code: public static AFPChain fastaToAfpChain(String sequence1, String sequence2, Structure structure1,
  			Structure structure2) throws StructureException, CompoundNotFoundException {
  		ProteinSequence s1 = new ProteinSequence(sequence1);
  		s1.setUserCollection(getAlignedUserCollection(sequence1));
  		ProteinSequence s2 = new ProteinSequence(sequence2);
  		s2.setUserCollection(getAlignedUserCollection(sequence2));
  		return fastaToAfpChain(s1, s2, structure1, structure2);
  	}
docs: TODO Write comment
  @param sequence1
  @param sequence2
  @param structure1
  @param structure2
  @return
  @throws StructureException
  @throws CompoundNotFoundException