code: private static final double scoreAfp(AFP afp, double badRmsd, double fragScore)
  	{
  		//longer AFP with low rmsd is better
  		double  s, w;
  		//s = (rmsdCut - afptmp.rmsd) * afptmp.len; //the same scroing strategy as that in the post-processing
  		w = afp.getRmsd() / badRmsd;
  		w = w * w;
  		s = fragScore * (1.0 - w);
  		return s;
  	}
docs: Assign score to each AFP