public class ProteinSearch {
	private final Protein cur;
	private Protein best;
	private int bestScore;

	public ProteinSearch(String chain) {
		cur = new Protein(chain);
		best = (Protein) cur.clone();
		bestScore = Integer.MIN_VALUE;
	}

	public Protein search() {
		search(0, cur.getLength() - 1, cur.getLength() - 1);
		return best;
	}

	private void search(int index, int row, int col) {
		cur.setLocation(index, row, col);
		if(index >= cur.getLength() - 1) { // we have placed final residue
			int score = cur.getScore();
			if(score > bestScore) {
				bestScore = score;
				best = (Protein) cur.clone();
			}
		} else {
			search(index + 1, row + 1, col); // try stepping south
			search(index + 1, row, col + 1); // or east
			search(index + 1, row - 1, col); // or north
			search(index + 1, row, col - 1); // or west
		}
	}
}