@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());
  }
Exemplo n.º 3
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 @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());
  }
Exemplo n.º 8
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  @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);
  }
Exemplo n.º 9
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 @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));
 }
Exemplo n.º 10
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  @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));
    }
  }
Exemplo n.º 11
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 /** 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);
  }
Exemplo n.º 13
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 /** 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);
 }
Exemplo n.º 14
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 /** 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);
 }
Exemplo n.º 15
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 @Test
 public void testSSSRFinder_IAtomContainer() {
   IAtomContainer molecule = MoleculeFactory.makeAlphaPinene();
   SSSRFinder finder = new SSSRFinder(molecule);
   Assert.assertNotNull(finder);
 }