Clazz.declarePackage("JV");
Clazz.load(["java.lang.Enum", "J.api.JmolViewer", "$.PlatformViewer", "J.atomdata.AtomDataServer", "java.util.Hashtable", "JU.P3"], "JV.Viewer", ["java.util.Arrays", "JU.AU", "$.BS", "$.CU", "$.DF", "$.Lst", "$.P3i", "$.PT", "$.Quat", "$.Rdr", "$.SB", "J.adapter.smarter.SmarterJmolAdapter", "J.api.Interface", "J.atomdata.RadiusData", "J.c.FIL", "$.STER", "$.VDW", "J.i18n.GT", "JM.Measurement", "$.ModelSet", "JS.SV", "$.T", "J.thread.TimeoutThread", "JU.BSUtil", "$.C", "$.CommandHistory", "$.Elements", "$.Escape", "$.GData", "$.JmolMolecule", "$.Logger", "$.Parser", "$.TempArray", "JV.ActionManager", "$.AnimationManager", "$.ColorManager", "$.FileManager", "$.GlobalSettings", "$.JC", "$.ModelManager", "$.SelectionManager", "$.ShapeManager", "$.StateManager", "$.StatusManager", "$.TransformManager", "JV.binding.Binding"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.testAsync = false;
this.autoExit = false;
this.haveDisplay = false;
this.isJSNoAWT = false;
this.isWebGL = false;
this.isSingleThreaded = false;
this.queueOnHold = false;
this.fullName = "";
this.compiler = null;
this.definedAtomSets = null;
this.ms = null;
this.fm = null;
this.isApplet = false;
this.isJNLP = false;
this.isSyntaxAndFileCheck = false;
this.isSyntaxCheck = false;
this.listCommands = false;
this.mustRender = false;
this.htmlName = "";
this.appletName = "";
this.tryPt = 0;
this.insertedCommand = "";
this.gdata = null;
this.html5Applet = null;
this.acm = null;
this.am = null;
this.cm = null;
this.dm = null;
this.shm = null;
this.slm = null;
this.rm = null;
this.g = null;
this.sm = null;
this.tm = null;
this.syncId = "";
this.logFilePath = "";
this.allowScripting = false;
this.isPrintOnly = false;
this.isSignedApplet = false;
this.isSignedAppletLocal = false;
this.isSilent = false;
this.multiTouch = false;
this.noGraphicsAllowed = false;
this.useCommandThread = false;
this.commandOptions = null;
this.vwrOptions = null;
this.display = null;
this.modelAdapter = null;
this.access = null;
this.commandHistory = null;
this.mm = null;
this.stm = null;
this.scm = null;
this.eval = null;
this.tempArray = null;
this.allowArrayDotNotation = false;
this.async = false;
this.executor = null;
this.screenWidth = 0;
this.screenHeight = 0;
this.defaultVdw = null;
this.rd = null;
this.chainMap = null;
this.chainList = null;
this.errorMessage = null;
this.errorMessageUntranslated = null;
this.privateKey = 0;
this.dataOnly = false;
this.maximumSize = 2147483647;
this.gRight = null;
this.isStereoSlave = false;
this.imageFontScaling = 1;
this.antialiased = false;
this.prevFrame = -2147483648;
this.prevMorphModel = 0;
this.haveJDX = false;
this.jsv = null;
this.outputManager = null;
this.jzt = null;
this.isPreviewOnly = false;
this.headless = false;
this.movableBitSet = null;
this.hasSelected = false;
this.mouse = null;
this.ligandModels = null;
this.ligandModelSet = null;
this.annotationParser = null;
this.dssrParser = null;
this.minimizer = null;
this.smilesMatcher = null;
this.jsc = null;
this.lastData = null;
this.motionEventNumber = 0;
this.inMotion = false;
this.refreshing = true;
this.axesAreTainted = false;
this.captureParams = null;
this.jsParams = null;
this.cirChecked = false;
this.hoverAtomIndex = -1;
this.hoverText = null;
this.hoverLabel = "%U";
this.hoverEnabled = true;
this.currentCursor = 0;
this.ptTemp = null;
this.selectionHalosEnabled = false;
this.frankOn = true;
this.noFrankEcho = true;
this.scriptEditorVisible = false;
this.appConsole = null;
this.scriptEditor = null;
this.jmolpopup = null;
this.modelkit = null;
this.headlessImageParams = null;
this.pm = null;
this.isTainted = true;
this.movingSelected = false;
this.showSelected = false;
this.ptScreen = null;
this.ptScreenNew = null;
this.ptNew = null;
this.atomHighlighted = -1;
this.creatingImage = false;
this.bsUserVdws = null;
this.userVdws = null;
this.userVdwMars = null;
this.currentShapeID = -1;
this.currentShapeState = null;
this.localFunctions = null;
this.$isKiosk = false;
this.displayLoadErrors = true;
this.$isParallel = false;
this.stateScriptVersionInt = 2147483647;
this.jsExporter3D = null;
this.timeouts = null;
this.chainCaseSpecified = false;
this.nmrCalculation = null;
this.logFileName = null;
this.jbr = null;
this.jcm = null;
this.jsonParser = null;
this.triangulator = null;
this.nboParser = null;
this.macros = null;
this.consoleFontScale = 1;
Clazz.instantialize(this, arguments);}, JV, "Viewer", J.api.JmolViewer, [J.atomdata.AtomDataServer, J.api.PlatformViewer]);
Clazz.prepareFields (c$, function(){
this.ptScreen =  new JU.P3();
this.ptScreenNew =  new JU.P3();
this.ptNew =  new JU.P3();
});
Clazz.makeConstructor(c$, 
function(info){
Clazz.superConstructor (this, JV.Viewer, []);
this.commandHistory =  new JU.CommandHistory();
this.rd =  new J.atomdata.RadiusData(null, 0, null, null);
this.defaultVdw = J.c.VDW.JMOL;
this.localFunctions =  new java.util.Hashtable();
this.privateKey = Math.random();
this.chainMap =  new java.util.Hashtable();
this.chainList =  new JU.Lst();
this.setOptions(info);
}, "java.util.Map");
Clazz.defineMethod(c$, "finalize", 
function(){
if (JU.Logger.debugging) JU.Logger.debug("vwr finalize " + this);
Clazz.superCall(this, JV.Viewer, "finalize", []);
});
Clazz.defineMethod(c$, "setInsertedCommand", 
function(strScript){
this.insertedCommand = strScript;
}, "~S");
c$.getJmolVersion = Clazz.overrideMethod(c$, "getJmolVersion", 
function(){
return (JV.Viewer.version_date == null ? JV.Viewer.version_date = JV.JC.version + "  " + JV.JC.date : JV.Viewer.version_date);
});
c$.allocateViewer = Clazz.defineMethod(c$, "allocateViewer", 
function(display, modelAdapter, fullName, documentBase, codeBase, commandOptions, statusListener, implementedPlatform){
var info =  new java.util.Hashtable();
info.put("display", display);
info.put("adapter", modelAdapter);
info.put("statusListener", statusListener);
info.put("platform", implementedPlatform);
info.put("options", commandOptions);
info.put("fullName", fullName);
info.put("documentBase", documentBase);
info.put("codeBase", codeBase);
return  new JV.Viewer(info);
}, "~O,J.api.JmolAdapter,~S,java.net.URL,java.net.URL,~S,J.api.JmolStatusListener,J.api.GenericPlatform");
Clazz.defineMethod(c$, "haveAccess", 
function(a){
return this.access === a;
}, "JV.Viewer.ACCESS");
Clazz.overrideMethod(c$, "getModelAdapter", 
function(){
return (this.modelAdapter == null ? this.modelAdapter =  new J.adapter.smarter.SmarterJmolAdapter() : this.modelAdapter);
});
Clazz.overrideMethod(c$, "getSmartsMatch", 
function(smarts, bsSelected){
if (bsSelected == null) bsSelected = this.bsA();
return this.getSmilesMatcher().getSubstructureSet(smarts, this.ms.at, this.ms.ac, bsSelected, 2);
}, "~S,JU.BS");
Clazz.defineMethod(c$, "isSubstructure", 
function(smarts, smiles){
try {
var map = this.getSmilesMatcher().find(smarts, smiles, 10);
return map != null && map.length > 0;
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
return false;
} else {
throw e;
}
}
}, "~S,~S");
Clazz.defineMethod(c$, "hasStructure", 
function(pattern, smiles, isSmarts){
try {
var ret = this.getSmilesMatcher().hasStructure(pattern,  Clazz.newArray(-1, [smiles]), (isSmarts ? 2 : 1) | 8);
return ret[0] == 1;
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
return false;
} else {
throw e;
}
}
}, "~S,~S,~B");
Clazz.defineMethod(c$, "getSmartsMatchForNodes", 
function(smarts, atoms){
return this.getSmilesMatcher().getSubstructureSet(smarts, atoms, atoms.length, null, 2);
}, "~S,~A");
Clazz.defineMethod(c$, "getSmartsMap", 
function(smilesOrSmarts, bsSelected, flags){
if (bsSelected == null) bsSelected = this.bsA();
if (flags == 0) flags = 2;
return this.getSmilesMatcher().getCorrelationMaps(smilesOrSmarts, this.ms.at, this.ms.ac, bsSelected, flags);
}, "~S,JU.BS,~N");
Clazz.defineMethod(c$, "setOptions", 
function(info){
this.vwrOptions = info;
if (JU.Logger.debugging) {
JU.Logger.debug("Viewer constructor " + this);
}this.modelAdapter = info.get("adapter");
var statusListener = info.get("statusListener");
this.fullName = info.get("fullName");
if (this.fullName == null) this.fullName = "";
var o = info.get("codePath");
if (o == null) o = "../java/";
JV.Viewer.appletCodeBase = o.toString();
JV.Viewer.appletIdiomaBase = JV.Viewer.appletCodeBase.substring(0, JV.Viewer.appletCodeBase.lastIndexOf("/", JV.Viewer.appletCodeBase.length - 2) + 1) + "idioma";
o = info.get("documentBase");
JV.Viewer.appletDocumentBase = (o == null ? "" : o.toString());
o = info.get("options");
this.commandOptions = (o == null ? "" : o.toString());
if (info.containsKey("debug") || this.commandOptions.indexOf("-debug") >= 0) JU.Logger.setLogLevel(5);
if (this.isApplet && info.containsKey("maximumSize")) this.setMaximumSize((info.get("maximumSize")).intValue());
this.isJNLP = this.checkOption2("isJNLP", "-jnlp");
if (this.isJNLP) JU.Logger.info("setting JNLP mode TRUE");
this.isSignedApplet = this.isJNLP || this.checkOption2("signedApplet", "-signed");
this.isApplet = this.isSignedApplet || this.checkOption2("applet", "-applet");
this.allowScripting = !this.checkOption2("noscripting", "-noscripting");
var i = this.fullName.indexOf("__");
this.htmlName = (i < 0 ? this.fullName : this.fullName.substring(0, i));
this.appletName = JU.PT.split(this.htmlName + "_", "_")[0];
this.syncId = (i < 0 ? "" : this.fullName.substring(i + 2, this.fullName.length - 2));
this.access = (this.checkOption2("access:READSPT", "-r") ? JV.Viewer.ACCESS.READSPT : this.checkOption2("access:NONE", "-R") ? JV.Viewer.ACCESS.NONE : JV.Viewer.ACCESS.ALL);
this.isPreviewOnly = info.containsKey("previewOnly");
if (this.isPreviewOnly) info.remove("previewOnly");
this.isPrintOnly = this.checkOption2("printOnly", "-p");
this.dataOnly = this.checkOption2("isDataOnly", "\0");
this.autoExit = this.checkOption2("exit", "-x");
o = info.get("platform");
var platform = "unknown";
if (o == null) {
o = (this.commandOptions.contains("platform=") ? this.commandOptions.substring(this.commandOptions.indexOf("platform=") + 9) : "J.awt.Platform");
}if ((typeof(o)=='string')) {
platform = o;
this.isWebGL = (platform.indexOf(".awtjs.") >= 0);
JV.Viewer.isJS = this.isJSNoAWT = this.isWebGL || (platform.indexOf(".awtjs2d.") >= 0);
this.async = !this.dataOnly && !this.autoExit && (this.testAsync || JV.Viewer.isJS && info.containsKey("async"));
var applet = null;
var jmol = null;
var javaver = "?";
{
if(self.Jmol) { jmol = Jmol; applet =
Jmol._applets[this.htmlName.split("_object")[0]]; javaver =
Jmol._version; }
}if (javaver != null) {
this.html5Applet = applet;
JV.Viewer.jmolObject = jmol;
JV.Viewer.strJavaVersion = javaver;
JV.Viewer.strJavaVendor = "Java2Script " + (this.isWebGL ? "(WebGL)" : "(HTML5)");
}o = J.api.Interface.getInterface(platform, this, "setOptions");
}this.apiPlatform = o;
this.display = info.get("display");
this.isSingleThreaded = this.apiPlatform.isSingleThreaded();
this.noGraphicsAllowed = this.checkOption2("noDisplay", "-n");
this.headless = this.apiPlatform.isHeadless();
this.haveDisplay = (this.isWebGL || this.display != null && !this.noGraphicsAllowed && !this.headless && !this.dataOnly);
this.noGraphicsAllowed = new Boolean (this.noGraphicsAllowed & (this.display == null)).valueOf();
this.headless = new Boolean (this.headless | this.noGraphicsAllowed).valueOf();
if (this.haveDisplay) {
this.mustRender = true;
this.multiTouch = this.checkOption2("multiTouch", "-multitouch");
{
if (!this.isWebGL) this.display =
document.getElementById(this.display);
}} else {
this.display = null;
}this.apiPlatform.setViewer(this, this.display);
o = info.get("graphicsAdapter");
if (o == null && !this.isWebGL) o = J.api.Interface.getOption("g3d.Graphics3D", this, "setOptions");
this.gdata = (o == null && (this.isWebGL || !JV.Viewer.isJS) ?  new JU.GData() : o);
this.gdata.initialize(this, this.apiPlatform);
this.stm =  new JV.StateManager(this);
this.cm =  new JV.ColorManager(this, this.gdata);
this.sm =  new JV.StatusManager(this);
var is4D = info.containsKey("4DMouse");
this.tm = JV.TransformManager.getTransformManager(this, 2147483647, 0, is4D);
this.slm =  new JV.SelectionManager(this);
if (this.haveDisplay) {
this.acm = (this.multiTouch ? J.api.Interface.getOption("multitouch.ActionManagerMT", null, null) :  new JV.ActionManager());
this.acm.setViewer(this, this.commandOptions + "-multitouch-" + info.get("multiTouch"));
this.mouse = this.apiPlatform.getMouseManager(this.privateKey, this.display);
if (this.multiTouch && !this.checkOption2("-simulated", "-simulated")) this.apiPlatform.setTransparentCursor(this.display);
}this.mm =  new JV.ModelManager(this);
this.shm =  new JV.ShapeManager(this);
this.tempArray =  new JU.TempArray();
this.am =  new JV.AnimationManager(this);
o = info.get("repaintManager");
if (o == null) o = J.api.Interface.getOption("render.RepaintManager", this, "setOptions");
if (JV.Viewer.isJS || o != null && !o.equals("")) (this.rm = o).set(this, this.shm);
this.ms =  new JM.ModelSet(this, null);
this.initialize(true, false);
this.fm =  new JV.FileManager(this);
this.definedAtomSets =  new java.util.Hashtable();
this.setJmolStatusListener(statusListener);
if (this.isApplet) {
JU.Logger.info("vwrOptions: \n" + JU.Escape.escapeMap(this.vwrOptions));
var path = this.vwrOptions.get("documentLocation");
if (!JV.Viewer.isJS && path != null && path.startsWith("file:/")) {
path = path.substring(0, path.substring(0, (path + "?").indexOf("?")).lastIndexOf("/"));
JU.Logger.info("setting current directory to " + path);
this.cd(path);
}path = JV.Viewer.appletDocumentBase;
i = path.indexOf("#");
if (i >= 0) path = path.substring(0, i);
i = path.lastIndexOf("?");
if (i >= 0) path = path.substring(0, i);
i = path.lastIndexOf("/");
if (i >= 0) path = path.substring(0, i);
JV.Viewer.jsDocumentBase = path;
this.fm.setAppletContext(JV.Viewer.appletDocumentBase);
var appletProxy = info.get("appletProxy");
if (appletProxy != null) this.setStringProperty("appletProxy", appletProxy);
if (this.isSignedApplet) {
this.logFilePath = JU.PT.rep(JV.Viewer.appletCodeBase, "file://", "");
this.logFilePath = JU.PT.rep(this.logFilePath, "file:/", "");
if (this.logFilePath.indexOf("//") >= 0) this.logFilePath = null;
 else this.isSignedAppletLocal = true;
} else if (!JV.Viewer.isJS) {
this.logFilePath = null;
} new J.i18n.GT(this, info.get("language"));
if (JV.Viewer.isJS) this.acm.createActions();
} else {
this.gdata.setBackgroundTransparent(this.checkOption2("backgroundTransparent", "-b"));
this.isSilent = this.checkOption2("silent", "-i");
if (this.isSilent) JU.Logger.setLogLevel(3);
if (this.headless && !this.isSilent) JU.Logger.info("Operating headless display=" + this.display + " nographicsallowed=" + this.noGraphicsAllowed);
this.isSyntaxAndFileCheck = this.checkOption2("checkLoad", "-C");
this.isSyntaxCheck = this.isSyntaxAndFileCheck || this.checkOption2("check", "-c");
this.listCommands = this.checkOption2("listCommands", "-l");
this.cd(".");
if (this.headless) {
this.headlessImageParams = info.get("headlessImage");
o = info.get("headlistMaxTimeMs");
if (o == null) o = Integer.$valueOf(60000);
this.setTimeout("" + Math.random(), (o).intValue(), "exitJmol");
}}this.useCommandThread = !this.headless && this.checkOption2("useCommandThread", "-threaded");
this.setStartupBooleans();
this.setIntProperty("_nProcessors", JV.Viewer.nProcessors);
if (!this.isSilent) {
JU.Logger.info("(C) 2015 Jmol Development" + "\nJmol Version: " + JV.Viewer.getJmolVersion() + "\njava.vendor: " + JV.Viewer.strJavaVendor + "\njava.version: " + JV.Viewer.strJavaVersion + "\nos.name: " + JV.Viewer.strOSName + "\nAccess: " + this.access + "\nmemory: " + this.getP("_memory") + "\nprocessors available: " + JV.Viewer.nProcessors + "\nuseCommandThread: " + this.useCommandThread + (!this.isApplet ? "" : "\nappletId:" + this.htmlName + (this.isSignedApplet ? " (signed)" : "")));
}this.zap(false, true, false);
this.g.setO("language", J.i18n.GT.getLanguage());
this.g.setO("_hoverLabel", this.hoverLabel);
this.stm.setJmolDefaults();
JU.Elements.covalentVersion = 1;
this.allowArrayDotNotation = true;
if (this.allowScripting) this.getScriptManager();
}, "java.util.Map");
Clazz.defineMethod(c$, "setMaximumSize", 
function(x){
this.maximumSize = Math.max(x, 100);
}, "~N");
Clazz.defineMethod(c$, "setStereo", 
function(isStereoSlave, gRight){
this.isStereoSlave = isStereoSlave;
this.gRight = gRight;
}, "~B,~O");
Clazz.defineMethod(c$, "getMenu", 
function(type){
this.getPopupMenu();
if (type.equals("\0")) {
this.popupMenu(this.screenWidth - 120, 0, 'j');
return "OK";
}return (this.jmolpopup == null ? "" : this.jmolpopup.jpiGetMenuAsString("Jmol version " + JV.Viewer.getJmolVersion() + "|_GET_MENU|" + type));
}, "~S");
Clazz.overrideMethod(c$, "resizeInnerPanel", 
function(width, height){
if (!this.autoExit && this.haveDisplay) return this.sm.resizeInnerPanel(width, height);
this.setScreenDimension(width, height);
return  Clazz.newIntArray(-1, [this.screenWidth, this.screenHeight]);
}, "~N,~N");
Clazz.overrideMethod(c$, "setScreenDimension", 
function(width, height){
height = Math.min(height, this.maximumSize);
width = Math.min(width, this.maximumSize);
if (this.tm.stereoDoubleFull) width = Clazz.doubleToInt((width + 1) / 2);
if (this.screenWidth == width && this.screenHeight == height) return;
this.resizeImage(width, height, false, false, true);
}, "~N,~N");
Clazz.defineMethod(c$, "resizeImage", 
function(width, height, isImageWrite, isExport, isReset){
if (!isImageWrite && this.creatingImage) return;
var wasAntialiased = this.antialiased;
this.antialiased = (isReset ? this.g.antialiasDisplay && this.checkMotionRendering(603979786) : isImageWrite && !isExport ? this.g.antialiasImages : false);
if (!isExport && !isImageWrite && (width > 0 || wasAntialiased != this.antialiased)) this.setShapeProperty(5, "clearBoxes", null);
this.imageFontScaling = (this.antialiased ? 2 : 1) * (isReset || this.tm.scale3D || width <= 0 ? 1 : (this.g.zoomLarge == (height > width) ? height : width) * 1 / this.getScreenDim());
if (width > 0) {
this.screenWidth = width;
this.screenHeight = height;
if (!isImageWrite) {
this.g.setI("_width", width);
this.g.setI("_height", height);
}} else {
width = (this.screenWidth == 0 ? this.screenWidth = 500 : this.screenWidth);
height = (this.screenHeight == 0 ? this.screenHeight = 500 : this.screenHeight);
}this.tm.setScreenParameters(width, height, isImageWrite || isReset ? this.g.zoomLarge : false, this.antialiased, false, false);
this.gdata.setWindowParameters(width, height, this.antialiased);
this.setModelkitPropertySafely("frameresized", null);
if (width > 0 && !isImageWrite) this.setStatusResized(width, height);
}, "~N,~N,~B,~B,~B");
Clazz.overrideMethod(c$, "getScreenWidth", 
function(){
return this.screenWidth;
});
Clazz.overrideMethod(c$, "getScreenHeight", 
function(){
return this.screenHeight;
});
Clazz.defineMethod(c$, "getScreenDim", 
function(){
return (this.g.zoomLarge == (this.screenHeight > this.screenWidth) ? this.screenHeight : this.screenWidth);
});
Clazz.defineMethod(c$, "setWidthHeightVar", 
function(){
this.g.setI("_width", this.screenWidth);
this.g.setI("_height", this.screenHeight);
});
Clazz.defineMethod(c$, "getBoundBoxCenterX", 
function(){
return Clazz.doubleToInt(this.screenWidth / 2);
});
Clazz.defineMethod(c$, "getBoundBoxCenterY", 
function(){
return Clazz.doubleToInt(this.screenHeight / 2);
});
Clazz.defineMethod(c$, "updateWindow", 
function(width, height){
if (!this.refreshing || this.creatingImage) return (this.refreshing ? false : !JV.Viewer.isJS);
if (this.isTainted || this.tm.slabEnabled) this.setModelVisibility();
this.isTainted = false;
if (this.rm != null) {
if (width != 0) this.setScreenDimension(width, height);
}return true;
}, "~N,~N");
Clazz.defineMethod(c$, "getImage", 
function(isStereo, isImageWrite){
var image = null;
try {
this.beginRendering(isStereo, isImageWrite);
this.render();
this.gdata.endRendering();
image = this.gdata.getScreenImage(isImageWrite);
} catch (e$$) {
if (Clazz.exceptionOf(e$$, Error)){
var er = e$$;
{
this.gdata.getScreenImage(isImageWrite);
this.handleError(er, false);
this.setErrorMessage("Error during rendering: " + er, null);
}
} else if (Clazz.exceptionOf(e$$, Exception)){
var e = e$$;
{
System.out.println("render error" + e);
}
} else {
throw e$$;
}
}
return image;
}, "~B,~B");
Clazz.defineMethod(c$, "beginRendering", 
function(isStereo, isImageWrite){
this.gdata.beginRendering(this.tm.getStereoRotationMatrix(isStereo), this.g.translucent, isImageWrite, !this.checkMotionRendering(603979967));
}, "~B,~B");
Clazz.defineMethod(c$, "render", 
function(){
if (this.mm.modelSet == null || !this.mustRender || !this.refreshing && !this.creatingImage || this.rm == null) return;
var antialias2 = this.antialiased && this.g.antialiasTranslucent;
var navMinMax = this.shm.finalizeAtoms(this.tm.bsSelectedAtoms, true);
if (this.isWebGL) {
this.rm.renderExport(this.gdata, this.ms, this.jsParams);
this.notifyViewerRepaintDone();
return;
}this.rm.render(this.gdata, this.ms, true, navMinMax);
if (this.gdata.setPass2(antialias2)) {
this.tm.setAntialias(antialias2);
this.rm.render(this.gdata, this.ms, false, null);
this.tm.setAntialias(this.antialiased);
}});
Clazz.defineMethod(c$, "drawImage", 
function(graphic, img, x, y, isDTI){
if (graphic != null && img != null) {
this.apiPlatform.drawImage(graphic, img, x, y, this.screenWidth, this.screenHeight, isDTI);
}this.gdata.releaseScreenImage();
}, "~O,~O,~N,~N,~B");
Clazz.defineMethod(c$, "getScreenImage", 
function(){
return this.getScreenImageBuffer(null, true);
});
Clazz.overrideMethod(c$, "getScreenImageBuffer", 
function(g, isImageWrite){
if (this.isWebGL) return (isImageWrite ? this.apiPlatform.allocateRgbImage(0, 0, null, 0, false, true) : null);
var isDouble = this.tm.stereoDoubleFull || this.tm.stereoDoubleDTI;
var isBicolor = this.tm.stereoMode.isBiColor();
var mergeImages = (g == null && isDouble);
var imageBuffer;
if (isBicolor) {
this.beginRendering(true, isImageWrite);
this.render();
this.gdata.endRendering();
this.gdata.snapshotAnaglyphChannelBytes();
this.beginRendering(false, isImageWrite);
this.render();
this.gdata.endRendering();
this.gdata.applyAnaglygh(this.tm.stereoMode, this.tm.stereoColors);
imageBuffer = this.gdata.getScreenImage(isImageWrite);
} else {
imageBuffer = this.getImage(isDouble, isImageWrite);
}var imageBuffer2 = null;
if (mergeImages) {
imageBuffer2 = this.apiPlatform.newBufferedImage(imageBuffer, (this.tm.stereoDoubleDTI ? this.screenWidth : this.screenWidth << 1), this.screenHeight);
g = this.apiPlatform.getGraphics(imageBuffer2);
}if (g != null) {
if (isDouble) {
if (this.tm.stereoMode === J.c.STER.DTI) {
this.drawImage(g, imageBuffer, this.screenWidth >> 1, 0, true);
imageBuffer = this.getImage(false, false);
this.drawImage(g, imageBuffer, 0, 0, true);
g = null;
} else {
this.drawImage(g, imageBuffer, this.screenWidth, 0, false);
imageBuffer = this.getImage(false, false);
}}if (g != null) this.drawImage(g, imageBuffer, 0, 0, false);
}return (mergeImages ? imageBuffer2 : imageBuffer);
}, "~O,~B");
Clazz.defineMethod(c$, "evalStringWaitStatusQueued", 
function(returnType, strScript, statusList, isQuiet, isQueued){
return (this.getScriptManager() == null ? null : this.scm.evalStringWaitStatusQueued(returnType, strScript, statusList, isQuiet, isQueued));
}, "~S,~S,~S,~B,~B");
Clazz.defineMethod(c$, "popupMenu", 
function(x, y, type){
if (!this.haveDisplay || !this.refreshing || this.isPreviewOnly || this.g.disablePopupMenu) return;
switch ((type).charCodeAt(0)) {
case 106:
try {
this.getPopupMenu();
this.jmolpopup.jpiShow(x, y);
} catch (e) {
JU.Logger.info(e.toString());
this.g.disablePopupMenu = true;
}
break;
case 97:
case 98:
case 109:
if (this.getModelkit(true) == null) {
return;
}this.modelkit.showMenu(x, y);
break;
}
}, "~N,~N,~S");
Clazz.defineMethod(c$, "getModelkit", 
function(andShow){
if (this.modelkit == null) {
(this.modelkit = J.api.Interface.getInterface("J.modelkit.ModelKit", this, "script")).setMenu(this.apiPlatform.getMenuPopup(null, 'm'));
} else if (andShow) {
this.modelkit.updateMenu();
}return this.modelkit;
}, "~B");
Clazz.defineMethod(c$, "getPopupMenu", 
function(){
if (this.g.disablePopupMenu) return null;
if (this.jmolpopup == null) {
this.jmolpopup = (this.allowScripting ? this.apiPlatform.getMenuPopup(this.menuStructure, 'j') : null);
if (this.jmolpopup == null) {
if (!this.async) this.g.disablePopupMenu = true;
return null;
}}if (this.isJSNoAWT) this.checkMenuUpdate();
return this.jmolpopup.jpiGetMenuAsObject();
});
Clazz.overrideMethod(c$, "setMenu", 
function(fileOrText, isFile){
if (isFile) JU.Logger.info("Setting menu " + (fileOrText.length == 0 ? "to Jmol defaults" : "from file " + fileOrText));
if (fileOrText.length == 0) fileOrText = null;
 else if (isFile) fileOrText = this.getFileAsString3(fileOrText, false, null);
this.getProperty("DATA_API", "setMenu", fileOrText);
this.sm.setCallbackFunction("menu", fileOrText);
}, "~S,~B");
Clazz.defineMethod(c$, "setStatusFrameChanged", 
function(isVib, doNotify){
if (isVib) {
this.prevFrame = -2147483648;
}this.tm.setVibrationPeriod(NaN);
var firstIndex = this.am.firstFrameIndex;
var lastIndex = this.am.lastFrameIndex;
var isMovie = this.am.isMovie;
var modelIndex = this.am.cmi;
if (firstIndex == lastIndex && !isMovie) modelIndex = firstIndex;
var frameID = this.getModelFileNumber(modelIndex);
var currentFrame = this.am.cmi;
var fileNo = frameID;
var modelNo = frameID % 1000000;
var firstNo = (isMovie ? firstIndex : this.getModelFileNumber(firstIndex));
var lastNo = (isMovie ? lastIndex : this.getModelFileNumber(lastIndex));
var strModelNo;
if (isMovie) {
strModelNo = "" + (currentFrame + 1);
} else if (fileNo == 0) {
strModelNo = this.getModelNumberDotted(firstIndex);
if (firstIndex != lastIndex) strModelNo += " - " + this.getModelNumberDotted(lastIndex);
if (Clazz.doubleToInt(firstNo / 1000000) == Clazz.doubleToInt(lastNo / 1000000)) fileNo = firstNo;
} else {
strModelNo = this.getModelNumberDotted(modelIndex);
}if (fileNo != 0) fileNo = (fileNo < 1000000 ? 1 : Clazz.doubleToInt(fileNo / 1000000));
if (!isMovie) {
this.g.setI("_currentFileNumber", fileNo);
this.g.setI("_currentModelNumberInFile", modelNo);
}var currentMorphModel = this.am.currentMorphModel;
this.g.setI("_currentFrame", currentFrame);
this.g.setI("_morphCount", this.am.morphCount);
this.g.setF("_currentMorphFrame", currentMorphModel);
this.g.setI("_frameID", frameID);
this.g.setI("_modelIndex", modelIndex);
this.g.setO("_modelNumber", strModelNo);
this.g.setO("_modelName", (modelIndex < 0 ? "" : this.getModelName(modelIndex)));
var title = (modelIndex < 0 ? "" : this.ms.getModelTitle(modelIndex));
this.g.setO("_modelTitle", title == null ? "" : title);
this.g.setO("_modelFile", (modelIndex < 0 ? "" : this.ms.getModelFileName(modelIndex)));
this.g.setO("_modelType", (modelIndex < 0 ? "" : this.ms.getModelFileType(modelIndex)));
if (currentFrame == this.prevFrame && currentMorphModel == this.prevMorphModel) return;
this.prevFrame = currentFrame;
this.prevMorphModel = currentMorphModel;
var entryName = this.getModelName(currentFrame);
if (isMovie) {
entryName = "" + (entryName === "" ? currentFrame + 1 : this.am.caf + 1) + ": " + entryName;
} else {
var script = "" + this.getModelNumberDotted(currentFrame);
if (!script.equals(entryName)) entryName = script + ": " + entryName;
}this.sm.setStatusFrameChanged(fileNo, modelNo, (this.am.animationDirection < 0 ? -firstNo : firstNo), (this.am.currentDirection < 0 ? -lastNo : lastNo), currentFrame, currentMorphModel, entryName);
if (this.doHaveJDX()) this.getJSV().setModel(modelIndex);
if (JV.Viewer.isJS) this.updateJSView(modelIndex, -1);
}, "~B,~B");
Clazz.defineMethod(c$, "doHaveJDX", 
function(){
return (this.haveJDX || (this.haveJDX = this.getBooleanProperty("_JSpecView".toLowerCase())));
});
Clazz.defineMethod(c$, "getJSV", 
function(){
if (this.jsv == null) {
this.jsv = J.api.Interface.getOption("jsv.JSpecView", this, "script");
this.jsv.setViewer(this);
}return this.jsv;
});
Clazz.defineMethod(c$, "getJDXBaseModelIndex", 
function(modelIndex){
if (!this.doHaveJDX()) return modelIndex;
return this.getJSV().getBaseModelIndex(modelIndex);
}, "~N");
Clazz.defineMethod(c$, "getJspecViewProperties", 
function(myParam){
var o = this.sm.getJspecViewProperties("" + myParam);
if (o != null) this.haveJDX = true;
return o;
}, "~O");
Clazz.defineMethod(c$, "scriptEcho", 
function(strEcho){
if (!JU.Logger.isActiveLevel(4)) return;
if (JV.Viewer.isJS) System.out.println(strEcho);
this.sm.setScriptEcho(strEcho, this.isScriptQueued());
if (this.listCommands && strEcho != null && strEcho.indexOf("$[") == 0) JU.Logger.info(strEcho);
}, "~S");
Clazz.defineMethod(c$, "isScriptQueued", 
function(){
return this.scm != null && this.scm.isScriptQueued();
});
Clazz.defineMethod(c$, "notifyError", 
function(errType, errMsg, errMsgUntranslated){
this.g.setO("_errormessage", errMsgUntranslated);
this.sm.notifyError(errType, errMsg, errMsgUntranslated);
}, "~S,~S,~S");
Clazz.defineMethod(c$, "jsEval", 
function(strEval){
return "" + this.sm.jsEval(strEval);
}, "~S");
Clazz.defineMethod(c$, "jsEvalSV", 
function(strEval){
return JS.SV.getVariable(JV.Viewer.isJS ? this.sm.jsEval(strEval) : this.jsEval(strEval));
}, "~S");
Clazz.defineMethod(c$, "setFileLoadStatus", 
function(ptLoad, fullPathName, fileName, modelName, strError, isAsync){
this.setErrorMessage(strError, null);
this.g.setI("_loadPoint", ptLoad.getCode());
var doCallback = (ptLoad !== J.c.FIL.CREATING_MODELSET);
if (doCallback) this.setStatusFrameChanged(false, false);
this.sm.setFileLoadStatus(fullPathName, fileName, modelName, strError, ptLoad.getCode(), doCallback, isAsync);
if (doCallback) {
if (this.doHaveJDX()) this.getJSV().setModel(this.am.cmi);
if (JV.Viewer.isJS) this.updateJSView(this.am.cmi, -2);
}}, "J.c.FIL,~S,~S,~S,~S,Boolean");
Clazz.defineMethod(c$, "getZapName", 
function(){
return (this.g.modelKitMode ? "Jmol Model Kit" : "zapped");
});
Clazz.defineMethod(c$, "setStatusMeasuring", 
function(status, intInfo, strMeasure, value){
this.sm.setStatusMeasuring(status, intInfo, strMeasure, value);
}, "~S,~N,~S,~N");
Clazz.defineMethod(c$, "notifyMinimizationStatus", 
function(){
var step = this.getP("_minimizationStep");
