class CalcHeteroNoePopup(BasePopup): """ **Calculate Heteronuclear NOE Values From Peak Intensities** The purpose of this popup window is to calculate the heteronuclear NOE for amide resonances based upon a comparison of the peak intensities in spectra that derive from an NOE saturated experiment and an unsaturated (reference) experiment. The basic idea of this tool is that three peak lists are chosen, two of which are for heteronuclear NOE experiments (H,N axes); unsaturated reference and saturated, and one which is the source of assignments and peak locations. This last "Assignment" peak list may be the same as one of the NOE peak lists, but may also be entirely separate. The "Assignment" peak list is used to specify which peak assignments and locations should be used for the calculation of the heteronuclear NOE values, and thus can be used to specify only a subset of the resonances for measurement. For example, it is common to copy an HQSC peak list for use as the "Assignment" peak list but remove overlapped and NH2 peaks so that the NOE values are only calculated for separated backbone amides. The calculation process involves taking each of these assigned peaks and finding peaks with the same assignment in the NOE peak lists, or if that fails finding peaks with a similar position (within the stated tolerances); new peaks may be picked if the "Pick new peaks?" option is set. The first "Peak Lists & Settings" tab allows the user to choose the peak lists and various options that will be used in the peak-finding and NOE calculation. The "Peaks" table allows the peaks from each of the three peak list selections to be displayed when one of the "Show" buttons is clicked. The [Separate Peak Table] function allows these peaks to be displayed in the main, separate `Peak Lists`_ table, which has many more peak manipulation options. The options below the table may be used to locate selected peaks within the spectrum window displays. The second "Peak Intensity Comparison" tab is where the heteronuclear NOE values are actually calculated. Assuming that two NOE experiment peak lists have been chosen and that some of their peaks match the assigned peak positions then the peak intensities are extracted and NOE values automatically calculated when the tab is opened. Although, a refresh of the table can be forced with [Find Matching Peaks] at the bottom If pairs of NOE saturated and reference peaks are found then the actual heteronuclear NOE value is displayed as the "Intensity Ratio" in the last, rightmost, column of the table. To store these values as a NOE measurement list; so that the data can be saved in the CCPN project without need for recalculation, the [Create Hetero NOE List] function can be used. The results are then available to view at any time via the `Measurement Lists`_ table. **Caveats & Tips** Erroneous peak intensity comparisons may be removed with the [Remove Pairs] function, but its is common to curate the "Assign" peak list first and avoid tidying afterwards. The "Closeness score" can be used to find peak positions where the compared NOE peaks are unexpectedly far from one another. .. _`Peak Lists`: EditPeakListsPopup.html .. _`Measurement Lists`: EditMeasurementListsPopup.html """ def __init__(self, parent, *args, **kw): self.guiParent = parent self.peakPairs = [] self.intensityType = 'height' self.selectedPair = None self.assignPeakList = None self.refPeakList = None self.satPeakList = None self.displayPeakList = None self.waiting = 0 BasePopup.__init__(self, parent, title="Data Analysis : Heteronuclear NOE", **kw) def body(self, guiFrame): self.geometry('700x700') guiFrame.expandGrid(0,0) options = ['Peak Lists & Settings','Peak Intensity Comparison'] tabbedFrame = TabbedFrame(guiFrame, options=options, callback=self.changeTab) tabbedFrame.grid(row=0, column=0, sticky='nsew') self.tabbedFrame = tabbedFrame frameA, frameB = tabbedFrame.frames row = 0 frameA.grid_columnconfigure(1, weight=1) frameA.grid_columnconfigure(3, weight=1) frameA.grid_columnconfigure(5, weight=1) frameA.grid_rowconfigure(5, weight=1) tipText = 'Number of reference peaks (no saturation)' self.peaksALabel = Label(frameA, text='Number of Ref Peaks: ', tipText=tipText) self.peaksALabel.grid(row=1,column=0,columnspan=2,sticky='w') tipText = 'Number of NOE saturation peaks' self.peaksBLabel = Label(frameA, text='Number of Sat Peaks: ', tipText=tipText) self.peaksBLabel.grid(row=1,column=2,columnspan=2,sticky='w') tipText = 'Number of peaks in assigned list' self.peaksCLabel = Label(frameA, text='Number of Assign Peaks: ', tipText=tipText) self.peaksCLabel.grid(row=1,column=4,columnspan=2,sticky='w') tipText = 'Selects which peak list is considered the NOE intensity reference (no saturation)' specALabel = Label(frameA, text='Ref Peak List: ') specALabel.grid(row=0,column=0,sticky='w') self.specAPulldown = PulldownList(frameA, callback=self.setRefPeakList, tipText=tipText) self.specAPulldown.grid(row=0,column=1,sticky='w') tipText = 'Selects which peak list is considered as NOE saturated.' specBLabel = Label(frameA, text='Sat Peak List: ') specBLabel.grid(row=0,column=2,sticky='w') self.specBPulldown = PulldownList(frameA, callback=self.setSatPeakList, tipText=tipText) self.specBPulldown.grid(row=0,column=3,sticky='w') tipText = 'Selects a peak list with assignments to use as a positional reference' specCLabel = Label(frameA, text='Assignment Peak List: ') specCLabel.grid(row=0,column=4,sticky='w') self.specCPulldown = PulldownList(frameA, callback=self.setAssignPeakList, tipText=tipText) self.specCPulldown.grid(row=0,column=5,sticky='w') frame0a = Frame(frameA) frame0a.grid(row=2,column=0,columnspan=6,sticky='nsew') frame0a.grid_columnconfigure(9, weight=1) tipText = '1H ppm tolerance for matching assigned peaks to reference & NOE saturation peaks' tolHLabel = Label(frame0a, text='Tolerances: 1H') tolHLabel.grid(row=0,column=0,sticky='w') self.tolHEntry = FloatEntry(frame0a,text='0.02', width=6, tipText=tipText) self.tolHEntry .grid(row=0,column=1,sticky='w') tipText = '15N ppm tolerance for matching assigned peaks to reference & NOE saturation peaks' tolNLabel = Label(frame0a, text=' 15N') tolNLabel .grid(row=0,column=2,sticky='w') self.tolNEntry = FloatEntry(frame0a,text='0.1', width=6, tipText=tipText) self.tolNEntry .grid(row=0,column=3,sticky='w') tipText = 'Whether to peak new peaks in reference & NOE saturated lists (at assignment locations)' label = Label(frame0a, text=' Pick new peaks?', grid=(0,4)) self.pickPeaksSelect = CheckButton(frame0a, tipText=tipText, grid=(0,5), selected=True) tipText = 'Whether to assign peaks in the peaks in the reference & NOE saturation lists, if not already assigned' label = Label(frame0a, text=' Assign peaks?') label.grid(row=0,column=6,sticky='w') self.assignSelect = CheckButton(frame0a, tipText=tipText) self.assignSelect.set(1) self.assignSelect.grid(row=0,column=7,sticky='w') tipText = 'Whether to consider peak height or volume in the heteronuclear NOE calculation' intensLabel = Label(frame0a, text=' Intensity Type:') intensLabel .grid(row=0,column=8,sticky='w') self.intensPulldown = PulldownList(frame0a, texts=['height','volume'], callback=self.setIntensityType, tipText=tipText) self.intensPulldown.grid(row=0,column=9,sticky='w') divider = LabelDivider(frameA, text='Peaks', grid=(3,0), gridSpan=(1,6)) tipTexts = ['Show the selected intensity reference peaks in the below table', 'Show the selected NOE saturation peaks in the below table', 'Show the selected assigned peak list in the below table', 'Show the displayed peaks in a separate peak table, where assignments etc. may be adjusted'] texts = ['Show Ref Peaks','Show Sat Peaks', 'Show Assign Peaks', 'Separate Peak Table'] commands = [self.viewRefPeakList, self.viewSatPeakList, self.viewAssignPeakList, self.viewSeparatePeakTable] self.viewPeaksButtons = ButtonList(frameA, expands=True, tipTexts=tipTexts, texts=texts, commands=commands) self.viewPeaksButtons.grid(row=4,column=0,columnspan=6,sticky='nsew') self.peakTable = PeakTableFrame(frameA, self.guiParent, grid=(5,0), gridSpan=(1,6)) self.peakTable.bottomButtons1.grid_forget() self.peakTable.bottomButtons2.grid_forget() #self.peakTable.topFrame.grid_forget() self.peakTable.topFrame.grid(row=2, column=0, sticky='ew') # Next tab frameB.expandGrid(0,0) tipTexts = ['Row number', 'Assignment annotation for NOE saturation peak', 'Assignment annotation for reference peak (no saturation)', '1H chemical shift of NOE saturation peak', '1H chemical shift of reference peak', '15N chemical shift of NOE saturation peak', '15N chemical shift of reference peak', 'The separation between compared peaks: square root of the sum of ppm differences squared', 'The intensity if the NOE saturation peak', 'The intensity of the reference peak (no saturation)', 'Ratio of peak intensities: saturated over reference', 'Residue(s) for reference peak'] colHeadings = ['#','Sat Peak','Ref Peak','1H shift A', '1H shift B','15N shift A','15N shift B', 'Closeness\nScore','Intensity A','Intensity B', 'Intensity\nRatio','Residue'] self.scrolledMatrix = ScrolledMatrix(frameB, multiSelect=True, headingList=colHeadings, callback=self.selectCell, tipTexts=tipTexts, grid=(0,0), deleteFunc=self.removePair) tipTexts = ['Force a manual update of the table; pair-up NOE saturation and reference peaks according to assigned peak positions', 'Remove the selected rows of peak pairs', 'Show peaks corresponding to the selected row in a table', 'Save the Heteronuclear NOE values in the CCPN project as a data list'] texts = ['Refresh Table','Remove Pairs', 'Show Peak Pair','Create Hetero NOE List'] commands = [self.matchPeaks,self.removePair, self.showPeakPair,self.makeNoeList] self.pairButtons = ButtonList(frameB, tipTexts=tipTexts, grid=(1,0), texts=texts, commands=commands) bottomButtons = UtilityButtonList(tabbedFrame.sideFrame, helpUrl=self.help_url) bottomButtons.grid(row=0, column=0, sticky='e') self.updatePulldowns() self.updateAfter() self.administerNotifiers(self.registerNotify) def administerNotifiers(self, notifyFunc): for func in ('__init__', 'delete','setName'): for clazz in ('ccp.nmr.Nmr.DataSource', 'ccp.nmr.Nmr.Experiment',): notifyFunc(self.updatePulldowns, clazz, func) for func in ('__init__', 'delete'): notifyFunc(self.updatePulldowns,'ccp.nmr.Nmr.PeakList', func) for func in ('__init__', 'delete','setAnnotation','setFigOfMerit'): notifyFunc(self.updatePeaks, 'ccp.nmr.Nmr.Peak', func) for func in ('setAnnotation','setPosition','setNumAliasing'): notifyFunc(self.updatePeakChild, 'ccp.nmr.Nmr.PeakDim', func) for func in ('__init__', 'delete', 'setValue'): notifyFunc(self.updatePeakChild, 'ccp.nmr.Nmr.PeakIntensity', func) def changeTab(self, index): if index == 1: self.matchPeaks() def open(self): self.updatePulldowns() self.updateAfter() BasePopup.open(self) def destroy(self): self.administerNotifiers(self.unregisterNotify) BasePopup.destroy(self) def updatePulldowns(self, *obj): index0 = 0 index1 = 0 index2 = 0 names, peakLists = self.getPeakLists() if names: if self.refPeakList not in peakLists: self.refPeakList = peakLists[0] if self.satPeakList not in peakLists: self.satPeakList = peakLists[0] if self.assignPeakList not in peakLists: self.assignPeakList = peakLists[0] index0 = peakLists.index(self.refPeakList) index1 = peakLists.index(self.satPeakList) index2 = peakLists.index(self.assignPeakList) self.specAPulldown.setup(names, peakLists, index0) self.specBPulldown.setup(names, peakLists, index1) self.specCPulldown.setup(names, peakLists, index2) def updatePeakChild(self,peakChild): if self.waiting: return self.updatePeaks(peakChild.peak) def updatePeaks(self, peak): if self.waiting: return if peak.peakList in (self.refPeakList,self.satPeakList,self.assignPeakList): if peak.isDeleted and (peak.peakList in (self.refPeakList,self.satPeakList) ): for peaks in self.peakPairs: if peak in peaks: self.peakPairs.remove(peaks) if self.selectedPair is peaks: self.selectedPair = None self.updateAfter() return self.updateAfter() def setIntensityType(self, intensityType): self.intensityType = intensityType self.updateAfter() def viewRefPeakList(self): if self.refPeakList: self.updatePeakTable(self.refPeakList) def viewSatPeakList(self): if self.satPeakList: self.updatePeakTable(self.satPeakList) def viewAssignPeakList(self): if self.assignPeakList: self.updatePeakTable(self.assignPeakList) def viewSeparatePeakTable(self): if self.displayPeakList: self.guiParent.editPeakList(peakList=self.displayPeakList) def setRefPeakList(self, refPeakList): if self.displayPeakList is self.refPeakList: self.updatePeakTable(refPeakList) self.refPeakList = refPeakList self.updateViewButtons() self.updateAfter() def setSatPeakList(self, satPeakList): if self.displayPeakList is self.satPeakList: self.updatePeakTable(satPeakList) self.satPeakList = satPeakList self.updateViewButtons() self.updateAfter() def setAssignPeakList(self, assignPeakList): if self.displayPeakList is self.assignPeakList: self.updatePeakTable(assignPeakList) self.assignPeakList = assignPeakList self.updateViewButtons() self.updateAfter() def getPeakListName(self, peakList): if peakList: spectrum = peakList.dataSource experiment = spectrum.experiment name = '%s:%s:%d' % (experiment.name, spectrum.name, peakList.serial) else: name = '<None>' return name def getPeakLists(self): names = [] peakLists = [] for experiment in self.nmrProject.sortedExperiments(): for dataSource in experiment.sortedDataSources(): if dataSource.numDim == 2: dimsN = findSpectrumDimsByIsotope(dataSource,'15N') dimsH = findSpectrumDimsByIsotope(dataSource,'1H') if len(dimsN) == 1 and len(dimsH) == 1: for peakList in dataSource.sortedPeakLists(): name = self.getPeakListName(peakList) names.append( name ) peakLists.append(peakList) return names, peakLists def showPeakPair(self): if self.selectedPair: self.guiParent.viewPeaks(self.selectedPair) def selectCell(self, object, row, col): self.selectedPair = object if self.selectedPair: self.pairButtons.buttons[1].enable() self.pairButtons.buttons[2].enable() else: self.pairButtons.buttons[1].disable() self.pairButtons.buttons[2].disable() def removePair(self, *event): pairs = self.scrolledMatrix.currentObjects if pairs: for pair in pairs: self.peakPairs.remove(pair) self.selectedPair = None self.updateAfter() def matchPeaks(self): # assign relative to reference if self.assignPeakList and self.assignPeakList.peaks and self.refPeakList and self.satPeakList: tolH = float( self.tolHEntry.get() ) tolN = float( self.tolNEntry.get() ) pickNewPeaks = self.pickPeaksSelect.get() doAssign = self.assignSelect.get() dimH = findSpectrumDimsByIsotope(self.assignPeakList.dataSource,'1H' )[0] dimHA = findSpectrumDimsByIsotope(self.refPeakList.dataSource,'1H' )[0] dimHB = findSpectrumDimsByIsotope(self.satPeakList.dataSource,'1H' )[0] dimN = 1-dimH dimNA = 1-dimHA dimNB = 1-dimHB tolerancesA = [0,0] tolerancesA[dimHA] = tolH tolerancesA[dimNA] = tolN tolerancesB = [0,0] tolerancesB[dimHB] = tolH tolerancesB[dimNB] = tolN self.peakPairs = matchHnoePeaks(self.assignPeakList,self.refPeakList, self.satPeakList,tolerancesA,tolerancesB, pickNewPeaks,doAssign) self.updateAfter() def makeNoeList(self): if self.refPeakList is self.satPeakList: showWarning('Same Peak List', 'Ref Peak List and Sat Peak List cannot be the same', parent=self) return if self.peakPairs: s1 = self.refPeakList.dataSource s2 = self.satPeakList.dataSource noiseRef = getSpectrumNoise(s1) noiseSat = getSpectrumNoise(s2) es = '%s-%s' % (s1.experiment.name,s2.experiment.name) if len(es) > 50: es = 'Expt(%d)-Expt(%d)' % (s1.experiment.serial,s2.experiment.serial) noeList = self.nmrProject.newNoeList(unit='None',name='Hetero NOE list for %s' % es) noeList.setExperiments([s1.experiment,]) if s1.experiment is not s2.experiment: noeList.addExperiment( s2.experiment ) # TBD: sf, noeValueType, refValue, refDescription resonancePairsSeen = set() for (peakA,peakB) in self.peakPairs: # peakA is sat intensA = getPeakIntensity(peakA,self.intensityType) intensB = getPeakIntensity(peakB,self.intensityType) value = float(intensA)/intensB error = abs(value) * sqrt((noiseSat/intensA)**2 + (noiseRef/intensB)**2) resonances = tuple(self.getPeakResonances(peakA)) frozenResonances = frozenset(resonances) if len(resonances) < 2: pl = peakA.peakList sp = pl.dataSource msg = 'Skipping %s:%s:%d peak %d it has too few resonances assigned' data = (sp.experiment.name, sp.name, pl.serial, peakA.serial) showWarning('Warning',msg % data, parent=self) elif len(resonances) > 2: pl = peakA.peakList sp = pl.dataSource resonanceText = ' '.join([makeResonanceGuiName(r) for r in resonances]) msg = 'Skipping %s:%s:%d peak %d it has too many resonances assigned (%s)' data = (sp.experiment.name, sp.name, pl.serial, peakA.serial, resonanceText) showWarning('Warning', msg % data, parent=self) elif frozenResonances not in resonancePairsSeen: resonancePairsSeen.add(frozenResonances) noeList.newNoe(value=value,resonances=resonances,peaks=[peakA,peakB],error=error) else: resonanceText = ' '.join([makeResonanceGuiName(r) for r in resonances]) msg = 'Skipping duplicate entry for resonances %s' % resonanceText showWarning('Warning', msg, parent=self) self.parent.editMeasurements(measurementList=noeList) def getPeakResonances(self,peak): resonances = [] for peakDim in peak.sortedPeakDims(): for contrib in peakDim.sortedPeakDimContribs(): resonances.append(contrib.resonance) return resonances def updateAfter(self, *opt): if self.waiting: return else: self.waiting = True self.after_idle(self.update) def updateViewButtons(self): if self.refPeakList: self.viewPeaksButtons.buttons[0].enable() else: self.viewPeaksButtons.buttons[0].disable() if self.satPeakList: self.viewPeaksButtons.buttons[1].enable() else: self.viewPeaksButtons.buttons[1].disable() if self.assignPeakList: self.viewPeaksButtons.buttons[2].enable() else: self.viewPeaksButtons.buttons[2].disable() def updatePeakTable(self, peakList): if peakList is not self.displayPeakList: self.displayPeakList = peakList self.peakTable.update(peaks=peakList.sortedPeaks()) def update(self): if self.refPeakList: self.peaksALabel.set( 'Number of Ref Peaks: %d' % len(self.refPeakList.peaks) ) else: self.peaksALabel.set( 'Number of Ref Peaks: %d' % 0 ) if self.satPeakList: self.peaksBLabel.set( 'Number of Sat Peaks: %d' % len(self.satPeakList.peaks) ) else: self.peaksBLabel.set( 'Number of Sat Peaks: %d' % 0 ) if self.assignPeakList: self.peaksCLabel.set( 'Number of Assign Peaks: %d' % len(self.assignPeakList.peaks) ) else: self.peaksCLabel.set( 'Number of Assign Peaks: %d' % 0 ) if self.refPeakList and self.satPeakList and self.assignPeakList: if self.refPeakList is self.satPeakList: self.pairButtons.buttons[0].disable() else: self.pairButtons.buttons[0].enable() else: self.pairButtons.buttons[0].disable() if self.selectedPair: self.pairButtons.buttons[1].enable() self.pairButtons.buttons[2].enable() else: self.pairButtons.buttons[1].disable() self.pairButtons.buttons[2].disable() if self.peakPairs: self.pairButtons.buttons[3].enable() dsA = self.peakPairs[0][0].peakList.dataSource dsB = self.peakPairs[0][1].peakList.dataSource dimHA = findSpectrumDimsByIsotope(dsA,'1H')[0] dimHB = findSpectrumDimsByIsotope(dsB,'1H')[0] dimNA = findSpectrumDimsByIsotope(dsA,'15N')[0] dimNB = findSpectrumDimsByIsotope(dsB,'15N')[0] else: self.pairButtons.buttons[3].disable() objectList = [] textMatrix = [] i = 0 for (peakA,peakB) in self.peakPairs: i += 1 peakDimsA = peakA.sortedPeakDims() peakDimsB = peakB.sortedPeakDims() ppm0 = peakDimsA[dimHA].value ppm1 = peakDimsB[dimHB].value ppm2 = peakDimsA[dimNA].value ppm3 = peakDimsB[dimNB].value d0 = abs(ppm0-ppm1) d1 = abs(ppm2-ppm3) intensA = getPeakIntensity(peakA,self.intensityType) intensB = getPeakIntensity(peakB,self.intensityType) datum = [] datum.append( i ) datum.append( getPeakAnnotation(peakA, doPeakDims=False) ) datum.append( getPeakAnnotation(peakB, doPeakDims=False) ) datum.append( ppm0 ) datum.append( ppm1 ) datum.append( ppm2 ) datum.append( ppm3 ) datum.append( sqrt((d0*d0)+(d1*d1)) ) datum.append( intensA ) datum.append( intensB ) if intensB: datum.append( float(intensA)/intensB ) else: datum.append( None ) seqCodes = ','.join(['%s' % seqCode for seqCode in getPeakSeqCodes(peakB)]) datum.append(seqCodes) objectList.append( (peakA,peakB) ) textMatrix.append( datum ) if not objectList: textMatrix.append([]) self.scrolledMatrix.update(objectList=objectList, textMatrix=textMatrix) self.waiting = False
class ViewResidueFrame(Frame): showAssign = True chemCompVar = None residue = None def __init__(self, parent, residue=None, resizeCallback=None, project=None, tipText=None, shiftList=None, *args, **kw): self.shiftList = shiftList Frame.__init__(self, parent, *args, **kw) self.grid_columnconfigure(2, weight=1) row = 0 self.label = Label(self, text='', grid=(row, 0)) self.assignSelect = CheckButton( self, callback=self.setDisplayAssign, grid=(row, 1), tipText='Whether to show chemical shifts of assigned atoms') label0 = Label(self, text='Show Assignments', grid=(row, 2)) row += 1 self.grid_rowconfigure(row, weight=1) self.varFrame = ViewChemCompVarFrame(self, chemCompVar=self.chemCompVar, project=project, tipText=tipText, grid=(row, 0), gridSpan=(1, 3)) self.assignSelect.set(True) def setDisplayAssign(self, trueOrFalse): self.showAssign = trueOrFalse self.update(self.residue) def setResidue(self, residue): self.residue = residue shiftList = self.shiftList if residue: self.varFrame.update(self.residue.chemCompVar) cAtomDict = self.varFrame.cAtomDict for atom in self.residue.atoms: chemAtom = atom.chemAtom cAtom = cAtomDict.get(chemAtom) if cAtom and self.showAssign: shifts = getAtomSetShifts(atom.atomSet, shiftList) label = '/'.join( ['%3.3f' % (shift.value) for shift in shifts]) cAtom.setAnnotation(chemAtom.name + ' ' + label) self.varFrame.drawStructure() chain = self.residue.chain self.label.set('Residue: %d%s ( %s %s )' % (self.residue.seqCode, getResidueCode(self.residue), chain.molSystem.code, chain.code)) else: self.varFrame.update(None) self.label.set('Residue: <None>') def update(self, residue=None, shiftList=None): self.shiftList = shiftList self.setResidue(residue) def printStructure(self): self.varFrame.printStructure()
class CingGui(BasePopup): def __init__(self, parent, options, *args, **kw): # Fill in below variable once run generates some results self.haveResults = None # store the options self.options = options BasePopup.__init__(self, parent=parent, title='CING Setup', **kw) # self.setGeometry(850, 750, 50, 50) self.project = None # self.tk_strictMotif( True) self.updateGui() # end def __init__ def body(self, guiFrame): row = 0 col =0 # frame = Frame( guiFrame ) # frame.grid(row=row, column=col, sticky='news') self.menuBar = Menu( guiFrame) self.menuBar.grid( row=row, column=col, sticky='ew') #---------------------------------------------------------------------------------- # Project frame #---------------------------------------------------------------------------------- # guiFrame.grid_columnconfigure(row, weight=1) # frame = LabelFrame(guiFrame, text='Project', font=medFont) row = +1 col =0 frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes ) print '>', frame.keys() frame.grid(row=row, column=col, sticky='nsew' ) frame.grid_columnconfigure(2, weight=1) # frame.grid_rowconfigure(0, weight=1) srow = 0 self.projectOptions = ['old','new from PDB','new from CCPN','new from CYANA'] self.projOptionsSelect = RadioButtons(frame, selected_index=0, entries=self.projectOptions, direction='vertical', select_callback=self.updateGui ) self.projOptionsSelect.grid(row=srow,column=0,rowspan=len(self.projectOptions),columnspan=2, sticky='w') if self.options.name: text = self.options.name else: text='' # end if self.projEntry = Entry(frame, bd=1, text=text, returnCallback=self.updateGui) self.projEntry.grid(row=srow,column=2,columnspan=2,sticky='ew') # self.projEntry.bind('<Key>', self.updateGui) self.projEntry.bind('<Leave>', self.updateGui) projButton = Button(frame, bd=1,command=self.chooseOldProjectFile, text='browse') projButton.grid(row=srow,column=3,sticky='ew') srow += 1 self.pdbEntry = Entry(frame, bd=1, text='') self.pdbEntry.grid(row=srow,column=2,sticky='ew') self.pdbEntry.bind('<Leave>', self.updateGui) pdbButton = Button(frame, bd=1,command=self.choosePdbFile, text='browse') pdbButton.grid(row=srow,column=3,sticky='ew') srow += 1 self.ccpnEntry = Entry(frame, bd=1, text='') self.ccpnEntry.grid(row=srow,column=2,sticky='ew') self.ccpnEntry.bind('<Leave>', self.updateGui) ccpnButton = Button(frame, bd=1,command=self.chooseCcpnFile, text='browse') ccpnButton.grid(row=srow,column=3,sticky='ew') srow += 1 self.cyanaEntry = Entry(frame, bd=1, text='') self.cyanaEntry.grid(row=srow,column=2,sticky='ew') self.cyanaEntry.bind('<Leave>', self.updateGui) cyanaButton = Button(frame, bd=1,command=self.chooseCyanaFile, text='browse') cyanaButton.grid(row=srow,column=3,sticky='ew') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') srow += 1 label = Label(frame, text='Project name:') label.grid(row=srow,column=0,sticky='nw') self.nameEntry = Entry(frame, bd=1, text='') self.nameEntry.grid(row=srow,column=2,sticky='w') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') srow += 1 self.openProjectButton = Button(frame, command=self.openProject, text='Open Project', **actionButtonAttributes ) self.openProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew') #---------------------------------------------------------------------------------- # status #---------------------------------------------------------------------------------- # guiFrame.grid_columnconfigure(1, weight=0) srow = 0 frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes) frame.grid( row=srow, column=1, sticky='wnes') self.projectStatus = Text(frame, height=11, width=70, borderwidth=0, relief='flat') self.projectStatus.grid(row=0, column=0, sticky='wen') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') srow += 1 self.closeProjectButton = Button(frame, command=self.closeProject, text='Close Project', **actionButtonAttributes) self.closeProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew') #---------------------------------------------------------------------------------- # Validate frame #---------------------------------------------------------------------------------- row +=1 col=0 frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes) # frame = LabelFrame(guiFrame, text='Validate', font=medFont) frame.grid(row=row, column=col, sticky='nsew') # frame.grid_columnconfigure(2, weight=1) frame.grid_rowconfigure(0, weight=1) srow = 0 # label = Label(frame, text='validation') # label.grid(row=srow,column=0,sticky='nw') # # self.selectDoValidation = CheckButton(frame) # self.selectDoValidation.grid(row=srow, column=1,sticky='nw' ) # self.selectDoValidation.set(True) # # srow += 1 # label = Label(frame, text='') # label.grid(row=srow,column=0,sticky='nw') # # srow += 1 label = Label(frame, text='checks') label.grid(row=srow,column=0,sticky='nw') self.selectCheckAssign = CheckButton(frame) self.selectCheckAssign.grid(row=srow, column=1,sticky='nw' ) self.selectCheckAssign.set(True) label = Label(frame, text='assignments and shifts') label.grid(row=srow,column=2,sticky='nw') # srow += 1 # self.selectCheckQueen = CheckButton(frame) # self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' ) # self.selectCheckQueen.set(False) # label = Label(frame, text='QUEEN') # label.grid(row=srow,column=5,sticky='nw') # # queenButton = Button(frame, bd=1,command=None, text='setup') # queenButton.grid(row=srow,column=6,sticky='ew') srow += 1 self.selectCheckResraint = CheckButton(frame) self.selectCheckResraint.grid(row=srow, column=1,sticky='nw' ) self.selectCheckResraint.set(True) label = Label(frame, text='restraints') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectCheckStructure = CheckButton(frame) self.selectCheckStructure.grid(row=srow, column=1,sticky='nw' ) self.selectCheckStructure.set(True) label = Label(frame, text='structural') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectMakeHtml = CheckButton(frame) self.selectMakeHtml.grid(row=srow, column=1,sticky='nw' ) self.selectMakeHtml.set(True) label = Label(frame, text='generate HTML') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectCheckScript = CheckButton(frame) self.selectCheckScript.grid(row=srow, column=1,sticky='nw' ) self.selectCheckScript.set(False) label = Label(frame, text='user script') label.grid(row=srow,column=0,sticky='nw') self.validScriptEntry = Entry(frame, bd=1, text='') self.validScriptEntry.grid(row=srow,column=2,columnspan=3, sticky='ew') scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse') scriptButton.grid(row=srow,column=5,sticky='ew') srow += 1 label = Label(frame, text='ranges') label.grid(row=srow,column=0,sticky='nw') self.rangesEntry = Entry( frame, text='' ) self.rangesEntry.grid( row=srow, column=2, columnspan=3, sticky='ew') # self.validScriptEntry = Entry(frame, bd=1, text='') # self.validScriptEntry.grid(row=srow,column=3,sticky='ew') # # scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse') # scriptButton.grid(row=srow,column=4,sticky='ew') srow += 1 texts = ['Run Validation','View Results','Setup QUEEN'] commands = [self.runCing, None, None] buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True) buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew') for button in buttonBar.buttons: button.config(**actionButtonAttributes) # end for self.runButton = buttonBar.buttons[0] self.viewResultButton = buttonBar.buttons[1] self.queenButton = buttonBar.buttons[2] #---------------------------------------------------------------------------------- # Miscellaneous frame #---------------------------------------------------------------------------------- row +=0 col=1 # frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont) frame = LabelFrame(guiFrame, text='Miscellaneous', **labelFrameAttributes) frame.grid(row=row, column=col, sticky='news') frame.grid_columnconfigure(2, weight=1) frame.grid_columnconfigure(4, weight=1,minsize=30) frame.grid_rowconfigure(0, weight=1) # Exports srow = 0 label = Label(frame, text='export to') label.grid(row=srow,column=0,sticky='nw') self.selectExportXeasy = CheckButton(frame) self.selectExportXeasy.grid(row=srow, column=1,sticky='nw' ) self.selectExportXeasy.set(True) label = Label(frame, text='Xeasy, Sparky, TALOS, ...') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectExportCcpn = CheckButton(frame) self.selectExportCcpn.grid(row=srow, column=1,sticky='nw' ) self.selectExportCcpn.set(True) label = Label(frame, text='CCPN') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectExportQueen = CheckButton(frame) self.selectExportQueen.grid(row=srow, column=1,sticky='nw' ) self.selectExportQueen.set(True) label = Label(frame, text='QUEEN') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectExportRefine = CheckButton(frame) self.selectExportRefine.grid(row=srow, column=1,sticky='nw' ) self.selectExportRefine.set(True) label = Label(frame, text='refine') label.grid(row=srow,column=2,sticky='nw') srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') # User script srow += 1 label = Label(frame, text='user script') label.grid(row=srow,column=0,sticky='nw') self.selectMiscScript = CheckButton(frame) self.selectMiscScript.grid(row=srow, column=1,sticky='nw' ) self.selectMiscScript.set(False) self.miscScriptEntry = Entry(frame, bd=1, text='') self.miscScriptEntry.grid(row=srow,column=3,sticky='ew') script2Button = Button(frame, bd=1,command=self.chooseMiscScript, text='browse') script2Button.grid(row=srow,column=4,sticky='ew') srow += 1 texts = ['Export','Run Script'] commands = [None, None] buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True) buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew') for button in buttonBar.buttons: button.config(**actionButtonAttributes) # end for self.exportButton = buttonBar.buttons[0] self.scriptButton = buttonBar.buttons[1] #---------------------------------------------------------------------------------- # Textarea #---------------------------------------------------------------------------------- row +=1 guiFrame.grid_rowconfigure(row, weight=1) self.outputTextBox = ScrolledText(guiFrame) self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew') self.redirectConsole() #---------------------------------------------------------------------------------- # Buttons #---------------------------------------------------------------------------------- row +=1 col=0 texts = ['Quit', 'Help'] commands = [self.close, None] self.buttonBar = ButtonList(guiFrame, texts=texts, commands=commands,expands=True) self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew') # self.openProjectButton = self.buttonBar.buttons[0] # self.closeProjectButton = self.buttonBar.buttons[1] # self.runButton = self.buttonBar.buttons[0] # self.viewResultButton = self.buttonBar.buttons[1] for button in self.buttonBar.buttons: button.config(**actionButtonAttributes) # end for # end def body def getGuiOptions(self): projectName = self.projEntry.get() index = self.projOptionsSelect.getIndex() if index > 0: makeNewProject = True projectImport = None if index > 1: i = index-2 format = ['PDB','CCPN','CYANA'][i] file = [self.pdbEntry, self.ccpnEntry, self.cyanaEntry][i].get() if not file: showWarning('Failure','No %s file selected' % format) return # end if projectImport = (format, file) # end if else: # Chould also check that any old project file exists makeNewProject = False projectImport = None # end if doValidation = self.selectDoValidation.get() checks = [] if doValidation: if self.selectCheckAssign.get(): checks.append('assignments') # end if if self.selectCheckResraint.get(): checks.append('restraints') # end if if self.selectCheckStructure.get(): checks.append('structural') # end if if self.selectMakeHtml.get(): checks.append('HTML') # end if if self.selectCheckScript.get(): script = self.validScriptEntry.get() if script: checks.append( ('script',script) ) # end if # end if if self.selectCheckQueen.get(): checks.append('queen') # end if # end if exports = [] if self.selectExportXeasy.get(): exports.append('Xeasy') # end if if self.selectExportCcpn.get(): exports.append('CCPN') # end if if self.selectExportQueen.get(): exports.append('QUEEN') # end if if self.selectExportRefine.get(): exports.append('refine') # end if miscScript = None if self.selectMiscScript.get(): script = self.miscScriptEntry.get() if script: miscScript = script # end if # end if return projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript # end def getGuiOptions def runCing(self): options = self.getGuiOptions() if options: projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript = options print 'Project name:', projectName print 'Make new project?', makeNewProject print 'Import source:', projectImport print 'Do vailidation?', doValidation print 'Validation checks:', ','.join(checks) print 'Export to:', ','.join(exports) print 'User script:', miscScript # end if # end def runCing # else there was already an error message def chooseOldProjectFile(self): fileTypes = [ FileType('CING', ['project.xml']), FileType('All', ['*']) ] popup = FileSelectPopup(self, file_types = fileTypes, title = 'Select CING project file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = popup.getFile() # dirName = popup.getDirectory() if len(fileName) > 0: # Put text into entry,name widgets dummy,name = cing.Project.rootPath(fileName) self.projEntry.configure(state='normal') self.projEntry.set(fileName) self.nameEntry.configure(state='normal') self.nameEntry.set(name) self.nameEntry.configure(state='disabled') # choose the correct radiobutton self.projOptionsSelect.setIndex(0) self.updateGui() # end if #nd if popup.destroy() # end def chooseOldProjectFile def choosePdbFile(self): fileTypes = [ FileType('PDB', ['*.pdb']), FileType('All', ['*'])] popup = FileSelectPopup(self, file_types = fileTypes, title = 'PDB file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = popup.getFile() if len(fileName)>0: # Put text into entry widget self.pdbEntry.configure(state='normal') self.pdbEntry.set(fileName) # Put text into name widget _dir,name,dummy = nTpath( fileName ) self.nameEntry.configure(state='normal') self.nameEntry.set(name) # choose the correct radiobutton self.projOptionsSelect.setIndex(1) self.updateGui() #end if popup.destroy() # end def choosePdbFile def chooseCcpnFile(self): fileTypes = [ FileType('XML', ['*.xml']), FileType('All', ['*'])] popup = FileSelectPopup(self, file_types = fileTypes, title = 'CCPN project XML file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = popup.getFile() if len(fileName)>0: self.pdbEntry.configure(state='normal') self.pdbEntry.set(fileName) self.projOptionsSelect.setIndex(1) _dir,name,dummy = nTpath( fileName ) self.nameEntry.set(name) #end if self.ccpnEntry.set(fileName) self.projOptionsSelect.setIndex(2) popup.destroy() # end def chooseCcpnFile def chooseCyanaFile(self): # Prepend default Cyana file extension below fileTypes = [ FileType('All', ['*']), ] popup = FileSelectPopup(self, file_types = fileTypes, title = 'CYANA fproject file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = popup.getFile() self.cyanaEntry.set(fileName) self.projOptionsSelect.setIndex(3) popup.destroy() # end def chooseCyanaFile def chooseValidScript(self): # Prepend default Cyana file extension below fileTypes = [ FileType('All', ['*']), ] popup = FileSelectPopup(self, file_types = fileTypes, title = 'Script file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = popup.getFile() self.validScriptEntry.set(fileName) popup.destroy() # end def chooseValidScript def chooseMiscScript(self): # Prepend default Cyana file extension below fileTypes = [ FileType('All', ['*']), ] popup = FileSelectPopup(self, file_types = fileTypes, title = 'Script file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = popup.getFile() self.miscScriptEntry.set(fileName) popup.destroy() # end def chooseMiscScript def openProject(self ): projOption = self.projOptionsSelect.get() if projOption == self.projectOptions[0]: self.openOldProject() elif projOption == self.projectOptions[1]: self.initPdb() # end if if self.project: self.project.gui = self # end if self.updateGui() #end def def openOldProject(self ): fName = self.projEntry.get() if not os.path.exists( fName ): nTerror('Error: file "%s" does not exist\n', fName) #end if if self.project: self.closeProject() # end if self.project = cing.Project.open( name=fName, status='old', verbose=False ) #end def def initPdb(self ): fName = self.pdbEntry.get() if not os.path.exists( fName ): nTerror('Error: file "%s" does not exist\n', fName) #end if self.project = cing.Project.open( self.nameEntry.get(), status='new' ) self.project.initPDB( pdbFile=fName, convention = 'PDB' ) #end def def closeProject(self): if self.project: self.project.close() # end if self.project = None self.updateGui() #end def def updateGui(self, event=None): projOption = self.projOptionsSelect.get() buttons = self.buttonBar.buttons # Disable entries for e in [self.projEntry, self.pdbEntry, self.ccpnEntry, self.cyanaEntry, self.nameEntry]: e.configure(state='disabled') #end for if projOption == self.projectOptions[0]: # Enable entries self.projEntry.configure(state='normal') if (len(self.projEntry.get()) > 0): self.openProjectButton.enable() self.runButton.enable() else: self.openProjectButton.disable() self.runButton.disable() #end if elif projOption == self.projectOptions[1]: # Enable entries self.pdbEntry.configure(state='normal') self.nameEntry.configure(state='normal') if (len(self.pdbEntry.get()) > 0 and len(self.nameEntry.get()) > 0): buttons[0].enable() buttons[1].enable() else: buttons[0].disable() buttons[1].disable() #end if #end if elif projOption == self.projectOptions[2]: # Enable entries self.ccpnEntry.configure(state='normal') self.nameEntry.configure(state='normal') if (len(self.ccpnEntry.get()) > 0 and len(self.nameEntry.get()) > 0): buttons[0].enable() buttons[1].enable() else: buttons[0].disable() buttons[1].disable() #end if #end if elif projOption == self.projectOptions[3]: # Enable entries self.cyanaEntry.configure(state='normal') self.nameEntry.configure(state='normal') if (len(self.cyanaEntry.get()) > 0 and len(self.nameEntry.get()) > 0): buttons[0].enable() buttons[1].enable() else: buttons[0].disable() buttons[1].disable() #end if #end if self.projectStatus.clear() if not self.project: self.projectStatus.setText('No open project') self.closeProjectButton.setText('Close Project') self.closeProjectButton.disable() else: self.projectStatus.setText(self.project.format()) self.closeProjectButton.enable() self.closeProjectButton.setText(sprintf('Close Project "%s"', self.project.name)) #end if #end def def redirectConsole(self): #pipe = TextPipe(self.inputTextBox.text_area) #sys.stdin = pipe pipe = TextPipe(self.outputTextBox.text_area) sys.stdout = pipe nTmessage.stream = pipe # end def redirectConsole # sys.stderr = pipe def resetConsole(self): #sys.stdin = stdin nTmessage.stream = stdout sys.stdout = stdout sys.stderr = stderr # end def resetConsole def open(self): self.redirectConsole() BasePopup.open(self) # end def open def close(self): geometry = self.getGeometry() self.resetConsole() BasePopup.close(self) print 'close:',geometry sys.exit(0) # remove later # end def close def destroy(self): geometry = self.getGeometry() self.resetConsole() BasePopup.destroy(self) print 'destroy:',geometry sys.exit(0) # remove later
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 CingGui(BasePopup): def __init__(self, parent, options, *args, **kw): # Fill in below variable once run generates some results self.haveResults = None # store the options self.options = options BasePopup.__init__(self, parent=parent, title='CING Setup', **kw) # self.setGeometry(850, 750, 50, 50) self.project = None # self.tk_strictMotif( True) self.updateGui() # end def __init__ def body(self, guiFrame): row = 0 col = 0 # frame = Frame( guiFrame ) # frame.grid(row=row, column=col, sticky='news') self.menuBar = Menu(guiFrame) self.menuBar.grid(row=row, column=col, sticky='ew') #---------------------------------------------------------------------------------- # Project frame #---------------------------------------------------------------------------------- # guiFrame.grid_columnconfigure(row, weight=1) # frame = LabelFrame(guiFrame, text='Project', font=medFont) row = +1 col = 0 frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes) print '>', frame.keys() frame.grid(row=row, column=col, sticky='nsew') frame.grid_columnconfigure(2, weight=1) # frame.grid_rowconfigure(0, weight=1) srow = 0 self.projectOptions = [ 'old', 'new from PDB', 'new from CCPN', 'new from CYANA' ] self.projOptionsSelect = RadioButtons(frame, selected_index=0, entries=self.projectOptions, direction='vertical', select_callback=self.updateGui) self.projOptionsSelect.grid(row=srow, column=0, rowspan=len(self.projectOptions), columnspan=2, sticky='w') if self.options.name: text = self.options.name else: text = '' # end if self.projEntry = Entry(frame, bd=1, text=text, returnCallback=self.updateGui) self.projEntry.grid(row=srow, column=2, columnspan=2, sticky='ew') # self.projEntry.bind('<Key>', self.updateGui) self.projEntry.bind('<Leave>', self.updateGui) projButton = Button(frame, bd=1, command=self.chooseOldProjectFile, text='browse') projButton.grid(row=srow, column=3, sticky='ew') srow += 1 self.pdbEntry = Entry(frame, bd=1, text='') self.pdbEntry.grid(row=srow, column=2, sticky='ew') self.pdbEntry.bind('<Leave>', self.updateGui) pdbButton = Button(frame, bd=1, command=self.choosePdbFile, text='browse') pdbButton.grid(row=srow, column=3, sticky='ew') srow += 1 self.ccpnEntry = Entry(frame, bd=1, text='') self.ccpnEntry.grid(row=srow, column=2, sticky='ew') self.ccpnEntry.bind('<Leave>', self.updateGui) ccpnButton = Button(frame, bd=1, command=self.chooseCcpnFile, text='browse') ccpnButton.grid(row=srow, column=3, sticky='ew') srow += 1 self.cyanaEntry = Entry(frame, bd=1, text='') self.cyanaEntry.grid(row=srow, column=2, sticky='ew') self.cyanaEntry.bind('<Leave>', self.updateGui) cyanaButton = Button(frame, bd=1, command=self.chooseCyanaFile, text='browse') cyanaButton.grid(row=srow, column=3, sticky='ew') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow, column=0, sticky='nw') srow += 1 label = Label(frame, text='Project name:') label.grid(row=srow, column=0, sticky='nw') self.nameEntry = Entry(frame, bd=1, text='') self.nameEntry.grid(row=srow, column=2, sticky='w') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow, column=0, sticky='nw') srow += 1 self.openProjectButton = Button(frame, command=self.openProject, text='Open Project', **actionButtonAttributes) self.openProjectButton.grid(row=srow, column=0, columnspan=4, sticky='ew') #---------------------------------------------------------------------------------- # status #---------------------------------------------------------------------------------- # guiFrame.grid_columnconfigure(1, weight=0) srow = 0 frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes) frame.grid(row=srow, column=1, sticky='wnes') self.projectStatus = Text(frame, height=11, width=70, borderwidth=0, relief='flat') self.projectStatus.grid(row=0, column=0, sticky='wen') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow, column=0, sticky='nw') srow += 1 self.closeProjectButton = Button(frame, command=self.closeProject, text='Close Project', **actionButtonAttributes) self.closeProjectButton.grid(row=srow, column=0, columnspan=4, sticky='ew') #---------------------------------------------------------------------------------- # Validate frame #---------------------------------------------------------------------------------- row += 1 col = 0 frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes) # frame = LabelFrame(guiFrame, text='Validate', font=medFont) frame.grid(row=row, column=col, sticky='nsew') # frame.grid_columnconfigure(2, weight=1) frame.grid_rowconfigure(0, weight=1) srow = 0 # label = Label(frame, text='validation') # label.grid(row=srow,column=0,sticky='nw') # # self.selectDoValidation = CheckButton(frame) # self.selectDoValidation.grid(row=srow, column=1,sticky='nw' ) # self.selectDoValidation.set(True) # # srow += 1 # label = Label(frame, text='') # label.grid(row=srow,column=0,sticky='nw') # # srow += 1 label = Label(frame, text='checks') label.grid(row=srow, column=0, sticky='nw') self.selectCheckAssign = CheckButton(frame) self.selectCheckAssign.grid(row=srow, column=1, sticky='nw') self.selectCheckAssign.set(True) label = Label(frame, text='assignments and shifts') label.grid(row=srow, column=2, sticky='nw') # srow += 1 # self.selectCheckQueen = CheckButton(frame) # self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' ) # self.selectCheckQueen.set(False) # label = Label(frame, text='QUEEN') # label.grid(row=srow,column=5,sticky='nw') # # queenButton = Button(frame, bd=1,command=None, text='setup') # queenButton.grid(row=srow,column=6,sticky='ew') srow += 1 self.selectCheckResraint = CheckButton(frame) self.selectCheckResraint.grid(row=srow, column=1, sticky='nw') self.selectCheckResraint.set(True) label = Label(frame, text='restraints') label.grid(row=srow, column=2, sticky='nw') srow += 1 self.selectCheckStructure = CheckButton(frame) self.selectCheckStructure.grid(row=srow, column=1, sticky='nw') self.selectCheckStructure.set(True) label = Label(frame, text='structural') label.grid(row=srow, column=2, sticky='nw') srow += 1 self.selectMakeHtml = CheckButton(frame) self.selectMakeHtml.grid(row=srow, column=1, sticky='nw') self.selectMakeHtml.set(True) label = Label(frame, text='generate HTML') label.grid(row=srow, column=2, sticky='nw') srow += 1 self.selectCheckScript = CheckButton(frame) self.selectCheckScript.grid(row=srow, column=1, sticky='nw') self.selectCheckScript.set(False) label = Label(frame, text='user script') label.grid(row=srow, column=0, sticky='nw') self.validScriptEntry = Entry(frame, bd=1, text='') self.validScriptEntry.grid(row=srow, column=2, columnspan=3, sticky='ew') scriptButton = Button(frame, bd=1, command=self.chooseValidScript, text='browse') scriptButton.grid(row=srow, column=5, sticky='ew') srow += 1 label = Label(frame, text='ranges') label.grid(row=srow, column=0, sticky='nw') self.rangesEntry = Entry(frame, text='') self.rangesEntry.grid(row=srow, column=2, columnspan=3, sticky='ew') # self.validScriptEntry = Entry(frame, bd=1, text='') # self.validScriptEntry.grid(row=srow,column=3,sticky='ew') # # scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse') # scriptButton.grid(row=srow,column=4,sticky='ew') srow += 1 texts = ['Run Validation', 'View Results', 'Setup QUEEN'] commands = [self.runCing, None, None] buttonBar = ButtonList(frame, texts=texts, commands=commands, expands=True) buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew') for button in buttonBar.buttons: button.config(**actionButtonAttributes) # end for self.runButton = buttonBar.buttons[0] self.viewResultButton = buttonBar.buttons[1] self.queenButton = buttonBar.buttons[2] #---------------------------------------------------------------------------------- # Miscellaneous frame #---------------------------------------------------------------------------------- row += 0 col = 1 # frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont) frame = LabelFrame(guiFrame, text='Miscellaneous', **labelFrameAttributes) frame.grid(row=row, column=col, sticky='news') frame.grid_columnconfigure(2, weight=1) frame.grid_columnconfigure(4, weight=1, minsize=30) frame.grid_rowconfigure(0, weight=1) # Exports srow = 0 label = Label(frame, text='export to') label.grid(row=srow, column=0, sticky='nw') self.selectExportXeasy = CheckButton(frame) self.selectExportXeasy.grid(row=srow, column=1, sticky='nw') self.selectExportXeasy.set(True) label = Label(frame, text='Xeasy, Sparky, TALOS, ...') label.grid(row=srow, column=2, sticky='nw') srow += 1 self.selectExportCcpn = CheckButton(frame) self.selectExportCcpn.grid(row=srow, column=1, sticky='nw') self.selectExportCcpn.set(True) label = Label(frame, text='CCPN') label.grid(row=srow, column=2, sticky='nw') srow += 1 self.selectExportQueen = CheckButton(frame) self.selectExportQueen.grid(row=srow, column=1, sticky='nw') self.selectExportQueen.set(True) label = Label(frame, text='QUEEN') label.grid(row=srow, column=2, sticky='nw') srow += 1 self.selectExportRefine = CheckButton(frame) self.selectExportRefine.grid(row=srow, column=1, sticky='nw') self.selectExportRefine.set(True) label = Label(frame, text='refine') label.grid(row=srow, column=2, sticky='nw') srow += 1 label = Label(frame, text='') label.grid(row=srow, column=0, sticky='nw') # User script srow += 1 label = Label(frame, text='user script') label.grid(row=srow, column=0, sticky='nw') self.selectMiscScript = CheckButton(frame) self.selectMiscScript.grid(row=srow, column=1, sticky='nw') self.selectMiscScript.set(False) self.miscScriptEntry = Entry(frame, bd=1, text='') self.miscScriptEntry.grid(row=srow, column=3, sticky='ew') script2Button = Button(frame, bd=1, command=self.chooseMiscScript, text='browse') script2Button.grid(row=srow, column=4, sticky='ew') srow += 1 texts = ['Export', 'Run Script'] commands = [None, None] buttonBar = ButtonList(frame, texts=texts, commands=commands, expands=True) buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew') for button in buttonBar.buttons: button.config(**actionButtonAttributes) # end for self.exportButton = buttonBar.buttons[0] self.scriptButton = buttonBar.buttons[1] #---------------------------------------------------------------------------------- # Textarea #---------------------------------------------------------------------------------- row += 1 guiFrame.grid_rowconfigure(row, weight=1) self.outputTextBox = ScrolledText(guiFrame) self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew') self.redirectConsole() #---------------------------------------------------------------------------------- # Buttons #---------------------------------------------------------------------------------- row += 1 col = 0 texts = ['Quit', 'Help'] commands = [self.close, None] self.buttonBar = ButtonList(guiFrame, texts=texts, commands=commands, expands=True) self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew') # self.openProjectButton = self.buttonBar.buttons[0] # self.closeProjectButton = self.buttonBar.buttons[1] # self.runButton = self.buttonBar.buttons[0] # self.viewResultButton = self.buttonBar.buttons[1] for button in self.buttonBar.buttons: button.config(**actionButtonAttributes) # end for # end def body def getGuiOptions(self): projectName = self.projEntry.get() index = self.projOptionsSelect.getIndex() if index > 0: makeNewProject = True projectImport = None if index > 1: i = index - 2 format = ['PDB', 'CCPN', 'CYANA'][i] file = [self.pdbEntry, self.ccpnEntry, self.cyanaEntry][i].get() if not file: showWarning('Failure', 'No %s file selected' % format) return # end if projectImport = (format, file) # end if else: # Chould also check that any old project file exists makeNewProject = False projectImport = None # end if doValidation = self.selectDoValidation.get() checks = [] if doValidation: if self.selectCheckAssign.get(): checks.append('assignments') # end if if self.selectCheckResraint.get(): checks.append('restraints') # end if if self.selectCheckStructure.get(): checks.append('structural') # end if if self.selectMakeHtml.get(): checks.append('HTML') # end if if self.selectCheckScript.get(): script = self.validScriptEntry.get() if script: checks.append(('script', script)) # end if # end if if self.selectCheckQueen.get(): checks.append('queen') # end if # end if exports = [] if self.selectExportXeasy.get(): exports.append('Xeasy') # end if if self.selectExportCcpn.get(): exports.append('CCPN') # end if if self.selectExportQueen.get(): exports.append('QUEEN') # end if if self.selectExportRefine.get(): exports.append('refine') # end if miscScript = None if self.selectMiscScript.get(): script = self.miscScriptEntry.get() if script: miscScript = script # end if # end if return projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript # end def getGuiOptions def runCing(self): options = self.getGuiOptions() if options: projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript = options print 'Project name:', projectName print 'Make new project?', makeNewProject print 'Import source:', projectImport print 'Do vailidation?', doValidation print 'Validation checks:', ','.join(checks) print 'Export to:', ','.join(exports) print 'User script:', miscScript # end if # end def runCing # else there was already an error message def chooseOldProjectFile(self): fileTypes = [FileType('CING', ['project.xml']), FileType('All', ['*'])] popup = FileSelectPopup(self, file_types=fileTypes, title='Select CING project file', dismiss_text='Cancel', selected_file_must_exist=True) fileName = popup.getFile() # dirName = popup.getDirectory() if len(fileName) > 0: # Put text into entry,name widgets dummy, name = cing.Project.rootPath(fileName) self.projEntry.configure(state='normal') self.projEntry.set(fileName) self.nameEntry.configure(state='normal') self.nameEntry.set(name) self.nameEntry.configure(state='disabled') # choose the correct radiobutton self.projOptionsSelect.setIndex(0) self.updateGui() # end if #nd if popup.destroy() # end def chooseOldProjectFile def choosePdbFile(self): fileTypes = [FileType('PDB', ['*.pdb']), FileType('All', ['*'])] popup = FileSelectPopup(self, file_types=fileTypes, title='PDB file', dismiss_text='Cancel', selected_file_must_exist=True) fileName = popup.getFile() if len(fileName) > 0: # Put text into entry widget self.pdbEntry.configure(state='normal') self.pdbEntry.set(fileName) # Put text into name widget _dir, name, dummy = nTpath(fileName) self.nameEntry.configure(state='normal') self.nameEntry.set(name) # choose the correct radiobutton self.projOptionsSelect.setIndex(1) self.updateGui() #end if popup.destroy() # end def choosePdbFile def chooseCcpnFile(self): fileTypes = [FileType('XML', ['*.xml']), FileType('All', ['*'])] popup = FileSelectPopup(self, file_types=fileTypes, title='CCPN project XML file', dismiss_text='Cancel', selected_file_must_exist=True) fileName = popup.getFile() if len(fileName) > 0: self.pdbEntry.configure(state='normal') self.pdbEntry.set(fileName) self.projOptionsSelect.setIndex(1) _dir, name, dummy = nTpath(fileName) self.nameEntry.set(name) #end if self.ccpnEntry.set(fileName) self.projOptionsSelect.setIndex(2) popup.destroy() # end def chooseCcpnFile def chooseCyanaFile(self): # Prepend default Cyana file extension below fileTypes = [ FileType('All', ['*']), ] popup = FileSelectPopup(self, file_types=fileTypes, title='CYANA fproject file', dismiss_text='Cancel', selected_file_must_exist=True) fileName = popup.getFile() self.cyanaEntry.set(fileName) self.projOptionsSelect.setIndex(3) popup.destroy() # end def chooseCyanaFile def chooseValidScript(self): # Prepend default Cyana file extension below fileTypes = [ FileType('All', ['*']), ] popup = FileSelectPopup(self, file_types=fileTypes, title='Script file', dismiss_text='Cancel', selected_file_must_exist=True) fileName = popup.getFile() self.validScriptEntry.set(fileName) popup.destroy() # end def chooseValidScript def chooseMiscScript(self): # Prepend default Cyana file extension below fileTypes = [ FileType('All', ['*']), ] popup = FileSelectPopup(self, file_types=fileTypes, title='Script file', dismiss_text='Cancel', selected_file_must_exist=True) fileName = popup.getFile() self.miscScriptEntry.set(fileName) popup.destroy() # end def chooseMiscScript def openProject(self): projOption = self.projOptionsSelect.get() if projOption == self.projectOptions[0]: self.openOldProject() elif projOption == self.projectOptions[1]: self.initPdb() # end if if self.project: self.project.gui = self # end if self.updateGui() #end def def openOldProject(self): fName = self.projEntry.get() if not os.path.exists(fName): nTerror('Error: file "%s" does not exist\n', fName) #end if if self.project: self.closeProject() # end if self.project = cing.Project.open(name=fName, status='old', verbose=False) #end def def initPdb(self): fName = self.pdbEntry.get() if not os.path.exists(fName): nTerror('Error: file "%s" does not exist\n', fName) #end if self.project = cing.Project.open(self.nameEntry.get(), status='new') self.project.initPDB(pdbFile=fName, convention='PDB') #end def def closeProject(self): if self.project: self.project.close() # end