Class SharingAnionReaction
java.lang.Object
org.openscience.cdk.reaction.ReactionEngine
org.openscience.cdk.reaction.type.SharingAnionReaction
- All Implemented Interfaces:
IReactionProcess
IReactionProcess which participate in movement resonance. This reaction could be represented as [A+]-B| => A=[B+]. Due to deficiency of charge of the atom A, the lone pair electron of the atom A is desplaced.
Make sure that the molecule has the correspond lone pair electrons for each atom. You can use the method:
LonePairElectronChecker
IAtomContainerSet setOfReactants = DefaultChemObjectBuilder.getInstance().newAtomContainerSet(); setOfReactants.addAtomContainer(new AtomContainer()); IReactionProcess type = new SharingAnionReaction(); Object[] params = {Boolean.FALSE}; type.setParameters(params); IReactionSet setOfReactions = type.initiate(setOfReactants, null);
We have the possibility to localize the reactive center. Good method if you want to localize the reaction in a fixed point
atoms[0].setFlag(CDKConstants.REACTIVE_CENTER,true);
Moreover you must put the parameter Boolean.TRUE
If the reactive center is not localized then the reaction process will try to find automatically the possible reactive center.
- Author:
- Miguel Rojas
- Source code:
- main
- Belongs to CDK module:
- reaction
- Created on:
- 2006-05-05
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Field Summary
Fields inherited from class org.openscience.cdk.reaction.ReactionEngine
mechanism, paramsMap, paramsMap2
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionGets the specification attribute of the SharingAnionReaction object.initiate
(IAtomContainerSet reactants, IAtomContainerSet agents) Initiate process.Methods inherited from class org.openscience.cdk.reaction.ReactionEngine
getParameterClass, getParameterList, setParameterList
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.openscience.cdk.reaction.IReactionProcess
getParameterClass, getParameterList, setParameterList
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Constructor Details
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SharingAnionReaction
public SharingAnionReaction()Constructor of the SharingAnionReaction object.
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Method Details
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getSpecification
Gets the specification attribute of the SharingAnionReaction object.- Specified by:
getSpecification
in interfaceIReactionProcess
- Returns:
- The specification value
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initiate
public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agents) throws CDKException Initiate process. It is needed to call the addExplicitHydrogensToSatisfyValency from the class tools.HydrogenAdder.- Specified by:
initiate
in interfaceIReactionProcess
- Parameters:
reactants
- reactants of the reaction.agents
- agents of the reaction (Must be in this case null).- Returns:
- the set of reactions.
- Throws:
CDKException
- Description of the Exception
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