def _testNmrStar(self):
"Testing conversion from CCPN to NMR-STAR using Wim Vranken's FC. Disabled test because only JFD uses it."
# failing entries: 1ai0, 1kr8 (same for 2hgh)
entryList = "1a4d".split()
# entryList = "1a4d 1a24 1afp 1ai0 1brv 1bus 1cjg 1hue 1ieh 1iv6 1kr8 2hgh 2k0e SRYBDNA Parvulustat".split()
#1iv6 needs better ccpn file from FC
# if you have a local copy you can use it; make sure to adjust the path setting below.
useNrgArchive = False # Default is 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 entryId in entryList:
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)
else:
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
self.assertTrue(project.initCcpn(ccpnFolder = ccpnFile))
self.assertTrue(project.save())
fileName = os.path.join( cingDirTmp, entryId + ".str")
nmrStar = NmrStar(project)
self.assertTrue( nmrStar )
self.assertTrue( nmrStar.toNmrStarFile( fileName ))
# 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))
def _testNmrStar(self):
"Testing conversion from CCPN to NMR-STAR using Wim Vranken's FC. Disabled test because only JFD uses it."
# failing entries: 1ai0, 1kr8 (same for 2hgh)
entryList = "1a4d".split()
# entryList = "1a4d 1a24 1afp 1ai0 1brv 1bus 1cjg 1hue 1ieh 1iv6 1kr8 2hgh 2k0e SRYBDNA Parvulustat".split()
#1iv6 needs better ccpn file from FC
# if you have a local copy you can use it; make sure to adjust the path setting below.
useNrgArchive = False # Default is 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 entryId in entryList:
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)
else:
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
self.assertTrue(project.initCcpn(ccpnFolder=ccpnFile))
self.assertTrue(project.save())
fileName = os.path.join(cingDirTmp, entryId + ".str")
nmrStar = NmrStar(project)
self.assertTrue(nmrStar)
self.assertTrue(nmrStar.toNmrStarFile(fileName))
# 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))
def _runWattos(project, ranges=None, tmp=None, parseOnly=False):
"""
Run and import the wattos results per model.
All models in the ensemble of the molecule will be checked.
Set wattos references for Molecule, Chain, Residue and Atom instances
or None if no wattos results exist
returns 1 on success or None on any failure.
"""
if not project.molecule:
nTerror("runWattos: no molecule defined")
return True
mol = project.molecule
if not mol:
nTerror("No project molecule in runWattos")
return None
if mol.modelCount == 0:
nTwarning('runWattos: no models for "%s"', mol)
return
path = project.path(mol.name, project.moleculeDirectories.wattos)
if not os.path.exists(path):
mol.wattos = None
for chain in mol.allChains():
chain.wattos = None
for res in mol.allResidues():
res.wattos = None
for atm in mol.allAtoms():
atm.wattos = None
return None
if ranges == None:
ranges = mol.ranges
wattos = Wattos(rootPath=path, molecule=mol, ranges=ranges)
del ranges # only use wattos.ranges now.
useRanges = mol.useRanges(wattos.ranges)
if mol == None:
nTerror('runWattos: no mol defined')
return None
if mol.modelCount == 0:
nTwarning('runWattos: no models for "%s"', mol)
return None
wattosDir = project.mkdir(mol.name, project.moleculeDirectories.wattos)
wattosStatus = project.wattosStatus
if not parseOnly:
wattosStatus.completed = False
wattosStatus.parsed = False
wattosStatus.time = None
wattosStatus.exitCode = None
fileName = 'project.str'
fullname = os.path.join(os.path.curdir, wattosDir, fileName)
fullname = os.path.abspath(fullname)
if os.path.exists(fullname):
if not os.unlink(fullname):
nTmessage("Removing existing file: %s" % fullname)
else:
nTerror("Failed to remove existing file: %s" % fullname)
return None
nmrStar = NmrStar(project)
if not nmrStar:
nTerror("Failed to create NmrStar(project)")
return None
if not nmrStar.toNmrStarFile(fullname):
nTmessage(
"Failed to nmrStar.toNmrStarFile (fine if there wasn't a CCPN project to start with)"
)
return None
if not os.path.exists(fullname):
nTerror("Failed to create file [%s] in nmrStar.toNmrStarFile" %
fullname)
return None
scriptComplete = wattos.scriptTemplate
scriptComplete = scriptComplete.replace("INPUT_STR_FILE", fileName)
scriptComplete = scriptComplete.replace("VERBOSITY",
repr(cing.verbosity))
rangesTxt = wattos.ranges
if not useRanges: # Wattos can't handle a None this way.
