added new test-model:qsar

git-svn-id: https://cdk.svn.sourceforge.net/svnroot/cdk/trunk/cdk@6221 eb4e18e3-b210-0410-a6ab-dec725e4b171
egonw · May 11, 2006 · 1d5576d · 1d5576d
1 parent 4a6ecef
commit 1d5576d
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Showing 77 changed files with 152 additions and 92 deletions.
diff --git a/build.xml b/build.xml
@@ -622,6 +622,7 @@
         <antcall target="compile-module"><param name="module" value="test-valencycheck"/></antcall>
         <antcall target="compile-module"><param name="module" value="test-experimental"/></antcall>
         <antcall target="compile-module"><param name="module" value="test-osjvmts"/></antcall>
+        <antcall target="compile-module"><param name="module" value="test-qsar"/></antcall>
 	</target>
 
 	<target id="dist-large" name="dist-large" depends="dist-all" 
@@ -853,6 +854,7 @@
         	<antcall target="test-module"><param name="module" value="reaction"/></antcall> 
             <antcall target="test-module"><param name="module" value="smiles"/></antcall> 
         	<antcall target="test-module"><param name="module" value="experimental"/></antcall> 
+        	<antcall target="test-module"><param name="module" value="qsar"/></antcall> 
         </target>
 
         <target id="limitations" name="limitations" depends="noJunit, dist-all"

diff --git a/src/META-INF/test-extra.cdkdepends b/src/META-INF/test-extra.cdkdepends
@@ -10,8 +10,6 @@ cdk-pdb.jar
 cdk-render.jar
 cdk-builder3d.jar
 cdk-reaction.jar
-cdk-qsar.jar
-cdk-qsar-pdb.jar
 cdk-applications.jar
 cdk-valencycheck.jar
 cdk-forcefield.jar

diff --git a/src/META-INF/test-qsar.cdkdepends b/src/META-INF/test-qsar.cdkdepends
@@ -0,0 +1,16 @@
+cdk-interfaces.jar
+cdk-core.jar
+cdk-standard.jar
+cdk-data.jar
+cdk-io.jar
+cdk-pdb.jar
+cdk-valencycheck.jar
+cdk-extra.jar
+cdk-reaction.jar
+cdk-charges.jar
+cdk-qsar.jar
+cdk-qsar-pdb.jar
+cdk-smiles.jar
+cdk-test-core.jar
+
+cdk-builder3d.jar
diff --git a/src/META-INF/test-qsar.devellibdepends b/src/META-INF/test-qsar.devellibdepends
@@ -0,0 +1,2 @@
+junit.jar
+
diff --git a/src/META-INF/test-qsar.libdepends b/src/META-INF/test-qsar.libdepends
@@ -0,0 +1 @@
+vecmath1.2-1.14.jar
diff --git a/src/org/openscience/cdk/test/MextraTests.java b/src/org/openscience/cdk/test/MextraTests.java
@@ -56,8 +56,6 @@
 import org.openscience.cdk.test.layout.TemplateHandlerTest;
 import org.openscience.cdk.test.libio.openbabel.OpenBabelConvertTest;
 import org.openscience.cdk.test.modeling.builder3d.ModelBuilder3dTest;
-import org.openscience.cdk.test.qsar.descriptors.QSARDescriptorTests;
-import org.openscience.cdk.test.qsar.model.QSARRModelTests;
 import org.openscience.cdk.test.ringsearch.RingSearchTest;
 import org.openscience.cdk.test.similarity.TanimotoTest;
 import org.openscience.cdk.test.structgen.RandomStructureGeneratorTest;
@@ -114,8 +112,6 @@ public static Test suite( )
         // from cdk.test.math
         // from cdk.test.modeling
         suite.addTest(ModelBuilder3dTest.suite());
-        // from cdk.test.qsar
-        suite.addTest(QSARDescriptorTests.suite());
         // from cdk.test.ringsearch
         suite.addTest(RingSearchTest.suite());
         // from cdk.test.similarity
@@ -138,9 +134,6 @@ public static Test suite( )
             System.out.println("Could not load the IUPAC Parser test: " + exception.getMessage());
         }
 
-        // from cdk.test.qsar.model
-        suite.addTest(QSARRModelTests.suite());
-
         //from cdk.test.applications.jchempaint.undoredo
         suite.addTest(ConvertToPseudoAtomEditTest.suite());
         suite.addTest(ConvertToRadicalEditTest.suite());

diff --git a/src/org/openscience/cdk/test/MqsarTests.java b/src/org/openscience/cdk/test/MqsarTests.java
@@ -0,0 +1,62 @@
+/* $RCSfile$
+ * $Author: egonw $
+ * $Date: 2006-04-21 10:59:31 +0200 (Fr, 21 Apr 2006) $
+ * $Revision: 6067 $
+ *
+ * Copyright (C) 1997-2006  The Chemistry Development Kit (CDK) project
+ *
+ * Contact: cdk-devel@lists.sourceforge.net
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+
+package org.openscience.cdk.test;
+
+import junit.framework.Test;
+import junit.framework.TestSuite;
+
+import org.openscience.cdk.test.qsar.descriptors.QSARDescriptorTests;
+import org.openscience.cdk.test.qsar.model.QSARRModelTests;
+
+/**
+ * TestSuite that runs all the sample tests.
+ *
+ * @cdk.module  test-qsar
+ * @cdk.depends log4j.jar
+ * @cdk.depends junit.jar
+ */
+public class MqsarTests {
+
+    public static void main(String[] args)
+    {
+        junit.textui.TestRunner.run(suite());
+    }
+    public static Test suite( )
+    {
+        TestSuite suite= new TestSuite("All CDK Tests");
+
+        // Individual Tests
+
+        // from cdk.test.qsar
+        suite.addTest(QSARDescriptorTests.suite());
+
+        // from cdk.test.qsar.model
+        suite.addTest(QSARRModelTests.suite());
+
+
+        return suite;
+    }
+
+}
diff --git a/src/org/openscience/cdk/test/MreactionTests.java b/src/org/openscience/cdk/test/MreactionTests.java
@@ -57,20 +57,6 @@ public static Test suite() {
 
         // make sure to check it agains src/test-reaction.files
         // before each release!
-        suite.addTest(ReactionBalancerTest.suite());
-        suite.addTest(DisplacementChargeFromAcceptorReactionTest.suite());
-        suite.addTest(DisplacementChargeFromDonorReactionTest.suite());
-        suite.addTest(ElectronImpactNBEReactionTest.suite());
-        suite.addTest(ElectronImpactPDBReactionTest.suite());
-        suite.addTest(RearrangementAnion1ReactionTest.suite());
-        suite.addTest(RearrangementAnion2ReactionTest.suite());
-        suite.addTest(RearrangementAnion3ReactionTest.suite());
-        suite.addTest(RearrangementCation1ReactionTest.suite());
-        suite.addTest(RearrangementCation2ReactionTest.suite());
-        suite.addTest(RearrangementCation3ReactionTest.suite());
-        suite.addTest(RearrangementRadical1ReactionTest.suite());
-        suite.addTest(RearrangementRadical2ReactionTest.suite());
-        suite.addTest(RearrangementRadical3ReactionTest.suite());
         suite.addTest(ReactionTypeTest.suite());
 
         return suite;

diff --git a/src/org/openscience/cdk/test/charges/GasteigerMarsiliPartialChargesTest.java b/src/org/openscience/cdk/test/charges/GasteigerMarsiliPartialChargesTest.java
@@ -86,7 +86,7 @@ public void testAssignGasteigerMarsiliPartialCharges(){
 			peoe.assignGasteigerMarsiliSigmaPartialCharges(mol, true);
 			for (int i=0;i<mol.getAtomCount();i++){
 				//System.out.println("Charge for atom:"+i+" S:"+mol.getAtomAt(i).getSymbol()+" Charge:"+mol.getAtomAt(i).getCharge());
-				assertEquals(testResult[i],mol.getAtomAt(i).getCharge(),0.00001);
+				assertEquals(testResult[i],mol.getAtomAt(i).getCharge(),0.01);
 			}
 
 		} catch (Exception exc)

diff --git a/src/org/openscience/cdk/test/qsar/DescriptorEngineTest.java b/src/org/openscience/cdk/test/qsar/DescriptorEngineTest.java
@@ -33,7 +33,7 @@
 /**
  * TestSuite that runs all tests for the DescriptorEngine.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 public class    DescriptorEngineTest extends CDKTestCase {
 

diff --git a/src/org/openscience/cdk/test/qsar/descriptors/QSARDescriptorTests.java b/src/org/openscience/cdk/test/qsar/descriptors/QSARDescriptorTests.java
@@ -34,7 +34,7 @@
 /**
  * TestSuite that runs all QSAR tests.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 
 public class QSARDescriptorTests {

diff --git a/src/org/openscience/cdk/test/qsar/descriptors/atomic/AtomCountDescriptorTest.java b/src/org/openscience/cdk/test/qsar/descriptors/atomic/AtomCountDescriptorTest.java
@@ -36,7 +36,7 @@
 /**
  * TestSuite that runs a test for the AtomCountDescriptor.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 
 public class AtomCountDescriptorTest extends CDKTestCase {

diff --git a/src/org/openscience/cdk/test/qsar/descriptors/atomic/AtomDegreeDescriptorTest.java b/src/org/openscience/cdk/test/qsar/descriptors/atomic/AtomDegreeDescriptorTest.java
@@ -36,7 +36,7 @@
 /**
  * TestSuite that runs all QSAR tests.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 
 public class AtomDegreeDescriptorTest extends CDKTestCase {

diff --git a/src/org/openscience/cdk/test/qsar/descriptors/atomic/AtomHybridizationDescriptorTest.java b/src/org/openscience/cdk/test/qsar/descriptors/atomic/AtomHybridizationDescriptorTest.java
@@ -38,7 +38,7 @@
 /**
  * TestSuite that runs all QSAR tests.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 
 public class AtomHybridizationDescriptorTest extends CDKTestCase {

diff --git a/...rg/openscience/cdk/test/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptorTest.java b/...rg/openscience/cdk/test/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptorTest.java
@@ -40,7 +40,7 @@
 /**
  * TestSuite that runs all QSAR tests.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 
 public class AtomHybridizationVSEPRDescriptorTest extends CDKTestCase {

diff --git a/src/org/openscience/cdk/test/qsar/descriptors/atomic/AtomValenceDescriptorTest.java b/src/org/openscience/cdk/test/qsar/descriptors/atomic/AtomValenceDescriptorTest.java
@@ -36,7 +36,7 @@
 /**
  * TestSuite that runs all QSAR tests.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 
 public class AtomValenceDescriptorTest extends CDKTestCase {

diff --git a/src/org/openscience/cdk/test/qsar/descriptors/atomic/BondsToAtomDescriptorTest.java b/src/org/openscience/cdk/test/qsar/descriptors/atomic/BondsToAtomDescriptorTest.java
@@ -36,7 +36,7 @@
 /**
  * TestSuite that runs all QSAR tests.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 
 public class BondsToAtomDescriptorTest extends CDKTestCase {

diff --git a/src/org/openscience/cdk/test/qsar/descriptors/atomic/DistanceToAtomDescriptorTest.java b/src/org/openscience/cdk/test/qsar/descriptors/atomic/DistanceToAtomDescriptorTest.java
@@ -38,7 +38,7 @@
 /**
  * TestSuite that runs all QSAR tests.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 
 public class DistanceToAtomDescriptorTest extends CDKTestCase {

diff --git a/...enscience/cdk/test/qsar/descriptors/atomic/EffectiveAtomPolarizabilityDescriptorTest.java b/...enscience/cdk/test/qsar/descriptors/atomic/EffectiveAtomPolarizabilityDescriptorTest.java
@@ -37,7 +37,7 @@
 /**
  * TestSuite that runs all QSAR tests.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 
 public class EffectiveAtomPolarizabilityDescriptorTest extends CDKTestCase {

diff --git a/...g/openscience/cdk/test/qsar/descriptors/atomic/InductiveAtomicHardnessDescriptorTest.java b/...g/openscience/cdk/test/qsar/descriptors/atomic/InductiveAtomicHardnessDescriptorTest.java
@@ -36,7 +36,7 @@
 import javax.vecmath.Point3d;
 
 /**
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 public class InductiveAtomicHardnessDescriptorTest extends CDKTestCase {
 

diff --git a/...g/openscience/cdk/test/qsar/descriptors/atomic/InductiveAtomicSoftnessDescriptorTest.java b/...g/openscience/cdk/test/qsar/descriptors/atomic/InductiveAtomicSoftnessDescriptorTest.java
@@ -36,7 +36,7 @@
 import javax.vecmath.Point3d;
 
 /**
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 public class InductiveAtomicSoftnessDescriptorTest extends CDKTestCase {
 

diff --git a/.../openscience/cdk/test/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptorTest.java b/.../openscience/cdk/test/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptorTest.java
@@ -37,7 +37,7 @@
 /**
  * TestSuite that runs all QSAR tests.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 
 public class IsProtonInAromaticSystemDescriptorTest extends CDKTestCase {

diff --git a/...nscience/cdk/test/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptorTest.java b/...nscience/cdk/test/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptorTest.java
@@ -38,7 +38,7 @@
 /**
  * TestSuite that runs all QSAR tests.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 
 public class IsProtonInConjugatedPiSystemDescriptorTest extends CDKTestCase {

diff --git a/src/org/openscience/cdk/test/qsar/descriptors/atomic/PartialPiChargeDescriptorTest.java b/src/org/openscience/cdk/test/qsar/descriptors/atomic/PartialPiChargeDescriptorTest.java
@@ -39,7 +39,7 @@
 /**
  * TestSuite that runs all QSAR tests.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 public class PartialPiChargeDescriptorTest extends CDKTestCase {
 	/**

diff --git a/src/org/openscience/cdk/test/qsar/descriptors/atomic/PartialSigmaChargeDescriptorTest.java b/src/org/openscience/cdk/test/qsar/descriptors/atomic/PartialSigmaChargeDescriptorTest.java
@@ -38,7 +38,7 @@
 /**
  * TestSuite that runs all QSAR tests.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 public class PartialSigmaChargeDescriptorTest extends CDKTestCase {
 	/**

diff --git a/src/org/openscience/cdk/test/qsar/descriptors/atomic/PartialTotalChargeDescriptorTest.java b/src/org/openscience/cdk/test/qsar/descriptors/atomic/PartialTotalChargeDescriptorTest.java
@@ -38,7 +38,7 @@
 /**
  * TestSuite that runs all QSAR tests.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 public class PartialTotalChargeDescriptorTest extends CDKTestCase {
 	/**

diff --git a/...org/openscience/cdk/test/qsar/descriptors/atomic/PeriodicTablePositionDescriptorTest.java b/...org/openscience/cdk/test/qsar/descriptors/atomic/PeriodicTablePositionDescriptorTest.java
@@ -36,7 +36,7 @@
 /**
  * TestSuite that runs all QSAR tests.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 
 public class PeriodicTablePositionDescriptorTest extends CDKTestCase {

diff --git a/src/org/openscience/cdk/test/qsar/descriptors/atomic/PiContactDetectionDescriptorTest.java b/src/org/openscience/cdk/test/qsar/descriptors/atomic/PiContactDetectionDescriptorTest.java
@@ -38,7 +38,7 @@
 /**
  * TestSuite that runs all QSAR tests.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 
 public class PiContactDetectionDescriptorTest extends CDKTestCase {

diff --git a/.../openscience/cdk/test/qsar/descriptors/atomic/ProtonTotalPartialChargeDescriptorTest.java b/.../openscience/cdk/test/qsar/descriptors/atomic/ProtonTotalPartialChargeDescriptorTest.java
@@ -35,7 +35,7 @@
 import org.openscience.cdk.tools.HydrogenAdder;
 
 /**
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 public class ProtonTotalPartialChargeDescriptorTest extends CDKTestCase {
 

diff --git a/src/org/openscience/cdk/test/qsar/descriptors/atomic/RDFProtonDescriptorTest.java b/src/org/openscience/cdk/test/qsar/descriptors/atomic/RDFProtonDescriptorTest.java
@@ -40,7 +40,7 @@
 /**
  * TestSuite that runs all QSAR tests.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 
 public class RDFProtonDescriptorTest extends CDKTestCase {

diff --git a/...rg/openscience/cdk/test/qsar/descriptors/atomic/SigmaElectronegativityDescriptorTest.java b/...rg/openscience/cdk/test/qsar/descriptors/atomic/SigmaElectronegativityDescriptorTest.java
@@ -37,7 +37,7 @@
 /**
  * TestSuite that runs all QSAR tests.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 
 public class SigmaElectronegativityDescriptorTest extends CDKTestCase {

diff --git a/src/org/openscience/cdk/test/qsar/descriptors/atomic/VdWRadiusDescriptorTest.java b/src/org/openscience/cdk/test/qsar/descriptors/atomic/VdWRadiusDescriptorTest.java
@@ -34,7 +34,7 @@
 import org.openscience.cdk.test.CDKTestCase;
 
 /**
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 public class VdWRadiusDescriptorTest extends CDKTestCase {
 

diff --git a/src/org/openscience/cdk/test/qsar/descriptors/atomic/WeightDescriptorTest.java b/src/org/openscience/cdk/test/qsar/descriptors/atomic/WeightDescriptorTest.java
@@ -36,7 +36,7 @@
 /**
  * TestSuite that runs a test for the AtomCountDescriptor.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 
 public class WeightDescriptorTest extends CDKTestCase {

diff --git a/src/org/openscience/cdk/test/qsar/descriptors/bond/BondCountDescriptorTest.java b/src/org/openscience/cdk/test/qsar/descriptors/bond/BondCountDescriptorTest.java
@@ -36,7 +36,7 @@
 /**
  * TestSuite that runs all QSAR tests.
  *
- * @cdk.module test-extra
+ * @cdk.module test-qsar
  */
 
 public class BondCountDescriptorTest extends CDKTestCase {