def printSequenceFromPdbFile(fn):
verbosityOriginal = cing.verbosity
cing.verbosity = cing.verbosityError
entryId = 'getSequenceFromPdbFile'
project = Project(entryId)
project.removeFromDisk()
project = Project.open(entryId, status='new')
project.initPDB(pdbFile=fn, convention=IUPAC)
fastaString = ''
for res in project.molecule.allResidues():
# db doesn't always exist.
fastaString += getDeepByKeysOrDefault(res, defaultPrintChainCode, 'db',
'shortName')
cing.verbosity = verbosityOriginal
nTmessage("Sequence from PDB file:")
nTmessage(fastaString)
for res in project.molecule.allResidues():
nTmessageNoEOL(res.shortName)
nTmessage('')
cing.verbosity = cing.verbosityError
project.removeFromDisk()
del project
cing.verbosity = verbosityOriginal
def test_pdb(self):
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
entryId = "1brv" # Small much studied PDB NMR entry
# entryId = "tightTurn_IIb"
# entryId = "1hy8" # small, single model, very low scoring entry
pdbDirectory = os.path.join(cingDirTestsData,"pdb", entryId)
pdbFileName = "pdb"+entryId+".ent"
pdbFilePath = os.path.join( pdbDirectory, pdbFileName)
# does it matter to import it just now?
project = Project( entryId )
self.failIf( project.removeFromDisk())
project = Project.open( entryId, status='new' )
project.initPDB( pdbFile=pdbFilePath, convention = IUPAC )
m = project.molecule
ranges = 'A.173-178'
nTdebug("m: %s" % m)
self.assertTrue( m.toPDB('m001.pdb', model=0, ranges=ranges, convention='XPLOR'))
# nTdebug("Manual reimport")
# m.initCoordinates()
# m.importFromPDB('m001.pdb',convention='XPLOR')
nTdebug("Reimport 1")
m.replaceCoordinatesByPdb(pdbFilePath, name = entryId+'_reimport', convention=IUPAC)
# nTdebug("Reimport 2")
# m.replaceCoordinatesByPdb(pdbFilePath, name = entryId+'_reimport', useModels = "1", convention=IUPAC)
self.assertFalse(project.mkMacros())
def test_pdb(self):
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
entryId = "1brv" # Small much studied PDB NMR entry
# entryId = "tightTurn_IIb"
# entryId = "1hy8" # small, single model, very low scoring entry
pdbDirectory = os.path.join(cingDirTestsData,"pdb", entryId)
pdbFileName = "pdb"+entryId+".ent"
pdbFilePath = os.path.join( pdbDirectory, pdbFileName)
# does it matter to import it just now?
project = Project( entryId )
self.failIf( project.removeFromDisk())
project = Project.open( entryId, status='new' )
project.initPDB( pdbFile=pdbFilePath, convention = IUPAC )
m = project.molecule
ranges = 'A.173-178'
nTdebug("m: %s" % m)
self.assertTrue( m.toPDB('m001.pdb', model=0, ranges=ranges, convention='XPLOR'))
# nTdebug("Manual reimport")
# m.initCoordinates()
# m.importFromPDB('m001.pdb',convention='XPLOR')
nTdebug("Reimport 1")
m.replaceCoordinatesByPdb(pdbFilePath, name = entryId+'_reimport', convention=IUPAC)
# nTdebug("Reimport 2")
# m.replaceCoordinatesByPdb(pdbFilePath, name = entryId+'_reimport', useModels = "1", convention=IUPAC)
self.assertFalse(project.mkMacros())
def testPdbFile(self):
nTwarning(
"This test case will take about 5 (+3 for 1v0e) minutes and is recommended to be done before major releases."
)
# entryId = "1ai0" # Most complex molecular system in any PDB NMR entry
# entryId = "1brv" # Small much studied PDB NMR entry
# entryId = "2hgh_1model"
# entryList = "1kr8".split()
# entryList = "1otz".split() # 61 chains of which one is ' '
# entryList = "1v0e".split()
# entryList = "1a4d 1a24 1afp 1ai0 1brv 1bus 1cjg 1hue 1ieh 1iv6 1kr8 1otz 2hgh 2k0e".split()
entryList = "1a4d 1ai0 1brv 1bus 1hue 1iv6 1kr8".split()
for entryId in entryList:
pdbDirectory = os.path.join(cingDirTestsData, "pdb", entryId)
pdbFileName = "pdb" + entryId + ".ent"
pdbFilePath = os.path.join(pdbDirectory, pdbFileName)
cingDirTmpTest = os.path.join(cingDirTmp, 'test2_pdb')
mkdirs(cingDirTmpTest)
os.chdir(cingDirTmpTest)
# does it matter to import it just now?
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
self.assertTrue(
project.initPDB(pdbFile=pdbFilePath,
convention=IUPAC,
allowNonStandardResidue=True))
self.assertTrue(project.save())
def testPdbFile(self):
nTwarning("This test case will take about 5 (+3 for 1v0e) minutes and is recommended to be done before major releases.")
