biojs-vis-pdbviewer/external/jmol-14.2.4/jsmol/j2s/JV/GlobalSettings.js

A BioJS 2.0 component to view protein structures

Clazz.declarePackage ("JV");
Clazz.load (["java.util.Hashtable", "JU.P3", "J.c.AXES", "$.CBK"], "JV.GlobalSettings", ["java.lang.Boolean", "$.Float", "JU.BS", "$.DF", "$.Lst", "$.PT", "$.SB", "J.c.STR", "JS.SV", "JU.BSUtil", "$.Escape", "$.Logger", "$.Txt", "JV.JC", "$.StateManager", "$.Viewer"], function () {
c$ = Clazz.decorateAsClass (function () {
this.vwr = null;
this.htNonbooleanParameterValues = null;
this.htBooleanParameterFlags = null;
this.htPropertyFlagsRemoved = null;
this.htUserVariables = null;
this.databases = null;
this.ambientPercent = 45;
this.diffusePercent = 84;
this.specular = true;
this.specularExponent = 6;
this.phongExponent = 64;
this.specularPercent = 22;
this.specularPower = 40;
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}){color structure}else{wireframe -0.1};if (!{visible}){spacefill 23%};select *}";
this.forceAutoBond = false;
this.fractionalRelative = true;
this.inlineNewlineChar = '|';
this.loadFormat = null;
this.loadLigandFormat = null;
this.nmrUrlFormat = null;
this.nmrPredictFormat = null;
this.smilesUrlFormat = null;
this.nihResolverFormat = null;
this.pubChemFormat = null;
this.edsUrlFormat = "http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap";
this.edsUrlCutoff = "http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.sfdat";
this.edsUrlOptions = "within 2.0 {*}";
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.allowRotateSelected = false;
this.allowMoveAtoms = false;
this.defaultPerspectiveDepth = true;
this.visualRange = 5;
this.solventOn = 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.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.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.partialDots = false;
this.bondModeOr = false;
this.hbondsBackbone = false;
this.hbondsAngleMinimum = 90;
this.hbondsDistanceMaximum = 3.25;
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.cartoonBaseEdges = false;
this.cartoonRockets = false;
this.backboneSteps = false;
this.cartoonFancy = false;
this.cartoonLadders = false;
this.cartoonRibose = false;
this.chainCaseSensitive = 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.allowGestures = false;
this.allowModelkit = true;
this.allowMultiTouch = true;
this.allowKeyStrokes = false;
this.animationFps = 10;
this.atomPicking = true;
this.autoFps = false;
this.axesMode = null;
this.axesScale = 2;
this.starWidth = 0.05;
this.bondPicking = false;
this.defaultCameraDepth = 3.0;
this.celShading = false;
this.celShadingPower = 10;
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 = 14;
this.disablePopupMenu = false;
this.dragSelected = false;
this.drawHover = false;
this.drawPicking = false;
this.dsspCalcHydrogen = true;
this.energyUnits = "kJ";
this.exportScale = 1;
this.helpPath = "http://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.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.showUnitCellDetails = true;
this.showUnitCellInfo = 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.useMinimizationThread = true;
this.useNumberLocalization = true;
this.useScriptQueue = true;
this.waitForMoveTo = true;
this.vectorScale = 1;
this.vectorSymmetry = false;
this.vectorsCentered = false;
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.objMad = 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.userDatabases = null;
this.bondingVersion = 0;
Clazz.instantialize (this, arguments);
}, JV, "GlobalSettings");
Clazz.prepareFields (c$, function () {
this.htUserVariables =  new java.util.Hashtable ();
this.ptDefaultLattice =  new JU.P3 ();
this.axesMode = J.c.AXES.BOUNDBOX;
this.objColors =  Clazz.newIntArray (8, 0);
this.objStateOn =  Clazz.newBooleanArray (8, false);
this.objMad =  Clazz.newIntArray (8, 0);
this.structureList =  new java.util.Hashtable ();
{
this.structureList.put (J.c.STR.TURN, [30, 90, -15, 95]);
