From: <mig...@us...> - 2006-05-30 09:34:06
|
Revision: 6324 Author: miguelrojasch Date: 2006-05-30 02:33:46 -0700 (Tue, 30 May 2006) ViewCVS: http://svn.sourceforge.net/cdk/?rev=6324&view=rev Log Message: ----------- generalization of dataSet input for weka librariy Modified Paths: -------------- trunk/cdk/src/data/arff/Table1.arff trunk/cdk/src/data/arff/Table2.arff trunk/cdk/src/org/openscience/cdk/libio/weka/Weka.java trunk/cdk/src/org/openscience/cdk/test/libio/weka/WekaTest.java Modified: trunk/cdk/src/data/arff/Table1.arff =================================================================== --- trunk/cdk/src/data/arff/Table1.arff 2006-05-29 13:13:18 UTC (rev 6323) +++ trunk/cdk/src/data/arff/Table1.arff 2006-05-30 09:33:46 UTC (rev 6324) @@ -1,27 +1,8 @@ @relation 'table1' -@attribute 'EffectivePolarizabilityDescriptor' real -@attribute 'SigmaElectronegativityDescriptor' real -@attribute 'ProtonTotalPartialChargeDescriptor' real -@attribute 'predicted valency' real -@data -0.39 , 9.62 , -0.15 ,12.74, -1.64 , 9.77 , -0.13 ,11.3 , -1.06 , 12.56 , -0.16 ,13.0 , -1.26 , 10.51 , -0.05 ,12.6 , -1.45 , 10.15 , -0.09 ,11.9 , -2.27 , 9.8 , -0.13 ,11.01, -1.89 , 10.54 , -0.05 ,12.5 , -1.06 , 10.15 , 0.01 ,12.9 , -2.59 , 9.81 , -0.13 ,10.88, -2.74 , 9.81 , -0.13 ,10.84, -2.79 , 9.85 , -0.12 ,11.21, -0.39 , 9.14 , -0.11 ,11.67, -1.64 , 9.28 , -0.1 ,10.53, -1.06 , 10.34 , 0.03 ,12.0 , -1.06 , 10.15 , 0.01 ,11.83, -2.27 , 9.31 , -0.09 ,10.28, -2.59 , 9.31 , -0.09 ,10.18, -2.74 , 9.31 , -0.09 ,10.15, -2.79 , 9.35 , -0.09 ,10.43, -0.39 , 9.06 , -0.11 ,10.38, -1.64 , 9.2 , -0.09 ,9.5 , +@attribute 'x1' real +@attribute 'x2' real +@attribute 'y3' real +@data 1,1,0, +3,3,2, +4,4,3, +6,6,5, \ No newline at end of file Modified: trunk/cdk/src/data/arff/Table2.arff =================================================================== --- trunk/cdk/src/data/arff/Table2.arff 2006-05-29 13:13:18 UTC (rev 6323) +++ trunk/cdk/src/data/arff/Table2.arff 2006-05-30 09:33:46 UTC (rev 6324) @@ -1,7 +1,6 @@ -@relation 'table1' -@attribute 'EffectivePolarizabilityDescriptor' real -@attribute 'SigmaElectronegativityDescriptor' real -@attribute 'ProtonTotalPartialChargeDescriptor' real -@attribute 'ProtonTotalPa' real -@data -0.39 , 9.06 , -0.11,0.0 +@relation 'table2' +@attribute 'x1' real +@attribute 'x2' real +@attribute 'y3' real +@data 2, 2 ,0 + 5,5,0 Modified: trunk/cdk/src/org/openscience/cdk/libio/weka/Weka.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/libio/weka/Weka.java 2006-05-29 13:13:18 UTC (rev 6323) +++ trunk/cdk/src/org/openscience/cdk/libio/weka/Weka.java 2006-05-30 09:33:46 UTC (rev 6324) @@ -46,15 +46,10 @@ * You have also the possibility to introduce directly values, done like: * <pre> * Classifier lr = new LinearRegression(); - * String[] attrib = {"aX","bX","cX","PY" }; + * String[] attrib = {"X1","X2","X3","Y" }; * int[] typAttrib = {Weka.NUMERIC,Weka.NUMERIC,Weka.NUMERIC,Weka.NUMERIC, }; - * double[][] x = {{0.39,9.62 ,-0.15 }, - * {1.64,9.77 ,-0.13}, - * {1.06,12.56,-0.16}, - * double[] y = {12.74,11.3 ,13.0}; * weka.setDataset(attrib, typAttrib, y, x, lr); - * double[] testX = {0.39,9.06,-0.11}; - * double resultY = weka.getPrediction(testX); + * double[] resultY = weka.getPrediction(testX); * </pre> * @author Miguel Rojas * @cdk.created 2006-05-23 @@ -66,11 +61,14 @@ public static final int NUMERIC = 0; public static final int NOMINAL = 1; + public static final int REGULAR = 2; + public static final int DATA = 3; + public static final int STRING = 4; /** type of classifier*/ - private Classifier classifier; + private Classifier classifier = null; - private Instances labeled; + private Instances instances; /** * Constructor of the Weka */ @@ -88,17 +86,10 @@ this.classifier = classifier; InputStream ins = this.getClass().getClassLoader().getResourceAsStream(pathTable); Reader insr = new InputStreamReader(ins); - Instances instances = new Instances(new BufferedReader(insr)); + instances = new Instances(new BufferedReader(insr)); instances.setClassIndex(instances.numAttributes() - 1); - - labeled = new Instances(instances); - classifier.buildClassifier(labeled); - - for (int i = 0; i < instances.numInstances(); i++) { - double clsLabel = classifier.classifyInstance(instances.instance(i)); - labeled.instance(i).setClassValue(clsLabel); - } - return labeled; + classifier.buildClassifier(instances); + return instances; } /** * @@ -107,14 +98,14 @@ * * @param attrib String with the attribut names * @param typAttrib Attribute type: NUMERICAL or NOMINAL. + * @param y An array containing the dependent variable. It is possible numeric or string. * @param x An array of independent variables. The observations should be in the rows * and the variables should be in the columns - * @param y An array containing the dependent variable. It is possible numeric or string. * @param classifier Type of Classifier * @return The Instances value * @throws Exception */ - public Instances setDataset(String[] attrib, int[] typAttrib, Object[]y, double[][] x, Classifier classifier) throws Exception{ + public Instances setDataset(String[] attrib, int[] typAttrib, Object[]y, Object[][] x, Classifier classifier) throws Exception{ return setDataset(attrib, typAttrib ,null,y,x,classifier); } /** @@ -125,26 +116,20 @@ * @param attrib String with the attribut names. * @param typAttrib Attribute type: NUMERICAL or NOMINAL. * @param classAttrib String with the attribut class. + * @param y An array containing the dependent variable. It is possible numeric or string. * @param x An array of independent variables. The observations should be in the rows * and the variables should be in the columns - * @param y An array containing the dependent variable. It is possible numeric or string. * @param classifier Type of classifier * @return The Instances value * @throws Exception */ - public Instances setDataset(String[] attrib, int[] typAttrib, String[] classAttrib, Object[]y, double[][] x, Classifier classifier) throws Exception{ + public Instances setDataset(String[] attrib, int[] typAttrib, String[] classAttrib, Object[]y, Object[][] x, Classifier classifier) throws Exception{ this.classifier = classifier; Reader reader = createAttributes(attrib,typAttrib,classAttrib,y,x); - Instances instances = new Instances(reader); + instances = new Instances(reader); instances.setClassIndex(instances.numAttributes() - 1); - labeled = new Instances(instances); - classifier.buildClassifier(labeled); - - for (int i = 0; i < instances.numInstances(); i++) { - double clsLabel = classifier.classifyInstance(instances.instance(i)); - labeled.instance(i).setClassValue(clsLabel); - } - return labeled; + classifier.buildClassifier(instances); + return instances; } /** * Return of the predicted value @@ -153,13 +138,21 @@ * @return Result of the prediction * @throws Exception */ - public double getPrediction(double[] value) throws Exception{ - Instance instance = new Instance(labeled.numAttributes()); - instance.setDataset(labeled); - for(int i = 0 ; i < value.length ; i++) - instance.setValue(i, value[i]); -// instance.setValue(value.length, 0.0); - return classifier.classifyInstance(instance); + public double[] getPrediction(Object[][] value) throws Exception{ + double[] results = new double[value.length]; + for(int j = 0 ; j < value.length ; j++){ + Instance instance = new Instance(instances.numAttributes()); + instance.setDataset(instances); + for(int i = 0 ; i < value[0].length ; i++){ + if(instance.attribute(i).isNumeric()) + instance.setValue(i, ((Double)value[j][i]).doubleValue()); + else if(instance.attribute(i).isString()) + instance.setValue(i, ""+value[j][i]); + } + instance.setValue(value[0].length, 0.0); + results[j] = classifier.classifyInstance(instance); + } + return results; } /** * Return of the predicted value @@ -173,9 +166,8 @@ Reader insr = new InputStreamReader(ins); Instances test = new Instances(new BufferedReader(insr)); double[] result = new double[test.numInstances()]; - for(int i = 0 ; i < test.numInstances(); i++){ + for(int i = 0 ; i < test.numInstances(); i++) result[i] = classifier.classifyInstance(test.instance(i)); - } return result; } /** @@ -188,7 +180,7 @@ * @return The Reader containing the attributes * @throws IOException */ - private Reader createAttributes(String[] attrib, int[] typAttrib, String[] classAttrib, Object[]y, double[][] x) throws IOException{ + private Reader createAttributes(String[] attrib, int[] typAttrib, String[] classAttrib, Object[]y, Object[][] x) throws IOException{ String string ="@relation table1 \n"; for(int i = 0; i < attrib.length ; i++){ string += ("@attribute "+attrib[i]); @@ -196,8 +188,14 @@ string += " numeric \n"; else if(typAttrib[i] == NOMINAL) string += " string \n"; + else if(typAttrib[i] == DATA) + string += " data \n"; + else if(typAttrib[i] == REGULAR) + string += " regular \n"; + else if(typAttrib[i] == STRING) + string += " string \n"; } - + if(classAttrib != null){ string += "@attribute class "; string += "{"; @@ -215,12 +213,11 @@ for(int i = 0 ; i < x[0].length ; i++){ string += x[j][i]+","; } - string += y[j]+", \n"; + string += y[j]+", \n"; } } - - Reader reader = new StringReader(string); return reader; } + } \ No newline at end of file Modified: trunk/cdk/src/org/openscience/cdk/test/libio/weka/WekaTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/libio/weka/WekaTest.java 2006-05-29 13:13:18 UTC (rev 6323) +++ trunk/cdk/src/org/openscience/cdk/test/libio/weka/WekaTest.java 2006-05-30 09:33:46 UTC (rev 6324) @@ -45,13 +45,11 @@ */ public class WekaTest extends CDKTestCase { - private Weka weka; /** * Constructor for the WekaTest object * */ public WekaTest() { - weka = new Weka(); } /** * A unit test suite for JUnit @@ -62,7 +60,7 @@ return new TestSuite(WekaTest.class); } /** - * A unit test for JUnit. Test usign file arff format, algorithm = Lineal Regression + * A unit test for JUnit. Test and prediction using file arff format, algorithm = Lineal Regression */ public void test1() throws ClassNotFoundException, CDKException, java.lang.Exception { LinearRegression lr = new LinearRegression(); @@ -72,12 +70,14 @@ options[2] = "-R"; options[3] = "0.00000008"; lr.setOptions(options); + Weka weka = new Weka(); weka.setDataset("data/arff/Table1.arff", lr); double[] result = weka.getPrediction("data/arff/Table2.arff"); assertNotNull(result); } /** - * A unit test for JUnit. Test using Array, algorithm = Lineal Regression + * A unit test for JUnit. Test using file arrf and prdiction using Array, + * algorithm = Lineal Regression */ public void test2() throws ClassNotFoundException, CDKException, java.lang.Exception { LinearRegression lr = new LinearRegression(); @@ -87,37 +87,42 @@ options[2] = "-R"; options[3] = "0.00000008"; lr.setOptions(options); + Weka weka = new Weka(); weka.setDataset("data/arff/Table1.arff", lr); - double[] testX = {0.39,9.06,-0.11}; - double result = weka.getPrediction(testX); -// assertNotNull(result); + Object[][] testX = {{new Double(2),new Double(2)}, + {new Double(5),new Double(5)} + }; + double[] result = weka.getPrediction(testX); + assertNotNull(result); } /** - * A unit test for JUnit. Test using Array, algorithm = Lineal Regression + * A unit test for JUnit. Test and prediction using Array, algorithm = Lineal Regression */ public void test3() throws ClassNotFoundException, CDKException, java.lang.Exception { LinearRegression lr = new LinearRegression(); - String[] attrib = {"aX","bX","cX", "PY" }; - int[] typAttrib = {Weka.NUMERIC,Weka.NUMERIC,Weka.NUMERIC,Weka.NUMERIC}; - double[][] x = {{0.39,9.62 ,-0.15 },{1.64 , 9.77 , -0.13},{1.06 , 12.56 , -0.16}, - {1.26 , 10.51 , -0.05},{1.45 , 10.15 , -0.09},{2.27 , 9.8 , -0.13}, - {1.89 , 10.54 , -0.05},{1.06 , 10.15 , 0.01},{2.59 , 9.81 , -0.13}, - {2.74 , 9.81 , -0.13},{2.79 , 9.85 , -0.12},{0.39 , 9.14 , -0.11}, - {1.64 , 9.28 , -0.1}, {1.06 , 10.34 , 0.03},{1.06 , 10.15 , 0.01}, - {2.27 , 9.31 , -0.09},{2.59 , 9.31 , -0.09},{2.74 , 9.31 , -0.09}, - {2.79 , 9.35 , -0.09},{0.39 , 9.06 , -0.11},{1.64 , 9.2 , -0.09}}; - double[] y = { 12.74,11.3 ,13.0 ,12.6 ,11.9 ,11.01,12.5 ,12.9 ,10.88,10.84,11.21,11.67, - 10.53,12.0 ,11.83,10.28,10.28,10.15,10.43,10.38,9.5 }; - Double[] yD = new Double[y.length]; + String[] attrib = {"X2","X1", "Y" }; + int[] typAttrib = {Weka.NUMERIC,Weka.NUMERIC,Weka.NUMERIC}; + double[][] x = {{ 1,1},{3,3},{4,4},{6,6} }; + Double[][] xD = new Double[x.length][x[0].length]; + for(int i = 0 ; i< xD.length; i++) + for(int j = 0 ; j < xD[i].length ; j++) + xD[i][j] = new Double(x[i][j]); + + double[] y = { 0,2,3,5}; + Double[] yD = new Double[y.length]; for(int i = 0 ; i< yD.length; i++) yD[i] = new Double(y[i]); - weka.setDataset(attrib, typAttrib, yD, x, lr); - double[] testX = {0.39,9.06,-0.11}; - double resultY = weka.getPrediction(testX); -// assertNotNull(resultY); + + Weka weka = new Weka(); + weka.setDataset(attrib, typAttrib, yD, xD, lr); + Double[][] testX = {{new Double(2),new Double(2)}, + {new Double(5),new Double(5)} + }; + double[] result = weka.getPrediction(testX); + assertNotNull(result); } /** - * A unit test for JUnit. Test using Array, algorithm = J48 + * A unit test for JUnit. Test prediction using Array, algorithm = J48 */ public void test4() throws ClassNotFoundException, CDKException, java.lang.Exception { String[] options = new String[1]; @@ -128,12 +133,18 @@ String[] attrib = {"aX","bX","cX"}; int[] typAttrib = {Weka.NUMERIC,Weka.NUMERIC,Weka.NUMERIC}; String[] classAttrib = {"A_","B_","C_"}; - double[][] x = {{10,10 ,10 },{10 , 10 , -10},{-10 , -10 , -10}, - {11,11 ,11 },{11 , 11 , -11},{-11 , -11 , -11}}; + double[][] x = {{10,10 ,10 },{10 , -10 , -10},{-10 , -10 , -10}, + {11,11 ,11 },{11 , -11 , -11},{-11 , -11 , -11}}; + Double[][] xD = new Double[x.length][x[0].length]; + for(int i = 0 ; i< xD.length; i++) + for(int j = 0 ; j < xD[i].length ; j++) + xD[i][j] = new Double(x[i][j]); String[] y = { "A_","B_" ,"C_","A_","B_" ,"C_"}; - weka.setDataset(attrib, typAttrib, classAttrib, y, x, j48); - double[] testX = {10,10,-11}; - double resultY = weka.getPrediction(testX); -// assertNotNull(resultY); + Weka weka = new Weka(); + weka.setDataset(attrib, typAttrib, classAttrib, y, xD, j48); + Double[][] testX = {{new Double(11),new Double(-11),new Double(-11)}, + {new Double(-10),new Double(-10),new Double(-10)}}; + double[] resultY = weka.getPrediction(testX); + assertNotNull(resultY); } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <mig...@us...> - 2006-05-30 12:22:25
|
Revision: 6326 Author: miguelrojasch Date: 2006-05-30 05:22:15 -0700 (Tue, 30 May 2006) ViewCVS: http://svn.sourceforge.net/cdk/?rev=6326&view=rev Log Message: ----------- table arff Added Paths: ----------- trunk/cdk/src/data/arff/Table3.arff trunk/cdk/src/data/arff/Table4.arff Added: trunk/cdk/src/data/arff/Table3.arff =================================================================== --- trunk/cdk/src/data/arff/Table3.arff (rev 0) +++ trunk/cdk/src/data/arff/Table3.arff 2006-05-30 12:22:15 UTC (rev 6326) @@ -0,0 +1,11 @@ +@relation 'table3' +@attribute 'x1' numeric +@attribute 'x2' numeric +@attribute 'x3' numeric +@attribute class {"A_","B_","C_"} +@data 10,10,10,A_, +10 ,-10 , -10,B_, +-10,-10 , -10,C_, +11 , 11 , 11,A_, +11 ,-11 , -11,B_, +-11,-11 , -11,C_, \ No newline at end of file Added: trunk/cdk/src/data/arff/Table4.arff =================================================================== --- trunk/cdk/src/data/arff/Table4.arff (rev 0) +++ trunk/cdk/src/data/arff/Table4.arff 2006-05-30 12:22:15 UTC (rev 6326) @@ -0,0 +1,7 @@ +@relation 'table4' +@attribute 'x1' numeric +@attribute 'x2' numeric +@attribute 'x3' numeric +@attribute class {"A_","B_","C_"} +@data 11,-11,-11,A_, + -10,-10,-10,A_, This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <mig...@us...> - 2006-06-02 07:22:16
|
Revision: 6333 Author: miguelrojasch Date: 2006-06-02 00:21:58 -0700 (Fri, 02 Jun 2006) ViewCVS: http://svn.sourceforge.net/cdk/?rev=6333&view=rev Log Message: ----------- new Descriptor. Try to calculate the Ionization potential for a atom. Up to now only possible heteroatoms. Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/test/MqsarTests.java Added Paths: ----------- trunk/cdk/src/data/arff/HeteroAtom1.arff trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPDescriptor.java trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPDescriptorTest.java Added: trunk/cdk/src/data/arff/HeteroAtom1.arff =================================================================== --- trunk/cdk/src/data/arff/HeteroAtom1.arff (rev 0) +++ trunk/cdk/src/data/arff/HeteroAtom1.arff 2006-06-02 07:21:58 UTC (rev 6333) @@ -0,0 +1,887 @@ +@relation HeteroAtom1 +@attribute SE numeric +@attribute SCH numeric +@attribute EE numeric +@attribute class {07_0,07_2,07_4,07_6,07_8,08_0,08_2,08_4,08_6,08_8,09_0,09_2,09_4,09_6,09_8,10_0,10_2,10_4,10_6,10_8,11_0,11_2,11_4,11_6,11_8,12_0,12_2,12_4,12_6,12_8,13_0,13_2,13_4,13_6,13_8,14_0,14_2,14_4,14_6,14_8} +@data +9.127746916005433 ,-0.11279410152034004 ,8.042125 ,07_6, +10.520703546695009 ,-0.0967346734621245 ,6.58671875 ,09_0, +10.52080477298224 ,-0.09672387779859191 ,6.1937500000000005 ,09_4, + 8.702547390185432 ,-0.2715070693588401 ,7.764625000000002 ,07_6, +10.256143306705784 ,-0.12506185953314314 ,6.912343750000001 ,08_8, +10.671878120324584 ,-0.15444540545901517 ,5.755343750000001 ,09_0, +10.197351566651683 ,-0.12608779032630876 ,5.2763437500000006 ,08_4, +11.45847238182544 ,-0.21564768357134897 ,4.463343750000001 ,08_2, +9.450539264055655 ,-0.0763981770374318 , 6.999343750000001 ,08_8, +11.418278235926532 ,-0.2189112648030682 ,5.624093750000002 ,08_2, +8.691627986927791 ,-0.27259034053376663 ,7.933875000000002 ,07_4, +9.578082025403772 ,-0.06212978383913348 ,6.859750000000001 ,08_8, +8.94127318300413 ,-0.13400982825989147 ,7.5165000000000015 ,08_6, +9.753669450961851 ,-0.3562492536155934 ,6.359125000000002 ,09_2, +13.029857633084225 ,-0.29596165470722147 ,5.254343750000001 ,08_4, +8.77873654600465 ,-0.26395743546368566 ,9.559187500000002 ,07_8, +13.01902078490945 ,-0.2967637057804767 ,4.5505 ,09_0, +13.371199477407584 ,-0.19644284435858958 ,5.049132812500001 ,08_8, +8.691627986927791 ,-0.27259034053376663 ,8.852875000000003 ,07_0, +8.805536155997904 ,-0.26130549025558025 ,9.106000000000002 ,08_2, +8.691627986927791 ,-0.27259034053376663 ,9.324437500000002 ,07_0, +8.691624697428043 ,-0.2725906669198539 ,8.707750000000003 ,08_0, +11.330026318307722 ,-0.3686562962567898 ,5.974843750000001 ,09_6, +9.350137105557799 ,-0.20781880462066427 , 8.301687500000002 ,08_2, + 9.900036483859179 ,-0.34399753889683105 ,7.488687500000001 ,09_0, +10.209999083682337 ,-0.1300258269846788 ,6.657171875000001 ,09_0, +9.3157493879685 ,-0.21117364816988674 ,6.533843750000001 ,08_6, +13.024843987198885 ,-0.2963327164507235 ,4.370421875 ,09_0, +8.751754002705725 ,-0.2666293971805795 ,7.791343750000002 ,07_6, +9.785552022268273 ,-0.35357753142780446 ,6.141500000000002 ,09_0, +11.458335962619305 ,-0.2156587561238227 ,4.1649609375 ,08_0, +11.413824374889172 ,-0.21927304602329512 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[truncated message content] |
From: <mig...@us...> - 2006-06-02 14:09:56
|
