def body(self, guiFrame):
self.geometry('500x500')
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(1, weight=1)
frame = LabelFrame(guiFrame, text='RDC protocol settings')
frame.grid(row=1, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
self.floatEntry = FloatEntry(self, returnCallback=self.setValue)
headingList = ['Parameter', 'Value', 'Description']
justifyList = ['center', 'center', 'left']
editWidgets = [None, self.floatEntry, None]
editGetCallbacks = [None, self.getValue, None]
editSetCallbacks = [None, self.setValue, None]
self.rdcMatrix = ScrolledMatrix(frame,
headingList=headingList,
justifyList=justifyList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
multiSelect=False,
initialRows=10,
passSelfToCallback=True,
callback=self.selectRdc)
self.rdcMatrix.grid(row=0, column=0, sticky='nsew')
self.rdcMatrix.refreshFunc = self.updateRdcSet
self.updateRdcSet()
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(1, weight=1)
frame = LabelFrame(guiFrame, text='Options')
frame.grid(row=0,column=0,sticky='ew')
frame.grid_columnconfigure(5, weight=1)
# Choose type of symmetry set to define or change (if allready present in the model)
self.molLabel = Label(frame, text='Symmetry Operator:')
self.molLabel.grid(row=0,column=2,sticky='w')
self.symmCodePulldown = PulldownMenu(frame, callback=self.setSymmCode, entries=['NCS','C2','C3','C5'], do_initial_callback=False)
self.symmCodePulldown.grid(row=0,column=3,sticky='w')
frame = LabelFrame(guiFrame, text='Symmetry Operations')
frame.grid(row=1,column=0,sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
self.molSysPulldown = PulldownMenu(self, callback=self.setMolSystem, do_initial_callback=False)
self.chainSelect = MultiWidget(self, CheckButton, callback=self.setChains, minRows=0, useImages=False)
self.segStartEntry = IntEntry(self, returnCallback=self.setSegStart, width=6)
self.segLengthEntry = IntEntry(self, returnCallback=self.setSegLength, width=6)
headings = ['#','Symmetry\noperator','Mol System','Chains','Start\nresidue','Segment\nlength']
editWidgets = [None, None, self.molSysPulldown, self.chainSelect, self.segStartEntry, self.segLengthEntry]
editGetCallbacks = [None, None, self.getMolSystem, self.getChains, self.getSegStart, self.getSegLength]
editSetCallbacks = [None, self.setSymmCode, self.setMolSystem, self.setChains, self.setSegStart, self.setSegLength]
self.symmetryMatrix = ScrolledMatrix(frame,headingList=headings,
callback=self.selectSymmetry,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks)
self.symmetryMatrix.grid(row=0,column=0,sticky='nsew')
texts = ['Add Symmetry Set','Remove Symmetry Set']
commands = [self.addSymmetrySet,self.removeSymmetrySet]
self.buttonList = createDismissHelpButtonList(guiFrame, texts=texts, commands=commands, expands=True)
self.buttonList.grid(row=2,column=0,sticky='ew')
self.updateMolPartners()
self.notify(self.registerNotify)
#Temporary report of parameters
print self.molSystem
print self.molecules
print self.symmetrySet
print self.symmetryOp
print self.symmetryCode
def body(self, guiFrame):
guiFrame.grid_rowconfigure(0, weight=1)
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame = LabelFrame(guiFrame, text='Matched Peak Groups')
frame.grid_rowconfigure(0, weight=1)
frame.grid_columnconfigure(0, weight=1)
frame.grid(row=row, sticky='nsew')
headingList, tipTexts = self.getHeadingList()
self.scrolledMatrix = ScrolledMatrix(frame, initialRows=15, multiSelect=True,
headingList=headingList, tipTexts=tipTexts,
grid=(0,0), gridSpan=(1,3))
tipTexts = ['Remove the selected peak groups from the table',
'Show 1D positional ruler lines for the selected groups',
'Remove any ruler lines previously added for peak group',
'Display selected peak groups within strips of selected window']
texts = ['Remove\nGroups','Show\nRulers',
'Delete\nRulers','Display Groups\nIn Strips']
commands = [self.removeGroups,self.addRulers,
self.removeRulers,self.stripGroups]
self.buttons = ButtonList(frame, texts=texts, commands=commands, tipTexts=tipTexts)
self.buttons.grid(row=1, column=0, sticky='ew')
tipText = 'Selects the spectrum window in which to display strips & ruler lines'
label = Label(frame, text='Target window:', grid=(1,1))
self.windowPulldown = PulldownList(frame, callback=None,
grid=(1,2), tipText=tipText)
row+= 1
bottomButtons = UtilityButtonList(guiFrame, helpUrl=self.help_url, expands=True, doClone=False)
bottomButtons.grid(row = row, sticky = 'ew')
self.update()
for func in ('__init__', 'delete', 'setName'):
self.registerNotify(self.updateWindowsAfter, 'ccpnmr.Analysis.SpectrumWindow', func)
def body(self, guiFrame):
fixedSpectrum = self.fixedPeak.peakList.dataSource
moveSpectrum = self.movePeak.peakList.dataSource
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame = LabelFrame(guiFrame,
text='Working Spectra',
grid=(row, 0),
sticky='ew')
frame.grid_columnconfigure(1, weight=1)
s = '%s:%-20s' % (fixedSpectrum.experiment.name, fixedSpectrum.name)
Label(frame, text='Fixed:', grid=(0, 0), sticky='e')
tipText = 'The experiment:spectrum name of the reference spectrum, which will not be moved'
Label(frame, text=s, grid=(0, 1), tipText=tipText)
s = '%s:%-20s' % (moveSpectrum.experiment.name, moveSpectrum.name)
Label(frame, text='Moving:', grid=(0, 2), sticky='e')
tipText = 'The experiment:spectrum name of the spectrum which will be re-referenced using peak positions'
Label(frame, text=s, grid=(0, 3), tipText=tipText)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame = LabelFrame(guiFrame,
text='Peak Position Mapping',
grid=(row, 0))
frame.expandGrid(0, 0)
tipText = 'Whether the more than one moving spectrum dimension may be mapped to the same fixed spectrum dimension; typically not used but can be useful for re-referencing with a diagonal peak'
self.fixedDimsButton = CheckButton(
frame,
text='Allow repeated fixed dim',
selected=False,
grid=(0, 0),
callback=self.changedFixedDimsButton,
tipText=tipText)
self.dimPulldown = PulldownList(self, callback=self.setDimMapping)
editWidgets = [None, None, self.dimPulldown, None, None, None]
editGetCallbacks = [None, None, self.getDimMapping, None, None, None]
editSetCallbacks = [None, None, self.setDimMapping, None, None, None]
tipTexts = [
'The dimension number of the spectrum being re-referenced',
'The isotope type that corresponds to both the fixed and re-reference spectrum dimensions',
'The dimension number of the fixed spectrum, used as a reference',
'The position of the moving peak in the relevant dimension, before any changes (for the spectrum being re-referenced)',
'The position of the fixed peak in the relevant dimension; potential new position of the moving peak after re-referencing changes',
'The chemical shift difference between the two peak positions on one dimension'
]
headingList = [
'Moving\nDim', 'Isotope', 'Fixed\nDim', 'Original\nPosition',
'New\nPosition', u'\u0394'
]
self.scrolledMatrix = ScrolledMatrix(frame,
headingList=headingList,
callback=self.selectPeakDim,
editWidgets=editWidgets,
maxRows=5,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
grid=(1, 0),
tipTexts=tipTexts)
row += 1
tipTexts = [
'Use the stated mapping of dimensions to re-reference the moving spectrum so that the selected peaks lie at the same position',
]
texts = ['Commit']
commands = [self.ok]
buttons = UtilityButtonList(guiFrame,
texts=texts,
commands=commands,
closeText='Cancel',
helpUrl=self.help_url,
grid=(row, 0),
tipTexts=tipTexts)
self.update()
def body(self, guiFrame):
guiFrame.grid_columnconfigure(3, weight=1)
self.progressBar = TypingEnsemblePopup(self,total=100)
self.progressBar.close()
row = 0
label = Label(guiFrame, text=' Chain: ', grid=(row,0))
tipText = 'Selects which molecular chain the spin system residue types will be predicted for; determines which range of types are available'
self.chainPulldown = PulldownList(guiFrame, self.changeChain,
grid=(row,1), tipText=tipText)
tipText = 'Selects which shift list will be used as the source of chemical shift information to make the residue type predictions'
label = Label(guiFrame, text='Shift List: ', grid=(row,2))
self.shiftListPulldown = PulldownList(guiFrame, callback=self.setShiftList,
grid=(row,3), tipText=tipText)
utilButtons = UtilityButtonList(guiFrame, helpUrl=self.help_url)
utilButtons.grid(row=row, column=4, sticky='w')
row += 1
frame = LabelFrame(guiFrame, text='Options', grid=(row,0), gridSpan=(1,5))
frame.grid_columnconfigure(3, weight=1)
frow = 0
label = Label(frame, text='Keep existing types?',
grid=(frow,0), sticky='e')
tipText = 'Whether any existing residue type information should be preserved, when predicting the type of others'
self.preserveTypesSelect = CheckButton(frame, grid=(frow,1), selected=False,
callback=self.selectPreserveTypes,
tipText=tipText)
label = Label(frame, text='Assignment threshold: ',
grid=(frow,2), sticky='e')
tipText = 'The lower limit for the predicted residue type to be set with "Assign Types"; needs to be adjusted according to result statistics and amount of shift data'
self.thresholdEntry = FloatEntry(frame, text=self.threshold,
width=8, grid=(frow,3), tipText=tipText)
frow += 1
label = Label(frame, text='Ensemble size: ', grid=(frow,0), sticky='e')
tipText = 'The number of best scoring residue type mappings, from the Monte Carlo search, to use un the prediction'
self.ensembleEntry = IntEntry(frame,text=20,width=4,
grid=(frow,1), tipText=tipText)
label = Label(frame, text='Num Search Steps: ', grid=(frow,2), sticky='e')
tipText = 'The number of iterative steps that will be used in the Monte Carlo search of best spin system to residue type mappings'
self.stepsEntry = IntEntry(frame, text=100000, width=8,
tipText=tipText, grid=(frow,3))
frow += 1
label = Label(frame, text='Isotope shifts to consider:',
grid=(frow,0), gridSpan=(1,4))
frow += 1
self.isotopes = ['1H','13C']
isos = ['1H','13C','15N']
colors = [COLOR_DICT[x] for x in isos]
tipText = 'Selects which kinds of resonances, in terms of isotope, the residue type predictions will be made with'
self.isotopeCheckButtons = PartitionedSelector(frame, labels=isos,
objects=isos, colors=colors,
callback=self.toggleIsotope,
selected=self.isotopes,
grid=(frow,0),
gridSpan=(1,4), tipText=tipText)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
labelFrame = LabelFrame(guiFrame, text='Spin Systems', grid=(row,0), gridSpan=(1,5))
labelFrame.expandGrid(0,0)
tipTexts = ['The spin system serial number',
'The residue to which the spin system may currently be assigned',
'Set whether to include a particular spin system in the type predictions',
'The spin system to residue type match score for a prediction; higher (less negative) is better',
'The predicted types of residue that the spin system may be',
'The chemical shifts in the spin system that will be used in the analysis']
headingList = ['#','Residue','Use?','Score','Types','Shifts']
justifyList = ['center','center','center','center','center','left']
editWidgets = [None, None, None, None, None, None]
editGetCallbacks = [None, None, self.toggleInclude, None, None, None]
editSetCallbacks = [None, None, None, None, None, None]
self.scrolledMatrix = ScrolledMatrix(labelFrame, headingList=headingList,
justifyList=justifyList,
editSetCallbacks=editSetCallbacks,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
callback=self.selectCell,
grid=(0,0), tipTexts=tipTexts)
row += 1
tipTexts = ['Execute the Monte Carlo search that will make the residue type predictions for the spin systems',
'Assign the residue type of spin systems with a unique type prediction and prediction score above the stated threshold',
'Show a residue type prediction for the selected spin system alone; only considers that spin system of shifts, not how all spin systems fit to the sequence',
'Show a table of peaks that are assigned to the resonances of the selected spin system']
texts = ['Run\nTyping','Assign\nTypes',
'Show Individual\nClassification',
'Show\nPeaks']
commands = [self.run, self.assign,
self.individualScore,
self.showPeaks]
bottomButtons = ButtonList(guiFrame, texts=texts, commands=commands,
grid=(row,0), gridSpan=(1,5), tipTexts=tipTexts)
self.runButton = bottomButtons.buttons[0]
self.assignButton = bottomButtons.buttons[1]
self.scoreButton = bottomButtons.buttons[2]
self.peaksButton = bottomButtons.buttons[2]
self.runButton.config(bg='#B0FFB0')
for func in ('__init__','delete'):
self.registerNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func)
self.registerNotify(self.updateShiftLists, 'ccp.nmr.Nmr.ShiftList', func)
for func in ('__init__','delete','setCcpCode',
'setResidue','addResonance', 'setName',
'removeResonance','setResonances'):
self.registerNotify(self.updateSpinSystemsAfter, 'ccp.nmr.Nmr.ResonanceGroup', func)
self.updateChains()
self.updateShiftLists()
self.updateSpinSystems()
def body(self, guiFrame):
'''This method describes the outline of the body of the
application.
args: guiFrame: frame the body should live in.
'''
self.geometry('800x530')
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(0, weight=0)
guiFrame.grid_rowconfigure(1, weight=2)
guiFrame.grid_rowconfigure(2, weight=1)
isotopeFrame = LabelFrame(guiFrame, text='Isotope Shift Correction CA and CB')
isotopeFrame.grid(row=0, column=0, sticky='nsew')
frameA = LabelFrame(guiFrame, text='Spin Systems')
frameA.grid(row=1, column=0, sticky='nsew')
frameA.grid_rowconfigure(0, weight=1)
frameA.grid_columnconfigure(0, weight=1)
frameA.grid_columnconfigure(1, weight=1)
frameA1 = LabelFrame(frameA, text='Spin System 1')
frameA1.grid(row=0, column=0, sticky='nsew')
frameA1.grid_columnconfigure(0, weight=1)
frameA1.grid_rowconfigure(0, weight=1)
frameA2 = LabelFrame(frameA, text='Spin System 2')
frameA2.grid(row=0, column=1, sticky='nsew')
frameA2.grid_columnconfigure(0, weight=1)
frameA2.grid_rowconfigure(0, weight=1)
frameB = LabelFrame(guiFrame, text='Comparison')
frameB.grid(row=2, column=0, sticky='nsew')
frameB.grid_rowconfigure(0, weight=1)
frameB.grid_columnconfigure(0, weight=1)
frameB.grid_columnconfigure(1, weight=2)
frameB.grid_columnconfigure(2, weight=1)
frameB1 = LabelFrame(frameB, text='Unique to Spin System 1')
frameB1.grid(row=0, column=0, sticky='nsew')
frameB1.expandGrid(0, 0)
frameB2 = LabelFrame(frameB, text='Intersection')
frameB2.grid(row=0, column=1, sticky='nsew')
frameB2.expandGrid(0, 0)
frameB3 = LabelFrame(frameB, text='Unique to Spin System 2')
frameB3.grid(row=0, column=2, sticky='nsew')
frameB3.expandGrid(0, 0)
# Settings for isotope shift correction
shiftLists = getShiftLists(self.nmrProject)
self.protonatedShiftList = shiftLists[0]
self.deuteratedShiftList = shiftLists[1]
shiftListNames = ['{}: {}'.format(shiftList.serial, shiftList.name) for shiftList in shiftLists]
Label(isotopeFrame, text='Correct for isotope shift:', grid=(0, 0))
self.correctCheck = CheckButton(isotopeFrame,
selected=True,
callback=self.setCorrection,
grid=(0, 1))
Label(isotopeFrame, text='Protonated shift list:', grid=(1, 0))
self.protonatedPulldown = PulldownList(isotopeFrame,
callback=self.setProtonatedShiftList,
texts=shiftListNames,
objects=shiftLists,
grid=(1, 1),
index=0)
Label(isotopeFrame, text='Deuterated shift list:', grid=(2, 0))
self.deuteratedPulldown = PulldownList(isotopeFrame,
callback=self.setDeuteratedShiftList,
texts=shiftListNames,
objects=shiftLists,
grid=(2, 1),
index=1)
# Table A1
headingList = ['#', 'shift lists', 'Assignment']
tipTexts = ['Spin System Serial',
'shift lists', 'The residue (tentatively) assigned to this spin system',
'The amount of spin systems that overlap with this spin system and have no violations']
editGetCallbacks = [self.setSpinSystem1]*3
editSetCallbacks = [None]*3
self.tableA1 = ScrolledMatrix(frameA1, headingList=headingList,
multiSelect=False,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
tipTexts=tipTexts)
self.tableA1.grid(row=0, column=0, sticky='nsew')
# Table A2
headingList = ['#', 'shift lists', 'Assignment', 'offset']
tipTexts = ['Spin System Serial', 'The residue (tentatively) assigned to this spin system',
'Root mean squared deviation of this spin system to the spin system selected in the table on the left.']
editGetCallbacks = [self.setSpinSystem2]*4
editSetCallbacks = [None]*4
self.tableA2 = ScrolledMatrix(frameA2, headingList=headingList,
#editWidgets=editWidgets,
multiSelect=False,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
tipTexts=tipTexts)
self.tableA2.grid(row=0, column=0, sticky='nsew')
# Table B1
headingList = ['atom', 'c.s.']
tipTexts = ['atom', 'chemical shift']
self.tableB1 = ScrolledMatrix(frameB1,
headingList=headingList,
multiSelect=False,
tipTexts=tipTexts)
self.tableB1.grid(row=0, column=0, sticky='nsew')
# Table B 2
headingList = ['atom', 'c.s. 1', 'c.s. 2', 'delta c.s.']
tipTexts = ['name of the atom', 'chemical shift of atom with this name in spin system 1',
'chemical shift of atom with this name in spin system 2',
'difference between the chemical shift of spin systems 1 and 2']
self.tableB2 = ScrolledMatrix(frameB2,
headingList=headingList,
tipTexts=tipTexts)
self.tableB2.grid(row=0, column=0, sticky='nsew')
# Table B 3
headingList = ['atom', 'c.s.']
tipTexts = ['atom', 'chemical shift.']
self.tableB3 = ScrolledMatrix(frameB3,
headingList=headingList,
multiSelect=False,
tipTexts=tipTexts)
self.tableB3.grid(row=0, column=0, sticky='nsew')
self.matchMatrix = {}
self.amountOfMatchesPerSpinSystem = {}
self.updateTableA1()
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1, minsize=500)
row = 0
frame = LabelFrame(guiFrame, text='General Options')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(1, weight=1)
label = Label(frame, text='Molecular System:')
label.grid(row=0, column=0, sticky='w')
self.molSystemPulldown = PulldownMenu(frame,
self.changeMolSystem,
do_initial_callback=False)
self.molSystemPulldown.grid(row=0, column=1, sticky='w')
label = Label(frame, text='Measured J coupling list:')
label.grid(row=0, column=2, sticky='w')
self.measureCouplingListPulldown = PulldownMenu(
frame, self.changeMeasureCouplingList)
self.measureCouplingListPulldown.grid(row=0, column=3, sticky='w')
label = Label(frame, text='Predicted J coupling list:')
label.grid(row=0, column=4, sticky='w')
self.predictCouplingListPulldown = PulldownMenu(
frame, self.changePredictCouplingList)
self.predictCouplingListPulldown.grid(row=0, column=5, sticky='w')
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame = LabelFrame(guiFrame, text='Angles & 3J Couplings')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
headingList = ['Residue', 'Phi', 'Chi^2']
editWidgets = [None, None, None]
editGetCallbacks = [None, None, None]
editSetCallbacks = [None, None, None]
self.jCouplingEntry = FloatEntry(
self, width=8, returnCallback=lambda event: self.setJCoupling())
i = 0
for names in couplingAtoms:
headingList.extend(
['Pred\nJ(%s,%s)' % names,
'Expt\nJ(%s,%s)' % names])
editWidgets.extend([None, self.jCouplingEntry])
editGetCallbacks.extend(
[None, lambda obj, i=i: self.getJCoupling(obj, i)])
editSetCallbacks.extend(
[None, lambda event, i=i: self.setJCoupling(i)])
i += 1
self.couplingMatrix = ScrolledMatrix(frame,
headingList=headingList,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
callback=self.selectJCoupling,
multiSelect=False)
self.couplingMatrix.grid(row=0, column=0, sticky='nsew')
self.couplingMatrix.doEditMarkExtraRules = self.doEditMarkExtraRules
row += 1
frame = LabelFrame(guiFrame, text='Karplus Coefficients')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
headingList = ['Phase']
editWidgets = [
None,
]
editGetCallbacks = [
None,
]
editSetCallbacks = [
None,
]
self.coefficientEntry = FloatEntry(
self, width=8, returnCallback=lambda event: self.setCoefficient())
for names in couplingAtoms:
headingList.append('J(%s,%s)' % names)
editWidgets.append(self.coefficientEntry)
editGetCallbacks.append(
lambda obj, n=names: self.getCoefficient(obj, n))
editSetCallbacks.append(
lambda event, n=names: self.setCoefficient(n))
headingList = [
'Phase', 'J(H,HA)', 'J(H,C)', 'J(H,CB)', 'J(C,HA)', 'J(C,C)',
'J(C,CB)'
]
self.coefficientMatrix = ScrolledMatrix(
frame,
headingList=headingList,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
callback=self.selectCoefficient,
maxRows=3,
multiSelect=False)
self.coefficientMatrix.grid(row=0, column=0, sticky='nsew')
row += 1
texts = []
commands = []
self.bottomButtons = UtilityButtonList(guiFrame,
commands=commands,
texts=texts,
helpUrl=self.help_url)
self.bottomButtons.grid(row=row, column=0, sticky='ew')
for func in ('__init__', 'delete', 'setValue', 'setError'):
for clazz in ('ccp.nmr.Nmr.JCoupling', ):
self.registerNotify(self.updateAfter, clazz, func)
for func in ('__init__', 'delete'):
for clazz in ('ccp.nmr.Nmr.JCouplingList', ):
self.registerNotify(self.updateJCouplingLists, clazz, func)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(2, weight=1)
row = 0
label = Label(guiFrame, text='Template window: ', grid=(row, 0))
tipText = 'Selects which window to use as the basis for making a new spectrum window; sets the axis types accordingly'
self.window_list = PulldownList(guiFrame,
grid=(row, 1),
callback=self.setAxisTypes,
tipText=tipText)
frame = LabelFrame(guiFrame,
text='Strips',
grid=(row, 2),
gridSpan=(2, 1))
buttons = UtilityButtonList(guiFrame,
doClone=False,
helpUrl=self.help_url,
grid=(row, 3))
row += 1
label = Label(guiFrame, text='New window name: ', grid=(row, 0))
tipText = 'A short name to identify the spectrum window, which will appear in the graphical interface'
self.nameEntry = Entry(guiFrame,
width=16,
grid=(row, 1),
tipText=tipText)
row += 1
label = Label(frame, text='Columns: ', grid=(0, 0))
tipText = 'The number of vertical strips/dividers to initially make in the spectrum window'
self.cols_menu = PulldownList(frame,
objects=STRIP_NUMS,
grid=(0, 1),
texts=[str(x) for x in STRIP_NUMS],
tipText=tipText)
label = Label(frame, text='Rows: ', grid=(0, 2))
tipText = 'The number of horizontal strips/dividers to initially make in the spectrum window'
self.rows_menu = PulldownList(frame,
objects=STRIP_NUMS,
grid=(0, 3),
texts=[str(x) for x in STRIP_NUMS],
tipText=tipText)
row += 1
div = LabelDivider(guiFrame,
text='Axes',
grid=(row, 0),
gridSpan=(1, 4))
row += 1
self.axis_lists = {}
frame = Frame(guiFrame, grid=(row, 0), gridSpan=(1, 4))
col = 0
self.axisTypes = {}
self.axisTypesIncludeNone = {}
for label in AXIS_LABELS:
self.axisTypes[label] = None
w = Label(frame, text=' ' + label)
w.grid(row=0, column=col, sticky='w')
col += 1
if label in ('x', 'y'):
includeNone = False
tipText = 'Sets the kind of measurement (typically ppm for a given isotope) that will be used along the window %s axis' % label
else:
includeNone = True
tipText = 'Where required, sets the kind of measurement (typically ppm for a given isotope) that will be used along the window %s axis' % label
self.axisTypesIncludeNone[label] = includeNone
getAxisTypes = lambda label=label: self.getAxisTypes(label)
callback = lambda axisType, label=label: self.changedAxisType(
label, axisType)
self.axis_lists[label] = PulldownList(frame,
callback=callback,
tipText=tipText)
self.axis_lists[label].grid(row=0, column=col, sticky='w')
col += 1
frame.grid_columnconfigure(col, weight=1)
row += 1
div = LabelDivider(guiFrame,
text='Viewed Spectra',
grid=(row, 0),
gridSpan=(1, 4))
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
editWidgets = [None, None, None, None]
editGetCallbacks = [None, self.toggleVisible, self.toggleToolbar, None]
editSetCallbacks = [None, None, None, None]
tipTexts = [
'The "experiment:spectrum" name for the spectrum that may be viewed in the new window, given the axis selections',
'Sets whether the spectrum contours will be visible in the new window',
'Sets whether the spectrum appears at all in the window; if not in the toolbar it cannot be displayed',
'The number of peak lists the spectrum contains'
]
headingList = ['Spectrum', 'Visible?', 'In Toolbar?', 'Peak Lists']
self.scrolledMatrix = ScrolledMatrix(guiFrame,
headingList=headingList,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
multiSelect=True,
grid=(row, 0),
gridSpan=(1, 4),
tipTexts=tipTexts)
row += 1
tipTexts = [
'Creates a new spectrum window with the specified parameters',
'Sets the contours of the selected spectra to be visible when the new window is made',
'Sets the contours of the selected spectra to not be displayed when the new window is made',
'Sets the selected spectra as absent from the window toolbar, and thus not displayable at all'
]
texts = [
'Create Window!', 'Selected\nVisible', 'Selected\nNot Visible',
'Selected\nNot In Toolbar'
]
commands = [
self.ok, self.setSelectedDisplay, self.setSelectedHide,
self.setSelectedAbsent
]
buttonList = ButtonList(guiFrame,
texts=texts,
grid=(row, 0),
commands=commands,
gridSpan=(1, 4),
tipTexts=tipTexts)
buttonList.buttons[0].config(bg='#B0FFB0')
self.updateAxisTypes()
self.updateWindow()
self.updateWindowName()
self.administerNotifiers(self.registerNotify)
self.updateAfter()
def body(self, guiFrame):
self.geometry('700x500')
guiFrame.expandGrid(1, 0)
row = 0
# TOP LEFT FRAME
frame = LabelFrame(guiFrame, text='Options')
frame.grid(row=row, column=0, sticky='nsew')
frame.columnconfigure(7, weight=1)
label = Label(frame, text='Chain')
label.grid(row=0, column=0, sticky='w')
self.chainPulldown = PulldownList(
frame,
callback=self.changeChain,
tipText='Choose the molecular system chain to make predictions for'
)
self.chainPulldown.grid(row=0, column=1, sticky='w')
label = Label(frame, text='Shift List')
label.grid(row=0, column=2, sticky='w')
self.shiftListPulldown = PulldownList(
frame,
callback=self.changeShiftList,
tipText='Select the shift list to take input chemical shifts from')
self.shiftListPulldown.grid(row=0, column=3, sticky='w')
label = Label(frame, text='Type')
label.grid(row=0, column=4, sticky='w')
self.scriptPulldown = PulldownList(
frame,
texts=SCRIPT_TEXTS,
callback=self.changeScript,
tipText='Select the algorithm script for this chain')
self.scriptPulldown.grid(row=0, column=5, sticky='w')
self.pHLabel = Label(frame, text='pH')
self.pHLabel.grid(row=0, column=6, sticky='w')
self.pHPulldown = PulldownList(
frame,
texts=SCRIPT_PHS,
tipText='Select the pH to make the prediction for')
self.pHPulldown.grid(row=0, column=7, sticky='w')
row += 1
# BOTTOM LEFT FRAME
frame = LabelFrame(guiFrame, text='Chemical Shift Predictions')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
tipTexts = [
'Residue number in chain', 'Residue type code', 'Atom name',
'Actual shift (first one it finds for atom in chosen shiftList)',
'CamCoil predicted shift', 'Predicted - Actual'
]
headingList = [
'Res\nNum', 'Res\nType', 'Atom\nName', 'Actual\nShift',
'Predicted\nShift', 'Difference'
]
n = len(headingList)
editWidgets = n * [None]
editGetCallbacks = n * [None]
editSetCallbacks = n * [None]
self.predictionMatrix = ScrolledMatrix(
frame,
headingList=headingList,
tipTexts=tipTexts,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks)
self.predictionMatrix.grid(row=0, column=0, sticky='nsew')
row += 1
tipTexts = [
'Run the CamCoil method to predict chemical shifts from sequence'
]
texts = ['Run CamCoil Prediction!']
commands = [self.runCamCoil]
self.buttonList = createDismissHelpButtonList(guiFrame,
texts=texts,
commands=commands,
help_url=self.help_url,
expands=True,
tipTexts=tipTexts)
self.buttonList.grid(row=row, column=0)
self.update()
self.notify(self.registerNotify)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(1, weight=1)
frame = LabelFrame(guiFrame, text='Options')
frame.grid(row=0, column=0, sticky='ew')
frame.grid_columnconfigure(5, weight=1)
label = Label(frame, text='MolSystem:')
label.grid(row=0, column=0, sticky='w')
self.molSystemPulldown = PulldownMenu(frame,
callback=self.selectMolSystem)
self.molSystemPulldown.grid(row=0, column=1, sticky='w')
self.molLabel = Label(frame, text='Molecule:')
self.molLabel.grid(row=0, column=2, sticky='w')
self.moleculePulldown = PulldownMenu(frame,
callback=self.selectMolecule)
self.moleculePulldown.grid(row=0, column=3, sticky='w')
label = Label(frame, text='Same Molecule Symmetry:')
label.grid(row=0, column=4, sticky='w')
self.molSelect = CheckButton(frame, callback=self.toggleSingleMolecule)
self.molSelect.grid(row=0, column=5, sticky='w')
self.molSelect.set(self.singleMolecule)
frame = LabelFrame(guiFrame, text='Symmetry Operations')
frame.grid(row=1, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
self.symmCodePulldown = PulldownMenu(self,
callback=self.setSymmCode,
do_initial_callback=False)
self.segLengthEntry = IntEntry(self,
returnCallback=self.setSegLength,
width=6)
self.setChainMulti = MultiWidget(self,
CheckButton,
callback=self.setChains,
minRows=0,
useImages=False)
self.setSegmentMulti = MultiWidget(self,
IntEntry,
callback=self.setSegments,
minRows=0,
useImages=False)
editWidgets = [
None, self.symmCodePulldown, self.segLengthEntry,
self.setChainMulti, self.setSegmentMulti
]
editGetCallbacks = [
None, self.getSymmCode, self.getSegLength, self.getChains,
self.getSegments
]
editSetCallbacks = [
None, self.setSymmCode, self.setSegLength, self.setChains,
self.setSegments
]
headings = [
'#', 'Symmetry\nType', 'Segment\nLength', 'Chains',
'Segment\nPositions'
]
self.symmetryMatrix = ScrolledMatrix(frame,
headingList=headings,
callback=self.selectSymmetry,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks)
self.symmetryMatrix.grid(row=0, column=0, sticky='nsew')
texts = ['Add Symmetry Op', 'Remove Symmetrey Op']
commands = [self.addSymmOp, self.removeSymmOp]
buttonList = createDismissHelpButtonList(guiFrame,
texts=texts,
commands=commands,
expands=True)
buttonList.grid(row=2, column=0, sticky='ew')
self.updateMolSystems()
self.updateMolecules()
self.updateSymmetriesAfter()
self.notify(self.registerNotify)
def body(self, guiFrame):
'''This method describes the outline of the body of the
application.
args: guiFrame: frame the body should live in.
