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

• GlobalSettings

  GlobalSettings​(Viewer vwr,
                 GlobalSettings g,
                 boolean clearUserVariables)

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)