Revision: 6335 Author: miguelrojasch Date: 2006-06-02 07:09:39 -0700 (Fri, 02 Jun 2006) ViewCVS: http://svn.sourceforge.net/cdk/?rev=6335&view=rev Log Message: ----------- Decrease of rank for the classification. between 0.1 eV. Modified Paths: -------------- trunk/cdk/src/data/arff/HeteroAtom1.arff trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPDescriptor.java trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPDescriptorTest.java Modified: trunk/cdk/src/data/arff/HeteroAtom1.arff =================================================================== --- trunk/cdk/src/data/arff/HeteroAtom1.arff 2006-06-02 13:29:29 UTC (rev 6334) +++ trunk/cdk/src/data/arff/HeteroAtom1.arff 2006-06-02 14:09:39 UTC (rev 6335) @@ -2,886 +2,783 @@ @attribute SE numeric @attribute SCH numeric @attribute EE numeric -@attribute class {07_0,07_2,07_4,07_6,07_8,08_0,08_2,08_4,08_6,08_8,09_0,09_2,09_4,09_6,09_8,10_0,10_2,10_4,10_6,10_8,11_0,11_2,11_4,11_6,11_8,12_0,12_2,12_4,12_6,12_8,13_0,13_2,13_4,13_6,13_8,14_0,14_2,14_4,14_6,14_8} +@attribute class {05_0,05_1,05_2,05_3,05_4,05_5,05_6,05_7,05_8,05_9,06_0,06_1,06_2,06_3,06_4,06_5,06_6,06_7,06_8,06_9,07_0,07_1,07_2,07_3,07_4,07_5,07_6,07_7,07_8,07_9,08_0,08_1,08_2,08_3,08_4,08_5,08_6,08_7,08_8,08_9,09_0,09_1,09_2,09_3,09_4,09_5,09_6,09_7,09_8,09_9,10_0,10_1,10_2,10_3,10_4,10_5,10_6,10_7,10_8,10_9,11_0,11_1,11_2,11_3,11_4,11_5,11_6,11_7,11_8,11_9,12_0,12_1,12_2,12_3,12_4,12_5,12_6,12_7,12_8,12_9,13_0,13_1,13_2,13_3,13_4,13_5,13_6,13_7,13_8,13_9,14_0,14_1,14_2,14_3,14_4,14_5,14_6,14_7,14_8,14_9} @data -9.127746916005433 ,-0.11279410152034004 ,8.042125 ,07_6, -10.520703546695009 ,-0.0967346734621245 ,6.58671875 ,09_0, -10.52080477298224 ,-0.09672387779859191 ,6.1937500000000005 ,09_4, - 8.702547390185432 ,-0.2715070693588401 ,7.764625000000002 ,07_6, -10.256143306705784 ,-0.12506185953314314 ,6.912343750000001 ,08_8, -10.671878120324584 ,-0.15444540545901517 ,5.755343750000001 ,09_0, -10.197351566651683 ,-0.12608779032630876 ,5.2763437500000006 ,08_4, -11.45847238182544 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[truncated message content] |
From: <mig...@us...> - 2006-06-06 13:31:14
|
Revision: 6347 Author: miguelrojasch Date: 2006-06-06 04:46:41 -0700 (Tue, 06 Jun 2006) ViewCVS: http://svn.sourceforge.net/cdk/?rev=6347&view=rev Log Message: ----------- implemented carbonyl group in IPAtomicDescriptor Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java Added Paths: ----------- trunk/cdk/src/data/arff/Carbonyl1.arff Added: trunk/cdk/src/data/arff/Carbonyl1.arff =================================================================== --- trunk/cdk/src/data/arff/Carbonyl1.arff (rev 0) +++ trunk/cdk/src/data/arff/Carbonyl1.arff 2006-06-06 11:46:41 UTC (rev 6347) @@ -0,0 +1,153 @@ +@relation Carbonyl1 +@attribute SE_c numeric +@attribute PCH_c numeric +@attribute SB numeric +@attribute SE_x numeric +@attribute PCH_x numeric +@attribute class {05_0,05_1,05_2,05_3,05_4,05_5,05_6,05_7,05_8,05_9,06_0,06_1,06_2,06_3,06_4,06_5,06_6,06_7,06_8,06_9,07_0,07_1,07_2,07_3,07_4,07_5,07_6,07_7,07_8,07_9,08_0,08_1,08_2,08_3,08_4,08_5,08_6,08_7,08_8,08_9,09_0,09_1,09_2,09_3,09_4,09_5,09_6,09_7,09_8,09_9,10_0,10_1,10_2,10_3,10_4,10_5,10_6,10_7,10_8,10_9,11_0,11_1,11_2,11_3,11_4,11_5,11_6,11_7,11_8,11_9,12_0,12_1,12_2,12_3,12_4,12_5,12_6,12_7,12_8,12_9,13_0,13_1,13_2,13_3,13_4,13_5,13_6,13_7,13_8,13_9,14_0,14_1,14_2,14_3,14_4,14_5,14_6,14_7,14_8,14_9} +@data +10.14223696457717 ,0.01254048559243616 ,0.4357614827468826 ,13.010144750817991 ,-0.01254048559243616 ,08_5, +10.115595009165439 , 0.0 ,0.433265930148359 ,13.00832193431444 , 0.0 ,09_0, +10.069206520828265 ,0.013010108066818708 ,0.4290106628067516 , 13.000881459331142 ,-0.013010108066818708 ,09_1, +10.053323843042925 , 0.0 ,0.427518527156048 , 12.999809313103185 , 0.0 ,09_1, +10.289068219060296 ,0.011679906623635335 ,0.4492797491334761 ,13.028926405386928 ,-0.011679906623635335 ,08_6, 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0.0 ,8.161601445273206 , 0.0 , 0.0 ,08_4, +10.121080306105117 , 0.0 ,0.43378292161867105 ,13.008642266718619 , 0.0 ,08_9, +10.13310870928706 , 0.0 ,0.4349156590665919 ,13.009268712659892 , 0.0 ,08_9, +10.058572486917585 , 0.0 ,0.4280148374543625 , 13.000120722689314 , 0.0 ,09_3, +9.957239332288003 , 0.0 ,0.42083663635016666 ,12.95445845936819 , 0.0 ,09_5, +10.050683727346291 , 0.0 ,0.4272682875425977 , 12.999662117402675 , 0.0 ,09_3, +9.95978667629054 , 0.0 ,0.4210794291291332 ,12.954603513581901 , 0.0 ,09_5, +10.05617011313598 , 0.0 ,0.4277868483770628 , 12.999961301652252 , 0.0 ,09_0, Modified: trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java 2006-06-06 08:55:35 UTC (rev 6346) +++ trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java 2006-06-06 11:46:41 UTC (rev 6347) @@ -30,9 +30,11 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; +import org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor; import org.openscience.cdk.qsar.model.weka.J48WModel; import org.openscience.cdk.qsar.result.DoubleResult; @@ -65,9 +67,15 @@ * @see J48WModel */ public class IPAtomicDescriptor implements IMolecularDescriptor { - /** Position of the atom in the AtomContainer*/ + /** Position of the target in the AtomContainer*/ private int targetPosition = 0; - + /** Type of the target in the AtomContainer*/ + private String targetType = ""; + /** Target which edintify with type IAtom target*/ + public static String AtomicTarget = "AtomicTarget"; + /** Target which edintify with type IBond target*/ + public static String BondTarget = "BondTarget"; + /** Hash map which contains the classAttribu = value of IP */ private HashMap hash = null; @@ -82,6 +90,7 @@ "12_0","12_1","12_2","12_3","12_4","12_5","12_6","12_7","12_8","12_9", "13_0","13_1","13_2","13_3","13_4","13_5","13_6","13_7","13_8","13_9", "14_0","14_1","14_2","14_3","14_4","14_5","14_6","14_7","14_8","14_9",}; + /** * Constructor for the IPAtomicDescriptor object */ @@ -108,17 +117,22 @@ /** * Sets the parameters attribute of the IPAtomicDescriptor object * - *@param params The parameter is the atom position + *@param params The parameter is the position and type the target (IAtom or IBond) *@exception CDKException Description of the Exception */ public void setParameters(Object[] params) throws CDKException { - if (params.length > 1) { - throw new CDKException("IPAtomicDescriptor only expects one parameter"); + if (params.length != 2) { + throw new CDKException("IPAtomicDescriptor expects two parameter. 1: the position and 2: type"); } if (!(params[0] instanceof Integer)) { throw new CDKException("The parameter must be of type Integer"); } + if (!(params[1] instanceof String) /* && ( + params[1].equals(AtomicTarget) ||params[1].equals(BondTarget))*/) { + throw new CDKException("The parameter must be of type String: BondTarget or AtomicTarget"); + } targetPosition = ((Integer) params[0]).intValue(); + targetType = (String) params[1]; } /** * Gets the parameters attribute of the IPAtomicDescriptor object @@ -126,31 +140,51 @@ *@return The parameters value */ public Object[] getParameters() { - Object[] params = new Object[1]; + Object[] params = new Object[2]; params[0] = new Integer(targetPosition); + params[1] = new String(targetType); return params; } /** * This method calculates the ionization potential of an atom. * - *@param container Parameter is the atom container. + *@param container Parameter is the IAtomContainer. *@return The ionization potential *@exception CDKException Description of the Exception */ public DescriptorValue calculate(IAtomContainer container) throws CDKException { double resultD = -1.0; - IAtom atom = container.getAtomAt(targetPosition); - if(atom.getSymbol().equals("F")|| - atom.getSymbol().equals("Cl")|| - atom.getSymbol().equals("Br")|| - atom.getSymbol().equals("I")|| - atom.getSymbol().equals("N")|| - atom.getSymbol().equals("S")|| - atom.getSymbol().equals("O")|| - atom.getSymbol().equals("P")){ - Double[][] resultsH = calculateHalogenDescriptor(container); - J48WModel j48 = new J48WModel("data/arff/HeteroAtom1.arff"); + boolean isTarget = false; + Double[][] resultsH = null; + String path = ""; + if(targetType.equals(AtomicTarget)){ + IAtom atom = container.getAtomAt(targetPosition); + if(atom.getSymbol().equals("F")|| + atom.getSymbol().equals("Cl")|| + atom.getSymbol().equals("Br")|| + atom.getSymbol().equals("I")|| + atom.getSymbol().equals("N")|| + atom.getSymbol().equals("S")|| + atom.getSymbol().equals("O")|| + atom.getSymbol().equals("P")){ + resultsH = calculateHeteroAtomDescriptor(container); + path = "data/arff/HeteroAtom1.arff"; + isTarget = true; + } + }else if(targetType.equals(BondTarget)){ + IBond bond = container.getBondAt(targetPosition); + IAtom[] atoms = bond.getAtoms(); + if((bond.getOrder() == 2) && + (((atoms[0].getSymbol().equals("C")) &&( !atoms[1].getSymbol().equals("C")))|| + ((atoms[1].getSymbol().equals("C")) && (!atoms[0].getSymbol().equals("C"))))) { + resultsH = calculateCarbonylDescriptor(container); + path = "data/arff/Carbonyl1.arff"; + isTarget = true; + } + } + if(isTarget){ + J48WModel j48 = new J48WModel(path); String[] options = new String[4]; options[0] = "-C"; options[1] = "0.25"; @@ -166,11 +200,11 @@ return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(resultD)); } /** - * Calculate the necessary descriptors for Halogens atoms + * Calculate the necessary descriptors for Heteratom atoms * @param atomContaine The IAtomContainer * @return Array with the values of the descriptors. */ - private Double[][] calculateHalogenDescriptor(IAtomContainer atomContainer) { + private Double[][] calculateHeteroAtomDescriptor(IAtomContainer atomContainer) { Double[][] results = new Double[1][3]; Integer[] params = new Integer[1]; Vector vector = new Vector(); @@ -190,6 +224,56 @@ return results; } /** + * Calculate the necessary descriptors for Carbonyl group + * @param atomContaine The IAtomContainer + * @return Array with the values of the descriptors. + */ + private Double[][] calculateCarbonylDescriptor(IAtomContainer atomContainer) { + Double[][] results = new Double[1][5]; + Integer[] params = new Integer[1]; + IBond bond = atomContainer.getBondAt(targetPosition); + IAtom[] atoms = bond.getAtoms(); + int positionC = 0; + int positionX = 0; + if((atoms[0].getSymbol().equals("C") && !atoms[1].getSymbol().equals("C"))){ + positionC = atomContainer.getAtomNumber(atoms[0]); + positionX = atomContainer.getAtomNumber(atoms[1]); + }else if((atoms[1].getSymbol().equals("C") && !atoms[0].getSymbol().equals("C"))){ + positionC = atomContainer.getAtomNumber(atoms[1]); + positionX = atomContainer.getAtomNumber(atoms[0]); + } + try { + /*0*/ + IMolecularDescriptor descriptor = new SigmaElectronegativityDescriptor(); + params[0] = new Integer(positionC); + descriptor.setParameters(params); + results[0][0]= new Double(((DoubleResult)descriptor.calculate(atomContainer).getValue()).doubleValue()); + /*1*/ + descriptor = new