java.lang.Object

org.jmol.scriptext.ScriptExt

org.jmol.scriptext.CmdExt

public class CmdExt extends ScriptExt

Field Summary

Fields

Modifier and Type

Field

Description

(package private) static final int

ERROR_invalidArgument

Fields inherited from class org.jmol.scriptext.ScriptExt
chk, e, slen, st, vwr
Constructor Summary

Constructors

Constructor

Description

CmdExt()
Method Summary

Modifier and Type

Method

Description

private void

assign()

Though a command, not documented.

private void

cache()

private void

calculate()

private void

capture()

private void

centerAt()

private int

checkPacked(int i, Map<String,Object> htParams, javajs.util.SB sOptions)

Process FILL and PACKED and all their variants.

private void

compare()

Compares one set of atoms to another, generating the matrix that takes that maps the first set's coordinates to the second's.

private void

configuration()

private void

connect(int index)

private void

console()

private void

data()

String

dispatch(int iTok, boolean flag, T[] st)

The command dispatcher for the set of commands extended by this class.

private void

ellipsoid()

boolean

evalParallel(ScriptContext context, ShapeManager shapeManager)

used for TRY command

private javajs.util.BS

expFor(int i, javajs.util.BS bsAtoms)

private String

filterShow(String msg, String name)

Object

getBitsetIdent(javajs.util.BS bs, String label, Object tokenValue, boolean useAtomMap, int index, boolean isExplicitlyAll)

Object

getBitsetIdentFull(javajs.util.BS bs, String label, Object tokenValue, boolean useAtomMap, int index, boolean isExplicitlyAll, String[] sout)

float[]

getBitsetPropertyFloat(javajs.util.BS bs, int tok, String property, float min, float max)

private String

getContext(boolean withVariables)

String

getCurrentModelFileAsString()

private Object

getIsosurfaceJvxl(int iShape, String type)

int

getLoadSymmetryParams(int i, javajs.util.SB sOptions, Map<String,Object> htParams)

private String

getMoJvxl(int ptMO, boolean isNBO)

private float

getPlotMinMax(float[] data, boolean isMax, int tok)

private String

getScriptID(ScriptContext context)

private javajs.util.P3[]

getUVBoxFromHKL(SymmetryInterface uc, javajs.util.P4 hkl, javajs.util.P4 plane)

create a uvw-space unit cell from an HKL plane

private void

image()

private void

invertSelected()

private void

macro()

private void

mapProperty()

private void

measure()

private void

minimize()

private void

modelkit()

Configure the ModelKitPopup for Crystallographic symmetry viewing and structure editing new 14.29.45 see modelkit.ModelKitPopup.java

private void

modulation()

Allows for setting one or more specific t-values as well as full unit-cell shifts (multiples of q).

private void

mutate()

private void

navigate()

private Object

parseDataArray(String str, boolean is3D)

private String

plot(T[] args)

private void

polyhedra()

javajs.util.Lst<Object>

prepareBinaryOutput(SV tvar)

private void

show()

private void

stereo()

private boolean

struts()

private static int

tokAtArray(int i, T[] args)

private T

tokenAt(int i, T[] args)

private void

unitcell(int i, boolean isModelkit)

private String

write(T[] args)

private String

writeMsg(String msg)

Methods inherited from class org.jmol.scriptext.ScriptExt
atomExpressionAt, bsToArray, centerParameter, checkLength, error, finalizeObject, floatParameter, getAllPoints, getColorTrans, getIntArray2, getPoint3f, getShapeProperty, getToken, init, intParameter, invArg, invPO, isFloatParameter, paramAsStr, setShapeId, setShapeProperty, showString, stringParameter, tokAt

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- ERROR_invalidArgument
  
  static final int ERROR_invalidArgument
  See Also:
  
  Constant Field Values
Constructor Details
- CmdExt
  
  public CmdExt()
Method Details
- dispatch
  
  public String dispatch(int iTok, boolean flag, T[] st) throws ScriptException
  
  The command dispatcher for the set of commands extended by this class. These commands can be from the Jmol command of their method name or another command or method working as though it were a command, with a non-GUI-generated compiled script.
  
  Specified by:
  
  dispatch in class ScriptExt
  
  Parameters:
  
  iTok - the current statement position, usually 1
  
  flag - a command-specific flag
  
  st - the compiled statement for this command
  
  Throws:
  
  ScriptException
- macro
  
  private void macro() throws ScriptException
  
  Throws:
  
  ScriptException
- evalParallel
  
  public boolean evalParallel(ScriptContext context, ShapeManager shapeManager)
  
  used for TRY command
  
  Parameters:
  
  context -
  
  shapeManager -
  
  Returns:
  
  true if successful; false if not
- getBitsetIdent
  
  public Object getBitsetIdent(javajs.util.BS bs, String label, Object tokenValue, boolean useAtomMap, int index, boolean isExplicitlyAll)
- getBitsetIdentFull
  
  public Object getBitsetIdentFull(javajs.util.BS bs, String label, Object tokenValue, boolean useAtomMap, int index, boolean isExplicitlyAll, String[] sout)
- getLoadSymmetryParams
  
  public int getLoadSymmetryParams(int i, javajs.util.SB sOptions, Map<String,Object> htParams) throws ScriptException
  
  Throws:
  
  ScriptException
- checkPacked
  
  private int checkPacked(int i, Map<String,Object> htParams, javajs.util.SB sOptions) throws ScriptException
  
  Process FILL and PACKED and all their variants.
  
  Parameters:
  
  i -
  
  htParams -
  
  sOptions -
  
  Returns:
  
  new token position
  
  Throws:
  
  ScriptException
- cache
  
  private void cache() throws ScriptException
  
  Throws:
  
  ScriptException
- calculate
  
  private void calculate() throws ScriptException
  
  Throws:
  
  ScriptException
- capture
  
  private void capture() throws ScriptException
  
  Throws:
  
  ScriptException
- centerAt
  
  private void centerAt() throws ScriptException
  
  Throws:
  
  ScriptException
- compare
  
  private void compare() throws ScriptException
  
  Compares one set of atoms to another, generating the matrix that takes that maps the first set's coordinates to the second's. Options TRANSLATE and ROTATE will generate an animation. See interactive documentation for more details.
  
  Throws:
  
  ScriptException
- configuration
  
  private void configuration() throws ScriptException
  
  Throws:
  
  ScriptException
- measure
  
  private void measure() throws ScriptException
  
  Throws:
  
  ScriptException
- connect
  
  private void connect(int index) throws ScriptException
  
  Parameters:
  
  index - 0 indicates hbond command
  
  Throws:
  
  ScriptException
- console
  
  private void console() throws ScriptException
  
  Throws:
  
  ScriptException
- data
  
  private void data() throws ScriptException
  
  Throws:
  
  ScriptException
- ellipsoid
  
  private void ellipsoid() throws ScriptException
  
  Throws:
  
  ScriptException
- image
  
  private void image() throws ScriptException
  
  Throws:
  
  ScriptException
- invertSelected
  
  private void invertSelected() throws ScriptException
  
  Throws:
  
  ScriptException
- mapProperty
  
  private void mapProperty() throws ScriptException
  
  Throws:
  
  ScriptException
- minimize
  
  private void minimize() throws ScriptException
  
  Throws:
  
  ScriptException
- modulation
  
  private void modulation() throws ScriptException
  
  Allows for setting one or more specific t-values as well as full unit-cell shifts (multiples of q).
  
