How to use org.openscience.cdk

@Override
public Object clone() throws CloneNotSupportedException {
  ChemSequence clone = (ChemSequence) super.clone();
  // clone the chemModels
  clone.chemModelCount = getChemModelCount();
  clone.chemModels = new ChemModel[clone.chemModelCount];
  for (int f = 0; f < clone.chemModelCount; f++) {
    clone.chemModels[f] = (ChemModel) ((ChemModel) chemModels[f]).clone();
  }
  return clone;
}

@Override
public void startDocument() {
  chemFile = new ChemFile();
  chemSequence = new ChemSequence();
  chemModel = new ChemModel();
  setOfMolecules = new AtomContainerSet();
}

/**
 * Access a set of candidates for a given key. Candidates match the
 * interface an number of parameters for the constructors. A key may
 * match when it's parameters are subclasses.
 *
 * @param key the key to find possible candidates for
 * @return set of constructors which 'could' match the given key
 */
public Set<ConstructorKey> getCandidates(ConstructorKey key) {
  return getCandidates(key.intf(), key.n());
}

  /**
   * {@inheritDoc}
   */
  @Override
  public IAtomContainer newAtomContainer() {
    if (CDK_LEGACY_AC)
      return new AtomContainer();
    else
      return new AtomContainer2();
  }
}

  @Override
  public IChemObject newTestObject() {
    return new Mapping(new Atom(), new Atom());
  }
});

@Override
public IAtom getAtom(int idx) {
  switch (idx) {
    case 0:
      return getBegin();
    case 1:
      return getEnd();
    default:
      return mol.getAtomRef(super.getAtom(idx));
  }
}

/**
 *{@inheritDoc}
 */
@Override
public T create(Object[] objects) throws InvocationTargetException, IllegalAccessException,
    InstantiationException {
  T instance = parent.create(objects);
  modifier.modify(instance);
  return instance;
}

/**
 * {@inheritDoc}
 */
@Override
public int indexOf(IAtom atom) {
  final AtomRef aref = getAtomRefUnsafe(atom);
  return aref == null ? -1 : aref.getIndex();
}

/**
 * {@inheritDoc}
 */
@Override
public IBond getBond(IAtom beg, IAtom end) {
  final AtomRef begref = getAtomRefUnsafe(beg);
  return begref != null ? begref.getBond(end) : null;
}

/**
 * {@inheritDoc}
 */
@Override
public int indexOf(IBond bond) {
  final BondRef bref = getBondRefUnsafe(bond);
  return bref == null ? -1 : bref.getIndex();
}

/**
 * Add an Atom and makes it the C-terminus atom.
 *
 * @param atom  The Atom that is the C-terminus
 *
 * @see    #getCTerminus
 */
@Override
public void addCTerminus(IAtom atom) {
  super.addAtom(atom);
  setCTerminus(atom);
}

/**
 * {@inheritDoc}
 */
@Override
public int getConnectedBondsCount(IAtom atom) {
  return getAtomRef(atom).getBondCount();
}

/**
 * Creates a constructor key for use in accessing constructors. The key
 * combines the interface and types in a single instance which we can then
 * use in a map.
 *
 * @param intf  the interface to build the key for
 * @param types the classes that the the constructor requires
 * @return a constructor key which can be used to lookup a constructor
 */
public static ConstructorKey key(Class<?> intf, Class<?>... types) {
  return new ClassBasedKey(intf, convert(types));
}

  /**
   * {@inheritDoc}
   */
  @Override
  public IAtomContainer newAtomContainer() {
    if (CDK_LEGACY_AC)
      return new AtomContainer();
    else
      return new AtomContainer2();
  }
}

@Override
public Object clone() throws CloneNotSupportedException {
  ChemSequence clone = (ChemSequence) super.clone();
  // clone the chemModels
  clone.chemModelCount = getChemModelCount();
  clone.chemModels = new ChemModel[clone.chemModelCount];
  for (int f = 0; f < clone.chemModelCount; f++) {
    clone.chemModels[f] = (ChemModel) ((ChemModel) chemModels[f]).clone();
  }
  return clone;
}

@Override
public IAtom getAtom(int idx) {
  switch (idx) {
    case 0:
      return getBegin();
    case 1:
      return getEnd();
    default:
      return mol.getAtomRef(super.getAtom(idx));
  }
}

/**
 *{@inheritDoc}
 */
@Override
public T create(Object[] objects) throws InvocationTargetException, IllegalAccessException,
    InstantiationException {
  T instance = parent.create(objects);
  modifier.modify(instance);
  return instance;
}

/**
 * {@inheritDoc}
 */
@Override
public int indexOf(IAtom atom) {
  final AtomRef aref = getAtomRefUnsafe(atom);
  return aref == null ? -1 : aref.getIndex();
}

/**
 * {@inheritDoc}
 */
@Override
public IBond getBond(IAtom beg, IAtom end) {
  final AtomRef begref = getAtomRefUnsafe(beg);
  return begref != null ? begref.getBond(end) : null;
}

/**
 * {@inheritDoc}
 */
@Override
public int getConnectedBondsCount(IAtom atom) {
  return getAtomRef(atom).getBondCount();
}