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
Source code:
main
Belongs to CDK module:
reaction
Created on:
2008-02-10
  • 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