Class HeterolyticCleavagePBReaction
- java.lang.Object
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- org.openscience.cdk.reaction.ReactionEngine
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- org.openscience.cdk.reaction.type.HeterolyticCleavagePBReaction
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- All Implemented Interfaces:
IReactionProcess
public class HeterolyticCleavagePBReaction extends ReactionEngine implements IReactionProcess
IReactionProcess which a bond is broken displacing the electron to one of the atoms. The mechanism will produce one atom with excess of charge and the other one deficiency. Depending of the bond order, the bond will be removed or simply the order decreased. As there are two directions for displacing a bond in a polar manner, each case is investigated twice:
A=B => [A+]-|[B-]
A=B => |[A-]-[B+]
It will not be created structures no possible, e.g; C=O => [C-][O+].
Below you have an example how to initiate the mechanism.
It is processed by the HeterolyticCleavageMechanism class
IAtomContainerSet setOfReactants = DefaultChemObjectBuilder.getInstance().newAtomContainerSet(); setOfReactants.addAtomContainer(new AtomContainer()); IReactionProcess type = new HeterolyticCleavagePBReaction(); 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 specify 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 specified then the reaction process will try to find automatically the possible reaction centers.
- Author:
- Miguel Rojas
- See Also:
HeterolyticCleavageMechanism
- Source code:
- main
- Belongs to CDK module:
- reaction
- Created on:
- 2006-06-09
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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 HeterolyticCleavagePBReaction()
Constructor of the HeterolyticCleavagePBReaction 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 HeterolyticCleavagePBReaction 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 HeterolyticCleavagePBReaction 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 reactionagents
- 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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