var ff = this.getP("_minimizationForceField");
var minStatus = this.getP("_minimizationStatus");
var starting = "starting".equals(minStatus);
var done = "done".equals(minStatus) || "failed".equals(minStatus);
var includeAtoms = (this.minimizer != null && (done || starting));
var bsAtoms = (includeAtoms ? this.minimizer.bsAtoms : null);
var atomIndex = (bsAtoms == null ? -1 : bsAtoms.nextSetBit(0));
var modelIndex = (atomIndex >= 0 ? this.getModelIndexForAtom(atomIndex) : -1);
if (starting && atomIndex >= 0) {
this.sm.setStatusStructureModified(atomIndex, modelIndex, 3, "minimize:" + minStatus, bsAtoms.cardinality(), bsAtoms);
}this.sm.notifyMinimizationStatus(minStatus, (typeof(step)=='string') ? Integer.$valueOf(0) : step, this.getP("_minimizationEnergy"), (step.toString().equals("0") ? Float.$valueOf(0) : this.getP("_minimizationEnergyDiff")), ff);
if (done && atomIndex >= 0) {
this.sm.setStatusStructureModified(atomIndex, modelIndex, -3, "minimize:" + minStatus, bsAtoms.cardinality(), bsAtoms);
}});
Clazz.defineMethod(c$, "setStatusAtomPicked", 
function(atomIndex, info, map, andSelect){
if (andSelect) this.setSelectionSet(JU.BSUtil.newAndSetBit(atomIndex));
if (info == null) {
info = this.g.pickLabel;
info = (info.length == 0 ? this.getAtomInfoXYZ(atomIndex, this.g.messageStyleChime ? 4 : 2) + (this.getOperativeSymmetry() == null ? "" : " (" + this.getAtomInfoXYZ(atomIndex, 3) + ")") : this.ms.getAtomInfo(atomIndex, info, this.ptTemp));
}this.setPicked(atomIndex, false);
if (atomIndex < 0) {
var m = this.getPendingMeasurement();
if (m != null) info = info.substring(0, info.length - 1) + ",\"" + m.getString() + "\"]";
}this.g.setO("_pickinfo", info);
this.sm.setStatusAtomPicked(atomIndex, info, map);
if (atomIndex < 0) return;
var syncMode = this.sm.getSyncMode();
if (syncMode == 1 && this.doHaveJDX()) this.getJSV().atomPicked(atomIndex);
if (JV.Viewer.isJS) this.updateJSView(this.ms.at[atomIndex].mi, atomIndex);
}, "~N,~S,java.util.Map,~B");
Clazz.overrideMethod(c$, "getProperty", 
function(returnType, infoType, paramInfo){
if (!"DATA_API".equals(returnType)) return this.getPropertyManager().getProperty(returnType, infoType, paramInfo);
switch (("scriptCheck.........consoleText.........scriptEditor........scriptEditorState...getAppConsole.......getScriptEditor.....setMenu.............spaceGroupInfo......disablePopupMenu....defaultDirectory....getPopupMenu........shapeManager........getPreference.......").indexOf(infoType)) {
case 0:
return this.scriptCheckRet(paramInfo, true);
case 20:
return (this.appConsole == null ? "" : this.appConsole.getText());
case 40:
this.showEditor(paramInfo);
return null;
case 60:
this.scriptEditorVisible = (paramInfo).booleanValue();
return null;
case 80:
if (this.$isKiosk) {
this.appConsole = null;
} else if (Clazz.instanceOf(paramInfo,"J.api.JmolAppConsoleInterface")) {
this.appConsole = paramInfo;
} else if (paramInfo != null && !(paramInfo).booleanValue()) {
this.appConsole = null;
} else if (this.appConsole == null && paramInfo != null && (paramInfo).booleanValue()) {
if (JV.Viewer.isJS) {
this.appConsole = J.api.Interface.getOption("consolejs.AppletConsole", this, "script");
}{
}if (this.appConsole != null) this.appConsole.start(this);
}this.scriptEditor = (JV.Viewer.isJS || this.appConsole == null ? null : this.appConsole.getScriptEditor());
return this.appConsole;
case 100:
if (this.appConsole == null && paramInfo != null && (paramInfo).booleanValue()) {
this.getProperty("DATA_API", "getAppConsole", Boolean.TRUE);
this.scriptEditor = (this.appConsole == null ? null : this.appConsole.getScriptEditor());
}return this.scriptEditor;
case 120:
if (this.jmolpopup != null) this.jmolpopup.jpiDispose();
this.jmolpopup = null;
return this.menuStructure = paramInfo;
case 140:
return this.getSymTemp().getSpaceGroupInfo(this.ms, null, -1, false, null);
case 160:
this.g.disablePopupMenu = true;
return null;
case 180:
return this.g.defaultDirectory;
case 200:
if ((typeof(paramInfo)=='string')) return this.getMenu(paramInfo);
return this.getPopupMenu();
case 220:
return this.shm.getProperty(paramInfo);
case 240:
return this.sm.syncSend("getPreference", paramInfo, 1);
}
JU.Logger.error("ERROR in getProperty DATA_API: " + infoType);
return null;
}, "~S,~S,~O");
Clazz.defineMethod(c$, "notifyMouseClicked", 
function(x, y, action, mode){
var modifiers = JV.binding.Binding.getButtonMods(action);
var clickCount = JV.binding.Binding.getClickCount(action);
this.g.setI("_mouseX", x);
this.g.setI("_mouseY", this.screenHeight - y);
this.g.setI("_mouseAction", action);
this.g.setI("_mouseModifiers", modifiers);
this.g.setI("_clickCount", clickCount);
return this.sm.setStatusClicked(x, this.screenHeight - y, action, clickCount, mode);
}, "~N,~N,~N,~N");
Clazz.defineMethod(c$, "getOutputManager", 
function(){
if (this.outputManager != null) return this.outputManager;
return (this.outputManager = J.api.Interface.getInterface("JV.OutputManager" + (JV.Viewer.isJS ? "JS" : "Awt"), this, "file")).setViewer(this, this.privateKey);
});
Clazz.defineMethod(c$, "getJzt", 
function(){
return (this.jzt == null ? this.jzt = J.api.Interface.getInterface("JU.ZipTools", this, "zip") : this.jzt);
});
Clazz.defineMethod(c$, "readFileAsMap", 
function(bis, map, name){
this.getJzt().readFileAsMap(bis, map, name);
}, "java.io.BufferedInputStream,java.util.Map,~S");
Clazz.defineMethod(c$, "getZipDirectoryAsString", 
function(fileName){
var t = this.fm.getBufferedInputStreamOrErrorMessageFromName(fileName, fileName, false, false, null, false, true);
return this.getJzt().getZipDirectoryAsStringAndClose(t);
}, "~S");
Clazz.overrideMethod(c$, "getImageAsBytes", 
function(type, width, height, quality, errMsg){
return this.getOutputManager().getImageAsBytes(type, width, height, quality, errMsg);
}, "~S,~N,~N,~N,~A");
Clazz.overrideMethod(c$, "releaseScreenImage", 
function(){
this.gdata.releaseScreenImage();
});
Clazz.defineMethod(c$, "setDisplay", 
function(canvas){
this.display = canvas;
this.apiPlatform.setViewer(this, canvas);
}, "~O");
Clazz.defineMethod(c$, "newMeasurementData", 
function(id, points){
return (J.api.Interface.getInterface("JM.MeasurementData", this, "script")).init(id, this, points);
}, "~S,JU.Lst");
Clazz.defineMethod(c$, "getDataManager", 
function(){
return (this.dm == null ? (this.dm = (J.api.Interface.getInterface("JV.DataManager", this, "script")).set(this)) : this.dm);
});
Clazz.defineMethod(c$, "getScriptManager", 
function(){
if (this.allowScripting && this.scm == null) {
this.scm = J.api.Interface.getInterface("JS.ScriptManager", this, "setOptions");
if (JV.Viewer.isJS && this.scm == null) throw  new NullPointerException();
if (this.scm == null) {
this.allowScripting = false;
return null;
}this.eval = this.scm.setViewer(this);
if (this.useCommandThread) this.scm.startCommandWatcher(true);
}return this.scm;
});
Clazz.defineMethod(c$, "checkOption2", 
function(key1, key2){
return (this.vwrOptions.containsKey(key1) && !this.vwrOptions.get(key1).toString().equals("false") || this.commandOptions.indexOf(key2) >= 0);
}, "~S,~S");
Clazz.defineMethod(c$, "setStartupBooleans", 
function(){
this.setBooleanProperty("_applet", this.isApplet);
this.setBooleanProperty("_JSpecView".toLowerCase(), false);
this.setBooleanProperty("_signedApplet", this.isSignedApplet);
this.setBooleanProperty("_headless", this.headless);
this.setStringProperty("_restrict", "\"" + this.access + "\"");
this.setBooleanProperty("_useCommandThread", this.useCommandThread);
this.setBooleanPropertyTok("doubleprecision", 603979831, false);
});
Clazz.defineMethod(c$, "getExportDriverList", 
function(){
return (this.haveAccess(JV.Viewer.ACCESS.ALL) ? this.g.getParameter("exportDrivers", true) : "");
});
Clazz.overrideMethod(c$, "dispose", 
function(){
this.gRight = null;
if (this.mouse != null) {
this.acm.dispose();
this.mouse.dispose();
this.mouse = null;
}this.clearScriptQueue();
this.clearThreads();
this.haltScriptExecution();
if (this.scm != null) this.scm.clear(true);
this.gdata.destroy();
if (this.jmolpopup != null) this.jmolpopup.jpiDispose();
if (this.modelkit != null) this.modelkit.dispose();
try {
if (this.appConsole != null) {
this.appConsole.dispose();
this.appConsole = null;
}if (this.scriptEditor != null) {
this.scriptEditor.dispose();
this.scriptEditor = null;
}} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
});
Clazz.defineMethod(c$, "reset", 
function(includingSpin){
this.ms.setBoundBox(null, null, true, 0);
this.axesAreTainted = true;
this.tm.homePosition(includingSpin);
if (this.ms.setCrystallographicDefaults()) this.stm.setCrystallographicDefaults();
 else this.setAxesMode(603979809);
this.prevFrame = -2147483648;
if (!this.tm.spinOn) this.setSync();
}, "~B");
Clazz.overrideMethod(c$, "homePosition", 
function(){
this.evalString("reset spin");
});
Clazz.defineMethod(c$, "initialize", 
function(clearUserVariables, isPyMOL){
this.g =  new JV.GlobalSettings(this, this.g, clearUserVariables);
this.setStartupBooleans();
this.setWidthHeightVar();
if (this.haveDisplay) {
this.g.setB("_is2D", JV.Viewer.isJS && !this.isWebGL);
this.g.setB("_multiTouchClient", this.acm.isMTClient());
this.g.setB("_multiTouchServer", this.acm.isMTServer());
}this.cm.setDefaultColors(false);
this.setObjectColor("background", "black");
this.setObjectColor("axis1", "red");
this.setObjectColor("axis2", "green");
this.setObjectColor("axis3", "blue");
this.am.setAnimationOn(false);
this.am.setAnimationFps(this.g.animationFps);
this.sm.playAudio(null);
this.sm.allowStatusReporting = this.g.statusReporting;
this.setBooleanPropertyTok("antialiasDisplay", 603979786, (isPyMOL ? true : this.g.antialiasDisplay));
this.stm.resetLighting();
this.tm.setDefaultPerspective();
}, "~B,~B");
Clazz.defineMethod(c$, "saveModelOrientation", 
function(){
this.ms.saveModelOrientation(this.am.cmi, this.stm.getOrientation());
});
Clazz.defineMethod(c$, "restoreModelOrientation", 
function(modelIndex){
var o = this.ms.getModelOrientation(modelIndex);
if (o != null) o.restore(-1, true);
}, "~N");
Clazz.defineMethod(c$, "restoreModelRotation", 
function(modelIndex){
var o = this.ms.getModelOrientation(modelIndex);
if (o != null) o.restore(-1, false);
}, "~N");
Clazz.defineMethod(c$, "getGLmolView", 
function(){
var tm = this.tm;
var center = tm.fixedRotationCenter;
var q = tm.getRotationQ();
var xtrans = tm.xTranslationFraction;
var ytrans = tm.yTranslationFraction;
var scale = tm.scalePixelsPerAngstrom;
var zoom = tm.zmPctSet;
var cd = tm.cameraDistance;
var pc = tm.screenPixelCount;
var pd = tm.perspectiveDepth;
var width = tm.width;
var height = tm.height;
{
return { center:center, quaternion:q, xtrans:xtrans,
ytrans:ytrans, scale:scale, zoom:zoom, cameraDistance:cd,
pixelCount:pc, perspective:pd, width:width, height:height };
}});
Clazz.defineMethod(c$, "setRotationRadius", 
function(angstroms, doAll){
if (doAll) angstroms = this.tm.setRotationRadius(angstroms, false);
if (this.ms.setRotationRadius(this.am.cmi, angstroms)) this.g.setF("rotationRadius", angstroms);
}, "~N,~B");
Clazz.defineMethod(c$, "setCenterBitSet", 
function(bsCenter, doScale){
if (this.isJmolDataFrame()) return;
this.tm.setNewRotationCenter((JU.BSUtil.cardinalityOf(bsCenter) > 0 ? this.ms.getAtomSetCenter(bsCenter) : null), doScale);
}, "JU.BS,~B");
Clazz.defineMethod(c$, "setNewRotationCenter", 
function(center){
if (!this.isJmolDataFrame()) this.tm.setNewRotationCenter(center, true);
}, "JU.P3");
Clazz.defineMethod(c$, "navigate", 
function(keyWhere, modifiers){
if (this.isJmolDataFrame()) return;
this.tm.navigateKey(keyWhere, modifiers);
if (!this.tm.vibrationOn && keyWhere != 0) this.refresh(1, "Viewer:navigate()");
}, "~N,~N");
Clazz.defineMethod(c$, "move", 
function(eval, dRot, dZoom, dTrans, dSlab, floatSecondsTotal, fps){
this.tm.move(eval, dRot, dZoom, dTrans, dSlab, floatSecondsTotal, fps);
this.moveUpdate(floatSecondsTotal);
}, "J.api.JmolScriptEvaluator,JU.V3,~N,JU.V3,~N,~N,~N");
Clazz.defineMethod(c$, "moveTo", 
function(eval, floatSecondsTotal, center, rotAxis, degrees, rotationMatrix, zoom, xTrans, yTrans, rotationRadius, navCenter, xNav, yNav, navDepth, cameraDepth, cameraX, cameraY){
if (!this.haveDisplay) floatSecondsTotal = 0;
this.setTainted(true);
this.tm.moveTo(eval, floatSecondsTotal, center, rotAxis, degrees, rotationMatrix, zoom, xTrans, yTrans, rotationRadius, navCenter, xNav, yNav, navDepth, cameraDepth, cameraX, cameraY);
}, "J.api.JmolScriptEvaluator,~N,JU.P3,JU.V3,~N,JU.M3,~N,~N,~N,~N,JU.P3,~N,~N,~N,~N,~N,~N");
Clazz.defineMethod(c$, "moveUpdate", 
function(floatSecondsTotal){
if (floatSecondsTotal > 0) this.requestRepaintAndWait("moveUpdate");
 else if (floatSecondsTotal == 0) this.setSync();
}, "~N");
Clazz.defineMethod(c$, "navigatePt", 
function(center){
this.tm.setNavigatePt(center);
this.setSync();
}, "JU.P3");
Clazz.defineMethod(c$, "navigateAxis", 
function(rotAxis, degrees){
this.tm.navigateAxis(rotAxis, degrees);
this.setSync();
}, "JU.V3,~N");
Clazz.defineMethod(c$, "navTranslatePercent", 
function(x, y){
if (this.isJmolDataFrame()) return;
this.tm.navTranslatePercentOrTo(0, x, y);
this.setSync();
}, "~N,~N");
Clazz.defineMethod(c$, "zoomBy", 
function(pixels){
this.tm.zoomBy(pixels);
this.refresh(2, this.sm.syncingMouse ? "Mouse: zoomBy " + pixels : "");
}, "~N");
Clazz.defineMethod(c$, "zoomByFactor", 
function(factor, x, y){
this.tm.zoomByFactor(factor, x, y);
this.refresh(2, !this.sm.syncingMouse ? "" : "Mouse: zoomByFactor " + factor + (x == 2147483647 ? "" : " " + x + " " + y));
}, "~N,~N,~N");
Clazz.defineMethod(c$, "rotateXYBy", 
function(degX, degY){
this.tm.rotateXYBy(degX, degY, null);
this.refresh(2, this.sm.syncingMouse ? "Mouse: rotateXYBy " + degX + " " + degY : "");
}, "~N,~N");
Clazz.defineMethod(c$, "spinXYBy", 
function(xDelta, yDelta, speed){
this.tm.spinXYBy(xDelta, yDelta, speed);
if (xDelta == 0 && yDelta == 0) return;
this.refresh(2, this.sm.syncingMouse ? "Mouse: spinXYBy " + xDelta + " " + yDelta + " " + speed : "");
}, "~N,~N,~N");
Clazz.defineMethod(c$, "rotateZBy", 
function(zDelta, x, y){
this.tm.rotateZBy(zDelta, x, y);
this.refresh(2, this.sm.syncingMouse ? "Mouse: rotateZBy " + zDelta + (x == 2147483647 ? "" : " " + x + " " + y) : "");
}, "~N,~N,~N");
Clazz.defineMethod(c$, "rotateSelected", 
function(deltaX, deltaY, bsSelected){
if (this.isJmolDataFrame()) return;
this.tm.rotateXYBy(deltaX, deltaY, this.setMovableBitSet(bsSelected, true));
this.refreshMeasures(true);
this.refresh(2, this.sm.syncingMouse ? "Mouse: rotateMolecule " + deltaX + " " + deltaY : "");
}, "~N,~N,JU.BS");
Clazz.defineMethod(c$, "setMovableBitSet", 
function(bsSelected, checkMolecule){
if (bsSelected == null) bsSelected = this.bsA();
bsSelected = JU.BSUtil.copy(bsSelected);
JU.BSUtil.andNot(bsSelected, this.getMotionFixedAtoms(null, null));
if (checkMolecule && !this.g.allowMoveAtoms) bsSelected = this.ms.getMoleculeBitSet(bsSelected);
return this.movableBitSet = bsSelected;
}, "JU.BS,~B");
Clazz.defineMethod(c$, "translateXYBy", 
function(xDelta, yDelta){
this.tm.translateXYBy(xDelta, yDelta);
this.refresh(2, this.sm.syncingMouse ? "Mouse: translateXYBy " + xDelta + " " + yDelta : "");
}, "~N,~N");
Clazz.overrideMethod(c$, "rotateFront", 
function(){
this.tm.resetRotation();
this.refresh(1, "Viewer:rotateFront()");
});
Clazz.defineMethod(c$, "translate", 
function(xyz, x, type, bsAtoms){
var xy = (type == '\0' ? x : type == '%' ? this.tm.percentToPixels(xyz, x) : this.tm.angstromsToPixels(x * (type == 'n' ? 10 : 1)));
if (bsAtoms != null) {
if (x == 0) return;
this.tm.setSelectedTranslation(bsAtoms, xyz, xy, x);
} else {
switch ((xyz).charCodeAt(0)) {
case 88:
case 120:
if (type == '\0') this.tm.translateToPercent('x', x);
 else this.tm.translateXYBy(Clazz.floatToInt(xy), 0);
break;
case 89:
case 121:
if (type == '\0') this.tm.translateToPercent('y', x);
 else this.tm.translateXYBy(0, Clazz.floatToInt(xy));
break;
case 90:
case 122:
if (type == '\0') this.tm.translateToPercent('z', x);
 else this.tm.translateZBy(Clazz.floatToInt(xy));
break;
}
}this.refresh(1, "Viewer:translate()");
}, "~S,~N,~S,JU.BS");
Clazz.defineMethod(c$, "slabByPixels", 
function(pixels){
this.tm.slabByPercentagePoints(pixels);
this.refresh(3, "slabByPixels");
}, "~N");
Clazz.defineMethod(c$, "depthByPixels", 
function(pixels){
this.tm.depthByPercentagePoints(pixels);
this.refresh(3, "depthByPixels");
}, "~N");
Clazz.defineMethod(c$, "slabDepthByPixels", 
function(pixels){
this.tm.slabDepthByPercentagePoints(pixels);
this.refresh(3, "slabDepthByPixels");
}, "~N");
Clazz.defineMethod(c$, "finalizeTransformParameters", 
function(){
this.tm.finalizeTransformParameters();
this.gdata.setSlabAndZShade(this.tm.slabValue, this.tm.depthValue, (this.tm.zShadeEnabled ? this.tm.zSlabValue : 2147483647), this.tm.zDepthValue, this.g.zShadePower);
});
Clazz.defineMethod(c$, "getScalePixelsPerAngstrom", 
function(asAntialiased){
return this.tm.scalePixelsPerAngstrom * (asAntialiased || !this.antialiased ? 1 : 0.5);
}, "~B");
Clazz.defineMethod(c$, "setSpin", 
function(key, value){
if (!JU.PT.isOneOf(key, ";x;y;z;fps;X;Y;Z;FPS;")) return;
var i = "x;y;z;fps;X;Y;Z;FPS".indexOf(key);
switch (i) {
case 0:
this.tm.setSpinXYZ(value, NaN, NaN);
break;
case 2:
this.tm.setSpinXYZ(NaN, value, NaN);
break;
case 4:
this.tm.setSpinXYZ(NaN, NaN, value);
break;
case 6:
default:
this.tm.setSpinFps(value);
break;
case 10:
this.tm.setNavXYZ(value, NaN, NaN);
break;
case 12:
this.tm.setNavXYZ(NaN, value, NaN);
break;
case 14:
this.tm.setNavXYZ(NaN, NaN, value);
break;
case 16:
this.tm.setNavFps(value);
break;
}
this.g.setI((i < 10 ? "spin" : "nav") + key, value);
}, "~S,~N");
Clazz.defineMethod(c$, "getSpinState", 
function(){
return this.getStateCreator().getSpinState(false);
});
Clazz.defineMethod(c$, "getOrientation", 
function(type, name, bs, points){
switch (type) {
case 1312817669:
case 1814695966:
case 1073741864:
case 1111492629:
case 1111492630:
case 1111492631:
case 134221850:
if (bs == null) bs = this.bsA();
if (bs.isEmpty()) return (type == 1312817669 ? "0" : type == 1814695966 || type == 1073741864 ? null :  new JU.Quat());
var q = this.ms.getBoundBoxOrientation(type, bs, points);
return (name === "best" && type != 1312817669 ? (q).div(this.tm.getRotationQ()) : q);
case 1073742034:
return this.stm.getSavedOrientationText(name);
default:
return this.tm.getOrientationText(type, name === "best");
}
}, "~N,~S,JU.BS,~A");
Clazz.defineMethod(c$, "getCurrentColorRange", 
function(){
return this.cm.getPropertyColorRange();
});
Clazz.defineMethod(c$, "setDefaultColors", 
function(isRasmol){
this.cm.setDefaultColors(isRasmol);
this.g.setB("colorRasmol", isRasmol);
this.g.setO("defaultColorScheme", (isRasmol ? "rasmol" : "jmol"));
}, "~B");
Clazz.defineMethod(c$, "setElementArgb", 
function(elementNumber, argb){
this.g.setO("=color " + JU.Elements.elementNameFromNumber(elementNumber), JU.Escape.escapeColor(argb));
this.cm.setElementArgb(elementNumber, argb);
}, "~N,~N");
Clazz.overrideMethod(c$, "setVectorScale", 
function(scale){
this.g.setF("vectorScale", scale);
this.g.vectorScale = scale;
}, "~N");
Clazz.overrideMethod(c$, "setVibrationScale", 
function(scale){
this.tm.setVibrationScale(scale);
this.g.vibrationScale = scale;
this.g.setF("vibrationScale", scale);
}, "~N");
Clazz.overrideMethod(c$, "setVibrationPeriod", 
function(period){
if (Double.isNaN(period)) {
period = this.g.vibrationPeriod;
}this.tm.setVibrationPeriod(period);
period = Math.abs(period);
this.g.vibrationPeriod = period;
this.g.setF("vibrationPeriod", period);
}, "~N");
Clazz.defineMethod(c$, "setObjectColor", 
function(name, colorName){
if (colorName == null || colorName.length == 0) return;
this.setObjectArgb(name, JU.CU.getArgbFromString(colorName));
}, "~S,~S");
Clazz.defineMethod(c$, "setObjectVisibility", 
function(name, b){
var objId = JV.StateManager.getObjectIdFromName(name);
if (objId >= 0) {
this.setShapeProperty(objId, "display", b ? Boolean.TRUE : Boolean.FALSE);
}}, "~S,~B");
Clazz.defineMethod(c$, "setObjectArgb", 
function(name, argb){
var objId = JV.StateManager.getObjectIdFromName(name);
if (objId < 0) {
if (name.equalsIgnoreCase("axes")) {
this.setObjectArgb("axis1", argb);
this.setObjectArgb("axis2", argb);
this.setObjectArgb("axis3", argb);
}return;
}this.g.objColors[objId] = argb;
switch (objId) {
case 0:
this.gdata.setBackgroundArgb(argb);
this.cm.setColixBackgroundContrast(argb);
break;
}
this.g.setO(name + "Color", JU.Escape.escapeColor(argb));
}, "~S,~N");
Clazz.defineMethod(c$, "setBackgroundImage", 
function(fileName, image){
this.g.backgroundImageFileName = fileName;
this.gdata.setBackgroundImage(image);
}, "~S,~O");
Clazz.defineMethod(c$, "getObjectColix", 
function(objId){
var argb = this.g.objColors[objId];
return (argb == 0 ? this.cm.colixBackgroundContrast : JU.C.getColix(argb));
}, "~N");
Clazz.overrideMethod(c$, "setColorBackground", 
function(colorName){
this.setObjectColor("background", colorName);
}, "~S");
Clazz.overrideMethod(c$, "getBackgroundArgb", 
function(){
return this.g.objColors[(0)];
});
Clazz.defineMethod(c$, "setObjectMad10", 
function(iShape, name, mad10){
var objId = JV.StateManager.getObjectIdFromName(name.equalsIgnoreCase("axes") ? "axis" : name);
if (objId < 0) return;
if (mad10 == -2 || mad10 == -4) {
var m = mad10 + 3;
mad10 = this.getObjectMad10(objId);
if (mad10 == 0) mad10 = m;
}this.g.setB("show" + name, mad10 != 0);
this.g.objStateOn[objId] = (mad10 != 0);
if (mad10 == 0) return;
this.g.objMad10[objId] = mad10;
this.setShapeSize(iShape, mad10, null);
}, "~N,~S,~N");
Clazz.defineMethod(c$, "getObjectMad10", 
function(objId){
return (this.g.objStateOn[objId] ? this.g.objMad10[objId] : 0);
}, "~N");
Clazz.defineMethod(c$, "setPropertyColorScheme", 
function(scheme, isTranslucent, isOverloaded){
this.g.propertyColorScheme = scheme;
if (scheme.startsWith("translucent ")) {
isTranslucent = true;
scheme = scheme.substring(12).trim();
}this.cm.setPropertyColorScheme(scheme, isTranslucent, isOverloaded);
}, "~S,~B,~B");
Clazz.defineMethod(c$, "getLightingState", 
function(){
return this.getStateCreator().getLightingState(true);
});
Clazz.defineMethod(c$, "getColorPointForPropertyValue", 
function(val){
return JU.CU.colorPtFromInt(this.gdata.getColorArgbOrGray(this.cm.ce.getColorIndex(val)), null);
}, "~N");
Clazz.defineMethod(c$, "select", 
function(bs, isGroup, addRemove, isQuiet){
if (isGroup) bs = this.getUndeletedGroupAtomBits(bs);
this.slm.select(bs, addRemove, isQuiet);
this.shm.setShapeSizeBs(1, 2147483647, null, null);
this.hasSelected = true;
}, "JU.BS,~B,~N,~B");
Clazz.overrideMethod(c$, "setSelectionSet", 
function(set){
this.selectStatus(set, false, 0, true, true);
}, "JU.BS");
Clazz.defineMethod(c$, "selectBonds", 
function(bs){
this.shm.setShapeSizeBs(1, 2147483647, null, bs);
}, "JU.BS");
Clazz.defineMethod(c$, "displayAtoms", 
function(bs, isDisplay, isGroup, addRemove, isQuiet){
if (isGroup) bs = this.getUndeletedGroupAtomBits(bs);
if (isDisplay) this.slm.display(this.ms, bs, addRemove, isQuiet);
 else this.slm.hide(this.ms, bs, addRemove, isQuiet);
}, "JU.BS,~B,~B,~N,~B");
Clazz.defineMethod(c$, "getUndeletedGroupAtomBits", 
function(bs){
bs = this.ms.getAtoms(1086324742, bs);
JU.BSUtil.andNot(bs, this.slm.bsDeleted);
return bs;
}, "JU.BS");
Clazz.defineMethod(c$, "reportSelection", 
function(msg){
if (this.selectionHalosEnabled) this.setTainted(true);
if (this.isScriptQueued() || this.g.debugScript) this.scriptStatus(msg);
}, "~S");
Clazz.defineMethod(c$, "clearAtomSets", 
function(){
this.slm.setSelectionSubset(null);
this.definedAtomSets.clear();
if (this.haveDisplay) this.acm.exitMeasurementMode("clearAtomSets");
});
Clazz.defineMethod(c$, "getDefinedAtomSet", 
function(name){
var o = this.definedAtomSets.get(name.toLowerCase());
return (Clazz.instanceOf(o,"JU.BS") ? o :  new JU.BS());
}, "~S");
Clazz.overrideMethod(c$, "selectAll", 
function(){
this.slm.selectAll(false);
});
Clazz.overrideMethod(c$, "clearSelection", 
function(){
this.slm.clearSelection(true);
this.g.setB("hideNotSelected", false);
});
Clazz.defineMethod(c$, "bsA", 
function(){
return this.slm.getSelectedAtoms();
});
Clazz.overrideMethod(c$, "addSelectionListener", 
function(listener){
this.slm.addListener(listener);
}, "J.api.JmolSelectionListener");
Clazz.overrideMethod(c$, "removeSelectionListener", 
function(listener){
this.slm.addListener(listener);
}, "J.api.JmolSelectionListener");
Clazz.defineMethod(c$, "getAtomBitSetEval", 
function(eval, atomExpression){
return (this.allowScripting ? this.getScriptManager().getAtomBitSetEval(eval, atomExpression) :  new JU.BS());
}, "J.api.JmolScriptEvaluator,~O");
Clazz.defineMethod(c$, "processTwoPointGesture", 
function(touches){
this.mouse.processTwoPointGesture(touches);
}, "~A");
Clazz.defineMethod(c$, "processMouseEvent", 
function(id, x, y, modifiers, time){
return this.mouse.processEvent(id, x, y, modifiers, time);
}, "~N,~N,~N,~N,~N");
Clazz.defineMethod(c$, "processKeyEvent", 
function(event){
this.mouse.processKeyEvent(event);
}, "~O");
Clazz.defineMethod(c$, "getRubberBandSelection", 
function(){
return (this.haveDisplay ? this.acm.getRubberBand() : null);
});
Clazz.defineMethod(c$, "isBound", 
function(mouseAction, jmolAction){
return (this.haveDisplay && this.acm.bnd(mouseAction, [jmolAction]));
}, "~N,~N");
Clazz.defineMethod(c$, "getCursorX", 
function(){
return (this.haveDisplay ? this.acm.getCurrentX() : 0);
});
Clazz.defineMethod(c$, "getCursorY", 
function(){
return (this.haveDisplay ? this.acm.getCurrentY() : 0);
});
Clazz.defineMethod(c$, "getDefaultDirectory", 
function(){
return this.g.defaultDirectory;
});
Clazz.defineMethod(c$, "getLocalUrl", 
function(fileName){
return this.apiPlatform.getLocalUrl(fileName);
}, "~S");
Clazz.defineMethod(c$, "getFileAsString", 
function(fileName){
return this.getAsciiFileOrNull(fileName);
}, "~S");
Clazz.overrideMethod(c$, "getBufferedInputStream", 
function(fullPathName){
return this.fm.getBufferedInputStream(fullPathName);
}, "~S");
Clazz.defineMethod(c$, "setLoadParameters", 
function(htParams, isAppend){
if (htParams == null) htParams =  new java.util.Hashtable();
htParams.put("vwr", this);
if (this.g.atomTypes.length > 0) htParams.put("atomTypes", this.g.atomTypes);
if (!htParams.containsKey("lattice")) htParams.put("lattice", this.g.ptDefaultLattice);
if (this.g.applySymmetryToBonds) htParams.put("applySymmetryToBonds", Boolean.TRUE);
if (this.g.pdbGetHeader) htParams.put("getHeader", Boolean.TRUE);
if (this.g.pdbSequential) htParams.put("isSequential", Boolean.TRUE);
if (this.g.legacyJavaFloat || this.g.doublePrecision) htParams.put("highPrecision", Boolean.TRUE);
if (!this.g.doublePrecision) htParams.put("lowPrecision", Boolean.TRUE);
htParams.put("stateScriptVersionInt", Integer.$valueOf(this.stateScriptVersionInt));
if (!htParams.containsKey("filter")) {
var filter = this.g.defaultLoadFilter;
if (filter.length > 0) htParams.put("filter", filter);
}var merging = (isAppend && !this.g.appendNew && this.ms.ac > 0);
htParams.put("baseAtomIndex", Integer.$valueOf(isAppend ? this.ms.ac : 0));
htParams.put("baseBondIndex", Integer.$valueOf(isAppend ? this.ms.bondCount : 0));
htParams.put("baseModelIndex", Integer.$valueOf(this.ms.ac == 0 ? 0 : this.ms.mc + (merging ? -1 : 0)));
if (merging) htParams.put("merging", Boolean.TRUE);
return htParams;
}, "java.util.Map,~B");
Clazz.overrideMethod(c$, "openFileAsyncSpecial", 
function(fileName, flags){
this.getScriptManager().openFileAsync(fileName, flags, null);
}, "~S,~N");
Clazz.overrideMethod(c$, "openFileAsyncSpecialType", 
function(fileName, flags, fileType){
this.getScriptManager().openFileAsync(fileName, flags, fileType);
}, "~S,~N,~S");
Clazz.overrideMethod(c$, "openFile", 
function(fileName){
this.zap(true, true, false);
return this.loadModelFromFileRepaint(null, fileName, null, null);
}, "~S");
Clazz.overrideMethod(c$, "openFiles", 
function(fileNames){
this.zap(true, true, false);
return this.loadModelFromFileRepaint(null, null, fileNames, null);
}, "~A");
Clazz.defineMethod(c$, "openReader", 
function(fullPathName, fileName, reader){
this.zap(true, true, false);
return this.loadModelFromFileRepaint(fullPathName, fileName, null, reader);
}, "~S,~S,~O");
Clazz.overrideMethod(c$, "openDOM", 
function(DOMNode){
this.zap(true, true, false);
return this.loadModelFromFileRepaint("?", "?", null, DOMNode);
}, "~O");
Clazz.defineMethod(c$, "loadModelFromFileRepaint", 
function(fullPathName, fileName, fileNames, reader){
var ret = this.loadModelFromFile(fullPathName, fileName, fileNames, reader, false, null, null, null, 0, " ");
this.refresh(1, "loadModelFromFileRepaint");
return ret;
}, "~S,~S,~A,~O");
Clazz.defineMethod(c$, "loadModelFromFile", 
function(fullPathName, fileName, fileNames, reader, isAppend, htParams, loadScript, sOptions, tokType, filecat){
if (htParams == null) htParams = this.setLoadParameters(null, isAppend);
if (tokType != 0) htParams.put("dataType", JS.T.nameOf(tokType));
if (filecat !== " ") htParams.put("concatenate", Boolean.TRUE);
var atomSetCollection;
var saveInfo = this.fm.getFileInfo();
if (fileNames != null) {
if (loadScript == null) {
loadScript =  new JU.SB().append("load files");
for (var i = 0; i < fileNames.length; i++) loadScript.append(i == 0 || filecat == null ? " " : filecat).append("/*file*/$FILENAME" + (i + 1) + "$");

if (sOptions.length() > 0) loadScript.append(" /*options*/ ").append(sOptions.toString());
}var timeBegin = System.currentTimeMillis();
atomSetCollection = this.fm.createAtomSetCollectionFromFiles(fileNames, this.setLoadParameters(htParams, isAppend), isAppend);
var ms = System.currentTimeMillis() - timeBegin;
JU.Logger.info("openFiles(" + fileNames.length + ") " + ms + " ms");
fileNames = htParams.get("fullPathNames");
var fileTypes = htParams.get("fileTypes");
var s = loadScript.toString();
for (var i = 0; i < fileNames.length; i++) {
var fname = fileNames[i];
if (fileTypes != null && fileTypes[i] != null) fname = fileTypes[i] + "::" + fname;
s = JU.PT.rep(s, "$FILENAME" + (i + 1) + "$", JU.PT.esc(JV.FileManager.fixDOSName(fname)));
}
loadScript =  new JU.SB().append(s);
} else if (reader == null) {
if (loadScript == null) loadScript =  new JU.SB().append("load /*file*/$FILENAME$");
atomSetCollection = this.openFileFull(fileName, isAppend, htParams, loadScript);
