def __init__(self, parent, label, entry='', separator=': ', label_width=20, entry_width=60, label_anchor=Tkinter.E, show='', returnCallback=None, tipText=None, *args, **kw): apply(Frame.__init__, (self, parent) + args, kw) self.grid_columnconfigure(1, weight=1) self.separator = separator text = label + separator self.label = Label(self, text=text, width=label_width, anchor=label_anchor) self.label.grid(row=0, column=0, sticky=Tkinter.EW) self.entry = Entry(self, show=show, width=entry_width, returnCallback=returnCallback, tipText=tipText) self.entry.insert(0, entry) self.entry.grid(row=0, column=1, sticky=Tkinter.EW)
def body(self, master): master.grid_columnconfigure(1, weight=1) row = 0 label = Label(master, text='Axis unit name: ', grid=(row, 0)) tipText = 'Short textual name for the unit, e.g. "KPa" or "ms"' self.nameEntry = Entry(master, width=10, grid=(row, 1), tipText=tipText) row += 1 label = Label(master, text='Unit is backwards: ', grid=(row, 0)) tipText = 'Whether the axis values decrease left to right & bottom to top. For example "ppm" does, but most units do not' self.backwardsMenu = BooleanPulldownMenu(master, grid=(row, 1), tipText=tipText) row += 1 tipTexts = [ 'Make a new unit specification using the stated options and close this popup' ] texts = ['Create'] commands = [self.ok] buttons = UtilityButtonList(master, texts=texts, commands=commands, closeText='Cancel', helpUrl=self.help_url, grid=(row, 0), gridSpan=(1, 2), tipTexts=tipTexts) master.grid_rowconfigure(row, weight=1)
def body(self, master): self.geometry('600x130') master.grid_columnconfigure(1, weight=1) for n in range(5): master.grid_rowconfigure(n, weight=1) row = 0 label = Label(master, text='Spectrum: ') label.grid(row=row, column=0, sticky='e') tipText = 'The spectrum for which the contour file is being added' self.expt_spectrum = PulldownList(master, callback=self.updateContourDir, tipText=tipText) self.expt_spectrum.grid(row=row, column=1, sticky='w') row = row + 1 tipText = 'The location of the directory where contour files are stored on disk' label = Label(master, text='Contour dir: ') label.grid(row=row, column=0, sticky='e') self.dir_label = Label(master, text='', tipText=tipText) self.dir_label.grid(row=row, column=1, sticky='w') row = row + 1 label = Label( master, text= '(file will be copied into Contour dir if it is not already in there)' ) label.grid(row=row, column=1, sticky='w') row = row + 1 tipText = 'Browse for a file store contour data' button = Button(master, text='File name: ', command=self.selectFile, tipText=tipText) button.grid(row=row, column=0, sticky='e') tipText = 'Enter the name of the file to store contour data' self.file_entry = Entry(master, tipText=tipText) self.file_entry.grid(row=row, column=1, sticky='ew') row = row + 1 texts = ['Add File'] commands = [self.addFile] tipTexts = [ 'Use the selected contour file in the current project, copying it to the contour directory if required', ] self.buttons = UtilityButtonList(master, texts=texts, doClone=False, tipTexts=tipTexts, commands=commands, helpUrl=self.help_url) self.buttons.grid(row=row, column=0, columnspan=2, sticky='ew') self.curateNotifiers(self.registerNotify) self.updateSpectrum()
def addLabelEntry(self, n, label='', entry='', show='', frozen=False, doGrid=True): text = label + self.separator l = Tkinter.Label(self, text=text, width=self.label_width, anchor=self.label_anchor) self.labels[n:n] = [l] e = Entry(self, text=entry, show=show, width=self.entry_width, returnCallback=lambda n=n: self.returnCallback(n)) if (frozen): e.config(bg='gray', state=Tkinter.DISABLED) e.bind('<Button>', lambda event, e=e: e.focus()) else: e.config(bg='white') self.entries[n:n] = [e] if (doGrid): self.gridAll()
def __init__(self, parent, width=70, height=20, xscroll=False, yscroll=True, *args, **kw): apply(Frame.__init__, (self, parent) + args, kw) self.grid_columnconfigure(1, weight=1) row = 0 texts = ('back', 'forward', 'load') commands = (self.prevUrl, self.nextUrl, self.loadUrl) self.buttons = ButtonList(self, texts=texts, commands=commands) self.buttons.grid(row=row, column=0) self.url_entry = Entry(self, returnCallback=self.loadUrl) self.url_entry.grid(row=row, column=1, columnspan=2, sticky=Tkinter.EW) row = row + 1 frame = Frame(self) frame.grid(row=row, column=0, columnspan=3, sticky=Tkinter.W) self.createFindFrame(frame) row = row + 1 self.grid_rowconfigure(row, weight=1) self.help_text = ScrolledHtml(self, width=width, height=height, xscroll=xscroll, yscroll=yscroll, startUrlCallback=self.startOpenUrl, endUrlCallback=self.endOpenUrl, enterLinkCallback=self.setLinkLabel, leaveLinkCallback=self.setLinkLabel) self.help_text.grid(row=row, column=0, columnspan=3, sticky=Tkinter.NSEW) row = row + 1 self.link_label = Label(self) self.link_label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W) button = memops.gui.Util.createDismissButton(self, dismiss_cmd=self.close) button.grid(row=row, column=2) self.urls = [] self.current = -1 self.updateUrlList = True self.setButtonState()
def body(self, guiParent): guiParent.grid_columnconfigure(0, weight=1) row = 0 guiParent.grid_rowconfigure(row, weight=1) inputFrame = LabelFrame(guiParent, text='Inputs:') inputFrame.grid(row=row, column=0, sticky=Tkinter.NSEW) label = Label(inputFrame, text='NOESY:') label.grid(row=0, column=0, sticky=Tkinter.NW) self.hNoesyPulldown = PulldownMenu(inputFrame,callback=self.setHNoesy) self.hNoesyPulldown.grid(row=0, column=1, sticky=Tkinter.NW) label = Label(inputFrame, text='15N NOESY:') label.grid(row=1, column=0, sticky=Tkinter.NW) self.nNoesyPulldown = PulldownMenu(inputFrame,callback=self.setNNoesy) self.nNoesyPulldown.grid(row=1, column=1, sticky=Tkinter.NW) label = Label(inputFrame, text='13C NOESY:') label.grid(row=2, column=0, sticky=Tkinter.NW) self.cNoesyPulldown = PulldownMenu(inputFrame,callback=self.setCNoesy) self.cNoesyPulldown.grid(row=2, column=1, sticky=Tkinter.NW) label = Label(inputFrame, text='Shift List:') label.grid(row=3, column=0, sticky=Tkinter.NW) self.shiftListPulldown = PulldownMenu(inputFrame,callback=self.setShiftList) self.shiftListPulldown.grid(row=3, column=1, sticky=Tkinter.NW) label = Label(inputFrame, text='2d BACUS executable:') label.grid(row=4, column=0, sticky=Tkinter.NW) self.executableEntry = Entry(inputFrame, text='/home/tjs23/clouds/justin/SpiBacusMidge/bacus/bacus_tjs.exe') self.executableEntry.grid(row=4, column=1, sticky=Tkinter.NW) self.executableButton = Button(inputFrame, text='Choose file', command=self.chooseExecutable) self.executableButton.grid(row=5, column=1, sticky=Tkinter.EW) row += 1 outputFrame = LabelFrame(guiParent, text='Output:') outputFrame.grid(row=row, column=0, sticky=Tkinter.NSEW) row += 1 texts = ['Run BACUS 2d','Run BACUS 3d'] commands = [self.runBacus,self.runBacus3d] self.bottomButtons = createDismissHelpButtonList(guiParent,texts=texts,commands=commands,expands=0,help_url=None) self.bottomButtons.grid(row=row, column=0, sticky=Tkinter.EW) self.update()
def body(self, guiParent): guiParent.grid_columnconfigure(1,weight=1) row = 0 file_types = [ FileType('Python', ['*.py']), FileType('All', ['*']) ] self.file_select = FileSelect(guiParent, file_types=file_types, single_callback=self.chooseFile, double_callback=self.chooseFile) self.file_select.grid(row=row, column=0, columnspan=2, sticky='nsew') row = row + 1 headingList=('Function',) self.scrolledMatrix = ScrolledMatrix(guiParent, initialRows=4, headingList=headingList, callback=self.selectFunction) self.scrolledMatrix.grid(row=row, column=0, columnspan=2, sticky='nsew') guiParent.grid_rowconfigure(row,weight=1) row = row + 1 self.moduleLabel1 = Label(guiParent, text='Module: ') self.moduleLabel1.grid(row=row, column=0, sticky='nw') self.moduleLabel2 = Label(guiParent, text=' ') self.moduleLabel2.grid(row=row, column=1, sticky='nw') row = row + 1 self.functionLabel1 = Label(guiParent, text='Function: ') self.functionLabel1.grid(row=row, column=0, sticky='nw') self.functionLabel2 = Label(guiParent, text=' ') self.functionLabel2.grid(row=row, column=1, sticky='nw') row = row + 1 self.nameLabel = Label(guiParent, text='Name: ') self.nameLabel.grid(row=row, column=0, sticky='nw') self.nameEntry = Entry(guiParent, text=' ', width=40) self.nameEntry.grid(row=row, column=1, sticky='nw') row = row + 1 texts = [ 'Load Macro' ] commands = [ self.loadMacro ] buttons = UtilityButtonList(guiParent, texts=texts, commands=commands, helpUrl=self.help_url) buttons.grid(row=row, column=0, columnspan=2, sticky='ew') self.loadButton = buttons.buttons[0] self.loadButton.disable() self.path = None self.module = None self.function = None
def body(self, master): master.grid_columnconfigure(2, weight=1) row = 0 label = Label(master, text='Data to export:') label.grid(row=row, column=0, columnspan=3, sticky=Tkinter.W) self.check_buttons = {} i = 0 for heading in self.headings: row = row + 1 isSelected = self.exportSelection.get(row, True) self.check_buttons[i] = c = CheckButton( master, selected=isSelected, callback=self.toggleCheckButton) c.grid(row=row, column=1) label = Label(master, text=heading) label.grid(row=row, column=2, sticky=Tkinter.W) i += 1 row = row + 1 button = Button(master, text='File:', command=self.findFile) button.grid(row=row, column=0, sticky=Tkinter.W) self.file_entry = Entry(master, text=self.file, width=30) self.file_entry.grid(row=row, column=1, columnspan=2, sticky=Tkinter.EW) row = row + 1 label = Label(master, text='Format:') label.grid(row=row, column=0, sticky=Tkinter.W) self.format_menu = PulldownMenu(master, entries=exportFormats) self.format_menu.grid(row=row, column=1, columnspan=2, sticky=Tkinter.W) row = row + 1 master.grid_rowconfigure(row, weight=1) texts = ['Save'] commands = [self.ok] buttons = createDismissHelpButtonList(master, texts=texts, commands=commands, dismiss_text='Cancel') buttons.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
def __init__(self, parent, values, initial_index=0, orient=Tkinter.HORIZONTAL, scale_length=200, entry_width=5, entry_format='%2.1f', set_callback=None, *args, **kw): assert len(values) > 0 self.entry_format = entry_format self.values = tuple(values) self.set_callback = set_callback apply(Frame.__init__, (self, parent) + args, kw) if (orient == Tkinter.HORIZONTAL): self.grid_columnconfigure(1, weight=1) sticky = Tkinter.EW row = 0 col = 1 else: self.grid_rowconfigure(1, weight=1) sticky = Tkinter.NS row = 1 col = 0 self.entry = Entry(self, width=entry_width) self.entry.grid(row=0, column=0, sticky=sticky) self.entry.bind('<KeyPress>', self.keyPress) self.scale = Tkinter.Scale(self, orient=orient, length=scale_length, from_=0, to=len(values) - 1, label='', showvalue=0, command=self.setCallback) self.scale.grid(row=row, column=col, sticky=sticky) self.set(initial_index)
def body(self, guiFrame): self.geometry('600x250+600+250') analysisProfile = self.analysisProfile userName = analysisProfile.userName userOrganisation = analysisProfile.userOrganisation userEmail = analysisProfile.userEmail guiFrame.grid_rowconfigure(0, weight=1) guiFrame.grid_columnconfigure(1, weight=1) explainText = 'To keep track of our users and which versions are being used\n' \ 'we would like you to register your details with us.\n' \ 'Collating the number of users is important for grant applications.\n' \ 'Please do not use accents in any of the information\n' \ 'because Python does not handle it gracefully.' row = 0 label = Label(guiFrame, text=explainText, grid=(row, 0), gridSpan=(1, 2), sticky='ew') row += 1 licenseAgreeText = 'I agree to abide by the rules of the CCPN licensing agreement.' self.agreeButton = CheckButton(guiFrame, licenseAgreeText, tipText=licenseAgreeText) self.agreeButton.grid(row=row, column=1, columnspan=1, sticky='nsew') row += 1 self.entryWidgets = [] for (text, value) in (('Name', userName), ('Organisation', userOrganisation), ('Email', userEmail)): label = Label(guiFrame, text=text + ':', grid=(row, 0)) entry = Entry(guiFrame, text=value or '', grid=(row, 1), sticky='ew', tipText='Your ' + text) self.entryWidgets.append(entry) row += 1 texts = ['Register Now', 'Read License', 'Register Later'] tipTexts = ['Register now', 'Read License', 'Register later'] commands = [self.register, self.openLicense, self.close] buttons = UtilityButtonList(guiFrame, helpUrl=self.help_url, grid=(row, 0), gridSpan=(1, 2), commands=commands, texts=texts, tipTexts=tipTexts) self.buttons = buttons
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)
class LabeledEntry(Frame): def __init__(self, parent, label, entry='', separator=': ', label_width=20, entry_width=60, label_anchor=Tkinter.E, show='', returnCallback=None, tipText=None, *args, **kw): apply(Frame.__init__, (self, parent) + args, kw) self.grid_columnconfigure(1, weight=1) self.separator = separator text = label + separator self.label = Label(self, text=text, width=label_width, anchor=label_anchor) self.label.grid(row=0, column=0, sticky=Tkinter.EW) self.entry = Entry(self, show=show, width=entry_width, returnCallback=returnCallback, tipText=tipText) self.entry.insert(0, entry) self.entry.grid(row=0, column=1, sticky=Tkinter.EW) def getLabel(self): text = self.label.get() n = text.find(self.separator) if (n >= 0): text = text[:n] return text def setLabel(self, text=''): text = text + self.separator self.label.set(text) def getEntry(self): return self.entry.get() def setEntry(self, text=''): self.entry.set(text)
def body(self, frame): label = Label(frame, text=self.prompt) if self.hide: entry = Entry(frame, text=self.initVal, bg='white', show='*') else: entry = Entry(frame, text=self.initVal, bg='white') label.grid(row=0, column=0, sticky=Tkinter.W) entry.grid(row=1, column=0, sticky=Tkinter.W) entry.focus_set() # for the keypresses return entry
def __init__(self, guiParent, dataText, dataObjects, dataValues, helpText, selectionText, **kw): Frame.__init__(self, guiParent, **kw) label = Label(self, text=dataText + ':', grid=(0, 0)) self.selectionList = PulldownList(self, objects=dataObjects, texts=dataValues, grid=(0, 1)) label = Label(self, text=helpText, grid=(1, 0), gridSpan=(1, 2)) label = Label(self, text=selectionText + ':', grid=(2, 0)) self.selectionEntry = Entry(self, grid=(2, 1))
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(1, weight=1) row = 0 label = Label(master, text='Panel name: ', grid=(row, 0)) tipText = 'Short text name for the new axis panel, e.g. "N2"' self.name_entry = Entry(master, width=15, grid=(row, 1), tipText=tipText) row += 1 label = Label(master, text='Axis type:', grid=(row, 0)) tipText = 'The type of axis (isotope, time, sampled etc.) represented by panel type' self.types_list = PulldownList(master, grid=(row, 1), tipText=tipText) row += 1 tipTexts = [ 'Create a new panel type object with the selected options & close the popup' ] texts = ['Create'] commands = [self.ok] buttons = UtilityButtonList(master, texts=texts, commands=commands, doClone=False, closeText='Cancel', helpUrl=self.help_url, grid=(row, 0), gridSpan=(1, 2), tipTexts=tipTexts) master.grid_rowconfigure(row, weight=1) self.administerNotifiers(self.registerNotify) self.update()
def createFindFrame(self, master): frame = Frame(master) frame.grid(row=0, column=0, sticky=Tkinter.W) arrow = ToggleArrow(frame, callback=self.toggleFindFrame) arrow.grid(row=0, column=0) button = Button(frame, text='find:', command=self.findPhrase) button.grid(row=0, column=1) self.find_entry = Entry(frame, width=20, returnCallback=self.findPhrase) self.find_entry.grid(row=0, column=2) self.find_frame = frame = Frame(master) entries = ('search forwards', 'search backwards') self.direction_buttons = PulldownMenu(frame, entries=entries) self.direction_buttons.grid(row=0, column=0, sticky=Tkinter.W, padx=5) self.forwards_entries = entries = ('wrap search', 'stop at end') self.backwards_entries = ('wrap search', 'stop at beginning') self.wrap_buttons = PulldownMenu(frame, entries=entries) self.wrap_buttons.grid(row=0, column=1, sticky=Tkinter.W, padx=5) self.direction_buttons.callback = self.setWrapText entries = ('case insensitive', 'case sensitive') self.case_buttons = PulldownMenu(frame, entries=entries) self.case_buttons.grid(row=0, column=2, sticky=Tkinter.W, padx=5) entries = ('literal search', 'regex search') self.pattern_buttons = PulldownMenu(frame, entries=entries) self.pattern_buttons.grid(row=0, column=3, sticky=Tkinter.W, padx=5) self.countVar = Tkinter.IntVar()
class CreatePanelTypePopup(BasePopup): def __init__(self, parent, *args, **kw): self.axisType = None BasePopup.__init__(self, parent=parent, title='Create panel type', modal=True, **kw) def body(self, master): master.grid_columnconfigure(1, weight=1) row = 0 label = Label(master, text='Panel name: ', grid=(row, 0)) tipText = 'Short text name for the new axis panel, e.g. "N2"' self.name_entry = Entry(master, width=15, grid=(row, 1), tipText=tipText) row += 1 label = Label(master, text='Axis type:', grid=(row, 0)) tipText = 'The type of axis (isotope, time, sampled etc.) represented by panel type' self.types_list = PulldownList(master, grid=(row, 1), tipText=tipText) row += 1 tipTexts = [ 'Create a new panel type object with the selected options & close the popup' ] texts = ['Create'] commands = [self.ok] buttons = UtilityButtonList(master, texts=texts, commands=commands, doClone=False, closeText='Cancel', helpUrl=self.help_url, grid=(row, 0), gridSpan=(1, 2), tipTexts=tipTexts) master.grid_rowconfigure(row, weight=1) self.administerNotifiers(self.registerNotify) self.update() def administerNotifiers(self, notifyFunc): for func in ('__init__', 'delete', 'setName'): notifyFunc(self.update, 'ccpnmr.Analysis.AxisType', func) def destroy(self): self.administerNotifiers(self.unregisterNotify) BasePopup.destroy(self) def update(self, *extra): axisType = self.axisType axisTypes = self.parent.getAxisTypes() names = [x.name for x in axisTypes] if axisTypes: if axisType not in axisTypes: self.axisType = axisType = axisTypes[0] index = axisTypes.index(axisType) else: index = 0 self.axisType = None self.types_list.setup(names, axisTypes, index) def apply(self): name = self.name_entry.get() if not name: showError('No name', 'Need to enter name', parent=self) return False names = [ panelType.name for panelType in self.analysisProject.panelTypes ] if name in names: showError('Repeated name', 'Name already used', parent=self) return False axisType = self.types_list.getObject() if not axisType: showError('No axis type', 'Need to create axis type', parent=self) return False self.analysisProject.newPanelType(name=name, axisType=axisType) return True
class CingFrame(NmrSimRunFrame): 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 downloadResults(self): if not self.run: msg = 'No current iCing run' showWarning('Failure', msg, parent=self) return credentials = self.serverCredentials if not credentials: msg = 'No current iCing server job' showWarning('Failure', msg, parent=self) return fileName = self.resultFileEntry.get() if not fileName: msg = 'No save file specified' showWarning('Failure', msg, parent=self) return if os.path.exists(fileName): msg = 'File %s already exists. Overwite?' % fileName if not showOkCancel('Query', msg, parent=self): return url = self.iCingBaseUrl iCingUrl = self.getServerUrl(url) logText = iCingRobot.iCingFetch(credentials, url, iCingUrl, fileName) print logText msg = 'Results saved to file %s\n' % fileName msg += 'Purge results from iCing server?' if showYesNo('Query',msg, parent=self): self.purgeCingServer() def getServerUrl(self, baseUrl): iCingUrl = os.path.join(baseUrl, 'icing/serv/iCingServlet') return iCingUrl def viewHtmlResults(self): resultsUrl = self.resultsUrl if not resultsUrl: msg = 'No current iCing results URL' showWarning('Failure', msg, parent=self) return webBrowser = WebBrowser(self.application, popup=self.application) webBrowser.open(self.resultsUrl) def runCingServer(self): if not self.project: return run = self.run if not run: msg = 'No CING run setup' showWarning('Failure', msg, parent=self) return structure = self.structure if not structure: msg = 'No structure ensemble selected' showWarning('Failure', msg, parent=self) return ensembleText = getModelsString(run) if not ensembleText: msg = 'No structural models selected from ensemble' showWarning('Failure', msg, parent=self) return residueText = getResiduesString(structure) if not residueText: msg = 'No active residues selected in structure' showWarning('Failure', msg, parent=self) return url = self.iCingBaseUrlPulldown.getObject() url.strip() if not url: msg = 'No iCing server URL specified' showWarning('Failure', msg, parent=self) self.iCingBaseUrl = None return msg = 'Submit job now? You will be informed when the job is done.' if not showOkCancel('Confirm', msg, parent=self): return self.iCingBaseUrl = url iCingUrl = self.getServerUrl(url) self.serverCredentials, results, tarFileName = iCingRobot.iCingSetup(self.project, userId='ccpnAp', url=iCingUrl) if not results: # Message already issued on failure self.serverCredentials = None self.resultsUrl = None self.update() return else: credentials = self.serverCredentials os.unlink(tarFileName) entryId = iCingRobot.iCingProjectName(credentials, iCingUrl).get(iCingRobot.RESPONSE_RESULT) baseUrl, htmlUrl, logUrl, zipUrl = iCingRobot.getResultUrls(credentials, entryId, url) self.resultsUrl = htmlUrl # Save server data in this run for persistence setRunParameter(run, iCingRobot.FORM_USER_ID, self.serverCredentials[0][1]) setRunParameter(run, iCingRobot.FORM_ACCESS_KEY, self.serverCredentials[1][1]) setRunParameter(run, ICING_BASE_URL, url) setRunParameter(run, HTML_RESULTS_URL, htmlUrl) self.update() run.inputStructures = structure.sortedModels() # select residues from the structure's chain #iCingRobot.iCingResidueSelection(credentials, iCingUrl, residueText) # Select models from ensemble #iCingRobot.iCingEnsembleSelection(credentials, iCingUrl, ensembleText) # Start the actual run self.serverDone = False iCingRobot.iCingRun(credentials, iCingUrl) # Fetch server progress occasionally, report when done # this function will call itself again and again self.after(CHECK_INTERVAL, self.timedCheckStatus) self.update() def timedCheckStatus(self): if not self.serverCredentials: return if self.serverDone: return status = iCingRobot.iCingStatus(self.serverCredentials, self.getServerUrl(self.iCingBaseUrl)) if not status: #something broke, already warned return result = status.get(iCingRobot.RESPONSE_RESULT) if result == iCingRobot.RESPONSE_DONE: self.serverDone = True msg = 'CING run is complete!' showInfo('Completion', msg, parent=self) return self.after(CHECK_INTERVAL, self.timedCheckStatus) def checkStatus(self): if not self.serverCredentials: return status = iCingRobot.iCingStatus(self.serverCredentials, self.getServerUrl(self.iCingBaseUrl)) if not status: #something broke, already warned return result = status.get(iCingRobot.RESPONSE_RESULT) if result == iCingRobot.RESPONSE_DONE: msg = 'CING run is complete!' showInfo('Completion', msg, parent=self) self.serverDone = True return else: msg = 'CING job is not done.' showInfo('Processing', msg, parent=self) self.serverDone = False return def purgeCingServer(self): if not self.project: return if not self.run: msg = 'No CING run setup' showWarning('Failure', msg, parent=self) return if not self.serverCredentials: msg = 'No current iCing server job' showWarning('Failure', msg, parent=self) return url = self.iCingBaseUrl results = iCingRobot.iCingPurge(self.serverCredentials, self.getServerUrl(url)) if results: showInfo('Info','iCing server results cleared') self.serverCredentials = None self.iCingBaseUrl = None self.serverDone = False deleteRunParameter(self.run, iCingRobot.FORM_USER_ID) deleteRunParameter(self.run, iCingRobot.FORM_ACCESS_KEY) deleteRunParameter(self.run, HTML_RESULTS_URL) else: showInfo('Info','Purge failed') self.update() def chooseZipFile(self): fileTypes = [ FileType('Zip', ['*.zip']), ] popup = FileSelectPopup(self, file_types=fileTypes, file=self.resultFileEntry.get(), title='Results zip file location', dismiss_text='Cancel', selected_file_must_exist=False) fileName = popup.getFile() if fileName: self.resultFileEntry.set(fileName) popup.destroy() def setZipFileName(self): zipFile = '%s_CING_report.zip' % self.project.name self.resultFileEntry.set(zipFile) def selectStructModel(self, model, row, col): self.model = model def selectResidue(self, residue, row, col): self.residue = residue def deactivateResidues(self): for residue in self.residueMatrix.currentObjects: residue.useInCing = False self.updateResidues() def activateResidues(self): for residue in self.residueMatrix.currentObjects: residue.useInCing = True self.updateResidues() def activateModels(self): if self.run: for model in self.modelTable.currentObjects: if model not in self.run.inputStructures: self.run.addInputStructure(model) self.updateModels() def disableModels(self): if self.run: for model in self.modelTable.currentObjects: if model in self.run.inputStructures: self.run.removeInputStructure(model) self.updateModels() def toggleModel(self, *opt): if self.model and self.run: if self.model in self.run.inputStructures: self.run.removeInputStructure(self.model) else: self.run.addInputStructure(self.model) self.updateModels() def toggleResidue(self, *opt): if self.residue: self.residue.useInCing = not self.residue.useInCing self.updateResidues() def updateResidues(self): if self.residue and (self.residue.topObject is not self.structure): self.residue = None textMatrix = [] objectList = [] colorMatrix = [] if self.chain: chainCode = self.chain.code for residue in self.chain.sortedResidues(): msResidue = residue.residue if not hasattr(residue, 'useInCing'): residue.useInCing = True if residue.useInCing: colors = [None, None, None, None, CING_BLUE] use = 'Yes' else: colors = [None, None, None, None, None] use = 'No' datum = [residue.seqCode, msResidue.ccpCode, msResidue.linking, msResidue.descriptor, use,] textMatrix.append(datum) objectList.append(residue) colorMatrix.append(colors) self.residueMatrix.update(objectList=objectList, textMatrix=textMatrix, colorMatrix=colorMatrix) def updateChains(self): index = 0 names = [] chains = [] chain = self.chain if self.structure: chains = self.structure.sortedCoordChains() names = [chain.code for chain in chains] if chains: if chain not in chains: chain = chains[0] index = chains.index(chain) self.changeChain(chain) self.chainPulldown.setup(names, chains, index) def updateStructures(self): index = 0 names = [] structures = [] structure = self.structure if self.run: model = self.run.findFirstInputStructure() if model: structure = model.structureEnsemble structures0 = [(s.ensembleId, s) for s in self.project.structureEnsembles] structures0.sort() for eId, structure in structures0: name = '%s:%s' % (structure.molSystem.code, eId) structures.append(structure) names.append(name) if structures: if structure not in structures: structure = structures[-1] index = structures.index(structure) self.changeStructure(structure) self.structurePulldown.setup(names, structures, index) def updateModels(self): textMatrix = [] objectList = [] colorMatrix = [] if self.structure and self.run: used = self.run.inputStructures for model in self.structure.sortedModels(): if model in used: colors = [None, CING_BLUE] use = 'Yes' else: colors = [None, None] use = 'No' datum = [model.serial,use] textMatrix.append(datum) objectList.append(model) colorMatrix.append(colors) self.modelTable.update(objectList=objectList, textMatrix=textMatrix, colorMatrix=colorMatrix) def changeStructure(self, structure): if self.project and (self.structure is not structure): self.project.currentEstructureEnsemble = structure self.structure = structure if self.run: self.run.inputStructures = structure.sortedModels() self.updateModels() self.updateChains() def changeChain(self, chain): if self.project and (self.chain is not chain): self.chain = chain self.updateResidues() def chooseValidScript(self): # Prepend default Cyana file extension below fileTypes = [ FileType('Python', ['*.py']), ] popup = FileSelectPopup(self, file_types = fileTypes, title='Python file', dismiss_text='Cancel', selected_file_must_exist = True) fileName = popup.getFile() self.validScriptEntry.set(fileName) popup.destroy() def updateAll(self, project=None): if project: self.project = project self.nmrProject = project.currentNmrProject simStore = project.findFirstNmrSimStore(application='CING') or \ project.newNmrSimStore(application='CING', name='CING') else: simStore = None if not self.project: return self.setZipFileName() if not self.project.currentNmrProject: name = self.project.name self.nmrProject = self.project.newNmrProject(name=name) else: self.nmrProject = self.project.currentNmrProject self.update(simStore) def update(self, simStore=None): NmrSimRunFrame.update(self, simStore) run = self.run urls = [DEFAULT_URL,] index = 0 if run: userId = getRunParameter(run, iCingRobot.FORM_USER_ID) accessKey = getRunParameter(run, iCingRobot.FORM_ACCESS_KEY) if userId and accessKey: self.serverCredentials = [(iCingRobot.FORM_USER_ID, userId), (iCingRobot.FORM_ACCESS_KEY, accessKey)] url = getRunParameter(run, ICING_BASE_URL) if url: htmlUrl = getRunParameter(run, HTML_RESULTS_URL) self.iCingBaseUrl = url self.resultsUrl = htmlUrl # May be None self.resultUrlEntry.set(self.resultsUrl) if self.iCingBaseUrl and self.iCingBaseUrl not in urls: index = len(urls) urls.append(self.iCingBaseUrl) self.iCingBaseUrlPulldown.setup(urls, urls, index) self.updateButtons() self.updateStructures() self.updateModels() self.updateChains() def updateButtons(self, event=None): buttons = self.buttonBar.buttons if self.project and self.run: buttons[0].enable() if self.resultsUrl and self.serverCredentials: buttons[1].enable() buttons[2].enable() buttons[3].enable() else: buttons[1].disable() buttons[2].disable() buttons[3].disable() else: buttons[0].disable() buttons[1].disable() buttons[2].disable() buttons[3].disable()
class NewWindowPopup(BasePopup): """ **Create New Windows to Display Spectra** This tool is used to make new windows for the graphical display of spectra, which will usually be as contours. It is notable that some spectrum windows will be made automatically when spectra are loaded if there is no existing appropriate window to display a spectrum. However, making new spectrum windows allows the user to specialise different windows for different tasks and gives complete freedom as to which types of axis go in which direction. For example the user may wish to make a new window so that a spectrum can be viewed from an orthogonal, rotated aspect. A new spectrum window is made by first considering whether it is similar to any existing windows. If so, then the user selects the appropriate template window to base the new one upon. The user then chooses a name for the window via the "New window name" field, although the name may be changed after the window is created. Usually the user does not need to consider the "Strips" section, but if required the new window can be created with starting strips and orthogonal sub-divisions (although these are not permanent). After setting the required axes and spectrum visibility, as described below, the user clicks on [Create Window!] to actually make the new spectrum display window. **Axes** The number and type of axes for the new window are chosen using the pulldown menus in the "Axes" section. The idea is that the user chooses which NMR isotopes should appear on the X, Y, & Z axes. Naturally, X and Y axes must always be set to something, to represent the plane of the screen, but the Z axes are optional. If not required, a Z axis may be set to "None" to indicate that it will not be used. Up to four Z axes may be specified, labelled as "z1", "z2" etc., and these represent extra dimensions orthogonal to the plane of the screen, which are often conceptualised as depth axes. It should be noted that the Y axis type may be set to "value", which refers to a spectrum intensity axis, rather than an NMR isotope axis. Setting the Y axis to "value" and only having the X axis set to an isotope is used to create windows that can show 1D spectra. Such value axes can also be used for 2D and higher dimensionality spectra, to show the data as an intensity graph (a "slice") rather than as contours. **Spectra** The lower "Viewed Spectra" section lists all of the spectra within the project that may be shown by a window with the selected axes. All spectra with isotopes in their data dimensions that match the isotope types of the window axes can potentially be displayed. This system also allows for displayed spectra to have fewer dimensions than the axes has windows, as long as at least the X and Y axes are present. For example a 2D H-N spectrum can be shown in a 3D H-N-H window, but not a 3D H-H-N. For spectra that have more than one data dimension of the same isotope, then which data dimension goes with which window axis is not always known to Analysis. Where there is ambiguity, this system will simply map the spectrum data dimensions in order to the next matching window axis. If this mapping turns out to be wrong, then it may be changed at any time via the main _Windows settings; toggling the "Dim. Mapping" of the "Spectrum & Peak List Mappings" tab. For the spectra listed in the lower table, which may be placed in the new window, the user has control over whether the spectra actually will appear. Firstly the user can change the "Visible?" column, either via a double-click or by using the appropriate lower buttons. By default spectra are set as not being visible in new windows, and the user toggles the ones that should be seen to "Yes". This basic spectrum visibility can readily be changed by the toggle buttons that appear in the "toolbar" at the top of the spectrum display, so the "Visible?" setting here is only about what initially appears. The "In Toolbar?" setting of a spectrum is a way of allowing the user to state that a spectrum should never appear in the window, and not even allow it to be toggled on later via the toolbar at the top of the windows. This is a way of reducing clutter, and allows certain windows to be used for particular subsets of spectra. For example the user may wish to put the spectra for a temperature series in one window, but not in other windows used for resonance assignment where they would get in the way. The "In Toolbar" setting can be changed after a window has been made, but only via the main Windows_ settings popup. .. _Windows: EditWindowPopup.html """ def __init__(self, parent, *args, **kw): self.visibleSpectra = parent.visibleSpectra self.toolbarSpectra = parent.toolbarSpectra self.waiting = False self.window = None BasePopup.__init__(self, parent=parent, title='Window : New Window', **kw) def body(self, guiFrame): guiFrame.grid_columnconfigure(2, weight=1) row = 0 label = Label(guiFrame, text='Template window: ', grid=(row, 0)) tipText = 'Selects which window to use as the basis for making a new spectrum window; sets the axis types accordingly' self.window_list = PulldownList(guiFrame, grid=(row, 1), callback=self.setAxisTypes, tipText=tipText) frame = LabelFrame(guiFrame, text='Strips', grid=(row, 2), gridSpan=(2, 1)) buttons = UtilityButtonList(guiFrame, doClone=False, helpUrl=self.help_url, grid=(row, 3)) row += 1 label = Label(guiFrame, text='New window name: ', grid=(row, 0)) tipText = 'A short name to identify the spectrum window, which will appear in the graphical interface' self.nameEntry = Entry(guiFrame, width=16, grid=(row, 1), tipText=tipText) row += 1 label = Label(frame, text='Columns: ', grid=(0, 0)) tipText = 'The number of vertical strips/dividers to initially make in the spectrum window' self.cols_menu = PulldownList(frame, objects=STRIP_NUMS, grid=(0, 1), texts=[str(x) for x in STRIP_NUMS], tipText=tipText) label = Label(frame, text='Rows: ', grid=(0, 2)) tipText = 'The number of horizontal strips/dividers to initially make in the spectrum window' self.rows_menu = PulldownList(frame, objects=STRIP_NUMS, grid=(0, 3), texts=[str(x) for x in STRIP_NUMS], tipText=tipText) row += 1 div = LabelDivider(guiFrame, text='Axes', grid=(row, 0), gridSpan=(1, 4)) row += 1 self.axis_lists = {} frame = Frame(guiFrame, grid=(row, 0), gridSpan=(1, 4)) col = 0 self.axisTypes = {} self.axisTypesIncludeNone = {} for label in AXIS_LABELS: self.axisTypes[label] = None w = Label(frame, text=' ' + label) w.grid(row=0, column=col, sticky='w') col += 1 if label in ('x', 'y'): includeNone = False tipText = 'Sets the kind of measurement (typically ppm for a given isotope) that will be used along the window %s axis' % label else: includeNone = True tipText = 'Where required, sets the kind of measurement (typically ppm for a given isotope) that will be used along the window %s axis' % label self.axisTypesIncludeNone[label] = includeNone getAxisTypes = lambda label=label: self.getAxisTypes(label) callback = lambda axisType, label=label: self.changedAxisType( label, axisType) self.axis_lists[label] = PulldownList(frame, callback=callback, tipText=tipText) self.axis_lists[label].grid(row=0, column=col, sticky='w') col += 1 frame.grid_columnconfigure(col, weight=1) row += 1 div = LabelDivider(guiFrame, text='Viewed Spectra', grid=(row, 0), gridSpan=(1, 4)) row += 1 guiFrame.grid_rowconfigure(row, weight=1) editWidgets = [None, None, None, None] editGetCallbacks = [None, self.toggleVisible, self.toggleToolbar, None] editSetCallbacks = [None, None, None, None] tipTexts = [ 'The "experiment:spectrum" name for the spectrum that may be viewed in the new window, given the axis selections', 'Sets whether the spectrum contours will be visible in the new window', 'Sets whether the spectrum appears at all in the window; if not in the toolbar it cannot be displayed', 'The number of peak lists the spectrum contains' ] headingList = ['Spectrum', 'Visible?', 'In Toolbar?', 'Peak Lists'] self.scrolledMatrix = ScrolledMatrix(guiFrame, headingList=headingList, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, multiSelect=True, grid=(row, 0), gridSpan=(1, 4), tipTexts=tipTexts) row += 1 tipTexts = [ 'Creates a new spectrum window with the specified parameters', 'Sets the contours of the selected spectra to be visible when the new window is made', 'Sets the contours of the selected spectra to not be displayed when the new window is made', 'Sets the selected spectra as absent from the window toolbar, and thus not displayable at all' ] texts = [ 'Create Window!', 'Selected\nVisible', 'Selected\nNot Visible', 'Selected\nNot In Toolbar' ] commands = [ self.ok, self.setSelectedDisplay, self.setSelectedHide, self.setSelectedAbsent ] buttonList = ButtonList(guiFrame, texts=texts, grid=(row, 0), commands=commands, gridSpan=(1, 4), tipTexts=tipTexts) buttonList.buttons[0].config(bg='#B0FFB0') self.updateAxisTypes() self.updateWindow() self.updateWindowName() self.administerNotifiers(self.registerNotify) self.updateAfter() def administerNotifiers(self, notifyFunc): self.registerNotify(self.updateWindowName, 'ccpnmr.Analysis.SpectrumWindow', '__init__') for clazz in ('ccp.nmr.Nmr.Experiment', 'ccp.nmr.Nmr.DataSource'): for func in ('__init__', 'delete', 'setName'): notifyFunc(self.updateAfter, clazz, func) for func in ('__init__', 'delete'): notifyFunc(self.updateAfter, 'ccp.nmr.Nmr.PeakList', func) for func in ('__init__', 'delete', 'setName', 'addSpectrumWindowGroup', 'removeSpectrumWindowGroup', 'setSpectrumWindowGroups'): notifyFunc(self.updateWindow, 'ccpnmr.Analysis.SpectrumWindow', func) for func in ('addSpectrumWindow', 'removeSpectrumWindow', 'setSpectrumWindows'): notifyFunc(self.updateWindow, 'ccpnmr.Analysis.SpectrumWindowGroup', func) for func in ('__init__', 'delete', 'setName'): notifyFunc(self.updateAxisTypes, 'ccpnmr.Analysis.AxisType', func) # Set visible contours, on commit, according to selection # Get hold of spectrumWindowView ASAP def destroy(self): self.administerNotifiers(self.unregisterNotify) BasePopup.destroy(self) def getSpectra(self): spectrumIsotopes = {} spectra = [] for experiment in self.nmrProject.sortedExperiments(): name = experiment.name for spectrum in experiment.sortedDataSources(): spectrumIsotopes[spectrum] = [] spectra.append(['%s:%s' % (name, spectrum.name), spectrum]) for dataDim in spectrum.dataDims: dimTypes = [] if dataDim.className != 'SampledDataDim': for dataDimRef in dataDim.dataDimRefs: expDimRef = dataDimRef.expDimRef isotopes = set() for isotopeCode in expDimRef.isotopeCodes: isotopes.add(isotopeCode) dimTypes.append( (expDimRef.measurementType.lower(), isotopes)) else: dimTypes.append('sampled') spectrumIsotopes[spectrum].append(dimTypes) axisIsotopes = {} for label in AXIS_LABELS: if label not in ('x', 'y'): if self.axis_lists[label].getSelectedIndex() == 0: continue axisType = self.axis_lists[label].getObject() axisIsotopes[label] = (axisType.measurementType.lower(), set(axisType.isotopeCodes)) spectraSel = [] axes = axisIsotopes.keys() axes.sort() for name, spectrum in spectra: dimIsotopes = spectrumIsotopes[spectrum] for label in axes: mType, selected = axisIsotopes[label] if label == 'y' and mType == 'none': continue # value axis for i, dimTypes in enumerate(dimIsotopes): for dimType in dimTypes: if dimType == 'sampled': if label != 'z1': continue axisType = self.axis_lists[label].getObject() if axisType.name != 'sampled': continue dimIsotopes.pop(i) break else: measurementType, isotopes = dimType if (mType == measurementType) and (selected <= isotopes): dimIsotopes.pop(i) break else: continue break else: if label in ('x', 'y'): break else: if not dimIsotopes: spectraSel.append([name, spectrum]) return spectraSel def setSelectedAbsent(self): for spectrum in self.scrolledMatrix.currentObjects: self.visibleSpectra[spectrum] = False self.toolbarSpectra[spectrum] = False self.updateAfter() def setSelectedDisplay(self): for spectrum in self.scrolledMatrix.currentObjects: self.visibleSpectra[spectrum] = True self.toolbarSpectra[spectrum] = True self.updateAfter() def setSelectedHide(self): for spectrum in self.scrolledMatrix.currentObjects: self.visibleSpectra[spectrum] = False self.toolbarSpectra[spectrum] = True self.updateAfter() def toggleToolbar(self, spectrum): boolean = not self.toolbarSpectra.get(spectrum, True) self.toolbarSpectra[spectrum] = boolean if boolean is False: self.visibleSpectra[spectrum] = False self.updateAfter() def toggleVisible(self, spectrum): boolean = not self.visibleSpectra.get(spectrum, False) self.visibleSpectra[spectrum] = boolean if boolean: if not self.toolbarSpectra.get(spectrum, True): self.toolbarSpectra[spectrum] = True self.updateAfter() def updateAfter(self, object=None): if self.waiting: return else: self.waiting = True self.after_idle(self.update) def update(self): for spectrum in self.visibleSpectra.keys(): if spectrum.isDeleted: del self.visibleSpectra[spectrum] textMatrix = [] objectList = [] colorMatrix = [] for name, spectrum in self.getSpectra(): colours = [None, None, None, None] if self.visibleSpectra.get(spectrum): colours[0] = '#60F060' isVisible = 'Yes' self.visibleSpectra[ spectrum] = True # do not need this but play safe in case above if changed else: isVisible = 'No' self.visibleSpectra[spectrum] = False if self.toolbarSpectra.get(spectrum, True): inToolbar = 'Yes' self.toolbarSpectra[spectrum] = True else: colours[0] = '#600000' inToolbar = 'No' self.toolbarSpectra[spectrum] = False datum = [ name, isVisible, inToolbar, ','.join(['%d' % pl.serial for pl in spectrum.peakLists]) ] textMatrix.append(datum) objectList.append(spectrum) colorMatrix.append(colours) self.scrolledMatrix.update(objectList=objectList, textMatrix=textMatrix, colorMatrix=colorMatrix) self.waiting = False def updateAxisTypes(self, *extra): for label in AXIS_LABELS: names = [] objects = [] includeNone = self.axisTypesIncludeNone[label] if includeNone: names.append('None') objects.append(None) axisType = self.axisTypes[label] axisTypes = self.getAxisTypes(label) objects.extend(axisTypes) if axisTypes: if axisType not in objects: axisType = objects[0] index = objects.index(axisType) names.extend([x.name for x in axisTypes]) else: index = 0 self.axis_lists[label].setup(names, objects, index) self.changedAxisType(label, axisType) def changedAxisType(self, label, axisType): if axisType is not self.axisTypes[label]: self.axisTypes[label] = axisType self.updateAfter() def updateWindow(self, *extra): window = self.window windows = self.parent.getWindows() if windows: if window not in windows: window = windows[0] index = windows.index(window) names = [x.name for x in windows] else: index = 0 names = [] self.window_list.setup(names, windows, index) self.setAxisTypes(window) def updateWindowName(self, *extra): self.nameEntry.set(WindowBasic.defaultWindowName(self.project)) def getAxisTypes(self, label): axisTypes = self.parent.getAxisTypes() if label == 'z1': axisTypes = [ axisType for axisType in axisTypes if axisType.name == 'sampled' or not axisType.isSampled ] else: axisTypes = [ axisType for axisType in axisTypes if not axisType.isSampled ] if label != 'y': axisTypes = [ at for at in axisTypes if at.name != WindowBasic.VALUE_AXIS_NAME ] return axisTypes def setAxisTypes(self, window): project = self.project if not project: return if window is self.window: return self.window = window if window: windowPanes = window.sortedSpectrumWindowPanes() if windowPanes: # might be empty because notifier called before windowPanes set up windowPane = windowPanes[0] for label in AXIS_LABELS: axisPanel = windowPane.findFirstAxisPanel(label=label) if axisPanel and axisPanel.panelType \ and axisPanel.panelType.axisType: self.axis_lists[label].setSelected( axisPanel.panelType.axisType) elif label not in ('x', 'y'): self.axis_lists[label].setIndex(0) self.updateAfter() def apply(self): project = self.project if not project: return False name = self.nameEntry.get().strip() if not name: showError('No name', 'Need to enter name', parent=self) return False names = [ window.name for window in self.analysisProject.spectrumWindows ] if (name in names): showError('Repeated name', 'Name already used', parent=self) return False axisTypes = [] for label in AXIS_LABELS: if label not in ('x', 'y'): if self.axis_lists[label].getSelectedIndex() == 0: continue axisType = self.axis_lists[label].getObject() axisTypes.append(axisType) ncols = self.cols_menu.getObject() nrows = self.rows_menu.getObject() window = WindowBasic.createSpectrumWindow(project, name, [ axisTypes, ], ncols=ncols, nrows=nrows) return True
def setupAtomFrame(self,resetFrame = False, resetStatus = True): frameRow = 0 self.atomWidgets = [] if resetFrame: self.atomFrame = ScrolledFrame(self.atomFrameMaster, width = self.frameWidth, height = 300, doExtraConfig = False) self.atomFrame.grid(row=self.atomFrameRow, column=0, columnspan = self.columnspan, sticky=Tkinter.NSEW) frame = self.atomFrame.frame # # Make fake info at top for col length... # colNum = 0 for chemCompAtomInfo in self.chemCompAtoms[0]: attrName = chemCompAtomInfo[0] label = Label(frame, text = '', width = len(attrName) + 2) label.grid(row=frameRow, column=colNum, sticky=Tkinter.EW) colNum += 1 # # Now atom info... # for chemCompAtom in self.chemCompAtoms: frameRow += 1 colNum = 0 self.atomWidgets.append([]) for chemCompAtomInfo in chemCompAtom: attrName = chemCompAtomInfo[0] if attrName == 'bondedAtoms': bondedAtomText = "" for otherAtom in chemCompAtomInfo[1]: bondedAtomText += otherAtom[0][1] + ',' label = Label(frame, text = bondedAtomText[:-1]) label.grid(row=frameRow, column=colNum, sticky=Tkinter.EW) else: if attrName in self.nonEntryAttributes: widgetInfo = self.nonEntryAttributes[attrName] if widgetInfo[0] == PulldownMenu: self.atomWidgets[-1].append(PulldownMenu(frame, entries = widgetInfo[1], selected_index = widgetInfo[1].index(chemCompAtomInfo[1]))) elif widgetInfo[0] == CheckButton: self.atomWidgets[-1].append(CheckButton(frame, selected = chemCompAtomInfo[1])) else: text = chemCompAtomInfo[1] if not text: text = '' self.atomWidgets[-1].append(Entry(frame, text = text, width = 5)) self.atomWidgets[-1][-1].grid(row=frameRow, column=colNum) colNum += 1
