code: public static final void rotate(Atom atom, double[][] m){
  
  		double x = atom.getX();
  		double y = atom.getY() ;
  		double z = atom.getZ();
  
  		double nx = m[0][0] * x + m[0][1] * y +  m[0][2] * z ;
  		double ny = m[1][0] * x + m[1][1] * y +  m[1][2] * z ;
  		double nz = m[2][0] * x + m[2][1] * y +  m[2][2] * z ;
  
  		atom.setX(nx);
  		atom.setY(ny);
  		atom.setZ(nz);
  	}
docs: Rotate a single Atom aroud a rotation matrix. The rotation Matrix must be
  a pre-multiplication 3x3 Matrix.
  
  If the matrix is indexed m[row][col], then the matrix will be
  pre-multiplied (y=atom*M)
  
  @param atom
  atom to be rotated
  @param m
  a rotation matrix represented as a double[3][3] array