class EDPluginExecDamaverv0_1(EDPluginExecProcessScript):
"""
Execution plugin running DAMAVER pipeline for alignment of input pdb models,
selecting the most typical one and building an averaged model
"""
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputDamaver)
self.__xsDataResult = XSDataResultDamaver()
self.__strSymmetry = ''
self.__bAutomatic = True
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
EDVerbose.DEBUG("EDPluginExecDamaverv0_1.checkParameters")
self.checkMandatoryParameters(self.getDataInput(),
"Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getPdbInputFiles(),
"PDB input files are missing")
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
EDVerbose.DEBUG("EDPluginExecDamaverv0_1.preProcess")
self.checkDamaverPath()
self.checkDamaverAutomaticInput()
self.checkDamaverSymmetryInput()
self.generateDamaverScript()
def checkDamaverPath(self):
if '.' in self.getScriptExecutable():
EDVerbose.WARNING(
'Damaver might not run properly when \'.\' is present in the path to launch it'
)
def checkDamaverAutomaticInput(self):
try:
if self.getDataInput().getAutomatic():
self.__bAutomatic = self.getDataInput().getAutomatic(
).getValue()
except Exception:
EDVerbose.WARNING(
"Running Damaver automation pipeline by default.")
def checkDamaverSymmetryInput(self):
EDVerbose.DEBUG("EDPluginExecDammifv0_1.checkDammifSymmetryInput")
knownSymmetry = []
knownSymmetry.extend(
itertools.imap(lambda i: 'P' + str(i), range(1, 20)))
knownSymmetry.extend(
itertools.imap(lambda i: 'P' + str(i) + '2', range(2, 13)))
try:
if self.getDataInput().getSymmetry().getValue() in knownSymmetry:
self.__strSymmetry = self.getDataInput().getSymmetry(
).getValue()
except Exception:
EDVerbose.WARNING(
"Symmetry wasn't specified. Setting symmetry to P1")
def process(self, _edObject=None):
EDPluginExecProcessScript.process(self)
EDVerbose.DEBUG("EDPluginExecDamaverv0_1.process")
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("EDPluginExecDamaverv0_1.postProcess")
# Create some output data
xsDataResult = XSDataResultDamaver()
self.setDataOutput(xsDataResult)
self.outputDamaverPdbFiles()
if self.__bAutomatic:
self.parseDamselLog()
self.setDataOutput(self.__xsDataResult)
def outputDamaverPdbFiles(self):
pathDamaverFile = XSDataString(
os.path.join(self.getWorkingDirectory(), "damaver.pdb"))
xsDamaverFile = XSDataFile(pathDamaverFile)
if os.path.exists(pathDamaverFile.getValue()):
self.__xsDataResult.setDamaverPdbFile(xsDamaverFile)
if self.__bAutomatic:
pathDamfilterFile = XSDataString(
os.path.join(self.getWorkingDirectory(), "damfilt.pdb"))
pathDamstartFile = XSDataString(
os.path.join(self.getWorkingDirectory(), "damstart.pdb"))
xsDamfilterFile = XSDataFile(pathDamfilterFile)
xsDamstartFile = XSDataFile(pathDamstartFile)
if os.path.exists(pathDamfilterFile.getValue()):
self.__xsDataResult.setDamfilterPdbFile(xsDamfilterFile)
if os.path.exists(pathDamstartFile.getValue()):
self.__xsDataResult.setDamstartPdbFile(xsDamstartFile)
def parseDamselLog(self):
