code: public static double getRMSD(MultipleAlignment alignment) {
  		List<Atom[]> trans = MultipleAlignmentTools.transformAtoms(alignment);
  		return getRMSD(trans);
  	}
docs: Calculates the RMSD of all-to-all structure comparisons (distances) of
  the given MultipleAlignment.
  <p>
  Complexity: T(n,l) = O(l*n^2), if n=number of structures and l=alignment
  length.
  <p>
  The formula used is just the sqroot of the average distance of all
  possible pairs of atoms. Thus, for R structures aligned over C columns
  without gaps, we have
  
  <pre>
  RMSD = \sqrt{1/(C*(R*(R-1)/2)) * \sum_{r1=1}^{R-1}
  \sum_{r2=r1+1}^{R-1} \sum_{j=0}^{C-1} (atom[r1][c]-atom[r2][c])^2}
  </pre>
  
  @param alignment
  @return double RMSD