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

Example 26 with IChemSequence

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

the class VASPReader method readChemFile.

private IChemFile readChemFile(IChemFile file) throws CDKException, IOException {
    IChemSequence seq = readChemSequence(file.getBuilder().newInstance(IChemSequence.class));
    file.addChemSequence(seq);
    return file;
}

Example 27 with IChemSequence

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

the class MDLRXNV2000Reader method read.

/**
 * Takes an object which subclasses IChemObject, e.g.Molecule, and will read
 * this (from file, database, internet etc). If the specific implementation
 * does not support a specific IChemObject it will throw an Exception.
 *
 * @param  object                              The object that subclasses
 *      IChemObject
 * @return                                     The IChemObject read
 * @exception  CDKException
 */
@Override
public <T extends IChemObject> T read(T object) throws CDKException {
    if (object instanceof IReaction) {
        return (T) readReaction(object.getBuilder());
    } else if (object instanceof IReactionSet) {
        IReactionSet reactionSet = object.getBuilder().newInstance(IReactionSet.class);
        reactionSet.addReaction(readReaction(object.getBuilder()));
        return (T) reactionSet;
    } else if (object instanceof IChemModel) {
        IChemModel model = object.getBuilder().newInstance(IChemModel.class);
        IReactionSet reactionSet = object.getBuilder().newInstance(IReactionSet.class);
        reactionSet.addReaction(readReaction(object.getBuilder()));
        model.setReactionSet(reactionSet);
        return (T) model;
    } else if (object instanceof IChemFile) {
        IChemFile chemFile = object.getBuilder().newInstance(IChemFile.class);
        IChemSequence sequence = object.getBuilder().newInstance(IChemSequence.class);
        sequence.addChemModel(read(object.getBuilder().newInstance(IChemModel.class)));
        chemFile.addChemSequence(sequence);
        return (T) chemFile;
    } else {
        throw new CDKException("Only supported are Reaction and ChemModel, and not " + object.getClass().getName() + ".");
    }
}

Example 28 with IChemSequence

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

the class SDFReaderTest method testMultipleDataFields.

@Test
public void testMultipleDataFields() throws Exception {
    String filename = "bug1587283.mol";
    InputStream ins = this.getClass().getResourceAsStream(filename);
    MDLV2000Reader reader = new MDLV2000Reader(ins);
    IChemFile fileContents = reader.read(new ChemFile());
    reader.close();
    Assert.assertEquals(1, fileContents.getChemSequenceCount());
    IChemSequence sequence = fileContents.getChemSequence(0);
    Assert.assertNotNull(sequence);
    Assert.assertEquals(1, sequence.getChemModelCount());
    IChemModel model = sequence.getChemModel(0);
    Assert.assertNotNull(model);
    IAtomContainerSet som = model.getMoleculeSet();
    Assert.assertNotNull(som);
    Assert.assertEquals(1, som.getAtomContainerCount());
    IAtomContainer m = som.getAtomContainer(0);
    Assert.assertNotNull(m);
    Assert.assertEquals("B02", m.getProperty("id_no"));
    Assert.assertEquals("2-2", m.getProperty("eductkey"));
    Assert.assertEquals("1", m.getProperty("Step"));
    Assert.assertEquals("2", m.getProperty("Pos"));
    Assert.assertEquals("B02", m.getProperty("Tag"));
}

Example 29 with IChemSequence

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

the class CML2Test method testCMLConciseFormula.

/**
 * Only Molecule with concise MolecularFormula
 */
@Test
public void testCMLConciseFormula() throws Exception {
    String filename = "cmlConciseFormula.cml";
    logger.info("Testing: " + filename);
    InputStream ins = this.getClass().getResourceAsStream(filename);
    CMLReader reader = new CMLReader(ins);
    IChemFile chemFile = reader.read(new ChemFile());
    reader.close();
    // test the resulting ChemFile content
    Assert.assertNotNull(chemFile);
    Assert.assertEquals(chemFile.getChemSequenceCount(), 1);
    IChemSequence seq = chemFile.getChemSequence(0);
    Assert.assertNotNull(seq);
    Assert.assertEquals(seq.getChemModelCount(), 1);
    IChemModel model = seq.getChemModel(0);
    Assert.assertNotNull(model);
    IAtomContainer mol = model.getMoleculeSet().getAtomContainer(0);
    Assert.assertNotNull(mol);
    // FIXME: REACT: It should return two different formulas
    Assert.assertEquals("[C 18 H 21 Cl 2 Mn 1 N 5 O 1]", mol.getProperty(CDKConstants.FORMULA).toString());
}

Example 30 with IChemSequence

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

the class CML2Test method testCMLWithFormula.

/**
 * @cdk.bug 1560486
 */
@Test
public void testCMLWithFormula() throws Exception {
    String filename = "cmlWithFormula.cml";
    logger.info("Testing: " + filename);
    InputStream ins = this.getClass().getResourceAsStream(filename);
    CMLReader reader = new CMLReader(ins);
    IChemFile chemFile = reader.read(new ChemFile());
    reader.close();
    // test the resulting ChemFile content
    Assert.assertNotNull(chemFile);
    Assert.assertEquals(chemFile.getChemSequenceCount(), 1);
    IChemSequence seq = chemFile.getChemSequence(0);
    Assert.assertNotNull(seq);
    Assert.assertEquals(seq.getChemModelCount(), 1);
    IChemModel model = seq.getChemModel(0);
    Assert.assertNotNull(model);
    IAtomContainer mol = model.getMoleculeSet().getAtomContainer(0);
    Assert.assertNotNull(mol);
    Assert.assertEquals("a", mol.getID());
    Assert.assertEquals("a1", mol.getAtom(0).getID());
    Assert.assertEquals(27, mol.getAtomCount());
    Assert.assertEquals(32, mol.getBondCount());
}