def doYasaraRewritePdb(entryCode):
"""Called from ipython"""
os.chdir(cingDirTmp)
inputDir = os.path.join(cingDirTestsData, "cyana")
pdbFileName = os.path.join(inputDir, entryCode, entryCode + '_org.pdb')
localPdbFileName = entryCode + "_org.pdb"
copy(pdbFileName, localPdbFileName)
yasara.info.mode = 'txt'
yasara.Console('off')
nTmessage('Using Yasara on %s' % entryCode)
# Read all models.
# obj = yasara.LoadPDB(localPdbFileName, center = 'No', correct = 'No', model=1)
obj = yasara.LoadPDB(localPdbFileName, center='No', correct='No')
# yasara.CleanAll() # needed for OptHydObj
# yasara.OptHydObj(obj,method='Yasara')
# yasara.AddHydObj(obj)
os.unlink(localPdbFileName)
newPdbFileName = entryCode + ".pdb"
# newPdbFileName = localPdbFileName
yasara.SavePDB(obj, newPdbFileName, format='IUPAC', transform='No')
yasara.Clear()
def copyFromCasp2CcpnArchive():
inputDir = '/Users/jd/CASP-NMR-CING/caspNmrDbDivided'
os.chdir(inputDir)
for entryCode in entryList:
# for entryCode in entryList[0:1]:
ch23 = entryCode[1:3]
for city in predList:
# for city in cityList[0:1]:
entryCodeNew = entryCode + city
nTmessage("Working on: %s" % entryCodeNew)
inputEntryDir = os.path.join(inputDir, ch23, entryCodeNew)
outputEntryDir = os.path.join(dataDir, ch23, entryCodeNew)
inputAuthorDir = os.path.join(outputEntryDir, 'Author')
outputNijmegenDir = os.path.join(outputEntryDir, 'Nijmegen')
if not os.path.exists(inputAuthorDir):
mkdirs(inputAuthorDir)
if not os.path.exists(outputNijmegenDir):
mkdirs(outputNijmegenDir)
# prevent junk
patternList = "*.pdb *.upl *.aco *.tbl".split()
fnList = globMultiplePatterns(inputEntryDir, patternList)
for fn in fnList:
orgFn = os.path.join(inputEntryDir, fn)
# nTmessage("Copying from %s" % fn)
# fnBaseName = os.path.basename(fn)
dstFn = os.path.join(inputAuthorDir, fn)
nTmessage("Copying from %s to %s" % (orgFn, dstFn))
copy(orgFn, dstFn)
def retrieveTgzFromUrl(entryId,
url,
archiveType=ARCHIVE_TYPE_FLAT,
formatFileName='%s.tgz'): # pylint: disable=W0613
"""Retrieves tgz file from url to current working dir assuming the
source is named: $url/$x/$x.tgz
Will skip the download if it's already present.
Returns True on failure or None on success.
"""
# fileNameTgz = entryId + extension
fileNameTgz = formatFileName % entryId
if os.path.exists(fileNameTgz):
nTmessage("Tgz already present, skipping download")
return
# nTdebug("fileNameTgz: %s" % fileNameTgz)
pathInsert = ''