this.structureList.put (J.c.STR.SHEET, [-180, -10, 70, 180, -180, -45, -180, -130, 140, 180, 90, 180]);
this.structureList.put (J.c.STR.HELIX, [-160, 0, -100, 45]);
}});
Clazz.makeConstructor (c$, 
function (vwr, gsOld, clearUserVariables) {
this.vwr = vwr;
this.registerAllValues (gsOld, clearUserVariables);
}, "JV.Viewer,JV.GlobalSettings,~B");
Clazz.defineMethod (c$, "clear", 
function () {
var e = this.htUserVariables.keySet ().iterator ();
while (e.hasNext ()) {
var key = e.next ();
if (key.charAt (0) == '@' || key.startsWith ("site_")) e.remove ();
}
this.setPicked (-1);
this.setI ("_atomhovered", -1);
this.setO ("_pickinfo", "");
this.setB ("selectionhalos", false);
this.setB ("hidenotselected", false);
this.setB ("measurementlabels", this.measurementLabels = true);
this.setB ("drawHover", this.drawHover = false);
this.vwr.stm.saveScene ("DELETE", null);
});
Clazz.defineMethod (c$, "registerAllValues", 
function (g, clearUserVariables) {
this.htNonbooleanParameterValues =  new java.util.Hashtable ();
this.htBooleanParameterFlags =  new java.util.Hashtable ();
this.htPropertyFlagsRemoved =  new java.util.Hashtable ();
if (g != null) {
if (!clearUserVariables) this.htUserVariables = g.htUserVariables;
this.debugScript = g.debugScript;
this.disablePopupMenu = g.disablePopupMenu;
this.messageStyleChime = g.messageStyleChime;
this.defaultDirectory = g.defaultDirectory;
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.bondingVersion = g.bondingVersion;
this.platformSpeed = g.platformSpeed;
this.useScriptQueue = g.useScriptQueue;
this.databases = g.databases;
this.showTiming = g.showTiming;
this.wireframeRotation = g.wireframeRotation;
this.testFlag1 = g.testFlag1;
this.testFlag2 = g.testFlag2;
this.testFlag3 = g.testFlag3;
this.testFlag4 = g.testFlag4;
}if (this.databases == null) {
this.databases =  new java.util.Hashtable ();
this.getDataBaseList (JV.JC.databases);
this.getDataBaseList (this.userDatabases);
}this.loadFormat = this.databases.get ("pdb");
this.loadLigandFormat = this.databases.get ("ligand");
this.nmrUrlFormat = this.databases.get ("nmr");
this.nmrPredictFormat = this.databases.get ("nmrdb");
this.smilesUrlFormat = this.databases.get ("nci") + "/file?format=sdf&get3d=True";
this.nihResolverFormat = this.databases.get ("nci");
this.pubChemFormat = this.databases.get ("pubchem");
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.setI ("historyLevel", 0);
this.setI ("depth", 0);
this.setF ("gestureSwipeFactor", 1.0);
this.setB ("hideNotSelected", false);
this.setO ("hoverLabel", "");
this.setB ("isKiosk", this.vwr.isKiosk ());
this.setO ("logFile", this.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.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.setI ("stereoDegrees", -5);
this.setI ("stateversion", 0);
this.setB ("syncScript", this.vwr.getStatusManager ().syncingScripts);
this.setB ("syncMouse", this.vwr.getStatusManager ().syncingMouse);
this.setB ("syncStereo", this.vwr.getStatusManager ().stereoSync);
this.setB ("windowCentered", true);
this.setB ("zoomEnabled", true);
this.setI ("zDepth", 0);
this.setB ("zShade", false);
this.setI ("zSlab", 50);
this.setI ("_version", JV.JC.versionInt);
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;Tachyon;Obj");
this.setI ("propertyAtomNumberColumnCount", 0);
this.setI ("propertyAtomNumberField", 0);
this.setI ("propertyDataColumnCount", 0);
this.setI ("propertyDataField", 0);
this.setB ("undo", true);
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 ("ambientPercent", this.ambientPercent);
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.getCode ());
this.setF ("axesScale", this.axesScale);
this.setB ("axesOrientationRasmol", this.axesOrientationRasmol);
this.setB ("backboneSteps", this.backboneSteps);
this.setB ("bondModeOr", this.bondModeOr);
this.setB ("bondPicking", this.bondPicking);
this.setI ("bondRadiusMilliAngstroms", this.bondRadiusMilliAngstroms);
this.setF ("bondTolerance", this.bondTolerance);
this.setF ("cameraDepth", this.defaultCameraDepth);
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 ("celShading", this.celShading);
this.setI ("celShadingPower", this.celShadingPower);
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.setI ("diffusePercent", this.diffusePercent);
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.setO ("edsUrlFormat", this.edsUrlFormat);
this.setO ("edsUrlCutoff", this.edsUrlCutoff);
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 ("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 ("hbondsDistanceMaximum", this.hbondsDistanceMaximum);
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 ("highResolution", this.highResolutionFlag);
this.setF ("hoverDelay", this.hoverDelayMs / 1000);
this.setB ("imageState", this.imageState);
this.setB ("isosurfaceKey", this.isosurfaceKey);
this.setB ("isosurfacePropertySmoothing", this.isosurfacePropertySmoothing);
this.setI ("isosurfacePropertySmoothingPower", this.isosurfacePropertySmoothingPower);
this.setB ("justifyMeasurements", this.justifyMeasurements);
this.setB ("legacyAutoBonding", this.legacyAutoBonding);
this.setB ("legacyHAddition", this.legacyHAddition);
this.setF ("loadAtomDataTolerance", this.loadAtomDataTolerance);
this.setO ("loadFormat", this.loadFormat);
this.setO ("loadLigandFormat", this.loadLigandFormat);
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 ("minimizationSteps", this.minimizationSteps);
this.setB ("minimizationRefresh", this.minimizationRefresh);
this.setB ("minimizationSilent", this.minimizationSilent);
this.setF ("minimizationCriterion", this.minimizationCriterion);
this.setB ("modelKitMode", this.modelKitMode);
this.setF ("modulationScale", this.modulationScale);
this.setB ("monitorEnergy", this.monitorEnergy);
this.setF ("multipleBondRadiusFactor", this.multipleBondRadiusFactor);
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.setO ("nmrPredictFormat", this.nmrPredictFormat);
this.setO ("nmrUrlFormat", this.nmrUrlFormat);
this.setB ("partialDots", this.partialDots);
this.setB ("pdbAddHydrogens", this.pdbAddHydrogens);
this.setB ("pdbGetHeader", this.pdbGetHeader);
this.setB ("pdbSequential", this.pdbSequential);
this.setB ("perspectiveDepth", this.defaultPerspectiveDepth);
this.setI ("percentVdwAtom", this.percentVdwAtom);
this.setI ("phongExponent", this.phongExponent);
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 ("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 ("smallMoleculeMaxAtoms", this.smallMoleculeMaxAtoms);
this.setO ("smilesUrlFormat", this.smilesUrlFormat);
this.setO ("nihResolverFormat", this.nihResolverFormat);
this.setO ("pubChemFormat", this.pubChemFormat);
this.setB ("showUnitCellDetails", this.showUnitCellDetails);
this.setB ("showUnitCellInfo", this.showUnitCellInfo);
this.setB ("solventProbe", this.solventOn);
this.setF ("solventProbeRadius", this.solventProbeRadius);
this.setB ("specular", this.specular);
this.setI ("specularExponent", this.specularExponent);
this.setI ("specularPercent", this.specularPercent);
this.setI ("specularPower", this.specularPower);
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 ("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.setF ("vibrationPeriod", this.vibrationPeriod);
this.setF ("vibrationScale", this.vibrationScale);
this.setF ("visualRange", this.visualRange);
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.GlobalSettings,~B");
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$, "setO", 
function (name, value) {
name = name.toLowerCase ();
if (value == null || this.htBooleanParameterFlags.containsKey (name)) return;
this.htNonbooleanParameterValues.put (name, value);
}, "~S,~O");
Clazz.defineMethod (c$, "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) return 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$, "getOrSetNewVariable", 
function (name, doSet) {
if (name == null || name.length == 0) name = "x";
var v = this.getParam (name, true);
return (v == null && doSet && name.charAt (0) != '_' ? this.setUserVariable (name, JS.SV.newV (4, "")) : JS.SV.getVariable (v));
}, "~S,~B");
Clazz.defineMethod (c$, "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$, "getStructureList", 
function () {
return this.structureList;
});
Clazz.defineMethod (c$, "setPicked", 
function (atomIndex) {
var pickedSet = null;
var pickedList = null;
if (atomIndex >= 0) {
this.setI ("_atompicked", atomIndex);
pickedSet = this.getParam ("picked", true);
pickedList = this.getParam ("pickedList", true);
}if (pickedSet == null || pickedSet.tok != 10) {
pickedSet = JS.SV.newV (10,  new JU.BS ());
pickedList = JS.SV.getVariableList ( new JU.Lst ());
this.setUserVariable ("picked", pickedSet);
this.setUserVariable ("pickedList", pickedList);
}if (atomIndex < 0) return;
JS.SV.getBitSet (pickedSet, false).set (atomIndex);
var p = pickedList.pushPop (null, null);
if (p.tok == 10) pickedList.pushPop (p, null);
if (p.tok != 10 || !(p.value).get (atomIndex)) pickedList.pushPop (JS.SV.newV (10, JU.BSUtil.newAndSetBit (atomIndex)), null);
}, "~N");
Clazz.defineMethod (c$, "resolveDataBase", 
function (database, id) {
var format = this.databases.get (database.toLowerCase ());
if (format == null) return null;
if (id.indexOf ("/") < 0) {
if (database.equals ("pubchem")) id = "name/" + id;
 else if (database.equals ("nci")) id += "/file?format=sdf&get3d=True";
}return (format.indexOf ("%FILE") < 0 ? format + id : JU.Txt.formatStringS (format, "FILE", id));
}, "~S,~S");
c$.doReportProperty = Clazz.defineMethod (c$, "doReportProperty", 
function (name) {
return (name.charAt (0) != '_' && JV.GlobalSettings.unreportedProperties.indexOf (";" + name + ";") < 0);
}, "~S");
Clazz.defineMethod (c$, "getDataBaseList", 
 function (list) {
if (list == null) return;
for (var i = 0; i < list.length; i += 2) this.databases.put (list[i].toLowerCase (), list[i + 1]);

}, "~A");
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.loadLigandFormat));
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 edsUrlFormat " + JU.PT.esc (this.edsUrlFormat));
this.app (str, "#set edsUrlCutoff " + JU.PT.esc (this.edsUrlCutoff));
this.app (str, "set bondingVersion " + this.bondingVersion);
this.app (str, "set legacyAutoBonding " + this.legacyAutoBonding);
this.app (str, "set legacyHAddition " + this.legacyHAddition);
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 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$, "app", 
 function (s, cmd) {
if (cmd.length == 0) return;
s.append ("  ").append (cmd).append (";\n");
}, "JU.SB,~S");
c$.unreportedProperties = c$.prototype.unreportedProperties = (";ambientpercent;animationfps;antialiasdisplay;antialiasimages;antialiastranslucent;appendnew;axescolor;axesposition;axesmolecular;axesorientationrasmol;axesunitcell;axeswindow;axis1color;axis2color;axis3color;backgroundcolor;backgroundmodel;bondsymmetryatoms;boundboxcolor;cameradepth;bondingversion;debug;debugscript;defaultlatttice;defaults;defaultdropscript;diffusepercent;;exportdrivers;exportscale;_filecaching;_filecache;fontcaching;fontscaling;forcefield;language;legacyautobonding;legacyhaddition;loglevel;logfile;loggestures;logcommands;measurestylechime;loadformat;loadligandformat;smilesurlformat;pubchemformat;nihresolverformat;edsurlformat;edsurlcutoff;multiprocessor;navigationmode;;pathforallfiles;perspectivedepth;phongexponent;perspectivemodel;platformspeed;preservestate;refreshing;repaintwaitms;rotationradius;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;propertycolorschemeoverload;radius;rgbblue;rgbgreen;rgbred;scaleangstromsperinch;selectionhalos;showscript;showselections;solvent;strandcount;spinx;spiny;spinz;spinfps;navx;navy;navz;navfps;" + J.c.CBK.getNameList () + ";undo;atompicking;drawpicking;bondpicking;pickspinrate;picklabel" + ";modelkitmode;allowgestures;allowkeystrokes;allowmultitouch;allowmodelkit" + ";").toLowerCase ();
});