code: public void identify(final Structure structure,
  			final Set<ProteinModification> potentialModifications) {
  		if (structure==null) {
  			throw new IllegalArgumentException("Null structure.");
  		}
  
  		identify(structure.getChains(), potentialModifications);
  	}
docs: Identify a set of modifications in a structure.
  @param structure query {@link Structure}.
  @param potentialModifications query {@link ProteinModification}s.