Setup.java

RandomAccessMDLReader reader = new RandomAccessMDLReader(new File(...));
EncodingFingerprint fingerprinter = new Encoding2DMolprint();

// We will use a pipeline in order to speedup the persisting process
Pipeline p = jedis.pipelined();

// Iterate the compounds one by one
for (int i = 0; i < reader.getSize(); i++) {

  // Retrieve the molecule and the fingerprints for this molecule
  Molecule molecule = reader.getMol(i);
  FeatureMap fingerprints = new FeatureMap(fingerprinter.getFingerprint(molecule));

  // Retrieve some of the compound properties we want to use later on
  String compound_cid = (String)molecule.getProperty("PUBCHEM_COMPOUND_CID");

  // Iterate the fingerprints
  for (IFeature fingerprint : fingerprints.getKeySet()) {

    // Check whether we already encountered the feature and create accordingly (
    String thefeaturestring = fingerprint.featureToString();
    if (!fingerprintlist.contains(thefeaturestring)) {
      fingerprintlist.add(thefeaturestring);
    }

    // Get the index of the fingerprint
    int fingerprintindex = fingerprintlist.indexOf(thefeaturestring);

    // Increment the weight of this fingerprint (number of occurences)
    p.incr(fingerprintindex + ":w");
    // Create the inverted indexes
    // Add the fingerprint to the set of fingerprints of this compound
    p.sadd((compound_cid + ":f"), fingerprintindex + "");
    // Add the compound to the set of compounds of this fingerprint
    p.sadd(fingerprintindex + ":c", compound_cid + "");

  }
  // Sync the changes
  p.sync();
}