def draw(self):
self.drawContours()
ScrolledGraph.draw(self)
plotRegion = self.getPlotRegion()
minX = self.minT1
maxX = self.maxT1
minY = self.minT2
maxY = self.maxT2
dataRegion = [minX, minY, maxX, maxY]
deltaXplot = plotRegion[2] - plotRegion[0]
deltaYplot = plotRegion[3] - plotRegion[1]
deltaXdata = dataRegion[2] - dataRegion[0]
deltaYdata = dataRegion[3] - dataRegion[1]
ppvX = deltaXplot/float(deltaXdata)
ppvY = deltaYplot/float(deltaYdata)
createText = self.canvas.create_text
for label, x, y in self.outlierLabels:
x0 = (x - dataRegion[0])*ppvX
y0 = (y - dataRegion[1])*ppvY
x0 += plotRegion[0]
y0 += plotRegion[1]
item = createText(x0+8,y0, text=label,
fill='#000000',anchor='w')
self.contourItems.add(item)
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')
class DangleGraphPopup(BasePopup):
def __init__(self, parent):
BasePopup.__init__(self, parent=parent, title=" Dangle Prediction Graph",
transient=False, borderwidth=6)
parent.protocol("WM_DELETE_WINDOW", self.close)
self.geometry('700x700+50+50')
def 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 update(self, phiData, psiData, islandData):
self.anglesGraph.update(dataSets=[phiData,psiData])
self.islandsGraph.update(dataSets=islandData)
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 __init__(self, parent, name, *args, **kw):
kw['title'] = '%s vs Residue Sequence' % name
kw['xLabel'] = 'Residue number'
kw['yLabel'] = '%s' % name
kw['width'] = 500
kw['height'] = 150
kw['xGrid'] = True
kw['yGrid'] = False
kw['graphType'] = 'histogram'
self.minRes = 0
self.maxRes = 100
self.minVal = -1.0
self.maxVal = 1.0
ScrolledGraph.__init__(self, parent, **kw)
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 getMinMaxValues(self, dataSets): minX,maxX,minY,maxY,maxN,minDx,minDy = ScrolledGraph.getMinMaxValues(self, dataSets) minX = self.minT1 maxX = self.maxT1 minY = self.minT2 maxY = self.maxT2 return minX,maxX,minY,maxY,maxN,minDx,minDy
def getMinMaxValues(self, dataSets): minX,maxX,minY,maxY,maxN,minDx,minDy = ScrolledGraph.getMinMaxValues(self, dataSets) minX = self.minRes maxX = self.maxRes #minY = self.minVal #maxY = self.maxVal return minX,maxX,minY,maxY,maxN,minDx,minDy
class MyPopup(BasePopup):
def __init__(self, parent, peakList, *args, **kw):
self.peakList = peakList
self.colours = ['red', 'green']
self.dataSets = []
BasePopup.__init__(self, parent=parent, title='Test Popup', **kw)
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 draw(self):
self.dataSets = self.getData()
self.graph.update(self.dataSets, self.colours)
def getData(self):
peakData = [(getPeakVolume(peak) or 0.0, peak)
for peak in self.peakList.peaks]
peakData.sort()
heights = []
volumes = []
i = 0
for volume, peak in peakData:
heights.append([i, getPeakHeight(peak) or 0.0])
volumes.append([i, volume])
i += 1
return [heights, volumes]
def __init__(self, parent, contourColorA='#FFC0B0', contourColorB='#B0C0FF', *args, **kw):
kw['title'] = u'%s vs %s Relaxation Analysis' % (T1, T2)
kw['xLabel'] = u'%s (ms)' % T1
kw['yLabel'] = u'%s (ms)' % T2
kw['width'] = 500
kw['height'] = 500
kw['xGrid'] = False
kw['yGrid'] = False
kw['graphType'] = 'scatter'
self.minT1 = 0.0
self.maxT1 = 1000.0
self.minT2 = 0.0
self.maxT2 = 1000.0
self.contourColorA = contourColorA
self.contourColorB = contourColorB
self.orderParamLines = []
self.rotCorrTimeLines = []
self.contourItems = set([])
self.outlierLabels = []
ScrolledGraph.__init__(self, parent, **kw)
def update(self, t1List, t2List, cSize, cDist, sf, lenNh, ict,
csaN, paramsS2, paramsRct, graphBounds):
self.calcContourLines(sf, lenNh, ict, csaN, paramsS2, paramsRct)
self.minT1, self.maxT1, self.minT2, self.maxT2 = graphBounds
dataSets = []
dataColors = []
symbols = []
outliers = []
nColors = len(CLUSTER_COLORS)
nSymbols = len(CLUSTER_SYMBOLS)
cDist2 = cDist**2
if t1List and t2List:
t1t2Points = []
resonancesT1 = {}
t1Unit = MS_UNIT_MULTIPLIERS[t1List.unit]
t2Unit = MS_UNIT_MULTIPLIERS[t2List.unit]
for t1 in t1List.measurements:
resonancesT1[t1.resonance] = t1
for t2 in t2List.measurements:
resonance = t2.resonance
t1 = resonancesT1.get(resonance)
if t1:
xyr = (t1Unit*t1.value,t2Unit*t2.value, resonance)
t1t2Points.append(xyr)
# Do clustering
clusters = [[pt,] for pt in t1t2Points]
nMerge = 1
while nMerge:
nMerge = 0
for i, clusterA in enumerate(clusters[:-1]):
for j in range(i+1,len(clusters)):
clusterB = clusters[j]
for x1, y1, r1 in clusterA:
for x2, y2, r2 in clusterB:
dx = x2-x1
dy = y2-y1
if (dx*dx) + (dy*dy) <= cDist2:
clusterA += clusterB
clusters[j] = []
nMerge += 1
break
else:
continue
break
clusters = [c for c in clusters if c]
self.outlierLabels = []
for c in clusters:
if len(c) < cSize:
for x,y,r in c:
outliers.append((x,y))
label = makeResonanceGuiName(r)
self.outlierLabels.append((label,x,y))
else:
data = [xyr[:2] for xyr in c]
dataSets.append(data)
dataSets.append(outliers)
for i, dataSet in enumerate(dataSets):
dataSet.sort()
dataColors.append(CLUSTER_COLORS[i % nColors])
symbols.append(CLUSTER_SYMBOLS[i % nSymbols])
if outliers:
symbols[-1] = 'star'
#else:
# dataSets.append([(0,0),(1000,1000)])
ScrolledGraph.update(self, dataSets, dataColors, symbols=symbols)
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)
class PopupTemplate(BasePopup):
def __init__(self, parent, project=None, *args, **kw):
self.project = project
self.parent = parent
self.objects = self.getObjects()
self.object = None
BasePopup.__init__(self, parent=parent, title='Popup Template', **kw)
self.updateObjects()
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 floatEntryReturn(self, event):
value = self.floatEntry.get()
self.textWindow.setText('%s\n' % value)
def selectObject(self, object, row, col):
self.object = object
def getKeywords(self, object):
if object :
values = object.keywords
self.multiWidget.set(values)
def setKeywords(self, event):
values = self.multiWidget.get()
self.object.keywords = values
self.updateObjects()
def getNumber(self, object):
if object :
self.intEntry.set(object.quantity)
def setNumber(self, event):
value = self.intEntry.get()
self.object.quantity = value
self.updateObjects()
def toggleFrame1(self, isHidden):
if isHidden:
self.scrolledMatrix.grid_forget()
self.toggleFrame.grid_forget()
else:
self.scrolledGraph.grid_forget()
self.scrolledCanvas.grid_forget()
self.scrolledMatrix.grid(row=0, column=0, sticky=Tkinter.NSEW)
self.toggleFrame.grid(row=self.toggleRow, column=1,sticky=Tkinter.NSEW)
self.toggleLabel2.arrowOff()
self.toggleLabel3.arrowOff()
def toggleFrame2(self, isHidden):
if isHidden:
self.scrolledGraph.grid_forget()
self.toggleFrame.grid_forget()
else:
self.scrolledMatrix.grid_forget()
self.scrolledCanvas.grid_forget()
self.scrolledGraph.grid(row=0, column=0, sticky=Tkinter.NSEW)
self.toggleFrame.grid(row=self.toggleRow, column=1,sticky=Tkinter.NSEW)
self.toggleLabel1.arrowOff()
self.toggleLabel3.arrowOff()
def toggleFrame3(self, isHidden):
if isHidden:
self.scrolledCanvas.grid_forget()
self.toggleFrame.grid_forget()
else:
self.scrolledMatrix.grid_forget()
self.scrolledGraph.grid_forget()
self.scrolledCanvas.grid(row=0, column=0, sticky=Tkinter.NSEW)
self.toggleFrame.grid(row=self.toggleRow, column=1,sticky=Tkinter.NSEW)
self.toggleLabel1.arrowOff()
self.toggleLabel2.arrowOff()
def valueRampCallback(self, value):
self.textWindow.setText('%s\n' % value)
def checkRadioButtons(self, value):
self.textWindow.setText('%s\n' % value)
def selectPulldown(self, index, name):
self.textWindow.setText('%d, %s\n' % (index, name))
def toggleSelector(self, value):
self.textWindow.setText('%s\n' % value)
def changedCheckButtons(self, values):
self.textWindow.setText(','.join(values) + '\n')
def getObjects(self):
objects = []
objects.append( Fruit('Lemon', '#FFFF00',1,keywords=['Bitter','Tangy'] ) )
objects.append( Fruit('Orange', '#FF8000',4 ) )
objects.append( Fruit('Banana', '#FFF000',5 ) )
objects.append( Fruit('Pinapple','#FFD000',9 ) )
objects.append( Fruit('Kiwi', '#008000',12) )
objects.append( Fruit('Lime', '#00FF00',2 ) )
objects.append( Fruit('Apple', '#800000',5,keywords=['Crunchy'] ) )
objects.append( Fruit('Pear', '#408000',6 ) )
objects.append( Fruit('Peach', '#FFE0C0',2,keywords=['Sweet','Furry'] ) )
objects.append( Fruit('Plumb', '#800080',7 ) )
return objects
def updateObjects(self, event=None):
textMatrix = []
objectList = []
colorMatrix = []
for object in self.objects:
datum = []
datum.append( object.name )
datum.append( None )
datum.append( object.quantity )
datum.append( ','.join(object.keywords) )
colors = [None, object.color, None, None]
textMatrix.append(datum)
objectList.append(object)
colorMatrix.append(colors)
if self.check.get():
self.scrolledMatrix.update(textMatrix=textMatrix, objectList=objectList)
else:
self.scrolledMatrix.update(textMatrix=textMatrix, objectList=objectList, colorMatrix=colorMatrix)
def selectFile(self):
fileSelectPopup = FileSelectPopup(self, title = 'Choose file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = fileSelectPopup.getFile()
self.textWindow.setText('File Selected: %s\n' % fileName)
def showWarning(self, eventObject):
self.textWindow.setText('Text Entry Return Pressed\n')
showWarning('Warning Title','Warning Message')
return
def pressButton(self):
self.textWindow.setText('Button Pressed\n')
if showYesNo('Title','Prompt: Clear text window?'):
self.textWindow.clear()
return
def quit(self):
BasePopup.destroy(self)
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()
class CloudHomologueAssignPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.project = parent.getProject()
self.molSystem = None
self.chain = None
self.assignment = None
self.scores = []
BasePopup.__init__(self, parent, title="Cloud Threader", **kw)
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 update(self):
if self.assignment and self.scores:
self.assignButton.enable()
else:
self.assignButton.disable()
def run(self):
if self.chain:
pattern = self.filenameEntry.get()
nSteps = self.numStepsEntry.get() or 4000
pdbFile = self.pdbEntry.get()
dist = self.distEntry.get() or 3.0
pgb = ProgressBar(self, text='Searching', total=nSteps)
files = getFileNamesFromPattern(pattern , '.')
if not files:
return
clouds = getCloudsFromFile(files, self.chain.root)
score, self.scores, self.assignment = cloudHomologueAssign(self.chain, clouds, pdbFile, dist, nSteps, self.graph, pgb)
pgb.destroy()
self.globalScoreLabel.set(str(score))
self.update()
def assignSpinSystems(self):
if self.assignment and self.scores:
if showWarning('Query','Are you sure?'):
threshold = self.thresholdEntry.get() or -4.0
i = 0
for residue in self.assignment.keys():
if self.scores[residue] > threshold:
spinSystem = self.assignment[residue]
assignSpinSystemResidue(spinSystem,residue=None)
for residue in self.assignment.keys():
if self.scores[residue] > threshold:
i += 1
spinSystem = self.assignment[residue]
assignSpinSystemResidue(spinSystem,residue=residue)
showWarning('Done','%d residues assigned' % i)
def getMolSystems(self):
names = []
for molSystem in self.project.molSystems:
if molSystem.chains:
names.append( '%s' % (molSystem.code) )
return names
def changeMolSystem(self, i, name):
self.molSystem = self.project.findFirstMolSystem(code=name)
def updateMolSystems(self, *opt):
names = self.getMolSystems()
if names:
if not self.molSystem:
self.molSystem = self.project.findFirstMolSystem(code=names[0])
self.molSysPulldown.setup(names, names.index(self.molSystem.code))
def getChains(self):
chains = []
if self.molSystem:
for chain in self.molSystem.chains:
chains.append( [chain.code, chain] )
return chains
def changeChain(self, i, name=None):
if not name:
i = self.chainPulldown.selected_index
chains = self.getChains()
if chains:
self.chain = chains[i][1]
def updateChains(self, *chain):
chains = self.getChains()
if chains:
names = [x[0] for x in chains]
if (not self.chain) or (self.chain.code not in names):
self.chain = chains[0][1]
self.chainPulldown.setup(names, names.index(self.chain.code) )
self.update()
def destroy(self):
for func in ('__init__','delete'):
Implementation.unregisterNotify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem', func)
Implementation.unregisterNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func)
BasePopup.destroy(self)
class BrowseReferenceShiftsPopup(BasePopup):
"""
**Graphs and Charts of Database Chemical Shift Data**
This popup window presents the user with the distributions of known chemical
shift values, for various kinds of atom, as they appear in the BioMagResBank
or re-referenced RefDB databases. This information is useful when attempting
to determine the type of a residue from its NMR spectra, for example when
performing protein sequence assignment.
The popup is divided into two tabs for two different kinds of graphical
display. The first "1D graphs" tab shows the distributions of chemical shift
value for either hydrogens or other "heavy" atoms within a given kind of
residue. The buttons that carry atom names above the main graph can be toggled
two switch the display for different kinds of atom on or off.
The second "Amino Acid CA CB" tab is a special display to assist in the
assignment of protein sequences when using triple-resonance experiments
like HNCA/CB. Data for all of the common amino acids is displayed, but
only for the alpha and beta carbons.
**Caveats & Tips**
Two dimensional correlations, e.g. between a 1H resonance and a covalently
bound 13C will be added to Analysis in the future.
DNA and RNA chemical shift distributions is not present in the RefDB data, but
are present in the BMRB data; to view the BMRB data change the pulldown menu
at the top-right.
Some of the atom types have a second, minor chemical shift distribution, far
from the main peak, that is erroneous (this data is still present in the
source databases). An example of this is for the NE atom of the amino acid
arginine at around 115 ppm, which in this instance is probably caused by peaks
being assigned in HSQC spectra in the normal backbone amide ppm range when the
NE peak is really an aliased harmonic and should be a spectrum width away,
nearer 85 ppm.
