Initiating only one time the function LonePairElectronChecker

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
egonw · Feb 1, 2010 · e71b52e · e71b52e
1 parent 4f5e8a1
commit e71b52e
Show file tree

Hide file tree

Showing 27 changed files with 55 additions and 45 deletions.
diff --git a/src/test/org/openscience/cdk/reaction/type/AdductionProtonLPReactionTest.java b/src/test/org/openscience/cdk/reaction/type/AdductionProtonLPReactionTest.java
@@ -57,7 +57,8 @@
  * @cdk.module test-reaction
  */
 public class AdductionProtonLPReactionTest extends ReactionProcessTest {
-
+
+	private final LonePairElectronChecker lpcheck = new LonePairElectronChecker();
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method
@@ -244,7 +245,7 @@ private IMoleculeSet getExampleReactants() {
         try {
 			AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
 
-	        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
+
 	        lpcheck.saturate(molecule);
 		} catch (CDKException e) {
 			e.printStackTrace();
@@ -281,7 +282,7 @@ private IMoleculeSet getExpectedProducts() {
         try {
 			AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
 
-	        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
+
 	        lpcheck.saturate(molecule);
 		} catch (CDKException e) {
 			e.printStackTrace();

diff --git a/src/test/org/openscience/cdk/reaction/type/AdductionProtonPBReactionTest.java b/src/test/org/openscience/cdk/reaction/type/AdductionProtonPBReactionTest.java
@@ -57,7 +57,8 @@
  * @cdk.module test-reaction
  */
 public class AdductionProtonPBReactionTest extends ReactionProcessTest {
-
+
+	private final LonePairElectronChecker lpcheck = new LonePairElectronChecker();
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method
@@ -244,7 +245,7 @@ private IMoleculeSet getExampleReactants() {
         try {
 			AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
 
-	        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
+
 	        lpcheck.saturate(molecule);
 		} catch (CDKException e) {
 			e.printStackTrace();
@@ -278,7 +279,7 @@ private IMoleculeSet getExpectedProducts() {
         try {
 			AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
 
-	        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
+
 	        lpcheck.saturate(molecule);
 		} catch (CDKException e) {
 			e.printStackTrace();

diff --git a/src/test/org/openscience/cdk/reaction/type/AdductionSodiumLPReactionTest.java b/src/test/org/openscience/cdk/reaction/type/AdductionSodiumLPReactionTest.java
@@ -57,7 +57,8 @@
  * @cdk.module test-reaction
  */
 public class AdductionSodiumLPReactionTest extends ReactionProcessTest {
-
+
+	private final LonePairElectronChecker lpcheck = new LonePairElectronChecker();
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method
@@ -252,7 +253,7 @@ private IMoleculeSet getExampleReactants() {
         try {
 			AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
 
-	        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
+
 	        lpcheck.saturate(molecule);
 		} catch (CDKException e) {
 			e.printStackTrace();
@@ -288,7 +289,7 @@ private IMoleculeSet getExpectedProducts() {
         try {
 			AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
 
-	        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
+
 	        lpcheck.saturate(molecule);
 		} catch (CDKException e) {
 			e.printStackTrace();

diff --git a/src/test/org/openscience/cdk/reaction/type/CarbonylEliminationReactionTest.java b/src/test/org/openscience/cdk/reaction/type/CarbonylEliminationReactionTest.java
@@ -58,7 +58,8 @@
  * @cdk.module test-reaction
  */
 public class CarbonylEliminationReactionTest extends ReactionProcessTest {
-
+
+	private final LonePairElectronChecker lpcheck = new LonePairElectronChecker();
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method
@@ -220,7 +221,7 @@ private IMoleculeSet getExampleReactants() {
 		try {
 			AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
 
-	        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
+
 	        lpcheck.saturate(molecule);
 			makeSureAtomTypesAreRecognized(molecule);
 		} catch (CDKException e) {

diff --git a/src/test/org/openscience/cdk/reaction/type/ElectronImpactSDBReactionTest.java b/src/test/org/openscience/cdk/reaction/type/ElectronImpactSDBReactionTest.java
@@ -53,7 +53,7 @@
  */
 
 public class ElectronImpactSDBReactionTest extends ReactionProcessTest {
-	
+
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method

diff --git a/src/test/org/openscience/cdk/reaction/type/HyperconjugationReactionTest.java b/src/test/org/openscience/cdk/reaction/type/HyperconjugationReactionTest.java
@@ -48,6 +48,7 @@
 import org.openscience.cdk.reaction.ReactionProcessTest;
 import org.openscience.cdk.reaction.type.parameters.IParameterReact;
 import org.openscience.cdk.reaction.type.parameters.SetReactionCenter;
+import org.openscience.cdk.tools.LonePairElectronChecker;
 import org.openscience.cdk.tools.manipulator.ReactionManipulator;
 
