From: <mig...@us...> - 2008-02-13 14:43:59
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Revision: 10086 http://cdk.svn.sourceforge.net/cdk/?rev=10086&view=rev Author: miguelrojasch Date: 2008-02-13 06:43:51 -0800 (Wed, 13 Feb 2008) Log Message: ----------- To initiate a mechanism is necessary to add a IMoleculeSet instead of IMolecule Modified Paths: -------------- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/IReactionMechanism.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/IReactionProcess.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/BreakingBondMechanism.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/CleavageBondMechanism.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RadicalSiteIonizationMechanism.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RadicalSiteRearrangementMechanism.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RearrangementCharge2Mechanism.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RemovingSEofBMechanism.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RemovingSEofNBMechanism.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/SharingChargeMechanism.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/SharingElectronMechanism.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/TautomerizationMechanism.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/BreakingBondReaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/CarbonylEliminationReaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/CleavageBondReaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/DisplacementChargeFromAcceptorReaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/ElectronImpactNBEReaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/ElectronImpactPDBReaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/ElectronImpactSDBReaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HydrogenRearrangementAlphaReaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HydrogenRearrangementBetaReaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HydrogenRearrangementDeltaReaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HydrogenRearrangementGammaReaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationReaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementAnion2Reaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementAnion3Reaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementCation2Reaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementCation3Reaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementRadical1Reaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementRadical2Reaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementRadical3Reaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/TautomerizationReaction.java branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/ReactionMechanismTest.java Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/IReactionMechanism.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/IReactionMechanism.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/IReactionMechanism.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -29,7 +29,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IBond; -import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.interfaces.IReaction; /** @@ -45,7 +45,7 @@ * Initiates the process for the given mechanism. The atoms to apply are mapped between * reactants and products. * - * @param molecule The IMolecule to apply the mechanism + * @param moleculeSet The IMoleculeSet to apply the mechanism * @param atomList The list of atoms taking part in the mechanism * @param bondList The list of bonds taking part in the mechanism * @return The Reaction mechanism @@ -53,6 +53,6 @@ * @throws CDKException if an error occurs during the reaction process. * See documentation for individual reaction processes */ - public IReaction initiate(IMolecule molecule, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) throws CDKException; + public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) throws CDKException; } Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/IReactionProcess.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/IReactionProcess.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/IReactionProcess.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -57,7 +57,7 @@ /** * Returns the names of the parameters for this reaction. * - * @return An array of String containing the names of the paraneters + * @return An array of String containing the names of the parameters * that this reaction can accept */ public String[] getParameterNames(); Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/BreakingBondMechanism.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/BreakingBondMechanism.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/BreakingBondMechanism.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -68,7 +68,7 @@ * Initiates the process for the given mechanism. The atoms to apply are mapped between * reactants and products. * - * @param molecule The IMolecule to apply the mechanism + * @param moleculeSet The IMolecule to apply the mechanism * @param atomList The list of atoms taking part in the mechanism. Only allowed two atoms. * The first atom receives the positive charge charge and the second * negative charge @@ -76,13 +76,17 @@ * @return The Reaction mechanism * */ - public IReaction initiate(IMolecule molecule, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + if (moleculeSet.getMoleculeCount() != 1) { + throw new CDKException("TautomerizationMechanism only expects one IMolecule"); + } if (atomList.size() != 2) { throw new CDKException("BreakingBondMechanism expects two atoms in the ArrayList"); } if (bondList.size() != 1) { throw new CDKException("BreakingBondMechanism only expect one bond in the ArrayList"); } + IMolecule molecule = moleculeSet.getMolecule(0); IMolecule reactantCloned; try { reactantCloned = (IMolecule) molecule.clone(); @@ -131,9 +135,9 @@ reaction.addMapping(mapping); reaction.addProduct(reactantCloned); } else{ - IMoleculeSet moleculeSet = ConnectivityChecker.partitionIntoMolecules(reactantCloned); - for(int z = 0; z < moleculeSet.getAtomContainerCount() ; z++){ - reaction.addProduct(moleculeSet.getMolecule(z)); + IMoleculeSet moleculeSetP = ConnectivityChecker.partitionIntoMolecules(reactantCloned); + for(int z = 0; z < moleculeSetP.getAtomContainerCount() ; z++){ + reaction.addProduct(moleculeSetP.getMolecule(z)); } } Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/CleavageBondMechanism.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/CleavageBondMechanism.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/CleavageBondMechanism.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -68,20 +68,24 @@ * Initiates the process for the given mechanism. The atoms to apply are mapped between * reactants and products. * - * @param molecule The IMolecule to apply the mechanism + * @param moleculeSet The IMolecule to apply the mechanism * @param atomList The list of atoms taking part in the mechanism. Only allowed two atoms. * Both atoms acquire a ISingleElectron * @param bondList The list of bonds taking part in the mechanism. Only allowed one bond * @return The Reaction mechanism * */ - public IReaction initiate(IMolecule molecule, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + if (moleculeSet.getMoleculeCount() != 1) { + throw new CDKException("TautomerizationMechanism only expects one IMolecule"); + } if (atomList.size() != 2) { throw new CDKException("CleavageBondMechanism expects two atoms in the ArrayList"); } if (bondList.size() != 1) { throw new CDKException("CleavageBondMechanism only expect one bond in the ArrayList"); } + IMolecule molecule = moleculeSet.getMolecule(0); IMolecule reactantCloned; try { reactantCloned = (IMolecule) molecule.clone(); @@ -127,9 +131,9 @@ reaction.addMapping(mapping); reaction.addProduct(reactantCloned); } else{ - IMoleculeSet moleculeSet = ConnectivityChecker.partitionIntoMolecules(reactantCloned); - for(int z = 0; z < moleculeSet.getAtomContainerCount() ; z++){ - reaction.addProduct(moleculeSet.getMolecule(z)); + IMoleculeSet moleculeSetP = ConnectivityChecker.partitionIntoMolecules(reactantCloned); + for(int z = 0; z < moleculeSetP.getAtomContainerCount() ; z++){ + reaction.addProduct(moleculeSetP.getMolecule(z)); } } Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RadicalSiteIonizationMechanism.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RadicalSiteIonizationMechanism.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RadicalSiteIonizationMechanism.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -70,7 +70,7 @@ * Initiates the process for the given mechanism. The atoms to apply are mapped between * reactants and products. * - * @param molecule The IMolecule to apply the mechanism + * @param moleculeSet The IMolecule to apply the mechanism * @param atomList The list of atoms taking part in the mechanism. Only allowed two atoms. * The first atom is the atom which contains the ISingleElectron and the second * third is the atom which will be removed @@ -80,13 +80,17 @@ * @return The Reaction mechanism * */ - public IReaction initiate(IMolecule molecule, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + if (moleculeSet.getMoleculeCount() != 1) { + throw new CDKException("TautomerizationMechanism only expects one IMolecule"); + } if (atomList.size() != 3) { throw new CDKException("RadicalSiteIonizationMechanism expects three atoms in the ArrayList"); } if (bondList.size() != 2) { throw new CDKException("RadicalSiteIonizationMechanism only expect one bond in the ArrayList"); } + IMolecule molecule = moleculeSet.getMolecule(0); IMolecule reactantCloned; try { reactantCloned = (IMolecule) molecule.clone(); @@ -138,9 +142,9 @@ mapping = DefaultChemObjectBuilder.getInstance().newMapping(bond1, reactantCloned.getBond(posBond1)); reaction.addMapping(mapping); - IMoleculeSet moleculeSet = ConnectivityChecker.partitionIntoMolecules(reactantCloned); - for(int z = 0; z < moleculeSet.getAtomContainerCount() ; z++) - reaction.addProduct(moleculeSet.getMolecule(z)); + IMoleculeSet moleculeSetP = ConnectivityChecker.partitionIntoMolecules(reactantCloned); + for(int z = 0; z < moleculeSetP.getAtomContainerCount() ; z++) + reaction.addProduct(moleculeSetP.getMolecule(z)); return reaction; } Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RadicalSiteRearrangementMechanism.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RadicalSiteRearrangementMechanism.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RadicalSiteRearrangementMechanism.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -32,6 +32,7 @@ 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.ISingleElectron; import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder; @@ -67,7 +68,7 @@ * Initiates the process for the given mechanism. The atoms to apply are mapped between * reactants and products. * - * @param molecule The IMolecule to apply the mechanism + * @param moleculeSet The IMolecule to apply the mechanism * @param atomList The list of atoms taking part in the mechanism. Only allowed two atoms. * The first atom is the atom which must be moved and the second * is the atom which receives the atom1 and the third is the atom which loss @@ -77,13 +78,17 @@ * @return The Reaction mechanism * */ - public IReaction initiate(IMolecule molecule, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + if (moleculeSet.getMoleculeCount() != 1) { + throw new CDKException("TautomerizationMechanism only expects one IMolecule"); + } if (atomList.size() != 3) { throw new CDKException("RadicalSiteRearrangementMechanism expects three atoms in the ArrayList"); } if (bondList.size() != 1) { throw new CDKException("RadicalSiteRearrangementMechanism only expect one bond in the ArrayList"); } + IMolecule molecule = moleculeSet.getMolecule(0); IMolecule reactantCloned; try { reactantCloned = (IMolecule) molecule.clone(); Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RearrangementCharge2Mechanism.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RearrangementCharge2Mechanism.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RearrangementCharge2Mechanism.