Distributions that are notably jagged, due to lack of data for a given atom
type should naturally not be relied upon to any great degree.
"""
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.sourceName = 'RefDB'
self.chemAtomNmrRefs = {}
BasePopup.__init__(self, parent=parent, title="Resonance : Reference Chemical Shifts", **kw)
def 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 open(self):
self.updateAfter()
BasePopup.open(self)
def changeSource(self, sourceName):
if sourceName is not self.sourceName:
self.sourceName = sourceName
self.updateCcpCodes()
self.updateAfter()
def getAtomColor(self, i,N):
h = i/float(N)
s = 1
v = 0.8
[r,g,b] = hsbToRgb(h,s,v)
return hexRepr(r,g,b)
def toggleAtom(self, atomName):
if self.atomNamesDict.get(atomName):
self.atomNamesDict[atomName] = False
else:
self.atomNamesDict[atomName] = True
self.updateAfter()
def getCcpCodes(self, molType):
sourceName = self.sourceName
ccpCodes = []
for nmrRef in self.project.findAllNmrReferenceStores(molType=molType):
chemCompNmrRef = nmrRef.findFirstChemCompNmrRef(sourceName=sourceName)
if chemCompNmrRef:
ccpCodes.append(nmrRef.ccpCode)
ccpCodes.sort()
return ccpCodes
def getCcpCodeData(self, ccpCode, molType=None, atomType=None):
if not molType:
molType = self.molType
dataDict = {}
project = self.project
sourceName = self.sourceName
nmrRefStore = project.findFirstNmrReferenceStore(molType=molType,ccpCode=ccpCode)
chemCompNmrRef = nmrRefStore.findFirstChemCompNmrRef(sourceName=sourceName)
if chemCompNmrRef:
chemCompVarNmrRef = chemCompNmrRef.findFirstChemCompVarNmrRef(linking='any',descriptor='any')
if chemCompVarNmrRef:
for chemAtomNmrRef in chemCompVarNmrRef.chemAtomNmrRefs:
atomName = chemAtomNmrRef.name
element = chemAtomNmrRef.findFirstChemAtom().elementSymbol
if not atomType:
dataDict[atomName] = chemAtomNmrRef
elif (atomType == 'Hydrogen' and element == 'H') or \
(atomType == 'Heavy' and element != 'H'):
dataDict[atomName] = chemAtomNmrRef
return dataDict
def changeMolType(self, molType):
self.molType = molType
self.updateCcpCodes()
def changeCcpCode(self, ccpCode):
self.ccpCode = ccpCode
self.updateAtomNames()
def changeAtomType(self, atomType):
self.atomType = atomType
self.updateAtomNames()
def updateAfter(self, *opt):
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.update)
def updateCcpCodes(self):
ccpCodes = self.getCcpCodes(self.molType)
if ccpCodes:
self.ccpCodePulldown.setup(ccpCodes, ccpCodes, 0)
self.changeCcpCode(ccpCodes[0])
else:
self.ccpCodePulldown.setup([], [], 0)
self.changeCcpCode(None)
def updateAtomNames(self):
if self.ccpCode:
self.chemAtomNmrRefs = self.getCcpCodeData(self.ccpCode, atomType=self.atomType)
atomNames = self.chemAtomNmrRefs.keys()
atomNames = greekSortAtomNames(atomNames, self.molType)
N = len(atomNames)
for atomName in atomNames:
if self.atomNamesDict.get(atomName) is None:
self.atomNamesDict[atomName] = True
colors = []
for i in range(N):
colors.append( self.getAtomColor(i,N) )
else:
colors = []
atomNames = []
N = 0
self.atomSelector.update(objects=atomNames,labels=atomNames,colors=colors)
for i in range(N):
if self.atomNamesDict[atomNames[i]]:
self.atomSelector.setButtonState(i, True)
else:
self.atomSelector.setButtonState(i, False)
self.updateAfter()
def destroy(self):
for func in ('__init__', 'delete'):
self.unregisterNotify(self.updateAfter, 'ccp.nmr.NmrReference.NmrReferenceStore', func)
BasePopup.destroy(self)
def update(self):
matrix, ppms = self.getCaCbMatrix()
self.cacbMatrix.xLabels = ppms
self.cacbMatrix.update(matrix)
self.updateAtomNames()
dataSets = []
colorList = []
atomsString = ''
if self.ccpCode:
c = 0
atomNames = self.chemAtomNmrRefs.keys()
N = len(atomNames)
for atomName in greekSortAtomNames(atomNames, self.molType):
if self.atomNamesDict[atomName]:
atomsString += '%s ' % atomName
chemAtomNmrRef = self.chemAtomNmrRefs[atomName]
distribution = chemAtomNmrRef.distribution
refPoint = chemAtomNmrRef.refPoint
refValue = chemAtomNmrRef.refValue
valuePerPoint = chemAtomNmrRef.valuePerPoint
data = []
for i in range(len(distribution)):
x = refValue + valuePerPoint*( i-refPoint)
y = distribution[i]
data.append( (x,y) )
dataSets.append(data)
colorList.append(self.getAtomColor(c,N))
c += 1
self.scrolledGraph.title = '%s %s Chemical shift distribution' % (self.ccpCode,atomsString)
else:
dataSets = [[(0,0)],]
self.scrolledGraph.title = 'Chemical shift distribution'
self.scrolledGraph.zoom = 1.0
self.scrolledGraph.update(dataSets=dataSets, dataColors=colorList)
self.waiting = False
def getCaCbMatrix(self):
ppms = range(73,14,-1)
blankCol = [0.0]*len(ppms)
matrix = [[0.0]*len(AMINO_ACIDS) for x in ppms]
for i, ccpCode in enumerate(AMINO_ACIDS):
atomRefDict = self.getCcpCodeData(ccpCode, molType='protein')
valueDict = {}
for atomName in ('CA','CB'):
valueDict[atomName] = blankCol[:]
chemAtomNmrRef = atomRefDict.get(atomName)
if not chemAtomNmrRef:
continue
distribution = chemAtomNmrRef.distribution
refPoint = chemAtomNmrRef.refPoint
refValue = chemAtomNmrRef.refValue
valuePerPoint = chemAtomNmrRef.valuePerPoint
for j, ppm in enumerate(ppms):
ppmMin = ppm-0.5
ppmMax = ppm+0.5
v = 0.0
n = 0.0
for k in range(len(distribution)):
y = refValue + valuePerPoint*(k-refPoint)
if ppmMin < y <= ppmMax:
v += distribution[k]
n += 1.0
elif y > ppmMax:
break
if n:
valueDict[atomName][j] = v/n
for j, ppm in enumerate(ppms):
matrix[j][i] = valueDict['CA'][j] - valueDict['CB'][j]
return matrix, ppms
def updateCrosshairs(self, event):
# code below is a bit dangerous
position = self.scrolledGraph.getPlotCoords(event)[0]
typeLocation = []
isHydrogen = (self.atomType == 'Hydrogen')
for panelType in self.analysisProject.panelTypes:
axisType = panelType.axisType
if isHydrogen:
if axisType.name in ('1H', '2H'):
typeLocation.append((panelType, position))
else:
if axisType.name not in ('1H', '2H'):
typeLocation.append((panelType, position))
self.scrolledGraph.mouseEnter(event)
self.parent.drawWindowCrosshairs(typeLocation)
def drawCrosshairs(self, typeLocation):
""" Draw crosshairs at specified locations.
