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 checkNmrEntryCompleteness(nmrEntry, textReport=False, submissionType='PDB'):
global starDict
global ccpn2StarDict
global ccpnLinkList
global ccpnObjDict
# starDict = nmrStarDict.sfDict
starDict = aditMandDict
starExport = NmrStarExport(nmrEntry)
ccpn2Star = Ccpn_To_NmrStar(starExport)
ccpn2StarDict = ccpn2Star.sfDict
ccpnLinkList = ccpn2Star.nmrEntryLinkList
# These are set in ccpnMap/ccpnLoop routines in Ccpn_To_NmrStar
ccpn2Star.nmrEntry = nmrEntry
ccpn2Star.authors = list(nmrEntry.authors)
#print 'DICTS: [%s] [%s]' % (starDict, ccpn2StarDict)
ccpnObjDict = checkCcpnObjects(nmrEntry, submissionType)
setCcpnVar(nmrEntry)
#print 'CCPN OBJ DICT: [%s]' % ccpnObjDict
finalInfoDict = {}
redColour = '#FF4040'
orangeColour = '#E0B040'
yellowColour = '#F0F020'
greenColour = '#B0FFB0'
for ccpnObj in ccpnObjDict.keys():
#print 'OBJ: [%s] [%s]' % (ccpnObj, ccpnObjDict[ccpnObj])
if ccpnObj == 'otherCitations':
continue
if ccpnObj == 'structureGenerations' and submissionType == 'BMRB':
continue
if not ccpnObjDict[ccpnObj][0]:
#print 'MISSING OBJ: [%s]' % ccpnObj
finalInfoDict[ccpnObj] = (ccpnObjDict[ccpnObj][1], 'No "' + ccpnObjDict[ccpnObj][2] + '" set/selected', redColour, False, 'Object', 0, ccpnObj, None, None)
else:
#print 'PRESENT OBJ: [%s]' % ccpnObj
finalInfoDict[ccpnObj] = (ccpnObjDict[ccpnObj][1], '"' + ccpnObjDict[ccpnObj][2] + '" done', greenColour, True, 'Object', 3, ccpnObj, None, None)
# TODO list:
# CCPN objects not in NMR-STAR
#'entryMolecules',
# CCPN objects that are not mandatory for NMR depositions - but required for structure depositions
#'structureEnsemble',
#'structureGenerations',
# Constraint objects
# NMR-STAR SF's/tables to be done - These aren't objects in CCPN - but are attributes.
#'SG_project', 'Struct_keywords',
#'Vendor', 'Task',
# Rough translation of NmrStar save frames/tables to CCPN objects.
starSf2CcpnDict = {'entry_information': 'nmrEntry',
'citations': 'primaryCitation', # 'otherCitations',
'assembly': 'molSystem',
'entity': 'molecule',
'natural_source': 'naturalSource',
'experimental_source': 'experimentalSource',
'sample': 'sample',
'sample_conditions': 'sampleConditionSet',
'software': 'software',
'NMR_spectrometer_list': 'spectrometer',
'experiment_list': 'experiments',
'assigned_chemical_shifts': 'shiftLists',
'chem_shift_reference': 'shiftReferences'}
starTable2CcpnDict = {'Contact_person': 'contactPersons', # 'personInGroups',
'Entry_author': 'authors',
#'SG_project': None,
#'Struct_keywords': 'keywords',
'Citation_author': 'citationAuthors',
'Entity_assembly': 'chains',
'Entity_natural_src': 'naturalSource',
'Entity_experimental_src': 'experimentalSource',
'Sample_component': 'sampleComponent',
'Sample_condition_variable': 'sampleConditions',
#'Vendor': 'software',
#'Task': 'software',
'NMR_spectrometer_view': 'spectrometer',
'Experiment': 'experiments',
'Chem_shift_experiment': 'shiftExperiments',
'Atom_chem_shift': 'shifts',
'Chem_shift_ref': 'shiftReferences'}
# Mandatory save frames/tables in NmrStar (ADIT-NMR).
# TODO: Eldon's ADIT-NMR dictionary doesn't include chem shift references,
# chem shift lists and structural (PDB) data.
mandSfList = ['entry_information',
'citations',
'assembly',
'entity',
'natural_source',
'experimental_source',
'sample',
'sample_conditions',
'software',
'NMR_spectrometer_list',
'experiment_list',
'chem_shift_reference',
'assigned_chemical_shifts']
mandTableDict = {'entry_information': ['Contact_person',
'Entry_author',
'SG_project',
'Struct_keywords'],
'citations': ['Citation_author'],
'assembly': ['Entity_assembly'],
'entity': [],
'natural_source': ['Entity_natural_src'],
'experimental_source': ['Entity_experimental_src'],
'sample': ['Sample_component'],
'sample_conditions': ['Sample_condition_variable'],
'software': ['Vendor',
'Task'],
'NMR_spectrometer_list': ['NMR_spectrometer_view'],
'experiment_list': ['Experiment'],
'chem_shift_reference': ['Chem_shift_ref'],
'assigned_chemical_shifts': ['Chem_shift_experiment',
'Atom_chem_shift']}
# These two dictionaries store the CCPN data.
global sfCcpnMapDict
global tableCcpnMapDict
sfCcpnMapDict = {}
tableCcpnMapDict = {}
sfTagDict = {}
for sfKey in nmrStarDict.sfList:
if sfKey not in mandSfList:
continue
if sfKey in starSf2CcpnDict:
ccpnObj = starSf2CcpnDict[sfKey]
#print 'SF KEY: [%s] [%s] [%s]' % (sfKey, ccpnObj, ccpnObjDict[ccpnObj])
