def importFromCyana(nmrCalcRun, targetDir):
c = cp.CyanaParser()
rootProject = nmrCalcRun.root
os.chdir(targetDir)
peakFiles = []
uplFiles = []
acoFiles = []
rdcFiles = []
cyaFiles = []
noaFiles = []
txtFiles = []
dataSources = []
ccpnConfigFile = open("Properties.ccpn.json")
ccpnConfig = json.load(ccpnConfigFile)
configFile = open("cyana2ccpn.json")
config = json.load(configFile)
runId = ccpnConfig['CCPN.nmrCalcId'].split('+')[1]
for peakList in ccpnConfig['PeakListData']:
peakListName = peakList['fileName'].split(
'.peaks')[0] + '-cycle7.peaks'
peakFiles.append(peakListName)
for distanceRestraintList in config["distanceRestraints"]:
uplFiles.append(distanceRestraintList)
for dihedralRestraintList in config["dihedralRestraints"]:
acoFiles.append(dihedralRestraintList)
for rdcRestraintList in config["rdcRestraints"]:
rdcFiles.append(rdcRestraintList)
for cyaFile in config["cyaFiles"]:
cyaFiles.append(cyaFile)
for noaFile in config["noaFiles"]:
noaFiles.append(noaFile)
seqFile = ccpnConfig['RunParameter']['fileNameSequence']
originalProtFile = ccpnConfig['MeasurementListData'][0]['fileName']
finalProtFile = originalProtFile.split(".prot")[0] + "-final.prot"
c.parse(seqFile=seqFile,
originalProtFile=originalProtFile,
finalProtFile=finalProtFile,
peakFiles=peakFiles,
rdcFiles=rdcFiles,
acoFiles=acoFiles,
cyaFiles=cyaFiles,
noaFiles=noaFiles)
nmrProject = rootProject.currentNmrProject
nmrConstraintStore = rootProject.newNmrConstraintStore(
nmrProject=nmrProject)
if rootProject.currentAnalysisProject is not None:
AnalysisProject = rootProject.currentAnalysisProject
else:
AnalysisProject = rootProject.newAnalysisProject(
name="analysisProject", nmrProject=nmrProject)
shiftListName = c.finalProtFile
molSystem = rootProject.findFirstMolSystem()
newShiftList = nmrProject.newShiftList(name=shiftListName)
atomToResonanceMap = createAtomtoResonanceMap(nmrProject)
resonanceDictionaries = assignResonances(c.resonances, atomToResonanceMap,
molSystem, newShiftList,
AnalysisProject,
nmrConstraintStore)
loadPdb(config['pdbFile'], molSystem)
# newPeakLists = []
for peakList in ccpnConfig['PeakListData']:
peakListName = peakList['fileName'].split('.peaks')[0]
experimentSerial = int(peakList['fileName'].split('_')[1])
ccpnExperiment = nmrProject.findFirstExperiment(
serial=experimentSerial)
cloneName = ccpnExperiment.name + '_run' + str(runId)
clonedExperiment = cloneExperiment(ccpnExperiment, cloneName)
spectrum = clonedExperiment.findFirstDataSource()
dataSources.append(spectrum)
setExperimentShiftList(clonedExperiment, newShiftList)
peakList = spectrum.newPeakList()
spectrum.activePeakList = peakList
for cingPeakList in c.peakLists:
if cingPeakList.name.split('-')[0] == peakListName:
peakList.name = cingPeakList.name
pickPeaksFromCing(cingPeakList, peakList,
resonanceDictionaries['resonanceDict'])
nmrCalcRun.newPeakListData(name=cingPeakList.name,
ioRole='output',
peakList=peakList)
# newPeakLists.append(peakList)
# for newPeakList in newPeakLists:
assignedPeakList = spectrum.newPeakList()
unassignedPeakList = spectrum.newPeakList()
assignedPeakList.details = 'assigned'
unassignedPeakList.details = 'unassigned'
splitAssignedUnassigned(peakList, assignedPeakList, unassignedPeakList)
loadChemShiftRestraints(c.chemicalShiftRestraints, originalProtFile,
nmrConstraintStore, atomToResonanceMap,
resonanceDictionaries['fixedResonanceDict'],
molSystem)
if len(c.distanceRestraintLists) != 0:
loadDistanceRestraints(c.distanceRestraintLists, nmrProject,
nmrCalcRun, nmrConstraintStore,
resonanceDictionaries['fixedResonanceDict'],
resonanceDictionaries['cingFixedResonanceDict'],
molSystem, AnalysisProject)
if len(c.violationLists) != 0:
violatedPeaks = loadViolatedDistanceRestraints(
c.violationLists, nmrProject, nmrCalcRun, nmrConstraintStore,
resonanceDictionaries['fixedResonanceDict'],
resonanceDictionaries['cingFixedResonanceDict'], molSystem,
AnalysisProject)
for peakList, peaks in violatedPeaks.iteritems():
spectrum = peakList.getDataSource()
newPeakList = spectrum.newPeakList()
newPeakList.details = 'violated'
copyPeakList(peakList, newPeakList, peaks=peaks)
if len(c.dihedralRestraintLists) != 0:
loadDihedralRestraints(c.dihedralRestraintLists, nmrConstraintStore,
nmrCalcRun,
resonanceDictionaries['cingFixedResonanceDict'],
molSystem)
if len(c.rdcRestraintLists) != 0:
loadRdcRestraints(c.rdcRestraintLists, nmrConstraintStore,
resonanceDictionaries['cingFixedResonanceDict'],
molSystem)
pluginModule = intUtil.getIntegratorPlugin(
ccpnConfig["CCPN.Run.wmsProtocolName"])
pluginModule.read.read(nmrCalcRun, targetDir)
print "Import Complete"
return dataSources
# set up input
junk, projectDir, nmrCalcRunId, protocolName = sys.argv[:4]
print '### input : ', projectDir, nmrCalcRunId, protocolName
masterRun = intIo.getNmrCalcRun(projectDir, nmrCalcRunId)
print '### masterRun', masterRun
if masterRun is None:
raise Exception("No NmrCalcRun found for %s, %s"
% (projectDir, nmrCalcRunId))
nmrCalcRun = intUtil.makeDerivedRun(masterRun)
print '### nmrCalcRun', nmrCalcRun
try:
pluginModule = intUtil.getIntegratorPlugin(protocolName)
intUtil.setRunParametersFromConfig(nmrCalcRun,
pluginModule.Util.defaultConfiguration)
except:
print 'WARNING, no python plugin found for %s' % protocolName
nmrCalcRun.wmsProtocolName = protocolName
intIo.doPrepareStdWmsRun(nmrCalcRun, pluginModule)
nmrCalcRun.root.saveModified()
else:
print "Usage: write projectDir NmrCalcRun.IDstring protocolName)"