forcefieldtests.java

化学图形处理软件

		double testResult_CCGSumEvdWAv = -0.01850601324794888;
		double[] testResult_gradientSumEvdW = {0.0,0.0,0.0,0.08689361826411737,-0.29019969341910473,-0.43372641964010566,
				0.17856051586843263,-0.03192618756787894,-0.3851429443130647,0.07502699191795303,-0.2145185420473048,
				-0.19094439695781296,0.0,0.0,0.0,-0.06217431032762669,0.2299101716788855,0.23770994928883152,
				-0.04530893553380176,0.2501302303266474,0.3169509609136706,-0.23299788018907458,0.0566040210287556,
				0.4551528507084811};
		double[] testResult_hessianSumEvdW = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 
				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				-0.49533950589829034, -0.49533950589829034, -0.49533950589829034, -0.6313613355244059, -0.8396575394554282, -0.87933019708822, 
				-0.49533950589829034, -0.49533950589829034, -0.49533950589829034, -0.49533950589829034, -0.49533950589829034, -0.49533950589829034, 
				-0.49533950589829034, -0.49533950589829034, -0.49533950589829034, -0.38956801034811495, -0.21396298051840593, -0.2182233583925277, 
				-0.43649700491524, -0.4404739425217814, -0.45492671577482213, -0.5239316728054003, -0.48726356109754576, -0.4288777523375914, 

				1.2214708065904647, 1.2214708065904647, 1.2214708065904647, 0.877152773033327, 1.5598471380761487, 1.6156438888325493, 
				1.2214708065904647, 1.2214708065904647, 1.2214708065904647, 1.2214708065904647, 1.2214708065904647, 1.2214708065904647, 
				1.2214708065904647, 1.2214708065904647, 1.2214708065904647, 1.502847331970349, 0.8368104957874781, 0.8529693074284388, 
				1.2763363699669736, 1.2540860897372723, 1.173225315243967, 1.2295467513912093, 1.2351395027609595, 1.2440447148569038, 

				2.1345402262911017, 2.1345402262911017, 2.1345402262911017, 1.7505495351011717, 2.5287133085331863, 2.9051286869238795, 
				2.1345402262911017, 2.1345402262911017, 2.1345402262911017, 2.1345402262911017, 2.1345402262911017, 2.1345402262911017, 
				2.1345402262911017, 2.1345402262911017, 2.1345402262911017, 2.4116563737968644, 1.7660387271290754, 1.7817021459939755, 
				2.1749530164145696, 2.0862947349446035, 1.7640975657000928, 2.2010019798518003, 2.1571141345575406, 2.0872325065464583, 

				-0.6297778101582324, -0.6297778101582324, -0.6297778101582324, -0.6297778101582324, -0.6297778101582324, -0.6297778101582324, 
				-0.6089325204028525, -0.8604451401401128, -1.279529368262116, -0.6297778101582324, -0.6297778101582324, -0.6297778101582324, 
				-0.6297778101582324, -0.6297778101582324, -0.6297778101582324, -0.6320285705874827, -0.6289559903994892, -0.629651963362336, 
				-0.6295391552100761, -0.6280490163314937, -0.6182458048153735, -0.6486109944325186, -0.40166109376183434, 0.008315895806895436, 

				0.34441611599074545, 0.34441611599074545, 0.34441611599074545, 0.34441611599074545, 0.34441611599074545, 0.34441611599074545, 
				0.11374878600886529, 0.15672812306998973, 0.2567881639921953, 0.34441611599074545, 0.34441611599074545, 0.34441611599074545, 
				0.34441611599074545, 0.34441611599074545, 0.34441611599074545, 0.3452379357494887, 0.36530464624691805, 0.36075931720585486, 
				0.3461449098174842, 0.34800561233253935, 0.36024665951668944, 0.5725328323871437, 0.5076260823135346, 0.39987032324824223, 

				1.7950970816508836, 1.7950970816508836, 1.7950970816508836, 1.7950970816508836, 1.7950970816508836, 1.7950970816508836, 
				1.145345523547, 1.7074691296523334, 2.6501399497449976, 1.7950970816508836, 1.7950970816508836, 1.7950970816508836, 
				1.7950970816508836, 1.7950970816508836, 1.7950970816508836, 1.79522292844678, 1.8114402828659928, 1.8077668750087206, 
				1.8066290869937425, 1.8109276251768274, 1.839206518925974, 2.4331907876160117, 1.8505512889083802, 0.8832749829238413, 

				-0.5439414689838414, -0.5439414689838414, -0.5439414689838414, -0.5439414689838414, -0.5439414689838414, -0.5439414689838414, 
				-0.5439414689838414, -0.5439414689838414, -0.5439414689838414, -0.573711549977258, -0.7815604539668985, -0.7807285851515327, 
				-0.5439414689838414, -0.5439414689838414, -0.5439414689838414, -0.5440124324947035, -0.5686587599124093, -0.5546135168962161, 
				-0.45567876653944217, -0.3290175063805018, -0.34810924538566984, -0.602363126923962, -0.4965291556755561, -0.492314528501947, 

