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