Examples with Reaction org.openscience.cdk.Reaction used on opensource projects

Example 26 with Reaction

use of org.openscience.cdk.Reaction in project cdk by cdk.

the class AbstractReactionLabeller method labelReaction.

public IReaction labelReaction(IReaction reaction, ICanonicalMoleculeLabeller labeller) {
    System.out.println("labelling");
    IReaction canonReaction = new Reaction();
    Map<IAtomContainer, int[]> permutationMap = new HashMap<>();
    IAtomContainerSet canonicalProducts = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainerSet.class);
    for (IAtomContainer product : reaction.getProducts().atomContainers()) {
        IAtomContainer canonicalForm = labeller.getCanonicalMolecule(product);
        if (fixAtomMappingCastType) {
            fixAtomMapping(canonicalForm);
        }
        IAtomContainer canonicalMolecule = canonicalForm.getBuilder().newInstance(IAtomContainer.class, canonicalForm);
        permutationMap.put(canonicalMolecule, labeller.getCanonicalPermutation(product));
        canonicalProducts.addAtomContainer(canonicalMolecule);
    }
    IAtomContainerSet canonicalReactants = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainerSet.class);
    for (IAtomContainer reactant : reaction.getReactants().atomContainers()) {
        IAtomContainer canonicalForm = labeller.getCanonicalMolecule(reactant);
        if (fixAtomMappingCastType) {
            fixAtomMapping(canonicalForm);
        }
        IAtomContainer canonicalMolecule = canonicalForm.getBuilder().newInstance(IAtomContainer.class, canonicalForm);
        permutationMap.put(canonicalMolecule, labeller.getCanonicalPermutation(reactant));
        canonicalReactants.addAtomContainer(canonicalMolecule);
    }
    canonReaction.setProducts(canonicalProducts);
    canonReaction.setReactants(canonicalReactants);
    cloneAndSortMappings(reaction, canonReaction, permutationMap);
    return canonReaction;
}

Example 27 with Reaction

use of org.openscience.cdk.Reaction in project cdk by cdk.

the class GeometryToolsTest method testShiftReactionVertical_IAtomContainer_Rectangle2D_Rectangle2D_double.

@Test
public void testShiftReactionVertical_IAtomContainer_Rectangle2D_Rectangle2D_double() throws Exception {
    IAtom atom1 = new Atom("C");
    atom1.setPoint2d(new Point2d(0, 1));
    IAtom atom2 = new Atom("C");
    atom2.setPoint2d(new Point2d(1, 0));
    IAtomContainer react1 = new AtomContainer();
    IReaction reaction = new Reaction();
    reaction.addReactant(react1);
    react1.addAtom(atom1);
    react1.addAtom(atom2);
    react1.addBond(0, 1, IBond.Order.SINGLE);
    IReaction reaction2 = (IReaction) reaction.clone();
    IAtomContainer react2 = reaction2.getReactants().getAtomContainer(0);
    // shift the second reaction up
    GeometryTools.shiftReactionVertical(reaction2, GeometryTools.getRectangle2D(react2), GeometryTools.getRectangle2D(react1), 1.0);
    // assert all coordinates of the second reaction moved up
    AtomContainerDiff.diff(react1, react2);
    LoggingToolFactory.createLoggingTool(getClass()).info("R1: " + GeometryTools.getRectangle2D(react1));
    LoggingToolFactory.createLoggingTool(getClass()).info("R2: " + GeometryTools.getRectangle2D(react2));
    for (int i = 0; i < 2; i++) {
        atom1 = react1.getAtom(0);
        atom2 = react2.getAtom(0);
        // so, x coordinates should be the same
        Assert.assertEquals(atom1.getPoint2d().x, atom2.getPoint2d().x, 0.0);
        // but, y coordinates should not
        Assert.assertTrue(atom1.getPoint2d().y < atom2.getPoint2d().y);
    }
}

Example 28 with Reaction

use of org.openscience.cdk.Reaction in project cdk by cdk.

the class GeometryToolsTest method testGetBondLengthAverage_MultiReaction.

