org.openscience.cdk.reaction.mechanism

Class RadicalSiteIonizationMechanism

java.lang.Object

org.openscience.cdk.reaction.mechanism.RadicalSiteIonizationMechanism

All Implemented Interfaces:

IReactionMechanism

public class RadicalSiteIonizationMechanism
extends Object
implements IReactionMechanism

This mechanism extracts an atom because of the stabilization of a radical. It returns the reaction mechanism which has been cloned the IAtomContainer.

This reaction could be represented as Y-B-[C*] => [Y*] + B=C

Author:

miguelrojasch

Source code:

master

Belongs to CDK module:

reaction

Created on:

2008-02-10

Constructor Summary

Constructors

Constructor and Description
RadicalSiteIonizationMechanism()

Method Summary

Modifier and Type	Method and 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 Detail

RadicalSiteIonizationMechanism

public RadicalSiteIonizationMechanism()

Method Detail

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 contains the ISingleElectron and the second third is the atom which will be removed 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