src/main/java/org/helm/notation2/parser/notation/polymer/MonomerNotationUnitRNA.java
private void setRNAContents(String str) throws NotationException {
    /* Nucleotide with all contents */
    String[] list;

    // if (str.contains("(")) {
    List<String> items = extractContents(str);
    for (String item : items) {
    	if(item.length()> 1){
    		if(!(item.startsWith("[") && item.endsWith("]"))){
    			throw new NotationException("Monomers have to be in brackets "+ item);
    		}
    	}
      contents.add(new MonomerNotationUnit(item, type));

    }

    // } /* nucleotide contains no base, but a modified sugar or phosphat */
    // else if (str.contains("[")) {
    // if (str.startsWith("[")) {
    // str = str.replace("]", "]$");
    // } else {
    // str = str.replace("[", "$[");
    // }
    // list = str.split("\\$");
    // for (int i = 0; i < list.length; i++) {
    // contents.add(new MonomerNotationUnit(list[i], type));
    // }
    // } /* nucleotide contains only standard sugar and/or phosphat */ else {
    // for (int i = 0; i < str.length(); i++) {
    // contents.add(new MonomerNotationUnit(Character.toString(str.charAt(i)),
    // type));
    // }
    // }

  }
private void setRNAContents(String str) throws NotationException {
    /* Nucleotide with all contents */
    String[] list;

    // if (str.contains("(")) {
    List<String> items = extractContents(str);
    for (String item : items) {
    	if(item.length()> 1){
    		if(!(item.startsWith("[") && item.endsWith("]"))){
    			throw new NotationException("Monomers have to be in brackets "+ item);
    		}
    	}
      contents.add(new MonomerNotationUnit(item, type));

    }

    // } /* nucleotide contains no base, but a modified sugar or phosphat */
    // else if (str.contains("[")) {
    // if (str.startsWith("[")) {
    // str = str.replace("]", "]$");
    // } else {
    // str = str.replace("[", "$[");
    // }
    // list = str.split("\\$");
    // for (int i = 0; i < list.length; i++) {
    // contents.add(new MonomerNotationUnit(list[i], type));
    // }
    // } /* nucleotide contains only standard sugar and/or phosphat */ else {
    // for (int i = 0; i < str.length(); i++) {
    // contents.add(new MonomerNotationUnit(Character.toString(str.charAt(i)),
    // type));
    // }
    // }

  }
method to set for each nucleotide the sugar, the base and the phosphat

@param str monomer notation
@throws NotationException if  single monomers are not in brackets