPMatrix method) (pyopenms.ConsensusIDAlgorithmRanks method) (pyopenms.ConsensusIDAlgorithmSimilarity method) (pyopenms.ConsensusIDAlgorithmWorst method) (pyopenms.CVReference method) (pyopenms.CVTerm method) (pyopenms.DIAScoring method) (pyopenms.DigestionEnzyme method) (pyopenms.DigestionEnzymeProtein method) (pyopenms.DigestionEnzymeRNA method) (pyopenms.Element method) (pyopenms.ElutionModelFitter method) (pyopenms.ElutionPeakDetection 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.FloatDataArray method) (pyopenms.GaussFilter method) (pyopenms.GNPSMGFFile method) (pyopenms.IDDecoyProbability method) (pyopenms.IDMapper method) (pyopenms.IDRipper method) (pyopenms.IMSAlphabet method) (pyopenms.IMSElement method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Instrument method) (pyopenms.IntegerDataArray method) (pyopenms.IsobaricChannelExtractor method) (pyopenms.IsobaricQuantifier method) (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.KDTreeFeatureMaps method) (pyopenms.LabeledPairFinder method) (pyopenms.LinearResampler 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.MorphologicalFilter method) (pyopenms.MRMFeatureFilter method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MRMMapping method) (pyopenms.MRMTransitionGroupPicker method) (pyopenms.MSChromatogram method) (pyopenms.MSPGenericFile method) (pyopenms.MSSpectrum method) (pyopenms.MultiplexDeltaMassesGenerator method) (pyopenms.NLargest method) (pyopenms.Normalizer method) (pyopenms.NucleicAcidSpectrumGenerator method) (pyopenms.OpenPepXLAlgorithm method) (pyopenms.OpenPepXLLFAlgorithm method) (pyopenms.PeakIntegrator method) (pyopenms.PeakPickerChromatogram method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) (pyopenms.PeptideAndProteinQuant method) (pyopenms.PeptideIndexing method) (pyopenms.PosteriorErrorProbabilityModel 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.SimpleSearchEngineAlgorithm method) (pyopenms.SimpleTSGXLMS method) (pyopenms.SiriusExportAlgorithm method) (pyopenms.Software method) (pyopenms.SpectraMerger method) (pyopenms.SpectrumAlignment method) (pyopenms.SpectrumAlignmentScore method) (pyopenms.SpectrumAnnotator method) (pyopenms.SqrtScaler method) (pyopenms.StablePairFinder method) (pyopenms.StringDataArray 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.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) getNeighborhood() (pyopenms.KDTreeFeatureMaps 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.SplineSpectrum_Navigator method) getNominalMass() (pyopenms.IMSElement method) (pyopenms.IMSIsotopeDistribution method) getNormalized_library_intensities_() (pyopenms.OpenSwathScoring 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.SpectrumAccessOpenMS method) (pyopenms.SpectrumAccessOpenMSCached method) (pyopenms.SpectrumAccessOpenMSInMemory method) (pyopenms.SpectrumAccessQuadMZTransforming method) (pyopenms.SpectrumAccessSqMass method) (pyopenms.SpectrumAccessTransforming 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.OnDiscMSExperiment method) (pyopenms.SpectrumAccessOpenMS method) (pyopenms.SpectrumAccessOpenMSCached method) (pyopenms.SpectrumAccessOpenMSInMemory method) (pyopenms.SpectrumAccessQuadMZTransforming method) (pyopenms.SpectrumAccessSqMass method) (pyopenms.SpectrumAccessTransforming 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) getNumberOfAtoms() (pyopenms.EmpiricalFormula method) getNumberOfChannels() (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.TMTEighteenPlexQuantitationMethod method) (pyopenms.TMTElevenPlexQuantitationMethod method) (pyopenms.TMTSixPlexQuantitationMethod method) (pyopenms.TMTSixteenPlexQuantitationMethod method) (pyopenms.TMTTenPlexQuantitationMethod method) getNumberOfColumns() (pyopenms.LPWrapper 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) getNumberOfNonZeroEntriesInRow() (pyopenms.LPWrapper method) getNumberOfResidues() (pyopenms.ResidueDB method) getNumberOfRows() (pyopenms.LPWrapper method) getNumberOfSamples() (pyopenms.ExperimentalDesign method) getNumberOfThreads() (pyopenms.XTandemInfile method) getNumberOfVariableModifications() (pyopenms.ModificationDefinitionsSet method) getNumpressConfigurationFloatDataArray() (pyopenms.PeakFileOptions method) getNumpressConfigurationIntensity() (pyopenms.PeakFileOptions method) getNumpressConfigurationMassTime() (pyopenms.PeakFileOptions method) getObjective() (pyopenms.LPWrapper method) getObjectiveSense() (pyopenms.LPWrapper method) getObjectiveValue() (pyopenms.LPWrapper 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 method) getOpenMPMaxNumThreads() (pyopenms.OpenMSBuildInfo method) getOpenMSDataPath() (pyopenms.File method) getOpenMSHomePath() (pyopenms.File method) getOptions() (pyopenms.ConsensusXMLFile method) (pyopenms.DTA2DFile method) (pyopenms.FeatureXMLFile method) (pyopenms.FileHandler method) (pyopenms.IndexedMzMLFileLoader method) (pyopenms.MzDataFile method) (pyopenms.MzMLFile method) (pyopenms.MzXMLFile method) (pyopenms.PlainMSDataWritingConsumer method) getOrder() (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) getOrganism() (pyopenms.Sample method) getOrigin() (pyopenms.ResidueModification method) (pyopenms.Ribonucleotide method) getOriginFullname() (pyopenms.RipFileIdentifier method) getOSAsString() (pyopenms.OpenMSOSInfo method) getOSInfo() (pyopenms.OpenMSOSInfo 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.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.ConsensusIDAlgorithm method) (pyopenms.ConsensusIDAlgorithmAverage method) (pyopenms.ConsensusIDAlgorithmBest method) (pyopenms.ConsensusIDAlgorithmIdentity method) (pyopenms.ConsensusIDAlgorithmPEPIons method) (pyopenms.ConsensusIDAlgorithmPEPMatrix method) (pyopenms.ConsensusIDAlgorithmRanks method) (pyopenms.ConsensusIDAlgorithmSimilarity method) (pyopenms.ConsensusIDAlgorithmWorst method) (pyopenms.DIAScoring method) (pyopenms.ElutionModelFitter method) (pyopenms.ElutionPeakDetection 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.GaussFilter method) (pyopenms.GNPSMGFFile method) (pyopenms.IDDecoyProbability method) (pyopenms.IDMapper method) (pyopenms.IDRipper method) (pyopenms.IsobaricChannelExtractor method) (pyopenms.IsobaricQuantifier method) (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.KDTreeFeatureMaps method) (pyopenms.LabeledPairFinder method) (pyopenms.LinearResampler 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.MorphologicalFilter method) (pyopenms.MRMFeatureFilter method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MRMMapping method) (pyopenms.MRMTransitionGroupPicker method) (pyopenms.MSPGenericFile method) (pyopenms.MultiplexDeltaMassesGenerator method) (pyopenms.NLargest method) (pyopenms.Normalizer method) (pyopenms.NucleicAcidSpectrumGenerator method) (pyopenms.OpenPepXLAlgorithm method) (pyopenms.OpenPepXLLFAlgorithm method) (pyopenms.PeakIntegrator method) (pyopenms.PeakPickerChromatogram method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) (pyopenms.PeptideAndProteinQuant method) (pyopenms.PeptideIndexing method) (pyopenms.PosteriorErrorProbabilityModel method) (pyopenms.QTClusterFinder method) (pyopenms.RankScaler method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.SimpleTSGXLMS method) (pyopenms.SiriusExportAlgorithm method) (pyopenms.SpectraMerger method) (pyopenms.SpectrumAlignment method) (pyopenms.SpectrumAlignmentScore method) (pyopenms.SpectrumAnnotator method) (pyopenms.SqrtScaler method) (pyopenms.StablePairFinder 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.WindowMower method) (pyopenms.XFDRAlgorithm method) getParentMass() (pyopenms.IMSWeights method) getParsingSuccess() (pyopenms.IndexedMzMLHandler method) getPartialSequence() (pyopenms.SequestInfile method) getPathToFile() (pyopenms.SourceFile method) getPeak() (pyopenms.PeakIndex method) getPeakAnnotations() (pyopenms.PeptideHit method) getPeakCount() (pyopenms.MassTraces method) getPeakMassTolerance() (pyopenms.InspectInfile method) (pyopenms.MascotInfile method) (pyopenms.SequestInfile 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.BaseFeature method) (pyopenms.ConsensusFeature method) (pyopenms.Feature method) (pyopenms.MRMFeature method) (pyopenms.MSSpectrum method) (pyopenms.RipFileContent method) (pyopenms.SpectrumSettings method) getPeptideMassUnit() (pyopenms.SequestInfile method) getPeptideRef() (pyopenms.IncludeExcludeTarget method) (pyopenms.LightTransition method) (pyopenms.ReactionMonitoringTransition method) getPeptides() (pyopenms.TargetedExperiment method) getPercentage() (pyopenms.Gradient method) getPh() (pyopenms.Digestion method) getPiValue() (pyopenms.Residue 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.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) getPrecision() (pyopenms.IMSWeights method) getPrecursor() (pyopenms.ChromatogramSettings method) (pyopenms.MSChromatogram method) getPrecursorAdduct() (pyopenms.SpectralMatch 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) getPrecursorMassErrorUnit() (pyopenms.XTandemInfile method) getPrecursorMassTolerance() (pyopenms.InspectInfile method) (pyopenms.MascotInfile method) (pyopenms.SequestInfile method) getPrecursorMassToleranceMinus() (pyopenms.XTandemInfile method) getPrecursorMassTolerancePlus() (pyopenms.XTandemInfile method) getPrecursorMZ() (pyopenms.IncludeExcludeTarget method) (pyopenms.LightTransition method) (pyopenms.ReactionMonitoringTransition method) getPrecursorMzTolerance() (pyopenms.SiriusExportAlgorithm method) getPrecursorRtTolerance() (pyopenms.SiriusExportAlgorithm method) getPrecursors() (pyopenms.BinnedSpectrum method) (pyopenms.MSSpectrum method) (pyopenms.PrecursorCorrection method) (pyopenms.SpectrumSettings method) getPrecursorSpectrum() (pyopenms.MSExperiment method) getPrediction() (pyopenms.IncludeExcludeTarget method) (pyopenms.ReactionMonitoringTransition method) getPrefix() (pyopenms.AASequence method) (pyopenms.NASequence 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) 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.