code: private static final double getEnd2EndDistance(Atom[] ca1, Atom[] ca2, int p1b, int p1e, int p2b, int p2e)
  	{
  
  		double min = 99;
  			double dist1 = Calc.getDistance(ca1[p1b], ca1[p1e]);
  			double dist2 = Calc.getDistance(ca2[p2b], ca2[p2e]);
  			min = dist1 - dist2;
  
  		return Math.abs(min);
  	}
docs: filter 1 for AFP extration: the distance of end-to-end
  @param p1b
  @param p1e
  @param p2b
  @param p2e
  @return