Class GlobalSettings

java.lang.Object
org.jmol.viewer.GlobalSettings

public class GlobalSettings extends Object
  • Field Details

    • vwr

      private final Viewer vwr
    • htNonbooleanParameterValues

      Map<String,Object> htNonbooleanParameterValues
    • htBooleanParameterFlags

      Map<String,Boolean> htBooleanParameterFlags
    • htPropertyFlagsRemoved

      Map<String,Boolean> htPropertyFlagsRemoved
    • htUserVariables

      Map<String,SV> htUserVariables
    • 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

      public String defaultLoadScript
    • defaultLoadFilter

      public String defaultLoadFilter
    • defaultDropScript

      public String defaultDropScript
    • 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 doublePrecision
      setting 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
    • hiddenLinesDashed

      boolean hiddenLinesDashed
    • 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

      public String energyUnits
    • 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

      public String measureDistanceUnits
    • 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 noDelay
      ensures 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
    • hideNavigationPoint

      boolean hideNavigationPoint
    • showNavigationPointAlways

      boolean showNavigationPointAlways
    • 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

      Map<STR,float[]> structureList
    • haveSetStructureList

      boolean haveSetStructureList
    • bondingVersion

      public int bondingVersion
    • unreportedProperties

      private static final String unreportedProperties
  • Constructor Details

  • Method Details

    • clear

      void clear()
    • setUnits

      void setUnits(String units)
    • isJmolVariable

      boolean isJmolVariable(String key)
    • resetValue

      private void resetValue(String name, GlobalSettings g)
    • setB

      public void setB(String name, boolean value)
    • setI

      void setI(String name, int value)
    • setF

      public void setF(String name, float value)
    • setO

      public void setO(String name, Object value)
    • removeParam

      public void removeParam(String key)
    • setUserVariable

      public SV setUserVariable(String key, SV var)
    • unsetUserVariable

      void unsetUserVariable(String key)
    • removeUserVariable

      void removeUserVariable(String key)
    • getUserVariable

      SV getUserVariable(String name)
    • getParameterEscaped

      String getParameterEscaped(String name, int nMax)
    • getParameter

      Object getParameter(String name, boolean nullAsString)
      strictly a getter
      Parameters:
      name -
      nullAsString - returns "" if not found
      Returns:
      a Integer, Float, String, BitSet, or Variable, or null
    • getAndSetNewVariable

      public SV getAndSetNewVariable(String name, boolean doSet)
      Parameters:
      name -
      doSet -
      Returns:
      a new variable if possible, but null if "_xxx"
    • getParam

      Object getParam(String name, boolean asVariable)
    • getVariableList

      public String getVariableList()
    • setStructureList

      public void setStructureList(float[] list, STR type)
    • getStructureList

      public Map<STR,float[]> getStructureList()
    • doReportProperty

      static boolean doReportProperty(String name)
    • getAllVariables

      Object getAllVariables()
    • getLoadState

      String getLoadState(Map<String,Object> htParams)
      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
    • app

      private void app(javajs.util.SB s, String cmd)
    • setCIR

      public void setCIR(String template, boolean notify)