Examples with SetReactionCenter org.openscience.cdk.reaction.type.parameters.SetReactionCenter used on opensource projects

Example 1 with SetReactionCenter

use of org.openscience.cdk.reaction.type.parameters.SetReactionCenter 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 2 with SetReactionCenter

use of org.openscience.cdk.reaction.type.parameters.SetReactionCenter 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));
}

Example 3 with SetReactionCenter

use of org.openscience.cdk.reaction.type.parameters.SetReactionCenter in project cdk by cdk.

the class RadicalSiteRrDeltaReactionTest 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 RadicalSiteRrDeltaReaction();
    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(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);
    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 4 with SetReactionCenter

use of org.openscience.cdk.reaction.type.parameters.SetReactionCenter in project cdk by cdk.

the class RadicalSiteRrGammaReactionTest method testMapping.

/**
 * A unit test suite for JUnit.
 */
@Test
public void testMapping() throws Exception {
    IReactionProcess type = new RadicalSiteRrGammaReaction();
    IAtomContainerSet setOfReactants = getExampleReactants();
    IAtomContainer molecule = setOfReactants.getAtomContainer(0);
    /* automatic search of the center active */
    molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER, true);
    molecule.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER, true);
    molecule.getAtom(5).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);
    IAtomContainer product = setOfReactions.getReaction(0).getProducts().getAtomContainer(0);
    Assert.assertEquals(22, setOfReactions.getReaction(0).getMappingCount());
    IAtom mappedProductA1 = (IAtom) ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(0));
    Assert.assertEquals(mappedProductA1, product.getAtom(0));
    IAtom mappedProductA2 = (IAtom) ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(1));
    Assert.assertEquals(mappedProductA2, product.getAtom(1));
    IAtom mappedProductA3 = (IAtom) ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(5));
    Assert.assertEquals(mappedProductA3, product.getAtom(5));
}

Example 5 with SetReactionCenter

use of org.openscience.cdk.reaction.type.parameters.SetReactionCenter in project cdk by cdk.

the class RadicalSiteRrGammaReactionTest 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 RadicalSiteRrGammaReaction();
    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(5).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);
}