Package org.jmol.adapter.readers.quantum

Class MOReader

  • All Implemented Interfaces:
    javajs.api.GenericLineReader
    Direct Known Subclasses:
    GamessReader, GaussianReader, GenNBOReader, JaguarReader, NWChemReader, PsiReader, QchemReader
    public class MOReader
extends BasisFunctionReader
    General methods for reading molecular orbital data, including embedded output from the NBO program. In particular, when the AONBO keyword is included. requires the following sort of construct: public AtomSetCollection readAtomSetCollection(BufferedReader reader) { readAtomSetCollection(reader, "some type"); } protected boolean checkLine() { if (line.indexOf(...)) { doThis(); return true/false; } if (line.indexOf(...)) { doThat(); return true/false; } return checkNboLine(); }

    • Field Detail

      • shellCount

        public int shellCount

      • gaussianCount

        public int gaussianCount

      • gaussians

        public float[][] gaussians

      • energyUnits

        protected java.lang.String energyUnits

      • moTypes

        protected javajs.util.Lst<java.lang.String> moTypes

      • getNBOs

        private boolean getNBOs

      • getNBOCharges

        private boolean getNBOCharges

      • haveNboCharges

        protected boolean haveNboCharges

      • haveNboOrbitals

        protected boolean haveNboOrbitals

      • orbitalsRead

        protected boolean orbitalsRead

      • lastMoData

        private java.util.Map<java.lang.String,​java.lang.Object> lastMoData

      • allowNoOrbitals

        protected boolean allowNoOrbitals

      • HEADER_GAMESS_OCCUPANCIES

        protected final int HEADER_GAMESS_OCCUPANCIES
        See Also:
        Constant Field Values

      • haveCoeffMap

        private boolean haveCoeffMap

      • FC_LIST

        private static java.lang.String FC_LIST

      • iMo0

        private int iMo0

    • Constructor Detail

      • MOReader

        public MOReader()

    • Method Detail

      • checkAndRemoveFilterKey

        public boolean checkAndRemoveFilterKey​(java.lang.String key)
        Prior to filterMO all extraneous filter keys must be removed.
        Parameters:
        key -
        Returns:
        true if the key existed; filter is set null if this is the only key

      • checkNboLine

        protected boolean checkNboLine()
                        throws java.lang.Exception
        Returns:
        true if need to read line
        Throws:
        java.lang.Exception

      • getNboCharges

        private void getNboCharges()
                    throws java.lang.Exception
        Throws:
        java.lang.Exception

      • getNboTypes

        protected void getNboTypes()
                    throws java.lang.Exception
        Throws:
        java.lang.Exception

      • readMolecularOrbitals

        protected void readMolecularOrbitals​(int headerType)
                              throws java.lang.Exception
        Throws:
        java.lang.Exception

      • addCoef

        public void addCoef​(java.util.Map<java.lang.String,​java.lang.Object> mo,
                    float[] coefs,
                    java.lang.String type,
                    float energy,
                    float occ,
                    int moCount)

      • getMOHeader

        protected void getMOHeader​(int headerType,
                           java.lang.String[] tokens,
                           java.util.Map<java.lang.String,​java.lang.Object>[] mos,
                           int nThisLine)
                    throws java.lang.Exception
        Throws:
        java.lang.Exception

      • addMOData

        protected void addMOData​(int nColumns,
                         javajs.util.Lst<java.lang.String>[] data,
                         java.util.Map<java.lang.String,​java.lang.Object>[] mos)

      • setMOData

        public void setMOData​(boolean clearOrbitals)

      • readSecondOrderData

        private void readSecondOrderData()
                          throws java.lang.Exception
        Throws:
        java.lang.Exception