} else if (Clazz.instanceOf(reader,"java.io.Reader") || Clazz.instanceOf(reader,"java.io.BufferedInputStream") || JU.AU.isAB(reader)) {
atomSetCollection = this.fm.createAtomSetCollectionFromReader(fullPathName, fileName, reader, this.setLoadParameters(htParams, isAppend));
} else {
return "ERROR - invalid reader";
}if (tokType != 0) {
this.fm.setFileInfo(saveInfo);
return this.loadAtomDataAndReturnError(atomSetCollection, tokType);
}if (htParams.containsKey("isData")) return atomSetCollection;
if (loadScript != null && !((typeof(atomSetCollection)=='string'))) {
var fname = htParams.get("fullPathName");
if (fname == null) fname = "";
if (htParams.containsKey("loadScript")) loadScript = htParams.get("loadScript");
htParams.put("loadScript", loadScript =  new JU.SB().append(JU.PT.rep(loadScript.toString(), "$FILENAME$", JU.PT.esc(JV.FileManager.fixDOSName(fname)))));
}return this.createModelSetAndReturnError(atomSetCollection, isAppend, loadScript, htParams);
}, "~S,~S,~A,~O,~B,java.util.Map,JU.SB,JU.SB,~N,~S");
Clazz.defineMethod(c$, "setLigandModel", 
function(key, data){
if (this.ligandModels == null) this.ligandModels =  new java.util.Hashtable();
this.ligandModels.put(key, data);
}, "~S,~S");
Clazz.defineMethod(c$, "getLigandModel", 
function(id, prefix, suffix, terminator){
if (id == null) {
if (this.ligandModelSet != null) {
var e = this.ligandModels.entrySet().iterator();
while (e.hasNext()) {
var entry = e.next();
if (Clazz.instanceOf(entry.getValue(), Boolean)) e.remove();
}
}return null;
}id = id.$replace('\\', '/');
var isLigand = prefix.equals("ligand_");
id = (id.indexOf("/cif") >= 0 ? id : isLigand ? id.toUpperCase() : id.substring(id.lastIndexOf("/") + 1));
if (this.ligandModelSet == null) this.ligandModelSet =  new java.util.Hashtable();
this.ligandModelSet.put(id, Boolean.TRUE);
if (this.ligandModels == null) this.ligandModels =  new java.util.Hashtable();
var pngPt = id.indexOf("|");
if (pngPt >= 0) id = id.substring(id.indexOf("|") + 1);
var model = (terminator == null ? this.ligandModels.get(id) : null);
var data;
var fname = null;
if (Clazz.instanceOf(model, Boolean)) return null;
if (model == null && (terminator == null || pngPt >= 0)) model = this.ligandModels.get(id + suffix);
var isError = false;
var isNew = (model == null);
if (isNew) {
var s;
if (isLigand) {
fname = this.setLoadFormat(false, "#" + id, '#', false);
if (fname.length == 0) return null;
this.scriptEcho("fetching " + fname);
s = this.getFileAsString3(fname, false, null);
} else {
this.scriptEcho("fetching " + prefix);
s = this.getFileAsString3(prefix, false, null);
var pt = (terminator == null ? -1 : s.indexOf(terminator));
if (pt >= 0) s = s.substring(0, pt);
}isError = (s.indexOf("java.") == 0);
model = s;
if (!isError) this.ligandModels.put(id + suffix, model);
}if (!isLigand) {
if (!isNew) this.scriptEcho(prefix + " loaded from cache");
return model;
}if (!isError && (typeof(model)=='string')) {
data = model;
if (data.length != 0) {
var htParams =  new java.util.Hashtable();
htParams.put("modelOnly", Boolean.TRUE);
model = this.getModelAdapter().getAtomSetCollectionReader("ligand", null, JU.Rdr.getBR(data), htParams);
isError = ((typeof(model)=='string'));
if (!isError) {
model = this.getModelAdapter().getAtomSetCollection(model);
isError = ((typeof(model)=='string'));
if (fname != null && !isError) this.scriptEcho(this.getModelAdapter().getAtomSetCollectionAuxiliaryInfo(model).get("modelLoadNote"));
}}}if (isError) {
this.scriptEcho(model.toString());
this.ligandModels.put(id, Boolean.FALSE);
return null;
}return model;
}, "~S,~S,~S,~S");
Clazz.defineMethod(c$, "openFileFull", 
function(fileName, isAppend, htParams, loadScript){
if (fileName == null) return null;
if (fileName.equals("String[]")) {
return null;
}var atomSetCollection;
var msg = "openFile(" + fileName + ")";
JU.Logger.startTimer(msg);
htParams = this.setLoadParameters(htParams, isAppend);
var isLoadVariable = fileName.startsWith("@");
var haveFileData = (htParams.containsKey("fileData"));
if (fileName.indexOf('$') == 0) htParams.put("smilesString", fileName.substring(1));
var isString = (fileName.equals("string") || fileName.equals("Jmol Model Kit"));
var strModel = null;
if (haveFileData) {
strModel = htParams.get("fileData");
if (htParams.containsKey("isData")) {
var o = this.loadInlineScript(strModel, '\0', isAppend, htParams);
this.lastData = (this.g.preserveState ? this.getDataManager().createFileData(strModel) : null);
return o;
}} else if (isString) {
strModel = this.ms.getInlineData(-1);
if (strModel == null) if (this.g.modelKitMode) strModel = "5\n\nC 0 0 0\nH .63 .63 .63\nH -.63 -.63 .63\nH -.63 .63 -.63\nH .63 -.63 -.63";
 else return "cannot find string data";
if (loadScript != null) htParams.put("loadScript", loadScript =  new JU.SB().append(JU.PT.rep(loadScript.toString(), "/*file*/$FILENAME$", "/*data*/data \"model inline\"\n" + strModel + "end \"model inline\"")));
}if (strModel != null) {
if (!isAppend) this.zap(true, false, false);
if (!isLoadVariable && (!haveFileData || isString)) this.getStateCreator().getInlineData(loadScript, strModel, isAppend, htParams.get("appendToModelIndex"), this.g.defaultLoadFilter);
atomSetCollection = this.fm.createAtomSetCollectionFromString(strModel, htParams, isAppend);
} else {
atomSetCollection = this.fm.createAtomSetCollectionFromFile(fileName, htParams, isAppend);
}JU.Logger.checkTimer(msg, false);
return atomSetCollection;
}, "~S,~B,java.util.Map,JU.SB");
Clazz.overrideMethod(c$, "openStringInline", 
function(strModel){
var ret = this.openStringInlineParamsAppend(strModel, null, false);
this.refresh(1, "openStringInline");
return ret;
}, "~S");
Clazz.defineMethod(c$, "loadInline", 
function(strModel){
return this.loadInlineScriptRepaint(strModel, this.g.inlineNewlineChar, false);
}, "~S");
Clazz.defineMethod(c$, "loadInline", 
function(strModel, newLine){
return this.loadInlineScriptRepaint(strModel, newLine, false);
}, "~S,~S");
Clazz.overrideMethod(c$, "loadInlineAppend", 
function(strModel, isAppend){
return this.loadInlineScriptRepaint(strModel, '\0', isAppend);
}, "~S,~B");
Clazz.defineMethod(c$, "loadInlineScriptRepaint", 
function(strModel, newLine, isAppend){
var ret = this.loadInlineScript(strModel, newLine, isAppend, null);
this.refresh(1, "loadInlineScript");
return ret;
}, "~S,~S,~B");
Clazz.defineMethod(c$, "loadInline", 
function(arrayModels){
return this.loadInline(arrayModels, false);
}, "~A");
Clazz.defineMethod(c$, "loadInline", 
function(arrayModels, isAppend){
if (arrayModels == null || arrayModels.length == 0) return null;
var ret = this.openStringsInlineParamsAppend(arrayModels,  new java.util.Hashtable(), isAppend);
this.refresh(1, "loadInline String[]");
return ret;
}, "~A,~B");
Clazz.defineMethod(c$, "loadInline", 
function(arrayData, isAppend){
if (arrayData == null || arrayData.size() == 0) return null;
if (!isAppend) this.zap(true, false, false);
var list =  new JU.Lst();
for (var i = 0; i < arrayData.size(); i++) list.addLast(arrayData.get(i));

var atomSetCollection = this.fm.createAtomSeCollectionFromArrayData(list, this.setLoadParameters(null, isAppend), isAppend);
var ret = this.createModelSetAndReturnError(atomSetCollection, isAppend, null,  new java.util.Hashtable());
this.refresh(1, "loadInline");
return ret;
}, "java.util.List,~B");
Clazz.defineMethod(c$, "loadInlineScript", 
function(strModel, newLine, isAppend, htParams){
if (strModel == null || strModel.length == 0) return null;
strModel = JV.Viewer.fixInlineString(strModel, newLine);
if (newLine.charCodeAt(0) != 0) JU.Logger.info("loading model inline, " + strModel.length + " bytes, with newLine character " + (newLine).charCodeAt(0) + " isAppend=" + isAppend);
if (JU.Logger.debugging) JU.Logger.debug(strModel);
var datasep = this.getDataSeparator();
var i;
if (datasep != null && datasep !== "" && (i = strModel.indexOf(datasep)) >= 0 && strModel.indexOf("# Jmol state") < 0) {
var n = 2;
while ((i = strModel.indexOf(datasep, i + 1)) >= 0) n++;

var strModels =  new Array(n);
var pt = 0;
var pt0 = 0;
for (i = 0; i < n; i++) {
pt = strModel.indexOf(datasep, pt0);
if (pt < 0) pt = strModel.length;
strModels[i] = strModel.substring(pt0, pt);
pt0 = pt + datasep.length;
}
return this.openStringsInlineParamsAppend(strModels, htParams, isAppend);
}return this.openStringInlineParamsAppend(strModel, htParams, isAppend);
}, "~S,~S,~B,java.util.Map");
c$.fixInlineString = Clazz.defineMethod(c$, "fixInlineString", 
function(strModel, newLine){
var i;
if (strModel.indexOf("\\/n") >= 0) {
strModel = JU.PT.rep(strModel, "\n", "");
strModel = JU.PT.rep(strModel, "\\/n", "\n");
newLine = String.fromCharCode( 0);
}if (newLine.charCodeAt(0) != 0 && newLine != '\n') {
var repEmpty = (strModel.indexOf('\n') >= 0);
var len = strModel.length;
for (i = 0; i < len && strModel.charAt(i) == ' '; ++i) {
}
if (i < len && strModel.charAt(i) == newLine) strModel = strModel.substring(i + 1);
if (repEmpty) strModel = JU.PT.rep(strModel, "" + newLine, "");
 else strModel = strModel.$replace(newLine, '\n');
}return strModel;
}, "~S,~S");
Clazz.defineMethod(c$, "openStringInlineParamsAppend", 
function(strModel, htParams, isAppend){
htParams = this.setLoadParameters(htParams, isAppend);
var type = this.getModelAdapter().getFileTypeName(htParams.get("filter"));
if (type == null && (type = this.getModelAdapter().getFileTypeName(JU.Rdr.getBR(strModel))) == null) return "unknown file type";
if (type.equals("spt")) {
return "cannot open script inline";
}var loadScript = htParams.get("loadScript");
var isLoadCommand = htParams.containsKey("isData");
if (loadScript == null) loadScript =  new JU.SB();
if (!isAppend) this.zap(true, false, false);
if (!isLoadCommand) this.getStateCreator().getInlineData(loadScript, strModel, isAppend, htParams.get("appendToModelIndex"), this.g.defaultLoadFilter);
var atomSetCollection = this.fm.createAtomSetCollectionFromString(strModel, htParams, isAppend);
return this.createModelSetAndReturnError(atomSetCollection, isAppend, loadScript, htParams);
}, "~S,java.util.Map,~B");
Clazz.defineMethod(c$, "openStringsInlineParamsAppend", 
function(arrayModels, htParams, isAppend){
var loadScript =  new JU.SB();
if (!isAppend) this.zap(true, false, false);
var atomSetCollection = this.fm.createAtomSeCollectionFromStrings(arrayModels, loadScript, this.setLoadParameters(htParams, isAppend), isAppend);
return this.createModelSetAndReturnError(atomSetCollection, isAppend, loadScript, htParams);
}, "~A,java.util.Map,~B");
Clazz.defineMethod(c$, "getInlineChar", 
function(){
return this.g.inlineNewlineChar;
});
Clazz.defineMethod(c$, "getDataSeparator", 
function(){
return this.g.getParameter("dataseparator", true);
});
Clazz.defineMethod(c$, "createModelSetAndReturnError", 
function(atomSetCollection, isAppend, loadScript, htParams){
JU.Logger.startTimer("creating model");
var fullPathName = this.fm.getFullPathName(false);
var fileName = this.fm.getFileName();
var errMsg;
if (loadScript == null) {
this.setBooleanPropertyTok("preserveState", 603979898, false);
loadScript =  new JU.SB().append("load \"???\"");
}if ((typeof(atomSetCollection)=='string')) {
errMsg = atomSetCollection;
this.setFileLoadStatus(J.c.FIL.NOT_LOADED, fullPathName, null, null, errMsg, null);
if (this.displayLoadErrors && !isAppend && !errMsg.equals("#CANCELED#") && !errMsg.startsWith(JV.JC.READER_NOT_FOUND)) this.zapMsg(errMsg);
return errMsg;
}if (isAppend) this.clearAtomSets();
 else if (this.g.modelKitMode && !fileName.equals("Jmol Model Kit")) this.setModelKitMode(false);
this.setFileLoadStatus(J.c.FIL.CREATING_MODELSET, fullPathName, fileName, null, null, null);
this.pushHoldRepaintWhy("createModelSet");
this.setErrorMessage(null, null);
try {
var bsNew =  new JU.BS();
this.mm.createModelSet(fullPathName, fileName, loadScript, atomSetCollection, bsNew, isAppend);
if (!bsNew.isEmpty()) {
var jmolScript = this.ms.getInfoM("jmolscript");
if (this.ms.getMSInfoB("doMinimize")) {
try {
var eval = htParams.get("eval");
var stereo = this.getAtomBitSet("_C & connected(3) & !connected(double)");
stereo.and(bsNew);
if (stereo.nextSetBit(0) >= 0) {
bsNew.or(this.addHydrogens(stereo, 41));
}this.minimize(eval, 2147483647, 0, bsNew, null, null, 0, 185);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
} else {
this.addHydrogens(bsNew, 9);
}if (jmolScript != null) this.ms.msInfo.put("jmolscript", jmolScript);
}this.initializeModel(isAppend);
} catch (er) {
if (Clazz.exceptionOf(er, Error)){
this.handleError(er, true);
errMsg = this.getShapeErrorState();
errMsg = ("ERROR creating model: " + er + (errMsg.length == 0 ? "" : "|" + errMsg));
this.zapMsg(errMsg);
this.setErrorMessage(errMsg, null);
} else {
throw er;
}
}
this.popHoldRepaint("createModelSet \u0001## REPAINT_IGNORE ##");
errMsg = this.getErrorMessage();
this.setFileLoadStatus(J.c.FIL.CREATED, fullPathName, fileName, this.ms.modelSetName, errMsg, htParams.get("async"));
if (isAppend) {
this.selectAll();
this.setTainted(true);
this.axesAreTainted = true;
}atomSetCollection = null;
JU.Logger.checkTimer("creating model", false);
System.gc();
return errMsg;
}, "~O,~B,JU.SB,java.util.Map");
Clazz.defineMethod(c$, "loadAtomDataAndReturnError", 
function(atomSetCollection, tokType){
if ((typeof(atomSetCollection)=='string')) return atomSetCollection;
this.setErrorMessage(null, null);
try {
var script = this.mm.createAtomDataSet(atomSetCollection, tokType);
switch (tokType) {
case 1145047049:
if (script != null) this.runScriptCautiously(script);
break;
case 4166:
this.setStatusFrameChanged(true, false);
break;
case 1648363544:
this.shm.deleteVdwDependentShapes(null);
break;
}
} catch (er) {
if (Clazz.exceptionOf(er, Error)){
this.handleError(er, true);
var errMsg = this.getShapeErrorState();
errMsg = ("ERROR adding atom data: " + er + (errMsg.length == 0 ? "" : "|" + errMsg));
this.zapMsg(errMsg);
this.setErrorMessage(errMsg, null);
this.setParallel(false);
} else {
throw er;
}
}
return this.getErrorMessage();
}, "~O,~N");
Clazz.defineMethod(c$, "getCurrentFileAsString", 
function(state){
var filename = this.fm.getFullPathName(false);
if (filename.equals("string") || filename.equals("Jmol Model Kit")) return this.ms.getInlineData(this.am.cmi);
if (filename.equals("String[]")) return filename;
if (filename === "JSNode") return "<DOM NODE>";
return this.getFileAsString4(filename, -1, true, false, false, state);
}, "~S");
Clazz.defineMethod(c$, "getFullPathNameOrError", 
function(filename){
var data =  new Array(2);
this.fm.getFullPathNameOrError(filename, false, data);
return data;
}, "~S");
Clazz.defineMethod(c$, "getFileAsString3", 
function(name, checkProtected, state){
return this.getFileAsString4(name, -1, false, false, checkProtected, state);
}, "~S,~B,~S");
Clazz.defineMethod(c$, "getFileAsString4", 
function(name, nBytesMax, doSpecialLoad, allowBinary, checkProtected, state){
if (name == null) return this.getCurrentFileAsString(state);
var data =  Clazz.newArray(-1, [name, null]);
this.fm.getFileDataAsString(data, nBytesMax, doSpecialLoad, allowBinary, checkProtected);
return data[1];
}, "~S,~N,~B,~B,~B,~S");
Clazz.defineMethod(c$, "getAsciiFileOrNull", 
function(name){
var data =  Clazz.newArray(-1, [name, null]);
return (this.fm.getFileDataAsString(data, -1, false, false, false) ? data[1] : null);
}, "~S");
Clazz.defineMethod(c$, "autoCalculate", 
function(tokProperty, dataType){
switch (tokProperty) {
case 1111490575:
this.ms.getSurfaceDistanceMax();
break;
case 1111490574:
this.ms.calculateStraightnessAll();
break;
case 1111490587:
this.ms.calculateDssrProperty(dataType);
}
}, "~N,~S");
Clazz.defineMethod(c$, "calculateStraightness", 
function(){
this.ms.haveStraightness = false;
this.ms.calculateStraightnessAll();
});
Clazz.defineMethod(c$, "calculateSurface", 
function(bsSelected, envelopeRadius){
if (bsSelected == null) bsSelected = this.bsA();
if (envelopeRadius == 3.4028235E38 || envelopeRadius == -1) this.ms.addStateScript("calculate surfaceDistance " + (envelopeRadius == 3.4028235E38 ? "FROM" : "WITHIN"), null, bsSelected, null, "", false, true);
return this.ms.calculateSurface(bsSelected, envelopeRadius);
}, "JU.BS,~N");
Clazz.defineMethod(c$, "getStructureList", 
function(){
return this.g.getStructureList();
});
Clazz.defineMethod(c$, "setStructureList", 
function(list, type){
this.g.setStructureList(list, type);
this.ms.setStructureList(this.getStructureList());
}, "~A,J.c.STR");
Clazz.defineMethod(c$, "calculateStructures", 
function(bsAtoms, asDSSP, setStructure, version){
if (bsAtoms == null) bsAtoms = this.bsA();
return this.ms.calculateStructures(bsAtoms, asDSSP, !this.am.animationOn, this.g.dsspCalcHydrogen, setStructure, version);
}, "JU.BS,~B,~B,~N");
Clazz.defineMethod(c$, "getAnnotationParser", 
function(isDSSR){
return (isDSSR ? (this.dssrParser == null ? (this.dssrParser = J.api.Interface.getOption("dssx.DSSR1", this, "script")) : this.dssrParser) : (this.annotationParser == null ? (this.annotationParser = J.api.Interface.getOption("dssx.AnnotationParser", this, "script")) : this.annotationParser));
}, "~B");
Clazz.overrideMethod(c$, "getSelectedAtomIterator", 
function(bsSelected, isGreaterOnly, modelZeroBased, isMultiModel){
return this.ms.getSelectedAtomIterator(bsSelected, isGreaterOnly, modelZeroBased, false, isMultiModel);
}, "JU.BS,~B,~B,~B");
Clazz.overrideMethod(c$, "setIteratorForAtom", 
function(iterator, atomIndex, distance){
this.ms.setIteratorForAtom(iterator, -1, atomIndex, distance, null);
}, "J.api.AtomIndexIterator,~N,~N");
Clazz.overrideMethod(c$, "setIteratorForPoint", 
function(iterator, modelIndex, pt, distance){
this.ms.setIteratorForPoint(iterator, modelIndex, pt, distance);
}, "J.api.AtomIndexIterator,~N,JU.T3,~N");
Clazz.overrideMethod(c$, "fillAtomData", 
function(atomData, mode){
atomData.programInfo = "Jmol Version " + JV.Viewer.getJmolVersion();
atomData.fileName = this.fm.getFileName();
this.ms.fillAtomData(atomData, mode);
}, "J.atomdata.AtomData,~N");
Clazz.defineMethod(c$, "addStateScript", 
function(script, addFrameNumber, postDefinitions){
return this.ms.addStateScript(script, null, null, null, null, addFrameNumber, postDefinitions);
}, "~S,~B,~B");
Clazz.defineMethod(c$, "getMinimizer", 
function(createNew){
return (this.minimizer == null && createNew ? (this.minimizer = J.api.Interface.getInterface("JM.Minimizer", this, "script")).setProperty("vwr", this) : this.minimizer);
}, "~B");
Clazz.defineMethod(c$, "getSmilesMatcher", 
function(){
return (this.smilesMatcher == null ? (this.smilesMatcher = J.api.Interface.getInterface("JS.SmilesMatcher", this, "script")) : this.smilesMatcher);
});
Clazz.defineMethod(c$, "clearModelDependentObjects", 
function(){
this.setFrameOffsets(null, false);
this.stopMinimization();
this.minimizer = null;
this.smilesMatcher = null;
if (this.modelkit != null) this.modelkit.clearAtomConstraints();
});
Clazz.defineMethod(c$, "zap", 
function(notify, resetUndo, zapModelKit){
this.clearThreads();
if (this.mm.modelSet == null) {
this.mm.zap();
} else {
this.ligandModelSet = null;
this.clearModelDependentObjects();
this.fm.clear();
this.clearRepaintManager(-1);
this.am.clear();
this.tm.clear();
this.slm.clear();
this.hasSelected = true;
this.clearAllMeasurements();
this.clearMinimization();
this.gdata.clear();
this.mm.zap();
if (this.scm != null) this.scm.clear(false);
if (this.nmrCalculation != null) this.getNMRCalculation().setChemicalShiftReference(null, 0);
if (this.haveDisplay) {
this.mouse.clear();
this.clearTimeouts();
this.acm.clear();
}this.stm.clear(this.g);
this.tempArray.clear();
this.chainMap.clear();
this.chainList.clear();
this.chainCaseSpecified = false;
this.definedAtomSets.clear();
this.lastData = null;
if (this.dm != null) this.dm.clear();
if (!this.g.doublePrecision && this.g.legacyJavaFloat) this.setBooleanPropertyTok("legacyjavafloat", 603979874, false);
if (resetUndo) {
if (zapModelKit) this.g.removeParam("_pngjFile");
if (zapModelKit && this.g.modelKitMode) {
this.loadDefaultModelKitModel(null);
} else {
this.setPickingMode(null, 1);
}this.undoMoveAction(4165, -2);
}System.gc();
}this.initializeModel(false);
if (notify) {
this.setFileLoadStatus(J.c.FIL.ZAPPED, null, (resetUndo ? "resetUndo" : this.getZapName()), null, null, null);
}if (JU.Logger.debugging) JU.Logger.checkMemory();
}, "~B,~B,~B");
Clazz.defineMethod(c$, "loadDefaultModelKitModel", 
function(htParams){
if (this.getModelkit(false).isHidden() || this.getOperativeSymmetry() != null) return;
this.openStringInlineParamsAppend(this.getModelkit(false).getDefaultModel(), htParams, true);
this.setRotationRadius(5.0, true);
this.setStringProperty("picking", "assignAtom_C");
this.setStringProperty("picking", "assignBond_p");
}, "java.util.Map");
Clazz.defineMethod(c$, "zapMsg", 
function(msg){
this.zap(true, true, false);
this.echoMessage(msg);
}, "~S");
Clazz.defineMethod(c$, "echoMessage", 
function(msg){
var iShape = 31;
this.shm.loadShape(iShape);
this.setShapeProperty(iShape, "font", this.getFont3D("SansSerif", "Plain", 20));
this.setShapeProperty(iShape, "target", "error");
this.setShapeProperty(iShape, "text", msg);
}, "~S");
Clazz.defineMethod(c$, "initializeModel", 
function(isAppend){
this.clearThreads();
if (isAppend) {
this.am.initializePointers(1);
return;
}this.reset(true);
this.selectAll();
this.setModelkitPropertySafely("initializemodel", null);
this.movingSelected = false;
this.slm.noneSelected = Boolean.FALSE;
this.setHoverEnabled(true);
this.setSelectionHalosEnabled(false);
this.tm.setCenter();
this.am.initializePointers(1);
this.setBooleanPropertyTok("multipleBondBananas", 603979886, false);
if (!this.ms.getMSInfoB("isPyMOL")) {
this.clearAtomSets();
this.setCurrentModelIndex(0);
}this.setBackgroundModelIndex(-1);
this.setFrankOn(this.getShowFrank());
this.shm.setScale();
this.startHoverWatcher(true);
this.setTainted(true);
this.finalizeTransformParameters();
}, "~B");
Clazz.defineMethod(c$, "startHoverWatcher", 
function(tf){
if (tf && this.inMotion || !this.haveDisplay || tf && (!this.hoverEnabled && !this.sm.haveHoverCallback() || this.am.animationOn)) return;
this.acm.startHoverWatcher(tf);
}, "~B");
Clazz.overrideMethod(c$, "getModelSetPathName", 
function(){
return this.mm.modelSetPathName;
});
Clazz.overrideMethod(c$, "getModelSetFileName", 
function(){
return (this.mm.fileName == null ? this.getZapName() : this.mm.fileName);
});
Clazz.defineMethod(c$, "getUnitCellInfoText", 
function(){
var c = this.getCurrentUnitCell();
return (c == null ? "not applicable" : c.getUnitCellInfo(true));
});
Clazz.defineMethod(c$, "getUnitCellInfo", 
function(infoType){
var symmetry = this.getCurrentUnitCell();
return (symmetry == null ? NaN : symmetry.getUnitCellInfoType(infoType));
}, "~N");
Clazz.defineMethod(c$, "getV0abc", 
function(iModel, def){
var uc = (iModel < 0 ? this.getCurrentUnitCell() : this.getUnitCell(iModel));
if (uc == null) uc = this.getSymTemp();
return (uc == null ? null : uc.getV0abc(def, null));
}, "~N,~O");
Clazz.defineMethod(c$, "getCurrentUnitCell", 
function(){
var iAtom = this.am.getUnitCellAtomIndex();
return (iAtom >= 0 ? this.ms.getUnitCellForAtom(iAtom) : this.getUnitCell(this.am.cmi));
});
Clazz.defineMethod(c$, "getUnitCell", 
function(modelIndex){
if (modelIndex >= 0) return this.ms.getUnitCell(modelIndex);
var models = this.getVisibleFramesBitSet();
var ucLast = null;
for (var i = models.nextSetBit(0); i >= 0; i = models.nextSetBit(i + 1)) {
var uc = this.ms.getUnitCell(i);
if (uc == null) continue;
if (ucLast == null) {
ucLast = uc;
continue;
}if (!ucLast.unitCellEquals(uc)) return null;
}
return ucLast;
}, "~N");
Clazz.defineMethod(c$, "getPolymerPointsAndVectors", 
function(bs, vList){
this.ms.getPolymerPointsAndVectors(bs, vList, this.g.traceAlpha, this.g.sheetSmoothing);
}, "JU.BS,JU.Lst");
Clazz.defineMethod(c$, "getHybridizationAndAxes", 
function(atomIndex, z, x, lcaoType){
return this.ms.getHybridizationAndAxes(atomIndex, 0, z, x, lcaoType, true, true, false, null);
}, "~N,JU.V3,JU.V3,~S");
Clazz.defineMethod(c$, "getAllAtoms", 
function(){
return this.getModelUndeletedAtomsBitSet(-1);
});
Clazz.defineMethod(c$, "getFrameAtoms", 
function(){
return this.getModelUndeletedAtomsBitSetBs(this.getVisibleFramesBitSet());
});
Clazz.overrideMethod(c$, "getVisibleFramesBitSet", 
function(){
var bs = JU.BSUtil.copy(this.am.bsVisibleModels);
if (this.ms.trajectory != null) this.ms.trajectory.selectDisplayed(bs);
return bs;
});
Clazz.defineMethod(c$, "getModelUndeletedAtomsBitSet", 
function(modelIndex){
return this.slm.excludeAtoms(this.ms.getModelAtomBitSetIncludingDeleted(modelIndex, true), false);
}, "~N");
Clazz.defineMethod(c$, "getModelUndeletedAtomsBitSetBs", 
function(bsModels){
return this.slm.excludeAtoms(this.ms.getModelAtomBitSetIncludingDeletedBs(bsModels), false);
}, "JU.BS");
Clazz.overrideMethod(c$, "getBoundBoxCenter", 
function(){
return this.ms.getBoundBoxCenter(this.am.cmi);
});
Clazz.defineMethod(c$, "calcBoundBoxDimensions", 
function(bs, scale){
this.ms.calcBoundBoxDimensions(bs, scale);
this.axesAreTainted = true;
}, "JU.BS,~N");
Clazz.overrideMethod(c$, "getBoundBoxCornerVector", 
function(){
return this.ms.getBoundBoxCornerVector();
});
Clazz.overrideMethod(c$, "getModelSetProperties", 
function(){
return this.ms.modelSetProperties;
});
Clazz.overrideMethod(c$, "getModelProperties", 
function(modelIndex){
return this.ms.am[modelIndex].properties;
}, "~N");
Clazz.defineMethod(c$, "getModelForAtomIndex", 
function(iatom){
return this.ms.am[this.ms.at[iatom].mi];
}, "~N");
Clazz.defineMethod(c$, "getModelIndexForAtom", 
function(iatom){
return this.ms.at[iatom].mi;
}, "~N");
Clazz.overrideMethod(c$, "getModelSetAuxiliaryInfo", 
function(){
return this.ms.getModelSetAuxiliaryInfo(null);
});
Clazz.overrideMethod(c$, "getModelNumber", 
function(modelIndex){
return (modelIndex < 0 ? modelIndex : this.ms.getModelNumber(modelIndex));
}, "~N");
Clazz.defineMethod(c$, "getModelFileNumber", 
function(modelIndex){
return (modelIndex < 0 ? 0 : this.ms.modelFileNumbers[modelIndex]);
}, "~N");
Clazz.overrideMethod(c$, "getModelNumberDotted", 
function(modelIndex){
return modelIndex < 0 ? "0" : this.ms.getModelNumberDotted(modelIndex);
}, "~N");
Clazz.overrideMethod(c$, "getModelName", 
function(modelIndex){
return this.ms.getModelName(modelIndex);
}, "~N");
Clazz.defineMethod(c$, "modelHasVibrationVectors", 
function(modelIndex){
return (this.ms.getLastVibrationVector(modelIndex, 4166) >= 0);
}, "~N");
Clazz.defineMethod(c$, "getBondsForSelectedAtoms", 
function(bsAtoms){
return this.ms.getBondsForSelectedAtoms(bsAtoms, this.g.bondModeOr || JU.BSUtil.cardinalityOf(bsAtoms) == 1);
}, "JU.BS");
Clazz.defineMethod(c$, "frankClicked", 
function(x, y){
return !this.g.disablePopupMenu && this.getShowFrank() && this.shm.checkFrankclicked(x, y);
}, "~N,~N");
Clazz.defineMethod(c$, "frankClickedModelKit", 
function(x, y){
return !this.g.disablePopupMenu && this.isModelKitOpen() && x >= 0 && y >= 0 && x < 40 && y < 104;
}, "~N,~N");
Clazz.overrideMethod(c$, "findNearestAtomIndex", 
function(x, y){
return this.findNearestAtomIndexMovable(x, y, false);
}, "~N,~N");
Clazz.defineMethod(c$, "findNearestAtomIndexMovable", 
function(x, y, mustBeMovable){
return (!this.g.atomPicking ? -1 : this.ms.findNearestAtomIndex(x, y, mustBeMovable ? this.slm.getMotionFixedAtoms() : null, this.g.minPixelSelRadius));
}, "~N,~N,~B");
Clazz.defineMethod(c$, "toCartesian", 
function(pt, ignoreOffset){
this.toCartesianUC(null, pt, ignoreOffset);
}, "JU.T3,~B");
Clazz.defineMethod(c$, "toCartesianUC", 
function(unitCell, pt, ignoreOffset){
if (unitCell == null) unitCell = this.getCurrentUnitCell();
if (unitCell != null) {
unitCell.toCartesian(pt, ignoreOffset);
if (!this.g.legacyJavaFloat) JU.PT.fixPtFloats(pt, 10000.0);
}}, "J.api.SymmetryInterface,JU.T3,~B");
Clazz.defineMethod(c$, "toFractional", 
function(pt, ignoreOffset){
this.toFractionalUC(null, pt, ignoreOffset);
}, "JU.T3,~B");
Clazz.defineMethod(c$, "toFractionalUC", 
function(unitCell, pt, ignoreOffset){
if (unitCell == null) unitCell = this.getCurrentUnitCell();
if (unitCell != null) {
unitCell.toFractional(pt, ignoreOffset);
if (!this.g.legacyJavaFloat) JU.PT.fixPtFloats(pt, 100000.0);
}}, "J.api.SymmetryInterface,JU.T3,~B");
Clazz.defineMethod(c$, "toUnitCell", 
function(pt, offset){
var unitCell = this.getCurrentUnitCell();
if (unitCell != null) unitCell.toUnitCell(pt, offset);
}, "JU.P3,JU.P3");
Clazz.defineMethod(c$, "setCurrentCage", 
function(isosurfaceId){
var data =  Clazz.newArray(-1, [isosurfaceId, null]);
this.shm.getShapePropertyData(24, "unitCell", data);
this.ms.setModelCage(this.am.cmi, data[1]);
}, "~S");
Clazz.defineMethod(c$, "addUnitCellOffset", 
function(pt){
var unitCell = this.getCurrentUnitCell();
if (unitCell == null) return;
pt.add(unitCell.getCartesianOffset());
}, "JU.P3");
Clazz.defineMethod(c$, "setAtomData", 
function(type, name, coordinateData, isDefault){
this.ms.setAtomData(type, name, coordinateData, isDefault);
if (type == 2) this.checkCoordinatesChanged(null);
this.refreshMeasures(true);
}, "~N,~S,~S,~B");
Clazz.overrideMethod(c$, "setCenterSelected", 
function(){
this.setCenterBitSet(this.bsA(), true);
});
Clazz.defineMethod(c$, "setApplySymmetryToBonds", 
function(TF){
this.g.applySymmetryToBonds = TF;
}, "~B");
Clazz.overrideMethod(c$, "setBondTolerance", 
function(bondTolerance){
this.g.setF("bondTolerance", bondTolerance);
this.g.bondTolerance = bondTolerance;
}, "~N");
Clazz.overrideMethod(c$, "setMinBondDistance", 
function(minBondDistance){
this.g.setF("minBondDistance", minBondDistance);
this.g.minBondDistance = minBondDistance;
}, "~N");
Clazz.defineMethod(c$, "getAtomsNearPt", 
function(distance, coord, bs){
if (bs == null) bs =  new JU.BS();
this.ms.getAtomsWithin(distance, coord, bs, -1);
return bs;
}, "~N,JU.P3,JU.BS");
Clazz.defineMethod(c$, "getBranchBitSet", 
function(atomIndex, atomIndexNot, allowCyclic){
if (atomIndex < 0 || atomIndex >= this.ms.ac) return  new JU.BS();
return JU.JmolMolecule.getBranchBitSet(this.ms.at, atomIndex, this.getModelUndeletedAtomsBitSet(this.ms.at[atomIndex].mi), null, atomIndexNot, allowCyclic, true);
}, "~N,~N,~B");
Clazz.overrideMethod(c$, "getElementsPresentBitSet", 
function(modelIndex){
return this.ms.getElementsPresentBitSet(modelIndex);
}, "~N");