'''
self.geometry('800x530')
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(0, weight=0)
guiFrame.grid_rowconfigure(1, weight=2)
guiFrame.grid_rowconfigure(2, weight=1)
isotopeFrame = LabelFrame(guiFrame,
text='Isotope Shift Correction CA and CB')
isotopeFrame.grid(row=0, column=0, sticky='nsew')
frameA = LabelFrame(guiFrame, text='Spin Systems')
frameA.grid(row=1, column=0, sticky='nsew')
frameA.grid_rowconfigure(0, weight=1)
frameA.grid_columnconfigure(0, weight=1)
frameA.grid_columnconfigure(1, weight=1)
frameA1 = LabelFrame(frameA, text='Spin System 1')
frameA1.grid(row=0, column=0, sticky='nsew')
frameA1.grid_columnconfigure(0, weight=1)
frameA1.grid_rowconfigure(0, weight=1)
frameA2 = LabelFrame(frameA, text='Spin System 2')
frameA2.grid(row=0, column=1, sticky='nsew')
frameA2.grid_columnconfigure(0, weight=1)
frameA2.grid_rowconfigure(0, weight=1)
frameB = LabelFrame(guiFrame, text='Comparison')
frameB.grid(row=2, column=0, sticky='nsew')
frameB.grid_rowconfigure(0, weight=1)
frameB.grid_columnconfigure(0, weight=1)
frameB.grid_columnconfigure(1, weight=2)
frameB.grid_columnconfigure(2, weight=1)
frameB1 = LabelFrame(frameB, text='Unique to Spin System 1')
frameB1.grid(row=0, column=0, sticky='nsew')
frameB1.expandGrid(0, 0)
frameB2 = LabelFrame(frameB, text='Intersection')
frameB2.grid(row=0, column=1, sticky='nsew')
frameB2.expandGrid(0, 0)
frameB3 = LabelFrame(frameB, text='Unique to Spin System 2')
frameB3.grid(row=0, column=2, sticky='nsew')
frameB3.expandGrid(0, 0)
# Settings for isotope shift correction
shiftLists = getShiftLists(self.nmrProject)
self.protonatedShiftList = shiftLists[0]
self.deuteratedShiftList = shiftLists[1]
shiftListNames = [
'{}: {}'.format(shiftList.serial, shiftList.name)
for shiftList in shiftLists
]
Label(isotopeFrame, text='Correct for isotope shift:', grid=(0, 0))
self.correctCheck = CheckButton(isotopeFrame,
selected=True,
callback=self.setCorrection,
grid=(0, 1))
Label(isotopeFrame, text='Protonated shift list:', grid=(1, 0))
self.protonatedPulldown = PulldownList(
isotopeFrame,
callback=self.setProtonatedShiftList,
texts=shiftListNames,
objects=shiftLists,
grid=(1, 1),
index=0)
Label(isotopeFrame, text='Deuterated shift list:', grid=(2, 0))
self.deuteratedPulldown = PulldownList(
isotopeFrame,
callback=self.setDeuteratedShiftList,
texts=shiftListNames,
objects=shiftLists,
grid=(2, 1),
index=1)
# Table A1
headingList = ['#', 'shift lists', 'Assignment']
tipTexts = [
'Spin System Serial', 'shift lists',
'The residue (tentatively) assigned to this spin system',
'The amount of spin systems that overlap with this spin system and have no violations'
]
editGetCallbacks = [self.setSpinSystem1] * 3
editSetCallbacks = [None] * 3
self.tableA1 = ScrolledMatrix(frameA1,
headingList=headingList,
multiSelect=False,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
tipTexts=tipTexts)
self.tableA1.grid(row=0, column=0, sticky='nsew')
# Table A2
headingList = ['#', 'shift lists', 'Assignment', 'offset']
tipTexts = [
'Spin System Serial',
'The residue (tentatively) assigned to this spin system',
'Root mean squared deviation of this spin system to the spin system selected in the table on the left.'
]
editGetCallbacks = [self.setSpinSystem2] * 4
editSetCallbacks = [None] * 4
self.tableA2 = ScrolledMatrix(
frameA2,
headingList=headingList,
#editWidgets=editWidgets,
multiSelect=False,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
tipTexts=tipTexts)
self.tableA2.grid(row=0, column=0, sticky='nsew')
# Table B1
headingList = ['atom', 'c.s.']
tipTexts = ['atom', 'chemical shift']
self.tableB1 = ScrolledMatrix(frameB1,
headingList=headingList,
multiSelect=False,
tipTexts=tipTexts)
self.tableB1.grid(row=0, column=0, sticky='nsew')
# Table B 2
headingList = ['atom', 'c.s. 1', 'c.s. 2', 'delta c.s.']
tipTexts = [
'name of the atom',
'chemical shift of atom with this name in spin system 1',
'chemical shift of atom with this name in spin system 2',
'difference between the chemical shift of spin systems 1 and 2'
]
self.tableB2 = ScrolledMatrix(frameB2,
headingList=headingList,
tipTexts=tipTexts)
self.tableB2.grid(row=0, column=0, sticky='nsew')
# Table B 3
headingList = ['atom', 'c.s.']
tipTexts = ['atom', 'chemical shift.']
self.tableB3 = ScrolledMatrix(frameB3,
headingList=headingList,
multiSelect=False,
tipTexts=tipTexts)
self.tableB3.grid(row=0, column=0, sticky='nsew')
self.matchMatrix = {}
self.amountOfMatchesPerSpinSystem = {}
self.updateTableA1()
def body(self, guiFrame):
self.fileSelect = None
names, objects = self.getShiftLists()
self.shiftListPulldown = PulldownList(self,
callback=self.setShiftList,
texts=names,
objects=objects)
self.windowPulldown = PulldownList(self,
texts=WINDOW_OPTS,
callback=self.setWindow)
self.experimentEntry = Entry(self,
width=16,
returnCallback=self.setExperiment)
self.spectrumEntry = Entry(self,
width=16,
returnCallback=self.setSpectrum)
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(0, weight=1)
guiFrame.grid_rowconfigure(1, weight=1)
leftFrame = LabelFrame(guiFrame, text='File Selection')
leftFrame.grid(row=0, column=0, sticky='nsew')
leftFrame.grid_columnconfigure(3, weight=1)
row = 0
label = Label(leftFrame, text='File format:')
label.grid(row=row, column=0, sticky='w')
tipText = 'Selects which kind of spectrum file is being loaded; what its data matrix format is'
self.formatPulldown = PulldownList(leftFrame,
callback=self.chooseFormat,
texts=file_formats,
tipText=tipText,
grid=(row, 1))
self.detailsLabel = Label(leftFrame, text='Show details:')
tipText = 'Whether to show an annotation that describes the spectrum in the file selection; currently only uses comment fields from Bruker spectra'
self.detailsSelect = CheckButton(leftFrame,
selected=False,
callback=self.showDetails,
tipText=tipText)
self.titleRow = row
self.detailsSelected = False
row = row + 1
leftFrame.grid_rowconfigure(row, weight=1)
file_types = [FileType('All', ['*'])]
self.fileSelect = FileSelect(leftFrame,
multiSelect=True,
file_types=file_types,
single_callback=self.chooseFiles,
extraHeadings=('Details', ),
extraJustifies=('left', ),
displayExtra=False,
getExtraCell=self.getDetails,
manualFileFilter=True)
self.fileSelect.grid(row=row, column=0, columnspan=6, sticky='nsew')
rightFrame = LabelFrame(guiFrame, text='Spectra To Open')
rightFrame.grid(row=1, column=0, sticky='nsew')
rightFrame.grid_columnconfigure(3, weight=1)
row = 0
label = Label(rightFrame,
text='Skip verification dialogs:',
grid=(row, 0))
tipText = 'Whether to allow the user to check file interpretation and referencing information before the spectrum is loaded'
self.verifySelect = CheckButton(rightFrame,
selected=False,
grid=(row, 1),
tipText=tipText)
label = Label(rightFrame, text='Use shared experiment:', grid=(row, 2))
tipText = 'When selecting multiple spectrum files, whether the loaded spectra will all belong to (derive from) the same experiment; useful for projection spectra etc.'
self.sharedExpSelect = CheckButton(rightFrame,
selected=False,
tipText=tipText,
callback=self.useShared,
grid=(row, 3))
row = row + 1
rightFrame.grid_rowconfigure(row, weight=1)
tipTexts = [
'A short textual name for the experiment record that the loaded spectrum will belong to; may be a new experiment or the name of an existing one',
'A short textual name to identify the spectrum within its experiment; typically a few characters or spectrum number, rather than a repeat of the experiment name',
'The location of the file, relative to the current directory, that the spectrum data will be loaded from',
'Sets which window or windows the spectrum will initially appear within once loaded',
'Sets which shift list the experiment (and hence loaded spectrum) will use to curate chemical shift information; can be changed after load time'
]
headingList = [
'Experiment', 'Spectrum', 'File', 'Windows', 'Shift List'
]
editWidgets = [
self.experimentEntry, self.spectrumEntry, None,
self.windowPulldown, self.shiftListPulldown
]
editGetCallbacks = [
self.getExperiment, self.getSpectrum, None, self.getWindow,
self.getShiftList
]
editSetCallbacks = [
self.setExperiment, self.setSpectrum, None, self.setWindow,
self.setShiftList
]
self.scrolledMatrix = ScrolledMatrix(rightFrame,
headingList=headingList,
callback=self.selectCell,
editWidgets=editWidgets,
multiSelect=True,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
tipTexts=tipTexts,
grid=(row, 0),
gridSpan=(1, 4))
row = row + 1
tipTexts = [
'Load spectrum or spectra into the CCPN project using the selected file(s)',
]
texts = ['Open Spectrum']
commands = [self.openSpectra]
bottomButtons = UtilityButtonList(guiFrame,
texts=texts,
tipTexts=tipTexts,
doClone=False,
commands=commands,
helpUrl=self.help_url)
bottomButtons.grid(row=row, column=0, columnspan=1, sticky='ew')
self.openButton = bottomButtons.buttons[0]
self.chooseFormat('Azara')
self.message()
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame = LabelFrame(guiFrame, text='Options')
frame.grid(row=row, column=0, sticky='ew')
frame.grid_columnconfigure(1, weight=1)
frame.grid_rowconfigure(1, weight=1)
label = Label(frame, text='Window:')
label.grid(row=0, column=0, sticky='nw')
self.windowPulldown = PulldownList(frame, callback=self.changeWindow)
self.windowPulldown.grid(row=0, column=1, sticky='nw')
label = Label(frame, text='Multiplet Pattern:')
label.grid(row=1, column=0, columnspan=2, sticky='nw')
self.multipletButtons = PartitionedSelector(frame,
callback=self.setMultiplet,
radio=True)
self.multipletButtons.grid(row=2, column=0, columnspan=2, sticky='ew')
row += 1
frame = LabelFrame(guiFrame, text='Active Peak Lists')
frame.grid(row=row, column=0, sticky='ew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
headingList = [
'Experiment', 'Spectrum', 'List', 'Coupled Dims', 'Experiment Type'
]
self.peakListMatrix = ScrolledMatrix(frame,
headingList=headingList,
callback=None,
multiSelect=False)
self.peakListMatrix.grid(row=0, column=0, sticky='nsew')
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame = LabelFrame(guiFrame, text='Multiplet Peak Clusters')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
headingList = [
'#', 'Main\nAssignment', 'Num\nPeaks', 'Coupling\nAssignment',
'Value', 'Value'
]
self.clusterMatrix = ScrolledMatrix(frame,
headingList=headingList,
callback=self.selectCluster,
multiSelect=True)
self.clusterMatrix.grid(row=0, column=0, sticky='nsew')
row += 1
texts = [
'Cluster Selected\nPeaks', 'Assign\nCouplings', 'List\nPeaks',
'Find\nPeaks', 'Delete\nClusters'
]
commands = [
self.clusterSelectedPeaks, self.assignCouplings, self.showPeaks,
self.findPeaks, self.deleteClusters
]
self.bottomButtons = UtilityButtonList(guiFrame,
texts=texts,
expands=True,
commands=commands,
helpUrl=self.help_url)
self.bottomButtons.grid(row=row, column=0, sticky='ew')
self.administerNotifiers(self.registerNotify)
class EditContourLevelsPopup(BasePopup):
"""
**Change Levels in Spectrum Contour Displays**
This popup window is used to specify which contour levels (lines of constant
intensity) are drawn for spectra within the spectrum windows of Analysis. A
spectrum can have both positive and negative levels, and the user can set
these on an individual basis or as a regular incremental (usually geometric)
series. It should be noted that spectrum contour colours, which may be
different for positive and negative levels, is set elsewhere, in the main
Spectra_ table.
In normal operation the user first selects the spectrum to change the contours
for in the upper left pulldown menu. Although contour levels are specified
for individual spectra, if there are several spectra that share the same
levels (for example if they form a series of some kind) then the user may
spread the contour level information from one to many via the [Propagate
Contours] function within the "Display Options" of the main Spectra_ table.
The user may also affect the contour levels of multiple spectra by changing
the "Global scale" settings. This global scale will affect *all spectra* in
the project; the scale value multiplies all of the contour levels for all
spectra, although in practice it is rarely changed. Using a global scale gives
the advantage of being able to specify smaller numbers for the levels.
The individual contour levels for a spectrum are listed in the "positive
levels" and "Negative levels" fields. They are multiplied by the global scale
factor when they are used for spectrum display. The user may type in values
for the levels directly into these field, or they can be filled using the
"Auto contour levels" mechanism. If manual levels are specified the user
should press [Apply manual Levels] when done to commit the changes and see the
results. The [Apply Auto Levels] function differs in that it always applies a
regular series of levels, according to the settings, and these will overwrite
any manual specifications when committed; the actual levels applied are always
displayed in the levels field.
The setting of "Auto" levels using a series involves choosing a base level,
which represents the first contour (closest to zero). This base level is
usually set according to the level of noise in the spectrum. Typically it is a
value just above most of the noise, so the noise is not seen, but it may be
set lower in some instances to show weak signals. The base level applies to
both positive and negative contour series, although for the negative side it
is naturally used with negative sign. The user sets how many levels there should be in total; the subsequent levels
start from the base level and move away from zero. Normally this involves a
geometric series, with a constant multiplication factor applied to a value to
generate the next in the series. This factor is set in the "Level multiplier",
although some of the commonly used values are quickly set via the adjacent
buttons. Under a few special circumstances it is helpful to have a constant
difference between levels, in which case "Add levels" may be used instead of
"Multiply levels".
**Caveats & Tips**
Often it is useful to initially setup contours using an "Auto" series, but
then manually remove some of the levels. For example having all the positive
levels but only the first negative level may be helpful to show where peaks
are truncated.
Note this system sets the levels that would be used to make any contour files
(an optional way of working, especially for 4D spectra etc.). However,
once contour files are made then this system will not affect the levels
within the files.
.. _Spectra: EditSpectrumPopup.html
"""
def __init__(self, parent, *args, **kw):
BasePopup.__init__(self,
parent=parent,
title='Spectrum Contour Levels',
**kw)
def body(self, guiFrame):
self.doUpdateForm = True
self.spectrum = None
guiFrame.grid_columnconfigure(1, weight=1)
row = 0
specFrame = LabelFrame(guiFrame, text='Spectrum', grid=(row, 0))
tipText = 'The spectrum for which you are setting the contour levels'
self.expt_spectrum = PulldownList(specFrame,
grid=(0, 0),
tipText=tipText,
callback=self.setSpectrumDetails)
tipText = 'Open the edit spectrum table to view and change other properties associated with the selected spectrum'
button = Button(specFrame,
text='Spectrum Properties',
command=self.editProperties,
borderwidth=1,
grid=(1, 0),
sticky='ew',
tipText=tipText)
globalFrame = LabelFrame(guiFrame, text='Global scale')
globalFrame.grid(row=row, column=1, sticky='nsew')
globalFrame.grid_columnconfigure(0, weight=1)
tipText = 'The value by which all contour levels in all spectra are multiplied; to give the actual contour level in terms of the stored spectrum data'
self.global_entry = FloatEntry(
globalFrame,
width=10,
tipText=tipText,
text=self.analysisProject.globalContourScale,
returnCallback=self.applyAuto,
grid=(0, 0),
gridSpan=(1, 2),
sticky='ew')
tipText = 'Divide the global scaling factor by two; moving all contour for all spectra levels closer to zero'
button = Button(globalFrame,
borderwidth=1,
text='/2',
sticky='ew',
tipText=tipText,
command=lambda: self.changeGlobalScale(0.5),
grid=(0, 2))
tipText = 'Multiple the global scaling factor by two; moving all contour for all spectra levels away from zero'
button = Button(globalFrame,
borderwidth=1,
text='*2',
sticky='ew',
tipText=tipText,
command=lambda: self.changeGlobalScale(2.0),
grid=(0, 3))
tipText = 'Set the global contour scale for all spectra to the default of 100,000'
button = Button(globalFrame,
borderwidth=1,
text='10^5',
tipText=tipText,
command=self.defaultGlobalScale,
grid=(1, 0))
tipText = 'Click to decrease "-" or increase "+" the global contour scale by small amounts'
frame = ValueRamp(globalFrame,
callback=self.changeGlobalScale,
tipText=tipText)
frame.grid(row=1, column=1, columnspan=3, sticky='e')
row += 1
self.autoFrame = LabelFrame(guiFrame, text='Auto contour levels')
self.autoFrame.grid(row=row, column=0, columnspan=5, sticky='nsew')
self.autoFrame.grid_columnconfigure(1, weight=1)
frow = 0
label = Label(self.autoFrame,
text='Base level:',
grid=(frow, 0),
sticky='e')
tipText = 'The first contour level (closest to zero) for an automated series of levels: the start of a geometric or arithmetic series defining levels'
self.base_entry = FloatEntry(self.autoFrame,
returnCallback=self.applyAuto,
width=10,
grid=(frow, 1),
sticky='ew',
tipText=tipText)
command = lambda: self.changeBaseLevel(0.5)
tipText = 'Lower the base contour level so that it is half of the previous value; moving the series of contour levels closer to zero'
button = Button(self.autoFrame,
borderwidth=1,
text='/2',
tipText=tipText,
command=command,
grid=(frow, 2),
sticky='ew')
command = lambda: self.changeBaseLevel(2.0)
tipText = 'Raise the base contour level so that it is double the previous value; moving the series of contour levels further from zero'
button = Button(self.autoFrame,
borderwidth=1,
text='*2',
tipText=tipText,
command=command,
grid=(frow, 3),
sticky='ew')
tipText = 'Click to decrease "-" or increase "+" the base contour level by small amounts'
frame = ValueRamp(self.autoFrame,
callback=self.changeBaseLevel,
tipText=tipText)
frame.grid(row=frow, column=4, columnspan=3, sticky='ew')
frow += 1
label = Label(self.autoFrame,
text='Number of levels:',
grid=(frow, 0),
sticky='e')
#self.numberEntry = IntEntry(guiFrame, text=numberLevels,
# returnCallback=self.applyAuto)
tipText = 'The number of contour levels to make in the automated series'
self.numberEntry = IntEntry(self.autoFrame,
returnCallback=self.applyAuto,
width=10,
grid=(frow, 1),
sticky='ew',
tipText=tipText)
command = lambda w=-1: self.changeNumberLevels(w)
tipText = 'Decrease the number of contour levels in the series by one'
button = Button(self.autoFrame,
borderwidth=1,
text='-1',
tipText=tipText,
command=command,
grid=(frow, 2),
sticky='ew')
command = lambda w=1: self.changeNumberLevels(w)
tipText = 'Increase the number of contour levels in the series by one'
button = Button(self.autoFrame,
borderwidth=1,
text='+1',
tipText=tipText,
command=command,
grid=(frow, 3),
sticky='ew')
n = 4
for w in (5, 10, 15, 20):
tipText = 'Set the number of contour levels in the series to %d' % w
command = lambda w=w: self.setNumberLevels(w)
button = Button(self.autoFrame,
borderwidth=1,
text='%d' % w,
command=command,
grid=(frow, n),
sticky='ew',
tipText=tipText)
n += 1
frow += 1
self.change_label = Label(self.autoFrame,
text='%s:' % multiplier_text,
grid=(frow, 0),
sticky='e')
tipText = 'The multiplication factor (or increment if adding levels) to repetitively apply to the base level to generate the series of levels'
self.change_entry = FloatEntry(self.autoFrame,
returnCallback=self.applyAuto,
width=10,
grid=(frow, 1),
sticky='ew',
tipText=tipText)
self.change_level_buttons = []
n = 2
for w in multiplier_changes:
tipText = 'Set the automated series multiplication factor or increment to %f' % w
command = lambda w=w: self.setChange(w)
button = Button(self.autoFrame,
borderwidth=1,
text=str(w),
command=command,
grid=(frow, n),
sticky='ew',
tipText=tipText)
self.change_level_buttons.append(button)
n += 1
frow += 1
frame = Frame(self.autoFrame,
grid=(frow, 0),
gridSpan=(1, 7),
sticky='ew')
tipTexts = [
'Toggles whether positive contour levels from the automated series will be used. Overrides any manual settings',
'Toggles whether negative contour levels from the automated series will be used. Overrides any manual settings'
]
entries = ('Positive', 'Negative')
selected = (True, False)
self.which_buttons = CheckButtons(frame,
entries,
selected=selected,
select_callback=self.applyAuto,
grid=(0, 0),
sticky='w',
tipTexts=tipTexts)
tipTexts = [
'Set the contour level generation to use a geometric series, starting from the base level and using the specified factor',
'Set the contour level generation to use an arithmetic series, starting from the base level and using the specified increment'
]
entries = ('Multiply levels', 'Add levels')
self.change_mode_buttons = RadioButtons(
frame,
entries,
grid=(0, 1),
sticky='ew',
select_callback=self.modeChanged,
tipTexts=tipTexts)
row += 1
manualFrame = LabelFrame(guiFrame,
text='Positive levels',
grid=(row, 0),
gridSpan=(1, 2))
manualFrame.expandGrid(None, 0)
tipText = 'The positive contour levels that will be used for the spectrum; filled in by the automation or set/modified manually'
self.posLevelsEntry = FloatEntry(manualFrame,
isArray=True,
width=60,
returnCallback=self.applyManual,
tipText=tipText,
grid=(0, 0),
sticky='ew')
row += 1
manualFrame = LabelFrame(guiFrame,
text='Negative levels',
grid=(row, 0),
gridSpan=(1, 2))
manualFrame.expandGrid(None, 0)
tipText = 'The negative contour levels that will be used for the spectrum; filled in by the automation or set/modified manually'
self.negLevelsEntry = FloatEntry(manualFrame,
isArray=True,
width=60,
returnCallback=self.applyManual,
tipText=tipText,
grid=(0, 0),
sticky='ew')
row += 1
tipTexts = [
'Set the spectrum contour levels, updating the display, to the automated series, ignoring any manual edits.',
'Set the spectrum contour levels, updating the display, to the values displayed in the level entry fields'
]
texts = ['Apply Auto Levels', 'Apply Manual Edits']
commands = [self.applyAuto, self.applyManual]
self.buttons = UtilityButtonList(guiFrame,
texts=texts,
commands=commands,
helpUrl=self.help_url,
grid=(row, 0),
gridSpan=(1, 2),
tipTexts=tipTexts)
guiFrame.grid_rowconfigure(row, weight=1)
self.curateNotifiers(self.registerNotify)
self.update()
def update(self, spectrum=None):
if not spectrum:
spectrum = self.spectrum
spectra = self.parent.getSpectra()
if spectra:
if spectrum not in spectra:
spectrum = spectra[0]
index = spectra.index(spectrum)
names = ['%s:%s' % (x.experiment.name, x.name) for x in spectra]
else:
index = 0
names = []
self.expt_spectrum.setup(names, spectra, index)
self.setSpectrumDetails(spectrum)
def updateNotifier(self, *extra):
self.update()
def open(self):
self.updateForm()
BasePopup.open(self)
def modeChanged(self, *entry):
spectrum = self.spectrum
if not spectrum or spectrum.isDeleted:
return
analysisSpectrum = spectrum.analysisSpectrum
changeMode = self.change_mode_buttons.getIndex(
) and 'add' or 'multiply'
if changeMode == 'add':
text = adder_text
changes = adder_changes
else:
text = multiplier_text
changes = multiplier_changes
self.change_label.set('%s:' % text)
n = 0
for button in self.change_level_buttons:
w = changes[n]
command = lambda w=w: self.setChange(w)
button.config(command=command)
button.setText(str(w))
n = n + 1
levelChanger = changes[2]
self.doUpdateForm = False
analysisSpectrum.autoLevelChanger = levelChanger
analysisSpectrum.autoLevelMode = changeMode
self.doUpdateForm = True
self.setContourLevels()
def defaultGlobalScale(self):
self.global_entry.set(100000)
self.applyAuto()
def close(self):
self.applyManual()
BasePopup.close(self)
def destroy(self):
self.curateNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
def curateNotifiers(self, notifyFunc):
notifyFunc(self.updateContourLevels,
'ccpnmr.Analysis.AnalysisSpectrum', 'setPosLevels')
notifyFunc(self.updateContourLevels,
'ccpnmr.Analysis.AnalysisSpectrum', 'setNegLevels')
notifyFunc(self.updateForm, 'ccpnmr.Analysis.AnalysisSpectrum',
'setAutoLevelChanger')
notifyFunc(self.updateForm, 'ccpnmr.Analysis.AnalysisSpectrum',
'setAutoLevelMode')
notifyFunc(self.updateForm, 'ccpnmr.Analysis.AnalysisSpectrum',
'setAutoNumLevels')
notifyFunc(self.updateForm, 'ccpnmr.Analysis.AnalysisSpectrum',
'setAutoBaseLevel')
notifyFunc(self.updateForm, 'ccpnmr.Analysis.AnalysisProject',
'setGlobalContourScale')
for clazz in ('Experiment', 'DataSource'):
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.updateNotifier, 'ccp.nmr.Nmr.%s' % clazz, func)
def editProperties(self):
self.parent.editSpectrum(self.spectrum)
def updateForm(self, *extra):
#print 'updateForm'
if (not self.doUpdateForm):
return
self.global_entry.set(self.analysisProject.globalContourScale)
spectrum = self.spectrum
if spectrum and not spectrum.isDeleted:
analysisSpectrum = spectrum.analysisSpectrum
self.base_entry.set(analysisSpectrum.autoBaseLevel)
self.numberEntry.set(analysisSpectrum.autoNumLevels)
self.change_entry.set(analysisSpectrum.autoLevelChanger)
if analysisSpectrum.autoLevelMode == 'add':
i = 1
else:
i = 0
self.change_mode_buttons.setIndex(i)
def updateContourLevels(self, analysisSpectrum):
spectrum = self.spectrum
if spectrum and not spectrum.isDeleted:
analysisSpectrum = spectrum.analysisSpectrum
posLevels = list(analysisSpectrum.posLevels)
negLevels = list(analysisSpectrum.negLevels)
self.posLevelsEntry.set(posLevels)
self.negLevelsEntry.set(negLevels)
self.doUpdateForm = False
updateSpectrumLevelParams(analysisSpectrum, posLevels, negLevels)
self.doUpdateForm = True
self.base_entry.set(analysisSpectrum.autoBaseLevel)
self.numberEntry.set(analysisSpectrum.autoNumLevels)
self.change_entry.set(analysisSpectrum.autoLevelChanger)
self.setWhichLevels(spectrum)
if analysisSpectrum.autoLevelMode == 'add':
i = 1
else:
i = 0
self.change_mode_buttons.setIndex(i)
def setWhichLevels(self, spectrum):
analysisSpectrum = spectrum.analysisSpectrum
posLevels = analysisSpectrum.posLevels
negLevels = analysisSpectrum.negLevels
if posLevels:
isSelected = True
else:
isSelected = False
self.which_buttons.setIndexSelection(0, isSelected)
if negLevels:
isSelected = True
else:
isSelected = False
self.which_buttons.setIndexSelection(1, isSelected)
def setSpectrum(self, spectrum):
if spectrum is not self.spectrum:
self.update(spectrum)
#if (spectrum and not spectrum.isDeleted):
# self.setWhichLevels(spectrum)
speed_scale = 6.0
speed_delay = 50 # msec
def changeGlobalScale(self, multiplier):
self.analysisProject.globalContourScale = multiplier * self.analysisProject.globalContourScale
def changeBaseLevel(self, multiplier):
spectrum = self.spectrum
if (not spectrum or spectrum.isDeleted is True):
return
analysisSpectrum = spectrum.analysisSpectrum
baseLevel = multiplier * analysisSpectrum.autoBaseLevel
self.base_entry.set(baseLevel)
self.doUpdateForm = False
analysisSpectrum.autoBaseLevel = abs(baseLevel)
self.doUpdateForm = True
self.setContourLevels()
def changeNumberLevels(self, change):
spectrum = self.spectrum
if not spectrum or spectrum.isDeleted is True:
return
analysisSpectrum = spectrum.analysisSpectrum
numberLevels = analysisSpectrum.autoNumLevels + change
self.numberEntry.set(numberLevels)
self.doUpdateForm = False
analysisSpectrum.autoNumLevels = numberLevels
self.doUpdateForm = True
self.setContourLevels()
def setChange(self, levelChanger):
spectrum = self.spectrum
if not spectrum or spectrum.isDeleted:
return
self.doUpdateForm = False
analysisSpectrum = spectrum.analysisSpectrum
analysisSpectrum.autoLevelChanger = levelChanger
self.doUpdateForm = True
self.setContourLevels()
def setNumberLevels(self, numberLevels):
spectrum = self.spectrum
if (not spectrum or spectrum.isDeleted is True):
return
self.doUpdateForm = False
analysisSpectrum = spectrum.analysisSpectrum
analysisSpectrum.autoNumLevels = numberLevels
self.doUpdateForm = True
self.setContourLevels()
def setSpectrumDetails(self, spectrum):
if spectrum is self.spectrum:
return
self.spectrum = spectrum
if spectrum and not spectrum.isDeleted:
analysisSpectrum = spectrum.analysisSpectrum
posLevels = list(analysisSpectrum.posLevels)
negLevels = list(analysisSpectrum.negLevels)
self.posLevelsEntry.set(posLevels)
self.negLevelsEntry.set(negLevels)
self.doUpdateForm = False
updateSpectrumLevelParams(analysisSpectrum, posLevels, negLevels)
self.doUpdateForm = True
self.base_entry.set(analysisSpectrum.autoBaseLevel)
self.numberEntry.set(analysisSpectrum.autoNumLevels)
self.change_entry.set(analysisSpectrum.autoLevelChanger)
self.autoFrame.setText('Auto contour levels - %s:%s' %
(spectrum.experiment.name, spectrum.name))
self.setWhichLevels(spectrum)
else:
self.posLevelsEntry.set('')
self.negLevelsEntry.set('')
self.autoFrame.setText('Auto contour levels')
def setContourLevels(self):
spectrum = self.spectrum
if not spectrum or spectrum.isDeleted is True:
return
try:
analysisSpectrum = spectrum.analysisSpectrum
baseLevel = analysisSpectrum.autoBaseLevel
numberLevels = analysisSpectrum.autoNumLevels
levelChanger = analysisSpectrum.autoLevelChanger
changeMode = analysisSpectrum.autoLevelMode
posLevels = []
if self.which_buttons.isIndexSelected(0):
posLevels.extend(
calcContourLevels(baseLevel, numberLevels, levelChanger,
changeMode))
negLevels = []
if self.which_buttons.isIndexSelected(1):
if changeMode == 'add':
levelChanger = -levelChanger
negLevels.extend(
calcContourLevels(-baseLevel, numberLevels, levelChanger,
changeMode))
self.posLevelsEntry.set(posLevels)
self.negLevelsEntry.set(negLevels)
analysisSpectrum.posLevels = posLevels
analysisSpectrum.negLevels = negLevels
except Implementation.ApiError, e:
showError('Contour levels error', e.error_msg, parent=self)
def body(self, guiFrame):
self.doUpdateForm = True
self.spectrum = None
guiFrame.grid_columnconfigure(1, weight=1)
row = 0
specFrame = LabelFrame(guiFrame, text='Spectrum', grid=(row, 0))
tipText = 'The spectrum for which you are setting the contour levels'
self.expt_spectrum = PulldownList(specFrame,
grid=(0, 0),
tipText=tipText,
callback=self.setSpectrumDetails)
tipText = 'Open the edit spectrum table to view and change other properties associated with the selected spectrum'
button = Button(specFrame,
text='Spectrum Properties',
command=self.editProperties,
borderwidth=1,
grid=(1, 0),
sticky='ew',
tipText=tipText)
globalFrame = LabelFrame(guiFrame, text='Global scale')
globalFrame.grid(row=row, column=1, sticky='nsew')
globalFrame.grid_columnconfigure(0, weight=1)
tipText = 'The value by which all contour levels in all spectra are multiplied; to give the actual contour level in terms of the stored spectrum data'
self.global_entry = FloatEntry(
globalFrame,
width=10,
tipText=tipText,
text=self.analysisProject.globalContourScale,
returnCallback=self.applyAuto,
grid=(0, 0),
gridSpan=(1, 2),
sticky='ew')
tipText = 'Divide the global scaling factor by two; moving all contour for all spectra levels closer to zero'
button = Button(globalFrame,
borderwidth=1,
text='/2',
sticky='ew',
tipText=tipText,
command=lambda: self.changeGlobalScale(0.5),
grid=(0, 2))
tipText = 'Multiple the global scaling factor by two; moving all contour for all spectra levels away from zero'
button = Button(globalFrame,
borderwidth=1,
text='*2',
sticky='ew',
tipText=tipText,
command=lambda: self.changeGlobalScale(2.0),
grid=(0, 3))
tipText = 'Set the global contour scale for all spectra to the default of 100,000'
button = Button(globalFrame,
borderwidth=1,
text='10^5',
tipText=tipText,
command=self.defaultGlobalScale,
grid=(1, 0))
tipText = 'Click to decrease "-" or increase "+" the global contour scale by small amounts'
frame = ValueRamp(globalFrame,
callback=self.changeGlobalScale,
tipText=tipText)
frame.grid(row=1, column=1, columnspan=3, sticky='e')
row += 1
self.autoFrame = LabelFrame(guiFrame, text='Auto contour levels')
self.autoFrame.grid(row=row, column=0, columnspan=5, sticky='nsew')
self.autoFrame.grid_columnconfigure(1, weight=1)
frow = 0
label = Label(self.autoFrame,
text='Base level:',
grid=(frow, 0),
sticky='e')
tipText = 'The first contour level (closest to zero) for an automated series of levels: the start of a geometric or arithmetic series defining levels'
self.base_entry = FloatEntry(self.autoFrame,
returnCallback=self.applyAuto,
width=10,
grid=(frow, 1),
sticky='ew',
tipText=tipText)
command = lambda: self.changeBaseLevel(0.5)
tipText = 'Lower the base contour level so that it is half of the previous value; moving the series of contour levels closer to zero'
button = Button(self.autoFrame,
borderwidth=1,
text='/2',
tipText=tipText,
command=command,
grid=(frow, 2),
sticky='ew')
command = lambda: self.changeBaseLevel(2.0)
tipText = 'Raise the base contour level so that it is double the previous value; moving the series of contour levels further from zero'
button = Button(self.autoFrame,
borderwidth=1,
text='*2',
tipText=tipText,
command=command,
grid=(frow, 3),
sticky='ew')
tipText = 'Click to decrease "-" or increase "+" the base contour level by small amounts'
frame = ValueRamp(self.autoFrame,
callback=self.changeBaseLevel,
tipText=tipText)
frame.grid(row=frow, column=4, columnspan=3, sticky='ew')
frow += 1
label = Label(self.autoFrame,
text='Number of levels:',
grid=(frow, 0),
sticky='e')
#self.numberEntry = IntEntry(guiFrame, text=numberLevels,
# returnCallback=self.applyAuto)
tipText = 'The number of contour levels to make in the automated series'
self.numberEntry = IntEntry(self.autoFrame,
returnCallback=self.applyAuto,
width=10,
grid=(frow, 1),
sticky='ew',
tipText=tipText)
command = lambda w=-1: self.changeNumberLevels(w)
tipText = 'Decrease the number of contour levels in the series by one'
button = Button(self.autoFrame,
borderwidth=1,
text='-1',
tipText=tipText,
command=command,
grid=(frow, 2),
sticky='ew')
command = lambda w=1: self.changeNumberLevels(w)
tipText = 'Increase the number of contour levels in the series by one'
button = Button(self.autoFrame,
borderwidth=1,
text='+1',
tipText=tipText,
command=command,
grid=(frow, 3),
sticky='ew')
n = 4
for w in (5, 10, 15, 20):
tipText = 'Set the number of contour levels in the series to %d' % w
command = lambda w=w: self.setNumberLevels(w)
button = Button(self.autoFrame,
borderwidth=1,
text='%d' % w,
command=command,
grid=(frow, n),
sticky='ew',
tipText=tipText)
n += 1
frow += 1
self.change_label = Label(self.autoFrame,
text='%s:' % multiplier_text,
grid=(frow, 0),
sticky='e')
tipText = 'The multiplication factor (or increment if adding levels) to repetitively apply to the base level to generate the series of levels'
self.change_entry = FloatEntry(self.autoFrame,
returnCallback=self.applyAuto,
width=10,
grid=(frow, 1),
sticky='ew',
tipText=tipText)
self.change_level_buttons = []
n = 2
for w in multiplier_changes:
tipText = 'Set the automated series multiplication factor or increment to %f' % w
command = lambda w=w: self.setChange(w)
button = Button(self.autoFrame,
borderwidth=1,
text=str(w),
command=command,
grid=(frow, n),
sticky='ew',
tipText=tipText)
self.change_level_buttons.append(button)
n += 1
frow += 1
frame = Frame(self.autoFrame,
grid=(frow, 0),
gridSpan=(1, 7),
sticky='ew')
tipTexts = [
'Toggles whether positive contour levels from the automated series will be used. Overrides any manual settings',
'Toggles whether negative contour levels from the automated series will be used. Overrides any manual settings'
]
entries = ('Positive', 'Negative')
selected = (True, False)
self.which_buttons = CheckButtons(frame,
entries,
selected=selected,
select_callback=self.applyAuto,
grid=(0, 0),
sticky='w',
tipTexts=tipTexts)
tipTexts = [
'Set the contour level generation to use a geometric series, starting from the base level and using the specified factor',
'Set the contour level generation to use an arithmetic series, starting from the base level and using the specified increment'
]
entries = ('Multiply levels', 'Add levels')
self.change_mode_buttons = RadioButtons(
frame,
entries,
grid=(0, 1),
sticky='ew',
select_callback=self.modeChanged,
tipTexts=tipTexts)
row += 1
manualFrame = LabelFrame(guiFrame,
text='Positive levels',
grid=(row, 0),
gridSpan=(1, 2))
manualFrame.expandGrid(None, 0)
tipText = 'The positive contour levels that will be used for the spectrum; filled in by the automation or set/modified manually'
self.posLevelsEntry = FloatEntry(manualFrame,
isArray=True,
width=60,
returnCallback=self.applyManual,
tipText=tipText,
grid=(0, 0),
sticky='ew')
row += 1
manualFrame = LabelFrame(guiFrame,
text='Negative levels',
grid=(row, 0),
gridSpan=(1, 2))
manualFrame.expandGrid(None, 0)
tipText = 'The negative contour levels that will be used for the spectrum; filled in by the automation or set/modified manually'
self.negLevelsEntry = FloatEntry(manualFrame,
isArray=True,
width=60,
returnCallback=self.applyManual,
tipText=tipText,
grid=(0, 0),
sticky='ew')
row += 1
tipTexts = [
'Set the spectrum contour levels, updating the display, to the automated series, ignoring any manual edits.',
'Set the spectrum contour levels, updating the display, to the values displayed in the level entry fields'
]
texts = ['Apply Auto Levels', 'Apply Manual Edits']
commands = [self.applyAuto, self.applyManual]
self.buttons = UtilityButtonList(guiFrame,
texts=texts,
commands=commands,
helpUrl=self.help_url,
grid=(row, 0),
gridSpan=(1, 2),
tipTexts=tipTexts)
guiFrame.grid_rowconfigure(row, weight=1)
self.curateNotifiers(self.registerNotify)
self.update()
def __init__(self,
guiParent,
project,
callback=None,
help_msg='',
help_url='',
dismiss_text='',
modal=False,
*args,
**kw):
self.project = project
self.callback = callback
self.help_msg = help_msg
self.help_url = help_url
self.dismiss_text = dismiss_text
self.modal = modal
self.did_save = False
Frame.__init__(self, guiParent, *args, **kw)
projDir = Io.getUserDataPath(self.project)
guiParent.grid_columnconfigure(1, weight=1)
row = 0
label = Label(guiParent, text='Project Name:')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.proj_name_entry = Entry(
guiParent,
text=self.project.name,
returnCallback=self.updateInfo,
leaveCallback=self.updateInfo,
tipText='The name used for the project save directory')
self.proj_name_entry.grid(row=row, column=1, sticky=Tkinter.EW)
row = row + 1
label = Label(guiParent, text='Project Directory:')
label.grid(row=row, column=0, sticky=Tkinter.E)
label = self.proj_dir_label = Label(guiParent, text=projDir)
label.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(
guiParent,
text='Note: Project Directory = Save Location + Project Name')
label.grid(row=row, column=1, sticky=Tkinter.W)
text = 'Save binary data with project'
tipText = 'Copy data files (e.g. for spectra) into new project directory if not already in current project directory: careful, this can take some time'
row = row + 1
self.dataCheckButton = CheckButton(guiParent,
text=text,
tipText=tipText)
self.dataCheckButton.grid(row=row,
column=0,
columnspan=2,
sticky=Tkinter.W)
row = row + 1
guiParent.grid_rowconfigure(row, weight=1)
labelFrame = LabelFrame(guiParent, text='Save Location')
labelFrame.grid(row=row, column=0, columnspan=2, sticky=Tkinter.NSEW)
labelFrame.grid_rowconfigure(0, weight=1)
labelFrame.grid_columnconfigure(0, weight=1)
directory = os.path.dirname(projDir)
self.proj_dir_select = FileSelect(
labelFrame,
directory=directory,
select_dir_callback=self.selectDir,
change_dir_callback=self.updateInfo,
should_change_dir_callback=self.shouldChangeDir,
getRowColor=self.getEntryColor,
show_file=False)
self.proj_dir_select.grid(row=0, column=0, sticky=Tkinter.NSEW)
row = row + 1
texts = ['Save']
tipTexts = ['Save project with specified name in specified directory']
commands = [self.save]
buttons = createDismissHelpButtonList(guiParent,
texts=texts,
tipTexts=tipTexts,
commands=commands,
help_msg=self.help_msg,
help_url=self.help_url,
dismiss_text=self.dismiss_text,
expands=True)
buttons.grid(row=row, column=0, columnspan=2, sticky=Tkinter.EW)
def body(self, guiParent):
now = datetime.date.today().strftime('%y%m%d')
filePrefix = '%s_%s' % (self.project.name, now)
projDir = getUserDataPath(self.project)
directory = os.path.dirname(projDir)
guiParent.grid_rowconfigure(0, weight=1)
guiParent.grid_columnconfigure(1, weight=1)
row = 0
label = Label(guiParent, text='Archive File:')
label.grid(row=row, column=0, sticky=Tkinter.E)
tipText = 'File name (excluding .tgz ending) for archive'
self.fileEntry = Entry(guiParent, text=filePrefix, tipText=tipText)
self.fileEntry.grid(row=row, column=1, sticky=Tkinter.EW)
label = Label(guiParent, text='.tgz (automatically appended)')
label.grid(row=row, column=2, sticky=Tkinter.W)
row = row + 1
self.backupCheck = CheckButton(
guiParent,
text='Include *.xml.bak files',
tipText='If checked include *.xml.bak files')
self.backupCheck.grid(row=row,
column=1,
columnspan=2,
sticky=Tkinter.W)
row = row + 1
self.dataCheck = CheckButton(
guiParent,
text='Include data files which are in project directory',
tipText=
'If checked include data files if they are located in project directory'
)
self.dataCheck.grid(row=row, column=1, columnspan=2, sticky=Tkinter.W)
row = row + 1
labelFrame = LabelFrame(guiParent, text='Archive Location')
labelFrame.grid(row=row, column=0, columnspan=3, sticky=Tkinter.NSEW)
labelFrame.grid_rowconfigure(0, weight=1)
labelFrame.grid_columnconfigure(0, weight=1)
self.dirSelect = FileSelect(labelFrame,
directory=directory,
show_file=False)
self.dirSelect.grid(row=0, column=0, sticky=Tkinter.NSEW)
guiParent.grid_rowconfigure(row, weight=1)
row = row + 1
texts = ['Save']
tipTexts = ['Create archive file']
commands = [self.save]
buttons = createDismissHelpButtonList(guiParent,
texts=texts,
tipTexts=tipTexts,
commands=commands,
help_msg=self.help_msg,
help_url=self.help_url,
dismiss_text=self.dismiss_text,
expands=True)
buttons.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
strucGenFrame = LabelFrame(guiFrame, text='Generation Runs')
strucGenFrame.grid(row=row, column=0, columnspan=1, sticky='nsew')
strucGenFrame.grid_columnconfigure(0, weight=1)
strucGenFrame.grid_rowconfigure(0, weight=1)
guiFrame.grid_rowconfigure(row, weight=0)
#self.editDetailsEntry = Entry(self,text='',returnCallback = self.setDetails, width=12)
#editWidgets = [None, None, None, None, None, self.editDetailsEntry]
#editGetCallbacks = [None, None, None, None, None, self.getDetails]
#editSetCallbacks = [None, None, None, None, None, self.setDetails]
colHeadings = [
'#', 'Constraint\nLists', 'Violation\nLists', 'Structures',
'Fixed\nAtom Sets', 'Fixes\nResonance Sets', 'Chain\nStates',
'Database\nEntries', 'Resonance\nClouds'
]
editWidgets = [None, None, None, None, None, None, None, None, None]
editGetCallbacks = [
None, None, None, None, None, None, None, None, None
]
editSetCallbacks = [
None, None, None, None, None, None, None, None, None
]
self.structGenMatrix = ScrolledMatrix(
strucGenFrame,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
initialRows=3,
initialCols=6,
headingList=colHeadings,
callback=self.selectStructGenCell,
objectList=[],
textMatrix=[
[],
])
self.structGenMatrix.grid(row=0, column=0, sticky='nsew')
texts = ['View Structures', 'Delete']
commands = [self.viewStructures, self.deleteStrucGen]
self.structGenButtons = ButtonList(strucGenFrame,
texts=texts,
expands=True,
commands=commands)
self.structGenButtons.grid(row=1, column=0, sticky='ew')
row += 1
constrFrame = LabelFrame(guiFrame, text='Constraint Lists')
constrFrame.grid(row=row, column=0, columnspan=1, sticky='nsew')
constrFrame.grid_columnconfigure(0, weight=1)
constrFrame.grid_rowconfigure(0, weight=1)
guiFrame.grid_rowconfigure(row, weight=1)
colHeadings = [
'#', 'Type', 'Name', 'Constraints', 'Experiments', 'Details',
'Unit'
]
editWidgets = [None, None, None, None, None, None, None]
editGetCallbacks = [None, None, None, None, None, None, None]
editSetCallbacks = [None, None, None, None, None, None, None]
self.constrListMatrix = ScrolledMatrix(
constrFrame,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
initialRows=10,
headingList=colHeadings,
callback=self.selectConstrListCell,
objectList=[],
textMatrix=[
[],
])
self.constrListMatrix.grid(row=0, column=0, sticky='nsew')
texts = ['View Constraints', 'Create List', 'Delete List']
commands = [
self.viewConstraints, self.createConstraints,
self.deleteConstraints
]
self.constrListButtons = ButtonList(constrFrame,
texts=texts,
expands=True,
commands=commands)
self.constrListButtons.grid(row=1, column=0, sticky='ew')
self.constrListButtons.buttons[1].disable()
row += 1
violFrame = LabelFrame(guiFrame, text='Violation Lists')
violFrame.grid(row=row, column=0, columnspan=1, sticky='nsew')
violFrame.grid_columnconfigure(0, weight=1)
violFrame.grid_rowconfigure(0, weight=1)
guiFrame.grid_rowconfigure(row, weight=1)
colHeadings = [
'#',
'Violations',
'Structures',
'Details',
]
editWidgets = [None, None, None, None]
editGetCallbacks = [None, None, None, None]
editSetCallbacks = [None, None, None, None]
self.violListMatrix = ScrolledMatrix(violFrame,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
initialRows=10,
headingList=colHeadings,
callback=self.selectViolListCell,
objectList=[],
textMatrix=[
[],
])
self.violListMatrix.grid(row=0, column=0, sticky='nsew')
texts = ['View Violations', 'Delete List']
commands = [self.viewViolations, self.deleteViolations]
self.violListButtons = ButtonList(violFrame,
texts=texts,
expands=True,
commands=commands)
self.violListButtons.grid(row=1, column=0, sticky='ew')
row += 1
self.bottomButtons = UtilityButtonList(guiFrame, helpUrl=self.help_url)
self.bottomButtons.grid(row=row, column=0, columnspan=1, sticky='ew')
self.update()
for func in ('__init__', 'delete', 'setName', 'setDetails', 'setUnit',
'setExperiments', 'addExperiment', 'removeExperiment'):
for clazz in ('ccp.nmr.Nmr.ChemShiftConstraintList',
'ccp.nmr.Nmr.DihedralConstraintList',
'ccp.nmr.Nmr.DistanceConstraintList',
'ccp.nmr.Nmr.HBondConstraintList',
'ccp.nmr.Nmr.JCouplingConstraintList',
'ccp.nmr.Nmr.RdcConstraintList'):
self.registerNotify(self.updateAfter, clazz, func)
for func in (
'__init__',
'delete',
):
for clazz in ('ccp.nmr.Nmr.ChemShiftConstraint',
'ccp.nmr.Nmr.DihedralConstraint',
'ccp.nmr.Nmr.DistanceConstraint',
'ccp.nmr.Nmr.HBondConstraint',
'ccp.nmr.Nmr.JCouplingConstraint',
'ccp.nmr.Nmr.RdcConstraint'):
self.registerNotify(self.updateAfter, clazz, func)
for func in ('__init__', 'delete', 'setChainStates', 'addChainState',
'removeChainState', 'addEntry', 'removeEntry',
'setResStructures', 'addResStructure', 'setEntries',
'removeResStructure', 'setStructures', 'addStructure',
'removeStructure'):
self.registerNotify(self.updateAfter,
'ccp.nmr.Nmr.StructureGeneration', func)
for func in ('__init__', 'delete', 'setDetails'):
for clazz in ('ccp.nmr.Nmr.ViolationList', ):
self.registerNotify(self.updateAfter, clazz, func)
for func in (
'__init__',
'delete',
):
for clazz in ('ccp.nmr.Nmr.Violation', ):
self.registerNotify(self.updateAfter, clazz, func)
def body(self, guiFrame):
self.specFreqEntry = IntEntry(self,
text=self.specFreq,
width=8,
returnCallback=self.setSpecFreq)
self.maxIterEntry = IntEntry(self,
text=self.maxIter,
width=8,
returnCallback=self.setMaxIter)
self.mixTimeEntry = FloatEntry(self,
text=self.mixTime,
width=8,
returnCallback=self.setMixTime)
self.corrTimeEntry = FloatEntry(self,
text=self.corrTime,
width=8,
returnCallback=self.setCorrTime)
self.leakRateEntry = FloatEntry(self,
text=self.leakRate,
width=8,
returnCallback=self.setLeakRate)
self.maxIntensEntry = IntEntry(self,
text=self.maxIntens,
width=8,
returnCallback=self.setMaxIntens)
self.mdInitTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdInitTemp)
self.mdFinTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdFinTemp)
self.mdCoolStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdCoolSteps)
self.mdSimStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdSimSteps)
self.mdTauEntry = FloatEntry(self,
text='',
returnCallback=self.setMdTau)
self.mdRepScaleEntry = FloatEntry(self,
text='',
returnCallback=self.setMdRepScale)
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame0 = LabelFrame(guiFrame, text='Setup peak lists')
frame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame0.grid_columnconfigure(1, weight=1)
f0row = 0
label00 = Label(frame0, text='1H-1H NOESY spectrum')
label00.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.noesyPulldown = PulldownMenu(frame0,
entries=self.getNoesys(),
callback=self.setNoesy,
selected_index=0,
do_initial_callback=0)
self.noesyPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label01 = Label(frame0, text='15N HSQC spectrum')
label01.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.hsqcPulldown = PulldownMenu(frame0,
entries=self.getHsqcs(),
callback=self.setHsqc,
selected_index=0,
do_initial_callback=0)
self.hsqcPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label02 = Label(frame0, text='15N HSQC TOCSY spectrum')
label02.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.tocsyPulldown = PulldownMenu(frame0,
entries=self.getTocsys(),
callback=self.setTocsy,
selected_index=0,
do_initial_callback=0)
self.tocsyPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label02 = Label(frame0, text='15N HSQC NOESY spectrum')
label02.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.noesy3dPulldown = PulldownMenu(frame0,
entries=self.getNoesy3ds(),
callback=self.setNoesy3d,
selected_index=0,
do_initial_callback=0)
self.noesy3dPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
texts = ['Setup resonances & peaks', 'Show Peaks', 'Show resonances']
commands = [self.setupResonances, self.showPeaks, self.showResonances]
self.setupButtons = ButtonList(frame0,
expands=1,
texts=texts,
commands=commands)
self.setupButtons.grid(row=f0row,
column=0,
columnspan=2,
sticky=Tkinter.NSEW)
f0row += 1
self.label03a = Label(frame0, text='Resonances found: 0')
self.label03a.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.label03b = Label(frame0, text='NOESY peaks found: 0')
self.label03b.grid(row=f0row, column=1, sticky=Tkinter.NW)
row += 1
frame1 = LabelFrame(guiFrame, text='Calculate distance constraints')
frame1.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame1.grid_columnconfigure(3, weight=1)
f1row = 0
frame1.grid_rowconfigure(f1row, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate, self.maxIntens
]
colHeadings = [
'Spectrometer\nfrequency', 'Max\niterations', 'Mixing\ntime (ms)',
'Correl.\ntime (ns)', 'Leak\nrate', 'Max\nintensity'
]
editWidgets = [
self.specFreqEntry,
self.maxIterEntry,
self.mixTimeEntry,
self.corrTimeEntry,
self.leakRateEntry,
self.maxIntensEntry,
]
editGetCallbacks = [
self.getSpecFreq,
self.getMaxIter,
self.getMixTime,
self.getCorrTime,
self.getLeakRate,
self.getMaxIntens,
]
editSetCallbacks = [
self.setSpecFreq,
self.setMaxIter,
self.setMixTime,
self.setCorrTime,
self.setLeakRate,
self.setMaxIntens,
]
self.midgeParamsMatrix = ScrolledMatrix(
frame1,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=1,
initialCols=5,
headingList=colHeadings,
callback=None,
objectList=[
'None',
],
textMatrix=[
data,
])
self.midgeParamsMatrix.grid(row=f1row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f1row += 1
label10 = Label(frame1, text='Benchmark structure')
label10.grid(row=f1row, column=0, sticky=Tkinter.NW)
self.structurePulldown = PulldownMenu(frame1,
entries=self.getStructures(),
callback=self.setStructure,
selected_index=0,
do_initial_callback=0)
self.structurePulldown.grid(row=f1row, column=1, sticky=Tkinter.NW)
label11 = Label(frame1, text='ADC atom types:')
label11.grid(row=f1row, column=2, sticky=Tkinter.NW)
self.adcAtomsPulldown = PulldownMenu(frame1,
entries=self.getAdcAtomTypes(),
callback=self.setAdcAtomTypes,
selected_index=0,
do_initial_callback=0)
self.adcAtomsPulldown.grid(row=f1row, column=3, sticky=Tkinter.NW)
f1row += 1
texts = [
'Calculate distances', 'Show distance\nconstraints',
'Show anti-distance\nconstraints'
]
commands = [
self.calculateDistances, self.showConstraints,
self.showAntiConstraints
]
self.midgeButtons = ButtonList(frame1,
expands=1,
texts=texts,
commands=commands)
self.midgeButtons.grid(row=f1row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f1row += 1
self.distConstrLabel = Label(frame1, text='Distance constraints:')
self.distConstrLabel.grid(row=f1row,
column=0,
columnspan=2,
sticky=Tkinter.NW)
self.antiConstrLabel = Label(frame1, text='Anti-distance constraints:')
self.antiConstrLabel.grid(row=f1row,
column=2,
columnspan=2,
sticky=Tkinter.NW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame2 = LabelFrame(guiFrame, text='Proton cloud molecular dynamics')
frame2.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame2.grid_columnconfigure(1, weight=1)
f2row = 0
frame2.grid_rowconfigure(f2row, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate
]
colHeadings = [
'Step', 'Initial temp.', 'Final temp.', 'Cooling steps',
'MD steps', 'MD tau', 'Rep. scale'
]
editWidgets = [
None, self.mdInitTempEntry, self.mdFinTempEntry,
self.mdCoolStepsEntry, self.mdSimStepsEntry, self.mdTauEntry,
self.mdRepScaleEntry
]
editGetCallbacks = [
None, self.getMdInitTemp, self.getMdFinTemp, self.getMdCoolSteps,
self.getMdSimSteps, self.getMdTau, self.getMdRepScale
]
editSetCallbacks = [
None, self.setMdInitTemp, self.setMdFinTemp, self.setMdCoolSteps,
self.setMdSimSteps, self.setMdTau, self.setMdRepScale
]
self.coolingSchemeMatrix = ScrolledMatrix(
frame2,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=9,
initialRows=12,
headingList=colHeadings,
callback=self.selectCoolingStep,
objectList=self.coolingScheme,
textMatrix=self.coolingScheme)
self.coolingSchemeMatrix.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f2row += 1
texts = ['Move earlier', 'Move later', 'Add step', 'Remove step']
commands = [
self.moveStepEarlier, self.moveStepLater, self.addCoolingStep,
self.removeCoolingStep
]
self.coolingSchemeButtons = ButtonList(frame2,
expands=1,
commands=commands,
texts=texts)
self.coolingSchemeButtons.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.EW)
f2row += 1
label20 = Label(frame2, text='Number of clouds:')
label20.grid(row=f2row, column=0, sticky=Tkinter.NW)
self.numCloudsEntry = FloatEntry(frame2,
text=100,
returnCallback=self.setNumClouds,
width=10)
self.numCloudsEntry.grid(row=f2row, column=1, sticky=Tkinter.NW)
label21 = Label(frame2, text='Cloud file prefix:')
label21.grid(row=f2row, column=2, sticky=Tkinter.NW)
self.filePrefixEntry = Entry(frame2,
text='cloud_',
returnCallback=self.setFilePrefix,
width=10)
self.filePrefixEntry.grid(row=f2row, column=3, sticky=Tkinter.NW)
f2row += 1
texts = ['Start molecular dynamics', 'Show dynamics progress']
commands = [self.startMd, self.showMdProgress]
self.mdButtons = ButtonList(frame2,
expands=1,
commands=commands,
texts=texts)
self.mdButtons.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
self.bottomButtons = createDismissHelpButtonList(guiFrame,
expands=0,
help_url=None)
self.bottomButtons.grid(row=row, column=0, sticky=Tkinter.EW)
self.setButtonStates()
def body(self, guiFrame):
self.specFreqEntry = IntEntry(self,
text=self.specFreq,
width=8,
returnCallback=self.setSpecFreq)
self.maxIterEntry = IntEntry(self,
text=self.maxIter,
width=8,
returnCallback=self.setMaxIter)
self.mixTimeEntry = FloatEntry(self,
text=self.mixTime,
width=8,
returnCallback=self.setMixTime)
self.corrTimeEntry = FloatEntry(self,
text=self.corrTime,
width=8,
returnCallback=self.setCorrTime)
self.leakRateEntry = FloatEntry(self,
text=self.leakRate,
width=8,
returnCallback=self.setLeakRate)
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(1, weight=1)
row = 0
labelFrame0 = LabelFrame(guiFrame, text='Input data')
labelFrame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
labelFrame0.grid_columnconfigure(3, weight=1)
label = Label(labelFrame0, text='Assigned NOESY spectrum')
label.grid(row=0, column=0, sticky=Tkinter.NW)
self.noesyPulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy,
selected_index=0,
do_initial_callback=0)
self.noesyPulldown.grid(row=0, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='H/D ratio: ')
label.grid(row=0, column=2, sticky=Tkinter.NW)
self.ratioHDEntry = FloatEntry(labelFrame0, text=self.ratioHD, width=6)
self.ratioHDEntry.grid(row=0, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='NOESY spectrum 1:')
label.grid(row=1, column=0, sticky=Tkinter.NW)
self.tmix1Pulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy1,
selected_index=-0,
do_initial_callback=0)
self.tmix1Pulldown.grid(row=1, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='Tmix (ms): ')
label.grid(row=1, column=2, sticky=Tkinter.NW)
self.tmix1Entry = FloatEntry(labelFrame0, text=60, width=6)
self.tmix1Entry.grid(row=1, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='NOESY spectrum 2:')
label.grid(row=2, column=0, sticky=Tkinter.NW)
self.tmix2Pulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy2,
selected_index=0,
do_initial_callback=0)
self.tmix2Pulldown.grid(row=2, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='Tmix (ms): ')
label.grid(row=2, column=2, sticky=Tkinter.NW)
self.tmix2Entry = FloatEntry(labelFrame0, text=120, width=6)
self.tmix2Entry.grid(row=2, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='NOESY spectrum 3:')
label.grid(row=3, column=0, sticky=Tkinter.NW)
self.tmix3Pulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy3,
selected_index=0,
do_initial_callback=0)
self.tmix3Pulldown.grid(row=3, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='Tmix (ms): ')
label.grid(row=3, column=2, sticky=Tkinter.NW)
self.tmix3Entry = FloatEntry(labelFrame0, text=200, width=6)
self.tmix3Entry.grid(row=3, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='3D NOESY:')
label.grid(row=4, column=0, sticky=Tkinter.NW)
self.noesy3dPulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys3d(),
callback=self.setNoesy3d,
selected_index=0,
do_initial_callback=0)
self.noesy3dPulldown.grid(row=4, column=1, sticky=Tkinter.NW)
label10 = Label(labelFrame0, text='Num peaks:')
label10.grid(row=5, column=0, sticky=Tkinter.NW)
self.numPeaksLabel = Label(labelFrame0, text='0')
self.numPeaksLabel.grid(row=5, column=1, sticky=Tkinter.NW)
label11 = Label(labelFrame0, text='Num resonances:')
label11.grid(row=5, column=2, sticky=Tkinter.NW)
self.numResonancesLabel = Label(labelFrame0, text='0')
self.numResonancesLabel.grid(row=5, column=3, sticky=Tkinter.NW)
row += 1
labelFrame1 = LabelFrame(guiFrame, text='Parameters')
labelFrame1.grid(row=row, column=0, sticky=Tkinter.NSEW)
labelFrame1.grid_columnconfigure(3, weight=1)
label = Label(labelFrame1, text='15N labelled sample:')
label.grid(row=0, column=0, sticky=Tkinter.NW)
self.nitrogenSelect = CheckButton(labelFrame1,
callback=self.setNitrogenLabel)
self.nitrogenSelect.grid(row=0, column=1, sticky=Tkinter.W)
self.nitrogenSelect.set(1)
label = Label(labelFrame1, text='13C labelled sample:')
label.grid(row=0, column=2, sticky=Tkinter.NW)
self.carbonSelect = CheckButton(labelFrame1,
callback=self.setCarbonLabel)
self.carbonSelect.grid(row=0, column=3, sticky=Tkinter.W)
self.carbonSelect.set(0)
labelFrame1.grid_rowconfigure(1, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate
]
colHeadings = [
'Spectrometer\nfrequency', 'Max\niterations', 'Mixing\ntime (ms)',
'Correl.\ntime (ns)', 'Leak\nrate'
]
editWidgets = [
self.specFreqEntry,
self.maxIterEntry,
self.mixTimeEntry,
self.corrTimeEntry,
self.leakRateEntry,
]
editGetCallbacks = [
self.getSpecFreq,
self.getMaxIter,
self.getMixTime,
self.getCorrTime,
self.getLeakRate,
]
editSetCallbacks = [
self.setSpecFreq,
self.setMaxIter,
self.setMixTime,
self.setCorrTime,
self.setLeakRate,
]
self.midgeParamsMatrix = ScrolledMatrix(
labelFrame1,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=1,
initialCols=5,
headingList=colHeadings,
callback=None,
objectList=[
'None',
],
textMatrix=[
data,
])
self.midgeParamsMatrix.grid(row=1,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
label10 = Label(labelFrame1, text='Benchmark structure')
label10.grid(row=2, column=0, sticky=Tkinter.NW)
self.structurePulldown = PulldownMenu(labelFrame1,
entries=self.getStructures(),
callback=self.setStructure,
selected_index=0,
do_initial_callback=0)
self.structurePulldown.grid(row=2, column=1, sticky=Tkinter.NW)
label11 = Label(labelFrame1, text='ADC atom types:')
label11.grid(row=2, column=2, sticky=Tkinter.NW)
self.adcAtomsPulldown = PulldownMenu(labelFrame1,
entries=self.getAdcAtomTypes(),
callback=self.setAdcAtomTypes,
selected_index=0,
do_initial_callback=0)
self.adcAtomsPulldown.grid(row=2, column=3, sticky=Tkinter.NW)
row += 1
labelFrame2 = LabelFrame(guiFrame, text='Output')
labelFrame2.grid(row=row, column=0, sticky=Tkinter.NSEW)
labelFrame2.grid_columnconfigure(3, weight=1)
label20 = Label(labelFrame2, text='Distance constraints:')
label20.grid(row=0, column=0, sticky=Tkinter.NW)
self.distConstrLabel = Label(labelFrame2, text='0')
self.distConstrLabel.grid(row=0, column=1, sticky=Tkinter.NW)
label21 = Label(labelFrame2, text='Anti-distance constraints:')
label21.grid(row=0, column=2, sticky=Tkinter.NW)
self.antiConstrLabel = Label(labelFrame2, text='0')
self.antiConstrLabel.grid(row=0, column=3, sticky=Tkinter.NW)
texts = [
'Calculate distances', 'Show distance\nconstraints',
'Show anti-distance\nconstraints'
]
commands = [
self.calculateDistances, self.showConstraints,
self.showAntiConstraints
]
self.midgeButtons = ButtonList(labelFrame2,
expands=1,
texts=texts,
commands=commands)
self.midgeButtons.grid(row=1,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
self.bottomButtons = createDismissHelpButtonList(guiFrame,
expands=0,
help_url=None)
self.bottomButtons.grid(row=row,
column=0,
columnspan=4,
sticky=Tkinter.EW)
self.getPeaks()
self.getResonances()
self.update()
self.geometry('600x400')
def body(self, mainFrame):
mainFrame.grid_columnconfigure(1, weight=1, minsize=100)
mainFrame.config(borderwidth=5, relief='solid')
row = 0
label = Label(mainFrame, text="Frame (with sub-widgets):")
label.grid(row=row, column=0, sticky=Tkinter.E)
frame = Frame(mainFrame, relief='raised', border=2, background='#8080D0')
# Frame expands East-West
frame.grid(row=row, column=1, sticky=Tkinter.EW)
# Last column expands => Widgets pusted to the West
frame.grid_columnconfigure(3, weight=1)
# Label is within the sub frame
label = Label(frame, text='label ')
label.grid(row=0, column=0, sticky=Tkinter.W)
entry = Entry(frame, text='Entry', returnCallback=self.showWarning)
entry.grid(row=0, column=1, sticky=Tkinter.W)
self.check = CheckButton(frame, text='Checkbutton', selected=True, callback=self.updateObjects)
self.check.grid(row=0, column=2, sticky=Tkinter.W)
# stick a button to the East wall
button = Button(frame, text='Button', command=self.pressButton)
button.grid(row=0, column=3, sticky=Tkinter.E)
row += 1
label = Label(mainFrame, text="Text:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.textWindow = Text(mainFrame, text='Initial Text\n', width=60, height=5)
self.textWindow.grid(row=row, column=1, sticky=Tkinter.NSEW)
row += 1
label = Label(mainFrame, text="CheckButtons:")
label.grid(row=row, column=0, sticky=Tkinter.E)
entries = ['Alpha','Beta','Gamma','Delta']
selected = entries[2:]
self.checkButtons = CheckButtons(mainFrame, entries, selected=selected,select_callback=self.changedCheckButtons)
self.checkButtons.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="PartitionedSelector:")
label.grid(row=row, column=0, sticky=Tkinter.E)
labels = ['Bool','Int','Float','String']
objects = [type(0),type(1),type(1.0),type('a')]
selected = [type('a')]
self.partitionedSelector= PartitionedSelector(mainFrame, labels=labels,
objects=objects,
colors = ['red','yellow','green','#000080'],
callback=self.toggleSelector,selected=selected)
self.partitionedSelector.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(mainFrame, text="PulldownMenu")
label.grid(row=row, column=0, sticky=Tkinter.E)
entries = ['Frodo','Pipin','Merry','Sam','Bill','Gandalf','Strider','Gimli','Legolas']
self.pulldownMenu = PulldownMenu(mainFrame, callback=self.selectPulldown,
entries=entries, selected_index=2,
do_initial_callback=False)
self.pulldownMenu.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="RadioButtons in a\nScrolledFrame.frame:")
label.grid(row=row, column=0, sticky=Tkinter.EW)
frame = ScrolledFrame(mainFrame, yscroll = False, doExtraConfig = True, width=100)
frame.grid(row=row, column=1, sticky=Tkinter.EW)
frame.grid_columnconfigure(0, weight=1)
self.radioButtons = RadioButtons(frame.frame, entries=entries,
select_callback=self.checkRadioButtons,
selected_index=1, relief='groove')
self.radioButtons.grid(row=0, column=0, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="LabelFrame with\nToggleLabels inside:")
label.grid(row=row, column=0, sticky=Tkinter.E)
labelFrame = LabelFrame(mainFrame, text='Frame Title')
labelFrame.grid(row=row, column=1, sticky=Tkinter.NSEW)
labelFrame.grid_rowconfigure(0, weight=1)
labelFrame.grid_columnconfigure(3, weight=1)
self.toggleLabel1 = ToggleLabel(labelFrame, text='ScrolledMatrix', callback=self.toggleFrame1)
self.toggleLabel1.grid(row=0, column=0, sticky=Tkinter.W)
self.toggleLabel1.arrowOn()
self.toggleLabel2 = ToggleLabel(labelFrame, text='ScrolledGraph', callback=self.toggleFrame2)
self.toggleLabel2.grid(row=0, column=1, sticky=Tkinter.W)
self.toggleLabel3 = ToggleLabel(labelFrame, text='ScrolledCanvas', callback=self.toggleFrame3)
self.toggleLabel3.grid(row=0, column=2, sticky=Tkinter.W)
row += 1
mainFrame.grid_rowconfigure(row, weight=1)
label = Label(mainFrame, text="changing/shrinking frames:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.toggleRow = row
self.toggleFrame = Frame(mainFrame)
self.toggleFrame.grid(row=row, column=1, sticky=Tkinter.NSEW)
self.toggleFrame.grid_rowconfigure(0, weight=1)
self.toggleFrame.grid_columnconfigure(0, weight=1)
# option 1
self.intEntry = IntEntry(self, returnCallback = self.setNumber, width=8)
self.multiWidget = MultiWidget(self, Entry, options=None,
values=None, callback=self.setKeywords,
minRows=3, maxRows=5)
editWidgets = [None, None, self.intEntry, self.multiWidget]
editGetCallbacks = [None, None, self.getNumber, self.getKeywords]
editSetCallbacks = [None, None, self.setNumber, self.setKeywords]
headingList = ['Name','Color','Number','Keywords']
self.scrolledMatrix = ScrolledMatrix(self.toggleFrame, headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=self.selectObject,
multiSelect=False)
self.scrolledMatrix.grid(row=0, column=0, sticky=Tkinter.NSEW)
# option 2
self.scrolledGraph = ScrolledGraph(self.toggleFrame, width=400,
height=300, symbolSize=5,
symbols=['square','circle'],
dataColors=['#000080','#800000'],
lineWidths=[0,1] )
self.scrolledGraph.setZoom(1.3)
dataSet1 = [[0,0],[1,1],[2,4],[3,9],[4,16],[5,25]]
dataSet2 = [[0,0],[1,3],[2,6],[3,9],[4,12],[5,15]]
self.scrolledGraph.update(dataSets=[dataSet1,dataSet2],
xLabel = 'X axis label',
yLabel = 'Y axis label',
title = 'Main Title')
self.scrolledGraph.draw()
# option 3
self.scrolledCanvas = ScrolledCanvas(self.toggleFrame,relief = 'groove', borderwidth = 2, resizeCallback=None)
canvas = self.scrolledCanvas.canvas
font = 'Helvetica 10'
box = canvas.create_rectangle(10,10,150,200, outline='grey', fill='grey90')
line = canvas.create_line(0,0,200,200,fill='#800000', width=2)
text = canvas.create_text(120,50, text='Text', font=font, fill='black')
circle = canvas.create_oval(30,30,50,50,outline='#008000',fill='#404040',width=3)
row += 1
label = Label(mainFrame, text="FloatEntry:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.floatEntry = FloatEntry(mainFrame, text=3.14159265, returnCallback=self.floatEntryReturn)
self.floatEntry.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="Scale:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.scale = Scale(mainFrame, from_=10, to=90, value=50, orient=Tkinter.HORIZONTAL)
self.scale.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="Value Ramp:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.valueRamp = ValueRamp(mainFrame, self.valueRampCallback, speed = 1.5, delay = 50)
self.valueRamp.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="ButtonList:")
label.grid(row=row, column=0, sticky=Tkinter.E)
texts = ['Select File','Close','Quit']
commands = [self.selectFile, self.close, self.quit]
bottomButtons = ButtonList(mainFrame, texts=texts, commands=commands, expands=True)
bottomButtons.grid(row=row, column=1, sticky=Tkinter.EW)
self.protocol('WM_DELETE_WINDOW', self.quit)
def __init__(self, parent, dangleGui, project=None, *args, **kw):
self.guiParent = parent
self.dangleGui = dangleGui
self.dangleDir = None
self.dangleChain = None
self.dangleResidue = None
#self.outDir = OUTDIR
self.row = None
self.col = None
self.project = project
self.nmrProject = None
self.colorScheme = 'red'
self.chain = None
self.shiftList = None
self.dangleStore = False # Not None
self.constraintSet = None
self.ensemble = None
Frame.__init__(self, parent=parent)
self.grid_columnconfigure(0, weight=1)
self.grid_rowconfigure(1, weight=1)
row = 0
# TOP LEFT FRAME
frame = LabelFrame(self, text='Options')
frame.grid(row=row, column=0, sticky='nsew')
frame.columnconfigure(5, weight=1)
label = Label(frame, text='Chain')
label.grid(row=0, column=0, sticky='w')
self.chainPulldown = PulldownList(
frame,
callback=self.changeChain,
tipText='Choose the molecular system chain to make predictions for'
)
self.chainPulldown.grid(row=0, column=1, sticky='w')
label = Label(frame, text='Shift List')
label.grid(row=0, column=2, sticky='w')
self.shiftListPulldown = PulldownList(
frame,
callback=self.changeShiftList,
tipText='Select the shift list to take input chemical shifts from')
self.shiftListPulldown.grid(row=0, column=3, sticky='w')
label = Label(frame, text='Max No. of Islands:')
label.grid(row=0, column=4, sticky='w')
sizes = range(10)
texts = [str(s) for s in sizes] + [
'Do not reject',
]
self.rejectPulldown = PulldownList(
frame,
texts=texts,
objects=sizes + [
None,
],
tipText=
'Select the maximum allowed number of disontinuous prediction islands'
)
self.rejectPulldown.set(DEFAULT_MAX_ISLANDS) # Actual value not index
self.rejectPulldown.grid(row=0, column=5, sticky='w')
label = Label(frame, text='Dangle Run:')
label.grid(row=1, column=0, sticky='w')
self.dangleStorePulldown = PulldownList(
frame,
callback=self.changeDangleStore,
tipText='Select a run number to store DANGLE results within')
self.dangleStorePulldown.grid(row=1, column=1, sticky='w')
label = Label(frame, text='Ensemble:')
label.grid(row=1, column=2, sticky='w')
self.ensemblePulldown = PulldownList(
frame,
callback=self.changeEnsemble,
tipText=
'Select the structure ensemble for superimposition of angle values on the GLE plots'
)
self.ensemblePulldown.grid(row=1, column=3, sticky='w')
label = Label(frame, text='Restraint Set:')
label.grid(row=1, column=4, sticky='w')
self.constrSetPulldown = PulldownList(
frame,
callback=self.changeConstraintSet,
tipText=
'Select the CCPN restraint set to store DANGLE dihedral angle restraints in'
)
self.constrSetPulldown.grid(row=1, column=5, sticky='w')
# TOP RIGHT FRAME
outerFrame = Frame(self)
outerFrame.grid(row=row, column=1, rowspan=2, sticky='nsew')
outerFrame.rowconfigure(0, weight=1)
outerFrame.columnconfigure(0, weight=1)
frame = LabelFrame(outerFrame, text='Global Likelihood Estimates')
frame.grid(row=0, column=0, sticky='nsew')
frame.rowconfigure(1, weight=1)
frame.columnconfigure(2, weight=1)
self.prevPlot = ViewRamachandranFrame(frame,
relief='sunken',
defaultPlot=False,
width=180,
height=180,
bgColor=self.cget('bg'),
nullColor='#000000',
titleText='Previous',
xTicks=False,
yTicks=False,
xLabel='',
yLabel='',
showCoords=False)
self.prevPlot.grid(row=0, column=0, sticky='nsew')
self.prevPlot.getPlotColor = self.getPlotColor
self.nextPlot = ViewRamachandranFrame(frame,
relief='sunken',
defaultPlot=False,
width=180,
height=180,
bgColor=self.cget('bg'),
nullColor='#000000',
titleText='Next',
xTicks=False,
yTicks=False,
xLabel='',
yLabel='',
showCoords=False)
self.nextPlot.grid(row=0, column=1, sticky='nsew')
self.nextPlot.getPlotColor = self.getPlotColor
self.plot = ViewRamachandranFrame(frame,
relief='sunken',
defaultPlot=False,
width=360,
height=360,
bgColor=self.cget('bg'),
nullColor='#000000')
self.plot.grid(row=1, column=0, columnspan=2, sticky='nsew')
self.plot.selectColor = '#FFB0B0'
self.plot.getPlotColor = self.getPlotColor
# BOTTOM RIGHT FRAME
frame = Frame(outerFrame)
frame.grid(row=1, column=0, sticky='nsew')
frame.rowconfigure(0, weight=1)
frame.columnconfigure(0, weight=1)
texts = ('Previous', ' Next ')
commands = (self.showPrevious, self.showNext)
tipTexts = [
'Show GLE plot of angle predictions for previous residue in chain',
'Show GLE plot of angle predictions for next residue in chain'
]
buttonList = ButtonList(frame, texts, commands, tipTexts=tipTexts)
buttonList.grid(row=0, column=0, sticky='nsew')
row += 1
# BOTTOM LEFT FRAME
frame = LabelFrame(self, text='Dihedral Angle Predictions')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
self.floatEntry = FloatEntry(self,
text='',
returnCallback=self.setFloatEntry,
width=10,
formatPlaces=9)
tipTexts = [
'Residue number in chain', 'Residue type code',
'Number of high scoring discontinuous angle predictions',
'Predicted secondary structure code',
'Predicted phi dihedral angle (CO-N-CA-CO)',
'Predicted psi dihedral angle (N-CA-CO-N)',
'Upper bound of phi angle prediction',
'Lower bound of phi angle prediction',
'Upper bound of psi angle prediction',
'Lower bound of phi angle prediction',
'Chemical shifts used in prediction'
]
headingList = [
'Res\nNum', 'Res\nType', 'No. of\nIslands', 'SS', 'Phi', 'Psi',
'Phi\nUpper', 'Phi\nLower', 'Psi\nUpper', 'Psi\nLower',
'Chemical Shifts'
]
editWidgets = [
None, None, None, None, self.floatEntry, self.floatEntry,
self.floatEntry, self.floatEntry, self.floatEntry, self.floatEntry
]
editGetCallbacks = [
None, None, None, None, self.getFloatEntry, self.getFloatEntry,
self.getFloatEntry, self.getFloatEntry, self.getFloatEntry,
self.getFloatEntry
]
editSetCallbacks = [
None, None, None, None, self.setFloatEntry, self.setFloatEntry,
self.setFloatEntry, self.setFloatEntry, self.setFloatEntry,
self.setFloatEntry
]
self.predictionMatrix = ScrolledMatrix(
frame,
headingList=headingList,
multiSelect=True,
callback=self.selectCell,
tipTexts=tipTexts,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks)
# doubleCallback=self.loadGLEs)
self.predictionMatrix.grid(row=0, column=0, sticky='nsew')
row += 1
tipTexts = [
'Remove the predictions for the selected residues',
'Run the DANGLE method to predict dihedral angles and secondary structure',
'Delete the DANGLE results stored under the current run number',
'Store the angle predictions and bounds in a new CCPN dihedral angle restraint list',
'Store the secondary structure predictions in the CCPN project'
]
texts = [
'Clear\nSelected', 'Run Prediction!', 'Delete\nCurrent Run',
'Commit\nRestraints', 'Commit\nSecondary Structure'
]
commands = [
self.clearSelected, self.runDangle, self.deleteRun,
self.storeDihedralConstraints, self.storeSecondaryStructure
]
self.buttonList = createDismissHelpButtonList(
self,
texts=texts,
commands=commands, # dismiss_text='Quit',
dismiss_cmd=self.dangleGui.quit,
help_url=self.dangleGui.help_url,
expands=True,
tipTexts=tipTexts)
self.buttonList.grid(row=row, column=0, columnspan=2, sticky='ew')
self.buttonList.buttons[1].config(bg='#C0FFFF')
self.updateProject(project)
self.notify(dangleGui.registerNotify)
def body(self, guiFrame):
self.geometry('700x500')
guiFrame.expandGrid(1, 0)
row = 0
# TOP LEFT FRAME
frame = LabelFrame(guiFrame, text='Options')
frame.grid(row=row, column=0, sticky='nsew')
frame.columnconfigure(5, weight=1)
label = Label(frame, text='Chain')
label.grid(row=0, column=0, sticky='w')
self.chainPulldown = PulldownList(
frame,
callback=self.changeChain,
tipText='Choose the molecular system chain to make predictions for'
)
self.chainPulldown.grid(row=0, column=1, sticky='w')
label = Label(frame, text='Shift List')
label.grid(row=0, column=2, sticky='w')
self.shiftListPulldown = PulldownList(
frame,
callback=self.changeShiftList,
tipText='Select the shift list to take input chemical shifts from')
self.shiftListPulldown.grid(row=0, column=3, sticky='w')
row += 1
# BOTTOM LEFT FRAME
frame = LabelFrame(guiFrame, text='Secondary Structure Predictions')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
tipTexts = ('Residue number in chain', 'Residue type code',
'Current stored secondary structure code',
'Predicted secondary structure code') + SEC_STRUC_TIPS
headingList = ('Res\nNum', 'Res\nType', 'Current\nSS',
'Predicted\nSS') + SEC_STRUC_KEYS
n = len(headingList)
editWidgets = n * [None]
editGetCallbacks = n * [None]
editSetCallbacks = n * [None]
self.predictionMatrix = ScrolledMatrix(
frame,
headingList=headingList,
tipTexts=tipTexts,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks)
self.predictionMatrix.grid(row=0, column=0, sticky='nsew')
row += 1
tipTexts = [
'Run the D2D method to predict secondary structure',
'Store the secondary structure predictions in the CCPN project'
]
texts = [
'Run D2D Prediction!', 'Commit Predicted\nSecondary Structure'
]
commands = [self.runD2D, self.storeSecondaryStructure]
self.buttonList = createDismissHelpButtonList(guiFrame,
texts=texts,
commands=commands,
help_url=self.help_url,
expands=True,
tipTexts=tipTexts)
self.buttonList.grid(row=row, column=0, columnspan=2, sticky='ew')
self.update()
self.notify(self.registerNotify)
def body(self, guiFrame):
self.mdInitTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdInitTemp)
self.mdFinTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdFinTemp)
self.mdCoolStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdCoolSteps)
self.mdSimStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdSimSteps)
self.mdTauEntry = FloatEntry(self,
text='',
returnCallback=self.setMdTau)
self.mdRepScaleEntry = FloatEntry(self,
text='',
returnCallback=self.setMdRepScale)
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
guiFrame.grid_rowconfigure(row, weight=1)
frame = LabelFrame(guiFrame, text='Input constraints')
frame.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame.grid_columnconfigure(2, weight=1)
srow = 0
label = Label(frame, text='Constraint set:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.constraintSetPulldown = PulldownMenu(
frame,
callback=self.changeConstraintSet,
selected_index=0,
do_initial_callback=0)
self.constraintSetPulldown.grid(row=srow, column=1, sticky=Tkinter.W)
srow += 1
label = Label(frame, text='Dist constraint list 1:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.distance1Pulldown = PulldownMenu(
frame,
callback=self.changeDistance1ConstraintList,
selected_index=0,
do_initial_callback=0)
self.distance1Pulldown.grid(row=srow, column=1, sticky=Tkinter.W)
self.numConstr1Label = Label(frame, text='Constraints: 0')
self.numConstr1Label.grid(row=srow, column=2, sticky=Tkinter.W)
srow += 1
label = Label(frame, text='Dist constraint list 2:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.distance2Pulldown = PulldownMenu(
frame,
callback=self.changeDistance2ConstraintList,
selected_index=0,
do_initial_callback=0)
self.distance2Pulldown.grid(row=srow, column=1, sticky=Tkinter.W)
self.numConstr2Label = Label(frame, text='Constraints: 0')
self.numConstr2Label.grid(row=srow, column=2, sticky=Tkinter.W)
srow += 1
label = Label(frame, text='Dist constraint list 3:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.distance3Pulldown = PulldownMenu(
frame,
callback=self.changeDistance3ConstraintList,
selected_index=0,
do_initial_callback=0)
self.distance3Pulldown.grid(row=srow, column=1, sticky=Tkinter.W)
self.numConstr3Label = Label(frame, text='Constraints: 0')
self.numConstr3Label.grid(row=srow, column=2, sticky=Tkinter.W)
srow += 1
label = Label(frame, text='Dist constraint list 4:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.distance4Pulldown = PulldownMenu(
frame,
callback=self.changeDistance4ConstraintList,
selected_index=0,
do_initial_callback=0)
self.distance4Pulldown.grid(row=srow, column=1, sticky=Tkinter.W)
self.numConstr4Label = Label(frame, text='Constraints: 0')
self.numConstr4Label.grid(row=srow, column=2, sticky=Tkinter.W)
row += 1
frame0 = LabelFrame(guiFrame, text='Cooling scheme')
frame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame0.grid_columnconfigure(1, weight=1)
f0row = 0
frame0.grid_rowconfigure(f0row, weight=1)
colHeadings = [
'Step', 'Initial\nTemp.', 'Final\nTemp.', 'Cooling\nSteps',
'MD Steps', 'MD Tau', 'Rep.\nScale'
]
editWidgets = [
None, self.mdInitTempEntry, self.mdFinTempEntry,
self.mdCoolStepsEntry, self.mdSimStepsEntry, self.mdTauEntry,
self.mdRepScaleEntry
]
editGetCallbacks = [
None, self.getMdInitTemp, self.getMdFinTemp, self.getMdCoolSteps,
self.getMdSimSteps, self.getMdTau, self.getMdRepScale
]
editSetCallbacks = [
None, self.setMdInitTemp, self.setMdFinTemp, self.setMdCoolSteps,
self.setMdSimSteps, self.setMdTau, self.setMdRepScale
]
self.coolingSchemeMatrix = ScrolledMatrix(
frame0,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=9,
initialRows=12,
headingList=colHeadings,
callback=self.selectCoolingStep,
objectList=self.coolingScheme,
textMatrix=self.coolingScheme)
self.coolingSchemeMatrix.grid(row=f0row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f0row += 1
texts = ['Move earlier', 'Move later', 'Add step', 'Remove step']
commands = [
self.moveStepEarlier, self.moveStepLater, self.addCoolingStep,
self.removeCoolingStep
]
self.coolingSchemeButtons = ButtonList(frame0,
expands=1,
commands=commands,
texts=texts)
self.coolingSchemeButtons.grid(row=f0row,
column=0,
columnspan=4,
sticky=Tkinter.EW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame1 = LabelFrame(guiFrame, text='Dynamics control')
frame1.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame1.grid_columnconfigure(1, weight=1)
f1row = 0
label20 = Label(frame1, text='Number of clouds:')
label20.grid(row=f1row, column=0, sticky=Tkinter.NW)
self.numCloudsEntry = IntEntry(frame1,
text=1,
returnCallback=self.setNumClouds,
width=10)
self.numCloudsEntry.grid(row=f1row, column=1, sticky=Tkinter.NW)
label21 = Label(frame1, text='Cloud file prefix:')
label21.grid(row=f1row, column=2, sticky=Tkinter.NW)
self.filePrefixEntry = Entry(frame1,
text='t_intra_',
returnCallback=self.setFilePrefix,
width=10)
self.filePrefixEntry.grid(row=f1row, column=3, sticky=Tkinter.NW)
f1row += 1
texts = ['Start molecular dynamics', 'Show dynamics progress']
commands = [self.startMd, self.showMdProgress]
self.mdButtons = ButtonList(frame1,
expands=1,
commands=commands,
texts=texts)
self.mdButtons.grid(row=f1row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
self.bottomButtons = createDismissHelpButtonList(guiFrame,
expands=0,
help_url=None)
self.bottomButtons.grid(row=row, column=0, sticky=Tkinter.EW)
self.update()
for func in ('__init__', 'delete', 'setName'):
for clazz in ('ccp.nmr.NmrConstraint.DistanceConstraintList', ):
Implementation.registerNotify(self.updateConstraintLists,
clazz, func)
for func in ('__init__', 'delete'):
Implementation.registerNotify(
self.updateConstraintSets,
'ccp.nmr.NmrConstraint.NmrConstraintStore', func)