@Test
public void testFingerprinter_int_int() throws java.lang.Exception {
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter(1024);
Assert.assertNotNull(fingerprinter);
IAtomContainer mol = MoleculeFactory.makeIndole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
BitSet bs = fingerprinter.getBitFingerprint(mol).asBitSet();
IAtomContainer frag1 = MoleculeFactory.makePyrrole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(frag1);
BitSet bs1 = fingerprinter.getBitFingerprint(frag1).asBitSet();
Assert.assertTrue(FingerprinterTool.isSubset(bs, bs1));
}
@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 testFindSSSR_IAtomContainer() {
IAtomContainer molecule = MoleculeFactory.makeAlphaPinene();
SSSRFinder sssrFinder = new SSSRFinder(molecule);
IRingSet ringSet = sssrFinder.findSSSR();
Assert.assertEquals(2, ringSet.getAtomContainerCount());
}
@Test
public void testViaFlags() throws Exception {
IMolecule molecule = MoleculeFactory.makeBenzene();
for (Iterator atoms = molecule.atoms().iterator(); atoms.hasNext(); ) {
((IAtom) atoms.next()).setFlag(CDKConstants.ISAROMATIC, true);
}
Assert.assertEquals(6, ((IntegerResult) descriptor.calculate(molecule).getValue()).intValue());
}
@Test
public void testRegression() throws Exception {
IAtomContainer mol1 = MoleculeFactory.makeIndole();
IAtomContainer mol2 = MoleculeFactory.makePyrrole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol1);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2);
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter();
IBitFingerprint bs1 = fingerprinter.getBitFingerprint(mol1);
Assert.assertEquals(
"Seems the fingerprint code has changed. This will cause a number of other tests to fail too!",
22,
bs1.cardinality());
IBitFingerprint bs2 = fingerprinter.getBitFingerprint(mol2);
Assert.assertEquals(
"Seems the fingerprint code has changed. This will cause a number of other tests to fail too!",
11,
bs2.cardinality());
}
@Test
public void testFingerprinterBitSetSize() throws Exception {
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter(1024);
Assert.assertNotNull(fingerprinter);
IAtomContainer mol = MoleculeFactory.makeIndole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
BitSet bs = fingerprinter.getBitFingerprint(mol).asBitSet();
Assert.assertEquals(1024, bs.length()); // highest set bit
Assert.assertEquals(1024, bs.size()); // actual bit set size
}
@Test
public void testgetBitFingerprint_IAtomContainer() throws java.lang.Exception {
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter();
IAtomContainer mol = MoleculeFactory.makeIndole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
IBitFingerprint bs = fingerprinter.getBitFingerprint(mol);
Assert.assertNotNull(bs);
Assert.assertEquals(fingerprinter.getSize(), bs.size());
}
@Test
public void testCyclohexaneWithHydrogens() {
IAtomContainer cyclohexane = MoleculeFactory.makeCyclohexane();
for (int i = 0; i < 6; i++) {
addHydrogens(cyclohexane, cyclohexane.getAtom(i), 2);
}
String expected =
"[C]([C]([C]([C,0]([H][H])[H][H])[H][H])" + "[C]([C]([C,0][H][H])[H][H])[H][H])";
String actual = this.canonicalStringFromMolecule(cyclohexane);
Assert.assertEquals(expected, actual);
}
@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));
}
@Test
public void testAtomPermutation2() throws CDKException {
IAtomContainer pamine = MoleculeFactory.makeCyclopentane();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(pamine);
ShortestPathFingerprinter fp = new ShortestPathFingerprinter();
IBitFingerprint bs1 = fp.getBitFingerprint(pamine);
AtomContainerAtomPermutor acp = new AtomContainerAtomPermutor(pamine);
while (acp.hasNext()) {
IAtomContainer container = acp.next();
IBitFingerprint bs2 = fp.getBitFingerprint(container);
Assert.assertTrue(bs1.equals(bs2));
}
}
/** A unit test for JUnit */
@Test
public void testEthylPropylPhenantren() throws Exception {
IAtomContainer mol1 = MoleculeFactory.makeEthylPropylPhenantren();
SmilesGenerator sg = new SmilesGenerator();
fixCarbonHCount(mol1);
String smiles1 = null;
if (standAlone) {
display(mol1);
}
smiles1 = sg.createSMILES(mol1);
if (standAlone) {
System.err.println("SMILES 1: " + smiles1);
}
Assert.assertNotNull(smiles1);
Assert.assertEquals("c2cc1c3ccc(cc3(ccc1c(c2)CC))CCC", smiles1);
}
@Test
public void testQuinone() throws Exception {
IAtomContainer mol = MoleculeFactory.makeQuinone();
Assert.assertNotNull("Created molecule was null", mol);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
CDKHueckelAromaticityDetector.detectAromaticity(mol);
EquivalentClassPartitioner partitioner = new EquivalentClassPartitioner(mol);
int[] eqCl = partitioner.getTopoEquivClassbyHuXu(mol);
Partition autP = ArrayToPartition.convert(eqCl, 1);
Assert.assertEquals("Wrong number of equivalent classes", 3, autP.size());
Partition expected = Partition.fromString("0,7|1,4|2,3,5,6");
Assert.assertEquals("Wrong class assignment", expected, autP);
}
/** A unit test for JUnit */
@Test
public void testSmilesGenerator() {
IAtomContainer mol2 = MoleculeFactory.makeAlphaPinene();
SmilesGenerator sg = new SmilesGenerator();
fixCarbonHCount(mol2);
String smiles2 = null;
if (standAlone) {
display(mol2);
}
try {
smiles2 = sg.createSMILES(mol2);
} catch (Exception exc) {
System.out.println(exc);
if (!standAlone) {
Assert.fail();
}
}
if (standAlone) {
System.err.println("SMILES 2: " + smiles2);
}
Assert.assertNotNull(smiles2);
Assert.assertEquals("C1=C(C)C2CC(C1)C2(C)(C)", smiles2);
}
/** A unit test for JUnit */
@Test
public void testPropylCycloPropane() {
IAtomContainer mol1 = MoleculeFactory.makePropylCycloPropane();
SmilesGenerator sg = new SmilesGenerator();
fixCarbonHCount(mol1);
String smiles1 = null;
if (standAlone) {
display(mol1);
}
try {
smiles1 = sg.createSMILES(mol1);
} catch (Exception exc) {
System.out.println(exc);
if (!standAlone) {
Assert.fail();
}
}
if (standAlone) {
System.err.println("SMILES 1: " + smiles1);
}
Assert.assertNotNull(smiles1);
Assert.assertEquals("CCCC1CC1", smiles1);
}
@Test
public void testSSSRFinder_IAtomContainer() {
IAtomContainer molecule = MoleculeFactory.makeAlphaPinene();
SSSRFinder finder = new SSSRFinder(molecule);
Assert.assertNotNull(finder);
}