code: private void orderTransformationsByChainId(Structure asymUnit, List<BiologicalAssemblyTransformation> transformations) {
  		final List<String> chainIds = getChainIds(asymUnit);
  		Collections.sort(transformations, new Comparator<BiologicalAssemblyTransformation>() {
  			@Override
  			public int compare(BiologicalAssemblyTransformation t1, BiologicalAssemblyTransformation t2) {
  				// set sort order only if the two ids are identical
  				if (t1.getId().equals(t2.getId())) {
  					 return chainIds.indexOf(t1.getChainId()) - chainIds.indexOf(t2.getChainId());
  				} else {
  					return t1.getId().compareTo(t2.getId());
  				}
  		    }
  		});
  	}
docs: Orders model transformations by chain ids in the same order as in the asymmetric unit
  @param asymUnit
  @param transformations