def createShift(self, resonance, chemShift):
keywds = {}
#
# Also set ambiguity code if listed
#
if chemShift.ambCode != None:
setUniqueAppData('AppDataInt', resonance, self.format,
'ambiguityCode', chemShift.ambCode)
#
# Shift error could be missing...
#
if hasattr(chemShift, 'error'):
keywds['error'] = chemShift.error
#
# Create shift linked to resonance
#
self.convertCount[self.mainCode][1][self.valueCode] += 1
return Nmr.Shift(self.measurementList,
value=chemShift.value,
resonance=resonance,
**keywds)
def createShift(self,resonance,chemShift):
#
# Also set ambiguity code if listed
#
if chemShift.ambCode != None:
setUniqueAppData('AppDataInt',resonance,self.format,'ambiguityCode',chemShift.ambCode)
#
# Create shift linked to resonance
#
return Nmr.Shift(self.measurementList, value = chemShift.value, resonance = resonance)
def createShift(self,resonance,chemShift):
#
# For xeasy also use chemShift to create atomSerial application data.
#
# Warning: if there is already an atomSerial available for this resonance
# it will be overwritten!!
#
applData = resonance.findFirstApplicationData(application = self.format, keyword = self.atomSerialKeyword)
if applData:
resonance.removeApplicationData(applData)
resonance.addApplicationData(Implementation.AppDataInt(application = self.format, keyword = self.atomSerialKeyword, value = chemShift.atomSerial))
#
# Create shift linked to resonance
#
return Nmr.Shift(self.measurementList, value = chemShift.value, error = chemShift.valueError, resonance = resonance)
def createChemShifts(peakLists,
guiParent=None,
messageReporter=None,
multiDialog=None,
shiftList=None,
useAllContribs=1,
defaultShiftError=None,
shiftListName='None'):
#
# Set up GUI or non-GuI user interaction if not passed in
#
if not messageReporter:
messageReporter = setupMessageReporter(guiParent)
if not multiDialog:
multiDialog = setupMultiDialog(guiParent)
#
# Initial checks
#
if not peakLists:
messageReporter.showError("Error", "No peaklist(s) provided.")
return False
for peakList in peakLists:
if not isinstance(peakList, Nmr.PeakList):
messageReporter.showError("Error", "Invalid peaklist provided.")
return False
#
# Initialize some stuff
#
if not defaultShiftError:
defaultShiftError = {}
for (nucl, defValue) in (('1H', 0.002), ('13C', 0.1), ('15N', 0.1)):
if not defaultShiftError.has_key(nucl):
defaultShiftError[nucl] = defValue
proj = peakLists[0].root
resonanceChemShifts = {}
experiments = []
#
# Read the chemshifts and link them to the relevant resonances
#
for peakList in peakLists:
if peakList.dataSource.experiment not in experiments:
experiments.append(peakList.dataSource.experiment)
for peak in peakList.sortedPeaks():
for peakDim in peak.sortedPeakDims():
chemShift = peakDim.value
peakDimContribs = tuple(peakDim.peakDimContribs)
if useAllContribs == 0 and len(peakDimContribs) > 1:
#
# First check if resonances for contribs connected through one resonanceSet
# If so, then set values anyway.
#
resonanceSet = peakDimContribs[0].resonance.resonanceSet
sameShiftGroup = 1
if resonanceSet:
resonanceSetResonances = resonanceSet.sortedResonances(
)
for peakDimContrib in peakDimContribs[1:]:
if peakDimContrib.resonance not in resonanceSetResonances:
sameShiftGroup = 0
break
if not sameShiftGroup:
#
# Ignore this peakDim - many contribs possible and not wanted (?)
#
print " Warning: ignoring peakDim %d for peak %d... more than one resonance contribution" % (
peakDim.dim, peak.serial)
continue
for peakDimContrib in peakDimContribs:
resonance = peakDimContrib.resonance
if not resonanceChemShifts.has_key(resonance):
resonanceChemShifts[resonance] = []
resonanceChemShifts[resonance].append(chemShift)
#
# Make a new chemical shift list if none passed in
#
if shiftList == None:
shiftList = Nmr.ShiftList(proj.currentNmrProject,
name=shiftListName,
unit='ppm',
experiments=experiments)
#
# Get the average (and standard dev) of the chemical shift for each resonance
# Create the chemical shifts
#
for resonance in resonanceChemShifts.keys():
chemShiftTotal = 0.0
for chemShift in resonanceChemShifts[resonance]:
chemShiftTotal += chemShift
chemShiftAverage = chemShiftTotal / len(resonanceChemShifts[resonance])
standardDev = getStandardDev(resonanceChemShifts[resonance],
chemShiftTotal)
if standardDev == None:
if defaultShiftError.has_key(resonance.isotopeCode):
shiftError = defaultShiftError[resonance.isotopeCode]
else:
shiftError = 0.1
else:
shiftError = standardDev * 2
#
# Set the chemical shift value
#
shift = shiftList.findFirstMeasurement(resonance=resonance)
if not shift:
Nmr.Shift(shiftList,
value=chemShiftAverage,
error=shiftError,
resonance=resonance)
else:
allowedErrorMargin = shiftError / 10
if shift.value + allowedErrorMargin < chemShiftAverage or chemShiftAverage < shift.value - allowedErrorMargin:
resName = getResNameText(resonance)
multiDialog.MeasurementSelect(guiParent, resName, resonance,
chemShiftAverage, shiftList,
'Shift')
return shiftList