@Test
public void testFingerprinter_int_int() throws java.lang.Exception {
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter(1024);
Assert.assertNotNull(fingerprinter);
IAtomContainer mol = TestMoleculeFactory.makeIndole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
BitSet bs = fingerprinter.getBitFingerprint(mol).asBitSet();
IAtomContainer frag1 = TestMoleculeFactory.makePyrrole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(frag1);
BitSet bs1 = fingerprinter.getBitFingerprint(frag1).asBitSet();
Assert.assertTrue(FingerprinterTool.isSubset(bs, bs1));
}
@Test
public void testRegression() throws Exception {
IAtomContainer mol1 = TestMoleculeFactory.makeIndole();
IAtomContainer mol2 = TestMoleculeFactory.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 testWriteSMILESFile() throws Exception {
StringWriter stringWriter = new StringWriter();
IAtomContainer benzene = TestMoleculeFactory.makeBenzene();
addImplicitHydrogens(benzene);
SMILESWriter smilesWriter = new SMILESWriter(stringWriter);
smilesWriter.write(benzene);
smilesWriter.close();
Assert.assertTrue(stringWriter.toString().contains("C=C"));
}
@Test
public void testFingerprinterBitSetSize() throws Exception {
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter(1024);
Assert.assertNotNull(fingerprinter);
IAtomContainer mol = TestMoleculeFactory.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 = TestMoleculeFactory.makeIndole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
IBitFingerprint bs = fingerprinter.getBitFingerprint(mol);
Assert.assertNotNull(bs);
Assert.assertEquals(fingerprinter.getSize(), bs.size());
}
@Test
public void testAtomPermutation2() throws CDKException {
IAtomContainer pamine = TestMoleculeFactory.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));
}
}
@Test
public void testWriteAromatic() throws Exception {
StringWriter stringWriter = new StringWriter();
IAtomContainer benzene = TestMoleculeFactory.makeBenzene();
addImplicitHydrogens(benzene);
CDKHueckelAromaticityDetector.detectAromaticity(benzene);
SMILESWriter smilesWriter = new SMILESWriter(stringWriter);
Properties prop = new Properties();
prop.setProperty("UseAromaticity", "true");
PropertiesListener listener = new PropertiesListener(prop);
smilesWriter.addChemObjectIOListener(listener);
smilesWriter.customizeJob();
smilesWriter.write(benzene);
smilesWriter.close();
Assert.assertFalse(stringWriter.toString().contains("C=C"));
Assert.assertTrue(stringWriter.toString().contains("ccc"));
}
@Test
public void imidazole_ignoreAromatic() throws Exception {
Graph g = convert(TestMoleculeFactory.makeImidazole(), true, true, false, true);
assertThat(g.toSmiles(), is("C=1NC=NC1"));
}
@Test
public void imidazole() throws Exception {
Graph g = convert(TestMoleculeFactory.makeImidazole(), true, true);
assertThat(g.toSmiles(), is("c1[nH]cnc1"));
}
@Test
public void benzene() throws Exception {
IAtomContainer ac = TestMoleculeFactory.makeBenzene();
Graph g = convert(ac, true, true);
assertThat(g.toSmiles(), is("c1ccccc1"));
}
@Test
public void benzene_kekule() throws Exception {
Graph g = convert(TestMoleculeFactory.makeBenzene());
assertThat(g.toSmiles(), is("C=1C=CC=CC1"));
}
@Test
public void adeneine() throws Exception {
Graph g = convert(TestMoleculeFactory.makeAdenine());
assertThat(g.toSmiles(), is("C12=C(N=CN=C1N)NC=N2"));
}