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)
      • 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