Class 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 Detail

      • RadicalSiteRearrangementMechanism

        public RadicalSiteRearrangementMechanism()
    • 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 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