# entryId = "1ai0" # Most complex molecular system in any PDB NMR entry
# entryId = "1brv" # Small much studied PDB NMR entry
# entryId = "2hgh_1model"
# entryList = "1kr8".split()
# entryList = "1otz".split() # 61 chains of which one is ' '
# entryList = "1v0e".split()
# entryList = "1a4d 1a24 1afp 1ai0 1brv 1bus 1cjg 1hue 1ieh 1iv6 1kr8 1otz 2hgh 2k0e".split()
entryList = "1a4d 1ai0 1brv 1bus 1hue 1iv6 1kr8".split()
for entryId in entryList:
pdbDirectory = os.path.join(cingDirTestsData,"pdb", entryId)
pdbFileName = "pdb"+entryId+".ent"
pdbFilePath = os.path.join( pdbDirectory, pdbFileName)
cingDirTmpTest = os.path.join( cingDirTmp, 'test2_pdb' )
mkdirs( cingDirTmpTest )
os.chdir(cingDirTmpTest)
# does it matter to import it just now?
project = Project( entryId )
self.failIf( project.removeFromDisk())
project = Project.open( entryId, status='new' )
self.assertTrue( project.initPDB( pdbFile=pdbFilePath, convention=IUPAC, allowNonStandardResidue=True ))
self.assertTrue( project.save() )
def test_xplor_nih(self):
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
entryId = "gb1"
pdbDirectory = os.path.join(cingDirTestsData,"xplor", entryId)
pdbFileName = entryId+".pdb"
pdbFilePath = os.path.join( pdbDirectory, pdbFileName)
project = Project( entryId )
self.failIf( project.removeFromDisk())
project = Project.open( entryId, status='new' )
project.initPDB( pdbFile=pdbFilePath, convention = XPLOR )
# project.validate(ranges, parseOnly, htmlOnly, doProcheck, doWhatif, doWattos, doTalos)
project.validate(htmlOnly=True, doProcheck=False, doWhatif=False, doWattos=False, doTalos=False)
project.save()
def test_superpose(self):
pdbConvention = IUPAC
entryId = "1brv"
# entryId = "2vb1_simple" # Protein solved by X-ray.
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
pdbDirectory = os.path.join(cingDirTestsData,"pdb", entryId)
pdbFileName = "pdb" + entryId + ".ent"
pdbFilePath = os.path.join( pdbDirectory, pdbFileName)
self.failIf( not os.path.exists(pdbFilePath), msg= "Failed to find file: "+pdbFilePath)
# does it matter to import it just now?
project = Project( entryId )
self.failIf( project.removeFromDisk())
project = Project.open( entryId, status='new' )
project.initPDB( pdbFile=pdbFilePath, convention = pdbConvention )
# Compare with molmol on 1brv's 48 models:
# mean global bb RMSD: 0.98 +/- 0.40 A ( 0.10.. 2.19 A)
# mean global heavy RMSD: 1.75 +/- 0.51 A ( 0.54.. 3.33 A)
# Note that in molmol the backbone protein atoms are defined: N, CA, C
# CING used to include the carbonyl atom
# using default parameters.
ens = project.molecule.superpose(backboneOnly=True, includeProtons = False, iterations=2)
nTdebug( 'ens %s' % ens)
nTdebug( 'ens.averageModel %s' % ens.averageModel)
self.assertAlmostEquals( 0.7643199324863148, ens.averageModel.rmsd, 3 )
# Confirmed to be the 'averaage RMSD to mean: 0.698' in molmol using command
# Fit 'to_mean'.
ens = project.molecule.superpose(backboneOnly=False, includeProtons = False,
iterations=3) # no improvement to do 3 over the default 2 but left in for speed checking.
nTdebug( 'ens.averageModel %s' % ens.averageModel)
self.assertAlmostEquals( 0.99383582432002637, ens.averageModel.rmsd, 3 )
def test_superpose(self):
pdbConvention = IUPAC
entryId = "1brv"
# entryId = "2vb1_simple" # Protein solved by X-ray.
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
pdbDirectory = os.path.join(cingDirTestsData,"pdb", entryId)
pdbFileName = "pdb" + entryId + ".ent"
pdbFilePath = os.path.join( pdbDirectory, pdbFileName)
self.failIf( not os.path.exists(pdbFilePath), msg= "Failed to find file: "+pdbFilePath)
# does it matter to import it just now?
project = Project( entryId )
self.failIf( project.removeFromDisk())
project = Project.open( entryId, status='new' )
project.initPDB( pdbFile=pdbFilePath, convention = pdbConvention )
# Compare with molmol on 1brv's 48 models:
# mean global bb RMSD: 0.98 +/- 0.40 A ( 0.10.. 2.19 A)
# mean global heavy RMSD: 1.75 +/- 0.51 A ( 0.54.. 3.33 A)
# Note that in molmol the backbone protein atoms are defined: N, CA, C
# CING used to include the carbonyl atom
# using default parameters.
ens = project.molecule.superpose(backboneOnly=True, includeProtons = False, iterations=2)
nTdebug( 'ens %s' % ens)
nTdebug( 'ens.averageModel %s' % ens.averageModel)
self.assertAlmostEquals( 0.7643199324863148, ens.averageModel.rmsd, 3 )
# Confirmed to be the 'averaage RMSD to mean: 0.698' in molmol using command
# Fit 'to_mean'.
ens = project.molecule.superpose(backboneOnly=False, includeProtons = False,
iterations=3) # no improvement to do 3 over the default 2 but left in for speed checking.
