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 DataFileImportFrame(Frame): """ TODO: should I also ask for sample conditions info with chemical shifts? Or do in ECI - possible? Check! """ # TODO should go where? email = '*****@*****.**' defaultSelectText = "Select file." fontOkColor = 'green3' fontCheckColor = 'orange3' fontBadColor = 'red3' fontDefaultColor = 'black' def __init__(self, parent, basePopup, *args, **kw): # # Variable initialisation # self.fcWrapper = basePopup.fcWrapper self.project = basePopup.project self.basePopup = basePopup # TODO necessary? if self.project: self.nmrProject = self.project.currentNmrProject self.entry = self.project.currentNmrEntryStore.findFirstEntry() if not self.entry: self.entry = self.project.currentNmrEntryStore.newEntry( name=self.project.name) else: self.nmrProject = None self.sequenceCoordinatesLoaded = False self.shiftsLoaded = False self.linkResDone = False self.currentShiftList = None self.shiftListChainPairs = [] self.moleculeList = [] self.moleculeDict = {} # # Frame setup # Frame.__init__(self, parent, **kw) self.grid_columnconfigure(1, weight=1) self.grid_rowconfigure(1, weight=1) options = ['Import', 'Deposition'] tabbedFrame = TabbedFrame(self, options=options, callback=self.selectTab) tabbedFrame.grid(row=1, column=0, columnspan=2, sticky='nsew') self.tabbedFrame = tabbedFrame frameA, frameD = tabbedFrame.frames # # Main # frameA.grid_columnconfigure(0, weight=1) #frameA.grid_columnconfigure(1, weight=1) # Change to 2 if want 2 columns frameA.grid_rowconfigure(12, weight=1) #frameA.grid_rowconfigure(12, weight=1) row = 0 div = LabelDivider( frameA, text= 'Select the full coordinate file or a sequence file (with info for a single molecule).', justify='center', grid=(row, 0), gridSpan=(1, 1)) row += 1 self.sequenceCoordinatesImport = Button( frameA, text=self.defaultSelectText, command=self.importSequenceOrCoords, foreground=self.fontDefaultColor) self.sequenceCoordinatesImport.grid(row=row, column=0, sticky='ew') row += 1 label = Label(frameA, text="") label.grid(row=row, column=0, sticky='ew') row += 1 div = LabelDivider( frameA, text='Select the molecule relevant for your chemical shift file.', justify='center', grid=(row, 0), gridSpan=(1, 1)) row += 1 self.moleculeSelect = Label( frameA, text="None available yet - import valid file first", foreground=self.fontBadColor) self.moleculeSelect.grid(row=row, column=0, sticky='ew') self.moleculeSelectRow = row row += 1 label = Label(frameA, text="") label.grid(row=row, column=0, sticky='ew') row += 1 div = LabelDivider( frameA, text= 'Select a chemical shift file with values only for the above molecule.', justify='center', grid=(row, 0), gridSpan=(1, 1)) row += 1 self.shiftImport = Button(frameA, text=self.defaultSelectText, command=self.importShifts, foreground=self.fontDefaultColor) self.shiftImport.grid(row=row, column=0, sticky='ew') row += 1 label = Label(frameA, text="") label.grid(row=row, column=0, sticky='ew') row += 1 div = LabelDivider( frameA, text='Consistency check between molecule and shift information.', justify='center', grid=(row, 0), gridSpan=(2, 1)) row += 1 self.linkResCheckInfo = Label(frameA, text='') self.linkResCheckInfo.grid(row=row, column=0, sticky='ew') row += 1 div = Separator(frameA, grid=(row, 0), gridSpan=(1, 1)) row += 1 texts = ['Import new sequence', 'Import new set of shifts'] commands = [self.resetSequenceImport, self.resetShiftImport] self.mainButtons = ButtonList(frameA, texts=texts, commands=commands) self.mainButtons.grid(row=row, column=0, columnspan=2, sticky='ew') self.mainButtons.buttons[0].config(foreground=self.fontDefaultColor) #print row self.frameA = frameA # # Not in use... # #frameX.grid_columnconfigure(0, weight=1) #frameX.grid_columnconfigure(1, weight=1) #frameX.grid_rowconfigure(1, weight=1) #frameX.grid_rowconfigure(3, weight=1) # # Deposition, is updated after each successful import run. # frameD.grid_columnconfigure(0, weight=1) frameD.grid_rowconfigure(5, weight=1) self.frameD = frameD row = 0 div = LabelDivider(frameD, text='Imported data.', justify='center', grid=(row, 0), gridSpan=(1, 2)) row += 1 self.depositionImportText = "\nImported %d shift list(s) for a total of %d shifts.