@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() ); }