Class BioShapeCollection

java.lang.Object
org.jmol.shape.Shape
org.jmol.shapebio.BioShapeCollection
Direct Known Subclasses:
Backbone, Ribbons, Rockets, Strands, Trace
public abstract class BioShapeCollection extends Shape
When a Cartoon is instantiated with a call to setSize(), it creates an BioShapeCollection for each BioPolymer in the model set. It is these shapes that are the real "shapes". Unlike other shapes, which are indexed by atom and throughout the entire model set, these shapes are indexed by residue and are restricted to a given BioPolymer within a given Model.

  • Field Details

    • bioShapes

      public BioShape[] bioShapes

  • Constructor Details

    • BioShapeCollection

      public BioShapeCollection()

  • Method Details

    • initModelSet

      public final void initModelSet()
      Overrides:
      initModelSet in class Shape

    • initShape

      public void initShape()
      Specified by:
      initShape in class Shape

    • getSizeG

      public int getSizeG(Group group)
      Overrides:
      getSizeG in class Shape
      Parameters:
      group -
      Returns:
      size

    • replaceGroup

      public void replaceGroup(Group g0, Group g1)
      Overrides:
      replaceGroup in class Shape
      Parameters:
      g0 -
      g1 -

    • setShapeSizeRD

      public void setShapeSizeRD(int size, RadiusData rd, BS bsSelected)
      Overrides:
      setShapeSizeRD in class Shape

    • setProperty

      public void setProperty(String propertyName, Object value, BS bsSelected)
      Specified by:
      setProperty in class Shape

    • setPropBSC

      protected void setPropBSC(String propertyName, Object value, BS bsSelected)

    • getShapeState

      public String getShapeState()
      Specified by:
      getShapeState in class Shape

    • findNearestAtomIndex

      public void findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, BS bsNot)
      Overrides:
      findNearestAtomIndex in class Shape
      Parameters:
      xMouse -
      yMouse -
      closest -
      bsNot -

    • setModelVisibilityFlags

      public void setModelVisibilityFlags(BS bsModels)
      Overrides:
      setModelVisibilityFlags in class Shape
      Parameters:
      bsModels -

    • setAtomClickability

      public void setAtomClickability()
      Overrides:
      setAtomClickability in class Shape

    • getBioShape

      public BioShape getBioShape(int i)