Examples with BitSetFingerprint org.openscience.cdk.fingerprint.BitSetFingerprint used on opensource projects

Example 1 with BitSetFingerprint

use of org.openscience.cdk.fingerprint.BitSetFingerprint in project cdk by cdk.

the class TanimotoTest method testCompareBitSetandBitFingerprintTanimoto.

@Test
public void testCompareBitSetandBitFingerprintTanimoto() throws Exception {
    IAtomContainer mol1 = TestMoleculeFactory.make123Triazole();
    IAtomContainer mol2 = TestMoleculeFactory.makeImidazole();
    Fingerprinter fingerprinter = new Fingerprinter(1024, 8);
    BitSet bs1 = fingerprinter.getBitFingerprint(mol1).asBitSet();
    BitSet bs2 = fingerprinter.getBitFingerprint(mol2).asBitSet();
    float tanimoto = Tanimoto.calculate(bs1, bs2);
    BitSetFingerprint fp1 = new BitSetFingerprint(bs1);
    BitSetFingerprint fp2 = new BitSetFingerprint(bs2);
    double tanimoto2 = Tanimoto.calculate(fp1, fp2);
    Assert.assertEquals(tanimoto, tanimoto2, 0.01);
    IntArrayFingerprint ifp1 = new IntArrayFingerprint(fp1);
    IntArrayFingerprint ifp2 = new IntArrayFingerprint(fp2);
    tanimoto2 = Tanimoto.calculate(ifp1, ifp2);
    Assert.assertEquals(tanimoto, tanimoto2, 0.01);
}

Example 2 with BitSetFingerprint

use of org.openscience.cdk.fingerprint.BitSetFingerprint in project cdk by cdk.

the class Tanimoto method calculate.

/**
 * Evaluates Tanimoto coefficient for two <code>IBitFingerprint</code>.
 * <p>
 * @param fingerprint1 fingerprint for the first molecule
 * @param fingerprint2 fingerprint for the second molecule
 * @return The Tanimoto coefficient
 * @throws IllegalArgumentException if bitsets are not of the same length
 */
public static double calculate(IBitFingerprint fingerprint1, IBitFingerprint fingerprint2) {
    if (fingerprint1.size() != fingerprint2.size()) {
        throw new IllegalArgumentException("Fingerprints must have the same size");
    }
    int cardinality1 = fingerprint1.cardinality();
    int cardinality2 = fingerprint2.cardinality();
    // If the fingerprint is an IntArrayFingeprint that could mean a big
    // fingerprint so let's take the safe way out and create a
    // new IntArrayfingerprint
    IBitFingerprint one_and_two = fingerprint1 instanceof IntArrayFingerprint ? new IntArrayFingerprint(fingerprint1) : new BitSetFingerprint(fingerprint1);
    one_and_two.and(fingerprint2);
    double cardinalityCommon = one_and_two.cardinality();
    return cardinalityCommon / (cardinality1 + cardinality2 - cardinalityCommon);
}

Example 3 with BitSetFingerprint

use of org.openscience.cdk.fingerprint.BitSetFingerprint in project cdk by cdk.

the class TemplateExtractor method makeFingerprintsFromSdf.

public List<IBitFingerprint> makeFingerprintsFromSdf(boolean anyAtom, boolean anyAtomAnyBond, Map<String, Integer> timings, BufferedReader fin, int limit) throws Exception {
    HybridizationFingerprinter fingerPrinter = new HybridizationFingerprinter(HybridizationFingerprinter.DEFAULT_SIZE, HybridizationFingerprinter.DEFAULT_SEARCH_DEPTH);
    fingerPrinter.setHashPseudoAtoms(true);
    IAtomContainer m;
    IteratingSDFReader imdl = null;
    // QueryAtomContainer query=null;
    IAtomContainer query;
    List<IBitFingerprint> data = new ArrayList<>();
    ILoggingTool logger = LoggingToolFactory.createLoggingTool(getClass());
    try {
        logger.info("Read data file in ...");
        imdl = new IteratingSDFReader(fin, builder);
        // fin.close();
        logger.info("ready");
    } catch (Exception exc) {
        System.out.println("Could not read Molecules from file" + " due to: " + exc.getMessage());
    }
    int moleculeCounter = 0;
    int fingerprintCounter = 0;
    logger.info("Generated Fingerprints: " + fingerprintCounter + "    ");
    while (imdl.hasNext() && (moleculeCounter < limit || limit == -1)) {
        m = imdl.next();
        moleculeCounter++;
        if (anyAtom && !anyAtomAnyBond) {
            query = QueryAtomContainerCreator.createAnyAtomContainer(m, false);
        } else {
            query = AtomContainerManipulator.anonymise(m);
        }
        try {
            long time = -System.currentTimeMillis();
            // query fp for anyAtom is probably not useful
            data.add(fingerPrinter.getBitFingerprint(query));
            fingerprintCounter = fingerprintCounter + 1;
            time += System.currentTimeMillis();
            // store the time
            String bin = Integer.toString((int) Math.floor(time / 10.0));
            if (timings.containsKey(bin)) {
                timings.put(bin, (timings.get(bin)) + 1);
            } else {
                timings.put(bin, 1);
            }
        } catch (Exception exc1) {
            logger.info("QueryFingerprintError: from molecule:" + moleculeCounter + " due to:" + exc1.getMessage());
            // OK, just adds a fingerprint with all ones, so that any
            // structure will match this template, and leave it up
            // to substructure match to figure things out
            IBitFingerprint allOnesFingerprint = new BitSetFingerprint(fingerPrinter.getSize());
            for (int i = 0; i < fingerPrinter.getSize(); i++) {
                allOnesFingerprint.set(i, true);
            }
            data.add(allOnesFingerprint);
            fingerprintCounter = fingerprintCounter + 1;
        }
        if (fingerprintCounter % 2 == 0)
            logger.info("\b" + "/");
        else
            logger.info("\b" + "\\");
        if (fingerprintCounter % 100 == 0)
            logger.info("\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b" + "Generated Fingerprints: " + fingerprintCounter + "   \n");
    }
    // while
    try {
        imdl.close();
    } catch (Exception exc2) {
        LoggingToolFactory.createLoggingTool(TemplateExtractor.class).warn("Unexpected Exception:", exc2);
    }
    logger.info("...ready with:" + moleculeCounter + " molecules\nWrite data...of data vector:" + data.size() + " fingerprintCounter:" + fingerprintCounter);
    return data;
}