PEATSA/Core/Environment.py
def __defaultConfiguration(self, writeFile=True):

		'''Creates a default ConfigParser object instances of this class can use
		
		Parameters -
			writeFile - If True writes a default configuration file in the current directory'''
	
		default = ConfigParser.SafeConfigParser()
		default.optionxform = str

		#Add default configuration values
		default.add_section('PKA SCAN PARAMETERS')
		default.add_section('PKA SCAN METHOD')
		default.add_section('PKA SCAN OUTPUT')
		default.add_section('PATHS')
		default.add_section('WORKING DIRECTORY')
		default.add_section('PDBS')
	    
		# pKa calculation parameters
		default.set('PKA SCAN PARAMETERS', 'pKMCsteps', str(200000))
		default.set('PKA SCAN PARAMETERS', 'pKMCsteps', str(200000))
		default.set('PKA SCAN PARAMETERS', 'recalc_intpka', str(1))
		default.set('PKA SCAN PARAMETERS', 'recalc_intpka_dist', str(20))
		default.set('PKA SCAN PARAMETERS', 'use_titration_curves', str(1))
		default.set('PKA SCAN PARAMETERS', 'calc_dpka', str(1))
		default.set('PKA SCAN PARAMETERS', 'generate_mutations', str(False))
		default.set('PKA SCAN PARAMETERS', 'save_temp_files', str(False))
		default.set('PKA SCAN PARAMETERS', 'mutation_quality', str(0.5))

		# Method
		default.set('PKA SCAN METHOD', 'dpKa_method', 'MC')
		default.set('PKA SCAN METHOD', 'tabulated', str(1))
		default.set('PKA SCAN METHOD', 'MCsteps', str(0))
		default.set('PKA SCAN METHOD', 'PBEsolver', 'DelPhi')

		# Be not-so-noisy
		default.set('PKA SCAN OUTPUT', 'verbose', str(1))
		# Do not save the solutions
		default.set('PKA SCAN OUTPUT', 'save_solutions', str(None))
			
		#Set a default location for the pKa Tools
		default.set('PATHS', 'pKa Tools', os.path.join(os.path.expanduser('~'), 'PEAT'))
		default.set('PATHS', 'uffbaps', os.path.join(os.path.expanduser('~'), 'PEAT/UFFBAPS'))
		
		#Working directory configuration (optional)
		#Users may not want to overwrite files in an existing working dir
		#These options configure this behaviour
		default.set('WORKING DIRECTORY', 'copyIfExists', str(0))
		default.set('WORKING DIRECTORY', 'copyLocation', os.getcwd())
		default.set('WORKING DIRECTORY', 'overwriteExistingCopies', str(0))
		default.set('WORKING DIRECTORY', 'useUniqueID', str(0))

		default.set('PDBS', 'pdbCleanProgram', 'WHATIF')
	
		#If requested write out this default configuration 
		#wherever the program is being run from
		if writeFile:
			file = open('proteinDesignTool.conf', 'w')
			default.write(file)
			file.close()
		
		return default
Creates a default ConfigParser object instances of this class can use
		