class AnnealingSettingsTab(object): '''This class describes the tab in the GUI where the user can change setting that govern the monte carlo / annleaing procedure. This also includes which information from the ccpn analysis project is used and which information is ignored. This includes: * present sequential assignments * tentative assignments * amino acid type information * whether to include untyped spin systems * assignments to peak dimensions ALso the chain can be selected here. Furthermore the user can set the temperature regime of the annealing, the amount of times the procedure is repeated to obtain statistics. The fraction of peaks that is left out in each run to diversify the results, the treshhold score for amino acid typing and the treshhold collabelling for a peak to be expected. ''' def __init__(self, parent, frame): '''Init. args: parent: the guiElement that this tab is part of. frame: the frame this part of the GUI lives in. ''' self.guiParent = parent self.frame = frame self.project = parent.project self.nmrProject = parent.nmrProject self.minIsoFrac = 0.1 self.leavePeaksOutFraction = 0.0 self.minTypeScore = 1.0 self.chain = None self.amountOfRepeats = 10 self.amountOfSteps = 10000 self.acceptanceConstantList = [0.0, 0.01, 0.015, 0.022, 0.033, 0.050, 0.075, 0.113, 0.170, 0.256, 0.384, 0.576, 0.864, 1.297, 1.946, 2.919, 4.378, 6.568, 9.852, 14.77, 22.16, 33.25] self.energyDataSets = [[]] self.residues = [] self.body() def body(self): '''describes the body of this tab. It bascically consists of some field to fill out for the user at the top and a ScrolledGraph that shows the progess of the annealing procedure a the bottom. ''' frame = self.frame # frame.expandGrid(13,0) frame.expandGrid(15, 1) row = 0 text = 'Calculate Assignment Suggestions' command = self.runCalculations self.startButton = Button(frame, command=command, text=text) self.startButton.grid(row=row, column=0, sticky='nsew', columnspan=2) row += 1 Label(frame, text='Amount of runs: ', grid=(row, 0)) tipText = 'The amount of times the whole optimization procedure is performed, each result is safed' self.repeatEntry = IntEntry(frame, grid=(row, 1), width=7, text=10, returnCallback=self.updateRepeatEntry, tipText=tipText, sticky='nsew') self.repeatEntry.bind('<Leave>', self.updateRepeatEntry, '+') row += 1 Label(frame, text='Temperature regime: ', grid=(row, 0)) tipText = 'This list of numbers govern the temperature steps during the annealing, every number represents 1/(kb*t), where kb is the Boltzmann constant and t the temperature of one step.' self.tempEntry = Entry(frame, text=map(str, self.acceptanceConstantList), width=64, grid=(row, 1), isArray=True, returnCallback=self.updateAcceptanceConstantList, tipText=tipText, sticky='nsew') row += 1 Label(frame, text='Amount of attempts per temperature:', grid=(row, 0)) tipText = 'The amount of attempts to switch the position of two spinsystems in the sequence are performed for each temperature point' self.NAStepEntry = IntEntry(frame, grid=(row, 1), width=7, text=10000, returnCallback=self.updateStepEntry, tipText=tipText, sticky='nsew') self.NAStepEntry.bind('<Leave>', self.updateStepEntry, '+') row += 1 Label(frame, text='Fraction of peaks to leave out:', grid=(row, 0)) tipText = 'In each run a fraction of the peaks can be left out of the optimization, thereby increasing the variability in the outcome and reducing false negatives. In each run this will be different randomly chosen sub-set of all peaks. 0.1 (10%) can be a good value.' self.leaveOutPeaksEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.0, returnCallback=self.updateLeavePeaksOutEntry, tipText=tipText, sticky='nsew') self.leaveOutPeaksEntry.bind( '<Leave>', self.updateLeavePeaksOutEntry, '+') row += 1 Label(frame, text='Minmal amino acid typing score:', grid=(row, 0)) tipText = 'If automatic amino acid typing is selected, a cut-off value has to set. Every amino acid type that scores higher than the cut-off is taken as a possible type. This is the same score as can be found under resonance --> spin systems --> predict type. Value should be between 0 and 100' self.minTypeScoreEntry = FloatEntry(frame, grid=(row, 1), width=7, text=1.0, returnCallback=self.updateMinTypeScoreEntry, tipText=tipText, sticky='nsew') self.minTypeScoreEntry.bind( '<Leave>', self.updateMinTypeScoreEntry, '+') row += 1 Label(frame, text='Minimal colabelling fraction:', grid=(row, 0)) tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.' self.minLabelEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.1, returnCallback=self.updateMinLabelEntry, tipText=tipText, sticky='nsew') self.minLabelEntry.bind('<Leave>', self.updateMinLabelEntry, '+') row += 1 Label(frame, text='Use sequential assignments:', grid=(row, 0)) tipText = 'When this option is select the present sequential assignments will be kept in place' self.useAssignmentsCheck = CheckButton( frame, selected=True, tipText=tipText, grid=(row, 1)) row += 1 Label(frame, text='Use tentative assignments:', grid=(row, 0)) tipText = 'If a spin system has tentative assignments this can be used to narrow down the amount of possible sequential assignments.' self.useTentativeCheck = CheckButton( frame, selected=True, tipText=tipText, grid=(row, 1)) row += 1 Label(frame, text='Use amino acid types:', grid=(row, 0)) tipText = 'Use amino acid types of the spin systems. If this option is not checked the spin systems are re-typed, only resonance names and frequencies are used' self.useTypeCheck = CheckButton( frame, selected=True, tipText=tipText, grid=(row, 1)) row += 1 Label(frame, text='Include untyped spin systems:', grid=(row, 0)) tipText = 'Also include spin system that have no type information. Amino acid typing will be done on the fly.' self.useAlsoUntypedSpinSystemsCheck = CheckButton( frame, selected=True, tipText=tipText, grid=(row, 1)) row += 1 Label(frame, text='Use dimensional assignments:', grid=(row, 0)) tipText = 'If one or more dimensions of a peak is already assigned, assume that this assignment is the only option. If not the check the program will consider all possibilities for the assignment of the dimension.' self.useDimensionalAssignmentsCheck = CheckButton( frame, selected=True, tipText=tipText, grid=(row, 1)) row += 1 Label(frame, text='Chain:', grid=(row, 0)) self.molPulldown = PulldownList( frame, callback=self.changeMolecule, grid=(row, 1)) self.updateChains() row += 1 Label(frame, text='Residue ranges: ', grid=(row, 0)) tipText = 'Which residues should be included. Example: "10-35, 62-100, 130".' self.residueRangeEntry = Entry(frame, text=None, width=64, grid=(row, 1), isArray=True, returnCallback=self.updateResidueRanges, tipText=tipText, sticky='nsew') self.updateResidueRanges(fromChain=True) row += 1 self.energyPlot = ScrolledGraph(frame, symbolSize=2, width=600, height=200, title='Annealing', xLabel='temperature step', yLabel='energy') self.energyPlot.grid(row=row, column=0, columnspan=2, sticky='nsew') def runCalculations(self): '''Run all calculations. Also triggers the disabling of some buttons and fields. ''' self.startButton.disable() self.disableIllegalButtonsAfterPrecalculations() self.guiParent.connector.runAllCalculations() self.startButton.configure(text='More runs') self.startButton.enable() def disableIllegalButtonsAfterPrecalculations(self): '''Disable buttons and field the user can not alter any longer after the model is set up and the 'pre-calculations' have finished. This is done because this part of the calculation should only be run once. All settings that would be changed after this point will not have any influence. ''' illegalButtons = [self.minTypeScoreEntry, self.minLabelEntry, self.useAlsoUntypedSpinSystemsCheck, self.useAssignmentsCheck, self.useTypeCheck, self.useDimensionalAssignmentsCheck, self.useTentativeCheck] for illegalButton in illegalButtons: illegalButton.configure(state='disabled') self.molPulldown.disable() def getChainName(self, chain): '''Get the name for a chain. args: chain: ccpn analysis chain object returns: chain name ''' return '%s:%s (%s)' % (chain.molSystem.code, chain.code, chain.molecule.molType) def getChains(self): '''Get all chains present in the project. returns: list of ccpn analysis chain objects ''' chains = [] if self.project: for molSystem in self.project.sortedMolSystems(): for chain in molSystem.sortedChains(): if chain.residues: chains.append(chain) return chains def updateChains(self, *opt): '''Updates the list of chains if a new one is added to or deleted from the project. Updates the pull down list where a chain can be selected. ''' index = 0 texts = [] chains = self.getChains() chain = self.chain if chains: if chain not in chains: chain = chains[0] texts = [self.getChainName(c) for c in chains] index = chains.index(chain) else: chain = None self.molPulldown.setup(texts, chains, index) if chain is not self.chain: self.chain = chain def changeMolecule(self, chain): '''Select a molecular chain.''' if chain is not self.chain: self.chain = chain self.updateResidueRanges(fromChain=True) def updateStepEntry(self, event=None): '''Update the value and entry that sets the amount of steps per temperature point. ''' value = self.NAStepEntry.get() if value == self.amountOfSteps: return if value < 1: self.NAStepEntry.set(1) self.amountOfSteps = 1 else: self.amountOfSteps = value self.NAStepEntry.set(value) def updateRepeatEntry(self, event=None): '''Update the value and entry of that sets the amount of times the whole annealing procedure is repeated in order to obtain statistics. ''' value = self.repeatEntry.get() if value == self.amountOfRepeats: return if value < 1: self.repeatEntry.set(1) self.amountOfRepeats = 1 else: self.amountOfRepeats = value self.repeatEntry.set(value) def updateMinTypeScoreEntry(self, event=None): '''Updates the value and the entry for the treshhold value for amino acid typing. ''' value = self.minTypeScoreEntry.get() if value == self.minTypeScore: return if value < 0: self.minTypeScoreEntry.set(0.0) self.minTypeScore = 0.0 elif value > 100: self.minTypeScoreEntry.set(100.0) self.minTypeScore = 100.0 else: self.minTypeScoreEntry.set(value) self.minTypeScore = value def updateMinLabelEntry(self, event=None): '''Updates the minimum colabelling fraction for which a peak is expected to be present in the spectra. ''' value = self.minLabelEntry.get() if value == self.minIsoFrac: return if value < 0: self.minIsoFrac = 0.0 self.minLabelEntry.set(0.0) elif value > 1: self.minIsoFrac = 1.0 self.minLabelEntry.set(1.0) else: self.minIsoFrac = value self.minLabelEntry.set(value) def updateLeavePeaksOutEntry(self, event=None): '''Updates the value and entry of the fraction of peaks that should be left out in each run in order to diversify the results. ''' value = self.leaveOutPeaksEntry.get() if value == self.leavePeaksOutFraction: return if value < 0: self.leavePeaksOutFraction = 0.0 self.leaveOutPeaksEntry.set(0.0) elif value > 1: self.leavePeaksOutFraction = 1.0 self.leaveOutPeaksEntry.set(1.0) else: self.leavePeaksOutFraction = value self.leaveOutPeaksEntry.set(value) def updateAcceptanceConstantList(self, event=None): '''Updates the list with constants that are used during the monte carlo procedure to decide whether a changed is accepted or not. ''' acList = self.tempEntry.get() newList = [] for constant in acList: try: number = float(constant) newList.append(number) except ValueError: string = constant + \ ' in temperature constants is not a number.' showWarning('Not A Number', string, parent=self.guiParent) return False self.acceptanceConstantList = newList return True def updateResidueRanges(self, event=None, fromChain=False): self.residues = set() subRanges = self.residueRangeEntry.get() if not subRanges or fromChain: self.residues = set(self.chain.residues) residues = self.chain.sortedResidues() text = '{}-{}'.format(residues[0].seqCode, residues[-1].seqCode) self.residueRangeEntry.set(text=text) return for subRange in subRanges: indeces = subRange.split('-') start = int(indeces[0]) stop = int(indeces[-1]) + 1 for seqCode in range(start, stop): residue = self.chain.findFirstResidue(seqCode=seqCode) if not residue: showWarning('Residue out of range.', 'There is no residue at position {}'.format(seqCode), parent=self.guiParent) self.residues = set() return self.residues.add(residue) def addEnergyPoint(self, energy, time): '''Adds a point to the graph that shows the progress of the annealling procedure. args: energy: the y-value time: the x-value ''' point = (time, energy * -1) # This means one run has finished if len(self.energyDataSets[-1]) / (len(self.acceptanceConstantList) + 1): self.energyDataSets.append([point]) else: self.energyDataSets[-1].append(point) colors = colorSeries Ncolors = len(colors) NdataSets = len(self.energyDataSets) colorList = (NdataSets / Ncolors) * colors + \ colors[:NdataSets % Ncolors] self.energyPlot.update(dataSets=self.energyDataSets, dataColors=colorList) # Forcing the graph to draw, eventhough calculations # are still running. Only do this with high numbers of # steps, otherwise drawing takes longer than annealling. if self.amountOfSteps >= 100000: self.energyPlot.draw()
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 body(self, guiFrame): self.specFreqEntry = IntEntry(self, text=self.specFreq, width=8, returnCallback=self.setSpecFreq) self.maxIterEntry = IntEntry(self, text=self.maxIter, width=8, returnCallback=self.setMaxIter) self.mixTimeEntry = FloatEntry(self, text=self.mixTime, width=8, returnCallback=self.setMixTime) self.corrTimeEntry = FloatEntry(self, text=self.corrTime, width=8, returnCallback=self.setCorrTime) self.leakRateEntry = FloatEntry(self, text=self.leakRate, width=8, returnCallback=self.setLeakRate) self.maxIntensEntry = IntEntry(self, text=self.maxIntens, width=8, returnCallback=self.setMaxIntens) self.mdInitTempEntry = FloatEntry(self, text='', returnCallback=self.setMdInitTemp) self.mdFinTempEntry = FloatEntry(self, text='', returnCallback=self.setMdFinTemp) self.mdCoolStepsEntry = IntEntry(self, text='', returnCallback=self.setMdCoolSteps) self.mdSimStepsEntry = IntEntry(self, text='', returnCallback=self.setMdSimSteps) self.mdTauEntry = FloatEntry(self, text='', returnCallback=self.setMdTau) self.mdRepScaleEntry = FloatEntry(self, text='', returnCallback=self.setMdRepScale) guiFrame.grid_columnconfigure(0, weight=1) row = 0 frame0 = LabelFrame(guiFrame, text='Setup peak lists') frame0.grid(row=row, column=0, sticky=Tkinter.NSEW) frame0.grid(row=row, column=0, sticky=Tkinter.NSEW) frame0.grid_columnconfigure(1, weight=1) f0row = 0 label00 = Label(frame0, text='1H-1H NOESY spectrum') label00.grid(row=f0row, column=0, sticky=Tkinter.NW) self.noesyPulldown = PulldownMenu(frame0, entries=self.getNoesys(), callback=self.setNoesy, selected_index=0, do_initial_callback=0) self.noesyPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW) f0row += 1 label01 = Label(frame0, text='15N HSQC spectrum') label01.grid(row=f0row, column=0, sticky=Tkinter.NW) self.hsqcPulldown = PulldownMenu(frame0, entries=self.getHsqcs(), callback=self.setHsqc, selected_index=0, do_initial_callback=0) self.hsqcPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW) f0row += 1 label02 = Label(frame0, text='15N HSQC TOCSY spectrum') label02.grid(row=f0row, column=0, sticky=Tkinter.NW) self.tocsyPulldown = PulldownMenu(frame0, entries=self.getTocsys(), callback=self.setTocsy, selected_index=0, do_initial_callback=0) self.tocsyPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW) f0row += 1 label02 = Label(frame0, text='15N HSQC NOESY spectrum') label02.grid(row=f0row, column=0, sticky=Tkinter.NW) self.noesy3dPulldown = PulldownMenu(frame0, entries=self.getNoesy3ds(), callback=self.setNoesy3d, selected_index=0, do_initial_callback=0) self.noesy3dPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW) f0row += 1 texts = ['Setup resonances & peaks', 'Show Peaks', 'Show resonances'] commands = [self.setupResonances, self.showPeaks, self.showResonances] self.setupButtons = ButtonList(frame0, expands=1, texts=texts, commands=commands) self.setupButtons.grid(row=f0row, column=0, columnspan=2, sticky=Tkinter.NSEW) f0row += 1 self.label03a = Label(frame0, text='Resonances found: 0') self.label03a.grid(row=f0row, column=0, sticky=Tkinter.NW) self.label03b = Label(frame0, text='NOESY peaks found: 0') self.label03b.grid(row=f0row, column=1, sticky=Tkinter.NW) row += 1 frame1 = LabelFrame(guiFrame, text='Calculate distance constraints') frame1.grid(row=row, column=0, sticky=Tkinter.NSEW) frame1.grid_columnconfigure(3, weight=1) f1row = 0 frame1.grid_rowconfigure(f1row, weight=1) data = [ self.specFreq, self.maxIter, self.mixTime, self.corrTime, self.leakRate, self.maxIntens ] colHeadings = [ 'Spectrometer\nfrequency', 'Max\niterations', 'Mixing\ntime (ms)', 'Correl.\ntime (ns)', 'Leak\nrate', 'Max\nintensity' ] editWidgets = [ self.specFreqEntry, self.maxIterEntry, self.mixTimeEntry, self.corrTimeEntry, self.leakRateEntry, self.maxIntensEntry, ] editGetCallbacks = [ self.getSpecFreq, self.getMaxIter, self.getMixTime, self.getCorrTime, self.getLeakRate, self.getMaxIntens, ] editSetCallbacks = [ self.setSpecFreq, self.setMaxIter, self.setMixTime, self.setCorrTime, self.setLeakRate, self.setMaxIntens, ] self.midgeParamsMatrix = ScrolledMatrix( frame1, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, maxRows=1, initialCols=5, headingList=colHeadings, callback=None, objectList=[ 'None', ], textMatrix=[ data, ]) self.midgeParamsMatrix.grid(row=f1row, column=0, columnspan=4, sticky=Tkinter.NSEW) f1row += 1 label10 = Label(frame1, text='Benchmark structure') label10.grid(row=f1row, column=0, sticky=Tkinter.NW) self.structurePulldown = PulldownMenu(frame1, entries=self.getStructures(), callback=self.setStructure, selected_index=0, do_initial_callback=0) self.structurePulldown.grid(row=f1row, column=1, sticky=Tkinter.NW) label11 = Label(frame1, text='ADC atom types:') label11.grid(row=f1row, column=2, sticky=Tkinter.NW) self.adcAtomsPulldown = PulldownMenu(frame1, entries=self.getAdcAtomTypes(), callback=self.setAdcAtomTypes, selected_index=0, do_initial_callback=0) self.adcAtomsPulldown.grid(row=f1row, column=3, sticky=Tkinter.NW) f1row += 1 texts = [ 'Calculate distances', 'Show distance\nconstraints', 'Show anti-distance\nconstraints' ] commands = [ self.calculateDistances, self.showConstraints, self.showAntiConstraints ] self.midgeButtons = ButtonList(frame1, expands=1, texts=texts, commands=commands) self.midgeButtons.grid(row=f1row, column=0, columnspan=4, sticky=Tkinter.NSEW) f1row += 1 self.distConstrLabel = Label(frame1, text='Distance constraints:') self.distConstrLabel.grid(row=f1row, column=0, columnspan=2, sticky=Tkinter.NW) self.antiConstrLabel = Label(frame1, text='Anti-distance constraints:') self.antiConstrLabel.grid(row=f1row, column=2, columnspan=2, sticky=Tkinter.NW) row += 1 guiFrame.grid_rowconfigure(row, weight=1) frame2 = LabelFrame(guiFrame, text='Proton cloud molecular dynamics') frame2.grid(row=row, column=0, sticky=Tkinter.NSEW) frame2.grid_columnconfigure(1, weight=1) f2row = 0 frame2.grid_rowconfigure(f2row, weight=1) data = [ self.specFreq, self.maxIter, self.mixTime, self.corrTime, self.leakRate ] colHeadings = [ 'Step', 'Initial temp.', 'Final temp.', 'Cooling steps', 'MD steps', 'MD tau', 'Rep. scale' ] editWidgets = [ None, self.mdInitTempEntry, self.mdFinTempEntry, self.mdCoolStepsEntry, self.mdSimStepsEntry, self.mdTauEntry, self.mdRepScaleEntry ] editGetCallbacks = [ None, self.getMdInitTemp, self.getMdFinTemp, self.getMdCoolSteps, self.getMdSimSteps, self.getMdTau, self.getMdRepScale ] editSetCallbacks = [ None, self.setMdInitTemp, self.setMdFinTemp, self.setMdCoolSteps, self.setMdSimSteps, self.setMdTau, self.setMdRepScale ] self.coolingSchemeMatrix = ScrolledMatrix( frame2, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, maxRows=9, initialRows=12, headingList=colHeadings, callback=self.selectCoolingStep, objectList=self.coolingScheme, textMatrix=self.coolingScheme) self.coolingSchemeMatrix.grid(row=f2row, column=0, columnspan=4, sticky=Tkinter.NSEW) f2row += 1 texts = ['Move earlier', 'Move later', 'Add step', 'Remove step'] commands = [ self.moveStepEarlier, self.moveStepLater, self.addCoolingStep, self.removeCoolingStep ] self.coolingSchemeButtons = ButtonList(frame2, expands=1, commands=commands, texts=texts) self.coolingSchemeButtons.grid(row=f2row, column=0, columnspan=4, sticky=Tkinter.EW) f2row += 1 label20 = Label(frame2, text='Number of clouds:') label20.grid(row=f2row, column=0, sticky=Tkinter.NW) self.numCloudsEntry = FloatEntry(frame2, text=100, returnCallback=self.setNumClouds, width=10) self.numCloudsEntry.grid(row=f2row, column=1, sticky=Tkinter.NW) label21 = Label(frame2, text='Cloud file prefix:') label21.grid(row=f2row, column=2, sticky=Tkinter.NW) self.filePrefixEntry = Entry(frame2, text='cloud_', returnCallback=self.setFilePrefix, width=10) self.filePrefixEntry.grid(row=f2row, column=3, sticky=Tkinter.NW) f2row += 1 texts = ['Start molecular dynamics', 'Show dynamics progress'] commands = [self.startMd, self.showMdProgress] self.mdButtons = ButtonList(frame2, expands=1, commands=commands, texts=texts) self.mdButtons.grid(row=f2row, column=0, columnspan=4, sticky=Tkinter.NSEW) row += 1 self.bottomButtons = createDismissHelpButtonList(guiFrame, expands=0, help_url=None) self.bottomButtons.grid(row=row, column=0, sticky=Tkinter.EW) self.setButtonStates()
def body(self): '''describes the body of this tab. It bascically consists of some field to fill out for the user at the top and a ScrolledGraph that shows the progess of the annealing procedure a the bottom. ''' frame = self.frame # frame.expandGrid(13,0) frame.expandGrid(15, 1) row = 0 text = 'Calculate Assignment Suggestions' command = self.runCalculations self.startButton = Button(frame, command=command, text=text) self.startButton.grid(row=row, column=0, sticky='nsew', columnspan=2) row += 1 Label(frame, text='Amount of runs: ', grid=(row, 0)) tipText = 'The amount of times the whole optimization procedure is performed, each result is safed' self.repeatEntry = IntEntry(frame, grid=(row, 1), width=7, text=10, returnCallback=self.updateRepeatEntry, tipText=tipText, sticky='nsew') self.repeatEntry.bind('<Leave>', self.updateRepeatEntry, '+') row += 1 Label(frame, text='Temperature regime: ', grid=(row, 0)) tipText = 'This list of numbers govern the temperature steps during the annealing, every number represents 1/(kb*t), where kb is the Boltzmann constant and t the temperature of one step.' self.tempEntry = Entry(frame, text=map(str, self.acceptanceConstantList), width=64, grid=(row, 1), isArray=True, returnCallback=self.updateAcceptanceConstantList, tipText=tipText, sticky='nsew') row += 1 Label(frame, text='Amount of attempts per temperature:', grid=(row, 0)) tipText = 'The amount of attempts to switch the position of two spinsystems in the sequence are performed for each temperature point' self.NAStepEntry = IntEntry(frame, grid=(row, 1), width=7, text=10000, returnCallback=self.updateStepEntry, tipText=tipText, sticky='nsew') self.NAStepEntry.bind('<Leave>', self.updateStepEntry, '+') row += 1 Label(frame, text='Fraction of peaks to leave out:', grid=(row, 0)) tipText = 'In each run a fraction of the peaks can be left out of the optimization, thereby increasing the variability in the outcome and reducing false negatives. In each run this will be different randomly chosen sub-set of all peaks. 0.1 (10%) can be a good value.' self.leaveOutPeaksEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.0, returnCallback=self.updateLeavePeaksOutEntry, tipText=tipText, sticky='nsew') self.leaveOutPeaksEntry.bind( '<Leave>', self.updateLeavePeaksOutEntry, '+') row += 1 Label(frame, text='Minmal amino acid typing score:', grid=(row, 0)) tipText = 'If automatic amino acid typing is selected, a cut-off value has to set. Every amino acid type that scores higher than the cut-off is taken as a possible type. This is the same score as can be found under resonance --> spin systems --> predict type. Value should be between 0 and 100' self.minTypeScoreEntry = FloatEntry(frame, grid=(row, 1), width=7, text=1.0, returnCallback=self.updateMinTypeScoreEntry, tipText=tipText, sticky='nsew') self.minTypeScoreEntry.bind( '<Leave>', self.updateMinTypeScoreEntry, '+') row += 1 Label(frame, text='Minimal colabelling fraction:', grid=(row, 0)) tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.' self.minLabelEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.1, returnCallback=self.updateMinLabelEntry, tipText=tipText, sticky='nsew') self.minLabelEntry.bind('<Leave>', self.updateMinLabelEntry, '+') row += 1 Label(frame, text='Use sequential assignments:', grid=(row, 0)) tipText = 'When this option is select the present sequential assignments will be kept in place' self.useAssignmentsCheck = CheckButton( frame, selected=True, tipText=tipText, grid=(row, 1)) row += 1 Label(frame, text='Use tentative assignments:', grid=(row, 0)) tipText = 'If a spin system has tentative assignments this can be used to narrow down the amount of possible sequential assignments.' self.useTentativeCheck = CheckButton( frame, selected=True, tipText=tipText, grid=(row, 1)) row += 1 Label(frame, text='Use amino acid types:', grid=(row, 0)) tipText = 'Use amino acid types of the spin systems. If this option is not checked the spin systems are re-typed, only resonance names and frequencies are used' self.useTypeCheck = CheckButton( frame, selected=True, tipText=tipText, grid=(row, 1)) row += 1 Label(frame, text='Include untyped spin systems:', grid=(row, 0)) tipText = 'Also include spin system that have no type information. Amino acid typing will be done on the fly.' self.useAlsoUntypedSpinSystemsCheck = CheckButton( frame, selected=True, tipText=tipText, grid=(row, 1)) row += 1 Label(frame, text='Use dimensional assignments:', grid=(row, 0)) tipText = 'If one or more dimensions of a peak is already assigned, assume that this assignment is the only option. If not the check the program will consider all possibilities for the assignment of the dimension.' self.useDimensionalAssignmentsCheck = CheckButton( frame, selected=True, tipText=tipText, grid=(row, 1)) row += 1 Label(frame, text='Chain:', grid=(row, 0)) self.molPulldown = PulldownList( frame, callback=self.changeMolecule, grid=(row, 1)) self.updateChains() row += 1 Label(frame, text='Residue ranges: ', grid=(row, 0)) tipText = 'Which residues should be included. Example: "10-35, 62-100, 130".' self.residueRangeEntry = Entry(frame, text=None, width=64, grid=(row, 1), isArray=True, returnCallback=self.updateResidueRanges, tipText=tipText, sticky='nsew') self.updateResidueRanges(fromChain=True) row += 1 self.energyPlot = ScrolledGraph(frame, symbolSize=2, width=600, height=200, title='Annealing', xLabel='temperature step', yLabel='energy') self.energyPlot.grid(row=row, column=0, columnspan=2, sticky='nsew')
def __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)
class HelpFrame(Frame): def __init__(self, parent, width=70, height=20, xscroll=False, yscroll=True, *args, **kw): apply(Frame.__init__, (self, parent) + args, kw) self.grid_columnconfigure(1, weight=1) row = 0 texts = ('back', 'forward', 'load') commands = (self.prevUrl, self.nextUrl, self.loadUrl) self.buttons = ButtonList(self, texts=texts, commands=commands) self.buttons.grid(row=row, column=0) self.url_entry = Entry(self, returnCallback=self.loadUrl) self.url_entry.grid(row=row, column=1, columnspan=2, sticky=Tkinter.EW) row = row + 1 frame = Frame(self) frame.grid(row=row, column=0, columnspan=3, sticky=Tkinter.W) self.createFindFrame(frame) row = row + 1 self.grid_rowconfigure(row, weight=1) self.help_text = ScrolledHtml(self, width=width, height=height, xscroll=xscroll, yscroll=yscroll, startUrlCallback=self.startOpenUrl, endUrlCallback=self.endOpenUrl, enterLinkCallback=self.setLinkLabel, leaveLinkCallback=self.setLinkLabel) self.help_text.grid(row=row, column=0, columnspan=3, sticky=Tkinter.NSEW) row = row + 1 self.link_label = Label(self) self.link_label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W) button = memops.gui.Util.createDismissButton(self, dismiss_cmd=self.close) button.grid(row=row, column=2) self.urls = [] self.current = -1 self.updateUrlList = True self.setButtonState() def close(self): if (self.popup): if (self.popup.modal): self.popup.do_grab() popup = self.parent while (not hasattr(popup, 'top')): popup = popup.parent popup.close() def createFindFrame(self, master): frame = Frame(master) frame.grid(row=0, column=0, sticky=Tkinter.W) arrow = ToggleArrow(frame, callback=self.toggleFindFrame) arrow.grid(row=0, column=0) button = Button(frame, text='find:', command=self.findPhrase) button.grid(row=0, column=1) self.find_entry = Entry(frame, width=20, returnCallback=self.findPhrase) self.find_entry.grid(row=0, column=2) self.find_frame = frame = Frame(master) entries = ('search forwards', 'search backwards') self.direction_buttons = PulldownMenu(frame, entries=entries) self.direction_buttons.grid(row=0, column=0, sticky=Tkinter.W, padx=5) self.forwards_entries = entries = ('wrap search', 'stop at end') self.backwards_entries = ('wrap search', 'stop at beginning') self.wrap_buttons = PulldownMenu(frame, entries=entries) self.wrap_buttons.grid(row=0, column=1, sticky=Tkinter.W, padx=5) self.direction_buttons.callback = self.setWrapText entries = ('case insensitive', 'case sensitive') self.case_buttons = PulldownMenu(frame, entries=entries) self.case_buttons.grid(row=0, column=2, sticky=Tkinter.W, padx=5) entries = ('literal search', 'regex search') self.pattern_buttons = PulldownMenu(frame, entries=entries) self.pattern_buttons.grid(row=0, column=3, sticky=Tkinter.W, padx=5) self.countVar = Tkinter.IntVar() def setWrapText(self, entry_ind, entry): if (entry_ind == 0): entries = self.forwards_entries else: entries = self.backwards_entries self.wrap_buttons.replace( entries, selected_index=self.wrap_buttons.getSelectedIndex()) def findPhrase(self, *extra): phrase = self.find_entry.get() if (not phrase): showError('No find phrase', 'Enter phrase in entry box.') return if (self.direction_buttons.getSelectedIndex() == 0): forwards = 1 backwards = 0 else: forwards = 0 backwards = 1 if (self.case_buttons.getSelectedIndex() == 0): nocase = 1 else: nocase = 0 if (self.pattern_buttons.getSelectedIndex() == 0): exact = 1 regexp = 0 else: exact = 0 regexp = 1 start = self.help_text.tag_nextrange(Tkinter.SEL, '1.0') if (start): start = start[0] if (forwards): start = '%s+1c' % start else: start = '%s-1c' % start else: start = Tkinter.CURRENT if (self.wrap_buttons.getSelectedIndex() == 0): match = self.help_text.search(phrase, start, count=self.countVar, forwards=forwards, backwards=backwards, nocase=nocase, exact=exact, regexp=regexp) elif (forwards): match = self.help_text.search(phrase, start, count=self.countVar, forwards=forwards, backwards=backwards, nocase=nocase, exact=exact, regexp=regexp, stopindex=Tkinter.END) else: match = self.help_text.search(phrase, start, count=self.countVar, forwards=forwards, backwards=backwards, nocase=nocase, exact=exact, regexp=regexp, stopindex='1.0') if (match): self.help_text.see(match) self.help_text.setSelection( match, '%s+%dc' % (match, self.countVar.get())) self.help_text.tag_config(Tkinter.SEL, background='gray70') else: showInfo('No match', 'No match found for phrase.') def toggleFindFrame(self, isClosed): if (isClosed): self.find_frame.grid_forget() else: self.find_frame.grid(row=1, column=0, sticky=Tkinter.W) def setButtonState(self): n = len(self.urls) if ((n >= 2) and (self.current > 0)): state = Tkinter.NORMAL else: state = Tkinter.DISABLED self.buttons.buttons[0].config(state=state) if ((n >= 2) and (self.current < (n - 1))): state = Tkinter.NORMAL else: state = Tkinter.DISABLED self.buttons.buttons[1].config(state=state) def setLinkLabel(self, url=''): self.link_label.set(url) def loadUrl(self, *extra): url = self.url_entry.get() if (url): if (url.find(':') == -1): if (url[:2] != '//'): url = '//' + url url = 'http:' + url self.showUrl(url, forceLoad=True) def newUrl(self, url): self.current = self.current + 1 self.urls[self.current:] = [[url, 0.0]] self.setButtonState() #print 'newUrl', self.current, self.urls def prevUrl(self): if (self.current > 0): # True if called via button (url, offset) = self.urls[self.current - 1] self.updateUrlList = False self.showUrl(url, offset=offset, allowModifyPath=False) self.updateUrlList = True self.current = self.current - 1 self.setButtonState() #print 'prevUrl', self.current, self.urls def nextUrl(self): if (self.current < (len(self.urls) - 1)): # True if called via button (url, offset) = self.urls[self.current + 1] self.updateUrlList = False self.showUrl(url, offset=offset, allowModifyPath=False) self.updateUrlList = True self.current = self.current + 1 self.setButtonState() #print 'nextUrl', self.current, self.urls def showText(self, message, popup=None): self.popup = popup if (popup): self.parent.modal = popup.modal self.help_text.setState(Tkinter.NORMAL) # so that can add text self.help_text.clear() # clear existing text self.help_text.append(message) self.help_text.setState(Tkinter.DISABLED) # make text read-only self.open() def startOpenUrl(self, yview): if (self.urls): self.urls[self.current][1] = yview[0] def endOpenUrl(self, url): #print 'endOpenUrl', url, self.updateUrlList self.url_entry.set(url) if (self.updateUrlList): self.newUrl(url) self.setLinkLabel() self.open() def showUrl(self, url, offset=None, forceLoad=False, allowModifyPath=True, popup=None): self.popup = popup if (popup): self.parent.modal = popup.modal self.help_text.openUrl(url, forceLoad=forceLoad, allowModifyPath=allowModifyPath) if (offset is not None): self.help_text.yview(Tkinter.MOVETO, str(offset))
class CingGui(BasePopup): def __init__(self, parent, options, *args, **kw): # Fill in below variable once run generates some results self.haveResults = None # store the options self.options = options BasePopup.__init__(self, parent=parent, title='CING Setup', **kw) # self.setGeometry(850, 750, 50, 50) self.project = None # self.tk_strictMotif( True) self.updateGui() # end def __init__ def body(self, guiFrame): row = 0 col =0 # frame = Frame( guiFrame ) # frame.grid(row=row, column=col, sticky='news') self.menuBar = Menu( guiFrame) self.menuBar.grid( row=row, column=col, sticky='ew') #---------------------------------------------------------------------------------- # Project frame #---------------------------------------------------------------------------------- # guiFrame.grid_columnconfigure(row, weight=1) # frame = LabelFrame(guiFrame, text='Project', font=medFont) row = +1 col =0 frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes ) print '>', frame.keys() frame.grid(row=row, column=col, sticky='nsew' ) frame.grid_columnconfigure(2, weight=1) # frame.grid_rowconfigure(0, weight=1) srow = 0 self.projectOptions = ['old','new from PDB','new from CCPN','new from CYANA'] self.projOptionsSelect = RadioButtons(frame, selected_index=0, entries=self.projectOptions, direction='vertical', select_callback=self.updateGui ) self.projOptionsSelect.grid(row=srow,column=0,rowspan=len(self.projectOptions),columnspan=2, sticky='w') if self.options.name: text = self.options.name else: text='' # end if self.projEntry = Entry(frame, bd=1, text=text, returnCallback=self.updateGui) self.projEntry.grid(row=srow,column=2,columnspan=2,sticky='ew') # self.projEntry.bind('<Key>', self.updateGui) self.projEntry.bind('<Leave>', self.updateGui) projButton = Button(frame, bd=1,command=self.chooseOldProjectFile, text='browse') projButton.grid(row=srow,column=3,sticky='ew') srow += 1 self.pdbEntry = Entry(frame, bd=1, text='') self.pdbEntry.grid(row=srow,column=2,sticky='ew') self.pdbEntry.bind('<Leave>', self.updateGui) pdbButton = Button(frame, bd=1,command=self.choosePdbFile, text='browse') pdbButton.grid(row=srow,column=3,sticky='ew') srow += 1 self.ccpnEntry = Entry(frame, bd=1, text='') self.ccpnEntry.grid(row=srow,column=2,sticky='ew') self.ccpnEntry.bind('<Leave>', self.updateGui) ccpnButton = Button(frame, bd=1,command=self.chooseCcpnFile, text='browse') ccpnButton.grid(row=srow,column=3,sticky='ew') srow += 1 self.cyanaEntry = Entry(frame, bd=1, text='') self.cyanaEntry.grid(row=srow,column=2,sticky='ew') self.cyanaEntry.bind('<Leave>', self.updateGui) cyanaButton = Button(frame, bd=1,command=self.chooseCyanaFile, text='browse') cyanaButton.grid(row=srow,column=3,sticky='ew') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') srow += 1 label = Label(frame, text='Project name:') label.grid(row=srow,column=0,sticky='nw') self.nameEntry = Entry(frame, bd=1, text='') self.nameEntry.grid(row=srow,column=2,sticky='w') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') srow += 1 self.openProjectButton = Button(frame, command=self.openProject, text='Open Project', **actionButtonAttributes ) self.openProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew') #---------------------------------------------------------------------------------- # status #---------------------------------------------------------------------------------- # guiFrame.grid_columnconfigure(1, weight=0) srow = 0 frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes) frame.grid( row=srow, column=1, sticky='wnes') self.projectStatus = Text(frame, height=11, width=70, borderwidth=0, relief='flat') self.projectStatus.grid(row=0, column=0, sticky='wen') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') srow += 1 self.closeProjectButton = Button(frame, command=self.closeProject, text='Close Project', **actionButtonAttributes) self.closeProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew') #---------------------------------------------------------------------------------- # Validate frame #---------------------------------------------------------------------------------- row +=1 col=0 frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes) # frame = LabelFrame(guiFrame, text='Validate', font=medFont) frame.grid(row=row, column=col, sticky='nsew') # frame.grid_columnconfigure(2, weight=1) frame.grid_rowconfigure(0, weight=1) srow = 0 # label = Label(frame, text='validation') # label.grid(row=srow,column=0,sticky='nw') # # self.selectDoValidation = CheckButton(frame) # self.selectDoValidation.grid(row=srow, column=1,sticky='nw' ) # self.selectDoValidation.set(True) # # srow += 1 # label = Label(frame, text='') # label.grid(row=srow,column=0,sticky='nw') # # srow += 1 label = Label(frame, text='checks') label.grid(row=srow,column=0,sticky='nw') self.selectCheckAssign = CheckButton(frame) self.selectCheckAssign.grid(row=srow, column=1,sticky='nw' ) self.selectCheckAssign.set(True) label = Label(frame, text='assignments and shifts') label.grid(row=srow,column=2,sticky='nw') # srow += 1 # self.selectCheckQueen = CheckButton(frame) # self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' ) # self.selectCheckQueen.set(False) # label = Label(frame, text='QUEEN') # label.grid(row=srow,column=5,sticky='nw') # # queenButton = Button(frame, bd=1,command=None, text='setup') # queenButton.grid(row=srow,column=6,sticky='ew') srow += 1 self.selectCheckResraint = CheckButton(frame) self.selectCheckResraint.grid(row=srow, column=1,sticky='nw' ) self.selectCheckResraint.set(True) label = Label(frame, text='restraints') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectCheckStructure = CheckButton(frame) self.selectCheckStructure.grid(row=srow, column=1,sticky='nw' ) self.selectCheckStructure.set(True) label = Label(frame, text='structural') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectMakeHtml = CheckButton(frame) self.selectMakeHtml.grid(row=srow, column=1,sticky='nw' ) self.selectMakeHtml.set(True) label = Label(frame, text='generate HTML') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectCheckScript = CheckButton(frame) self.selectCheckScript.grid(row=srow, column=1,sticky='nw' ) self.selectCheckScript.set(False) label = Label(frame, text='user script') label.grid(row=srow,column=0,sticky='nw') self.validScriptEntry = Entry(frame, bd=1, text='') self.validScriptEntry.grid(row=srow,column=2,columnspan=3, sticky='ew') scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse') scriptButton.grid(row=srow,column=5,sticky='ew') srow += 1 label = Label(frame, text='ranges') label.grid(row=srow,column=0,sticky='nw') self.rangesEntry = Entry( frame, text='' ) self.rangesEntry.grid( row=srow, column=2, columnspan=3, sticky='ew') # self.validScriptEntry = Entry(frame, bd=1, text='') # self.validScriptEntry.grid(row=srow,column=3,sticky='ew') # # scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse') # scriptButton.grid(row=srow,column=4,sticky='ew') srow += 1 texts = ['Run Validation','View Results','Setup QUEEN'] commands = [self.runCing, None, None] buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True) buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew') for button in buttonBar.buttons: button.config(**actionButtonAttributes) # end for self.runButton = buttonBar.buttons[0] self.viewResultButton = buttonBar.buttons[1] self.queenButton = buttonBar.buttons[2] #---------------------------------------------------------------------------------- # Miscellaneous frame #---------------------------------------------------------------------------------- row +=0 col=1 # frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont) frame = LabelFrame(guiFrame, text='Miscellaneous', **labelFrameAttributes) frame.grid(row=row, column=col, sticky='news') frame.grid_columnconfigure(2, weight=1) frame.grid_columnconfigure(4, weight=1,minsize=30) frame.grid_rowconfigure(0, weight=1) # Exports srow = 0 label = Label(frame, text='export to') label.grid(row=srow,column=0,sticky='nw') self.selectExportXeasy = CheckButton(frame) self.selectExportXeasy.grid(row=srow, column=1,sticky='nw' ) self.selectExportXeasy.set(True) label = Label(frame, text='Xeasy, Sparky, TALOS, ...') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectExportCcpn = CheckButton(frame) self.selectExportCcpn.grid(row=srow, column=1,sticky='nw' ) self.selectExportCcpn.set(True) label = Label(frame, text='CCPN') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectExportQueen = CheckButton(frame) self.selectExportQueen.grid(row=srow, column=1,sticky='nw' ) self.selectExportQueen.set(True) label = Label(frame, text='QUEEN') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectExportRefine = CheckButton(frame) self.selectExportRefine.grid(row=srow, column=1,sticky='nw' ) self.selectExportRefine.set(True) label = Label(frame, text='refine') label.grid(row=srow,column=2,sticky='nw') srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') # User script srow += 1 label = Label(frame, text='user script') label.grid(row=srow,column=0,sticky='nw') self.selectMiscScript = CheckButton(frame) self.selectMiscScript.grid(row=srow, column=1,sticky='nw' ) self.selectMiscScript.set(False) self.miscScriptEntry = Entry(frame, bd=1, text='') self.miscScriptEntry.grid(row=srow,column=3,sticky='ew') script2Button = Button(frame, bd=1,command=self.chooseMiscScript, text='browse') script2Button.grid(row=srow,column=4,sticky='ew') srow += 1 texts = ['Export','Run Script'] commands = [None, None] buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True) buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew') for button in buttonBar.buttons: button.config(**actionButtonAttributes) # end for self.exportButton = buttonBar.buttons[0] self.scriptButton = buttonBar.buttons[1] #---------------------------------------------------------------------------------- # Textarea #---------------------------------------------------------------------------------- row +=1 guiFrame.grid_rowconfigure(row, weight=1) self.outputTextBox = ScrolledText(guiFrame) self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew') self.redirectConsole() #---------------------------------------------------------------------------------- # Buttons #---------------------------------------------------------------------------------- row +=1 col=0 texts = ['Quit', 'Help'] commands = [self.close, None] self.buttonBar = ButtonList(guiFrame, texts=texts, commands=commands,expands=True) self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew') # self.openProjectButton = self.buttonBar.buttons[0] # self.closeProjectButton = self.buttonBar.buttons[1] # self.runButton = self.buttonBar.buttons[0] # self.viewResultButton = self.buttonBar.buttons[1] for button in self.buttonBar.buttons: button.config(**actionButtonAttributes) # end for # end def body def getGuiOptions(self): projectName = self.projEntry.get() index = self.projOptionsSelect.getIndex() if index > 0: makeNewProject = True projectImport = None if index > 1: i = index-2 format = ['PDB','CCPN','CYANA'][i] file = [self.pdbEntry, self.ccpnEntry, self.cyanaEntry][i].get() if not file: showWarning('Failure','No %s file selected' % format) return # end if projectImport = (format, file) # end if else: # Chould also check that any old project file exists makeNewProject = False projectImport = None # end if doValidation = self.selectDoValidation.get() checks = [] if doValidation: if self.selectCheckAssign.get(): checks.append('assignments') # end if if self.selectCheckResraint.get(): checks.append('restraints') # end if if self.selectCheckStructure.get(): checks.append('structural') # end if if self.selectMakeHtml.get(): checks.append('HTML') # end if if self.selectCheckScript.get(): script = self.validScriptEntry.get() if script: checks.append( ('script',script) ) # end if # end if if self.selectCheckQueen.get(): checks.append('queen') # end if # end if exports = [] if self.selectExportXeasy.get(): exports.append('Xeasy') # end if if self.selectExportCcpn.get(): exports.append('CCPN') # end if if self.selectExportQueen.get(): exports.append('QUEEN') # end if if self.selectExportRefine.get(): exports.append('refine') # end if miscScript = None if self.selectMiscScript.get(): script = self.miscScriptEntry.get() if script: miscScript = script # end if # end if return projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript # end def getGuiOptions def runCing(self): options = self.getGuiOptions() if options: projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript = options print 'Project name:', projectName print 'Make new project?', makeNewProject print 'Import source:', projectImport print 'Do vailidation?', doValidation print 'Validation checks:', ','.join(checks) print 'Export to:', ','.join(exports) print 'User script:', miscScript # end if # end def runCing # else there was already an error message def chooseOldProjectFile(self): fileTypes = [ FileType('CING', ['project.xml']), FileType('All', ['*']) ] popup = FileSelectPopup(self, file_types = fileTypes, title = 'Select CING project file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = popup.getFile() # dirName = popup.getDirectory() if len(fileName) > 0: # Put text into entry,name widgets dummy,name = cing.Project.rootPath(fileName) self.projEntry.configure(state='normal') self.projEntry.set(fileName) self.nameEntry.configure(state='normal') self.nameEntry.set(name) self.nameEntry.configure(state='disabled') # choose the correct radiobutton self.projOptionsSelect.setIndex(0) self.updateGui() # end if #nd if popup.destroy() # end def chooseOldProjectFile def choosePdbFile(self): fileTypes = [ FileType('PDB', ['*.pdb']), FileType('All', ['*'])] popup = FileSelectPopup(self, file_types = fileTypes, title = 'PDB file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = popup.getFile() if len(fileName)>0: # Put text into entry widget self.pdbEntry.configure(state='normal') self.pdbEntry.set(fileName) # Put text into name widget _dir,name,dummy = nTpath( fileName ) self.nameEntry.configure(state='normal') self.nameEntry.set(name) # choose the correct radiobutton self.projOptionsSelect.setIndex(1) self.updateGui() #end if popup.destroy() # end def choosePdbFile def chooseCcpnFile(self): fileTypes = [ FileType('XML', ['*.xml']), FileType('All', ['*'])] popup = FileSelectPopup(self, file_types = fileTypes, title = 'CCPN project XML file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = popup.getFile() if len(fileName)>0: self.pdbEntry.configure(state='normal') self.pdbEntry.set(fileName) self.projOptionsSelect.setIndex(1) _dir,name,dummy = nTpath( fileName ) self.nameEntry.set(name) #end if self.ccpnEntry.set(fileName) self.projOptionsSelect.setIndex(2) popup.destroy() # end def chooseCcpnFile def chooseCyanaFile(self): # Prepend default Cyana file extension below fileTypes = [ FileType('All', ['*']), ] popup = FileSelectPopup(self, file_types = fileTypes, title = 'CYANA fproject file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = popup.getFile() self.cyanaEntry.set(fileName) self.projOptionsSelect.setIndex(3) popup.destroy() # end def chooseCyanaFile def chooseValidScript(self): # Prepend default Cyana file extension below fileTypes = [ FileType('All', ['*']), ] popup = FileSelectPopup(self, file_types = fileTypes, title = 'Script file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = popup.getFile() self.validScriptEntry.set(fileName) popup.destroy() # end def chooseValidScript def chooseMiscScript(self): # Prepend default Cyana file extension below fileTypes = [ FileType('All', ['*']), ] popup = FileSelectPopup(self, file_types = fileTypes, title = 'Script file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = popup.getFile() self.miscScriptEntry.set(fileName) popup.destroy() # end def chooseMiscScript def openProject(self ): projOption = self.projOptionsSelect.get() if projOption == self.projectOptions[0]: self.openOldProject() elif projOption == self.projectOptions[1]: self.initPdb() # end if if self.project: self.project.gui = self # end if self.updateGui() #end def def openOldProject(self ): fName = self.projEntry.get() if not os.path.exists( fName ): nTerror('Error: file "%s" does not exist\n', fName) #end if if self.project: self.closeProject() # end if self.project = cing.Project.open( name=fName, status='old', verbose=False ) #end def def initPdb(self ): fName = self.pdbEntry.get() if not os.path.exists( fName ): nTerror('Error: file "%s" does not exist\n', fName) #end if self.project = cing.Project.open( self.nameEntry.get(), status='new' ) self.project.initPDB( pdbFile=fName, convention = 'PDB' ) #end def def closeProject(self): if self.project: self.project.close() # end if self.project = None self.updateGui() #end def def updateGui(self, event=None): projOption = self.projOptionsSelect.get() buttons = self.buttonBar.buttons # Disable entries for e in [self.projEntry, self.pdbEntry, self.ccpnEntry, self.cyanaEntry, self.nameEntry]: e.configure(state='disabled') #end for if projOption == self.projectOptions[0]: # Enable entries self.projEntry.configure(state='normal') if (len(self.projEntry.get()) > 0): self.openProjectButton.enable() self.runButton.enable() else: self.openProjectButton.disable() self.runButton.disable() #end if elif projOption == self.projectOptions[1]: # Enable entries self.pdbEntry.configure(state='normal') self.nameEntry.configure(state='normal') if (len(self.pdbEntry.get()) > 0 and len(self.nameEntry.get()) > 0): buttons[0].enable() buttons[1].enable() else: buttons[0].disable() buttons[1].disable() #end if #end if elif projOption == self.projectOptions[2]: # Enable entries self.ccpnEntry.configure(state='normal') self.nameEntry.configure(state='normal') if (len(self.ccpnEntry.get()) > 0 and len(self.nameEntry.get()) > 0): buttons[0].enable() buttons[1].enable() else: buttons[0].disable() buttons[1].disable() #end if #end if elif projOption == self.projectOptions[3]: # Enable entries self.cyanaEntry.configure(state='normal') self.nameEntry.configure(state='normal') if (len(self.cyanaEntry.get()) > 0 and len(self.nameEntry.get()) > 0): buttons[0].enable() buttons[1].enable() else: buttons[0].disable() buttons[1].disable() #end if #end if self.projectStatus.clear() if not self.project: self.projectStatus.setText('No open project') self.closeProjectButton.setText('Close Project') self.closeProjectButton.disable() else: self.projectStatus.setText(self.project.format()) self.closeProjectButton.enable() self.closeProjectButton.setText(sprintf('Close Project "%s"', self.project.name)) #end if #end def def redirectConsole(self): #pipe = TextPipe(self.inputTextBox.text_area) #sys.stdin = pipe pipe = TextPipe(self.outputTextBox.text_area) sys.stdout = pipe nTmessage.stream = pipe # end def redirectConsole # sys.stderr = pipe def resetConsole(self): #sys.stdin = stdin nTmessage.stream = stdout sys.stdout = stdout sys.stderr = stderr # end def resetConsole def open(self): self.redirectConsole() BasePopup.open(self) # end def open def close(self): geometry = self.getGeometry() self.resetConsole() BasePopup.close(self) print 'close:',geometry sys.exit(0) # remove later # end def close def destroy(self): geometry = self.getGeometry() self.resetConsole() BasePopup.destroy(self) print 'destroy:',geometry sys.exit(0) # remove later
