structureresonancegeneratortest.java

化学图形处理软件

	 * @return    The test suite
	 */
	public void testGetStructures2() throws ClassNotFoundException, CDKException, java.lang.Exception {
		IMolecule molecule = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("CCC(=O)C(C)=O");
	    HydrogenAdder adder = new HydrogenAdder();
        adder.addExplicitHydrogensToSatisfyValency(molecule);
        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
        lpcheck.newSaturate(molecule);
        
        IAtom atom =  molecule.getAtom(3);
        molecule.addSingleElectron(new SingleElectron(atom));
        atom.setFormalCharge(1);
        List selectron = molecule.getConnectedLonePairsList(atom);
		molecule.removeLonePair((ILonePair)selectron.get(0));

		StructureResonanceGenerator gRI = new StructureResonanceGenerator();
		IAtomContainerSet setOfMolecules = gRI.getStructures(molecule);

		Assert.assertEquals(2,setOfMolecules.getAtomContainerCount());
		
		IMolecule molecule1 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("CCC(=O)C(C)=O");
		adder = new HydrogenAdder();
		adder.addExplicitHydrogensToSatisfyValency(molecule1);
		lpcheck.newSaturate(molecule1);

        IAtom atom1 =  molecule1.getAtom(6);
        molecule1.addSingleElectron(new SingleElectron(atom1));
        atom1.setFormalCharge(1);
        selectron = molecule.getConnectedLonePairsList(atom);
		molecule.removeLonePair((ILonePair)selectron.get(0));

		QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule1);
		Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getAtomContainer(1),qAC));
	
	}
	/**
	 * A unit test suite for JUnit: Resonance C-C=C-[C+]-C-C=C-[C+] <=> C-[C+]-C=C-C-C=C-[C+]
	 *
	 * @return    The test suite
	 */
	public void testFlagActiveCenter1() throws ClassNotFoundException, CDKException, java.lang.Exception {
		IMolecule molecule = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("CC=C[C+]-C-C=C-C=C");
        
        molecule.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
		molecule.getBond(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
		molecule.getAtom(2).setFlag(CDKConstants.REACTIVE_CENTER,true);
		molecule.getBond(2).setFlag(CDKConstants.REACTIVE_CENTER,true);
		molecule.getAtom(3).setFlag(CDKConstants.REACTIVE_CENTER,true);
		
        StructureResonanceGenerator gRI = new StructureResonanceGenerator();
		IAtomContainerSet setOfMolecules = gRI.getStructures(molecule);
        
		Assert.assertEquals(2,setOfMolecules.getAtomContainerCount());

        IMolecule molecule2 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("C-[C+]-C=C-C-C=C-C=C");
        
        QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule2);
        Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getAtomContainer(1),qAC));
	}
	/**
	 * A unit test suite for JUnit: Resonance C-C=C-[C-] <=> C=C-[C-]-C
	 *
	 * @return    The test suite
	 */
	public void testFlagActiveCenter2() throws ClassNotFoundException, CDKException, java.lang.Exception {
		IMolecule molecule = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("C-C=C-[C-]");
		molecule.addLonePair(new LonePair(molecule.getAtom(3)));
		
        IAtomContainerSet setOfMolecules = gR.getStructures(molecule);
        
		Assert.assertEquals(2,setOfMolecules.getAtomContainerCount());

        IMolecule molecule2 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("C=C-[C-]-C");
        molecule.addLonePair(new LonePair(molecule.getAtom(2)));
		
        QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule2);
        Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getAtomContainer(1),qAC));
	}
	/**
	 * A unit test suite for JUnit: Resonance Formic acid  C(=O)O <=> [C-](-[O+])O <=> [C+](-[O-])O <=> C([O-])=[O+]
	 *
	 * @return    The test suite
	 */
	public void testResonanceFormicAcid() throws ClassNotFoundException, CDKException, java.lang.Exception {
		IMolecule molecule = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("C(=O)O");
	    HydrogenAdder adder = new HydrogenAdder();
        adder.addImplicitHydrogensToSatisfyValency(molecule);
        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
        lpcheck.newSaturate(molecule);
        
