def setupMultiProtocol(argServer,
procNames=(
'CYANA_SS1',
'CYANA_PEAKLIST',
'ROSETTA_MULTI',
'UNIO_CANDID',
'ASDP_XPLOR',
),
prelimProtocolName=prelimProtocolName,
executeProc=False):
""" Run multiple, connected protocols in one run
"""
intIo.setupMultiInteractive(argServer, procNames, prelimProtocolName)
def setupAsdpXplor(argServer):
project = argServer.getProject()
run = None
#runIndex = None
runIndex = 88
if runIndex:
for store in reversed(project.sortedNmrCalcStores()):
run = store.findFirstRun(serial=runIndex)
if run:
break
intIo.setupSingleInteractive(argServer,
protocolName='ASDP_XPLOR',
prelimProtocolName=prelimProtocolName,
masterRun=run)
def setupCyanaPeaklist(argServer):
project = argServer.getProject()
run = None
#runIndex = None
runIndex = 88
if runIndex:
for store in reversed(project.sortedNmrCalcStores()):
run = store.findFirstRun(serial=runIndex)
if run:
break
intIo.setupSingleInteractive(argServer,
protocolName='CYANA_PEAKLIST',
prelimProtocolName=prelimProtocolName,
masterRun=run)
def setupCandid(argServer):
project = argServer.getProject()
run = None
#runIndex = None
runIndex = 55
if runIndex:
for store in reversed(project.sortedNmrCalcStores()):
run = store.findFirstRun(serial=runIndex)
if run:
break
intIo.setupSingleInteractive(argServer,
protocolName='UNIO_CANDID',
prelimProtocolName=prelimProtocolName,
masterRun=run)
def runCyana2CcpnDialogue(argServer):
calculationData = intIo.runCyana2CcpnDialogue(
argServer,
protocolName='CYANA_SS4',
)
return calculationData
def write(nmrCalcRun, targetDir):
""" Write input files for Program run
Input:
nmrCalcRun: NmrCalc.Run
targetDir: destination directory.
"""
intIo.writeDataFiles(nmrCalcRun, targetDir)
jsonDict = intIo.makeJsonDict(nmrCalcRun)
# write properties file (must be done at the end
propFile = uniIo.joinPath(targetDir, intIo.propFileName)
print 'About to write', propFile
open(propFile,'w').write(json.dumps(jsonDict, sort_keys=True,
indent=intIo.propIndent))
def oldwrite(nmrCalcRun, topDir=None):
""" Write input files for Program run
Input:
nmrCalcRun: NmrCalc.Run
topDir: optional destination directory.
"""
targetDir = intIo.createTargetDir(nmrCalcRun, topDir=topDir)
# write Properties file
propDict, dummy = intIo.makeParameterDict(nmrCalcRun)
propFile = uniIo.joinPath(targetDir, intIo.propFileName)
open(propFile,'w').write(json.dumps(propDict, sort_keys=True,
indent=intIo.propIndent))
# Write data file
# get file
inpFile = propDict.get('INPUT_FILE')
if inpFile:
talosInputFile = uniIo.joinPath(targetDir, inpFile)
else:
raise Exception("No code=INPUT_FILE RunParameter in nmrCalcRun")
# Get shiftList
shiftList = intUtil.getMeasurementList(nmrCalcRun)
if shiftList is None:
raise Exception("Run must have exactly one shift list, %s found" % len(ll))
# Get residues
ll = list(nmrCalcRun.findAllData(className='MolResidueData'))
if len(ll) == 1:
obj = ll.pop()
residues = list(obj.residues)
residues.sort(key=operator.attrgetter('seqId'))
if len(set(obj.chainCodes)) != 1:
raise Exception("Run MolResidueData did not have a (single) chain" )
else:
raise Exception("Run must have excactly one MolResidueData, %s found" % len(ll))
#
talosIo.writeShiftFile(open(talosInputFile,'w'), residues, shiftList,
propDict.get('minShiftQuality'))
def write(nmrCalcRun, targetDir):
""" Write input files for Program run
Input:
nmrCalcRun: NmrCalc.Run
targetDir: destination directory.
"""
intIo.writeDataFiles(nmrCalcRun, targetDir)
jsonDict = intIo.makeJsonDict(nmrCalcRun)
# write properties file
propFile = uniIo.joinPath(targetDir, intIo.propFileName)
open(propFile, 'w').write(
json.dumps(jsonDict, sort_keys=True, indent=intIo.propIndent))
# Write program setup file
fileNameObj = nmrCalcRun.findFirstRunParameter(name='fileNameSetup')
if fileNameObj is not None:
filePath = uniIo.joinPath(targetDir, fileNameObj.textValue)
writeSetupFile(filePath, jsonDict)
def write(nmrCalcRun, targetDir):
""" Write input files for Program run
Input:
nmrCalcRun: NmrCalc.Run
targetDir: destination directory.
