Package org.openscience.cdk.reaction.mechanism

Class RadicalSiteRearrangementMechanism

java.lang.Object

org.openscience.cdk.reaction.mechanism.RadicalSiteRearrangementMechanism

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

Created on:

2008-02-10

Constructor Summary

Constructors

Constructor	Description
RadicalSiteRearrangementMechanism()

Method Summary

Modifier and Type	Method	Description
IReaction	initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)	Initiates the process for the given mechanism.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

RadicalSiteRearrangementMechanism

public RadicalSiteRearrangementMechanism()

Method Details

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 interface IReactionMechanism

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 atom

bondList - 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