Examples with AtomEnvironmentsDistance ambit2.similarity.measure.AtomEnvironmentsDistance used on opensource projects

Example 1 with AtomEnvironmentsDistance

use of ambit2.similarity.measure.AtomEnvironmentsDistance in project ambit-mirror by ideaconsult.

the class AtomEnvironmentHammingDistanceTest method testGetDistance.

/**
 * Test method for {@link ambit2.similarity.AtomEnvironmentHammingDistance#getDistance(ambit2.data.descriptors.AtomEnvironmentList, ambit2.data.descriptors.AtomEnvironmentList)}.
 */
@Test
public void testGetDistance() throws Exception {
    IAtomContainer mol = MoleculeFactory.makeAlkane(3);
    IAtomContainer mol1 = MoleculeFactory.makeAlkane(3);
    SmilesParserWrapper p = SmilesParserWrapper.getInstance();
    IAtomContainer mol2 = p.parseSmiles("CCCC");
    AtomEnvironmentGenerator g = new AtomEnvironmentGenerator();
    g.setUseHydrogens(true);
    g.setMaxLevels(3);
    AtomEnvironmentList ae = g.generateProperty(mol);
    AtomEnvironmentList ae1 = g.generateProperty(mol1);
    AtomEnvironmentList ae2 = g.generateProperty(mol2);
    AtomEnvironmentsDistance hd = new AtomEnvironmentsDistance();
    Assert.assertEquals(1.0, hd.getDistance(ae, ae1), 1E-10);
    Assert.assertEquals(hd.getDistance(ae1, ae), hd.getDistance(ae, ae1), 1E-10);
    System.out.println(ae);
    System.out.println(ae2);
    float d = hd.getDistance(ae, ae2);
    // System.out.println(d);
    Assert.assertTrue(d < 1.0);
    Assert.assertEquals(hd.getDistance(ae2, ae), hd.getDistance(ae1, ae2), 1E-10);
}

Example 2 with AtomEnvironmentsDistance

use of ambit2.similarity.measure.AtomEnvironmentsDistance in project ambit-mirror by ideaconsult.

the class MySelector method testCH3difference.

public void testCH3difference(boolean display) throws Exception {
    IMolecularDescriptor descriptor = new AtomEnvironmentDescriptor();
    int maxLevel = 3;
    Object[] params = { null, new Integer(maxLevel), new Boolean(true), new Boolean(true) };
    SmilesParserWrapper sp = SmilesParserWrapper.getInstance();
    // IAtomContainer mol = sp.parseSmiles("O=N(=O)c1ccc(O)c(N)c1");
    // Amino-2nitro-3.4-5 hydroxy-methyl benzene (ANMB)
    // IAtomContainer mol1 = sp.parseSmiles("Cc1c(C)c(cc(N)c1(O))N(=O)=O");
    IAtomContainer molecule1 = sp.parseSmiles("Nc1c(C)cccc1");
    // Amino-2nitro-3.4-5 hydroxy-methyl benzene (ANMB)
    IAtomContainer molecule2 = sp.parseSmiles("Nc1c(O)cccc1");
    // Amino-2nitro-3.4-5 hydroxy-methyl benzene (ANMB)
    AtomEnvironmentGenerator g = new AtomEnvironmentGenerator();
    g.setNoDuplicates(false);
    g.setUseHydrogens(true);
    g.setMaxLevels(maxLevel);
    AtomEnvironmentList ae = g.generateProperty(molecule1);
    AtomEnvironmentList ae1 = g.generateProperty(molecule2);
    Collections.sort(ae);
    Collections.sort(ae1);
    AtomEnvironmentsDistance d = new AtomEnvironmentsDistance();
    System.out.println("distance " + d.getDistance(ae, ae1));
    Set<AtomEnvironment> set = new TreeSet<AtomEnvironment>();
    Set<AtomEnvironment> set1 = new TreeSet<AtomEnvironment>();
    for (int i = 0; i < ae.size(); i++) set.add(ae.get(i));
    for (int i = 0; i < ae1.size(); i++) set1.add(ae1.get(i));
    System.out.println(set);
    System.out.println();
    System.out.println(set1);
    Assert.assertNotSame(set, set1);
    Set intersection = (Set) ((TreeSet) set1).clone();
    intersection.retainAll(set);
    System.out.println("Intersection\t" + intersection.size());
    System.out.println(intersection);
    if (display)
        displayAE(molecule1, ae, molecule2, ae1);
    Assert.assertNotNull(ae);
    Assert.assertNotNull(ae1);
}