partialpichargedescriptortest.java

化学图形处理软件

	public void testPartialPiChargeDescriptoCharge_2() throws ClassNotFoundException, CDKException, java.lang.Exception {
		double [] testResult={-0.0822,0.02,0.0,0.0423,0.0,0.02,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0};/* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
		double [] testResultMy={-0.1090,0.04283,-0.0139,0.05130,-0.01397,0.042839,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0};/* my */
		IAtomicDescriptor descriptor = new PartialPiChargeDescriptor();
        
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("n1ccccc1");

		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(mol.getAtom(i).getSymbol()+"-result: "+result);
	        
	        if(testResultMy[i] == 0.0)
				assertTrue(result == 0.0);
			else {
				assertTrue(result != 0.0);
				assertEquals(getSign(testResultMy[i]),getSign(result), 0.00001);
			}
			assertEquals(testResultMy[i],result, 0.03);
		}
	}
	/**
	 *  A unit test for JUnit. This molecule break. With PETRA as well.
	 */
	public void testPartialPiChargeDescriptoCharge_3() throws ClassNotFoundException, CDKException, java.lang.Exception {
		double [] testResult={-0.0379,-0.0032,0.0,-0.0078,0.0,0.0488,0.0,0.0};/* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
		IAtomicDescriptor descriptor = new PartialPiChargeDescriptor();
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("O=C([H])[C+]([H])[C-]([H])[H]");
		
		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(mol.getAtom(i).getSymbol()+"-result: "+result);

	        if(i == 0 || i == 1 || i == 3)/*not get same signus like Gasteiger*/
	        	continue;
	        
	        if(testResult[i] == 0.0)
				assertTrue(result == 0.0);
			else {
				assertTrue(result != 0.0);
				assertEquals(getSign(testResult[i]),getSign(result), 0.00001);
			}
			assertEquals(testResult[i],result, 0.15);
		}
	}

	/**
	 *  A unit test for JUnit. This molecule break. With PETRA as well.
	 */
	public void testPartialPiChargeDescripto4() throws ClassNotFoundException, CDKException, java.lang.Exception {
		double [] testResult={0.0};/* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
		IAtomicDescriptor descriptor = new PartialPiChargeDescriptor();
        
		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++){
	        double result= ((DoubleResult)descriptor.calculate(mol.getAtom(i),mol).getValue()).doubleValue();
//	        logger.debug(mol.getAtom(i).getSymbol()+"-result: "+result);

			assertEquals(testResult[0],result, 0.0001);
		}
	}
	/**
	 *  A unit test for JUnit with 
	 */
	public void testArticle1() throws ClassNotFoundException, CDKException, java.lang.Exception {
		IAtomicDescriptor descriptor = new PartialPiChargeDescriptor();
        double[] testResult = {0.0,0.0216,-0.1644,0.1428,0.0,0.0,0.0,0.0,0.0,0.0}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("CC(=O)N");
		HydrogenAdder hAdder = new HydrogenAdder();
		hAdder.addExplicitHydrogensToSatisfyValency(mol);
		Object[] object = {new Integer(6),new Boolean(true)};
		descriptor.setParameters(object);
		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(mol.getAtom(i).getSymbol()+",result: "+result);

			if(testResult[i] == 0.0)
				assertTrue(result == 0.0);
			else {
				assertTrue(result != 0.0);
				assertEquals(getSign(testResult[i]),getSign(result), 0.00001);
			}
			assertEquals(testResult[i],result,0.1);
		}
	}
	/**
	 *  A unit test for JUnit with FC(=O)CCc1cccc(F)c1(C)
	 */
	public void testSousa() throws ClassNotFoundException, CDKException, java.lang.Exception {
		IAtomicDescriptor descriptor = new PartialPiChargeDescriptor();
        double[] testResult = {0.0914,0.0193,-0.1107,0.0,0.0,0.0,-0.0063,0.0,-0.0101,0.0,0.0262,-0.0098,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("FC(=O)CCc1cccc(F)c1(C)");
		HydrogenAdder hAdder = new HydrogenAdder();
		hAdder.addExplicitHydrogensToSatisfyValency(mol);
		Object[] object = {new Integer(6),new Boolean(true)};
		descriptor.setParameters(object);
		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(mol.getAtom(i).getSymbol()+",result: "+result);

			if(testResult[i] == 0.0)
				assertTrue(result == 0.0);
			else {
				assertTrue(result != 0.0);
				assertEquals(getSign(testResult[i]),getSign(result), 0.00001);
			}
			assertEquals(testResult[i],result,0.07);
		}
	}
	/**
	 *  A unit test for JUnit with [H]C([H])=C([H])C([H])([H])C([H])=O
	 */
	public void testBondNotConjugated() throws ClassNotFoundException, CDKException, java.lang.Exception {
		IAtomicDescriptor descriptor = new PartialPiChargeDescriptor();
        double[] testResult = {0.0,0.0004,0.0,-0.0004,0.0,0.0,0.0,0.0,0.0277,0.0,-0.0277}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("[H]C([H])=C([H])C([H])([H])C([H])=O");
		Object[] object = {new Integer(6),new Boolean(true)};
		descriptor.setParameters(object);
		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(mol.getAtom(i).getSymbol()+",result: "+result);
			