 /**
@@ -57,7 +58,7 @@
  * @cdk.module test-reaction
  */
 public class HyperconjugationReactionTest extends ReactionProcessTest {
-	
+
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method

diff --git a/src/test/org/openscience/cdk/reaction/type/PiBondingMovementReactionTest.java b/src/test/org/openscience/cdk/reaction/type/PiBondingMovementReactionTest.java
@@ -59,7 +59,7 @@
  * @cdk.module test-reaction
  */
 public class PiBondingMovementReactionTest extends ReactionProcessTest {
-	
+
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method

diff --git a/src/test/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationHReactionTest.java b/src/test/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationHReactionTest.java
@@ -58,7 +58,7 @@
  * @cdk.module test-reaction
  */
 public class RadicalChargeSiteInitiationHReactionTest extends ReactionProcessTest {
-	
+
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method

diff --git a/src/test/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationReactionTest.java b/src/test/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationReactionTest.java
@@ -55,7 +55,7 @@
  * @cdk.module test-reaction
  */
 public class RadicalChargeSiteInitiationReactionTest extends ReactionProcessTest {
-	
+
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method

diff --git a/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrAlphaReactionTest.java b/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrAlphaReactionTest.java
@@ -58,7 +58,7 @@
  * @cdk.module test-reaction
  */
 public class RadicalSiteHrAlphaReactionTest extends ReactionProcessTest {
-	
+
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method

diff --git a/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrBetaReactionTest.java b/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrBetaReactionTest.java
@@ -58,7 +58,7 @@
  * @cdk.module test-reaction
  */
 public class RadicalSiteHrBetaReactionTest extends ReactionProcessTest {
-	
+
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method

diff --git a/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrDeltaReactionTest.java b/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrDeltaReactionTest.java
@@ -59,7 +59,7 @@
  * @cdk.module test-reaction
  */
 public class RadicalSiteHrDeltaReactionTest extends ReactionProcessTest {
-	
+
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method

diff --git a/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrGammaReactionTest.java b/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrGammaReactionTest.java
@@ -59,7 +59,7 @@
  * @cdk.module test-reaction
  */
 public class RadicalSiteHrGammaReactionTest extends ReactionProcessTest {
-	
+
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method

diff --git a/src/test/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReactionTest.java b/src/test/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReactionTest.java
@@ -59,7 +59,7 @@
  * @cdk.module test-reaction
  */
 public class RadicalSiteInitiationHReactionTest extends ReactionProcessTest {
-	
+
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method

diff --git a/src/test/org/openscience/cdk/reaction/type/RadicalSiteInitiationReactionTest.java b/src/test/org/openscience/cdk/reaction/type/RadicalSiteInitiationReactionTest.java
@@ -59,7 +59,7 @@
  * @cdk.module test-reaction
  */
 public class RadicalSiteInitiationReactionTest extends ReactionProcessTest {
-	
+
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method

diff --git a/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrAlphaReactionTest.java b/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrAlphaReactionTest.java
@@ -58,7 +58,7 @@
  * @cdk.module test-reaction
  */
 public class RadicalSiteRrAlphaReactionTest extends ReactionProcessTest {
-	
+
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method

diff --git a/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrBetaReactionTest.java b/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrBetaReactionTest.java
@@ -58,7 +58,7 @@
  * @cdk.module test-reaction
  */
 public class RadicalSiteRrBetaReactionTest extends ReactionProcessTest {
-	
+
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method

diff --git a/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrDeltaReactionTest.java b/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrDeltaReactionTest.java
@@ -58,7 +58,7 @@
  * @cdk.module test-reaction
  */
 public class RadicalSiteRrDeltaReactionTest extends ReactionProcessTest {
-	
+
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method

diff --git a/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrGammaReactionTest.java b/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrGammaReactionTest.java
@@ -58,7 +58,7 @@
  * @cdk.module test-reaction
  */
 public class RadicalSiteRrGammaReactionTest extends ReactionProcessTest {
-	
+
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method

diff --git a/src/test/org/openscience/cdk/reaction/type/RearrangementAnionReactionTest.java b/src/test/org/openscience/cdk/reaction/type/RearrangementAnionReactionTest.java
@@ -90,7 +90,8 @@
  */
 
 public class RearrangementAnionReactionTest extends ReactionProcessTest {
-
+
+	private final LonePairElectronChecker lpcheck = new LonePairElectronChecker();
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method
@@ -290,7 +291,7 @@ public  RearrangementAnionReactionTest()  throws Exception {
 		molecule.addBond(6, 1, IBond.Order.SINGLE);
 
 		addExplicitHydrogens(molecule);
-        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
+
 		AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
         lpcheck.saturate(molecule);
 

diff --git a/src/test/org/openscience/cdk/reaction/type/RearrangementCationReactionTest.java b/src/test/org/openscience/cdk/reaction/type/RearrangementCationReactionTest.java
@@ -59,7 +59,7 @@
  * @cdk.module test-reaction
  */
 public class RearrangementCationReactionTest extends ReactionProcessTest {
-	
+
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method

diff --git a/src/test/org/openscience/cdk/reaction/type/RearrangementLonePairReactionTest.java b/src/test/org/openscience/cdk/reaction/type/RearrangementLonePairReactionTest.java
@@ -91,7 +91,8 @@
  */
 
 public class RearrangementLonePairReactionTest extends ReactionProcessTest {
-
+
+	private final LonePairElectronChecker lpcheck = new LonePairElectronChecker();
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method
@@ -304,7 +305,7 @@ private IMoleculeSet getExampleReactants() {
 			addExplicitHydrogens(molecule);
 			AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
 
-	        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
+
 	        lpcheck.saturate(molecule);
 		} catch (Exception e) {
 			e.printStackTrace();
@@ -338,7 +339,7 @@ private IMoleculeSet getExpectedProducts() {
 			addExplicitHydrogens(molecule);
 			AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
 
-	        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
+
 	        lpcheck.saturate(molecule);
 
 		} catch (Exception e) {
@@ -392,7 +393,7 @@ private void makeSureAtomTypesAreRecognized(IMolecule molecule) throws Exception
 
 		addExplicitHydrogens(molecule);
 		AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
-        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
+
         lpcheck.saturate(molecule);
 
 		IReactionProcess type = new RearrangementLonePairReaction();

diff --git a/src/test/org/openscience/cdk/reaction/type/RearrangementRadicalReactionTest.java b/src/test/org/openscience/cdk/reaction/type/RearrangementRadicalReactionTest.java
@@ -59,7 +59,7 @@
  * @cdk.module test-reaction
  */
 public class RearrangementRadicalReactionTest extends ReactionProcessTest {
-	
+
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method

diff --git a/src/test/org/openscience/cdk/reaction/type/SharingAnionReactionTest.java b/src/test/org/openscience/cdk/reaction/type/SharingAnionReactionTest.java
@@ -60,7 +60,8 @@
  */
 
 public class SharingAnionReactionTest extends ReactionProcessTest {
-
+
+	private final LonePairElectronChecker lpcheck = new LonePairElectronChecker();
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method
@@ -171,7 +172,7 @@ public  SharingAnionReactionTest()  throws Exception {
 
 		addExplicitHydrogens(molecule);
 		AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
-        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
+
         lpcheck.saturate(molecule);
 
 		IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
@@ -308,7 +309,7 @@ private IMoleculeSet getExampleReactants() {
 		try {
 			addExplicitHydrogens(molecule);
 			AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
-	        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
+
 	        lpcheck.saturate(molecule);
 		} catch (Exception e) {
 			e.printStackTrace();
@@ -333,7 +334,7 @@ private IMoleculeSet getExpectedProducts() {
 		try {
 			addExplicitHydrogens(molecule);
 			AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
-	        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
+
 	        lpcheck.saturate(molecule);
 		} catch (Exception e) {
 			e.printStackTrace();

diff --git a/src/test/org/openscience/cdk/reaction/type/SharingChargeDBReactionTest.java b/src/test/org/openscience/cdk/reaction/type/SharingChargeDBReactionTest.java
@@ -59,7 +59,8 @@
  * @cdk.module test-reaction
  */
 public class SharingChargeDBReactionTest extends ReactionProcessTest {
-
+
+	private final LonePairElectronChecker lpcheck = new LonePairElectronChecker();
 	private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
 	/**
 	 *  The JUnit setup method
@@ -254,7 +255,7 @@ private IMoleculeSet getExampleReactants() {
 		try {
 			addExplicitHydrogens(molecule);
 
-	        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
+
 			AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
 	        lpcheck.saturate(molecule);
 		} catch (Exception e) {
@@ -281,7 +282,7 @@ private IMoleculeSet getExpectedProducts() {
 
 		try {
 			addExplicitHydrogens(molecule);
-	        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
+
 			AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
 	        lpcheck.saturate(molecule);
 		} catch (Exception e) {