Class CIPData

java.lang.Object
org.jmol.symmetry.CIPData
Direct Known Subclasses:
CIPDataSmiles, CIPDataTracker

public class CIPData extends Object
A helper class to handle application-specific analysis and store information needed by CIPChirality and CIPDataSmiles. Subclassed as CIPDataSmiles to also allow Jmol's "...SMILES...".find("SMILES","chirality")
  • Field Details

    • testRule6Full

      public boolean testRule6Full
      A flag that, if set, returns rr for bicyclo[2.2.2]octane
    • vNorm

      protected V3 vNorm
    • vTemp

      protected V3 vTemp
  • Constructor Details

    • CIPData

      public CIPData()
  • Method Details

    • isTracker

      protected boolean isTracker()
      Subclass identifier
      Returns:
      true for CIPDataTracker
    • set

      public CIPData set(Viewer vwr, BS bsAtoms)
      Actual constructor.
      Parameters:
      vwr - Jmol viewer
      bsAtoms - selected atoms
      Returns:
      this
    • init

      protected void init()
      initializer -- called also by CIPDataSmiles
    • getList

      protected BS[] getList(String smarts) throws Exception
      Retrieve an array of bit sets that match a given SMARTS
      Parameters:
      smarts -
      Returns:
      array of matching bit sets
      Throws:
      Exception
    • match

      protected BS match(String smarts) throws Exception
      Return a bit set corresponding to a SMARTS
      Parameters:
      smarts -
      Returns:
      bit set matching this SMARTS
      Throws:
      Exception
    • setRule6Full

      public void setRule6Full(boolean rrrr)