typeLocation = tuple of (PanelType, position)
"""
isHydrogen = (self.atomType == ATOM_TYPES[0])
positions = []
for (panelType, position) in typeLocation:
axisType = panelType.axisType
if axisType.measurementType != 'Shift':
continue
if position is None:
continue
if isHydrogen:
if axisType.name in ('1H', '2H'):
positions.append(position)
else:
if axisType.name not in ('1H', '2H'):
positions.append(position)
self.scrolledGraph.drawVerticalLines(positions)
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 update(self, t1List, t2List):
nColors = len(CLUSTER_COLORS)
dataSets = []
dataColors = []
dataNames = []
seqNums = set()
values = set()
if t1List and t2List:
t1t2Points = {}
resonancesT1 = {}
t1Unit = MS_UNIT_MULTIPLIERS[t1List.unit]
t2Unit = MS_UNIT_MULTIPLIERS[t2List.unit]
for t1 in t1List.measurements:
resonancesT1[t1.resonance] = t1
for t2 in t2List.measurements:
resonance = t2.resonance
if not resonance.resonanceSet:
continue
t1 = resonancesT1.get(resonance)
if t1:
residue = resonance.resonanceSet.findFirstAtomSet().findFirstAtom().residue
value = (t1Unit*t1.value) / (t2Unit*t2.value)
chain = residue.chain
if chain not in t1t2Points:
t1t2Points[chain] = []
seqCode = residue.seqCode
t1t2Points[chain].append((seqCode, value))
seqNums.add(seqCode)
values.add(value)
chains = t1t2Points.keys()
molSystems = set([c.molSystem for c in chains])
if len(molSystems) > 1:
chainLabels = [('Chain %s:%s' % (c.molSystem.code, c.code), c) for c in chains]
chainLabels.sort()
else:
chainLabels = [('Chain %s' % c.code, c) for c in chains]
chainLabels.sort()
for label, chain in chainLabels:
data = t1t2Points[chain]
data.sort()
dataSets.append(data)
dataNames.append(label)
for i, dataSet in enumerate(dataSets):
dataColors.append(CLUSTER_COLORS[i % nColors])
res = [c.sortedResidues() for c in chains]
if seqNums:
self.minRes = min(seqNums) - 1
self.maxRes = max(seqNums) + 1
if values:
self.minVal = 0.0 # min(values)
self.maxVal = int(max(values) + 1)
if len(dataNames) < 2:
dataNames = None
ScrolledGraph.update(self, dataSets, dataColors, dataNames=dataNames)
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 update(self, mList):
nColors = len(CLUSTER_COLORS)
dataSets = []
dataColors = []
dataNames = []
seqNums = set()
values = set()
if mList:
points = {}
for measurement in mList.measurements:
resonance = list(measurement.resonances)[0]
if not resonance.resonanceSet:
continue
residue = resonance.resonanceSet.findFirstAtomSet().findFirstAtom().residue
value = measurement.value
chain = residue.chain
if chain not in points:
points[chain] = []
seqCode = residue.seqCode
points[chain].append((seqCode, value))
seqNums.add(seqCode)
values.add(value)
chains = points.keys()
molSystems = set([c.molSystem for c in chains])
if len(molSystems) > 1:
chainLabels = [('Chain %s:%s' % (c.molSystem.code, c.code), c) for c in chains]
chainLabels.sort()
else:
chainLabels = [('Chain %s' % c.code, c) for c in chains]
chainLabels.sort()
for label, chain in chainLabels:
data = points[chain]
data.sort()
dataSets.append(data)
dataNames.append(label)
for i, dataSet in enumerate(dataSets):
dataColors.append(CLUSTER_COLORS[i % nColors])
res = [c.sortedResidues() for c in chains]
if seqNums:
self.minRes = min(seqNums) - 1
self.maxRes = max(seqNums) + 1
if values:
self.minVal = int(min(values))
self.maxVal = int(max(values) + 1)
if len(dataNames) < 2:
dataNames = None
ScrolledGraph.update(self, dataSets, dataColors, dataNames=dataNames)
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()
class RelaxationAnalysisPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.t1List = None
self.t2List = None
self.noeList = None
self.waiting = False
BasePopup.__init__(self, parent, title="Relaxation Analyses", **kw)
periodicTable = self.project.currentChemElementStore
nitrogen = periodicTable.findFirstChemElement(elementSymbol='N')
hydrogen = periodicTable.findFirstChemElement(elementSymbol='H')
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)
def open(self):
self.updateRelaxationLists()
self.drawAfter()
BasePopup.open(self)
def destroy(self):
self.administerNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
def getSanitisedParams(self):
cDist = self.clusterDictEntry.get() or 0.0
lenNh = max(min(self.lenNhEntry.get() or 1.015, 1.2), 0.8)
ict = self.ictEntry.get() or 0.0
csaN = self.csaNEntry.get() or -180.0
if csaN > 0:
csaN *= -1.0
minS2 = max(min(self.minS2Entry.get() or 0.0, 0.9), 0.0)
maxS2 = max(min(self.maxS2Entry.get() or 1.0, 1.0), 0.1)
if minS2 > maxS2:
maxS2, minS2 = minS2, maxS2
stepS2 = max(self.stepS2Entry.get() or 0.1, (maxS2-minS2)/100)
minRct = self.minRctEntry.get()
maxRct = self.maxRctEntry.get()
if minRct > maxRct:
maxRct, minRct = minRct, maxRct
stepRct = max(self.stepRctEntry.get() or 0.1, (maxRct-minRct)/100)
cluster = max(abs(self.clusterSizeEntry.get() or 10), 1)
minT1 = self.minT1Entry.get() or 300.0
maxT1 = self.maxT1Entry.get() or 1000.0
minT2 = self.minT2Entry.get() or 0.0
maxT2 = self.maxT2Entry.get() or 600.0
if minT1 < 0:
minT1 = 0.0
if minT2 < 0:
minT2 = 0.0
if maxT1 < 0:
maxT1 = 0.0
if maxT2 < 0:
maxT2 = 0.0
if minT1 > maxT1:
minT1, maxT1 = maxT1, minT1
if minT2 > maxT2:
minT2, maxT2 = maxT2, minT2
if minT1 == maxT1:
maxT1 += 100
if minT2 == maxT2:
maxT2 += 100
self.clusterSizeEntry.set(cluster)
self.minT1Entry.set(minT1)
self.maxT1Entry.set(maxT1)
self.minT2Entry.set(minT2)
self.maxT2Entry.set(maxT2)
self.clusterDictEntry.set(cDist)
self.lenNhEntry.set(lenNh)
self.ictEntry.set(ict)
self.csaNEntry.set(csaN)
self.minS2Entry.set(minS2)
self.maxS2Entry.set(maxS2)
self.stepS2Entry.set(stepS2)
self.minRctEntry.set(minRct)
self.maxRctEntry.set(maxRct)
self.stepRctEntry.set(stepRct)
paramsS2 = (minS2, maxS2, stepS2)
paramsRct = (minRct, maxRct, stepRct)
tBounds = (minT1, maxT1, minT2, maxT2)
return cluster, cDist, lenNh, ict, csaN, paramsS2, paramsRct, tBounds
def administerNotifiers(self, notifyFunc):
for func in ('__init__', 'delete','setName'):
for clazz in ('ccp.nmr.Nmr.T1List','ccp.nmr.Nmr.T2List'):
notifyFunc(self.updateRelaxationLists,clazz, func)
for func in ('__init__', 'delete', 'setValue'):
notifyFunc(self.updateMeasurementAfter,'ccp.nmr.Nmr.T1', func)
notifyFunc(self.updateMeasurementAfter,'ccp.nmr.Nmr.T2', func)
def showT1List(self):
if self.t1List:
self.guiParent.editMeasurements(self.t1List)
def showT2List(self):
if self.t2List:
self.guiParent.editMeasurements(self.t2List)
def toggleTab(self, index):
if index == 0:
self.drawAfter()
def updateMeasurementAfter(self, measurement):
if measurement.parentList in (self.t1List, self.t2List):
self.drawAfter()
def updateRelaxationLists(self, obj=None):
mLists = self.nmrProject.sortedMeasurementLists()
# T1
t1List = self.t1List
t1Lists = [ml for ml in mLists if ml.className == 'T1List']
index = 0
names = []
if t1Lists:
if t1List not in t1Lists:
t1List = t1Lists[0]
index = t1Lists.index(t1List)
names = [ml.name or 'List %d' % ml.serial for ml in t1Lists]
else:
t1List = None
self.selectT1List(t1List)
self.t1Pulldown.setup(names, t1Lists, index)
# T2
t2List = self.t2List
t2Lists = [ml for ml in mLists if ml.className == 'T2List']
index = 0
names = []
if t2Lists:
if t2List not in t2Lists:
t2List = t2Lists[0]
index = t2Lists.index(t2List)
names = [ml.name or 'List %d' % ml.serial for ml in t2Lists]
else:
t2List = None
self.selectT2List(t2List)
self.t2Pulldown.setup(names, t2Lists, index)
# NOE
noeList = self.noeList
noeLists = [ml for ml in mLists if ml.className == 'NoeList']
index = 0
names = []
if noeLists:
if noeList not in noeLists:
noeList = noeLists[0]
index = noeLists.index(noeList)
names = [ml.name or 'List %d' % ml.serial for ml in noeLists]
else:
noeList = None
self.selectNoeList(noeList)
self.noePulldown.setup(names, noeLists, index)
def drawAfter(self):
if self.waiting:
return
self.waiting = True
self.after_idle(self.draw)
def selectT1List(self, t1List):
if t1List is not self.t1List:
self.t1List = t1List
self.sfEntry.set(t1List.sf)
values = [m.value for m in t1List.measurements]
values.sort()
minVal = self.minT1Entry.get()
maxVal = self.maxT1Entry.get()
minVal0 = values[0]*MS_UNIT_MULTIPLIERS[t1List.unit]
maxVal0 = values[-1]*MS_UNIT_MULTIPLIERS[t1List.unit]
if minVal0 < minVal:
self.minT1Entry.set(max(minVal0 - 100, 0))
if maxVal0 > maxVal:
self.maxT1Entry.set(maxVal0 + 100)
self.drawAfter()
def selectT2List(self, t2List):
if t2List is not self.t2List:
self.t2List = t2List
self.sfEntry.set(t2List.sf)
values = [m.value for m in t2List.measurements]
values.sort()
values.sort()
minVal = self.minT2Entry.get()
maxVal = self.maxT2Entry.get()
minVal0 = values[0]*MS_UNIT_MULTIPLIERS[t2List.unit]
maxVal0 = values[-1]*MS_UNIT_MULTIPLIERS[t2List.unit]
if minVal0 < minVal:
self.minT2Entry.set(max(minVal0 - 50, 0))
if maxVal0 > maxVal:
self.maxT2Entry.set(maxVal0 + 50)
self.drawAfter()
def selectNoeList(self, noeList):
if noeList is not self.noeList:
self.noeList = noeList
self.sfEntry.set(noeList.sf)
#self.drawAfter()
def draw(self):
params = self.getSanitisedParams()
cSize, cDist, lenNh, ict, csaN, paramsS2, paramsRct, tBounds = params
sf = abs(self.sfEntry.get() or 500.010)
self.t1t2Graph.update(self.t1List, self.t2List, cSize, cDist, sf, lenNh,
ict, csaN, paramsS2, paramsRct, tBounds)
self.t1t2GraphB.update(self.t1List, self.t2List)
self.t1Graph.update(self.t1List)
self.t2Graph.update(self.t2List)
self.noeGraph.update(self.noeList)
self.waiting = False
def mc(self):
sf = abs(self.sfEntry.get() or 500.010)
if not self.t1List and self.t2List:
return
chains = set([])
t1t2Points = {}
resonancesT1 = {}
resonancesNoe = {}
residueResonances = {}
t1Unit = MS_UNIT_MULTIPLIERS[self.t1List.unit]
t2Unit = MS_UNIT_MULTIPLIERS[self.t2List.unit]
if self.noeList:
for noe in self.noeList.measurements:
for resonance in noe.resonances:
resonancesNoe[resonance] = noe
for t1 in self.t1List.measurements:
resonancesT1[t1.resonance] = t1
for t2 in self.t2List.measurements:
resonance = t2.resonance
if not resonance.resonanceSet:
continue
residue = resonance.resonanceSet.findFirstAtomSet().findFirstAtom().residue
t1 = resonancesT1.get(resonance)
noe = resonancesNoe.get(resonance)
if t1 and noe:
t1t2Points[residue] = 1e-3*t1Unit*t1.value, 1e-3*t2Unit*t2.value, noe.value
chains.add(residue.chain)
residueResonances[residue] = resonance
if t1:
t1t2Points[residue] = 1e-3*t1Unit*t1.value, 1e-3*t2Unit*t2.value, None
chains.add(residue.chain)
residueResonances[residue] = resonance
for chain in chains:
residues = chain.sortedResidues()
t1Values = []
t2Values = []
noeValues = []
n = len(residues)
n2 = n-1
jj = range(n)
s2Best = [0.0] * n
teBest = [0.0] * n
rexBest = [0.0] * n
print ''
for residue in residues:
t1,t2, noe = t1t2Points.get(residue, (None, None, None))
t1Values.append(t1)
t2Values.append(t2)
noeValues.append(noe)
t1s = [v for v in t1Values if v]
t2s = [v for v in t2Values if v]
noes = [v for v in noeValues if v]
m = len(t1s)
t1 = sum(t1s)/float(m)
t2 = sum(t2s)/float(m)
noe = sum(noes)/float(m)
t12 = [v/t2s[i] for i, v in enumerate(t1s) if v]
t12m = sum(t12)/float(len(t12))
deltas = [abs(v-t12m)/t12m for v in t12]
w = [1.0/(v*v) for v in deltas]
t1 = sum([ t1s[j]*w[j] for j in range(m)])/sum(w)
t2 = sum([ t2s[j]*w[j] for j in range(m)])/sum(w)
if noes:
noe = sum([ noes[j]*w[j] for j in range(m)])/sum(w)
else:
noe = None
i, ensemble = self.fitT1T2(t1, t2, noe, sf, tmFix=None, teFix=None, s2Fix=None,
tmMin=1e-9, tmMax=100e-9, teMin=1e-12, teMax=1e-10,
rexFix=0.0)
ensemble.sort()
score, s2, te0, tm0, rex, t1t, t2t, noet = ensemble[0]
data = (s2, te0*1e12, tm0*1e9, rex, t1, t1t, t2, t2t, noe or 0.0, noet, score, i)
print 'Mean A S2:%5.3f Te:%5.1f Tm:%5.3f Rex:%5.3f T1:%5.3f %5.3f T2:%5.3f %5.3f NOE:%5.3f %5.3f %e %6d' % data
rexCheck = 999 # 1.40 * t1/t2
# Prior is mean, then region
for j in jj:
t1 = t1Values[j]
t2 = t2Values[j]
noe = noeValues[j]
if t1 is None:
continue
residue = residues[j]
print '%3d%s' % (residue.seqCode, residue.ccpCode),
i, ensemble = self.fitT1T2(t1, t2, noe, sf, tmFix=tm0, teFix=None, s2Fix=None,
tmMin=tm0*0.1, tmMax=tm0*5, teMin=te0/100, teMax=te0*20,
rexFix=0.0, rexMax=15.0)
ensemble.sort()
score, s2, te, tm, rex, t1t, t2t, noet = ensemble[0]
if s2 > 0.995:
i, ensemble = self.fitT1T2(t1, t2, noe, sf, tmFix=tm0, teFix=None, s2Fix=None,
teMin=te/10, teMax=te*10,
rexFix=None, rexMax=15.0)
ensemble.sort()
score, s2, te, tm, rex, t1t, t2t, noet = ensemble[0]
teBest[j] = te
s2Best[j] = s2
rexBest[j] = rex
data = (s2, te*1e12, tm*1e9, rex, t1, t1t, t2, t2t, noe or 0.0, noet, score, i)
print 'S2:%5.3f Te:%5.1f Tm:%5.3f Rex:%5.3f T1:%5.3f %5.3f T2:%5.3f %5.3f NOE:%5.3f %5.3f %e %6d' % data
dataSet1 = []
dataSet2 = []
dataSet3 = []
for j in jj:
residue = residues[j]
resonance = residueResonances.get(residue)
if not resonance:
continue
dataSet1.append((residue.seqCode, s2Best[j]))
dataSet2.append((residue.seqCode, teBest[j]*1e9))
dataSet3.append((residue.seqCode, rexBest[j]))
self.s2Graph.update([dataSet1,])
self.teGraph.update([dataSet2,])
self.rexGraph.update([dataSet3,])
self.tabbedFrame.select(3)
def fitT1T2(self, t1, t2, noe, sf, tmFix=None, teFix=None, s2Fix=None,
tmMin=1e-9, tmMax=100e-9, teMin=1e-12, teMax=1e-9,
rexFix=None, rexMax=15.0, niter=10000):
# Could have multiple sf
rNH = 1.015
csaN = 160*1e-6 # 160 ppm
omegaH = sf * 2 * PI * 1e6 # Rad/s
omegaN = omegaH * GAMMA_N/GAMMA_H
gammaHN = GAMMA_H/GAMMA_N
A = REDUCED_PERM_VACUUM * REDUCED_PLANK * GAMMA_N * GAMMA_H * 1e30 # Cubic Angstrom adjust
A /= rNH**3.0
A = A*A/4.0
C = omegaN * omegaN * csaN * csaN
C /= 3.0
# Init params
if s2Fix is None:
s2Start = [x*0.05 for x in range(1,20)]
else:
s2Start = [s2Fix,]
if teFix is None:
teStart = [x*1e-12 for x in [10,30,70,100,300,700,1000]]
else:
teStart = [teFix,]
if tmFix is None:
tmStart = [x*1e-9 for x in range(1,30)]
else:
tmStart = [tmFix,]
if rexFix is None:
rexStart = [float(x) for x in range(int(rexMax))]
else:
rexStart = [rexFix,]
# Init ensemble of solutions
ensemble = []
for s2 in s2Start:
for te in teStart:
for tm in tmStart:
for rex in rexStart:
ensemble.append((None, s2, te, tm, rex))
# Init scores
for k, (score, s2, te, tm, rex) in enumerate(ensemble):
jH = getSpectralDensity(s2, tm, te, omegaH)
jN = getSpectralDensity(s2, tm, te, omegaN)
jHpN = getSpectralDensity(s2, tm, te, omegaH+omegaN)
jHmN = getSpectralDensity(s2, tm, te, omegaH-omegaN)
j0 = getSpectralDensity(s2, tm, te, 0.0)
r1 = A*( (3*jN) + (6*jHpN) + jHmN ) + C*jN
r2 = 0.5*A*( (4*j0) + (3*jN) + (6*jHpN) + (6*jH) + jHmN ) + C*( 2*j0/3.0 + 0.5*jN ) + rex
t1p = 1.0/r1
t2p = 1.0/r2
d1 = (t1p-t1)/t1
d2 = (t2p-t2)/t2
score = (d1*d1) + (d2*d2)
if noe is None:
noep = 0.0
else:
noep = 1.0 + ( A * gammaHN * t1 * ((6*jHpN)-jHmN) )
dn = (noep-noe)/2.0
score += (dn*dn)
ensemble[k] = (score, s2, te, tm, rex, t1p, t2p, noep)
# Matrix
#
# Pred Jh
# R1
# R2
# NOE
# r = 1.0/rct + 1.0/ict
# t = 1.0/r
# j = (s2*rct) / (1.0 + w*w*rct*rct)
# j += ((1.0-s2)*t) / (1.0 + w*w*t*t)
#
# return j*0.4
ensemble.sort()
ensemble = ensemble[:10]
ensembleSize = len(ensemble)
bestScore = 1e99
for i in xrange(niter):
f = i/float(niter)
f = exp(-10.0*f)
# Mutate
ensemble.sort()
prevScore, s2, te, tm, rex, t1p, t2p, noep = ensemble[-1] #Biggest is worst
if ensemble[0][0] < 1e-10:
break
if not s2Fix:
#d = ((random() + 0.618 - 1.0) * f) + 1.0
d = ((random() - 0.382) * f) + 1.0
s2 = max(0.0, min(1.0, s2*d))
if not tmFix:
d = ((random() - 0.382) * f) + 1.0
tm = max(tmMin, min(tmMax, tm*d))
if not teFix:
d = ((random() - 0.382) * f) + 1.0
te = max(teMin, min(teMax, te*d))
d = ((random() - 0.382) * f) + 1.0
rex = max(0.0, min(rexMax, rex*d))
jH = getSpectralDensity(s2, tm, te, omegaH)
jN = getSpectralDensity(s2, tm, te, omegaN)
jHpN = getSpectralDensity(s2, tm, te, omegaH+omegaN)
jHmN = getSpectralDensity(s2, tm, te, omegaH-omegaN)
j0 = getSpectralDensity(s2, tm, te, 0.0)
r1 = A*( (3*jN) + (6*jHpN) + jHmN ) + C*jN
r2 = 0.5*A*( (4*j0) + (3*jN) + (6*jHpN) + (6*jH) + jHmN ) + C*( 2*j0/3.0 + 0.5*jN ) + rex
t1p = 1.0/r1
t2p = 1.0/r2
d1 = (t1p-t1)/t1
d2 = (t2p-t2)/t2
score = (d1*d1) + (d2*d2)
if noe is None:
noep = 0.0
else:
noep = 1.0 + ( A * gammaHN * t1 * ((6*jHpN)-jHmN) )
dn = (noep-noe)/2.0
score += (dn*dn)
ratio = exp(prevScore-score)
if ratio > 1.0: # random():
ensemble[-1] = (score, s2, te, tm, rex, t1p, t2p, noep)
else:
k = randint(0,ensembleSize-1)
score, s2, te, tm, rex, t1p, t2p, noep = ensemble[k]
ensemble[-1] = (score, s2, te, tm, rex, t1p, t2p, noep)
if score < bestScore:
bestScore = score
#print bestScore, ', '.join(['%.3e' % x[0] for x in ensemble])
return i, ensemble
class EditFitGraphPopup(BasePopup):
"""
**Analyse Function Curve Fitting to Peak Series Data**
This popup is used to display the fit of a curve, of the displayed equation
type, to data that has been extracted for a group of spectrum peaks from an
NMR series. Precisely which kind of data is being fitted depends on the parent
tool that this popup window was launched from. For example, for the `Follow
Intensity Changes`_ tool the displayed graph is of a time or frequency value
on the "X" axis (e.g. T1) verses peak intensity. For the `Follow Shift
Changes`_ system the plot is for the parameters of the experiment titration on
the "X" axis (e.g concentration) verses chemical shift distance.
The upper graph shows the peak data that was used; the blue points, and the
points of the fitted theoretical curve; red points. The lower table lists the
data points for all of the peaks in the group, to which the data relates.
There will be one peak for each row of the table, and hence point on the "X"
axis. For each data point in the table the corresponding peak from which the
data was extracted may be located with the "Follow in window" option, using
the stated spectrum window and making marker lines as desired. Alternatively,
the peak may be viewed in a table with [Show Peak]
In general operation this system is used to check how well the selected
function curve fits the peak data. The data that is displayed comes from the
analysis tool that launched this popup. Any outliers may be removed using
[Remove Point] (only with good reason) or the peaks themselves may be
corrected if something has gone awry. Given that the display is launched from
the selection of a specific group of peaks from a popup like `Follow Shift
Changes`_ or `Follow Intensity Changes`_ and there are usually several peak
groups that need to be analysed, the [Previous Set] and [Next Set] buttons can
be used to quickly jump to the next peak group and see the next curve in the
analysis results.
.. _`Follow Intensity Changes`: CalcRatesPopup.html
.. _`Follow Shift Changes`: FollowShiftChangesPopup.html
"""
def __init__(self,
parent,
dataFitting,
getXYfunction,
updateFunction,
xLabel,
yLabel,
showObjectFunction=None,
nextSetFunction=None,
prevSetFunction=None,
graphTitle='',
**kw):
self.guiParent = parent
self.getXYfunction = getXYfunction
self.updateFunction = updateFunction
self.nextSetFunction = nextSetFunction
self.prevSetFunction = prevSetFunction
self.dataFitting = dataFitting
self.object = None
self.xLabel = xLabel
self.yLabel = yLabel
self.x = []
self.y = []
self.yFit = []
self.params = ()
self.chiSq = 0
self.method = dataFitting.fitFunction
self.waiting = False
self.noiseLevel = dataFitting.noiseLevel
self.graphTitle = graphTitle
self.windowPane = None
self.mark = None
BasePopup.__init__(self, parent=parent, title='Fit Graph', **kw)
parent.protocol("WM_DELETE_WINDOW", self.close)
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 destroy(self):
for func in ('__init__', 'delete', 'setName'):
self.unregisterNotify(self.updateWindows,
'ccpnmr.Analysis.SpectrumWindow', func)
BasePopup.destroy(self)
def nextSet(self):
if self.nextSetFunction:
self.nextSetFunction()
self.windowPaneNavigate()
def prevSet(self):
if self.prevSetFunction:
self.prevSetFunction()
self.windowPaneNavigate()
def windowPaneNavigate(self, event=None):
if self.followSelect.get() and self.dataFitting:
peaks = self.dataFitting.objects
if self.windowPane and peaks:
peak = peaks[int(len(peaks) / 2)]
windowFrame = self.windowPane.getWindowFrame()
windowFrame.gotoPeak(peak)
if self.markSelect.get():
if self.mark and not self.mark.isDeleted:
self.mark.delete()
self.mark = createPeakMark(self.dataFitting.refObject)
def getWindows(self):
peaks = self.scrolledMatrix.objectList
windowPanes = []
if peaks:
peak = peaks[0]
project = peak.root
spectrum = peak.peakList.dataSource
tryWindows = getActiveWindows(project)
for window in tryWindows:
for windowPane in window.sortedSpectrumWindowPanes():
if isSpectrumInWindowPane(windowPane, spectrum):
windowPanes.append(windowPane)
return windowPanes
def changeWindow(self, windowPane):
if windowPane is not self.windowPane:
self.windowPane = windowPane
self.windowPaneNavigate()
def updateWindows(self, window=None):
windowPanes = self.getWindows()
index = -1
names = [getWindowPaneName(wp) for wp in windowPanes]
windowPane = self.windowPane
if windowPanes:
if windowPane not in windowPanes:
windowPane = windowPanes[0]
index = windowPanes.index(windowPane)
if windowPane is not self.windowPane:
self.windowPane = windowPane
self.windowPaneNavigate()
self.windowPanePulldown.setup(names, windowPanes, index)
def showObject(self):
if self.object and (self.object.className == 'Peak'):
peaks = [self.object]
self.guiParent.guiParent.viewPeaks(peaks)
def close(self):
BasePopup.close(self)
def changeMethod(self, index):
if self.dataFitting:
self.method = index
self.dataFitting.fitFunction = self.method
self.updateAfter()
def updateMethods(self, *opt):
n = len(METHOD_NAMES)
if self.method >= n:
self.method = 1
self.methodPulldown.setup(METHOD_NAMES, range(n), self.method)
def selectObject(self, object, row, col):
if object:
self.object = object
self.updateButtons()
def removePoint(self):
if self.object and (len(self.dataFitting.objects) > 2):
self.dataFitting.objects.remove(self.object)
if showYesNo('Query',
'Delete the corresponding %s?' %
(self.object.className),
parent=self):
self.object.delete()
self.updateAfter()
def draw(self, *junk):
title = '%s Function fit %s' % (self.graphTitle,
METHOD_NAMES[self.method])
dataSet1 = []
dataSet2 = []
useErr = self.yErrorSelect.isSelected()
if not useErr:
useErr = None
for i in range(len(self.scrolledMatrix.textMatrix)):
row = self.scrolledMatrix.textMatrix[i]
x = row[1]
y = row[2]
y2 = row[3]
err = useErr and row[5]
dataSet1.append([x, y, err])
dataSet2.append([x, y2])
dataSet1.sort()
dataSet2.sort()
if dataSet1 and dataSet2:
drawOriginX = self.xOriginSelect.isSelected()
drawOriginY = self.yOriginSelect.isSelected()
self.scrolledGraph.update(dataSets=[dataSet1, dataSet2],
xLabel=self.xLabel,
yLabel=self.yLabel,
title=title,
drawOriginX=drawOriginX,
drawOriginY=drawOriginY)
self.scrolledGraph.draw()
def updateAfter(self, *object):
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.update)
def update(self,
dataFitting=None,
xLabel=None,
yLabel=None,
graphTitle=None,
force=False):
if (not force) and dataFitting and (self.dataFitting is dataFitting):
if (self.method, self.xLabel, self.yLabel, self.noiseLevel) == \
(self.dataFitting.fitFunction, xLabel, yLabel, self.dataFitting.noiseLevel):
self.waiting = False
return
if dataFitting:
self.dataFitting = dataFitting
self.xLabel = xLabel or self.xLabel
self.yLabel = yLabel or self.yLabel
self.graphTitle = graphTitle or self.graphTitle
if not self.dataFitting:
self.waiting = False
return
else:
dataFitting = self.dataFitting
dataFitting = self.getXYfunction(dataFitting)
if dataFitting.fitFunction is not None:
self.method = dataFitting.fitFunction
self.noiseLevel = dataFitting.noiseLevel or self.noiseLevel
self.updateMethods()
isFitted = dataFitting.fit()
textMatrix = []
objectList = []
if isFitted and self.method:
methodInfo = getFitMethodInfo()[self.method - 1]
textFormat, indices = methodInfo[2]
textParams = [dataFitting.parameters[i] or 0 for i in indices]
equationText = textFormat % tuple(textParams)
errorText = '%4f' % dataFitting.fitError
x = dataFitting.dataX
y = dataFitting.dataY
yFit = dataFitting.fittedY
N = len(x)
err = hasattr(dataFitting, 'dataErr') and dataFitting.dataErr
if not err:
err = None
# wb104: 10 Mar 2014: not sure why the below was here, it isn't needed
#if self.method == 10:
# x = [sqrt(v) for v in x]
data = [(x[i], y[i], yFit[i], y[i] - yFit[i],
dataFitting.objects[i], err and err[i]) for i in range(N)]
data.sort()
for i in range(N):
xi, yi, yFiti, deltai, object, erri = data[i]
textMatrix.append([i + 1, xi, yi, yFiti, deltai, erri])
objectList.append(object)
else:
equationText = 'Equation: <No Fit>'
errorText = '<None>'
x = dataFitting.dataX
y = dataFitting.dataY
for i, x in enumerate(x):
textMatrix.append([i + 1, x, y[i], None, None, None])
objectList.append(dataFitting.objects[i])
self.equationLabel.set('Equation: %s' % equationText)
self.errorLabel.set('Fit Error: %s' % errorText)
self.scrolledMatrix.update(textMatrix=textMatrix,
objectList=objectList)
self.updateWindows()
self.updateButtons()
self.draw()
if self.updateFunction:
self.updateFunction(dataFitting)
self.waiting = False
def updateButtons(self):
if self.object:
self.removeButton.enable()
else:
self.removeButton.disable()
class AnnealingSettingsTab(object):
'''This class describes the tab in the GUI where the user
can change setting that govern the monte carlo / annleaing
procedure. This also includes which information from the ccpn
analysis project is used and which information is
ignored. This includes:
* present sequential assignments
* tentative assignments
* amino acid type information
* whether to include untyped spin systems
* assignments to peak dimensions
ALso the chain can be selected here.
Furthermore the user can set the temperature
regime of the annealing, the amount of times the procedure
is repeated to obtain statistics. The fraction of peaks
that is left out in each run to diversify the results,
the treshhold score for amino acid typing and the treshhold
collabelling for a peak to be expected.
'''
def __init__(self, parent, frame):
'''Init. args: parent: the guiElement that this
tab is part of.
frame: the frame this part of the
GUI lives in.
'''
self.guiParent = parent
self.frame = frame
self.project = parent.project
self.nmrProject = parent.nmrProject
self.minIsoFrac = 0.1
self.leavePeaksOutFraction = 0.0
self.minTypeScore = 1.0
self.chain = None
self.amountOfRepeats = 10
self.amountOfSteps = 10000
self.acceptanceConstantList = [0.0, 0.01, 0.015, 0.022,
0.033, 0.050, 0.075, 0.113,
0.170, 0.256, 0.384, 0.576,
0.864, 1.297, 1.946, 2.919,
4.378, 6.568, 9.852, 14.77,
22.16, 33.25]
self.energyDataSets = [[]]
self.residues = []
self.body()
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 runCalculations(self):
'''Run all calculations. Also triggers the disabling of
some buttons and fields.
'''
self.startButton.disable()
self.disableIllegalButtonsAfterPrecalculations()
self.guiParent.connector.runAllCalculations()
self.startButton.configure(text='More runs')
self.startButton.enable()
def disableIllegalButtonsAfterPrecalculations(self):
'''Disable buttons and field the user can not alter
any longer after the model is set up and the
'pre-calculations' have finished.
This is done because this part of the calculation
should only be run once. All settings that would
be changed after this point will not have any influence.
'''
illegalButtons = [self.minTypeScoreEntry, self.minLabelEntry,
self.useAlsoUntypedSpinSystemsCheck, self.useAssignmentsCheck,
self.useTypeCheck, self.useDimensionalAssignmentsCheck,
self.useTentativeCheck]
for illegalButton in illegalButtons:
illegalButton.configure(state='disabled')
self.molPulldown.disable()
def getChainName(self, chain):
'''Get the name for a chain.
args: chain: ccpn analysis
chain object
returns: chain name
'''
return '%s:%s (%s)' % (chain.molSystem.code, chain.code, chain.molecule.molType)
def getChains(self):
'''Get all chains present in the project.
returns: list of ccpn analysis chain objects
'''
chains = []
if self.project:
for molSystem in self.project.sortedMolSystems():
for chain in molSystem.sortedChains():
if chain.residues:
chains.append(chain)
return chains
def updateChains(self, *opt):
'''Updates the list of chains if a new one is added
to or deleted from the project. Updates the
pull down list where a chain can be selected.
'''
index = 0
texts = []
chains = self.getChains()
chain = self.chain
if chains:
if chain not in chains:
chain = chains[0]
texts = [self.getChainName(c) for c in chains]
index = chains.index(chain)
else:
chain = None
self.molPulldown.setup(texts, chains, index)
if chain is not self.chain:
self.chain = chain
def changeMolecule(self, chain):
'''Select a molecular chain.'''
if chain is not self.chain:
self.chain = chain
self.updateResidueRanges(fromChain=True)
def updateStepEntry(self, event=None):
'''Update the value and entry that sets the amount of
steps per temperature point.
'''
value = self.NAStepEntry.get()
if value == self.amountOfSteps:
return
if value < 1:
self.NAStepEntry.set(1)
self.amountOfSteps = 1
else:
self.amountOfSteps = value
self.NAStepEntry.set(value)
def updateRepeatEntry(self, event=None):
'''Update the value and entry of that sets
the amount of times the whole annealing
procedure is repeated in order
to obtain statistics.
'''
value = self.repeatEntry.get()
if value == self.amountOfRepeats:
return
if value < 1:
self.repeatEntry.set(1)
self.amountOfRepeats = 1
else:
self.amountOfRepeats = value
self.repeatEntry.set(value)
def updateMinTypeScoreEntry(self, event=None):
'''Updates the value and the entry for the
treshhold value for amino acid typing.
'''
value = self.minTypeScoreEntry.get()
if value == self.minTypeScore:
return
if value < 0:
self.minTypeScoreEntry.set(0.0)
self.minTypeScore = 0.0
elif value > 100:
self.minTypeScoreEntry.set(100.0)
self.minTypeScore = 100.0
else:
self.minTypeScoreEntry.set(value)
self.minTypeScore = value
def updateMinLabelEntry(self, event=None):
'''Updates the minimum colabelling fraction
for which a peak is expected to be present
in the spectra.
'''
value = self.minLabelEntry.get()
if value == self.minIsoFrac:
return
if value < 0:
self.minIsoFrac = 0.0
self.minLabelEntry.set(0.0)
elif value > 1:
self.minIsoFrac = 1.0
self.minLabelEntry.set(1.0)
else:
self.minIsoFrac = value
self.minLabelEntry.set(value)
def updateLeavePeaksOutEntry(self, event=None):
'''Updates the value and entry of the fraction
of peaks that should be left out in each
run in order to diversify the results.
'''
value = self.leaveOutPeaksEntry.get()
if value == self.leavePeaksOutFraction:
return
if value < 0:
self.leavePeaksOutFraction = 0.0
self.leaveOutPeaksEntry.set(0.0)
elif value > 1:
self.leavePeaksOutFraction = 1.0
self.leaveOutPeaksEntry.set(1.0)
else:
self.leavePeaksOutFraction = value
self.leaveOutPeaksEntry.set(value)
def updateAcceptanceConstantList(self, event=None):
'''Updates the list with constants that are used
during the monte carlo procedure to decide whether
a changed is accepted or not.
'''
acList = self.tempEntry.get()
newList = []
for constant in acList:
try:
number = float(constant)
newList.append(number)
except ValueError:
string = constant + \
' in temperature constants is not a number.'
showWarning('Not A Number', string, parent=self.guiParent)
return False
self.acceptanceConstantList = newList
return True
def updateResidueRanges(self, event=None, fromChain=False):
self.residues = set()
subRanges = self.residueRangeEntry.get()
if not subRanges or fromChain:
self.residues = set(self.chain.residues)
residues = self.chain.sortedResidues()
text = '{}-{}'.format(residues[0].seqCode, residues[-1].seqCode)
self.residueRangeEntry.set(text=text)
return
for subRange in subRanges:
indeces = subRange.split('-')
start = int(indeces[0])
stop = int(indeces[-1]) + 1
for seqCode in range(start, stop):
residue = self.chain.findFirstResidue(seqCode=seqCode)
if not residue:
showWarning('Residue out of range.',
'There is no residue at position {}'.format(seqCode),
parent=self.guiParent)
self.residues = set()
return
self.residues.add(residue)
def addEnergyPoint(self, energy, time):
'''Adds a point to the graph that shows the progress
of the annealling procedure.
args: energy: the y-value
time: the x-value
'''
point = (time, energy * -1)
# This means one run has finished
if len(self.energyDataSets[-1]) / (len(self.acceptanceConstantList) + 1):
self.energyDataSets.append([point])
else:
self.energyDataSets[-1].append(point)
colors = colorSeries
Ncolors = len(colors)
NdataSets = len(self.energyDataSets)
colorList = (NdataSets / Ncolors) * colors + \
colors[:NdataSets % Ncolors]
self.energyPlot.update(dataSets=self.energyDataSets,
dataColors=colorList)
# Forcing the graph to draw, eventhough calculations
# are still running. Only do this with high numbers of
# steps, otherwise drawing takes longer than annealling.
if self.amountOfSteps >= 100000:
self.energyPlot.draw()
