code: public static void hybridize(HELM2Notation helm2notation) throws NotationException, RNAUtilsException,
  			HELM2HandledException, org.helm.notation2.exception.NotationException, ChemistryException {
  		if (HELM2NotationUtils.getAllBasePairConnections(helm2notation.getListOfConnections()).isEmpty()
  				&& HELM2NotationUtils.getRNAPolymers(helm2notation.getListOfPolymers()).size() == 2) {
  			List<ConnectionNotation> connections = RNAUtils.hybridize(
  					HELM2NotationUtils.getRNAPolymers(helm2notation.getListOfPolymers()).get(0),
  					HELM2NotationUtils.getRNAPolymers(helm2notation.getListOfPolymers()).get(1));
  			for (ConnectionNotation connection : connections) {
  				addConnection(connection, helm2notation.getListOfConnections().size(), helm2notation);
  			}
  		}
  	}
docs: this method will automatically add base pair info into notation only if
  it contains two RNA polymer notations and there is no base pairing info
  
  @param helm2notation
  HELM2Notation object
  @throws NotationException
  if notation is not valid
  @throws RNAUtilsException
  if the polymer is not a RNA/DNA
  @throws HELM2HandledException
  if it contains HELM2 specific features, so that it can not be
  casted to HELM1 Format
  @throws org.helm.notation2.exception.NotationException
  if notation is not valid
  @throws ChemistryException
  if chemistry engine can not be initialized