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

Example 11 with ChemModel

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

the class AbstractReaderFactoryTest method expectReader.

void expectReader(String filename, IResourceFormat expectedFormat, int expectedAtomCount, int expectedBondCount) throws Exception {
    InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
    Assert.assertNotNull("Cannot find file: " + filename, ins);
    if (expectedFormat instanceof IChemFormatMatcher) {
        factory.registerFormat((IChemFormatMatcher) expectedFormat);
    }
    ISimpleChemObjectReader reader = factory.createReader(ins);
    Assert.assertNotNull(reader);
    Assert.assertEquals(((IChemFormat) expectedFormat).getReaderClassName(), reader.getClass().getName());
    // now try reading something from it
    IChemObject[] objects = { new ChemFile(), new ChemModel(), new AtomContainer(), new Reaction() };
    boolean read = false;
    for (int i = 0; (i < objects.length && !read); i++) {
        if (reader.accepts(objects[i].getClass())) {
            IChemObject chemObject = reader.read(objects[i]);
            Assert.assertNotNull("Reader accepted a " + objects[i].getClass().getName() + " but failed to read it", chemObject);
            assertAtomCount(expectedAtomCount, chemObject);
            assertBondCount(expectedBondCount, chemObject);
            read = true;
        }
    }
    if (read) {
    // ok, reseting worked
    } else {
        Assert.fail("Reading an IChemObject from the Reader did not work properly.");
    }
}

Example 12 with ChemModel

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

the class MDLRXNReaderTest method testRDFModel.

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

Example 13 with ChemModel

use of org.openscience.cdk.ChemModel 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 14 with ChemModel

use of org.openscience.cdk.ChemModel 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));
}

Example 15 with ChemModel

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

the class ChemModelManipulatorTest method testGetAllAtomContainers_IChemModel_WithReactions.

@Test
public void testGetAllAtomContainers_IChemModel_WithReactions() throws Exception {
    String filename = "0024.stg02.rxn";
    logger.info("Testing: " + filename);
    InputStream ins = this.getClass().getResourceAsStream(filename);
    MDLRXNV2000Reader reader = new MDLRXNV2000Reader(ins, Mode.STRICT);
    ChemModel chemFile = (ChemModel) reader.read((ChemObject) new ChemModel());
    Assert.assertNotNull(chemFile);
    List<IAtomContainer> containersList = ChemModelManipulator.getAllAtomContainers(chemFile);
    Assert.assertEquals(2, containersList.size());
}