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

Example 1 with IReaction

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

the class ReactionTest method testReaction.

@Test
public void testReaction() {
    IReaction reaction = new Reaction();
    Assert.assertNotNull(reaction);
    Assert.assertEquals(0, reaction.getReactantCount());
    Assert.assertEquals(0, reaction.getProductCount());
    Assert.assertEquals(IReaction.Direction.FORWARD, reaction.getDirection());
}

Example 2 with IReaction

use of org.openscience.cdk.interfaces.IReaction 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 3 with IReaction

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

the class DebugReactionTest method testDebugReaction.

@Test
public void testDebugReaction() {
    IReaction polymer = new DebugReaction();
    Assert.assertTrue(polymer instanceof DebugReaction);
}

Example 4 with IReaction

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

the class ReactionScheme method clone.

/**
 * Clones this ReactionScheme object and its content.
 *
 * @return    The cloned object
 */
@Override
public Object clone() throws CloneNotSupportedException {
    IReactionScheme clone = new ReactionScheme();
    for (IReactionScheme scheme : this.reactionSchemes()) {
        clone.add((IReactionScheme) scheme.clone());
    }
    for (IReaction reaction : reactions()) {
        clone.addReaction((IReaction) reaction.clone());
    }
    // clone the properties
    if (getProperties() != null) {
        Map<Object, Object> properties = getProperties();
        Map<Object, Object> clonedHashtable = new HashMap<>();
        for (Object key : properties.keySet()) {
            Object value = properties.get(key);
            clonedHashtable.put(key, value);
        }
        clone.addProperties(clonedHashtable);
    }
    return clone;
}

Example 5 with IReaction

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

the class ReactionSet method toString.

@Override
public String toString() {
    StringBuilder buffer = new StringBuilder(32);
    buffer.append("ReactionSet(");
    buffer.append(this.hashCode());
    buffer.append(", R=").append(getReactionCount()).append(", ");
    for (IReaction reaction : reactions()) {
        buffer.append(reaction.toString());
    }
    buffer.append(')');
    return buffer.toString();
}