# TODO: check
# Commented out the next lines for NRG-CING but not certain this will work for all uses of this script.
# if archiveType == ARCHIVE_TYPE_BY_ENTRY:
# pathInsert = '/%s' % entryId
# if archiveType == ARCHIVE_TYPE_BY_CH23_BY_ENTRY:
## entryCodeChar2and3 = entryId[1:3]
# pathInsert = '/%s/%s' % (entryCodeChar2and3, entryId)
if url.startswith('file://'):
pathSource = url.replace('file://', '')
fullPathSource = "%s%s/%s" % (pathSource, pathInsert, fileNameTgz)
nTmessage("copying file: %s to: %s" % (fullPathSource, fileNameTgz))
if not os.path.exists(fullPathSource):
nTerror("%s does not exist." % (fullPathSource))
return True
if not os.path.isfile(fullPathSource):
nTerror("%s is not a file" % (fullPathSource))
return True
if os.path.exists(fileNameTgz):
nTmessage('Removing old copy: %s' % fileNameTgz)
os.unlink(fileNameTgz)
copy(fullPathSource, fileNameTgz)
elif url.startswith('http://'):
urlNameTgz = "%s%s/%s" % (url, pathInsert, fileNameTgz)
nTmessage("downloading url: %s to: %s" % (urlNameTgz, fileNameTgz))
urllib.urlretrieve(urlNameTgz, fileNameTgz)
elif url.startswith('ssh://'):
urlNameTgz = "%s%s/%s" % (url, pathInsert, fileNameTgz)
nTmessage("Retrieving by ssh: %s to: %s" % (urlNameTgz, fileNameTgz))
if getFileBySsh(urlNameTgz, fileNameTgz, ntriesMax=2):
nTerror("Giving up ")
else:
nTerror("url has to start with http:/ or file:/ but was: %s" % (url))
return True
if os.path.exists(fileNameTgz):
return
nTerror("Failed to download: " + urlNameTgz)
return True
def copyFromCasp2CcpnArchive():
inputDir = '/Users/jd/CASP-NMR-CING/caspNmrDbDivided'
os.chdir(inputDir)
for entryCode in entryList:
# for entryCode in entryList[0:1]:
ch23 = entryCode[1:3]
for city in predList:
# for city in cityList[0:1]:
entryCodeNew = entryCode + city
nTmessage("Working on: %s" % entryCodeNew)
inputEntryDir = os.path.join(inputDir, ch23, entryCodeNew)
outputEntryDir = os.path.join(dataDir, ch23, entryCodeNew)
inputAuthorDir = os.path.join(outputEntryDir, 'Author')
outputNijmegenDir = os.path.join(outputEntryDir, 'Nijmegen')
if not os.path.exists(inputAuthorDir):
mkdirs(inputAuthorDir)
if not os.path.exists(outputNijmegenDir):
mkdirs(outputNijmegenDir)
# prevent junk
patternList = "*.pdb *.upl *.aco *.tbl".split()
fnList = globMultiplePatterns(inputEntryDir, patternList)
for fn in fnList:
orgFn = os.path.join(inputEntryDir, fn)
# nTmessage("Copying from %s" % fn)
# fnBaseName = os.path.basename(fn)
dstFn = os.path.join(inputAuthorDir, fn)
nTmessage("Copying from %s to %s" % (orgFn, dstFn))
copy(orgFn, dstFn)
def export2gif(molecule, pathMolGif, project = None):
"""Return True on error but will still put a default image in."""
check_type(molecule, 'Molecule')
check_string(pathMolGif)
if project:
check_type(project, 'Project')
# nTdebug("Now in cing.Plugincode.molgrap#export2gif")
m = Molgrap(project = project)
m.run(molecule, pathMolGif)
failed = False
if not os.path.exists(pathMolGif):
failed = True
src = os.path.join( cingPythonCingDir, 'PluginCode', DATA_STR, 'UnknownImage.gif' )
# if os.path.exists(pathMolGif): # disable when done testing.
# os.unlink(pathMolGif)
nTmessage("copying default image from %s to %s" % (src, pathMolGif))
# os.link(src, pathMolGif) # us a real copy JFD: fails between 2 filesystems
disk.copy(src, pathMolGif) # us a real copy
# os.symlink(src, pathMolGif) # funny, the extension on mac fails to show up for this file only; other extensions are shown ok...
# end if
pathMolGifPinup = pathMolGif[:-4] + '_pin.gif'
if convertImageMagick(pathMolGif, pathMolGifPinup, options='-geometry 114x80'):
nTerror("convertImageMagick failed for: " + pathMolGifPinup)
# end if
if failed:
return True
return None
def doYasaraRewritePdb( entryCode ):
"""Called from ipython"""
os.chdir(cingDirTmp)
inputDir = os.path.join(cingDirTestsData, "cyana" )
pdbFileName = os.path.join(inputDir, entryCode, entryCode+'_org.pdb')
localPdbFileName = entryCode+"_org.pdb"
copy(pdbFileName, localPdbFileName)
yasara.info.mode = 'txt'
yasara.Console('off')
nTmessage('Using Yasara on %s' % entryCode)
# Read all models.
# obj = yasara.LoadPDB(localPdbFileName, center = 'No', correct = 'No', model=1)
obj = yasara.LoadPDB(localPdbFileName, center = 'No', correct = 'No')
# yasara.CleanAll() # needed for OptHydObj
# yasara.OptHydObj(obj,method='Yasara')
# yasara.AddHydObj(obj)
os.unlink(localPdbFileName)
newPdbFileName = entryCode+".pdb"
# newPdbFileName = localPdbFileName
yasara.SavePDB(obj,newPdbFileName,format='IUPAC', transform='No')
yasara.Clear()
def retrieveTgzFromUrl(entryId, url, archiveType=ARCHIVE_TYPE_FLAT, formatFileName='%s.tgz'): # pylint: disable=W0613
"""Retrieves tgz file from url to current working dir assuming the
source is named: $url/$x/$x.tgz
Will skip the download if it's already present.