PartialSigmaChargeDescriptor(); + descriptor.setParameters(params); + results[0][1]= new Double(((DoubleResult)descriptor.calculate(atomContainer).getValue()).doubleValue()); + /*2*/ + descriptor = new BondPartialSigmaChargeDescriptor(); + params[0] = new Integer(targetPosition); + descriptor.setParameters(params); + results[0][2]= new Double(((DoubleResult)descriptor.calculate(atomContainer).getValue()).doubleValue()); + /*3*/ + descriptor = new SigmaElectronegativityDescriptor(); + params[0] = new Integer(positionX); + descriptor.setParameters(params); + results[0][3]= new Double(((DoubleResult)descriptor.calculate(atomContainer).getValue()).doubleValue()); + /*4*/ + descriptor = new PartialSigmaChargeDescriptor(); + descriptor.setParameters(params); + results[0][4]= new Double(((DoubleResult)descriptor.calculate(atomContainer).getValue()).doubleValue()); + + } catch (CDKException e) { + e.printStackTrace(); + } + return results; + } + + /** * Gets the parameterNames attribute of the IPAtomicDescriptor object * *@return The parameterNames value Modified: trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java 2006-06-06 08:55:35 UTC (rev 6346) +++ trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java 2006-06-06 11:46:41 UTC (rev 6347) @@ -62,7 +62,7 @@ */ public void testIPDescriptor_1() throws ClassNotFoundException, CDKException, java.lang.Exception{ IMolecularDescriptor descriptor = new IPAtomicDescriptor(); - Integer[] params = new Integer[1]; + Object[] params = new Object[2]; SmilesParser sp = new SmilesParser(); Molecule mol = sp.parseSmiles("C-Cl"); @@ -74,6 +74,7 @@ lpcheck.newSaturate(mol); params[0] = new Integer(1); + params[1] = new String(IPAtomicDescriptor.AtomicTarget); descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 11.26; @@ -84,7 +85,7 @@ */ public void testIPDescriptor_2() throws ClassNotFoundException, CDKException, java.lang.Exception{ IMolecularDescriptor descriptor = new IPAtomicDescriptor(); - Integer[] params = new Integer[1]; + Object[] params = new Object[2]; SmilesParser sp = new SmilesParser(); Molecule mol = sp.parseSmiles("C-C-Br"); @@ -96,6 +97,7 @@ lpcheck.newSaturate(mol); params[0] = new Integer(2); + params[1] = IPAtomicDescriptor.AtomicTarget; descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 11.29; @@ -106,7 +108,7 @@ */ public void testIPDescriptor_3() throws ClassNotFoundException, CDKException, java.lang.Exception{ IMolecularDescriptor descriptor = new IPAtomicDescriptor(); - Integer[] params = new Integer[1]; + Object[] params = new Object[2]; SmilesParser sp = new SmilesParser(); Molecule mol = sp.parseSmiles("C-C-C-I"); @@ -118,6 +120,7 @@ lpcheck.newSaturate(mol); params[0] = new Integer(3); + params[1] = IPAtomicDescriptor.AtomicTarget; descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 9.27; @@ -128,7 +131,7 @@ */ public void testIPDescriptor_4() throws ClassNotFoundException, CDKException, java.lang.Exception{ IMolecularDescriptor descriptor = new IPAtomicDescriptor(); - Integer[] params = new Integer[1]; + Object[] params = new Object[2]; SmilesParser sp = new SmilesParser(); Molecule mol = sp.parseSmiles("C-C-O"); @@ -140,6 +143,7 @@ lpcheck.newSaturate(mol); params[0] = new Integer(2); + params[1] = IPAtomicDescriptor.AtomicTarget; descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 10.48; @@ -149,7 +153,7 @@ */ public void testIPDescriptor_5() throws ClassNotFoundException, CDKException, java.lang.Exception{ IMolecularDescriptor descriptor = new IPAtomicDescriptor(); - Integer[] params = new Integer[1]; + Object[] params = new Object[2]; SmilesParser sp = new SmilesParser(); Molecule mol = sp.parseSmiles("C-O-C"); @@ -161,6 +165,7 @@ lpcheck.newSaturate(mol); params[0] = new Integer(1); + params[1] = IPAtomicDescriptor.AtomicTarget; descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 10.025; @@ -171,7 +176,7 @@ */ public void testIPDescriptor_6() throws ClassNotFoundException, CDKException, java.lang.Exception{ IMolecularDescriptor descriptor = new IPAtomicDescriptor(); - Integer[] params = new Integer[1]; + Object[] params = new Object[2]; SmilesParser sp = new SmilesParser(); Molecule mol = sp.parseSmiles("C-N-C"); @@ -183,6 +188,7 @@ lpcheck.newSaturate(mol); params[0] = new Integer(1); + params[1] = IPAtomicDescriptor.AtomicTarget; descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 8.24; @@ -193,7 +199,7 @@ */ public void testIPDescriptor_7() throws ClassNotFoundException, CDKException, java.lang.Exception{ IMolecularDescriptor descriptor = new IPAtomicDescriptor(); - Integer[] params = new Integer[1]; + Object[] params = new Object[2]; SmilesParser sp = new SmilesParser(); Molecule mol = sp.parseSmiles("C-C-N"); @@ -205,6 +211,7 @@ lpcheck.newSaturate(mol); params[0] = new Integer(2); + params[1] = IPAtomicDescriptor.AtomicTarget; descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 8.9; @@ -215,7 +222,7 @@ */ public void testIPDescriptor_8() throws ClassNotFoundException, CDKException, java.lang.Exception{ IMolecularDescriptor descriptor = new IPAtomicDescriptor(); - Integer[] params = new Integer[1]; + Object[] params = new Object[2]; SmilesParser sp = new SmilesParser(); Molecule mol = sp.parseSmiles("C-C-P-C-C"); @@ -227,11 +234,57 @@ lpcheck.newSaturate(mol); params[0] = new Integer(2); + params[1] = IPAtomicDescriptor.AtomicTarget; descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 8.5; assertEquals(result, resultAccordingNIST, 0.4); } + /** + * A unit test for JUnit with CCCCC(=O)CC + */ + public void testIPDescriptor_9() throws ClassNotFoundException, CDKException, java.lang.Exception{ + IMolecularDescriptor descriptor = new IPAtomicDescriptor(); + Object[] params = new Object[2]; + + SmilesParser sp = new SmilesParser(); + Molecule mol = sp.parseSmiles("CCCCC(=O)CC"); + HydrogenAdder hAdder = new HydrogenAdder(); + hAdder.addExplicitHydrogensToSatisfyValency(mol); + + LonePairElectronChecker lpcheck = new LonePairElectronChecker(); + lpcheck.newSaturate(mol); + params[0] = new Integer(4); + params[1] = IPAtomicDescriptor.BondTarget; + descriptor.setParameters(params); + double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); + double resultAccordingNIST = 9.15; + assertEquals(result, resultAccordingNIST, 1); + } + /** + * A unit test for JUnit with O=C1CCCC1 + */ + public void testIPDescriptor_10() throws ClassNotFoundException, CDKException, java.lang.Exception{ + IMolecularDescriptor descriptor = new IPAtomicDescriptor(); + Object[] params = new Object[2]; + + SmilesParser sp = new SmilesParser(); + Molecule mol = sp.parseSmiles("O=C1CCCC1"); + + HydrogenAdder hAdder = new HydrogenAdder(); + hAdder.addExplicitHydrogensToSatisfyValency(mol); + + LonePairElectronChecker lpcheck = new LonePairElectronChecker(); + lpcheck.newSaturate(mol); + params[0] = new Integer(0); + params[1] = IPAtomicDescriptor.BondTarget; + descriptor.setParameters(params); + double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); + double resultAccordingNIST = 9.26; + assertEquals(result, resultAccordingNIST, 15); + } + + } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <mig...@us...> - 2006-06-28 11:41:28
|
Revision: 6522 Author: miguelrojasch Date: 2006-06-28 04:41:10 -0700 (Wed, 28 Jun 2006) ViewCVS: http://svn.sourceforge.net/cdk/?rev=6522&view=rev Log Message: ----------- added a new descriptor for the calcualtion of IPAtomicDescriptor with learning machine. Modified Paths: -------------- trunk/cdk/src/data/arff/Carbonyl1.arff trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java Modified: trunk/cdk/src/data/arff/Carbonyl1.arff =================================================================== --- trunk/cdk/src/data/arff/Carbonyl1.arff 2006-06-27 08:45:28 UTC (rev 6521) +++ trunk/cdk/src/data/arff/Carbonyl1.arff 2006-06-28 11:41:10 UTC (rev 6522) @@ -4,150 +4,151 @@ @attribute SB numeric @attribute SE_x numeric @attribute PCH_x numeric +@attribute RES_c numeric @attribute class {05_0,05_1,05_2,05_3,05_4,05_5,05_6,05_7,05_8,05_9,06_0,06_1,06_2,06_3,06_4,06_5,06_6,06_7,06_8,06_9,07_0,07_1,07_2,07_3,07_4,07_5,07_6,07_7,07_8,07_9,08_0,08_1,08_2,08_3,08_4,08_5,08_6,08_7,08_8,08_9,09_0,09_1,09_2,09_3,09_4,09_5,09_6,09_7,09_8,09_9,10_0,10_1,10_2,10_3,10_4,10_5,10_6,10_7,10_8,10_9,11_0,11_1,11_2,11_3,11_4,11_5,11_6,11_7,11_8,11_9,12_0,12_1,12_2,12_3,12_4,12_5,12_6,12_7,12_8,12_9,13_0,13_1,13_2,13_3,13_4,13_5,13_6,13_7,13_8,13_9,14_0,14_1,14_2,14_3,14_4,14_5,14_6,14_7,14_8,14_9} @data -10.14223696457717 ,0.01254048559243616 ,0.4357614827468826 ,13.010144750817991 ,-0.01254048559243616 ,08_5, -10.115595009165439 , 0.0 ,0.433265930148359 ,13.00832193431444 , 0.0 ,09_0, -10.069206520828265 ,0.013010108066818708 ,0.4290106628067516 , 13.000881459331142 ,-0.013010108066818708 ,09_1, -10.053323843042925 , 0.0 ,0.427518527156048 , 12.999809313103185 , 0.0 ,09_1, -10.289068219060296 ,0.011679906623635335 ,0.4492797491334761 ,13.028926405386928 ,-0.011679906623635335 ,08_6, 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trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java 2006-06-27 08:45:28 UTC (rev 6521) +++ trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java 2006-06-28 11:41:10 UTC (rev 6522) @@ -32,7 +32,9 @@ import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; import org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor; +import org.openscience.cdk.qsar.descriptors.bond.ResonancePositiveChargeDescriptor; import org.openscience.cdk.qsar.model.weka.J48WModel; +import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.qsar.result.DoubleResult; import java.util.HashMap; @@ -170,6 +172,7 @@ atom.getSymbol().equals("S")|| atom.getSymbol().equals("O")|| atom.getSymbol().equals("P")){ + resultsH = calculateHeteroAtomDescriptor(container); path = "data/arff/HeteroAtom1.arff"; isTarget = true; @@ -177,12 +180,16 @@ }else if(targetType.equals(BondTarget)){ IBond bond = container.getBondAt(targetPosition); IAtom[] atoms = bond.getAtoms(); - if((bond.getOrder() == 