hueckelaromaticitydetectortest.java

化学图形处理软件

				true
				};
		Molecule molecule = MoleculeFactory.makeAzulene();
		boolean isAromatic = false;
		boolean result = false;
		isAromatic = HueckelAromaticityDetector.detectAromaticity(molecule);
		for (int f = 0; f < molecule.getAtomCount(); f++)
		{
			result = (molecule.getAtom(f).getFlag(CDKConstants.ISAROMATIC) == testResult[f]);
			assertTrue(result);
			logger.debug("Result for atom " + f + " is correct?: " + result);
		}
		if (standAlone && isAromatic)
		{
			System.out.println("Azulene is aromatic");
		}
	}


	/**
	 *  A unit test for JUnit. The N has to be counted correctly
	 */
	public void testIndole() throws Exception
	{
		Molecule molecule = MoleculeFactory.makeIndole();
		boolean testResults[] = {
				true,
				true,
				true,
				true,
				true,
				true,
				true,
				true,
				true
				};
		//boolean isAromatic = false;
		HueckelAromaticityDetector.detectAromaticity(molecule);
		for (int f = 0; f < molecule.getAtomCount(); f++)
		{
			assertTrue(molecule.getAtom(f).getFlag(CDKConstants.ISAROMATIC) == testResults[f]);
		}
	}

	/**
	 *  A unit test for JUnit. The N has to be counted correctly
	 */
	public void testPyrrole() throws Exception
	{
		Molecule molecule = MoleculeFactory.makePyrrole();
		boolean testResults[] = {
				true,
				true,
				true,
				true,
				true
				};
		//boolean isAromatic = false;
		HueckelAromaticityDetector.detectAromaticity(molecule);
		for (int f = 0; f < molecule.getAtomCount(); f++)
		{
			assertTrue(molecule.getAtom(f).getFlag(CDKConstants.ISAROMATIC) == testResults[f]);
		}
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testThiazole() throws Exception
	{
		Molecule molecule = MoleculeFactory.makeThiazole();
		boolean[] testResults = {true, true, true, true, true};
		HueckelAromaticityDetector.detectAromaticity(molecule);
		for (int f = 0; f < molecule.getAtomCount(); f++)
		{
			assertTrue(molecule.getAtom(f).getFlag(CDKConstants.ISAROMATIC) == testResults[f]);
		}

	}


	/**
	 *  A unit test for JUnit
	 */
	public void testTetraDehydroDecaline() throws Exception
	{
		boolean isAromatic = false;
		//boolean testResults[] = {true, false, false};
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());

		IMolecule mol = sp.parseSmiles("C1CCCc2c1cccc2");
		IRingSet rs = (new AllRingsFinder()).findAllRings(mol);
		//logger.debug("rs.size(): " + rs.size());
		HueckelAromaticityDetector.detectAromaticity(mol, rs, true);
		IRing r = null;
		int i = 0, aromacount = 0;
		java.util.Iterator rings = rs.atomContainers();
		while (rings.hasNext()) {
			r = (IRing)rings.next();
			isAromatic = r.getFlag(CDKConstants.ISAROMATIC);

			if (standAlone && isAromatic)
			{
				System.out.println("Ring " + i + " in test molecule is aromatic.");
			} else if (standAlone && !isAromatic)
			{
				System.out.println("Ring " + i + " in test molecule is not aromatic.");
			}
			if (isAromatic) aromacount++;
			i++;
		}
		assertEquals(aromacount, 1);
	}

    /**
     * This is a bug reported for JCP.
     */
    public void testSFBug956924() throws Exception {
    	SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());

    	IMolecule mol = sp.parseSmiles("[cH+]1cccccc1"); // tropylium cation
    	assertTrue(HueckelAromaticityDetector.detectAromaticity(mol));
    	assertEquals(7, mol.getAtomCount());
    	for (int f = 0; f < mol.getAtomCount(); f++) {
    		assertTrue(mol.getAtom(f).getFlag(CDKConstants.ISAROMATIC));
    	}
	}

    /**
     * This is a bug reported for JCP.
     */
    public void testSFBug956923() throws Exception {
		boolean testResults[] = {false, false, false, false, false, false, false, false};
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());

		IMolecule mol = sp.parseSmiles("O=c1cccccc1"); // tropone
		assertFalse(HueckelAromaticityDetector.detectAromaticity(mol));
		assertEquals(testResults.length, mol.getAtomCount());
		for (int f = 0; f < mol.getAtomCount(); f++) {
			assertTrue(mol.getAtom(f).getFlag(CDKConstants.ISAROMATIC) == testResults[f]);
		}
	}

	/**
	 *  A unit test for JUnit
	 */
	public void testPorphyrine() throws Exception
	{
		IMolecule molecule = null;
		boolean isAromatic = false;
		boolean testResults[] = {
				false,
				false,
				false,
				false,
				false,
				true,
				true,
				true,
				true,
				true,
				false,
				true,
				true,
				true,
				false,
				true,
				true,
				false,
				false,
				true,
				true,
				false,
				false,
				false,
				true,
				true,
				false,
				false,
				false,
				true,
				true,
				false,
				false,
				false,
				false,
				true,
				true,
				true,
				true,
				false,
				false,
				false
				};

		String filename = "data/mdl/porphyrin.mol";
		InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
		MDLReader reader = new MDLReader(ins);
		molecule = (Molecule) reader.read((ChemObject) new Molecule());

		isAromatic = HueckelAromaticityDetector.detectAromaticity(molecule);
		for (int f = 0; f < molecule.getAtomCount(); f++)
		{
			assertEquals(testResults[f], molecule.getAtom(f).getFlag(CDKConstants.ISAROMATIC));
		}
		assertTrue(isAromatic);
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testBug698152() throws Exception
	{
		Molecule molecule = null;
		//boolean isAromatic = false;
		boolean[] testResults = {true,
				true,
				true,
				true,
				true,
				true,
				false,
				false,
				false,
				false,
				false,
				false,
				false,
				false,
				false,
				false,
				false,
				false};

		String filename = "data/mdl/bug698152.mol";
		InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
		MDLReader reader = new MDLReader(ins);
		molecule = (Molecule) reader.read((ChemObject) new Molecule());

		HueckelAromaticityDetector.detectAromaticity(molecule);
		for (int f = 0; f < molecule.getAtomCount(); f++)
		{
			assertTrue(molecule.getAtom(f).getFlag(CDKConstants.ISAROMATIC) == testResults[f]);
		}
	}

	/**
	 *  A test for the fix of bug #716259, where a quinone ring 
	 *  was falsely detected as aromatic
	 */
	public void testBug716259() throws Exception
	{
		Molecule molecule = null;
		//boolean isAromatic = false;
		boolean[] testResults = {
			true,
			true,
			true,
			true,
			true,
			true,
			true,
			true,
			true,
			true,
			false,
			false,
			false,
			false,
			false,
			false,
			false,
			false,
			false
		};

		String filename = "data/mdl/bug716259.mol";
		InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
		MDLReader reader = new MDLReader(ins);
		molecule = (Molecule) reader.read((ChemObject) new Molecule());

		HueckelAromaticityDetector.detectAromaticity(molecule);
		for (int f = 0; f < molecule.getAtomCount(); f++)
		{
			assertTrue(molecule.getAtom(f).getFlag(CDKConstants.ISAROMATIC) == testResults[f]);
		}

	}
	
	
	/**
	 *  A unit test for JUnit
	 */
	public void testQuinone() throws Exception
	{
		Molecule molecule = MoleculeFactory.makeQuinone();
		//boolean isAromatic = false;
		boolean[] testResults = {false, false, false, false, false, false, false, false};

		HueckelAromaticityDetector.detectAromaticity(molecule);
		for (int f = 0; f < molecule.getAtomCount(); f++)
		{
			assertTrue(molecule.getAtom(f).getFlag(CDKConstants.ISAROMATIC) == testResults[f]);
		}

	}
  
  public void testBug1328739() throws Exception {
      String filename = "data/mdl/bug1328739.mol";
      InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
      MDLReader reader = new MDLReader(ins);
      Molecule molecule = (Molecule) reader.read(new Molecule());
      HueckelAromaticityDetector.detectAromaticity(molecule);
      assertEquals(15, molecule.getBondCount());
      assertTrue(molecule.getBond(0).getFlag(CDKConstants.ISAROMATIC));
      assertTrue(molecule.getBond(1).getFlag(CDKConstants.ISAROMATIC));
      assertTrue(molecule.getBond(2).getFlag(CDKConstants.ISAROMATIC));
      assertTrue(molecule.getBond(3).getFlag(CDKConstants.ISAROMATIC));
      assertTrue(molecule.getBond(4).getFlag(CDKConstants.ISAROMATIC));
      assertTrue(molecule.getBond(6).getFlag(CDKConstants.ISAROMATIC));
  }

	/**
	 *  A unit test for JUnit
	 */
	public void testBenzene() throws Exception
	{
		Molecule molecule = MoleculeFactory.makeBenzene();
		//boolean isAromatic = false;
		boolean[] testResults = {true,true,true,true,true,true};

		HueckelAromaticityDetector.detectAromaticity(molecule);
		for (int f = 0; f < molecule.getAtomCount(); f++)
		{
			assertTrue(molecule.getAtom(f).getFlag(CDKConstants.ISAROMATIC) == testResults[f]);
		}

	}

	private IMolecule makeAromaticMolecule()
	{
		  IMolecule mol = new Molecule();
		  IAtom a1 = mol.getBuilder().newAtom("C");
		  a1.setPoint2d(new Point2d(329.99999999999994, 971.0));  mol.addAtom(a1);
		  IAtom a2 = mol.getBuilder().newAtom("C");
		  a2.setPoint2d(new Point2d(298.8230854637602, 989.0));  mol.addAtom(a2);
		  IAtom a3 = mol.getBuilder().newAtom("C");
		  a3.setPoint2d(new Point2d(298.8230854637602, 1025.0));  mol.addAtom(a3);
		  IAtom a4 = mol.getBuilder().newAtom("C");
		  a4.setPoint2d(new Point2d(330.0, 1043.0));  mol.addAtom(a4);
		  IAtom a5 = mol.getBuilder().newAtom("C");
		  a5.setPoint2d(new Point2d(361.1769145362398, 1025.0));  mol.addAtom(a5);
		  IAtom a6 = mol.getBuilder().newAtom("C");
		  a6.setPoint2d(new Point2d(361.1769145362398, 989.0));  mol.addAtom(a6);
		  IAtom a7 = mol.getBuilder().newAtom("C");
		  a7.setPoint2d(new Point2d(392.3538290724796, 971.0));  mol.addAtom(a7);
		  IAtom a8 = mol.getBuilder().newAtom("C");
		  a8.setPoint2d(new Point2d(423.5307436087194, 989.0));  mol.addAtom(a8);
		  IAtom a9 = mol.getBuilder().newAtom("C");
		  a9.setPoint2d(new Point2d(423.5307436087194, 1025.0));  mol.addAtom(a9);
		  IAtom a10 = mol.getBuilder().newAtom("C");
		  a10.setPoint2d(new Point2d(392.3538290724796, 1043.0));  mol.addAtom(a10);
		  IBond b1 = mol.getBuilder().newBond(a1, a2, 2.0);
		  mol.addBond(b1);
		  IBond b2 = mol.getBuilder().newBond(a2, a3, 1.0);
		  mol.addBond(b2);
		  IBond b3 = mol.getBuilder().newBond(a3, a4, 2.0);
		  mol.addBond(b3);
		  IBond b4 = mol.getBuilder().newBond(a4, a5, 1.0);
		  mol.addBond(b4);
		  IBond b5 = mol.getBuilder().newBond(a5, a6, 2.0);
		  mol.addBond(b5);
		  IBond b6 = mol.getBuilder().newBond(a6, a1, 1.0);
		  mol.addBond(b6);
		  IBond b7 = mol.getBuilder().newBond(a6, a7, 1.0);
		  mol.addBond(b7);
		  IBond b8 = mol.getBuilder().newBond(a7, a8, 1.0);
		  mol.addBond(b8);
		  IBond b9 = mol.getBuilder().newBond(a8, a9, 1.0);
		  mol.addBond(b9);
		  IBond b10 = mol.getBuilder().newBond(a9, a10, 1.0);
		  mol.addBond(b10);
		  IBond b11 = mol.getBuilder().newBond(a10, a5, 1.0);
		  mol.addBond(b11);
		  return mol;
	}
	
}