X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples-jbake%2Fassets%2Fjmol%2FJmol.js;fp=examples-jbake%2Fassets%2Fjmol%2FJmol.js;h=0000000000000000000000000000000000000000;hb=1ae4cc763bcf09b68274ca3954c42c513217a5fe;hp=fbc36383c0c28f85791481c4dc398856a784d575;hpb=00346db020eaed84154f33016a2203fb3a002c7b;p=jalview.git

diff --git a/examples-jbake/assets/jmol/Jmol.js b/examples-jbake/assets/jmol/Jmol.js
deleted file mode 100644
index fbc3638..0000000
--- a/examples-jbake/assets/jmol/Jmol.js
+++ /dev/null
@@ -1,1705 +0,0 @@
-/* Jmol 12.0 script library Jmol.js 9:48 PM 1/31/2011 Bob Hanson
-
- checkbox heirarchy -- see http://chemapps.stolaf.edu/jmol/docs/examples-11/check.htm
-
-    based on:
- *
- * Copyright (C) 2004-2005  Miguel, Jmol Development, www.jmol.org
- *
- * Contact: hansonr@stolaf.edu
- *
- *  This library is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public
- *  License as published by the Free Software Foundation; either
- *  version 2.1 of the License, or (at your option) any later version.
- *
- *  This library is distributed in the hope that it will be useful,
- *  but WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this library; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
- *  02111-1307  USA.
- */
-
-// for documentation see www.jmol.org/jslibrary
-
-try{if(typeof(_jmol)!="undefined")exit()
-
-// place "?NOAPPLET" on your command line to check applet control action with a textarea
-// place "?JMOLJAR=xxxxx" to use a specific jar file
-
-// bob hanson -- jmolResize(w,h) -- resizes absolutely or by percent (w or h 0.5 means 50%)
-//    angel herraez -- update of jmolResize(w,h,targetSuffix) so it is not tied to first applet
-// bob hanson -- jmolEvaluate -- evaluates molecular math 8:37 AM 2/23/2007
-// bob hanson -- jmolScriptMessage -- returns all "scriptStatus" messages 8:37 AM 2/23/2007
-// bob hanson -- jmolScriptEcho -- returns all "scriptEcho" messages 8:37 AM 2/23/2007
-// bob hanson -- jmolScriptWait -- 11:31 AM 5/2/2006
-// bob hanson -- remove trailing separatorHTML in radio groups -- 12:18 PM 5/6/2006
-// bob hanson -- adds support for dynamic DOM script nodes 7:04 AM 5/19/2006
-// bob hanson -- adds try/catch for wiki - multiple code passes 7:05 AM 5/19/2006
-// bob hanson -- auto-initiates to defaultdir/defaultjar -- change as desired.
-// bob hanson -- adding save/restore orientation w/ and w/o delay 11:49 AM 5/25/2006
-// bob hanson -- adding AjaxJS service 11:16 AM 6/3/2006
-// bob hanson -- fix for iframes not available for finding applet
-// bob hanson -- added applet fake ?NOAPPLET URL flag
-// bob hanson -- added jmolSetCallback(calbackName, funcName) 3:32 PM 6/13/2006
-//			used PRIOR to jmolApplet() or jmolAppletInline()
-//               added 4th array element in jmolRadioGroup -- title
-//               added <span> and id around link, checkbox, radio, menu
-//               fixing AJAX loads for MSIE/Opera-Mozilla incompatibility
-//            -- renamed Jmol-11.js from Jmol-new.js; JmolApplet.jar from JmolAppletProto.jar
-//	 	 renamed Jmol.js for Jmol 11 distribution
-//            -- modified jmolRestoreOrientation() to be immediate, no 1-second delay
-// bob hanson -- jmolScriptWait always returns a string -- 11:23 AM 9/16/2006
-// bh         -- jmolCommandInput()
-// bh         -- jmolSetTranslation(TF) -- forces translation even if there might be message callback issues
-// bh         -- minor fixes suggested by Angel
-// bh         -- adds jmolSetSyncId() and jmolGetSyncId()
-// bh 3/2008  -- adds jmolAppendInlineScript() and jmolAppendInlineArray()
-// bh 3/2008  -- fixes IE7 bug in relation to jmolLoadInlineArray()
-// bh 6/2008  -- adds jmolSetAppletWindow()
-// Angel H. 6/2008  -- added html <label> tags to checkboxes and radio buttons [in jmolCheckbox() and _jmolRadio() functions]
-// bh 7/2008  -- code fix "for(i..." not "for(var i..."
-// bh 12/2008 -- jmolLoadInline, jmolLoadInlineArray, jmolLoadInlineScript, jmolAppendInlineScript, jmolAppendInlineArray all return error message or null (Jmol 11.7.16)
-// bh 12/2008 -- jmolScriptWaitOutput() -- waits for script to complete and delivers output normally sent to console
-
-// bh 5/2009  -- Support for XHTML using jmolSetXHTML(id)
-// ah & bh 6/2009 -- New jmolResizeApplet() more flexible, similar to jmolApplet() size syntax
-// bh 11/2009 -- care in accessing top.document
-// bh 12/2009 -- added jmolSetParameter(name, value)
-// bh 12/2009 -- added PARAMS=name:value;name:value;name:value... for command line
-// bh 12/2009 -- overhaul of target checking
-// bh 1/2010  -- all _xxxx() methods ALWAYS have complete argument list
-// bh 1/2010  -- adds option to run a JavaScript function from any Jmol control. 
-//               This is accomplished by passing an array rather than a script:
-//               jmolHref([myfunc,"my param 1", "my param 2"], "testing")
-//               function myfunc(jmolControlObject, [myfunc,"my param 1", "my param 2"], target){...}
-//               and allows much more flexibility with responding to controls
-// bh 4/2010  -- added jmolSetMemoryMb(nMb)
-// ah 1/2011  -- wider detection of browsers; more browsers now use the object tag instead of the applet tag; 
-//               fix of object tag (removed classid) accounts for change of behavior in Chrome
-// bh 3/2011  -- added jmolLoadAjax_STOLAF_NIH
-
-var defaultdir = "."
-var defaultjar = "JmolApplet.jar"
-
-
-// Note added 12:41 PM 9/21/2008 by Bob Hanson, hansonr@stolaf.edu:
-
-// JMOLJAR=xxxxx.jar on the URL for this page will override
-// the JAR file specified in the jmolInitialize() call.
-
-// The idea is that it can be very useful to test a web page with different JAR files
-// Or for an expert user to substitute a signed applet for an unsigned one
-// so as to use a broader range of models or to create JPEG files, for example.
-
-// If the JAR file is not in the current directory (has any sort of "/" in its name)
-// then the user is presented with a warning and asked whether it is OK to change Jar files.
-// The default action, if the user just presses "OK" is to NOT allow the change. 
-// The user must type the word "yes" in the prompt box for the change to be approved.
-
-// If you don't want people to be able to switch in their own JAR file on your page,
-// simply set this next line to read "var allowJMOLJAR = false".
-
-
-var undefined; // for IE 5 ... wherein undefined is undefined
-
-////////////////////////////////////////////////////////////////
-// Basic Scripting infrastruture
-////////////////////////////////////////////////////////////////
-
-function jmolInitialize(codebaseDirectory, fileNameOrUseSignedApplet) {
-  if (_jmol.initialized)
-    return;
-  _jmol.initialized = true;
-  if(_jmol.jmoljar) {
-    var f = _jmol.jmoljar;
-    if (f.indexOf("/") >= 0) {
-      alert ("This web page URL is requesting that the applet used be " + f + ". This is a possible security risk, particularly if the applet is signed, because signed applets can read and write files on your local machine or network.")
-      var ok = prompt("Do you want to use applet " + f + "? ","yes or no")
-      if (ok == "yes") {
-        codebaseDirectory = f.substring(0, f.lastIndexOf("/"));
-        fileNameOrUseSignedApplet = f.substring(f.lastIndexOf("/") + 1);
-      } else {
-	_jmolGetJarFilename(fileNameOrUseSignedApplet);
-        alert("The web page URL was ignored. Continuing using " + _jmol.archivePath + ' in directory "' + codebaseDirectory + '"');
-      }
-    } else {
-      fileNameOrUseSignedApplet = f;
-    }
-  }
-  _jmolSetCodebase(codebaseDirectory);
-  _jmolGetJarFilename(fileNameOrUseSignedApplet);
-  _jmolOnloadResetForms();
-}
-
-function jmolSetTranslation(TF) {
-  _jmol.params.doTranslate = ''+TF;
-}
-
-function _jmolGetJarFilename(fileNameOrFlag) {
-  _jmol.archivePath =
-    (typeof(fileNameOrFlag) == "string"  ? fileNameOrFlag : (fileNameOrFlag ?  "JmolAppletSigned" : "JmolApplet") + "0.jar");
-}
-
-function jmolSetDocument(doc) {
-  _jmol.currentDocument = doc;
-}
-
-function jmolSetAppletColor(boxbgcolor, boxfgcolor, progresscolor) {
-  _jmolInitCheck();
-  _jmol.params.boxbgcolor = boxbgcolor;
-  if (boxfgcolor)
-    _jmol.params.boxfgcolor = boxfgcolor
-  else if (boxbgcolor == "white" || boxbgcolor == "#FFFFFF")
-    _jmol.params.boxfgcolor = "black";
-  else
-    _jmol.params.boxfgcolor = "white";
-  if (progresscolor)
-    _jmol.params.progresscolor = progresscolor;
-  if (_jmol.debugAlert)
-    alert(" boxbgcolor=" + _jmol.params.boxbgcolor +
-          " boxfgcolor=" + _jmol.params.boxfgcolor +
-          " progresscolor=" + _jmol.params.progresscolor);
-}
-
-function jmolSetAppletWindow(w) {
-  _jmol.appletWindow = w;
-}
-
-function jmolApplet(size, script, nameSuffix) {
-  _jmolInitCheck();
-  return _jmolApplet(size, null, script, nameSuffix);
-}
-
-////////////////////////////////////////////////////////////////
-// Basic controls
-////////////////////////////////////////////////////////////////
-
-// undefined means it wasn't there; null means it was explicitly listed as null (so as to skip it)
-
-function jmolButton(script, label, id, title) {
-  _jmolInitCheck();
-  id != undefined && id != null || (id = "jmolButton" + _jmol.buttonCount);
-  label != undefined && label != null || (label = script.substring(0, 32));
-  ++_jmol.buttonCount;
-  var scriptIndex = _jmolAddScript(script);
-  var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input type='button' name='" + id + "' id='" + id +
-          "' value='" + label +
-          "' onclick='_jmolClick(this," + scriptIndex + _jmol.targetText +
-          ")' onmouseover='_jmolMouseOver(" + scriptIndex +
-          ");return true' onmouseout='_jmolMouseOut()' " +
-          _jmol.buttonCssText + " /></span>";
-  if (_jmol.debugAlert)
-    alert(t);
-  return _jmolDocumentWrite(t);
-}
-
-function jmolCheckbox(scriptWhenChecked, scriptWhenUnchecked,
-                      labelHtml, isChecked, id, title) {
-  _jmolInitCheck();
-  id != undefined && id != null || (id = "jmolCheckbox" + _jmol.checkboxCount);
-  ++_jmol.checkboxCount;
-  if (scriptWhenChecked == undefined || scriptWhenChecked == null ||
-      scriptWhenUnchecked == undefined || scriptWhenUnchecked == null) {
-    alert("jmolCheckbox requires two scripts");
-    return;
-  }
-  if (labelHtml == undefined || labelHtml == null) {
-    alert("jmolCheckbox requires a label");
-    return;
-  }
-  var indexChecked = _jmolAddScript(scriptWhenChecked);
-  var indexUnchecked = _jmolAddScript(scriptWhenUnchecked);
-  var eospan = "</span>"
-  var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input type='checkbox' name='" + id + "' id='" + id +
-          "' onclick='_jmolCbClick(this," +
-          indexChecked + "," + indexUnchecked + _jmol.targetText +
-          ")' onmouseover='_jmolCbOver(this," + indexChecked + "," +
-          indexUnchecked +
-          ");return true' onmouseout='_jmolMouseOut()' " +
-	  (isChecked ? "checked='true' " : "")+ _jmol.checkboxCssText + " />" 
-  if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
-	t += eospan
-	eospan = "";
-  }
-  t += "<label for=\"" + id + "\">" + labelHtml + "</label>" +eospan;
-  if (_jmol.debugAlert)
-    alert(t);
-  return _jmolDocumentWrite(t);
-}
-
-function jmolStartNewRadioGroup() {
-  ++_jmol.radioGroupCount;
-}
-
-function jmolRadioGroup(arrayOfRadioButtons, separatorHtml, groupName, id, title) {
-  /*
-
-    array: [radio1,radio2,radio3...]
-    where radioN = ["script","label",isSelected,"id","title"]
-
-  */
-
-  _jmolInitCheck();
-  var type = typeof arrayOfRadioButtons;
-  if (type != "object" || type == null || ! arrayOfRadioButtons.length) {
-    alert("invalid arrayOfRadioButtons");
-    return;
-  }
-  separatorHtml != undefined && separatorHtml != null || (separatorHtml = "&nbsp; ");
-  var len = arrayOfRadioButtons.length;
-  jmolStartNewRadioGroup();
-  groupName || (groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1));
-  var t = "<span id='"+(id ? id : groupName)+"'>";
-  for (var i = 0; i < len; ++i) {
-    if (i == len - 1)
-      separatorHtml = "";
-    var radio = arrayOfRadioButtons[i];
-    type = typeof radio;
-    if (type == "object") {
-      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);
-    } else {
-      t += _jmolRadio(radio, null, null, separatorHtml, groupName, (id ? id : groupName)+"_"+i, title);
-    }
-  }
-  t+="</span>"
-  if (_jmol.debugAlert)
-    alert(t);
-  return _jmolDocumentWrite(t);
-}
-
-
-function jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
-  _jmolInitCheck();
-  if (_jmol.radioGroupCount == 0)
-    ++_jmol.radioGroupCount;
-  var t = _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, (id ? id : groupName + "_" + _jmol.radioCount), title ? title : 0);
-  if (_jmol.debugAlert)
-    alert(t);
-  return _jmolDocumentWrite(t);
-}
-
-function jmolLink(script, label, id, title) {
-  _jmolInitCheck();
-  id != undefined && id != null || (id = "jmolLink" + _jmol.linkCount);
-  label != undefined && label != null || (label = script.substring(0, 32));
-  ++_jmol.linkCount;
-  var scriptIndex = _jmolAddScript(script);
-  var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><a name='" + id + "' id='" + id + 
-          "' href='javascript:_jmolClick(this," + scriptIndex + _jmol.targetText + ");' onmouseover='_jmolMouseOver(" + scriptIndex +
-          ");return true;' onmouseout='_jmolMouseOut()' " +
-          _jmol.linkCssText + ">" + label + "</a></span>";
-  if (_jmol.debugAlert)
-    alert(t);
-  return _jmolDocumentWrite(t);
-}
-
-function jmolCommandInput(label, size, id, title) {
-  _jmolInitCheck();
-  id != undefined && id != null || (id = "jmolCmd" + _jmol.cmdCount);
-  label != undefined && label != null || (label = "Execute");
-  size != undefined && !isNaN(size) || (size = 60);
-  ++_jmol.cmdCount;
-  var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input name='" + id + "' id='" + id + 
-          "' size='"+size+"' onkeypress='_jmolCommandKeyPress(event,\""+id+"\"" + _jmol.targetText + ")'><input type=button value = '"+label+"' onclick='jmolScript(document.getElementById(\""+id+"\").value" + _jmol.targetText + ")' /></span>";
-  if (_jmol.debugAlert)
-    alert(t);
-  return _jmolDocumentWrite(t);
-}
-
-function _jmolCommandKeyPress(e, id, target) {
