📄 forcefieldtests.java

📁 化学图形处理软件
💻 JAVA
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				}			} else if (coord <= 0.66) {				if (Math.random() <= 0.) {					coordinate.y += positiveShift;				} else {					coordinate.y -= negativeShift;				}			} else {				if (Math.random() <= 0.) {					coordinate.z += positiveShift;				} else {					coordinate.z -= negativeShift;				}			}		}		return molecule;	}	/**	 *  A unit test for JUnit	 */	public void testForceField() throws Exception, CDKException {			}	/**	 *  A unit test for JUnit (Torsions)	 */	public void testTorsions() throws ClassNotFoundException, CDKException, java.lang.Exception {		//logger.debug("");		//logger.debug("FORCEFIELDTESTS with Torsions");		double testResult_MMFF94SumET = 11.369615843222473;		double[] testResult_gradientSumET = {-2.9021441715059266,0.365841131889513,-1.3798123459631118,2.334296171767999,				-7.741921297512765E-4,0.9419919236223522,-1.0919747760635934,-1.4243907634213469,0.3741346043388054,				0.8706944865031971,1.081124943590873,-0.2670804663450631,1.9172157299433363,0.1735281313651372,				0.6740797133199399,-1.0891396653529841,0.12919063902722416,-0.5131917159860654,0.2969423891730237,				-1.1492480840394526,0.7770108103021226,-0.33589016359430374,0.8247281932428495,-0.6071325229723439};		double[] testResult_hessianSumET = {0.618245987948552, 0.618245987948552, 0.618245987948552, 0.618245987948552, 0.618245987948552, 				0.618245987948552, 0.618245987948552, 0.618245987948552, 0.618245987948552, 0.618245987948552, 0.618245987948552, 				0.618245987948552, 0.618245987948552, 0.618245987948552, 0.618245987948552, 0.618245987948552, 0.618245987948552, 				0.618245987948552, 0.618245987948552, 0.618245987948552, 0.618245987948552, 0.618245987948552, 0.618245987948552, 				0.618245987948552, 				-1.9559306031700696, -1.9559306031700696, -1.9559306031700696, -1.9559306031700696, -1.9559306031700696, -1.9559306031700696, 				-1.9559306031700696, -1.9559306031700696, -1.9559306031700696, -1.9559306031700696, -1.9559306031700696, -1.9559306031700696, 				-1.9559306031700696, -1.9559306031700696, -1.9559306031700696, -1.9559306031700696, -1.9559306031700696, -1.9559306031700696, 				-1.9559306031700696, -1.9559306031700696, -1.9559306031700696, -1.9559306031700696, -1.9559306031700696, -1.9559306031700696, 				1.3679397254378274, 1.3679397254378274, 1.3679397254378274, 1.3679397254378274, 1.3679397254378274, 1.3679397254378274, 				1.3679397254378274, 1.3679397254378274, 1.3679397254378274, 1.3679397254378274, 1.3679397254378274, 1.3679397254378274, 				1.3679397254378274, 1.3679397254378274, 1.3679397254378274, 1.3679397254378274, 1.3679397254378274, 1.3679397254378274, 				1.3679397254378274, 1.3679397254378274, 1.3679397254378274, 1.3679397254378274, 1.3679397254378274, 1.3679397254378274, 				-1.9611727123824523, -1.9611727123824523, -1.9611727123824523, -1.9611727123824523, -1.9611727123824523, -1.9611727123824523, 				-1.9611727123824523, -1.9611727123824523, -1.9611727123824523, -1.9611727123824523, -1.9611727123824523, -1.9611727123824523, 				-1.9611727123824523, -1.9611727123824523, -1.9611727123824523, -1.9611727123824523, -1.9611727123824523, -1.9611727123824523, 				-1.9611727123824523, -1.9611727123824523, -1.9611727123824523, -1.9611727123824523, -1.9611727123824523, -1.9611727123824523, 				6.504419782056093E-4, 6.504419782056093E-4, 6.504419782056093E-4, 6.504419782056093E-4, 6.504419782056093E-4, 6.504419782056093E-4, 				6.504419782056093E-4, 6.504419782056093E-4, 6.504419782056093E-4, 6.504419782056093E-4, 6.504419782056093E-4, 6.504419782056093E-4, 				6.504419782056093E-4, 6.504419782056093E-4, 6.504419782056093E-4, 6.504419782056093E-4, 6.504419782056093E-4, 6.504419782056093E-4, 				6.504419782056093E-4, 6.504419782056093E-4, 6.504419782056093E-4, 6.504419782056093E-4, 6.504419782056093E-4, 6.504419782056093E-4, 				-0.7914200768597389, -0.7914200768597389, -0.7914200768597389, -0.7914200768597389, -0.7914200768597389, -0.7914200768597389, 				-0.7914200768597389, -0.7914200768597389, -0.7914200768597389, -0.7914200768597389, -0.7914200768597389, -0.7914200768597389, 				-0.7914200768597389, -0.7914200768597389, -0.7914200768597389, -0.7914200768597389, -0.7914200768597389, -0.7914200768597389, 				-0.7914200768597389, -0.7914200768597389, -0.7914200768597389, -0.7914200768597389, -0.7914200768597389, -0.7914200768597389, 				-1.651798423864038, -1.651798423864038, -1.651798423864038, -1.651798423864038, -1.651798423864038, -1.651798423864038, 				-1.651798423864038, -1.651798423864038, -1.651798423864038, -1.651798423864038, -1.651798423864038, -1.651798423864038, 				-1.651798423864038, -1.651798423864038, -1.651798423864038, -1.651798423864038, -1.651798423864038, -1.651798423864038, 				-1.651798423864038, -1.651798423864038, -1.651798423864038, -1.651798423864038, -1.651798423864038, -1.651798423864038, 				-2.154634400475277, -2.154634400475277, -2.154634400475277, -2.154634400475277, -2.154634400475277, -2.154634400475277, 				-2.154634400475277, -2.154634400475277, -2.154634400475277, -2.154634400475277, -2.154634400475277, -2.154634400475277, 				-2.154634400475277, -2.154634400475277, -2.154634400475277, -2.154634400475277, -2.154634400475277, -2.154634400475277, 				-2.154634400475277, -2.154634400475277, -2.154634400475277, -2.154634400475277, -2.154634400475277, -2.154634400475277, 				0.5659425137028654, 0.5659425137028654, 0.5659425137028654, 0.5659425137028654, 0.5659425137028654, 0.5659425137028654, 				0.5659425137028654, 0.5659425137028654, 0.5659425137028654, 0.5659425137028654, 0.5659425137028654, 0.5659425137028654, 				0.5659425137028654, 0.5659425137028654, 0.5659425137028654, 0.5659425137028654, 0.5659425137028654, 0.5659425137028654, 				0.5659425137028654, 0.5659425137028654, 0.5659425137028654, 0.5659425137028654, 0.5659425137028654, 0.5659425137028654, 				3.378802068568724, 3.378802068568724, 3.378802068568724, 3.378802068568724, 3.378802068568724, 3.378802068568724, 				3.378802068568724, 3.378802068568724, 3.378802068568724, 3.378802068568724, 3.378802068568724, 3.378802068568724, 				3.378802068568724, 3.378802068568724, 3.378802068568724, 3.378802068568724, 3.378802068568724, 3.378802068568724, 				3.378802068568724, 3.378802068568724, 3.378802068568724, 3.378802068568724, 3.378802068568724, 3.378802068568724, 				4.195394885123073, 4.195394885123073, 4.195394885123073, 4.195394885123073, 4.195394885123073, 4.195394885123073, 				4.195394885123073, 4.195394885123073, 4.195394885123073, 4.195394885123073, 4.195394885123073, 4.195394885123073, 				4.195394885123073, 4.195394885123073, 4.195394885123073, 4.195394885123073, 4.195394885123073, 4.195394885123073, 				4.195394885123073, 4.195394885123073, 4.195394885123073, 4.195394885123073, 4.195394885123073, 4.195394885123073, 				-1.0364278700844103, -1.0364278700844103, -1.0364278700844103, -1.0364278700844103, -1.0364278700844103, -1.0364278700844103, 				-1.0364278700844103, -1.0364278700844103, -1.0364278700844103, -1.0364278700844103, -1.0364278700844103, -1.0364278700844103, 				-1.0364278700844103, -1.0364278700844103, -1.0364278700844103, -1.0364278700844103, -1.0364278700844103, -1.0364278700844103, 				-1.0364278700844103, -1.0364278700844103, -1.0364278700844103, -1.0364278700844103, -1.0364278700844103, -1.0364278700844103, 				-0.4839472141487817, -0.4839472141487817, -0.4839472141487817, -0.4839472141487817, -0.4839472141487817, -0.4839472141487817, 				