@Test public void testDiff() throws Exception { ICDKMolecule mol1 = (ICDKMolecule) cdk.fromSMILES("C"); ICDKMolecule mol2 = (ICDKMolecule) cdk.fromSMILES("C"); debug.diff(mol1, mol2); // would like to test more, but the method does not return anything }
@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 }