Examples with IReactionSet org.openscience.cdk.interfaces.IReactionSet used on opensource projects

Example 1 with IReactionSet

use of org.openscience.cdk.interfaces.IReactionSet in project cdk by cdk.

the class IDCreator method createIDsForChemModel.

private static void createIDsForChemModel(IChemModel model, List<String> tabuList) {
    if (tabuList == null)
        tabuList = ChemModelManipulator.getAllIDs(model);
    if (null == model.getID()) {
        chemModelCount = setID(CHEMMODEL_PREFIX, chemModelCount, model, tabuList);
    }
    ICrystal crystal = model.getCrystal();
    if (crystal != null) {
        if (policy == OBJECT_UNIQUE_POLICY) {
            atomCount = 0;
            bondCount = 0;
        }
        createIDsForAtomContainer(crystal, tabuList);
    }
    IAtomContainerSet moleculeSet = model.getMoleculeSet();
    if (moleculeSet != null) {
        if (policy == OBJECT_UNIQUE_POLICY) {
            atomContainerSetCount = 0;
            atomContainerCount = 0;
        }
        createIDsForAtomContainerSet(moleculeSet, tabuList);
    }
    IReactionSet reactionSet = model.getReactionSet();
    if (reactionSet != null) {
        if (policy == OBJECT_UNIQUE_POLICY) {
            reactionSetCount = 0;
            reactionCount = 0;
        }
        createIDsForReactionSet(reactionSet, tabuList);
    }
}

Example 2 with IReactionSet

use of org.openscience.cdk.interfaces.IReactionSet in project cdk by cdk.

the class ReactionSetTest method testReactionSet.

@Test
public void testReactionSet() {
    IReactionSet reactionSet = new ReactionSet();
    Assert.assertNotNull(reactionSet);
}

Example 3 with IReactionSet

use of org.openscience.cdk.interfaces.IReactionSet in project cdk by cdk.

the class ChemModelTest method testChemModel.

@Test
public void testChemModel() {
    IChemModel chemModel = new ChemModel();
    Assert.assertNotNull(chemModel);
    Assert.assertTrue(chemModel.isEmpty());
    IAtom atom = new Atom("N");
    IAtomContainer mol = new AtomContainer();
    IAtomContainerSet mset = new AtomContainerSet();
    mol.addAtom(atom);
    mset.addAtomContainer(mol);
    chemModel.setMoleculeSet(mset);
    Assert.assertFalse(chemModel.isEmpty());
    mol.removeAtomOnly(atom);
    Assert.assertFalse(chemModel.isEmpty());
    chemModel.setMoleculeSet(null);
    Assert.assertTrue(chemModel.isEmpty());
    IChemModel model1 = new ChemModel();
    mol.addAtom(atom);
    IReaction react = new Reaction();
    react.addReactant(mol);
    IReactionSet rset = new ReactionSet();
    rset.addReaction(react);
    model1.setReactionSet(rset);
    Assert.assertFalse(model1.isEmpty());
    mol.removeAtomOnly(atom);
    Assert.assertFalse(model1.isEmpty());
    model1.setReactionSet(null);
    Assert.assertTrue(model1.isEmpty());
    IChemModel model2 = new ChemModel();
    mol.addAtom(atom);
    IRingSet ringset = new RingSet();
    ringset.add(mset);
    model2.setRingSet(ringset);
    Assert.assertFalse(model2.isEmpty());
    mol.removeAtomOnly(atom);
    Assert.assertFalse(model2.isEmpty());
    model2.setRingSet(null);
    Assert.assertTrue(model2.isEmpty());
    IChemModel model3 = new ChemModel();
    mol.addAtom(atom);
    ICrystal cry = new Crystal(mol);
    model3.setCrystal(cry);
    Assert.assertFalse(model3.isEmpty());
    mol.removeAtomOnly(atom);
    Assert.assertFalse(model3.isEmpty());
    model3.setCrystal(null);
    Assert.assertTrue(model3.isEmpty());
}

Example 4 with IReactionSet

use of org.openscience.cdk.interfaces.IReactionSet in project cdk by cdk.

the class RadicalSiteRrBetaReactionTest method testInitiate_IAtomContainerSet_IAtomContainerSet.

