diff --git a/src/test/org/openscience/cdk/reaction/type/AdductionProtonLPReactionTest.java b/src/test/org/openscience/cdk/reaction/type/AdductionProtonLPReactionTest.java index 8a5f3485224..e3a9854fa5e 100644 --- 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 index 179d220b2f7..c831b4ac3f5 100644 --- 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 index 01835c8ead7..d0c07698627 100644 --- 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 index 1758e5b4967..8d5779e634e 100644 --- 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 index 0d96290e7df..9ba3e470f38 100644 --- 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 index 19d05f1c5fe..a094c331850 100644 --- 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 index 5a12a1ab79d..5384553dd82 100644 --- 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 index 31e59e5268d..2482c81e259 100644 --- 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 index f8206dbb4b2..b719a513f1f 100644 --- 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 index 0c4be0d651d..e6585e392ce 100644 --- 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 index e84e0939ad2..4ceb3f0848f 100644 --- 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 index a60bce817b8..af63113f4f9 100644 --- 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 index 9418f4f6e0e..2e0508276da 100644 --- 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 index 3ccee232db4..859515d6d8d 100644 --- 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 index 24b22515290..def137fdfe7 100644 --- 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 index ad4eee5fc06..26f630e3764 100644 --- 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 index 77efb889029..23c5aafbfd4 100644 --- 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 index f73507eb7bd..5094c0056ab 100644 --- 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 index ae2dc135109..2d38a08808f 100644 --- 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 index 90b6faead57..b939ecab669 100644 --- 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 index a50493fe7df..e3801ddf7d0 100644 --- 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 index 3d66af4ddc6..281a8b74b28 100644 --- 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 index 8b558a513c9..848c3ed4963 100644 --- 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 index 4b91fa90ecd..faa3b0465e8 100644 --- 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 index add5771ba28..effb6a3a96a 100644 --- 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) { diff --git a/src/test/org/openscience/cdk/reaction/type/SharingLonePairReactionTest.java b/src/test/org/openscience/cdk/reaction/type/SharingLonePairReactionTest.java index 3ff2bde9689..5c04d64781d 100644 --- a/src/test/org/openscience/cdk/reaction/type/SharingLonePairReactionTest.java +++ b/src/test/org/openscience/cdk/reaction/type/SharingLonePairReactionTest.java @@ -60,7 +60,8 @@ */ public class SharingLonePairReactionTest extends ReactionProcessTest { - + + private final LonePairElectronChecker lpcheck = new LonePairElectronChecker(); private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance(); /** * The JUnit setup method @@ -255,7 +256,7 @@ private IMoleculeSet getExampleReactants() { try { addExplicitHydrogens(molecule); AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule); - LonePairElectronChecker lpcheck = new LonePairElectronChecker(); + lpcheck.saturate(molecule); } catch (Exception e) { e.printStackTrace(); @@ -280,7 +281,7 @@ 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/TautomerizationReactionTest.java b/src/test/org/openscience/cdk/reaction/type/TautomerizationReactionTest.java index 10a7d64ce02..66fc973d98a 100644 --- a/src/test/org/openscience/cdk/reaction/type/TautomerizationReactionTest.java +++ b/src/test/org/openscience/cdk/reaction/type/TautomerizationReactionTest.java @@ -56,7 +56,7 @@ * @cdk.module test-reaction */ public class TautomerizationReactionTest extends ReactionProcessTest { - + private IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance(); /** * The JUnit setup method