Clazz.declarePackage("JS");
Clazz.load(["JS.ScriptExpr"], "JS.ScriptEval", ["java.util.Arrays", "$.Hashtable", "JU.AU", "$.BArray", "$.BS", "$.Base64", "$.Lst", "$.M3", "$.M4", "$.Measure", "$.P3", "$.P4", "$.PT", "$.Quat", "$.SB", "$.V3", "J.api.Interface", "J.atomdata.RadiusData", "J.c.PAL", "$.STR", "$.VDW", "J.i18n.GT", "JM.BondSet", "$.Group", "$.Measurement", "JS.SV", "$.ScriptCompiler", "$.ScriptContext", "$.ScriptDelayThread", "$.ScriptInterruption", "$.ScriptManager", "$.ScriptMathProcessor", "$.T", "JU.BSUtil", "$.ColorEncoder", "$.Edge", "$.Elements", "$.Escape", "$.Font", "$.Logger", "$.Parser", "$.SimpleUnitCell", "JV.ActionManager", "$.FileManager", "$.JC", "$.StateManager", "$.Viewer"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.sm = null;
this.isJS = false;
this.fdThread = null;
this.scriptDelayThread = null;
this.allowJSThreads = true;
this.isFuncReturn = false;
this.historyDisabled = false;
this.debugScript = false;
this.isCmdLine_C_Option = false;
this.isCmdLine_c_or_C_Option = false;
this.listCommands = false;
this.tQuiet = false;
this.executionStopped = false;
this.executionPaused = false;
this.executionStepping = false;
this.executing = false;
this.isEditor = false;
this.timeBeginExecution = 0;
this.timeEndExecution = 0;
this.mustResumeEval = false;
this.currentThread = null;
this.compiler = null;
this.outputBuffer = null;
this.contextPath = "";
this.scriptFileName = null;
this.functionName = null;
this.$isStateScript = false;
this.scriptLevel = 0;
this.aatoken = null;
this.lineNumbers = null;
this.lineIndices = null;
this.script = null;
this.scriptExtensions = null;
this.pc = 0;
this.thisCommand = null;
this.fullCommand = null;
this.lineEnd = 0;
this.pcEnd = 0;
this.forceNoAddHydrogens = false;
this.isEmbedded = false;
this.isGUI = false;
this.parallelProcessor = null;
this.pcResume = -1;
Clazz.instantialize(this, arguments);}, JS, "ScriptEval", JS.ScriptExpr);
Clazz.makeConstructor(c$, 
function(){
Clazz.superConstructor (this, JS.ScriptEval, []);
this.currentThread = Thread.currentThread();
});
Clazz.overrideMethod(c$, "getAllowJSThreads", 
function(){
return this.allowJSThreads;
});
Clazz.defineMethod(c$, "setAllowJSThreads", 
function(b){
this.allowJSThreads = b;
}, "~B");
Clazz.defineMethod(c$, "doReport", 
function(){
return (!this.tQuiet && this.scriptLevel <= JS.ScriptEval.scriptReportingLevel);
});
Clazz.overrideMethod(c$, "isStateScript", 
function(){
return this.$isStateScript;
});
Clazz.overrideMethod(c$, "setStatic", 
function(tok, ival){
switch (tok) {
case 553648167:
if (ival >= 10) JS.ScriptEval.contextDepthMax = ival;
return JS.ScriptEval.contextDepthMax;
case 553648144:
if (ival >= 0) JS.ScriptEval.commandHistoryLevelMax = ival;
return JS.ScriptEval.commandHistoryLevelMax;
case 553648168:
if (ival >= 0) JS.ScriptEval.scriptReportingLevel = ival;
return JS.ScriptEval.scriptReportingLevel;
}
return 0;
}, "~N,~N");
Clazz.overrideMethod(c$, "getScript", 
function(){
return this.script;
});
Clazz.overrideMethod(c$, "setViewer", 
function(vwr){
this.vwr = vwr;
this.compiler = (this.compiler == null ? vwr.compiler : this.compiler);
this.isJS = vwr.isSingleThreaded;
return this;
}, "JV.Viewer");
Clazz.overrideMethod(c$, "setCompiler", 
function(){
this.vwr.compiler = this.compiler =  new JS.ScriptCompiler(this.vwr);
});
Clazz.overrideMethod(c$, "compileScriptString", 
function(script, tQuiet){
this.clearState(tQuiet);
this.contextPath = "[script]";
return this.compileScript(null, script, this.debugScript);
}, "~S,~B");
Clazz.overrideMethod(c$, "evaluateCompiledScript", 
function(params, isCmdLine_c_or_C_Option, isCmdLine_C_Option, historyDisabled, listCommands, outputBuffer, allowThreads){
var tempOpen = this.isCmdLine_C_Option;
this.isCmdLine_C_Option = isCmdLine_C_Option;
this.chk = this.isCmdLine_c_or_C_Option = isCmdLine_c_or_C_Option;
this.historyDisabled = historyDisabled;
this.outputBuffer = outputBuffer;
this.privateFuncs = null;
this.currentThread = Thread.currentThread();
this.setAllowJSThreads( new Boolean (allowThreads & !this.vwr.getBoolean(603979892)).valueOf());
this.listCommands = listCommands;
this.timeBeginExecution = System.currentTimeMillis();
this.executionStopped = this.executionPaused = false;
this.executionStepping = false;
this.executing = true;
this.vwr.pushHoldRepaintWhy("runEval" + (params == null ? "" : "+params"));
this.setScriptExtensions();
this.vwr.hasSelected = false;
this.executeCommands(params, false, true);
this.isCmdLine_C_Option = tempOpen;
if (this.$isStateScript) JS.ScriptManager.setStateScriptVersion(this.vwr, null);
if (this.vwr.hasSelected && this.isGUI) this.vwr.setStatusSelect(null);
this.vwr.hasSelected = false;
}, "~A,~B,~B,~B,~B,JU.SB,~B");
Clazz.defineMethod(c$, "useThreads", 
function(allowWaitFor){
return (!this.chk && (allowWaitFor && this.vwr.g.waitForMoveTo || !this.vwr.headless && !this.vwr.autoExit && this.vwr.haveDisplay && this.outputBuffer == null && this.allowJSThreads));
}, "~B");
Clazz.defineMethod(c$, "executeCommands", 
function(params, isTry, reportCompletion){
var haveError = false;
try {
if (params != null) {
this.pushContext(null, "runCallback");
this.contextPath += " >> " + params[0] + "callback ";
this.setScriptArguments(params, true);
}if (!this.dispatchCommands(false, false, isTry)) return -1;
if (params != null) {
this.popContext(false, false);
}} catch (e$$) {
if (Clazz.exceptionOf(e$$,"JS.ScriptException")){
var e = e$$;
{
if (Clazz.instanceOf(e,"JS.ScriptInterruption") && (!isTry || !e.isError)) {
return -1;
}if (isTry) {
this.vwr.setStringProperty("_errormessage", "" + e);
return 1;
}this.setErrorMessage(e.toString());
this.errorMessageUntranslated = e.getErrorMessageUntranslated();
this.report(this.errorMessage, true);
this.vwr.notifyError((this.errorMessage != null && this.errorMessage.indexOf("java.lang.OutOfMemoryError") >= 0 ? "Error" : "ScriptException"), this.errorMessage, this.errorMessageUntranslated);
haveError = true;
}
} else {
var er = e$$;
{
this.vwr.handleError(er, false);
this.setErrorMessage("" + er + " " + this.vwr.getShapeErrorState());
this.errorMessageUntranslated = "" + er;
this.report(this.errorMessage, true);
haveError = true;
}
}
}
if (haveError || !this.isJS || !this.allowJSThreads || params != null) {
this.vwr.setTainted(true);
this.vwr.popHoldRepaint("CLEAR HOLD - executeCommands" + " " + (this.scriptLevel > 0 ? "\u0001## REPAINT_IGNORE ##" : ""));
if (haveError) this.resumeViewer("exception", true);
}this.timeEndExecution = System.currentTimeMillis();
if (this.errorMessage == null && this.executionStopped) this.setErrorMessage("execution interrupted");
 else if (!this.tQuiet && reportCompletion) this.vwr.scriptStatus("Script completed");
this.executing = this.chk = this.isCmdLine_c_or_C_Option = this.historyDisabled = false;
var msg = this.getErrorMessageUntranslated();
this.vwr.setErrorMessage(this.errorMessage, msg);
if (!this.tQuiet && reportCompletion) this.vwr.setScriptStatus("Jmol script terminated", this.errorMessage, 1 + (this.timeEndExecution - this.timeBeginExecution), msg);
return (haveError ? 1 : 0);
}, "~A,~B,~B");
Clazz.overrideMethod(c$, "resumeEval", 
function(sco){
var sc = sco;
this.setErrorMessage(null);
if (this.executionStopped || sc == null || !sc.mustResumeEval) {
this.resumeViewer("resumeEval", this.executionStopped);
return;
}this.thisContext = sc;
if (sc.scriptLevel > 0 && sc.why !== "getEvalContextAndHoldQueue") this.scriptLevel = sc.scriptLevel - 1;
if (sc.isTryCatch) {
this.postProcessTry(null);
this.pcResume = -1;
} else {
if (!this.executionPaused) sc.pc++;
this.restoreScriptContext(sc, true, false, false);
this.pcResume = sc.pc;
}switch (this.executeCommands(null, this.thisContext != null && this.thisContext.isTryCatch, this.scriptLevel <= 0)) {
case -1:
break;
case 1:
case 0:
this.postProcessTry(null);
if (this.executing) this.executeCommands(null, true, false);
break;
}
this.pcResume = -1;
}, "~O");
Clazz.defineMethod(c$, "resumeViewer", 
function(why, andStopQueue){
this.vwr.setTainted(true);
this.vwr.popHoldRepaint(why + (this.chk ? "\u0001## REPAINT_IGNORE ##" : ""));
this.vwr.queueOnHold = false;
if (andStopQueue) {
this.vwr.clearScriptQueue();
this.vwr.scm.queueThreadFinished(-1);
}}, "~S,~B");
Clazz.overrideMethod(c$, "runScript", 
function(script){
if (!this.vwr.isPreviewOnly) this.runScriptBuffer(script, this.outputBuffer, false);
}, "~S");
Clazz.overrideMethod(c$, "runScriptBuffer", 
function(script, outputBuffer, isFuncReturn){
this.pushContext(null, "runScriptBuffer");
this.contextPath += " >> script() ";
this.outputBuffer = outputBuffer;
this.setAllowJSThreads(false);
var fret = this.isFuncReturn;
this.isFuncReturn = new Boolean (this.isFuncReturn | isFuncReturn).valueOf();
if (this.compileScript(null, script + "\u0001## EDITOR_IGNORE ##" + "\u0001## REPAINT_IGNORE ##", false)) this.dispatchCommands(false, false, false);
this.popContext(false, false);
this.isFuncReturn = fret;
}, "~S,JU.SB,~B");
Clazz.overrideMethod(c$, "checkScriptSilent", 
function(script){
var sc = this.compiler.compile(null, script, false, true, false, true);
if (sc.errorType != null) return sc;
this.restoreScriptContext(sc, false, false, false);
this.chk = true;
this.isCmdLine_c_or_C_Option = this.isCmdLine_C_Option = false;
this.pc = 0;
try {
this.dispatchCommands(false, false, false);
} catch (e) {
if (Clazz.exceptionOf(e,"JS.ScriptException")){
this.setErrorMessage(e.toString());
sc = this.getScriptContext("checkScriptSilent");
} else {
throw e;
}
}
this.chk = false;
return sc;
}, "~S");
c$.getContextTrace = Clazz.defineMethod(c$, "getContextTrace", 
function(vwr, sc, sb, isTop){
if (sb == null) sb =  new JU.SB();
var pc = (sc.lineNumbers == null ? sc.pc : Math.min(sc.pc, sc.lineNumbers[sc.lineNumbers.length - 1]));
sb.append(JS.ScriptError.getErrorLineMessage(sc.functionName, sc.scriptFileName, (sc.lineNumbers == null ? 0 : sc.lineNumbers[pc]), pc, JS.ScriptEval.statementAsString(vwr, sc.statement, (isTop ? sc.iToken : 9999), false)));
if (sc.parentContext != null) JS.ScriptEval.getContextTrace(vwr, sc.parentContext, sb, false);
return sb;
}, "JV.Viewer,JS.ScriptContext,JU.SB,~B");
Clazz.overrideMethod(c$, "setDebugging", 
function(){
this.debugScript = this.vwr.getBoolean(603979825);
this.debugHigh = (this.debugScript && JU.Logger.debugging);
});
Clazz.overrideMethod(c$, "haltExecution", 
function(){
if (this.isEmbedded) {
this.vwr.setBooleanProperty("allowEmbeddedScripts", true);
this.isEmbedded = false;
}this.resumePausedExecution();
this.executionStopped = true;
});
Clazz.overrideMethod(c$, "pauseExecution", 
function(withDelay){
if (this.chk || this.vwr.headless) return;
if (withDelay && !this.isJS) this.delayScript(-100);
this.vwr.popHoldRepaint("pauseExecution " + withDelay);
this.executionStepping = false;
this.executionPaused = true;
}, "~B");
Clazz.overrideMethod(c$, "stepPausedExecution", 
function(){
this.executionStepping = true;
this.executionPaused = false;
});
Clazz.overrideMethod(c$, "resumePausedExecution", 
function(){
this.executionPaused = false;
this.executionStepping = false;
if (!this.tQuiet) this.vwr.setScriptStatus("Jmol script resumed", this.errorMessage, 1 + (this.timeEndExecution - this.timeBeginExecution), "resumed");
});
Clazz.overrideMethod(c$, "isExecuting", 
function(){
return this.executing && !this.executionStopped;
});
Clazz.overrideMethod(c$, "isPaused", 
function(){
return this.executionPaused;
});
Clazz.overrideMethod(c$, "isStepping", 
function(){
return this.executionStepping;
});
Clazz.overrideMethod(c$, "isStopped", 
function(){
return this.executionStopped || !this.isJS && this.currentThread !== Thread.currentThread();
});
Clazz.overrideMethod(c$, "getNextStatement", 
function(){
return (this.pc < this.aatoken.length ? JS.ScriptError.getErrorLineMessage(this.functionName, this.scriptFileName, this.getLinenumber(null), this.pc, JS.ScriptEval.statementAsString(this.vwr, this.aatoken[this.pc], -9999, this.debugHigh)) : "");
});
Clazz.defineMethod(c$, "getCommand", 
function(pc, allThisLine, addSemi){
if (pc >= this.lineIndices.length) return "";
if (allThisLine) {
var pt0 = -1;
var s = this.script;
var pt1 = s.length;
for (var i = 0; i < this.lineNumbers.length; i++) {
if (this.lineNumbers[i] == this.lineNumbers[pc]) {
if (pt0 < 0) pt0 = this.lineIndices[i][0];
pt1 = this.lineIndices[i][1];
} else if (this.lineNumbers[i] == 0 || this.lineNumbers[i] > this.lineNumbers[pc]) {
break;
}}
if (s.indexOf('\1') >= 0) s = s.substring(0, s.indexOf('\1'));
var len = s.length;
if (pt1 == len - 1 && s.endsWith("}")) pt1++;
return (pt0 >= len || pt1 < pt0 || pt1 < 0 ? "" : s.substring(Math.max(pt0, 0), Math.min(len, pt1)));
}var ichBegin = this.lineIndices[pc][0];
var ichEnd = this.lineIndices[pc][1];
var s = "";
if (ichBegin < 0 || ichEnd <= ichBegin || ichEnd > this.script.length) return "";
try {
s = this.script.substring(ichBegin, ichEnd);
if (s.indexOf("\\\n") >= 0) s = JU.PT.rep(s, "\\\n", "  ");
if (s.indexOf("\\\r") >= 0) s = JU.PT.rep(s, "\\\r", "  ");
if (s.length > 0 && !s.endsWith(";")) s += ";";
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
JU.Logger.error("darn problem in Eval getCommand: ichBegin=" + ichBegin + " ichEnd=" + ichEnd + " len = " + this.script.length + "\n" + e);
} else {
throw e;
}
}
return s;
}, "~N,~B,~B");
Clazz.defineMethod(c$, "logDebugScript", 
function(st, ifLevel){
var itok = this.iToken;
this.iToken = -9999;
if (this.debugHigh) {
if (st.length > 0) JU.Logger.debug(st[0].toString());
for (var i = 1; i < st.length; ++i) if (st[i] != null) JU.Logger.debug(st[i].toString());

var strbufLog =  new JU.SB();
var s = (ifLevel > 0 ? "                          ".substring(0, ifLevel * 2) : "");
strbufLog.append(s).append(JS.ScriptEval.statementAsString(this.vwr, st, this.iToken, this.debugHigh));
this.vwr.scriptStatus(strbufLog.toString());
} else {
var cmd = this.getCommand(this.pc, false, false);
if (cmd !== "") this.vwr.scriptStatus(cmd);
}this.iToken = itok;
}, "~A,~N");
Clazz.overrideMethod(c$, "evaluateExpression", 
function(expr, asVariable, compileOnly){
var e = ( new JS.ScriptEval()).setViewer(this.vwr);
try {
e.thisContext = this.thisContext;
e.contextVariables = this.contextVariables;
e.pushContext(null, "evalExp");
e.setAllowJSThreads(false);
} catch (e1) {
if (Clazz.exceptionOf(e1,"JS.ScriptException")){
} else {
throw e1;
}
}
var exec0 = this.executing;
var o = (e.evaluate(expr, asVariable, compileOnly));
this.executing = exec0;
return o;
}, "~O,~B,~B");
Clazz.defineMethod(c$, "runBufferedSafely", 
function(script, outputBuffer){
if (outputBuffer == null) outputBuffer = this.outputBuffer;
var e = ( new JS.ScriptEval()).setViewer(this.vwr);
var exec0 = this.executing;
try {
e.runScriptBuffer(script, outputBuffer, false);
} catch (e1) {
if (Clazz.exceptionOf(e1,"JS.ScriptException")){
e1.printStackTrace();
} else {
throw e1;
}
}
this.executing = exec0;
}, "~S,JU.SB");
c$.runUserAction = Clazz.defineMethod(c$, "runUserAction", 
function(functionName, params, vwr){
var ev = ( new JS.ScriptEval()).setViewer(vwr);
var func = vwr.getFunction(functionName.toLowerCase());
if (func == null) return null;
try {
var svparams = JS.SV.getVariableAO(params).getList();
ev.restoreFunction(func, svparams, null);
ev.dispatchCommands(false, true, false);
} catch (e) {
if (Clazz.exceptionOf(e,"JS.ScriptException")){
return null;
} else {
throw e;
}
}
var ret = ev.getContextVariableAsVariable("_retval", false);
return (ret == null ? JS.SV.vT : ret);
}, "~S,~A,JV.Viewer");
Clazz.defineMethod(c$, "evaluate", 
function(expr, asVariable, compileOnly){
try {
if ((typeof(expr)=='string')) {
if (this.compileScript(null, (compileOnly ? "w_h_e_r_e" : "e_x_p_r_e_s_s_i_o_n") + " = " + expr, false)) {
if (compileOnly) return this.aatoken[0];
this.setStatement(this.aatoken[0], 1);
return (asVariable ? this.parameterExpressionList(2, -1, false).get(0) : this.parameterExpressionString(2, 0));
}} else if (Clazz.instanceOf(expr,Array) && Clazz.instanceOf((expr)[0],Array)) {
this.setStatement((expr)[0], 1);
return (asVariable ? this.parameterExpressionList(0, -1, false).get(0) : this.parameterExpressionString(0, -1));
} else if (Clazz.instanceOf(expr,Array)) {
var bs = this.atomExpression(expr, 0, 0, true, false, null, false);
return (asVariable ? JS.SV.newV(10, bs) : bs);
}} catch (ex) {
if (Clazz.exceptionOf(ex, Exception)){
JU.Logger.error("Error evaluating: " + expr + "\n" + ex);
} else {
throw ex;
}
}
return (asVariable ? JS.SV.getVariable("ERROR") : "ERROR");
}, "~O,~B,~B");
Clazz.overrideMethod(c$, "checkSelect", 
function(h, where){
var ok = false;
try {
this.pushContext(null, "checkSelect");
ok = this.parameterExpressionSelect(h, where);
} catch (ex) {
if (Clazz.exceptionOf(ex, Exception)){
} else {
throw ex;
}
}
this.popContext(false, false);
return ok;
}, "java.util.Map,~A");
Clazz.overrideMethod(c$, "getAtomBitSet", 
function(atomExpression){
if (Clazz.instanceOf(atomExpression,"JU.BS")) return atomExpression;
if ((typeof(atomExpression)=='string') && (atomExpression).startsWith(";base90+35,")) return JS.SV.decodeBase90_35(atomExpression);
var bs =  new JU.BS();
var executing = this.executing;
try {
this.pushContext(null, "getAtomBitSet");
var scr = "select (" + atomExpression + ")";
scr = JU.PT.replaceAllCharacters(scr, "\n\r", "),(");
scr = JU.PT.rep(scr, "()", "(none)");
if (this.compileScript(null, scr, false)) {
this.st = this.aatoken[0];
this.setStatement(this.st, 0);
bs = this.atomExpression(this.st, 1, 0, false, false, null, true);
}this.popContext(false, false);
} catch (ex) {
if (Clazz.exceptionOf(ex, Exception)){
JU.Logger.error("getAtomBitSet " + atomExpression + "\n" + ex);
} else {
throw ex;
}
}
this.executing = executing;
return bs;
}, "~O");
Clazz.defineMethod(c$, "compileScript", 
function(filename, strScript, debugCompiler){
this.scriptFileName = filename;
strScript = this.fixScriptPath(strScript, filename);
var sc = this.compiler.compile(filename, strScript, false, false, debugCompiler && JU.Logger.debugging, false);
this.addFunction(null);
var pf = this.privateFuncs;
this.restoreScriptContext(sc, false, false, false);
this.privateFuncs = null;
if (this.thisContext != null) this.thisContext.privateFuncs = pf;
this.$isStateScript = this.compiler.isStateScript;
this.forceNoAddHydrogens = (this.$isStateScript && this.script.indexOf("pdbAddHydrogens") < 0);
var s = this.script;
this.isGUI = (s.indexOf("; ## GUI ##") >= 0);
if (this.isGUI) {
s = JU.PT.rep(s, "; ## GUI ##", "");
}this.pc = this.setScriptExtensions();
if (!this.chk && this.vwr.scriptEditorVisible && strScript.indexOf("\u0001## EDITOR_IGNORE ##") < 0) this.vwr.scriptStatus("");
this.script = s;
return !this.$error;
}, "~S,~S,~B");
Clazz.defineMethod(c$, "fixScriptPath", 
function(strScript, filename){
if (filename != null && strScript.indexOf("$SCRIPT_PATH$") >= 0) {
var path = filename;
var pt = Math.max(filename.lastIndexOf("|"), filename.lastIndexOf("/"));
path = path.substring(0, pt + 1);
strScript = JU.PT.rep(strScript, "$SCRIPT_PATH$/", path);
strScript = JU.PT.rep(strScript, "$SCRIPT_PATH$", path);
}return strScript;
}, "~S,~S");
Clazz.defineMethod(c$, "setScriptExtensions", 
function(){
this.fromMenu = false;
var extensions = this.scriptExtensions;
if (extensions == null) return 0;
this.fromMenu = (extensions.indexOf("\u0001##MENU") >= 0);
if (extensions.indexOf("\u0001##SCRIPT_STEP") >= 0) this.executionStepping = true;
var pt = extensions.indexOf("\u0001##SCRIPT_START");
if (pt < 0) return 0;
pt = JU.PT.parseInt(extensions.substring(pt + "\u0001##SCRIPT_START".length));
if (pt == -2147483648) return 0;
for (this.pc = 0; this.pc < this.lineIndices.length; this.pc++) {
if (this.lineIndices[this.pc][0] > pt || this.lineIndices[this.pc][1] >= pt) break;
}
if (this.pc > 0 && this.pc < this.lineIndices.length && this.lineIndices[this.pc][0] > pt) --this.pc;
return this.pc;
});
Clazz.defineMethod(c$, "getScriptFileInternal", 
function(filename, localPath, remotePath, scriptPath){
if (filename.toLowerCase().indexOf("javascript:") == 0) {
return this.vwr.jsEval(filename.substring(11));
}var data =  new Array(2);
data[0] = filename;
if (!this.vwr.fm.getFileDataAsString(data, -1, false, true, false)) {
this.setErrorMessage("io error reading " + data[0] + ": " + data[1]);
return null;
}var movieScript = "";
if (("\n" + data[1]).indexOf("\nJmolManifest.txt\n") >= 0) {
var path;
if (filename.endsWith(".all.pngj") || filename.endsWith(".all.png")) {
path = "|state.spt";
filename += "|";
} else {
if (data[1].indexOf("movie.spt") >= 0) {
data[0] = filename + "|movie.spt";
if (this.vwr.fm.getFileDataAsString(data, -1, false, true, false)) {
movieScript = data[1];
}}filename += "|JmolManifest.txt";
data[0] = filename;
if (!this.vwr.fm.getFileDataAsString(data, -1, false, true, false)) {
this.setErrorMessage("io error reading " + data[0] + ": " + data[1]);
return null;
}path = JV.FileManager.getManifestScriptPath(data[1]);
}if (path != null && path.length > 0) {
data[0] = filename = filename.substring(0, filename.lastIndexOf("|")) + path;
if (!this.vwr.fm.getFileDataAsString(data, -1, false, true, false)) {
this.setErrorMessage("io error reading " + data[0] + ": " + data[1]);
return null;
}}if (filename.endsWith("|state.spt")) {
this.vwr.g.setO("_pngjFile", filename.substring(0, filename.length - 10) + "?");
}}this.scriptFileName = filename;
data[1] = JV.FileManager.getEmbeddedScript(data[1]);
var script = this.fixScriptPath(data[1], data[0]);
var pt = -1;
var path = scriptPath;
if (scriptPath == null) {
path = this.vwr.fm.getFilePath(filename, false, false);
scriptPath = path.substring(0, Math.max((pt = path.lastIndexOf("|")), path.lastIndexOf("/")));
if (pt > 0) {
script = this.checkFixBondDelete(script);
this.vwr.setAccessInternal(path.substring(0, pt));
}}return JV.FileManager.setScriptFileReferences(script, localPath, remotePath, scriptPath) + movieScript;
}, "~S,~S,~S,~S");
Clazz.defineMethod(c$, "checkFixBondDelete", 
function(script){
var pt = script.indexOf("select BONDS ({");
if (pt < 0) return script;
var pt2 = script.indexOf("delete ({", pt + 20);
if (pt2 < 0) return script;
var line1 = script.substring(pt, script.indexOf("\n\n", pt) + 2);
pt2 = script.indexOf("\n", pt2);
script = script.substring(0, pt2 + 1) + line1.$replace("select BONDS", "select /*FIXED*/ BONDS") + script.substring(pt2 + 2);
script = script.substring(0, pt) + script.substring(pt + line1.length);
return script;
}, "~S");
Clazz.overrideMethod(c$, "evalFunctionFloat", 
function(func, params, values){
try {
var p = params;
for (var i = 0; i < values.length; i++) p.get(i).value = Float.$valueOf(values[i]);

var f = func;
return JS.SV.fValue(this.runFunctionAndRet(f, f.name, p, null, true, false, false));
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
return NaN;
} else {
throw e;
}
}
}, "~O,~O,~A");
Clazz.defineMethod(c$, "getUserFunctionResult", 
function(name, params, tokenAtom){
return this.runFunctionAndRet(null, name, params, tokenAtom, true, true, false);
}, "~S,JU.Lst,JS.SV");
Clazz.defineMethod(c$, "runFunctionAndRet", 
function($function, name, params, tokenAtom, getReturn, setContextPath, allowThreads){
if ($function == null) {
name = name.toLowerCase();
$function = this.getFunction(name);
if ($function == null) return null;
if (setContextPath) this.contextPath += " >> function " + name;
} else if (setContextPath) {
this.contextPath += " >> " + name;
}this.pushContext(null, "runFunctionAndRet ");
if (this.allowJSThreads) this.setAllowJSThreads(allowThreads);
var isTry = ($function.getTok() == 364558);
this.thisContext.isTryCatch = isTry;
this.thisContext.isFunction = !isTry;
this.functionName = name;
if (isTry) {
this.resetError();
this.thisContext.displayLoadErrorsSave = this.vwr.displayLoadErrors;
this.thisContext.tryPt = ++this.vwr.tryPt;
this.vwr.displayLoadErrors = false;
this.restoreFunction($function, params, tokenAtom);
this.contextVariables.put("_breakval", JS.SV.newI(2147483647));
this.contextVariables.put("_errorval", JS.SV.newS(""));
var cv = this.contextVariables;
switch (this.executeCommands(null, true, false)) {
case -1:
break;
case 1:
case 0:
this.postProcessTry(cv);
}
return null;
} else if (Clazz.instanceOf($function,"J.api.JmolParallelProcessor")) {
{
this.parallelProcessor = $function;
this.restoreFunction($function, params, tokenAtom);
this.dispatchCommands(false, true, false);
($function).runAllProcesses(this.vwr);
}} else {
this.restoreFunction($function, params, tokenAtom);
this.dispatchCommands(false, true, false);
}var v = (getReturn ? this.getContextVariableAsVariable("_retval", false) : null);
this.popContext(false, false);
return v;
}, "J.api.JmolScriptFunction,~S,JU.Lst,JS.SV,~B,~B,~B");
Clazz.defineMethod(c$, "postProcessTry", 
function(cv){
if (this.thisContext == null) return;
while (this.thisContext.tryPt > this.vwr.tryPt) this.popContext(false, false);

var isJSReturn = (cv == null);
if (isJSReturn) {
cv = this.contextVariables;
}this.vwr.displayLoadErrors = this.thisContext.displayLoadErrorsSave;
this.popContext(false, false);
var err = this.vwr.getP("_errormessage");
if (err.length > 0) {
cv.put("_errorval", JS.SV.newS(err));
this.resetError();
}cv.put("_tryret", cv.get("_retval"));
var ret = cv.get("_tryret");
if (ret.value != null || ret.intValue != 2147483647) {
try {
this.cmdReturn(ret);
} catch (e) {
if (Clazz.exceptionOf(e,"JS.ScriptException")){
e.printStackTrace();
} else {
throw e;
}
}
return;
}var errMsg = (cv.get("_errorval")).value;
if (errMsg.length == 0) {
var iBreak = (cv.get("_breakval")).intValue;
if (iBreak != 2147483647) {
this.breakAt(this.pc - iBreak);
return;
}}if (this.pc + 1 < this.aatoken.length && this.aatoken[this.pc + 1][0].tok == 102412) {
var ct = this.aatoken[this.pc + 1][0];
if (ct.contextVariables != null && ct.name0 != null) ct.contextVariables.put(ct.name0, JS.SV.newS(errMsg));
ct.intValue = (errMsg.length > 0 ? 1 : -1) * Math.abs(ct.intValue);
}if (isJSReturn) this.pc++;
}, "java.util.Map");
Clazz.defineMethod(c$, "breakAt", 
function(pt){
if (pt < 0) {
this.getContextVariableAsVariable("_breakval", false).intValue = -pt;
this.pcEnd = this.pc;
return;
}var ptEnd = Math.abs(this.aatoken[pt][0].intValue);
var tok = this.aatoken[pt][0].tok;
if (tok == 102411 || tok == 102413) {
this.theToken = this.aatoken[ptEnd--][0];
var ptNext = Math.abs(this.theToken.intValue);
if (this.theToken.tok != 102409) this.theToken.intValue = -ptNext;
} else {
this.pc = -1;
while (this.pc != pt && this.thisContext != null) {
while (this.thisContext != null && !JS.ScriptCompiler.isBreakableContext(this.thisContext.token.tok)) this.popContext(true, false);

this.pc = this.thisContext.pc;
this.popContext(true, false);
}
}this.pc = ptEnd;
}, "~N");
Clazz.defineMethod(c$, "restoreFunction", 
function(f, params, tokenAtom){
var $function = f;
this.aatoken = $function.aatoken;
this.lineNumbers = $function.lineNumbers;
this.lineIndices = $function.lineIndices;
this.script = $function.script;
this.pc = 0;
if ($function.names != null) {
this.contextVariables =  new java.util.Hashtable();
$function.setVariables(this.contextVariables, params);
}if (tokenAtom != null) this.contextVariables.put("_x", tokenAtom);
}, "J.api.JmolScriptFunction,JU.Lst,JS.SV");
Clazz.defineMethod(c$, "clearDefinedVariableAtomSets", 
function(){
this.vwr.definedAtomSets.remove("# variable");
});
Clazz.defineMethod(c$, "defineSets", 
function(){
if (!this.vwr.definedAtomSets.containsKey("# static")) {
for (var i = 0; i < JV.JC.predefinedStatic.length; i++) this.defineAtomSet(JV.JC.predefinedStatic[i]);

this.defineAtomSet("# static");
}if (this.vwr.definedAtomSets.containsKey("# variable")) return;
for (var i = 0; i < JV.JC.predefinedVariable.length; i++) this.defineAtomSet(JV.JC.predefinedVariable[i]);

for (var i = JU.Elements.elementNumberMax; --i >= 0; ) {
var definition = " elemno=" + i;
this.defineAtomSet("@" + JU.Elements.elementNameFromNumber(i) + definition);
this.defineAtomSet("@_" + JU.Elements.elementSymbolFromNumber(i) + definition);
}
for (var i = 4; --i >= 0; ) {
var definition = "@" + JU.Elements.altElementNameFromIndex(i) + " _e=" + JU.Elements.altElementNumberFromIndex(i);
this.defineAtomSet(definition);
}
for (var i = JU.Elements.altElementMax; --i >= 4; ) {
var ei = JU.Elements.altElementNumberFromIndex(i);
var def = " _e=" + ei;
var definition = "@_" + JU.Elements.altElementSymbolFromIndex(i);
this.defineAtomSet(definition + def);
definition = "@_" + JU.Elements.altIsotopeSymbolFromIndex(i);
this.defineAtomSet(definition + def);
definition = "@_" + JU.Elements.altIsotopeSymbolFromIndex2(i);
this.defineAtomSet(definition + def);
definition = "@" + JU.Elements.altElementNameFromIndex(i);
if (definition.length > 1) this.defineAtomSet(definition + def);
var e = JU.Elements.getElementNumber(ei);
ei = JU.Elements.getNaturalIsotope(e);
if (ei > 0) {
def = JU.Elements.elementSymbolFromNumber(e);
this.defineAtomSet("@_" + def + ei + " _e=" + e);
this.defineAtomSet("@_" + ei + def + " _e=" + e);
}}
this.defineAtomSet("# variable");
});
Clazz.defineMethod(c$, "defineAtomSet", 
function(script){
if (script.indexOf("#") == 0) {
this.vwr.definedAtomSets.put(script, Boolean.TRUE);
return;
}var sc = this.compiler.compile("#predefine", script, true, false, false, false);
if (sc.errorType != null) {
this.vwr.scriptStatus("JmolConstants.java ERROR: predefined set compile error:" + script + "\ncompile error:" + sc.errorMessageUntranslated);
return;
}if (sc.getTokenCount() != 1) {
this.vwr.scriptStatus("JmolConstants.java ERROR: predefinition does not have exactly 1 command:" + script);
return;
}var statement = sc.getToken(0);
if (statement.length <= 2) {
this.vwr.scriptStatus("JmolConstants.java ERROR: bad predefinition length:" + script);
return;
}var tok = statement[1].tok;
if (!JS.T.tokAttr(tok, 1073741824) && !JS.T.tokAttr(tok, 2097152)) {
this.vwr.scriptStatus("JmolConstants.java ERROR: invalid variable name:" + script);
return;
}var name = (statement[1].value).toLowerCase();
if (name.startsWith("dynamic_")) name = "!" + name.substring(8);
this.vwr.definedAtomSets.put(name, statement);
}, "~S");
Clazz.defineMethod(c$, "lookupIdentifierValue", 
function(identifier){
var bs = this.lookupValue(identifier, false);
if (bs != null) return JU.BSUtil.copy(bs);
bs = this.getAtomBits(1073741824, identifier);
return (bs == null ?  new JU.BS() : bs);
}, "~S");
Clazz.defineMethod(c$, "lookupValue", 
function(setName, plurals){
if (this.chk) {
return  new JU.BS();
}this.defineSets();
setName = setName.toLowerCase();
var value = this.vwr.definedAtomSets.get(setName);
var isDynamic = false;
if (value == null) {
value = this.vwr.definedAtomSets.get("!" + setName);
isDynamic = (value != null);
}if (Clazz.instanceOf(value,"JU.BS")) return value;
if (Clazz.instanceOf(value,Array)) {
this.pushContext(null, "lookupValue");
var bs = this.atomExpression(value, -2, 0, true, false, null, true);
this.popContext(false, false);
if (!isDynamic) this.vwr.definedAtomSets.put(setName, bs);
return bs;
}if (setName.equals("water")) {
var bs = this.vwr.ms.getAtoms(1612709912, null);
if (!isDynamic) this.vwr.definedAtomSets.put(setName, bs);
return bs;
}if (plurals) return null;
var len = setName.length;
if (len < 5) return null;
if (setName.charAt(len - 1) != 's') return null;
if (setName.endsWith("ies")) setName = setName.substring(0, len - 3) + 'y';
 else setName = setName.substring(0, len - 1);
return this.lookupValue(setName, true);
}, "~S,~B");
Clazz.overrideMethod(c$, "deleteAtomsInVariables", 
function(bsDeleted){
for (var entry, $entry = this.vwr.definedAtomSets.entrySet().iterator (); $entry.hasNext()&& ((entry = $entry.next ()) || true);) {
var value = entry.getValue();
if (Clazz.instanceOf(value,"JU.BS")) {
JU.BSUtil.deleteBits(value, bsDeleted);
if (!entry.getKey().startsWith("!")) this.vwr.g.setUserVariable("@" + entry.getKey(), JS.SV.newV(10, value));
}}
}, "JU.BS");
Clazz.overrideMethod(c$, "getThisContext", 
function(){
return this.thisContext;
});
Clazz.defineMethod(c$, "clearState", 
function(tQuiet){
this.thisContext = null;
this.scriptLevel = 0;
this.setErrorMessage(null);
this.contextPath = "";
this.tQuiet = tQuiet;
}, "~B");
Clazz.overrideMethod(c$, "pushContextDown", 
function(why){
this.scriptLevel--;
this.pushContext2(null, why);
}, "~S");
Clazz.defineMethod(c$, "pushContext", 
function(token, why){
if (this.scriptLevel == JS.ScriptEval.contextDepthMax) this.error(44);
this.pushContext2(token, why);
}, "JS.ContextToken,~S");
Clazz.defineMethod(c$, "pushContext2", 
function(token, why){
this.thisContext = this.getScriptContext(why);
this.thisContext.token = token;
if (token == null) {
this.scriptLevel = ++this.thisContext.scriptLevel;
} else {
this.thisContext.scriptLevel = -1;
this.contextVariables =  new java.util.Hashtable();
if (token.contextVariables != null) for (var key, $key = token.contextVariables.keySet().iterator (); $key.hasNext()&& ((key = $key.next ()) || true);) JS.ScriptCompiler.addContextVariable(this.contextVariables, key);

}if (this.debugHigh || this.isCmdLine_c_or_C_Option) JU.Logger.info("-->>----------------------".substring(0, Math.min(15, this.scriptLevel + 5)) + this.scriptLevel + " " + this.scriptFileName + " " + token + " " + this.thisContext.id + " " + why + " path=" + this.thisContext.contextPath);
}, "JS.ContextToken,~S");
Clazz.overrideMethod(c$, "getScriptContext", 
function(why){
var context =  new JS.ScriptContext();
if (this.debugHigh) JU.Logger.info("creating context " + context.id + " for " + why + " path=" + this.contextPath);
context.why = why;
context.scriptLevel = this.scriptLevel;
context.parentContext = this.thisContext;
context.contextPath = this.contextPath;
context.scriptFileName = this.scriptFileName;
context.parallelProcessor = this.parallelProcessor;
context.functionName = this.functionName;
context.script = this.script;
context.lineNumbers = this.lineNumbers;
context.lineIndices = this.lineIndices;
context.saveTokens(this.aatoken);
context.statement = this.st;
context.statementLength = this.slen;
context.pc = context.pc0 = this.pc;
context.lineEnd = this.lineEnd;
context.pcEnd = this.pcEnd;
context.iToken = this.iToken;
context.theToken = this.theToken;
context.theTok = this.theTok;
context.outputBuffer = this.outputBuffer;
context.vars = this.contextVariables;
context.isStateScript = this.$isStateScript;
context.errorMessage = this.errorMessage;
context.errorType = this.errorType;
context.iCommandError = this.iCommandError;
context.chk = this.chk;
context.executionStepping = this.executionStepping;
context.executionPaused = this.executionPaused;
context.scriptExtensions = this.scriptExtensions;
context.isEditor = this.isEditor;
context.mustResumeEval = this.mustResumeEval;
context.allowJSThreads = this.allowJSThreads;
return context;
}, "~S");
Clazz.defineMethod(c$, "popContext", 
function(isFlowCommand, statementOnly){
if (this.thisContext == null) return;
if (this.thisContext.scriptLevel > 0) this.scriptLevel = this.thisContext.scriptLevel - 1;
var scTemp = (isFlowCommand ? this.getScriptContext("popFlow") : null);
this.restoreScriptContext(this.thisContext, true, isFlowCommand, statementOnly);
if (scTemp != null) this.restoreScriptContext(scTemp, true, false, true);
if (this.debugHigh || this.isCmdLine_c_or_C_Option) JU.Logger.info("--<<------------".substring(0, Math.min(15, this.scriptLevel + 5)) + (this.scriptLevel + 1) + " " + this.scriptFileName + " isFlow " + isFlowCommand + " thisContext=" + (this.thisContext == null ? "" : "" + this.thisContext.id) + " pc=" + this.pc + "-->" + this.pc + " path=" + (this.thisContext == null ? "" : this.thisContext.contextPath));
}, "~B,~B");
Clazz.defineMethod(c$, "restoreScriptContext", 
function(context, isPopContext, isFlowCommand, statementOnly){
this.executing = !this.chk;
if (context == null) return;
if (!isFlowCommand) {
this.st = context.statement;
this.slen = context.statementLength;
this.pc = context.pc;
this.lineEnd = context.lineEnd;
this.pcEnd = context.pcEnd;
if (statementOnly) return;
}if (context.privateFuncs != null) this.privateFuncs = context.privateFuncs;
this.mustResumeEval = context.mustResumeEval;
this.script = context.script;
this.lineNumbers = context.lineNumbers;
this.lineIndices = context.lineIndices;
this.aatoken = context.restoreTokens();
this.contextVariables = context.vars;
this.scriptExtensions = context.scriptExtensions;
this.isEditor = context.isEditor;
if (isPopContext) {
this.contextPath = context.contextPath;
var pt = (this.contextPath == null ? -1 : this.contextPath.indexOf(" >> "));
if (pt >= 0) this.contextPath = this.contextPath.substring(0, pt);
this.scriptFileName = context.scriptFileName;
this.parallelProcessor = context.parallelProcessor;
this.functionName = context.functionName;
this.iToken = context.iToken;
this.theToken = context.theToken;
this.theTok = context.theTok;
this.outputBuffer = context.outputBuffer;
this.$isStateScript = context.isStateScript;
this.thisContext = context.parentContext;
this.allowJSThreads = context.allowJSThreads;
if (this.debugHigh || this.isCmdLine_c_or_C_Option) JU.Logger.info("--r------------".substring(0, Math.min(15, this.scriptLevel + 5)) + this.scriptLevel + " " + this.scriptFileName + " isPop " + isPopContext + " isFlow " + isFlowCommand + " context.id=" + context.id + " pc=" + this.pc + "-->" + context.pc + " " + this.contextPath);
} else {
this.$error = (context.errorType != null);
this.errorMessage = context.errorMessage;
this.errorMessageUntranslated = context.errorMessageUntranslated;
this.iCommandError = context.iCommandError;
this.errorType = context.errorType;
}}, "JS.ScriptContext,~B,~B,~B");
Clazz.defineMethod(c$, "setException", 
function(sx, msg, untranslated){
sx.untranslated = (untranslated == null ? msg : untranslated);
var isThrown = "!".equals(untranslated);
this.errorType = msg;
this.iCommandError = this.pc;
if (sx.message == null) {
sx.message = "";
return;
}var s = JS.ScriptEval.getContextTrace(this.vwr, this.getScriptContext("setException"), null, true).toString();
while (this.thisContext != null && !this.thisContext.isTryCatch) this.popContext(false, false);

if (sx.message.indexOf(s) < 0) {
sx.message += s;
sx.untranslated += s;
}var done = (isThrown || this.thisContext != null || this.chk || msg.indexOf("NOTE: file recognized as a script file: ") >= 0);
this.resumeViewer(isThrown ? "throw context" : "scriptException", isThrown);
if (done) return;
this.isFuncReturn = false;
if (s.indexOf("w_h_e_r_e =") < 0) JU.Logger.error("eval ERROR: " + s + "\n" + this.toString());
this.vwr.setAccessInternal(null);
if (this.vwr.autoExit) this.vwr.exitJmol();
}, "JS.ScriptException,~S,~S");
c$.statementAsString = Clazz.defineMethod(c$, "statementAsString", 
function(vwr, statement, iTok, doLogMessages){
if (statement == null || statement.length == 0) return "";
var sb =  new JU.SB();
var tok = statement[0].tok;
switch (tok) {
case 0:
return statement[0].value;
case 102409:
if (statement.length == 2 && (statement[1].tok == 134320141 || statement[1].tok == 102436)) return ((statement[1].value)).toString();
}
var useBraces = true;
var inBrace = false;
var inClauseDefine = false;
var setEquals = (statement.length > 1 && tok == 36867 && statement[0].value.equals("") && (statement[0].intValue == 61 || statement[0].intValue == 35) && statement[1].tok != 1073742325);
var len = statement.length;
for (var i = 0; i < len; ++i) {
var token = statement[i];
if (token == null) {
len = i;
break;
}if (iTok == i - 1) sb.append(" <<");
if (i != 0) sb.appendC(' ');
if (i == 2 && setEquals) {
if ((setEquals = (token.tok != 268440324)) || statement[0].intValue == 35) {
sb.append(setEquals ? "= " : "== ");
if (!setEquals) continue;
}}var tval = token.value;
switch (token.tok) {
case 1073742325:
if (useBraces) sb.append("{");
continue;
case 1073742326:
if (inClauseDefine && i == statement.length - 1) useBraces = false;
if (useBraces) sb.append("}");
continue;
case 268437504:
case 268437505:
break;
case 1073742332:
case 1073742338:
inBrace = (token.tok == 1073742332);
break;
case 12290:
if (i > 0 && (token.value).equals("define")) {
sb.append("@");
if (i + 1 < statement.length && statement[i + 1].tok == 1073742325) {
if (!useBraces) inClauseDefine = true;
useBraces = true;
}continue;
}break;
case 1073742335:
sb.append("true");
tval = null;
break;
case 1073742334:
sb.append("false");
tval = null;
break;
case 1275082241:
break;
case 2:
sb.appendI(token.intValue);
tval = null;
break;
case 8:
case 9:
case 10:
sb.append(JS.SV.sValue(token));
tval = null;
break;
case 6:
if (Boolean.TRUE === (token.value).get("$_BINARY_$")) {
sb.append("<BINARY DATA>");
tval = null;
break;
}case 7:
sb.append((token).escape());
tval = null;
break;
case 5:
sb.appendC('^');
tval = null;
break;
case 1073742363:
if (token.intValue != 2147483647) sb.appendI(token.intValue);
 else sb.append(JM.Group.getSeqcodeStringFor(JS.ScriptExpr.getSeqCode(token)));
token = statement[++i];
sb.appendC(' ');
sb.append(inBrace ? "-" : "- ");
case 1073742362:
if (token.intValue != 2147483647) sb.appendI(token.intValue);
 else sb.append(JM.Group.getSeqcodeStringFor(JS.ScriptExpr.getSeqCode(token)));
tval = null;
break;
case 1073742357:
sb.append("*:");
sb.append(vwr.getChainIDStr(token.intValue));
tval = null;
break;
case 1073742355:
sb.append("*%");
if (token.value != null) sb.append(token.value.toString());
tval = null;
break;
case 1073742358:
sb.append("*/");
case 1073742359:
case 3:
if (token.intValue < 2147483647) {
sb.append(JU.Escape.escapeModelFileNumber(token.intValue));
} else {
sb.append("" + token.value);
}tval = null;
break;
case 1073742361:
sb.appendC('[');
var ptr = token.intValue * 6 + 1;
sb.append(JM.Group.standardGroupList.substring(ptr, ptr + 3).trim());
sb.appendC(']');
tval = null;
break;
case 1073742360:
sb.appendC('[');
sb.appendO(token.value);
sb.appendC(']');
tval = null;
break;
case 1073742356:
sb.append("*.");
break;
case 1094713349:
if (Clazz.instanceOf(token.value,"JU.P3")) {
var pt = token.value;
sb.append("cell=").append(JU.Escape.eP(pt));
tval = null;
break;
}break;
case 4:
sb.append("\"").appendO(token.value).append("\"");
tval = null;
break;
case 268440324:
case 268440322:
case 268440321:
case 268440320:
case 268440323:
case 268440325:
if (token.intValue == 1715472409) {
sb.append(statement[++i].value).append(" ");
} else if (token.intValue != 2147483647) sb.append(JS.T.nameOf(token.intValue)).append(" ");
break;
case 364558:
tval = null;
break;
case 102409:
sb.append("end");
tval = null;
break;
default:
if (JS.T.tokAttr(token.tok, 1073741824) || !doLogMessages) break;
sb.appendC('\n').append(token.toString()).appendC('\n');
tval = null;
break;
}
if (tval != null) sb.append(token.value.toString());
if (iTok == i) sb.append("<<<<");
}
return sb.toString();
}, "JV.Viewer,~A,~N,~B");
Clazz.overrideMethod(c$, "setObjectPropSafe", 
function(id, tokCommand){
try {
return this.setObjectProp(id, tokCommand, -1);
} catch (e) {
if (Clazz.exceptionOf(e,"JS.ScriptException")){
return null;
} else {
throw e;
}
}
}, "~S,~N");
Clazz.defineMethod(c$, "setAtomProp", 
function(prop, value, bs){
this.setShapePropertyBs(0, prop, value, bs);
}, "~S,~O,JU.BS");
Clazz.defineMethod(c$, "restrictSelected", 
function(isBond, doInvert){
if (!this.chk) this.sm.restrictSelected(isBond, doInvert);
}, "~B,~B");
Clazz.defineMethod(c$, "showString", 
function(str){
this.showStringPrint(str, false);
}, "~S");
Clazz.overrideMethod(c$, "showStringPrint", 
function(s, mustDo){
if (this.chk || s == null) return;
if (this.outputBuffer == null) this.vwr.showString(s, mustDo);
 else this.appendBuffer(s, mustDo);
}, "~S,~B");
Clazz.defineMethod(c$, "report", 
function(s, isError){
if (this.chk || isError && s.indexOf(" of try:") >= 0) return;
if (this.outputBuffer == null) this.vwr.scriptStatus(s);
 else this.appendBuffer(s, isError);
}, "~S,~B");
Clazz.defineMethod(c$, "appendBuffer", 
function(str, mustDo){
if (mustDo || this.isFuncReturn || JU.Logger.isActiveLevel(4)) this.outputBuffer.append(str).appendC('\n');
}, "~S,~B");
Clazz.defineMethod(c$, "addProcess", 
function(vProcess, pc, pt){
if (this.parallelProcessor == null) return;
var statements =  new Array(pt);
for (var i = 0; i < vProcess.size(); i++) statements[i + 1 - pc] = vProcess.get(i);

var context = this.getScriptContext("addProcess");
context.saveTokens(statements);
context.pc = 1 - pc;
context.pcEnd = pt;
this.parallelProcessor.addProcess("p" + (++JS.ScriptEval.iProcess), context);
}, "JU.Lst,~N,~N");
Clazz.defineMethod(c$, "checkContinue", 
function(){
if (this.executionStopped) return false;
if (this.executionStepping && this.isCommandDisplayable(this.pc)) {
this.vwr.scriptStatusMsg("Next: " + this.getNextStatement(), "stepping -- type RESUME to continue");
this.executionPaused = true;
} else if (!this.executionPaused) {
return true;
}if (JU.Logger.debugging) {
JU.Logger.debug("script execution paused at command " + (this.pc + 1) + " level " + this.scriptLevel + ": " + this.thisCommand);
}this.refresh(false);
var doShowPC = true;
while (this.executionPaused) {
if (!this.isJS) {
Thread.yield();
}if (this.isEditor && doShowPC) this.notifyScriptEditor(this.pc);
doShowPC = false;
this.vwr.popHoldRepaint("pause \u0001## REPAINT_IGNORE ##");
var script = this.vwr.getInsertedCommand();
if (script.length > 0) {
this.resumePausedExecution();
this.setErrorMessage(null);
var scSave = this.getScriptContext("script insertion");
this.pc--;
try {
this.runScript(script);
} catch (e$$) {
if (Clazz.exceptionOf(e$$, Exception)){
var e = e$$;
{
this.setErrorMessage("" + e);
}
} else if (Clazz.exceptionOf(e$$, Error)){
var er = e$$;
{
this.setErrorMessage("" + er);
}
} else {
throw e$$;
}
}
if (this.$error) {
this.report(this.errorMessage, true);
this.setErrorMessage(null);
}this.restoreScriptContext(scSave, true, false, false);
if (!script.startsWith("resume\1") && !script.startsWith("step\1")) this.pauseExecution(false);
}this.doDelay(-100, null);
this.vwr.pushHoldRepaintWhy("pause");
}
this.notifyResumeStatus();
return !this.$error && !this.executionStopped;
});
Clazz.defineMethod(c$, "delayScript", 
function(millis){
this.delayScriptAndRun(millis, null);
}, "~N");
Clazz.defineMethod(c$, "delayScriptAndRun", 
function(millis, script){
if (this.vwr.autoExit) return;
this.stopScriptThreads();
if (this.vwr.captureParams != null && millis > 0) {
this.vwr.captureParams.put("captureDelayMS", Integer.$valueOf(millis));
}this.scriptDelayThread =  new JS.ScriptDelayThread(this, this.vwr, millis);
this.scriptDelayThread.setScript(script);
if (this.isJS && this.allowJSThreads) {
this.pc = this.aatoken.length;
}this.scriptDelayThread.run();
}, "~N,~S");
Clazz.defineMethod(c$, "doDelay", 
function(millis, script){
if (!this.useThreads(false)) return;
if (this.isJS) throw  new JS.ScriptInterruption(this, "delay" + (script == null ? "" : ":" + script), millis);
this.delayScriptAndRun(millis, script);
}, "~N,~S");
Clazz.overrideMethod(c$, "evalParallel", 
function(context, shapeManager){
return this.getCmdExt().evalParallel(context, shapeManager);
}, "JS.ScriptContext,JV.ShapeManager");
Clazz.defineMethod(c$, "isCommandDisplayable", 
function(i){
if (i >= this.aatoken.length || i >= this.pcEnd || this.aatoken[i] == null) return false;
return (this.lineIndices[i][1] > this.lineIndices[i][0]);
}, "~N");
Clazz.overrideMethod(c$, "loadFileResourceAsync", 
function(fileName){
this.loadFileAsync(null, fileName, -Math.abs(fileName.hashCode()), false);
}, "~S");
Clazz.defineMethod(c$, "loadFileAsync", 
function(prefix, filename, i, doClear){
if (!filename.startsWith("?")) {
var fullPathNameOrError = this.vwr.getFullPathNameOrError(filename);
filename = fullPathNameOrError[0];
if (fullPathNameOrError[1] != null) this.errorStr(17, filename + ":" + fullPathNameOrError[1]);
}if (this.vwr.fm.cacheGet(filename, false) != null) {
this.cancelFDThread("FileLoad");
return filename;
}if (prefix != null) prefix = "cache://" + "local" + prefix;
var key = this.pc + "_" + i + "_" + filename;
var cacheName;
if (this.thisContext == null) {
this.pushContext(null, "FileLoad");
}if (this.thisContext.htFileCache == null) {
this.thisContext.htFileCache =  new java.util.Hashtable();
}cacheName = this.thisContext.htFileCache.get(key);
if (cacheName != null && cacheName.length > 0) {
this.cancelFDThread("FileLoad");
this.vwr.queueOnHold = false;
if ("#CANCELED#".equals(cacheName) || "#CANCELED#".equals(this.vwr.fm.cacheGet(cacheName, false))) this.evalError("#CANCELED#", null);
return cacheName;
}this.thisContext.htFileCache.put(key, cacheName = prefix + System.currentTimeMillis());
if (doClear) this.vwr.cacheFileByName(prefix + "*", false);
this.fdThread = (this.newAsyncThread("FileLoad")).initialize(this, this.vwr, filename, key, cacheName);
if (this.vwr.testAsync) this.fdThread.start();
 else this.fdThread.run();
if (i < 0) this.fdThread = null;
throw  new JS.ScriptInterruption(this, "load", 1);
}, "~S,~S,~N,~B");
Clazz.defineMethod(c$, "cancelFDThread", 
function(name){
this.fdThread = null;
if (this.thisContext != null && this.thisContext.why === name) {
this.popContext(false, false);
}}, "~S");
Clazz.overrideMethod(c$, "promptAsync", 
function(label, options){
if (this.thisContext == null) {
this.pushContext(null, "Dialog");
}if (this.thisContext.htFileCache == null) {
this.thisContext.htFileCache =  new java.util.Hashtable();
}var key = "cache:// DIALOG";
var value = this.thisContext.htFileCache.get(key);
if (value != null) {
this.cancelFDThread("Dialog");
return (value === "#CANCELED#" ? null : value);
}this.fdThread = (this.newAsyncThread("Dialog")).initialize(this, this.vwr, label, options);
this.fdThread.run();
this.fdThread = null;
throw  new JS.ScriptInterruption(this, "prompt", 1);
}, "~S,~A");
Clazz.defineMethod(c$, "newAsyncThread", 
function(name){
return J.api.Interface.getInterface("JS." + name + "Thread", null, "async");
}, "~S");
Clazz.defineMethod(c$, "logLoadInfo", 
function(msg, isData){
if (msg.length > 0) JU.Logger.info(msg);
var sb =  new JU.SB();
var modelCount = this.vwr.ms.mc;
if (modelCount > 1 && !isData) sb.append((this.vwr.am.isMovie ? this.vwr.am.getFrameCount() + " frames" : modelCount + " models") + "\n");
for (var i = 0; i < modelCount; i++) {
var moData = this.vwr.ms.getInfo(i, "moData");
if (moData == null || !moData.containsKey("mos")) continue;
sb.appendI((moData.get("mos")).size()).append(" molecular orbitals in model ").append(this.vwr.getModelNumberDotted(i)).append("\n");
}
if (sb.length() > 0) this.showString(sb.toString());
}, "~S,~B");
Clazz.overrideMethod(c$, "notifyResumeStatus", 
function(){
if (!this.chk && !this.executionStopped && !this.executionStepping && !this.executionPaused) {
var isInterrupt = (this.$error || this.executionStopped);
this.vwr.scriptStatus("script execution " + (isInterrupt ? "interrupted" : "resumed"));
}});
Clazz.defineMethod(c$, "refresh", 
function(doDelay){
if (this.chk) return;
this.vwr.setTainted(true);
this.vwr.requestRepaintAndWait("refresh cmd");
if (this.isJS && doDelay) this.doDelay(10, null);
}, "~B");
Clazz.overrideMethod(c$, "stopScriptThreads", 
function(){
if (this.scriptDelayThread != null) {
this.scriptDelayThread.interrupt();
this.scriptDelayThread = null;
}if (this.fdThread != null) {
this.fdThread.interrupt();
this.fdThread.resumeEval();
this.cancelFDThread("FileLoad");
this.cancelFDThread("Dialog");
}});
Clazz.defineMethod(c$, "getErrorLineMessage2", 
function(){
return JS.ScriptError.getErrorLineMessage(this.functionName, this.scriptFileName, this.getLinenumber(null), this.pc, JS.ScriptEval.statementAsString(this.vwr, this.st, -9999, this.debugHigh));
});
Clazz.defineMethod(c$, "getLinenumber", 
function(c){
return (c == null ? this.lineNumbers[this.pc] : c.lineNumbers[c.pc]);
}, "JS.ScriptContext");
Clazz.defineMethod(c$, "dispatchCommands", 
function(isSpt, fromFunc, isTry){
if (this.sm == null) this.sm = this.vwr.shm;
this.debugScript = this.debugHigh = false;
if (!this.chk) this.setDebugging();
if (this.pcEnd == 0) this.pcEnd = 2147483647;
if (this.lineEnd == 0) this.lineEnd = 2147483647;
if (this.aatoken == null) return true;
if (!this.tQuiet) {
this.tQuiet = (this.vwr.getInt(536870922) < 0);
}var allowJSInterrupt = (this.isJS && !fromFunc && this.useThreads(false) && this.vwr.getInt(536870922) >= 0);
this.commandLoop(allowJSInterrupt);
if (this.chk) return true;
var script = this.vwr.getInsertedCommand();
if (!"".equals(script)) this.runScriptBuffer(script, null, false);
 else if (isSpt && this.debugScript && this.vwr.getBoolean(603979879)) this.vwr.getChimeMessenger().update(null);
if (!this.mustResumeEval && !allowJSInterrupt || fromFunc) return true;
if (!isTry && this.mustResumeEval || this.thisContext == null) {
var done = (this.thisContext == null);
this.resumeEval(this.thisContext);
this.mustResumeEval = false;
return done;
}return true;
}, "~B,~B,~B");
Clazz.defineMethod(c$, "commandLoop", 
function(allowJSInterrupt){
var lastCommand = "";
var isForCheck = false;
var vProcess = null;
var lastTime = System.currentTimeMillis();
if (this.debugScript && this.debugHigh && !this.chk) {
for (var i = this.pc; i < this.aatoken.length && i < this.pcEnd; i++) {
JU.Logger.info("Command " + i);
if (this.debugScript) this.logDebugScript(this.aatoken[i], 0);
}
JU.Logger.info("-----");
}var isFirst = true;
for (; this.pc < this.aatoken.length && this.pc < this.pcEnd; this.pc++) {
if (allowJSInterrupt) {
if (!this.executionPaused && System.currentTimeMillis() - lastTime > 1000000) {
this.pc--;
this.doDelay(-1, null);
}lastTime = System.currentTimeMillis();
}if (!this.chk && (!this.executionStepping || !isFirst) && !this.checkContinue()) break;
isFirst = false;
if (this.pc >= this.lineNumbers.length || this.lineNumbers[this.pc] > this.lineEnd) break;
if (this.debugHigh) {
var timeBegin = 0;
timeBegin = System.currentTimeMillis();
this.vwr.scriptStatus("Eval.dispatchCommands():" + timeBegin);
this.vwr.scriptStatus(this.script);
}if (this.debugScript && !this.chk) JU.Logger.info("Command " + this.pc + (this.thisContext == null ? "" : " path=" + this.thisContext.contextPath));
this.theToken = (this.aatoken[this.pc].length == 0 ? null : this.aatoken[this.pc][0]);
if (!this.historyDisabled && !this.chk && this.scriptLevel <= JS.ScriptEval.commandHistoryLevelMax && !this.tQuiet) {
var cmdLine = this.getCommand(this.pc, true, true);
if (this.theToken != null && cmdLine.length > 0 && !cmdLine.equals(lastCommand) && (this.theToken.tok == 134320141 || this.theToken.tok == 102436 || !JS.T.tokAttr(this.theToken.tok, 102400))) this.vwr.addCommand(lastCommand = cmdLine);
}if (!this.chk && allowJSInterrupt) {
var script = this.vwr.getInsertedCommand();
if (!"".equals(script)) this.runScript(script);
}if (!this.setStatement(this.aatoken[this.pc], 1)) {
continue;
}this.thisCommand = this.getCommand(this.pc, false, true);
if (this.debugHigh || this.debugScript) JU.Logger.info(this.thisCommand);
var nextCommand = this.getCommand(this.pc + 1, false, true);
this.fullCommand = this.thisCommand + (nextCommand.startsWith("#") ? nextCommand : "");
this.getToken(0);
this.iToken = 0;
if ((this.listCommands || !this.chk && this.scriptLevel > 0) && !this.isJS) {
var milliSecDelay = this.vwr.getInt(536870922);
if (this.listCommands || milliSecDelay > 0) {
if (milliSecDelay > 0) this.delayScript(-milliSecDelay);
this.vwr.scriptEcho("$[" + this.scriptLevel + "." + this.lineNumbers[this.pc] + "." + (this.pc + 1) + "] " + this.thisCommand);
}}if (vProcess != null && (this.theTok != 102409 || this.slen < 2 || this.st[1].tok != 102439)) {
vProcess.addLast(this.st);
continue;
}if (this.chk) {
if (this.isCmdLine_c_or_C_Option) JU.Logger.info(this.thisCommand);
if (this.slen == 1 && this.st[0].tok != 134320141 && this.st[0].tok != 102436) continue;
} else {
if (this.debugScript) this.logDebugScript(this.st, 0);
if (this.scriptLevel == 0 && this.vwr.g.logCommands) this.vwr.log(this.thisCommand);
if (this.debugHigh && this.theToken != null) JU.Logger.debug(this.theToken.toString());
if (!this.isJS && this.isEditor && this.scriptLevel == 0) {
this.notifyScriptEditor(this.pc);
try {
Thread.sleep(100);
} catch (e) {
if (Clazz.exceptionOf(e,"InterruptedException")){
} else {
throw e;
}
}
}}if (this.theToken == null) continue;
var tok = this.theToken.tok;
switch (tok) {
case 36867:
this.cmdSet();
continue;
case 134320648:
isForCheck = this.cmdFor(tok, isForCheck);
continue;
case 102439:
this.pushContext(this.theToken, "PROCESS");
if (this.parallelProcessor != null) vProcess =  new JU.Lst();
continue;
default:
if (JS.T.tokAttr(tok, 102400)) {
isForCheck = this.cmdFlow(tok, isForCheck, vProcess);
if (this.theTok == 102439) vProcess = null;
continue;
}this.processCommand(tok);
this.setCursorWait(false);
if (tok != 266298 && this.executionStepping) {
this.executionPaused = (this.isCommandDisplayable(this.pc + 1));
}}
}
}, "~B");
Clazz.defineMethod(c$, "notifyScriptEditor", 
function(pc){
this.vwr.notifyScriptEditor((this.lineIndices[pc][0] << 16) | this.lineIndices[pc][1], null);
}, "~N");
Clazz.defineMethod(c$, "processCommand", 
function(tok){
if (JS.T.tokAttr(this.theToken.tok, 135168)) {
this.processShapeCommand(tok);
return;
}switch (tok) {
case 0:
if (!this.chk && this.vwr.getBoolean(603979879)) this.vwr.getChimeMessenger().showHash(this.outputBuffer, this.theToken.value);
break;
case 1275335685:
this.pushContext(this.theToken, "PUSH");
break;
case 1275334681:
this.popContext(true, false);
break;
case 268436482:
break;
case 4097:
this.cmdAnimation();
break;
case 1610616835:
this.cmdBackground(1);
break;
case 4100:
this.cmdBind();
break;
case 4101:
this.cmdBondorder();
break;
case 20488:
this.cmdCD();
break;
case 12289:
this.cmdCenter(1);
break;
case 1765808134:
this.cmdColor();
break;
case 12290:
this.cmdDefine();
break;
case 528397:
this.cmdDelay();
break;
case 12291:
this.cmdDelete();
break;
case 554176526:
this.cmdSlab(true);
break;
case 1610625028:
this.cmdDisplay(true);
break;
case 266255:
case 266281:
if (this.chk) break;
if (this.pc > 0 && this.theToken.tok == 266255 && !this.vwr.autoExit) {
this.vwr.clearScriptQueue();
}this.executionStopped = (this.pc > 0 || !this.vwr.g.useScriptQueue);
break;
case 266256:
if (this.chk) return;
if (this.outputBuffer != null) JU.Logger.warn(this.outputBuffer.toString());
this.vwr.exitJmol();
break;
case 1228935687:
this.cmdFile();
break;
case 12293:
this.cmdFixed();
break;
case 4114:
this.cmdFont(-1, 0);
break;
case 4115:
case 1094717454:
this.cmdModel(1);
break;
case 1073741824:
this.cmdFunc();
break;
case 1275072526:
this.cmdGetProperty();
break;
case 20500:
if (this.vwr.headless) break;
this.cmdGoto(true);
break;
case 20482:
this.cmdHelp();
break;
case 12294:
this.cmdDisplay(false);
break;
case 1613238294:
this.cmdHbond();
break;
case 1610616855:
this.cmdHistory(1);
break;
case 544771:
this.cmdHover();
break;
case 4121:
switch (this.slen) {
case 1:
if (!this.chk) this.vwr.initialize(!this.$isStateScript, false);
break;
case 2:
if (this.tokAt(1) == 1275068433) {
this.vwr.getInchi(null, null, null);
if (this.chk) {
} else {
if (JV.Viewer.isJS) {
this.vwr.showString("InChI module initialized", false);
this.doDelay(1, null);
}}break;
}default:
this.bad();
}
break;
case 134238732:
this.cmdScript(134238732, null, null, null);
break;
case 134223363:
this.cmdLoad();
break;
case 36869:
this.cmdLog();
break;
case 528411:
this.cmdLoop();
break;
case 20485:
this.cmdMessage();
break;
case 4128:
this.cmdMove();
break;
case 4129:
this.cmdMoveto();
break;
case 20487:
this.cmdPause();
break;
case 36865:
this.cmdPrint();
break;
case 134256129:
this.cmdPrompt();
break;
case 536875059:
this.cmdScale(1);
break;
case 603984065:
case 4139:
case 4140:
case 4165:
this.cmdUndoRedo(tok);
break;
case 266284:
this.refresh(true);
break;
case 4141:
this.cmdReset();
break;
case 12295:
this.cmdRestrict();
break;
case 4143:
if (this.slen == 1) {
if (!this.chk) this.resumePausedExecution();
break;
}case 4142:
this.cmdRestore();
break;
case 36866:
this.cmdReturn(null);
break;
case 528432:
this.cmdRotate(false, false);
break;
case 4145:
this.cmdRotate(false, true);
break;
case 4146:
this.cmdSave();
break;
case 134222850:
this.cmdScript(134222850, null, null, null);
break;
case 1275082241:
this.cmdSelect(1);
break;
case 1611141172:
this.cmdSelectionHalos(1);
break;
case 554176565:
this.cmdSlab(false);
break;
case 1095241729:
this.cmdRotate(true, false);
break;
case 1611141176:
this.cmdSsbond();
break;
case 266298:
if (this.cmdPause()) this.stepPausedExecution();
break;
case 1639976963:
this.cmdStructure();
break;
case 2109448:
this.cmdSubset();
break;
case 36870:
this.cmdThrow();
break;
case 536875070:
this.cmdTimeout(1);
break;
case 4160:
this.cmdTranslate(false);
break;
case 4162:
this.cmdTranslate(true);
break;
case 4163:
this.cmdUnbind();
break;
case 36868:
break;
case 4166:
this.cmdVibration();
break;
case 12297:
this.cmdZap(true);
break;
case 4168:
this.cmdZoom(false);
break;
case 4170:
this.cmdZoom(true);
break;
default:
this.checkExtension(this.theToken.tok);
}
}, "~N");
Clazz.defineMethod(c$, "checkExtension", 
function(tok){
switch (tok) {
case 4098:
case 4108:
case 134221829:
case 4102:
case 4103:
case 4105:
case 134221831:
case 1094717448:
case 4106:
case 528395:
case 1613238294:
case 4120:
case 4122:
case 528443:
case 4124:
case 4125:
case 4126:
case 603983903:
case 1275072532:
case 4130:
case 134221834:
case 4131:
case 4133:
case 134221850:
case 4138:
case 134222350:
case 4156:
case 20489:
case 134221856:
this.getCmdExt().dispatch(tok, false, this.st);
break;
default:
System.out.println(JS.T.nameOf(tok) + " is not a command");
this.error(47);
}
}, "~N");
Clazz.defineMethod(c$, "processShapeCommand", 
function(tok){
var iShape = 0;
switch (tok) {
case 1611272194:
iShape = 34;
break;
case 1114249217:
iShape = 9;
break;
case 1812599299:
iShape = 32;
break;
case 1112152066:
iShape = 11;
break;
case 135174:
iShape = 23;
break;
case 134353926:
iShape = 25;
break;
case 135175:
iShape = 17;
break;
case 1112150019:
iShape = 16;
break;
case 135176:
iShape = 22;
break;
case 537022465:
iShape = 31;
break;
case 1112150020:
iShape = 20;
break;
case 1611272202:
iShape = 36;
break;
case 1112150021:
iShape = 19;
break;
case 1112152070:
iShape = 8;
break;
case 135180:
iShape = 24;
break;
case 1825200146:
iShape = 5;
break;
case 135182:
iShape = 26;
break;
case 537006096:
case 1745489939:
iShape = 6;
break;
case 1112152071:
iShape = 13;
break;
case 1073877010:
iShape = 27;
break;
case 1073877011:
iShape = 28;
break;
case 135190:
iShape = 30;
break;
case 135188:
iShape = 29;
break;
case 1275203608:
iShape = 21;
break;
case 1112152073:
iShape = 14;
break;
case 1112152074:
iShape = 15;
break;
case 1112152075:
iShape = 0;
break;
case 1112152076:
iShape = 7;
break;
case 1649022989:
iShape = 12;
break;
case 659482:
iShape = 4;
break;
case 1112152078:
iShape = 10;
break;
case 1814695966:
iShape = 33;
break;
case 135198:
iShape = 18;
break;
case 659488:
iShape = 1;
break;
default:
this.error(47);
}
if (this.sm.getShape(iShape) == null && this.slen == 2) {
switch (this.st[1].tok) {
case 1073742334:
case 12291:
case 1073742333:
return;
}
}switch (tok) {
case 1114249217:
case 1112152066:
case 1112152071:
case 1112152073:
case 1112152074:
case 1649022989:
case 1112152078:
this.setSizeBio(iShape);
return;
case 1112150019:
case 1112150021:
this.cmdDots(iShape);
return;
case 1112152070:
case 1112152075:
case 1112152076:
this.setSize(iShape, (tok == 1112152070 ? -1000.0 : 1));
return;
case 1825200146:
this.cmdLabel(1, null);
return;
case 135198:
this.cmdVector();
return;
case 659488:
this.cmdWireframe();
return;
}
switch (tok) {
case 1611272194:
this.cmdAxes(1);
return;
case 1812599299:
this.cmdBoundbox(1);
return;
case 537022465:
this.cmdEcho(1);
return;
case 1611272202:
this.cmdFrank(1);
return;
case 1814695966:
this.cmdUnitcell(1);
return;
case 1112150020:
case 537006096:
case 1745489939:
case 1275203608:
case 659482:
this.getCmdExt().dispatch(iShape, false, this.st);
return;
case 135174:
case 134353926:
case 135175:
case 135176:
case 135180:
case 135182:
case 1073877010:
case 1073877011:
case 135190:
case 135188:
this.getIsoExt().dispatch(iShape, false, this.st);
return;
}
}, "~N");
Clazz.defineMethod(c$, "cmdAnimation", 
function(){
var animate = false;
switch (this.getToken(1).tok) {
case 1073742335:
animate = true;
case 1073742334:
if (!this.chk) this.vwr.setAnimationOn(animate);
break;
case 1073742029:
var morphCount = Clazz.floatToInt(this.floatParameter(2));
if (!this.chk) this.vwr.am.setMorphCount(Math.abs(morphCount));
break;
case 1610625028:
this.iToken = 2;
var bs = (this.tokAt(2) == 1073742327 ? null : this.atomExpressionAt(2));
this.checkLength(this.iToken + 1);
if (!this.chk) this.vwr.setAnimDisplay(bs);
return;
case 4115:
if (this.isArrayParameter(2)) this.setFrameSet(2);
 else this.cmdModel(2);
break;
case 1073742024:
var startDelay = 1;
var endDelay = 1;
if (this.slen > 5) this.bad();
var animationMode = JS.T.getTokFromName(this.paramAsStr(2));
switch (animationMode) {
case 1073742070:
startDelay = endDelay = 0;
break;
case 528411:
case 1073742082:
break;
default:
this.invArg();
}
if (this.slen >= 4) {
startDelay = endDelay = this.floatParameter(3);
if (this.slen == 5) endDelay = this.floatParameter(4);
}if (!this.chk) this.vwr.am.setAnimationReplayMode(animationMode, startDelay, endDelay);
break;
case 1073741918:
var i = 2;
var direction = 0;
switch (this.tokAt(i)) {
case 268440576:
direction = -this.intParameter(++i);
break;
case 268440577:
direction = this.intParameter(++i);
break;
case 2:
direction = this.intParameter(i);
break;
default:
this.invArg();
}
this.checkLength(++i);
if (direction != 1 && direction != -1) this.errorStr2(35, "-1", "1");
if (!this.chk) this.vwr.am.setAnimationDirection(direction);
break;
case 1073741950:
this.setIntProperty("animationFps", this.intParameter(this.checkLast(2)));
break;
default:
this.frameControl(1);
}
});
Clazz.defineMethod(c$, "setFrameSet", 
function(i){
var frames = this.expandFloatArray(this.floatParameterSet(i, 0, 2147483647), 1, false);
this.checkLength(this.iToken + 1);
if (this.chk) return;
var movie =  new java.util.Hashtable();
if (frames.length > 0) movie.put("frames", frames);
movie.put("currentFrame", Integer.$valueOf(0));
this.vwr.am.setMovie(movie);
}, "~N");
Clazz.defineMethod(c$, "cmdAxes", 
function(index){
var tickInfo = this.tickParamAsStr(index, true, true, false);
index = this.iToken + 1;
var tok = this.tokAt(index);
var type = this.optParameterAsString(index).toLowerCase();
if (this.slen == index + 1 && JU.PT.isOneOf(type, ";window;unitcell;molecular;")) {
this.setBooleanProperty("axes" + type, true);
return;
}switch (tok) {
case 1073742066:
this.setFloatProperty("axisOffset", this.floatParameter(++index));
this.checkLast(this.iToken);
return;
case 12289:
this.setShapeProperty(34, "origin", this.centerParameter(index + 1, null));
this.checkLast(this.iToken);
return;
case 1140850696:
var s = this.stringParameter(index + 1);
if (!JU.PT.isOneOf(s, ";a;b;c;ab;ac;bc;abc;")) s = null;
this.setShapeProperty(34, "type", s);
this.checkLast(this.iToken);
return;
case 536875059:
this.setFloatProperty("axesScale", this.floatParameter(this.checkLast(++index)));
return;
case 1825200146:
switch (tok = this.tokAt(index + 1)) {
case 1073742334:
case 1073742335:
this.checkLength(index + 2);
this.setShapeProperty(34, "labels" + (tok == 1073742335 ? "On" : "Off"), null);
return;
}
var sOrigin = null;
switch (this.slen - index) {
case 7:
this.setShapeProperty(34, "labels",  Clazz.newArray(-1, [this.paramAsStr(++index), this.paramAsStr(++index), this.paramAsStr(++index), this.paramAsStr(++index), this.paramAsStr(++index), this.paramAsStr(++index)]));
break;
case 5:
sOrigin = this.paramAsStr(index + 4);
case 4:
this.setShapeProperty(34, "labels",  Clazz.newArray(-1, [this.paramAsStr(++index), this.paramAsStr(++index), this.paramAsStr(++index), sOrigin]));
break;
default:
this.bad();
}
return;
}
if (type.equals("position")) {
var xyp;
if (this.tokAt(++index) == 1073742334) {
xyp =  new JU.P3();
} else {
xyp = this.xypParameter(index);
if (xyp == null) this.invArg();
index = this.iToken;
this.setShapeProperty(34, "axes2", (this.tokAt(index + 1) == 4 ? this.stringParameter(++index) : null));
}this.setShapeProperty(34, "position", xyp);
return;
}var mad10 = this.getSetAxesTypeMad10(index);
if (this.chk || mad10 == 2147483647) return;
this.setObjectMad10(34, "axes", mad10);
if (tickInfo != null) this.setShapeProperty(34, "tickInfo", tickInfo);
}, "~N");
Clazz.defineMethod(c$, "cmdBackground", 
function(i){
this.getToken(i);
var argb;
if (this.theTok == 4120) {
var o = null;
switch (this.tokAt(++i)) {
case 15:
case 6:
o = this.getToken(i).value;
break;
default:
var file = this.paramAsStr(this.checkLast(i));
if (this.chk) return;
if (file.equalsIgnoreCase("none") || file.length == 0) {
this.vwr.setBackgroundImage(null, null);
return;
}o = (file.startsWith(";base64,") ?  new JU.BArray(JU.Base64.decodeBase64(file)) : file);
}
if (this.vwr.fm.loadImage(o, null, !this.useThreads(false))) throw  new JS.ScriptInterruption(this, "backgroundImage", 1);
return;
}if (this.theTok == 1073742333 || this.isColorParam(i)) {
argb = this.getArgbParamLast(i, true);
if (this.chk) return;
this.setObjectArgb("background", argb);
this.vwr.setBackgroundImage(null, null);
return;
}this.colorShape(-this.theTok, i + 1, true);
}, "~N");
Clazz.defineMethod(c$, "cmdBind", 
function(){
var mouseAction = this.stringParameter(1);
var name = this.paramAsStr(2);
this.checkLength(3);
if (!this.chk) this.vwr.bindAction(mouseAction, name);
});
Clazz.defineMethod(c$, "cmdBondorder", 
function(){
this.checkLength(-3);
var order = 0;
switch (this.getToken(1).tok) {
case 2:
case 3:
if ((order = JU.Edge.getBondOrderFromFloat(this.floatParameter(1))) == 131071) this.invArg();
break;
default:
if ((order = JU.Edge.getBondOrderFromString(this.paramAsStr(1))) == 131071) this.invArg();
if (order == 33 && this.tokAt(2) == 3) {
order = JU.Edge.getPartialBondOrderFromFloatEncodedInt(this.st[2].intValue);
}}
this.setShapeProperty(1, "bondOrder", Integer.$valueOf(order));
});
Clazz.defineMethod(c$, "cmdBoundbox", 
function(index){
var tickInfo = this.tickParamAsStr(index, false, true, false);
index = this.iToken + 1;
var scale = 1;
if (this.tokAt(index) == 536875059) {
scale = this.floatParameter(++index);
index++;
if (index == this.slen) {
if (!this.chk) this.vwr.ms.setBoundBox(null, null, true, scale);
return;
}} else if (this.tokAt(index) == 4141) {
if (!this.chk) this.vwr.ms.setBoundBox(null, null, true, 0);
return;
}var byCorner = (this.tokAt(index) == 1073741902);
if (byCorner) index++;
if (this.isCenterParameter(index)) {
var ret =  new Array(1);
var index0 = index;
var pt1 = this.centerParameter(index, ret);
index = this.iToken + 1;
if (byCorner || this.isCenterParameter(index)) {
var pt2 = (byCorner ? this.centerParameter(index, ret) : this.getPoint3f(index, true, true));
index = this.iToken + 1;
if (!this.chk) this.vwr.ms.setBoundBox(pt1, pt2, byCorner, scale);
} else if (ret[0] != null && Clazz.instanceOf(ret[0],"JU.BS")) {
if (!this.chk) this.vwr.calcBoundBoxDimensions(ret[0], scale);
} else if (ret[0] == null && this.tokAt(index0) == 1073742330) {
if (this.chk) return;
var bbox = this.getObjectBoundingBox(this.objectNameParameter(++index0));
if (bbox == null) this.invArg();
this.vwr.ms.setBoundBox(bbox[0], bbox[1], true, scale);
index = this.iToken + 1;
} else {
this.invArg();
}if (index == this.slen) return;
}var mad10 = this.getSetAxesTypeMad10(index);
if (this.chk || mad10 == 2147483647) return;
if (tickInfo != null) this.setShapeProperty(32, "tickInfo", tickInfo);
this.setObjectMad10(32, "boundbox", mad10);
}, "~N");
Clazz.defineMethod(c$, "cmdCD", 
function(){
if (this.chk) return;
var dir = (this.slen == 1 ? null : this.paramAsStr(1));
this.showString(this.vwr.cd(dir));
});
Clazz.defineMethod(c$, "cmdCenter", 
function(i){
if (this.slen == 1) {
this.vwr.setNewRotationCenter(null);
return;
}if (this.slen == 4 && this.tokAt(2) == 1814695966) i = 2;
var center = this.centerParameter(i, null);
if (center == null) this.invArg();
if (!this.chk) this.vwr.setNewRotationCenter(center);
}, "~N");
Clazz.defineMethod(c$, "cmdColor", 
function(){
var i = 1;
var strColor = (this.tokAt(1) == 4 ? this.stringParameter(1) : null);
if (this.isColorParam(1)) {
this.theTok = 1153433601;
} else {
var argb = 0;
i = 2;
var tok = this.getToken(1).tok;
if (tok == 4) {
tok = JS.T.getTokFromName(strColor);
if (tok == 0 || tok == 1073742186) tok = 4;
}switch (tok) {
case 1073742330:
this.setObjectProperty();
return;
case 1086324739:
case 2097154:
case 2097166:
case 1086326788:
case 1073741946:
case 1631586315:
case 1086324742:
case 1113589786:
case 1086324746:
case 1073741991:
case 1094713360:
case 1094713361:
case 1073742333:
case 1073742074:
case 1111492619:
case 1094713362:
case 1715472409:
case 1073742116:
case 1073742110:
case 1275082241:
case 1112152075:
case 1073742144:
case 1111490574:
case 1639976963:
case 1111490575:
case 1111492620:
case 1111490588:
case 1648363544:
case 1145047055:
this.theTok = 1153433601;
i = 1;
break;
case 4:
i = 2;
if (this.isArrayParameter(i)) {
strColor = strColor += "=" + JS.SV.sValue(JS.SV.getVariableAS(this.stringParameterSet(i))).$replace('\n', ' ');
i = this.iToken + 1;
}var isTranslucent = (this.tokAt(i) == 1111490588);
if (!this.chk) this.vwr.setPropertyColorScheme(strColor, isTranslucent, true);
if (isTranslucent) ++i;
if (this.tokAt(i) == 1073742114 || this.tokAt(i) == 1073741826) {
var min = this.floatParameter(++i);
var max = this.floatParameter(++i);
if (!this.chk) this.vwr.cm.setPropertyColorRange(min, max);
}return;
case 1073742114:
case 1073741826:
var min = this.floatParameter(2);
var max = this.floatParameter(this.checkLast(3));
if (!this.chk) this.vwr.cm.setPropertyColorRange(min, max);
return;
case 1610616835:
argb = this.getArgbParamLast(2, true);
if (!this.chk) this.setObjectArgb("background", argb);
return;
case 12290:
case 10:
case 1073742325:
i = -1;
this.theTok = 1153433601;
break;
case 1073742134:
argb = this.getArgbParamLast(2, false);
if (!this.chk) this.vwr.cm.setRubberbandArgb(argb);
return;
case 536870920:
case 1611141172:
i = 2;
if (this.tokAt(2) == 1073742074) i++;
argb = this.getArgbParamLast(i, true);
if (this.chk) return;
this.sm.loadShape(8);
this.setShapeProperty(8, (tok == 1611141172 ? "argbSelection" : "argbHighlight"), Integer.$valueOf(argb));
return;
case 1611272194:
case 1812599299:
case 1814695966:
case 1073741824:
case 1612709900:
var str = this.paramAsStr(1);
if (this.checkToken(2)) {
argb = this.getToken(2).tok;
switch (argb) {
case 1073742333:
argb = 1073741991;
break;
case 1073741991:
case 1073742116:
case 1073742110:
break;
default:
argb = this.getArgbParam(2);
}
}if (argb == 0) this.error(9);
this.checkLast(this.iToken);
if (str.equalsIgnoreCase("axes") || JV.StateManager.getObjectIdFromName(str) >= 0) {
this.setObjectArgb(str, argb);
return;
}if (this.setElementColor(str, argb)) return;
this.invArg();
break;
case 135180:
case 134353926:
this.setShapeProperty(JV.JC.shapeTokenIndex(tok), "thisID", "+PREVIOUS_MESH+");
break;
}
}this.colorShape(-this.theTok, i, false);
});
Clazz.defineMethod(c$, "cmdDefine", 
function(){
if (this.slen < 3 || !((typeof(this.getToken(1).value)=='string'))) this.invArg();
var setName = (this.getToken(1).value).toLowerCase();
if (JU.PT.parseInt(setName) != -2147483648) this.invArg();
if (this.chk) return;
var isSite = setName.startsWith("site_");
var isDynamic = (setName.indexOf("dynamic_") == 0);
if (isDynamic || isSite) {
var code =  new Array(this.slen);
for (var i = this.slen; --i >= 0; ) code[i] = this.st[i];

this.vwr.definedAtomSets.put("!" + (isSite ? setName : setName.substring(8)), code);
} else {
var bs = this.atomExpressionAt(2);
this.vwr.definedAtomSets.put(setName, bs);
if (!this.chk) this.vwr.g.setUserVariable("@" + setName, JS.SV.newV(10, bs));
}});
Clazz.defineMethod(c$, "cmdDelay", 
function(){
var millis = 0;
switch (this.getToken(1).tok) {
case 1073742335:
millis = 1;
break;
case 2:
millis = this.intParameter(1) * 1000;
break;
case 3:
millis = Clazz.floatToInt(this.floatParameter(1) * 1000);
break;
default:
this.error(34);
}
this.refresh(false);
this.doDelay(Math.abs(millis), (this.slen == 3 && this.tokAt(2) == 4 ? JS.SV.sValue(this.getToken(2)) : null));
});
Clazz.defineMethod(c$, "cmdDelete", 
function(){
if (this.tokAt(1) == 1073742330) {
if (this.slen == 4 && this.optParameterAsString(2).equals("saved") && this.slen == 4) {
this.vwr.stm.deleteSaved(this.optParameterAsString(3));
if (this.doReport()) this.report(J.i18n.GT.o(J.i18n.GT.$("show saved: {0}"), this.vwr.stm.listSavedStates()), false);
return;
}this.setObjectProperty();
return;
}var bs = (this.slen == 1 ? null : this.atomExpression(this.st, 1, 0, true, false, null, false));
if (this.chk) return;
if (bs == null) bs = this.vwr.getAllAtoms();
var nDeleted = this.vwr.deleteAtoms(bs, false);
if (this.doReport()) this.report(J.i18n.GT.i(J.i18n.GT.$("{0} atoms deleted"), nDeleted), false);
});
Clazz.defineMethod(c$, "cmdDisplay", 
function(isDisplay){
var bs = null;
var addRemove = 0;
var i = 1;
var tok;
switch (tok = this.tokAt(1)) {
case 1275069441:
case 1073742119:
addRemove = tok;
tok = this.tokAt(++i);
break;
}
var isGroup = (tok == 1086324742);
if (isGroup) tok = this.tokAt(++i);
switch (tok) {
case 1073742330:
this.setObjectProperty();
return;
case 0:
break;
default:
if (this.slen == 4 && this.tokAt(2) == 1677721602) bs = JM.BondSet.newBS(JU.BSUtil.newBitSet2(0, this.vwr.ms.bondCount));
 else bs = this.atomExpressionAt(i);
}
if (this.chk) return;
if (Clazz.instanceOf(bs,"JM.BondSet")) {
this.vwr.ms.displayBonds(bs, isDisplay);
return;
}this.vwr.displayAtoms(bs, isDisplay, isGroup, addRemove, this.tQuiet);
}, "~B");
Clazz.defineMethod(c$, "cmdDots", 
function(iShape){
if (!this.chk) this.sm.loadShape(iShape);
this.setShapeProperty(iShape, "init", null);
var value = NaN;
var type = J.atomdata.RadiusData.EnumType.ABSOLUTE;
var ipt = 1;
var isOnly = false;
while (true) {
switch (this.getToken(ipt).tok) {
case 1073742072:
isOnly = true;
case 1073742335:
value = 1;
type = J.atomdata.RadiusData.EnumType.FACTOR;
break;
case 1073742334:
value = 0;
break;
case 1073741976:
this.setShapeProperty(iShape, "ignore", this.atomExpressionAt(ipt + 1));
ipt = this.iToken + 1;
continue;
case 3:
isOnly = (this.tokAt(ipt + 1) == 1073742072 || this.floatParameter(ipt) < 0);
break;
case 2:
var dotsParam = this.intParameter(ipt);
if (this.tokAt(ipt + 1) == 1665140738) {
ipt++;
this.setShapeProperty(iShape, "atom", Integer.$valueOf(dotsParam));
this.setShapeProperty(iShape, "radius", Float.$valueOf(this.floatParameter(++ipt)));
if (this.tokAt(++ipt) == 1765808134) {
this.setShapeProperty(iShape, "colorRGB", Integer.$valueOf(this.getArgbParam(++ipt)));
ipt++;
}if (this.getToken(ipt).tok != 10) this.invArg();
this.setShapeProperty(iShape, "dots", this.st[ipt].value);
return;
}break;
}
break;
}
var rd = (Float.isNaN(value) ? this.encodeRadiusParameter(ipt, isOnly, true) :  new J.atomdata.RadiusData(null, value, type, J.c.VDW.AUTO));
if (rd == null) return;
if (Float.isNaN(rd.value)) this.invArg();
if (isOnly) {
this.restrictSelected(false, false);
}this.setShapeSize(iShape, rd);
}, "~N");
Clazz.defineMethod(c$, "cmdEcho", 
function(index){
if (this.chk) return;
var text = this.optParameterAsString(index);
var doRefresh = true;
if (this.vwr.ms.getEchoStateActive()) {
if (text.startsWith("\1")) {
text = text.substring(1);
doRefresh = false;
}if (text != null) this.setShapeProperty(31, "text", text);
}if (doRefresh && this.vwr.getRefreshing() && text != null && !text.startsWith("%SCALE")) this.showString(this.vwr.formatText(text));
}, "~N");
Clazz.defineMethod(c$, "cmdFile", 
function(){
var file = this.intParameter(this.checkLast(1));
if (this.chk) return;
var modelIndex = this.vwr.ms.getModelNumberIndex(file * 1000000 + 1, false, false);
var modelIndex2 = -1;
if (modelIndex >= 0) {
modelIndex2 = this.vwr.ms.getModelNumberIndex((file + 1) * 1000000 + 1, false, false);
if (modelIndex2 < 0) modelIndex2 = this.vwr.ms.mc;
modelIndex2--;
}this.vwr.setAnimationOn(false);
this.vwr.am.setAnimationDirection(1);
this.vwr.setAnimationRange(modelIndex, modelIndex2);
this.vwr.setCurrentModelIndex(-1);
});
Clazz.defineMethod(c$, "cmdFixed", 
function(){
var bs = (this.slen == 1 ? null : this.atomExpressionAt(1));
if (this.chk) return;
this.vwr.setMotionFixedAtoms(bs);
});
Clazz.defineMethod(c$, "cmdFor", 
function(tok, isForCheck){
var cmdToken = this.theToken;
var pt = this.st[0].intValue;
var forVars = cmdToken.forVars;
var pts =  Clazz.newIntArray (2, 0);
var bsOrList = null;
var forVal = null;
var forVar = null;
var inTok = 0;
var isOK = true;
var isMinusMinus = false;
var j = 0;
var key = null;
if (isForCheck && forVars != null) {
tok = 1275068432;
forVar = forVars[0];
forVal = forVars[1];
bsOrList = forVars[1].value;
j = ++forVal.intValue;
if (forVal.tok == 2) {
isMinusMinus = (j < 0);
var i1 = (bsOrList)[0];
var i2 = (bsOrList)[1];
isOK = (i1 != i2 && (i2 < i1) == isMinusMinus);
if (isOK) forVar.intValue = (bsOrList)[0] = i1 + (isMinusMinus ? -1 : 1);
j = -1;
} else if (forVal.tok == 7) {
isOK = (j <= (bsOrList).size());
if (isOK) forVar.setv(JS.SV.selectItemVar(forVal));
j = -1;
} else {
this.isBondSet = Clazz.instanceOf(bsOrList,"JM.BondSet");
j = (bsOrList).nextSetBit(j);
isOK = (j >= 0);
}} else {
var isLocal = false;
for (var i = 1, nSkip = 0; i < this.slen && j < 2; i++) {
switch (tok = this.tokAt(i)) {
case 36868:
isLocal = true;
break;
case 1073742339:
if (nSkip > 0) nSkip--;
 else pts[j++] = i;
break;
case 1275068432:
case 1073741952:
key = this.paramAsStr(i - 1);
nSkip -= 2;
if (this.isAtomExpression(++i)) {
inTok = 10;
bsOrList = this.atomExpressionAt(i);
if (this.isBondSet) bsOrList = JM.BondSet.newBS(bsOrList);
isOK = ((bsOrList).nextSetBit(0) >= 0);
} else {
var what = this.parameterExpressionList(-i, 1, false);
if (what == null || what.size() < 1) this.invArg();
var vl = what.get(0);
switch (inTok = vl.tok) {
case 10:
bsOrList = vl.value;
isOK = !(bsOrList).isEmpty();
break;
case 7:
var v = vl.getList();
j = v.size();
isOK = (j > 0);
if (isOK && tok == 1073741952) {
var i12 =  Clazz.newIntArray(-1, [JS.SV.iValue(v.get(0)), JS.SV.iValue(v.get(j - 1))]);
isMinusMinus = (i12[1] < i12[0]);
bsOrList = i12;
tok = 1275068432;
inTok = 2;
} else {
bsOrList = v;
}break;
case 6:
var m = vl.getMap();
var n = m.keySet().size();
isOK = (n > 0);
if (isOK) {
var keys =  new Array(n);
m.keySet().toArray(keys);
java.util.Arrays.sort(keys);
bsOrList = keys;
}break;
default:
this.invArg();
}
}i = this.iToken;
break;
case 1275082241:
nSkip += 2;
break;
}
}
if (!isForCheck) {
this.pushContext(cmdToken, "FOR");
this.thisContext.forVars = forVars;
forVars = null;
}if (key == null) {
if (isForCheck) {
j = (bsOrList == null ? pts[1] + 1 : 2);
} else {
j = 2;
}if (this.tokAt(j) == 36868) j++;
key = this.paramAsStr(j);
isMinusMinus = key.equals("--") || key.equals("++");
if (isMinusMinus) key = this.paramAsStr(++j);
}if (isOK) if (tok == 1275068432) {
forVar = this.getContextVariableAsVariable(key, isLocal);
if (forVar == null && !isLocal) forVar = this.vwr.g.getAndSetNewVariable(key, false);
if (forVar == null || forVar.myName == null) {
if (key.startsWith("_")) this.invArg();
if (isLocal) this.contextVariables.put(key.toLowerCase(), forVar = JS.SV.newI(0));
 else forVar = this.vwr.g.getAndSetNewVariable(key, true);
}if (inTok == 2) {
forVar.tok = 2;
forVar.intValue = (bsOrList)[0];
forVal = JS.SV.newV(2, bsOrList);
forVal.intValue = (isMinusMinus ? -2147483648 : 0);
j = -1;
} else {
forVal = JS.SV.getVariable(bsOrList);
if (inTok == 10) {
j = (bsOrList).nextSetBit(0);
forVal.intValue = 0;
} else {
forVal.intValue = 1;
forVar.setv(JS.SV.selectItemVar(forVal));
j = -1;
}}if (forVars == null) forVars = cmdToken.forVars =  new Array(2);
forVars[0] = forVar;
forVars[1] = forVal;
} else {
var vtok = this.tokAt(j);
if (vtok != 1073742339 && (JS.T.tokAttr(vtok, 1073741824) || (forVal = this.getContextVariableAsVariable(key, false)) != null)) {
if (!isMinusMinus && this.getToken(++j).tok != 268440324) this.invArg();
if (isMinusMinus) j -= 2;
this.setVariable(++j, this.slen - 1, key, false);
}isOK = (pts[0] + 1 == pts[1] || this.parameterExpressionBoolean(pts[0] + 1, pts[1]));
}}if (isOK && tok == 1275068432 && j >= 0) {
forVal.intValue = j;
forVar.tok = 10;
if (this.isBondSet) {
forVar.value =  new JM.BondSet();
(forVar.value).set(j);
} else {
forVar.value = JU.BSUtil.newAndSetBit(j);
}}pt++;
if (!isOK) {
cmdToken.forVars = this.thisContext.forVars;
this.popContext(true, false);
}isForCheck = false;
if (!isOK && !this.chk) this.pc = Math.abs(pt) - 1;
return isForCheck;
}, "~N,~B");
Clazz.defineMethod(c$, "cmdFlow", 
function(tok, isForCheck, vProcess){
var ct;
var pt = this.st[0].intValue;
var isDone = (pt < 0 && !this.chk);
var continuing = true;
var ptNext = 0;
switch (tok) {
case 134320141:
case 102436:
this.cmdFunc();
return isForCheck;
case 364558:
return isForCheck;
case 102412:
ct = this.theToken;
this.pushContext(ct, "CATCH");
if (!isDone && ct.name0 != null) this.contextVariables.put(ct.name0, ct.contextVariables.get(ct.name0));
continuing = !isDone;
this.st[0].intValue = -Math.abs(pt);
break;
case 102410:
case 102413:
case 102411:
ptNext = Math.abs(this.aatoken[Math.abs(pt)][0].intValue);
switch (isDone ? 0 : this.cmdFlowSwitch(this.theToken, tok)) {
case 0:
ptNext = -ptNext;
continuing = false;
break;
case -1:
continuing = false;
break;
case 1:
}
this.aatoken[this.pc][0].intValue = Math.abs(pt);
this.theToken = this.aatoken[Math.abs(pt)][0];
if (this.theToken.tok != 102409) this.theToken.intValue = ptNext;
break;
case 134320649:
case 102402:
continuing = (!isDone && this.parameterExpressionBoolean(1, 0));
if (this.chk) break;
ptNext = Math.abs(this.aatoken[Math.abs(pt)][0].intValue);
ptNext = (isDone || continuing ? -ptNext : ptNext);
this.aatoken[Math.abs(pt)][0].intValue = ptNext;
if (tok == 102412) this.aatoken[this.pc][0].intValue = -pt;
break;
case 364547:
this.checkLength(1);
if (pt < 0 && !this.chk) this.pc = -pt - 1;
break;
case 364548:
this.checkLength(1);
break;
case 102406:
if (!isForCheck) this.pushContext(this.theToken, "WHILE");
isForCheck = false;
if (!this.parameterExpressionBoolean(1, 0) && !this.chk) {
this.pc = pt;
this.popContext(true, false);
}break;
case 102407:
if (!this.chk) {
this.breakAt(pt);
break;
}if (this.slen == 1) break;
var n = this.intParameter(this.checkLast(1));
if (this.chk) break;
for (var i = 0; i < n; i++) this.popContext(true, false);

break;
case 102408:
isForCheck = true;
if (!this.chk) this.pc = pt - 1;
if (this.slen > 1) this.intParameter(this.checkLast(1));
break;
case 102409:
switch (this.getToken(this.checkLast(1)).tok) {
case 364558:
var trycmd = this.getToken(1).value;
if (this.chk) return false;
this.runFunctionAndRet(trycmd, "try", null, null, true, true, true);
return false;
case 134320141:
case 102436:
this.addFunction(this.theToken.value);
return isForCheck;
case 102412:
this.popContext(true, false);
break;
case 102439:
this.addProcess(vProcess, pt, this.pc);
this.popContext(true, false);
break;
case 102410:
if (pt > 0 && this.cmdFlowSwitch(this.aatoken[pt][0], 0) == -1) {
for (; pt < this.pc; pt++) if ((tok = this.aatoken[pt][0].tok) != 102413 && tok != 102411) break;

continuing = (this.pc == pt);
}break;
case 134320649:
break;
case 134320648:
case 102406:
continuing = false;
isForCheck = true;
break;
}
break;
}
if (!continuing && !this.chk) this.pc = Math.abs(pt) - 1;
return isForCheck;
}, "~N,~B,JU.Lst");
Clazz.defineMethod(c$, "cmdFlowSwitch", 
function(c, tok){
if (tok == 102410) c.addName("_var");
var $var = c.contextVariables.get("_var");
if ($var == null) return 1;
if (tok == 0) {
c.contextVariables.remove("_var");
return -1;
}if (tok == 102413) return -1;
var v = this.parameterExpressionToken(1);
if (tok == 102411) {
var isOK = JS.SV.areEqual($var, v);
if (isOK) c.contextVariables.remove("_var");
return isOK ? 1 : -1;
}c.contextVariables.put("_var", v);
return 1;
}, "JS.ContextToken,~N");
Clazz.defineMethod(c$, "cmdFont", 
function(shapeType, fontsize){
var fontface = "SansSerif";
var fontstyle = "Plain";
var name = "font";
var sizeAdjust = 0;
var scaleAngstromsPerPixel = -1;
switch (this.iToken = this.slen) {
case 6:
scaleAngstromsPerPixel = this.floatParameter(5);
if (scaleAngstromsPerPixel >= 5) scaleAngstromsPerPixel = this.vwr.tm.getZoomSetting() / scaleAngstromsPerPixel / this.vwr.getScalePixelsPerAngstrom(false);
case 5:
if (this.getToken(4).tok != 1073741824) this.invArg();
fontstyle = this.paramAsStr(4);
case 4:
if (this.getToken(3).tok != 1073741824) this.invArg();
fontface = this.paramAsStr(3);
if (!this.isFloatParameter(2)) this.error(34);
fontsize = this.floatParameter(2);
shapeType = -1;
break;
case 3:
if (!this.isFloatParameter(2)) this.error(34);
if (shapeType == -1) {
fontsize = this.floatParameter(2);
} else {
if (fontsize >= 1) fontsize += (sizeAdjust = 5);
fontface = null;
}break;
case 2:
default:
if (shapeType == 5) {
fontsize = 13;
name = "fontsize";
break;
}this.bad();
}
var isScale = (this.tokAt(1) == 536875059);
if (shapeType == -1) shapeType = (isScale ? 31 : this.getShapeType(this.getToken(1).tok));
if (shapeType == 5) {
if (fontsize == 0 || fontsize >= 1 && (fontsize < 6 || fontsize > 63)) {
this.integerOutOfRange(6 - sizeAdjust, 63 - sizeAdjust);
return;
}if (!this.chk) this.setShapeProperty(5, "setDefaults", fontsize == 0 ? this.vwr.slm.noneSelected : Boolean.FALSE);
}if (this.chk) return;
var value;
if (name === "font") {
if (JU.Font.getFontStyleID(fontface) >= 0) {
fontstyle = fontface;
fontface = "SansSerif";
}value = this.vwr.getFont3D(fontface, fontstyle, fontsize);
} else {
value = Float.$valueOf(fontsize);
}this.sm.loadShape(shapeType);
if (isScale) this.setShapeProperty(31, "target", "%SCALE");
this.setShapeProperty(shapeType, name, value);
if (scaleAngstromsPerPixel >= 0) this.setShapeProperty(shapeType, "scalereference", Float.$valueOf(scaleAngstromsPerPixel));
if (isScale) this.setShapeProperty(31, "thisID", null);
}, "~N,~N");
Clazz.defineMethod(c$, "cmdFrank", 
function(i){
var b = true;
if (this.slen > i) switch (this.getToken(this.checkLast(i)).tok) {
case 1073742335:
break;
case 1073742334:
b = false;
break;
default:
this.error(5);
}
this.setBooleanProperty("frank", b);
}, "~N");
Clazz.defineMethod(c$, "cmdFunc", 
function(){
if (this.chk && !this.isCmdLine_c_or_C_Option) return;
var name = (this.getToken(0).value).toLowerCase();
if (this.tokAt(1) == 268440324 && this.tokAt(2) == 1073742333) {
this.vwr.removeFunction(name);
return;
}if (!this.isFunction(name)) this.error(10);
var params = (this.slen == 1 || this.slen == 3 && this.tokAt(1) == 268435968 && this.tokAt(2) == 268435969 ? null : this.parameterExpressionList(1, -1, false));
if (this.chk) return;
this.runFunctionAndRet(null, name, params, null, false, true, true);
});
Clazz.defineMethod(c$, "cmdGetProperty", 
function(){
if (this.chk) return;
var retValue = "";
var property = this.optParameterAsString(1);
var name = property;
if (name.indexOf(".") >= 0) name = name.substring(0, name.indexOf("."));
if (name.indexOf("[") >= 0) name = name.substring(0, name.indexOf("["));
var propertyID = this.vwr.getPropertyNumber(name);
var param = "";
switch (this.tokAt(2)) {
default:
param = this.optParameterAsString(2);
break;
case 12290:
case 1073742325:
case 10:
param = this.atomExpressionAt(2);
if (property.equalsIgnoreCase("bondInfo") && this.isAtomExpression(++this.iToken)) param =  Clazz.newArray(-1, [param, this.atomExpressionAt(this.iToken)]);
break;
}
if (property.length > 0 && propertyID < 0) {
property = "";
param = "";
} else if (propertyID >= 0 && this.slen < 3) {
if ((param = this.vwr.getDefaultPropertyParam(propertyID)).equals("(visible)")) param = this.vwr.ms.getVisibleSet(true);
} else if (propertyID == this.vwr.getPropertyNumber("fileContents")) {
var s = param.toString();
for (var i = 3; i < this.slen; i++) s += this.paramAsStr(i);

param = s;
}retValue = this.vwr.getProperty("readable", property, param);
this.showString(retValue);
});
Clazz.defineMethod(c$, "cmdGoto", 
function(isCmd){
var strTo = (isCmd ? this.paramAsStr(this.checkLast(1)) : null);
var pcTo = (strTo == null ? this.aatoken.length - 1 : -1);
var s = null;
for (var i = pcTo + 1; i < this.aatoken.length; i++) {
var tokens = this.aatoken[i];
var tok = tokens[0].tok;
switch (tok) {
case 20485:
case 0:
s = tokens[tokens.length - 1].value;
if (tok == 0) s = s.substring(s.startsWith("#") ? 1 : 2);
break;
default:
continue;
}
if (s.equalsIgnoreCase(strTo)) {
pcTo = i;
break;
}}
if (pcTo < 0) this.invArg();
if (strTo == null) pcTo = 0;
var di = (pcTo < this.pc ? 1 : -1);
var nPush = 0;
for (var i = pcTo; i != this.pc; i += di) {
switch (this.aatoken[i][0].tok) {
case 1275335685:
case 102439:
case 134320648:
case 102412:
case 102406:
nPush++;
break;
case 1275334681:
nPush--;
break;
case 102409:
switch (this.aatoken[i][1].tok) {
case 102439:
case 134320648:
case 102412:
case 102406:
nPush--;
}
break;
}
}
if (strTo == null) {
pcTo = 2147483647;
for (; nPush > 0; --nPush) this.popContext(false, false);

}if (nPush != 0) this.invArg();
if (!this.chk) this.pc = pcTo - 1;
}, "~B");
Clazz.defineMethod(c$, "cmdHbond", 
function(){
if (this.slen == 2 && this.getToken(1).tok == 4102) {
if (this.chk) return;
var n = this.vwr.autoHbond(null, null, false);
this.report(J.i18n.GT.i(J.i18n.GT.$("{0} hydrogen bonds"), Math.abs(n)), false);
return;
}if (this.slen == 2 && this.getToken(1).tok == 12291) {
if (this.chk) return;
this.checkExtension(1613238294);
return;
}var mad = this.getMadParameter();
if (mad == 2147483647) return;
this.setShapeProperty(1, "type", Integer.$valueOf(30720));
this.setShapeSizeBs(1, mad, null);
this.setShapeProperty(1, "type", Integer.$valueOf(1023));
});
Clazz.defineMethod(c$, "cmdHelp", 
function(){
if (this.chk) return;
var what = this.optParameterAsString(1).toLowerCase();
var pt = 0;
if (what.startsWith("mouse") && (pt = what.indexOf(" ")) >= 0 && pt == what.lastIndexOf(" ")) {
this.showString(this.vwr.getBindingInfo(what.substring(pt + 1)));
return;
}if (JS.T.tokAttr(JS.T.getTokFromName(what), 4096)) what = "?command=" + what;
this.vwr.getHelp(what);
});
Clazz.defineMethod(c$, "cmdHistory", 
function(pt){
if (this.slen == 1) {
this.showString(this.vwr.getSetHistory(2147483647));
return;
}if (pt == 2) {
var n = this.intParameter(this.checkLast(2));
if (n < 0) this.invArg();
if (!this.chk) this.vwr.getSetHistory(n == 0 ? 0 : -2 - n);
return;
}switch (this.getToken(this.checkLast(1)).tok) {
case 1073742335:
case 1073741882:
if (!this.chk) this.vwr.getSetHistory(-2147483648);
return;
case 1073742334:
if (!this.chk) this.vwr.getSetHistory(0);
break;
default:
this.errorStr(24, "ON, OFF, CLEAR");
}
}, "~N");
Clazz.defineMethod(c$, "cmdHover", 
function(){
if (this.chk) return;
var strLabel = (this.slen == 1 ? "on" : this.paramAsStr(1));
if (strLabel.equalsIgnoreCase("on")) strLabel = "%U";
 else if (strLabel.equalsIgnoreCase("off")) strLabel = null;
this.vwr.setHoverLabel(strLabel);
});
Clazz.defineMethod(c$, "cmdLabel", 
function(index, bs){
if (this.chk) return;
this.sm.loadShape(5);
var strLabel = null;
switch (this.getToken(index).tok) {
case 1073742335:
strLabel = this.vwr.getStandardLabelFormat(0);
break;
case 1073742334:
break;
case 12294:
case 1610625028:
this.setShapeProperty(5, "display", this.theTok == 1610625028 ? Boolean.TRUE : Boolean.FALSE);
return;
case 7:
strLabel = this.theToken.value;
break;
default:
strLabel = this.paramAsStr(index);
}
this.sm.setLabel(strLabel, bs == null ? this.vwr.bsA() : bs);
}, "~N,JU.BS");
Clazz.defineMethod(c$, "cmdLoad", 
function(){
var doLoadFiles = (!this.chk || this.isCmdLine_C_Option);
var isAppend = false;
var isInline = false;
var isSmiles = false;
var isMutate = false;
var isData = false;
var isAsync = this.vwr.async;
var isConcat = false;
var doOrient = false;
var appendNew = this.vwr.getBoolean(603979792);
var filename = null;
var bsModels;
var i = (this.tokAt(0) == 134221834 ? 0 : 1);
var filter = null;
var modelCount0 = this.vwr.ms.mc - (this.vwr.fm.getFileName().equals("zapped") ? 1 : 0);
var ac0 = this.vwr.ms.ac;
var loadScript =  new JU.SB().append("load");
var nFiles = 1;
var htParams =  new java.util.Hashtable();
if (this.$isStateScript) {
htParams.put("isStateScript", Boolean.TRUE);
if (this.forceNoAddHydrogens) htParams.put("doNotAddHydrogens", Boolean.TRUE);
}var modelName = null;
var filenames = null;
var tempFileInfo = null;
var errMsg = null;
var sOptions =  new JU.SB();
var tokType = 0;
var tok;
if (this.slen == 1) {
i = 0;
} else {
modelName = (this.tokAt(1) == 6 ? "@" : this.paramAsStr(i));
if (this.slen == 2 && !this.chk) {
if (modelName.endsWith(".spt") || modelName.endsWith(".png") || modelName.endsWith(".pngj")) {
this.cmdScript(0, modelName, null, null);
return;
}}tok = this.tokAt(i);
switch (tok) {
case 1073742077:
doOrient = true;
loadScript.append(" orientation");
this.vwr.stm.saveOrientation("preload", null);
modelName = this.paramAsStr(++i);
tok = JS.T.getTokFromName(modelName);
break;
}
switch (tok) {
case 1073741839:
var ami = (this.tokAt(++i) == 2 ? this.intParameter(i++) : -1);
modelName = this.optParameterAsString(i);
isAppend = (!this.$isStateScript || this.vwr.ms.mc > 0);
if (isAppend) {
loadScript.append(" append");
if (ami >= 0) {
loadScript.append(" " + ami);
appendNew = false;
htParams.put("appendToModelIndex", Integer.$valueOf(ami));
}}tok = JS.T.getTokFromName(modelName);
break;
case 4108:
this.checkExtension(4108);
return;
case 1073877011:
case 1610616855:
case 1073742015:
var m = this.paramAsStr(this.checkLast(2));
if (!this.chk) {
switch (tok) {
case 1073877011:
htParams.put("service", "nbo");
htParams.put("mode", Integer.$valueOf(1));
htParams.put("action", "load");
htParams.put("value", m);
htParams.put("sync", Boolean.TRUE);
this.vwr.sm.processService(htParams);
this.runScript(htParams.get("ret"));
break;
case 1610616855:
this.vwr.setHistory(m);
break;
case 1073742015:
this.vwr.setMenu(m, true);
break;
}
}return;
case 4130:
isMutate = isAppend = true;
appendNew = false;
loadScript.append(" mutate");
modelName = this.optParameterAsString(++i);
tok = JS.T.getTokFromName(modelName);
htParams.put("appendToModelIndex", Integer.$valueOf(this.vwr.am.cmi));
break;
case 1073741824:
i++;
loadScript.append(" " + modelName);
tokType = (tok == 1073741824 && JU.PT.isOneOf(modelName.toLowerCase(), ";xyz;vxyz;vibration;temperature;occupancy;partialcharge;") ? JS.T.getTokFromName(modelName) : 0);
if (tokType != 0) {
htParams.put("atomDataOnly", Boolean.TRUE);
htParams.put("modelNumber", Integer.$valueOf(1));
if (tokType == 4166) tokType = 1145047055;
tempFileInfo = this.vwr.fm.getFileInfo();
isAppend = true;
}}
switch (tok) {
case 36868:
var $var = this.paramAsStr(++i);
filename = "@" + $var;
break;
case 1228935687:
i++;
loadScript.append(" " + modelName);
if (this.optParameterAsString(i).equals("+")) {
isConcat = true;
i++;
loadScript.append(" +");
}if (this.optParameterAsString(i).equals("-")) {
isConcat = true;
i++;
loadScript.append(" -");
}if (this.tokAt(i) == 7) {
filenames = this.stringParameterSet(i);
i = this.iToken;
if (i + 1 != this.slen) this.invArg();
if (filenames != null) nFiles = filenames.length;
}break;
case 134217764:
if (this.slen < i + 4) this.invArg();
i -= 2;
filename = "0";
htParams.put("isEmptyLoad", Boolean.TRUE);
case 1073741984:
isInline = true;
i++;
loadScript.append(" inline");
break;
case 134218757:
isSmiles = true;
i++;
break;
case 1073741849:
isAsync = true;
htParams.put("async", Boolean.TRUE);
i++;
break;
case 536870926:
case 1094717454:
i++;
loadScript.append(" " + modelName);
if (tok == 536870926) htParams.put("isTrajectory", Boolean.TRUE);
if (this.isPoint3f(i)) {
var pt = this.getPoint3f(i, false, true);
i = this.iToken + 1;
htParams.put("firstLastStep",  Clazz.newIntArray(-1, [Clazz.floatToInt(pt.x), Clazz.floatToInt(pt.y), Clazz.floatToInt(pt.z)]));
loadScript.append(" " + JU.Escape.eP(pt));
} else {
switch (this.tokAt(i)) {
case 10:
bsModels = this.getToken(i++).value;
htParams.put("bsModels", bsModels);
loadScript.append(" " + JU.Escape.eBS(bsModels));
break;
default:
htParams.put("firstLastStep",  Clazz.newIntArray(-1, [0, -1, 1]));
}
}break;
case 1073741824:
break;
case 134221834:
var key = this.stringParameter(++i).toLowerCase();
modelName = this.optParameterAsString(i + 1);
isAppend = key.startsWith("append");
if (isAppend && key.startsWith("append modelindex=")) {
var ami = JU.PT.parseInt(key.substring(18));
if (ami >= 0) {
appendNew = false;
htParams.put("appendToModelIndex", Integer.$valueOf(ami));
}}doOrient = (key.indexOf("orientation") >= 0);
i = this.addLoadData(loadScript, key, htParams, i);
isData = true;
break;
default:
modelName = "fileset";
}
if (!isInline && filename == null && filenames == null && this.getToken(i).tok != 4) this.error(16);
}var filePt = i;
var ptAs = i + 1;
var localName = null;
if (this.tokAt(ptAs) == 1073741848) {
localName = this.stringParameter(i = ptAs + 1);
if (this.vwr.fm.getPathForAllFiles() !== "") {
localName = null;
filePt = i;
}}var appendedData = null;
var appendedKey = null;
if (isSmiles && this.tokAt(i + 1) == 1073741940) {
++i;
filter = this.stringParameter(++i);
}if (this.slen == i + 1) {
if (filename == null && (i == 0 || filenames == null && (filename = this.paramAsStr(filePt)).length == 0)) filename = this.getFullPathName(true);
if (filename == null && filenames == null) {
this.cmdZap(false);
return;
}if (filenames == null && !isInline) {
if (isSmiles) {
filename = "$" + filename;
} else {
if (filename.equals("String[]")) return;
if (filename.indexOf("[") == 0) {
filenames = JU.Escape.unescapeStringArray(filename);
if (filenames != null) {
if (i == 1) loadScript.append(" files");
nFiles = filenames.length;
}}}}if (filenames != null) for (var j = 0; j < nFiles; j++) loadScript.append(" /*file*/").append(JU.PT.esc(filenames[j]));

