def __init__(self, parent, *args, **kw):
self.waiting = False
self.molSystem = None
self.residue = None
self.jCouplings = []
self.atomNames = []
self.measureJCouplingList = None
self.predictJCouplingList = None
self.coeffAtomNames = []
self.coefficients = {}
self.coefficient = None
for i in range(3):
self.coefficients[i] = {}
BasePopup.__init__(
self,
parent=parent,
title='Predict Karplus Coefficients from J Coupling',
**kw)
self.updateJCouplingLists()
self.updateMolSystems()
self.updateAfter()
def __init__(self, parent, *args, **kw):
self.spectrumConditions = []
self.col = None
self.spectrum = None
BasePopup.__init__(self, parent=parent, title='New Contour File', **kw)
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.sourceName = 'RefDB'
self.chemAtomNmrRefs = {}
BasePopup.__init__(self, parent=parent, title="Resonance : Reference Chemical Shifts", **kw)
def __init__(self, parent, *args, **kw):
BasePopup.__init__(self,
parent=parent,
title='Create axis unit',
modal=True,
**kw)
def __init__(self, parent, *args, **kw):
self.spectrum = None
BasePopup.__init__(self,
parent=parent,
title='Peak : Peak Finding',
**kw)
def __init__(self, parent):
BasePopup.__init__(self, parent=parent, title=" Dangle Prediction Graph",
transient=False, borderwidth=6)
parent.protocol("WM_DELETE_WINDOW", self.close)
self.geometry('700x700+50+50')
def __init__(self, parent, isModal=False, *args, **kw):
title = 'Project : Register with CCPN'
BasePopup.__init__(self,
parent=parent,
title=title,
modal=isModal,
**kw)
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.expSeries = None
self.conditionPoint = None
self.waiting = 0
BasePopup.__init__(self, parent, title="Experiment : NMR Series", **kw)
def __init__(self, parent, *args, **kw):
self.spectrum = None
BasePopup.__init__(self,
parent=parent,
title='Add existing contour file',
**kw)
def __init__(self, parent, *args, **kw):
self.measurementType = None
BasePopup.__init__(self,
parent=parent,
title='Create axis type',
modal=True,
**kw)
def __init__(self, parent, *args, **kw):
self.chain = None
self.shiftList = None
self.predictionDict = {}
BasePopup.__init__(self,
parent=parent,
title='Structure : Predict Secondary Structure')
def __init__(self, parent, *args, **kw):
self.axisType = None
BasePopup.__init__(self,
parent=parent,
title='Create panel type',
modal=True,
**kw)
def __init__(self, parent, *args, **kw):
self.waiting = False
self.contourFileDir = None
BasePopup.__init__(self,
parent=parent,
title='Spectrum Contour Files',
**kw)
def __init__(self, parent, *args, **kw):
self.experiment = None
self.currentObject = None
#self.currentObjects = [] # looks obsolete
BasePopup.__init__(self,
parent=parent,
title='Experiment : Open Spectra',
**kw)
def __init__(self, parent, *args, **kw):
self.residue = None
self.chain = None
self.shiftList = None
BasePopup.__init__(self,
parent=parent,
title="Molecule : Residue Information",
**kw)
def __init__(self, parent, dataDim, position):
self.dataDim = dataDim
self.position = position
BasePopup.__init__(self,
parent=parent,
title='Set spectrum referencing',
modal=True,
transient=True)
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.peakLists = []
self.constraintLists = []
self.constraintSet = None
BasePopup.__init__(self,
parent=parent,
title="Chart : Residue Interaction Matrix",
**kw)
def __init__(self, parent, *args, **kw):
self.chain = None
self.shiftList = None
self.predictionDict = {}
BasePopup.__init__(
self,
parent=parent,
title='Data Analysis : Predict Shifts from Sequence')
def __init__(self, parent, peak=None, *args, **kw):
self.peak = peak
self.peakDim = None
self.guiParent = parent
BasePopup.__init__(self,
parent=parent,
title="Edit Peak Aliasing",
**kw)
def __init__(self, parent, *args, **kw):
self.visibleSpectra = parent.visibleSpectra
self.toolbarSpectra = parent.toolbarSpectra
self.waiting = False
self.window = None
BasePopup.__init__(self,
parent=parent,
title='Window : New Window',
**kw)
def __init__(self, parent, *args, **kw):
self.font = 'Helvetica 10'
self.sFont = 'Helvetica %d'
self.project = parent.project
