code: public static void calculateScores(MultipleAlignment alignment)
  			throws StructureException {
  
  		// Put RMSD
  		List<Atom[]> trans = MultipleAlignmentTools.transformAtoms(alignment);
  		alignment.putScore(RMSD, getRMSD(trans));
  
  		// Put AvgTM-Score
  		List<Integer> lengths = new ArrayList<Integer>(alignment.size());
  		for (Atom[] atoms : alignment.getAtomArrays()) {
  			lengths.add(atoms.length);
  		}
  		alignment.putScore(AVGTM_SCORE, getAvgTMScore(trans, lengths));
  	}
docs: Calculates and puts the RMSD and the average TM-Score of the
  MultipleAlignment.
  
  @param alignment
  @throws StructureException
  @see #getAvgTMScore(MultipleAlignment)
  @see #getRMSD(MultipleAlignment)