Class NBOParser

java.lang.Object
org.jmol.adapter.readers.quantum.NBOParser
public class NBOParser extends Object

  • Constructor Details

    • NBOParser

      public NBOParser()

  • Method Details

    • set

      public NBOParser set(Viewer vwr)

    • getAllStructures

      public Lst<Object> getAllStructures(String output, Lst<Object> list)

    • getStructures46

      public static void getStructures46(String[] tokens, String type, Lst<Object> structures, int nAtoms)
      Use the .46 file NBO alpha/beta labels to identify bonds, lone pairs, and lone valences.
      Parameters:
      tokens -
      type -
      structures -
      nAtoms -

    • getStructures

      public int getStructures(String data, String nrtType, Lst<Object> list)
      Reads the $NRTSTR $NRTSTRA, $NRTSTRB, and $CHOOSE blocks. Creates a Lst of Hashtables
      Parameters:
      data - NBO output block not including $END
      nrtType - "CHOOSE", "NRTSTRA", "NRTSTRB"
      list - to fill
      Returns:
      number of structures found or -1 for an error

    • isOpenShell

      public boolean isOpenShell()

    • getStructureMap

      public static Map<String,Object> getStructureMap(Lst<Object> structureList, String type, int index)
      Find the map for a specified structure, producing a structure that can be used to generate lone pairs and bonds for a Lewis structure
      Parameters:
      structureList - a list of structural information from this class created from an NBO file
      type - topoa, topob, nrtstra, nrtstrb, alpha, beta -- last two are from CHOOSE
      index - 0-based index for this type
      Returns:
      Hashtable or null

    • connectNBO

      public boolean connectNBO(int modelIndex, String type)
      Parameters:
      modelIndex -
      type - one of alpha|beta|choosea|chooseb|nrtstr_n|nrtstra_n|topo_n|topoa_n| topob_n
      Returns:
      true if successful

    • getNBOAtomLabel

      public String getNBOAtomLabel(Atom a)
      get the
      Parameters:
      a -
      Returns:
      label including (lp), (lv), and (if not open-spin) formal charge