self.guiParent = parent
self.chemCompDict = {}
self.createChemCompDict()
self.waiting = False
BasePopup.__init__(self, parent,
title="Residue Type Probabilities", **kw)
def __init__(self, parent, *args, **kw):
self.groups = []
self.variableDim = 1
self.windowPane = None
self.rulers = []
self.peakLists = []
self.orthogonalDict = {}
self.parent = parent
self.searchPeaks = []
BasePopup.__init__(self, parent, title= "Peak Groups", borderwidth=5, **kw)
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.strucGen = None
self.violList = None
self.constrList = None
self.waiting = 0
BasePopup.__init__(self,
parent=parent,
title="Structure Generation Runs",
**kw)
def __init__(self, parent, *args, **kw):
self.molSystem = None
self.structure = None
self.model = None
self.waiting = False
self.colorScheme = None
self.ccpCode = None # Which Rama background to use
self.residue = None
self.labelMode = LABEL_MODES[1]
BasePopup.__init__(self, parent=parent, title='Chart : Ramachandran Plot', **kw)
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.structure = None
self.name = None
self.clouds = []
self.rmsds = []
self.names = []
self.atomTypes = None
self.waiting = 0
BasePopup.__init__(self, parent=parent, title="Filter Clouds", **kw)
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.chain = None
self.waiting = False
self.shiftList = None
self.spinSystem = None
self.preserveTypes = 0
self.progressBar = None
self.scoresPopup = None
self.threshold = -20.0
BasePopup.__init__(self, parent, title="Assignment : Spin System Typing", **kw)
def __init__(self, parent, *args, **kw):
'''Init. Args: parent: guiParent.
'''
self.guiParent = parent
self.spinSystem1 = None
self.spinSystem2 = None
self.correction = True
self.protonatedShiftList = None
self.deuteratedShiftList = None
BasePopup.__init__(self, parent, title="Compare Spin Systems", **kw)
self.waiting = False
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.peakPairs = []
self.intensityType = 'height'
self.selectedPair = None
self.assignPeakList = None
self.refPeakList = None
self.satPeakList = None
self.displayPeakList = None
self.waiting = 0
BasePopup.__init__(self, parent, title="Data Analysis : Heteronuclear NOE", **kw)
def __init__(self, parent, fixedPeak, movePeak, *args, **kw):
self.movePeakDim = None
self.fixedPeak = fixedPeak
self.movePeak = movePeak
self.setupDimMapping()
BasePopup.__init__(self,
parent=parent,
title='Reference By Peak',
modal=True,
*args,
**kw)
def __init__(self, root, programName=PROGRAM_NAME, **kw):
self.parent = root
self.programName = programName
# Application object needed to store application-specific data with project
self.application = Application(name=PROGRAM_NAME)
self.versionInfo = 'Version ' + VERSION
self.graphPopup = None
self.analysisProfile = None
# Application popup is a superclass of memops.editor.BasePoup
BasePopup.__init__(self, parent=root, title=PROGRAM_NAME,
location='+100+100', class_=self.application.name, **kw)
def __init__(self, parent, *args, **kw):
'''Init. Args: parent: guiParent.
'''
self.guiParent = parent
self.spinSystem1 = None
self.spinSystem2 = None
self.correction = True
self.protonatedShiftList = None
self.deuteratedShiftList = None
BasePopup.__init__(self, parent, title="Compare Spin Systems", **kw)
self.waiting = False
def __init__(self, parent, *args, **kw):
self.font = 'Helvetica 10'
self.sFont = 'Helvetica %d'
self.project = parent.project
self.guiParent = parent
self.chemCompDict = {}
self.createChemCompDict()
self.waiting = False
BasePopup.__init__(self,
parent,
title="Residue Type Probabilities",
**kw)
def __init__(self, parent, controler, *args, **kw):
self.font = 'Helvetica 10'
self.sFont = 'Helvetica %d'
self.project = parent.project
self.guiParent = parent
self.sourceName = 'RefDB'
self.connector = controler
self.tabbedFrame = None
self.saveLoadTab = None
self.assignTab = None
self.spectrumSelectionTab = None
self.resultsTab = None
self.annealingSettingsTab = None
self.infoLabel = None
self.waiting = False
BasePopup.__init__(self, parent, title="Assignment Suggestions", **kw)