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.ConsensusMap method) (pyopenms.ExperimentalSettings method) (pyopenms.FeatureMap method) (pyopenms.MSExperiment method) (pyopenms.RipFileContent method) getProteinMassFilter() (pyopenms.SequestInfile method) getProteins() (pyopenms.LightTargetedExperiment method) (pyopenms.TargetedExperiment method) getPSIID() (pyopenms.DigestionEnzymeProtein method) getPSIMODAccession() (pyopenms.ResidueModification method) getPublications() (pyopenms.TargetedExperiment method) getQuality() (pyopenms.BaseFeature method) (pyopenms.ConsensusFeature method) (pyopenms.Feature method) (pyopenms.MRMFeature method) (pyopenms.QTCluster method) getQuantMethod() (pyopenms.Kernel_MassTrace method) getQuantMethods() (pyopenms.AbsoluteQuantitation method) getQueryMass() (pyopenms.AccurateMassSearchResult method) getRank() (pyopenms.PeptideHit method) (pyopenms.ProteinHit method) getRatios() (pyopenms.ConsensusFeature method) getReagentName() (pyopenms.Modification method) getReferenceChannel() (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.TMTEighteenPlexQuantitationMethod method) (pyopenms.TMTElevenPlexQuantitationMethod method) (pyopenms.TMTSixPlexQuantitationMethod method) (pyopenms.TMTSixteenPlexQuantitationMethod method) (pyopenms.TMTTenPlexQuantitationMethod method) getReferencingHits() (pyopenms.PeptideIdentification 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) getRemovePrecursorNearPeaks() (pyopenms.SequestInfile 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 method) getResolution() (pyopenms.IonDetector method) (pyopenms.MassAnalyzer method) getResolutionMethod() (pyopenms.MassAnalyzer method) getResolutionType() (pyopenms.MassAnalyzer 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 method) getRibonucleotide() (pyopenms.RibonucleotideDB method) getRibonucleotideAlternatives() (pyopenms.RibonucleotideDB method) getRibonucleotidePrefix() (pyopenms.RibonucleotideDB method) getROBB760107() (pyopenms.AAIndex method) getRoundMasses() (pyopenms.CoarseIsotopePatternGenerator method) getRow() (pyopenms.CsvFile method) getRowIndex() (pyopenms.LPWrapper method) getRowLowerBound() (pyopenms.LPWrapper method) getRowName() (pyopenms.LPWrapper method) getRowUpperBound() (pyopenms.LPWrapper method) getRT() (pyopenms.BaseFeature method) (pyopenms.CalibrationData method) (pyopenms.ChromatogramPeak method) (pyopenms.ConsensusFeature method) (pyopenms.Feature method) (pyopenms.FeatureHandle 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) getRTRange() (pyopenms.FeatureFileOptions method) (pyopenms.PeakFileOptions method) getRTRanges() (pyopenms.FeatureFinderMetaboIdentCompound method) getRTs() (pyopenms.FeatureFinderMetaboIdentCompound method) getRTShift() (pyopenms.Adduct method) (pyopenms.Compomer method) getRunID() (pyopenms.MzMLSqliteHandler method) getRunIDs() (pyopenms.QcMLFile method) getRunNames() (pyopenms.QcMLFile method) getSample() (pyopenms.ExperimentalDesign method) (pyopenms.ExperimentalSettings method) (pyopenms.MSExperiment method) getSamples() (pyopenms.ExperimentalDesign_SampleSection method) getSampleSection() (pyopenms.ExperimentalDesign method) getScale() (pyopenms.LinearInterpolation method) getScale_0() (pyopenms.BilinearInterpolation method) getScale_1() (pyopenms.BilinearInterpolation method) getScalingFactor() (pyopenms.EmgModel method) (pyopenms.InterpolationModel method) getScanDirection() (pyopenms.MassAnalyzer method) getScanLaw() (pyopenms.MassAnalyzer method) getScanMode() (pyopenms.InstrumentSettings method) getScanRate() (pyopenms.MassAnalyzer method) getScanTime() (pyopenms.MassAnalyzer method) getScanWindows() (pyopenms.InstrumentSettings method) getScopePath() (pyopenms.CVMappingRule method) getScore() (pyopenms.PeptideHit method) (pyopenms.ProteinHit method) getScores() (pyopenms.MRMFeature method) getScoreType() (pyopenms.PeptideIdentification method) (pyopenms.PercolatorOutfile method) (pyopenms.ProteinIdentification method) getSearchEngine() (pyopenms.ProteinIdentification method) getSearchEngineAndVersion() (pyopenms.InspectOutfile method) getSearchEngineVersion() (pyopenms.ProteinIdentification method) getSearchParameters() (pyopenms.ProteinIdentification method) getSearchType() (pyopenms.MascotInfile method) getSecondaryIdentifier() (pyopenms.SpectralMatch method) getSectionDescription() (pyopenms.Param method) getSeed() (pyopenms.UniqueIdGenerator method) getSequence() (pyopenms.IMSElement method) (pyopenms.NASequence method) (pyopenms.PeptideHit method) (pyopenms.ProteinHit method) getSequenceHeaderFilter() (pyopenms.SequestInfile method) getSequences() (pyopenms.InspectOutfile method) (pyopenms.SequestOutfile 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.Kernel_MassTrace method) (pyopenms.MSExperiment method) getSizeOnly() (pyopenms.FeatureFileOptions method) getSkipXMLChecks() (pyopenms.PeakFileOptions method) getSmallestScore() (pyopenms.PosteriorErrorProbabilityModel method) getSMILESString() (pyopenms.SpectralMatch method) getSmoothedIntensities() (pyopenms.Kernel_MassTrace method) getSoftware() (pyopenms.DataProcessing method) (pyopenms.Instrument method) (pyopenms.TargetedExperiment method) getSolver() (pyopenms.LPWrapper 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 method) (pyopenms.ProteaseDigestion method) (pyopenms.RNaseDigestion method) getSpecificityType() (pyopenms.Modification method) getSpectra() (pyopenms.InspectInfile method) (pyopenms.MSExperiment method) getSpectraByRT() (pyopenms.SpectrumAccessOpenMS method) (pyopenms.SpectrumAccessOpenMSCached method) (pyopenms.SpectrumAccessOpenMSInMemory method) (pyopenms.SpectrumAccessQuadMZTransforming method) (pyopenms.SpectrumAccessSqMass method) (pyopenms.SpectrumAccessTransforming method) getSpectraIndex() (pyopenms.CachedMzMLHandler method) getSpectraIndicesbyRT() (pyopenms.MzMLSqliteHandler method) getSpectrum() (pyopenms.CachedmzML method) (pyopenms.MSExperiment method) (pyopenms.NucleicAcidSpectrumGenerator method) (pyopenms.OnDiscMSExperiment method) (pyopenms.PeakIndex method) (pyopenms.TheoreticalSpectrumGenerator method) getSpectrumAccessOpenMSPtr() (pyopenms.SimpleOpenMSSpectraFactory static method) getSpectrumAlignment() (pyopenms.SpectrumAlignment method) getSpectrumAlignmentFastCharge() (pyopenms.OPXLSpectrumProcessingAlgorithms method) getSpectrumAlignmentSimple() (pyopenms.OPXLSpectrumProcessingAlgorithms method) getSpectrumById() (pyopenms.IndexedMzMLHandler method) (pyopenms.OnDiscMSExperiment method) (pyopenms.SpectrumAccessOpenMS method) (pyopenms.SpectrumAccessOpenMSCached method) (pyopenms.SpectrumAccessOpenMSInMemory method) (pyopenms.SpectrumAccessQuadMZTransforming method) (pyopenms.SpectrumAccessSqMass method) (pyopenms.SpectrumAccessTransforming method) getSpectrumByNativeId() (pyopenms.OnDiscMSExperiment method) getSpectrumMetaData() (pyopenms.SpectrumMetaDataLookup method) getSpectrumPtr() (pyopenms.SwathMap method) getStart() (pyopenms.PeptideEvidence method) getState() (pyopenms.Sample method) getStatistics() (pyopenms.PeptideAndProteinQuant method) (pyopenms.TransformationDescription method) getStatus() (pyopenms.LPWrapper method) getString() (pyopenms.StringView method) getStringDataArrays() (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.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.ConsensusIDAlgorithm method) (pyopenms.ConsensusIDAlgorithmAverage method) (pyopenms.ConsensusIDAlgorithmBest method) (pyopenms.ConsensusIDAlgorithmIdentity method) (pyopenms.ConsensusIDAlgorithmPEPIons method) (pyopenms.ConsensusIDAlgorithmPEPMatrix method) (pyopenms.ConsensusIDAlgorithmRanks method) (pyopenms.ConsensusIDAlgorithmSimilarity method) (pyopenms.ConsensusIDAlgorithmWorst method) (pyopenms.DIAScoring method) (pyopenms.ElutionModelFitter method) (pyopenms.ElutionPeakDetection 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.GaussFilter method) (pyopenms.GNPSMGFFile method) (pyopenms.IDDecoyProbability method) (pyopenms.IDMapper method) (pyopenms.IDRipper method) (pyopenms.IsobaricChannelExtractor method) (pyopenms.IsobaricQuantifier method) (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.KDTreeFeatureMaps method) (pyopenms.LabeledPairFinder method) (pyopenms.LinearResampler 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.MorphologicalFilter method) (pyopenms.MRMFeatureFilter method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MRMMapping method) (pyopenms.MRMTransitionGroupPicker method) (pyopenms.MSPGenericFile method) (pyopenms.MultiplexDeltaMassesGenerator method) (pyopenms.NLargest method) (pyopenms.Normalizer method) (pyopenms.NucleicAcidSpectrumGenerator method) (pyopenms.OpenPepXLAlgorithm method) (pyopenms.OpenPepXLLFAlgorithm method) (pyopenms.PeakIntegrator method) (pyopenms.PeakPickerChromatogram method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) (pyopenms.PeptideAndProteinQuant method) (pyopenms.PeptideIndexing method) (pyopenms.PosteriorErrorProbabilityModel method) (pyopenms.QTClusterFinder method) (pyopenms.RankScaler method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.SimpleTSGXLMS method) (pyopenms.SiriusExportAlgorithm method) (pyopenms.SpectraMerger method) (pyopenms.SpectrumAlignment method) (pyopenms.SpectrumAlignmentScore method) (pyopenms.SpectrumAnnotator method) (pyopenms.SqrtScaler method) (pyopenms.StablePairFinder 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.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 method) getTag() (pyopenms.Tagger method) getTagCount() (pyopenms.InspectInfile method) getTags() (pyopenms.Param method) getTargetCVTerms() (pyopenms.TargetedExperiment method) getTaxon() (pyopenms.XTandemInfile method) getTaxonomy() (pyopenms.MascotInfile method) getTaxonomyFilename() (pyopenms.XTandemInfile method) getTempDirectory() (pyopenms.File method) getTemperature() (pyopenms.Digestion method) (pyopenms.HPLC method) getTemporaryFile() (pyopenms.File 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 method) getTimeArray() (pyopenms.OSChromatogram method) getTimepoints() (pyopenms.Gradient method) getTOFTotalPathLength() (pyopenms.MassAnalyzer method) getTotalProbability() (pyopenms.FineIsotopePatternGenerator method) getTraceLength() (pyopenms.Kernel_MassTrace method) getTransformationModel() (pyopenms.AbsoluteQuantitationMethod method) getTransformationModelParams() (pyopenms.AbsoluteQuantitationMethod method) getTransformations() (pyopenms.FeatureFinderAlgorithmMetaboIdent method) getTransition() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) getTransitionGroupID() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) getTransitions() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.LightTargetedExperiment method) (pyopenms.MRMTransitionGroupCP method) (pyopenms.TargetedExperiment method) getTransitionsMuteable() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) getType() (pyopenms.FileHandler method) (pyopenms.IonDetector method) (pyopenms.MassAnalyzer method) (pyopenms.Modification method) (pyopenms.MSSpectrum method) (pyopenms.ProteinProteinCrossLink method) (pyopenms.SpectrumSettings method) getTypeByContent() (pyopenms.FileHandler method) getTypeByFileName() (pyopenms.FileHandler method) getULOD() (pyopenms.AbsoluteQuantitationMethod method) getULOQ() (pyopenms.AbsoluteQuantitationMethod method) getUnassignedPeptideIdentifications() (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) getUnchargedMass() (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 method) getUniqueName() (pyopenms.File method) getUnit() (pyopenms.CVTerm method) (pyopenms.DataValue method) (pyopenms.MetaInfoRegistry method) getUnitType() (pyopenms.DataValue method) getUpperRTBound() (pyopenms.GaussTraceFitter method) getURL() (pyopenms.ContactPerson method) getUserDirectory() (pyopenms.File 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.MascotInfile method) (pyopenms.ModificationDefinitionsSet method) getVariant() (pyopenms.Tagging method) getVASM830103() (pyopenms.AAIndex method) getVendor() (pyopenms.Instrument method) getVersion() (pyopenms.MascotXMLFile method) (pyopenms.OMSSAXMLFile method) (pyopenms.QcMLFile method) (pyopenms.Software method) (pyopenms.UnimodXMLFile method) (pyopenms.VersionInfo method) (pyopenms.XMLFile method) (pyopenms.XQuestResultXMLFile method) getVersionStruct() (pyopenms.VersionInfo 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.MRMFeature method) getWILM950102() (pyopenms.AAIndex method) getWriteIndex() (pyopenms.PeakFileOptions method) getWriteSupplementalData() (pyopenms.PeakFileOptions method) getXCoord() (pyopenms.QTCluster method) getXLinkIonSpectrum() (pyopenms.SimpleTSGXLMS method) (pyopenms.TheoreticalSpectrumGeneratorXLMS method) getXRefTypeName() (pyopenms.CVTerm_ControlledVocabulary method) getXTandemID() (pyopenms.DigestionEnzymeProtein method) getYCoord() (pyopenms.QTCluster method) getZoomScan() (pyopenms.InstrumentSettings method) GNPSMetaValueFile (class in pyopenms) GNPSMGFFile (class in pyopenms) GNPSQuantificationFile (class in pyopenms) Gradient (class in pyopenms) GRAVITATIONAL_CONSTANT (in module pyopenms.Constants) GridBasedCluster (class in pyopenms) group() (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.FeatureGroupingAlgorithmLabeled method) (pyopenms.FeatureGroupingAlgorithmQT method) (pyopenms.FeatureGroupingAlgorithmUnlabeled method) GUI (pyopenms.LogType attribute) H handlePTMs() (pyopenms.InspectInfile method) (pyopenms.SequestInfile method) HARDKLOER (pyopenms.FileType attribute) has() (pyopenms.AASequence method) (pyopenms.CrossLinksDB method) (pyopenms.ModificationsDB method) has_unit_accession (pyopenms.SemanticValidator_CVTerm attribute) has_unit_name (pyopenms.SemanticValidator_CVTerm attribute) has_value (pyopenms.SemanticValidator_CVTerm attribute) 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.Protein method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation 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) hasIntensityRange() (pyopenms.FeatureFileOptions method) (pyopenms.PeakFileOptions 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) 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) hasPrecursorChromatogram() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) hasPrecursorCVTerms() (pyopenms.ReactionMonitoringTransition method) hasPrediction() (pyopenms.ReactionMonitoringTransition method) hasPrefix() (pyopenms.AASequence method) hasProtein() (pyopenms.TargetedExperiment method) hasRegEx() (pyopenms.ProteaseDB method) (pyopenms.RNaseDB 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) hasSubsequence() (pyopenms.AASequence method) hasSuffix() (pyopenms.AASequence method) hasTag() (pyopenms.Param method) hasTermWithName() (pyopenms.ControlledVocabulary method) hasTransition() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) hasUnit() (pyopenms.CVTerm method) (pyopenms.DataValue method) hasValidExtension() (pyopenms.FileHandler 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) hasValue() (pyopenms.CVTerm method) HCD (pyopenms.ActivationMethod attribute) HCID (pyopenms.ActivationMethod attribute) headerMatches() (pyopenms.FASTAEntry method) HEAVY (pyopenms.IsotopeVariant attribute) height (pyopenms.PI_PeakArea attribute) (pyopenms.PI_PeakBackground attribute) high performance liquid chromatography higher_is_better (pyopenms.PeptideHit_AnalysisResult attribute) HPLC (class in pyopenms) HTML (pyopenms.FileType attribute) hull_points (pyopenms.PI_PeakArea attribute) HyperScore (class in pyopenms) I IBSpectraFile (class in pyopenms) id (pyopenms.Attachment attribute) (pyopenms.ChannelInfo attribute) (pyopenms.Compound attribute) (pyopenms.Contact attribute) (pyopenms.CV attribute) (pyopenms.CVTerm_ControlledVocabulary attribute) (pyopenms.ExtractionCoordinates attribute) (pyopenms.IsobaricChannelInformation attribute) (pyopenms.LightCompound attribute) (pyopenms.LightProtein attribute) (pyopenms.OSChromatogramMeta attribute) (pyopenms.OSSpectrumMeta attribute) (pyopenms.Peptide attribute) (pyopenms.Protein attribute) (pyopenms.Publication attribute) (pyopenms.QualityParameter attribute) (pyopenms.TargetedExperiment_Instrument attribute) ID_MERGE_INDEX (pyopenms.OriginAnnotationFormat attribute) IDConflictResolverAlgorithm (class in pyopenms) IDDecoyProbability (class in pyopenms) IdentificationRuns (class in pyopenms) identified (pyopenms.IDMapper_SpectraIdentificationState attribute) identifier (pyopenms.FASTAEntry attribute) identifying_transition (pyopenms.LightTransition attribute) IDFilter (class in pyopenms) IDMapper (class in pyopenms) IDMapper_SpectraIdentificationState (class in pyopenms) IDRipper (class in pyopenms) IDXML (pyopenms.FileType attribute) IdXMLFile (class in pyopenms) ILPDCWrapper (class in pyopenms) im_extraction_window (pyopenms.OSW_ChromExtractParams attribute) IMD (pyopenms.ActivationMethod attribute) IMFormat (class in pyopenms) IMSAlphabet (class in pyopenms) IMSElement (class in pyopenms) IMSIsotopeDistribution (class in pyopenms) IMSIsotopeDistribution_Peak (class in pyopenms) IMSWeights (class in pyopenms) IMTypes (class in pyopenms) IncludeExcludeTarget (class in pyopenms) index (pyopenms.OSChromatogramMeta attribute) (pyopenms.OSSpectrumMeta attribute) index2key() (pyopenms.LinearInterpolation method) index2key_0() (pyopenms.BilinearInterpolation method) index2key_1() (pyopenms.BilinearInterpolation method) IndexedMzMLDecoder (class in pyopenms) IndexedMzMLFileLoader (class in pyopenms) IndexedMzMLHandler (class in pyopenms) infer() (pyopenms.ProteinInference method) inferFromPeptides() (pyopenms.ModificationDefinitionsSet method) inferPosteriorProbabilities() (pyopenms.BayesianProteinInferenceAlgorithm method) INI (pyopenms.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 method) initPlots() (pyopenms.PosteriorErrorProbabilityModel method) initPluginParam() (pyopenms.Param method) InletType (pyopenms.IonSource 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.ActivationMethod attribute) InspectInfile (class in pyopenms) InspectOutfile (class in pyopenms) install Instrument (class in pyopenms) instrument_ref (pyopenms.Configuration attribute) InstrumentSettings (class in pyopenms) INT_LIST (pyopenms.DataType attribute) (pyopenms.ValueType attribute) int_sum (pyopenms.CrossLinkSpectrumMatch attribute) INT_VALUE (pyopenms.DataType attribute) (pyopenms.ValueType attribute) IntegerDataArray (class in pyopenms) integratePeak() (pyopenms.PeakIntegrator method) intensity (pyopenms.IsotopePattern attribute) (pyopenms.OpenSwath_Scores attribute) (pyopenms.PeptideHit_PeakAnnotation attribute) (pyopenms.Seed attribute) (pyopenms.TheoreticalIsotopePattern attribute) intensity() (pyopenms.KDTreeFeatureMaps method) intensity_l (pyopenms.MRMFQC_ComponentGroupQCs attribute) (pyopenms.MRMFQC_ComponentQCs attribute) intensity_u (pyopenms.MRMFQC_ComponentGroupQCs attribute) (pyopenms.MRMFQC_ComponentQCs attribute) intensityInRange() (pyopenms.MSSpectrum method) IntensityThresholdCalculation (pyopenms.SignalToNoiseEstimatorMeanIterative attribute) (pyopenms.SignalToNoiseEstimatorMedianChrom attribute) Interfaces (class in pyopenms) interfering_peak_count (pyopenms.PurityScores attribute) interfering_peaks (pyopenms.PurityScores attribute) Internal_MzMLValidator (class in pyopenms) InternalCalibration (class in pyopenms) InternalCalibration_LockMass (class in pyopenms) InterpolationModel (class in pyopenms) Intersects (pyopenms.DRangeIntersection attribute) intsum_alpha (pyopenms.CrossLinkSpectrumMatch attribute) intsum_beta (pyopenms.CrossLinkSpectrumMatch attribute) invert() (pyopenms.TransformationDescription method) (pyopenms.TransformationModelLinear method) ion_mobility (pyopenms.ExtractionCoordinates attribute) ion_ratio_feature_name (pyopenms.MRMFQC_ComponentGroupQCs attribute) ion_ratio_l (pyopenms.MRMFQC_ComponentGroupQCs attribute) ion_ratio_pair_name_1 (pyopenms.MRMFQC_ComponentGroupQCs attribute) ion_ratio_pair_name_2 (pyopenms.MRMFQC_ComponentGroupQCs attribute) ion_ratio_u (pyopenms.MRMFQC_ComponentGroupQCs attribute) IonDetector (class in pyopenms) IonIdentityMolecularNetworking (class in pyopenms) IonizationMethod (pyopenms.IonSource attribute) IonOpticsType (class in pyopenms) IonSource (class in pyopenms) iontype (pyopenms.TargetedExperiment_Interpretation attribute) IS_actual_concentration (pyopenms.AQS_featureConcentration attribute) (pyopenms.AQS_runConcentration attribute) IS_component_name (pyopenms.AQS_runConcentration attribute) IS_feature (pyopenms.AQS_featureConcentration attribute) isActive() (pyopenms.ChargePair method) (pyopenms.DataFilters method) (pyopenms.OpenSwathOSWWriter method) isCharged() (pyopenms.EmpiricalFormula method) isChildOf() (pyopenms.ControlledVocabulary method) isCompatible() (pyopenms.AMSE_AdductInfo method) (pyopenms.BinnedSpectrum method) (pyopenms.ModificationDefinitionsSet method) isConflicting() (pyopenms.Compomer method) isDetectingTransition() (pyopenms.LightTransition method) (pyopenms.ReactionMonitoringTransition method) isDirectory() (pyopenms.File 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) isHigherBetterScore() (pyopenms.CVTerm_ControlledVocabulary method) isHigherScoreBetter() (pyopenms.PeptideIdentification method) (pyopenms.ProteinIdentification method) isIdentifyingTransition() (pyopenms.LightTransition method) (pyopenms.ReactionMonitoringTransition method) isInPackage() (pyopenms.SplinePackage method) isInResidueSet() (pyopenms.Residue method) isInstantiated() (pyopenms.CrossLinksDB method) (pyopenms.ModificationsDB method) isInternallyConsistent() (pyopenms.LightMRMTransitionGroupCP method) (pyopenms.MRMTransitionGroupCP method) isIntersected() (pyopenms.DRange1 method) (pyopenms.DRange2 method) isInvalid() (pyopenms.QTCluster 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.Instrument method) (pyopenms.InstrumentSettings method) (pyopenms.IntegerDataArray method) (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) (pyopenms.MetaInfoDescription method) (pyopenms.MetaInfoInterface method) (pyopenms.Modification 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.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.SpectrumSettings method) (pyopenms.StringDataArray method) (pyopenms.TraMLProduct method) isModified() (pyopenms.AASequence method) (pyopenms.Residue method) (pyopenms.Ribonucleotide method) isNoMasstraceInfoIsotopePattern() (pyopenms.SiriusExportAlgorithm method) isNonEmptyCell() (pyopenms.ClusteringGrid method) iso_number_ms2_negative (pyopenms.IsobaricQuantifierStatistics attribute) iso_number_reporter_different (pyopenms.IsobaricQuantifierStatistics attribute) iso_number_reporter_negative (pyopenms.IsobaricQuantifierStatistics attribute) iso_solution_different_intensity (pyopenms.IsobaricQuantifierStatistics attribute) iso_total_intensity_negative (pyopenms.IsobaricQuantifierStatistics attribute) IsobaricChannelExtractor (class in pyopenms) IsobaricChannelInformation (class in pyopenms) IsobaricIsotopeCorrector (class in pyopenms) IsobaricNormalizer (class in pyopenms) IsobaricQuantifier (class in pyopenms) IsobaricQuantifierStatistics (class in pyopenms) isoPeakMeans() (pyopenms.OPXLHelper method) isOpenMPEnabled() (pyopenms.OpenMSBuildInfo method) isotope_correlation (pyopenms.OpenSwath_Scores attribute) isotope_overlap (pyopenms.OpenSwath_Scores attribute) IsotopeCluster (class in pyopenms) IsotopeDistribution (class in pyopenms) IsotopeFitter1D (class in pyopenms) IsotopeLabelingMDVs (class in pyopenms) IsotopeModel (class in pyopenms) IsotopePattern (class in pyopenms) IsotopeVariant (class in pyopenms) isotopicCorrection() (pyopenms.IsotopeLabelingMDVs method) isotopicCorrections() (pyopenms.IsotopeLabelingMDVs method) isPeptide() (pyopenms.LightCompound method) isPrefix() (pyopenms.PeptideIndexing method) isProductChargeStateSet() (pyopenms.LightTransition method) (pyopenms.ReactionMonitoringTransition method) isQuantifyingTransition() (pyopenms.LightTransition method) (pyopenms.ReactionMonitoringTransition method) isRTset() (pyopenms.RetentionTime method) isSemanticallyValid() (pyopenms.MzDataFile method) (pyopenms.MzIdentMLFile method) (pyopenms.MzMLFile method) (pyopenms.TraMLFile method) isSingleAdduct() (pyopenms.Compomer method) isSorted() (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) isSupported() (pyopenms.FileHandler method) isTrained() (pyopenms.MZTrafoModel method) isUserDefined() (pyopenms.ResidueModification method) isValid() (pyopenms.BaseFeature method) (pyopenms.ClusterProxyKD method) (pyopenms.ConsensusFeature method) (pyopenms.ConsensusMap method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.FeatureMap method) (pyopenms.Gradient method) (pyopenms.MassTrace method) (pyopenms.MassTraces method) (pyopenms.MRMFeature method) (pyopenms.PeakIndex method) (pyopenms.RichPeak2D method) isValidModel() (pyopenms.MZTrafoModel method) isValidProduct() (pyopenms.EnzymaticDigestion method) (pyopenms.ProteaseDigestion method) (pyopenms.RNaseDigestion method) items() (pyopenms.Param method) iTRAQ ITRAQ_TYPES (class in pyopenms) ItraqConstants (class in pyopenms) ItraqEightPlexQuantitationMethod (class in pyopenms) ItraqFourPlexQuantitationMethod (class in pyopenms) J JavaInfo (class in pyopenms) JOULE_PER_CAL (in module pyopenms.Constants) K k (pyopenms.RANSACParam attribute) KDTreeFeatureMaps (class in pyopenms) KDTreeFeatureNode (class in pyopenms) keepBestPeptideHits() (pyopenms.IDFilter method) keepBestPerPeptide() (pyopenms.IDFilter method) keepBestPerPeptidePerRun() (pyopenms.IDFilter method) keepHitsMatchingProteins() (pyopenms.IDFilter method) keepNativeSpectrumName() (pyopenms.PepXMLFile method) keepNBestHits() (pyopenms.IDFilter method) keepNBestSpectra() (pyopenms.IDFilter method) keepPeptidesWithMatchingModifications() (pyopenms.IDFilter method) keepPeptidesWithMatchingSequences() (pyopenms.IDFilter method) keepUniquePeptidesPerProtein() (pyopenms.IDFilter method) Kernel_MassTrace (class in pyopenms) key2index() (pyopenms.LinearInterpolation method) key2index_0() (pyopenms.BilinearInterpolation method) key2index_1() (pyopenms.BilinearInterpolation method) keys() (pyopenms.Param method) KINETIC_ENERGY_ANALYZER (pyopenms.IonOpticsType attribute) KNIME KROENIK (pyopenms.FileType attribute) KroenikFile (class in pyopenms) L label (pyopenms.ColumnHeader attribute) (pyopenms.ExperimentalDesign_MSFileSectionEntry attribute) LabeledPairFinder (class in pyopenms) LC LC-MS LC-MS/MS LCID (pyopenms.ActivationMethod attribute) LCMS LEFT (pyopenms.SIDE attribute) library_corr (pyopenms.OpenSwath_Scores attribute) library_dotprod (pyopenms.OpenSwath_Scores attribute) library_intensity (pyopenms.LightTransition attribute) library_manhattan (pyopenms.OpenSwath_Scores attribute) library_norm_manhattan (pyopenms.OpenSwath_Scores attribute) library_rootmeansquare (pyopenms.OpenSwath_Scores attribute) library_sangle (pyopenms.OpenSwath_Scores attribute) LIFT (pyopenms.ActivationMethod attribute) LIGHT (pyopenms.IsotopeVariant 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) LINEAR (pyopenms.MZTrafoModel_MODELTYPE attribute) linear_fp_mass_acc (pyopenms.NumpressConfig attribute) (pyopenms.SqMassConfig attribute) LINEAR_WEIGHTED (pyopenms.MZTrafoModel_MODELTYPE attribute) LinearInterpolation (class in pyopenms) LinearResampler (class in pyopenms) LinearResamplerAlign (class in pyopenms) liquid chromatography liquid chromatography coupled tandem mass spectrometry load() (pyopenms.AbsoluteQuantitationMethodFile method) (pyopenms.AbsoluteQuantitationStandardsFile method) (pyopenms.CachedmzML method) (pyopenms.ChromeleonFile method) (pyopenms.ConsensusXMLFile method) (pyopenms.CsvFile method) (pyopenms.CVMappingFile method) (pyopenms.DTA2DFile method) (pyopenms.DTAFile method) (pyopenms.EDTAFile method) (pyopenms.ExperimentalDesignFile method) (pyopenms.FASTAFile method) (pyopenms.FeatureXMLFile method) (pyopenms.IdXMLFile method) (pyopenms.IMSAlphabet method) (pyopenms.IndexedMzMLFileLoader method) (pyopenms.InspectOutfile method) (pyopenms.KroenikFile method) (pyopenms.MascotGenericFile method) (pyopenms.MascotInfile 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.OMSSACSVFile method) (pyopenms.OMSSAXMLFile method) (pyopenms.ParamXMLFile method) (pyopenms.PepXMLFile method) (pyopenms.PercolatorOutfile method) (pyopenms.ProtXMLFile method) (pyopenms.QcMLFile method) (pyopenms.SequestOutfile method) (pyopenms.SqMassFile method) (pyopenms.TextFile method) (pyopenms.TraMLFile method) (pyopenms.TransformationXMLFile method) (pyopenms.XQuestResultXMLFile method) (pyopenms.XTandemXMLFile method) loadBuffer() (pyopenms.MzMLFile method) loadExperiment() (pyopenms.FileHandler method) loadFeatures() (pyopenms.FileHandler method) loadFromOBO() (pyopenms.ControlledVocabulary method) loadMzML() (pyopenms.SwathFile method) loadMzXML() (pyopenms.SwathFile method) loads (pyopenms.SysInfo attribute) loadSize() (pyopenms.FeatureXMLFile method) loadSplit() (pyopenms.SwathFile method) locateTerm() (pyopenms.SemanticValidator method) location (pyopenms.LightModification attribute) (pyopenms.TargetedExperiment_Modification attribute) log_occupancy (pyopenms.CrossLinkSpectrumMatch attribute) log_occupancy_alpha (pyopenms.CrossLinkSpectrumMatch attribute) log_occupancy_beta (pyopenms.CrossLinkSpectrumMatch attribute) log_sn_score (pyopenms.OpenSwath_Scores attribute) LogConfigHandler (class in pyopenms) logFeatureSpectraNumber() (pyopenms.SiriusExportAlgorithm method) logOccupancyProb() (pyopenms.XQuestScores method) LogType (class in pyopenms) long_name (pyopenms.MultiplexDeltaMassesGenerator_Label attribute) lower (pyopenms.SwathMap attribute) LowessSmoothing (class in pyopenms) LPWrapper (class in pyopenms) LPWrapper_Type (pyopenms.LPWrapper attribute) LuciphorAdapter M M_PER_FOOT (in module pyopenms.Constants) MAGNETIC_DEFLECTION (pyopenms.IonOpticsType attribute) main_score (pyopenms.PeptideHit_AnalysisResult attribute) manhatt_score_dia (pyopenms.OpenSwath_Scores attribute) map2csv() (pyopenms.QcMLFile method) MAP_INDEX (pyopenms.OriginAnnotationFormat attribute) MapAlignmentAlgorithmIdentification (class in pyopenms) MapAlignmentAlgorithmKD (class in pyopenms) MapAlignmentAlgorithmPoseClustering (class in pyopenms) MapAlignmentEvaluationAlgorithmPrecision (class in pyopenms) MapAlignmentEvaluationAlgorithmRecall (class in pyopenms) MapAlignmentTransformer (class in pyopenms) MapConversion (class in pyopenms) mapExperiment() (pyopenms.MRMMapping method) mapIndex() (pyopenms.KDTreeFeatureMaps method) mapPrecursorsToIdentifications() (pyopenms.IDMapper method) MascotAdapter MascotGenericFile (class in pyopenms) MascotInfile (class in pyopenms) MASCOTXML (pyopenms.FileType attribute) MascotXMLFile (class in pyopenms) mass (pyopenms.IMSIsotopeDistribution_Peak attribute) Mass Spectrometry mass spectrum mass_type (pyopenms.SearchParameters attribute) MassAnalyzer (class in pyopenms) MassDecomposition (class in pyopenms) MassDecompositionAlgorithm (class in pyopenms) massdev_score (pyopenms.OpenSwath_Scores attribute) MassExplainer (class in pyopenms) MassIntensityType (pyopenms.XQuestResultXMLFile attribute) MASSSPECTRUM (pyopenms.ScanMode attribute) MassTrace (class in pyopenms) MasstraceCorrelator (class in pyopenms) MassTraceDetection (class in pyopenms) MassTraces (class in pyopenms) MassType (pyopenms.XTandemInfile attribute) match_odds (pyopenms.CrossLinkSpectrumMatch attribute) match_odds_alpha (pyopenms.CrossLinkSpectrumMatch attribute) match_odds_beta (pyopenms.CrossLinkSpectrumMatch attribute) matched_linear_alpha (pyopenms.CrossLinkSpectrumMatch attribute) matched_linear_beta (pyopenms.CrossLinkSpectrumMatch attribute) matched_xlink_alpha (pyopenms.CrossLinkSpectrumMatch attribute) matched_xlink_beta (pyopenms.CrossLinkSpectrumMatch attribute) matchedCurrentChain() (pyopenms.XQuestScores method) matches (pyopenms.MorpheusScore_Result attribute) matchOddsScore() (pyopenms.XQuestScores method) MatrixDouble (class in pyopenms) max (pyopenms.TheoreticalIsotopePattern attribute) max_float (pyopenms.ParamEntry attribute) max_int (pyopenms.ParamEntry attribute) max_rt (pyopenms.MassTrace attribute) max_trace (pyopenms.MassTraces attribute) maxPosition() (pyopenms.DBoundingBox2 method) MD5 (pyopenms.ChecksumType attribute) Measure (class in pyopenms) MEASURE_DA (pyopenms.Measure attribute) MEASURE_PPM (pyopenms.Measure attribute) median() (pyopenms.CalibrationData method) mem_unit (pyopenms.SysInfo attribute) merge() (pyopenms.IsotopeDistribution method) (pyopenms.Param method) (pyopenms.QcMLFile method) mergeAnnotatedSpectra() (pyopenms.OPXLSpectrumProcessingAlgorithms method) mergeFeatures() (pyopenms.TargetedSpectraExtractor method) mergeMULTISEPeptideIds() (pyopenms.PercolatorFeatureSetHelper method) mergeMULTISEProteinIds() (pyopenms.PercolatorFeatureSetHelper method) mergeSpectraBlockWise() (pyopenms.SpectraMerger method) mergeSpectraPrecursors() (pyopenms.SpectraMerger method) message_level (pyopenms.SolverParam attribute) meta_name (pyopenms.DataFilter attribute) MetaboliteFeatureDeconvolution (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) MetaInfo (class in pyopenms) MetaInfoDescription (class in pyopenms) MetaInfoInterface (class in pyopenms) MetaInfoRegistry (class in pyopenms) metaRegistry() (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.Instrument method) (pyopenms.InstrumentSettings method) (pyopenms.IntegerDataArray method) (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) (pyopenms.MetaInfoDescription method) (pyopenms.MetaInfoInterface method) (pyopenms.Modification 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.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.SpectrumSettings method) (pyopenms.StringDataArray method) (pyopenms.TraMLProduct 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.Instrument method) (pyopenms.InstrumentSettings method) (pyopenms.IntegerDataArray method) (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) (pyopenms.MetaInfoDescription method) (pyopenms.MetaInfoInterface method) (pyopenms.Modification 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.