Clazz.declarePackage("JV");
Clazz.load(["java.util.Hashtable", "JU.P3", "J.c.CBK"], "JV.GlobalSettings", ["JU.DF", "$.PT", "$.SB", "J.c.STR", "JS.SV", "JU.Escape", "$.Logger", "JV.JC", "$.StateManager", "$.Viewer"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.vwr = null;
this.htNonbooleanParameterValues = null;
this.htBooleanParameterFlags = null;
this.htPropertyFlagsRemoved = null;
this.htUserVariables = null;
this.zDepth = 0;
this.zShadePower = 3;
this.zSlab = 50;
this.slabByMolecule = false;
this.slabByAtom = false;
this.allowEmbeddedScripts = true;
this.appendNew = true;
this.appletProxy = "";
this.applySymmetryToBonds = false;
this.atomTypes = "";
this.autoBond = true;
this.axesOrientationRasmol = false;
this.bondRadiusMilliAngstroms = 150;
this.bondTolerance = 0.45;
this.defaultDirectory = "";
this.defaultStructureDSSP = true;
this.ptDefaultLattice = null;
this.defaultLoadScript = "";
this.defaultLoadFilter = "";
this.defaultDropScript = "zap; load SYNC \"%FILE\";if (%ALLOWCARTOONS && _loadScript == \'\' && defaultLoadScript == \'\' && _filetype == \'Pdb\') {if ({(protein or nucleic)&*/1.1} && {*/1.1}[1].groupindex != {*/1.1}[0].groupindex){select protein or nucleic;cartoons only;}if ({visible && cartoons > 0}){color structure}else{wireframe -0.1};if (!{visible}){spacefill 23%};select *}";
this.forceAutoBond = false;
this.fractionalRelative = true;
this.inlineNewlineChar = '|';
this.loadFormat = null;
this.pdbLoadFormat = null;
this.pdbLoadLigandFormat = null;
this.nmrUrlFormat = null;
this.nmrPredictFormat = null;
this.smilesUrlFormat = null;
this.nihResolverFormat = null;
this.pubChemFormat = null;
this.macroDirectory = null;
this.resolverResolver = null;
this.checkCIR = false;
this.minBondDistance = 0.4;
this.minPixelSelRadius = 6;
this.pdbAddHydrogens = false;
this.pdbGetHeader = false;
this.pdbSequential = false;
this.percentVdwAtom = 23;
this.smallMoleculeMaxAtoms = 40000;
this.smartAromatic = true;
this.zeroBasedXyzRasmol = false;
this.legacyAutoBonding = false;
this.legacyHAddition = false;
this.legacyJavaFloat = false;
this.doublePrecision = false;
this.jmolInJSpecView = true;
this.modulateOccupancy = true;
this.allowRotateSelected = false;
this.allowMoveAtoms = false;
this.dotSolvent = false;
this.defaultAngleLabel = "%VALUE %UNITS";
this.defaultDistanceLabel = "%VALUE %UNITS";
this.defaultTorsionLabel = "%VALUE %UNITS";
this.justifyMeasurements = false;
this.measureAllModels = false;
this.minimizationSteps = 100;
this.minimizationRefresh = true;
this.minimizationSilent = false;
this.minimizationCriterion = 0.001;
this.minimizationMaxAtoms = 200;
this.minimizationReportSteps = 10;
this.infoFontSize = 20;
this.antialiasDisplay = false;
this.antialiasImages = true;
this.imageState = true;
this.antialiasTranslucent = true;
this.displayCellParameters = true;
this.dotsSelectedOnly = false;
this.dotSurface = true;
this.dotDensity = 3;
this.dotScale = 1;
this.meshScale = 1;
this.mode2d = false;
this.greyscaleRendering = false;
this.isosurfaceKey = false;
this.isosurfacePropertySmoothing = true;
this.isosurfacePropertySmoothingPower = 7;
this.platformSpeed = 10;
this.repaintWaitMs = 1000;
this.showHiddenSelectionHalos = false;
this.showKeyStrokes = true;
this.showMeasurements = true;
this.showTiming = false;
this.zoomLarge = true;
this.zoomHeight = false;
this.backgroundImageFileName = null;
this.occupancyThreshold = 50;
this.partialDots = false;
this.bondModeOr = false;
this.hbondsBackbone = false;
this.hbondsAngleMinimum = 90;
this.hbondNODistanceMaximum = 3.25;
this.hbondHXDistanceMaximum = 2.5;
this.hbondsRasmol = true;
this.hbondsSolid = false;
this.modeMultipleBond = 2;
this.showHydrogens = true;
this.showMultipleBonds = true;
this.ssbondsBackbone = false;
this.multipleBondSpacing = -1;
this.multipleBondRadiusFactor = 0;
this.multipleBondBananas = false;
this.nboCharges = true;
this.cartoonBaseEdges = false;
this.cartoonRockets = false;
this.cartoonBlockHeight = 0.5;
this.cartoonBlocks = false;
this.cartoonSteps = false;
this.cartoonFancy = false;
this.cartoonLadders = false;
this.cartoonRibose = false;
this.chainCaseSensitive = false;
this.cipRule6Full = false;
this.hermiteLevel = 0;
this.highResolutionFlag = false;
this.rangeSelected = false;
this.rasmolHydrogenSetting = true;
this.rasmolHeteroSetting = true;
this.ribbonAspectRatio = 16;
this.ribbonBorder = false;
this.rocketBarrels = false;
this.sheetSmoothing = 1;
this.traceAlpha = true;
this.translucent = true;
this.twistedSheets = false;
this.autoplayMovie = true;
this.allowAudio = true;
this.allowGestures = false;
this.allowModelkit = true;
this.allowMultiTouch = true;
this.allowKeyStrokes = false;
