Ejemplo n.º 1
0
  @Test
  public void testReading() throws Exception {
    String filename = "data/asn/pubchem/cid1145.xml";
    logger.info("Testing: " + filename);
    InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
    PCCompoundXMLReader reader = new PCCompoundXMLReader(ins);
    IMolecule molecule = (IMolecule) reader.read(new Molecule());
    Assert.assertNotNull(molecule);

    // check atom stuff
    Assert.assertEquals(14, molecule.getAtomCount());
    Assert.assertEquals("O", molecule.getAtom(0).getSymbol());
    Assert.assertEquals(Integer.valueOf(-1), molecule.getAtom(0).getFormalCharge());
    Assert.assertEquals("N", molecule.getAtom(1).getSymbol());
    Assert.assertEquals(Integer.valueOf(1), molecule.getAtom(1).getFormalCharge());

    // check bond stuff
    Assert.assertEquals(13, molecule.getBondCount());
    Assert.assertNotNull(molecule.getBond(3));

    // coordinates
    Assert.assertNull(molecule.getAtom(0).getPoint3d());
    Point2d point = molecule.getAtom(0).getPoint2d();
    Assert.assertNotNull(point);
    Assert.assertEquals(3.7320508956909, point.x, 0.00000001);
    Assert.assertEquals(0.5, point.y, 0.00000001);
  }
Ejemplo n.º 2
0
  /**
   * Test for SF bug #1309731.
   *
   * @cdk.bug 1309731
   */
  @Test
  public void testModelBuilder3D_keepChemObjectIDs() throws Exception {
    ModelBuilder3D mb3d = ModelBuilder3D.getInstance();

    IMolecule methanol = new org.openscience.cdk.Molecule();
    IChemObjectBuilder builder = methanol.getBuilder();

    IAtom carbon1 = builder.newInstance(IAtom.class, "C");
    carbon1.setID("carbon1");
    methanol.addAtom(carbon1);
    for (int i = 0; i < 3; i++) {
      IAtom hydrogen = builder.newInstance(IAtom.class, "H");
      methanol.addAtom(hydrogen);
      methanol.addBond(builder.newInstance(IBond.class, carbon1, hydrogen, IBond.Order.SINGLE));
    }
    IAtom oxygen1 = builder.newInstance(IAtom.class, "O");
    oxygen1.setID("oxygen1");
    methanol.addAtom(oxygen1);
    methanol.addBond(builder.newInstance(IBond.class, carbon1, oxygen1, IBond.Order.SINGLE));
    IAtom hydrogen = builder.newInstance(IAtom.class, "H");
    methanol.addAtom(hydrogen);
    methanol.addBond(builder.newInstance(IBond.class, hydrogen, oxygen1, IBond.Order.SINGLE));

    Assert.assertEquals(6, methanol.getAtomCount());
    Assert.assertEquals(5, methanol.getBondCount());

    mb3d.generate3DCoordinates(methanol, false);

    checkAverageBondLength(methanol);
    Assert.assertEquals("carbon1", carbon1.getID());
    Assert.assertEquals("oxygen1", oxygen1.getID());
  }
Ejemplo n.º 3
0
 @Test
 public void testNNMolecule_int_int_int_int() {
   IMolecule m = new NNMolecule(5, 5, 1, 1);
   Assert.assertNotNull(m);
   Assert.assertEquals(0, m.getAtomCount());
   Assert.assertEquals(0, m.getBondCount());
   Assert.assertEquals(0, m.getLonePairCount());
   Assert.assertEquals(0, m.getSingleElectronCount());
 }
Ejemplo n.º 4
0
  @Test
  public void testBondStereo() throws Exception {
    String cmlString =
        "<molecule id='m1'><atomArray><atom id='a1'/><atom id='a2'/></atomArray><bondArray><bond id='b1' atomRefs2='a1 a2'><bondStereo dictRef='cml:H'/></bond></bondArray></molecule>";
    IChemFile chemFile = parseCMLString(cmlString);
    IMolecule mol = checkForSingleMoleculeFile(chemFile);

    Assert.assertEquals(2, mol.getAtomCount());
    Assert.assertEquals(1, mol.getBondCount());
    IBond bond = mol.getBond(0);
    Assert.assertEquals(IBond.Stereo.DOWN, bond.getStereo());
  }
Ejemplo n.º 5
0
  @Test
  public void testBondAromatic2() throws Exception {
    String cmlString =
        "<molecule id='m1'><atomArray atomID='a1 a2'/><bondArray><bond atomRefs='a1 a2' order='2'><bondType dictRef='cdk:aromaticBond'/></bond></bondArray></molecule>";
    IChemFile chemFile = parseCMLString(cmlString);
    IMolecule mol = checkForSingleMoleculeFile(chemFile);

    Assert.assertEquals(2, mol.getAtomCount());
    Assert.assertEquals(1, mol.getBondCount());
    org.openscience.cdk.interfaces.IBond bond = mol.getBond(0);
    Assert.assertEquals(CDKConstants.BONDORDER_DOUBLE, bond.getOrder());
    Assert.assertTrue(bond.getFlag(CDKConstants.ISAROMATIC));
  }
Ejemplo n.º 6
0
  @Test
  public void testBondId() throws Exception {
    String cmlString =
        "<molecule id='m1'><atomArray><atom id='a1'/><atom id='a2'/></atomArray><bondArray><bond id='b1' atomRefs2='a1 a2'/></bondArray></molecule>";

    IChemFile chemFile = parseCMLString(cmlString);
    IMolecule mol = checkForSingleMoleculeFile(chemFile);

    Assert.assertEquals(2, mol.getAtomCount());
    Assert.assertEquals(1, mol.getBondCount());
    org.openscience.cdk.interfaces.IBond bond = mol.getBond(0);
    Assert.assertEquals("b1", bond.getID());
  }
Ejemplo n.º 7
0
  @Test
  public void testBond5() throws Exception {
    String cmlString =
        "<molecule id='m1'><atomArray atomID='a1 a2 a3'/><bondArray atomRef1='a1 a1' atomRef2='a2 a3' order='1 1'/></molecule>";

    IChemFile chemFile = parseCMLString(cmlString);
    IMolecule mol = checkForSingleMoleculeFile(chemFile);

    Assert.assertEquals(3, mol.getAtomCount());
    Assert.assertEquals(2, mol.getBondCount());
    org.openscience.cdk.interfaces.IBond bond = mol.getBond(0);
    Assert.assertEquals(2, bond.getAtomCount());
    Assert.assertEquals(IBond.Order.SINGLE, bond.getOrder());
    bond = mol.getBond(1);
    Assert.assertEquals(2, bond.getAtomCount());
    Assert.assertEquals(IBond.Order.SINGLE, bond.getOrder());
  }
Ejemplo n.º 8
0
  @Test
  public void testBond4() throws Exception {
    String cmlString =
        "<molecule id='m1'><atomArray atomID='a1 a2 a3'/><bondArray atomRef1='a1 a1' atomRef2='a2 a3' bondID='b1 b2'/></molecule>";

    IChemFile chemFile = parseCMLString(cmlString);
    IMolecule mol = checkForSingleMoleculeFile(chemFile);

    Assert.assertEquals(3, mol.getAtomCount());
    Assert.assertEquals(2, mol.getBondCount());
    org.openscience.cdk.interfaces.IBond bond = mol.getBond(0);
    Assert.assertEquals(2, bond.getAtomCount());
    IAtom atom1 = bond.getAtom(0);
    IAtom atom2 = bond.getAtom(1);
    Assert.assertEquals("a1", atom1.getID());
    Assert.assertEquals("a2", atom2.getID());
    Assert.assertEquals("b2", mol.getBond(1).getID());
  }
Ejemplo n.º 9
0
  @Test
  public void testNNMolecule_IAtomContainer() {
    IAtomContainer acetone = new org.openscience.cdk.AtomContainer();
    IAtom c1 = acetone.getBuilder().newAtom("C");
    IAtom c2 = acetone.getBuilder().newAtom("C");
    IAtom o = acetone.getBuilder().newAtom("O");
    IAtom c3 = acetone.getBuilder().newAtom("C");
    acetone.addAtom(c1);
    acetone.addAtom(c2);
    acetone.addAtom(c3);
    acetone.addAtom(o);
    IBond b1 = acetone.getBuilder().newBond(c1, c2, IBond.Order.SINGLE);
    IBond b2 = acetone.getBuilder().newBond(c1, o, IBond.Order.DOUBLE);
    IBond b3 = acetone.getBuilder().newBond(c1, c3, IBond.Order.SINGLE);
    acetone.addBond(b1);
    acetone.addBond(b2);
    acetone.addBond(b3);

