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src/b/i/biskit-2.4/Biskit/AmberParmBuilder.py   biskit(Download)
 
        cleaner = PDBCleaner( m, log=self.log, verbose=self.verbose )
        m = cleaner.process( keep_hetatoms=hetatm, amber=1 )
 
        m.renumberResidues( addChainId=1 )