Clazz.defineMethod(c$, "getFileHeader", 
function(){
return this.ms.getFileHeader(this.am.cmi);
});
Clazz.defineMethod(c$, "getFileData", 
function(){
return this.ms.getFileData(this.am.cmi);
});
Clazz.defineMethod(c$, "getCifData", 
function(modelIndex){
return this.readCifData(this.ms.getModelFileName(modelIndex), this.ms.getModelFileType(modelIndex).toUpperCase());
}, "~N");
Clazz.defineMethod(c$, "readCifData", 
function(fileName, type){
var fname = (fileName == null ? this.ms.getModelFileName(this.am.cmi) : fileName);
if (type == null && fname != null && fname.toUpperCase().indexOf("BCIF") >= 0) {
var is = this.fm.getBufferedInputStream(fname);
try {
return (J.api.Interface.getInterface("JU.MessagePackReader", this, "script")).getMapForStream(is);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
e.printStackTrace();
return  new java.util.Hashtable();
} else {
throw e;
}
}
}var data = (fileName == null || fileName.length == 0 ? this.getCurrentFileAsString("script") : this.getFileAsString3(fileName, false, null));
if (data == null || data.length < 2) return null;
var rdr = JU.Rdr.getBR(data);
if (type == null) type = this.getModelAdapter().getFileTypeName(rdr);
return (type == null ? null : this.readCifData(null, rdr, type));
}, "~S,~S");
Clazz.defineMethod(c$, "readCifData", 
function(fileName, rdrOrStringData, type){
if (rdrOrStringData == null) rdrOrStringData = this.getFileAsString(fileName);
var rdr = (Clazz.instanceOf(rdrOrStringData,"java.io.BufferedReader") ? rdrOrStringData : JU.Rdr.getBR(rdrOrStringData));
return JU.Rdr.readCifData(J.api.Interface.getInterface(("Cif2".equals(type) ? "J.adapter.readers.cif.Cif2DataParser" : "JU.CifDataParser"), this, "script"), rdr);
}, "~S,~O,~S");
Clazz.defineMethod(c$, "getStateCreator", 
function(){
if (this.jsc == null) (this.jsc = J.api.Interface.getInterface("JV.StateCreator", this, "script")).setViewer(this);
return this.jsc;
});
Clazz.defineMethod(c$, "getWrappedStateScript", 
function(){
return this.getOutputManager().getWrappedState(null, null, null, null);
});
Clazz.overrideMethod(c$, "getStateInfo", 
function(){
return this.getStateInfo3(null, 0, 0);
});
Clazz.defineMethod(c$, "getStateInfo3", 
function(type, width, height){
return (this.g.preserveState ? this.getStateCreator().getStateScript(type, width, height) : "");
}, "~S,~N,~N");
Clazz.defineMethod(c$, "getStructureState", 
function(){
return this.getStateCreator().getModelState(null, false, true);
});
Clazz.defineMethod(c$, "getCoordinateState", 
function(bsSelected){
return this.getStateCreator().getAtomicPropertyState(2, bsSelected);
}, "JU.BS");
Clazz.defineMethod(c$, "setCurrentColorRange", 
function(label){
var data = this.getDataObj(label, null, 1);
var bs = (data == null ? null : (this.getDataObj(label, null, -1))[2]);
if (bs != null && this.g.rangeSelected) bs.and(this.bsA());
this.cm.setPropertyColorRangeData(data, bs);
}, "~S");
Clazz.defineMethod(c$, "setData", 
function(key, data, dataType, matchField, matchFieldColumnCount, dataField, dataFieldColumnCount){
this.getDataManager().setData(key, this.lastData = data, dataType, this.ms.ac, matchField, matchFieldColumnCount, dataField, dataFieldColumnCount);
}, "~S,~A,~N,~N,~N,~N,~N");
Clazz.defineMethod(c$, "getDataObj", 
function(key, bsSelected, dataType){
return (key == null && dataType == -2 ? this.lastData : this.getDataManager().getData(key, bsSelected, dataType));
}, "~S,JU.BS,~N");
Clazz.defineMethod(c$, "autoHbond", 
function(bsFrom, bsTo, onlyIfHaveCalculated){
if (bsFrom == null) bsFrom = bsTo = this.bsA();
return this.ms.autoHbond(bsFrom, bsTo, onlyIfHaveCalculated);
}, "JU.BS,JU.BS,~B");
Clazz.defineMethod(c$, "getDefaultMeasurementLabel", 
function(nPoints){
switch (nPoints) {
case 2:
return this.g.defaultDistanceLabel;
case 3:
return this.g.defaultAngleLabel;
default:
return this.g.defaultTorsionLabel;
}
}, "~N");
Clazz.overrideMethod(c$, "getMeasurementCount", 
function(){
var count = this.getShapePropertyAsInt(6, "count");
return count <= 0 ? 0 : count;
});
Clazz.overrideMethod(c$, "getMeasurementStringValue", 
function(i){
return "" + this.shm.getShapePropertyIndex(6, "stringValue", i);
}, "~N");
Clazz.defineMethod(c$, "getMeasurementInfoAsString", 
function(){
return this.getShapeProperty(6, "infostring");
});
Clazz.overrideMethod(c$, "getMeasurementCountPlusIndices", 
function(i){
return this.shm.getShapePropertyIndex(6, "countPlusIndices", i);
}, "~N");
Clazz.defineMethod(c$, "setPendingMeasurement", 
function(mp){
this.shm.loadShape(6);
this.setShapeProperty(6, "pending", mp);
}, "JM.MeasurementPending");
Clazz.defineMethod(c$, "getPendingMeasurement", 
function(){
return this.getShapeProperty(6, "pending");
});
Clazz.defineMethod(c$, "clearAllMeasurements", 
function(){
this.setShapeProperty(6, "clear", null);
});
Clazz.overrideMethod(c$, "clearMeasurements", 
function(){
this.evalString("measures delete");
});
Clazz.defineMethod(c$, "setAnimation", 
function(tok){
switch (tok) {
case 1073742098:
this.am.reverseAnimation();
case 1073742096:
case 4143:
if (!this.am.animationOn) this.am.resumeAnimation();
return;
case 20487:
if (this.am.animationOn && !this.am.animationPaused) this.am.pauseAnimation();
return;
case 1073742037:
this.am.setAnimationNext();
return;
case 1073742108:
this.am.setAnimationPrevious();
return;
case 1073741942:
case 1073742125:
this.am.rewindAnimation();
return;
case 1073741993:
this.am.setAnimationLast();
return;
}
}, "~N");
Clazz.overrideMethod(c$, "setAnimationFps", 
function(fps){
this.am.setAnimationFps(fps);
}, "~N");
Clazz.defineMethod(c$, "setAnimationMode", 
function(mode){
if (mode.equalsIgnoreCase("once")) {
this.am.setAnimationReplayMode(1073742070, 0, 0);
} else if (mode.equalsIgnoreCase("loop")) {
this.am.setAnimationReplayMode(528411, 1, 1);
} else if (mode.startsWith("pal")) {
this.am.setAnimationReplayMode(1073742082, 1, 1);
}}, "~S");
Clazz.defineMethod(c$, "setAnimationOn", 
function(animationOn){
var wasAnimating = this.am.animationOn;
if (animationOn == wasAnimating) return;
this.am.setAnimationOn(animationOn);
}, "~B");
Clazz.defineMethod(c$, "setAnimationRange", 
function(modelIndex1, modelIndex2){
this.am.setAnimationRange(modelIndex1, modelIndex2);
}, "~N,~N");
Clazz.defineMethod(c$, "defineAtomSets", 
function(info){
this.definedAtomSets.putAll(info);
}, "java.util.Map");
Clazz.defineMethod(c$, "setAnimDisplay", 
function(bs){
this.am.setDisplay(bs);
if (!this.am.animationOn) this.am.morph(this.am.currentMorphModel + 1);
}, "JU.BS");
Clazz.defineMethod(c$, "setCurrentModelIndex", 
function(modelIndex){
if (modelIndex == -2147483648) {
this.prevFrame = -2147483648;
this.setCurrentModelIndexClear(this.am.cmi, true);
return;
}this.am.setModel(modelIndex, true);
}, "~N");
Clazz.defineMethod(c$, "getTrajectoryState", 
function(){
return (this.ms.trajectory == null ? "" : this.ms.trajectory.getState());
});
Clazz.defineMethod(c$, "setFrameOffsets", 
function(bsAtoms, isFull){
this.tm.bsFrameOffsets = null;
if (isFull) this.clearModelDependentObjects();
 else this.tm.bsFrameOffsets = bsAtoms;
this.tm.frameOffsets = this.ms.getFrameOffsets(bsAtoms, isFull);
}, "JU.BS,~B");
Clazz.defineMethod(c$, "setCurrentModelIndexClear", 
function(modelIndex, clearBackground){
this.am.setModel(modelIndex, clearBackground);
}, "~N,~B");
Clazz.defineMethod(c$, "haveFileSet", 
function(){
return (this.ms.mc > 1 && this.getModelNumber(2147483647) > 2000000);
});
Clazz.defineMethod(c$, "setBackgroundModelIndex", 
function(modelIndex){
this.am.setBackgroundModelIndex(modelIndex);
this.g.setO("backgroundModel", this.ms.getModelNumberDotted(modelIndex));
}, "~N");
Clazz.defineMethod(c$, "setFrameVariables", 
function(){
this.g.setO("animationMode", JS.T.nameOf(this.am.animationReplayMode));
this.g.setI("animationFps", this.am.animationFps);
this.g.setO("_firstFrame", this.am.getModelSpecial(-1));
this.g.setO("_lastFrame", this.am.getModelSpecial(1));
this.g.setF("_animTimeSec", this.am.getAnimRunTimeSeconds());
this.g.setB("_animMovie", this.am.isMovie);
});
Clazz.defineMethod(c$, "getInMotion", 
function(includeAnim){
return (this.inMotion || includeAnim && this.am.animationOn);
}, "~B");
Clazz.overrideMethod(c$, "getMotionEventNumber", 
function(){
return this.motionEventNumber;
});
Clazz.overrideMethod(c$, "setInMotion", 
function(inMotion){
if ( new Boolean (this.inMotion ^ inMotion).valueOf()) {
this.inMotion = inMotion;
this.resizeImage(0, 0, false, false, true);
if (inMotion) {
this.startHoverWatcher(false);
++this.motionEventNumber;
} else {
this.startHoverWatcher(true);
this.refresh(3, "vwr setInMotion " + inMotion);
}}}, "~B");
Clazz.defineMethod(c$, "setRefreshing", 
function(TF){
this.refreshing = TF;
}, "~B");
Clazz.defineMethod(c$, "getRefreshing", 
function(){
return this.refreshing;
});
Clazz.overrideMethod(c$, "pushHoldRepaint", 
function(){
this.pushHoldRepaintWhy(null);
});
Clazz.defineMethod(c$, "pushHoldRepaintWhy", 
function(why){
if (this.rm != null) this.rm.pushHoldRepaint(why);
}, "~S");
Clazz.overrideMethod(c$, "popHoldRepaint", 
function(why){
if (this.rm != null) {
this.rm.popHoldRepaint(why.indexOf("\u0001## REPAINT_IGNORE ##") < 0, why);
}}, "~S");
Clazz.overrideMethod(c$, "refresh", 
function(mode, strWhy){
if (this.rm == null || !this.refreshing || mode == 6 && this.getInMotion(true) || !this.isWebGL && mode == 7) return;
if (this.isWebGL) {
switch (mode) {
case 1:
case 2:
case 7:
this.tm.finalizeTransformParameters();
if (this.html5Applet == null) return;
this.html5Applet._refresh();
if (mode == 7) return;
break;
}
} else {
this.rm.repaintIfReady("refresh " + mode + " " + strWhy);
}if (this.sm.doSync()) this.sm.setSync(mode == 2 ? strWhy : null);
}, "~N,~S");
Clazz.defineMethod(c$, "requestRepaintAndWait", 
function(why){
if (this.rm == null) return;
if (!this.haveDisplay) {
this.setModelVisibility();
this.shm.finalizeAtoms(null, true);
return;
}this.rm.requestRepaintAndWait(why);
this.setSync();
}, "~S");
Clazz.defineMethod(c$, "clearShapeRenderers", 
function(){
this.clearRepaintManager(-1);
});
Clazz.defineMethod(c$, "isRepaintPending", 
function(){
return (this.rm == null ? false : this.rm.isRepaintPending());
});
Clazz.overrideMethod(c$, "notifyViewerRepaintDone", 
function(){
if (this.rm != null) this.rm.repaintDone();
this.am.repaintDone();
});
Clazz.defineMethod(c$, "areAxesTainted", 
function(){
var TF = this.axesAreTainted;
this.axesAreTainted = false;
return TF;
});
Clazz.overrideMethod(c$, "generateOutputForExport", 
function(params){
return (this.noGraphicsAllowed || this.rm == null ? null : this.getOutputManager().getOutputFromExport(params));
}, "java.util.Map");
Clazz.defineMethod(c$, "clearRepaintManager", 
function(iShape){
if (this.rm != null) this.rm.clear(iShape);
}, "~N");
Clazz.defineMethod(c$, "renderScreenImage", 
function(g, width, height){
this.renderScreenImageStereo(g, false, width, height);
}, "~O,~N,~N");
Clazz.defineMethod(c$, "renderScreenImageStereo", 
function(gLeft, checkStereoSlave, width, height){
if (this.updateWindow(width, height)) {
if (!checkStereoSlave || this.gRight == null) {
this.getScreenImageBuffer(gLeft, false);
} else {
this.drawImage(this.gRight, this.getImage(true, false), 0, 0, this.tm.stereoDoubleDTI);
this.drawImage(gLeft, this.getImage(false, false), 0, 0, this.tm.stereoDoubleDTI);
}}if (this.captureParams != null && Boolean.FALSE !== this.captureParams.get("captureEnabled")) {
this.captureParams.remove("imagePixels");
var t = (this.captureParams.get("endTime")).longValue();
if (t > 0 && System.currentTimeMillis() + 50 > t) this.captureParams.put("captureMode", "end");
this.processWriteOrCapture(this.captureParams);
}this.notifyViewerRepaintDone();
}, "~O,~B,~N,~N");
Clazz.defineMethod(c$, "updateJS", 
function(){
if (this.isWebGL) {
if (this.jsParams == null) {
this.jsParams =  new java.util.Hashtable();
this.jsParams.put("type", "JS");
}if (this.updateWindow(0, 0)) this.render();
this.notifyViewerRepaintDone();
} else {
if (this.isStereoSlave) return;
this.renderScreenImageStereo(this.apiPlatform.getGraphics(null), true, 0, 0);
}});
Clazz.defineMethod(c$, "updateJSView", 
function(imodel, iatom){
if (this.html5Applet == null) return;
var applet = this.html5Applet;
var doViewPick = true;
{
doViewPick = (applet != null && applet._viewSet != null);
}if (doViewPick) this.html5Applet._atomPickedCallback(imodel, iatom);
}, "~N,~N");
Clazz.overrideMethod(c$, "evalFile", 
function(strFilename){
return this.evalFileArgs(strFilename, null);
}, "~S");
Clazz.overrideMethod(c$, "evalFileArgs", 
function(strFilename, args){
return (this.allowScripting && this.getScriptManager() != null ? this.scm.evalFileArgs(strFilename, args) : null);
}, "~S,~S");
Clazz.defineMethod(c$, "getInsertedCommand", 
function(){
var s = this.insertedCommand;
this.insertedCommand = "";
if (JU.Logger.debugging && s !== "") JU.Logger.debug("inserting: " + s);
return s;
});
Clazz.overrideMethod(c$, "script", 
function(strScript){
return this.evalStringQuietSync(strScript, false, true);
}, "~S");
Clazz.overrideMethod(c$, "evalString", 
function(strScript){
return this.evalStringQuietSync(strScript, false, true);
}, "~S");
Clazz.overrideMethod(c$, "evalStringQuiet", 
function(strScript){
return this.evalStringQuietSync(strScript, true, true);
}, "~S");
Clazz.defineMethod(c$, "evalStringQuietSync", 
function(strScript, isQuiet, allowSyncScript){
return (this.getScriptManager() == null ? null : this.scm.evalStringQuietSync(strScript, isQuiet, allowSyncScript));
}, "~S,~B,~B");
Clazz.defineMethod(c$, "clearScriptQueue", 
function(){
if (this.scm != null) this.scm.clearQueue();
});
Clazz.defineMethod(c$, "setScriptQueue", 
function(TF){
this.g.useScriptQueue = TF;
if (!TF) this.clearScriptQueue();
}, "~B");
Clazz.overrideMethod(c$, "checkHalt", 
function(str, isInsert){
return (this.scm != null && this.scm.checkHalt(str, isInsert));
}, "~S,~B");
Clazz.overrideMethod(c$, "scriptWait", 
function(strScript){
return this.evalWait("JSON", strScript, "+scriptStarted,+scriptStatus,+scriptEcho,+scriptTerminated");
}, "~S");
Clazz.overrideMethod(c$, "scriptWaitStatus", 
function(strScript, statusList){
return this.evalWait("object", strScript, statusList);
}, "~S,~S");
Clazz.defineMethod(c$, "evalWait", 
function(returnType, strScript, statusList){
if (this.getScriptManager() == null) return null;
this.scm.waitForQueue();
var doTranslateTemp = J.i18n.GT.setDoTranslate(false);
var ret = this.evalStringWaitStatusQueued(returnType, strScript, statusList, false, false);
J.i18n.GT.setDoTranslate(doTranslateTemp);
return ret;
}, "~S,~S,~S");
Clazz.defineMethod(c$, "exitJmol", 
function(){
if (this.isApplet && !this.isJNLP) return;
if (this.headlessImageParams != null) {
try {
if (this.headless) this.outputToFile(this.headlessImageParams);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
}if (JU.Logger.debugging) JU.Logger.debug("exitJmol -- exiting");
System.out.flush();
System.exit(0);
});
Clazz.defineMethod(c$, "scriptCheckRet", 
function(strScript, returnContext){
return (this.getScriptManager() == null ? null : this.scm.scriptCheckRet(strScript, returnContext));
}, "~S,~B");
Clazz.overrideMethod(c$, "scriptCheck", 
function(strScript){
return this.scriptCheckRet(strScript, false);
}, "~S");
Clazz.overrideMethod(c$, "isScriptExecuting", 
function(){
return (this.eval != null && this.eval.isExecuting());
});
Clazz.overrideMethod(c$, "haltScriptExecution", 
function(){
if (this.eval != null) {
this.eval.haltExecution();
this.eval.stopScriptThreads();
}this.setStringPropertyTok("pathForAllFiles", 545259572, "");
this.clearTimeouts();
});
Clazz.defineMethod(c$, "pauseScriptExecution", 
function(){
if (this.eval != null) this.eval.pauseExecution(true);
});
Clazz.defineMethod(c$, "resolveDatabaseFormat", 
function(fileName){
return (JV.Viewer.hasDatabasePrefix(fileName) || fileName.indexOf("cactus.nci.nih.gov/chemical/structure") >= 0 ? this.setLoadFormat(false, fileName, fileName.charAt(0), false) : fileName);
}, "~S");
c$.hasDatabasePrefix = Clazz.defineMethod(c$, "hasDatabasePrefix", 
function(fileName){
return (fileName.length != 0 && JV.Viewer.isDatabaseCode(fileName.charAt(0)));
}, "~S");
c$.isDatabaseCode = Clazz.defineMethod(c$, "isDatabaseCode", 
function(ch){
return (ch == '*' || ch == '$' || ch == '=' || ch == ':');
}, "~S");
Clazz.defineMethod(c$, "setLoadFormat", 
function(isSurface, name, type, withPrefix){
var format = null;
var id = name.substring(1);
switch ((type).charCodeAt(0)) {
case 99:
return name;
case 104:
if (this.g.checkCIR) this.checkCIR(false);
return this.g.nihResolverFormat + name.substring(name.indexOf("/structure") + 10);
case 61:
if (name.startsWith("==")) {
id = id.substring(1);
if (id.equals("?") && (id = this.getDBID("chemical component from RCSB")) == null) return null;
type = '#';
} else {
if (id.equals("?") && (id = this.getDBID("PDB ID from RCSB")) == null) return null;
if (id.indexOf("/") > 0) {
try {
var pt = id.indexOf("/");
var database = id.substring(0, pt);
id = id.substring(pt + 1);
if (database.equalsIgnoreCase("aflowlib")) {
var index = 1;
pt = id.indexOf('.');
if (pt >= 0) {
index = JU.PT.parseInt(id.substring(pt + 1));
id = id.substring(0, pt);
}if (id.indexOf("_") < 0) id = this.getSymTemp().getSpaceGroupJSON(this, "AFLOW", id, index);
}id = JV.JC.resolveDataBase(database, id, null);
if (id != null && id.startsWith("'")) id = this.evaluateExpression(id).toString();
return (id == null || id.length == 0 ? name : id);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
return name;
} else {
throw e;
}
}
}if (!isSurface && id.endsWith(".bcif")) {
id = id.substring(0, id.indexOf(".bcif"));
return JV.JC.resolveDataBase("bcif", id.toLowerCase(), null);
}if (id.endsWith(".mmtf")) {
id = id.substring(0, id.indexOf(".mmtf"));
return JV.JC.resolveDataBase("mmtf", id.toUpperCase(), null);
}format = this.g.loadFormat;
}case 35:
if (format == null) format = this.g.pdbLoadLigandFormat;
return JV.JC.resolveDataBase(null, id, format);
case 42:
if (id.equals("?") && (id = this.getDBID("PDB ID from EBI")) == null) return null;
var pt = name.lastIndexOf("/");
if (name.startsWith("*dom/")) {
id = name.substring(pt + 1);
format = (pt > 4 ? name.substring(5) : "mappings");
return JU.PT.rep(JV.JC.resolveDataBase("map", id, null), "%TYPE", format);
} else if (name.startsWith("*val/")) {
id = name.substring(pt + 1);
format = (pt > 4 ? name.substring(5) : "validation/outliers/all");
return JU.PT.rep(JV.JC.resolveDataBase("map", id, null), "%TYPE", format);
} else if (name.startsWith("*rna3d/")) {
id = name.substring(pt + 1);
format = (pt > 6 ? name.substring(6) : "loops");
return JU.PT.rep(JV.JC.resolveDataBase("rna3d", id, null), "%TYPE", format);
} else if (name.startsWith("*dssr--")) {
id = name.substring(pt + 1);
id = JV.JC.resolveDataBase("dssr", id, null);
return id + "%20" + JU.PT.rep(name.substring(5, pt), " ", "%20");
} else if (name.startsWith("*dssr/")) {
id = name.substring(pt + 1);
return JV.JC.resolveDataBase("dssr", id, null);
} else if (name.startsWith("*dssr1/")) {
id = name.substring(pt + 1);
return JV.JC.resolveDataBase("dssr1", id, null);
}var pdbe = "pdbe";
if (id.length == 5 && id.charAt(4) == '*') {
pdbe = "pdbe2";
id = id.substring(0, 4);
}return JV.JC.resolveDataBase(pdbe, id, null);
case 58:
format = this.g.pubChemFormat;
if (id.equals("?") && (id = this.getDBID("structure from PubChem")) == null) return null;
if (id === "") {
try {
id = "smiles:" + this.getOpenSmiles(this.bsA());
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
}var fl = id.toLowerCase();
var fi = -2147483648;
try {
fi = Integer.parseInt(id);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
if (fi != -2147483648) {
id = "cid/" + fi;
} else {
if (fl.startsWith("smiles:")) {
format += "?POST?smiles=" + id.substring(7);
id = "smiles";
} else if (id.startsWith("cid:") || id.startsWith("inchikey:") || id.startsWith("cas:")) {
id = id.$replace(':', '/');
} else {
if (fl.startsWith("name:")) id = id.substring(5);
id = "name/" + JU.PT.escapeUrl(id);
}}return JU.PT.formatStringS(format, "FILE", id);
case 36:
this.checkCIR(false);
if (id.equals("?") && (id = this.getDBID("structure from NCI/CADD")) == null) return null;
if (name.equals("$")) {
try {
id = this.getOpenSmiles(this.bsA());
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
} else if (name.startsWith("$$")) {
id = id.substring(1);
if (id.length == 0) {
try {
id = this.getOpenSmiles(this.bsA());
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
}format = JU.PT.rep(this.g.smilesUrlFormat, "get3d", "get2d");
return JU.PT.formatStringS(format, "FILE", JU.PT.escapeUrl(id));
}case 77:
case 78:
case 50:
case 73:
case 75:
case 83:
case 84:
case 47:
id = JU.PT.escapeUrl(id);
switch ((type).charCodeAt(0)) {
case 77:
case 78:
format = this.g.nihResolverFormat + "/%FILE/names";
break;
case 50:
format = this.g.nihResolverFormat + "/%FILE/image";
break;
case 73:
case 84:
format = this.g.nihResolverFormat + "/%FILE/stdinchi";
break;
case 75:
format = this.g.nihResolverFormat + "/%FILE/inchikey";
break;
case 83:
format = this.g.nihResolverFormat + "/%FILE/stdinchikey";
break;
case 47:
format = this.g.nihResolverFormat + "/%FILE/";
break;
default:
format = this.g.smilesUrlFormat;
break;
}
return (withPrefix ? "MOL3D::" : "") + JU.PT.formatStringS(format, "FILE", id);
case 63:
case 45:
case 95:
var isDiff = id.startsWith("*") || id.startsWith("=");
if (isDiff) id = id.substring(1);
var ciftype = null;
pt = id.indexOf(".");
if (pt >= 0) {
ciftype = id.substring(pt + 1);
id = id.substring(0, pt);
}var checkXray = id.startsWith("density");
if (checkXray) id = "em" + id.substring(7);
if (id.equals("emdb") || id.equals("em")) id += "/";
if (id.startsWith("em/")) id = "emdb" + id.substring(2);
if (id.startsWith("emdb/")) {
id = id.substring(5);
if (id.length == 0) id = "=";
 else if (id.startsWith("*")) id = "=" + id.substring(1);
var emdext = "#-sigma=10";
if (id.startsWith("=")) {
id = (id.equals("=") ? this.getPdbID() : id.substring(1));
if (id == null || type == '?') return id;
var q = JV.JC.resolveDataBase("emdbquery", id, null);
var data = this.fm.cacheGet(q, false);
if (data == null) {
this.showString("retrieving " + q, false);
data = this.getFileAsString(q);
if (data == null) {
this.showString("EM retrieve failed for " + id, false);
if (!checkXray) return null;
data = "FAILED";
} else {
this.showString(data, false);
}this.fm.cachePut(q, data);
}pt = data.indexOf("EMD-");
if (pt >= 0) {
id = data.substring(pt + 4);
pt = id.indexOf('\n');
if (pt > 0) id = id.substring(0, pt);
pt = id.indexOf(",");
if (pt > 0) {
emdext = "#-cutoff=" + id.substring(pt + 1);
id = id.substring(0, pt);
}} else {
if (!checkXray) return null;
emdext = null;
}}if (emdext != null) return JV.JC.resolveDataBase("emdbmap" + (type == '-' ? "server" : ""), id, null) + emdext;
}id = JV.JC.resolveDataBase((isDiff ? "pdbemapdiff" : "pdbemap") + (type == '-' ? "server" : ""), id, null);
if ("cif".equals(ciftype)) {
id = id.$replace("bcif", "cif");
}break;
}
return id;
}, "~B,~S,~S,~B");
Clazz.defineMethod(c$, "getDBID", 
function(type){
return this.prompt("load a " + type, "", null, false);
}, "~S");
Clazz.defineMethod(c$, "checkCIR", 
function(forceCheck){
if (this.cirChecked && !forceCheck || this.g.resolverResolver == null) return;
try {
this.g.removeParam("_cirStatus");
var m = this.getModelSetAuxiliaryInfo();
m.remove("cirInfo");
var s = this.getFileAsString(this.g.resolverResolver);
System.out.println(s);
var map = this.parseJSONMap(s);
m.put("cirInfo", map);
this.ms.msInfo = m;
s = map.get("status");
this.g.setO("_cirStatus", s);
this.g.setCIR(map.get("rfc6570Template"), !this.isSilent);
if (!this.isSilent) JU.Logger.info("Viewer.checkCIR _.cirInfo.status = " + s);
} catch (t) {
System.out.println("Viewer.checkCIR failed at " + this.g.resolverResolver + ": " + t);
}
this.cirChecked = true;
}, "~B");
Clazz.defineMethod(c$, "getStandardLabelFormat", 
function(type){
switch (type) {
default:
case 0:
return "%[identify]";
case 1:
return this.g.defaultLabelXYZ;
case 2:
return this.g.defaultLabelPDB;
}
}, "~N");
Clazz.defineMethod(c$, "getAdditionalHydrogens", 
function(bsAtoms, vConnections, flags){
if (bsAtoms == null) bsAtoms = this.bsA();
var nTotal =  Clazz.newIntArray (1, 0);
var pts = this.ms.calculateHydrogens(bsAtoms, nTotal, vConnections, flags);
var points =  new Array(nTotal[0]);
for (var i = 0, pt = 0; i < pts.length; i++) if (pts[i] != null) for (var j = 0; j < pts[i].length; j++) points[pt++] = pts[i][j];


return points;
}, "JU.BS,JU.Lst,~N");
Clazz.overrideMethod(c$, "setMarBond", 
function(marBond){
this.g.bondRadiusMilliAngstroms = marBond;
this.g.setI("bondRadiusMilliAngstroms", marBond);
this.setShapeSize(1, marBond * 2, JU.BSUtil.setAll(this.ms.ac));
}, "~N");
Clazz.defineMethod(c$, "setHoverLabel", 
function(strLabel){
this.shm.loadShape(35);
this.setShapeProperty(35, "label", strLabel);
this.setHoverEnabled(strLabel != null);
this.g.setO("_hoverLabel", this.hoverLabel = strLabel);
if (!this.hoverEnabled && !this.sm.haveHoverCallback()) this.startHoverWatcher(false);
}, "~S");
Clazz.defineMethod(c$, "setHoverEnabled", 
function(tf){
this.hoverEnabled = tf;
this.g.setB("_hoverEnabled", tf);
}, "~B");
Clazz.defineMethod(c$, "hoverOn", 
function(atomIndex, isLabel){
this.g.removeParam("_objecthovered");
this.g.setI("_atomhovered", atomIndex);
this.g.setO("_hoverLabel", this.hoverLabel);
this.g.setUserVariable("hovered", JS.SV.getVariable(JU.BSUtil.newAndSetBit(atomIndex)));
if (this.sm.haveHoverCallback()) this.sm.setStatusAtomHovered(atomIndex, this.getAtomInfoXYZ(atomIndex, 2));
if (!this.hoverEnabled || this.eval != null && this.isScriptExecuting() || atomIndex == this.hoverAtomIndex || this.g.hoverDelayMs == 0 || !this.slm.isInSelectionSubset(atomIndex)) return;
var label = (isLabel ? J.i18n.GT.$("Drag to move label") : this.isModelKitOpen() || this.isModelkitPickingActive() ? this.getModelkit(false).setProperty("hoverlabel", Integer.$valueOf(atomIndex)) : null);
this.shm.loadShape(35);
if (label != null && (!isLabel || this.ms.at[atomIndex].isVisible(512))) {
this.setShapeProperty(35, "specialLabel", label);
}this.setShapeProperty(35, "text", this.hoverText = null);
this.setShapeProperty(35, "target", Integer.$valueOf(this.hoverAtomIndex = atomIndex));
this.refresh(3, "hover on atom");
}, "~N,~B");
Clazz.defineMethod(c$, "isModelkitPickingActive", 
function(){
if (this.acm.getAtomPickingMode() == 32) return true;
switch (this.acm.getBondPickingMode()) {
case 34:
case 33:
case 8:
case 35:
return this.g.bondPicking;
}
return false;
});
Clazz.defineMethod(c$, "isModelkitPickingRotateBond", 
function(){
return (this.acm.getBondPickingMode() == 34);
});
Clazz.defineMethod(c$, "hoverOnPt", 
function(x, y, text, id, pt){
if (this.eval != null && this.isScriptExecuting()) return;
this.g.setO("_hoverLabel", text);
if (id != null && pt != null) {
this.g.setO("_objecthovered", id);
this.g.setI("_atomhovered", -1);
this.g.setUserVariable("hovered", JS.SV.getVariable(pt));
if (this.sm.haveHoverCallback()) this.sm.setStatusObjectHovered(id, text, pt);
}if (!this.hoverEnabled) return;
this.shm.loadShape(35);
if (this.gdata.antialiasEnabled) {
x <<= 1;
y <<= 1;
}this.setShapeProperty(35, "xy", JU.P3i.new3(x, y, 0));
this.setShapeProperty(35, "target", null);
this.setShapeProperty(35, "specialLabel", null);
this.setShapeProperty(35, "text", text);
this.hoverAtomIndex = -1;
this.hoverText = text;
this.refresh(3, "hover on point");
}, "~N,~N,~S,~S,JU.T3");
Clazz.defineMethod(c$, "hoverOff", 
function(){
try {
if ((this.isModelKitOpen() || this.modelkit != null && this.modelkit.wasRotating()) && !this.isModelkitPickingRotateBond()) this.highlight(null);
if (!this.hoverEnabled) return;
var isHover = (this.hoverText != null || this.hoverAtomIndex >= 0);
if (this.hoverAtomIndex >= 0) {
this.setShapeProperty(35, "target", null);
this.hoverAtomIndex = -1;
}if (this.hoverText != null) {
this.setShapeProperty(35, "text", null);
this.hoverText = null;
}this.setShapeProperty(35, "specialLabel", null);
if (isHover) this.refresh(3, "hover off");
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
});
Clazz.overrideMethod(c$, "setDebugScript", 
function(debugScript){
this.g.debugScript = debugScript;
this.g.setB("debugScript", debugScript);
if (this.eval != null) this.eval.setDebugging();
}, "~B");
Clazz.defineMethod(c$, "clearClickCount", 
function(){
this.setTainted(true);
});
Clazz.defineMethod(c$, "setCursor", 
function(cursor){
if (this.$isKiosk || this.currentCursor == cursor || this.multiTouch || !this.haveDisplay) return;
this.apiPlatform.setCursor(this.currentCursor = cursor, this.display);
}, "~N");
Clazz.defineMethod(c$, "setPickingMode", 
function(strMode, pickingMode){
if (!this.haveDisplay) return;
var mode = this.acm.getAtomPickingMode();
this.showSelected = false;
var option = null;
if (strMode != null) {
var pt = strMode.indexOf("_");
if (pt >= 0) {
option = strMode.substring(pt + 1);
strMode = strMode.substring(0, pt);
}pickingMode = JV.ActionManager.getPickingMode(strMode);
}if (pickingMode < 0) pickingMode = 1;
this.acm.setPickingMode(pickingMode);
var name = JV.ActionManager.getPickingModeName(this.acm.getAtomPickingMode());
this.g.setO("picking", name);
if (this.modelkit != null) {
this.modelkit.setProperty("atompickingmode", name);
this.acm.setPickingMode(pickingMode);
switch (pickingMode) {
case 1:
if (pickingMode != mode) this.setModelKitMode(false);
break;
case 8:
case 35:
this.modelkit.setProperty("bondpickingmode", strMode.toLowerCase());
break;
}
}if (option == null || option.length == 0) return;
option = Character.toUpperCase(option.charAt(0)) + (option.length == 1 ? "" : option.substring(1, 2));
switch (pickingMode) {
case 32:
this.getModelkit(false).setProperty("atomtype", option);
break;
case 33:
this.setBooleanPropertyTok("bondPicking", 603979814, true);
this.getModelkit(false).setProperty("bondtype", option);
break;
default:
JU.Logger.error("Bad picking mode: " + strMode + "_" + option);
}
}, "~S,~N");
Clazz.defineMethod(c$, "getPickingMode", 
function(){
return (this.haveDisplay ? this.acm.getAtomPickingMode() : 0);
});
Clazz.defineMethod(c$, "setPickingStyle", 
function(style, pickingStyle){
if (!this.haveDisplay) return;
if (style != null) pickingStyle = JV.ActionManager.getPickingStyleIndex(style);
