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- version 11.2.13 of Jmol

    1: 
    2: /* Jmol 11.0 script library Jmol.js (aka Jmol-11.js) 1:34 AM 3/19/2007
    3: 
    4:  checkbox heirarchy -- see http://www.stolaf.edu/academics/jmol/docs/examples-11/check.htm
    5: 
    6:     based on:
    7:  *
    8:  * Copyright (C) 2004-2005  Miguel, Jmol Development, www.jmol.org
    9:  *
   10:  * Contact: hansonr@stolaf.edu
   11:  *
   12:  *  This library is free software; you can redistribute it and/or
   13:  *  modify it under the terms of the GNU Lesser General Public
   14:  *  License as published by the Free Software Foundation; either
   15:  *  version 2.1 of the License, or (at your option) any later version.
   16:  *
   17:  *  This library is distributed in the hope that it will be useful,
   18:  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
   19:  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
   20:  *  Lesser General Public License for more details.
   21:  *
   22:  *  You should have received a copy of the GNU Lesser General Public
   23:  *  License along with this library; if not, write to the Free Software
   24:  *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
   25:  *  02111-1307  USA.
   26:  */
   27: 
   28: // for documentation see www.jmol.org/jslibrary
   29: 
   30: try{if(typeof(_jmol)!="undefined")exit()
   31: 
   32: // place "?NOAPPLET" on your command line to check applet control action with a textarea
   33: 
   34: // bob hanson -- jmolResize(w,h) -- resizes absolutely or by percent (w or h 0.5 means 50%)
   35: // bob hanson -- jmolEvaluate -- evaluates molecular math 8:37 AM 2/23/2007
   36: // bob hanson -- jmolScriptMessage -- returns all "scriptStatus" messages 8:37 AM 2/23/2007
   37: // bob hanson -- jmolScriptEcho -- returns all "scriptEcho" messages 8:37 AM 2/23/2007
   38: // bob hanson -- jmolScriptWait -- 11:31 AM 5/2/2006
   39: // bob hanson -- remove trailing separatorHTML in radio groups -- 12:18 PM 5/6/2006
   40: // bob hanson -- adds support for dynamic DOM script nodes 7:04 AM 5/19/2006
   41: // bob hanson -- adds try/catch for wiki - multiple code passes 7:05 AM 5/19/2006
   42: // bob hanson -- auto-initiates to defaultdir/defaultjar -- change as desired.
   43: // bob hanson -- adding save/restore orientation w/ and w/o delay 11:49 AM 5/25/2006
   44: // bob hanson -- adding AjaxJS service 11:16 AM 6/3/2006
   45: // bob hanson -- fix for iframes not available for finding applet
   46: // bob hanson -- added applet fake ?NOAPPLET URL flag
   47: // bob hanson -- added jmolSetCallback(calbackName, funcName) 3:32 PM 6/13/2006
   48: //			used PRIOR to jmolApplet() or jmolAppletInline()
   49: //               added 4th array element in jmolRadioGroup -- title
   50: //               added <span> and id around link, checkbox, radio, menu
   51: //               fixing AJAX loads for MSIE/Opera-Mozilla incompatibility
   52: //            -- renamed Jmol-11.js from Jmol-new.js; JmolApplet.jar from JmolAppletProto.jar
   53: //	 	 renamed Jmol.js for Jmol 11 distribution
   54: //            -- modified jmolRestoreOrientation() to be immediate, no 1-second delay
   55: // bob hanson -- jmolScriptWait always returns a string -- 11:23 AM 9/16/2006
   56: // bh         -- jmolCommandInput()
   57: // bh         -- jmolSetTranslation(TF) -- forces translation even if there might be message callback issues
   58: // bh         -- minor fixes suggested by Angel
   59: 	  	
   60: var defaultdir = "."
   61: var defaultjar = "JmolApplet.jar"
   62: 
   63: var undefined; // for IE 5 ... wherein undefined is undefined
   64: 
   65: ////////////////////////////////////////////////////////////////
   66: // Basic Scripting infrastruture
   67: ////////////////////////////////////////////////////////////////
   68: 
   69: function jmolInitialize(codebaseDirectory, fileNameOrUseSignedApplet) {
   70:   if (_jmol.initialized) {
   71:     //alert("jmolInitialize() should only be called *ONCE* within a page");
   72:     return;
   73:   }
   74:   if (! codebaseDirectory) {
   75:     alert("codebaseDirectory is a required parameter to jmolInitialize");
   76:     codebaseDirectory = ".";
   77:   }
   78: 
   79:   if (codebaseDirectory.indexOf("http://") == 0 ||
   80:       codebaseDirectory.indexOf("https://") == 0)
   81:     alert("In general, an absolute URL is not recommended for codebaseDirectory.\n" +
   82: 	  "A directory- or docroot-relative reference is recommended.\n\n" +
   83: 	  "If you need to use an absolute URL (because, for example, the JAR and data\n" +
   84: 	  "files are on another server), then insert a space before\n" +
   85: 	  "\"http\" in your URL to avoid this warning message.");
   86: 
   87:   _jmolSetCodebase(codebaseDirectory);
   88:   _jmolGetJarFilename(fileNameOrUseSignedApplet);
   89:   _jmolOnloadResetForms();
   90:   _jmol.initialized = true;
   91: }
   92: 
   93: function jmolSetTranslation(TF) {
   94:   _jmol.params.doTranslate = ''+TF;
   95: }
   96: 
   97: function _jmolGetJarFilename(fileNameOrFlag) {
   98:   _jmol.archivePath =
   99:     (typeof(fileNameOrFlag) == "string"  ? fileNameOrFlag : (fileNameOrFlag ?  "JmolAppletSigned" : "JmolApplet") + "0.jar");
  100: }
  101: 
  102: function jmolSetDocument(doc) {
  103:   _jmol.currentDocument = doc;
  104: }
  105: 
  106: function jmolSetAppletColor(boxbgcolor, boxfgcolor, progresscolor) {
  107:   _jmolInitCheck();
  108:   _jmol.params.boxbgcolor = boxbgcolor;
  109:   if (boxfgcolor)
  110:     _jmol.params.boxfgcolor = boxfgcolor
  111:   else if (boxbgcolor == "white" || boxbgcolor == "#FFFFFF")
  112:     _jmol.params.boxfgcolor = "black";
  113:   else
  114:     _jmol.params.boxfgcolor = "white";
  115:   if (progresscolor)
  116:     _jmol.params.progresscolor = progresscolor;
  117:   if (_jmol.debugAlert)
  118:     alert(" boxbgcolor=" + _jmol.params.boxbgcolor +
  119:           " boxfgcolor=" + _jmol.params.boxfgcolor +
  120:           " progresscolor=" + _jmol.params.progresscolor);
  121: }
  122: 
  123: function jmolApplet(size, script, nameSuffix) {
  124:   _jmolInitCheck();
  125:   return _jmolApplet(size, null, script, nameSuffix);
  126: }
  127: 
  128: ////////////////////////////////////////////////////////////////
  129: // Basic controls
  130: ////////////////////////////////////////////////////////////////
  131: 
  132: function jmolButton(script, label, id, title) {
  133:   _jmolInitCheck();
  134:   if (id == undefined || id == null)
  135:     id = "jmolButton" + _jmol.buttonCount;
  136:   if (label == undefined || label == null)
  137:     label = script.substring(0, 32);
  138:   ++_jmol.buttonCount;
  139:   var scriptIndex = _jmolAddScript(script);
  140:   var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><input type='button' name='" + id + "' id='" + id +
  141:           "' value='" + label +
  142:           "' onClick='_jmolClick(" + scriptIndex + _jmol.targetText +
  143:           ")' onMouseover='_jmolMouseOver(" + scriptIndex +
  144:           ");return true' onMouseout='_jmolMouseOut()' " +
  145:           _jmol.buttonCssText + "/></span>";
  146:   if (_jmol.debugAlert)
  147:     alert(t);
  148:   return _jmolDocumentWrite(t);
  149: }
  150: 
  151: function jmolCheckbox(scriptWhenChecked, scriptWhenUnchecked,
  152:                       labelHtml, isChecked, id, title) {
  153:   _jmolInitCheck();
  154:   if (id == undefined || id == null)
  155:     id = "jmolCheckbox" + _jmol.checkboxCount;
  156:   ++_jmol.checkboxCount;
  157:   if (scriptWhenChecked == undefined || scriptWhenChecked == null ||
  158:       scriptWhenUnchecked == undefined || scriptWhenUnchecked == null) {
  159:     alert("jmolCheckbox requires two scripts");
  160:     return;
  161:   }
  162:   if (labelHtml == undefined || labelHtml == null) {
  163:     alert("jmolCheckbox requires a label");
  164:     return;
  165:   }
  166:   var indexChecked = _jmolAddScript(scriptWhenChecked);
  167:   var indexUnchecked = _jmolAddScript(scriptWhenUnchecked);
  168:   var eospan = "</span>"
  169:   var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><input type='checkbox' name='" + id + "' id='" + id +
  170:           "' onClick='_jmolCbClick(this," +
  171:           indexChecked + "," + indexUnchecked + _jmol.targetText +
  172:           ")' onMouseover='_jmolCbOver(this," + indexChecked + "," +
  173:           indexUnchecked +
  174:           ");return true' onMouseout='_jmolMouseOut()' " +
  175: 	  (isChecked ? "checked " : "") + _jmol.checkboxCssText + "/>" 
  176:   if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
  177: 	t += eospan
  178: 	eospan = "";
  179:   }
  180:   t += labelHtml +eospan;
  181:   if (_jmol.debugAlert)
  182:     alert(t);
  183:   return _jmolDocumentWrite(t);
  184: }
  185: 
  186: function jmolStartNewRadioGroup() {
  187:   ++_jmol.radioGroupCount;
  188: }
  189: 
  190: function jmolRadioGroup(arrayOfRadioButtons, separatorHtml, groupName, id, title) {
  191:   /*
  192: 
  193:     array: [radio1,radio2,radio3...]
  194:     where radioN = ["script","label",isSelected,"id","title"]
  195: 
  196:   */
  197: 
  198:   _jmolInitCheck();
  199:   var type = typeof arrayOfRadioButtons;
  200:   if (type != "object" || type == null || ! arrayOfRadioButtons.length) {
  201:     alert("invalid arrayOfRadioButtons");
  202:     return;
  203:   }
  204:   if (separatorHtml == undefined || separatorHtml == null)
  205:     separatorHtml = "&nbsp; ";
  206:   var len = arrayOfRadioButtons.length;
  207:   jmolStartNewRadioGroup();
  208:   if (!groupName)
  209:     groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1);
  210:   var t = "<span id='"+(id ? id : groupName)+"'>";
  211:   for (var i = 0; i < len; ++i) {
  212:     if (i == len - 1)
  213:       separatorHtml = "";
  214:     var radio = arrayOfRadioButtons[i];
  215:     type = typeof radio;
  216:     if (type == "object") {
  217:       t += _jmolRadio(radio[0], radio[1], radio[2], separatorHtml, groupName, (radio.length > 3 ? radio[3]: (id ? id : groupName)+"_"+i), (radio.length > 4 ? radio[4] : 0), title);
  218:     } else {
  219:       t += _jmolRadio(radio, null, null, separatorHtml, groupName, (id ? id : groupName)+"_"+i, title);
  220:     }
  221:   }
  222:   t+="</span>"
  223:   if (_jmol.debugAlert)
  224:     alert(t);
  225:   return _jmolDocumentWrite(t);
  226: }
  227: 
  228: 
  229: function jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
  230:   _jmolInitCheck();
  231:   if (_jmol.radioGroupCount == 0)
  232:     ++_jmol.radioGroupCount;
  233:   var t = _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, (id ? id : groupName + "_" + _jmol.radioCount), title ? title : 0);
  234:   if (_jmol.debugAlert)
  235:     alert(t);
  236:   return _jmolDocumentWrite(t);
  237: }
  238: 
  239: function jmolLink(script, label, id, title) {
  240:   _jmolInitCheck();
  241:   if (id == undefined || id == null)
  242:     id = "jmolLink" + _jmol.linkCount;
  243:   if (label == undefined || label == null)
  244:     label = script.substring(0, 32);
  245:   ++_jmol.linkCount;
  246:   var scriptIndex = _jmolAddScript(script);
  247:   var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><a name='" + id + "' id='" + id + 
  248:           "' href='javascript:_jmolClick(" + scriptIndex + _jmol.targetText + ");' onMouseover='_jmolMouseOver(" + scriptIndex +
  249:           ");return true;' onMouseout='_jmolMouseOut()' " +
  250:           _jmol.linkCssText + ">" + label + "</a></span>";
  251:   if (_jmol.debugAlert)
  252:     alert(t);
  253:   return _jmolDocumentWrite(t);
  254: }
  255: 
  256: function jmolCommandInput(label, size, id, title) {
  257:   _jmolInitCheck();
  258:   if (id == undefined || id == null)
  259:     id = "jmolCmd" + _jmol.cmdCount;
  260:   if (label == undefined || label == null)
  261:     label = "Execute";
  262:   if (size == undefined || isNaN(size))
  263:     size = 60;
  264:   ++_jmol.cmdCount;
  265:   var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><input name='" + id + "' id='" + id + 
  266:           "' size='"+size+"'><input type=button value = '"+label+"' onClick='jmolScript(document.getElementById(\""+id+"\").value" + _jmol.targetText + ")'/></span>";
  267:   if (_jmol.debugAlert)
  268:     alert(t);
  269:   return _jmolDocumentWrite(t);
  270: }
  271: 
  272: function jmolMenu(arrayOfMenuItems, size, id, title) {
  273:   _jmolInitCheck();
  274:   if (id == undefined || id == null)
  275:     id = "jmolMenu" + _jmol.menuCount;
  276:   ++_jmol.menuCount;
  277:   var type = typeof arrayOfMenuItems;
  278:   if (type != null && type == "object" && arrayOfMenuItems.length) {
  279:     var len = arrayOfMenuItems.length;
  280:     if (typeof size != "number" || size == 1)
  281:       size = null;
  282:     else if (size < 0)
  283:       size = len;
  284:     var sizeText = size ? " size='" + size + "' " : "";
  285:     var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><select name='" + id + "' id='" + id +
  286:             "' onChange='_jmolMenuSelected(this" + _jmol.targetText + ")'" +
  287:             sizeText + _jmol.menuCssText + ">";
  288:     for (var i = 0; i < len; ++i) {
  289:       var menuItem = arrayOfMenuItems[i];
  290:       type = typeof menuItem;
  291:       var script, text;
  292:       var isSelected = undefined;
  293:       if (type == "object" && menuItem != null) {
  294:         script = menuItem[0];
  295:         text = menuItem[1];
  296:         isSelected = menuItem[2];
  297:       } else {
  298:         script = text = menuItem;
  299:       }
  300:       if (text == undefined || text == null)
  301:         text = script;		
  302: 	  if (script=="#optgroup") {
  303:         t += "<optgroup label='" + text + "'>";	  
  304: 	  } else if (script=="#optgroupEnd") {
  305:         t += "</optgroup>";	  
  306: 	  } else {		
  307:         var scriptIndex = _jmolAddScript(script);
  308:         var selectedText = isSelected ? "' selected>" : "'>";
  309:         t += "<option value='" + scriptIndex + selectedText + text + "</option>";
  310: 	  }
  311:     }
  312:     t += "</select></span>";
  313:     if (_jmol.debugAlert)
  314:       alert(t);
  315:     return _jmolDocumentWrite(t);
  316:   }
  317: }
  318: 
  319: function jmolHtml(html) {
  320:   return _jmolDocumentWrite(html);
  321: }
  322: 
  323: function jmolBr() {
  324:   return _jmolDocumentWrite("<br />");
  325: }
  326: 
  327: ////////////////////////////////////////////////////////////////
  328: // advanced scripting functions
  329: ////////////////////////////////////////////////////////////////
  330: 
  331: function jmolDebugAlert(enableAlerts) {
  332:   _jmol.debugAlert = (enableAlerts == undefined || enableAlerts)
  333: }
  334: 
  335: function jmolAppletInline(size, inlineModel, script, nameSuffix) {
  336:   _jmolInitCheck();
  337:   return _jmolApplet(size, _jmolSterilizeInline(inlineModel),
  338:                      script, nameSuffix);
  339: }
  340: 
  341: function jmolSetTarget(targetSuffix) {
  342:   _jmol.targetSuffix = targetSuffix;
  343:   _jmol.targetText = targetSuffix ? ",\"" + targetSuffix + "\"" : "";
  344: }
  345: 
  346: function jmolScript(script, targetSuffix) {
  347:   if (script) {
  348:     _jmolCheckBrowser();
  349:     if (targetSuffix == "all") {
  350:       with (_jmol) {
  351: 	for (var i = 0; i < appletSuffixes.length; ++i) {
  352: 	  var applet = _jmolGetApplet(appletSuffixes[i]);
  353:           if (applet) applet.script(script);
  354:         }
  355:       }
  356:     } else {
  357:       var applet=_jmolGetApplet(targetSuffix);
  358:       if (applet) applet.script(script);
  359:     }
  360:   }
  361: }
  362: 
  363: function jmolLoadInline(model, targetSuffix) {
  364:   if (!model)return
  365:   var applet=_jmolGetApplet(targetSuffix);
  366:   if (applet)applet.loadInline(model);
  367: }
  368: 
  369: function jmolLoadInlineScript(model, script, targetSuffix) {
  370:   if (!model)return
  371:   var applet=_jmolGetApplet(targetSuffix);
  372:   if (applet)applet.loadInline(model, script);
  373: }
  374: 
  375: function jmolLoadInlineArray(ModelArray, script, targetSuffix) {
  376:   if (!model)return
  377:   if (!script)script=""
  378:   var applet=_jmolGetApplet(targetSuffix);
  379:   if (applet)applet.loadInlineArray(ModelArray, script);
  380: }
  381: 
  382: function jmolCheckBrowser(action, urlOrMessage, nowOrLater) {
  383:   if (typeof action == "string") {
  384:     action = action.toLowerCase();
  385:     if (action != "alert" && action != "redirect" && action != "popup")
  386:       action = null;
  387:   }
  388:   if (typeof action != "string")
  389:     alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +
  390:           "action must be 'alert', 'redirect', or 'popup'");
  391:   else {
  392:     if (typeof urlOrMessage != "string")
  393:       alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +
  394:             "urlOrMessage must be a string");
  395:     else {
  396:       _jmol.checkBrowserAction = action;
  397:       _jmol.checkBrowserUrlOrMessage = urlOrMessage;
  398:     }
  399:   }
  400:   if (typeof nowOrLater == "string" && nowOrLater.toLowerCase() == "now")
  401:     _jmolCheckBrowser();
  402: }
  403: 
  404: ////////////////////////////////////////////////////////////////
  405: // Cascading Style Sheet Class support
  406: ////////////////////////////////////////////////////////////////
  407: 
  408: function jmolSetAppletCssClass(appletCssClass) {
  409:   if (_jmol.hasGetElementById) {
  410:     _jmol.appletCssClass = appletCssClass;
  411:     _jmol.appletCssText = appletCssClass ? "class='" + appletCssClass + "' " : "";
  412:   }
  413: }
  414: 
  415: function jmolSetButtonCssClass(buttonCssClass) {
  416:   if (_jmol.hasGetElementById) {
  417:     _jmol.buttonCssClass = buttonCssClass;
  418:     _jmol.buttonCssText = buttonCssClass ? "class='" + buttonCssClass + "' " : "";
  419:   }
  420: }
  421: 
  422: function jmolSetCheckboxCssClass(checkboxCssClass) {
  423:   if (_jmol.hasGetElementById) {
  424:     _jmol.checkboxCssClass = checkboxCssClass;
  425:     _jmol.checkboxCssText = checkboxCssClass ? "class='" + checkboxCssClass + "' " : "";
  426:   }
  427: }
  428: 
  429: function jmolSetRadioCssClass(radioCssClass) {
  430:   if (_jmol.hasGetElementById) {
  431:     _jmol.radioCssClass = radioCssClass;
  432:     _jmol.radioCssText = radioCssClass ? "class='" + radioCssClass + "' " : "";
  433:   }
  434: }
  435: 
  436: function jmolSetLinkCssClass(linkCssClass) {
  437:   if (_jmol.hasGetElementById) {
  438:     _jmol.linkCssClass = linkCssClass;
  439:     _jmol.linkCssText = linkCssClass ? "class='" + linkCssClass + "' " : "";
  440:   }
  441: }
  442: 
  443: function jmolSetMenuCssClass(menuCssClass) {
  444:   if (_jmol.hasGetElementById) {
  445:     _jmol.menuCssClass = menuCssClass;
  446:     _jmol.menuCssText = menuCssClass ? "class='" + menuCssClass + "' " : "";
  447:   }
  448: }
  449: 
  450: ////////////////////////////////////////////////////////////////
  451: // functions for INTERNAL USE ONLY which are subject to change
  452: // use at your own risk ... you have been WARNED!
  453: ////////////////////////////////////////////////////////////////
  454: var _jmol = {
  455:   currentDocument: document,
  456: 
  457:   debugAlert: false,
  458:   
  459:   codebase: ".",
  460:   modelbase: ".",
  461:   
  462:   appletCount: 0,
  463:   appletSuffixes: [],
  464:   
  465:   buttonCount: 0,
  466:   checkboxCount: 0,
  467:   linkCount: 0,
  468:   cmdCount: 0,
  469:   menuCount: 0,
  470:   radioCount: 0,
  471:   radioGroupCount: 0,
  472:   
  473:   appletCssClass: null,
  474:   appletCssText: "",
  475:   buttonCssClass: null,
  476:   buttonCssText: "",
  477:   checkboxCssClass: null,
  478:   checkboxCssText: "",
  479:   radioCssClass: null,
  480:   radioCssText: "",
  481:   linkCssClass: null,
  482:   linkCssText: "",
  483:   menuCssClass: null,
  484:   menuCssText: "",
  485:   
  486:   targetSuffix: 0,
  487:   targetText: "",
  488:   scripts: [""],
  489:   params: {
  490: 	progressbar: "true",
  491: 	progresscolor: "blue",
  492: 	boxbgcolor: "black",
  493: 	boxfgcolor: "white",
  494: 	boxmessage: "Downloading JmolApplet ..."
  495:   },
  496:   ua: navigator.userAgent.toLowerCase(),
  497:   uaVersion: parseFloat(navigator.appVersion),
  498:   
  499:   os: "unknown",
  500:   browser: "unknown",
  501:   browserVersion: 0,
  502:   hasGetElementById: !!document.getElementById,
  503:   isJavaEnabled: navigator.javaEnabled(),
  504:   isNetscape47Win: false,
  505:   isIEWin: false,
  506:   useIEObject: false,
  507:   useHtml4Object: false,
  508:   
  509:   windowsClassId: "clsid:8AD9C840-044E-11D1-B3E9-00805F499D93",
  510:   windowsCabUrl:
  511:    "http://java.sun.com/update/1.5.0/jinstall-1_5_0_05-windows-i586.cab",
  512: 
  513:   isBrowserCompliant: false,
  514:   isJavaCompliant: false,
  515:   isFullyCompliant: false,
  516: 
  517:   initialized: false,
  518:   initChecked: false,
  519:   
  520:   browserChecked: false,
  521:   checkBrowserAction: "alert",
  522:   checkBrowserUrlOrMessage: null,
  523: 
  524:   archivePath: null, // JmolApplet0.jar OR JmolAppletSigned0.jar
  525: 
  526:   previousOnloadHandler: null,
  527:   ready: {}
  528: }
  529: 
  530: with (_jmol) {
  531: 
  532:   function _jmolTestUA(candidate) {
  533:     var ua = _jmol.ua;
  534:     var index = ua.indexOf(candidate);
  535:     if (index < 0)
  536:       return false;
  537:     _jmol.browser = candidate;
  538:     _jmol.browserVersion = parseFloat(ua.substring(index+candidate.length+1));
  539:     return true;
  540:   }
  541:   
  542:   function _jmolTestOS(candidate) {
  543:     if (_jmol.ua.indexOf(candidate) < 0)
  544:       return false;
  545:     _jmol.os = candidate;
  546:     return true;
  547:   }
  548:   
  549:   _jmolTestUA("konqueror") ||
  550:   _jmolTestUA("safari") ||
  551:   _jmolTestUA("omniweb") ||
  552:   _jmolTestUA("opera") ||
  553:   _jmolTestUA("webtv") ||
  554:   _jmolTestUA("icab") ||
  555:   _jmolTestUA("msie") ||
  556:   (_jmol.ua.indexOf("compatible") < 0 && _jmolTestUA("mozilla"));
  557:   
  558:   _jmolTestOS("linux") ||
  559:   _jmolTestOS("unix") ||
  560:   _jmolTestOS("mac") ||
  561:   _jmolTestOS("win");
  562: 
  563:   isNetscape47Win = (os == "win" && browser == "mozilla" &&
  564:                      browserVersion >= 4.78 && browserVersion <= 4.8);
  565: 
  566:   if (os == "win") {
  567:     isBrowserCompliant = hasGetElementById;
  568:   } else if (os == "mac") { // mac is the problem child :-(
  569:     if (browser == "mozilla" && browserVersion >= 5) {
  570:       // miguel 2004 11 17
  571:       // checking the plugins array does not work because
  572:       // Netscape 7.2 OS X still has Java 1.3.1 listed even though
  573:       // javaplugin.sf.net is installed to upgrade to 1.4.2
  574:       eval("try {var v = java.lang.System.getProperty('java.version');" +
  575:            " _jmol.isBrowserCompliant = v >= '1.4.2';" +
  576:            " } catch (e) { }");
  577:     } else if (browser == "opera" && browserVersion <= 7.54) {
  578:       isBrowserCompliant = false;
  579:     } else {
  580:       isBrowserCompliant = hasGetElementById &&
  581:         !((browser == "msie") ||
  582:           (browser == "safari" && browserVersion < 125.12));
  583:     }
  584:   } else if (os == "linux" || os == "unix") {
  585:     if (browser == "konqueror" && browserVersion <= 3.3)
  586:       isBrowserCompliant = false;
  587:     else
  588:       isBrowserCompliant = hasGetElementById;
  589:   } else { // other OS
  590:     isBrowserCompliant = hasGetElementById;
  591:   }
  592: 
  593:   // possibly more checks in the future for this
  594:   isJavaCompliant = isJavaEnabled;
  595: 
  596:   isFullyCompliant = isBrowserCompliant && isJavaCompliant;
  597: 
  598:   // IE5.5 works just fine ... but let's push them to Sun Java
  599:   isIEWin = (os == "win" && browser == "msie" && browserVersion >= 5.5);
  600:   useIEObject = isIEWin;
  601:   useHtml4Object =
  602:    (os != "mac" && browser == "mozilla" && browserVersion >= 5) ||
  603:    (os == "win" && browser == "opera" && browserVersion >= 8) ||
  604:    (os == "mac" && browser == "safari" && browserVersion >= 412.2);
  605: 
  606:  doTranslate = true;
  607:  haveSetTranslate = false;
  608: }
  609: 
  610: function jmolSetCallback(callbackName,funcName) {
  611:   _jmol.params[callbackName] = funcName
  612: }
  613: 
  614: function jmolSetLogLevel(n) {
  615:   _jmol.params.logLevel = ''+n;
  616: }
  617: 
  618: 	/*  AngelH, mar2007:
  619: 		By (re)setting these variables in the webpage before calling jmolApplet(), 
  620: 		a custom message can be provided (e.g. localized for user's language) when no Java is installed.
  621: 	*/
  622: if (noJavaMsg==undefined) var noJavaMsg = 
  623:         "You do not have Java applets enabled in your web browser, or your browser is blocking this applet.<br />\n" +
  624:         "Check the warning message from your browser and/or enable Java applets in<br />\n" +
  625:         "your web browser preferences, or install the Java Runtime Environment from <a href='http://www.java.com'>www.java.com</a><br />";
  626: if (noJavaMsg2==undefined) var noJavaMsg2 = 
  627:         "You do not have the<br />\n" +
  628:         "Java Runtime Environment<br />\n" +
  629:         "installed for applet support.<br />\n" +
  630:         "Visit <a href='http://www.java.com'>www.java.com</a>";
  631: function _jmolApplet(size, inlineModel, script, nameSuffix) {
  632: 	/*  AngelH, mar2007
  633: 		Fixed percent / pixel business, to avoid browser errors:
  634: 		put "px" where needed, avoid where not.		
  635: 	*/
  636:   with (_jmol) {
  637:     if (! nameSuffix)
  638:       nameSuffix = appletCount;
  639:     appletSuffixes.push(nameSuffix);
  640:     ++appletCount;
  641:     if (! script)
  642:       script = "select *";
  643:     var sz = _jmolGetAppletSize(size);
  644:     var widthAndHeight = " width='" + sz[0] + "' height='" + sz[1] + "' ";
  645:     var tHeader, tFooter;
  646: 
  647:     if (useIEObject || useHtml4Object) {
  648:       params.name = 'jmolApplet' + nameSuffix;
  649:       params.archive = archivePath;
  650:       params.mayscript = 'true';
  651:       params.codebase = codebase;
  652:     }
  653:     if (useIEObject) { // use MSFT IE6 object tag with .cab file reference
  654:       winCodebase = (windowsCabUrl ? " codebase='" + windowsCabUrl + "'\n" : "");
  655:       tHeader = 
  656:         "<object name='jmolApplet" + nameSuffix +
  657:         "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
  658: 	" classid='" + windowsClassId + "'\n" + winCodebase + widthAndHeight + ">\n";
  659:         params.code = 'JmolApplet';
  660:       tFooter = "</object>";
  661:     } else if (useHtml4Object) { // use HTML4 object tag
  662:       tHeader = 
  663:         "<object name='jmolApplet" + nameSuffix +
  664:         "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
  665: 	" classid='java:JmolApplet'\n" +
  666:         " type='application/x-java-applet'\n" +
  667:         widthAndHeight + ">\n";
  668:       tFooter = "</object>";
  669:     } else { // use applet tag
  670:       tHeader = 
  671:         "<applet name='jmolApplet" + nameSuffix +
  672:         "' id='jmolApplet" + nameSuffix +
  673:         "' " + appletCssText +
  674:         " code='JmolApplet'" +
  675:         " archive='" + archivePath + "' codebase='" + codebase + "'\n" +
  676: 		widthAndHeight +
  677:         " mayscript='true'>\n";
  678:       tFooter = "</applet>";
  679:     }
  680:     var visitJava;
  681:     if (isIEWin || useHtml4Object) {
  682: 		var szX = "width:" + sz[0]
  683: 		if ( szX.indexOf("%")==-1 ) szX+="px" 
  684: 		var szY = "height:" + sz[1]
  685: 		if ( szY.indexOf("%")==-1 ) szY+="px" 
  686:       visitJava =
  687:         "<p style='background-color:yellow; color:black; " +
  688: 		szX + ";" + szY + ";" +
  689:         // why doesn't this vertical-align work?
