ccpn.framework package

Module Documentation here

Subpackages

Submodules

ccpn.framework.Application module

Module Documentation here

class ccpn.framework.Application.ApplicationContainer(*args, **kwargs)[source]

Bases: object

A singleton class used to register the application (eg AnalysisScreen) and properties defining the top objects application, project, current and mainWindow

application = None
property current

- None, immutable -

property mainWindow

- None, immutable -

property project

- None, immutable -

register(application)[source]
class ccpn.framework.Application.Arguments(projectPath=None, **kwds)[source]

Bases: object

Class for setting FrameWork input arguments directly

debug = False
debug2 = False
debug3 = False
interface = 'NoUi'
language = 'English-UK'
nologging = True
projectPath = None
skipUserPreferences = True
ccpn.framework.Application.defineProgramArguments()[source]

Define the arguments of the program return argparse instance

ccpn.framework.Application.getApplication()[source]

Return the application instance

ccpn.framework.Application.getCurrent()[source]

Return the Current instance

ccpn.framework.Application.getMainWindow()[source]

Return the MainWindow instance (if present

ccpn.framework.Application.getProject()[source]

Return the active Project instance

ccpn.framework.AutoBackup module

This file contains AutoBackup class

class ccpn.framework.AutoBackup.AutoBackup(q, backupFunction, sleepTime=1)[source]

Bases: threading.Thread

class MainThreadAccess[source]

Bases: PyQt5.QtCore.QObject

emit(func)[source]
runOnMainThread
run()[source]

Method representing the thread’s activity.

You may override this method in a subclass. The standard run() method invokes the callable object passed to the object’s constructor as the target argument, if any, with sequential and keyword arguments taken from the args and kwargs arguments, respectively.

ccpn.framework.Current module

class ccpn.framework.Current.Current(project)[source]

Bases: object

The current object gives access to the collection of active or selected objects and values.

Currently implemented:

chain (last selected chain); chains (all selected chains); chemicalShift (last selected chemicalShift); chemicalShifts (all selected chemicalShifts); chemicalShiftList (last selected chemicalShiftList); chemicalShiftLists (all selected chemicalShiftLists); collection (last selected collection); collections (all selected collections); dataTable (last selected dataTable); dataTables (all selected dataTables); integral (last selected integral); integrals (all selected integrals); multiplet (last selected multiplet); multiplets (all selected multiplets); nmrAtom (last selected nmrAtom); nmrAtoms (all selected nmrAtoms); nmrChain (last selected nmrChain); nmrChains (all selected nmrChains); nmrResidue (last selected nmrResidue); nmrResidues (all selected nmrResidues); peak (last selected peak); peaks (all selected peaks); residue (last selected residue); residues (all selected residues); restraint (last selected restraint); restraints (all selected restraints); sample (last selected sample); samples (all selected samples); spectrumGroup (last selected spectrumGroup); spectrumGroups (all selected spectrumGroups); spectrumHit (last selected spectrumHit); strip (last selected strip); substance (last selected substance); substances (all selected substances); violationTable (last selected violationTable); violationTables (all selected violationTables); _OldChemicalShift (last selected _OldChemicalShift); _oldChemicalShifts (all selected _oldChemicalShifts); axisCode (last selected axisCode); cursorPosition (last cursor cursorPosition - (posX,posY) tuple); guiTabl (last selected guiTabl, of any obj kind); macroFile (last selected macroFile, of any obj kind); macroFiles (last selected macroFiles, of any obj kind); pcaComponent (last selected pcaComponent, of any obj kind); pcaComponents (last selected pcaComponents, of any obj kind); position (last cursor position); positions (last cursor positions)

Use print(current) to get a list of attribute, value pairs’)

addChain(value)
addChemicalShift(value)
addChemicalShiftList(value)
addCollection(value)
addDataTable(value)
addIntegral(value)
addMacroFile(value)
addMultiplet(value)
addNmrAtom(value)
addNmrChain(value)
addNmrResidue(value)
addPcaComponent(value)
addPeak(value)
addPosition(value)
addResidue(value)
addRestraint(value)
addSample(value)
addSpectrumGroup(value)
addSubstance(value)
addViolationTable(value)
add_OldChemicalShift(value)
asString()[source]

Return string representation of self listing all attribute, value pairs

property axisCode

- None, mutable - Current axisCode

property chain

- None, mutable - Current chain

property chains

- None, mutable - Current chains

property chemicalShift

- None, mutable - Current chemicalShift

property chemicalShiftList

- None, mutable - Current chemicalShiftList

property chemicalShiftLists

- None, mutable - Current chemicalShiftLists

property chemicalShifts

- None, mutable - Current chemicalShifts

className = 'Current'
clearChains()
clearChemicalShiftLists()
clearChemicalShifts()
clearCollections()
clearDataTables()
clearIntegrals()
clearMacroFiles()
clearMultiplets()
clearNmrAtoms()
clearNmrChains()
clearNmrResidues()
clearPcaComponents()
clearPeaks()
clearPositions()
clearResidues()
clearRestraints()
clearSamples()
clearSpectrumGroups()
clearSubstances()
clearViolationTables()
clear_oldChemicalShifts()
cls

alias of ccpn.core._OldChemicalShift._OldChemicalShift

property collection

- None, mutable - Current collection

property collections

- None, mutable - Current collections

property cursorPosition

- None, mutable - Current cursorPosition

property dataTable

- None, mutable - Current dataTable

property dataTables

- None, mutable - Current dataTables

dd = {'docTemplate': 'last cursor %s'}
decreaseBlanking()[source]
field = 'positions'
property guiTabl

- None, mutable - Current guiTabl

increaseBlanking()[source]
property integral

- None, mutable - Current integral

property integrals

- None, mutable - Current integrals

ll = ['\nchain (last selected chain)', 'chains (all selected chains)', '\nchemicalShift (last selected chemicalShift)', 'chemicalShifts (all selected chemicalShifts)', '\nchemicalShiftList (last selected chemicalShiftList)', 'chemicalShiftLists (all selected chemicalShiftLists)', '\ncollection (last selected collection)', 'collections (all selected collections)', '\ndataTable (last selected dataTable)', 'dataTables (all selected dataTables)', '\nintegral (last selected integral)', 'integrals (all selected integrals)', '\nmultiplet (last selected multiplet)', 'multiplets (all selected multiplets)', '\nnmrAtom (last selected nmrAtom)', 'nmrAtoms (all selected nmrAtoms)', '\nnmrChain (last selected nmrChain)', 'nmrChains (all selected nmrChains)', '\nnmrResidue (last selected nmrResidue)', 'nmrResidues (all selected nmrResidues)', '\npeak (last selected peak)', 'peaks (all selected peaks)', '\nresidue (last selected residue)', 'residues (all selected residues)', '\nrestraint (last selected restraint)', 'restraints (all selected restraints)', '\nsample (last selected sample)', 'samples (all selected samples)', '\nspectrumGroup (last selected spectrumGroup)', 'spectrumGroups (all selected spectrumGroups)', '\nspectrumHit (last selected spectrumHit)', '\nstrip (last selected strip)', '\nsubstance (last selected substance)', 'substances (all selected substances)', '\nviolationTable (last selected violationTable)', 'violationTables (all selected violationTables)', '\n_OldChemicalShift (last selected _OldChemicalShift)', '_oldChemicalShifts (all selected _oldChemicalShifts)', '\naxisCode (last selected axisCode)', '\ncursorPosition (last cursor cursorPosition - (posX,posY) tuple)', '\nguiTabl (last selected guiTabl, of any obj kind)', '\nmacroFile (last selected macroFile, of any obj kind)', 'macroFiles (last selected macroFiles, of any obj kind)', '\npcaComponent (last selected pcaComponent, of any obj kind)', 'pcaComponents (last selected pcaComponents, of any obj kind)', '\nposition (last cursor position)', 'positions (last cursor positions)']
property macroFile

- None, mutable - Current macroFile

property macroFiles

- None, mutable - Current macroFiles

property multiplet

- None, mutable - Current multiplet

property multiplets

- None, mutable - Current multiplets

property nmrAtom

- None, mutable - Current nmrAtom

property nmrAtoms

- None, mutable - Current nmrAtoms

property nmrChain

- None, mutable - Current nmrChain

property nmrChains

- None, mutable - Current nmrChains

property nmrResidue

- None, mutable - Current nmrResidue

property nmrResidues

- None, mutable - Current nmrResidues

property pcaComponent

- None, mutable - Current pcaComponent

property pcaComponents

- None, mutable - Current pcaComponents

property peak

- None, mutable - Current peak

property peaks

- None, mutable - Current peaks

property pid

- None, immutable -

property position

- None, mutable - Current position

property positions

- None, mutable - Current positions

property project

- None, immutable - Project attached to current

registerNotify(notify, field)[source]

Register notifier function ‘notify’ to be called on field ‘field’

Return notify

E.g. current.registerNotify(highlightSelectedPeaks, ‘peaks’) Where highlightSelectedPeaks is a function that takes a list of peaks as its only input

Notifiers are attached to the Current OBJECT, not to the class They are therefore removed when a new project is created/loaded Otherwise it is the responsibility of the adder to remove them when no longer relevant for which the notifier function object must be kept around. The function is attached to the field and is executed after the field value changes In practice this goes through the setter for (the equivalent of) Current.spectra The notifier function is passed the new value of the field as its only parameter. If you need a graphics object (e.g. a module) you must make and register a bound method on the module.

removeChain(value)
removeChemicalShift(value)
removeChemicalShiftList(value)
removeCollection(value)
removeDataTable(value)
removeIntegral(value)
removeMacroFile(value)
removeMultiplet(value)
removeNmrAtom(value)
removeNmrChain(value)
removeNmrResidue(value)
removePcaComponent(value)
removePeak(value)
removePosition(value)
removeResidue(value)
removeRestraint(value)
removeSample(value)
removeSpectrumGroup(value)
removeSubstance(value)
removeViolationTable(value)
remove_OldChemicalShift(value)
property residue

- None, mutable - Current residue

property residues

- None, mutable - Current residues

property restraint

- None, mutable - Current restraint

property restraints

- None, mutable - Current restraints

property sample

- None, mutable - Current sample

property samples

- None, mutable - Current samples

shortClassName = 'CU'

Short class name, for PID.

property spectrumGroup

- None, mutable - Current spectrumGroup

property spectrumGroups

- None, mutable - Current spectrumGroups

property spectrumHit

- None, mutable - Current spectrumHit

ss = 'positions'
property state

- None, immutable - Returns a storable representation of current objs in a ordered Dict. Keys the class name, values: pids, float/int or Nones. [] for plural cases. Used to dump in json file to save a restore the state when opening/closing a project

property strip

- None, mutable - Current strip

property substance

- None, mutable - Current substance

property substances

- None, mutable - Current substances

unRegisterNotify(notify, field)[source]

Remove notifier for field

property violationTable

- None, mutable - Current violationTable

property violationTables

- None, mutable - Current violationTables

ccpn.framework.Current.noCap(string)[source]

return de-capitalised string

ccpn.framework.Framework module

class ccpn.framework.Framework.Framework(args=<ccpn.framework.Application.Arguments object>)[source]

Bases: ccpn.core.lib.Notifiers.NotifierBase, ccpn.ui.gui.GuiBase.GuiBase

The Framework class is the base class for all applications.

applicationName = None
applicationVersion = None
property archivesPath: ccpn.util.Path.Path

- ccpn.util.Path.Path, immutable - :return: the absolute path to the archives sub-directory of the current project

as a Path instance

copyStrip()[source]
property current: ccpn.framework.Current.Current

- ccpn.framework.Current.Current, immutable - Current contains selected peaks, selected restraints, cursor position, etc. see Current.py for detailed descriptiom :return the Current object

property dataPath: ccpn.util.Path.Path

- ccpn.util.Path.Path, immutable - :return: the absolute path to the data sub-directory of the current project

as a Path instance

defineUserShortcuts()[source]
get(identifier)[source]

General method to obtain object (either gui or data) from identifier (pid, gid, obj-string) :param identifier: a Pid, Gid or string object identifier :return a Version-3 core data or graphics object

getByGid(gid)[source]

Legacy; obtain graphics object from identifier (gid or obj-string) replaced by get(identifier). :param gid: a Gid or string object identifier :return a Version-3 graphics object

getByPid(pid)[source]

Legacy; obtain data object from identifier (pid or obj-string) replaced by get(identifier). :param pid: a Pid or string object identifier :return a Version-3 core data object

property hasGui: bool

- bool, immutable - :return True if application has a gui

inspectMolecule()[source]
loadData(*paths, pathFilter=None) → list[source]

Loads data from paths. Optionally filter for dataFormat(s) :param *paths: argument list of path’s (str or Path instances) :param pathFilter: keyword argument: list/tuple of dataFormat strings :returns list of loaded objects

loadProject(path=None) → ccpn.core.Project.Project[source]

Load project defined by path :return a Project instance

loadSpectra(*paths) → list[source]

Load all the spectra found in paths.