if (pickingStyle < 0) pickingStyle = 0;
this.acm.setPickingStyle(pickingStyle);
this.g.setO("pickingStyle", JV.ActionManager.getPickingStyleName(this.acm.getPickingStyle()));
}, "~S,~N");
Clazz.defineMethod(c$, "getDrawHover", 
function(){
return this.haveDisplay && this.g.drawHover;
});
Clazz.defineMethod(c$, "getAtomInfo", 
function(atomOrPointIndex){
if (this.ptTemp == null) this.ptTemp =  new JU.P3();
return (atomOrPointIndex >= 0 ? this.ms.getAtomInfo(atomOrPointIndex, null, this.ptTemp) : this.shm.getShapePropertyIndex(6, "pointInfo", -atomOrPointIndex));
}, "~N");
Clazz.defineMethod(c$, "getAtomInfoXYZ", 
function(atomIndex, mode){
var atom = this.ms.at[atomIndex];
if (mode == 4) return this.getChimeMessenger().getInfoXYZ(atom);
if (this.ptTemp == null) this.ptTemp =  new JU.P3();
return atom.getIdentityXYZ(this.ptTemp, mode);
}, "~N,~N");
Clazz.defineMethod(c$, "setSync", 
function(){
if (this.sm.doSync()) this.sm.setSync(null);
});
Clazz.overrideMethod(c$, "setJmolCallbackListener", 
function(listener){
this.sm.cbl = listener;
}, "J.api.JmolCallbackListener");
Clazz.overrideMethod(c$, "setJmolStatusListener", 
function(listener){
this.sm.cbl = this.sm.jsl = listener;
}, "J.api.JmolStatusListener");
Clazz.defineMethod(c$, "getStatusChanged", 
function(statusNameList){
return (statusNameList == null ? null : this.sm.getStatusChanged(statusNameList));
}, "~S");
Clazz.defineMethod(c$, "menuEnabled", 
function(){
return (!this.g.disablePopupMenu && this.getPopupMenu() != null);
});
Clazz.defineMethod(c$, "setStatusDragDropped", 
function(mode, x, y, fileName, retType){
if (mode == 0) {
this.g.setO("_fileDropped", fileName);
this.g.setUserVariable("doDrop", JS.SV.vT);
this.g.setUserVariable("dropFileType", JS.SV.newS(""));
this.g.setUserVariable("dropFileName", JS.SV.newS(fileName));
}var handled = this.sm.setStatusDragDropped(mode, x, y, fileName, retType);
var type = this.getP("dropFileType").toString();
if (type.length > 0 && retType != null) {
retType[0] = type;
}return (!handled || this.getP("doDrop").toString().equals("true"));
}, "~N,~N,~N,~S,~A");
Clazz.defineMethod(c$, "setStatusResized", 
function(width, height){
this.sm.setStatusResized(width, height);
}, "~N,~N");
Clazz.defineMethod(c$, "scriptStatus", 
function(strStatus){
this.setScriptStatus(strStatus, "", 0, null);
}, "~S");
Clazz.defineMethod(c$, "scriptStatusMsg", 
function(strStatus, statusMessage){
this.setScriptStatus(strStatus, statusMessage, 0, null);
}, "~S,~S");
Clazz.defineMethod(c$, "setScriptStatus", 
function(strStatus, statusMessage, msWalltime, strErrorMessageUntranslated){
this.sm.setScriptStatus(strStatus, statusMessage, msWalltime, strErrorMessageUntranslated);
}, "~S,~S,~N,~S");
Clazz.overrideMethod(c$, "showUrl", 
function(urlString){
if (urlString == null) return;
if (urlString.indexOf(":") < 0) {
var base = this.fm.getAppletDocumentBase();
if (base === "") base = this.fm.getFullPathName(false);
if (base.indexOf("/") >= 0) {
base = base.substring(0, base.lastIndexOf("/") + 1);
} else if (base.indexOf("\\") >= 0) {
base = base.substring(0, base.lastIndexOf("\\") + 1);
}urlString = base + urlString;
}JU.Logger.info("showUrl:" + urlString);
this.sm.showUrl(urlString);
}, "~S");
Clazz.defineMethod(c$, "setMeshCreator", 
function(meshCreator){
this.shm.loadShape(24);
this.setShapeProperty(24, "meshCreator", meshCreator);
}, "~O");
Clazz.defineMethod(c$, "showConsole", 
function(showConsole){
if (!this.haveDisplay) return;
try {
if (this.appConsole == null && showConsole) this.getConsole();
this.appConsole.setVisible(true);
} catch (e) {
}
}, "~B");
Clazz.defineMethod(c$, "getConsole", 
function(){
this.getProperty("DATA_API", "getAppConsole", Boolean.TRUE);
return this.appConsole;
});
Clazz.overrideMethod(c$, "getParameter", 
function(key){
return this.getP(key);
}, "~S");
Clazz.defineMethod(c$, "getP", 
function(key){
return this.g.getParameter(key, true);
}, "~S");
Clazz.defineMethod(c$, "getPOrNull", 
function(key){
return this.g.getParameter(key, false);
}, "~S");
Clazz.defineMethod(c$, "unsetProperty", 
function(key){
key = key.toLowerCase();
if (key.equals("all") || key.equals("variables")) this.fm.setPathForAllFiles("");
this.g.unsetUserVariable(key);
}, "~S");
Clazz.overrideMethod(c$, "notifyStatusReady", 
function(isReady){
System.out.println("Jmol applet " + this.fullName + (isReady ? " ready" : " destroyed"));
if (!isReady) this.dispose();
this.sm.setStatusAppletReady(this.fullName, isReady);
}, "~B");
Clazz.overrideMethod(c$, "getBooleanProperty", 
function(key){
key = key.toLowerCase();
if (this.g.htBooleanParameterFlags.containsKey(key)) return this.g.htBooleanParameterFlags.get(key).booleanValue();
if (key.endsWith("p!")) {
if (this.acm == null) return false;
var s = this.acm.getPickingState().toLowerCase();
key = key.substring(0, key.length - 2) + ";";
return (s.indexOf(key) >= 0);
}if (key.equalsIgnoreCase("executionPaused")) return (this.eval != null && this.eval.isPaused());
if (key.equalsIgnoreCase("executionStepping")) return (this.eval != null && this.eval.isStepping());
if (key.equalsIgnoreCase("haveBFactors")) return (this.ms.getBFactors() != null);
if (key.equalsIgnoreCase("colorRasmol")) return this.cm.isDefaultColorRasmol;
if (key.equalsIgnoreCase("frank")) return this.getShowFrank();
if (key.equalsIgnoreCase("spinOn")) return this.tm.spinOn;
if (key.equalsIgnoreCase("isNavigating")) return this.tm.isNavigating();
if (key.equalsIgnoreCase("showSelections")) return this.selectionHalosEnabled;
if (this.g.htUserVariables.containsKey(key)) {
var t = this.g.getUserVariable(key);
if (t.tok == 1073742335) return true;
if (t.tok == 1073742334) return false;
}JU.Logger.error("vwr.getBooleanProperty(" + key + ") - unrecognized");
return false;
}, "~S");
Clazz.overrideMethod(c$, "getInt", 
function(tok){
switch (tok) {
case 553648132:
return this.am.animationFps;
case 553648139:
return this.g.dotDensity;
case 553648140:
return this.g.dotScale;
case 553648142:
return this.g.helixStep;
case 553648145:
return this.g.infoFontSize;
case 553648147:
return this.g.labelPointerWidth;
case 553648149:
return this.g.meshScale;
case 553648150:
return this.g.minimizationReportSteps;
case 553648153:
return this.g.minPixelSelRadius;
case 553648154:
return this.g.percentVdwAtom;
case 553648157:
return this.g.pickingSpinRate;
case 553648166:
return this.g.ribbonAspectRatio;
case 536870922:
return this.g.scriptDelay;
case 553648152:
return this.g.minimizationMaxAtoms;
case 553648170:
return this.g.smallMoleculeMaxAtoms;
case 553648183:
return this.g.strutSpacing;
case 553648184:
return this.stm.getUndoMax();
case 553648185:
return this.g.vectorTrail;
}
JU.Logger.error("viewer.getInt(" + JS.T.nameOf(tok) + ") - not listed");
return 0;
}, "~N");
Clazz.defineMethod(c$, "getDelayMaximumMs", 
function(){
return (this.haveDisplay ? this.g.delayMaximumMs : 1);
});
Clazz.defineMethod(c$, "getHermiteLevel", 
function(){
return (this.tm.spinOn && this.g.hermiteLevel > 0 ? 0 : this.g.hermiteLevel);
});
Clazz.defineMethod(c$, "getHoverDelay", 
function(){
return (this.isModelKitOpen() || this.isModelkitPickingActive() || this.getDrawHover() ? 20 : this.g.hoverDelayMs);
});
Clazz.overrideMethod(c$, "getBoolean", 
function(tok){
switch (tok) {
case 603979970:
return this.g.useMinimizationThread;
case 603979891:
return this.g.nboCharges;
case 603979856:
return this.g.hiddenLinesDashed;
case 1073742086:
return this.ms.getMSInfoB(JV.JC.getBoolName(4));
case 603979802:
return this.g.autoplayMovie;
case 603979797:
return !this.headless && this.g.allowAudio;
case 603979780:
return this.g.allowGestures;
case 603979784:
return this.g.allowMultiTouch;
case 603979785:
return this.g.allowRotateSelected;
case 603979792:
return this.g.appendNew;
case 603979794:
return this.g.applySymmetryToBonds;
case 603979796:
return this.g.atomPicking;
case 603979798:
return this.g.autoBond;
case 603979800:
return this.g.autoFps;
case 603979806:
return this.g.axesOrientationRasmol;
case 603979811:
return this.g.cartoonSteps;
case 603979810:
return this.g.cartoonBlocks;
case 603979821:
return this.g.checkCIR;
case 603979812:
return this.g.bondModeOr;
case 603979815:
return this.g.cartoonBaseEdges;
case 603979816:
return this.g.cartoonFancy;
case 603979817:
return this.g.cartoonLadders;
case 603979818:
return this.g.cartoonRibose;
case 603979819:
return this.g.cartoonRockets;
case 603979822:
return this.g.chainCaseSensitive || this.chainCaseSpecified;
case 603979823:
return this.g.cipRule6Full;
case 603979825:
return this.g.debugScript;
case 603979826:
return this.g.defaultStructureDSSP;
case 603979827:
return this.g.disablePopupMenu;
case 603979828:
return this.g.displayCellParameters;
case 603979830:
return this.g.dotSurface;
case 603979829:
return this.g.dotsSelectedOnly;
case 603979831:
return this.g.doublePrecision;
case 603979834:
return this.g.drawPicking;
case 603979838:
return this.g.elementKey;
case 603979846:
return this.g.fontCaching;
case 603979847:
return this.g.fontScaling;
case 603979848:
return this.g.forceAutoBond;
case 603979849:
return false;
case 603979850:
return this.g.greyscaleRendering;
case 603979852:
return this.g.hbondsBackbone;
case 603979853:
return this.g.hbondsRasmol;
case 603979854:
return this.g.hbondsSolid;
case 1612709894:
return this.g.rasmolHeteroSetting;
case 603979858:
return this.g.hideNameInPopup;
case 603979864:
return this.g.highResolutionFlag;
case 1612709900:
return this.g.rasmolHydrogenSetting;
case 603979867:
return this.g.isosurfaceKey;
case 603979869:
return this.g.jmolInJSpecView;
case 603979870:
return this.g.justifyMeasurements;
case 603979872:
return this.g.legacyAutoBonding;
case 603979873:
return this.g.legacyHAddition;
case 603979874:
return this.g.legacyJavaFloat;
case 603979876:
return this.g.logGestures;
case 603979877:
return this.g.measureAllModels;
case 603979878:
return this.g.measurementLabels;
case 603979879:
return this.g.messageStyleChime;
case 603983903:
return this.g.modelKitMode;
case 603979886:
return this.g.multipleBondBananas;
case 603979889:
return this.g.navigationMode;
case 603979890:
return this.g.navigationPeriodic;
case 603979893:
return this.g.partialDots;
case 603979894:
return this.g.pdbAddHydrogens;
case 603979896:
return this.g.pdbSequential;
case 603979898:
return this.g.preserveState;
case 603979900:
return this.refreshing;
case 603979901:
return this.g.ribbonBorder;
case 603979902:
return this.g.rocketBarrels;
case 603979892:
return this.g.noDelay;
case 603979906:
return this.g.selectAllModels;
case 603979920:
return this.g.showHiddenSelectionHalos;
case 603979922:
return this.g.showHydrogens;
case 603979926:
return this.g.showMeasurements;
case 603979927:
return this.g.showModVecs;
case 603979928:
return this.g.showMultipleBonds;
case 603979934:
return this.g.showTiming;
case 603979937:
return this.g.showUnitCellDetails;
case 603979939:
return this.g.slabByAtom;
case 603979940:
return this.g.slabByMolecule;
case 603979944:
return this.g.smartAromatic;
case 603979948:
return this.g.dotSolvent;
case 603979952:
return this.g.ssbondsBackbone;
case 603979955:
return this.g.strutsMultiple;
case 603979956:
return this.g.symmetryHermannMauguin;
case 603979960:
return this.g.testFlag1;
case 603979962:
return this.g.testFlag2;
case 603979964:
return this.g.testFlag3;
case 603979965:
return this.g.testFlag4;
case 603979966:
return this.g.traceAlpha;
case 603979967:
return this.g.translucent;
case 603979968:
return this.g.twistedSheets;
case 603979972:
return this.g.vectorsCentered;
case 603979973:
return this.g.vectorSymmetry;
case 603979975:
return this.g.waitForMoveTo;
case 603979978:
return this.g.zeroBasedXyzRasmol;
}
JU.Logger.error("viewer.getBoolean(" + JS.T.nameOf(tok) + ") - not listed");
return false;
}, "~N");
Clazz.defineMethod(c$, "allowEmbeddedScripts", 
function(){
return (this.g.allowEmbeddedScripts && !this.isPreviewOnly);
});
Clazz.defineMethod(c$, "getDragSelected", 
function(){
return (this.g.dragSelected && !this.g.modelKitMode);
});
Clazz.defineMethod(c$, "getBondsPickable", 
function(){
return (this.g.bondPicking || this.isModelkitPickingActive() || this.isModelKitOpen() && this.getModelkitPropertySafely("ismolecular") === Boolean.TRUE);
});
Clazz.defineMethod(c$, "isModelKitOpen", 
function(){
return this.g.modelKitMode && this.modelkit != null && !this.modelkit.isHidden();
});
Clazz.defineMethod(c$, "useMinimizationThread", 
function(){
return (this.g.useMinimizationThread && !this.autoExit);
});
Clazz.overrideMethod(c$, "getFloat", 
function(tok){
switch (tok) {
case 1153433601:
return this.g.particleRadius;
case 570425345:
return this.g.axesOffset;
case 570425346:
return this.g.axesScale;
case 570425348:
return this.g.bondTolerance;
case 570425353:
return this.g.defaultTranslucent;
case 570425352:
return this.g.defaultDrawArrowScale;
case 570425354:
return this.g.dipoleScale;
case 570425355:
return this.g.drawFontSize;
case 570425357:
return this.g.exportScale;
case 570425359:
return this.g.hbondsAngleMinimum;
case 570425361:
return this.g.hbondHXDistanceMaximum;
case 570425360:
return this.g.hbondNODistanceMaximum;
case 570425363:
return this.g.loadAtomDataTolerance;
case 570425364:
return this.g.minBondDistance;
case 1275072532:
return this.g.modulationScale;
case 570425370:
return this.g.multipleBondSpacing;
case 570425369:
return this.g.multipleBondRadiusFactor;
case 570425374:
return this.g.navigationSpeed;
case 570425382:
return this.g.pointGroupDistanceTolerance;
case 570425384:
return this.g.pointGroupLinearTolerance;
case 570425388:
return this.tm.modelRadius;
case 570425392:
return this.g.sheetSmoothing;
case 570425394:
return this.g.solventProbeRadius;
case 570425403:
return this.g.starWidth;
case 570425406:
return this.g.strutDefaultRadius;
case 570425408:
return this.g.strutLengthMaximum;
case 1648361473:
return this.g.vectorScale;
case 570425412:
return this.g.vibrationPeriod;
case 570425347:
return this.g.cartoonBlockHeight;
}
JU.Logger.error("viewer.getFloat(" + JS.T.nameOf(tok) + ") - not listed");
return 0;
}, "~N");
Clazz.overrideMethod(c$, "setStringProperty", 
function(key, value){
if (value == null || key == null || key.length == 0) return;
if (key.charAt(0) == '_') {
this.g.setO(key, value);
return;
}var tok = JS.T.getTokFromName(key);
switch (JS.T.getParamType(tok)) {
case 603979776:
this.setBooleanPropertyTok(key, tok, JS.SV.newV(4, value).asBoolean());
break;
case 553648128:
this.setIntPropertyTok(key, tok, JS.SV.newV(4, value).asInt());
break;
case 570425344:
this.setFloatPropertyTok(key, tok, JU.PT.parseFloat(value));
break;
default:
this.setStringPropertyTok(key, tok, value);
}
}, "~S,~S");
Clazz.defineMethod(c$, "setStringPropertyTok", 
function(key, tok, value){
switch (tok) {
case 545259567:
this.g.macroDirectory = value = (value == null || value.length == 0 ? "https://chemapps.stolaf.edu/jmol/macros" : value);
this.macros = null;
break;
case 545259570:
this.g.nihResolverFormat = value;
break;
case 545259521:
this.setAnimationMode(value);
return;
case 545259569:
this.g.nmrPredictFormat = value;
break;
case 545259548:
this.g.defaultDropScript = value;
break;
case 545259572:
value = this.fm.setPathForAllFiles(value);
break;
case 545259558:
this.setUnits(value, false);
return;
case 545259560:
if (!this.g.forceField.equals(value)) {
this.g.forceField = value = ("UFF".equalsIgnoreCase(value) ? "UFF" : "UFF2D".equalsIgnoreCase(value) ? "UFF2D" : "MMFF2D".equalsIgnoreCase(value) ? "MMFF2D" : "MMFF");
this.minimizer = null;
}break;
case 545259571:
this.g.nmrUrlFormat = value;
break;
case 545259568:
this.setUnits(value, true);
return;
case 545259565:
this.g.pdbLoadLigandFormat = value;
break;
case 545259543:
this.g.defaultLabelPDB = value;
break;
case 545259544:
this.g.defaultLabelXYZ = value;
break;
case 545259549:
this.g.defaultLoadFilter = value;
break;
case 545259566:
value = this.getOutputManager().setLogFile(value);
if (value == null) return;
break;
case 545259559:
break;
case 545259524:
this.g.atomTypes = value;
break;
case 545259538:
break;
case 545259576:
this.g.pickLabel = value;
break;
case 545259580:
if (value.length == 2 && value.startsWith("R")) this.g.quaternionFrame = value.substring(0, 2);
 else this.g.quaternionFrame = "" + (value.toLowerCase() + "p").charAt(0);
if (!JU.PT.isOneOf(this.g.quaternionFrame, "RC;RP;a;b;c;n;p;q;x;")) this.g.quaternionFrame = "p";
this.ms.haveStraightness = false;
break;
case 545259555:
this.setVdwStr(value);
return;
case 545259563:
 new J.i18n.GT(this, value);
var language = J.i18n.GT.getLanguage();
this.modelkit = null;
if (this.jmolpopup != null) {
this.jmolpopup.jpiDispose();
this.jmolpopup = null;
this.getPopupMenu();
}this.sm.setCallbackFunction("language", language);
value = J.i18n.GT.getLanguage();
break;
case 545259564:
this.g.loadFormat = value;
break;
case 545259534:
this.setObjectColor("background", value);
return;
case 545259528:
this.setObjectColor("axis1", value);
return;
case 545259530:
this.setObjectColor("axis2", value);
return;
case 545259532:
this.setObjectColor("axis3", value);
return;
case 545259536:
this.setObjectColor("boundbox", value);
return;
case 545259586:
this.setObjectColor("unitcell", value);
return;
case 545259578:
this.setPropertyColorScheme(value, false, false);
break;
case 545259562:
this.shm.loadShape(35);
this.setShapeProperty(35, "atomLabel", value);
break;
case 545259547:
this.g.defaultDistanceLabel = value;
break;
case 545259542:
this.g.defaultAngleLabel = value;
break;
case 545259554:
this.g.defaultTorsionLabel = value;
break;
case 545259550:
this.g.defaultLoadScript = value;
break;
case 545259522:
this.fm.setAppletProxy(value);
break;
case 545259546:
if (value == null) value = "";
value = value.$replace('\\', '/');
this.g.defaultDirectory = value;
break;
case 545259561:
this.g.helpPath = value;
break;
case 545259552:
if (!value.equalsIgnoreCase("RasMol") && !value.equalsIgnoreCase("PyMOL")) value = "Jmol";
this.setDefaultsType(value);
break;
case 545259545:
this.setDefaultColors(value.equalsIgnoreCase("rasmol"));
return;
case 545259573:
this.setPickingMode(value, 0);
return;
case 545259574:
this.setPickingStyle(value, 0);
return;
case 545259540:
break;
default:
if (key.toLowerCase().endsWith("callback")) {
this.sm.setCallbackFunction(key, (value.length == 0 || value.equalsIgnoreCase("none") ? null : value));
break;
}if (!this.g.htNonbooleanParameterValues.containsKey(key.toLowerCase())) {
this.g.setUserVariable(key, JS.SV.newV(4, value));
return;
}break;
}
this.g.setO(key, value);
}, "~S,~N,~S");
Clazz.overrideMethod(c$, "setFloatProperty", 
function(key, value){
if (key == null || key.length == 0) return;
if (key.charAt(0) == '_') {
this.g.setF(key, value);
return;
}var tok = JS.T.getTokFromName(key);
switch (JS.T.getParamType(tok)) {
case 545259520:
this.setStringPropertyTok(key, tok, "" + value);
break;
case 603979776:
this.setBooleanPropertyTok(key, tok, value != 0);
break;
case 553648128:
this.setIntPropertyTok(key, tok, Clazz.floatToInt(value));
break;
case 570425344:
if (Float.isNaN(value)) return;
default:
this.setFloatPropertyTok(key, tok, value);
}
}, "~S,~N");
Clazz.defineMethod(c$, "setFloatPropertyTok", 
function(key, tok, value){
switch (tok) {
case 570425347:
this.g.cartoonBlockHeight = value;
break;
case 570425366:
this.ms.setModulation(null, false, null, false);
this.g.modulationScale = value = Math.max(0.1, value);
this.ms.setModulation(null, true, null, false);
break;
case 570425381:
this.g.particleRadius = Math.abs(value);
break;
case 570425355:
this.g.drawFontSize = value;
this.shm.setShapePropertyBs(22, "font", null, null);
break;
case 570425357:
this.g.exportScale = value;
break;
case 570425403:
this.g.starWidth = value;
break;
case 570425369:
this.g.multipleBondRadiusFactor = value;
break;
case 570425370:
this.g.multipleBondSpacing = value;
break;
case 570425393:
this.tm.setSlabRange(value);
break;
case 570425365:
this.g.minimizationCriterion = value;
break;
case 570425358:
if (this.haveDisplay) this.acm.setGestureSwipeFactor(value);
break;
case 570425367:
if (this.haveDisplay) this.acm.setMouseDragFactor(value);
break;
case 570425368:
if (this.haveDisplay) this.acm.setMouseWheelFactor(value);
break;
case 570425408:
this.g.strutLengthMaximum = value;
break;
case 570425406:
this.g.strutDefaultRadius = value;
break;
case 570425376:
this.setSpin("X", Clazz.floatToInt(value));
break;
case 570425378:
this.setSpin("Y", Clazz.floatToInt(value));
break;
case 570425380:
this.setSpin("Z", Clazz.floatToInt(value));
break;
case 570425371:
if (Float.isNaN(value)) return;
this.setSpin("FPS", Clazz.floatToInt(value));
break;
case 570425363:
this.g.loadAtomDataTolerance = value;
break;
case 570425359:
this.g.hbondsAngleMinimum = value;
break;
case 570425361:
this.g.hbondHXDistanceMaximum = value;
break;
case 570425360:
this.g.hbondNODistanceMaximum = value;
break;
case 570425382:
this.g.pointGroupDistanceTolerance = value;
break;
case 570425384:
this.g.pointGroupLinearTolerance = value;
break;
case 570425356:
this.g.ellipsoidAxisDiameter = value;
break;
case 570425398:
this.setSpin("x", Clazz.floatToInt(value));
break;
case 570425400:
this.setSpin("y", Clazz.floatToInt(value));
break;
case 570425402:
this.setSpin("z", Clazz.floatToInt(value));
break;
case 570425396:
this.setSpin("fps", Clazz.floatToInt(value));
break;
case 570425352:
this.g.defaultDrawArrowScale = value;
break;
case 570425353:
this.g.defaultTranslucent = value;
break;
case 570425345:
this.setAxesScale(tok, value);
break;
case 570425346:
this.setAxesScale(tok, value);
break;
case 570425416:
this.tm.visualRangeAngstroms = value;
this.refresh(1, "set visualRange");
break;
case 570425372:
this.setNavigationDepthPercent(value);
break;
case 570425374:
this.g.navigationSpeed = value;
break;
case 570425373:
this.tm.setNavigationSlabOffsetPercent(value);
break;
case 570425350:
this.tm.setCameraDepthPercent(value, false);
this.refresh(1, "set cameraDepth");
return;
case 570425388:
this.setRotationRadius(value, true);
return;
case 570425362:
this.g.hoverDelayMs = Clazz.floatToInt(value * 1000);
break;
case 570425392:
this.g.sheetSmoothing = value;
break;
case 570425354:
value = JV.Viewer.checkFloatRange(value, -10, 10);
this.g.dipoleScale = value;
break;
case 570425404:
this.tm.setStereoDegrees(value);
break;
case 1648361473:
this.setVectorScale(value);
return;
case 570425412:
this.setVibrationPeriod(value);
return;
case 570425414:
this.setVibrationScale(value);
return;
case 570425348:
this.setBondTolerance(value);
return;
case 570425364:
this.setMinBondDistance(value);
return;
case 570425390:
this.tm.setScaleAngstromsPerInch(value);
break;
case 570425394:
value = JV.Viewer.checkFloatRange(value, 0, 10);
this.g.solventProbeRadius = value;
break;
default:
if (!this.g.htNonbooleanParameterValues.containsKey(key.toLowerCase())) {
this.g.setUserVariable(key, JS.SV.newF(value));
return;
}}
this.g.setF(key, value);
}, "~S,~N,~N");
Clazz.overrideMethod(c$, "setIntProperty", 
function(key, value){
if (value == -2147483648 || key == null || key.length == 0) return;
if (key.charAt(0) == '_') {
this.g.setI(key, value);
return;
}var tok = JS.T.getTokFromName(key);
switch (JS.T.getParamType(tok)) {
case 545259520:
this.setStringPropertyTok(key, tok, "" + value);
break;
case 603979776:
this.setBooleanPropertyTok(key, tok, value != 0);
break;
case 570425344:
this.setFloatPropertyTok(key, tok, value);
break;
default:
this.setIntPropertyTok(key, tok, value);
}
}, "~S,~N");
Clazz.defineMethod(c$, "setIntPropertyTok", 
function(key, tok, value){
switch (tok) {
case 553648150:
this.g.minimizationReportSteps = Math.min(Math.max(value, 1), 20);
break;
case 553648184:
this.stm.setUndoMax(value);
break;
case 553648147:
this.g.labelPointerWidth = value;
break;
case 553648152:
this.g.minimizationMaxAtoms = value;
break;
case 553648145:
this.g.infoFontSize = Math.max(0, value);
break;
case 553648167:
case 553648144:
case 553648168:
value = this.eval.setStatic(tok, value);
break;
case 553648185:
this.g.vectorTrail = value;
break;
case 553648136:
value = (value == 0 ? 0 : 1);
this.g.bondingVersion = JU.Elements.bondingVersion = value;
break;
case 553648135:
this.gdata.setCelPower(value);
break;
case 553648129:
this.gdata.setAmbientOcclusion(value);
break;
case 553648158:
this.g.platformSpeed = Math.min(Math.max(value, 0), 10);
break;
case 553648149:
this.g.meshScale = value;
break;
case 553648153:
this.g.minPixelSelRadius = value;
break;
case 553648146:
this.g.isosurfacePropertySmoothingPower = value;
break;
case 553648165:
this.g.repaintWaitMs = value;
break;
case 553648170:
this.g.smallMoleculeMaxAtoms = value;
break;
case 553648151:
this.g.minimizationSteps = value;
break;
case 553648183:
this.g.strutSpacing = value;
break;
case 553648156:
value = JV.Viewer.checkIntRange(value, 0, 1000);
this.gdata.setPhongExponent(value);
break;
case 553648142:
this.g.helixStep = value;
this.ms.haveStraightness = false;
break;
case 553648140:
this.g.dotScale = value;
break;
case 553648139:
this.g.dotDensity = value;
break;
case 553648137:
this.g.delayMaximumMs = value;
break;
case 553648148:
JU.Logger.setLogLevel(value);
JU.Logger.info("logging level set to " + value);
this.g.setI("logLevel", value);
if (this.eval != null) this.eval.setDebugging();
return;
case 553648133:
this.setAxesMode(value == 2 ? 603979808 : value == 1 ? 603979804 : 603979809);
return;
case 553648178:
this.setStrandCount(0, value);
return;
case 553648182:
this.setStrandCount(12, value);
return;
case 553648180:
this.setStrandCount(13, value);
return;
case 553648155:
return;
case 536870922:
this.g.scriptDelay = value;
break;
case 553648176:
if (value < 0) value = JV.Viewer.checkIntRange(value, -10, -1);
 else value = JV.Viewer.checkIntRange(value, 0, 100);
this.gdata.setSpecularPower(value);
break;
case 553648172:
value = JV.Viewer.checkIntRange(-value, -10, -1);
this.gdata.setSpecularPower(value);
break;
case 553648134:
this.setMarBond(value);
return;
case 536870924:
this.setBooleanPropertyTok(key, tok, value == 1);
return;
case 553648174:
value = JV.Viewer.checkIntRange(value, 0, 100);
this.gdata.setSpecularPercent(value);
break;
case 553648138:
value = JV.Viewer.checkIntRange(value, 0, 100);
this.gdata.setDiffusePercent(value);
break;
case 553648130:
value = JV.Viewer.checkIntRange(value, 0, 100);
this.gdata.setAmbientPercent(value);
break;
case 553648186:
this.tm.zDepthToPercent(value);
break;
case 553648188:
this.tm.zSlabToPercent(value);
break;
case 554176526:
this.tm.depthToPercent(value);
break;
case 554176565:
this.tm.slabToPercent(value);
break;
case 553648190:
this.g.zShadePower = value = Math.max(value, 0);
break;
case 553648166:
this.g.ribbonAspectRatio = value;
break;
case 553648157:
this.g.pickingSpinRate = (value < 1 ? 1 : value);
break;
case 553648132:
this.setAnimationFps(value);
return;
case 553648154:
this.setPercentVdwAtom(value);
break;
case 553648143:
this.g.hermiteLevel = value;
break;
case 553648141:
case 553648161:
case 553648160:
case 553648162:
case 553648164:
break;
default:
if (!this.g.htNonbooleanParameterValues.containsKey(key)) {
this.g.setUserVariable(key, JS.SV.newI(value));
return;
}}
this.g.setI(key, value);
}, "~S,~N,~N");
c$.checkIntRange = Clazz.defineMethod(c$, "checkIntRange", 
function(value, min, max){
return (value < min ? min : value > max ? max : value);
}, "~N,~N,~N");
c$.checkFloatRange = Clazz.defineMethod(c$, "checkFloatRange", 
function(value, min, max){
return (value < min ? min : value > max ? max : value);
}, "~N,~N,~N");
Clazz.overrideMethod(c$, "setBooleanProperty", 
function(key, value){
if (key == null || key.length == 0) return;
if (key.charAt(0) == '_') {
this.g.setB(key, value);
return;
}var tok = JS.T.getTokFromName(key);
switch (JS.T.getParamType(tok)) {
case 545259520:
this.setStringPropertyTok(key, tok, "");
break;
case 553648128:
this.setIntPropertyTok(key, tok, value ? 1 : 0);
break;
case 570425344:
this.setFloatPropertyTok(key, tok, value ? 1 : 0);
break;
default:
this.setBooleanPropertyTok(key, tok, value);
}
}, "~S,~B");
Clazz.defineMethod(c$, "setBooleanPropertyTok", 
function(key, tok, value){
var doRepaint = true;
switch (tok) {
case 603979838:
this.g.elementKey = value;
this.getModelkit(false).setProperty("setelementkey", Boolean.$valueOf(value));
break;
case 603979956:
this.g.symmetryHermannMauguin = value;
break;
case 603979831:
value = new Boolean (value & JV.Viewer.isJS).valueOf();
this.g.doublePrecision = value;
JV.Viewer.isHighPrecision = this.g.doublePrecision;
this.setBooleanPropertyTok("legacyJavaFloat", 603979874, value);
break;
case 603979821:
this.g.checkCIR = value;
if (value) {
this.checkCIR(true);
}break;
case 603979823:
this.g.cipRule6Full = value;
break;
case 603979802:
this.g.autoplayMovie = value;
break;
case 603979797:
value = false;
this.g.allowAudio = value;
break;
case 603979892:
this.g.noDelay = value;
break;
case 603979891:
this.g.nboCharges = value;
break;
case 603979856:
this.g.hiddenLinesDashed = value;
break;
case 603979886:
this.g.multipleBondBananas = value;
break;
case 603979884:
this.g.modulateOccupancy = value;
break;
case 603979874:
if (value || !this.g.doublePrecision) this.g.legacyJavaFloat = value;
value = this.g.legacyJavaFloat;
break;
case 603979927:
this.g.showModVecs = value;
break;
case 603979937:
this.g.showUnitCellDetails = value;
break;
case 603979849:
doRepaint = false;
break;
case 603979972:
this.g.vectorsCentered = value;
break;
case 603979810:
this.g.cartoonBlocks = value;
break;
case 603979811:
this.g.cartoonSteps = value;
break;
case 603979818:
this.g.cartoonRibose = value;
break;
case 603979840:
this.g.ellipsoidArrows = value;
break;
case 603979967:
this.g.translucent = value;
break;
case 603979817:
this.g.cartoonLadders = value;
break;
case 603979968:
var b = this.g.twistedSheets;
this.g.twistedSheets = value;
if (b != value) this.checkCoordinatesChanged(null);
break;
case 603979820:
this.gdata.setCel(value);
break;
case 603979816:
this.g.cartoonFancy = value;
break;
case 603979934:
this.g.showTiming = value;
break;
case 603979973:
this.g.vectorSymmetry = value;
break;
case 603979867:
this.g.isosurfaceKey = value;
break;
case 603979893:
this.g.partialDots = value;
break;
case 603979872:
this.g.legacyAutoBonding = value;
break;
case 603979826:
this.g.defaultStructureDSSP = value;
