Class ShapeManager

java.lang.Object
org.jmol.viewer.ShapeManager
public class ShapeManager extends Object

  • Field Details

    • shapes

      public Shape[] shapes

    • vwr

      public Viewer vwr

    • bsRenderableAtoms

      public final BS bsRenderableAtoms

    • bsSlabbedInternal

      public final BS bsSlabbedInternal

  • Constructor Details

    • ShapeManager

      public ShapeManager(Viewer vwr)

  • Method Details

    • setParallel

      public void setParallel()

    • findNearestShapeAtomIndex

      public void findNearestShapeAtomIndex(int x, int y, Atom[] closest, BS bsNot)

    • getShapePropertyIndex

      public Object getShapePropertyIndex(int shapeID, String propertyName, int index)

    • getShapePropertyData

      public boolean getShapePropertyData(int shapeID, String propertyName, Object[] data)

    • getShapeIdFromObjectName

      public int getShapeIdFromObjectName(String objectName)
      Returns the shape type index for a shape object given the object name.
      Parameters:
      objectName - (string) string name of object
      Returns:
      shapeType (int) integer corresponding to the shape type index see ShapeManager.shapes[].

    • loadDefaultShapes

      public void loadDefaultShapes(ModelSet newModelSet)

    • loadShape

      public Shape loadShape(int shapeID)

    • notifyAtomPositionsChanged

      public void notifyAtomPositionsChanged(int baseModel, BS bs, M4 mat)

    • releaseShape

      public void releaseShape(int shapeID)

    • setScale

      public void setScale()

    • resetShapes

      public void resetShapes(boolean cacheScale)

    • setShapeProperties

      public void setShapeProperties(int shapeID, Object[]... values)

    • setShapeSizeBs

      public void setShapeSizeBs(int shapeID, int size, RadiusData rd, BS bsSelected)
      Parameters:
      shapeID -
      size - in milliangstroms
      rd -
      bsSelected -

    • setLabel

      public void setLabel(Object strLabel, BS bsSelection)

    • setShapePropertyBs

      public void setShapePropertyBs(int shapeID, String propertyName, Object value, BS bsSelected)

    • deleteShapeAtoms

      public void deleteShapeAtoms(Object[] value, BS bs)

    • notifyAtoms

      public void notifyAtoms(String prop, BS[] atomsAndModels)

    • getAtomShapeValue

      public float getAtomShapeValue(int tok, Group group, int atomIndex)

    • replaceGroup

      public void replaceGroup(Group g0, Group g1)

    • getShape

      public Shape getShape(int i)

    • resetBioshapes

      public void resetBioshapes(BS bsAllAtoms)

    • setAtomLabel

      public void setAtomLabel(String strLabel, int i)

    • finalizeAtoms

      public int[] finalizeAtoms(BS bsTranslateSelected, boolean finalizeParams)

    • setModelSet

      public void setModelSet(ModelSet modelSet)

    • checkInheritedShapes

      public void checkInheritedShapes()
      starting with Jmol 13.1.13, isosurfaces can use "property color" to inherit the color of the underlying atoms. This is then dynamic

    • restrictSelected

      public void restrictSelected(boolean isBond, boolean doInvert)