def body(self, guiFrame): guiFrame.grid_columnconfigure(0, weight=1) guiFrame.grid_rowconfigure(1, weight=1) frame = LabelFrame(guiFrame, text='Options') frame.grid(row=0,column=0,sticky='ew') frame.grid_columnconfigure(5, weight=1) # Choose type of symmetry set to define or change (if allready present in the model) self.molLabel = Label(frame, text='Symmetry Operator:') self.molLabel.grid(row=0,column=2,sticky='w') self.symmCodePulldown = PulldownMenu(frame, callback=self.setSymmCode, entries=['NCS','C2','C3','C5'], do_initial_callback=False) self.symmCodePulldown.grid(row=0,column=3,sticky='w') frame = LabelFrame(guiFrame, text='Symmetry Operations') frame.grid(row=1,column=0,sticky='nsew') frame.grid_columnconfigure(0, weight=1) frame.grid_rowconfigure(0, weight=1) self.molSysPulldown = PulldownMenu(self, callback=self.setMolSystem, do_initial_callback=False) self.chainSelect = MultiWidget(self, CheckButton, callback=self.setChains, minRows=0, useImages=False) self.segStartEntry = IntEntry(self, returnCallback=self.setSegStart, width=6) self.segLengthEntry = IntEntry(self, returnCallback=self.setSegLength, width=6) headings = ['#','Symmetry\noperator','Mol System','Chains','Start\nresidue','Segment\nlength'] editWidgets = [None, None, self.molSysPulldown, self.chainSelect, self.segStartEntry, self.segLengthEntry] editGetCallbacks = [None, None, self.getMolSystem, self.getChains, self.getSegStart, self.getSegLength] editSetCallbacks = [None, self.setSymmCode, self.setMolSystem, self.setChains, self.setSegStart, self.setSegLength] self.symmetryMatrix = ScrolledMatrix(frame,headingList=headings, callback=self.selectSymmetry, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks) self.symmetryMatrix.grid(row=0,column=0,sticky='nsew') texts = ['Add Symmetry Set','Remove Symmetry Set'] commands = [self.addSymmetrySet,self.removeSymmetrySet] self.buttonList = createDismissHelpButtonList(guiFrame, texts=texts, commands=commands, expands=True) self.buttonList.grid(row=2,column=0,sticky='ew') self.updateMolPartners() self.notify(self.registerNotify) #Temporary report of parameters print self.molSystem print self.molecules print self.symmetrySet print self.symmetryOp print self.symmetryCode
def body(self, master): self.alarm_id = None self.root_widget = getRoot(self) row = 0 label = Label(master, text='Widget count:') label.grid(row=row, column=0, sticky=Tkinter.W) self.count_label = Label(master, text='', tipText='Number of Tkinter widget objects') self.count_label.grid(row=row, column=1, sticky=Tkinter.W) row = row + 1 ind = 1 label = Label(master, text='Auto count:') label.grid(row=row, column=0, sticky=Tkinter.W) self.on_off_buttons = RadioButtons(master, entries=self.on_off_entries, select_callback=self.applyAuto, selected_index=ind) self.on_off_buttons.grid(row=row, column=1, sticky=Tkinter.EW) row = row + 1 label = Label(master, text='Auto frequency:') label.grid(row=row, column=0, sticky=Tkinter.W) self.freq_entry = IntEntry(master, text=60, returnCallback=self.applyAuto) self.freq_entry.grid(row=row, column=1, sticky=Tkinter.EW) label = Label(master, text='seconds') label.grid(row=row, column=2, sticky=Tkinter.W) row = row + 1 texts = ['Do Immediate Count'] commands = [self.applyManual] buttons = createDismissHelpButtonList(master, texts=texts, commands=commands, help_msg=self.help_msg, help_url=self.help_url) buttons.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW) self.doCount()
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()
class PopupTemplate(BasePopup): def __init__(self, parent, project=None, *args, **kw): self.project = project self.parent = parent self.objects = self.getObjects() self.object = None BasePopup.__init__(self, parent=parent, title='Popup Template', **kw) self.updateObjects() def body(self, mainFrame): mainFrame.grid_columnconfigure(1, weight=1, minsize=100) mainFrame.config(borderwidth=5, relief='solid') row = 0 label = Label(mainFrame, text="Frame (with sub-widgets):") label.grid(row=row, column=0, sticky=Tkinter.E) frame = Frame(mainFrame, relief='raised', border=2, background='#8080D0') # Frame expands East-West frame.grid(row=row, column=1, sticky=Tkinter.EW) # Last column expands => Widgets pusted to the West frame.grid_columnconfigure(3, weight=1) # Label is within the sub frame label = Label(frame, text='label ') label.grid(row=0, column=0, sticky=Tkinter.W) entry = Entry(frame, text='Entry', returnCallback=self.showWarning) entry.grid(row=0, column=1, sticky=Tkinter.W) self.check = CheckButton(frame, text='Checkbutton', selected=True, callback=self.updateObjects) self.check.grid(row=0, column=2, sticky=Tkinter.W) # stick a button to the East wall button = Button(frame, text='Button', command=self.pressButton) button.grid(row=0, column=3, sticky=Tkinter.E) row += 1 label = Label(mainFrame, text="Text:") label.grid(row=row, column=0, sticky=Tkinter.E) self.textWindow = Text(mainFrame, text='Initial Text\n', width=60, height=5) self.textWindow.grid(row=row, column=1, sticky=Tkinter.NSEW) row += 1 label = Label(mainFrame, text="CheckButtons:") label.grid(row=row, column=0, sticky=Tkinter.E) entries = ['Alpha','Beta','Gamma','Delta'] selected = entries[2:] self.checkButtons = CheckButtons(mainFrame, entries, selected=selected,select_callback=self.changedCheckButtons) self.checkButtons.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="PartitionedSelector:") label.grid(row=row, column=0, sticky=Tkinter.E) labels = ['Bool','Int','Float','String'] objects = [type(0),type(1),type(1.0),type('a')] selected = [type('a')] self.partitionedSelector= PartitionedSelector(mainFrame, labels=labels, objects=objects, colors = ['red','yellow','green','#000080'], callback=self.toggleSelector,selected=selected) self.partitionedSelector.grid(row=row, column=1, sticky=Tkinter.EW) row += 1 label = Label(mainFrame, text="PulldownMenu") label.grid(row=row, column=0, sticky=Tkinter.E) entries = ['Frodo','Pipin','Merry','Sam','Bill','Gandalf','Strider','Gimli','Legolas'] self.pulldownMenu = PulldownMenu(mainFrame, callback=self.selectPulldown, entries=entries, selected_index=2, do_initial_callback=False) self.pulldownMenu.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="RadioButtons in a\nScrolledFrame.frame:") label.grid(row=row, column=0, sticky=Tkinter.EW) frame = ScrolledFrame(mainFrame, yscroll = False, doExtraConfig = True, width=100) frame.grid(row=row, column=1, sticky=Tkinter.EW) frame.grid_columnconfigure(0, weight=1) self.radioButtons = RadioButtons(frame.frame, entries=entries, select_callback=self.checkRadioButtons, selected_index=1, relief='groove') self.radioButtons.grid(row=0, column=0, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="LabelFrame with\nToggleLabels inside:") label.grid(row=row, column=0, sticky=Tkinter.E) labelFrame = LabelFrame(mainFrame, text='Frame Title') labelFrame.grid(row=row, column=1, sticky=Tkinter.NSEW) labelFrame.grid_rowconfigure(0, weight=1) labelFrame.grid_columnconfigure(3, weight=1) self.toggleLabel1 = ToggleLabel(labelFrame, text='ScrolledMatrix', callback=self.toggleFrame1) self.toggleLabel1.grid(row=0, column=0, sticky=Tkinter.W) self.toggleLabel1.arrowOn() self.toggleLabel2 = ToggleLabel(labelFrame, text='ScrolledGraph', callback=self.toggleFrame2) self.toggleLabel2.grid(row=0, column=1, sticky=Tkinter.W) self.toggleLabel3 = ToggleLabel(labelFrame, text='ScrolledCanvas', callback=self.toggleFrame3) self.toggleLabel3.grid(row=0, column=2, sticky=Tkinter.W) row += 1 mainFrame.grid_rowconfigure(row, weight=1) label = Label(mainFrame, text="changing/shrinking frames:") label.grid(row=row, column=0, sticky=Tkinter.E) self.toggleRow = row self.toggleFrame = Frame(mainFrame) self.toggleFrame.grid(row=row, column=1, sticky=Tkinter.NSEW) self.toggleFrame.grid_rowconfigure(0, weight=1) self.toggleFrame.grid_columnconfigure(0, weight=1) # option 1 self.intEntry = IntEntry(self, returnCallback = self.setNumber, width=8) self.multiWidget = MultiWidget(self, Entry, options=None, values=None, callback=self.setKeywords, minRows=3, maxRows=5) editWidgets = [None, None, self.intEntry, self.multiWidget] editGetCallbacks = [None, None, self.getNumber, self.getKeywords] editSetCallbacks = [None, None, self.setNumber, self.setKeywords] headingList = ['Name','Color','Number','Keywords'] self.scrolledMatrix = ScrolledMatrix(self.toggleFrame, headingList=headingList, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, callback=self.selectObject, multiSelect=False) self.scrolledMatrix.grid(row=0, column=0, sticky=Tkinter.NSEW) # option 2 self.scrolledGraph = ScrolledGraph(self.toggleFrame, width=400, height=300, symbolSize=5, symbols=['square','circle'], dataColors=['#000080','#800000'], lineWidths=[0,1] ) self.scrolledGraph.setZoom(1.3) dataSet1 = [[0,0],[1,1],[2,4],[3,9],[4,16],[5,25]] dataSet2 = [[0,0],[1,3],[2,6],[3,9],[4,12],[5,15]] self.scrolledGraph.update(dataSets=[dataSet1,dataSet2], xLabel = 'X axis label', yLabel = 'Y axis label', title = 'Main Title') self.scrolledGraph.draw() # option 3 self.scrolledCanvas = ScrolledCanvas(self.toggleFrame,relief = 'groove', borderwidth = 2, resizeCallback=None) canvas = self.scrolledCanvas.canvas font = 'Helvetica 10' box = canvas.create_rectangle(10,10,150,200, outline='grey', fill='grey90') line = canvas.create_line(0,0,200,200,fill='#800000', width=2) text = canvas.create_text(120,50, text='Text', font=font, fill='black') circle = canvas.create_oval(30,30,50,50,outline='#008000',fill='#404040',width=3) row += 1 label = Label(mainFrame, text="FloatEntry:") label.grid(row=row, column=0, sticky=Tkinter.E) self.floatEntry = FloatEntry(mainFrame, text=3.14159265, returnCallback=self.floatEntryReturn) self.floatEntry.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="Scale:") label.grid(row=row, column=0, sticky=Tkinter.E) self.scale = Scale(mainFrame, from_=10, to=90, value=50, orient=Tkinter.HORIZONTAL) self.scale.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="Value Ramp:") label.grid(row=row, column=0, sticky=Tkinter.E) self.valueRamp = ValueRamp(mainFrame, self.valueRampCallback, speed = 1.5, delay = 50) self.valueRamp.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="ButtonList:") label.grid(row=row, column=0, sticky=Tkinter.E) texts = ['Select File','Close','Quit'] commands = [self.selectFile, self.close, self.quit] bottomButtons = ButtonList(mainFrame, texts=texts, commands=commands, expands=True) bottomButtons.grid(row=row, column=1, sticky=Tkinter.EW) self.protocol('WM_DELETE_WINDOW', self.quit) def floatEntryReturn(self, event): value = self.floatEntry.get() self.textWindow.setText('%s\n' % value) def selectObject(self, object, row, col): self.object = object def getKeywords(self, object): if object : values = object.keywords self.multiWidget.set(values) def setKeywords(self, event): values = self.multiWidget.get() self.object.keywords = values self.updateObjects() def getNumber(self, object): if object : self.intEntry.set(object.quantity) def setNumber(self, event): value = self.intEntry.get() self.object.quantity = value self.updateObjects() def toggleFrame1(self, isHidden): if isHidden: self.scrolledMatrix.grid_forget() self.toggleFrame.grid_forget() else: self.scrolledGraph.grid_forget() self.scrolledCanvas.grid_forget() self.scrolledMatrix.grid(row=0, column=0, sticky=Tkinter.NSEW) self.toggleFrame.grid(row=self.toggleRow, column=1,sticky=Tkinter.NSEW) self.toggleLabel2.arrowOff() self.toggleLabel3.arrowOff() def toggleFrame2(self, isHidden): if isHidden: self.scrolledGraph.grid_forget() self.toggleFrame.grid_forget() else: self.scrolledMatrix.grid_forget() self.scrolledCanvas.grid_forget() self.scrolledGraph.grid(row=0, column=0, sticky=Tkinter.NSEW) self.toggleFrame.grid(row=self.toggleRow, column=1,sticky=Tkinter.NSEW) self.toggleLabel1.arrowOff() self.toggleLabel3.arrowOff() def toggleFrame3(self, isHidden): if isHidden: self.scrolledCanvas.grid_forget() self.toggleFrame.grid_forget() else: self.scrolledMatrix.grid_forget() self.scrolledGraph.grid_forget() self.scrolledCanvas.grid(row=0, column=0, sticky=Tkinter.NSEW) self.toggleFrame.grid(row=self.toggleRow, column=1,sticky=Tkinter.NSEW) self.toggleLabel1.arrowOff() self.toggleLabel2.arrowOff() def valueRampCallback(self, value): self.textWindow.setText('%s\n' % value) def checkRadioButtons(self, value): self.textWindow.setText('%s\n' % value) def selectPulldown(self, index, name): self.textWindow.setText('%d, %s\n' % (index, name)) def toggleSelector(self, value): self.textWindow.setText('%s\n' % value) def changedCheckButtons(self, values): self.textWindow.setText(','.join(values) + '\n') def getObjects(self): objects = [] objects.append( Fruit('Lemon', '#FFFF00',1,keywords=['Bitter','Tangy'] ) ) objects.append( Fruit('Orange', '#FF8000',4 ) ) objects.append( Fruit('Banana', '#FFF000',5 ) ) objects.append( Fruit('Pinapple','#FFD000',9 ) ) objects.append( Fruit('Kiwi', '#008000',12) ) objects.append( Fruit('Lime', '#00FF00',2 ) ) objects.append( Fruit('Apple', '#800000',5,keywords=['Crunchy'] ) ) objects.append( Fruit('Pear', '#408000',6 ) ) objects.append( Fruit('Peach', '#FFE0C0',2,keywords=['Sweet','Furry'] ) ) objects.append( Fruit('Plumb', '#800080',7 ) ) return objects def updateObjects(self, event=None): textMatrix = [] objectList = [] colorMatrix = [] for object in self.objects: datum = [] datum.append( object.name ) datum.append( None ) datum.append( object.quantity ) datum.append( ','.join(object.keywords) ) colors = [None, object.color, None, None] textMatrix.append(datum) objectList.append(object) colorMatrix.append(colors) if self.check.get(): self.scrolledMatrix.update(textMatrix=textMatrix, objectList=objectList) else: self.scrolledMatrix.update(textMatrix=textMatrix, objectList=objectList, colorMatrix=colorMatrix) def selectFile(self): fileSelectPopup = FileSelectPopup(self, title = 'Choose file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = fileSelectPopup.getFile() self.textWindow.setText('File Selected: %s\n' % fileName) def showWarning(self, eventObject): self.textWindow.setText('Text Entry Return Pressed\n') showWarning('Warning Title','Warning Message') return def pressButton(self): self.textWindow.setText('Button Pressed\n') if showYesNo('Title','Prompt: Clear text window?'): self.textWindow.clear() return def quit(self): BasePopup.destroy(self)
def body(self): '''Describes the body of this tab. It consists out of a number of radio buttons, check buttons and number entries that allow the user to indicate which assignments should be transferred. ''' # self.frame.expandColumn(0) self.frame.expandGrid(8, 0) self.frame.expandGrid(8, 1) typeOfAssignmentFrame = LabelFrame( self.frame, text='type of assignment') typeOfAssignmentFrame.grid(row=0, column=0, sticky='nesw') # typeOfAssignmentFrame.expandGrid(0,5) peakSelectionFrame = LabelFrame( self.frame, text='which peaks to assign') peakSelectionFrame.grid(row=0, column=1, sticky='nesw', rowspan=2) spinSystemSelectionFrame = LabelFrame(self.frame, text='Which spin-systems to use') spinSystemSelectionFrame.grid(row=2, column=0, sticky='nesw') tipText = 'What to do when a residue has already a spin system assigned to it.' assignedResidueFrame = LabelFrame(self.frame, text='if residue already has spin-system', tipText=tipText) assignedResidueFrame.grid(row=2, column=1, sticky='nesw') spectrumSelectionFrame = LabelFrame(self.frame, text='spectra') spectrumSelectionFrame.grid(row=1, column=0, sticky='nesw') row = 0 Label(typeOfAssignmentFrame, text='Resonances to Peak Dimensions', grid=(row, 0)) self.peaksCheckButton = CheckButton(typeOfAssignmentFrame, selected=True, grid=(row, 1)) row += 1 Label(typeOfAssignmentFrame, text='SpinSystems to Residues', grid=(row, 0)) self.residuesCheckButton = CheckButton( typeOfAssignmentFrame, selected=True, grid=(row, 1)) row = 0 Label(peakSelectionFrame, text='Intra-Residual', grid=(row, 0)) self.intraCheckButton = CheckButton( peakSelectionFrame, selected=True, grid=(row, 1)) row += 1 Label(peakSelectionFrame, text='Sequential', grid=(row, 0)) self.sequentialCheckButton = CheckButton( peakSelectionFrame, selected=True, grid=(row, 1)) row += 1 Label(peakSelectionFrame, text='Do not assign diagonal peaks', grid=(row, 0)) self.noDiagonalCheckButton = CheckButton( peakSelectionFrame, selected=True, grid=(row, 1)) entries = ['Only assigned spin systems', 'All that have a score of at least: ', 'User Defined', 'Solution number:'] tipTexts = ['Only assign resonances of spin systems that already have a sequential assignment for the assignment of peak dimensions. Spin system to residue assignment is not relevant in this case.', 'Assign all spin systems that have a score of at least a given percentage. 50% or lower is not possible, because than spin systems might have to be assigned to more than 1 residue, which is impossible.', "As defined in the lower row of buttons in the 'results' tab.", 'One of the single solutions of the annealing.'] self.spinSystemTypeSelect = RadioButtons(spinSystemSelectionFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(4, 1), tipTexts=tipTexts) tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.' self.minScoreEntry = FloatEntry(spinSystemSelectionFrame, grid=(1, 1), width=7, text=str(self.minScore), returnCallback=self.changeMinScore, tipText=tipText) self.minScoreEntry.bind('<Leave>', self.changeMinScore, '+') self.solutionNumberEntry = IntEntry(spinSystemSelectionFrame, grid=(3, 1), width=7, text=1, returnCallback=self.solutionUpdate, tipText=tipText) self.solutionNumberEntry.bind('<Leave>', self.solutionUpdate, '+') #self.solutionPullDown = PulldownList(spinSystemSelectionFrame, None, grid=(3,1), sticky='w') entries = ['all spectra', 'only:'] tipTexts = ['Assign peaks in all the spectra that where selected before the annealing ran.', 'Only assign peaks in one particular spectrum. You can of course repeat this multiple times for different spectra.'] self.spectrumSelect = RadioButtons(spectrumSelectionFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(2, 1), tipTexts=tipTexts) self.spectraPullDown = PulldownList(spectrumSelectionFrame, self.changeSpectrum, grid=(1, 1), sticky='w') entries = ['skip this residue', 'de-assign old spin system from residue', 'assign, but never merge', 'warn to merge'] tipTexts = ["Don't assign the new spin system to the residue. The residue is not skipped when the old spin system does not contain any resonances", "De-assign old spin system from residue, unless the old spin system is a spin system without any resonances.", "Don't merge any spin systems, merging can be performed later if nescesary in the Resonance --> SpinSystems window.", "Ask to merge individually for each spin system, this might result in clicking on a lot of popups."] self.assignedResidueStrategySelect = RadioButtons(assignedResidueFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(2, 1), tipTexts=tipTexts) texts = ['Transfer Assignments'] commands = [self.transferAssignments] self.transferButton = ButtonList( self.frame, commands=commands, texts=texts) self.transferButton.grid(row=5, column=0, sticky='nsew', columnspan=2)
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 body(self, guiFrame): guiFrame.grid_columnconfigure(0, weight=1) guiFrame.grid_rowconfigure(1, weight=1) frame = LabelFrame(guiFrame, text='Options') frame.grid(row=0, column=0, sticky='ew') frame.grid_columnconfigure(5, weight=1) label = Label(frame, text='MolSystem:') label.grid(row=0, column=0, sticky='w') self.molSystemPulldown = PulldownMenu(frame, callback=self.selectMolSystem) self.molSystemPulldown.grid(row=0, column=1, sticky='w') self.molLabel = Label(frame, text='Molecule:') self.molLabel.grid(row=0, column=2, sticky='w') self.moleculePulldown = PulldownMenu(frame, callback=self.selectMolecule) self.moleculePulldown.grid(row=0, column=3, sticky='w') label = Label(frame, text='Same Molecule Symmetry:') label.grid(row=0, column=4, sticky='w') self.molSelect = CheckButton(frame, callback=self.toggleSingleMolecule) self.molSelect.grid(row=0, column=5, sticky='w') self.molSelect.set(self.singleMolecule) frame = LabelFrame(guiFrame, text='Symmetry Operations') frame.grid(row=1, column=0, sticky='nsew') frame.grid_columnconfigure(0, weight=1) frame.grid_rowconfigure(0, weight=1) self.symmCodePulldown = PulldownMenu(self, callback=self.setSymmCode, do_initial_callback=False) self.segLengthEntry = IntEntry(self, returnCallback=self.setSegLength, width=6) self.setChainMulti = MultiWidget(self, CheckButton, callback=self.setChains, minRows=0, useImages=False) self.setSegmentMulti = MultiWidget(self, IntEntry, callback=self.setSegments, minRows=0, useImages=False) editWidgets = [ None, self.symmCodePulldown, self.segLengthEntry, self.setChainMulti, self.setSegmentMulti ] editGetCallbacks = [ None, self.getSymmCode, self.getSegLength, self.getChains, self.getSegments ] editSetCallbacks = [ None, self.setSymmCode, self.setSegLength, self.setChains, self.setSegments ] headings = [ '#', 'Symmetry\nType', 'Segment\nLength', 'Chains', 'Segment\nPositions' ] self.symmetryMatrix = ScrolledMatrix(frame, headingList=headings, callback=self.selectSymmetry, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks) self.symmetryMatrix.grid(row=0, column=0, sticky='nsew') texts = ['Add Symmetry Op', 'Remove Symmetrey Op'] commands = [self.addSymmOp, self.removeSymmOp] buttonList = createDismissHelpButtonList(guiFrame, texts=texts, commands=commands, expands=True) buttonList.grid(row=2, column=0, sticky='ew') self.updateMolSystems() self.updateMolecules() self.updateSymmetriesAfter() self.notify(self.registerNotify)
def body(self): frame = self.frame self.resultsResidueNumber = 1 frame.expandGrid(5, 0) resultTopFrame = LabelFrame(frame, text='Which results to show') resultTopFrame.grid(row=0, column=0, sticky='ew') self.resultsResidueNumber = 3 texts = [' < '] commands = [self.resultsPrevResidue] self.resultsPreviousButton = ButtonList(resultTopFrame, commands=commands, texts=texts) self.resultsPreviousButton.grid(row=0, column=1, sticky='nsew') tipText = 'The Number of the residue in the sequence to display results for' self.resultsResidueNumberEntry = IntEntry( resultTopFrame, grid=(0, 2), width=7, text=3, returnCallback=self.resultsUpdateAfterEntry, tipText=tipText) #self.resultsResidueNumberEntry.bind('<Leave>', self.resultsUpdateAfterEntry, '+') texts = [' > '] commands = [self.resultsNextResidue] self.resultsNextButton = ButtonList(resultTopFrame, commands=commands, texts=texts) self.resultsNextButton.grid(row=0, column=3, sticky='nsew') selectCcpCodes = ['residue'] + AMINO_ACIDS self.resultsSelectedCcpCode = 'residue' tipText = 'Instead of going through the sequence residue by residue, jump directly to next amino acid of a specific type.' resultsSelectCcpCodeLabel = Label( resultTopFrame, text='Directly jump to previous/next:', grid=(0, 4)) self.resultsSelectCcpCodePulldown = PulldownList( resultTopFrame, callback=self.resultsChangeSelectedCcpCode, texts=selectCcpCodes, index=selectCcpCodes.index(self.resultsSelectedCcpCode), grid=(0, 5), tipText=tipText) self.selectedSolution = 1 runLabel = Label(resultTopFrame, text='run:') runLabel.grid(row=0, column=6) texts = [' < '] commands = [self.resultsPrevSolution] self.resultsPreviousSolutionButton = ButtonList(resultTopFrame, commands=commands, texts=texts) self.resultsPreviousSolutionButton.grid(row=0, column=7, sticky='nsew') tipText = 'If you ran the algorithm more than once, you can select the solution given by the different runs.' self.resultsSolutionNumberEntry = IntEntry( resultTopFrame, grid=(0, 8), width=7, text=1, returnCallback=self.solutionUpdateAfterEntry, tipText=tipText) #self.resultsSolutionNumberEntry.bind('<Leave>', self.solutionUpdateAfterEntry, '+') texts = [' > '] commands = [self.resultsNextSolution] self.resultsNextSolutionButton = ButtonList(resultTopFrame, commands=commands, texts=texts) self.resultsNextSolutionButton.grid(row=0, column=9, sticky='nsew') self.energyLabel = Label(resultTopFrame, text='energy:') self.energyLabel.grid(row=0, column=10) texts = ['template for puzzling'] commands = [self.adoptSolution] self.adoptButton = ButtonList(resultTopFrame, commands=commands, texts=texts) self.adoptButton.grid(row=0, column=11, sticky='nsew') # LabelFrame(frame, text='Spin Systems') resultsSecondFrame = Frame(frame) resultsSecondFrame.grid(row=2, column=0, sticky='nsew') resultsSecondFrame.grid_columnconfigure(0, weight=1) resultsSecondFrame.grid_columnconfigure(1, weight=1) resultsSecondFrame.grid_columnconfigure(2, weight=1) resultsSecondFrame.grid_columnconfigure(3, weight=1) resultsSecondFrame.grid_columnconfigure(4, weight=1) headingList = ['#', '%'] tipTexts = [ 'Spinsystem number {} indicates serial of the spinsystem. If the spinsystem was already assigned to a residue, the residue number is shown aswell', 'percentage of the solutions that connected this spinsystem to this residue' ] editWidgets = [None, None, None] self.displayResultsTables = [] self.residueLabels = [] for i in range(5): label = Label(resultsSecondFrame, text='residue') label.grid(row=0, column=i) #editGetCallbacks = [createCallbackFunction(i)]*3 displayResultsTable = ScrolledMatrix( resultsSecondFrame, headingList=headingList, multiSelect=False, tipTexts=tipTexts, callback=self.selectSpinSystemForTable, passSelfToCallback=True) displayResultsTable.grid(row=2, column=i, sticky='nsew') displayResultsTable.sortDown = False self.residueLabels.append(label) self.displayResultsTables.append(displayResultsTable) # LabelFrame(frame, text='Sequence Fragment') resultsFirstFrame = Frame(resultsSecondFrame) resultsFirstFrame.grid(row=1, column=0, sticky='ew', columnspan=5) resultsFirstFrame.grid_rowconfigure(0, weight=1) resultsFirstFrame.grid_rowconfigure(1, weight=1) resultsFirstFrame.grid_columnconfigure(0, weight=1) texts = [ ' res 1 ', ' links ', ' res 2 ', ' links ', ' res 3 ', ' links ', ' res 4 ', ' links ', ' res 5 ' ] commands = [ lambda: self.selectRelativeResidue(1, True), lambda: self.selectLink(1, True), lambda: self.selectRelativeResidue(2, True), lambda: self.selectLink(2, True), lambda: self.selectRelativeResidue(3, True), lambda: self.selectLink(3, True), lambda: self.selectRelativeResidue(4, True), lambda: self.selectLink(4, True), lambda: self.selectRelativeResidue(5, True) ] self.sequenceButtons = ButtonList(resultsFirstFrame, commands=commands, texts=texts) self.sequenceButtons.grid(row=0, column=0, sticky='nsew') for n, button in enumerate(self.sequenceButtons.buttons): if n % 2: button.grid(column=n, sticky='ns') self.sequenceButtons.grid_columnconfigure(n, weight=0) else: self.sequenceButtons.grid_columnconfigure(n, uniform=2) spacer = Spacer(resultsFirstFrame) spacer.grid(row=1, column=0, sticky='nsew') texts = [ ' res 1 ', ' links ', ' res 2 ', ' links ', ' res 3 ', ' links ', ' res 4 ', ' links ', ' res 5 ' ] commands = commands = [ lambda: self.selectRelativeResidue(1, False), lambda: self.selectLink(1, False), lambda: self.selectRelativeResidue(2, False), lambda: self.selectLink(2, False), lambda: self.selectRelativeResidue(3, False), lambda: self.selectLink(3, False), lambda: self.selectRelativeResidue(4, False), lambda: self.selectLink(4, False), lambda: self.selectRelativeResidue(5, False) ] self.sequenceButtonsB = ButtonList(resultsFirstFrame, commands=commands, texts=texts) self.sequenceButtonsB.grid(row=2, column=0, sticky='nsew') for n, button in enumerate(self.sequenceButtonsB.buttons): if n % 2: button.grid(column=n, sticky='ns') self.sequenceButtonsB.grid_columnconfigure(n, weight=0) else: self.sequenceButtonsB.grid_columnconfigure(n, uniform=2) frame.grid_rowconfigure(3, weight=2) resultsThirdFrame = Frame(frame) resultsThirdFrame.grid(row=3, column=0, sticky='nsew') resultsThirdFrame.grid_rowconfigure(0, weight=1) resultsThirdFrame.grid_columnconfigure(0, weight=1) tabbedFrameB = TabbedFrame(resultsThirdFrame, options=['Peaks', 'Spin System'], callback=self.toggleTab, grid=(0, 0)) #self.tabbedFrameB = tabbedFrame PeakFrame, SpinSystemFrame = tabbedFrameB.frames SpinSystemFrame.grid_rowconfigure(0, weight=1) PeakFrame.grid_rowconfigure(1, weight=1) SpinSystemFrame.grid_columnconfigure(0, weight=1) PeakFrame.grid_columnconfigure(0, weight=1) headingList = [ 'residue', 'assigned to in project', 'user defined sequence', 'selected annealing result', '%' ] tipTexts = [None, None, None, None, None] editWidgets = [None, None, None, None, None] editGetCallbacks = [None, None, None, None, None] editSetCallbacks = [None, None, None, None, None] self.spinSysTable = ScrolledMatrix(SpinSystemFrame, headingList=headingList, editWidgets=editWidgets, multiSelect=False, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, tipTexts=tipTexts) self.spinSysTable.grid(row=0, column=0, sticky='nsew') buttonFrameinPeakFrame = Frame(PeakFrame) buttonFrameinPeakFrame.grid(sticky='ew') self.findButton = Button( buttonFrameinPeakFrame, text=' Go to Peak ', borderwidth=1, padx=2, pady=1, command=self.findPeak, tipText='Locate the currently selected peak in the specified window' ) self.findButton.grid(row=0, column=0, sticky='e') label = Label(buttonFrameinPeakFrame, text='in window:') label.grid(row=0, column=1, sticky='w') self.windowPulldown = PulldownList( buttonFrameinPeakFrame, callback=self.selectWindowPane, tipText='Choose the spectrum window for locating peaks or strips') self.windowPulldown.grid(row=0, column=2, sticky='w') self.assignSelectedPeaksButton = Button( buttonFrameinPeakFrame, text='Assign Resonances to Peak(s)', borderwidth=1, padx=2, pady=1, command=self.assignSelectedPeaks, tipText= 'Assign resonances to peak dimensions, this of course only works when the peak is found in the spectrum.' ) self.assignSelectedPeaksButton.grid(row=0, column=3, sticky='ew') self.assignSelectedSpinSystemsToResiduesButton = Button( buttonFrameinPeakFrame, text='Assign Spinsystems to Residues', borderwidth=1, padx=2, pady=1, command=self.assignSelectedSpinSystemsToResidues, tipText='Assign spinsystems to residues') self.assignSelectedSpinSystemsToResiduesButton.grid(row=0, column=4, sticky='ew') headingList = [ '#', 'spectrum', 'Dim1', 'Dim2', 'Dim3', 'c.s. dim1', 'c.s. dim2', 'c.s. dim3', 'colabelling' ] tipTexts = [ 'Peak number, only present when the peak was actually found in the spectrum.', 'Name of the spectrum', 'Name of atomSet measured in this dimension. Dimension number corresponds to Ref Exp Dim as indicated by going in the main menu to Experiment-->Experiments-->Experiment Type', 'Name of atomSet measured in this dimension. Dimension number corresponds to Ref Exp Dim as indicated by going in the main menu to Experiment-->Experiments-->Experiment Type', 'Name of atomSet measured in this dimension. Dimension number corresponds to Ref Exp Dim as indicated by going in the main menu to Experiment-->Experiments-->Experiment Type', 'Chemical Shift', 'Chemical Shift', 'Chemical Shift', 'Colabbeling fraction over all nuclei that are on the magnetization transfer pathway during the experiment that gave rise to the peak, including visited nuclei that were not measured in any of the peak dimensions' ] #editWidgets = [None, None, None, None, None, None, None, None, None] editGetCallbacks = [ None, None, None, None, None, None, None, None, None ] #editGetCallbacks = [self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak] editSetCallbacks = [ None, None, None, None, None, None, None, None, None ] self.displayPeakTable = ScrolledMatrix(PeakFrame, headingList=headingList, multiSelect=True, tipTexts=tipTexts) #editWidgets=editWidgets, multiSelect=True, # editGetCallbacks=editGetCallbacks, # editSetCallbacks=editSetCallbacks, # tipTexts=tipTexts) self.displayPeakTable.grid(row=1, column=0, sticky='nsew') self.windowPane = None self.updateWindows()
