def checkProject(self,
ccpnProject=None,
ccpnDir=None,
structureEnsembleId=None,
shiftListSerial=None):
if self.showMessages:
print drawBox(" VASCO: calculating rereferencing...")
#
# Get info from CCPN project
#
if ccpnProject:
self.ccpnProject = ccpnProject
elif ccpnDir:
self.ccpnProject = loadProject(ccpnDir)
elif self.ccpnDir:
self.ccpnProject = loadProject(self.ccpnDir)
else:
from memops.editor.OpenProjectPopup import OpenProjectPopup
_popup = OpenProjectPopup(self.guiParent,
callback=self.initProject,
modal=True)
#
# Get the relevant structureEnsemble
#
self.selectStructureEnsemble(structureEnsembleId=structureEnsembleId)
#
# Get the right shift list
#
self.selectShiftList(shiftListSerial=shiftListSerial)
#
# Prep the data
#
self.prepareData()
#
# Create a dictionary to run VASCO on
#
self.createEntryDict()
#
# Get VASCO reref data
#
self.getVascoRerefInfo()
def checkProject(self,ccpnProject=None,ccpnDir=None,structureEnsembleId=None,shiftListSerial=None):
if self.showMessages:
print drawBox(" VASCO: calculating rereferencing...")
#
# Get info from CCPN project
#
if ccpnProject:
self.ccpnProject = ccpnProject
elif ccpnDir:
self.ccpnProject = loadProject(ccpnDir)
elif self.ccpnDir:
self.ccpnProject = loadProject(self.ccpnDir)
else:
from memops.editor.OpenProjectPopup import OpenProjectPopup
_popup = OpenProjectPopup(self.guiParent, callback = self.initProject, modal=True)
#
# Get the relevant structureEnsemble
#
self.selectStructureEnsemble(structureEnsembleId=structureEnsembleId)
#
# Get the right shift list
#
self.selectShiftList(shiftListSerial=shiftListSerial)
#
# Prep the data
#
self.prepareData()
#
# Create a dictionary to run VASCO on
#
self.createEntryDict()
#
# Get VASCO reref data
#
self.getVascoRerefInfo()
def launchApplication(projectDir=None):
global top
root = Tkinter.Tk()
root.withdraw()
top = EntryCompletionGui(root)
project = None
if projectDir:
projectDir = normalisePath(projectDir)
askdir = lambda title, prompt, initial_value, default_dir: askDir(title, prompt,
initial_value, parent=top, extra_dismiss_text='Skip')
askfile = lambda title, prompt, initial_value: askFile(title, prompt,
initial_value, parent=top, extra_dismiss_text='Skip')
try:
project = loadProject(path=projectDir, showWarning=showWarning, askDir=askdir, askFile=askfile)
userRepos = project.findFirstRepository(name='userData')
chemCompPackLoc = project.findFirstPackageLocator(targetName='ccp.molecule.ChemComp')
if userRepos not in chemCompPackLoc.repositories:
chemCompPackLoc.addRepository(userRepos)
except ApiError, e:
showError('Reading project', e.error_msg, parent=top)
def checkAllShiftLists(self):
"""
Return True on error
"""
if not self.showMessages:
# print 'switching messaging off temporarily.'
switchOutput(False)
ccpnProject = loadProject(self.ccpnDir)
if not self.showMessages:
print 'switching messaging on again.'
switchOutput(True)
if ccpnProject == None:
nTerror("Failed to load CCPN project from: %s" % self.ccpnDir)
return True
# shiftLoL = ccpnProject.currentNmrProject.findAllMeasurementLists(className='ShiftList')
# Use sorting by CCPN.
shiftLoL = filterListByObjectClassName(
ccpnProject.currentNmrProject.sortedMeasurementLists(),
Ccpn.CCPN_CS_LIST)
# nTdebug("Working on shiftLoL %s", str(shiftLoL))
for i, shiftList in enumerate(shiftLoL):
shiftListSerial = shiftList.serial
# nTdebug("Working on shiftListSerial %s", shiftListSerial)
self.checkProject(ccpnProject=ccpnProject,
shiftListSerial=shiftListSerial)
self.tagProject()
if self.tagCingProject(shiftList, i):
return True
def launchApplication(projectDir=None):
global top
root = Tkinter.Tk()
root.withdraw(
) # get rid of the root window Tkinter would otherwise put up
top = ApplicationPopup(
root) # creates our controlled window (this class in fact)
project = None
if projectDir:
projectDir = normalisePath(projectDir)
askdir = lambda title, prompt, initial_value, default_dir: askDir(
title,
prompt,
initial_value,
parent=top,
extra_dismiss_text='Skip')
askfile = lambda title, prompt, initial_value: askFile(
title,
prompt,
initial_value,
parent=top,
extra_dismiss_text='Skip')
try:
project = loadProject(path=projectDir,
showWarning=showWarning,
askDir=askdir,
askFile=askfile)
except ApiError, e:
showError('Reading project', e.error_msg, parent=top)
def checkAllShiftLists(self):
"""
Return True on error
"""
if not self.showMessages:
# print 'switching messaging off temporarily.'
switchOutput(False)
ccpnProject = loadProject(self.ccpnDir)
if not self.showMessages:
print 'switching messaging on again.'
switchOutput(True)
if ccpnProject == None:
nTerror("Failed to load CCPN project from: %s" % self.ccpnDir)
return True
# shiftLoL = ccpnProject.currentNmrProject.findAllMeasurementLists(className='ShiftList')
# Use sorting by CCPN.
shiftLoL = filterListByObjectClassName( ccpnProject.currentNmrProject.sortedMeasurementLists(), Ccpn.CCPN_CS_LIST )
# nTdebug("Working on shiftLoL %s", str(shiftLoL))
for i,shiftList in enumerate(shiftLoL):
shiftListSerial=shiftList.serial
# nTdebug("Working on shiftListSerial %s", shiftListSerial)
self.checkProject(ccpnProject=ccpnProject, shiftListSerial=shiftListSerial)
self.tagProject()
if self.tagCingProject(shiftList, i):
return True
def launchApplication(filename=None):
global top
root = Tkinter.Tk()
root.withdraw()
top = ApplicationPopup(root)
project = None
if filename:
file = normalisePath(filename)
askdir = lambda title, prompt, initial_value, default_dir: askDir(
title,
prompt,
initial_value,
parent=top,
extra_dismiss_text='Skip',
default_dir=default_dir)
askfile = lambda title, prompt, initial_value: askFile(
title,
prompt,
initial_value,
parent=top,
extra_dismiss_text='Skip')
try:
project = loadProject(path=file,
showWarning=showWarning,
askDir=askdir,
askFile=askfile)
except ApiError, e:
showError('Reading project', e.error_msg)
def __init__(self,
parent,
title='Project : Open',
callback=None,
help_msg='',
help_url='',
load_project=None,
*args,
**kw):
self.callback = callback
self.help_msg = help_msg
self.help_url = help_url
self.project = None
if not load_project:
askdir = lambda title, prompt, initial_value: askDir(
title,
prompt,
initial_value,
parent=self,
extra_dismiss_text='Skip')
askfile = lambda title, prompt, initial_value: askFile(
title,
prompt,
initial_value,
parent=self,
extra_dismiss_text='Skip')
load_project = lambda path: loadProject(
path, showWarning=showWarning, askDir=askdir, askFile=askfile)
self.load_project = load_project
BasePopup.__init__(self, parent=parent, title=title, *args, **kw)
def convert(projectName, inputDir, projectNameNew):
"Testing doc strings"
# Adjust the parameters below!
removeOriginalStructureEnsemble = True
addStructureEnsemble = True # From all *.pdb files in inputDir.
ccpnPath = os.path.join(inputDir, projectName)
ccpnProject = loadProject(ccpnPath)
ccpnMolSystem = ccpnProject.findFirstMolSystem()
nTmessage( 'found ccpnMolSystem: %s' % ccpnMolSystem )
# print 'status: %s' % ccpnMolSystem.setCode(projectName) # impossible; reported to ccpn team.
if removeOriginalStructureEnsemble:
structureEnsemble = ccpnProject.findFirstStructureEnsemble()
if structureEnsemble:
nTmessage("Removing first found structureEnsemble -A-")
structureEnsemble.delete()
else:
nTwarning("No structureEnsemble found; can't remove it.")
if addStructureEnsemble:
structureGeneration = ccpnProject.newStructureGeneration()
guiRoot = Tkinter.Tk()
format = PseudoPdbFormat(ccpnProject, guiRoot, verbose = 1)
globPattern = inputDir + '/*.pdb'
fileList = glob(globPattern)
nTdebug("From %s will read files: %s" % (globPattern,fileList))
format.readCoordinates(fileList, strucGen = structureGeneration, minimalPrompts = 1, linkAtoms = 0)
nTmessage( 'saving to new path if all checks are valid' )
# the newPath basename will be taken according to ccpn code doc.
ccpnPathNew = os.path.join(inputDir, projectNameNew)
saveProject(ccpnProject, checkValid=True, newPath=ccpnPathNew, removeExisting=True)
def setupProject(self, dirPath, projectName):
self.projectDirPath = dirPath
try:
self.ccpnProject = loadProject(dirPath)
print "Read existing CCPN project..."
except:
print "Creating new CCPN project..."
projectName = returnMemopsWord(projectName)
self.ccpnProject = Implementation.MemopsRoot(name=projectName)
self.nmrProject = self.ccpnProject.newNmrProject(
name=self.ccpnProject.name)
if not os.path.exists(dirPath):
os.mkdir(dirPath)
repository = self.ccpnProject.findFirstRepository(name='userData')
if not repository.url.path == dirPath:
url = Implementation.Url(path=dirPath)
repository.url = url
# TODO: check name of project: if not same CRASH OUT!
return self.ccpnProject
def unpackCcpnProjectTgz(self, tgzFileName, removeFile=False):
"""
Unpack a CCPN project and read it
"""
textOutput = self.unpackTgzFile(tgzFileName)
lines = textOutput.split("\n")
ccpnProjectId = lines[0]
ccpnProject = loadProject(ccpnProjectId)
return ccpnProject
def convert(projectName, inputDir, projectNameNew):
"Testing doc strings"
# Adjust the parameters below!
removeOriginalStructureEnsemble = True
addStructureEnsemble = True # From all *.pdb files in inputDir.
ccpnPath = os.path.join(inputDir, projectName)
ccpnProject = loadProject(ccpnPath)
ccpnMolSystem = ccpnProject.findFirstMolSystem()
nTmessage('found ccpnMolSystem: %s' % ccpnMolSystem)
# print 'status: %s' % ccpnMolSystem.setCode(projectName) # impossible; reported to ccpn team.
if removeOriginalStructureEnsemble:
structureEnsemble = ccpnProject.findFirstStructureEnsemble()
if structureEnsemble:
nTmessage("Removing first found structureEnsemble -A-")
structureEnsemble.delete()
else:
nTwarning("No structureEnsemble found; can't remove it.")
if addStructureEnsemble:
structureGeneration = ccpnProject.newStructureGeneration()
guiRoot = Tkinter.Tk()
format = PseudoPdbFormat(ccpnProject, guiRoot, verbose=1)
globPattern = inputDir + '/*.pdb'
fileList = glob(globPattern)
nTdebug("From %s will read files: %s" % (globPattern, fileList))
format.readCoordinates(fileList,
strucGen=structureGeneration,
minimalPrompts=1,
linkAtoms=0)
nTmessage('saving to new path if all checks are valid')
