def body(self, guiFrame):
ProgressBar.body(self, guiFrame)
guiFrame.expandGrid(2,3)
self.stepLabel = Label(guiFrame, text='Best step: ', grid=(0,3))
frame = LabelFrame(guiFrame, text='Best mappings', grid=(1,0), gridSpan=(1,4))
row = 0
for i in range(self.ensembleSize):
label = Label(frame, text='', pady=0, font='Courier 10',
borderwidth=0, grid=(row,0), sticky='ew')
self.labels.append(label)
row +=1
guiFrame.grid_rowconfigure(2, weight=1)
self.graph = ScrolledGraph(guiFrame, width=450, height=300,
graphType='scatter', title='Typing Scores',
xLabel='Spin System', yLabel='Score',
grid=(2,0), gridSpan=(1,4))
self.buttonList = ButtonList(guiFrame, texts=['Close',], commands=[self.done],
grid=(3,0), gridSpan=(1,4))
self.buttonList.buttons[0].disable()
def body(self, guiFrame):
guiFrame.expandGrid(0,0)
guiFrame.expandGrid(1,0)
self.anglesGraph = ScrolledGraph(guiFrame, xLabel='Residue',yLabel='Angle',
relief='flat', symbolSize=1, grid=(0,0),
zoom=1.0,width=500,height=200,
dataColors=['#D00000','#0000D0'],
dataNames=['Phi','Psi'])
self.anglesGraph.draw()
self.islandsGraph = ScrolledGraph(guiFrame, xLabel='Residue',yLabel='No. Islands',
relief='flat', graphType='histogram',
zoom=1.0,width=500,height=200 ,grid=(1,0),
dataColors=['#8080FF','#FFFF00','#E00000'],
dataNames=['1','2-3','4+'],)
self.islandsGraph.draw()
def body(self, guiParent):
row = 0
self.graph = ScrolledGraph(guiParent)
self.graph.grid(row=row, column=0, sticky='NSEW')
row += 1
texts = ['Draw graph', 'Goodbye']
commands = [self.draw, self.destroy]
buttons = ButtonList(guiParent, texts=texts, commands=commands)
buttons.grid(row=row, column=0, sticky='NSEW')
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
self.scrolledGraph = ScrolledGraph(guiFrame,
width=400,
height=300,
symbolSize=5,
symbols=['square', 'circle'],
dataColors=['#000080', '#800000'],
lineWidths=[0, 1],
grid=(row, 0))
#self.scrolledGraph.setZoom(0.7)
row += 1
frame = Frame(guiFrame, grid=(row, 0), sticky='ew')
label = Label(frame, text='Fitting Function:', grid=(0, 0))
tipText = 'Selects which form of function to fit to the experimental data'
self.methodPulldown = PulldownList(frame,
self.changeMethod,
grid=(0, 1),
tipText=tipText)
row += 1
frame = Frame(guiFrame, grid=(row, 0), sticky='ew')
tipText = 'The effective equation of the final fitted graph, incorporating all parameters'
self.equationLabel = Label(frame,
text='Equation:',
grid=(0, 0),
tipText=tipText)
tipText = 'The error in the fit of the selected parameterised function to the experimental data'
self.errorLabel = Label(frame,
text='Fit Error:',
grid=(0, 1),
tipText=tipText)
row += 1
frame = Frame(guiFrame, grid=(row, 0), sticky='ew')
label = Label(frame, text='Include x origin?:', grid=(0, 0))
tipText = 'Whether to include the x=0 point in the drawing'
self.xOriginSelect = CheckButton(frame,
callback=self.draw,
grid=(0, 1),
selected=False,
tipText=tipText)
label = Label(frame, text='Include y origin?:', grid=(0, 2))
tipText = 'Whether to include the y=0 point in the drawing'
self.yOriginSelect = CheckButton(frame,
callback=self.draw,
grid=(0, 3),
selected=False,
tipText=tipText)
label = Label(frame, text='Include y error?:', grid=(0, 4))
tipText = 'Whether to include the y error bars in the drawing (if these exist)'
self.yErrorSelect = CheckButton(frame,
callback=self.draw,
grid=(0, 5),
selected=False,
tipText=tipText)
row += 1
frame = Frame(guiFrame, grid=(row, 0), sticky='ew')
label = Label(frame, text='Navigation Window:', grid=(0, 0))
tipText = 'Selects which spectrum window will be used for navigating to peak positions'
self.windowPanePulldown = PulldownList(frame,
self.changeWindow,
grid=(0, 1),
tipText=tipText)
label = Label(frame, text='Follow in window?:', grid=(0, 2))
tipText = 'Whether to navigate to the position of the reference peak (for the group), in the selected window'
self.followSelect = CheckButton(frame,
callback=self.windowPaneNavigate,
grid=(0, 3),
selected=False,
tipText=tipText)
label = Label(frame, text='Mark Ref Peak?:', grid=(0, 4))
tipText = 'Whether to put a multi-dimensional cross-mark through the reference peak position, so it can be identified in spectra'
self.markSelect = CheckButton(frame,
callback=None,
tipText=tipText,
grid=(0, 5),
selected=False)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
tipTexts = [
'The number of the data point, in order of increasing X-axis value',
'For each point, the value of the parameter which is varied in the NMR series, e.g. T1, temperature, concentration etc.',
'For each point, the experimental value being fitted, e.g. peak intensity of chemical shift distance',
'The value of the best-fit function at the X-axis location',
'The difference between the experimental (Y-axis) value and the fitted value',
'The error in the experimental (Y-axis) value'
]
headingList = ['Point', 'x', 'y', 'Fitted y', u'\u0394', 'y error']
self.scrolledMatrix = ScrolledMatrix(guiFrame,
headingList=headingList,
callback=self.selectObject,
tipTexts=tipTexts,
grid=(row, 0))
row += 1
tipTexts = [
'Remove the selected data point, optionally removing the underlying peak',
'Show a table of spectrum peaks that correspond to the selected data point'
]
texts = ['Remove Point', 'Show Peak']
commands = [self.removePoint, self.showObject]
if self.prevSetFunction:
texts.append('Previous Set')
tipTexts.append(
'Move to the previous set of fitted values; the next group of peaks, often corresponding to a different residue or resonance'
)
commands.append(self.prevSet)
if self.nextSetFunction:
tipTexts.append(
'Move to the next set of fitted values; the next group of peaks, often corresponding to a different residue or resonance'
)
texts.append('Next Set')
commands.append(self.nextSet)
bottomButtons = UtilityButtonList(guiFrame,
texts=texts,
commands=commands,
helpUrl=self.help_url,
tipTexts=tipTexts,
grid=(row, 0),
doClone=False)
self.removeButton = bottomButtons.buttons[0]
for func in ('__init__', 'delete', 'setName'):
self.registerNotify(self.updateWindows,
'ccpnmr.Analysis.SpectrumWindow', func)
self.update()
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 body(self, guiFrame):
guiFrame.grid_columnconfigure(3, weight=1)
row = 0
label = Label(guiFrame, text='Molecular system: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.molSysPulldown = PulldownMenu(guiFrame, self.changeMolSystem, selected_index=-1, do_initial_callback=0)
self.molSysPulldown.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Clouds files: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.filenameEntry = Entry(guiFrame,text='perfect00.pdb')
self.filenameEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Chain: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.chainPulldown = PulldownMenu(guiFrame, self.changeChain, selected_index=-1, do_initial_callback=0)
self.chainPulldown.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Thread steps: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.numStepsEntry = IntEntry(guiFrame,text=3000)
self.numStepsEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Homologue PDB file: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.pdbEntry = Entry(guiFrame,text='')
self.pdbEntry.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Dist. Threshold: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.distEntry = FloatEntry(guiFrame,text=3.0)
self.distEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Global score: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.globalScoreLabel = Label(guiFrame, text='')
self.globalScoreLabel.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Assignment Threshold: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.thresholdEntry = FloatEntry(guiFrame,text=-4.5)
self.thresholdEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
self.graph = ScrolledGraph(guiFrame, width=300, height=200)
self.graph.grid(row=row, column=0, columnspan=4, sticky = Tkinter.NSEW)
row += 1
texts = ['Run','Assign!']
commands = [self.run, self.assignSpinSystems]
bottomButtons = createDismissHelpButtonList(guiFrame,texts=texts,commands=commands,expands=0,help_url=None)
bottomButtons.grid(row=row, column=0, columnspan=4, sticky=Tkinter.EW)
self.assignButton = bottomButtons.buttons[1]
for func in ('__init__','delete'):
Implementation.registerNotify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem', func)
Implementation.registerNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func)
self.updateMolSystems()
self.updateChains()
def body(self, guiFrame):
self.geometry("775x500")
guiFrame.expandGrid(0,0)
options = ['1D Graphs','Amino Acid CA CB']
tipTexts = ['Simple graphs of how chemical shift values are distributed for a given atom type',
'Density plots of alpha a & beta carbon shift distributions for common amnio acids']
tabbedFrame = TabbedFrame(guiFrame, options=options, grid=(0,0), tipTexts=tipTexts)
frameA, frameB = tabbedFrame.frames
# # # # # # # 1D GRAPHS # # # # # # #
row = 0
MolType = self.project.metaclass.metaObjFromQualName('ccp.molecule.ChemComp.MolType')
molTypes = MolType.enumeration
molTypes.remove('other')
molTypes.remove('carbohydrate')
self.molType = 'protein'
ccpCodes = self.getCcpCodes(self.molType) or [None,]
self.ccpCode = 'Ala'
self.atomType = ATOM_TYPES[0]
self.atomNamesDict = {}
self.chemAtomNmrRefs = self.getCcpCodeData(self.ccpCode, atomType=self.atomType)
tipText = 'Which of the common bio-polymer types to show data for'
self.molTypeLabel = Label(frameA, text = 'Molecule Type:', grid=(row,0))
self.molTypePulldown = PulldownList(frameA, callback=self.changeMolType,
texts=molTypes, grid=(row,1), tipText=tipText)
tipText = 'Which residue code to show chemical shift distributions for'
self.ccpCodeLabel = Label(frameA, text = 'Residue Code:', grid=(row,2))
self.ccpCodePulldown = PulldownList(frameA, callback=self.changeCcpCode, texts=ccpCodes,
index=ccpCodes.index(self.ccpCode),
grid=(row,3), tipText=tipText)
tipText = 'Whether to show distributions for hydrogen atoms or other atoms'
self.atomTypeLabel = Label(frameA, text = 'Atom Type:', grid=(row,4))
self.atomTypePulldown = PulldownList(frameA, callback=self.changeAtomType,
texts=ATOM_TYPES, tipText=tipText,
grid=(row,5))
row += 1
tipText = 'The selection of atom name to display distributions for'
self.atomSelector = PartitionedSelector(frameA, self.toggleAtom,
tipText=tipText, maxRowObjects=20)
self.atomSelector.grid(row=row, column=0, columnspan=6, sticky='ew')
row += 1
frameA.expandGrid(row,5)
self.scrolledGraph = ScrolledGraph(frameA, symbolSize=2, reverseX=True, width=650,
height=300, title='Chemical shift distribution',
xLabel='Chemical shift', yLabel='proportion',
motionCallback=self.updateCrosshairs)
self.scrolledGraph.grid(row=row, column=0, columnspan=6, sticky='nsew')
# # # # # # # PROTEIN CA CB # # # # # # #
frameB.expandGrid(0,0)
matrix, ppms = self.getCaCbMatrix()
title = 'Amino Acid CA & CB Chemical Shifts'
self.cacbMatrix = ScrolledDensityMatrix(frameB, matrix=matrix, boxSize=14,
title=title,
xLabels=ppms, yLabels=AMINO_ACIDS,
borderColor='grey', zoom=1.0,
labelAxes=True, barPlot=False,
doLegend=False, grid=(0,0))
sdm = self.cacbMatrix
font = sdm.boldFont
x0, y0 = (470,370)
sdm.canvas.create_rectangle(x0+170,y0-6,x0+182,y0+6,fill='#4040A0',
outline=sdm.borderColor, width=1)
sdm.canvas.create_text(x0+200, y0, text='CA', font=font)
sdm.canvas.create_rectangle(x0+220,y0-6,x0+232,y0+6,fill='#A04040',
outline=sdm.borderColor, width=1)
sdm.canvas.create_text(x0+250, y0, text='CB', font=font)
sdm.canvas.create_text(x0, y0, text='13C PPM +/- 0.5', font=font)
# # # # # # # M A I N # # # # # # #
tipText = 'Whether to use chemical shift data from the BMRB (unfiltered) or RefDB sets'
label = Label(tabbedFrame.sideFrame, text='Source Database:', grid=(0,0), sticky='e')
index = SOURCE_NAMES.index(self.sourceName)
self.sourcePulldown = PulldownList(tabbedFrame.sideFrame, self.changeSource,
texts=SOURCE_NAMES, index=index,
grid=(0,1), sticky='e', tipText=tipText)
self.bottomButtons = UtilityButtonList(tabbedFrame.sideFrame, expands=True,
helpUrl=self.help_url, sticky='e',
grid=(0,2))
self.waiting = False
self.updateAfter()
for func in ('__init__', 'delete'):
self.registerNotify(self.updateAfter, 'ccp.nmr.NmrReference.NmrReferenceStore', func)
def body(self):
'''describes the body of this tab. It bascically consists
of some field to fill out for the user at the top and
a ScrolledGraph that shows the progess of the annealing
procedure a the bottom.
'''
frame = self.frame
# frame.expandGrid(13,0)
frame.expandGrid(15, 1)
row = 0
text = 'Calculate Assignment Suggestions'
command = self.runCalculations
self.startButton = Button(frame, command=command, text=text)
self.startButton.grid(row=row, column=0, sticky='nsew', columnspan=2)
row += 1
Label(frame, text='Amount of runs: ', grid=(row, 0))
tipText = 'The amount of times the whole optimization procedure is performed, each result is safed'
self.repeatEntry = IntEntry(frame, grid=(row, 1), width=7, text=10,
returnCallback=self.updateRepeatEntry,
tipText=tipText, sticky='nsew')
self.repeatEntry.bind('<Leave>', self.updateRepeatEntry, '+')
row += 1
Label(frame, text='Temperature regime: ', grid=(row, 0))
tipText = 'This list of numbers govern the temperature steps during the annealing, every number represents 1/(kb*t), where kb is the Boltzmann constant and t the temperature of one step.'
self.tempEntry = Entry(frame, text=map(str, self.acceptanceConstantList), width=64,
grid=(row, 1), isArray=True, returnCallback=self.updateAcceptanceConstantList,
tipText=tipText, sticky='nsew')
row += 1
Label(frame, text='Amount of attempts per temperature:', grid=(row, 0))
tipText = 'The amount of attempts to switch the position of two spinsystems in the sequence are performed for each temperature point'
self.NAStepEntry = IntEntry(frame, grid=(row, 1), width=7, text=10000,
returnCallback=self.updateStepEntry,
tipText=tipText, sticky='nsew')
self.NAStepEntry.bind('<Leave>', self.updateStepEntry, '+')
row += 1
Label(frame, text='Fraction of peaks to leave out:', grid=(row, 0))
tipText = 'In each run a fraction of the peaks can be left out of the optimization, thereby increasing the variability in the outcome and reducing false negatives. In each run this will be different randomly chosen sub-set of all peaks. 0.1 (10%) can be a good value.'
self.leaveOutPeaksEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.0,
returnCallback=self.updateLeavePeaksOutEntry,
tipText=tipText, sticky='nsew')
self.leaveOutPeaksEntry.bind(
'<Leave>', self.updateLeavePeaksOutEntry, '+')
row += 1
Label(frame, text='Minmal amino acid typing score:', grid=(row, 0))
tipText = 'If automatic amino acid typing is selected, a cut-off value has to set. Every amino acid type that scores higher than the cut-off is taken as a possible type. This is the same score as can be found under resonance --> spin systems --> predict type. Value should be between 0 and 100'
self.minTypeScoreEntry = FloatEntry(frame, grid=(row, 1), width=7, text=1.0,
returnCallback=self.updateMinTypeScoreEntry,
tipText=tipText, sticky='nsew')
self.minTypeScoreEntry.bind(
'<Leave>', self.updateMinTypeScoreEntry, '+')
row += 1
Label(frame, text='Minimal colabelling fraction:', grid=(row, 0))
tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.'
self.minLabelEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.1,
returnCallback=self.updateMinLabelEntry,
tipText=tipText, sticky='nsew')
self.minLabelEntry.bind('<Leave>', self.updateMinLabelEntry, '+')
row += 1
Label(frame, text='Use sequential assignments:', grid=(row, 0))
tipText = 'When this option is select the present sequential assignments will be kept in place'
self.useAssignmentsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use tentative assignments:', grid=(row, 0))
tipText = 'If a spin system has tentative assignments this can be used to narrow down the amount of possible sequential assignments.'
self.useTentativeCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use amino acid types:', grid=(row, 0))
tipText = 'Use amino acid types of the spin systems. If this option is not checked the spin systems are re-typed, only resonance names and frequencies are used'
self.useTypeCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Include untyped spin systems:', grid=(row, 0))
tipText = 'Also include spin system that have no type information. Amino acid typing will be done on the fly.'
self.useAlsoUntypedSpinSystemsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use dimensional assignments:', grid=(row, 0))
tipText = 'If one or more dimensions of a peak is already assigned, assume that this assignment is the only option. If not the check the program will consider all possibilities for the assignment of the dimension.'
self.useDimensionalAssignmentsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Chain:', grid=(row, 0))
self.molPulldown = PulldownList(
frame, callback=self.changeMolecule, grid=(row, 1))
self.updateChains()
row += 1
Label(frame, text='Residue ranges: ', grid=(row, 0))
tipText = 'Which residues should be included. Example: "10-35, 62-100, 130".'
self.residueRangeEntry = Entry(frame, text=None, width=64,
grid=(row, 1), isArray=True, returnCallback=self.updateResidueRanges,
tipText=tipText, sticky='nsew')
self.updateResidueRanges(fromChain=True)
row += 1
self.energyPlot = ScrolledGraph(frame, symbolSize=2, width=600,
height=200, title='Annealing',
xLabel='temperature step', yLabel='energy')
self.energyPlot.grid(row=row, column=0, columnspan=2, sticky='nsew')
def body(self, guiFrame):
self.geometry('700x840')
guiFrame.expandGrid(1,0)
# Top frame
frame = Frame(guiFrame, grid=(0,0))
frame.expandGrid(None,8)
label = Label(frame, text=u' %s List:' % T1, grid=(0,0))
self.t1Pulldown = PulldownList(frame, callback=self.selectT1List, grid=(0,1))
label = Label(frame, text=u' %s List:' % T2, grid=(0,2))
self.t2Pulldown = PulldownList(frame, callback=self.selectT2List, grid=(0,3))
label = Label(frame, text=' NOE List:', grid=(0,4))
self.noePulldown = PulldownList(frame, callback=self.selectNoeList, grid=(0,5))
label = Label(frame, text=' Spectrometer Freq (MHz):', grid=(0,6))
self.sfEntry = FloatEntry(frame, grid=(0,7), text=600.00, width=6)
UtilityButtonList(frame, grid=(0,9), sticky='e')
# Tabs
options = [u'%s vs %s Scatter' % (T1, T2),
u'%s,%s & NOE Graphs' % (T1, T2) ,
u'%s/%s Graph' % (T1, T2),
u'%s Estimate Graph' % S2,
'Options']
self.tabbedFrame = TabbedFrame(guiFrame, options=options,
callback=self.toggleTab, grid=(1,0))
frameA, frameD, frameC, frameE, frameB = self.tabbedFrame.frames
# T1 vs T2 Graph
frameA.expandGrid(0,0)
self.t1t2Graph = T1VersesT2Plot(frameA, grid=(0,0))
# T1 & T2 Graph
frameD.expandGrid(0,0)
frameD.expandGrid(1,0)
frameD.expandGrid(2,0)
self.t1Graph = MeasurementPlot(frameD, T1, grid=(0,0))
self.t2Graph = MeasurementPlot(frameD, T2, grid=(1,0))
self.noeGraph = NoePlot(frameD, 'NOE', grid=(2,0))
# T1 over T2 Graph
frameC.expandGrid(0,0)
self.t1t2GraphB = T1OverT2Plot(frameC, grid=(0,0))
# Order params graph
frameE.expandGrid(0,0)
frameE.expandGrid(1,0)
frameE.expandGrid(2,0)
self.s2Graph = ScrolledGraph(frameE, title=u'%s vs Residue Sequence' % S2,
xLabel='Residue number', yLabel=S2,
width=500, height=150, graphType='histogram',
xGrid=True, yGrid=False, grid=(0,0),
dataColors=['#0000A0','#808000'],
dataNames=['Isotropic',])
self.teGraph = ScrolledGraph(frameE, title=u'%s vs Residue Sequence' % Te,
xLabel='Residue number', yLabel=u'%s (ps)' % Te,
width=500, height=150, graphType='histogram',
xGrid=True, yGrid=False, grid=(1,0),
dataColors=['#008000',])
self.rexGraph = ScrolledGraph(frameE, title=u'%s vs Residue Sequence' % 'Rex',
xLabel='Residue number', yLabel='Rex',
width=500, height=150, graphType='histogram',
xGrid=True, yGrid=False, grid=(2,0),
dataColors=['#900000',])
# Options
frameB.expandGrid(4,2)
frame = LabelFrame(frameB, text='Physical Params', grid=(0,0))
frame.expandGrid(None,3)
label = Label(frame, text=u'N-H bond length (\u00C5)', grid=(0,0))
self.lenNhEntry = FloatEntry(frame, text=1.015, grid=(0,1), width=8)
label = Label(frame, text=u'Internal correlation\ntime, \u03C4e (ps)', grid=(1,0))
self.ictEntry = FloatEntry(frame, text=50.0, grid=(1,1), width=8)
label = Label(frame, text=u'15N Chemical Shift\nAnisotopy,\u0394N (ppm)',
grid=(2,0))
self.csaNEntry = FloatEntry(frame, text=-160.0, grid=(2,1), width=8)
frame = LabelFrame(frameB, text=u'%s vs %s Scatter' % (T1, T2), grid=(1,0))
label = Label(frame, text='Max cluster difference (ms):', grid=(0,0))
self.clusterDictEntry = FloatEntry(frame, text=20.0, grid=(0,1), width=8)
label = Label(frame, text='Min cluster size:', grid=(1,0))
self.clusterSizeEntry = FloatEntry(frame, text=5, grid=(1,1), width=8)
label = Label(frame, text=u'Min graph %s (ms):' % T1, grid=(2,0))
self.minT1Entry = FloatEntry(frame, text=300.0, grid=(2,1), width=8)
label = Label(frame, text=u'Max graph %s (ms):' % T1, grid=(3,0))
self.maxT1Entry = FloatEntry(frame, text=1000.0, grid=(3,1), width=8)
label = Label(frame, text=u'Min graph %s (ms):' % T2, grid=(4,0))
self.minT2Entry = FloatEntry(frame, text=0.0, grid=(4,1), width=8)
label = Label(frame, text=u'Max graph %s (ms):' % T2, grid=(5,0))
self.maxT2Entry = FloatEntry(frame, text=600.0, grid=(5,1), width=8)
frame = LabelFrame(frameB, text=u'%s Contours' % S2, grid=(0,1))
frame.expandGrid(4,3)
label = Label(frame, text='(Order Parameter Lines)',
grid=(0,0), gridSpan=(1,2))
label = Label(frame, text='Min value:', grid=(1,0))
self.minS2Entry = FloatEntry(frame, text=0.3, grid=(1,1), width=8)
label = Label(frame, text='Max value:', grid=(2,0))
self.maxS2Entry = FloatEntry(frame, text=1.0, grid=(2,1), width=8)
label = Label(frame, text='Step:', grid=(3,0))
self.stepS2Entry = FloatEntry(frame, text=0.1, grid=(3,1), width=8)
frame = LabelFrame(frameB, text=u'\u03C4m Contours', grid=(1,1))
frame.expandGrid(4,3)
label = Label(frame, text='(Rotational Correlation Time Lines)',
grid=(0,0), gridSpan=(1,2))
label = Label(frame, text='Min value (ns):', grid=(1,0))
self.minRctEntry = FloatEntry(frame, text=5.0, grid=(1,1), width=8)
label = Label(frame, text='Max value (ns):', grid=(2,0))
self.maxRctEntry = FloatEntry(frame, text=14.0, grid=(2,1), width=8)
label = Label(frame, text='Step (ns):', grid=(3,0))
self.stepRctEntry = FloatEntry(frame, text=1.0, grid=(3,1), width=8)
# Bottom frame
texts = [u'Show %s Table' % T1,u'Show %s Table' % T2, u'Estimate %s' % S2]
commands = [self.showT1List, self.showT2List, self.mc]
buttonList = ButtonList(guiFrame, grid=(2,0), texts=texts, commands=commands)
# Update
self.updateRelaxationLists()
self.drawAfter()
self.administerNotifiers(self.registerNotify)