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): self.geometry("500x250") self.numAliasingEntry = IntEntry(self, text='', returnCallback=self.setNumAliasing, width=4) guiFrame.expandGrid(1, 0) div = LabelDivider(guiFrame, text='Peak Dimension Positions', grid=(0, 0)) utilButtons = UtilityButtonList(guiFrame, doClone=False, closeCmd=self.close, helpUrl=self.help_url, grid=(0, 1)) tipTexts = [ 'The peak/spectrum dimension number', 'The kind of isotope measured in the dimension', 'The position of the peak in this dimension, in units of ppm', 'The frequency position of the peak in this dimension, in units of Hz', 'The data point position (in the spectrum matrix) of the peak in this dimension', 'Sets the number of spectrum sweep withs to add to the peak dimension position to locate it at its real ppm value. Note an aliasing of "1" moves a peak to a lower ppm', 'The assignment annotation for the peak dimension' ] headingList = [ 'Dimension', 'Isotope', 'ppm', 'Hz', 'Points', 'Num.\nAliasing', 'Annotation' ] editWidgets = [ None, None, None, None, None, self.numAliasingEntry, None ] editGetCallbacks = [ None, None, None, None, None, self.getNumAliasing, None ] editSetCallbacks = [ None, None, None, None, None, self.setNumAliasing, None ] self.scrolledMatrix = ScrolledMatrix(guiFrame, tipTexts=tipTexts, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, initialCols=5, initialRows=3, headingList=headingList, callback=self.selectCell, grid=(1, 0), gridSpan=(1, 2)) for func in ('__init__', 'delete', 'setAnnotation', 'setNumAliasing', 'setPosition'): self.registerNotify(self.updateAfter, 'ccp.nmr.Nmr.PeakDim', func) self.waiting = False self.updateAfter(self.peak)
class EditPeakAliasingPopup(BasePopup): """ **Move Aliased Peaks to Their Underlying Resonance Position** This popup window is used to move aliased 'ghost' peaks to their real underlying resonance locations by adding or subtracting a whole number of spectrum widths to the position in one or more peak dimensions. This is used when a resonance, that causes a peak, lies outside the normal recorded bounds of the spectrum but the peak nonetheless still appears within the spectrum, as an aliased signal that re-appears as if wrapped back onto the opposite side of the spectrum. The minimum and maximum aliased frequency values for a spectrum dimension, as edited in the "Referencing" table of the main Spectra_ popup, may be set extend the contour display beyond the normal sweep width (ppm range) of the spectrum and thus cover the real ppm position of peaks that have been unaliased. In such instances the contours are extended by tiling; one or more copies of the contours (not mirror image) are made and placed sequentially next to the normal, fundamental region. If a peak is unaliased to a position outside the displayed spectrum limits then the contour display will naturally be extended to cover the new peak position; all peaks will be visible within the spectrum by default. However, the user may at any time reset the minimum and maximum aliased frequency for a spectrum display (see the Spectra_ popup); deleting all values will reset bounds to the original sweep with, but any values may be chosen, within reason. A peak can be moved to the unaliased position of its underlying resonances by editing the "Num. Aliasing" column of this popup; double-clicking and typing in the appropriate number. When this number is changed for a peak dimension the peak will be instantly moved to its new location. An aliasing value of zero means that the peak lies within the sweep width of the spectrum. For a ppm scale having a positive aliasing value will *reduce* the ppm value, placing the peak a number of spectrum widths above or to the right of the spectrum bounds. Likewise a negative aliasing value will place a peak at a higher ppm value; below or to the left. Often aliasing values will be 1 or -1, where a peak has just fallen off the edge of a spectrum. For example a glycine amide nitrogen really at 100 ppm may be just outside the top of a 15N HSQC and be wrapped back into the bottom to appear as a peak at around 135 ppm, which means that the aliasing value should be set to 1, moving the peaks position up by a sweep with of 35 ppm, from 135 ppm to 100 ppm. The sign of the aliasing number may seem to be backwards, but it is perhaps the ppm scale that is 'backwards'. More complex aliasing is often seen in 3D 13C spectra where the 13C axis can be folded (wrapped) to reduce the sweep width that needs to be recorded, but still avoiding peak overlap because of the way shifts correlate. For example a 13C HSQC NOESY may be recorded with a sweep with that covers the CA, CB range 25-75 ppm but aliased methyl carbons below 25 ppm and aromatic carbons between 110 ppm and 140 ppm will be present; the methyls will have aliasing values of 1, and the aromatics -1 or -2. It should be noted that picking peaks in the tiled copies of a contour display, i.e. outside the sweep width, will automatically set the aliasing value for the peak to reflect the displayed chemical shift value. Thus, the user does not need to explicitly unalias the peak position. Any peaks that are moved by virtue of being unaliased will have their contribution to the chemical shifts, of any assigned resonances, adjusted automatically. Chemical shift values are always calculated using the underlying resonance positions, not the apparent peak position. Also, if it is known that many peaks share the same aliasing values, i.e. are in the same sweep width tile, then the user can propagate the aliasing value from one peak to many others in a single step via the right-click window menu; "Peak::Unaliasing propagate". .. _Spectra: EditSpectrumPopup.html """ def __init__(self, parent, peak=None, *args, **kw): self.peak = peak self.peakDim = None self.guiParent = parent BasePopup.__init__(self, parent=parent, title="Edit Peak Aliasing", **kw) def body(self, guiFrame): self.geometry("500x250") self.numAliasingEntry = IntEntry(self, text='', returnCallback=self.setNumAliasing, width=4) guiFrame.expandGrid(1, 0) div = LabelDivider(guiFrame, text='Peak Dimension Positions', grid=(0, 0)) utilButtons = UtilityButtonList(guiFrame, doClone=False, closeCmd=self.close, helpUrl=self.help_url, grid=(0, 1)) tipTexts = [ 'The peak/spectrum dimension number', 'The kind of isotope measured in the dimension', 'The position of the peak in this dimension, in units of ppm', 'The frequency position of the peak in this dimension, in units of Hz', 'The data point position (in the spectrum matrix) of the peak in this dimension', 'Sets the number of spectrum sweep withs to add to the peak dimension position to locate it at its real ppm value. Note an aliasing of "1" moves a peak to a lower ppm', 'The assignment annotation for the peak dimension' ] headingList = [ 'Dimension', 'Isotope', 'ppm', 'Hz', 'Points', 'Num.\nAliasing', 'Annotation' ] editWidgets = [ None, None, None, None, None, self.numAliasingEntry, None ] editGetCallbacks = [ None, None, None, None, None, self.getNumAliasing, None ] editSetCallbacks = [ None, None, None, None, None, self.setNumAliasing, None ] self.scrolledMatrix = ScrolledMatrix(guiFrame, tipTexts=tipTexts, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, initialCols=5, initialRows=3, headingList=headingList, callback=self.selectCell, grid=(1, 0), gridSpan=(1, 2)) for func in ('__init__', 'delete', 'setAnnotation', 'setNumAliasing', 'setPosition'): self.registerNotify(self.updateAfter, 'ccp.nmr.Nmr.PeakDim', func) self.waiting = False self.updateAfter(self.peak) def open(self): self.updateAfter() BasePopup.open(self) def setNumAliasing(self, event): value = self.numAliasingEntry.get() if (value is not None) and self.peakDim: setPeakDimNumAliasing(self.peakDim, value) self.updateAfter() def getNumAliasing(self, peakDim): if peakDim: self.numAliasingEntry.set(peakDim.numAliasing) def selectCell(self, object, row, col): self.peakDim = object def updateAfter(self, object=None): if object: if object.className == 'Peak': self.peak = object elif object.peak is not self.peak: # object is peakDim & function was called by notifier # return if not my peak return if self.waiting: return else: self.waiting = True self.after_idle(self.update) def update(self): objectList = [] textMatrix = [] colorMatrix = [] colors = [None] * 7 colors[5] = '#B0FFB0' if self.peak: for peakDim in self.peak.sortedPeakDims(): dataDimRef = peakDim.dataDimRef if dataDimRef: objectList.append(peakDim) else: textMatrix.append([]) for peakDim in objectList: dataDimRef = peakDim.dataDimRef expDimRef = dataDimRef.expDimRef position = aliasedPeakDimPosition(peakDim) datum = [ peakDim.dim, '/'.join(expDimRef.isotopeCodes), unit_converter[('point', 'ppm')](position, dataDimRef), unit_converter[('point', 'Hz')](position, dataDimRef), position, peakDim.numAliasing, peakDim.annotation ] textMatrix.append(datum) colorMatrix.append(colors) self.scrolledMatrix.update(objectList=objectList, textMatrix=textMatrix, colorMatrix=colorMatrix) self.waiting = False def destroy(self): for func in ('__init__', 'delete', 'setAnnotation', 'setNumAliasing', 'setPosition'): self.unregisterNotify(self.updateAfter, 'ccp.nmr.Nmr.PeakDim', func) BasePopup.destroy(self)
class SpinSystemTypingPopup(BasePopup): """ **Predict Which Types of Residue Spin Systems Represent** This popup window uses chemical shift information, obtained from the resonances of a spin system group, to predict which kind of residue a spin system could be. Naturally, the more resonances/shifts there are in a spin system the better the prediction will be. Predictions are either made for a single spin system in isolation, or for a whole chain; by shuffling the residue to spin system mapping to give the optimum arrangement. Prediction for individual spin systems, as accessed by [Show Individual Classification], is covered in the `Spin System Type Scores`_ popup and will not be discussed here. .. _`Spin System Type Scores`: ../popups/SpinSystemTypeScoresPopup.html **Finding the Optimal Arrangement of Residue Types** This system attempts to find the best match of spin system to residue type by performing a Monte Carlo search to arrange each group of chemical shifts amongst the residue types found in the chain. The main principle is that the chain's residues dictate how many spin systems of a given type may be found, such that for example if there is only one Threonine residue then only one spin system may be predicted to be of Threonine type. This result comes naturally from shuffling the spin systems, with their chemical shifts, amongst the residue slots (disregarding sequence position). The prediction is made my selecting the chain and shift list to use, then which kinds of isotope to consider, by toggling the relevant buttons, choosing various Monte Carlo search options and finally selecting [Run Typing]. The prediction may take some time to run, depending upon the number of residues and spin systems that are being matched, but gives a graphical output of the progress. If the final prediction looks good the "Highest Scoring Mappings" display may be closed and [Assign Types] may be used to set the residue types for all of the spin systems in the main table that match only a single type and have a score above the assignment threshold value. Spin systems that already have a type or full residue assignment will not be affected. The default Monte Carlo search options ought to be appropriate for a small protein (100 residues) with 1H and 13C chemical shift information. Increasing the number of search steps may help if the search does not converge; still swaps between optimal assignments toward the end of the search. Increasing the ensemble size (how many test mappings are optimised at the same time) may help if the prediction gets stuck in local minima; different runs predict different arrangement, but larger ensembles require more search steps to converge. Where a spin system has multiple residue types predicted these are the types that come out of the final ensemble for that set of shifts, i.e. at this point the ensemble of solutions differ. Overall, it should be noted that if a human being cannot readily predict the probably types of a spin system from its shifts alone, then this search tool cannot be expected to do a good job; it is merely an optimiser to address the problem of shuffling spin systems within a chain. The scores are currently unnormalised log-odds values and are not especially meaningful in the human sense, other than higher is better (closer to zero for negative values). This issue will be addressed in the future. Spin systems without a unique type prediction will not get a final score. """ def __init__(self, parent, *args, **kw): self.guiParent = parent self.chain = None self.waiting = False self.shiftList = None self.spinSystem = None self.preserveTypes = 0 self.progressBar = None self.scoresPopup = None self.threshold = -20.0 BasePopup.__init__(self, parent, title="Assignment : Spin System Typing", **kw) def body(self, guiFrame): guiFrame.grid_columnconfigure(3, weight=1) self.progressBar = TypingEnsemblePopup(self,total=100) self.progressBar.close() row = 0 label = Label(guiFrame, text=' Chain: ', grid=(row,0)) tipText = 'Selects which molecular chain the spin system residue types will be predicted for; determines which range of types are available' self.chainPulldown = PulldownList(guiFrame, self.changeChain, grid=(row,1), tipText=tipText) tipText = 'Selects which shift list will be used as the source of chemical shift information to make the residue type predictions' label = Label(guiFrame, text='Shift List: ', grid=(row,2)) self.shiftListPulldown = PulldownList(guiFrame, callback=self.setShiftList, grid=(row,3), tipText=tipText) utilButtons = UtilityButtonList(guiFrame, helpUrl=self.help_url) utilButtons.grid(row=row, column=4, sticky='w') row += 1 frame = LabelFrame(guiFrame, text='Options', grid=(row,0), gridSpan=(1,5)) frame.grid_columnconfigure(3, weight=1) frow = 0 label = Label(frame, text='Keep existing types?', grid=(frow,0), sticky='e') tipText = 'Whether any existing residue type information should be preserved, when predicting the type of others' self.preserveTypesSelect = CheckButton(frame, grid=(frow,1), selected=False, callback=self.selectPreserveTypes, tipText=tipText) label = Label(frame, text='Assignment threshold: ', grid=(frow,2), sticky='e') tipText = 'The lower limit for the predicted residue type to be set with "Assign Types"; needs to be adjusted according to result statistics and amount of shift data' self.thresholdEntry = FloatEntry(frame, text=self.threshold, width=8, grid=(frow,3), tipText=tipText) frow += 1 label = Label(frame, text='Ensemble size: ', grid=(frow,0), sticky='e') tipText = 'The number of best scoring residue type mappings, from the Monte Carlo search, to use un the prediction' self.ensembleEntry = IntEntry(frame,text=20,width=4, grid=(frow,1), tipText=tipText) label = Label(frame, text='Num Search Steps: ', grid=(frow,2), sticky='e') tipText = 'The number of iterative steps that will be used in the Monte Carlo search of best spin system to residue type mappings' self.stepsEntry = IntEntry(frame, text=100000, width=8, tipText=tipText, grid=(frow,3)) frow += 1 label = Label(frame, text='Isotope shifts to consider:', grid=(frow,0), gridSpan=(1,4)) frow += 1 self.isotopes = ['1H','13C'] isos = ['1H','13C','15N'] colors = [COLOR_DICT[x] for x in isos] tipText = 'Selects which kinds of resonances, in terms of isotope, the residue type predictions will be made with' self.isotopeCheckButtons = PartitionedSelector(frame, labels=isos, objects=isos, colors=colors, callback=self.toggleIsotope, selected=self.isotopes, grid=(frow,0), gridSpan=(1,4), tipText=tipText) row += 1 guiFrame.grid_rowconfigure(row, weight=1) labelFrame = LabelFrame(guiFrame, text='Spin Systems', grid=(row,0), gridSpan=(1,5)) labelFrame.expandGrid(0,0) tipTexts = ['The spin system serial number', 'The residue to which the spin system may currently be assigned', 'Set whether to include a particular spin system in the type predictions', 'The spin system to residue type match score for a prediction; higher (less negative) is better', 'The predicted types of residue that the spin system may be', 'The chemical shifts in the spin system that will be used in the analysis'] headingList = ['#','Residue','Use?','Score','Types','Shifts'] justifyList = ['center','center','center','center','center','left'] editWidgets = [None, None, None, None, None, None] editGetCallbacks = [None, None, self.toggleInclude, None, None, None] editSetCallbacks = [None, None, None, None, None, None] self.scrolledMatrix = ScrolledMatrix(labelFrame, headingList=headingList, justifyList=justifyList, editSetCallbacks=editSetCallbacks, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, callback=self.selectCell, grid=(0,0), tipTexts=tipTexts) row += 1 tipTexts = ['Execute the Monte Carlo search that will make the residue type predictions for the spin systems', 'Assign the residue type of spin systems with a unique type prediction and prediction score above the stated threshold', 'Show a residue type prediction for the selected spin system alone; only considers that spin system of shifts, not how all spin systems fit to the sequence', 'Show a table of peaks that are assigned to the resonances of the selected spin system'] texts = ['Run\nTyping','Assign\nTypes', 'Show Individual\nClassification', 'Show\nPeaks'] commands = [self.run, self.assign, self.individualScore, self.showPeaks] bottomButtons = ButtonList(guiFrame, texts=texts, commands=commands, grid=(row,0), gridSpan=(1,5), tipTexts=tipTexts) self.runButton = bottomButtons.buttons[0] self.assignButton = bottomButtons.buttons[1] self.scoreButton = bottomButtons.buttons[2] self.peaksButton = bottomButtons.buttons[2] self.runButton.config(bg='#B0FFB0') for func in ('__init__','delete'): self.registerNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func) self.registerNotify(self.updateShiftLists, 'ccp.nmr.Nmr.ShiftList', func) for func in ('__init__','delete','setCcpCode', 'setResidue','addResonance', 'setName', 'removeResonance','setResonances'): self.registerNotify(self.updateSpinSystemsAfter, 'ccp.nmr.Nmr.ResonanceGroup', func) self.updateChains() self.updateShiftLists() self.updateSpinSystems() def individualScore(self): if self.scoresPopup: self.scoresPopup.open() self.scoresPopup.update(self.spinSystem, self.chain) else: self.scoresPopup = SpinSystemTypeScoresPopup(self.guiParent, spinSystem=self.spinSystem, chain=self.chain) def showPeaks(self): if self.spinSystem: peaks = [] for resonance in self.spinSystem.resonances: for contrib in resonance.peakDimContribs: peaks.append(contrib.peakDim.peak) if len(peaks) > 0: self.guiParent.viewPeaks(peaks) def assign(self): for spinSystem in self.scrolledMatrix.objectList: if spinSystem.sstSelected == 'Yes': if (len(spinSystem.sstTypes) == 1) and (spinSystem.ssScore > self.threshold): ccpCode = spinSystem.sstTypes[0] if spinSystem.residue and (spinSystem.residue.ccpCode != ccpCode): assignSpinSystemResidue(spinSystem,residue=None) if spinSystem.ccpCode != ccpCode: assignSpinSystemType(spinSystem,ccpCode,'protein') self.updateSpinSystems() def toggleIsotope(self, isotope): if isotope in self.isotopes: self.isotopes.remove(isotope) else: self.isotopes.append(isotope) self.updateSpinSystemsAfter() def selectPreserveTypes(self, boolean): self.preserveTypes = boolean def toggleInclude(self, *obj): if self.spinSystem: if self.spinSystem.sstSelected == 'Yes': self.spinSystem.sstSelected = 'No' else: self.spinSystem.sstSelected = 'Yes' self.updateSpinSystemsAfter() def selectCell(self, spinSystem, row, col): self.spinSystem = spinSystem self.updateButtons() def updateShiftLists(self, *opt): shiftLists = getShiftLists(self.nmrProject) names = ['Shift List %d' % x.serial for x in shiftLists] index = 0 if shiftLists: if self.shiftList not in shiftLists: self.shiftList = shiftLists[0] index = shiftLists.index(self.shiftList) self.shiftListPulldown.setup(names, shiftLists, index) def setShiftList(self, shiftList): self.shiftList = shiftList self.updateSpinSystemsAfter() def updateButtons(self): if self.chain and self.scrolledMatrix.objectList: self.runButton.enable() self.assignButton.enable() else: self.runButton.enable() self.assignButton.enable() if self.spinSystem: self.scoreButton.enable() self.peaksButton.enable() else: self.scoreButton.disable() self.peaksButton.disable() def updateSpinSystemsAfter(self, spinSystem=None): if spinSystem: spinSystem.sstTypes = [] spinSystem.ssScore = None spinSystem.codeScoreDict = {} if self.waiting: return else: self.waiting = True self.after_idle(self.updateSpinSystems) def updateSpinSystems(self): textMatrix = [] objectList = [] if self.project: for spinSystem in self.nmrProject.resonanceGroups: if not spinSystem.resonances: continue if self.chain: if spinSystem.residue and (spinSystem.residue.chain is not self.chain): continue if spinSystem.chains and (self.chain not in spinSystem.chains): continue if hasattr(spinSystem, 'sstSelected'): includeText = spinSystem.sstSelected else: spinSystem.sstSelected = 'Yes' includeText = 'Yes' if not hasattr(spinSystem, 'sstTypes'): spinSystem.sstTypes = [] if not hasattr(spinSystem, 'ssScore'): spinSystem.ssScore = None if spinSystem.ssScore: scoreText = '%.2f' % spinSystem.ssScore else: scoreText = None typesText = ' '.join(spinSystem.sstTypes) residueText = '' if spinSystem.residue: resCode = getResidueCode(spinSystem.residue) residueText = '%d%s' % (spinSystem.residue.seqCode,resCode) elif spinSystem.residueProbs: resTexts = [] resSeqs = [] resCodes = set() for residueProb in spinSystem.residueProbs: if not residueProb.weight: continue residue = residueProb.possibility seq = residue.seqCode resCode = getResidueCode(residue) resText = '%d?%s' % (seq, resCode) resTexts.append(resText) resSeqs.append('%d?' % seq) resCodes.add(resCode) if len(resCodes) == 1: residueText = '/'.join(resSeqs) + resCodes.pop() else: residueText = '/'.join(resTexts) elif spinSystem.ccpCode: getResidueCode(spinSystem) shifts = [] if self.shiftList: for resonance in spinSystem.resonances: if resonance.isotopeCode in self.isotopes: shift = resonance.findFirstShift(parentList = self.shiftList) if shift: shifts.append('%.2f' % shift.value) shifts.sort() shiftsText = ' '.join(shifts) data = [] data.append(spinSystem.serial) data.append(residueText) data.append(includeText) data.append(scoreText) data.append(typesText) data.append(shiftsText) objectList.append(spinSystem) textMatrix.append(data) self.scrolledMatrix.update(textMatrix=textMatrix, objectList=objectList) self.updateButtons() self.waiting = False def getChains(self): chains = [] if self.project: for molSystem in self.project.sortedMolSystems(): for chain in molSystem.sortedChains(): if chain.molecule.molType in ('protein',None): # None moltype may be mixed, including protein component text = '%s:%s' % (molSystem.code, chain.code) chains.append( [text, chain] ) return chains def changeChain(self, chain): self.chain = chain self.updateSpinSystemsAfter() def updateChains(self, *chain): data = self.getChains() names = [x[0] for x in data] chains = [x[1] for x in data] index = 0 if chains: if self.chain not in chains: if self.spinSystem: if self.spinSystem.residue: self.chain = self.spinSystem.residue.chain else: self.chain = chains[0] index = chains.index(self.chain) self.chainPulldown.setup(names, chains, index) self.updateButtons() def run(self): spinSystems = [] for spinSystem in self.scrolledMatrix.objectList: if spinSystem.sstSelected == 'Yes': spinSystems.append(spinSystem) if self.chain and spinSystems: if self.progressBar: self.progressBar.destroy() self.progressBar = TypingEnsemblePopup(self,total=100) residues = self.chain.sortedResidues() numBest = self.ensembleEntry.get() or 20 numSteps = max(100, self.stepsEntry.get() or 100000) graph = self.progressBar.graph typeScores, cc0 = getSpinSystemTypes(residues, spinSystems, self.preserveTypes, isotopes=self.isotopes, shiftList=self.shiftList, numSteps=numSteps, numBest=numBest, graph=graph, progressBar=self.progressBar) threshold = self.thresholdEntry.get() for ss in typeScores.keys(): ss.sstTypes = [] ss.ssScore = None for ccpCode in typeScores[ss].keys(): if ccpCode and typeScores[ss][ccpCode] > threshold: if ccpCode not in ss.sstTypes: ss.sstTypes.append(ccpCode) if len(ss.sstTypes) == 1: ss.ssScore = typeScores[ss][ss.sstTypes[0]] self.updateSpinSystemsAfter() def destroy(self): for func in ('__init__','delete'): self.unregisterNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func) self.unregisterNotify(self.updateShiftLists, 'ccp.nmr.Nmr.ShiftList', func) for func in ('__init__','delete','setCcpCode', 'setResidue','setName','addResonance', 'removeResonance','setResonances'): self.unregisterNotify(self.updateSpinSystemsAfter, 'ccp.nmr.Nmr.ResonanceGroup', func) if self.scoresPopup: self.scoresPopup.destroy() BasePopup.destroy(self)
def body(self, guiFrame): guiFrame.grid_columnconfigure(3, weight=1) self.progressBar = TypingEnsemblePopup(self,total=100) self.progressBar.close() row = 0 label = Label(guiFrame, text=' Chain: ', grid=(row,0)) tipText = 'Selects which molecular chain the spin system residue types will be predicted for; determines which range of types are available' self.chainPulldown = PulldownList(guiFrame, self.changeChain, grid=(row,1), tipText=tipText) tipText = 'Selects which shift list will be used as the source of chemical shift information to make the residue type predictions' label = Label(guiFrame, text='Shift List: ', grid=(row,2)) self.shiftListPulldown = PulldownList(guiFrame, callback=self.setShiftList, grid=(row,3), tipText=tipText) utilButtons = UtilityButtonList(guiFrame, helpUrl=self.help_url) utilButtons.grid(row=row, column=4, sticky='w') row += 1 frame = LabelFrame(guiFrame, text='Options', grid=(row,0), gridSpan=(1,5)) frame.grid_columnconfigure(3, weight=1) frow = 0 label = Label(frame, text='Keep existing types?', grid=(frow,0), sticky='e') tipText = 'Whether any existing residue type information should be preserved, when predicting the type of others' self.preserveTypesSelect = CheckButton(frame, grid=(frow,1), selected=False, callback=self.selectPreserveTypes, tipText=tipText) label = Label(frame, text='Assignment threshold: ', grid=(frow,2), sticky='e') tipText = 'The lower limit for the predicted residue type to be set with "Assign Types"; needs to be adjusted according to result statistics and amount of shift data' self.thresholdEntry = FloatEntry(frame, text=self.threshold, width=8, grid=(frow,3), tipText=tipText) frow += 1 label = Label(frame, text='Ensemble size: ', grid=(frow,0), sticky='e') tipText = 'The number of best scoring residue type mappings, from the Monte Carlo search, to use un the prediction' self.ensembleEntry = IntEntry(frame,text=20,width=4, grid=(frow,1), tipText=tipText) label = Label(frame, text='Num Search Steps: ', grid=(frow,2), sticky='e') tipText = 'The number of iterative steps that will be used in the Monte Carlo search of best spin system to residue type mappings' self.stepsEntry = IntEntry(frame, text=100000, width=8, tipText=tipText, grid=(frow,3)) frow += 1 label = Label(frame, text='Isotope shifts to consider:', grid=(frow,0), gridSpan=(1,4)) frow += 1 self.isotopes = ['1H','13C'] isos = ['1H','13C','15N'] colors = [COLOR_DICT[x] for x in isos] tipText = 'Selects which kinds of resonances, in terms of isotope, the residue type predictions will be made with' self.isotopeCheckButtons = PartitionedSelector(frame, labels=isos, objects=isos, colors=colors, callback=self.toggleIsotope, selected=self.isotopes, grid=(frow,0), gridSpan=(1,4), tipText=tipText) row += 1 guiFrame.grid_rowconfigure(row, weight=1) labelFrame = LabelFrame(guiFrame, text='Spin Systems', grid=(row,0), gridSpan=(1,5)) labelFrame.expandGrid(0,0) tipTexts = ['The spin system serial number', 'The residue to which the spin system may currently be assigned', 'Set whether to include a particular spin system in the type predictions', 'The spin system to residue type match score for a prediction; higher (less negative) is better', 'The predicted types of residue that the spin system may be', 'The chemical shifts in the spin system that will be used in the analysis'] headingList = ['#','Residue','Use?','Score','Types','Shifts'] justifyList = ['center','center','center','center','center','left'] editWidgets = [None, None, None, None, None, None] editGetCallbacks = [None, None, self.toggleInclude, None, None, None] editSetCallbacks = [None, None, None, None, None, None] self.scrolledMatrix = ScrolledMatrix(labelFrame, headingList=headingList, justifyList=justifyList, editSetCallbacks=editSetCallbacks, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, callback=self.selectCell, grid=(0,0), tipTexts=tipTexts) row += 1 tipTexts = ['Execute the Monte Carlo search that will make the residue type predictions for the spin systems', 'Assign the residue type of spin systems with a unique type prediction and prediction score above the stated threshold', 'Show a residue type prediction for the selected spin system alone; only considers that spin system of shifts, not how all spin systems fit to the sequence', 'Show a table of peaks that are assigned to the resonances of the selected spin system'] texts = ['Run\nTyping','Assign\nTypes', 'Show Individual\nClassification', 'Show\nPeaks'] commands = [self.run, self.assign, self.individualScore, self.showPeaks] bottomButtons = ButtonList(guiFrame, texts=texts, commands=commands, grid=(row,0), gridSpan=(1,5), tipTexts=tipTexts) self.runButton = bottomButtons.buttons[0] self.assignButton = bottomButtons.buttons[1] self.scoreButton = bottomButtons.buttons[2] self.peaksButton = bottomButtons.buttons[2] self.runButton.config(bg='#B0FFB0') for func in ('__init__','delete'): self.registerNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func) self.registerNotify(self.updateShiftLists, 'ccp.nmr.Nmr.ShiftList', func) for func in ('__init__','delete','setCcpCode', 'setResidue','addResonance', 'setName', 'removeResonance','setResonances'): self.registerNotify(self.updateSpinSystemsAfter, 'ccp.nmr.Nmr.ResonanceGroup', func) self.updateChains() self.updateShiftLists() self.updateSpinSystems()
