Class 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 Detail

      • atoms

        Atom[] atoms
      • madOn

        short madOn
      • madHelixSheet

        short madHelixSheet
      • madTurnRandom

        short madTurnRandom
      • madDnaRna

        short madDnaRna
      • isActive

        boolean isActive
      • bioShapes

        public BioShape[] bioShapes
    • Constructor Detail

      • BioShapeCollection

        public BioShapeCollection()
    • Method Detail

      • 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
      • 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)
      • 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
      • getMpsShapeCount

        int getMpsShapeCount()
      • getBioShape

        public BioShape getBioShape​(int i)