Examples with SMARTSQueryTool org.openscience.cdk.smiles.smarts.SMARTSQueryTool used on opensource projects

Example 6 with SMARTSQueryTool

use of org.openscience.cdk.smiles.smarts.SMARTSQueryTool in project cdk by cdk.

the class RecursiveTest method testRecursive28_cdkAromaticModel.

@Test
public void testRecursive28_cdkAromaticModel() throws Exception {
    SMARTSQueryTool sqt = smarts("[NX3;H2,H1;!$(NC=O)]");
    IAtomContainer smi = smiles("Cc1ccc[n+]2c1[nH]cc(c2=O)c1n[nH]nn1");
    sqt.setAromaticity(new Aromaticity(ElectronDonation.cdk(), Cycles.cdkAromaticSet()));
    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(smi);
    int[] result = SMARTSSearchTest.match(sqt, smi);
    Assert.assertEquals(1, result[0]);
    Assert.assertEquals(1, result[1]);
}

Example 7 with SMARTSQueryTool

use of org.openscience.cdk.smiles.smarts.SMARTSQueryTool in project cdk by cdk.

the class RecursiveTest method testRecursiveSmarts26.

@Test
public void testRecursiveSmarts26() throws Exception {
    SMARTSQueryTool sqt = smarts("[NX3;H2,H1;!$(NC=O)]");
    IAtomContainer smi = smiles("CCCc1cc(=O)nc([nH]1)S");
    int[] result = SMARTSSearchTest.match(sqt, smi);
    Assert.assertEquals(0, result[0]);
    Assert.assertEquals(0, result[1]);
}

Example 8 with SMARTSQueryTool

use of org.openscience.cdk.smiles.smarts.SMARTSQueryTool in project cdk by cdk.

the class RecursiveTest method testRecursive29.

@Test
public void testRecursive29() throws Exception {
    SMARTSQueryTool sqt = smarts("[NX3;H2,H1;!$(NC=O)]");
    IAtomContainer smi = smiles("Cc1cc(=O)c(c[nH]1)C(=O)NC(c1ccc(cc1)O)C(=O)NC1C(=O)N2C1SCC(=C2C(=O)O)CSc1nnnn1C");
    int[] result = SMARTSSearchTest.match(sqt, smi);
    Assert.assertEquals(0, result[0]);
    Assert.assertEquals(0, result[1]);
}

Example 9 with SMARTSQueryTool

use of org.openscience.cdk.smiles.smarts.SMARTSQueryTool in project cdk by cdk.

the class SMARTSSearchTest method testPropertyR2.

@Test
public void testPropertyR2() throws Exception {
    SMARTSQueryTool sqt = smarts("[R2]");
    // default for daylight
    sqt.useSmallestSetOfSmallestRings();
    int[] results = match(sqt, smiles("COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34"));
    Assert.assertEquals(6, results[0]);
    Assert.assertEquals(6, results[1]);
}

Example 10 with SMARTSQueryTool

use of org.openscience.cdk.smiles.smarts.SMARTSQueryTool in project cdk by cdk.

the class SMARTSSearchTest method testLogicalOrLowAnd6_cdkAromaticity.

@Test
public void testLogicalOrLowAnd6_cdkAromaticity() throws Exception {
    SMARTSQueryTool sqt = smarts("[#7,C;+0,+1]");
    IAtomContainer smi = smiles("[Na+].[Na+].[O-]C(=O)c1ccccc1c2c3ccc([O-])cc3oc4cc(=O)ccc24");
    sqt.setAromaticity(new Aromaticity(ElectronDonation.cdk(), Cycles.cdkAromaticSet()));
    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(smi);
    int[] results = match(sqt, smi);
    Assert.assertEquals(8, results[0]);
}