2) && - (((atoms[0].getSymbol().equals("C")) &&( !atoms[1].getSymbol().equals("C")))|| - ((atoms[1].getSymbol().equals("C")) && (!atoms[0].getSymbol().equals("C"))))) { - resultsH = calculateCarbonylDescriptor(container); - path = "data/arff/Carbonyl1.arff"; - isTarget = true; + if((bond.getOrder() == 2)){ + if((atoms[0].getSymbol().equals("C")) && ( atoms[1].getSymbol().equals("C"))) { +// resultsH = calculatePiSystWithoutHeteroDescriptor(container); +// path = "data/arff/PiSystWithoutHetero.arff"; +// isTarget = true; + }else { + resultsH = calculateCarbonylDescriptor(container); + path = "data/arff/Carbonyl1.arff"; + isTarget = true; + } } } if(isTarget){ @@ -231,7 +238,7 @@ * @return Array with the values of the descriptors. */ private Double[][] calculateCarbonylDescriptor(IAtomContainer atomContainer) { - Double[][] results = new Double[1][5]; + Double[][] results = new Double[1][6]; Integer[] params = new Integer[1]; IBond bond = atomContainer.getBondAt(targetPosition); IAtom[] atoms = bond.getAtoms(); @@ -268,6 +275,56 @@ descriptor = new PartialSigmaChargeDescriptor(); descriptor.setParameters(params); results[0][4]= new Double(((DoubleResult)descriptor.calculate(atomContainer).getValue()).doubleValue()); + /*5*/ + descriptor = new ResonancePositiveChargeDescriptor(); + params[0] = new Integer(targetPosition); + descriptor.setParameters(params); + DoubleArrayResult dar = ((DoubleArrayResult)descriptor.calculate(atomContainer).getValue()); + double datT = (dar.get(0)+dar.get(1))/2; + results[0][5] = datT; + + } catch (CDKException e) { + e.printStackTrace(); + } + return results; + } + /** + * Calculate the necessary descriptors for pi systems without heteroatom + * + * @param atomContainer The IAtomContainer + * @return Array with the values of the descriptors. + */ + private Double[][] calculatePiSystWithoutHeteroDescriptor(IAtomContainer atomContainer) { + Double[][] results = new Double[1][5]; + Integer[] params = new Integer[1]; + IBond bond = atomContainer.getBondAt(targetPosition); + IAtom[] atoms = bond.getAtoms(); + int positionC = atomContainer.getAtomNumber(atoms[0]); + int positionX = atomContainer.getAtomNumber(atoms[1]); + try { + /*0*/ + IMolecularDescriptor descriptor = new SigmaElectronegativityDescriptor(); + params[0] = new Integer(positionC); + descriptor.setParameters(params); + results[0][0]= new Double(((DoubleResult)descriptor.calculate(atomContainer).getValue()).doubleValue()); + /*1*/ + descriptor = new PartialSigmaChargeDescriptor(); + descriptor.setParameters(params); + results[0][1]= new Double(((DoubleResult)descriptor.calculate(atomContainer).getValue()).doubleValue()); + /*2*/ + descriptor = new BondPartialSigmaChargeDescriptor(); + params[0] = new Integer(targetPosition); + descriptor.setParameters(params); + results[0][2]= new Double(((DoubleResult)descriptor.calculate(atomContainer).getValue()).doubleValue()); + /*3*/ + descriptor = new SigmaElectronegativityDescriptor(); + params[0] = new Integer(positionX); + descriptor.setParameters(params); + results[0][3]= new Double(((DoubleResult)descriptor.calculate(atomContainer).getValue()).doubleValue()); + /*4*/ + descriptor = new PartialSigmaChargeDescriptor(); + descriptor.setParameters(params); + results[0][4]= new Double(((DoubleResult)descriptor.calculate(atomContainer).getValue()).doubleValue()); } catch (CDKException e) { e.printStackTrace(); Modified: trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java 2006-06-27 08:45:28 UTC (rev 6521) +++ trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java 2006-06-28 11:41:10 UTC (rev 6522) @@ -101,7 +101,7 @@ descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 11.29; - assertEquals(result, resultAccordingNIST, 1.3); + assertEquals(result, resultAccordingNIST, 1.2); } /** * A unit test for JUnit with C-C-C-I @@ -124,7 +124,7 @@ descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 9.27; - assertEquals(result, resultAccordingNIST, 0.4); + assertEquals(result, resultAccordingNIST, 0.03); } /** * A unit test for JUnit with C-C-O @@ -169,7 +169,7 @@ descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 10.025; - assertEquals(result, resultAccordingNIST, 0.05); + assertEquals(result, resultAccordingNIST, 0.03); } /** * A unit test for JUnit with C-N-C @@ -215,7 +215,7 @@ descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 8.9; - assertEquals(result, resultAccordingNIST, 3.1); + assertEquals(result, resultAccordingNIST, 0.5); } /** * A unit test for JUnit with C-C-P-C-C @@ -283,7 +283,7 @@ descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 9.26; - assertEquals(result, resultAccordingNIST, 15); + assertEquals(result, resultAccordingNIST, 1.2); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <mig...@us...> - 2006-06-28 13:19:48
|
Revision: 6523 Author: miguelrojasch Date: 2006-06-28 06:19:30 -0700 (Wed, 28 Jun 2006) ViewCVS: http://svn.sourceforge.net/cdk/?rev=6523&view=rev Log Message: ----------- implementetion in IPAtomicDescriptor the possibility to calculate the ionization of double bond without added heteroatoms and Tests Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java Added Paths: ----------- trunk/cdk/src/data/arff/PySystWithoutHetero.arff Added: trunk/cdk/src/data/arff/PySystWithoutHetero.arff =================================================================== --- trunk/cdk/src/data/arff/PySystWithoutHetero.arff (rev 0) +++ trunk/cdk/src/data/arff/PySystWithoutHetero.arff 2006-06-28 13:19:30 UTC (rev 6523) @@ -0,0 +1,276 @@ +@relation PySystWithoutHetero +@attribute SE_1 numeric +@attribute SCH_1 numeric +@attribute SE_2 numeric +@attribute SCH_2 numeric +@attribute RES_c1 numeric +@attribute RES_c2 numeric +@attribute class {05_0,05_1,05_2,05_3,05_4,05_5,05_6,05_7,05_8,05_9,06_0,06_1,06_2,06_3,06_4,06_5,06_6,06_7,06_8,06_9,07_0,07_1,07_2,07_3,07_4,07_5,07_6,07_7,07_8,07_9,08_0,08_1,08_2,08_3,08_4,08_5,08_6,08_7,08_8,08_9,09_0,09_1,09_2,09_3,09_4,09_5,09_6,09_7,09_8,09_9,10_0,10_1,10_2,10_3,10_4,10_5,10_6,10_7,10_8,10_9,11_0,11_1,11_2,11_3,11_4,11_5,11_6,11_7,11_8,11_9,12_0,12_1,12_2,12_3,12_4,12_5,12_6,12_7,12_8,12_9,13_0,13_1,13_2,13_3,13_4,13_5,13_6,13_7,13_8,13_9,14_0,14_1,14_2,14_3,14_4,14_5,14_6,14_7,14_8,14_9} +@data + 7.989618076133143 , -0.08912810810949996 , 8.118275659390836 , -0.07497523502429623 , 0.0 , 0.0 ,08_4, + 7.991638041288278 , -0.08890538471160767 , 7.991638041288278 , -0.08890538471160767 , 0.0 , 0.0 ,08_8, + 7.991657321469534 , -0.08890325893945959 , 8.022184204338759 , -0.08553935846554848 , 0.0 , 0.0 ,08_7, + 8.0194974231284 , -0.08583527543085695 , 8.0194974231284 , -0.08583527543085695 , 0.0 , 0.0 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-0.10017519190924389 , 0.0 , 0.0 ,08_8, + 8.087808302809579 , -0.07832072635757308 , 7.987163346107584 , -0.08939879150477933 , 0.0 , 0.0 ,08_5, + 8.0194974231284 , -0.08583527543085695 , 8.0194974231284 , -0.08583527543085695 , 0.0 , 0.0 ,09_0, + 7.989034514222297 , -0.08919245533098699 , 7.989034514222297 , -0.08919245533098699 , 0.0 , 0.0 ,08_8, + 7.989034514222297 , -0.08919245533098699 , 7.989034514222297 , -0.08919245533098699 , 0.0 , 0.0 ,09_0, + 7.989034514222297 , -0.08919245533098699 , 7.989034514222297 , -0.08919245533098699 , 0.0 , 0.0 ,08_8, + 7.989034514222297 , -0.08919245533098699 , 7.989034514222297 , -0.08919245533098699 , 0.0 , 0.0 ,08_9, Modified: trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java 2006-06-28 11:41:10 UTC (rev 6522) +++ trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java 2006-06-28 13:19:30 UTC (rev 6523) @@ -182,9 +182,9 @@ IAtom[] atoms = bond.getAtoms(); if((bond.getOrder() == 2)){ if((atoms[0].getSymbol().equals("C")) && ( atoms[1].getSymbol().equals("C"))) { -// resultsH = calculatePiSystWithoutHeteroDescriptor(container); -// path = "data/arff/PiSystWithoutHetero.arff"; -// isTarget = true; + resultsH = calculatePiSystWithoutHeteroDescriptor(container); + path = "data/arff/PySystWithoutHetero.arff"; + isTarget = true; }else { resultsH = calculateCarbonylDescriptor(container); path = "data/arff/Carbonyl1.arff"; @@ -295,37 +295,42 @@ * @return Array with the values of the descriptors. */ private Double[][] calculatePiSystWithoutHeteroDescriptor(IAtomContainer atomContainer) { - Double[][] results = new Double[1][5]; + Double[][] results = new Double[1][6]; Integer[] params = new Integer[1]; IBond bond = atomContainer.getBondAt(targetPosition); IAtom[] atoms = bond.getAtoms(); int positionC = atomContainer.getAtomNumber(atoms[0]); int positionX = atomContainer.getAtomNumber(atoms[1]); try { - /*0*/ + /*0_1*/ IMolecularDescriptor descriptor = new SigmaElectronegativityDescriptor(); params[0] = new Integer(positionC); descriptor.setParameters(params); results[0][0]= new Double(((DoubleResult)descriptor.calculate(atomContainer).getValue()).doubleValue()); - /*1*/ + /*1_1*/ descriptor = new PartialSigmaChargeDescriptor(); descriptor.setParameters(params); results[0][1]= new Double(((DoubleResult)descriptor.calculate(atomContainer).getValue()).doubleValue()); - /*2*/ - descriptor = new BondPartialSigmaChargeDescriptor(); - params[0] = new Integer(targetPosition); - descriptor.setParameters(params); - results[0][2]= new Double(((DoubleResult)descriptor.calculate(atomContainer).getValue()).doubleValue()); - /*3*/ + + /*0_2*/ descriptor = new SigmaElectronegativityDescriptor(); params[0] = new Integer(positionX); descriptor.setParameters(params); - results[0][3]= new Double(((DoubleResult)descriptor.calculate(atomContainer).getValue()).doubleValue()); - /*4*/ + results[0][2]= new Double(((DoubleResult)descriptor.calculate(atomContainer).getValue()).doubleValue()); + /*1_2*/ descriptor = new PartialSigmaChargeDescriptor(); descriptor.setParameters(params); - results[0][4]= new Double(((DoubleResult)descriptor.calculate(atomContainer).getValue()).doubleValue()); + results[0][3]= new Double(((DoubleResult)descriptor.calculate(atomContainer).getValue()).doubleValue()); + /* */ + descriptor = new ResonancePositiveChargeDescriptor(); + params[0] = new Integer(targetPosition); + descriptor.setParameters(params); + DoubleArrayResult