this.hiddenLinesDashed = false;
this.animationFps = 10;
this.atomPicking = true;
this.autoFps = false;
this.axesMode = 603979809;
this.axesScale = 2;
this.axesOffset = 0;
this.starWidth = 0.05;
this.bondPicking = false;
this.dataSeparator = "~~~";
this.debugScript = false;
this.defaultDrawArrowScale = 0.5;
this.defaultLabelXYZ = "%a";
this.defaultLabelPDB = "%m%r";
this.defaultTranslucent = 0.5;
this.delayMaximumMs = 0;
this.dipoleScale = 1;
this.drawFontSize = 16.0;
this.disablePopupMenu = false;
this.dragSelected = false;
this.drawHover = false;
this.drawPicking = false;
this.dsspCalcHydrogen = true;
this.elementKey = false;
this.labelKey = false;
this.energyUnits = "kJ";
this.exportScale = 0;
this.helpPath = "https://chemapps.stolaf.edu/jmol/docs/index.htm";
this.fontScaling = false;
this.fontCaching = true;
this.forceField = "MMFF";
this.helixStep = 1;
this.hideNameInPopup = false;
this.hoverDelayMs = 500;
this.labelPointerWidth = 2;
this.loadAtomDataTolerance = 0.01;
this.logCommands = false;
this.logGestures = false;
this.measureDistanceUnits = "nanometers";
this.measurementLabels = true;
this.messageStyleChime = false;
this.monitorEnergy = false;
this.modulationScale = 1;
this.multiProcessor = true;
this.particleRadius = 20;
this.pickingSpinRate = 10;
this.pickLabel = "";
this.pointGroupDistanceTolerance = 0.2;
this.pointGroupLinearTolerance = 8.0;
this.preserveState = true;
this.propertyColorScheme = "roygb";
this.quaternionFrame = "p";
this.saveProteinStructureState = true;
this.showModVecs = false;
this.showUnitCellDetails = true;
this.solventProbeRadius = 1.2;
this.scriptDelay = 0;
this.selectAllModels = true;
this.statusReporting = true;
this.strandCountForStrands = 5;
this.strandCountForMeshRibbon = 7;
this.strutSpacing = 6;
this.strutLengthMaximum = 7.0;
this.strutDefaultRadius = 0.3;
this.strutsMultiple = false;
this.symmetryHermannMauguin = false;
this.useMinimizationThread = true;
this.useNumberLocalization = true;
this.useScriptQueue = true;
this.waitForMoveTo = true;
this.noDelay = false;
this.vectorScale = 1;
this.vectorSymmetry = false;
this.vectorsCentered = false;
this.vectorTrail = 0;
this.vibrationPeriod = 1;
this.vibrationScale = 1;
this.wireframeRotation = false;
this.hideNavigationPoint = false;
this.navigationMode = false;
this.navigationPeriodic = false;
this.navigationSpeed = 5;
this.showNavigationPointAlways = false;
this.stereoState = null;
this.modelKitMode = false;
this.objColors = null;
this.objStateOn = null;
this.objMad10 = null;
this.ellipsoidAxes = false;
this.ellipsoidDots = false;
this.ellipsoidArcs = false;
this.ellipsoidArrows = false;
this.ellipsoidFill = false;
this.ellipsoidBall = true;
this.ellipsoidDotCount = 200;
this.ellipsoidAxisDiameter = 0.02;
this.testFlag1 = false;
this.testFlag2 = false;
this.testFlag3 = false;
this.testFlag4 = false;
this.structureList = null;
this.haveSetStructureList = false;
this.bondingVersion = 0;
Clazz.instantialize(this, arguments);}, JV, "GlobalSettings", null);
Clazz.prepareFields (c$, function(){
this.htUserVariables =  new java.util.Hashtable();
this.ptDefaultLattice =  new JU.P3();
this.objColors =  Clazz.newIntArray (7, 0);
this.objStateOn =  Clazz.newBooleanArray(7, false);
this.objMad10 =  Clazz.newIntArray (7, 0);
this.structureList =  new java.util.Hashtable();
{
this.structureList.put(J.c.STR.TURN,  Clazz.newFloatArray(-1, [30, 90, -15, 95]));
this.structureList.put(J.c.STR.SHEET,  Clazz.newFloatArray(-1, [-180, -10, 70, 180, -180, -45, -180, -130, 140, 180, 90, 180]));
this.structureList.put(J.c.STR.HELIX,  Clazz.newFloatArray(-1, [-160, 0, -100, 45]));
}});
Clazz.makeConstructor(c$, 
function(vwr, g, clearUserVariables){
this.vwr = vwr;
this.htNonbooleanParameterValues =  new java.util.Hashtable();
this.htBooleanParameterFlags =  new java.util.Hashtable();
this.htPropertyFlagsRemoved =  new java.util.Hashtable();
this.loadFormat = this.pdbLoadFormat = JV.JC.databases.get("pdb");
this.pdbLoadLigandFormat = JV.JC.databases.get("ligand");
this.nmrUrlFormat = JV.JC.databases.get("nmr");
this.nmrPredictFormat = JV.JC.databases.get("nmrdb");
this.pubChemFormat = JV.JC.databases.get("pubchem");
this.resolverResolver = JV.JC.databases.get("resolverresolver");
this.macroDirectory = "https://chemapps.stolaf.edu/jmol/macros";
if (g == null) {
this.setB("undoAuto", !vwr.isApplet);
} else {
this.setB("undoAuto", vwr.getBooleanProperty("undoAuto"));
if (!clearUserVariables) {
this.setO("_pngjFile", g.getParameter("_pngjFile", false));
this.htUserVariables = g.htUserVariables;
}this.debugScript = g.debugScript;
this.disablePopupMenu = g.disablePopupMenu;
this.messageStyleChime = g.messageStyleChime;
