clear the conflicts between charges and reactions

git-svn-id: https://cdk.svn.sourceforge.net/svnroot/cdk/trunk/cdk@6214 eb4e18e3-b210-0410-a6ab-dec725e4b171
egonw · May 10, 2006 · 3bdf862 · 3bdf862
1 parent ea81af7
commit 3bdf862
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Showing 5 changed files with 10 additions and 8 deletions.
diff --git a/build.xml b/build.xml
@@ -592,16 +592,16 @@
             <antcall target="compile-module"><param name="module" value="pdb"/></antcall>
             <antcall target="compile-module"><param name="module" value="valencycheck"/></antcall>
             <antcall target="compile-module"><param name="module" value="extra"/></antcall>
-	    <antcall target="compile-module"><param name="module" value="charges"/></antcall>
             <antcall target="compile-module"><param name="module" value="smiles"/></antcall>
             <antcall target="compile-module"><param name="module" value="libio-cml"/></antcall>
             <antcall target="compile-module"><param name="module" value="pdb-cml"/></antcall>
+            <antcall target="compile-module"><param name="module" value="reaction"/></antcall>
+    	    <antcall target="compile-module"><param name="module" value="charges"/></antcall>
             <antcall target="compile-module"><param name="module" value="qsar"/></antcall>
             <antcall target="compile-module"><param name="module" value="qsar-cml"/></antcall>
             <antcall target="compile-module"><param name="module" value="qsar-pdb"/></antcall>
             <antcall target="compile-module"><param name="module" value="forcefield"/></antcall>
             <antcall target="compile-module"><param name="module" value="builder3d"/></antcall>
-            <antcall target="compile-module"><param name="module" value="reaction"/></antcall>
             <antcall target="compile-module"><param name="module" value="svg"/></antcall>
             <antcall target="compile-module"><param name="module" value="experimental"/></antcall>
             <antcall target="compile-module"><param name="module" value="applications"/></antcall>

diff --git a/src/META-INF/charges.cdkdepends b/src/META-INF/charges.cdkdepends
@@ -4,3 +4,4 @@ cdk-extra.jar
 cdk-interfaces.jar
 cdk-io.jar
 cdk-standard.jar
+cdk-reaction.jar
diff --git a/src/META-INF/qsar.cdkdepends b/src/META-INF/qsar.cdkdepends
@@ -4,4 +4,5 @@ cdk-core.jar
 cdk-standard.jar
 cdk-valencycheck.jar
 cdk-extra.jar
+cdk-reaction.jar
 cdk-charges.jar
diff --git a/src/org/openscience/cdk/test/tools/StructureResonanceGeneratorTest.java b/src/org/openscience/cdk/test/tools/StructureResonanceGeneratorTest.java
@@ -225,7 +225,7 @@ public void testGetStructures2() throws ClassNotFoundException, CDKException, ja
 	 * @return    The test suite
 	 */
 	public void testFlagActiveCenter1() throws ClassNotFoundException, CDKException, java.lang.Exception {
-		Molecule molecule = (new SmilesParser()).parseSmiles("CC=C[C+]-C-C=C-[C+]");
+		Molecule molecule = (new SmilesParser()).parseSmiles("CC=C[C+]-C-C=C-C");
 	    HydrogenAdder adder = new HydrogenAdder();
         adder.addImplicitHydrogensToSatisfyValency(molecule);
 
@@ -240,7 +240,7 @@ public void testFlagActiveCenter1() throws ClassNotFoundException, CDKException,
 
 		Assert.assertEquals(2,setOfMolecules.getAtomContainerCount());
 
-        Molecule molecule2 = (new SmilesParser()).parseSmiles("C-[C+]-C=C-C-C=C-[C+]");
+        Molecule molecule2 = (new SmilesParser()).parseSmiles("C-[C+]-C=C-C-C=C-C");
         adder.addImplicitHydrogensToSatisfyValency(molecule2);
 
         QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule2);

diff --git a/src/org/openscience/cdk/tools/StructureResonanceGenerator.java b/src/org/openscience/cdk/tools/StructureResonanceGenerator.java
@@ -41,9 +41,9 @@
  * <p>If the reactive center is not localized then the reaction process will
  * try to find automatically the posible reactive center.</p>
  *  
- * @author      Miguel Rojas
- * @cdk.created     2006-5-05
- * @cdk.module reaction
+ * @author       Miguel Rojas
+ * @cdk.created  2006-5-05
+ * @cdk.module   reaction
  * 
  * @see DisplacementChargeFromAcceptorReaction
  * @see DisplacementChargeFromDonorReaction
@@ -103,7 +103,7 @@ public StructureResonanceGenerator(
 	 * @return The different resonance structures
 	 */
 	public ISetOfAtomContainers getStructures(IAtomContainer atomContainer) {
-		ISetOfAtomContainers setOfAC = DefaultChemObjectBuilder.getInstance().newSetOfAtomContainers();
+		ISetOfAtomContainers setOfAC = atomContainer.getBuilder().newSetOfAtomContainers();
 
 		ISetOfAtomContainers set = getAllStructures(atomContainer); 
 		/*analize sum of bonds */