def importFullStarProjects(starFileName, projectName, inputDir='.', outputDir='.', guiRoot=None, allowPopups=0,minimalPrompts=1,verbose=1):
'''Returns a full CCPN project rooted in inputDir/projectName that will be created and saved.
Input will be from inputDir/starFileName
Returns False for error.
'''
if not os.path.exists(inputDir):
nTerror("Failed to find inputDir: %s" % inputDir)
return False
starFileNameFull = os.path.join(inputDir, starFileName)
if not os.path.exists(starFileNameFull):
nTerror("Failed to find starFileNameFull: %s" % starFileNameFull)
return False
if not os.path.exists(outputDir):
os.mkdir(outputDir)
os.chdir(outputDir)
ccpnProjectPath = os.path.join(outputDir, projectName)
if os.path.exists(ccpnProjectPath):
shutil.rmtree(ccpnProjectPath)
ccpnProject = Implementation.MemopsRoot(name=projectName)
# 'linkAtoms': (True,False,'If set to False (off), unrecognized coordinate atoms will not be linked.'),
keywds = {'minimalPrompts': minimalPrompts, 'allowPopups': allowPopups, 'linkAtoms':0}
formatNmrStarFormat = NmrStarFormat(ccpnProject, guiRoot, verbose=verbose, **keywds)
formatNmrStarFormat.version = '3.1'
entryTitle = 'Project from NMR-STAR for %s' % projectName
entryDetails = "Created by Wim Vranken's FormatConverter embedded in CING"
formatNmrStarFormat.getFullProject( starFileNameFull, title = entryTitle, details = entryDetails, **keywds)
# nmrConstraintStore = shiftList.nmrConstraintStore
# structureGeneration = nmrConstraintStore.findFirstStructureGeneration()
# formatNmrStarFormat.linkResonances(
# forceDefaultChainMapping=1, # may be overwritten by using forceChainMappings.
# globalStereoAssign=1,
# setSingleProchiral=1,
# setSinglePossEquiv=1,
## strucGen=structureGeneration,
# allowPopups=allowPopups, minimalPrompts=minimalPrompts, verbose=verbose, **keywds)
# Catch entries like mentioned in issue
try:
ccpnProject.checkAllValid()
except ApiError:
nTtracebackError()
nTerror("Failed ccpnProject.checkAllValid")
nTerror("See issue: %s%d" % (issueListUrl, 266))
return False
ccpnProject.saveModified()
if not os.path.exists(ccpnProjectPath):
nTerror("Failed to find new CCPN project directory: %s" % ccpnProjectPath)
return False
tgzFileName = projectName + ".tgz"
cmd = "tar -czf %s %s" % (tgzFileName, projectName)
do_cmd(cmd)
return ccpnProject
def _test_anneal(self):
'Test the anneal'
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
inputArchiveDir = os.path.join(cingDirTestsData, "xplor")
for _i, entryId in enumerate(AllChecks.entryList):
nTmessage('Doing entry %s' % entryId)
cingDirTmpTestEntry = entryId
mkdirs(cingDirTmpTestEntry)
self.failIf(
os.chdir(cingDirTmpTestEntry),
msg="Failed to change to test entry directory for files: " +
cingDirTmpTestEntry)
do_cmd("rm -f *_extended_*.pdb* >& /dev/null")
inputDir = os.path.join(inputArchiveDir, entryId)
self.failIf(not os.path.exists(inputDir),
"Missing input dir " + inputDir)
nTmessage('Trying to copy input files')
copydir(os.path.join(inputDir, '*'), '.')
xplorExecutable = '/Users/jd/workspace/xplor-nih-2.27/bin/xplor'
xplorScript = '$CINGROOT/python/xplorcing/anneal.py'
cmd = 'env -i PATH=$PATH HOME=$HOME USER=$USER %s -py %s %s >& anneal.log' % (
xplorExecutable,
xplorScript,
entryId,
# os.getcwd(), # inputDir
# os.getcwd(), # outputDir
)
if do_cmd(cmd):
nTerror("Failed anneal")
else:
nTmessage("Succeeded anneal")
def convert(projectName, rootDir):
datasetDir = os.path.join(rootDir, projectName)
nijmegenDir = os.path.join(datasetDir, "Nijmegen")
authorDir = os.path.join(datasetDir, "Authors")
os.chdir(nijmegenDir)
projectPath = os.path.join(nijmegenDir, projectName)
if os.path.exists(projectPath):
shutil.rmtree(projectPath)
project = Implementation.MemopsRoot(name = projectName)
nmrProject = project.newNmrProject(name = project.name)
structureGeneration = nmrProject.newStructureGeneration()
guiRoot = Tkinter.Tk()
format = PseudoPdbFormat(project, guiRoot, verbose = 1)
globPattern = authorDir + '/*.pdb'
fileList = glob(globPattern)
nTdebug("From %s will read files: %s" % (globPattern,fileList))
format.readCoordinates(fileList, strucGen = structureGeneration, minimalPrompts = 1, linkAtoms = 0)
project.saveModified()
tgzFileName = "../"+projectName + ".tgz"
cmd = "tar -czf %s %s" % (tgzFileName, projectName)
do_cmd(cmd)
def convert(projectName, rootDir):
datasetDir = os.path.join(rootDir, projectName)
nijmegenDir = os.path.join(datasetDir, "Nijmegen")
authorDir = os.path.join(datasetDir, "Authors")
os.chdir(nijmegenDir)
projectPath = os.path.join(nijmegenDir, projectName)
if os.path.exists(projectPath):
shutil.rmtree(projectPath)
project = Implementation.MemopsRoot(name=projectName)
nmrProject = project.newNmrProject(name=project.name)
structureGeneration = nmrProject.newStructureGeneration()
guiRoot = Tkinter.Tk()
format = PseudoPdbFormat(project, guiRoot, verbose=1)
globPattern = authorDir + '/*.pdb'
fileList = glob(globPattern)
nTdebug("From %s will read files: %s" % (globPattern, fileList))
format.readCoordinates(fileList,
strucGen=structureGeneration,
minimalPrompts=1,
linkAtoms=0)
project.saveModified()
tgzFileName = "../" + projectName + ".tgz"
cmd = "tar -czf %s %s" % (tgzFileName, projectName)
do_cmd(cmd)
def _test_anneal(self):
'Test the anneal'
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
inputArchiveDir = os.path.join(cingDirTestsData, "xplor")
for _i,entryId in enumerate(AllChecks.entryList):
nTmessage('Doing entry %s' % entryId)
cingDirTmpTestEntry = entryId
mkdirs( cingDirTmpTestEntry )
self.failIf(os.chdir(cingDirTmpTestEntry), msg =
"Failed to change to test entry directory for files: " + cingDirTmpTestEntry)
do_cmd( "rm -f *_extended_*.pdb* >& /dev/null" )
inputDir = os.path.join(inputArchiveDir, entryId )
self.failIf( not os.path.exists(inputDir), "Missing input dir " + inputDir)
nTmessage('Trying to copy input files' )
copydir( os.path.join(inputDir, '*'), '.')