/**
 * Tests if the bond length average is calculated based on all
 * {@link IAtomContainer}s in the IReaction.
 */
@Test
public void testGetBondLengthAverage_MultiReaction() {
    IReaction reaction = new Reaction();
    // mol 1
    IAtom atom1 = new Atom("C");
    atom1.setPoint2d(new Point2d(0, 0));
    IAtom atom2 = new Atom("C");
    atom2.setPoint2d(new Point2d(1, 0));
    IAtomContainer acont = new AtomContainer();
    reaction.addReactant(acont);
    acont.addAtom(atom1);
    acont.addAtom(atom2);
    acont.addBond(0, 1, IBond.Order.SINGLE);
    // mol 2
    atom1 = new Atom("C");
    atom1.setPoint2d(new Point2d(0, 0));
    atom2 = new Atom("C");
    atom2.setPoint2d(new Point2d(3, 0));
    acont = new AtomContainer();
    reaction.addProduct(acont);
    acont.addAtom(atom1);
    acont.addAtom(atom2);
    acont.addBond(0, 1, IBond.Order.SINGLE);
    Assert.assertEquals(2.0, GeometryTools.getBondLengthAverage(reaction), 0.0);
}

Example 29 with Reaction

use of org.openscience.cdk.Reaction in project cdk by cdk.

the class ChemFileManipulatorTest method setUp.

@Before
public void setUp() {
    molecule1 = new AtomContainer();
    atomInMol1 = new Atom("Cl");
    molecule1.addAtom(atomInMol1);
    molecule1.addAtom(new Atom("Cl"));
    bondInMol1 = new Bond(atomInMol1, molecule1.getAtom(1));
    molecule1.addBond(bondInMol1);
    molecule2 = new AtomContainer();
    atomInMol2 = new Atom("O");
    atomInMol2.setImplicitHydrogenCount(2);
    molecule2.addAtom(atomInMol2);
    moleculeSet = new AtomContainerSet();
    moleculeSet.addAtomContainer(molecule1);
    moleculeSet.addAtomContainer(molecule2);
    reaction = new Reaction();
    reaction.addReactant(molecule1);
    reaction.addProduct(molecule2);
    reactionSet = new ReactionSet();
    reactionSet.addReaction(reaction);
    chemModel = new ChemModel();
    chemModel.setMoleculeSet(moleculeSet);
    chemModel.setReactionSet(reactionSet);
    chemSequence1 = new ChemSequence();
    chemSequence1.addChemModel(chemModel);
    chemSequence2 = new ChemSequence();
    chemFile = new ChemFile();
    chemFile.addChemSequence(chemSequence1);
    chemFile.addChemSequence(chemSequence2);
}

Example 30 with Reaction

use of org.openscience.cdk.Reaction in project cdk by cdk.

the class ChemModelManipulatorTest method testRemoveAtomAndConnectedElectronContainers_IChemModel_IAtom.

@Test
public void testRemoveAtomAndConnectedElectronContainers_IChemModel_IAtom() {
    IAtomContainer mol1 = new AtomContainer();
    IAtom atom1 = new Atom("Cl");
    mol1.addAtom(atom1);
    mol1.addAtom(new Atom("Cl"));
    IBond bond1 = new Bond(mol1.getAtom(0), mol1.getAtom(1));
    mol1.addBond(bond1);
    IAtomContainer mol2 = new AtomContainer();
    IAtom atom2 = new Atom("I");
    mol2.addAtom(atom2);
    mol2.addAtom(new Atom("I"));
    IBond bond2 = new Bond(mol2.getAtom(0), mol2.getAtom(1));
    mol2.addBond(bond2);
    IAtomContainerSet molSet = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainerSet.class);
    molSet.addAtomContainer(mol1);
    IReaction r = new Reaction();
    r.addProduct(mol2);
    IReactionSet rSet = new ReactionSet();
    rSet.addReaction(r);
    IChemModel model = new ChemModel();
    model.setMoleculeSet(molSet);
    model.setReactionSet(rSet);
    IAtom otherAtom = new Atom("Cl");
    Assert.assertEquals(2, ChemModelManipulator.getBondCount(model));
    Assert.assertEquals(4, ChemModelManipulator.getAtomCount(model));
    ChemModelManipulator.removeAtomAndConnectedElectronContainers(model, otherAtom);
    Assert.assertEquals(2, ChemModelManipulator.getBondCount(model));
    Assert.assertEquals(4, ChemModelManipulator.getAtomCount(model));
    ChemModelManipulator.removeAtomAndConnectedElectronContainers(model, atom1);
    Assert.assertEquals(1, ChemModelManipulator.getBondCount(model));
    Assert.assertEquals(3, ChemModelManipulator.getAtomCount(model));
    ChemModelManipulator.removeAtomAndConnectedElectronContainers(model, atom2);
    Assert.assertEquals(0, ChemModelManipulator.getBondCount(model));
    Assert.assertEquals(2, ChemModelManipulator.getAtomCount(model));
}