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

Example 21 with AtomContainerSet

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

the class SDFWriterTest method testWrite_IAtomContainerSet_Properties.

@Test
public void testWrite_IAtomContainerSet_Properties() throws Exception {
    StringWriter writer = new StringWriter();
    IAtomContainerSet molSet = new AtomContainerSet();
    IAtomContainer molecule = new AtomContainer();
    molecule.addAtom(new Atom("C"));
    molecule.setProperty("foo", "bar");
    molSet.addAtomContainer(molecule);
    SDFWriter sdfWriter = new SDFWriter(writer);
    sdfWriter.write(molSet);
    sdfWriter.close();
    Assert.assertTrue(writer.toString().contains("<foo>"));
    Assert.assertTrue(writer.toString().contains("bar"));
}

Example 22 with AtomContainerSet

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

the class SDFWriterTest method testWrite_IAtomContainerSet_MultIAtomContainer.

@Test
public void testWrite_IAtomContainerSet_MultIAtomContainer() throws Exception {
    StringWriter writer = new StringWriter();
    IAtomContainerSet molSet = new AtomContainerSet();
    IAtomContainer molecule = new AtomContainer();
    molecule.addAtom(new Atom("C"));
    molSet.addAtomContainer(molecule);
    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 23 with AtomContainerSet

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

the class MoleculeSetManipulatorTest method testRemoveAtomAndConnectedElectronContainers_IAtomContainerSet_IAtom.

@Test
public void testRemoveAtomAndConnectedElectronContainers_IAtomContainerSet_IAtom() {
    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);
    IAtom atom = mol.getAtom(0);
    ms.addAtomContainer(mol);
    IAtom otherAtom = new Atom("O");
    MoleculeSetManipulator.removeAtomAndConnectedElectronContainers(ms, otherAtom);
    Assert.assertEquals(1, MoleculeSetManipulator.getBondCount(ms));
    Assert.assertEquals(2, MoleculeSetManipulator.getAtomCount(ms));
    MoleculeSetManipulator.removeAtomAndConnectedElectronContainers(ms, atom);
    Assert.assertEquals(0, MoleculeSetManipulator.getBondCount(ms));
    Assert.assertEquals(1, MoleculeSetManipulator.getAtomCount(ms));
}

Example 24 with AtomContainerSet

use of org.openscience.cdk.AtomContainerSet 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 25 with AtomContainerSet

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

the class CMLRoundTripTest method testMoleculeSet.

@Test
public void testMoleculeSet() throws Exception {
    IAtomContainerSet list = new AtomContainerSet();
    list.addAtomContainer(new AtomContainer());
    list.addAtomContainer(new AtomContainer());
    IChemModel model = new ChemModel();
    model.setMoleculeSet(list);
    IChemModel roundTripped = CMLRoundTripTool.roundTripChemModel(convertor, model);
    IAtomContainerSet newList = roundTripped.getMoleculeSet();
    Assert.assertNotNull(newList);
    Assert.assertEquals(2, newList.getAtomContainerCount());
    Assert.assertNotNull(newList.getAtomContainer(0));
    Assert.assertNotNull(newList.getAtomContainer(1));
}