xplorExecutable = '/Users/jd/workspace/xplor-nih-2.27/bin/xplor'
xplorScript = '$CINGROOT/python/xplorcing/anneal.py'
cmd = 'env -i PATH=$PATH HOME=$HOME USER=$USER %s -py %s %s >& anneal.log' % (
xplorExecutable, xplorScript,
entryId,
# os.getcwd(), # inputDir
# os.getcwd(), # outputDir
)
if do_cmd( cmd ):
nTerror("Failed anneal")
else:
nTmessage("Succeeded anneal")
def convertStar2Ccpn(projectName, rootDir, inputDir="XPLOR", outputDir="CCPN"):
"""The structure when done will be:
rootDir -> -> inputDir -> xxxx.pdb etc.
-> outputDir -> xxxx -> ccp etc.
-> xxxx.tgz (the resulting CCPN data)
E.g.
taf3Piscataway -> Authors -> all.pdb etc.
-> Nijmegen -> taf3Piscataway -> ccp etc.
-> taf3Piscataway.tgz
Or in iCingSetup the rootDir is eg: /Library/WebServer/Documents/tmp/cing/ano/WjtXOz
with project name gb1
WjtXOz -> XPLOR -> gb1.pdb etc.
-> CCPN -> gb1 -> ccpn etc.
-> gb1.tgz
The in and out paths are relative to the rootDir.
"""
nTerror("This routine is untested and shouldn't be used without.")
inputDir = os.path.join(rootDir, inputDir)
outputDir = os.path.join(rootDir, outputDir)
if not os.path.exists(inputDir):
nTerror("Failed to find")
if os.path.exists(outputDir):
shutil.rmtree(outputDir)
os.mkdir(outputDir)
os.chdir(outputDir)
ccpnProjectPath = os.path.join(outputDir, projectName)
if os.path.exists(ccpnProjectPath):
shutil.rmtree(ccpnProjectPath)
project = Implementation.MemopsRoot(name=projectName)
guiRoot = Tkinter.Tk() # headless possible?
importStarChemicalShifts(project,
inputDir,
guiRoot,
allowPopups=0,
minimalPrompts=1,
verbose=0)
project.saveModified()
tgzFileName = "../" + projectName + ".tgz"
cmd = "tar -czf %s %s" % (tgzFileName, projectName)
do_cmd(cmd)
guiRoot.destroy()
def convertStar2Ccpn(projectName, rootDir, inputDir="XPLOR", outputDir="CCPN"):
"""The structure when done will be:
rootDir -> -> inputDir -> xxxx.pdb etc.
-> outputDir -> xxxx -> ccp etc.
-> xxxx.tgz (the resulting CCPN data)
E.g.
taf3Piscataway -> Authors -> all.pdb etc.
-> Nijmegen -> taf3Piscataway -> ccp etc.
-> taf3Piscataway.tgz
Or in iCingSetup the rootDir is eg: /Library/WebServer/Documents/tmp/cing/ano/WjtXOz
with project name gb1
WjtXOz -> XPLOR -> gb1.pdb etc.
-> CCPN -> gb1 -> ccpn etc.
-> gb1.tgz
The in and out paths are relative to the rootDir.
"""
nTerror("This routine is untested and shouldn't be used without.")
inputDir = os.path.join(rootDir, inputDir)
outputDir = os.path.join(rootDir, outputDir)
if not os.path.exists(inputDir):
nTerror("Failed to find")
if os.path.exists(outputDir):
shutil.rmtree(outputDir)
os.mkdir(outputDir)
os.chdir(outputDir)
ccpnProjectPath = os.path.join(outputDir, projectName)
if os.path.exists(ccpnProjectPath):
shutil.rmtree(ccpnProjectPath)
project = Implementation.MemopsRoot(name=projectName)
guiRoot = Tkinter.Tk() # headless possible?
importStarChemicalShifts(project, inputDir, guiRoot, allowPopups=0, minimalPrompts=1, verbose=0)
project.saveModified()
tgzFileName = "../" + projectName + ".tgz"
cmd = "tar -czf %s %s" % (tgzFileName, projectName)
do_cmd(cmd)
guiRoot.destroy()
def runSpecific(self):
""" Returns True on error """
entryCodeChar2and3 = self.idCode[1:3]
projectDirectory = os.path.join(dir_S, entryCodeChar2and3, self.idCode)
os.chdir(projectDirectory)
curDir = os.getcwd() #@UnusedVariable
nTdebug("curDir: %s" % curDir)
# ccpnDir = self.baseName #@UnusedVariable
# Read the existing CCPN project, set up format object dict
self.loadProject()
self.createFormatObjects()
self.entry = self.ccpnProject.findFirstNmrEntryStore().findFirstEntry()
self.molSystem = self.ccpnProject.findFirstMolSystem()
self.nmrProject = self.ccpnProject.findFirstNmrProject()
self.strucGen = self.nmrProject.findFirstStructureGeneration()
bmrbCodesLength = len(self.bmrbCodes)
if not bmrbCodesLength:
nTerror("Not a single BMRB entry presented.")
return
if bmrbCodesLength > 1:
nTwarning("Currently NRG-CING only loads a single BMRB entry's CS. Skipping others.")
# Read the BMRB NMR-STAR file (only chem shift data)
# for bmrbCode in self.bmrbCodes:
bmrbFile = self.bmrbCodes[0]
bmrbCode = bmrbFile.split('_')[0]
self.initShiftPresets(bmrbCode)
# bmrbNmrStarFile = os.path.join(bmrbArchiveDataDir, self.bmrbFileFormat % bmrbCode)
# bmrb_id = int(bmrbCode[3:])
# digits12 = "%02d" % (bmrb_id % 100)
# inputStarDir = os.path.join(bmrbDir, digits12)
# inputStarDir = os.path.join(bmrbDir, bmrbCode)
# if not os.path.exists(bmrbFile):
# nTerror("Input star dir not found: %s" % bmrbFile)
# return True
inputStarFile = bmrbFile
if not os.path.exists(inputStarFile):
nTerror("inputStarFile not found: %s" % inputStarFile)
return True
nTdebug("Start readNmrStarFile")
self.readNmrStarFile(inputStarFile, components=['measurements'])
# Try to autoset mapping...
nTdebug("Start setBmrbNmrStarMapping")
self.setBmrbNmrStarMapping(inputStarFile)
# Run linkResonances, using custom keywds set above
nTdebug("Start runLinkResonances")
self.runLinkResonances(resonanceType='nmr')
# Save project in new location
newPath = self.baseName
nTmessage('Saving to new path: %s in cwd: %s' % (newPath, os.getcwd()))
saveProject(self.ccpnProject, removeExisting=True, newPath=newPath, newProjectName=self.baseName)
ccpnTgzFile = "%s.tgz" % self.idCode
cmd = "tar -czf %s %s" % (ccpnTgzFile, newPath)
if do_cmd(cmd):
nTerror("Failed tar")
return None
nTmessage("Saved ccpn project to tgz: %s" % ccpnTgzFile)
def convertCyana2Ccpn(projectName, rootDir):
guiRoot = Tkinter.Tk()
datasetDir = os.path.join(rootDir, projectName)
nijmegenDir = os.path.join(datasetDir, "Nijmegen")
authorDir = os.path.join(datasetDir, "Authors")
os.chdir(nijmegenDir)
projectPath = os.path.join(nijmegenDir, projectName)
if os.path.exists(projectPath):
shutil.rmtree(projectPath)
project = Implementation.MemopsRoot(name=projectName)
importCyanaCoorAndRes(project, authorDir, guiRoot)
project.saveModified()
tgzFileName = "../" + projectName + ".tgz"
cmd = "tar -czf %s %s" % (tgzFileName, projectName)
do_cmd(cmd)
guiRoot.destroy()
def convertCyana2Ccpn(projectName, rootDir):
guiRoot = Tkinter.Tk()
datasetDir = os.path.join(rootDir, projectName)
nijmegenDir = os.path.join(datasetDir, "Nijmegen")
authorDir = os.path.join(datasetDir, "Authors")
os.chdir(nijmegenDir)
projectPath = os.path.join(nijmegenDir, projectName)
if os.path.exists(projectPath):
shutil.rmtree(projectPath)
project = Implementation.MemopsRoot(name=projectName)
importCyanaCoorAndRes(project, authorDir, guiRoot)
project.saveModified()
tgzFileName = "../" + projectName + ".tgz"
cmd = "tar -czf %s %s" % (tgzFileName, projectName)
do_cmd(cmd)
guiRoot.destroy()
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 importFullStarProjects(starFileName,
projectName,
inputDir='.',
outputDir='.',
guiRoot=None,
allowPopups=0,
minimalPrompts=1,
verbose=1):
'''Returns a full CCPN project rooted in inputDir/projectName that will be created and saved.
Input will be from inputDir/starFileName
Returns False for error.
'''
if not os.path.exists(inputDir):
nTerror("Failed to find inputDir: %s" % inputDir)
return False
starFileNameFull = os.path.join(inputDir, starFileName)
if not os.path.exists(starFileNameFull):
nTerror("Failed to find starFileNameFull: %s" % starFileNameFull)
return False
if not os.path.exists(outputDir):
os.mkdir(outputDir)
os.chdir(outputDir)
ccpnProjectPath = os.path.join(outputDir, projectName)
if os.path.exists(ccpnProjectPath):
shutil.rmtree(ccpnProjectPath)
ccpnProject = Implementation.MemopsRoot(name=projectName)
# 'linkAtoms': (True,False,'If set to False (off), unrecognized coordinate atoms will not be linked.'),
keywds = {
'minimalPrompts': minimalPrompts,
'allowPopups': allowPopups,
'linkAtoms': 0
}
formatNmrStarFormat = NmrStarFormat(ccpnProject,
guiRoot,
verbose=verbose,
**keywds)
formatNmrStarFormat.version = '3.1'
entryTitle = 'Project from NMR-STAR for %s' % projectName
entryDetails = "Created by Wim Vranken's FormatConverter embedded in CING"
formatNmrStarFormat.getFullProject(starFileNameFull,
title=entryTitle,
details=entryDetails,
**keywds)
# nmrConstraintStore = shiftList.nmrConstraintStore
# structureGeneration = nmrConstraintStore.findFirstStructureGeneration()
# formatNmrStarFormat.linkResonances(
# forceDefaultChainMapping=1, # may be overwritten by using forceChainMappings.
# globalStereoAssign=1,
# setSingleProchiral=1,
# setSinglePossEquiv=1,
## strucGen=structureGeneration,
# allowPopups=allowPopups, minimalPrompts=minimalPrompts, verbose=verbose, **keywds)
# Catch entries like mentioned in issue
try:
ccpnProject.checkAllValid()
except ApiError:
nTtracebackError()
nTerror("Failed ccpnProject.checkAllValid")
nTerror("See issue: %s%d" % (issueListUrl, 266))
return False
ccpnProject.saveModified()
if not os.path.exists(ccpnProjectPath):
nTerror("Failed to find new CCPN project directory: %s" %
ccpnProjectPath)
return False
tgzFileName = projectName + ".tgz"
cmd = "tar -czf %s %s" % (tgzFileName, projectName)
do_cmd(cmd)
return ccpnProject
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 _test_CombineRestraints(self):
'''
This unit test is by default disabled because we haven't figured out yet how to disable the output from
Yasara yet.
Input is a CING project from the test data.
'''
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
# Original project
# entryId = 'H2_2Ca_64_100'
_basicStats = """
pdb e.res_count b.deposition_date c.name r.number r.name a1.name a2.name
csd chi1_avg chi2_avg chi1_cv chi2_cv
1brv 32 1996-03-29 A 180 LEU CD1 CD2 0.0 270.3 170.5 0.000 0.000 no SSA delta
1brv 32 1996-03-29 A 183 LEU CD1 CD2 2.3 285.2 180.6 0.000 0.000 no SSA delta
1brv 32 1996-03-29 A 185 LEU CD1 CD2 0.4 313.5 172.1 0.054 0.045 no SSA delta/beta
2loj 63 2012-01-24 A 20 LEU CD1 CD2 1.3 302.2 178.2 0.002 0.001
2loj 63 2012-01-24 A 33 LEU CD1 CD2 -1.5 72.0 168.8 0.001 0.002
2loj 63 2012-01-24 A 34 LEU CD1 CD2 3.0 295.7 176.1 0.001 0.001
2loj <= 63 2012-01-24 A 50 LEU CD1 CD2 -2.2 184.2 283.6 0.002 0.001 chi2 > 240
2loj 63 2012-01-24 A 51 LEU CD1 CD2 -1.3 181.5 59.6 0.001 0.001
2loj 63 2012-01-24 A 59 LEU CD1 CD2 2.2 286.8 174.6 0.001 0.001
2loj 63 2012-01-24 A 60 LEU CD1 CD2 -0.3 203.4 66.6 0.049 0.002
2loj <= 63 2012-01-24 A 61 LEU CD1 CD2 -1.6 197.5 289.6 0.001 0.001 chi2 > 240 no SSA beta
2fwu 159 2006-02-03 A 526 LEU CD1 CD2 2.2 297.3 306.8 0.003 0.001 chi2 > 240
2fwu 159 2006-02-03 A 560 LEU CD1 CD2 1.8 293.8 173.6 0.002 0.001
2fwu 159 2006-02-03 A 589 LEU CD1 CD2 -1.1 205.0 301.3 0.001 0.000 chi2 > 240
2fwu 159 2006-02-03 A 596 LEU CD1 CD2 -0.5 220.3 318.1 0.002 0.002 chi2 > 240
2fwu 159 2006-02-03 A 642 LEU CD1 CD2 -4.1 178.5 70.9 0.001 0.000
"""
entryId = '2fwu'
# entryId = '1brv'
# entryId = '2loj'
# entryId = 'H2_2Ca_64_100'
modelCount = 20 # DEFAULT: 20 Not valid for starting from CING project.
doCcpn = True # Test entry starting from CCPN project e.g. from NRG-CING.
threshold = 0 # minimal violation, necessary to classify the restraints.
deasHB = True # first deassign all HBs in the specified leucines
dihrCHI2 = True # add a dihedral restraint on the leucines.
useAll = False # DEFAULT: False. use all leucines regardless of state
useLeuList = False # If useAll is False and useLeuList is False then the leucines will be automatically detected
doPrepCingProject = False # DEFAULT: True # NB If False this script will prefer a restore from the virgin .tgz
doRunRotateLeucines = False # DEFAULT: True # NB If False this script will prefer a restore from the virgin .tgz
# No changes needed below. ################################################################################################
if entryId == 'H2_2Ca_64_100' or entryId == '2fwu':
useLeuList = (('A', 589), ('A', 596), ('A', 618))
# elif entryId == '1brv':
# useLeuList = (('A', 180),('A', 185),)
# elif entryId == '2loj': # Commented out will lead to automatic detection.
# useLeuList = (('A', 50),('A', 61),)
# end if
nTmessage("Starting %s" % getCallerName())
nTmessage("entryId %s" % entryId)
nTmessage("modelCount %s" % modelCount)
nTmessage("doCcpn %s" % doCcpn)
nTmessage("threshold %s" % threshold)
nTmessage("deasHB %s" % deasHB)
nTmessage("dihrCHI2 %s" % dihrCHI2)
nTmessage("useAll %s" % useAll)
nTmessage("useLeuList %s" % str(useLeuList))
nTmessage("doPrepCingProject %s" % doPrepCingProject)
nTmessage("doRunRotateLeucines %s" % doRunRotateLeucines)
# project with rotated leucines (created with RotateLeucines).
entry2Id = entryId + '_' + ROTL_STR
# NO CHANGES NEEDED BELOW THIS LINE.
if doCcpn:
nTmessage("Creating project from CCPN first.")
if doPrepCingProject:
project = Project.open(entryId, status='new')
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
project.initCcpn(ccpnFolder=ccpnFile, modelCount=modelCount)
project.close()
del project
do_cmd('tar -czf %s.cing.tgz %s.cing' % (entryId, entryId))
# end if
inputCingArchiveDir = cingDirTmpTest # cwd.is input dir.
else:
inputCingArchiveDir = os.path.join(cingDirTestsData, "cing")
# end if
# Create a copy of the original cing project locally
# Then duplicate the project to a cing project that has rotated leucines.
# It will also close and GC the large objects for efficiency.
if doRunRotateLeucines:
status = runRotateLeucines(cingDirTmpTest,
inputCingArchiveDir,
entryId,
useAll=useAll,
useLeuList=useLeuList)
self.assertFalse(status)
# end if
# Restore the 2 projects. The first project will be modified based on the info in the second project.
proj1 = Project.open(
entryId,
status='old') # NB Will prefer a restore from the virgin .tgz
proj2 = Project.open(entry2Id, status='old')
self.assertTrue(proj1 and proj2)
project = proj1
#### BLOCK BEGIN repeated in rotateLeucines
if not useAll and useLeuList:
leuList = project.decodeResidueList(useLeuList)
if not leuList:
nTerror('Failed to decodeResidueList')
return True
# end if
else:
leuList = selectBadLeucineList(project,
CV_THRESHOLD_SELECTION,
useAll=useAll)
# end if
if leuList == None:
nTerror('Failed to selectBadLeucineList')
return True
# end if
#### BLOCK BEGIN
status = alterRestraintsForLeus(leuList, proj1, proj2, threshold,
deasHB, dihrCHI2)
self.assertTrue(status)
proj1.save()
def mainCasd(entryId, *extraArgList):
"""inputDir may be a directory or a url. A url needs to start with http://.