		Parameters -
			writeFile - If True writes a default configuration file in the current directory
Creates a default ConfigParser object instances of this class can use
Parameters
writeFile - If True writes a default configuration file in the current directory
Creates a default ConfigParser object instances of this class can use Parameters writeFile - If True writes a default configuration file in the current directory
def __defaultConfiguration(self, writeFile=True):
		default = ConfigParser.SafeConfigParser()
		default.optionxform = str
		default.add_section('PKA SCAN PARAMETERS')
		default.add_section('PKA SCAN METHOD')
		default.add_section('PKA SCAN OUTPUT')
		default.add_section('PATHS')
		default.add_section('WORKING DIRECTORY')
		default.add_section('PDBS')
		default.set('PKA SCAN PARAMETERS', 'pKMCsteps', str(200000))
		default.set('PKA SCAN PARAMETERS', 'pKMCsteps', str(200000))
		default.set('PKA SCAN PARAMETERS', 'recalc_intpka', str(1))
		default.set('PKA SCAN PARAMETERS', 'recalc_intpka_dist', str(20))
		default.set('PKA SCAN PARAMETERS', 'use_titration_curves', str(1))
		default.set('PKA SCAN PARAMETERS', 'calc_dpka', str(1))
		default.set('PKA SCAN PARAMETERS', 'generate_mutations', str(False))
		default.set('PKA SCAN PARAMETERS', 'save_temp_files', str(False))
		default.set('PKA SCAN PARAMETERS', 'mutation_quality', str(0.5))
		default.set('PKA SCAN METHOD', 'dpKa_method', 'MC')
		default.set('PKA SCAN METHOD', 'tabulated', str(1))
		default.set('PKA SCAN METHOD', 'MCsteps', str(0))
		default.set('PKA SCAN METHOD', 'PBEsolver', 'DelPhi')
		default.set('PKA SCAN OUTPUT', 'verbose', str(1))
		default.set('PKA SCAN OUTPUT', 'save_solutions', str(None))
		default.set('PATHS', 'pKa Tools', os.path.join(os.path.expanduser('~'), 'PEAT'))
		default.set('PATHS', 'uffbaps', os.path.join(os.path.expanduser('~'), 'PEAT/UFFBAPS'))
		default.set('WORKING DIRECTORY', 'copyIfExists', str(0))
		default.set('WORKING DIRECTORY', 'copyLocation', os.getcwd())
		default.set('WORKING DIRECTORY', 'overwriteExistingCopies', str(0))
		default.set('WORKING DIRECTORY', 'useUniqueID', str(0))
		default.set('PDBS', 'pdbCleanProgram', 'WHATIF')
		if writeFile:
			file = open('proteinDesignTool.conf', 'w')
			default.write(file)
			file.close()
		return default
def __defaultConfiguration ( self , writeFile = True ) : default = ConfigParser . SafeConfigParser ( ) default . optionxform = str default . add_section ( 'PKA SCAN PARAMETERS' ) default . add_section ( 'PKA SCAN METHOD' ) default . add_section ( 'PKA SCAN OUTPUT' ) default . add_section ( 'PATHS' ) default . add_section ( 'WORKING DIRECTORY' ) default . add_section ( 'PDBS' ) default . set ( 'PKA SCAN PARAMETERS' , 'pKMCsteps' , str ( 200000 ) ) default . set ( 'PKA SCAN PARAMETERS' , 'pKMCsteps' , str ( 200000 ) ) default . set ( 'PKA SCAN PARAMETERS' , 'recalc_intpka' , str ( 1 ) ) default . set ( 'PKA SCAN PARAMETERS' , 'recalc_intpka_dist' , str ( 20 ) ) default . set ( 'PKA SCAN PARAMETERS' , 'use_titration_curves' , str ( 1 ) ) default . set ( 'PKA SCAN PARAMETERS' , 'calc_dpka' , str ( 1 ) ) default . set ( 'PKA SCAN PARAMETERS' , 'generate_mutations' , str ( False ) ) default . set ( 'PKA SCAN PARAMETERS' , 'save_temp_files' , str ( False ) ) default . set ( 'PKA SCAN PARAMETERS' , 'mutation_quality' , str ( 0.5 ) ) default . set ( 'PKA SCAN METHOD' , 'dpKa_method' , 'MC' ) default . set ( 'PKA SCAN METHOD' , 'tabulated' , str ( 1 ) ) default . set ( 'PKA SCAN METHOD' , 'MCsteps' , str ( 0 ) ) default . set ( 'PKA SCAN METHOD' , 'PBEsolver' , 'DelPhi' ) default . set ( 'PKA SCAN OUTPUT' , 'verbose' , str ( 1 ) ) default . set ( 'PKA SCAN OUTPUT' , 'save_solutions' , str ( None ) ) default . set ( 'PATHS' , 'pKa Tools' , os . path . join ( os . path . expanduser ( '~' ) , 'PEAT' ) ) default . set ( 'PATHS' , 'uffbaps' , os . path . join ( os . path . expanduser ( '~' ) , 'PEAT/UFFBAPS' ) ) default . set ( 'WORKING DIRECTORY' , 'copyIfExists' , str ( 0 ) ) default . set ( 'WORKING DIRECTORY' , 'copyLocation' , os . getcwd ( ) ) default . set ( 'WORKING DIRECTORY' , 'overwriteExistingCopies' , str ( 0 ) ) default . set ( 'WORKING DIRECTORY' , 'useUniqueID' , str ( 0 ) ) default . set ( 'PDBS' , 'pdbCleanProgram' , 'WHATIF' ) if writeFile : file = open ( 'proteinDesignTool.conf' , 'w' ) default . write ( file ) file . close ( ) return default
Creates a default ConfigParser object instances of this class can use
Parameters
writeFile - If True writes a default configuration file in the current directory
Creates a default ConfigParser object instances of this class can use Parameters writeFile - If True writes a default configuration file in the current directory
'''Creates a default ConfigParser object instances of this class can use
		
		Parameters -
			writeFile - If True writes a default configuration file in the current directory''' #Add default configuration values # pKa calculation parameters # Method # Be not-so-noisy # Do not save the solutions #Set a default location for the pKa Tools #Working directory configuration (optional) #Users may not want to overwrite files in an existing working dir #These options configure this behaviour #If requested write out this default configuration  #wherever the program is being run from
self
writeFile