Package org.openscience.cdk.isomorphism.matchers

Interface IRGroupList

  • All Known Implementing Classes:
    RGroupList
    public interface IRGroupList
    Represents a list of Rgroup substitutes to be associated with some key in an IRGroupQuery.
    Author:
    John Mayfield

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      String getOccurrence()
      Occurrence required: n : exactly n ; n - m : n through m ; > n : greater than n ; < n : fewer than n ; default (blank) is > 0 ; Any non-contradictory combination of the preceding values is also allowed; for example "1, 3-7, 9, >11".
      int getRequiredRGroupNumber()
      Access the dependant Rgroup number if R1 then R2.
      int getRGroupNumber()
      Get the Rgroup number, for example R1 => 1.
      List<IRGroup> getRGroups()
      Access the list of possible RGroups.
      boolean isRestH()
      Indicates that sites labeled with this Rgroup may only be substituted with a member of the Rgroup or with hydrogen.
      List<Integer> matchOccurence​(int maxAttachments)
      Matches the 'occurrence' condition with a provided maximum number of RGroup attachments.

    • Method Detail

      • getRGroupNumber

        int getRGroupNumber()
        Get the Rgroup number, for example R1 => 1.
        Returns:
        the Rgroup number

      • getRequiredRGroupNumber

        int getRequiredRGroupNumber()
        Access the dependant Rgroup number if R1 then R2.
        Returns:
        the required Rgroup number.

      • getRGroups

        List<IRGroup> getRGroups()
        Access the list of possible RGroups.
        Returns:
        the rgroups.

      • isRestH

        boolean isRestH()
        Indicates that sites labeled with this Rgroup may only be substituted with a member of the Rgroup or with hydrogen.

      • matchOccurence

        List<Integer> matchOccurence​(int maxAttachments)
        Matches the 'occurrence' condition with a provided maximum number of RGroup attachments. Returns the valid occurrences (numeric) for these two combined. If none found, returns empty list.
        Example: if R1 occurs 3 times attached to some root structure, then stating ">5" as an occurrence for that RGoupList does not make sense: the example R1 can occur 0..3 times. Empty would be returned.
        If the occurence would be >2, then 3 would be returned. Etcetera.
        Parameters:
        maxAttachments - number of attachments
        Returns:
        valid values by combining a max for R# with the occurrence cond.

      • getOccurrence

        String getOccurrence()
        Occurrence required:
        • n : exactly n ;
        • n - m : n through m ;
        • > n : greater than n ;
        • < n : fewer than n ;
        • default (blank) is > 0 ;
        Any non-contradictory combination of the preceding values is also allowed; for example "1, 3-7, 9, >11".