How to use

doubleValue

method

in

org.openscience.cdk.qsar.result.DoubleResult

@Test
public void testDoubleValue() {
  DoubleResult result = new DoubleResult(5);
  Assert.assertEquals(5.0, result.doubleValue(), 0.000001);
}

@Test
public void testno1000() throws ClassNotFoundException, CDKException, java.lang.Exception {
  Object[] params = {new Boolean(true), new Boolean(false)};
  descriptor.setParameters(params);
  SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  IAtomContainer mol = sp.parseSmiles("Clc1cccc(c1)/C=C/[N+](=O)[O-]"); // xlogp training set molecule no1000
  assertAtomTypesPerceived(mol);
  addExplicitHydrogens(mol);
  //logger.debug("no10000:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
  Assert.assertEquals(2.809, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 1.0); //at:  16
}

@Test
public void testApirinBug1296383() throws ClassNotFoundException, CDKException, java.lang.Exception {
  Object[] params = {new Boolean(true), new Boolean(false)};
  descriptor.setParameters(params);
  SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  IAtomContainer mol = sp.parseSmiles("CC(=O)OC1=CC=CC=C1C(=O)O"); // aspirin
  assertAtomTypesPerceived(mol);
  addExplicitHydrogens(mol);
  //logger.debug("Aspirin:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
  Assert.assertEquals(1.422, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
}

@Test
public void testno1596() throws ClassNotFoundException, CDKException, java.lang.Exception {
  // the xlogp program value is 0.44 because of paralleled donor pair correction factor
  Object[] params = {new Boolean(true), new Boolean(false)};
  descriptor.setParameters(params);
  SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  IAtomContainer mol = sp.parseSmiles("Nc2ccc(S(=O)(=O)c1ccc(N)cc1)cc2"); // xlogp training set molecule no1596
  assertAtomTypesPerceived(mol);
  addExplicitHydrogens(mol);
  //logger.debug("no1596:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
  Assert.assertEquals(0.86, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 1.0); //at:  16
}

@Test
public void testno1429() throws ClassNotFoundException, CDKException, java.lang.Exception {
  Object[] params = {new Boolean(true), new Boolean(false)};
  descriptor.setParameters(params);
  SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  IAtomContainer mol = sp.parseSmiles("O=C(OC)CNC(=O)c1ccc(N)cc1"); // xlogp training set molecule no1429
  assertAtomTypesPerceived(mol);
  addExplicitHydrogens(mol);
  //logger.debug("no1429:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
  Assert.assertEquals(0.31, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 1.0); //at:  16
}

@Test
public void testAprindine() throws ClassNotFoundException, CDKException, java.lang.Exception {
  //even here the amid assignment is very strange
  Object[] params = {new Boolean(true), new Boolean(false)};
  descriptor.setParameters(params);
  SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  IAtomContainer mol = sp.parseSmiles("CCN(CC)CCCN(C2Cc1ccccc1C2)c3ccccc3"); // xlogp training set molecule Aprindine
  assertAtomTypesPerceived(mol);
  addExplicitHydrogens(mol);
  //logger.debug("Aprindine:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
  Assert.assertEquals(5.03, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 1.0); //at:  16
}

@Test
public void testTPSA5() throws Exception {
  IAtomContainer mol = sp.parseSmiles("c1ccncc1");
  addExplicitHydrogens(mol);
  Assert.assertEquals(12.892, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.01);
}

@Ignore
@Test
public void testno688() throws ClassNotFoundException, CDKException, java.lang.Exception {
  Object[] params = {new Boolean(true), new Boolean(false)};
  descriptor.setParameters(params);
  SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  IAtomContainer mol = sp.parseSmiles("O=C(O)c1[nH0]cccc1"); // xlogp training set molecule no688
  assertAtomTypesPerceived(mol);
  addExplicitHydrogens(mol);
  //logger.debug("no688:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
  Assert.assertEquals(-1.69, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
}