# the newPath basename will be taken according to ccpn code doc.
ccpnPathNew = os.path.join(inputDir, projectNameNew)
saveProject(ccpnProject,
checkValid=True,
newPath=ccpnPathNew,
removeExisting=True)
def loadProject(self):
# This is the directory where the original CCPN project lives
origCcpnProjectDir = os.path.join(self.projectDirectory, self.idCode)
# This is the zipped CCPN project location
zippedCcpnProject = os.path.join(origCcpnProjectDir, 'linkNmrStarData.zip')
# Unzip into the original CCPN project directory
try:
curTarFile = tarfile.open(zippedCcpnProject, 'r:gz')
curTarFile.extractall(origCcpnProjectDir)
except Exception:
curZipFile = zipfile.ZipFile(zippedCcpnProject)
curZipFile.extractall(origCcpnProjectDir)
self.ccpnProjectDir = os.path.join(origCcpnProjectDir, 'linkNmrStarData')
assert os.path.exists(self.ccpnProjectDir), 'Project did not unzip correctly'
self.ccpnProject = loadProject(self.ccpnProjectDir)
def loadProject(self):
# This is the directory where the original CCPN project lives
origCcpnProjectDir = os.path.join(self.projectDirectory, self.idCode)
# This is the zipped CCPN project location
zippedCcpnProject = os.path.join(origCcpnProjectDir,
'linkNmrStarData.zip')
# Unzip into the original CCPN project directory
try:
curTarFile = tarfile.open(zippedCcpnProject, 'r:gz')
curTarFile.extractall(origCcpnProjectDir)
except Exception:
curZipFile = zipfile.ZipFile(zippedCcpnProject)
curZipFile.extractall(origCcpnProjectDir)
self.ccpnProjectDir = os.path.join(origCcpnProjectDir,
'linkNmrStarData')
assert os.path.exists(
self.ccpnProjectDir), 'Project did not unzip correctly'
self.ccpnProject = loadProject(self.ccpnProjectDir)
return finalInfoList2
def listCol6Cmp(x, y):
return cmp(x[5], y[5])
if __name__ == '__main__':
argv = sys.argv[:]
argc = len(argv)
mr = None
if argc > 1:
projectDir = argv[1]
mr = loadProject(projectDir)
else:
projectDir = None
nmrEntry = mr.currentNmrEntryStore.findFirstEntry()
if nmrEntry:
finalInfoList = checkNmrEntryCompleteness(nmrEntry)
#print finalInfoList
for row in finalInfoList:
print row #[0], row[3:]
def process(self):
rootProject = loadProject(self._projectDir)
rootProject.saveModified()
print 'must specify project directory'
sys.exit()
path = sys.argv[1]
import Tkinter
from memops.gui.DataEntry import askDir, askFile
from memops.gui.MessageReporter import showWarning
from memops.general.Io import loadProject
from memops.universal.Io import normalisePath
# This needs to be above loadProject because that can pop up
# dialogs, and it will create a root if one has not been created
# already, and that will lead to the later code crashing
r = Tkinter.Tk()
path = normalisePath(path)
askdir = lambda title, prompt, initial_value: askDir(
title, prompt, initial_value, parent=top, extra_dismiss_text='Skip')
askfile = lambda title, prompt, initial_value: askFile(
title, prompt, initial_value, parent=top, extra_dismiss_text='Skip')
project = loadProject(path,
showWarning=showWarning,
askDir=askdir,
askFile=askfile)
popup = DataLocationPopup(r, project)
r.withdraw()
r.mainloop()
from memops.universal.Io import joinPath
###################
# Main of program #
###################
if __name__ == "__main__":
#
# Load a CCPN project
#
projectName = 'test'
projectDir = os.path.join(os.getcwd(),'local',projectName)
ccpnProject = loadProject(projectDir,projectName)
#
# Because the original project was saved in a different directory structure,
# the paths have to be reset first... here I am resetting everything 'hardcoded'
# based on the examples and/or data directory.
#
localDataPaths = {}
localDataPaths['examples'] = os.path.abspath('.')
localDataPaths['data'] = joinPath(getTopDirectory(),'data')
for repository in ccpnProject.repositories:
for findName in ('examples','data'):
findNameIndex = repository.url.path.find(findName)
if findNameIndex>= 0:
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 initialiseWorkflow(
self,
ccpnProject=None, # One of these top three is obligatory!
ccpnProjectTgz=None,
identifier=None,
useGui=False,
overwrite=True,
initializeObjects=True, # Set to False if don't want to automatically set NmrProject and constraint stuff. Should probably do this differently anyway! More options...
verbose=True):
self.verbose = verbose
#
# Need either an existing CCPN project or an identifier for it - note that this
# can be set as part of the class if required.
#
if not hasattr(self, 'identifier') and identifier:
self.identifier = identifier
if not ccpnProject and not self.identifier and not ccpnProjectTgz:
raise self.WorkFlowError(
"No CCPN project or identifier given - aborting workflow.")
#
# Set day/time when workflow was run
#
self.timeFlag = self.getTimeString()
#
# Set CCPN project - this is obligatory, and the CCPN project is unpacked if
# tgz file. Is this smart? Should I always start from a loaded project?
# And always pack it (temporary file) if have to send off? Probably best!
#
self.ccpnProject = None
if ccpnProject:
self.ccpnProject = ccpnProject
elif ccpnProjectTgz:
self.ccpnProject = self.unpackCcpnProjectTgz(ccpnProjectTgz)
else:
try:
tmpCcpnProject = loadProject(self.identifier)
except:
tmpCcpnProject = None
if tmpCcpnProject:
if not overwrite:
print(" Warning: using existing project!")
self.ccpnProject = tmpCcpnProject
else:
print(" Warning: overwriting existing project!")
shutil.rmtree(self.identifier)
if not self.ccpnProject:
self.ccpnProject = Implementation.MemopsRoot(
name=self.identifier)
#
# Set other CCPN objects (if required)
#
if initializeObjects:
# NMR project
setCurrentStore(self.ccpnProject, 'NmrProject')
self.nmrProject = self.ccpnProject.currentNmrProject
nmrConstraintStores = self.ccpnProject.sortedNmrConstraintStores()
if not nmrConstraintStores:
self.nmrConstraintStore = None
else:
if len(nmrConstraintStores) > 1:
raise self.WorkFlowError(
"Only one NMR constraint store allowed for running workflow. Please modify input."
)
self.nmrConstraintStore = nmrConstraintStores[0]
# TODO nmrEntry?
#
# Set graphical interface, if required
#
self.useGui = useGui
if useGui:
import Tkinter
self.guiRoot = Tkinter.Tk()
else:
self.guiRoot = None
#
# Run other <programShortCode>__init__
#
for program in programList:
programInit = '%s__init__' % program.lower()
if hasattr(self, programInit):
getattr(self, programInit)()
import os
# Import the loadProject() function.
from memops.general.Io import loadProject
from memops.universal import Io as uniIo
# Import the Url class.
from memops.api.Implementation import Url
if __name__ == '__main__':
# Load the old project - need to specify the correct directory name.
project = loadProject('topObjectTest')
print 'Project: [%s]\n' % project
# Find the right repository that contains the project data.
projectRepos = project.findFirstRepository(name='userData')
# Specify a new location to save the project in.
newPath = uniIo.normalisePath(
os.path.join(os.path.abspath('.'), 'newDir', 'newSubDir'))
# Make a new Url pointing to the new location and link it to the
# 'userData' repository.
def test_ccpn(self):
# cing.verbosity = verbosityDebug
# if you have a local copy you can use it; make sure to adjust the path setting below.
fastestTest = True # DEFAULT: True. Not passed to the validate routine in order to customize checks for speed.
modelCount = 99 # DEFAULT: 99
redoFromCingProject = False # DEFAULT: False
htmlOnly = False # DEFAULT: False # default is False but enable it for faster runs without some actual data.
doWhatif = True # DEFAULT: True # disables whatif actual run
doProcheck = True # DEFAULT: True
doWattos = True # DEFAULT: True
doQueeny = True # DEFAULT: True
doTalos = True # DEFAULT: True
filterVasco = True # DEFAULT: True
filterTopViolations = True # DEFAULT: True
useNrgArchive = False # DEFAULT: False
ranges = CV_STR # DEFAULT: CV_STR
# ranges='173-177'
# ranges='6-13,29-45' # 1bus
doSwapCheck = False
doRestoreCheck = False
doStoreCheck = False # DEFAULT: False Requires sqlAlchemy
doSave = not redoFromCingProject # DEFAULT: False Requires sqlAlchemy
if fastestTest:
modelCount = 2 # DEFAULT 2
# redoFromCingProject = False
htmlOnly = True # DEFAULT: True
doWhatif = False # DEFAULT: False
doProcheck = False # DEFAULT: False
doWattos = False # DEFAULT: False
doQueeny = False # DEFAULT: False
doTalos = False # DEFAULT: False
filterVasco = False # DEFAULT: False
doRestoreCheck = False # DEFAULT: False
doStoreCheck = False # DEFAULT: False
if redoFromCingProject:
useNrgArchive = False
doWhatif = False
doProcheck = False
doWattos = False
doTalos = False
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
for i, entryId in enumerate(AllChecks.entryList):
if i:
nTmessage('\n\n')
if redoFromCingProject:
project = Project.open(entryId, status='old')
else:
project = Project.open(entryId, status='new')
self.assertTrue(project, 'Failed opening project: ' + entryId)
if useNrgArchive: # default is False
# inputArchiveDir = os.path.join('/Library/WebServer/Documents/NRG-CING/recoordSync', entryId)
# Mounted from nmr.cmbi.ru.nl
# inputArchiveDir = os.path.join('/Volumes/tria1/Library/WebServer/Documents/NRG-CING/recoordSync', entryId)
inputArchiveDir = os.path.join(
'/Users/jd/ccpn_tmp/data/recoord', entryId)
else:
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
if not os.path.exists(ccpnFile):
ccpnFile = os.path.join(inputArchiveDir,
entryId + ".tar.gz")
if not os.path.exists(ccpnFile):
self.fail("Neither %s or the .tgz exist" % ccpnFile)
if doSwapCheck: # Need to start with ccpn without loading into CING api yet.
if os.path.exists(entryId):
nTmessage("Removing previous directory: %s" % entryId)
rmtree(entryId)
do_cmd("tar -xzf " +
ccpnFile) # will extract to local dir.
if os.path.exists('linkNmrStarData'):
nTmessage(
"Renaming standard directory linkNmrStarData to entry: %s"
% entryId)
os.rename('linkNmrStarData', entryId)
ccpnProject = loadProject(entryId)
if not ccpnProject:
self.fail("Failed to read project: %s" % entryId)
# constraintsHandler = ConstraintsHandler()
nmrConstraintStore = ccpnProject.findFirstNmrConstraintStore(
)
structureEnsemble = ccpnProject.findFirstStructureEnsemble(
)
numSwapCheckRuns = 2
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)
nTmessage('Saving to new path')
# checkValid=True,
saveProject(ccpnProject,
newPath=entryId,
removeExisting=True)
ccpnFile = entryId # set to local dir now.
# end if doSwapCheck
self.assertTrue(
project.initCcpn(ccpnFolder=ccpnFile,
modelCount=modelCount))
# if doSave:
# self.assertTrue(project.save())
if False:
ranges = "173-183"
# residueOfInterest = range(171,174)
# for residue in project.molecule.A.allResidues():
# if residue.resNum not in residueOfInterest:
# # nTmessage("Removing residue of no interest")
# project.molecule.A.removeResidue(residue)
if False:
ccpnProject = project.ccpn
printSequenceFromCcpnProject(ccpnProject)
if True:
self.assertFalse(project.molecule.setRanges(ranges))
nTdebug('In test_ccpn.py: ranges: %s' %
str(project.molecule.ranges))
project.molecule.rangesToMmCifRanges(ranges)
if True:
self.assertFalse(
project.validate(
htmlOnly=htmlOnly,
ranges=ranges,
# fastestTest=fastestTest, # disabled
doProcheck=doProcheck,
doWhatif=doWhatif,
doWattos=doWattos,
doQueeny=doQueeny,
doTalos=doTalos,
filterVasco=filterVasco,
filterTopViolations=filterTopViolations))
if doWattos and False:
mol = project.molecule
completenessMol = mol.getDeepByKeys(
WATTOS_STR, COMPLCHK_STR, VALUE_LIST_STR)
nTdebug("completenessMol: %s" % completenessMol)
for res in mol.allResidues():
completenessRes = res.getDeepByKeys(
WATTOS_STR, COMPLCHK_STR, VALUE_LIST_STR)
nTdebug("%s: %s" % (res, completenessRes))
# end for
# end if
color = project.molecule.getRogColor()
nTdebug("The color of this molecule is: %s" % color)
self.assertFalse(color == COLOR_RED) # ;-)
# end if
# self.assertTrue(project.exportValidation2ccpn())
# self.assertFalse(project.removeCcpnReferences())
# Do not leave the old CCPN directory laying around since it might get added to by another test.
# if os.path.exists(entryId):
# self.assertFalse(shutil.rmtree(entryId))
if False:
self.assertTrue(project.save())
self.assertTrue(project.saveCcpn(entryId))
if doRestoreCheck:
del project
project = Project.open(entryId, status='old')
self.assertTrue(project,
'Failed reopening project: ' + entryId)
if doStoreCheck:
# # Does require below import which is used here to trigger import warning in case it's not installed.
# pylint: disable=W0612
from cing.PluginCode.sqlAlchemy import CsqlAlchemy #@UnusedImport # pylint: disable=W0404
if doStoreCING2db(entryId, ARCHIVE_NRG_ID, project=project):
nTerror(
"Failed to store CING project's data to DB but continuing."
)
if doSave:
self.assertTrue(project.save())
def fcProcessEntry( entry_code, ccpnTgzFile, outputCcpnTgzFile, functionToRun='swapCheck'):
"""
E.g.
entry_code 1brv
ccpnTgzFile /NRG-CING/prep/S/br/1brv/1brv.tgz Full path
outputCcpnTgzFile 1brv_assign.tgz but inside the project will still be keyed and named 1brv.
Return True on error
Can be extended later on to run a different function.
Will run in cwd.