-0.4839472141487817, -0.4839472141487817, -0.4839472141487817, -0.4839472141487817, -0.4839472141487817, -0.4839472141487817, 				-0.4839472141487817, -0.4839472141487817, -0.4839472141487817, -0.4839472141487817, -0.4839472141487817, -0.4839472141487817, 				-0.4839472141487817, -0.4839472141487817, -0.4839472141487817, -0.4839472141487817, -0.4839472141487817, -0.4839472141487817, 				-2.625665858605127, -2.625665858605127, -2.625665858605127, -2.625665858605127, -2.625665858605127, -2.625665858605127, 				-2.625665858605127, -2.625665858605127, -2.625665858605127, -2.625665858605127, -2.625665858605127, -2.625665858605127, 				-2.625665858605127, -2.625665858605127, -2.625665858605127, -2.625665858605127, -2.625665858605127, -2.625665858605127, 				-2.625665858605127, -2.625665858605127, -2.625665858605127, -2.625665858605127, -2.625665858605127, -2.625665858605127, 				1.3063765272395833, 1.3063765272395833, 1.3063765272395833, 1.3063765272395833, 1.3063765272395833, 1.3063765272395833, 				1.3063765272395833, 1.3063765272395833, 1.3063765272395833, 1.3063765272395833, 1.3063765272395833, 1.3063765272395833, 				1.3063765272395833, 1.3063765272395833, 1.3063765272395833, 1.3063765272395833, 1.3063765272395833, 1.3063765272395833, 				1.3063765272395833, 1.3063765272395833, 1.3063765272395833, 1.3063765272395833, 1.3063765272395833, 1.3063765272395833, 				1.4130145712631725, 1.4130145712631725, 1.4130145712631725, 1.4130145712631725, 1.4130145712631725, 1.4130145712631725, 				1.4130145712631725, 1.4130145712631725, 1.4130145712631725, 1.4130145712631725, 1.4130145712631725, 1.4130145712631725, 				1.4130145712631725, 1.4130145712631725, 1.4130145712631725, 1.4130145712631725, 1.4130145712631725, 1.4130145712631725, 				1.4130145712631725, 1.4130145712631725, 1.4130145712631725, 1.4130145712631725, 1.4130145712631725, 1.4130145712631725, 				-0.16760775622175592, -0.16760775622175592, -0.16760775622175592, -0.16760775622175592, -0.16760775622175592, -0.16760775622175592, 				-0.16760775622175592, -0.16760775622175592, -0.16760775622175592, -0.16760775622175592, -0.16760775622175592, -0.16760775622175592, 				-0.16760775622175592, -0.16760775622175592, -0.16760775622175592, -0.16760775622175592, -0.16760775622175592, -0.16760775622175592, 				-0.16760775622175592, -0.16760775622175592, -0.16760775622175592, -0.16760775622175592, -0.16760775622175592, -0.16760775622175592, 				0.6657983322868645, 0.6657983322868645, 0.6657983322868645, 0.6657983322868645, 0.6657983322868645, 0.6657983322868645, 				0.6657983322868645, 0.6657983322868645, 0.6657983322868645, 0.6657983322868645, 0.6657983322868645, 0.6657983322868645, 				0.6657983322868645, 0.6657983322868645, 0.6657983322868645, 0.6657983322868645, 0.6657983322868645, 0.6657983322868645, 				0.6657983322868645, 0.6657983322868645, 0.6657983322868645, 0.6657983322868645, 0.6657983322868645, 0.6657983322868645, 				0.36499296253183455, 0.36499296253183455, 0.36499296253183455, 0.36499296253183455, 0.36499296253183455, 0.36499296253183455, 				0.36499296253183455, 0.36499296253183455, 0.36499296253183455, 0.36499296253183455, 0.36499296253183455, 0.36499296253183455, 				0.36499296253183455, 0.36499296253183455, 0.36499296253183455, 0.36499296253183455, 0.36499296253183455, 0.36499296253183455, 				0.36499296253183455, 0.36499296253183455, 0.36499296253183455, 0.36499296253183455, 0.36499296253183455, 0.36499296253183455, 				-1.4126223743318331, -1.4126223743318331, -1.4126223743318331, -1.4126223743318331, -1.4126223743318331, -1.4126223743318331, 				-1.4126223743318331, -1.4126223743318331, -1.4126223743318331, -1.4126223743318331, -1.4126223743318331, -1.4126223743318331, 				