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) guiFrame.grid_columnconfigure(0, weight=1) guiFrame.grid_rowconfigure(1, weight=1) row = 0 labelFrame0 = LabelFrame(guiFrame, text='Input data') labelFrame0.grid(row=row, column=0, sticky=Tkinter.NSEW) labelFrame0.grid_columnconfigure(3, weight=1) label = Label(labelFrame0, text='Assigned NOESY spectrum') label.grid(row=0, column=0, sticky=Tkinter.NW) self.noesyPulldown = PulldownMenu(labelFrame0, entries=self.getNoesys(), callback=self.setNoesy, selected_index=0, do_initial_callback=0) self.noesyPulldown.grid(row=0, column=1, sticky=Tkinter.NW) label = Label(labelFrame0, text='H/D ratio: ') label.grid(row=0, column=2, sticky=Tkinter.NW) self.ratioHDEntry = FloatEntry(labelFrame0, text=self.ratioHD, width=6) self.ratioHDEntry.grid(row=0, column=3, sticky=Tkinter.NW) label = Label(labelFrame0, text='NOESY spectrum 1:') label.grid(row=1, column=0, sticky=Tkinter.NW) self.tmix1Pulldown = PulldownMenu(labelFrame0, entries=self.getNoesys(), callback=self.setNoesy1, selected_index=-0, do_initial_callback=0) self.tmix1Pulldown.grid(row=1, column=1, sticky=Tkinter.NW) label = Label(labelFrame0, text='Tmix (ms): ') label.grid(row=1, column=2, sticky=Tkinter.NW) self.tmix1Entry = FloatEntry(labelFrame0, text=60, width=6) self.tmix1Entry.grid(row=1, column=3, sticky=Tkinter.NW) label = Label(labelFrame0, text='NOESY spectrum 2:') label.grid(row=2, column=0, sticky=Tkinter.NW) self.tmix2Pulldown = PulldownMenu(labelFrame0, entries=self.getNoesys(), callback=self.setNoesy2, selected_index=0, do_initial_callback=0) self.tmix2Pulldown.grid(row=2, column=1, sticky=Tkinter.NW) label = Label(labelFrame0, text='Tmix (ms): ') label.grid(row=2, column=2, sticky=Tkinter.NW) self.tmix2Entry = FloatEntry(labelFrame0, text=120, width=6) self.tmix2Entry.grid(row=2, column=3, sticky=Tkinter.NW) label = Label(labelFrame0, text='NOESY spectrum 3:') label.grid(row=3, column=0, sticky=Tkinter.NW) self.tmix3Pulldown = PulldownMenu(labelFrame0, entries=self.getNoesys(), callback=self.setNoesy3, selected_index=0, do_initial_callback=0) self.tmix3Pulldown.grid(row=3, column=1, sticky=Tkinter.NW) label = Label(labelFrame0, text='Tmix (ms): ') label.grid(row=3, column=2, sticky=Tkinter.NW) self.tmix3Entry = FloatEntry(labelFrame0, text=200, width=6) self.tmix3Entry.grid(row=3, column=3, sticky=Tkinter.NW) label = Label(labelFrame0, text='3D NOESY:') label.grid(row=4, column=0, sticky=Tkinter.NW) self.noesy3dPulldown = PulldownMenu(labelFrame0, entries=self.getNoesys3d(), callback=self.setNoesy3d, selected_index=0, do_initial_callback=0) self.noesy3dPulldown.grid(row=4, column=1, sticky=Tkinter.NW) label10 = Label(labelFrame0, text='Num peaks:') label10.grid(row=5, column=0, sticky=Tkinter.NW) self.numPeaksLabel = Label(labelFrame0, text='0') self.numPeaksLabel.grid(row=5, column=1, sticky=Tkinter.NW) label11 = Label(labelFrame0, text='Num resonances:') label11.grid(row=5, column=2, sticky=Tkinter.NW) self.numResonancesLabel = Label(labelFrame0, text='0') self.numResonancesLabel.grid(row=5, column=3, sticky=Tkinter.NW) row += 1 labelFrame1 = LabelFrame(guiFrame, text='Parameters') labelFrame1.grid(row=row, column=0, sticky=Tkinter.NSEW) labelFrame1.grid_columnconfigure(3, weight=1) label = Label(labelFrame1, text='15N labelled sample:') label.grid(row=0, column=0, sticky=Tkinter.NW) self.nitrogenSelect = CheckButton(labelFrame1, callback=self.setNitrogenLabel) self.nitrogenSelect.grid(row=0, column=1, sticky=Tkinter.W) self.nitrogenSelect.set(1) label = Label(labelFrame1, text='13C labelled sample:') label.grid(row=0, column=2, sticky=Tkinter.NW) self.carbonSelect = CheckButton(labelFrame1, callback=self.setCarbonLabel) self.carbonSelect.grid(row=0, column=3, sticky=Tkinter.W) self.carbonSelect.set(0) labelFrame1.grid_rowconfigure(1, weight=1) data = [ self.specFreq, self.maxIter, self.mixTime, self.corrTime, self.leakRate ] colHeadings = [ 'Spectrometer\nfrequency', 'Max\niterations', 'Mixing\ntime (ms)', 'Correl.\ntime (ns)', 'Leak\nrate' ] editWidgets = [ self.specFreqEntry, self.maxIterEntry, self.mixTimeEntry, self.corrTimeEntry, self.leakRateEntry, ] editGetCallbacks = [ self.getSpecFreq, self.getMaxIter, self.getMixTime, self.getCorrTime, self.getLeakRate, ] editSetCallbacks = [ self.setSpecFreq, self.setMaxIter, self.setMixTime, self.setCorrTime, self.setLeakRate, ] self.midgeParamsMatrix = ScrolledMatrix( labelFrame1, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, maxRows=1, initialCols=5, headingList=colHeadings, callback=None, objectList=[ 'None', ], textMatrix=[ data, ]) self.midgeParamsMatrix.grid(row=1, column=0, columnspan=4, sticky=Tkinter.NSEW) label10 = Label(labelFrame1, text='Benchmark structure') label10.grid(row=2, column=0, sticky=Tkinter.NW) self.structurePulldown = PulldownMenu(labelFrame1, entries=self.getStructures(), callback=self.setStructure, selected_index=0, do_initial_callback=0) self.structurePulldown.grid(row=2, column=1, sticky=Tkinter.NW) label11 = Label(labelFrame1, text='ADC atom types:') label11.grid(row=2, column=2, sticky=Tkinter.NW) self.adcAtomsPulldown = PulldownMenu(labelFrame1, entries=self.getAdcAtomTypes(), callback=self.setAdcAtomTypes, selected_index=0, do_initial_callback=0) self.adcAtomsPulldown.grid(row=2, column=3, sticky=Tkinter.NW) row += 1 labelFrame2 = LabelFrame(guiFrame, text='Output') labelFrame2.grid(row=row, column=0, sticky=Tkinter.NSEW) labelFrame2.grid_columnconfigure(3, weight=1) label20 = Label(labelFrame2, text='Distance constraints:') label20.grid(row=0, column=0, sticky=Tkinter.NW) self.distConstrLabel = Label(labelFrame2, text='0') self.distConstrLabel.grid(row=0, column=1, sticky=Tkinter.NW) label21 = Label(labelFrame2, text='Anti-distance constraints:') label21.grid(row=0, column=2, sticky=Tkinter.NW) self.antiConstrLabel = Label(labelFrame2, text='0') self.antiConstrLabel.grid(row=0, column=3, sticky=Tkinter.NW) texts = [ 'Calculate distances', 'Show distance\nconstraints', 'Show anti-distance\nconstraints' ] commands = [ self.calculateDistances, self.showConstraints, self.showAntiConstraints ] self.midgeButtons = ButtonList(labelFrame2, expands=1, texts=texts, commands=commands) self.midgeButtons.grid(row=1, 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, columnspan=4, sticky=Tkinter.EW) self.getPeaks() self.getResonances() self.update() self.geometry('600x400')
class MidgePopup(BasePopup): def __init__(self, parent, *args, **kw): self.guiParent = parent self.project = parent.getProject() self.waiting = 0 self.specFreq = 800.13 self.maxIter = 15 self.mixTime = 60 self.corrTime = 11.5 self.leakRate = 2.0 self.ratioHD = 0.9 self.peakListDict = {} self.peakListDict3d = {} self.noesyPeakList = None self.noesy3dPeakList = None self.carbonLabel = 0 self.nitrogenLabel = 1 self.noesyPeakList1 = None self.noesyPeakList2 = None self.noesyPeakList3 = None self.noesyPeakList3d = None self.resonances = None self.noesyPeaks = None self.distanceConstraintList = None self.antiDistConstraintList = None self.adcAtomTypes = None self.structure = None BasePopup.__init__(self, parent, title="Relaxation Matrix Optimisation", **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) guiFrame.grid_columnconfigure(0, weight=1) guiFrame.grid_rowconfigure(1, weight=1) row = 0 labelFrame0 = LabelFrame(guiFrame, text='Input data') labelFrame0.grid(row=row, column=0, sticky=Tkinter.NSEW) labelFrame0.grid_columnconfigure(3, weight=1) label = Label(labelFrame0, text='Assigned NOESY spectrum') label.grid(row=0, column=0, sticky=Tkinter.NW) self.noesyPulldown = PulldownMenu(labelFrame0, entries=self.getNoesys(), callback=self.setNoesy, selected_index=0, do_initial_callback=0) self.noesyPulldown.grid(row=0, column=1, sticky=Tkinter.NW) label = Label(labelFrame0, text='H/D ratio: ') label.grid(row=0, column=2, sticky=Tkinter.NW) self.ratioHDEntry = FloatEntry(labelFrame0, text=self.ratioHD, width=6) self.ratioHDEntry.grid(row=0, column=3, sticky=Tkinter.NW) label = Label(labelFrame0, text='NOESY spectrum 1:') label.grid(row=1, column=0, sticky=Tkinter.NW) self.tmix1Pulldown = PulldownMenu(labelFrame0, entries=self.getNoesys(), callback=self.setNoesy1, selected_index=-0, do_initial_callback=0) self.tmix1Pulldown.grid(row=1, column=1, sticky=Tkinter.NW) label = Label(labelFrame0, text='Tmix (ms): ') label.grid(row=1, column=2, sticky=Tkinter.NW) self.tmix1Entry = FloatEntry(labelFrame0, text=60, width=6) self.tmix1Entry.grid(row=1, column=3, sticky=Tkinter.NW) label = Label(labelFrame0, text='NOESY spectrum 2:') label.grid(row=2, column=0, sticky=Tkinter.NW) self.tmix2Pulldown = PulldownMenu(labelFrame0, entries=self.getNoesys(), callback=self.setNoesy2, selected_index=0, do_initial_callback=0) self.tmix2Pulldown.grid(row=2, column=1, sticky=Tkinter.NW) label = Label(labelFrame0, text='Tmix (ms): ') label.grid(row=2, column=2, sticky=Tkinter.NW) self.tmix2Entry = FloatEntry(labelFrame0, text=120, width=6) self.tmix2Entry.grid(row=2, column=3, sticky=Tkinter.NW) label = Label(labelFrame0, text='NOESY spectrum 3:') label.grid(row=3, column=0, sticky=Tkinter.NW) self.tmix3Pulldown = PulldownMenu(labelFrame0, entries=self.getNoesys(), callback=self.setNoesy3, selected_index=0, do_initial_callback=0) self.tmix3Pulldown.grid(row=3, column=1, sticky=Tkinter.NW) label = Label(labelFrame0, text='Tmix (ms): ') label.grid(row=3, column=2, sticky=Tkinter.NW) self.tmix3Entry = FloatEntry(labelFrame0, text=200, width=6) self.tmix3Entry.grid(row=3, column=3, sticky=Tkinter.NW) label = Label(labelFrame0, text='3D NOESY:') label.grid(row=4, column=0, sticky=Tkinter.NW) self.noesy3dPulldown = PulldownMenu(labelFrame0, entries=self.getNoesys3d(), callback=self.setNoesy3d, selected_index=0, do_initial_callback=0) self.noesy3dPulldown.grid(row=4, column=1, sticky=Tkinter.NW) label10 = Label(labelFrame0, text='Num peaks:') label10.grid(row=5, column=0, sticky=Tkinter.NW) self.numPeaksLabel = Label(labelFrame0, text='0') self.numPeaksLabel.grid(row=5, column=1, sticky=Tkinter.NW) label11 = Label(labelFrame0, text='Num resonances:') label11.grid(row=5, column=2, sticky=Tkinter.NW) self.numResonancesLabel = Label(labelFrame0, text='0') self.numResonancesLabel.grid(row=5, column=3, sticky=Tkinter.NW) row += 1 labelFrame1 = LabelFrame(guiFrame, text='Parameters') labelFrame1.grid(row=row, column=0, sticky=Tkinter.NSEW) labelFrame1.grid_columnconfigure(3, weight=1) label = Label(labelFrame1, text='15N labelled sample:') label.grid(row=0, column=0, sticky=Tkinter.NW) self.nitrogenSelect = CheckButton(labelFrame1, callback=self.setNitrogenLabel) self.nitrogenSelect.grid(row=0, column=1, sticky=Tkinter.W) self.nitrogenSelect.set(1) label = Label(labelFrame1, text='13C labelled sample:') label.grid(row=0, column=2, sticky=Tkinter.NW) self.carbonSelect = CheckButton(labelFrame1, callback=self.setCarbonLabel) self.carbonSelect.grid(row=0, column=3, sticky=Tkinter.W) self.carbonSelect.set(0) labelFrame1.grid_rowconfigure(1, weight=1) data = [ self.specFreq, self.maxIter, self.mixTime, self.corrTime, self.leakRate ] colHeadings = [ 'Spectrometer\nfrequency', 'Max\niterations', 'Mixing\ntime (ms)', 'Correl.\ntime (ns)', 'Leak\nrate' ] editWidgets = [ self.specFreqEntry, self.maxIterEntry, self.mixTimeEntry, self.corrTimeEntry, self.leakRateEntry, ] editGetCallbacks = [ self.getSpecFreq, self.getMaxIter, self.getMixTime, self.getCorrTime, self.getLeakRate, ] editSetCallbacks = [ self.setSpecFreq, self.setMaxIter, self.setMixTime, self.setCorrTime, self.setLeakRate, ] self.midgeParamsMatrix = ScrolledMatrix( labelFrame1, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, maxRows=1, initialCols=5, headingList=colHeadings, callback=None, objectList=[ 'None', ], textMatrix=[ data, ]) self.midgeParamsMatrix.grid(row=1, column=0, columnspan=4, sticky=Tkinter.NSEW) label10 = Label(labelFrame1, text='Benchmark structure') label10.grid(row=2, column=0, sticky=Tkinter.NW) self.structurePulldown = PulldownMenu(labelFrame1, entries=self.getStructures(), callback=self.setStructure, selected_index=0, do_initial_callback=0) self.structurePulldown.grid(row=2, column=1, sticky=Tkinter.NW) label11 = Label(labelFrame1, text='ADC atom types:') label11.grid(row=2, column=2, sticky=Tkinter.NW) self.adcAtomsPulldown = PulldownMenu(labelFrame1, entries=self.getAdcAtomTypes(), callback=self.setAdcAtomTypes, selected_index=0, do_initial_callback=0) self.adcAtomsPulldown.grid(row=2, column=3, sticky=Tkinter.NW) row += 1 labelFrame2 = LabelFrame(guiFrame, text='Output') labelFrame2.grid(row=row, column=0, sticky=Tkinter.NSEW) labelFrame2.grid_columnconfigure(3, weight=1) label20 = Label(labelFrame2, text='Distance constraints:') label20.grid(row=0, column=0, sticky=Tkinter.NW) self.distConstrLabel = Label(labelFrame2, text='0') self.distConstrLabel.grid(row=0, column=1, sticky=Tkinter.NW) label21 = Label(labelFrame2, text='Anti-distance constraints:') label21.grid(row=0, column=2, sticky=Tkinter.NW) self.antiConstrLabel = Label(labelFrame2, text='0') self.antiConstrLabel.grid(row=0, column=3, sticky=Tkinter.NW) texts = [ 'Calculate distances', 'Show distance\nconstraints', 'Show anti-distance\nconstraints' ] commands = [ self.calculateDistances, self.showConstraints, self.showAntiConstraints ] self.midgeButtons = ButtonList(labelFrame2, expands=1, texts=texts, commands=commands) self.midgeButtons.grid(row=1, 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, columnspan=4, sticky=Tkinter.EW) self.getPeaks() self.getResonances() self.update() self.geometry('600x400') def setCarbonLabel(self, boolean): self.carbonLabel = boolean def setNitrogenLabel(self, boolean): self.nitrogenLabel = boolean def update(self): if self.resonances and ( (self.noesyPeaks and self.noesyPeakList1 and self.noesyPeakList2 and self.noesyPeakList3) or self.noesyPeakList3d): self.midgeButtons.buttons[0].enable() else: self.midgeButtons.buttons[0].disable() if self.distanceConstraintList: self.distConstrLabel.set( str(len(self.distanceConstraintList.constraints))) self.midgeButtons.buttons[1].enable() else: self.distConstrLabel.set('') self.midgeButtons.buttons[1].disable() if self.antiDistConstraintList: self.antiConstrLabel.set( str(len(self.antiDistConstraintList.constraints))) self.midgeButtons.buttons[2].enable() else: self.antiConstrLabel.set('') self.midgeButtons.buttons[2].disable() if self.resonances: self.numResonancesLabel.set(str(len(self.resonances))) else: self.numResonancesLabel.set('') if self.noesyPeaks: self.numPeaksLabel.set(str(len(self.noesyPeaks))) else: self.numPeaksLabel.set('') 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 ['<None>', 'HN', 'HN HA', 'HN HA HB'] def setAdcAtomTypes(self, index, name=None): if name is None: name = self.adcAtomsPulldown.getSelected() if name == '<None>': name = None self.adcAtomTypes = name def getResonances(self): resonanceDict = {} if self.noesyPeaks: for peak in self.noesyPeaks: for peakDim in peak.peakDims: for contrib in peakDim.peakDimContribs: resonanceDict[contrib.resonance] = 1 # TBD: Set resonance.name for typing self.resonances = resonanceDict.keys() def getPeaks(self): if self.noesyPeakList: self.noesyPeaks = self.noesyPeakList.sortedPeaks() def calculateDistances(self): resonances = list(self.resonances) resDict = {} for resonance in resonances: resDict[resonance.serial] = resonance ratioHD = self.ratioHDEntry.get() or self.ratioHD tmix1 = self.tmix1Entry.get() or 60 tmix2 = self.tmix2Entry.get() or 120 tmix3 = self.tmix3Entry.get() or 200 data = [(tmix1, self.noesyPeakList1), (tmix2, self.noesyPeakList2), (tmix3, self.noesyPeakList3)] data.sort() mixingTimes = [x[0] for x in data] peakLists = [x[1] for x in data] # get a clean, symmetric and normalised NOE matrix noeMatrix = getNoeMatrixFromPeaks(self.noesyPeaks, resonances, peakLists, mixingTimes, ratioHD=ratioHD, analysis=self.guiParent) # optimiseRelaxation will remove unconstrained resonances self.distanceConstraintList, resonances = optimiseRelaxation( resonances, noeMatrix, self.mixTime, self.specFreq, self.corrTime, self.leakRate, self.carbonLabel, self.nitrogenLabel, maxIter=self.maxIter) #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 and self.noesyPeakList: constraintHead = self.distanceConstraintList.nmrConstraintStore if self.adcAtomTypes: adcDict = { 'HN': ['H'], 'HN HA': ['H', 'HA', 'HA1', 'HA2'], 'HN HA HB': ['H', 'HA', 'HA1', 'HA2', 'HB', 'HB2', 'HB3'] } allowedAtomTypes = adcDict[self.adcAtomTypes] print "Making ADCs" self.antiDistConstraintList = makeNoeAdcs( resonances[:], self.noesyPeakList.dataSource, constraintHead, allowedAtomTypes=allowedAtomTypes) print "Done ADCs" 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: item = constraint.findFirstItem() resonances = list(item.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.setOrigData(distance) self.update() 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 getNoesys3d(self): peakLists = getThroughSpacePeakLists(self.project) names = [ '<None>', ] for peakList in peakLists: spectrum = peakList.dataSource if spectrum.numDim != 3: continue name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name, peakList.serial) names.append(name) self.peakListDict3d[name] = peakList if not self.noesyPeakList: self.noesyPeakList = peakList return names def getNoesys(self): peakLists = getThroughSpacePeakLists(self.project) names = [ '<None>', ] for peakList in peakLists: spectrum = peakList.dataSource 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() if name == '<None>': self.noesyPeakList = None else: self.noesyPeakList = self.peakListDict[name] self.getPeaks() self.getResonances() self.update() def setNoesy1(self, index, name=None): if not name: name = self.tmix1Pulldown.getSelected() if name != '<None>': self.noesyPeakList1 = self.peakListDict[name] else: self.noesyPeakList1 = None self.update() def setNoesy2(self, index, name=None): if not name: name = self.tmix2Pulldown.getSelected() if name != '<None>': self.noesyPeakList2 = self.peakListDict[name] else: self.noesyPeakList2 = None self.update() def setNoesy3(self, index, name=None): if not name: name = self.tmix3Pulldown.getSelected() if name != '<None>': self.noesyPeakList3 = self.peakListDict[name] else: self.noesyPeakList3 = None self.update() def setNoesy3d(self, index, name=None): if not name: name = self.noesy3dPulldown.getSelected() if name != '<None>': self.noesyPeakList3d = self.peakListDict3d[name] self.noesyPeaks = self.noesyPeakList3d.sortedPeaks() else: self.noesyPeakList3d = None self.noesyPeaks = [] self.getResonances() self.update() def updateMidgeParams(self): data = [ self.specFreq, self.maxIter, self.mixTime, self.corrTime, self.leakRate ] 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 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 destroy(self): BasePopup.destroy(self)
class EditSymmetryPopup(BasePopup): def __init__(self, parent, project): self.parent = parent self.project = project self.singleMolecule = True self.molSystem = None self.molecules = [] self.symmetrySet = None self.symmetryOp = None self.waiting = False BasePopup.__init__(self, parent=parent, title='Symmetry Operations') def body(self, guiFrame): guiFrame.grid_columnconfigure(0, weight=1) guiFrame.grid_rowconfigure(1, weight=1) frame = LabelFrame(guiFrame, text='Options') frame.grid(row=0, column=0, sticky='ew') frame.grid_columnconfigure(5, weight=1) label = Label(frame, text='MolSystem:') label.grid(row=0, column=0, sticky='w') self.molSystemPulldown = PulldownMenu(frame, callback=self.selectMolSystem) self.molSystemPulldown.grid(row=0, column=1, sticky='w') self.molLabel = Label(frame, text='Molecule:') self.molLabel.grid(row=0, column=2, sticky='w') self.moleculePulldown = PulldownMenu(frame, callback=self.selectMolecule) self.moleculePulldown.grid(row=0, column=3, sticky='w') label = Label(frame, text='Same Molecule Symmetry:') label.grid(row=0, column=4, sticky='w') self.molSelect = CheckButton(frame, callback=self.toggleSingleMolecule) self.molSelect.grid(row=0, column=5, sticky='w') self.molSelect.set(self.singleMolecule) frame = LabelFrame(guiFrame, text='Symmetry Operations') frame.grid(row=1, column=0, sticky='nsew') frame.grid_columnconfigure(0, weight=1) frame.grid_rowconfigure(0, weight=1) self.symmCodePulldown = PulldownMenu(self, callback=self.setSymmCode, do_initial_callback=False) self.segLengthEntry = IntEntry(self, returnCallback=self.setSegLength, width=6) self.setChainMulti = MultiWidget(self, CheckButton, callback=self.setChains, minRows=0, useImages=False) self.setSegmentMulti = MultiWidget(self, IntEntry, callback=self.setSegments, minRows=0, useImages=False) editWidgets = [ None, self.symmCodePulldown, self.segLengthEntry, self.setChainMulti, self.setSegmentMulti ] editGetCallbacks = [ None, self.getSymmCode, self.getSegLength, self.getChains, self.getSegments ] editSetCallbacks = [ None, self.setSymmCode, self.setSegLength, self.setChains, self.setSegments ] headings = [ '#', 'Symmetry\nType', 'Segment\nLength', 'Chains', 'Segment\nPositions' ] self.symmetryMatrix = ScrolledMatrix(frame, headingList=headings, callback=self.selectSymmetry, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks) self.symmetryMatrix.grid(row=0, column=0, sticky='nsew') texts = ['Add Symmetry Op', 'Remove Symmetrey Op'] commands = [self.addSymmOp, self.removeSymmOp] buttonList = createDismissHelpButtonList(guiFrame, texts=texts, commands=commands, expands=True) buttonList.grid(row=2, column=0, sticky='ew') self.updateMolSystems() self.updateMolecules() self.updateSymmetriesAfter() self.notify(self.registerNotify) def open(self): self.updateMolSystems() self.updateMolecules() self.updateSymmetriesAfter() BasePopup.open(self) def notify(self, notifyFunc): for func in ('__init__', 'delete', 'setSymmetryCode', 'setSegmentLength'): notifyFunc(self.updateSymmetriesAfter, 'molsim.Symmetry.Symmetry', func) for func in ('__init__', 'delete', 'setfirstSeqId'): notifyFunc(self.updateSymmetriesAfter, 'molsim.Symmetry.Segment', func) def getSymmCode(self, symmetryOp): """Get allowed symmetry operators from the model""" symmetryOpCodes = symmetryOp.parent.metaclass.container.getElement( 'SymmetryOpCode').enumeration index = 0 if symmetryOp.symmetryCode in symmetryOpCodes: index = symmetryOpCodes.index(symmetryOp.symmetryCode) self.symmCodePulldown.setup(symmetryOpCodes, index) def getSegLength(self, symmetryOp): if symmetryOp and symmetryOp.segmentLength: self.segLengthEntry.set(symmetryOp.segmentLength) def getChains(self, symmetryOp): chains = [] for chain in self.molSystem.chains: if chain.residues: if chain.molecule in self.molecules: chains.append(chain.code) chains.sort() values = [] for chain in chains: if symmetryOp.findFirstSegment(chainCode=chain): values.append(True) else: values.append(False) self.setChainMulti.set(values=values, options=chains) def getSegments(self, symmetryOp): values = [] names = [] if symmetryOp: for segment in symmetryOp.sortedSegments(): names.append(segment.chainCode) values.append(segment.firstSeqId) n = len(values) self.setSegmentMulti.maxRows = n self.setSegmentMulti.minRows = n self.setSegmentMulti.set(values=values, options=names) def setSymmCode(self, index, name=None): """Set the symmetry code as NCS,C2,C3,C4,C5,C6""" if self.symmetryOp: symmCode = self.symmCodePulldown.getSelected() self.symmetryOp.symmetryCode = symmCode def setSegLength(self, event): value = self.segLengthEntry.get() or 1 self.symmetryOp.segmentLength = value def setChains(self, obj): if self.symmetryOp and obj: codes = self.setChainMulti.options segment = self.symmetryOp.findFirstSegment() values = self.setChainMulti.get() if segment: seqId0 = segment.firstSeqId else: seqId0 = 1 for i in range(len(values)): segment = self.symmetryOp.findFirstSegment(chainCode=codes[i]) if segment and not values[i]: segment.delete() elif values[i] and not segment: chain = self.molSystem.findFirstChain(code=codes[i]) residue = chain.findFirstResidue(seqid=seqId0) if residue: seqId = seqId0 else: residue = chain.sortedResidues()[0] seqId = residue.seqId residue2 = chain.findFirstResidue( seqid=seqId + self.symmetryOp.segmentLength) if not residue2: residue2 = chain.sortedResidues()[-1] self.symmetryOp.segmentLength = (residue2.seqId - seqId) + 1 segment = self.symmetryOp.newSegment(chainCode=codes[i], firstSeqId=seqId) self.symmetryMatrix.keyPressEscape() def setSegments(self, obj): if self.symmetryOp and obj: segments = self.symmetryOp.sortedSegments() values = self.setSegmentMulti.get() for i in range(len(values)): seqCode = values[i] chain = self.molSystem.findFirstChain( code=segments[i].chainCode) residue = chain.findFirstResidue(seqCode=seqCode) if residue: seqId = residue.seqId if segments[i].firstSeqId != seqId: segments[i].delete() segments[i] = self.symmetryOp.newSegment( chainCode=chain.code, firstSeqId=seqId) self.symmetryMatrix.keyPressEscape() def selectSymmetry(self, obj, row, col): self.symmetryOp = obj def addSymmOp(self): if self.molSystem: if not self.symmetrySet: self.symmetrySet = self.molSystem.findFirstMolSystemSymmetrySet( ) if not self.symmetrySet: objGen = self.project.newMolSystemSymmetrySet self.symmetrySet = objGen(symmetrySetId=1, molSystem=self.molSystem) segLen = len(self.molSystem.findFirstChain().residues) symmetry = self.symmetrySet.newSymmetry(segmentLength=segLen) def removeSymmOp(self): if self.symmetryOp: self.symmetryOp.delete() def toggleSingleMolecule(self, boolean): self.singleMolecule = not boolean self.updateMolSystems() self.updateMolecules() def setMolecules(self, molecules): self.molecules = molecules if self.symmetrySet: for symmetryOp in self.symmetrySet.symmetries: for segment in symmetryOp.segments: chain = self.molSystem.findFirstChain( code=segment.chainCode) if chain and (chain.molecule not in molecules): segment.delete() def selectMolecule(self, index, name): self.setMolecules(self.getMolecules()[index]) self.updateSymmetries() def getMolecules(self): counts = {} moleculesList = [] for chain in self.molSystem.chains: molecule = chain.molecule counts[molecule] = counts.get(molecule, 0) + 1 molecules = counts.keys() if self.singleMolecule: for molecule in counts: if counts[molecule] > 1: moleculesList.append([ molecule, ]) elif molecules: molecules = counts.keys() n = len(molecules) moleculesList.append([ molecules[0], ]) if n > 1: moleculesList.append([ molecules[1], ]) moleculesList.append([molecules[0], molecules[1]]) if n > 2: moleculesList.append([ molecules[2], ]) moleculesList.append([molecules[1], molecules[2]]) moleculesList.append( [molecules[0], molecules[1], molecules[2]]) if n > 3: moleculesList.append([ molecules[3], ]) moleculesList.append([molecules[0], molecules[3]]) moleculesList.append([molecules[1], molecules[3]]) moleculesList.append([molecules[2], molecules[3]]) moleculesList.append( [molecules[0], molecules[1], molecules[3]]) moleculesList.append( [molecules[0], molecules[2], molecules[3]]) moleculesList.append( [molecules[1], molecules[2], molecules[3]]) moleculesList.append( [molecules[0], molecules[1], molecules[2], molecules[3]]) return moleculesList def updateMolecules(self): names = [] index = -1 moleculesList = self.getMolecules() if moleculesList: if self.molecules not in moleculesList: self.setMolecules(moleculesList[0]) self.symmetrySet = self.molSystem.findFirstMolSystemSymmetrySet( ) index = moleculesList.index(self.molecules) names = [] for molecules in moleculesList: names.append(','.join([mol.name for mol in molecules])) else: self.molecules = [] self.moleculePulldown.setup(names, index) def selectMolSystem(self, index, name): self.molSystem = self.getMolSystems()[index] self.symmetrySet = self.molSystem.findFirstMolSystemSymmetrySet() self.updateSymmetries() def getMolSystems(self): molSystems = [] for molSystem in self.project.sortedMolSystems(): n = len(molSystem.chains) if self.singleMolecule and (n > 1): molSystems.append(molSystem) elif n > 0: molSystems.append(molSystem) return molSystems def updateMolSystems(self): names = [] index = -1 molSystems = self.getMolSystems() if molSystems: if self.molSystem not in molSystems: self.molSystem = molSystems[0] index = molSystems.index(self.molSystem) names = [ms.code for ms in molSystems] else: self.molSystem = None self.molSystemPulldown.setup(names, index) def updateSymmetriesAfter(self, obj=None): if self.waiting: return else: self.waiting = True self.after_idle(self.updateSymmetries) def updateSymmetries(self): textMatrix = [] objectList = [] if self.symmetrySet: for symmetryOp in self.symmetrySet.symmetries: chains = [] segments = [] length = symmetryOp.segmentLength for segment in symmetryOp.sortedSegments(): code = segment.chainCode chain = self.molSystem.findFirstChain(code=code) if chain: chains.append(code) seqId = segment.firstSeqId residue1 = chain.findFirstResidue(seqId=seqId) residue2 = chain.findFirstResidue(seqId=seqId + length - 1) segments.append( '%s:%d-%d' % (code, residue1.seqCode, residue2.seqCode)) datum = [ symmetryOp.serial, symmetryOp.symmetryCode, length, '\n'.join(chains), '\n'.join(segments) ] objectList.append(symmetryOp) textMatrix.append(datum) self.symmetryMatrix.update(objectList=objectList, textMatrix=textMatrix) self.waiting = False def destroy(self): self.notify(self.unregisterNotify) BasePopup.destroy(self)
def body(self, guiFrame): guiFrame.grid_columnconfigure(3, weight=1) row = 0 label = Label(guiFrame, text='Molecular system: ') label.grid(row=row, column=0, sticky=Tkinter.NW) self.molSysPulldown = PulldownMenu(guiFrame, self.changeMolSystem, selected_index=-1, do_initial_callback=0) self.molSysPulldown.grid(row=row, column=1, sticky=Tkinter.NW) label = Label(guiFrame, text='Clouds files: ') label.grid(row=row, column=2, sticky=Tkinter.NW) self.filenameEntry = Entry(guiFrame,text='perfect00.pdb') self.filenameEntry.grid(row=row, column=3, sticky=Tkinter.NW) row += 1 label = Label(guiFrame, text='Chain: ') label.grid(row=row, column=0, sticky=Tkinter.NW) self.chainPulldown = PulldownMenu(guiFrame, self.changeChain, selected_index=-1, do_initial_callback=0) self.chainPulldown.grid(row=row, column=1, sticky=Tkinter.NW) label = Label(guiFrame, text='Thread steps: ') label.grid(row=row, column=2, sticky=Tkinter.NW) self.numStepsEntry = IntEntry(guiFrame,text=3000) self.numStepsEntry.grid(row=row, column=3, sticky=Tkinter.NW) row += 1 label = Label(guiFrame, text='Homologue PDB file: ') label.grid(row=row, column=0, sticky=Tkinter.NW) self.pdbEntry = Entry(guiFrame,text='') self.pdbEntry.grid(row=row, column=1, sticky=Tkinter.NW) label = Label(guiFrame, text='Dist. Threshold: ') label.grid(row=row, column=2, sticky=Tkinter.NW) self.distEntry = FloatEntry(guiFrame,text=3.0) self.distEntry.grid(row=row, column=3, sticky=Tkinter.NW) row += 1 label = Label(guiFrame, text='Global score: ') label.grid(row=row, column=0, sticky=Tkinter.NW) self.globalScoreLabel = Label(guiFrame, text='') self.globalScoreLabel.grid(row=row, column=1, sticky=Tkinter.NW) label = Label(guiFrame, text='Assignment Threshold: ') label.grid(row=row, column=2, sticky=Tkinter.NW) self.thresholdEntry = FloatEntry(guiFrame,text=-4.5) self.thresholdEntry.grid(row=row, column=3, sticky=Tkinter.NW) row += 1 guiFrame.grid_rowconfigure(row, weight=1) self.graph = ScrolledGraph(guiFrame, width=300, height=200) self.graph.grid(row=row, column=0, columnspan=4, sticky = Tkinter.NSEW) row += 1 texts = ['Run','Assign!'] commands = [self.run, self.assignSpinSystems] bottomButtons = createDismissHelpButtonList(guiFrame,texts=texts,commands=commands,expands=0,help_url=None) bottomButtons.grid(row=row, column=0, columnspan=4, sticky=Tkinter.EW) self.assignButton = bottomButtons.buttons[1] for func in ('__init__','delete'): Implementation.registerNotify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem', func) Implementation.registerNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func) self.updateMolSystems() self.updateChains()
class NmrPipePseudoPopup(BasePopup): pseudoEntries = ('Is Pseudo Expt', 'Is Not Pseudo Expt') def __init__(self, parent, params, dim, fileName='', *args, **kw): self.dim = dim self.params = params self.fileName = fileName m = template_re.match(fileName) if m: n = len(m.groups(2)) ss = '%%0%dd' % n template = re.sub(template_re, r'\1%s\3' % ss, fileName) else: template = fileName self.template = template BasePopup.__init__(self, parent=parent, title='NMRPipe Pseudo Data', modal=True, **kw) def body(self, master): fileName = self.fileName directory = os.path.dirname(fileName) if not directory: directory = os.getcwd() fileName = os.path.basename(fileName) m = template_re.match(fileName) if m: n = len(m.groups(2)) ss = '%%0%dd' % n template = re.sub(template_re, r'\1%s\3' % ss, fileName) else: template = fileName master.rowconfigure(0, weight=1) master.rowconfigure(1, weight=1) master.columnconfigure(1, weight=1) tipTexts = [ 'The experiment is pseudo-N dimensional, with a sampled axis', 'The experiment is the regular kind with only NMR frequency axes' ] self.pseudoButton = RadioButtons( master, entries=self.pseudoEntries, select_callback=self.changedPseudoMode, grid=(0, 0), sticky='nw', tipTexts=tipTexts) frame = self.pseudoFrame = Frame(master) self.pseudoFrame.grid(row=1, column=0, sticky='nsew') row = 0 npts = self.params.npts[self.dim] tipText = 'Number of data points (planes) along sampled axis' label = Label(frame, text='Number of points: ') label.grid(row=row, column=0, sticky='e') self.nptsEntry = IntEntry(frame, text=npts, tipText=tipText, width=8, grid=(row, 1)) tipText = 'Load the values for the sampled axis from a text file containing a list of numeric values' Button(frame, text='Load values from text file', command=self.loadValues, tipText=tipText, grid=(row, 2), sticky='ew') row = row + 1 tipText = 'The values (e.g. T1, T2) corresponding to each data point (plane) along sampled axis' label = Label(frame, text='Point values: ') label.grid(row=row, column=0, sticky='e') self.valueEntry = FloatEntry(frame, isArray=True, tipText=tipText) self.valueEntry.grid(row=row, column=1, columnspan=2, sticky='ew') row = row + 1 tipText = 'Fetch the Point values from the files given by the NMRPipe template' button = Button( frame, text='Fetch values from file(s) specified by template below', command=self.fetchValues, tipText=tipText) button.grid(row=row, column=1, columnspan=2, sticky='w') row = row + 1 tipText = 'The directory where the data files reside' button = Button(frame, text='Data directory: ', command=self.chooseDirectory) button.grid(row=row, column=0, sticky='e') self.directoryEntry = Entry(frame, text=directory, width=40, tipText=tipText) self.directoryEntry.grid(row=row, column=1, columnspan=2, sticky='ew') row = row + 1 tipText = 'The NMRPipe template for the data files, if you want to use these to fetch the point values from' button = Button(frame, text='NMRPipe template: ', command=self.chooseFile) button.grid(row=row, column=0, sticky='e') self.templateEntry = Entry(frame, text=template, tipText=tipText) self.templateEntry.grid(row=row, column=1, columnspan=2, sticky='ew') for n in range(row): frame.rowconfigure(n, weight=1) frame.columnconfigure(1, weight=1) buttons = UtilityButtonList(master, closeText='Ok', doClone=False, closeCmd=self.updateParams, helpUrl=self.help_url) buttons.grid(row=2, column=0, sticky='ew') def loadValues(self): directory = self.parent.fileSelect.getDirectory() fileSelectPopup = FileSelectPopup(self, title='Select Sampled Data File', dismiss_text='Cancel', selected_file_must_exist=True, multiSelect=False, directory=directory) fileName = fileSelectPopup.file_select.getFile() if not fileName: return fileObj = open(fileName, 'rU') data = '' line = fileObj.readline() while line: data += line line = fileObj.readline() fileObj.close() data = re.sub(',\s+', ',', data) data = re.sub('\s+', ',', data) data = re.sub(',,', ',', data) data = re.sub('[^0-9,.\-+eE]', '', data) self.valueEntry.set(data) def chooseDirectory(self): directory = os.path.dirname(self.fileName) if not directory: directory = os.getcwd() popup = FileSelectPopup(self, directory=directory, show_file=False) directory = popup.getDirectory() popup.destroy() if directory: self.directoryEntry.set(directory) def chooseFile(self): directory = self.directoryEntry.get() if not directory: directory = os.getcwd() popup = FileSelectPopup(self, directory=directory) file = popup.getFile() popup.destroy() if file: template = os.path.basename(file) self.templateEntry.set(template) def updateParams(self): params = self.params if self.pseudoButton.get() == self.pseudoEntries[0]: npts = self.nptsEntry.get() params.npts[self.dim] = npts values = self.valueEntry.get() try: params.setSampledDim(self.dim, values) except ApiError, e: showError('Set Sampled Dim', e.error_msg, parent=self) return params.fixNullDims(ignoreDim=self.dim) else:
class ResultsTab(object): def __init__(self, parent, frame): self.guiParent = parent self.frame = frame self.project = parent.project self.nmrProject = parent.nmrProject self.selectedLinkA = None self.selectedLinkB = None self.selectedResidueA = None self.selectedResidueB = None self.selectedLink = None self.dataModel = self.guiParent.connector.results self.body() def body(self): frame = self.frame self.resultsResidueNumber = 1 frame.expandGrid(5, 0) resultTopFrame = LabelFrame(frame, text='Which results to show') resultTopFrame.grid(row=0, column=0, sticky='ew') self.resultsResidueNumber = 3 texts = [' < '] commands = [self.resultsPrevResidue] self.resultsPreviousButton = ButtonList(resultTopFrame, commands=commands, texts=texts) self.resultsPreviousButton.grid(row=0, column=1, sticky='nsew') tipText = 'The Number of the residue in the sequence to display results for' self.resultsResidueNumberEntry = IntEntry( resultTopFrame, grid=(0, 2), width=7, text=3, returnCallback=self.resultsUpdateAfterEntry, tipText=tipText) #self.resultsResidueNumberEntry.bind('<Leave>', self.resultsUpdateAfterEntry, '+') texts = [' > '] commands = [self.resultsNextResidue] self.resultsNextButton = ButtonList(resultTopFrame, commands=commands, texts=texts) self.resultsNextButton.grid(row=0, column=3, sticky='nsew') selectCcpCodes = ['residue'] + AMINO_ACIDS self.resultsSelectedCcpCode = 'residue' tipText = 'Instead of going through the sequence residue by residue, jump directly to next amino acid of a specific type.' resultsSelectCcpCodeLabel = Label( resultTopFrame, text='Directly jump to previous/next:', grid=(0, 4)) self.resultsSelectCcpCodePulldown = PulldownList( resultTopFrame, callback=self.resultsChangeSelectedCcpCode, texts=selectCcpCodes, index=selectCcpCodes.index(self.resultsSelectedCcpCode), grid=(0, 5), tipText=tipText) self.selectedSolution = 1 runLabel = Label(resultTopFrame, text='run:') runLabel.grid(row=0, column=6) texts = [' < '] commands = [self.resultsPrevSolution] self.resultsPreviousSolutionButton = ButtonList(resultTopFrame, commands=commands, texts=texts) self.resultsPreviousSolutionButton.grid(row=0, column=7, sticky='nsew') tipText = 'If you ran the algorithm more than once, you can select the solution given by the different runs.' self.resultsSolutionNumberEntry = IntEntry( resultTopFrame, grid=(0, 8), width=7, text=1, returnCallback=self.solutionUpdateAfterEntry, tipText=tipText) #self.resultsSolutionNumberEntry.bind('<Leave>', self.solutionUpdateAfterEntry, '+') texts = [' > '] commands = [self.resultsNextSolution] self.resultsNextSolutionButton = ButtonList(resultTopFrame, commands=commands, texts=texts) self.resultsNextSolutionButton.grid(row=0, column=9, sticky='nsew') self.energyLabel = Label(resultTopFrame, text='energy:') self.energyLabel.grid(row=0, column=10) texts = ['template for puzzling'] commands = [self.adoptSolution] self.adoptButton = ButtonList(resultTopFrame, commands=commands, texts=texts) self.adoptButton.grid(row=0, column=11, sticky='nsew') # LabelFrame(frame, text='Spin Systems') resultsSecondFrame = Frame(frame) resultsSecondFrame.grid(row=2, column=0, sticky='nsew') resultsSecondFrame.grid_columnconfigure(0, weight=1) resultsSecondFrame.grid_columnconfigure(1, weight=1) resultsSecondFrame.grid_columnconfigure(2, weight=1) resultsSecondFrame.grid_columnconfigure(3, weight=1) resultsSecondFrame.grid_columnconfigure(4, weight=1) headingList = ['#', '%'] tipTexts = [ 'Spinsystem number {} indicates serial of the spinsystem. If the spinsystem was already assigned to a residue, the residue number is shown aswell', 'percentage of the solutions that connected this spinsystem to this residue' ] editWidgets = [None, None, None] self.displayResultsTables = [] self.residueLabels = [] for i in range(5): label = Label(resultsSecondFrame, text='residue') label.grid(row=0, column=i) #editGetCallbacks = [createCallbackFunction(i)]*3 displayResultsTable = ScrolledMatrix( resultsSecondFrame, headingList=headingList, multiSelect=False, tipTexts=tipTexts, callback=self.selectSpinSystemForTable, passSelfToCallback=True) displayResultsTable.grid(row=2, column=i, sticky='nsew') displayResultsTable.sortDown = False self.residueLabels.append(label) self.displayResultsTables.append(displayResultsTable) # LabelFrame(frame, text='Sequence Fragment') resultsFirstFrame = Frame(resultsSecondFrame) resultsFirstFrame.grid(row=1, column=0, sticky='ew', columnspan=5) resultsFirstFrame.grid_rowconfigure(0, weight=1) resultsFirstFrame.grid_rowconfigure(1, weight=1) resultsFirstFrame.grid_columnconfigure(0, weight=1) texts = [ ' res 1 ', ' links ', ' res 2 ', ' links ', ' res 3 ', ' links ', ' res 4 ', ' links ', ' res 5 ' ] commands = [ lambda: self.selectRelativeResidue(1, True), lambda: self.selectLink(1, True), lambda: self.selectRelativeResidue(2, True), lambda: self.selectLink(2, True), lambda: self.selectRelativeResidue(3, True), lambda: self.selectLink(3, True), lambda: self.selectRelativeResidue(4, True), lambda: self.selectLink(4, True), lambda: self.selectRelativeResidue(5, True) ] self.sequenceButtons = ButtonList(resultsFirstFrame, commands=commands, texts=texts) self.sequenceButtons.grid(row=0, column=0, sticky='nsew') for n, button in enumerate(self.sequenceButtons.buttons): if n % 2: button.grid(column=n, sticky='ns') self.sequenceButtons.grid_columnconfigure(n, weight=0) else: self.sequenceButtons.grid_columnconfigure(n, uniform=2) spacer = Spacer(resultsFirstFrame) spacer.grid(row=1, column=0, sticky='nsew') texts = [ ' res 1 ', ' links ', ' res 2 ', ' links ', ' res 3 ', ' links ', ' res 4 ', ' links ', ' res 5 ' ] commands = commands = [ lambda: self.selectRelativeResidue(1, False), lambda: self.selectLink(1, False), lambda: self.selectRelativeResidue(2, False), lambda: self.selectLink(2, False), lambda: self.selectRelativeResidue(3, False), lambda: self.selectLink(3, False), lambda: self.selectRelativeResidue(4, False), lambda: self.selectLink(4, False), lambda: self.selectRelativeResidue(5, False) ] self.sequenceButtonsB = ButtonList(resultsFirstFrame, commands=commands, texts=texts) self.sequenceButtonsB.grid(row=2, column=0, sticky='nsew') for n, button in enumerate(self.sequenceButtonsB.buttons): if n % 2: button.grid(column=n, sticky='ns') self.sequenceButtonsB.grid_columnconfigure(n, weight=0) else: self.sequenceButtonsB.grid_columnconfigure(n, uniform=2) frame.grid_rowconfigure(3, weight=2) resultsThirdFrame = Frame(frame) resultsThirdFrame.grid(row=3, column=0, sticky='nsew') resultsThirdFrame.grid_rowconfigure(0, weight=1) resultsThirdFrame.grid_columnconfigure(0, weight=1) tabbedFrameB = TabbedFrame(resultsThirdFrame, options=['Peaks', 'Spin System'], callback=self.toggleTab, grid=(0, 0)) #self.tabbedFrameB = tabbedFrame PeakFrame, SpinSystemFrame = tabbedFrameB.frames SpinSystemFrame.grid_rowconfigure(0, weight=1) PeakFrame.grid_rowconfigure(1, weight=1) SpinSystemFrame.grid_columnconfigure(0, weight=1) PeakFrame.grid_columnconfigure(0, weight=1) headingList = [ 'residue', 'assigned to in project', 'user defined sequence', 'selected annealing result', '%' ] tipTexts = [None, None, None, None, None] editWidgets = [None, None, None, None, None] editGetCallbacks = [None, None, None, None, None] editSetCallbacks = [None, None, None, None, None] self.spinSysTable = ScrolledMatrix(SpinSystemFrame, headingList=headingList, editWidgets=editWidgets, multiSelect=False, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, tipTexts=tipTexts) self.spinSysTable.grid(row=0, column=0, sticky='nsew') buttonFrameinPeakFrame = Frame(PeakFrame) buttonFrameinPeakFrame.grid(sticky='ew') self.findButton = Button( buttonFrameinPeakFrame, text=' Go to Peak ', borderwidth=1, padx=2, pady=1, command=self.findPeak, tipText='Locate the currently selected peak in the specified window' ) self.findButton.grid(row=0, column=0, sticky='e') label = Label(buttonFrameinPeakFrame, text='in window:') label.grid(row=0, column=1, sticky='w') self.windowPulldown = PulldownList( buttonFrameinPeakFrame, callback=self.selectWindowPane, tipText='Choose the spectrum window for locating peaks or strips') self.windowPulldown.grid(row=0, column=2, sticky='w') self.assignSelectedPeaksButton = Button( buttonFrameinPeakFrame, text='Assign Resonances to Peak(s)', borderwidth=1, padx=2, pady=1, command=self.assignSelectedPeaks, tipText= 'Assign resonances to peak dimensions, this of course only works when the peak is found in the spectrum.' ) self.assignSelectedPeaksButton.grid(row=0, column=3, sticky='ew') self.assignSelectedSpinSystemsToResiduesButton = Button( buttonFrameinPeakFrame, text='Assign Spinsystems to Residues', borderwidth=1, padx=2, pady=1, command=self.assignSelectedSpinSystemsToResidues, tipText='Assign spinsystems to residues') self.assignSelectedSpinSystemsToResiduesButton.grid(row=0, column=4, sticky='ew') headingList = [ '#', 'spectrum', 'Dim1', 'Dim2', 'Dim3', 'c.s. dim1', 'c.s. dim2', 'c.s. dim3', 'colabelling' ] tipTexts = [ 'Peak number, only present when the peak was actually found in the spectrum.', 'Name of the spectrum', 'Name of atomSet measured in this dimension. Dimension number corresponds to Ref Exp Dim as indicated by going in the main menu to Experiment-->Experiments-->Experiment Type', 'Name of atomSet measured in this dimension. Dimension number corresponds to Ref Exp Dim as indicated by going in the main menu to Experiment-->Experiments-->Experiment Type', 'Name of atomSet measured in this dimension. Dimension number corresponds to Ref Exp Dim as indicated by going in the main menu to Experiment-->Experiments-->Experiment Type', 'Chemical Shift', 'Chemical Shift', 'Chemical Shift', 'Colabbeling fraction over all nuclei that are on the magnetization transfer pathway during the experiment that gave rise to the peak, including visited nuclei that were not measured in any of the peak dimensions' ] #editWidgets = [None, None, None, None, None, None, None, None, None] editGetCallbacks = [ None, None, None, None, None, None, None, None, None ] #editGetCallbacks = [self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak] editSetCallbacks = [ None, None, None, None, None, None, None, None, None ] self.displayPeakTable = ScrolledMatrix(PeakFrame, headingList=headingList, multiSelect=True, tipTexts=tipTexts) #editWidgets=editWidgets, multiSelect=True, # editGetCallbacks=editGetCallbacks, # editSetCallbacks=editSetCallbacks, # tipTexts=tipTexts) self.displayPeakTable.grid(row=1, column=0, sticky='nsew') self.windowPane = None self.updateWindows() def selectSpinSystemForTable(self, spinSystem, row, column, table): table_number = self.displayResultsTables.index(table) self.selectSpinSystem(table_number, spinSystem) @lockUntillResults def showResults(self): self.updateResultsTable() @lockUntillResults def selectLink(self, number, topRow): if topRow: self.selectedResidueA = None self.selectedResidueB = None self.selectedLinkA = number self.selectedLinkB = None else: self.selectedResidueA = None self.selectedResidueB = None self.selectedLinkA = None self.selectedLinkB = number self.updateButtons() self.updateLink() @lockUntillResults def selectRelativeResidue(self, number, topRow): if topRow: self.selectedResidueA = number self.selectedResidueB = None self.selectedLinkA = None self.selectedLinkB = None else: self.selectedResidueA = None self.selectedResidueB = number self.selectedLinkA = None self.selectedLinkB = None self.updateButtons() self.updateLink() def updateLink(self): ''' Checks for any selected link (self.selectedLinkA or self.selectedLinkB) and calls updatePeakTable with the correct residue Object and spinsystem Objects. ''' number = self.selectedLinkA or self.selectedLinkB or self.selectedResidueA or self.selectedResidueB if not number: self.emptyPeakTable() return dataModel = self.dataModel resNumber = self.resultsResidueNumber chain = dataModel.chain residues = chain.residues solutionNumber = self.selectedSolution - 1 if self.selectedResidueA: res = residues[resNumber - 4 + number] spinSystem = res.solutions[solutionNumber] self.selectedLink = None if res and spinSystem: self.selectedLink = res.getIntraLink(spinSystem) #self.updatePeakTableIntra(res, spinSystem) self.updateSpinSystemTable(spinSystem) elif self.selectedResidueB: res = residues[resNumber - 4 + number] spinSystem = res.userDefinedSolution self.selectedLink = None if res and spinSystem: self.selectedLink = res.getIntraLink(spinSystem) #self.updatePeakTableIntra(res, spinSystem) self.updateSpinSystemTable(spinSystem) elif self.selectedLinkA: resA = residues[resNumber - 4 + number] resB = residues[resNumber - 3 + number] spinSystemA = resA.solutions[solutionNumber] spinSystemB = resB.solutions[solutionNumber] self.selectedLink = None if resA and spinSystemA and spinSystemB: self.selectedLink = resA.getLink(spinSystemA, spinSystemB) #self.updatePeakTable(resA, spinSystemA, spinSystemB) # and resA.userDefinedSolution and resB.userDefinedSolution: elif self.selectedLinkB: resA = residues[resNumber - 4 + number] resB = residues[resNumber - 3 + number] spinSystemA = resA.userDefinedSolution spinSystemB = resB.userDefinedSolution self.selectedLink = None if resA and spinSystemA and spinSystemB: self.selectedLink = resA.getLink(spinSystemA, spinSystemB) #self.updatePeakTable(resA, spinSystemA, spinSystemB) self.updatePeakTable() def emptyPeakTable(self): self.displayPeakTable.update(objectList=[], textMatrix=[], colorMatrix=[]) def updatePeakTable(self): ''' Updates the peak table to show the peaks that are found for a sequencial pair of spinsystems A and B. If there is not a linkobject found for spinsystems A and B the table is emptied. Also sets the selected peak to None. ''' link = self.selectedLink if not link: self.emptyPeakTable() else: resA, resB = link.getResidues() spinSystemA, spinSystemB = link.getSpinSystems() data = [] objectList = [] peakLinks = link.getAllPeakLinks() if not peakLinks: self.emptyPeakTable() return maxDimenionality = max([ len(peakLink.getSimulatedPeak().getContribs()) for peakLink in peakLinks ]) for peakLink in peakLinks: serial = None realPeak = peakLink.getPeak() simPeak = peakLink.getSimulatedPeak() atomTexts = [None] * maxDimenionality chemicalShifts = [None] * maxDimenionality for simulatedPeakContrib in simPeak.getContribs(): atomName = simulatedPeakContrib.getAtomName() #ccpCode = simulatedPeakContrib.getCcpCode() dimNumber = simulatedPeakContrib.getDimNumber() if resA is simulatedPeakContrib.getResidue(): spinSystemDescription = spinSystemA.getDescription( noSerialWhenSeqCodeIsPresent=True) else: spinSystemDescription = spinSystemB.getDescription( noSerialWhenSeqCodeIsPresent=True) atomTexts[dimNumber - 1] = '%s %s' % (spinSystemDescription, atomName) if realPeak: serial = realPeak.getSerial() for dim in realPeak.getDimensions(): chemicalShifts[dim.getDimNumber() - 1] = dim.getChemicalShift() else: shiftListSerial = simPeak.getSpectrum().getShiftListSerial( ) for resonance, simulatedPeakContrib in zip( peakLink.getResonances(), simPeak.getContribs()): if resonance: chemicalShifts[simulatedPeakContrib.getDimNumber() - 1] = resonance.getChemicalShift( shiftListSerial) else: chemicalShifts[simulatedPeakContrib.getDimNumber() - 1] = '?' data.append([serial, simPeak.getSpectrum().name] + atomTexts + chemicalShifts + [simPeak.colabelling]) objectList.append(peakLink) headingList = ['#', 'spectrum'] + [ 'dim%s' % a for a in range(1, maxDimenionality + 1) ] + ['c.s. dim%s' % a for a in range(1, maxDimenionality + 1)] + ['colabbeling'] self.displayPeakTable.update(objectList=objectList, textMatrix=data, headingList=headingList) def findPeak(self): if not self.windowPane: return selectedPeakLinks = self.displayPeakTable.currentObjects if not selectedPeakLinks: self.guiParent.updateInfoText('Please select a peak first.') return if len(selectedPeakLinks) > 1: self.guiParent.updateInfoText('Can only go to one peak at a time.') return selectedPeakLink = selectedPeakLinks[0] selectedPeak = selectedPeakLink.getPeak() if selectedPeak: ccpnPeak = selectedPeak.getCcpnPeak() createPeakMark(ccpnPeak, lineWidth=2.0) windowFrame = self.windowPane.getWindowFrame() windowFrame.gotoPeak(ccpnPeak) else: simPeak = selectedPeakLink.getSimulatedPeak() spectrum = simPeak.getSpectrum() ccpnSpectrum = spectrum.getCcpnSpectrum() view = getSpectrumWindowView(self.windowPane, ccpnSpectrum) if not view: self.guiParent.updateInfoText( 'This peak cannot be displayed in the window you chose.') axisMappingByRefExpDimNumber = {} for axisMapping in view.axisMappings: refExpDimNumber = axisMapping.analysisDataDim.dataDim.expDim.refExpDim.dim axisMappingByRefExpDimNumber[refExpDimNumber] = axisMapping positionToGoTo = {} markPosition = [] axisTypes = [] for resonance, contrib in zip(selectedPeakLink.getResonances(), simPeak.getContribs()): dimNumber = contrib.getDimNumber() axisMapping = axisMappingByRefExpDimNumber.get(dimNumber) label = axisMapping.label if resonance: axisType = axisMapping.axisPanel.axisType chemicalShift = resonance.getChemicalShift() positionToGoTo[label] = chemicalShift markPosition.append(chemicalShift) axisTypes.append(axisType) # Not drawing a mark at this chemical shift, just hoovering to # the good region in the spectrum else: ccpCode = contrib.getResidue().getCcpCode() atomName = contrib.getAtomName() medianChemicalShift = self.getMedianChemicalShift( ccpCode, atomName) if medianChemicalShift: positionToGoTo[label] = medianChemicalShift if positionToGoTo: windowFrame = self.windowPane.getWindowFrame() windowFrame.gotoPosition(positionToGoTo) if markPosition: createNonPeakMark(markPosition, axisTypes) def assignSelectedPeaks(self): selectedPeakLinks = self.displayPeakTable.currentObjects for pl in selectedPeakLinks: peak = pl.getPeak() if peak: for resonance, dimension in zip(pl.getResonances(), peak.getDimensions()): ccpnResonance = resonance.getCcpnResonance() ccpnDimension = dimension.getCcpnDimension() if ccpnResonance and ccpnDimension: assignResToDim(ccpnDimension, ccpnResonance) def assignSelectedSpinSystemsToResidues(self): link = self.selectedLink if link: residues = link.getResidues() spinSystems = link.getSpinSystems() ccpnSpinSystems = [] ccpnResidues = [] for spinSys, res in zip(spinSystems, residues): if spinSys and res: ccpnSpinSystems.append(spinSys.getCcpnResonanceGroup()) ccpnResidues.append(res.getCcpnResidue()) assignSpinSystemstoResidues(ccpnSpinSystems, ccpnResidues, guiParent=self.guiParent) self.updateButtons() self.updateButtons() self.updateResultsTable() self.updatePeakTable() def getMedianChemicalShift(self, ccpCode, atomName): nmrRefStore = self.project.findFirstNmrReferenceStore( molType='protein', ccpCode=ccpCode) chemCompNmrRef = nmrRefStore.findFirstChemCompNmrRef( sourceName='RefDB') chemCompVarNmrRef = chemCompNmrRef.findFirstChemCompVarNmrRef( linking='any', descriptor='any') if chemCompVarNmrRef: chemAtomNmrRef = chemCompVarNmrRef.findFirstChemAtomNmrRef( name=atomName) if chemAtomNmrRef: distribution = chemAtomNmrRef.distribution maxIndex = max([ (value, index) for index, value in enumerate(distribution) ])[1] return chemAtomNmrRef.refValue + chemAtomNmrRef.valuePerPoint * ( maxIndex - chemAtomNmrRef.refPoint) return None def selectWindowPane(self, windowPane): if windowPane is not self.windowPane: self.windowPane = windowPane def updateWindows(self): index = 0 windowPane = None windowPanes = [] names = [] peakList = None tryWindows = WindowBasic.getActiveWindows(self.project) windowData = [] getName = WindowBasic.getWindowPaneName for window in tryWindows: for windowPane0 in window.spectrumWindowPanes: # if WindowBasic.isSpectrumInWindowPane(windowPane0, spectrum): windowData.append((getName(windowPane0), windowPane0)) windowData.sort() names = [x[0] for x in windowData] windowPanes = [x[1] for x in windowData] if windowPanes: if windowPane not in windowPanes: windowPane = windowPanes[0] index = windowPanes.index(windowPane) else: windowPane = None self.selectWindowPane(windowPane) self.windowPulldown.setup(names, windowPanes, index) def selectSpinSystem(self, number, spinSystem): res = self.dataModel.chain.residues[self.resultsResidueNumber - 3 + number] oldSpinSystemForResidue = res.userDefinedSolution if oldSpinSystemForResidue and res.getSeqCode( ) in oldSpinSystemForResidue.userDefinedSolutions: oldSpinSystemForResidue.userDefinedSolutions.remove( res.getSeqCode()) res.userDefinedSolution = spinSystem spinSystem.userDefinedSolutions.append(res.getSeqCode()) # self.updateSpinSystemTable(spinSystem) self.updateLink() self.updateButtons() def updateSpinSystemTable(self, spinSystem): if not spinSystem: self.emptySpinSystemTable() return dataModel = self.dataModel residues = dataModel.chain.residues data = [] colorMatrix = [] for residue in spinSystem.allowedResidues: oneRow = [] oneRowColor = [] string = str(residue.getSeqCode()) + ' ' + residue.getCcpCode() oneRow.append(string) resonanceGroup = spinSystem.getCcpnResonanceGroup() ccpnResidue = residue.ccpnResidue # Assigned in the project to this residue if resonanceGroup and resonanceGroup.residue and resonanceGroup.residue is ccpnResidue: oneRow.append('x') else: oneRow.append(None) # The user selected this res for this spinsystem (could be more # than one res for which this happens) if residue.getSeqCode() in spinSystem.userDefinedSolutions: oneRow.append('x') else: oneRow.append(None) if residue.solutions[self.selectedSolution - 1] == spinSystem: oneRow.append('x') else: oneRow.append(None) if spinSystem.solutions: percentage = spinSystem.solutions.count( residue.getSeqCode()) / float(len( spinSystem.solutions)) * 100.0 else: percentage = 0 oneRow.append(int(percentage + 0.5)) color = pick_color_by_percentage(percentage) oneRowColor = [color] * 5 data.append(oneRow) colorMatrix.append(oneRowColor) self.spinSysTable.update(objectList=data, textMatrix=data, colorMatrix=colorMatrix) self.spinSysTable.sortDown = False self.spinSysTable.sortLine(-1, noUpdate=True) def emptySpinSystemTable(self): self.spinSysTable.update(objectList=[], textMatrix=[], colorMatrix=[]) @lockUntillResults def adoptSolution(self): dataModel = self.dataModel selectedSolution = self.selectedSolution for res in dataModel.chain.residues: spinSystem = res.solutions[selectedSolution - 1] res.userDefinedSolution = spinSystem spinSystem.userDefinedSolutions = [res.getSeqCode()] self.updateLink() self.updateButtons() @lockUntillResults