this.measureDistanceUnits = g.measureDistanceUnits;
this.defaultDirectory = g.defaultDirectory;
this.autoplayMovie = g.autoplayMovie;
this.allowAudio = g.allowAudio;
this.allowGestures = g.allowGestures;
this.allowModelkit = g.allowModelkit;
this.allowMultiTouch = g.allowMultiTouch;
this.allowKeyStrokes = g.allowKeyStrokes;
this.legacyAutoBonding = g.legacyAutoBonding;
this.legacyHAddition = g.legacyHAddition;
this.legacyJavaFloat = g.legacyJavaFloat;
this.minimizationReportSteps = g.minimizationReportSteps;
this.doublePrecision = g.doublePrecision;
this.bondingVersion = g.bondingVersion;
this.platformSpeed = g.platformSpeed;
this.useScriptQueue = g.useScriptQueue;
this.showTiming = g.showTiming;
this.wireframeRotation = g.wireframeRotation;
this.testFlag1 = g.testFlag1;
this.testFlag2 = g.testFlag2;
this.testFlag3 = g.testFlag3;
this.testFlag4 = g.testFlag4;
this.nihResolverFormat = g.nihResolverFormat;
}if (this.nihResolverFormat == null) this.nihResolverFormat = JV.JC.databases.get("nci");
this.setCIR(this.nihResolverFormat, false);
for (var item, $item = 0, $$item = J.c.CBK.values(); $item < $$item.length && ((item = $$item[$item]) || true); $item++) this.resetValue(item.name() + "Callback", g);

this.setF("cameraDepth", 3.0);
this.setI("undoMax", vwr.stm.getUndoMax());
this.setI("contextDepthMax", 100);
this.setI("depth", 0);
this.setF("gestureSwipeFactor", 1.0);
this.setB("hideNotSelected", false);
this.setI("historyLevel", 0);
this.setO("hoverLabel", "");
this.setB("isKiosk", vwr.isKiosk());
this.setO("logFile", vwr.getLogFileName());
this.setI("logLevel", JU.Logger.getLogLevel());
this.setF("mouseWheelFactor", 1.15);
this.setF("mouseDragFactor", 1.0);
this.setI("navFps", 10);
this.setI("navigationDepth", 0);
this.setI("navigationSlab", 0);
this.setI("navX", 0);
this.setI("navY", 0);
this.setI("navZ", 0);
this.setO("pathForAllFiles", "");
this.setB("perspectiveDepth", true);
this.setI("perspectiveModel", 11);
this.setO("picking", "identify");
this.setO("pickingStyle", "toggle");
this.setB("refreshing", true);
this.setI("rotationRadius", 0);
this.setI("scaleAngstromsPerInch", 0);
this.setI("scriptReportingLevel", 0);
this.setB("selectionHalos", false);
this.setB("showaxes", false);
this.setB("showboundbox", false);
this.setB("showfrank", false);
this.setB("showUnitcell", false);
this.setI("slab", 100);
this.setB("slabEnabled", false);
this.setF("slabrange", 0);
this.setI("spinX", 0);
this.setI("spinY", 30);
this.setI("spinZ", 0);
this.setI("spinFps", 30);
this.setF("visualRange", 5.0);
this.setI("stereoDegrees", -5);
this.setB("syncScript", vwr.sm.syncingScripts);
this.setB("syncMouse", vwr.sm.syncingMouse);
this.setB("syncStereo", vwr.sm.stereoSync);
this.setB("windowCentered", true);
this.setB("zoomEnabled", true);
this.setI("_version", JV.JC.versionInt);
this.setO("_versionDate", JV.Viewer.getJmolVersion());
this.setB("axesWindow", true);
this.setB("axesMolecular", false);
this.setB("axesPosition", false);
this.setB("axesUnitcell", false);
this.setI("backgroundModel", 0);
this.setB("colorRasmol", false);
this.setO("currentLocalPath", "");
this.setO("defaultLattice", "{0 0 0}");
this.setO("defaultColorScheme", "Jmol");
this.setO("defaultDirectoryLocal", "");
this.setO("defaults", "Jmol");
this.setO("defaultVDW", "Jmol");
this.setO("exportDrivers", "Idtf;Maya;Povray;Vrml;X3d;Stl;Tachyon;Obj");
this.setI("propertyAtomNumberColumnCount", 0);
this.setI("propertyAtomNumberField", 0);
this.setI("propertyDataColumnCount", 0);
this.setI("propertyDataField", 0);
this.setI("undoMax", vwr.stm.getUndoMax());
this.setB("allowEmbeddedScripts", this.allowEmbeddedScripts);
this.setB("allowGestures", this.allowGestures);
this.setB("allowKeyStrokes", this.allowKeyStrokes);
this.setB("allowModelkit", this.allowModelkit);
this.setB("allowMultiTouch", this.allowMultiTouch);
this.setB("allowRotateSelected", this.allowRotateSelected);
this.setB("allowMoveAtoms", this.allowMoveAtoms);
this.setI("animationFps", this.animationFps);
this.setB("antialiasImages", this.antialiasImages);
this.setB("antialiasDisplay", this.antialiasDisplay);
this.setB("antialiasTranslucent", this.antialiasTranslucent);
this.setB("appendNew", this.appendNew);
this.setO("appletProxy", this.appletProxy);
this.setB("applySymmetryToBonds", this.applySymmetryToBonds);
this.setB("atomPicking", this.atomPicking);
this.setO("atomTypes", this.atomTypes);
this.setB("autoBond", this.autoBond);
this.setB("autoFps", this.autoFps);
this.setI("axesMode", this.axesMode == 603979808 ? 2 : this.axesMode == 603979804 ? 1 : 0);
this.setF("axesScale", this.axesScale);
this.setF("axesOffset", this.axesOffset);
this.setB("axesOrientationRasmol", this.axesOrientationRasmol);
this.setF("cartoonBlockHeight", this.cartoonBlockHeight);
this.setB("cartoonBlocks", this.cartoonBlocks);
this.setB("cartoonSteps", this.cartoonSteps);
this.setB("bondModeOr", this.bondModeOr);
this.setB("bondPicking", this.bondPicking);
this.setI("bondRadiusMilliAngstroms", this.bondRadiusMilliAngstroms);
this.setF("bondTolerance", this.bondTolerance);
this.setB("cartoonBaseEdges", this.cartoonBaseEdges);
this.setB("cartoonFancy", this.cartoonFancy);
this.setB("cartoonLadders", this.cartoonLadders);
this.setB("cartoonLadders", this.cartoonRibose);
this.setB("cartoonRockets", this.cartoonRockets);
this.setB("chainCaseSensitive", this.chainCaseSensitive);
this.setB("cipRule6Full", this.cipRule6Full);
this.setI("bondingVersion", this.bondingVersion);
this.setO("dataSeparator", this.dataSeparator);
this.setB("debugScript", this.debugScript);
this.setO("defaultAngleLabel", this.defaultAngleLabel);
this.setF("defaultDrawArrowScale", this.defaultDrawArrowScale);
this.setO("defaultDirectory", this.defaultDirectory);
this.setO("defaultDistanceLabel", this.defaultDistanceLabel);
this.setO("defaultDropScript", this.defaultDropScript);
this.setO("defaultLabelPDB", this.defaultLabelPDB);
this.setO("defaultLabelXYZ", this.defaultLabelXYZ);
this.setO("defaultLoadFilter", this.defaultLoadFilter);
this.setO("defaultLoadScript", this.defaultLoadScript);
this.setB("defaultStructureDSSP", this.defaultStructureDSSP);
this.setO("defaultTorsionLabel", this.defaultTorsionLabel);
this.setF("defaultTranslucent", this.defaultTranslucent);
this.setI("delayMaximumMs", this.delayMaximumMs);
this.setF("dipoleScale", this.dipoleScale);
this.setB("disablePopupMenu", this.disablePopupMenu);
this.setB("displayCellParameters", this.displayCellParameters);
this.setI("dotDensity", this.dotDensity);
this.setI("dotScale", this.dotScale);
this.setB("dotsSelectedOnly", this.dotsSelectedOnly);
this.setB("dotSurface", this.dotSurface);
this.setB("dragSelected", this.dragSelected);
this.setB("drawHover", this.drawHover);
this.setF("drawFontSize", this.drawFontSize);
this.setB("drawPicking", this.drawPicking);
this.setB("dsspCalculateHydrogenAlways", this.dsspCalcHydrogen);
this.setB("elementkey", this.elementKey);
this.setB("labelkey", this.labelKey);
this.setB("ellipsoidArcs", this.ellipsoidArcs);
this.setB("ellipsoidArrows", this.ellipsoidArrows);
this.setB("ellipsoidAxes", this.ellipsoidAxes);
this.setF("ellipsoidAxisDiameter", this.ellipsoidAxisDiameter);
this.setB("ellipsoidBall", this.ellipsoidBall);
this.setI("ellipsoidDotCount", this.ellipsoidDotCount);
this.setB("ellipsoidDots", this.ellipsoidDots);
this.setB("ellipsoidFill", this.ellipsoidFill);
this.setO("energyUnits", this.energyUnits);
this.setF("exportScale", this.exportScale);
this.setB("doublePrecision", this.doublePrecision);
this.setB("fontScaling", this.fontScaling);
this.setB("fontCaching", this.fontCaching);
this.setB("forceAutoBond", this.forceAutoBond);
this.setO("forceField", this.forceField);
this.setB("fractionalRelative", this.fractionalRelative);
this.setF("particleRadius", this.particleRadius);
this.setB("greyscaleRendering", this.greyscaleRendering);
this.setF("hbondsAngleMinimum", this.hbondsAngleMinimum);
this.setF("hbondHXDistanceMaximum", this.hbondHXDistanceMaximum);
this.setF("hbondsDistanceMaximum", this.hbondNODistanceMaximum);
this.setB("hbondsBackbone", this.hbondsBackbone);
this.setB("hbondsRasmol", this.hbondsRasmol);
this.setB("hbondsSolid", this.hbondsSolid);
this.setI("helixStep", this.helixStep);
this.setO("helpPath", this.helpPath);
this.setI("hermiteLevel", this.hermiteLevel);
this.setB("hideNameInPopup", this.hideNameInPopup);
this.setB("hideNavigationPoint", this.hideNavigationPoint);
this.setB("hiddenLinesDashed", this.hiddenLinesDashed);
this.setB("highResolution", this.highResolutionFlag);
this.setF("hoverDelay", this.hoverDelayMs / 1000);
this.setB("imageState", this.imageState);
this.setI("infoFontSize", this.infoFontSize);
this.setB("isosurfaceKey", this.isosurfaceKey);
this.setB("isosurfacePropertySmoothing", this.isosurfacePropertySmoothing);
this.setI("isosurfacePropertySmoothingPower", this.isosurfacePropertySmoothingPower);
this.setB("jmolInJSpecView", this.jmolInJSpecView);
this.setI("labelPointerWidth", this.labelPointerWidth);
this.setB("justifyMeasurements", this.justifyMeasurements);
this.setB("legacyAutoBonding", this.legacyAutoBonding);
this.setB("legacyHAddition", this.legacyHAddition);
this.setB("legacyJavaFloat", this.legacyJavaFloat);
this.setF("loadAtomDataTolerance", this.loadAtomDataTolerance);
this.setO("loadFormat", this.loadFormat);
this.setO("loadLigandFormat", this.pdbLoadLigandFormat);
this.setB("logCommands", this.logCommands);
this.setB("logGestures", this.logGestures);
this.setB("measureAllModels", this.measureAllModels);
this.setB("measurementLabels", this.measurementLabels);
this.setO("measurementUnits", this.measureDistanceUnits);
this.setI("meshScale", this.meshScale);
this.setB("messageStyleChime", this.messageStyleChime);
this.setF("minBondDistance", this.minBondDistance);
this.setI("minPixelSelRadius", this.minPixelSelRadius);
this.setI("minimizationReportSteps", this.minimizationReportSteps);
this.setI("minimizationSteps", this.minimizationSteps);
this.setB("minimizationRefresh", this.minimizationRefresh);
this.setB("minimizationSilent", this.minimizationSilent);
this.setF("minimizationCriterion", this.minimizationCriterion);
this.setB("mode2d", this.mode2d);
this.setB("modelKitMode", this.modelKitMode);
this.setF("modulationScale", this.modulationScale);
this.setB("monitorEnergy", this.monitorEnergy);
this.setF("multipleBondRadiusFactor", this.multipleBondRadiusFactor);
this.setB("multipleBondBananas", this.multipleBondBananas);
this.setF("multipleBondSpacing", this.multipleBondSpacing);
this.setB("multiProcessor", this.multiProcessor && (JV.Viewer.nProcessors > 1));
this.setB("navigationMode", this.navigationMode);
this.setB("navigationPeriodic", this.navigationPeriodic);
this.setF("navigationSpeed", this.navigationSpeed);
this.setB("nboCharges", this.nboCharges);
this.setB("noDelay", this.noDelay);
this.setO("nmrPredictFormat", this.nmrPredictFormat);
this.setO("nmrUrlFormat", this.nmrUrlFormat);
this.setI("occupancyThreshold", this.occupancyThreshold);
this.setB("partialDots", this.partialDots);
this.setB("pdbAddHydrogens", this.pdbAddHydrogens);
this.setB("pdbGetHeader", this.pdbGetHeader);
this.setB("pdbSequential", this.pdbSequential);
this.setI("percentVdwAtom", this.percentVdwAtom);
this.setI("pickingSpinRate", this.pickingSpinRate);
this.setO("pickLabel", this.pickLabel);
this.setI("platformSpeed", this.platformSpeed);
this.setF("pointGroupLinearTolerance", this.pointGroupLinearTolerance);
this.setF("pointGroupDistanceTolerance", this.pointGroupDistanceTolerance);
this.setB("preserveState", this.preserveState);
this.setO("propertyColorScheme", this.propertyColorScheme);
this.setO("quaternionFrame", this.quaternionFrame);
this.setB("rangeSelected", this.rangeSelected);
this.setI("repaintWaitMs", this.repaintWaitMs);
this.setI("ribbonAspectRatio", this.ribbonAspectRatio);
this.setB("ribbonBorder", this.ribbonBorder);
this.setB("rocketBarrels", this.rocketBarrels);
this.setB("saveProteinStructureState", this.saveProteinStructureState);
this.setB("scriptqueue", this.useScriptQueue);
this.setB("selectAllModels", this.selectAllModels);
this.setB("selectHetero", this.rasmolHeteroSetting);
this.setB("selectHydrogen", this.rasmolHydrogenSetting);
this.setF("sheetSmoothing", this.sheetSmoothing);
this.setB("showHiddenSelectionHalos", this.showHiddenSelectionHalos);
this.setB("showHydrogens", this.showHydrogens);
this.setB("showKeyStrokes", this.showKeyStrokes);
this.setB("showMeasurements", this.showMeasurements);
this.setB("showModulationVectors", this.showModVecs);
this.setB("showMultipleBonds", this.showMultipleBonds);
this.setB("showNavigationPointAlways", this.showNavigationPointAlways);
this.setI("showScript", this.scriptDelay);
this.setB("showtiming", this.showTiming);
this.setB("slabByMolecule", this.slabByMolecule);
this.setB("slabByAtom", this.slabByAtom);
this.setB("smartAromatic", this.smartAromatic);
this.setI("minimizationMaxAtoms", this.minimizationMaxAtoms);
this.setI("smallMoleculeMaxAtoms", this.smallMoleculeMaxAtoms);
this.setO("smilesUrlFormat", this.smilesUrlFormat);
this.setO("macroDirectory", this.macroDirectory);
this.setO("nihResolverFormat", this.nihResolverFormat);
this.setO("pubChemFormat", this.pubChemFormat);
this.setB("showUnitCellDetails", this.showUnitCellDetails);
this.setB("solventProbe", this.dotSolvent);
this.setF("solventProbeRadius", this.solventProbeRadius);
this.setB("ssbondsBackbone", this.ssbondsBackbone);
this.setF("starWidth", this.starWidth);
this.setB("statusReporting", this.statusReporting);
this.setI("strandCount", this.strandCountForStrands);
this.setI("strandCountForStrands", this.strandCountForStrands);
this.setI("strandCountForMeshRibbon", this.strandCountForMeshRibbon);
this.setF("strutDefaultRadius", this.strutDefaultRadius);
this.setF("strutLengthMaximum", this.strutLengthMaximum);
this.setI("strutSpacing", this.strutSpacing);
this.setB("strutsMultiple", this.strutsMultiple);
this.setB("symmetryhermannmauguin", this.symmetryHermannMauguin);
