code: public static final double getDistance(Atom a, Atom b) {
  		double x = a.getX() - b.getX();
  		double y = a.getY() - b.getY();
  		double z = a.getZ() - b.getZ();
  
  		double s  = x * x  + y * y + z * z;
  
  		return Math.sqrt(s);
  	}
docs: calculate distance between two atoms.
  
  @param a
  an Atom object
  @param b
  an Atom object
  @return a double