code: public String toPDB(Structure s1, Structure s2){
  
  
  		Structure newpdb = getAlignedStructure(s1, s2);
  
  		return newpdb.toPDB();
  	}
docs: converts the alignment to a PDB file
  each of the structures will be represented as a model.
  
  
  @param s1
  @param s2
  @return a PDB file as a String