pielectronegativitydescriptortest.java

化学图形处理软件

	 */
	public void testPiElectronegativityDescriptor_Formaldehyde() throws ClassNotFoundException, CDKException, java.lang.Exception {
		double [] testResult={6.3012,8.0791,0.0,0.0,0.0};/* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
		IAtomicDescriptor descriptor = new PiElectronegativityDescriptor();
		Integer[] params = new Integer[1];
        
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("C=O");
		HydrogenAdder hAdder = new HydrogenAdder();
		hAdder.addExplicitHydrogensToSatisfyValency(mol);
		LonePairElectronChecker lpcheck = new LonePairElectronChecker();
		lpcheck.newSaturate(mol);
		
		for (int i = 0 ; i < mol.getAtomCount(); i++){
			params[0] = new Integer(10);
	        descriptor.setParameters(params);
			double result= ((DoubleResult)descriptor.calculate(mol.getAtom(i),mol).getValue()).doubleValue();
//			logger.debug("result: "+result);
			if(result == 0.0)
				assertEquals(testResult[i],result, 0.0001);
			else {
				assertTrue(result != 0.0);
				assertEquals(testResult[i],result, 0.55);
			}
		}
	}
	/**
	 *  A unit test for JUnit with Ethylene
	 */
	public void testPiElectronegativityDescriptor_Ethylene() throws ClassNotFoundException, CDKException, java.lang.Exception {
		
		double [] testResult={5.1519,5.1519,0.0,0.0,0.0,0.0,0.0,0.0};/* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
		IAtomicDescriptor descriptor = new PiElectronegativityDescriptor();
        
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("C=C");

		HydrogenAdder hAdder = new HydrogenAdder();
		hAdder.addExplicitHydrogensToSatisfyValency(mol);
		
		LonePairElectronChecker lpcheck = new LonePairElectronChecker();
		lpcheck.newSaturate(mol);
		for (int i = 0 ; i < 3 ; i++){
	        double result= ((DoubleResult)descriptor.calculate(mol.getAtom(i),mol).getValue()).doubleValue();

//	        logger.debug("result: "+result);
			if(result == 0.0)
				assertEquals(testResult[i],result, 0.0001);
			else {
				assertTrue(result != 0.0);
				assertEquals(testResult[i],result, 0.02);
			}
		}
	}

	/**
	 *  A unit test for JUnit with Fluoroethylene
	 */
	public void testPiElectronegativityDescriptor_Fluoroethylene() throws ClassNotFoundException, CDKException, java.lang.Exception {
		double [] testResult={4.7796,5.9414,5.0507,0.0,0.0,0.0};/* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
		IAtomicDescriptor descriptor = new PiElectronegativityDescriptor();
        
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("F-C=C");

		HydrogenAdder hAdder = new HydrogenAdder();
		hAdder.addExplicitHydrogensToSatisfyValency(mol);
		
		LonePairElectronChecker lpcheck = new LonePairElectronChecker();
		lpcheck.newSaturate(mol);
		
		for (int i = 0 ; i < 3 ; i++){
	        double result= ((DoubleResult)descriptor.calculate(mol.getAtom(i),mol).getValue()).doubleValue();
//	        logger.debug("result: "+result);
			if(result == 0.0)
				assertEquals(testResult[i],result, 0.0001);
			else {
				assertTrue(result != 0.0);
				assertEquals(testResult[i],result, 0.7);
			}
		}
	}
	/**
	 *  A unit test for JUnit with Formic Acid
	 */
	public void testPiElectronegativityDescriptor_FormicAcid() throws ClassNotFoundException, CDKException, java.lang.Exception {
		double [] testResult={6.8954,7.301,4.8022,0.0,0.0};/* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
		IAtomicDescriptor descriptor = new PiElectronegativityDescriptor();
        
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("C(=O)O");

		HydrogenAdder hAdder = new HydrogenAdder();
		hAdder.addExplicitHydrogensToSatisfyValency(mol);
		
