def body(self, guiFrame):
self.geometry('700x700')
guiFrame.expandGrid(0,0)
options = ['Peak Lists & Settings','Peak Intensity Comparison']
tabbedFrame = TabbedFrame(guiFrame, options=options, callback=self.changeTab)
tabbedFrame.grid(row=0, column=0, sticky='nsew')
self.tabbedFrame = tabbedFrame
frameA, frameB = tabbedFrame.frames
row = 0
frameA.grid_columnconfigure(1, weight=1)
frameA.grid_columnconfigure(3, weight=1)
frameA.grid_columnconfigure(5, weight=1)
frameA.grid_rowconfigure(5, weight=1)
tipText = 'Number of reference peaks (no saturation)'
self.peaksALabel = Label(frameA, text='Number of Ref Peaks: ', tipText=tipText)
self.peaksALabel.grid(row=1,column=0,columnspan=2,sticky='w')
tipText = 'Number of NOE saturation peaks'
self.peaksBLabel = Label(frameA, text='Number of Sat Peaks: ', tipText=tipText)
self.peaksBLabel.grid(row=1,column=2,columnspan=2,sticky='w')
tipText = 'Number of peaks in assigned list'
self.peaksCLabel = Label(frameA, text='Number of Assign Peaks: ', tipText=tipText)
self.peaksCLabel.grid(row=1,column=4,columnspan=2,sticky='w')
tipText = 'Selects which peak list is considered the NOE intensity reference (no saturation)'
specALabel = Label(frameA, text='Ref Peak List: ')
specALabel.grid(row=0,column=0,sticky='w')
self.specAPulldown = PulldownList(frameA, callback=self.setRefPeakList, tipText=tipText)
self.specAPulldown.grid(row=0,column=1,sticky='w')
tipText = 'Selects which peak list is considered as NOE saturated.'
specBLabel = Label(frameA, text='Sat Peak List: ')
specBLabel.grid(row=0,column=2,sticky='w')
self.specBPulldown = PulldownList(frameA, callback=self.setSatPeakList, tipText=tipText)
self.specBPulldown.grid(row=0,column=3,sticky='w')
tipText = 'Selects a peak list with assignments to use as a positional reference'
specCLabel = Label(frameA, text='Assignment Peak List: ')
specCLabel.grid(row=0,column=4,sticky='w')
self.specCPulldown = PulldownList(frameA, callback=self.setAssignPeakList, tipText=tipText)
self.specCPulldown.grid(row=0,column=5,sticky='w')
frame0a = Frame(frameA)
frame0a.grid(row=2,column=0,columnspan=6,sticky='nsew')
frame0a.grid_columnconfigure(9, weight=1)
tipText = '1H ppm tolerance for matching assigned peaks to reference & NOE saturation peaks'
tolHLabel = Label(frame0a, text='Tolerances: 1H')
tolHLabel.grid(row=0,column=0,sticky='w')
self.tolHEntry = FloatEntry(frame0a,text='0.02', width=6, tipText=tipText)
self.tolHEntry .grid(row=0,column=1,sticky='w')
tipText = '15N ppm tolerance for matching assigned peaks to reference & NOE saturation peaks'
tolNLabel = Label(frame0a, text=' 15N')
tolNLabel .grid(row=0,column=2,sticky='w')
self.tolNEntry = FloatEntry(frame0a,text='0.1', width=6, tipText=tipText)
self.tolNEntry .grid(row=0,column=3,sticky='w')
tipText = 'Whether to peak new peaks in reference & NOE saturated lists (at assignment locations)'
label = Label(frame0a, text=' Pick new peaks?', grid=(0,4))
self.pickPeaksSelect = CheckButton(frame0a, tipText=tipText,
grid=(0,5), selected=True)
tipText = 'Whether to assign peaks in the peaks in the reference & NOE saturation lists, if not already assigned'
label = Label(frame0a, text=' Assign peaks?')
label.grid(row=0,column=6,sticky='w')
self.assignSelect = CheckButton(frame0a, tipText=tipText)
self.assignSelect.set(1)
self.assignSelect.grid(row=0,column=7,sticky='w')
tipText = 'Whether to consider peak height or volume in the heteronuclear NOE calculation'
intensLabel = Label(frame0a, text=' Intensity Type:')
intensLabel .grid(row=0,column=8,sticky='w')
self.intensPulldown = PulldownList(frame0a, texts=['height','volume'],
callback=self.setIntensityType,
tipText=tipText)
self.intensPulldown.grid(row=0,column=9,sticky='w')
divider = LabelDivider(frameA, text='Peaks', grid=(3,0),
gridSpan=(1,6))
tipTexts = ['Show the selected intensity reference peaks in the below table',
'Show the selected NOE saturation peaks in the below table',
'Show the selected assigned peak list in the below table',
'Show the displayed peaks in a separate peak table, where assignments etc. may be adjusted']
texts = ['Show Ref Peaks','Show Sat Peaks',
'Show Assign Peaks', 'Separate Peak Table']
commands = [self.viewRefPeakList, self.viewSatPeakList,
self.viewAssignPeakList, self.viewSeparatePeakTable]
self.viewPeaksButtons = ButtonList(frameA, expands=True, tipTexts=tipTexts,
texts=texts, commands=commands)
self.viewPeaksButtons.grid(row=4,column=0,columnspan=6,sticky='nsew')
self.peakTable = PeakTableFrame(frameA, self.guiParent, grid=(5,0),
gridSpan=(1,6))
self.peakTable.bottomButtons1.grid_forget()
self.peakTable.bottomButtons2.grid_forget()
#self.peakTable.topFrame.grid_forget()
self.peakTable.topFrame.grid(row=2, column=0, sticky='ew')
# Next tab
frameB.expandGrid(0,0)
tipTexts = ['Row number',
'Assignment annotation for NOE saturation peak',
'Assignment annotation for reference peak (no saturation)',
'1H chemical shift of NOE saturation peak',
'1H chemical shift of reference peak',
'15N chemical shift of NOE saturation peak',
'15N chemical shift of reference peak',
'The separation between compared peaks: square root of the sum of ppm differences squared',
'The intensity if the NOE saturation peak',
'The intensity of the reference peak (no saturation)',
'Ratio of peak intensities: saturated over reference',
'Residue(s) for reference peak']
colHeadings = ['#','Sat Peak','Ref Peak','1H shift A',
'1H shift B','15N shift A','15N shift B',
'Closeness\nScore','Intensity A','Intensity B',
'Intensity\nRatio','Residue']
self.scrolledMatrix = ScrolledMatrix(frameB, multiSelect=True,
headingList=colHeadings,
callback=self.selectCell,
tipTexts=tipTexts,
grid=(0,0),
deleteFunc=self.removePair)
tipTexts = ['Force a manual update of the table; pair-up NOE saturation and reference peaks according to assigned peak positions',
'Remove the selected rows of peak pairs',
'Show peaks corresponding to the selected row in a table',
'Save the Heteronuclear NOE values in the CCPN project as a data list']
texts = ['Refresh Table','Remove Pairs',
'Show Peak Pair','Create Hetero NOE List']
commands = [self.matchPeaks,self.removePair,
self.showPeakPair,self.makeNoeList]
self.pairButtons = ButtonList(frameB, tipTexts=tipTexts, grid=(1,0),
texts=texts, commands=commands)
bottomButtons = UtilityButtonList(tabbedFrame.sideFrame, helpUrl=self.help_url)
bottomButtons.grid(row=0, column=0, sticky='e')
self.updatePulldowns()
self.updateAfter()
self.administerNotifiers(self.registerNotify)
class ExtendNmrFrame(Frame):
def __init__(self, guiParent, basePopup, project=None):
# Base popup required to handle notification of data model changes
# e.g. new peak lists, so that the GUI can update to the latest
# state
self.basePopup = basePopup
self.guiParent = guiParent
# FIXME JMCI
# need to work through this far more carefully
self.project = project
# shortcuts to this layer
self.basePopup.frameShortcuts['Task'] = self
# shortcuts to layer below. We should set these in the
# initMethod methods
self.frameShortcuts = {}
# TODO understand what these are doing
self.registerNotify = basePopup.registerNotify
self.unregisterNotify = basePopup.unregisterNotify
Frame.__init__(self, guiParent)
self.grid_rowconfigure(1, weight=1)
self.grid_columnconfigure(0, weight=1)
# Logos. Code nicked from ExtendNMR GUI
ccpnDir = getTopDirectory()
imageDir = os.path.join(ccpnDir, 'python', 'extendNmr', 'images')
# basically nicked from Extend-NMR
softwareOpts = [
'Test1Task', 'ARIA 2', 'Auremol', 'CING', ' ECI ', 'HADDOCK',
' ISD ', 'PRODECOMP'
]
self.tabbedFrame = TabbedFrame(guiParent,
options=softwareOpts,
toggleOff=False,
selected=0)
self.tabbedFrame.grid(row=1, column=0, sticky='nsew')
frames = self.tabbedFrame.frames
# Logos
ccpnDir = getTopDirectory()
imageDir = os.path.join(ccpnDir, 'python', 'extendNmr', 'images')
imageFile = os.path.join(imageDir, 'Fp6Logo.gif')
self.fp6Logo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'CingLogo.gif')
self.cingLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'AriaLogo.gif')
self.ariaLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'IsdLogo.gif')
self.isdLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'HaddockLogo.gif')
self.haddockLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'AuremolLogo.gif')
self.auremolLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'CcpnLogo.gif')
self.ccpnLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'ProdecompLogo.gif')
self.prodecompLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'MddLogo.gif')
self.mddLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'BrukerLogo.gif')
self.brukerLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'MsdLogo.gif')
self.msdLogo = Tkinter.PhotoImage(file=imageFile)
# don't know what this does
self.updateFuncs = []
self.projButtons = []
# basically nicked from Extend-NMR
self.initTest1(frames[0])
self.initAria(frames[1])
self.initAuremol(frames[2])
self.initCing(frames[3])
#self.initEci(frames[4])
#self.initHaddock(frames[5])
self.initIsd(frames[6])
self.initProdecomp(frames[7])
def initTest1(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
# FIXME JMCI
# Provide the basePopup for navigation purposes right now However,
# there is a strong case for not making the method-specific Frames
# dependent on the master. It might therefore be better to pass
# the critical information directly, rather than passing a
# reference to the basePopup which can then be used to extract it
# indirectly
test1Frame = Test1Frame(frame, self.basePopup)
test1Frame.grid(row=1, column=0, sticky='nsew')
self.frameShortcuts['Test1'] = test1Frame
#self.projButtons.extend(cingFrame.buttonBar.buttons)
self.updateFuncs.append(test1Frame.updateAll)
def initAria(self, frame):
welcomeMessage = \
"""ARIA Version 2.2. Authors: Benjamin Bardiaux, Michael Habeck,
Jens Linge, Therese Malliavin, Sean O'Donoghue, Wolfgang Rieping,
and Michael Nilges.
Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E.,
Nilges M.(2007) ARIA2: automated NOE assignment and data
integration in NMR structure calculation. Bioinformatics 23:381-382"""
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
canvas = Tkinter.Canvas(frame, width=700, height=114, bg='#FFFFFF')
canvas.grid(row=0, column=0, sticky='ew')
canvas.create_image(0, 0, anchor='nw', image=self.ariaLogo)
canvas.create_text(250, 10, anchor='nw', text=welcomeMessage)
ariaFrame = AriaFrame(frame, self)
ariaFrame.grid(row=1, column=0, sticky='nsew')
self.frameShortcuts['ARIA'] = ariaFrame
#self.projButtons.extend(ariaFrame.buttons)
self.updateFuncs.append(ariaFrame.updateAll)
def initAuremol(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
auremolFrame = AuremolFrame(frame, self.project)
auremolFrame.grid(row=0, column=0, sticky='nsew')
self.frameShortcuts['AUREMOL'] = auremolFrame
#self.projButtons.extend(isdFrame.buttons)
self.updateFuncs.append(auremolFrame.updateAll)
def initCing(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
canvas = Tkinter.Canvas(frame, width=702, height=77)
canvas.grid(row=0, column=0)
canvas.create_image(0, 0, anchor='nw', image=self.cingLogo)
cingFrame = CingFrame(frame, self.project)
cingFrame.grid(row=1, column=0, sticky='nsew')
self.frameShortcuts['CING'] = cingFrame
#self.projButtons.extend(cingFrame.buttonBar.buttons)
self.updateFuncs.append(cingFrame.updateAll)
def initEci(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
frame.parent = self # For notifiers
canvas = Tkinter.Canvas(frame, width=753, height=73, bg='#FFFFFF')
canvas.grid(row=0, column=0)
canvas.create_image(10, 10, anchor='nw', image=self.msdLogo)
eciFrame = EntryCompletionFrame(frame, basePopup=self)
eciFrame.grid(row=1, column=0, sticky='nsew')
self.frameShortcuts['ECI'] = eciFrame
#self.projButtons.extend(isdFrame.buttons)
self.updateFuncs.append(eciFrame.updateAll)
def initHaddock(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
frame.parent = self # For notifiers
canvas = Tkinter.Canvas(frame, width=753, height=92)
canvas.grid(row=0, column=0)
canvas.create_image(0, 0, anchor='nw', image=self.haddockLogo)
haddockFrame = HaddockFrame(frame, self.project)
haddockFrame.grid(row=1, column=0, sticky='nsew')
self.frameShortcuts['HADDOCK'] = haddockFrame
#self.projButtons.extend(isdFrame.buttons)
self.updateFuncs.append(haddockFrame.updateAll)
def initIsd(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
canvas = Tkinter.Canvas(frame, width=700, height=91, bg='#FFFFFF')
canvas.grid(row=0, column=0, sticky='ew')
canvas.create_image(0, 0, anchor='nw', image=self.isdLogo)
isdFrame = IsdFrame(frame, self.project)
isdFrame.grid(row=1, column=0, sticky='nsew')
self.frameShortcuts['ISD'] = isdFrame
#self.projButtons.extend(isdFrame.buttons)
self.updateFuncs.append(isdFrame.updateAll)
def initProdecomp(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
canvas = Tkinter.Canvas(frame, width=700, height=90, bg='#FFFFFF')
canvas.grid(row=0, column=0)
canvas.create_image(0, 0, anchor='nw', image=self.prodecompLogo)
prodecompFrame = ProdecompFrame(frame,
basePopup=self,
ccpnProject=self.project)
prodecompFrame.grid(row=1, column=0, sticky='nsew')
self.frameShortcuts['PRODECOMP'] = prodecompFrame
#self.projButtons.extend(isdFrame.buttons)
self.updateFuncs.append(prodecompFrame.updateAll)
# need to understand this method a little bit better
def administerNotifiers(self, notifyFunc):
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.Experiment', func)
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.DataSource', func)
def updateAllAfter(self, obj):
self.after_idle(self.updateAll)
def updateAll(self, project=None):
if project:
self.project = project
self.nmrProject = project.currentNmrProject
if not self.nmrProject:
self.nmrProject = project.newNmrProject(name=project.name)
if not self.project:
return
def quit(self):
self.guiParent.parent.destroy()
def destroy(self):
self.administerNotifiers(self.basePopup.unregisterNotify)
Frame.destroy(self)
def body(self, guiFrame):
self.geometry('600x350')
project = self.project
analysisProject = self.analysisProject
guiFrame.grid_columnconfigure(1, weight=1)
row = 0
frame = Frame(guiFrame, grid=(0,0))
label = Label(frame, text=' Window:', grid=(0,0))
self.windowPulldown = PulldownList(frame, grid=(0,1),
tipText='The window that will be printed out',
callback=self.selectWindow)
tipTexts = ['For the window pulldown, show all of the spectrum windows in the current project, irrespective of the active group',
'For the window pulldown, show only spectrum windows that are in the currently active window group']
self.whichWindows = RadioButtons(frame, grid=(0,2),
entries=ACTIVE_OPTIONS, tipTexts=tipTexts,
select_callback=self.updateWindows)
texts = [ 'Save Print File' ]
tipTexts = [ 'Save the printout to the specified file' ]
commands = [ self.saveFile ]
buttons = UtilityButtonList(guiFrame, helpUrl=self.help_url, grid=(row,2),
commands=commands, texts=texts, tipTexts=tipTexts)
self.buttons = buttons
buttons.buttons[0].config(bg='#B0FFB0')
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
options = ['Options', 'Spectra', 'Peak Lists', 'Region']
tipTexts = ['Optional settings for spectra', 'Optional settings for peak lists', 'Optional settings for the region']
tabbedFrame = TabbedFrame(guiFrame, options=options, tipTexts=tipTexts)
tabbedFrame.grid(row=row, column=0, columnspan=3, sticky='nsew')
self.tabbedFrame = tabbedFrame
optionFrame, spectrumFrame, peakListFrame, regionFrame = tabbedFrame.frames
optionFrame.expandGrid(0, 0)
getOption = lambda key, defaultValue: PrintBasic.getPrintOption(analysisProject, key, defaultValue)
setOption = lambda key, value: PrintBasic.setPrintOption(analysisProject, key, value)
self.printFrame = PrintFrame(optionFrame, getOption=getOption,
grid=(0,0), gridSpan=(1,1),
setOption=setOption, haveTicks=True,
doOutlineBox=False)
spectrumFrame.expandGrid(0, 0)
frame = Frame(spectrumFrame, grid=(0,0), gridSpan=(1,1))
frame.expandGrid(1,0)
self.overrideSpectrum = CheckButton(frame,
text='Use below settings when printing',
tipText='Use below settings when printing instead of the window values',
grid=(0,0), sticky='w')
tipText = 'Change the settings of the selected spectra back to their window values'
button = Button(frame, text='Reset Selected', tipText=tipText,
command=self.resetSelected, grid=(0,1), sticky='e')
self.posColorPulldown = PulldownList(self, callback=self.setPosColor)
self.negColorPulldown = PulldownList(self, callback=self.setNegColor)
headings = ['Spectrum', 'Pos. Contours\nDrawn', 'Neg. Contours\nDrawn', 'Positive\nColours', 'Negative\nColours']
tipTexts = ['Spectrum in window', 'Whether the positive contours should be drawn', 'Whether the negative contours should be drawn',
'Colour scheme for positive contours (can be a single colour)', 'Colour scheme for negative contours (can be a single colour)']
editWidgets = [ None, None, None, self.posColorPulldown, self.negColorPulldown]
editGetCallbacks = [ None, self.togglePos, self.toggleNeg, self.getPosColor, self.getNegColor]
editSetCallbacks = [ None, None, None, self.setPosColor, self.setNegColor]
self.spectrumTable = ScrolledMatrix(frame, headingList=headings,
tipTexts=tipTexts,
multiSelect=True,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
grid=(1,0), gridSpan=(1,2))
peakListFrame.expandGrid(0, 0)
frame = Frame(peakListFrame, grid=(0,0), gridSpan=(1,3))
frame.expandGrid(1,0)
self.overridePeakList = CheckButton(frame,
text='Use below settings when printing',
tipText='Use below settings when printing instead of the window values',
grid=(0,0))
tipText = 'Change the settings of the selected peak lists back to their window values'
button = Button(frame, text='Reset Selected', tipText=tipText,
command=self.resetSelected, grid=(0,1), sticky='e')
colors = Color.standardColors
self.peakColorPulldown = PulldownList(self, callback=self.setPeakColor,
texts=[c.name for c in colors],
objects=[c.hex for c in colors],
colors=[c.hex for c in colors])
headings = [ 'Peak List', 'Symbols Drawn', 'Peak Font', 'Peak Colour']
self.fontMenu = FontList(self, mode='Print', extraTexts=[no_peak_text])
editWidgets = [ None, None, self.fontMenu, self.peakColorPulldown]
editGetCallbacks = [ None, self.togglePeaks, self.getPeakFont, self.getPeakColor ]
editSetCallbacks = [ None, None, self.setPeakFont, self.setPeakColor ]
self.peakListTable = ScrolledMatrix(frame, headingList=headings,
multiSelect=True,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
grid=(1,0), gridSpan=(1,2))
regionFrame.expandGrid(0, 0)
frame = Frame(regionFrame, grid=(0,0), gridSpan=(1,3))
frame.expandGrid(3,0)
tipText = 'Use the specified override region when printing rather than the window values'
self.overrideButton = CheckButton(frame, text='Use override region when printing',
tipText=tipText,
callback=self.toggledOverride, grid=(0,0))
tipTexts = ('Use min and max to specify override region', 'Use center and width to specify override region')
self.use_entry = USE_ENTRIES[0]
self.useButtons = RadioButtons(frame, entries=USE_ENTRIES,
tipTexts=tipTexts,
select_callback=self.changedUseEntry,
grid=(1,0))
texts = ('Set Region from Window', 'Set Center from Window', 'Set Width from Window')
tipTexts = ('Set the override region to be the current window region',
'Set the center of the override region to be the center of the current window region',
'Set the width of the override region to be the width of the current window region')
commands = (self.setRegionFromWindow, self.setCenterFromWindow, self.setWidthFromWindow)
self.setRegionButton = ButtonList(frame, texts=texts,
tipTexts=tipTexts,
commands=commands, grid=(2,0))