"""
fastestTest = False # default: False
# ranges=AUTO_STR # default is None retrieved from DBMS csv files.
htmlOnly = False # default: False but enable it for faster runs without some actual data.
doWhatif = True # disables whatif actual run
doProcheck = True
doWattos = True
doTalos = True
# doStoreCheck = True # DEFAULT: True Requires sqlAlchemy
doStoreCheck = False # DEFAULT: True Requires sqlAlchemy
tgzCing = True # default: True # Create a tgz for the cing project. In case of a CING project input it will be overwritten.
modelCount = None # default setting is None
if fastestTest:
modelCount = 3
htmlOnly = True
doWhatif = False
doProcheck = False
doWattos = False
doTalos = False
fORCE_REDO = True
fORCE_RETRIEVE_INPUT = False
nTmessage(header)
nTmessage(getStartMessage())
expectedArgumentList = [ 'inputDir', 'outputDir', 'pdbConvention', 'restraintsConvention', 'archiveType', 'projectType' ]
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
entryCodeChar2and3 = entryId[1:3]
inputDir = extraArgList[0]
outputDir = os.path.join(extraArgList[1], DATA_STR, entryCodeChar2and3, entryId)
pdbConvention = extraArgList[2] #@UnusedVariable
restraintsConvention = extraArgList[3]
archiveType = extraArgList[4]
projectType = extraArgList[5]
if archiveType == ARCHIVE_TYPE_FLAT:
pass
# default
elif archiveType == ARCHIVE_TYPE_BY_ENTRY:
inputDir = os.path.join(inputDir, entryId)
elif archiveType == ARCHIVE_TYPE_BY_CH23:
inputDir = os.path.join(inputDir, entryCodeChar2and3)
elif archiveType == ARCHIVE_TYPE_BY_CH23_BY_ENTRY:
inputDir = os.path.join(inputDir, entryCodeChar2and3, entryId)
ranges = CasdScripts.getRangesForEntry(entryId)
nTdebug("Using:")
nTdebug("inputDir: %s" % inputDir)
nTdebug("outputDir: %s" % outputDir)
nTdebug("pdbConvention: %s" % pdbConvention)
nTdebug("restraintsConvention: %s" % restraintsConvention)
nTdebug("archiveType: %s" % archiveType)
nTdebug("projectType: %s" % projectType)
nTdebug("modelCount: %s" % modelCount)
nTdebug("ranges: %s" % ranges)
# presume the directory still needs to be created.
cingEntryDir = entryId + ".cing"
if os.path.isdir(cingEntryDir):
if fORCE_REDO:
nTmessage("Enforcing a redo")
rmtree(cingEntryDir)
else:
mainIndexFile = os.path.join(cingEntryDir, "index.html")
isDone = os.path.isfile(mainIndexFile)
if isDone:
nTmessage("SKIPPING ENTRY ALREADY DONE")
return
nTmessage("REDOING BECAUSE VALIDATION CONSIDERED NOT DONE.")
rmtree(cingEntryDir)
# end if.
# end if.
os.chdir(outputDir)
project = Project(entryId)
if project.removeFromDisk():
nTerror("Failed to remove existing project (if present)")
return True
# end if.
# extension = '.tgz'
formatFileName = '%s.tgz'
# fileNameTgz = entryId + '.tgz'
if projectType == PROJECT_TYPE_CING:
# fileNameTgz = entryId + '.cing.tgz'
formatFileName = '%s.cing.tgz'
elif projectType == PROJECT_TYPE_PDB:
formatFileName = 'pdb%s.ent.gz'
fileNameTgz = formatFileName % entryId
# nTdebug("fileNameTgz: %s" % fileNameTgz)
# if true will do retrieveTgzFromUrl.
if inputDir.startswith("http") or inputDir.startswith("file"):
stillToRetrieve = False
if os.path.exists(fileNameTgz):
if fORCE_RETRIEVE_INPUT:
os.unlink(fileNameTgz)
stillToRetrieve = True
# end if
else:
stillToRetrieve = True
# end if
if stillToRetrieve:
retrieveTgzFromUrl(entryId, inputDir, archiveType=archiveType, formatFileName=formatFileName)
# end if
if not os.path.exists(fileNameTgz):
nTerror("Tgz should already have been present skipping entry")
return
# end if
# end if.
# retrieveTgzFromUrl(entryId, inputDir)
if projectType == PROJECT_TYPE_CING:
# Needs to be copied because the open method doesn't take a directory argument..
fullFileNameTgz = os.path.join(inputDir, fileNameTgz)
shutil.copy(fullFileNameTgz, '.')
project = Project.open(entryId, status='old')
if not project:
nTerror("Failed to init old project")
return True
elif projectType == PROJECT_TYPE_CCPN:
project = Project.open(entryId, status='new')
if not project.initCcpn(ccpnFolder=fileNameTgz, modelCount=modelCount):
#nmrCalcName='CING'):
#nmrCalcName='CASD-NMR'):
nTerror("Failed to init project from ccpn")
return True
# Temporary debug
# project.saveCcpn(os.path.join('/home/rf118/tmpdata/',entryId))
elif projectType == PROJECT_TYPE_PDB:
project = Project.open(entryId, status='new')
# pdbFileFormats = [ entryId + ".pdb", "pdb" + entryId + ".ent.gz" ]
# for pdbFileName in pdbFileFormats:
# pdbFileName = "pdb" + entryId + ".ent.gz"
# # pdbFilePath = os.path.join( inputDir, pdbFileName)
# pdbFilePath = os.path.join(inputDir, pdbFileName)
# if os.path.exists(pdbFilePath):
# break
# tmpPdbFile = None
# if pdbFileName.endswith('.gz'):
pdbFilePath = entryId + ".pdb"
# tmpPdbFile = pdbFilePath
# if os.path.exists(pdbFilePath):
# os.unlink(pdbFilePath)
gunzip(fileNameTgz, outputFileName=pdbFilePath, removeOriginal=True)
project.initPDB(pdbFile=pdbFilePath, convention=IUPAC, nmodels=modelCount)
# if tmpPdbFile:
if True:
nTdebug("Removing tmp: %s" % pdbFilePath)
os.unlink(pdbFilePath)
# if inputDirOrg == inputDirCASD_NMR:
# if True: # Default is False for this is specific to CASD-NMR
# nTmessage("Renaming molecule name to entry id: %s" % entryId)
# project.molecule.name = entryId # insufficient since all data is already initialized to disk.
# project.updateProject()
# project.molecule.rename( entryId )
# project.save()
# project.molecule.ranges = ranges # JFD: this doesn't seem to be set there exactly.
# nTdebug("mainCasd: Molecule starts with ranges %s" % project.molecule.ranges)
project.molecule.superpose(ranges=ranges)
if True:
if project.validate(htmlOnly=htmlOnly, ranges=ranges, doProcheck=doProcheck, doWhatif=doWhatif,
doWattos=doWattos, doTalos=doTalos):
nTerror("Failed to validate project read")
return True
# if True:
# project.runRpf(
# doAlised=DEFAULT_CONSIDER_ALIASED_POSITIONS,
# distThreshold=DEFAULT_DISTANCE_THRESHOLD,
# prochiralExclusion=DEFAULT_PROCHIRAL_EXCLUSION_SHIFT,
# diagonalExclusion=DEFAULT_DIAGONAL_EXCLUSION_SHIFT
# )
if doStoreCheck:
if doStoreCING2db( entryId, ARCHIVE_CASD_ID, project=project):
nTerror("Failed to store CING project's data to DB but continuing.")
project.save()
if projectType == PROJECT_TYPE_CCPN:
# fileNameTgz = entryId + '.tgz'
# os.unlink(fileNameTgz) # temporary ccpn tgz
# pass
rmdir(entryId) # temporary ccpn dir
if tgzCing:
directoryNameCing = entryId + ".cing"
tgzFileNameCing = directoryNameCing + ".tgz"
if os.path.exists(tgzFileNameCing):
nTwarning("Overwriting: " + tgzFileNameCing)
cmd = "tar -czf %s %s" % (tgzFileNameCing, directoryNameCing)
do_cmd(cmd)
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()
def mainCasd(entryId, *extraArgList):
"""inputDir may be a directory or a url. A url needs to start with http://.
"""
fastestTest = False # default: False
# ranges=AUTO_STR # default is None retrieved from DBMS csv files.
htmlOnly = False # default: False but enable it for faster runs without some actual data.
doWhatif = True # disables whatif actual run
doProcheck = True
doWattos = True
doTalos = True
# doStoreCheck = True # DEFAULT: True Requires sqlAlchemy
doStoreCheck = False # DEFAULT: True Requires sqlAlchemy
tgzCing = True # default: True # Create a tgz for the cing project. In case of a CING project input it will be overwritten.
modelCount = None # default setting is None
if fastestTest:
modelCount = 3
htmlOnly = True
doWhatif = False
doProcheck = False
doWattos = False
doTalos = False
fORCE_REDO = True
fORCE_RETRIEVE_INPUT = False
nTmessage(header)
nTmessage(getStartMessage())
expectedArgumentList = [
'inputDir', 'outputDir', 'pdbConvention', 'restraintsConvention',
'archiveType', 'projectType'
]
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
entryCodeChar2and3 = entryId[1:3]
inputDir = extraArgList[0]
outputDir = os.path.join(extraArgList[1], DATA_STR, entryCodeChar2and3,
entryId)
pdbConvention = extraArgList[2] #@UnusedVariable
restraintsConvention = extraArgList[3]
archiveType = extraArgList[4]
projectType = extraArgList[5]
if archiveType == ARCHIVE_TYPE_FLAT:
pass
# default
elif archiveType == ARCHIVE_TYPE_BY_ENTRY:
inputDir = os.path.join(inputDir, entryId)
elif archiveType == ARCHIVE_TYPE_BY_CH23:
inputDir = os.path.join(inputDir, entryCodeChar2and3)
elif archiveType == ARCHIVE_TYPE_BY_CH23_BY_ENTRY:
inputDir = os.path.join(inputDir, entryCodeChar2and3, entryId)
ranges = CasdScripts.getRangesForEntry(entryId)
nTdebug("Using:")
nTdebug("inputDir: %s" % inputDir)
nTdebug("outputDir: %s" % outputDir)
nTdebug("pdbConvention: %s" % pdbConvention)
nTdebug("restraintsConvention: %s" % restraintsConvention)
nTdebug("archiveType: %s" % archiveType)
nTdebug("projectType: %s" % projectType)
nTdebug("modelCount: %s" % modelCount)
nTdebug("ranges: %s" % ranges)
# presume the directory still needs to be created.
cingEntryDir = entryId + ".cing"
if os.path.isdir(cingEntryDir):
if fORCE_REDO:
nTmessage("Enforcing a redo")
rmtree(cingEntryDir)
else:
mainIndexFile = os.path.join(cingEntryDir, "index.html")
isDone = os.path.isfile(mainIndexFile)
if isDone:
nTmessage("SKIPPING ENTRY ALREADY DONE")
return
nTmessage("REDOING BECAUSE VALIDATION CONSIDERED NOT DONE.")
