code: private static void addAdHocMonomer(MonomerNotation monomerNotation) throws IOException, JDOMException, ChemistryException {
      Monomer monomer = MonomerFactory.getInstance().getMonomerStore().getMonomer(monomerNotation.getType(), monomerNotation.getUnit().replace("[", "").replace("]", ""));
      if (monomer.isAdHocMonomer()) {
        set.add(monomer);
      }
  
    }
docs: method to add the monomer to the database if it is an adhoc monomer
  
  @param monomerNotation MonomerNotation
  @throws JDOMException jdome error
  @throws IOException IO error
  @throws ChemistryException if chemistry engine can not be initialized
  @throws CTKException general ChemToolKit exception passed to HELMToolKit