\n\nImported %d molecule(s) and %d chain(s).\n\nImported %d model(s) for a total of %d atom coordinates.\n\nLinked %.2f%% of imported NMR information to %d chain(s)." self.depositionImportLoc = (row, 0) # These used for setting text above... self.depositionImportNums = [0, 0, 0, 0, 0, 0, 0.0, 0] self.importedShiftLists = [] self.connectedChains = [] self.depositionImportLabel = Label(frameD, text=self.depositionImportText % tuple(self.depositionImportNums), foreground=self.fontBadColor) self.depositionImportLabel.grid(row=row, column=0, sticky='ew') row += 1 label = Label(frameD, text="") label.grid(row=row, column=0, sticky='ew') # # Finalize the import part, proceed to ECI. # row += 1 div = LabelDivider( frameD, text= 'Import completed, save project and start Entry Completion Interface.', justify='center', grid=(row, 0), gridSpan=(1, 1)) row += 1 self.eciStart = Button(frameD, text="Finalise import", command=self.finaliseImport, foreground=self.fontBadColor) self.eciStart.grid(row=row, column=0, sticky='ew') def finaliseImport(self): if not self.depositionImportNums[6]: showWarning('Failure', 'Need connected molecule and shift information first') return if showYesNo( "Save project and continue annotation", "Are you sure you want to save this project and continue?", parent=self): if self.depositionImportNums[5] or showYesNo( "No coordinates", "No coordinates are available - are you sure you want to continue?", parent=self): showInfo("Project name", "Your project will be saved in the %s directory." % self.project.name, parent=self) self.project.saveModified() #userData = self.project.findFirstRepository(name='userData') #currentPath = userData.url.path #currentProjectName = self.project.name #projectDir = os.path.join(currentPath,currentProjectName) eci = EntryCompletionGui(self.basePopup.root) eci.initProject(self.project) # # File type determination and import # def createFileTypes(self, dataTypes): fileTypes = [FileType('all', ['*'])] for dataType in dataTypes: formatNames = fileTypeDict[dataType].keys() formatNames.sort() for formatName in formatNames: if formatName in self.fcWrapper.formatNameLists[dataType]: fileTypes.append( FileType(formatName, fileTypeDict[dataType][formatName])) return fileTypes def getFileName(self, title, fileTypes): fileSelectPopup = FileSelectPopup( self, file_types=fileTypes, title=title, dismiss_text='Cancel', selected_file_must_exist=True, multiSelect=False, ) self.fileName = fileSelectPopup.getFile() if not self.fileName: showWarning('Failure', 'Please select an existing file.', parent=self) return False return True def importSequenceOrCoords(self): dataTypes = ['sequence', 'coordinates'] fileTypes = self.createFileTypes(dataTypes) if self.getFileName('Import sequence or coordinate file', fileTypes): formatNameSuggestions = {} for dataType in dataTypes: tmpList = self.fcWrapper.determineFormatNamesForFile( dataType, self.fileName) if tmpList: formatNameSuggestions[dataType] = tmpList if not formatNameSuggestions: showWarning( 'Failure', 'This file cannot be read by this software.