Index

A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z

A

acquisitionAxisCode (ccpn.core.Spectrum.Spectrum attribute)
add() (ccpn.AnalysisMetabolomics.lib.commands.Command method)
(ccpn.util.OrderedSet.OrderedSet method)
addApplicationMenuSpec() (ccpn.framework.Framework.Framework method)
addAssignment() (ccpn.core.Peak.Peak method)
addAtomId() (ccpn.core.StructureEnsemble.StructureEnsemble method)
addAtomIds() (ccpn.core.StructureEnsemble.StructureEnsemble method)
addBlankDisplay() (ccpn.framework.Framework.Framework method)
addChain() (ccpn.core.StructureEnsemble.StructureEnsemble method)
addColumn() (ccpn.util.Bmrb.bmrb.loop method)
addData() (ccpn.util.Bmrb.bmrb.loop method)
addDataByColumn() (ccpn.util.Bmrb.bmrb.loop method)
addFiles() (ccpn.framework.update.UpdateAgent.UpdateAgent method)
addInterAtomBond() (ccpn.core.Atom.Atom method)
additionalLowerLimit (ccpn.core.Restraint.Restraint attribute)
(ccpn.core.RestraintContribution.RestraintContribution attribute)
additionalUpperLimit (ccpn.core.Restraint.Restraint attribute)
(ccpn.core.RestraintContribution.RestraintContribution attribute)
addLoop() (ccpn.util.Bmrb.bmrb.saveframe method)
addMenu() (ccpn.ui.Ui.Ui method)
addMethod() (ccpn.AnalysisMetabolomics.MetabolomicsPipeline.PipelineWidgets method)
addNmratom() (ccpn.framework.Current.Current method)
addNmrchain() (ccpn.framework.Current.Current method)
addNmrChainToPulldown() (ccpn.AnalysisAssign.modules.SequenceGraph.SequenceGraph method)
addNmrresidue() (ccpn.framework.Current.Current method)
addPeak() (ccpn.framework.Current.Current method)
addPosition() (ccpn.framework.Current.Current method)
addResidue() (ccpn.AnalysisAssign.modules.SequenceGraph.SequenceGraph method)
addRestraintItem() (ccpn.core.RestraintContribution.RestraintContribution method)
addRow() (ccpn.AnalysisMetabolomics.MetabolomicsPipeline.PipelineWidgets method)
addSaveframe() (ccpn.util.Bmrb.bmrb.entry method)
addSideChainAtoms() (ccpn.AnalysisAssign.modules.SequenceGraph.SequenceGraph method)
addTag() (ccpn.util.Bmrb.bmrb.saveframe method)
addTags() (ccpn.util.Bmrb.bmrb.saveframe method)
aliasingLimits (ccpn.core.Spectrum.Spectrum attribute)
alignNmrChain() (in module ccpn.core.lib.DataIo)
AlignSpectra (class in ccpn.AnalysisMetabolomics.GuiPipeLine)
alignSpectra() (in module ccpn.AnalysisMetabolomics.Pipeline)
AlignToReference (class in ccpn.AnalysisMetabolomics.GuiPipeLine)
alignToReference() (in module ccpn.AnalysisMetabolomics.Pipeline)
allCombinations() (in module ccpn.AnalysisScreen.lib.MixtureGeneration)
amount (ccpn.core.Sample.Sample attribute)
amountUnit (ccpn.core.Sample.Sample attribute)
annealMixtures() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
annotation (ccpn.core.Integral.Integral attribute)
(ccpn.core.Peak.Peak attribute)
applyPreferences() (ccpn.framework.Framework.Framework method)
archiveProject() (ccpn.framework.Framework.Framework method)
Arguments (class in ccpn.framework.Framework)
Assign (class in ccpn.AnalysisAssign.AnalysisAssign)
assignAlphas() (in module ccpn.core.lib.AssignmentLib)
assignAndMove() (ccpn.AnalysisMetabolomics.IntegralAssignment.IntegralAssignment method)
(ccpn.AnalysisMetabolomics.PeakAssignment.PeakAssignment method)
assignBetas() (in module ccpn.core.lib.AssignmentLib)
assignConnectedResidues() (ccpn.core.NmrChain.NmrChain method)
assignDimension() (ccpn.core.Peak.Peak method)
assignedNmrAtoms (ccpn.core.Peak.Peak attribute)
assignedPeaks (ccpn.core.NmrAtom.NmrAtom attribute)
assignIntegral() (ccpn.AnalysisMetabolomics.IntegralAssignment.IntegralAssignment method)
AssignmentLine (class in ccpn.AnalysisAssign.modules.SequenceGraph)
assignmentTolerances (ccpn.core.Spectrum.Spectrum attribute)
assignPeak() (ccpn.AnalysisMetabolomics.PeakAssignment.PeakAssignment method)
assignTo() (ccpn.core.NmrAtom.NmrAtom method)
(ccpn.core.NmrResidue.NmrResidue method)
atom (ccpn.core.NmrAtom.NmrAtom attribute)
Atom (class in ccpn.core.Atom)
atomCount (ccpn.core.Substance.Substance attribute)
atomIds (ccpn.core.StructureEnsemble.StructureEnsemble attribute)
AtomIdTuple (class in ccpn.core.lib.Util)
atomLabelingFractions() (in module ccpn.core.lib.LabelingLib)
atomName (ccpn.core.lib.Util.AtomIdTuple attribute)
atomNameData (ccpn.core.Model.Model attribute)
(ccpn.core.StructureEnsemble.StructureEnsemble attribute)
atomPairLabelingFractions() (in module ccpn.core.lib.LabelingLib)
atoms (ccpn.core.Chain.Chain attribute)
(ccpn.core.Project.Project attribute)
(ccpn.core.Residue.Residue attribute)
AtomSelector (class in ccpn.AnalysisAssign.modules.AtomSelector)
attachedObject (ccpn.core.Data.Data attribute)
attachedObjectPid (ccpn.core.Data.Data attribute)
AttrDict (class in ccpn.util.AttrDict)
autodoc_process_docstring() (in module ccpn.util.SphinxExtensions)
autodoc_process_signature() (in module ccpn.util.SphinxExtensions)
automaticIntegration() (ccpn.core.Spectrum.Spectrum method)
AutoPick (class in ccpn.AnalysisMetabolomics.PickandFit)
autoScale() (in module ccpn.AnalysisMetabolomics.lib.scaling)
(in module ccpn.AnalysisMetabolomics.Pipeline)
autoUpdate (ccpn.core.ChemicalShiftList.ChemicalShiftList attribute)
axes (ccpn.core.Project.Project attribute)
axial (ccpn.util.Tensor.Tensor attribute)
axisCode (ccpn.core.PseudoDimension.PseudoDimension attribute)
(ccpn.core.SpectrumReference.SpectrumReference attribute)
axisCodes (ccpn.core.Integral.Integral attribute)
(ccpn.core.Peak.Peak attribute)
(ccpn.core.Spectrum.Spectrum attribute)
axisParameter (ccpn.core.PseudoDimension.PseudoDimension attribute)
axisUnit (ccpn.core.PseudoDimension.PseudoDimension attribute)
(ccpn.core.SpectrumReference.SpectrumReference attribute)
axisUnits (ccpn.core.Spectrum.Spectrum attribute)

B

BackboneAssignmentModule (class in ccpn.AnalysisAssign.modules.BackboneAssignmentModule)
batchIdentifier (ccpn.core.Sample.Sample attribute)
bestMatch() (in module ccpn.AnalysisScreen.lib.MixtureGeneration)
bFactorData (ccpn.core.Model.Model attribute)
(ccpn.core.StructureEnsemble.StructureEnsemble attribute)
bias (ccpn.core.Integral.Integral attribute)
Bin (class in ccpn.AnalysisMetabolomics.GuiPipeLine)
bin() (in module ccpn.AnalysisMetabolomics.Pipeline)
blankNotification() (ccpn.core.Project.Project method)
blocking (ccpn.util.Undo.Undo attribute)
bmrb_id (ccpn.util.Bmrb.bmrb.entry attribute)
bondCount (ccpn.core.Substance.Substance attribute)
Borg (class in ccpn.AnalysisMetabolomics.lib.persistence)
boundAtoms (ccpn.core.Atom.Atom attribute)
boundNmrAtoms (ccpn.core.NmrAtom.NmrAtom attribute)
boxWidths (ccpn.core.Peak.Peak attribute)
bruker1dDict() (in module ccpn.AnalysisMetabolomics.lib.persistence)
buildSourceData() (ccpn.AnalysisMetabolomics.Decomposition.Decomposition method)

