Class Reactor


  • public class Reactor
    extends java.lang.Object
    • Constructor Summary

      Constructors 
      Constructor Description
      Reactor​(Reaction reaction)
      Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants.
      Reactor​(Reaction reaction, boolean retainCoordinates)
      Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants.
      Reactor​(Reaction reaction, boolean retainCoordinates, boolean fullyMapReactions, int maxProducts, boolean uniqueOnly)
      Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants.
    • Constructor Detail

      • Reactor

        public Reactor​(Reaction reaction)
        Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants. Reactors built with this constructor will not use product atom coordinates from the generic products, nor will they be able to generate fully mapped reactions. They will produce and return all unique products or reactions.
        Parameters:
        reaction - generic reactions consisting of reactant substructures with optional query features
      • Reactor

        public Reactor​(Reaction reaction,
                       boolean retainCoordinates)
        Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants. Reactors built with this constructor will be able to generate fully mapped reactions, They will produce and return all unique products or reactions.
        Parameters:
        reaction - generic reactions consisting of reactant substructures with optional query features
        retainCoordinates - if true, then atom coordinates from the generic products are taken into the real world products
      • Reactor

        public Reactor​(Reaction reaction,
                       boolean retainCoordinates,
                       boolean fullyMapReactions,
                       int maxProducts,
                       boolean uniqueOnly)
        Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants. The reactor may or may not use atoms coordinates from the generic products, when generating clean product atom coordinates.
        Parameters:
        reaction - generic reactions consisting of reactant substructures with optional query features
        retainCoordinates - if true, then atom coordinates from the generic products are taken into the real world products
        fullyMapReactions - if true, then real world reactants and products will have valid mapping numbers after product generation
        maxProducts - maximum number of products/reactions to be enumerated
        uniqueOnly - whether to skip duplicate products/reactions because of starting material symmetry
    • Method Detail

      • setReactant

        public void setReactant​(int no,
                                StereoMolecule reactant)
      • getProductIDCodes

        public java.lang.String[][] getProductIDCodes()
      • getFullyMappedReactions

        public Reaction[] getFullyMappedReactions()
        After instantiating the Reactor with fullyMappedReaction==true and after supplying real reactants, this method may be used to construct the fully mapped reaction. If one or more reactants have multiple matches of their generic reactants, then multiple reactions leading to isomeric products are returned. After calling this method, one or more new real reactants may provided with setReactant() before calling this method again.
        Returns:
        array with one or more reactions