"""
# Adjust the parameters below
isInteractive = False
doSwapCheck = True
doSaveProject = True
doExport = True
minimalPrompts = True
verbose = True
allowPopups = False
if isInteractive:
allowPopups = True
minimalPrompts = False
print 'entry_code ', entry_code
# print 'bmrb_id ', bmrb_id
print 'allowPopups ', allowPopups
print 'isInteractive ', isInteractive
print 'minimalPrompts ', minimalPrompts
print 'verbose ', verbose
print 'doSwapCheck ', doSwapCheck
print 'doSaveProject ', doSaveProject
print 'doExport ', doExport
guiRoot = None
if allowPopups:
guiRoot = Tkinter.Tk()
if not os.path.exists(ccpnTgzFile):
nTerror("Input file not found: %s" % ccpnTgzFile)
return True
nTdebug("Looking at %s" % entry_code)
if os.path.exists(entry_code):
nTmessage("Removing previous directory: %s" % entry_code)
rmtree(entry_code)
do_cmd("tar -xzf " + ccpnTgzFile) # will unpack to cwd.
if os.path.exists('linkNmrStarData'):
nTmessage("Renaming standard directory linkNmrStarData to entry: %s" % entry_code)
os.rename('linkNmrStarData', entry_code)
ccpnProject = loadProject(entry_code)
if not ccpnProject:
nTerror("Failed to read project: %s" % entry_code)
return True
if doSwapCheck:
# constraintsHandler = ConstraintsHandler()
nmrConstraintStore = ccpnProject.findFirstNmrConstraintStore()
structureEnsemble = ccpnProject.findFirstStructureEnsemble()
if nmrConstraintStore:
if structureEnsemble:
swapCheck(nmrConstraintStore, structureEnsemble)
else:
nTmessage("Failed to find structureEnsemble; skipping swapCheck")
else:
nTmessage("Failed to find nmrConstraintStore; skipping swapCheck")
# constraintsHandler.swapCheck(nmrConstraintStore, structureEnsemble, numSwapCheckRuns)
# end if doSwapCheck
if doSaveProject:
nTmessage('Saving to new path: %s' % entry_code)
saveProject(ccpnProject, newPath=entry_code, removeExisting=True)
if doExport:
if os.path.exists(outputCcpnTgzFile):
nTmessage("Overwriting: " + outputCcpnTgzFile)
myTar = tarfile.open(outputCcpnTgzFile, mode='w:gz') # overwrites
myTar.add(entry_code)
myTar.close()
if guiRoot:
guiRoot.destroy()
residue = chain.newResidue(seqId=seqId, seqCode=molSysResidue.seqCode)
# create MolStructure.Atoms
for molSysAtom in molSysResidue.atoms:
chemAtom = molSysAtom.chemAtom
if chemAtom.elementSymbol != 'H':
atom = residue.newAtom(name=molSysAtom.name)
# create MolStructure.Coord
coord = atom.newCoord(model=model)
coord.x = random.random()
coord.y = random.random()
coord.z = random.random()
#root.saveModified()
if __name__ == '__main__':
import sys
if len(sys.argv) == 1:
from memops.api.Implementation import MemopsRoot
root = MemopsRoot(name='testNmr')
elif len(sys.argv) == 2:
from memops.general.Io import loadProject
repositoryPath = sys.argv[1]
root = loadProject(path=repositoryPath)
main(root)
def replaceCoordinates():
cityList = [
'Cheshire', 'Frankfurt', 'Lyon', 'Paris', 'Piscataway', 'Seattle',
'Utrecht'
]
maxCities = 1
maxEntries = 1
# Adjust the parameters below!
removeOriginalStructureEnsemble = True
addStructureEnsemble = True # From all *.pdb files in inputDir.
dataOrgDir = os.path.join(baseDir, DATA_STR)
dataDividedDir = os.path.join(baseDir, DATA_STR)
# _scriptName = sys.argv[0]
# parameters for doScriptOnEntryList
startDir = '/Library/WebServer/Documents/' + CASD_NMR_BASE_NAME
entryListFileName = os.path.join(startDir, 'list', 'entry_list_todo.csv')
entryList = readLinesFromFile(entryListFileName) #@UnusedVariable
entryList = ['ET109Aox']
for entryCode in entryList[0:maxEntries]:
ch23 = entryCode[1:3]
dataOrgEntryDir = os.path.join(dataOrgDir, entryCode)
ccpnFile = os.path.join(dataOrgEntryDir, entryCode + ".tgz")
for city in cityList[0:maxCities]:
entryCodeNew = entryCode + city
dataDividedXDir = os.path.join(dataDividedDir, ch23)
inputAuthorDir = os.path.join(dataDividedXDir, entryCodeNew,
'Author')
outputNijmegenDir = os.path.join(dataDividedXDir, entryCodeNew,
'Nijmegen')
globPattern = inputAuthorDir + '/*.pdb'
pdbFileList = glob(globPattern)
if not pdbFileList:
nTmessage("Skipping because there is no PDB file in: " +
os.getcwd())
continue
if not os.path.exists(inputAuthorDir):
mkdirs(inputAuthorDir)
if not os.path.exists(outputNijmegenDir):
mkdirs(outputNijmegenDir)
os.chdir(outputNijmegenDir)
if False:
# By reading the ccpn tgz into cing it is also untarred/tested.
project = Project.open(entryCode, status='new')
project.initCcpn(ccpnFolder=ccpnFile, modelCount=1)
project.removeFromDisk()
project.close(save=False)
if True:
ccpnProject = loadProject(entryCode)
nmrProject = ccpnProject.currentNmrProject
ccpnMolSystem = ccpnProject.findFirstMolSystem()
nTmessage('found ccpnMolSystem: %s' % ccpnMolSystem)
# print 'status: %s' % ccpnMolSystem.setCode(projectName) # impossible; reported to ccpn team.
if removeOriginalStructureEnsemble:
structureEnsemble = ccpnProject.findFirstStructureEnsemble(
)
if structureEnsemble:
nTmessage("Removing first found structureEnsemble")
structureEnsemble.delete()
else:
nTwarning(
"No structureEnsemble found; can't remove it.")
if addStructureEnsemble:
structureGeneration = nmrProject.newStructureGeneration()
fileList = None
nTdebug("From %s will read files: %s" %
(globPattern, fileList))
guiRoot = Tkinter.Tk()
format = PseudoPdbFormat(ccpnProject, guiRoot, verbose=1)
format.readCoordinates(fileList,
strucGen=structureGeneration,
minimalPrompts=1,
linkAtoms=0)
nTmessage('saving to new path if all checks are valid')
# the newPath basename will be taken according to ccpn code doc.
saveProject(ccpnProject,
checkValid=True,
newPath=entryCodeNew,
removeExisting=True)
#
# - Print out the residue type, position and all the atoms found in
# each residue.
#
# - Check that the project is valid.
#
# - Hint: Look at class methods for MemopsRoot objects.
#
from memops.general.Io import loadProject
if __name__ == '__main__':
# Load the project with the DNA molecule.
project = loadProject('dnaTest')
# Locate the DNA molecule in the project.
molecule = project.findFirstMolecule(name = 'myDnaMoleculeName')
# Make a new molSystem top object.
keywds = {'code': 'myMolecularSystemCode',
'name': 'My molecular system name'}
molSystem = project.newMolSystem(**keywds)
# Make a chain for this molSystem that is linked to the reference
# DNA molecule.
chain = molSystem.newChain(code = 'A', molecule = molecule)
ccpnProjectDir, ariaProjectPath = cmdArgs[:2]
workingDir = None
tempDir = None
if nArgs > 2:
workingDir = cmdArgs[2]
if nArgs > 3:
tempDir = cmdArgs[3]
from memops.general.Io import loadProject
if not os.path.exists(ccpnProjectDir):
raise Exception(FAIL + 'CCPN project directory does not exist')
if not os.path.isdir(ccpnProjectDir):
raise Exception(FAIL + 'CCPN project location is not a directory')
try:
ccpnProject = loadProject(ccpnProjectDir)
except Exception, err:
raise Exception(FAIL + 'CCPN project failed to load. original error:' +
err)
makeAriaProject(ccpnProject,
ariaProjectPath,
workingDir=workingDir,
tempDir=tempDir)
print 'Done. Saved ARIA project to: %s' % ariaProjectPath
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 test_ccpn(self):
# cing.verbosity = verbosityDebug
# if you have a local copy you can use it; make sure to adjust the path setting below.
fastestTest = True # DEFAULT: True. Not passed to the validate routine in order to customize checks for speed.
modelCount=99 # DEFAULT: 99
redoFromCingProject = False # DEFAULT: False
htmlOnly = False # DEFAULT: False # default is False but enable it for faster runs without some actual data.
doWhatif = True # DEFAULT: True # disables whatif actual run
doProcheck = True # DEFAULT: True
doWattos = True # DEFAULT: True
doQueeny = True # DEFAULT: True
doTalos = True # DEFAULT: True
filterVasco = True # DEFAULT: True
filterTopViolations = True # DEFAULT: True
useNrgArchive = False # DEFAULT: False
ranges = CV_STR # DEFAULT: CV_STR
# ranges='173-177'
# ranges='6-13,29-45' # 1bus
doSwapCheck = False
doRestoreCheck = False
doStoreCheck = False # DEFAULT: False Requires sqlAlchemy
doSave = not redoFromCingProject # DEFAULT: False Requires sqlAlchemy
if fastestTest:
modelCount=2 # DEFAULT 2
# redoFromCingProject = False
htmlOnly = True # DEFAULT: True
doWhatif = False # DEFAULT: False
doProcheck = False # DEFAULT: False
doWattos = False # DEFAULT: False
doQueeny = False # DEFAULT: False
doTalos = False # DEFAULT: False
filterVasco = False # DEFAULT: False
doRestoreCheck = False # DEFAULT: False
doStoreCheck = False # DEFAULT: False
if redoFromCingProject:
useNrgArchive = False
doWhatif = False
doProcheck = False
doWattos = False
doTalos = False
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
for i,entryId in enumerate(AllChecks.entryList):
if i:
nTmessage('\n\n')
if redoFromCingProject:
project = Project.open(entryId, status = 'old')
else:
project = Project.open(entryId, status = 'new')
self.assertTrue(project, 'Failed opening project: ' + entryId)
if useNrgArchive: # default is False
# inputArchiveDir = os.path.join('/Library/WebServer/Documents/NRG-CING/recoordSync', entryId)
# Mounted from nmr.cmbi.ru.nl
# inputArchiveDir = os.path.join('/Volumes/tria1/Library/WebServer/Documents/NRG-CING/recoordSync', entryId)
inputArchiveDir = os.path.join('/Users/jd/ccpn_tmp/data/recoord', entryId)
else:
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
if not os.path.exists(ccpnFile):
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tar.gz")
if not os.path.exists(ccpnFile):
self.fail("Neither %s or the .tgz exist" % ccpnFile)
if doSwapCheck: # Need to start with ccpn without loading into CING api yet.
if os.path.exists(entryId):
nTmessage("Removing previous directory: %s" % entryId)
rmtree(entryId)
do_cmd("tar -xzf " + ccpnFile) # will extract to local dir.
if os.path.exists('linkNmrStarData'):
nTmessage("Renaming standard directory linkNmrStarData to entry: %s" % entryId)
os.rename('linkNmrStarData', entryId)
ccpnProject = loadProject(entryId)
if not ccpnProject:
self.fail("Failed to read project: %s" % entryId)
# constraintsHandler = ConstraintsHandler()
nmrConstraintStore = ccpnProject.findFirstNmrConstraintStore()
structureEnsemble = ccpnProject.findFirstStructureEnsemble()
numSwapCheckRuns = 2
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)
nTmessage('Saving to new path')
# checkValid=True,
saveProject(ccpnProject, newPath=entryId, removeExisting=True)
ccpnFile = entryId # set to local dir now.
# end if doSwapCheck
self.assertTrue(project.initCcpn(ccpnFolder = ccpnFile, modelCount=modelCount))
# if doSave:
# self.assertTrue(project.save())
if False:
ranges = "173-183"
# residueOfInterest = range(171,174)
# for residue in project.molecule.A.allResidues():
# if residue.resNum not in residueOfInterest:
# # nTmessage("Removing residue of no interest")
# project.molecule.A.removeResidue(residue)
if False:
ccpnProject = project.ccpn
printSequenceFromCcpnProject(ccpnProject)
if True:
self.assertFalse(project.molecule.setRanges(ranges))
nTdebug('In test_ccpn.py: ranges: %s' % str(project.molecule.ranges))
project.molecule.rangesToMmCifRanges(ranges)
if True:
self.assertFalse(project.validate(htmlOnly = htmlOnly,
ranges=ranges,
# fastestTest=fastestTest, # disabled
doProcheck = doProcheck,
doWhatif = doWhatif,
doWattos=doWattos,
doQueeny = doQueeny,
doTalos=doTalos,
filterVasco=filterVasco,
filterTopViolations = filterTopViolations
))
if doWattos and False:
mol = project.molecule
completenessMol = mol.getDeepByKeys( WATTOS_STR, COMPLCHK_STR, VALUE_LIST_STR)
nTdebug("completenessMol: %s" % completenessMol)
for res in mol.allResidues():
completenessRes = res.getDeepByKeys( WATTOS_STR, COMPLCHK_STR, VALUE_LIST_STR)
nTdebug("%s: %s" % (res, completenessRes))
# end for
# end if
color = project.molecule.getRogColor()
nTdebug("The color of this molecule is: %s" % color)
self.assertFalse( color == COLOR_RED ) # ;-)