				1.1359183917803006, 1.1359183917803006, 1.1359183917803006, 1.1359183917803006, 1.1359183917803006, 1.1359183917803006, 
				1.1359183917803006, 1.1359183917803006, 1.1359183917803006, 0.8982994067972434, 1.4602334223259112, 1.4163747768880244, 
				1.1359183917803006, 1.1359183917803006, 1.1359183917803006, 1.1112011008517326, 1.1871127634614052, 1.143852859823585, 
				1.3508423543836399, 0.760355344848344, 0.8493598586029334, 1.183330705088586, 1.135972036485542, 1.1340860718066597, 

				0.9564440551953459, 0.9564440551953459, 0.9564440551953459, 0.9564440551953459, 0.9564440551953459, 0.9564440551953459, 
				0.9564440551953459, 0.9564440551953459, 0.9564440551953459, 0.7196569390276547, 1.2369004403030694, 1.1769215835558002, 
				0.9564440551953459, 0.9564440551953459, 0.9564440551953459, 0.9457720072829713, 0.9643785232386305, 0.9537751974833226, 
				1.1522762787935175, 0.6698855220179788, 0.7425966131227676, 1.0080709956772402, 0.9546117352217048, 0.9524828266194932, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.26913213005937325, 0.26913213005937325, 0.26913213005937325, 0.3749036256095486, 0.5505086554392575, 0.5462482775651357, 
				0.26688136963012293, 0.26995394981811643, 0.26925797685526975, 0.2690611665485111, 0.2444148391308054, 0.2584600821469985, 
				0.26913213005937325, 0.26913213005937325, 0.26913213005937325, 0.16568235844931034, 0.011651075849313478, 0.0025621836700887995, 
				0.26913213005937325, 0.26913213005937325, 0.26913213005937325, 0.26913213005937325, 0.26913213005937325, 0.26913213005937325, 

				-1.2155125612018092, -1.2155125612018092, -1.2155125612018092, -0.934136035821925, -1.6001728720047956, -1.584014060363835, 
				-1.2146907414430659, -1.1946240309456364, -1.1991693599866997, -1.2402298521303772, -1.1643181895207046, -1.2075780931585247, 
				-1.2155125612018092, -1.2155125612018092, -1.2155125612018092, -1.4729936154118688, -0.9029351523361, -0.8712887312981772, 
				-1.2155125612018092, -1.2155125612018092, -1.2155125612018092, -1.2155125612018092, -1.2155125612018092, -1.2155125612018092, 

				-1.1356750227757766, -1.1356750227757766, -1.1356750227757766, -0.858558875270014, -1.5041765219378027, -1.4885131030729026, 
				-1.13554917597988, -1.1193318215606671, -1.1230052294179393, -1.1463470706881513, -1.1277405547324921, -1.1383438804877999, 
				-1.1356750227757766, -1.1356750227757766, -1.1356750227757766, -1.402244969165061, -0.7914511928721446, -0.7928378781244645, 
				-1.1356750227757766, -1.1356750227757766, -1.1356750227757766, -1.1356750227757766, -1.1356750227757766, -1.1356750227757766, 

				0.1389109884602232, 0.1389109884602232, 0.1389109884602232, 0.1977534894432735, 0.19377655183673212, 0.17932377858369142, 
				0.13914964340837963, 0.14063978228696195, 0.15044299380308213, 0.22717369090462247, 0.3538349510635629, 0.33474321205839475, 
				0.1389109884602232, 0.1389109884602232, 0.1389109884602232, 0.1389109884602232, 0.1389109884602232, 0.1389109884602232, 
				-0.008432869915382862, -0.13260733134636407, -0.10886603060427552, 0.1389109884602232, 0.1389109884602232, 0.1389109884602232, 

				-1.199176020429921, -1.199176020429921, -1.199176020429921, -1.1443104570534122, -1.1665607372831137, -1.247421511776419, 
				-1.1974472266031824, -1.1955865240881272, -1.1833454769039773, -0.9842520578265814, -1.5747390673618775, -1.4857345536072883, 
				-1.199176020429921, -1.199176020429921, -1.199176020429921, -1.199176020429921, -1.199176020429921, -1.199176020429921, 
				-1.4706943402365082, -0.8598177529865658, -0.8802025394320001, -1.199176020429921, -1.199176020429921, -1.199176020429921, 

				-1.6780627528193968, -1.6780627528193968, -1.6780627528193968, -1.6376499626959284, -1.7263082441658946, -2.0485054134104055, 
				-1.6665307474765376, -1.6622322092934527, -1.6339533155443058, -1.482230529221225, -1.9646212859967638, -1.891910194891975, 
				-1.6780627528193968, -1.6780627528193968, -1.6780627528193968, -1.6780627528193968, -1.6780627528193968, -1.6780627528193968, 
				-1.9258397718838953, -1.3590892718214755, -1.1378820874309001, -1.6780627528193968, -1.6780627528193968, -1.6780627528193968, 

