ccpn.AnalysisScreen.pipes package

Submodules

ccpn.AnalysisScreen.pipes.AnnotatePeaks module

class ccpn.AnalysisScreen.pipes.AnnotatePeaks.SetPeakAnnotationsFromSpectrumGuiPipe(name='Annotate Peaks', parent=None, project=None, **kw)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Annotate Peaks'
class ccpn.AnalysisScreen.pipes.AnnotatePeaks.SetPeakAnnotationsFromSpectrumPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

Annotate peaks in the input spectra using available options:

  • parent spectrum Name

  • reference Substance name linked to the parent spectrum

  • others to be implemented ( such as a free entry Regex text )

guiPipe

alias of ccpn.AnalysisScreen.pipes.AnnotatePeaks.SetPeakAnnotationsFromSpectrumGuiPipe

pipeCategory = 'AnalysisScreen'
pipeName = 'Annotate Peaks'
runPipe(spectra)[source]
Parameters

spectra – inputData

Returns

spectra

ccpn.AnalysisScreen.pipes.CopyPeakListsBetweenSG module

class ccpn.AnalysisScreen.pipes.CopyPeakListsBetweenSG.CopyPeakListsBetweenSGroupsGuiPipe(name='Copy PeakLists', parent=None, project=None, **kw)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Copy PeakLists'
class ccpn.AnalysisScreen.pipes.CopyPeakListsBetweenSG.CopyPeakListsBetweenSGroupsPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

Apply phasing to all the spectra in the pipeline

guiPipe

alias of ccpn.AnalysisScreen.pipes.CopyPeakListsBetweenSG.CopyPeakListsBetweenSGroupsGuiPipe

pipeCategory = 'AnalysisScreen'
pipeName = 'Copy PeakLists'
runPipe(spectra)[source]
Parameters

spectra – inputData

Returns

spectra

ccpn.AnalysisScreen.pipes.CreateSTD module

class ccpn.AnalysisScreen.pipes.CreateSTD.STDCreator(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

guiPipe

alias of ccpn.AnalysisScreen.pipes.CreateSTD.STDCreatorGuiPipe

pipeCategory = 'AnalysisScreen'
pipeName = 'STD Creator'
runPipe(spectra)[source]
Parameters

spectra – inputData

Returns

aligned spectra

class ccpn.AnalysisScreen.pipes.CreateSTD.STDCreatorGuiPipe(name='STD Creator', parent=None, project=None, **kwds)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'STD Creator'
ccpn.AnalysisScreen.pipes.CreateSTD.spectrumDifference(spectrumA, spectrumB)[source]
Parameters

  • spectrumA – first spectrum

  • spectrumB – second spectrum

Returns

diff. An array with the abs intensity difference between the two spectra Spectrum A and B must have the same number of position points.

This array can be used for create a new spectrum. Like an STD

ccpn.AnalysisScreen.pipes.HitFinder module

ccpn.AnalysisScreen.pipes.LinkSubstancesToSpectrum module

class ccpn.AnalysisScreen.pipes.LinkSubstancesToSpectrum.LinkSubstancesToSpectrumGuiPipe(name='Link Substances To Spectrum', parent=None, project=None, **kw)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Link Substances To Spectrum'
class ccpn.AnalysisScreen.pipes.LinkSubstancesToSpectrum.LinkSubstancesToSpectrumPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

Link substances to a spectrum recorded for a mixture of screening substances. Normally a substance has a link to the reference spectrum for one single compound. 1:1 link

The spectrum recorded for a mixture is linked to sample. The sample is made by components linked to substances of same name. In this pipe all those substances will be directly linked to to the mixture spectrum

MixtureSpectrum -> ReferenceSubstances = [Empty] MixtureSpectrum -> Sample -> SampleComponent -> Substance -> ReferenceSpectrum

new link from this pipe: MixtureSpectrum -> ReferenceSubstances = [all substances in the MixtureSpectrum.sample]

