Examples with IteratingSMILESReader org.openscience.cdk.io.iterator.IteratingSMILESReader used on opensource projects

Example 1 with IteratingSMILESReader

use of org.openscience.cdk.io.iterator.IteratingSMILESReader in project cdk by cdk.

the class RecursiveTest method testBasicAmineOnDrugs_cdkAromaticModel.

@Category(SlowTest.class)
@Test
public void testBasicAmineOnDrugs_cdkAromaticModel() throws Exception {
    String filename = "drugs.smi";
    InputStream ins = this.getClass().getResourceAsStream(filename);
    IteratingSMILESReader reader = new IteratingSMILESReader(ins, DefaultChemObjectBuilder.getInstance());
    SMARTSQueryTool sqt = new SMARTSQueryTool("[NX3;H2,H1;!$(NC=O)]", DefaultChemObjectBuilder.getInstance());
    sqt.setAromaticity(new Aromaticity(ElectronDonation.cdk(), Cycles.cdkAromaticSet()));
    int nmatch = 0;
    int nmol = 0;
    READ: while (reader.hasNext()) {
        IAtomContainer container = reader.next();
        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(container);
        // model
        for (IAtom atom : container.atoms()) {
            if (atom.getAtomTypeName() == null) {
                continue READ;
            }
        }
        if (sqt.matches(container)) {
            nmatch++;
        }
        nmol++;
    }
    reader.close();
    Assert.assertEquals(141, nmol);
    Assert.assertEquals(4, nmatch);
}