Examples with AtomTypeFactory org.openscience.cdk.config.AtomTypeFactory used on opensource projects

Example 16 with AtomTypeFactory

use of org.openscience.cdk.config.AtomTypeFactory in project cdk by cdk.

the class CDKAtomTypeMatcherTest method testAllElementsRepresented.

/**
 * Test if all elements up to and including Uranium have atom types.
 *
 * @throws Exception
 */
@Test
public void testAllElementsRepresented() throws Exception {
    AtomTypeFactory factory = AtomTypeFactory.getInstance("org/openscience/cdk/dict/data/cdk-atom-types.owl", SilentChemObjectBuilder.getInstance());
    Assert.assertTrue("Could not read the atom types", factory.getSize() != 0);
    String errorMessage = "Elements without atom type(s) defined in the XML:";
    // TODO: 92 ?
    final int testUptoAtomicNumber = 36;
    int elementsMissingTypes = 0;
    for (int i = 1; i < testUptoAtomicNumber; i++) {
        String symbol = PeriodicTable.getSymbol(i);
        IAtomType[] expectedTypes = factory.getAtomTypes(symbol);
        if (expectedTypes.length == 0) {
            errorMessage += " " + symbol;
            elementsMissingTypes++;
        }
    }
    Assert.assertEquals(errorMessage, 0, elementsMissingTypes);
}