# If no CCPN object, then we don't need to check for missing attributes.
# Need to tell people to make a new CCPN object first.
if ccpnObj in ccpnObjDict and not ccpnObjDict[ccpnObj][0]:
#print 'NO SF CCPN OBJ: [%s] [%s]' % (sfKey, ccpnObj)
continue
sfTagDict = checkSfTags(sfKey)
sfMappingDict = checkMappingSfTags(sfTagDict)
# TODO: add me
#print 'MAPPING SF DICT: [%s] [%s]' % (sfKey, sfMappingDict)
if sfKey not in starDict or not 'tableNames' in starDict[sfKey]:
continue
for tableName in starDict[sfKey]['tableNames']:
if tableName not in mandTableDict[sfKey]:
continue
if tableName in starTable2CcpnDict:
ccpnObj = starTable2CcpnDict[tableName]
#print 'TABLE KEY: [%s] [%s] [%s] [%s]' % (sfKey, tableName, ccpnObj, ccpnObjDict[ccpnObj])
# Again if no CCPN object...
if ccpnObj in ccpnObjDict and not ccpnObjDict[ccpnObj][0]:
if ccpnObj == 'contactPersons':
if 'personInGroups' in ccpnObjDict and not ccpnObjDict['personInGroups'][0]:
#print 'NO TABLE CCPN OBJ: [%s] [%s/personInGroups]' % (sfKey, tableName, ccpnObj)
continue
else:
#print 'NO TABLE CCPN OBJ: [%s] [%s]' % (sfKey, tableName, ccpnObj)
continue
tableTagDict = checkTableTags(sfKey, tableName)
tableMappingDict = checkMappingTableTags(tableTagDict)
# TODO: add me
#print 'MAPPING TABLE DICT: [%s] [%s] [%s]' % (sfKey, tableName, tableMappingDict)
for sfKey in sfCcpnMapDict:
for tagName in sfCcpnMapDict[sfKey]:
ccpnData = sfCcpnMapDict[sfKey][tagName]
starInfo = starDict[sfKey]['tags'][tagName][3].strip()
#print 'SF DATA: [%s] [%s] [%s] [%s]' % (sfKey, tagName, ccpnData, starInfo)
emptyFlag = True
if None in ccpnData:
ccpnData.remove(None)
elif '' in ccpnData:
ccpnData.remove('')
else:
emptyFlag = False
if not ccpnData:
finalInfoDict[sfKey + '_' + tagName] = (STAR_TO_CCPN_SF_NAMES[sfKey] + ' [' + tagName + ']', 'No "' + starInfo + '" attribute set/selected', orangeColour, False, 'SF Attr', 1, sfKey, None, tagName)
elif emptyFlag:
finalInfoDict[sfKey + '_' + tagName] = (STAR_TO_CCPN_SF_NAMES[sfKey] + ' [' + tagName + ']', 'Some "' + starInfo + '" attributes not set/selected', yellowColour, False, 'SF Attr', 2, sfKey, None, tagName)
#else:
# finalInfoDict[sfKey + '_' + tagName] = (sfKey + ': ' + tagName, starInfo + ' attribute set/selected', greenColour, True, 'SF Attr')
for sfKey in tableCcpnMapDict:
for tableName in tableCcpnMapDict[sfKey]:
for tagName in tableCcpnMapDict[sfKey][tableName]:
ccpnData = tableCcpnMapDict[sfKey][tableName][tagName]
starInfo = starDict[sfKey]['tables'][tableName]['tags'][tagName][3].strip()
#print 'TABLE DATA1: [%s] [%s] [%s] [%s] [%s]' % (sfKey, tableName, tagName, ccpnData, starInfo)
emptyFlag = True
if None in ccpnData:
ccpnData.remove(None)
elif '' in ccpnData:
ccpnData.remove('')
else:
emptyFlag = False
if not ccpnData:
finalInfoDict[sfKey + '_' + tableName + '_' + tagName] = (STAR_TO_CCPN_TABLE_NAMES[tableName] + ' [' + tagName + ']', 'No "' + starInfo + '" attribute set/selected', orangeColour, False, 'Table Attr', 1, sfKey, tableName, tagName)
elif emptyFlag:
finalInfoDict[sfKey + '_' + tableName + '_' + tagName] = (STAR_TO_CCPN_TABLE_NAMES[tableName] + ' [' + tagName + ']', 'Some "' + starInfo + '" attributes not set/selected', yellowColour, False, 'Table Attr', 2, sfKey, tableName, tagName)
#else:
# finalInfoDict[sfKey + '_' + tableName + '_' + tagName] = (sfKey + '/' + tableName + ': ' + tagName, starInfo + ' attribute set/selected', greenColour, True, 'Table Attr')
finalInfoList = []
for key in sorted(finalInfoDict.keys() ):
finalInfoList.append(finalInfoDict[key])
finalInfoList.sort(listCol6Cmp)
if not textReport:
finalInfoList2 = []
for row in finalInfoList:
finalInfoList2.append(row[:3])
return finalInfoList2
else:
finalInfoList3 = []
for row in finalInfoList:
finalInfoList3.append(row)
return finalInfoList3
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)
