code: private static Matrix4d getTransformForClusterSubunitMap(
  			List<SubunitCluster> clusters,
  			Map<Integer, Map<Integer, Integer>> clusterSubunitMap)
  			throws StructureException {
  
  		Pair<Atom[]> pair = getAlignedAtomsForClusterSubunitMap(clusters,
  				clusterSubunitMap);
  
  		return SuperPositions.superpose(Calc.atomsToPoints(pair.getFirst()),
  				Calc.atomsToPoints(pair.getSecond()));
  
  	}
docs: Returns the transformation matrix corresponding to the alignment of
  subunit matchings.
  <p>
  Utility method to cumulative calculate the alignment transformation.
  
  @param clusters
  List of SubunitClusters
  @param clusterSubunitMap
  map from cluster id to subunit matching
  @return transformation matrix
  @throws StructureException