code: private void rotateShiftAtoms(Atom[] ca){
  
  		for (int i  = 0 ; i < ca.length; i++){
  			Atom c = ca[i];
  
  			Calc.rotate(c,currentRotMatrix);
  			Calc.shift(c,currentTranMatrix);
  			//System.out.println("after " + c);
  			ca[i] = c;
  		}
  		//System.out.println("after " + ca[0]);
  	}
docs: rotate and shift atoms with currentRotMatrix and current Tranmatrix
  
  @param ca