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.SpectrumSettings method) (pyopenms.StringDataArray method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TraMLProduct method) MGF (pyopenms.FileType attribute) mi_score (pyopenms.OpenSwath_Scores attribute) MIC (pyopenms.MorpheusScore_Result attribute) MILLISECOND (pyopenms.DriftTimeUnit attribute) min_float (pyopenms.ParamEntry attribute) min_int (pyopenms.ParamEntry attribute) min_upper_edge_dist (pyopenms.OSW_ChromExtractParams attribute) minPosition() (pyopenms.DBoundingBox2 method) mip_gap (pyopenms.SolverParam attribute) mirror_plot_spectrum() (in module pyopenms.plotting) missed_cleavages (pyopenms.SearchParameters attribute) MIXED (pyopenms.IMFormat attribute) MM_PER_INCH (in module pyopenms.Constants) Modification (class in pyopenms) Modification_SpecificityType (pyopenms.Modification attribute) ModificationDefinition (class in pyopenms) ModificationDefinitionsSet (class in pyopenms) modifications (pyopenms.LightCompound attribute) ModificationsDB (class in pyopenms) ModifiedPeptideGenerator (class in pyopenms) ModifiedPeptideGenerator_MapToResidueType (class in pyopenms) mods (pyopenms.Peptide attribute) module pyopenms pyopenms.Constants pyopenms.plotting molecular_formula (pyopenms.Compound attribute) mono_mass_delta (pyopenms.TargetedExperiment_Modification attribute) MorpheusScore (class in pyopenms) MorpheusScore_Result (class in pyopenms) MorphologicalFilter (class in pyopenms) MRM (pyopenms.FileType attribute) MRMAssay (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) 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 MS/MS MS1 ms1 (pyopenms.SwathMap attribute) ms1_isotope_correlation (pyopenms.OpenSwath_Scores attribute) ms1_isotope_overlap (pyopenms.OpenSwath_Scores attribute) ms1_mi_combined_score (pyopenms.OpenSwath_Scores attribute) ms1_mi_contrast_score (pyopenms.OpenSwath_Scores attribute) ms1_mi_score (pyopenms.OpenSwath_Scores attribute) ms1_ppm_score (pyopenms.OpenSwath_Scores attribute) ms1_xcorr_coelution_combined_score (pyopenms.OpenSwath_Scores attribute) ms1_xcorr_coelution_contrast_score (pyopenms.OpenSwath_Scores attribute) ms1_xcorr_coelution_score (pyopenms.OpenSwath_Scores attribute) ms1_xcorr_shape_combined_score (pyopenms.OpenSwath_Scores attribute) ms1_xcorr_shape_contrast_score (pyopenms.OpenSwath_Scores attribute) ms1_xcorr_shape_score (pyopenms.OpenSwath_Scores attribute) MS1SPECTRUM (pyopenms.ScanMode attribute) MS2 (pyopenms.FileType attribute) MS2File (class in pyopenms) MS3 ms_level (pyopenms.InternalCalibration_LockMass attribute) (pyopenms.OSSpectrumMeta attribute) (pyopenms.SpectrumMetaData attribute) 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) MSGFPlusAdapter MsInspectFile (class in pyopenms) MSNSPECTRUM (pyopenms.ScanMode attribute) MSNumpressCoder (class in pyopenms) MSP (pyopenms.FileType attribute) MSPFile (class in pyopenms) MSPGenericFile (class in pyopenms) MSSpectrum (class in pyopenms) MSstatsFile (class in pyopenms) MT_QUANT_AREA (pyopenms.MT_QUANTMETHOD attribute) MT_QUANT_MEDIAN (pyopenms.MT_QUANTMETHOD attribute) MT_QUANTMETHOD (class in pyopenms) MULTIPLE_SPECTRA (pyopenms.IMFormat attribute) MultiplexDeltaMasses (class in pyopenms) MultiplexDeltaMasses_DeltaMass (class in pyopenms) MultiplexDeltaMassesGenerator (class in pyopenms) MultiplexDeltaMassesGenerator_Label (class in pyopenms) MultiplexIsotopicPeakPattern (class in pyopenms) MZ (pyopenms.DimensionDescription attribute) mz (pyopenms.ExtractionCoordinates attribute) (pyopenms.InternalCalibration_LockMass attribute) (pyopenms.PeptideHit_PeakAnnotation attribute) (pyopenms.SimplePeak attribute) mz() (pyopenms.KDTreeFeatureMaps method) mz_extraction_window (pyopenms.OSW_ChromExtractParams attribute) mz_max (pyopenms.PeakBoundary attribute) mz_min (pyopenms.PeakBoundary attribute) mz_precursor (pyopenms.ExtractionCoordinates attribute) mz_score (pyopenms.IsotopePattern attribute) mz_start (pyopenms.NoiseEstimator attribute) mzData mzdata MZDATA (pyopenms.FileType attribute) MzDataFile (class in pyopenms) MZIDENTML (pyopenms.FileType attribute) MzIdentMLFile (class in pyopenms) mzML mzml MZML (pyopenms.FileType attribute) MzMLFile (class in pyopenms) MzMLSpectrumDecoder (class in pyopenms) MzMLSqliteHandler (class in pyopenms) MzMLSwathFileConsumer (class in pyopenms) MzQCFile (class in pyopenms) MzTab (class in pyopenms) MzTabFile (class in pyopenms) MzTabM (class in pyopenms) MzTabMFile (class in pyopenms) MZTrafoModel (class in pyopenms) MZTrafoModel_MODELTYPE (class in pyopenms) mzXML mzxml MZXML (pyopenms.FileType attribute) MzXMLFile (class in pyopenms) N n (pyopenms.RANSACParam attribute) n_detecting_l (pyopenms.MRMFQC_ComponentGroupQCs attribute) n_detecting_u (pyopenms.MRMFQC_ComponentGroupQCs attribute) n_heavy_l (pyopenms.MRMFQC_ComponentGroupQCs attribute) n_heavy_u (pyopenms.MRMFQC_ComponentGroupQCs attribute) n_identifying_l (pyopenms.MRMFQC_ComponentGroupQCs attribute) n_identifying_u (pyopenms.MRMFQC_ComponentGroupQCs attribute) n_light_l (pyopenms.MRMFQC_ComponentGroupQCs attribute) n_light_u (pyopenms.MRMFQC_ComponentGroupQCs attribute) n_peaks (pyopenms.MorpheusScore_Result attribute) n_quantifying_l (pyopenms.MRMFQC_ComponentGroupQCs attribute) n_quantifying_u (pyopenms.MRMFQC_ComponentGroupQCs attribute) n_samples (pyopenms.PeptideAndProteinQuant_Statistics attribute) n_transitions_l (pyopenms.MRMFQC_ComponentGroupQCs attribute) n_transitions_u (pyopenms.MRMFQC_ComponentGroupQCs attribute) name (pyopenms.Attachment attribute) (pyopenms.ChannelInfo attribute) (pyopenms.CVTerm_ControlledVocabulary attribute) (pyopenms.IsobaricChannelInformation attribute) (pyopenms.ParamEntry attribute) (pyopenms.ParamNode attribute) (pyopenms.QualityParameter attribute) (pyopenms.SemanticValidator_CVTerm attribute) (pyopenms.TraceInfo attribute) (pyopenms.Unit attribute) name() (pyopenms.ControlledVocabulary method) nameToEnum() (pyopenms.MZTrafoModel method) nameToType() (pyopenms.FileTypes method) NASequence (class in pyopenms) NASFragmentType (pyopenms.NASequence attribute) native_id (pyopenms.SpectrumMetaData attribute) NEUTRON_MASS (in module pyopenms.Constants) NEUTRON_MASS_U (in module pyopenms.Constants) nextProgress() (pyopenms.AccurateMassSearchEngine method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.CachedMzMLHandler method) (pyopenms.ChromatogramExtractor method) (pyopenms.ChromatogramExtractorAlgorithm method) (pyopenms.DTA2DFile method) (pyopenms.ElutionPeakDetection method) (pyopenms.FeatureFindingMetabo method) (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.GaussFilter method) (pyopenms.InternalCalibration method) (pyopenms.LabeledPairFinder method) (pyopenms.LinearResampler method) (pyopenms.LinearResamplerAlign method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) (pyopenms.MascotGenericFile method) (pyopenms.MascotInfile method) (pyopenms.MasstraceCorrelator method) (pyopenms.MassTraceDetection method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.MorphologicalFilter method) (pyopenms.MRMAssay method) (pyopenms.MRMDecoy method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MS2File method) (pyopenms.MzDataFile method) (pyopenms.MzIdentMLFile method) (pyopenms.MzMLFile method) (pyopenms.MzXMLFile method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) (pyopenms.ProgressLogger method) (pyopenms.QcMLFile method) (pyopenms.QTClusterFinder method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.StablePairFinder method) (pyopenms.SwathFile method) (pyopenms.TransitionTSVFile method) nightly snapshot NLargest (class in pyopenms) NM_SCALE (pyopenms.NormalizationMethod attribute) NM_SHIFT (pyopenms.NormalizationMethod attribute) no_precursors (pyopenms.IDMapper_SpectraIdentificationState attribute) nodes (pyopenms.ParamNode attribute) NoiseEstimator (class in pyopenms) NONE (pyopenms.DriftTimeUnit attribute) (pyopenms.IMFormat attribute) (pyopenms.LogType attribute) (pyopenms.QuotingMethod attribute) (pyopenms.XRefType_CVTerm_ControlledVocabulary attribute) NonNegativeLeastSquaresSolver (class in pyopenms) NoopMSDataWritingConsumer (class in pyopenms) norm_rt_score (pyopenms.OpenSwath_Scores attribute) NormalizationMethod (class in pyopenms) normalize() (pyopenms.IMSIsotopeDistribution method) (pyopenms.IsobaricNormalizer method) normalized_experimental_rt (pyopenms.OpenSwath_Scores attribute) normalizeMaps() (pyopenms.ConsensusMapNormalizerAlgorithmMedian method) (pyopenms.ConsensusMapNormalizerAlgorithmQuantile method) (pyopenms.ConsensusMapNormalizerAlgorithmThreshold method) Normalizer (class in pyopenms) note (pyopenms.TM_DataPoint attribute) now() (pyopenms.DateTime method) np_compression (pyopenms.NumpressConfig attribute) nr_peaks (pyopenms.OpenSwath_Scores attribute) nr_windows (pyopenms.NoiseEstimator attribute) NucleicAcidSpectrumGenerator (class in pyopenms) num_iso_peaks_mean (pyopenms.CrossLinkSpectrumMatch attribute) num_iso_peaks_mean_linear_alpha (pyopenms.CrossLinkSpectrumMatch attribute) num_iso_peaks_mean_linear_beta (pyopenms.CrossLinkSpectrumMatch attribute) num_iso_peaks_mean_xlinks_alpha (pyopenms.CrossLinkSpectrumMatch attribute) num_iso_peaks_mean_xlinks_beta (pyopenms.CrossLinkSpectrumMatch attribute) number_ms2_empty (pyopenms.IsobaricQuantifierStatistics attribute) number_ms2_total (pyopenms.IsobaricQuantifierStatistics attribute) NUMBER_OF_TERM_SPECIFICITY (pyopenms.TermSpecificityNuc attribute) numerator_ref_ (pyopenms.Ratio attribute) numMaps() (pyopenms.KDTreeFeatureMaps method) numpress NumpressCompression (pyopenms.MSNumpressCoder attribute) NumpressConfig (class in pyopenms) numpressErrorTolerance (pyopenms.NumpressConfig attribute) numpressFixedPoint (pyopenms.NumpressConfig attribute) O OBO (pyopenms.FileType attribute) obsolete (pyopenms.CVTerm_ControlledVocabulary attribute) octadecyl ok() (pyopenms.BSpline2d method) OMSSACSVFile (class in pyopenms) OMSSAXML (pyopenms.FileType attribute) OMSSAXMLFile (class in pyopenms) OnDiscMSExperiment (class in pyopenms) op (pyopenms.DataFilter attribute) opened (pyopenms.TraceInfo attribute) openFile() (pyopenms.IndexedMzMLHandler method) (pyopenms.OnDiscMSExperiment method) OpenMS API OpenMSBuildInfo (class in pyopenms) OpenMSOSInfo (class in pyopenms) OpenPepXLAlgorithm (class in pyopenms) OpenPepXLAlgorithm_ExitCodes (pyopenms.OpenPepXLAlgorithm attribute) OpenPepXLLFAlgorithm (class in pyopenms) OpenPepXLLFAlgorithm_ExitCodes (pyopenms.OpenPepXLLFAlgorithm 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) optimizeCalibrationCurveIterative() (pyopenms.AbsoluteQuantitation method) optimizeSingleCalibrationCurve() (pyopenms.AbsoluteQuantitation method) optimizeTree() (pyopenms.KDTreeFeatureMaps method) optional_begin (pyopenms.TheoreticalIsotopePattern attribute) optional_end (pyopenms.TheoreticalIsotopePattern attribute) OPXL_PreprocessedPairSpectra (class in pyopenms) OPXLDataStructs (class in pyopenms) OPXLHelper (class in pyopenms) OPXLSpectrumProcessingAlgorithms (class in pyopenms) orbitrap ordinal (pyopenms.TargetedExperiment_Interpretation attribute) OriginAnnotationFormat (class in pyopenms) OSBinaryDataArray (class in pyopenms) OSChromatogram (class in pyopenms) OSChromatogramMeta (class in pyopenms) OSSpectrum (class in pyopenms) OSSpectrumMeta (class in pyopenms) OSW (pyopenms.FileType attribute) OSW_ChromExtractParams (class in pyopenms) OSWFile (class in pyopenms) OTHER (pyopenms.UnitType attribute) output_delay (pyopenms.SolverParam attribute) output_freq (pyopenms.SolverParam attribute) overall_quality_l (pyopenms.MRMFQC_ComponentGroupQCs attribute) (pyopenms.MRMFQC_ComponentQCs attribute) overall_quality_u (pyopenms.MRMFQC_ComponentGroupQCs attribute) (pyopenms.MRMFQC_ComponentQCs attribute) P padding (pyopenms.SysInfo attribute) pairCompoundWithAnnotatedTDSpectraPairs() (pyopenms.MetaboTargetedAssay method) Param (class in pyopenms) ParamCTDFile (class in