		LonePairElectronChecker lpcheck = new LonePairElectronChecker();
		lpcheck.newSaturate(mol);
		
		for (int i = 0 ; i < mol.getAtomCount() ; i++){
			double result= ((DoubleResult)descriptor.calculate(mol.getAtom(i),mol).getValue()).doubleValue();
//			logger.debug("result: "+result);
			if(result == 0.0)
				assertEquals(testResult[i],result, 0.0001);
			else {
				assertTrue(result != 0.0);
				assertEquals(testResult[i],result,  2);
			}
		}
	}
	/**
	 *  A unit test for JUnit with Methoxyethylene
	 */
	public void testPiElectronegativityDescriptor_Methoxyethylene() throws ClassNotFoundException, CDKException, java.lang.Exception {
		double [] testResult={4.916,5.7345,3.971,0.0,0.0,0.0,0.0,0.0,0.0,0.0};/* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
		IAtomicDescriptor descriptor = new PiElectronegativityDescriptor();
		Integer[] params = new Integer[1];
        
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("C=C-O-C");

		HydrogenAdder hAdder = new HydrogenAdder();
		hAdder.addExplicitHydrogensToSatisfyValency(mol);
		
		LonePairElectronChecker lpcheck = new LonePairElectronChecker();
		lpcheck.newSaturate(mol);
		
		for (int i = 0 ; i < mol.getAtomCount(); i++){
//			params[0] = new Integer(10);
//	        descriptor.setParameters(params);
	        double result= ((DoubleResult)descriptor.calculate(mol.getAtom(i),mol).getValue()).doubleValue();
//	        logger.debug("result: "+result);
			if(result == 0.0)
				assertEquals(testResult[i],result, 0.0001);
			else {
				assertTrue(result != 0.0);
				assertEquals(testResult[i],result, 0.5);
			}
		}
	}
	/**
	 *  A unit test for JUnit with F[C+][C-]
	 */
	public void testPiElectronegativity1() throws ClassNotFoundException, CDKException, java.lang.Exception {
		double [] testResult={5.1788,5.465,5.2475,0.0,0.0,0.0,0.0,0.0,0.0,0.0};/* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
		IAtomicDescriptor descriptor = new PiElectronegativityDescriptor();
		Integer[] params = new Integer[1];
        
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("F[C+][C-]");

		HydrogenAdder hAdder = new HydrogenAdder();
		hAdder.addExplicitHydrogensToSatisfyValency(mol);
		
		LonePairElectronChecker lpcheck = new LonePairElectronChecker();
		lpcheck.newSaturate(mol);
		
		for (int i = 0 ; i < mol.getAtomCount(); i++){
			params[0] = new Integer(6);
	        descriptor.setParameters(params);
	        double result= ((DoubleResult)descriptor.calculate(mol.getAtom(i),mol).getValue()).doubleValue();
//	        logger.debug(mol.getAtomAt(i).getSymbol()+"-result: "+result);
			if(result == 0.0)
				assertEquals(testResult[i],result, 0.0001);
			else {
				assertTrue(result != 0.0);
				assertEquals(testResult[i],result, 1.2);
			}
		}
	}
	/**
	 *  A unit test for JUnit with CCOCCCO
	 */
	public void testPiElectronegativity2() throws ClassNotFoundException, CDKException, java.lang.Exception {
		double [] testResult={0.0,0.0,3.2849,0.0,0.0,0.0,3.2849,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0};/* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
		IAtomicDescriptor descriptor = new PiElectronegativityDescriptor();
		Integer[] params = new Integer[1];
        
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("CCOCCCO");

		HydrogenAdder hAdder = new HydrogenAdder();
		hAdder.addExplicitHydrogensToSatisfyValency(mol);
		
		LonePairElectronChecker lpcheck = new LonePairElectronChecker();
		lpcheck.newSaturate(mol);
		
		for (int i = 0 ; i < mol.getAtomCount(); i++){
			params[0] = new Integer(6);
	        descriptor.setParameters(params);
	        double result= ((DoubleResult)descriptor.calculate(mol.getAtom(i),mol).getValue()).doubleValue();
//	        logger.debug(mol.getAtom(i).getSymbol()+"-result: "+result);
			if(result == 0.0)
				assertEquals(testResult[i],result, 0.0001);
			else {
				assertTrue(result != 0.0);
				assertEquals(testResult[i],result, 0.2);
			}
		}
	}
}