} else if (this.isLoadOption(this.getToken(i + 1).tok)) {
if (filename == null && (filename = this.paramAsStr(filePt)).length == 0 && (filename = this.getFullPathName(true)) == null) {
this.cmdZap(false);
return;
}if (filePt == i || localName != null) i++;
if (filename.equals("String[]")) return;
if ((tok = this.tokAt(i)) == 1073742010) {
var manifest = this.stringParameter(++i);
htParams.put("manifest", manifest);
sOptions.append(" MANIFEST " + JU.PT.esc(manifest));
tok = this.tokAt(++i);
}switch (tok) {
case 2:
case 7:
case 268437504:
case 1073742195:
i = this.getLoadModelIndex(i, sOptions, htParams);
break;
}
i = this.getCmdExt().getLoadSymmetryParams(i, sOptions, htParams);
if (this.tokAt(i) == 1073741839) {
if (this.tokAt(++i) == 134221834) {
i += 2;
appendedData = this.getToken(i++).value;
appendedKey = this.stringParameter(++i);
++i;
} else {
appendedKey = this.stringParameter(i++);
appendedData = this.stringParameter(i++);
}htParams.put(appendedKey, appendedData);
}if (this.tokAt(i) == 1073741940) filter = this.stringParameter(++i);
} else {
var fNames =  new JU.Lst();
if (i == 1) {
if (this.tokAt(i + 1) == 268440577 || this.tokAt(i + 1) == 268440576) {
modelName = "files";
} else {
i++;
}loadScript.append(" " + modelName);
}if (this.tokAt(i + 1) == 268440576) isConcat = true;
filter = this.getLoadFilesList(i, loadScript, sOptions, htParams, fNames);
filenames = fNames.toArray( new Array(nFiles = fNames.size()));
if (!isConcat && loadScript.indexOf("/*concat*/") >= 0) isConcat = true;
}if (!doLoadFiles) return;
if (filenames != null) filename = "fileSet";
if (appendedData != null) {
sOptions.append(" APPEND data \"" + appendedKey + "\"\n" + appendedData + (appendedData.endsWith("\n") ? "" : "\n") + "end \"" + appendedKey + "\"");
}if (filter == null) filter = this.vwr.g.defaultLoadFilter;
if (filter.length > 0) {
if (filter.toUpperCase().indexOf("DOCACHE") >= 0) {
if (!this.$isStateScript && !isAppend && !JV.Viewer.isJS) this.vwr.cacheClear();
}htParams.put("filter", filter);
if (filter.equalsIgnoreCase("2d")) filter = "2D-noMin";
sOptions.append(" FILTER " + JU.PT.esc(filter));
}var isVariable = false;
if (filenames == null) {
if (this.vwr.am.cmi >= 0 && ("::" + filename).endsWith("::string")) {
filename = this.vwr.getCurrentModelFile("null", false);
loadScript =  new JU.SB().append("load inline ");
isInline = true;
}if (isInline) {
htParams.put("fileData", filename);
} else if (filename.startsWith("@") && filename.length > 1) {
var o = this.getVarParameter(filename.substring(1), false);
if (Clazz.instanceOf(o,"java.util.Map") && (o).containsKey("state.spt")) {
this.checkLength(i + 1);
this.loadPNGJVar(filename, o, htParams);
return;
}isVariable = true;
if (Clazz.instanceOf(o,"java.util.Map") && (o).containsKey("_DATA_")) {
o = (o).get("_DATA_");
o = JU.Base64.getBase64((o).data);
} else {
o = "" + o;
}loadScript =  new JU.SB().append("{\n    var ").append(filename.substring(1)).append(" = ").append(JU.PT.esc(o)).append(";\n    ").appendSB(loadScript);
htParams.put("fileData", o);
} else if (!isData && !((filename.startsWith("=") || filename.startsWith("*")) && filename.indexOf("/") > 0)) {
var type = "";
var pt = filename.indexOf("::");
if (pt > 0 && pt < 20) {
type = filename.substring(0, pt + 2);
filename = filename.substring(pt + 2);
}if (filename.startsWith("cache://")) {
localName = null;
} else if (!isMutate || filename.length > 0) {
filename = this.checkFileExists("LOAD" + (isAppend ? "_APPEND_" : "_"), isAsync, filename, filePt, !isAppend && this.pc != this.pcResume);
if (filename == null) this.error(57);
filename = type + filename;
}if (filename.startsWith("cache://")) localName = null;
}}var out = null;
var filecat = null;
if (localName != null) {
if (localName.equals(".")) localName = this.vwr.fm.getFilePath(filename, false, true);
if (localName.length == 0 || this.vwr.fm.getFilePath(localName, false, false).equalsIgnoreCase(this.vwr.fm.getFilePath(filename, false, false))) this.invArg();
var fullPath =  Clazz.newArray(-1, [localName]);
out = this.vwr.getOutputChannel(localName, fullPath);
if (out == null) JU.Logger.error("Could not create output stream for " + fullPath[0]);
 else htParams.put("outputChannel", out);
}if (filenames == null && tokType == 0) {
loadScript.append(" ");
if (isVariable || isInline) {
loadScript.append(filename.indexOf('\n') >= 0 || isVariable ? JU.PT.esc(filename) : filename);
} else if (!isData) {
if (localName != null) localName = this.vwr.fm.getFilePath(localName, false, false);
if (!filename.equals("String[]")) loadScript.append("/*file*/").append((localName != null ? JU.PT.esc(localName) : "$FILENAME$"));
}if (!isConcat && (filename.startsWith("=") || filename.startsWith("*")) && filename.indexOf("/") > 0) {
isConcat = true;
var pt = filename.indexOf("/");
var id;
if (pt == 1 && (id = this.vwr.getPdbID()) != null) {
filename = filename.substring(0, 1) + id + filename.substring(1);
pt = filename.indexOf("/");
} else {
id = filename.substring(1, pt);
}var ext = filename.substring(pt + 1);
filename = filename.substring(0, pt);
if ((pt = filename.indexOf(".")) >= 0) filename = filename.substring(0, pt);
if (";dssr;rna3d;dom;val;".indexOf(";" + ext + ";") >= 0 || ext.startsWith("dssr--")) {
if (filename.startsWith("=")) filename += ".cif";
filenames = (ext.equals("all") ?  Clazz.newArray(-1, [filename, "*dom/" + id, "*val/" + id]) :  Clazz.newArray(-1, [filename, "*" + ext + "/" + id]));
filename = "fileSet";
loadScript = null;
isVariable = false;
filecat = "-";
} else {
filename += "/" + ext;
}}if (loadScript != null) {
if (sOptions.length() > 0) loadScript.append(" /*options*/ ").append(sOptions.toString());
if (isVariable) loadScript.append("\n  }");
htParams.put("loadScript", loadScript);
}}this.setCursorWait(true);
var timeMsg = this.vwr.getBoolean(603979934);
if (timeMsg) JU.Logger.startTimer("load");
if (!this.$isStateScript && !isAppend && !this.vwr.getBoolean(603979831)) this.vwr.setBooleanProperty("legacyJavaFloat", false);
if (isMutate) htParams.put("isMutate", Boolean.TRUE);
htParams.put("eval", this);
errMsg = this.vwr.loadModelFromFile(null, filename, filenames, null, isAppend, htParams, loadScript, sOptions, tokType, filecat != null ? filecat : isConcat ? "+" : " ");
if (timeMsg) this.showString(JU.Logger.getTimerMsg("load", 0));
if (out != null) {
this.vwr.fm.setFileInfo( Clazz.newArray(-1, [localName]));
JU.Logger.info(J.i18n.GT.o(J.i18n.GT.$("file {0} created"), localName));
this.showString(this.vwr.fm.getFilePath(localName, false, false) + " created");
out.closeChannel();
}if (tokType > 0) {
this.vwr.fm.setFileInfo(tempFileInfo);
if (errMsg != null && !this.isCmdLine_c_or_C_Option) this.evalError(errMsg, null);
return;
}if (errMsg != null && !this.isCmdLine_c_or_C_Option) {
if (errMsg.indexOf("NOTE: file recognized as a script file: ") == 0) {
filename = errMsg.substring("NOTE: file recognized as a script file: ".length).trim();
if (filename.indexOf("png|") >= 0 && filename.endsWith("pdb|state.spt")) {
filename = filename.substring(0, filename.lastIndexOf("|"));
filename += filename.substring(filename.lastIndexOf("|"));
this.runScript("load \"" + filename + "\"");
return;
}this.cmdScript(0, filename, null, null);
return;
}if (this.vwr.async && errMsg.startsWith("File reader was not found:")) {
throw  new JS.ScriptInterruption(this, "async", 1);
}this.evalError(errMsg, null);
}if (this.debugHigh) this.report("Successfully loaded:" + (filenames == null ? htParams.get("fullPathName") : modelName), false);
this.finalizeLoad(isAppend, appendNew, isConcat, doOrient, nFiles, ac0, modelCount0, isData);
});
Clazz.defineMethod(c$, "checkFileExists", 
function(prefix, isAsync, filename, i, doClear){
if (this.chk || filename.startsWith("cache://")) return filename;
if ((this.vwr.testAsync || JV.Viewer.isJS) && (isAsync || filename.startsWith("?")) || this.vwr.apiPlatform.forceAsyncLoad(filename)) {
filename = this.loadFileAsync(prefix, filename, i, doClear);
}var fullPathNameOrError = this.vwr.getFullPathNameOrError(filename);
filename = fullPathNameOrError[0];
if (filename == null) return null;
if (fullPathNameOrError[1] != null) this.errorStr(17, filename + ":" + fullPathNameOrError[1]);
return filename;
}, "~S,~B,~S,~N,~B");
Clazz.defineMethod(c$, "addLoadData", 
function(loadScript, key, htParams, i){
loadScript.append(" /*data*/ data");
var ptVar = key.indexOf("@");
if (ptVar >= 0) key = key.$replace('@', '_');
loadScript.append(" ").append(JU.PT.esc(key));
var strModel = (ptVar >= 0 ? "" + this.getParameter(key.substring(ptVar + 1), 4, true) : this.paramAsStr(++i));
if (!strModel.startsWith(";base64,")) strModel = JV.Viewer.fixInlineString(strModel, this.vwr.getInlineChar());
htParams.put("fileData", strModel);
htParams.put("isData", Boolean.TRUE);
loadScript.appendC('\n').append(strModel).append(" end ").append(JU.PT.esc(key));
if (ptVar < 0) i += 2;
return i;
}, "JU.SB,~S,java.util.Map,~N");
Clazz.defineMethod(c$, "loadPNGJVar", 
function(varName, o, htParams){
var av =  Clazz.newArray(-1, [JS.SV.newV(6, o)]);
this.getCmdExt().dispatch(1073741866, false, av);
htParams.put("imageData", av[0].value);
var out = this.vwr.getOutputChannel(null, null);
htParams.put("outputChannel", out);
this.vwr.createZip("", "ZIPDATA", htParams);
var modelName = "cache://" + "VAR_" + varName;
this.vwr.cacheFileByName("cache://VAR_*", false);
this.vwr.cachePut(modelName, out.toByteArray());
this.cmdScript(0, modelName, null, null);
}, "~S,~O,java.util.Map");
Clazz.defineMethod(c$, "getLoadFilesList", 
function(i, loadScript, sOptions, htParams, fNames){
var firstLastSteps = null;
var filter = null;
var pt = null;
var bs = null;
while (i < this.slen) {
switch (this.tokAt(i)) {
case 268440577:
loadScript.append("/*concat*/ +");
++i;
continue;
case 268440576:
loadScript.append(" -");
++i;
continue;
case 2:
case 7:
case 268437504:
case 1073742195:
i = this.getLoadModelIndex(i, sOptions, htParams);
continue;
case 1073741940:
filter = this.stringParameter(++i);
++i;
continue;
case 1073742329:
htParams.remove("isTrajectory");
if (firstLastSteps == null) {
firstLastSteps =  new JU.Lst();
pt = JU.P3.new3(0, -1, 1);
}if (this.isPoint3f(++i)) {
pt = this.getPoint3f(i, false, true);
i = this.iToken + 1;
} else if (this.tokAt(i) == 10) {
bs = this.getToken(i).value;
pt = null;
i = this.iToken + 1;
}break;
case 1073741824:
this.invArg();
}
fNames.addLast(this.paramAsStr(i++));
if (pt != null) {
firstLastSteps.addLast( Clazz.newIntArray(-1, [Clazz.floatToInt(pt.x), Clazz.floatToInt(pt.y), Clazz.floatToInt(pt.z)]));
loadScript.append(" COORD " + JU.Escape.eP(pt));
} else if (bs != null) {
firstLastSteps.addLast(bs);
loadScript.append(" COORD " + JU.Escape.eBS(bs));
}loadScript.append(" /*file*/$FILENAME" + fNames.size() + "$");
}
if (firstLastSteps != null) htParams.put("firstLastSteps", firstLastSteps);
return filter;
}, "~N,JU.SB,JU.SB,java.util.Map,JU.Lst");
Clazz.defineMethod(c$, "isLoadOption", 
function(tok){
switch (tok) {
case 1073742010:
case 2:
case 7:
case 268437504:
case 1073742195:
case 1073742332:
case 8:
case 1073742080:
case 1094713350:
case 1073742163:
case 1073741938:
case 1073742114:
case 134217764:
case 1814695966:
case 1073742066:
case 134221834:
case 1073741839:
return true;
case 1073741940:
case 1073741824:
return (this.tokAt(this.iToken + 2) != 1073742329);
}
return false;
}, "~N");
Clazz.defineMethod(c$, "getLoadModelIndex", 
function(i, sOptions, htParams){
var n;
switch (this.tokAt(i)) {
case 2:
htParams.remove("firstLastStep");
htParams.remove("bsModel");
htParams.put("useFileModelNumbers", Boolean.TRUE);
n = this.intParameter(i);
sOptions.append(" ").appendI(n);
if (n < 0) htParams.put("vibrationNumber", Integer.$valueOf(-n));
 else htParams.put("modelNumber", Integer.$valueOf(n));
break;
case 7:
case 268437504:
case 1073742195:
htParams.remove("firstLastStep");
var data = this.floatParameterSet(i, 1, 2147483647);
var bs =  new JU.BS();
var iArray =  Clazz.newIntArray (data.length, 0);
for (var j = 0; j < data.length; j++) {
n = Clazz.floatToInt(data[j]);
if (data[j] >= 1 && data[j] == n) bs.set(n - 1);
 else this.invArg();
iArray[j] = n;
}
sOptions.append(" " + JU.Escape.eAI(iArray));
htParams.put("bsModels", bs);
htParams.put("useFileModelNumbers", Boolean.TRUE);
break;
}
return this.iToken + 1;
}, "~N,JU.SB,java.util.Map");
Clazz.defineMethod(c$, "finalizeLoad", 
function(isAppend, appendNew, isConcat, doOrient, nFiles, ac0, modelCount0, isData){
var bs = JU.BSUtil.newBitSet2(isAppend ? ac0 : 0, this.vwr.ms.ac);
if (isAppend && (appendNew || nFiles > 1)) {
this.vwr.setAnimationRange(-1, -1);
this.vwr.setCurrentModelIndex(modelCount0);
}this.vwr.setModelkitPropertySafely("updateatomkeys", bs);
var msg;
if (this.scriptLevel == 0 && !isAppend && (isConcat || nFiles < 2) && (msg = this.vwr.ms.getInfoM("modelLoadNote")) != null) {
this.showString(msg);
}var centroid = this.vwr.ms.getInfoM("centroidMinMax");
if (JU.AU.isAI(centroid) && this.vwr.ms.ac > 0) {
this.vwr.ms.setCentroid(bs, centroid);
}var script = this.vwr.g.defaultLoadScript;
msg = "";
if (script.length > 0) msg += "\nUsing defaultLoadScript: " + script;
var embeddedScript;
var info = this.vwr.ms.msInfo;
if (info != null && this.vwr.allowEmbeddedScripts() && (embeddedScript = info.remove("jmolscript")) != null && embeddedScript.length > 0) {
msg += "\nAdding embedded #jmolscript: " + embeddedScript;
script += ";" + embeddedScript;
this.setStringProperty("_loadScript", script);
script = "allowEmbeddedScripts = false;try{" + script + "} allowEmbeddedScripts = true;";
this.isEmbedded = !this.isCmdLine_c_or_C_Option;
} else {
this.setStringProperty("_loadScript", "");
}this.logLoadInfo(msg, isData);
var siteScript = (info == null ? null : info.remove("sitescript"));
if (siteScript != null) script = siteScript + ";" + script;
if (doOrient) script += ";restore orientation preload";
if (script.length > 0 && !this.isCmdLine_c_or_C_Option) this.runScript(script);
this.isEmbedded = false;
}, "~B,~B,~B,~B,~N,~N,~N,~B");
Clazz.defineMethod(c$, "cmdLog", 
function(){
if (this.slen == 1) this.bad();
if (this.chk) return;
var s = this.parameterExpressionString(1, 0);
if (this.tokAt(1) == 1073742334) this.setStringProperty("logFile", "");
 else this.vwr.log(s);
});
Clazz.defineMethod(c$, "cmdLoop", 
function(){
if (this.vwr.headless) return;
if (!this.chk) this.pc = -1;
this.cmdDelay();
});
Clazz.defineMethod(c$, "cmdMessage", 
function(){
var text = this.paramAsStr(this.checkLast(1));
if (this.chk) return;
var s = this.vwr.formatText(text);
if (this.outputBuffer == null && !this.vwr.isPrintOnly) JU.Logger.warn(s);
if (!s.startsWith("_")) this.report(s, false);
});
Clazz.defineMethod(c$, "cmdModel", 
function(offset){
var isFrame = (this.theTok == 4115 || this.vwr.ms.mc > 1);
var frameList =  Clazz.newIntArray(-1, [-1, -1]);
var nFrames = 0;
var useModelNumber = true;
var modelIndex = -1;
if (this.slen == 1 && offset == 1) {
modelIndex = this.vwr.am.cmi;
var m;
if (!this.chk && modelIndex >= 0 && (m = this.vwr.ms.getJmolDataSourceFrame(modelIndex)) >= 0) this.vwr.setCurrentModelIndex(m == modelIndex ? -2147483648 : m);
return;
}switch (this.tokAt(1)) {
case 1073877010:
if (!this.chk && isFrame && this.slen == 2) {
while (++modelIndex < this.vwr.ms.mc) {
if (!this.vwr.ms.am[modelIndex].auxiliaryInfo.containsKey("moData")) continue;
this.vwr.am.setFrame(modelIndex);
this.showString("Frame set to " + (modelIndex + 1));
return;
}
this.showString("No molecular orbitals");
}return;
case 2:
if (isFrame && this.slen == 2) {
if (!this.chk) this.vwr.am.setFrame(this.intParameter(1) - 1);
return;
}break;
case 1073742325:
case 10:
modelIndex = this.atomExpressionAt(1).nextSetBit(0);
if (this.chk || modelIndex < 0 || modelIndex >= this.vwr.ms.ac) return;
modelIndex = this.vwr.ms.at[modelIndex].mi;
if (this.iToken + 1 == this.slen) {
this.vwr.setCurrentModelIndex(modelIndex);
return;
}frameList[nFrames++] = modelIndex;
offset = this.iToken + 1;
useModelNumber = false;
break;
case 1073741904:
this.iToken = 1;
var n = (this.tokAt(2) == 2 ? this.intParameter(++this.iToken) : 1);
this.checkLength(this.iToken + 1);
if (!this.chk && n > 0) this.vwr.ms.createModels(n);
return;
case 1073741974:
this.checkLength(3);
var id = this.stringParameter(2);
if (JU.PT.parseInt(id) != -2147483648) this.invArg();
if (!this.chk) this.vwr.setCurrentModelID(id);
return;
case 528397:
var millis = 0;
this.checkLength(3);
switch (this.getToken(2).tok) {
case 2:
case 3:
millis = Clazz.floatToLong(this.floatParameter(2) * 1000);
break;
default:
this.error(20);
}
if (!this.chk) this.vwr.setFrameDelayMs(millis);
return;
case 1073742166:
if (this.checkLength23() > 0) if (!this.chk) this.vwr.setFrameTitleObj(this.slen == 2 ? "@{_modelName}" : (this.tokAt(2) == 7 ? JS.SV.strListValue(this.st[2]) : this.paramAsStr(2)));
return;
case 1073742077:
if (this.tokAt(2) == 3 && this.tokAt(3) == 12) {
modelIndex = this.vwr.ms.getModelNumberIndex(this.getToken(2).intValue, false, false);
var mat4 = this.getToken(3).value;
if (modelIndex >= 0) this.vwr.ms.am[modelIndex].mat4 = mat4;
return;
}break;
case 1073741832:
var isNone = (this.tokAt(2) == 1073742333);
var bs = (this.slen == 2 || isNone ? null : this.atomExpressionAt(2));
if (isNone) this.iToken = 2;
var isFixed = (this.tokAt(this.iToken + 1) == 12293);
this.checkLength(this.iToken + (isFixed ? 2 : 1));
if (!this.chk) this.vwr.setFrameOffsets(bs, isFixed);
return;
}
if (this.getToken(offset).tok == 268440576) {
++offset;
if (this.getToken(this.checkLast(offset)).tok != 2 || this.intParameter(offset) != 1) this.invArg();
if (!this.chk) this.vwr.setAnimation(1073742108);
return;
}var isPlay = false;
var isRange = false;
var isSplit = false;
var propName = null;
var prop = null;
var isAll = false;
var isHyphen = false;
var fFrame = 0;
var frameAlign = null;
var haveFileSet = this.vwr.haveFileSet();
if (this.isArrayParameter(1)) {
this.setFrameSet(1);
isAll = true;
} else {
for (var i = offset; i < this.slen; i++) {
switch (this.getToken(i).tok) {
case 1275069447:
switch (i == this.slen - 1 ? nFrames : -1) {
case 2:
break;
case 0:
if (this.vwr.ms.mc == 2) {
frameList[0] = 0;
frameList[1] = 1;
nFrames = 2;
break;
}default:
this.invArg();
}
isSplit = true;
break;
case 1073741832:
if (i != 2) this.invArg();
frameAlign = this.centerParameter(3, null);
this.checkLength(i = this.iToken + 1);
break;
case 1073742327:
case 268441089:
this.checkLength(offset + (isRange ? 2 : 1));
isAll = true;
break;
case 268440576:
if (nFrames != 1) this.invArg();
isHyphen = true;
break;
case 1073742333:
this.checkLength(offset + 1);
break;
case 3:
useModelNumber = false;
if ((fFrame = this.floatParameter(i)) < 0) {
this.checkLength(i + 1);
if (!this.chk) this.vwr.am.morph(-fFrame);
return;
}case 2:
case 4:
if (nFrames == 2) this.invArg();
var iFrame = (this.theTok == 4 ? JU.Edge.getFloatEncodedInt(this.theToken.value) : this.theToken.intValue);
if (iFrame < 0 && nFrames == 1) {
isHyphen = true;
iFrame = -iFrame;
if (haveFileSet && iFrame < 1000000) iFrame *= 1000000;
}if (this.theTok == 3 && haveFileSet && fFrame == Clazz.floatToInt(fFrame)) iFrame = Clazz.floatToInt(fFrame) * 1000000;
if (iFrame == 2147483647) {
useModelNumber = false;
frameList[nFrames++] = (this.chk || i != 1 ? 0 : this.vwr.getModelIndexFromId(this.theToken.value.toString()));
break;
}if (iFrame == -1) {
this.checkLength(offset + 1);
if (!this.chk) this.vwr.setAnimation(1073742108);
return;
}if (iFrame >= 1000 && iFrame < 1000000 && haveFileSet) iFrame = (Clazz.doubleToInt(iFrame / 1000)) * 1000000 + (iFrame % 1000);
if (!useModelNumber && iFrame == 0 && nFrames == 0) isAll = true;
if (iFrame >= 1000000) useModelNumber = false;
frameList[nFrames++] = iFrame;
break;
case 1073742096:
isPlay = true;
break;
case 1073742114:
isRange = true;
break;
case 1715472409:
if (modelIndex < 0 && (modelIndex = this.vwr.am.cmi) < 0) return;
propName = this.paramAsStr(++i);
var sv = this.setVariable(++i, -1, "", false);
if (sv != null && !this.chk) {
if (propName.equalsIgnoreCase("dssr")) {
this.loadDssr(modelIndex, sv.value);
return;
}prop = JS.SV.oValue(sv);
}if (!this.chk) this.vwr.ms.setInfo(modelIndex, propName, prop);
return;
default:
this.frameControl(offset);
return;
}
}
}if (this.chk) return;
if (isRange && nFrames == 0) isAll = true;
if (isAll) {
this.vwr.setAnimationOn(false);
this.vwr.setAnimationRange(-1, -1);
if (!isRange) this.vwr.setCurrentModelIndex(-1);
return;
}if (nFrames == 2 && !isRange && !isSplit) isHyphen = true;
if (haveFileSet) useModelNumber = false;
 else if (useModelNumber) for (var i = 0; i < nFrames; i++) if (frameList[i] >= 0) frameList[i] %= 1000000;

modelIndex = this.vwr.ms.getModelNumberIndex(frameList[0], useModelNumber, false);
if (frameAlign != null) {
if (modelIndex >= 0) {
this.vwr.ms.translateModel(modelIndex, null);
this.vwr.ms.translateModel(modelIndex, frameAlign);
}return;
}var modelIndex2 = -1;
if (haveFileSet && modelIndex < 0 && frameList[0] != 0) {
if (frameList[0] < 1000000) frameList[0] *= 1000000;
if (nFrames == 2 && frameList[1] < 1000000) frameList[1] *= 1000000;
if (frameList[0] % 1000000 == 0) {
frameList[0]++;
modelIndex = this.vwr.ms.getModelNumberIndex(frameList[0], false, false);
if (modelIndex >= 0) {
var i2 = (nFrames == 1 ? frameList[0] + 1000000 : frameList[1] == 0 ? -1 : frameList[1] % 1000000 == 0 ? frameList[1] + 1000001 : frameList[1] + 1);
modelIndex2 = this.vwr.ms.getModelNumberIndex(i2, false, false);
if (modelIndex2 < 0) modelIndex2 = this.vwr.ms.mc;
modelIndex2--;
if (isRange) nFrames = 2;
 else if (!isHyphen && modelIndex2 != modelIndex) isHyphen = true;
isRange = isRange || modelIndex == modelIndex2;
}} else {
return;
}}if (!isPlay && !isRange || modelIndex >= 0) this.vwr.setCurrentModelIndexClear(modelIndex, false);
if (isPlay && nFrames == 2 || isRange || isHyphen || isSplit) {
if (modelIndex2 < 0) modelIndex2 = this.vwr.ms.getModelNumberIndex(frameList[1], useModelNumber, false);
this.vwr.setAnimationOn(false);
this.vwr.am.setAnimationDirection(1);
if (!isSplit) this.vwr.setAnimationRange(modelIndex, modelIndex2);
this.vwr.setCurrentModelIndexClear(isHyphen && !isRange ? -1 : modelIndex >= 0 ? modelIndex : 0, false);
}if (isSplit) {
this.vwr.am.setSplitFrame(modelIndex, modelIndex2);
} else {
this.vwr.am.setSplitFrame(-1, -1);
}if (isPlay) this.vwr.setAnimation(4143);
}, "~N");
Clazz.defineMethod(c$, "loadDssr", 
function(modelIndex, data){
if (modelIndex < 0 && (modelIndex = this.vwr.am.cmi) < 0) this.errorStr(30, "load <dssr file>");
if (!data.startsWith("{")) data = this.vwr.getFileAsString3(data, true, "script");
this.clearDefinedVariableAtomSets();
var map = this.vwr.parseJSONMap(data);
this.showString(this.vwr.getAnnotationParser(1111490587).fixDSSRJSONMap(map));
this.vwr.ms.setInfo(modelIndex, "dssr", map);
}, "~N,~S");
Clazz.defineMethod(c$, "cmdMove", 
function(){
this.checkLength(-11);
var dRot = JU.V3.new3(this.floatParameter(1), this.floatParameter(2), this.floatParameter(3));
var dZoom = this.floatParameter(4);
var dTrans = JU.V3.new3(this.intParameter(5), this.intParameter(6), this.intParameter(7));
var dSlab = this.floatParameter(8);
var secondsTotal = this.floatParameter(9);
var fps = (this.slen == 11 ? this.intParameter(10) : 30);
if (this.chk) return;
this.refresh(false);
if (!this.useThreads(true)) secondsTotal = 0;
this.vwr.move(this, dRot, dZoom, dTrans, dSlab, secondsTotal, fps);
if (secondsTotal > 0 && this.isJS) throw  new JS.ScriptInterruption(this, "move", 1);
});
Clazz.defineMethod(c$, "cmdMoveto", 
function(){
if (this.slen == 2 && this.tokAt(1) == 1073742162) {
if (!this.chk) this.vwr.tm.stopMotion();
return;
}var secondsTotal;
if (this.slen == 2 && this.isFloatParameter(1)) {
secondsTotal = this.floatParameter(1);
if (this.chk) return;
if (!this.useThreads(true)) secondsTotal = 0;
if (secondsTotal > 0) this.refresh(false);
this.vwr.movetoHome(this, secondsTotal);
if (this.isJS && secondsTotal > 0 && this.vwr.g.waitForMoveTo) throw  new JS.ScriptInterruption(this, "moveTo", 1);
return;
}var axis = JU.V3.new3(NaN, 0, 0);
var center = null;
var i = 1;
secondsTotal = (this.isFloatParameter(i) ? this.floatParameter(i++) : 2.0);
var degrees = 90;
var bsCenter = null;
var isChange = true;
var isMolecular = false;
var isUnitCell = false;
var planeUVW = null;
var uvw = null;
var abc = null;
var xTrans = 0;
var yTrans = 0;
var zoom = NaN;
var rotationRadius = NaN;
var zoom0 = this.vwr.tm.getZoomSetting();
var navCenter = null;
var xNav = NaN;
var yNav = NaN;
var navDepth = NaN;
var cameraDepth = NaN;
var cameraX = NaN;
var cameraY = NaN;
var pymolView = null;
var q = null;
var tok = this.getToken(i).tok;
switch (tok) {
case 1073742110:
pymolView = this.floatParameterSet(++i, 18, 21);
i = this.iToken + 1;
if (this.chk && this.checkLength(i) > 0) return;
break;
case 134221850:
if (this.tokAt(++i) == 1073742028) {
isMolecular = true;
i++;
}if (this.isAtomExpression(i)) {
isMolecular = true;
var ret =  new Array(1);
center = this.centerParameter(i, ret);
if (!(Clazz.instanceOf(ret[0],"JU.BS"))) this.invArg();
bsCenter = ret[0];
q = (this.chk ?  new JU.Quat() : this.vwr.ms.getQuaternion(bsCenter.nextSetBit(0), this.vwr.getQuaternionFrame()));
} else {
q = this.getQuaternionParameter(i, null, false);
}i = this.iToken + 1;
if (q == null) this.invArg();
break;
case 9:
case 8:
case 1073742332:
if (this.isPoint3f(i)) {
axis.setT(this.getPoint3f(i, true, true));
i = this.iToken + 1;
degrees = this.floatParameter(i++);
} else {
var pt4 = this.getPoint4f(i);
i = this.iToken + 1;
axis.set(pt4.x, pt4.y, pt4.z);
degrees = (pt4.x == 0 && pt4.y == 0 && pt4.z == 0 ? NaN : pt4.w);
}break;
case 1073741954:
axis.set(1, 0, 0);
degrees = 0;
this.checkLength(++i);
break;
case 1073741858:
axis.set(0, 1, 0);
degrees = 180;
this.checkLength(++i);
break;
case 1073741996:
axis.set(0, 1, 0);
this.checkLength(++i);
break;
case 1073742126:
axis.set(0, -1, 0);
this.checkLength(++i);
break;
case 1073742172:
axis.set(1, 0, 0);
this.checkLength(++i);
break;
case 1073741871:
axis.set(-1, 0, 0);
this.checkLength(++i);
break;
case 134219777:
case 1073742187:
isMolecular = true;
isUnitCell = true;
uvw =  new JU.P3();
planeUVW = this.hklParameter(i + 1, null, true, uvw);
if (Double.isNaN(uvw.x)) uvw = null;
this.checkLength(i = this.iToken + 1);
break;
case 134217750:
case 1073741918:
var v = this.planeParameter(i, false);
var x = JU.V3.new3(0, 0, 1);
x.cross(x, v);
if (x.length() < 0.001) {
x.set(0, 1, 0);
x.cross(x, v);
}v.cross(x, v);
q = JU.Quat.getQuaternionFrame(null, v, x).inv();
i = this.iToken + 1;
break;
case 1073741854:
abc = this.paramAsStr(++i);
if (abc.equals("-")) abc += this.paramAsStr(++i);
this.checkLength(++i);
switch ("xyz".indexOf(abc)) {
case 0:
q = JU.Quat.new4(0.5, 0.5, 0.5, -0.5);
break;
case 1:
q = JU.Quat.new4(0.5, 0.5, 0.5, 0.5);
break;
case 2:
q = JU.Quat.new4(0, 0, 0, 1);
break;
default:
isUnitCell = true;
break;
}
break;
default:
axis = JU.V3.new3(this.floatParameter(i++), this.floatParameter(i++), this.floatParameter(i++));
degrees = this.floatParameter(i++);
}
if (isUnitCell) {
var uc = this.vwr.getCurrentUnitCell();
if (planeUVW == null) {
if (uc == null) uc = this.vwr.getSymTemp().setUnitCellFromParams(null, false, NaN);
q = uc.getQuaternionRotation(abc);
} else if (uc != null) {
q = uc.getQuaternionRotationForUVW(uvw, planeUVW);
}if (q == null) this.invArg();
}if (q != null) {
var aa;
aa = q.toAxisAngle4f();
axis.set(aa.x, aa.y, aa.z);
degrees = (isMolecular ? -1 : 1) * (aa.angle * 180.0 / 3.141592653589793);
}if (Float.isNaN(axis.x) || Float.isNaN(axis.y) || Float.isNaN(axis.z)) axis.set(0, 0, 0);
 else if (axis.length() == 0 && degrees == 0) degrees = NaN;
isChange = (tok == 134221850 || !this.vwr.tm.isInPosition(axis, degrees));
if (this.isFloatParameter(i)) zoom = this.floatParameter(i++);
if (this.isFloatParameter(i) && !this.isCenterParameter(i)) {
xTrans = this.floatParameter(i++);
yTrans = this.floatParameter(i++);
if (!isChange && Math.abs(xTrans - this.vwr.tm.getTranslationXPercent()) >= 1) isChange = true;
if (!isChange && Math.abs(yTrans - this.vwr.tm.getTranslationYPercent()) >= 1) isChange = true;
}if (bsCenter == null && i != this.slen) {
var ret =  new Array(1);
center = this.centerParameter(i, ret);
if (Clazz.instanceOf(ret[0],"JU.BS")) bsCenter = ret[0];
i = this.iToken + 1;
}if (center != null) {
if (!isChange && center.distance(this.vwr.tm.fixedRotationCenter) >= 0.1) isChange = true;
if (this.isFloatParameter(i)) rotationRadius = this.floatParameter(i++);
if (!this.isCenterParameter(i)) {
if ((rotationRadius == 0 || Float.isNaN(rotationRadius)) && (zoom == 0 || Float.isNaN(zoom))) {
var newZoom = Math.abs(this.getZoom(0, i, bsCenter, (zoom == 0 ? 0 : zoom0)));
i = this.iToken + 1;
zoom = newZoom;
} else {
if (!isChange && Math.abs(rotationRadius - this.vwr.getFloat(570425388)) >= 0.1) isChange = true;
}}if (zoom == 0 || Float.isNaN(zoom)) zoom = 100;
if (Float.isNaN(rotationRadius)) rotationRadius = 0;
if (!isChange && Math.abs(zoom - zoom0) >= 1) isChange = true;
if (i != this.slen) {
navCenter = this.centerParameter(i, null);
i = this.iToken + 1;
if (i != this.slen) {
xNav = this.floatParameter(i++);
yNav = this.floatParameter(i++);
}if (i != this.slen) navDepth = this.floatParameter(i++);
if (i != this.slen) {
cameraDepth = this.floatParameter(i++);
if (!isChange && Math.abs(cameraDepth - this.vwr.tm.getCameraDepth()) >= 0.01) isChange = true;
}if (i + 1 < this.slen) {
cameraX = this.floatParameter(i++);
cameraY = this.floatParameter(i++);
if (!isChange && Math.abs(cameraX - this.vwr.tm.camera.x) >= 0.01) isChange = true;
if (!isChange && Math.abs(cameraY - this.vwr.tm.camera.y) >= 0.01) isChange = true;
}}}this.checkLength(i);
if (this.chk) return;
if (!isChange) secondsTotal = 0;
if (secondsTotal > 0) this.refresh(false);
if (!this.useThreads(true)) secondsTotal = 0;
if (cameraDepth == 0) {
cameraDepth = cameraX = cameraY = NaN;
}if (pymolView != null) this.vwr.tm.moveToPyMOL(this, secondsTotal, pymolView);
 else this.vwr.moveTo(this, secondsTotal, center, axis, degrees, null, zoom, xTrans, yTrans, rotationRadius, navCenter, xNav, yNav, navDepth, cameraDepth, cameraX, cameraY);
if (this.isJS && secondsTotal > 0 && this.vwr.g.waitForMoveTo) throw  new JS.ScriptInterruption(this, "moveTo", 1);
});
Clazz.defineMethod(c$, "isAtomExpression", 
function(i){
switch (this.tokAt(i)) {
case 12290:
case 10:
case 1073742325:
return true;
default:
return false;
}
}, "~N");
Clazz.defineMethod(c$, "cmdPause", 
function(){
if (this.chk || this.isJS && !this.allowJSThreads) return false;
var msg = this.optParameterAsString(1);
if (!this.vwr.getBooleanProperty("_useCommandThread")) {
}if (this.vwr.autoExit || !this.vwr.haveDisplay && !this.vwr.isWebGL) return false;
if (this.scriptLevel == 0 && this.pc == this.aatoken.length - 1) {
this.vwr.scriptStatus("nothing to pause: " + msg);
return false;
}msg = (msg.length == 0 ? ": RESUME to continue." : ": " + this.vwr.formatText(msg));
this.pauseExecution(true);
this.vwr.scriptStatusMsg("script execution paused" + msg, "script paused for RESUME");
return true;
});
Clazz.defineMethod(c$, "cmdPrint", 
function(){
if (this.slen == 1) {
if (!this.chk) this.showStringPrint("\0", true);
return;
}this.showStringPrint(this.parameterExpressionString(1, 0), true);
});
Clazz.defineMethod(c$, "cmdPrompt", 
function(){
var msg = null;
if (this.slen == 1) {
if (!this.chk) msg = JS.ScriptEval.getContextTrace(this.vwr, this.getScriptContext("prompt"), null, true).toString();
} else {
msg = this.parameterExpressionString(1, 0);
}if (!this.chk) this.vwr.prompt(msg, null, false);
});
Clazz.defineMethod(c$, "cmdReset", 
function(){
if (this.slen == 3 && this.tokAt(1) == 134320141) {
if (!this.chk) this.vwr.removeFunction(this.stringParameter(2));
return;
}this.checkLength(-2);
if (this.chk) return;
if (this.slen == 1) {
this.vwr.reset(false);
return;
}switch (this.tokAt(1)) {
case 36865:
if (this.outputBuffer != null) this.outputBuffer.setLength(0);
return;
case 134221829:
this.vwr.cacheClear();
return;
case 1073741936:
this.resetError();
return;
case 1073741995:
this.vwr.stm.resetLighting();
return;
case 1086324748:
this.vwr.resetShapes(true);
return;
case 134320141:
this.vwr.clearFunctions();
return;
case 1812599299:
this.vwr.ms.setBoundBox(null, null, true, 0);
return;
case 1639976963:
var bsModified =  new JU.BS();
this.runScript(this.vwr.ms.getDefaultStructure(this.vwr.bsA(), bsModified));
this.vwr.shm.resetBioshapes(bsModified);
return;
case 1648363544:
this.vwr.setData("element_vdw",  Clazz.newArray(-1, [null, ""]), 0, 0, 0, 0, 0);
return;
case 1075838996:
this.vwr.ms.resetAromatic();
return;
case 1095241729:
this.vwr.reset(true);
return;
case 135198:
this.vwr.rotateModelSpinVectors(-1, null);
return;
}
var $var = this.paramAsStr(1);
if ($var.charAt(0) == '_') this.invArg();
this.vwr.unsetProperty($var);
});
Clazz.defineMethod(c$, "resetError", 
function(){
this.vwr.g.removeParam("_errormessage");
});
Clazz.defineMethod(c$, "cmdRestrict", 
function(){
var isBond = (this.tokAt(1) == 1677721602);
this.cmdSelect(isBond ? 2 : 1);
this.restrictSelected(isBond, true);
});
Clazz.defineMethod(c$, "cmdReturn", 
function(tv){
if (this.chk) return;
var t = this.getContextVariableAsVariable("_retval", false);
if (t != null) {
var v = (tv != null || this.slen == 1 ? null : this.parameterExpressionToken(1));
if (tv == null) tv = (v == null ? JS.SV.newI(0) : v);
t.value = tv.value;
t.intValue = tv.intValue;
t.tok = tv.tok;
}this.cmdGoto(false);
}, "JS.SV");
Clazz.defineMethod(c$, "cmdRotate", 
function(isSpin, isSelected){
var is2d = this.vwr.is2D();
if (isSpin && is2d) return;
if (this.slen == 2) switch (this.getToken(1).tok) {
case 1073742335:
if (!this.chk) this.vwr.tm.setSpinOn();
return;
case 1073742334:
if (!this.chk) this.vwr.tm.setSpinOff();
return;
case 135198:
if (isSpin) break;
if (!this.chk) {
this.vwr.rotateModelSpinVectors(-1, null);
}return;
}
var bsAtoms = null;
var bsBest = null;
var degreesPerSecond = 1.4E-45;
var nPoints = 0;
var model = -1;
var endDegrees = 3.4028235E38;
var isMolecular = false;
var haveRotation = false;
var isVector = false;
var dihedralList = null;
var ptsA = null;
var points =  new Array(2);
var rotAxis = JU.V3.new3(0, 1, 0);
var translation = null;
var m4 = null;
var m3 = null;
var is4x4 = false;
var direction = 1;
var tok;
var q = null;
var helicalPath = false;
var isDegreesPerSecond = false;
var isSeconds = false;
var ptsB = null;
var bsCompare = null;
var invPoint = null;
var invPlane = null;
var axesOrientationRasmol = this.vwr.getBoolean(603979806);
var checkModelKit = false;
for (var i = 1; i < this.slen; ++i) {
switch (tok = this.getToken(i).tok) {
case 528432:
case 4145:
checkModelKit = (this.vwr.getOperativeSymmetry() != null);
continue;
case 12290:
case 10:
case 1073742325:
bsBest = this.atomExpressionAt(i);
if (translation != null || q != null || nPoints == 2) {
bsAtoms = bsBest;
ptsB = null;
isSelected = true;
break;
}case 1073742332:
case 8:
case 1073742330:
haveRotation = true;
if (nPoints == 2) nPoints = 0;
if (isVector) {
if (nPoints == 1) this.invArg();
rotAxis = JU.V3.newV(this.getPoint3f(i, true, true));
if (isSpin && this.slen == this.iToken + 1) {
degreesPerSecond = 2;
}break;
}var pt1 = this.centerParameterForModel(i, this.vwr.am.cmi, null);
if (!this.chk && tok == 1073742330 && this.tokAt(i + 2) != 268437504) {
isMolecular = true;
var data =  Clazz.newArray(-1, [this.objectNameParameter(++i), Integer.$valueOf(this.vwr.am.cmi), null]);
rotAxis = (this.getShapePropertyData(22, "getSpinAxis", data) ? data[2] : null);
}points[nPoints++] = pt1;
break;
case 135198:
isVector = true;
isMolecular = true;
m3 = this.getMatrixParam(i + 1, 3, false);
if (m3 == null) {
var p4 = this.getPoint4fNoError(i + 1);
if (p4 != null) {
q = JU.Quat.newP4(p4);
}}i = this.iToken;
if (this.isFloatParameter(i + 1)) {
rotAxis.x = NaN;
}break;
case 1095241729:
isSpin = true;
continue;
case 1073741988:
case 1073742028:
isMolecular = true;
continue;
case 1113589787:
isSelected = true;
break;
case 268436992:
continue;
case 2:
case 3:
if (isSpin) {
if (degreesPerSecond == 1.4E-45) {
degreesPerSecond = this.floatParameter(i);
} else if (endDegrees == 3.4028235E38) {
endDegrees = degreesPerSecond;
degreesPerSecond = this.floatParameter(i);
} else {
this.invArg();
}} else {
if (endDegrees == 3.4028235E38) {
endDegrees = this.floatParameter(i);
} else if (degreesPerSecond == 1.4E-45) {
degreesPerSecond = this.floatParameter(i);
isSpin = true;
} else {
this.invArg();
}}if (i == this.slen - 2 && (this.tokAt(i + 1) == 1073741824 || this.tokAt(i + 1) == 4)) {
var s = this.paramAsStr(++i).toLowerCase();
if (s.equals("dps")) {
isDegreesPerSecond = true;
} else if (s.equals("sec")) {
isSeconds = true;
}}break;
case 268440576:
direction = -1;
continue;
case 1111492629:
if (is2d) return;
haveRotation = true;
rotAxis.set(direction, 0, 0);
continue;
case 1111492630:
if (is2d) return;
haveRotation = true;
rotAxis.set(0, direction, 0);
continue;
case 1111492631:
haveRotation = true;
rotAxis.set(0, 0, (axesOrientationRasmol && !isMolecular ? -direction : direction));
continue;
case 9:
case 134221850:
case 1073741864:
if (tok == 134221850) i++;
haveRotation = true;
if ((q = this.getQuaternionParameter(i, bsBest, tok == 1073741864)) != null) {
if (q.q0 == 0) q.q0 = 1e-10;
rotAxis.setT(q.getNormal());
endDegrees = q.getTheta();
}break;
case 134217750:
var pts;
var n;
if (this.paramAsStr(i + 1).equalsIgnoreCase("picked")) {
i++;
var lst = this.vwr.getPOrNull("pickedList");
n = lst.size();
if (n < 3) return;
pts =  new Array(3);
for (var j = 0; j < 3; j++) pts[j] = this.vwr.ms.getAtomSetCenter(JS.SV.getBitSet(lst.get(n - 3 + j), false));