Returns True on failure or None on success.
"""
# fileNameTgz = entryId + extension
fileNameTgz = formatFileName % entryId
if os.path.exists(fileNameTgz):
nTmessage("Tgz already present, skipping download")
return
# nTdebug("fileNameTgz: %s" % fileNameTgz)
pathInsert = ''
# TODO: check
# Commented out the next lines for NRG-CING but not certain this will work for all uses of this script.
# if archiveType == ARCHIVE_TYPE_BY_ENTRY:
# pathInsert = '/%s' % entryId
# if archiveType == ARCHIVE_TYPE_BY_CH23_BY_ENTRY:
## entryCodeChar2and3 = entryId[1:3]
# pathInsert = '/%s/%s' % (entryCodeChar2and3, entryId)
if url.startswith('file://'):
pathSource = url.replace('file://', '')
fullPathSource = "%s%s/%s" % (pathSource, pathInsert, fileNameTgz)
nTmessage("copying file: %s to: %s" % (fullPathSource, fileNameTgz))
if not os.path.exists(fullPathSource):
nTerror("%s does not exist." % (fullPathSource))
return True
if not os.path.isfile(fullPathSource):
nTerror("%s is not a file" % (fullPathSource))
return True
if os.path.exists(fileNameTgz):
nTmessage('Removing old copy: %s' % fileNameTgz)
os.unlink(fileNameTgz)
copy(fullPathSource, fileNameTgz)
elif url.startswith('http://'):
urlNameTgz = "%s%s/%s" % (url, pathInsert, fileNameTgz)
nTmessage("downloading url: %s to: %s" % (urlNameTgz, fileNameTgz))
urllib.urlretrieve(urlNameTgz, fileNameTgz)
elif url.startswith('ssh://'):
urlNameTgz = "%s%s/%s" % (url, pathInsert, fileNameTgz)
nTmessage("Retrieving by ssh: %s to: %s" % (urlNameTgz, fileNameTgz))
if getFileBySsh(urlNameTgz, fileNameTgz, ntriesMax = 2):
nTerror( "Giving up ")
else:
nTerror("url has to start with http:/ or file:/ but was: %s" % (url))
return True
if os.path.exists(fileNameTgz):
return
nTerror("Failed to download: " + urlNameTgz)
return True
def copyFromCasdNmr2CcpnArchive():
#inputDir = '/Users/jd/CASD-NMR-CING/casdNmrDbDivided'
programHoH = convertToProgram(participationTable)
os.chdir(inputDir)
for entryCode in entryList:
# for entryCode in entryList[0:1]:
ch23 = entryCode[1:3]
for city in cityList:
# for city in cityList[0:1]:
entryCodeNew = entryCode + city
programId = getDeepByKeys(programHoH, entryCode, city)
if not (city == 'Test' or programId):
# nTdebug("Skipping %s" % entryCodeNew)
continue
# else:
# nTdebug("Looking at %s" % entryCodeNew)
# continue # TODO disable premature stop.
nTmessage("Working on: %s" % entryCodeNew)
inputEntryDir = os.path.join(inputDir, ch23, entryCodeNew)
outputEntryDir = os.path.join(dataDir, ch23, entryCodeNew)
inputAuthorDir = os.path.join(outputEntryDir, 'Author')
outputNijmegenDir = os.path.join(outputEntryDir, 'Nijmegen')
if not os.path.exists(inputAuthorDir):
mkdirs(inputAuthorDir)
if not os.path.exists(outputNijmegenDir):
mkdirs(outputNijmegenDir)
# prevent junk
patternList = "*.pdb *.upl *.aco *.tbl".split()
fnList = globMultiplePatterns(inputEntryDir, patternList)
for fn in fnList:
orgFn = os.path.join(inputEntryDir, fn)
# nTmessage("Copying from %s" % fn)
# fnBaseName = os.path.basename(fn)
dstFn = os.path.join(inputAuthorDir, fn)
nTmessage("Copying from %s to %s" % (orgFn, dstFn))
copy(orgFn, dstFn)
def copyFromCasdNmr2CcpnArchive():
#inputDir = '/Users/jd/CASD-NMR-CING/casdNmrDbDivided'
programHoH = convertToProgram(participationTable)
os.chdir(inputDir)
for entryCode in entryList:
# for entryCode in entryList[0:1]:
ch23 = entryCode[1:3]
for city in cityList:
# for city in cityList[0:1]:
entryCodeNew = entryCode + city
programId = getDeepByKeys(programHoH, entryCode, city)
if not (city == 'Test' or programId):