@Ignore
@Test
public void testno937() throws ClassNotFoundException, CDKException, java.lang.Exception {
  Object[] params = {new Boolean(true), new Boolean(false)};
  descriptor.setParameters(params);
  SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  IAtomContainer mol = sp.parseSmiles("ClCC(O)C[nH0]1c([nH0]cc1[N+](=O)[O-])C"); // xlogp training set molecule no937
  assertAtomTypesPerceived(mol);
  addExplicitHydrogens(mol);
  //logger.debug("no937:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
  Assert.assertEquals(0.66, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
}

@Test
public void testTPSA4() throws Exception {
  IAtomContainer mol = sp.parseSmiles("C#N=CC(CNC)N1CC1");
  addExplicitHydrogens(mol);
  Assert.assertEquals(28.632, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.01);
}

@Test
public void testTPSA7() throws java.lang.Exception {
  IAtomContainer mol = sp.parseSmiles("C(I)I");//at:  16
  addExplicitHydrogens(mol);
  Assert.assertEquals(0.0, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
}

  @Test
  public void testCompound() throws Exception {
    SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
    IAtomContainer mol = sp.parseSmiles("CCCCC1CCCCC1");
    Assert.assertThat(((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), closeTo(4.322, 0.001));
  }
}

@Test
public void testPyridine() throws CDKException {
  parser = new SmilesParser(SilentChemObjectBuilder.getInstance());
  IAtomContainer struct = parseSmiles("c1ncccc1");
  JPlogPDescriptor desc = new JPlogPDescriptor();
  DescriptorValue answer = desc.calculate(struct);
  DoubleResult result = (DoubleResult) answer.getValue();
  double output = result.doubleValue();
  assertEquals(0.9, output, 0.1);
}

@Test
public void testCyclic() throws Exception {
  SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  IAtomContainer mol = sp.parseSmiles("C1CCC2CCCCC2C1");
  Assert.assertThat(((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), closeTo(4.459, 0.001));
}

@Test
public void testWeightDescriptor() throws ClassNotFoundException, CDKException, java.lang.Exception {
  Object[] params = {"*"};
  descriptor.setParameters(params);
  SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  IAtomContainer mol = sp.parseSmiles("CCC");
  Assert.assertEquals(44.06, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1);
}

@Test
public void testFluorobenzene() throws CDKException {
  parser = new SmilesParser(SilentChemObjectBuilder.getInstance());
  IAtomContainer struct = parseSmiles("Fc1ccccc1");
  JPlogPDescriptor desc = new JPlogPDescriptor();
  DescriptorValue answer = desc.calculate(struct);
  DoubleResult result = (DoubleResult) answer.getValue();
  double output = result.doubleValue();
  assertEquals(2.0, output, 0.1);
}

@Test
public void testDescriptor1() throws InvalidSmilesException {
  SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  IAtomContainer mol1 = sp.parseSmiles("CC");
  double value = ((DoubleResult) descriptor.calculate(mol1.getBond(0), mol1).getValue()).doubleValue();
  Assert.assertEquals(0, value, 0.0000);
}

@Test
public void testMethane() {
  IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
  IAtomContainer methane = builder.newInstance(IAtomContainer.class);
  methane.addAtom(builder.newInstance(IAtom.class, "C"));
  IDescriptorResult result = descriptor.calculate(methane).getValue();
  Assert.assertTrue(result instanceof DoubleResult);
  Assert.assertEquals(1.57, ((DoubleResult) result).doubleValue(), 0.01);
}

@Test
public void testClenbuterol() throws Exception {
  SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  IAtomContainer mol = sp.parseSmiles("Clc1cc(cc(Cl)c1N)C(O)CNC(C)(C)C");
  AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
  Aromaticity.cdkLegacy().apply(mol);
  DoubleResult result = (DoubleResult) descriptor.calculate(mol).getValue();
  Assert.assertEquals(0.353, result.doubleValue(), 0.01);
}

@Test
public void testAromaticBenzene() throws java.lang.Exception {
  Object[] params = {false, true};
  descriptor.setParameters(params);
  SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  IAtomContainer mol = sp.parseSmiles("C1=CC=CC=C1"); // benzene
  Aromaticity aromaticity = new Aromaticity(ElectronDonation.daylight(), Cycles.all());
  aromaticity.apply(mol);
  assertAtomTypesPerceived(mol);
  addExplicitHydrogens(mol);
  Assert.assertThat(((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), closeTo(2.02, 0.01));
}