Examples with CMLWriter org.openscience.cdk.io.CMLWriter used on opensource projects

Example 1 with CMLWriter

use of org.openscience.cdk.io.CMLWriter in project ambit-mirror by ideaconsult.

the class TestCML method writeCML.

protected String writeCML(IAtomContainer mol) throws Exception {
    StringWriter output = new StringWriter();
    CMLWriter cmlwriter = new CMLWriter(output);
    cmlwriter.write(mol);
    cmlwriter.close();
    return output.toString();
}

Example 2 with CMLWriter

use of org.openscience.cdk.io.CMLWriter in project ambit-mirror by ideaconsult.

the class TestCML method testCML1.

public static void testCML1(String smiles) throws Exception {
    IAtomContainer mol = SmartsHelper.getMoleculeFromSmiles(smiles);
    mol.getAtom(0).setProperty("Prop1", "Test1");
    mol.getAtom(0).setProperty("Prop2", "Test2");
    printAtomProperties(mol.getAtom(0));
    try {
        System.out.println("Writing " + smiles + " to CML ");
        StringWriter output = new StringWriter();
        CMLWriter cmlwriter = new CMLWriter(output);
        cmlwriter.write(mol);
        cmlwriter.close();
        String cmlcode = output.toString();
        System.out.println(cmlcode);
        IChemFile chemFile = parseCMLString(cmlcode);
        IAtomContainer mol2 = chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getAtomContainer(0);
        printAtomProperties(mol2.getAtom(0));
    } catch (Exception e) {
        System.out.println(e.toString());
    }
}

Example 3 with CMLWriter

use of org.openscience.cdk.io.CMLWriter in project ambit-mirror by ideaconsult.

the class TestCML method testCML2.

public static void testCML2(String smiles) throws Exception {
    IAtomContainer mol = SmartsHelper.getMoleculeFromSmiles(smiles);
    printAromaticity(mol);
    try {
        System.out.println("Writing " + smiles + " to CML ");
        StringWriter output = new StringWriter();
        CMLWriter cmlwriter = new CMLWriter(output);
        cmlwriter.write(mol);
        cmlwriter.close();
        String cmlcode = output.toString();
        System.out.println(cmlcode);
        IChemFile chemFile = parseCMLString(cmlcode);
        IAtomContainer mol2 = chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getAtomContainer(0);
        printAromaticity(mol2);
    } catch (Exception e) {
        System.out.println(e.toString());
    }
}

Example 4 with CMLWriter

use of org.openscience.cdk.io.CMLWriter in project cdk by cdk.

the class SmilesGeneratorTest method testSFBug1014344.

/**
 * @cdk.bug 1014344
 */
@Category(SlowTest.class)
// MDL -> CML (slow) -> SMILES round tripping
@Test
public void testSFBug1014344() throws Exception {
    String filename = "bug1014344-1.mol";
    InputStream ins = this.getClass().getResourceAsStream(filename);
    MDLReader reader = new MDLReader(ins, Mode.STRICT);
    IAtomContainer mol1 = reader.read(new AtomContainer());
    addImplicitHydrogens(mol1);
    SmilesGenerator sg = new SmilesGenerator();
    String molSmiles = sg.create(mol1);
    StringWriter output = new StringWriter();
    CMLWriter cmlWriter = new CMLWriter(output);
    cmlWriter.write(mol1);
    CMLReader cmlreader = new CMLReader(new ByteArrayInputStream(output.toString().getBytes()));
    IAtomContainer mol2 = ((IChemFile) cmlreader.read(new ChemFile())).getChemSequence(0).getChemModel(0).getMoleculeSet().getAtomContainer(0);
    addImplicitHydrogens(mol2);
    String cmlSmiles = sg.create(new AtomContainer(mol2));
    Assert.assertEquals(molSmiles, cmlSmiles);
}

Example 5 with CMLWriter

use of org.openscience.cdk.io.CMLWriter in project cdk by cdk.

the class CML2WriterTest method testHydrogenCount.

/**
 * Test example with one explicit carbon, and four implicit hydrogens.
 *
 * @cdk.bug 1655045
 */
@Test
public void testHydrogenCount() throws Exception {
    StringWriter writer = new StringWriter();
    // methane
    IAtomContainer molecule = new AtomContainer();
    molecule.addAtom(molecule.getBuilder().newInstance(IAtom.class, Elements.CARBON));
    molecule.getAtom(0).setImplicitHydrogenCount(4);
    CMLWriter cmlWriter = new CMLWriter(writer);
    cmlWriter.write(molecule);
    cmlWriter.close();
    logger.debug("****************************** testHydrogenCount()");
    logger.debug(writer.toString());
    logger.debug("******************************");
    Assert.assertTrue(writer.toString().contains("hydrogenCount=\"4\""));
}