From: <mig...@us...> - 2006-10-10 16:55:39
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Revision: 7101 http://svn.sourceforge.net/cdk/?rev=7101&view=rev Author: miguelrojasch Date: 2006-10-10 09:55:21 -0700 (Tue, 10 Oct 2006) Log Message: ----------- cleared remove singleElectrons Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/reaction/type/DisplacementChargeFromDonorReaction.java trunk/cdk/src/org/openscience/cdk/reaction/type/ElectronImpactNBEReaction.java trunk/cdk/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationReaction.java trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementAnion1Reaction.java trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementCation1Reaction.java trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementRadical1Reaction.java trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementRadical2Reaction.java trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementRadical3Reaction.java Modified: trunk/cdk/src/org/openscience/cdk/reaction/type/DisplacementChargeFromDonorReaction.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/reaction/type/DisplacementChargeFromDonorReaction.java 2006-10-10 16:53:32 UTC (rev 7100) +++ trunk/cdk/src/org/openscience/cdk/reaction/type/DisplacementChargeFromDonorReaction.java 2006-10-10 16:55:21 UTC (rev 7101) @@ -190,8 +190,8 @@ int charge = acCloned.getAtom(atom0P).getFormalCharge(); acCloned.getAtom(atom0P).setFormalCharge(charge+1); - ILonePair[] lpelectron = acCloned.getLonePairs(acCloned.getAtom(atom0P)); - acCloned.removeElectronContainer(lpelectron[0]); + ILonePair[] selectron = acCloned.getLonePairs(acCloned.getAtom(atom0P)); + acCloned.removeElectronContainer(selectron[selectron.length -1]); double order = acCloned.getBond(bond1P).getOrder(); acCloned.getBond(bond1P).setOrder(order+1); Modified: trunk/cdk/src/org/openscience/cdk/reaction/type/ElectronImpactNBEReaction.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/reaction/type/ElectronImpactNBEReaction.java 2006-10-10 16:53:32 UTC (rev 7100) +++ trunk/cdk/src/org/openscience/cdk/reaction/type/ElectronImpactNBEReaction.java 2006-10-10 16:55:21 UTC (rev 7101) @@ -170,7 +170,7 @@ } ILonePair[] lps = reactantCloned.getLonePairs(reactantCloned.getAtom(posA)); - reactantCloned.removeElectronContainer(lps[0]); + reactantCloned.removeElectronContainer(lps[lps.length - 1]); reactantCloned.addElectronContainer(new SingleElectron(reactantCloned.getAtom(posA))); reactantCloned.getAtom(posA).setFormalCharge(1); Modified: trunk/cdk/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationReaction.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationReaction.java 2006-10-10 16:53:32 UTC (rev 7100) +++ trunk/cdk/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationReaction.java 2006-10-10 16:55:21 UTC (rev 7101) @@ -193,7 +193,7 @@ } ISingleElectron[] selectron = acCloned.getSingleElectron(acCloned.getAtom(atom0P)); - acCloned.removeElectronContainer(selectron[0]); + acCloned.removeElectronContainer(selectron[selectron.length -1]); acCloned.addElectronContainer(new SingleElectron(acCloned.getAtom(atom2P))); Modified: trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementAnion1Reaction.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementAnion1Reaction.java 2006-10-10 16:53:32 UTC (rev 7100) +++ trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementAnion1Reaction.java 2006-10-10 16:55:21 UTC (rev 7101) @@ -203,7 +203,7 @@ acCloned.getAtom(atom1P).setFormalCharge(charge-1); ILonePair[] selectron = acCloned.getLonePairs(acCloned.getAtom(atom0P)); - acCloned.removeElectronContainer(selectron[0]); + acCloned.removeElectronContainer(selectron[selectron.length -1]); /* mapping */ IMapping mapping = DefaultChemObjectBuilder.getInstance().newMapping(atomi, acCloned.getAtom(atom0P)); Modified: trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementCation1Reaction.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementCation1Reaction.java 2006-10-10 16:53:32 UTC (rev 7100) +++ trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementCation1Reaction.java 2006-10-10 16:55:21 UTC (rev 7101) @@ -208,7 +208,7 @@ acCloned.getAtom(atom1P).setFormalCharge(charge+1); ILonePair[] selectron = acCloned.getLonePairs(acCloned.getAtom(atom1P)); - acCloned.removeElectronContainer(selectron[0]); + acCloned.removeElectronContainer(selectron[selectron.length -1]); /* mapping */ IMapping mapping = DefaultChemObjectBuilder.getInstance().newMapping(atomi, acCloned.getAtom(atom0P)); Modified: trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementRadical1Reaction.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementRadical1Reaction.java 2006-10-10 16:53:32 UTC (rev 7100) +++ trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementRadical1Reaction.java 2006-10-10 16:55:21 UTC (rev 7101) @@ -193,7 +193,7 @@ acCloned.addElectronContainer(new SingleElectron(acCloned.getAtom(atom1P))); ILonePair[] lpelectron = acCloned.getLonePairs(acCloned.getAtom(atom1P)); - acCloned.removeElectronContainer(lpelectron[0]); + acCloned.removeElectronContainer(lpelectron[selectron.length -1]); double order = acCloned.getBond(bond1P).getOrder(); acCloned.getBond(bond1P).setOrder(order+1); Modified: trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementRadical2Reaction.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementRadical2Reaction.java 2006-10-10 16:53:32 UTC (rev 7100) +++ trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementRadical2Reaction.java 2006-10-10 16:55:21 UTC (rev 7101) @@ -194,7 +194,7 @@ } ISingleElectron[] selectron = acCloned.getSingleElectron(acCloned.getAtom(atom0P)); - acCloned.removeElectronContainer(selectron[0]); + acCloned.removeElectronContainer(selectron[selectron.length -1]); acCloned.addElectronContainer(new SingleElectron(acCloned.getAtom(atom2P))); Modified: trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementRadical3Reaction.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementRadical3Reaction.java 2006-10-10 16:53:32 UTC (rev 7100) +++ trunk/cdk/src/org/openscience/cdk/reaction/type/RearrangementRadical3Reaction.java 2006-10-10 16:55:21 UTC (rev 7101) @@ -27,6 +27,7 @@ import org.openscience.cdk.CDKConstants; import org.openscience.cdk.DefaultChemObjectBuilder; +import org.openscience.cdk.LonePair; import org.openscience.cdk.SingleElectron; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; @@ -34,8 +35,8 @@ import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IMapping; import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.interfaces.IReaction; -import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.interfaces.IReactionSet; import org.openscience.cdk.interfaces.ISingleElectron; import org.openscience.cdk.reaction.IReactionProcess; @@ -185,7 +186,8 @@ } ISingleElectron[] selectron = acCloned.getSingleElectron(acCloned.getAtom(atom0P)); - acCloned.removeElectronContainer(selectron[0]); + acCloned.removeElectronContainer(selectron[selectron.length -1]); + acCloned.addElectronContainer(new LonePair(acCloned.getAtom(atom0P))); acCloned.addElectronContainer(new SingleElectron(acCloned.getAtom(atom1P))); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |