gistfile1.java

static IAtomContainer mykekule(IAtomContainer org) throws Exception {
        
    final IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
    final SmilesParser smipar = new SmilesParser(bldr);
    final SmilesGenerator smigen = SmilesGenerator.unique();

    final int n = org.getAtomCount();
    int[] ordering = new int[n];
        
    // generate a kekule assignment via SMILES and store the output order (a permutation of
    // atom indices)
    IAtomContainer cpy = smipar.parseSmiles(smigen.create(org, ordering));
        
    // index atoms for lookup
    final Map<IAtom,Integer> atomIndexMap = new HashMap<>();
    for (IAtom atom : org.atoms())
        atomIndexMap.put(atom, atomIndexMap.size());

    // util to get atom index -> bond map
    EdgeToBondMap bondMap = EdgeToBondMap.withSpaceFor(cpy);
    GraphUtil.toAdjList(cpy, bondMap);
        
    for (IBond bond : org.bonds()) {
            
        // atom indices
        int u = atomIndexMap.get(bond.getAtom(0));
        int v = atomIndexMap.get(bond.getAtom(1));
            
        // atom indices in 'cpy'
        int uCpy = ordering[u];
        int vCpy = ordering[v];
            
        // propagate the assigned bond order
        bond.setOrder(bondMap.get(uCpy, vCpy).getOrder());
            
        // note the following would also work to get the cpy bond
        // cpy.getBond(cpy.getAtom(uCpy), cpy.getAtom(vCpy));
    }
        
    return org;
}