code: public static AFPChain fastaStringToAfpChain(String sequence1, String sequence2, Structure structure1,
  			Structure structure2) throws StructureException, CompoundNotFoundException {
  		ProteinSequence seq1 = new ProteinSequence(sequence1);
  		ProteinSequence seq2 = new ProteinSequence(sequence2);
  		return fastaToAfpChain(seq1, seq2, structure1, structure2);
  	}
docs: Returns an AFPChain corresponding to the alignment between {@code structure1} and {@code structure2}, which is given by the gapped protein sequences {@code sequence1} and {@code sequence2}. The
  sequences need not correspond to the entire structures, since local alignment is performed to match the sequences to structures.
  @throws StructureException
  @throws CompoundNotFoundException