code: public double getRmsd() {
  
  		if (alignment == null)
  			return -1.0;
  		if (alignment.getScore(MultipleAlignmentScorer.RMSD) == null)
  			return MultipleAlignmentScorer.getRMSD(alignment);
  
  		return alignment.getScore(MultipleAlignmentScorer.RMSD);
  	}
docs: The RMSD between the equivalent residues of the equivalent Subunits after
  superposition of the Subunit groups. This is equivalent to
  multipleAlignment.getScore(MultipleAlignmentScorer.RMSD).
  
  @return rmsd