code: public static final void rotate(Structure structure,
  			double[][] rotationmatrix) throws StructureException {
  
  		if ( rotationmatrix.length != 3 ) {
  			throw new StructureException ("matrix does not have size 3x3 !");
  		}
  		AtomIterator iter = new AtomIterator(structure) ;
  		while (iter.hasNext()) {
  			Atom atom = iter.next() ;
  			Calc.rotate(atom,rotationmatrix);
  		}
  	}
docs: Rotate a structure. The rotation Matrix must be a pre-multiplication
  Matrix.
  
  @param structure
  a Structure object
  @param rotationmatrix
  an array (3x3) of double representing the rotation matrix.
  @throws StructureException
  ...