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

    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 Details

    • 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".