def writeNmrStarFile(entry, nmrStarFileName, nmrStarVersion='3.0'):
from pdbe.nmrStar.IO.NmrStarExport import NmrStarExport
nmrStarExport = NmrStarExport(entry, nmrStarVersion=nmrStarVersion)
nmrStarExport.createFile(nmrStarFileName)
nmrStarExport.writeFile()
# 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')
if not os.path.exists(nmrStarDir):
os.mkdir(nmrStarDir)
outNmrStarFile = os.path.join(nmrStarDir, 'nmrStar4.str')
nmrStarExport = NmrStarExport(entry, nmrStarVersion='3.1')
nmrStarExport.createFile(outNmrStarFile)
nmrStarExport.writeFile()
def convert(projectName,
inputDir,
outputFile,
excludeSaveFrames=('general_distance_constraints', )):
print "projectName: %s" % projectName
print "inputDir: %s" % inputDir
print "outputFile: %s" % outputFile
print "excludeSaveFrames: %s" % excludeSaveFrames
ccpnPath = os.path.join(inputDir, projectName)
ccpnProject = loadProject(ccpnPath)
nmrEntryStore = ccpnProject.newNmrEntryStore(name="newNmrEntryStoreName")
molSystem = ccpnProject.findFirstMolSystem()
nmrEntry = nmrEntryStore.newEntry(molSystem=molSystem,
name='newNmrEntryName')
nmrProject = ccpnProject.currentNmrProject
nmrEntry.structureGenerations = nmrProject.sortedStructureGenerations()
if nmrEntry.structureGenerations:
print "Using structureGenerations from nmrProject"
else:
ncs = ccpnProject.findFirstNmrConstraintStore()
sG = None
if not ncs:
print "Failed to find any NmrConstraintStore from project"
else:
sG = ncs.findFirstStructureGeneration()
if sG:
nmrEntry.addStructureGeneration(sG)
print "Using structureGenerations from nmrProject"
else:
print "Failed to find nmrEntry.structureGenerations from nmrProject or nmrConstraintStore; creating a new one."
strucGen = nmrProject.newStructureGeneration()
nmrEntry.addStructureGeneration(strucGen)
# end if
# end if
# end if
try: # ccpn stable as 08 Jul 2009
nmrEntry.structureAnalyses = nmrProject.sortedStructureAnalysiss(
) # watch out for misspelling.
except AttributeError: # ccpn trunk fixed misspelled function
nmrEntry.structureAnalyses = nmrProject.sortedStructureAnalyses()
if not nmrEntry.structureAnalyses:
print "Failed to find nmrEntry.structureAnalyses"
nmrEntry.measurementLists = nmrProject.sortedMeasurementLists()
if not nmrEntry.measurementLists:
print "Failed to find nmrEntry.measurementLists"
# Hack to hook up coordinates, hopefully correctly (Wim 30/04/2009)
if nmrEntry.structureGenerations:
hasStructureEnsemble = False
for strucGen in nmrEntry.structureGenerations:
if strucGen.structureEnsemble:
hasStructureEnsemble = True
break
# end if
# end for
print "hasStructureEnsemble: %s" % hasStructureEnsemble
# This will only work dependably if there is one structureGeneration, one structureEnsemble...
# Take the one that was created last in any case, fingers crossed that they match up!
if not hasStructureEnsemble and ccpnProject.structureEnsembles:
nmrEntry.sortedStructureGenerations(
)[-1].structureEnsemble = ccpnProject.sortedStructureEnsembles(
)[-1]
# end if
# end if
for ne in nmrProject.sortedExperiments(): # will be sortedNmrExperiments
for ds in ne.sortedDataSources():
for pl in ds.sortedPeakLists():
nmrEntry.addPeakList(pl)
nmrStarExport = NmrStarExport(nmrEntry,
nmrStarVersion='3.1',
forceEntryId='1')
nmrStarExport.createFile(outputFile,
excludeSaveFrames=excludeSaveFrames,
verbose=True)
# Set the header comment - only set this if you need a standard header!
topComment = "# File written for CING by NmrStarExport.py code"
nmrStarExport.writeFile(title="CING", topComment=topComment, verbose=True)
def convert(projectName,
inputDir,
outputFile,
excludeSaveFrames=('general_distance_constraints', )):
print "projectName: %s" % projectName
print "inputDir: %s" % inputDir
print "outputFile: %s" % outputFile
print "excludeSaveFrames: %s" % excludeSaveFrames
ccpnPath = os.path.join(inputDir, projectName)
ccpnProject = loadProject(ccpnPath)
# Try to find the CING setup info in the project.
cingCalcStore = ccpnProject.findFirstNmrCalcStore(name='CING')
if cingCalcStore is not None:
nmrProject = cingCalcStore.nmrProject
run = cingCalcStore.findFirstRun(status='pending')
nmrConstraintStore = run.findFirstData(
className='ConstraintStoreData').nmrConstraintStore
molSystem = (
run.findFirstData(className='MolSystemData') or run.findFirstData(
className='StructureEnsembleData').structureEnsemble
or run.findFirstData(
className='MolResidueData').findFirstChain()).molSystem
nmrEntryStore = (
ccpnProject.findFirstNmrEntryStore(name='newNmrEntryStoreName')
or ccpnProject.newNmrEntryStore(name='newNmrEntryStoreName'))
nmrEntry = nmrEntryStore.newEntry(molSystem=molSystem,
name='newNmrEntryName')
structureGeneration = nmrProject.newStructureGeneration(
name='newNmrStructureGeneration',
nmrConstraintStore=nmrConstraintStore)
nmrEntry.addStructureGeneration(structureGeneration)
nmrEntry.measurementLists = [
x.measurementList
for x in run.findAllData(className='MeasurementListData')
]
nmrEntry.structureAnalyses = nmrProject.sortedStructureAnalyses()
nmrEntry.peakLists = [
x.peakList for x in run.findAllData(className='PeakListData')
]
structureGeneration.structureEnsemble = run.findFirstData(
className='StructureEnsembleData').structureEnsemble
else:
nmrEntryStore = ccpnProject.newNmrEntryStore(
name="newNmrEntryStoreName")
molSystem = ccpnProject.findFirstMolSystem()
nmrEntry = nmrEntryStore.newEntry(molSystem=molSystem,
name='newNmrEntryName')
nmrProject = ccpnProject.currentNmrProject
#
# nmrEntry.structureGenerations = nmrProject.sortedStructureGenerations()
# if nmrEntry.structureGenerations:
# print "Using structureGenerations from nmrProject"
structureGenerations = nmrProject.sortedStructureGenerations()
if structureGenerations:
# NBNB RHF October 2014. WATTOS breaks if there is more than one structureGeneration
# Add the newest ony, and let the pre-existing code take care of ensembles
nmrEntry.addStructureGeneration(structureGenerations[-1])
else:
ncs = ccpnProject.findFirstNmrConstraintStore()
sG = None
if not ncs:
print "Failed to find any NmrConstraintStore from project"
else:
sG = ncs.findFirstStructureGeneration()
if sG:
nmrEntry.addStructureGeneration(sG)
print "Using structureGenerations from nmrProject"
else:
print "Failed to find nmrEntry.structureGenerations from nmrProject or nmrConstraintStore; creating a new one."
strucGen = nmrProject.newStructureGeneration()
nmrEntry.addStructureGeneration(strucGen)
# end if
# end if
# end if
try: # ccpn stable as 08 Jul 2009
nmrEntry.structureAnalyses = nmrProject.sortedStructureAnalysiss(
) # watch out for misspelling.
except AttributeError: # ccpn trunk fixed misspelled function
nmrEntry.structureAnalyses = nmrProject.sortedStructureAnalyses()
if not nmrEntry.structureAnalyses:
print "Failed to find nmrEntry.structureAnalyses"
nmrEntry.measurementLists = nmrProject.sortedMeasurementLists()
if not nmrEntry.measurementLists:
print "Failed to find nmrEntry.measurementLists"
# TJR, RHF 16 Oct 2014
# DIfferent hack. We now have only ever allow 1 (ONE) structureGeneration.
assert len(nmrEntry.root.sortedStructureEnsembles()
) == 1, "Must have one and only one ensemble"
assert len(nmrProject.sortedNmrConstraintStores()
) == 1, "Must have one and only one set of constraints"
#
# Hack to hook up coordinates, hopefully correctly (Wim 30/04/2009)
# if nmrEntry.structureGenerations:
# hasStructureEnsemble = False
# for strucGen in nmrEntry.structureGenerations:
# if strucGen.structureEnsemble:
# hasStructureEnsemble = True
# break
# # end if
# # end for
#
# print "hasStructureEnsemble: %s" % hasStructureEnsemble
# # This will only work dependably if there is one structureGeneration, one structureEnsemble...
# # Take the one that was created last in any case, fingers crossed that they match up!
# if not hasStructureEnsemble and ccpnProject.structureEnsembles:
# nmrEntry.sortedStructureGenerations()[-1].structureEnsemble = ccpnProject.sortedStructureEnsembles()[-1]
# # end if
# # end if
for ne in nmrProject.sortedExperiments(
): # will be sortedNmrExperiments
for ds in ne.sortedDataSources():
for pl in ds.sortedPeakLists():
nmrEntry.addPeakList(pl)
nmrStarExport = NmrStarExport(nmrEntry,
nmrStarVersion='3.1',
forceEntryId='1')
nmrStarExport.createFile(outputFile,
excludeSaveFrames=excludeSaveFrames,
verbose=True)
# Set the header comment - only set this if you need a standard header!
topComment = "# File written for CING by NmrStarExport.py code"
nmrStarExport.writeFile(title="CING", topComment=topComment, verbose=True)
def convert(projectName, inputDir, outputFile, excludeSaveFrames = ('general_distance_constraints',) ):
print "projectName: %s" % projectName
print "inputDir: %s" % inputDir
print "outputFile: %s" % outputFile
print "excludeSaveFrames: %s" % excludeSaveFrames
ccpnPath = os.path.join(inputDir, projectName)
ccpnProject = loadProject(ccpnPath)
# Try to find the CING setup info in the project.
cingCalcStore = ccpnProject.findFirstNmrCalcStore(name='CING')
if cingCalcStore is not None:
nmrProject = cingCalcStore.nmrProject
run = cingCalcStore.findFirstRun(status='pending')
nmrConstraintStore = run.findFirstData(className='ConstraintStoreData').nmrConstraintStore
molSystem = (run.findFirstData(className='MolSystemData') or
run.findFirstData(className='StructureEnsembleData').structureEnsemble or
run.findFirstData(className='MolResidueData').findFirstChain()).molSystem
nmrEntryStore = (ccpnProject.findFirstNmrEntryStore(name='newNmrEntryStoreName') or
ccpnProject.newNmrEntryStore(name='newNmrEntryStoreName'))
nmrEntry = nmrEntryStore.newEntry(molSystem=molSystem, name='newNmrEntryName')
structureGeneration = nmrProject.newStructureGeneration(name='newNmrStructureGeneration',
nmrConstraintStore=nmrConstraintStore)
nmrEntry.addStructureGeneration(structureGeneration)
nmrEntry.measurementLists = [x.measurementList for x in run.findAllData(className='MeasurementListData')]
nmrEntry.structureAnalyses = nmrProject.sortedStructureAnalyses()
nmrEntry.peakLists = [x.peakList for x in run.findAllData(className='PeakListData')]
structureGeneration.structureEnsemble = run.findFirstData(className='StructureEnsembleData').structureEnsemble
else:
nmrEntryStore = ccpnProject.newNmrEntryStore(name = "newNmrEntryStoreName")
molSystem = ccpnProject.findFirstMolSystem()
nmrEntry = nmrEntryStore.newEntry( molSystem = molSystem, name = 'newNmrEntryName')
nmrProject = ccpnProject.currentNmrProject
#
# nmrEntry.structureGenerations = nmrProject.sortedStructureGenerations()
# if nmrEntry.structureGenerations:
# print "Using structureGenerations from nmrProject"
structureGenerations = nmrProject.sortedStructureGenerations()
if structureGenerations:
# NBNB RHF October 2014. WATTOS breaks if there is more than one structureGeneration
# Add the newest ony, and let the pre-existing code take care of ensembles
nmrEntry.addStructureGeneration(structureGenerations[-1])
else:
ncs = ccpnProject.findFirstNmrConstraintStore()
sG = None
if not ncs:
print "Failed to find any NmrConstraintStore from project"
else:
sG = ncs.findFirstStructureGeneration()
if sG:
nmrEntry.addStructureGeneration( sG )
print "Using structureGenerations from nmrProject"
else:
print "Failed to find nmrEntry.structureGenerations from nmrProject or nmrConstraintStore; creating a new one."
strucGen = nmrProject.newStructureGeneration()
nmrEntry.addStructureGeneration(strucGen)
# end if
# end if
# end if
try: # ccpn stable as 08 Jul 2009
nmrEntry.structureAnalyses = nmrProject.sortedStructureAnalysiss() # watch out for misspelling.
except AttributeError: # ccpn trunk fixed misspelled function
nmrEntry.structureAnalyses = nmrProject.sortedStructureAnalyses()
if not nmrEntry.structureAnalyses:
print "Failed to find nmrEntry.structureAnalyses"
nmrEntry.measurementLists = nmrProject.sortedMeasurementLists()
if not nmrEntry.measurementLists:
print "Failed to find nmrEntry.measurementLists"
# TJR, RHF 16 Oct 2014
# DIfferent hack. We now have only ever allow 1 (ONE) structureGeneration.
assert len(nmrEntry.root.sortedStructureEnsembles()) == 1, "Must have one and only one ensemble"
assert len(nmrProject.sortedNmrConstraintStores()) == 1, "Must have one and only one set of constraints"
