@Test
public void testSybylAtomTypePerceptionBenzene()
throws CDKException, FileNotFoundException, IOException, BioclipseException, CoreException,
InvocationTargetException {
IAtomContainer ac = MoleculeFactory.makeBenzene();
ICDKMolecule mol = new CDKMolecule(ac);
debug.perceiveSybylAtomTypes(mol);
System.out.println("** BENZENE **");
System.out.println(AtomContainerDiff.diff(ac, mol.getAtomContainer()));
for (int i = 0; i < mol.getAtomContainer().getAtomCount(); i++) {
IAtom a = mol.getAtomContainer().getAtom(i);
System.out.println("Atom: " + a.getSymbol() + i + ", type=" + a.getAtomTypeName());
}
assertEquals("C.ar", mol.getAtomContainer().getAtom(0).getAtomTypeName());
assertEquals("C.ar", mol.getAtomContainer().getAtom(1).getAtomTypeName());
assertEquals("C.ar", mol.getAtomContainer().getAtom(2).getAtomTypeName());
assertEquals("C.ar", mol.getAtomContainer().getAtom(3).getAtomTypeName());
assertEquals("C.ar", mol.getAtomContainer().getAtom(4).getAtomTypeName());
assertEquals("C.ar", mol.getAtomContainer().getAtom(5).getAtomTypeName());
}
@Test
public void testSybylAtomTypePerceptionFromSMILES()
throws FileNotFoundException, IOException, BioclipseException, CoreException,
InvocationTargetException {
ICDKMolecule mol = cdk.fromSMILES("C1CCCCC1CCOC");
debug.perceiveSybylAtomTypes(mol);
for (int i = 0; i < mol.getAtomContainer().getAtomCount(); i++) {
IAtom a = mol.getAtomContainer().getAtom(i);
System.out.println("Atom: " + a.getSymbol() + i + ", type=" + a.getAtomTypeName());
}
}
@Test
public void testSybylAtomTypePerception()
throws FileNotFoundException, IOException, BioclipseException, CoreException,
InvocationTargetException {
String path = getClass().getResource("/testFiles/atp.mol").getPath();
ICDKMolecule mol = cdk.loadMolecule(new MockIFile(path));
System.out.println("mol: " + mol.toString());
debug.perceiveSybylAtomTypes(mol);
for (int i = 0; i < mol.getAtomContainer().getAtomCount(); i++) {
IAtom a = mol.getAtomContainer().getAtom(i);
System.out.println("Atom: " + a.getSymbol() + i + ", type=" + a.getAtomTypeName());
}
}
/**
* Test that sybyl atom typing for 232 mols in an SDF does not throw exception
*
* @throws Exception
*/
@Test
public void testDepictSybylAtomTypesFromSDF() throws Exception {
URI uri = getClass().getResource("/testFiles/m2d_ref_232.sdf").toURI();
URL url = FileLocator.toFileURL(uri.toURL());
String path = url.getFile();
List<ICDKMolecule> mols = cdk.loadMolecules(path);
int cnt = 0;
for (ICDKMolecule mol : mols) {
try {
debug.perceiveSybylAtomTypes(mol);
} catch (InvocationTargetException e) {
System.out.println("Atom typing of molecule " + cnt + " failed.");
e.printStackTrace();
fail("Atom typing of molecule " + cnt + " failed due to: " + e.getMessage());
} catch (NullPointerException e) {
System.out.println("Atom typing of molecule " + cnt + " failed.");
e.printStackTrace();
fail("Atom typing of molecule " + cnt + " failed due to NPE: " + e.getMessage());
}
// would like to test more, but the method does not return anything
cnt++;
}
}
@Test
public void testDepictSybylAtomTypes() throws Exception {
ICDKMolecule mol = (ICDKMolecule) cdk.fromSMILES("CNCO");
debug.perceiveSybylAtomTypes(mol);
// would like to test more, but the method does not return anything
}