-	var keycode = (window.event ? window.event.keyCode : e ? e.which : 0);
-	if (keycode == 13) {
-		var inputBox = document.getElementById(id)
-		_jmolScriptExecute(inputBox, inputBox.value, target)
-	}
-}
-
-function _jmolScriptExecute(element,script,target) {
-	if (typeof(script) == "object")
-		script[0](element, script, target)
-	else
-		jmolScript(script, target) 
-}
-
-function jmolMenu(arrayOfMenuItems, size, id, title) {
-  _jmolInitCheck();
-  id != undefined && id != null || (id = "jmolMenu" + _jmol.menuCount);
-  ++_jmol.menuCount;
-  var type = typeof arrayOfMenuItems;
-  if (type != null && type == "object" && arrayOfMenuItems.length) {
-    var len = arrayOfMenuItems.length;
-    if (typeof size != "number" || size == 1)
-      size = null;
-    else if (size < 0)
-      size = len;
-    var sizeText = size ? " size='" + size + "' " : "";
-    var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><select name='" + id + "' id='" + id +
-            "' onChange='_jmolMenuSelected(this" + _jmol.targetText + ")'" +
-            sizeText + _jmol.menuCssText + ">";
-    for (var i = 0; i < len; ++i) {
-      var menuItem = arrayOfMenuItems[i];
-      type = typeof menuItem;
-      var script, text;
-      var isSelected = undefined;
-      if (type == "object" && menuItem != null) {
-        script = menuItem[0];
-        text = menuItem[1];
-        isSelected = menuItem[2];
-      } else {
-        script = text = menuItem;
-      }
-      text != undefined && text != null || (text = script);		
-      if (script=="#optgroup") {
-        t += "<optgroup label='" + text + "'>";	  
-	  } else if (script=="#optgroupEnd") {
-        t += "</optgroup>";	  
-	  } else {		
-        var scriptIndex = _jmolAddScript(script);
-        var selectedText = isSelected ? "' selected='true'>" : "'>";
-        t += "<option value='" + scriptIndex + selectedText + text + "</option>";
-      }
-    }
-    t += "</select></span>";
-    if (_jmol.debugAlert)
-      alert(t);
-    return _jmolDocumentWrite(t);
-  }
-}
-
-function jmolHtml(html) {
-  return _jmolDocumentWrite(html);
-}
-
-function jmolBr() {
-  return _jmolDocumentWrite("<br />");
-}
-
-////////////////////////////////////////////////////////////////
-// advanced scripting functions
-////////////////////////////////////////////////////////////////
-
-function jmolDebugAlert(enableAlerts) {
-  _jmol.debugAlert = (enableAlerts == undefined || enableAlerts)
-}
-
-function jmolAppletInline(size, inlineModel, script, nameSuffix) {
-  _jmolInitCheck();
-  return _jmolApplet(size, _jmolSterilizeInline(inlineModel),
-                     script, nameSuffix);
-}
-
-function jmolSetTarget(targetSuffix) {
-  _jmol.targetSuffix = targetSuffix;
-  _jmol.targetText = targetSuffix ? ",\"" + targetSuffix + "\"" : ",0";
-}
-
-function jmolScript(script, targetSuffix) {
-  if (script) {
-    _jmolCheckBrowser();
-    if (targetSuffix == "all") {
-      with (_jmol) {
-	for (var i = 0; i < appletSuffixes.length; ++i) {
-	  var applet = _jmolGetApplet(appletSuffixes[i]);
-          if (applet) applet.script(script);
-        }
-      }
-    } else {
-      var applet=_jmolGetApplet(targetSuffix);
-      if (applet) applet.script(script);
-    }
-  }
-}
-
-function jmolLoadInline(model, targetSuffix) {
-  if (!model)return "ERROR: NO MODEL"
-  var applet=_jmolGetApplet(targetSuffix);
-  if (!applet)return "ERROR: NO APPLET"
-  if (typeof(model) == "string")
-    return applet.loadInlineString(model, "", false);
-  else
-    return applet.loadInlineArray(model, "", false);
-}
-
-
-function jmolLoadInlineScript(model, script, targetSuffix) {
-  if (!model)return "ERROR: NO MODEL"
-  var applet=_jmolGetApplet(targetSuffix);
-  if (!applet)return "ERROR: NO APPLET"
-  return applet.loadInlineString(model, script, false);
-}
-
-
-function jmolLoadInlineArray(ModelArray, script, targetSuffix) {
-  if (!model)return "ERROR: NO MODEL"
-  script || (script="")
-  var applet=_jmolGetApplet(targetSuffix);
-  if (!applet)return "ERROR: NO APPLET"
-  try {
-    return applet.loadInlineArray(ModelArray, script, false);
-  } catch (err) {
-    //IE 7 bug
-    return applet.loadInlineString(ModelArray.join("\n"), script, false);
-  }
-}
-
-function jmolAppendInlineArray(ModelArray, script, targetSuffix) {
-  if (!model)return "ERROR: NO MODEL"
-  script || (script="")
-  var applet=_jmolGetApplet(targetSuffix);
-  if (!applet)return "ERROR: NO APPLET"
-  try {
-    return applet.loadInlineArray(ModelArray, script, true);
-  } catch (err) {
-    //IE 7 bug
-    return applet.loadInlineString(ModelArray.join("\n"), script, true);
-  }
-}
-
-function jmolAppendInlineScript(model, script, targetSuffix) {
-  if (!model)return "ERROR: NO MODEL"
-  var applet=_jmolGetApplet(targetSuffix);
-  if (!applet)return "ERROR: NO APPLET"
-  return applet.loadInlineString(model, script, true);
-}
-
-function jmolCheckBrowser(action, urlOrMessage, nowOrLater) {
-  if (typeof action == "string") {
-    action = action.toLowerCase();
-    action == "alert" || action == "redirect" || action == "popup" || (action = null);
-  }
-  if (typeof action != "string")
-    alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +
-          "action must be 'alert', 'redirect', or 'popup'");
-  else {
-    if (typeof urlOrMessage != "string")
-      alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +
-            "urlOrMessage must be a string");
-    else {
-      _jmol.checkBrowserAction = action;
-      _jmol.checkBrowserUrlOrMessage = urlOrMessage;
-    }
-  }
-  if (typeof nowOrLater == "string" && nowOrLater.toLowerCase() == "now")
-    _jmolCheckBrowser();
-}
-
-////////////////////////////////////////////////////////////////
-// Cascading Style Sheet Class support
-////////////////////////////////////////////////////////////////
-
-function jmolSetAppletCssClass(appletCssClass) {
-  if (_jmol.hasGetElementById) {
-    _jmol.appletCssClass = appletCssClass;
-    _jmol.appletCssText = appletCssClass ? "class='" + appletCssClass + "' " : "";
-  }
-}
-
-function jmolSetButtonCssClass(buttonCssClass) {
-  if (_jmol.hasGetElementById) {
-    _jmol.buttonCssClass = buttonCssClass;
-    _jmol.buttonCssText = buttonCssClass ? "class='" + buttonCssClass + "' " : "";
-  }
-}
-
-function jmolSetCheckboxCssClass(checkboxCssClass) {
-  if (_jmol.hasGetElementById) {
-    _jmol.checkboxCssClass = checkboxCssClass;
-    _jmol.checkboxCssText = checkboxCssClass ? "class='" + checkboxCssClass + "' " : "";
-  }
-}
-
-function jmolSetRadioCssClass(radioCssClass) {
-  if (_jmol.hasGetElementById) {
-    _jmol.radioCssClass = radioCssClass;
-    _jmol.radioCssText = radioCssClass ? "class='" + radioCssClass + "' " : "";
-  }
-}
-
-function jmolSetLinkCssClass(linkCssClass) {
-  if (_jmol.hasGetElementById) {
-    _jmol.linkCssClass = linkCssClass;
-    _jmol.linkCssText = linkCssClass ? "class='" + linkCssClass + "' " : "";
-  }
-}
-
-function jmolSetMenuCssClass(menuCssClass) {
-  if (_jmol.hasGetElementById) {
-    _jmol.menuCssClass = menuCssClass;
-    _jmol.menuCssText = menuCssClass ? "class='" + menuCssClass + "' " : "";
-  }
-}
-
-////////////////////////////////////////////////////////////////
-// functions for INTERNAL USE ONLY which are subject to change
-// use at your own risk ... you have been WARNED!
