# As usual, create the BMRB Entry object.
entryStore = project.newNmrEntryStore(name=project.name)
entry = entryStore.newEntry(name=project.name)
# Get the molSystem object, and link to it.
molSystem = project.sortedMolSystems()[0]
entry.setMolSystem(molSystem)
# Link the structureGeneration object so that the restraints
# are part of the BMRB Entry object.
entry.addStructureGeneration(strucGen)
# Make a test NOESY experiment.
refExpType = 'noesy_hsqc_HNH.hhn'
refExp = getRefExpFromOldExpType(project, refExpType)
nmrExp = createExperiment(project, 'noesyTest', refExp)
nmrExp.addMolSystem(molSystem)
# Link the experiment to the BMRB Entry.
entry.addExperiment(nmrExp)
# Save the project to XML files using a sub routine - see above.
saveProject(project, name='testSave', subDir='../data/cnsOut')
# Sub routine to print where data for the CCPN project is saved.
printReposUrls(project)
curDir = os.path.abspath('../data')
nmrStarDir = os.path.join(curDir, 'nmrStar')
sequenceFile = os.path.join(dataDir,inputSequenceFileName) 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.
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
def ccpNmrConversion(self):
ccpNmrConv = Tool()
ccpNmrConv.setupProject(self.xmlFile.conversion.project.filename,
self.xmlFile.conversion.project.name)
ccpNmrConv.setupMolSystem(
self.xmlFile.conversion.molecular_system.name)
self.tagAriaInput(ccpNmrConv.molSystem)
#
# Molecules
#
molecules = self.xmlFile.conversion.molecular_system.molecule
if type(molecules) != type([]):
molecules = [molecules]
for molecule in molecules:
ccpNmrConv.setupFormat(molecule.sequence_format)
if not hasattr(molecule, 'segID'):
segID = defaultMolCode
else:
segID = molecule.segID
ccpNmrConv.readSequence(molecule.sequence_filename, molecule.name,
molecule.type, segID,
molecule.first_residue_number)
#
# Spectra
#
spectra = self.xmlFile.conversion.spectrum
if type(spectra) != type([]):
spectra = [spectra]
for spectrum in spectra:
ccpNmrConv.setupFormat(spectrum.data_files_format)
if spectrum.chemical_shifts.filename:
shiftList = ccpNmrConv.readShifts(
spectrum.chemical_shifts.filename, spectrum.name)
else:
shiftList = ccpNmrConv.createChemShiftsFromPeakList(
spectrum.name)
self.tagAriaInput(shiftList)
peakListDimOrder = [
spectrum.cross_peaks.proton1, spectrum.cross_peaks.proton2,
spectrum.cross_peaks.hetero1, spectrum.cross_peaks.hetero2
]
# TODO TODO Should the names not directly reflect the ones from the data model?!?! Better...
# or have alternative system for this at least
refExperiment = getRefExpFromOldExpType(ccpNmrConv.ccpnProject,
spectrum.type)
if not refExperiment:
print " Error unknown experiment type %s... not created." % spectrum.type
peakLists = ccpNmrConv.readPeakList(spectrum.cross_peaks.filename,
refExperiment, spectrum.name,
peakListDimOrder)
self.tagAriaInput(peakLists[0])
if spectrum.cross_peaks_assignments.filename:
ccpNmrConv.readPeakListAssignments(
spectrum.cross_peaks_assignments.filename)
#
# Link resonances to atoms
#
ccpNmrConv.linkResonances(
self.xmlFile.conversion.project.naming_system,
setSinglePossEquiv=0,
setSingleProchiral=0,
useIupacMatching=1,
minimalPrompts=1)
self.ccpNmrConv = ccpNmrConv
sequenceFile = os.path.join(dataDir,inputSequenceFileName) 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.
def fcSetPeaksInformation(self, formatName, filePath, addKeywords):
"""
Handling of peak lists - can use specific addKeywords that make it easier to select
reference experiments and set the peak list to reference experiment dimension mappings.
"""
from ccpnmr.format.general.Util import getRefExpFromOldExpType
#
# Step 1, preparse the file and get info out
#
(fileRead, fileInformation) = self.formatConversion.preparseFile(
'peaks', formatName, filePath, addKeywords=addKeywords)
if not fileRead:
raise self.FcWorkFlowError(
"Could not read peak list file %s in format %s:\n%s" %
(filePath, formatName, fileRead))
else:
peakListNames = fileInformation.keys()
if len(peakListNames) > 1:
if not addKeywords.has_key("peakListName"):
raise self.FcWorkFlowError(
"Multiple peak lists in file %s, and no specific 'peakListName' defined in addKeywords."
% (filePath))
else:
peakListName = addKeywords['peakListName']
if peakListName not in peakListNames:
raise self.FcWorkFlowError(
"Multiple peak lists in file %s, and 'peakListName' %s not in list of peak list names from file."
% (filePath, peakListName))
else:
peakListName = peakListNames[0]
peakPpmRanges = fileInformation[peakListName]['peakPpmRanges']
dimCodes = fileInformation[peakListName]['dimensionCodes']
#
# Step 2, set the reference experiment.
#
if addKeywords.has_key('oldExpType'):
refExperiment = getRefExpFromOldExpType(
self.formatConversion.ccpnProject, addKeywords['oldExpType'])
if not refExperiment:
raise self.FcWorkFlowError(
"Could not find reference experiment 'old' name %s." %
(addKeywords['oldExpType']))
del (addKeywords['oldExpType'])
elif addKeywords.has_key('expTypeInfo'):
(expPrototypeName, refExpName) = addKeywords['expTypeInfo']
refExperiment = None
expPrototype = project.findFirstNmrExpPrototype(
name=expPrototypeName)
if expPrototype:
refExperiment = expPrototype.findFirstRefExperiment(
name=refExpName)
if not refExperiment:
raise self.FcWorkFlowError(
"Could not find reference experiment with (prototype,experiment) names %s."
% (addKeywords['expTypeInfo']))
del (addKeywords['expTypeInfo'])
else:
raise self.FcWorkFlowError(
"No reference experiment defined for %s:\nNeed to set an 'oldExpType' or 'expTypeInfo' variable in addKeywords in self.dataFiles."
% (filePath))
addKeywords['refExperiment'] = refExperiment
refExperimentInfo = self.formatConversion.getRefExperimentInfo(
addKeywords['refExperiment'])
#
# Step 3 set the peak list to reference experiment dimension mapping, if necessary
#
# uniqueMatches gives the unique (shift matches) connection between the CCPN dimension (as number) and the peak dimension (as list index)
# matches gives all possible shift matches
#
# Basically, web side has to allow all possibilities in 'matches', but should set the 'uniqueMatches' match as default.
#
# Only run this if not manually set!
if not addKeywords.has_key(
'expDimToPeakDim') or not addKeywords['expDimToPeakDim']:
(matches,
uniqueMatches) = self.formatConversion.matchFormatAndCcpnPeakDims(
peakPpmRanges, dimCodes, refExperimentInfo['ppmRange'])
if uniqueMatches:
addKeywords['expDimToPeakDim'] = uniqueMatches
else:
raise self.FcWorkFlowError(
"No reference experiment dimension to peak list dimension mapping set or a unique match found. Possibilities are:\n%s\n\nReference experiment info is:\n%s\n\nPeak ppm ranges:\n%s\n"
% (str(matches), refExperimentInfo, str(peakPpmRanges)))