C

calcHashCode() (in module ccpn.framework.update.UpdateAgent)
calculateOverlapCount() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
calculateTotalScore() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
calculationStep (ccpn.core.Data.Data attribute)
CalculationStep (class in ccpn.core.CalculationStep)
calculationSteps (ccpn.core.DataSet.DataSet attribute)
(ccpn.core.Project.Project attribute)
callback() (ccpn.AnalysisMetabolomics.PeakAssignment.PeakAssignment method)
canRedo() (ccpn.util.Undo.Undo method)
canUndo() (ccpn.util.Undo.Undo method)
casNumber (ccpn.core.Substance.Substance attribute)
category (ccpn.util.Bmrb.bmrb.loop attribute)
ccpn (module)
ccpn.AnalysisAssign (module)
ccpn.AnalysisAssign.AnalysisAssign (module)
ccpn.AnalysisAssign.modules (module)
ccpn.AnalysisAssign.modules.AtomSelector (module)
ccpn.AnalysisAssign.modules.BackboneAssignmentModule (module)
ccpn.AnalysisAssign.modules.ModifyAssignmentModule (module)
ccpn.AnalysisAssign.modules.PickAndAssignModule (module)
ccpn.AnalysisAssign.modules.SequenceGraph (module)
ccpn.AnalysisAssign.modules.SideChainAssignmentModule (module)
ccpn.AnalysisMetabolomics (module)
ccpn.AnalysisMetabolomics.AnalysisMetabolomics (module)
ccpn.AnalysisMetabolomics.Decomposition (module)
ccpn.AnalysisMetabolomics.GuiPipeLine (module)
ccpn.AnalysisMetabolomics.IntegralAssignment (module)
ccpn.AnalysisMetabolomics.Integration (module)
ccpn.AnalysisMetabolomics.lib (module)
ccpn.AnalysisMetabolomics.lib.centering (module)
ccpn.AnalysisMetabolomics.lib.commands (module)
ccpn.AnalysisMetabolomics.lib.decomposition (module)
ccpn.AnalysisMetabolomics.lib.normalisation (module)
ccpn.AnalysisMetabolomics.lib.persistence (module)
ccpn.AnalysisMetabolomics.lib.pipeline (module)
ccpn.AnalysisMetabolomics.lib.scaling (module)
ccpn.AnalysisMetabolomics.lib.transformations (module)
ccpn.AnalysisMetabolomics.MetabolomicsPipeline (module)
ccpn.AnalysisMetabolomics.PeakAssignment (module)
ccpn.AnalysisMetabolomics.PickandFit (module)
ccpn.AnalysisMetabolomics.Pipeline (module)
ccpn.AnalysisScreen (module)
ccpn.AnalysisScreen.AnalysisScreen (module)
ccpn.AnalysisScreen.lib (module)
ccpn.AnalysisScreen.lib.MixtureGeneration (module)
ccpn.AnalysisScreen.lib.MixturesGeneration (module)
ccpn.AnalysisScreen.lib.Screening (module)
ccpn.AnalysisScreen.lib.SimulatedAnnealing (module)
ccpn.AnalysisScreen.modules (module)
ccpn.AnalysisScreen.modules.Display1DWidget (module)
ccpn.AnalysisScreen.modules.MixtureOptimisation (module)
ccpn.AnalysisScreen.popups (module)
ccpn.AnalysisScreen.popups.LookupSetupPopup (module)
ccpn.core (module)
ccpn.core.Atom (module)
ccpn.core.CalculationStep (module)
ccpn.core.Chain (module)
ccpn.core.ChemicalShift (module)
ccpn.core.ChemicalShiftList (module)
ccpn.core.Complex (module)
ccpn.core.Data (module)
ccpn.core.DataSet (module)
ccpn.core.Integral (module)
ccpn.core.IntegralList (module)
ccpn.core.lib (module)
ccpn.core.lib.AssignmentLib (module)
ccpn.core.lib.CcpnNefIo (module)
ccpn.core.lib.CcpnSorting (module)
ccpn.core.lib.DataIo (module)
ccpn.core.lib.Documentation (module)
ccpn.core.lib.LabelingLib (module)
ccpn.core.lib.MoleculeLib (module)
ccpn.core.lib.Pid (module)
ccpn.core.lib.RestraintLib (module)
ccpn.core.lib.SpectrumLib (module)
ccpn.core.lib.Util (module)
ccpn.core.Model (module)
ccpn.core.NmrAtom (module)
ccpn.core.NmrChain (module)
ccpn.core.NmrResidue (module)
ccpn.core.Note (module)
ccpn.core.Peak (module)
ccpn.core.PeakList (module)
ccpn.core.Project (module)
ccpn.core.PseudoDimension (module)
ccpn.core.Residue (module)
ccpn.core.Restraint (module)
ccpn.core.RestraintContribution (module)
ccpn.core.RestraintList (module)
ccpn.core.Sample (module)
ccpn.core.SampleComponent (module)
ccpn.core.Spectrum (module)
ccpn.core.SpectrumGroup (module)
ccpn.core.SpectrumHit (module)
ccpn.core.SpectrumReference (module)
ccpn.core.StructureEnsemble (module)
ccpn.core.Substance (module)
ccpn.framework (module)
ccpn.framework.Current (module)
ccpn.framework.Framework (module)
ccpn.framework.languages (module)
ccpn.framework.languages.Chinese (module)
ccpn.framework.languages.Dutch (module)
ccpn.framework.languages.French (module)
ccpn.framework.languages.Italiano (module)
ccpn.framework.PathsAndUrls (module)
ccpn.framework.Translation (module)
ccpn.framework.update (module)
ccpn.framework.update.UpdateAgent (module)
ccpn.framework.update.UpdatePopup (module)
ccpn.framework.Version (module)
ccpn.ui (module)
ccpn.ui.Ui (module)
ccpn.util (module)
ccpn.util.Anchor (module)
ccpn.util.AttrDict (module)
ccpn.util.Bmrb (module)
ccpn.util.Bmrb.bmrb (module)
ccpn.util.Bmrb.passthrough (module)
ccpn.util.Bmrb.testNef (module)
ccpn.util.Colour (module)
ccpn.util.Common (module)
ccpn.util.Constants (module)
ccpn.util.Graph (module)
ccpn.util.Hdf5 (module)
ccpn.util.jsonIo (module)
ccpn.util.LocalShutil (module)
ccpn.util.Logging (module)
ccpn.util.OrderedSet (module)
ccpn.util.Path (module)
ccpn.util.Phasing (module)
ccpn.util.recursive_import (module)
ccpn.util.Register (module)
ccpn.util.Sorting (module)
ccpn.util.SphinxExtensions (module)
ccpn.util.Tensor (module)
ccpn.util.Ticks (module)
ccpn.util.Time (module)
ccpn.util.Undo (module)
ccpn.util.updateHeader (module)
ccpn.util.Url (module)
CcpnNefReader (class in ccpn.core.lib.CcpnNefIo)
CcpnNefWriter (class in ccpn.core.lib.CcpnNefIo)
center() (ccpn.AnalysisMetabolomics.Decomposition.Decomposition method)
centering (ccpn.AnalysisMetabolomics.Decomposition.Decomposition attribute)
Centre (class in ccpn.AnalysisMetabolomics.GuiPipeLine)
chain (ccpn.core.NmrChain.NmrChain attribute)
(ccpn.core.Residue.Residue attribute)
Chain (class in ccpn.core.Chain)
chainCode (ccpn.core.lib.Util.AtomIdTuple attribute)
chains (ccpn.core.Project.Project attribute)
(ccpn.core.Substance.Substance attribute)
chains2Nef() (ccpn.core.lib.CcpnNefIo.CcpnNefWriter method)
checkFilePath() (in module ccpn.util.Path)
ChemicalShift (class in ccpn.core.ChemicalShift)
chemicalShiftList (ccpn.core.ChemicalShift.ChemicalShift attribute)
(ccpn.core.PeakList.PeakList attribute)
(ccpn.core.Spectrum.Spectrum attribute)
ChemicalShiftList (class in ccpn.core.ChemicalShiftList)
chemicalShiftList2Nef() (ccpn.core.lib.CcpnNefIo.CcpnNefWriter method)
chemicalShiftLists (ccpn.core.Project.Project attribute)
chemicalShifts (ccpn.core.ChemicalShiftList.ChemicalShiftList attribute)
(ccpn.core.NmrAtom.NmrAtom attribute)
(ccpn.core.Project.Project attribute)
className (ccpn.core.Atom.Atom attribute)
(ccpn.core.CalculationStep.CalculationStep attribute)
(ccpn.core.Chain.Chain attribute)
(ccpn.core.ChemicalShift.ChemicalShift attribute)
(ccpn.core.ChemicalShiftList.ChemicalShiftList attribute)
(ccpn.core.Complex.Complex attribute)
(ccpn.core.Data.Data attribute)
(ccpn.core.DataSet.DataSet attribute)
(ccpn.core.Integral.Integral attribute)
(ccpn.core.IntegralList.IntegralList attribute)
(ccpn.core.Model.Model attribute)
(ccpn.core.NmrAtom.NmrAtom attribute)
(ccpn.core.NmrChain.NmrChain attribute)
(ccpn.core.NmrResidue.NmrResidue attribute)
(ccpn.core.Note.Note attribute)
(ccpn.core.Peak.Peak attribute)
(ccpn.core.PeakList.PeakList attribute)
(ccpn.core.Project.Project attribute)
(ccpn.core.PseudoDimension.PseudoDimension attribute)
(ccpn.core.Residue.Residue attribute)
(ccpn.core.Restraint.Restraint attribute)
(ccpn.core.RestraintContribution.RestraintContribution attribute)
(ccpn.core.RestraintList.RestraintList attribute)
(ccpn.core.Sample.Sample attribute)
(ccpn.core.SampleComponent.SampleComponent attribute)
(ccpn.core.Spectrum.Spectrum attribute)
(ccpn.core.SpectrumGroup.SpectrumGroup attribute)
(ccpn.core.SpectrumHit.SpectrumHit attribute)
(ccpn.core.SpectrumReference.SpectrumReference attribute)
(ccpn.core.StructureEnsemble.StructureEnsemble attribute)
(ccpn.core.Substance.Substance attribute)
cleanUpDocrProject() (in module ccpn.core.lib.DataIo)
clear() (ccpn.util.Undo.Undo method)
clearAllItems() (ccpn.AnalysisAssign.modules.SequenceGraph.SequenceGraph method)
clearData() (ccpn.util.Bmrb.bmrb.loop method)
clearLogFile() (ccpn.framework.Framework.Framework method)
clearNmratoms() (ccpn.framework.Current.Current method)
clearNmrchains() (ccpn.framework.Current.Current method)
clearNmrresidues() (ccpn.framework.Current.Current method)
clearParameters() (ccpn.core.Data.Data method)
clearPeaks() (ccpn.framework.Current.Current method)
clearPositions() (ccpn.framework.Current.Current method)
clearRecentMacros() (ccpn.framework.Framework.Framework method)
clearRecentProjects() (ccpn.framework.Framework.Framework method)
clone() (ccpn.core.Chain.Chain method)
(ccpn.core.lib.Pid.Pid method)
closeModule() (ccpn.AnalysisAssign.modules.BackboneAssignmentModule.BackboneAssignmentModule method)
(ccpn.AnalysisAssign.modules.SequenceGraph.SequenceGraph method)
collapseXH3Groups() (in module ccpn.core.lib.DataIo)
Colour (class in ccpn.util.Colour)
columnNumber (ccpn.core.Sample.Sample attribute)
columns (ccpn.util.Bmrb.bmrb.loop attribute)
combinationId (ccpn.core.RestraintContribution.RestraintContribution attribute)
Command (class in ccpn.AnalysisMetabolomics.lib.commands)
commandParameterString() (in module ccpn.core.lib.Util)
comment (ccpn.core.Chain.Chain attribute)
(ccpn.core.ChemicalShift.ChemicalShift attribute)
(ccpn.core.ChemicalShiftList.ChemicalShiftList attribute)
(ccpn.core.DataSet.DataSet attribute)
(ccpn.core.Integral.Integral attribute)
(ccpn.core.IntegralList.IntegralList attribute)
(ccpn.core.Model.Model attribute)
(ccpn.core.NmrChain.NmrChain attribute)
(ccpn.core.NmrResidue.NmrResidue attribute)
(ccpn.core.Peak.Peak attribute)
(ccpn.core.PeakList.PeakList attribute)
(ccpn.core.PseudoDimension.PseudoDimension attribute)
(ccpn.core.Residue.Residue attribute)
(ccpn.core.Restraint.Restraint attribute)
(ccpn.core.RestraintList.RestraintList attribute)
(ccpn.core.Sample.Sample attribute)
(ccpn.core.SampleComponent.SampleComponent attribute)
(ccpn.core.Spectrum.Spectrum attribute)
(ccpn.core.SpectrumHit.SpectrumHit attribute)
(ccpn.core.StructureEnsemble.StructureEnsemble attribute)
(ccpn.core.Substance.Substance attribute)
comment() (ccpn.util.Bmrb.passthrough.Handler method)
commitChosen() (ccpn.framework.update.UpdateAgent.UpdateAgent method)
commitUpdate() (ccpn.framework.update.UpdateAgent.UpdateFile method)
commitUpdateDb() (ccpn.framework.update.UpdateAgent.UpdateAgent method)
commonSuperDirectory() (in module ccpn.util.Path)
compare() (ccpn.util.Bmrb.bmrb.entry method)
(ccpn.util.Bmrb.bmrb.loop method)
(ccpn.util.Bmrb.bmrb.saveframe method)
Complex (class in ccpn.core.Complex)
complexStoredBy (ccpn.core.Spectrum.Spectrum attribute)
compoundName (ccpn.core.Chain.Chain attribute)
concentration (ccpn.core.SampleComponent.SampleComponent attribute)
(ccpn.core.SpectrumHit.SpectrumHit attribute)
concentrationError (ccpn.core.SampleComponent.SampleComponent attribute)
(ccpn.core.SpectrumHit.SpectrumHit attribute)
concentrationUnit (ccpn.core.SampleComponent.SampleComponent attribute)
(ccpn.core.SpectrumHit.SpectrumHit attribute)
confidenceLimit (ccpn.AnalysisMetabolomics.lib.decomposition.PCA attribute)
confidenceLimits_ (ccpn.AnalysisMetabolomics.lib.decomposition.PCA attribute)
connectNext() (ccpn.core.NmrResidue.NmrResidue method)
connectPrevious() (ccpn.core.NmrResidue.NmrResidue method)
converseSplitPath() (in module ccpn.util.Path)
convert2NefString() (in module ccpn.core.lib.CcpnNefIo)
convertBmrbAmbiguousAtoms() (in module ccpn.core.lib.DataIo)
convertDataToHdf5() (in module ccpn.util.Hdf5)
convertStringToFileName() (in module ccpn.util.Common)
coordinateData (ccpn.core.Model.Model attribute)
(ccpn.core.StructureEnsemble.StructureEnsemble attribute)
copyPeakAssignments() (in module ccpn.core.lib.AssignmentLib)
copyPeakListAssignments() (in module ccpn.core.lib.AssignmentLib)
copytree() (in module ccpn.util.LocalShutil)
createChain() (ccpn.core.Project.Project method)
(ccpn.core.Substance.Substance method)
created (ccpn.core.Note.Note attribute)
createDummySpectrum() (ccpn.core.Project.Project method)
createId() (in module ccpn.core.lib.Pid)
createLogger() (in module ccpn.util.Logging)
createNewProject() (ccpn.framework.Framework.Framework method)
createPid() (in module ccpn.core.lib.Pid)
createPolymerSubstance() (ccpn.core.Project.Project method)
createSample() (in module ccpn.AnalysisScreen.lib.MixtureGeneration)
createSimpleRestraint() (ccpn.core.RestraintList.RestraintList method)
(in module ccpn.core.Restraint)
createSpectrum() (in module ccpn.core.lib.CcpnNefIo)
createStdDifferenceSpectrum() (in module ccpn.AnalysisScreen.lib.Screening)
creationDate (ccpn.core.DataSet.DataSet attribute)
(ccpn.core.Sample.Sample attribute)
Current (class in ccpn.framework.Current)
currentSpectrumGroup() (ccpn.AnalysisMetabolomics.MetabolomicsPipeline.GoArea method)
cursorPosition (ccpn.framework.Current.Current attribute)