if self.project = None self.updateGui() #end def def updateGui(self, event=None): projOption = self.projOptionsSelect.get() buttons = self.buttonBar.buttons # Disable entries for e in [ self.projEntry, self.pdbEntry, self.ccpnEntry, self.cyanaEntry, self.nameEntry ]: e.configure(state='disabled') #end for if projOption == self.projectOptions[0]: # Enable entries self.projEntry.configure(state='normal') if (len(self.projEntry.get()) > 0): self.openProjectButton.enable() self.runButton.enable() else: self.openProjectButton.disable() self.runButton.disable() #end if elif projOption == self.projectOptions[1]: # Enable entries self.pdbEntry.configure(state='normal') self.nameEntry.configure(state='normal') if (len(self.pdbEntry.get()) > 0 and len(self.nameEntry.get()) > 0): buttons[0].enable() buttons[1].enable() else: buttons[0].disable() buttons[1].disable() #end if #end if elif projOption == self.projectOptions[2]: # Enable entries self.ccpnEntry.configure(state='normal') self.nameEntry.configure(state='normal') if (len(self.ccpnEntry.get()) > 0 and len(self.nameEntry.get()) > 0): buttons[0].enable() buttons[1].enable() else: buttons[0].disable() buttons[1].disable() #end if #end if elif projOption == self.projectOptions[3]: # Enable entries self.cyanaEntry.configure(state='normal') self.nameEntry.configure(state='normal') if (len(self.cyanaEntry.get()) > 0 and len(self.nameEntry.get()) > 0): buttons[0].enable() buttons[1].enable() else: buttons[0].disable() buttons[1].disable() #end if #end if self.projectStatus.clear() if not self.project: self.projectStatus.setText('No open project') self.closeProjectButton.setText('Close Project') self.closeProjectButton.disable() else: self.projectStatus.setText(self.project.format()) self.closeProjectButton.enable() self.closeProjectButton.setText( sprintf('Close Project "%s"', self.project.name)) #end if #end def def redirectConsole(self): #pipe = TextPipe(self.inputTextBox.text_area) #sys.stdin = pipe pipe = TextPipe(self.outputTextBox.text_area) sys.stdout = pipe nTmessage.stream = pipe # end def redirectConsole # sys.stderr = pipe def resetConsole(self): #sys.stdin = stdin nTmessage.stream = stdout sys.stdout = stdout sys.stderr = stderr # end def resetConsole def open(self): self.redirectConsole() BasePopup.open(self) # end def open def close(self): geometry = self.getGeometry() self.resetConsole() BasePopup.close(self) print 'close:', geometry sys.exit(0) # remove later # end def close def destroy(self): geometry = self.getGeometry() self.resetConsole() BasePopup.destroy(self) print 'destroy:', geometry sys.exit(0) # remove later
class ViewChemicalShiftsPopup(BasePopup): """ **A Table of Chemical Shifts for Export** This section is designed to make a layout of a table for chemical shifts on a per-residue basis which may them be exported as either PostScript, for printing and graphical manipulation, or as plain text for import into other software or computer scripts. The user chooses the molecular chain (which sequence) and the shift list to use at the top of the popup, together with a few other options that control how things are rendered. Then buttons are toggled to select which kinds of atom will be displayed in aligned columns; other kinds will simply be listed to the right of the columns. Thus for example if the shift list does not contain any carbonyl resonances in a protein chain then the user may toggle the empty "C" column off. Once the desired layout is achieved the user then uses the [Export PostScript] or [Export Text] buttons to write the data into a file of the appropriate type. The user will be presented wit ha file browser to specify the location and the name of the file to be saved. It should be noted that although the graphical display in the popup itself is somewhat limited, e.g. the gaps and spacing doesn't always look perfect, the PostScript version that is exported is significantly neater. **Caveats & Tips** If you need a chemical shift list represented in a particular format, specific for a particular external NMR program then you should use the FormatConverter software. Chemical shifts may also be exported from any table in Analysis that contains such data by clicking the right mouse button over the table and selecting the export option. """ def __init__(self, parent, *args, **kw): self.shiftList = None self.font = 'Helvetica 10' self.boldFont = 'Helvetica 10 bold' self.symbolFont = 'Symbol 8' self.smallFont = 'Helvetica 8' self.chain = None self.textOut = '' self.textMatrix = [] BasePopup.__init__(self, parent=parent, title='Chart : Chemical Shifts Table') def body(self, guiFrame): row = 0 frame = Frame(guiFrame, grid=(row, 0)) frame.expandGrid(None, 6) label = Label(frame, text='Chain:', grid=(0, 0)) tipText = 'Selects which molecular chain to show residues and chemical shift values for' self.chainPulldown = PulldownList(frame, callback=self.changeChain, grid=(0, 1), tipText=tipText) label = Label(frame, text=' Shift List:', grid=(0, 2)) tipText = 'Selects which shift list is used to derive the displayed chemical shift values' self.shiftListPulldown = PulldownList(frame, callback=self.changeShiftList, grid=(0, 3), tipText=tipText) label = Label(frame, text=' List all shifts:', grid=(0, 4)) tipText = 'Sets whether to display all the chemical shifts for residues or just for the nominated atom types in columns' self.otherShiftsSelect = CheckButton(frame, callback=self.draw, grid=(0, 5), tipText=tipText) utilButtons = UtilityButtonList(frame, helpUrl=self.help_url, grid=(0, 7)) row += 1 frame = Frame(guiFrame, grid=(row, 0)) frame.expandGrid(None, 6) label = Label(frame, text=' 1-letter codes:', grid=(0, 0)) tipText = 'Whether to use 1-letter residue codes in the table, or otherwise Ccp/three-letter codes' self.oneLetterSelect = CheckButton(frame, callback=self.draw, grid=(0, 1), selected=False, tipText=tipText) precisions = [0.1, 0.01, 0.001] texts = [str(t) for t in precisions] label = Label(frame, text=' 1H precision:', grid=(0, 2)) tipText = 'Specifies how many decimal places to use when displaying 1H chemical shift values' self.protonPrecisionSelect = PulldownList(frame, texts=texts, objects=precisions, callback=self.draw, index=1, grid=(0, 3), tipText=tipText) label = Label(frame, text=' Other precision:') label.grid(row=0, column=4, sticky='w') tipText = 'Specifies how many decimal places to use when displaying chemical shift values for isotopes other than 1H' self.otherPrecisionSelect = PulldownList(frame, texts=texts, objects=precisions, callback=self.draw, index=1, grid=(0, 5), tipText=tipText) row += 1 frame = Frame(guiFrame, grid=(row, 0)) frame.expandGrid(None, 1) label = Label(frame, text='Column\nAtoms:', grid=(0, 0)) tipText = 'Selects which kinds of atoms are displayed in aligned columns, or otherwise displayed at the end of the residue row (if "List all shifts" is set)' self.optSelector = PartitionedSelector(frame, self.toggleOpt, tipText=tipText, maxRowObjects=10, grid=(0, 1), sticky='ew') options = ['H', 'N', 'C', 'CA', 'CB', 'CG'] self.optSelector.update(objects=options, labels=options, selected=['H', 'N', 'CA']) row += 1 guiFrame.expandGrid(row, 0) self.canvasFrame = ScrolledCanvas(guiFrame, relief='groove', width=650, borderwidth=2, resizeCallback=None, grid=(row, 0), padx=1, pady=1) self.canvas = self.canvasFrame.canvas #self.canvas.bind('<Button-1>', self.toggleResidue) row += 1 tipTexts = [ 'Output information from the table as PostScript file, for printing etc.', 'Output information from the table as a whitespace separated plain text file' ] commands = [self.makePostScript, self.exportText] texts = ['Export PostScript', 'Export Text'] buttonList = ButtonList(guiFrame, commands=commands, texts=texts, grid=(row, 0), tipTexts=tipTexts) chains = self.getChains() if len(chains) > 1: self.chain = chains[1] else: self.chain = None self.updateShiftLists() self.updateChains() self.otherShiftsSelect.set(True) self.update() for func in ('__init__', 'delete'): self.registerNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func) for func in ('__init__', 'delete'): self.registerNotify(self.updateShiftLists, 'ccp.nmr.Nmr.ShiftList', func) def changeShiftList(self, shiftList): if shiftList is not self.shiftList: self.shiftList = shiftList self.update() def updateShiftLists(self, *opt): names = [] index = 0 shiftLists = getShiftLists(self.nmrProject) shiftList = self.shiftList if shiftLists: names = [ '%s [%d]' % (sl.name or '<No name>', sl.serial) for sl in shiftLists ] if shiftList not in shiftLists: shiftList = shiftLists[0] index = shiftLists.index(shiftList) if self.shiftList is not shiftList: self.shiftList = shiftList self.shiftListPulldown.setup(names, shiftLists, index) def getChains(self): chains = [ None, ] for molSystem in self.project.sortedMolSystems(): for chain in molSystem.sortedChains(): if len(chain.residues) > 1: chains.append(chain) return chains def changeChain(self, chain): if chain is not self.chain: self.chain = chain self.update() def updateChains(self, *opt): names = [] index = -1 chains = self.getChains() chain = self.chain if len(chains) > 1: names = [ 'None', ] + ['%s:%s' % (ch.molSystem.code, ch.code) for ch in chains[1:]] if chain not in chains: chain = chains[1] index = chains.index(chain) else: chain = None self.chainPulldown.setup(names, chains, index) def destroy(self): for func in ('__init__', 'delete'): self.unregisterNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func) for func in ('__init__', 'delete'): self.unregisterNotify(self.updateShiftLists, 'ccp.nmr.Nmr.ShiftList', func) BasePopup.destroy(self) def exportText(self, *event): from memops.gui.FileSelect import FileType from memops.gui.FileSelectPopup import FileSelectPopup if self.textOut: fileTypes = [ FileType('Text', ['*.txt']), FileType('CSV', ['*.csv']), FileType('All', ['*']) ] fileSelectPopup = FileSelectPopup(self, file_types=fileTypes, title='Save table as text', dismiss_text='Cancel', selected_file_must_exist=False) fileName = fileSelectPopup.getFile() if fileName: file = open(fileName, 'w') if fileName.endswith('.csv'): for textRow in self.textMatrix: file.write(','.join(textRow) + '\n') else: file.write(self.textOut) def toggleOpt(self, selected): self.draw() def makePostScript(self): self.canvasFrame.printCanvas() def update(self): colors = [] selected = set() atomNames = set() if self.chain: for residue in self.chain.sortedResidues(): for atom in residue.atoms: chemAtom = atom.chemAtom if colorDict.get(chemAtom.elementSymbol) is None: continue if chemAtom.waterExchangeable: continue atomNames.add(atom.name[:2]) molType = residue.molResidue.molType if molType == 'protein': selected.add('H') selected.add('N') selected.add('CA') selected.add('C') elif molType == 'DNA': selected.add("C1'") elif molType == 'RNA': selected.add("C1'") elif molType == 'carbohydrate': selected.add("C1") else: for spinSystem in self.shiftList.nmrProject.resonanceGroups: if not spinSystem.residue: for resonance in spinSystem.resonances: for name in resonance.assignNames: atomNames.add(name) options = list(atomNames) molType = 'protein' if self.chain: molType = self.chain.molecule.molType options = greekSortAtomNames(options, molType=molType) if 'H' in options: options.remove('H') options = [ 'H', ] + options colors = [colorDict.get(n[0]) for n in options] if options and not selected: selected = [ options[0], ] self.optSelector.update(objects=options, labels=options, colors=colors, selected=list(selected)) self.draw() def draw(self, *opt): if not self.shiftList: return nmrProject = self.shiftList.nmrProject shiftList = self.shiftList font = self.font bfont = self.boldFont symbolFont = self.symbolFont sFont = self.smallFont bbox = self.canvas.bbox doOthers = self.otherShiftsSelect.get() spc = 4 gap = 14 x = gap y = gap ct = self.canvas.create_text cl = self.canvas.create_line cc = self.canvas.coords self.canvas.delete('all') ssDict = {} formatDict = { 0.1: '%.1f', 0.01: '%.2f', 0.001: '%.3f', } protonFormat = formatDict[self.protonPrecisionSelect.getObject()] otherFormat = formatDict[self.otherPrecisionSelect.getObject()] uSpinSystems = [] chains = set() molSystems = set() for spinSystem in nmrProject.resonanceGroups: residue = spinSystem.residue if residue: ssDict[residue] = ssDict.get(residue, []) + [ spinSystem, ] else: uSpinSystems.append((spinSystem.serial, spinSystem)) uSpinSystems.sort() commonAtoms = self.optSelector.getSelected() N = len(commonAtoms) chain = self.chain if chain: spinSystems = [] for residue in chain.sortedResidues(): spinSystems0 = ssDict.get(residue, []) for spinSystem in spinSystems0: if spinSystem and spinSystem.resonances: spinSystems.append([residue, spinSystem]) else: spinSystems = uSpinSystems strings = [] doOneLetter = self.oneLetterSelect.get() if spinSystems: x = gap y += gap numItems = [] codeItems = [] commonItems = [] otherItems = [] numWidth = 0 codeWidth = 0 commonWidths = [0] * N commonCounts = [0] * N for residue, spinSystem in spinSystems: if type(residue) is type(1): seqNum = '{%d}' % residue if doOneLetter: ccpCode = '-' else: ccpCode = spinSystem.ccpCode or '' else: if doOneLetter: ccpCode = residue.chemCompVar.chemComp.code1Letter else: ccpCode = getResidueCode(residue) seqNum = str(residue.seqCode) subStrings = [] subStrings.append(seqNum) subStrings.append(ccpCode) item = ct(x, y, text=seqNum, font=font, anchor='se') box = bbox(item) iWidth = box[2] - box[0] numWidth = max(numWidth, iWidth) numItems.append(item) item = ct(x, y, text=ccpCode, font=font, anchor='sw') box = bbox(item) iWidth = box[2] - box[0] codeWidth = max(codeWidth, iWidth) codeItems.append(item) commonShifts, commonElements, otherShifts = self.getShiftData( spinSystem, shiftList, commonAtoms) items = [] for i in range(N): values = commonShifts[i] element = commonElements[i] if element == 'H': shiftFormat = protonFormat else: shiftFormat = otherFormat subItems = [] for value in values: text = shiftFormat % value if text: item = ct(x, y, text=text, font=font, anchor='se') box = bbox(item) iWidth = box[2] - box[0] commonWidths[i] = max(commonWidths[i], iWidth) commonCounts[i] += 1 subItems.append(item) subStrings.append( ','.join([shiftFormat % v for v in values]) or '-') items.append(subItems) commonItems.append(items) if doOthers: items0 = [] i = 0 I = len(otherShifts) for atomLabel, element, value in otherShifts: label = atomLabel if label[0] == '?': label = label[3:-1] if element == 'H': shiftFormat = protonFormat else: shiftFormat = otherFormat subStrings.append('%6s:%-4s' % (shiftFormat % value, label)) i += 1 atoms = atomLabel.split('|') items = [] j = 0 for atom in atoms: text = element if j > 0: text = '/' + text item = ct(x, y, text=text, font=font, anchor='sw') box = bbox(item) iWidth = box[2] - box[0] - 3 items.append((iWidth, item, 0)) p = len(element) if len(atom) > p: letter = atom[p] if letter not in ('0123456789'): item = ct(x, y, text=letter.lower(), font=symbolFont, anchor='sw') box = bbox(item) iWidth = box[2] - box[0] - 2 items.append((iWidth, item, -4)) p += 1 text = atom[p:] if text: item = ct(x, y, text=text, font=sFont, anchor='sw') box = bbox(item) iWidth = box[2] - box[0] - 2 items.append((iWidth, item, -4)) j += 1 text = ' ' + shiftFormat % value if i != I: text += ',' item = ct(x, y, text=text, font=font, anchor='sw') box = bbox(item) iWidth = box[2] - box[0] - 4 items.append((iWidth, item, 0)) items0.append(items) otherItems.append(items0) strings.append(subStrings) y0 = y x = x0 = gap + numWidth + codeWidth + spc + spc for i in range(N): if not commonCounts[i]: continue x += commonWidths[i] + spc + spc element = commonElements[i] iWidth = 0 text = commonAtoms[i][len(element):].lower() if text: item = ct(x, y, text=text, font=symbolFont, anchor='se') box = bbox(item) iWidth = box[2] - box[0] - 2 ct(x - iWidth, y, text=element, font=font, anchor='se') y += gap for i in range(len(numItems)): x = gap + numWidth + spc cc(numItems[i], x, y) x += spc cc(codeItems[i], x, y) x += codeWidth x1 = x + spc yM = y for j in range(N): if not commonCounts[j]: continue x += commonWidths[j] + spc + spc items = commonItems[i][j] yB = y - gap for item in items: yB += gap cc(item, x, yB) yM = max(yB, yM) x += gap if doOthers: x += spc x3 = x for items in otherItems[i]: if x > 550: x = x3 y += gap for iWidth, item, dy in items: cc(item, x, y + dy) x += iWidth y = max(y, yM) y += gap x = x0 for i in range(N): if not commonCounts[i]: continue x += commonWidths[i] + spc + spc cl(x + 8, y0, x + 8, y - gap, width=0.3, fill='#808080') cl(x1, y0, x1, y - gap, width=0.3, fill='#808080') cl(0, 0, 550, 0, width=0.3, fill='#FFFFFF') y += gap textWidths = {} for subStrings in strings: for i, text in enumerate(subStrings): if text and len(text) > textWidths.get(i, 0): textWidths[i] = len(text) else: textWidths[i] = 0 formats = {} for i in textWidths.keys(): formats[i] = ' %%%ds' % max(6, textWidths[i]) textOut = '!' textRow = ['', ''] textMatrix = [textRow] textOut += ' ' * (max(6, textWidths.get(0, 6)) + max(6, textWidths.get(1, 6)) + 1) i = 2 for atom in commonAtoms: if i in formats: textOut += formats[i] % atom textRow.append((formats[i] % atom).strip()) i += 1 textOut += '\n' for subStrings in strings: textRow = [] textMatrix.append(textRow) i = 0 for text in subStrings: textOut += formats[i] % text textRow.append((formats[i] % text).strip()) i += 1 textOut += '\n' self.textOut = textOut self.textMatrix = textMatrix def getShiftData(self, spinSystem, shiftList, commonAtoms=('H', 'N', 'CA', 'CB')): commonShifts = [] commonResonances = {} commonElements = [] for atomName in commonAtoms: elements = set() resonances = [] for resonance in spinSystem.resonances: resonanceSet = resonance.resonanceSet if resonanceSet: for atomSet in resonanceSet.atomSets: for atom in atomSet.atoms: if atomName == atom.name[:2]: resonances.append(resonance) break else: continue break else: for assignName in resonance.assignNames: if atomName == assignName[:2]: resonances.append(resonance) break shiftValues = [] for resonance in resonances: isotope = resonance.isotope if isotope: elements.add(isotope.chemElement.symbol) commonResonances[resonance] = True shift = resonance.findFirstShift(parentList=shiftList) if shift: shiftValues.append(shift.value) if not elements: element = atomName[0] else: element = elements.pop() commonElements.append(element) commonShifts.append(shiftValues) otherShifts = [] for resonance in spinSystem.resonances: if not commonResonances.get(resonance): shift = resonance.findFirstShift(parentList=shiftList) if shift: isotope = resonance.isotope if isotope: element = isotope.chemElement.symbol else: element = '??' if resonance.assignNames or resonance.resonanceSet: name = getResonanceName(resonance) else: name = '??[%d]' % resonance.serial otherShifts.append((name, element, shift.value)) molType = 'protein' if spinSystem.residue: molType = spinSystem.residue.molResidue.molType otherShifts = greekSortAtomNames(otherShifts, molType) return commonShifts, commonElements, otherShifts
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)
class EditPeakDrawParamsPopup(BasePopup): """ **Control How Peak Symbols and Annotations Are Drawn** This popup window controls the display of picked peak positions within spectrum windows and also how their annotations are displayed in many of the tables throughout the rest of Analysis. **Peak Annotations** The "Annotation Style" tab, as the name suggests, controls which bits of information go to form the assignment annotation that is used to label peaks in spectra and when listing their identities in tables. The user can toggle various options on or off to dictate what should be included. With no options selected at all peaks will show only resonance number information like "[123],[45]", irrespective of any atomic assignments. Switching the atom assignments on will substitute the atom and residue name for the resonance names. The spin system toggle is used to control the display of spin system numbers like the curly bracketed numbers of "{89}[123],[45]" or a residue name if the spin system is assigned, although the atom assignment option will also give any residue name. The chain and molecular system toggles are used when there are several sequences in the assignment that need to be distinguished, so that you can identify "A25LsyH,N" separately to "B25LysH,N" or even "MS2:A25LysH,N". The details toggle allows the user to contribute to peak annotations; such details are set in the relevant column of the peak tables (e.g. `Selected Peaks`_)or the "Peak::Set details" option of the right-click window menu. The last "Minimal Annotations" option is special because it gives a quick replacement for spectrum annotations that overrides all other settings, for example "25LysH,N" becomes "25K", which is useful to reduce clutter when printing out an HSQC. It should be noted that, with the exception of the "Minimal Annotations" option, any changes to the annotation options for existing peak assignments will not be visible until [Update Full Annotations] is pressed, which can take a while to update if the number of peaks in the project is large. Any new assignments will observe the current settings. **Draw Size** The second tab controls how the peak cross symbols, which indicate the pick position, are drawn in the spectrum display. Here, the user has four choices: the default is to use a fixed number of screen pixels, so that all symbols are the same size, irrespective of zoom level; uniform size in ppm (with the appropriate values for each isotope set in the lower table that appears) allows the peak symbol maintain a constant size relative to the contours, and thus differ in on-screen size according to the contour zoom level; and two choices for a "scaled" size where the peak symbol is larger or smaller depending on the intensity of the peak, either relative to its peak list or an absolute globally applied value. **Figure of Merit** The last "Merit Symbols" tab allows the user to add textual markers to a peak depending on the figure-of-merit value, which is an indication of reliability (although the precise context is at the discretion of the user). The merit value for a peak is set via the peak tables or the "Peak::Set merit" option of the right-click window menu. Aside from display purposes the merit value is used at a few points throughout Analysis to optionally exclude peaks. Typically a peak with a merit value of 0.0 may be ignored during certain analyses, e.g. for making NOE derived distance restraints. **Caveats & Tips** When assigning peaks via the `Assignment Panel`_ the resonance annotation will always display spin system information, given that this grouping is critical to assignment, but the chain and atom assignment will reflect the peak display, and thus these details may be missing if unset in this Draw Parameters popup. .. _`Assignment Panel`: EditAssignmentPopup.html .. _`Selected Peaks`: SelectedPeaksPopup.html """ def __init__(self, parent, *args, **kw): BasePopup.