/**
 * A unit test suite for JUnit. Reaction:
 * Manually put of the center active.
 */
@Test
@Override
public void testInitiate_IAtomContainerSet_IAtomContainerSet() throws Exception {
    IReactionProcess type = new RadicalSiteRrBetaReaction();
    IAtomContainerSet setOfReactants = getExampleReactants();
    IAtomContainer molecule = setOfReactants.getAtomContainer(0);
    /* initiate */
    molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER, true);
    molecule.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER, true);
    molecule.getAtom(4).setFlag(CDKConstants.REACTIVE_CENTER, true);
    molecule.getBond(0).setFlag(CDKConstants.REACTIVE_CENTER, true);
    List<IParameterReact> paramList = new ArrayList<>();
    IParameterReact param = new SetReactionCenter();
    param.setParameter(Boolean.TRUE);
    paramList.add(param);
    type.setParameterList(paramList);
    IReactionSet setOfReactions = type.initiate(setOfReactants, null);
    Assert.assertEquals(1, setOfReactions.getReactionCount());
    Assert.assertEquals(1, setOfReactions.getReaction(0).getProductCount());
    IAtomContainer product = setOfReactions.getReaction(0).getProducts().getAtomContainer(0);
    IAtomContainer molecule2 = getExpectedProducts().getAtomContainer(0);
    assertEquals(molecule2, product);
}

Example 5 with IReactionSet

use of org.openscience.cdk.interfaces.IReactionSet in project cdk by cdk.

the class RadicalSiteRrDeltaReactionTest method testCDKConstants_REACTIVE_CENTER.

/**
 * A unit test suite for JUnit.
 */
@Test
public void testCDKConstants_REACTIVE_CENTER() throws Exception {
    IReactionProcess type = new RadicalSiteRrDeltaReaction();
    IAtomContainerSet setOfReactants = getExampleReactants();
    IAtomContainer molecule = setOfReactants.getAtomContainer(0);
    /* manually put the reactive center */
    molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER, true);
    molecule.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER, true);
    molecule.getAtom(6).setFlag(CDKConstants.REACTIVE_CENTER, true);
    molecule.getBond(0).setFlag(CDKConstants.REACTIVE_CENTER, true);
    List<IParameterReact> paramList = new ArrayList<>();
    IParameterReact param = new SetReactionCenter();
    param.setParameter(Boolean.TRUE);
    paramList.add(param);
    type.setParameterList(paramList);
    /* initiate */
    IReactionSet setOfReactions = type.initiate(setOfReactants, null);
    Assert.assertEquals(1, setOfReactions.getReactionCount());
    IAtomContainer reactant = setOfReactions.getReaction(0).getReactants().getAtomContainer(0);
    Assert.assertTrue(molecule.getAtom(0).getFlag(CDKConstants.REACTIVE_CENTER));
    Assert.assertTrue(reactant.getAtom(0).getFlag(CDKConstants.REACTIVE_CENTER));
    Assert.assertTrue(molecule.getAtom(1).getFlag(CDKConstants.REACTIVE_CENTER));
    Assert.assertTrue(reactant.getAtom(1).getFlag(CDKConstants.REACTIVE_CENTER));
    Assert.assertTrue(molecule.getAtom(6).getFlag(CDKConstants.REACTIVE_CENTER));
    Assert.assertTrue(reactant.getAtom(6).getFlag(CDKConstants.REACTIVE_CENTER));
    Assert.assertTrue(molecule.getBond(0).getFlag(CDKConstants.REACTIVE_CENTER));
    Assert.assertTrue(reactant.getBond(0).getFlag(CDKConstants.REACTIVE_CENTER));
}