# nTdebug("Skipping %s" % entryCodeNew)
continue
# else:
# nTdebug("Looking at %s" % entryCodeNew)
# continue # TODO disable premature stop.
nTmessage("Working on: %s" % entryCodeNew)
inputEntryDir = os.path.join(inputDir, ch23, entryCodeNew)
outputEntryDir = os.path.join(dataDir, ch23, entryCodeNew)
inputAuthorDir = os.path.join(outputEntryDir, 'Author')
outputNijmegenDir = os.path.join(outputEntryDir, 'Nijmegen')
if not os.path.exists(inputAuthorDir):
mkdirs(inputAuthorDir)
if not os.path.exists(outputNijmegenDir):
mkdirs(outputNijmegenDir)
# prevent junk
patternList = "*.pdb *.upl *.aco *.tbl".split()
fnList = globMultiplePatterns(inputEntryDir, patternList)
for fn in fnList:
orgFn = os.path.join(inputEntryDir, fn)
# nTmessage("Copying from %s" % fn)
# fnBaseName = os.path.basename(fn)
dstFn = os.path.join(inputAuthorDir, fn)
nTmessage("Copying from %s to %s" % (orgFn, dstFn))
copy(orgFn, dstFn)
def run(self, ranges=None, export = True, createPlots=True, runAqua=True):
"""
Run procheck analysis.
Ranges: GWV 25 Sep 2008: does work ok, using modified script to only implement for tplot call
Return True on error (None on success; Python default)
"""
#
if self.molecule.modelCount == 0:
nTwarning('Procheck run: no models for "%s"', self.molecule)
return
# It's actually important not to write any to Procheck then because
# there might be more than 200 stretches which upsets PC.
nTmessage('==> Running procheck_nmr')
useRanges = self.molecule.useRanges(ranges)
if useRanges:
self.ranges = ranges
# nTdebug("pc.ranges: %s" % self.ranges)
# Convert the ranges and translate into procheck format
selectedResidues = self.molecule.setResiduesFromRanges(ranges)
if selectedResidues == None:
nTerror( 'In procheck.run selectedResidues None for ranges: %s' % ranges)
return True
rangesTxtPlugin = self.rangesForPlugin(ranges)
if rangesTxtPlugin == None:
nTerror('Procheck.run: Failed to get rangesTxtPlugin for ranges: [%s]' % ranges)
return True
writeTextToFile(os.path.join(self.rootPath, self.rangesFileName), rangesTxtPlugin)
#end if
#copy script
source = os.path.join(cingPythonCingDir, 'PluginCode', DATA_STR, self.procheckScript)
destination = os.path.join(self.rootPath, self.procheckScript)
try:
copy(source, destination)
except:
nTerror('Procheck.run: Failed to copy (by exception) "%s"', source)
return True
# Copy parameter file
pcNmrParameterFileOrg = 'procheck_nmr.prm'
if not createPlots:
pcNmrParameterFileOrg = 'procheck_nmr_nada.prm'
pcNmrParameterFile = os.path.join(cingPythonCingDir, 'PluginCode', DATA_STR, pcNmrParameterFileOrg)
pcNmrParameterFileDestination = os.path.join(self.rootPath, 'procheck_nmr.prm')
if os.path.exists(pcNmrParameterFileDestination):
# nTdebug("Removing existing pcNmrParameterFileDestination:"+ pcNmrParameterFileDestination)
os.unlink(pcNmrParameterFileDestination)
# nTdebug("Copying "+pcNmrParameterFile+" to: " + pcNmrParameterFileDestination)
try: # Don't allow this to mess up CING.1
if copy(pcNmrParameterFile, pcNmrParameterFileDestination):
# if os.link(pcNmrParameterFile, pcNmrParameterFileDestination): # don't use link in python for this.
nTerror("Procheck.run: Failed to copy from " +pcNmrParameterFile+" to: " + pcNmrParameterFileDestination)
return True
except:
nTerror("Procheck.run: Failed to copy (by exception) from " +pcNmrParameterFile+" to: " + pcNmrParameterFileDestination)
return True
max_models = self.getMaxModelCount()
path = os.path.join(self.rootPath, self.molecule.name + '.pdb')
if export:
self.molecule.toPDB(path, convention=AQUA, max_models = max_models)
