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)
