Class GenNBOReader

  • All Implemented Interfaces:
    javajs.api.GenericLineReader

    public class GenNBOReader
    extends MOReader
    NBO file nn reader will pull in other files as necessary acknowledgments: Grange Hermitage, Frank Weinhold upgrade to NBO 6 allows reading of resonance structures, including base structure
    Author:
    hansonr
    • Field Detail

      • isOutputFile

        private boolean isOutputFile
      • nboType

        private java.lang.String nboType
      • nOrbitals0

        private int nOrbitals0
      • is47File

        private boolean is47File
      • isOpenShell

        private boolean isOpenShell
      • alphaOnly

        private boolean alphaOnly
      • betaOnly

        private boolean betaOnly
      • nAOs

        private int nAOs
      • nNOs

        private int nNOs
      • topoType

        private java.lang.String topoType
      • nStructures

        private int nStructures
      • addBetaSet

        private boolean addBetaSet
      • P_LIST

        private static java.lang.String P_LIST
      • SP_LIST

        private static java.lang.String SP_LIST
      • DS_LIST

        private static java.lang.String DS_LIST
      • DC_LIST

        private static java.lang.String DC_LIST
      • FS_LIST

        private static java.lang.String FS_LIST
      • FC_LIST

        private static java.lang.String FC_LIST
      • GS_LIST

        private static java.lang.String GS_LIST
      • GC_LIST

        private static java.lang.String GC_LIST
      • HS_LIST

        private static java.lang.String HS_LIST
      • HC_LIST

        private static java.lang.String HC_LIST
      • IS_LIST

        private static java.lang.String IS_LIST
      • IC_LIST

        private static java.lang.String IC_LIST
    • Constructor Detail

      • GenNBOReader

        public GenNBOReader()
    • Method Detail

      • initializeReader

        protected void initializeReader()
                                 throws java.lang.Exception
        Overrides:
        initializeReader in class MOReader
        Throws:
        java.lang.Exception
      • checkLine

        protected boolean checkLine()
                             throws java.lang.Exception
        Overrides:
        checkLine in class AtomSetCollectionReader
        Returns:
        true if need to read new line
        Throws:
        java.lang.Exception
      • getStructures

        private void getStructures​(java.lang.String type)
                            throws java.lang.Exception
        Throws:
        java.lang.Exception
      • getStructureList

        private javajs.util.Lst<java.lang.Object> getStructureList()
      • getFileData

        private java.lang.String getFileData​(java.lang.String ext)
                                      throws java.lang.Exception
        Throws:
        java.lang.Exception
      • getFile31

        private boolean getFile31()
                           throws java.lang.Exception
        Throws:
        java.lang.Exception
      • getFile46

        private void getFile46()
                        throws java.lang.Exception
        read the labels from xxxx.46
        Throws:
        java.lang.Exception
      • readData47

        private void readData47()
                         throws java.lang.Exception
        Throws:
        java.lang.Exception
      • getIntData

        private int[] getIntData()
                          throws java.lang.Exception
        Throws:
        java.lang.Exception
      • fillSlater

        private boolean fillSlater​(int[] slater,
                                   int n,
                                   int pt,
                                   int ng)
      • getAlphasAndExponents

        private void getAlphasAndExponents()
                                    throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readData31

        private boolean readData31​(java.lang.String line1)
                            throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readData46

        private void readData46()
                         throws java.lang.Exception
        read labels and not proper number of NOs, nNOs, for this nboType
        Throws:
        java.lang.Exception
      • getLabelKey

        private static java.lang.String getLabelKey​(java.lang.String labelKey)
      • readNBOCoefficients

        public static boolean readNBOCoefficients​(java.util.Map<java.lang.String,​java.lang.Object> moData,
                                                  java.lang.String nboType,
                                                  Viewer vwr)
        Called by setNBOType in IsoExt when use issues NBO TYPE xxx
        Parameters:
        moData -
        nboType -
        vwr -
        Returns:
        true if sucessful or false if required file is missing
      • getNBOOccupanciesStatic

        private static void getNBOOccupanciesStatic​(javajs.util.Lst<java.util.Map<java.lang.String,​java.lang.Object>> orbitals,
                                                    int nAOs,
                                                    int pt,
                                                    java.lang.String data,
                                                    int len,
                                                    int[] next)
      • readMOs

        private void readMOs()
                      throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readNBO37Occupancies

        private void readNBO37Occupancies​(int pt)
                                   throws java.lang.Exception
        Read occupancies from .37 file. Called by readMOs.
        Parameters:
        pt -
        Throws:
        java.lang.Exception
      • setNboLabels

        public static void setNboLabels​(java.lang.String[] tokens,
                                        int nLabels,
                                        javajs.util.Lst<java.util.Map<java.lang.String,​java.lang.Object>> orbitals,
                                        int nOrbitals0,
                                        java.lang.String moType)