  690: 	"text-align:center;vertical-align:middle;'>\n" +
  691: 		noJavaMsg +
  692:         "</p>";
  693:     } else {
  694:       visitJava =
  695:         "<table bgcolor='yellow'><tr>" +
  696:         "<td align='center' valign='middle' " + widthAndHeight + "><font color='black'>\n" +
  697: 		noJavaMsg2 +
  698:         "</font></td></tr></table>";
  699:     }
  700:     params.loadInline = (inlineModel ? inlineModel : "");
  701:     params.script = (script ? _jmolSterilizeScript(script) : "");
  702:     var t = tHeader + _jmolParams() + visitJava + tFooter;
  703:     jmolSetTarget(nameSuffix);
  704:     ready["jmolApplet" + nameSuffix] = false;
  705:     if (_jmol.debugAlert)
  706:       alert(t);
  707:     return _jmolDocumentWrite(t);
  708:   }
  709: }
  710: 
  711: function _jmolParams() {
  712:  var t = "";
  713:  for (i in _jmol.params)
  714: 	if(_jmol.params[i]!="")
  715: 		 t+="  <param name='"+i+"' value='"+_jmol.params[i]+"' />\n";
  716:  return t
  717: }
  718: 
  719: function _jmolInitCheck() {
  720:   if (_jmol.initChecked)
  721:     return;
  722:   _jmol.initChecked = true;
  723:   if (_jmol.initialized)
  724:     return;
  725:   jmolInitialize(defaultdir, defaultjar)
  726: }
  727: 
  728: function _jmolCheckBrowser() {
  729:   with (_jmol) {
  730:     if (browserChecked)
  731:       return;
  732:     browserChecked = true;
  733:   
  734:     if (isFullyCompliant)
  735:       return true;
  736: 
  737:     if (checkBrowserAction == "redirect")
  738:       location.href = checkBrowserUrlOrMessage;
  739:     else if (checkBrowserAction == "popup")
  740:       _jmolPopup(checkBrowserUrlOrMessage);
  741:     else {
  742:       var msg = checkBrowserUrlOrMessage;
  743:       if (msg == null)
  744:         msg = "Your web browser is not fully compatible with Jmol\n\n" +
  745:               "browser: " + browser +
  746:               "   version: " + browserVersion +
  747:               "   os: " + os +
  748:               "\n\n" + ua;
  749:       alert(msg);
  750:     }
  751:   }
  752:   return false;
  753: }
  754: 
  755: function _jmolDocumentWrite(text) {
  756:   if (_jmol.currentDocument)
  757:     _jmol.currentDocument.write(text);
  758:   return text;
  759: }
  760: 
  761: function _jmolPopup(url) {
  762:   var popup = window.open(url, "JmolPopup",
  763:                           "left=150,top=150,height=400,width=600," +
  764:                           "directories=yes,location=yes,menubar=yes," +
  765:                           "toolbar=yes," +
  766:                           "resizable=yes,scrollbars=yes,status=yes");
  767:   if (popup.focus)
  768:     poup.focus();
  769: }
  770: 
  771: function _jmolReadyCallback(name) {
  772:   if (_jmol.debugAlert)
  773:     alert(name + " is ready");
  774:   _jmol.ready["" + name] = true;
  775: }
  776: 
  777: function _jmolSterilizeScript(script) {
  778:   var inlineScript = script.replace(/'/g, "&#39;");
  779:   if (_jmol.debugAlert)
  780:     alert("script:\n" + inlineScript);
  781:   return inlineScript;
  782: }
  783: 
  784: function _jmolSterilizeInline(model) {
  785:   var inlineModel =
  786:     model.replace(/\r|\n|\r\n/g, "|").replace(/'/g, "&#39;");
  787:   if (_jmol.debugAlert)
  788:     alert("inline model:\n" + inlineModel);
  789:   return inlineModel;
  790: }
  791: 
  792: 	/*  AngelH, mar2007:
  793: 		By (re)setting this variable in the webpage before calling jmolApplet(), limits for applet size can be overriden.
  794: 	*/
  795: 
  796: 	/* hansonr, jun2007:
  797: 		2048 standard for GeoWall (http://geowall.geo.lsa.umich.edu/home.html)
  798: 	*/
  799: 
  800: if (allowedJmolSize==undefined) var allowedJmolSize = [25, 2048, 300]   // min, max, default (pixels)
  801: function _jmolGetAppletSize(size) {
  802: 	/*  AngelH, mar2007
  803: 		Accepts single number or 2-value array, each one can be either:
  804: 	   percent (text string ending %), decimal 0 to 1 (percent/100), number, or text string (interpreted as nr.)
  805: 	   Size is now returned as string or number, no "px".
  806: 	*/
  807:   var width, height;
  808:   if ( (typeof size) == "object" && size != null ) {
  809:     width = size[0]; height = size[1];
  810:   } else {
  811:     width = height = size;
  812:   }
  813:   // if percent, leave it as it is:
  814:   if ( width.toString().charAt(width.toString().length-1) != "%" ) {
  815:     width = parseFloat(width);	// convert to nr., or strip text, or make zero
  816: 	if ( width <= 1 && width > 0 ) { width = (width*100)+"%" }	// decimal: convert to percent and quit
  817: 	else if ( width >= allowedJmolSize[0] && width <= allowedJmolSize[1] ) { width = parseInt(width) }	// accept only that range (pixels)
  818: 	else { width = allowedJmolSize[2] }	// default size 300 pixels
  819:   }
  820:   if ( height.toString().charAt(height.toString().length-1) != "%" ) {
  821:     height = parseFloat(height);
  822: 	if ( height <= 1 && height > 0 ) { height = (height*100)+"%" }
  823: 	else if ( height >= allowedJmolSize[0] && height <= allowedJmolSize[1] ) { height = parseInt(height) }
  824: 	else { height = allowedJmolSize[2] }
  825:   }
  826:   return [width, height];
  827: }
  828: 
  829: function _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
  830:   ++_jmol.radioCount;
  831:   if (groupName == undefined || groupName == null)
  832:     groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1);
  833:   if (!script)
  834:     return "";
  835:   if (labelHtml == undefined || labelHtml == null)
  836:     labelHtml = script.substring(0, 32);
  837:   if (! separatorHtml)
  838:     separatorHtml = "";
  839:   var scriptIndex = _jmolAddScript(script);
  840:   var eospan = "</span>"
  841:   var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><input name='" 
  842: 	+ groupName + "' id='"+id+"' type='radio' onClick='_jmolClick(" +
  843:          scriptIndex + _jmol.targetText + ");return true;' onMouseover='_jmolMouseOver(" +
  844:          scriptIndex + ");return true;' onMouseout='_jmolMouseOut()' " +
  845: 	 (isChecked ? "checked " : "") + _jmol.radioCssText + "/>"
  846:   if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
  847: 	t += eospan
  848: 	eospan = "";
  849:   }
  850:   t += labelHtml +eospan + separatorHtml;
  851:   return t;
  852: }
  853: 
  854: function _jmolFindApplet(target) {
  855:   // first look for the target in the current window
  856:   var applet = _jmolFindAppletInWindow(window, target);
  857:   // THEN look for the target in child frames
  858:   if (applet == undefined)
  859:     applet = _jmolSearchFrames(window, target);
  860:   // FINALLY look for the target in sibling frames
  861:   if (applet == undefined)
  862:     applet = _jmolSearchFrames(top, target); // look starting in top frame
  863:   return applet;
  864: }
  865: 
  866: function _jmolGetApplet(targetSuffix){
  867:  var target = "jmolApplet" + (targetSuffix ? targetSuffix : "0");
  868:  var applet = _jmolFindApplet(target);
  869:  if (applet) return applet
  870:  if(!_jmol.alerted)alert("could not find applet " + target);
  871:  _jmol.alerted = true;
  872:  return null
  873: }
  874: 
  875: function _jmolSearchFrames(win, target) {
  876:   var applet;
  877:   var frames = win.frames;
  878:   if (frames && frames.length) { // look in all the frames below this window
  879:     for (var i = 0; i < frames.length; ++i) {
  880:       applet = _jmolSearchFrames(frames[i], target);
  881:       if (applet)
  882:         break;
  883:     }
  884:   } else { // look for the applet in this window
  885:    applet = _jmolFindAppletInWindow(win, target)
  886:   }
  887:   return applet;
  888: }
  889: 
  890: function _jmolFindAppletInWindow(win, target) {
  891:     var doc = win.document;
  892:     // getElementById fails on MacOSX Safari & Mozilla	
  893:     if (_jmol.useHtml4Object || _jmol.useIEObject)
  894:       return doc.getElementById(target);
  895:     else if (doc.applets)
  896:       return doc.applets[target];
  897:     else
  898:       return doc[target]; 
  899: }
  900: 
  901: function _jmolAddScript(script) {
  902:   if (! script)
  903:     return 0;
  904:   var index = _jmol.scripts.length;
  905:   _jmol.scripts[index] = script;
  906:   return index;
  907: }
  908: 
  909: function _jmolClick(scriptIndex, targetSuffix) {
  910:   jmolScript(_jmol.scripts[scriptIndex], targetSuffix);
  911: }
  912: 
  913: function _jmolMenuSelected(menuObject, targetSuffix) {
  914:   var scriptIndex = menuObject.value;
  915:   if (scriptIndex != undefined) {
  916:     jmolScript(_jmol.scripts[scriptIndex], targetSuffix);
  917:     return;
  918:   }
  919:   var len = menuObject.length;
  920:   if (typeof len == "number") {
  921:     for (var i = 0; i < len; ++i) {
  922:       if (menuObject[i].selected) {
  923:         _jmolClick(menuObject[i].value, targetSuffix);
  924: 	return;
  925:       }
  926:     }
  927:   }
  928:   alert("?Que? menu selected bug #8734");
  929: }
  930: 
  931: 
  932: _jmol.checkboxMasters = new Array();
  933: _jmol.checkboxItems = new Array();
  934: 
  935: function jmolSetCheckboxGroup(chkMaster,chkBox) {
  936: 	var id = chkMaster;
  937: 	if(typeof(id)=="number")id = "jmolCheckbox" + id;
  938: 	chkMaster = document.getElementById(id);
  939: 	if (!chkMaster)alert("jmolSetCheckboxGroup: master checkbox not found: " + id);
  940: 	var m = _jmol.checkboxMasters[id] = new Array();
  941: 	m.chkMaster = chkMaster;
  942: 	m.chkGroup = new Array();
  943: 	for (var i = 1; i < arguments.length; i++){
  944: 		var id = arguments[i];
  945: 		if(typeof(id)=="number")id = "jmolCheckbox" + id;
  946: 		checkboxItem = document.getElementById(id);
  947: 		if (!checkboxItem)alert("jmolSetCheckboxGroup: group checkbox not found: " + id);
  948: 		m.chkGroup[id] = checkboxItem;
  949: 		_jmol.checkboxItems[id] = m;
  950: 	}
  951: }
  952: 
  953: function _jmolNotifyMaster(m){
  954: 	//called when a group item is checked
  955: 	var allOn = true;
  956: 	var allOff = true;
  957: 	for (var chkBox in m.chkGroup){
  958: 		if(m.chkGroup[chkBox].checked)
  959: 			allOff = false;
  960: 		else
  961: 			allOn = false;
  962: 	}
  963: 	if (allOn)m.chkMaster.checked = true;	
  964: 	if (allOff)m.chkMaster.checked = false;
  965: 	if ((allOn || allOff) && _jmol.checkboxItems[m.chkMaster.id])
  966: 		_jmolNotifyMaster(_jmol.checkboxItems[m.chkMaster.id])
  967: }
  968: 
  969: function _jmolNotifyGroup(m, isOn){
  970: 	//called when a master item is checked
  971: 	for (var chkBox in m.chkGroup){
  972: 		var item = m.chkGroup[chkBox]
  973: 		item.checked = isOn;
  974: 		if (_jmol.checkboxMasters[item.id])
  975: 			_jmolNotifyGroup(_jmol.checkboxMasters[item.id], isOn)
  976: 	}
  977: }
  978: 
  979: function _jmolCbClick(ckbox, whenChecked, whenUnchecked, targetSuffix) {
  980:   _jmolClick(ckbox.checked ? whenChecked : whenUnchecked, targetSuffix);
  981:   if(_jmol.checkboxMasters[ckbox.id])
  982: 	_jmolNotifyGroup(_jmol.checkboxMasters[ckbox.id], ckbox.checked)
  983:   if(_jmol.checkboxItems[ckbox.id])
  984: 	_jmolNotifyMaster(_jmol.checkboxItems[ckbox.id])
  985: }
  986: 
  987: function _jmolCbOver(ckbox, whenChecked, whenUnchecked) {
  988:   window.status = _jmol.scripts[ckbox.checked ? whenUnchecked : whenChecked];
  989: }
  990: 
  991: function _jmolMouseOver(scriptIndex) {
  992:   window.status = _jmol.scripts[scriptIndex];
  993: }
  994: 
  995: function _jmolMouseOut() {
  996:   window.status = " ";
  997:   return true;
  998: }
  999: 
 1000: function _jmolSetCodebase(codebase) {
 1001:   _jmol.codebase = codebase ? codebase : ".";
 1002:   if (_jmol.debugAlert)
 1003:     alert("jmolCodebase=" + _jmol.codebase);
 1004: }
 1005: 
 1006: function _jmolOnloadResetForms() {
 1007:   _jmol.previousOnloadHandler = window.onload;
 1008:   window.onload =
 1009:   function() {
 1010:     with (_jmol) {
 1011:       if (buttonCount+checkboxCount+menuCount+radioCount+radioGroupCount > 0) {
 1012:         var forms = document.forms;
 1013:         for (var i = forms.length; --i >= 0; )
 1014:           forms[i].reset();
 1015:       }
 1016:       if (previousOnloadHandler)
 1017:         previousOnloadHandler();
 1018:     }
 1019:   }
 1020: }
 1021: 
 1022: ////////////////////////////////////
 1023: /////extensions for getProperty/////
 1024: ////////////////////////////////////
 1025: 
 1026: 
 1027: function _jmolEvalJSON(s,key){
 1028:  s=s+""
 1029:  if(!s)return []
 1030:  if(s.charAt(0)!="{"){
 1031: 	if(s.indexOf(" | ")>=0)s=s.replace(/\ \|\ /g, "\n")
 1032: 	return s
 1033:  }
 1034:  var A = eval("("+s+")")
 1035:  if(!A)return
 1036:  if(key && A[key])A=A[key]
 1037:  return A
 1038: }
 1039: 
 1040: function _jmolEnumerateObject(A,key){
 1041:  var sout=""
 1042:  if(typeof(A) == "string" && A!="null"){
 1043: 	sout+="\n"+key+"=\""+A+"\""
 1044:  }else if(!isNaN(A)||A==null){
 1045: 	sout+="\n"+key+"="+(A+""==""?"null":A)
 1046:  }else if(A.length){
 1047:     sout+=key+"=new Array()"
 1048:     for(var i=0;i<A.length;i++){
 1049: 	sout+="\n"
 1050: 	if(typeof(A[i]) == "object"||typeof(A[i]) == "array"){
 1051: 		sout+=_jmolEnumerateObject(A[i],key+"["+i+"]")
 1052: 	}else{
 1053: 		sout+=key+"["+i+"]="+(typeof(A[i]) == "string" && A[i]!="null"?"\""+A[i].replace(/\"/g,"\\\"")+"\"":A[i])
 1054: 	}
 1055:     }
 1056:  }else{
 1057:     if(key != ""){
 1058: 	sout+=key+"=new Array()"
 1059: 	key+="."
