code: public synchronized Map<String, Map<String, Monomer>> getMonomerDB(boolean includeNewMonomers) {
  		if (includeNewMonomers) {
  			return monomerDB;
  		} else {
  			Map<String, Map<String, Monomer>> reducedMonomerDB = new TreeMap<String, Map<String, Monomer>>(
  					String.CASE_INSENSITIVE_ORDER);
  			for (String polymerType : monomerDB.keySet()) {
  				Map<String, Monomer> monomerMap = monomerDB.get(polymerType);
  				reducedMonomerDB.put(polymerType, excludeNewMonomers(monomerMap));
  			}
  			return reducedMonomerDB;
  		}
  	}
docs: returns the monomer database including monomers that where temporary
  marked as new, else without those monomers
  
  @param includeNewMonomers
  if true, then the new monomers will be added to the monomer db
  @return Map as {@code Map<String, Map<String, Monomer>>}