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

Example 11 with Reaction

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

the class ExtraReaderFactoryTest method expectReader.

void expectReader(String filename, IResourceFormat expectedFormat) 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);
            read = true;
        }
    }
    Assert.assertTrue("Reading an IChemObject from the Reader did not work properly.", read);
}

Example 12 with Reaction

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

the class MDLRXNV3000ReaderTest method testReadReactions1.

/**
 * @cdk.bug 1849925
 */
@Test
public void testReadReactions1() throws Exception {
    String filename1 = "reaction_v3.rxn";
    logger.info("Testing: " + filename1);
    InputStream ins1 = this.getClass().getResourceAsStream(filename1);
    MDLRXNV3000Reader reader1 = new MDLRXNV3000Reader(ins1, Mode.STRICT);
    IReaction reaction1 = new Reaction();
    reaction1 = reader1.read(reaction1);
    reader1.close();
    Assert.assertNotNull(reaction1);
    Assert.assertEquals(1, reaction1.getReactantCount());
    Assert.assertEquals(1, reaction1.getProductCount());
    IAtomContainer reactant = reaction1.getReactants().getAtomContainer(0);
    Assert.assertNotNull(reactant);
    Assert.assertEquals(32, reactant.getAtomCount());
    Assert.assertEquals(29, reactant.getBondCount());
    IAtomContainer product = reaction1.getProducts().getAtomContainer(0);
    Assert.assertNotNull(product);
    Assert.assertEquals(32, product.getAtomCount());
    Assert.assertEquals(29, product.getBondCount());
}

Example 13 with Reaction

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

the class MDLRXNReaderTest method testReadReactions2.

@Test
public void testReadReactions2() throws Exception {
    String filename2 = "reaction-2.rxn";
    logger.info("Testing: " + filename2);
    InputStream ins2 = this.getClass().getResourceAsStream(filename2);
    MDLRXNReader reader2 = new MDLRXNReader(ins2);
    IReaction reaction2 = new Reaction();
    reaction2 = reader2.read(reaction2);
    reader2.close();
    Assert.assertNotNull(reaction2);
    Assert.assertEquals(2, reaction2.getReactantCount());
    Assert.assertEquals(2, reaction2.getProductCount());
}

Example 14 with Reaction

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

the class MDLRXNReaderTest method testReadReactions1.

@Test
public void testReadReactions1() throws Exception {
    String filename1 = "reaction-1.rxn";
    logger.info("Testing: " + filename1);
    InputStream ins1 = this.getClass().getResourceAsStream(filename1);
    MDLRXNReader reader1 = new MDLRXNReader(ins1);
    IReaction reaction1 = new Reaction();
    reaction1 = reader1.read(reaction1);
    reader1.close();
    Assert.assertNotNull(reaction1);
    Assert.assertEquals(2, reaction1.getReactantCount());
    Assert.assertEquals(1, reaction1.getProductCount());
    IAtomContainerSet educts = reaction1.getReactants();
    // Check Atom symbols of first educt
    String[] atomSymbolsOfEduct1 = { "C", "C", "O", "Cl" };
    for (int i = 0; i < educts.getAtomContainer(0).getAtomCount(); i++) {
        Assert.assertEquals(atomSymbolsOfEduct1[i], educts.getAtomContainer(0).getAtom(i).getSymbol());
    }
    // Check Atom symbols of second educt
    for (int i = 0; i < educts.getAtomContainer(1).getAtomCount(); i++) {
        Assert.assertEquals("C", educts.getAtomContainer(1).getAtom(i).getSymbol());
    }
    // Check Atom symbols of first product
    IAtomContainerSet products = reaction1.getProducts();
    String[] atomSymbolsOfProduct1 = { "C", "C", "C", "C", "C", "C", "C", "O", "C" };
    for (int i = 0; i < products.getAtomContainer(0).getAtomCount(); i++) {
        Assert.assertEquals(atomSymbolsOfProduct1[i], products.getAtomContainer(0).getAtom(i).getSymbol());
    }
}

Example 15 with Reaction

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

the class MDLRXNV2000ReaderTest method testAgentParts.

@Test
public void testAgentParts() throws Exception {
    try (InputStream in = this.getClass().getResourceAsStream("ethylesterification.mol");
        MDLRXNV2000Reader rdr = new MDLRXNV2000Reader(in)) {
        IReaction reaction = rdr.read(new Reaction());
        assertThat(reaction.getAgents().getAtomContainerCount(), is(1));
    }
}