rangesTxt = ALL_RANGES_STR
rangesTxtWattos = project.molecule.rangesToMmCifRanges(rangesTxt)
if rangesTxtWattos == None:
rangesTxtWattos = ALL_RANGES_STR
if rangesTxt != rangesTxtWattos:
nTmessage(
"==> Translating ranges %s to mmCIF numbering scheme: %s" %
(rangesTxt, rangesTxtWattos))
scriptComplete = scriptComplete.replace("RANGES", rangesTxtWattos)
# Let's ask the user to be nice and not kill us
# estimate to do **0.5 residues per minutes as with entry 1bus on dual core intel Mac.
timeRunEstimatedInSeconds = 0.025 * mol.modelCount * len(
mol.allResidues())
timeRunEstimatedList = timedelta2Hms(timeRunEstimatedInSeconds)
msg = '==> Running Wattos for an estimated (5,000 atoms/s): %s hours, %s minutes and %s seconds; please wait' % timeRunEstimatedList
nTmessage(msg)
scriptFileName = "wattos.script"
scriptFullFileName = os.path.join(wattosDir, scriptFileName)
open(scriptFullFileName, "w").write(scriptComplete)
wattosPath = "%s Wattos.CloneWars.UserInterface -at" % JVM_CMD_STD
logFileName = "wattos_compl.log"
wattosProgram = ExecuteProgram(wattosPath,
rootPath=wattosDir,
redirectOutputToFile=logFileName,
redirectInputFromFile=scriptFileName)
# The last argument becomes a necessary redirection into fouling Wattos into
# thinking it's running interactively.
now = time.time()
wattosExitCode = wattosProgram()
# nTdebug("Took number of seconds: " + sprintf("%8.1f", time.time() - now))
wattosStatus.exitCode = wattosExitCode
wattosStatus.time = sprintf("%.1f", time.time() - now)
wattosStatus.keysformat()
if wattosExitCode:
nTerror("Failed wattos checks with exit code: " +
repr(wattosExitCode))
return None
wattosStatus.completed = True
# end if not parseOnly
if not project.hasDistanceRestraints():
return wattos
fullname = os.path.join(wattosDir, wattos.completeness_check_file_name)
if not os.path.exists(fullname):
nTwarning("Failed to find wattos completeness check result file: %s" %
fullname)
return None
# nTmessage('==> Parsing checks')
if wattos._processComplCheck(fullname):
nTerror("\nrunWattos Failed to parse check %s", fullname)
return None
pathOutSurplus = os.path.join(
path, wattos.surplus_check_file_name_base + '_summary.txt')
if not os.path.exists(
pathOutSurplus
): # Happened for 1ao2 on production machine; not on development...
nTerror("Path does not exist: %s" % (pathOutSurplus))
return True
# nTdebug('> parsing ' + pathOutSurplus)
fullTextSurplus = open(pathOutSurplus, 'r').read()
if not fullTextSurplus:
nTerror('Failed to parse Wattos surplus summary file')
return True
startString = 'SUMMARY:'
surplusSummary = getTextBetween(fullTextSurplus,
startString,
endString=None,
startIncl=False,
endIncl=False)
if not surplusSummary:
nTerror("Failed to find surplusSummary in surplusSummary[:80]: [%s]" %
surplusSummary[:80])
return True
surplusSummary = "Wattos Surplus Analysis Summary\n\n" + surplusSummary.strip(
)
