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

Example 1 with SMARTSQueryTool

use of org.openscience.cdk.smiles.smarts.SMARTSQueryTool in project MetFragRelaunched by ipb-halle.

the class SmartsGroup method removeDuplicates.

public void removeDuplicates() {
    java.util.ArrayList<Object> newList = new java.util.ArrayList<Object>();
    java.util.ArrayList<String> newSmiles = new java.util.ArrayList<String>();
    for (int i = 0; i < this.list.size(); i++) {
        String current = ((SMARTSQueryTool) this.list.get(i)).getSmarts();
        if (!newList.contains(current)) {
            newList.add(current);
            newSmiles.add(this.smiles.get(i));
        }
    }
    this.list = new java.util.ArrayList<Object>();
    for (int i = 0; i < newList.size(); i++) {
        SMARTSQueryTool sqt = new SMARTSQueryTool((String) newList.get(i), DefaultChemObjectBuilder.getInstance());
        this.list.add(sqt);
    }
    this.smiles = newSmiles;
}

Example 2 with SMARTSQueryTool

use of org.openscience.cdk.smiles.smarts.SMARTSQueryTool in project MetFragRelaunched by ipb-halle.

the class SmartsSubstructureExclusionScoreInitialiser method initScoreParameters.

@Override
public void initScoreParameters(Settings settings) {
    String[] excludedSmarts = (String[]) settings.get(VariableNames.SCORE_SMARTS_EXCLUSION_LIST_NAME);
    SMARTSQueryTool[] smartsQuerytools = null;
    if (excludedSmarts != null && excludedSmarts.length != 0) {
        smartsQuerytools = new SMARTSQueryTool[excludedSmarts.length];
        for (int i = 0; i < excludedSmarts.length; i++) {
            smartsQuerytools[i] = new SMARTSQueryTool(excludedSmarts[i], DefaultChemObjectBuilder.getInstance());
        }
        settings.set(VariableNames.SMARTS_SUBSTRUCTURE_EXCLUSION_SCORE_LIST_NAME, smartsQuerytools);
    }
}

Example 3 with SMARTSQueryTool

use of org.openscience.cdk.smiles.smarts.SMARTSQueryTool in project MetFragRelaunched by ipb-halle.

the class SmartsSubstructureInclusionScoreInitialiser method initScoreParameters.

@Override
public void initScoreParameters(Settings settings) {
    String[] excludedSmarts = (String[]) settings.get(VariableNames.SCORE_SMARTS_INCLUSION_LIST_NAME);
    SMARTSQueryTool[] smartsQuerytools = null;
    if (excludedSmarts != null && excludedSmarts.length != 0) {
        smartsQuerytools = new SMARTSQueryTool[excludedSmarts.length];
        for (int i = 0; i < excludedSmarts.length; i++) {
            smartsQuerytools[i] = new SMARTSQueryTool(excludedSmarts[i], DefaultChemObjectBuilder.getInstance());
        }
        settings.set(VariableNames.SMARTS_SUBSTRUCTURE_INCLUSION_SCORE_LIST_NAME, smartsQuerytools);
    }
}

Example 4 with SMARTSQueryTool

use of org.openscience.cdk.smiles.smarts.SMARTSQueryTool in project ambit-mirror by ideaconsult.

the class StructureKeysBitSetGeneratorTest method testBiphenyl4CDK.

