Class ModelKit

Method Details

• getKey

  protected static String getKey(int modelIndex, char ext)

• actionRotateBond

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

  Actually rotate the bond.

  Parameters:

  deltaX -

  deltaY -

  x -

  y -

  forceFull -

• addLockedAtoms

  public void addLockedAtoms(SymmetryInterface sg, BS bsLocked)

  Only for the current model

  Parameters:

  sg -

  bsLocked -

• checkMovedAtoms

  public int checkMovedAtoms(BS bsFixed, BS bsAtoms, P3[] apos0)

  Something has changed atom positions. Check to see that this is allowed and, if it is, move all equivalent atoms appropriately. If it is not, then revert.

  Parameters:

  bsFixed -

  bsAtoms -

  apos0 - original positions

  Returns:

  number of atoms moved, possibly 0

• checkOption

  public boolean checkOption(char type, String key)

  MODELKIT SET options for syntax checking.

  Parameters:

  type - 'M' menu, 'S' symmetry 'U' unit cell, 'B' boolean

  key -

  Returns:

  true if the type exists

• clearAtomConstraints

  public void clearAtomConstraints()

• clickAssignAtom

  public void clickAssignAtom(int atomIndex, String element, P3 ptNew)

  From Mouse or handleAtomOrBondBicked

  Parameters:

  atomIndex - initiating atom clicked or dragged from

  element - chemical symbol or "X" for delete, or one of the pickAssignTypes, such as increase/decrease charge

  ptNew - if dragged to a new location to create a bond

• cmdAssignAddAtoms

  public int cmdAssignAddAtoms(String type, P3[] pts, BS bsAtoms, float packing, String cmd)

  MODELKIT ADD @3 ... MODELKIT ADD _C wyckoff invalid input: '<'[a-zAG] MODELKIT ADD C | this model only

  Parameters:

  type - | "_" | ":"invalid input: '<'Wyckoff letter [a-zAG]

  pts - one or more new points, may be null

  bsAtoms - the atoms to process, presumably from different sites

  packing -

  cmd - the command generating this call

  Returns:

  the number of atoms added

• cmdAssignAtom

  public void cmdAssignAtom(BS bs, P3 pt, String type, String cmd)

  A versatile method that allows changing element, setting charge, setting position, adding or deleting an atom via MODELKIT ASSIGN ATOM

  Parameters:

  bs - 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

• cmdAssignBond

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

• cmdAssignConnect

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

  Parameters:

  index -

  index2 -

  type -

  cmd -

• cmdAssignSpaceGroup

  public void cmdAssignSpaceGroup(String transform, SB sb, String cmd, float packing, boolean doDraw)

  MODELKIT SPACEGROUP

  Parameters:

  transform -

  sb -

  cmd -

  packing -

  doDraw -

• cmdAssignDeleteAtoms

  public int cmdAssignDeleteAtoms(BS bs)

  Delete all atoms that are equivalent to this atom.

  Parameters:

  bs -

  Returns:

  number of deleted atoms

• cmdPackUnitCell

  public void cmdPackUnitCell(SymmetryInterface sym, BS bsAtoms, float packing)

  MODELKIT {1 0 0} PACKED

  Parameters:

  sym -

  bsAtoms -

  packing -

• cmdFillOABC

  public int cmdFillOABC(T3[] oabc, float packing, String cmd)

• cmdAssignMoveAtoms

  public int cmdAssignMoveAtoms(BS bsSelected, int iatom, P3 p, P3[] pts, boolean allowProjection, boolean isMolecule, boolean isCommand)

• cmdMinimize

  public void cmdMinimize(JmolScriptEvaluator eval, BS bsBasis, int steps, float crit, float rangeFixed, int flags) throws Exception

  Minimize a unit cell with full symmetry constraints. The model will be loaded with a 27-cell packing, but only the basis atoms themselves will be loaded.

  Parameters:

  eval -

  bsBasis -

  steps -

  crit -

  rangeFixed -

  flags -

  Throws:

  Exception

• cmdRotateAtoms

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

• dispose

  public void dispose()

• getActiveMenu

  public String getActiveMenu()

  for the thin box on the top left of the window

  Returns:

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

• getDefaultModel

  public String getDefaultModel()

• getProperty

  public Object getProperty(String name)

  Get a property of the modelkit.

  Parameters:

  name -

  Returns:

  value

• getRotateBondIndex

  public int getRotateBondIndex()

• getSym

  public SymmetryInterface getSym(int iatom)

• 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

• hasConstraint

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

• isHidden

  public boolean isHidden()

• isPickAtomAssignCharge

  public boolean isPickAtomAssignCharge()

• minimizeEnd

  public void minimizeEnd(BS bsBasis2, boolean isEnd)

• moveMinConstrained

  public int moveMinConstrained(int iatom, P3 p, BS bsAtoms)

• setBondMeasure

  public MeasurementPending setBondMeasure(int bi, MeasurementPending mp)

• setMenu

  public void setMenu(ModelKitPopup menu)

• 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

• showMenu

  public void showMenu(int x, int y)

• updateMenu

  public void updateMenu()

• wasRotating

  public boolean wasRotating()

• checkNewModel

  protected boolean checkNewModel()

• clickProcessXtal

  protected void clickProcessXtal(String id, String action)

• exitBondRotation

  protected void exitBondRotation(String text)

• getAllOperators

  protected String[] getAllOperators()

• getBasisAtom

  protected Atom getBasisAtom(int iatom)

• getCenterText

  protected String getCenterText()

• getElementFromUser

  protected String getElementFromUser()

• getMKState

  protected int getMKState()

• getSymEditState

  protected int getSymEditState()

• getSymopText

  protected String getSymopText()

• getSymViewState

  protected int getSymViewState()

• getUnitCellState

  protected int getUnitCellState()

• isXtalState

  protected boolean isXtalState()

• processMKPropertyItem

  protected void processMKPropertyItem(String name, boolean TF)

• processSymop

  protected boolean processSymop(String id, boolean isFocus)

• resetAtomPickType

  protected void resetAtomPickType()

• setConstraint

  protected org.jmol.modelkit.ModelKit.Constraint setConstraint(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

• setHasUnitCell

  protected boolean setHasUnitCell()

• setHoverLabel

  protected void setHoverLabel(String mode, String text)

• setMKState

  protected void setMKState(int bits)

• transformAtomsToUnitCell

  public boolean transformAtomsToUnitCell(SymmetryInterface sym, T3[] oabc, String ucname)

  Transform the atoms to fractional coordinate, set the unit cell to a new cell, and then transform them back to Cartesians.

  Parameters:

  sym -

  oabc -

  ucname -

  Returns:

  true if this is a "reset" with no atoms or sym == null

• drawSymop

  public void drawSymop(int a1, int a2)

  from set picking symop

  Parameters:

  a1 -

  a2 -

• addAtomSet

  public void addAtomSet(String data)

• drawUnitCell

  public void drawUnitCell(String id, T3 ucLattice, String swidth)

  Parameters:

  id -

  ucLattice -

  swidth -

• drawAxes

  public void drawAxes(P3[] points, String id, String swidth)

• drawSymmetry

  public String drawSymmetry(String thisId, boolean isSymop, int iatom, String xyz, int iSym, P3 trans, P3 center, P3 target, int intScale, int nth, int options, int[] opList, boolean isModelkit)