def body(self, mainFrame): mainFrame.grid_columnconfigure(1, weight=1, minsize=100) mainFrame.config(borderwidth=5, relief='solid') row = 0 label = Label(mainFrame, text="Frame (with sub-widgets):") label.grid(row=row, column=0, sticky=Tkinter.E) frame = Frame(mainFrame, relief='raised', border=2, background='#8080D0') # Frame expands East-West frame.grid(row=row, column=1, sticky=Tkinter.EW) # Last column expands => Widgets pusted to the West frame.grid_columnconfigure(3, weight=1) # Label is within the sub frame label = Label(frame, text='label ') label.grid(row=0, column=0, sticky=Tkinter.W) entry = Entry(frame, text='Entry', returnCallback=self.showWarning) entry.grid(row=0, column=1, sticky=Tkinter.W) self.check = CheckButton(frame, text='Checkbutton', selected=True, callback=self.updateObjects) self.check.grid(row=0, column=2, sticky=Tkinter.W) # stick a button to the East wall button = Button(frame, text='Button', command=self.pressButton) button.grid(row=0, column=3, sticky=Tkinter.E) row += 1 label = Label(mainFrame, text="Text:") label.grid(row=row, column=0, sticky=Tkinter.E) self.textWindow = Text(mainFrame, text='Initial Text\n', width=60, height=5) self.textWindow.grid(row=row, column=1, sticky=Tkinter.NSEW) row += 1 label = Label(mainFrame, text="CheckButtons:") label.grid(row=row, column=0, sticky=Tkinter.E) entries = ['Alpha','Beta','Gamma','Delta'] selected = entries[2:] self.checkButtons = CheckButtons(mainFrame, entries, selected=selected,select_callback=self.changedCheckButtons) self.checkButtons.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="PartitionedSelector:") label.grid(row=row, column=0, sticky=Tkinter.E) labels = ['Bool','Int','Float','String'] objects = [type(0),type(1),type(1.0),type('a')] selected = [type('a')] self.partitionedSelector= PartitionedSelector(mainFrame, labels=labels, objects=objects, colors = ['red','yellow','green','#000080'], callback=self.toggleSelector,selected=selected) self.partitionedSelector.grid(row=row, column=1, sticky=Tkinter.EW) row += 1 label = Label(mainFrame, text="PulldownMenu") label.grid(row=row, column=0, sticky=Tkinter.E) entries = ['Frodo','Pipin','Merry','Sam','Bill','Gandalf','Strider','Gimli','Legolas'] self.pulldownMenu = PulldownMenu(mainFrame, callback=self.selectPulldown, entries=entries, selected_index=2, do_initial_callback=False) self.pulldownMenu.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="RadioButtons in a\nScrolledFrame.frame:") label.grid(row=row, column=0, sticky=Tkinter.EW) frame = ScrolledFrame(mainFrame, yscroll = False, doExtraConfig = True, width=100) frame.grid(row=row, column=1, sticky=Tkinter.EW) frame.grid_columnconfigure(0, weight=1) self.radioButtons = RadioButtons(frame.frame, entries=entries, select_callback=self.checkRadioButtons, selected_index=1, relief='groove') self.radioButtons.grid(row=0, column=0, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="LabelFrame with\nToggleLabels inside:") label.grid(row=row, column=0, sticky=Tkinter.E) labelFrame = LabelFrame(mainFrame, text='Frame Title') labelFrame.grid(row=row, column=1, sticky=Tkinter.NSEW) labelFrame.grid_rowconfigure(0, weight=1) labelFrame.grid_columnconfigure(3, weight=1) self.toggleLabel1 = ToggleLabel(labelFrame, text='ScrolledMatrix', callback=self.toggleFrame1) self.toggleLabel1.grid(row=0, column=0, sticky=Tkinter.W) self.toggleLabel1.arrowOn() self.toggleLabel2 = ToggleLabel(labelFrame, text='ScrolledGraph', callback=self.toggleFrame2) self.toggleLabel2.grid(row=0, column=1, sticky=Tkinter.W) self.toggleLabel3 = ToggleLabel(labelFrame, text='ScrolledCanvas', callback=self.toggleFrame3) self.toggleLabel3.grid(row=0, column=2, sticky=Tkinter.W) row += 1 mainFrame.grid_rowconfigure(row, weight=1) label = Label(mainFrame, text="changing/shrinking frames:") label.grid(row=row, column=0, sticky=Tkinter.E) self.toggleRow = row self.toggleFrame = Frame(mainFrame) self.toggleFrame.grid(row=row, column=1, sticky=Tkinter.NSEW) self.toggleFrame.grid_rowconfigure(0, weight=1) self.toggleFrame.grid_columnconfigure(0, weight=1) # option 1 self.intEntry = IntEntry(self, returnCallback = self.setNumber, width=8) self.multiWidget = MultiWidget(self, Entry, options=None, values=None, callback=self.setKeywords, minRows=3, maxRows=5) editWidgets = [None, None, self.intEntry, self.multiWidget] editGetCallbacks = [None, None, self.getNumber, self.getKeywords] editSetCallbacks = [None, None, self.setNumber, self.setKeywords] headingList = ['Name','Color','Number','Keywords'] self.scrolledMatrix = ScrolledMatrix(self.toggleFrame, headingList=headingList, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, callback=self.selectObject, multiSelect=False) self.scrolledMatrix.grid(row=0, column=0, sticky=Tkinter.NSEW) # option 2 self.scrolledGraph = ScrolledGraph(self.toggleFrame, width=400, height=300, symbolSize=5, symbols=['square','circle'], dataColors=['#000080','#800000'], lineWidths=[0,1] ) self.scrolledGraph.setZoom(1.3) dataSet1 = [[0,0],[1,1],[2,4],[3,9],[4,16],[5,25]] dataSet2 = [[0,0],[1,3],[2,6],[3,9],[4,12],[5,15]] self.scrolledGraph.update(dataSets=[dataSet1,dataSet2], xLabel = 'X axis label', yLabel = 'Y axis label', title = 'Main Title') self.scrolledGraph.draw() # option 3 self.scrolledCanvas = ScrolledCanvas(self.toggleFrame,relief = 'groove', borderwidth = 2, resizeCallback=None) canvas = self.scrolledCanvas.canvas font = 'Helvetica 10' box = canvas.create_rectangle(10,10,150,200, outline='grey', fill='grey90') line = canvas.create_line(0,0,200,200,fill='#800000', width=2) text = canvas.create_text(120,50, text='Text', font=font, fill='black') circle = canvas.create_oval(30,30,50,50,outline='#008000',fill='#404040',width=3) row += 1 label = Label(mainFrame, text="FloatEntry:") label.grid(row=row, column=0, sticky=Tkinter.E) self.floatEntry = FloatEntry(mainFrame, text=3.14159265, returnCallback=self.floatEntryReturn) self.floatEntry.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="Scale:") label.grid(row=row, column=0, sticky=Tkinter.E) self.scale = Scale(mainFrame, from_=10, to=90, value=50, orient=Tkinter.HORIZONTAL) self.scale.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="Value Ramp:") label.grid(row=row, column=0, sticky=Tkinter.E) self.valueRamp = ValueRamp(mainFrame, self.valueRampCallback, speed = 1.5, delay = 50) self.valueRamp.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="ButtonList:") label.grid(row=row, column=0, sticky=Tkinter.E) texts = ['Select File','Close','Quit'] commands = [self.selectFile, self.close, self.quit] bottomButtons = ButtonList(mainFrame, texts=texts, commands=commands, expands=True) bottomButtons.grid(row=row, column=1, sticky=Tkinter.EW) self.protocol('WM_DELETE_WINDOW', self.quit)
def body(self, guiFrame): row = 0 col =0 # frame = Frame( guiFrame ) # frame.grid(row=row, column=col, sticky='news') self.menuBar = Menu( guiFrame) self.menuBar.grid( row=row, column=col, sticky='ew') #---------------------------------------------------------------------------------- # Project frame #---------------------------------------------------------------------------------- # guiFrame.grid_columnconfigure(row, weight=1) # frame = LabelFrame(guiFrame, text='Project', font=medFont) row = +1 col =0 frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes ) print '>', frame.keys() frame.grid(row=row, column=col, sticky='nsew' ) frame.grid_columnconfigure(2, weight=1) # frame.grid_rowconfigure(0, weight=1) srow = 0 self.projectOptions = ['old','new from PDB','new from CCPN','new from CYANA'] self.projOptionsSelect = RadioButtons(frame, selected_index=0, entries=self.projectOptions, direction='vertical', select_callback=self.updateGui ) self.projOptionsSelect.grid(row=srow,column=0,rowspan=len(self.projectOptions),columnspan=2, sticky='w') if self.options.name: text = self.options.name else: text='' # end if self.projEntry = Entry(frame, bd=1, text=text, returnCallback=self.updateGui) self.projEntry.grid(row=srow,column=2,columnspan=2,sticky='ew') # self.projEntry.bind('<Key>', self.updateGui) self.projEntry.bind('<Leave>', self.updateGui) projButton = Button(frame, bd=1,command=self.chooseOldProjectFile, text='browse') projButton.grid(row=srow,column=3,sticky='ew') srow += 1 self.pdbEntry = Entry(frame, bd=1, text='') self.pdbEntry.grid(row=srow,column=2,sticky='ew') self.pdbEntry.bind('<Leave>', self.updateGui) pdbButton = Button(frame, bd=1,command=self.choosePdbFile, text='browse') pdbButton.grid(row=srow,column=3,sticky='ew') srow += 1 self.ccpnEntry = Entry(frame, bd=1, text='') self.ccpnEntry.grid(row=srow,column=2,sticky='ew') self.ccpnEntry.bind('<Leave>', self.updateGui) ccpnButton = Button(frame, bd=1,command=self.chooseCcpnFile, text='browse') ccpnButton.grid(row=srow,column=3,sticky='ew') srow += 1 self.cyanaEntry = Entry(frame, bd=1, text='') self.cyanaEntry.grid(row=srow,column=2,sticky='ew') self.cyanaEntry.bind('<Leave>', self.updateGui) cyanaButton = Button(frame, bd=1,command=self.chooseCyanaFile, text='browse') cyanaButton.grid(row=srow,column=3,sticky='ew') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') srow += 1 label = Label(frame, text='Project name:') label.grid(row=srow,column=0,sticky='nw') self.nameEntry = Entry(frame, bd=1, text='') self.nameEntry.grid(row=srow,column=2,sticky='w') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') srow += 1 self.openProjectButton = Button(frame, command=self.openProject, text='Open Project', **actionButtonAttributes ) self.openProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew') #---------------------------------------------------------------------------------- # status #---------------------------------------------------------------------------------- # guiFrame.grid_columnconfigure(1, weight=0) srow = 0 frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes) frame.grid( row=srow, column=1, sticky='wnes') self.projectStatus = Text(frame, height=11, width=70, borderwidth=0, relief='flat') self.projectStatus.grid(row=0, column=0, sticky='wen') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') srow += 1 self.closeProjectButton = Button(frame, command=self.closeProject, text='Close Project', **actionButtonAttributes) self.closeProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew') #---------------------------------------------------------------------------------- # Validate frame #---------------------------------------------------------------------------------- row +=1 col=0 frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes) # frame = LabelFrame(guiFrame, text='Validate', font=medFont) frame.grid(row=row, column=col, sticky='nsew') # frame.grid_columnconfigure(2, weight=1) frame.grid_rowconfigure(0, weight=1) srow = 0 # label = Label(frame, text='validation') # label.grid(row=srow,column=0,sticky='nw') # # self.selectDoValidation = CheckButton(frame) # self.selectDoValidation.grid(row=srow, column=1,sticky='nw' ) # self.selectDoValidation.set(True) # # srow += 1 # label = Label(frame, text='') # label.grid(row=srow,column=0,sticky='nw') # # srow += 1 label = Label(frame, text='checks') label.grid(row=srow,column=0,sticky='nw') self.selectCheckAssign = CheckButton(frame) self.selectCheckAssign.grid(row=srow, column=1,sticky='nw' ) self.selectCheckAssign.set(True) label = Label(frame, text='assignments and shifts') label.grid(row=srow,column=2,sticky='nw') # srow += 1 # self.selectCheckQueen = CheckButton(frame) # self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' ) # self.selectCheckQueen.set(False) # label = Label(frame, text='QUEEN') # label.grid(row=srow,column=5,sticky='nw') # # queenButton = Button(frame, bd=1,command=None, text='setup') # queenButton.grid(row=srow,column=6,sticky='ew') srow += 1 self.selectCheckResraint = CheckButton(frame) self.selectCheckResraint.grid(row=srow, column=1,sticky='nw' ) self.selectCheckResraint.set(True) label = Label(frame, text='restraints') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectCheckStructure = CheckButton(frame) self.selectCheckStructure.grid(row=srow, column=1,sticky='nw' ) self.selectCheckStructure.set(True) label = Label(frame, text='structural') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectMakeHtml = CheckButton(frame) self.selectMakeHtml.grid(row=srow, column=1,sticky='nw' ) self.selectMakeHtml.set(True) label = Label(frame, text='generate HTML') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectCheckScript = CheckButton(frame) self.selectCheckScript.grid(row=srow, column=1,sticky='nw' ) self.selectCheckScript.set(False) label = Label(frame, text='user script') label.grid(row=srow,column=0,sticky='nw') self.validScriptEntry = Entry(frame, bd=1, text='') self.validScriptEntry.grid(row=srow,column=2,columnspan=3, sticky='ew') scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse') scriptButton.grid(row=srow,column=5,sticky='ew') srow += 1 label = Label(frame, text='ranges') label.grid(row=srow,column=0,sticky='nw') self.rangesEntry = Entry( frame, text='' ) self.rangesEntry.grid( row=srow, column=2, columnspan=3, sticky='ew') # self.validScriptEntry = Entry(frame, bd=1, text='') # self.validScriptEntry.grid(row=srow,column=3,sticky='ew') # # scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse') # scriptButton.grid(row=srow,column=4,sticky='ew') srow += 1 texts = ['Run Validation','View Results','Setup QUEEN'] commands = [self.runCing, None, None] buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True) buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew') for button in buttonBar.buttons: button.config(**actionButtonAttributes) # end for self.runButton = buttonBar.buttons[0] self.viewResultButton = buttonBar.buttons[1] self.queenButton = buttonBar.buttons[2] #---------------------------------------------------------------------------------- # Miscellaneous frame #---------------------------------------------------------------------------------- row +=0 col=1 # frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont) frame = LabelFrame(guiFrame, text='Miscellaneous', **labelFrameAttributes) frame.grid(row=row, column=col, sticky='news') frame.grid_columnconfigure(2, weight=1) frame.grid_columnconfigure(4, weight=1,minsize=30) frame.grid_rowconfigure(0, weight=1) # Exports srow = 0 label = Label(frame, text='export to') label.grid(row=srow,column=0,sticky='nw') self.selectExportXeasy = CheckButton(frame) self.selectExportXeasy.grid(row=srow, column=1,sticky='nw' ) self.selectExportXeasy.set(True) label = Label(frame, text='Xeasy, Sparky, TALOS, ...') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectExportCcpn = CheckButton(frame) self.selectExportCcpn.grid(row=srow, column=1,sticky='nw' ) self.selectExportCcpn.set(True) label = Label(frame, text='CCPN') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectExportQueen = CheckButton(frame) self.selectExportQueen.grid(row=srow, column=1,sticky='nw' ) self.selectExportQueen.set(True) label = Label(frame, text='QUEEN') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectExportRefine = CheckButton(frame) self.selectExportRefine.grid(row=srow, column=1,sticky='nw' ) self.selectExportRefine.set(True) label = Label(frame, text='refine') label.grid(row=srow,column=2,sticky='nw') srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') # User script srow += 1 label = Label(frame, text='user script') label.grid(row=srow,column=0,sticky='nw') self.selectMiscScript = CheckButton(frame) self.selectMiscScript.grid(row=srow, column=1,sticky='nw' ) self.selectMiscScript.set(False) self.miscScriptEntry = Entry(frame, bd=1, text='') self.miscScriptEntry.grid(row=srow,column=3,sticky='ew') script2Button = Button(frame, bd=1,command=self.chooseMiscScript, text='browse') script2Button.grid(row=srow,column=4,sticky='ew') srow += 1 texts = ['Export','Run Script'] commands = [None, None] buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True) buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew') for button in buttonBar.buttons: button.config(**actionButtonAttributes) # end for self.exportButton = buttonBar.buttons[0] self.scriptButton = buttonBar.buttons[1] #---------------------------------------------------------------------------------- # Textarea #---------------------------------------------------------------------------------- row +=1 guiFrame.grid_rowconfigure(row, weight=1) self.outputTextBox = ScrolledText(guiFrame) self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew') self.redirectConsole() #---------------------------------------------------------------------------------- # Buttons #---------------------------------------------------------------------------------- row +=1 col=0 texts = ['Quit', 'Help'] commands = [self.close, None] self.buttonBar = ButtonList(guiFrame, texts=texts, commands=commands,expands=True) self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew') # self.openProjectButton = self.buttonBar.buttons[0] # self.closeProjectButton = self.buttonBar.buttons[1] # self.runButton = self.buttonBar.buttons[0] # self.viewResultButton = self.buttonBar.buttons[1] for button in self.buttonBar.buttons: button.config(**actionButtonAttributes)
def body(self, guiFrame): guiFrame.grid_columnconfigure(2, weight=1) row = 0 label = Label(guiFrame, text='Template window: ', grid=(row, 0)) tipText = 'Selects which window to use as the basis for making a new spectrum window; sets the axis types accordingly' self.window_list = PulldownList(guiFrame, grid=(row, 1), callback=self.setAxisTypes, tipText=tipText) frame = LabelFrame(guiFrame, text='Strips', grid=(row, 2), gridSpan=(2, 1)) buttons = UtilityButtonList(guiFrame, doClone=False, helpUrl=self.help_url, grid=(row, 3)) row += 1 label = Label(guiFrame, text='New window name: ', grid=(row, 0)) tipText = 'A short name to identify the spectrum window, which will appear in the graphical interface' self.nameEntry = Entry(guiFrame, width=16, grid=(row, 1), tipText=tipText) row += 1 label = Label(frame, text='Columns: ', grid=(0, 0)) tipText = 'The number of vertical strips/dividers to initially make in the spectrum window' self.cols_menu = PulldownList(frame, objects=STRIP_NUMS, grid=(0, 1), texts=[str(x) for x in STRIP_NUMS], tipText=tipText) label = Label(frame, text='Rows: ', grid=(0, 2)) tipText = 'The number of horizontal strips/dividers to initially make in the spectrum window' self.rows_menu = PulldownList(frame, objects=STRIP_NUMS, grid=(0, 3), texts=[str(x) for x in STRIP_NUMS], tipText=tipText) row += 1 div = LabelDivider(guiFrame, text='Axes', grid=(row, 0), gridSpan=(1, 4)) row += 1 self.axis_lists = {} frame = Frame(guiFrame, grid=(row, 0), gridSpan=(1, 4)) col = 0 self.axisTypes = {} self.axisTypesIncludeNone = {} for label in AXIS_LABELS: self.axisTypes[label] = None w = Label(frame, text=' ' + label) w.grid(row=0, column=col, sticky='w') col += 1 if label in ('x', 'y'): includeNone = False tipText = 'Sets the kind of measurement (typically ppm for a given isotope) that will be used along the window %s axis' % label else: includeNone = True tipText = 'Where required, sets the kind of measurement (typically ppm for a given isotope) that will be used along the window %s axis' % label self.axisTypesIncludeNone[label] = includeNone getAxisTypes = lambda label=label: self.getAxisTypes(label) callback = lambda axisType, label=label: self.changedAxisType( label, axisType) self.axis_lists[label] = PulldownList(frame, callback=callback, tipText=tipText) self.axis_lists[label].grid(row=0, column=col, sticky='w') col += 1 frame.grid_columnconfigure(col, weight=1) row += 1 div = LabelDivider(guiFrame, text='Viewed Spectra', grid=(row, 0), gridSpan=(1, 4)) row += 1 guiFrame.grid_rowconfigure(row, weight=1) editWidgets = [None, None, None, None] editGetCallbacks = [None, self.toggleVisible, self.toggleToolbar, None] editSetCallbacks = [None, None, None, None] tipTexts = [ 'The "experiment:spectrum" name for the spectrum that may be viewed in the new window, given the axis selections', 'Sets whether the spectrum contours will be visible in the new window', 'Sets whether the spectrum appears at all in the window; if not in the toolbar it cannot be displayed', 'The number of peak lists the spectrum contains' ] headingList = ['Spectrum', 'Visible?', 'In Toolbar?', 'Peak Lists'] self.scrolledMatrix = ScrolledMatrix(guiFrame, headingList=headingList, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, multiSelect=True, grid=(row, 0), gridSpan=(1, 4), tipTexts=tipTexts) row += 1 tipTexts = [ 'Creates a new spectrum window with the specified parameters', 'Sets the contours of the selected spectra to be visible when the new window is made', 'Sets the contours of the selected spectra to not be displayed when the new window is made', 'Sets the selected spectra as absent from the window toolbar, and thus not displayable at all' ] texts = [ 'Create Window!', 'Selected\nVisible', 'Selected\nNot Visible', 'Selected\nNot In Toolbar' ] commands = [ self.ok, self.setSelectedDisplay, self.setSelectedHide, self.setSelectedAbsent ] buttonList = ButtonList(guiFrame, texts=texts, grid=(row, 0), commands=commands, gridSpan=(1, 4), tipTexts=tipTexts) buttonList.buttons[0].config(bg='#B0FFB0') self.updateAxisTypes() self.updateWindow() self.updateWindowName() self.administerNotifiers(self.registerNotify) self.updateAfter()
class MeccanoPopup(BasePopup): def __init__(self, parent, project, *args, **kw): self.alignMedium = None self.chain = None self.constraint = None self.constraintSet = None self.molSystem = None self.project = project self.run = None self.shiftList = None self.tensor = None BasePopup.__init__(self, parent=parent, title='MECCANO', *args, **kw) self.curateNotifiers(self.registerNotify) 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() def close(self): self.updateRunParams() BasePopup.close(self) def destroy(self): self.updateRunParams() self.curateNotifiers(self.unregisterNotify) BasePopup.destroy(self) def curateNotifiers(self, notifyFunc): for func in ('__init__', 'delete'): notifyFunc(self.updateConstraintSetsAfter, 'ccp.nmr.NmrConstraint.NmrConstraintStore', func) for func in ('__init__', 'delete','setName','setConditionState'): for clazz in ('ccp.nmr.NmrConstraint.CsaConstraintList', 'ccp.nmr.NmrConstraint.DihedralConstraintList', 'ccp.nmr.NmrConstraint.DistanceConstraintList', 'ccp.nmr.NmrConstraint.HBondConstraintList', 'ccp.nmr.NmrConstraint.JCouplingConstraintList', 'ccp.nmr.NmrConstraint.RdcConstraintList'): notifyFunc(self.updateConstraintListsAfter, clazz, func) for func in ('__init__', 'delete',): for clazz in ('ccp.nmr.NmrConstraint.CsaConstraint', 'ccp.nmr.NmrConstraint.DihedralConstraint', 'ccp.nmr.NmrConstraint.DistanceConstraint', 'ccp.nmr.NmrConstraint.HBondConstraint', 'ccp.nmr.NmrConstraint.JCouplingConstraint', 'ccp.nmr.NmrConstraint.RdcConstraint'): notifyFunc(self.updateConstraintsAfter, clazz, func) for func in ('__init__', 'delete'): notifyFunc(self.updateShiftListsAfter,'ccp.nmr.Nmr.ShiftList', func) for func in ('__init__', 'delete'): notifyFunc(self.updateMolSystemsAfter,'ccp.molecule.MolSystem.MolSystem', func) for func in ('__init__', 'delete'): notifyFunc(self.updateChainsAfter,'ccp.molecule.MolSystem.Chain', func) for func in ('__init__', 'delete','setDynamicAlignment', 'setStaticAlignment','setName','setDetails'): notifyFunc(self.updateAlignMediaAfter,'ccp.nmr.NmrConstraint.ConditionState', func) def updateAlignMediaAfter(self, alignMedium): if alignMedium.nmrConstraintStore is self.constraintSet: self.after_idle(self.updateAlignMedia) if alignMedium is self.alignMedium: self.after_idle(self.updateTensors) def updateConstraintSetsAfter(self, constraintSet): self.after_idle(self.updateConstraintSets) def updateShiftListsAfter(self, shiftList): self.after_idle(self.updateShiftLists) def updateMolSystemsAfter(self, molSystem): self.after_idle(self.updateMolSystems) def updateChainsAfter(self, chain): self.after_idle(self.updateChains) def updateConstraintsAfter(self, constraint): if constraint.parent.parent is self.constraintSet: self.after_idle(self.updateConstraintLists) def updateConstraintListsAfter(self, constraintList): if constraintList.parent is self.constraintSet: self.after_idle(self.updateConstraintLists) def runMeccano(self): # # # Input checks first # # warning = '' if not self.molSystem: warning += 'No molecular system selected\n' if not self.chain: warning += 'No chain selected\n' if not self.constraintSet: warning += 'No selected constraint set\n' else: constraintLists = [cl for cl in self.constraintSet.constraintLists if cl.useForMeccano] if not constraintLists: warning += 'No constraint lists selected for use\n' first, last = self.updateResidueRanges() if (last-first) < 2: warning += 'Too few peptide planes selected\n' if warning: showWarning('Cannot run MECCANO','Encountered the following problems:\n' + warning) return if not self.run: self.run = self.makeSimRun() self.updateRunParams() if self.toggleCopyShifts.get() and self.shiftList: shiftList = self.run.findFirstOutputMeasurementList(className='ShiftList') if not shiftList: shiftList = self.project.currentNmrProject.newShiftList(name='Meccano Input') self.run.setOutputMeasurementLists([shiftList,]) shiftDict = {} for shift in shiftList.shifts: shiftDict[shift.resonance] = shift for shift in self.shiftList.shifts: resonance = shift.resonance resonanceSet = resonance.resonanceSet if resonanceSet: atom = resonanceSet.findFirstAtomSet().findFirstAtom() if (atom.name == 'C') and (atom.residue.molResidue.molType == 'protein'): shift2 = shiftDict.get(resonance) if shift2: shift2.value = shift.value shift2.error = shift.error else: shiftList.newShift(resonance=resonance, value=shift.value, error=shift.error) # # # Accumulate data from CCPN data model & GUI # # # Sequence residues = self.chain.sortedResidues() residueDict = {} seqData = [] for residue in residues: molResidue = residue.molResidue code1Letter = molResidue.chemComp.code1Letter if not code1Letter: msg = 'Encountered non-standard residue type: %s' showWarning('Cannot run MECCANO', msg % residue.ccpCode) return seqCode = residue.seqCode seqData.append((seqCode, code1Letter)) residueDict[seqCode] = residue.chemCompVar.chemComp.code3Letter # Media, RDCs & Dihedrals rdcLists = [] dihedralLists = [] for constraintList in constraintLists: if constraintList.className == 'RdcConsraintList': if constraintList.conditionState: rdcLists.append(constraintList) elif constraintList.className == 'DihedralConstraintList': dihedralLists.append(dihedralLists) f = PI_OVER_180 mediaData = [] for constraintList in rdcLists: medium = constraintList.conditionState dynamicTensor = medium.dynamicAlignment staticTensor = medium.staticAlignment if not (dynamicTensor or staticTensor): continue if dynamicTensor: dynamicTensorData = ['Dynamic', dynamicTensor.aAxial, dynamicTensor.aRhombic, f*dynamicTensor.alpha, f*dynamicTensor.beta, f*dynamicTensor.gamma] if staticTensor: staticTensorData = ['Static', staticTensor.aAxial, staticTensor.aRhombic, f*staticTensor.alpha, f*staticTensor.beta, f*staticTensor.gamma] if not dynamicTensor: dynamicTensorData = staticTensorData elif not staticTensor: staticTensorData = dynamicTensorData rdcData = [] for restraint in constraintList.constraints: items = list(restraint.items) if len(items) != 1: continue resonanceA, resonanceB = [fr.resonance for fr in items[0].resonances] resonanceSetA = resonanceA.resonanceSet if not resonanceSetA: continue resonanceSetB = resonanceB.resonanceSet if not resonanceSetB: continue resNameA = getResonanceName(resonanceA) resNameB = getResonanceName(resonanceB) residueA = resonanceSetA.findFirstAtomSet().findFirstAtom().residue residueB = resonanceSetB.findFirstAtomSet().findFirstAtom().residue seqA = residueA.seqCode seqB = residueB.seqCode value = restraint.targetValue error = restraint.error if error is None: key = [resNameA,resNameB] key.sort() sigma = DEFAULT_ERRORS.get(tuple(key), 1.0) rdcData.append([seqA, resNameA, seqB, resNameB, value, error]) mediaData.append((dynamicTensorData,staticTensorData,rdcData)) oneTurn = 360.0 dihedralDict = {} for constraintList in dihedralLists: for restraint in constraintList.constraints: items = list(restraint.items) if len(items) != 1: continue item = items[0] resonances = [fr.resonance for fr in item.resonances] resonanceSets = [r.resonanceSet for r in resonances] if None in resonanceSets: continue atoms = [rs.findFirstAtomSet().findFirstAtom() for rs in resonanceSets] atomNames = [a.name for a in atoms] if atomNames == PHI_ATOM_NAMES: isPhi = True elif atomNames == PSI_ATOM_NAMES: isPhi = False else: continue residue = atoms[2].residue if residue.chain is not self.chain: continue if isPhi: residuePrev = getLinkedResidue(residue, linkCode='prev') if not residuePrev: continue atomC0 = residuePrev.findFirstAtom(name='C') atomN = residue.findFirstAtom(name='N') atomCa = residue.findFirstAtom(name='CA') atomC = residue.findFirstAtom(name='C') atoms2 = [atomC0, atomN, atomCa, atomC] else: residueNext = getLinkedResidue(residue, linkCode='next') if not residueNext: continue atomN = residue.findFirstAtom(name='N') atomCa = residue.findFirstAtom(name='CA') atomC = residue.findFirstAtom(name='C') atomN2 = residueNext.findFirstAtom(name='N') atoms2 = [atomN, atomCa, atomC, atomN2] if atoms != atoms2: continue value = item.targetValue error = item.error if error is None: upper = item.upperLimit lower = item.lowerLimit if (upper is not None) and (lower is not None): dUpper = angleDifference(value, lower, oneTurn) dLower = angleDifference(upper, value, oneTurn) error = max(dUpper, dLower) elif lower is not None: error = angleDifference(value, lower, oneTurn) elif upper is not None: error = angleDifference(upper, value, oneTurn) else: error = 30.0 # Arbitrary, but sensible for TALOS, DANGLE seqCode = residue.seqCode if not dihedralDict.has_key(seqCode): dihedralDict[seqCode] = [None, None, None, None] # Phi, Psi, PhiErr, PsiErr if isPhi: dihedralDict[seqCode][0] = value dihedralDict[seqCode][2] = error else: dihedralDict[seqCode][1] = value dihedralDict[seqCode][3] = error phipsiData = [] seqCodes = dihedralDict.keys() seqCodes.sort() for seqCode in seqCodes: data = dihedralDict[seqCode] if None not in data: phi, psi, phiErr, psiErr = data phipsiData.append((seqCode, phi, psi, phiErr, psiErr)) # User options firstPPlaneFrag = self.firstResEntry.get() or 1 lastPPlaneFrag = self.lastResEntry.get() or 1 ppNbMin = self.numOptPlaneEntry.get() or 1 minValueBest = self.numOptHitsEntry.get() or 2 maxValueBest = self.maxOptStepEntry.get() or 5 strucData = Meccano.runFwd(firstPPlaneFrag, lastPPlaneFrag, ppNbMin, minValueBest, maxValueBest, RAMACHANDRAN_DATABASE, seqData, mediaData, phipsiData) if strucData: fileName = 'CcpnMeccanoPdb%f.pdb' % time.time() fileObj = open(fileName, 'w') ch = self.chain.pdbOneLetterCode.strip() if not ch: ch = self.chain.code[0].upper() i = 1 for atomType, resNb, x, y, z in strucData: resType = residueDict.get(resNb, '???') line = PDB_FORMAT % ('ATOM',i,'%-3s' % atomType,'',resType,ch,resNb,'',x,y,z,1.0,1.0) i += 1 fileObj.close() ensemble = getStructureFromFile(self.molSystem, fileName) if not self.toggleWritePdbFile.get(): os.unlink(fileName) self.run.outputEnsemble = ensemble self.run = None self.updateRuns() def getMediumName(self, alignMedium): self.mediumNameEntry.set(alignMedium.name) def getMediumDetails(self, alignMedium): self.mediumDetailsEntry.set(alignMedium.details) def setMediumName(self, event): value = self.mediumNameEntry.get() self.alignMedium.name = value or None def setMediumDetails(self, event): value = self.mediumDetailsEntry.get() self.alignMedium.details = value or None def setAlignMedium(self, alignMedium): if self.constraintSet: self.constraintSet.conditionState = alignMedium def getAlignMedium(self, constraintList): media = self.getAlignmentMedia() names = [am.name for am in media] if constraintList.conditionState in media: index = media.index(constraintList.conditionState) else: index = 0 self.alignMediumPulldown.setup(names, media, index) def toggleUseRestraints(self, constraintList): bool = constraintList.useForMeccano bool = not bool if bool and (not constraintList.conditionState) \ and (constraintList.className == 'RdcConsraintList'): msg = 'Cannot use RDC restraint list for Meccano ' msg += 'unless it is first associated with an amigment medium' showWarning('Warning', msg, parent=self) else: constraintList.useForMeccano = bool self.updateConstraintLists() def addStaticTensor(self): if self.alignMedium: tensor = Implementation.SymmTracelessMatrix(aAxial=0.0,aRhombic=0.0, alpha=0.0,beta=0.0, gamma=0.0) self.alignMedium.staticAlignment = tensor self.updateAlignMediaAfter(self.alignMedium) def addDynamicTensor(self): if self.alignMedium: tensor = Implementation.SymmTracelessMatrix(aAxial=0.0,aRhombic=0.0, alpha=0.0,beta=0.0, gamma=0.0) self.alignMedium.dynamicAlignment = tensor self.updateAlignMediaAfter(self.alignMedium) def removeTensor(self): if self.alignMedium and self.tensor: if self.tensor is self.alignMedium.dynamicAlignment: self.alignMedium.dynamicAlignment = None elif self.tensor is self.alignMedium.staticAlignment: self.alignMedium.staticAlignment = None self.updateAlignMediaAfter(self.alignMedium) def addAlignMedium(self): if self.constraintSet: medium = self.constraintSet.newConditionState() medium.name = 'Align Medium %d' % medium.serial def removeAlignMedium(self): if self.alignMedium: self.alignMedium.delete() def updateTensor(self, aAxial=None, aRhombic=None, alpha=None, beta=None, gamma=None): aAxial = aAxial or self.tensor.aAxial aRhombic = aRhombic or self.tensor.aRhombic alpha = alpha or self.tensor.alpha beta = beta or self.tensor.beta gamma = gamma or self.tensor.gamma tensor = Implementation.SymmTracelessMatrix(aAxial=aAxial, aRhombic=aRhombic, alpha=alpha,beta=beta, gamma=gamma) if self.alignMedium: if self.tensor is self.alignMedium.dynamicAlignment: self.alignMedium.dynamicAlignment = tensor elif self.tensor is self.alignMedium.staticAlignment: self.alignMedium.staticAlignment = tensor self.tensor = tensor def setAxial(self, event): value = self.editAxialEntry.get() self.updateTensor(aAxial=value) self.updateTensors() def setRhombic(self, event): value = self.editRhombicEntry.get() self.updateTensor(aRhombic=value) self.updateTensors() def setEulerAlpha(self, event): value = self.editAlphaEulerEntry.get() self.updateTensor(alpha=value) self.updateTensors() def setEulerBeta(self, event): value = self.editBetaEulerEntry.get() self.updateTensor(beta=value) self.updateTensors() def setEulerGamma(self, event): value = self.editGammaEulerEntry.get() self.updateTensor(gamma=value) self.updateTensors() def getAxial(self, tensor): value = tensor.aAxial self.editAxialEntry.set(value) def getRhombic(self, tensor): value = tensor.aRhombic self.editRhombicEntry.set(value) def getEulerAlpha(self, tensor): value = tensor.alpha self.editAlphaEulerEntry.set(value) def getEulerBeta(self, tensor): value = tensor.beta self.editBetaEulerEntry.set(value) def getEulerGamma(self, tensor): value = tensor.gamma self.editGammaEulerEntry.set(value) def selectTensor(self, tensor, row, col): self.tensor = tensor def selectAlignMedium(self, alignMedium, row, col): self.alignMedium = alignMedium self.updateTensors() def getAlignmentMedia(self): if self.constraintSet: return self.constraintSet.sortedConditionStates() else: return [] def updateAlignMedia(self): textMatrix = [] objectList = [] if self.constraintSet: objectList = self.getAlignmentMedia() for conditionState in objectList: staticTensor = None dyamicTensor = None tensor = conditionState.dynamicAlignment if tensor: vals = (tensor.aAxial, tensor.aRhombic, tensor.alpha, tensor.beta, tensor.gamma) dyamicTensor = u'\u03B6:%.3f \u03B7:%.3f \u03B1:%.3f \u03B2:%.3f \u03B3:%.3f ' % vals tensor = conditionState.staticAlignment if tensor: vals = (tensor.aAxial, tensor.aRhombic, tensor.alpha, tensor.beta, tensor.gamma) staticTensor = u'\u03B6:%.3f \u03B7:%.3f \u03B1:%.3f \u03B2:%.3f \u03B3:%.3f ' % vals datum = [conditionState.serial, conditionState.name, conditionState.details, dyamicTensor, staticTensor] textMatrix.append(datum) if dyamicTensor or staticTensor: if not self.alignMedium: self.alignMedium = conditionState self.mediaMatrix.update(textMatrix=textMatrix, objectList=objectList) if self.alignMedium: self.mediaMatrix.selectObject(self.alignMedium) def updateTensors(self): textMatrix = [] objectList = [] conditionState = self.alignMedium if conditionState: tensor = conditionState.dynamicAlignment if tensor: datum = ['Dynamic', tensor.aAxial, tensor.aRhombic, tensor.alpha, tensor.beta, tensor.gamma] textMatrix.append(datum) objectList.append(tensor) tensor = conditionState.staticAlignment if tensor: datum = ['Static', tensor.aAxial, tensor.aRhombic, tensor.alpha, tensor.beta, tensor.gamma] textMatrix.append(datum) objectList.append(tensor) self.tensorMatrix.update(textMatrix=textMatrix, objectList=objectList) def getMolSystems(self): molSystems = [] for molSystem in self.project.sortedMolSystems(): if molSystem.chains: molSystems.append(molSystem) return molSystems def updateMolSystems(self, *notifyObj): index = 0 names = [] molSystems = self.getMolSystems() molSystem = self.molSystem if molSystems: if molSystem not in molSystems: molSystem = molSystems[0] index = molSystems.index(molSystem) names = [ms.code for ms in molSystems] else: self.molSystem = None if self.molSystem is not molSystem: if self.run: self.run.molSystem = molSystem self.molSystem = molSystem self.updateChains() self.molSystemPulldown.setup(texts=names, objects=molSystems, index=index) def selectMolSystem(self, molSystem): if self.molSystem is not molSystem: if self.run: self.run.molSystem = molSystem self.molSystem = molSystem self.updateChains() def updateChains(self, *notifyObj): index = 0 names = [] chains = [] chain = self.chain if self.molSystem: chains = [c for c in self.molSystem.sortedChains() if c.residues] if chains: if chain not in chains: chain = chains[0] index = chains.index(chain) names = [c.code for c in chains] if chain is not self.chain: self.chain = chain self.updateResidueRanges() self.chainPulldown.setup(texts=names, objects=chains, index=index) def selectChain(self, chain): if chain is not self.chain: self.chain = chain self.updateResidueRanges() def updateResidueRanges(self): first = self.firstResEntry.get() last = self.lastResEntry.get() if self.chain: residues = self.chain.sortedResidues() firstSeq = residues[0].seqCode lastSeq = residues[-2].seqCode if first < firstSeq: first = firstSeq if last == first: last = lastSeq elif last > lastSeq: last = lastSeq if first > last: last, first = first, last self.firstResEntry.set(first) self.lastResEntry.set(last) return first, last def getConstraintSets(self): constraintSets = [] nmrProject = self.project.currentNmrProject for constraintSet in nmrProject.sortedNmrConstraintStores(): for constraintList in constraintSet.constraintLists: if constraintList.className not in ('ChemShiftConstraintList','somethingElse'): constraintSets.append(constraintSet) break return constraintSets def updateConstraintSets(self, *notifyObj): index = 0 names = [] constraintSets = self.getConstraintSets() constraintSet = self.constraintSet if constraintSets: if constraintSet not in constraintSets: constraintSet = constraintSets[0] index = constraintSets.index(constraintSet) names = ['%d' % cs.serial for cs in constraintSets] if constraintSet is not self.constraintSet: if self.run: self.run.inputConstraintStore = constraintSet self.constraintSet = constraintSet self.updateConstraintLists() self.constraintSetPulldown.setup(texts=names, objects=constraintSets, index=index) def selectConstraintSet(self, constraintSet): if self.constraintSet is not constraintSet: if self.run: self.run.inputConstraintStore = constraintSet self.constraintSet = constraintSet self.updateConstraintLists() def getConstraintLists(self): constraintLists = [] if self.constraintSet: for constraintList in self.constraintSet.sortedConstraintLists(): if constraintList.className not in ('ChemShiftConstraintList','somethingElse'): constraintLists.append(constraintList) return constraintLists def updateConstraintLists(self, *notifyObj): textMatrix = [] objectList = self.getConstraintLists() for constraintList in objectList: if not hasattr(constraintList, 'useForMeccano'): if constraintList.conditionState \ or (constraintList.className != 'RdcConstraintList'): bool = True else: bool = False constraintList.useForMeccano = bool if constraintList.conditionState: alignMedium = constraintList.conditionState.name else: alignMedium = None datum = [constraintList.serial, constraintList.className[:-14], constraintList.useForMeccano and 'Yes' or 'No', alignMedium, len(constraintList.constraints)] textMatrix.append(datum) self.restraintMatrix.update(textMatrix=textMatrix, objectList=objectList) def selectConstraint(self, obj, row, column): if self.constraint is not obj: self.constraint = obj def getSimStore(self): simStore = self.project.findFirstNmrSimStore(name='meccano') if not simStore: simStore = self.project.newNmrSimStore(name='meccano') return simStore def getRuns(self): runs = [None, ] if self.molSystem and self.constraintSet: simStore = self.getSimStore() runs += simStore.sortedRuns() return runs def updateRuns(self, *notifyObj): index = 0 names = ['<New>'] runs = self.getRuns() run = self.run if runs: if run not in runs: run = runs[0] index = runs.index(run) names += [r.serial for r in runs if r] if run is not self.run: self.updateConstraintSets() self.updateMolSystems() self.updateShiftLists() self.runPulldown.setup(names, runs, index) def updateRunParams(self, event=None): if self.run and self.molSystem and self.constraintSet: simRun = self.run simRun.inputConstraintStore = self.constraintSet simRun.molSystem = self.molSystem if self.shiftList: simRun.setInputMeasurementLists([self.shiftList,]) simRun.newRunParameter(code='FirstPepPlane',id=1, intValue=self.firstResEntry.get() or 0) simRun.newRunParameter(code='LastPepPlane' ,id=1, intValue=self.lastResEntry.get() or 0) simRun.newRunParameter(code='MaxOptSteps', id=1, intValue=self.maxOptStepEntry.get() or 0) simRun.newRunParameter(code='NumOptPlanes', id=1, intValue=self.numOptPlaneEntry.get() or 0) simRun.newRunParameter(code='MinOptHits', id=1, intValue=self.numOptHitsEntry.get() or 0) def makeSimRun(self, template=None): simStore = self.getSimStore() if template: molSystem = template.molSystem constraintSet = template.inputConstraintStore shiftList = template.findFirstInputMeasurementList(className='ShiftList') protocol = template.annealProtocol else: molSystem = self.molSystem constraintSet = self.constraintSet shiftList = self.shiftList protocol = self.annealProtocol simRun = simStore.newRun(annealProtocol=protocol, molSystem=molSystem, inputConstraintStore=protocol) if shiftList: simRun.addInputMeasurementList(shiftList) if template: for param in template.runParameters: simRun.newRunParameter(code=param.code, id=param.id, booleanValue=param.booleanValue, floatValue=param.floatValue, intValue=param.intValue, textValue=param.textValue) else: if self.chain: chainCode = self.chain.code else: chaincode = 'A' simRun.newRunParameter(code='FirstPepPlane',id=1, intValue=self.firstResEntry.get() or 0) simRun.newRunParameter(code='LastPepPlane' ,id=1, intValue=self.lastResEntry.get() or 0) simRun.newRunParameter(code='MaxOptSteps', id=1, intValue=self.maxOptStepEntry.get() or 0) simRun.newRunParameter(code='NumOptPlanes', id=1, intValue=self.numOptPlaneEntry.get() or 0) simRun.newRunParameter(code='MinOptHits', id=1, intValue=self.numOptHitsEntry.get() or 0) simRun.newRunParameter(code='ChainCode', id=1, textValue=chainCode) return simRun def selectRun(self, simRun): if self.run is not simRun: if simRun: if simRun.outputEnsemble: msg = 'Selected run has already been used to generate a structure.' msg += 'A new run will be setup based on the selection.' showWarning('Warning',msg) simRun = self.makeSimRun(template=simRun) molSystem = simRun.molSystem constraintSet = simRun.inputConstraintStore shiftList = simRun.findFirstInputMeasurementList(className='ShiftList') if molSystem and (self.molSystem is not molSystem): self.molSystem = molSystem self.updateMolSystems() if constraintSet and (self.constraintSet is not constraintSet): self.constraintSet = constraintSet self.updateConstraintSets() if shiftList and (self.shiftList is not shiftList): self.shiftList = shiftList self.updateShiftLists() firstPepPlane = simRun.findFirstrunParameter(code='FirstPepPlane') lastPepPlane = simRun.findFirstrunParameter(code='LastPepPlane') maxOptSteps = simRun.findFirstrunParameter(code='MaxOptSteps') numOptPlanes = simRun.findFirstrunParameter(code='NumOptPlanes') minOptHits = simRun.findFirstrunParameter(code='MinOptHits') chainCode = simRun.findFirstrunParameter(code='ChainCode') if firstPepPlane is not None: self.firstResEntry.set(firstPepPlane.intValue or 0) if lastPepPlane is not None: self.lastResEntry.set(lastPepPlane.intValue or 0) if maxOptSteps is not None: self.maxOptStepEntry.set(maxOptSteps.intValue or 0) if numOptPlanes is not None: self.numOptPlaneEntry.set(numOptPlanes.intValue or 0) if minOptHits is not None: self.numOptHitsEntry.set(minOptHits.intValue or 0) if chainCode is not None: chainCode = chainCode.textValue or 'A' if self.molSystem: chain = self.molSystem.findFirsChain(code=chainCode) if chain: self.selectChain(chain) self.run = simRun def updateShiftLists(self, *notifyObj): index = 0 names = [] nmrProject = self.project.currentNmrProject shiftLists = nmrProject.findAllMeasurementLists(className='ShiftList') shiftLists = [(sl.serial, sl) for sl in shiftLists] shiftLists.sort() shiftLists = [x[1] for x in shiftLists] shiftList = self.shiftList if shiftLists: if shiftList not in shiftLists: shiftList = shiftLists[0] index = shiftLists.index(shiftList) names = ['%d'% sl.serial for sl in shiftLists] if shiftList is not self.shiftList: if self.run: self.run.setInputMeasurementLists([shiftList]) self.shiftListPulldown.setup(texts=names, objects=shiftLists, index=index) def selectShiftList(self, shiftList): if shiftList is not self.shiftList: if self.run: self.run.setInputMeasurementLists([shiftList]) self.shiftList = shiftList
class CloudsPopup(BasePopup): def __init__(self, parent, *args, **kw): self.guiParent = parent self.project = parent.getProject() self.waiting = 0 self.specFreq = 800.13 self.maxIter = 50 self.mixTime = 60 self.corrTime = 11.5 self.leakRate = 2.0 self.peakListDict = {} self.noesyPeakList = None self.tocsyPeakList = None self.noesy3dPeakList = None self.hsqcPeakList = None self.maxIntens = 37000000 self.resonances = None self.origResonances = None self.noesyPeaks = None self.distanceConstraintList = None self.antiDistConstraintList = None self.numClouds = 100 self.filePrefix = 'cloud_' self.cloudsFiles = [] self.adcAtomTypes = 'HN' self.structure = None # step num, initial temp, final temp, cooling steps, MD steps, MD tau, rep scale self.coolingScheme = [] self.coolingScheme.append([1, 1, 1, 3, 500, 0.001, 0]) self.coolingScheme.append([2, 80000, 4000, 19, 1000, 0.001, 0]) self.coolingScheme.append([3, 4000, 1, 5, 500, 0.001, 0]) self.coolingScheme.append([4, 15000, 1, 3, 1000, 0.001, 0]) self.coolingScheme.append([5, 1, 1, 5, 500, 0.001, 0]) self.coolingScheme.append([6, 8000, 1, 3, 1000, 0.001, 0]) self.coolingScheme.append([7, 1, 1, 5, 500, 0.001, 0]) self.coolingScheme.append([8, 3000, 25, 60, 2500, 0.001, 1]) self.coolingScheme.append([9, 25, 25, 1, 7500, 0.001, 1]) self.coolingScheme.append([10, 10, 10, 1, 7500, 0.001, 1]) self.coolingScheme.append([11, 0.01, 0.01, 1, 7500, 0.0005, 1]) self.coolingStep = None BasePopup.__init__(self, parent, title="Resonance Clouds Analysis", **kw) def body(self, guiFrame): self.specFreqEntry = IntEntry(self, text=self.specFreq, width=8, returnCallback=self.setSpecFreq) self.maxIterEntry = IntEntry(self, text=self.maxIter, width=8, returnCallback=self.setMaxIter) self.mixTimeEntry = FloatEntry(self, text=self.mixTime, width=8, returnCallback=self.setMixTime) self.corrTimeEntry = FloatEntry(self, text=self.corrTime, width=8, returnCallback=self.setCorrTime) self.leakRateEntry = FloatEntry(self, text=self.leakRate, width=8, returnCallback=self.setLeakRate) self.maxIntensEntry = IntEntry(self, text=self.maxIntens, width=8, returnCallback=self.setMaxIntens) self.mdInitTempEntry = FloatEntry(self, text='', returnCallback=self.setMdInitTemp) self.mdFinTempEntry = FloatEntry(self, text='', returnCallback=self.setMdFinTemp) self.mdCoolStepsEntry = IntEntry(self, text='', returnCallback=self.setMdCoolSteps) self.mdSimStepsEntry = IntEntry(self, text='', returnCallback=self.setMdSimSteps) self.mdTauEntry = FloatEntry(self, text='', returnCallback=self.setMdTau) self.mdRepScaleEntry = FloatEntry(self, text='', returnCallback=self.setMdRepScale) guiFrame.grid_columnconfigure(0, weight=1) row = 0 frame0 = LabelFrame(guiFrame, text='Setup peak lists') frame0.grid(row=row, column=0, sticky=Tkinter.NSEW) frame0.grid(row=row, column=0, sticky=Tkinter.NSEW) frame0.grid_columnconfigure(1, weight=1) f0row = 0 label00 = Label(frame0, text='1H-1H NOESY spectrum') label00.grid(row=f0row, column=0, sticky=Tkinter.NW) self.noesyPulldown = PulldownMenu(frame0, entries=self.getNoesys(), callback=self.setNoesy, selected_index=0, do_initial_callback=0) self.noesyPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW) f0row += 1 label01 = Label(frame0, text='15N HSQC spectrum') label01.grid(row=f0row, column=0, sticky=Tkinter.NW) self.hsqcPulldown = PulldownMenu(frame0, entries=self.getHsqcs(), callback=self.setHsqc, selected_index=0, do_initial_callback=0) self.hsqcPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW) f0row += 1 label02 = Label(frame0, text='15N HSQC TOCSY spectrum') label02.grid(row=f0row, column=0, sticky=Tkinter.NW) self.tocsyPulldown = PulldownMenu(frame0, entries=self.getTocsys(), callback=self.setTocsy, selected_index=0, do_initial_callback=0) self.tocsyPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW) f0row += 1 label02 = Label(frame0, text='15N HSQC NOESY spectrum') label02.grid(row=f0row, column=0, sticky=Tkinter.NW) self.noesy3dPulldown = PulldownMenu(frame0, entries=self.getNoesy3ds(), callback=self.setNoesy3d, selected_index=0, do_initial_callback=0) self.noesy3dPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW) f0row += 1 texts = ['Setup resonances & peaks', 'Show Peaks', 'Show resonances'] commands = [self.setupResonances, self.showPeaks, self.showResonances] self.setupButtons = ButtonList(frame0, expands=1, texts=texts, commands=commands) self.setupButtons.grid(row=f0row, column=0, columnspan=2, sticky=Tkinter.NSEW) f0row += 1 self.label03a = Label(frame0, text='Resonances found: 0') self.label03a.grid(row=f0row, column=0, sticky=Tkinter.NW) self.label03b = Label(frame0, text='NOESY peaks found: 0') self.label03b.grid(row=f0row, column=1, sticky=Tkinter.NW) row += 1 frame1 = LabelFrame(guiFrame, text='Calculate distance constraints') frame1.grid(row=row, column=0, sticky=Tkinter.NSEW) frame1.grid_columnconfigure(3, weight=1) f1row = 0 frame1.grid_rowconfigure(f1row, weight=1) data = [ self.specFreq, self.maxIter, self.mixTime, self.corrTime, self.leakRate, self.maxIntens ] colHeadings = [ 'Spectrometer\nfrequency', 'Max\niterations', 'Mixing\ntime (ms)', 'Correl.\ntime (ns)', 'Leak\nrate', 'Max\nintensity' ] editWidgets = [ self.specFreqEntry, self.maxIterEntry, self.mixTimeEntry, self.corrTimeEntry, self.leakRateEntry, self.maxIntensEntry, ] editGetCallbacks = [ self.getSpecFreq, self.getMaxIter, self.getMixTime, self.getCorrTime, self.getLeakRate, self.getMaxIntens, ] editSetCallbacks = [ self.setSpecFreq, self.setMaxIter, self.setMixTime, self.setCorrTime, self.setLeakRate, self.setMaxIntens, ] self.midgeParamsMatrix = ScrolledMatrix( frame1, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, maxRows=1, initialCols=5, headingList=colHeadings, callback=None, objectList=[ 'None', ], textMatrix=[ data, ]) self.midgeParamsMatrix.grid(row=f1row, column=0, columnspan=4, sticky=Tkinter.NSEW) f1row += 1 label10 = Label(frame1, text='Benchmark structure') label10.grid(row=f1row, column=0, sticky=Tkinter.NW) self.structurePulldown = PulldownMenu(frame1, entries=self.getStructures(), callback=self.setStructure, selected_index=0, do_initial_callback=0) self.structurePulldown.grid(row=f1row, column=1, sticky=Tkinter.NW) label11 = Label(frame1, text='ADC atom types:') label11.grid(row=f1row, column=2, sticky=Tkinter.NW) self.adcAtomsPulldown = PulldownMenu(frame1, entries=self.getAdcAtomTypes(), callback=self.setAdcAtomTypes, selected_index=0, do_initial_callback=0) self.adcAtomsPulldown.grid(row=f1row, column=3, sticky=Tkinter.NW) f1row += 1 texts = [ 'Calculate distances', 'Show distance\nconstraints', 'Show anti-distance\nconstraints' ] commands = [ self.calculateDistances, self.showConstraints, self.showAntiConstraints ] self.midgeButtons = ButtonList(frame1, expands=1, texts=texts, commands=commands) self.midgeButtons.grid(row=f1row, column=0, columnspan=4, sticky=Tkinter.NSEW) f1row += 1 self.distConstrLabel = Label(frame1, text='Distance constraints:') self.distConstrLabel.grid(row=f1row, column=0, columnspan=2, sticky=Tkinter.NW) self.antiConstrLabel = Label(frame1, text='Anti-distance constraints:') self.antiConstrLabel.grid(row=f1row, column=2, columnspan=2, sticky=Tkinter.NW) row += 1 guiFrame.grid_rowconfigure(row, weight=1) frame2 = LabelFrame(guiFrame, text='Proton cloud molecular dynamics') frame2.grid(row=row, column=0, sticky=Tkinter.NSEW) frame2.grid_columnconfigure(1, weight=1) f2row = 0 frame2.grid_rowconfigure(f2row, weight=1) data = [ self.specFreq, self.maxIter, self.mixTime, self.corrTime, self.leakRate ] colHeadings = [ 'Step', 'Initial temp.', 'Final temp.', 'Cooling steps', 'MD steps', 'MD tau', 'Rep. scale' ] editWidgets = [ None, self.mdInitTempEntry, self.mdFinTempEntry, self.mdCoolStepsEntry, self.mdSimStepsEntry, self.mdTauEntry, self.mdRepScaleEntry ] editGetCallbacks = [ None, self.getMdInitTemp, self.getMdFinTemp, self.getMdCoolSteps, self.getMdSimSteps, self.getMdTau, self.getMdRepScale ] editSetCallbacks = [ None, self.setMdInitTemp, self.setMdFinTemp, self.setMdCoolSteps, self.setMdSimSteps, self.setMdTau, self.setMdRepScale ] self.coolingSchemeMatrix = ScrolledMatrix( frame2, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, maxRows=9, initialRows=12, headingList=colHeadings, callback=self.selectCoolingStep, objectList=self.coolingScheme, textMatrix=self.coolingScheme) self.coolingSchemeMatrix.grid(row=f2row, column=0, columnspan=4, sticky=Tkinter.NSEW) f2row += 1 texts = ['Move earlier', 'Move later', 'Add step', 'Remove step'] commands = [ self.moveStepEarlier, self.moveStepLater, self.addCoolingStep, self.removeCoolingStep ] self.coolingSchemeButtons = ButtonList(frame2, expands=1, commands=commands, texts=texts) self.coolingSchemeButtons.grid(row=f2row, column=0, columnspan=4, sticky=Tkinter.EW) f2row += 1 label20 = Label(frame2, text='Number of clouds:') label20.grid(row=f2row, column=0, sticky=Tkinter.NW) self.numCloudsEntry = FloatEntry(frame2, text=100, returnCallback=self.setNumClouds, width=10) self.numCloudsEntry.grid(row=f2row, column=1, sticky=Tkinter.NW) label21 = Label(frame2, text='Cloud file prefix:') label21.grid(row=f2row, column=2, sticky=Tkinter.NW) self.filePrefixEntry = Entry(frame2, text='cloud_', returnCallback=self.setFilePrefix, width=10) self.filePrefixEntry.grid(row=f2row, column=3, sticky=Tkinter.NW) f2row += 1 texts = ['Start molecular dynamics', 'Show dynamics progress'] commands = [self.startMd, self.showMdProgress] self.mdButtons = ButtonList(frame2, expands=1, commands=commands, texts=texts) self.mdButtons.grid(row=f2row, column=0, columnspan=4, sticky=Tkinter.NSEW) row += 1 self.bottomButtons = createDismissHelpButtonList(guiFrame, expands=0, help_url=None) self.bottomButtons.grid(row=row, column=0, sticky=Tkinter.EW) self.setButtonStates() def getStructures(self): names = [ '<None>', ] for molSystem in self.project.sortedMolSystems(): for structure in molSystem.sortedStructureEnsembles(): names.append('%s:%d' % (molSystem.name, structure.ensembleId)) return names def setStructure(self, index, name=None): if index < 1: self.structure = None else: structures = [] for molSystem in self.project.molSystems: for structure in molSystem.structureEnsembles: structures.append(structure) self.structure = structures[index - 1] def getAdcAtomTypes(self): return ['HN', 'HN HA', 'HN HA HB'] def setAdcAtomTypes(self, index, name=None): if name is None: name = self.adcAtomsPulldown.getSelected() self.adcAtomTypes = name def startMd(self): self.setNumClouds() self.setFilePrefix() if (self.distanceConstraintList and self.antiDistConstraintList and (self.numClouds > 0) and self.filePrefix): resDict = {} for resonance in self.guiParent.project.currentNmrProject.resonances: resDict[resonance.serial] = resonance resonances = [] for constraint in self.distanceConstraintList.constraints: for item in constraint.items: for fixedResonance in item.resonances: if resDict.get( fixedResonance.resonanceSerial) is not None: resonances.append( resDict[fixedResonance.resonanceSerial]) resDict[fixedResonance.resonanceSerial] = None startMdProcess(self.numClouds, self.distanceConstraintList, resonances, self.coolingScheme, self.filePrefix) #structGen = self.distanceConstraintList.structureGeneration serials = [] for resonance in resonances: serials.append(resonance.serial) clouds = [] for i in range(self.numClouds): clouds.append('%s%3.3d.pdb' % (self.filePrefix, i)) self.guiParent.application.setValues( self.distanceConstraintList.nmrConstraintStore, 'clouds', values=clouds) self.guiParent.application.setValues( self.distanceConstraintList.nmrConstraintStore, 'cloudsResonances', values=serials) # do better than this check for creation def showMdProgress(self): n = 0 m = self.numClouds for i in range(m): pdbFileName = '%s%3.3d.pdb' % (self.filePrefix, i) if os.path.exists(pdbFileName): n += 1 p = n * 100 / float(m) text = 'Done %d of %d clouds (%1.2f)%%' % (n, m, p) showInfo('MD Progress', text) def setFilePrefix(self, text=None): if not text: text = self.filePrefixEntry.get() if text: self.filePrefix = text def setNumClouds(self, n=None, *event): if not n: n = self.numCloudsEntry.get() if n: self.numClouds = int(n) def calculateDistances(self): # setup normalisation factor intensityMax # self.maxIter # what if failure ? resDict = {} for resonance in self.project.currentNmrProject.resonances: resDict[resonance.serial] = resonance self.resonances = self.origResonances intensityFactors = [1.0 for x in range(len(self.resonances))] # optimiseRelaxation will remove unconstrained resonances self.distanceConstraintList = optimiseRelaxation( self.resonances, self.noesyPeaks, intensityMax=self.maxIntens, intensityFactors=intensityFactors, tmix=self.mixTime, sf=self.specFreq, tcor=self.corrTime, rleak=self.leakRate) constrainSpinSystems(self.distanceConstraintList) # for testing calculate distances from structure overrides any resonances: uses assigned ones #(self.distanceConstraintList, self.resonances) = self.cheatForTesting() #self.antiDistConstraintList = self.distanceConstraintList protonNumbs = {'CH3': 3, 'Haro': 2, 'HN': 1, 'H': 1} PI = 3.1415926535897931 GH = 2.6752e4 HB = 1.05459e-27 CONST = GH * GH * GH * GH * HB * HB tc = 1.0e-9 * self.corrTime wh = 2.0 * PI * self.specFreq * 1.0e6 j0 = CONST * tc j1 = CONST * tc / (1.0 + wh * wh * tc * tc) j2 = CONST * tc / (1.0 + 4.0 * wh * wh * tc * tc) #jself = 6.0*j2 + 3.0*j1 + j0 jcross = 6.0 * j2 - j0 if self.distanceConstraintList: constraintStore = self.distanceConstraintList.nmrConstraintStore dict = { 'HN': ['H'], 'HN HA': ['H', 'HA', 'HA1', 'HA2'], 'HN HA HB': ['H', 'HA', 'HA1', 'HA2', 'HB', 'HB2', 'HB3'] } self.antiDistConstraintList = makeNoeAdcs( self.resonances, self.noesyPeakList.dataSource, constraintStore, allowedAtomTypes=dict[self.adcAtomTypes]) if self.structure: N = len(self.resonances) sigmas = [[] for i in range(N)] for i in range(N): sigmas[i] = [0.0 for j in range(N)] for constraint in self.distanceConstraintList.constraints: resonances = list(constraint, findFirstItem().resonances) ri = resDict[resonances[0].resonanceSerial] rj = resDict[resonances[1].resonanceSerial] i = self.resonances.index(ri) j = self.resonances.index(rj) atomSets1 = list(ri.resonanceSet.atomSets) atomSets2 = list(rj.resonanceSet.atomSets) if atomSets1 == atomSets2: ass = list(atomSets1) atomSets1 = [ ass[0], ] atomSets2 = [ ass[-1], ] distance = getAtomSetsDistance(atomSets1, atomSets2, self.structure) r = distance * 1e-8 nhs = protonNumbs[rj.name] sigma = 0.1 * jcross * nhs / (r**6) sigmas[i][j] = sigma constraint.setDetails('Known Dist: %4.3f' % (distance)) #for constraint in self.antiDistConstraintList.constraints: # atomSets1 = list(resonances[0].resonanceSet.atomSets) # atomSets2 = list(resonances[1].resonanceSet.atomSets) # distance = getAtomSetsDistance(atomSets1, atomSets2, self.structure) # constraint.setDetails('Known Dist: %4.3f' % (distance)) fp = open('sigmas.out', 'w') for i in range(N - 1): for j in range(i + 1, N): if sigmas[i][j] != 0.0: fp.write('%3.1d %3.1d %9.2e\n' % (i, j, sigmas[i][j])) #fp.write('\n') fp.close() self.setButtonStates() def cheatForTesting(self, atomSelection='H'): """ Makes a perfect cloud from a structure. """ project = self.project structure = self.guiParent.argumentServer.getStructure() constraintStore = makeNmrConstraintStore(project) distConstraintList = NmrConstraint.DistanceConstraintList( constraintStore) chain = structure.findFirstCoodChain() structureGeneration.hydrogenResonances = [] molSystem = structure.molSystem atomSets = [] resonances = [] i = 0 for resonance in project.currentNmrProject.resonances: if resonance.isotopeCode == '1H': if resonance.resonanceSet: atomSet = resonance.resonanceSet.findFirstAtomSet() atom = atomSet.findFirstAtom() seqId = atom.residue.seqId if (seqId < 9) or (seqId > 78): continue if atom.residue.chain.molSystem is molSystem: if atomSelection == 'methyl': if len(atomSet.atoms) == 3: if atom.residue.ccpCode not in ('Ala', 'Val', 'Ile', 'Leu', 'Thr', 'Met'): continue elif atom.name != 'H': continue elif atomSelection == 'amide': if atom.name != 'H': continue if atom.name == 'H': resonance.name = 'HN' else: resonance.name = 'H' resonances.append(resonance) atomSets.append(list(resonance.resonanceSet.atomSets)) i += 1 print "Found %d atomSets" % (len(atomSets)) weight = 1 adcWeight = 1 constrDict = {} N = len(atomSets) for i in range(N - 1): atomSets0 = atomSets[i] residue0 = atomSets0[0].findFirstAtom().residue.seqId print "R", residue0 for j in range(i + 1, N): if j == i: continue atomSets1 = atomSets[j] dist = getAtomSetsDistance(atomSets0, atomSets1, structure) if not dist: continue if dist < 5.5: fixedResonance0 = getFixedResonance( constraintStore, resonances[i]) fixedResonance1 = getFixedResonance( constraintStore, resonances[j]) constrDict[i] = 1 constrDict[j] = 1 constraint = NmrConstraint.DistanceConstraint( distConstraintList, weight=weight, targetValue=dist, upperLimit=dist + (dist / 10), lowerLimit=dist - (dist / 10), error=dist / 5) item = NmrConstraint.DistanceConstraintItem( constraint, resonances=[fixedResonance0, fixedResonance1]) elif (atomSets1[0].findFirstAtom().name == 'H') and (atomSets0[0].findFirstAtom().name == 'H') and (dist > 7): #else: fixedResonance0 = getFixedResonance( constraintStore, resonances[i]) fixedResonance1 = getFixedResonance( constraintStore, resonances[j]) constrDict[i] = 1 constrDict[j] = 1 constraint = NmrConstraint.DistanceConstraint( distConstraintList, weight=adcWeight, targetValue=75, upperLimit=175, lowerLimit=5.0, error=94.5) item = NmrConstraint.DistanceConstraintItem( constraint, resonances=[fixedResonance0, fixedResonance1]) return (distConstraintList, resonances) def showConstraints(self): if self.distanceConstraintList: self.guiParent.browseConstraints( constraintList=self.distanceConstraintList) def showAntiConstraints(self): if self.antiDistConstraintList: self.guiParent.browseConstraints( constraintList=self.antiDistConstraintList) def showPeaks(self): self.guiParent.viewPeaks(peaks=self.noesyPeaks) def showResonances(self): pass #self.guiParent.viewResonances(resonances=self.resonances) def setupResonances(self): if self.noesyPeakList and self.noesy3dPeakList and self.tocsyPeakList and self.hsqcPeakList: disambiguateNoesyPeaks(self.noesyPeakList, self.noesy3dPeakList, self.tocsyPeakList, self.hsqcPeakList) (self.origResonances, self.noesyPeaks, null) = getCloudsResonanceList(self.guiParent.argumentServer, hsqcPeakList=self.hsqcPeakList, tocsy3dPeakList=self.tocsyPeakList, noesy2dPeakList=self.noesyPeakList) self.setButtonStates() def setButtonStates(self): if self.origResonances: self.label03a.set('Resonances found: %d' % (len(self.origResonances))) if self.noesyPeaks: self.label03b.set('NOESY peaks found: %d' % (len(self.noesyPeaks))) if self.noesyPeakList and self.tocsyPeakList and self.hsqcPeakList: self.setupButtons.buttons[0].enable() else: self.setupButtons.buttons[0].disable() if self.noesyPeaks: self.setupButtons.buttons[1].enable() else: self.setupButtons.buttons[1].disable() if self.origResonances: self.setupButtons.buttons[2].enable() else: self.setupButtons.buttons[2].disable() if self.noesyPeaks and self.origResonances: self.midgeButtons.buttons[0].enable() else: self.midgeButtons.buttons[0].disable() if self.distanceConstraintList: self.midgeButtons.buttons[1].enable() self.distConstrLabel.set( 'Distance constraints: %d' % len(self.distanceConstraintList.constraints)) else: self.distConstrLabel.set('Distance constraints:') self.midgeButtons.buttons[1].disable() if self.antiDistConstraintList: self.antiConstrLabel.set( 'Anti-distance constraints: %d' % len(self.antiDistConstraintList.constraints)) self.midgeButtons.buttons[2].enable() else: self.antiConstrLabel.set('Anti-distance constraints:') self.midgeButtons.buttons[2].disable() if (self.distanceConstraintList and self.antiDistConstraintList and (self.numClouds > 0) and self.filePrefix): self.mdButtons.buttons[0].enable() self.mdButtons.buttons[1].enable() else: self.mdButtons.buttons[0].disable() self.mdButtons.buttons[1].disable() def getNoesys(self): names = [] spectra = getSpectraByType(self.project, '2dNOESY') for spectrum in spectra: for peakList in spectrum.peakLists: name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name, peakList.serial) names.append(name) self.peakListDict[name] = peakList if not self.noesyPeakList: self.noesyPeakList = peakList return names def setNoesy(self, index, name=None): if not name: name = self.noesyPulldown.getSelected() self.noesyPeakList = self.peakListDict[name] self.setButtonStates() def getTocsys(self): names = [] spectra = getSpectraByType(self.project, '3dTOCSY') for spectrum in spectra: for peakList in spectrum.peakLists: name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name, peakList.serial) names.append(name) self.peakListDict[name] = peakList if not self.tocsyPeakList: self.tocsyPeakList = peakList return names def getNoesy3ds(self): names = [] spectra = getSpectraByType(self.project, '3dNOESY') for spectrum in spectra: for peakList in spectrum.peakLists: name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name, peakList.serial) names.append(name) self.peakListDict[name] = peakList if not self.noesy3dPeakList: self.noesy3dPeakList = peakList return names def setTocsy(self, index, name=None): if not name: name = self.tocsyPulldown.getSelected() self.tocsyPeakList = self.peakListDict[name] self.setButtonStates() def setNoesy3d(self, index, name=None): if not name: name = self.noesy3dPulldown.getSelected() self.noesy3dPeakList = self.peakListDict[name] self.setButtonStates() def getHsqcs(self): names = [] spectra = getSpectraByType(self.project, 'HSQC') for spectrum in spectra: for peakList in spectrum.peakLists: name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name, peakList.serial) names.append(name) self.peakListDict[name] = peakList if not self.hsqcPeakList: self.hsqcPeakList = peakList return names def setHsqc(self, index, name=None): if not name: name = self.hsqcPulldown.getSelected() self.hsqcPeakList = self.peakListDict[name] self.setButtonStates() def getMdInitTemp(self, coolingStep): self.mdInitTempEntry.set(coolingStep[1]) def getMdFinTemp(self, coolingStep): self.mdFinTempEntry.set(coolingStep[2]) def getMdCoolSteps(self, coolingStep): self.mdCoolStepsEntry.set(coolingStep[3]) def getMdSimSteps(self, coolingStep): self.mdSimStepsEntry.set(coolingStep[4]) def getMdTau(self, coolingStep): self.mdTauEntry.set(coolingStep[5]) def getMdRepScale(self, coolingStep): self.mdRepScaleEntry.set(coolingStep[6]) def setMdInitTemp(self, event): value = self.mdInitTempEntry.get() if value is not None: self.coolingStep[1] = value self.updateCoolingScheme() def setMdFinTemp(self, event): value = self.mdFinTempEntry.get() if value is not None: self.coolingStep[2] = value self.updateCoolingScheme() def setMdCoolSteps(self, event): value = self.mdCoolStepsEntry.get() if value is not None: self.coolingStep[3] = value self.updateCoolingScheme() def setMdSimSteps(self, event): value = self.mdSimStepsEntry.get() if value is not None: self.coolingStep[4] = value self.updateCoolingScheme() def setMdTau(self, event): value = self.mdTauEntry.get() if value is not None: self.coolingStep[5] = value self.updateCoolingScheme() def setMdRepScale(self, event): value = self.mdRepScaleEntry.get() if value is not None: self.coolingStep[6] = value self.updateCoolingScheme() def selectCoolingStep(self, object, row, col): self.coolingStep = object def moveStepEarlier(self): if self.coolingStep: i = self.coolingStep[0] - 1 if i > 0: coolingStep = self.coolingScheme[i - 1] coolingStep[0] = i + 1 self.coolingStep[0] = i self.coolingScheme[i - 1] = self.coolingStep self.coolingScheme[i] = coolingStep self.updateCoolingScheme() self.coolingSchemeMatrix.hilightObject(self.coolingStep) def moveStepLater(self): if self.coolingStep: i = self.coolingStep[0] - 1 if i < len(self.coolingScheme) - 1: coolingStep = self.coolingScheme[i + 1] coolingStep[0] = i + 1 self.coolingStep[0] = i + 2 self.coolingScheme[i + 1] = self.coolingStep self.coolingScheme[i] = coolingStep self.updateCoolingScheme() self.coolingSchemeMatrix.hilightObject(self.coolingStep) def addCoolingStep(self): i = len(self.coolingScheme) + 1 datum = [i, 3000, 100, 10, 2500, 0.001, 1] self.coolingScheme.append(datum) self.updateCoolingScheme() def removeCoolingStep(self): if self.coolingStep: coolingScheme = [] i = 0 for coolingStep in self.coolingScheme: if coolingStep is not self.coolingStep: i += 1 coolingStep[0] = i coolingScheme.append(coolingStep) self.coolingScheme = coolingScheme self.updateCoolingScheme() def updateCoolingScheme(self): objectList = self.coolingScheme textMatrix = self.coolingScheme self.coolingSchemeMatrix.update(objectList=objectList, textMatrix=textMatrix) def updateMidgeParams(self): data = [ self.specFreq, self.maxIter, self.mixTime, self.corrTime, self.leakRate, self.maxIntens ] self.midgeParamsMatrix.update(textMatrix=[ data, ]) def getSpecFreq(self, obj): self.specFreqEntry.set(self.specFreq) def getMaxIter(self, obj): self.maxIterEntry.set(self.maxIter) def getMixTime(self, obj): self.mixTimeEntry.set(self.mixTime) def getCorrTime(self, obj): self.corrTimeEntry.set(self.corrTime) def getLeakRate(self, obj): self.leakRateEntry.set(self.leakRate) def getMaxIntens(self, obj): self.maxIntensEntry.set(self.maxIntens) def setSpecFreq(self, event): value = self.specFreqEntry.get() if value is not None: self.specFreq = value self.updateMidgeParams() def setMaxIter(self, event): value = self.maxIterEntry.get() if value is not None: self.maxIter = value self.updateMidgeParams() def setMixTime(self, event): value = self.mixTimeEntry.get() if value is not None: self.mixTime = value self.updateMidgeParams() def setCorrTime(self, event): value = self.corrTimeEntry.get() if value is not None: self.corrTime = value self.updateMidgeParams() def setLeakRate(self, event): value = self.leakRateEntry.get() if value is not None: self.leakRate = value self.updateMidgeParams() def setMaxIntens(self, event): value = self.maxIntensEntry.get() if value is not None: self.maxIntens = value self.updateMidgeParams() def destroy(self): BasePopup.destroy(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 EditExperimentSeriesPopup(BasePopup): """ **Setup Experiment Series for Chemical Shift and Intensity Changes** The purpose of this popup is to setup ordered groups of experiments that are related by the variation in some condition or parameter, but otherwise the kind of experiment being run is the same. For example the user could setup experiments for a temperature series, ligand binding titration or relaxation rate measurement. The layout is divided into two tables. The upper table shows all of the series that are known to the current project and the lower table shows all of the experiments or planes that comprise the selected series. These series relate to both groups of separate experiments (and hence spectra) and also single experiment where one dimension is not for NMR frequency but rather a "sampled" dimension and thus effectively combines many experiments (e.g. for different T1 values) as different planes. A stack of effectively 2D experiments combined in this manner is typically referred to as pseudo-3D. - The experiment is 3D but there are only two NMR dimensions. Series which are stacks of planes in a single experiment entity are automatically detected and entered into the table once they are loaded. Series that are constructed from multiple, separate experiments however must be setup by the user. To setup a new series of this kind [Add Series] makes a new, empty NMR series. Next the user should change the "Parameter varied" column to specify what type of thing is varied between the different experiments. The user then adds experiments into this series with the [Add Series Point] function at the bottom. Once the points have been added to the series the name of the experiment for each point may be changed. Initially, arbitrary experiments appear for the series points, so these almost always have to be adjusted. Once a stacked-plane experiment or series of experiments is setup, the user next sets (or checks) the value of the parameter associated with each point in the lower table. When loading stacked-plane experiments these values may come though automatically, if they are present in the spectrum header or parameter file. Given a completed NMR series specification the user may then extract the relevant data from the series using one of the analysis tools like `Follow Intensity Changes`_ or `Follow Shift Changes`_. **Caveats & Tips** Make sure the "Parameter Varied" for a given NMR series is appropriate to the type of analysis being performed. Many tools that extract T1 or Kd measurements for example look for specific types of series. The "Set/Unset Ref Plane" function is only used in certain kinds of series such as those that use trains of CPMG pulses. .. _`Follow Intensity Changes`: CalcRatesPopup.html .. _`Follow Shift Changes`: FollowShiftChangesPopup.html """ def __init__(self, parent, *args, **kw): self.guiParent = parent self.expSeries = None self.conditionPoint = None self.waiting = 0 BasePopup.__init__(self, parent, title="Experiment : NMR Series", **kw) 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 administerNotifiers(self, notifyFunc): #for func in ('__init__', 'delete','setName'): for func in ('__init__', 'delete','setName','setConditionNames', 'addConditionName','removeConditionName'): notifyFunc(self.updateAfter,'ccp.nmr.Nmr.NmrExpSeries', func) for func in ('__init__', 'delete','setName'): notifyFunc(self.updateExperiments,'ccp.nmr.Nmr.Experiment', func) for func in ('__init__', 'delete'): notifyFunc(self.updateDataDim,'ccp.nmr.Nmr.SampledDataDim', func) for func in ('__init__', 'delete','setCondition','setUnit','setValue','setError'): notifyFunc(self.updateConditionsAfter,'ccp.nmr.Nmr.SampleCondition', func) for func in ('__init__', 'delete','setCondition'): notifyFunc(self.updateAfter,'ccp.nmr.Nmr.SampleCondition', func) for func in ('setConditionVaried', 'setPointErrors', 'addPointError', 'removePointError', 'setPointValues','addPointValue', 'removePointValue','setUnit'): notifyFunc(self.updateAfter,'ccp.nmr.Nmr.SampledDataDim', func) for func in ('__init__', 'delete'): notifyFunc(self.updateColorSchemes,'ccpnmr.AnalysisProfile.ColorScheme', func) def open(self): self.updateAfter() BasePopup.open(self) def updateColorSchemes(self, scheme=None): index = 0 prevScheme = self.colorSchemePulldown.getObject() schemes = getHueSortedColorSchemes(self.analysisProfile) schemes = [s for s in schemes if len(s.colors) > 1] colors = [list(s.colors) for s in schemes] if schemes: names = [s.name for s in schemes] if prevScheme in schemes: index = schemes.index(prevScheme) else: names = [] self.colorSchemePulldown.setup(names, schemes, index, colors) def autoColorSpectra(self): if self.expSeries and (self.expSeries.className != 'Experiment'): scheme = self.colorSchemePulldown.getObject() if scheme: colors = scheme.colors else: colors = ['#FF0000','#00FF00','#0000FF'] cdict = getNmrExpSeriesSampleConditions(self.expSeries) conditionName = list(self.expSeries.conditionNames)[0] expList = [] for sampleCondition in cdict.get(conditionName, []): expList.append( (sampleCondition.value, sampleCondition.parent.experiments) ) expList.sort() m = len(expList)-1.0 c = len(colors)-1 for i, (value, experiments) in enumerate(expList): p = c*i/m j = int(p) r1, g1, b1 = Color.hexToRgb(colors[j]) r2, g2, b2 = Color.hexToRgb(colors[min(c,j+1)]) f2 = p-j f1 = 1.0-f2 r = (r1*f1)+(r2*f2) g = (g1*f1)+(g2*f2) b = (b1*f1)+(b2*f2) hexColor = Color.hexRepr(r,g,b) for experiment in experiments: for spectrum in experiment.dataSources: if spectrum.dataType == 'processed': analysisSpec = getAnalysisSpectrum(spectrum) if analysisSpec.posColors: analysisSpec.posColors = [hexColor,] elif analysisSpec.negColors: analysisSpec.negColors = [hexColor,] def getUnusedExperiments(self): sampleExperiments = getSampledDimExperiments(self.nmrProject) experiments = [] for experiment in self.nmrProject.sortedExperiments(): if experiment in sampleExperiments: continue if self.expSeries and (self.expSeries.className != 'Experiment'): if experiment in self.expSeries.experiments: continue experiments.append(experiment) return experiments def conditionTableShow(self, object, row, col): if type(object) is type(()): dataDim, index = object refPlane = dataDim.analysisDataDim.refSamplePlane if refPlane == index: return False if col == 1: return False return True def setSampledReferencePlane(self): if self.expSeries and (self.expSeries.className == 'Experiment'): if self.conditionPoint: dataDim, point = self.conditionPoint analysisDataDim = dataDim.analysisDataDim refPoint = analysisDataDim.refSamplePlane if refPoint == point: analysisDataDim.refSamplePlane = None else: analysisDataDim.refSamplePlane = point self.updateAfter() def checkAddSampleCondition(self, experiment): conditionSet = getExperimentConditionSet(experiment) conditionName = self.expSeries.conditionNames[0] condDict = getNmrExpSeriesSampleConditions(self.expSeries) sampleConditions = condDict.get(conditionName, []) units = [sc.unit for sc in sampleConditions if sc.unit] if units: sortList = list(set(units)) sortList.sort(key = lambda u:units.count(u)) unit = sortList[-1] else: unit = CONDITION_UNITS_DICT[conditionName][0] condition = conditionSet.findFirstSampleCondition(condition=conditionName) if not condition: condition = conditionSet.newSampleCondition(condition=conditionName, unit=unit, value=0.0, error=0.0) def addConditionPoint(self): if self.expSeries and (self.expSeries.className != 'Experiment'): experiments = self.getUnusedExperiments() if not experiments: showWarning('Warning','No experiments available', parent=self) return experiment = experiments[0] if experiment not in self.expSeries.experiments: self.expSeries.addExperiment(experiment) self.checkAddSampleCondition(experiment) self.updateAfter() def deleteConditionPoint(self, *event): if self.conditionPoint and (self.expSeries.className != 'Experiment'): if showOkCancel('Confirm','Really delete series point?', parent=self): conditionSet = self.conditionPoint.sampleConditionSet experiments = [e for e in conditionSet.experiments if e in self.expSeries.experiments] for experiment in experiments: self.expSeries.removeExperiment(experiment) for experiment in experiments: for expSeries in experiment.nmrExpSeries: if self.conditionPoint.condition in self.expSeries.conditionNames: break else: continue break else: self.conditionPoint.delete() self.conditionPoint = None def selectConditionPoint(self, object, row, col): if object: self.conditionPoint = object self.updateButtons() def selectExpSeries(self, object, row, col): if object: self.expSeries = object self.checkExperimentConditionsConsistent() self.updateConditions() def checkExperimentConditionsConsistent(self): if self.expSeries.className != 'Experiment': for experiment in self.expSeries.experiments: self.checkAddSampleCondition(experiment) def getUnits(self): units = [] if self.expSeries: if self.expSeries.className == 'Experiment': conditionName = getExperimentSampledDim(self.expSeries).conditionVaried else: conditionName = self.expSeries.conditionNames[0] units = CONDITION_UNITS_DICT.get(conditionName) if not units: units = ['?',] return units def getUnit(self, sampleCondition): index = -1 units = self.getUnits() if units: if sampleCondition: if type(sampleCondition) is type(()): dataDim, index = sampleCondition unit = dataDim.unit else: unit = sampleCondition.unit if unit not in units: unit = units[0] index = units.index(unit) self.unitPulldown.setup(units,units,index) def setUnit(self, obj): name = self.unitPulldown.getObject() if self.conditionPoint: if type(self.conditionPoint) is type(()): dataDim, index = self.conditionPoint dataDim.setUnit(name) else: self.conditionPoint.setUnit(name) def getConditionNames(self): if self.expSeries and (self.expSeries.className == 'Experiment'): names = ['delay time','mixing time','num delays','pulsing frequency','gradient strength'] else: names = CONDITION_UNITS_DICT.keys() names.sort() return names def setConditionName(self, obj): name = self.conditionNamesPulldown.getObject() if self.expSeries: if self.expSeries.className == 'Experiment': dataDim = getExperimentSampledDim(self.expSeries) dataDim.conditionVaried = name else: self.expSeries.setConditionNames([name,]) def getConditionName(self, expSeries): index = 0 names = self.getConditionNames() if names: if expSeries: if expSeries.className == 'Experiment': name = getExperimentSampledDim(expSeries).conditionVaried else: name = expSeries.conditionNames[0] if name: index = names.index(name) else: index = 0 self.conditionNamesPulldown.setup(names,names,index) def getName(self, expSeries): if expSeries : self.nameEntry.set(expSeries.name) def setName(self, event): text = self.nameEntry.get() if text and text != ' ': self.expSeries.setName( text ) def getValue(self, conditionPoint): if conditionPoint: if type(self.conditionPoint) is type(()): dataDim, index = conditionPoint value = dataDim.pointValues[index] else: value = conditionPoint.value self.valueEntry.set(value) def setValue(self, event): value = self.valueEntry.get() if value is not None: if type(self.conditionPoint) is type(()): dataDim, index = self.conditionPoint values = list(dataDim.pointValues) values[index] = value dataDim.setPointValues(values) else: self.conditionPoint.setValue( value ) def getError(self, conditionPoint): if conditionPoint: if type(self.conditionPoint) is type(()): dataDim, index = conditionPoint if index < len(dataDim.pointErrors): error = dataDim.pointValues[index] else: error = 0.0 else: error = conditionPoint.error self.errorEntry.set(error) def setError(self, event): value = self.errorEntry.get() if value is not None: if type(self.conditionPoint) is type(()): dataDim, index = self.conditionPoint pointErrors = dataDim.pointErrors if pointErrors: values = list(pointErrors) else: values = [0.0] * dataDim.numPoints values[index] = value dataDim.setPointErrors(values) else: self.conditionPoint.setError( value ) def getDetails(self, expSeries): if expSeries : self.detailsEntry.set(expSeries.details) def setDetails(self, event): text = self.detailsEntry.get() if text and text != ' ': self.expSeries.setDetails( text ) def addExpSeries(self): expSeries = self.nmrProject.newNmrExpSeries(conditionNames=['delay time',]) def deleteExpSeries(self, *event): if self.expSeries and (self.expSeries.className != 'Experiment'): if showOkCancel('Confirm','Really delete series?', parent=self): self.expSeries.delete() self.expSeries = None self.conditionPoint = None def getExperiments(self): if self.expSeries and (self.expSeries.className == 'Experiment'): return [self.expSeries,] else: return self.nmrProject.sortedExperiments() def getExperiment(self, sampleCondition): index = 0 names = [] if self.conditionPoint and (type(self.conditionPoint) != type(())): index = 0 experiment = self.conditionPoint.parent.findFirstExperiment() experiments = self.getUnusedExperiments() name = experiment.name names = [name] + [e.name for e in experiments] experiments = [experiment,] + experiments self.experimentPulldown.setup(names,experiments,index) def setExperiment(self, obj): experiment = self.experimentPulldown.getObject() if self.conditionPoint and (type(self.conditionPoint) != type(())): conditionSet = getExperimentConditionSet(experiment) if conditionSet is not self.conditionPoint.parent: if experiment not in self.expSeries.experiments: self.expSeries.addExperiment(experiment) unit = self.conditionPoint.unit if not unit: unit = CONDITION_UNITS_DICT[self.expSeries.conditionNames[0]] condition = self.conditionPoint.condition experiments = set(self.expSeries.experiments) for experiment0 in self.conditionPoint.parent.experiments: if experiment0 in experiments: experiments.remove(experiment0) self.expSeries.experiments = experiments value = self.conditionPoint.value error = self.conditionPoint.error self.conditionPoint.delete() self.conditionPoint = conditionSet.findFirstSampleCondition(condition=condition) if self.conditionPoint: self.conditionPoint.unit = unit self.updateAfter() else: self.conditionPoint = conditionSet.newSampleCondition(condition=condition,unit=unit, value=value,error=error) def updateDataDim(self, sampledDataDim): experiment = sampledDataDim.dataSource.experiment self.updateExperiments(experiment) def updateExperiments(self, experiment): experiments = self.getExperiments() names = [e.name for e in experiments] self.experimentPulldown.setup(names, experiments,0) if getExperimentSampledDim(experiment): self.updateAfter() elif self.expSeries: if self.expSeries.className == 'Experiment': if experiment is self.expSeries: self.updateConditionsAfter() elif experiment in self.expSeries.experiments: self.updateConditionsAfter() def updateConditionsAfter(self, sampleCondition=None): if self.waitingConditions: return if sampleCondition: experiments = sampleCondition.sampleConditionSet.experiments for experiment in experiments: if self.expSeries.className == 'Experiment': if experiment is self.expSeries: self.waitingConditions = True self.after_idle(self.updateConditions) break elif experiment in self.expSeries.experiments: self.waitingConditions = True self.after_idle(self.updateConditions) break else: self.waitingConditions = True self.after_idle(self.updateConditions) def updateConditions(self): self.updateButtons() objectList = [] textMatrix = [] colorMatrix = [] nCols = len(self.conditionPointsMatrix.headingList) defaultColors = [None] * nCols if self.expSeries: if self.expSeries.className == 'Experiment': dataDim = getExperimentSampledDim(self.expSeries) analysisDataDim = getAnalysisDataDim(dataDim) conditionVaried = dataDim.conditionVaried expName = self.expSeries.name unit = dataDim.unit pointValues = dataDim.pointValues pointErrors = dataDim.pointErrors refPlane = analysisDataDim.refSamplePlane for i in range(dataDim.numPoints): if i < len(pointErrors): error = pointErrors[i] else: error = None pointText = ':%3d' % (i+1) if i == refPlane: datum = ['* Ref Plane *', expName+pointText, None, None, None] colorMatrix.append(['#f08080'] * nCols) else: datum = [conditionVaried , expName+pointText, pointValues[i], error, unit] colorMatrix.append(defaultColors) textMatrix.append(datum) objectList.append((dataDim, i)) else: condDict = getNmrExpSeriesSampleConditions(self.expSeries) conditionNames = self.expSeries.conditionNames for conditionName in conditionNames: for sampleCondition in condDict.get(conditionName, []): datum = [sampleCondition.condition, ' '.join([e.name for e in sampleCondition.parent.experiments]), sampleCondition.value, sampleCondition.error, sampleCondition.unit] textMatrix.append(datum) objectList.append(sampleCondition) colorMatrix.append(defaultColors) self.conditionPointsMatrix.update(objectList=objectList, colorMatrix=colorMatrix, textMatrix=textMatrix) self.waitingConditions = 0 def updateAfter(self, object=None): if self.waiting: return else: self.waiting = True self.after_idle(self.update) def updateButtons(self): if self.expSeries is None: self.seriesButtons.buttons[1].disable() self.seriesButtons.buttons[2].disable() self.conditionPointsButtons.buttons[0].disable() self.conditionPointsButtons.buttons[1].disable() self.conditionPointsButtons.buttons[2].disable() elif self.expSeries.className == 'Experiment': self.seriesButtons.buttons[1].disable() self.seriesButtons.buttons[2].disable() self.conditionPointsButtons.buttons[0].disable() self.conditionPointsButtons.buttons[1].disable() self.conditionPointsButtons.buttons[2].enable() else: self.seriesButtons.buttons[1].enable() self.seriesButtons.buttons[2].enable() self.conditionPointsButtons.buttons[0].enable() self.conditionPointsButtons.buttons[2].disable() if self.conditionPoint is None: self.conditionPointsButtons.buttons[1].disable() else: self.conditionPointsButtons.buttons[1].enable() def update(self): self.updateButtons() objectList = [] textMatrix = [] for experiment in getSampledDimExperiments(self.nmrProject): getExperimentConditionSet(experiment) sampledDim = getExperimentSampledDim(experiment) datum = [None, experiment.name, 1, sampledDim.conditionVaried, sampledDim.numPoints] textMatrix.append(datum) objectList.append(experiment) for expSeries in self.nmrProject.sortedNmrExpSeries(): experiments = expSeries.experiments conditionSets = len([e.sampleConditionSet for e in experiments if e.sampleConditionSet]) datum = [expSeries.serial, expSeries.name or ' ', len(experiments), ','.join(expSeries.conditionNames), conditionSets] textMatrix.append(datum) objectList.append(expSeries) self.seriesMatrix.update(objectList=objectList, textMatrix=textMatrix) self.updateConditions() self.waiting = False def destroy(self): self.administerNotifiers(self.unregisterNotify) BasePopup.destroy(self)
def body(self, master): self.geometry('600x400') columnspan = 5 row = 0 label = Label(master, text="AutoAssign project file setup window.") label.grid(row=row, column=0, columnspan=columnspan, sticky=Tkinter.W) # # Set up the spectra # row += 1 label = Label(master, text="Spectrum type") label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W) label = Label(master, text="CCPN peak list") label.grid(row=row, column=2, columnspan=2, sticky=Tkinter.W) label = Label(master, text="Phase") # TODO What's this? label.grid(row=row, column=4, sticky=Tkinter.W) self.spectrumSelectWidget = {} self.spectrumPhaseWidget = {} for i in range(len(self.autoAssignProjectFile.defaultSpectra)): row += 1 specType = self.autoAssignProjectFile.defaultSpectra[i][0] if i == 0: labelText = "%s (root)" % specType else: labelText = "%s" % specType label = Label(master, text=labelText) label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W) self.spectrumSelectWidget[specType] = PulldownMenu( master, entries=self.peakNameList) self.spectrumSelectWidget[specType].grid(row=row, column=2, columnspan=2, sticky=Tkinter.W) self.spectrumPhaseWidget[specType] = Entry(master, text="", width=4) self.spectrumPhaseWidget[specType].grid(row=row, column=4, sticky=Tkinter.W) # # Make a break... # row += 1 separator = Separator(master, height=3) separator.setColor('black', bgColor='black') separator.grid(row=row, column=0, columnspan=columnspan, sticky=Tkinter.EW) # # Set up the tolerances # row += 1 label = Label(master, text="Atom tolerances") label.grid(row=row, column=0, columnspan=columnspan, sticky=Tkinter.EW) toleranceAtoms = self.autoAssignProjectFile.toleranceAtoms toleranceDefault = self.autoAssignProjectFile.toleranceDefault self.toleranceWidget = {} for i in range(0, len(toleranceAtoms), 2): row += 1 for j in range(2): curPos = i + j if curPos == len(toleranceAtoms): break toleranceAtom = toleranceAtoms[curPos] label = Label(master, text=toleranceAtom) label.grid(row=row, column=2 * j, sticky=Tkinter.E) self.toleranceWidget[toleranceAtom] = Entry( master, text=str(toleranceDefault[curPos]), width=6) self.toleranceWidget[toleranceAtom].grid(row=row, column=1 + 2 * j, sticky=Tkinter.W) # # Make a break... # row += 1 separator = Separator(master, height=3) separator.setColor('black', bgColor='black') separator.grid(row=row, column=0, columnspan=columnspan, sticky=Tkinter.EW) row += 1 label = Label( master, text="Will save the peak files in the project file directory.", fg='red') label.grid(row=row, column=0, columnspan=columnspan, sticky=Tkinter.EW) row += 1 texts = ['OK'] commands = [ self.ok ] # This calls 'ok' in BasePopup, this then calls 'apply' in here buttons = createDismissHelpButtonList(master, texts=texts, commands=commands, help_url=self.help_url) buttons.grid(row=row, columnspan=columnspan, column=0)