 1060:     }
 1061:     
 1062:     for(var i in A){
 1063: 	sout+="\n"
 1064: 	if(typeof(A[i]) == "object"||typeof(A[i]) == "array"){
 1065: 		sout+=_jmolEnumerateObject(A[i],key+i)
 1066: 	}else{
 1067: 		sout+=key+i+"="+(typeof(A[i]) == "string" && A[i]!="null"?"\""+A[i].replace(/\"/g,"\\\"")+"\"":A[i])
 1068: 	}
 1069:     }
 1070:  } 
 1071:  return sout
 1072: }
 1073: 
 1074: 
 1075: function _jmolSortKey0(a,b){
 1076:  return (a[0]<b[0]?1:a[0]>b[0]?-1:0)
 1077: }
 1078: 
 1079: function _jmolSortMessages(A){
 1080:  if(!A || typeof(A)!="object")return []
 1081:  var B = new Array()
 1082:  for(var i=A.length-1;i>=0;i--)for(var j=0;j<A[i].length;j++)B[B.length]=A[i][j]
 1083:  if(B.length == 0) return
 1084:  B=B.sort(_jmolSortKey0)
 1085:  return B
 1086: }
 1087: 
 1088: /////////additional extensions //////////
 1089: 
 1090: 
 1091: function _jmolDomScriptLoad(URL){
 1092:  //open(URL) //to debug
 1093:  _jmol.servercall=URL
 1094:  var node = document.getElementById("_jmolScriptNode")
 1095:  if (node && _jmol.browser!="msie"){
 1096:     document.getElementsByTagName("HEAD")[0].removeChild(node)
 1097:     node=null
 1098:  }
 1099:  if (node) {
 1100:    node.setAttribute("src",URL)
 1101:  } else {
 1102:    node=document.createElement("script")
 1103:    node.setAttribute("id","_jmolScriptNode")
 1104:    node.setAttribute("type","text/javascript")
 1105:    node.setAttribute("src",URL)
 1106:    document.getElementsByTagName("HEAD")[0].appendChild(node)
 1107:  }
 1108: }
 1109: 
 1110: 
 1111: function _jmolExtractPostData(url){
 1112:  S=url.split("&POST:")
 1113:  var s=""
 1114:  for(var i=1;i<S.length;i++){
 1115: 	KV=S[i].split("=")
 1116: 	s+="&POSTKEY"+i+"="+KV[0]
 1117: 	s+="&POSTVALUE"+i+"="+KV[1]
 1118:  }
 1119:  return "&url="+escape(S[0])+s
 1120: }
 1121: 
 1122: function _jmolLoadModel(targetSuffix,remoteURL,array,isError,errorMessage){
 1123:  //called by server, but in client
 1124:  //overload this function to customize return
 1125:  _jmol.remoteURL=remoteURL
 1126:  if(isError)alert(errorMessage)
 1127:  jmolLoadInlineScript(array.join("\n"),_jmol.optionalscript,targetSuffix)
 1128: }
 1129: 
 1130: //////////user property/status functions/////////
 1131: 
 1132: function jmolGetStatus(strStatus,targetSuffix){
 1133:  return _jmolSortMessages(jmolGetPropertyAsArray("jmolStatus",strStatus,targetSuffix))
 1134: }
 1135: 
 1136: function jmolGetPropertyAsArray(sKey,sValue,targetSuffix) {
 1137:  return _jmolEvalJSON(jmolGetPropertyAsJSON(sKey,sValue,targetSuffix),sKey)
 1138: }
 1139: 
 1140: function jmolGetPropertyAsString(sKey,sValue,targetSuffix) {
 1141:  var applet = _jmolGetApplet(targetSuffix);
 1142:  if(!sValue)sValue=""
 1143:  return (applet ? applet.getPropertyAsString(sKey,sValue) + "" : "")
 1144: }
 1145: 
 1146: function jmolGetPropertyAsJSON(sKey,sValue,targetSuffix) {
 1147:  if(!sValue)sValue = ""
 1148:  var applet = _jmolGetApplet(targetSuffix);
 1149:  try {
 1150:   return (applet ? applet.getPropertyAsJSON(sKey,sValue) + "" : "")
 1151:  } catch(e) {
 1152:   return ""
 1153:  }
 1154: }
 1155: 
 1156: function jmolGetPropertyAsJavaObject(sKey,sValue,targetSuffix) {
 1157:  if(!sValue)sValue = ""
 1158:  var applet = _jmolGetApplet(targetSuffix);
 1159:  return (applet ? applet.getProperty(sKey,sValue) : null)
 1160: }
 1161: 
 1162: 
 1163: function jmolDecodeJSON(s) {
 1164:  return _jmolEnumerateObject(_jmolEvalJSON(s),"")
 1165: }
 1166: 
 1167: 
 1168: ///////// synchronous scripting ////////
 1169: 
 1170: function jmolScriptWait(script, targetSuffix) {
 1171:   if(!targetSuffix)targetSuffix="0"
 1172:   var Ret=jmolScriptWaitAsArray(script, targetSuffix)
 1173:   var s = ""
 1174:   for(i=Ret.length;--i>=0;)
 1175:   for(j=0;j< Ret[i].length;j++)
 1176: 	s+=Ret[i][j]+"\n"
 1177:   return s
 1178: }
 1179: 
 1180: function jmolEvaluate(molecularMath, targetSuffix) {
 1181: 
 1182:   //carries out molecular math on a model
 1183: 
 1184:   if(!targetSuffix)targetSuffix="0"
 1185:   var result = "" + jmolGetPropertyAsJavaObject("evaluate", molecularMath, targetSuffix);
 1186:   var s = result.replace(/\-*\d+/,"")
 1187:   if (s == "" && !isNaN(parseInt(result)))return parseInt(result);
 1188:   var s = result.replace(/\-*\d*\.\d*/,"")
 1189:   if (s == "" && !isNaN(parseFloat(result)))return parseFloat(result);
 1190:   return result;
 1191: }
 1192: 
 1193: function jmolScriptEcho(script, targetSuffix) {
 1194:   // returns a newline-separated list of all echos from a script
 1195:   if(!targetSuffix)targetSuffix="0"
 1196:   var Ret=jmolScriptWaitAsArray(script, targetSuffix)
 1197:   var s = ""
 1198:   for(i=Ret.length;--i>=0;)
 1199:   for(j=Ret[i].length;--j>=0;)
 1200:         if (Ret[i][j][1] == "scriptEcho")s+=Ret[i][j][3]+"\n"
 1201:   return s.replace(/ \| /g, "\n")
 1202: }
 1203: 
 1204: 
 1205: function jmolScriptMessage(script, targetSuffix) {
 1206:   // returns a newline-separated list of all messages from a script, ending with "script completed\n"
 1207:   if(!targetSuffix)targetSuffix="0"
 1208:   var Ret=jmolScriptWaitAsArray(script, targetSuffix)
 1209:   var s = ""
 1210:   for(i=Ret.length;--i>=0;)
 1211:   for(j=Ret[i].length;--j>=0;)
 1212:         if (Ret[i][j][1] == "scriptStatus")s+=Ret[i][j][3]+"\n"
 1213:   return s.replace(/ \| /g, "\n")
 1214: }
 1215: 
 1216: 
 1217: function jmolScriptWaitAsArray(script, targetSuffix) {
 1218:  var ret = ""
 1219:  try{
 1220:   jmolGetStatus("scriptEcho,scriptMessage,scriptStatus,scriptError",targetSuffix)
 1221:   if (script) {
 1222:     _jmolCheckBrowser();
 1223:     var applet=_jmolGetApplet(targetSuffix);
 1224:     if (applet) ret += applet.scriptWait(script);
 1225:     ret = _jmolEvalJSON(ret,"jmolStatus")
 1226:     if(typeof ret == "object")
 1227: 	return ret
 1228:   }
 1229:  }catch(e){
 1230:  }
 1231:   return [[ret]]
 1232: }
 1233: 
 1234: 
 1235: 
 1236: ////////////   save/restore orientation   /////////////
 1237: 
 1238: function jmolSaveOrientation(id, targetSuffix) {  
 1239:  if(!targetSuffix)targetSuffix="0"
 1240:   return _jmol["savedOrientation"+id] = jmolGetPropertyAsArray("orientationInfo","info",targetSuffix).moveTo
 1241: }
 1242: 
 1243: function jmolRestoreOrientation(id, targetSuffix) {
 1244:  if(!targetSuffix)targetSuffix="0"
 1245:  var s=_jmol["savedOrientation"+id]
 1246:  if (!s || s == "")return
 1247:  s=s.replace(/1\.0/,"0")
 1248:  return jmolScriptWait(s,targetSuffix)
 1249: }
 1250: 
 1251: function jmolRestoreOrientationDelayed(id, delay, targetSuffix) {
 1252:  if(arguments.length < 2)delay=1;
 1253:  if(!targetSuffix)targetSuffix="0"
 1254:  var s=_jmol["savedOrientation"+id]
 1255:  if (!s || s == "")return
 1256:  s=s.replace(/1\.0/,delay)
 1257:  return jmolScriptWait(s,targetSuffix)
 1258: }
 1259: 
 1260: ////////////  add parameter /////////////
 1261: /*
 1262:  * for adding callbacks or other parameters. Use:
 1263: 
 1264:    jmolSetDocument(0)
 1265:    var s= jmolApplet(....)