damselLog = open(os.path.join(self.getWorkingDirectory(),
"damsel.log"))
for line in damselLog:
wordsLine = [
tmpStr for tmpStr in line.split(' ') if tmpStr is not ''
]
if wordsLine[:4] == ['Mean', 'value', 'of', 'NSD']:
self.__xsDataResult.setMeanNSD(
XSDataDouble(float(wordsLine[-1])))
if wordsLine[:3] == ['Variation', 'of', 'NSD']:
self.__xsDataResult.setVariationNSD(
XSDataDouble(float(wordsLine[-1])))
def generateDamaverScript(self):
EDVerbose.DEBUG("*** EDPluginExecDammifv0_1.generateDammifScript")
dataFileNames = []
for idx, pdbInputFile in enumerate(
self.getDataInput().getPdbInputFiles()):
tmpInputFileName = pdbInputFile.getPath().getValue()
os.symlink(
tmpInputFileName,
os.path.join(self.getWorkingDirectory(),
'dammif-' + str(idx + 1) + '.pdb'))
dataFileNames.append('dammif-' + str(idx + 1) + '.pdb')
if self.__bAutomatic:
commandScriptLine = ['/a', self.__strSymmetry]
else:
damsupLog = open(
os.path.join(self.getWorkingDirectory(), "damsup.log"), 'w')
damsupLog.write('\n'.join(dataFileNames))
damsupLog.close()
commandScriptLine = ['damsup.log']
self.setScriptCommandline(' '.join(commandScriptLine))
def generateExecutiveSummary(self, __edPlugin=None):
self.addExecutiveSummaryLine(
"Results of model averaging using DAMAVER pipeline")
self.addExecutiveSummarySeparator()
self.addExecutiveSummaryLine(
"DAMAVER output pdb model : %s" %
os.path.join(self.getWorkingDirectory(), "damaver.pdb"))
if self.__bAutomatic:
self.addExecutiveSummaryLine(
"DAMFILT output pdb model : %s" %
os.path.join(self.getWorkingDirectory(), "damfilt.pdb"))
self.addExecutiveSummaryLine(
"DAMSTART output pdb model : %s" %
os.path.join(self.getWorkingDirectory(), "damstart.pdb"))
damselLog = open(
os.path.join(self.getWorkingDirectory(), "damsel.log"))
for line in damselLog:
self.addExecutiveSummaryLine(line)
self.addExecutiveSummarySeparator()
class EDPluginExecDamaverv0_1(EDPluginExecProcessScript):
"""
Execution plugin running DAMAVER pipeline for alignment of input pdb models,
selecting the most typical one and building an averaged model
"""
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputDamaver)
self.__xsDataResult = XSDataResultDamaver()
self.__strSymmetry = ''
self.__bAutomatic = True
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
EDVerbose.DEBUG("EDPluginExecDamaverv0_1.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getPdbInputFiles(), "PDB input files are missing")
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
EDVerbose.DEBUG("EDPluginExecDamaverv0_1.preProcess")
self.checkDamaverPath()
self.checkDamaverAutomaticInput()
self.checkDamaverSymmetryInput()
self.generateDamaverScript()
def checkDamaverPath(self):
if '.' in self.getScriptExecutable():
EDVerbose.WARNING('Damaver might not run properly when \'.\' is present in the path to launch it')
def checkDamaverAutomaticInput(self):
try:
if self.getDataInput().getAutomatic():
self.__bAutomatic = self.getDataInput().getAutomatic().getValue()
except Exception:
EDVerbose.WARNING("Running Damaver automation pipeline by default.")
def checkDamaverSymmetryInput(self):
EDVerbose.DEBUG("EDPluginExecDammifv0_1.checkDammifSymmetryInput")
knownSymmetry = []
knownSymmetry.extend(itertools.imap(lambda i: 'P' + str(i), range(1, 20)))
knownSymmetry.extend(itertools.imap(lambda i: 'P' + str(i) + '2', range(2, 13)))
try:
if self.getDataInput().getSymmetry().getValue() in knownSymmetry:
self.__strSymmetry = self.getDataInput().getSymmetry().getValue()
except Exception:
EDVerbose.WARNING("Symmetry wasn't specified. Setting symmetry to P1")
def process(self, _edObject=None):
EDPluginExecProcessScript.process(self)
EDVerbose.DEBUG("EDPluginExecDamaverv0_1.process")
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("EDPluginExecDamaverv0_1.postProcess")
# Create some output data
xsDataResult = XSDataResultDamaver()
self.setDataOutput(xsDataResult)
self.outputDamaverPdbFiles()
if self.__bAutomatic:
self.parseDamselLog()
self.setDataOutput(self.__xsDataResult)
def outputDamaverPdbFiles(self):
pathDamaverFile = XSDataString(os.path.join(self.getWorkingDirectory(), "damaver.pdb"))
xsDamaverFile = XSDataFile(pathDamaverFile)
if os.path.exists(pathDamaverFile.getValue()):
self.__xsDataResult.setDamaverPdbFile(xsDamaverFile)
if self.__bAutomatic:
pathDamfilterFile = XSDataString(os.path.join(self.getWorkingDirectory(), "damfilt.pdb"))
pathDamstartFile = XSDataString(os.path.join(self.getWorkingDirectory(), "damstart.pdb"))
xsDamfilterFile = XSDataFile(pathDamfilterFile)
xsDamstartFile = XSDataFile(pathDamstartFile)
if os.path.exists(pathDamfilterFile.getValue()):
self.__xsDataResult.setDamfilterPdbFile(xsDamfilterFile)
if os.path.exists(pathDamstartFile.getValue()):
self.__xsDataResult.setDamstartPdbFile(xsDamstartFile)
def parseDamselLog(self):
damselLog = open(os.path.join(self.getWorkingDirectory(), "damsel.log"))
for line in damselLog:
wordsLine = [tmpStr for tmpStr in line.split(' ') if tmpStr is not '']
if wordsLine[:4] == ['Mean', 'value', 'of', 'NSD']:
self.__xsDataResult.setMeanNSD(XSDataDouble(float(wordsLine[-1])))
if wordsLine[:3] == ['Variation', 'of', 'NSD']:
self.__xsDataResult.setVariationNSD(XSDataDouble(float(wordsLine[-1])))
def generateDamaverScript(self):
EDVerbose.DEBUG("*** EDPluginExecDammifv0_1.generateDammifScript")
dataFileNames = []
for idx, pdbInputFile in enumerate(self.getDataInput().getPdbInputFiles()):
tmpInputFileName = pdbInputFile.getPath().getValue()
os.symlink(tmpInputFileName, os.path.join(self.getWorkingDirectory(), 'dammif-' + str(idx + 1) + '.pdb'))
dataFileNames.append('dammif-' + str(idx + 1) + '.pdb')
if self.__bAutomatic:
commandScriptLine = ['/a', self.__strSymmetry]
else:
damsupLog = open(os.path.join(self.getWorkingDirectory(), "damsup.log"), 'w')
damsupLog.write('\n'.join(dataFileNames))
damsupLog.close()
commandScriptLine = ['damsup.log']
self.setScriptCommandline(' '.join(commandScriptLine))
def generateExecutiveSummary(self, __edPlugin=None):
self.addExecutiveSummaryLine("Results of model averaging using DAMAVER pipeline")
self.addExecutiveSummarySeparator()
self.addExecutiveSummaryLine("DAMAVER output pdb model : %s" % os.path.join(self.getWorkingDirectory(), "damaver.pdb"))
if self.__bAutomatic:
self.addExecutiveSummaryLine("DAMFILT output pdb model : %s" % os.path.join(self.getWorkingDirectory(), "damfilt.pdb"))
self.addExecutiveSummaryLine("DAMSTART output pdb model : %s" % os.path.join(self.getWorkingDirectory(), "damstart.pdb"))
damselLog = open(os.path.join(self.getWorkingDirectory(), "damsel.log"))
for line in damselLog:
self.addExecutiveSummaryLine(line)
self.addExecutiveSummarySeparator()
