PEATSA/Core/ProteinDesignTool.py
def runScan(self, mutantCollection, ionisableGroups=None, resultsName='ScanResults', verbose=False):
	
		'''Calculates the effect of the mutations in mutantCollection on the pKa of ionisable groups.
		
		Parameters:
			mutantCollection - A MutantCollection instance representing the mutations to be scanned.
			ionisableGroups - A list of the residue codes of the groups that will be checked
			resultsName - The results matrix will be added to the dataDirectory with this name.
			verbose - If True the scan will output more verbose information on the
				progress of the calculation. Default - False.'''
			
		scanner = self.scanTool()
		if ionisableGroups is not None:
			scanner.setIonisableResidues(ionisableGroups)
	
		runpka = False
		try:
			scanner.scan(mutantCollection=mutantCollection, verbose=verbose)
			self.environment.output("[PEAT-SA] Finished scan - %s" % datetime.datetime.now().strftime('%H:%M:%S'))
		except Exceptions.MissingPKADataError, data:
			self.environment.output('\n[PEAT-SA] Detected error setting up scan\n%s.' % data)
			self.environment.output('\n[PEAT-SA] Initial pKa calculation required - running now.')
			runpka = True
			raise
		
		if runpka is True:
			try:
				#The initial design run wasn't done - Do it now
				pKaRun = Programs.PKARun(self.workingDirectory, 
						self.outputDirectory,
						configuration=self.configuration,
						filename=self.pdbFile)
				pKaRun.run(cleanPDB=False)
				#Retry
				scanner.scan(mutantCollection=mutantCollection, verbose=verbose)
			except BaseException, data:
				self.environment.output('\n[PEAT-SA] Caught exception while running scan (%d)' % data)
				raise
			
		self.dataDirectory.addMatrix(matrix=scanner.scanResults(), name=resultsName)
Calculates the effect of the mutations in mutantCollection on the pKa of ionisable groups.
		
		Parameters:
			mutantCollection - A MutantCollection instance representing the mutations to be scanned.
			ionisableGroups - A list of the residue codes of the groups that will be checked
			resultsName - The results matrix will be added to the dataDirectory with this name.
			verbose - If True the scan will output more verbose information on the
				progress of the calculation. Default - False.
Calculates the effect of the mutations in mutantCollection on the pKa of ionisable groups.
Parameters:
mutantCollection - A MutantCollection instance representing the mutations to be scanned.
ionisableGroups - A list of the residue codes of the groups that will be checked
resultsName - The results matrix will be added to the dataDirectory with this name.
verbose - If True the scan will output more verbose information on the
progress of the calculation. Default - False.
Calculates the effect of the mutations in mutantCollection on the pKa of ionisable groups . Parameters : mutantCollection - A MutantCollection instance representing the mutations to be scanned . ionisableGroups - A list of the residue codes of the groups that will be checked resultsName - The results matrix will be added to the dataDirectory with this name . verbose - If True the scan will output more verbose information on the progress of the calculation . Default - False .
def runScan(self, mutantCollection, ionisableGroups=None, resultsName='ScanResults', verbose=False):
		scanner = self.scanTool()
		if ionisableGroups is not None:
			scanner.setIonisableResidues(ionisableGroups)
		runpka = False
		try:
			scanner.scan(mutantCollection=mutantCollection, verbose=verbose)
			self.environment.output("[PEAT-SA] Finished scan - %s" % datetime.datetime.now().strftime('%H:%M:%S'))
		except Exceptions.MissingPKADataError, data:
			self.environment.output('\n[PEAT-SA] Detected error setting up scan\n%s.' % data)
			self.environment.output('\n[PEAT-SA] Initial pKa calculation required - running now.')
			runpka = True
			raise
		if runpka is True:
			try:
				pKaRun = Programs.PKARun(self.workingDirectory, 
						self.outputDirectory,
						configuration=self.configuration,
						filename=self.pdbFile)
				pKaRun.run(cleanPDB=False)
				scanner.scan(mutantCollection=mutantCollection, verbose=verbose)
			except BaseException, data:
				self.environment.output('\n[PEAT-SA] Caught exception while running scan (%d)' % data)
				raise
		self.dataDirectory.addMatrix(matrix=scanner.scanResults(), name=resultsName)
def runScan ( self , mutantCollection , ionisableGroups = None , resultsName = 'ScanResults' , verbose = False ) : scanner = self . scanTool ( ) if ionisableGroups is not None : scanner . setIonisableResidues ( ionisableGroups ) runpka = False try : scanner . scan ( mutantCollection = mutantCollection , verbose = verbose ) self . environment . output ( "[PEAT-SA] Finished scan - %s" % datetime . datetime . now ( ) . strftime ( '%H:%M:%S' ) ) except Exceptions . MissingPKADataError , data : self . environment . output ( '\n[PEAT-SA] Detected error setting up scan\n%s.' % data ) self . environment . output ( '\n[PEAT-SA] Initial pKa calculation required - running now.' ) runpka = True raise if runpka is True : try : pKaRun = Programs . PKARun ( self . workingDirectory , self . outputDirectory , configuration = self . configuration , filename = self . pdbFile ) pKaRun . run ( cleanPDB = False ) scanner . scan ( mutantCollection = mutantCollection , verbose = verbose ) except BaseException , data : self . environment . output ( '\n[PEAT-SA] Caught exception while running scan (%d)' % data ) raise self . dataDirectory . addMatrix ( matrix = scanner . scanResults ( ) , name = resultsName )
Calculates the effect of the mutations in mutantCollection on the pKa of ionisable groups.
Calculates the effect of the mutations in mutantCollection on the pKa of ionisable groups .
'''Calculates the effect of the mutations in mutantCollection on the pKa of ionisable groups.
		
		Parameters:
			mutantCollection - A MutantCollection instance representing the mutations to be scanned.
			ionisableGroups - A list of the residue codes of the groups that will be checked
			resultsName - The results matrix will be added to the dataDirectory with this name.
			verbose - If True the scan will output more verbose information on the
				progress of the calculation. Default - False.''' #The initial design run wasn't done - Do it now #Retry
self
mutantCollection
ionisableGroups
resultsName
verbose