code: public static AFPChain fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>, AminoAcidCompound> alignment,
  			Structure structure1, Structure structure2) throws StructureException {
  		List<AlignedSequence<Sequence<AminoAcidCompound>, AminoAcidCompound>> seqs = alignment.getAlignedSequences();
  		StringBuilder sb1 = new StringBuilder();
  		for (AminoAcidCompound a : seqs.get(0)) {
  			sb1.append(a.getBase());
  		}
  		try {
  			ProteinSequence seq1 = new ProteinSequence(sb1.toString());
  			StringBuilder sb2 = new StringBuilder();
  			for (AminoAcidCompound a : seqs.get(1)) {
  				sb1.append(a.getBase());
  			}
  			ProteinSequence seq2 = new ProteinSequence(sb2.toString());
  			LinkedHashMap<String, ProteinSequence> map = new LinkedHashMap<String, ProteinSequence>();
  			map.put(structure1.getName(), seq1);
  			map.put(structure2.getName(), seq2);
  			return fastaToAfpChain(map, structure1, structure2);
  		} catch (CompoundNotFoundException e) {
  			logger.error("Unexpected error while creating protein sequences: {}. This is most likely a bug.",e.getMessage());
  			return null;
  		}
  	}
docs: Provided only for convenience.
  
  @see #fastaToAfpChain(ProteinSequence, ProteinSequence, Structure, Structure)
  @throws StructureException