/**
* Test for SF bug #1309731.
*
* @cdk.bug 1309731
*/
@Test
public void testModelBuilder3D_keepChemObjectIDs() throws Exception {
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
IMolecule methanol = new org.openscience.cdk.Molecule();
IChemObjectBuilder builder = methanol.getBuilder();
IAtom carbon1 = builder.newInstance(IAtom.class, "C");
carbon1.setID("carbon1");
methanol.addAtom(carbon1);
for (int i = 0; i < 3; i++) {
IAtom hydrogen = builder.newInstance(IAtom.class, "H");
methanol.addAtom(hydrogen);
methanol.addBond(builder.newInstance(IBond.class, carbon1, hydrogen, IBond.Order.SINGLE));
}
IAtom oxygen1 = builder.newInstance(IAtom.class, "O");
oxygen1.setID("oxygen1");
methanol.addAtom(oxygen1);
methanol.addBond(builder.newInstance(IBond.class, carbon1, oxygen1, IBond.Order.SINGLE));
IAtom hydrogen = builder.newInstance(IAtom.class, "H");
methanol.addAtom(hydrogen);
methanol.addBond(builder.newInstance(IBond.class, hydrogen, oxygen1, IBond.Order.SINGLE));
Assert.assertEquals(6, methanol.getAtomCount());
Assert.assertEquals(5, methanol.getBondCount());
mb3d.generate3DCoordinates(methanol, false);
checkAverageBondLength(methanol);
Assert.assertEquals("carbon1", carbon1.getID());
Assert.assertEquals("oxygen1", oxygen1.getID());
}
/** A unit test for JUnit with ethoxyethane */
@Test
public void testPartialTotalChargeDescriptor_Ethoxyethane()
throws ClassNotFoundException, CDKException, java.lang.Exception {
double[] testResult = {
0.28, -0.56, 0.28,
}; /* from Merck Molecular Force Field. II. Thomas A. Halgren*/
IAtomicDescriptor descriptor = new PartialTChargeMMFF94Descriptor();
// IMolecule mol = sp.parseSmiles("COC");
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom carbon = builder.newInstance(IAtom.class, Elements.CARBON);
IAtom oxygen = builder.newInstance(IAtom.class, Elements.OXYGEN);
IAtom carbon2 = builder.newInstance(IAtom.class, Elements.CARBON);
// making sure the order matches the test results
mol.addAtom(carbon);
mol.addAtom(oxygen);
mol.addAtom(carbon2);
mol.addBond(builder.newInstance(IBond.class, carbon, oxygen, CDKConstants.BONDORDER_SINGLE));
mol.addBond(builder.newInstance(IBond.class, carbon2, oxygen, CDKConstants.BONDORDER_SINGLE));
addExplicitHydrogens(mol);
for (int i = 0; i < 3; i++) {
double result =
((DoubleResult) descriptor.calculate(mol.getAtom(i), mol).getValue()).doubleValue();
Assert.assertEquals(testResult[i], result, METHOD_ERROR);
}
}
/**
* Get the Ethene structure.
*
* @return The IMolecule
* @throws CDKException
*/
private IMolecule getEthene() throws Exception {
IMolecule molecule = builder.newMolecule();
molecule.addAtom(builder.newAtom("C"));
molecule.addAtom(builder.newAtom("C"));
molecule.addBond(0, 1, IBond.Order.DOUBLE);
molecule.addAtom(builder.newAtom("H"));
molecule.addAtom(builder.newAtom("H"));
molecule.addAtom(builder.newAtom("H"));
molecule.addAtom(builder.newAtom("H"));
molecule.addBond(0, 2, IBond.Order.SINGLE);
molecule.addBond(0, 3, IBond.Order.SINGLE);
molecule.addBond(1, 4, IBond.Order.SINGLE);
molecule.addBond(1, 5, IBond.Order.SINGLE);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
LonePairElectronChecker lpcheck = new LonePairElectronChecker();
lpcheck.saturate(molecule);
return molecule;
}
/** A unit test for JUnit with Benzene */
@Test
public void testPartialTotalChargeDescriptor_Benzene()
throws ClassNotFoundException, CDKException, java.lang.Exception {
double[] testResult = {
-0.15, -0.15, -0.15, -0.15, -0.15, -0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15
}; /* from Merck Molecular Force Field. II. Thomas A. Halgren*/
IAtomicDescriptor descriptor = new PartialTChargeMMFF94Descriptor();
// IMolecule mol = sp.parseSmiles("c1ccccc1");
IMolecule mol = builder.newInstance(IMolecule.class);
for (int i = 0; i < 6; i++) {
IAtom carbon = builder.newInstance(IAtom.class, Elements.CARBON);
carbon.setFlag(CDKConstants.ISAROMATIC, true);
// making sure the order matches the test results
mol.addAtom(carbon);
}
IBond ringBond =
builder.newInstance(
IBond.class, mol.getAtom(0), mol.getAtom(1), CDKConstants.BONDORDER_DOUBLE);
ringBond.setFlag(CDKConstants.ISAROMATIC, true);
mol.addBond(ringBond);
ringBond =
builder.newInstance(
IBond.class, mol.getAtom(1), mol.getAtom(2), CDKConstants.BONDORDER_SINGLE);
ringBond.setFlag(CDKConstants.ISAROMATIC, true);
mol.addBond(ringBond);
ringBond =
builder.newInstance(
IBond.class, mol.getAtom(2), mol.getAtom(3), CDKConstants.BONDORDER_DOUBLE);
ringBond.setFlag(CDKConstants.ISAROMATIC, true);
mol.addBond(ringBond);
ringBond =
builder.newInstance(
IBond.class, mol.getAtom(3), mol.getAtom(4), CDKConstants.BONDORDER_SINGLE);
ringBond.setFlag(CDKConstants.ISAROMATIC, true);
mol.addBond(ringBond);
ringBond =
builder.newInstance(
IBond.class, mol.getAtom(4), mol.getAtom(5), CDKConstants.BONDORDER_DOUBLE);
ringBond.setFlag(CDKConstants.ISAROMATIC, true);
mol.addBond(ringBond);
ringBond =
builder.newInstance(
IBond.class, mol.getAtom(5), mol.getAtom(0), CDKConstants.BONDORDER_SINGLE);
ringBond.setFlag(CDKConstants.ISAROMATIC, true);
mol.addBond(ringBond);
addExplicitHydrogens(mol);
for (int i = 0; i < 12; i++) {
double result =
((DoubleResult) descriptor.calculate(mol.getAtom(i), mol).getValue()).doubleValue();
Assert.assertEquals(testResult[i], result, METHOD_ERROR);
}
}
/** A unit test for JUnit with Water */
@Test
public void testPartialTotalChargeDescriptor_Water()
throws ClassNotFoundException, CDKException, java.lang.Exception {
double[] testResult = {
-0.86, 0.43, 0.43
}; /* from Merck Molecular Force Field. II. Thomas A. Halgren*/
IAtomicDescriptor descriptor = new PartialTChargeMMFF94Descriptor();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom oxygen = builder.newInstance(IAtom.class, Elements.OXYGEN);
// making sure the order matches the test results
mol.addAtom(oxygen);
addExplicitHydrogens(mol);
for (int i = 0; i < 3; i++) {
double result =
((DoubleResult) descriptor.calculate(mol.getAtom(i), mol).getValue()).doubleValue();
Assert.assertEquals(testResult[i], result, METHOD_ERROR);
}
}