# self.molecule.toPDBfile(path, convention=AQUA) #GV removed because not implemented in toPDBfile; 12 Jan 09 Try-again
# Can't use IUPAC here because aqua doesn't understand difference between
# G and DG.(oxy/deoxy).
canAqpc = True
if cingPaths.aqpc == None or cingPaths.aqpc == PLEASE_ADD_EXECUTABLE_HERE:
nTmessage("No aqpc installed so skipping this step")
canAqpc = False
if canAqpc:
# Save restraints for Aqua
if self.project.export2aqua():
canAqpc = False
nTwarning("Failed to export restraints to Aqua; will run pc without restraints")
else:
hasRestraints = False
for extensionRestraintFile in [ "noe", "tor" ]:
srcDir = os.path.join(self.project.rootPath(self.project.name)[0], self.project.directories.aqua )
if not os.path.exists(srcDir):
nTcodeerror("Aqua export dir is absent")
return True
fileName = self.project.name +'.' + extensionRestraintFile
path = os.path.join(srcDir, fileName )
if not os.path.exists(path):
# nTdebug("No "+ path+" file found (in Aqua export dir)")
pass
else:
# Map from Aqua per project file to Cing per molecule file.
dstFileName = self.molecule.name + '.' + extensionRestraintFile
dstPath = os.path.join( self.rootPath, dstFileName )
if os.path.exists(dstPath):
# nTdebug("Removing existing copy: " + dstPath)
os.unlink(dstPath)
# nTdebug("Trying to copy from: " + path+" to: "+dstPath)
# if os.link(path, dstPath):# don't use link in python for this.
if disk.copy(path, dstPath):# don't use link in python for this.
nTcodeerror("Failed to copy from: " + path+" to: "+self.rootPath)
return True
hasRestraints = True
# run aqpc
if not canAqpc:
nTwarning("Skipping aqpc because failed to convert restraints to Aqua")
elif not hasRestraints:
pass
# nTdebug("Skipping aqpc because no Aqua restraints were copied for Aqua")
else:
# nTdebug("Trying aqpc")
if self.aqpc( '-r6sum 1 ' + self.molecule.name + '.pdb'):
nTcodeerror("Failed to run aqpc; please consult the log file aqpc.log etc. in the molecules procheck directory.")
return True
else:
nTmessage("==> Finished aqpc successfully")
# nTdebug("Trying procheck_nmr")
cmd = self.molecule.name +'.pdb'
if useRanges:
cmd += ' ' + self.rangesFileName
if self.procheck(cmd):
nTerror('Failed to run procheck_nmr successfully; please consult the log file (.log, .out0 etc). in the "%s" directory.',
self.rootPath)
return True
if self.parseResult():
nTerror('Failed to procheck_nmr parseResult.')
return False
# Remove temp files in case the run was successful and parsed ok.
removeTempFiles(self.rootPath)
# Store in project file that we ran procheck successfully
self.project.procheckStatus.completed = True
if useRanges:
self.project.procheckStatus.ranges = ranges
else:
self.project.procheckStatus.ranges = None
nTmessage("==> Finished procheck_nmr successfully")
return True
def doSetup(config, project, basePath, options):
"""Generate the directory setup and parameter.py file from project and basePath
Export the data from project.
Return parameters or None on error.
"""
nTmessage("\n-- doSetup --")
if os.path.exists(basePath):
removedir(basePath)
#end if
xplor = Xplor(config, basePath=basePath, project=project
) # generates the directories and initialize parameter setup
# Set some defaults
optionNameList = 'modelsAnneal models bestModels'.split()
modelCount = project.molecule.modelCount
modelsStr = '0'
if modelCount != 1:
modelsStr += '-%d' % (modelCount - 1)
for optionName in optionNameList: # DEFAULT: number of molecules in current project
xplor[optionName] = modelsStr
setParametersFromOptions(
project, options,
xplor) # Do here for the first time and every time refine is called.
# copy xplor parameter and topology files
for fname in os.listdir(os.path.join(xplor.refinePath, 'toppar')):
if not fnmatch(fname, '.*'):
# print '>>',fname
copy(os.path.join(xplor.refinePath, 'toppar', fname),
xplor.joinPath(xplor.directories.toppar, fname))
