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 int ERROR_invalidArgument
- Fields inherited from class org.jmol.scriptext.ScriptExt
  chk, e, slen, st, vwr

Constructor Summary

Constructors
Constructor Description

CmdExt()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
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, java.util.Map<java.lang.String,java.lang.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()`
`java.lang.String`	`dispatch(int iTok, boolean b, T[] st)`
`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 java.lang.String`	`filterShow(java.lang.String msg, java.lang.String name)`
`java.lang.Object`	`getBitsetIdent(javajs.util.BS bs, java.lang.String label, java.lang.Object tokenValue, boolean useAtomMap, int index, boolean isExplicitlyAll)`
`java.lang.Object`	`getBitsetIdentFull(javajs.util.BS bs, java.lang.String label, java.lang.Object tokenValue, boolean useAtomMap, int index, boolean isExplicitlyAll, java.lang.String[] sout)`
`float[]`	`getBitsetPropertyFloat(javajs.util.BS bs, int tok, java.lang.String property, float min, float max)`
`private java.lang.String`	`getContext(boolean withVariables)`
`private java.lang.Object`	`getIsosurfaceJvxl(int iShape, java.lang.String type)`
`int`	`getLoadSymmetryParams(int i, javajs.util.SB sOptions, java.util.Map<java.lang.String,java.lang.Object> htParams)`
`private java.lang.String`	`getMoJvxl(int ptMO, boolean isNBO)`
`private float`	`getPlotMinMax(float[] data, boolean isMax, int tok)`
`private java.lang.String`	`getScriptID(ScriptContext context)`
`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 java.lang.Object`	`parseDataArray(java.lang.String str, boolean is3D)`
`private java.lang.String`	`plot(T[] args)`
`private void`	`polyhedra()`
`javajs.util.Lst<java.lang.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)`
`private java.lang.String`	`write(T[] args)`
`private java.lang.String`	`writeMsg(java.lang.String msg)`

Methods inherited from class org.jmol.scriptext.ScriptExt
atomExpressionAt, 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 Detail
- ERROR_invalidArgument
```
static final int ERROR_invalidArgument
```
  See Also:
  
  Constant Field Values

Constructor Detail
- CmdExt
```
public CmdExt()
```

Method Detail

dispatch

public java.lang.String dispatch(int iTok,
                                 boolean b,
                                 T[] st)
                          throws ScriptException

Specified by:: dispatch in class ScriptExt
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

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

getBitsetIdentFull

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

getLoadSymmetryParams

public int getLoadSymmetryParams(int i,
                                 javajs.util.SB sOptions,
                                 java.util.Map<java.lang.String,java.lang.Object> htParams)
                          throws ScriptException

Throws:: ScriptException

checkPacked

private int checkPacked(int i,
                        java.util.Map<java.lang.String,java.lang.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 java.lang.String plot(T[] args)
                       throws ScriptException

Throws:: ScriptException

polyhedra

private void polyhedra()
                throws ScriptException

Throws:: ScriptException

write

private java.lang.String write(T[] args)
                        throws ScriptException

Parameters:: args -
Returns:: string for write() function
Throws:: ScriptException

prepareBinaryOutput

public javajs.util.Lst<java.lang.Object> prepareBinaryOutput(SV tvar)

writeMsg

private java.lang.String writeMsg(java.lang.String msg)
                           throws ScriptException

Throws:: ScriptException

show

private void show()
           throws ScriptException

Throws:: ScriptException

filterShow

private java.lang.String filterShow(java.lang.String msg,
                                    java.lang.String name)

stereo

private void stereo()
             throws ScriptException

Throws:: ScriptException

struts

private boolean struts()
                throws ScriptException

Throws:: ScriptException

unitcell

private void unitcell(int i)
               throws ScriptException

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 java.lang.String getContext(boolean withVariables)

getIsosurfaceJvxl

private java.lang.Object getIsosurfaceJvxl(int iShape,
                                           java.lang.String type)

getMoJvxl

private java.lang.String getMoJvxl(int ptMO,
                                   boolean isNBO)
                            throws ScriptException

Throws:: ScriptException

getScriptID

private java.lang.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 java.lang.Object parseDataArray(java.lang.String str,
                                        boolean is3D)

getBitsetPropertyFloat

public float[] getBitsetPropertyFloat(javajs.util.BS bs,
                                      int tok,
                                      java.lang.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 Detail

ERROR_invalidArgument

Constructor Detail

CmdExt

Method Detail

dispatch

modelkit

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

filterShow

stereo

struts

unitcell

assign

expFor

getContext

getIsosurfaceJvxl

getMoJvxl

getScriptID

tokenAt

tokAtArray

getPlotMinMax

parseDataArray

getBitsetPropertyFloat