break;
case 603979835:
this.g.dsspCalcHydrogen = value;
break;
case 603979782:
this.g.allowModelkit = value;
if (!value) this.setModelKitMode(false);
break;
case 603983903:
this.setModelKitMode(value);
break;
case 603979887:
this.g.multiProcessor = value && (JV.Viewer.nProcessors > 1);
break;
case 603979885:
this.g.monitorEnergy = value;
break;
case 603979853:
this.g.hbondsRasmol = value;
break;
case 603979880:
this.g.minimizationRefresh = value;
break;
case 603979881:
this.g.minimizationSilent = value;
break;
case 603979866:
if (value) {
this.$isKiosk = true;
this.g.disablePopupMenu = true;
if (this.display != null) this.apiPlatform.setTransparentCursor(this.display);
}break;
case 603979975:
this.g.waitForMoveTo = value;
break;
case 603979875:
this.g.logCommands = true;
break;
case 603979876:
this.g.logGestures = true;
break;
case 603979784:
this.g.allowMultiTouch = value;
break;
case 603979898:
this.g.preserveState = value;
this.ms.setPreserveState(value);
this.undoMoveAction(4165, -2);
break;
case 603979955:
this.g.strutsMultiple = value;
break;
case 603979845:
break;
case 603979939:
this.g.slabByAtom = value;
break;
case 603979940:
this.g.slabByMolecule = value;
break;
case 603979903:
this.g.saveProteinStructureState = value;
break;
case 603979780:
this.g.allowGestures = value;
break;
case 603979865:
this.g.imageState = value;
break;
case 603979970:
this.g.useMinimizationThread = value;
break;
case 603979781:
this.g.allowKeyStrokes = value;
break;
case 603979832:
this.g.dragSelected = value;
this.showSelected = false;
break;
case 603979924:
this.g.showKeyStrokes = value;
break;
case 603979846:
this.g.fontCaching = value;
break;
case 603979796:
this.g.atomPicking = value;
break;
case 603979814:
this.highlight(null);
this.g.bondPicking = value;
break;
case 603979906:
this.g.selectAllModels = value;
if (value) this.slm.setSelectionSubset(null);
 else this.am.setSelectAllSubset(false);
break;
case 603979879:
this.g.messageStyleChime = value;
break;
case 603979896:
this.g.pdbSequential = value;
break;
case 603979894:
this.g.pdbAddHydrogens = value;
break;
case 603979895:
this.g.pdbGetHeader = value;
break;
case 603979841:
this.g.ellipsoidAxes = value;
break;
case 603979839:
this.g.ellipsoidArcs = value;
break;
case 603979842:
this.g.ellipsoidBall = value;
break;
case 603979843:
this.g.ellipsoidDots = value;
break;
case 603979844:
this.g.ellipsoidFill = value;
break;
case 603979847:
this.g.fontScaling = value;
break;
case 603979957:
this.setSyncTarget(0, value);
break;
case 603979958:
this.setSyncTarget(1, value);
break;
case 603979977:
this.g.wireframeRotation = value;
break;
case 603979868:
this.g.isosurfacePropertySmoothing = value;
break;
case 603979834:
this.g.drawPicking = value;
break;
case 603979786:
case 603979790:
case 603979788:
this.setAntialias(tok, value);
break;
case 603979944:
this.g.smartAromatic = value;
break;
case 603979794:
this.setApplySymmetryToBonds(value);
break;
case 603979792:
this.g.appendNew = value;
break;
case 603979800:
this.g.autoFps = value;
break;
case 603979971:
JU.DF.setUseNumberLocalization(this.g.useNumberLocalization = value);
break;
case 603979918:
case 1611272202:
key = "showFrank";
this.setFrankOn(value);
break;
case 1612709912:
key = "solventProbe";
this.g.dotSolvent = value;
break;
case 603979948:
this.g.dotSolvent = value;
break;
case 603979785:
this.g.allowRotateSelected = value;
break;
case 603979783:
this.g.allowMoveAtoms = value;
this.showSelected = false;
break;
case 536870922:
this.setIntPropertyTok("showScript", tok, value ? 1 : 0);
return;
case 603979778:
this.g.allowEmbeddedScripts = value;
break;
case 603979890:
this.g.navigationPeriodic = value;
break;
case 603979984:
this.tm.setZShadeEnabled(value);
return;
case 603979833:
if (this.haveDisplay) this.g.drawHover = value;
break;
case 603979889:
this.setNavigationMode(value);
break;
case 603979888:
return;
case 603979860:
this.g.hideNavigationPoint = value;
break;
case 603979930:
this.g.showNavigationPointAlways = value;
break;
case 603979900:
this.setRefreshing(value);
break;
case 603979869:
this.g.jmolInJSpecView = value;
break;
case 603979870:
this.g.justifyMeasurements = value;
break;
case 603979952:
this.g.ssbondsBackbone = value;
break;
case 603979852:
this.g.hbondsBackbone = value;
break;
case 603979854:
this.g.hbondsSolid = value;
break;
case 536870924:
this.gdata.setSpecular(value);
break;
case 603979942:
this.tm.setSlabEnabled(value);
return;
case 603979980:
this.tm.setZoomEnabled(value);
return;
case 603979864:
this.g.highResolutionFlag = value;
break;
case 603979966:
this.g.traceAlpha = value;
break;
case 603979983:
this.g.zoomLarge = value;
this.tm.setZoomHeight(this.g.zoomHeight, value);
break;
case 603979982:
this.g.zoomHeight = value;
this.tm.setZoomHeight(value, this.g.zoomLarge);
break;
case 603979871:
J.i18n.GT.setDoTranslate(value);
break;
case 603979862:
this.slm.setHideNotSelected(value);
break;
case 603979904:
this.setScriptQueue(value);
break;
case 603979830:
this.g.dotSurface = value;
break;
case 603979829:
this.g.dotsSelectedOnly = value;
break;
case 1611141172:
this.setSelectionHalosEnabled(value);
break;
case 603979910:
this.g.rasmolHydrogenSetting = value;
break;
case 603979908:
this.g.rasmolHeteroSetting = value;
break;
case 603979928:
this.g.showMultipleBonds = value;
break;
case 603979920:
this.g.showHiddenSelectionHalos = value;
break;
case 603979976:
this.tm.setWindowCentered(value);
break;
case 603979828:
this.g.displayCellParameters = value;
break;
case 603979960:
this.g.testFlag1 = value;
break;
case 603979962:
this.g.testFlag2 = value;
break;
case 603979964:
this.g.testFlag3 = value;
break;
case 603979965:
this.jmolTest();
this.g.testFlag4 = value;
break;
case 603979901:
this.g.ribbonBorder = value;
break;
case 603979815:
this.g.cartoonBaseEdges = value;
break;
case 603979819:
this.g.cartoonRockets = value;
break;
case 603979902:
this.g.rocketBarrels = value;
break;
case 603979850:
this.gdata.setGreyscaleMode(this.g.greyscaleRendering = value);
break;
case 603979878:
this.g.measurementLabels = value;
break;
case 603979809:
case 603979804:
case 603979808:
this.setAxesMode(tok);
return;
case 603979806:
this.setAxesOrientationRasmol(value);
return;
case 603979824:
this.setStringPropertyTok("defaultcolorscheme", 545259545, value ? "rasmol" : "jmol");
return;
case 603979825:
this.setDebugScript(value);
return;
case 603979897:
this.setPerspectiveDepth(value);
return;
case 603979798:
this.setAutoBond(value);
return;
case 603979914:
this.setShowAxes(value);
return;
case 603979916:
this.setShowBbcage(value);
return;
case 603979922:
this.setShowHydrogens(value);
return;
case 603979926:
this.setShowMeasurements(value);
return;
case 603979936:
this.setShowUnitCell(value);
return;
case 603979812:
doRepaint = false;
this.g.bondModeOr = value;
break;
case 603979978:
doRepaint = false;
this.g.zeroBasedXyzRasmol = value;
this.reset(true);
break;
case 603979899:
doRepaint = false;
this.g.rangeSelected = value;
break;
case 603979877:
doRepaint = false;
this.g.measureAllModels = value;
break;
case 603979954:
doRepaint = false;
this.sm.allowStatusReporting = value;
break;
case 603979822:
doRepaint = false;
this.g.chainCaseSensitive = value;
break;
case 603979858:
doRepaint = false;
this.g.hideNameInPopup = value;
break;
case 603979827:
doRepaint = false;
this.g.disablePopupMenu = value;
break;
case 603979848:
doRepaint = false;
this.g.forceAutoBond = value;
break;
default:
if (!this.g.htBooleanParameterFlags.containsKey(key.toLowerCase())) {
this.g.setUserVariable(key, JS.SV.getBoolean(value));
return;
}}
this.g.setB(key, value);
if (doRepaint) this.setTainted(true);
}, "~S,~N,~B");
Clazz.defineMethod(c$, "setModelKitMode", 
function(value){
if (this.acm == null || !this.allowScripting) return;
if (value || this.g.modelKitMode) {
this.setPickingMode(null, value ? 33 : 1);
this.setPickingMode(null, value ? 32 : 1);
}var isChange = (this.g.modelKitMode != value);
this.g.modelKitMode = value;
this.g.setB("modelkitmode", value);
this.highlight(null);
if (isChange) {
this.setModelkitPropertySafely("constraint", null);
}if (value) {
this.setNavigationMode(false);
this.selectAll();
this.setStringProperty("picking", "assignAtom_C");
this.setStringProperty("picking", "assignBond_p");
if (!this.isApplet) this.popupMenu(10, 0, 'm');
if (isChange) this.sm.setStatusModelKit(1);
this.g.modelKitMode = true;
if (this.getOperativeSymmetry() != null) {
} else if (this.ms.ac == 0) {
this.zap(false, true, true);
} else if (this.am.cmi >= 0 && this.getModelUndeletedAtomsBitSet(this.am.cmi).isEmpty()) {
var htParams =  new java.util.Hashtable();
htParams.put("appendToModelIndex", Integer.$valueOf(this.am.cmi));
this.loadDefaultModelKitModel(htParams);
}} else {
this.acm.setPickingMode(-1);
if (isChange) {
this.sm.setStatusModelKit(0);
} else if (!value) {
this.getModelkit(false).setProperty("hidemenu", null);
}}}, "~B");
Clazz.defineMethod(c$, "setSmilesString", 
function(s){
if (s == null) this.g.removeParam("_smilesString");
 else this.g.setO("_smilesString", s);
}, "~S");
Clazz.defineMethod(c$, "removeUserVariable", 
function(key){
this.g.removeUserVariable(key);
if (key.endsWith("callback")) this.sm.setCallbackFunction(key, null);
}, "~S");
Clazz.defineMethod(c$, "jmolTest", 
function(){
});
Clazz.defineMethod(c$, "showParameter", 
function(key, ifNotSet, nMax){
var sv = "" + this.g.getParameterEscaped(key, nMax);
if (ifNotSet || sv.indexOf("<not defined>") < 0) this.showString(key + " = " + sv, false);
}, "~S,~B,~N");
Clazz.defineMethod(c$, "showString", 
function(str, isPrint){
if (!JV.Viewer.isJS && this.isScriptQueued() && (!this.isSilent || isPrint) && !"\0".equals(str)) {
JU.Logger.warn(str);
}this.scriptEcho(str);
}, "~S,~B");
Clazz.defineMethod(c$, "getAllSettings", 
function(prefix){
return this.getStateCreator().getAllSettings(prefix);
}, "~S");
Clazz.defineMethod(c$, "getBindingInfo", 
function(qualifiers){
return (this.haveDisplay ? this.acm.getBindingInfo(qualifiers) : "");
}, "~S");
Clazz.defineMethod(c$, "getIsosurfacePropertySmoothing", 
function(asPower){
return (asPower ? this.g.isosurfacePropertySmoothingPower : this.g.isosurfacePropertySmoothing ? 1 : 0);
}, "~B");
Clazz.defineMethod(c$, "setNavigationDepthPercent", 
function(percent){
this.tm.setNavigationDepthPercent(percent);
this.refresh(1, "set navigationDepth");
}, "~N");
Clazz.defineMethod(c$, "getShowNavigationPoint", 
function(){
if (!this.g.navigationMode) return false;
return (this.tm.isNavigating() && !this.g.hideNavigationPoint || this.g.showNavigationPointAlways || this.getInMotion(true));
});
Clazz.overrideMethod(c$, "setPerspectiveDepth", 
function(perspectiveDepth){
this.tm.setPerspectiveDepth(perspectiveDepth);
}, "~B");
Clazz.overrideMethod(c$, "setAxesOrientationRasmol", 
function(TF){
this.g.setB("axesOrientationRasmol", TF);
this.g.axesOrientationRasmol = TF;
this.reset(true);
}, "~B");
Clazz.defineMethod(c$, "setAxesScale", 
function(tok, val){
val = JV.Viewer.checkFloatRange(val, -100, 100);
if (tok == 570425345) this.g.axesOffset = val;
 else this.g.axesScale = val;
this.axesAreTainted = true;
}, "~N,~N");
Clazz.defineMethod(c$, "setAxesMode", 
function(mode){
this.g.axesMode = mode;
this.axesAreTainted = true;
switch (mode) {
case 603979808:
this.g.removeParam("axesmolecular");
this.g.removeParam("axeswindow");
this.g.setB("axesUnitcell", true);
mode = 2;
break;
case 603979804:
this.g.removeParam("axesunitcell");
this.g.removeParam("axeswindow");
this.g.setB("axesMolecular", true);
mode = 1;
break;
case 603979809:
this.g.removeParam("axesunitcell");
this.g.removeParam("axesmolecular");
this.g.setB("axesWindow", true);
mode = 0;
}
this.g.setI("axesMode", mode);
}, "~N");
Clazz.defineMethod(c$, "getSelectionHalosEnabled", 
function(){
return this.selectionHalosEnabled;
});
Clazz.defineMethod(c$, "setSelectionHalosEnabled", 
function(TF){
if (this.selectionHalosEnabled == TF) return;
this.g.setB("selectionHalos", TF);
this.shm.loadShape(8);
this.selectionHalosEnabled = TF;
}, "~B");
Clazz.defineMethod(c$, "getShowSelectedOnce", 
function(){
var flag = this.showSelected;
this.showSelected = false;
return flag;
});
Clazz.defineMethod(c$, "setStrandCount", 
function(type, value){
value = JV.Viewer.checkIntRange(value, 0, 20);
switch (type) {
case 12:
this.g.strandCountForStrands = value;
break;
case 13:
this.g.strandCountForMeshRibbon = value;
break;
default:
this.g.strandCountForStrands = value;
this.g.strandCountForMeshRibbon = value;
break;
}
this.g.setI("strandCount", value);
this.g.setI("strandCountForStrands", this.g.strandCountForStrands);
this.g.setI("strandCountForMeshRibbon", this.g.strandCountForMeshRibbon);
}, "~N,~N");
Clazz.defineMethod(c$, "getStrandCount", 
function(type){
return (type == 12 ? this.g.strandCountForStrands : this.g.strandCountForMeshRibbon);
}, "~N");
Clazz.defineMethod(c$, "setNavigationMode", 
function(TF){
this.g.navigationMode = TF;
this.tm.setNavigationMode(TF);
}, "~B");
Clazz.overrideMethod(c$, "setAutoBond", 
function(TF){
this.g.setB("autobond", TF);
this.g.autoBond = TF;
}, "~B");
Clazz.defineMethod(c$, "makeConnections", 
function(minDistance, maxDistance, order, connectOperation, bsA, bsB, bsBonds, isBonds, addGroup, energy){
this.clearModelDependentObjects();
this.clearMinimization();
return this.ms.makeConnections(minDistance, maxDistance, order, connectOperation, bsA, bsB, bsBonds, isBonds, addGroup, energy);
}, "~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");
Clazz.overrideMethod(c$, "rebond", 
function(){
this.rebondState(false);
});
Clazz.defineMethod(c$, "rebondState", 
function(isStateScript){
this.clearModelDependentObjects();
this.ms.deleteAllBonds();
var isLegacy = isStateScript && this.g.legacyAutoBonding;
this.ms.autoBondBs4(null, null, null, null, this.getMadBond(), isLegacy, null);
this.addStateScript((isLegacy ? "set legacyAutoBonding TRUE;connect;set legacyAutoBonding FALSE;" : "connect;"), false, true);
}, "~B");
Clazz.overrideMethod(c$, "setPercentVdwAtom", 
function(value){
this.g.setI("percentVdwAtom", value);
this.g.percentVdwAtom = value;
this.rd.value = value / 100;
this.rd.factorType = J.atomdata.RadiusData.EnumType.FACTOR;
this.rd.vdwType = J.c.VDW.AUTO;
this.shm.setShapeSizeBs(0, 0, this.rd, null);
}, "~N");
Clazz.overrideMethod(c$, "getMadBond", 
function(){
return (this.g.bondRadiusMilliAngstroms * 2);
});
Clazz.overrideMethod(c$, "setShowHydrogens", 
function(TF){
this.g.setB("showHydrogens", TF);
this.g.showHydrogens = TF;
}, "~B");
Clazz.defineMethod(c$, "setShowBbcage", 
function(value){
this.setObjectMad10(32, "boundbox", (value ? -4 : 0));
this.g.setB("showBoundBox", value);
}, "~B");
Clazz.defineMethod(c$, "getShowBbcage", 
function(){
return this.getObjectMad10(4) != 0;
});
Clazz.defineMethod(c$, "setShowUnitCell", 
function(value){
this.setObjectMad10(33, "unitcell", (value ? -2 : 0));
this.g.setB("showUnitCell", value);
}, "~B");
Clazz.defineMethod(c$, "getShowUnitCell", 
function(){
return this.getObjectMad10(5) != 0;
});
Clazz.defineMethod(c$, "setShowAxes", 
function(value){
this.setObjectMad10(34, "axes", (value ? -2 : 0));
this.g.setB("showAxes", value);
}, "~B");
Clazz.defineMethod(c$, "getShowAxes", 
function(){
return this.getObjectMad10(1) != 0;
});
Clazz.overrideMethod(c$, "setFrankOn", 
function(TF){
if (this.isPreviewOnly) TF = false;
this.frankOn = TF;
this.setObjectMad10(36, "frank", (TF ? 1 : 0));
}, "~B");
Clazz.defineMethod(c$, "getShowFrank", 
function(){
if (this.isPreviewOnly || this.isApplet && this.creatingImage) return false;
return (this.isSignedApplet && !this.isSignedAppletLocal && !JV.Viewer.isJS || this.frankOn);
});
Clazz.overrideMethod(c$, "setShowMeasurements", 
function(TF){
this.g.setB("showMeasurements", TF);
this.g.showMeasurements = TF;
}, "~B");
Clazz.defineMethod(c$, "setUnits", 
function(units, isDistance){
var isDefault = "default".equals(units);
if (!isDistance || !isDefault) this.g.setUnits(units);
if (isDistance) {
this.setShapeProperty(6, "reformatDistances", units);
}}, "~S,~B");
Clazz.overrideMethod(c$, "setRasmolDefaults", 
function(){
this.setDefaultsType("RasMol");
});
Clazz.overrideMethod(c$, "setJmolDefaults", 
function(){
this.setDefaultsType("Jmol");
});
Clazz.defineMethod(c$, "setDefaultsType", 
function(type){
if (type.equalsIgnoreCase("RasMol")) {
this.stm.setRasMolDefaults();
return;
}if (type.equalsIgnoreCase("PyMOL")) {
this.stm.setPyMOLDefaults();
return;
}this.stm.setJmolDefaults();
this.setIntProperty("bondingVersion", 0);
this.shm.setShapeSizeBs(0, 0, this.rd, this.getAllAtoms());
}, "~S");
Clazz.defineMethod(c$, "setAntialias", 
function(tok, TF){
var isChanged = false;
switch (tok) {
case 603979786:
isChanged = (this.g.antialiasDisplay != TF);
this.g.antialiasDisplay = TF;
break;
case 603979790:
isChanged = (this.g.antialiasTranslucent != TF);
this.g.antialiasTranslucent = TF;
break;
case 603979788:
this.g.antialiasImages = TF;
return;
}
if (isChanged) {
this.resizeImage(0, 0, false, false, true);
this.refresh(3, "Viewer:setAntialias()");
}}, "~N,~B");
Clazz.defineMethod(c$, "allocTempPoints", 
function(size){
return this.tempArray.allocTempPoints(size);
}, "~N");
Clazz.defineMethod(c$, "freeTempPoints", 
function(tempPoints){
this.tempArray.freeTempPoints(tempPoints);
}, "~A");
Clazz.defineMethod(c$, "allocTempScreens", 
function(size){
return this.tempArray.allocTempScreens(size);
}, "~N");
Clazz.defineMethod(c$, "freeTempScreens", 
function(tempScreens){
this.tempArray.freeTempScreens(tempScreens);
}, "~A");
Clazz.defineMethod(c$, "allocTempEnum", 
function(size){
return this.tempArray.allocTempEnum(size);
}, "~N");
Clazz.defineMethod(c$, "freeTempEnum", 
function(temp){
this.tempArray.freeTempEnum(temp);
}, "~A");
Clazz.defineMethod(c$, "getFont3D", 
function(fontFace, fontStyle, fontSize){
return this.gdata.getFont3DFSS(fontFace, fontStyle, fontSize);
}, "~S,~S,~N");
Clazz.defineMethod(c$, "getAtomGroupQuaternions", 
function(bsAtoms, nMax){
return this.ms.getAtomGroupQuaternions(bsAtoms, nMax, this.getQuaternionFrame());
}, "JU.BS,~N");
Clazz.defineMethod(c$, "setStereoMode", 
function(twoColors, stereoMode, degrees){
this.setFloatProperty("stereoDegrees", degrees);
this.setBooleanPropertyTok("greyscaleRendering", 603979850, stereoMode.isBiColor());
if (twoColors != null) this.tm.setStereoMode2(twoColors);
 else this.tm.setStereoMode(stereoMode);
}, "~A,J.c.STER,~N");
Clazz.defineMethod(c$, "getChimeInfo", 
function(tok){
return this.getPropertyManager().getChimeInfo(tok, this.bsA());
}, "~N");
Clazz.defineMethod(c$, "getModelFileInfo", 
function(){
return this.getPropertyManager().getModelFileInfo(this.getVisibleFramesBitSet());
});
Clazz.defineMethod(c$, "getModelFileInfoAll", 
function(){
return this.getPropertyManager().getModelFileInfo(null);
});
Clazz.defineMethod(c$, "showEditor", 
function(file_text){
var scriptEditor = this.getProperty("DATA_API", "getScriptEditor", Boolean.TRUE);
if (scriptEditor == null) return;
scriptEditor.show(file_text);
}, "~A");
Clazz.defineMethod(c$, "getPropertyManager", 
function(){
if (this.pm == null) (this.pm = J.api.Interface.getInterface("JV.PropertyManager", this, "prop")).setViewer(this);
return this.pm;
});
Clazz.defineMethod(c$, "setTainted", 
function(TF){
this.isTainted = this.axesAreTainted = (TF && (this.refreshing || this.creatingImage));
}, "~B");
Clazz.defineMethod(c$, "checkObjectClicked", 
function(x, y, modifiers){
return this.shm.checkObjectClicked(x, y, modifiers, this.getVisibleFramesBitSet(), this.g.drawPicking);
}, "~N,~N,~N");
Clazz.defineMethod(c$, "checkObjectHovered", 
function(x, y){
return (x >= 0 && this.shm != null && this.shm.checkObjectHovered(x, y, this.getVisibleFramesBitSet(), this.getBondsPickable()));
}, "~N,~N");
Clazz.defineMethod(c$, "checkObjectDragged", 
function(prevX, prevY, x, y, action){
var iShape = 0;
switch (this.getPickingMode()) {
case 2:
iShape = 5;
break;
case 4:
iShape = 22;
break;
}
if (this.shm.checkObjectDragged(prevX, prevY, x, y, action, this.getVisibleFramesBitSet(), iShape)) {
this.refresh(1, "checkObjectDragged");
if (iShape == 22) this.scriptEcho(this.getShapeProperty(22, "command"));
return true;
}return false;
}, "~N,~N,~N,~N,~N");
Clazz.defineMethod(c$, "rotateAxisAngleAtCenter", 
function(eval, rotCenter, rotAxis, degreesPerSecond, endDegrees, isSpin, bsSelected){
var isOK = this.tm.rotateAxisAngleAtCenter(eval, rotCenter, rotAxis, degreesPerSecond, endDegrees, isSpin, bsSelected);
if (isOK) this.setSync();
return isOK;
}, "J.api.JmolScriptEvaluator,JU.P3,JU.V3,~N,~N,~B,JU.BS");
Clazz.defineMethod(c$, "rotateAboutPointsInternal", 
function(eval, point1, point2, degreesPerSecond, endDegrees, isSpin, bsSelected, translation, finalPoints, dihedralList, m4, useModelKit){
if (eval == null) eval = this.eval;
if (this.headless) {
if (isSpin && endDegrees == 3.4028235E38) return false;
isSpin = false;
}var isOK = this.tm.rotateAboutPointsInternal(eval, point1, point2, degreesPerSecond, endDegrees, false, isSpin, bsSelected, false, translation, finalPoints, dihedralList, m4, useModelKit);
if (isOK) this.setSync();
return isOK;
}, "J.api.JmolScriptEvaluator,JU.P3,JU.P3,~N,~N,~B,JU.BS,JU.V3,JU.Lst,~A,JU.M4,~B");
Clazz.defineMethod(c$, "startSpinningAxis", 
function(pt1, pt2, isClockwise){
if (this.tm.spinOn || this.tm.navOn) {
this.tm.setSpinOff();
this.tm.setNavOn(false);
return;
}this.tm.rotateAboutPointsInternal(null, pt1, pt2, this.g.pickingSpinRate, 3.4028235E38, isClockwise, true, null, false, null, null, null, null, false);
}, "JU.T3,JU.T3,~B");
Clazz.defineMethod(c$, "getModelDipole", 
function(){
return this.ms.getModelDipole(this.am.cmi);
});
Clazz.defineMethod(c$, "calculateMolecularDipole", 
function(bsAtoms){
try {
return this.ms.calculateMolecularDipole(this.am.cmi, bsAtoms);
} catch (e) {
if (Clazz.exceptionOf(e,"JV.JmolAsyncException")){
if (this.eval != null) this.eval.loadFileResourceAsync(e.getFileName());
return null;
} else {
throw e;
}
}
}, "JU.BS");
Clazz.defineMethod(c$, "setDefaultLattice", 
function(p){
if (!Float.isNaN(p.x + p.y + p.z)) this.g.ptDefaultLattice.setT(p);
this.g.setO("defaultLattice", JU.Escape.eP(p));
}, "JU.P3");
Clazz.defineMethod(c$, "getDefaultLattice", 
function(){
return this.g.ptDefaultLattice;
});
Clazz.defineMethod(c$, "getModelExtract", 
function(atomExpression, doTransform, isModelKit, type){
return this.getPropertyManager().getModelExtract(this.getAtomBitSet(atomExpression), doTransform, isModelKit, type, false);
}, "~O,~B,~B,~S");
Clazz.overrideMethod(c$, "getData", 
function(atomExpression, type){
return this.getModelFileData(atomExpression, type, true);
}, "~S,~S");
Clazz.defineMethod(c$, "getModelFileData", 
function(atomExpression, type, allTrajectories){
return this.getPropertyManager().getAtomData(atomExpression, type, allTrajectories);
}, "~S,~S,~B");
Clazz.defineMethod(c$, "getModelCml", 
function(bs, nAtomsMax, addBonds, doTransform){
return this.getPropertyManager().getModelCml(bs, nAtomsMax, addBonds, doTransform, false);
}, "JU.BS,~N,~B,~B");
Clazz.defineMethod(c$, "getPdbAtomData", 
function(bs, out, asPQR, doTransform){
return this.getPropertyManager().getPdbAtomData(bs == null ? this.bsA() : bs, out, asPQR, doTransform, false);
}, "JU.BS,JU.OC,~B,~B");
Clazz.defineMethod(c$, "isJmolDataFrame", 
function(){
return this.ms.isJmolDataFrameForModel(this.am.cmi);
});
Clazz.defineMethod(c$, "setFrameTitle", 
function(modelIndex, title){
this.ms.setFrameTitle(JU.BSUtil.newAndSetBit(modelIndex), title);
}, "~N,~S");
Clazz.defineMethod(c$, "setFrameTitleObj", 
function(title){
this.shm.loadShape(31);
this.ms.setFrameTitle(this.getVisibleFramesBitSet(), title);
}, "~O");
Clazz.defineMethod(c$, "getFrameTitle", 
function(){
return this.ms.getFrameTitle(this.am.cmi);
});
Clazz.defineMethod(c$, "setAtomProperty", 
function(bs, tok, iValue, fValue, sValue, values, list){
if (tok == 1648363544) this.shm.deleteVdwDependentShapes(bs);
this.clearMinimization();
this.ms.setAtomProperty(bs, tok, iValue, fValue, sValue, values, list);
switch (tok) {
case 1086326789:
this.setModelkitPropertySafely("updateatomkeys", bs);
case 1111492609:
case 1111492610:
case 1111492611:
case 1111492612:
case 1111492613:
case 1111492614:
case 1111490577:
case 1111490578:
case 1111490579:
this.refreshMeasures(true);
}
}, "JU.BS,~N,~N,~N,~S,~A,~A");
Clazz.defineMethod(c$, "checkCoordinatesChanged", 
function(bsAtoms){
this.ms.recalculatePositionDependentQuantities(bsAtoms, null);
this.refreshMeasures(true);
}, "JU.BS");
Clazz.defineMethod(c$, "setAtomCoords", 
function(bs, tokType, xyzValues){
if (bs.isEmpty()) return;
var atom = this.ms.at[bs.nextSetBit(0)];
var n = bs.cardinality();
this.sm.setStatusStructureModified(atom.i, atom.mi, 3, "setAtomCoords", n, bs);
this.ms.setAtomCoords(bs, tokType, xyzValues);
this.setStatusAtomMoved(true, bs);
this.sm.setStatusStructureModified(atom.i, atom.mi, -3, "OK", n, bs);
}, "JU.BS,~N,~O");
Clazz.defineMethod(c$, "setAtomCoordsRelative", 
function(offset, bs){
if (bs == null) bs = this.bsA();
if (bs.isEmpty()) return;
var doNotify = (offset.lengthSquared() != 0);
var atom = this.ms.at[bs.nextSetBit(0)];
var n = bs.cardinality();
if (doNotify) {
this.sm.setStatusStructureModified(atom.i, atom.mi, 3, "setAtomCoords", n, bs);
}this.ms.setAtomCoordsRelative(offset, bs);
this.checkMinimization();
if (doNotify) {
this.setStatusAtomMoved(false, bs);
this.sm.setStatusStructureModified(atom.i, atom.mi, -3, "OK", n, bs);
}}, "JU.T3,JU.BS");
Clazz.defineMethod(c$, "invertAtomCoord", 
function(pt, plane, bs, ringAtomIndex, isClick){
if (ringAtomIndex >= 0) {
bs = JU.JmolMolecule.getBranchesForInversion(this.ms.at, ringAtomIndex, this.ms.getMoleculeBitSetForAtom(ringAtomIndex));
var nb = bs.cardinality();
switch (nb) {
case 0:
case 1:
return;
case 2:
break;
case 3:
case 4:
var lengths =  Clazz.newIntArray (nb, 0);
var points =  Clazz.newIntArray (nb, 0);
var ni = 0;
for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1), ni++) {
lengths[ni] = this.getBranchBitSet(i, ringAtomIndex, true).cardinality();
points[ni] = i;
}
for (var j = 0; j < nb - 2; j++) {
var max = -2147483648;
var imax = 0;
for (var i = 0; i < nb; i++) if (lengths[i] >= max && bs.get(points[i])) {
imax = points[i];
max = lengths[i];
}
bs.clear(imax);
}
}
if (isClick && !bs.isEmpty()) this.undoMoveActionClear(ringAtomIndex, 2, true);
}var n = bs.cardinality();
if (n == 0) return;
var atom = this.ms.at[bs.nextSetBit(0)];
this.sm.setStatusStructureModified(atom.i, atom.mi, 3, "invertAtomCoords", n, bs);
this.ms.invertSelected(pt, plane, ringAtomIndex, bs);
this.setStatusAtomMoved(true, bs);
this.sm.setStatusStructureModified(atom.i, atom.mi, -3, "OK", n, bs);
if (isClick) this.setStatusAtomPicked(ringAtomIndex, "inverted: " + JU.Escape.eBS(bs), null, false);
}, "JU.P3,JU.P4,JU.BS,~N,~B");
Clazz.defineMethod(c$, "invertSelected", 
function(pt, plane, iAtom, bsAtoms){
if (bsAtoms == null) bsAtoms = this.bsA();
if (bsAtoms.isEmpty()) return;
this.ms.invertSelected(pt, plane, iAtom, bsAtoms);
this.setStatusAtomMoved(true, bsAtoms);
}, "JU.P3,JU.P4,~N,JU.BS");
Clazz.defineMethod(c$, "moveAtoms", 
function(m4, mNew, rotation, translation, center, isInternal, bsAtoms, translationOnly, useModelKit){
if (bsAtoms.isEmpty()) return;
var bsFixed = this.getMotionFixedAtoms(null, null);
if (bsAtoms.intersects(bsFixed)) return;
var uc = (useModelKit ? this.getOperativeSymmetry() : null);
var apos0 = null;
if (uc != null) {
apos0 = this.ms.saveAtomPositions();
}this.ms.moveAtoms(m4, mNew, rotation, translation, bsAtoms, center, isInternal, translationOnly);
if (uc != null) {
this.getModelkit(false).checkMovedAtoms(bsFixed, bsAtoms, apos0);
}this.setStatusAtomMoved(true, bsAtoms);
}, "JU.M4,JU.M3,JU.M3,JU.V3,JU.P3,~B,JU.BS,~B,~B");
Clazz.defineMethod(c$, "moveSelectedXY", 
function(deltaX, deltaY, modifiers){
this.moveSelected(deltaX, deltaY, -2147483648, -2147483648, -2147483648, null, null, null, false, false, modifiers);
}, "~N,~N,~N");
Clazz.defineMethod(c$, "moveSelected", 
function(deltaX, deltaY, deltaZ, x, y, bsSelected, ptOld, ptNew, isTranslation, asAtoms, modifiers){
if (deltaZ == 0 && ptNew == null || this.isJmolDataFrame()) return 0;
if (ptNew == null) {
if (x == -2147483648 && this.modelkit != null) this.setModelkitPropertySafely("rotatebondindex", Integer.$valueOf(-2147483648));
if (deltaX == -2147483648) {
this.showSelected = true;
this.movableBitSet = this.setMovableBitSet(null, !asAtoms);
this.shm.loadShape(8);
this.refresh(6, "moveSelected");
return 0;
}if (deltaX == 2147483647) {
if (!this.showSelected) return 0;
this.showSelected = false;
this.movableBitSet = null;
this.refresh(6, "moveSelected");
return 0;
}}if (this.movingSelected) return 0;
this.movingSelected = true;
this.stopMinimization();
if (ptNew == null && x != -2147483648 && this.modelkit != null && this.modelkit.getProperty("rotatebondindex") != null) {
this.modelkit.actionRotateBond(deltaX, deltaY, x, y, (modifiers & 16) != 0);
} else {
if (bsSelected == null) bsSelected = this.bsA();
var iatom = bsSelected.nextSetBit(0);
bsSelected = this.setMovableBitSet(bsSelected, !asAtoms);
if (bsSelected.isEmpty()) {
bsSelected.set(iatom);
this.sm.setStatusStructureModified(iatom, this.getModelIndexForAtom(iatom), -3, "FAILED", 1, bsSelected);
} else {
if (isTranslation) {
var ptCenter = (ptOld == null ? this.ms.getAtomSetCenter(bsSelected) : ptOld);
if (ptNew == null) {
this.tm.finalizeTransformParameters();
var f = (this.g.antialiasDisplay ? 2 : 1);
this.tm.transformPt3f(ptCenter, this.ptScreen);
if (deltaZ != -2147483648) this.ptScreenNew.set(this.ptScreen.x, this.ptScreen.y, this.ptScreen.z + deltaZ);
 else this.ptScreenNew.set(this.ptScreen.x + deltaX * f, this.ptScreen.y + deltaY * f, this.ptScreen.z);
this.tm.unTransformPoint(this.ptScreenNew, this.ptNew);
ptNew = this.ptNew;
var uc = this.getOperativeSymmetry();
if (uc != null) {
ptNew.sub(ptCenter);
ptNew.add(this.ms.at[iatom]);
this.getModelkit(false).cmdAssignMoveAtoms(bsSelected, iatom, ptNew, null, true, !asAtoms);
}}if (!Float.isNaN(ptNew.x)) {
ptNew.sub(ptCenter);
this.setAtomCoordsRelative(ptNew, bsSelected);
}} else {
this.tm.rotateXYBy(deltaX, deltaY, bsSelected);
}}}this.refresh(2, "");
this.movingSelected = false;
return (bsSelected == null ? 0 : bsSelected.cardinality());
