Class BinaryDcdReader

  • All Implemented Interfaces:
    javajs.api.GenericLineReader

    public class BinaryDcdReader
    extends AtomSetCollectionReader
    DCD binary trajectory file reader. see http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dcdplugin.html and http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5651.html Bob Hanson 2/18/2011 requires PDB file load trajectory "c:/temp/t.pdb" coord "c:/temp/t.dcd"
    • Field Detail

      • nModels

        private int nModels
      • nAtoms

        private int nAtoms
      • nFree

        private int nFree
      • bsFree

        private javajs.util.BS bsFree
      • xAll

        private float[] xAll
      • yAll

        private float[] yAll
      • zAll

        private float[] zAll
      • crystGroup

        private int crystGroup
    • Constructor Detail

      • BinaryDcdReader

        public BinaryDcdReader()
    • Method Detail

      • setup

        protected void setup​(java.lang.String fullPath,
                             java.util.Map<java.lang.String,​java.lang.Object> htParams,
                             java.lang.Object reader)
        Overrides:
        setup in class AtomSetCollectionReader
      • trimString

        private java.lang.String trimString​(java.lang.String s)
      • readFloatArray

        private float[] readFloatArray()
                                throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readDoubleArray

        private double[] readDoubleArray()
                                  throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readCoordinates

        private void readCoordinates()
                              throws java.lang.Exception
        Throws:
        java.lang.Exception
      • getTrajectoryStep

        private boolean getTrajectoryStep​(javajs.util.P3[] trajectoryStep)
                                   throws java.lang.Exception
        Throws:
        java.lang.Exception
      • calcUnitCell

        private float[] calcUnitCell​(double[] abc)