def body(self, guiFrame):
'''Describes where all the GUI element are.'''
self.geometry('400x500')
guiFrame.expandGrid(0, 0)
tableFrame = Frame(guiFrame)
tableFrame.grid(
row=0,
column=0,
sticky='nsew',
)
tableFrame.expandGrid(0, 0)
buttonFrame = Frame(guiFrame)
buttonFrame.grid(
row=1,
column=0,
sticky='nsew',
)
headingList = ['Spinsystem Number', 'Assignment', 'Residue Type Probs']
self.table = ScrolledMatrix(tableFrame,
headingList=headingList,
callback=self.updateSpinSystemSelection,
multiSelect=True)
self.table.grid(row=0, column=0, sticky='nsew')
texts = ['Add Prob']
commands = [self.addProb]
self.AddProbButton = ButtonList(buttonFrame,
commands=commands,
texts=texts)
self.AddProbButton.grid(row=0, column=0, sticky='nsew')
texts = ['Remove Prob']
commands = [self.removeProb]
self.AddProbButton = ButtonList(buttonFrame,
commands=commands,
texts=texts)
self.AddProbButton.grid(row=0, column=2, sticky='nsew')
selectCcpCodes = sorted(self.chemCompDict.keys())
tipText = 'select ccpCode'
self.selectCcpCodePulldown = PulldownList(buttonFrame,
texts=selectCcpCodes,
grid=(0, 1),
tipText=tipText)
selectCcpCodes = ['All Residue Types']
tipText = 'select ccpCode'
self.selectCcpCodeRemovePulldown = PulldownList(buttonFrame,
texts=selectCcpCodes,
index=0,
grid=(0, 3),
tipText=tipText)
self.updateTable()
def body(self, guiFrame):
'''Describes where all the GUI element are.'''
self.geometry('400x500')
guiFrame.expandGrid(0, 0)
tableFrame = Frame(guiFrame)
tableFrame.grid(row=0, column=0, sticky='nsew', )
tableFrame.expandGrid(0, 0)
buttonFrame = Frame(guiFrame)
buttonFrame.grid(row=1, column=0, sticky='nsew', )
headingList = ['Spinsystem Number', 'Assignment', 'Residue Type Probs']
self.table = ScrolledMatrix(tableFrame, headingList=headingList,
callback=self.updateSpinSystemSelection,
multiSelect=True)
self.table.grid(row=0, column=0, sticky='nsew')
texts = ['Add Prob']
commands = [self.addProb]
self.AddProbButton = ButtonList(buttonFrame, commands=commands,
texts=texts)
self.AddProbButton.grid(row=0, column=0, sticky='nsew')
texts = ['Remove Prob']
commands = [self.removeProb]
self.AddProbButton = ButtonList(buttonFrame, commands=commands,
texts=texts)
self.AddProbButton.grid(row=0, column=2, sticky='nsew')
selectCcpCodes = sorted(self.chemCompDict.keys())
tipText = 'select ccpCode'
self.selectCcpCodePulldown = PulldownList(buttonFrame,
texts=selectCcpCodes,
grid=(0, 1),
tipText=tipText)
selectCcpCodes = ['All Residue Types']
tipText = 'select ccpCode'
self.selectCcpCodeRemovePulldown = PulldownList(buttonFrame,
texts=selectCcpCodes,
index=0,
grid=(0, 3),
tipText=tipText)
self.updateTable()
def body(self, guiFrame):
self.geometry("500x500")
self.nameEntry = Entry(self, text='', returnCallback=self.setName, width=12)
self.detailsEntry = Entry(self, text='', returnCallback=self.setDetails, width=16)
self.valueEntry = FloatEntry(self, text='', returnCallback=self.setValue, width=10)
self.errorEntry = FloatEntry(self, text='', returnCallback=self.setError, width=8)
self.conditionNamesPulldown = PulldownList(self, callback=self.setConditionName,
texts=self.getConditionNames())
self.unitPulldown = PulldownList(self, callback=self.setUnit,
texts=self.getUnits())
self.experimentPulldown = PulldownList(self, callback=self.setExperiment)
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame = Frame(guiFrame, grid=(row, 0))
frame.expandGrid(None,0)
div = LabelDivider(frame, text='Current Series', grid=(0, 0))
utilButtons = UtilityButtonList(frame, helpUrl=self.help_url, grid=(0,1))
row += 1
frame0 = Frame(guiFrame, grid=(row, 0))
frame0.expandGrid(0,0)
tipTexts = ['The serial number of the experiment series, but left blank if the series as actually a pseudo-nD experiment (with a sampled non-frequency axis)',
'The name of the experiment series, which may be a single pseudo-nD experiment',
'The number of separate experiments (and hence spectra) present in the series',
'The kind of quantity that varies for different experiments/planes within the NMR series, e.g. delay time, temperature, ligand concentration etc.',
'The number of separate points, each with a separate experiment/plane and parameter value, in the series']
headingList = ['#','Name','Experiments','Parameter\nVaried','Num\nPoints']
editWidgets = [None, self.nameEntry, None, self.conditionNamesPulldown, None]
editGetCallbacks = [None, self.getName, None, self.getConditionName, None]
editSetCallbacks = [None, self.setName, None, self.setConditionName, None]
self.seriesMatrix = ScrolledMatrix(frame0, tipTexts=tipTexts,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=headingList,
callback=self.selectExpSeries,
deleteFunc=self.deleteExpSeries,
grid=(0,0), gridSpan=(None, 3))
tipTexts = ['Make a new, blank NMR series specification in the CCPN project',
'Delete the selected NMR series from the project, although any component experiments remain. Note you cannot delete pseudo-nD series; delete the actual experiment instead',
'Colour the spectrum contours for each experiment in the selected series (not pseudo-nD) using a specified scheme']
texts = ['Add Series','Delete Series',
'Auto Colour Spectra']
commands = [self.addExpSeries,self.deleteExpSeries,
self.autoColorSpectra]
self.seriesButtons = ButtonList(frame0, texts=texts, commands=commands,
grid=(1,0), tipTexts=tipTexts)
label = Label(frame0, text='Scheme:', grid=(1,1))
tipText = 'Selects which colour scheme to apply to the contours of (separate) experiments within an NMR series'
self.colorSchemePulldown = PulldownList(frame0, grid=(1,2), tipText=tipText)
row += 1
div = LabelDivider(guiFrame, text='Experimental Parameters & Conditions', grid=(row, 0))
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame1 = Frame(guiFrame, grid=(row, 0))
frame1.expandGrid(0,0)
tipTexts = ['The kind of experimental parameter that is being used to define the NMR series',
'The experiment that corresponds to the specified parameter value; can be edited from an arbitrary initial experiment',