self.minRegionWidget = FloatEntry(self, returnCallback=self.setMinRegion, width=10)
self.maxRegionWidget = FloatEntry(self, returnCallback=self.setMaxRegion, width=10)
headings = MIN_MAX_HEADINGS
editWidgets = [ None, None, self.minRegionWidget, self.maxRegionWidget ]
editGetCallbacks = [ None, None, self.getMinRegion, self.getMaxRegion ]
editSetCallbacks = [ None, None, self.setMinRegion, self.setMaxRegion ]
self.regionTable = RegionScrolledMatrix(frame, headingList=headings,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
grid=(3,0))
self.updateWindows()
self.updateAfter()
self.administerNotifiers(self.registerNotify)
class AuremolFrame(Frame):
def __init__(self, guiParent, ccpnProject=None, **kw):
self.guiParent = guiParent
self.project = ccpnProject
self.spectrum = None
self.peakMode = 0
if ccpnProject:
self.nmrProject = ccpnProject.currentNmrProject
else:
self.nmrProject = None
Frame.__init__(self, guiParent, **kw)
self.expandGrid(0,0)
options = ['Peak Picking',] #,'About Auremol' 'NOE assignment','Homology Modelling',]
self.tabbedFrame = TabbedFrame(self, options=options)
self.tabbedFrame.grid(row=0,column=0,sticky='nsew')
frameA = self.tabbedFrame.frames[0]
#frameC.grid_columnconfigure(0, weight=1)
#frameC.grid_rowconfigure(0, weight=1)
#frameD.grid_columnconfigure(0, weight=1)
#frameD.grid_rowconfigure(0, weight=1)
#
# Frame A
#
frameA.expandGrid(2,0)
frameA.expandGrid(3,0)
frameA.expandGrid(4,0)
frameA.expandGrid(5,0)
frame = Frame(frameA, grid=(0,0))
frame.expandGrid(0,4)
label = Label(frame, text='Spectrum:', grid=(0,0))
self.spectrumPulldown = PulldownList(frame, self.changeSpectrum, grid=(0,1))
label = Label(frame, text=' Use Peak Sign:', grid=(0,2))
self.peakModePulldown = PulldownList(frame, self.changePeakMode, texts=PEAK_MODES,
objects=[0,1,2], grid=(0,3))
frame = Frame(frameA, grid=(1,0))
frame.expandGrid(0,4)
label = Label(frame, text='Integration Depth (Relative to max):', grid=(1,0))
self.segLevelEntry = FloatEntry(frame, text=0.1, grid=(1,1), width=8)
label = Label(frame, text='Threshold (Threshold only):', grid=(1,3))
self.thresholdEntry = IntEntry(frame, text=100000, grid=(1,4), width=8)
label = Label(frame, text='Keep Peaks (Adaptive only):', grid=(1,5))
self.keepPeakEntry = IntEntry(frame, text=4000, grid=(1,6), width=8)
texts = ['Threshold\nPeak Pick','Adaptive\nPeak Pick']
commands = [self.pickThreshold, self.pickAdaptive]
self.buttons = ButtonList(frameA, texts=texts, commands=commands,
grid=(2,0), sticky='NSEW')
frame = Frame(frameA, grid=(3,0))
frame.expandGrid(0,0)
frame = Frame(frameA, grid=(4,0))
frame.expandGrid(0,0)
frame = Frame(frameA, grid=(5,0))
frame.expandGrid(0,0)
#
# About
"""
frameB.expandGrid(4,0)
label = Label(frameB, text='References', font='Helvetica 12 bold')
label.grid(row=0, column=0, sticky='w')
text =
* Gronwald W, Brunner K, Kirchhofer R, Nasser A, Trenner J, Ganslmeier B,
Riepl H, Ried A, Scheiber J, Elsner R, Neidig K-P, Kalbitzer HR
AUREMOL, a New Program for the Automated Structure Elucidation of Biological Macromolecules
Bruker Reports 2004; 154/155: 11-14
* Ried A, Gronwald W, Trenner JM, Brunner K, Neidig KP, Kalbitzer HR
Improved simulation of NOESY spectra by RELAX-JT2 including effects of J-coupling,
transverse relaxation and chemical shift anisotrophy
J Biomol NMR. 2004 Oct;30(2):121-31
* Gronwald W, Moussa S, Elsner R, Jung A, Ganslmeier B, Trenner J, Kremer W, Neidig KP, Kalbitzer HR
Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE)
J Biomol NMR. 2002 Aug;23(4):271-87
* Gronwald W, Kirchhofer R, Gorler A, Kremer W, Ganslmeier B, Neidig KP, Kalbitzer HR
RFAC, a program for automated NMR R-factor estimation
J Biomol NMR. 2000 Jun;17(2):137-51
label = Label(frameB, text=text)
label.grid(row=1, column=0, sticky='w')
"""
#
# Frame C
#
#
# Frame D
#
self.updateAll()
def getEntryData(self):
segLevel = self.segLevelEntry.get() or 0.001
threshold = self.thresholdEntry.get() or 100000
maxPeaks = self.keepPeakEntry.get() or 1
segLevel = min(1.0, segLevel)
self.segLevelEntry.set(segLevel)
self.thresholdEntry.set(threshold)
self.keepPeakEntry.set(maxPeaks)
return segLevel, threshold, maxPeaks
def pickThreshold(self):
if self.spectrum:
segLevel, threshold, maxPeaks = self.getEntryData()
try:
findAuremolPeaksThreshold(spectrum=self.spectrum, mode=self.peakMode,
useAutoThreshold=0, threshold=threshold, seglevel=segLevel)
except Exception, e:
showError('pickThreshold', str(e), parent=self)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(0, weight=1)
options = ['Parameters','Restraints','Alignment Media & Tensors','About Meccano']
tabbedFrame = TabbedFrame(guiFrame, options=options)
tabbedFrame.grid(row=0, column=0, sticky='nsew')
frameA, frameB, frameC, frameD = tabbedFrame.frames
frameA.grid_columnconfigure(1, weight=1)
frameA.grid_rowconfigure(13, weight=1)
frameB.grid_columnconfigure(1, weight=1)
frameB.grid_rowconfigure(1, weight=1)
frameC.grid_columnconfigure(0, weight=1)
frameC.grid_rowconfigure(1, weight=1)
frameD.grid_columnconfigure(0, weight=1)
frameD.grid_rowconfigure(0, weight=1)
texts = ['Run MECCANO!']
commands = [self.runMeccano]
bottomButtons = createDismissHelpButtonList(guiFrame, texts=texts,
commands=commands, expands=True)
bottomButtons.grid(row=1, column=0, sticky='ew')
if not Meccano:
bottomButtons.buttons[0].disable()
# Parameters
row = 0
label = Label(frameA, text='Calculation Run:')
label.grid(row=row,column=0,sticky='w')
self.runPulldown = PulldownList(frameA, callback=self.selectRun)
self.runPulldown.grid(row=row,column=1,sticky='w')
row += 1
label = Label(frameA, text='Shift List (for CO):')
label.grid(row=row,column=0,sticky='w')
self.shiftListPulldown = PulldownList(frameA, callback=self.selectShiftList)
self.shiftListPulldown.grid(row=row,column=1,sticky='w')
row += 1
label = Label(frameA, text='Keep Copy of Used Shifts:')
label.grid(row=row,column=0,sticky='w')
self.toggleCopyShifts = CheckButton(frameA)
self.toggleCopyShifts.grid(row=row,column=1,sticky='w')
self.toggleCopyShifts.set(True)
row += 1
label = Label(frameA, text='Molecular System:')
label.grid(row=row,column=0,sticky='w')
self.molSystemPulldown = PulldownList(frameA, callback=self.selectMolSystem)
self.molSystemPulldown.grid(row=row,column=1,sticky='w')
row += 1
label = Label(frameA, text='Chain:')
label.grid(row=row,column=0,sticky='w')
self.chainPulldown = PulldownList(frameA, callback=self.selectChain)
self.chainPulldown.grid(row=row,column=1,sticky='w')
self.chainPulldown.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='First Peptide Plane:')
label.grid(row=row,column=0,sticky='w')
self.firstResEntry = IntEntry(frameA, text=None, width=8)
self.firstResEntry.grid(row=row,column=1,sticky='w')
self.firstResEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Last Peptide Plane:')
label.grid(row=row,column=0,sticky='w')
self.lastResEntry = IntEntry(frameA, text=None, width=8)
self.lastResEntry.grid(row=row,column=1,sticky='w')
self.lastResEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Max Num Optimisation Steps:')
label.grid(row=row,column=0,sticky='w')
self.maxOptStepEntry = IntEntry(frameA, text=500, width=8)
self.maxOptStepEntry.grid(row=row,column=1,sticky='w')
self.maxOptStepEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Num Optimisation Peptide Planes:')
label.grid(row=row,column=0,sticky='w')
self.numOptPlaneEntry = IntEntry(frameA, text=2, width=8)
self.numOptPlaneEntry.grid(row=row,column=1,sticky='w')
self.numOptPlaneEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Min Num Optimisation Hits:')
label.grid(row=row,column=0,sticky='w')
self.numOptHitsEntry = IntEntry(frameA, text=5, width=8)
self.numOptHitsEntry.grid(row=row,column=1,sticky='w')
self.numOptHitsEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='File Name Prefix:')
label.grid(row=row,column=0,sticky='w')
self.pdbFileEntry = Entry(frameA, text='Meccano', width=8)
self.pdbFileEntry.grid(row=row,column=1,sticky='w')
self.pdbFileEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Write Output File (.out):')
label.grid(row=row,column=0,sticky='w')
self.toggleWriteOutFile = CheckButton(frameA)
self.toggleWriteOutFile.grid(row=row,column=1,sticky='w')
self.toggleWriteOutFile.set(False)
self.toggleWriteOutFile.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Write PDB File (.pdb):')
label.grid(row=row,column=0,sticky='w')
self.toggleWritePdbFile = CheckButton(frameA)
self.toggleWritePdbFile.grid(row=row,column=1,sticky='w')
self.toggleWritePdbFile.set(True)
self.toggleWritePdbFile.bind('<Leave>', self.updateRunParams)
if not Meccano:
row += 1
label = Label(frameA, text='The Meccano executable is not available (it needs to be compiled)', fg='red')
label.grid(row=row,column=0,columnspan=2,sticky='w')
# Restraints
label = Label(frameB, text='Constraint Set:')
label.grid(row=0,column=0,sticky='w')
self.constraintSetPulldown = PulldownList(frameB, callback=self.selectConstraintSet)
self.constraintSetPulldown.grid(row=0,column=1,sticky='w')
self.alignMediumPulldown= PulldownList(self, callback=self.setAlignMedium)
headingList = ['#','List Type','Use?','Alignment\nMedium','Num\nRestraints']
editWidgets = [None,None,None,self.alignMediumPulldown,None]
editGetCallbacks = [None,None,self.toggleUseRestraints,self.getAlignMedium,None]
editSetCallbacks = [None,None,None,self.setAlignMedium,None]
self.restraintMatrix = ScrolledMatrix(frameB,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=None,
multiSelect=True)
self.restraintMatrix.grid(row=1,column=0,columnspan=2,sticky='nsew')
# Alignment Media
div = LabelDivider(frameC,text='Alignment Media')
div.grid(row=0,column=0,sticky='ew')
self.mediumNameEntry = Entry(self, returnCallback=self.setMediumName)