nTdebug( 'ens.averageModel %s' % ens.averageModel)
self.assertAlmostEquals( 0.99383582432002637, ens.averageModel.rmsd, 3 )
def test_xplor_nih(self):
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
entryId = "gb1"
pdbDirectory = os.path.join(cingDirTestsData, "xplor", entryId)
pdbFileName = entryId + ".pdb"
pdbFilePath = os.path.join(pdbDirectory, pdbFileName)
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
project.initPDB(pdbFile=pdbFilePath, convention=XPLOR)
# project.validate(ranges, parseOnly, htmlOnly, doProcheck, doWhatif, doWattos, doTalos)
project.validate(htmlOnly=True,
doProcheck=False,
doWhatif=False,
doWattos=False,
doTalos=False)
project.save()
def printSequenceFromPdbFile(fn):
verbosityOriginal = cing.verbosity
cing.verbosity = cing.verbosityError
entryId = 'getSequenceFromPdbFile'
project = Project(entryId)
project.removeFromDisk()
project = Project.open(entryId, status='new')
project.initPDB(pdbFile=fn, convention=IUPAC)
fastaString = ''
for res in project.molecule.allResidues():
# db doesn't always exist.
fastaString += getDeepByKeysOrDefault(res, defaultPrintChainCode, 'db', 'shortName')
cing.verbosity = verbosityOriginal
nTmessage("Sequence from PDB file:")
nTmessage(fastaString)
for res in project.molecule.allResidues():
nTmessageNoEOL(res.shortName)
nTmessage('')
cing.verbosity = cing.verbosityError
project.removeFromDisk()
del project
cing.verbosity = verbosityOriginal
def plotDihedralD1D2():
dihedralName1 = 'Cb4N'
dihedralName2 = 'Cb4C'
graphicsFormat = "png"
entryId = "1brv" # Small much studied PDB NMR entry
# entryId = "1hy8" # small, single model, very low scoring entry
pdbDirectory = os.path.join(cingDirTestsData, "pdb", entryId)
pdbFileName = "pdb" + entryId + ".ent"
pdbFilePath = os.path.join(pdbDirectory, pdbFileName)
# does it matter to import it just now?
project = Project(entryId)
project.removeFromDisk()
project = Project.open(entryId, status='new')
project.initPDB(pdbFile=pdbFilePath, convention=IUPAC)
# ssType = 'E'
# resType = 'GLY'
# for ssType in histRamaBySsAndResType.keys():
# ssTypeForFileName = ssType.replace(' ', '_')
titleStr = 'd1d2 all resType'
nTmessage("plotting: %s" % titleStr)
# hist = histd1d2BySsAndResType[ssType][resType]
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (500, 500)
# residueName = resType + ""
x = NTlist(-45, -80, 125) # outside the range.
y = NTlist(-65, -63, -125)
# important to switch to temp space before starting to generate files for the project.
# project = Project('testPlotHistoDihedrald1d2')
plotparams1 = project.plotParameters.getdefault(dihedralName1,
'dihedralDefault')
plotparams2 = project.plotParameters.getdefault(dihedralName2,
'dihedralDefault')
x.limit(plotparams1.min, plotparams1.max)
y.limit(plotparams2.min, plotparams2.max)
plot = NTplot(title=titleStr,
xRange=(plotparams1.min, plotparams1.max),
xTicks=range(int(plotparams1.min), int(plotparams1.max + 1),
plotparams1.ticksize),
xLabel=dihedralName1,
yRange=(plotparams2.min, plotparams2.max),
yTicks=range(int(plotparams2.min), int(plotparams2.max + 1),
plotparams2.ticksize),
yLabel=dihedralName2)
ps.addPlot(plot)
# Plot a density background
histList = []
ssTypeList = hPlot.histd1BySs0.keys(
) # TODO: check this histd1BySs0 attribute. UNTESTED.
ssTypeList.sort() # in place sort to: space, H, S
for ssType in ssTypeList:
hist = getDeepByKeys(hPlot.histd1BySs0, ssType)
if hist != None:
nTdebug('appending [%s]' % ssType)
histList.append(hist)
if histList:
plot.dihedralComboPlot(histList)
# fn = os.path.join('bySsAndResType', ( ssTypeForFileName+"_"+resType+"."+graphicsFormat))
# fn = os.path.join('byResType', ( resType+"."+graphicsFormat))
fpGood = open(project.name + '.testCb2Good.out', 'w')
fpBad = open(project.name + '.testCb2Bad.out', 'w')
mCount = project.molecule.modelCount
for res in project.molecule.A.allResidues():
triplet = NTlist()
for i in [-1, 0, 1]:
triplet.append(res.sibling(i))
if None in triplet:
nTdebug('Skipping ' % res)
else:
ca_atms = triplet.zap('CA')
cb_atms = triplet.zap('CB')
nTdebug("%s %s %s %s" % (res, triplet, ca_atms, cb_atms))
if None in cb_atms: # skip Gly for now
nTdebug('Skipping %s' % res)
else:
d1 = Dihedral(res, 'Cb4N', range=[0.0, 360.0])
d1.atoms = [cb_atms[0], ca_atms[0], ca_atms[1], cb_atms[1]]
d1.calculateValues()
res['Cb4N'] = d1 # append dihedral to residue
d2 = Dihedral(res, 'Cb4C', range=[0.0, 360.0])
d2.atoms = [cb_atms[1], ca_atms[1], ca_atms[2], cb_atms[2]]
d2.calculateValues()
res['Cb4C'] = d2 # append dihedral to residue
bb = getDeepByKeys(res, WHATIF_STR, BBCCHK_STR, VALUE_LIST_STR,
0) # check first one.
