code: public void startObject(String objectType) {
          logger.debug("START:" + objectType);
          if (objectType.equals("Molecule")) {
              currentMolecule = builder.newInstance(IAtomContainer.class);
              atomEnumeration = new Hashtable<String, Integer>();
          } else if (objectType.equals("Atom")) {
              currentAtom = builder.newInstance(IAtom.class, "H");
              logger.debug("Atom # " + numberOfAtoms);
              numberOfAtoms++;
          } else if (objectType.equals("Bond")) {
              bond_id = null;
              bond_stereo = (IBond.Stereo) CDKConstants.UNSET;
          }
      }
docs: Procedure required by the CDOInterface. This function is only
  supposed to be called by the JCFL library