org.openscience.cdk.AtomContainerSet.<init> java code examples

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private void myMethod () {
 ArrayList a =new ArrayList<Object>()
Collection collection;new ArrayList<>(collection)
Lists.newArrayList()
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}

  @Override
  public IChemObject newTestObject() {
    return new AtomContainerSet();
  }
});

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

@BeforeClass
public static void setUp() {
  setTestObjectBuilder(new ITestObjectBuilder() {
    @Override
    public IChemObject newTestObject() {
      return new AtomContainerSet();
    }
  });
}

@Test
public void testExampleFile_SupportColumns() throws Exception {
  String filename = "data/moss/TKO.mossoutput";
  InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
  MoSSOutputReader reader = new MoSSOutputReader(ins);
  IAtomContainerSet moleculeSet = new AtomContainerSet();
  moleculeSet = reader.read(moleculeSet);
  Assert.assertEquals(5.06, Double
      .valueOf(moleculeSet.getAtomContainer(0).getProperty("focusSupport").toString()).doubleValue(), 0.01);
  Assert.assertEquals(1.74,
      Double.valueOf(moleculeSet.getAtomContainer(0).getProperty("complementSupport").toString())
          .doubleValue(), 0.01);
}

@Test
public void testReadingSmiFile_1() throws Exception {
  String filename = "data/smiles/smiles.smi";
  logger.info("Testing: " + filename);
  InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
  SMILESReader reader = new SMILESReader(ins);
  IAtomContainerSet som = reader.read(new AtomContainerSet());
  String name = null;
  IAtomContainer thisMol = som.getAtomContainer(0);
  name = ((String) thisMol.getProperty("SMIdbNAME")).toString();
  Assert.assertEquals("benzene", name);
}

@Test
public void testReading() throws Exception {
  String filename = "data/smiles/smiles.smi";
  logger.info("Testing: " + filename);
  InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
  SMILESReader reader = new SMILESReader(ins);
  IAtomContainerSet som = reader.read(new AtomContainerSet());
  Assert.assertEquals(8, som.getAtomContainerCount());
}

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

@Test
public void testExampleFile_MolReading() throws Exception {
  String filename = "data/moss/TKO.mossoutput";
  InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
  MoSSOutputReader reader = new MoSSOutputReader(ins);
  IAtomContainerSet moleculeSet = new AtomContainerSet();
  moleculeSet = reader.read(moleculeSet);
  Assert.assertEquals(19, moleculeSet.getAtomContainerCount());
  for (IAtomContainer mol : moleculeSet.atomContainers()) {
    Assert.assertEquals(Integer.valueOf(mol.getProperty("atomCount").toString()).intValue(), mol.getAtomCount());
    Assert.assertEquals(Integer.valueOf(mol.getProperty("bondCount").toString()).intValue(), mol.getBondCount());
  }
}

@Test
public void testReadingSmiFile_2() throws Exception {
  String filename = "data/smiles/smiles.smi";
  logger.info("Testing: " + filename);
  InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
  SMILESReader reader = new SMILESReader(ins);
  IAtomContainerSet som = reader.read(new AtomContainerSet());
  IAtomContainer thisMol = som.getAtomContainer(1);
  Assert.assertNull(thisMol.getProperty("SMIdbNAME"));
}

@Test
public void testAtomContainerSet() {
  IAtomContainerSet som = new AtomContainerSet();
  Assert.assertNotNull(som);
  Assert.assertEquals(0, som.getAtomContainerCount());
}

@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().indexOf("$$$$") != -1);
}

@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().indexOf("<foo>") != -1);
  Assert.assertTrue(writer.toString().indexOf("bar") != -1);
}

@Test
public void testWrite_IAtomContainerSet_CDKProperties() throws Exception {
  StringWriter writer = new StringWriter();
  IAtomContainerSet molSet = new AtomContainerSet();
  IAtomContainer molecule = new AtomContainer();
  molecule.addAtom(new Atom("C"));
  molecule.setProperty(InvPair.CANONICAL_LABEL, "bar");
  molSet.addAtomContainer(molecule);
  SDFWriter sdfWriter = new SDFWriter(writer);
  sdfWriter.write(molSet);
  sdfWriter.close();
  Assert.assertTrue(writer.toString().indexOf(InvPair.CANONICAL_LABEL) == -1);
}

@Test
public void testWrite_IAtomContainerSet_Properties_Off() 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);
  Properties sdfWriterProps = new Properties();
  sdfWriterProps.put("writeProperties", "false");
  sdfWriter.addChemObjectIOListener(new PropertiesListener(sdfWriterProps));
  sdfWriter.customizeJob();
  sdfWriter.write(molSet);
  sdfWriter.close();
  String result = writer.toString();
  Assert.assertFalse(result.contains("<foo>"));
}

@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().indexOf("$$$$") != -1);
}

@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));
}

@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());
  AtomContainerSetManipulator.removeElectronContainer(ms, otherBond);
  Assert.assertEquals(1, AtomContainerSetManipulator.getBondCount(ms));
  AtomContainerSetManipulator.removeElectronContainer(ms, bond);
  Assert.assertEquals(0, AtomContainerSetManipulator.getBondCount(ms));
}

@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));
}

@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));
}

@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");
  AtomContainerSetManipulator.removeAtomAndConnectedElectronContainers(ms, otherAtom);
  Assert.assertEquals(1, AtomContainerSetManipulator.getBondCount(ms));
  Assert.assertEquals(2, AtomContainerSetManipulator.getAtomCount(ms));
  AtomContainerSetManipulator.removeAtomAndConnectedElectronContainers(ms, atom);
  Assert.assertEquals(0, AtomContainerSetManipulator.getBondCount(ms));
  Assert.assertEquals(1, AtomContainerSetManipulator.getAtomCount(ms));
}

Javadoc

Constructs an empty AtomContainerSet.

Popular methods of AtomContainerSet

addAtomContainer
Adds an atomContainer to this container with the given multiplier.
clone
Clones this AtomContainerSet and its content.
getAtomContainerCount
Returns the number of AtomContainers in this Container.
getMultiplier
Returns the multiplier of the given AtomContainer.
notifyChanged
removeAtomContainer
Removes an AtomContainer from this container.
setMultiplier
Sets the coefficient of a AtomContainer to a given value.
add
Adds all atomContainers in the AtomContainerSet to this container.
addListener
addProperties
atomContainers
Get an iterator for this AtomContainerSet.
getAtomContainer
Returns the AtomContainer at position number in the container.

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org.openscience.cdk.AtomContainerSet
constructor