#print ">>", xplor
# restore the data
# project.restore() # JFD: why ? I get doubling of restraint lists by this.
nTmessage(project.format())
if project.molecule == None:
nTerror('doSetup: No molecule defined for project %s\n', project)
return
#end if
project.validateRestraints(toFile=True)
if xplor.superpose and len(xplor.superpose) > 0:
project.molecule.superpose(ranges=xplor.superpose)
# export the data
# nTmessage('\n' + dots * 10)
nTmessage('==> Exporting %s to %s for refinement', project, basePath)
for drl in project.distances:
if drl.status == 'keep':
drl.renameToXplorCompatible()
xplor.noeRestraints.append(refineNoeParameters(drl.name))
fname = xplor.joinPath(xplor.directories.tables, drl.name + '.tbl')
drl.export2xplor(fname)
#end if
#end for
for drl in project.dihedrals:
if ((drl.name == TALOSPLUS_LIST_STR) & (drl.status != 'noRefine')):
drl.status = 'noRefine'
#end if
if drl.status == 'keep':
drl.renameToXplorCompatible()
xplor.dihedralRestraints.append(refineDihedralParameters(drl.name))
fname = xplor.joinPath(xplor.directories.tables, drl.name + '.tbl')
drl.export2xplor(fname)
#end if
#end for
# export structures in Xplor-PDB format
xplor.baseName = project.molecule.name + '_%03d.pdb'
# Only used for psf generation:
xplor.baseNameByChain = project.molecule.name + '_%s_%03d.pdb'
pathByChain = xplor.joinPath(xplor.directories.converted,
xplor.baseNameByChain)
nTmessage('==> -A- Exporting first model of %s to XPLOR PDB-files (%s)',
project.molecule, pathByChain)
project.molecule.export2xplor(pathByChain,
chainName=ALL_CHAINS_STR,
model=0)
path = xplor.joinPath(xplor.directories.converted, xplor.baseName)
nTmessage('==> -B- Exporting all models of %s to XPLOR PDB-files (%s)',
project.molecule, path)
project.molecule.export2xplor(path)
# PSF file
xplor.psfFile = project.molecule.name + '.psf'
# Set the patches for the psf file
for res in project.molecule.residuesWithProperties('HIS'):
xplor.patchHISD.append((res.chain.name, res.resNum))
for res in project.molecule.residuesWithProperties('HISE'):
xplor.patchHISE.append((res.chain.name, res.resNum))
for res in project.molecule.residuesWithProperties('cPRO'):
xplor.patchCISP.append((res.chain.name, res.resNum))
disulfide_bridges = project.molecule.idDisulfides(toFile=False,
applyBonds=False)
if disulfide_bridges == True:
nTerror("Failed to analyze disulfide bridges.")
elif disulfide_bridges:
nTmessage("==> Located disulfide bridges %s" % str(disulfide_bridges))
for (res1, res2) in disulfide_bridges:
xplor.patchDISU.append(
((res1.chain.name, res1.resNum), (res2.chain.name, res2.resNum)))
parfile = xplor.joinPath(PARAMETERS_FILE_NAME)
xplor.toFile(parfile)
nTmessage("==> Saved the parameter file %s" % parfile)
# nTmessage('\n==> Generated setup under "%s"\nEdit "%s" before continuing\n', basePath, parfile ) # Not in all setups relevant.
return xplor
def run(self, ranges=None, export=True, createPlots=True, runAqua=True):
"""
Run procheck analysis.
Ranges: GWV 25 Sep 2008: does work ok, using modified script to only implement for tplot call
Return True on error (None on success; Python default)
"""
#
if self.molecule.modelCount == 0:
nTwarning('Procheck run: no models for "%s"', self.molecule)
return
# It's actually important not to write any to Procheck then because
# there might be more than 200 stretches which upsets PC.
nTmessage('==> Running procheck_nmr')
useRanges = self.molecule.useRanges(ranges)
if useRanges:
self.ranges = ranges
# nTdebug("pc.ranges: %s" % self.ranges)
# Convert the ranges and translate into procheck format
selectedResidues = self.molecule.setResiduesFromRanges(ranges)
if selectedResidues == None:
nTerror(
'In procheck.run selectedResidues None for ranges: %s' %
ranges)
return True
rangesTxtPlugin = self.rangesForPlugin(ranges)
if rangesTxtPlugin == None:
nTerror(
'Procheck.run: Failed to get rangesTxtPlugin for ranges: [%s]'
% ranges)
return True
writeTextToFile(os.path.join(self.rootPath, self.rangesFileName),
rangesTxtPlugin)
#end if
#copy script
source = os.path.join(cingPythonCingDir, 'PluginCode', DATA_STR,
self.procheckScript)
destination = os.path.join(self.rootPath, self.procheckScript)
try:
copy(source, destination)
except:
nTerror('Procheck.run: Failed to copy (by exception) "%s"', source)
return True
# Copy parameter file
pcNmrParameterFileOrg = 'procheck_nmr.prm'
if not createPlots:
pcNmrParameterFileOrg = 'procheck_nmr_nada.prm'
pcNmrParameterFile = os.path.join(cingPythonCingDir, 'PluginCode',
DATA_STR, pcNmrParameterFileOrg)
pcNmrParameterFileDestination = os.path.join(self.rootPath,
'procheck_nmr.prm')
if os.path.exists(pcNmrParameterFileDestination):
# nTdebug("Removing existing pcNmrParameterFileDestination:"+ pcNmrParameterFileDestination)
os.unlink(pcNmrParameterFileDestination)
# nTdebug("Copying "+pcNmrParameterFile+" to: " + pcNmrParameterFileDestination)
try: # Don't allow this to mess up CING.1
if copy(pcNmrParameterFile, pcNmrParameterFileDestination):
