Field Detail

• ms

  private ModelSet ms

• shapes

  public Shape[] shapes

• vwr

  public Viewer vwr

• hoverable

  private static final int[] hoverable

• clickableMax

  private static int clickableMax

• bsRenderableAtoms

  public final BS bsRenderableAtoms

• bsSlabbedInternal

  public final BS bsSlabbedInternal

• navMinMax

  private final int[] navMinMax

Constructor Detail

• ShapeManager

  public ShapeManager​(Viewer vwr)

Method Detail

• setParallel

  public void setParallel()

• findNearestShapeAtomIndex

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

• getShapePropertyIndex

  public java.lang.Object getShapePropertyIndex​(int shapeID,
                                                java.lang.String propertyName,
                                                int index)

• getShapePropertyData

  public boolean getShapePropertyData​(int shapeID,
                                      java.lang.String propertyName,
                                      java.lang.Object[] data)

• getShapeIdFromObjectName

  public int getShapeIdFromObjectName​(java.lang.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,
                                         javajs.util.M4 mat)

• releaseShape

  public void releaseShape​(int shapeID)

• resetShapes

  public void resetShapes()

• setShapeSizeBs

  public void setShapeSizeBs​(int shapeID,
                             int size,
                             RadiusData rd,
                             BS bsSelected)

  Parameters:

  shapeID -

  size - in milliangstroms

  rd -

  bsSelected -

• setLabel

  public void setLabel​(java.lang.Object strLabel,
                       BS bsSelection)

• setShapePropertyBs

  public void setShapePropertyBs​(int shapeID,
                                 java.lang.String propertyName,
                                 java.lang.Object value,
                                 BS bsSelected)

• checkFrankclicked

  boolean checkFrankclicked​(int x,
                            int y)

• checkObjectClicked

  java.util.Map<java.lang.String,​java.lang.Object> checkObjectClicked​(int x,
                                                                            int y,
                                                                            int modifiers,
                                                                            BS bsVisible,
                                                                            boolean drawPicking)

• checkObjectDragged

  boolean checkObjectDragged​(int prevX,
                             int prevY,
                             int x,
                             int y,
                             int modifiers,
                             BS bsVisible,
                             int iShape)

• checkObjectHovered

  boolean checkObjectHovered​(int x,
                             int y,
                             BS bsVisible,
                             boolean checkBonds)

• deleteShapeAtoms

  public void deleteShapeAtoms​(java.lang.Object[] value,
                               BS bs)

• deleteVdwDependentShapes

  void deleteVdwDependentShapes​(BS bs)

• getAtomShapeValue

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

• replaceGroup

  public void replaceGroup​(Group g0,
                           Group g1)

• getObjectMap

  void getObjectMap​(java.util.Map<java.lang.String,​?> map,
                    boolean withDollar)

• getProperty

  java.lang.Object getProperty​(java.lang.Object paramInfo)

• getShape

  public Shape getShape​(int i)

• resetBioshapes

  public void resetBioshapes​(BS bsAllAtoms)

• setAtomLabel

  public void setAtomLabel​(java.lang.String strLabel,
                           int i)

• setModelVisibility

  void setModelVisibility()

  Sets shape visibility flags, including ATOM_VIS_INFRAME and ATOM_VIS_NOTHIDDEN.

• setShapeVis

  private void setShapeVis()

• 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)