} else if (this.isArrayParameter(i + 1)) {
pts = this.getPointArray(++i, -1, false, true);
i = this.iToken;
} else {
pts =  new Array(3);
for (var j = 0; j < 3; j++) {
pts[j] = this.centerParameter(++i, null);
i = this.iToken;
}
}n = pts.length;
if (n < 3) return;
q = JU.Quat.getQuaternionFrame(pts[n - 3], pts[n - 2], pts[n - 1]);
q = JU.Quat.new4(1, 0, 0, 0).mulQ(q.inv().div(this.vwr.tm.getRotationQ()));
rotAxis.setT(q.getNormal());
endDegrees = q.getTheta();
break;
case 134217731:
haveRotation = true;
if (this.isPoint3f(++i)) {
rotAxis.setT(this.centerParameter(i, null));
break;
}var p4 = this.getPoint4f(i);
rotAxis.set(p4.x, p4.y, p4.z);
endDegrees = p4.w;
q = JU.Quat.newVA(rotAxis, endDegrees);
break;
case 1073742328:
isSelected = true;
isMolecular = true;
haveRotation = true;
if (this.isArrayParameter(++i)) {
dihedralList = this.floatParameterSet(i, 6, 2147483647);
i = this.iToken;
} else {
var iAtom1 = this.atomExpressionAt(i).nextSetBit(0);
var iAtom2 = this.atomExpressionAt(++this.iToken).nextSetBit(0);
if (iAtom1 < 0 || iAtom2 < 0) return;
bsAtoms = this.vwr.getBranchBitSet(iAtom2, iAtom1, true);
points[0] = this.vwr.ms.at[iAtom1];
points[1] = this.vwr.ms.at[iAtom2];
nPoints = 2;
}break;
case 4160:
translation = JU.V3.newV(this.centerParameter(++i, null));
isMolecular = isSelected = true;
break;
case 136314895:
helicalPath = true;
continue;
case 1296041986:
var symop = this.intParameter(++i);
if (this.chk) continue;
var info = this.vwr.getSymTemp().getSpaceGroupInfo(this.vwr.ms, null, -1, false, null);
var op = (info == null ? null : info.get("operations"));
if (symop == 0 || op == null || op.length < Math.abs(symop)) this.invArg();
op = op[Math.abs(symop) - 1];
translation = op[5];
invPoint = op[6];
points[0] = op[7];
if (op[8] != null) rotAxis = op[8];
endDegrees = (op[9]).intValue();
if (symop < 0) {
endDegrees = -endDegrees;
if (translation != null) translation.scale(-1);
}if (endDegrees == 0 && points[0] != null) {
rotAxis.normalize();
JU.Measure.getPlaneThroughPoint(points[0], rotAxis, invPlane =  new JU.P4());
}q = JU.Quat.newVA(rotAxis, endDegrees);
nPoints = (points[0] == null ? 0 : 1);
isMolecular = true;
haveRotation = true;
isSelected = true;
continue;
case 134221831:
bsCompare = this.atomExpressionAt(++i);
ptsA = this.vwr.ms.getAtomPointVector(bsCompare);
if (ptsA == null) {
this.iToken = i;
this.invArg();
}i = this.iToken;
ptsB = this.getPointVector(this.getToken(++i), i);
if (ptsB == null || ptsA.size() != ptsB.size()) {
this.iToken = i;
this.invArg();
}m4 =  new JU.M4();
points[0] =  new JU.P3();
nPoints = 1;
J.api.Interface.getInterface("JU.Eigen", this.vwr, "script");
var stddev = (this.chk ? 0 : JU.Measure.getTransformMatrix4(ptsA, ptsB, m4, points[0]));
if (stddev > 0.001) ptsB = null;
case 12:
case 11:
haveRotation = true;
m3 =  new JU.M3();
if (tok == 12) {
is4x4 = true;
m4 = this.theToken.value;
}if (m4 != null) {
points[0] = null;
bsAtoms = bsBest;
ptsB = null;
nPoints = 0;
translation =  new JU.V3();
m4.getTranslation(translation);
m4.getRotationScale(m3);
} else {
m3 = this.theToken.value;
}q = (this.chk ?  new JU.Quat() : JU.Quat.newM(m3));
rotAxis.setT(q.getNormal());
endDegrees = q.getTheta();
isMolecular = true;
break;
default:
this.invArg();
}
i = this.iToken;
}
if (this.chk) return;
if (dihedralList != null) {
if (endDegrees != 3.4028235E38) {
isSpin = true;
degreesPerSecond = endDegrees;
}}if (isSelected && bsAtoms == null) bsAtoms = this.vwr.bsA();
if (bsCompare != null) {
isSelected = true;
if (bsAtoms == null) bsAtoms = bsCompare;
}if (q != null && !isSeconds && !isDegreesPerSecond) {
isDegreesPerSecond = (degreesPerSecond > 0);
isSeconds = !isDegreesPerSecond;
}var rate = (degreesPerSecond == 1.4E-45 ? 10 : endDegrees == 3.4028235E38 ? degreesPerSecond : isDegreesPerSecond ? degreesPerSecond : isSeconds ? (endDegrees < 0 ? -1 : 1) * Math.abs(endDegrees / degreesPerSecond) : (degreesPerSecond < 0) == (q == null ? endDegrees > 0 : true) ? -endDegrees / degreesPerSecond : degreesPerSecond);
if (q == null && endDegrees < 0 && rate > 0) rate = -rate;
if (dihedralList != null) {
if (!isSpin) {
this.vwr.setDihedrals(dihedralList, null, 1);
return;
}translation = null;
}if (q != null) {
if (nPoints == 0 && translation != null && !is4x4) points[0] = this.vwr.ms.getAtomSetCenter(bsAtoms != null ? bsAtoms : isSelected ? this.vwr.bsA() : this.vwr.getAllAtoms());
if (helicalPath && translation != null) {
points[1] = JU.P3.newP(points[0]);
points[1].add(translation);
var ret = JU.Measure.computeHelicalAxis(points[0], points[1], q);
points[0] = ret[0];
var theta = (ret[3]).x;
if (theta != 0) {
translation = ret[1];
rotAxis = JU.V3.newV(translation);
if (theta < 0) rotAxis.scale(-1);
}m4 = null;
}if (isSpin && m4 == null) m4 = JS.ScriptMathProcessor.getMatrix4f(q.getMatrix(), translation);
if (points[0] != null) nPoints = 1;
}if (invPoint != null || invPlane != null) {
this.vwr.invertAtomCoord(invPoint, null, bsAtoms, -1, false);
if (rotAxis == null) return;
}var requiresThread = (isSpin && (!this.vwr.headless || endDegrees == 3.4028235E38));
if (isSpin && !requiresThread) isSpin = false;
if (!checkModelKit && nPoints < 2 && dihedralList == null) {
if (!isMolecular) {
if (requiresThread && bsAtoms == null && !this.useThreads(true)) {
isSpin = false;
if (endDegrees == 3.4028235E38) return;
}if (this.vwr.rotateAxisAngleAtCenter(this, points[0], rotAxis, rate, endDegrees, isSpin, bsAtoms)) {
if (this.isJS && isSpin && bsAtoms == null && this.vwr.g.waitForMoveTo && endDegrees != 3.4028235E38) throw  new JS.ScriptInterruption(this, "rotate", 1);
}return;
}if (nPoints == 0) points[0] =  new JU.P3();
points[1] = JU.P3.newP(points[0]);
points[1].add(rotAxis);
nPoints = 2;
}if (nPoints == 0) points[0] =  new JU.P3();
if (nPoints < 2 || points[0].distance(points[1]) == 0) {
points[1] = JU.P3.newP(points[0]);
points[1].y += 1.0;
}if (endDegrees == 3.4028235E38) endDegrees = 0;
if (checkModelKit) {
if (endDegrees == 0) return;
if (bsAtoms == null || nPoints != 2 || isSpin || translation != null || dihedralList != null || ptsB != null || is4x4) this.invArg();
var na = this.vwr.getModelkit(false).cmdRotateAtoms(bsAtoms, points, endDegrees);
if (this.doReport()) this.report(J.i18n.GT.i(J.i18n.GT.$("{0} atoms rotated"), na), false);
return;
}if (endDegrees != 0 && translation != null && !haveRotation) translation.scale(endDegrees / translation.length());
if (isSpin && translation != null && (endDegrees == 0 || degreesPerSecond == 0)) {
endDegrees = 0.01;
rate = (degreesPerSecond == 1.4E-45 ? 0.01 : degreesPerSecond < 0 ? -endDegrees / degreesPerSecond : degreesPerSecond * 0.01 / translation.length());
degreesPerSecond = 0.01;
}if (bsAtoms != null && isSpin && ptsB == null && m4 != null) {
ptsA = this.vwr.ms.getAtomPointVector(bsAtoms);
ptsB = JU.Measure.transformPoints(ptsA, m4, points[0]);
}if (bsAtoms != null && !isSpin && ptsB != null) {
this.vwr.setAtomCoords(bsAtoms, 1145047049, ptsB);
} else {
if (requiresThread && !this.useThreads(false)) return;
if (isVector) {
if (model < 0 && this.vwr.am.cmi < 0) this.errorStr(30, "rotate VECTOR");
if (q == null && endDegrees == 1.7976931348623157E308) this.invArg();
var deg = (isSpin ? degreesPerSecond : endDegrees);
if (q == null) {
q = (m3 == null ? JU.Quat.newVA(rotAxis, deg) : JU.Quat.newM(m3));
}m3 = q.getMatrix();
if (rotAxis.lengthSquared() == 0) {
m3.m00 = NaN;
}if (Float.isNaN(m3.getElement(0, 0))) m3.setElement(1, 1, deg);
if (!isSpin || degreesPerSecond <= 0) {
this.vwr.tm.setSpinOff();
this.vwr.rotateModelSpinVectors(model, m3);
return;
}}if (this.vwr.rotateAboutPointsInternal(this, points[0], points[1], rate, endDegrees, isSpin, bsAtoms, translation, ptsB, dihedralList, (isVector ? m3 : null), is4x4 ? m4 : null, false, null) && this.isJS && isSpin) {
throw  new JS.ScriptInterruption(this, "rotate", 1);
}}}, "~B,~B");
Clazz.defineMethod(c$, "cmdRestore", 
function(){
if (this.slen > 1) {
var saveName = this.optParameterAsString(2);
var tok = this.tokAt(1);
switch (tok) {
case 1073742077:
case 1073742132:
case 1073742139:
var secondsTotal = (this.slen > 3 ? this.floatParameter(3) : 0);
if (secondsTotal < 0) this.invArg();
if (this.chk) return;
var type = "";
switch (tok) {
case 1073742077:
type = "Orientation";
this.vwr.stm.restoreOrientation(saveName, secondsTotal, true);
break;
case 1073742132:
type = "Rotation";
this.vwr.stm.restoreOrientation(saveName, secondsTotal, false);
break;
case 1073742139:
type = "Scene";
this.vwr.stm.restoreScene(saveName, secondsTotal);
break;
}
if (this.isJS && secondsTotal > 0 && this.vwr.g.waitForMoveTo) throw  new JS.ScriptInterruption(this, "restore" + type, 1);
return;
}
this.checkLength23();
switch (tok) {
case 1677721602:
if (!this.chk) this.vwr.stm.restoreBonds(saveName);
return;
case 14:
if (this.chk) return;
var sc = this.vwr.stm.getContext(saveName);
if (sc != null) {
this.restoreScriptContext(sc, true, false, false);
if (this.thisContext != null) {
this.thisContext.setMustResume();
this.mustResumeEval = true;
this.tQuiet = true;
}}return;
case 1073742329:
if (this.chk) return;
var script = this.vwr.stm.getSavedCoordinates(saveName);
if (script == null) this.invArg();
this.runScript(script);
this.vwr.checkCoordinatesChanged(null);
return;
case 1073742140:
if (!this.chk) this.vwr.stm.restoreSelection(saveName);
return;
case 1073742158:
if (this.chk) return;
var state;
state = this.vwr.stm.getSavedState(saveName);
if (state == null) {
if (saveName.equalsIgnoreCase("UNDO")) return;
this.invArg();
}this.runScript(state);
return;
case 1639976963:
if (this.chk) return;
var shape = this.vwr.stm.getSavedStructure(saveName);
if (shape == null) this.invArg();
this.runScript(shape);
return;
case 1814695966:
if (!this.chk) this.vwr.stm.restoreUnitCell(saveName);
return;
}
}this.errorStr2(53, "RESTORE", "bonds? context? coordinates? orientation? rotation? selection? state? structure?");
});
Clazz.defineMethod(c$, "cmdSave", 
function(){
if (this.slen > 1) {
var saveName = this.optParameterAsString(2);
switch (this.tokAt(1)) {
case 1677721602:
if (!this.chk) this.vwr.stm.saveBonds(saveName);
return;
case 14:
if (!this.chk) this.saveContext(saveName);
return;
case 1073742329:
if (!this.chk) this.vwr.stm.saveCoordinates(saveName, this.vwr.bsA());
return;
case 1073742077:
case 1073742132:
if (!this.chk) this.vwr.stm.saveOrientation(saveName, null);
return;
case 1073742140:
if (!this.chk) {
this.vwr.stm.saveSelection(saveName, this.vwr.bsA());
this.vwr.stm.restoreSelection(saveName);
}return;
case 1073742158:
if (!this.chk && this.vwr.getBoolean(603979898)) {
this.vwr.stm.saveState(saveName);
if (saveName.length == 0) {
this.showString(this.vwr.stm.getUndoInfo());
}}return;
case 1639976963:
if (!this.chk) this.vwr.stm.saveStructure(saveName);
return;
case 1814695966:
if (!this.chk) this.vwr.stm.saveUnitCell(saveName);
return;
}
}this.errorStr2(53, "SAVE", "bonds? context? coordinates? orientation? rotation? selection? state? structure?");
});
Clazz.defineMethod(c$, "cmdScript", 
function(tok, filename, theScript, params){
if (tok == 134238732) {
if (this.vwr.haveAccessInternal(null)) this.error(10);
this.checkLength(2);
if (!this.chk) this.vwr.jsEval(this.paramAsStr(1));
return;
}var loadCheck = true;
var isCheck = false;
var doStep = false;
var isAsync = this.vwr.async;
var lineNumber = 0;
var pc = 0;
var lineEnd = 0;
var pcEnd = 0;
var i = 1;
var localPath = null;
var remotePath = null;
var scriptPath = null;
if (tok == 4124) {
i = -2;
}if (filename == null && theScript == null) {
tok = this.tokAt(i);
if (tok != 4) this.error(16);
filename = this.paramAsStr(i);
if (filename.equalsIgnoreCase("async")) {
isAsync = true;
filename = this.paramAsStr(++i);
}if (filename.equalsIgnoreCase("applet")) {
filename = null;
var appID = this.paramAsStr(++i);
theScript = this.parameterExpressionString(++i, 0);
this.checkLast(this.iToken);
if (this.chk) return;
if (appID.length == 0 || appID.equals("all")) appID = "*";
if (!appID.equals(".")) {
this.vwr.jsEval(appID + "\1" + theScript);
if (!appID.equals("*")) return;
}} else {
tok = this.tokAt(this.slen - 1);
doStep = (tok == 266298);
if (filename.equalsIgnoreCase("inline")) {
filename = null;
theScript = this.parameterExpressionString(++i, (doStep ? this.slen - 1 : 0));
i = this.iToken;
} else {
while (filename.equalsIgnoreCase("localPath") || filename.equalsIgnoreCase("remotePath") || filename.equalsIgnoreCase("scriptPath")) {
if (filename.equalsIgnoreCase("localPath")) localPath = this.paramAsStr(++i);
 else if (filename.equalsIgnoreCase("scriptPath")) scriptPath = this.paramAsStr(++i);
 else remotePath = this.paramAsStr(++i);
filename = this.paramAsStr(++i);
}
if (filename.startsWith("spt::")) filename = filename.substring(5);
filename = this.checkFileExists("SCRIPT_", isAsync, filename, i, true);
}if ((tok = this.tokAt(++i)) == 1073741877) {
isCheck = true;
tok = this.tokAt(++i);
}if (tok == 1073742050) {
loadCheck = false;
tok = this.tokAt(++i);
}if (tok == 1073741998 || tok == 1140850692) {
i++;
lineEnd = lineNumber = Math.max(this.intParameter(i++), 0);
if (this.checkToken(i)) {
if (this.getToken(i).tok == 268440576) lineEnd = (this.checkToken(++i) ? this.intParameter(i++) : 0);
 else lineEnd = -this.intParameter(i++);
if (lineEnd <= 0) this.invArg();
}} else if (tok == 1073741890 || tok == 1073741892) {
i++;
pc = Math.max(this.intParameter(i++) - 1, 0);
pcEnd = pc + 1;
if (this.checkToken(i)) {
if (this.getToken(i).tok == 268440576) pcEnd = (this.checkToken(++i) ? this.intParameter(i++) : 0);
 else pcEnd = -this.intParameter(i++);
if (pcEnd <= 0) this.invArg();
}}i = -i;
}} else if (filename != null && isAsync) {
filename = this.checkFileExists("SCRIPT_", isAsync, filename, i, true);
}if (i < 0) {
if (this.tokAt(i = -i) == 268435968) {
params = this.parameterExpressionList(i, -1, false);
i = this.iToken + 1;
}this.checkLength(doStep ? i + 1 : i);
}if (this.chk && !this.isCmdLine_c_or_C_Option) return;
if (this.isCmdLine_c_or_C_Option) isCheck = true;
var isPNGJ = false;
if (theScript == null) {
theScript = this.getScriptFileInternal(filename, localPath, remotePath, scriptPath);
if (theScript == null) this.invArg();
isPNGJ = this.vwr.haveAccessInternal(null);
}if (this.isMenu(theScript)) {
this.vwr.setMenu(theScript, false);
return;
}var wasSyntaxCheck = this.chk;
var wasScriptCheck = this.isCmdLine_c_or_C_Option;
if (isCheck) this.chk = this.isCmdLine_c_or_C_Option = true;
this.pushContext(null, "SCRIPT");
this.contextPath += " >> " + filename;
if (this.compileScript(filename, theScript, filename != null && this.debugScript)) {
this.pcEnd = pcEnd;
this.lineEnd = lineEnd;
while (pc < this.lineNumbers.length && this.lineNumbers[pc] < lineNumber) pc++;

this.pc = pc;
var saveLoadCheck = this.isCmdLine_C_Option;
this.isCmdLine_C_Option = new Boolean (this.isCmdLine_C_Option & loadCheck).valueOf();
this.executionStepping = new Boolean (this.executionStepping | doStep).valueOf();
this.setScriptArguments(params, false);
if (isCheck) this.listCommands = true;
var timeMsg = this.vwr.getBoolean(603979934);
if (timeMsg) JU.Logger.startTimer("script");
this.privateFuncs = null;
this.dispatchCommands(false, false, false);
if (this.$isStateScript) JS.ScriptManager.setStateScriptVersion(this.vwr, null);
if (isPNGJ) this.vwr.setAccessInternal(null);
if (timeMsg) this.showString(JU.Logger.getTimerMsg("script", 0));
this.isCmdLine_C_Option = saveLoadCheck;
this.popContext(false, false);
} else {
JU.Logger.error(J.i18n.GT.$("script ERROR: ") + this.errorMessage);
this.popContext(false, false);
if (wasScriptCheck) {
this.setErrorMessage(null);
} else {
this.evalError(null, null);
}}this.chk = wasSyntaxCheck;
this.isCmdLine_c_or_C_Option = wasScriptCheck;
}, "~N,~S,~S,JU.Lst");
Clazz.defineMethod(c$, "isMenu", 
function(s){
var pt = (s == null ? -1 : s.indexOf("Menu Structure"));
return (pt > 0 && s.startsWith("#") && pt < s.indexOf("\n"));
}, "~S");
Clazz.defineMethod(c$, "cmdSelect", 
function(i){
if (this.slen == 1) {
this.vwr.selectStatus(null, false, 0, !this.doReport(), false);
return;
}if (this.slen == 2 && this.tokAt(1) == 1073742072) return;
var tok = this.tokAt(2);
var bs = null;
switch (tok) {
case 10:
if (Clazz.instanceOf(this.getToken(2).value,"JM.BondSet") || tok == 1677721602 && this.getToken(3).tok == 10) {
if (this.slen != this.iToken + 2) this.invArg();
if (!this.chk) this.vwr.selectBonds(this.theToken.value);
return;
}break;
case 1745489939:
case 1677721602:
if (this.slen == 5 && this.tokAt(3) == 10) {
bs = this.getToken(3).value;
if (this.thisCommand != null && this.thisCommand.indexOf("/*FIXED*/") > 0) bs = this.vwr.ms.fixDeletedBonds(bs);
this.iToken++;
} else if (this.isArrayParameter(4)) {
i = -4;
} else if (this.isArrayParameter(3)) {
i = -3;
}if (i < 0) {
bs =  new JU.BS();
var a = this.expandFloatArray(this.floatParameterSet(-i, 0, 2147483647), 0, false);
for (var ii = a.length; --ii >= 0; ) if (a[ii] >= 0) bs.set(a[ii]);

if (i == -3) this.iToken++;
}this.checkLast(this.iToken);
if (this.chk) return;
if (bs == null) this.invArg();
if (tok == 1745489939) this.setShapeProperty(6, "select", bs);
 else this.vwr.selectBonds(bs);
return;
}
var addRemove = 0;
var isGroup = false;
var reportStatus = (this.tokAt(i) == 268436992);
if (reportStatus) i++;
if (this.getToken(1).intValue == 0 && this.theTok != 1073742334) {
var v = this.parameterExpressionToken(0).value;
if (!(Clazz.instanceOf(v,"JU.BS"))) this.invArg();
this.checkLast(this.iToken);
bs = v;
} else {
tok = this.tokAt(i);
switch (tok) {
case 1073742335:
case 1073742334:
if (!this.chk) this.vwr.setSelectionHalosEnabled(tok == 1073742335);
tok = this.tokAt(++i);
if (tok == 0) return;
break;
}
switch (tok) {
case 1275069441:
case 1073742119:
addRemove = tok;
tok = this.tokAt(++i);
}
isGroup = (tok == 1086324742);
if (isGroup) tok = this.tokAt(++i);
bs = this.atomExpressionAt(i);
}if (this.chk) return;
if (this.isBondSet) {
this.vwr.selectBonds(bs);
} else {
if (bs.length() > this.vwr.ms.ac) {
var bs1 = this.vwr.getAllAtoms();
bs1.and(bs);
bs = bs1;
}this.vwr.selectStatus(bs, isGroup, addRemove, !this.doReport(), reportStatus);
this.vwr.slm.noneSelected = Boolean.$valueOf(this.slen == 4 && this.tokAt(2) == 1073742333);
}}, "~N");
Clazz.defineMethod(c$, "cmdSelectionHalos", 
function(pt){
var showHalo = false;
switch (pt == this.slen ? 1073742335 : this.getToken(pt).tok) {
case 1073742335:
case 1113589787:
showHalo = true;
case 1073742334:
case 1073742333:
case 1073742056:
this.setBooleanProperty("selectionHalos", showHalo);
break;
default:
this.invArg();
}
}, "~N");
Clazz.defineMethod(c$, "cmdSet", 
function(){
if (this.slen == 1) {
this.showString(this.vwr.getAllSettings(null));
return;
}var isJmolSet = (this.paramAsStr(0).equals("set"));
var key = this.optParameterAsString(1);
if (isJmolSet && this.slen == 2 && key.indexOf("?") >= 0) {
this.showString(this.vwr.getAllSettings(key.substring(0, key.indexOf("?"))));
return;
}var tok = this.getToken(1).tok;
var newTok = 0;
var sval;
var ival = 2147483647;
var b;
var pt;
var showing = (!this.chk && this.doReport() && !(this.st[0].value).equals("var"));
switch (tok) {
case 553648144:
case 603979865:
case 603979903:
case 603979924:
case 603979960:
case 603979962:
case 603979964:
case 603979965:
case 603979970:
if (this.$isStateScript) return;
break;
case 1611272194:
this.cmdAxes(2);
return;
case 1610616835:
this.cmdBackground(2);
return;
case 1812599299:
this.cmdBoundbox(2);
return;
case 1611272202:
this.cmdFrank(2);
return;
case 1610616855:
this.cmdHistory(2);
return;
case 1825200146:
this.cmdLabel(2, null);
return;
case 1814695966:
this.cmdUnitcell(2);
return;
case 536870920:
this.sm.loadShape(8);
this.setShapeProperty(8, "highlight", (this.tokAt(2) == 1073742334 ? null : this.atomExpressionAt(2)));
return;
case 1610625028:
case 1611141172:
this.cmdSelectionHalos(2);
return;
case 536875070:
this.cmdTimeout(2);
return;
case 536870932:
var o = (this.isArrayParameter(2) ? this.floatParameterSet(2, 2, 2) : this.tokAt(2) == 2 ?  Clazz.newFloatArray(-1, [this.intParameter(2), this.intParameter(3)]) : this.stringParameter(2));
this.checkLast(this.iToken);
if (this.chk) return;
if ((typeof(o)=='string')) {
if (this.vwr.fm.loadImage(o, "\0windowImage", !this.useThreads(false))) throw  new JS.ScriptInterruption(this, "windowImage", 1);
} else {
this.vwr.setWindowDimensions(o);
}return;
case 1639976963:
var type = J.c.STR.getProteinStructureType(this.paramAsStr(2));
if (type === J.c.STR.NOT) this.invArg();
var data = this.floatParameterSet(3, 0, 2147483647);
if (data.length % 4 != 0) this.invArg();
this.vwr.setStructureList(data, type);
this.checkLast(this.iToken);
return;
case 1111490588:
if (this.slen > 3) this.checkLast(2);
this.setBooleanProperty("translucent", this.slen == 2 || JS.SV.bValue(this.getToken(2)));
return;
case 545259526:
ival = this.getArgbParam(2);
if (!this.chk) this.setObjectArgb("axes", ival);
return;
case 1610612737:
b = false;
switch (this.getToken(this.checkLast(2)).tok) {
case 268438528:
break;
case 268438016:
b = true;
break;
default:
this.invArg();
}
this.setBooleanProperty("bondModeOr", b);
return;
case 536870916:
case 536870917:
if (this.chk) return;
var iLevel = (this.tokAt(2) == 1073742334 || this.tokAt(2) == 2 && this.intParameter(2) == 0 ? 4 : (tok == 536870917 ? 6 : 5));
JU.Logger.setLogLevel(iLevel);
this.setIntProperty("logLevel", iLevel);
if (iLevel == 4) {
this.vwr.setDebugScript(false);
if (showing) this.vwr.showParameter("debugScript", true, 80);
}this.setDebugging();
if (showing) this.vwr.showParameter("logLevel", true, 80);
return;
case 537022465:
this.cmdSetEcho(0);
return;
case 536875059:
this.cmdScale(2);
return;
case 1610612738:
this.cmdFont(5, this.checkLength23() == 2 ? 0 : this.floatParameter(2));
return;
case 1613238294:
var bool = false;
switch (this.tokAt(this.checkLast(2))) {
case 1114249217:
bool = true;
case 2097178:
this.setBooleanProperty("hbondsBackbone", bool);
break;
case 1073742150:
bool = true;
case 1073741926:
this.setBooleanProperty("hbondsSolid", bool);
break;
default:
this.invArg();
}
return;
case 1745489939:
case 537006096:
switch (tok = this.tokAt(this.checkLast(2))) {
case 1073742335:
case 1073742334:
this.setBooleanProperty("measurementlabels", tok == 1073742335);
return;
case 1073741926:
case 2:
case 3:
this.vwr.shm.loadShape(6);
var mad10 = this.getSetAxesTypeMad10(2);
if (mad10 != 2147483647) this.setShapeSizeBs(6, tok == 3 ? Clazz.doubleToInt(mad10 / 10) : mad10, null);
return;
}
this.setUnits(this.paramAsStr(2), 545259568);
return;
case 1611141176:
b = false;
switch (this.tokAt(this.checkLast(2))) {
case 1114249217:
b = true;
break;
case 2097178:
break;
default:
this.invArg();
}
this.setBooleanProperty("ssbondsBackbone", b);
return;
case 1610612741:
this.cmdSetLabel("toggle");
return;
case 536870930:
var v =  new JU.Lst();
for (var i = 2; i < this.slen; i++) {
var argb = this.getArgbParam(i);
v.addLast(Integer.$valueOf(argb));
i = this.iToken;
}
if (this.chk) return;
var n = v.size();
var scale =  Clazz.newIntArray (n, 0);
for (var i = n; --i >= 0; ) scale[i] = v.get(i).intValue();

this.vwr.cm.ce.setUserScale(scale);
return;
case 553648188:
if (this.isFloatParameter(2)) {
this.checkLength(3);
this.setIntProperty("zSlab", Clazz.floatToInt(this.floatParameter(2)));
pt = null;
} else {
if (!this.isCenterParameter(2)) this.invArg();
pt = this.centerParameter(2, null);
this.checkLength(this.iToken + 1);
}if (!this.chk) this.vwr.tm.zSlabPoint = (pt == null ? null : JU.P3.newP(pt));
return;
}
var justShow = true;
switch (tok) {
case 536870914:
if (this.slen > 2) {
var modelDotted = this.getSettingStr(2, false);
var modelNumber;
var useModelNumber = false;
if (modelDotted.indexOf(".") < 0) {
modelNumber = JU.PT.parseInt(modelDotted);
useModelNumber = true;
} else {
modelNumber = JU.Edge.getFloatEncodedInt(modelDotted);
}if (this.chk) return;
var modelIndex = this.vwr.ms.getModelNumberIndex(modelNumber, useModelNumber, true);
this.vwr.setBackgroundModelIndex(modelIndex);
return;
}break;
case 1648363544:
if (this.chk) return;
this.vwr.setAtomProperty(this.vwr.getAllAtoms(), 1648363544, -1, NaN, null, null, null);
if (this.slen > 2 && "probe".equalsIgnoreCase(this.getSettingStr(2, false))) {
this.runScript("#VDW radii for PROBE;{_H}.vdw = 1.0;{_H and connected(_C) and not connected(within(smiles,\'[a]\'))}.vdw = 1.17;{_C}.vdw = 1.75;{_C and connected(3) and connected(_O)}.vdw = 1.65;{_N}.vdw = 1.55;{_O}.vdw = 1.4;{_P}.vdw = 1.8;{_S}.vdw = 1.8;message VDW radii for H, C, N, O, P, and S set according to Word, et al., J. Mol. Biol. (1999) 285, 1711-1733");
return;
}newTok = 545259555;
case 545259555:
if (this.slen > 2) {
sval = this.paramAsStr(2);
if (this.slen == 3 && J.c.VDW.getVdwType(sval) == null && J.c.VDW.getVdwType(sval = this.getSettingStr(2, false)) == null) this.invArg();
this.setStringProperty(key, sval);
}break;
case 536870918:
if (this.slen > 2) {
var $var = this.parameterExpressionToken(2);
if ($var.tok == 8) pt = $var.value;
 else {
pt =  new JU.P3();
var ijk = $var.asInt();
if (ijk >= 100) JU.SimpleUnitCell.ijkToPoint3f(ijk, pt, -1, 0);
}if (!this.chk) this.vwr.setDefaultLattice(pt);
}break;
case 545259552:
case 545259545:
if (this.slen > 2) {
if ((this.theTok = this.tokAt(2)) == 1073741991 || this.theTok == 1073742116) {
sval = this.paramAsStr(this.checkLast(2));
} else {
sval = this.getSettingStr(2, false);
}this.setStringProperty(key, sval);
}break;
case 1631586315:
ival = this.getSettingInt(2);
if (ival == -2147483648) this.invArg();
if (!this.chk) this.vwr.ms.setFormalCharges(this.vwr.bsA(), ival);
return;
case 545259563:
if (this.slen > 2) this.setStringProperty(key, this.getSettingStr(2, isJmolSet));
break;
case 545259568:
case 545259558:
if (this.slen > 2) this.setUnits(this.getSettingStr(2, isJmolSet), tok);
break;
case 545259573:
if (!this.chk) this.vwr.setPicked(-1, false);
if (this.slen > 2) {
this.cmdSetPicking();
return;
}break;
case 545259574:
if (this.slen > 2) {
this.cmdSetPickingStyle();
return;
}break;
case 1715472409:
break;
case 536870924:
ival = this.getSettingInt(2);
if (ival == -2147483648 || ival == 0 || ival == 1) {
justShow = false;
break;
}tok = 553648174;
key = "specularPercent";
this.setIntProperty(key, ival);
break;
case 1649022989:
tok = 553648178;
key = "strandCount";
this.setIntProperty(key, this.getSettingInt(2));
break;
default:
justShow = false;
}
if (justShow && !showing) return;
var isContextVariable = (!justShow && !isJmolSet && this.getContextVariableAsVariable(key, false) != null);
if (!justShow && !isContextVariable) {
switch (tok) {
case 1677721602:
newTok = 603979928;
break;
case 1612709894:
newTok = 603979908;
break;
case 1612709900:
newTok = 603979910;
break;
case 1610612739:
newTok = 603979878;
break;
case 1665140738:
newTok = 570425394;
this.setFloatProperty("solventProbeRadius", this.getSettingFloat(2));
justShow = true;
break;
case 1610612740:
newTok = 570425390;
break;
case 1612709912:
newTok = 603979948;
break;
case 1765808134:
newTok = 545259545;
break;
case 1095241729:
sval = this.paramAsStr(2).toLowerCase();
switch ("x;y;z;fps;".indexOf(sval + ";")) {
case 0:
newTok = 570425398;
break;
case 2:
newTok = 570425400;
break;
case 4:
newTok = 570425402;
break;
case 6:
newTok = 570425396;
break;
default:
this.errorStr2(50, "set SPIN ", sval);
}
if (!this.chk) this.vwr.setSpin(sval, Clazz.floatToInt(this.floatParameter(this.checkLast(3))));
justShow = true;
break;
}
}if (newTok != 0) {
key = JS.T.nameOf(tok = newTok);
} else if (isContextVariable) {
} else if (!justShow) {
if (key.length == 0 || key.charAt(0) == '_' && this.tokAt(2) != 268437504) this.error(56);
var lckey = key.toLowerCase();
if (lckey.indexOf("label") == 0 && JU.PT.isOneOf(lckey.substring(5), ";front;group;atom;offset;offsetexact;offsetabsolute;pointer;alignment;toggle;scalereference;for;")) {
if (this.cmdSetLabel(lckey.substring(5))) return;
}if (isJmolSet && lckey.indexOf("shift_") == 0) {
var f = this.floatParameter(2);
this.checkLength(3);
if (!this.chk) this.vwr.getNMRCalculation().setChemicalShiftReference(lckey.substring(6), f);
return;
}if (lckey.endsWith("callback")) tok = 536870912;
}if (isJmolSet && !JS.T.tokAttr(tok, 536870912)) {
this.iToken = 1;
if (!this.$isStateScript) this.errorStr2(50, "SET", key);
this.warning(51, "SET", key);
}if (!justShow && isJmolSet) {
switch (this.slen) {
case 2:
this.setBooleanProperty(key, true);
justShow = true;
break;
case 3:
if (ival != 2147483647) {
this.setIntProperty(key, ival);
justShow = true;
}break;
}
}if (!justShow && !isJmolSet && this.tokAt(2) == 1073742333) {
if (!this.chk) this.vwr.removeUserVariable(key.toLowerCase());
justShow = true;
}if (!justShow) {
this.setVariable(1, 0, key, true);
if (!isJmolSet) return;
}if (showing) this.vwr.showParameter(key, true, 80);
});
Clazz.defineMethod(c$, "cmdScale", 
function(pt){
if (this.chk) return;
var text = "%SCALE";
switch (this.tokAt(pt)) {
case 1073742334:
this.setShapeProperty(31, "%SCALE", null);
this.checkLast(pt);
return;
case 1073742335:
pt++;
break;
default:
var units = JM.Measurement.fixUnits(this.optParameterAsString(pt));
if (JM.Measurement.fromUnits(1, units) != 0) {
text += " " + units;
pt++;
} else {
text = null;
}break;
}
this.setShapeProperty(31, "thisID", "%SCALE");
if (this.tokAt(pt) == 0) {
this.vwr.ms.setEchoStateActive(true);
var echo = this.vwr.shm.loadShape(31);
if (echo.scaleObject == null) this.setShapeProperty(31, "target", "bottom");
} else {
this.setShapeProperty(31, "target", "%SCALE");
this.cmdSetEcho(pt);
}if (text != null) this.setShapeProperty(31, "text", text);
this.setShapeProperty(31, "thisID", null);
this.refresh(false);
}, "~N");
Clazz.defineMethod(c$, "cmdSetEcho", 
function(i){
var propertyName = null;
var propertyValue = null;
var id = null;
var echoShapeActive = true;
var isScale = (i > 0);
var pt = (i == 0 ? 2 : i);
switch (isScale ? 0 : this.getToken(pt).tok) {
case 1073742334:
id = propertyName = "allOff";
this.checkLength(++pt);
break;
case 1073742333:
echoShapeActive = false;
case 1073742327:
id = this.paramAsStr(2);
this.checkLength(++pt);
break;
}
switch (isScale ? this.tokAt(2) : this.getToken(2).tok) {
case 1073741974:
pt++;
case 1073741996:
case 12289:
case 1073742126:
case 1073742172:
case 1073742019:
case 1073741871:
case 1073741824:
case 4:
id = this.paramAsStr(pt++);
break;
}
if (!this.chk) {
this.vwr.ms.setEchoStateActive(echoShapeActive);
this.sm.loadShape(31);
if (id != null) {
if (propertyName == null && !isScale) this.setShapeProperty(31, "thisID", null);
this.setShapeProperty(31, propertyName == null ? "target" : propertyName, id);
}}if (pt < this.slen) {
if (isScale) {
switch (this.tokAt(pt)) {
case 536875059:
case 4120:
case 4:
this.invArg();
}
}switch (this.getToken(pt++).tok) {
case 1073741832:
propertyName = "align";
switch (this.getToken(pt).tok) {
case 1073741996:
case 1073742126:
case 12289:
propertyValue = this.paramAsStr(pt++);
break;
default:
this.invArg();
}
break;
case 12289:
case 1073741996:
case 1073742126:
propertyName = "align";
propertyValue = this.paramAsStr(pt - 1);
break;
case 554176526:
propertyName = "%zpos";
propertyValue = Integer.$valueOf(Clazz.floatToInt(this.floatParameter(pt++)));
break;
case 1610625028:
case 2097192:
case 1073742335:
propertyName = "hidden";
propertyValue = Boolean.FALSE;
break;
case 12294:
case 2097194:
propertyName = "hidden";
propertyValue = Boolean.TRUE;
break;
case 1094717454:
var modelIndex = this.modelNumberParameter(pt++);
if (modelIndex >= this.vwr.ms.mc) this.invArg();
propertyName = "model";
propertyValue = Integer.$valueOf(modelIndex);
break;
case 268437504:
case 1073742195:
propertyName = "xypos";
propertyValue = this.xypParameter(--pt);
if (propertyValue == null) this.invArg();
pt = this.iToken + 1;
break;
case 2:
var posx = this.intParameter(pt - 1);
var namex = "xpos";
if (this.tokAt(pt) == 268441090) {
namex = "%xpos";
pt++;
}propertyName = "ypos";
propertyValue = Integer.$valueOf(this.intParameter(pt++));
if (this.tokAt(pt) == 268441090) {
propertyName = "%ypos";
pt++;
}this.checkLength(pt);
this.setShapeProperty(31, namex, Integer.$valueOf(posx));
break;
case 1073742066:
propertyName = "offset";
if (this.isPoint3f(pt)) {
var pt3 = this.getPoint3f(pt, false, true);
propertyValue =  Clazz.newFloatArray(-1, [-1, pt3.x, pt3.y, pt3.z, 0, 0, 0]);
pt = this.iToken + 1;
} else if (this.isArrayParameter(pt)) {
propertyValue = this.floatParameterSet(pt, 7, 7);
pt = this.iToken + 1;
} else if (this.tokAt(pt) == 1073742333) {
pt++;
}break;
case 1073742334:
propertyName = "off";
break;
case 536875059:
propertyName = "scale";
propertyValue = Float.$valueOf(this.floatParameter(pt++));
break;
case 134222850:
propertyName = "script";
propertyValue = this.paramAsStr(pt++);
break;
case 4120:
pt++;
case 4:
var isImage = (this.theTok != 4);
this.checkLength(pt--);
if (isImage) {
if (id == null) {
var data =  new Array(1);
this.getShapePropertyData(31, "currentTarget", data);
id = data[0];
}if (!this.chk && this.vwr.ms.getEchoStateActive() && this.vwr.fm.loadImage(this.getToken(pt).value, id, !this.useThreads(false))) throw  new JS.ScriptInterruption(this, "setEchoImage", 1);
return;
}this.cmdEcho(pt);
return;
case 134217751:
propertyName = "point";
propertyValue = (this.isCenterParameter(pt) ? this.centerParameter(pt, null) : null);
pt = this.iToken + 1;
break;
default:
if (this.isCenterParameter(pt - 1)) {
propertyName = "xyz";
propertyValue = this.centerParameter(pt - 1, null);
pt = this.iToken + 1;
break;
}this.invArg();
}
}this.checkLength(pt);
if (!this.chk && propertyName != null) this.setShapeProperty(31, propertyName, propertyValue);
}, "~N");
Clazz.defineMethod(c$, "cmdSetLabel", 
function(str){
this.sm.loadShape(5);
var propertyValue = null;
this.setShapeProperty(5, "setDefaults", this.vwr.slm.noneSelected);
while (true) {
if (str.equals("for")) {
var bs = this.atomExpressionAt(2);
this.cmdLabel(this.iToken + 1, bs);
return true;
}if (str.equals("scalereference")) {
var scaleAngstromsPerPixel = this.floatParameter(2);
if (scaleAngstromsPerPixel >= 5) scaleAngstromsPerPixel = this.vwr.tm.getZoomSetting() / scaleAngstromsPerPixel / this.vwr.getScalePixelsPerAngstrom(false);
propertyValue = Float.$valueOf(scaleAngstromsPerPixel);
break;
}var isAbsolute = false;
if (str.equals("offset") || (isAbsolute = (str.equals("offsetabsolute") || str.equals("offsetexact")))) {
str = "offset";
if (this.isPoint3f(2)) {
var pt = this.getPoint3f(2, false, true);
propertyValue =  Clazz.newFloatArray(-1, [-1, pt.x, pt.y, pt.z, 0, 0, 0]);
} else if (this.isArrayParameter(2)) {
propertyValue = this.floatParameterSet(2, 7, 7);
} else {
var xOffset = this.intParameterRange(2, -500, 500);
var yOffset = this.intParameterRange(3, -500, 500);
if (xOffset == 2147483647 || yOffset == 2147483647) return true;
propertyValue = Integer.$valueOf(JV.JC.getOffset(xOffset, yOffset, isAbsolute));
}break;
}if (str.equals("alignment")) {
switch (this.getToken(2).tok) {
case 1073741996:
case 1073742126:
case 12289:
str = "align";
propertyValue = this.theToken.value;
break;
default:
this.invArg();
}
break;
}if (str.equals("pointer")) {
var flags = 0;
switch (this.getToken(2).tok) {
case 1073742334:
case 1073742333:
break;
case 1610616835:
flags |= 2;
case 1073742335:
flags |= 1;
break;
default:
this.invArg();
}
propertyValue = Integer.$valueOf(flags);
break;
}if (str.equals("toggle")) {
this.iToken = 1;
var bs = (this.slen == 2 ? this.vwr.bsA() : this.atomExpressionAt(2));
this.checkLast(this.iToken);
if (this.chk) return true;
this.vwr.shm.loadShape(5);
this.vwr.shm.setShapePropertyBs(5, "toggleLabel", null, bs);
return true;
}this.iToken = 1;
var TF = (this.slen == 2 || this.getToken(2).tok == 1073742335);
if (str.equals("front") || str.equals("group")) {
if (!TF && this.tokAt(2) != 1073742334) this.invArg();
if (!TF) str = "front";
propertyValue = (TF ? Boolean.TRUE : Boolean.FALSE);
break;
}if (str.equals("atom")) {
if (!TF && this.tokAt(2) != 1073742334) this.invArg();
str = "front";
propertyValue = (TF ? Boolean.FALSE : Boolean.TRUE);
break;
}return false;
}
var bs = (this.iToken + 1 < this.slen ? this.atomExpressionAt(++this.iToken) : null);
this.checkLast(this.iToken);
if (this.chk) return true;
if (bs == null) this.setShapeProperty(5, str, propertyValue);
 else this.setShapePropertyBs(5, str, propertyValue, bs);
return true;
}, "~S");
Clazz.defineMethod(c$, "cmdSetPicking", 
function(){
if (this.slen == 2) {
this.setStringProperty("picking", "identify");
return;
}if (this.slen > 4 || this.tokAt(2) == 4) {
this.setStringProperty("picking", this.getSettingStr(2, false));
return;
}var i = 2;
var type = "SELECT";
switch (this.getToken(2).tok) {
case 1275082241:
case 1745489939:
case 1095241729:
if (this.checkLength34() == 4) {
type = this.paramAsStr(2).toUpperCase();
if (type.equals("SPIN")) this.setIntProperty("pickingSpinRate", this.intParameter(3));
 else i = 3;
}break;
case 12291:
break;
default:
this.checkLength(3);
}
var str = this.paramAsStr(i);
switch (this.getToken(i).tok) {
case 1073742335:
case 1073742056:
str = "identify";
break;
case 1073742334:
case 1073742333:
str = "off";
break;
case 1275082241:
str = "atom";
break;
case 1825200146:
str = "label";
break;
case 1677721602:
str = "bond";
break;
case 12291:
this.checkLength(4);
if (this.tokAt(3) != 1677721602) this.invArg();
str = "deleteBond";
break;
}
var mode = ((mode = str.indexOf("_")) >= 0 ? mode : str.length);
mode = JV.ActionManager.getPickingMode(str.substring(0, mode));
if (mode < 0) this.errorStr2(50, "SET PICKING " + type, str);
this.setStringProperty("picking", str);
});
Clazz.defineMethod(c$, "cmdSetPickingStyle", 
function(){
if (this.slen > 4 || this.tokAt(2) == 4) {
this.setStringProperty("pickingStyle", this.getSettingStr(2, false));
return;
}var i = 2;
var isMeasure = false;
var type = "SELECT";
switch (this.getToken(2).tok) {
case 1745489939:
isMeasure = true;
type = "MEASURE";
case 1275082241:
if (this.checkLength34() == 4) i = 3;
break;
default:
this.checkLength(3);
}
var str = this.paramAsStr(i);
switch (this.getToken(i).tok) {
case 1073742333:
case 1073742334:
str = (isMeasure ? "measureoff" : "toggle");
break;
case 1073742335:
if (isMeasure) str = "measure";
break;
}
if (JV.ActionManager.getPickingStyleIndex(str) < 0) this.errorStr2(50, "SET PICKINGSTYLE " + type, str);
this.setStringProperty("pickingStyle", str);
});
Clazz.defineMethod(c$, "cmdSlab", 
function(isDepth){
var TF = false;
var plane = null;
var str;
if (this.isCenterParameter(1) || this.tokAt(1) == 9) plane = this.planeParameter(1, false);
 else switch (this.getToken(1).tok) {
case 2:
var percent = this.intParameter(this.checkLast(1));
if (!this.chk) if (isDepth) this.vwr.tm.depthToPercent(percent);
 else this.vwr.tm.slabToPercent(percent);
return;
case 1073742335:
TF = true;
case 1073742334:
this.checkLength(2);
this.setBooleanProperty("slabEnabled", TF);
return;
case 4141:
this.checkLength(2);
if (this.chk) return;
this.vwr.tm.slabReset();
this.setBooleanProperty("slabEnabled", true);
return;
case 36867:
this.checkLength(2);
if (!this.chk) this.vwr.tm.setSlabDepthInternal(isDepth);
return;
case 268440576:
str = this.paramAsStr(2);
if (str.equalsIgnoreCase("hkl")) plane = this.hklParameter(3, null, true, null);
 else if (str.equalsIgnoreCase("plane")) plane = this.planeParameter(2, false);
if (plane == null) this.invArg();
plane.scale4(-1);
break;
case 134217750:
switch (this.getToken(2).tok) {
case 1073742333:
break;
default:
plane = this.planeParameter(1, false);
}
break;
case 134219777:
plane = (this.getToken(2).tok == 1073742333 ? null : this.hklParameter(2, null, true, null));
break;
case 1073742118:
return;
default:
this.invArg();
}
if (!this.chk) this.vwr.tm.slabInternal(plane, isDepth);
}, "~B");
Clazz.defineMethod(c$, "cmdSsbond", 
function(){
var mad = this.getMadParameter();
if (mad == 2147483647) return;
this.setShapeProperty(1, "type", Integer.$valueOf(256));
this.setShapeSizeBs(1, mad, null);
this.setShapeProperty(1, "type", Integer.$valueOf(1023));
});
Clazz.defineMethod(c$, "cmdStructure", 
function(){
var type = J.c.STR.getProteinStructureType(this.paramAsStr(1));
if (type === J.c.STR.NOT) this.invArg();
var bs = null;
switch (this.tokAt(2)) {
case 12290:
case 10:
case 1073742325:
bs = this.atomExpressionAt(2);
this.checkLast(this.iToken);
break;
default:
this.checkLength(2);
}
if (this.chk) return;
this.clearDefinedVariableAtomSets();
this.vwr.setProteinType(type, bs);
});
Clazz.defineMethod(c$, "cmdSubset", 
function(){
var bs = null;
if (!this.chk) this.vwr.slm.setSelectionSubset(null);
if (this.slen != 1 && (this.slen != 4 || !this.getToken(2).value.equals("off"))) bs = this.atomExpressionAt(1);
if (!this.chk) this.vwr.slm.setSelectionSubset(bs);
});
Clazz.defineMethod(c$, "cmdThrow", 
function(){
if (this.chk) return;
var pt = (this.tokAt(1) == 14 ? 2 : 1);
var v = (pt == 1 ? this.setVariable(1, this.slen, "thrown_value", false) : this.vwr.g.setUserVariable("thrown_value", JS.SV.newS(this.optParameterAsString(2))));
var info = v.asString();
if (info.length == 0 && (info = this.optParameterAsString(1)).length == 0) info = "context";
if (pt == 2) {
this.saveContext(info);
if (this.doReport()) this.report(J.i18n.GT.o(J.i18n.GT.$("to resume, enter: &{0}"), info), false);
throw  new JS.ScriptInterruption(this, info, -2147483648);
}this.evalError(info, null);
});
Clazz.defineMethod(c$, "saveContext", 
function(saveName){
var sc = this.getScriptContext("Context_" + saveName);
this.vwr.stm.saveContext(saveName, sc);
this.vwr.g.setUserVariable(saveName, JS.SV.newV(14, sc));
return sc;
}, "~S");
Clazz.defineMethod(c$, "cmdTimeout", 
function(index){
var name = null;
var script = null;
var mSec = 0;
if (this.slen == index) {
this.showString(this.vwr.showTimeout(null));
return;
}for (var i = index; i < this.slen; i++) switch (this.getToken(i).tok) {
case 1073741974:
name = this.paramAsStr(++i);
if (this.slen == 3) {
if (!this.chk) this.vwr.triggerTimeout(name);
return;
}break;
case 1073742334:
break;
case 2:
mSec = this.intParameter(i);
break;
case 3:
mSec = Math.round(this.floatParameter(i) * 1000);
break;
default:
if (name == null) name = this.paramAsStr(i);
 else if (script == null) script = this.paramAsStr(i);
 else this.invArg();
break;
}

if (!this.chk) this.vwr.setTimeout(name, mSec, script);
}, "~N");
Clazz.defineMethod(c$, "cmdTranslate", 
function(isSelected){
var bs = null;
var i = 1;
var i0 = 0;
if (this.tokAt(1) == 1113589787) {
isSelected = true;
i0 = 1;
i = 2;
}if (this.isPoint3f(i)) {
var pt = this.getPoint3f(i, true, true);
bs = (this.iToken + 1 < this.slen ? this.atomExpressionAt(++this.iToken) : null);
this.checkLast(this.iToken);
if (!this.chk) this.vwr.setAtomCoordsRelative(pt, bs);
return;
}var xyz = (this.paramAsStr(i).toLowerCase() + " ").charAt(0);
if ("xyz".indexOf(xyz) < 0) this.error(0);
var amount = this.floatParameter(++i);
var type;
switch (this.tokAt(++i)) {
case 0:
case 12290:
case 10:
case 1073742325:
type = '\0';
break;
default:
type = (this.optParameterAsString(i).toLowerCase() + '\0').charAt(0);
}
if (amount == 0 && type != '\0') return;
this.iToken = i0 + (type == '\0' ? 2 : 3);
bs = (isSelected ? this.vwr.bsA() : this.iToken + 1 < this.slen ? this.atomExpressionAt(++this.iToken) : null);
this.checkLast(this.iToken);
if (!this.chk) {
this.vwr.translate(xyz, amount, type, bs);
this.refresh(false);
}}, "~B");
Clazz.defineMethod(c$, "cmdUnbind", 
function(){
if (this.slen != 1) this.checkLength23();
var mouseAction = this.optParameterAsString(1);
var name = this.optParameterAsString(2);
if (mouseAction.length == 0 || this.tokAt(1) == 1073742327) mouseAction = null;
if (name.length == 0 || this.tokAt(2) == 1073742327) name = null;
if (name == null && mouseAction != null && JV.ActionManager.getActionFromName(mouseAction) >= 0) {
name = mouseAction;
mouseAction = null;
}if (!this.chk) this.vwr.unBindAction(mouseAction, name);
});
Clazz.defineMethod(c$, "cmdUndoRedo", 
function(tok){
var n = 1;
var len = 2;
switch (tok) {
case 603984065:
case 4139:
var state = this.vwr.stm.getUndoRedoState(tok);
if (state != null) this.runScript(state);
return;
case 4165:
case 4140:
break;
}
switch (this.tokAt(1)) {
case 0:
len = 1;
break;
case 1073742327:
n = 0;
break;
case 2:
n = this.intParameter(1);
break;
default:
this.invArg();
}
this.checkLength(len);
if (!this.chk) this.vwr.undoMoveAction(tok, n);
}, "~N");
Clazz.defineMethod(c$, "cmdUnitcell", 
function(i){
this.getCmdExt().dispatch(1814695966, i == 2, null);
}, "~N");
Clazz.defineMethod(c$, "cmdVector", 
function(){
var type = J.atomdata.RadiusData.EnumType.SCREEN;
var value = 1;
this.checkLength(-3);
switch (this.iToken = this.slen) {
case 1:
break;
case 2:
switch (this.getToken(1).tok) {
case 1073742335:
break;
case 1073742334:
value = 0;
break;
case 2:
var d = this.intParameterRange(1, 0, 19);
if (d == 2147483647) return;
value = d;
break;
case 3:
type = J.atomdata.RadiusData.EnumType.ABSOLUTE;
if (Float.isNaN(value = this.floatParameterRange(1, 0, 3))) return;
break;
default:
this.error(6);
}
break;
case 3:
switch (this.tokAt(1)) {
case 1112152078:
this.setIntProperty("vectorTrace", this.intParameterRange(2, 0, 20));
return;
case 536875059:
if (!Float.isNaN(value = this.floatParameterRange(2, -100, 100))) this.setFloatProperty("vectorScale", value);
return;
case 64:
var max = this.floatParameter(2);
if (!this.chk) this.vwr.ms.scaleVectorsToMax(max);
return;
}
break;
}
this.setShapeSize(18,  new J.atomdata.RadiusData(null, value, type, null));
});
Clazz.defineMethod(c$, "cmdVibration", 
function(){
this.checkLength(-3);
var period = 0;
switch (this.getToken(1).tok) {
case 1073742335:
this.checkLength(2);
period = this.vwr.getFloat(570425412);
break;
case 1073742334:
this.checkLength(2);
period = 0;
break;
case 2:
case 3:
this.checkLength(2);
period = this.floatParameter(1);
break;
case 536875059:
if (!Float.isNaN(period = this.floatParameterRange(2, -100, 100))) this.setFloatProperty("vibrationScale", period);
return;
case 64:
var max = this.floatParameter(2);
if (!this.chk) this.vwr.ms.scaleVectorsToMax(max);
break;
case 1073742090:
this.setFloatProperty("vibrationPeriod", this.floatParameter(2));
return;
case 1073741824:
this.invArg();
break;
default:
period = -1;
}
if (period < 0) this.invArg();
if (this.chk) return;
if (period == 0) {
this.vwr.tm.setVibrationPeriod(0);
return;
}this.vwr.setVibrationPeriod(-period);
});
Clazz.defineMethod(c$, "cmdWireframe", 
function(){
var mad = -2147483648;
if (this.tokAt(1) == 4141) this.checkLast(1);
 else mad = this.getMadParameter();
if (this.chk || mad == 2147483647) return;
this.setShapeProperty(1, "type", Integer.$valueOf(1023));
this.setShapeSizeBs(1, mad == -2147483648 ? 300 : mad, null);
});
Clazz.defineMethod(c$, "cmdZap", 
function(isZapCommand){
if (this.slen == 1 || !isZapCommand) {
var doAll = (isZapCommand && !this.$isStateScript);
if (doAll) this.vwr.cacheClear();
this.vwr.zap(true, doAll, true);
this.refresh(false);
return;
}var bs = this.atomExpressionAt(1);
if (this.chk) return;
if (bs.nextSetBit(0) < 0 && this.slen == 4 && this.tokAt(2) == 1073742359) {
var iModel = this.vwr.ms.getModelNumberIndex(this.getToken(2).intValue, false, true);
if (iModel >= 0) this.vwr.deleteModels(iModel, null);
return;
}var nDeleted = this.vwr.deleteAtoms(bs, true);
var isQuiet = !this.doReport();
if (!isQuiet) this.report(J.i18n.GT.i(J.i18n.GT.$("{0} atoms deleted"), nDeleted), false);
this.vwr.selectStatus(null, false, 0, isQuiet, false);
}, "~B");
Clazz.defineMethod(c$, "cmdZoom", 
function(isZoomTo){
if (!isZoomTo) {
var tok = (this.slen > 1 ? this.getToken(1).tok : 1073742335);
switch (tok) {
case 1275068432:
case 1073742079:
break;
case 1073742335:
case 1073742334:
if (this.slen > 2) this.bad();
if (!this.chk) this.setBooleanProperty("zoomEnabled", tok == 1073742335);
return;
}
}var center = null;
var i = 1;
var secondsTotal = (isZoomTo ? (this.isFloatParameter(i) ? this.floatParameter(i++) : 1) : 0);
if (secondsTotal < 0) {
i--;
secondsTotal = 0;
}var ptCenter = 0;
var bsCenter = null;
if (this.tokAt(i) == 1814695966 || this.isCenterParameter(i)) {
ptCenter = i;
var ret =  new Array(1);
center = this.centerParameter(i, ret);
if (Clazz.instanceOf(ret[0],"JU.BS")) bsCenter = ret[0];
i = this.iToken + 1;
} else if (this.tokAt(i) == 2 && this.getToken(i).intValue == 0) {
bsCenter = this.vwr.getAtomBitSet("visible");
center = this.vwr.ms.getAtomSetCenter(bsCenter);
}var zoom = this.vwr.tm.getZoomSetting();
var newZoom = this.getZoom(ptCenter, i, bsCenter, zoom);
i = this.iToken + 1;
var xTrans = NaN;
var yTrans = NaN;
if (i != this.slen) {
xTrans = this.floatParameter(i++);
yTrans = this.floatParameter(i++);
}if (i != this.slen) this.invArg();
if (newZoom < 0) {
newZoom = -newZoom;
if (isZoomTo) {
if (this.slen == 1) newZoom *= 2;
 else if (center == null) newZoom /= 2;
}}var max = 200000;
if (newZoom < 5 || newZoom > max) this.numberOutOfRange(5, max);
if (!this.vwr.tm.isWindowCentered()) {
if (center != null) {
var bs = this.atomExpressionAt(ptCenter);
if (!this.chk) this.vwr.setCenterBitSet(bs, false);
}center = this.vwr.tm.fixedRotationCenter;
if (Float.isNaN(xTrans)) xTrans = this.vwr.tm.getTranslationXPercent();
if (Float.isNaN(yTrans)) yTrans = this.vwr.tm.getTranslationYPercent();
}if (this.chk) return;
if (Float.isNaN(xTrans)) xTrans = 0;
if (Float.isNaN(yTrans)) yTrans = 0;
if (!this.useThreads(true)) secondsTotal = 0;
this.vwr.moveTo(this, secondsTotal, center, JV.JC.center, NaN, null, newZoom, xTrans, yTrans, NaN, null, NaN, NaN, NaN, NaN, NaN, NaN);
if (this.isJS && secondsTotal > 0 && this.vwr.g.waitForMoveTo) throw  new JS.ScriptInterruption(this, "zoomTo", 1);
}, "~B");
Clazz.defineMethod(c$, "colorShape", 
function(shapeType, index, isBackground){
var isScale = (Math.abs(shapeType) == 536875059);
if (isScale) {
shapeType = 31;
} else if (shapeType < 0) {
shapeType = this.getShapeType(-shapeType);
}var translucency = null;
var colorvalue = null;
var colorvalue1 = null;
var bs = null;
var prefix = (index == 2 && this.tokAt(1) == 1073741859 ? "ball" : "");
var isIsosurface = (shapeType == 24 || shapeType == 25);
var doClearBondSet = false;
var translucentLevel = 3.4028235E38;
if (index < 0) {
bs = this.atomExpressionAt(-index);
index = this.iToken + 1;
if (this.isBondSet) {
doClearBondSet = true;
shapeType = 1;
}}var tok = this.getToken(index).tok;
var isColorSelect = (tok == 1275082241);
if (isColorSelect) {
tok = this.getToken(++index).tok;
}if (isBackground) this.getToken(index);
 else if ((isBackground = (tok == 1610616835)) == true) this.getToken(++index);
if (isBackground) prefix = "bg";
 else if (isIsosurface) {
var isVertices = false;
if (this.theTok == 1073742194) {
this.getToken(++index);
isVertices = true;
}switch (this.theTok) {
case 1073742018:
this.getToken(++index);
prefix = "mesh";
break;
case 1073742094:
var argb = this.getArgbParamOrNone(++index, false);
colorvalue1 = (argb == 0 ? null : Integer.$valueOf(argb));
this.getToken(index = this.iToken + 1);
break;
case 12290:
case 10:
case 1073742325:
if (Clazz.instanceOf(this.theToken.value,"JM.BondSet")) {
bs = this.theToken.value;
prefix = "vertex";
} else if (isVertices && Clazz.instanceOf(this.theToken.value,"JU.BS")) {
bs = this.theToken.value;
prefix = "vertex";
} else {
bs = this.atomExpressionAt(index);
prefix = "atom";
}this.getToken(index = this.iToken + 1);
break;
}
}if (!this.chk && (shapeType == 27 || shapeType == 28) && this.getIsoExt().dispatch(shapeType, true, this.st) != null) return;
var isTranslucent = (this.theTok == 1111490588);
if (isTranslucent || this.theTok == 1073742074) {
if (translucentLevel == 1.4E-45) this.invArg();
translucency = this.paramAsStr(index++);
if (isTranslucent && this.isFloatParameter(index)) translucentLevel = this.getTranslucentLevel(index++);
}tok = 0;
var isColor = (index < this.slen && this.tokAt(index) != 1073742335 && this.tokAt(index) != 1073742334);
if (isColor) {
var argb = 0;
var argb1 = 0;
tok = this.getToken(index).tok;
if ((!isIsosurface || this.tokAt(index + 1) != 1073742170) && (isColorSelect && tok == 1073742333 || this.isColorParam(index))) {
argb = this.getArgbParamOrNone(index, isColorSelect);
colorvalue = (argb == 0 ? null : Integer.$valueOf(argb));
if (this.tokAt(index = this.iToken + 1) != 0 && translucency == null) {
this.getToken(index);
isTranslucent = (this.theTok == 1111490588);
if (isTranslucent || this.theTok == 1073742074) {
translucency = this.paramAsStr(index++);
if (isTranslucent && this.isFloatParameter(index)) translucentLevel = this.getTranslucentLevel(index++);
}}tok = this.tokAt(index);
if (isColorSelect && tok == 1073742333 || this.isColorParam(index)) {
argb1 = this.getArgbParamOrNone(index, isColorSelect);
colorvalue1 = (argb1 == 0 ? null : Integer.$valueOf(argb1));
index = this.iToken + 1;
}this.checkLength(index);
if (isColorSelect) {
if (!this.chk) this.vwr.setSelectionColors(colorvalue, colorvalue1, translucency, translucentLevel);
return;
}} else if (shapeType == 26) {
this.iToken--;
} else {
var name = this.paramAsStr(index).toLowerCase();
var isByElement = (name.indexOf("byelement") == 0);
var isColorIndex = (isByElement || name.indexOf("byresidue") == 0);
var pal = (isColorIndex || isIsosurface ? J.c.PAL.PROPERTY : tok == 1112152075 ? J.c.PAL.CPK : J.c.PAL.getPalette(name));
if (pal === J.c.PAL.UNKNOWN || (pal === J.c.PAL.TYPE || pal === J.c.PAL.ENERGY) && shapeType != 2) this.invArg();
var data = null;
var bsSelected = (pal !== J.c.PAL.PROPERTY && pal !== J.c.PAL.VARIABLE || !this.vwr.g.rangeSelected ? null : this.vwr.bsA());
if (pal === J.c.PAL.PROPERTY) {
if (isColorIndex) {
if (!this.chk) {
data = this.getBitsetPropertyFloat(bsSelected, (isByElement ? 1094715402 : 1094713356) | 256, null, NaN, NaN);
}} else {
var isPropertyExplicit = name.equals("property");
if (isPropertyExplicit && JS.T.tokAttr((tok = this.getToken(++index).tok), 1077936128) && (tok == 1086324754 || !JS.T.tokAttr(tok, 1086324736))) {
tok = this.getToken(index).tok;
var type = (tok == 1111490587 ? "property_dssr." + this.getToken(++index).value.toString() : tok == 1086324754 || tok == 1145047055 ? "color" : null);
if (!this.chk) {
data = this.getBitsetPropertyFloat(bsSelected, tok | 256, type, NaN, NaN);
}index++;
} else if (!isPropertyExplicit && !isIsosurface) {
index++;
}}} else if (pal === J.c.PAL.VARIABLE) {
index++;
name = this.paramAsStr(index++);
data =  Clazz.newFloatArray (this.vwr.ms.ac, 0);
JU.Parser.parseStringInfestedFloatArray("" + this.getParameter(name, 4, true), null, data);
pal = J.c.PAL.PROPERTY;
}if (pal === J.c.PAL.PROPERTY) {
var scheme = null;
if (this.tokAt(index) == 4) {
scheme = this.paramAsStr(index++);
if (scheme.indexOf("/") < 0) scheme = scheme.toLowerCase();
if (this.isArrayParameter(index)) {
scheme += "=" + JS.SV.sValue(JS.SV.getVariableAS(this.stringParameterSet(index))).$replace('\n', ' ');
index = this.iToken + 1;
}} else if (isIsosurface && this.isColorParam(index)) {
scheme = this.getColorRange(index);
index = this.iToken + 1;
}if (scheme != null && !isIsosurface) {
this.setStringProperty("propertyColorScheme", (isTranslucent && translucentLevel == 3.4028235E38 ? "translucent " : "") + scheme);
isColorIndex = (scheme.indexOf("byelement") == 0 || scheme.indexOf("byresidue") == 0);
}var min = 0;
var max = 3.4028235E38;
if (!isColorIndex && (this.tokAt(index) == 1073741826 || this.tokAt(index) == 1073742114)) {
min = this.floatParameter(index + 1);
max = this.floatParameter(index + 2);
index += 3;
if (min == max && isIsosurface) {
var range = this.getShapeProperty(shapeType, "dataRange");
if (range != null) {
min = range[0];
max = range[1];
}} else if (min == max) {
max = 3.4028235E38;
}}if (isIsosurface) {
} else if (data == null) {
if (!this.chk) this.vwr.setCurrentColorRange(name);
} else {
if (!this.chk) this.vwr.cm.setPropertyColorRangeData(data, bsSelected);
}if (isIsosurface) {
this.checkLength(index);
if (this.chk) return;
isColor = false;
var ce = (scheme == null ? this.getShapeProperty(shapeType, "colorEncoder") : null);
if (ce == null && (ce = this.vwr.cm.getColorEncoder(scheme)) == null) return;
ce.isTranslucent = (isTranslucent && translucentLevel == 3.4028235E38);
ce.setRange(min, max, min > max);
if (max == 3.4028235E38) ce.hi = max;
this.setShapeProperty(shapeType, "remapColor", ce);
this.showString((this.getShapeProperty(shapeType, "dataRangeStr")).$replace('\n', ' '));
if (translucentLevel == 3.4028235E38) return;
} else if (max != 3.4028235E38) {
this.vwr.cm.setPropertyColorRange(min, max);
}} else {
index++;
}this.checkLength(index);
colorvalue = pal;
}}if (this.chk || shapeType < 0) return;
if (isScale) this.setShapeProperty(31, "target", "%SCALE");
var typeMask;
switch (shapeType) {
case 4:
typeMask = 32768;
break;
case 2:
typeMask = 30720;
break;
case 3:
typeMask = 256;
break;
case 1:
typeMask = 1023;
break;
default:
typeMask = 0;
}
if (typeMask == 0) {
this.sm.loadShape(shapeType);
if (shapeType == 5) this.setShapeProperty(5, "setDefaults", this.vwr.slm.noneSelected);
} else {
if (bs != null) {
this.vwr.selectBonds(bs);
bs = null;
}shapeType = 1;
this.setShapeProperty(shapeType, "type", Integer.$valueOf(typeMask));
}if (isColor) {
switch (tok) {
case 1111492619:
this.getPartialCharges(bs);
break;
case 1111490575:
case 1111490574:
this.vwr.autoCalculate(tok, null);
break;
case 1111492620:
if (this.vwr.g.rangeSelected) this.vwr.ms.clearBfactorRange();
break;
case 1086324742:
this.vwr.ms.calcSelectedGroupsCount();
break;
case 1094713362:
case 1094713361:
this.vwr.ms.calcSelectedMonomersCount();
break;
case 1639976963:
this.vwr.ms.getStructureAssignments();
break;
case 1094713360:
this.vwr.ms.calcSelectedMoleculesCount();
break;
}
if (colorvalue1 != null && (isIsosurface || shapeType == 11 || shapeType == 14 || shapeType == 21)) this.setShapeProperty(shapeType, "colorPhase",  Clazz.newArray(-1, [colorvalue1, colorvalue]));
 else if (bs == null) this.setShapeProperty(shapeType, prefix + "color", colorvalue);
 else if (prefix === "vertex") this.setShapePropertyBs(shapeType, "vertexcolor",  Clazz.newArray(-1, [colorvalue, Double.$valueOf(translucentLevel)]), bs);
 else this.setShapePropertyBs(shapeType, prefix + "color", colorvalue, bs);
}if (translucency != null && prefix !== "vertex") this.setShapeTranslucency(shapeType, prefix, translucency, translucentLevel, bs);
if (isScale) this.setShapeProperty(31, "thisID", null);
if (typeMask != 0) this.setShapeProperty(1, "type", Integer.$valueOf(1023));
if (doClearBondSet) this.vwr.selectBonds(null);
if (shapeType == 0) {
this.vwr.shm.checkInheritedShapes();
this.vwr.sm.setStatusStructureModified(-1, -1, 1, null, 0, bs);
}}, "~N,~N,~B");
Clazz.defineMethod(c$, "getPartialCharges", 
function(bs){
try {
this.vwr.getOrCalcPartialCharges(bs, null);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
throw  new JS.ScriptInterruption(this, "partialcharge", 1);
} else {
throw e;
}
}
}, "JU.BS");
Clazz.defineMethod(c$, "encodeRadiusParameter", 
function(index, isOnly, allowAbsolute){
var value = NaN;
var factorType = J.atomdata.RadiusData.EnumType.ABSOLUTE;
var vdwType = null;
var tok = (index == -1 ? 1648363544 : this.getToken(index).tok);
switch (tok) {
case 1111490561:
case 1111490562:
case 1111492618:
case 1113589786:
case 1111492620:
case 1648363544:
value = 1;
factorType = J.atomdata.RadiusData.EnumType.FACTOR;
vdwType = (tok == 1648363544 ? null : J.c.VDW.getVdwType2(JS.T.nameOf(tok)));
tok = this.tokAt(++index);
break;
}
switch (tok) {
case 4141:
return this.vwr.rd;
case 1073741852:
case 1073742116:
case 1073741856:
case 1073741857:
case 1073741991:
value = 1;
factorType = J.atomdata.RadiusData.EnumType.FACTOR;
this.iToken = index - 1;
break;
case 268440577:
case 2:
case 3:
if (tok == 268440577) {
index++;
} else if (this.tokAt(index + 1) == 268441090) {
value = Math.round(this.floatParameter(index));
this.iToken = ++index;
factorType = J.atomdata.RadiusData.EnumType.FACTOR;
if (Math.abs(value) > 200) {
this.integerOutOfRange(0, 200);
return null;
}if (isOnly) value = -value;
value /= 100;
break;
} else if (tok == 2) {
value = this.intParameter(index);
if (value > 749 || value < -200) {
this.integerOutOfRange(-200, 749);
return null;
}if (value > 0) {
value /= 250;
factorType = J.atomdata.RadiusData.EnumType.ABSOLUTE;
} else {
value /= -100;
factorType = J.atomdata.RadiusData.EnumType.FACTOR;
}break;
}var max;
if (tok == 268440577 || !allowAbsolute) {
factorType = J.atomdata.RadiusData.EnumType.OFFSET;
max = 16;
} else {
factorType = J.atomdata.RadiusData.EnumType.ABSOLUTE;
vdwType = J.c.VDW.NADA;
max = 100;
}value = this.floatParameterRange(index, (isOnly || !allowAbsolute ? -max : 0), max);
if (Float.isNaN(value)) return null;
if (isOnly) value = -value;
if (value > 16) value = 16.1;
break;
default:
if (value == 1) index--;
}
if (vdwType == null) {
vdwType = J.c.VDW.getVdwType(this.optParameterAsString(++this.iToken));
if (vdwType == null) {
this.iToken = index;
vdwType = J.c.VDW.AUTO;
}}return  new J.atomdata.RadiusData(null, value, factorType, vdwType);
}, "~N,~B,~B");
Clazz.defineMethod(c$, "expandFloatArray", 
function(a, min, asBS){
var n = a.length;
var haveNeg = false;
var bs = (asBS ?  new JU.BS() : null);
try {
for (var i = 0; i < a.length; i++) if (a[i] < 0) {
n += Math.abs(a[i - 1] + a[i]) - 1;
haveNeg = true;
}
if (haveNeg) {
var b = (asBS ? null :  Clazz.newFloatArray (n, 0));
for (var pt = 0, i = 0; i < a.length; i++) {
n = Clazz.floatToInt(a[i]);
if (n >= 0) {
if (n < min) this.invArg();
if (asBS) bs.set(n - 1);
 else b[pt++] = n;
} else {
var j = Clazz.floatToInt(a[i - 1]);
var dir = (j <= -n ? 1 : -1);
for (var j2 = -n; j != j2; j += dir, pt++) if (!asBS) b[pt] = j + dir;
 else bs.set(j);

}}
a = b;
if (!asBS) n = a.length;
}if (asBS) {
for (var i = n; --i >= 0; ) bs.set(Clazz.floatToInt(a[i]) - 1);

return bs;
}var ia =  Clazz.newIntArray (n, 0);
for (var i = n; --i >= 0; ) ia[i] = Clazz.floatToInt(a[i]);

return ia;
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
this.invArg();
return null;
} else {
throw e;
}
}
}, "~A,~N,~B");
Clazz.defineMethod(c$, "frameControl", 
function(i){
switch (this.getToken(this.checkLast(i)).tok) {
case 1073742098:
case 1073742096:
case 4143:
case 20487:
case 1073742037:
case 1073742108:
case 1073742125:
case 1073741942:
case 1073741993:
if (!this.chk) this.vwr.setAnimation(this.theTok);
return;
}
this.invArg();
}, "~N");
Clazz.defineMethod(c$, "getColorRange", 
function(i){
var color1 = this.getArgbParam(i);
if (this.tokAt(++this.iToken) != 1073742170) this.invArg();
var color2 = this.getArgbParam(++this.iToken);
var nColors = (this.tokAt(this.iToken + 1) == 2 ? this.intParameter(++this.iToken) : 0);
return JU.ColorEncoder.getColorSchemeList(JU.ColorEncoder.getPaletteAtoB(color1, color2, nColors));
}, "~N");
Clazz.defineMethod(c$, "getFullPathName", 
function(withType){
var filename = (!this.chk || this.isCmdLine_C_Option ? this.vwr.fm.getFullPathName(true) : "test.xyz");
if (filename == null) this.invArg();
if (withType && !"string".equals(filename) && !"zapped".equals(filename)) {
var ft = this.vwr.fm.getLastReadFileType();
if (ft != null && ft.length > 0) filename = ft + "::" + filename;
}return filename;
}, "~B");
Clazz.defineMethod(c$, "getObjectBoundingBox", 
function(id){
var data =  Clazz.newArray(-1, [id, null, null]);
return (this.getShapePropertyData(24, "getBoundingBox", data) || this.getShapePropertyData(29, "getBoundingBox", data) || this.getShapePropertyData(25, "getBoundingBox", data) || this.getShapePropertyData(28, "getBoundingBox", data) || this.getShapePropertyData(27, "getBoundingBox", data) ? data[2] : null);
}, "~S");
Clazz.defineMethod(c$, "getObjectCenter", 
function(axisID, index, modelIndex){
var data =  Clazz.newArray(-1, [axisID, Integer.$valueOf(index), Integer.$valueOf(modelIndex)]);
return (this.getShapePropertyData(22, "getCenter", data) || this.getShapePropertyData(24, "getCenter", data) || this.getShapePropertyData(29, "getCenter", data) || this.getShapePropertyData(25, "getCenter", data) || this.getShapePropertyData(28, "getCenter", data) || this.getShapePropertyData(27, "getCenter", data) ? data[2] : null);
}, "~S,~N,~N");
Clazz.defineMethod(c$, "getPlaneForObject", 
function(id, vAB){
var shapeType = this.sm.getShapeIdFromObjectName(id);
switch (shapeType) {
case 22:
this.setShapeProperty(22, "thisID", id);
var points = this.getShapeProperty(22, "vertices");
if (points == null || points.length < 3 || points[0] == null || points[1] == null || points[2] == null) break;
return JU.Measure.getPlaneThroughPoints(points[0], points[1], points[2],  new JU.V3(), vAB,  new JU.P4());
case 24:
this.setShapeProperty(24, "thisID", id);
return this.getShapeProperty(24, "plane");
}
return null;
}, "~S,JU.V3");
Clazz.defineMethod(c$, "getQuaternionArray", 
function(quaternionOrSVData, itype){
var data;
switch (itype) {
case 134221850:
data = quaternionOrSVData;
break;
case 9:
var pts = quaternionOrSVData;
data =  new Array(pts.length);
for (var i = 0; i < pts.length; i++) data[i] = JU.Quat.newP4(pts[i]);

break;
case 1073742001:
var sv = quaternionOrSVData;
data =  new Array(sv.size());
for (var i = 0; i < sv.size(); i++) {
var pt = JS.SV.pt4Value(sv.get(i));
if (pt == null) return null;
data[i] = JU.Quat.newP4(pt);
}
break;
default:
return null;
}
return data;
}, "~O,~N");
Clazz.defineMethod(c$, "getSetAxesTypeMad10", 
function(index){
if (index == this.slen) return 1;
switch (this.getToken(this.checkLast(index)).tok) {
case 1073742335:
return 1;
case 1073742334:
return 0;
case 1073741926:
return -1;
case 2:
return this.intParameterRange(index, -1, 19);
case 3:
var angstroms = this.floatParameterRange(index, 0, 2);
return (Float.isNaN(angstroms) ? 2147483647 : Clazz.doubleToInt(Math.floor(angstroms * 10000 * 2)));
}
if (!this.chk) this.errorStr(7, "\"DOTTED\"");
return 0;
}, "~N");
Clazz.defineMethod(c$, "getSettingFloat", 
function(pt){
return (pt >= this.slen ? NaN : JS.SV.fValue(this.parameterExpressionToken(pt)));
}, "~N");
Clazz.defineMethod(c$, "getSettingInt", 
function(pt){
return (pt >= this.slen ? -2147483648 : this.parameterExpressionToken(pt).asInt());
}, "~N");
Clazz.defineMethod(c$, "getSettingStr", 
function(pt, isJmolSet){
return (isJmolSet && this.slen == pt + 1 ? this.paramAsStr(pt) : this.parameterExpressionToken(pt).asString());
}, "~N,~B");
Clazz.defineMethod(c$, "getShapeProperty", 
function(shapeType, propertyName){
return this.sm.getShapePropertyIndex(shapeType, propertyName, -2147483648);
}, "~N,~S");
Clazz.defineMethod(c$, "getShapePropertyData", 
function(shapeType, propertyName, data){
return this.sm.getShapePropertyData(shapeType, propertyName, data);
}, "~N,~S,~A");
Clazz.defineMethod(c$, "getShapeType", 
function(tok){
var iShape = JV.JC.shapeTokenIndex(tok);
if (iShape < 0) this.error(49);
return iShape;
}, "~N");
Clazz.defineMethod(c$, "getTranslucentLevel", 
function(i){
var f = this.floatParameter(i);
return (this.theTok == 2 && f > 0 && f < 9 ? f + 1 : f);
}, "~N");
Clazz.defineMethod(c$, "getZoom", 
function(ptCenter, i, bs, currentZoom){
var zoom = (this.isFloatParameter(i) ? this.floatParameter(i++) : NaN);
if (zoom == 0 || currentZoom == 0) {
var r = NaN;
if (bs == null) {
switch (this.tokAt(ptCenter)) {
case 1814695966:
var uc = this.vwr.getCurrentUnitCell();
if (uc == null) this.invArg();
var pts = uc.getUnitCellVerticesNoOffset();
var center =  new JU.P3();
for (var j = 0; j < 8; j++) {
center.add(pts[j]);
}
center.scale(0.125);
r = 0;
for (var j = 0; j < 8; j++) {
var d = pts[j].distanceSquared(center);
if (d > r) r = d;
}
if (r == 0) this.invArg();
r = Math.sqrt(r);
break;
case 1073742330:
var bbox = this.getObjectBoundingBox(this.objectNameParameter(ptCenter + 1));
if (bbox == null || (r = bbox[0].distance(bbox[1]) / 2) == 0) this.invArg();
break;
}
} else {
r = this.vwr.ms.calcRotationRadiusBs(bs);
}if (Float.isNaN(r)) this.invArg();
currentZoom = this.vwr.getFloat(570425388) / r * 100;
zoom = NaN;
}if (zoom < 0) {
zoom += currentZoom;
} else if (Float.isNaN(zoom)) {
var tok = this.tokAt(i);
switch (tok) {
case 1073742079:
case 1275068432:
zoom = currentZoom * (tok == 1073742079 ? 0.5 : 2);
i++;
break;
case 268441088:
case 268441089:
case 268440577:
var value = this.floatParameter(++i);
i++;
switch (tok) {
case 268441088:
zoom = currentZoom / value;
break;
case 268441089:
zoom = currentZoom * value;
break;
case 268440577:
zoom = currentZoom + value;
break;
}
break;
default:
zoom = (bs == null ? -currentZoom : currentZoom);
}
}this.iToken = i - 1;
return zoom;
}, "~N,~N,JU.BS,~N");
Clazz.defineMethod(c$, "setElementColor", 
function(str, argb){
var n = -1;
var isSym = (str.charAt(0) == '_');
out : while (true) {
if (isSym) {
str = str.substring(1);
for (var i = JU.Elements.elementNumberMax; --i >= 0; ) {
if (str.equalsIgnoreCase(JU.Elements.elementSymbolFromNumber(i))) {
n = i;
break out;
}}
for (var i = JU.Elements.altElementMax; --i >= 4; ) {
if (str.equalsIgnoreCase(JU.Elements.altElementSymbolFromIndex(i)) || str.equalsIgnoreCase(JU.Elements.altIsotopeSymbolFromIndex(i))) {
n = JU.Elements.altElementNumberFromIndex(i);
break out;
}}
} else {
for (var i = JU.Elements.elementNumberMax; --i >= 0; ) {
if (str.equalsIgnoreCase(JU.Elements.elementNameFromNumber(i))) {
n = i;
break out;
}}
for (var i = JU.Elements.altElementMax; --i >= 0; ) {
if (str.equalsIgnoreCase(JU.Elements.altElementNameFromIndex(i))) {
n = JU.Elements.altElementNumberFromIndex(i);
break out;
}}
}break;
}
if (this.chk || n < 0) {
return false;
}this.vwr.setElementArgb(n, argb);
return true;
}, "~S,~N");
Clazz.defineMethod(c$, "setMeshDisplayProperty", 
function(shape, i, tok){
var propertyName = null;
var propertyValue = null;
var allowCOLOR = (shape == 25);
var checkOnly = (i == 0);
if (!checkOnly) tok = this.getToken(i).tok;
switch (tok) {
case 1765808134:
if (allowCOLOR) this.iToken++;
 else break;
case 1073742074:
case 1111490588:
if (!checkOnly) this.colorShape(shape, this.iToken, false);
return true;
case 0:
case 12291:
case 1073742335:
case 1073742072:
case 1073742334:
case 12294:
case 2097194:
case 1610625028:
case 2097192:
if (this.iToken == 1 && shape >= 0 && this.tokAt(2) == 0) this.setShapeProperty(shape, "thisID", null);
if (tok == 0) return (this.iToken == 1);
if (checkOnly) return true;
switch (tok) {
case 12291:
this.setShapeProperty(shape, "delete", null);
return true;
case 2097194:
case 12294:
tok = 1073742334;
break;
case 2097192:
tok = 1073742335;
break;
case 1610625028:
if (i + 1 == this.slen) tok = 1073742335;
break;
}
case 1073741958:
case 1073741861:
case 1073741964:
case 1073741898:
case 1073742039:
case 1112150019:
case 1073742042:
case 1073742018:
case 1073742052:
case 1073741938:
case 1073742046:
case 1073741862:
case 1073742057:
case 1073742182:
case 1073742060:
case 1073741960:
case 1073742058:
propertyName = "token";
propertyValue = Integer.$valueOf(tok);
break;
}
if (propertyName == null) return false;
if (checkOnly) return true;
this.setShapeProperty(shape, propertyName, propertyValue);
if ((this.tokAt(this.iToken + 1)) != 0) {
if (!this.setMeshDisplayProperty(shape, ++this.iToken, 0)) --this.iToken;
}return true;
}, "~N,~N,~N");
Clazz.defineMethod(c$, "setObjectArgb", 
function(str, argb){
if (this.chk) return;
this.vwr.setObjectArgb(str, argb);
}, "~S,~N");
Clazz.defineMethod(c$, "setObjectMad10", 
function(iShape, name, mad10){
if (!this.chk) this.vwr.setObjectMad10(iShape, name, mad10);
}, "~N,~S,~N");
Clazz.defineMethod(c$, "setObjectProp", 
function(id, tokCommand, ptColor){
var data =  Clazz.newArray(-1, [id, null]);
var s = "";
var isWild = JU.PT.isWild(id);
for (var iShape = 17; ; ) {
if (this.getShapePropertyData(iShape, "checkID", data)) {
this.setShapeProperty(iShape, "thisID", id);
switch (tokCommand) {
case 12291:
this.setShapeProperty(iShape, "delete", null);
break;
case 12294:
case 1610625028:
this.setShapeProperty(iShape, "hidden", tokCommand == 1610625028 ? Boolean.FALSE : Boolean.TRUE);
break;
case 134222350:
s += this.getShapeProperty(iShape, "command") + "\n";
break;
case 1765808134:
if (ptColor >= 0) this.colorShape(iShape, ptColor + 1, false);
break;
}
if (!isWild) break;
}switch (iShape) {
case 17:
iShape = 20;
continue;
case 20:
iShape = 32;
}
switch (--iShape) {
case 27:
iShape--;
break;
case 28:
iShape -= 2;
break;
}
if (iShape < 21) break;
}
return s;
}, "~S,~N,~N");
Clazz.defineMethod(c$, "setObjectProperty", 
function(){
var id = this.setShapeNameParameter(2);
return (this.chk ? "" : this.setObjectProp(id, this.tokAt(0), this.iToken));
});
Clazz.defineMethod(c$, "setShapeNameParameter", 
function(i){
var id = this.paramAsStr(i);
var isWild = id.equals("*");
if (id.length == 0) this.invArg();
if (isWild) {
switch (this.tokAt(i + 1)) {
case 0:
case 1073742335:
case 1073742072:
case 1073742334:
case 2097192:
case 2097194:
case 1765808134:
case 12291:
break;
default:
if (this.setMeshDisplayProperty(-1, 0, this.tokAt(i + 1))) break;
id += this.optParameterAsString(++i);
}
}if (this.tokAt(i + 1) == 268441089) id += this.paramAsStr(++i);
this.iToken = i;
return id;
}, "~N");
Clazz.defineMethod(c$, "setShapeProperty", 
function(shapeType, propertyName, propertyValue){
if (!this.chk) this.sm.setShapePropertyBs(shapeType, propertyName, propertyValue, null);
}, "~N,~S,~O");
Clazz.defineMethod(c$, "setShapePropertyBs", 
function(iShape, propertyName, propertyValue, bs){
if (!this.chk) this.sm.setShapePropertyBs(iShape, propertyName, propertyValue, bs);
}, "~N,~S,~O,JU.BS");
Clazz.defineMethod(c$, "setShapeSize", 
function(shapeType, rd){
if (!this.chk) this.sm.setShapeSizeBs(shapeType, 0, rd, null);
}, "~N,J.atomdata.RadiusData");
Clazz.defineMethod(c$, "setShapeSizeBs", 
function(shapeType, size, bs){
if (!this.chk) this.sm.setShapeSizeBs(shapeType, size, null, bs);
}, "~N,~N,JU.BS");
Clazz.defineMethod(c$, "setShapeTranslucency", 
function(shapeType, prefix, translucency, translucentLevel, bs){
if (translucentLevel == 3.4028235E38) translucentLevel = this.vwr.getFloat(570425353);
this.setShapeProperty(shapeType, "translucentLevel", Float.$valueOf(translucentLevel));
if (prefix == null) return;
if (bs == null) this.setShapeProperty(shapeType, prefix + "translucency", translucency);
 else if (!this.chk) this.setShapePropertyBs(shapeType, prefix + "translucency", translucency, bs);
}, "~N,~S,~S,~N,JU.BS");
Clazz.defineMethod(c$, "setSize", 
function(shape, scale){
var rd = null;
var tok = this.tokAt(1);
var isOnly = false;
switch (tok) {
case 1073742072:
this.restrictSelected(false, false);
case 1073742335:
break;
case 1073742334:
scale = 0;
break;
case 3:
case 2:
isOnly = (this.floatParameter(1) < 0 && (tok == 3 || this.tokAt(2) == 268441090));
default:
rd = this.encodeRadiusParameter(1, isOnly, true);
if (rd == null) return;
if (Float.isNaN(rd.value)) this.invArg();
}
if (rd == null) rd =  new J.atomdata.RadiusData(null, scale, J.atomdata.RadiusData.EnumType.FACTOR, J.c.VDW.AUTO);
if (isOnly) this.restrictSelected(false, false);
this.setShapeSize(shape, rd);
}, "~N,~N");
Clazz.defineMethod(c$, "setSizeBio", 
function(iShape){
var mad = 0;
switch (this.getToken(1).tok) {
case 1073742072:
this.restrictSelected(false, false);
case 1073742335:
mad = -1;
break;
case 1073742334:
break;
case 1639976963:
mad = -2;
break;
case 1111492620:
case 1073741922:
mad = -4;
break;
case 2:
if ((mad = (this.intParameterRange(1, 0, 1000) * 8)) == 2147483647) return;
break;
case 3:
mad = Math.round(this.floatParameterRange(1, -4.0, 4.0) * 2000);
if (mad == 2147483647) return;
if (mad < 0) {
this.restrictSelected(false, false);
mad = -mad;
}break;
case 10:
if (!this.chk) this.sm.loadShape(iShape);
this.setShapeProperty(iShape, "bitset", this.theToken.value);
return;
default:
this.error(6);
}
this.setShapeSizeBs(iShape, mad, null);
}, "~N");
Clazz.defineMethod(c$, "setUnits", 
function(units, tok){
if (tok == 545259568 && (units.toLowerCase().endsWith("hz") || JU.PT.isOneOf(units.toLowerCase(), ";default;angstroms;au;bohr;nanometers;nm;picometers;pm;vanderwaals;vdw;"))) {
if (!this.chk) this.vwr.setUnits(units, true);
} else if (tok == 545259558 && JU.PT.isOneOf(units.toLowerCase(), ";kcal;kj;")) {
if (!this.chk) this.vwr.setUnits(units, false);
} else {
this.errorStr2(50, "set " + JS.T.nameOf(tok), units);
}return true;
}, "~S,~N");
Clazz.defineMethod(c$, "toString", 
function(){
var str =  new JU.SB();
str.append("Eval\n pc:");
str.appendI(this.pc);
str.append("\n");
str.appendI(this.aatoken.length);
str.append(" statements\n");
for (var i = 0; i < this.aatoken.length; ++i) {
str.append("----\n");
var atoken = this.aatoken[i];
for (var j = 0; j < atoken.length; ++j) {
str.appendO(atoken[j]);
str.appendC('\n');
}
str.appendC('\n');
}
str.append("END\n");
return str.toString();
});
c$.iProcess = 0;
c$.commandHistoryLevelMax = 0;
c$.contextDepthMax = 100;
c$.scriptReportingLevel = 0;
});
;//5.0.1-v7 Thu Aug 27 08:24:49 CDT 2026
