Class ReactionSetManipulator

    • Constructor Detail

      • ReactionSetManipulator

        public ReactionSetManipulator()
    • Method Detail

      • getAtomCount

        public static int getAtomCount​(IReactionSet set)
      • getBondCount

        public static int getBondCount​(IReactionSet set)
      • removeAtomAndConnectedElectronContainers

        public static void removeAtomAndConnectedElectronContainers​(IReactionSet set,
                                                                    IAtom atom)
      • getAllMolecules

        public static IAtomContainerSet getAllMolecules​(IReactionSet set)
        get all Molecules object from a set of Reactions.
        Parameters:
        set - The set of reaction to inspect
        Returns:
        The IAtomContanerSet
      • getAllAtomContainers

        public static List<IAtomContainer> getAllAtomContainers​(IReactionSet set)
        Returns all the AtomContainer's of a Reaction.
        Parameters:
        set - the reaction set to get the molecules from
        Returns:
        a List containing the IAtomContainer objects in the IReactionSet
      • getRelevantReactions

        public static IReactionSet getRelevantReactions​(IReactionSet reactSet,
                                                        IAtomContainer molecule)
        Get all Reactions object containing a Molecule from a set of Reactions.
        Parameters:
        reactSet - The set of reaction to inspect
        molecule - The molecule to find
        Returns:
        The IReactionSet
      • getRelevantReactionsAsReactant

        public static IReactionSet getRelevantReactionsAsReactant​(IReactionSet reactSet,
                                                                  IAtomContainer molecule)
        Get all Reactions object containing a Molecule as a Reactant from a set of Reactions.
        Parameters:
        reactSet - The set of reaction to inspect
        molecule - The molecule to find as a reactant
        Returns:
        The IReactionSet
      • getRelevantReactionsAsProduct

        public static IReactionSet getRelevantReactionsAsProduct​(IReactionSet reactSet,
                                                                 IAtomContainer molecule)
        Get all Reactions object containing a Molecule as a Product from a set of Reactions.
        Parameters:
        reactSet - The set of reaction to inspect
        molecule - The molecule to find as a product
        Returns:
        The IReactionSet
      • getReactionByAtomContainerID

        public static IReaction getReactionByAtomContainerID​(IReactionSet reactionSet,
                                                             String id)
        Gets a reaction from a ReactionSet by ID of any product or reactant. If several exist, only the first one will be returned.
        Parameters:
        reactionSet - The reactionSet to search in
        id - The id to search for.
        Returns:
        The Reaction or null;
      • getReactionByReactionID

        public static IReaction getReactionByReactionID​(IReactionSet reactionSet,
                                                        String id)
        Gets a reaction from a ReactionSet by ID. If several exist, only the first one will be returned.
        Parameters:
        reactionSet - The reactionSet to search in
        id - The id to search for.
        Returns:
        The Reaction or null;