Class GlobalSettings


  • public class GlobalSettings
    extends java.lang.Object
    • Field Detail

      • vwr

        private final Viewer vwr
      • htNonbooleanParameterValues

        java.util.Map<java.lang.String,​java.lang.Object> htNonbooleanParameterValues
      • htBooleanParameterFlags

        java.util.Map<java.lang.String,​java.lang.Boolean> htBooleanParameterFlags
      • htPropertyFlagsRemoved

        java.util.Map<java.lang.String,​java.lang.Boolean> htPropertyFlagsRemoved
      • htUserVariables

        java.util.Map<java.lang.String,​SV> htUserVariables
      • databases

        java.util.Map<java.lang.String,​java.lang.String> databases
      • zDepth

        int zDepth
      • zShadePower

        int zShadePower
      • zSlab

        int zSlab
      • slabByMolecule

        boolean slabByMolecule
      • slabByAtom

        boolean slabByAtom
      • allowEmbeddedScripts

        boolean allowEmbeddedScripts
      • appendNew

        public boolean appendNew
      • appletProxy

        java.lang.String appletProxy
      • applySymmetryToBonds

        boolean applySymmetryToBonds
      • atomTypes

        java.lang.String atomTypes
      • autoBond

        boolean autoBond
      • axesOrientationRasmol

        boolean axesOrientationRasmol
      • bondRadiusMilliAngstroms

        short bondRadiusMilliAngstroms
      • bondTolerance

        float bondTolerance
      • defaultDirectory

        java.lang.String defaultDirectory
      • defaultStructureDSSP

        boolean defaultStructureDSSP
      • ptDefaultLattice

        final javajs.util.P3 ptDefaultLattice
      • defaultLoadScript

        public java.lang.String defaultLoadScript
      • defaultLoadFilter

        public java.lang.String defaultLoadFilter
      • defaultDropScript

        public java.lang.String defaultDropScript
      • forceAutoBond

        boolean forceAutoBond
      • fractionalRelative

        boolean fractionalRelative
      • inlineNewlineChar

        char inlineNewlineChar
      • loadFormat

        java.lang.String loadFormat
      • pdbLoadFormat

        java.lang.String pdbLoadFormat
      • pdbLoadFormat0

        java.lang.String pdbLoadFormat0
      • pdbLoadLigandFormat

        java.lang.String pdbLoadLigandFormat
      • nmrUrlFormat

        java.lang.String nmrUrlFormat
      • nmrPredictFormat

        java.lang.String nmrPredictFormat
      • smilesUrlFormat

        java.lang.String smilesUrlFormat
      • nihResolverFormat

        java.lang.String nihResolverFormat
      • pubChemFormat

        java.lang.String pubChemFormat
      • edsUrlFormat

        java.lang.String edsUrlFormat
      • edsUrlFormatDiff

        java.lang.String edsUrlFormatDiff
      • edsUrlCutoff

        java.lang.String edsUrlCutoff
      • minBondDistance

        float minBondDistance
      • minPixelSelRadius

        int minPixelSelRadius
      • pdbAddHydrogens

        boolean pdbAddHydrogens
      • pdbGetHeader

        boolean pdbGetHeader
      • pdbSequential

        boolean pdbSequential
      • percentVdwAtom

        int percentVdwAtom
      • smallMoleculeMaxAtoms

        int smallMoleculeMaxAtoms
      • smartAromatic

        boolean smartAromatic
      • zeroBasedXyzRasmol

        boolean zeroBasedXyzRasmol
      • legacyAutoBonding

        boolean legacyAutoBonding
      • legacyHAddition

        public boolean legacyHAddition
      • legacyJavaFloat

        public boolean legacyJavaFloat
      • modulateOccupancy

        boolean modulateOccupancy
      • allowRotateSelected

        boolean allowRotateSelected
      • allowMoveAtoms

        boolean allowMoveAtoms
      • solventOn

        boolean solventOn
      • defaultAngleLabel

        java.lang.String defaultAngleLabel
      • defaultDistanceLabel

        java.lang.String defaultDistanceLabel
      • defaultTorsionLabel

        java.lang.String defaultTorsionLabel
      • justifyMeasurements

        boolean justifyMeasurements
      • measureAllModels

        boolean measureAllModels
      • minimizationSteps

        int minimizationSteps
      • minimizationRefresh

        boolean minimizationRefresh
      • minimizationSilent

        boolean minimizationSilent
      • minimizationCriterion

        float minimizationCriterion
      • antialiasDisplay

        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

        java.lang.String backgroundImageFileName
      • partialDots

        boolean partialDots
      • bondModeOr

        boolean bondModeOr
      • hbondsBackbone

        boolean hbondsBackbone
      • hbondsAngleMinimum

        float hbondsAngleMinimum
      • hbondsDistanceMaximum

        float hbondsDistanceMaximum
      • 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
      • cartoonBaseEdges

        boolean cartoonBaseEdges
      • cartoonRockets

        boolean cartoonRockets
      • backboneSteps

        boolean backboneSteps
      • cartoonFancy

        boolean cartoonFancy
      • cartoonLadders

        boolean cartoonLadders
      • cartoonRibose

        boolean cartoonRibose
      • chainCaseSensitive

        boolean chainCaseSensitive
      • 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
      • 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

        java.lang.String dataSeparator
      • debugScript

        boolean debugScript
      • defaultDrawArrowScale

        float defaultDrawArrowScale
      • defaultLabelXYZ

        java.lang.String defaultLabelXYZ
      • defaultLabelPDB

        java.lang.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 java.lang.String energyUnits
      • exportScale

        float exportScale
      • helpPath

        java.lang.String helpPath
      • fontScaling

        boolean fontScaling
      • fontCaching

        boolean fontCaching
      • forceField

        java.lang.String forceField
      • helixStep

        int helixStep
      • hideNameInPopup

        boolean hideNameInPopup
      • hoverDelayMs

        int hoverDelayMs
      • loadAtomDataTolerance

        float loadAtomDataTolerance
      • logCommands

        public boolean logCommands
      • logGestures

        public boolean logGestures
      • measureDistanceUnits

        public java.lang.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

        java.lang.String pickLabel
      • pointGroupDistanceTolerance

        float pointGroupDistanceTolerance
      • pointGroupLinearTolerance

        float pointGroupLinearTolerance
      • preserveState

        public boolean preserveState
      • propertyColorScheme

        java.lang.String propertyColorScheme
      • quaternionFrame

        java.lang.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
      • vectorScale

        float vectorScale
      • vectorSymmetry

        boolean vectorSymmetry
      • vectorsCentered

        boolean vectorsCentered
      • vectorTrail

        int vectorTrail
      • vibrationPeriod

        float vibrationPeriod
      • vibrationScale

        float vibrationScale
      • wireframeRotation

        boolean wireframeRotation
      • hideNavigationPoint

        boolean hideNavigationPoint
      • navigationMode

        boolean navigationMode
      • navigationPeriodic

        boolean navigationPeriodic
      • navigationSpeed

        float navigationSpeed
      • showNavigationPointAlways

        boolean showNavigationPointAlways
      • stereoState

        java.lang.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

        java.util.Map<STR,​float[]> structureList
      • haveSetStructureList

        boolean haveSetStructureList
      • userDatabases

        private java.lang.String[] userDatabases
      • bondingVersion

        public int bondingVersion
      • unreportedProperties

        private static final java.lang.String unreportedProperties
    • Constructor Detail

    • Method Detail

      • clear

        void clear()
      • setUnits

        void setUnits​(java.lang.String units)
      • isJmolVariable

        boolean isJmolVariable​(java.lang.String key)
      • resetValue

        private void resetValue​(java.lang.String name,
                                GlobalSettings g)
      • setB

        public void setB​(java.lang.String name,
                         boolean value)
      • setI

        void setI​(java.lang.String name,
                  int value)
      • setF

        public void setF​(java.lang.String name,
                         float value)
      • setO

        void setO​(java.lang.String name,
                  java.lang.Object value)
      • removeParam

        public void removeParam​(java.lang.String key)
      • setUserVariable

        public SV setUserVariable​(java.lang.String key,
                                  SV var)
      • unsetUserVariable

        void unsetUserVariable​(java.lang.String key)
      • removeUserVariable

        void removeUserVariable​(java.lang.String key)
      • getUserVariable

        SV getUserVariable​(java.lang.String name)
      • getParameterEscaped

        java.lang.String getParameterEscaped​(java.lang.String name,
                                             int nMax)
      • getParameter

        java.lang.Object getParameter​(java.lang.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​(java.lang.String name,
                                       boolean doSet)
        Parameters:
        name -
        doSet -
        Returns:
        a new variable if possible, but null if "_xxx"
      • getParam

        java.lang.Object getParam​(java.lang.String name,
                                  boolean asVariable)
      • getVariableList

        public java.lang.String getVariableList()
      • setStructureList

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

        public java.util.Map<STR,​float[]> getStructureList()
      • resolveDataBase

        java.lang.String resolveDataBase​(java.lang.String database,
                                         java.lang.String id,
                                         java.lang.String format)
      • fixSurfaceFileNameVariables

        public java.lang.String[] fixSurfaceFileNameVariables​(java.lang.String id)
      • doReportProperty

        static boolean doReportProperty​(java.lang.String name)
      • getDataBaseList

        private void getDataBaseList​(java.lang.String[] list)
      • getAllVariables

        java.lang.Object getAllVariables()
      • getLoadState

        java.lang.String getLoadState​(java.util.Map<java.lang.String,​java.lang.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,
                         java.lang.String cmd)