As a result, references don’t need be loaded for screening Analysis. See Recurrent Screening Analyses Manual

guiPipe

alias of ccpn.AnalysisScreen.pipes.LinkSubstancesToSpectrum.LinkSubstancesToSpectrumGuiPipe

pipeCategory = 'AnalysisScreen'
pipeName = 'Link Substances To Spectrum'
runPipe(spectra)[source]
Parameters

spectra – inputData

Returns

spectra

ccpn.AnalysisScreen.pipes.OutputHits module

class ccpn.AnalysisScreen.pipes.OutputHits.OutputHitsGuiPipe(name='Output Hits', parent=None, project=None, **kwds)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Output Hits'
class ccpn.AnalysisScreen.pipes.OutputHits.OutputHitsPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

guiPipe

alias of ccpn.AnalysisScreen.pipes.OutputHits.OutputHitsGuiPipe

pipeCategory = 'AnalysisScreen'
pipeName = 'Output Hits'
runPipe(spectra)[source]

ccpn.AnalysisScreen.pipes.PropagateFromReferences module

class ccpn.AnalysisScreen.pipes.PropagateFromReferences.PropagatePeaksFromReferencesGuiPipe(name='Propagate Peaks From References', parent=None, project=None, **kw)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Propagate Peaks From References'
class ccpn.AnalysisScreen.pipes.PropagateFromReferences.PropagatePeaksFromReferencesPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

Apply phasing to all the spectra in the pipeline

guiPipe

alias of ccpn.AnalysisScreen.pipes.PropagateFromReferences.PropagatePeaksFromReferencesGuiPipe

pipeCategory = 'AnalysisScreen'
pipeName = 'Propagate Peaks From References'
runPipe(spectra)[source]
Parameters

spectra – inputData

Returns

spectra

ccpn.AnalysisScreen.pipes.SetPeaksFigureOfMerit module

class ccpn.AnalysisScreen.pipes.SetPeaksFigureOfMerit.SetFigureOfMeritGuiPipe(name='Set Peak Figure of Merit', parent=None, project=None, **kw)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Set Peak Figure of Merit'
class ccpn.AnalysisScreen.pipes.SetPeaksFigureOfMerit.SetFigureOfMeritPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

Apply phasing to all the spectra in the pipeline

guiPipe

alias of ccpn.AnalysisScreen.pipes.SetPeaksFigureOfMerit.SetFigureOfMeritGuiPipe

pipeCategory = 'AnalysisScreen'
pipeName = 'Set Peak Figure of Merit'
runPipe(spectra)[source]
Parameters

spectra – inputData

Returns

spectra

This pipe could have other generic conditions.

ccpn.AnalysisScreen.pipes.SetupNmrAtomsPipeFromSG module

class ccpn.AnalysisScreen.pipes.SetupNmrAtomsPipeFromSG.SetupNmrAtomsFromSGroupGuiPipe(name='Setup NmrAtoms from Peaks', parent=None, project=None, **kwds)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Setup NmrAtoms from Peaks'
class ccpn.AnalysisScreen.pipes.SetupNmrAtomsPipeFromSG.SetupNmrAtomsFromSGroupPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

guiPipe

alias of ccpn.AnalysisScreen.pipes.SetupNmrAtomsPipeFromSG.SetupNmrAtomsFromSGroupGuiPipe

pipeCategory = 'AnalysisScreen'
pipeName = 'Setup NmrAtoms from Peaks'
runPipe(spectra)[source]

ccpn.AnalysisScreen.pipes.setupScreeningDataset module

class ccpn.AnalysisScreen.pipes.setupScreeningDataset.SetupScreeningDatasetGuiPipe(name='Setup Screening dataset', parent=None, project=None, **kw)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Setup Screening dataset'
class ccpn.AnalysisScreen.pipes.setupScreeningDataset.SetupScreeningDatasetPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

Apply phasing to all the spectra in the pipeline

guiPipe

alias of ccpn.AnalysisScreen.pipes.setupScreeningDataset.SetupScreeningDatasetGuiPipe

pipeCategory = 'AnalysisScreen'
pipeName = 'Setup Screening dataset'
runPipe(spectra)[source]
Parameters

spectra – inputData

Returns

spectra

# tbd: in theory this pipe should return a df or dataset