java.lang.Object
org.openscience.cdk.isomorphism.matchers.RGroup
All Implemented Interfaces:
IRGroup

public class RGroup extends Object implements IRGroup
Represents a single substitute structure in an RGroupList.

The order of attachment points is provided (first and second only, conform RGFile spec). This order is relevant when the structure connects to the root with more than one bond.

See also RGroupList and RGroupQuery.

Author:
Mark Rijnbeek
Source code:
main
Belongs to CDK module:
isomorphism
Keywords:
Rgroup, R group, R-group
  • Field Details

    • ROOT_LABEL

      public static final String ROOT_LABEL
      Standard label/title to be used for the root atom container.
      See Also:
  • Constructor Details

    • RGroup

      public RGroup()
  • Method Details

    • makeLabel

      public static String makeLabel(int rgroupNum)
      Makes a label/title to be used for a substituent.
      Parameters:
      rgroupNum - R-Group number (1..32)
      Returns:
      label for substituent, like "R3"
    • setFirstAttachmentPoint

      public void setFirstAttachmentPoint(IAtom firstAttachmentPoint)
    • getFirstAttachmentPoint

      public IAtom getFirstAttachmentPoint()
      Description copied from interface: IRGroup
      Get the first attachment point of the RGroup.
      Specified by:
      getFirstAttachmentPoint in interface IRGroup
      Returns:
      the first attachment point
    • setSecondAttachmentPoint

      public void setSecondAttachmentPoint(IAtom secondAttachmentPoint)
    • getSecondAttachmentPoint

      public IAtom getSecondAttachmentPoint()
      Description copied from interface: IRGroup
      Get the optional second attachment point of the RGroup.
      Specified by:
      getSecondAttachmentPoint in interface IRGroup
      Returns:
      the second attachment point or null.
    • setGroup

      public void setGroup(IAtomContainer group)
    • getGroup

      public IAtomContainer getGroup()
      Description copied from interface: IRGroup
      Get the connection table of atoms/bonds for this Rgroup.
      Specified by:
      getGroup in interface IRGroup
      Returns:
      the connection table