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

Example 1 with ReactionSet

use of org.openscience.cdk.ReactionSet 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 ReactionSet

use of org.openscience.cdk.ReactionSet 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 ReactionSet

use of org.openscience.cdk.ReactionSet 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 ReactionSet

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

the class MDLRXNReaderTest method testRDFReactioniSet.

/**
 */
@Test
public void testRDFReactioniSet() throws Exception {
    String filename = "qsar-reaction-test.rdf";
    logger.info("Testing: " + filename);
    InputStream ins = this.getClass().getResourceAsStream(filename);
    MDLRXNReader reader = new MDLRXNReader(ins);
    IReactionSet reactionSet = reader.read(new ReactionSet());
    reader.close();
    Assert.assertNotNull(reactionSet);
    Assert.assertEquals(2, reactionSet.getReactionCount());
    Assert.assertEquals(2, reactionSet.getReaction(0).getReactantCount());
    Assert.assertEquals(3, reactionSet.getReaction(0).getReactants().getAtomContainer(0).getAtomCount());
    Assert.assertEquals(2, reactionSet.getReaction(0).getReactants().getAtomContainer(1).getAtomCount());
    Assert.assertEquals(2, reactionSet.getReaction(0).getProductCount());
    Assert.assertEquals(2, reactionSet.getReaction(0).getProducts().getAtomContainer(0).getAtomCount());
    Assert.assertEquals(2, reactionSet.getReaction(0).getProducts().getAtomContainer(1).getAtomCount());
    Assert.assertEquals(1, reactionSet.getReaction(1).getReactantCount());
    Assert.assertEquals(3, reactionSet.getReaction(1).getReactants().getAtomContainer(0).getAtomCount());
    Assert.assertEquals(1, reactionSet.getReaction(1).getProductCount());
    Assert.assertEquals(2, reactionSet.getReaction(1).getProducts().getAtomContainer(0).getAtomCount());
}

Example 5 with ReactionSet

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

the class MDLRXNReaderTest method testAsadExamples.

/**
 * This test checks of different numbering for the same mapping gives the same result.
 */
@Test
public void testAsadExamples() throws Exception {
    String filename = "output.rxn";
    logger.info("Testing: " + filename);
    InputStream ins = this.getClass().getResourceAsStream(filename);
    MDLRXNReader reader = new MDLRXNReader(ins);
    IReactionSet reactionSet = reader.read(new ReactionSet());
    reader.close();
    filename = "output_Cleaned.rxn";
    logger.info("Testing: " + filename);
    ins = this.getClass().getResourceAsStream(filename);
    reader = new MDLRXNReader(ins);
    IReactionSet reactionSet2 = reader.read(new ReactionSet());
    reader.close();
    Assert.assertEquals(reactionSet.getReaction(0).getMappingCount(), reactionSet2.getReaction(0).getMappingCount());
    for (int i = 0; i < reactionSet.getReaction(0).getMappingCount(); i++) {
        Assert.assertEquals(getAtomNumber(reactionSet, reactionSet.getReaction(0).getMapping(i).getChemObject(0)), getAtomNumber(reactionSet2, reactionSet2.getReaction(0).getMapping(i).getChemObject(0)));
        Assert.assertEquals(getAtomNumber(reactionSet, reactionSet.getReaction(0).getMapping(i).getChemObject(1)), getAtomNumber(reactionSet2, reactionSet2.getReaction(0).getMapping(i).getChemObject(1)));
    }
}