Class HomolyticCleavageReaction
- java.lang.Object
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- org.openscience.cdk.reaction.ReactionEngine
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- org.openscience.cdk.reaction.type.HomolyticCleavageReaction
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- All Implemented Interfaces:
IReactionProcess
public class HomolyticCleavageReaction extends ReactionEngine implements IReactionProcess
IReactionProcess which breaks the bond homogeneously leading to radical ions. It is also called homogeneous bond-breaking.Depending of the bond order, the bond will be removed or simply the order decreased.
A-B => [A*] + [B*]
It is processed by the HomolyticCleavageMechanism class
IAtomContainerSet setOfReactants = DefaultChemObjectBuilder.getInstance().newAtomContainerSet(); setOfReactants.addAtomContainer(new AtomContainer()); IReactionProcess type = new HomolyticCleavageReaction(); 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
- See Also:
HomolyticCleavageMechanism
- Source code:
- main
- Belongs to CDK module:
- reaction
- Created on:
- 2006-10-27
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Field Summary
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Fields inherited from class org.openscience.cdk.reaction.ReactionEngine
mechanism, paramsMap, paramsMap2
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Constructor Summary
Constructors Constructor Description HomolyticCleavageReaction()
Constructor of the HomolyticCleavageReaction object.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description ReactionSpecification
getSpecification()
Gets the specification attribute of the HomolyticCleavageReaction object.IReactionSet
initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.-
Methods inherited from class org.openscience.cdk.reaction.ReactionEngine
getParameterClass, getParameterList, setParameterList
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.reaction.IReactionProcess
getParameterClass, getParameterList, setParameterList
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Method Detail
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getSpecification
public ReactionSpecification getSpecification()
Gets the specification attribute of the HomolyticCleavageReaction 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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