Class SRSearcher


  • public class SRSearcher
    extends java.lang.Object
    The SRSearcher class handles reaction-sub-structure searches. Correctly, the class should be named SuperReactionSearcher, because it is rather a search for super reactions for a given query reaction. The query reaction may also be called transformation and may contain atom or bond based query features.
    • Constructor Summary

      Constructors 
      Constructor Description
      SRSearcher()  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      boolean isQueryInReaction()
      Performs a reaction substructure search with the SSSearcher.cDefaultMatchMode
      boolean isQueryInReaction​(int matchMode)  
      void setQuery​(byte[] rxncode, byte[] rxnmapping, byte[] rxncoords, long[] reactantFFP, long[] productFFP)  
      void setQuery​(Reaction query)
      This defines the query reaction (or transformation).
      void setQuery​(Reaction query, long[] reactantFFP, long[] productFFP)
      This defines the query reaction (or transformation).
      void setReaction​(byte[] rxncode, byte[] rxnmapping, byte[] rxncoords, long[] reactantFFP, long[] productFFP)  
      void setReaction​(Reaction reaction)  
      void setReaction​(Reaction reaction, long[] reactantFFP, long[] productFFP)
      This defines the query reaction (or transformation).
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • SRSearcher

        public SRSearcher()
    • Method Detail

      • setQuery

        public void setQuery​(byte[] rxncode,
                             byte[] rxnmapping,
                             byte[] rxncoords,
                             long[] reactantFFP,
                             long[] productFFP)
      • setReaction

        public void setReaction​(byte[] rxncode,
                                byte[] rxnmapping,
                                byte[] rxncoords,
                                long[] reactantFFP,
                                long[] productFFP)
      • setQuery

        public void setQuery​(Reaction query,
                             long[] reactantFFP,
                             long[] productFFP)
        This defines the query reaction (or transformation). Typically, this method is called once, while setReaction() is called many times, if a reaction collection is searched for hits. For acceleration through ffp based pre-screening, you should use this method to supply query ffps. If the query reaction contains multiple reactants or multiple products, these are merged into one molecule each. Thus, for a maximum of performance you may avoid this step by parsing a reaction that contains one reactant and one product only.
        Parameters:
        query -
        reactantFFP -
        productFFP -
      • setReaction

        public void setReaction​(Reaction reaction,
                                long[] reactantFFP,
                                long[] productFFP)
        This defines the query reaction (or transformation). Typically, this method is called once, while setReaction() is called many times, if a reaction collection is searched for hits. For acceleration through ffp based pre-screening, you should use this method to supply query ffps. If the query reaction contains multiple reactants or multiple products, these are merged into one molecule each. Thus, for a maximum of performance you may avoid this step by parsing a reaction that contains one reactant and one product only.
        Parameters:
        reaction -
        reactantFFP -
        productFFP -
      • setQuery

        public void setQuery​(Reaction query)
        This defines the query reaction (or transformation). Typically, this method is called once, while setReaction() is called many times, if a reaction collection is searched for hits. If the query reaction contains multiple reactants or multiple products, these are merged into one molecule each. Thus, for a maximum of performance you may avoid this step by parsing a reaction that contains one reactant and one product only.
        Parameters:
        query -
      • setReaction

        public void setReaction​(Reaction reaction)
      • isQueryInReaction

        public boolean isQueryInReaction()
        Performs a reaction substructure search with the SSSearcher.cDefaultMatchMode
        Returns:
      • isQueryInReaction

        public boolean isQueryInReaction​(int matchMode)
        Parameters:
        matchMode - cDefaultMatchMode or combination of cMatchAtomCharge, cMatchAtomMass, cMatchDBondToDelocalized, cMatchAromDBondToDelocalized
        Returns: