Examples with SymbolQueryAtom org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom used on opensource projects

Example 1 with SymbolQueryAtom

use of org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom in project cdk by cdk.

the class SMARTSTest method testSMARTS.

@Test
public void testSMARTS() throws Exception {
    IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
    SmilesParser sp = new SmilesParser(builder);
    // acetic acid anhydride
    IAtomContainer atomContainer = sp.parseSmiles("CC(=O)OC(=O)C");
    QueryAtomContainer query = new QueryAtomContainer(builder);
    AnyAtom atom1 = new AnyAtom(builder);
    SymbolQueryAtom atom2 = new SymbolQueryAtom(builder);
    atom2.setSymbol("C");
    query.addAtom(atom1);
    query.addAtom(atom2);
    query.addBond(new OrderQueryBond(atom1, atom2, IBond.Order.DOUBLE, builder));
    Assert.assertTrue(uiTester.isSubgraph(atomContainer, query));
}

Example 2 with SymbolQueryAtom

use of org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom in project cdk by cdk.

the class CDKMCSTest method testSFBug1708336.

/**
 * @cdk.bug 1708336
 * @throws Exception
 */
@Test
public void testSFBug1708336() throws Exception {
    IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
    IAtomContainer atomContainer = builder.newInstance(IAtomContainer.class);
    atomContainer.addAtom(builder.newInstance(IAtom.class, "C"));
    atomContainer.addAtom(builder.newInstance(IAtom.class, "C"));
    atomContainer.addAtom(builder.newInstance(IAtom.class, "N"));
    atomContainer.addBond(0, 1, IBond.Order.SINGLE);
    atomContainer.addBond(1, 2, IBond.Order.SINGLE);
    IQueryAtomContainer query = new QueryAtomContainer(DefaultChemObjectBuilder.getInstance());
    IQueryAtom a1 = new SymbolQueryAtom(DefaultChemObjectBuilder.getInstance());
    a1.setSymbol("C");
    AnyAtom a2 = new AnyAtom(DefaultChemObjectBuilder.getInstance());
    IBond b1 = new OrderQueryBond(a1, a2, IBond.Order.SINGLE, DefaultChemObjectBuilder.getInstance());
    IQueryAtom a3 = new SymbolQueryAtom(DefaultChemObjectBuilder.getInstance());
    a3.setSymbol("C");
    IBond b2 = new OrderQueryBond(a2, a3, IBond.Order.SINGLE, DefaultChemObjectBuilder.getInstance());
    query.addAtom(a1);
    query.addAtom(a2);
    query.addAtom(a3);
    query.addBond(b1);
    query.addBond(b2);
    List<List<CDKRMap>> list = CDKMCS.getSubgraphMaps(atomContainer, query, true);
    Assert.assertTrue(list.isEmpty());
}

Example 3 with SymbolQueryAtom

use of org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom in project cdk by cdk.

the class SMARTSTest method testMatchInherited.

@Test
public void testMatchInherited() {
    try {
        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
        SymbolQueryAtom c1 = new SymbolQueryAtom(new org.openscience.cdk.Atom("C"));
        SymbolAndChargeQueryAtom c2 = new SymbolAndChargeQueryAtom(new org.openscience.cdk.Atom("C"));
        IAtomContainer c = TestMoleculeFactory.makeAlkane(2);
        QueryAtomContainer query1 = new QueryAtomContainer(builder);
        query1.addAtom(c1);
        query1.addAtom(c2);
        query1.addBond(new OrderQueryBond(c1, c2, Order.SINGLE, builder));
        Assert.assertTrue(uiTester.isSubgraph(c, query1));
        QueryAtomContainer query = new QueryAtomContainer(builder);
        query.addAtom(c1);
        query.addAtom(c2);
        query.addBond(new AnyOrderQueryBond(c1, c2, Order.SINGLE, builder));
        Assert.assertTrue(uiTester.isSubgraph(c, query));
    } catch (CDKException exception) {
        Assert.fail(exception.getMessage());
    }
}

Example 4 with SymbolQueryAtom

use of org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom in project cdk by cdk.

the class SMARTSTest method testStrictSMARTS.

@Test
public void testStrictSMARTS() throws Exception {
    IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
    SmilesParser sp = new SmilesParser(builder);
    // acetic acid anhydride
    IAtomContainer atomContainer = sp.parseSmiles("CC(=O)OC(=O)C");
    QueryAtomContainer query = new QueryAtomContainer(builder);
    SymbolQueryAtom atom1 = new SymbolQueryAtom(builder);
    atom1.setSymbol("N");
    SymbolQueryAtom atom2 = new SymbolQueryAtom(builder);
    atom2.setSymbol("C");
    query.addAtom(atom1);
    query.addAtom(atom2);
    query.addBond(new OrderQueryBond(atom1, atom2, IBond.Order.DOUBLE, builder));
    Assert.assertFalse(uiTester.isSubgraph(atomContainer, query));
}