Field Detail

• hasUnitCell

  private boolean hasUnitCell

• allOperators

  private java.lang.String[] allOperators

• currentModelIndex

  private int currentModelIndex

• alertedNoEdit

  private boolean alertedNoEdit

• atomHoverLabel

  private java.lang.String atomHoverLabel

• bondHoverLabel

  private java.lang.String bondHoverLabel

• xtalHoverLabel

  private java.lang.String xtalHoverLabel

• activeMenu

  private java.lang.String activeMenu

• lastModelSet

  protected ModelSet lastModelSet

• pickAtomAssignType

  private java.lang.String pickAtomAssignType

• lastElementType

  private java.lang.String lastElementType

• pickBondAssignType

  private java.lang.String pickBondAssignType

• isPickAtomAssignCharge

  private boolean isPickAtomAssignCharge

• bsHighlight

  private javajs.util.BS bsHighlight

• bondIndex

  private int bondIndex

• bondAtomIndex1

  private int bondAtomIndex1

• bondAtomIndex2

  private int bondAtomIndex2

• bsRotateBranch

  private javajs.util.BS bsRotateBranch

• branchAtomIndex

  private int branchAtomIndex

• isRotateBond

  private boolean isRotateBond

• screenXY

  private int[] screenXY

• mkdata

  private java.util.Map<java.lang.String,​java.lang.Object> mkdata

• showSymopInfo

  private boolean showSymopInfo

• addXtalHydrogens

  private boolean addXtalHydrogens

  when TRUE, add H atoms to C when added to the modelSet.

• clickToSetElement

  private boolean clickToSetElement

  Except for H atoms, do not allow changes to elements just by clicking them. This protects against doing that inadvertently when editing.

• centerPoint

  private javajs.util.P3 centerPoint

• spherePoint

  private javajs.util.P3 spherePoint

• viewOffset

  private javajs.util.P3 viewOffset

• centerDistance

  private float centerDistance

• symop

  private java.lang.Object symop

• centerAtomIndex

  private int centerAtomIndex

• secondAtomIndex

  private int secondAtomIndex

• atomIndexSphere

  private int atomIndexSphere

• drawData

  private java.lang.String drawData

• drawScript

  private java.lang.String drawScript

• iatom0

  private int iatom0

• MAX_LABEL

  private static final int MAX_LABEL

  See Also:

  Constant Field Values

• ATOM_MENU

  static final java.lang.String ATOM_MENU

  See Also:

  Constant Field Values

• BOND_MENU

  static final java.lang.String BOND_MENU

  See Also:

  Constant Field Values

• XTAL_MENU

  static final java.lang.String XTAL_MENU

  See Also:

  Constant Field Values

• bundle

  private static PopupResource bundle

• STATE_BITS_XTAL

  public static final int STATE_BITS_XTAL

  See Also:

  Constant Field Values

• STATE_MOLECULAR

  public static final int STATE_MOLECULAR

  See Also:

  Constant Field Values

• STATE_XTALVIEW

  public static final int STATE_XTALVIEW

  See Also:

  Constant Field Values

• STATE_XTALEDIT

  public static final int STATE_XTALEDIT

  See Also:

  Constant Field Values

• STATE_BITS_SYM_VIEW

  public static final int STATE_BITS_SYM_VIEW

  See Also:

  Constant Field Values

• STATE_SYM_NONE

  public static final int STATE_SYM_NONE

  See Also:

  Constant Field Values

• STATE_SYM_SHOW

  public static final int STATE_SYM_SHOW

  See Also:

  Constant Field Values

• STATE_BITS_SYM_EDIT

  public static final int STATE_BITS_SYM_EDIT

  See Also:

  Constant Field Values

• STATE_SYM_APPLYLOCAL

  public static final int STATE_SYM_APPLYLOCAL

  See Also:

  Constant Field Values

• STATE_SYM_RETAINLOCAL

  public static final int STATE_SYM_RETAINLOCAL

  See Also:

  Constant Field Values

• STATE_SYM_APPLYFULL

  public static final int STATE_SYM_APPLYFULL

  See Also:

  Constant Field Values

• STATE_BITS_UNITCELL

  public static final int STATE_BITS_UNITCELL

  See Also:

  Constant Field Values

• STATE_UNITCELL_PACKED

  public static final int STATE_UNITCELL_PACKED

  See Also:

  Constant Field Values

• STATE_UNITCELL_EXTEND

  public static final int STATE_UNITCELL_EXTEND

  See Also:

  Constant Field Values

• MODE_OPTIONS

  public static final java.lang.String MODE_OPTIONS

  See Also:

  Constant Field Values

• SYMMETRY_OPTIONS

  public static final java.lang.String SYMMETRY_OPTIONS

  See Also:

  Constant Field Values

• UNITCELL_OPTIONS

  public static final java.lang.String UNITCELL_OPTIONS

  See Also:

  Constant Field Values

• BOOLEAN_OPTIONS

  public static final java.lang.String BOOLEAN_OPTIONS

  See Also:

  Constant Field Values

• SET_OPTIONS

  public static final java.lang.String SET_OPTIONS

  See Also:

  Constant Field Values

• Pt000

  private static final javajs.util.P3 Pt000

• state

  private int state

• rotationDeg

  private float rotationDeg

• lastCenter

  private java.lang.String lastCenter

• lastOffset

  private java.lang.String lastOffset

Constructor Detail

• ModelKitPopup

  public ModelKitPopup()

Method Detail

• initialize

  protected void initialize​(Viewer vwr,
                            PopupResource bundle,
                            java.lang.String title)

  Overrides:

  initialize in class JmolGenericPopup

• getBundle

  protected PopupResource getBundle​(java.lang.String menu)

  Specified by:

  getBundle in class JmolGenericPopup

• initializeForModel

  public void initializeForModel()

• jpiUpdateComputedMenus

  public void jpiUpdateComputedMenus()

• appUpdateForShow

  protected void appUpdateForShow()

  Specified by:

  appUpdateForShow in class GenericPopup

• updateOperatorMenu

  protected void updateOperatorMenu()

• addAllCheckboxItems

  private void addAllCheckboxItems​(SC menu,
                                   java.lang.String[] labels)

• updateAllXtalMenuOptions

  protected void updateAllXtalMenuOptions()

• setLabel

  private void setLabel​(java.lang.String key,
                        java.lang.String label)

• getActiveMenu

  public java.lang.String getActiveMenu()

  for FrankRender -- the thin box on the top left

  Returns:

  [ "atomMenu" | "bondMenu" | "xtalMenu" | null ]

• setActiveMenu

  public java.lang.String setActiveMenu​(java.lang.String name)

  Set the active menu and request a repaint.

  Parameters:

  name -

  Returns:

  activeMenu or null

• appUpdateSpecialCheckBoxValue

  protected void appUpdateSpecialCheckBoxValue​(SC source,
                                               java.lang.String actionCommand,
                                               boolean selected)

  Set the active menu based on updating a value -- usually by the user, but also during setup (ignored).

  Specified by:

  appUpdateSpecialCheckBoxValue in class GenericPopup

• isXtalState

  private boolean isXtalState()

• setMKState

  private void setMKState​(int bits)

• getMKState

  private int getMKState()

• setSymEdit

  private void setSymEdit​(int bits)

• getSymEditState

  private int getSymEditState()

• getViewState

  private int getViewState()

• setSymViewState

  private void setSymViewState​(int bits)

• getSymViewState

  private int getSymViewState()

• setUnitCell

  private void setUnitCell​(int bits)

• getUnitCellState

  private int getUnitCellState()

• isPickAtomAssignCharge

  public boolean isPickAtomAssignCharge()

• getProperty

  public java.lang.Object getProperty​(java.lang.Object data)

  Get a property of the modelkit.

  Parameters:

  data - a name or an array with [name, value]

  Returns:

  value

• setProperty

  public java.lang.Object setProperty​(java.lang.String name,
                                      java.lang.Object value)

  Modify the state by setting a property -- primarily from CmdExt.modelkit. Also can be used for "get" purposes.

  Parameters:

  name -

  value -

  Returns:

  null or "get" value

• isTrue

  private static boolean isTrue​(java.lang.Object value)

• getData

  private java.lang.Object getData​(java.lang.String key)

  Parameters:

  key -

  Returns:

• addData

  private void addData​(java.lang.String key,
                       java.lang.Object value)

• processAtomClick

  private boolean processAtomClick​(int atomIndex)

  An atom has been clicked -- handle it. Called from CmdExt.assignAtom from the script created in ActionManager.assignNew from Actionmanager.checkReleaseAction

  Parameters:

  atomIndex -

  Returns:

  true if handled

• getHoverLabel

  private java.lang.String getHoverLabel​(int atomIndex)

  Called by Viewer.hoverOn to set the special label if desired.

  Parameters:

  atomIndex -

  Returns:

  special label or null

• setDefaultState

  private void setDefaultState​(int mode)

• appGetBooleanProperty

  protected boolean appGetBooleanProperty​(java.lang.String name)

  Overrides:

  appGetBooleanProperty in class JmolGenericPopup

• getUnknownCheckBoxScriptToRun

  public java.lang.String getUnknownCheckBoxScriptToRun​(SC item,
                                                        java.lang.String name,
                                                        java.lang.String what,
                                                        boolean TF)

  From JmolGenericPopup.appRunSpecialCheckBox when name starts with "mk" or has "??" in it.

  Specified by:

  getUnknownCheckBoxScriptToRun in class GenericPopup

• processMKPropertyItem

  private void processMKPropertyItem​(java.lang.String name,
                                     boolean TF)

• showXtalSymmetry

  private void showXtalSymmetry()

  Draw the symmetry element

• assignAtom

  private void assignAtom​(int atomIndex,
                          java.lang.String type,
                          boolean autoBond,
                          boolean addHsAndBond,
                          boolean isClick)

  Original ModelKitPopup functionality -- assign an atom.

  Parameters:

  atomIndex -

  type -

  autoBond -

  addHsAndBond -

  isClick - whether this is a click or not

• assignBond

  private javajs.util.BS assignBond​(int bondIndex,
                                    char type)

  Original ModelKit functionality -- assign a bond.

  Parameters:

  bondIndex -

  type -

  Returns:

  bit set of atoms to modify

• isVwrRotateBond

  private boolean isVwrRotateBond()

• getRotateBondIndex

  public int getRotateBondIndex()

• resetBondFields

  private void resetBondFields​(java.lang.String where)

  Parameters:

  where -

• setBondIndex

  private void setBondIndex​(int index,
                            boolean isRotate)

  Set the bond for rotation -- called by Sticks.checkObjectHovered via Viewer.highlightBond.

  Parameters:

  index -

  isRotate -

• actionRotateBond

  public void actionRotateBond​(int deltaX,
                               int deltaY,
                               int x,
                               int y,
                               boolean forceFull)

  Actually rotate the bond. Called by ActionManager.checkDragWheelAction.

  Parameters:

  deltaX -

  deltaY -

  x -

  y -

  forceFull -

• menuFocusCallback

  public void menuFocusCallback​(java.lang.String name,
                                java.lang.String actionCommand,
                                boolean gained)

  Specified by:

  menuFocusCallback in class GenericPopup

• menuClickCallback

  public void menuClickCallback​(SC source,
                                java.lang.String script)

  Overrides:

  menuClickCallback in class GenericPopup

• doMenuClickCallbackMK

  public void doMenuClickCallbackMK​(SC source,
                                    java.lang.String script)

• getScriptForCallback

  protected java.lang.String getScriptForCallback​(SC source,
                                                  java.lang.String id,
                                                  java.lang.String script)

  Secondary processing of menu item click

  Specified by:

  getScriptForCallback in class GenericPopup

• processXtalClick

  private void processXtalClick​(java.lang.String id,
                                java.lang.String action)

• processSelOpClick

  private void processSelOpClick​(java.lang.String action)

• processSymop

  private boolean processSymop​(java.lang.String id,
                               boolean isFocus)

• showSymop

  private void showSymop​(java.lang.Object symop)

• processModeClick

  private void processModeClick​(java.lang.String action)

• processSelClick

  private void processSelClick​(java.lang.String action)

• processSymClick

  private void processSymClick​(java.lang.String action)

• processUCClick

  private void processUCClick​(java.lang.String action)

• handleDragAtom

  public boolean handleDragAtom​(MouseState pressed,
                                MouseState dragged,
                                int[] countPlusIndices)

  Called from ActionManager for a drag-drop

  Parameters:

  pressed -

  dragged -

  countPlusIndices -

  Returns:

  true if handled here

• pointFromTriad

  private static javajs.util.P3 pointFromTriad​(java.lang.String pos)

• notImplemented

  private static void notImplemented​(java.lang.String action)

• promptUser

  private java.lang.String promptUser​(java.lang.String msg,
                                      java.lang.String def)

• runScriptBuffered

  private java.lang.String runScriptBuffered​(java.lang.String script)

• handleAssignNew

  public boolean handleAssignNew​(MouseState pressed,
                                 MouseState dragged,
                                 MeasurementPending mp,
                                 int dragAtomIndex)

  C

  Parameters:

  pressed -

  dragged -

  mp -

  dragAtomIndex -

  Returns:

  true if we should do a refresh now

• cmdAssignAtom

  public void cmdAssignAtom​(int atomIndex,
                            javajs.util.P3 pt,
                            java.lang.String type,
                            java.lang.String cmd,
                            boolean isClick)

• cmdAssignBond

  public void cmdAssignBond​(int bondIndex,
                            char type,
                            java.lang.String cmd)

• cmdAssignConnect

  public void cmdAssignConnect​(int index,
                               int index2,
                               java.lang.String cmd,
                               boolean isClick)

• assignAtomClick

  public void assignAtomClick​(int atomIndex,
                              java.lang.String element,
                              javajs.util.P3 ptNew)

• appRunSpecialCheckBox

  protected boolean appRunSpecialCheckBox​(SC item,
                                          java.lang.String basename,
                                          java.lang.String script,
                                          boolean TF)

  Overrides:

  appRunSpecialCheckBox in class JmolGenericPopup