PEATSA/Tools/ExampleFunction.py
def DeltaStability(inputFile, mutationList, configurationFile=None, workingDirectory=os.getcwd(), outputDirectory=os.getcwd()):

	'''Calculates the stability difference between a protein and set of mutants
	
	Parameters:
		inputFile: A PDB file of the protein
		mutationList: A list of Data.MutationSet instances. Each represents a mutant of the protein.
		configurationFile: The location of a proteinDesignTool.conf file - defaults to home directory.
		workingDirectory: Where the calculation will be run. 
		outputDirectory: Where the results will be written.
		
	Returns
		A Data.DataSet instance containing one matrix, stabilityResults.
		Each row of this matrix corresponds to a mutant defined in the mutationList argument.'''

	#Create the ProteinDesignTool instance
	tool = Core.ProteinDesignTool.ProteinDesignTool(configurationFile, 
			workingDirectory=workingDirectory,
			pdbFile=inputFile, 
			outputDirectory=outputDirectory)
	
	#The above cleans the pdb file and copies it to the working directory.
	#Use this pdb from now on.
	inputFile = tool.pdbFile
	
	#Create the mutants
	mutantCollection = Core.Data.MutantCollection(pdbFile=inputFile,
					mutationList=mutationList,
					location=outputDirectory,
					temporary=True)
					
	#Run stability calculation
	#The results are added to the ProteinDesignTool instance's dataDirectory attribute
	#This is an instance of Data.DataSet class
	tool.runStabilityCalculation(mutantFiles=mutantCollection.mutantFiles())

	#Clean up - Deletes files copied to the working directory for Uffbaps
	tool.cleanUp()
	
	return tool.dataDirectory
Calculates the stability difference between a protein and set of mutants
	
	Parameters:
		inputFile: A PDB file of the protein
		mutationList: A list of Data.MutationSet instances. Each represents a mutant of the protein.
		configurationFile: The location of a proteinDesignTool.conf file - defaults to home directory.
		workingDirectory: Where the calculation will be run. 
		outputDirectory: Where the results will be written.
		
	Returns
		A Data.DataSet instance containing one matrix, stabilityResults.
		Each row of this matrix corresponds to a mutant defined in the mutationList argument.
Calculates the stability difference between a protein and set of mutants
Calculates the stability difference between a protein and set of mutants
def DeltaStability(inputFile, mutationList, configurationFile=None, workingDirectory=os.getcwd(), outputDirectory=os.getcwd()):
	tool = Core.ProteinDesignTool.ProteinDesignTool(configurationFile, 
			workingDirectory=workingDirectory,
			pdbFile=inputFile, 
			outputDirectory=outputDirectory)
	inputFile = tool.pdbFile
	mutantCollection = Core.Data.MutantCollection(pdbFile=inputFile,
					mutationList=mutationList,
					location=outputDirectory,
					temporary=True)
	tool.runStabilityCalculation(mutantFiles=mutantCollection.mutantFiles())
	tool.cleanUp()
	return tool.dataDirectory
def DeltaStability ( inputFile , mutationList , configurationFile = None , workingDirectory = os . getcwd ( ) , outputDirectory = os . getcwd ( ) ) : tool = Core . ProteinDesignTool . ProteinDesignTool ( configurationFile , workingDirectory = workingDirectory , pdbFile = inputFile , outputDirectory = outputDirectory ) inputFile = tool . pdbFile mutantCollection = Core . Data . MutantCollection ( pdbFile = inputFile , mutationList = mutationList , location = outputDirectory , temporary = True ) tool . runStabilityCalculation ( mutantFiles = mutantCollection . mutantFiles ( ) ) tool . cleanUp ( ) return tool . dataDirectory
Calculates the stability difference between a protein and set of mutants
Calculates the stability difference between a protein and set of mutants
'''Calculates the stability difference between a protein and set of mutants
	
	Parameters:
		inputFile: A PDB file of the protein
		mutationList: A list of Data.MutationSet instances. Each represents a mutant of the protein.
		configurationFile: The location of a proteinDesignTool.conf file - defaults to home directory.
		workingDirectory: Where the calculation will be run. 
		outputDirectory: Where the results will be written.
		
	Returns
		A Data.DataSet instance containing one matrix, stabilityResults.
		Each row of this matrix corresponds to a mutant defined in the mutationList argument.''' #Create the ProteinDesignTool instance #The above cleans the pdb file and copies it to the working directory. #Use this pdb from now on. #Create the mutants #Run stability calculation #The results are added to the ProteinDesignTool instance's dataDirectory attribute #This is an instance of Data.DataSet class #Clean up - Deletes files copied to the working directory for Uffbaps
inputFile
A PDB file of the protein
A PDB file of the protein
mutationList
A list of Data.MutationSet instances. Each represents a mutant of the protein.
A list of Data . MutationSet instances . Each represents a mutant of the protein .
configurationFile
The location of a proteinDesignTool.conf file - defaults to home directory.
The location of a proteinDesignTool . conf file - defaults to home directory .
workingDirectory
None
outputDirectory
None