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

Example 1 with Reaction

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

the class ChemModelManipulatorTest method setUp.

@Before
public void setUp() {
    molecule1 = new AtomContainer();
    atomInMol1 = new Atom("Cl");
    atomInMol1.setCharge(-1.0);
    atomInMol1.setFormalCharge(-1);
    atomInMol1.setImplicitHydrogenCount(1);
    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 = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainerSet.class);
    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);
}

Example 2 with Reaction

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

the class ChemModelManipulatorTest method testRemoveElectronContainer_IChemModel_IElectronContainer.

@Test
public void testRemoveElectronContainer_IChemModel_IElectronContainer() {
    IAtomContainer mol1 = new AtomContainer();
    mol1.addAtom(new Atom("Cl"));
    mol1.addAtom(new Atom("Cl"));
    IBond bond1 = new Bond(mol1.getAtom(0), mol1.getAtom(1));
    mol1.addBond(bond1);
    IAtomContainer mol2 = new AtomContainer();
    mol2.addAtom(new Atom("I"));
    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);
    IBond otherBond = new Bond();
    Assert.assertEquals(2, ChemModelManipulator.getBondCount(model));
    ChemModelManipulator.removeElectronContainer(model, otherBond);
    Assert.assertEquals(2, ChemModelManipulator.getBondCount(model));
    ChemModelManipulator.removeElectronContainer(model, bond1);
    Assert.assertEquals(1, ChemModelManipulator.getBondCount(model));
    ChemModelManipulator.removeElectronContainer(model, bond2);
    Assert.assertEquals(0, ChemModelManipulator.getBondCount(model));
}

Example 3 with Reaction

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

the class ChemSequenceManipulatorTest 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 = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainerSet.class);
    moleculeSet.addAtomContainer(molecule1);
    moleculeSet.addAtomContainer(molecule2);
    reaction = new Reaction();
    reaction.addReactant(molecule1);
    reaction.addProduct(molecule2);
    reactionSet = new ReactionSet();
    reactionSet.addReaction(reaction);
    chemModel1 = new ChemModel();
    chemModel1.setMoleculeSet(moleculeSet);
    chemModel2 = new ChemModel();
    chemModel2.setReactionSet(reactionSet);
    chemSequence = new ChemSequence();
    chemSequence.addChemModel(chemModel1);
    chemSequence.addChemModel(chemModel2);
}

Example 4 with Reaction

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

the class ReactionManipulatorTest method testGetAllIDs_IReaction.

@Test
public void testGetAllIDs_IReaction() {
    Reaction reaction = new Reaction();
    reaction.setID("r1");
    IAtomContainer water = new AtomContainer();
    water.setID("m1");
    Atom oxygen = new Atom("O");
    oxygen.setID("a1");
    water.addAtom(oxygen);
    reaction.addReactant(water);
    reaction.addProduct(water);
    List<String> ids = ReactionManipulator.getAllIDs(reaction);
    Assert.assertNotNull(ids);
    Assert.assertEquals(5, ids.size());
}

Example 5 with Reaction

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

the class ReactionManipulatorTest method testReverse_IReaction.

@Test
public void testReverse_IReaction() {
    Reaction reaction = new Reaction();
    reaction.setDirection(IReaction.Direction.BACKWARD);
    IAtomContainer water = new AtomContainer();
    reaction.addReactant(water, 3.0);
    reaction.addReactant(new AtomContainer());
    reaction.addProduct(new AtomContainer());
    Reaction reversedReaction = (Reaction) ReactionManipulator.reverse(reaction);
    Assert.assertEquals(IReaction.Direction.FORWARD, reversedReaction.getDirection());
    Assert.assertEquals(2, reversedReaction.getProductCount());
    Assert.assertEquals(1, reversedReaction.getReactantCount());
    Assert.assertEquals(3.0, reversedReaction.getProductCoefficient(water), 0.00001);
}