Class JmolObject


  • class JmolObject
    extends java.lang.Object
    a class to store rendering information prior to finishing file loading, specifically designed for reading PyMOL PSE files. More direct than a script
    • Field Summary

      Fields 
      Modifier and Type Field Description
      (package private) int argb  
      private BS bsAtoms  
      java.lang.String cacheID  
      private java.lang.Object[] colors  
      (package private) int id  
      private java.lang.Object info  
      (package private) java.lang.String jmolName  
      (package private) int modelIndex  
      (package private) RadiusData rd  
      private int size  
      (package private) float translucency  
      (package private) boolean visible  
    • Constructor Summary

      Constructors 
      Constructor Description
      JmolObject​(int id, java.lang.String branchNameID, BS bsAtoms, java.lang.Object info)  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      (package private) void finalizeObject​(PyMOLScene pymolScene, ModelSet m, java.lang.String mepList, boolean doCache)  
      private int getModelIndex​(ModelSet m)  
      (package private) void offset​(int modelOffset, int atomOffset)
      offset is carried out in ModelLoader when the "script" is processed to move the bits to skip the base atom index.
      (package private) void setColors​(short[] colixes, float translucency)  
      (package private) void setSize​(float size)  
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Field Detail

      • id

        int id
      • bsAtoms

        private BS bsAtoms
      • info

        private java.lang.Object info
      • size

        private int size
      • colors

        private java.lang.Object[] colors
      • modelIndex

        int modelIndex
      • jmolName

        java.lang.String jmolName
      • argb

        int argb
      • translucency

        float translucency
      • visible

        boolean visible
      • cacheID

        public java.lang.String cacheID
    • Constructor Detail

      • JmolObject

        JmolObject​(int id,
                   java.lang.String branchNameID,
                   BS bsAtoms,
                   java.lang.Object info)
        Parameters:
        id - A Token or JmolConstants.SHAPE_XXXX
        branchNameID -
        bsAtoms -
        info - optional additional information for the shape
    • Method Detail

      • offset

        void offset​(int modelOffset,
                    int atomOffset)
        offset is carried out in ModelLoader when the "script" is processed to move the bits to skip the base atom index.
        Parameters:
        modelOffset -
        atomOffset -
      • finalizeObject

        void finalizeObject​(PyMOLScene pymolScene,
                            ModelSet m,
                            java.lang.String mepList,
                            boolean doCache)
      • getModelIndex

        private int getModelIndex​(ModelSet m)
      • setColors

        void setColors​(short[] colixes,
                       float translucency)
      • setSize

        void setSize​(float size)