def body(self, master):
#
# Popup window
#
row = 0
if self.topText:
label = Label(master, text= self.topText)
label.grid(row=row, column=0, columnspan = 2, sticky=Tkinter.EW)
row = row + 1
label = Label(master, text= self.text)
label.grid(row=row, column=0, sticky=Tkinter.EW)
self.menu = PulldownMenu(master, entries = self.selectionList, selected_index = self.selectedIndex)
self.menu.grid(row=row, column=1, sticky=Tkinter.E, ipadx = 20)
row = row + 1
texts = [ 'OK' ]
commands = [ self.ok ] # This calls 'ok' in BasePopup, this then calls 'apply' in here
if self.dismissButton:
buttons = createDismissHelpButtonList(master, texts=texts, commands=commands, dismiss_text = self.dismissText, help_url=self.help_url)
else:
buttons = createHelpButtonList(master, texts=texts, commands=commands, help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan = 3)
def body(self, master):
master.grid_columnconfigure(0, weight=1)
for i in range(3):
master.grid_rowconfigure(i, weight=1)
self.geometry('600x400')
# Master is the owner widget (not self.parent) - parent of the widget here
row = 0
label = Label(master,
text="Residue %s-%d" %
(self.nmrRes.molResidue.ccpCode, self.nmrRes.seqCode))
label.grid(row=row, column=0, sticky=Tkinter.W)
row = row + 1
label = Label(master, text=self.message)
label.grid(row=row, column=0, sticky=Tkinter.W)
row = row + 1
self.menu = PulldownMenu(master, entries=self.optionList)
self.menu.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
texts = ['OK']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, column=0)
def body(self, master):
#
# Popup window
#
self.widgets = []
row = 0
label = Label(master, text= "ChemComp formula '%s'" % self.formula)
label.grid(row=row, column=0, columnspan = 2, sticky=Tkinter.EW)
row = row + 1
label = Label(master, text= "Number of bonds: %d" % self.bondNumber)
label.grid(row=row, column=0, columnspan = 2, sticky=Tkinter.EW)
#
# Show relevant attributes...
#
for chemCompAttrInfo in self.chemCompInfo:
row = row + 1
attrName = chemCompAttrInfo[0]
label = Label(master, text = attrName)
label.grid(row=row, column=0, sticky=Tkinter.EW)
if attrName in self.nonEntryAttributes:
widgetInfo = self.nonEntryAttributes[attrName]
if widgetInfo[0] == PulldownMenu:
self.widgets.append(PulldownMenu(master, entries = widgetInfo[1], selected_index = widgetInfo[1].index(chemCompAttrInfo[1])))
elif widgetInfo[0] == CheckButton:
self.widgets.append(CheckButton(master, selected = widgetInfo[1]))
else:
text = chemCompAttrInfo[1]
if not text:
text = ''
self.widgets.append(Entry(master, text = text))
self.widgets[-1].grid(row=row, column=1, sticky=Tkinter.EW)
row = row + 1
texts = [ 'OK' ]
commands = [ self.ok ] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createHelpButtonList(master, texts=texts, commands=commands, help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan = 2)
def body(self, master):
self.text = ScrolledText(master)
self.text.pack(side=Tkinter.TOP, expand=Tkinter.YES, fill=Tkinter.BOTH)
texts = ['Save text']
commands = [self.saveText]
buttons = createHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.pack()
def body(self, master):
#
# Popup window
#
row = 0
label = Label(master, text=self.topText)
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.EW)
row = row + 1
self.valueWidgets = []
for i in range(0, len(self.valueList)):
value = self.valueList[i]
labelText = self.valueInfo[i]
label = Label(master, text=labelText)
label.grid(row=row, column=0, sticky=Tkinter.EW)
self.valueWidgets.append(Entry(master, text=str(value)))