# if os.link(pcNmrParameterFile, pcNmrParameterFileDestination): # don't use link in python for this.
nTerror("Procheck.run: Failed to copy from " +
pcNmrParameterFile + " to: " +
pcNmrParameterFileDestination)
return True
except:
nTerror("Procheck.run: Failed to copy (by exception) from " +
pcNmrParameterFile + " to: " +
pcNmrParameterFileDestination)
return True
max_models = self.getMaxModelCount()
path = os.path.join(self.rootPath, self.molecule.name + '.pdb')
if export:
self.molecule.toPDB(path, convention=AQUA, max_models=max_models)
# self.molecule.toPDBfile(path, convention=AQUA) #GV removed because not implemented in toPDBfile; 12 Jan 09 Try-again
# Can't use IUPAC here because aqua doesn't understand difference between
# G and DG.(oxy/deoxy).
canAqpc = True
if cingPaths.aqpc == None or cingPaths.aqpc == PLEASE_ADD_EXECUTABLE_HERE:
nTmessage("No aqpc installed so skipping this step")
canAqpc = False
if canAqpc:
# Save restraints for Aqua
if self.project.export2aqua():
canAqpc = False
nTwarning(
"Failed to export restraints to Aqua; will run pc without restraints"
)
else:
hasRestraints = False
for extensionRestraintFile in ["noe", "tor"]:
srcDir = os.path.join(
self.project.rootPath(self.project.name)[0],
self.project.directories.aqua)
if not os.path.exists(srcDir):
nTcodeerror("Aqua export dir is absent")
return True
fileName = self.project.name + '.' + extensionRestraintFile
path = os.path.join(srcDir, fileName)
if not os.path.exists(path):
# nTdebug("No "+ path+" file found (in Aqua export dir)")
pass
else:
# Map from Aqua per project file to Cing per molecule file.
dstFileName = self.molecule.name + '.' + extensionRestraintFile
dstPath = os.path.join(self.rootPath, dstFileName)
if os.path.exists(dstPath):
# nTdebug("Removing existing copy: " + dstPath)
os.unlink(dstPath)
# nTdebug("Trying to copy from: " + path+" to: "+dstPath)
# if os.link(path, dstPath):# don't use link in python for this.
if disk.copy(
path,
dstPath): # don't use link in python for this.
nTcodeerror("Failed to copy from: " + path +
" to: " + self.rootPath)
return True
hasRestraints = True
# run aqpc
if not canAqpc:
nTwarning(
"Skipping aqpc because failed to convert restraints to Aqua"
)
elif not hasRestraints:
pass
# nTdebug("Skipping aqpc because no Aqua restraints were copied for Aqua")
else:
# nTdebug("Trying aqpc")
if self.aqpc('-r6sum 1 ' + self.molecule.name + '.pdb'):
nTcodeerror(
"Failed to run aqpc; please consult the log file aqpc.log etc. in the molecules procheck directory."
)
return True
else:
nTmessage("==> Finished aqpc successfully")
# nTdebug("Trying procheck_nmr")
cmd = self.molecule.name + '.pdb'
if useRanges:
cmd += ' ' + self.rangesFileName
if self.procheck(cmd):
nTerror(
'Failed to run procheck_nmr successfully; please consult the log file (.log, .out0 etc). in the "%s" directory.',
self.rootPath)
return True
if self.parseResult():
nTerror('Failed to procheck_nmr parseResult.')
return False
# Remove temp files in case the run was successful and parsed ok.
removeTempFiles(self.rootPath)
# Store in project file that we ran procheck successfully
self.project.procheckStatus.completed = True
if useRanges:
self.project.procheckStatus.ranges = ranges
else:
self.project.procheckStatus.ranges = None
nTmessage("==> Finished procheck_nmr successfully")
return True
def doSetup(config, project, basePath, options):
"""Generate the directory setup and parameter.py file from project and basePath
Export the data from project.
Return parameters or None on error.
"""
nTmessage("\n-- doSetup --")
if os.path.exists(basePath):
removedir(basePath)
#end if
xplor = Xplor(config, basePath=basePath, project=project) # generates the directories and initialize parameter setup
# Set some defaults
optionNameList = 'modelsAnneal models bestModels'.split()
modelCount = project.molecule.modelCount
modelsStr = '0'
if modelCount != 1:
modelsStr += '-%d' % (modelCount-1)
for optionName in optionNameList: # DEFAULT: number of molecules in current project
xplor[ optionName ] = modelsStr
setParametersFromOptions(project, options, xplor) # Do here for the first time and every time refine is called.
# copy xplor parameter and topology files
for fname in os.listdir(os.path.join(xplor.refinePath, 'toppar')):
if not fnmatch(fname, '.*'):
# print '>>',fname
copy(os.path.join(xplor.refinePath, 'toppar', fname), xplor.joinPath(xplor.directories.toppar, fname))
#print ">>", xplor
# restore the data
# project.restore() # JFD: why ? I get doubling of restraint lists by this.
nTmessage(project.format())
if project.molecule == None:
nTerror('doSetup: No molecule defined for project %s\n', project)
return
#end if
project.validateRestraints(toFile=True)
if xplor.superpose and len(xplor.superpose) > 0:
project.molecule.superpose(ranges=xplor.superpose)
# export the data
# nTmessage('\n' + dots * 10)
nTmessage('==> Exporting %s to %s for refinement', project, basePath)
for drl in project.distances:
if drl.status == 'keep':
drl.renameToXplorCompatible()
xplor.noeRestraints.append(refineNoeParameters(drl.name))
fname = xplor.joinPath(xplor.directories.tables, drl.name + '.tbl')
drl.export2xplor(fname)
#end if
#end for
for drl in project.dihedrals:
if ((drl.name == TALOSPLUS_LIST_STR) & (drl.status != 'noRefine')) :
drl.status = 'noRefine'
#end if
if drl.status == 'keep':
drl.renameToXplorCompatible()
xplor.dihedralRestraints.append(refineDihedralParameters(drl.name))
fname = xplor.joinPath(xplor.directories.tables, drl.name + '.tbl')
drl.export2xplor(fname)
#end if
#end for
# export structures in Xplor-PDB format
xplor.baseName = project.molecule.name + '_%03d.pdb'
# Only used for psf generation:
xplor.baseNameByChain = project.molecule.name + '_%s_%03d.pdb'
pathByChain = xplor.joinPath(xplor.directories.converted, xplor.baseNameByChain)
nTmessage('==> -A- Exporting first model of %s to XPLOR PDB-files (%s)', project.molecule, pathByChain)
project.molecule.export2xplor(pathByChain, chainName = ALL_CHAINS_STR, model = 0)
path = xplor.joinPath(xplor.directories.converted, xplor.baseName)
nTmessage('==> -B- Exporting all models of %s to XPLOR PDB-files (%s)', project.molecule, path)
project.molecule.export2xplor(path)
# PSF file
xplor.psfFile = project.molecule.name + '.psf'
# Set the patches for the psf file
for res in project.molecule.residuesWithProperties('HIS'):
xplor.patchHISD.append((res.chain.name, res.resNum))
for res in project.molecule.residuesWithProperties('HISE'):
xplor.patchHISE.append((res.chain.name, res.resNum))
for res in project.molecule.residuesWithProperties('cPRO'):
xplor.patchCISP.append((res.chain.name, res.resNum))
disulfide_bridges = project.molecule.idDisulfides(toFile=False, applyBonds=False)
if disulfide_bridges == True:
nTerror("Failed to analyze disulfide bridges.")
elif disulfide_bridges:
nTmessage("==> Located disulfide bridges %s" % str(disulfide_bridges))
for (res1, res2) in disulfide_bridges:
xplor.patchDISU.append( ((res1.chain.name, res1.resNum),
(res2.chain.name, res2.resNum)))
parfile = xplor.joinPath(PARAMETERS_FILE_NAME)
xplor.toFile(parfile)
nTmessage("==> Saved the parameter file %s" % parfile)
# nTmessage('\n==> Generated setup under "%s"\nEdit "%s" before continuing\n', basePath, parfile ) # Not in all setups relevant.
return xplor
