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 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 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
def getCloseSingleShiftMatches(peakList,
network,
covalent,
labelling=None,
minLabelFraction=0.1,
intensityType='height',
progressBar=None):
spectrum = peakList.dataSource
experiment = spectrum.experiment
shiftList = experiment.shiftList
hDims = findSpectrumDimsByIsotope(spectrum, '1H')
tolerances = getDimTolerances(spectrum)
bondedDims = getBondedDimsDict(spectrum)
meanIntensity = getMeanPeakIntensity(peakList.peaks,
intensityType=intensityType)
info = (experiment.name, spectrum.name, peakList.serial,
len(peakList.peaks))
if progressBar:
progressBar.setText('Unique shift matches for\n%s:%s:%d - %d peaks' %
info)
progressBar.set(0)
progressBar.total = len(peakList.peaks)
progressBar.open()
progressBar.update_idletasks()
else:
print 'Determining unique shift matches for %s:%s:%d - %d peaks' % info
for peak in peakList.peaks:
if progressBar:
progressBar.increment()
hResonances = []
peakDims = peak.sortedPeakDims()
boundResonances = {}
for dim in hDims:
peakDim = peakDims[dim]
if peakDim.peakDimContribs:
hResonances.append(
[contrib.resonance for contrib in peakDim.peakDimContribs])
else:
resonances = []
shifts = findMatchingPeakDimShifts(peakDim,
shiftRanges=None,
tolerance=tolerances[dim],
aliasing=True,
findAssigned=False)
dim2 = bondedDims.get(dim)
peakDim2 = None
if dim2 is not None:
peakDim2 = peakDims[dim2]
shifts2 = []
if peakDim2.peakDimContribs:
for contrib in peakDim2.peakDimContribs:
shift = contrib.resonance.findFirstShift(
parentList=shiftList)
if shift:
shifts2.append(shift)
else:
shifts2 = findMatchingPeakDimShifts(
peakDim2,
shiftRanges=None,
tolerance=tolerances[dim2],
aliasing=True,
findAssigned=False)
for shift in shifts:
resonance1 = shift.resonance
for shift2 in shifts2:
resonance2 = shift2.resonance
if areResonancesBound(resonance1, resonance2):
if labelling:
fraction = getResonancePairLabellingFraction(
resonance1, resonance2, labelling)
if fraction < minLabelFraction:
continue
resonances.append(resonance1)
boundResonances[resonance1] = resonance2
break
else:
for shift in shifts:
resonance = shift.resonance
if labelling:
fraction = getResonanceLabellingFraction(
resonance, labelling)
if fraction < minLabelFraction:
continue
resonances.append(resonance)
if len(resonances) == 1:
#resonance = resonances[0]
#assignResToDim(peakDim,resonance,doWarning=False)
#resonance2 = boundResonances.get(resonance)
#if peakDim2 and (resonance2 is not None):
# assignResToDim(peakDim2,resonance2,doWarning=False)
hResonances.append(resonances)
if len(hResonances) == 2:
peakIntensity = peak.findFirstPeakIntensity(
intensityType=intensityType)
if peakIntensity:
intensity = peakIntensity.value
intensity /= float(len(hResonances[0]))
intensity /= float(len(hResonances[1]))
intensity /= meanIntensity
for resonance1 in hResonances[0]:
if network.get(resonance1) is None:
covalent[resonance1] = {}
network[resonance1] = {}
intensity2 = intensity
if resonance1.resonanceSet:
intensity2 /= float(
len(resonance1.resonanceSet.findFirstAtomSet().
atoms))
for resonance2 in hResonances[1]:
if network.get(resonance2) is None:
network[resonance2] = {}
covalent[resonance2] = {}
if resonance2.resonanceSet:
intensity2 /= float(
len(resonance2.resonanceSet.findFirstAtomSet().
atoms))
network[resonance1][resonance2] = [intensity2, peak]
network[resonance2][resonance1] = [intensity2, peak]
return network, covalent
def assignCloseSingleShiftMatches(peakList):
spectrum = peakList.dataSource
experiment = spectrum.experiment
shiftList = experiment.shiftList
hDims = findSpectrumDimsByIsotope(spectrum, '1H')
tolerances = getDimTolerances(spectrum)
bondedDims = getBondedDimsDict(spectrum)
info = (experiment.name, spectrum.name, peakList.serial,
len(peakList.peaks))
print 'Assigning obvious shift matches for %s:%s:%d - %d peaks' % info
c = 0
for peak in peakList.peaks:
if c and (c % 100 == 0):
print ' %d' % (c, )
c += 1
peakDims = peak.sortedPeakDims()
boundResonances = {}
for dim in hDims:
peakDim = peakDims[dim]
if not peakDim.peakDimContribs:
resonances = []
shifts = findMatchingPeakDimShifts(peakDim,
shiftRanges=None,
tolerance=tolerances[dim],
aliasing=True,
findAssigned=False)
dim2 = bondedDims.get(dim)
peakDim2 = None
if dim2 is not None:
peakDim2 = peakDims[dim2]
shifts2 = []
if peakDim2.peakDimContribs:
for contrib in peakDim2.peakDimContribs:
shift = contrib.resonance.findFirstShift(
parentList=shiftList)
if shift:
shifts2.append(shift)
else:
shifts2 = findMatchingPeakDimShifts(
peakDim2,
shiftRanges=None,
tolerance=tolerances[dim2],
aliasing=True,
findAssigned=False)
for shift in shifts:
resonance1 = shift.resonance
for shift2 in shifts2:
resonance2 = shift2.resonance
if areResonancesBound(resonance1, resonance2):
resonances.append(resonance1)
boundResonances[resonance1] = resonance2
break
else:
for shift in shifts:
resonances.append(shift.resonance)
if len(resonances) == 1:
resonance = resonances[0]
assignResToDim(peakDim, resonance, doWarning=False)
resonance2 = boundResonances.get(resonance)
if peakDim2 and (resonance2 is not None):
assignResToDim(peakDim2, resonance2, doWarning=False)