@Test
public void testLoadingOfBondDescriptors() {
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.BOND);
Assert.assertNotNull(engine);
int loadedDescriptors = engine.getDescriptorInstances().size();
Assert.assertNotSame(0, loadedDescriptors);
Assert.assertEquals(loadedDescriptors, engine.getDescriptorClassNames().size());
Assert.assertEquals(loadedDescriptors, engine.getDescriptorSpecifications().size());
}
@Test
public void testLoadingOfMolecularDescriptors() {
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
Assert.assertNotNull(engine);
int loadedDescriptors = engine.getDescriptorInstances().size();
Assert.assertTrue("Could not load any descriptors", 0 != loadedDescriptors);
Assert.assertEquals(loadedDescriptors, engine.getDescriptorClassNames().size());
Assert.assertEquals(loadedDescriptors, engine.getDescriptorSpecifications().size());
}
/**
* @cdk.bug 1965254
* @throws Exception
*/
@Test
public void testjunk() throws Exception {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer molecule = sp.parseSmiles("COC1=CC2=C(C=C1)NC3=C2CCNC3");
TemplateHandler3D template = TemplateHandler3D.getInstance();
ModelBuilder3D mb3d = ModelBuilder3D.getInstance(template, "mm2");
molecule = mb3d.generate3DCoordinates(molecule, true);
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
engine.process(molecule);
}
@Test
public void testDictionaryType() {
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
String className = "org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor";
DescriptorSpecification specRef =
new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#zagrebIndex",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
Assert.assertEquals("molecularDescriptor", engine.getDictionaryType(className));
Assert.assertEquals("molecularDescriptor", engine.getDictionaryType(specRef));
}
@Test
public void checkUniqueMolecularDescriptorNames() throws Exception {
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
List<DescriptorSpecification> specs = engine.getDescriptorSpecifications();
// we work with a simple molecule with 3D coordinates
String filename = "data/mdl/lobtest2.sdf";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
ISimpleChemObjectReader reader = new MDLV2000Reader(ins);
ChemFile content = (ChemFile) reader.read(new ChemFile());
List cList = ChemFileManipulator.getAllAtomContainers(content);
IAtomContainer ac = (IAtomContainer) cList.get(0);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ac);
engine.process(ac);
int ncalc = 0;
List<String> descNames = new ArrayList<String>();
for (DescriptorSpecification spec : specs) {
DescriptorValue value = (DescriptorValue) ac.getProperty(spec);
if (value == null) continue;
ncalc++;
String[] names = value.getNames();
descNames.addAll(Arrays.asList(names));
}
List<String> dups = new ArrayList<String>();
Set<String> uniqueNames = new HashSet<String>();
for (String name : descNames) {
if (!uniqueNames.add(name)) dups.add(name);
}
Assert.assertEquals(specs.size(), ncalc);
Assert.assertEquals(descNames.size(), uniqueNames.size());
if (dups.size() != 0) {
System.out.println("Following names were duplicated");
for (String dup : dups) {
System.out.println("dup = " + dup);
}
}
}
@Test
public void testDictionaryClass() {
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
String className = "org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor";
DescriptorSpecification specRef =
new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#tpsa",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
String[] dictClass = engine.getDictionaryClass(className);
Assert.assertEquals(2, dictClass.length);
Assert.assertEquals("topologicalDescriptor", dictClass[0]);
Assert.assertEquals("electronicDescriptor", dictClass[1]);
dictClass = engine.getDictionaryClass(specRef);
Assert.assertEquals(2, dictClass.length);
Assert.assertEquals("topologicalDescriptor", dictClass[0]);
Assert.assertEquals("electronicDescriptor", dictClass[1]);
}
@Test
public void testAvailableClass() {
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
String[] availClasses = engine.getAvailableDictionaryClasses();
Assert.assertEquals(5, availClasses.length);
}