# nTdebug('got surplusSummary: \n' + surplusSummary)
# pathOutCompleteness = os.path.join(path, 'wattos_completeness_chk.str')
# if not os.path.exists(pathOutCompleteness): # Happened for 1ao2 on production machine; not on development...
# nTerror("Path does not exist: %s" % (pathOutCompleteness))
# return True
# nTdebug('> parsing ' + pathOutCompleteness)
# fullTextCompleteness = open(pathOutCompleteness, 'r').read()
# if not fullTextCompleteness:
# nTerror('Failed to parse Wattos completeness summary file')
# return True
#
# startString = '_NOE_completeness_shell.Type'
# endString = 'stop_'
# completenessSummary = getTextBetween(fullTextCompleteness, startString, endString, endIncl = False)
# if not completenessSummary:
# nTerror("Failed to find completenessSummary in fullText[:80]: [%s]" % fullTextCompleteness[:80])
# return True
# completenessSummary = '\n'.join([HTML_TAG_PRE,
# completenessSummary.strip(),
# '---------------------------------------------',
# HTML_TAG_PRE2])
#
# nTdebug('got completenessSummary: \n' + completenessSummary)
# intro = '----------- Wattos summary -----------'
completenessMolStr = NaNstring
completenessMol = mol.getDeepByKeys(WATTOS_STR, COMPLCHK_STR,
VALUE_LIST_STR)
if completenessMol:
completenessMolStr = val2Str(completenessMol, "%.2f")
complStatement = 'Overall NOE completeness is %s percent\n' % completenessMolStr
summary = '\n\n'.join([surplusSummary, complStatement])
if setDeepByKeys(mol, summary, WATTOS_SUMMARY_STR):
nTerror('Failed to set Wattos summary')
return True
wattosStatus.parsed = True
# nTdebug("In runWattos: project.wattosStatus.completed: %s" % project.wattosStatus.completed)
return wattos # Success
def _runWattos(project, ranges=None, tmp = None, parseOnly=False):
"""
Run and import the wattos results per model.
All models in the ensemble of the molecule will be checked.
Set wattos references for Molecule, Chain, Residue and Atom instances
or None if no wattos results exist
returns 1 on success or None on any failure.
"""
if not project.molecule:
nTerror("runWattos: no molecule defined")
return True
mol = project.molecule
if not mol:
nTerror("No project molecule in runWattos")
return None
if mol.modelCount == 0:
nTwarning('runWattos: no models for "%s"', mol)
return
path = project.path(mol.name, project.moleculeDirectories.wattos)
if not os.path.exists(path):
mol.wattos = None
for chain in mol.allChains():
chain.wattos = None
for res in mol.allResidues():
res.wattos = None
for atm in mol.allAtoms():
atm.wattos = None
return None
if ranges == None:
ranges = mol.ranges
wattos = Wattos(rootPath = path, molecule = mol, ranges = ranges)
del ranges # only use wattos.ranges now.
useRanges = mol.useRanges(wattos.ranges)
if mol == None:
nTerror('runWattos: no mol defined')
return None
if mol.modelCount == 0:
nTwarning('runWattos: no models for "%s"', mol)
return None
wattosDir = project.mkdir(mol.name, project.moleculeDirectories.wattos)
wattosStatus = project.wattosStatus
if not parseOnly:
wattosStatus.completed = False
wattosStatus.parsed = False
wattosStatus.time = None
wattosStatus.exitCode = None
fileName = 'project.str'
fullname = os.path.join(os.path.curdir, wattosDir, fileName)
fullname = os.path.abspath(fullname)
if os.path.exists(fullname):
if not os.unlink(fullname):
nTmessage("Removing existing file: %s" % fullname)
else:
nTerror("Failed to remove existing file: %s" % fullname)
return None
nmrStar = NmrStar(project)
if not nmrStar:
nTerror("Failed to create NmrStar(project)")
return None
if not nmrStar.toNmrStarFile(fullname):
nTmessage("Failed to nmrStar.toNmrStarFile (fine if there wasn't a CCPN project to start with)")
return None
if not os.path.exists(fullname):
nTerror("Failed to create file [%s] in nmrStar.toNmrStarFile" % fullname)
return None
scriptComplete = wattos.scriptTemplate
scriptComplete = scriptComplete.replace("INPUT_STR_FILE", fileName)
scriptComplete = scriptComplete.replace("VERBOSITY", repr(cing.verbosity))
rangesTxt = wattos.ranges
if not useRanges: # Wattos can't handle a None this way.
rangesTxt = ALL_RANGES_STR
rangesTxtWattos = project.molecule.rangesToMmCifRanges(rangesTxt)
if rangesTxtWattos == None:
rangesTxtWattos = ALL_RANGES_STR
if rangesTxt != rangesTxtWattos:
nTmessage("==> Translating ranges %s to mmCIF numbering scheme: %s" % (rangesTxt, rangesTxtWattos ))
scriptComplete = scriptComplete.replace("RANGES", rangesTxtWattos)