pyopenms) ParamEntry (class in pyopenms) ParamNode (class in pyopenms) params (pyopenms.MRMFP_ComponentGroupParams attribute) (pyopenms.MRMFP_ComponentParams attribute) ParamValue (class in pyopenms) PARAMXML (pyopenms.FileType attribute) ParamXMLFile (class in pyopenms) parents (pyopenms.CVTerm_ControlledVocabulary attribute) parse() (pyopenms.LogConfigHandler method) passes() (pyopenms.DataFilters method) path (pyopenms.ExperimentalDesign_MSFileSectionEntry attribute) path() (pyopenms.File method) PD (pyopenms.ActivationMethod attribute) peak (pyopenms.PeakIndex attribute) (pyopenms.Seed attribute) Peak1D (class in pyopenms) Peak2D (class in pyopenms) peak_depth (pyopenms.ProbablePhosphoSites attribute) PeakBoundary (class in pyopenms) PeakFileOptions (class in pyopenms) PeakIndex (class in pyopenms) PeakIntegrator (class in pyopenms) PeakMap (in module pyopenms) PeakMassType (pyopenms.ProteinIdentification attribute) PeakPickerChromatogram (class in pyopenms) PeakPickerHiRes (class in pyopenms) PeakPickerIterative (class in pyopenms) peaks (pyopenms.IsotopeCluster attribute) PeakSpectrum (in module pyopenms) PeakTypeEstimator (class in pyopenms) PeakWidthEstimator (class in pyopenms) pep_indices (pyopenms.PeptideProteinResolution_ConnectedComponent attribute) PEPLIST (pyopenms.FileType attribute) PepNovo Peptide (class in pyopenms) peptide-spectrum match peptide_group_label (pyopenms.LightCompound attribute) peptide_id_index (pyopenms.CrossLinkSpectrumMatch attribute) peptide_identifications_to_df() (in module pyopenms) peptide_mass (pyopenms.AASeqWithMass attribute) peptide_ref (pyopenms.LightTransition attribute) peptide_seq (pyopenms.AASeqWithMass attribute) 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) PeptideIndexing (class in pyopenms) PeptideIndexing_ExitCodes (pyopenms.PeptideIndexing attribute) PeptidePosition (pyopenms.OPXLDataStructs attribute) PeptideProteinResolution (class in pyopenms) PeptideProteinResolution_ConnectedComponent (class in pyopenms) PEPXML (pyopenms.FileType attribute) PepXMLFile (class in pyopenms) PepXMLFileMascot (class in pyopenms) percentiles_after (pyopenms.TransformationStatistics attribute) percentiles_before (pyopenms.TransformationStatistics attribute) PercolatorFeatureSetHelper (class in pyopenms) PercolatorInfile (class in pyopenms) PercolatorOutfile (class in pyopenms) PercolatorOutfile_ScoreType (pyopenms.PercolatorOutfile attribute) percTIC (pyopenms.CrossLinkSpectrumMatch attribute) PHD (pyopenms.ActivationMethod attribute) PI (in module pyopenms.Constants) PI_PeakArea (class in pyopenms) PI_PeakBackground (class in pyopenms) PI_PeakShapeMetrics (class in pyopenms) pick() (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) pickChromatogram() (pyopenms.PeakPickerChromatogram method) pickExperiment() (pyopenms.MRMFeatureFinderScoring method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) pickSpectrum() (pyopenms.TargetedSpectraExtractor method) pickTransitionGroup() (pyopenms.MRMTransitionGroupPicker 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) PNG (pyopenms.FileType attribute) points_across_baseline (pyopenms.PI_PeakShapeMetrics attribute) points_across_half_height (pyopenms.PI_PeakShapeMetrics attribute) polar() (pyopenms.AAIndex method) Polarity (pyopenms.IonSource attribute) pos_neg_mean_weighted_posteriors() (pyopenms.PosteriorErrorProbabilityModel method) position (pyopenms.AASeqWithMass attribute) PosteriorErrorProbabilityModel (class in pyopenms) ppm (pyopenms.OSW_ChromExtractParams attribute) ppm_error_abs_sum (pyopenms.CrossLinkSpectrumMatch attribute) ppm_error_abs_sum_alpha (pyopenms.CrossLinkSpectrumMatch attribute) ppm_error_abs_sum_beta (pyopenms.CrossLinkSpectrumMatch attribute) ppm_error_abs_sum_linear (pyopenms.CrossLinkSpectrumMatch attribute) ppm_error_abs_sum_linear_alpha (pyopenms.CrossLinkSpectrumMatch attribute) ppm_error_abs_sum_linear_beta (pyopenms.CrossLinkSpectrumMatch attribute) ppm_error_abs_sum_xlinks (pyopenms.CrossLinkSpectrumMatch attribute) ppm_error_abs_sum_xlinks_alpha (pyopenms.CrossLinkSpectrumMatch attribute) ppm_error_abs_sum_xlinks_beta (pyopenms.CrossLinkSpectrumMatch attribute) PQD (pyopenms.ActivationMethod attribute) PQP (pyopenms.FileType attribute) pre_release_identifier (pyopenms.VersionDetails attribute) pre_score (pyopenms.CrossLinkSpectrumMatch attribute) Precursor (class in pyopenms) PRECURSOR (pyopenms.ScanMode attribute) precursor_charge (pyopenms.SpectrumMetaData attribute) precursor_correction (pyopenms.CrossLinkSpectrumMatch attribute) (pyopenms.ProteinProteinCrossLink attribute) precursor_error_ppm (pyopenms.CrossLinkSpectrumMatch attribute) PRECURSOR_ERROR_PPM_USERPARAM (in module pyopenms.Constants) precursor_mass (pyopenms.XLPrecursor attribute) precursor_mass_tolerance (pyopenms.SearchParameters attribute) precursor_mass_tolerance_ppm (pyopenms.SearchParameters attribute) precursor_mz (pyopenms.LightTransition attribute) (pyopenms.SpectrumMetaData attribute) precursor_residual_peak_count (pyopenms.CrossLinkSpectrumMatch attribute) precursor_rt (pyopenms.SpectrumMetaData attribute) precursor_signal_proportion (pyopenms.CrossLinkSpectrumMatch attribute) precursor_target_intensity (pyopenms.CrossLinkSpectrumMatch attribute) precursor_target_peak_count (pyopenms.CrossLinkSpectrumMatch attribute) precursor_total_intensity (pyopenms.CrossLinkSpectrumMatch attribute) PrecursorCorrection (class in pyopenms) precursorMzToleranceUnitIsPPM() (pyopenms.SiriusExportAlgorithm method) PrecursorPurity (class in pyopenms) predict() (pyopenms.MZTrafoModel method) Prediction (class in pyopenms) prepareLine() (pyopenms.OpenSwathOSWWriter method) prepareProteinPeptideMaps_() (pyopenms.MRMFeatureFinderScoring method) preprocess() (pyopenms.SpectraSTSimilarityScore method) preprocessing() (pyopenms.SiriusExportAlgorithm method) preprocessing_tech (pyopenms.SolverParam attribute) preprocessSpectra() (pyopenms.OPXLSpectrumProcessingAlgorithms method) preScore() (pyopenms.XQuestScores method) probability (pyopenms.ProteinGroup attribute) ProbablePhosphoSites (class in pyopenms) ProcessingAction (pyopenms.DataProcessing attribute) procs (pyopenms.SysInfo attribute) PROD (pyopenms.AggregationMethod attribute) Product (class in pyopenms) product_mz (pyopenms.LightTransition attribute) ProgressLogger (class in pyopenms) prot_grp_indices (pyopenms.PeptideProteinResolution_ConnectedComponent attribute) ProteaseDB (class in pyopenms) ProteaseDigestion (class in pyopenms) Protein (class in pyopenms) protein_refs (pyopenms.LightCompound attribute) (pyopenms.Peptide attribute) ProteinGroup (class in pyopenms) ProteinHit (class in pyopenms) ProteinIdentification (class in pyopenms) ProteinInference (class in pyopenms) ProteinProteinCrossLink (class in pyopenms) ProteinProteinCrossLinkType (pyopenms.OPXLDataStructs attribute) proteins (pyopenms.LightTargetedExperiment attribute) ProteoWizard PROTON_MASS (in module pyopenms.Constants) PROTON_MASS_U (in module pyopenms.Constants) PROTXML (pyopenms.FileType attribute) ProtXMLFile (class in pyopenms) PScore (class in pyopenms) PSD (pyopenms.ActivationMethod attribute) PSM psm_count (pyopenms.PeptideAndProteinQuant_PeptideData attribute) (pyopenms.PeptideAndProteinQuant_ProteinData attribute) PSMS (pyopenms.FileType attribute) PSQ (pyopenms.FileType attribute) Publication (class in pyopenms) PurityScores (class in pyopenms) push_back() (pyopenms.AcquisitionInfo method) (pyopenms.ConsensusMap method) (pyopenms.FeatureMap method) (pyopenms.FloatDataArray method) (pyopenms.IMSAlphabet method) (pyopenms.IntegerDataArray method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) (pyopenms.StringDataArray method) pyopenms module pyopenms.Constants module pyopenms.plotting module Q QCML (pyopenms.FileType attribute) QcMLFile (class in pyopenms) QTCluster (class in pyopenms) QTClusterFinder (class in pyopenms) QUADRATIC (pyopenms.MZTrafoModel_MODELTYPE attribute) QUADRATIC_WEIGHTED (pyopenms.MZTrafoModel_MODELTYPE attribute) quadrupole QualityParameter (class in pyopenms) qualityRef (pyopenms.Attachment attribute) quant_features (pyopenms.PeptideAndProteinQuant_Statistics attribute) quant_peptides (pyopenms.PeptideAndProteinQuant_Statistics attribute) quant_proteins (pyopenms.PeptideAndProteinQuant_Statistics attribute) quantify() (pyopenms.IsobaricQuantifier method) quantifyComponents() (pyopenms.AbsoluteQuantitation method) quantifying_transition (pyopenms.LightTransition attribute) quantifyPeptides() (pyopenms.PeptideAndProteinQuant method) quantifyProteins() (pyopenms.PeptideAndProteinQuant method) queryByConsensusFeature() (pyopenms.AccurateMassSearchEngine method) queryByFeature() (pyopenms.AccurateMassSearchEngine method) queryByMZ() (pyopenms.AccurateMassSearchEngine method) queryRegion() (pyopenms.KDTreeFeatureMaps method) QuotingMethod (class in pyopenms) R RAD_PER_DEG (in module pyopenms.Constants) RangeIntensity (class in pyopenms) RangeMobility (class in pyopenms) RangeMZ (class in pyopenms) rank (pyopenms.CrossLinkSpectrumMatch attribute) (pyopenms.TargetedExperiment_Interpretation attribute) 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.LinearResampler method) (pyopenms.LinearResamplerAlign method) rasterExperiment() (pyopenms.LinearResampler method) (pyopenms.LinearResamplerAlign method) Ratio (class in pyopenms) ratio_value_ (pyopenms.Ratio attribute) raw_rt_score (pyopenms.OpenSwath_Scores attribute) ReactionMonitoringTransition (class in pyopenms) readable() (pyopenms.File method) readChromatograms() (pyopenms.MzMLSqliteHandler method) readExperiment() (pyopenms.MzMLSqliteHandler method) readFromOBOFile() (pyopenms.CrossLinksDB method) readMemdump() (pyopenms.CachedMzMLHandler method) readNext() (pyopenms.FASTAFile method) readOutHeader() (pyopenms.InspectOutfile method) readProblem() (pyopenms.LPWrapper method) readQuantData() (pyopenms.PeptideAndProteinQuant method) readSpectra() (pyopenms.MzMLSqliteHandler method) (pyopenms.SpectrumLookup method) (pyopenms.SpectrumMetaDataLookup method) readStart() (pyopenms.FASTAFile method) readSwathWindows() (pyopenms.SwathWindowLoader method) RealMassDecomposer (class in pyopenms) reannotateTransitions() (pyopenms.MRMAssay method) reduce() (pyopenms.DistanceMatrix method) REFLECTRON (pyopenms.IonOpticsType attribute) ReflectronState (pyopenms.MassAnalyzer attribute) registerName() (pyopenms.MetaInfoRegistry method) registerRun() (pyopenms.QcMLFile method) registerSet() (pyopenms.QcMLFile method) registry() (pyopenms.MetaInfo method) RegularSwathFileConsumer (class in pyopenms) relative_d (pyopenms.RANSACParam attribute) remove() (pyopenms.DataFilters method) (pyopenms.File method) (pyopenms.Param method) remove_overlapping_features() (pyopenms.MRMTransitionGroupPicker method) removeAdduct() (pyopenms.Compomer method) removeAll() (pyopenms.Param method) removeAllAttachments() (pyopenms.QcMLFile method) removeAllClusters() (pyopenms.ClusteringGrid method) removeAttachment() (pyopenms.QcMLFile method) removeBetaPeptideHits() (pyopenms.OPXLHelper method) removeCluster() (pyopenms.ClusteringGrid method) removeDecoyHits() (pyopenms.IDFilter method) removeDirRecursively() (pyopenms.File method) removeDuplicatePeptideHits() (pyopenms.IDFilter method) removeEmptyIdentifications() (pyopenms.IDFilter method) removeHitsMatchingProteins() (pyopenms.IDFilter 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.Instrument method) (pyopenms.InstrumentSettings method) (pyopenms.IntegerDataArray method) (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) (pyopenms.MetaInfoDescription method) (pyopenms.MetaInfoInterface method) (pyopenms.Modification 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.