Package org.jmol.shapebio

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
Mps stands for Model-Polymer-Shape When a Cartoon is instantiated with a call to setSize(), it creates an MpsShape 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. Model

  • Field Details

    • atoms

      Atom[] atoms

    • madOn

      short madOn

    • madHelixSheet

      short madHelixSheet

    • madTurnRandom

      short madTurnRandom

    • madDnaRna

      short madDnaRna

    • isActive

      boolean isActive

    • 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
      Returns:
      size

    • replaceGroup

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

    • setShapeSizeRD

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

    • setProperty

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

    • setPropBSC

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

    • getShapeState

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

    • initialize

      void initialize()

    • findNearestAtomIndex

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

    • setModelVisibilityFlags

      public void setModelVisibilityFlags(javajs.util.BS bsModels)
      Overrides:
      setModelVisibilityFlags in class Shape

    • setAtomClickability

      public void setAtomClickability()
      Overrides:
      setAtomClickability in class Shape

    • getMpsShapeCount

      int getMpsShapeCount()

    • getBioShape

      public BioShape getBioShape(int i)