Package org.jmol.adapter.readers.pymol

Class JmolObject

java.lang.Object
org.jmol.adapter.readers.pymol.JmolObject
class JmolObject extends 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 Details

    • id

      int id

    • bsAtoms

      private javajs.util.BS bsAtoms

    • info

      private Object info

    • size

      private int size

    • colors

      private Object[] colors

    • modelIndex

      int modelIndex

    • jmolName

      String jmolName

    • argb

      int argb

    • translucency

      float translucency

    • visible

      boolean visible

    • rd

      RadiusData rd

    • cacheID

      public String cacheID

  • Constructor Details

    • JmolObject

      JmolObject(int id, String branchNameID, javajs.util.BS bsAtoms, Object info)
      Parameters:
      id - A Token or JmolConstants.SHAPE_XXXX
      branchNameID -
      bsAtoms -
      info - optional additional information for the shape

  • Method Details

    • 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, String mepList, boolean doCache)

    • getModelIndex

      private int getModelIndex(ModelSet m)

    • setColors

      void setColors(short[] colixes, float translucency)

    • setSize

      void setSize(float size)