this.setB("testFlag1", this.testFlag1);
this.setB("testFlag2", this.testFlag2);
this.setB("testFlag3", this.testFlag3);
this.setB("testFlag4", this.testFlag4);
this.setB("traceAlpha", this.traceAlpha);
this.setB("translucent", this.translucent);
this.setB("twistedSheets", this.twistedSheets);
this.setB("useMinimizationThread", this.useMinimizationThread);
this.setB("useNumberLocalization", this.useNumberLocalization);
this.setB("vectorsCentered", this.vectorsCentered);
this.setF("vectorScale", this.vectorScale);
this.setB("vectorSymmetry", this.vectorSymmetry);
this.setI("vectorTrail", this.vectorTrail);
this.setF("vibrationPeriod", this.vibrationPeriod);
this.setF("vibrationScale", this.vibrationScale);
this.setB("waitForMoveTo", this.waitForMoveTo);
this.setB("wireframeRotation", this.wireframeRotation);
this.setI("zDepth", this.zDepth);
this.setB("zeroBasedXyzRasmol", this.zeroBasedXyzRasmol);
this.setB("zoomHeight", this.zoomHeight);
this.setB("zoomLarge", this.zoomLarge);
this.setI("zShadePower", this.zShadePower);
this.setI("zSlab", this.zSlab);
}, "JV.Viewer,JV.GlobalSettings,~B");
Clazz.defineMethod(c$, "clear", 
function(){
var e = this.htUserVariables.keySet().iterator();
while (e.hasNext()) {
var key = e.next();
if (key.charAt(0) == '@' || key.startsWith("site_")) e.remove();
}
this.vwr.setPicked(-1, false);
this.setI("_atomhovered", -1);
this.setO("_pickinfo", "");
this.setB("selectionhalos", false);
this.setB("hidenotselected", false);
this.setB("measurementlabels", this.measurementLabels = true);
this.setB("drawHover", this.drawHover = false);
this.vwr.stm.saveScene("DELETE", null);
});
Clazz.defineMethod(c$, "setUnits", 
function(units){
var mu = this.measureDistanceUnits;
var eu = this.energyUnits;
if (units.equalsIgnoreCase("angstroms")) this.measureDistanceUnits = "angstroms";
 else if (units.equalsIgnoreCase("nanometers") || units.equalsIgnoreCase("nm")) this.measureDistanceUnits = "nanometers";
 else if (units.equalsIgnoreCase("picometers") || units.equalsIgnoreCase("pm")) this.measureDistanceUnits = "picometers";
 else if (units.equalsIgnoreCase("bohr") || units.equalsIgnoreCase("au")) this.measureDistanceUnits = "au";
 else if (units.equalsIgnoreCase("vanderwaals") || units.equalsIgnoreCase("vdw")) this.measureDistanceUnits = "vdw";
 else if (units.toLowerCase().endsWith("hz") || units.toLowerCase().endsWith("khz")) this.measureDistanceUnits = units.toLowerCase();
 else if (units.equalsIgnoreCase("kj")) this.energyUnits = "kJ";
 else if (units.equalsIgnoreCase("kcal")) this.energyUnits = "kcal";
if (!mu.equalsIgnoreCase(this.measureDistanceUnits)) this.setO("measurementUnits", this.measureDistanceUnits);
 else if (!eu.equalsIgnoreCase(this.energyUnits)) this.setO("energyUnits", this.energyUnits);
}, "~S");
Clazz.defineMethod(c$, "isJmolVariable", 
function(key){
return key.charAt(0) == '_' || this.htNonbooleanParameterValues.containsKey(key = key.toLowerCase()) || this.htBooleanParameterFlags.containsKey(key) || JV.GlobalSettings.unreportedProperties.indexOf(";" + key + ";") >= 0;
}, "~S");
Clazz.defineMethod(c$, "resetValue", 
function(name, g){
this.setO(name, g == null ? "" : g.getParameter(name, true));
}, "~S,JV.GlobalSettings");
Clazz.defineMethod(c$, "setB", 
function(name, value){
name = name.toLowerCase();
if (this.htNonbooleanParameterValues.containsKey(name)) return;
this.htBooleanParameterFlags.put(name, value ? Boolean.TRUE : Boolean.FALSE);
}, "~S,~B");
Clazz.defineMethod(c$, "setI", 
function(name, value){
if (value != 2147483647) this.setO(name, Integer.$valueOf(value));
}, "~S,~N");
Clazz.defineMethod(c$, "setF", 
function(name, value){
if (!Float.isNaN(value)) this.setO(name, Float.$valueOf(value));
}, "~S,~N");
Clazz.defineMethod(c$, "setOrRemoveO", 
function(name, value){
if (value == null) this.removeParam(name);
 else this.setO(name, value);
}, "~S,~O");
Clazz.defineMethod(c$, "setO", 
function(name, value){
name = name.toLowerCase();
if (value == null || this.htBooleanParameterFlags.containsKey(name)) return;
this.htNonbooleanParameterValues.put(name, value);
}, "~S,~O");
Clazz.defineMethod(c$, "removeParam", 
function(key){
key = key.toLowerCase();
if (this.htBooleanParameterFlags.containsKey(key)) {
this.htBooleanParameterFlags.remove(key);
if (!this.htPropertyFlagsRemoved.containsKey(key)) this.htPropertyFlagsRemoved.put(key, Boolean.FALSE);
return;
}if (this.htNonbooleanParameterValues.containsKey(key)) this.htNonbooleanParameterValues.remove(key);
}, "~S");
Clazz.defineMethod(c$, "setUserVariable", 
function(key, $var){
if ($var != null) {
key = key.toLowerCase();
this.htUserVariables.put(key, $var.setName(key));
}return $var;