#
# Hack to hook up coordinates, hopefully correctly (Wim 30/04/2009)
# if nmrEntry.structureGenerations:
# hasStructureEnsemble = False
# for strucGen in nmrEntry.structureGenerations:
# if strucGen.structureEnsemble:
# hasStructureEnsemble = True
# break
# # end if
# # end for
#
# print "hasStructureEnsemble: %s" % hasStructureEnsemble
# # This will only work dependably if there is one structureGeneration, one structureEnsemble...
# # Take the one that was created last in any case, fingers crossed that they match up!
# if not hasStructureEnsemble and ccpnProject.structureEnsembles:
# nmrEntry.sortedStructureGenerations()[-1].structureEnsemble = ccpnProject.sortedStructureEnsembles()[-1]
# # end if
# # end if
for ne in nmrProject.sortedExperiments(): # will be sortedNmrExperiments
for ds in ne.sortedDataSources():
for pl in ds.sortedPeakLists():
nmrEntry.addPeakList(pl)
nmrStarExport = NmrStarExport(nmrEntry, nmrStarVersion = '3.1', forceEntryId = '1')
nmrStarExport.createFile(outputFile, excludeSaveFrames= excludeSaveFrames, verbose = True)
# Set the header comment - only set this if you need a standard header!
topComment = "# File written for CING by NmrStarExport.py code"
nmrStarExport.writeFile(title = "CING", topComment=topComment, verbose = True)
def convert(projectName, inputDir, outputFile, excludeSaveFrames=("general_distance_constraints",)):
print "projectName: %s" % projectName
print "inputDir: %s" % inputDir
print "outputFile: %s" % outputFile
print "excludeSaveFrames: %s" % excludeSaveFrames
ccpnPath = os.path.join(inputDir, projectName)
ccpnProject = loadProject(ccpnPath)
nmrEntryStore = ccpnProject.newNmrEntryStore(name="newNmrEntryStoreName")
molSystem = ccpnProject.findFirstMolSystem()
nmrEntry = nmrEntryStore.newEntry(molSystem=molSystem, name="newNmrEntryName")
nmrProject = ccpnProject.currentNmrProject
nmrEntry.structureGenerations = nmrProject.sortedStructureGenerations()
if nmrEntry.structureGenerations:
print "Using structureGenerations from nmrProject"
else:
ncs = ccpnProject.findFirstNmrConstraintStore()
sG = None
if not ncs:
print "Failed to find any NmrConstraintStore from project"
else:
sG = ncs.findFirstStructureGeneration()
if sG:
nmrEntry.addStructureGeneration(sG)
print "Using structureGenerations from nmrProject"
else:
print "Failed to find nmrEntry.structureGenerations from nmrProject or nmrConstraintStore; creating a new one."
strucGen = nmrProject.newStructureGeneration()
nmrEntry.addStructureGeneration(strucGen)
# end if
# end if
# end if
try: # ccpn stable as 08 Jul 2009
nmrEntry.structureAnalyses = nmrProject.sortedStructureAnalysiss() # watch out for misspelling.
except AttributeError: # ccpn trunk fixed misspelled function
nmrEntry.structureAnalyses = nmrProject.sortedStructureAnalyses()
if not nmrEntry.structureAnalyses:
print "Failed to find nmrEntry.structureAnalyses"
nmrEntry.measurementLists = nmrProject.sortedMeasurementLists()
if not nmrEntry.measurementLists:
print "Failed to find nmrEntry.measurementLists"
# Hack to hook up coordinates, hopefully correctly (Wim 30/04/2009)
if nmrEntry.structureGenerations:
hasStructureEnsemble = False
for strucGen in nmrEntry.structureGenerations:
if strucGen.structureEnsemble:
hasStructureEnsemble = True
break
# end if
# end for
print "hasStructureEnsemble: %s" % hasStructureEnsemble
# This will only work dependably if there is one structureGeneration, one structureEnsemble...
# Take the one that was created last in any case, fingers crossed that they match up!
if not hasStructureEnsemble and ccpnProject.structureEnsembles:
nmrEntry.sortedStructureGenerations()[-1].structureEnsemble = ccpnProject.sortedStructureEnsembles()[-1]
# end if
# end if
for ne in nmrProject.sortedExperiments(): # will be sortedNmrExperiments
for ds in ne.sortedDataSources():
for pl in ds.sortedPeakLists():
nmrEntry.addPeakList(pl)
nmrStarExport = NmrStarExport(nmrEntry, nmrStarVersion="3.1", forceEntryId="1")
nmrStarExport.createFile(outputFile, excludeSaveFrames=excludeSaveFrames, verbose=True)
# Set the header comment - only set this if you need a standard header!
topComment = "# File written for CING by NmrStarExport.py code"
nmrStarExport.writeFile(title="CING", topComment=topComment, verbose=True)