	        if(i == 1 || i == 3)/*not get same signus like Gasteiger*/
	        	continue;
			
	        if(testResult[i] == 0.0)
				assertTrue(result == 0.0);
			else {
				assertTrue(result != 0.0);
				assertEquals(getSign(testResult[i]),getSign(result), 0.00001);
			}
			assertEquals(testResult[i],result,0.02);
		}
	}
	/**
	 *  A unit test for JUnit with [H]C([H])=C([H])C([H])([H])C([H])=O
	 */
	public void testBondNotConjugated1() throws ClassNotFoundException, CDKException, java.lang.Exception {
		IAtomicDescriptor descriptor = new PartialPiChargeDescriptor();
        double[] testResult = {0.0,-0.0009,0.0,0.0009,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("[H]C([H])=C([H])C([H])([H])[H]");
		Object[] object = {new Integer(6),new Boolean(true)};
		descriptor.setParameters(object);
		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(mol.getAtom(i).getSymbol()+",result: "+result);

	        if(i == 8)/*not get same signus like Gasteiger*/
	        	continue;
			
			if(testResult[i] == 0.0)
				assertTrue(result == 0.0);
			else {
				assertTrue(result != 0.0);
				assertEquals(getSign(testResult[i]),getSign(result), 0.00001);
			}
			assertEquals(testResult[i],result,0.02);
		}
	}
	/**
	 *  A unit test for JUnit with [H]C([H])=C([H])[C+]([H])[H]
	 */
	public void testBondNotConjugated2() throws ClassNotFoundException, CDKException, java.lang.Exception {
		IAtomicDescriptor descriptor = new PartialPiChargeDescriptor();
        double[] testResult = {0.0,0.25,0.0,0.0,0.0,0.25,0.0,0.0,0.0,0.0,0.0,0.0,}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("[H]C([H])=C([H])[C+]([H])[H]");
		Object[] object = {new Integer(6),new Boolean(true)};
		descriptor.setParameters(object);
		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(mol.getAtom(i).getSymbol()+",result: "+result);

	        if(i == 5)/*not get same signus like Gasteiger*/
	        	continue;
	        
			if(testResult[i] == 0.0)
				assertTrue(result == 0.0);
			else {
				assertTrue(result != 0.0);
				assertEquals(getSign(testResult[i]),getSign(result), 0.00001);
			}
			assertEquals(testResult[i],result,0.21);
		}
	}


	/**
	 *  A unit test for JUnit with [C]=C=C=O
	 */
	public void testWithRadical() throws ClassNotFoundException, CDKException, java.lang.Exception {
		IAtomicDescriptor descriptor = new PartialPiChargeDescriptor();
        double[] testResult = {0.0,0.25,0.0,0.0,0.0,0.25,0.0,0.0,0.0,0.0,0.0,0.0,}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("[C]=C=C=O");
//		mol.addElectronContainer(new SingleElectron(mol.getAtom(0)));
		mol.addLonePair(new LonePair(mol.getAtom(3)));
		Object[] object = {new Integer(6),new Boolean(false)};
		descriptor.setParameters(object);

		for (int i = 0 ; i < mol.getAtomCount() ; i++){
			double result= ((DoubleResult)descriptor.calculate(mol.getAtom(i), mol).getValue()).doubleValue();
//			logger.debug(mol.getAtom(i).getSymbol()+",result: "+result);
			
	        if(i == 1 || i == 2 || i == 3)/*not get same signus like Gasteiger*/
	        	continue;
			
			if(testResult[i] == 0.0)
				assertTrue(result == 0.0);
			else {
				assertTrue(result != 0.0);
				assertEquals(getSign(testResult[i]),getSign(result), 0.00001);
			}
			assertEquals(testResult[i],result,0.21);
		}
	}
	
	/**
	 *  A unit test for JUnit with c1ccc(cc1)n3c4ccccc4(c2ccccc23)
	 */
	public void testLangCalculation() throws ClassNotFoundException, CDKException, java.lang.Exception {
		IAtomicDescriptor descriptor = new PartialPiChargeDescriptor();
//        double[] testResult = {0.0,0.25,0.0,0.0,0.0,0.25,0.0,0.0,0.0,0.0,0.0,0.0,}; /* from Petra online: http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml*/
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("c1ccc(cc1)n3c4ccccc4(c2ccccc23)");
		HydrogenAdder hAdder = new HydrogenAdder();
		hAdder.addExplicitHydrogensToSatisfyValency(mol);
		LonePairElectronChecker lpcheck = new LonePairElectronChecker();
		lpcheck.newSaturate(mol);
		
		Object[] object = {new Integer(6),new Boolean(false)};
		descriptor.setParameters(object);

		for (int i = 0 ; i < mol.getAtomCount() ; i++){
			double result= ((DoubleResult)descriptor.calculate(mol.getAtom(i), mol).getValue()).doubleValue();
//			logger.debug(mol.getAtom(i).getSymbol()+",result_: "+result);
			
		}
	}

}