# end if
# self.assertTrue(project.exportValidation2ccpn())
# self.assertFalse(project.removeCcpnReferences())
# Do not leave the old CCPN directory laying around since it might get added to by another test.
# if os.path.exists(entryId):
# self.assertFalse(shutil.rmtree(entryId))
if False:
self.assertTrue(project.save())
self.assertTrue(project.saveCcpn(entryId))
if doRestoreCheck:
del project
project = Project.open(entryId, status = 'old')
self.assertTrue(project, 'Failed reopening project: ' + entryId)
if doStoreCheck:
# # Does require below import which is used here to trigger import warning in case it's not installed.
# pylint: disable=W0612
from cing.PluginCode.sqlAlchemy import CsqlAlchemy #@UnusedImport # pylint: disable=W0404
if doStoreCING2db( entryId, ARCHIVE_NRG_ID, project=project):
nTerror("Failed to store CING project's data to DB but continuing.")
if doSave:
self.assertTrue(project.save())
def replaceCoordinates():
cityList = [ 'Cheshire', 'Frankfurt', 'Lyon', 'Paris', 'Piscataway', 'Seattle', 'Utrecht' ]
maxCities = 1
maxEntries = 1
# Adjust the parameters below!
removeOriginalStructureEnsemble = True
addStructureEnsemble = True # From all *.pdb files in inputDir.
dataOrgDir = os.path.join(baseDir,DATA_STR)
dataDividedDir = os.path.join(baseDir,DATA_STR)
# _scriptName = sys.argv[0]
# parameters for doScriptOnEntryList
startDir = '/Library/WebServer/Documents/' + CASD_NMR_BASE_NAME
entryListFileName = os.path.join(startDir, 'list', 'entry_list_todo.csv')
entryList = readLinesFromFile(entryListFileName) #@UnusedVariable
entryList = ['ET109Aox']
for entryCode in entryList[0:maxEntries]:
ch23 = entryCode[1:3]
dataOrgEntryDir = os.path.join( dataOrgDir, entryCode )
ccpnFile = os.path.join(dataOrgEntryDir, entryCode+".tgz")
for city in cityList[0:maxCities]:
entryCodeNew = entryCode + city
dataDividedXDir = os.path.join(dataDividedDir, ch23)
inputAuthorDir = os.path.join(dataDividedXDir, entryCodeNew, 'Author')
outputNijmegenDir = os.path.join(dataDividedXDir, entryCodeNew, 'Nijmegen')
globPattern = inputAuthorDir + '/*.pdb'
pdbFileList = glob(globPattern)
if not pdbFileList:
nTmessage("Skipping because there is no PDB file in: " + os.getcwd())
continue
if not os.path.exists(inputAuthorDir):
mkdirs(inputAuthorDir)
if not os.path.exists(outputNijmegenDir):
mkdirs(outputNijmegenDir)
os.chdir(outputNijmegenDir)
if False:
# By reading the ccpn tgz into cing it is also untarred/tested.
project = Project.open(entryCode, status = 'new')
project.initCcpn(ccpnFolder = ccpnFile, modelCount=1)
project.removeFromDisk()
project.close(save=False)
if True:
ccpnProject = loadProject(entryCode)
nmrProject = ccpnProject.currentNmrProject
ccpnMolSystem = ccpnProject.findFirstMolSystem()
nTmessage( 'found ccpnMolSystem: %s' % ccpnMolSystem )
# print 'status: %s' % ccpnMolSystem.setCode(projectName) # impossible; reported to ccpn team.
if removeOriginalStructureEnsemble:
structureEnsemble = ccpnProject.findFirstStructureEnsemble()
if structureEnsemble:
nTmessage("Removing first found structureEnsemble")
structureEnsemble.delete()
else:
nTwarning("No structureEnsemble found; can't remove it.")
if addStructureEnsemble:
structureGeneration = nmrProject.newStructureGeneration()
fileList = None
nTdebug("From %s will read files: %s" % (globPattern,fileList))
guiRoot = Tkinter.Tk()
format = PseudoPdbFormat(ccpnProject, guiRoot, verbose = 1)
format.readCoordinates(fileList, strucGen = structureGeneration, minimalPrompts = 1, linkAtoms = 0)
nTmessage( 'saving to new path if all checks are valid' )
# the newPath basename will be taken according to ccpn code doc.
saveProject(ccpnProject, checkValid=True, newPath=entryCodeNew, removeExisting=True)
def annotateEntry(entry_code, bmrb_id, *extraArgList):
'Return True on error'
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
# entry_code, city = entryCodePlusCity.split('_')
# Adjust the parameters below
isInteractive = False
checkOrgProject = False
doSwapCheck = False
doSaveProject = True
doExport = True
minimalPrompts = True
verbose = True
allowPopups = False
if isInteractive:
allowPopups = True
minimalPrompts = False
# verbose = True
else:
pass
# minimalPrompts = True
# verbose = False
print 'entry_code ', entry_code
print 'bmrb_id ', bmrb_id
print 'allowPopups ', allowPopups
print 'isInteractive ', isInteractive
print 'minimalPrompts ', minimalPrompts
print 'verbose ', verbose
print 'checkOrgProject ', checkOrgProject
print 'doSwapCheck ', doSwapCheck
print 'doSaveProject ', doSaveProject
print 'doExport ', doExport
guiRoot = None
if allowPopups:
guiRoot = Tkinter.Tk()
ch23 = entry_code[1:3]
dataOrgEntryDir = os.path.join(results_dir, 'recoordSync', entry_code)
ccpnFile = os.path.join(dataOrgEntryDir, entry_code + ".tgz")
if not os.path.exists(ccpnFile):
nTerror("Input file not found: %s" % ccpnFile)
return True
nTdebug("Looking at %s" % entry_code)
# continue # TODO disable premature stop.
bmrb_code = 'bmr'+bmrb_id
digits12 ="%02d" % ( bmrb_id % 100 )
inputStarDir = os.path.join(bmrbDir, digits12)
if not os.path.exists(inputStarDir):
nTerror("Input star dir not found: %s" % inputStarDir)
return True
inputStarFile = os.path.join(inputStarDir, '%s.str'%bmrb_code)
if not os.path.exists(inputStarFile):
nTerror("inputStarFile not found: %s" % inputStarFile)
return True
dataDividedXDir = os.path.join(nrgPlusDir, ch23)
entryDir = os.path.join(dataDividedXDir, entry_code)
outputNijmegenDir = os.path.join(entryDir, 'Nijmegen')
if not os.path.exists(outputNijmegenDir):
mkdirs(outputNijmegenDir)
os.chdir(outputNijmegenDir)
presets = getDeepByKeysOrDefault(presetDict, {}, bmrb_code)
if presets:
nTmessage("In annotateLoop using preset values...")
