Package org.jmol.scriptext
Class CmdExt
java.lang.Object
org.jmol.scriptext.ScriptExt
org.jmol.scriptext.CmdExt
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Field Summary
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionprivate void
assign()
Though a command, not documented.private void
cache()
private void
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
private void
connect
(int index) private void
console()
private void
data()
The command dispatcher for the set of commands extended by this class.private void
boolean
evalParallel
(ScriptContext context, ShapeManager shapeManager) used for TRY commandprivate javajs.util.BS
expFor
(int i, javajs.util.BS bsAtoms) private String
filterShow
(String msg, String name) getBitsetIdent
(javajs.util.BS bs, String label, Object tokenValue, boolean useAtomMap, int index, boolean isExplicitlyAll) 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) 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 planeprivate void
image()
private void
private void
macro()
private void
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.javaprivate void
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
private void
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
private void
unitcell
(int i, boolean isModelkit) private String
private String
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
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Field Details
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ERROR_invalidArgument
static final int ERROR_invalidArgument- See Also:
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Constructor Details
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CmdExt
public CmdExt()
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Method Details
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dispatch
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 classScriptExt
- Parameters:
iTok
- the current statement position, usually 1flag
- a command-specific flagst
- the compiled statement for this command- Throws:
ScriptException
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macro
- Throws:
ScriptException
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evalParallel
used for TRY command- Parameters:
context
-shapeManager
-- Returns:
- true if successful; false if not
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getBitsetIdent
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getBitsetIdentFull
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getLoadSymmetryParams
public int getLoadSymmetryParams(int i, javajs.util.SB sOptions, Map<String, Object> htParams) throws ScriptException- Throws:
ScriptException
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checkPacked
private int checkPacked(int i, Map<String, Object> htParams, javajs.util.SB sOptions) throws ScriptExceptionProcess FILL and PACKED and all their variants.- Parameters:
i
-htParams
-sOptions
-- Returns:
- new token position
- Throws:
ScriptException
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cache
- Throws:
ScriptException
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calculate
- Throws:
ScriptException
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capture
- Throws:
ScriptException
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centerAt
- Throws:
ScriptException
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compare
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
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configuration
- Throws:
ScriptException
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measure
- Throws:
ScriptException
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connect
- Parameters:
index
- 0 indicates hbond command- Throws:
ScriptException
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console
- Throws:
ScriptException
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data
- Throws:
ScriptException
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ellipsoid
- Throws:
ScriptException
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image
- Throws:
ScriptException
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invertSelected
- Throws:
ScriptException
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mapProperty
- Throws:
ScriptException
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minimize
- Throws:
ScriptException
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modulation
Allows for setting one or more specific t-values as well as full unit-cell shifts (multiples of q).- Throws:
ScriptException
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mutate
- Throws:
ScriptException
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plot
- Throws:
ScriptException
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polyhedra
- Throws:
ScriptException
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write
- Parameters:
args
-- Returns:
- string for write() function
- Throws:
ScriptException
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prepareBinaryOutput
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writeMsg
- Throws:
ScriptException
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show
- Throws:
ScriptException
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getCurrentModelFileAsString
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filterShow
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stereo
- Throws:
ScriptException
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struts
- Throws:
ScriptException
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unitcell
- Throws:
ScriptException
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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
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modelkit
Configure the ModelKitPopup for Crystallographic symmetry viewing and structure editing new 14.29.45 see modelkit.ModelKitPopup.java- Throws:
ScriptException
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assign
Though a command, not documented. Use the MODELKIT command instead- Throws:
ScriptException
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expFor
- Throws:
ScriptException
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getContext
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getIsosurfaceJvxl
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getMoJvxl
- Throws:
ScriptException
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getScriptID
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tokenAt
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tokAtArray
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getPlotMinMax
private float getPlotMinMax(float[] data, boolean isMax, int tok) -
parseDataArray
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getBitsetPropertyFloat
public float[] getBitsetPropertyFloat(javajs.util.BS bs, int tok, String property, float min, float max) throws ScriptException - Throws:
ScriptException
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