Package org.jmol.jvxl.readers

Class BCifDensityReader

  • All Implemented Interfaces:
    VertexDataServer
    Direct Known Subclasses:
    CifDensityReader
    class BCifDensityReader
extends MapFileReader
    Binary CIF density reader. See https://www.ebi.ac.uk/pdbe/densities/x-ray/1eve/box, for example: https://www.ebi.ac.uk/pdbe/densities/x-ray/1eve/box/-4.413,55.607,64.124/-0.4130001,59.607,68.124?space=cartesian&encoding=bcif Reads a MessagePack file and extracts either 2Fo-Fc or Fo-Fc.

    • Field Detail

      • header

        private java.lang.String header

      • pt

        private int pt

      • checkSum

        float checkSum

      • values

        protected float[] values

      • cifData

        public java.util.Map<java.lang.String,​java.lang.Object> cifData

      • thisData

        public java.util.Map<java.lang.String,​java.lang.Object> thisData

      • isDiff

        private boolean isDiff

    • Constructor Detail

      • BCifDensityReader

        BCifDensityReader()

    • Method Detail

      • getCifData

        protected void getCifData​(java.lang.String fileName,
                          java.lang.Object data)

      • readCifP3

        protected javajs.util.P3 readCifP3​(java.lang.String key,
                                   javajs.util.P3 p3)

      • getCifMap

        protected java.util.Map<java.lang.String,​java.lang.Object> getCifMap​(java.lang.String type)

      • getCifString

        protected java.lang.String getCifString​(java.lang.String key)

      • getCifFloat

        protected float getCifFloat​(java.lang.String key)

      • readCifFloats

        protected float[] readCifFloats​(java.lang.String key,
                                float[] values)

      • readParameters

        protected void readParameters()
                       throws java.lang.Exception
        Specified by:
        readParameters in class VolumeFileReader
        Throws:
        java.lang.Exception

      • getXYZ

        private float getXYZ​(javajs.util.P3 a,
                     float x)

      • nextVoxel

        protected float nextVoxel()
                   throws java.lang.Exception
        Overrides:
        nextVoxel in class VolumeFileReader
        Throws:
        java.lang.Exception

      • skipData

        protected void skipData​(int nPoints)
                 throws java.lang.Exception
        Overrides:
        skipData in class VolumeFileReader
        Throws:
        java.lang.Exception