}, "~S,JS.SV");
Clazz.defineMethod(c$, "unsetUserVariable", 
function(key){
if (key.equals("all") || key.equals("variables")) {
this.htUserVariables.clear();
JU.Logger.info("all user-defined variables deleted");
} else if (this.htUserVariables.containsKey(key)) {
JU.Logger.info("variable " + key + " deleted");
this.htUserVariables.remove(key);
}}, "~S");
Clazz.defineMethod(c$, "removeUserVariable", 
function(key){
this.htUserVariables.remove(key);
}, "~S");
Clazz.defineMethod(c$, "getUserVariable", 
function(name){
if (name == null) return null;
name = name.toLowerCase();
return this.htUserVariables.get(name);
}, "~S");
Clazz.defineMethod(c$, "getParameterEscaped", 
function(name, nMax){
name = name.toLowerCase();
if (this.htNonbooleanParameterValues.containsKey(name)) {
var v = this.htNonbooleanParameterValues.get(name);
return JV.StateManager.varClip(name, JU.Escape.e(v), nMax);
}if (this.htBooleanParameterFlags.containsKey(name)) return this.htBooleanParameterFlags.get(name).toString();
if (this.htUserVariables.containsKey(name)) return this.htUserVariables.get(name).escape();
if (this.htPropertyFlagsRemoved.containsKey(name)) return "false";
return "<not defined>";
}, "~S,~N");
Clazz.defineMethod(c$, "getParameter", 
function(name, nullAsString){
var v = this.getParam(name, false);
return (v == null && nullAsString ? "" : v);
}, "~S,~B");
Clazz.defineMethod(c$, "getAndSetNewVariable", 
function(name, doSet){
if (name == null || name.length == 0) name = "x";
var v = this.getParam(name, true);
return (v == null && doSet && name.charAt(0) != '_' ? this.setUserVariable(name, JS.SV.newV(4, "")) : JS.SV.getVariable(v));
}, "~S,~B");
Clazz.defineMethod(c$, "getParam", 
function(name, asVariable){
name = name.toLowerCase();
if (name.equals("_memory")) {
var bTotal = 0;
var bFree = 0;
{
}var value = JU.DF.formatDecimal(bTotal - bFree, 1) + "/" + JU.DF.formatDecimal(bTotal, 1);
this.htNonbooleanParameterValues.put("_memory", value);
}if (this.htNonbooleanParameterValues.containsKey(name)) return this.htNonbooleanParameterValues.get(name);
if (this.htBooleanParameterFlags.containsKey(name)) return this.htBooleanParameterFlags.get(name);
if (this.htPropertyFlagsRemoved.containsKey(name)) return Boolean.FALSE;
if (this.htUserVariables.containsKey(name)) {
var v = this.htUserVariables.get(name);
return (asVariable ? v : JS.SV.oValue(v));
}return null;
}, "~S,~B");
Clazz.defineMethod(c$, "getVariableList", 
function(){
return JV.StateManager.getVariableList(this.htUserVariables, 0, true, false);
});
Clazz.defineMethod(c$, "setStructureList", 
function(list, type){
this.haveSetStructureList = true;
this.structureList.put(type, list);
}, "~A,J.c.STR");
Clazz.defineMethod(c$, "getStructureList", 
function(){
return this.structureList;
});
c$.doReportProperty = Clazz.defineMethod(c$, "doReportProperty", 
function(name){
return (name.charAt(0) != '_' && JV.GlobalSettings.unreportedProperties.indexOf(";" + name + ";") < 0);
}, "~S");
Clazz.defineMethod(c$, "getAllVariables", 
function(){
var map =  new java.util.Hashtable();
map.putAll(this.htBooleanParameterFlags);
map.putAll(this.htNonbooleanParameterValues);
map.putAll(this.htUserVariables);
return map;
});
Clazz.defineMethod(c$, "getLoadState", 
function(htParams){
var str =  new JU.SB();
this.app(str, "set allowEmbeddedScripts false");
if (this.allowEmbeddedScripts) this.setB("allowEmbeddedScripts", true);
this.app(str, "set appendNew " + this.appendNew);
this.app(str, "set appletProxy " + JU.PT.esc(this.appletProxy));
this.app(str, "set applySymmetryToBonds " + this.applySymmetryToBonds);
if (this.atomTypes.length > 0) this.app(str, "set atomTypes " + JU.PT.esc(this.atomTypes));
this.app(str, "set autoBond " + this.autoBond);
if (this.axesOrientationRasmol) this.app(str, "set axesOrientationRasmol true");
this.app(str, "set bondRadiusMilliAngstroms " + this.bondRadiusMilliAngstroms);
this.app(str, "set bondTolerance " + this.bondTolerance);
this.app(str, "set defaultLattice " + JU.Escape.eP(this.ptDefaultLattice));
this.app(str, "set defaultLoadFilter " + JU.PT.esc(this.defaultLoadFilter));
this.app(str, "set defaultLoadScript \"\"");
if (this.defaultLoadScript.length > 0) this.setO("defaultLoadScript", this.defaultLoadScript);
this.app(str, "set defaultStructureDssp " + this.defaultStructureDSSP);
var sMode = this.vwr.getDefaultVdwNameOrData(-2147483648, null, null);
this.app(str, "set defaultVDW " + sMode);
if (sMode.equals("User")) this.app(str, this.vwr.getDefaultVdwNameOrData(2147483647, null, null));
this.app(str, "set forceAutoBond " + this.forceAutoBond);
this.app(str, "#set defaultDirectory " + JU.PT.esc(this.defaultDirectory));
