Package org.jmol.viewer
Class GlobalSettings
java.lang.Object
org.jmol.viewer.GlobalSettings
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Field Summary
FieldsModifier and TypeFieldDescription(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) int
boolean
(package private) boolean
(package private) boolean
boolean
(package private) String
(package private) boolean
(package private) boolean
(package private) String
(package private) boolean
(package private) boolean
(package private) boolean
int
(package private) float
(package private) boolean
(package private) float
(package private) String
int
(package private) boolean
(package private) boolean
(package private) short
(package private) float
(package private) boolean
(package private) float
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) String
(package private) boolean
(package private) String
(package private) String
(package private) String
(package private) float
(package private) String
(package private) String
(package private) boolean
(package private) String
(package private) float
(package private) int
(package private) float
(package private) boolean
(package private) boolean
(package private) int
(package private) int
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
setting doublePrecision will also toggle legacyJavaFloat to doublePrecision in order to avoid any rounding(package private) boolean
(package private) float
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) float
(package private) boolean
(package private) int
(package private) boolean
(package private) boolean
(package private) float
(package private) boolean
(package private) boolean
(package private) boolean
(package private) String
(package private) boolean
(package private) boolean
(package private) boolean
(package private) float
(package private) float
(package private) float
(package private) boolean
(package private) boolean
(package private) boolean
(package private) int
(package private) String
(package private) int
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) int
(package private) boolean
(package private) int
(package private) char
(package private) boolean
(package private) boolean
(package private) int
(package private) boolean
(package private) boolean
int
(package private) boolean
(package private) boolean
boolean
(package private) float
(package private) String
boolean
boolean
(package private) String
(package private) boolean
(package private) boolean
(package private) int
(package private) boolean
(package private) float
(package private) float
(package private) int
(package private) boolean
(package private) boolean
(package private) int
(package private) int
(package private) boolean
byte
(package private) boolean
float
(package private) boolean
(package private) boolean
(package private) float
(package private) float
(package private) boolean
(package private) boolean
(package private) boolean
(package private) float
(package private) boolean
(package private) String
(package private) String
(package private) String
boolean
ensures that ScriptManager.allowJSThreads is false so that ScriptManager.useThreads() returns false; Jmol 14.21.1(package private) int[]
(package private) int[]
(package private) boolean[]
(package private) boolean
(package private) float
(package private) boolean
(package private) boolean
(package private) String
(package private) String
(package private) boolean
(package private) int
(package private) int
(package private) String
(package private) int
(package private) float
(package private) float
boolean
(package private) String
(package private) final javajs.util.P3
(package private) String
(package private) String
boolean
(package private) boolean
(package private) boolean
int
(package private) String
(package private) int
(package private) boolean
(package private) boolean
(package private) boolean
(package private) int
(package private) boolean
(package private) float
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) int
(package private) boolean
(package private) String
(package private) float
(package private) boolean
(package private) float
(package private) boolean
(package private) String
(package private) int
(package private) int
(package private) float
(package private) float
(package private) boolean
(package private) int
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
(package private) boolean
private static final String
(package private) boolean
(package private) boolean
boolean
(package private) float
(package private) boolean
(package private) boolean
(package private) int
(package private) float
(package private) float
private final Viewer
boolean
(package private) boolean
(package private) int
(package private) boolean
(package private) boolean
(package private) boolean
(package private) int
(package private) int
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate void
(package private) void
clear()
(package private) static boolean
doReportProperty
(String name) (package private) Object
getAndSetNewVariable
(String name, boolean doSet) (package private) String
getLoadState
(Map<String, Object> htParams) these settings are determined when the file is loaded and are kept even though they might later change.(package private) Object
(package private) Object
getParameter
(String name, boolean nullAsString) strictly a getter(package private) String
getParameterEscaped
(String name, int nMax) (package private) SV
getUserVariable
(String name) (package private) boolean
isJmolVariable
(String key) void
removeParam
(String key) (package private) void
removeUserVariable
(String key) private void
resetValue
(String name, GlobalSettings g) void
void
void
(package private) void
void
void
setStructureList
(float[] list, STR type) (package private) void
setUserVariable
(String key, SV var) (package private) void
unsetUserVariable
(String key)
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Field Details
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vwr
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htNonbooleanParameterValues
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htBooleanParameterFlags
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htPropertyFlagsRemoved
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htUserVariables
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zDepth
int zDepth -
zShadePower
int zShadePower -
zSlab
int zSlab -
slabByMolecule
boolean slabByMolecule -
slabByAtom
boolean slabByAtom -
allowEmbeddedScripts
boolean allowEmbeddedScripts -
appendNew
public boolean appendNew -
appletProxy
String appletProxy -
applySymmetryToBonds
boolean applySymmetryToBonds -
atomTypes
String atomTypes -
autoBond
boolean autoBond -
axesOrientationRasmol
boolean axesOrientationRasmol -
bondRadiusMilliAngstroms
short bondRadiusMilliAngstroms -
bondTolerance
float bondTolerance -
defaultDirectory
String defaultDirectory -
defaultStructureDSSP
boolean defaultStructureDSSP -
ptDefaultLattice
final javajs.util.P3 ptDefaultLattice -
defaultLoadScript
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defaultLoadFilter
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defaultDropScript
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forceAutoBond
boolean forceAutoBond -
fractionalRelative
boolean fractionalRelative -
inlineNewlineChar
char inlineNewlineChar -
loadFormat
String loadFormat -
pdbLoadFormat
String pdbLoadFormat -
pdbLoadLigandFormat
String pdbLoadLigandFormat -
nmrUrlFormat
String nmrUrlFormat -
nmrPredictFormat
String nmrPredictFormat -
smilesUrlFormat
String smilesUrlFormat -
nihResolverFormat
String nihResolverFormat -
pubChemFormat
String pubChemFormat -
macroDirectory
String macroDirectory -
resolverResolver
String resolverResolver -
checkCIR
boolean checkCIR -
minBondDistance
float minBondDistance -
minPixelSelRadius
int minPixelSelRadius -
pdbAddHydrogens
boolean pdbAddHydrogens -
pdbGetHeader
boolean pdbGetHeader -
pdbSequential
boolean pdbSequential -
percentVdwAtom
int percentVdwAtom -
smallMoleculeMaxAtoms
int smallMoleculeMaxAtoms -
minimizationMaxAtoms
int minimizationMaxAtoms -
smartAromatic
boolean smartAromatic -
zeroBasedXyzRasmol
boolean zeroBasedXyzRasmol -
legacyAutoBonding
boolean legacyAutoBonding -
legacyHAddition
boolean legacyHAddition -
legacyJavaFloat
public boolean legacyJavaFloat -
doublePrecision
boolean doublePrecisionsetting doublePrecision will also toggle legacyJavaFloat to doublePrecision in order to avoid any rounding -
jmolInJSpecView
boolean jmolInJSpecView -
modulateOccupancy
boolean modulateOccupancy -
allowRotateSelected
boolean allowRotateSelected -
allowMoveAtoms
boolean allowMoveAtoms -
dotSolvent
boolean dotSolvent -
defaultAngleLabel
String defaultAngleLabel -
defaultDistanceLabel
String defaultDistanceLabel -
defaultTorsionLabel
String defaultTorsionLabel -
justifyMeasurements
boolean justifyMeasurements -
measureAllModels
boolean measureAllModels -
minimizationSteps
int minimizationSteps -
minimizationRefresh
boolean minimizationRefresh -
minimizationSilent
boolean minimizationSilent -
minimizationCriterion
float minimizationCriterion -
infoFontSize
int infoFontSize -
antialiasDisplay
public boolean antialiasDisplay -
antialiasImages
boolean antialiasImages -
imageState
boolean imageState -
antialiasTranslucent
boolean antialiasTranslucent -
displayCellParameters
boolean displayCellParameters -
dotsSelectedOnly
boolean dotsSelectedOnly -
dotSurface
boolean dotSurface -
dotDensity
int dotDensity -
dotScale
int dotScale -
meshScale
int meshScale -
greyscaleRendering
boolean greyscaleRendering -
isosurfaceKey
boolean isosurfaceKey -
isosurfacePropertySmoothing
boolean isosurfacePropertySmoothing -
isosurfacePropertySmoothingPower
int isosurfacePropertySmoothingPower -
platformSpeed
int platformSpeed -
repaintWaitMs
public int repaintWaitMs -
showHiddenSelectionHalos
boolean showHiddenSelectionHalos -
showKeyStrokes
boolean showKeyStrokes -
showMeasurements
boolean showMeasurements -
showTiming
public boolean showTiming -
zoomLarge
boolean zoomLarge -
zoomHeight
boolean zoomHeight -
backgroundImageFileName
String backgroundImageFileName -
partialDots
boolean partialDots -
bondModeOr
boolean bondModeOr -
hbondsBackbone
boolean hbondsBackbone -
hbondsAngleMinimum
float hbondsAngleMinimum -
hbondNODistanceMaximum
float hbondNODistanceMaximum -
hbondHXDistanceMaximum
float hbondHXDistanceMaximum -
hbondsRasmol
boolean hbondsRasmol -
hbondsSolid
boolean hbondsSolid -
modeMultipleBond
public byte modeMultipleBond -
showHydrogens
boolean showHydrogens -
showMultipleBonds
boolean showMultipleBonds -
ssbondsBackbone
boolean ssbondsBackbone -
multipleBondSpacing
float multipleBondSpacing -
multipleBondRadiusFactor
float multipleBondRadiusFactor -
multipleBondBananas
boolean multipleBondBananas -
nboCharges
boolean nboCharges -
cartoonBaseEdges
boolean cartoonBaseEdges -
cartoonRockets
boolean cartoonRockets -
cartoonBlockHeight
float cartoonBlockHeight -
cartoonBlocks
boolean cartoonBlocks -
cartoonSteps
boolean cartoonSteps -
cartoonFancy
boolean cartoonFancy -
cartoonLadders
boolean cartoonLadders -
cartoonRibose
boolean cartoonRibose -
chainCaseSensitive
boolean chainCaseSensitive -
cipRule6Full
boolean cipRule6Full -
hermiteLevel
int hermiteLevel -
highResolutionFlag
boolean highResolutionFlag -
rangeSelected
public boolean rangeSelected -
rasmolHydrogenSetting
boolean rasmolHydrogenSetting -
rasmolHeteroSetting
boolean rasmolHeteroSetting -
ribbonAspectRatio
int ribbonAspectRatio -
ribbonBorder
boolean ribbonBorder -
rocketBarrels
boolean rocketBarrels -
sheetSmoothing
float sheetSmoothing -
traceAlpha
boolean traceAlpha -
translucent
boolean translucent -
twistedSheets
boolean twistedSheets -
autoplayMovie
boolean autoplayMovie -
allowAudio
boolean allowAudio -
allowGestures
boolean allowGestures -
allowModelkit
boolean allowModelkit -
allowMultiTouch
boolean allowMultiTouch -
allowKeyStrokes
boolean allowKeyStrokes -
animationFps
int animationFps -
atomPicking
boolean atomPicking -
autoFps
boolean autoFps -
axesMode
public int axesMode -
axesScale
float axesScale -
axesOffset
float axesOffset -
starWidth
float starWidth -
bondPicking
boolean bondPicking -
dataSeparator
String dataSeparator -
debugScript
boolean debugScript -
defaultDrawArrowScale
float defaultDrawArrowScale -
defaultLabelXYZ
String defaultLabelXYZ -
defaultLabelPDB
String defaultLabelPDB -
defaultTranslucent
float defaultTranslucent -
delayMaximumMs
int delayMaximumMs -
dipoleScale
float dipoleScale -
drawFontSize
float drawFontSize -
disablePopupMenu
boolean disablePopupMenu -
dragSelected
boolean dragSelected -
drawHover
boolean drawHover -
drawPicking
boolean drawPicking -
dsspCalcHydrogen
boolean dsspCalcHydrogen -
energyUnits
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exportScale
float exportScale -
helpPath
String helpPath -
fontScaling
boolean fontScaling -
fontCaching
boolean fontCaching -
forceField
String forceField -
helixStep
int helixStep -
hideNameInPopup
boolean hideNameInPopup -
hoverDelayMs
int hoverDelayMs -
labelPointerWidth
public int labelPointerWidth -
loadAtomDataTolerance
float loadAtomDataTolerance -
logCommands
public boolean logCommands -
logGestures
public boolean logGestures -
measureDistanceUnits
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measurementLabels
boolean measurementLabels -
messageStyleChime
boolean messageStyleChime -
monitorEnergy
boolean monitorEnergy -
modulationScale
public float modulationScale -
multiProcessor
boolean multiProcessor -
particleRadius
float particleRadius -
pickingSpinRate
int pickingSpinRate -
pickLabel
String pickLabel -
pointGroupDistanceTolerance
float pointGroupDistanceTolerance -
pointGroupLinearTolerance
float pointGroupLinearTolerance -
preserveState
public boolean preserveState -
propertyColorScheme
String propertyColorScheme -
quaternionFrame
String quaternionFrame -
saveProteinStructureState
boolean saveProteinStructureState -
showModVecs
boolean showModVecs -
showUnitCellDetails
boolean showUnitCellDetails -
solventProbeRadius
float solventProbeRadius -
scriptDelay
int scriptDelay -
selectAllModels
boolean selectAllModels -
statusReporting
boolean statusReporting -
strandCountForStrands
int strandCountForStrands -
strandCountForMeshRibbon
int strandCountForMeshRibbon -
strutSpacing
int strutSpacing -
strutLengthMaximum
float strutLengthMaximum -
strutDefaultRadius
float strutDefaultRadius -
strutsMultiple
boolean strutsMultiple -
useMinimizationThread
boolean useMinimizationThread -
useNumberLocalization
boolean useNumberLocalization -
useScriptQueue
public boolean useScriptQueue -
waitForMoveTo
public boolean waitForMoveTo -
noDelay
public boolean noDelayensures that ScriptManager.allowJSThreads is false so that ScriptManager.useThreads() returns false; Jmol 14.21.1 -
vectorScale
float vectorScale -
vectorSymmetry
boolean vectorSymmetry -
vectorsCentered
boolean vectorsCentered -
vectorTrail
int vectorTrail -
vibrationPeriod
float vibrationPeriod -
vibrationScale
float vibrationScale -
wireframeRotation
boolean wireframeRotation -
stereoState
String stereoState -
modelKitMode
boolean modelKitMode -
objColors
int[] objColors -
objStateOn
boolean[] objStateOn -
objMad10
int[] objMad10 -
ellipsoidAxes
boolean ellipsoidAxes -
ellipsoidDots
boolean ellipsoidDots -
ellipsoidArcs
boolean ellipsoidArcs -
ellipsoidArrows
boolean ellipsoidArrows -
ellipsoidFill
boolean ellipsoidFill -
ellipsoidBall
boolean ellipsoidBall -
ellipsoidDotCount
int ellipsoidDotCount -
ellipsoidAxisDiameter
float ellipsoidAxisDiameter -
testFlag1
boolean testFlag1 -
testFlag2
boolean testFlag2 -
testFlag3
boolean testFlag3 -
testFlag4
boolean testFlag4 -
structureList
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haveSetStructureList
boolean haveSetStructureList -
bondingVersion
public int bondingVersion -
unreportedProperties
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Constructor Details
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GlobalSettings
GlobalSettings(Viewer vwr, GlobalSettings g, boolean clearUserVariables)
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Method Details
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clear
void clear() -
setUnits
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isJmolVariable
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resetValue
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setB
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setI
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setF
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setO
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removeParam
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setUserVariable
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unsetUserVariable
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removeUserVariable
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getUserVariable
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getParameterEscaped
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getParameter
strictly a getter- Parameters:
name
-nullAsString
- returns "" if not found- Returns:
- a Integer, Float, String, BitSet, or Variable, or null
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getAndSetNewVariable
- Parameters:
name
-doSet
-- Returns:
- a new variable if possible, but null if "_xxx"
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getParam
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getVariableList
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setStructureList
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getStructureList
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doReportProperty
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getAllVariables
Object getAllVariables() -
getLoadState
these settings are determined when the file is loaded and are kept even though they might later change. So we list them here and ALSO let them be defined in the settings. 10.9.98 missed this.- Parameters:
htParams
-- Returns:
- script command
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app
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setCIR
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