-1.4126223743318331, -1.4126223743318331, -1.4126223743318331, -1.4126223743318331, -1.4126223743318331, -1.4126223743318331, 				-1.4126223743318331, -1.4126223743318331, -1.4126223743318331, -1.4126223743318331, -1.4126223743318331, -1.4126223743318331, 				0.9550791263416403, 0.9550791263416403, 0.9550791263416403, 0.9550791263416403, 0.9550791263416403, 0.9550791263416403, 				0.9550791263416403, 0.9550791263416403, 0.9550791263416403, 0.9550791263416403, 0.9550791263416403, 0.9550791263416403, 				0.9550791263416403, 0.9550791263416403, 0.9550791263416403, 0.9550791263416403, 0.9550791263416403, 0.9550791263416403, 				0.9550791263416403, 0.9550791263416403, 0.9550791263416403, 0.9550791263416403, 0.9550791263416403, 0.9550791263416403, 				-1.6781372399120633, -1.6781372399120633, -1.6781372399120633, -1.6781372399120633, -1.6781372399120633, -1.6781372399120633, 				-1.6781372399120633, -1.6781372399120633, -1.6781372399120633, -1.6781372399120633, -1.6781372399120633, -1.6781372399120633, 				-1.6781372399120633, -1.6781372399120633, -1.6781372399120633, -1.6781372399120633, -1.6781372399120633, -1.6781372399120633, 				-1.6781372399120633, -1.6781372399120633, -1.6781372399120633, -1.6781372399120633, -1.6781372399120633, -1.6781372399120633, 				4.1204156663162665, 4.1204156663162665, 4.1204156663162665, 4.1204156663162665, 4.1204156663162665, 4.1204156663162665, 				4.1204156663162665, 4.1204156663162665, 4.1204156663162665, 4.1204156663162665, 4.1204156663162665, 4.1204156663162665, 				4.1204156663162665, 4.1204156663162665, 4.1204156663162665, 4.1204156663162665, 4.1204156663162665, 4.1204156663162665, 				4.1204156663162665, 4.1204156663162665, 4.1204156663162665, 4.1204156663162665, 4.1204156663162665, 4.1204156663162665, 				-3.0332882772928316, -3.0332882772928316, -3.0332882772928316, -3.0332882772928316, -3.0332882772928316, -3.0332882772928316, 				-3.0332882772928316, -3.0332882772928316, -3.0332882772928316, -3.0332882772928316, -3.0332882772928316, -3.0332882772928316, 				-3.0332882772928316, -3.0332882772928316, -3.0332882772928316, -3.0332882772928316, -3.0332882772928316, -3.0332882772928316, 				-3.0332882772928316, -3.0332882772928316, -3.0332882772928316, -3.0332882772928316, -3.0332882772928316, -3.0332882772928316};		Torsions t = new Torsions();		t.setMMFF94TorsionsParameters(molecule, mmff94Tables);		//logger.debug("functionMMFF94SumET = " + t.functionMMFF94SumET(moleculeCoordinates));		assertEquals(testResult_MMFF94SumET, t.functionMMFF94SumET(moleculeCoordinates), 0.00001);		t.set2ndOrderErrorApproximateGradientMMFF94SumET(moleculeCoordinates);		//logger.debug("t.get2ndOrderErrorApproximateGradientMMFF94SumET() = " + t.get2ndOrderErrorApproximateGradientMMFF94SumET());		for (int i = 0; i < testResult_gradientSumET.length; i++) {			assertEquals(testResult_gradientSumET[i], t.get2ndOrderErrorApproximateGradientMMFF94SumET().getElement(i), 0.00001);		}		t.set2ndOrderErrorApproximateHessianMMFF94SumET(moleculeCoordinates);		//logger.debug("HessianMMFF94SumET = ");		for (int i = 0; i < 24; i++) {			//logger.debug("");			//logger.debug("");			for (int j = 0; j < 24; j++) {				//logger.debug(t.get2ndOrderErrorApproximateHessianMMFF94SumET().getElement(i, j) + ", ");				assertEquals(testResult_hessianSumET[i * 24 + j], t.get2ndOrderErrorApproximateHessianMMFF94SumET().getElement(i, j), 0.00001);			}		}	}	/**	 *  A unit test for JUnit (VanDerWaalsInteraction)	 */	public void testVanDerWaalsInteraction() throws ClassNotFoundException, CDKException, java.lang.Exception {		//logger.debug("");		//logger.debug("FORCEFIELDTESTS with VanDerWaalsInteraction");		double testResult_MMFF94SumEvdW = -0.018315208443555175;		double testResult_CCGSumEvdWSK = -0.018315208443555175;
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