def createPpmFreqDataSource(exp,dsName,dsType,numDim):
ds = Nmr.DataSource(exp,name = dsName, numDim = numDim, dataType = dsType)
for dim in range(0,numDim):
expDim = exp.findFirstExpDim(dim = (dim + 1))
expDimRefs = expDim.sortedExpDimRefs()
refIsotopeCode = expDimRefs[0].isotopeCodes[0]
# User first expDimRef to set number of points
# Set numPoints, numPointsOrig to 20 for H, 250 for C,N!
if refIsotopeCode == '1H':
numPoints = 1024
valuePerPoint = 6.5
else:
numPoints = 256
if refIsotopeCode == '13C':
valuePerPoint = 100.0
elif refIsotopeCode== '15N':
valuePerPoint = 40.0
else:
valuePerPoint = 1.0
# Setting up empty freqdatadim and associated datadimref...
# Assuming that imaginary data will be deleted!
freqDataDim = Nmr.FreqDataDim(ds, expDim = expDim, dim = (dim + 1), isComplex = True,valuePerPoint = valuePerPoint, numPoints = numPoints, numPointsOrig = numPoints)
# Tag to mark that this is a 'default' freqDataDim
freqDataDim.addApplicationData(Implementation.AppDataBoolean(application = ccpNmr_kw, keyword = 'default', value = True))
# Set sensible dataDimRef info.
setDataDimRefs(ds)
return ds
def tagAsFresh(ccpnObject):
appData = ccpnObject.findFirstApplicationData(keyword = freshTag)
if not appData:
appData = Implementation.AppDataBoolean(application = 'pdbeCcGeneration', keyword = freshTag, value = True)
ccpnObject.addApplicationData(appData)
appData.value = True
def tagAriaInput(self, object):
appData = object.findFirstApplicationData(application=ccpNmr_kw,
keyword=isAriaInput_kw)
if not appData:
object.addApplicationData(
Implementation.AppDataBoolean(application=ccpNmr_kw,
keyword=isAriaInput_kw,
value=True))
def createExperiment(proj,expName,refExperiment,unit = 'ppm'):
#
# Create a default experiment based on a reference experiment...
#
numDim = len(refExperiment.refExpDims)
isReversed = refExperiment.isReversed
# Make sure experiment name fits Ccp Line
expName = returnMemopsLine(expName)
# Create the experiment
exp = Nmr.Experiment(proj.currentNmrProject,name = expName, numDim = numDim, refExperiment = refExperiment)
# Tag to mark that this is a 'default' experiment
exp.addApplicationData(Implementation.AppDataBoolean(application = ccpNmr_kw, keyword = 'default', value = True))
#
# Set expDimRefs
#
atomSiteList = []
acquisitionDim = None
for i in range(0,numDim):
expDim = exp.findFirstExpDim(dim = i + 1)
refExpDim = refExperiment.findFirstRefExpDim(dim = i + 1)
expDim.refExpDim = refExpDim
atomSiteList.append([])
for refExpDimRef in refExpDim.refExpDimRefs:
# TODO Here catch things like ConstantTimePeriod for editing!!!!?!?!
expMeasurement = refExpDimRef.expMeasurement
isotopeCodes = []
for atomSite in expMeasurement.atomSites:
isotopeCodes.append(atomSite.isotopeCode)
if isotopeCodes.count('1H'):
sf = baseFrequency = 500.0
elif isotopeCodes.count('13C'):
sf = baseFrequency = 125.7367377
elif isotopeCodes.count('15N'):
sf = baseFrequency = 50.670637
else:
sf = baseFrequency = 1.0
#
# Setting paramaters correctly goes via GUI interface... these are 'defaults'
#
expDimRef = Nmr.ExpDimRef(expDim, unit = unit,
sf = sf,
baseFrequency = baseFrequency,
measurementType = expMeasurement.measurementType,
isotopeCodes = isotopeCodes,
refExpDimRef = refExpDimRef)
# Tag to mark that this is a 'default' expDimRef
expDimRef.addApplicationData(Implementation.AppDataBoolean(application = ccpNmr_kw, keyword = 'default', value = True))
#
# Keep track for expTransfer settings...
#
atomSiteList[-1].append((expDimRef,expMeasurement.atomSites))
#
# Set acquisition dimension. Is the expMeasurement connected to the last
# expStep (or first expStep in case isReversed).
#
expDim = None
for expGraph in refExperiment.nmrExpPrototype.expGraphs:
expStepNums = []
for expStep in expGraph.expSteps:
expStepNums.append(expStep.stepNumber)
expStepNums.sort()
if not isReversed:
expStepNums.reverse()
for expStepNum in expStepNums:
expStep = expGraph.findFirstExpStep(stepNumber = expStepNum)
for refExpDimRef in expStep.expMeasurement.refExpDimRefs:
refExpDim = refExpDimRef.refExpDim
expDim = exp.findFirstExpDim(refExpDim = refExpDim)
if expDim:
break
if expDim:
break
if expDim:
break
if expDim:
expDim.isAcquisition = True
#
# Set expTransfers...
#
for i in range(0,len(atomSiteList)-1):
for (expDimRef,atomSites) in atomSiteList[i]:
for otherAtomSiteList in atomSiteList[i+1:]:
for (otherExpDimRef,otherAtomSites) in otherAtomSiteList:
for expGraph in atomSites[0].nmrExpPrototype.expGraphs:
#
# Transfers are only set in simple case: direct transfer between single atomSites corresponding to expDimRefs
#
expDimRefSet = set([expDimRef,otherExpDimRef])
sites = frozenset([atomSites[0],otherAtomSites[0]])
refExpTransfer = expGraph.findFirstExpTransfer(atomSites = sites)
if refExpTransfer:
expTransfer = exp.findFirstExpTransfer(transferType = refExpTransfer.transferType, expDimRefs = expDimRefSet)
if not expTransfer:
expTransfer = exp.newExpTransfer(transferType = refExpTransfer.transferType, expDimRefs = expDimRefSet)
return exp