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.SpectrumSettings method) (pyopenms.StringDataArray method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TraMLProduct method) removeOutliersIterative() (pyopenms.MRMRTNormalizer method) removeOutliersRANSAC() (pyopenms.MRMRTNormalizer method) removePeaks() (pyopenms.SpectrumHelper method) removePeptidesWithMatchingModifications() (pyopenms.IDFilter method) removePeptidesWithMatchingSequences() (pyopenms.IDFilter method) removeQualityParameter() (pyopenms.QcMLFile method) removeTreatment() (pyopenms.Sample method) removeUnreferencedProteins() (pyopenms.IDFilter method) removeValue() (pyopenms.MetaInfo method) rename() (pyopenms.File method) renormalize() (pyopenms.IsotopeDistribution method) 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.Protein method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation 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.Protein method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TraMLProduct method) RequirementLevel (pyopenms.CVMappingRule attribute) resample() (pyopenms.ConsensusMapNormalizerAlgorithmQuantile method) reserve() (pyopenms.ConsensusMap method) (pyopenms.FloatDataArray method) (pyopenms.IntegerDataArray method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) reserveSpaceChromatograms() (pyopenms.MSExperiment method) reserveSpaceSpectra() (pyopenms.MSExperiment method) reset() (pyopenms.IsobaricQuantifierStatistics method) (pyopenms.MSExperiment method) (pyopenms.QcMLFile method) (pyopenms.XMLHandler method) resetInterpretations() (pyopenms.TraMLProduct method) Residue (class in pyopenms) ResidueDB (class in pyopenms) ResidueModification (class in pyopenms) ResidueType (pyopenms.Residue attribute) residueTypeToIonLetter() (pyopenms.Residue method) resize() (pyopenms.AcquisitionInfo method) (pyopenms.DistanceMatrix method) (pyopenms.FloatDataArray method) (pyopenms.IntegerDataArray method) (pyopenms.IsotopeDistribution method) (pyopenms.MatrixDouble method) (pyopenms.MSChromatogram method) (pyopenms.MSExperiment method) (pyopenms.MSSpectrum method) (pyopenms.StringDataArray method) resolution_l (pyopenms.MRMFQC_ComponentGroupPairQCs attribute) resolution_pair_name (pyopenms.MRMFQC_ComponentGroupPairQCs attribute) resolution_u (pyopenms.MRMFQC_ComponentGroupPairQCs attribute) ResolutionMethod (pyopenms.MassAnalyzer attribute) ResolutionType (pyopenms.MassAnalyzer attribute) resolve() (pyopenms.IDConflictResolverAlgorithm method) resolveBetweenFeatures() (pyopenms.IDConflictResolverAlgorithm method) resolveConnectedComponent() (pyopenms.PeptideProteinResolution method) resolveGraph() (pyopenms.PeptideProteinResolution method) resolveOverlappingTargetDecoyMassesByDecoyMassShift() (pyopenms.MetaboTargetedTargetDecoy method) restrictTransitions() (pyopenms.MRMAssay method) result_windows_even (pyopenms.NoiseEstimator attribute) result_windows_odd (pyopenms.NoiseEstimator attribute) retention_time_l (pyopenms.MRMFQC_ComponentGroupQCs attribute) (pyopenms.MRMFQC_ComponentQCs attribute) retention_time_type (pyopenms.RetentionTime attribute) retention_time_u (pyopenms.MRMFQC_ComponentGroupQCs attribute) (pyopenms.MRMFQC_ComponentQCs attribute) retention_time_unit (pyopenms.RetentionTime attribute) RetentionTime (class in pyopenms) retrieveSwathMaps() (pyopenms.CachedSwathFileConsumer method) (pyopenms.MzMLSwathFileConsumer method) (pyopenms.RegularSwathFileConsumer method) RETURN_STATUS (pyopenms.NonNegativeLeastSquaresSolver attribute) reversePeptides() (pyopenms.DecoyGenerator method) reverseProtein() (pyopenms.DecoyGenerator method) Ribonucleotide (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) RNaseDB (class in pyopenms) RNaseDigestion (class in pyopenms) rocN() (pyopenms.FalseDiscoveryRate method) rows() (pyopenms.MatrixDouble method) RT (pyopenms.DimensionDescription attribute) rt (pyopenms.LightCompound attribute) RT (pyopenms.OSSpectrumMeta attribute) rt (pyopenms.SpectrumMetaData attribute) rt() (pyopenms.KDTreeFeatureMaps method) rt_diff_l (pyopenms.MRMFQC_ComponentGroupPairQCs attribute) rt_diff_u (pyopenms.MRMFQC_ComponentGroupPairQCs attribute) rt_difference (pyopenms.OpenSwath_Scores attribute) rt_end (pyopenms.ExtractionCoordinates attribute) rt_extraction_window (pyopenms.OSW_ChromExtractParams attribute) rt_start (pyopenms.ExtractionCoordinates attribute) rt_tolerance (pyopenms.SpectrumLookup attribute) rts (pyopenms.Compound attribute) (pyopenms.Peptide attribute) RTType (pyopenms.RetentionTime attribute) RTUnit (pyopenms.RetentionTime attribute) run() (pyopenms.AccurateMassSearchEngine method) (pyopenms.BasicProteinInferenceAlgorithm 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.FineIsotopePatternGenerator method) (pyopenms.LabeledPairFinder method) (pyopenms.MassTraceDetection method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.OpenPepXLAlgorithm method) (pyopenms.OpenPepXLLFAlgorithm method) (pyopenms.PeptideIndexing method) (pyopenms.PeptideProteinResolution method) (pyopenms.QTClusterFinder method) (pyopenms.SiriusExportAlgorithm method) (pyopenms.StablePairFinder method) (pyopenms.XFDRAlgorithm method) runOnCandidates() (pyopenms.FeatureFinderIdentificationAlgorithm method) S sameNrOfMSFilesPerFraction() (pyopenms.ExperimentalDesign method) Sample (class in pyopenms) sample (pyopenms.ExperimentalDesign_MSFileSectionEntry attribute) sample_name (pyopenms.AQS_runConcentration attribute) SampleState (pyopenms.Sample attribute) SavitzkyGolayFilter (class in pyopenms) scan_index_heavy (pyopenms.CrossLinkSpectrumMatch attribute) scan_index_light (pyopenms.CrossLinkSpectrumMatch attribute) scan_number (pyopenms.SpectrumMetaData attribute) ScanDirection (pyopenms.MassAnalyzer attribute) ScanLaw (pyopenms.MassAnalyzer attribute) ScanMode (class in pyopenms) scans (pyopenms.IsotopeCluster attribute) ScanWindow (class in pyopenms) score (pyopenms.CrossLinkSpectrumMatch attribute) (pyopenms.MorpheusScore_Result attribute) (pyopenms.TSE_Match attribute) score_type (pyopenms.PeptideHit_AnalysisResult attribute) score_with_isotopes() (pyopenms.DIAScoring method) scoreMap() (pyopenms.ConfidenceScoring method) scorePeakgroups() (pyopenms.MRMFeatureFinderScoring method) scoreSpectra() (pyopenms.TargetedSpectraExtractor method) search() (pyopenms.SimpleSearchEngineAlgorithm method) searchModifications() (pyopenms.CrossLinksDB method) (pyopenms.ModificationsDB method) searchModificationsByDiffMonoMass() (pyopenms.CrossLinksDB method) (pyopenms.ModificationsDB method) SearchParameters (class in pyopenms) searchSpectrum() (pyopenms.TargetedSpectraExtractor method) second (pyopenms.ProbablePhosphoSites attribute) (pyopenms.TM_DataPoint attribute) Seed (class in pyopenms) SeedListGenerator (class in pyopenms) select() (pyopenms.MSSpectrum method) SELECTED_ION_FLOW_TUBE (pyopenms.IonOpticsType attribute) selectSpectra() (pyopenms.TargetedSpectraExtractor method) SemanticValidator (class in pyopenms) SemanticValidator_CVTerm (class in pyopenms) Sense (pyopenms.LPWrapper attribute) seq_1 (pyopenms.ProbablePhosphoSites attribute) seq_2 (pyopenms.ProbablePhosphoSites attribute) sequence (pyopenms.FASTAEntry attribute) (pyopenms.LightCompound attribute) (pyopenms.LightProtein attribute) (pyopenms.Peptide attribute) (pyopenms.Protein attribute) 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) set_matrix() (pyopenms.MatrixDouble method) set_peaks() (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum 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) setAffectedAminoAcids() (pyopenms.Modification method) setAllowChildren() (pyopenms.CVMappingTerm method) setAllowIsotopeError() (pyopenms.XTandemInfile method) setAmount() (pyopenms.Adduct method) setAnalysisResults() (pyopenms.PeptideHit method) setAtomicNumber() (pyopenms.Element method) setAverageMass() (pyopenms.ResidueModification method) setAverageWeight() (pyopenms.Element method) (pyopenms.Residue method) setAvgMass() (pyopenms.Ribonucleotide method) setBackboneBasicityLeft() (pyopenms.Residue method) setBackboneBasicityRight() (pyopenms.Residue method) setBaselossFormula() (pyopenms.Ribonucleotide method) setBaseName() (pyopenms.PeptideIdentification method) setBlind() (pyopenms.InspectInfile method) setBoundary() (pyopenms.MascotInfile method) setCalculatedMZ() (pyopenms.AccurateMassSearchResult method) setCentroidSD() (pyopenms.Kernel_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) setCharges() (pyopenms.MascotInfile 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.MSExperiment method) setChromatogramType() (pyopenms.ChromatogramSettings method) (pyopenms.MSChromatogram method) setCleavage() (pyopenms.MascotInfile method) setCleavageSite() (pyopenms.XTandemInfile method) setCode() (pyopenms.Ribonucleotide method) setCoefficientLimits() (pyopenms.MZTrafoModel method) setCoefficients() (pyopenms.MZTrafoModel method) setColumn() (pyopenms.HPLC method) setColumnBounds() (pyopenms.LPWrapper method) setColumnHeaders() (pyopenms.ConsensusMap method) setColumnName() (pyopenms.LPWrapper method) setColumnType() (pyopenms.LPWrapper method) setCombinationsLogic() (pyopenms.CVMappingRule method) setCometID() (pyopenms.DigestionEnzymeProtein method) setComment() (pyopenms.ChromatogramSettings method) (pyopenms.ExperimentalSettings method) (pyopenms.HPLC method) (pyopenms.Modification 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.Protein method) (pyopenms.Publication method) (pyopenms.ReactionMonitoringTransition method) (pyopenms.RetentionTime method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation 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) setDB() (pyopenms.MascotInfile 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) setDigestionTime() (pyopenms.Digestion method) setDriftTime() (pyopenms.LightCompound method) (pyopenms.MSSpectrum method) (pyopenms.Precursor method) setDriftTimeUnit() (pyopenms.MSSpectrum method) setDriftTimeWindowLowerOffset() (pyopenms.Precursor method) setDriftTimeWindowUpperOffset() (pyopenms.Precursor method) setEdgeScore() (pyopenms.ChargePair method) setElement() (pyopenms.IMSAlphabet method) (pyopenms.LPWrapper method) setElementIndex() (pyopenms.ChargePair method) setElementPath() (pyopenms.CVMappingRule method) setEmail() (pyopenms.ContactPerson method) setEmpiricalFormula() (pyopenms.AccurateMassSearchResult method) setEnd() (pyopenms.PeptideEvidence method) setEnzyme() (pyopenms.Digestion method) (pyopenms.EnzymaticDigestion method) (pyopenms.InspectInfile method) (pyopenms.ProteaseDigestion method) (pyopenms.RNaseDigestion method) (pyopenms.SequestInfile method) setExcludeTargets() (pyopenms.TargetedExperiment method) setExpectedSize() (pyopenms.CachedSwathFileConsumer 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.