Package org.openscience.cdk.tools.manipulator

Class ReactionSetManipulator

java.lang.Object
org.openscience.cdk.tools.manipulator.ReactionSetManipulator
public class ReactionSetManipulator extends Object
See Also:

  • Constructor Details

    • ReactionSetManipulator

      public ReactionSetManipulator()

  • Method Details

    • getAtomCount

      public static int getAtomCount(IReactionSet set)

    • getBondCount

      public static int getBondCount(IReactionSet set)

    • removeAtomAndConnectedElectronContainers

      public static void removeAtomAndConnectedElectronContainers(IReactionSet set, IAtom atom)

    • removeElectronContainer

      public static void removeElectronContainer(IReactionSet set, IElectronContainer electrons)

    • 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

    • getAllIDs

      public static List<String> getAllIDs(IReactionSet set)

    • 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

    • getRelevantReaction

      public static IReaction getRelevantReaction(IReactionSet set, IAtom atom)

    • getRelevantReaction

      public static IReaction getRelevantReaction(IReactionSet set, IBond bond)

    • 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

    • getRelevantAtomContainer

      public static IAtomContainer getRelevantAtomContainer(IReactionSet set, IAtom atom)

    • getRelevantAtomContainer

      public static IAtomContainer getRelevantAtomContainer(IReactionSet set, IBond bond)

    • setAtomProperties

      public static void setAtomProperties(IReactionSet set, Object propKey, Object propVal)

    • getAllChemObjects

      public static List<IChemObject> getAllChemObjects(IReactionSet set)

    • 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;