conjugatedpisystemsdetectortest.java

化学图形处理软件

        String filename = "data/mdl/piSystemCumulative.mol";
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLReader reader = new MDLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read((ChemObject)new ChemFile());
        mol = chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0);    

        HueckelAromaticityDetector.detectAromaticity(mol);
        
        AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol);
        
        assertEquals(2, acSet.getAtomContainerCount());
        IAtomContainer ac1 = acSet.getAtomContainer(0);
        assertEquals(4, ac1.getAtomCount());
        assertEquals(3, ac1.getBondCount());
        
        for (int i = 0; i < ac1.getAtomCount(); i++) {
            assertTrue(mol.contains(ac1.getAtom(i)));
        }
        
        for (int i = 0; i < ac1.getBondCount(); i++) {
            assertTrue(mol.contains(ac1.getBond(i)));
        }
        
        IAtomContainer ac2 = acSet.getAtomContainer(0);
        assertEquals(4, ac2.getAtomCount());
        assertEquals(3, ac2.getBondCount());
        
        for (int i = 0; i < ac2.getAtomCount(); i++) {
            assertTrue(mol.contains(ac1.getAtom(i)));
        }
        
        for (int i = 0; i < ac2.getBondCount(); i++) {
            assertTrue(mol.contains(ac1.getBond(i)));
        }
        
	}

    /**
	 *  A unit test for JUnit
	 *
	 *@return    Description of the Return Value
	 */
    public void testAceticAcid() throws Exception
	{
    	IMolecule mol = null;
    	mol = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("CC(=O)O");
    	HydrogenAdder adder = new HydrogenAdder();
    	adder.addImplicitHydrogensToSatisfyValency(mol);
    	LonePairElectronChecker lpcheck = new LonePairElectronChecker();
    	lpcheck.newSaturate(mol);
    	HueckelAromaticityDetector.detectAromaticity(mol);
        
        AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol);
        
        assertEquals(1, acSet.getAtomContainerCount());
        IAtomContainer ac1 = acSet.getAtomContainer(0);
        assertEquals(3, ac1.getAtomCount());
        assertEquals(2, ac1.getBondCount());
        
        for (int i = 0; i < ac1.getAtomCount(); i++) {
            assertTrue(mol.contains(ac1.getAtom(i)));
        }
        
        for (int i = 0; i < ac1.getBondCount(); i++) {
            assertTrue(mol.contains(ac1.getBond(i)));
        }
        
	}
    /**
	 *  A unit test for JUnit
	 *
	 *@return    Description of the Return Value
	 */
    public void testNN_dimethylaniline_cation() throws Exception
	{
    	IMolecule mol = null;
    	String filename = "data/mdl/NN_dimethylaniline.mol";
    	InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
    	MDLReader reader = new MDLReader(ins);
    	IChemFile chemFile = (IChemFile)reader.read((ChemObject)new ChemFile());
    	mol = chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0);  
//    	for(int i =0;i<mol.getAtomCount();i++)
//    		System.out.println(i+", "+mol.getAtom(i).getSymbol()+" "+mol.getAtom(i).getHydrogenCount());

//  	mol.getAtomAt(6).setFormalCharge(1);
    	HydrogenAdder adder = new HydrogenAdder();
    	adder.addImplicitHydrogensToSatisfyValency(mol);
    	LonePairElectronChecker lpcheck = new LonePairElectronChecker();
    	lpcheck.newSaturate(mol);
    	HueckelAromaticityDetector.detectAromaticity(mol);
        
        AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol);
        
        assertEquals(1, acSet.getAtomContainerCount());
        IAtomContainer ac1 = acSet.getAtomContainer(0);
        assertEquals(6, ac1.getAtomCount());
        assertEquals(5, ac1.getBondCount());
        
	}

    /**
	 *  A unit test for JUnit
	 *
	 *@return    Description of the Return Value
	 */
    public void test1_fluorobutadienene() throws Exception
	{
    	IMolecule mol = null;
    	mol = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("FC=CC=C");
    	HydrogenAdder adder = new HydrogenAdder();
    	adder.addImplicitHydrogensToSatisfyValency(mol);
    	LonePairElectronChecker lpcheck = new LonePairElectronChecker();
    	lpcheck.newSaturate(mol);
    	HueckelAromaticityDetector.detectAromaticity(mol);
        
        AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol);
        
        assertEquals(1, acSet.getAtomContainerCount());
        IAtomContainer ac1 = acSet.getAtomContainer(0);
        assertEquals(5, ac1.getAtomCount());
        assertEquals(4, ac1.getBondCount());
        
	}
    /**
	 *  A unit test for JUnit
	 *
	 *@return    Description of the Return Value
	 */
    public void testEthyne_difluoro() throws Exception
	{
    	IMolecule mol = null;
    	mol = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("FC#CF");
    	HydrogenAdder adder = new HydrogenAdder();
    	adder.addImplicitHydrogensToSatisfyValency(mol);
    	LonePairElectronChecker lpcheck = new LonePairElectronChecker();
    	lpcheck.newSaturate(mol);
    	HueckelAromaticityDetector.detectAromaticity(mol);
        
        AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol);
        
        assertEquals(1, acSet.getAtomContainerCount());
        IAtomContainer ac1 = acSet.getAtomContainer(0);
        assertEquals(4, ac1.getAtomCount());
        assertEquals(3, ac1.getBondCount());
        
        
        
	}
    /**
	 *  A unit test for JUnit
	 *
	 *@return    Description of the Return Value
	 */
    public void test3Aminomethane_cation() throws Exception
	{
    	IMolecule mol = null;
    	mol = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("CN(C)C(N(C)C)N(C)C");
    	mol.getAtom(3).setFormalCharge(+1);
    	HydrogenAdder adder = new HydrogenAdder();
    	adder.addImplicitHydrogensToSatisfyValency(mol);
    	LonePairElectronChecker lpcheck = new LonePairElectronChecker();
    	lpcheck.newSaturate(mol);
    	HueckelAromaticityDetector.detectAromaticity(mol);
        
        AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol);
        
        assertEquals(1, acSet.getAtomContainerCount());
        IAtomContainer ac1 = acSet.getAtomContainer(0);
        assertEquals(4, ac1.getAtomCount());
        assertEquals(3, ac1.getBondCount());
        
        
        
	}
    /**
	 *  A unit test for JUnit
	 *
	 *@return    Description of the Return Value
	 */
    private IMolecule readCMLMolecule(String filename) throws Exception {
    	IMolecule mol = null;
    	logger.debug("Filename: " + filename);
    	InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
    	CMLReader reader = new CMLReader(ins);

    	IChemFile file = (IChemFile)reader.read(new ChemFile());
    	assertNotNull(file);
    	assertEquals(1, file.getChemSequenceCount());
    	IChemSequence sequence = file.getChemSequence(0);
    	assertNotNull(sequence);
    	assertEquals(1, sequence.getChemModelCount());
    	IChemModel chemModel = sequence.getChemModel(0);
    	assertNotNull(chemModel);
    	IMoleculeSet moleculeSet = chemModel.getMoleculeSet();
    	assertNotNull(moleculeSet);
    	assertEquals(1, moleculeSet.getMoleculeCount());
    	mol = moleculeSet.getMolecule(0);
    	assertNotNull(mol);
        
        return mol;
    	
    }
    
    /**
	 *  A unit test for JUnit: Cyanoallene
	 *
	 *@return    Description of the Return Value
	 */
    public void testCyanoallene() throws Exception
	{
    	IMolecule mol = null;
    	mol = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("C=C=CC#N");
    	HydrogenAdder adder = new HydrogenAdder();
    	adder.addImplicitHydrogensToSatisfyValency(mol);
    	LonePairElectronChecker lpcheck = new LonePairElectronChecker();
    	lpcheck.newSaturate(mol);
    	HueckelAromaticityDetector.detectAromaticity(mol);
        
        AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol);
        
        assertEquals(1, acSet.getAtomContainerCount());
        IAtomContainer ac1 = acSet.getAtomContainer(0);
        assertEquals(4, ac1.getAtomCount());
        assertEquals(3, ac1.getBondCount());
        
        for (int i = 0; i < ac1.getAtomCount(); i++) {
            assertTrue(mol.contains(ac1.getAtom(i)));
        }
        
        for (int i = 0; i < ac1.getBondCount(); i++) {
            assertTrue(mol.contains(ac1.getBond(i)));
        }
        
	}
    
}