Field Detail

• locked

  static ModelKit.Constraint locked

• none

  static ModelKit.Constraint none

• vwr

  private Viewer vwr

• menu

  private ModelKitPopup menu

• 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

• STATE_MOLECULAR

  static final int STATE_MOLECULAR

  See Also:

  Constant Field Values

• STATE_XTALVIEW

  static final int STATE_XTALVIEW

  See Also:

  Constant Field Values

• STATE_XTALEDIT

  static final int STATE_XTALEDIT

  See Also:

  Constant Field Values

• STATE_BITS_XTAL

  static final int STATE_BITS_XTAL

  See Also:

  Constant Field Values

• STATE_BITS_SYM_VIEW

  static final int STATE_BITS_SYM_VIEW

  See Also:

  Constant Field Values

• STATE_SYM_NONE

  static final int STATE_SYM_NONE

  See Also:

  Constant Field Values

• STATE_SYM_SHOW

  static final int STATE_SYM_SHOW

  See Also:

  Constant Field Values

• STATE_BITS_SYM_EDIT

  static final int STATE_BITS_SYM_EDIT

  See Also:

  Constant Field Values

• STATE_SYM_APPLYLOCAL

  static final int STATE_SYM_APPLYLOCAL

  See Also:

  Constant Field Values

• STATE_SYM_RETAINLOCAL

  static final int STATE_SYM_RETAINLOCAL

  See Also:

  Constant Field Values

• STATE_SYM_APPLYFULL

  static final int STATE_SYM_APPLYFULL

  See Also:

  Constant Field Values

• STATE_BITS_UNITCELL

  static final int STATE_BITS_UNITCELL

  See Also:

  Constant Field Values

• STATE_UNITCELL_PACKED

  static final int STATE_UNITCELL_PACKED

  See Also:

  Constant Field Values

• STATE_UNITCELL_EXTEND

  static final int STATE_UNITCELL_EXTEND

  See Also:

  Constant Field Values

• Pt000

  private static final javajs.util.P3 Pt000

• state

  int state

• rotationDeg

  float rotationDeg

• atomHoverLabel

  java.lang.String atomHoverLabel

• bondHoverLabel

  java.lang.String bondHoverLabel

• xtalHoverLabel

  java.lang.String xtalHoverLabel

• hasUnitCell

  boolean hasUnitCell

• allOperators

  java.lang.String[] allOperators

• currentModelIndex

  int currentModelIndex

• alertedNoEdit

  boolean alertedNoEdit

• lastModelSet

  protected ModelSet lastModelSet

• pickAtomAssignType

  java.lang.String pickAtomAssignType

• lastElementType

  java.lang.String lastElementType

• pickBondAssignType

  char pickBondAssignType

• isPickAtomAssignCharge

  boolean isPickAtomAssignCharge

• bsHighlight

  javajs.util.BS bsHighlight

• bondIndex

  int bondIndex

• bondAtomIndex1

  int bondAtomIndex1

• bondAtomIndex2

  int bondAtomIndex2

• bsRotateBranch

  javajs.util.BS bsRotateBranch

• branchAtomIndex

  int branchAtomIndex

• isRotateBond

  boolean isRotateBond

• screenXY

  int[] screenXY

• showSymopInfo

  boolean showSymopInfo

• addXtalHydrogens

  boolean addXtalHydrogens

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

• clickToSetElement

  boolean clickToSetElement

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

• autoBond

  boolean autoBond

  set to true for proximity-based autobonding (prior to 14.32.4/15.2.4 the default was TRUE

• centerPoint

  javajs.util.P3 centerPoint

• spherePoint

  javajs.util.P3 spherePoint

• viewOffset

  javajs.util.P3 viewOffset

• centerDistance

  float centerDistance

• symop

  java.lang.Object symop

• centerAtomIndex

  int centerAtomIndex

• secondAtomIndex

  int secondAtomIndex

• atomIndexSphere

  int atomIndexSphere

• drawData

  java.lang.String drawData

• drawScript

  java.lang.String drawScript

• iatom0

  int iatom0

• bondRotationName

  java.lang.String bondRotationName

• lastCenter

  java.lang.String lastCenter

• lastOffset

  java.lang.String lastOffset

• a0

  private Atom a0

• a3

  private Atom a3

• constraint

  private ModelKit.Constraint constraint

• atomConstraints

  private ModelKit.Constraint[] atomConstraints

• GET

  private static int GET

• GET_CREATE

  private static int GET_CREATE

• GET_DELETE

  private static int GET_DELETE

Constructor Detail

• ModelKit

  public ModelKit()

Method Detail

• setMenu

  public void setMenu​(ModelKitPopup menu)

• initializeForModel

  public void initializeForModel()

• showMenu

  public void showMenu​(int x,
                       int y)

• getDefaultModel

  public java.lang.String getDefaultModel()

• updateMenu

  public void updateMenu()

• dispose

  public void dispose()

• isPickAtomAssignCharge

  public boolean isPickAtomAssignCharge()

• isHidden

  public boolean isHidden()

• getActiveMenu

  public java.lang.String getActiveMenu()

  for the thin box on the top left of the window

  Returns:

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

• getRotateBondIndex

  public int getRotateBondIndex()

• getProperty

  public java.lang.Object getProperty​(java.lang.String name)

  Get a property of the modelkit.

  Parameters:

  name -

  Returns:

  value

• setProperty

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

  Modify the state by setting a property. Also can be used for "get" purposes.

  Parameters:

  key -

  value - to set, or null to simply return the current value

  Returns:

  null or "get" value

• setBondMeasure

  public MeasurementPending setBondMeasure​(int bi,
                                           MeasurementPending mp)

• actionRotateBond

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

  Actually rotate the bond.

  Parameters:

  deltaX -

  deltaY -

  x -

  y -

  forceFull -

• handleAssignNew

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

  handle a mouse-generated assignNew event

  Parameters:

  pressed -

  dragged -

  mp -

  dragAtomIndex -

  Returns:

  true if we should do a refresh now

• isXtalState

  boolean isXtalState()

• setMKState

  void setMKState​(int bits)

• getMKState

  int getMKState()

• setSymEdit

  void setSymEdit​(int bits)

• getSymEditState

  int getSymEditState()

• setSymViewState

  void setSymViewState​(int bits)

• getSymViewState

  int getSymViewState()

• setUnitCell

  void setUnitCell​(int bits)

• getUnitCellState

  int getUnitCellState()

• exitBondRotation

  void exitBondRotation​(java.lang.String text)

• resetBondFields

  void resetBondFields()

• processXtalClick

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

• processSymop

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

• setDefaultState

  void setDefaultState​(int mode)

• getAllOperators

  java.lang.String[] getAllOperators()

• setHasUnitCell

  boolean setHasUnitCell()

• checkNewModel

  boolean checkNewModel()

• getSymopText

  java.lang.String getSymopText()

• getCenterText

  java.lang.String getCenterText()

• resetAtomPickType

  void resetAtomPickType()

• setHoverLabel

  void setHoverLabel​(java.lang.String activeMenu,
                     java.lang.String text)

• getElementFromUser

  java.lang.String getElementFromUser()

• processMKPropertyItem

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

• assignAtom

  private int assignAtom​(int atomIndex,
                         java.lang.String type,
                         boolean autoBond,
                         boolean addHsAndBond,
                         boolean isClick,
                         javajs.util.BS bsAtoms)

  Original ModelKitPopup functionality -- assign an atom.

  Parameters:

  atomIndex -

  type -

  autoBond -

  addHsAndBond -

  isClick - whether this is a click or not

  bsAtoms -

  Returns:

  atomicNumber or -1

• cmdAssignSpaceGroup

  public java.lang.String cmdAssignSpaceGroup​(javajs.util.BS bs,
                                              java.lang.String name,
                                              int mi)

  Assign a given space group, currently only "P1"

  Parameters:

  bs - atoms in the set defining the space group

  name - "P1" or "1" or ignored

  Returns:

  new name or "" or error message

• cmdAssignDeleteAtoms

  public int cmdAssignDeleteAtoms​(javajs.util.BS bs)

  Delete all atoms that are equivalent to this atom.

  Parameters:

  bs -

  Returns:

  number of deleted atoms

• setBondIndex

  private void setBondIndex​(int index,
                            boolean isRotate)

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

  Parameters:

  index -

  isRotate -

• handleDragAtom

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

  Parameters:

  pressed -

  dragged -

  countPlusIndices -

  Returns:

  true if handled here

• showSymop

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

• showXtalSymmetry

  private void showXtalSymmetry()

  Draw the symmetry element

• getinfo

  private java.lang.Object getinfo()

• addInfo

  private void addInfo​(java.util.Map<java.lang.String,​java.lang.Object> info,
                       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

• processModeClick

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

• processSelClick

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

• processSelOpClick

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

• processSymClick

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

• processUCClick

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

• 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

• getBondLabel

  private java.lang.String getBondLabel​(Atom[] atoms)

• getOtherAtomIndex

  private Atom getOtherAtomIndex​(Atom a1,
                                 Atom a2)

• isVwrRotateBond

  private boolean isVwrRotateBond()

• promptUser

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

• appRunScript

  private void appRunScript​(java.lang.String script)

• runScriptBuffered

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

• isTrue

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

• pointFromTriad

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

• notImplemented

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

• cmdAssignAtom

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

  A versatile method that allows changing element, setting charge, setting position, adding or deleting an atom by clicking or dragging or via the MODELKIT ASSIGN ATOM command.