rmtree(cingEntryDir)
# end if.
# end if.
os.chdir(outputDir)
project = Project(entryId)
if project.removeFromDisk():
nTerror("Failed to remove existing project (if present)")
return True
# end if.
# extension = '.tgz'
formatFileName = '%s.tgz'
# fileNameTgz = entryId + '.tgz'
if projectType == PROJECT_TYPE_CING:
# fileNameTgz = entryId + '.cing.tgz'
formatFileName = '%s.cing.tgz'
elif projectType == PROJECT_TYPE_PDB:
formatFileName = 'pdb%s.ent.gz'
fileNameTgz = formatFileName % entryId
# nTdebug("fileNameTgz: %s" % fileNameTgz)
# if true will do retrieveTgzFromUrl.
if inputDir.startswith("http") or inputDir.startswith("file"):
stillToRetrieve = False
if os.path.exists(fileNameTgz):
if fORCE_RETRIEVE_INPUT:
os.unlink(fileNameTgz)
stillToRetrieve = True
# end if
else:
stillToRetrieve = True
# end if
if stillToRetrieve:
retrieveTgzFromUrl(entryId,
inputDir,
archiveType=archiveType,
formatFileName=formatFileName)
# end if
if not os.path.exists(fileNameTgz):
nTerror("Tgz should already have been present skipping entry")
return
# end if
# end if.
# retrieveTgzFromUrl(entryId, inputDir)
if projectType == PROJECT_TYPE_CING:
# Needs to be copied because the open method doesn't take a directory argument..
fullFileNameTgz = os.path.join(inputDir, fileNameTgz)
shutil.copy(fullFileNameTgz, '.')
project = Project.open(entryId, status='old')
if not project:
nTerror("Failed to init old project")
return True
elif projectType == PROJECT_TYPE_CCPN:
project = Project.open(entryId, status='new')
if not project.initCcpn(ccpnFolder=fileNameTgz, modelCount=modelCount):
#nmrCalcName='CING'):
#nmrCalcName='CASD-NMR'):
nTerror("Failed to init project from ccpn")
return True
# Temporary debug
# project.saveCcpn(os.path.join('/home/rf118/tmpdata/',entryId))
elif projectType == PROJECT_TYPE_PDB:
project = Project.open(entryId, status='new')
# pdbFileFormats = [ entryId + ".pdb", "pdb" + entryId + ".ent.gz" ]
# for pdbFileName in pdbFileFormats:
# pdbFileName = "pdb" + entryId + ".ent.gz"
# # pdbFilePath = os.path.join( inputDir, pdbFileName)
# pdbFilePath = os.path.join(inputDir, pdbFileName)
# if os.path.exists(pdbFilePath):
# break
# tmpPdbFile = None
# if pdbFileName.endswith('.gz'):
pdbFilePath = entryId + ".pdb"
# tmpPdbFile = pdbFilePath
# if os.path.exists(pdbFilePath):
# os.unlink(pdbFilePath)
gunzip(fileNameTgz, outputFileName=pdbFilePath, removeOriginal=True)
project.initPDB(pdbFile=pdbFilePath,
convention=IUPAC,
nmodels=modelCount)
# if tmpPdbFile:
if True:
nTdebug("Removing tmp: %s" % pdbFilePath)
os.unlink(pdbFilePath)
# if inputDirOrg == inputDirCASD_NMR:
# if True: # Default is False for this is specific to CASD-NMR
# nTmessage("Renaming molecule name to entry id: %s" % entryId)
# project.molecule.name = entryId # insufficient since all data is already initialized to disk.
# project.updateProject()
# project.molecule.rename( entryId )
# project.save()
# project.molecule.ranges = ranges # JFD: this doesn't seem to be set there exactly.
# nTdebug("mainCasd: Molecule starts with ranges %s" % project.molecule.ranges)
project.molecule.superpose(ranges=ranges)
if True:
if project.validate(htmlOnly=htmlOnly,
ranges=ranges,
doProcheck=doProcheck,
doWhatif=doWhatif,
doWattos=doWattos,
doTalos=doTalos):
nTerror("Failed to validate project read")
return True
# if True:
# project.runRpf(
# doAlised=DEFAULT_CONSIDER_ALIASED_POSITIONS,
# distThreshold=DEFAULT_DISTANCE_THRESHOLD,
# prochiralExclusion=DEFAULT_PROCHIRAL_EXCLUSION_SHIFT,
# diagonalExclusion=DEFAULT_DIAGONAL_EXCLUSION_SHIFT
# )
if doStoreCheck:
if doStoreCING2db(entryId, ARCHIVE_CASD_ID, project=project):
nTerror(
"Failed to store CING project's data to DB but continuing.")
project.save()
if projectType == PROJECT_TYPE_CCPN:
# fileNameTgz = entryId + '.tgz'
# os.unlink(fileNameTgz) # temporary ccpn tgz
# pass
rmdir(entryId) # temporary ccpn dir
if tgzCing:
directoryNameCing = entryId + ".cing"
tgzFileNameCing = directoryNameCing + ".tgz"
if os.path.exists(tgzFileNameCing):
nTwarning("Overwriting: " + tgzFileNameCing)
cmd = "tar -czf %s %s" % (tgzFileNameCing, directoryNameCing)
do_cmd(cmd)
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 _test_CombineRestraints(self):
'''
This unit test is by default disabled because we haven't figured out yet how to disable the output from
Yasara yet.
Input is a CING project from the test data.
'''
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest), msg=
"Failed to change to test directory for files: " + cingDirTmpTest)
# Original project
# entryId = 'H2_2Ca_64_100'
_basicStats = """
pdb e.res_count b.deposition_date c.name r.number r.name a1.name a2.name
csd chi1_avg chi2_avg chi1_cv chi2_cv
1brv 32 1996-03-29 A 180 LEU CD1 CD2 0.0 270.3 170.5 0.000 0.000 no SSA delta
1brv 32 1996-03-29 A 183 LEU CD1 CD2 2.3 285.2 180.6 0.000 0.000 no SSA delta
1brv 32 1996-03-29 A 185 LEU CD1 CD2 0.4 313.5 172.1 0.054 0.045 no SSA delta/beta
2loj 63 2012-01-24 A 20 LEU CD1 CD2 1.3 302.2 178.2 0.002 0.001
2loj 63 2012-01-24 A 33 LEU CD1 CD2 -1.5 72.0 168.8 0.001 0.002
2loj 63 2012-01-24 A 34 LEU CD1 CD2 3.0 295.7 176.1 0.001 0.001
2loj <= 63 2012-01-24 A 50 LEU CD1 CD2 -2.2 184.2 283.6 0.002 0.001 chi2 > 240
2loj 63 2012-01-24 A 51 LEU CD1 CD2 -1.3 181.5 59.6 0.001 0.001
2loj 63 2012-01-24 A 59 LEU CD1 CD2 2.2 286.8 174.6 0.001 0.001
2loj 63 2012-01-24 A 60 LEU CD1 CD2 -0.3 203.4 66.6 0.049 0.002
2loj <= 63 2012-01-24 A 61 LEU CD1 CD2 -1.6 197.5 289.6 0.001 0.001 chi2 > 240 no SSA beta
2fwu 159 2006-02-03 A 526 LEU CD1 CD2 2.2 297.3 306.8 0.003 0.001 chi2 > 240
2fwu 159 2006-02-03 A 560 LEU CD1 CD2 1.8 293.8 173.6 0.002 0.001
2fwu 159 2006-02-03 A 589 LEU CD1 CD2 -1.1 205.0 301.3 0.001 0.000 chi2 > 240
2fwu 159 2006-02-03 A 596 LEU CD1 CD2 -0.5 220.3 318.1 0.002 0.002 chi2 > 240
2fwu 159 2006-02-03 A 642 LEU CD1 CD2 -4.1 178.5 70.9 0.001 0.000
"""
entryId = '2fwu'
# entryId = '1brv'
# entryId = '2loj'
# entryId = 'H2_2Ca_64_100'
modelCount = 20 # DEFAULT: 20 Not valid for starting from CING project.
doCcpn = True # Test entry starting from CCPN project e.g. from NRG-CING.
threshold = 0 # minimal violation, necessary to classify the restraints.
deasHB = True # first deassign all HBs in the specified leucines
dihrCHI2 = True # add a dihedral restraint on the leucines.
useAll = False # DEFAULT: False. use all leucines regardless of state
useLeuList = False # If useAll is False and useLeuList is False then the leucines will be automatically detected
doPrepCingProject = False # DEFAULT: True # NB If False this script will prefer a restore from the virgin .tgz
doRunRotateLeucines = False # DEFAULT: True # NB If False this script will prefer a restore from the virgin .tgz
# No changes needed below. ################################################################################################
if entryId == 'H2_2Ca_64_100' or entryId == '2fwu':
useLeuList = (('A', 589), ('A', 596), ('A', 618))
# elif entryId == '1brv':
# useLeuList = (('A', 180),('A', 185),)
# elif entryId == '2loj': # Commented out will lead to automatic detection.
# useLeuList = (('A', 50),('A', 61),)
# end if
nTmessage("Starting %s" % getCallerName())
nTmessage("entryId %s" % entryId )
nTmessage("modelCount %s" % modelCount )
nTmessage("doCcpn %s" % doCcpn )
nTmessage("threshold %s" % threshold )
nTmessage("deasHB %s" % deasHB )
nTmessage("dihrCHI2 %s" % dihrCHI2 )
nTmessage("useAll %s" % useAll )
nTmessage("useLeuList %s" % str(useLeuList))
nTmessage("doPrepCingProject %s" % doPrepCingProject )
nTmessage("doRunRotateLeucines %s" % doRunRotateLeucines)
# project with rotated leucines (created with RotateLeucines).
entry2Id = entryId + '_' + ROTL_STR
# NO CHANGES NEEDED BELOW THIS LINE.
if doCcpn:
nTmessage("Creating project from CCPN first.")
if doPrepCingProject:
project = Project.open(entryId, status='new')
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
project.initCcpn(ccpnFolder=ccpnFile, modelCount=modelCount)
project.close()
del project
do_cmd('tar -czf %s.cing.tgz %s.cing' % (entryId, entryId))
# end if
inputCingArchiveDir = cingDirTmpTest # cwd.is input dir.
else:
inputCingArchiveDir = os.path.join(cingDirTestsData, "cing")
# end if
# Create a copy of the original cing project locally
# Then duplicate the project to a cing project that has rotated leucines.
# It will also close and GC the large objects for efficiency.
if doRunRotateLeucines:
status = runRotateLeucines(cingDirTmpTest, inputCingArchiveDir, entryId, useAll=useAll, useLeuList=useLeuList)
self.assertFalse(status)
# end if
# Restore the 2 projects. The first project will be modified based on the info in the second project.
proj1 = Project.open(entryId, status='old') # NB Will prefer a restore from the virgin .tgz
proj2 = Project.open(entry2Id, status='old')
self.assertTrue(proj1 and proj2)
project = proj1
#### BLOCK BEGIN repeated in rotateLeucines
if not useAll and useLeuList:
leuList = project.decodeResidueList(useLeuList)
if not leuList:
nTerror('Failed to decodeResidueList')
return True
# end if
else:
leuList = selectBadLeucineList(project, CV_THRESHOLD_SELECTION, useAll=useAll)
# end if
if leuList == None:
nTerror('Failed to selectBadLeucineList')
return True
# end if
#### BLOCK BEGIN
status = alterRestraintsForLeus(leuList, proj1, proj2, threshold, deasHB, dihrCHI2)
self.assertTrue(status)
proj1.save()
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()
nTmessage("Removing existing file.")
else:
nTerror("Failed because found remote file: %s" % remoteFile)
sys.exit(1)
tarring = ExecuteProgram('tar', rootPath=localDir, redirectOutputToFile = remoteFile)
tar_cmd = '-cpBf - %s.vmwarevm | gzip --fast' % vmName
nTmessage("Running tar with options: %s" % tar_cmd)
if tarring( tar_cmd ):
nTerror("Failed to run tar with options: " + tar_cmd)
sys.exit(1)
if doLink:
local_cmd = "'cd %s/%s; ln -f %s %s'" % ( dDir, VCsecret, fileName, dstFile )
if workLocally:
if do_cmd(local_cmd):
nTerror("Failed to link locally: " + local_cmd)
sys.exit(1)
else:
sshing = ExecuteProgram('ssh', redirectOutput = False)
ssh_cmd = ' [email protected] %s' % local_cmd
nTmessage("Running ssh with options: %s" % ssh_cmd)
if sshing( ssh_cmd ):
nTerror("Failed to run ssh with options: " + ssh_cmd)
sys.exit(1)
else:
nTmessage("No linking done yet, do manually.")