D

data (ccpn.core.DataSet.DataSet attribute)
(ccpn.core.Project.Project attribute)
(ccpn.util.Bmrb.bmrb.loop attribute)
Data (class in ccpn.core.Data)
data() (ccpn.util.Bmrb.passthrough.Handler method)
dataPath (ccpn.core.DataSet.DataSet attribute)
dataSet (ccpn.core.CalculationStep.CalculationStep attribute)
(ccpn.core.RestraintList.RestraintList attribute)
DataSet (class in ccpn.core.DataSet)
dataSets (ccpn.core.Project.Project attribute)
deassign() (ccpn.core.NmrAtom.NmrAtom method)
(ccpn.core.NmrChain.NmrChain method)
(ccpn.core.NmrResidue.NmrResidue method)
deassignAndMove() (ccpn.AnalysisMetabolomics.IntegralAssignment.IntegralAssignment method)
(ccpn.AnalysisMetabolomics.PeakAssignment.PeakAssignment method)
deassignIntegral() (ccpn.AnalysisMetabolomics.IntegralAssignment.IntegralAssignment method)
deassignPeak() (ccpn.AnalysisMetabolomics.PeakAssignment.PeakAssignment method)
decodePid() (in module ccpn.core.lib.Pid)
decompose() (ccpn.AnalysisMetabolomics.Decomposition.Decomposition method)
Decomposition (class in ccpn.AnalysisMetabolomics.Decomposition)
decreaseBlocking() (ccpn.util.Undo.Undo method)
decrement() (ccpn.core.lib.Pid.Pid method)
defineProgramArguments() (in module ccpn.framework.Framework)
defineShortcut() (ccpn.framework.Framework.Framework method)
defineUserShortcuts() (ccpn.framework.Framework.Framework method)
delete() (ccpn.core.Project.Project method)
deleteCurrentVirtualSamples() (ccpn.AnalysisScreen.modules.MixtureOptimisation.MixtureOptimisation method)
deleteDataByTagValue() (ccpn.util.Bmrb.bmrb.loop method)
deleteObjects() (ccpn.core.Project.Project method)
deleteParameter() (ccpn.core.Data.Data method)
deletePath() (in module ccpn.util.Path)
deleteTag() (ccpn.util.Bmrb.bmrb.saveframe method)
descriptor (ccpn.core.Residue.Residue attribute)
dictionaryProduct() (in module ccpn.util.Common)
diff() (in module ccpn.util.Bmrb.bmrb)
diffUpdates() (ccpn.framework.update.UpdateAgent.UpdateAgent method)
dihedralName() (in module ccpn.core.lib.RestraintLib)
dimension (ccpn.core.PseudoDimension.PseudoDimension attribute)
(ccpn.core.SpectrumReference.SpectrumReference attribute)
dimension1 (ccpn.core.lib.SpectrumLib.MagnetisationTransferTuple attribute)
dimension2 (ccpn.core.lib.SpectrumLib.MagnetisationTransferTuple attribute)
dimensionCount (ccpn.core.Spectrum.Spectrum attribute)
dimensionNmrAtoms (ccpn.core.Peak.Peak attribute)
dimensionType (ccpn.core.PseudoDimension.PseudoDimension attribute)
(ccpn.core.SpectrumReference.SpectrumReference attribute)
dimensionTypes (ccpn.core.Spectrum.Spectrum attribute)
disableAddButton() (ccpn.AnalysisMetabolomics.MetabolomicsPipeline.PipelineWidgets method)
discard() (ccpn.util.OrderedSet.OrderedSet method)
disconnect() (ccpn.core.NmrResidue.NmrResidue method)
disconnectNext() (ccpn.core.NmrResidue.NmrResidue method)
disconnectNextNmrResidue() (ccpn.AnalysisAssign.modules.SequenceGraph.SequenceGraph method)
disconnectNmrResidue() (ccpn.AnalysisAssign.modules.SequenceGraph.SequenceGraph method)
disconnectPrevious() (ccpn.core.NmrResidue.NmrResidue method)
disconnectPreviousNmrResidue() (ccpn.AnalysisAssign.modules.SequenceGraph.SequenceGraph method)
Display1DWidget (class in ccpn.AnalysisScreen.modules.Display1DWidget)
displayProjectSummary() (ccpn.framework.Framework.Framework method)
divide() (ccpn.AnalysisMetabolomics.lib.commands.Command method)
downloadFile() (in module ccpn.framework.update.UpdateAgent)
dump() (in module ccpn.util.jsonIo)
dumps() (in module ccpn.util.jsonIo)
duplicateAtomBonds() (in module ccpn.core.lib.MoleculeLib)
duplicateNotifier() (ccpn.core.Project.Project method)

E

echoCommands() (ccpn.ui.Ui.TestUi method)
(ccpn.ui.Ui.Ui method)
eigenvalues_ (ccpn.AnalysisMetabolomics.lib.decomposition.PCA attribute)
empiricalFormula (ccpn.core.Substance.Substance attribute)
enableAddButton() (ccpn.AnalysisMetabolomics.MetabolomicsPipeline.PipelineWidgets method)
endData() (ccpn.util.Bmrb.passthrough.Handler method)
endLoop() (ccpn.util.Bmrb.passthrough.Handler method)
endSaveframe() (ccpn.util.Bmrb.passthrough.Handler method)
ensembleId (ccpn.core.StructureEnsemble.StructureEnsemble attribute)
entry (class in ccpn.util.Bmrb.bmrb)
error (ccpn.core.Restraint.Restraint attribute)
(ccpn.core.RestraintContribution.RestraintContribution attribute)
estimateNoise() (ccpn.core.Spectrum.Spectrum method)
(in module ccpn.AnalysisScreen.lib.Screening)
ExcludeBaselinePoints (class in ccpn.AnalysisMetabolomics.GuiPipeLine)
excludeBaselinePoints() (in module ccpn.AnalysisMetabolomics.Pipeline)
excludeRegions() (in module ccpn.AnalysisMetabolomics.Pipeline)
ExcludeSignalFreeRegions (class in ccpn.AnalysisMetabolomics.GuiPipeLine)
excludeSignalFreeRegions() (in module ccpn.AnalysisMetabolomics.Pipeline)
execute() (ccpn.core.Project.Project method)
expandDollarFilePath() (in module ccpn.core.lib.Util)
experimentName (ccpn.core.Spectrum.Spectrum attribute)
experimentType (ccpn.core.Spectrum.Spectrum attribute)
explainedVariance_ (ccpn.AnalysisMetabolomics.lib.decomposition.PCA attribute)
exponentialCooling() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
exportDataSet() (ccpn.core.lib.CcpnNefIo.CcpnNefWriter method)
exportProject() (ccpn.core.lib.CcpnNefIo.CcpnNefWriter method)
extend() (ccpn.core.lib.Pid.Pid method)
extraBoundAtomPairs() (in module ccpn.core.lib.MoleculeLib)
extractCyanaRestraints() (in module ccpn.core.lib.DataIo)

F

fetchDataSet() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
fetchNefSubstance() (ccpn.core.Project.Project method)
fetchNmrAtom() (ccpn.core.NmrResidue.NmrResidue method)
fetchNmrChain() (ccpn.core.Project.Project method)
fetchNmrResidue() (ccpn.core.NmrChain.NmrChain method)
fetchSubstance() (ccpn.core.Project.Project method)
fetchUpdateDb() (ccpn.framework.update.UpdateAgent.UpdateAgent method)
fetchUrl() (in module ccpn.util.Url)
fields (ccpn.core.lib.Pid.Pid attribute)
figureOfMerit (ccpn.core.ChemicalShift.ChemicalShift attribute)
(ccpn.core.Integral.Integral attribute)
(ccpn.core.Peak.Peak attribute)
(ccpn.core.Restraint.Restraint attribute)
(ccpn.core.SpectrumHit.SpectrumHit attribute)
filename2module() (in module ccpn.util.recursive_import)
filePath (ccpn.core.Spectrum.Spectrum attribute)
fillSubstanceTable() (ccpn.AnalysisMetabolomics.IntegralAssignment.IntegralAssignment method)
find_all_pyfiles() (in module ccpn.util.recursive_import)
find_pyfiles() (in module ccpn.util.recursive_import)
findBestMixtures() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
findClosePeaks() (in module ccpn.core.lib.AssignmentLib)
findTicks() (in module ccpn.util.Ticks)
Fit (class in ccpn.AnalysisMetabolomics.PickandFit)
flattenIfNumpy() (in module ccpn.util.Common)
foldingMode (ccpn.core.SpectrumReference.SpectrumReference attribute)
foldingModes (ccpn.core.Spectrum.Spectrum attribute)
frame_list (ccpn.util.Bmrb.bmrb.entry attribute)
frameDict() (ccpn.util.Bmrb.bmrb.entry method)
Framework (class in ccpn.framework.Framework)
frequency (ccpn.AnalysisScreen.lib.Screening.Peak attribute)
fromDatabase() (ccpn.util.Bmrb.bmrb.entry class method)
fromFile() (ccpn.util.Bmrb.bmrb.entry class method)
(ccpn.util.Bmrb.bmrb.loop class method)
(ccpn.util.Bmrb.bmrb.saveframe class method)
fromScratch() (ccpn.util.Bmrb.bmrb.entry class method)
(ccpn.util.Bmrb.bmrb.loop class method)
(ccpn.util.Bmrb.bmrb.saveframe class method)
fromString() (ccpn.util.Bmrb.bmrb.entry class method)
(ccpn.util.Bmrb.bmrb.loop class method)
(ccpn.util.Bmrb.bmrb.saveframe class method)
(ccpn.util.Time.Time static method)

G

gaussianBroadenings (ccpn.core.Spectrum.Spectrum attribute)
generatePeakPositions() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
generateSimpleCompounds() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
getActiveDisplays() (ccpn.AnalysisAssign.modules.PickAndAssignModule.SpectrumSelectionWidget method)
getAllOverlappedPositions() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
getAtom() (ccpn.core.Chain.Chain method)
(ccpn.core.Project.Project method)
(ccpn.core.Residue.Residue method)
getAtomBFactors() (ccpn.core.StructureEnsemble.StructureEnsemble method)
getAtomCoordinates() (ccpn.core.StructureEnsemble.StructureEnsemble method)
getAtomOccupancies() (ccpn.core.StructureEnsemble.StructureEnsemble method)
getAtomSpecificNames() (ccpn.core.StructureEnsemble.StructureEnsemble method)
getAxis() (ccpn.core.Project.Project method)
getBoundNmrAtomPairs() (in module ccpn.core.lib.AssignmentLib)
getByGid() (ccpn.framework.Framework.Framework method)
getByPid() (ccpn.framework.Framework.Framework method)
getCalculationStep() (ccpn.core.DataSet.DataSet method)
(ccpn.core.Project.Project method)
getCcpFileString() (in module ccpn.util.Common)
getChain() (ccpn.core.Project.Project method)
getChemicalShift() (ccpn.core.ChemicalShiftList.ChemicalShiftList method)
(ccpn.core.Project.Project method)
getChemicalShiftList() (ccpn.core.Project.Project method)
getColumns() (ccpn.AnalysisAssign.modules.ModifyAssignmentModule.ModifyAssignmentModule method)
getCompounds() (in module ccpn.AnalysisScreen.lib.MixturesGeneration)
getData() (ccpn.core.DataSet.DataSet method)
(ccpn.core.Project.Project method)
getDataAsCSV() (ccpn.util.Bmrb.bmrb.loop method)
(ccpn.util.Bmrb.bmrb.saveframe method)
getDataByTag() (ccpn.util.Bmrb.bmrb.loop method)
getDataSet() (ccpn.core.Project.Project method)
getFramework() (in module ccpn.framework.Framework)
getHashCode() (in module ccpn.util.Register)
getIntegral() (ccpn.core.IntegralList.IntegralList method)
(ccpn.core.Project.Project method)
(ccpn.core.Spectrum.Spectrum method)
getIntegralList() (ccpn.core.Project.Project method)
(ccpn.core.Spectrum.Spectrum method)
getLogger() (in module ccpn.util.Logging)
getLoopByCategory() (ccpn.util.Bmrb.bmrb.saveframe method)
getLoopsByCategory() (ccpn.util.Bmrb.bmrb.entry method)
getMark() (ccpn.core.Project.Project method)
getMixtureInfo() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
getModel() (ccpn.core.Project.Project method)
(ccpn.core.StructureEnsemble.StructureEnsemble method)
getModule() (ccpn.core.Project.Project method)
getNamedSubdirectories() (in module ccpn.core.lib.Documentation)
getNComponentsPerSample() (ccpn.AnalysisScreen.lib.MixtureGeneration.ObjectClustering method)
getNefData() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
getNmrAtom() (ccpn.core.NmrChain.NmrChain method)
(ccpn.core.NmrResidue.NmrResidue method)
(ccpn.core.Project.Project method)
getNmrAtomPrediction() (in module ccpn.core.lib.AssignmentLib)
getNmrChain() (ccpn.core.Project.Project method)
getNmrResidue() (ccpn.core.NmrChain.NmrChain method)
(ccpn.core.Project.Project method)
getNmrResiduePrediction() (in module ccpn.core.lib.AssignmentLib)
getNote() (ccpn.core.Project.Project method)
getNSamples() (ccpn.AnalysisScreen.lib.MixtureGeneration.ObjectClustering method)
getOffsetNmrResidue() (ccpn.core.NmrResidue.NmrResidue method)
getOverlappedCount() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
getParams() (ccpn.AnalysisMetabolomics.GuiPipeLine.AlignSpectra method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.AlignToReference method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.Bin method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.Centre method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.ExcludeBaselinePoints method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.ExcludeSignalFreeRegions method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.NormaliseSpectra method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.PolyBaseline method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.Scale method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.SegmentalAlign method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.WhittakerBaseline method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.WhittakerSmooth method)
(ccpn.AnalysisMetabolomics.Integration.IntegrationWidget method)
getPathToImport() (in module ccpn.util.Path)
getPeak() (ccpn.core.PeakList.PeakList method)
(ccpn.core.Project.Project method)
(ccpn.core.Spectrum.Spectrum method)
getPeakList() (ccpn.core.Project.Project method)
(ccpn.core.Spectrum.Spectrum method)
getPeakListView() (ccpn.core.Project.Project method)
getPlaneData() (ccpn.core.Spectrum.Spectrum method)
getPluginMenuItems() (ccpn.framework.Framework.Framework method)
getPreferences() (in module ccpn.framework.Framework)
getProbability() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
getProject() (in module ccpn.core.lib.DataIo)
getPseudoDimension() (ccpn.core.Project.Project method)
(ccpn.core.Spectrum.Spectrum method)
getPythonDirectory() (in module ccpn.util.Path)
getResidue() (ccpn.core.Chain.Chain method)
(ccpn.core.Project.Project method)
getRestraint() (ccpn.core.DataSet.DataSet method)
(ccpn.core.Project.Project method)
(ccpn.core.RestraintList.RestraintList method)
getRestraintContribution() (ccpn.core.DataSet.DataSet method)
(ccpn.core.Project.Project method)
(ccpn.core.Restraint.Restraint method)
(ccpn.core.RestraintList.RestraintList method)
getRestraintList() (ccpn.core.DataSet.DataSet method)
(ccpn.core.Project.Project method)
getSample() (ccpn.core.Project.Project method)
getSampleComponent() (ccpn.core.Project.Project method)
(ccpn.core.Sample.Sample method)
getSaveDirectory() (in module ccpn.framework.Framework)
getSaveframeByName() (ccpn.util.Bmrb.bmrb.entry method)
getSaveframesByCategory() (ccpn.util.Bmrb.bmrb.entry method)
getSaveframesByTagAndValue() (ccpn.util.Bmrb.bmrb.entry method)
getSliceData() (ccpn.core.Spectrum.Spectrum method)
getSourceData() (ccpn.AnalysisMetabolomics.Decomposition.Decomposition method)
getSpectrum() (ccpn.core.Project.Project method)
getSpectrumCluster() (in module ccpn.AnalysisMetabolomics.lib.normalisation)
getSpectrumDisplay() (ccpn.core.Project.Project method)
getSpectrumGroup() (ccpn.core.Project.Project method)
getSpectrumHit() (ccpn.core.Project.Project method)
(ccpn.core.Spectrum.Spectrum method)
getSpectrumReference() (ccpn.core.Project.Project method)
(ccpn.core.Spectrum.Spectrum method)
getSpectrumView() (ccpn.core.Project.Project method)
getSpinSystemsLocation() (in module ccpn.core.lib.AssignmentLib)
getStrip() (ccpn.core.Project.Project method)
getStructureEnsemble() (ccpn.core.Project.Project method)
getStyleSheet() (ccpn.framework.Framework.Framework method)
getSubstance() (ccpn.core.Project.Project method)
getTag() (ccpn.util.Bmrb.bmrb.entry method)
(ccpn.util.Bmrb.bmrb.loop method)
(ccpn.util.Bmrb.bmrb.saveframe method)
getTask() (ccpn.core.Project.Project method)
getTimeStamp() (in module ccpn.util.Common)
getTopDirectory() (in module ccpn.util.Path)
getTranslator() (in module ccpn.framework.Translation)
getUuid() (in module ccpn.util.Common)
getWindow() (ccpn.core.Project.Project method)
GoArea (class in ccpn.AnalysisMetabolomics.MetabolomicsPipeline)
greedyMixtures() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
GuiNmrAtom (class in ccpn.AnalysisAssign.modules.SequenceGraph)
GuiNmrResidue (class in ccpn.AnalysisAssign.modules.SequenceGraph)