\nPlease send the file with an explanation to %s.' % self.email, parent=self) return False # # Let user select if multiple options, otherwise take default # if len(formatNameSuggestions) == 1 and len(formatNameSuggestions[ formatNameSuggestions.keys()[0]]) == 1: dataType = formatNameSuggestions.keys()[0] formatName = formatNameSuggestions[dataType][0] if not showYesNo( 'File type detected', 'Reading as %s file in %s format. Is this correct?' % (dataType, formatName), parent=self): showWarning( 'Failure', 'This file cannot be read by this software.\nPlease send the file with an explanation to %s.' % self.email, parent=self) return False else: # # Create a selection (hopefully user-understandable) # selectionList = [] selectionDict = {} for dataType in dataTypes: dataTypeString = dataType if formatNameSuggestions.has_key(dataType): formatNames = formatNameSuggestions[dataType] formatNames.sort() for formatName in formatNames: selectionString = "%s file in %s format." % ( dataTypeString, formatName) selectionList.append(selectionString) selectionDict[selectionString] = (dataType, formatName) interaction = SelectionListPopup(self, selectionList, title='File format selection', text='This is a:', selectionDict=selectionDict, dismissButton=True, modal=True) # # Check if anything was selected... # dataType = formatName = None if interaction.isSelected: (dataType, formatName) = interaction.selection else: showWarning( 'Failure', 'This file cannot by read without a format selection.\nIf the correct format is not available, please send the file with an explanation to %s' % self.email, parent=self) return False # # Now read the file, need to do some field updates! # (fileRead, fileInformation) = self.fcWrapper.readFile( dataType, formatName, self.fileName) if not fileRead: showWarning( 'Failure', 'This file cannot be read by this software:%s\nPlease send the file with an explanation to %s.' % (fileInformation, self.email), parent=self) return False (conversionInfo, conversionSuccess) = ( self.fcWrapper.formatConversion.conversionInfo, self.fcWrapper.formatConversion.conversionSuccess) if not conversionSuccess: showWarning( 'Failure', 'This file was read by the software but contains invalid information.\nPlease send the file with an explanation to %s.' % self.email, parent=self) return False # # Set info if import worked OK # conversionLines = conversionInfo.split(": ") showInfo("Import coordinate and/or sequence information", ":\n".join(conversionLines), parent=self) if dataType == 'sequence': chains = self.fcWrapper.importReturns[dataType] models = [] elif dataType == 'coordinates': models = self.fcWrapper.importReturns[dataType] chains = [ cChain.chain for cChain in models[0].structureEnsemble.coordChains ] self.sequenceCoordinatesImport.setText( self.fileName) # TODO change color or something? self.sequenceCoordinatesImport.configure( foreground=self.fontOkColor) self.sequenceCoordinatesLoaded = True # # Reset to list selector for further use # moleculeName = None for chain in chains: if chain in self.moleculeDict.values(): continue numResidues = len(chain.residues) if numResidues == 1: residueText = "%s residue" % chain.findFirstResidue( ).ccpCode else: residueText = "%d residues" % numResidues moleculeName = "%s (chain '%s', %s)" % ( chain.molecule.name, chain.code, residueText) self.moleculeList.append(moleculeName) self.moleculeDict[moleculeName] = chain self.moleculeList.sort() self.moleculeSelect.destroy() if len(chains) == 1 and moleculeName: selectedIndex = self.moleculeList.index(moleculeName) else: selectedIndex = 0 self.moleculeSelect = PulldownList(self.frameA, texts=self.moleculeList, index=selectedIndex, sticky='ew') self.moleculeSelect.grid(row=self.moleculeSelectRow, column=0) # # Now update Deposition tab # molecules = [] for chain in chains: if not chain.molecule in molecules: molecules.append(chain.molecule) numCoords = 0 for model in models: numCoords += len(model.coords) self.updateDepositionImportLabel(molecules=len(molecules), chains=len(chains), models=len(models), coordinates=numCoords) # Add