self.valueWidgets[-1].grid(row=row,
column=1,
sticky=Tkinter.E,
ipadx=20)
row = row + 1
texts = ['OK']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
if self.dismissButton:
buttons = createDismissHelpButtonList(
master,
texts=texts,
commands=commands,
dismiss_text=self.dismissText,
help_url=self.help_url)
else:
buttons = createHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=3)
def body(self, master):
master.grid_columnconfigure(0, weight=1)
master.grid_columnconfigure(1, weight=1)
self.geometry('600x400')
#
# Popup window
#
row = 0
label = Label(master, text="Residue type '%s'" % self.ccpCode)
label.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
label = Label(
master,
text=
"Please select resonances that belong together (remaining ones are also grouped)"
)
label.grid(row=row, column=0, sticky=Tkinter.EW)
for resName in self.resonanceNameList:
row = row + 1
label = Label(master, text="Resonance '%s'" % resName)
label.grid(row=row, column=0, sticky=Tkinter.EW)
self.checkButtons.append(CheckButton(master))
self.checkButtons[-1].grid(row=row, column=1, sticky=Tkinter.EW)
row = row + 1
texts = ['OK']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, column=0)
for i in range(row):
master.grid_rowconfigure(i, weight=1)
def body(self, master):
#
# Initialize
#
#
# Get relevant dataDimRefs AND chemical shift ranges for each
#
self.dataDimRefDict = {}
dataDimRefList = []
dataDimRefSelection = self.numDim * ['']
for peak in self.peakList.sortedPeaks():
for peakDim in peak.sortedPeakDims():
dataDim = peakDim.dataDim
if dataDim.className == 'SampledDataDim':
continue
dataDimRef = peakDim.dataDimRef
if dataDim.dim == 1:
addInfo = " (acqu)"
else:
addInfo = ""
isotopeString = '/'.join(dataDimRef.expDimRef.isotopeCodes)
selectionString = "Dim %d, nucl %s%s" % (
dataDim.dim, isotopeString, addInfo)
if dataDimRefList.count(selectionString) == 0:
dataDimRefList.append(selectionString)
self.dataDimRefDict[selectionString] = dataDimRef
if dataDimRef in self.dataDimRefs:
dataDimRefSelection[self.dataDimRefs.index(
dataDimRef)] = selectionString
else:
dataDimRefSelection[(peakDim.dim -
1)] = selectionString
#
# Popup info
#
#
# Header labels
#
row = 0
label = Label(master, text="%s peak dim" % self.format)
label.grid(row=row, column=0, sticky=Tkinter.EW)
label = Label(master, text="PeakDim selection")
label.grid(row=row, column=1, sticky=Tkinter.EW)
#
# Selection per peakDim
#
self.dataDimRefMenu = []
for peakDim in range(0, self.numDim):
row = row + 1
label = Label(master, text=str(peakDim))
label.grid(row=row, column=0, sticky=Tkinter.EW)
peakDimIndex = self.order[peakDim]
self.dataDimRefMenu.append(
PulldownMenu(master,
entries=dataDimRefList,
selected_index=dataDimRefList.index(
dataDimRefSelection[peakDimIndex])))
self.dataDimRefMenu[-1].grid(row=row,
column=1,
sticky=Tkinter.W,
ipadx=20)
row = row + 1
texts = ['OK']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=2)
def body(self, master):
#
# Popup window
#
self.columnspan = len(self.chemCompAtoms[0])
row = 0
label = Label(master, text= "Molecule type '%s', ccp code '%s'" % (self.chemCompInfo[0][1],self.chemCompInfo[1][1]))
label.grid(row=row, column=0, columnspan = self.columnspan, sticky=Tkinter.EW)
#
# Warning message if necessary!
#
if self.obligatoryAtoms:
row += 1
label = Label(master, text= "Warning: have to define atoms: %s!" % string.join(self.obligatoryAtoms,', '), fg = 'red')
label.grid(row=row, column=0, columnspan = self.columnspan, sticky=Tkinter.EW)
#
# Show top information...
#
row = row + 1
colNum = 0
self.frameWidth = 0
for chemCompAtomInfo in self.chemCompAtoms[0]:
attrName = chemCompAtomInfo[0]
label = Label(master, text = attrName, width = len(attrName) + 2)
label.grid(row=row, column=colNum, sticky=Tkinter.EW)
self.frameWidth += len(attrName) + 2
colNum += 1
#
# Separator
#
row += 1
separator = Separator(master, height = 3)
separator.setColor('black', bgColor = 'black')
separator.grid(row = row, columnspan = self.columnspan, sticky = Tkinter.EW)
#
# Separate frame for info (have to be able to scroll)
#
row += 1
# THIS BIT TELLS MASTER TO CONFIGURE WINDOW ON INSIDE WIDGET!!
master.grid_rowconfigure(row,weight = 1)
for i in range(self.columnspan):
master.grid_columnconfigure(i,weight = 1)
self.atomFrame = ScrolledFrame(master, width = self.frameWidth, height = 300, doExtraConfig = False)
self.atomFrame.grid(row=row, column=0, columnspan = self.columnspan, sticky=Tkinter.NSEW)
self.atomFrameRow = row
self.atomFrameMaster = master
#
# Separator
#
row += 1
separator = Separator(master, height = 3)
separator.setColor('black', bgColor = 'black')
separator.grid(row = row, columnspan = self.columnspan, sticky = Tkinter.EW)
#
# End bit...
#
row = row + 1
texts = [ 'OK', 'Update' ]
commands = [ self.ok, self.update ] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createHelpButtonList(master, texts=texts, commands=commands, help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan = self.columnspan)
self.setupAtomFrame()
def body(self, master):
#
# Initialize
#
#
# Get chem shift range
#
peakChemShiftRange = []
if not self.peaks:
return
elif hasattr(self.peaks[0], 'ppm'):
peakUnit = 'ppm'
elif hasattr(self.peaks[0], 'point'):
peakUnit = 'point'
else:
return
for peak in self.peaks:
peakInfo = getattr(peak, peakUnit)
for dim in range(0, len(peakInfo)):
if len(peakChemShiftRange) < dim + 1:
peakChemShiftRange.append([999999, -999999])
if peakChemShiftRange[dim][0] > peakInfo[dim]:
peakChemShiftRange[dim][0] = peakInfo[dim]
if peakChemShiftRange[dim][1] < peakInfo[dim]:
peakChemShiftRange[dim][1] = peakInfo[dim]
#
# Make datadimref lists
#
dataDimRefList = []
self.dataDimRefDict = {}
dataDimRefSelection = []
for i in self.order:
dataDim = self.dataSource.sortedDataDims()[i]
if dataDim.dim == 1:
addInfo = " (acqu)"
else:
addInfo = ""
for dataDimRef in dataDim.dataDimRefs:
# Note: key for dataDimRef is expDimRef!
isotopeString = string.join(dataDimRef.expDimRef.isotopeCodes,
dirsep)
selectionString = "Dim %d, nucl %s, refValue %s%s" % (
dataDim.dim, isotopeString, dataDimRef.refValue, addInfo)
# In principle this could go wrong if one expDim has two expDimRefs with same isotopelist
# (but what would be the use? Is this a good constraint?)
dataDimRefList.append(selectionString)
self.dataDimRefDict[selectionString] = dataDimRef
dataDimRefSelection.append(dataDimRefList[-1])
#
# Add on a None dimension if necessary
#
if self.numDim < len(peakChemShiftRange):
dataDimRefSelection.append('None')
dataDimRefList.append('None')
self.dataDimRefDict['None'] = None
#
# Popup info
#
#
# Header labels
#
row = 0
label = Label(master, text="Peak dim")
label.grid(row=row, column=0, sticky=Tkinter.EW)
label = Label(master, text="Chem. shift range")
label.grid(row=row, column=1, sticky=Tkinter.EW)
# TODO: add in peak dim column headers if known (for nmrView for example)
label = Label(master, text="DataDimRef selection")
label.grid(row=row, column=2, sticky=Tkinter.EW)
#
# Selection per peakDim
#
self.dataDimRefMenu = []
for peakDim in range(0, len(peakChemShiftRange)):
row = row + 1
label = Label(master, text=str(peakDim))
label.grid(row=row, column=0, sticky=Tkinter.EW)
label = Label(master,
text="%.3f - %.3f %s" %
(peakChemShiftRange[peakDim][0],
peakChemShiftRange[peakDim][1], peakUnit))
label.grid(row=row, column=1, sticky=Tkinter.EW)
if peakDim < len(dataDimRefList):
selectedIndex = dataDimRefList.index(
dataDimRefSelection[peakDim])
else:
selectedIndex = len(dataDimRefList) - 1
self.dataDimRefMenu.append(
PulldownMenu(master,
entries=dataDimRefList,
selected_index=selectedIndex))
self.dataDimRefMenu[-1].grid(row=row,
column=2,
sticky=Tkinter.E,
ipadx=20)
row = row + 1
texts = ['OK']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=3)
def body(self, master):
#
# Setup header
#
row = 0
label = Label(master, text="Data model", fg='blue')
label.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
label = Label(master, text="Export")
label.grid(row=row, column=3, columnspan=2, sticky=Tkinter.EW)
row += 1
label = Label(master, text="Sequence ID (code)", fg='blue')
label.grid(row=row, column=1, columnspan=2, sticky=Tkinter.EW)
row += 1
label = Label(master, text="Ccp chain code", fg='blue')
label.grid(row=row, column=0, sticky=Tkinter.W)
label = Label(master, text="start", fg='blue')
label.grid(row=row, column=1, sticky=Tkinter.EW)
label = Label(master, text="end", fg='blue')
label.grid(row=row, column=2, sticky=Tkinter.EW)
column = 3
columnspan = 2
if self.requireChainCode:
label = Label(master, text=self.requireChainCode)
label.grid(row=row, column=column, sticky=Tkinter.W)
column += 1
columnspan -= 1
label = Label(master, text="Sequence code start")
label.grid(row=row,
column=column,
columnspan=columnspan,
sticky=Tkinter.W)
#
# Setup list of ccp chains labels
#
ccpChainLabels = self.ccpChainLabelDict.keys()
ccpChainLabels.sort()
#
# Currently only linking start in ccp chain (ONLY ONE!) to start in chain read in from file
# Assuming sequential order thereafter.
#
for ccpChainLabel in ccpChainLabels:
row = row + 1
chain = self.ccpChainLabelDict[ccpChainLabel]
ccpCodeLow = "%d (%d)" % (
self.ccpChainSeqIDCodes[ccpChainLabel][0][0],
self.ccpChainSeqIDCodes[ccpChainLabel][1][0])
ccpCodeHigh = "%d (%d)" % (
self.ccpChainSeqIDCodes[ccpChainLabel][0][-1],
self.ccpChainSeqIDCodes[ccpChainLabel][1][-1])
label = Label(master, text=ccpChainLabel, fg='blue')
label.grid(row=row, column=0, sticky=Tkinter.W)
label = Label(master, text=ccpCodeLow, fg='blue')
label.grid(row=row, column=1, sticky=Tkinter.W)
label = Label(master, text=ccpCodeHigh, fg='blue')
label.grid(row=row, column=2, sticky=Tkinter.W)
column = 3
columnspan = 2
suggestedFirstSeqCode = str(
self.ccpChainSeqIDCodes[ccpChainLabel][1][0])
if self.requireChainCode:
if self.requireChainCode == 'molecule name':
chainCodeText = chain.molecule.name
width = 20
else:
chainCodeText = chain.code
width = 4
self.exportChainCode[chain] = Entry(master,
text=chainCodeText,
width=width)
self.exportChainCode[chain].grid(row=row,
column=column,
sticky=Tkinter.W)
column += 1
columnspan -= 1
suggestedFirstSeqCode = '1'
self.exportFirstSeqCode[chain] = Entry(master,
text=suggestedFirstSeqCode,
width=4)
self.exportFirstSeqCode[chain].grid(row=row,
column=column,
columnspan=columnspan,
sticky=Tkinter.W)
row = row + 1
texts = ['OK']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=4)
def body(self, master):
#
# Initialize
#
#
# Make expDimRef lists
#
expDimRefList = []
self.expDimRefDict = {}
expDimRefSelection = {}
for expDim in self.experiment.sortedExpDims():
if expDim.dim == 1:
addInfo = " (acqu)"
else:
addInfo = ""
for expDimRef in expDim.expDimRefs:
isotopeString = string.join(expDimRef.isotopeCodes, dirsep)
selectionString = "Dim %d, nucl %s %s" % (
expDim.dim, isotopeString, addInfo)
expDimRefList.append(selectionString)
self.expDimRefDict[selectionString] = expDimRef
expDimRefSelection[expDimRef] = len(expDimRefList) - 1
#
# Popup info
#
#
# Header labels
#
columnspan = 4
row = 0
if self.fPars.has_key('inputFile'):
text = "Processing file %s" % (self.fPars['inputFile'])
else:
text = "Processing experiment %s" % (self.experiment.name)
label = Label(master, text=text)
label.grid(row=row, column=0, columnspan=columnspan, sticky=Tkinter.EW)
row += 1
label = Label(master, text="NumPoints")
label.grid(row=row, column=0, sticky=Tkinter.EW)
label = Label(master, text="SW")
label.grid(row=row, column=1, sticky=Tkinter.EW)
label = Label(master, text="Isotope")
label.grid(row=row, column=2, sticky=Tkinter.EW)
label = Label(master, text="ExpDimRef selection")
label.grid(row=row, column=3, sticky=Tkinter.EW)
#
# Selection per dimension from the procpar file
#
self.expDimRefMenu = []
for dim in range(0, len(self.fPars['nucleus'])):
row = row + 1
label = Label(master, text=str(self.fPars['numPoints'][dim]))
label.grid(row=row, column=0, sticky=Tkinter.EW)
label = Label(master,
text="%.1f" % self.fPars['spectralWidth'][dim])
label.grid(row=row, column=1, sticky=Tkinter.EW)
label = Label(master, text=self.fPars['nucleus'][dim])
label.grid(row=row, column=2, sticky=Tkinter.EW)
expDimRef = self.linkDict[dim]
selectedIndex = expDimRefSelection[expDimRef]
self.expDimRefMenu.append(
PulldownMenu(master,
entries=expDimRefList,
selected_index=selectedIndex))
self.expDimRefMenu[-1].grid(row=row,
column=3,
sticky=Tkinter.E,
ipadx=20)
row = row + 1
texts = ['OK']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=columnspan)
def body(self, master):
#
# Initialize
#
contentList = []
for (fullName, attrName, func) in self.columnContents:
contentList.append(fullName)
#
# Popup info
#
#
# Header labels
#
row = 0
label = Label(master, text="Column number")
label.grid(row=row, column=0, sticky=Tkinter.EW)
label = Label(master, text="Column data range")
label.grid(row=row, column=1, sticky=Tkinter.EW)
label = Label(master, text="Column content selection")
label.grid(row=row, column=2, sticky=Tkinter.EW)
#
# Selection per column
#
self.columnInfoWidgets = []
for colIndex in range(0, self.columnLen):
row = row + 1
label = Label(master, text=str(colIndex + 1))
label.grid(row=row, column=0, sticky=Tkinter.EW)
label = Label(master,
text="%s - %s" % (str(self.columnData[colIndex][0]),
str(self.columnData[colIndex][1])))
label.grid(row=row, column=1, sticky=Tkinter.EW)
self.columnInfoWidgets.append(
PulldownMenu(master, entries=contentList))
self.columnInfoWidgets[-1].grid(row=row,
column=2,
sticky=Tkinter.W,
ipadx=20)
row = row + 1
texts = ['OK']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=3)