nmrViewFormat.readSequence(sequenceFile, minimalPrompts = 1) # # Read in the chemical shifts (set minimalPrompts = 0 for more user interaction during this process) # chemShiftFile = os.path.join(dataDir,inputChemShiftFileName) nmrViewFormat.readShifts(chemShiftFile, minimalPrompts = 1) # # Create an NMR experiment. This is based on the NmrExpPrototype setup. # refExp = getRefExpFromOldExpType(ccpnProject,expTypeName) nmrExp = createExperiment(ccpnProject,expName,refExp) nmrDataSource = createPpmFreqDataSource(nmrExp,'test','processed',nmrExp.numDim) # # Read in a peak list (connected to the experiment that was just created) # peakListFile = os.path.join(dataDir,inputPeakListFileName) nmrViewFormat.readPeaks(peakListFile, dataSource = nmrDataSource,minimalPrompts = 1) # # Run linkresonances... before running this there is on the one hand the NMR # information (peaks, shifts) linked to the 'Resonance' objects, and on the # other hand the sequence information (molecules, chains, residues, atoms), but # they are not linked to each other. # # LinkResonances links up the NMR information to the atom information - so basically
# Should print 'H_H[N].NOESY'.
print 'New experiment type name: [%s]' % refExp.name
# Create a real NMR experiment from this object and link it to the
# CCPN project.
keywds = {'expName': 'noesyTest', 'refExperiment': refExp}
nmrExp = createExperiment(project, **keywds)
# Create a dataSource object (with the right number of dimensions etc.)
# to hold peak list information.
keywds2 = {
'dsName': 'test',
'dsType': 'processed',
'numDim': nmrExp.numDim
}
nmrDataSource = createPpmFreqDataSource(nmrExp, **keywds2)
# Read in a peak list connected to the experiment/dataSource that
# was just created.
nmrViewPeakLists = 'nmrView.xpk'
nmrViewPeakListFile = os.path.join(nmrViewDir, nmrViewPeakLists)
# Do the reading - this will throw up a Tkinter popup window.
nmrViewObj.readPeaks(nmrViewPeakListFile,
dataSource=nmrDataSource,
minimalPrompts=1)
# Find and print this peakList in the CCPN data model.
peakLists = nmrDataSource.sortedPeakLists()
print 'Peaklists: [%s]' % peakLists
def readPeakList(self, fileName, refExperimentOldName, spectrumName,
peakListDimOrder):
if self.fileNameDict.has_key(fileName):
self.peakList = self.fileNameDict[fileName]
else:
refExperiment = getRefExpFromOldExpType(self.ccpnProject,
refExperimentOldName)
self.experiment = self.ccpnProject.currentNmrProject.findFirstExperiment(
name=spectrumName, refExperiment=refExperiment)
if not self.experiment:
self.experiment = createExperiment(self.ccpnProject,
spectrumName, refExperiment)
self.dataSource = self.experiment.findFirstDataSource(
dataType='processed')
if not self.dataSource:
self.dataSource = createPpmFreqDataSource(
self.experiment, spectrumName, 'processed',
self.experiment.numDim)
self.peakList = self.dataSource.findFirstPeakList(
name=spectrumName)
#
# Determine the peak list relationship
# In ccp data model setup assuming that:
# - first dim is acquisition
# - first hetero dim belongs to acquisition dim
#
protonDims = []
heteroDims = []
for dataDim in self.dataSource.sortedDataDims():
if '1H' in dataDim.findFirstDataDimRef(
).expDimRef.isotopeCodes:
protonDims.append(dataDim.findFirstDataDimRef())
else:
heteroDims.append(dataDim.findFirstDataDimRef())
dataDimRefs = self.experiment.numDim * ['']
for dim in range(0, len(peakListDimOrder)):
peakListDim = returnInt(peakListDimOrder[dim])
if peakListDim:
if dim >= 2:
dataDimRef = heteroDims[dim - 2]
else:
dataDimRef = protonDims[dim - 2]
dataDimRefs[peakListDim - 1] = dataDimRef
self.peakLists = self.format.readPeaks(fileName,
dataSource=self.dataSource,
dataDimRefs=dataDimRefs,
specName=spectrumName,
peakList=self.peakList,
minimalPrompts=1)
if self.experiment not in self.chemShiftList.experiments:
self.chemShiftList.addExperiment(self.experiment)
return self.peakLists
nmrViewChemShifts = 'ppm.out'
nmrViewChemShiftFile = os.path.join(nmrViewDir, nmrViewChemShifts)
nmrViewObj.readShifts(nmrViewChemShiftFile, minimalPrompts = 1)
refExpType = 'noesy_hsqc_HNH.hhn'
refExp = getRefExpFromOldExpType(project, refExpType)
nmrExp = createExperiment(project, 'noesyTest', refExp)
# Find the molSystem object in the CCPN project.
molSystem = project.sortedMolSystems()[0]
# Make a link between the molSystem and the experiment objects.
nmrExp.addMolSystem(molSystem)
nmrDataSource = createPpmFreqDataSource(nmrExp, 'test', 'processed',
nmrExp.numDim)
nmrViewPeakLists = 'nmrView.xpk'
nmrViewPeakListFile = os.path.join(nmrViewDir, nmrViewPeakLists)
nmrViewObj.readPeaks(nmrViewPeakListFile,
dataSource = nmrDataSource,
minimalPrompts = 1)
nmrViewObj.linkResonances(setSingleProchiral = 0,
setSinglePossEquiv = 0,
minimalPrompts = 1)
# New part of the code - need a BMRB Entry object for writing to
# an NMR-STAR file.
entryStore = project.newNmrEntryStore(name = project.name)