sandbox/ProteinComplexTool_parallel.py
def DeltaStability(self,inputFile, mutationList, configurationFile, workingDirectory, outputDirectory):
             
            '''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,
                            removeHeterogens=True)

            #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(self,inputFile, mutationList, configurationFile, workingDirectory, outputDirectory):
            tool = Core.ProteinDesignTool.ProteinDesignTool(configurationFile, 
                            workingDirectory=workingDirectory,
                            pdbFile=inputFile, 
                            outputDirectory=outputDirectory,
                            removeHeterogens=True)
            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 ( self , inputFile , mutationList , configurationFile , workingDirectory , outputDirectory ) : tool = Core . ProteinDesignTool . ProteinDesignTool ( configurationFile , workingDirectory = workingDirectory , pdbFile = inputFile , outputDirectory = outputDirectory , removeHeterogens = True ) 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
self
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