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

Example 1 with ExtendedFingerprinter

use of org.openscience.cdk.fingerprint.ExtendedFingerprinter in project ambit-mirror by ideaconsult.

the class FingerPrintGeneratorTest method testPolyAromatics.

@Test
public void testPolyAromatics() throws Exception {
    MoleculeReader molreader = new MoleculeReader();
    FingerprintGenerator gen = new FingerprintGenerator(new Fingerprinter());
    InputStream in = FingerPrintGeneratorTest.class.getClassLoader().getResourceAsStream("ambit2/core/data/fp/polyaromatics.sdf");
    RawIteratingSDFReader reader = new RawIteratingSDFReader(new InputStreamReader(in));
    while (reader.hasNext()) {
        IStructureRecord record = reader.nextRecord();
        IAtomContainer mol = molreader.process(record);
        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
        CDKHydrogenAdder.getInstance(SilentChemObjectBuilder.getInstance()).addImplicitHydrogens(mol);
        CDKHueckelAromaticityDetector.detectAromaticity(mol);
        gen.setHydrogens(false);
        mol = AtomContainerManipulator.removeHydrogensPreserveMultiplyBonded(mol);
        BitSet bs1 = gen.process(mol);
        System.out.println(bs1);
        ExtendedFingerprinter efp = new ExtendedFingerprinter();
        System.out.println(efp.getClass().getName());
        System.out.println(efp.getBitFingerprint(mol).asBitSet());
        PubchemFingerprinter pfp = new PubchemFingerprinter(SilentChemObjectBuilder.getInstance());
        System.out.println(pfp.getClass().getName());
        System.out.println(pfp.getBitFingerprint(mol).asBitSet());
        EStateFingerprinter esfp = new EStateFingerprinter();
        System.out.println(esfp.getClass().getName());
        System.out.println(esfp.getBitFingerprint(mol).asBitSet());
        MACCSFingerprinter mfp = new MACCSFingerprinter();
        System.out.println(mfp.getClass().getName());
        System.out.println(mfp.getBitFingerprint(mol).asBitSet());
        SubstructureFingerprinter sfp = new SubstructureFingerprinter();
        System.out.println(sfp.getClass().getName());
        System.out.println(sfp.getBitFingerprint(mol).asBitSet());
        HybridizationFingerprinter hfp = new HybridizationFingerprinter();
        System.out.println(hfp.getClass().getName());
        System.out.println(hfp.getBitFingerprint(mol).asBitSet());
    /*
			BigInteger[] h16 = new BigInteger[16];
			MoleculeTools.bitset2bigint16(bs1,64,h16);
			new Random(10000);
			BitSet bs2 = gen.process(molreader.process(record));
			Assert.assertEquals(bs1,bs2);
			MoleculeTools.bitset2bigint16(bs2,64,h16);
			for (int i=0; i <16;i++) {
				Assert.assertEquals(expected[i], h16[i]);
			}
			*/
    }
    /*
		IStructureRecord record = new StructureRecord();
		record.setContent();
		MoleculeReader reader = new MoleculeReader();
		reader.process(target)
		*/
    reader.close();
}