}, "~N,~N,~N,~N,~N,JU.BS,JU.P3,JU.P3,~B,~B,~N");
Clazz.defineMethod(c$, "highlightBond", 
function(index, closestAtomIndex, x, y){
if (!this.hoverEnabled) return;
var bs = null;
if (index >= 0) {
var b = this.ms.bo[index];
var i = b.atom2.i;
bs = JU.BSUtil.newAndSetBit(i);
bs.set(b.atom1.i);
}this.highlight(bs);
this.getModelkit(false);
this.setModelkitPropertySafely("screenxy",  Clazz.newIntArray(-1, [x, y]));
this.setModelkitPropertySafely("bondindex", Integer.$valueOf(index));
var text = this.setModelkitPropertySafely("hoverlabel", Integer.$valueOf(-2 - index));
if (text != null) this.hoverOnPt(x, y, text, null, null);
this.refresh(3, "highlightBond");
}, "~N,~N,~N,~N");
Clazz.defineMethod(c$, "highlight", 
function(bs){
this.atomHighlighted = (bs != null && bs.cardinality() == 1 ? bs.nextSetBit(0) : -1);
if (bs == null) {
this.setCursor(0);
} else {
this.shm.loadShape(8);
this.setCursor(12);
}this.setModelkitPropertySafely("highlight", bs);
this.setShapeProperty(8, "highlight", bs);
}, "JU.BS");
Clazz.defineMethod(c$, "refreshMeasures", 
function(andStopMinimization){
this.setShapeProperty(6, "refresh", null);
this.setStatusMeasuring("refreshed", -3, "", 0);
if (andStopMinimization) this.stopMinimization();
}, "~B");
Clazz.defineMethod(c$, "functionXY", 
function(functionName, nX, nY){
var data = null;
if (functionName.indexOf("file:") == 0) data = this.getFileAsString3(functionName.substring(5), false, null);
 else if (functionName.indexOf("data2d_") != 0) return this.sm.functionXY(functionName, nX, nY);
nX = Math.abs(nX);
nY = Math.abs(nY);
var fdata;
if (data == null) {
fdata = this.getDataObj(functionName, null, 2);
if (fdata != null) return fdata;
data = "";
}fdata =  Clazz.newFloatArray (nX, nY, 0);
var f =  Clazz.newFloatArray (nX * nY, 0);
JU.Parser.parseStringInfestedFloatArray(data, null, f);
for (var i = 0, n = 0; i < nX; i++) for (var j = 0; j < nY; j++) fdata[i][j] = f[n++];


return fdata;
}, "~S,~N,~N");
Clazz.defineMethod(c$, "functionXYZ", 
function(functionName, nX, nY, nZ){
var data = null;
if (functionName.indexOf("file:") == 0) data = this.getFileAsString3(functionName.substring(5), false, null);
 else if (functionName.indexOf("data3d_") != 0) return this.sm.functionXYZ(functionName, nX, nY, nZ);
nX = Math.abs(nX);
nY = Math.abs(nY);
nZ = Math.abs(nZ);
var xyzdata;
if (data == null) {
xyzdata = this.getDataObj(functionName, null, 2);
if (xyzdata != null) return xyzdata;
data = "";
}xyzdata =  Clazz.newFloatArray (nX, nY, nZ, 0);
var f =  Clazz.newFloatArray (nX * nY * nZ, 0);
JU.Parser.parseStringInfestedFloatArray(data, null, f);
for (var i = 0, n = 0; i < nX; i++) for (var j = 0; j < nY; j++) for (var k = 0; k < nZ; k++) xyzdata[i][j][k] = f[n++];



return xyzdata;
}, "~S,~N,~N,~N");
Clazz.overrideMethod(c$, "extractMolData", 
function(what){
if (what == null) {
var i = this.am.cmi;
if (i < 0 || this.ms.ac == 0) return null;
what = this.getModelNumberDotted(i);
}return this.getModelExtract(what, true, false, "V2000");
}, "~S");
Clazz.defineMethod(c$, "getNMRPredict", 
function(type){
type = type.toUpperCase();
if (type.equals("H") || type.equals("1H") || type.equals("")) type = "H1";
 else if (type.equals("C") || type.equals("13C")) type = "C13";
if (!type.equals("NONE")) {
if (!type.equals("C13") && !type.equals("H1")) return "Type must be H1 or C13";
var molFile = this.getModelExtract("selected", true, false, "V2000");
var pt = molFile.indexOf("\n");
if (pt < 0) return null;
molFile = "Jmol " + JV.Viewer.version_date + molFile.substring(pt);
if (this.isApplet) {
this.showUrl(this.g.nmrUrlFormat + molFile);
return "opening " + this.g.nmrUrlFormat;
}}this.syncScript("true", "*", 0);
this.syncScript(type + "Simulate:", ".", 0);
return "sending request to JSpecView";
}, "~S");
Clazz.defineMethod(c$, "getHelp", 
function(what){
if (this.g.helpPath.indexOf("?") < 0) {
if (what.length > 0 && what.indexOf("?") != 0) what = "?search=" + JU.PT.rep(what, " ", "%20");
what += (what.length == 0 ? "?ver=" : "&ver=") + JV.JC.majorVersion;
} else {
what = "&" + what;
}this.showUrl(this.g.helpPath + what);
}, "~S");
Clazz.defineMethod(c$, "getChemicalInfo", 
function(smiles, info, bsAtoms){
info = info.toLowerCase();
var type = '/';
switch (";inchi;inchikey;stdinchi;stdinchikey;name;image;drawing;names;".indexOf(";" + info + ";")) {
case 0:
type = 'I';
break;
case 6:
type = 'K';
break;
case 15:
type = 'T';
break;
case 24:
type = 'S';
break;
case 36:
type = 'M';
break;
case 41:
case 47:
type = '2';
break;
case 55:
type = 'N';
break;
}
var s = this.setLoadFormat(false, "_" + smiles, type, false);
if (type == '2') {
this.fm.loadImage(s, "\1" + smiles, false);
return s;
}if (type == '/') {
if (JU.PT.isOneOf(info, ";alc;cdxml;cerius;charmm;cif;cml;ctx;gjf;gromacs;hyperchem;jme;maestro;mol;mol2;sybyl2;mrv;pdb;sdf;sdf3000;sln;smiles;xyz")) s += "file?format=" + info;
 else s += JU.PT.rep(info, " ", "%20");
}s = this.getFileAsString4(s, -1, false, false, false, "file");
if (type == 'M' && s.indexOf("\n") > 0) s = s.substring(0, s.indexOf("\n"));
 else if (info.equals("jme")) s = this.getPropertyManager().fixJMEFormalCharges(bsAtoms, s);
return s;
}, "~S,~S,JU.BS");
Clazz.defineMethod(c$, "addCommand", 
function(command){
if (this.autoExit || !this.haveDisplay || !this.getPreserveState()) return;
if (command.startsWith("pause ") || command.equals("pause")) command = "resume";
this.commandHistory.addCommand(JU.PT.replaceAllCharacters(command, "\r\n\t", " "));
}, "~S");
Clazz.defineMethod(c$, "pushState", 
function(){
if (this.autoExit || !this.haveDisplay || !this.getPreserveState()) return;
this.commandHistory.pushState(this.getStateInfo());
});
Clazz.defineMethod(c$, "popState", 
function(){
if (this.autoExit || !this.haveDisplay || !this.getPreserveState()) return;
var state = this.commandHistory.popState();
if (state != null) this.evalStringQuiet(state);
});
Clazz.defineMethod(c$, "removeCommand", 
function(){
return this.commandHistory.removeCommand();
});
Clazz.overrideMethod(c$, "getSetHistory", 
function(howFarBack){
return this.commandHistory.getSetHistory(howFarBack);
}, "~N");
Clazz.defineMethod(c$, "historyFind", 
function(cmd, dir){
return this.commandHistory.find(cmd, dir);
}, "~S,~N");
Clazz.defineMethod(c$, "setHistory", 
function(fileName){
this.commandHistory.getSetHistory(-2147483648);
this.commandHistory.addCommand(this.getFileAsString4(fileName, -1, false, false, true, null));
}, "~S");
Clazz.defineMethod(c$, "getOutputChannel", 
function(localName, fullPath){
return this.getOutputManager().getOutputChannel(localName, fullPath);
}, "~S,~A");
Clazz.overrideMethod(c$, "writeTextFile", 
function(fileName, data){
return this.writeFile(fileName, data, "txt");
}, "~S,~S");
Clazz.defineMethod(c$, "writeFile", 
function(fileName, data, type){
var params =  new java.util.Hashtable();
params.put("fileName", fileName);
params.put("type", type);
params.put(((typeof(data)=='string') ? "text" : "bytes"), data);
return this.outputToFile(params);
}, "~S,~O,~S");
Clazz.overrideMethod(c$, "clipImageOrPasteText", 
function(text){
if (!this.haveAccess(JV.Viewer.ACCESS.ALL)) return "no";
return this.getOutputManager().clipImageOrPasteText(text);
}, "~S");
Clazz.overrideMethod(c$, "getClipboardText", 
function(){
if (!this.haveAccess(JV.Viewer.ACCESS.ALL)) return "no";
try {
return this.getOutputManager().getClipboardText();
} catch (er) {
if (Clazz.exceptionOf(er, Error)){
return J.i18n.GT.$("clipboard is not accessible -- use signed applet");
} else {
throw er;
}
}
});
Clazz.defineMethod(c$, "processWriteOrCapture", 
function(params){
return this.getOutputManager().processWriteOrCapture(params);
}, "java.util.Map");
Clazz.defineMethod(c$, "createZip", 
function(fileName, type, params){
var state = this.getStateInfo();
var data = params.get("data");
if (fileName != null) params.put("fileName", fileName);
params.put("type", type);
params.put("text", state);
if (Clazz.instanceOf(data,Array)) params.put("scripts", data);
 else if (Clazz.instanceOf(data,"JU.Lst")) params.put("imageData", data);
return this.getOutputManager().outputToFile(params);
}, "~S,~S,java.util.Map");
Clazz.overrideMethod(c$, "outputToFile", 
function(params){
return this.getOutputManager().outputToFile(params);
}, "java.util.Map");
Clazz.defineMethod(c$, "setSyncTarget", 
function(mode, TF){
switch (mode) {
case 0:
this.sm.syncingMouse = TF;
break;
case 1:
this.sm.syncingScripts = TF;
break;
case 2:
this.sm.syncSend(TF ? "GET_GRAPHICS" : "SET_GRAPHICS_OFF", "*", 0);
if (Float.isNaN(this.tm.stereoDegrees)) this.setFloatProperty("stereoDegrees", -5);
if (TF) {
this.setBooleanProperty("_syncMouse", false);
this.setBooleanProperty("_syncScript", false);
}return;
}
if (!this.sm.syncingScripts && !this.sm.syncingMouse) this.setSync();
}, "~N,~B");
Clazz.overrideMethod(c$, "syncScript", 
function(script, applet, port){
this.sm.syncScript(script, applet, port);
}, "~S,~S,~N");
Clazz.overrideMethod(c$, "getModelIndexFromId", 
function(id){
return this.ms.getModelIndexFromId(id);
}, "~S");
Clazz.defineMethod(c$, "setSyncDriver", 
function(mode){
this.sm.setSyncDriver(mode);
}, "~N");
Clazz.defineMethod(c$, "setProteinType", 
function(type, bs){
this.ms.setProteinType(bs == null ? this.bsA() : bs, type);
}, "J.c.STR,JU.BS");
Clazz.defineMethod(c$, "getVanderwaalsMar", 
function(i){
return (this.defaultVdw === J.c.VDW.USER ? this.userVdwMars[i] : JU.Elements.getVanderwaalsMar(i, this.defaultVdw));
}, "~N");
Clazz.defineMethod(c$, "getVanderwaalsMarType", 
function(atomicAndIsotopeNumber, type){
if (type == null) type = this.defaultVdw;
 else switch (type) {
case J.c.VDW.AUTO:
case J.c.VDW.AUTO_BABEL:
case J.c.VDW.AUTO_JMOL:
case J.c.VDW.AUTO_RASMOL:
if (this.defaultVdw !== J.c.VDW.AUTO) type = this.defaultVdw;
break;
default:
break;
}
if (type === J.c.VDW.USER && this.bsUserVdws == null) type = J.c.VDW.JMOL;
return (type === J.c.VDW.USER ? this.userVdwMars[atomicAndIsotopeNumber & 127] : JU.Elements.getVanderwaalsMar(atomicAndIsotopeNumber, type));
}, "~N,J.c.VDW");
Clazz.defineMethod(c$, "setVdwStr", 
function(name){
var type = J.c.VDW.getVdwType(name);
if (type == null) type = J.c.VDW.AUTO;
switch (type) {
case J.c.VDW.JMOL:
case J.c.VDW.BABEL:
case J.c.VDW.RASMOL:
case J.c.VDW.AUTO:
case J.c.VDW.USER:
break;
default:
type = J.c.VDW.JMOL;
}
if (type !== this.defaultVdw && type === J.c.VDW.USER && this.bsUserVdws == null) this.setUserVdw(this.defaultVdw);
this.defaultVdw = type;
this.g.setO("defaultVDW", type.getVdwLabel());
}, "~S");
Clazz.defineMethod(c$, "setUserVdw", 
function(mode){
this.userVdwMars =  Clazz.newIntArray (JU.Elements.elementNumberMax, 0);
this.userVdws =  Clazz.newFloatArray (JU.Elements.elementNumberMax, 0);
this.bsUserVdws =  new JU.BS();
if (mode === J.c.VDW.USER) mode = J.c.VDW.JMOL;
for (var i = 1; i < JU.Elements.elementNumberMax; i++) {
this.userVdwMars[i] = JU.Elements.getVanderwaalsMar(i, mode);
this.userVdws[i] = this.userVdwMars[i] / 1000;
}
}, "J.c.VDW");
Clazz.defineMethod(c$, "getDefaultVdwNameOrData", 
function(mode, type, bs){
switch (mode) {
case -2147483648:
return this.defaultVdw.getVdwLabel();
case 2147483647:
if ((bs = this.bsUserVdws) == null) return "";
type = J.c.VDW.USER;
break;
}
if (type == null || type === J.c.VDW.AUTO) type = this.defaultVdw;
if (type === J.c.VDW.USER && this.bsUserVdws == null) this.setUserVdw(this.defaultVdw);
return this.getDataManager().getDefaultVdwNameOrData(type, bs);
}, "~N,J.c.VDW,JU.BS");
Clazz.defineMethod(c$, "deleteAtoms", 
function(bsAtoms, fullModels){
var atomIndex = (bsAtoms == null ? -1 : bsAtoms.nextSetBit(0));
if (atomIndex < 0) return 0;
this.clearModelDependentObjects();
var a = this.ms.at[atomIndex];
if (a == null) return 0;
var mi = a.mi;
if (fullModels) {
return this.deleteModels(mi, bsAtoms);
}this.sm.setStatusStructureModified(atomIndex, a.mi, 4, "deleting atoms " + bsAtoms, bsAtoms.cardinality(), bsAtoms);
this.ms.deleteAtoms(bsAtoms);
var n = this.slm.deleteAtoms(bsAtoms);
this.setTainted(true);
this.sm.setStatusStructureModified(atomIndex, mi, -4, "OK", n, bsAtoms);
return n;
}, "JU.BS,~B");
Clazz.defineMethod(c$, "deleteModels", 
function(modelIndex, bsAtoms){
var bsModels = (bsAtoms == null ? JU.BSUtil.newAndSetBit(modelIndex) : this.ms.getModelBS(bsAtoms, false));
this.clearModelDependentObjects();
bsAtoms = this.getModelUndeletedAtomsBitSetBs(bsModels);
var n = bsAtoms.cardinality();
var currentModel = this.am.cmi;
this.setCurrentModelIndexClear(0, false);
this.am.setAnimationOn(false);
var bsD0 = JU.BSUtil.copy(this.slm.bsDeleted);
var bsDeleted = this.ms.deleteModels(bsModels);
if (bsDeleted == null) {
this.setCurrentModelIndexClear(currentModel, false);
return 0;
}this.sm.setStatusStructureModified(-1, modelIndex, 5, "deleting model " + this.getModelNumberDotted(modelIndex), n, bsAtoms);
this.slm.processDeletedModelAtoms(bsDeleted);
if (this.eval != null) this.eval.deleteAtomsInVariables(bsDeleted);
this.setAnimationRange(0, 0);
this.clearRepaintManager(-1);
this.am.clear();
this.am.initializePointers(1);
this.setCurrentModelIndexClear(this.ms.mc > 1 ? -1 : 0, this.ms.mc > 1);
this.hoverAtomIndex = -1;
this.setFileLoadStatus(J.c.FIL.DELETED, null, null, null, null, null);
this.refreshMeasures(true);
if (bsD0 != null) bsDeleted.andNot(bsD0);
n = JU.BSUtil.cardinalityOf(bsDeleted);
this.sm.setStatusStructureModified(-1, modelIndex, -5, "OK", n, bsDeleted);
return n;
}, "~N,JU.BS");
Clazz.defineMethod(c$, "deleteBonds", 
function(bsDeleted){
var modelIndex = this.ms.bo[bsDeleted.nextSetBit(0)].atom1.mi;
var n = bsDeleted.cardinality();
if (n == 0) return;
this.sm.setStatusStructureModified(-1, modelIndex, 2, "delete bonds " + JU.Escape.eBond(bsDeleted), bsDeleted.cardinality(), bsDeleted);
this.ms.deleteBonds(bsDeleted, false);
this.sm.setStatusStructureModified(-1, modelIndex, -2, "OK", bsDeleted.cardinality(), bsDeleted);
}, "JU.BS");
Clazz.defineMethod(c$, "deleteModelAtoms", 
function(modelIndex, firstAtomIndex, nAtoms, bsModelAtoms){
var n = bsModelAtoms.cardinality();
if (n == 0) return;
this.sm.setStatusStructureModified(-1, modelIndex, 7, "delete atoms " + JU.Escape.eBS(bsModelAtoms), n, bsModelAtoms);
JU.BSUtil.deleteBits(this.tm.bsFrameOffsets, bsModelAtoms);
this.getDataManager().deleteModelAtoms(firstAtomIndex, nAtoms, bsModelAtoms);
this.sm.setStatusStructureModified(-1, modelIndex, -7, "OK", n, bsModelAtoms);
}, "~N,~N,~N,JU.BS");
Clazz.defineMethod(c$, "getQuaternionFrame", 
function(){
return this.g.quaternionFrame.charAt(this.g.quaternionFrame.length == 2 ? 1 : 0);
});
Clazz.defineMethod(c$, "loadImageData", 
function(image, nameOrError, echoName, sco){
var sc = sco;
if (image == null && nameOrError != null) this.scriptEcho(nameOrError);
if (echoName == null) {
this.setBackgroundImage((image == null ? null : nameOrError), image);
} else if (echoName.startsWith("\1")) {
this.sm.showImage(echoName, image);
} else if (echoName.startsWith("\0")) {
if (image != null) {
this.setWindowDimensions( Clazz.newFloatArray(-1, [this.apiPlatform.getImageWidth(image), this.apiPlatform.getImageHeight(image)]));
}} else {
this.shm.loadShape(31);
this.setShapeProperty(31, "text", nameOrError);
if (image != null) this.setShapeProperty(31, "image", image);
}if (JV.Viewer.isJS && sc != null) {
sc.mustResumeEval = true;
this.eval.resumeEval(sc);
}return false;
}, "~O,~S,~S,~O");
Clazz.defineMethod(c$, "cd", 
function(dir){
if (dir == null) {
dir = ".";
} else if (dir.length == 0) {
this.setStringProperty("defaultDirectory", "");
dir = ".";
}dir = this.fm.getDefaultDirectory(dir + (dir.equals("=") ? "" : dir.endsWith("/") ? "X.spt" : "/X.spt"));
if (dir.length > 0) this.setStringProperty("defaultDirectory", dir);
var path = this.fm.getFilePath(dir + "/", true, false);
if (path.startsWith("file:/")) JV.FileManager.setLocalPath(this, dir, false);
return dir;
}, "~S");
Clazz.defineMethod(c$, "setErrorMessage", 
function(errMsg, errMsgUntranslated){
this.errorMessageUntranslated = errMsgUntranslated;
if (errMsg != null) this.eval.stopScriptThreads();
return (this.errorMessage = errMsg);
}, "~S,~S");
Clazz.overrideMethod(c$, "getErrorMessage", 
function(){
return this.errorMessage;
});
Clazz.overrideMethod(c$, "getErrorMessageUn", 
function(){
return this.errorMessageUntranslated == null ? this.errorMessage : this.errorMessageUntranslated;
});
Clazz.defineMethod(c$, "setShapeErrorState", 
function(shapeID, state){
this.currentShapeID = shapeID;
this.currentShapeState = state;
}, "~N,~S");
Clazz.defineMethod(c$, "getShapeErrorState", 
function(){
if (this.currentShapeID < 0) return "";
this.shm.releaseShape(this.currentShapeID);
this.clearRepaintManager(this.currentShapeID);
return JV.JC.getShapeClassName(this.currentShapeID, false) + " " + this.currentShapeState;
});
Clazz.defineMethod(c$, "handleError", 
function(er, doClear){
try {
if (doClear) this.zapMsg("" + er);
this.undoMoveAction(4165, -2);
if (JU.Logger.getLogLevel() == 0) JU.Logger.setLogLevel(4);
this.setCursor(0);
this.setBooleanPropertyTok("refreshing", 603979900, true);
this.fm.setPathForAllFiles("");
JU.Logger.error("vwr handling error condition: " + er + "  ");
this.notifyError("Error", "doClear=" + doClear + "; " + er, "" + er);
} catch (e1) {
try {
JU.Logger.error("Could not notify error " + er + ": due to " + e1);
} catch (er2) {
}
}
}, "Throwable,~B");
Clazz.defineMethod(c$, "getFunctions", 
function(isStatic){
return (isStatic ? JV.Viewer.staticFunctions : this.localFunctions);
}, "~B");
Clazz.defineMethod(c$, "removeFunction", 
function(name){
name = name.toLowerCase();
var $function = this.getFunction(name);
if ($function == null) return;
JV.Viewer.staticFunctions.remove(name);
this.localFunctions.remove(name);
}, "~S");
Clazz.defineMethod(c$, "getFunction", 
function(name){
if (name == null) return null;
var $function = (JV.Viewer.isStaticFunction(name) ? JV.Viewer.staticFunctions : this.localFunctions).get(name);
return ($function == null || $function.geTokens() == null ? null : $function);
}, "~S");
c$.isStaticFunction = Clazz.defineMethod(c$, "isStaticFunction", 
function(name){
return name.startsWith("static_");
}, "~S");
Clazz.defineMethod(c$, "isFunction", 
function(name){
return (JV.Viewer.isStaticFunction(name) ? JV.Viewer.staticFunctions : this.localFunctions).containsKey(name);
}, "~S");
Clazz.defineMethod(c$, "clearFunctions", 
function(){
JV.Viewer.staticFunctions.clear();
this.localFunctions.clear();
});
Clazz.defineMethod(c$, "addFunction", 
function($function){
var name = $function.getName();
(JV.Viewer.isStaticFunction(name) ? JV.Viewer.staticFunctions : this.localFunctions).put(name, $function);
}, "J.api.JmolScriptFunction");
Clazz.defineMethod(c$, "getFunctionCalls", 
function(selectedFunction){
return this.getStateCreator().getFunctionCalls(selectedFunction);
}, "~S");
Clazz.defineMethod(c$, "checkPrivateKey", 
function(privateKey){
return privateKey == this.privateKey;
}, "~N");
Clazz.defineMethod(c$, "bindAction", 
function(desc, name){
if (this.haveDisplay) this.acm.bind(desc, name);
}, "~S,~S");
Clazz.defineMethod(c$, "unBindAction", 
function(desc, name){
if (this.haveDisplay) this.acm.unbindAction(desc, name);
}, "~S,~S");
Clazz.defineMethod(c$, "calculateStruts", 
function(bs1, bs2){
return this.ms.calculateStruts(bs1 == null ? this.bsA() : bs1, bs2 == null ? this.bsA() : bs2);
}, "JU.BS,JU.BS");
Clazz.defineMethod(c$, "getPreserveState", 
function(){
return (this.g.preserveState && this.scm != null);
});
Clazz.defineMethod(c$, "isKiosk", 
function(){
return this.$isKiosk;
});
Clazz.defineMethod(c$, "hasFocus", 
function(){
return (this.haveDisplay && (this.$isKiosk || this.apiPlatform.hasFocus(this.display)));
});
Clazz.defineMethod(c$, "setFocus", 
function(){
if (this.haveDisplay && !this.apiPlatform.hasFocus(this.display)) this.apiPlatform.requestFocusInWindow(this.display);
});
Clazz.defineMethod(c$, "stopMinimization", 
function(){
if (this.minimizer != null) {
this.minimizer.setProperty("stop", null);
}});
Clazz.defineMethod(c$, "clearMinimization", 
function(){
if (this.minimizer != null) this.minimizer.setProperty("clear", null);
});
Clazz.defineMethod(c$, "getMinimizationInfo", 
function(){
return (this.minimizer == null ? "" : this.minimizer.getProperty("log", 0));
});
Clazz.defineMethod(c$, "checkMinimization", 
function(){
this.refreshMeasures(true);
if (!this.g.monitorEnergy) return;
try {
this.minimize(null, 0, 0, this.getFrameAtoms(), null, null, 0, 1);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
this.echoMessage(this.getP("_minimizationForceField") + " Energy = " + this.getP("_minimizationEnergy"));
});
Clazz.defineMethod(c$, "minimize", 
function(eval, steps, crit, bsSelected, bsFixed, bsInFrame, rangeFixed, flags){
var isSelectionExplicit = (bsSelected != null);
if (isSelectionExplicit) {
flags |= 2;
}var addHydrogen = (flags & 16) != 0;
var isModelkitCmd = (flags & 256) != 0;
var isSilent = (flags & 1) != 0;
var isQuick = (flags & 8) != 0;
var groupSelected = (flags & 64) != 0;
var selectedOnly = groupSelected || (flags & 32) != 0;
var isFixExplicit = (bsFixed != null);
if (this.isModelKitOpen()) this.setModelkitPropertySafely("constraint", null);
if (bsInFrame == null) bsInFrame = this.getFrameAtoms();
if (!isQuick && !addHydrogen && isSelectionExplicit && !isFixExplicit && !selectedOnly) {
var bs = JU.BSUtil.copy(bsInFrame);
bsFixed = JU.BSUtil.copy(bs);
bsFixed.andNot(bsSelected);
bsSelected = bs;
isFixExplicit = true;
}if (!isSelectionExplicit) {
bsSelected = this.getThisModelAtoms();
if (selectedOnly) bsSelected.and(this.bsA());
} else if (!isQuick) {
bsSelected.and(bsInFrame);
}if (bsSelected.isEmpty()) return;
var bsBasis = (isModelkitCmd || !selectedOnly ? JU.BSUtil.copy(this.ms.am[this.ms.at[bsSelected.nextSetBit(0)].mi].bsAsymmetricUnit) : null);
if (isModelkitCmd && bsBasis == null) {
this.scriptStatusMsg("MODELKIT MINIMIZE is only applicable to crystal structures.", "minimization: not a crystal structure");
return;
}try {
if (isModelkitCmd) {
this.getModelkit(false).cmdMinimize(eval, bsBasis, steps, crit, rangeFixed, flags);
return;
}var ff = (bsBasis == null ? this.g.forceField : "UFF");
this.getModelForAtomIndex(bsSelected.nextSetBit(0)).auxiliaryInfo.put("dimension", "3D");
if (isQuick) {
bsInFrame = bsSelected;
}var bsMotionFixed = JU.BSUtil.copy(isFixExplicit ? bsFixed : this.slm.getMotionFixedAtoms());
var haveFixed = !bsMotionFixed.isEmpty();
if (haveFixed) bsSelected.andNot(bsMotionFixed);
var bsNearby = (bsBasis != null && isModelkitCmd ? this.getThisModelAtoms() : selectedOnly || !haveFixed ?  new JU.BS() : this.ms.getAtomsWithinRadius((rangeFixed <= 0 ? 5.0 : rangeFixed), bsSelected, true, null, null));
bsNearby.andNot(bsSelected);
if (haveFixed) {
bsMotionFixed.and(bsNearby);
} else {
bsMotionFixed = bsNearby;
}bsMotionFixed.and(bsInFrame);
flags |= ((haveFixed ? 4 : 0) | (this.getBooleanProperty("minimizationSilent") ? 1 : 0));
if (isQuick && this.getBoolean(603979962)) return;
if (isQuick) {
{
try {
if (!isSilent) JU.Logger.info("Minimizing " + bsSelected.cardinality() + " atoms");
this.getMinimizer(true).minimize(steps, crit, bsSelected, bsMotionFixed, null, flags, "UFF");
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
JU.Logger.error("Minimization error: " + e.toString());
e.printStackTrace();
} else {
throw e;
}
}
}}if (addHydrogen) {
var bsH = this.addHydrogens(bsSelected, flags);
if (!isQuick) bsSelected.or(bsH);
}var n = bsSelected.cardinality();
if (ff.equals("MMFF") && n > this.g.minimizationMaxAtoms) {
this.scriptStatusMsg("Too many atoms for minimization (" + n + ">" + this.g.minimizationMaxAtoms + "); use 'set minimizationMaxAtoms' to increase this limit", "minimization: too many atoms");
return;
}if (groupSelected) {
bsMotionFixed.or(this.ms.getConnectingAtoms(bsSelected, bsMotionFixed));
bsSelected.andNot(bsMotionFixed);
}if (!isSilent) JU.Logger.info("Minimizing " + bsSelected.cardinality() + " atoms");
this.getMinimizer(true).minimize(steps, crit, bsSelected, bsMotionFixed, bsBasis, flags, (isQuick ? "MMFF" : ff));
if (isQuick) {
this.g.forceField = "MMFF";
this.setHydrogens(bsSelected);
var ffUsed = this.getMinimizer(false).getForceFieldUsed();
if (ffUsed != null) this.showString("Minimized by Jmol using " + ffUsed, false);
}} catch (e$$) {
if (Clazz.exceptionOf(e$$,"JV.JmolAsyncException")){
var e = e$$;
{
if (eval != null) eval.loadFileResourceAsync(e.getFileName());
}
} else if (Clazz.exceptionOf(e$$, Exception)){
var e = e$$;
{
JU.Logger.error("Minimization error: " + e.toString());
e.printStackTrace();
}
} else {
throw e$$;
}
}
}, "J.api.JmolScriptEvaluator,~N,~N,JU.BS,JU.BS,JU.BS,~N,~N");
Clazz.defineMethod(c$, "setHydrogens", 
function(bsAtoms){
var nTotal =  Clazz.newIntArray (1, 0);
var hatoms = this.ms.calculateHydrogens(bsAtoms, nTotal, null, 2056);
for (var i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms.nextSetBit(i + 1)) {
var pts = hatoms[i];
if (pts == null || pts.length == 0) continue;
var a = this.ms.at[i];
var b = a.bonds;
for (var j = 0, pt = 0, n = a.getBondCount(); j < n; j++) {
var h = b[j].getOtherAtom(a);
if (h.getAtomicAndIsotopeNumber() == 1) {
var p = pts[pt++];
if (p != null) this.ms.setAtomCoord(h.i, p.x, p.y, p.z);
}}
}
this.ms.resetMolecules();
}, "JU.BS");
Clazz.defineMethod(c$, "setMotionFixedAtoms", 
function(bs){
this.slm.setMotionFixedAtoms(bs);
}, "JU.BS");
Clazz.defineMethod(c$, "setMotionFixed", 
function(bs){
this.slm.setMotionFixedAtoms(bs);
}, "JU.BS");
Clazz.defineMethod(c$, "getMotionFixedAtoms", 
function(sym, bsFixed){
if (this.am.cmi < 0) return  new JU.BS();
if (bsFixed == null) bsFixed =  new JU.BS();
bsFixed.or(this.slm.getMotionFixedAtoms());
bsFixed.and(this.getThisModelAtoms());
if (sym == null) sym = this.getOperativeSymmetry();
if (sym != null && this.getModelkit(false) != null) this.modelkit.addLockedAtoms(sym, bsFixed);
return bsFixed;
}, "J.api.SymmetryInterface,JU.BS");
Clazz.defineMethod(c$, "getAtomicPropertyState", 
function(commands, type, bs, name, data){
this.getStateCreator().getAtomicPropertyStateBuffer(commands, type, bs, name, data);
}, "JU.SB,~N,JU.BS,~S,~A");
Clazz.defineMethod(c$, "getCenterAndPoints", 
function(atomSets, addCenter){
return this.ms.getCenterAndPoints(atomSets, addCenter);
}, "JU.Lst,~B");
Clazz.defineMethod(c$, "writeFileData", 
function(fileName, type, modelIndex, parameters){
return this.getOutputManager().writeFileData(fileName, type, modelIndex, parameters);
}, "~S,~S,~N,~A");
Clazz.defineMethod(c$, "getPdbData", 
function(modelIndex, type, bsAtoms, parameters, oc, getStructure){
return this.getPropertyManager().getPdbData(modelIndex, type, bsAtoms == null ? this.bsA() : bsAtoms, parameters, oc, getStructure);
}, "~N,~S,JU.BS,~A,JU.OC,~B");
Clazz.defineMethod(c$, "getGroupsWithin", 
function(nResidues, bs){
return this.ms.getGroupsWithin(nResidues, bs);
}, "~N,JU.BS");
Clazz.defineMethod(c$, "setShapeSize", 
function(shapeID, madOrMad10, bsSelected){
if (bsSelected == null) bsSelected = this.bsA();
this.shm.setShapeSizeBs(shapeID, madOrMad10, null, bsSelected);
}, "~N,~N,JU.BS");
Clazz.defineMethod(c$, "setShapeProperty", 
function(shapeID, propertyName, value){
if (shapeID >= 0) this.shm.setShapePropertyBs(shapeID, propertyName, value, null);
}, "~N,~S,~O");
Clazz.defineMethod(c$, "getShapeProperty", 
function(shapeType, propertyName){
return this.shm.getShapePropertyIndex(shapeType, propertyName, -2147483648);
}, "~N,~S");
Clazz.defineMethod(c$, "getShapePropertyAsInt", 
function(shapeID, propertyName){
var value = this.getShapeProperty(shapeID, propertyName);
return value == null || !(Clazz.instanceOf(value, Integer)) ? -2147483648 : (value).intValue();
}, "~N,~S");
Clazz.defineMethod(c$, "setModelVisibility", 
function(){
if (this.shm != null) this.shm.setModelVisibility();
});
Clazz.defineMethod(c$, "resetShapes", 
function(andCreateNew){
this.shm.resetShapes(!andCreateNew);
if (andCreateNew) {
this.shm.loadDefaultShapes(this.ms);
this.clearRepaintManager(-1);
}}, "~B");
Clazz.defineMethod(c$, "setParallel", 
function(TF){
return (this.$isParallel = this.g.multiProcessor && TF);
}, "~B");
Clazz.defineMethod(c$, "isParallel", 
function(){
return this.g.multiProcessor && this.$isParallel;
});
Clazz.defineMethod(c$, "undoMoveAction", 
function(action, n){
return (this.g.preserveState ? this.getStateCreator().undoMoveAction(action, n) : 0);
}, "~N,~N");
Clazz.defineMethod(c$, "undoMoveActionClear", 
function(taintedAtom, type, clearRedo){
if (this.g.preserveState && this.getOperativeSymmetry() == null) this.getStateCreator().undoMoveActionClear(taintedAtom, type, clearRedo);
}, "~N,~N,~B");
Clazz.defineMethod(c$, "moveAtomWithHydrogens", 
function(atomIndex, deltaX, deltaY, deltaZ, ptNew, bsAtoms){
this.stopMinimization();
var modelkitNoAddH = (ptNew != null && deltaX == 0);
var atom = this.ms.at[atomIndex];
if (bsAtoms == null) {
bsAtoms = JU.BSUtil.newAndSetBit(atomIndex);
var addH = (this.getOperativeSymmetry() == null || this.isModelKitOpen() && !this.modelkit.hasConstraint(atomIndex, true, false));
if (addH && !modelkitNoAddH) this.ms.addConnectedHAtoms(atom, bsAtoms);
}return this.moveSelected(deltaX, deltaY, deltaZ, -2147483648, -2147483648, bsAtoms, atom, ptNew, true, true, 0);
}, "~N,~N,~N,~N,JU.P3,JU.BS");
Clazz.defineMethod(c$, "isModelPDB", 
function(i){
return this.ms.am[i].isBioModel;
}, "~N");
Clazz.overrideMethod(c$, "deleteMeasurement", 
function(i){
this.setShapeProperty(6, "delete", Integer.$valueOf(i));
}, "~N");
Clazz.overrideMethod(c$, "getSmiles", 
function(bs){
return this.getSmilesOpt(bs, -1, -1, 16 | (bs == null && JU.Logger.debugging ? 131072 : 0), null);
}, "JU.BS");
Clazz.overrideMethod(c$, "getOpenSmiles", 
function(bs){
return this.getSmilesOpt(bs, -1, -1, 5 | (bs == null && JU.Logger.debugging ? 131072 : 0), "/open///");
}, "JU.BS");
Clazz.defineMethod(c$, "getBioSmiles", 
function(bs){
return this.getSmilesOpt(bs, -1, -1, 3145728 | 5242880 | 17825792 | (JU.Logger.debugging ? 131072 : 0), null);
}, "JU.BS");
Clazz.defineMethod(c$, "getSmilesOpt", 
function(bsSelected, index1, index2, flags, options){
var bioComment = ((flags & 17825792) == 17825792 ? JV.Viewer.getJmolVersion() + " " + this.getModelName(this.am.cmi) : options);
var atoms = this.ms.at;
if (bsSelected == null) {
if (index1 < 0 || index2 < 0) {
bsSelected = this.bsA();
} else {
