def importCyanaCoorAndRes(ccpnProject, inputDir, guiRoot, replaceCoordinates=1, replaceRestraints=1, allowPopups=1,
minimalPrompts=0, verbose=1, **presets):
if replaceCoordinates:
status = importPseudoPdb(ccpnProject, inputDir, guiRoot, allowPopups=allowPopups,
minimalPrompts=minimalPrompts, verbose=verbose, **presets)
if status:
nTerror("Failed importCyanaCoorAndRes")
return True
if not replaceRestraints:
return
formatCyana = CyanaFormat(ccpnProject, guiRoot, verbose=verbose, minimalPrompts=minimalPrompts, allowPopups=allowPopups)
ccpnConstraintListOfList = []
globPattern = inputDir + '/*.upl'
fileList = glob(globPattern)
nTdebug("From %s will read files: %s" % (globPattern, fileList))
for fn in fileList:
fnBaseName = os.path.basename(fn).split('.')[0]
ccpnConstraintList = formatCyana.readDistanceConstraints(fn, minimalPrompts=minimalPrompts, verbose=verbose)
ccpnConstraintList.setName(fnBaseName)
ccpnConstraintListOfList.append(ccpnConstraintList)
globPattern = inputDir + '/*.aco'
fileList = glob(globPattern)
nTdebug("From %s will read in total files: %s" % (globPattern, fileList))
for fn in fileList:
fnBaseName = os.path.basename(fn).split('.')[0]
ccpnConstraintList = formatCyana.readDihedralConstraints(fn, minimalPrompts=minimalPrompts,allowPopups=allowPopups,verbose=verbose)
ccpnConstraintList.setName(fnBaseName)
ccpnConstraintListOfList.append(ccpnConstraintList)
ccpnConstraintList = getDeepByKeys(ccpnConstraintListOfList, 0) # no need to repeat
nTdebug("ccpnConstraintList: %s" % ccpnConstraintList)
if ccpnConstraintList:
nmrConstraintStore = ccpnConstraintList.nmrConstraintStore
structureGeneration = nmrConstraintStore.findFirstStructureGeneration()
formatCyana.linkResonances(
forceDefaultChainMapping=1,
globalStereoAssign=1,
setSingleProchiral=1,
setSinglePossEquiv=1,
strucGen=structureGeneration,
allowPopups=allowPopups, minimalPrompts=minimalPrompts, verbose=verbose)
def importXplorCoorAndRes(ccpnProject, inputDir, guiRoot, replaceCoordinates=1, replaceRestraints=1,
allowPopups=1, minimalPrompts=0, verbose=1, **presets):
if replaceCoordinates:
status = importPseudoPdb(ccpnProject, inputDir, guiRoot, allowPopups=allowPopups, minimalPrompts=minimalPrompts,
verbose=verbose, **presets)
if status:
nTerror("Failed importXplorCoorAndRes")
return True
if not replaceRestraints:
return
formatCns = CnsFormat(ccpnProject, guiRoot, verbose=verbose, minimalPrompts=minimalPrompts, allowPopups=allowPopups)
ccpnConstraintListOfList = []
# Will overwrite the settings given to formatCns.linkResonances( below
globPattern = inputDir + '/*_noe.tbl'
fileList = glob(globPattern)
nTdebug("From %s will read files: %s" % (globPattern, fileList))
# for fn in fileList[0:1]: # TODO:
for fn in fileList:
fnBaseName = os.path.basename(fn).split('.')[0]
ccpnConstraintList = formatCns.readDistanceConstraints(fn, minimalPrompts=minimalPrompts, verbose=verbose)
ccpnConstraintList.setName(fnBaseName)
ccpnConstraintListOfList.append(ccpnConstraintList)
if not ccpnConstraintList:
nTerror("Failed to read")
return True
# globPattern = inputDir + '/*_hbond.tblXXXX' # TODO:
globPattern = inputDir + '/*_hbond.tbl'
fileList = glob(globPattern)
nTdebug("From %s will read in files: %s" % (globPattern, fileList))
for fn in fileList:
fnBaseName = os.path.basename(fn).split('.')[0]
ccpnConstraintList = formatCns.readDistanceConstraints(fn, minimalPrompts=minimalPrompts, verbose=verbose)
ccpnConstraintList.setName(fnBaseName)
ccpnConstraintListOfList.append(ccpnConstraintList)
# globPattern = inputDir + '/*_dihe.tblXXXX' # TODO:
globPattern = inputDir + '/*_dihe.tbl'
fileList = glob(globPattern)
nTdebug("From %s will read in total files: %s" % (globPattern, fileList))
for fn in fileList:
fnBaseName = os.path.basename(fn).split('.')[0]
ccpnConstraintList = formatCns.readDihedralConstraints(fn, minimalPrompts=minimalPrompts, verbose=verbose)
ccpnConstraintList.setName(fnBaseName)
ccpnConstraintListOfList.append(ccpnConstraintList)
keywds = getDeepByKeysOrDefault(presets, {}, LINK_RESONANCES, KEYWORDS)
nTdebug("From getDeepByKeysOrDefault keywds: %s" % repr(keywds))
ccpnConstraintList = getDeepByKeys(ccpnConstraintListOfList, 0) # no need to repeat
nTdebug("First ccpnConstraintList: %s" % ccpnConstraintList)
if ccpnConstraintList != None:
# for i, ccpnConstraintList in enumerate(ccpnConstraintListOfList):
keywds = getDeepByKeysOrDefault(presets, {}, LINK_RESONANCES, KEYWORDS)
nTdebug("From getDeepByKeysOrDefault keywds: %s" % repr(keywds))
nTdebug("ccpnConstraintList: %s" % ccpnConstraintList)
nmrConstraintStore = ccpnConstraintList.nmrConstraintStore
structureGeneration = nmrConstraintStore.findFirstStructureGeneration()
formatCns.linkResonances(
forceDefaultChainMapping=1, # may be overwritten by using forceChainMappings.
globalStereoAssign=1,
setSingleProchiral=1,
setSinglePossEquiv=1,
strucGen=structureGeneration,
allowPopups=allowPopups, minimalPrompts=minimalPrompts, verbose=verbose, **keywds)
def annotateEntry(entryCodeNew, *extraArgList):
nTmessage(header)
nTmessage(getStartMessage())
expectedArgumentList = []
expectedNumberOfArguments = len(expectedArgumentList)
if len(extraArgList) != expectedNumberOfArguments:
nTerror("Got arguments: " + repr(extraArgList))
nTerror("Failed to get expected number of arguments: %d got %d" % (
expectedNumberOfArguments, len(extraArgList)))
nTerror("Expected arguments: %s" % expectedArgumentList)
return True
# entryCode, city = entryCodePlusCity.split('_')
# Adjust the parameters below
isInteractive = False
sourceIsOrgProject = True
checkOrgProject = False
replaceCoordinates = True # From all *.pdb files in inputDir.
replaceRestraints = True
doSwapCheck = True
doSaveProject = True
doExport = True
minimalPrompts = True
verbose = True
if isInteractive:
allowPopups = True
minimalPrompts = False
# verbose = True
else:
allowPopups = False
# minimalPrompts = True
# verbose = False
print 'allowPopups ', allowPopups
print 'isInteractive ', isInteractive
print 'minimalPrompts ', minimalPrompts
print 'verbose ', verbose
print 'sourceIsOrgProject (or new CCPN file) ', sourceIsOrgProject
print 'checkOrgProject ', checkOrgProject
print 'replaceCoordinates ', replaceCoordinates
print 'replaceRestraints ', replaceRestraints
print 'doSwapCheck ', doSwapCheck
print 'doSaveProject ', doSaveProject
print 'doExport ', doExport
guiRoot = None
if allowPopups:
guiRoot = Tkinter.Tk()
entryCode,city = mapEntrycodeNew2EntrycodeAndCity[entryCodeNew]
ch23 = entryCode[1:3]
entryCodeOrg = entryCode + 'Org'
dataOrgEntryDir = os.path.join(dataDir, ch23, entryCodeOrg)
ccpnFile = os.path.join(dataOrgEntryDir, entryCodeOrg + ".tgz")
# entryCodeNew = entryCode + city
programId = getDeepByKeys(programHoH, entryCode, city)
if not (city == 'Test' or programId):
# nTdebug("Skipping %s" % entryCodeNew)
nTerror("Neither City is 'Test' or programId given")
return
else:
nTdebug("Looking at %s" % entryCodeNew)
# continue # TODO disable premature stop.
dataDividedXDir = os.path.join(dataDir, ch23)
entryDir = os.path.join(dataDividedXDir, entryCodeNew)
inputAuthorDir = os.path.join(entryDir, 'Author')
outputNijmegenDir = os.path.join(entryDir, 'Nijmegen')
if not os.path.exists(inputAuthorDir):
mkdirs(inputAuthorDir)
if not os.path.exists(outputNijmegenDir):
mkdirs(outputNijmegenDir)
os.chdir(outputNijmegenDir)
presets = getDeepByKeysOrDefault(presetDict, {}, entryCodeNew)
if presets:
nTmessage("In annotateLoop using preset values...")
# end if
if sourceIsOrgProject:
if os.path.exists(entryCodeOrg):
nTmessage("Removing previous Org directory: %s" % entryCodeOrg)
rmtree(entryCodeOrg)
do_cmd("tar -xzf " + ccpnFile)
if os.path.exists(entryCodeNew):
nTmessage("Removing previous directory: %s" % entryCodeNew)
rmtree(entryCodeNew)
copytree(entryCodeOrg, entryCodeNew)
if checkOrgProject:
# By reading the ccpn tgz into cing it is also untarred/tested.
project = Project.open(entryCodeOrg, status='new')
if not project.initCcpn(ccpnFolder=ccpnFile, modelCount=1):
nTerror("Failed check of original project")
return
project.removeFromDisk()
project.close(save=False)
ccpnProject = loadProject(entryCodeNew)
if not ccpnProject:
nTerror("Failed to read project: %s" % entryCodeNew)
