code: public static final void rotate(Atom atom, Matrix m){
  
  		double x = atom.getX();
  		double y = atom.getY();
  		double z = atom.getZ();
  		double[][] ad = new double[][]{{x,y,z}};
  
  		Matrix am = new Matrix(ad);
  		Matrix na = am.times(m);
  
  		atom.setX(na.get(0,0));
  		atom.setY(na.get(0,1));
  		atom.setZ(na.get(0,2));
  
  	}
docs: Rotate an Atom around a Matrix object. The rotation Matrix must be a
  pre-multiplication Matrix.
  
  @param atom
  atom to be rotated
  @param m
  rotation matrix to be applied to the atom