code: public AminoAcid mutateResidue(AminoAcid oldAmino, String newType)
  	throws PDBParseException {
  
  		AminoAcid newgroup = new AminoAcidImpl();
  
  		newgroup.setResidueNumber(oldAmino.getResidueNumber());
  		newgroup.setPDBName(newType);
  
  
  		AtomIterator aiter =new AtomIterator(oldAmino);
  		while (aiter.hasNext()){
  			Atom a = aiter.next();
  			if ( supportedAtoms.contains(a.getName())){
  				newgroup.addAtom(a);
  			}
  		}
  
  		return newgroup;
  
  	}
docs: create a new residue which is of the new type.
  Only the atoms N, Ca, C, O, Cb will be considered.
  @param oldAmino
  @param newType
  @return a new, mutated, residue
  @throws PDBParseException