				1.2610156665207677, 1.2610156665207677, 1.2610156665207677, 1.2324234996136578, 1.2690916113215123, 1.3274774200814667, 
				1.2421824822464815, 1.489132382917166, 1.8991093724858958, 1.2025940085806472, 1.308427979829053, 1.3126426070026622, 
				1.2610156665207677, 1.2610156665207677, 1.2610156665207677, 1.2610156665207677, 1.2610156665207677, 1.2610156665207677, 
				1.2610156665207677, 1.2610156665207677, 1.2610156665207677, 1.3668626756422846, 0.9774106920153398, 0.5048332665130466, 

				-0.2871167327297804, -0.2871167327297804, -0.2871167327297804, -0.27904078792903586, -0.2734480365592854, -0.26454282446334115, 
				-0.0590000163333822, -0.12390676640699119, -0.23166252547228358, -0.23970441942149506, -0.28706308802453917, -0.28894905270342147, 
				-0.2871167327297804, -0.2871167327297804, -0.2871167327297804, -0.2871167327297804, -0.2871167327297804, -0.2871167327297804, 
				-0.2871167327297804, -0.2871167327297804, -0.2871167327297804, -0.5707217072352084, -0.4640490399283057, -0.3633125282800753, 

				-2.0723435875421576, -2.0723435875421576, -2.0723435875421576, -2.0058818339814586, -2.0497696792757183, -2.1196513072868006, 
				-1.4342498815770297, -2.016889380284661, -2.9841656862691996, -2.0207166470602633, -2.074175907515799, -2.0763048161180104, 
				-2.0723435875421576, -2.0723435875421576, -2.0723435875421576, -2.0723435875421576, -2.0723435875421576, -2.0723435875421576, 
				-2.0723435875421576, -2.0723435875421576, -2.0723435875421576, -2.828525987549879, -2.1485393830924524, -1.1092525404946196};

		VanDerWaalsInteractions vdwi = new VanDerWaalsInteractions();
		vdwi.setMMFF94VanDerWaalsParameters(molecule, mmff94Tables);
		vdwi.setAtomDistance(moleculeCoordinates);

		SmoothingFunctions sf = new SmoothingFunctions();
		sf.setSmoothingFunction(vdwi.getAtomDistance());

		vdwi.setFunctionMMFF94SumEvdW(moleculeCoordinates);
		//logger.debug("functionMMFF94SumEvdW = " + vdwi.getFunctionMMFF94SumEvdW());
		//logger.debug("functionCCGSumEvdWSK = " + vdwi.functionCCGSumEvdWSK(moleculeCoordinates,sf.getSmoothingFunction()));
		//logger.debug("functionCCGSumEvdWAv = " + vdwi.functionCCGSumEvdWAv(moleculeCoordinates,sf.getSmoothingFunction()));

		assertEquals(testResult_MMFF94SumEvdW, vdwi.getFunctionMMFF94SumEvdW(), 0.00001);
		assertEquals(testResult_CCGSumEvdWSK, vdwi.functionCCGSumEvdWSK(moleculeCoordinates, sf.getSmoothingFunction()), 0.00001);
		assertEquals(testResult_CCGSumEvdWAv, vdwi.functionCCGSumEvdWAv(moleculeCoordinates, sf.getSmoothingFunction()), 0.00001);

		vdwi.setGradientMMFF94SumEvdW(moleculeCoordinates);
		//logger.debug("vdwi.gradientMMFF94SumEvdW(moleculeCoordinates) = " + vdwi.getGradientMMFF94SumEvdW());
		for (int i = 0; i < testResult_gradientSumEvdW.length; i++) {
			assertEquals(testResult_gradientSumEvdW[i], vdwi.getGradientMMFF94SumEvdW().getElement(i), 0.00001);
		}

		vdwi.setHessianMMFF94SumEvdW(moleculeCoordinates);
		//logger.debug("HessianMMFF94SumEQ = ");
		for (int i = 0; i < 24; i++) {
			//logger.debug("");
			//logger.debug("");
			for (int j = 0; j < 24; j++) {
				//logger.debug(vdwi.getHessianMMFF94SumEvdW().getElement(i, j) + ", ");
				assertEquals(testResult_hessianSumEvdW[i * 24 + j], vdwi.getHessianMMFF94SumEvdW().getElement(i, j), 0.00001);
			}
		}
	}


	/**
	 *  A unit test for JUnit (ElectrostaticInteraction)
	 */
	public void testElectrostaticInteraction() throws ClassNotFoundException, CDKException, java.lang.Exception {

		//logger.debug("");
		//logger.debug("FORCEFIELDTESTS with ElectrostaticInteraction");

		double testResult_MMFF94SumEQ = 0.0;
		double[] testResult_gradientSumEQ = {0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0};
		double[] testResult_hessianSumEQ = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 
				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 

				0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.