H

Handler (class in ccpn.util.Bmrb.passthrough)
has_duplicates() (ccpn.AnalysisAssign.modules.SideChainAssignmentModule.SideChainAssignmentModule method)
haveWriteAccess() (ccpn.framework.update.UpdateAgent.UpdateAgent method)
hBondAcceptorCount (ccpn.core.Substance.Substance attribute)
hBondDonorCount (ccpn.core.Substance.Substance attribute)
header (ccpn.core.Note.Note attribute)
headers (ccpn.util.Bmrb.bmrb.schema attribute)
headerSize (ccpn.core.Spectrum.Spectrum attribute)
height (ccpn.core.Peak.Peak attribute)
heightError (ccpn.core.Peak.Peak attribute)
hex() (ccpn.util.Colour.Colour method)
hexToRgb() (in module ccpn.util.Colour)
hideSequenceModule() (ccpn.framework.Framework.Framework method)

I

id (ccpn.core.lib.Pid.Pid attribute)
importAllPyfiles() (in module ccpn.util.recursive_import)
importCyanaRestraints() (in module ccpn.core.lib.DataIo)
importers (ccpn.core.lib.CcpnNefIo.CcpnNefReader attribute)
importNewProject() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
inChi (ccpn.core.Substance.Substance attribute)
increaseBlocking() (ccpn.util.Undo.Undo method)
increment() (ccpn.core.lib.Pid.Pid method)
incrementName() (in module ccpn.util.Common)
initGraphics() (ccpn.framework.Framework.Framework method)
initialiseClusters() (ccpn.AnalysisScreen.lib.MixtureGeneration.ObjectClustering method)
initialize() (ccpn.ui.Ui.Ui method)
inputCalculationSteps (ccpn.core.DataSet.DataSet attribute)
inputDataSet (ccpn.core.CalculationStep.CalculationStep attribute)
inputDataUuid (ccpn.core.CalculationStep.CalculationStep attribute)
inspectMolecule() (ccpn.framework.Framework.Framework method)
installChosen() (ccpn.framework.update.UpdateAgent.UpdateAgent method)
installUpdate() (ccpn.framework.update.UpdateAgent.UpdateFile method)
installUpdates() (ccpn.framework.update.UpdateAgent.UpdateAgent method)
instance (ccpn.AnalysisMetabolomics.lib.persistence.MetabolomicsPersistenceDict attribute)
Integral (class in ccpn.AnalysisMetabolomics.IntegralAssignment)
(class in ccpn.core.Integral)
IntegralAssignment (class in ccpn.AnalysisMetabolomics.IntegralAssignment)
integralCallback() (ccpn.AnalysisMetabolomics.IntegralAssignment.IntegralTable method)
integralList (ccpn.core.Integral.Integral attribute)
IntegralList (class in ccpn.core.IntegralList)
integralLists (ccpn.core.Project.Project attribute)
(ccpn.core.Spectrum.Spectrum attribute)
integrals (ccpn.core.IntegralList.IntegralList attribute)
(ccpn.core.Project.Project attribute)
(ccpn.core.Spectrum.Spectrum attribute)
IntegralTable (class in ccpn.AnalysisMetabolomics.IntegralAssignment)
IntegrationTable (class in ccpn.AnalysisMetabolomics.Integration)
IntegrationWidget (class in ccpn.AnalysisMetabolomics.Integration)
intensities (ccpn.core.Spectrum.Spectrum attribute)
intensity (ccpn.AnalysisScreen.lib.Screening.Peak attribute)
interface (ccpn.framework.Framework.Arguments attribute)
ionicStrength (ccpn.core.Sample.Sample attribute)
isAcquisition (ccpn.core.SpectrumReference.SpectrumReference attribute)
isClose() (in module ccpn.util.Common)
isComplex (ccpn.core.Spectrum.Spectrum attribute)
isConfirmed (ccpn.core.SpectrumHit.SpectrumHit attribute)
isConnected (ccpn.core.NmrChain.NmrChain attribute)
isCyclic (ccpn.core.Chain.Chain attribute)
isDistanceDependent (ccpn.core.RestraintContribution.RestraintContribution attribute)
isHazardous (ccpn.core.Sample.Sample attribute)
isIndirect (ccpn.core.lib.SpectrumLib.MagnetisationTransferTuple attribute)
isInterOnlyExpt() (in module ccpn.core.lib.AssignmentLib)
isNewRegistration() (in module ccpn.util.Register)
isotopeCode (ccpn.core.NmrAtom.NmrAtom attribute)
isotopeCodes (ccpn.core.Spectrum.Spectrum attribute)
(ccpn.core.SpectrumReference.SpectrumReference attribute)
isotropic (ccpn.util.Tensor.Tensor attribute)
isSimulated (ccpn.core.ChemicalShiftList.ChemicalShiftList attribute)
(ccpn.core.PeakList.PeakList attribute)
isUpdateDifferent() (ccpn.framework.update.UpdateAgent.UpdateAgent method)
isValid() (ccpn.core.lib.Pid.Pid static method)
isVirtual (ccpn.core.Sample.Sample attribute)
isWindowsOS() (in module ccpn.util.Common)
iterateAnnealing() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)

J

joinPath() (in module ccpn.util.Path)

L

label (ccpn.core.NmrChain.NmrChain attribute)
labeling (ccpn.core.SampleComponent.SampleComponent attribute)
(ccpn.core.Substance.Substance attribute)
language (ccpn.framework.Framework.Arguments attribute)
lastModified (ccpn.core.Note.Note attribute)
lastModifiedTime() (in module ccpn.framework.update.UpdateAgent)
levelScale() (in module ccpn.AnalysisMetabolomics.lib.scaling)
limits (ccpn.core.Integral.Integral attribute)
linearCooling() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
lineMoved() (ccpn.AnalysisMetabolomics.GuiPipeLine.ExcludeBaselinePoints method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.PolyBaseline method)
linewidth (ccpn.AnalysisScreen.lib.Screening.Peak attribute)
lineWidths (ccpn.core.Peak.Peak attribute)
linking (ccpn.core.Residue.Residue attribute)
load() (in module ccpn.util.jsonIo)
load_ccpn_assignments() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_ccpn_dataset() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_ccpn_integral_list() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_ccpn_notes() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_ccpn_sample() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_ccpn_spectrum_dimension() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_ccpn_spectrum_group() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_ccpn_substance() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_nef_chemical_shift() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_nef_chemical_shift_list() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_nef_covalent_links() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_nef_molecular_system() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_nef_nmr_meta_data() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_nef_nmr_spectrum() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_nef_peak() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_nef_peak_restraint_link() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_nef_peak_restraint_links() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_nef_restraint() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_nef_restraint_list() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_nef_sequence() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
load_nef_spectrum_dimension_transfer() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
loadCasdData() (in module ccpn.core.lib.DataIo)
loadCasdPeakList() (in module ccpn.core.lib.DataIo)
loadCasdRdcList() (in module ccpn.core.lib.DataIo)
loadCyanaPeakList() (in module ccpn.core.lib.DataIo)
loadData() (ccpn.core.Project.Project method)
(ccpn.framework.Framework.Framework method)
loadDict() (in module ccpn.util.Register)
loadDocrProject() (in module ccpn.core.lib.DataIo)
loadings (ccpn.AnalysisMetabolomics.Decomposition.Decomposition attribute)
loadings_ (ccpn.AnalysisMetabolomics.lib.decomposition.PCA attribute)
loadNmrStarChemicalShifts() (in module ccpn.core.lib.DataIo)
loadProject() (ccpn.core.Project.Project method)
(ccpn.framework.Framework.Framework method)
loads() (in module ccpn.util.jsonIo)
loadSpectrum() (ccpn.core.Project.Project method)
logPartitionCoefficient (ccpn.core.Substance.Substance attribute)
logTransform() (in module ccpn.AnalysisMetabolomics.lib.transformations)
LookupSetupPopup (class in ccpn.AnalysisScreen.popups.LookupSetupPopup)
loop (class in ccpn.util.Bmrb.bmrb)
loopDict() (ccpn.util.Bmrb.bmrb.saveframe method)
loopIterator() (ccpn.util.Bmrb.bmrb.saveframe method)
loops (ccpn.util.Bmrb.bmrb.saveframe attribute)
lorentzian() (in module ccpn.AnalysisScreen.lib.Screening)
lorentzianBroadenings (ccpn.core.Spectrum.Spectrum attribute)
lowerLimit (ccpn.core.Restraint.Restraint attribute)
(ccpn.core.RestraintContribution.RestraintContribution attribute)
lr1Moved() (ccpn.AnalysisMetabolomics.PickandFit.PickandFitTable method)
lr2Moved() (ccpn.AnalysisMetabolomics.PickandFit.PickandFitTable method)
lr3Moved() (ccpn.AnalysisMetabolomics.PickandFit.PickandFitTable method)

M

magnetisationTransfers (ccpn.core.Spectrum.Spectrum attribute)
MagnetisationTransferTuple (class in ccpn.core.lib.SpectrumLib)
main() (in module ccpn.util.recursive_import)
mainNmrResidue (ccpn.core.NmrResidue.NmrResidue attribute)
mainNmrResidues (ccpn.core.NmrChain.NmrChain attribute)
makeNefAxisCodes() (in module ccpn.core.lib.CcpnNefIo)
makeNefMetaData() (ccpn.core.lib.CcpnNefIo.CcpnNefWriter method)
marks (ccpn.core.Project.Project attribute)
matchedPosition() (in module ccpn.AnalysisScreen.lib.Screening)
maxAliasedFrequency (ccpn.core.SpectrumReference.SpectrumReference attribute)
meanCenter() (in module ccpn.AnalysisMetabolomics.lib.centering)
meanCentre() (in module ccpn.AnalysisMetabolomics.Pipeline)
measurementType (ccpn.core.RestraintList.RestraintList attribute)
(ccpn.core.SpectrumReference.SpectrumReference attribute)
measurementTypes (ccpn.core.Spectrum.Spectrum attribute)
medianCenter() (in module ccpn.AnalysisMetabolomics.lib.centering)
mediateRefresh() (ccpn.AnalysisAssign.modules.SideChainAssignmentModule.SideChainAssignmentModule method)
meritCode (ccpn.core.SpectrumHit.SpectrumHit attribute)
Metabolomics (class in ccpn.AnalysisMetabolomics.AnalysisMetabolomics)
MetabolomicsModule (class in ccpn.AnalysisMetabolomics.MetabolomicsPipeline)
MetabolomicsPersistenceDict (class in ccpn.AnalysisMetabolomics.lib.persistence)
method (ccpn.AnalysisMetabolomics.Decomposition.Decomposition attribute)
minAliasedFrequency (ccpn.core.SpectrumReference.SpectrumReference attribute)
minimumStepPath() (in module ccpn.util.Graph)
MixtureOptimisation (class in ccpn.AnalysisScreen.modules.MixtureOptimisation)
mixTwoMixturesDict() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
Model (class in ccpn.core.Model)
models (ccpn.core.Project.Project attribute)
(ccpn.core.StructureEnsemble.StructureEnsemble attribute)
modify() (ccpn.core.lib.Pid.Pid method)
ModifyAssignmentModule (class in ccpn.AnalysisAssign.modules.ModifyAssignmentModule)
modules (ccpn.core.Project.Project attribute)
molecularMass (ccpn.core.Substance.Substance attribute)
mouseDoubleClickEvent() (ccpn.AnalysisAssign.modules.SequenceGraph.GuiNmrAtom method)
mouseMoveEvent() (ccpn.AnalysisAssign.modules.SequenceGraph.GuiNmrResidue method)
mousePressEvent() (ccpn.AnalysisAssign.modules.SequenceGraph.GuiNmrResidue method)
moveRowDown() (ccpn.AnalysisMetabolomics.MetabolomicsPipeline.PipelineWidgets method)
moveRowUp() (ccpn.AnalysisMetabolomics.MetabolomicsPipeline.PipelineWidgets method)
moveToNmrChain() (ccpn.core.NmrResidue.NmrResidue method)
multiply() (ccpn.AnalysisMetabolomics.lib.commands.Command method)
MyThread (class in ccpn.AnalysisMetabolomics.MetabolomicsPipeline)

N

name (ccpn.core.Atom.Atom attribute)
(ccpn.core.ChemicalShiftList.ChemicalShiftList attribute)
(ccpn.core.Data.Data attribute)
(ccpn.core.NmrAtom.NmrAtom attribute)
(ccpn.core.Note.Note attribute)
(ccpn.core.Project.Project attribute)
(ccpn.core.RestraintList.RestraintList attribute)
(ccpn.core.Sample.Sample attribute)
(ccpn.core.SampleComponent.SampleComponent attribute)
(ccpn.core.Spectrum.Spectrum attribute)
(ccpn.core.SpectrumGroup.SpectrumGroup attribute)
(ccpn.core.Substance.Substance attribute)
(ccpn.util.Bmrb.bmrb.saveframe attribute)
nameMap (ccpn.core.lib.Pid.Pid attribute)
nComponents (ccpn.AnalysisMetabolomics.lib.decomposition.PCA attribute)
nefString() (ccpn.util.Bmrb.bmrb.entry method)
negativeContourBase (ccpn.core.Spectrum.Spectrum attribute)
negativeContourColour (ccpn.core.Spectrum.Spectrum attribute)
negativeContourCount (ccpn.core.Spectrum.Spectrum attribute)
negativeContourFactor (ccpn.core.Spectrum.Spectrum attribute)
new() (ccpn.core.lib.Pid.Pid static method)
newCalculationStep() (ccpn.core.DataSet.DataSet method)
newChemicalShift() (ccpn.core.ChemicalShiftList.ChemicalShiftList method)
newChemicalShiftList() (ccpn.core.Project.Project method)
newData() (ccpn.core.DataSet.DataSet method)
newDataSet() (ccpn.core.Project.Project method)
newIntegral() (ccpn.core.IntegralList.IntegralList method)
newIntegralList() (ccpn.core.Spectrum.Spectrum method)
newItem() (ccpn.util.Undo.Undo method)
newMacroFromConsole() (ccpn.framework.Framework.Framework method)
newMacroFromLog() (ccpn.framework.Framework.Framework method)
newModel() (ccpn.core.StructureEnsemble.StructureEnsemble method)
newNmrAtom() (ccpn.core.NmrResidue.NmrResidue method)
newNmrChain() (ccpn.core.Project.Project method)
newNmrResidue() (ccpn.core.NmrChain.NmrChain method)
newNote() (ccpn.core.Project.Project method)
newPeak() (ccpn.core.PeakList.PeakList method)
newPeakList() (ccpn.core.Spectrum.Spectrum method)
newProject() (ccpn.framework.Framework.Framework method)
newRestraint() (ccpn.core.RestraintList.RestraintList method)
newRestraintContribution() (ccpn.core.Restraint.Restraint method)
newRestraintList() (ccpn.core.DataSet.DataSet method)
newSample() (ccpn.core.Project.Project method)
newSampleComponent() (ccpn.core.Sample.Sample method)
newSpectrum() (ccpn.core.Project.Project method)
newSpectrumGroup() (ccpn.core.Project.Project method)
newSpectrumHit() (ccpn.core.Spectrum.Spectrum method)
newSpectrumReference() (ccpn.core.Spectrum.Spectrum method)
newStructureEnsemble() (ccpn.core.Project.Project method)
newSubstance() (ccpn.core.Project.Project method)
newTask() (ccpn.core.Project.Project method)
newUndoPoint() (ccpn.core.Project.Project method)
newWaypoint() (ccpn.util.Undo.Undo method)
newWindow() (ccpn.core.Project.Project method)
nextNmrResidue (ccpn.core.NmrResidue.NmrResidue attribute)
nextResidue (ccpn.core.Residue.Residue attribute)
nmrAtom (ccpn.core.Atom.Atom attribute)
(ccpn.core.ChemicalShift.ChemicalShift attribute)
(ccpn.framework.Current.Current attribute)
NmrAtom (class in ccpn.core.NmrAtom)
nmrAtomPairsByDimensionTransfer() (in module ccpn.core.lib.AssignmentLib)
nmrAtoms (ccpn.core.NmrChain.NmrChain attribute)
(ccpn.core.NmrResidue.NmrResidue attribute)
(ccpn.core.Project.Project attribute)
(ccpn.framework.Current.Current attribute)
nmrChain (ccpn.core.Chain.Chain attribute)
(ccpn.core.NmrResidue.NmrResidue attribute)
(ccpn.framework.Current.Current attribute)
NmrChain (class in ccpn.core.NmrChain)
nmrChains (ccpn.core.Project.Project attribute)
(ccpn.framework.Current.Current attribute)
nmrResidue (ccpn.core.NmrAtom.NmrAtom attribute)
(ccpn.core.Residue.Residue attribute)
(ccpn.framework.Current.Current attribute)
NmrResidue (class in ccpn.core.NmrResidue)
nmrResidues (ccpn.core.NmrChain.NmrChain attribute)
(ccpn.core.Project.Project attribute)
(ccpn.framework.Current.Current attribute)
no_op() (in module ccpn.util.Undo)
noCap() (in module ccpn.framework.Current)
nologging (ccpn.framework.Framework.Arguments attribute)
normalise() (in module ccpn.AnalysisMetabolomics.Pipeline)
normalisedChange (ccpn.core.SpectrumHit.SpectrumHit attribute)
normalisePath() (in module ccpn.util.Path)
NormaliseSpectra (class in ccpn.AnalysisMetabolomics.GuiPipeLine)
normalization (ccpn.AnalysisMetabolomics.Decomposition.Decomposition attribute)
normalize() (ccpn.AnalysisMetabolomics.Decomposition.Decomposition method)
Note (class in ccpn.core.Note)
notes (ccpn.core.Project.Project attribute)
notes2Nef() (ccpn.core.lib.CcpnNefIo.CcpnNefWriter method)
NoUi (class in ccpn.ui.Ui)
now() (in module ccpn.util.Time)
numberType (ccpn.core.Spectrum.Spectrum attribute)

O

ObjectClustering (class in ccpn.AnalysisScreen.lib.MixtureGeneration)
occupancyData (ccpn.core.Model.Model attribute)
(ccpn.core.StructureEnsemble.StructureEnsemble attribute)
offsetNmrResidues (ccpn.core.NmrResidue.NmrResidue attribute)
openProject() (ccpn.framework.Framework.Framework method)
orderedSamples (ccpn.core.PseudoDimension.PseudoDimension attribute)
OrderedSet (class in ccpn.util.OrderedSet)
orientationMatrix (ccpn.util.Tensor.Tensor attribute)
origin (ccpn.core.RestraintList.RestraintList attribute)
outputCalculationSteps (ccpn.core.DataSet.DataSet attribute)
outputDataSet (ccpn.core.CalculationStep.CalculationStep attribute)
outputDataUuid (ccpn.core.CalculationStep.CalculationStep attribute)

P

parameters (ccpn.core.Data.Data attribute)
paretoScale() (in module ccpn.AnalysisMetabolomics.lib.scaling)
parseCyanaPeakList() (in module ccpn.core.lib.DataIo)
parseNmrPipeScript() (in module ccpn.core.lib.DataIo)
parseSequenceCode() (in module ccpn.util.Common)
path (ccpn.core.Project.Project attribute)
PCA (class in ccpn.AnalysisMetabolomics.lib.decomposition)
peak (ccpn.framework.Current.Current attribute)
Peak (class in ccpn.AnalysisScreen.lib.Screening)
(class in ccpn.core.Peak)
PeakAssignment (class in ccpn.AnalysisMetabolomics.PeakAssignment)
peakList (ccpn.core.Peak.Peak attribute)
PeakList (class in ccpn.core.PeakList)
peakList2Nef() (ccpn.core.lib.CcpnNefIo.CcpnNefWriter method)
peakLists (ccpn.core.Project.Project attribute)
(ccpn.core.Spectrum.Spectrum attribute)
peakListViews (ccpn.core.PeakList.PeakList attribute)
(ccpn.core.Project.Project attribute)
peakRestraintLinks2Nef() (ccpn.core.lib.CcpnNefIo.CcpnNefWriter method)
peaks (ccpn.core.PeakList.PeakList attribute)
(ccpn.core.Project.Project attribute)
(ccpn.core.Restraint.Restraint attribute)
(ccpn.core.Spectrum.Spectrum attribute)
(ccpn.framework.Current.Current attribute)
pH (ccpn.core.Sample.Sample attribute)
phase (ccpn.AnalysisScreen.lib.Screening.Peak attribute)
phaseComplexData() (in module ccpn.util.Phasing)
phaseRealData() (in module ccpn.util.Phasing)
phases0 (ccpn.core.Spectrum.Spectrum attribute)
phases1 (ccpn.core.Spectrum.Spectrum attribute)
PickAndAssignModule (class in ccpn.AnalysisAssign.modules.PickAndAssignModule)
PickandFit (class in ccpn.AnalysisMetabolomics.PickandFit)
PickandFitTable (class in ccpn.AnalysisMetabolomics.PickandFit)
pickPeaks1d() (ccpn.core.PeakList.PeakList method)
pickPeaks1dFiltered() (ccpn.core.PeakList.PeakList method)
pickPeaksNd() (ccpn.core.PeakList.PeakList method)
Pid (class in ccpn.core.lib.Pid)
pid2PluralName() (in module ccpn.core.lib.Util)
pipeline() (in module ccpn.AnalysisMetabolomics.lib.pipeline)
PipelineWidgets (class in ccpn.AnalysisMetabolomics.MetabolomicsPipeline)
plateIdentifier (ccpn.core.Sample.Sample attribute)
pointCount (ccpn.core.PseudoDimension.PseudoDimension attribute)
pointCounts (ccpn.core.Spectrum.Spectrum attribute)
pointErrors (ccpn.core.PseudoDimension.PseudoDimension attribute)
pointlimits (ccpn.core.Integral.Integral attribute)
pointNumber (ccpn.core.SpectrumHit.SpectrumHit attribute)
pointOffsets (ccpn.core.Spectrum.Spectrum attribute)
pointPosition (ccpn.core.Peak.Peak attribute)
pointValues (ccpn.core.PseudoDimension.PseudoDimension attribute)
polarSurfaceArea (ccpn.core.Substance.Substance attribute)
PolyBaseline (class in ccpn.AnalysisMetabolomics.GuiPipeLine)
polyBaseLine() (in module ccpn.AnalysisMetabolomics.Pipeline)
pop() (ccpn.util.OrderedSet.OrderedSet method)
populatePathWidget() (ccpn.AnalysisScreen.popups.LookupSetupPopup.LookupSetupPopup method)
position (ccpn.core.Peak.Peak attribute)
(ccpn.framework.Current.Current attribute)
positionError (ccpn.core.Peak.Peak attribute)
positions (ccpn.core.Spectrum.Spectrum attribute)
(ccpn.framework.Current.Current attribute)
positiveContourBase (ccpn.core.Spectrum.Spectrum attribute)
positiveContourColour (ccpn.core.Spectrum.Spectrum attribute)
positiveContourCount (ccpn.core.Spectrum.Spectrum attribute)
positiveContourFactor (ccpn.core.Spectrum.Spectrum attribute)
potentialType (ccpn.core.RestraintList.RestraintList attribute)
powerTransform() (in module ccpn.AnalysisMetabolomics.lib.transformations)
pqn() (in module ccpn.AnalysisMetabolomics.lib.normalisation)
predictions_ (ccpn.AnalysisMetabolomics.lib.decomposition.PCA attribute)
predictSequencePosition() (ccpn.AnalysisAssign.modules.SequenceGraph.SequenceGraph method)
preloadAssignmentData() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
presenter (ccpn.AnalysisMetabolomics.Decomposition.Decomposition attribute)
previousNmrResidue (ccpn.core.NmrResidue.NmrResidue attribute)
previousResidue (ccpn.core.Residue.Residue attribute)
printCreditsText() (in module ccpn.framework.Framework)
printToFile() (ccpn.framework.Framework.Framework method)
printTree() (ccpn.util.Bmrb.bmrb.entry method)
(ccpn.util.Bmrb.bmrb.loop method)
(ccpn.util.Bmrb.bmrb.saveframe method)
probableResidues (ccpn.core.NmrResidue.NmrResidue attribute)
probableResidueTypes (ccpn.core.NmrResidue.NmrResidue attribute)
process() (ccpn.AnalysisMetabolomics.lib.commands.Command method)
process_nef_spectrum_dimension_transfer() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
produceNmrAtom() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
produceNmrChain() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
produceNmrResidue() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
programName (ccpn.core.CalculationStep.CalculationStep attribute)
(ccpn.core.DataSet.DataSet attribute)
(ccpn.core.Project.Project attribute)
programVersion (ccpn.core.CalculationStep.CalculationStep attribute)
(ccpn.core.DataSet.DataSet attribute)
project (ccpn.framework.Current.Current attribute)
Project (class in ccpn.core.Project)
projectedPlaneData() (ccpn.core.Spectrum.Spectrum method)
projectedToFile() (ccpn.core.Spectrum.Spectrum method)
projectPath (ccpn.framework.Framework.Arguments attribute)
propagateAssignments() (in module ccpn.core.lib.AssignmentLib)
pseudoDimension (ccpn.core.SpectrumHit.SpectrumHit attribute)
PseudoDimension (class in ccpn.core.PseudoDimension)
pseudoDimensionNumber (ccpn.core.SpectrumHit.SpectrumHit attribute)
pseudoDimensions (ccpn.core.Project.Project attribute)
(ccpn.core.Sample.Sample attribute)
(ccpn.core.Spectrum.Spectrum attribute)
purity (ccpn.core.SampleComponent.SampleComponent attribute)

Q

qConfLimit (ccpn.AnalysisMetabolomics.lib.decomposition.PCA attribute)
qScores_ (ccpn.AnalysisMetabolomics.lib.decomposition.PCA attribute)

R

randomDictMixtures() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
rangeScale() (in module ccpn.AnalysisMetabolomics.lib.scaling)
read_nef_spectrum_dimension() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
read_nef_spectrum_dimension_transfer() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
readNmrStarChemicalShifts() (in module ccpn.core.lib.DataIo)
recursiveImport() (in module ccpn.util.Common)
redo() (ccpn.framework.Framework.Framework method)
(ccpn.util.Undo.Undo method)
referencePoint (ccpn.core.SpectrumReference.SpectrumReference attribute)
referencePoints (ccpn.core.Spectrum.Spectrum attribute)
referenceSerial (ccpn.core.SpectrumReference.SpectrumReference attribute)
referenceSpectra (ccpn.core.Substance.Substance attribute)
referenceSubstance (ccpn.core.Spectrum.Spectrum attribute)
referenceValue (ccpn.core.SpectrumReference.SpectrumReference attribute)
referenceValues (ccpn.core.Spectrum.Spectrum attribute)
refit() (ccpn.core.PeakList.PeakList method)
refreshSourceDataOptions() (ccpn.AnalysisMetabolomics.Decomposition.Decomposition method)
refreshSphinxDocumentation() (in module ccpn.core.lib.Documentation)
registerNotifier() (ccpn.core.Project.Project method)
registerNotifiers() (ccpn.AnalysisMetabolomics.Decomposition.Decomposition method)
registerNotify() (ccpn.framework.Current.Current method)
relativeOffset (ccpn.core.NmrResidue.NmrResidue attribute)
remapRestraintItems() (in module ccpn.core.lib.DataIo)
removeAtomId() (ccpn.core.StructureEnsemble.StructureEnsemble method)
removeAtomIds() (ccpn.core.StructureEnsemble.StructureEnsemble method)
removeNmratom() (ccpn.framework.Current.Current method)
removeNmrchain() (ccpn.framework.Current.Current method)
removeNmrChainFromPulldown() (ccpn.AnalysisAssign.modules.SequenceGraph.SequenceGraph method)
removeNmrresidue() (ccpn.framework.Current.Current method)
removeNotifier() (ccpn.core.Project.Project method)
removePeak() (ccpn.framework.Current.Current method)
removePosition() (ccpn.framework.Current.Current method)
removeRow() (ccpn.AnalysisMetabolomics.MetabolomicsPipeline.PipelineWidgets method)
rename() (ccpn.core.Chain.Chain method)
(ccpn.core.ChemicalShiftList.ChemicalShiftList method)
(ccpn.core.Data.Data method)
(ccpn.core.NmrAtom.NmrAtom method)
(ccpn.core.NmrChain.NmrChain method)
(ccpn.core.NmrResidue.NmrResidue method)
(ccpn.core.Note.Note method)
(ccpn.core.Residue.Residue method)
(ccpn.core.RestraintList.RestraintList method)
(ccpn.core.Sample.Sample method)
(ccpn.core.Spectrum.Spectrum method)
(ccpn.core.SpectrumGroup.SpectrumGroup method)
(ccpn.core.Substance.Substance method)
renameObject() (ccpn.core.Project.Project method)
renamePipeline() (ccpn.AnalysisMetabolomics.MetabolomicsPipeline.GoArea method)
renumberRows() (ccpn.util.Bmrb.bmrb.loop method)
replaceAtomIds() (ccpn.core.StructureEnsemble.StructureEnsemble method)
resetAssignmentTolerances() (ccpn.core.Spectrum.Spectrum method)
resetFromServer() (ccpn.framework.update.UpdateAgent.UpdateAgent method)
(ccpn.framework.update.UpdatePopup.UpdatePopup method)
resetUndo() (in module ccpn.util.Undo)
resetZoom() (ccpn.framework.Framework.Framework method)
residualEigenvalues_ (ccpn.AnalysisMetabolomics.lib.decomposition.PCA attribute)
residuals_ (ccpn.AnalysisMetabolomics.lib.decomposition.PCA attribute)
residue (ccpn.core.Atom.Atom attribute)
(ccpn.core.NmrResidue.NmrResidue attribute)
Residue (class in ccpn.core.Residue)
residueIds (ccpn.core.StructureEnsemble.StructureEnsemble attribute)
residues (ccpn.core.Chain.Chain attribute)
(ccpn.core.Project.Project attribute)
residueType (ccpn.core.lib.Util.AtomIdTuple attribute)
(ccpn.core.NmrResidue.NmrResidue attribute)
(ccpn.core.Residue.Residue attribute)
residueVariant (ccpn.core.Residue.Residue attribute)
restoreBackup() (ccpn.framework.Framework.Framework method)
restoreOriginalLinks() (in module ccpn.util.Undo)
restraint (ccpn.core.RestraintContribution.RestraintContribution attribute)
Restraint (class in ccpn.core.Restraint)
RestraintContribution (class in ccpn.core.RestraintContribution)
restraintContributions (ccpn.core.DataSet.DataSet attribute)
(ccpn.core.Project.Project attribute)
(ccpn.core.Restraint.Restraint attribute)
(ccpn.core.RestraintList.RestraintList attribute)
restraintItemLength (ccpn.core.RestraintList.RestraintList attribute)
restraintItems (ccpn.core.RestraintContribution.RestraintContribution attribute)
restraintList (ccpn.core.Restraint.Restraint attribute)
RestraintList (class in ccpn.core.RestraintList)
restraintList2Nef() (ccpn.core.lib.CcpnNefIo.CcpnNefWriter method)
restraintLists (ccpn.core.DataSet.DataSet attribute)
(ccpn.core.Project.Project attribute)
restraints (ccpn.core.DataSet.DataSet attribute)
(ccpn.core.Peak.Peak attribute)
(ccpn.core.Project.Project attribute)
(ccpn.core.RestraintList.RestraintList attribute)
restraintType (ccpn.core.RestraintList.RestraintList attribute)
restrictedPick() (ccpn.core.PeakList.PeakList method)
resumeNotification() (ccpn.core.Project.Project method)
rgba() (ccpn.util.Colour.Colour method)
(in module ccpn.util.Colour)
rgbaToHex() (in module ccpn.util.Colour)
rgbToHex() (in module ccpn.util.Colour)
rhombic (ccpn.util.Tensor.Tensor attribute)
ringCount (ccpn.core.Substance.Substance attribute)
role (ccpn.core.Chain.Chain attribute)
(ccpn.core.SampleComponent.SampleComponent attribute)
rowNumber (ccpn.core.Sample.Sample attribute)
run() (ccpn.AnalysisMetabolomics.MetabolomicsPipeline.MyThread method)
runCooling() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
runMacro() (ccpn.framework.Framework.Framework method)
runPipeline() (ccpn.AnalysisMetabolomics.MetabolomicsPipeline.MetabolomicsModule method)