__init__(self, parent=parent, title='Peak : Draw Parameters', **kw) def body(self, guiParent): self.geometry('380x250') analysisProject = self.analysisProject self.smallFont = '-schumacher-clean-medium-r-normal--14-140-75-75-c-70-iso646.1991-irv' guiParent.grid_columnconfigure(0, weight=1) guiParent.grid_rowconfigure(0, weight=1) row = 0 tipTexts = ['Options specifying how peak annotations are drawn in spectrum windows and in tables etc.', 'Options to specify how large the peak crosses/symbols are drawn in spectrum windows', 'Enables the user to specify special symbols to annotate peaks according to quality'] options=['Annotation Style','Draw Size','Merit Symbols'] tabbedFrame = TabbedFrame(guiParent, options=options, grid=(row,0), tipTexts=tipTexts) frame1, frame2, frame3 = tabbedFrame.frames frame1.expandGrid(7,1) frame2.expandGrid(2,0) frame3.expandGrid(3,1) self.drawFrame = frame2 # Annotations tipText = 'Whether to show unassigned spin system numbers like "{123}" in peak annotations; does not affect the display of full residue assignments' self.spinSystAnnoSelect = CheckButton(frame1, callback=self.setSpinSystAnno, grid=(0,0), selected=analysisProject.doSpinSystemAnnotations, tipText=tipText) spinSystAnnoLabel = Label(frame1, text='Spin System Info', grid=(0,1)) tipText = 'Whether to show assigned atom names in peak annotations rather than resonance numbers, e.g. "21LeuH,N" or "21Leu[55],[56]"' self.resonanceAnnoSelect = CheckButton(frame1, callback=self.setResonanceAnno, grid=(1,0), selected=analysisProject.doAssignmentAnnotations, tipText=tipText) resonanceAnnoLabel = Label(frame1, text='Atom Assignment', grid=(1,1)) tipText = 'Whether to show the molecular chain code letter in peak annotations, e.g. "21LeuH,N" or "A21LeuH,N"' self.chainAnnoSelect = CheckButton(frame1, callback=self.setChainAnno, grid=(2,0), selected=analysisProject.doChainAnnotations, tipText=tipText) chainAnnoLabel = Label(frame1, text='Chain Assignment', grid=(2,1)) tipText = 'Whether to show the molecular system code name in peak annotations, e.g. "MS1:21LeuH,N" or "21LeuH,N"' self.molSysAnnoSelect = CheckButton(frame1, callback=self.setMolSysAnno, grid=(3,0), selected=analysisProject.doMolSysAnnotations, tipText=tipText) molSysAnnoLabel = Label(frame1, text='Molecular System', grid=(3,1)) tipText = 'Whether to show a symbol indicating the quality of a peak; these symbols must be set in the "Merit Symbols" tab' self.meritAnnoSelect = CheckButton(frame1, callback=self.setMeritAnno, grid=(4,0), selected=analysisProject.doMeritAnnotations, tipText=tipText) meritAnnoLabel = Label(frame1, text='Merit Symbol', grid=(4,1)) tipText = 'Whether to show the details text for a peak in spectrum windows (set in the peak tables)' self.detailAnnoSelect = CheckButton(frame1, callback=self.setDetailAnno, grid=(5,0), selected=analysisProject.doDetailAnnotations, tipText=tipText) detailAnnoLabel = Label(frame1, text='Details', grid=(5,1)) tipText = 'Whether to ignore above settings, and use a short peak annotation using only residue numbers and one-letter codes, e.g. "21L"' self.simpleAnnoSelect = CheckButton(frame1, callback=self.setSimpleAnnotations, grid=(6,0), tipText=tipText, selected=analysisProject.doMinimalAnnotations) simpleAnnoLabel = Label(frame1, text='Minimal Annotations (overriding option)', grid=(6,1)) tipText = 'Manually cause an update of all peak annotations; may take some time but recommended to see the immediate effect of changes' self.updateFullAnnoButton = Button(frame1, text='Update Full Annotations', command=self.updateAnnotations, grid=(7,0), gridSpan=(1,2), sticky='nsew', tipText=tipText) # Size tipText = 'The width of the displayed peak cross/symbol in screen pixels; the number of pixels from the centre point' self.pixel_entry = LabeledEntry(frame2, label='Number of pixels', entry=analysisProject.peakPixelSize, returnCallback=self.updatePixelSize, entry_width=8, tipText=tipText) tipText = 'Specifies which peak height corresponds to the specific per-isotope ppm size; actual peak symbol sizes are scaled, according to relative height (and volume)' self.intensity_entry = LabeledEntry(frame2, label='Height scale', entry=analysisProject.peakIntensityScale, returnCallback=self.updateIntensityScale, entry_width=8, tipText=tipText) tipText = 'Specifies which peak volume corresponds to the specific per-isotope ppm size; actual peak symbol sizes are scaled, according to relative volume (and height)' self.volume_entry = LabeledEntry(frame2, label='Volume scale', entry=analysisProject.peakVolumeScale, returnCallback=self.updateVolumeScale, entry_width=8, tipText=tipText) tipTexts = ['The kind of nuclear isotope, as found on the axis if a spectrum window', 'The ppm width of the peak cross/symbol along the specific kind of isotope axis'] headings = ['Isotope', 'Peak Size (ppm)'] self.peakSizeEntry = FloatEntry(self, returnCallback=self.setPeakSize, width=10) editWidgets = [None, self.peakSizeEntry] editGetCallbacks = [None, self.getPeakSize] editSetCallbacks = [None, self.setPeakSize] self.peak_size_table = ScrolledMatrix(frame2, headingList=headings, initialRows=5, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, tipTexts=tipTexts) self.selected_method = None self.method_widgets = {} self.method_widgets[peak_draw_methods[0]] = [self.pixel_entry] self.method_widgets[peak_draw_methods[1]] = [self.peak_size_table] self.method_widgets[peak_draw_methods[2]] = [self.intensity_entry, self.volume_entry, self.peak_size_table] self.method_widgets[peak_draw_methods[3]] = [self.peak_size_table] self.method_widgets[peak_draw_methods[4]] = [] self.method_widgets[peak_draw_methods[5]] = [] selected_index = peak_draw_methods.index(analysisProject.peakDrawMethod) tipText = 'Selects which mode to use for determining peak cross/symbol sizes; a fixed pixel/ppm value or scaled by intensity for all peaks or just one peak list' self.method_menu = PulldownList(frame2, texts=peak_draw_methods, gridSpan=(1,2), grid=(0,0), tipText=tipText, callback=self.setMethod, index=selected_index) # Merit symbol label = Label(frame3, text='Good merit (>0.66)', grid=(0,0)) tipText = 'Although typically blank, sets a symbol to display for good quality peaks (merit value > 0.66), if the relevant option is selected in the "Annotation Style" tab' self.meritGoodEntry = Entry(frame3, text=analysisProject.meritAnnotationGood, width=8, grid=(0,1), sticky='ew', tipText=tipText, returnCallback=self.setMeritAnnotation) label = Label(frame3, text='Medium merit', grid=(1,0)) tipText = 'Sets a symbol to display for mediocre quality peaks (merit value between 0.34 & 0.66), if the relevant option is selected in the "Annotation Style" tab' self.meritUglyEntry = Entry(frame3, text=analysisProject.meritAnnotationMediocre, width=8, grid=(1,1), sticky='ew', tipText=tipText, returnCallback=self.setMeritAnnotation) label = Label(frame3, text='Poor merit (<0.34)', grid=(2,0)) tipText = 'Sets a symbol to display for poor quality peaks (merit value < 0.34), if the relevant option is selected in the "Annotation Style" tab' self.meritBadEntry = Entry(frame3, text=analysisProject.meritAnnotationBad, width=8, grid=(2,1), sticky='ew', tipText=tipText, returnCallback=self.setMeritAnnotation) tipText = 'Commit the changes to the merit symbols; this will not automatically update the display - see the "Annotation Style" tab' setButton = Button(frame3, text='Set symbols', command=self.setMeritAnnotation, grid=(3,0), gridSpan=(1,2), tipText=tipText, sticky='nsew') buttons = UtilityButtonList(tabbedFrame.sideFrame, grid=(0,0), helpUrl=self.help_url, sticky='e') self.updatePeakSizeTable() self.updateMethod() for func in ('__init__', 'delete', ''): self.registerNotify(self.updatePeakSizeTable, 'ccpnmr.Analysis.AxisType', func) self.registerNotify(self.changedDoSpinSystemAnnotations, 'ccpnmr.Analysis.AnalysisProject', 'setDoSpinSystemAnnotations') self.registerNotify(self.changedDoAssignmentAnnotations, 'ccpnmr.Analysis.AnalysisProject', 'setDoAssignmentAnnotations') self.registerNotify(self.changedDoChainAnnotations, 'ccpnmr.Analysis.AnalysisProject', 'setDoChainAnnotations') self.registerNotify(self.changedPeakDrawMethod, 'ccpnmr.Analysis.AnalysisProject', 'setPeakDrawMethod') self.registerNotify(self.changedPeakPixelSize, 'ccpnmr.Analysis.AnalysisProject', 'setPeakPixelSize') def open(self): self.updatePeakSizeTable() self.updateMethod() BasePopup.open(self) def close(self): self.setMeritAnnotation() BasePopup.close(self) def destroy(self): for func in ('__init__', 'delete', ''): self.unregisterNotify(self.updatePeakSizeTable, 'ccpnmr.Analysis.AxisType', func) self.unregisterNotify(self.changedDoSpinSystemAnnotations, 'ccpnmr.Analysis.AnalysisProject', 'setDoSpinSystemAnnotations') self.unregisterNotify(self.changedDoAssignmentAnnotations, 'ccpnmr.Analysis.AnalysisProject', 'setDoAssignmentAnnotations') self.unregisterNotify(self.changedDoChainAnnotations, 'ccpnmr.Analysis.AnalysisProject', 'setDoChainAnnotations') self.unregisterNotify(self.changedPeakDrawMethod, 'ccpnmr.Analysis.AnalysisProject', 'setPeakDrawMethod') self.unregisterNotify(self.changedPeakPixelSize, 'ccpnmr.Analysis.AnalysisProject', 'setPeakPixelSize') BasePopup.destroy(self) def setMeritAnnotation(self, *opt): analysisProject = self.analysisProject analysisProject.meritAnnotationGood = self.meritGoodEntry.get() or None analysisProject.meritAnnotationMediocre = self.meritUglyEntry.get() or None analysisProject.meritAnnotationBad = self.meritBadEntry.get() or None def updateAnnotations(self): self.setMeritAnnotation() refreshPeakAnnotations(self.project) def setSimpleAnnotations(self, trueOrFalse): self.analysisProject.doMinimalAnnotations = trueOrFalse def setSpinSystAnno(self, trueOrFalse): self.analysisProject.doSpinSystemAnnotations = trueOrFalse def setResonanceAnno(self, trueOrFalse): self.analysisProject.doAssignmentAnnotations = trueOrFalse def setMolSysAnno(self, trueOrFalse): self.analysisProject.doMolSysAnnotations = trueOrFalse def setChainAnno(self, trueOrFalse): self.analysisProject.doChainAnnotations = trueOrFalse def setMeritAnno(self, trueOrFalse): self.analysisProject.doMeritAnnotations = trueOrFalse def setDetailAnno(self, trueOrFalse): self.analysisProject.doDetailAnnotations = trueOrFalse def changedDoSpinSystemAnnotations(self, analysisProject): self.spinSystAnnoSelect.set(analysisProject.doSpinSystemAnnotations) def changedDoAssignmentAnnotations(self, analysisProject): self.resonanceAnnoSelect.set(analysisProject.doAssignmentAnnotations) def changedDoChainAnnotations(self, analysisProject): self.chainAnnoSelect.set(analysisProject.doChainAnnotations) def changedPeakDrawMethod(self, analysisProject): self.updateMethod() def changedPeakPixelSize(self, analysisProject): self.pixel_entry.setEntry(analysisProject.peakPixelSize) def setMethod(self, text): self.analysisProject.peakDrawMethod = text def updateMethod(self): selected = self.analysisProject.peakDrawMethod if selected == self.selected_method: return self.unsetMethod() widgets = self.method_widgets[selected] row = 1 for widget in widgets: if isinstance(widget, ScrolledMatrix): widget.grid(row=row, column=0, sticky='nsew') self.drawFrame.grid_rowconfigure(row, weight=1) else: widget.grid(row=row, column=0, sticky='new') self.drawFrame.grid_rowconfigure(row, weight=0) row += 1 self.selected_method = selected def unsetMethod(self): selected = self.selected_method if selected is None: return widgets = self.method_widgets[selected] for widget in widgets: widget.grid_forget() self.selected_method = None def updatePeakSizeTable(self, *extra): axisTypes = self.parent.getAxisTypes() textMatrix = [] n = 0 for axisType in axisTypes: if (len(axisType.isotopeCodes) == 1): n = n + 1 text = [] text.append(', '.join(axisType.isotopeCodes)) text.append(axisType.peakSize) textMatrix.append(text) self.peak_size_table.update(objectList=axisTypes, textMatrix=textMatrix) def getPeakSize(self, axisType): self.peakSizeEntry.set(axisType.peakSize) def setPeakSize(self, *extra): axisType = self.getAxisType() try: axisType.peakSize = self.peakSizeEntry.get() except Implementation.ApiError, e: showError('Setting peak size', e.error_msg, parent=self)