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -32,6 +32,7 @@ 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.ISingleElectron; import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder; @@ -69,7 +70,7 @@ * Initiates the process for the given mechanism. The atoms to apply are mapped between * reactants and products. * - * @param molecule The IMolecule to apply the mechanism + * @param moleculeSet The IMolecule to apply the mechanism * @param atomList The list of atoms taking part in the mechanism. Only allowed two three. * The first atom is the atom which must contain the charge to be moved, the second * is the atom which is in the middle and the third is the atom which acquires the new charge @@ -80,13 +81,17 @@ * @return The Reaction mechanism * */ - public IReaction initiate(IMolecule molecule, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + if (moleculeSet.getMoleculeCount() != 1) { + throw new CDKException("TautomerizationMechanism only expects one IMolecule"); + } if (atomList.size() != 3) { throw new CDKException("RearrangementCharge2Mechanism expects three atoms in the ArrayList"); } if (bondList.size() != 2) { throw new CDKException("RearrangementCharge2Mechanism only expect one bond in the ArrayList"); } + IMolecule molecule = moleculeSet.getMolecule(0); IMolecule reactantCloned; try { reactantCloned = (IMolecule) molecule.clone(); Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RemovingSEofBMechanism.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RemovingSEofBMechanism.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RemovingSEofBMechanism.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -69,21 +69,24 @@ * Initiates the process for the given mechanism. The atoms to apply are mapped between * reactants and products. * - * @param molecule The IMolecule to apply the mechanism + * @param moleculeSet The IMolecule to apply the mechanism * @param atomList The list of atoms taking part in the mechanism. Only allowed two atoms. * The first atom receives the charge and the second the single electron * @param bondList The list of bonds taking part in the mechanism. Only allowed one bond * @return The Reaction mechanism * */ - public IReaction initiate(IMolecule molecule, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + if (moleculeSet.getMoleculeCount() != 1) { + throw new CDKException("TautomerizationMechanism only expects one IMolecule"); + } if (atomList.size() != 2) { throw new CDKException("RemovingSEofBMechanism expects two atoms in the ArrayList"); } if (bondList.size() != 1) { throw new CDKException("RemovingSEofBMechanism only expects one bond in the ArrayList"); } - + IMolecule molecule = moleculeSet.getMolecule(0); IMolecule reactantCloned; try { reactantCloned = (IMolecule) molecule.clone(); @@ -129,9 +132,9 @@ reaction.addMapping(mapping); reaction.addProduct(reactantCloned); }else{ - IMoleculeSet moleculeSet = ConnectivityChecker.partitionIntoMolecules(reactantCloned); - for(int z = 0; z < moleculeSet.getAtomContainerCount() ; z++){ - reaction.addProduct(moleculeSet.getMolecule(z)); + IMoleculeSet moleculeSetP = ConnectivityChecker.partitionIntoMolecules(reactantCloned); + for(int z = 0; z < moleculeSetP.getAtomContainerCount() ; z++){ + reaction.addProduct(moleculeSetP.getMolecule(z)); } } Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RemovingSEofNBMechanism.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RemovingSEofNBMechanism.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/RemovingSEofNBMechanism.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -33,6 +33,7 @@ import org.openscience.cdk.interfaces.ILonePair; 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.nonotify.NoNotificationChemObjectBuilder; import org.openscience.cdk.reaction.IReactionMechanism; @@ -67,19 +68,23 @@ * Initiates the process for the given mechanism. The atoms to apply are mapped between * reactants and products. * - * @param molecule The IMolecule to apply the mechanism + * @param moleculeSet The IMolecule to apply the mechanism * @param atomList The list of atoms taking part in the mechanism. Only allowed one atom * @param bondList The list of bonds taking part in the mechanism. Only allowed one Bond * @return The Reaction mechanism * */ - public IReaction initiate(IMolecule molecule, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + if (moleculeSet.getMoleculeCount() != 1) { + throw new CDKException("TautomerizationMechanism only expects one IMolecule"); + } if (atomList.size() != 1) { throw new CDKException("RemovingSEofNBMechanism only expects one atom in the ArrayList"); } if (bondList != null) { throw new CDKException("RemovingSEofNBMechanism don't expect any bond in the ArrayList"); } + IMolecule molecule = moleculeSet.getMolecule(0); IMolecule reactantCloned; try { reactantCloned = (IMolecule) molecule.clone(); Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/SharingChargeMechanism.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/SharingChargeMechanism.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/SharingChargeMechanism.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -34,6 +34,7 @@ import org.openscience.cdk.interfaces.ILonePair; 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.ISingleElectron; import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder; @@ -71,20 +72,24 @@ * Initiates the process for the given mechanism. The atoms to apply are mapped between * reactants and products. * - * @param molecule The IMolecule to apply the mechanism + * @param moleculeSet The IMolecule to apply the mechanism * @param atomList The list of atoms taking part in the mechanism. Only allowed two atoms. * Both atoms acquire a ISingleElectron * @param bondList The list of bonds taking part in the mechanism. Only allowed one bond * @return The Reaction mechanism * */ - public IReaction initiate(IMolecule molecule, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + if (moleculeSet.getMoleculeCount() != 1) { + throw new CDKException("TautomerizationMechanism only expects one IMolecule"); + } if (atomList.size() != 2) { throw new CDKException("SharingChargeMechanism expects two atoms in the ArrayList"); } if (bondList.size() != 1) { throw new CDKException("SharingChargeMechanism only expect one bond in the ArrayList"); } + IMolecule molecule = moleculeSet.getMolecule(0); IMolecule reactantCloned; try { reactantCloned = (IMolecule) molecule.clone(); Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/SharingElectronMechanism.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/SharingElectronMechanism.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/SharingElectronMechanism.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -24,7 +24,6 @@ import java.util.List; import org.openscience.cdk.DefaultChemObjectBuilder; -import org.openscience.cdk.LonePair; import org.openscience.cdk.SingleElectron; import org.openscience.cdk.atomtype.CDKAtomTypeMatcher; import org.openscience.cdk.exception.CDKException; @@ -34,6 +33,7 @@ import org.openscience.cdk.interfaces.ILonePair; 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.ISingleElectron; import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder; @@ -71,19 +71,23 @@ * Initiates the process for the given mechanism. The atoms to apply are mapped between * reactants and products. * - * @param molecule The IMolecule to apply the mechanism + * @param moleculeSet The IMolecule to apply the mechanism * @param atomList The list of atoms taking part in the mechanism. Only allowed two atoms * @param bondList The list of bonds taking part in the mechanism. Only allowed one bond * @return The Reaction mechanism * */ - public IReaction initiate(IMolecule molecule, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + if (moleculeSet.getMoleculeCount() != 1) { + throw new CDKException("TautomerizationMechanism only expects one IMolecule"); + } if (atomList.size() != 2) { throw new CDKException("SharingElectronMechanism expects two atoms in the ArrayList"); } if (bondList.size() != 1) { throw new CDKException("SharingElectronMechanism only expect one bond in the ArrayList"); } + IMolecule molecule = moleculeSet.getMolecule(0); IMolecule reactantCloned; try { reactantCloned = (IMolecule) molecule.clone(); Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/TautomerizationMechanism.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/TautomerizationMechanism.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/mechanism/TautomerizationMechanism.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -30,6 +30,7 @@ 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.nonotify.NoNotificationChemObjectBuilder; import org.openscience.cdk.reaction.IReactionMechanism; @@ -65,7 +66,7 @@ * Initiates the process for the given mechanism. The atoms and bonds to apply are mapped between * reactants and products. * - * @param molecule The IMolecule to apply the mechanism + * @param moleculeSet The IMolecule to apply the mechanism * @param atomList The list of atoms taking part in the mechanism. Only allowed fourth atoms. * @param bondList The list of bonds taking part in the mechanism. Only allowed two bond. * The first bond is the bond to decrease the order and the second is the bond @@ -74,13 +75,17 @@ * @return The Reaction mechanism * */ - public IReaction initiate(IMolecule molecule, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException { + if (moleculeSet.getMoleculeCount() != 1) { + throw new CDKException("TautomerizationMechanism only expects one IMolecule"); + } if (atomList.size() != 4) { throw new CDKException("TautomerizationMechanism expects four atoms in the ArrayList"); } if (bondList.size() != 3) { throw new CDKException("TautomerizationMechanism expects three bonds in the ArrayList"); } + IMolecule molecule = moleculeSet.getMolecule(0); IMolecule reactantCloned; try { reactantCloned = (IMolecule) molecule.clone(); Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/BreakingBondReaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/BreakingBondReaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/BreakingBondReaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -190,7 +190,9 @@ ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(bondi); - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/CarbonylEliminationReaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/CarbonylEliminationReaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/CarbonylEliminationReaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -185,8 +185,10 @@ atomList.add(atomj); ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(bondj); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/CleavageBondReaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/CleavageBondReaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/CleavageBondReaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -170,8 +170,10 @@ atomList.add(bondi.getAtom(1)); ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(bondi); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/DisplacementChargeFromAcceptorReaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/DisplacementChargeFromAcceptorReaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/DisplacementChargeFromAcceptorReaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -181,8 +181,10 @@ } ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(bondi); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/ElectronImpactNBEReaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/ElectronImpactNBEReaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/ElectronImpactNBEReaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -169,7 +169,9 @@ ArrayList<IAtom> atomList = new ArrayList<IAtom>(); atomList.add(atom); - IReaction reaction = mechanism.initiate(reactant, atomList, null); + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, null); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/ElectronImpactPDBReaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/ElectronImpactPDBReaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/ElectronImpactPDBReaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -178,8 +178,10 @@ } ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(bond); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/ElectronImpactSDBReaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/ElectronImpactSDBReaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/ElectronImpactSDBReaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -177,8 +177,10 @@ } ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(bond); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HydrogenRearrangementAlphaReaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HydrogenRearrangementAlphaReaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HydrogenRearrangementAlphaReaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -203,8 +203,10 @@ atomList.add(atoml); ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(reactant.getBond(atomh, atoml)); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HydrogenRearrangementBetaReaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HydrogenRearrangementBetaReaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HydrogenRearrangementBetaReaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -203,8 +203,10 @@ atomList.add(atoml); ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(reactant.getBond(atomh, atoml)); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HydrogenRearrangementDeltaReaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HydrogenRearrangementDeltaReaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HydrogenRearrangementDeltaReaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -203,8 +203,10 @@ atomList.add(atoml); ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(reactant.getBond(atomh, atoml)); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HydrogenRearrangementGammaReaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HydrogenRearrangementGammaReaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/HydrogenRearrangementGammaReaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -203,8 +203,10 @@ atomList.add(atoml); ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(reactant.getBond(atomh, atoml)); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -191,8 +191,10 @@ ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(bondi); bondList.add(bondj); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationReaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationReaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RadicalSiteInitiationReaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -192,8 +192,10 @@ ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(bondi); bondList.add(bondj); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementAnion2Reaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementAnion2Reaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementAnion2Reaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -198,8 +198,10 @@ ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(bondi); bondList.add(bondj); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementAnion3Reaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementAnion3Reaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementAnion3Reaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -187,8 +187,10 @@ atomList.add(atomj); ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(bondi); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementCation2Reaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementCation2Reaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementCation2Reaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -200,8 +200,10 @@ ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(bondi); bondList.add(bondj); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementCation3Reaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementCation3Reaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementCation3Reaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -189,8 +189,10 @@ atomList.add(atomj); ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(bondi); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementRadical1Reaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementRadical1Reaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementRadical1Reaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -184,8 +184,10 @@ atomList.add(atomj); ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(bondi); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementRadical2Reaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementRadical2Reaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementRadical2Reaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -200,8 +200,10 @@ ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(bondi); bondList.add(bondj); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementRadical3Reaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementRadical3Reaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/RearrangementRadical3Reaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -184,8 +184,10 @@ atomList.add(atomj); ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(bondi); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/TautomerizationReaction.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/TautomerizationReaction.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/reaction/type/TautomerizationReaction.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -201,8 +201,10 @@ bondList.add(bondi); bondList.add(bondj); bondList.add(bondk); - - IReaction reaction = mechanism.initiate(reactant, atomList, bondList); + + IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); + moleculeSet.addMolecule(reactant); + IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if(reaction == null) continue; else Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/ReactionMechanismTest.java =================================================================== --- branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/ReactionMechanismTest.java 2008-02-13 12:21:18 UTC (rev 10085) +++ branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/ReactionMechanismTest.java 2008-02-13 14:43:51 UTC (rev 10086) @@ -66,7 +66,7 @@ @Test public void testInitiate_IMolecule_ArrayList_ArrayList() throws Exception { ArrayList<IAtom> atomList = new ArrayList<IAtom>(); ArrayList<IBond> bondList = new ArrayList<IBond>(); - IReaction reaction = reactionMechanism.initiate(builder.newMolecule(), atomList, bondList); + IReaction reaction = reactionMechanism.initiate(builder.newMoleculeSet(), atomList, bondList); Assert.assertNotNull(reaction); } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |