Examples with XLogPDescriptor org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor used on opensource projects

Example 1 with XLogPDescriptor

use of org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor in project ambit-mirror by ideaconsult.

the class DbDescriptorValuesWriterTest method testWriteDescriptorValue.

/**
 * Test method for
 * {@link ambit2.db.processors.DbDescriptorWriter#write(org.openscience.cdk.qsar.DescriptorValue)}
 * .
 */
@Test
public void testWriteDescriptorValue() throws Exception {
    setUpDatabaseFromResource("ambit2/db/processors/test/descriptors-datasets.xml");
    IDatabaseConnection c = getConnection();
    ITable names = c.createQueryTable("EXPECTED_NAMES", "SELECT * FROM properties");
    Assert.assertEquals(5, names.getRowCount());
    ITable values = c.createQueryTable("EXPECTED_VALUES", "SELECT * FROM property_values");
    Assert.assertEquals(2, values.getRowCount());
    ITable templates = c.createQueryTable("EXPECTED_TEMPLATES", "SELECT * FROM template");
    Assert.assertEquals(5, templates.getRowCount());
    ITable dictionary = c.createQueryTable("EXPECTED_ONTOLOGY", "SELECT * FROM dictionary");
    Assert.assertEquals(3, dictionary.getRowCount());
    writer.setConnection(c.getConnection());
    writer.open();
    XLogPDescriptor xlogp = new XLogPDescriptor();
    writer.setStructure(new StructureRecord(7, 100211, "", ""));
    writer.write(xlogp.calculate(MoleculeFactory.makeAlkane(10)));
    names = c.createQueryTable("EXPECTED_NAMES", "SELECT * FROM properties");
    Assert.assertEquals(6, names.getRowCount());
    values = c.createQueryTable("EXPECTED_VALUES", "SELECT * FROM property_values");
    Assert.assertEquals(3, values.getRowCount());
    DescriptorValue v = new DescriptorValue(new DescriptorSpecification("XLogPReference", "XLogPTitle", "XLogPIdentifier", "XLogPVendor"), new String[] {}, new Object[] {}, new DoubleResult(5.01), new String[] { "XLogP" });
    writer.setStructure(new StructureRecord(10, 100214, "", ""));
    writer.write(v);
    // one more time
    writer.write(v);
    c.close();
    c = getConnection();
    names = c.createQueryTable("EXPECTED_NAMES", "SELECT * FROM properties");
    Assert.assertEquals(7, names.getRowCount());
    values = c.createQueryTable("EXPECTED_VALUES", "SELECT value_num FROM property_values WHERE idstructure=100214");
    Assert.assertEquals(1, values.getRowCount());
    Assert.assertEquals(5.01, (Double) DataType.DOUBLE.typeCast(values.getValue(0, "value_num")), 1E-4);
    c.close();
}

Example 2 with XLogPDescriptor

use of org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor in project ambit-mirror by ideaconsult.

the class DbDescriptorValuesWriterTest method testReadWriteProperty.

@Test
public void testReadWriteProperty() throws Exception {
    setUpDatabaseFromResource("ambit2/db/processors/test/experiments-datasets.xml");
    IDatabaseConnection c = getConnection();
    ITable names = c.createQueryTable("EXPECTED_FIELDS", "SELECT * FROM property_values");
    Assert.assertEquals(0, names.getRowCount());
    XLogPDescriptor xlogp = new XLogPDescriptor();
    RepositoryReader reader = new RepositoryReader();
    reader.setConnection(c.getConnection());
    writer.setConnection(c.getConnection());
    writer.open();
    reader.open();
    int records = 0;
    long now = System.currentTimeMillis();
    IChemObjectBuilder b = SilentChemObjectBuilder.getInstance();
    IStructureRecord o;
    while (reader.hasNext()) {
        o = reader.next();
        String content = reader.getStructure(o.getIdstructure());
        if (content == null)
            continue;
        IIteratingChemObjectReader mReader = new IteratingSDFReader(new StringReader(content), b);
        if (mReader.hasNext()) {
            Object mol = mReader.next();
            if (mol instanceof IAtomContainer) {
                writer.setStructure(o);
                writer.write(xlogp.calculate((IAtomContainer) mol));
            }
        }
        o.clear();
        mReader.close();
        mReader = null;
        records++;
    }
    reader.close();
    writer.close();
    now = System.currentTimeMillis() - now;
    c = getConnection();
    names = c.createQueryTable("EXPECTED_FIELDS", "SELECT * FROM property_values where value_num is not null");
    Assert.assertEquals(2, names.getRowCount());
    names = c.createQueryTable("EXPECTED_FIELDS", "SELECT * FROM property_values  where idstructure in (105095,109287)");
    Assert.assertEquals(2, names.getRowCount());
    c.close();
}

Example 3 with XLogPDescriptor

use of org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor in project ambit-mirror by ideaconsult.

the class DbDescriptorWriterTest method testWriteAllDescriptors.

@Test
public void testWriteAllDescriptors() throws Exception {
    setUpDatabaseFromResource("ambit2/db/processors/test/descriptors-datasets.xml");
    DbDescriptorWriter writer = new DbDescriptorWriter();
    IDatabaseConnection c = getConnection();
    ITable names = c.createQueryTable("EXPECTED_NAMES", "SELECT * FROM properties");
    Assert.assertEquals(5, names.getRowCount());
    writer.setConnection(c.getConnection());
    writer.open();
    XLogPDescriptor xlogp = new XLogPDescriptor();
    writer.write(xlogp.calculate(MoleculeFactory.makeAlkane(10)));
    DescriptorValue v = new DescriptorValue(new DescriptorSpecification("XLogPReference", "XLogPTitle", "XLogPIdentifier", "XLogPVendor"), new String[] {}, new Object[] {}, new DoubleResult(5), new String[] { "XLogP" });
    writer.write(xlogp.calculate(MoleculeFactory.makeAlkane(10)));
    writer.write(v);
    c.close();
    c = getConnection();
    names = c.createQueryTable("EXPECTED_NAMES", "SELECT * FROM properties");
    Assert.assertEquals(7, names.getRowCount());
    ITable values = c.createQueryTable("EXPECTED_VALUES", "SELECT * FROM property_values");
    Assert.assertEquals(2, values.getRowCount());
    c.close();
}

Example 4 with XLogPDescriptor

use of org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor in project ambit-mirror by ideaconsult.

the class DbDescriptorValuesWriterTest method testWriteStringDescriptorValue.

@Test
public void testWriteStringDescriptorValue() throws Exception {
    setUpDatabaseFromResource("ambit2/db/processors/test/descriptors-datasets.xml");
    IDatabaseConnection c = getConnection();
    ITable names = c.createQueryTable("EXPECTED_NAMES", "SELECT * FROM properties");
    Assert.assertEquals(5, names.getRowCount());
    ITable values = c.createQueryTable("EXPECTED_VALUES", "SELECT * FROM property_values");
    Assert.assertEquals(2, values.getRowCount());
    writer.setConnection(c.getConnection());
    writer.open();
    XLogPDescriptor xlogp = new XLogPDescriptor();
    writer.setStructure(new StructureRecord(7, 100211, "", ""));
    writer.write(xlogp.calculate(MoleculeFactory.makeAlkane(10)));
    names = c.createQueryTable("EXPECTED_NAMES", "SELECT * FROM properties");
    Assert.assertEquals(6, names.getRowCount());
    values = c.createQueryTable("EXPECTED_VALUES", "SELECT * FROM property_values");
    Assert.assertEquals(3, values.getRowCount());
    DescriptorValue v = new DescriptorValue(new DescriptorSpecification("XLogPReference", "XLogPTitle", "XLogPIdentifier", "XLogPVendor"), new String[] {}, new Object[] {}, new StringDescriptorResultType("TESTVALUE"), new String[] { "XLogP" });
    writer.setStructure(new StructureRecord(10, 100214, "", ""));
    writer.write(v);
    // one more time
    writer.write(v);
    c.close();
    c = getConnection();
    names = c.createQueryTable("EXPECTED_NAMES", "SELECT * FROM properties");
    Assert.assertEquals(7, names.getRowCount());
    values = c.createQueryTable("EXPECTED_VALUES", "SELECT value FROM values_string WHERE idstructure=100214");
    Assert.assertEquals(1, values.getRowCount());
    Object o = values.getValue(0, "value");
    if (o instanceof String)
        Assert.assertEquals("TESTVALUE", (String) o);
    else
        Assert.assertEquals("TESTVALUE", new String((byte[]) o));
    c.close();
}

Example 5 with XLogPDescriptor

use of org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor in project ambit-mirror by ideaconsult.

the class DbDescriptorWriterTest method test.

@Test
public void test() throws Exception {
    setUpDatabaseFromResource("ambit2/db/processors/test/descriptors-datasets.xml");
    DbDescriptorWriter writer = new DbDescriptorWriter();
    IDatabaseConnection c = getConnection();
    ITable names = c.createQueryTable("EXPECTED_NAMES", "SELECT * FROM properties");
    Assert.assertEquals(5, names.getRowCount());
    writer.setConnection(c.getConnection());
    writer.open();
    XLogPDescriptor xlogp = new XLogPDescriptor();
    writer.write(xlogp.calculate(MoleculeFactory.makeAlkane(10)));
    DescriptorValue v = new DescriptorValue(new DescriptorSpecification("XLogPReference", "XLogPTitle", "XLogPIdentifier", "XLogPVendor"), new String[] {}, new Object[] {}, new DoubleResult(5), new String[] { "XLogP" });
    writer.write(xlogp.calculate(MoleculeFactory.makeAlkane(10)));
    writer.write(v);
    c.close();
    c = getConnection();
    names = c.createQueryTable("EXPECTED_NAMES", "SELECT * FROM properties");
    Assert.assertEquals(7, names.getRowCount());
    ITable values = c.createQueryTable("EXPECTED_VALUES", "SELECT * FROM property_values");
    Assert.assertEquals(2, values.getRowCount());
    c.close();
}