code: public static double getAngle(AFPChain afpChain, Atom[] ca1, Atom[] ca2) {
  		Matrix rotation = afpChain.getBlockRotationMatrix()[0];
  		return Math.acos(rotation.trace() - 1) * 180 / Math.PI;
  	}
docs: Returns the <em>magnitude</em> of the angle between the first and second
  blocks of {@code afpChain}, measured in degrees. This is always a
  positive value (unsigned).
  
  @param afpChain
  @param ca1
  @param ca2
  @return