'The numeric value of the parameter (condition) that relates to the experiment or point in the NMR series',
'The estimated error in value of the condition',
'The measurement unit in which the value of the condition is represented']
headingList = ['Parameter','Experiment','Value','Error','Unit']
editWidgets = [None,self.experimentPulldown,self.valueEntry,self.errorEntry, self.unitPulldown]
editGetCallbacks = [None,self.getExperiment, self.getValue, self.getError, self.getUnit]
editSetCallbacks = [None,self.setExperiment, self.setValue, self.setError, self.setUnit]
self.conditionPointsMatrix = ScrolledMatrix(frame1, grid=(0,0), tipTexts=tipTexts,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=headingList,
callback=self.selectConditionPoint,
deleteFunc=self.deleteConditionPoint)
self.conditionPointsMatrix.doEditMarkExtraRules = self.conditionTableShow
tipTexts = ['Add a new point to the NMR series with an associated parameter value and experiment',
'Remove the selected point from the series, including any associated parameter value',
'For appropriate kinds of NMR series, set or unset a point as representing the plane to use as a reference']
texts = ['Add Series Point','Delete Series Point','Set/Unset Ref Plane']
commands = [self.addConditionPoint,self.deleteConditionPoint,self.setSampledReferencePlane]
self.conditionPointsButtons = ButtonList(frame1, texts=texts, commands=commands,
tipTexts=tipTexts, grid=(1,0))
self.updateAfter()
self.updateColorSchemes()
self.administerNotifiers(self.registerNotify)
def __init__(self,
parent,
file_types=None,
directory=None,
single_callback=None,
double_callback=None,
select_dir_callback=None,
change_dir_callback=None,
should_change_dir_callback=None,
prompt=None,
show_file=True,
file='',
multiSelect=False,
default_dir=None,
getRowColor=None,
getExtraCell=None,
extraHeadings=None,
extraJustifies=None,
displayExtra=True,
manualFileFilter=False,
extraTipTexts=None,
*args,
**kw):
if file_types is None:
file_types = [FileType("All", ["*"])]
if manualFileFilter:
self.manualFilter = FileType("Manual")
file_types.append(self.manualFilter)
else:
self.manualFilter = None
if directory is None:
directory = normalisePath(os.getcwd())
if extraHeadings is None:
extraHeadings = ()
else:
extraHeadings = tuple(extraHeadings)
if extraJustifies is None:
extraJustifies = ()
else:
extraJustifies = tuple(extraJustifies)
if extraHeadings or extraJustifies:
assert len(extraHeadings) == len(extraJustifies)
assert getExtraCell
self.extraHeadings = extraHeadings
self.extraJustifies = extraJustifies
self.extraTipTexts = extraTipTexts or []
self.displayExtra = displayExtra
Frame.__init__(self, parent, *args, **kw)
self.file_types = file_types
self.fileType = file_types[0]
self.single_callback = single_callback
self.double_callback = double_callback
self.select_dir_callback = select_dir_callback
self.change_dir_callback = change_dir_callback
self.should_change_dir_callback = should_change_dir_callback
self.show_file = show_file
self.directory = None
self.historyBack = []
self.historyFwd = []
self.determineDir(directory)
self.default_dir = default_dir
self.getRowColor = getRowColor
self.getExtraCell = getExtraCell
self.grid_columnconfigure(0, weight=1)
row = 0
if prompt:
label = Label(self, text=prompt, grid=(row, 0))
row += 1
self.grid_rowconfigure(row, weight=1)
if show_file:
headings = ('Name', 'Size', 'Date')
justifies = ('left', 'right', 'right')
tipTexts = [
'Name of file, directory or link', 'Size of file in bytes',
'Date of last modification'
]
else:
headings = ('Directory', )
justifies = ('left', )
tipTexts = ['Name of directory']
self.normalHeadings = headings
self.normalJustifies = justifies
self.normalTipTexts = tipTexts
headings = headings + extraHeadings
justifies = justifies + extraJustifies
tipTexts += [None] * len(extraHeadings)
self.fileList = ScrolledMatrix(self,
headingList=headings,
justifyList=justifies,
initialRows=10,
callback=self.singleCallback,
doubleCallback=self.doubleCallback,
tipTexts=tipTexts,
multiSelect=multiSelect,
grid=(row, 0))
row += 1
tipTexts = [
'Go to previous location in history',
'Go forward in location history', 'Go up one directory level',
'Go to root directory', 'Go to home directory',
'Make a new directory', 'Refresh directory listing'
]
texts = ['Back', 'Forward', 'Up', 'Top', 'Home', 'New', 'Refresh']
commands = [
self.backDir, self.fwdDir, self.upDir, self.topDir, self.homeDir,
self.createDir, self.updateFileList
]
if self.default_dir:
texts.append('Default')
commands.append(self.setDefaultDir)
tipTexts.append('Set the current directory as the default')
self.icons = []
for name in ICON_NAMES:
icon = Tkinter.PhotoImage(
file=os.path.join(GFX_DIR, name + '.gif'))
self.icons.append(icon)
self.buttons = ButtonList(self,
texts=texts,
commands=commands,
images=self.icons,
grid=(row, 0),
tipTexts=tipTexts)
if show_file:
row += 1
self.file_entry = LabeledEntry(self,
label='File name',
label_width=10,
entry_width=40,
returnCallback=self.setSelectedFile)
self.file_entry.grid(row=row, column=0, sticky=Tkinter.EW)
else:
self.file_entry = None
row += 1
self.directory_entry = LabeledEntry(self,
label='Directory',
entry=directory,
label_width=10,
entry_width=40,
returnCallback=self.entryDir)
self.directory_entry.grid(row=row, column=0, sticky=Tkinter.EW)
row += 1
subFrame = Frame(self, grid=(row, 0))
subFrame.expandGrid(None, 6)
if show_file:
label = Label(subFrame, text='File type:', grid=(0, 0))
type_labels = self.determineTypeLabels()
self.fileType_menu = PulldownList(
subFrame,
callback=self.typeCallback,
texts=type_labels,
objects=self.file_types,
grid=(0, 1),
tipText='Restrict listed files to selected suffix')
label = Label(subFrame, text=' Show hidden:', grid=(0, 2))
self.hidden_checkbutton = CheckButton(
subFrame,
text='',
selected=False,
callback=self.updateFileList,
grid=(0, 3),
tipText='Show hidden files beginning with "." etc.')
label = Label(subFrame, text='Dir path:', grid=(0, 4))
self.pathMenu = PulldownList(
subFrame,
callback=self.dirCallback,
objects=range(len(self.dirs)),
texts=self.dirs,
index=len(self.dirs) - 1,
indent=' ',
prefix=dirsep,
grid=(0, 5),
tipText='Directory navigation to current location')
if show_file and self.manualFilter is not None:
row += 1
self.manual_filter_entry = LabeledEntry(
self,
label='Manual Select',
entry=defaultFilter,
label_width=13,
entry_width=40,
returnCallback=self.entryFilter,
tipText=
'Path specification with wildcards to select multiple files')
self.manual_filter_entry.grid(row=row, column=0, sticky=Tkinter.EW)
self.updateFileList()
self.updateButtons()
if file:
self.setFile(file)
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 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)
def __init__(self, parent, application, *args, **kw):
project = application.project
simStore = project.findFirstNmrSimStore(application=APP_NAME) or \
project.newNmrSimStore(application=APP_NAME, name=APP_NAME)
self.application = application
self.residue = None
self.structure = None
self.serverCredentials = None
self.iCingBaseUrl = DEFAULT_URL
self.resultsUrl = None
self.chain = None
self.nmrProject = application.nmrProject
self.serverDone = False
NmrSimRunFrame.__init__(self, parent, project, simStore, *args, **kw)
# # # # # # New Structure Frame # # # # #
self.structureFrame.grid_forget()
tab = self.tabbedFrame.frames[0]
frame = Frame(tab, grid=(1,0))
frame.expandGrid(2,1)
div = LabelDivider(frame, text='Structures', grid=(0,0), gridSpan=(1,2))
label = Label(frame, text='Ensemble: ', grid=(1,0))
self.structurePulldown = PulldownList(frame, callback=self.changeStructure, grid=(1,1))
headingList = ['Model','Use']
editWidgets = [None,None]
editGetCallbacks = [None,self.toggleModel]
editSetCallbacks = [None,None,]
self.modelTable = ScrolledMatrix(frame, grid=(2,0), gridSpan=(1,2),
callback=self.selectStructModel,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
headingList=headingList)
texts = ['Activate Selected','Inactivate Selected']
commands = [self.activateModels, self.disableModels]
buttons = ButtonList(frame, texts=texts, commands=commands, grid=(3,0), gridSpan=(1,2))
# # # # # # Submission frame # # # # # #
tab = self.tabbedFrame.frames[1]
tab.expandGrid(1,0)
frame = LabelFrame(tab, text='Server Job Submission', grid=(0,0))
frame.expandGrid(None,2)
srow = 0
label = Label(frame, text='iCing URL:', grid=(srow, 0))
urls = [DEFAULT_URL,]
self.iCingBaseUrlPulldown = PulldownList(frame, texts=urls, objects=urls, index=0, grid=(srow,1))
srow +=1
label = Label(frame, text='Results File:', grid=(srow, 0))
self.resultFileEntry = Entry(frame, bd=1, text='', grid=(srow,1), width=50)
self.setZipFileName()
button = Button(frame, text='Choose File', bd=1, sticky='ew',
command=self.chooseZipFile, grid=(srow, 2))
srow +=1
label = Label(frame, text='Results URL:', grid=(srow, 0))
self.resultUrlEntry = Entry(frame, bd=1, text='', grid=(srow,1), width=50)
button = Button(frame, text='View Results HTML', bd=1, sticky='ew',
command=self.viewHtmlResults, grid=(srow, 2))
srow +=1
texts = ['Submit Project!', 'Check Run Status',
'Purge Server Result', 'Download Results']
commands = [self.runCingServer, self.checkStatus,
self.purgeCingServer, self.downloadResults]
self.buttonBar = ButtonList(frame, texts=texts, commands=commands,
grid=(srow, 0), gridSpan=(1,3))
for button in self.buttonBar.buttons[:1]:
button.config(bg=CING_BLUE)
# # # # # # Residue frame # # # # # #
frame = LabelFrame(tab, text='Residue Options', grid=(1,0))
frame.expandGrid(1,1)
label = Label(frame, text='Chain: ')
label.grid(row=0,column=0,sticky='w')
self.chainPulldown = PulldownList(frame, callback=self.changeChain)
self.chainPulldown.grid(row=0,column=1,sticky='w')
headingList = ['#','Residue','Linking','Decriptor','Use?']
editWidgets = [None,None,None,None,None]
editGetCallbacks = [None,None,None,None,self.toggleResidue]
editSetCallbacks = [None,None,None,None,None,]
self.residueMatrix = ScrolledMatrix(frame,
headingList=headingList,
multiSelect=True,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
callback=self.selectResidue)
self.residueMatrix.grid(row=1, column=0, columnspan=2, sticky = 'nsew')
texts = ['Activate Selected','Inactivate Selected']
commands = [self.activateResidues, self.deactivateResidues]
self.resButtons = ButtonList(frame, texts=texts, commands=commands,)
self.resButtons.grid(row=2, column=0, columnspan=2, sticky='ew')
"""
# # # # # # Validate frame # # # # # #
frame = LabelFrame(tab, text='Validation Options', grid=(2,0))
frame.expandGrid(None,2)
srow = 0
self.selectCheckAssign = CheckButton(frame)
self.selectCheckAssign.grid(row=srow, column=0,sticky='nw' )
self.selectCheckAssign.set(True)
label = Label(frame, text='Assignments and shifts')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckResraint = CheckButton(frame)
self.selectCheckResraint.grid(row=srow, column=0,sticky='nw' )
self.selectCheckResraint.set(True)
label = Label(frame, text='Restraints')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckQueen = CheckButton(frame)
self.selectCheckQueen.grid(row=srow, column=0,sticky='nw' )
self.selectCheckQueen.set(False)
label = Label(frame, text='QUEEN')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckScript = CheckButton(frame)
self.selectCheckScript.grid(row=srow, column=0,sticky='nw' )
self.selectCheckScript.set(False)
label = Label(frame, text='User Python script\n(overriding option)')
label.grid(row=srow,column=1,sticky='nw')
self.validScriptEntry = Entry(frame, bd=1, text='')
self.validScriptEntry.grid(row=srow,column=2,sticky='ew')
scriptButton = Button(frame, bd=1,
command=self.chooseValidScript,
text='Browse')
scriptButton.grid(row=srow,column=3,sticky='ew')
"""
# # # # # # # # # #
self.update(simStore)
self.administerNotifiers(application.registerNotify)
def body(self, guiFrame):
self.geometry('550x600')
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame = Frame(guiFrame, grid=(row, 0))
frame.expandGrid(0, 4)
label = Label(frame, text='Peak List:', grid=(0, 0))
tipText = 'For spectra with (mostly) one peak per residue, selects which peak list to initialise; by adding anonymous resonance and spin system numbers'
self.peakListPulldown = PulldownList(frame,
self.changePeakList,
grid=(0, 1),
tipText=tipText)
label = Label(frame, text='15N tolerance (ppm):', grid=(0, 2))
tipText = 'The upper limit in the difference between 15N ppm positions for two peaks to be considered as a potential amide'
self.tolEntry = FloatEntry(frame,
text=0.02,
width=8,
grid=(0, 3),
sticky='ew',
tipText=tipText)
frame2 = Frame(frame, grid=(1, 0), gridSpan=(1, 4), sticky='ew')
frame2.grid_columnconfigure(5, weight=1)
label = Label(frame2, text='Follow Amides:', grid=(0, 0))
tipText = 'Sets whether to follow the H-N locations of potential amide peaks when clicking in rows of the table'
self.followSelect = CheckButton(frame2,
callback=None,
grid=(0, 1),
selected=True,
tipText=tipText)
self.windowLabel = Label(frame2, text='Window:', grid=(0, 2))
tipText = 'Selects the spectrum window in which to show positions of potential amide peaks'
self.windowPulldown = PulldownList(frame2,
self.selectWindowPane,
grid=(0, 3),
tipText=tipText)
label = Label(frame2, text='Mark Amides:', grid=(0, 4))
tipText = 'Whether to put a multi-dimensional cross mark though the H-N positions of the selected peak pair'
self.markSelect = CheckButton(frame2,
callback=None,
grid=(0, 5),
selected=True,
tipText=tipText)
utilButtons = UtilityButtonList(guiFrame,
grid=(row, 1),
sticky='ne',
helpUrl=self.help_url)
row += 1
tipTexts = [
'For the stated peak list, considering confirmed amide side chain peaks, add spin system and resonance numbers to all peaks',
]
commands = [
self.initialisePeakList,
]
texts = [
'Initialise Peak List!',
]
self.initButtons = ButtonList(guiFrame,
commands=commands,
grid=(row, 0),
texts=texts,
gridSpan=(1, 2),
tipTexts=tipTexts)
self.initButtons.buttons[0].config(bg='#B0FFB0')
row += 1
div = LabelDivider(guiFrame,
text='Amide Side Chain Peaks',
gridSpan=(1, 2),
grid=(row, 0))
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame = Frame(guiFrame, gridSpan=(1, 2), grid=(row, 0))
frame.expandGrid(0, 0)
editSetCallbacks = [None] * 8
editGetCallbacks = [None] * 8
editWidgets = [None] * 8
editGetCallbacks[1] = self.toggleConfirm
#self.userCodeEntry = Entry(self,text='', returnCallback=self.setResidueCode, width=6)
tipTexts = [
'Number of the peak pair for the table',
'Whether the peak pair is confirmed as being from an amide side chain; a common nitrogen by different hydrogens',
'The difference in 15N ppm position between the two peaks of the pair',
'The assignment annotation of the first peak in the pair',
'The assignment annotation of the second peak in the pair',
'The average 15N position of the peaks in the pair',
'The 1H chemical shift of the first peak in the pair',
'The 1H chemical shift of the second peak in the pair'
]
headingList = [
'#', 'Confirmed?', u'15N\n\u0394ppm', 'Peak 1', 'Peak 2',
'Shift N', 'Shift H1', 'Shift H2'
]
self.amidePairMatrix = ScrolledMatrix(
frame,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=self.selectAmidePair,
multiSelect=True,
grid=(0, 0),
tipTexts=tipTexts)
tipTexts = [
'Confirm the selected peak pairs as being amide side chain peaks; a common nitrogen by different hydrogens',
'remove any conformation for the selected peak pairs being amide side chain peaks',
'Manually force an update the table of potential pairs of amide side chain peaks'
]
commands = [
self.confirmAmidePairs, self.unconfirmAmidePairs,
self.predictAmidePairs
]
texts = ['Confirm\nSelected', 'Unconfirm\nSelected', 'Update\nTable']
self.amideButtons = ButtonList(frame,
texts=texts,
commands=commands,
grid=(1, 0),
tipTexts=tipTexts)
self.updatePeakLists()
self.administerNotifiers(self.registerNotify)
def body(self, guiFrame):
row = 0
frame = Frame(guiFrame, grid=(row, 0))
frame.expandGrid(None, 6)
label = Label(frame, text='Chain:', grid=(0, 0))
tipText = 'Selects which molecular chain to show residues and chemical shift values for'
self.chainPulldown = PulldownList(frame,
callback=self.changeChain,
grid=(0, 1),
tipText=tipText)
label = Label(frame, text=' Shift List:', grid=(0, 2))
tipText = 'Selects which shift list is used to derive the displayed chemical shift values'
self.shiftListPulldown = PulldownList(frame,
callback=self.changeShiftList,
grid=(0, 3),
tipText=tipText)
label = Label(frame, text=' List all shifts:', grid=(0, 4))
tipText = 'Sets whether to display all the chemical shifts for residues or just for the nominated atom types in columns'
self.otherShiftsSelect = CheckButton(frame,
callback=self.draw,
grid=(0, 5),
tipText=tipText)
utilButtons = UtilityButtonList(frame,
helpUrl=self.help_url,
grid=(0, 7))
row += 1
frame = Frame(guiFrame, grid=(row, 0))
frame.expandGrid(None, 6)
label = Label(frame, text=' 1-letter codes:', grid=(0, 0))
tipText = 'Whether to use 1-letter residue codes in the table, or otherwise Ccp/three-letter codes'
self.oneLetterSelect = CheckButton(frame,
callback=self.draw,
grid=(0, 1),
selected=False,
tipText=tipText)
precisions = [0.1, 0.01, 0.001]
texts = [str(t) for t in precisions]
label = Label(frame, text=' 1H precision:', grid=(0, 2))
tipText = 'Specifies how many decimal places to use when displaying 1H chemical shift values'
self.protonPrecisionSelect = PulldownList(frame,
texts=texts,
objects=precisions,
callback=self.draw,
index=1,
grid=(0, 3),
tipText=tipText)
label = Label(frame, text=' Other precision:')
label.grid(row=0, column=4, sticky='w')
tipText = 'Specifies how many decimal places to use when displaying chemical shift values for isotopes other than 1H'
self.otherPrecisionSelect = PulldownList(frame,
texts=texts,
objects=precisions,
callback=self.draw,
index=1,
grid=(0, 5),
tipText=tipText)
row += 1
frame = Frame(guiFrame, grid=(row, 0))
frame.expandGrid(None, 1)
label = Label(frame, text='Column\nAtoms:', grid=(0, 0))
tipText = 'Selects which kinds of atoms are displayed in aligned columns, or otherwise displayed at the end of the residue row (if "List all shifts" is set)'
self.optSelector = PartitionedSelector(frame,
self.toggleOpt,
tipText=tipText,
maxRowObjects=10,
grid=(0, 1),
sticky='ew')
options = ['H', 'N', 'C', 'CA', 'CB', 'CG']
self.optSelector.update(objects=options,
labels=options,
selected=['H', 'N', 'CA'])
row += 1
guiFrame.expandGrid(row, 0)
self.canvasFrame = ScrolledCanvas(guiFrame,
relief='groove',
width=650,
borderwidth=2,
resizeCallback=None,
grid=(row, 0),
padx=1,
pady=1)
self.canvas = self.canvasFrame.canvas
#self.canvas.bind('<Button-1>', self.toggleResidue)
row += 1
tipTexts = [
'Output information from the table as PostScript file, for printing etc.',
'Output information from the table as a whitespace separated plain text file'
]
commands = [self.makePostScript, self.exportText]
texts = ['Export PostScript', 'Export Text']
buttonList = ButtonList(guiFrame,
commands=commands,
texts=texts,
grid=(row, 0),
tipTexts=tipTexts)
chains = self.getChains()
if len(chains) > 1:
self.chain = chains[1]
else:
self.chain = None
self.updateShiftLists()
self.updateChains()
self.otherShiftsSelect.set(True)
self.update()
for func in ('__init__', 'delete'):
self.registerNotify(self.updateChains,
'ccp.molecule.MolSystem.Chain', func)
for func in ('__init__', 'delete'):
self.registerNotify(self.updateShiftLists, 'ccp.nmr.Nmr.ShiftList',
func)
def __init__(self, parent, file_types = None, directory = None,
single_callback = None, double_callback = None,
prompt = None, show_file = True, file = '', multiSelect=False,
default_dir = None, getRowColor = None,
getExtraCell = None, extraHeadings = None, extraJustifies = None,
displayExtra = True, *args, **kw):
if file_types is None:
file_types = [ FileType("All", ["*"]) ]
if directory is None:
directory = normalisePath(os.getcwd())
if extraHeadings is None:
extraHeadings = ()
else:
extraHeadings = tuple(extraHeadings)
if extraJustifies is None:
extraJustifies = ()
else:
extraJustifies = tuple(extraJustifies)
if extraHeadings or extraJustifies:
assert len(extraHeadings) == len(extraJustifies)
assert getExtraCell
self.extraHeadings = extraHeadings
self.extraJustifies = extraJustifies
self.displayExtra = displayExtra
Frame.__init__(self, parent, *args, **kw)
self.file_types = file_types
self.fileType = file_types[0]
self.single_callback = single_callback
self.double_callback = double_callback
self.show_file = show_file
self.directory = None
self.historyBack = []
self.historyFwd = []
self.determineDir(directory)
self.default_dir = default_dir
self.getRowColor = getRowColor
self.getExtraCell = getExtraCell
self.grid_columnconfigure(0, weight=1)
row = 0
if prompt:
label = Label(self, text=prompt, grid=(row,0))
row += 1
self.grid_rowconfigure(row, weight=1)
if show_file:
headings = ('Name', 'Size', 'Date')
justifies = ('left','right','right')
else:
headings = ('Directory',)
justifies = ('left',)
self.normalHeadings = headings
self.normalJustifies = justifies
headings = headings + extraHeadings
justifies = justifies + extraJustifies
self.fileList = ScrolledMatrix(self, headingList=headings, justifyList=justifies,
initialRows=10, callback=self.singleCallback,
doubleCallback=self.doubleCallback,
multiSelect=multiSelect, grid=(row,0))
row += 1
texts = ['Back', 'Up', 'Forward', 'Top', 'Home', 'New', 'Refresh']
commands = [self.backDir, self.fwdDir, self.upDir, self.topDir,
self.homeDir, self.createDir, self.updateFileList ]
if self.default_dir:
texts.append('Default')
commands.append(self.setDefaultDir)
self.icons = []
for name in ICON_NAMES:
icon = Tkinter.PhotoImage(file=os.path.join(GFX_DIR,name+'.gif'))
self.icons.append(icon)
self.buttons = ButtonList(self, texts=texts, commands=commands,
images=self.icons, grid=(row,0))
if show_file:
row += 1
self.file_entry = LabeledEntry(self, label='File name',
label_width=10, entry_width=40,
returnCallback=self.setSelectedFile)
self.file_entry.grid(row=row, column=0, sticky=Tkinter.EW)
else:
self.file_entry = None
row += 1
self.directory_entry = LabeledEntry(self, label='Directory',
entry = directory,
label_width=10, entry_width=40,
returnCallback=self.entryDir)
self.directory_entry.grid(row=row, column=0, sticky=Tkinter.EW)
row += 1
subFrame = Frame(self, grid=(row,0))
subFrame.expandGrid(None,6)
if show_file:
label = Label(subFrame, text='File type:', grid=(0,0))
type_labels = self.determineTypeLabels()
self.fileType_menu = PulldownList(subFrame, callback=self.typeCallback,
texts=type_labels, objects=self.file_types,
grid=(0,1))
label = Label(subFrame, text=' Show hidden:', grid=(0,2))
self.hidden_checkbutton = CheckButton(subFrame, text='', selected=False,
callback=self.updateFileList, grid=(0,3))
label = Label(subFrame, text='Dir path:', grid=(0,4))
self.pathMenu = PulldownList(subFrame, callback=self.dirCallback,
objects=range(len(self.dirs)),
texts=self.dirs, index=len(self.dirs)-1,
indent=' ', prefix=dirsep, grid=(0,5))
self.updateFileList()
self.updateButtons()
if file:
self.setFile(file)
def __init__(self, parent, project, calcStore, *args, **kw):
NmrCalcRunFrame.__init__(self, parent, project, calcStore,
inputTypes=(PEAK_DATA, CONSTRAINT_DATA),
chainSelection=True, *args, **kw)
self.calcStore = calcStore
self.optPeakList = None
self.optConstraintList = None
frame = self.tabbedFrame.frames[1]
headingList = ['PeakList','Filter\nViolated?',
'Keep\nAssignments?','Shift List']
editWidgets = [None, None, None, None]
editGetCallbacks = [None, self.toggleFilterViol,
self.toggleKeepAssign, None]
editSetCallbacks = [None, None, None, None]
row = 0
subFrame = Frame(frame, grid=(row,0))
subFrame.expandGrid(0,1)
label = Label(subFrame, text='File Name Prefix:', grid=(0,0))
self.filePrefixEntry = Entry(subFrame, text='aria', grid=(0,1), sticky="ew")
self.filePrefixEntry.bind('<Leave>', self.updateEntryParams)
label = Label(subFrame, text='CNS Executable:', grid=(1,0))
self.cnsExeEntry = Entry(subFrame, text='', grid=(1,1), sticky="ew")
self.cnsExeEntry.bind('<Leave>', self.updateEntryParams)
button = Button(subFrame, text='Select File',bd=1,bg='#C0E0FF',
command=self.selectCnsExe, grid=(1,2))
label = Label(subFrame, text='Working Directory:', grid=(2,0))
self.workingDirEntry = Entry(subFrame, text='', grid=(2,1), sticky="ew")
self.workingDirEntry.bind('<Leave>', self.updateEntryParams)
button = Button(subFrame, text='Select File',bd=1,bg='#C0E0FF',
command=self.selectWorkingDir, grid=(2,2))
label = Label(subFrame, text='Temporary Directory:', grid=(3,0))
self.tempDirEntry = Entry(subFrame, text='', grid=(3,1), sticky="ew")
self.tempDirEntry.bind('<Leave>', self.updateEntryParams)
button = Button(subFrame, text='Select File',bd=1,bg='#C0E0FF',
command=self.selectTempDir, grid=(3,2))
row += 1
frame.expandGrid(row,0)
self.grid_rowconfigure(row, weight=1)
self.optPeakListMatrix = ScrolledMatrix(frame, headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
multiSelect=True, grid=(row,0),
callback=self.selectOptPeakList)
row += 1
frame.expandGrid(row,0)
headingList = ['Constraint List',
'Name',
'Filter\nViolated?',
'Ambiguous\nProtocol?',]
editWidgets = [None, None, None, None]
editGetCallbacks = [None, None, self.toggleFilterViol, self.toggleAmbig]
editSetCallbacks = [None, None, None, None]
self.optConstraintMatrix = ScrolledMatrix(frame, headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
multiSelect=True, grid=(row,0),
callback=self.selectConstraintList)
self.optConstraintMatrix.doEditMarkExtraRules = self.doEditMarkExtraRules
self.update(calcStore)
def body(self, guiFrame):
self.geometry('700x600')
guiFrame.expandGrid(0, 0)
tipTexts = [
'A table of all of the reference isotope scheme definitions available to the project',
'A list of the residue isotopomers that comprise the selected isotope labelling scheme',
'A three-dimensional representation of residues and their isotopomer labelling'
]
options = ['Reference Schemes', 'Isotopomers', 'Isotopomer Structure']
tabbedFrame = TabbedFrame(guiFrame,
options=options,
grid=(0, 0),
tipTexts=tipTexts)
self.tabbedFrame = tabbedFrame
frameA, frameB, frameC = tabbedFrame.frames
#
# Schemes
#
frameA.expandGrid(0, 0)
tipTexts = [
'A short textual code that identifies the reference isotope scheme in graphical displays',
'The full name for the isotope scheme',
'A detailed description of the isotope scheme including user comments',
'The name of the CCPN data repository in which the isotope scheme is saved; "refData" is in the CCPn installation'
]
headingList = ['Code', 'Name', 'Description', 'Save Location']
self.schemeNameEntry = Entry(self,
text='',
returnCallback=self.setSchemeName,
width=20)
self.schemeDetailsEntry = Entry(self,
text='',
returnCallback=self.setSchemeDetails,
width=20)
editWidgets = [
None, self.schemeNameEntry, self.schemeDetailsEntry, None
]
editGetCallbacks = [
None, self.getSchemeName, self.getSchemeDetails, None
]
editSetCallbacks = [
None, self.setSchemeName, self.setSchemeDetails, None
]
self.schemeMatrix = ScrolledMatrix(frameA,
headingList=headingList,
callback=self.selectScheme,
editWidgets=editWidgets,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
multiSelect=False,
grid=(0, 0),
tipTexts=tipTexts)
self.schemeMatrix.doEditMarkExtraRules = self.schemeEditRules
tipTexts = [
'Make a new reference isotope scheme definition based on a copy of the scheme currently selected',
'Delete the selected isotope scheme',
'Make a new, blank isotope scheme'
]
texts = ['Copy', 'Delete', 'New']
commands = [self.copyScheme, self.removeScheme, self.makeNewScheme]
self.schemeButtons = ButtonList(frameA,
texts=texts,
commands=commands,
grid=(1, 0),
tipTexts=tipTexts)
#
# Isotopomers
#
frameB.expandGrid(3, 0)
row = 0
frame = Frame(frameB, grid=(row, 0))
frame.expandGrid(0, 2)
tipText = 'Selects which of the available isotope schemes to view/edit'
label = Label(frame, text='Reference Scheme:', grid=(0, 0))
self.schemePulldown = PulldownList(frame,
callback=self.setLabellingScheme,
grid=(0, 1),
tipText=tipText)
row += 1
div = LabelDivider(frameB, text='Isotopomers', grid=(row, 0))
row += 1
frame = Frame(frameB, grid=(row, 0))
frame.expandGrid(1, 2)
self.isotopomerFrame = frame
self.abundanceWidget = MultiWidget(self,
FloatEntry,
relief='raised',
borderwidth=2,
callback=self.setDefaultAbundances,
useImages=False)
tipText = 'Opens a panel that allows you to set the basis/default abundances for C, H & N isotopes; used as the starting point for new isotopomer definitions'
self.abundanceButton = Button(frame,
text='Set Default\nAbundances',
borderwidth=1,
command=self.enterDefaultAbundances,
grid=(0, 0),
tipText=tipText)
tipText = 'Sets the basis/default abundances for C, H & N isotopes to their natural abundance proportions'
button = Button(frame,
text='Set Natural\nAbundance Default',
borderwidth=1,
command=self.resetDefaultAbundance,
grid=(0, 1),
sticky='ew',
tipText=tipText)
label = Label(frame, text='Molecule Type:', grid=(0, 2), sticky='e')
entries = standardResidueCcpCodes.keys()
entries.sort()
entries.reverse()
tipText = 'Selects which type of bio-polymer to define residue isotopomer labelling for'
self.molTypePulldown = PulldownList(frame,
callback=self.setMolType,
texts=entries,
grid=(0, 3),
tipText=tipText)
row += 1
tipTexts = [
'The CCPN code that identifies the kind of residue the isotopomer relates to',
'The number of the particular isotopomer (isotope pattern) within its residue type',
'The fraction of the total residues, of its kind, that the isotopomer make up'
]
headingList = ['Ccp Code', 'Variant', 'Weight']
self.isotopomerWeightEntry = FloatEntry(
self, text='', returnCallback=self.setIsotopomerWeight, width=6)
editWidgets = [None, None, self.isotopomerWeightEntry]
editGetCallbacks = [None, None, self.getIsotopomerWeight]
editSetCallbacks = [None, None, self.setIsotopomerWeight]
self.isotopomerMatrix = ScrolledMatrix(
frameB,
tipTexts=tipTexts,
headingList=headingList,
callback=self.selectIsotopomer,
editWidgets=editWidgets,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
multiSelect=True,
grid=(row, 0))
self.isotopomerMatrix.doEditMarkExtraRules = self.isotopomerEditRules
row += 1
frame = Frame(frameB, grid=(row, 0), sticky='ew')
frame.expandGrid(0, 0)
tipTexts = [
'Delete the selected residue isotopomers from the current isotope scheme',
'Make a new residue isotopomer definition by copying the details of the last selected isotopomer',
'Add a complete set of isotopomers to the isotope scheme, one for each residue type, based on the states default isotope abundances',
'For all residue isotopomers in the scheme, set the labelling of one kind of atom (the user is prompted) to its default isotopic incorporation ',
'Add a new residue isotopomer definition that uses the default isotopic incorporation'
]
texts = [
'Delete\nSelected', 'Copy\nSelected', 'Add Default\nAbundance Set',
'Set Atom Type\nTo Default', 'Add\nNew:'
]
commands = [
self.removeIsotopomers, self.duplicateResidues,
self.addDefaultIsotopomers, self.setAtomTypeDefault,
self.addNewIsotopomer
]
self.isotopomerButtons = ButtonList(frame,
texts=texts,
commands=commands,
grid=(0, 0),
tipTexts=tipTexts)
tipText = 'Selects which kind of residue isotopomer may be added to the current isotope scheme'
self.ccpCodePulldown = PulldownList(frame,
callback=None,
grid=(0, 1),
sticky='e',
tipText=tipText)
row += 1
div = LabelDivider(frameB, text='Atom Labels', grid=(row, 0))
row += 1
frame = Frame(frameB, grid=(row, 0))
frame.expandGrid(1, 3)
label = Label(frame, text='Chemical Element:', grid=(0, 0))
tipText = 'Selects which kind of atoms to select from the selected residue isotopomer; to display isotopic incorporation in the below table'
self.elementPulldown = PulldownList(frame,
callback=self.changeChemElement,
grid=(0, 1),
tipText=tipText)
self.updateChemElements()
label = Label(frame, text='Water Exchangeable Atoms:', grid=(0, 2))
tipText = 'Sets whether to show atoms considered as being "water exchangeable"; their isotopic labelling will rapidly equilibrate with aqueous solvent'
self.exchangeCheck = CheckButton(frame,
callback=self.updateAtomLabelsAfter,
grid=(0, 3),
selected=False,
tipText=tipText)
row += 1
# Tip texts set on update
headingList = [
'Atom\nName', 'Weighting\n13C'
'Weighting\n12C', '%12C', '%13C'
]
self.atomLabelTupleWeightEntry = FloatEntry(
self, text='', width=6, returnCallback=self.setAtomLabelWeight)
self.atomsMatrix = ScrolledMatrix(frameB,
headingList=headingList,
callback=self.selectAtomLabel,
multiSelect=True,
grid=(row, 0))
self.atomsMatrix.doEditMarkExtraRules = self.atomsEditRules
row += 1
tipTexts = [
'For the selected atom sites, in the current isotopomer, set their isotopic incorporation to the default values',
'Spread the isotopic incorporation values from the last selected atom site to all selected atoms sites'
]
texts = ['Reset Selected to Default Abundance', 'Propagate Abundances']
commands = [self.setAtomLabelsDefault, self.propagateAbundances]
self.atomButtons = ButtonList(frameB,
texts=texts,
commands=commands,
grid=(row, 0),
tipTexts=tipTexts)
#
# View Frame
#
frameC.expandGrid(1, 0)
row = 0
frame = Frame(frameC, grid=(row, 0), sticky='ew')
frame.grid_columnconfigure(3, weight=1)
label = Label(frame, text='Residue Type:', grid=(0, 0))
tipText = 'Selects which kind of residue, within the current isotope scheme, to show isotopomer structures for'
self.viewCcpCodePulldown = PulldownList(
frame,
callback=self.selectViewCcpcode,
grid=(0, 1),
tipText=tipText)
label = Label(frame, text='Isotopomer:', grid=(0, 2))
tipText = 'Selects which kind of isotopomer (labelling pattern) to display, from the selected residue type.'
