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 getPdbString(model,
chains,
chainRename=None,
blankchain=False,
fileEnd='END'):
"""Description: Convert a CCPN molEnsemble into a PDB formatted string Atom names will use IUPAC nomenclature
Input: MolStructure.StructureEnsemble, list of chains (pdb One Letter Code) to check if we need to
write only a subset of chains of the MolStructure. The chainID can be set to the haddock partner
code by using the chainRename argument. If the chain argument is set to True both chain and segid
are printed (needed for parameter file).
Output: PDB structure String
"""
project = model.root
cnsFormat = CnsFormat(project, guiParent=None)
if chainRename: forceExportSegId = chainRename
else: forceExportSegId = " "
if blankchain: forceExportChainId = " "
else: forceExportChainId = forceExportSegId
if not chains: chainlist = project.findFirstMolSystem().sortedChains()
cnsFormat.writeCoordinates('void',
structures=[model],
forceExportSegId=forceExportSegId,
forceExportChainId=forceExportChainId,
resetMapping=True,
exportChains=chains,
minimalPrompts=True,
noWrite=True)
cnsFormat.coordinateFile.write(endStatement=fileEnd, writeString=True)
return cnsFormat.coordinateFile.coordFileString
def getCnsObject(project):
from ccpnmr.format.converters.CnsFormat import CnsFormat
cnsObj = CnsFormat(project, None, allowPopups=False)
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)
print '\nUrls:'
for repos in project.sortedRepositories():
print repos.name, repos.url.path
print
if __name__ == '__main__':
# This code follows on from ex7.py.
project = MemopsRoot(name='constraintsTest')
guiRoot = Tkinter.Tk()
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)
from memops.api.Implementation import MemopsRoot
from ccpnmr.format.converters.CnsFormat import CnsFormat
from ccpnmr.format.general.Util import (createExperiment,
getRefExpFromOldExpType)
from msd.nmrStar.IO.NmrStarExport import NmrStarExport
if __name__ == '__main__':
# Similar start to code as that found in ex6.py.
project = MemopsRoot(name='sampleTest')
guiRoot = Tkinter.Tk()
cnsObj = CnsFormat(project, guiRoot)
nmrProject = project.currentNmrProject = \
project.newNmrProject(name = project.name)
strucGen = nmrProject.newStructureGeneration()
cnsDir = '../data/cns'
cnsFile = os.path.join(cnsDir, 'cns_1.pdb')
cnsObj.readCoordinates([cnsFile],
strucGen=strucGen,
minimalPrompts=1,
linkAtoms=0)
# Find molecule made by readCoordinates and set isFinalised to True.
molecule = project.findFirstMolecule()
(oldUrlPath, baseName) = uniIo.splitPath(repository.url.path)
newUrlPath = uniIo.joinPath(projectDir, baseName)
repository.url = Implementation.Url(path=newUrlPath)
#
# Open a Tk window for handling the popups...
#
root = Tkinter.Tk()
#
# Create the FormatConverter CnsFormat object
#
cnsFormat = CnsFormat(ccpnProject, root)
#
# Read in a sequence - this will create the molecular system with
# 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
fileDict[strucNum] = file
strucNumList.append(strucNum)
strucNumList.sort()
fileList = []
for strucNum in strucNumList:
fileList.append(os.path.join(dataDir, fileDict[strucNum]))
#
# Create the format converter CNS format
#
cnsFormat = CnsFormat(project, guiRoot, verbose=1)
#
# Now read in the structures... this will also create the Molecules and Molecular system via readSequence()
#
cnsFormat.readCoordinates(fileList,
strucGen=structureGeneration,
minimalPrompts=1,
linkAtoms=0)
#
# Create the format converter PDB format
#
pdbFormat = PdbFormat(project, guiRoot, verbose=1)
(oldUrlPath,baseName) = uniIo.splitPath(repository.url.path)
newUrlPath = uniIo.joinPath(projectDir,baseName)
repository.url = Implementation.Url(path = newUrlPath)
#
# Open a Tk window for handling the popups...
#
root = Tkinter.Tk()
#
# Create the FormatConverter CnsFormat object
#
cnsFormat = CnsFormat(ccpnProject,root)
#
# Read in a sequence - this will create the molecular system with
# 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
fileDict[strucNum] = file
strucNumList.append(strucNum)
strucNumList.sort()
fileList = []
for strucNum in strucNumList:
fileList.append(os.path.join(dataDir,fileDict[strucNum]))
#
# Create the format converter CNS format
#
cnsFormat = CnsFormat(project,guiRoot,verbose = 1)
#
# Now read in the structures... this will also create the Molecules and Molecular system via readSequence()
#
cnsFormat.readCoordinates(fileList,strucGen = structureGeneration, minimalPrompts = 1, linkAtoms = 0)
#
# Create the format converter PDB format
#
pdbFormat = PdbFormat(project,guiRoot,verbose = 1)
#
# Make sure the outputDir exists...