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) setFeatureName() (pyopenms.AbsoluteQuantitationMethod 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.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) setFormVersion() (pyopenms.MascotInfile method) setFoundAdduct() (pyopenms.AccurateMassSearchResult 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) setFullId() (pyopenms.ResidueModification method) setFullName() (pyopenms.ResidueModification method) setGradient() (pyopenms.HPLC method) setHigherScoreBetter() (pyopenms.PeptideIdentification method) (pyopenms.ProteinIdentification method) setHits() (pyopenms.MascotInfile method) (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) setInchiString() (pyopenms.SpectralMatch method) setIncludeTargets() (pyopenms.TargetedExperiment 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.MascotInfile method) (pyopenms.MSExperiment method) setInstruments() (pyopenms.TargetedExperiment method) setInstrumentSettings() (pyopenms.ChromatogramSettings method) (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) (pyopenms.SpectrumSettings method) setIntegerDataArrays() (pyopenms.MSChromatogram method) (pyopenms.MSSpectrum method) setIntensity() (pyopenms.BaseFeature method) (pyopenms.ChromatogramPeak method) (pyopenms.ConsensusFeature method) (pyopenms.Feature method) (pyopenms.FeatureHandle method) (pyopenms.MRMFeature method) (pyopenms.Peak1D method) (pyopenms.Peak2D method) (pyopenms.Precursor method) (pyopenms.RichPeak2D method) setIntensity32Bit() (pyopenms.PeakFileOptions method) setIntensityArray() (pyopenms.OSChromatogram method) (pyopenms.OSSpectrum method) setIntensityRange() (pyopenms.FeatureFileOptions method) (pyopenms.PeakFileOptions method) setIntermediateProducts() (pyopenms.ReactionMonitoringTransition method) setInterpolationStep() (pyopenms.EmgModel method) (pyopenms.InterpolationModel 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) setIsotopeDistribution() (pyopenms.Element method) (pyopenms.IMSElement method) setIsotopesSimScore() (pyopenms.AccurateMassSearchResult method) setIsRepeatable() (pyopenms.CVMappingTerm method) setLabel() (pyopenms.Kernel_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.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.CachedMzMLHandler method) (pyopenms.ChromatogramExtractor method) (pyopenms.ChromatogramExtractorAlgorithm method) (pyopenms.DTA2DFile method) (pyopenms.ElutionPeakDetection method) (pyopenms.FeatureFindingMetabo method) (pyopenms.FeatureGroupingAlgorithmKD method) (pyopenms.GaussFilter method) (pyopenms.InternalCalibration method) (pyopenms.LabeledPairFinder method) (pyopenms.LinearResampler method) (pyopenms.LinearResamplerAlign method) (pyopenms.MapAlignmentAlgorithmIdentification method) (pyopenms.MapAlignmentAlgorithmPoseClustering method) (pyopenms.MascotGenericFile method) (pyopenms.MascotInfile method) (pyopenms.MasstraceCorrelator method) (pyopenms.MassTraceDetection method) (pyopenms.MetaboliteSpectralMatching method) (pyopenms.MorphologicalFilter method) (pyopenms.MRMAssay method) (pyopenms.MRMDecoy method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MS2File method) (pyopenms.MzDataFile method) (pyopenms.MzIdentMLFile method) (pyopenms.MzMLFile method) (pyopenms.MzXMLFile method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) (pyopenms.ProgressLogger method) (pyopenms.QcMLFile method) (pyopenms.QTClusterFinder method) (pyopenms.SavitzkyGolayFilter method) (pyopenms.SimpleSearchEngineAlgorithm method) (pyopenms.StablePairFinder method) (pyopenms.SwathFile 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.Modification method) (pyopenms.Sample method) setMassAnalyzers() (pyopenms.Instrument method) setMassDiff() (pyopenms.ChargePair method) setMassShift() (pyopenms.Tagging method) setMasstraceIntensities() (pyopenms.AccurateMassSearchResult method) setMassType() (pyopenms.MascotInfile 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) setMaxAAPerModPerPeptide() (pyopenms.SequestInfile method) setMaxCharge() (pyopenms.Tagger method) setMaxDataPoolSize() (pyopenms.PeakFileOptions method) setMaxFloat() (pyopenms.Param method) setMaxInt() (pyopenms.Param method) setMaxInternalCleavageSites() (pyopenms.SequestInfile method) setMaxIsotope() (pyopenms.CoarseIsotopePatternGenerator method) setMaxModifications() (pyopenms.ModificationDefinitionsSet method) setMaxModsPerPeptide() (pyopenms.SequestInfile method) setMaxOccurrences() (pyopenms.ModificationDefinition method) setMaxPrecursorCharge() (pyopenms.XTandemInfile method) setMaxPTMsize() (pyopenms.InspectInfile method) setMaxValidEValue() (pyopenms.XTandemInfile 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.Instrument method) (pyopenms.InstrumentSettings method) (pyopenms.IntegerDataArray method) (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) (pyopenms.MetaInfoDescription method) (pyopenms.MetaInfoInterface method) (pyopenms.Modification 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.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.SpectrumSettings method) (pyopenms.StringDataArray method) (pyopenms.TargetedExperiment_Instrument method) (pyopenms.TargetedExperiment_Interpretation method) (pyopenms.TraMLProduct method) setMetaValues() (pyopenms.MetaInfoInterface method) setMethodOfCombination() (pyopenms.AcquisitionInfo method) setMinFloat() (pyopenms.Param method) setMinInt() (pyopenms.Param method) setMissedCleavages() (pyopenms.EnzymaticDigestion method) (pyopenms.MascotInfile method) (pyopenms.ProteaseDigestion method) (pyopenms.RNaseDigestion 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.MascotInfile method) (pyopenms.ModificationDefinitionsSet method) (pyopenms.XTandemInfile method) setModificationsPerPeptide() (pyopenms.InspectInfile method) setMonoMass() (pyopenms.ResidueModification method) (pyopenms.Ribonucleotide method) setMonoWeight() (pyopenms.Element method) (pyopenms.Residue method) setMS1Map() (pyopenms.MRMFeatureFinderScoring method) setMSData() (pyopenms.FeatureFinderAlgorithmMetaboIdent method) (pyopenms.FeatureFinderIdentificationAlgorithm method) setMSFileSection() (pyopenms.ExperimentalDesign method) setMSGFID() (pyopenms.DigestionEnzymeProtein method) setMSLevel() (pyopenms.MSSpectrum method) setMSLevels() (pyopenms.PeakFileOptions 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) setMZErrorPPM() (pyopenms.AccurateMassSearchResult method) setMZRange() (pyopenms.FeatureFileOptions method) (pyopenms.PeakFileOptions method) setName() (pyopenms.AbsoluteQuantitation method) (pyopenms.AccurateMassSearchEngine method) (pyopenms.AScore method) (pyopenms.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.ConsensusIDAlgorithm method) (pyopenms.ConsensusIDAlgorithmAverage method) (pyopenms.ConsensusIDAlgorithmBest method) (pyopenms.ConsensusIDAlgorithmIdentity method) (pyopenms.ConsensusIDAlgorithmPEPIons method) (pyopenms.ConsensusIDAlgorithmPEPMatrix method) (pyopenms.ConsensusIDAlgorithmRanks method) (pyopenms.ConsensusIDAlgorithmSimilarity method) (pyopenms.ConsensusIDAlgorithmWorst method) (pyopenms.ContactPerson method) (pyopenms.CVReference method) (pyopenms.CVTerm method) (pyopenms.DIAScoring method) (pyopenms.DigestionEnzyme method) (pyopenms.DigestionEnzymeProtein method) (pyopenms.DigestionEnzymeRNA method) (pyopenms.Element method) (pyopenms.ElutionModelFitter method) (pyopenms.ElutionPeakDetection 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.FloatDataArray method) (pyopenms.GaussFilter method) (pyopenms.GNPSMGFFile method) (pyopenms.IDDecoyProbability method) (pyopenms.IDMapper method) (pyopenms.IDRipper method) (pyopenms.IMSElement method) (pyopenms.IncludeExcludeTarget method) (pyopenms.Instrument method) (pyopenms.IntegerDataArray method) (pyopenms.IsobaricChannelExtractor method) (pyopenms.IsobaricQuantifier method) (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.KDTreeFeatureMaps method) (pyopenms.LabeledPairFinder method) (pyopenms.LinearResampler 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.MorphologicalFilter method) (pyopenms.MRMFeatureFilter method) (pyopenms.MRMFeatureFinderScoring method) (pyopenms.MRMMapping method) (pyopenms.MRMTransitionGroupPicker method) (pyopenms.MSChromatogram method) (pyopenms.MSPGenericFile method) (pyopenms.MSSpectrum method) (pyopenms.MultiplexDeltaMassesGenerator method) (pyopenms.NLargest method) (pyopenms.Normalizer method) (pyopenms.NucleicAcidSpectrumGenerator method) (pyopenms.OpenPepXLAlgorithm method) (pyopenms.OpenPepXLLFAlgorithm method) (pyopenms.PeakIntegrator method) (pyopenms.PeakPickerChromatogram method) (pyopenms.PeakPickerHiRes method) (pyopenms.PeakPickerIterative method) (pyopenms.PeptideAndProteinQuant method) (pyopenms.PeptideIndexing method) (pyopenms.PosteriorErrorProbabilityModel 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.SimpleSearchEngineAlgorithm method) (pyopenms.SimpleTSGXLMS method) (pyopenms.SiriusExportAlgorithm method) (pyopenms.Software method) (pyopenms.SpectraMerger method) (pyopenms.SpectrumAlignment method) (pyopenms.SpectrumAlignmentScore method) (pyopenms.SpectrumAnnotator method) (pyopenms.SqrtScaler method) (pyopenms.StablePairFinder method) (pyopenms.StringDataArray 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.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 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) setObjective() (pyopenms.LPWrapper method) setObjectiveSense() (pyopenms.LPWrapper 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 method) setOptions() (pyopenms.FeatureXMLFile method) (pyopenms.FileHandler method) (pyopenms.IndexedMzMLFileLoader method) (pyopenms.MzDataFile method) (pyopenms.MzMLFile method) (pyopenms.MzXMLFile method) (pyopenms.PlainMSDataWritingConsumer method) setOrder() (pyopenms.IonDetector method) (pyopenms.IonSource method) (pyopenms.MassAnalyzer method) setOrganism() (pyopenms.Sample method) setOrigin() (pyopenms.ResidueModification method) (pyopenms.Ribonucleotide 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.BasicProteinInferenceAlgorithm method) (pyopenms.BayesianProteinInferenceAlgorithm method) (pyopenms.ConsensusIDAlgorithm method) (pyopenms.ConsensusIDAlgorithmAverage method) (pyopenms.ConsensusIDAlgorithmBest method) (pyopenms.ConsensusIDAlgorithmIdentity method) (pyopenms.ConsensusIDAlgorithmPEPIons method) (pyopenms.ConsensusIDAlgorithmPEPMatrix method) (pyopenms.ConsensusIDAlgorithmRanks method) (pyopenms.ConsensusIDAlgorithmSimilarity method) (pyopenms.ConsensusIDAlgorithmWorst method) (pyopenms.DIAScoring method) (pyopenms.ElutionModelFitter method) (pyopenms.ElutionPeakDetection 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.GaussFilter method) (pyopenms.GNPSMGFFile method) (pyopenms.IDDecoyProbability method) (pyopenms.IDMapper method) (pyopenms.IDRipper method) (pyopenms.IsobaricChannelExtractor method) (pyopenms.IsobaricQuantifier method) (pyopenms.ItraqEightPlexQuantitationMethod method) (pyopenms.ItraqFourPlexQuantitationMethod method) (pyopenms.KDTreeFeatureMaps method) (pyopenms.LabeledPairFinder method) (pyopenms.LinearResampler 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 meth