# Let's ask the user to be nice and not kill us
# estimate to do **0.5 residues per minutes as with entry 1bus on dual core intel Mac.
timeRunEstimatedInSeconds = 0.025 * mol.modelCount * len(mol.allResidues())
timeRunEstimatedInSeconds *= 60
timeRunEstimatedList = timedelta2Hms(timeRunEstimatedInSeconds)
msg = '==> Running Wattos for an estimated (5,000 atoms/s): %s hours, %s minutes and %s seconds; please wait' % timeRunEstimatedList
nTmessage(msg)
scriptFileName = "wattos.script"
scriptFullFileName = os.path.join(wattosDir, scriptFileName)
open(scriptFullFileName, "w").write(scriptComplete)
wattosPath = "%s Wattos.CloneWars.UserInterface -at" % JVM_CMD_STD
logFileName = "wattos_compl.log"
wattosProgram = ExecuteProgram(wattosPath, rootPath = wattosDir,
redirectOutputToFile = logFileName,
redirectInputFromFile = scriptFileName)
# The last argument becomes a necessary redirection into fouling Wattos into
# thinking it's running interactively.
now = time.time()
wattosExitCode = wattosProgram()
# nTdebug("Took number of seconds: " + sprintf("%8.1f", time.time() - now))
wattosStatus.exitCode = wattosExitCode
wattosStatus.time = sprintf("%.1f", time.time() - now)
wattosStatus.keysformat()
if wattosExitCode:
nTerror("Failed wattos checks with exit code: " + repr(wattosExitCode))
return None
wattosStatus.completed = True
# end if not parseOnly
if not project.hasDistanceRestraints():
return wattos
fullname = os.path.join(wattosDir, wattos.completeness_check_file_name)
if not os.path.exists(fullname):
nTwarning("Failed to find wattos completeness check result file: %s" % fullname)
return None
# nTmessage('==> Parsing checks')
if wattos._processComplCheck(fullname):
nTerror("\nrunWattos Failed to parse check %s", fullname)
return None
pathOutSurplus = os.path.join(path, wattos.surplus_check_file_name_base + '_summary.txt')
if not os.path.exists(pathOutSurplus): # Happened for 1ao2 on production machine; not on development...
nTerror("Path does not exist: %s" % (pathOutSurplus))
return True
# nTdebug('> parsing ' + pathOutSurplus)
fullTextSurplus = open(pathOutSurplus, 'r').read()
if not fullTextSurplus:
nTerror('Failed to parse Wattos surplus summary file')
return True
startString = 'SUMMARY:'
surplusSummary = getTextBetween(fullTextSurplus, startString, endString = None, startIncl = False, endIncl = False)
if not surplusSummary:
nTerror("Failed to find surplusSummary in surplusSummary[:80]: [%s]" % surplusSummary[:80])
return True
surplusSummary = "Wattos Surplus Analysis Summary\n\n" + surplusSummary.strip()
# nTdebug('got surplusSummary: \n' + surplusSummary)
# pathOutCompleteness = os.path.join(path, 'wattos_completeness_chk.str')
# if not os.path.exists(pathOutCompleteness): # Happened for 1ao2 on production machine; not on development...
# nTerror("Path does not exist: %s" % (pathOutCompleteness))
# return True
# nTdebug('> parsing ' + pathOutCompleteness)
# fullTextCompleteness = open(pathOutCompleteness, 'r').read()
# if not fullTextCompleteness:
# nTerror('Failed to parse Wattos completeness summary file')
# return True
#
# startString = '_NOE_completeness_shell.Type'
# endString = 'stop_'
# completenessSummary = getTextBetween(fullTextCompleteness, startString, endString, endIncl = False)
# if not completenessSummary:
# nTerror("Failed to find completenessSummary in fullText[:80]: [%s]" % fullTextCompleteness[:80])
# return True
# completenessSummary = '\n'.join([HTML_TAG_PRE,
# completenessSummary.strip(),
# '---------------------------------------------',
# HTML_TAG_PRE2])
#
# nTdebug('got completenessSummary: \n' + completenessSummary)
# intro = '----------- Wattos summary -----------'
completenessMolStr = NaNstring
completenessMol = mol.getDeepByKeys( WATTOS_STR, COMPLCHK_STR, VALUE_LIST_STR)
if completenessMol:
completenessMolStr = val2Str(completenessMol, "%.2f")
complStatement = 'Overall NOE completeness is %s percent\n' % completenessMolStr
summary = '\n\n'.join([surplusSummary, complStatement])
if setDeepByKeys(mol, summary, WATTOS_SUMMARY_STR):
nTerror('Failed to set Wattos summary')
return True
wattosStatus.parsed = True
# nTdebug("In runWattos: project.wattosStatus.completed: %s" % project.wattosStatus.completed)
return wattos # Success