@Test
public void testBiphenyl4CDK() throws Exception {
    IteratingSDFReader reader = new IteratingSDFReader(new InputStreamReader(getClass().getClassLoader().getResourceAsStream("biphenyl.sdf")), SilentChemObjectBuilder.getInstance());
    IAtomContainer biphenyl_kekule = null;
    while (reader.hasNext()) {
        IChemObject o = reader.next();
        Assert.assertTrue(o instanceof IAtomContainer);
        biphenyl_kekule = (IAtomContainer) o;
        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(biphenyl_kekule);
        // well, Hydrogens are already in the file, but we need to mimic the
        // generic read/processing workflow
        CDKHydrogenAdder hAdder = CDKHydrogenAdder.getInstance(biphenyl_kekule.getBuilder());
        hAdder.addImplicitHydrogens(biphenyl_kekule);
        CDKHueckelAromaticityDetector.detectAromaticity(biphenyl_kekule);
        MoleculeTools.convertImplicitToExplicitHydrogens(biphenyl_kekule);
        biphenyl_kekule.setID("biphenyl_kekule");
        break;
    }
    reader.close();
    Assert.assertNotNull(biphenyl_kekule);
    // get the biphenyl as aromatic smiles
    SmilesParser parser = new SmilesParser(SilentChemObjectBuilder.getInstance());
    IAtomContainer biphenyl_aromaticsmiles = parser.parseSmiles("c1ccccc1c2ccccc2");
    biphenyl_aromaticsmiles.setID("biphenyl_aromatic");
    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(biphenyl_aromaticsmiles);
    CDKHydrogenAdder hAdder = CDKHydrogenAdder.getInstance(biphenyl_aromaticsmiles.getBuilder());
    hAdder.addImplicitHydrogens(biphenyl_aromaticsmiles);
    CDKHueckelAromaticityDetector.detectAromaticity(biphenyl_aromaticsmiles);
    MoleculeTools.convertImplicitToExplicitHydrogens(biphenyl_aromaticsmiles);
    // get the biphenyl as Kekule smiles
    IAtomContainer biphenyl_kekulesmiles = parser.parseSmiles("C1=C(C=CC=C1)C2=CC=CC=C2");
    biphenyl_kekulesmiles.setID("biphenyl_kekulesmiles");
    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(biphenyl_kekulesmiles);
    hAdder = CDKHydrogenAdder.getInstance(biphenyl_kekulesmiles.getBuilder());
    hAdder.addImplicitHydrogens(biphenyl_kekulesmiles);
    CDKHueckelAromaticityDetector.detectAromaticity(biphenyl_kekulesmiles);
    MoleculeTools.convertImplicitToExplicitHydrogens(biphenyl_kekulesmiles);
    UniversalIsomorphismTester uit = new UniversalIsomorphismTester();
    Assert.assertTrue(uit.isIsomorph(biphenyl_aromaticsmiles, biphenyl_kekule));
    Assert.assertTrue(uit.isIsomorph(biphenyl_aromaticsmiles, biphenyl_kekulesmiles));
    Assert.assertTrue(uit.isIsomorph(biphenyl_kekulesmiles, biphenyl_kekule));
    // #1 with the latest fix, we'll not find double bonds :)
    ISmartsPattern smartsPattern_ambit = SmartsPatternFactory.createSmartsPattern(SmartsParser.smarts_nk, "[#6]=[#6]", false);
    Assert.assertTrue(smartsPattern_ambit.match(biphenyl_aromaticsmiles) == 0);
    Assert.assertTrue(smartsPattern_ambit.match(biphenyl_kekule) == 0);
    Assert.assertTrue(smartsPattern_ambit.match(biphenyl_kekulesmiles) == 0);
    // #1 with the latest fix, we'll not find double bonds :)
    ISmartsPattern smartsPattern_fast = SmartsPatternFactory.createSmartsPattern(SmartsParser.smarts_fast, "[#6]=[#6]", false);
    Assert.assertTrue(smartsPattern_fast.match(biphenyl_aromaticsmiles) == 0);
    Assert.assertTrue(smartsPattern_fast.match(biphenyl_kekule) == 0);
    Assert.assertTrue(smartsPattern_fast.match(biphenyl_kekulesmiles) == 0);
    // #3 cdk does find double bonds in kekule representation
    ISmartsPattern smartsPattern_cdk = SmartsPatternFactory.createSmartsPattern(SmartsParser.smarts_cdk, "[#6]=[#6]", false);
    Assert.assertTrue(smartsPattern_cdk.match(biphenyl_aromaticsmiles) == 0);
    // this is fixed in cdk 1.4.4
    Assert.assertTrue(smartsPattern_cdk.match(biphenyl_kekule) == 0);
    Assert.assertTrue(smartsPattern_cdk.match(biphenyl_kekulesmiles) == 0);
    // same as #3 but using CDK code only
    SMARTSQueryTool sqt = new SMARTSQueryTool("[#6]=[#6]", SilentChemObjectBuilder.getInstance());
    // there is no any double bond in biphenyl, created via aromatic smiles
    // Fixed in cdk 1.4.4
    Assert.assertFalse(sqt.matches(biphenyl_aromaticsmiles));
    // there is at least one :) double bond in the biphenyl , read from SDF
    Assert.assertFalse(sqt.matches(biphenyl_kekule));
    // there is at least one :) double bond in the biphenyl , read from SDF
    Assert.assertFalse(sqt.matches(biphenyl_kekulesmiles));
}

Example 5 with SMARTSQueryTool

use of org.openscience.cdk.smiles.smarts.SMARTSQueryTool 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);
}