 1266:    s = jmolAppletAddParam(s,"messageCallback", "myFunctionName")
 1267:    document.write(s)
 1268:    jmolSetDocument(document) // if you want to then write buttons and such normally
 1269:  
 1270:  */
 1271: 
 1272: function jmolAppletAddParam(appletCode,name,value){
 1273:   if(value == "")return appletCode
 1274:   return appletCode.replace(/\<param/,"\n<param name='"+name+"' value='"+value+"' />\n<param")
 1275: }
 1276: 
 1277: ///////////////auto load Research Consortium for Structural Biology (RCSB) data ///////////
 1278: 
 1279: function jmolLoadAjax_STOLAF_RCSB(fileformat,pdbid,optionalscript,targetSuffix){
 1280: 
 1281:  if(!_jmol.thismodel)_jmol.thismodel = "1crn"
 1282:  if(!_jmol.serverURL)_jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm"
 1283:  if(!_jmol.RCSBserver)_jmol.RCSBserver="http://www.rcsb.org"
 1284:  if(!_jmol.defaultURL_RCSB)_jmol.defaultURL_RCSB=_jmol.RCSBserver+"/pdb/files/1CRN.CIF"
 1285:  if(!fileformat)fileformat="PDB"
 1286:  if(!pdbid)pdbid=prompt("Enter a 4-digit PDB ID:",_jmol.thismodel)
 1287:  if(!pdbid || pdbid.length != 4)return ""
 1288:  if(!targetSuffix)targetSuffix="0"
 1289:  if(!optionalscript)optionalscript=""
 1290:  var url=_jmol.defaultURL_RCSB.replace(/1CRN/g,pdbid.toUpperCase())
 1291:  if(fileformat!="CIF")url=url.replace(/CIF/,fileformat)
 1292:  _jmol.optionalscript=optionalscript
 1293:  _jmol.thismodel=pdbid
 1294:  _jmol.thistargetsuffix=targetSuffix
 1295:  _jmol.thisurl=url
 1296:  _jmol.modelArray = new Array()
 1297:  url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)
 1298:  _jmolDomScriptLoad(url)
 1299:  return url
 1300: }
 1301: 
 1302: /////////////// St. Olaf College AJAX server -- ANY URL ///////////
 1303: 
 1304: function jmolLoadAjax_STOLAF_ANY(url, userid, optionalscript,targetSuffix){
 1305:  _jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm"
 1306:  if(!_jmol.thisurlANY)_jmol.thisurlANY = "http://www.stolaf.edu/depts/chemistry/mo/struc/data/ycp3-1.mol"
 1307:  if(!url)url=prompt("Enter any (uncompressed file) URL:", _jmol.thisurlANY)
 1308:  if(!userid)userid="0"
 1309:  if(!targetSuffix)targetSuffix="0"
 1310:  if(!optionalscript)optionalscript=""
 1311:  _jmol.optionalscript=optionalscript
 1312:  _jmol.thistargetsuffix=targetSuffix
 1313:  _jmol.modelArray = new Array()
 1314:  _jmol.thisurl = url
 1315:  url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)
 1316:  _jmolDomScriptLoad(url)
 1317: }
 1318: 
 1319: 
 1320: /////////////// Mineralogical Society of America (MSA) data /////////
 1321: 
 1322: function jmolLoadAjax_MSA(key,value,optionalscript,targetSuffix){
 1323: 
 1324:  if(!_jmol.thiskeyMSA)_jmol.thiskeyMSA = "mineral"
 1325:  if(!_jmol.thismodelMSA)_jmol.thismodelMSA = "quartz"
 1326:  if(!_jmol.ajaxURL_MSA)_jmol.ajaxURL_MSA="http://rruff.geo.arizona.edu/AMS/result.php?mineral=quartz&viewing=ajaxjs"
 1327:  if(!key)key=prompt("Enter a field:", _jmol.thiskeyMSA)
 1328:  if(!key)return ""
 1329:  if(!value)value=prompt("Enter a "+key+":", _jmol.thismodelMSA)
 1330:  if(!value)return ""
 1331:  if(!targetSuffix)targetSuffix="0"
 1332:  if(!optionalscript)optionalscript=""
 1333:  if(optionalscript == 1)optionalscript='load "" {1 1 1}'
 1334:  var url=_jmol.ajaxURL_MSA.replace(/mineral/g,key).replace(/quartz/g,value)
 1335:  _jmol.optionalscript=optionalscript
 1336:  _jmol.thiskeyMSA=key
 1337:  _jmol.thismodelMSA=value
 1338:  _jmol.thistargetsuffix=targetSuffix
 1339:  _jmol.thisurl=url
 1340:  _jmol.modelArray = new Array()
 1341:  loadModel=_jmolLoadModel
 1342:  _jmolDomScriptLoad(url)
 1343:  return url
 1344: }
 1345: 
 1346: 
 1347: 
 1348: function jmolLoadAjaxJS(url, userid, optionalscript,targetSuffix){
 1349:  if(!userid)userid="0"
 1350:  if(!targetSuffix)targetSuffix="0"
 1351:  if(!optionalscript)optionalscript=""
 1352:  _jmol.optionalscript=optionalscript
 1353:  _jmol.thismodel=userid
 1354:  _jmol.thistargetsuffix=targetSuffix
 1355:  _jmol.modelArray = new Array()
 1356:  _jmol.thisurl = url
 1357:  url+="&returnFunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix
 1358:  _jmolDomScriptLoad(url)
 1359: }
 1360: 
 1361: 
 1362: //// in case Jmol library has already been loaded:
 1363: 
 1364: }catch(e){}
 1365: 
 1366: ///////////////moving atoms //////////////
 1367: 
 1368: // HIGHLY experimental!!
 1369: 
 1370: function jmolSetAtomCoord(i,x,y,z,targetSuffix){
 1371:     _jmolCheckBrowser();
 1372:       var applet=_jmolGetApplet(targetSuffix);
 1373:       if (applet) applet.getProperty('jmolViewer').setAtomCoord(i,x,y,z)
 1374: }
 1375: 
 1376: function jmolSetAtomCoordRelative(i,x,y,z,targetSuffix){
 1377:     _jmolCheckBrowser();
 1378:       var applet=_jmolGetApplet(targetSuffix);
 1379:       if (applet) applet.getProperty('jmolViewer').setAtomCoordRelative(i,x,y,z)
 1380: }
 1381: 
 1382: 
 1383: ///////////////applet fake for testing buttons/////////////
 1384: 
 1385: 
 1386: if(document.location.search.indexOf("NOAPPLET")>=0){
 1387: 	jmolApplet = function(w){
 1388: 		var s="<table style='background-color:black' width="+w+"><tr height="+w+">"
 1389: 		+"<td align=center valign=center style='background-color:white'>"
 1390: 		+"Applet would be here"
 1391: 		+"<p><textarea id=fakeApplet rows=5 cols=50></textarea>"
 1392: 		+"</td></tr></table>"
 1393: 		return _jmolDocumentWrite(s)
 1394: 	}
 1395: 
 1396: 	_jmolFindApplet = function(){return jmolApplet0}
 1397: 
 1398: 	jmolApplet0 = {
 1399: 	 script: function(script){document.getElementById("fakeApplet").value="\njmolScript:\n"+script}
 1400: 	,scriptWait: function(script){document.getElementById("fakeApplet").value="\njmolScriptWait:\n"+script}	
 1401: 	,loadInline: function(data,script){document.getElementById("fakeApplet").value="\njmolLoadInline data:\n"+data+"\n\nscript:\n"+script}
 1402: 	}
 1403: }
 1404: 
 1405: 
 1406: ///////////////////////////////////////////
 1407: 
 1408: //new 9:49 AM 3/6/2007:
 1409: 
 1410: //both w and h are optional. 
 1411: //if either is between 0 and 1, then it is taken as percent/100.
 1412: //if either is greater than 1, then it is taken as a size. 
 1413: function jmolResize(w,h) {
 1414:  _jmol.alerted = true;
 1415:  var percentW = (!w ? 100 : w <= 1  && w > 0 ? w * 100 : 0)
 1416:  var percentH = (!h ? percentW : h <= 1 && h > 0 ? h * 100 : 0)
 1417:  if (_jmol.browser=="msie") {
 1418:    var width=document.body.clientWidth;
 1419:    var height=document.body.clientHeight;
 1420:  } else {
 1421:    var netscapeScrollWidth=15;
 1422:    var width=window.innerWidth - netscapeScrollWidth;
 1423:    var height=window.innerHeight-netscapeScrollWidth;
 1424:  }
 1425:  var applet = _jmolGetApplet(0);
 1426:  if(!applet)return;
 1427:  applet.style.width = (percentW ? width * percentW/100 : w)+"px"
 1428:  applet.style.height = (percentH ? height * percentH/100 : h)+"px"
 1429:  title=width +  " " + height + " " + (new Date())
 1430: }
 1431: