Package chemaxon.struc

Interface RgMoleculeGraph

All Known Implementing Classes:
RgMolecule
@PublicApi public interface RgMoleculeGraph
R-group container interface. This interface is for internal use only, please do not implement it!
Since:
Marvin 4.1, 11/24/2005

  • Method Details

    • getRootG

      MoleculeGraph getRootG()
      Gets the root structure.
      Returns:
      the root structure

    • getRgroupCount

      int getRgroupCount()
      Gets the number of R-groups.
      Returns:
      number of R-groups

    • getRgroupMemberCount

      int getRgroupMemberCount(int i)
      Gets the number of R-group members.
      Parameters:
      i - R-group index
      Returns:
      number of R-group members

    • getRgroupMemberG

      MoleculeGraph getRgroupMemberG(int i, int j)
      Gets an R-group member.
      Parameters:
      i - R-group index
      j - member index
      Returns:
      the R-group member

    • getRgroupId

      int getRgroupId(int i)
      Gets the ID of an R-group.
      Parameters:
      i - R-group index
      Returns:
      number between 0 and MolAtom.RGROUP_MAX

    • getRgroupIndex

      default int getRgroupIndex(int rgid)
      Finds R-group R#. This is an alias for findRgroupIndex(int).
      Parameters:
      rgid - number between 0 and MolAtom.RGROUP_MAX
      Returns:
      R-group index, or -1 if not found

    • findRgroupIndex

      int findRgroupIndex(int rgid)
      Finds R-group R#.
      Parameters:
      rgid - number between 0 and MolAtom.RGROUP_MAX
      Returns:
      R-group index, or -1 if not found

    • getRlogic

      int getRlogic(int i)
      Gets R-logic flags.
      Parameters:
      i - R-group index
      Returns:
      R-logic flags

    • getRlogicRange

      String getRlogicRange(int i)
      Gets R-logic occurrence range.
      Parameters:
      i - R-group index
      Returns:
      the occurrence range

    • rgroupIdOf

      int rgroupIdOf(MolAtom node)
      Finds the ID of the R-group (the number in R#) that contains the specified atom.
      Parameters:
      node - the atom
      Returns:
      the R-group ID if found or -1 if not found

    • rgroupIndexOf

      int rgroupIndexOf(MolAtom node)
      Finds the index of the R-group (the number in R#) that contains the specified atom.
      Parameters:
      node - the atom
      Returns:
      the R-group index if found or -1 if not found

    • getRgroupMemberId

      long getRgroupMemberId(MolAtom node)
      Gets the unique indentifier of the R-group member that contains the specified atom.
      Parameters:
      node - the atom
      Returns:
      the ID or -1

    • getRgroupIndexFromMemberId

      default int getRgroupIndexFromMemberId(long id)
      Gets the R-group index from the R-group member ID.
      Parameters:
      id - the R-group member ID or -1
      Returns:
      the R-group ID or -1

    • getRgroupMemberIndexFromMemberId

      default int getRgroupMemberIndexFromMemberId(long id)
      Gets the R-group member index from the R-group member ID.
      Parameters:
      id - the R-group member ID or -1
      Returns:
      the R-group member index or -1

    • cleanupRemovedRgroupMember

      void cleanupRemovedRgroupMember(MoleculeGraph m, int f)
      Clean-up after R-group removal.
      Parameters:
      m - the removed R-group member

    • getRgroupDisplayLabel

      String getRgroupDisplayLabel(int rgroupIndex)
      Returns the display label of an R-group. For example, "R5" for an ordinary R-group and "R1+R2" for an R-group bridge.
      Parameters:
      rgroupIndex - index of the R-group
      Returns:
      the display label of the R-group

    • getRgroupId

      int getRgroupId(RgroupBridgeId bridgeId)
      Returns the ID of the ordinary R-group that actually represents the given R-group bridge.
      Parameters:
      bridgeId - R-group bridge ID
      Returns:
      the id of the ordinary R-group that actually represents the given R-group bridge or -1 if the given bridge is not defined in the structure
      Since:
      Marvin 14.10.21.
      See Also: