Substructure search

SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  // Benzene
  IAtomContainer A1 = sp.parseSmiles("C1=CC=CC=C1");
  // Napthalene
  IAtomContainer A2 = sp.parseSmiles("C1=CC2=C(C=C1)C=CC=C2");
  //Turbo mode search
  //Bond Sensitive is set true
  SMSD comparison = new SMSD(Algorithm.SubStructure, true);
  // set molecules and remove hydrogens
  comparison.init(A1, A2, true);
  // set chemical filter true
  comparison.setChemFilters(false, false, false);
  if (comparison.isSubgraph()) {
  //Get similarity score
   System.out.println("Tanimoto coefficient:  " + comparison.getTanimotoSimilarity());
   System.out.println("A1 is a subgraph of A2:  " + comparison.isSubgraph());
  //Get Modified AtomContainer
   IAtomContainer Mol1 = comparison.getReactantMolecule();
   IAtomContainer Mol2 = comparison.getProductMolecule();
  // Print the mapping between molecules
   System.out.println(" Mappings: ");
   for (Map.Entry  mapping : comparison.getFirstMapping().entrySet()) {
      System.out.println((mapping.getKey() + 1) + " " + (mapping.getValue() + 1));

      IAtom eAtom = Mol1.getAtom(mapping.getKey());
      IAtom pAtom = Mol2.getAtom(mapping.getValue());
      System.out.println(eAtom.getSymbol() + " " + pAtom.getSymbol());
   }
   System.out.println("");
  }