this.app(str, "#set loadFormat " + JU.PT.esc(this.loadFormat));
this.app(str, "#set loadLigandFormat " + JU.PT.esc(this.pdbLoadLigandFormat));
this.app(str, "#set smilesUrlFormat " + JU.PT.esc(this.smilesUrlFormat));
this.app(str, "#set nihResolverFormat " + JU.PT.esc(this.nihResolverFormat));
this.app(str, "#set pubChemFormat " + JU.PT.esc(this.pubChemFormat));
this.app(str, "set bondingVersion " + this.bondingVersion);
this.app(str, "set legacyAutoBonding " + this.legacyAutoBonding);
this.app(str, "set legacyAutoBonding " + this.legacyAutoBonding);
this.app(str, "set legacyHAddition " + this.legacyHAddition);
this.app(str, "set legacyJavaFloat " + this.legacyJavaFloat);
this.app(str, "set minBondDistance " + this.minBondDistance);
this.app(str, "set minimizationCriterion  " + this.minimizationCriterion);
this.app(str, "set minimizationSteps  " + this.minimizationSteps);
this.app(str, "set multipleBondBananas false");
this.app(str, "set pdbAddHydrogens " + (htParams != null && htParams.get("pdbNoHydrogens") !== Boolean.TRUE ? this.pdbAddHydrogens : false));
this.app(str, "set pdbGetHeader " + this.pdbGetHeader);
this.app(str, "set pdbSequential " + this.pdbSequential);
this.app(str, "set percentVdwAtom " + this.percentVdwAtom);
this.app(str, "set smallMoleculeMaxAtoms " + this.smallMoleculeMaxAtoms);
this.app(str, "set smartAromatic " + this.smartAromatic);
if (this.zeroBasedXyzRasmol) this.app(str, "set zeroBasedXyzRasmol true");
return str.toString();
}, "java.util.Map");
Clazz.defineMethod(c$, "app", 
function(s, cmd){
if (cmd.length == 0) return;
s.append("  ").append(cmd).append(";\n");
}, "JU.SB,~S");
Clazz.defineMethod(c$, "setCIR", 
function(template, notify){
if (template == null || template.equals(this.nihResolverFormat) && this.smilesUrlFormat != null) return;
var pt = template.indexOf("/structure");
if (pt > 0) {
this.nihResolverFormat = template.substring(0, pt + 10);
this.smilesUrlFormat = this.nihResolverFormat + "/%FILE/file?format=sdf&get3d=true";
if (notify) JU.Logger.info("CIR resolver set to " + this.nihResolverFormat + " template=" + template);
}}, "~S,~B");
c$.unreportedProperties = (";ambientpercent;animationfps;antialiasdisplay;antialiasimages;antialiastranslucent;appendnew;axescolor;axesposition;axesmolecular;axesorientationrasmol;axesunitcell;axeswindow;axis1color;axis2color;axis3color;backgroundcolor;backgroundmodel;bondsymmetryatoms;boundboxcolor;cameradepth;bondingversion;ciprule6full;contextdepthmax;debug;debugscript;defaultlatttice;defaults;defaultdropscript;diffusepercent;;exportdrivers;exportscale;_filecaching;_filecache;fontcaching;fontscaling;forcefield;language;hbondsDistanceMaximum;hbondsangleminimum;jmolinJSV;legacyautobonding;legacyhaddition;legacyjavafloat;loglevel;logfile;loggestures;logcommands;measurestylechime;loadformat;loadligandformat;macrodirectory;mkaddhydrogens;minimizationmaxatoms;smilesurlformat;pubchemformat;nihresolverformat;edsurlformat;edsurlcutoff;multiprocessor;navigationmode;;nodelay;pathforallfiles;perspectivedepth;phongexponent;perspectivemodel;platformspeed;preservestate;refreshing;repaintwaitms;rotationradius;selectallmodels;showaxes;showaxis1;showaxis2;showaxis3;showboundbox;showfrank;showtiming;showunitcell;slabenabled;slab;slabrange;depth;zshade;zshadepower;specular;specularexponent;specularpercent;celshading;celshadingpower;specularpower;stateversion;statusreporting;stereo;stereostate;vibrationperiod;unitcellcolor;visualrange;windowcentered;zerobasedxyzrasmol;zoomenabled;mousedragfactor;mousewheelfactor;scriptqueue;scriptreportinglevel;syncscript;syncmouse;syncstereo;defaultdirectory;currentlocalpath;defaultdirectorylocal;ambient;bonds;colorrasmol;diffuse;fractionalrelative;frank;hetero;hidenotselected;hoverlabel;hydrogen;languagetranslation;measurementunits;navigationdepth;navigationslab;picking;pickingstyle;propertycolorscheme;radius;rgbblue;rgbgreen;rgbred;scaleangstromsperinch;selectionhalos;showscript;showselections;solvent;strandcount;spinx;spiny;spinz;spinfps;navx;navy;navz;navfps;" + J.c.CBK.getNameList() + ";undo;undoauto;undomax;atompicking;drawpicking;bondpicking;pickspinrate;picklabel" + ";modelkitmode;autoplaymovie;allowaudio;allowgestures;allowkeystrokes;allowmultitouch;allowmodelkit" + ";dodrop;hovered;historylevel;imagestate;iskiosk;useminimizationthread" + ";checkcir;resolverresolver;showkeystrokes;saveproteinstructurestate;testflag1;testflag2;testflag3;testflag4" + ";selecthetero;selecthydrogen" + ";pointgrouplineartolerance;pointgroupdistancetolerance" + ";minimizationreportsteps;labelkey;elementkey;symmetryhermannmauguin;mode2d;").toLowerCase();
});
;//5.0.1-v7 Tue Feb 10 12:29:49 CST 2026
