code: private static void section1(List<PolymerNotation> polymers, Map<String, String> mapIds) throws NotationException {
      for (PolymerNotation polymer : polymers) {
        if (mapIds.containsKey(polymer.getPolymerID().getId())) {
          /* change id */
          PolymerNotation newpolymer = new PolymerNotation(mapIds.get(polymer.getPolymerID().getId()));
          newpolymer = new PolymerNotation(newpolymer.getPolymerID(), polymer.getPolymerElements());
          helm2notation.addPolymer(newpolymer);
        } else {
          helm2notation.addPolymer(polymer);
        }
  
      }
  
    }
docs: method to add PolymerNotations to the existent
  
  @param polymers PolymerNotation
  @param mapIds Map of old and new Ids
  @throws NotationException if notation is not valid