if ((flags & 1048576) == 1048576) {
if (index1 > index2) {
var i = index1;
index1 = index2;
index2 = i;
}index1 = atoms[index1].group.firstAtomIndex;
index2 = atoms[index2].group.lastAtomIndex;
}bsSelected =  new JU.BS();
bsSelected.setBits(index1, index2 + 1);
}}flags |= (this.isModel2D(bsSelected) ? 134217728 : 0);
var sm = this.getSmilesMatcher();
if (JV.JC.isSmilesCanonical(options)) {
var smiles = sm.getSmiles(atoms, this.ms.ac, bsSelected, "/noAromatic/", flags);
return this.getChemicalInfo(smiles, "smiles", null).trim();
}return sm.getSmiles(atoms, this.ms.ac, bsSelected, bioComment, flags);
}, "JU.BS,~N,~N,~N,~S");
Clazz.defineMethod(c$, "isModel2D", 
function(bs){
var m = this.getModelForAtomIndex(bs.nextSetBit(0));
return (m != null && "2D".equals(m.auxiliaryInfo.get("dimension")));
}, "JU.BS");
Clazz.defineMethod(c$, "alert", 
function(msg){
this.prompt(msg, null, null, true);
}, "~S");
Clazz.defineMethod(c$, "prompt", 
function(label, data, list, asButtons){
return (this.$isKiosk ? "null" : this.apiPlatform.prompt(label, data, list, asButtons));
}, "~S,~S,~A,~B");
Clazz.defineMethod(c$, "dialogAsk", 
function(type, fileName, params){
{
return prompt(type, fileName);
}}, "~S,~S,java.util.Map");
Clazz.defineMethod(c$, "initializeExporter", 
function(params){
var isJS = params.get("type").equals("JS");
if (isJS) {
if (this.jsExporter3D != null) {
this.jsExporter3D.initializeOutput(this, this.privateKey, params);
return this.jsExporter3D;
}} else {
var fileName = params.get("fileName");
var fullPath = params.get("fullPath");
var out = this.getOutputChannel(fileName, fullPath);
if (out == null) return null;
params.put("outputChannel", out);
}var export3D = J.api.Interface.getOption("export.Export3D", this, "export");
if (export3D == null) return null;
var exporter = export3D.initializeExporter(this, this.privateKey, this.gdata, params);
if (isJS && exporter != null) this.jsExporter3D = export3D;
return (exporter == null ? null : export3D);
}, "java.util.Map");
Clazz.defineMethod(c$, "getMouseEnabled", 
function(){
return this.refreshing && !this.creatingImage;
});
Clazz.overrideMethod(c$, "calcAtomsMinMax", 
function(bs, boxInfo){
this.ms.calcAtomsMinMax(bs, boxInfo);
}, "JU.BS,JU.BoxInfo");
Clazz.defineMethod(c$, "getObjectMap", 
function(map, c){
switch ((c).charCodeAt(0)) {
case 123:
if (this.getScriptManager() != null) {
var m = map;
if (this.definedAtomSets != null) m.putAll(this.definedAtomSets);
JS.T.getTokensType(m, 2097152);
}return;
case 36:
case 48:
this.shm.getObjectMap(map, c == '$');
return;
}
}, "java.util.Map,~S");
Clazz.defineMethod(c$, "setPicked", 
function(atomIndex, andReset){
var pickedSet = null;
var pickedList = null;
if (atomIndex >= 0) {
if (andReset) this.setPicked(-1, false);
this.g.setI("_atompicked", atomIndex);
pickedSet = this.g.getParam("picked", true);
pickedList = this.g.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.g.setUserVariable("picked", pickedSet);
this.g.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(null, p);
if (p.tok != 10 || !(p.value).get(atomIndex)) pickedList.pushPop(null, JS.SV.newV(10, JU.BSUtil.newAndSetBit(atomIndex)));
}, "~N,~B");
Clazz.overrideMethod(c$, "runScript", 
function(script){
return "" + this.evaluateExpression( Clazz.newArray(-1, [ Clazz.newArray(-1, [JS.T.tokenScript, JS.T.tokenLeftParen, JS.SV.newS(script), JS.T.tokenRightParen])]));
}, "~S");
Clazz.overrideMethod(c$, "runScriptCautiously", 
function(script){
var outputBuffer =  new JU.SB();
try {
if (this.getScriptManager() == null) return null;
this.eval.runScriptBuffer(script, outputBuffer, false);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
return this.eval.getErrorMessage();
} else {
throw e;
}
}
return outputBuffer.toString();
}, "~S");
Clazz.defineMethod(c$, "setFrameDelayMs", 
function(millis){
this.ms.setFrameDelayMs(millis, this.getVisibleFramesBitSet());
}, "~N");
Clazz.defineMethod(c$, "getBaseModelBitSet", 
function(){
return this.ms.getModelAtomBitSetIncludingDeleted(this.getJDXBaseModelIndex(this.am.cmi), true);
});
Clazz.defineMethod(c$, "clearTimeouts", 
function(){
if (this.timeouts != null) J.thread.TimeoutThread.clear(this.timeouts);
});
Clazz.defineMethod(c$, "setTimeout", 
function(name, mSec, script){
if (!this.haveDisplay || this.headless || this.autoExit) return;
if (name == null) {
this.clearTimeouts();
return;
}if (this.timeouts == null) {
this.timeouts =  new java.util.Hashtable();
}J.thread.TimeoutThread.setTimeout(this, this.timeouts, name, mSec, script);
}, "~S,~N,~S");
Clazz.defineMethod(c$, "triggerTimeout", 
function(name){
if (!this.haveDisplay || this.timeouts == null) return;
J.thread.TimeoutThread.trigger(this.timeouts, name);
}, "~S");
Clazz.defineMethod(c$, "clearTimeout", 
function(name){
this.setTimeout(name, 0, null);
}, "~S");
Clazz.defineMethod(c$, "showTimeout", 
function(name){
return (this.haveDisplay ? J.thread.TimeoutThread.showTimeout(this.timeouts, name) : "");
}, "~S");
Clazz.defineMethod(c$, "getOrCalcPartialCharges", 
function(bsSelected, bsIgnore){
if (bsSelected == null) bsSelected = this.bsA();
bsSelected = JU.BSUtil.copy(bsSelected);
JU.BSUtil.andNot(bsSelected, bsIgnore);
JU.BSUtil.andNot(bsSelected, this.ms.bsPartialCharges);
if (!bsSelected.isEmpty()) this.calculatePartialCharges(bsSelected);
return this.ms.getPartialCharges();
}, "JU.BS,JU.BS");
Clazz.defineMethod(c$, "calculatePartialCharges", 
function(bsSelected){
if (bsSelected == null || bsSelected.isEmpty()) bsSelected = this.getFrameAtoms();
if (bsSelected.isEmpty()) return;
JU.Logger.info("Calculating MMFF94 partial charges for " + bsSelected.cardinality() + " atoms");
this.getMinimizer(true).calculatePartialCharges(this.ms, bsSelected, null);
}, "JU.BS");
Clazz.defineMethod(c$, "setCurrentModelID", 
function(id){
var modelIndex = this.am.cmi;
if (modelIndex >= 0) this.ms.setInfo(modelIndex, "modelID", id);
}, "~S");
Clazz.defineMethod(c$, "cacheClear", 
function(){
this.fm.cacheClear();
this.ligandModelSet = null;
this.ligandModels = null;
this.ms.clearCache();
this.cm.ce.clearCache();
});
Clazz.defineMethod(c$, "cachePut", 
function(key, data){
JU.Logger.info("Viewer cachePut " + key);
this.fm.cachePut(key, data);
}, "~S,~O");
Clazz.defineMethod(c$, "cacheFileByName", 
function(fileName, isAdd){
if (fileName == null) {
this.cacheClear();
return -1;
}return this.fm.cacheFileByNameAdd(fileName, isAdd);
}, "~S,~B");
Clazz.defineMethod(c$, "clearThreads", 
function(){
if (this.eval != null) this.eval.stopScriptThreads();
this.stopMinimization();
this.tm.clearThreads();
this.setAnimationOn(false);
});
Clazz.defineMethod(c$, "getEvalContextAndHoldQueue", 
function(eval){
if (eval == null || !(JV.Viewer.isJS || this.testAsync)) return null;
eval.pushContextDown("getEvalContextAndHoldQueue");
var sc = eval.getThisContext();
sc.setMustResume();
sc.isJSThread = true;
this.queueOnHold = true;
return sc;
}, "J.api.JmolScriptEvaluator");
Clazz.defineMethod(c$, "getDefaultPropertyParam", 
function(propertyID){
return this.getPropertyManager().getDefaultPropertyParam(propertyID);
}, "~N");
Clazz.defineMethod(c$, "getPropertyNumber", 
function(name){
return this.getPropertyManager().getPropertyNumber(name);
}, "~S");
Clazz.defineMethod(c$, "checkPropertyParameter", 
function(name){
return this.getPropertyManager().checkPropertyParameter(name);
}, "~S");
Clazz.defineMethod(c$, "extractProperty", 
function(property, args, pt){
return this.getPropertyManager().extractProperty(property, args, pt, null, false);
}, "~O,~O,~N");
Clazz.defineMethod(c$, "addHydrogens", 
function(bsAtoms, flags){
var isSilent = ((flags & 1) == 1);
var isQuick = ((flags & 8) == 8);
var doAll = (bsAtoms == null);
if (bsAtoms == null) bsAtoms = this.getModelUndeletedAtomsBitSet(this.getVisibleFramesBitSet().length() - 1);
var bsB =  new JU.BS();
if (bsAtoms.isEmpty()) return bsB;
var vConnections =  new JU.Lst();
var pts = this.getAdditionalHydrogens(bsAtoms, vConnections, flags | (doAll ? 256 : 0));
var wasAppendNew = false;
wasAppendNew = this.g.appendNew;
if (pts.length > 0) {
this.clearModelDependentObjects();
try {
bsB = (isQuick && vConnections.get(0).mi == this.ms.mc - 1 ? this.ms.addHydrogens(vConnections, pts) : this.addHydrogensInline(bsAtoms, vConnections, pts, null));
this.setModelkitPropertySafely("updateatomkeys", bsAtoms);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
System.out.println(e.toString());
} else {
throw e;
}
}
if (wasAppendNew) this.g.appendNew = true;
}if (!isSilent) this.scriptStatus(J.i18n.GT.i(J.i18n.GT.$("{0} hydrogens added"), pts.length));
return bsB;
}, "JU.BS,~N");
Clazz.defineMethod(c$, "addHydrogensInline", 
function(bsAtoms, vConnections, pts, htParams){
if (this.getScriptManager() == null) return null;
return this.scm.addHydrogensInline(bsAtoms, vConnections, pts, htParams);
}, "JU.BS,JU.Lst,~A,java.util.Map");
Clazz.overrideMethod(c$, "evalFunctionFloat", 
function(func, params, values){
return (this.getScriptManager() == null ? 0 : this.eval.evalFunctionFloat(func, params, values));
}, "~O,~O,~A");
Clazz.defineMethod(c$, "evalParallel", 
function(context, shapeManager){
this.displayLoadErrors = false;
var isOK = this.getScriptManager() != null && this.eval.evalParallel(context, (shapeManager == null ? this.shm : shapeManager));
this.displayLoadErrors = true;
return isOK;
}, "JS.ScriptContext,JV.ShapeManager");
Clazz.overrideMethod(c$, "evaluateExpression", 
function(stringOrTokens){
return (this.getScriptManager() == null ? null : this.eval.evaluateExpression(stringOrTokens, false, false));
}, "~O");
Clazz.overrideMethod(c$, "evaluateExpressionAsVariable", 
function(stringOrTokens){
return (this.getScriptManager() == null ? null : this.eval.evaluateExpression(stringOrTokens, true, false));
}, "~O");
Clazz.defineMethod(c$, "getAtomBitSet", 
function(atomExpression){
if (Clazz.instanceOf(atomExpression,"JU.BS")) return this.slm.excludeAtoms(atomExpression, false);
this.getScriptManager();
return this.getAtomBitSetEval(this.eval, atomExpression);
}, "~O");
Clazz.defineMethod(c$, "getScriptContext", 
function(why){
return (this.getScriptManager() == null ? null : this.eval.getScriptContext(why));
}, "~S");
Clazz.defineMethod(c$, "getAtomDefs", 
function(names){
var keys =  new JU.Lst();
for (var e, $e = names.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) if (Clazz.instanceOf(e.getValue(),"JU.BS")) keys.addLast("{" + e.getKey() + "} <" + (e.getValue()).cardinality() + " atoms>\n");

var n = keys.size();
var k =  new Array(n);
keys.toArray(k);
java.util.Arrays.sort(k);
var sb =  new JU.SB();
for (var i = 0; i < n; i++) sb.append(k[i]);

return sb.append("\n").toString();
}, "java.util.Map");
Clazz.defineMethod(c$, "setCGO", 
function(info){
this.shm.loadShape(23);
this.shm.setShapePropertyBs(23, "setCGO", info, null);
}, "JU.Lst");
Clazz.defineMethod(c$, "setModelSet", 
function(modelSet){
this.ms = this.mm.modelSet = modelSet;
}, "JM.ModelSet");
Clazz.defineMethod(c$, "setObjectProp", 
function(id, tokCommand){
this.getScriptManager();
if (id == null) id = "*";
return (this.eval == null ? null : this.eval.setObjectPropSafe(id, tokCommand));
}, "~S,~N");
Clazz.defineMethod(c$, "setDihedrals", 
function(dihedralList, bsBranches, rate){
if (bsBranches == null) bsBranches = this.ms.getBsBranches(dihedralList);
this.ms.setDihedrals(dihedralList, bsBranches, rate);
}, "~A,~A,~N");
Clazz.defineMethod(c$, "getChainID", 
function(id, isAssign){
var iboxed = this.chainMap.get(id);
if (iboxed != null) return iboxed.intValue();
var i = (id.charAt(0)).charCodeAt(0);
if (id.length > 1) {
i = 300 + this.chainList.size();
} else if ((isAssign || this.chainCaseSpecified) && 97 <= i && i <= 122) {
i += 159;
}if (i >= 256) {
iboxed = this.chainMap.get(id);
if (iboxed != null) return iboxed.intValue();
this.chainCaseSpecified = new Boolean (this.chainCaseSpecified | isAssign).valueOf();
this.chainList.addLast(id);
}iboxed = Integer.$valueOf(i);
this.chainMap.put(iboxed, id);
this.chainMap.put(id, iboxed);
return i;
}, "~S,~B");
Clazz.defineMethod(c$, "getChainIDStr", 
function(id){
return this.chainMap.get(Integer.$valueOf(id));
}, "~N");
Clazz.defineMethod(c$, "getScriptQueueInfo", 
function(){
return (this.scm != null && this.scm.isQueueProcessing() ? Boolean.TRUE : Boolean.FALSE);
});
Clazz.defineMethod(c$, "getNMRCalculation", 
function(){
return (this.nmrCalculation == null ? (this.nmrCalculation = J.api.Interface.getOption("quantum.NMRCalculation", this, "script")).setViewer(this) : this.nmrCalculation);
});
Clazz.defineMethod(c$, "getDistanceUnits", 
function(s){
if (s == null) s = this.getDefaultMeasurementLabel(2);
var pt = s.indexOf("//");
return (pt < 0 ? this.g.measureDistanceUnits : s.substring(pt + 2));
}, "~S");
Clazz.defineMethod(c$, "calculateFormalCharges", 
function(bs){
return this.ms.fixFormalCharges(bs == null ? this.bsA() : bs);
}, "JU.BS");
Clazz.defineMethod(c$, "setModulation", 
function(bs, isOn, t1, isQ){
if (isQ) this.g.setO("_modt", JU.Escape.eP(t1));
this.ms.setModulation(bs == null ? this.getAllAtoms() : bs, isOn, t1, isQ);
this.refreshMeasures(true);
}, "JU.BS,~B,JU.P3,~B");
Clazz.defineMethod(c$, "checkInMotion", 
function(state){
switch (state) {
case 0:
this.setTimeout("_SET_IN_MOTION_", 0, null);
break;
case 1:
if (!this.inMotion) this.setTimeout("_SET_IN_MOTION_", this.g.hoverDelayMs * 2, "!setInMotion");
break;
case 2:
this.setInMotion(true);
this.refresh(3, "timeoutThread set in motion");
break;
}
}, "~N");
Clazz.defineMethod(c$, "checkMotionRendering", 
function(tok){
if (!this.getInMotion(true) && !this.tm.spinOn && !this.tm.vibrationOn && !this.am.animationOn) return true;
if (this.g.wireframeRotation) return false;
var n = 0;
switch (tok) {
case 1677721602:
case 1153433601:
n = 2;
break;
case 1112150020:
n = 3;
break;
case 1112150021:
n = 4;
break;
case 1112152066:
n = 5;
break;
case 1073742018:
n = 6;
break;
case 603979967:
n = 7;
break;
case 603979786:
n = 8;
break;
}
return this.g.platformSpeed >= n;
}, "~N");
Clazz.defineMethod(c$, "openExportChannel", 
function(privateKey, fileName, asWriter){
return this.getOutputManager().openOutputChannel(privateKey, fileName, asWriter, false);
}, "~N,~S,~B");
Clazz.overrideMethod(c$, "log", 
function(data){
if (data != null) this.getOutputManager().logToFile(data);
}, "~S");
Clazz.defineMethod(c$, "getLogFileName", 
function(){
return (this.logFileName == null ? "" : this.logFileName);
});
Clazz.defineMethod(c$, "getCommands", 
function(htDefine, htMore, select){
return this.getStateCreator().getCommands(htDefine, htMore, select);
}, "java.util.Map,java.util.Map,~S");
Clazz.defineMethod(c$, "allowCapture", 
function(){
return !this.isApplet || this.isSignedApplet;
});
Clazz.defineMethod(c$, "compileExpr", 
function(expr){
var o = (this.getScriptManager() == null ? null : this.eval.evaluateExpression(expr, false, true));
return (Clazz.instanceOf(o,Array) ? o :  Clazz.newArray(-1, [JS.T.o(4, expr)]));
}, "~S");
Clazz.defineMethod(c$, "checkSelect", 
function(h, value){
return this.getScriptManager() != null && this.eval.checkSelect(h, value);
}, "java.util.Map,~A");
Clazz.defineMethod(c$, "getAnnotationInfo", 
function(d, match, type){
return this.getAnnotationParser(type == 1111490587).getAnnotationInfo(this, d, match, type, this.am.cmi);
}, "JS.SV,~S,~N");
Clazz.defineMethod(c$, "getAtomValidation", 
function(type, atom){
return this.getAnnotationParser(false).getAtomValidation(this, type, atom);
}, "~S,JM.Atom");
Clazz.defineMethod(c$, "dragMinimizeAtom", 
function(iAtom){
this.stopMinimization();
var flags = 0;
var sym = this.getOperativeSymmetry();
if (sym != null) {
flags = 256;
}var bs = (flags != 0 ? null : (this.getMotionFixedAtoms(sym, null).isEmpty() ? this.ms.getAtoms((this.ms.isAtomPDB(iAtom) ? 1086324742 : 1094713360), JU.BSUtil.newAndSetBit(iAtom)) : JU.BSUtil.setAll(this.ms.ac)));
try {
this.minimize(this.eval, 2147483647, 0, bs, null, null, 0, flags);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
if (!this.async) return;
var me = this;
var r = ((Clazz.isClassDefined("JV.Viewer$1") ? 0 : JV.Viewer.$Viewer$1$ ()), Clazz.innerTypeInstance(JV.Viewer$1, this, Clazz.cloneFinals("me", me, "iAtom", iAtom)));
{
setTimeout(function(){r.run()}, 100);
}} else {
throw e;
}
}
}, "~N");
Clazz.defineMethod(c$, "getJBR", 
function(){
return (this.jbr == null ? this.jbr = (J.api.Interface.getInterface("JM.BioResolver", this, "file")).setViewer(this) : this.jbr);
});
Clazz.defineMethod(c$, "checkMenuUpdate", 
function(){
if (this.jmolpopup != null) this.jmolpopup.jpiUpdateComputedMenus();
});
Clazz.defineMethod(c$, "getChimeMessenger", 
function(){
return (this.jcm == null ? this.jcm = (J.api.Interface.getInterface("JV.ChimeMessenger", this, "script")).set(this) : this.jcm);
});
Clazz.defineMethod(c$, "getModelSetAuxiliaryInfoForAtoms", 
function(atomExpression){
return this.ms.getModelSetAuxiliaryInfo(this.ms.getModelBS(this.getAtomBitSet(atomExpression), false));
}, "~O");
Clazz.defineMethod(c$, "getJSJSONParser", 
function(){
return (this.jsonParser == null ? this.jsonParser = J.api.Interface.getInterface("JU.JSJSONParser", this, "script") : this.jsonParser);
});
Clazz.defineMethod(c$, "parseJSON", 
function(str){
return (str == null ? null : (str = str.trim()).startsWith("{") ? this.parseJSONMap(str) : this.parseJSONArray(str));
}, "~S");
Clazz.defineMethod(c$, "parseJSONMap", 
function(jsonMap){
return this.getJSJSONParser().parseMap(jsonMap, true);
}, "~S");
Clazz.defineMethod(c$, "parseJSONArray", 
function(jsonArray){
return this.getJSJSONParser().parse(jsonArray, true);
}, "~S");
Clazz.defineMethod(c$, "getSymTemp", 
function(){
return J.api.Interface.getSymmetry(this, "ms");
});
Clazz.defineMethod(c$, "getSymStatic", 
function(){
return (JV.Viewer.symStatic == null ? (JV.Viewer.symStatic = J.api.Interface.getSymmetry(this, "ms")) : JV.Viewer.symStatic);
});
Clazz.defineMethod(c$, "setWindowDimensions", 
function(dims){
this.resizeInnerPanel(Clazz.floatToInt(dims[0]), Clazz.floatToInt(dims[1]));
}, "~A");
Clazz.defineMethod(c$, "getTriangulator", 
function(){
return (this.triangulator == null ? (this.triangulator = J.api.Interface.getUtil("Triangulator", this, "script")) : this.triangulator);
});
Clazz.defineMethod(c$, "getCurrentModelAuxInfo", 
function(){
return (this.am.cmi >= 0 ? this.ms.getModelAuxiliaryInfo(this.am.cmi) : null);
});
Clazz.defineMethod(c$, "startNBO", 
function(options){
var htParams =  new java.util.Hashtable();
htParams.put("service", "nbo");
htParams.put("action", "showPanel");
htParams.put("options", options);
this.sm.processService(htParams);
}, "~S");
Clazz.defineMethod(c$, "startPlugin", 
function(plugin){
if ("nbo".equalsIgnoreCase(plugin)) this.startNBO("all");
}, "~S");
Clazz.defineMethod(c$, "connectNBO", 
function(type){
if (this.am.cmi < 0) return;
this.getNBOParser().connectNBO(this.am.cmi, type);
}, "~S");
Clazz.defineMethod(c$, "getNBOParser", 
function(){
return (this.nboParser == null ? this.nboParser = (J.api.Interface.getInterface("J.adapter.readers.quantum.NBOParser", this, "script")).set(this) : this.nboParser);
});
Clazz.defineMethod(c$, "getNBOAtomLabel", 
function(atom){
return this.getNBOParser().getNBOAtomLabel(atom);
}, "JM.Atom");
Clazz.defineMethod(c$, "calculateChirality", 
function(bsAtoms){
if (bsAtoms == null) bsAtoms = this.bsA();
return this.ms.calculateChiralityForAtoms(bsAtoms, true);
}, "JU.BS");
Clazz.defineMethod(c$, "getSubstructureSetArray", 
function(pattern, bsSelected, flags){
return this.getSmilesMatcher().getSubstructureSetArray(pattern, this.ms.at, this.ms.ac, bsSelected, null, flags);
}, "~S,JU.BS,~N");
Clazz.defineMethod(c$, "getSubstructureSetArrayForNodes", 
function(pattern, nodes, flags){
return this.getSmilesMatcher().getSubstructureSetArray(pattern, nodes, nodes.length, null, null, flags);
}, "~S,~A,~N");
Clazz.defineMethod(c$, "getSmilesAtoms", 
function(smiles){
return this.getSmilesMatcher().getAtoms(smiles);
}, "~S");
Clazz.defineMethod(c$, "calculateChiralityForSmiles", 
function(smiles){
try {
return J.api.Interface.getSymmetry(this, "ms").calculateCIPChiralityForSmiles(this, smiles);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
return null;
} else {
throw e;
}
}
}, "~S");
Clazz.defineMethod(c$, "getPdbID", 
function(){
return (this.ms.getInfo(this.am.cmi, JV.JC.getBoolName(4)) === Boolean.TRUE ? this.ms.getInfo(this.am.cmi, "pdbID") : null);
});
Clazz.defineMethod(c$, "getModelInfo", 
function(key){
return this.ms.getInfo(this.am.cmi, key);
}, "~S");
Clazz.defineMethod(c$, "notifyScriptEditor", 
function(msWalltime, data){
if (this.scriptEditor != null) {
this.scriptEditor.notify(msWalltime, data);
}}, "~N,~A");
Clazz.defineMethod(c$, "sendConsoleMessage", 
function(msg){
if (this.appConsole != null) this.appConsole.sendConsoleMessage(msg);
}, "~S");
Clazz.defineMethod(c$, "getModelkitPropertySafely", 
function(name){
return (this.modelkit == null ? null : this.modelkit.getProperty(name));
}, "~S");
Clazz.defineMethod(c$, "setModelkitPropertySafely", 
function(key, value){
return (this.modelkit == null ? null : this.modelkit.setProperty(key, value));
}, "~S,~O");
Clazz.defineMethod(c$, "isModelKitOption", 
function(type, value){
return this.modelkit != null && this.modelkit.checkOption(type, value);
}, "~S,~S");
Clazz.defineMethod(c$, "getSymmetryInfo", 
function(iatom, xyz, iOp, translation, pt1, pt2, type, desc, scaleFactor, nth, options, opList){
try {
return this.getSymTemp().getSymmetryInfoAtom(this.ms, iatom, xyz, iOp, translation, pt1, pt2, desc, type, scaleFactor, nth, options, opList);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
System.out.println("Exception in Viewer.getSymmetryInfo: " + e);
if (!JV.Viewer.isJS) e.printStackTrace();
return null;
} else {
throw e;
}
}
}, "~N,~S,~N,JU.P3,JU.P3,JU.P3,~N,~S,~N,~N,~N,~A");
Clazz.defineMethod(c$, "getMacro", 
function(key){
if (this.macros == null || this.macros.isEmpty()) {
try {
var s = this.getAsciiFileOrNull(this.g.macroDirectory + "/macros.json");
this.macros = this.parseJSON(s);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
this.macros =  new java.util.Hashtable();
} else {
throw e;
}
}
}if (key == null) {
var s =  new JU.SB();
for (var k, $k = this.macros.keySet().iterator (); $k.hasNext()&& ((k = $k.next ()) || true);) {
var a = this.macros.get(k);
s.append(k).append("\t").appendO(a).append("\n");
}
return s.toString();
}key = key.toLowerCase();
return this.macros.containsKey(key) ? (this.macros.get(key)).get("path").toString() : null;
}, "~S");
Clazz.defineMethod(c$, "getConsoleFontScale", 
function(){
return this.consoleFontScale;
});
Clazz.defineMethod(c$, "setConsoleFontScale", 
function(scale){
this.consoleFontScale = scale;
}, "~N");
Clazz.defineMethod(c$, "confirm", 
function(msg, msgNo){
return this.apiPlatform.confirm(msg, msgNo);
}, "~S,~S");
Clazz.defineMethod(c$, "evalStringGUI", 
function(script){
this.evalStringQuiet(script + "; ## GUI ##");
}, "~S");
Clazz.defineMethod(c$, "selectStatus", 
function(bs, isGroup, addRemove, isQuiet, reportStatus){
this.select(bs, isGroup, addRemove, isQuiet);
if (reportStatus) {
this.setStatusSelect(bs);
}}, "JU.BS,~B,~N,~B,~B");
Clazz.defineMethod(c$, "setStatusSelect", 
function(bs){
this.hasSelected = false;
this.sm.setStatusSelect(bs == null ? this.bsA() : bs);
}, "JU.BS");
Clazz.defineMethod(c$, "wasmInchiHack", 
function(cmd){
if (JV.Viewer.isJS && (cmd.indexOf("inchi") >= 0 || cmd.indexOf("INCHI") >= 0) || cmd.indexOf("TAUTOMER") >= 0 || cmd.indexOf("tautomer") >= 0) {
this.getInchi(null, null, null);
}return cmd;
}, "~S");
Clazz.defineMethod(c$, "getInchi", 
function(atoms, molData, options){
try {
var inch = this.apiPlatform.getInChI();
if (atoms == null && molData == null) {
return "";
}if ((typeof(molData)=='string')) {
var data = molData;
if (data.startsWith("$") || data.startsWith(":")) {
molData = this.getFileAsString4(data, -1, false, false, true, "script");
} else if (!data.startsWith("InChI=") && data.indexOf(" ") < 0) {
data = this.setLoadFormat(false, "$" + molData, '$', false);
molData = this.getFileAsString4(data, -1, false, false, true, "script");
}}return inch.getInchi(this, atoms, molData, options);
} catch (t) {
return "";
}
}, "JU.BS,~O,~S");
Clazz.defineMethod(c$, "findSpaceGroup", 
function(sym, bsAtoms, xyzList, unitCellParams, origin, oabc, flags){
var ret = null;
if (bsAtoms == null && xyzList == null || (flags & 2) != 0) bsAtoms = this.getThisModelAtoms();
if (xyzList == null) {
if (!bsAtoms.isEmpty()) {
var uc = (sym == null ? this.getOperativeSymmetry() : sym);
ret = (uc == null ? null : uc.findSpaceGroup(this, bsAtoms, null, unitCellParams, null, oabc, flags));
}} else {
ret = this.getSymTemp().findSpaceGroup(this, bsAtoms, xyzList, unitCellParams, origin, oabc, flags);
}return (ret == null && (flags & 1) != 0 ? "" : ret);
}, "J.api.SymmetryInterface,JU.BS,~S,~A,JU.T3,~A,~N");
Clazz.defineMethod(c$, "restrictToModel", 
function(bs, mi){
if (bs == null) bs = this.bsA();
var isEmpty = bs.isEmpty();
if (isEmpty && mi >= 0) return bs;
if (mi == -1) mi = this.am.cmi;
if (mi < 0) {
if (isEmpty) {
return this.getThisModelAtoms();
}mi = this.ms.at[bs.nextSetBit(0)].getModelIndex();
}var bsm = this.getModelUndeletedAtomsBitSet(mi);
bsm.and(bs);
return bsm;
}, "JU.BS,~N");
Clazz.defineMethod(c$, "getThisModelAtoms", 
function(){
return this.getModelUndeletedAtomsBitSet(this.getVisibleFramesBitSet().nextSetBit(0));
});
Clazz.defineMethod(c$, "getSymmetryEquivPoints", 
function(pt, flags){
var uc = this.getCurrentUnitCell();
return (uc == null ?  new JU.Lst() : uc.getEquivPoints(null, pt, flags));
}, "JU.P3,~S");
Clazz.defineMethod(c$, "getSymmetryEquivPointList", 
function(pts, flags){
var uc = this.getCurrentUnitCell();
if (uc == null) return  new JU.Lst();
uc.getEquivPointList(pts, 0, flags.toLowerCase(), null);
return pts;
}, "JU.Lst,~S");
Clazz.defineMethod(c$, "getOperativeSymmetry", 
function(){
var sg = this.getCurrentUnitCell();
return (sg == null || sg.getSymmetryOperations() == null ? null : sg);
});
Clazz.defineMethod(c$, "formatText", 
function(text0){
var i;
if ((i = text0.indexOf("@{")) < 0 && (i = text0.indexOf("%{")) < 0) return text0;
var text = text0;
var isEscaped = (text.indexOf("\\") >= 0);
if (isEscaped) {
text = JU.PT.rep(text, "\\%", "\1");
text = JU.PT.rep(text, "\\@", "\2");
isEscaped = !text.equals(text0);
}text = JU.PT.rep(text, "%{", "@{");
var name;
while ((i = text.indexOf("@{")) >= 0) {
i++;
var i0 = i + 1;
var len = text.length;
var nP = 1;
var chFirst = '\u0000';
var chLast = '\u0000';
while (nP > 0 && ++i < len) {
var ch = text.charAt(i);
if (chFirst != '\0') {
if (chLast == '\\') {
ch = '\0';
} else if (ch == chFirst) {
chFirst = '\0';
}chLast = ch;
continue;
}switch ((ch).charCodeAt(0)) {
case 39:
case 34:
chFirst = ch;
break;
case 123:
nP++;
break;
case 125:
nP--;
break;
}
}
if (i >= len) return text;
name = text.substring(i0, i);
if (name.length == 0) return text;
var v = this.evaluateExpression(name);
if (Clazz.instanceOf(v,"JU.P3")) v = JU.Escape.eP(v);
text = text.substring(0, i0 - 2) + v.toString() + text.substring(i + 1);
}
if (isEscaped) {
text = JU.PT.rep(text, "\2", "@");
text = JU.PT.rep(text, "\1", "%");
}return text;
}, "~S");
Clazz.defineMethod(c$, "getScaleText", 
function(units, isAntialiased, min, ret){
var relativeScale = 1;
var u = JM.Measurement.fixUnits(units.length > 0 ? ((units.startsWith("//") ? units.substring(2) : units).toLowerCase()) : this.g.measureDistanceUnits.equals("vdw") ? "angstroms" : this.g.measureDistanceUnits);
if (JM.Measurement.fromUnits(1, u) == 0) {
u = JM.Measurement.fixUnits(this.g.measureDistanceUnits);
}if (ret == null) return u;
var d = this.tm.modelRadius * this.tm.scaleDefaultPixelsPerAngstrom / this.tm.scalePixelsPerAngstrom / 4;
var af = (isAntialiased ? 2 : 1);
var m = 0;
var p = 0;
var e = 0;
var mp = 0;
min = min * this.imageFontScaling / af * relativeScale * 2;
while (p < min) {
e = JM.Measurement.toUnits(d, u, false);
m = Clazz.doubleToInt(Math.floor(Math.log10(e)));
mp = Math.pow(10, m);
e = JM.Measurement.fromUnits(mp + 0.000001, u);
p = Clazz.floatToInt(e * this.tm.scalePixelsPerAngstrom / af);
if (p < min) {
d *= 10;
}}
var se = (m >= 0 ? " " + Clazz.floatToInt(mp) + " " : " 0." + "000000000".substring(0, -1 - m) + "1 ");
ret[0] = p;
ret[1] = e;
return se + u;
}, "~S,~B,~N,~A");
Clazz.defineMethod(c$, "setStatusAtomMoved", 
function(andCheckMinimize, bs){
if (andCheckMinimize) this.checkMinimization();
this.sm.setStatusAtomMoved(bs);
}, "~B,JU.BS");
Clazz.defineMethod(c$, "getFormulaForAtoms", 
function(bs, type, isEmpirical){
return JU.JmolMolecule.getMolecularFormulaAtoms(this.ms.at, bs, ("CELLFORMULA".equals(type) ? this.ms.getCellWeights(bs) : null), isEmpirical);
}, "JU.BS,~S,~B");
Clazz.defineMethod(c$, "evalCallback", 
function(cmd, params, doWait){
if (this.getScriptManager() != null) this.scm.evalCallback(cmd, params, doWait);
}, "~S,~A,~B");
Clazz.defineMethod(c$, "checkConsoleScript", 
function(strScript){
{
if (strScript.indexOf("JSCONSOLE") == 0) {
this.html5Applet._showInfo(strScript.indexOf("CLOSE")<0); if
(strScript.indexOf("CLEAR") >= 0)
this.html5Applet._clearConsole(); return true; }
}return false;
}, "~S");
c$.$Viewer$1$=function(){
/*if5*/;(function(){
var c$ = Clazz.declareAnonymous(JV, "Viewer$1", null, Runnable);
Clazz.overrideMethod(c$, "run", 
function(){
this.f$.me.dragMinimizeAtom(this.f$.iAtom);
});
/*eoif5*/})();
};
/*if2*/;(function(){
var c$ = Clazz.declareType(JV.Viewer, "ACCESS", Enum);
Clazz.defineEnumConstant(c$, "NONE", 0, []);
Clazz.defineEnumConstant(c$, "READSPT", 1, []);
Clazz.defineEnumConstant(c$, "ALL", 2, []);
/*eoif2*/})();
{
{
self.Jmol && Jmol.extend && Jmol.extend("vwr",
JV.Viewer.prototype);
}}c$.isJS = false;
c$.isSwingJS = false;
c$.appletDocumentBase = "";
c$.appletCodeBase = "";
c$.appletIdiomaBase = null;
c$.jsDocumentBase = "";
c$.jmolObject = null;
c$.strJavaVendor = "Java: " + System.getProperty("java.vendor", "j2s");
c$.strOSName = System.getProperty("os.name", "");
c$.strJavaVersion = "Java " + System.getProperty("java.version", "");
c$.version_date = null;
c$.staticFunctions =  new java.util.Hashtable();
c$.nProcessors = 1;
c$.isHighPrecision = false;
{
{
}}c$.symStatic = null;
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
