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Runs the pKa calculation. This method does not return until the run is finished which may take some time.

Parameters:
        cleanPDB - If True the all waters and ligands are removed from the pdbfile before the run.
                Default is True.

src/p/e/PEATDB-2.3/PEATSA/Core/ProteinDesignTool.py   PEATDB(Download)
						configuration=self.configuration,
						filename=self.pdbFile)
			pKaRun.run(cleanPDB=False)
		else:
			raise Exceptions.EnvironmentError, "Cannot run a pKa calculation in a parallel environment"
						configuration=self.configuration,
						filename=self.pdbFile)
				pKaRun.run(cleanPDB=False)
				#Retry
				scanner.scan(mutantCollection=mutantCollection, verbose=verbose)