if bb == None:
nTdebug('Skipping without BB %s' % res)
continue
if d1.cv < 0.03 and d2.cv < 0.03: # Only include structured residues
for i in range(mCount): # Consider each model individually
# bb = res.Whatif.bbNormality.valueList[i]
bb = getDeepByKeys(res, WHATIF_STR, BBCCHK_STR,
VALUE_LIST_STR, i)
if bb == None:
nTdebug('Skipping without BB %s' % res)
continue
angles = NTlist() # store phi, psi, chi1, chi2
for angle in ['PHI', 'PSI', 'CHI1', 'CHI2']:
if res.has_key(angle):
angles.append(res[angle][i])
else:
angles.append(0.0)
#end for
if bb < 20.0: # Arbitrary 20 bb occurences as cuttoff for now
fprintf(fpBad,
'%4d %7.2f %7.2f %7.2f %s %s %s\n',
res.resNum, d1[i], d2[i], bb,
angles.format("%7.2f "), res,
res.dssp.consensus)
else:
fprintf(fpGood,
'%4d %7.2f %7.2f %7.2f %s %s %s\n',
res.resNum, d1[i], d2[i], bb,
angles.format("%7.2f "), res,
res.dssp.consensus)
#end if
#end if
#end if
#end for
fpBad.close()
fpGood.close()
fn = "allRestype_d1d2." + graphicsFormat
ps.hardcopy(fn, graphicsFormat)
def main(entryId, *extraArgList):
"""inputDir may be a directory or a url. A url needs to start with http://.
"""
fastestTest = False # default: False
htmlOnly = False # default: False but enable it for faster runs without some actual data.
doWhatif = True # disables whatif actual run
doProcheck = True
doWattos = True
doQueeny = True
doTalos = True
tgzCing = True # default: True # Create a tgz for the cing project. In case of a CING project input it will be overwritten.
# NB leave this set to True or modify code below.
removeCcpnDirectory = 1 # perhaps not so in the future.
modelCount = None # default setting is None
# ranges = None
if fastestTest:
modelCount = 2 # if this is more and there is only one model present it leads to an error message.
htmlOnly = True
doWhatif = False
doProcheck = False
doWattos = False
doQueeny = False
doTalos = False
forceRedo = True
forceRetrieveInput = True
nTmessage(header)
nTmessage(getStartMessage())
# Sync below code with nrgCing#createToposTokens
expectedArgumentList = """
verbosity inputDir outputDir
pdbConvention restraintsConvention archiveType projectType
storeCING2db ranges filterTopViolations filterVasco
singleCoreOperation
""".split()
expectedNumberOfArguments = len(expectedArgumentList)
if len(extraArgList) != expectedNumberOfArguments:
nTmessage("consider updating code to include all sequential parameters: %s" % str(expectedArgumentList))
if len(extraArgList) > expectedNumberOfArguments:
nTerror("Got arguments: " + str(extraArgList))
nTerror("Failed to get expected number of arguments: %d got %d" % (
expectedNumberOfArguments, len(extraArgList)))
nTerror("Expected arguments: %s" % expectedArgumentList)
return True
# end if
# end if
entryCodeChar2and3 = entryId[1:3]
cing.verbosity = int( extraArgList[IDX_VERBOSITY] )
inputDir = extraArgList[IDX_INPUT]
outputDir = os.path.join(extraArgList[IDX_OUTPUT], DATA_STR, entryCodeChar2and3, entryId)
pdbConvention = extraArgList[IDX_PDB] #@UnusedVariable
restraintsConvention = extraArgList[IDX_RESTRAINTS]
archiveType = extraArgList[IDX_ARCHIVE] # Only used for deriving the input location not the output.
projectType = extraArgList[IDX_PROJECT_TYPE]
storeCING2db = stringMeansBooleanTrue( getDeepByKeysOrAttributes(extraArgList, IDX_STORE_DB))
ranges = getDeepByKeysOrAttributes(extraArgList, IDX_RANGES)
filterTopViolations = getDeepByKeysOrAttributes(extraArgList, IDX_FILTER_TOP)
if filterTopViolations:
filterTopViolations = int(filterTopViolations) # change '0' to 0
filterVasco = getDeepByKeysOrAttributes(extraArgList, IDX_FILTER_VASCO)
if filterVasco:
filterVasco = int(filterVasco)
else:
filterVasco = 1 # Default should be True
# end if
singleCoreOperation = getDeepByKeysOrAttributes(extraArgList, IDX_SINGLE_CORE_OPERATION )
if singleCoreOperation:
singleCoreOperation = int(singleCoreOperation)
else:
singleCoreOperation = 0 # Default should be True
# end if
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)
isRemoteOutputDir = False
if '@' in outputDir:
isRemoteOutputDir = True
# end if
# vc = vCing('.') # argument is a fake master_ssh_url not needed here.
archive_id = getArchiveIdFromDirectoryName( outputDir )
nTdebug("Using program arguments:")
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("storeCING2db: %s" % storeCING2db)
nTdebug("ranges: %s" % ranges)
nTdebug("filterTopViolations: %s" % filterTopViolations)
nTdebug("filterVasco: %s" % filterVasco)
nTdebug("singleCoreOperation: %s" % singleCoreOperation)
nTdebug("")
nTdebug("Using derived settings:")
nTdebug("modelCount: %s" % modelCount)
nTdebug("isRemoteOutputDir: %s" % isRemoteOutputDir)
nTdebug("archive_id: %s" % archive_id)
# For NMR_REDO required as most efficient.
if singleCoreOperation:
setToSingleCoreOperation()
# presume the directory still needs to be created.
cingEntryDir = entryId + ".cing"
if os.path.isdir(cingEntryDir):
if forceRedo:
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.