nTdebug(str(presets))
if os.path.exists(entry_code):
nTmessage("Removing previous directory: %s" % entry_code)
rmtree(entry_code)
do_cmd("tar -xzf " + ccpnFile)
if os.path.exists('linkNmrStarData'):
nTmessage("Renaming standard directory linkNmrStarData to entry: %s" % entry_code)
os.rename('linkNmrStarData', entry_code)
if checkOrgProject:
# By reading the ccpn tgz into cing it is also untarred/tested.
project = Project.open(entry_code, status='new')
if not project.initCcpn(ccpnFolder=ccpnFile, modelCount=1):
nTerror("Failed check of original project")
return True
project.removeFromDisk()
project.close(save=False)
ccpnProject = loadProject(entry_code)
if not ccpnProject:
nTerror("Failed to read project: %s" % entry_code)
return True
# nmrProject = ccpnProject.currentNmrProject
# ccpnMolSystem = ccpnProject.findFirstMolSystem()
# nTmessage('found ccpnMolSystem: %s' % ccpnMolSystem)
# print 'status: %s' % ccpnMolSystem.setCode(projectName) # impossible; reported to ccpn team.
importStarChemicalShifts(ccpnProject, inputStarDir, guiRoot, allowPopups=allowPopups, minimalPrompts=minimalPrompts,
verbose=verbose, **presets)
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')
# checkValid=True,
saveProject(ccpnProject, newPath=entry_code, removeExisting=True)
if doExport:
tarPath = os.path.join(entryDir, entry_code + ".tgz")
if os.path.exists(tarPath):
nTmessage("Overwriting: " + tarPath)
myTar = tarfile.open(tarPath, mode='w:gz') # overwrites
myTar.add(entry_code)
myTar.close()
if guiRoot:
guiRoot.destroy()
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 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 annotateEntry(entry_code, bmrb_id, *extraArgList):
'Return True on error'
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
# entry_code, city = entryCodePlusCity.split('_')
# Adjust the parameters below
isInteractive = False
checkOrgProject = False
doSwapCheck = False
doSaveProject = True
doExport = True
minimalPrompts = True
verbose = True
allowPopups = False
if isInteractive:
allowPopups = True
minimalPrompts = False
# verbose = True
else:
pass
# minimalPrompts = True
# verbose = False
print 'entry_code ', entry_code
print 'bmrb_id ', bmrb_id
print 'allowPopups ', allowPopups
print 'isInteractive ', isInteractive
print 'minimalPrompts ', minimalPrompts
print 'verbose ', verbose
print 'checkOrgProject ', checkOrgProject
print 'doSwapCheck ', doSwapCheck
print 'doSaveProject ', doSaveProject
print 'doExport ', doExport
guiRoot = None
if allowPopups:
guiRoot = Tkinter.Tk()
ch23 = entry_code[1:3]
dataOrgEntryDir = os.path.join(results_dir, 'recoordSync', entry_code)
ccpnFile = os.path.join(dataOrgEntryDir, entry_code + ".tgz")
if not os.path.exists(ccpnFile):
nTerror("Input file not found: %s" % ccpnFile)
return True
nTdebug("Looking at %s" % entry_code)
# continue # TODO disable premature stop.
bmrb_code = 'bmr' + bmrb_id
digits12 = "%02d" % (bmrb_id % 100)
inputStarDir = os.path.join(bmrbDir, digits12)
if not os.path.exists(inputStarDir):
nTerror("Input star dir not found: %s" % inputStarDir)
return True
inputStarFile = os.path.join(inputStarDir, '%s.str' % bmrb_code)
if not os.path.exists(inputStarFile):
nTerror("inputStarFile not found: %s" % inputStarFile)
return True
dataDividedXDir = os.path.join(nrgPlusDir, ch23)
entryDir = os.path.join(dataDividedXDir, entry_code)
outputNijmegenDir = os.path.join(entryDir, 'Nijmegen')
if not os.path.exists(outputNijmegenDir):
mkdirs(outputNijmegenDir)
os.chdir(outputNijmegenDir)
presets = getDeepByKeysOrDefault(presetDict, {}, bmrb_code)
if presets:
nTmessage("In annotateLoop using preset values...")
nTdebug(str(presets))
if os.path.exists(entry_code):
nTmessage("Removing previous directory: %s" % entry_code)
rmtree(entry_code)
do_cmd("tar -xzf " + ccpnFile)
if os.path.exists('linkNmrStarData'):
nTmessage("Renaming standard directory linkNmrStarData to entry: %s" %
entry_code)
os.rename('linkNmrStarData', entry_code)
if checkOrgProject:
# By reading the ccpn tgz into cing it is also untarred/tested.
project = Project.open(entry_code, status='new')
if not project.initCcpn(ccpnFolder=ccpnFile, modelCount=1):
nTerror("Failed check of original project")
return True
project.removeFromDisk()
project.close(save=False)
ccpnProject = loadProject(entry_code)
if not ccpnProject:
nTerror("Failed to read project: %s" % entry_code)
return True
# nmrProject = ccpnProject.currentNmrProject
# ccpnMolSystem = ccpnProject.findFirstMolSystem()
# nTmessage('found ccpnMolSystem: %s' % ccpnMolSystem)
# print 'status: %s' % ccpnMolSystem.setCode(projectName) # impossible; reported to ccpn team.
importStarChemicalShifts(ccpnProject,
inputStarDir,
guiRoot,
allowPopups=allowPopups,
minimalPrompts=minimalPrompts,
verbose=verbose,
**presets)
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')
# checkValid=True,
saveProject(ccpnProject, newPath=entry_code, removeExisting=True)
if doExport:
tarPath = os.path.join(entryDir, entry_code + ".tgz")
if os.path.exists(tarPath):
nTmessage("Overwriting: " + tarPath)
myTar = tarfile.open(tarPath, mode='w:gz') # overwrites
myTar.add(entry_code)
myTar.close()
if guiRoot:
guiRoot.destroy()
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)