def candidNmrCalcRun(nmrCalcRun):
""" Modify nmrCalcRun from generic MultiStructure form to CANDID-specific
Input:
nmrCalcRun: NmrCalc.Run
"""
xx = nmrCalcRun.findFirstRunParameter(name='shiftFormat')
if xx is None:
raise Exception("shiftFormat must be set for UNIO_CANDID protocols")
else:
shiftFormat = xx.textValue
xx = nmrCalcRun.findFirstRunParameter(name='peakFormat')
if xx is None:
raise Exception("peakFormat must be set for UNIO_CANDID protocols")
else:
peakFormat = xx.textValue
shiftFileSuffix = intUtil.getFileFormatData(shiftFormat,
'shift')['shiftExt']
peakFileSuffix = intUtil.getFileFormatData(peakFormat, 'peak')['peakExt']
# name : code dictionary for resetting code values
codeRemapping = {
'solvent': 'SolventType',
'spectrumType': 'PeakType',
'spectrumKind': 'PeakKind',
'numDataSets': 'NoPeakList',
}
# set proper codes for existing data parameters
for runParameter in nmrCalcRun.sortedRunParameters():
newCode = codeRemapping.get(runParameter.name)
if newCode is not None:
runParameter.code = newCode
# Reset spectrumType strings
for runParameter in nmrCalcRun.findAllRunParameters(name='spectrumType'):
ss = runParameter.textValue
if ss in spectrumTypes:
# Spectrum type should be remapped
runParameter.textValue = spectrumTypes[ss]
# get data sets
peakListObjs = [
x for x in nmrCalcRun.sortedData() if x.className == 'PeakListData'
]
shiftListObjs = {}
for datum in nmrCalcRun.findAllData(className='MeasurementListData'):
measurementList = datum.measurementList
if measurementList.className == 'ShiftList':
shiftListObjs[measurementList] = datum
# create data set files and parameters
numDataSets = 0
usePeakListObjs = []
for peakListData in peakListObjs:
numDataSets += 1
# check and set spectrum kind
dataSource = peakListData.dataSource
spectrumKind = getSpectrumKind(dataSource)
if spectrumKind is None:
print 'WARNING, incorrect spectrum type. Removing %s' % peakListData
for runParameter in peakListData.runParameters:
runParameter.delete()
peakListData.delete()
numDataSets -= 1
continue
# note in order to select shiftlist later
usePeakListObjs.append(peakListData)
# Reset connected parameters
#for runParameter in peakListData.runParameters:
# code = runParameter.code
# if code:
# runParameter.code = code + '[%s]' % numDataSets
nmrCalcRun.newRunParameter(
name='spectrumKind',
data=peakListData,
code=codeRemapping['spectrumKind'], # + '[%s]' % numDataSets),
textValue=spectrumKind)
# check and set shiftlist and related parameters
experiment = dataSource.experiment
shiftList = experiment.shiftList
shiftListData = shiftListObjs.get(shiftList)
if shiftListData is None:
shiftListData = nmrCalcRun.newMeasurementListData(
name='shiftList', measurementList=shiftList)
shiftListObjs[shiftList] = shiftListData
shiftFile = intUtil.objectFileName(shiftList,
suffix=shiftFileSuffix,
compact=True)
nmrCalcRun.newRunParameter(name='fileName',
textValue=shiftFile,
data=shiftListData)
nmrCalcRun.newRunParameter(name='fileFormat',
textValue=shiftFormat,
data=shiftListData)
useFormat = shiftFormat
else:
shiftFile = shiftListData.findFirstRunParameter(
name='fileName').textValue
useFormat = shiftListData.findFirstRunParameter(
name='fileFormat').textValue
nmrCalcRun.newRunParameter(name='fileNameShift',
textValue=shiftFile,
code='fileNameShift',
data=peakListData)
nmrCalcRun.newRunParameter(name='fileFormatShift',
textValue=shiftFormat,
code='fileFormatShift',
data=peakListData)
fileNamePeakList = intUtil.objectFileName(peakListData.peakList,
suffix=peakFileSuffix,
compact=True)
nmrCalcRun.newRunParameter(name='fileName',
textValue=fileNamePeakList,
code='fileNamePeak',
data=peakListData)
nmrCalcRun.newRunParameter(name='fileFormat',
textValue=peakFormat,
code='fileFormatPeak',
data=peakListData)
# number of data sets
nmrCalcRun.newRunParameter(name='numDataSets',
code=codeRemapping['numDataSets'],
intValue=numDataSets)
# choose shift list for backbone
if shiftListObjs:
if len(shiftListObjs) == 1:
shiftData = list(shiftListObjs.items())[0][1]
fileName = shiftData.findFirstRunParameter(
name='fileName').textValue
fileFormat = shiftData.findFirstRunParameter(
name='fileFormat').textValue
else:
shiftListScore = 0
for peakListData in usePeakListObjs:
# check preferred shiftlist
spectrumKind = peakListData.findFirstRunParameter(
name='spectrumKind').textValue
spectrumType = peakListData.findFirstRunParameter(
name='spectrumType').textValue
shiftFileWeight = (preferredShiftWeights.get(spectrumKind, 0) +
preferredShiftWeights.get(spectrumType, 0))
if shiftFileWeight > shiftListScore:
shiftListScore = shiftFileWeight
fileName = peakListData.findFirstRunParameter(
name='fileNameShift').textValue
fileFormat = peakListData.findFirstRunParameter(
name='fileFormatShift').textValue
# main shift list
nmrCalcRun.newRunParameter(name='fileNameShift',
code='fileNameCaCbShift',
textValue=fileName)
nmrCalcRun.newRunParameter(name='fileFormatShift',
code='fileFormatCaCbShift',
textValue=fileFormat)
def asdpNmrCalcRun(nmrCalcRun):
""" Modify nmrCalcRun from generic MultiStructure form to ASDP-specific
Input:
nmrCalcRun: NmrCalc.Run
"""
# CCPN params
xx = nmrCalcRun.findFirstRunParameter(name='shiftFormat')
if xx is None:
raise Exception("shiftFormat must be set for ASDP protocols")
else:
shiftFormat = xx.textValue
xx = nmrCalcRun.findFirstRunParameter(name='peakFormat')
if xx is None:
raise Exception("peakFormat must be set for ASDP protocols")
else:
peakFormat = xx.textValue
shiftFileSuffix = intUtil.getFileFormatData(shiftFormat,
'shift')['shiftExt']
peakFileSuffix = intUtil.getFileFormatData(peakFormat, 'peak')['peakExt']
# name : code dictionary for resetting code values
codeRemapping = {
#'spectrumType':'x1.type',
'jobName': 'proteinName',
#'numDataSets':None,
}
# set proper codes for existing data parameters
for runParameter in nmrCalcRun.sortedRunParameters():
name = runParameter.name
if name in codeRemapping:
runParameter.code = codeRemapping[name]
# get data sets
peakListObjs = [
x for x in nmrCalcRun.sortedData() if x.className == 'PeakListData'
]
shiftListObjs = {}
for datum in nmrCalcRun.findAllData(className='MeasurementListData'):
measurementList = datum.measurementList
if measurementList.className == 'ShiftList':
shiftListObjs[measurementList] = datum
defaultTol = 1.0
runParam = nmrCalcRun.findFirstRunParameter(name='defaultTolPoints')
if runParam:
val = runParam.floatValue
if val:
defaultTol = val
minTol = 0.02
runParam = nmrCalcRun.findFirstRunParameter(name='minTolPpm')
if runParam:
val = runParam.floatValue
if val:
minTol = val
# create data set files and parameters
for peakListData in peakListObjs:
dataSource = peakListData.dataSource
experiment = dataSource.experiment
dimCodes = getDimCodes(dataSource)
if (None in dimCodes or not experiment.findFirstExpTransfer(
transferType='through-space')):
print("Removed spectrum %s: not recognised as 2D-4D NOESY" %
dataSource)
for runParameter in peakListData.runParameters:
runParameter.delete()
peakListData.delete()
continue
# peak file name
fileNamePeakList = intUtil.objectFileName(peakListData.peakList,
suffix=peakFileSuffix,
compact=True)
nmrCalcRun.newRunParameter(name='fileName',
textValue=fileNamePeakList,
code='fileNamePeak',
data=peakListData)
nmrCalcRun.newRunParameter(name='fileFormat',
textValue=peakFormat,
data=peakListData)
nmrCalcRun.newRunParameter(name='numDim',
code='dimension',
intValue=dataSource.numDim,
data=peakListData)
# interchain NOEs not supported
nmrCalcRun.newRunParameter(name='haveInterChain',
code='haveIC',
intValue=0,
data=peakListData)
nmrCalcRun.newRunParameter(name='interChain',
code='IC',
intValue=0,
data=peakListData)
# Solvent
runParameter = peakListData.findFirstRunParameter(name='solvent')
if runParameter.textValue == 'h2o':
val = 1
else:
val = 0
nmrCalcRun.newRunParameter(name='solventH2O',
code='waterFlag',
intValue=val,
data=peakListData)
runParameter.delete()
# column data
nmrCalcRun.newRunParameter(name='intensityColumn',
code='col.intensity',
intValue=dataSource.numDim + 4,
data=peakListData)
isotopeCodes = getIsotopeCodesList(dataSource)
tolerances = AssignmentBasic.estimateAssignmentTolerances(
dataSource, defPoints=defaultTol, minTol=minTol)
# Dimension parameters:
for ii, dataDim in enumerate(dataSource.sortedDataDims()):
dimCode = dimCodes[ii]
# Peak position column column
tag = 'col.%s' % dimCode
nmrCalcRun.newRunParameter(name='PositionColumn',
code=tag,
intValue=ii + 2,
data=peakListData)
# Shift correction (set to default)
tag = '%s.shift' % dimCode
nmrCalcRun.newRunParameter(name='ShiftCorrection',
code=tag,
floatValue=0.0,
data=peakListData)
# sign (meaning ???) (set to default)
tag = '%s.sign' % dimCode
nmrCalcRun.newRunParameter(name=tag,
code=tag,
intValue=0,
data=peakListData)
# Assignment tolerance
tag = '%s.tol' % dimCode
nmrCalcRun.newRunParameter(name='AssignTolerance',
code=tag,
floatValue=tolerances[ii],
data=peakListData)
# sw in ppm
tag = '%s.sw' % dimCode
swOrig = 1000.0
# NBNB program probably assumes that all shifts are within SW.
# As long as peak positions are correct, swOrig is not useful.
# Leave at default
#for dataDimRef in dataDim.sortedDataDimRefs():
# if dataDimRef.expDimRef.measurementType in ('shift','Shift'):
# swOrig = dataDimRef.spectralWidthOrig
nmrCalcRun.newRunParameter(name='swPpm',
code=tag,
floatValue=swOrig,
data=peakListData)
# dimension type
isotopeCode = isotopeCodes[ii]
if isotopeCode == '1H':
dimType = 'H'
elif isotopeCode == '13C':
dimType = 'C13'
specTypeObj = peakListData.findFirstRunParameter(
name='spectrumType')
if specTypeObj:
dimType = spectrumTypes.get(
specTypeObj.textValue) or dimType
else:
ii = 0
while isotopeCode[ii] in '0123456789':
ii += 1
dimType = isotopeCode[ii:] + isotopeCode[:ii]
tag = '%s.type' % dimCode
nmrCalcRun.newRunParameter(name='dimensionType',
code=tag,
textValue=dimType,
data=peakListData)
# check and set shiftlist and related parameters
shiftList = experiment.shiftList
shiftListData = shiftListObjs.get(shiftList)
if shiftListData is None:
shiftListData = nmrCalcRun.newMeasurementListData(
name='shiftList', measurementList=shiftList)
shiftListObjs[shiftList] = shiftListData
shiftFile = intUtil.objectFileName(shiftList,
suffix=shiftFileSuffix,
compact=True)
nmrCalcRun.newRunParameter(name='fileName',
textValue=shiftFile,
data=shiftListData)
nmrCalcRun.newRunParameter(name='fileFormat',
textValue=shiftFormat,
data=shiftListData)
useFormat = shiftFormat
# main shift list
if shiftListObjs:
if len(shiftListObjs) == 1:
shiftData = list(shiftListObjs.items())[0][1]
fileName = shiftData.findFirstRunParameter(
name='fileName').textValue
fileFormat = shiftData.findFirstRunParameter(
name='fileFormat').textValue
nmrCalcRun.newRunParameter(name='fileNameShift',
code='chemicalShiftFile',
textValue=fileName,
data=shiftData)
nmrCalcRun.newRunParameter(name='fileFormatShift',
code='fileFormatShift',
textValue=fileFormat,
data=shiftData)
else:
raise Exception("All spectra must use same shift list for ASDP")