S

sample (ccpn.core.SampleComponent.SampleComponent attribute)
(ccpn.core.Spectrum.Spectrum attribute)
(ccpn.core.SpectrumHit.SpectrumHit attribute)
Sample (class in ccpn.core.Sample)
sample2Nef() (ccpn.core.lib.CcpnNefIo.CcpnNefWriter method)
sampleComponent (ccpn.core.SpectrumHit.SpectrumHit attribute)
SampleComponent (class in ccpn.core.SampleComponent)
sampleComponents (ccpn.core.Project.Project attribute)
(ccpn.core.Sample.Sample attribute)
(ccpn.core.Substance.Substance attribute)
sampleLabelingFractions() (in module ccpn.core.lib.LabelingLib)
samplePairLabelingFractions() (in module ccpn.core.lib.LabelingLib)
samples (ccpn.core.Project.Project attribute)
save() (ccpn.core.Project.Project method)
saveBackup() (ccpn.framework.Framework.Framework method)
saveDict() (in module ccpn.util.Register)
saveframe (class in ccpn.util.Bmrb.bmrb)
saveLoadingsToSpectra() (ccpn.AnalysisMetabolomics.Decomposition.Decomposition method)
saveLogFile() (ccpn.framework.Framework.Framework method)
saveNefProject() (in module ccpn.core.lib.CcpnNefIo)
saveProject() (ccpn.framework.Framework.Framework method)
saveProjectAs() (ccpn.framework.Framework.Framework method)
scale (ccpn.core.RestraintContribution.RestraintContribution attribute)
(ccpn.core.Spectrum.Spectrum attribute)
Scale (class in ccpn.AnalysisMetabolomics.GuiPipeLine)
scale() (ccpn.AnalysisMetabolomics.Decomposition.Decomposition method)
(in module ccpn.AnalysisMetabolomics.Pipeline)
scaledRgba() (ccpn.util.Colour.Colour method)
(in module ccpn.util.Colour)
scaling (ccpn.AnalysisMetabolomics.Decomposition.Decomposition attribute)
schema (ccpn.util.Bmrb.bmrb.schema attribute)
(class in ccpn.util.Bmrb.bmrb)
schema_file (ccpn.util.Bmrb.bmrb.schema attribute)
schema_order (ccpn.util.Bmrb.bmrb.schema attribute)
scoreCompound() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
scoreMixture() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
scores (ccpn.AnalysisMetabolomics.Decomposition.Decomposition attribute)
scores_ (ccpn.AnalysisMetabolomics.lib.decomposition.PCA attribute)
scoring() (in module ccpn.AnalysisScreen.lib.MixtureGeneration)
Screen (class in ccpn.AnalysisScreen.AnalysisScreen)
script (ccpn.core.CalculationStep.CalculationStep attribute)
scriptName (ccpn.core.CalculationStep.CalculationStep attribute)
SegmentalAlign (class in ccpn.AnalysisMetabolomics.GuiPipeLine)
segmentalAlign() (in module ccpn.AnalysisMetabolomics.Pipeline)
sequenceCode (ccpn.core.lib.Util.AtomIdTuple attribute)
(ccpn.core.NmrResidue.NmrResidue attribute)
(ccpn.core.Residue.Residue attribute)
SequenceGraph (class in ccpn.AnalysisAssign.modules.SequenceGraph)
sequenceMatchOffset() (in module ccpn.core.lib.MoleculeLib)
sequenceString (ccpn.core.Substance.Substance attribute)
serial (ccpn.core.CalculationStep.CalculationStep attribute)
(ccpn.core.ChemicalShiftList.ChemicalShiftList attribute)
(ccpn.core.DataSet.DataSet attribute)
(ccpn.core.Integral.Integral attribute)
(ccpn.core.IntegralList.IntegralList attribute)
(ccpn.core.Model.Model attribute)
(ccpn.core.NmrAtom.NmrAtom attribute)
(ccpn.core.NmrChain.NmrChain attribute)
(ccpn.core.NmrResidue.NmrResidue attribute)
(ccpn.core.Note.Note attribute)
(ccpn.core.Peak.Peak attribute)
(ccpn.core.PeakList.PeakList attribute)
(ccpn.core.Restraint.Restraint attribute)
(ccpn.core.RestraintContribution.RestraintContribution attribute)
(ccpn.core.RestraintList.RestraintList attribute)
setAtomBFactors() (ccpn.core.StructureEnsemble.StructureEnsemble method)
setAtomCoordinates() (ccpn.core.StructureEnsemble.StructureEnsemble method)
setAtomOccupancies() (ccpn.core.StructureEnsemble.StructureEnsemble method)
setAtomSpecificNames() (ccpn.core.StructureEnsemble.StructureEnsemble method)
setAvailablePlotData() (ccpn.AnalysisMetabolomics.Decomposition.Decomposition method)
setButtons() (ccpn.AnalysisScreen.popups.LookupSetupPopup.LookupSetupPopup method)
setCategory() (ccpn.util.Bmrb.bmrb.loop method)
setCurrentPeak() (ccpn.AnalysisAssign.modules.ModifyAssignmentModule.ModifyAssignmentModule method)
setDashedLineBoundaries() (ccpn.AnalysisMetabolomics.PickandFit.PickandFitTable method)
setHashCode() (in module ccpn.util.Register)
setLinePosition() (ccpn.AnalysisMetabolomics.GuiPipeLine.ExcludeBaselinePoints method)
setMode() (ccpn.AnalysisAssign.modules.SequenceGraph.SequenceGraph method)
setNmrChainDisplay() (ccpn.AnalysisAssign.modules.SequenceGraph.SequenceGraph method)
setParameter() (ccpn.core.Data.Data method)
setPathDetectorWidget() (ccpn.AnalysisScreen.popups.LookupSetupPopup.LookupSetupPopup method)
setPositions() (ccpn.AnalysisMetabolomics.GuiPipeLine.AlignToReference method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.PolyBaseline method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.SegmentalAlign method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.WhittakerBaseline method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.WhittakerSmooth method)
(ccpn.AnalysisMetabolomics.Integration.IntegrationWidget method)
setRegionLimits() (ccpn.AnalysisMetabolomics.PickandFit.PickandFitTable method)
setSubstancename() (ccpn.AnalysisMetabolomics.IntegralAssignment.SubstanceTable method)
setTagPrefix() (ccpn.util.Bmrb.bmrb.saveframe method)
setUp() (ccpn.ui.Ui.Ui class method)
setupAreaView() (ccpn.AnalysisMetabolomics.Integration.IntegrationTable method)
setupMenus() (ccpn.AnalysisAssign.AnalysisAssign.Assign method)
(ccpn.AnalysisMetabolomics.AnalysisMetabolomics.Metabolomics method)
(ccpn.AnalysisScreen.AnalysisScreen.Screen method)
(ccpn.framework.Framework.Framework method)
setupSamples() (in module ccpn.AnalysisScreen.lib.MixtureGeneration)
setupSpectralView() (ccpn.AnalysisMetabolomics.Integration.IntegrationTable method)
setValueInValueList() (ccpn.AnalysisMetabolomics.GuiPipeLine.PolyBaseline method)
shortClassName (ccpn.core.Atom.Atom attribute)
(ccpn.core.CalculationStep.CalculationStep attribute)
(ccpn.core.Chain.Chain attribute)
(ccpn.core.ChemicalShift.ChemicalShift attribute)
(ccpn.core.ChemicalShiftList.ChemicalShiftList attribute)
(ccpn.core.Complex.Complex attribute)
(ccpn.core.Data.Data attribute)
(ccpn.core.DataSet.DataSet attribute)
(ccpn.core.Integral.Integral attribute)
(ccpn.core.IntegralList.IntegralList attribute)
(ccpn.core.Model.Model attribute)
(ccpn.core.NmrAtom.NmrAtom attribute)
(ccpn.core.NmrChain.NmrChain attribute)
(ccpn.core.NmrResidue.NmrResidue attribute)
(ccpn.core.Note.Note attribute)
(ccpn.core.Peak.Peak attribute)
(ccpn.core.PeakList.PeakList attribute)
(ccpn.core.Project.Project attribute)
(ccpn.core.PseudoDimension.PseudoDimension attribute)
(ccpn.core.Residue.Residue attribute)
(ccpn.core.Restraint.Restraint attribute)
(ccpn.core.RestraintContribution.RestraintContribution attribute)
(ccpn.core.RestraintList.RestraintList attribute)
(ccpn.core.Sample.Sample attribute)
(ccpn.core.SampleComponent.SampleComponent attribute)
(ccpn.core.Spectrum.Spectrum attribute)
(ccpn.core.SpectrumGroup.SpectrumGroup attribute)
(ccpn.core.SpectrumHit.SpectrumHit attribute)
(ccpn.core.SpectrumReference.SpectrumReference attribute)
(ccpn.core.StructureEnsemble.StructureEnsemble attribute)
(ccpn.core.Substance.Substance attribute)
shortName (ccpn.core.Chain.Chain attribute)
(ccpn.core.NmrChain.NmrChain attribute)
(ccpn.core.Residue.Residue attribute)
showAboutCcpn() (ccpn.framework.Framework.Framework method)
showAboutPopup() (ccpn.framework.Framework.Framework method)
showApplicationPreferences() (ccpn.framework.Framework.Framework method)
showAtomSelector() (ccpn.framework.Framework.Framework method)
showBackboneAssignmentModule() (ccpn.AnalysisAssign.AnalysisAssign.Assign method)
showBackboneTutorial() (ccpn.framework.Framework.Framework method)
showBackupPopup() (ccpn.framework.Framework.Framework method)
showBeginnersTutorial() (ccpn.framework.Framework.Framework method)
showCcpnLicense() (ccpn.framework.Framework.Framework method)
showChemicalShiftTable() (ccpn.framework.Framework.Framework method)
showCodeInspectionPopup() (ccpn.framework.Framework.Framework method)
showCommandHelp() (ccpn.framework.Framework.Framework method)
showDecompositionModule() (ccpn.AnalysisMetabolomics.AnalysisMetabolomics.Metabolomics method)
showExperimentTypePopup() (ccpn.framework.Framework.Framework method)
showFeedbackPopup() (ccpn.framework.Framework.Framework method)
showHitAnalysisModule() (ccpn.AnalysisScreen.AnalysisScreen.Screen method)
showIntegrationModule() (ccpn.framework.Framework.Framework method)
showIssuesList() (ccpn.framework.Framework.Framework method)
showLicense() (ccpn.framework.Framework.Framework method)
showMacroEditor() (ccpn.framework.Framework.Framework method)
showMixtureGenerationPopup() (ccpn.AnalysisScreen.AnalysisScreen.Screen method)
showModifyAssignmentModule() (ccpn.AnalysisAssign.AnalysisAssign.Assign method)
showMoleculePopup() (ccpn.framework.Framework.Framework method)
showNmrResidueTable() (ccpn.framework.Framework.Framework method)
showParassignSetup() (ccpn.framework.Framework.Framework method)
showPeakAssigner() (ccpn.AnalysisAssign.AnalysisAssign.Assign method)
showPeakPickPopup() (ccpn.framework.Framework.Framework method)
showPeakTable() (ccpn.framework.Framework.Framework method)
showPickAndAssignModule() (ccpn.AnalysisAssign.AnalysisAssign.Assign method)
showPickPeakPopup() (ccpn.AnalysisScreen.AnalysisScreen.Screen method)
showPipeline() (ccpn.AnalysisMetabolomics.AnalysisMetabolomics.Metabolomics method)
showProjectionPopup() (ccpn.framework.Framework.Framework method)
showRefChemicalShifts() (ccpn.framework.Framework.Framework method)
showResidueInformation() (ccpn.AnalysisAssign.AnalysisAssign.Assign method)
showSampleAnalysis() (ccpn.AnalysisScreen.AnalysisScreen.Screen method)
showScoresOnListWidget() (ccpn.AnalysisScreen.modules.MixtureOptimisation.MixtureOptimisation method)
showScoresPerMixture() (in module ccpn.AnalysisScreen.lib.SimulatedAnnealing)
showScreeningSetup() (ccpn.AnalysisScreen.AnalysisScreen.Screen method)
showSequenceGraph() (ccpn.AnalysisAssign.AnalysisAssign.Assign method)
(ccpn.framework.Framework.Framework method)
showSequenceModule() (ccpn.framework.Framework.Framework method)
showSetupNmrResiduesPopup() (ccpn.AnalysisAssign.AnalysisAssign.Assign method)
showShortcuts() (ccpn.framework.Framework.Framework method)
showSidechainAssignmentModule() (ccpn.AnalysisAssign.AnalysisAssign.Assign method)
showSpectrumGroupsPopup() (ccpn.framework.Framework.Framework method)
showSubmitMacroPopup() (ccpn.framework.Framework.Framework method)
showUpdatePopup() (ccpn.framework.Framework.Framework method)
showVersion3Documentation() (ccpn.framework.Framework.Framework method)
SideChainAssignmentModule (class in ccpn.AnalysisAssign.modules.SideChainAssignmentModule)
SimulatedAnnealingWidgets (class in ccpn.AnalysisScreen.modules.MixtureOptimisation)
sineWindowShifts (ccpn.core.Spectrum.Spectrum attribute)
skipUserPreferences (ccpn.framework.Framework.Arguments attribute)
sliceColour (ccpn.core.Spectrum.Spectrum attribute)
slopes (ccpn.core.Integral.Integral attribute)
smiles (ccpn.core.Substance.Substance attribute)
sortNmrAtomPairs() (ccpn.AnalysisAssign.modules.SideChainAssignmentModule.SideChainAssignmentModule method)
sortRows() (ccpn.util.Bmrb.bmrb.loop method)
sortTags() (ccpn.util.Bmrb.bmrb.saveframe method)
sources (ccpn.AnalysisMetabolomics.Decomposition.Decomposition attribute)
spectra (ccpn.core.ChemicalShiftList.ChemicalShiftList attribute)
(ccpn.core.Project.Project attribute)
(ccpn.core.Sample.Sample attribute)
(ccpn.core.SpectrumGroup.SpectrumGroup attribute)
spectraDicToBrukerExperiment() (in module ccpn.AnalysisMetabolomics.lib.persistence)
spectralWidth (ccpn.core.SpectrumReference.SpectrumReference attribute)
spectralWidths (ccpn.core.Spectrum.Spectrum attribute)
spectralWidthsHz (ccpn.core.Spectrum.Spectrum attribute)
spectrometerFrequencies (ccpn.core.Spectrum.Spectrum attribute)
spectrometerFrequency (ccpn.core.SpectrumReference.SpectrumReference attribute)
spectrum (ccpn.core.IntegralList.IntegralList attribute)
(ccpn.core.PeakList.PeakList attribute)
(ccpn.core.PseudoDimension.PseudoDimension attribute)
(ccpn.core.SpectrumHit.SpectrumHit attribute)
(ccpn.core.SpectrumReference.SpectrumReference attribute)
Spectrum (class in ccpn.core.Spectrum)
spectrum2Nef() (ccpn.core.lib.CcpnNefIo.CcpnNefWriter method)
spectrumDisplays (ccpn.core.Project.Project attribute)
spectrumFromPeaks() (in module ccpn.AnalysisScreen.lib.Screening)
spectrumGroup (ccpn.framework.Current.Current attribute)
SpectrumGroup (class in ccpn.core.SpectrumGroup)
spectrumGroups (ccpn.core.Project.Project attribute)
(ccpn.core.Spectrum.Spectrum attribute)
SpectrumHit (class in ccpn.core.SpectrumHit)
spectrumHits (ccpn.core.Project.Project attribute)
(ccpn.core.PseudoDimension.PseudoDimension attribute)
(ccpn.core.Sample.Sample attribute)
(ccpn.core.SampleComponent.SampleComponent attribute)
(ccpn.core.Spectrum.Spectrum attribute)
spectrumLimits (ccpn.core.Spectrum.Spectrum attribute)
SpectrumReference (class in ccpn.core.SpectrumReference)
spectrumReferences (ccpn.core.Project.Project attribute)
(ccpn.core.Spectrum.Spectrum attribute)
SpectrumSelectionWidget (class in ccpn.AnalysisAssign.modules.PickAndAssignModule)
spectrumViews (ccpn.core.Project.Project attribute)
(ccpn.core.Spectrum.Spectrum attribute)
spinningRate (ccpn.core.Spectrum.Spectrum attribute)
splitId() (in module ccpn.core.lib.Pid)
splitIntFromChars() (in module ccpn.util.Common)
splitPath() (in module ccpn.util.Path)
start() (ccpn.framework.Framework.Framework method)
(ccpn.ui.Ui.Ui method)
startData() (ccpn.util.Bmrb.passthrough.Handler method)
startLoop() (ccpn.util.Bmrb.passthrough.Handler method)
startMacroRecord() (ccpn.framework.Framework.Framework method)
startSaveframe() (ccpn.util.Bmrb.passthrough.Handler method)
str (ccpn.core.lib.Pid.Pid attribute)
stringSortKey() (in module ccpn.core.lib.CcpnSorting)
(in module ccpn.util.Sorting)
stringToIdentifier() (in module ccpn.util.Common)
strip (ccpn.framework.Current.Current attribute)
strips (ccpn.core.Project.Project attribute)
structureEnsemble (ccpn.core.Model.Model attribute)
StructureEnsemble (class in ccpn.core.StructureEnsemble)
structureEnsembles (ccpn.core.Project.Project attribute)
substance (ccpn.core.Chain.Chain attribute)
(ccpn.core.SampleComponent.SampleComponent attribute)
Substance (class in ccpn.AnalysisMetabolomics.IntegralAssignment)
(class in ccpn.AnalysisMetabolomics.PeakAssignment)
(class in ccpn.core.Substance)
substance2Nef() (ccpn.core.lib.CcpnNefIo.CcpnNefWriter method)
substanceCallback() (ccpn.AnalysisMetabolomics.IntegralAssignment.SubstanceTable method)
(ccpn.AnalysisMetabolomics.PeakAssignment.SubstanceTable method)
substanceName (ccpn.core.SpectrumHit.SpectrumHit attribute)
substances (ccpn.core.Project.Project attribute)
SubstanceTable (class in ccpn.AnalysisMetabolomics.IntegralAssignment)
(class in ccpn.AnalysisMetabolomics.PeakAssignment)
substanceType (ccpn.core.Substance.Substance attribute)
subtract() (ccpn.AnalysisMetabolomics.lib.commands.Command method)
subtractPeakLists() (ccpn.core.PeakList.PeakList method)
suggestFileLocations() (in module ccpn.util.Path)
suspendNotification() (ccpn.core.Project.Project method)
symbolColour (ccpn.core.IntegralList.IntegralList attribute)
(ccpn.core.PeakList.PeakList attribute)
symbolStyle (ccpn.core.PeakList.PeakList attribute)
synonyms (ccpn.core.Substance.Substance attribute)