        IAtomContainerSet setOfMolecules = gR.getAllStructures(molecule);
        
		Assert.assertEquals(3,setOfMolecules.getAtomContainerCount());

//        Molecule molecule1 = (new SmilesParser()).parseSmiles("[C-](-[O+])O");
//        adder.addImplicitHydrogensToSatisfyValency(molecule1);
//        lpcheck.newSaturate(molecule1);
//        QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule1);
//        Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getAtomContainer(1),qAC));

		IMolecule molecule2 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("[C+](-[O-])O");
        adder.addImplicitHydrogensToSatisfyValency(molecule2);
        lpcheck.newSaturate(molecule2);
        QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule2);
        Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getAtomContainer(1),qAC));
        
        IMolecule molecule3 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("C([O-])=[O+]");
        adder.addImplicitHydrogensToSatisfyValency(molecule3);
        lpcheck.newSaturate(molecule3);
        
        qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule3);
        Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getAtomContainer(2),qAC));
	}

	/**
	 * A unit test suite for JUnit: Resonance Formic acid  F-C=C <=> [F+]=C-[C-]
	 *
	 * @return    The test suite
	 */
	public void testResonanceFluoroethylene() throws ClassNotFoundException, CDKException, java.lang.Exception {
		IMolecule molecule = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("F-C=C");
	    HydrogenAdder adder = new HydrogenAdder();
        adder.addImplicitHydrogensToSatisfyValency(molecule);
        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
        lpcheck.newSaturate(molecule);
        
        IAtomContainerSet setOfMolecules = gR.getAllStructures(molecule);
        
		Assert.assertEquals(2,setOfMolecules.getAtomContainerCount());

        IMolecule molecule1 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("[F+]=C-[C-]");
        adder.addImplicitHydrogensToSatisfyValency(molecule1);
        lpcheck.newSaturate(molecule1);
        QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule1);
        Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getAtomContainer(1),qAC));
	}
	/**
	 * A unit test suite for JUnit: Resonance Fluorobenzene  Fc1ccccc1 <=> ...
	 *
	 * @return    The test suite
	 */
	public void testResonanceFluorobenzene() throws ClassNotFoundException, CDKException, java.lang.Exception {
		IMolecule molecule = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("Fc1ccccc1");
	    HydrogenAdder adder = new HydrogenAdder();
        adder.addImplicitHydrogensToSatisfyValency(molecule);
        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
        lpcheck.newSaturate(molecule);
        
        StructureResonanceGenerator gRI = new StructureResonanceGenerator();
		IAtomContainerSet setOfMolecules = gRI.getAllStructures(molecule);
        
		Assert.assertEquals(4,setOfMolecules.getAtomContainerCount());

        IMolecule molecule1 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("[F+]=C1C=CC=C[C-]1");
        adder.addImplicitHydrogensToSatisfyValency(molecule1);
        lpcheck.newSaturate(molecule1);
        QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule1);
        Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getAtomContainer(1),qAC));
        
        IMolecule molecule2 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("[F+]=C1-C=C-[C-]-C=C1");
        adder.addImplicitHydrogensToSatisfyValency(molecule2);
        lpcheck.newSaturate(molecule2);
        qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule2);
        Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getAtomContainer(2),qAC));
	}
	/**
	 * A unit test suite for JUnit: Resonance   n1ccccc1 <=> ...
	 *
	 * @return    The test suite
	 */
	public void test_n1ccccc1() throws ClassNotFoundException, CDKException, java.lang.Exception {
		IMolecule molecule = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("n1ccccc1");
	    HydrogenAdder adder = new HydrogenAdder();
        adder.addImplicitHydrogensToSatisfyValency(molecule);
        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
        lpcheck.newSaturate(molecule);
        
        StructureResonanceGenerator gRI = new StructureResonanceGenerator();
		 IAtomContainerSet setOfMolecules = gRI.getAllStructures(molecule);
        
		Assert.assertEquals(10,setOfMolecules.getAtomContainerCount());
	}
}