Class RadicalSiteRearrangementMechanism
- java.lang.Object
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- org.openscience.cdk.reaction.mechanism.RadicalSiteRearrangementMechanism
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- All Implemented Interfaces:
IReactionMechanism
public class RadicalSiteRearrangementMechanism extends Object implements IReactionMechanism
This mechanism displaces an Atom or substructure (R) from one position to an other. It returns the reaction mechanism which has been cloned the
IAtomContainer
.This reaction could be represented as [A*]-(X)_n-Y-Z => A(Z)-(X)_n-[Y*]
- Author:
- miguelrojasch
- Source code:
- main
- Belongs to CDK module:
- reaction
- Created on:
- 2008-02-10
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Constructor Summary
Constructors Constructor Description RadicalSiteRearrangementMechanism()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description IReaction
initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
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Method Detail
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initiate
public IReaction initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) throws CDKException
Initiates the process for the given mechanism. The atoms to apply are mapped between reactants and products.- Specified by:
initiate
in interfaceIReactionMechanism
- Parameters:
atomContainerSet
-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 the first atombondList
- The list of bonds taking part in the mechanism. Only allowed one bond. It is the bond which is moved- Returns:
- The Reaction mechanism
- Throws:
CDKException
- if an error occurs during the reaction process. See documentation for individual reaction processes
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