self.viewIsotopomerPulldown = PulldownList(
frame,
callback=self.selectViewIsotopomer,
grid=(0, 3),
tipText=tipText)
row += 1
self.viewIsotopomerFrame = ViewIsotopomerFrame(frameC,
None,
grid=(row, 0))
#
# Main
#
tipTexts = [
'Save all changes to the reference isotope scheme to disk; the saves ALL changes to the CCPN installation for all projects to use',
]
texts = ['Save Schemes']
commands = [self.saveSchemes]
self.bottomButtons = UtilityButtonList(tabbedFrame.sideFrame,
texts=texts,
commands=commands,
helpUrl=self.help_url,
grid=(0, 0),
sticky='e',
tipTexts=tipTexts)
self.updateChemElements()
self.updateCcpCodes()
self.updateSchemes()
self.administerNotifiers(self.registerNotify)
def body(self, guiFrame):
self.geometry('700x840')
guiFrame.expandGrid(1,0)
# Top frame
frame = Frame(guiFrame, grid=(0,0))
frame.expandGrid(None,8)
label = Label(frame, text=u' %s List:' % T1, grid=(0,0))
self.t1Pulldown = PulldownList(frame, callback=self.selectT1List, grid=(0,1))
label = Label(frame, text=u' %s List:' % T2, grid=(0,2))
self.t2Pulldown = PulldownList(frame, callback=self.selectT2List, grid=(0,3))
label = Label(frame, text=' NOE List:', grid=(0,4))
self.noePulldown = PulldownList(frame, callback=self.selectNoeList, grid=(0,5))
label = Label(frame, text=' Spectrometer Freq (MHz):', grid=(0,6))
self.sfEntry = FloatEntry(frame, grid=(0,7), text=600.00, width=6)
UtilityButtonList(frame, grid=(0,9), sticky='e')
# Tabs
options = [u'%s vs %s Scatter' % (T1, T2),
u'%s,%s & NOE Graphs' % (T1, T2) ,
u'%s/%s Graph' % (T1, T2),
u'%s Estimate Graph' % S2,
'Options']
self.tabbedFrame = TabbedFrame(guiFrame, options=options,
callback=self.toggleTab, grid=(1,0))
frameA, frameD, frameC, frameE, frameB = self.tabbedFrame.frames
# T1 vs T2 Graph
frameA.expandGrid(0,0)
self.t1t2Graph = T1VersesT2Plot(frameA, grid=(0,0))
# T1 & T2 Graph
frameD.expandGrid(0,0)
frameD.expandGrid(1,0)
frameD.expandGrid(2,0)
self.t1Graph = MeasurementPlot(frameD, T1, grid=(0,0))
self.t2Graph = MeasurementPlot(frameD, T2, grid=(1,0))
self.noeGraph = NoePlot(frameD, 'NOE', grid=(2,0))
# T1 over T2 Graph
frameC.expandGrid(0,0)
self.t1t2GraphB = T1OverT2Plot(frameC, grid=(0,0))
# Order params graph
frameE.expandGrid(0,0)
frameE.expandGrid(1,0)
frameE.expandGrid(2,0)
self.s2Graph = ScrolledGraph(frameE, title=u'%s vs Residue Sequence' % S2,
xLabel='Residue number', yLabel=S2,
width=500, height=150, graphType='histogram',
xGrid=True, yGrid=False, grid=(0,0),
dataColors=['#0000A0','#808000'],
dataNames=['Isotropic',])
self.teGraph = ScrolledGraph(frameE, title=u'%s vs Residue Sequence' % Te,
xLabel='Residue number', yLabel=u'%s (ps)' % Te,
width=500, height=150, graphType='histogram',
xGrid=True, yGrid=False, grid=(1,0),
dataColors=['#008000',])
self.rexGraph = ScrolledGraph(frameE, title=u'%s vs Residue Sequence' % 'Rex',
xLabel='Residue number', yLabel='Rex',
width=500, height=150, graphType='histogram',
xGrid=True, yGrid=False, grid=(2,0),
dataColors=['#900000',])
# Options
frameB.expandGrid(4,2)
frame = LabelFrame(frameB, text='Physical Params', grid=(0,0))
frame.expandGrid(None,3)
label = Label(frame, text=u'N-H bond length (\u00C5)', grid=(0,0))
self.lenNhEntry = FloatEntry(frame, text=1.015, grid=(0,1), width=8)
label = Label(frame, text=u'Internal correlation\ntime, \u03C4e (ps)', grid=(1,0))
self.ictEntry = FloatEntry(frame, text=50.0, grid=(1,1), width=8)
label = Label(frame, text=u'15N Chemical Shift\nAnisotopy,\u0394N (ppm)',
grid=(2,0))
self.csaNEntry = FloatEntry(frame, text=-160.0, grid=(2,1), width=8)
frame = LabelFrame(frameB, text=u'%s vs %s Scatter' % (T1, T2), grid=(1,0))
label = Label(frame, text='Max cluster difference (ms):', grid=(0,0))
self.clusterDictEntry = FloatEntry(frame, text=20.0, grid=(0,1), width=8)
label = Label(frame, text='Min cluster size:', grid=(1,0))
self.clusterSizeEntry = FloatEntry(frame, text=5, grid=(1,1), width=8)
label = Label(frame, text=u'Min graph %s (ms):' % T1, grid=(2,0))
self.minT1Entry = FloatEntry(frame, text=300.0, grid=(2,1), width=8)
label = Label(frame, text=u'Max graph %s (ms):' % T1, grid=(3,0))
self.maxT1Entry = FloatEntry(frame, text=1000.0, grid=(3,1), width=8)
label = Label(frame, text=u'Min graph %s (ms):' % T2, grid=(4,0))
self.minT2Entry = FloatEntry(frame, text=0.0, grid=(4,1), width=8)
label = Label(frame, text=u'Max graph %s (ms):' % T2, grid=(5,0))
self.maxT2Entry = FloatEntry(frame, text=600.0, grid=(5,1), width=8)
frame = LabelFrame(frameB, text=u'%s Contours' % S2, grid=(0,1))
frame.expandGrid(4,3)
label = Label(frame, text='(Order Parameter Lines)',
grid=(0,0), gridSpan=(1,2))
label = Label(frame, text='Min value:', grid=(1,0))
self.minS2Entry = FloatEntry(frame, text=0.3, grid=(1,1), width=8)
label = Label(frame, text='Max value:', grid=(2,0))
self.maxS2Entry = FloatEntry(frame, text=1.0, grid=(2,1), width=8)
label = Label(frame, text='Step:', grid=(3,0))
self.stepS2Entry = FloatEntry(frame, text=0.1, grid=(3,1), width=8)
frame = LabelFrame(frameB, text=u'\u03C4m Contours', grid=(1,1))
frame.expandGrid(4,3)
label = Label(frame, text='(Rotational Correlation Time Lines)',
grid=(0,0), gridSpan=(1,2))
label = Label(frame, text='Min value (ns):', grid=(1,0))
self.minRctEntry = FloatEntry(frame, text=5.0, grid=(1,1), width=8)
label = Label(frame, text='Max value (ns):', grid=(2,0))
self.maxRctEntry = FloatEntry(frame, text=14.0, grid=(2,1), width=8)
label = Label(frame, text='Step (ns):', grid=(3,0))
self.stepRctEntry = FloatEntry(frame, text=1.0, grid=(3,1), width=8)
# Bottom frame
texts = [u'Show %s Table' % T1,u'Show %s Table' % T2, u'Estimate %s' % S2]
commands = [self.showT1List, self.showT2List, self.mc]
buttonList = ButtonList(guiFrame, grid=(2,0), texts=texts, commands=commands)
# Update
self.updateRelaxationLists()
self.drawAfter()
self.administerNotifiers(self.registerNotify)