return
# nmrProject = ccpnProject.currentNmrProject
# ccpnMolSystem = ccpnProject.findFirstMolSystem()
# nTmessage('found ccpnMolSystem: %s' % ccpnMolSystem)
# print 'status: %s' % ccpnMolSystem.setCode(projectName) # impossible; reported to ccpn team.
if replaceCoordinates or replaceRestraints:
if programId == CYANA:
importCyanaCoorAndRes(ccpnProject, inputAuthorDir, guiRoot,
replaceCoordinates=replaceCoordinates, replaceRestraints=replaceRestraints,
allowPopups=allowPopups, minimalPrompts=minimalPrompts, verbose=verbose, **presets)
elif programId == XPLOR:
importXplorCoorAndRes(ccpnProject, inputAuthorDir, guiRoot,
replaceCoordinates=replaceCoordinates, replaceRestraints=replaceRestraints,
allowPopups=allowPopups, minimalPrompts=minimalPrompts, verbose=verbose, **presets)
elif programId == PDB:
importPseudoPdb(ccpnProject, inputAuthorDir, guiRoot,
allowPopups=allowPopups, minimalPrompts=minimalPrompts, verbose=verbose, **presets)
else:
nTerror("Failed to doImportCoordinatesAndRestraints because action for program Id not coded for: %s" % programId)
nTerror("Skipping entry")
return
if doSwapCheck:
# constraintsHandler = ConstraintsHandler()
nmrConstraintStore = ccpnProject.findFirstNmrConstraintStore()
structureEnsemble = ccpnProject.findFirstStructureEnsemble()
numSwapCheckRuns = 3
if nmrConstraintStore:
if structureEnsemble:
swapCheck(nmrConstraintStore, structureEnsemble, numSwapCheckRuns)
else:
nTmessage("Failed to find structureEnsemble; skipping swapCheck")
else:
nTmessage("Failed to find nmrConstraintStore; skipping swapCheck")
# constraintsHandler.swapCheck(nmrConstraintStore, structureEnsemble, numSwapCheckRuns)
if doSaveProject:
# nTmessage('Checking validity and saving to new path')
nTmessage('Saving to new path: %s' % entryCodeNew)
# checkValid=True,
saveProject(ccpnProject, newPath=entryCodeNew, removeExisting=True)
if doExport:
tarPath = os.path.join(entryDir, entryCodeNew + ".tgz")
if os.path.exists(tarPath):
nTmessage("Overwriting: " + tarPath)
myTar = tarfile.open(tarPath, mode='w:gz') # overwrites
myTar.add(entryCodeNew)
myTar.close()
if guiRoot:
guiRoot.destroy()
def importCyanaCoorAndRes(ccpnProject,
inputDir,
guiRoot,
replaceCoordinates=1,
replaceRestraints=1,
allowPopups=1,
minimalPrompts=0,
verbose=1,
**presets):
if replaceCoordinates:
status = importPseudoPdb(ccpnProject,
inputDir,
guiRoot,
allowPopups=allowPopups,
minimalPrompts=minimalPrompts,
verbose=verbose,
**presets)
if status:
nTerror("Failed importCyanaCoorAndRes")
return True
if not replaceRestraints:
return
formatCyana = CyanaFormat(ccpnProject,
guiRoot,
verbose=verbose,
minimalPrompts=minimalPrompts,
allowPopups=allowPopups)
ccpnConstraintListOfList = []
globPattern = inputDir + '/*.upl'
fileList = glob(globPattern)
nTdebug("From %s will read files: %s" % (globPattern, fileList))
for fn in fileList:
fnBaseName = os.path.basename(fn).split('.')[0]
ccpnConstraintList = formatCyana.readDistanceConstraints(
fn, minimalPrompts=minimalPrompts, verbose=verbose)
ccpnConstraintList.setName(fnBaseName)
ccpnConstraintListOfList.append(ccpnConstraintList)
globPattern = inputDir + '/*.aco'
fileList = glob(globPattern)
nTdebug("From %s will read in total files: %s" % (globPattern, fileList))
for fn in fileList:
fnBaseName = os.path.basename(fn).split('.')[0]
ccpnConstraintList = formatCyana.readDihedralConstraints(
fn,
minimalPrompts=minimalPrompts,
allowPopups=allowPopups,
verbose=verbose)
ccpnConstraintList.setName(fnBaseName)
ccpnConstraintListOfList.append(ccpnConstraintList)
ccpnConstraintList = getDeepByKeys(ccpnConstraintListOfList,
0) # no need to repeat
nTdebug("ccpnConstraintList: %s" % ccpnConstraintList)
if ccpnConstraintList:
nmrConstraintStore = ccpnConstraintList.nmrConstraintStore
structureGeneration = nmrConstraintStore.findFirstStructureGeneration()
formatCyana.linkResonances(forceDefaultChainMapping=1,
globalStereoAssign=1,
setSingleProchiral=1,
setSinglePossEquiv=1,
strucGen=structureGeneration,
allowPopups=allowPopups,
minimalPrompts=minimalPrompts,
verbose=verbose)
