Class MoldenReader

  • All Implemented Interfaces:
    javajs.api.GenericLineReader
    Direct Known Subclasses:
    QCJSONReader

    public class MoldenReader
    extends MopacSlaterReader
    A molecular structure and orbital reader for MolDen files. See http://www.cmbi.ru.nl/molden/molden_format.html updated by Bob Hanson for Jmol 12.0/12.1 adding [spacegroup] [operators] [cell] [cellaxes] for Jmol 14.3.7
    Author:
    Matthew Zwier
    • Field Detail

      • loadGeometries

        protected boolean loadGeometries
      • loadVibrations

        protected boolean loadVibrations
      • vibOnly

        protected boolean vibOnly
      • optOnly

        protected boolean optOnly
      • doSort

        protected boolean doSort
      • orbitalType

        protected java.lang.String orbitalType
      • modelAtomCount

        protected int modelAtomCount
      • bsAtomOK

        private javajs.util.BS bsAtomOK
      • bsBadIndex

        private javajs.util.BS bsBadIndex
      • nSPDF

        private int[] nSPDF
      • haveEnergy

        private boolean haveEnergy
    • Constructor Detail

      • MoldenReader

        public MoldenReader()
    • Method Detail

      • 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
      • checkSymmetry

        private boolean checkSymmetry()
                               throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readAtoms

        private void readAtoms()
                        throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readSlaterBasis

        boolean readSlaterBasis()
                         throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readGaussianBasis

        private boolean readGaussianBasis()
                                   throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readMolecularOrbitals

        private boolean readMolecularOrbitals()
                                       throws java.lang.Exception
        Throws:
        java.lang.Exception
      • sortMOs

        private void sortMOs()
      • getMoTokens

        private java.lang.String[] getMoTokens​(java.lang.String line)
                                        throws java.lang.Exception
        Throws:
        java.lang.Exception
      • checkOrbitalType

        private boolean checkOrbitalType​(java.lang.String line)
      • fixOrbitalType

        private void fixOrbitalType()
      • readFreqsAndModes

        private boolean readFreqsAndModes()
                                   throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readGeometryOptimization

        private boolean readGeometryOptimization()
                                          throws java.lang.Exception
        Throws:
        java.lang.Exception
      • skipTo

        private void skipTo​(java.lang.String key)
                     throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readAtomSet

        private void readAtomSet​(java.lang.String atomSetName,
                                 boolean isBohr,
                                 boolean asClone)
                          throws java.lang.Exception
        Throws:
        java.lang.Exception