  Parameters:

  atomIndex - may be -1

  pt - a Cartesian position for a new atom or when moving an atom to a new position

  type - one of: an element symbol, "X" (delete), "Mi" (decrement charge), "Pl" (increment charge), "." (from connect; just adding hydrogens)

  cmd - reference command given; may be null

  isClick - if this is a user-generated click event

• assignAtoms

  private void assignAtoms​(javajs.util.P3 pt,
                           boolean newPoint,
                           int atomIndex,
                           java.lang.String type,
                           java.lang.String cmd,
                           boolean isClick,
                           javajs.util.BS bs,
                           int atomicNo,
                           int site,
                           SymmetryInterface uc,
                           javajs.util.Lst<javajs.util.P3> points,
                           java.lang.String packing)

  Change element, charge, and deleting an atom by clicking on it or via the MODELKIT ASSIGN ATOM command. null n bs ASSIGN ATOM @1 "N" pt -1 null ASSIGN ATOM "N" {x,y,z} pt -1 bs ADD ATOM @1 "N" {x,y,z}

  Parameters:

  pt -

  newPoint -

  atomIndex -

  type -

  cmd -

  isClick -

  bs -

  atomicNo -

  site -

  uc - a SymmetryInterface or null

  points -

  packing -

• cmdAssignBond

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

• assignBond

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

  Original ModelKit functionality -- assign a bond.

  Parameters:

  bondIndex -

  type -

  bsAtoms -

  Returns:

  bit set of atoms to modify

• cmdAssignConnect

  public void cmdAssignConnect​(int index,
                               int index2,
                               char type,
                               java.lang.String cmd)

• assignAtomClick

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

• cmdAssignAddAtoms

  public int cmdAssignAddAtoms​(java.lang.String type,
                               javajs.util.P3 pt,
                               javajs.util.BS bsAtoms,
                               java.lang.String packing,
                               java.lang.String cmd,
                               boolean isClick)

  MODELKIT ADD @3 ...

  Parameters:

  type -

  pt - the new point

  bsAtoms - the atoms to process, presumably from different sites

  packing - "packed" or ""

  cmd - the command generating this call

  isClick -

  Returns:

  the number of atoms added

• cmdAssignMoveAtoms

  public int cmdAssignMoveAtoms​(javajs.util.BS bsSelected,
                                int iatom,
                                javajs.util.P3 p)

  Move all atoms that are equivalent to this atom PROVIDED that they have the same symmetry-invariant properties.

  Parameters:

  bsSelected - could be a single atom or a molecule

  iatom - atom index

  p0 - new position for this atom, which may be modified

  Returns:

• assignMoveAtom

  public int assignMoveAtom​(int iatom,
                            javajs.util.P3 pt,
                            javajs.util.BS bsFixed)

• fillPointsForMove

  private boolean fillPointsForMove​(SymmetryInterface sg,
                                    javajs.util.BS bseq,
                                    int i0,
                                    javajs.util.P3 a,
                                    javajs.util.P3 pt,
                                    javajs.util.P3[] points)

  Find the operator that transforms fractional point fa to one of its symmetry-equivalent points, and then also transform pt by that same matrix. Optionally, save the transformed points in a compact array.

  Parameters:

  sg -

  bseq -

  i0 -

  a -

  pt -

  points -

  Returns:

  false if there is a failure to find a transform

• clearAtomConstraints

  public void clearAtomConstraints()

• hasConstraint

  public boolean hasConstraint​(int iatom,
                               boolean ignoreGeneral,
                               boolean addNew)

• moveConstrained

  public int moveConstrained​(int iatom,
                             javajs.util.P3 ptNew,
                             boolean doAssign)

  This is the main method from viewer.moveSelected.

  Parameters:

  iatom -

  ptNew -

  bsFixed -

  doAssign - allow for exit with setting ptNew but not creating atoms

  Returns:

  number of atoms moved

• getConstraint

  private ModelKit.Constraint getConstraint​(SymmetryInterface sym,
                                            int ia,
                                            int mode)

  This constraint will be set for the site only.

  Parameters:

  sym -

  ia -

  mode - GET, GET_CREATE, or GET_DELETE

  Returns:

  a Constraint, or possibly null if not createNew

• addConstraint

  private ModelKit.Constraint addConstraint​(int iatom,
                                            ModelKit.Constraint c)

• addLockedAtoms

  public void addLockedAtoms​(javajs.util.BS bs)