Class QCJSONReader

  • All Implemented Interfaces:
    javajs.api.GenericLineReader

    public class QCJSONReader
    extends MoldenReader
    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

      • job

        private java.util.Map<java.lang.String,​java.lang.Object> job
      • jobCount

        private int jobCount
      • modelCount

        private int modelCount
      • lastBasisID

        java.lang.String lastBasisID
    • Constructor Detail

      • QCJSONReader

        public QCJSONReader()
    • Method Detail

      • processJob

        private void processJob​(java.util.Map<java.lang.String,​java.lang.Object> job)
                         throws java.lang.Exception
        Parameters:
        job -
        Throws:
        java.lang.Exception
      • readSteps

        private void readSteps()
                        throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readFreqsAndModesQC

        private boolean readFreqsAndModesQC​(java.util.ArrayList<java.lang.Object> vibrations)
                                     throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readMolecularOrbitalsQC

        private boolean readMolecularOrbitalsQC​(java.util.Map<java.lang.String,​java.lang.Object> molecular_orbitals)
                                         throws java.lang.Exception
        Read basis and orbital information.
        Parameters:
        molecular_orbitals -
        Returns:
        true if successful
        Throws:
        java.lang.Exception
      • toFloatArray

        private float[] toFloatArray​(double[] da)
      • readBasisQC

        private boolean readBasisQC​(java.lang.String moBasisID)
                             throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readSlaterBasisQC

        boolean readSlaterBasisQC​(java.util.ArrayList<java.lang.Object> listS)
                           throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readGaussianBasisQC

        private boolean readGaussianBasisQC​(java.util.ArrayList<java.lang.Object> listG,
                                            java.util.ArrayList<java.lang.Object> listS)
                                     throws java.lang.Exception
        Throws:
        java.lang.Exception
      • getMapSafely

        private static java.util.Map<java.lang.String,​java.lang.Object> getMapSafely​(java.util.Map<java.lang.String,​java.lang.Object> map,
                                                                                           java.lang.String key)
        Safely get a Map from a Map using a key.
        Parameters:
        map -
        key -
        Returns:
        the Map or null