if isRemoteOutputDir:
os.chdir(cingDirTmp)
else:
os.chdir(outputDir)
project = Project(entryId)
if project.removeFromDisk():
nTerror("Failed to remove existing project (if present)")
return True
# end if.
formatFileName = '%s.tgz'
if projectType == PROJECT_TYPE_CING:
formatFileName = '%s.cing.tgz'
elif projectType == PROJECT_TYPE_PDB:
formatFileName = 'pdb%s.ent.gz'
fileNameTgz = formatFileName % entryId
# nTdebug("fileNameTgz: %s" % fileNameTgz)
allowedInputProtocolList = 'http file ssh'.split()
inputProtocal = string.split( inputDir, ':' )[0]
if inputProtocal in allowedInputProtocolList:
stillToRetrieve = False
if os.path.exists(fileNameTgz):
if forceRetrieveInput:
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
else:
nTdebug("Entry not retrieved which might be normal in some situations.")
# end if.
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):
nTerror("Failed to init project from ccpn")
return True
elif projectType == PROJECT_TYPE_PDB:
project = Project.open(entryId, status='new')
pdbFilePath = entryId + ".pdb"
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)
# end if
if ranges is not None:
project.molecule.setRanges(ranges)
# end if
if archive_id:
project.molecule.setArchiveId(archive_id)
# end if
project.molecule.superpose(ranges=ranges)
if filterTopViolations and not project.filterHighRestraintViol():
nTerror("Failed to filterHighRestraintViol")
####> MAIN UTILITY HERE
if 0: # DEFAULT 0
project.save()
if project.validate(htmlOnly=htmlOnly, ranges=ranges, doProcheck=doProcheck, doWhatif=doWhatif,
doWattos=doWattos, doQueeny = doQueeny, doTalos=doTalos, filterVasco = filterVasco ):
nTerror("Failed to validate project read")
return True
# end if filterVasco
# Write a single PDB file containing all models
# according to IUPAC conventions
project.export2PDB()
project.save()
if storeCING2db and archive_id:
# Does require:
#from cing.PluginCode.sqlAlchemy import csqlAlchemy
# and should never crash run.
# archive_id = ARCHIVE_DEV_NRG_ID
# if isProduction:
# archive_id = ARCHIVE_NRG_ID
try:
if doStoreCING2db( entryId, archive_id, project=project):
nTerror("Failed to store CING project's data to DB but continuing.")
except:
nTtracebackError()
nTerror("Failed to store CING project's data due to above traceback error.")
if projectType == PROJECT_TYPE_CCPN:
# fileNameTgz = entryId + '.tgz'
os.unlink(fileNameTgz) # temporary ccpn tgz
if removeCcpnDirectory:
rmdir(entryId) # ccpn dir may contain vasco info.
if tgzCing:
directoryNameCing = entryId + ".cing"
tgzFileNameCing = directoryNameCing + ".tgz"
if os.path.exists(tgzFileNameCing):
nTwarning("Overwriting: " + tgzFileNameCing)
cmd = "tar -czf %s %s" % (tgzFileNameCing, directoryNameCing)
nTdebug("cmd: %s" % cmd)
# do_cmd(cmd)
status, result = commands.getstatusoutput(cmd)
if status:
nTerror("Failed to tar status: %s with result %s" % (status, result))
return True
if isRemoteOutputDir:
if putFileBySsh(tgzFileNameCing, outputDir, ntriesMax = 2):
nTerror("Failed to send File By Scp status: %s with result %s" % (status, result))
nTerror("Maintaining results.")
return True
# end if
nTmessage("Removing tgz result: %s" % tgzFileNameCing)
os.remove(tgzFileNameCing)
nTmessage("Removing cing dir itself: %s" % directoryNameCing)
rmdir(directoryNameCing)
else: # do NOT remove local copy
pass
def main(entryId, *extraArgList):
"""inputDir may be a directory or a url. A url needs to start with http://.
