Package org.openscience.cdk.tools.manipulator

Class ReactionSchemeManipulator

java.lang.Object
org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
public class ReactionSchemeManipulator extends Object
See Also:
Source code:
main
Belongs to CDK module:
standard

  • Constructor Details

    • ReactionSchemeManipulator

      public ReactionSchemeManipulator()

  • Method Details

    • 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