    IMolecule m = new NNMolecule(acetone);
    Assert.assertNotNull(m);
    Assert.assertEquals(4, m.getAtomCount());
    Assert.assertEquals(3, m.getBondCount());
  }
  /**
   * Get the container which is found resonance from a IMolecule. It is based on looking if the
   * order of the bond changes.
   *
   * @param molecule The IMolecule to analyze
   * @return The different containers
   */
  @TestMethod("testGetContainers_IMolecule")
  public IAtomContainerSet getContainers(IMolecule molecule) {
    IAtomContainerSet setOfCont = molecule.getBuilder().newAtomContainerSet();
    IMoleculeSet setOfMol = getStructures(molecule);

    if (setOfMol.getMoleculeCount() == 0) return setOfCont;

    /*extraction of all bonds which has been produced a changes of order*/
    List<IBond> bondList = new ArrayList<IBond>();
    for (int i = 1; i < setOfMol.getMoleculeCount(); i++) {
      IMolecule mol = setOfMol.getMolecule(i);
      for (int j = 0; j < mol.getBondCount(); j++) {
        IBond bond = molecule.getBond(j);
        if (!mol.getBond(j).getOrder().equals(bond.getOrder())) {
          if (!bondList.contains(bond)) bondList.add(bond);
        }
      }
    }

    if (bondList.size() == 0) return null;

    int[] flagBelonging = new int[bondList.size()];
    for (int i = 0; i < flagBelonging.length; i++) flagBelonging[i] = 0;
    int[] position = new int[bondList.size()];
    int maxGroup = 1;

    /*Analysis if the bond are linked together*/
    List<IBond> newBondList = new ArrayList<IBond>();
    newBondList.add(bondList.get(0));

    int pos = 0;
    for (int i = 0; i < newBondList.size(); i++) {

      if (i == 0) flagBelonging[i] = maxGroup;
      else {
        if (flagBelonging[position[i]] == 0) {
          maxGroup++;
          flagBelonging[position[i]] = maxGroup;
        }
      }

      IBond bondA = newBondList.get(i);
      for (int ato = 0; ato < 2; ato++) {
        IAtom atomA1 = bondA.getAtom(ato);
        List<IBond> bondA1s = molecule.getConnectedBondsList(atomA1);
        for (int j = 0; j < bondA1s.size(); j++) {
          IBond bondB = bondA1s.get(j);
          if (!newBondList.contains(bondB))
            for (int k = 0; k < bondList.size(); k++)
              if (bondList.get(k).equals(bondB))
                if (flagBelonging[k] == 0) {
                  flagBelonging[k] = maxGroup;
                  pos++;
                  newBondList.add(bondB);
                  position[pos] = k;
                }
        }
      }
      // if it is final size and not all are added
      if (newBondList.size() - 1 == i)
        for (int k = 0; k < bondList.size(); k++)
          if (!newBondList.contains(bondList.get(k))) {
            newBondList.add(bondList.get(k));
            position[i + 1] = k;
            break;
          }
    }
    /*creating containers according groups*/
    for (int i = 0; i < maxGroup; i++) {
      IAtomContainer container = molecule.getBuilder().newAtomContainer();
      for (int j = 0; j < bondList.size(); j++) {
        if (flagBelonging[j] != i + 1) continue;
        IBond bond = bondList.get(j);
        IAtom atomA1 = bond.getAtom(0);
        IAtom atomA2 = bond.getAtom(1);
        if (!container.contains(atomA1)) container.addAtom(atomA1);
        if (!container.contains(atomA2)) container.addAtom(atomA2);
        container.addBond(bond);
      }
      setOfCont.addAtomContainer(container);
    }
    return setOfCont;
  }