def importCnsDistance(self):
if not self.project:
showWarning('Failure','Please create a new CCPN project.', parent=self)
return
fileTypes = [ FileType('CNS', ['*.tbl']),
FileType('All', ['*']) ]
fileSelectPopup = FileSelectPopup(self, file_types=fileTypes,
title='Import CNS distance restraints file', dismiss_text='Cancel',
selected_file_must_exist=True, multiSelect=False,)
fileName = fileSelectPopup.getFile()
if not os.path.exists(fileName):
showWarning('Failure','No such file.', parent=self)
return
if fileName:
name = os.path.split(fileName)[1]
if '.' in name:
name = name.split('.')[0]
cnsObj = CnsFormat(self.project, self, verbose=True)
cnsObj.readDistanceConstraints(fileName, minimalPrompts=True)
self.eciFrame.updateAll()
return cnsObj
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)
cnsObj = CnsFormat(project, guiRoot)
cnsDir = '../data/cns'
cnsCoord = 'cns_1.pdb'
cnsCoordFile = os.path.join(cnsDir, cnsCoord)
# 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.
# all the atom information.
#
# Note that a lot of the popups can be avoided when the right information
# is passed in (see ccpnmr.format.converters.DataFormat, the readSequence
# function in the DataFormat class)
#
coordinateFile = os.path.join(dataDir, coordinateFileName)
ccpnChains = cnsFormat.readSequence(coordinateFile)
#
# Read in a distance constraint list
#
distanceConstraintFile = os.path.join(dataDir, distanceConstraintFileName)
ccpnConstraintList = cnsFormat.readDistanceConstraints(
distanceConstraintFile)
#
# Do some preliminary Data Model navigation to get input parameters for
# linkResonances
#
# An nmrConstraintStore links a group of constraint files
# A structureGeneration links an nmrConstraintStore with a set of structures
#
nmrConstraintStore = ccpnConstraintList.nmrConstraintStore
structureGeneration = nmrConstraintStore.findFirstStructureGeneration()
#
# Run linkResonances (this will generate a lot of output to the shell)
#
# Set the location of the CNS files.
cnsDir = '../data/cns'
# Read in a sequence to set molecule and molSystem objects.
cnsCoord = 'cns_1.pdb'
cnsCoordFile = os.path.join(cnsDir, cnsCoord)
# readSequence() returns a list of chains.
chains = cnsObj.readSequence(cnsCoordFile, minimalPrompts=1)
# Read in a distance constraint list.
distConst = 'n15noesy.tbl'
distConstFile = os.path.join(cnsDir, distConst)
constList = cnsObj.readDistanceConstraints(distConstFile, minimalPrompts=1)
# Do some preliminary data model navigation to get input parameters for
# linkResonances.
# An nmrConstraintStore links a group of constraint files.
# A structureGeneration links an nmrConstraintStore with a set
# of structures.
nmrConstStore = constList.nmrConstraintStore
strucGen = nmrConstStore.findFirstStructureGeneration()
# Run linkResonances (this will generate a lot of output to the shell).
# The current options are the 'safest' to maintain the original
# information, although bear in mind that all atoms in the original
# list are considered to be stereospecifically assigned.
# all the atom information. # # Note that a lot of the popups can be avoided when the right information # is passed in (see ccpnmr.format.converters.DataFormat, the readSequence # function in the DataFormat class) # coordinateFile = os.path.join(dataDir,coordinateFileName) ccpnChains = cnsFormat.readSequence(coordinateFile) # # Read in a distance constraint list # distanceConstraintFile = os.path.join(dataDir,distanceConstraintFileName) ccpnConstraintList = cnsFormat.readDistanceConstraints(distanceConstraintFile) # # Do some preliminary Data Model navigation to get input parameters for # linkResonances # # An nmrConstraintStore links a group of constraint files # A structureGeneration links an nmrConstraintStore with a set of structures # nmrConstraintStore = ccpnConstraintList.nmrConstraintStore structureGeneration = nmrConstraintStore.findFirstStructureGeneration() # # Run linkResonances (this will generate a lot of output to the shell) #