"""
fastestTest = True # 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
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 = True
nTmessage(cing.cingDefinitions.getHeaderString())
nTmessage(cing.systemDefinitions.getStartMessage())
expectedArgumentList = [ 'inputDir', 'outputDir', 'pdbConvention', 'restraintsConvention', 'archiveType','projectType','storeCING2db']
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]
storeCING2db = False
if len(extraArgList) >= expectedNumberOfArguments:
storeCING2db = extraArgList[6]
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 = None
# targetId = getTargetForFullEntryName(entryId)
# if not targetId:
# nTerror("Failed to getTargetForFullEntryName for entryId: %s" % entryId)
# return True
# ranges = getRangesForTarget(targetId)
# if ranges == None:
# nTerror("Failed to getRangesForTarget for targetId: %s" % targetId)
# return True
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("storeCING2db: %s" % storeCING2db)
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):
nTerror("Failed to init project from ccpn")
return True
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.molecule.rename( entryId )
# project.save()
# project.molecule.ranges = ranges # JFD: this doesn't seem to be set there exactly.
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 storeCING2db:
# Does require:
#from cing.PluginCode.sqlAlchemy import csqlAlchemy
# and should never crash run.
try:
if doStoreCING2db( entryId, ARCHIVE_CASP_ID, project=project):
nTerror("Failed to store CING project's data to DB but continuing.")
except:
nTtracebackError()
nTerror("Failed to store CING project's data due to above traceback error.")
project.save()
if projectType == PROJECT_TYPE_CCPN:
# fileNameTgz = entryId + '.tgz'
# os.unlink(fileNameTgz) # temporary ccpn tgz
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 plotDihedralD1D2():
dihedralName1 = 'Cb4N'
dihedralName2 = 'Cb4C'
graphicsFormat = "png"
entryId = "1brv" # Small much studied PDB NMR entry
# entryId = "1hy8" # small, single model, very low scoring entry
pdbDirectory = os.path.join(cingDirTestsData, "pdb", entryId)
pdbFileName = "pdb" + entryId + ".ent"
pdbFilePath = os.path.join(pdbDirectory, pdbFileName)
# does it matter to import it just now?
project = Project(entryId)
project.removeFromDisk()
project = Project.open(entryId, status='new')
project.initPDB(pdbFile=pdbFilePath, convention=IUPAC)
# ssType = 'E'
# resType = 'GLY'
# for ssType in histRamaBySsAndResType.keys():
# ssTypeForFileName = ssType.replace(' ', '_')
titleStr = 'd1d2 all resType'
nTmessage("plotting: %s" % titleStr)
# hist = histd1d2BySsAndResType[ssType][resType]
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (500, 500)
# residueName = resType + ""
x = NTlist(-45, -80, 125) # outside the range.
y = NTlist(-65, -63, -125)
# important to switch to temp space before starting to generate files for the project.
# project = Project('testPlotHistoDihedrald1d2')
plotparams1 = project.plotParameters.getdefault(dihedralName1, 'dihedralDefault')
plotparams2 = project.plotParameters.getdefault(dihedralName2, 'dihedralDefault')
x.limit(plotparams1.min, plotparams1.max)
y.limit(plotparams2.min, plotparams2.max)
plot = NTplot(title=titleStr,
xRange=(plotparams1.min, plotparams1.max),
xTicks=range(int(plotparams1.min), int(plotparams1.max + 1), plotparams1.ticksize),
xLabel=dihedralName1,
yRange=(plotparams2.min, plotparams2.max),
yTicks=range(int(plotparams2.min), int(plotparams2.max + 1), plotparams2.ticksize),
yLabel=dihedralName2)
ps.addPlot(plot)
# Plot a density background
histList = []
ssTypeList = hPlot.histd1BySs0.keys() # TODO: check this histd1BySs0 attribute. UNTESTED.
ssTypeList.sort() # in place sort to: space, H, S
for ssType in ssTypeList:
hist = getDeepByKeys(hPlot.histd1BySs0, ssType)
if hist != None:
nTdebug('appending [%s]' % ssType)
histList.append(hist)
if histList:
plot.dihedralComboPlot(histList)
# fn = os.path.join('bySsAndResType', ( ssTypeForFileName+"_"+resType+"."+graphicsFormat))
# fn = os.path.join('byResType', ( resType+"."+graphicsFormat))
fpGood = open(project.name + '.testCb2Good.out', 'w')
fpBad = open(project.name + '.testCb2Bad.out', 'w')
mCount = project.molecule.modelCount
for res in project.molecule.A.allResidues():
triplet = NTlist()
for i in [-1, 0, 1]:
triplet.append(res.sibling(i))
if None in triplet:
nTdebug('Skipping ' % res)
else:
ca_atms = triplet.zap('CA')
cb_atms = triplet.zap('CB')
nTdebug("%s %s %s %s" % (res, triplet, ca_atms, cb_atms))
if None in cb_atms: # skip Gly for now
nTdebug('Skipping %s' % res)
else:
d1 = Dihedral(res, 'Cb4N', range=[0.0, 360.0])
d1.atoms = [cb_atms[0], ca_atms[0], ca_atms[1], cb_atms[1]]
d1.calculateValues()
res['Cb4N'] = d1 # append dihedral to residue
d2 = Dihedral(res, 'Cb4C', range=[0.0, 360.0])
d2.atoms = [cb_atms[1], ca_atms[1], ca_atms[2], cb_atms[2]]
d2.calculateValues()
res['Cb4C'] = d2 # append dihedral to residue
bb = getDeepByKeys(res, WHATIF_STR, BBCCHK_STR, VALUE_LIST_STR, 0) # check first one.
if bb == None:
nTdebug('Skipping without BB %s' % res)
continue
if d1.cv < 0.03 and d2.cv < 0.03: # Only include structured residues
for i in range(mCount): # Consider each model individually
# bb = res.Whatif.bbNormality.valueList[i]
bb = getDeepByKeys(res, WHATIF_STR, BBCCHK_STR, VALUE_LIST_STR, i)
if bb == None:
nTdebug('Skipping without BB %s' % res)
continue
angles = NTlist() # store phi, psi, chi1, chi2
for angle in ['PHI', 'PSI', 'CHI1', 'CHI2']:
if res.has_key(angle):
angles.append(res[angle][i])
else:
angles.append(0.0)
#end for
if bb < 20.0: # Arbitrary 20 bb occurences as cuttoff for now
fprintf(fpBad, '%4d %7.2f %7.2f %7.2f %s %s %s\n',
res.resNum, d1[i], d2[i], bb, angles.format("%7.2f "), res, res.dssp.consensus)
else:
fprintf(fpGood, '%4d %7.2f %7.2f %7.2f %s %s %s\n',
res.resNum, d1[i], d2[i], bb, angles.format("%7.2f "), res, res.dssp.consensus)
#end if
#end if
#end if
#end for
fpBad.close()
fpGood.close()
fn = "allRestype_d1d2." + graphicsFormat
ps.hardcopy(fn, graphicsFormat)
def main(entryId, *extraArgList):
"""inputDir may be a directory or a url. A url needs to start with http://.
"""
fastestTest = False # default: False
htmlOnly = False # default: False but enable it for faster runs without some actual data.
doWhatif = True # disables whatif actual run
doProcheck = True
doWattos = True
doQueeny = True
doTalos = True
tgzCing = True # default: True # Create a tgz for the cing project. In case of a CING project input it will be overwritten.
# NB leave this set to True or modify code below.
removeCcpnDirectory = 1 # perhaps not so in the future.
modelCount = None # default setting is None
# ranges = None
if fastestTest:
modelCount = 2 # if this is more and there is only one model present it leads to an error message.
htmlOnly = True
doWhatif = False
doProcheck = False
doWattos = False
doQueeny = False
doTalos = False
forceRedo = True
forceRetrieveInput = True
nTmessage(header)
nTmessage(getStartMessage())
# Sync below code with nrgCing#createToposTokens
expectedArgumentList = """
verbosity inputDir outputDir
pdbConvention restraintsConvention archiveType projectType
storeCING2db ranges filterTopViolations filterVasco
singleCoreOperation
""".split()
expectedNumberOfArguments = len(expectedArgumentList)
if len(extraArgList) != expectedNumberOfArguments:
nTmessage(
"consider updating code to include all sequential parameters: %s" %
str(expectedArgumentList))
if len(extraArgList) > expectedNumberOfArguments:
nTerror("Got arguments: " + str(extraArgList))
nTerror("Failed to get expected number of arguments: %d got %d" %
(expectedNumberOfArguments, len(extraArgList)))
nTerror("Expected arguments: %s" % expectedArgumentList)
return True
# end if
# end if
entryCodeChar2and3 = entryId[1:3]
cing.verbosity = int(extraArgList[IDX_VERBOSITY])
inputDir = extraArgList[IDX_INPUT]
outputDir = os.path.join(extraArgList[IDX_OUTPUT], DATA_STR,
entryCodeChar2and3, entryId)
pdbConvention = extraArgList[IDX_PDB] #@UnusedVariable
restraintsConvention = extraArgList[IDX_RESTRAINTS]
archiveType = extraArgList[
IDX_ARCHIVE] # Only used for deriving the input location not the output.
projectType = extraArgList[IDX_PROJECT_TYPE]
storeCING2db = stringMeansBooleanTrue(
getDeepByKeysOrAttributes(extraArgList, IDX_STORE_DB))
ranges = getDeepByKeysOrAttributes(extraArgList, IDX_RANGES)
filterTopViolations = getDeepByKeysOrAttributes(extraArgList,
IDX_FILTER_TOP)
if filterTopViolations:
filterTopViolations = int(filterTopViolations) # change '0' to 0
filterVasco = getDeepByKeysOrAttributes(extraArgList, IDX_FILTER_VASCO)
if filterVasco:
filterVasco = int(filterVasco)
else:
filterVasco = 1 # Default should be True
# end if
singleCoreOperation = getDeepByKeysOrAttributes(extraArgList,
IDX_SINGLE_CORE_OPERATION)
if singleCoreOperation:
singleCoreOperation = int(singleCoreOperation)
else:
singleCoreOperation = 0 # Default should be True
# end if
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)
isRemoteOutputDir = False
if '@' in outputDir:
isRemoteOutputDir = True
# end if
# vc = vCing('.') # argument is a fake master_ssh_url not needed here.
archive_id = getArchiveIdFromDirectoryName(outputDir)
nTdebug("Using program arguments:")
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("storeCING2db: %s" % storeCING2db)
nTdebug("ranges: %s" % ranges)
nTdebug("filterTopViolations: %s" % filterTopViolations)
nTdebug("filterVasco: %s" % filterVasco)
nTdebug("singleCoreOperation: %s" % singleCoreOperation)
nTdebug("")
nTdebug("Using derived settings:")
nTdebug("modelCount: %s" % modelCount)
nTdebug("isRemoteOutputDir: %s" % isRemoteOutputDir)
nTdebug("archive_id: %s" % archive_id)
# For NMR_REDO required as most efficient.
if singleCoreOperation:
setToSingleCoreOperation()
# presume the directory still needs to be created.
cingEntryDir = entryId + ".cing"
if os.path.isdir(cingEntryDir):
if forceRedo:
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.
if isRemoteOutputDir:
os.chdir(cingDirTmp)
else:
os.chdir(outputDir)
project = Project(entryId)
if project.removeFromDisk():
nTerror("Failed to remove existing project (if present)")
return True
# end if.
formatFileName = '%s.tgz'
if projectType == PROJECT_TYPE_CING:
formatFileName = '%s.cing.tgz'
elif projectType == PROJECT_TYPE_PDB:
formatFileName = 'pdb%s.ent.gz'
fileNameTgz = formatFileName % entryId
# nTdebug("fileNameTgz: %s" % fileNameTgz)
allowedInputProtocolList = 'http file ssh'.split()
inputProtocal = string.split(inputDir, ':')[0]
if inputProtocal in allowedInputProtocolList:
stillToRetrieve = False
if os.path.exists(fileNameTgz):
if forceRetrieveInput:
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
else:
nTdebug(
"Entry not retrieved which might be normal in some situations.")
# end if.
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):
nTerror("Failed to init project from ccpn")
return True
elif projectType == PROJECT_TYPE_PDB:
project = Project.open(entryId, status='new')
pdbFilePath = entryId + ".pdb"
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)
# end if
if ranges is not None:
project.molecule.setRanges(ranges)
# end if
if archive_id:
project.molecule.setArchiveId(archive_id)
# end if
project.molecule.superpose(ranges=ranges)
if filterTopViolations and not project.filterHighRestraintViol():
nTerror("Failed to filterHighRestraintViol")
####> MAIN UTILITY HERE
if 0: # DEFAULT 0
project.save()
if project.validate(htmlOnly=htmlOnly,
ranges=ranges,
doProcheck=doProcheck,
doWhatif=doWhatif,
doWattos=doWattos,
doQueeny=doQueeny,
doTalos=doTalos,
filterVasco=filterVasco):
nTerror("Failed to validate project read")
return True
# end if filterVasco
# Write a single PDB file containing all models
# according to IUPAC conventions
project.export2PDB()
project.save()
if storeCING2db and archive_id:
# Does require:
#from cing.PluginCode.sqlAlchemy import csqlAlchemy
# and should never crash run.
# archive_id = ARCHIVE_DEV_NRG_ID
# if isProduction:
# archive_id = ARCHIVE_NRG_ID
try:
if doStoreCING2db(entryId, archive_id, project=project):
nTerror(
"Failed to store CING project's data to DB but continuing."
)
except:
nTtracebackError()
nTerror(
"Failed to store CING project's data due to above traceback error."
)
if projectType == PROJECT_TYPE_CCPN:
# fileNameTgz = entryId + '.tgz'
os.unlink(fileNameTgz) # temporary ccpn tgz
if removeCcpnDirectory:
rmdir(entryId) # ccpn dir may contain vasco info.
if tgzCing:
directoryNameCing = entryId + ".cing"
tgzFileNameCing = directoryNameCing + ".tgz"
if os.path.exists(tgzFileNameCing):
nTwarning("Overwriting: " + tgzFileNameCing)
cmd = "tar -czf %s %s" % (tgzFileNameCing, directoryNameCing)
nTdebug("cmd: %s" % cmd)
# do_cmd(cmd)
status, result = commands.getstatusoutput(cmd)
if status:
nTerror("Failed to tar status: %s with result %s" %
(status, result))
return True
if isRemoteOutputDir:
if putFileBySsh(tgzFileNameCing, outputDir, ntriesMax=2):
nTerror(
"Failed to send File By Scp status: %s with result %s" %
(status, result))
nTerror("Maintaining results.")
return True
# end if
nTmessage("Removing tgz result: %s" % tgzFileNameCing)
os.remove(tgzFileNameCing)
nTmessage("Removing cing dir itself: %s" % directoryNameCing)
rmdir(directoryNameCing)
else: # do NOT remove local copy
pass
def main(entryId, *extraArgList):
"""inputDir may be a directory or a url. A url needs to start with http://.
"""
fastestTest = True # 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
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 = True
nTmessage(header)
nTmessage(getStartMessage())
expectedArgumentList = [
'inputDir', 'outputDir', 'pdbConvention', 'restraintsConvention',
'archiveType', 'projectType', 'storeCING2db'
]
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]
storeCING2db = False
if len(extraArgList) >= expectedNumberOfArguments:
storeCING2db = extraArgList[6]
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 = None
# targetId = getTargetForFullEntryName(entryId)
# if not targetId:
# nTerror("Failed to getTargetForFullEntryName for entryId: %s" % entryId)
# return True
# ranges = getRangesForTarget(targetId)
# if ranges == None:
# nTerror("Failed to getRangesForTarget for targetId: %s" % targetId)
# return True
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("storeCING2db: %s" % storeCING2db)
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):
nTerror("Failed to init project from ccpn")
return True
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.
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 storeCING2db:
# Does require:
#from cing.PluginCode.sqlAlchemy import csqlAlchemy
# and should never crash run.
try:
if doStoreCING2db(entryId, ARCHIVE_CASP_ID, project=project):
nTerror(
"Failed to store CING project's data to DB but continuing."
)
except:
nTtracebackError()
nTerror(
"Failed to store CING project's data due to above traceback error."
)
project.save()
if projectType == PROJECT_TYPE_CCPN:
# fileNameTgz = entryId + '.tgz'
# os.unlink(fileNameTgz) # temporary ccpn tgz
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)
