Class ReactionSchemeManipulator

    • Constructor Detail

      • ReactionSchemeManipulator

        public ReactionSchemeManipulator()
    • Method Detail

      • getAllAtomContainers

        public static IAtomContainerSet getAllAtomContainers​(IReactionScheme scheme,
                                                             IAtomContainerSet molSet)
        Get all molecule objects from a set of Reactions given a IAtomContainerSet to add.
        Parameters:
        scheme - The set of reaction to inspect
        molSet - The set of molecules to be added
        Returns:
        The IAtomContainerSet
      • getAllAtomContainers

        public static IAtomContainerSet getAllAtomContainers​(IReactionScheme scheme)
        get all AtomContainers object from a set of Reactions.
        Parameters:
        scheme - The scheme of reaction to inspect
        Returns:
        The IAtomContainerSet
      • getAllIDs

        public static List<String> getAllIDs​(IReactionScheme scheme)
        Get all ID of this IReactionSet.
        Parameters:
        scheme - The IReactionScheme to analyze
        Returns:
        A List with all ID
      • getAllReactions

        public static IReactionSet getAllReactions​(IReactionScheme scheme)
        Get all IReaction's object from a given IReactionScheme.
        Parameters:
        scheme - The IReactionScheme to extract
        Returns:
        The IReactionSet
      • createReactionScheme

        public static IReactionScheme createReactionScheme​(IReactionSet reactionSet)
        Create a IReactionScheme give a IReactionSet object.
        Parameters:
        reactionSet - The IReactionSet
        Returns:
        The IReactionScheme
      • extractTopReactions

        public static IReactionSet extractTopReactions​(IReactionScheme reactionScheme)
        Extract a set of Reactions which are in top of a IReactionScheme. The top reactions are those which any of their reactants are participating in other reactions as a products.
        Parameters:
        reactionScheme - The IReactionScheme
        Returns:
        The set of top reactions
      • getAtomContainerSet

        public static ArrayList<IAtomContainerSet> getAtomContainerSet​(IAtomContainer origenMol,
                                                                       IAtomContainer finalMol,
                                                                       IReactionScheme reactionScheme)
        Extract the list of AtomContainers taking part in the IReactionScheme to originate a product given a reactant.
        Parameters:
        origenMol - The start IAtomContainer
        finalMol - The end IAtomContainer
        reactionScheme - The IReactionScheme containing the AtomContainers
        Returns:
        A List of IAtomContainerSet given the path