@Test
public void testInterruption() {
fbot.setInterrupted(false);
Assert.assertFalse(fbot.isInterrupted());
fbot.setInterrupted(true);
Assert.assertTrue(fbot.isInterrupted());
fbot.setInterrupted(false);
}
/**
* Just to ensure it doesn't throw exceptions
*
* @throws Exception
*/
@Test(timeout = 1000)
public void testAcyclic() throws Exception {
String smiles = "CCCCCCC";
SmilesParser smilesParser = new SmilesParser(SilentChemObjectBuilder.getInstance());
IAtomContainer molecule = smilesParser.parseSmiles(smiles);
molecule = fbot.kekuliseAromaticRings(molecule);
Assert.assertNotNull(molecule);
}
/** @cdk.inchi InChI=1/C4H5N/c1-2-4-5-3-1/h1-5H */
@Test
public void xtestPyrrole() throws Exception {
IAtomContainer enol = new AtomContainer();
// atom block
IAtom atom1 = new Atom(Elements.CARBON);
atom1.setHybridization(Hybridization.SP2);
IAtom atom2 = new Atom(Elements.CARBON);
atom2.setHybridization(Hybridization.SP2);
IAtom atom3 = new Atom(Elements.CARBON);
atom3.setHybridization(Hybridization.SP2);
IAtom atom4 = new Atom(Elements.CARBON);
atom4.setHybridization(Hybridization.SP2);
IAtom atom5 = new Atom(Elements.NITROGEN);
atom5.setHybridization(Hybridization.SP2);
atom5.setImplicitHydrogenCount(1);
// bond block
IBond bond1 = new Bond(atom1, atom2);
IBond bond2 = new Bond(atom2, atom3);
IBond bond3 = new Bond(atom3, atom4);
IBond bond4 = new Bond(atom4, atom5);
IBond bond5 = new Bond(atom5, atom1);
enol.addAtom(atom1);
enol.addAtom(atom2);
enol.addAtom(atom3);
enol.addAtom(atom4);
enol.addAtom(atom5);
enol.addBond(bond1);
enol.addBond(bond2);
enol.addBond(bond3);
enol.addBond(bond4);
enol.addBond(bond5);
// perceive atom types
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(enol);
// now have the algorithm have a go at it
enol = fbot.kekuliseAromaticRings(enol);
Assert.assertNotNull(enol);
// Assert.assertTrue(fbot.isOK(enol));
// now check whether it did the right thing
Assert.assertEquals(CDKConstants.BONDORDER_DOUBLE, enol.getBond(0).getOrder());
;
Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, enol.getBond(1).getOrder());
;
Assert.assertEquals(CDKConstants.BONDORDER_DOUBLE, enol.getBond(2).getOrder());
;
Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, enol.getBond(3).getOrder());
;
Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, enol.getBond(4).getOrder());
;
}
@Test(timeout = 1000)
public void testPyrrole_Silent() throws Exception {
String smiles = "c2ccc3n([H])c1ccccc1c3(c2)";
SmilesParser smilesParser = new SmilesParser(SilentChemObjectBuilder.getInstance());
IAtomContainer molecule = smilesParser.parseSmiles(smiles);
molecule = fbot.kekuliseAromaticRings(molecule);
Assert.assertNotNull(molecule);
molecule = (IAtomContainer) AtomContainerManipulator.removeHydrogens(molecule);
int doubleBondCount = 0;
for (int i = 0; i < molecule.getBondCount(); i++) {
IBond bond = molecule.getBond(i);
Assert.assertTrue(bond.getFlag(CDKConstants.ISAROMATIC));
if (bond.getOrder() == Order.DOUBLE) doubleBondCount++;
}
Assert.assertEquals(6, doubleBondCount);
}
@Test
public void testLargeRingSystem() throws Exception {
String smiles = "O=C1Oc6ccccc6(C(O)C1C5c2ccccc2CC(c3ccc(cc3)c4ccccc4)C5)";
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer molecule = smilesParser.parseSmiles(smiles);
molecule = fbot.kekuliseAromaticRings(molecule);
Assert.assertNotNull(molecule);
molecule = (IAtomContainer) AtomContainerManipulator.removeHydrogens(molecule);
Assert.assertEquals(34, molecule.getAtomCount());
// we should have 14 double bonds
int doubleBondCount = 0;
for (int i = 0; i < molecule.getBondCount(); i++) {
IBond bond = molecule.getBond(i);
if (bond.getOrder() == Order.DOUBLE) doubleBondCount++;
}
Assert.assertEquals(13, doubleBondCount);
}
/** @cdk.bug 3506770 */
@Test
public void testLargeBioclipseUseCase() throws Exception {
String smiles =
"COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56";
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer molecule = smilesParser.parseSmiles(smiles);
molecule = fbot.kekuliseAromaticRings(molecule);
Assert.assertNotNull(molecule);
molecule = (IAtomContainer) AtomContainerManipulator.removeHydrogens(molecule);
Assert.assertEquals(40, molecule.getAtomCount());
// we should have 14 double bonds
int doubleBondCount = 0;
for (int i = 0; i < molecule.getBondCount(); i++) {
IBond bond = molecule.getBond(i);
if (bond.getOrder() == Order.DOUBLE) doubleBondCount++;
}
Assert.assertEquals(10, doubleBondCount);
}