@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());
}
public String diff(ICDKMolecule mol, ICDKMolecule mol2) {
return AtomContainerDiff.diff(
mol.getAtomContainer(), mol2.getAtomContainer()
);
}