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

Example 6 with AtomContainerSet

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

the class MoleculeSetManipulatorTest method testRemoveElectronContainer_IAtomContainerSet_IElectronContainer.

@Test
public void testRemoveElectronContainer_IAtomContainerSet_IElectronContainer() {
    IAtomContainerSet ms = new AtomContainerSet();
    IAtomContainer mol = new AtomContainer();
    mol.addAtom(new Atom("O"));
    mol.addAtom(new Atom("O"));
    mol.addBond(0, 1, IBond.Order.DOUBLE);
    IBond bond = mol.getBond(0);
    ms.addAtomContainer(mol);
    IBond otherBond = new Bond(new Atom(), new Atom());
    MoleculeSetManipulator.removeElectronContainer(ms, otherBond);
    Assert.assertEquals(1, MoleculeSetManipulator.getBondCount(ms));
    MoleculeSetManipulator.removeElectronContainer(ms, bond);
    Assert.assertEquals(0, MoleculeSetManipulator.getBondCount(ms));
}

Example 7 with AtomContainerSet

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

the class SDFWriterTest method testWrite_IAtomContainerSet_SingleMolecule.

@Test
public void testWrite_IAtomContainerSet_SingleMolecule() throws Exception {
    StringWriter writer = new StringWriter();
    IAtomContainerSet molSet = new AtomContainerSet();
    IAtomContainer molecule = new AtomContainer();
    molecule.addAtom(new Atom("C"));
    molSet.addAtomContainer(molecule);
    SDFWriter sdfWriter = new SDFWriter(writer);
    sdfWriter.write(molSet);
    sdfWriter.close();
    Assert.assertTrue(writer.toString().contains("$$$$"));
}

Example 8 with AtomContainerSet

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

the class CMLRoundTripTest method testChemModel.

/**
 * @cdk.bug 1455346
 */
@Test
public void testChemModel() throws Exception {
    ChemModel model = new ChemModel();
    IAtomContainerSet moleculeSet = new AtomContainerSet();
    IAtomContainer mol = new AtomContainer();
    PseudoAtom atom = new PseudoAtom("N");
    mol.addAtom(atom);
    moleculeSet.addAtomContainer(mol);
    model.setMoleculeSet(moleculeSet);
    IChemModel roundTrippedModel = CMLRoundTripTool.roundTripChemModel(convertor, model);
    IAtomContainerSet roundTrippedMolSet = roundTrippedModel.getMoleculeSet();
    Assert.assertNotNull(roundTrippedMolSet);
    Assert.assertEquals(1, roundTrippedMolSet.getAtomContainerCount());
    IAtomContainer roundTrippedMolecule = roundTrippedMolSet.getAtomContainer(0);
    Assert.assertNotNull(roundTrippedMolecule);
    Assert.assertEquals(1, roundTrippedMolecule.getAtomCount());
}

Example 9 with AtomContainerSet

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

the class INChIHandler method startDocument.

@Override
public void startDocument() {
    chemFile = new ChemFile();
    chemSequence = new ChemSequence();
    chemModel = new ChemModel();
    setOfMolecules = new AtomContainerSet();
}

Example 10 with AtomContainerSet

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

the class SMILESReaderTest method testReadingSmiFile_3.

@Test
public void testReadingSmiFile_3() throws Exception {
    String filename = "test3.smi";
    logger.info("Testing: " + filename);
    InputStream ins = this.getClass().getResourceAsStream(filename);
    SMILESReader reader = new SMILESReader(ins);
    IAtomContainerSet som = reader.read(new AtomContainerSet());
    Assert.assertEquals(5, som.getAtomContainerCount());
}