T

t2ConfLimit (ccpn.AnalysisMetabolomics.lib.decomposition.PCA attribute)
t2Scores_ (ccpn.AnalysisMetabolomics.lib.decomposition.PCA attribute)
tableCallback() (ccpn.AnalysisMetabolomics.Integration.IntegrationWidget method)
(ccpn.AnalysisMetabolomics.PickandFit.PickandFitTable method)
tag_prefix (ccpn.util.Bmrb.bmrb.saveframe attribute)
tagIterator() (ccpn.util.Bmrb.bmrb.saveframe method)
tags (ccpn.util.Bmrb.bmrb.saveframe attribute)
targetValue (ccpn.core.Restraint.Restraint attribute)
(ccpn.core.RestraintContribution.RestraintContribution attribute)
tasks (ccpn.core.Project.Project attribute)
tensor (ccpn.core.RestraintList.RestraintList attribute)
Tensor (class in ccpn.util.Tensor)
tensorChainCode (ccpn.core.RestraintList.RestraintList attribute)
tensorIsotropicValue (ccpn.core.RestraintList.RestraintList attribute)
tensorMagnitude (ccpn.core.RestraintList.RestraintList attribute)
tensorResidueType (ccpn.core.RestraintList.RestraintList attribute)
tensorRhombicity (ccpn.core.RestraintList.RestraintList attribute)
tensorSequenceCode (ccpn.core.RestraintList.RestraintList attribute)
TestUi (class in ccpn.ui.Ui)
text (ccpn.core.Note.Note attribute)
textColour (ccpn.core.IntegralList.IntegralList attribute)
(ccpn.core.PeakList.PeakList attribute)
Time (class in ccpn.util.Time)
title (ccpn.core.DataSet.DataSet attribute)
(ccpn.core.IntegralList.IntegralList attribute)
(ccpn.core.Model.Model attribute)
(ccpn.core.PeakList.PeakList attribute)
toggleConsole() (ccpn.framework.Framework.Framework method)
togglePhaseConsole() (ccpn.framework.Framework.Framework method)
togglePicking() (ccpn.AnalysisMetabolomics.GuiPipeLine.AlignToReference method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.ExcludeBaselinePoints method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.PolyBaseline method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.SegmentalAlign method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.WhittakerBaseline method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.WhittakerSmooth method)
(ccpn.AnalysisMetabolomics.Integration.IntegrationWidget method)
toggleSequenceModule() (ccpn.framework.Framework.Framework method)
toggleToolbar() (ccpn.framework.Framework.Framework method)
totalPointCounts (ccpn.core.Spectrum.Spectrum attribute)
transferType (ccpn.core.lib.SpectrumLib.MagnetisationTransferTuple attribute)
tsa() (in module ccpn.AnalysisMetabolomics.lib.normalisation)
turnOffPositionPicking() (ccpn.AnalysisMetabolomics.GuiPipeLine.AlignToReference method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.ExcludeBaselinePoints method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.PolyBaseline method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.SegmentalAlign method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.WhittakerBaseline method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.WhittakerSmooth method)
(ccpn.AnalysisMetabolomics.Integration.IntegrationWidget method)
turnOnPositionPicking() (ccpn.AnalysisMetabolomics.GuiPipeLine.AlignToReference method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.ExcludeBaselinePoints method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.PolyBaseline method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.SegmentalAlign method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.WhittakerBaseline method)
(ccpn.AnalysisMetabolomics.GuiPipeLine.WhittakerSmooth method)
(ccpn.AnalysisMetabolomics.Integration.IntegrationWidget method)
type (ccpn.core.lib.Pid.Pid attribute)
types (ccpn.util.Bmrb.bmrb.schema attribute)

U

Ui (class in ccpn.ui.Ui)
unblankNotification() (ccpn.core.Project.Project method)
Undo (class in ccpn.util.Undo)
undo() (ccpn.framework.Framework.Framework method)
(ccpn.util.Undo.Undo method)
uniquify() (in module ccpn.util.Common)
unit (ccpn.core.ChemicalShiftList.ChemicalShiftList attribute)
(ccpn.core.RestraintList.RestraintList attribute)
unitVarianceScale() (in module ccpn.AnalysisMetabolomics.lib.scaling)
universalNaturalSortKey() (in module ccpn.util.Sorting)
universalSortKey() (in module ccpn.core.lib.CcpnSorting)
(in module ccpn.util.Sorting)
unnormalisePath() (in module ccpn.util.Path)
unprocess() (ccpn.AnalysisMetabolomics.lib.commands.Command method)
unRegisterNotifier() (ccpn.core.Project.Project method)
unRegisterNotify() (ccpn.framework.Current.Current method)
UpdateAgent (class in ccpn.framework.update.UpdateAgent)
updated (ccpn.AnalysisMetabolomics.MetabolomicsPipeline.MyThread attribute)
UpdateFile (class in ccpn.framework.update.UpdateAgent)
updateFile() (in module ccpn.util.updateHeader)
updateLayout() (ccpn.AnalysisMetabolomics.GuiPipeLine.PolyBaseline method)
(ccpn.AnalysisMetabolomics.MetabolomicsPipeline.PipelineWidgets method)
(ccpn.AnalysisMetabolomics.PickandFit.AutoPick method)
(ccpn.AnalysisMetabolomics.PickandFit.Fit method)
updateMetaData() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
updateModule() (ccpn.AnalysisAssign.modules.ModifyAssignmentModule.ModifyAssignmentModule method)
updateModules() (ccpn.AnalysisAssign.modules.SideChainAssignmentModule.SideChainAssignmentModule method)
updateNmrResidueTable() (ccpn.AnalysisAssign.modules.SequenceGraph.SequenceGraph method)
updateParameters() (ccpn.core.Data.Data method)
updatePeakTable() (ccpn.AnalysisAssign.modules.ModifyAssignmentModule.ModifyAssignmentModule method)
updatePipeline() (ccpn.AnalysisMetabolomics.MetabolomicsPipeline.MetabolomicsModule method)
UpdatePopup (class in ccpn.framework.update.UpdatePopup)
updateRegion() (ccpn.AnalysisMetabolomics.GuiPipeLine.AlignToReference method)
updateServer() (in module ccpn.util.Register)
updateSpectrumCluster() (in module ccpn.AnalysisMetabolomics.lib.normalisation)
uploadData() (in module ccpn.framework.update.UpdateAgent)
uploadFile() (in module ccpn.framework.update.UpdateAgent)
(in module ccpn.util.Url)
upperLimit (ccpn.core.Restraint.Restraint attribute)
(ccpn.core.RestraintContribution.RestraintContribution attribute)
userCode (ccpn.core.Substance.Substance attribute)
uuid (ccpn.core.DataSet.DataSet attribute)

V

validate() (ccpn.util.Bmrb.bmrb.entry method)
(ccpn.util.Bmrb.bmrb.loop method)
(ccpn.util.Bmrb.bmrb.saveframe method)
(in module ccpn.util.Bmrb.bmrb)
valType() (ccpn.util.Bmrb.bmrb.schema method)
value (ccpn.core.ChemicalShift.ChemicalShift attribute)
(ccpn.core.Integral.Integral attribute)
valueError (ccpn.core.ChemicalShift.ChemicalShift attribute)
(ccpn.core.Integral.Integral attribute)
varianceScale() (in module ccpn.AnalysisMetabolomics.lib.scaling)
vastScale() (in module ccpn.AnalysisMetabolomics.lib.scaling)
vectorLength (ccpn.core.Restraint.Restraint attribute)
visitDirectory() (in module ccpn.util.updateHeader)
volume (ccpn.core.Peak.Peak attribute)
volumeError (ccpn.core.Peak.Peak attribute)

W

warning() (ccpn.core.lib.CcpnNefIo.CcpnNefReader method)
weight (ccpn.core.Restraint.Restraint attribute)
(ccpn.core.RestraintContribution.RestraintContribution attribute)
WhittakerBaseline (class in ccpn.AnalysisMetabolomics.GuiPipeLine)
whittakerBaseline() (in module ccpn.AnalysisMetabolomics.Pipeline)
WhittakerSmooth (class in ccpn.AnalysisMetabolomics.GuiPipeLine)
whittakerSmooth() (in module ccpn.AnalysisMetabolomics.Pipeline)
windowFunctions (ccpn.core.Spectrum.Spectrum attribute)
windows (ccpn.core.Project.Project attribute)
writeBruker() (in module ccpn.AnalysisMetabolomics.lib.persistence)
(in module ccpn.AnalysisScreen.lib.Screening)

X

xx (ccpn.util.Tensor.Tensor attribute)

Y

yy (ccpn.util.Tensor.Tensor attribute)

Z

zz (ccpn.util.Tensor.Tensor attribute)