the molSystem to the entry! if chains and not chains[0].molSystem == self.entry.molSystem: self.entry.molSystem = chains[0].molSystem self.updateAll() def importShifts(self): currentChain = self.getCurrentChain() if not currentChain: showWarning( 'Failure', 'Please first read in a sequence or coordinate file and select the molecule relevant for this shift list.', parent=self) return elif self.currentShiftList: shiftListChainPair = (self.currentShiftList, currentChain) if shiftListChainPair in self.shiftListChainPairs: showWarning( 'Failure', "You already read in chemical shifts for this chain.\nPlease read in related shifts for the other chain(s), if present, or press the 'Import new set of shifts' button to read in a new set of shifts.", parent=self) return dataType = 'shifts' fileTypes = self.createFileTypes([dataType]) if self.getFileName('Import chemical shift file', fileTypes): formatNameSuggestions = self.fcWrapper.determineFormatNamesForFile( dataType, self.fileName) if not formatNameSuggestions: showWarning( 'Failure', 'This file cannot be read by this software.\nPlease send the file with an explanation to %s.' % self.email, parent=self) return False # # Let user select if multiple options, otherwise take default # if len(formatNameSuggestions) == 1: formatName = formatNameSuggestions[0] if not showYesNo( 'File type detected', 'Reading as a chemical shift file in %s format. Is this correct?' % formatName, parent=self): showWarning( 'Failure', 'This file cannot be read by this software.\nPlease send the file with an explanation to %s.' % self.email, parent=self) return False else: # # Create a selection (hopefully user-understandable) # selectionList = [] selectionDict = {} formatNameSuggestions.sort() for formatName in formatNameSuggestions: selectionString = "chemical shift file in %s format." % ( formatName) selectionList.append(selectionString) selectionDict[selectionString] = formatName interaction = SelectionListPopup(self, selectionList, title='File format selection', text='This is a:', selectionDict=selectionDict, dismissButton=True, modal=True) # # Check if anything was selected... # formatName = None if interaction.isSelected: formatName = interaction.selection else: showWarning( 'Failure', 'This file cannot by read without a format selection.\nIf the correct format is not available, please send the file with an explanation to %s' % self.email, parent=self) return False # # Now read the file, need to do some field updates! Also make sure to re-use shift list for other molecules... # (fileRead, fileInformation) = self.fcWrapper.readFile( dataType, formatName, self.fileName, addKeywords={'measurementList': self.currentShiftList}) if not fileRead: showWarning( 'Failure', 'This file cannot be read by this software:%s\nPlease send the file with an explanation to %s.' % (fileInformation, self.email), parent=self) return False (conversionInfo, conversionSuccess) = ( self.fcWrapper.formatConversion.conversionInfo, self.fcWrapper.formatConversion.conversionSuccess) if not conversionSuccess: showWarning( 'Failure', 'This file was read by the software but contains invalid information.\nPlease send the file with an explanation to %s.' % self.email, parent=self) return False # # Set info if import worked OK # conversionLines = conversionInfo.split(": ") showInfo("Import chemical shift information", ":\n".join(conversionLines), parent=self) self.shiftImport.setText( self.fileName) # TODO change color or something? self.shiftImport.configure(foreground=self.fontOkColor) self.shiftsLoaded = True self.shiftsFormatName = formatName shiftList = self.fcWrapper.importReturns[dataType] if not self.currentShiftList: self.currentShiftList = shiftList self.shiftListChainPairs.append( (self.currentShiftList, currentChain)) self.updateDepositionImportLabel(shiftList=shiftList) if not shiftList in self.entry.measurementLists: print shiftList self.entry.addMeasurementList(shiftList) print self.entry.measurementLists self.updateAll() # # Updaters # def selectTab(self, index): funcsDict = { 0: (self.updateMain, ), 1: (self.updateCoordinates, ), 2: (self.updateDeposition, ) } for func in funcsDict[index]: func() def updateMain(self): pass def updateCoordinates(self): pass def updateDeposition(self): pass def updateAll(self): self.selectTab(self.tabbedFrame.selected) if self.sequenceCoordinatesLoaded and self.shiftsLoaded: if showYesNo( 'Connect shifts to sequence', 'You have to check whether the chemical shift information matches the sequence. Do you want to this now?', parent=self): self.connectShiftsSequence() self.waiting = False def getCurrentChain(self): if len(self.moleculeList) == 1: chain = self.moleculeDict.values()[0] else: try: moleculeSelected = self.moleculeSelect.getText() chain = self.moleculeDict[moleculeSelected] except: chain = None return chain def connectShiftsSequence(self): if not self.linkResDone: changeResetColor = False # # Get chain mapping and run linkResonances # chain = self.getCurrentChain() forceChainMappings = self.fcWrapper.linkResonancesToSequence( chain=chain) self.fcWrapper.formatConversion.linkResonances( forceChainMappings=forceChainMappings, guiParent=self) # # Get information about the linking process # # TODO Should only have an nmrProject (no restraint import, should be included?) # In any case, is always the LAST info in numResonancesLinked info numResonancesLinked = self.fcWrapper.formatConversion.numResonancesLinked (origLinked, origUnlinked, linked, unlinked) = (numResonancesLinked['origLinked'][-1], numResonancesLinked['origUnlinked'][-1], numResonancesLinked['linked'][-1], numResonancesLinked['unlinked'][-1]) # # Track number of new resonances, and reset for new import # if self.fcWrapper.formatConversion.allResonancesLinked: status = 'All information matches (for all imports).' foreground = self.fontOkColor changeResetColor = True else: if origUnlinked - unlinked == self.fcWrapper.numNewResonances: status = 'All information matches (for this import)' foreground = self.fontOkColor changeResetColor = True else: if origUnlinked != unlinked: status = 'Not all information matches (for this and/or another import).' foreground = self.fontCheckColor changeResetColor = True else: status = 'No information matches (for this import).' foreground = self.fontBadColor otherUnlinked = (origUnlinked - self.fcWrapper.numNewResonances) notLinked = unlinked - otherUnlinked status += "\nUnable to link %d out of %d imported shifts (%.2f%%)." % ( notLinked, self.fcWrapper.numNewResonances, (notLinked * 100.0) / self.fcWrapper.numNewResonances) self.linkResCheckInfo.set("Status: %s" % status) self.linkResCheckInfo.config(foreground=foreground) self.linkResDone = True # # Change the color of the reset button to indicate OK to do next one # if changeResetColor: self.mainButtons.buttons[0].config(foreground=self.fontOkColor) self.updateDepositionImportLabel( shiftList=None, percentageLinked=(linked * 100.0 / (unlinked + linked)), connectedChain=chain) def updateDepositionImportLabel(self, shiftList=None, molecules=0, chains=0, models=0, coordinates=0, percentageLinked=None, connectedChain=None): if shiftList and shiftList not in self.importedShiftLists: self.importedShiftLists.append(shiftList) self.depositionImportNums[0] += 1 shifts = 0 for shiftList in self.importedShiftLists: shifts += len(shiftList.measurements) self.depositionImportNums[1] += shifts self.depositionImportNums[2] += molecules self.depositionImportNums[3] += chains self.depositionImportNums[4] += models self.depositionImportNums[5] += coordinates if percentageLinked != None: self.depositionImportNums[6] = percentageLinked if connectedChain and connectedChain not in self.connectedChains: self.depositionImportNums[7] += 1 self.connectedChains.append(connectedChain) self.depositionImportLabel.destroy() finalForeground = self.fontBadColor if self.depositionImportNums[0] == 0 and self.depositionImportNums[ 2] == 0: # Nothing imported foreground = self.fontBadColor elif self.depositionImportNums[6]: # Linked shifts available - TODO base this on % of shifts linked? foreground = self.fontOkColor if self.depositionImportNums[5]: finalForeground = self.fontOkColor else: finalForeground = self.fontCheckColor else: # Intermediate state foreground = self.fontCheckColor self.depositionImportLabel = Label(self.frameD, text=self.depositionImportText % tuple(self.depositionImportNums), foreground=foreground) self.depositionImportLabel.grid(row=self.depositionImportLoc[0], column=self.depositionImportLoc[1], sticky='ew') self.eciStart.configure(foreground=finalForeground) def resetSequenceImport(self): doReset = True if not self.linkResDone and self.sequenceCoordinatesLoaded and self.shiftsLoaded: if showYesNo( 'Shifts not connected to sequence', 'You have not checked whether the imported chemical shift information matches the imported sequence. Do you want to this first? If not, the last imported data will be invalid.', parent=self): self.connectShiftsSequence() doReset = False if doReset: self.mainButtons.buttons[0].config( foreground=self.fontDefaultColor) self.sequenceCoordinatesLoaded = self.shiftsLoaded = self.linkResDone = False self.sequenceCoordinatesImport.setText(self.defaultSelectText) self.sequenceCoordinatesImport.configure( foreground=self.fontDefaultColor) self.moleculeSelect.destroy() self.moleculeSelect = Label( self.frameA, text="None available yet - import valid file first", foreground=self.fontBadColor) self.moleculeSelect.grid(row=self.moleculeSelectRow, column=0, sticky='ew') self.shiftImport.setText(self.defaultSelectText) self.shiftImport.configure(foreground=self.fontDefaultColor) self.linkResCheckInfo.set("") def resetShiftImport(self): doReset = True if not self.linkResDone and self.sequenceCoordinatesLoaded and self.shiftsLoaded: if showYesNo( 'Shifts not connected to sequence', 'You have not checked whether the imported chemical shift information matches the imported sequence. Do you want to this first? If not, the last imported data will be invalid.', parent=self): self.connectShiftsSequence() doReset = False if doReset: self.mainButtons.buttons[1].config( foreground=self.fontDefaultColor) self.shiftsLoaded = self.linkResDone = False self.currentShiftList = None self.shiftImport.setText(self.defaultSelectText) self.shiftImport.configure(foreground=self.fontDefaultColor) self.linkResCheckInfo.set("") def destroy(self): Frame.destroy(self) # # Instructions # def showMainInstructions(self): popup = getPopup(self) message = """Use this tab to import the chemical shifts and the coordinate and/or sequence information for your molecular chains. The imported chemical shift file should contain information for only *one* molecular chain to make it easier to connect the molecule information to the chemical shift information. You therefore have to select a single chain for each shift list from the dropdown menu that will appear after you imported a coordinate or sequence file. For example, when using sequence files for a dimer, import the information for the chemical shifts for each chain separately: 1. Import the sequence for the first molecular chain. 2. Import a chemical shift file with shifts only for this molecular chain. 3. Reset using the 'Import new sequence' button 4. Import the sequence for the second molecular chain 5. Import a chemical shift file with shifts only for this second chain Alternatively, it is possible to read in the molecule information from a full coordinate file: 1. Import a coordinate file with all molecular information, including coordinates. 2. Select a molecular chain. 3. Import a chemical shift file with shifts only for the selected molecular chain. 4. Go back to step 2. if necessary. You can also import multiple sets of chemical shifts (e.g. for the sample in different conditions). In this case, you have to import all chemical shift information that belongs together for all molecular chains, then press the 'Import new set of shifts' button. Notes: 1. This application always creates a new CCPN project. It is not possible to import files into existing projects. 2. If your chemical shift file contains information for multiple chains, you have to edit it manually to split up the information per chain. """ showHelpText(self, message, popup=popup) def showFormats(self): popup = getPopup(self) message = """For chemical shifts, the following formats are recognised: *** Auremol *** section_sequenzdefinition _Residue_seq_code _Atom_num_code _Residue_label _Atom_name _Atom_type _Atom_alias _Atom_equivalent _Atom_CSA 1 1 MET HN H - - 8.95 1 2 MET N N - - 157.00 1 3 MET CA C - - 40.00 *** Autoassign *** AA HN N15 CO-1 CA-1 CB-1 HA-1 CO CA CB HA A31 8.14 121.4 51.3 19.6 (GS178 115.HSQC) D32 8.88 122.9 51.3 19.5 55.4 39.6 (GS271 22.HSQC) *** CNS *** do ( store1 = 53.13218 ) ( resid 78 and name CA ) do ( store1 = 0.7356673 ) ( resid 15 and name HD1# ) do ( store1 = 120.5381 ) ( resid 8 and name N ) do ( store1 = 121.1414 ) ( resid 78 and name N ) *** Cosmos *** CS_VALUES 3 C_ALA 176.6 CA_ALA 51.66 CB_ALA 17.26 END *** CSI *** # A HA CA CO CB Consensus # 1 MET 0 C 0 C NA 0 C 0 C 2 GLY 0 C 0 C NA 0 C 0 C *** MARS *** H N CO-1 CA CA-1 PR_2 8.900 123.220 170.540 55.080 54.450 PR_4 8.320 115.340 175.920 - 55.080 *** MONTE *** 1 102.544 8.211 45.853 54.925 0.000 18.069 180.112 2 103.276 8.580 45.334 54.154 0.000 35.650 175.087 3 103.997 7.407 45.165 0.000 0.000 0.000 0.000 *** NMR-STAR *** data_test save_shifts1 _Saveframe_category assigned_chemical_shifts loop_ _Atom_shift_assign_ID _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 ASP CA C 52.000 0.02 1 2 1 ASP HA H 4.220 0.02 1 stop_ save_ *** NMRVIEW *** 2.CG1 18.549 0 2.CG2 18.844 0 2.HG1# 0.800 0 2.HG2# 0.723 0 3.HG2 2.298 0 3.HG1 2.298 0 *** PIPP *** RES_ID 1 RES_TYPE MET SPIN_SYSTEM_ID 1 CA 55.9920 CB 33.1470 HA 4.1141 HB# 2.0492 HG# 2.4250 END_RES_DEF *** PISTACHIO *** 1 1 GLY C C 172.621 1.000 0 2 1 GLY CA C 44.308 1.000 0 3 2 SER N N 122.241 1.000 0 *** PRONTO *** Spin system HN HA Other: 1: Val-1 3.76 HB: 1.945, HG1: 0.770, HG2: 0.608 2: Ile-2 8.80 4.26 HB: 1.526, HG1: 1.278, HG2: 0.728, HD: 0.918 *** SHIFTX *** NUM RES HA H N CA CB C --- --- ------ ------ -------- ------- ------- -------- 2 T 4.4161 8.1749 111.0443 61.8324 70.3867 172.5362 3 Y 4.9022 9.0239 120.2106 56.0493 41.4218 173.0761 NUM RES H HA HB HB2 HB3 HD1 HD2 HD21 HD22 HD3 HE HE1 HE2 HE21 HE22 HE3 HG HG1 HG12 HG13 HG2 HG3 HZ 2 T 8.17 4.42 4.24 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.21 0.00 0.00 3 Y 9.02 4.90 0.00 2.22 2.20 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 *** SPARKY *** Group Atom Nuc Shift SDev Assignments R2 CA 13C 56.539 0.003 3 R2 CB 13C 30.808 0.009 3 *** TALOS *** VARS RESID RESNAME PHI PSI DPHI DPSI DIST COUNT CLASS FORMAT %4d %s %8.3f %8.3f %8.3f %8.3f %8.3f %2d %s 1 Q 9999.000 9999.000 0.000 0.000 0.000 0 None 2 N -85.000 124.000 23.000 28.000 85.920 10 Good ***XEASY/CYANA: 1 117.803 0.000 N 1 2 8.208 0.002 HN 1 3 56.508 0.055 CA 1 4 999.000 0.000 HA 1 5 29.451 0.004 CB 1 """ showHelpText(self, message, popup=popup)