CmdExt

java.lang.Object
- org.jmol.scriptext.ScriptExt
- - org.jmol.scriptext.CmdExt

```
public class CmdExt
extends ScriptExt
```

Field Summary

Fields
Modifier and Type Field and Description

(package private) static int ERROR_invalidArgument
- Fields inherited from class org.jmol.scriptext.ScriptExt
  chk, e, slen, st, vwr

Fields
Modifier and Type	Field and Description
`(package private) static int`	`ERROR_invalidArgument`

Constructor Summary

Constructors
Constructor and Description

CmdExt()

Constructors
Constructor and Description
`CmdExt()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`private void`	`assign()`
`private void`	`assignAtom(int atomIndex, javajs.util.P3 pt, String type)`
`private void`	`assignBond(int bondIndex, char type)`
`private void`	`assignConnect(int index, int index2)`
`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()`
`private void`	`configuration()`
`private void`	`connect(int index)`
`private void`	`console()`
`private void`	`data()`
`String`	`dispatch(int iTok, boolean b, T[] st)`
`private void`	`ellipsoid()`
`boolean`	`evalParallel(ScriptContext context, ShapeManager shapeManager)` used for TRY command
`private String`	`filterShow(String msg, String name)`
`Object`	`getBitsetIdent(BS bs, String label, Object tokenValue, boolean useAtomMap, int index, boolean isExplicitlyAll)`
`float[]`	`getBitsetPropertyFloat(BS bs, int tok, String property, float min, float max)`
`private String`	`getContext(boolean withVariables)`
`private String`	`getIsosurfaceJvxl(boolean asMesh, int iShape)`
`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 Object`	`getShapePropertyIndex(int shapeType, String propertyName, int index)`
`private void`	`image()`
`private void`	`macro()`
`private void`	`mapProperty()`
`private void`	`measure()`
`private void`	`minimize()`
`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)`
`private String`	`write(T[] args)`
`private String`	`writeMsg(String msg)`

Methods inherited from class org.jmol.scriptext.ScriptExt
atomExpressionAt, centerParameter, checkLength, error, finalizeObject, floatParameter, getColorTrans, 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 String dispatch(int iTok,
                       boolean b,
                       T[] st)
                throws ScriptException

Specified by:: dispatch in class ScriptExt
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(BS bs,
                             String label,
                             Object tokenValue,
                             boolean useAtomMap,
                             int index,
                             boolean isExplicitlyAll)

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

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

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

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)
               throws ScriptException

Throws:: ScriptException

assign

private void assign()
             throws ScriptException

Throws:: ScriptException

assignAtom

private void assignAtom(int atomIndex,
                        javajs.util.P3 pt,
                        String type)

assignBond

private void assignBond(int bondIndex,
                        char type)

assignConnect

private void assignConnect(int index,
                           int index2)

getContext

private String getContext(boolean withVariables)

getIsosurfaceJvxl

private String getIsosurfaceJvxl(boolean asMesh,
                                 int iShape)

getMoJvxl

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

Throws:: ScriptException

getScriptID

private String getScriptID(ScriptContext context)

getShapePropertyIndex

private Object getShapePropertyIndex(int shapeType,
                                     String propertyName,
                                     int index)

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(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 Detail

ERROR_invalidArgument

Constructor Detail

CmdExt

Method Detail

dispatch

macro

evalParallel

getBitsetIdent

getLoadSymmetryParams

checkPacked

cache

calculate

capture

centerAt

compare

configuration

measure

connect

console

data

ellipsoid

image

mapProperty

minimize

modulation

mutate

navigate

plot

polyhedra

write

prepareBinaryOutput

writeMsg

show

filterShow

stereo

struts

unitcell

assign

assignAtom

assignBond

assignConnect

getContext

getIsosurfaceJvxl

getMoJvxl

getScriptID

getShapePropertyIndex

tokenAt

tokAtArray

getPlotMinMax

parseDataArray

getBitsetPropertyFloat