Class ModelKit

Method Details

• checkOption

  public boolean checkOption(char type, String value)

• setMenu

  public void setMenu(ModelKitPopup menu)

• initializeForModel

  public void initializeForModel()

• showMenu

  public void showMenu(int x, int y)

• getDefaultModel

  public String getDefaultModel()

• updateMenu

  public void updateMenu()

• dispose

  public void dispose()

• isPickAtomAssignCharge

  public boolean isPickAtomAssignCharge()

• isHidden

  public boolean isHidden()

• getActiveMenu

  public String getActiveMenu()

  for the thin box on the top left of the window

  Returns:

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

• getRotateBondIndex

  public int getRotateBondIndex()

• getProperty

  public Object getProperty(String name)

  Get a property of the modelkit.

  Parameters:

  name -

  Returns:

  value

• setProperty

  public Object setProperty(String key, 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, int key)

  handle a mouse-generated assignNew event

  Parameters:

  pressed -

  dragged -

  mp -

  dragAtomIndex -

  key - from a key press

  Returns:

  true if we should do a refresh now

• keyToElement

  private static String keyToElement(int key)

  Convert key sequence from ActionManager into an element symbol. Element is (char 1) (char 2) or just (char 1)

  Parameters:

  key - (char 2 << 8) + (char 1), all caps

  Returns:

  valid element symbol or null

• 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(String text)

• resetBondFields

  void resetBondFields()

• processXtalClick

  void processXtalClick(String id, String action)

• processSymop

  boolean processSymop(String id, boolean isFocus)

• setDefaultState

  void setDefaultState(int mode)

• getAllOperators

  String[] getAllOperators()

• setHasUnitCell

  boolean setHasUnitCell()

• checkNewModel

  boolean checkNewModel()

• getSymopText

  String getSymopText()

• getCenterText

  String getCenterText()

• resetAtomPickType

  void resetAtomPickType()

• setHoverLabel

  void setHoverLabel(String mode, String text)

• getElementFromUser

  String getElementFromUser()

• processMKPropertyItem

  void processMKPropertyItem(String name, boolean TF)

• assignAtom

  private int assignAtom(int atomIndex, 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 String cmdAssignSpaceGroup(javajs.util.BS bs, 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

  mi -

  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(Object symop)

• showXtalSymmetry

  private void showXtalSymmetry()

  Draw the symmetry element

• getinfo

  private Object getinfo()

• addInfo

  private void addInfo(Map<String,Object> info, String key, 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(String action)

• processSelClick

  private void processSelClick(String action)

• processSelOpClick

  private String processSelOpClick(String action)

• processSymClick

  private void processSymClick(String action)

• processUCClick

  private void processUCClick(String action)

• getHoverLabel

  private String getHoverLabel(int atomIndex)

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

  Parameters:

  atomIndex -

  Returns:

  special label or null

• setBranchAtom

  private void setBranchAtom(int atomIndex, boolean isClick)

  Parameters:

  atomIndex -

  isClick -

• getBondLabel

  private String getBondLabel(Atom[] atoms)

• getOtherAtomIndex

  private Atom getOtherAtomIndex(Atom a1, Atom a2)

• promptUser

  private String promptUser(String msg, String def)

• appRunScript

  private void appRunScript(String script)

• runScriptBuffered

  private String runScriptBuffered(String script)

• isTrue

  private static boolean isTrue(Object value)

• pointFromTriad

  private static javajs.util.P3 pointFromTriad(String pos)

• notImplemented

  private static void notImplemented(String action)

• cmdAssignAtom

  public void cmdAssignAtom(int atomIndex, javajs.util.P3 pt, String type, 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, String type, String cmd, boolean isClick, javajs.util.BS bs, int atomicNo, int site, SymmetryInterface uc, javajs.util.Lst<javajs.util.P3> points, 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 -

• connectAtoms

  private void connectAtoms(float bd, int bondOrder, javajs.util.BS bs1, javajs.util.BS bs2)

• cmdAssignBond

  public void cmdAssignBond(int bondIndex, char type, String cmd)

• assignBondAndType

  public void assignBondAndType(int bondIndex, int bondOrder, char type, String cmd)

• assignBond

  private boolean assignBond(int bondIndex, int bondOrder, javajs.util.BS bsAtoms)

  Original ModelKit functionality -- assign a bond.

  Parameters:

  bondIndex -

  bondOrder -

  bsAtoms -

  Returns:

  bit set of atoms to modify

• getBondOrder

  private int getBondOrder(char type, Bond bond)

• cmdAssignConnect

  public void cmdAssignConnect(int index, int index2, char type, String cmd)

• assignConnect

  private void assignConnect(javajs.util.BS bs, int modelIndex, float[][] connections, char type, String cmd)

• assignAtomClick

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

• cmdAssignAddAtoms

  public int cmdAssignAddAtoms(String type, javajs.util.P3[] pts, javajs.util.BS bsAtoms, String packing, String cmd, boolean isClick)

  MODELKIT ADD @3 ...

  Parameters:

  type -

  pts - one or more new points

  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, boolean allowProjection)

  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

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

  allowProjection - always true here

  Returns:

  number of atoms moved

• 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, boolean allowProjection)

  This is the main method from viewer.moveSelected.

  Parameters:

  iatom -

  ptNew -

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

  allowProjection -

  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)

• cmdRotateAtoms

  public int cmdRotateAtoms(javajs.util.BS bsAtoms, javajs.util.P3[] points, float endDegrees)

• getText

  static String getText(String key)

• wasRotating

  public boolean wasRotating()