Parameters

paths – list of paths

:return a list of Spectra instances

property mainWindow

- None, immutable - :returns: MainWindow instance if application has a Gui or None otherwise

makeStripPlotPopup(includePeakLists=True, includeNmrChains=True, includeNmrChainPullSelection=True)[source]
newProject(name: str = 'default') → ccpn.core.Project.Project[source]

Create new, empty project with name :return a Project instance

property pipelinePath: ccpn.util.Path.Path

- ccpn.util.Path.Path, immutable - :return: the absolute path to the state/pipeline sub-directory of

the current project as a Path instance

property pluginDataPath: ccpn.util.Path.Path

- ccpn.util.Path.Path, immutable - :return: the absolute path to the data/plugins sub-directory of the

current project as a Path instance

property project: ccpn.core.Project.Project

- ccpn.core.Project.Project, immutable - :return currently active project

redo()[source]
resetZoom()[source]
restoreFromArchive(archivePath) → ccpn.core.Project.Project[source]

Restore a project from archive path :return the restored project or None on error

runMacro(macroFile: Optional[str] = None)[source]

Runs a macro if a macro is specified, or opens a dialog box for selection of a macro file and then runs the selected macro.

saveProject() → bool[source]

Save project. :return True if successful

saveProjectAs(newPath, overwrite: bool = False) → bool[source]

Save project to newPath :param newPath: new path to save project (str | Path instance) :param overwrite: flag to indicate overwriting of existing path :return True if successful

saveToArchive() → ccpn.util.Path.Path[source]

Archive the project. :return location of the archive as a Path instance

property scriptsPath: ccpn.util.Path.Path

- ccpn.util.Path.Path, immutable - :return: the absolute path to the script sub-directory of the current project

as a Path instance

showChemicalShiftMapping(position: str = 'top', relativeTo: Optional[ccpn.ui.gui.modules.CcpnModule.CcpnModule] = None)[source]
showChemicalShiftTable(position: str = 'bottom', relativeTo: ccpn.ui.gui.modules.CcpnModule.CcpnModule = None, chemicalShiftList=None, selectFirstItem=False)[source]

Displays Chemical Shift table.

showCollectionModule(position='bottom', relativeTo=None, collection=None, selectFirstItem=False)[source]

Displays Collection Module

showCopyPeakListPopup()[source]
showCopyPeaks()[source]
showCreateChainPopup()[source]

Displays sequence creation popup.

showDataTable(position='bottom', relativeTo=None, dataTable=None, selectFirstItem=False)[source]

Displays DataTable Table

showEstimateVolumesPopup()[source]

Displays Estimate Volumes Popup.

showExperimentTypePopup()[source]

Displays experiment type popup.

showFlipArbitraryAxisPopup()[source]
showIntegralTable(position: str = 'left', relativeTo: ccpn.ui.gui.modules.CcpnModule.CcpnModule = None, integralList: ccpn.core.IntegralList.IntegralList = None, selectFirstItem=False)[source]

Displays integral table on left of main window with specified list selected.

showMultipletTable(position: str = 'left', relativeTo: ccpn.ui.gui.modules.CcpnModule.CcpnModule = None, multipletList: ccpn.core.MultipletList.MultipletList = None, selectFirstItem=False)[source]

Displays multipletList table on left of main window with specified list selected.

showNmrResidueTable(position='bottom', relativeTo=None, nmrChain=None, selectFirstItem=False)[source]

Displays Nmr Residue Table

showNotesEditor(position: str = 'bottom', relativeTo: ccpn.ui.gui.modules.CcpnModule.CcpnModule = None, note=None, selectFirstItem=False)[source]

Displays Notes Editing Table

showPeakPick1DPopup()[source]

Displays Peak Picking 1D Popup.

showPeakPickNDPopup()[source]

Displays Peak Picking ND Popup.

showPeakTable(position: str = 'left', relativeTo: ccpn.ui.gui.modules.CcpnModule.CcpnModule = None, peakList: ccpn.core.PeakList.PeakList = None, selectFirstItem=False)[source]

Displays Peak table on left of main window with specified list selected.

showPrintSpectrumDisplayPopup()[source]

Show the print spectrumDisplay dialog

showProjectionPopup()[source]
showReferenceChemicalShifts(position='left', relativeTo=None)[source]

Displays Reference Chemical Shifts module.

showReorderPeakListAxesPopup()[source]

Displays Reorder PeakList Axes Popup.

showResidueInformation(position: str = 'bottom', relativeTo: ccpn.ui.gui.modules.CcpnModule.CcpnModule = None)[source]

Displays Residue Information module.

showResidueTable(position='bottom', relativeTo=None, chain=None, selectFirstItem=False)[source]

Displays Residue Table

showRestraintAnalysisTable(position: str = 'bottom', relativeTo: ccpn.ui.gui.modules.CcpnModule.CcpnModule = None, peakList=None, selectFirstItem=False)[source]

Displays restraint analysis table.