  Throws:
  
  ScriptException
- mutate
  
  private void mutate() throws ScriptException
  
  Throws:
  
  ScriptException
- navigate
  
  private void navigate() throws ScriptException
  
  Throws:
  
  ScriptException
- plot
  
  private String plot(T[] args) throws ScriptException
  
  Throws:
  
  ScriptException
- polyhedra
  
  private void polyhedra() throws ScriptException
  
  Throws:
  
  ScriptException
- write
  
  private String write(T[] args) throws ScriptException
  
  Parameters:
  
  args -
  
  Returns:
  
  string for write() function
  
  Throws:
  
  ScriptException
- prepareBinaryOutput
  
  public javajs.util.Lst<Object> prepareBinaryOutput(SV tvar)
- writeMsg
  
  private String writeMsg(String msg) throws ScriptException
  
  Throws:
  
  ScriptException
- show
  
  private void show() throws ScriptException
  
  Throws:
  
  ScriptException
- getCurrentModelFileAsString
  
  public String getCurrentModelFileAsString()
- filterShow
  
  private String filterShow(String msg, String name)
- stereo
  
  private void stereo() throws ScriptException
  
  Throws:
  
  ScriptException
- struts
  
  private boolean struts() throws ScriptException
  
  Throws:
  
  ScriptException
- unitcell
  
  private void unitcell(int i, boolean isModelkit) throws ScriptException
  
  Throws:
  
  ScriptException
- getUVBoxFromHKL
  
  private javajs.util.P3[] getUVBoxFromHKL(SymmetryInterface uc, javajs.util.P4 hkl, javajs.util.P4 plane) throws ScriptException
  
  create a uvw-space unit cell from an HKL plane
  
  Parameters:
  
  uc -
  
  hkl -
  
  plane -
  
  Returns:
  
  [o a b c]
  
  Throws:
  
  ScriptException
- modelkit
  
  private void modelkit() throws ScriptException
  
  Configure the ModelKitPopup for Crystallographic symmetry viewing and structure editing new 14.29.45 see modelkit.ModelKitPopup.java
  
  Throws:
  
  ScriptException
- assign
  
  private void assign() throws ScriptException
  
  Though a command, not documented. Use the MODELKIT command instead
  
  Throws:
  
  ScriptException
- expFor
  
  private javajs.util.BS expFor(int i, javajs.util.BS bsAtoms) throws ScriptException
  
  Throws:
  
  ScriptException
- getContext
  
  private String getContext(boolean withVariables)
- getIsosurfaceJvxl
  
  private Object getIsosurfaceJvxl(int iShape, String type)
- getMoJvxl
  
  private String getMoJvxl(int ptMO, boolean isNBO) throws ScriptException
  
  Throws:
  
  ScriptException
- getScriptID
  
  private String getScriptID(ScriptContext context)
- tokenAt
  
  private T tokenAt(int i, T[] args)
- tokAtArray
  
  private static int tokAtArray(int i, T[] args)
- getPlotMinMax
  
  private float getPlotMinMax(float[] data, boolean isMax, int tok)
- parseDataArray
  
  private Object parseDataArray(String str, boolean is3D)
- getBitsetPropertyFloat
  
  public float[] getBitsetPropertyFloat(javajs.util.BS bs, int tok, String property, float min, float max) throws ScriptException
  
  Throws:
  
  ScriptException

Class CmdExt

Field Summary

Fields inherited from class org.jmol.scriptext.ScriptExt

Constructor Summary

Method Summary

Methods inherited from class org.jmol.scriptext.ScriptExt

Methods inherited from class java.lang.Object

Field Details

ERROR_invalidArgument

Constructor Details

CmdExt

Method Details

dispatch

macro

evalParallel

getBitsetIdent

getBitsetIdentFull

getLoadSymmetryParams

checkPacked

cache

calculate

capture

centerAt

compare

configuration

measure

connect

console

data

ellipsoid

image

invertSelected

mapProperty

minimize

modulation

mutate

navigate

plot

polyhedra

write

prepareBinaryOutput

writeMsg

show

getCurrentModelFileAsString

filterShow

stereo

struts

unitcell

getUVBoxFromHKL

modelkit

assign

expFor

getContext

getIsosurfaceJvxl

getMoJvxl

getScriptID

tokenAt

tokAtArray

getPlotMinMax

parseDataArray

getBitsetPropertyFloat