self.mediumDetailsEntry = Entry(self, returnCallback=self.setMediumDetails)
headingList = ['#','Name','Details','Static Tensor','Dynamic Tensor']
editWidgets = [None, self.mediumNameEntry, self.mediumDetailsEntry, None, None]
editGetCallbacks = [None, self.getMediumName, self.getMediumDetails, None, None]
editSetCallbacks = [None, self.setMediumName, self.setMediumDetails, None, None]
self.mediaMatrix = ScrolledMatrix(frameC,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=self.selectAlignMedium,
multiSelect=True)
self.mediaMatrix.grid(row=1,column=0,sticky='nsew')
texts = ['Add Alignment medium','Remove Alignment Medium']
commands = [self.addAlignMedium,self.removeAlignMedium]
buttonList = ButtonList(frameC, texts=texts, commands=commands, expands=True)
buttonList.grid(row=2,column=0,sticky='nsew')
self.editAxialEntry = FloatEntry(self, returnCallback=self.setAxial)
self.editRhombicEntry = FloatEntry(self, returnCallback=self.setRhombic)
self.editAlphaEulerEntry = FloatEntry(self, returnCallback=self.setEulerAlpha)
self.editBetaEulerEntry = FloatEntry(self, returnCallback=self.setEulerBeta)
self.editGammaEulerEntry = FloatEntry(self, returnCallback=self.setEulerGamma)
div = LabelDivider(frameC,text='Alignment Tensors')
div.grid(row=3,column=0,sticky='ew')
headingList = ['Type', u'Axial (\u03B6)',u'Rhombic (\u03B7)',
u'Euler \u03B1',u'Euler \u03B2',u'Euler \u03B3']
editWidgets = [None,self.editAxialEntry,
self.editRhombicEntry,self.editAlphaEulerEntry,
self.editBetaEulerEntry,self.editGammaEulerEntry]
editSetCallbacks = [None,self.setAxial,self.setRhombic,
self.setEulerAlpha,self.setEulerBeta,self.setEulerGamma]
editGetCallbacks = [None,self.getAxial,self.getRhombic,
self.getEulerAlpha,self.getEulerBeta,self.getEulerGamma]
self.tensorMatrix = ScrolledMatrix(frameC, maxRows=2,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=self.selectTensor,
multiSelect=True)
self.tensorMatrix.grid(row=4,column=0,sticky='nsew')
texts = ['Add Static Tensor','Add Dynamic Tensor','Remove Tensor']
commands = [self.addStaticTensor,self.addDynamicTensor,self.removeTensor]
buttonList = ButtonList(frameC,texts=texts, commands=commands, expands=True)
buttonList.grid(row=5,column=0,sticky='ew')
# About
label = Label(frameD, text='About Meccano...')
label.grid(row=0,column=0,sticky='w')
#
self.geometry('500x400')
self.updateShiftLists()
self.updateMolSystems()
self.updateResidueRanges()
self.updateConstraintSets()
self.updateAlignMedia()
self.updateRuns()
class ApplicationPopup(BasePopup):
help_url = 'http://www.ccpn.ac.uk'
def __init__(self, root, programName='Ccpn Workflow Management System'):
self.programName = programName
self.font = DEFAULT_FONT
# Application object needed to store application-specific data with project
self.application = Application(name=PROGRAM_NAME)
self.versionInfo = 'Version ' + VERSION
self.ariaProjectFile = None
self.username = None
# what do these do??
self.updateFuncs = []
self.projButtons = []
# may need these in the end
self.ariaPaths = []
self.isdPaths = []
# FIXME JMCI
# hard code this for now. this should be initialised from file
# read during GUI login and then extended using the menu options
# should set a placeholder. In fact, this placeholder will also have
# a default user (guest) so that there is always a structure to
# extend should the user wish to start from scratch and not log in
self.repList = RepositoryList()
self.currentTask = None
# going to stick in shortcuts to frames for quick access
self.frameShortcuts = {}
# Application popup is a superclass of memops.editor.BasePoup
BasePopup.__init__(self,
parent=root,
title=PROGRAM_NAME,
location='+100+100',
class_=self.application.name)
self.setTitle(PROGRAM_NAME)
def body(self, guiParent):
self.geometry('700x600')
# Ensure that the first row and column in popup expand
guiParent.grid_rowconfigure(0, weight=1)
guiParent.grid_columnconfigure(0, weight=1, minsize=200)
frame = Frame(guiParent) # Body widgets can be put in this frame
frame.grid()
# this is going to set up the options on the tabs. Really we need
# stronger bookeeping between the options and the frames. it
# might make sense to define a master dictionary with option_name
# => index. We can use this dictionary to build up the software
# options and can also use it to define any refreshes etc (although
# these would be better done through notifiers)
softwareOpts = [
'Repository', 'Project', 'Process', 'Client Tasks', 'Server Tasks',
'Data Exchange', 'Workflow', 'Protocols', 'User'
]
# FIXME JMCI
# we should have a tidier tabbed frame. ned to discuss rules with
# tjs but it would seem to make sense to have the tabs stretch
# across the entire top of the frame. Check the existing options
# first, though
self.tabbedFrame = TabbedFrame(guiParent,
options=softwareOpts,
toggleOff=False,
selected=0)
self.tabbedFrame.grid(row=0, column=0, sticky='nsew')
frames = self.tabbedFrame.frames
# Logos
ccpnDir = getTopDirectory()
imageDir = os.path.join(ccpnDir, 'python', 'extendNmr', 'images')
imageFile = os.path.join(imageDir, 'CcpnLogo.gif')
self.ccpnLogo = Tkinter.PhotoImage(file=imageFile)
# Dictionary to store popups opened by this application - e.g. need to close upon quit
self.popups = {}
# Default font
self.font = 'Helvetica 10'
# Closing the window from the desktop environment calls the proper quit
self.protocol('WM_DELETE_WINDOW', self.quit)
# jmci we are going to have to change these drastically
self.mainMenu = Menu(self)
self.userMenu = self.makeUserMenu()
self.repositoryMenu = self.makeRepositoryMenu()
self.otherMenu = self.makeOtherMenu()
# Put the top level menu
self.config(menu=self.mainMenu)
self.initRepository(frames[0])
self.initProjectFrame(frames[1])
self.initWms(frames[2])
self.initTasks(frames[3])
self.initDataExch(frames[5])
self.initWorkflow(frames[6])
self.initProtocol(frames[7])
self.initUserFrame(frames[8])
self.initProject()
if not self.project:
for button in self.projButtons:
button.disable()
# the main client side daemon. This is going to run in the background
# and control the task processing
self.taskDaemon = TaskManager(self)
self.taskDaemon.active = False
self.taskDaemon.start()
## THE TABBED FRAMES ##
def initRepository(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
repositoryFrame = RepositoryFrame(frame, basePopup=self)
repositoryFrame.grid(row=1, column=0, sticky='nsew')
self.updateFuncs.append(repositoryFrame.updateAll)
def initProjectFrame(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
self.projectFrame = ProjectFrame(frame, basePopup=self)
self.projectFrame.grid(row=1, column=0, sticky='nsew')
self.updateFuncs.append(self.projectFrame.updateAll)
def initWms(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
extendNmrFrame = ExtendNmrFrame(frame, basePopup=self)
extendNmrFrame.grid(row=1, column=0, sticky='nsew')
self.updateFuncs.append(extendNmrFrame.updateAll)
def initTasks(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
tasksFrame = TasksFrame(frame, self)
tasksFrame.grid(row=1, column=0, sticky='nsew')
self.updateFuncs.append(tasksFrame.updateAll)
def initDataExch(self, frame):
row = 0
frame.config(bg='#E6E6E6')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
dataExchFrame = DataExchFrame(frame, basePopup=self)
dataExchFrame.grid(row=1, column=0, sticky='nsew')
self.updateFuncs.append(dataExchFrame.updateAll)
def initWorkflow(self, frame):
row = 0
frame.config(bg='#FFFFFF')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
workflowFrame = WorkflowFrame(frame, basePopup=self)
workflowFrame.grid(row=1, column=0, sticky='nsew')
self.updateFuncs.append(workflowFrame.updateAll)
def initProtocol(self, frame):
row = 0
frame.config(bg='#FFFFFF')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
protocolFrame = ProtocolFrame(frame, basePopup=self)
protocolFrame.grid(row=1, column=0, sticky='nsew')
self.updateFuncs.append(protocolFrame.updateAll)
def initUserFrame(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
row = 0
frame.config(bg='#FFFFFF')
userFrame = UserFrame(frame, basePopup=self)
userFrame.grid(row=1, column=0, sticky='nsew')
self.updateFuncs.append(userFrame.updateAll)
## The Menu ##
def makeUserMenu(self):
menu = Menu(self.mainMenu, tearoff=0)
menu.add_command(label='Log In',
shortcut='I',
command=self.openLoginPopup)
menu.add_command(label='Log Out', shortcut='O', command=self.logout)
menu.add_command(label='Save Profile',
shortcut='S',
command=self.tmpCall)
menu.add_command(label='View Profile',
shortcut='V',
command=self.tmpCall)
menu.add_command(label='Create Profile',
shortcut='C',
command=self.tmpCall)
menu.add_command(label='Edit Profile',
shortcut='E',
command=self.tmpCall)
self.mainMenu.add_cascade(label='User', shortcut='U', menu=menu)
menu.options = [
'Log In', 'Log Out', 'Save Profile', 'View Profile',
'Create Profile', 'Edit Profile'
]
return menu
def makeRepositoryMenu(self):
self.repMenu = Menu(self.mainMenu, tearoff=0)
# Add various options to the menu and state the functions they call
self.repMenu.add_command(label='Manager',
shortcut='M',
command=self.tmpCall)
self.repMenu.add_command(label='Connect',
shortcut='C',
command=self.openRepository)
# doesn't really work to have a disconnect; we do not have a list
# of repositories and so would it refer to? Better to do this from
# within the RepositoryFrame
self.repMenu.add_command(label='Disconnect',
shortcut='D',
command=self.tmpCall)
# again, this is functionality that would make sense but which it is hard to put
# in the top level menu because it is not obvious which repository it refers
# to
self.repMenu.add_command(label='Import Project',
shortcut='I',
command=self.tmpCall)
self.repMenu.add_command(label='Export Project',
shortcut='E',
command=self.tmpCall)
# FIXME JMCI
# the quit option needs to be tied to a dialogue box that asks whether
# the current connection state should be saved. This will have to be
# secured and so means that the GUI should have a login itself (beyond
# the logins for the various resources).
self.repMenu.add_command(label='Quit', shortcut='Q', command=self.quit)
self.mainMenu.add_cascade(label='Repository',
shortcut='R',
menu=self.repMenu)
self.repMenu.options = [
'Connect', 'Disconnect', 'Import Project', 'Export Project', 'Quit'
]
return self.repMenu
def makeProjectMenu(self):
# Submenu of the min menu
menu = Menu(self.mainMenu, tearoff=0)
# Add various options to the menu and state the functions they call
menu.add_command(label='New', shortcut='N', command=self.newProject)
menu.add_command(label='Open', shortcut='O', command=self.openProject)
menu.add_command(label='Close',
shortcut='C',
command=self.closeProject)
menu.add_command(label='Save', shortcut='S', command=self.saveProject)
menu.add_command(label='Save As',
shortcut='A',
command=self.saveAsProject)
menu.add_command(label='Quit', shortcut='Q', command=self.quit)
menu.add_command(label='Version',
shortcut='V',
command=self.showVersion)
self.mainMenu.add_cascade(label='Project', shortcut='P', menu=menu)
menu.options = [
'New', 'Open', 'Close', 'Save', 'Save As', 'Quit', 'Version'
]
return menu
def makeOtherMenu(self):
# The fonts menu is a pre-created widget
fontsMenu = FontMenu(self.mainMenu,
self.setFont,
sizes=(8, 10, 12),
doItalic=0,
doBoldItalic=0,
tearoff=0)
# Submenu of the min menu
menu = Menu(self.mainMenu, tearoff=0)
# Only Fonts option so far
menu.add_cascade(label='Fonts', shortcut='F', menu=fontsMenu)
self.mainMenu.add_cascade(label='Options', shortcut='O', menu=menu)
menu.options = [
'Fonts',
]
return menu
def makeCcpNmrMenu(self):
try:
from ccpnmr.analysis.AnalysisPopup import AnalysisPopup
haveAnalysis = True
except ImportError:
haveAnalysis = False
try:
from ccpnmr.format.gui.FormatConverter import FormatConverter
from ccpnmr.format.gui.DataShifter import DataShifter
haveFormatConv = True
except ImportError:
haveFormatConv = False
menu = Menu(self.mainMenu, tearoff=0)
if haveAnalysis:
menu.add_command(label='Analysis',
shortcut='A',
command=self.ccpNmrAnalysis)
else:
menu.add_command(label='Analysis ** NOT INSTALLED **',
shortcut='A',
command=None)
if haveFormatConv:
menu.add_command(label='Format Converter',
shortcut='F',
command=self.ccpNmrFormatConverter)
menu.add_command(label='Data Shifter',
shortcut='D',
command=self.ccpNmrDataShifter)
else:
menu.add_command(label='Format Converter ** NOT INSTALLED **',
shortcut='F',
command=None)
menu.add_command(label='Data Shifter ** NOT INSTALLED **',
shortcut='D',
command=None)
self.mainMenu.add_cascade(label='CcpNmr', shortcut='C', menu=menu)
menu.options = ['Analysis', 'Format Converter', 'Data Shifter']
return menu
def ccpNmrAnalysis(self, cacheSize=64):
from ccpnmr.analysis.AnalysisPopup import AnalysisPopup
analysis = AnalysisPopup(self, cache_size=cacheSize, glDirect=None)
analysis.update_idletasks() # fast
if self.project:
analysis.initProject(self.project)
def ccpNmrFormatConverter(self):
from ccpnmr.format.gui.FormatConverter import FormatConverter
fc = FormatConverter(self, threading=False, project=self.project)
fc.open()
if self.project:
fc.initProject(self.project)
def ccpNmrDataShifter(self):
from ccpnmr.format.gui.DataShifter import DataShifter
ds = DataShifter(self)
ds.open()
def newProject(self):
if self.project:
# Project already present
if not self.closeProject():
# If we don't close the current project do nothing
return
name = askString(title='Project name',
prompt='Enter project name:',
parent=self)
if name:
# Make the API Project object
project = Implementation.MemopsRoot(name=name)
nmrProject = project.newNmrProject(name=name)
self.initProject(project)
# placeholder method until we write code
def tmpCall(self):
return
def openProject(self):
if self.project:
if not self.closeProject():
return
self.openPopup('open_project',
OpenProjectPopup,
callback=self.initProject)
def openLoginPopup(self):
# at the moment we do this through methods in the popup. It
# would be much more sensible to do this through some
# sort of callback.
login_popup = LoginPopup(self)
# really we want to imoblise the rest. how to do?
def setRepository(self, rep):
self.repList.currentRepository = rep
if self.frameShortcuts.has_key('Repository'):
self.frameShortcuts['Repository'].drawFrame()
if self.frameShortcuts.has_key('Tasks'):
self.frameShortcuts['Tasks'].drawFrame()
#for ff in self.tabbedFrame.frames[0].children.values():
# ff.draw()
#for ff in self.tabbedFrame.frames[3].children.values():
# ff.draw()
for ff in self.tabbedFrame.frames[8].children.values():
ff.draw()
def openRepository(self):
rep_popup = RepositoryPropertiesPopup(self)
def closeRepository(self):
pass
def logout(self):
self.setUsername(None)
self.repList = RepositoryList()
print 'in logout ', self.repList
print '#########################'
print self.tabbedFrame.frames[0].__dict__
print '#########################'
if self.frameShortcuts.has_key('Repository'):
self.frameShortcuts['Repository'].drawFrame()
#for ff in self.tabbedFrame.frames[0].children.values():
# ff.draw()
for ff in self.tabbedFrame.frames[8].children.values():
ff.draw()
def openPopup(self, popup_name, clazz, oldStyle=False, *args, **kw):
popup = self.popups.get(popup_name)
if (popup):
popup.open()
else:
if self.project:
analysisProfile = self.analysisProfile
else:
analysisProfile = None
if analysisProfile:
transient = analysisProfile.transientDialogs
else:
transient = True
name = popup_name
if (oldStyle):
popup = self.popups[popup_name] = clazz(self,
transient=transient,
*args,
**kw)
else:
popup = self.popups[popup_name] = clazz(self,
project=self.project,
popup_name=name,
transient=transient,
*args,
**kw)
# above automatically opens popup
return popup
def closeProject(self, queryClose=True, querySave=True):
if queryClose:
if not showYesNo(
'Close project', 'Close current project?', parent=self):
return False
if querySave:
if not self.checkSaving():
return False
self.destroyPopups()
self.initProject()
return True
def saveProject(self):
self.saveFile()
# NBNB Rasmus 22/8/08 changed to fit AnalysisPopup (and removed 'isStored' bug)
#if (self.project.isStored):
# self.saveFile()
#else:
# self.askSaveFile()
def saveAsProject(self):
self.askSaveFile()
def showVersion(self):
showInfo('Version', self.versionInfo, parent=self)
def changeFont(self, analysisProfile):
if analysisProfile is self.analysisProfile:
if self.font != analysisProfile.font:
self.font = analysisProfile.font or DEFAULT_FONT
self.setFont()
def selectFont(self, font): # Only called from main menu option
if self.project:
self.analysisProfile.font = font
def setFont(self, font=None, popup=None):
if font is None:
font = self.font or DEFAULT_FONT
else:
self.font = font
if not popup:
popup = self
childList = popup.children.values()
classes = [
Tkinter.Button, Tkinter.Label, Tkinter.Menu, Tkinter.Entry,
Tkinter.Checkbutton, Tkinter.Radiobutton
]
for child in childList:
for clazz in classes:
if isinstance(child, clazz):
if hasattr(child, 'font'):
if not child.font:
child.config(font=font)
else:
child.config(font=font)
break
if isinstance(child, Tkinter.Frame):
child.font = font
elif isinstance(child, ScrolledMatrix):
child.setFont(font)
if hasattr(child, 'children'):
childList.extend(child.children.values())
def initProject(self, project=None):
self.project = project
if project:
self.initTopObjects(self.project)
self.project.application = self.application
self.setFont()
webBrowser = ProjectWebBrowser(self.top,
popup=self,
project=project)
#self.helpButton.config(command = lambda url=self.help_url: webBrowser.open(url) )
for i, func in enumerate(self.updateFuncs):
func(project)
for button in self.projButtons:
button.enable()
self.setupSoftware()
else:
for button in self.projButtons:
button.disable()
self.setMenuState()
def setUsername(self, name):
self.username = name
print 'set username ', self.username
# jmci FIXME
# need to look into this carefully and analyse the possible
# states
def setMenuState(self):
if self.project:
state = Tkinter.NORMAL
else:
state = Tkinter.DISABLED
# Disable bits of the project menu if there's no project
#for option in ('Save','Save As','Close'):
# i = self.projectMenu.options.index(option)
# self.projectMenu.entryconfig(i, state=state)
# Disable other manus if there's no project
#for menu in [self.otherMenu,]: # Include more menus in this list
# for i in range(len(menu.options)):
# menu.entryconfig(i, state=state)
def setupSoftware(self):
project = self.project
methodStore = project.currentMethodStore or \
project.findFirstMethodStore() or \
project.newMethodStore(name=project.name)
software = methodStore.findFirstSoftware(name=PROGRAM_NAME,
version=VERSION)
if not software:
software = methodStore.newSoftware(name=PROGRAM_NAME,
version=VERSION)
#software.vendorName = 'PDBe & CCPN'
#software.vendorAddress = ''
#software.vendorWebAddress = 'http:'
#software.details = ''
def askSaveFile(self):
popup = self.openPopup('save_project', SaveProjectPopup)
popup.refresh()
def modalAskSaveFile(self):
popup = SaveProjectPopup(self,
project=self.project,
dismiss_text='Cancel Quit',
modal=True)
did_save = popup.did_save
popup.destroy()
return did_save
def quitSaveProject(self):
if (self.project.activeRepositories):
return self.saveFile()
else:
return self.modalAskSaveFile()
def destroyPopups(self):
for key in self.popups.keys():
popup = self.popups[key]
popup.destroy()
self.popups = {}
## WMS methods
# should maybe merge this with setUsername
# this will read a config file that stores user setups. How this
# is done TBD so hack for now and just return
def readConfig(self, userName):
# this should return the full RepositoryList structure. In reality this
# will parse from file. set it by hand from here for now for speed
repList = RepositoryList(userName)
rep1 = repList.newRepository('remote', 'localhost:8080/HalxService',
'ccpn', 'remote')
repList.currentRepository = rep1
# should these be directory objects?
repList.current_export_dir = '/home/jionides/work/CCPN/test_JMCI_data'
repList.current_import_dir = '/home/jionides/work/CCPN/test_EXP_data'
self.repList = repList
print 'in readconfig '
self.setRepository(rep1)
# really should be done through notifiers
if self.frameShortcuts.has_key('Repository'):
self.frameShortcuts['Repository'].drawFrame()
if self.frameShortcuts.has_key('Tasks'):
self.frameShortcuts['Tasks'].drawFrame()
if self.frameShortcuts.has_key('DataExch'):
self.frameShortcuts['DataExch'].drawFrame()
for ff in self.tabbedFrame.frames[8].children.values():
ff.draw()
# want to update the top menu. The idea should be to add a bar item
# and then to list all the repositories underneath. Clicking on a given
# repository will set the home repository as current. That seems to
# be a good sensible way of simplifying the interface in a expected
# way. We could, alternatively, use tabs.
opts = {}
self.repMenu.add('separator', **opts)
for rep in repList.repositories:
item = {
'command': lambda rep=rep: self.setRepository(rep),
'label': rep.name
}
self.repMenu.add('comman', **item)
self.repMenu.config()
## end WMS methods
def copyModifiedStorages(self):
modifiedStorages = [
storage for storage in self.project.storages if storage.isModified
]
if (self.project.isModified):
modifiedStorages.append(self.project)
for storage in modifiedStorages:
self.copyStorage(storage)
def saveFile(self):
if not self.project:
return False
try:
saveProject(self.project, createFallback=True)
print 'successfully saved project'
return True
except IOError, e:
showError('Saving file', str(e), parent=self)
return False
def body(self, guiFrame):
self.geometry('450x500')
guiFrame.grid_rowconfigure(0, weight=1)
guiFrame.grid_columnconfigure(0, weight=1)
options = ['Peak Separator', 'Advanced Settings']
tabbedFrame = TabbedFrame(guiFrame, options=options)
tabbedFrame.grid(row=0, column=0, sticky='nsew')
buttons = UtilityButtonList(tabbedFrame.sideFrame,
helpUrl=self.help_url)
buttons.grid(row=0, column=0, sticky='e')
self.tabbedFrame = tabbedFrame
frameA, frameB = tabbedFrame.frames
#
# FrameA : Main Settings
#
frameA.grid_columnconfigure(1, weight=1)
row = 0 # Label row
row += 1
div = LabelDivider(frameA, text='Peak Separator Parameters')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
label = Label(frameA, text='Min. number of peaks:')
label.grid(row=row, column=0, sticky='w')
self.minPeaksEntry = IntEntry(frameA, returnCallback=self.applyChange, width=10, \
tipText='Minimum number of peaks to find (must be > 0)')
self.minPeaksEntry.grid(row=row, column=1, sticky='n')
self.minPeaksEntry.bind('<Leave>', self.applyChange, '+')
row += 1
label = Label(frameA, text='Max. number of peaks:')
label.grid(row=row, column=0, sticky='w')
self.maxPeaksEntry = IntEntry(frameA, returnCallback=self.applyChange, width=10, \
tipText='Maximum number of peaks to find (0 is unlimited - not recommended)')
self.maxPeaksEntry.grid(row=row, column=1, sticky='n')
self.maxPeaksEntry.bind('<Leave>', self.applyChange, '+')
row += 1
label = Label(frameA, text='Only pick positive peaks:')
label.grid(row=row, column=0, sticky='w')
entries = ['False', 'True']
self.posPeaksButtons = RadioButtons(
frameA,
entries=entries,
select_callback=self.applyChange,
direction='horizontal',
tipTexts=[
'Search for both positive and negative intensity peaks',
'Limit search to only positive peaks'
])
self.posPeaksButtons.grid(row=row, column=1, sticky='n')
row += 1
label = Label(frameA, text='Peak Model:')
label.grid(row=row, column=0, sticky='w')
### G/L Mixture works, but volume calculation involves Gamma function
# entries = ['Gaussian', 'Lorentzian', 'G/L Mixture']
entries = ['Gaussian', 'Lorentzian']
self.shapeButtons = RadioButtons(
frameA,
entries=entries,
select_callback=self.applyChange,
direction='horizontal',
tipTexts=[
'Choose a Gaussian model peak shape to fit to peaks',
'Choose a Lorentzian model peak shape to fit to peaks'
])
self.shapeButtons.grid(row=row, column=1, sticky='n')
row += 1
div = LabelDivider(frameA,
text='Region',
tipText='Region that search will limit itself to')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
label = Label(frameA, text='Peak List:')
label.grid(row=row, column=0, sticky='nw')
self.peakListPulldown = PulldownList(
frameA,
callback=self.setManuallyPickPeakList,
tipText='Select which peak list new peaks are to be added to')
self.peakListPulldown.grid(row=row, column=1, sticky='nw')
# tricky scrolled matrix
row += 1
self.regionTable = None
frameA.grid_rowconfigure(row, weight=1)
headings = ('dim.', 'start (ppm)', 'end (ppm)', 'actual size')
self.editDimEntry = IntEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Dimension number')
self.editStartEntry = FloatEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Search area lower bound')
self.editEndEntry = FloatEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Search area upper bound')
editWidgets = [
self.editDimEntry, self.editStartEntry, self.editEndEntry, None
]
editGetCallbacks = [None, None, None, None]
editSetCallbacks = [None, None, None, None]
self.regionTable = ScrolledMatrix(frameA,
headingList=headings,
multiSelect=False,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
initialRows=5)
self.regionTable.grid(row=row, column=0, columnspan=2, sticky='nsew')
# Run Button
row += 1
texts = ['Add Region']
commands = [self.updateFromRegion]
self.addResetButtons = ButtonList(
frameA,
texts=texts,
commands=commands,
tipTexts=['Add selected specrtral region'])
self.addResetButtons.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
texts = ['Separate Peaks']
commands = [self.runPeakSeparator]
self.runButton = ButtonList(frameA,
texts=texts,
commands=commands,
expands=True,
tipTexts=['Run peak search now'])
self.runButton.grid(row=row, column=0, columnspan=2, sticky='nsew')
#
# FrameB : Further Settings
#
frameB.grid_columnconfigure(0, weight=1)
row = 0
div = LabelDivider(frameB, text='Rate:')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
label = Label(frameB, text='Rate of MCMC step size change')
label.grid(row=row, column=0, columnspan=1, sticky='w')
self.rateEntry = FloatEntry(frameB, returnCallback=self.applyChange, width=10, \
tipText='Rate effects speed of run, smaller values take longer but may produce better results')
self.rateEntry.grid(row=row, column=1, sticky='n')
self.rateEntry.bind('<Leave>', self.applyChange, '+')
self.rateEntry.set(self.params.rate)
# tricky scrolled matrix for line width
row += 2
div = LabelDivider(frameB, text='Line Width (Hz):')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
label = Label(frameB, text="Descr.")
label.grid(row=row, rowspan=2, column=0, sticky='w')
row += 1
self.lineWidthTable = None
frameB.grid_rowconfigure(row, weight=1)
lineWidthHeadings = ('dim.', 'min. σ (Hz)', 'max. σ (Hz)')
self.editMinSigmaEntry = FloatEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Minimum line width (Hz)')
self.editMaxSigmaEntry = FloatEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Maximum line width (Hz)')
# self.editDimEntry is also from regionTable
initialWidthRows = 4
editLineWidthWidgets = [
None, self.editMinSigmaEntry, self.editMaxSigmaEntry
]
editLineWidthGetCallbacks = [None, self.getSigmaMin, self.getSigmaMax]
editLineWidthSetCallbacks = [None, self.setSigmaMin, self.setSigmaMax]
self.lineWidthTable = ScrolledMatrix(
frameB,
headingList=lineWidthHeadings,
multiSelect=False,
editWidgets=editLineWidthWidgets,
editGetCallbacks=editLineWidthGetCallbacks,
editSetCallbacks=editLineWidthSetCallbacks,
initialRows=initialWidthRows)
self.lineWidthTable.grid(row=row,
column=0,
columnspan=2,
sticky='nsew')
# option to 'repick' exisiting peak list
row += initialWidthRows
div = LabelDivider(frameB, text='(optional - repick entire peak list)')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
self.repickListPulldown = PulldownList(
frameB,
callback=self.setRePickPeakList,
tipText=
'Select which peak list to repick (new peaks will be put into a new peak list)'
)
self.repickListPulldown.grid(row=row, column=0, sticky='nw')
texts = ['Repick Peak List']
commands = [self.runRepickPeaks]
self.runButton = ButtonList(
frameB,
texts=texts,
commands=commands,
expands=True,
tipTexts=['Repick selected peak list into a new peak list.'])
self.runButton.grid(row=row, column=1, columnspan=1, sticky='nsew')
row += 1
div = LabelDivider(frameB)
row += 1
texts = ['Separate Peaks']
commands = [self.runPeakSeparator]
self.runButton = ButtonList(frameB,
texts=texts,
commands=commands,
expands=True,
tipTexts=['Run peak search now'])
self.runButton.grid(row=row, column=0, columnspan=2, sticky='nsew')
self.setWidgetEntries()
self.administerNotifiers(self.registerNotify)
class ApplicationPopup(AnalysisPopup):
help_url = 'http://www.ccpn.ac.uk'
allowedCallbackFuncnames = ('init', 'save', 'close')
def __init__(self, root, programName='Extend-NMR Interface'):
self.font = DEFAULT_FONT
# Application object needed to store application-specific data with project
self.application = Application(name=PROGRAM_NAME)
self.versionInfo = 'Version' + VERSION
self.ariaProjectFile = None
self.doneAnalysisInfo = False
self.updateFuncs = []
self.projButtons = []
self.ariaPaths = []
self.isdPaths = []
AnalysisPopup.__init__(self, root)
self.program_name = PROGRAM_NAME
self.setTitle(PROGRAM_NAME)
def printAnalysisCommandLineInfo(self, event):
if not self.doneAnalysisInfo:
Analysis.printCommandLineInfo(self)
self.doneAnalysisInfo = True
def printCommandLineInfo(self):
print """
For program documentation see:
http://www.extend-nmr.eu
"""
def body(self, guiParent):
self.menus = {}
self.menu_items = {}
self.fixedActiveMenus = {}
self.popups = {}
self.callbacksDict = {}
self.selected_objects = []
self.menubar = menubar = Menu(guiParent)
self.font = DEFAULT_FONT
self.setProjectMenu()
#
menu = Menu(self.menubar, tearoff=0)
menu.bind('<Button>', self.printAnalysisCommandLineInfo)
self.menubar.add_cascade(label='CcpNmr Analysis',
shortcut='C',
menu=menu)
self.menubar.add_command(label='FormatConverter',
shortcut='F',
command=self.runFormatConverter)
self.menubar = menu
self.initProject()
self.setPeaksMenu()
self.setMoleculeMenu()
self.setAssignMenu()
self.setResonanceMenu()
self.setDataMenu()
self.setStructureMenu()
self.setChartMenu()
self.setMacroMenu()
self.setOtherMenu()
self.setMenuState() # need to do it again because of OtherMenu state
# Help Submenu
helpMenu = Menu(self.menubar, tearoff=0)
helpMenu.add_command(label='Version',
shortcut='V',
command=self.showVersion)
helpMenu.add_command(label='About',
shortcut='A',
command=self.showAbout)
helpMenu.add_command(label='Help', shortcut='H', command=self.showHelp)
menu.add_separator()
menu.add_command(label='CCPN Updates',
shortcut='U',
image=self.iconRefresh,
compound='left',
command=self.updateAnalysis,
tipText='Get any new patches and updates to CcpNmr')
menu.add_cascade(label='CCPN Help',
shortcut='H',
image=self.iconHelp,
compound='left',
menu=helpMenu)
self.config(menu=menubar)
# Ensure that the first row and column in popup expand
guiParent.grid_rowconfigure(0, weight=1)
guiParent.grid_columnconfigure(0, weight=1, minsize=200)
frame = Frame(guiParent) # Body widgets can be put in this frame
frame.grid()
softwareOpts = [
'Extend-NMR', 'ARIA 2', 'Auremol', 'CING', ' ECI ', 'HADDOCK',
' ISD ', 'PRODECOMP'
]
self.tabbedFrame = TabbedFrame(guiParent,
options=softwareOpts,
toggleOff=False,
selected=0,
callback=self.toggleTab)
self.tabbedFrame.grid(row=0, column=0, sticky='nsew')
frames = self.tabbedFrame.frames
# Logos
ccpnDir = getTopDirectory()
imageDir = os.path.join(ccpnDir, 'python', 'extendNmr', 'images')
imageFile = os.path.join(imageDir, 'Fp6Logo.gif')
self.fp6Logo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'CingLogo.gif')
self.cingLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'AriaLogo.gif')
self.ariaLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'IsdLogo.gif')
self.isdLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'HaddockLogo.gif')
self.haddockLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'AuremolLogo.gif')
self.auremolLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'CcpnLogo.gif')
self.ccpnLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'ProdecompLogo.gif')
self.prodecompLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'MddLogo.gif')
self.mddLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'BrukerLogo.gif')
self.brukerLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'MsdLogo.gif')
self.msdLogo = Tkinter.PhotoImage(file=imageFile)
self.initExtendNmr(frames[0])
self.initAria(frames[1])
self.initAuremol(frames[2])
self.initCing(frames[3])
self.initEci(frames[4])
self.initHaddock(frames[5])
self.initIsd(frames[6])
self.initProdecomp(frames[7])
self.initProject(self.project)
if not self.project:
for button in self.projButtons:
button.disable()
self.geometry('680x670')
def setProjectMenu(self):
ProjectMenu = 'Project'
# Imports submenu
importsMenu = Menu(self.menubar, tearoff=False)
importsMenu.add_command(label='Via Format Converter',
shortcut='F',
command=self.runFormatConverter)
importsMenu.add_command(label='NMR-STAR 2.1.1',
command=self.importNmrStar211)
importsMenu.add_command(label='NMR-STAR 3.1',
shortcut='N',
command=self.importNmrStar31)
importsMenu.add_command(label='PDB 3.20',
shortcut='P',
command=self.importPdb)
importsMenu.add_command(label='Coordinates (PDB-style)',
shortcut='C',
command=self.importCoordinates)
# Preferences submenu
fontsMenu = FontMenu(self.menubar,
self.selectFont,
sizes=(8, 10, 12),
doItalic=False,
doBoldItalic=False,
tearoff=0)
prefsMenu = Menu(self.menubar, tearoff=False)
prefsMenu.add_cascade(
label='Fonts',
shortcut='F',
image=self.iconFont,
compound='left',
menu=fontsMenu,
tipText='Select font to use in the graphical interface')
prefsMenu.add_command(label='Colour Schemes',
image=self.iconTable,
compound='left',
shortcut='C',
tipText='Edit and create colour schemes',
command=self.editColorSchemes)
prefsMenu.add_command(
label='Residue Codes',
image=self.iconTable,
compound='left',
shortcut='R',
tipText=
'User-specified codes that override the standard residue names',
command=self.editResidueCodes)
prefsMenu.add_command(label='User Options',
image=self.iconTable,
compound='left',
shortcut='U',
tipText='General options for Analysis behaviour',
command=self.editProfiles)
#
menu = Menu(self.menubar, tearoff=0)
menu.add_command(
label='New',
shortcut='N',
image=self.iconNewWindow,
compound='left',
command=self.newProject,
tipText='Create a new, blank CCPN project (closes any open project)'
)
menu.add_command(
label='Open Project',
shortcut='O',
image=self.iconOpen,
compound='left',
command=self.openProject,
tipText=
'Open a new CCPN project by selecting a project directory on disk')
menu.add_command(
label='Open Spectra',
shortcut='p',
image=self.iconOpenFile,
compound='left',
command=self.openSpectrum,
tipText=
'Open spectrum data fom disk, creating a default CCPN project if needed'
)
menu.add_command(label='Save',
shortcut='S',
image=self.iconSave,
compound='left',
command=self.saveProject,
tipText='Save the current CCPN project on disk')
menu.add_command(
label='Save As',
shortcut='A',
image=self.iconSaveAs,
compound='left',
command=self.saveAsProject,
tipText=
'Save the current CCPN project under a different name (project directory)'
)
menu.add_cascade(label='Import',
shortcut='I',
image=self.iconImport,
compound='left',
menu=importsMenu)
menu.add_command(label='Close',
shortcut='C',
image=self.iconClose,
compound='left',
command=self.closeProject,
tipText='Close the current CCPN project')
menu.add_command(
label='Quit',
shortcut='Q',
image=self.iconQuit,
compound='left',
command=self.quit,
tipText='Quit Extend-NMR, closing any open CCPN project')
menu.add_separator()
menu.add_cascade(label='Preferences',
shortcut='P',
image=self.iconPrefs,
compound='left',
menu=prefsMenu)
menu.add_command(
label='Validate',
shortcut='V',
image=self.iconTool,
compound='left',
command=self.validateProject,
tipText=
'Check the current CCPN project for data model consistency errors')
menu.add_command(
label='Backup',
shortcut='B',
image=self.iconTool,
compound='left',
command=self.backupProject,
tipText='Setup options for automated backup of CCPN project data')
menu.add_command(
label='Archive',
shortcut='r',
image=self.iconTool,
compound='left',
command=self.archiveProject,
tipText=
'Save the current CCPN project in an archived form, e.g. tar gzipped'
)
self.menubar.add_cascade(label=ProjectMenu, shortcut='j', menu=menu)
self.menus[ProjectMenu] = menu
self.menu_items[ProjectMenu] = [
'New',
'Open Project',
'Open Spectra',
'Save',
'Save As',
'Import',
'Close',
'Quit',
'Preferences',
'Validate',
'Backup',
'Archive',
]
# Menus that area ctive in absence of a project
#for ii in (0,1,2,7,13,15):
for ii in (
0,
1,
2,
7,
):
self.fixedActiveMenus[(ProjectMenu, ii)] = True
def setPopupGeometries(self):
for key in self.popups.keys():
popup = self.popups[key]
if not key.startswith(window_popup_prefix): # bit of a hack
not self.setPopupGeometry(popup, key)
def toggleTab(self, index):
if (index > 0) and not self.project:
showWarning('Warning', 'No active project', parent=self)
self.tabbedFrame.select(0)
return
frame = self.tabbedFrame.frames[index]
if hasattr(frame, 'printOutDocString'):
print frame.printOutDocString
# only print it once
del frame.printOutDocString
def initCing(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
canvas = Tkinter.Canvas(frame, width=702, height=77)
canvas.grid(row=0, column=0, sticky='ew')
canvas.create_image(0, 0, anchor='nw', image=self.cingLogo)
cingFrame = CingFrame(frame, self)
cingFrame.grid(row=1, column=0, sticky='nsew')
#self.projButtons.extend(cingFrame.buttonBar.buttons)
self.updateFuncs.append(cingFrame.updateAll)
def initProdecomp(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
frame.configure(bg='#FFFFFF')
canvas = Tkinter.Canvas(frame, width=1024, height=90, bg='#FFFFFF')
canvas.grid(row=0, column=0, sticky='ew')
canvas.create_image(0, 0, anchor='nw', image=self.prodecompLogo)
prodecompFrame = ProdecompFrame(frame,
basePopup=self,
ccpnProject=self.project)
prodecompFrame.grid(row=1, column=0, sticky='nsew')
# set printOutDocString:
frame.printOutDocString = prodecompFrame.printOutDocString
#self.projButtons.extend(isdFrame.buttons)
self.updateFuncs.append(prodecompFrame.updateAll)
def initAuremol(self, frame):
frame.expandGrid(1, 0)
refText = """Gronwald W, Brunner K, Kirchhofer R, Nasser A, Trenner J, Ganslmeier B,
Riepl H, Ried A, Scheiber J, Elsner R, Neidig K-P, Kalbitzer HR
AUREMOL, a New Program for the Automated Structure Elucidation of
Biological Macromolecules. Bruker Reports 2004; 154/155: 11-14
"""
canvas = Tkinter.Canvas(frame, width=700, height=160, bg='#FFFFFF')
canvas.grid(row=0, column=0, sticky='ew')
canvas.create_image(12, 12, anchor='nw', image=self.auremolLogo)
canvas.create_text(200, 10, anchor='nw', text=refText)
auremolFrame = AuremolFrame(frame, self.project, grid=(1, 0))
#self.projButtons.extend(isdFrame.buttons)
self.updateFuncs.append(auremolFrame.updateAll)
def initEci(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
frame.parent = self # For notifiers
frame.configure(bg='#FFFFFF')
canvas = Tkinter.Canvas(frame,
width=800,
height=73,
bd=3,
bg='#FFFFFF')
canvas.grid(row=0, column=0, sticky='ew')
canvas.create_image(10, 10, anchor='nw', image=self.msdLogo)
eciFrame = EntryCompletionFrame(frame, basePopup=self)
eciFrame.grid(row=1, column=0, sticky='nsew')
#self.projButtons.extend(isdFrame.buttons)
self.updateFuncs.append(eciFrame.updateAll)
def initHaddock(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
frame.parent = self # For notifiers
canvas = Tkinter.Canvas(frame, width=753, height=92)
canvas.grid(row=0, column=0, sticky='ew')
canvas.create_image(0, 0, anchor='nw', image=self.haddockLogo)
haddockFrame = HaddockFrame(frame, self.project)
haddockFrame.grid(row=1, column=0, sticky='nsew')
#self.projButtons.extend(isdFrame.buttons)
self.updateFuncs.append(haddockFrame.updateAll)
def initIsd(self, frame):
global isd
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
frame.configure(bg='#FFFFFF')
canvas = Tkinter.Canvas(frame,
width=800,
height=91,
bd=3,
bg='#FFFFFF')
canvas.grid(row=0, column=0, sticky='ew', padx=0)
canvas.create_image(0, 0, anchor='nw', image=self.isdLogo)
isdFrame = IsdFrame(frame, self.project)
isdFrame.grid(row=1, column=0, sticky='nsew')
self.isd = isdFrame
isd = self.isd
#self.projButtons.extend(isdFrame.buttons)
self.updateFuncs.append(isdFrame.updateAll)
def initExtendNmr(self, frame):
row = 0
frame.config(bd=5)
canvas = Tkinter.Canvas(frame,
width=640,
height=600,
bg='#FFFFFF',
bd=5)
canvas.grid(row=row, column=0, sticky='nsew')
canvas.create_image(15, 15, anchor='nw', image=self.fp6Logo)
canvas.create_image(330, 15, anchor='nw', image=self.prodecompLogo)
canvas.create_image(330, 115, anchor='nw', image=self.mddLogo)
canvas.create_image(20, 200, anchor='nw', image=self.ccpnLogo)
canvas.create_image(230, 220, anchor='nw', image=self.msdLogo)
canvas.create_image(450, 200, anchor='nw', image=self.brukerLogo)
canvas.create_image(5, 310, anchor='nw', image=self.isdLogo)
canvas.create_image(230, 300, anchor='nw', image=self.ariaLogo)
canvas.create_image(450, 290, anchor='nw', image=self.auremolLogo)
canvas.create_image(5, 420, anchor='nw', image=self.haddockLogo)
canvas.create_image(5, 520, anchor='nw', image=self.cingLogo)
#row += 1
#l1 = Label(frame, text='Welcome to the Extend NMR suite')
#l1.grid(row=row, column=0, sticky='ew')
def initAria(self, frame):
welcomeMessage = \
"""ARIA Version 2.3. Authors: Benjamin Bardiaux, Michael Habeck,
Jens Linge, Therese Malliavin, Sean O'Donoghue, Wolfgang Rieping,
and Michael Nilges.
Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E.,
Nilges M.(2007) ARIA2: automated NOE assignment and data
integration in NMR structure calculation. Bioinformatics 23:381-382"""
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
canvas = Tkinter.Canvas(frame, width=700, height=114, bg='#FFFFFF')
canvas.grid(row=0, column=0, sticky='ew')
canvas.create_image(0, 0, anchor='nw', image=self.ariaLogo)
canvas.create_text(250, 10, anchor='nw', text=welcomeMessage)
ariaFrame = AriaFrame(frame, self)
ariaFrame.grid(row=1, column=0, sticky='nsew')
self.projButtons.extend(ariaFrame.buttons)
self.updateFuncs.append(ariaFrame.updateAll)
def openPopup(self, popup_name, clazz, oldStyle=False, *args, **kw):
popup = self.popups.get(popup_name)
if (popup):
popup.open()
else:
if self.project:
analysisProfile = self.analysisProfile
else:
analysisProfile = None
if analysisProfile:
if popup_name.startswith(window_popup_prefix): # bit of a hack
transient = analysisProfile.transientWindows
else:
transient = analysisProfile.transientDialogs
else:
transient = True
name = popup_name
if (oldStyle):
popup = self.popups[popup_name] = clazz(self,
transient=transient,
*args,
**kw)
else:
popup = self.popups[popup_name] = clazz(self,
project=self.project,
popup_name=name,
transient=transient,
*args,
**kw)
# above automatically opens popup
return popup
def initProject(self, project=None):
AnalysisPopup.initProject(self, project, False)
self.project = project
if project:
for i, func in enumerate(self.updateFuncs):
func(project)
for button in self.projButtons:
button.enable()
else:
for button in self.projButtons:
button.disable()
def setupSoftware(self):
return
project = self.project
methodStore = project.currentMethodStore or \
project.findFirstMethodStore() or \
project.newMethodStore(name=project.name)
software = methodStore.findFirstSoftware(name=PROGRAM_NAME,
version=VERSION)
if not software:
software = methodStore.newSoftware(name=PROGRAM_NAME,
version=VERSION)
software.task = 'data pipeline'
software.vendorName = 'The Extend-NMR Project'
#software.vendorAddress = ''
software.vendorWebAddress = 'http://www.extend-nmr.eu'
def __init__(self, parent, basePopup, *args, **kw):
#
# Variable initialisation
#
self.fcWrapper = basePopup.fcWrapper
self.project = basePopup.project
self.basePopup = basePopup
# TODO necessary?
if self.project:
self.nmrProject = self.project.currentNmrProject
self.entry = self.project.currentNmrEntryStore.findFirstEntry()
if not self.entry:
self.entry = self.project.currentNmrEntryStore.newEntry(
name=self.project.name)
else:
self.nmrProject = None
self.sequenceCoordinatesLoaded = False
self.shiftsLoaded = False
self.linkResDone = False
self.currentShiftList = None
self.shiftListChainPairs = []
self.moleculeList = []
self.moleculeDict = {}
#
# Frame setup
#
Frame.__init__(self, parent, **kw)
self.grid_columnconfigure(1, weight=1)
self.grid_rowconfigure(1, weight=1)
options = ['Import', 'Deposition']
tabbedFrame = TabbedFrame(self,
options=options,
callback=self.selectTab)
tabbedFrame.grid(row=1, column=0, columnspan=2, sticky='nsew')
self.tabbedFrame = tabbedFrame
frameA, frameD = tabbedFrame.frames
#
# Main
#
frameA.grid_columnconfigure(0, weight=1)
#frameA.grid_columnconfigure(1, weight=1) # Change to 2 if want 2 columns
frameA.grid_rowconfigure(12, weight=1)
#frameA.grid_rowconfigure(12, weight=1)
row = 0
div = LabelDivider(
frameA,
text=
'Select the full coordinate file or a sequence file (with info for a single molecule).',
justify='center',
grid=(row, 0),
gridSpan=(1, 1))
row += 1
self.sequenceCoordinatesImport = Button(
frameA,
text=self.defaultSelectText,
command=self.importSequenceOrCoords,
foreground=self.fontDefaultColor)
self.sequenceCoordinatesImport.grid(row=row, column=0, sticky='ew')
row += 1
label = Label(frameA, text="")
label.grid(row=row, column=0, sticky='ew')
row += 1
div = LabelDivider(
frameA,
text='Select the molecule relevant for your chemical shift file.',
justify='center',
grid=(row, 0),
gridSpan=(1, 1))
row += 1
self.moleculeSelect = Label(
frameA,
text="None available yet - import valid file first",
foreground=self.fontBadColor)
self.moleculeSelect.grid(row=row, column=0, sticky='ew')
self.moleculeSelectRow = row
row += 1
label = Label(frameA, text="")
label.grid(row=row, column=0, sticky='ew')
row += 1
div = LabelDivider(
frameA,
text=
'Select a chemical shift file with values only for the above molecule.',
justify='center',
grid=(row, 0),
gridSpan=(1, 1))
row += 1
self.shiftImport = Button(frameA,
text=self.defaultSelectText,
command=self.importShifts,
foreground=self.fontDefaultColor)
self.shiftImport.grid(row=row, column=0, sticky='ew')
row += 1
label = Label(frameA, text="")
label.grid(row=row, column=0, sticky='ew')
row += 1
div = LabelDivider(
frameA,
text='Consistency check between molecule and shift information.',
justify='center',
grid=(row, 0),
gridSpan=(2, 1))
row += 1
self.linkResCheckInfo = Label(frameA, text='')
self.linkResCheckInfo.grid(row=row, column=0, sticky='ew')
row += 1
div = Separator(frameA, grid=(row, 0), gridSpan=(1, 1))
row += 1
texts = ['Import new sequence', 'Import new set of shifts']
commands = [self.resetSequenceImport, self.resetShiftImport]
self.mainButtons = ButtonList(frameA, texts=texts, commands=commands)
self.mainButtons.grid(row=row, column=0, columnspan=2, sticky='ew')
self.mainButtons.buttons[0].config(foreground=self.fontDefaultColor)
#print row
self.frameA = frameA
#
# Not in use...
#
#frameX.grid_columnconfigure(0, weight=1)
#frameX.grid_columnconfigure(1, weight=1)
#frameX.grid_rowconfigure(1, weight=1)
#frameX.grid_rowconfigure(3, weight=1)
#
# Deposition, is updated after each successful import run.
#
frameD.grid_columnconfigure(0, weight=1)
frameD.grid_rowconfigure(5, weight=1)
self.frameD = frameD
row = 0
div = LabelDivider(frameD,
text='Imported data.',
justify='center',
grid=(row, 0),
gridSpan=(1, 2))
row += 1
self.depositionImportText = "\nImported %d shift list(s) for a total of %d shifts.\n\nImported %d molecule(s) and %d chain(s).\n\nImported %d model(s) for a total of %d atom coordinates.\n\nLinked %.2f%% of imported NMR information to %d chain(s)."
self.depositionImportLoc = (row, 0)
# These used for setting text above...
self.depositionImportNums = [0, 0, 0, 0, 0, 0, 0.0, 0]
self.importedShiftLists = []
self.connectedChains = []
self.depositionImportLabel = Label(frameD,
text=self.depositionImportText %
tuple(self.depositionImportNums),
foreground=self.fontBadColor)
self.depositionImportLabel.grid(row=row, column=0, sticky='ew')
row += 1
label = Label(frameD, text="")
label.grid(row=row, column=0, sticky='ew')
#
# Finalize the import part, proceed to ECI.
#
row += 1
div = LabelDivider(
frameD,
text=
'Import completed, save project and start Entry Completion Interface.',
justify='center',
grid=(row, 0),
gridSpan=(1, 1))
row += 1
self.eciStart = Button(frameD,
text="Finalise import",
command=self.finaliseImport,
foreground=self.fontBadColor)
self.eciStart.grid(row=row, column=0, sticky='ew')