showRestraintTable(position: str = 'bottom', relativeTo: ccpn.ui.gui.modules.CcpnModule.CcpnModule = None, restraintTable: ccpn.core.PeakList.PeakList = None, selectFirstItem=False)[source]

Displays Peak table on left of main window with specified list selected.

showSpectrumGroupsPopup()[source]
showStructureTable(position='bottom', relativeTo=None, structureEnsemble=None, selectFirstItem=False)[source]

Displays Structure Table

showValidateSpectraPopup(spectra=None, defaultSelected=None)[source]

Displays validate spectra popup.

showViolationTable(position: str = 'bottom', relativeTo: ccpn.ui.gui.modules.CcpnModule.CcpnModule = None, violationTable: ccpn.core.PeakList.PeakList = None, selectFirstItem=False)[source]

Displays Peak table on left of main window with specified list selected.

property spectraPath

- None, immutable - :return: the absolute path to the data sub-directory of the current project

as a Path instance

property statePath: ccpn.util.Path.Path

- ccpn.util.Path.Path, immutable - :return: the absolute path to the state sub-directory of the current project

as a Path instance

property tempMacrosPath: ccpn.util.Path.Path

- ccpn.util.Path.Path, immutable - :return: the absolute path to the ~/.ccpn/macros directory

as a Path instance

togglePhaseConsole()[source]
toggleSpectrumToolbar()[source]
toggleToolbar()[source]
undo()[source]
class ccpn.framework.Framework.MyProgramme(args=<ccpn.framework.Application.Arguments object>)[source]

Bases: ccpn.framework.Framework.Framework

My first app

applicationName = 'CcpNmr'
applicationVersion = '3.1.0.beta1'
ccpn.framework.Framework.createFramework(projectPath=None, **kwds)[source]
ccpn.framework.Framework.testMain()[source]

ccpn.framework.PathsAndUrls module

This file contains path definitions and Url definitions

ccpn.framework.Preferences module

This file contains the Preference object and related methods;

class ccpn.framework.Preferences.Preferences(*args, **kwargs)[source]

Bases: ccpn.util.AttrDict.AttrDict

A singleton class to hold the preferences, implemented as a AttrDict-of-AttrDict-of-AttrDict

dashes = '-----'
get(key, default=None)[source]

Return the value for key if key is in the dictionary, else default. Check for key to be a “dotted” one; e.g. “aap.noot” If so, recusively decent.

print()[source]

Print items of self

ccpn.framework.Preferences.getPreferences()[source]

Return the Preferences instance

ccpn.framework.Translation module

Translation and translation dictionary handling

the application can import the translator instance for translation and use:

translator.setLanguage(language) translator.translate(text)

To silence the message, e.g. when initiating dynamical menus with recent files use: translator.setSilent() translator.setLoud()

To have both defaultLanguage and translated language: translator.setDebug(True)

there are translation dictionaries associated with this module for really common words like “Help”

ccpn.framework.Translation.getTranslator(language)[source]

ccpn.framework.Version module

Top level application version file

class ccpn.framework.Version.VersionString(string: str, **kwds)[source]

Bases: str

Version-string routines, adapted from path idea in: Python Cookbook, A. Martelli and D. Ascher (eds), O’Reilly 2002, pgs 140-142

A VersionString is a string with extra functionality. It consists of three non-empty and one optional substrings separated by a mandatory dot ‘.’ character:

majorVersion.minorVersion.microVersion[.release]

Examples: 3.0.4; 3.1.0.alpha

The isValid function checks for validity

The majorVersion, minorVersion, microVersion and release fields are available as properties.

A VersionString instance supports comparisons with either another VersionString instance or a suitable formatted string; e.g.

VersionString(‘3.1.0.alpha’) > VersionString(‘3.0.4’) yields True VersionString(‘3.1.0.alpha’) < ‘3.0.2’ yields False

property asStr: str

- str, immutable - Convenience: return as string rather than object; allows to do things as obj.asPid.str rather then str(obj.asPid)

property fields: tuple

- tuple, immutable - Return a tuple of the fields of self

property majorVersion: str

- str, immutable - return majorVersion field of self

property microVersion: str

- str, immutable - return microVersion field of self

property minorVersion: str

- str, immutable - return minorVersion field of self

property release: str

- str, immutable - return release field of self, or None if it does not exist

withoutRelease() → str[source]

Convenience: return self as str with the release field

ccpn.framework.constants module

ccpn.framework.credits module

This module defines the code for creating the credits

ccpn.framework.credits.printCreditsText(fp, programName, version)[source]

Initial text to terminal