"""
intIo.writeDataFiles(nmrCalcRun, targetDir)
jsonDict = intIo.makeJsonDict(nmrCalcRun)
# write properties file
propFile = uniIo.joinPath(targetDir, intIo.propFileName)
print 'About to write', propFile
open(propFile, 'w').write(
json.dumps(jsonDict, sort_keys=True, indent=intIo.propIndent))
# Write program setup file
fileNameObj = nmrCalcRun.findFirstRunParameter(name='fileNameSetup')
importJsonName = 'cyana2ccpn.json'
if fileNameObj is not None:
# write init.cya
initFile = uniIo.joinPath(targetDir, initFileName)
rmsdrange = jsonDict['RunParameter'].pop('rmsdrange')
seqFile = jsonDict['RunParameter'].pop('fileNameSequence')
text = """# Cyana init file - Generated by CcpNmr Integrator
rmsdrange:=%s
cyanalib
read seq %s
""" % (rmsdrange, seqFile)
open(initFile, 'w').write(text)
# write main command file
filePath = uniIo.joinPath(targetDir, fileNameObj.textValue)
importFilePath = uniIo.joinPath(targetDir, importJsonName)
writeSetupFile(filePath, jsonDict)
writeImportJson(importFilePath, jsonDict)
def runCyanaPeaklist(argServer):
intIo.runCyana2Ccpn(
argServer,
protocolName='CYANA_SS4',
)
def runCandid(argServer):
intIo.runSingleInteractive(argServer,
protocolName='UNIO_CANDID_XPLOR_TEST',
prelimProtocolName=prelimProtocolName)
def setupPreviousCalculation(argServer):
intIo.setupPreviousCalculation(argServer, protocolName='CYANA_SS4')
def importDataFromCyana(argServer, calculationData=None):
if calculationData == None:
dataSources = intIo.importDataFromCyana(argServer)
else:
dataSources = intIo.importDataFromCyana(calculationData)
return dataSources
def runPreviousCalculation(argServer):
intIo.runPreviousCalculation(argServer, protocolName='CYANA_SS4')
===========================REFERENCE END===============================
"""
import sys
from ccpnmr.integrator.core import Util as intUtil
from ccpnmr.integrator.core import Io as intIo
if __name__ == '__main__':
""" Merge multiple projectfiles (directories or .tgz) as output from WMS).
"""
if len(sys.argv) >= 3:
#
# set up input
nmrCalcRunId = sys.argv[1]
projectFiles = sys.argv[2:]
intIo.mergeParallelRuns(nmrCalcRunId, projectFiles)
else:
print "Usage: merge NmrCalcRun.IDstring projectFiles* "
def runAsdpXplor(argServer):
intIo.runSingleInteractive(argServer,
protocolName='ASDP_XPLOR',
prelimProtocolName=prelimProtocolName)
def setupRosetta(argServer):
intIo.setupSingleInteractive(argServer,
protocolName='ROSETTA_MULTI',
prelimProtocolName=prelimProtocolName)
details=docTemplate % ss)
# Make Nmr.StructureCalculation
nmrProject = nmrCalcRun.nmrCalcStore.nmrProject
nmrCalcRun.structureGeneration = nmrProject.newStructureGeneration(
generationType='denovo', name='CSRosetta', structureEnsemble=ensemble)
if __name__ == '__main__':
""" Run read function from command line.
Input is projectDir NmrCalcRun.IDstring, Rosetta.outputdir
projectDir must contain the desired project (and no others)
NmrCalcRun.IDstring is of the form
'%s+%s' % (NmrCalcStore.guid, Run.serial)
"""
if len(sys.argv) == 4:
# set up input
junk, projectDir, nmrCalcRunId, rosettaDir = sys.argv
nmrCalcRun = intIo.getNmrCalcRun(projectDir, nmrCalcRunId)
if nmrCalcRun is None:
print "No NmrCalcRun found. Aborting"
else:
read(nmrCalcRun, rosettaDir)
nmrCalcRun.root.saveModified()
else:
print "Usage: read projectDir NmrCalcRun.IDstring RosettaDataDir"
def setupCyanaCalculation(argServer):
intIo.setupSingleInteractive(
argServer,
protocolName='CYANA_SS4',
)
def setupCyanaCalculationDialogue(argServer):
intIo.setupCyana2CcpnDialogue(
argServer,
protocolName='CYANA_SS4',
)
if __name__ == '__main__':
""" Run write function from command line.
Input is projectDir NmrCalcRun.IDstring
projectDir must contain the desired project (and no others)
NmrCalcRun.IDstring is of the form
'%s+%s' % (NmrCalcStore.guid, Run.serial)
"""
from memops.general import Io as genIo
if len(sys.argv) >= 3:
# set up input
junk, projectDir, nmrCalcRunId = sys.argv
if len(sys.argv) >= 4:
targetDir = sys.argv[3]
else:
targetDir = None
#intIo.prepareStdWmsRun(pluginName, projectDir, nmrCalcRunId, targetDir)
# NB necessary.
# As side effect prints message that passes newCalcId to WMS Java
nmrCalcRun = intIo.getNmrCalcRun(projectDir, nmrCalcRunId, pluginName)
else:
#print "Usage: write projectDir NmrCalcRun.IDstring"
print "Usage: write projectDir NmrCalcRun.IDstring targetDir(optional)"
if __name__ == '__main__':
""" Copy master NmrCalcRun and add default configuration parameters to copy
Input
"""
if len(sys.argv) >= 4:
#
# 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