/** Tests whether the saturation checker gets a proton right. */
@Test
public void testIsSaturated_Proton() throws Exception {
// test H+
IAtomContainer m = new AtomContainer();
Atom h = new Atom("H");
h.setFormalCharge(+1);
m.addAtom(h);
Assert.assertTrue(satcheck.isSaturated(h, m));
}
@Test
public void testCalculateMissingHydrogens_Aromatic() throws Exception {
IAtomContainer pyrrole = MoleculeFactory.makePyrrole();
IAtom n = pyrrole.getAtom(1);
IRingSet rs = (new SSSRFinder(pyrrole)).findSSSR();
IRing ring = (IRing) rs.getAtomContainer(0);
for (int j = 0; j < ring.getBondCount(); j++) {
ring.getBond(j).setFlag(CDKConstants.ISAROMATIC, true);
}
Assert.assertEquals(5, ring.getBondCount());
Assert.assertEquals(1, satcheck.calculateNumberOfImplicitHydrogens(n, pyrrole));
}
/** Tests the method saturate(). */
@Test
public void testSaturate_NumberingProblem() throws Exception {
IAtomContainer mol = new AtomContainer();
Atom a1 = new Atom("C");
mol.addAtom(a1);
Atom a2 = new Atom("C");
mol.addAtom(a2);
Atom a3 = new Atom("C");
mol.addAtom(a3);
Atom a4 = new Atom("H");
mol.addAtom(a4);
Atom a5 = new Atom("C");
mol.addAtom(a5);
Atom a6 = new Atom("H");
mol.addAtom(a6);
Atom a7 = new Atom("S");
mol.addAtom(a7);
Atom a8 = new Atom("H");
mol.addAtom(a8);
Atom a9 = new Atom("H");
mol.addAtom(a9);
Bond b1 = new Bond(a1, a2, IBond.Order.SINGLE);
mol.addBond(b1);
Bond b2 = new Bond(a1, a3, IBond.Order.SINGLE);
mol.addBond(b2);
Bond b3 = new Bond(a1, a4, IBond.Order.SINGLE);
mol.addBond(b3);
Bond b4 = new Bond(a5, a2, IBond.Order.SINGLE);
mol.addBond(b4);
Bond b5 = new Bond(a2, a6, IBond.Order.SINGLE);
mol.addBond(b5);
Bond b6 = new Bond(a3, a7, IBond.Order.SINGLE);
mol.addBond(b6);
Bond b7 = new Bond(a3, a8, IBond.Order.SINGLE);
mol.addBond(b7);
Bond b8 = new Bond(a7, a5, IBond.Order.SINGLE);
mol.addBond(b8);
Bond b9 = new Bond(a5, a9, IBond.Order.SINGLE);
mol.addBond(b9);
satcheck.saturate(mol);
Assert.assertEquals(IBond.Order.SINGLE, b1.getOrder());
Assert.assertEquals(IBond.Order.DOUBLE, b2.getOrder());
Assert.assertEquals(IBond.Order.SINGLE, b6.getOrder());
Assert.assertEquals(IBond.Order.SINGLE, b8.getOrder());
Assert.assertEquals(IBond.Order.DOUBLE, b4.getOrder());
}
/** Tests the method saturate(). */
@Test
public void testSaturate_WithNitrate() throws Exception {
IAtomContainer mol = new AtomContainer();
Atom a1 = new Atom("O");
mol.addAtom(a1);
Atom a2 = new Atom("N");
mol.addAtom(a2);
Atom a3 = new Atom("O");
mol.addAtom(a3);
Atom a4 = new Atom("C");
mol.addAtom(a4);
Atom a5 = new Atom("C");
mol.addAtom(a5);
Atom a6 = new Atom("C");
mol.addAtom(a6);
Atom a7 = new Atom("H");
mol.addAtom(a7);
Atom a8 = new Atom("C");
mol.addAtom(a8);
Atom a9 = new Atom("C");
mol.addAtom(a9);
Atom a10 = new Atom("H");
mol.addAtom(a10);
Atom a11 = new Atom("H");
mol.addAtom(a11);
Atom a12 = new Atom("C");
mol.addAtom(a12);
Atom a13 = new Atom("H");
mol.addAtom(a13);
Atom a14 = new Atom("N");
mol.addAtom(a14);
Atom a15 = new Atom("H");
mol.addAtom(a15);
Atom a16 = new Atom("H");
mol.addAtom(a16);
Bond b1 = new Bond(a2, a1, IBond.Order.SINGLE);
mol.addBond(b1);
Bond b2 = new Bond(a3, a2, IBond.Order.SINGLE);
mol.addBond(b2);
Bond b3 = new Bond(a2, a4, IBond.Order.SINGLE);
mol.addBond(b3);
Bond b4 = new Bond(a5, a4, IBond.Order.SINGLE);
mol.addBond(b4);
Bond b5 = new Bond(a4, a6, IBond.Order.SINGLE);
mol.addBond(b5);
Bond b6 = new Bond(a7, a5, IBond.Order.SINGLE);
mol.addBond(b6);
Bond b7 = new Bond(a8, a5, IBond.Order.SINGLE);
mol.addBond(b7);
Bond b8 = new Bond(a6, a9, IBond.Order.SINGLE);
mol.addBond(b8);
Bond b9 = new Bond(a6, a10, IBond.Order.SINGLE);
mol.addBond(b9);
Bond b10 = new Bond(a11, a8, IBond.Order.SINGLE);
mol.addBond(b10);
Bond b11 = new Bond(a8, a12, IBond.Order.SINGLE);
mol.addBond(b11);
Bond b12 = new Bond(a9, a13, IBond.Order.SINGLE);
mol.addBond(b12);
Bond b13 = new Bond(a12, a9, IBond.Order.SINGLE);
mol.addBond(b13);
Bond b14 = new Bond(a14, a12, IBond.Order.SINGLE);
mol.addBond(b14);
Bond b15 = new Bond(a15, a14, IBond.Order.SINGLE);
mol.addBond(b15);
Bond b16 = new Bond(a14, a16, IBond.Order.SINGLE);
mol.addBond(b16);
satcheck.saturate(mol);
Assert.assertEquals(IBond.Order.DOUBLE, b1.getOrder());
Assert.assertEquals(IBond.Order.DOUBLE, b2.getOrder());
}