def resultsPrevSolution(self): if self.selectedSolution != 1: self.selectedSolution = self.selectedSolution - 1 self.resultsSolutionNumberEntry.set(self.selectedSolution) self.updateLink() self.updateButtons() self.updateEnergy() @lockUntillResults def resultsNextSolution(self): amountOfRepeats = len(self.dataModel.chain.residues[0].solutions) if self.selectedSolution < amountOfRepeats: self.selectedSolution = self.selectedSolution + 1 self.resultsSolutionNumberEntry.set(self.selectedSolution) self.updateLink() self.updateButtons() self.updateEnergy() @lockUntillResults def resultsPrevResidue(self): residues = self.dataModel.chain.residues #chainLength = len(residues) new_value = self.resultsResidueNumber if self.resultsSelectedCcpCode == 'residue': if self.resultsResidueNumber != 3: new_value = self.resultsResidueNumber - 1 else: for res in residues: if res.getSeqCode() == self.resultsResidueNumber: break elif res.getCcpCode() == self.resultsSelectedCcpCode: new_value = res.getSeqCode() if new_value < 3: new_value = 3 if self.resultsResidueNumber != new_value: self.resultsResidueNumber = new_value self.resultsResidueNumberEntry.set(self.resultsResidueNumber) self.updateLink() self.updateButtons() self.updateButtons() self.updateResultsTable() self.updateResidueLabels() @lockUntillResults def resultsNextResidue(self): residues = self.dataModel.chain.residues chainLength = len(residues) new_value = self.resultsResidueNumber if self.resultsSelectedCcpCode == 'residue': if self.resultsResidueNumber != chainLength - 2: new_value = self.resultsResidueNumber + 1 else: for res in residues[(self.resultsResidueNumber):]: if res.getCcpCode() == self.resultsSelectedCcpCode: new_value = res.getSeqCode() if new_value > chainLength - 2: new_value = chainLength - 2 break if self.resultsResidueNumber != new_value: self.resultsResidueNumber = new_value self.resultsResidueNumberEntry.set(self.resultsResidueNumber) self.updateLink() self.updateButtons() self.updateButtons() self.updateResultsTable() self.updateResidueLabels() def resultsChangeSelectedCcpCode(self, ccpCode): self.resultsSelectedCcpCode = ccpCode @lockUntillResults def resultsUpdateAfterEntry(self, event=None): ''' Update for entry of residue number in strip plots ''' residues = self.dataModel.chain.residues value = self.resultsResidueNumberEntry.get() if value == self.resultsResidueNumber: return else: self.resultsResidueNumber = value if value < 3: self.resultsResidueNumberEntry.set(3) self.resultsResidueNumber = 3 elif value > len(residues) - 2: self.resultsResidueNumber = len(residues) - 2 self.resultsResidueNumberEntry.set(self.resultsResidueNumber) else: self.resultsResidueNumberEntry.set(self.resultsResidueNumber) self.updateLink() self.updateButtons() self.updateButtons() self.updateResultsTable() self.updateResidueLabels() @lockUntillResults def solutionUpdateAfterEntry(self, event=None): ''' Update for entry of residue number in strip plots ''' Nsolutions = len(self.dataModel.chain.residues[0].solutions) value = self.resultsSolutionNumberEntry.get() if value == self.selectedSolution: return else: self.selectedSolution = value if value < 1: self.resultsSolutionNumberEntry.set(1) self.selectedSolution = 1 elif value > Nsolutions: self.selectedSolution = Nsolutions self.resultsSolutionNumberEntry.set(self.selectedSolution) else: self.resultsSolutionNumberEntry.set(self.selectedSolution) self.updateLink() self.updateButtons() def update(self): self.updateLink() self.updateResidueLabels() self.updateResultsTable() self.updateButtons() self.updateButtons() self.updateEnergy() def updateResultsTable(self): resNumber = self.resultsResidueNumber dataModel = self.dataModel chain = dataModel.chain residues = chain.residues resA = residues[resNumber - 3] resB = residues[resNumber - 2] resC = residues[resNumber - 1] resD = residues[resNumber] resE = residues[resNumber + 1] resList = [resA, resB, resC, resD, resE] tableList = self.displayResultsTables for res, table in zip(resList, tableList): ccpCode = res.ccpCode spinSystemsWithThisCcpCode = dataModel.getSpinSystems()[ccpCode] data = [] colorMatrix = [] objectList = [] jokers = [] realSpinSystems = [] for spinSys in spinSystemsWithThisCcpCode: if spinSys.getIsJoker(): jokers.append(spinSys) else: realSpinSystems.append(spinSys) for spinsys in realSpinSystems: oneRow = [] oneRowColor = [] # self.getStringDescriptionOfSpinSystem(spinsys) spinSystemInfo = spinsys.getDescription() oneRow.append(spinSystemInfo) assignmentPercentage = int( float(res.solutions.count(spinsys)) / len(res.solutions) * 100.0) oneRow.append(assignmentPercentage) objectList.append(spinsys) color = pick_color_by_percentage(assignmentPercentage) oneRowColor = [color, color] data.append(oneRow) colorMatrix.append(oneRowColor) if jokers: oneRow = ['Joker'] NumberOfAssignmentsToJoker = 0 for spinSys in jokers: NumberOfAssignmentsToJoker += res.solutions.count(spinSys) assignmentPercentage = int( float(NumberOfAssignmentsToJoker) / len(res.solutions) * 100.0) oneRow.append(assignmentPercentage) color = pick_color_by_percentage(assignmentPercentage) oneRowColor = [color, color] data.append(oneRow) colorMatrix.append(oneRowColor) objectList.append(jokers[0]) percentages = [datapoint[1] for datapoint in data] tableData = sorted(zip(percentages, data, objectList, colorMatrix), reverse=True) percentage, data, objectList, colorMatrix = zip(*tableData) table.update(objectList=objectList, textMatrix=data, colorMatrix=colorMatrix) def updateResidueLabels(self): resList = self.getCurrentlyDisplayedResidues() labels = self.residueLabels for residue, label in zip(resList, labels): text = str(residue.getSeqCode()) + ' ' + residue.getCcpCode() label.set(text) def updateButtons(self): self.updateButtonHighLights() self.updateResultsTopRowButtons() self.updateResultsBottomRowButtons() def updateResultsTopRowButtons(self): resList = self.getCurrentlyDisplayedResidues() buttons = self.sequenceButtons.buttons[::2] for button, res in zip(buttons, resList): spinsys = res.solutions[self.selectedSolution - 1] # str(res.getSeqCode()) + ' ' + res.getCcpCode() + ': ' + # spinsys.getDescription() # self.getStringDescriptionOfSpinSystem(spinsys) text = spinsys.getDescription(noSerialWhenSeqCodeIsPresent=False) button.config(text=text) def updateResultsBottomRowButtons(self): resList = self.getCurrentlyDisplayedResidues() buttons = self.sequenceButtonsB.buttons[::2] for button, res in zip(buttons, resList): if res.userDefinedSolution: selectedSpinSystem = res.userDefinedSolution text = selectedSpinSystem.getDescription( noSerialWhenSeqCodeIsPresent=False) if len(selectedSpinSystem.userDefinedSolutions) > 1: # The red color signals that the spinssystem is used in # more than 1 place in the sequence button.config(text=text, bg=highLightRed) else: button.config(text=text) else: # str(res.getSeqCode()) + ' ' + res.getCcpCode() + ': -' text = '-' button.config(text=text) def updateButtonHighLights(self): self.setAllButtonsToGrey() if self.selectedResidueA: buttons = [ self.sequenceButtons.buttons[0], self.sequenceButtons.buttons[2], self.sequenceButtons.buttons[4], self.sequenceButtons.buttons[6], self.sequenceButtons.buttons[8] ] buttons[self.selectedResidueA - 1].config(bg=highLightYellow) elif self.selectedResidueB: buttons = [ self.sequenceButtonsB.buttons[0], self.sequenceButtonsB.buttons[2], self.sequenceButtonsB.buttons[4], self.sequenceButtonsB.buttons[6], self.sequenceButtonsB.buttons[8] ] buttons[self.selectedResidueB - 1].config(bg=highLightYellow) elif self.selectedLinkA: buttons = [ self.sequenceButtons.buttons[1], self.sequenceButtons.buttons[3], self.sequenceButtons.buttons[5], self.sequenceButtons.buttons[7] ] buttons[self.selectedLinkA - 1].config(bg=highLightYellow) elif self.selectedLinkB: buttons = [ self.sequenceButtonsB.buttons[1], self.sequenceButtonsB.buttons[3], self.sequenceButtonsB.buttons[5], self.sequenceButtonsB.buttons[7] ] buttons[self.selectedLinkB - 1].config(bg=highLightYellow) def updateEnergy(self): text = 'energy: %s' % int( self.dataModel.getEnergy(self.selectedSolution - 1) + 0.5) self.energyLabel.set(text) self.energyLabel.update() def setAllButtonsToGrey(self): for button in self.sequenceButtons.buttons + self.sequenceButtonsB.buttons: button.config(bg='grey83') def setAllRedButtonsToGrey(self): for button in self.sequenceButtons.buttons + self.sequenceButtonsB.buttons: if button.enableFg == highLightRed: button.config(bg='grey83') def getCurrentlyDisplayedResidues(self): resNumber = self.resultsResidueNumber residues = self.dataModel.chain.residues[resNumber - 3:resNumber + 2] return residues def toggleTab(self, index): pass
def body(self, master): fileName = self.fileName directory = os.path.dirname(fileName) if not directory: directory = os.getcwd() fileName = os.path.basename(fileName) m = template_re.match(fileName) if m: n = len(m.groups(2)) ss = '%%0%dd' % n template = re.sub(template_re, r'\1%s\3' % ss, fileName) else: template = fileName master.rowconfigure(0, weight=1) master.rowconfigure(1, weight=1) master.columnconfigure(1, weight=1) tipTexts = [ 'The experiment is pseudo-N dimensional, with a sampled axis', 'The experiment is the regular kind with only NMR frequency axes' ] self.pseudoButton = RadioButtons( master, entries=self.pseudoEntries, select_callback=self.changedPseudoMode, grid=(0, 0), sticky='nw', tipTexts=tipTexts) frame = self.pseudoFrame = Frame(master) self.pseudoFrame.grid(row=1, column=0, sticky='nsew') row = 0 npts = self.params.npts[self.dim] tipText = 'Number of data points (planes) along sampled axis' label = Label(frame, text='Number of points: ') label.grid(row=row, column=0, sticky='e') self.nptsEntry = IntEntry(frame, text=npts, tipText=tipText, width=8, grid=(row, 1)) tipText = 'Load the values for the sampled axis from a text file containing a list of numeric values' Button(frame, text='Load values from text file', command=self.loadValues, tipText=tipText, grid=(row, 2), sticky='ew') row = row + 1 tipText = 'The values (e.g. T1, T2) corresponding to each data point (plane) along sampled axis' label = Label(frame, text='Point values: ') label.grid(row=row, column=0, sticky='e') self.valueEntry = FloatEntry(frame, isArray=True, tipText=tipText) self.valueEntry.grid(row=row, column=1, columnspan=2, sticky='ew') row = row + 1 tipText = 'Fetch the Point values from the files given by the NMRPipe template' button = Button( frame, text='Fetch values from file(s) specified by template below', command=self.fetchValues, tipText=tipText) button.grid(row=row, column=1, columnspan=2, sticky='w') row = row + 1 tipText = 'The directory where the data files reside' button = Button(frame, text='Data directory: ', command=self.chooseDirectory) button.grid(row=row, column=0, sticky='e') self.directoryEntry = Entry(frame, text=directory, width=40, tipText=tipText) self.directoryEntry.grid(row=row, column=1, columnspan=2, sticky='ew') row = row + 1 tipText = 'The NMRPipe template for the data files, if you want to use these to fetch the point values from' button = Button(frame, text='NMRPipe template: ', command=self.chooseFile) button.grid(row=row, column=0, sticky='e') self.templateEntry = Entry(frame, text=template, tipText=tipText) self.templateEntry.grid(row=row, column=1, columnspan=2, sticky='ew') for n in range(row): frame.rowconfigure(n, weight=1) frame.columnconfigure(1, weight=1) buttons = UtilityButtonList(master, closeText='Ok', doClone=False, closeCmd=self.updateParams, helpUrl=self.help_url) buttons.grid(row=2, column=0, sticky='ew')
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()
class AssignMentTransferTab(object): '''the tab in the GUI where assignments can be transferred in bulk to the ccpn analysis project. A difference is made between two types of assignments: 1) spin systems to residues, which also implies resonanceSets to atomSets. 2) resonances to peak dimensions. The user is able to configure which assignments should be transferred to the project. Attributes: guiParent: gui object this tab is part of. frame: the frame in which this element lives. dataModel(src.cython.malandro.DataModel): dataModel object describing the assignment proposed by the algorithm. selectedSolution (int): The index of the solution/run that is used asa the template to make the assignments. resonanceToDimension (bool): True if resonances should be assigned to peak dimensions. False if not. spinSystemToResidue (bool): True if spin system to residue assignment should be carried out. minScore (float): The minimal score of a spin system assignment to a residue to be allowed to transfer this assignment to the project intra (bool): True if intra-residual peaks should be assigned. sequential (bool): True if sequential peaks should be assigned. noDiagonal (bool): If True, purely diagonal peaks are ignored during the transfer of assignments. allSpectra (bool): If True, all spectra will be assigned. If False, one specified spectrum will be assigned. spectrum (src.cython.malandro.Spectrum): The spectrum that should be assigned. ''' 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 # Buttons and fields, # will be set in body(): self.peaksCheckButton = None self.residuesCheckButton = None self.intraCheckButton = None self.sequentialCheckButton = None self.noDiagonalCheckButton = None self.spinSystemTypeSelect = None self.minScoreEntry = None self.solutionNumberEntry = None self.spectrumSelect = None self.spectraPullDown = None self.assignedResidueStrategySelect = None self.transferButton = None # Settings that determine how assignments # are transferred to the analysis project: self.minScore = 80.0 self.dataModel = None self.spectrum = None self.selectedSolution = 1 self.body() self.resonanceToDimension = True self.spinSystemToResidue = True self.intra = True self.sequential = True self.noDiagonal = True self.allSpectra = True self.spinSystemType = 0 self.strategy = 0 def body(self): '''Describes the body of this tab. It consists out of a number of radio buttons, check buttons and number entries that allow the user to indicate which assignments should be transferred. ''' # self.frame.expandColumn(0) self.frame.expandGrid(8, 0) self.frame.expandGrid(8, 1) typeOfAssignmentFrame = LabelFrame(self.frame, text='type of assignment') typeOfAssignmentFrame.grid(row=0, column=0, sticky='nesw') # typeOfAssignmentFrame.expandGrid(0,5) peakSelectionFrame = LabelFrame(self.frame, text='which peaks to assign') peakSelectionFrame.grid(row=0, column=1, sticky='nesw', rowspan=2) spinSystemSelectionFrame = LabelFrame(self.frame, text='Which spin-systems to use') spinSystemSelectionFrame.grid(row=2, column=0, sticky='nesw') tipText = 'What to do when a residue has already a spin system assigned to it.' assignedResidueFrame = LabelFrame( self.frame, text='if residue already has spin-system', tipText=tipText) assignedResidueFrame.grid(row=2, column=1, sticky='nesw') spectrumSelectionFrame = LabelFrame(self.frame, text='spectra') spectrumSelectionFrame.grid(row=1, column=0, sticky='nesw') row = 0 Label(typeOfAssignmentFrame, text='Resonances to Peak Dimensions', grid=(row, 0)) self.peaksCheckButton = CheckButton(typeOfAssignmentFrame, selected=True, grid=(row, 1)) row += 1 Label(typeOfAssignmentFrame, text='SpinSystems to Residues', grid=(row, 0)) self.residuesCheckButton = CheckButton(typeOfAssignmentFrame, selected=True, grid=(row, 1)) row = 0 Label(peakSelectionFrame, text='Intra-Residual', grid=(row, 0)) self.intraCheckButton = CheckButton(peakSelectionFrame, selected=True, grid=(row, 1)) row += 1 Label(peakSelectionFrame, text='Sequential', grid=(row, 0)) self.sequentialCheckButton = CheckButton(peakSelectionFrame, selected=True, grid=(row, 1)) row += 1 Label(peakSelectionFrame, text='Do not assign diagonal peaks', grid=(row, 0)) self.noDiagonalCheckButton = CheckButton(peakSelectionFrame, selected=True, grid=(row, 1)) entries = [ 'Only assigned spin systems', 'All that have a score of at least: ', 'User Defined', 'Solution number:' ] tipTexts = [ 'Only assign resonances of spin systems that already have a sequential assignment for the assignment of peak dimensions. Spin system to residue assignment is not relevant in this case.', 'Assign all spin systems that have a score of at least a given percentage. 50% or lower is not possible, because than spin systems might have to be assigned to more than 1 residue, which is impossible.', "As defined in the lower row of buttons in the 'results' tab.", 'One of the single solutions of the annealing.' ] self.spinSystemTypeSelect = RadioButtons(spinSystemSelectionFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(4, 1), tipTexts=tipTexts) tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.' self.minScoreEntry = FloatEntry(spinSystemSelectionFrame, grid=(1, 1), width=7, text=str(self.minScore), returnCallback=self.changeMinScore, tipText=tipText) self.minScoreEntry.bind('<Leave>', self.changeMinScore, '+') self.solutionNumberEntry = IntEntry(spinSystemSelectionFrame, grid=(3, 1), width=7, text=1, returnCallback=self.solutionUpdate, tipText=tipText) self.solutionNumberEntry.bind('<Leave>', self.solutionUpdate, '+') #self.solutionPullDown = PulldownList(spinSystemSelectionFrame, None, grid=(3,1), sticky='w') entries = ['all spectra', 'only:'] tipTexts = [ 'Assign peaks in all the spectra that where selected before the annealing ran.', 'Only assign peaks in one particular spectrum. You can of course repeat this multiple times for different spectra.' ] self.spectrumSelect = RadioButtons(spectrumSelectionFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(2, 1), tipTexts=tipTexts) self.spectraPullDown = PulldownList(spectrumSelectionFrame, self.changeSpectrum, grid=(1, 1), sticky='w') entries = [ 'skip this residue', 'de-assign old spin system from residue', 'assign, but never merge', 'warn to merge' ] tipTexts = [ "Don't assign the new spin system to the residue. The residue is not skipped when the old spin system does not contain any resonances", "De-assign old spin system from residue, unless the old spin system is a spin system without any resonances.", "Don't merge any spin systems, merging can be performed later if nescesary in the Resonance --> SpinSystems window.", "Ask to merge individually for each spin system, this might result in clicking on a lot of popups." ] self.assignedResidueStrategySelect = RadioButtons(assignedResidueFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(2, 1), tipTexts=tipTexts) texts = ['Transfer Assignments'] commands = [self.transferAssignments] self.transferButton = ButtonList(self.frame, commands=commands, texts=texts) self.transferButton.grid(row=5, column=0, sticky='nsew', columnspan=2) def update(self): '''Update the nescesary elements in the tab. Is called when the algorithm has produced possible assignments. The only thing that has to be updated in practice in this tab is the pulldown with spectra. ''' self.dataModel = self.guiParent.connector.results self.updateSpectra() def setDataModel(self, dataModel): '''Here the dataModel, which is the dataModel containing the suggested assignments body the algorithm, can be set. ''' self.dataModel = dataModel self.update() def updateSpectra(self, *opt): '''Updates the spectra shown in the spectra pulldown. These are only the spectra that were used by the algorithm. All other spectra in the project are not relevant since for those no simulated peaks have been matched to real peaks. ''' if not self.dataModel: return spectrum = self.spectrum spectra = self.dataModel.getSpectra() if spectra: names = [spectrum.name for spectrum in spectra] index = 0 if self.spectrum not in spectra: self.spectrum = spectra[0] else: index = spectra.index(self.spectrum) self.spectraPullDown.setup(names, spectra, index) def changeSpectrum(self, spectrum): '''Select a spectum to be assigned.''' self.spectrum = spectrum def solutionUpdate(self, event=None, value=None): '''Select a solution. A solution is a one to one mapping of spin systems to residues produced by one run of the algorithm. args: event: event object, this is one of the values the number entry calls his callback function with. value: the index of the solution/run. ''' if not self.dataModel: return Nsolutions = len(self.dataModel.chain.residues[0].solutions) if value is None: value = self.solutionNumberEntry.get() if value == self.selectedSolution: return else: self.selectedSolution = value if value < 1: self.solutionNumberEntry.set(1) self.selectedSolution = 1 elif value > Nsolutions: self.selectedSolution = Nsolutions self.solutionNumberEntry.set(self.selectedSolution) else: self.solutionNumberEntry.set(self.selectedSolution) def fetchOptions(self): '''Fetches user set options from the gui in one go and stores them in their corresponding instance variables. ''' self.resonanceToDimension = self.peaksCheckButton.get() self.spinSystemToResidue = self.residuesCheckButton.get() self.intra = self.intraCheckButton.get() self.sequential = self.sequentialCheckButton.get() self.noDiagonal = self.noDiagonalCheckButton.get() self.spinSystemType = self.spinSystemTypeSelect.getIndex() self.strategy = ['skip', 'remove', 'noMerge', None][self.assignedResidueStrategySelect.getIndex()] self.allSpectra = [True, False][self.spectrumSelect.getIndex()] def changeMinScore(self, event=None): '''Set the minimal score for which a spin system to residue assignment gets transferred to the ccpn analysis project. ''' newMinScore = self.minScoreEntry.get() if self.minScore != newMinScore: if newMinScore <= 50.0: self.minScore = 51.0 self.minScoreEntry.set(51.0) elif newMinScore > 100.0: self.minScore = 100.0 self.minScoreEntry.set(100.0) else: self.minScore = newMinScore def transferAssignments(self): '''Transfer assignments to project depending on the settings from the GUI. ''' self.fetchOptions() if not self.dataModel or (not self.resonanceToDimension and not self.spinSystemToResidue): return strategy = self.strategy lookupSpinSystem = [ self.getAssignedSpinSystem, self.getBestScoringSpinSystem, self.getUserDefinedSpinSystem, self.getSelectedSolutionSpinSystem ][self.spinSystemType] residues = self.dataModel.chain.residues spinSystemSequence = [lookupSpinSystem(res) for res in residues] ccpnSpinSystems = [] ccpnResidues = [] # if self.spinSystemType == 0 it means that it for sure already # assigned like this if self.spinSystemToResidue and not self.spinSystemType == 0: for spinSys, res in zip(spinSystemSequence, residues): if spinSys and res: ccpnSpinSystems.append(spinSys.getCcpnResonanceGroup()) ccpnResidues.append(res.getCcpnResidue()) assignSpinSystemstoResidues(ccpnSpinSystems, ccpnResidues, strategy=strategy, guiParent=self.guiParent) if self.resonanceToDimension: allSpectra = self.allSpectra if self.intra: for residue, spinSystem in zip(residues, spinSystemSequence): if not spinSystem: continue intraLink = residue.getIntraLink(spinSystem) for pl in intraLink.getPeakLinks(): peak = pl.getPeak() if not allSpectra and peak.getSpectrum( ) is not self.spectrum: continue if not peak: continue resonances = pl.getResonances() if self.noDiagonal and len( set(resonances)) < len(resonances): continue for resonance, dimension in zip( resonances, peak.getDimensions()): ccpnResonance = resonance.getCcpnResonance() ccpnDimension = dimension.getCcpnDimension() assignResToDim(ccpnDimension, ccpnResonance) if self.sequential: for residue, spinSystemA, spinSystemB in zip( residues, spinSystemSequence, spinSystemSequence[1:]): if not spinSystemA or not spinSystemB: continue link = residue.getLink(spinSystemA, spinSystemB) for pl in link.getPeakLinks(): peak = pl.getPeak() if not allSpectra and peak.getSpectrum( ) is not self.spectrum: continue if not peak: continue resonances = pl.getResonances() if self.noDiagonal and len( set(resonances)) < len(resonances): continue for resonance, dimension in zip( resonances, peak.getDimensions()): ccpnResonance = resonance.getCcpnResonance() ccpnDimension = dimension.getCcpnDimension() assignResToDim(ccpnDimension, ccpnResonance) self.guiParent.resultsTab.update() def getAssignedSpinSystem(self, residue): '''Get the spinSystem that is assigned in the project to a residue. args: residue (src.cython.malandro.Residue) return: spinSystem (src.cython.malandro.SpinSystem) ''' ccpCode = residue.ccpCode seqCode = residue.getSeqCode() spinSystems = self.dataModel.getSpinSystems()[ccpCode] ccpnResidue = residue.getCcpnResidue() if ccpnResidue: assignedResonanceGroups = ccpnResidue.getResonanceGroups() if len(assignedResonanceGroups) > 1: print 'There is more than one spin system assigned to residue %s, did not know which one to use to assign peaks. Therefor this residue is skipped.' % ( seqCode) return assignedResonanceGroup = ccpnResidue.findFirstResonanceGroup() if assignedResonanceGroup: for spinSystem in spinSystems: if spinSystem.getSerial() == assignedResonanceGroup.serial: # Just checking to make sure, analysis project could # have changed if not self.skipResidue(residue, spinSystem): return spinSystem def getBestScoringSpinSystem(self, residue): '''Get the spinSystem that scores the highest, i.e. is assigned in most of the runs to the given residue. args: residue (src.cython.malandro.Residue) return: spinSystem (src.cython.malandro.SpinSystem) ''' solutions = residue.solutions weigth = 1.0 / len(solutions) score, bestSpinSystem = max([ (solutions.count(solution) * weigth * 100.0, solution) for solution in solutions ]) if score >= self.minScore and not bestSpinSystem.getIsJoker( ) and not self.skipResidue(residue, bestSpinSystem): return bestSpinSystem return None def getUserDefinedSpinSystem(self, residue): '''Get the spinSystem that is defined by the user (probably in the resultsTab) as the correct assignment of the given residue. args: residue (src.cython.malandro.Residue) return: spinSystem (src.cython.malandro.SpinSystem) ''' userDefinedSpinSystem = residue.userDefinedSolution if userDefinedSpinSystem and not userDefinedSpinSystem.getIsJoker( ) and not self.skipResidue(residue, userDefinedSpinSystem): return userDefinedSpinSystem return None def getSelectedSolutionSpinSystem(self, residue): '''I a solution corresponding to one specific run of the algorithm is defined, return which spinSystem in that run got assigned to the given residue. args: residue (src.cython.malandro.Residue) return: spinSystem (src.cython.malandro.SpinSystem) ''' solutions = residue.solutions spinSystem = solutions[self.selectedSolution - 1] if not spinSystem.getIsJoker() and not self.skipResidue( residue, spinSystem): return spinSystem return None def skipResidue(self, residue, spinSystem): '''One strategy is to skip all residues that already have a spin system assignment. If that is the case determine whether to skip the given residue. args: residue (src.cython.malandro.Residue) spinSystem (src.cython.malandro.SpinSystem) return: boolean, True if residue should be skipped. ''' if self.strategy == 0: assignedGroups = residue.getCcpnResidue().getResonanceGroups() assignedSerials = set( [spinSys.serial for spinSys in assignedGroups]) if assignedSerials and spinSystem.getSerial( ) not in assignedSerials: return True return False
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 EditPeakFindParamsPopup(BasePopup): """ ** Peak Settings and Non-Interactive Peak Finding ** The purpose of this dialog is to allow the user to select settings for finding and integrating peaks, and also to be able to find peaks in an arbitrary region that is specified in a table rather than via a spectrum window. ** Find Parameters tab ** This can be used to specify how peak finding works. First of all, you can search for just positive peaks, just negative peaks or both, and the default is that it is just positive peaks. However, this is further filtered by what the contour levels are. If there are no positive contour levels for a given spectrum then positive peaks are not found even if this dialog says they can be, and similarly if there are no negative contour levels for a given spectrum then negative peaks are not found even if this dialog says they can be. The peak finding algorithm looks for local extrema (maximum for positive peaks and minima for negative peaks). But on a grid there are various ways to define what you mean by an extremum. Suppose you are trying to determine if point p is a maximum (similar considerations apply for minimum). You would want the intensity at all nearby points to be less than or equal to the intensity at p. You can just check points that are just +- one point from p in each dimension, or you can also check "diagonal" points. For example, if you are looking at point p = (x, y) in 2D, then the former would mean checking the four points (x-1, y), (x+1, y) (x, y-1) and (x, y+1), whereas for the latter you would also have to check (x-1, y-1), (x-1, y+1), (x+1, y-1) and (x+1, y+1). In N dimensions the "diagonal" method involves checking 3^N-1 points whereas the "non-diagonal" method involves checking only 2N points. In general the "non-diagonal" method is probably the one to use, and it is the default. Peaks are only found above (for positive peaks) or below (for negative peaks) some threshold. By default this is determined by the contour level for the spectrum. For positive peaks the threshold is the minimum positive contour level, and for negative peaks the threshold is the maximum negative contour level. However these levels can be scaled up (or down) using the "Scale relative to contour levels" option (default value 1). For example, if you have drawn the contour levels low to show a bit of noise, but do not want the noise picked as peaks, then you could select a scale of 2 (or whatever) to increase the threshold. The "Exclusion buffer around peaks" is so that in crowded regions you do not get too many peaks near one location. By default the exclusion buffer is 1 point in each dimension, but this can be increased to make the algorithm find fewer peaks. By default the peak finding only looks at the orthogonal region that is displayed in the given window where peak finding is taking place. Sometimes it looks like a peak should be found because in x, y you can see an extremum, but unless it is also an extremum in the orthogonal dimensions it is not picked. You can widen out the points being examined in the orthogonal dimensions by using the "Extra thickness in orthogonal dims" option, which is specified in points. The "Minimum drop factor" is by what factor the intensity needs to drop from its extreme value for there to be considered to be a peak. This could help remove sinc wiggle peaks, for example. The default is that the drop factor is 0, which in effect means that there is no condition. The "Volume method" is what is used to estimate the volume of peaks that are found. The default is "box sum", which just looks at a fixed size box around the peak centre and sums the intensities in that. The size of the box is set in the table in the Spectrum Widths tab. The "truncated box sum" is the same as "box sum" except that the summing stops in a given direction when (if) the intensities start increasing. The "parabolic" fit fits a quadratic equation in each dimension to the intensity at the peak centre and ad +- 1 points and then uses the equivalent Gaussian fit to estimate the volume. ** Spectrum Widths ** This can be used to specify minimum linewidths (in Hz) for there to be considered a peak to exist in the peak finding algorithm. It is also where the Boxwidth for each dimension in each spectrum is specified. ** Diagonal Exclusions ** This can be used to exclude peaks from being found in regions near the diagonal (so in homonuclear experiments). The exclusion region is specified in ppm and is independent of spectrum. ** Region Peak Find ** This can be used to find peaks non-interactively (so not having to control shift drag inside a spectrum window). The region being analysed is specified in the table. There are two types of conditions that can be specified, "include" for regions that should be included and "exclude" for regions that should be excluded. The regions are specified in ppm. The "Whole Region" button will set the selected row in the table to be the entire fundamental region of the spectrum. The "Add Region" button adds an extra row to the table, and the "Delete Region" button removes the selected row. The "Adjust Params" button goes to the Find Parameters tab. The "Find Peaks!" button does the peak finding. """ def __init__(self, parent, *args, **kw): self.spectrum = None BasePopup.__init__(self, parent=parent, title='Peak : Peak Finding', **kw) def body(self, guiFrame): self.geometry('600x350') guiFrame.expandGrid(0, 0) tipTexts = ['', '', '', ''] options = [ 'Find Parameters', 'Spectrum Widths', 'Diagonal Exclusions', 'Region Peak Find' ] tabbedFrame = TabbedFrame(guiFrame, options=options, grid=(0, 0)) frameA, frameB, frameC, frameD = tabbedFrame.frames self.tabbedFrame = tabbedFrame # Find Params frameA.expandGrid(2, 0) row = 0 label = LabelFrame(frameA, text='Extrema to search for:', grid=(row, 0), gridSpan=(1, 2)) label.expandGrid(0, 1) entries = ['positive and negative', 'positive only', 'negative only'] tipTexts = [ 'Sets whether peak picking within spectra find intensity maxima, minima or both maxima and minima', ] self.extrema_buttons = RadioButtons(label, entries=entries, select_callback=self.apply, direction='horizontal', grid=(0, 0), tipTexts=tipTexts) row += 1 label = LabelFrame(frameA, text='Nearby points to check:', grid=(row, 0), gridSpan=(1, 2)) label.expandGrid(None, 1) entries = ['+-1 in at most one dim', '+-1 allowed in any dim'] tipTexts = [ 'Sets how permissive the peak picking in when searching for intensity extrema; by adding extra points to the selected search region', ] self.adjacent_buttons = RadioButtons(label, entries=entries, select_callback=self.apply, direction='horizontal', grid=(0, 0), tipTexts=tipTexts) row += 1 labelFrame = LabelFrame(frameA, text='Other parameters:', grid=(row, 0), gridSpan=(1, 2)) labelFrame.expandGrid(5, 2) frow = 0 label = Label(labelFrame, text='Scale relative to contour levels:', grid=(frow, 0), sticky='e') tipText = 'Threshold above which peaks are picked, relative to the lowest displayed contour; 1.0 means picking exactly what is visible' self.scale_entry = FloatEntry(labelFrame, grid=(frow, 1), tipText=tipText, returnCallback=self.apply, width=10) self.scale_entry.bind('<Leave>', self.apply, '+') frow += 1 label = Label(labelFrame, text='Exclusion buffer around peaks (in points):', grid=(frow, 0), sticky='e') tipText = 'The size of the no-pick region, in data points, around existing picked peaks; eliminates duplicate picking' self.buffer_entry = IntEntry(labelFrame, returnCallback=self.apply, grid=(frow, 1), width=10, tipText=tipText) self.buffer_entry.bind('<Leave>', self.apply, '+') frow += 1 label = Label(labelFrame, text='Extra thickness in orthogonal dims (in points):', grid=(frow, 0), sticky='e') tipText = 'Sets whether to consider any additional planes (Z dimension) when calculating peak volume integrals' self.thickness_entry = IntEntry(labelFrame, returnCallback=self.apply, width=10, grid=(frow, 1), tipText=tipText) self.thickness_entry.bind('<Leave>', self.apply, '+') frow += 1 label = Label(labelFrame, text='Minimum drop factor (0.0-1.0):', grid=(frow, 0), sticky='e') tipText = '' self.drop_entry = FloatEntry(labelFrame, returnCallback=self.apply, width=10, grid=(frow, 1), tipText=tipText) self.drop_entry.bind('<Leave>', self.apply, '+') frow += 1 label = Label(labelFrame, text='Volume method:', grid=(frow, 0), sticky='e') tipText = 'Selects which method to use to calculate peak volume integrals when peaks are picked; box sizes are specified in "Spectrum Widths"' self.method_menu = PulldownList(labelFrame, texts=PeakBasic.PEAK_VOLUME_METHODS, grid=(frow, 1), callback=self.apply, tipText=tipText) # Spectrum widths frameB.expandGrid(1, 1) label = Label(frameB, text='Spectrum: ') label.grid(row=0, column=0, sticky='e') tipText = 'The spectrum which determines the widths being shown' self.expt_spectrum = PulldownList(frameB, tipText=tipText, callback=self.setSpectrumProperties) self.expt_spectrum.grid(row=0, column=1, sticky='w') self.editLinewidthEntry = FloatEntry(self, text='', returnCallback=self.setLinewidth, width=10) self.editBoxwidthEntry = FloatEntry(self, text='', returnCallback=self.setBoxwidth, width=10) tipTexts = [ 'The number of the spectrum dimension to which the settings apply', 'The nuclear isotope measures in the spectrum dimension', 'The smallest value for the linewidth of a peak for it to be picked', 'The size of the spectrum region to perform the volume integral over' ] headingList = [ 'Dimension', 'Isotope', 'Minimum Linewidth (Hz)', 'Boxwidth' ] editSetCallbacks = [None, None, self.setLinewidth, self.setBoxwidth] editGetCallbacks = [None, None, self.getLinewidth, self.getBoxwidth] editWidgets = [ None, None, self.editLinewidthEntry, self.editBoxwidthEntry ] self.spectrumMatrix = ScrolledMatrix(frameB, initialRows=6, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, headingList=headingList, callback=self.selectCell, tipTexts=tipTexts) self.spectrumMatrix.grid(row=1, column=0, columnspan=2, sticky='nsew') # Diagonal Exclusions frameC.expandGrid(0, 0) tipTexts = [ 'The isotope as measures on the axis of a spectrum window', 'The distance from the homonuclear diagonal line within which no peak picking can occur' ] self.exclusionEntry = FloatEntry(self, text='', returnCallback=self.setExclusion, width=10) headingList = ['Isotope', 'Diagonal Exclusion (ppm)'] editSetCallbacks = [None, self.setExclusion] editGetCallbacks = [None, self.getExclusion] editWidgets = [None, self.exclusionEntry] self.isotopeMatrix = ScrolledMatrix(frameC, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, headingList=headingList, grid=(0, 0), tipTexts=tipTexts) # Region peak find self.regionFindPeakList = None self.regionCondition = None self.regionConditions = [] self.regionCol = 1 row = 0 label = Label(frameD, text='Peak List: ', grid=(0, 0)) tipText = 'Selects which peak list to perform region-wide peak picking for' self.regionPeakListPulldown = PulldownList( frameD, callback=self.changeRegionPeakList, grid=(0, 1), tipText=tipText) row += 1 frameD.expandGrid(row, 1) self.regionEntry = FloatEntry(self, text='', returnCallback=self.setRegion, width=10) self.conditionMenu = PulldownList(self, texts=('include', 'exclude'), callback=self.setCondition) tipTexts = [ 'Whether to include or exclude the states region from region-wide peak picking', ] headingList = ['Condition'] editSetCallbacks = [None] editGetCallbacks = [None] editWidgets = [self.conditionMenu] self.regionFindMatrix = ScrolledMatrix( frameD, headingList=headingList, callback=self.selectRegionCell, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, grid=(row, 0), gridSpan=(1, 2)) row += 1 tipTexts = [ 'Sets the currently selected region row to cover the whole spectrum', 'Add a new region row, which may them be set for exclusion or inclusion when peak picking large areas', 'Remove the selected region specification', 'Go to the panel for setting the parameters that control how peaks extrema are picked', 'Using the stated regions and parameters, perform region-wide peak picking' ] texts = [ 'Whole Region', 'Add Region', 'Delete Region', 'Adjust Params', 'Find Peaks!' ] commands = [ self.wholeRegion, self.addCondition, self.deleteCondition, self.adjustParams, self.regionFindPeaks ] buttons = ButtonList(frameD, texts=texts, commands=commands, grid=(row, 0), gridSpan=(1, 2), tipTexts=tipTexts) buttons.buttons[4].config(bg='#B0FFB0') utilButtons = UtilityButtonList(tabbedFrame.sideFrame, grid=(0, 0), helpUrl=self.help_url, sticky='e') self.dataDim = None self.setParamsEntries() self.updateSpectrum() self.setIsotopeProperties() self.updateRegionPeakLists() self.administerNotifiers(self.registerNotify) def administerNotifiers(self, notifyFunc): # Many more needed here, esp on the AnalysisProject prams for func in ('__init__', 'delete', 'setName'): notifyFunc(self.updateRegionPeakLists, 'ccp.nmr.Nmr.DataSource', func) notifyFunc(self.updateRegionPeakLists, 'ccp.nmr.Nmr.Experiment', func) for func in ('__init__', 'delete'): notifyFunc(self.updateRegionPeakLists, 'ccp.nmr.Nmr.PeakList', func) for clazz in ('Experiment', 'DataSource'): for func in ('__init__', 'delete', 'setName'): notifyFunc(self.updateSpectrumTable, 'ccp.nmr.Nmr.%s' % clazz, func) for func in ('setPeakFindBoxWidth', 'setPeakFindMinLineWidth'): notifyFunc(self.updateSpectrumTable, 'ccpnmr.Analysis.AnalysisDataDim', func) def destroy(self): self.administerNotifiers(self.unregisterNotify) BasePopup.destroy(self) def updateSpectrum(self, spectrum=None): if not spectrum: spectrum = self.spectrum spectra = self.parent.getSpectra() if spectra: if spectrum not in spectra: spectrum = spectra[0] index = spectra.index(spectrum) names = ['%s:%s' % (x.experiment.name, x.name) for x in spectra] else: index = 0 names = [] self.expt_spectrum.setup(names, spectra, index) self.setSpectrumProperties(spectrum) def updateNotifier(self, *extra): self.updateSpectrum() def setLinewidth(self, *event): value = self.editLinewidthEntry.get() if value is not None: PeakFindParams.setPeakFindMinLinewidth(self.dataDim, value) self.setSpectrumProperties(self.dataDim.dataSource) def getLinewidth(self, dataDim): if dataDim: self.editLinewidthEntry.set( PeakFindParams.getPeakFindMinLinewidth(self.dataDim)) def setBoxwidth(self, *event): value = self.editBoxwidthEntry.get() if value is not None: PeakFindParams.setPeakFindBoxwidth(self.dataDim, value) self.setSpectrumProperties(self.dataDim.dataSource) def getBoxwidth(self, dataDim): if dataDim: self.editBoxwidthEntry.set( PeakFindParams.getPeakFindBoxwidth(self.dataDim)) def selectCell(self, object, row, col): self.dataDim = object def setExclusion(self, *extra): isotope = self.isotopeMatrix.currentObject if not isotope: return value = self.exclusionEntry.get() if value is not None: setIsotopeExclusion(isotope, value) self.setIsotopeProperties() def getExclusion(self, isotope): value = getIsotopeExclusion(isotope) self.exclusionEntry.set(value) def setParamsEntries(self): project = self.project params = PeakFindParams.getPeakFindParams(project) self.scale_entry.set(params['scale']) self.buffer_entry.set(params['buffer']) self.thickness_entry.set(params['thickness']) self.drop_entry.set(params['drop']) volumeMethod = params['volumeMethod'] if volumeMethod == 'parabolic fit': volumeMethod = PeakBasic.PEAK_VOLUME_METHODS[0] self.method_menu.set(params['volumeMethod']) if (params['nonadjacent']): n = 1 else: n = 0 self.adjacent_buttons.setIndex(n) have_high = params['haveHigh'] have_low = params['haveLow'] if (have_high and have_low): n = 0 elif (have_high): n = 1 else: n = 2 self.extrema_buttons.setIndex(n) def apply(self, *extra): params = {} params['scale'] = self.scale_entry.get() params['buffer'] = self.buffer_entry.get() params['thickness'] = self.thickness_entry.get() params['drop'] = self.drop_entry.get() params['volumeMethod'] = self.method_menu.getText() n = self.adjacent_buttons.getIndex() if (n == 0): nonadjacent = False else: nonadjacent = True params['nonadjacent'] = nonadjacent n = self.extrema_buttons.getIndex() if (n == 0): have_high = True have_low = True elif (n == 1): have_high = True have_low = False elif (n == 2): have_high = False have_low = True params['haveHigh'] = have_high params['haveLow'] = have_low project = self.project try: PeakFindParams.setPeakFindParams(project, params) except Implementation.ApiError, e: showError('Parameter error', e.error_msg, parent=self)
def body(self): '''Describes the body of this tab. It consists out of a number of radio buttons, check buttons and number entries that allow the user to indicate which assignments should be transferred. ''' # self.frame.expandColumn(0) self.frame.expandGrid(8, 0) self.frame.expandGrid(8, 1) typeOfAssignmentFrame = LabelFrame(self.frame, text='type of assignment') typeOfAssignmentFrame.grid(row=0, column=0, sticky='nesw') # typeOfAssignmentFrame.expandGrid(0,5) peakSelectionFrame = LabelFrame(self.frame, text='which peaks to assign') peakSelectionFrame.grid(row=0, column=1, sticky='nesw', rowspan=2) spinSystemSelectionFrame = LabelFrame(self.frame, text='Which spin-systems to use') spinSystemSelectionFrame.grid(row=2, column=0, sticky='nesw') tipText = 'What to do when a residue has already a spin system assigned to it.' assignedResidueFrame = LabelFrame( self.frame, text='if residue already has spin-system', tipText=tipText) assignedResidueFrame.grid(row=2, column=1, sticky='nesw') spectrumSelectionFrame = LabelFrame(self.frame, text='spectra') spectrumSelectionFrame.grid(row=1, column=0, sticky='nesw') row = 0 Label(typeOfAssignmentFrame, text='Resonances to Peak Dimensions', grid=(row, 0)) self.peaksCheckButton = CheckButton(typeOfAssignmentFrame, selected=True, grid=(row, 1)) row += 1 Label(typeOfAssignmentFrame, text='SpinSystems to Residues', grid=(row, 0)) self.residuesCheckButton = CheckButton(typeOfAssignmentFrame, selected=True, grid=(row, 1)) row = 0 Label(peakSelectionFrame, text='Intra-Residual', grid=(row, 0)) self.intraCheckButton = CheckButton(peakSelectionFrame, selected=True, grid=(row, 1)) row += 1 Label(peakSelectionFrame, text='Sequential', grid=(row, 0)) self.sequentialCheckButton = CheckButton(peakSelectionFrame, selected=True, grid=(row, 1)) row += 1 Label(peakSelectionFrame, text='Do not assign diagonal peaks', grid=(row, 0)) self.noDiagonalCheckButton = CheckButton(peakSelectionFrame, selected=True, grid=(row, 1)) entries = [ 'Only assigned spin systems', 'All that have a score of at least: ', 'User Defined', 'Solution number:' ] tipTexts = [ 'Only assign resonances of spin systems that already have a sequential assignment for the assignment of peak dimensions. Spin system to residue assignment is not relevant in this case.', 'Assign all spin systems that have a score of at least a given percentage. 50% or lower is not possible, because than spin systems might have to be assigned to more than 1 residue, which is impossible.', "As defined in the lower row of buttons in the 'results' tab.", 'One of the single solutions of the annealing.' ] self.spinSystemTypeSelect = RadioButtons(spinSystemSelectionFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(4, 1), tipTexts=tipTexts) tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.' self.minScoreEntry = FloatEntry(spinSystemSelectionFrame, grid=(1, 1), width=7, text=str(self.minScore), returnCallback=self.changeMinScore, tipText=tipText) self.minScoreEntry.bind('<Leave>', self.changeMinScore, '+') self.solutionNumberEntry = IntEntry(spinSystemSelectionFrame, grid=(3, 1), width=7, text=1, returnCallback=self.solutionUpdate, tipText=tipText) self.solutionNumberEntry.bind('<Leave>', self.solutionUpdate, '+') #self.solutionPullDown = PulldownList(spinSystemSelectionFrame, None, grid=(3,1), sticky='w') entries = ['all spectra', 'only:'] tipTexts = [ 'Assign peaks in all the spectra that where selected before the annealing ran.', 'Only assign peaks in one particular spectrum. You can of course repeat this multiple times for different spectra.' ] self.spectrumSelect = RadioButtons(spectrumSelectionFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(2, 1), tipTexts=tipTexts) self.spectraPullDown = PulldownList(spectrumSelectionFrame, self.changeSpectrum, grid=(1, 1), sticky='w') entries = [ 'skip this residue', 'de-assign old spin system from residue', 'assign, but never merge', 'warn to merge' ] tipTexts = [ "Don't assign the new spin system to the residue. The residue is not skipped when the old spin system does not contain any resonances", "De-assign old spin system from residue, unless the old spin system is a spin system without any resonances.", "Don't merge any spin systems, merging can be performed later if nescesary in the Resonance --> SpinSystems window.", "Ask to merge individually for each spin system, this might result in clicking on a lot of popups." ] self.assignedResidueStrategySelect = RadioButtons(assignedResidueFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(2, 1), tipTexts=tipTexts) texts = ['Transfer Assignments'] commands = [self.transferAssignments] self.transferButton = ButtonList(self.frame, commands=commands, texts=texts) self.transferButton.grid(row=5, column=0, sticky='nsew', columnspan=2)
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 body(self, guiFrame): self.geometry('600x350') guiFrame.expandGrid(0, 0) tipTexts = ['', '', '', ''] options = [ 'Find Parameters', 'Spectrum Widths', 'Diagonal Exclusions', 'Region Peak Find' ] tabbedFrame = TabbedFrame(guiFrame, options=options, grid=(0, 0)) frameA, frameB, frameC, frameD = tabbedFrame.frames self.tabbedFrame = tabbedFrame # Find Params frameA.expandGrid(2, 0) row = 0 label = LabelFrame(frameA, text='Extrema to search for:', grid=(row, 0), gridSpan=(1, 2)) label.expandGrid(0, 1) entries = ['positive and negative', 'positive only', 'negative only'] tipTexts = [ 'Sets whether peak picking within spectra find intensity maxima, minima or both maxima and minima', ] self.extrema_buttons = RadioButtons(label, entries=entries, select_callback=self.apply, direction='horizontal', grid=(0, 0), tipTexts=tipTexts) row += 1 label = LabelFrame(frameA, text='Nearby points to check:', grid=(row, 0), gridSpan=(1, 2)) label.expandGrid(None, 1) entries = ['+-1 in at most one dim', '+-1 allowed in any dim'] tipTexts = [ 'Sets how permissive the peak picking in when searching for intensity extrema; by adding extra points to the selected search region', ] self.adjacent_buttons = RadioButtons(label, entries=entries, select_callback=self.apply, direction='horizontal', grid=(0, 0), tipTexts=tipTexts) row += 1 labelFrame = LabelFrame(frameA, text='Other parameters:', grid=(row, 0), gridSpan=(1, 2)) labelFrame.expandGrid(5, 2) frow = 0 label = Label(labelFrame, text='Scale relative to contour levels:', grid=(frow, 0), sticky='e') tipText = 'Threshold above which peaks are picked, relative to the lowest displayed contour; 1.0 means picking exactly what is visible' self.scale_entry = FloatEntry(labelFrame, grid=(frow, 1), tipText=tipText, returnCallback=self.apply, width=10) self.scale_entry.bind('<Leave>', self.apply, '+') frow += 1 label = Label(labelFrame, text='Exclusion buffer around peaks (in points):', grid=(frow, 0), sticky='e') tipText = 'The size of the no-pick region, in data points, around existing picked peaks; eliminates duplicate picking' self.buffer_entry = IntEntry(labelFrame, returnCallback=self.apply, grid=(frow, 1), width=10, tipText=tipText) self.buffer_entry.bind('<Leave>', self.apply, '+') frow += 1 label = Label(labelFrame, text='Extra thickness in orthogonal dims (in points):', grid=(frow, 0), sticky='e') tipText = 'Sets whether to consider any additional planes (Z dimension) when calculating peak volume integrals' self.thickness_entry = IntEntry(labelFrame, returnCallback=self.apply, width=10, grid=(frow, 1), tipText=tipText) self.thickness_entry.bind('<Leave>', self.apply, '+') frow += 1 label = Label(labelFrame, text='Minimum drop factor (0.0-1.0):', grid=(frow, 0), sticky='e') tipText = '' self.drop_entry = FloatEntry(labelFrame, returnCallback=self.apply, width=10, grid=(frow, 1), tipText=tipText) self.drop_entry.bind('<Leave>', self.apply, '+') frow += 1 label = Label(labelFrame, text='Volume method:', grid=(frow, 0), sticky='e') tipText = 'Selects which method to use to calculate peak volume integrals when peaks are picked; box sizes are specified in "Spectrum Widths"' self.method_menu = PulldownList(labelFrame, texts=PeakBasic.PEAK_VOLUME_METHODS, grid=(frow, 1), callback=self.apply, tipText=tipText) # Spectrum widths frameB.expandGrid(1, 1) label = Label(frameB, text='Spectrum: ') label.grid(row=0, column=0, sticky='e') tipText = 'The spectrum which determines the widths being shown' self.expt_spectrum = PulldownList(frameB, tipText=tipText, callback=self.setSpectrumProperties) self.expt_spectrum.grid(row=0, column=1, sticky='w') self.editLinewidthEntry = FloatEntry(self, text='', returnCallback=self.setLinewidth, width=10) self.editBoxwidthEntry = FloatEntry(self, text='', returnCallback=self.setBoxwidth, width=10) tipTexts = [ 'The number of the spectrum dimension to which the settings apply', 'The nuclear isotope measures in the spectrum dimension', 'The smallest value for the linewidth of a peak for it to be picked', 'The size of the spectrum region to perform the volume integral over' ] headingList = [ 'Dimension', 'Isotope', 'Minimum Linewidth (Hz)', 'Boxwidth' ] editSetCallbacks = [None, None, self.setLinewidth, self.setBoxwidth] editGetCallbacks = [None, None, self.getLinewidth, self.getBoxwidth] editWidgets = [ None, None, self.editLinewidthEntry, self.editBoxwidthEntry ] self.spectrumMatrix = ScrolledMatrix(frameB, initialRows=6, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, headingList=headingList, callback=self.selectCell, tipTexts=tipTexts) self.spectrumMatrix.grid(row=1, column=0, columnspan=2, sticky='nsew') # Diagonal Exclusions frameC.expandGrid(0, 0) tipTexts = [ 'The isotope as measures on the axis of a spectrum window', 'The distance from the homonuclear diagonal line within which no peak picking can occur' ] self.exclusionEntry = FloatEntry(self, text='', returnCallback=self.setExclusion, width=10) headingList = ['Isotope', 'Diagonal Exclusion (ppm)'] editSetCallbacks = [None, self.setExclusion] editGetCallbacks = [None, self.getExclusion] editWidgets = [None, self.exclusionEntry] self.isotopeMatrix = ScrolledMatrix(frameC, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, headingList=headingList, grid=(0, 0), tipTexts=tipTexts) # Region peak find self.regionFindPeakList = None self.regionCondition = None self.regionConditions = [] self.regionCol = 1 row = 0 label = Label(frameD, text='Peak List: ', grid=(0, 0)) tipText = 'Selects which peak list to perform region-wide peak picking for' self.regionPeakListPulldown = PulldownList( frameD, callback=self.changeRegionPeakList, grid=(0, 1), tipText=tipText) row += 1 frameD.expandGrid(row, 1) self.regionEntry = FloatEntry(self, text='', returnCallback=self.setRegion, width=10) self.conditionMenu = PulldownList(self, texts=('include', 'exclude'), callback=self.setCondition) tipTexts = [ 'Whether to include or exclude the states region from region-wide peak picking', ] headingList = ['Condition'] editSetCallbacks = [None] editGetCallbacks = [None] editWidgets = [self.conditionMenu] self.regionFindMatrix = ScrolledMatrix( frameD, headingList=headingList, callback=self.selectRegionCell, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, grid=(row, 0), gridSpan=(1, 2)) row += 1 tipTexts = [ 'Sets the currently selected region row to cover the whole spectrum', 'Add a new region row, which may them be set for exclusion or inclusion when peak picking large areas', 'Remove the selected region specification', 'Go to the panel for setting the parameters that control how peaks extrema are picked', 'Using the stated regions and parameters, perform region-wide peak picking' ] texts = [ 'Whole Region', 'Add Region', 'Delete Region', 'Adjust Params', 'Find Peaks!' ] commands = [ self.wholeRegion, self.addCondition, self.deleteCondition, self.adjustParams, self.regionFindPeaks ] buttons = ButtonList(frameD, texts=texts, commands=commands, grid=(row, 0), gridSpan=(1, 2), tipTexts=tipTexts) buttons.buttons[4].config(bg='#B0FFB0') utilButtons = UtilityButtonList(tabbedFrame.sideFrame, grid=(0, 0), helpUrl=self.help_url, sticky='e') self.dataDim = None self.setParamsEntries() self.updateSpectrum() self.setIsotopeProperties() self.updateRegionPeakLists() self.administerNotifiers(self.registerNotify)
class EditSymmetryPopup(BasePopup): def __init__(self, parent, project): self.parent = parent self.ccpnProject = project self.hProject = project.currentHaddockProject self.molPartner = None self.molecules = [] self.symmetrySet = None self.symmetryOp = None self.symmetryCode = None self.waiting = False BasePopup.__init__(self, parent=parent, title='Symmetry Operations') self.font = 'Helvetica 12' self.setFont() def body(self, guiFrame): guiFrame.grid_columnconfigure(0, weight=1) guiFrame.grid_rowconfigure(1, weight=1) frame = LabelFrame(guiFrame, text='Options') frame.grid(row=0,column=0,sticky='ew') frame.grid_columnconfigure(5, weight=1) # Choose type of symmetry set to define or change (if allready present in the model) self.molLabel = Label(frame, text='Symmetry Operator:') self.molLabel.grid(row=0,column=2,sticky='w') self.symmCodePulldown = PulldownMenu(frame, callback=self.setSymmCode, entries=['NCS','C2','C3','C5'], do_initial_callback=False) self.symmCodePulldown.grid(row=0,column=3,sticky='w') frame = LabelFrame(guiFrame, text='Symmetry Operations') frame.grid(row=1,column=0,sticky='nsew') frame.grid_columnconfigure(0, weight=1) frame.grid_rowconfigure(0, weight=1) self.molSysPulldown = PulldownMenu(self, callback=self.setMolSystem, do_initial_callback=False) self.chainSelect = MultiWidget(self, CheckButton, callback=self.setChains, minRows=0, useImages=False) self.segStartEntry = IntEntry(self, returnCallback=self.setSegStart, width=6) self.segLengthEntry = IntEntry(self, returnCallback=self.setSegLength, width=6) headings = ['#','Symmetry\noperator','Mol System','Chains','Start\nresidue','Segment\nlength'] editWidgets = [None, None, self.molSysPulldown, self.chainSelect, self.segStartEntry, self.segLengthEntry] editGetCallbacks = [None, None, self.getMolSystem, self.getChains, self.getSegStart, self.getSegLength] editSetCallbacks = [None, self.setSymmCode, self.setMolSystem, self.setChains, self.setSegStart, self.setSegLength] self.symmetryMatrix = ScrolledMatrix(frame,headingList=headings, callback=self.selectSymmetry, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks) self.symmetryMatrix.grid(row=0,column=0,sticky='nsew') texts = ['Add Symmetry Set','Remove Symmetry Set'] commands = [self.addSymmetrySet,self.removeSymmetrySet] self.buttonList = createDismissHelpButtonList(guiFrame, texts=texts, commands=commands, expands=True) self.buttonList.grid(row=2,column=0,sticky='ew') self.updateMolPartners() self.notify(self.registerNotify) #Temporary report of parameters print self.molSystem print self.molecules print self.symmetrySet print self.symmetryOp print self.symmetryCode def getMolSystem(self, partner): """Select molecular system from list of molsystems stored in the project""" names = []; index = -1 molSystem = partner.molSystem molSystems = self.ccpnProject.sortedMolSystems() if molSystems: names = [ms.code for ms in molSystems] if molSystem not in molSystems: molSystem = molSystems[0] index = molSystems.index(molSystem) self.molSysPulldown.setup(names, index) def getChains(self, partner): names = [] values = [] molSystem = partner.molSystem if molSystem: for chain in molSystem.sortedChains(): names.append(chain.code) if not partner.chains: values.append(True) elif partner.findFirstChain(chain=chain): values.append(True) else: values.append(False) self.chainSelect.set(values=values,options=names) else: showWarning('Warning','Set Mol System or ensemble first',parent=self) self.symmetryMatrix.keyPressEscape() def getSegLength(self, symmetryOp): if symmetryOp and symmetryOp.segmentLength: self.segLengthEntry.set(symmetryOp.segmentLength) def getSegStart(self): pass def setMolSystem(self, partner, name=None): """Get all molsystems as stored in the project as list""" index = self.molSysPulldown.getSelectedIndex() molSystems = self.ccpnProject.sortedMolSystems() if molSystems: molSystem = molSystems[index] self.molPartner.molSystem = molSystem chains = molSystem.sortedChains() if (not self.molPartner.chains) and chains: setPartnerChains(self.molPartner,chains) self.updateAllAfter() def setChains(self, obj): """Get the list of chains for the selected molsystem""" if self.molPartner and self.molPartner.molSystem: if obj is not None: chains = self.molPartner.molSystem.sortedChains() values = self.chainSelect.get() chains = [chains[i] for i in range(len(values)) if values[i]] setPartnerChains(self.molPartner,chains) self.symmetryMatrix.keyPressEscape() self.updateAllAfter() def setSegLength(self, event): value = self.segLengthEntry.get() or 1 self.symmetryOp.segmentLength = value def setSegStart(self): pass def setSymmCode(self, index, name=None): self.symmetryCode = self.symmCodePulldown.getSelected() def selectSymmetry(self, obj, row, col): self.symmetryOp = obj self.updateMolSysPulldown() def notify(self, notifyFunc): for func in ('__init__', 'delete', 'setSymmetryCode','setSegmentLength'): notifyFunc(self.updateAllAfter, 'molsim.Symmetry.Symmetry', func) for func in ('__init__', 'delete','setfirstSeqId'): notifyFunc(self.updateAllAfter, 'molsim.Symmetry.Segment', func) def addSymmetrySet(self): if not self.ccpnProject.molSystems: showWarning('Warning','No molecular systems present in CCPN project',parent=self) return molSystem = self.ccpnProject.findFirstMolSystem() partner = self.hProject.newHaddockPartner(code=molSystem.code, molSystem=molSystem) setPartnerChains(partner, molSystem.chains) self.updateAllAfter() def removeSymmetrySet(self): pass def updateAllAfter(self, obj=None): if self.waiting: return else: self.waiting = True self.after_idle(self.updateSymmetries, self.updateMolPartners) def updateMolPartners(self): textMatrix = [] objectList = [] for partner in self.hProject.sortedHaddockPartners(): datum = [partner.code, self.symmetryCode, partner.molSystem.code, ','.join([c.chain.code for c in partner.chains]), partner.autoHistidinePstate and 'Yes' or 'No', partner.isDna and 'Yes' or 'No'] objectList.append(partner) textMatrix.append(datum) self.symmetryMatrix.update(objectList=objectList, textMatrix=textMatrix) self.updateMolSysPulldown() def updateMolSysPulldown(self): names = [] index = -1 partners = self.hProject.sortedHaddockPartners() if partners: if self.molPartner not in partners: self.molPartner = partners[0] names = ['Partner %s' % p.code for p in partners] index = partners.index(self.molPartner) else: self.molPartner = None self.molSysPulldown.setup(names, index) def updateSymmetries(self): textMatrix = []; objectList = [] if self.symmetrySet: for symmetryOp in self.symmetrySet.symmetries: chains = []; segments = [] length = symmetryOp.segmentLength for segment in symmetryOp.sortedSegments(): code = segment.chainCode chain = self.molSystem.findFirstChain(code=code) if chain: chains.append(code) seqId = segment.firstSeqId residue1 = chain.findFirstResidue(seqId=seqId) residue2 = chain.findFirstResidue(seqId=seqId+length-1) segments.append('%s:%d-%d' % (code,residue1.seqCode,residue2.seqCode)) datum = [symmetryOp.serial, symmetryOp.symmetryCode, length, '\n'.join(chains), '\n'.join(segments)] objectList.append(symmetryOp) textMatrix.append(datum) self.symmetryMatrix.update(objectList=objectList, textMatrix=textMatrix) self.waiting = False def destroy(self): self.notify(self.unregisterNotify) BasePopup.destroy(self)
def body(self, mainFrame): mainFrame.grid_columnconfigure(1, weight=1, minsize=100) mainFrame.config(borderwidth=5, relief='solid') row = 0 label = Label(mainFrame, text="Frame (with sub-widgets):") label.grid(row=row, column=0, sticky=Tkinter.E) frame = Frame(mainFrame, relief='raised', border=2, background='#8080D0') # Frame expands East-West frame.grid(row=row, column=1, sticky=Tkinter.EW) # Last column expands => Widgets pusted to the West frame.grid_columnconfigure(3, weight=1) # Label is within the sub frame label = Label(frame, text='label ') label.grid(row=0, column=0, sticky=Tkinter.W) entry = Entry(frame, text='Entry', returnCallback=self.showWarning) entry.grid(row=0, column=1, sticky=Tkinter.W) self.check = CheckButton(frame, text='Checkbutton', selected=True, callback=self.updateObjects) self.check.grid(row=0, column=2, sticky=Tkinter.W) # stick a button to the East wall button = Button(frame, text='Button', command=self.pressButton) button.grid(row=0, column=3, sticky=Tkinter.E) row += 1 label = Label(mainFrame, text="Text:") label.grid(row=row, column=0, sticky=Tkinter.E) self.textWindow = Text(mainFrame, text='Initial Text\n', width=60, height=5) self.textWindow.grid(row=row, column=1, sticky=Tkinter.NSEW) row += 1 label = Label(mainFrame, text="CheckButtons:") label.grid(row=row, column=0, sticky=Tkinter.E) entries = ['Alpha','Beta','Gamma','Delta'] selected = entries[2:] self.checkButtons = CheckButtons(mainFrame, entries, selected=selected,select_callback=self.changedCheckButtons) self.checkButtons.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="PartitionedSelector:") label.grid(row=row, column=0, sticky=Tkinter.E) labels = ['Bool','Int','Float','String'] objects = [type(0),type(1),type(1.0),type('a')] selected = [type('a')] self.partitionedSelector= PartitionedSelector(mainFrame, labels=labels, objects=objects, colors = ['red','yellow','green','#000080'], callback=self.toggleSelector,selected=selected) self.partitionedSelector.grid(row=row, column=1, sticky=Tkinter.EW) row += 1 label = Label(mainFrame, text="PulldownMenu") label.grid(row=row, column=0, sticky=Tkinter.E) entries = ['Frodo','Pipin','Merry','Sam','Bill','Gandalf','Strider','Gimli','Legolas'] self.pulldownMenu = PulldownMenu(mainFrame, callback=self.selectPulldown, entries=entries, selected_index=2, do_initial_callback=False) self.pulldownMenu.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="RadioButtons in a\nScrolledFrame.frame:") label.grid(row=row, column=0, sticky=Tkinter.EW) frame = ScrolledFrame(mainFrame, yscroll = False, doExtraConfig = True, width=100) frame.grid(row=row, column=1, sticky=Tkinter.EW) frame.grid_columnconfigure(0, weight=1) self.radioButtons = RadioButtons(frame.frame, entries=entries, select_callback=self.checkRadioButtons, selected_index=1, relief='groove') self.radioButtons.grid(row=0, column=0, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="LabelFrame with\nToggleLabels inside:") label.grid(row=row, column=0, sticky=Tkinter.E) labelFrame = LabelFrame(mainFrame, text='Frame Title') labelFrame.grid(row=row, column=1, sticky=Tkinter.NSEW) labelFrame.grid_rowconfigure(0, weight=1) labelFrame.grid_columnconfigure(3, weight=1) self.toggleLabel1 = ToggleLabel(labelFrame, text='ScrolledMatrix', callback=self.toggleFrame1) self.toggleLabel1.grid(row=0, column=0, sticky=Tkinter.W) self.toggleLabel1.arrowOn() self.toggleLabel2 = ToggleLabel(labelFrame, text='ScrolledGraph', callback=self.toggleFrame2) self.toggleLabel2.grid(row=0, column=1, sticky=Tkinter.W) self.toggleLabel3 = ToggleLabel(labelFrame, text='ScrolledCanvas', callback=self.toggleFrame3) self.toggleLabel3.grid(row=0, column=2, sticky=Tkinter.W) row += 1 mainFrame.grid_rowconfigure(row, weight=1) label = Label(mainFrame, text="changing/shrinking frames:") label.grid(row=row, column=0, sticky=Tkinter.E) self.toggleRow = row self.toggleFrame = Frame(mainFrame) self.toggleFrame.grid(row=row, column=1, sticky=Tkinter.NSEW) self.toggleFrame.grid_rowconfigure(0, weight=1) self.toggleFrame.grid_columnconfigure(0, weight=1) # option 1 self.intEntry = IntEntry(self, returnCallback = self.setNumber, width=8) self.multiWidget = MultiWidget(self, Entry, options=None, values=None, callback=self.setKeywords, minRows=3, maxRows=5) editWidgets = [None, None, self.intEntry, self.multiWidget] editGetCallbacks = [None, None, self.getNumber, self.getKeywords] editSetCallbacks = [None, None, self.setNumber, self.setKeywords] headingList = ['Name','Color','Number','Keywords'] self.scrolledMatrix = ScrolledMatrix(self.toggleFrame, headingList=headingList, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, callback=self.selectObject, multiSelect=False) self.scrolledMatrix.grid(row=0, column=0, sticky=Tkinter.NSEW) # option 2 self.scrolledGraph = ScrolledGraph(self.toggleFrame, width=400, height=300, symbolSize=5, symbols=['square','circle'], dataColors=['#000080','#800000'], lineWidths=[0,1] ) self.scrolledGraph.setZoom(1.3) dataSet1 = [[0,0],[1,1],[2,4],[3,9],[4,16],[5,25]] dataSet2 = [[0,0],[1,3],[2,6],[3,9],[4,12],[5,15]] self.scrolledGraph.update(dataSets=[dataSet1,dataSet2], xLabel = 'X axis label', yLabel = 'Y axis label', title = 'Main Title') self.scrolledGraph.draw() # option 3 self.scrolledCanvas = ScrolledCanvas(self.toggleFrame,relief = 'groove', borderwidth = 2, resizeCallback=None) canvas = self.scrolledCanvas.canvas font = 'Helvetica 10' box = canvas.create_rectangle(10,10,150,200, outline='grey', fill='grey90') line = canvas.create_line(0,0,200,200,fill='#800000', width=2) text = canvas.create_text(120,50, text='Text', font=font, fill='black') circle = canvas.create_oval(30,30,50,50,outline='#008000',fill='#404040',width=3) row += 1 label = Label(mainFrame, text="FloatEntry:") label.grid(row=row, column=0, sticky=Tkinter.E) self.floatEntry = FloatEntry(mainFrame, text=3.14159265, returnCallback=self.floatEntryReturn) self.floatEntry.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="Scale:") label.grid(row=row, column=0, sticky=Tkinter.E) self.scale = Scale(mainFrame, from_=10, to=90, value=50, orient=Tkinter.HORIZONTAL) self.scale.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="Value Ramp:") label.grid(row=row, column=0, sticky=Tkinter.E) self.valueRamp = ValueRamp(mainFrame, self.valueRampCallback, speed = 1.5, delay = 50) self.valueRamp.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="ButtonList:") label.grid(row=row, column=0, sticky=Tkinter.E) texts = ['Select File','Close','Quit'] commands = [self.selectFile, self.close, self.quit] bottomButtons = ButtonList(mainFrame, texts=texts, commands=commands, expands=True) bottomButtons.grid(row=row, column=1, sticky=Tkinter.EW) self.protocol('WM_DELETE_WINDOW', self.quit)
def body(self, guiFrame): self.geometry('450x500') guiFrame.grid_rowconfigure(0, weight=1) guiFrame.grid_columnconfigure(0, weight=1) options = ['Peak Separator', 'Advanced Settings'] tabbedFrame = TabbedFrame(guiFrame, options=options) tabbedFrame.grid(row=0, column=0, sticky='nsew') buttons = UtilityButtonList(tabbedFrame.sideFrame, helpUrl=self.help_url) buttons.grid(row=0, column=0, sticky='e') self.tabbedFrame = tabbedFrame frameA, frameB = tabbedFrame.frames # # FrameA : Main Settings # frameA.grid_columnconfigure(1, weight=1) row = 0 # Label row row += 1 div = LabelDivider(frameA, text='Peak Separator Parameters') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 label = Label(frameA, text='Min. number of peaks:') label.grid(row=row, column=0, sticky='w') self.minPeaksEntry = IntEntry(frameA, returnCallback=self.applyChange, width=10, \ tipText='Minimum number of peaks to find (must be > 0)') self.minPeaksEntry.grid(row=row, column=1, sticky='n') self.minPeaksEntry.bind('<Leave>', self.applyChange, '+') row += 1 label = Label(frameA, text='Max. number of peaks:') label.grid(row=row, column=0, sticky='w') self.maxPeaksEntry = IntEntry(frameA, returnCallback=self.applyChange, width=10, \ tipText='Maximum number of peaks to find (0 is unlimited - not recommended)') self.maxPeaksEntry.grid(row=row, column=1, sticky='n') self.maxPeaksEntry.bind('<Leave>', self.applyChange, '+') row += 1 label = Label(frameA, text='Only pick positive peaks:') label.grid(row=row, column=0, sticky='w') entries = ['False', 'True'] self.posPeaksButtons = RadioButtons( frameA, entries=entries, select_callback=self.applyChange, direction='horizontal', tipTexts=[ 'Search for both positive and negative intensity peaks', 'Limit search to only positive peaks' ]) self.posPeaksButtons.grid(row=row, column=1, sticky='n') row += 1 label = Label(frameA, text='Peak Model:') label.grid(row=row, column=0, sticky='w') ### G/L Mixture works, but volume calculation involves Gamma function # entries = ['Gaussian', 'Lorentzian', 'G/L Mixture'] entries = ['Gaussian', 'Lorentzian'] self.shapeButtons = RadioButtons( frameA, entries=entries, select_callback=self.applyChange, direction='horizontal', tipTexts=[ 'Choose a Gaussian model peak shape to fit to peaks', 'Choose a Lorentzian model peak shape to fit to peaks' ]) self.shapeButtons.grid(row=row, column=1, sticky='n') row += 1 div = LabelDivider(frameA, text='Region', tipText='Region that search will limit itself to') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 label = Label(frameA, text='Peak List:') label.grid(row=row, column=0, sticky='nw') self.peakListPulldown = PulldownList( frameA, callback=self.setManuallyPickPeakList, tipText='Select which peak list new peaks are to be added to') self.peakListPulldown.grid(row=row, column=1, sticky='nw') # tricky scrolled matrix row += 1 self.regionTable = None frameA.grid_rowconfigure(row, weight=1) headings = ('dim.', 'start (ppm)', 'end (ppm)', 'actual size') self.editDimEntry = IntEntry(self, returnCallback=self.applyChange, width=5, tipText='Dimension number') self.editStartEntry = FloatEntry(self, returnCallback=self.applyChange, width=5, tipText='Search area lower bound') self.editEndEntry = FloatEntry(self, returnCallback=self.applyChange, width=5, tipText='Search area upper bound') editWidgets = [ self.editDimEntry, self.editStartEntry, self.editEndEntry, None ] editGetCallbacks = [None, None, None, None] editSetCallbacks = [None, None, None, None] self.regionTable = ScrolledMatrix(frameA, headingList=headings, multiSelect=False, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, initialRows=5) self.regionTable.grid(row=row, column=0, columnspan=2, sticky='nsew') # Run Button row += 1 texts = ['Add Region'] commands = [self.updateFromRegion] self.addResetButtons = ButtonList( frameA, texts=texts, commands=commands, tipTexts=['Add selected specrtral region']) self.addResetButtons.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 texts = ['Separate Peaks'] commands = [self.runPeakSeparator] self.runButton = ButtonList(frameA, texts=texts, commands=commands, expands=True, tipTexts=['Run peak search now']) self.runButton.grid(row=row, column=0, columnspan=2, sticky='nsew') # # FrameB : Further Settings # frameB.grid_columnconfigure(0, weight=1) row = 0 div = LabelDivider(frameB, text='Rate:') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 label = Label(frameB, text='Rate of MCMC step size change') label.grid(row=row, column=0, columnspan=1, sticky='w') self.rateEntry = FloatEntry(frameB, returnCallback=self.applyChange, width=10, \ tipText='Rate effects speed of run, smaller values take longer but may produce better results') self.rateEntry.grid(row=row, column=1, sticky='n') self.rateEntry.bind('<Leave>', self.applyChange, '+') self.rateEntry.set(self.params.rate) # tricky scrolled matrix for line width row += 2 div = LabelDivider(frameB, text='Line Width (Hz):') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 label = Label(frameB, text="Descr.") label.grid(row=row, rowspan=2, column=0, sticky='w') row += 1 self.lineWidthTable = None frameB.grid_rowconfigure(row, weight=1) lineWidthHeadings = ('dim.', 'min. σ (Hz)', 'max. σ (Hz)') self.editMinSigmaEntry = FloatEntry(self, returnCallback=self.applyChange, width=5, tipText='Minimum line width (Hz)') self.editMaxSigmaEntry = FloatEntry(self, returnCallback=self.applyChange, width=5, tipText='Maximum line width (Hz)') # self.editDimEntry is also from regionTable initialWidthRows = 4 editLineWidthWidgets = [ None, self.editMinSigmaEntry, self.editMaxSigmaEntry ] editLineWidthGetCallbacks = [None, self.getSigmaMin, self.getSigmaMax] editLineWidthSetCallbacks = [None, self.setSigmaMin, self.setSigmaMax] self.lineWidthTable = ScrolledMatrix( frameB, headingList=lineWidthHeadings, multiSelect=False, editWidgets=editLineWidthWidgets, editGetCallbacks=editLineWidthGetCallbacks, editSetCallbacks=editLineWidthSetCallbacks, initialRows=initialWidthRows) self.lineWidthTable.grid(row=row, column=0, columnspan=2, sticky='nsew') # option to 'repick' exisiting peak list row += initialWidthRows div = LabelDivider(frameB, text='(optional - repick entire peak list)') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 self.repickListPulldown = PulldownList( frameB, callback=self.setRePickPeakList, tipText= 'Select which peak list to repick (new peaks will be put into a new peak list)' ) self.repickListPulldown.grid(row=row, column=0, sticky='nw') texts = ['Repick Peak List'] commands = [self.runRepickPeaks] self.runButton = ButtonList( frameB, texts=texts, commands=commands, expands=True, tipTexts=['Repick selected peak list into a new peak list.']) self.runButton.grid(row=row, column=1, columnspan=1, sticky='nsew') row += 1 div = LabelDivider(frameB) row += 1 texts = ['Separate Peaks'] commands = [self.runPeakSeparator] self.runButton = ButtonList(frameB, texts=texts, commands=commands, expands=True, tipTexts=['Run peak search now']) self.runButton.grid(row=row, column=0, columnspan=2, sticky='nsew') self.setWidgetEntries() self.administerNotifiers(self.registerNotify)
def __init__(self, guiParent, ccpnProject=None, **kw): self.guiParent = guiParent self.project = ccpnProject self.spectrum = None self.peakMode = 0 if ccpnProject: self.nmrProject = ccpnProject.currentNmrProject else: self.nmrProject = None Frame.__init__(self, guiParent, **kw) self.expandGrid(0,0) options = ['Peak Picking',] #,'About Auremol' 'NOE assignment','Homology Modelling',] self.tabbedFrame = TabbedFrame(self, options=options) self.tabbedFrame.grid(row=0,column=0,sticky='nsew') frameA = self.tabbedFrame.frames[0] #frameC.grid_columnconfigure(0, weight=1) #frameC.grid_rowconfigure(0, weight=1) #frameD.grid_columnconfigure(0, weight=1) #frameD.grid_rowconfigure(0, weight=1) # # Frame A # frameA.expandGrid(2,0) frameA.expandGrid(3,0) frameA.expandGrid(4,0) frameA.expandGrid(5,0) frame = Frame(frameA, grid=(0,0)) frame.expandGrid(0,4) label = Label(frame, text='Spectrum:', grid=(0,0)) self.spectrumPulldown = PulldownList(frame, self.changeSpectrum, grid=(0,1)) label = Label(frame, text=' Use Peak Sign:', grid=(0,2)) self.peakModePulldown = PulldownList(frame, self.changePeakMode, texts=PEAK_MODES, objects=[0,1,2], grid=(0,3)) frame = Frame(frameA, grid=(1,0)) frame.expandGrid(0,4) label = Label(frame, text='Integration Depth (Relative to max):', grid=(1,0)) self.segLevelEntry = FloatEntry(frame, text=0.1, grid=(1,1), width=8) label = Label(frame, text='Threshold (Threshold only):', grid=(1,3)) self.thresholdEntry = IntEntry(frame, text=100000, grid=(1,4), width=8) label = Label(frame, text='Keep Peaks (Adaptive only):', grid=(1,5)) self.keepPeakEntry = IntEntry(frame, text=4000, grid=(1,6), width=8) texts = ['Threshold\nPeak Pick','Adaptive\nPeak Pick'] commands = [self.pickThreshold, self.pickAdaptive] self.buttons = ButtonList(frameA, texts=texts, commands=commands, grid=(2,0), sticky='NSEW') frame = Frame(frameA, grid=(3,0)) frame.expandGrid(0,0) frame = Frame(frameA, grid=(4,0)) frame.expandGrid(0,0) frame = Frame(frameA, grid=(5,0)) frame.expandGrid(0,0) # # About """ frameB.expandGrid(4,0) label = Label(frameB, text='References', font='Helvetica 12 bold') label.grid(row=0, column=0, sticky='w') text = * Gronwald W, Brunner K, Kirchhofer R, Nasser A, Trenner J, Ganslmeier B, Riepl H, Ried A, Scheiber J, Elsner R, Neidig K-P, Kalbitzer HR AUREMOL, a New Program for the Automated Structure Elucidation of Biological Macromolecules Bruker Reports 2004; 154/155: 11-14 * Ried A, Gronwald W, Trenner JM, Brunner K, Neidig KP, Kalbitzer HR Improved simulation of NOESY spectra by RELAX-JT2 including effects of J-coupling, transverse relaxation and chemical shift anisotrophy J Biomol NMR. 2004 Oct;30(2):121-31 * Gronwald W, Moussa S, Elsner R, Jung A, Ganslmeier B, Trenner J, Kremer W, Neidig KP, Kalbitzer HR Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE) J Biomol NMR. 2002 Aug;23(4):271-87 * Gronwald W, Kirchhofer R, Gorler A, Kremer W, Ganslmeier B, Neidig KP, Kalbitzer HR RFAC, a program for automated NMR R-factor estimation J Biomol NMR. 2000 Jun;17(2):137-51 label = Label(frameB, text=text) label.grid(row=1, column=0, sticky='w') """ # # Frame C # # # Frame D # self.updateAll()
class PeakSeparatorGui(BasePopup): """ **Separate Merged Peaks Using Peak Models** The Peak Separator code uses a Markov Chain Monte Carlo search which, using idealised peak shapes, attempts to deconvolve overlapped peak regions into their separate constituent peaks. This routine is also suitable for accurately fitting model shapes to single peaks in order to calculate precise intensities. **Options Peak Separator Parameters** *Min. Number of peaks* is by default set to one, it is not possible to set this to a value less than one. *Max. Number of peaks* is by default set to one, increasing this value allows the search routine to fit more models. The best fit may be found with fewer than the maximum number models. Higher numbers slow the routine, and setting this value to 0 allows the routine to (effectively) fit unlimited peaks. *Only pick positive peaks*. If you are not interested in negative peaks, removing the possibility of fitting negative peaks can reduce search time. *Peak Model* fits the spectra with either a Gaussian peak model or a Lorentzian peak model. **Options Region** *Peak List* choose which peak list newly picked peaks should be added to. Peaks picked using this method will have their details appended with 'PeakSepartor' so you know where they came from. *Region Table* shows which area of the current spectrum is about to be searched. *Add Region*. Once an area of spectra has been highlighted clicking this button will pass it's details on to the Peak Separator. *Reset All* will reset all search parameters. *Separate Peaks* will run the Peak Separator code with your current settings. This may take a few minutes to run, depending on the size of the spectral region being searched, the number of peaks being fitted and the speed of your machine. Please wait while this completes. After a successful Peak Separation run, the found peaks will be added to the selected peak list. These peaks intensties (volume) have been found using the peak model selected. **Advanced Settings Tab** *Rate* affects the speed of the Markov Chain Monte Carlo routine. A smaller value results in longer execution, but possibly higher quality results. The default setting is deemed sensible for the majority of runs. *Line Width* offers a finer degree of control over maximum and minimum peak widths for each dimension. The default values are *very* stupid and could do with re-checking for each experiment. *Re-Pick Entire Peak List* if you would like to use the Peak Separator to repick *every* peak in your peak list, try this option - but note that this may take a very long time! """ def __init__(self, parent, programName='Peak Separator', **kw): self.parent = parent self.programName = programName self.versionInfo = 'Version 0.2' self.help_url = 'http://www.ccpn.ac.uk/' self.window = None self.waiting = False self.rootWindow = None # just used for display - PeakSeparator will not see this self._minSigmaHz = None self._maxSigmaHz = None self.customSigma = False self.rePickPeakList = False self._sampleStartPpm = None self._sampleEndPpm = None try: self.project = parent.project except: pass self.params = PeakSeparatorParams() BasePopup.__init__(self, parent=parent, title=programName, location='+100+100', **kw) if not self.analysisProject: print '&&& init: No analysis project found ...' try: if parent.argumentServer: self.argServer = parent.argumentServer else: print '&&& init: No argument server found...' except: print '&&& init: Test' ########################################################################### def body(self, guiFrame): self.geometry('450x500') guiFrame.grid_rowconfigure(0, weight=1) guiFrame.grid_columnconfigure(0, weight=1) options = ['Peak Separator', 'Advanced Settings'] tabbedFrame = TabbedFrame(guiFrame, options=options) tabbedFrame.grid(row=0, column=0, sticky='nsew') buttons = UtilityButtonList(tabbedFrame.sideFrame, helpUrl=self.help_url) buttons.grid(row=0, column=0, sticky='e') self.tabbedFrame = tabbedFrame frameA, frameB = tabbedFrame.frames # # FrameA : Main Settings # frameA.grid_columnconfigure(1, weight=1) row = 0 # Label row row += 1 div = LabelDivider(frameA, text='Peak Separator Parameters') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 label = Label(frameA, text='Min. number of peaks:') label.grid(row=row, column=0, sticky='w') self.minPeaksEntry = IntEntry(frameA, returnCallback=self.applyChange, width=10, \ tipText='Minimum number of peaks to find (must be > 0)') self.minPeaksEntry.grid(row=row, column=1, sticky='n') self.minPeaksEntry.bind('<Leave>', self.applyChange, '+') row += 1 label = Label(frameA, text='Max. number of peaks:') label.grid(row=row, column=0, sticky='w') self.maxPeaksEntry = IntEntry(frameA, returnCallback=self.applyChange, width=10, \ tipText='Maximum number of peaks to find (0 is unlimited - not recommended)') self.maxPeaksEntry.grid(row=row, column=1, sticky='n') self.maxPeaksEntry.bind('<Leave>', self.applyChange, '+') row += 1 label = Label(frameA, text='Only pick positive peaks:') label.grid(row=row, column=0, sticky='w') entries = ['False', 'True'] self.posPeaksButtons = RadioButtons( frameA, entries=entries, select_callback=self.applyChange, direction='horizontal', tipTexts=[ 'Search for both positive and negative intensity peaks', 'Limit search to only positive peaks' ]) self.posPeaksButtons.grid(row=row, column=1, sticky='n') row += 1 label = Label(frameA, text='Peak Model:') label.grid(row=row, column=0, sticky='w') ### G/L Mixture works, but volume calculation involves Gamma function # entries = ['Gaussian', 'Lorentzian', 'G/L Mixture'] entries = ['Gaussian', 'Lorentzian'] self.shapeButtons = RadioButtons( frameA, entries=entries, select_callback=self.applyChange, direction='horizontal', tipTexts=[ 'Choose a Gaussian model peak shape to fit to peaks', 'Choose a Lorentzian model peak shape to fit to peaks' ]) self.shapeButtons.grid(row=row, column=1, sticky='n') row += 1 div = LabelDivider(frameA, text='Region', tipText='Region that search will limit itself to') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 label = Label(frameA, text='Peak List:') label.grid(row=row, column=0, sticky='nw') self.peakListPulldown = PulldownList( frameA, callback=self.setManuallyPickPeakList, tipText='Select which peak list new peaks are to be added to') self.peakListPulldown.grid(row=row, column=1, sticky='nw') # tricky scrolled matrix row += 1 self.regionTable = None frameA.grid_rowconfigure(row, weight=1) headings = ('dim.', 'start (ppm)', 'end (ppm)', 'actual size') self.editDimEntry = IntEntry(self, returnCallback=self.applyChange, width=5, tipText='Dimension number') self.editStartEntry = FloatEntry(self, returnCallback=self.applyChange, width=5, tipText='Search area lower bound') self.editEndEntry = FloatEntry(self, returnCallback=self.applyChange, width=5, tipText='Search area upper bound') editWidgets = [ self.editDimEntry, self.editStartEntry, self.editEndEntry, None ] editGetCallbacks = [None, None, None, None] editSetCallbacks = [None, None, None, None] self.regionTable = ScrolledMatrix(frameA, headingList=headings, multiSelect=False, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, initialRows=5) self.regionTable.grid(row=row, column=0, columnspan=2, sticky='nsew') # Run Button row += 1 texts = ['Add Region'] commands = [self.updateFromRegion] self.addResetButtons = ButtonList( frameA, texts=texts, commands=commands, tipTexts=['Add selected specrtral region']) self.addResetButtons.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 texts = ['Separate Peaks'] commands = [self.runPeakSeparator] self.runButton = ButtonList(frameA, texts=texts, commands=commands, expands=True, tipTexts=['Run peak search now']) self.runButton.grid(row=row, column=0, columnspan=2, sticky='nsew') # # FrameB : Further Settings # frameB.grid_columnconfigure(0, weight=1) row = 0 div = LabelDivider(frameB, text='Rate:') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 label = Label(frameB, text='Rate of MCMC step size change') label.grid(row=row, column=0, columnspan=1, sticky='w') self.rateEntry = FloatEntry(frameB, returnCallback=self.applyChange, width=10, \ tipText='Rate effects speed of run, smaller values take longer but may produce better results') self.rateEntry.grid(row=row, column=1, sticky='n') self.rateEntry.bind('<Leave>', self.applyChange, '+') self.rateEntry.set(self.params.rate) # tricky scrolled matrix for line width row += 2 div = LabelDivider(frameB, text='Line Width (Hz):') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 label = Label(frameB, text="Descr.") label.grid(row=row, rowspan=2, column=0, sticky='w') row += 1 self.lineWidthTable = None frameB.grid_rowconfigure(row, weight=1) lineWidthHeadings = ('dim.', 'min. σ (Hz)', 'max. σ (Hz)') self.editMinSigmaEntry = FloatEntry(self, returnCallback=self.applyChange, width=5, tipText='Minimum line width (Hz)') self.editMaxSigmaEntry = FloatEntry(self, returnCallback=self.applyChange, width=5, tipText='Maximum line width (Hz)') # self.editDimEntry is also from regionTable initialWidthRows = 4 editLineWidthWidgets = [ None, self.editMinSigmaEntry, self.editMaxSigmaEntry ] editLineWidthGetCallbacks = [None, self.getSigmaMin, self.getSigmaMax] editLineWidthSetCallbacks = [None, self.setSigmaMin, self.setSigmaMax] self.lineWidthTable = ScrolledMatrix( frameB, headingList=lineWidthHeadings, multiSelect=False, editWidgets=editLineWidthWidgets, editGetCallbacks=editLineWidthGetCallbacks, editSetCallbacks=editLineWidthSetCallbacks, initialRows=initialWidthRows) self.lineWidthTable.grid(row=row, column=0, columnspan=2, sticky='nsew') # option to 'repick' exisiting peak list row += initialWidthRows div = LabelDivider(frameB, text='(optional - repick entire peak list)') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 self.repickListPulldown = PulldownList( frameB, callback=self.setRePickPeakList, tipText= 'Select which peak list to repick (new peaks will be put into a new peak list)' ) self.repickListPulldown.grid(row=row, column=0, sticky='nw') texts = ['Repick Peak List'] commands = [self.runRepickPeaks] self.runButton = ButtonList( frameB, texts=texts, commands=commands, expands=True, tipTexts=['Repick selected peak list into a new peak list.']) self.runButton.grid(row=row, column=1, columnspan=1, sticky='nsew') row += 1 div = LabelDivider(frameB) row += 1 texts = ['Separate Peaks'] commands = [self.runPeakSeparator] self.runButton = ButtonList(frameB, texts=texts, commands=commands, expands=True, tipTexts=['Run peak search now']) self.runButton.grid(row=row, column=0, columnspan=2, sticky='nsew') self.setWidgetEntries() self.administerNotifiers(self.registerNotify) def administerNotifiers(self, notifyFunc): for func in ('__init__', 'delete'): notifyFunc(self.updateAfter, 'ccp.nmr.Nmr.PeakList', func) notifyFunc(self.updateAfter, 'ccp.nmr.Nmr.Experiment', 'setName') notifyFunc(self.updateAfter, 'ccp.nmr.Nmr.DataSource', 'setName') def destroy(self): self.administerNotifiers(self.unregisterNotify) BasePopup.destroy(self) ########################################################################### # update parameters from PS Region def updateFromRegion(self): if not self.params.peakList: print '&&& update from region: Need a peak list' return if (self.argServer.parent.currentRegion) == None: showError('No Region', 'Please select a peak region to be separated') return self.rePickPeakList = False getRegionParams(self.params, argServer=self.argServer) if not self.customSigma: self.initSigmaParams() self.setWidgetEntries() ########################################################################### # update parameters from PS PeakList def updateFromPeakList(self): if not self.params.peakList: print '&&& update from peakList: Need a peak list' return getPeakListParams(self.params) if not self.customSigma: self.initSigmaParams() self.setWidgetEntries() ########################################################################### # Run the C library! def runPeakSeparator(self): """ run the peak separator """ # hack for Macs - focus isn't always lost on mouse move # so bind event not always called. Shouldn't affect other OS. self.applyChange() if not self.params.peakList: print '&&& Peak list not yet set' else: # SeparatePeakRoutine(self.params, self.params.peakList, routine='pymc' ) SeparatePeakRoutine(self.params, self.params.peakList, routine='bayesys') def runRepickPeaks(self): """ Run the Peak Separator on entire chosen peak list """ # hack for Macs - focus isn't always lost on mouse move # so bind event not always called. Shouldn't affect other OS. self.applyChange() if not self.params.peakList: print '&&& Peak list not yet set' else: SeparatePeaksInPeakList(self.params) ########################################################################### def setWidgetEntries(self): ### Page One widgets self.minPeaksEntry.set(self.params.minAtoms) self.maxPeaksEntry.set(self.params.maxAtoms) if self.params.positivePeaks == 1: self.posPeaksButtons.set('True') # only pick pos peaks else: self.posPeaksButtons.set('False') # do something fancy if different shapes for each dim! n = self.params.peakShape - 3 # shape is only 3, 4, (5) self.shapeButtons.setIndex(n) if self.project is not None: self.updatePeakListList() self.updateSpectrumWindow() if self.params.sampleStart and self.params.peakList: if not self.rePickPeakList: objectList = [] textMatrix = [] if len(self.params.samplePpmStart) != self.params.Ndim: return for i in range(self.params.Ndim): dim_entry = [] dim_entry.append('%2d' % (i + 1)) dim_entry.append('%7.3f' % self.params.samplePpmStart[i]) dim_entry.append('%7.3f' % self.params.samplePpmEnd[i]) dim_entry.append('%3d' % self.params.sampleSize[i]) textMatrix.append(dim_entry) self.regionTable.update(textMatrix=textMatrix, objectList=objectList) ### Page Two widgets self.rateEntry.set(self.params.rate) if self.params.peakList and self.params.Ndim: textMatrix = [] objectList = [] for i in range(self.params.Ndim): if self.params.isFreqDim[i]: dim_entry = [] objectList.append(i) dim_entry.append('%2d' % (i + 1)) dim_entry.append('%7.3f' % self._minSigmaHz[i]) dim_entry.append('%7.3f' % self._maxSigmaHz[i]) textMatrix.append(dim_entry) self.lineWidthTable.update(textMatrix=textMatrix, objectList=objectList) def applyChange(self, *event): """ Upon change, add settings to params """ # Page One apply changes self.params.minAtoms = self.minPeaksEntry.get() self.params.maxAtoms = self.maxPeaksEntry.get() if self.posPeaksButtons.get() == 'True': # asked only pick pos peaks self.params.positivePeaks = 1 else: self.params.positivePeaks = 0 # do something fancy if different shapes for each dim! n = self.shapeButtons.getIndex() # shape is only 3, 4, (5) self.params.peakShape = n + 3 # Page Two apply changes self.params.rate = float(self.rateEntry.get()) self.updateSigmaParams() ########################################################################### # Peak list functions provide PeakSeparator some inherited params def getPeakListList(self): """ given a spectrum, get list of peak lists """ project = self.project peakLists = [] for experiment in self.nmrProject.experiments: for spectrum in experiment.dataSources: for peakList in spectrum.peakLists: peakLists.append([ '%s:%s:%d' % (experiment.name, spectrum.name, peakList.serial), peakList ]) peakLists.sort() return peakLists def updatePeakListList(self): """ set the peaklist list in the pulldown menu """ peakListData = self.getPeakListList() index = -1 names = [] peakList = self.params.peakList if peakListData: names = [x[0] for x in peakListData] peakLists = [x[1] for x in peakListData] if peakList not in peakLists: peakList = peakLists[0] index = peakLists.index(peakList) else: peakList = None peakLists = [] if peakList is not self.params.peakList: self.params.peakList = peakList self.peakListPulldown.setup(names, peakLists, index) self.repickListPulldown.setup(names, peakLists, index) def setRePickPeakList(self, peakList): """ Set the peak list to be repicked (and hit a Flag) """ self.rePickPeakList = True self.setPeakList(peakList) def setManuallyPickPeakList(self, peakList): """ Set the peak list to add new peaks to (and hit a Flag) """ self.rePickPeakList = False self.setPeakList(peakList) def setPeakList(self, peakList): """ Sets the Peak List """ if peakList is not self.params.peakList: self.params.peakList = peakList # # interrogate the peak list and get all the usefull parameters out self.updateFromPeakList() self.updateSpectrumWindow() self.setWidgetEntries() ########################################################################### # TBD I suspect this is for matching region with peak list, but may be obsolete now def getSpectrumWindowList(self): """ get list of windows which spectrum could be in """ windows = {} if self.params.peakList: views = getSpectrumViews(self.params.peakList.dataSource) for view in views: windows[view.spectrumWindowPane.spectrumWindow] = None return [[w.name, w] for w in windows.keys()] def updateSpectrumWindow(self): """ update the spectrum window """ windowData = self.getSpectrumWindowList() index = -1 names = [] window = self.rootWindow if windowData: names = [x[0] for x in windowData] windows = [x[1] for x in windowData] if window not in windows: window = windows[0] index = windows.index(window) else: window = None windows = [] if window is not self.rootWindow: self.rootWindow = window ########################################################################### # get and set sigma stuff def setSigmaMin(self, dim): value = self.editMinSigmaEntry.get() self._minSigmaHz[dim] = value # dont go and re-write users settings self.customSigma = True # make sure changes are in params object self.updateSigmaParams(dim) self.setWidgetEntries() def getSigmaMin(self, dim): if dim is not None: self.editMinSigmaEntry.set(self._minSigmaHz[dim]) def setSigmaMax(self, dim): value = self.editMaxSigmaEntry.get() self._maxSigmaHz[dim] = value # dont go and re-write users settings self.customSigma = True # make sure changes are in params object self.updateSigmaParams(dim) self.setWidgetEntries() def getSigmaMax(self, dim): if dim is not None: self.editMaxSigmaEntry.set(self._maxSigmaHz[dim]) def updateSigmaParams(self, dim=None): """ updateSigmaParams Just updates the parameters (params obj) for sigma values. If dim is None, do this for each dim """ dataDimRefs = self.params.dataDimRefs if not dataDimRefs: return if not self.params.minSigma or len( self.params.minSigma) != self.params.Ndim: self.params.minSigma = [0.] * self.params.Ndim if not self.params.maxSigma or len( self.params.maxSigma) != self.params.Ndim: self.params.maxSigma = [0.] * self.params.Ndim def updateSigmaParam(dim, dataDimRefs): """ Convert and update sigma for dim """ if self.params.isFreqDim[dim]: # note factor of two! self.params.minSigma[dim] = self.rHz2pnt( self._minSigmaHz[dim], dataDimRefs[dim]) / 2. self.params.maxSigma[dim] = self.rHz2pnt( self._maxSigmaHz[dim], dataDimRefs[dim]) / 2. else: self.params.minSigma[dim] = 1.0 self.params.maxSigma[dim] = 1.0 if dim: updateSigmaParam(dim, dataDimRefs) else: for dim in range(self.params.Ndim): updateSigmaParam(dim, dataDimRefs) # utility functions for sigma values def pnt2rHz(self, point, dataDimRef): """ Point to relative Hz frequency relative to frequency at Zeroeth point Necessary when (for example) looking for width of peak in Hz """ assert point, dataDimRef sigmaBase = pnt2hz(0, dataDimRef) sigmaHz = pnt2hz(point, dataDimRef) return abs(sigmaHz - sigmaBase) def rHz2pnt(self, freq, dataDimRef): """ Relative Hz to point frequency relative to frequency at Zeroeth point Necessary when (for example) looking for width of peak in Hz """ assert freq, dataDimRef sigmaBase = hz2pnt(0, dataDimRef) sigmaPoint = hz2pnt(freq, dataDimRef) return abs(sigmaPoint - sigmaBase) def initSigmaParams(self): """ Set some initial default values for sigma """ self._minSigmaHz = [] self._maxSigmaHz = [] if self.params.Ndim: for dim in range(self.params.Ndim): self._minSigmaHz.append(6.) self._maxSigmaHz.append(28.) ########################################################################### def updateAll(self): self.updateSpectrumWindow() self.updatePeakListList() self.waiting = False def updateAfter(self, obj=None): if self.waiting: return else: self.waiting = True self.after_idle(self.updateAll)
class AssignMentTransferTab(object): '''the tab in the GUI where assignments can be transferred in bulk to the ccpn analysis project. A difference is made between two types of assignments: 1) spin systems to residues, which also implies resonanceSets to atomSets. 2) resonances to peak dimensions. The user is able to configure which assignments should be transferred to the project. Attributes: guiParent: gui object this tab is part of. frame: the frame in which this element lives. dataModel(src.cython.malandro.DataModel): dataModel object describing the assignment proposed by the algorithm. selectedSolution (int): The index of the solution/run that is used asa the template to make the assignments. resonanceToDimension (bool): True if resonances should be assigned to peak dimensions. False if not. spinSystemToResidue (bool): True if spin system to residue assignment should be carried out. minScore (float): The minimal score of a spin system assignment to a residue to be allowed to transfer this assignment to the project intra (bool): True if intra-residual peaks should be assigned. sequential (bool): True if sequential peaks should be assigned. noDiagonal (bool): If True, purely diagonal peaks are ignored during the transfer of assignments. allSpectra (bool): If True, all spectra will be assigned. If False, one specified spectrum will be assigned. spectrum (src.cython.malandro.Spectrum): The spectrum that should be assigned. ''' 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 # Buttons and fields, # will be set in body(): self.peaksCheckButton = None self.residuesCheckButton = None self.intraCheckButton = None self.sequentialCheckButton = None self.noDiagonalCheckButton = None self.spinSystemTypeSelect = None self.minScoreEntry = None self.solutionNumberEntry = None self.spectrumSelect = None self.spectraPullDown = None self.assignedResidueStrategySelect = None self.transferButton = None # Settings that determine how assignments # are transferred to the analysis project: self.minScore = 80.0 self.dataModel = None self.spectrum = None self.selectedSolution = 1 self.body() self.resonanceToDimension = True self.spinSystemToResidue = True self.intra = True self.sequential = True self.noDiagonal = True self.allSpectra = True self.spinSystemType = 0 self.strategy = 0 def body(self): '''Describes the body of this tab. It consists out of a number of radio buttons, check buttons and number entries that allow the user to indicate which assignments should be transferred. ''' # self.frame.expandColumn(0) self.frame.expandGrid(8, 0) self.frame.expandGrid(8, 1) typeOfAssignmentFrame = LabelFrame( self.frame, text='type of assignment') typeOfAssignmentFrame.grid(row=0, column=0, sticky='nesw') # typeOfAssignmentFrame.expandGrid(0,5) peakSelectionFrame = LabelFrame( self.frame, text='which peaks to assign') peakSelectionFrame.grid(row=0, column=1, sticky='nesw', rowspan=2) spinSystemSelectionFrame = LabelFrame(self.frame, text='Which spin-systems to use') spinSystemSelectionFrame.grid(row=2, column=0, sticky='nesw') tipText = 'What to do when a residue has already a spin system assigned to it.' assignedResidueFrame = LabelFrame(self.frame, text='if residue already has spin-system', tipText=tipText) assignedResidueFrame.grid(row=2, column=1, sticky='nesw') spectrumSelectionFrame = LabelFrame(self.frame, text='spectra') spectrumSelectionFrame.grid(row=1, column=0, sticky='nesw') row = 0 Label(typeOfAssignmentFrame, text='Resonances to Peak Dimensions', grid=(row, 0)) self.peaksCheckButton = CheckButton(typeOfAssignmentFrame, selected=True, grid=(row, 1)) row += 1 Label(typeOfAssignmentFrame, text='SpinSystems to Residues', grid=(row, 0)) self.residuesCheckButton = CheckButton( typeOfAssignmentFrame, selected=True, grid=(row, 1)) row = 0 Label(peakSelectionFrame, text='Intra-Residual', grid=(row, 0)) self.intraCheckButton = CheckButton( peakSelectionFrame, selected=True, grid=(row, 1)) row += 1 Label(peakSelectionFrame, text='Sequential', grid=(row, 0)) self.sequentialCheckButton = CheckButton( peakSelectionFrame, selected=True, grid=(row, 1)) row += 1 Label(peakSelectionFrame, text='Do not assign diagonal peaks', grid=(row, 0)) self.noDiagonalCheckButton = CheckButton( peakSelectionFrame, selected=True, grid=(row, 1)) entries = ['Only assigned spin systems', 'All that have a score of at least: ', 'User Defined', 'Solution number:'] tipTexts = ['Only assign resonances of spin systems that already have a sequential assignment for the assignment of peak dimensions. Spin system to residue assignment is not relevant in this case.', 'Assign all spin systems that have a score of at least a given percentage. 50% or lower is not possible, because than spin systems might have to be assigned to more than 1 residue, which is impossible.', "As defined in the lower row of buttons in the 'results' tab.", 'One of the single solutions of the annealing.'] self.spinSystemTypeSelect = RadioButtons(spinSystemSelectionFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(4, 1), tipTexts=tipTexts) tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.' self.minScoreEntry = FloatEntry(spinSystemSelectionFrame, grid=(1, 1), width=7, text=str(self.minScore), returnCallback=self.changeMinScore, tipText=tipText) self.minScoreEntry.bind('<Leave>', self.changeMinScore, '+') self.solutionNumberEntry = IntEntry(spinSystemSelectionFrame, grid=(3, 1), width=7, text=1, returnCallback=self.solutionUpdate, tipText=tipText) self.solutionNumberEntry.bind('<Leave>', self.solutionUpdate, '+') #self.solutionPullDown = PulldownList(spinSystemSelectionFrame, None, grid=(3,1), sticky='w') entries = ['all spectra', 'only:'] tipTexts = ['Assign peaks in all the spectra that where selected before the annealing ran.', 'Only assign peaks in one particular spectrum. You can of course repeat this multiple times for different spectra.'] self.spectrumSelect = RadioButtons(spectrumSelectionFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(2, 1), tipTexts=tipTexts) self.spectraPullDown = PulldownList(spectrumSelectionFrame, self.changeSpectrum, grid=(1, 1), sticky='w') entries = ['skip this residue', 'de-assign old spin system from residue', 'assign, but never merge', 'warn to merge'] tipTexts = ["Don't assign the new spin system to the residue. The residue is not skipped when the old spin system does not contain any resonances", "De-assign old spin system from residue, unless the old spin system is a spin system without any resonances.", "Don't merge any spin systems, merging can be performed later if nescesary in the Resonance --> SpinSystems window.", "Ask to merge individually for each spin system, this might result in clicking on a lot of popups."] self.assignedResidueStrategySelect = RadioButtons(assignedResidueFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(2, 1), tipTexts=tipTexts) texts = ['Transfer Assignments'] commands = [self.transferAssignments] self.transferButton = ButtonList( self.frame, commands=commands, texts=texts) self.transferButton.grid(row=5, column=0, sticky='nsew', columnspan=2) def update(self): '''Update the nescesary elements in the tab. Is called when the algorithm has produced possible assignments. The only thing that has to be updated in practice in this tab is the pulldown with spectra. ''' self.dataModel = self.guiParent.connector.results self.updateSpectra() def setDataModel(self, dataModel): '''Here the dataModel, which is the dataModel containing the suggested assignments body the algorithm, can be set. ''' self.dataModel = dataModel self.update() def updateSpectra(self, *opt): '''Updates the spectra shown in the spectra pulldown. These are only the spectra that were used by the algorithm. All other spectra in the project are not relevant since for those no simulated peaks have been matched to real peaks. ''' if not self.dataModel: return spectrum = self.spectrum spectra = self.dataModel.getSpectra() if spectra: names = [spectrum.name for spectrum in spectra] index = 0 if self.spectrum not in spectra: self.spectrum = spectra[0] else: index = spectra.index(self.spectrum) self.spectraPullDown.setup(names, spectra, index) def changeSpectrum(self, spectrum): '''Select a spectum to be assigned.''' self.spectrum = spectrum def solutionUpdate(self, event=None, value=None): '''Select a solution. A solution is a one to one mapping of spin systems to residues produced by one run of the algorithm. args: event: event object, this is one of the values the number entry calls his callback function with. value: the index of the solution/run. ''' if not self.dataModel: return Nsolutions = len(self.dataModel.chain.residues[0].solutions) if value is None: value = self.solutionNumberEntry.get() if value == self.selectedSolution: return else: self.selectedSolution = value if value < 1: self.solutionNumberEntry.set(1) self.selectedSolution = 1 elif value > Nsolutions: self.selectedSolution = Nsolutions self.solutionNumberEntry.set(self.selectedSolution) else: self.solutionNumberEntry.set(self.selectedSolution) def fetchOptions(self): '''Fetches user set options from the gui in one go and stores them in their corresponding instance variables. ''' self.resonanceToDimension = self.peaksCheckButton.get() self.spinSystemToResidue = self.residuesCheckButton.get() self.intra = self.intraCheckButton.get() self.sequential = self.sequentialCheckButton.get() self.noDiagonal = self.noDiagonalCheckButton.get() self.spinSystemType = self.spinSystemTypeSelect.getIndex() self.strategy = ['skip', 'remove', 'noMerge', None][ self.assignedResidueStrategySelect.getIndex()] self.allSpectra = [True, False][self.spectrumSelect.getIndex()] def changeMinScore(self, event=None): '''Set the minimal score for which a spin system to residue assignment gets transferred to the ccpn analysis project. ''' newMinScore = self.minScoreEntry.get() if self.minScore != newMinScore: if newMinScore <= 50.0: self.minScore = 51.0 self.minScoreEntry.set(51.0) elif newMinScore > 100.0: self.minScore = 100.0 self.minScoreEntry.set(100.0) else: self.minScore = newMinScore def transferAssignments(self): '''Transfer assignments to project depending on the settings from the GUI. ''' self.fetchOptions() if not self.dataModel or (not self.resonanceToDimension and not self.spinSystemToResidue): return strategy = self.strategy lookupSpinSystem = [self.getAssignedSpinSystem, self.getBestScoringSpinSystem, self.getUserDefinedSpinSystem, self.getSelectedSolutionSpinSystem][self.spinSystemType] residues = self.dataModel.chain.residues spinSystemSequence = [lookupSpinSystem(res) for res in residues] ccpnSpinSystems = [] ccpnResidues = [] # if self.spinSystemType == 0 it means that it for sure already # assigned like this if self.spinSystemToResidue and not self.spinSystemType == 0: for spinSys, res in zip(spinSystemSequence, residues): if spinSys and res: ccpnSpinSystems.append(spinSys.getCcpnResonanceGroup()) ccpnResidues.append(res.getCcpnResidue()) assignSpinSystemstoResidues(ccpnSpinSystems, ccpnResidues, strategy=strategy, guiParent=self.guiParent) if self.resonanceToDimension: allSpectra = self.allSpectra if self.intra: for residue, spinSystem in zip(residues, spinSystemSequence): if not spinSystem: continue intraLink = residue.getIntraLink(spinSystem) for pl in intraLink.getPeakLinks(): peak = pl.getPeak() if not allSpectra and peak.getSpectrum() is not self.spectrum: continue if not peak: continue resonances = pl.getResonances() if self.noDiagonal and len(set(resonances)) < len(resonances): continue for resonance, dimension in zip(resonances, peak.getDimensions()): ccpnResonance = resonance.getCcpnResonance() ccpnDimension = dimension.getCcpnDimension() assignResToDim(ccpnDimension, ccpnResonance) if self.sequential: for residue, spinSystemA, spinSystemB in zip(residues, spinSystemSequence, spinSystemSequence[1:]): if not spinSystemA or not spinSystemB: continue link = residue.getLink(spinSystemA, spinSystemB) for pl in link.getPeakLinks(): peak = pl.getPeak() if not allSpectra and peak.getSpectrum() is not self.spectrum: continue if not peak: continue resonances = pl.getResonances() if self.noDiagonal and len(set(resonances)) < len(resonances): continue for resonance, dimension in zip(resonances, peak.getDimensions()): ccpnResonance = resonance.getCcpnResonance() ccpnDimension = dimension.getCcpnDimension() assignResToDim(ccpnDimension, ccpnResonance) self.guiParent.resultsTab.update() def getAssignedSpinSystem(self, residue): '''Get the spinSystem that is assigned in the project to a residue. args: residue (src.cython.malandro.Residue) return: spinSystem (src.cython.malandro.SpinSystem) ''' ccpCode = residue.ccpCode seqCode = residue.getSeqCode() spinSystems = self.dataModel.getSpinSystems()[ccpCode] ccpnResidue = residue.getCcpnResidue() if ccpnResidue: assignedResonanceGroups = ccpnResidue.getResonanceGroups() if len(assignedResonanceGroups) > 1: print 'There is more than one spin system assigned to residue %s, did not know which one to use to assign peaks. Therefor this residue is skipped.' % (seqCode) return assignedResonanceGroup = ccpnResidue.findFirstResonanceGroup() if assignedResonanceGroup: for spinSystem in spinSystems: if spinSystem.getSerial() == assignedResonanceGroup.serial: # Just checking to make sure, analysis project could # have changed if not self.skipResidue(residue, spinSystem): return spinSystem def getBestScoringSpinSystem(self, residue): '''Get the spinSystem that scores the highest, i.e. is assigned in most of the runs to the given residue. args: residue (src.cython.malandro.Residue) return: spinSystem (src.cython.malandro.SpinSystem) ''' solutions = residue.solutions weigth = 1.0 / len(solutions) score, bestSpinSystem = max([(solutions.count(solution) * weigth * 100.0, solution) for solution in solutions]) if score >= self.minScore and not bestSpinSystem.getIsJoker() and not self.skipResidue(residue, bestSpinSystem): return bestSpinSystem return None def getUserDefinedSpinSystem(self, residue): '''Get the spinSystem that is defined by the user (probably in the resultsTab) as the correct assignment of the given residue. args: residue (src.cython.malandro.Residue) return: spinSystem (src.cython.malandro.SpinSystem) ''' userDefinedSpinSystem = residue.userDefinedSolution if userDefinedSpinSystem and not userDefinedSpinSystem.getIsJoker() and not self.skipResidue(residue, userDefinedSpinSystem): return userDefinedSpinSystem return None def getSelectedSolutionSpinSystem(self, residue): '''I a solution corresponding to one specific run of the algorithm is defined, return which spinSystem in that run got assigned to the given residue. args: residue (src.cython.malandro.Residue) return: spinSystem (src.cython.malandro.SpinSystem) ''' solutions = residue.solutions spinSystem = solutions[self.selectedSolution - 1] if not spinSystem.getIsJoker() and not self.skipResidue(residue, spinSystem): return spinSystem return None def skipResidue(self, residue, spinSystem): '''One strategy is to skip all residues that already have a spin system assignment. If that is the case determine whether to skip the given residue. args: residue (src.cython.malandro.Residue) spinSystem (src.cython.malandro.SpinSystem) return: boolean, True if residue should be skipped. ''' if self.strategy == 0: assignedGroups = residue.getCcpnResidue().getResonanceGroups() assignedSerials = set([spinSys.serial for spinSys in assignedGroups]) if assignedSerials and spinSystem.getSerial() not in assignedSerials: return True return False
class CloudHomologueAssignPopup(BasePopup): def __init__(self, parent, *args, **kw): self.guiParent = parent self.project = parent.getProject() self.molSystem = None self.chain = None self.assignment = None self.scores = [] BasePopup.__init__(self, parent, title="Cloud Threader", **kw) def body(self, guiFrame): guiFrame.grid_columnconfigure(3, weight=1) row = 0 label = Label(guiFrame, text='Molecular system: ') label.grid(row=row, column=0, sticky=Tkinter.NW) self.molSysPulldown = PulldownMenu(guiFrame, self.changeMolSystem, selected_index=-1, do_initial_callback=0) self.molSysPulldown.grid(row=row, column=1, sticky=Tkinter.NW) label = Label(guiFrame, text='Clouds files: ') label.grid(row=row, column=2, sticky=Tkinter.NW) self.filenameEntry = Entry(guiFrame,text='perfect00.pdb') self.filenameEntry.grid(row=row, column=3, sticky=Tkinter.NW) row += 1 label = Label(guiFrame, text='Chain: ') label.grid(row=row, column=0, sticky=Tkinter.NW) self.chainPulldown = PulldownMenu(guiFrame, self.changeChain, selected_index=-1, do_initial_callback=0) self.chainPulldown.grid(row=row, column=1, sticky=Tkinter.NW) label = Label(guiFrame, text='Thread steps: ') label.grid(row=row, column=2, sticky=Tkinter.NW) self.numStepsEntry = IntEntry(guiFrame,text=3000) self.numStepsEntry.grid(row=row, column=3, sticky=Tkinter.NW) row += 1 label = Label(guiFrame, text='Homologue PDB file: ') label.grid(row=row, column=0, sticky=Tkinter.NW) self.pdbEntry = Entry(guiFrame,text='') self.pdbEntry.grid(row=row, column=1, sticky=Tkinter.NW) label = Label(guiFrame, text='Dist. Threshold: ') label.grid(row=row, column=2, sticky=Tkinter.NW) self.distEntry = FloatEntry(guiFrame,text=3.0) self.distEntry.grid(row=row, column=3, sticky=Tkinter.NW) row += 1 label = Label(guiFrame, text='Global score: ') label.grid(row=row, column=0, sticky=Tkinter.NW) self.globalScoreLabel = Label(guiFrame, text='') self.globalScoreLabel.grid(row=row, column=1, sticky=Tkinter.NW) label = Label(guiFrame, text='Assignment Threshold: ') label.grid(row=row, column=2, sticky=Tkinter.NW) self.thresholdEntry = FloatEntry(guiFrame,text=-4.5) self.thresholdEntry.grid(row=row, column=3, sticky=Tkinter.NW) row += 1 guiFrame.grid_rowconfigure(row, weight=1) self.graph = ScrolledGraph(guiFrame, width=300, height=200) self.graph.grid(row=row, column=0, columnspan=4, sticky = Tkinter.NSEW) row += 1 texts = ['Run','Assign!'] commands = [self.run, self.assignSpinSystems] bottomButtons = createDismissHelpButtonList(guiFrame,texts=texts,commands=commands,expands=0,help_url=None) bottomButtons.grid(row=row, column=0, columnspan=4, sticky=Tkinter.EW) self.assignButton = bottomButtons.buttons[1] for func in ('__init__','delete'): Implementation.registerNotify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem', func) Implementation.registerNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func) self.updateMolSystems() self.updateChains() def update(self): if self.assignment and self.scores: self.assignButton.enable() else: self.assignButton.disable() def run(self): if self.chain: pattern = self.filenameEntry.get() nSteps = self.numStepsEntry.get() or 4000 pdbFile = self.pdbEntry.get() dist = self.distEntry.get() or 3.0 pgb = ProgressBar(self, text='Searching', total=nSteps) files = getFileNamesFromPattern(pattern , '.') if not files: return clouds = getCloudsFromFile(files, self.chain.root) score, self.scores, self.assignment = cloudHomologueAssign(self.chain, clouds, pdbFile, dist, nSteps, self.graph, pgb) pgb.destroy() self.globalScoreLabel.set(str(score)) self.update() def assignSpinSystems(self): if self.assignment and self.scores: if showWarning('Query','Are you sure?'): threshold = self.thresholdEntry.get() or -4.0 i = 0 for residue in self.assignment.keys(): if self.scores[residue] > threshold: spinSystem = self.assignment[residue] assignSpinSystemResidue(spinSystem,residue=None) for residue in self.assignment.keys(): if self.scores[residue] > threshold: i += 1 spinSystem = self.assignment[residue] assignSpinSystemResidue(spinSystem,residue=residue) showWarning('Done','%d residues assigned' % i) def getMolSystems(self): names = [] for molSystem in self.project.molSystems: if molSystem.chains: names.append( '%s' % (molSystem.code) ) return names def changeMolSystem(self, i, name): self.molSystem = self.project.findFirstMolSystem(code=name) def updateMolSystems(self, *opt): names = self.getMolSystems() if names: if not self.molSystem: self.molSystem = self.project.findFirstMolSystem(code=names[0]) self.molSysPulldown.setup(names, names.index(self.molSystem.code)) def getChains(self): chains = [] if self.molSystem: for chain in self.molSystem.chains: chains.append( [chain.code, chain] ) return chains def changeChain(self, i, name=None): if not name: i = self.chainPulldown.selected_index chains = self.getChains() if chains: self.chain = chains[i][1] def updateChains(self, *chain): chains = self.getChains() if chains: names = [x[0] for x in chains] if (not self.chain) or (self.chain.code not in names): self.chain = chains[0][1] self.chainPulldown.setup(names, names.index(self.chain.code) ) self.update() def destroy(self): for func in ('__init__','delete'): Implementation.unregisterNotify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem', func) Implementation.unregisterNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func) BasePopup.destroy(self)