Package org.jmol.viewer

Class GlobalSettings

  • public class GlobalSettings
extends Object

    • Field Detail

      • vwr

        private final Viewer vwr

      • htNonbooleanParameterValues

        Map<String,​Object> htNonbooleanParameterValues

      • 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

      • 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

      • 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

        public boolean legacyHAddition

      • legacyJavaFloat

        public boolean legacyJavaFloat

      • jmolInJSpecView

        boolean jmolInJSpecView

      • modulateOccupancy

        boolean modulateOccupancy

      • allowRotateSelected

        boolean allowRotateSelected

      • allowMoveAtoms

        boolean allowMoveAtoms

      • solventOn

        boolean solventOn

      • 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

        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

      • 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

      • 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

      • fontScaling

        boolean fontScaling

      • fontCaching

        boolean fontCaching

      • forceField

        String forceField

      • helixStep

        int helixStep

      • hideNameInPopup

        boolean hideNameInPopup

      • hoverDelayMs

        int hoverDelayMs

      • 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

      • 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

      • navigationMode

        boolean navigationMode

      • navigationPeriodic

        boolean navigationPeriodic

      • navigationSpeed

        float navigationSpeed

      • 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 Detail

    • Method Detail

      • clear

        void clear()

      • setUnits

        void setUnits​(String units)

      • isJmolVariable

        boolean isJmolVariable​(String key)

      • setB

        public void setB​(String name,
                 boolean value)

      • setI

        void setI​(String name,
          int value)

      • setF

        public void setF​(String name,
                 float 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)