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)
#
# Run linkResonances (this will generate a lot of output to the shell)
#
# Many options are available - see ccpnmr.format.process.linkResonances
#
# The current options are the 'safest' to maintain the original information,
# although bear in mind that here all atoms in the original list are
# considered to be stereospecifically assigned
#
# Set forceDefaultChainMapping to 0 if you want to interactively link the
# chains in the CCPN data model to the information from the constraint file
#
cnsFormat.linkResonances(forceDefaultChainMapping=1,
globalStereoAssign=1,
setSingleProchiral=1,
setSinglePossEquiv=1,
strucGen=structureGeneration)
#
# Save the CCPN project as XML files
#
ccpnProject.saveModified()
#
# Navigate the Data Model, get a list of atoms per constraint item
#
for distConstr in ccpnConstraintList.sortedConstraints():
# To make a molSystem object.
chains = cnsObj.readSequence(cnsCoordFile)
distConst = 'n15noesy.tbl'
distConstFile = os.path.join(cnsDir, distConst)
# To make a structureGeneration object.
constList = cnsObj.readDistanceConstraints(distConstFile)
nmrConstStore = constList.nmrConstraintStore
strucGen = nmrConstStore.findFirstStructureGeneration()
cnsObj.linkResonances(forceDefaultChainMapping=1,
globalStereoAssign=1,
setSingleProchiral=1,
setSinglePossEquiv=1,
strucGen=strucGen)
# As usual, create the BMRB Entry object.
entryStore = project.newNmrEntryStore(name=project.name)
entry = entryStore.newEntry(name=project.name)
# Get the molSystem object, and link to it.
molSystem = project.sortedMolSystems()[0]
entry.setMolSystem(molSystem)
# Link the structureGeneration object so that the restraints
# are part of the BMRB Entry object.
entry.addStructureGeneration(strucGen)
#
# Many options are available - see ccpnmr.format.process.linkResonances
#
# The current options are the 'safest' to maintain the original information,
# although bear in mind that here all atoms in the original list are
# considered to be stereospecifically assigned
#
# Set forceDefaultChainMapping to 0 if you want to interactively link the
# chains in the CCPN data model to the information from the constraint file
#
cnsFormat.linkResonances(
forceDefaultChainMapping = 1,
globalStereoAssign = 1,
setSingleProchiral = 1,
setSinglePossEquiv = 1,
strucGen = structureGeneration
)
#
# Save the CCPN project as XML files
#
ccpnProject.saveModified()
#
# Navigate the Data Model, get a list of atoms per constraint item
#