dar = ((DoubleArrayResult)descriptor.calculate(atomContainer).getValue()); + results[0][4] = dar.get(0); + results[0][5] = dar.get(1); + + } catch (CDKException e) { e.printStackTrace(); } Modified: trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java 2006-06-28 11:41:10 UTC (rev 6522) +++ trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java 2006-06-28 13:19:30 UTC (rev 6523) @@ -285,6 +285,52 @@ double resultAccordingNIST = 9.26; assertEquals(result, resultAccordingNIST, 1.2); } + /** + * A unit test for JUnit with CCCC=CCCCC + */ + public void testIPDescriptor_11() throws ClassNotFoundException, CDKException, java.lang.Exception{ + IMolecularDescriptor descriptor = new IPAtomicDescriptor(); + Object[] params = new Object[2]; + + SmilesParser sp = new SmilesParser(); + Molecule mol = sp.parseSmiles("CCCC=CCCCC"); + HydrogenAdder hAdder = new HydrogenAdder(); + hAdder.addExplicitHydrogensToSatisfyValency(mol); + + LonePairElectronChecker lpcheck = new LonePairElectronChecker(); + lpcheck.newSaturate(mol); + + params[0] = new Integer(3); + params[1] = IPAtomicDescriptor.BondTarget; + descriptor.setParameters(params); + double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); + double resultAccordingNIST = 8.80; + assertEquals(result, resultAccordingNIST, 0.05); + } + /** + * A unit test for JUnit with CC1CCC=C1 + */ + public void testIPDescriptor_12() throws ClassNotFoundException, CDKException, java.lang.Exception{ + IMolecularDescriptor descriptor = new IPAtomicDescriptor(); + Object[] params = new Object[2]; + + SmilesParser sp = new SmilesParser(); + Molecule mol = sp.parseSmiles("CC1CCC=C1"); + HydrogenAdder hAdder = new HydrogenAdder(); + hAdder.addExplicitHydrogensToSatisfyValency(mol); + + LonePairElectronChecker lpcheck = new LonePairElectronChecker(); + lpcheck.newSaturate(mol); + + params[0] = new Integer(4); + params[1] = IPAtomicDescriptor.BondTarget; + descriptor.setParameters(params); + double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); + double resultAccordingNIST = 8.95; + assertEquals(result, resultAccordingNIST, 0.11); + } + + } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <mig...@us...> - 2006-07-21 08:07:19
|
Revision: 6696 Author: miguelrojasch Date: 2006-07-21 01:07:09 -0700 (Fri, 21 Jul 2006) ViewCVS: http://svn.sourceforge.net/cdk/?rev=6696&view=rev Log Message: ----------- update table arff for prediction of Ionization potential. Modified Paths: -------------- trunk/cdk/src/data/arff/Carbonyl1.arff trunk/cdk/src/data/arff/HeteroAtom1.arff trunk/cdk/src/data/arff/PySystWithoutHetero.arff Modified: trunk/cdk/src/data/arff/Carbonyl1.arff =================================================================== --- trunk/cdk/src/data/arff/Carbonyl1.arff 2006-07-21 08:05:08 UTC (rev 6695) +++ trunk/cdk/src/data/arff/Carbonyl1.arff 2006-07-21 08:07:09 UTC (rev 6696) @@ -7,148 +7,147 @@ @attribute RES_c numeric @attribute class {05_0,05_1,05_2,05_3,05_4,05_5,05_6,05_7,05_8,05_9,06_0,06_1,06_2,06_3,06_4,06_5,06_6,06_7,06_8,06_9,07_0,07_1,07_2,07_3,07_4,07_5,07_6,07_7,07_8,07_9,08_0,08_1,08_2,08_3,08_4,08_5,08_6,08_7,08_8,08_9,09_0,09_1,09_2,09_3,09_4,09_5,09_6,09_7,09_8,09_9,10_0,10_1,10_2,10_3,10_4,10_5,10_6,10_7,10_8,10_9,11_0,11_1,11_2,11_3,11_4,11_5,11_6,11_7,11_8,11_9,12_0,12_1,12_2,12_3,12_4,12_5,12_6,12_7,12_8,12_9,13_0,13_1,13_2,13_3,13_4,13_5,13_6,13_7,13_8,13_9,14_0,14_1,14_2,14_3,14_4,14_5,14_6,14_7,14_8,14_9} @data - 10.14223696457717 , 0.01254048559243616 , 0.4357614827468826 , 13.010144750817991 , -0.01254048559243616 , 8.694842308483691 ,08_5, - 10.115595009165439 , 0.0 , 0.433265930148359 , 13.00832193431444 , 0.0 , 8.879729046328267 ,09_0, - 10.069206520828265 , 0.013010108066818708 , 0.4290106628067516 , 13.000881459331142 , -0.013010108066818708 , 9.169262273229904 ,09_1, - 10.053323843042925 , 0.0 , 0.427518527156048 , 12.999809313103185 , 0.0 , 9.288434798469119 ,09_1, - 10.289068219060296 , 0.011679906623635335 , 0.4492797491334761 , 13.028926405386928 , -0.011679906623635335 , 7.874971251625103 ,08_6, - 8.024100674579385 , 0.0 , 0.010091041816101959 , 8.282969831068904 , 0.0 , 101.77817428387631 ,09_7, - 10.026033886745763 , 0.0 , 0.42500423855023695 , 12.995791602861736 , 0.0 , 9.480488382024069 ,09_3, - 10.028586962263011 , 0.0 , 0.4252470668350704 , 12.995937410169796 , 0.0 , 9.462590984008926 ,09_3, - 10.06088316880118 , 0.0 , 0.4282373365521245 , 13.000243792786874 , 0.0 , 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0.029776309298128682 , 0.4337732812364117 , 13.008639340883757 , -0.029776309298128682 , 1.1132943143812708 ,08_7, + 10.055911639901261 , 0.030357734611010496 , 0.42776257636294873 , 12.999971749181361 , -0.030357734611010496 , 0.5566471571906354 ,09_5, + 9.954694393651287 , 0.012129439766988985 , 0.42059405438555525 , 12.954313548668747 , -0.012129439766988985 , 1.1132943143812708 ,09_7, + 10.023491774799673 , 0.03064733903964851 , 0.42476249588304227 , 12.995646836819134 , -0.03064733903964851 , 0.5566471571906354 ,09_5, + 11.062472836423165 , 0.02501169843462819 , 0.5142531869546936 , 13.207586338582468 , 0.0 , 0.0 ,08_6, + 10.159162238145829 , 0.015268920131677263 , 0.43723309549496436 , 13.015835854653117 , -0.015268920131677263 , 0.0 ,08_6, + 10.134791381391095 , 0.014547484547165925 , 0.43506706364309866 , 13.00957525069415 , -0.014547484547165925 , 0.44531772575250833 ,08_7, + 10.026131302572084 , 0.030515107355948482 , 0.4250128699354545 , 12.995793923392686 , -0.030515107355948482 , 0.5566471571906354 ,09_3, + 10.055967307696625 , 0.030348685666762635 , 0.42776899177711325 , 12.999956550128417 , -0.030348685666762635 , 0.5566471571906354 ,08_9, + 8.292339755779297 , 0.0442186107343548 , 0.01214340462182844 , 9.524856581933687 , -0.0442186107343548 , 0.0 ,09_3, + 8.664584353934035 , 0.030596785373637116 , 0.043915759033837175 , 9.601430568440042 , -0.030596785373637116 , 0.0 ,08_4, + 10.121080306105117 , 0.029762943246791854 , 0.43378292161867105 , 13.008642266718619 , -0.029762943246791854 , 1.1132943143812708 ,08_9, + 10.13310870928706 , 0.029076786272534016 , 0.4349156590665919 , 13.009268712659892 , 0.0 , 0.5566471571906354 ,08_9, + 10.058572486917585 , 0.030227923645947473 , 0.4280148374543625 , 13.000120722689314 , -0.030227923645947473 , 0.5566471571906354 ,09_3, + 9.957239332288003 , 0.01201179798358135 , 0.42083663635016666 , 12.95445845936819 , -0.01201179798358135 , 1.1132943143812708 ,09_5, + 10.050683727346291 , 0.030613003621118125 , 0.4272682875425977 , 12.999662117402675 , -0.030613003621118125 , 0.5566471571906354 ,09_3, + 9.95978667629054 , 0.011894269739974006 , 0.4210794291291332 , 12.954603513581901 , -0.011894269739974006 , 1.1132943143812708 ,09_5, + 10.05617011313598 , 0.030317058437990072 , 0.4277868483770628 , 12.999961301652252 , -0.030317058437990072 , 0.5566471571906354 ,09_0, Modified: trunk/cdk/src/data/arff/HeteroAtom1.arff =================================================================== --- trunk/cdk/src/data/arff/HeteroAtom1.arff 2006-07-21 08:05:08 UTC (rev 6695) +++ trunk/cdk/src/data/arff/HeteroAtom1.arff 2006-07-21 08:07:09 UTC (rev 6696) @@ -1,784 +1,786 @@ -@relation HeteroAtom1 -@attribute SE numeric -@attribute SCH numeric -@attribute EE numeric -@attribute class {05_0,05_1,05_2,05_3,05_4,05_5,05_6,05_7,05_8,05_9,06_0,06_1,06_2,06_3,06_4,06_5,06_6,06_7,06_8,06_9,07_0,07_1,07_2,07_3,07_4,07_5,07_6,07_7,07_8,07_9,08_0,08_1,08_2,08_3,08_4,08_5,08_6,08_7,08_8,08_9,09_0,09_1,09_2,09_3,09_4,09_5,09_6,09_7,09_8,09_9,10_0,10_1,10_2,10_3,10_4,10_5,10_6,10_7,10_8,10_9,11_0,11_1,11_2,11_3,11_4,11_5,11_6,11_7,11_8,11_9,12_0,12_1,12_2,12_3,12_4,12_5,12_6,12_7,12_8,12_9,13_0,13_1,13_2,13_3,13_4,13_5,13_6,13_7,13_8,13_9,14_0,14_1,14_2,14_3,14_4,14_5,14_6,14_7,14_8,14_9} -@data -8.358226088454181 ,-0.3058196694098954 ,7.764625000000002 ,07_7, -10.135709179671531 ,-0.13803220193332338 ,6.912343750000001 ,08_9, -10.529331185905713 ,-0.16821521283505064 ,5.755343750000001 ,09_1, -8.15693894385922 ,-0.3260278273836952 ,5.2763437500000006 ,08_4, -9.341246198368871 ,-0.3909609899878817 ,4.463343750000001 ,08_2, -8.59344661500769 ,-0.1739669663086838 , 6.999343750000001 ,08_8, -9.383054614828 ,-0.38742928835128587 ,5.624093750000002 ,08_3, -8.388337594005247 ,-0.3028061890826569 ,7.933875000000002 ,07_5, -8.70936821085626 ,-0.1605939270680286 ,7.5165000000000015 ,08_7, -9.505410020768332 ,-0.3771102857779075 ,6.359125000000002 ,09_2, -13.010144750817991 ,-0.2974206674616146 ,5.254343750000001 ,08_5, -8.448039755662744 ,-0.29683864817822053 ,9.559187500000002 ,07_8, -13.00832193431444 ,-0.2975555873562002 ,4.5505 ,09_0, -13.370802947844462 ,-0.19647643122972394 ,5.049132812500001 ,08_8, -8.387759922128712 ,-0.3028639777181398 ,8.852875000000003 ,07_0, - 8.503325955305005 ,-0.2913211199439496 ,9.106000000000002 ,08_3, -8.38804323034907 ,-0.3028356362638783 ,9.324437500000002 ,07_0, -8.390534868818051 ,-0.302586388321885 ,8.707750000000003 ,08_1, -10.925317017468707 ,-0.4026419182614658 ,5.974843750000001 ,09_6, -8.337583721562401 ,-0.30788693277501916 , 8.301687500000002 ,08_2, -9.57600033913808 ,-0.371168286161644 ,7.488687500000001 ,09_1, -10.090620192227325 ,-0.14290038299754748 ,6.657171875000001 ,09_0, -8.267354050528503 ,-0.31492893411152895 ,6.533843750000001 ,08_7, - 13.000881459331142 ,-0.29810632411110416 ,4.370421875 ,09_1, -8.375440038494302 ,-0.3040966399089681 ,7.791343750000002 ,07_6, -9.467108150525696 ,-0.380337840800761 ,6.141500000000002 ,09_1, -9.334113990576235 ,-0.39156376488915307 ,4.1649609375 ,08_1, -9.372084339436311 ,-0.38835570208422093 ,4.672125000000001 ,09_6, -10.529331203150011 ,-0.1682152111659219 , 5.7953906250000005 ,08_7, -9.418061256272665 ,-0.3844744067539614 ,6.252843750000002 ,08_0, -8.090240425386556 ,-0.332748715029036 ,3.5085000000000006 ,06_2, - 12.999809313103185 ,-0.29818568507654547 ,4.35103125 ,09_1, -13.028926405386928 ,-0.2960305744812244 ,5.36 ,08_6, -9.560638239820227 ,-0.37246070073301957 ,4.509125000000001 ,10_1, -10.087231504788887 ,-0.14326652486754932 ,6.087625000000001 ,10_1, -10.129672324522863 ,-0.13868360238142985 ,6.172000000000001 ,10_0, -10.217437422204354 ,-0.1292251775414925 ,5.9586250000000005 ,10_4, -8.551425415204589 ,-0.17882876313228188 ,6.174625000000001 ,09_2, -10.52258616894475 ,-0.16886814618629142 ,5.015000000000001 ,10_0, -9.210253787308913 ,-0.08510576598333318 ,8.377625 ,09_2, -8.117629296810437 ,-0.329987372350079 ,4.451625000000001 ,08_5, -8.151819836824801 ,-0.3265432167914418 ,4.536000000000001 ,09_4, -13.358909911994196 ,-0.1974837718942036 ,3.505625 ,11_8, -9.33386993320511 ,-0.39158439278397533 ,3.7230000000000003 ,09_6, -9.434243257393495 ,-0.38310918943815214 ,3.5096250000000007 ,10_4, -8.74648742325209 ,-0.15632374513612035 ,6.730750000000001 ,08_6, -8.387222851963761 ,-0.3029177054901521 ,5.636500000000002 ,09_2, -8.282969831068904 ,-0.07523725818032645 ,2.7727500000000003 ,09_7, -8.8060597543675 ,-0.14948263136960932 ,10.261500000000002 ,08_2, -8.593633233043601 ,-0.17394539167233006 ,7.371015625 ,08_0, - 12.995791602861736 ,-0.29848308251602246 ,3.9580625000000005 ,09_3, - 12.995937410169796 ,-0.2984722895145756 ,4.1152500000000005 ,09_3, - 8.30091434294074 ,-0.3115621216987585 ,7.281000000000002 ,07_6, -9.526852766593828 ,-0.37530445062054485 ,6.468000000000002 ,09_2, - 13.000243792786874 ,-0.29815352455321065 ,4.744000000000001 ,09_0, -10.121469424588476 ,-0.13956891990336917 ,7.115375000000001 ,09_8, -8.142501022640447 ,-0.3274816176347653 ,5.479375000000001 ,08_4, -9.323362428013741 ,-0.39247258909620514 ,4.666375000000001 ,10_0, - 12.999956550232218 ,-0.29817478646193946 , 4.1998750000000005 ,09_1, -8.281538469689297 ,-0.3135055572184893 ,6.821500000000002 ,07_9, - 12.995957565774757 ,-0.29847079754971173 ,4.05775 ,09_5, -10.087323152945537 ,-0.14325662194195762 ,6.244812500000001 ,10_1, -10.475438509039716 ,-0.1734356394424199 ,5.087812500000001 ,10_6, -8.11771505136608 ,-0.3299787298687019 ,4.608812500000001 ,08_7, -13.359026955562685 ,-0.19747385852488247 ,3.6628125000000002 ,11_8, -13.363094834344434 ,-0.1971293140776928 ,3.7050000000000005 ,10_2, -8.551508380827155 ,-0.1788191566779825 ,6.331812500000002 ,09_1, -8.251812643810032 ,-0.31648911714599687 ,6.023500000000002 ,07_9, -8.326175254070225 ,-0.30902995205679873 ,5.942500000000001 ,08_6, -9.46377744309678 ,-0.3806186224120376 ,5.017000000000001 ,09_4, - 8.702488299973192 ,-0.1613860263226812 ,7.553000000000002 ,08_6, - 12.995796231041266 ,-0.298482739927114 ,4.1152500000000005 ,09_2, - 12.9957939233456 ,-0.29848291074826067 ,4.075953125000001 ,09_2, -10.087324520674773 ,-0.143256474153916 ,6.3234062500000014 ,10_1, -8.117716175861895 ,-0.32997861654034977 ,4.68740625 ,09_3, -12.950438474714261 ,-0.30184062167553827 , 3.3959062500000003 ,09_7, -8.256984614790861 ,-0.3159698354342966 ,6.192750000000002 ,08_0, -8.26183120014585 ,-0.3154832902590167 ,7.281000000000002 ,07_8, - 12.995793923392641 ,-0.2984829107447786 , 4.095601562499999 ,09_4, -10.087324528938465 ,-0.1432564732609945 ,6.362703125 ,10_0, -8.117716180460109 ,-0.329978616076935 ,4.726703125000002 ,08_6, -9.285132568127938 ,-0.39570571347548694 ,3.913703125000001 ,10_3, -9.46351262389956 ,-0.38064094769984114 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[truncated message content] |
From: <mig...@us...> - 2006-07-21 08:37:47
|
Revision: 6698 Author: miguelrojasch Date: 2006-07-21 01:36:52 -0700 (Fri, 21 Jul 2006) ViewCVS: http://svn.sourceforge.net/cdk/?rev=6698&view=rev Log Message: ----------- improve for the prediction of ionization of potential. Modified Paths: -------------- trunk/cdk/src/data/arff/HeteroAtom1.arff trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java Modified: trunk/cdk/src/data/arff/HeteroAtom1.arff =================================================================== --- trunk/cdk/src/data/arff/HeteroAtom1.arff 2006-07-21 08:25:41 UTC (rev 6697) +++ trunk/cdk/src/data/arff/HeteroAtom1.arff 2006-07-21 08:36:52 UTC (rev 6698) @@ -197,7 +197,6 @@ 12.90081352345769 , -0.30551530746905936 , 2.2170000000000005 ,10_9, 9.724911223935267 , -0.3586605870999855 , 7.1016875000000015 ,08_6, 9.42219772630527 , -0.38412538604138846 , 4.581750000000001 ,09_6, - 7.617165405740187 , -0.38077857216722133 , 3.8955 ,null, 9.42219772630527 , -0.38412538604138846 , 4.581750000000001 ,06_5, 8.521991829091817 , -0.1822386933141923 , 5.2315000000000005 ,07_5, 9.56145195841657 , -0.3723922327265118 , 5.129500000000002 ,09_1, @@ -758,7 +757,6 @@ 8.300497253111853 , -0.31160394572218564 , 7.020468750000003 ,08_5, 13.009268712659892 , -0.29748550925318734 , 5.135312500000001 ,08_9, 8.376114053530067 , -0.3040291908461817 , 7.9097500000000025 ,08_0, - 7.524780042922308 , -0.3902332190189361 , 2.6380000000000003 ,null, 9.281832565711683 , -0.3959849121258387 , 3.324250000000001 ,10_4, 8.327659070694997 , -0.3088812676839582 , 7.123812500000002 ,08_3, 9.29646389260295 , -0.39474715961540285 , 3.731312500000001 ,09_6, Modified: trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java 2006-07-21 08:25:41 UTC (rev 6697) +++ trunk/cdk/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java 2006-07-21 08:36:52 UTC (rev 6698) @@ -38,7 +38,6 @@ import org.openscience.cdk.qsar.result.DoubleResult; import java.util.HashMap; -import java.util.Vector; /** * This class returns the ionization potential of an atom. It is Modified: trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java 2006-07-21 08:25:41 UTC (rev 6697) +++ trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/atomic/IPAtomicDescriptorTest.java 2006-07-21 08:36:52 UTC (rev 6698) @@ -78,7 +78,8 @@ descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 11.26; - assertEquals(result, resultAccordingNIST, 0.05); +// System.out.println(resultAccordingNIST+"="+result); + assertEquals(result, resultAccordingNIST, 0.02); } /** * A unit test for JUnit with C-C-Br @@ -101,7 +102,8 @@ descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 11.29; - assertEquals(result, resultAccordingNIST, 1.2); +// System.out.println(resultAccordingNIST+"="+result); + assertEquals(result, resultAccordingNIST, 1.05); } /** * A unit test for JUnit with C-C-C-I @@ -124,6 +126,7 @@ descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 9.27; +// System.out.println(resultAccordingNIST+"="+result); assertEquals(result, resultAccordingNIST, 0.03); } /** @@ -147,6 +150,7 @@ descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 10.48; +// System.out.println(resultAccordingNIST+"="+result); assertEquals(result, resultAccordingNIST, 0.05); }/** * A unit test for JUnit with C-O-C @@ -169,6 +173,7 @@ descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 10.025; +// System.out.println(resultAccordingNIST+"="+result); assertEquals(result, resultAccordingNIST, 0.03); } /** @@ -192,6 +197,7 @@ descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 8.24; +// System.out.println(resultAccordingNIST+"="+result); assertEquals(result, resultAccordingNIST, 3.1); } /** @@ -215,6 +221,7 @@ descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 8.9; +// System.out.println(resultAccordingNIST+"="+result); assertEquals(result, resultAccordingNIST, 0.5); } /** @@ -238,6 +245,7 @@ descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 8.5; +// System.out.println(resultAccordingNIST+"="+result); assertEquals(result, resultAccordingNIST, 0.4); } @@ -261,7 +269,8 @@ descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 9.15; - assertEquals(result, resultAccordingNIST, 1); +// System.out.println(resultAccordingNIST+"="+result); + assertEquals(result, resultAccordingNIST, 0.01); } /** * A unit test for JUnit with O=C1CCCC1 @@ -283,7 +292,8 @@ descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 9.26; - assertEquals(result, resultAccordingNIST, 1.2); +// System.out.println(resultAccordingNIST+"="+result); + assertEquals(result, resultAccordingNIST, 0.2); } /** * A unit test for JUnit with CCCC=CCCCC @@ -306,6 +316,7 @@ descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 8.80; +// System.out.println(resultAccordingNIST+"="+result); assertEquals(result, resultAccordingNIST, 0.05); } /** @@ -329,6 +340,7 @@ descriptor.setParameters(params); double result= ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(); double resultAccordingNIST = 8.95; +// System.out.println(resultAccordingNIST+"="+result); assertEquals(result, resultAccordingNIST, 0.11); } /** This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <mig...@us...> - 2006-09-07 12:24:53
|
Revision: 6839 http://svn.sourceforge.net/cdk/?rev=6839&view=rev Author: miguelrojasch Date: 2006-09-07 05:24:38 -0700 (Thu, 07 Sep 2006) Log Message: ----------- update of the files arff for prediction of Ionization potential Modified Paths: -------------- trunk/cdk/src/data/arff/Carbonyl1.arff trunk/cdk/src/data/arff/HeteroAtom1.arff trunk/cdk/src/data/arff/PySystWithoutHetero.arff Modified: trunk/cdk/src/data/arff/Carbonyl1.arff =================================================================== --- trunk/cdk/src/data/arff/Carbonyl1.arff 2006-09-06 13:29:01 UTC (rev 6838) +++ trunk/cdk/src/data/arff/Carbonyl1.arff 2006-09-07 12:24:38 UTC (rev 6839) @@ -7,147 +7,56 @@ @attribute RES_c numeric @attribute class {05_0,05_1,05_2,05_3,05_4,05_5,05_6,05_7,05_8,05_9,06_0,06_1,06_2,06_3,06_4,06_5,06_6,06_7,06_8,06_9,07_0,07_1,07_2,07_3,07_4,07_5,07_6,07_7,07_8,07_9,08_0,08_1,08_2,08_3,08_4,08_5,08_6,08_7,08_8,08_9,09_0,09_1,09_2,09_3,09_4,09_5,09_6,09_7,09_8,09_9,10_0,10_1,10_2,10_3,10_4,10_5,10_6,10_7,10_8,10_9,11_0,11_1,11_2,11_3,11_4,11_5,11_6,11_7,11_8,11_9,12_0,12_1,12_2,12_3,12_4,12_5,12_6,12_7,12_8,12_9,13_0,13_1,13_2,13_3,13_4,13_5,13_6,13_7,13_8,13_9,14_0,14_1,14_2,14_3,14_4,14_5,14_6,14_7,14_8,14_9} @data - 10.14223696457717 , 0.014375359490302008 , 0.4357614827468826 , 13.010144750817991 , -0.014375359490302008 , 0.15904204491161006 ,08_5, - 10.115595009165439 , 0.030036254484584527 , 0.433265930148359 , 13.00832193431444 , -0.030036254484584527 , 0.5566471571906354 ,09_0, - 10.069206520828265 , 0.014857098728605701 , 0.4290106628067516 , 13.000881459331142 , -0.014857098728605701 , 0.24739873652917127 ,09_1, - 10.053323843042925 , 0.030481383669501205 , 0.427518527156048 , 12.999809313103185 , -0.030481383669501205 , 0.5566471571906354 ,09_1, - 10.289068219060296 , 0.013502157885677749 , 0.4492797491334761 , 13.028926405386928 , -0.013502157885677749 , 0.2783235785953177 ,08_6, - 8.024100674579385 , 2.7920942192701776 , 0.010091041816101959 , 8.282969831068904 , -2.7920942192701776 , 1.1132943143812708 ,09_7, - 10.026033886745763 , 0.030529769766583607 , 0.42500423855023695 , 12.995791602861736 , -0.030529769766583607 , 0.5566471571906354 ,09_3, - 10.028586962263011 , 0.03041299881886391 , 0.4252470668350704 , 12.995937410169796 , -0.03041299881886391 , 0.5566471571906354 ,09_3, - 10.06088316880118 , 0.030144614857738592 , 0.4282373365521245 , 13.000243792786874 , -0.030144614857738592 , 0.5566471571906354 ,09_0, - 10.055967332703583 , 0.030348668878102468 , 0.4277689927875876 , 12.999956550232218 , -0.030348668878102468 , 0.5566471571906354 ,09_1, - 10.029157498089255 , 0.03034729622823242 , 0.42529884499824955 , 12.995957565774757 , 0.0 , 0.5566471571906354 ,09_5, - 10.026226269382743 , 0.030501470916229612 , 0.42502133901408096 , 12.995796231041266 , -0.030501470916229612 , 0.5566471571906354 ,09_2, - 10.026131291500178 , 0.030515114688239305 , 0.42501286947117667 , 12.9957939233456 , -0.030515114688239305 , 0.5566471571906354 ,09_2, - 9.930173557608919 , 0.012817585707726512 , 0.4183343038198407 , 12.950438474714261 , -0.012817585707726512 , 1.1132943143812708 ,09_7, - 10.026131302539845 , 0.03051510738634019 , 0.42501286993545445 , 12.995793923392641 , -0.03051510738634019 , 0.5566471571906354 ,09_4, - 9.930175120358061 , 0.012816988774519564 , 0.4183344171562495 , 12.950438490869567 , -0.012816988774519564 , 1.1132943143812708 ,09_6, - 9.930269786929722 , 0.012799247806622208 , 0.41834288452537216 , 12.950440789109889 , -0.012799247806622208 , 1.1132943143812708 ,09_8, - 10.026131302572116 , 0.030515107355948482 , 0.4250128699354545 , 12.995793923392686 , -0.030515107355948482 , 0.5566471571906354 ,09_2, - 10.115595009165439 , 0.030036254484584527 , 0.433265930148359 , 13.00832193431444 , -0.030036254484584527 , 0.5566471571906354 ,09_2, - 10.161012886890456 , 0.029206203441354068 , 0.4374720659446574 , 13.013618733609128 , 0.0 , 1.1132943143812708 ,08_9, - 10.093175912802899 , 0.029877742821928222 , 0.43120988170262076 , 13.004730990550904 , 0.0 , 0.44531772575250833 ,09_1, - 10.130420565550153 , 0.014703539540414276 , 0.43464956765354507 , 13.009509662915168 , -0.014703539540414276 , 0.2783235785953177 ,08_2, - 10.056223158166366 , 0.0303015206120995 , 0.42779090932452424 , 12.999962052752455 , -0.0303015206120995 , 0.5566471571906354 ,09_4, - 10.169935777442715 , 0.015000104391745329 , 0.43824978567891354 , 13.016434786438277 , -0.015000104391745329 , 0.0 ,08_8, - 10.055971030610777 , 0.030347303208813445 , 0.4277692513813015 , 12.99995658677092 , -0.030347303208813445 , 0.5566471571906354 ,09_2, - 9.973259897329552 , 0.005606373038410509 , 0.4223470979559885 , 12.955515112303287 , -0.005606373038410509 , 0.31808408982322023 ,09_3, - 9.957335322284623 , 0.011997685806357789 , 0.42084518672631427 , 12.95446076679854 , -0.011997685806357789 , 1.1132943143812708 ,09_7, - 10.055772282962447 , 0.030378004710248162 , 0.4277517285430902 , 12.999951904368778 , -0.030378004710248162 , 0.5566471571906354 ,09_1, - 9.92754062805054 , 0.013071664412142876 , 0.4180837415240912 , 12.950291928624345 , -0.013071664412142876 , 1.1132943143812708 ,09_9, - 9.930078014775631 , 0.012835833767728087 , 0.41832578768406464 , 12.95043617980971 , -0.012835833767728087 , 1.1132943143812708 ,09_8, - 10.142807937791822 , 0.030011821928424186 , 0.4357628952054311 , 13.012378470845295 , -0.030011821928424186 , 1.1132943143812708 ,08_8, - 9.933408114349119 , 0.006233196055761297 , 0.41863947133275675 , 12.950606489422318 , -0.006233196055761297 , 1.1132943143812708 ,08_7, - 10.061278633795576 , 0.030084697459071844 , 0.4282722902016855 , 13.000253175940621 , -0.030084697459071844 , 0.5566471571906354 ,09_2, - 10.115588034599794 , 0.03003874029383303 , 0.43326543642377513 , 13.008321864004165 , -0.03003874029383303 , 0.5566471571906354 ,08_9, - 10.130207417295116 , 0.029440164141601142 , 0.4346308632030557 , 13.009504685757793 , 0.0 , 0.37109810479375693 ,09_4, - 10.140052817044495 , 0.028576883462660692 , 0.43556173359696315 , 13.009606961581559 , -0.028576883462660692 , 0.5566471571906354 ,08_4, - 10.055967307696625 , 0.030348685666762635 , 0.42776899177711325 , 12.999956550128417 , -0.030348685666762635 , 0.5566471571906354 ,09_1, - 10.082983412577843 , 0.0303435529440055 , 0.43025194925072874 , 13.004018826299452 , -0.0303435529440055 , 1.1132943143812708 ,09_3, - 9.92754062805054 , 0.006535832206071438 , 0.4180837415240912 , 12.950291928624345 , -0.006535832206071438 , 1.1132943143812708 ,06_6, - 8.62389914739769 , 0.0 , 0.2949283947611918 , 9.43958855008736 , 0.0 , 0.0 ,09_4, - 9.93272238263547 , 0.012581947984459784 , 0.41857748244814413 , 12.950583776873179 , -0.012581947984459784 , 1.1132943143812708 ,09_9, - 10.08593145065085 , 0.030173234339375903 , 0.4305295116352289 , 13.004174547877533 , -0.030173234339375903 , 1.1132943143812708 ,08_8, - 10.11855349506123 , 0.029863898585237445 , 0.43354409984582676 , 13.0084782204764 , -0.029863898585237445 , 0.5566471571906354 ,08_8, - 9.041208694495825 , 0.02957934693745509 , 0.07528760613858912 , 9.681268874166234 , -0.02957934693745509 , 0.0 ,08_8, - 10.090790269187131 , 0.02997643947100667 , 0.43099519952033744 , 13.00442807105895 , -0.02997643947100667 , 0.5566471571906354 ,09_8, - 9.930286550112157 , 0.006397125914174465 , 0.41834422220143047 , 12.950441064567892 , -0.006397125914174465 , 1.1132943143812708 ,08_8, - 10.936332825006174 , -0.03623180605148446 , 0.502853388245659 , 13.19310619257268 , 0.0 , 0.0 ,08_8, - 9.959982015805766 , 0.011864968824332646 , 0.42109677559156755 , 12.95460816618311 , -0.011864968824332646 , 1.1132943143812708 ,09_6, - 8.62389914739769 , 0.016985397312086703 , 0.2949283947611918 , 9.43958855008736 , -0.016985397312086703 , 0.0 ,09_8, - 10.08021706834077 , 0.03049174298431059 , 0.4299908127153823 , 13.00386781343683 , -0.03049174298431059 , 1.1132943143812708 ,09_0, - 8.724789389490919 , 0.04998312302408295 , 0.30277695935678 , 9.472589693963172 , -0.04998312302408295 , 1.1132943143812708 ,10_1, - 10.12867558176142 , 0.029450035205618265 , 0.4344925709285653 , 13.009251820011245 , 0.0 , 0.44531772575250833 ,08_9, - 10.026243091948466 , 0.015248561062802896 , 0.4250226774380089 , 12.99579650765508 , -0.015248561062802896 , 0.5566471571906354 ,09_0, - 10.053252980504885 , 0.030491812852840226 , 0.42751079985426077 , 12.999823754552924 , -0.030491812852840226 , 0.5566471571906354 ,09_2, - 10.029370949525912 , 0.015156708797084984 , 0.42531760342201974 , 12.995962527192663 , -0.015156708797084984 , 0.5566471571906354 ,09_0, - 10.085960212257511 , 0.030165128555503552 , 0.430534822617881 , 13.00414225042995 , -0.030165128555503552 , 0.5566471571906354 ,08_9, - 9.962344977474677 , 0.0117775377633666 , 0.4213233094708757 , 12.954749610043388 , -0.0117775377633666 , 1.1132943143812708 ,09_4, - 10.088422622911224 , 0.030062073910407657 , 0.43076912487793495 , 13.004286007216503 , -0.030062073910407657 , 0.5566471571906354 ,09_0, - 9.935185475022818 , 0.012364929987177408 , 0.41881312744105736 , 12.95072779198975 , -0.012364929987177408 , 1.1132943143812708 ,09_6, - 10.088531288121494 , 0.030047660258066544 , 0.43077878460175023 , 13.004289064376238 , -0.030047660258066544 , 0.5566471571906354 ,09_0, - 9.900329262065231 , 0.007183975223245206 , 0.4155644081063608 , 12.946287204169645 , -0.007183975223245206 , 1.1132943143812708 ,08_0, - 10.029252767276528 , 0.030332979616527683 , 0.42530728509744836 , 12.995959834606943 , 0.0 , 0.5566471571906354 ,09_4, - 10.138359961854515 , 0.028777187193696506 , 0.43540893696499294 , 13.009552556580147 , -0.028777187193696506 , 0.5566471571906354 ,09_3, - 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1.1132943143812708 ,09_6, + 8.62063866107877 , 0.043010916779213544 , 0.2972630726633395 , 9.43356304720823 , -0.043010916779213544 , 0.0 ,09_8, + 10.076984611518249 , 0.039719218593216386 , 0.43300469432625466 , 12.99041718716767 , -0.039719218593216386 , 1.1132943143812708 ,09_0, + 8.721454071890493 , 0.04136841470209696 , 0.3051151309200609 , 9.466613032136298 , -0.04136841470209696 , 1.1132943143812708 ,10_1, + 10.124481702629478 , 0.03990659328852543 , 0.43742496538944226 , 12.995688719197835 , -0.03990659328852543 , 0.44531772575250833 ,08_9, + 10.0230 \ No newline at end of file Modified: trunk/cdk/src/data/arff/HeteroAtom1.arff =================================================================== --- trunk/cdk/src/data/arff/HeteroAtom1.arff 2006-09-06 13:29:01 UTC (rev 6838) +++ trunk/cdk/src/data/arff/HeteroAtom1.arff 2006-09-07 12:24:38 UTC (rev 6839) @@ -5,84 +5,84 @@ @attribute class {05_0,05_1,05_2,05_3,05_4,05_5,05_6,05_7,05_8,05_9,06_0,06_1,06_2,06_3,06_4,06_5,06_6,06_7,06_8,06_9,07_0,07_1,07_2,07_3,07_4,07_5,07_6,07_7,07_8,07_9,08_0,08_1,08_2,08_3,08_4,08_5,08_6,08_7,08_8,08_9,09_0,09_1,09_2,09_3,09_4,09_5,09_6,09_7,09_8,09_9,10_0,10_1,10_2,10_3,10_4,10_5,10_6,10_7,10_8,10_9,11_0,11_1,11_2,11_3,11_4,11_5,11_6,11_7,11_8,11_9,12_0,12_1,12_2,12_3,12_4,12_5,12_6,12_7,12_8,12_9,13_0,13_1,13_2,13_3,13_4,13_5,13_6,13_7,13_8,13_9,14_0,14_1,14_2,14_3,14_4,14_5,14_6,14_7,14_8,14_9} @data 8.358226088454181 , -0.3058196694098954 , 7.764625000000002 ,07_7, - 10.135709179671531 , -0.13803220193332338 , 6.912343750000001 ,08_9, - 10.529331185905713 , -0.16821521283505064 , 5.755343750000001 ,09_1, - 8.15693894385922 , -0.3260278273836952 , 5.2763437500000006 ,08_4, - 9.341246198368871 , -0.3909609899878817 , 4.463343750000001 ,08_2, - 8.59344661500769 , -0.1739669663086838 , 6.999343750000001 ,08_8, - 9.383054614828 , -0.38742928835128587 , 5.624093750000002 ,08_3, + 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