org.openscience.cdk.reaction

Interface IReactionMechanism

All Known Implementing Classes:

AdductionLPMechanism, AdductionPBMechanism, HeterolyticCleavageMechanism, HomolyticCleavageMechanism, RadicalSiteIonizationMechanism, RadicalSiteRearrangementMechanism, RearrangementChargeMechanism, RemovingSEofBMechanism, RemovingSEofNBMechanism, SharingElectronMechanism, TautomerizationMechanism

public interface IReactionMechanism

Classes that implement this interface are reaction mechanisms.

Author:

Miguel Rojas

Method Summary

Methods

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

Method Detail

initiate

IReaction initiate(IMoleculeSet moleculeSet,
                 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.

Parameters:

moleculeSet - The IMoleculeSet to apply the mechanism

atomList - The list of atoms taking part in the mechanism

bondList - The list of bonds taking part in the mechanism

Returns:

The Reaction mechanism

Throws:

CDKException - if an error occurs during the reaction process. See documentation for individual reaction processes