-////////////////////////////////////////////////////////////////
-var _jmol = {
-  currentDocument: document,
-
-  debugAlert: false,
-  
-  codebase: "",
-  modelbase: ".",
-  
-  appletCount: 0,
-  appletSuffixes: [],
-  appletWindow: null,
-  allowedJmolSize: [25, 2048, 300],   // min, max, default (pixels)
-	  /*  By setting the _jmol.allowedJmolSize[] variable in the webpage 
-	      before calling jmolApplet(), limits for applet size can be overriden.
-		    2048 standard for GeoWall (http://geowall.geo.lsa.umich.edu/home.html)
-	  */  
-  buttonCount: 0,
-  checkboxCount: 0,
-  linkCount: 0,
-  cmdCount: 0,
-  menuCount: 0,
-  radioCount: 0,
-  radioGroupCount: 0,
-  
-  appletCssClass: null,
-  appletCssText: "",
-  buttonCssClass: null,
-  buttonCssText: "",
-  checkboxCssClass: null,
-  checkboxCssText: "",
-  java_arguments: "-Xmx512m",
-  radioCssClass: null,
-  radioCssText: "",
-  linkCssClass: null,
-  linkCssText: "",
-  menuCssClass: null,
-  menuCssText: "",
-  
-  targetSuffix: 0,
-  targetText: ",0",
-  scripts: [""],
-  params: {
-	syncId: ("" + Math.random()).substring(3),
-	progressbar: "true",
-	progresscolor: "blue",
-	boxbgcolor: "black",
-	boxfgcolor: "white",
-	boxmessage: "Downloading JmolApplet ..."
-  },
-  ua: navigator.userAgent.toLowerCase(),
-  // uaVersion: parseFloat(navigator.appVersion),  // not used
-  
-  os: "unknown",
-  browser: "unknown",
-  browserVersion: 0,
-  hasGetElementById: !!document.getElementById,
-  isJavaEnabled: navigator.javaEnabled(),
-  // isNetscape47Win: false,  // not used, N4.7 is no longer supported even for detection
-  useIEObject: false,
-  useHtml4Object: false,
-  
-  windowsClassId: "clsid:8AD9C840-044E-11D1-B3E9-00805F499D93",
-  windowsCabUrl:
-   "http://java.sun.com/update/1.6.0/jinstall-6u22-windows-i586.cab",
-
-  isBrowserCompliant: false,
-  isJavaCompliant: false,
-  isFullyCompliant: false,
-
-  initialized: false,
-  initChecked: false,
-  
-  browserChecked: false,
-  checkBrowserAction: "alert",
-  checkBrowserUrlOrMessage: null,
-
-  archivePath: null, // JmolApplet0.jar OR JmolAppletSigned0.jar
-
-  previousOnloadHandler: null,
-
-  jmoljar: null,  
-  useNoApplet: false,
-
-  ready: {}
-}
-
-with (_jmol) {
-  function _jmolTestUA(candidate) {
-    var ua = _jmol.ua;
-    var index = ua.indexOf(candidate);
-    if (index < 0)
-      return false;
-    _jmol.browser = candidate;
-    _jmol.browserVersion = parseFloat(ua.substring(index+candidate.length+1));
-    return true;
-  }
-  
-  function _jmolTestOS(candidate) {
-    if (_jmol.ua.indexOf(candidate) < 0)
-      return false;
-    _jmol.os = candidate;
-    return true;
-  }
-  
-  _jmolTestUA("konqueror") ||
-  _jmolTestUA("webkit") ||
-  _jmolTestUA("omniweb") ||
-  _jmolTestUA("opera") ||
-  _jmolTestUA("webtv") ||
-  _jmolTestUA("icab") ||
-  _jmolTestUA("msie") ||
-  (_jmol.ua.indexOf("compatible") < 0 && _jmolTestUA("mozilla")); //Netscape, Mozilla, Seamonkey, Firefox and anything assimilated
-  
-  _jmolTestOS("linux") ||
-  _jmolTestOS("unix") ||
-  _jmolTestOS("mac") ||
-  _jmolTestOS("win");
-
-  /* not used:
-	isNetscape47Win = (os == "win" && browser == "mozilla" &&
-                     browserVersion >= 4.78 && browserVersion <= 4.8);
-	*/
-
-  if (os == "win") {
-    isBrowserCompliant = hasGetElementById;
-  } else if (os == "mac") { // mac is the problem child :-(
-    if (browser == "mozilla" && browserVersion >= 5) {
-      // miguel 2004 11 17
-      // checking the plugins array does not work because
-      // Netscape 7.2 OS X still has Java 1.3.1 listed even though
-      // javaplugin.sf.net is installed to upgrade to 1.4.2
-      eval("try {var v = java.lang.System.getProperty('java.version');" +
-           " _jmol.isBrowserCompliant = v >= '1.4.2';" +
-           " } catch (e) { }");
-    } else if (browser == "opera" && browserVersion <= 7.54) {
-      isBrowserCompliant = false;
-    } else {
-      isBrowserCompliant = hasGetElementById &&
-        !((browser == "msie") ||
-          (browser == "webkit" && browserVersion < 125.12));
-    }
-  } else if (os == "linux" || os == "unix") {
-    if (browser == "konqueror" && browserVersion <= 3.3)
-      isBrowserCompliant = false;
-    else
-      isBrowserCompliant = hasGetElementById;
-  } else { // other OS
-    isBrowserCompliant = hasGetElementById;
-  }
-
-  // possibly more checks in the future for this
-  isJavaCompliant = isJavaEnabled;
-
-  isFullyCompliant = isBrowserCompliant && isJavaCompliant;
-
-  useIEObject = (os == "win" && browser == "msie" && browserVersion >= 5.5);
-  useHtml4Object =
-   (browser == "mozilla" && browserVersion >= 5) ||
-   (browser == "opera" && browserVersion >= 8) ||
-   (browser == "webkit" && browserVersion >= 412.2);
- try {
-  if (top.location.search.indexOf("JMOLJAR=")>=0)
-    jmoljar = top.location.search.split("JMOLJAR=")[1].split("&")[0];
- } catch(e) {
-  // can't access top.location
- }
- try {
-  useNoApplet = (top.location.search.indexOf("NOAPPLET")>=0);
- } catch(e) {
-  // can't access top.document
- }
-}
-
-function jmolSetMemoryMb(nMb) {
-  _jmol.java_arguments = "-Xmx" + Math.round(nMb) + "m"
-}
-
-function jmolSetParameter(name,value) {
-  _jmol.params[name] = value
-}
-
-function jmolSetCallback(callbackName,funcName) {
-  _jmol.params[callbackName] = funcName
-}
-
- try {
-// note this is done FIRST, so it cannot override a setting done by the developer
-  if (top.location.search.indexOf("PARAMS=")>=0) {
-    var pars = unescape(top.location.search.split("PARAMS=")[1].split("&")[0]).split(";");
-    for (var i = 0; i < pars.length; i++) {
-      var p = pars[i].split(":");
-      jmolSetParameter(p[0],p[1]);
-    }
-  }
- } catch(e) {
-  // can't access top.location
- }
-
-function jmolSetSyncId(n) {
-  return _jmol.params["syncId"] = n
-}
-
-function jmolGetSyncId() {
-  return _jmol.params["syncId"]
-}
-
-function jmolSetLogLevel(n) {
-  _jmol.params.logLevel = ''+n;
-}
-
-	/*  AngelH, mar2007:
-		By (re)setting these variables in the webpage before calling jmolApplet(), 
-		a custom message can be provided (e.g. localized for user's language) when no Java is installed.
-	*/
-if (noJavaMsg==undefined) var noJavaMsg = 
-        "You do not have Java applets enabled in your web browser, or your browser is blocking this applet.<br />\n" +
-        "Check the warning message from your browser and/or enable Java applets in<br />\n" +
-        "your web browser preferences, or install the Java Runtime Environment from <a href='http://www.java.com'>www.java.com</a><br />";
-if (noJavaMsg2==undefined) var noJavaMsg2 = 
-        "You do not have the<br />\n" +
-        "Java Runtime Environment<br />\n" +
-        "installed for applet support.<br />\n" +
-        "Visit <a href='http://www.java.com'>www.java.com</a>";
-function _jmolApplet(size, inlineModel, script, nameSuffix) {
-	/*  AngelH, mar2007
-		Fixed percent / pixel business, to avoid browser errors:
-		put "px" where needed, avoid where not.
-
-	    Bob Hanson, 1/2010
-		Fixed inline escape changing returns to |		
-	*/
-  with (_jmol) {
-    nameSuffix == undefined && (nameSuffix = appletCount);
-    appletSuffixes.push(nameSuffix);
-    ++appletCount;
-    script || (script = "select *");
-    var sz = _jmolGetAppletSize(size);
-    var widthAndHeight = " width='" + sz[0] + "' height='" + sz[1] + "' ";
-    var tHeader, tFooter;
-    codebase || jmolInitialize(".");
-    if (useIEObject || useHtml4Object) {
-      params.archive = archivePath;
-      params.mayscript = 'true';
-      params.codebase = codebase;
-      params.code = 'JmolApplet';
-      tHeader = 
-        "<object name='jmolApplet" + nameSuffix +
-        "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
-				widthAndHeight + "\n";
-      tFooter = "</object>";
-    }
-    if (java_arguments)
-      params.java_arguments = java_arguments;
-    if (useIEObject) { // use MSFT IE6 object tag with .cab file reference
-      tHeader += " classid='" + windowsClassId + "'\n" +
-      (windowsCabUrl ? " codebase='" + windowsCabUrl + "'\n" : "") + ">\n";
-    } else if (useHtml4Object) { // use HTML4 object tag
-      tHeader += " type='application/x-java-applet'\n>\n";
-				/*	" classid='java:JmolApplet'\n" +	AH removed this
-				  Chromium Issue 62076: 	Java Applets using an <object> with a classid paramater don't load.
-					http://code.google.com/p/chromium/issues/detail?id=62076
-					They say this is the correct behavior according to the spec, and there's no indication at this point 
-					that WebKit will be changing the handling, so eventually Safari will acquire this behavior too.
-					Removing the classid parameter seems to be well tolerated by all browsers (even IE!).
-				*/
-    } else { // use applet tag
-      tHeader = 
-        "<applet name='jmolApplet" + nameSuffix +
-        "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
-				widthAndHeight + "\n" +
-        " code='JmolApplet'" +
-        " archive='" + archivePath + "' codebase='" + codebase + "'\n" +
-        " mayscript='true'>\n";
-      tFooter = "</applet>";
-    }
-    var visitJava;
-    if (useIEObject || useHtml4Object) {
-		var szX = "width:" + sz[0]
-		if ( szX.indexOf("%")==-1 ) szX+="px" 
-		var szY = "height:" + sz[1]
-		if ( szY.indexOf("%")==-1 ) szY+="px" 
-      visitJava =
-        "<p style='background-color:yellow; color:black; " +
-		szX + ";" + szY + ";" +
-        // why doesn't this vertical-align work?
-	"text-align:center;vertical-align:middle;'>\n" +
-		noJavaMsg +
-        "</p>";
-    } else {
-      visitJava =
-        "<table bgcolor='yellow'><tr>" +
-        "<td align='center' valign='middle' " + widthAndHeight + "><font color='black'>\n" +
-		noJavaMsg2 +
-        "</font></td></tr></table>";
-    }
-    params.loadInline = (inlineModel ? inlineModel : "");
-    params.script = (script ? _jmolSterilizeScript(script) : "");
-    var t = tHeader + _jmolParams() + visitJava + tFooter;
-    jmolSetTarget(nameSuffix);
-    ready["jmolApplet" + nameSuffix] = false;
-    if (_jmol.debugAlert)
-      alert(t);
-    return _jmolDocumentWrite(t);
-  }
-}
-
-function _jmolParams() {
- var t = "";
- for (var i in _jmol.params)
-	if(_jmol.params[i]!="")
-		 t+="  <param name='"+i+"' value='"+_jmol.params[i]+"' />\n";
- return t
-}
-
-function _jmolInitCheck() {
-  if (_jmol.initChecked)
-    return;
-  _jmol.initChecked = true;
-  jmolInitialize(defaultdir, defaultjar)
-}
-
-function _jmolCheckBrowser() {
-  with (_jmol) {
-    if (browserChecked)
-      return;
-    browserChecked = true;
-  
-    if (isFullyCompliant)
-      return true;
-
-    if (checkBrowserAction == "redirect")
-      location.href = checkBrowserUrlOrMessage;
-    else if (checkBrowserAction == "popup")
-      _jmolPopup(checkBrowserUrlOrMessage);
-    else {
-      var msg = checkBrowserUrlOrMessage;
-      if (msg == null)
-        msg = "Your web browser is not fully compatible with Jmol\n\n" +
-              "browser: " + browser +
-              "   version: " + browserVersion +
-              "   os: " + os +
-              "   isBrowserCompliant: " + isBrowserCompliant +
-              "   isJavaCompliant: " + isJavaCompliant +
-              "\n\n" + ua;
-      alert(msg);
-    }
-  }
-  return false;
-}
-
-function jmolSetXHTML(id) {
-	_jmol.isXHTML = true
-	_jmol.XhtmlElement = null
-	_jmol.XhtmlAppendChild = false
-	if (id){
-		_jmol.XhtmlElement = document.getElementById(id)
-		_jmol.XhtmlAppendChild = true
-	}
-}
-
-function _jmolDocumentWrite(text) {
-	if (_jmol.currentDocument) {
-		if (_jmol.isXHTML && !_jmol.XhtmlElement) {
-			var s = document.getElementsByTagName("script")
-			_jmol.XhtmlElement = s.item(s.length - 1)
-			_jmol.XhtmlAppendChild = false
-		}
-		if (_jmol.XhtmlElement) {
-			_jmolDomDocumentWrite(text)
-		} else {
-			_jmol.currentDocument.write(text);
-		}
-	}
-	return text;
-}
-
-function _jmolDomDocumentWrite(data) {
-	var pt = 0
-	var Ptr = []
-	Ptr[0] = 0
-	while (Ptr[0] < data.length) {
-		var child = _jmolGetDomElement(data, Ptr)
-		if (!child)break
-		if (_jmol.XhtmlAppendChild)
-			_jmol.XhtmlElement.appendChild(child)
-		else
-			_jmol.XhtmlElement.parentNode.insertBefore(child, _jmol.XhtmlElement); 
-	}
-}
-function _jmolGetDomElement(data, Ptr, closetag, lvel) {
-	var e = document.createElement("span")
-	e.innerHTML = data
-	Ptr[0] = data.length
-	return e
-
-//unnecessary?
-
-	closetag || (closetag = "")
-	lvel || (lvel = 0)
-	var pt0 = Ptr[0]
-	var pt = pt0
-	while (pt < data.length && data.charAt(pt) != "<") pt++
-	if (pt != pt0) {
-		var text = data.substring(pt0, pt)
-		Ptr[0] = pt
-		return document.createTextNode(text)
-	}	
-	pt0 = ++pt
-	var ch
-	while (pt < data.length && "\n\r\t >".indexOf(ch = data.charAt(pt)) < 0) pt++
-	var tagname = data.substring(pt0, pt)
-	var e = (tagname == closetag  || tagname == "/" ? "" 
-		: document.createElementNS ? document.createElementNS('http://www.w3.org/1999/xhtml', tagname)
-		: document.createElement(tagname));
-	if (ch == ">") {
-		Ptr[0] = ++pt
-		return e
-	}
-	while (pt < data.length && (ch = data.charAt(pt)) != ">") {
-		while (pt < data.length && "\n\r\t ".indexOf(ch = data.charAt(pt)) >= 0) pt++
-		pt0 = pt
-		while (pt < data.length && "\n\r\t =/>".indexOf(ch = data.charAt(pt)) < 0) pt++
-		var attrname = data.substring(pt0, pt).toLowerCase()
-		if (attrname && ch != "=") 
-			e.setAttribute(attrname, "true")
-		while (pt < data.length && "\n\r\t ".indexOf(ch = data.charAt(pt)) >= 0) pt++
-		if (ch == "/") {
-			Ptr[0] = pt + 2
-			return e
-		} else if (ch == "=") {
-			var quote = data.charAt(++pt)
-			pt0 = ++pt
-			while (pt < data.length && (ch = data.charAt(pt)) != quote) pt++
-			var attrvalue = data.substring(pt0, pt)
-			e.setAttribute(attrname, attrvalue)
-			pt++
-		}
-	}
-	Ptr[0] = ++pt
-	while (Ptr[0] < data.length) {
-		var child = _jmolGetDomElement(data, Ptr, "/" + tagname, lvel+1)
-		if (!child)break
-		e.appendChild(child)
-	}
-	return e
-}
-
-function _jmolPopup(url) {
-  var popup = window.open(url, "JmolPopup",
-                          "left=150,top=150,height=400,width=600," +
-                          "directories=yes,location=yes,menubar=yes," +
-                          "toolbar=yes," +
-                          "resizable=yes,scrollbars=yes,status=yes");
-  if (popup.focus)
-    poup.focus();
-}
-
-function _jmolReadyCallback(name) {
-  if (_jmol.debugAlert)
-    alert(name + " is ready");
-  _jmol.ready["" + name] = true;
-}
-
-function _jmolSterilizeScript(script) {
-  script = script.replace(/'/g, "&#39;");
-  if (_jmol.debugAlert)
-    alert("script:\n" + script);
-  return script;
-}
-
-function _jmolSterilizeInline(model) {
-  model = model.replace(/\r|\n|\r\n/g, (model.indexOf("|") >= 0 ? "\\/n" : "|")).replace(/'/g, "&#39;");
-  if (_jmol.debugAlert)
-    alert("inline model:\n" + model);
-  return model;
-}
-
-function _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
-  ++_jmol.radioCount;
-  groupName != undefined && groupName != null || (groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1));
-  if (!script)
-    return "";
-  labelHtml != undefined && labelHtml != null || (labelHtml = script.substring(0, 32));
-  separatorHtml || (separatorHtml = "")
-  var scriptIndex = _jmolAddScript(script);
-  var eospan = "</span>"
-  var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input name='" 
-	+ groupName + "' id='"+id+"' type='radio' onclick='_jmolClick(this," +
-         scriptIndex + _jmol.targetText + ");return true;' onmouseover='_jmolMouseOver(" +
-         scriptIndex + ");return true;' onmouseout='_jmolMouseOut()' " +
-	 (isChecked ? "checked='true' " : "") + _jmol.radioCssText + " />"
-  if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
-	t += eospan
-	eospan = "";
-  }
-  t += "<label for=\"" + id + "\">" + labelHtml + "</label>" +eospan + separatorHtml;
-
-  return t;
-}
-
-function _jmolFindApplet(target) {
-  // first look for the target in the current window
-  var applet = _jmolFindAppletInWindow(_jmol.appletWindow != null ? _jmol.appletWindow : window, target);
-  // THEN look for the target in child frames
-  if (applet == undefined)
-    applet = _jmolSearchFrames(window, target);
-  // FINALLY look for the target in sibling frames
-  if (applet == undefined)
-    applet = _jmolSearchFrames(top, target); // look starting in top frame
-  return applet;
-}
-
-function _jmolGetApplet(targetSuffix){
- var target = "jmolApplet" + (targetSuffix ? targetSuffix : "0");
- var applet = _jmolFindApplet(target);
- if (applet) return applet
- _jmol.alerted || alert("could not find applet " + target);
- _jmol.alerted = true;
- return null
-}
-
-function _jmolSearchFrames(win, target) {
-  var applet;
-  var frames = win.frames;
-  if (frames && frames.length) { // look in all the frames below this window
-   try{
-    for (var i = 0; i < frames.length; ++i) {
-      applet = _jmolSearchFrames(frames[i], target);
-      if (applet)
-        return applet;
-    }
-   }catch(e) {
-	if (_jmol.debugAlert)
-		alert("Jmol.js _jmolSearchFrames cannot access " + win.name + ".frame[" + i + "] consider using jmolSetAppletWindow()") 
-   }
-  }
-  return applet = _jmolFindAppletInWindow(win, target)
-}
-
-function _jmolFindAppletInWindow(win, target) {
-    var doc = win.document;
-		if (doc.getElementById(target))
-      return doc.getElementById(target);
-    else if (doc.applets)
-      return doc.applets[target];
-    else
-      return doc[target]; 
-}
-
-function _jmolAddScript(script) {
-  if (!script)
-    return 0;
-  var index = _jmol.scripts.length;
-  _jmol.scripts[index] = script;
-  return index;
-}
-
-function _jmolClick(elementClicked, scriptIndex, targetSuffix) {
-  _jmol.element = elementClicked;
-  _jmolScriptExecute(elementClicked, _jmol.scripts[scriptIndex], targetSuffix);
-}
-
-function _jmolMenuSelected(menuObject, targetSuffix) {
-  var scriptIndex = menuObject.value;
-  if (scriptIndex != undefined) {
-    _jmolScriptExecute(menuObject, _jmol.scripts[scriptIndex], targetSuffix);
-    return;
-  }
-  var len = menuObject.length;
-  if (typeof len == "number") {
-    for (var i = 0; i < len; ++i) {
-      if (menuObject[i].selected) {
-        _jmolClick(menuObject[i], menuObject[i].value, targetSuffix);
-	return;
-      }
-    }
-  }
-  alert("?Que? menu selected bug #8734");
-}
-
-
-_jmol.checkboxMasters = {};
-_jmol.checkboxItems = {};
-
-function jmolSetCheckboxGroup(chkMaster,chkBox) {
-	var id = chkMaster;
-	if(typeof(id)=="number")id = "jmolCheckbox" + id;
-	chkMaster = document.getElementById(id);
-	if (!chkMaster)alert("jmolSetCheckboxGroup: master checkbox not found: " + id);
-	var m = _jmol.checkboxMasters[id] = {};
-	m.chkMaster = chkMaster;
-	m.chkGroup = {};
-	for (var i = 1; i < arguments.length; i++){
-		var id = arguments[i];
-		if(typeof(id)=="number")id = "jmolCheckbox" + id;
-		checkboxItem = document.getElementById(id);
-		if (!checkboxItem)alert("jmolSetCheckboxGroup: group checkbox not found: " + id);
-		m.chkGroup[id] = checkboxItem;
-		_jmol.checkboxItems[id] = m;
-	}
-}
-
-function _jmolNotifyMaster(m){
-	//called when a group item is checked
-	var allOn = true;
-	var allOff = true;
-	for (var chkBox in m.chkGroup){
-		if(m.chkGroup[chkBox].checked)
-			allOff = false;
-		else
-			allOn = false;
-	}
-	if (allOn)m.chkMaster.checked = true;	
-	if (allOff)m.chkMaster.checked = false;
-	if ((allOn || allOff) && _jmol.checkboxItems[m.chkMaster.id])
-		_jmolNotifyMaster(_jmol.checkboxItems[m.chkMaster.id])
-}
-
-function _jmolNotifyGroup(m, isOn){
-	//called when a master item is checked
-	for (var chkBox in m.chkGroup){
-		var item = m.chkGroup[chkBox]
-		item.checked = isOn;
-		if (_jmol.checkboxMasters[item.id])
-			_jmolNotifyGroup(_jmol.checkboxMasters[item.id], isOn)
-	}
-}
-
-function _jmolCbClick(ckbox, whenChecked, whenUnchecked, targetSuffix) {
-  _jmol.control = ckbox
-  _jmolClick(ckbox, ckbox.checked ? whenChecked : whenUnchecked, targetSuffix);
-  if(_jmol.checkboxMasters[ckbox.id])
-	_jmolNotifyGroup(_jmol.checkboxMasters[ckbox.id], ckbox.checked)
-  if(_jmol.checkboxItems[ckbox.id])
-	_jmolNotifyMaster(_jmol.checkboxItems[ckbox.id])
-}
-
-function _jmolCbOver(ckbox, whenChecked, whenUnchecked) {
-  window.status = _jmol.scripts[ckbox.checked ? whenUnchecked : whenChecked];
-}
-
-function _jmolMouseOver(scriptIndex) {
-  window.status = _jmol.scripts[scriptIndex];
-}
-
-function _jmolMouseOut() {
-  window.status = " ";
-  return true;
-}
-
-function _jmolSetCodebase(codebase) {
-  _jmol.codebase = codebase ? codebase : ".";
-  if (_jmol.debugAlert)
-    alert("jmolCodebase=" + _jmol.codebase);
-}
-
-function _jmolOnloadResetForms() {
-  // must be evaluated ONLY once
-  _jmol.previousOnloadHandler = window.onload;
-  window.onload =
-  function() {
-    with (_jmol) {
-      if (buttonCount+checkboxCount+menuCount+radioCount+radioGroupCount > 0) {
-        var forms = document.forms;
-        for (var i = forms.length; --i >= 0; )
-          forms[i].reset();
-      }
-      if (previousOnloadHandler)
-        previousOnloadHandler();
-    }
-  }
-}
-
-////////////////////////////////////
-/////extensions for getProperty/////
-////////////////////////////////////
-
-
-function _jmolEvalJSON(s,key){
- s=s+""
- if(!s)return []
- if(s.charAt(0)!="{"){
-	if(s.indexOf(" | ")>=0)s=s.replace(/\ \|\ /g, "\n")
-	return s
- }
- var A = eval("("+s+")")
- if(!A)return
- if(key && A[key])A=A[key]
- return A
-}
-
-function _jmolEnumerateObject(A,key){
- var sout=""
- if(typeof(A) == "string" && A!="null"){
-	sout+="\n"+key+"=\""+A+"\""
- }else if(!isNaN(A)||A==null){
-	sout+="\n"+key+"="+(A+""==""?"null":A)
- }else if(A.length){
-    sout+=key+"=[]"
-    for(var i=0;i<A.length;i++){
-	sout+="\n"
-	if(typeof(A[i]) == "object"||typeof(A[i]) == "array"){
-		sout+=_jmolEnumerateObject(A[i],key+"["+i+"]")
-	}else{
-		sout+=key+"["+i+"]="+(typeof(A[i]) == "string" && A[i]!="null"?"\""+A[i].replace(/\"/g,"\\\"")+"\"":A[i])
-	}
-    }
- }else{
-    if(key != ""){
-	sout+=key+"={}"
-	key+="."
-    }
-    
-    for(var i in A){
-	sout+="\n"
-	if(typeof(A[i]) == "object"||typeof(A[i]) == "array"){
-		sout+=_jmolEnumerateObject(A[i],key+i)
-	}else{
-		sout+=key+i+"="+(typeof(A[i]) == "string" && A[i]!="null"?"\""+A[i].replace(/\"/g,"\\\"")+"\"":A[i])
-	}
-    }
- } 
- return sout
-}
-
-
-function _jmolSortKey0(a,b){
- return (a[0]<b[0]?1:a[0]>b[0]?-1:0)
-}
-
-function _jmolSortMessages(A){
- if(!A || typeof(A)!="object")return []
- var B = []
- for(var i=A.length-1;i>=0;i--)for(var j=0;j<A[i].length;j++)B[B.length]=A[i][j]
- if(B.length == 0) return
- B=B.sort(_jmolSortKey0)
- return B
-}
-
-/////////additional extensions //////////
-
-
-function _jmolDomScriptLoad(URL){
- //open(URL) //to debug
- _jmol.servercall=URL
- var node = document.getElementById("_jmolScriptNode")
- if (node && _jmol.browser!="msie"){
-    document.getElementsByTagName("HEAD")[0].removeChild(node)
-    node=null
- }
- if (node) {
-   node.setAttribute("src",URL)
- } else {
-   node=document.createElement("script")
-   node.setAttribute("id","_jmolScriptNode")
-   node.setAttribute("type","text/javascript")
-   node.setAttribute("src",URL)
-   document.getElementsByTagName("HEAD")[0].appendChild(node)
- }
-}
-
-
-function _jmolExtractPostData(url){
- S=url.split("&POST:")
- var s=""
- for(var i=1;i<S.length;i++){
-	KV=S[i].split("=")
-	s+="&POSTKEY"+i+"="+KV[0]
-	s+="&POSTVALUE"+i+"="+KV[1]
- }
- return "&url="+escape(S[0])+s
-}
-
-function _jmolLoadModel(targetSuffix,remoteURL,array,isError,errorMessage){
- //called by server, but in client
- //overload this function to customize return
- _jmol.remoteURL=remoteURL
- isError && alert(errorMessage)
- jmolLoadInlineScript(array.join("\n"),_jmol.optionalscript,targetSuffix)
-}
-
-//////////user property/status functions/////////
-
-function jmolGetStatus(strStatus,targetSuffix){
- return _jmolSortMessages(jmolGetPropertyAsArray("jmolStatus",strStatus,targetSuffix))
-}
-
-function jmolGetPropertyAsArray(sKey,sValue,targetSuffix) {
- return _jmolEvalJSON(jmolGetPropertyAsJSON(sKey,sValue,targetSuffix),sKey)
-}
-
-function jmolGetPropertyAsString(sKey,sValue,targetSuffix) {
- var applet = _jmolGetApplet(targetSuffix);
- sValue == undefined && (sValue="");
- return (applet ? applet.getPropertyAsString(sKey,sValue) + "" : "")
-}
-
-function jmolGetPropertyAsJSON(sKey,sValue,targetSuffix) {
- sValue == undefined && (sValue = "")
- var applet = _jmolGetApplet(targetSuffix);
- try {
-  return (applet ? applet.getPropertyAsJSON(sKey,sValue) + "" : "")
- } catch(e) {
-  return ""
- }
-}
-
-function jmolGetPropertyAsJavaObject(sKey,sValue,targetSuffix) {
- sValue == undefined && (sValue = "")
- var applet = _jmolGetApplet(targetSuffix);
- return (applet ? applet.getProperty(sKey,sValue) : null)
-}
-
-
-function jmolDecodeJSON(s) {
- return _jmolEnumerateObject(_jmolEvalJSON(s),"")
-}
-
-
-///////// synchronous scripting ////////
-
-function jmolScriptWait(script, targetSuffix) {
-  targetSuffix == undefined && (targetSuffix="0")
-  var Ret=jmolScriptWaitAsArray(script, targetSuffix)
-  var s = ""
-  for(var i=Ret.length;--i>=0;)
-  for(var j=0;j< Ret[i].length;j++)
-	s+=Ret[i][j]+"\n"
-  return s
-}
-
-function jmolScriptWaitOutput(script, targetSuffix) {
-  targetSuffix == undefined && (targetSuffix="0")
-  var ret = ""
-  try{
-   if (script) {
-    _jmolCheckBrowser();
-    var applet=_jmolGetApplet(targetSuffix);
-    if (applet) ret += applet.scriptWaitOutput(script);
-   }
-  }catch(e){
-  }
- return ret;
-}
-
-function jmolEvaluate(molecularMath, targetSuffix) {
-
-  //carries out molecular math on a model
-
-  targetSuffix == undefined && (targetSuffix="0")
-  var result = "" + jmolGetPropertyAsJavaObject("evaluate", molecularMath, targetSuffix);
-  var s = result.replace(/\-*\d+/,"")
-  if (s == "" && !isNaN(parseInt(result)))return parseInt(result);
-  var s = result.replace(/\-*\d*\.\d*/,"")
-  if (s == "" && !isNaN(parseFloat(result)))return parseFloat(result);
-  return result;
-}
-
-function jmolScriptEcho(script, targetSuffix) {
-  // returns a newline-separated list of all echos from a script
-  targetSuffix == undefined && (targetSuffix="0")
-  var Ret=jmolScriptWaitAsArray(script, targetSuffix)
-  var s = ""
-  for(var i=Ret.length;--i>=0;)
-  for(var j=Ret[i].length;--j>=0;)
-        if (Ret[i][j][1] == "scriptEcho")s+=Ret[i][j][3]+"\n"
-  return s.replace(/ \| /g, "\n")
-}
-
-
-function jmolScriptMessage(script, targetSuffix) {
-  // returns a newline-separated list of all messages from a script, ending with "script completed\n"
-  targetSuffix == undefined && (targetSuffix="0")
-  var Ret=jmolScriptWaitAsArray(script, targetSuffix)
-  var s = ""
-  for(var i=Ret.length;--i>=0;)
-  for(var j=Ret[i].length;--j>=0;)
-        if (Ret[i][j][1] == "scriptStatus")s+=Ret[i][j][3]+"\n"
-  return s.replace(/ \| /g, "\n")
-}
-
-
-function jmolScriptWaitAsArray(script, targetSuffix) {
- var ret = ""
- try{
-  jmolGetStatus("scriptEcho,scriptMessage,scriptStatus,scriptError",targetSuffix)
-  if (script) {
-    _jmolCheckBrowser();
-    var applet=_jmolGetApplet(targetSuffix);
-    if (applet) ret += applet.scriptWait(script);
-    ret = _jmolEvalJSON(ret,"jmolStatus")
-    if(typeof ret == "object")
-	return ret
-  }
- }catch(e){
- }
-  return [[ret]]
-}
-
-
-
-////////////   save/restore orientation   /////////////
-
-function jmolSaveOrientation(id, targetSuffix) {  
- targetSuffix == undefined && (targetSuffix="0")
- return _jmol["savedOrientation"+id] = jmolGetPropertyAsArray("orientationInfo","info",targetSuffix).moveTo
-}
-
-function jmolRestoreOrientation(id, targetSuffix) {
- targetSuffix == undefined && (targetSuffix="0")
- var s=_jmol["savedOrientation"+id]
- if (!s || s == "")return
- s=s.replace(/1\.0/,"0")
- return jmolScriptWait(s,targetSuffix)
-}
-
-function jmolRestoreOrientationDelayed(id, delay, targetSuffix) {
- arguments.length < 2 && (delay=1)
- targetSuffix == undefined && (targetSuffix="0")
- var s=_jmol["savedOrientation"+id]
- if (!s || s == "")return
- s=s.replace(/1\.0/,delay)
- return jmolScriptWait(s,targetSuffix)
-}
-
-////////////  add parameter /////////////
-/*
- * for adding callbacks or other parameters. Use:
-
-   jmolSetDocument(0)
-   var s= jmolApplet(....)
-   s = jmolAppletAddParam(s,"messageCallback", "myFunctionName")
-   document.write(s)
-   jmolSetDocument(document) // if you want to then write buttons and such normally
- 
- */
-
-function jmolAppletAddParam(appletCode,name,value){
-  return (value == "" ? appletCode : appletCode.replace(/\<param/,"\n<param name='"+name+"' value='"+value+"' />\n<param"))
-}
-
-///////////////auto load Research Consortium for Structural Biology (RCSB) data ///////////
-
-function jmolLoadAjax_STOLAF_RCSB(fileformat,pdbid,optionalscript,targetSuffix){
-
- _jmol.thismodel || (_jmol.thismodel = "1crn")
- _jmol.serverURL || (_jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm")
- _jmol.RCSBserver || (_jmol.RCSBserver="http://www.rcsb.org")
- _jmol.defaultURL_RCSB || (_jmol.defaultURL_RCSB=_jmol.RCSBserver+"/pdb/files/1CRN.CIF")
- fileformat || (fileformat="PDB")
- pdbid || (pdbid=prompt("Enter a 4-digit PDB ID:",_jmol.thismodel))
- if(!pdbid || pdbid.length != 4)return ""
- targetSuffix || (targetSuffix="0")
- optionalscript || (optionalscript="")
- var url=_jmol.defaultURL_RCSB.replace(/1CRN/g,pdbid.toUpperCase())
- fileformat=="CIF" || (url=url.replace(/CIF/,fileformat))
- _jmol.optionalscript=optionalscript
- _jmol.thismodel=pdbid
- _jmol.thistargetsuffix=targetSuffix
- _jmol.thisurl=url
- _jmol.modelArray = []
- url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)
- _jmolDomScriptLoad(url)
- return url
-}
-
-
-///////////////auto load NIH CACTVS data -- compound name or SMILES ///////////
-
-function jmolLoadAjax_STOLAF_NIH(compoundid,optionalscript,targetSuffix){
- _jmol.thismodel || (_jmol.thismodel = "aspirin")
- _jmol.serverURL || (_jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm")
- _jmol.defaultURL_NIH || (_jmol.defaultURL_NIH="http://cactus.nci.nih.gov/chemical/structure/FILE/file?format=sdf&get3d=True")
- compoundid || (compoundid=prompt("Enter a compound name or a SMILES string:",_jmol.thismodel))
- if(!compoundid)return ""
- targetSuffix || (targetSuffix="0")
- optionalscript || (optionalscript="")
- var url=_jmol.defaultURL_NIH.replace(/FILE/g,compoundid)
- _jmol.optionalscript=optionalscript
- _jmol.thismodel=compoundid
- _jmol.thistargetsuffix=targetSuffix
- _jmol.thisurl=url
- _jmol.modelArray = []
- url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)
- _jmolDomScriptLoad(url)
- return url
-}
-
-
-/////////////// St. Olaf College AJAX server -- ANY URL ///////////
-
-function jmolLoadAjax_STOLAF_ANY(url, userid, optionalscript,targetSuffix){
- _jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm"
- _jmol.thisurlANY || (_jmol.thisurlANY = "http://www.stolaf.edu/depts/chemistry/mo/struc/data/ycp3-1.mol")
- url || (url=prompt("Enter any (uncompressed file) URL:", _jmol.thisurlANY))
- userid || (userid="0")
- targetSuffix || (targetSuffix="0")
- optionalscript || (optionalscript="")
- _jmol.optionalscript=optionalscript
- _jmol.thistargetsuffix=targetSuffix
- _jmol.modelArray = []
- _jmol.thisurl = url
- url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)
- _jmolDomScriptLoad(url)
-}
-
-
-/////////////// Mineralogical Society of America (MSA) data /////////
-
-function jmolLoadAjax_MSA(key,value,optionalscript,targetSuffix){
-
- _jmol.thiskeyMSA || (_jmol.thiskeyMSA = "mineral")
- _jmol.thismodelMSA || (_jmol.thismodelMSA = "quartz")
- _jmol.ajaxURL_MSA || (_jmol.ajaxURL_MSA="http://rruff.geo.arizona.edu/AMS/result.php?mineral=quartz&viewing=ajaxjs")
- key || (key=prompt("Enter a field:", _jmol.thiskeyMSA))
- if(!key)return ""
- value || (value=prompt("Enter a "+key+":", _jmol.thismodelMSA))
- if(!value)return ""
- targetSuffix || (targetSuffix="0")
- optionalscript || (optionalscript="")
- optionalscript == 1 && (optionalscript='load "" {1 1 1}')
- var url=_jmol.ajaxURL_MSA.replace(/mineral/g,key).replace(/quartz/g,value)
- _jmol.optionalscript=optionalscript
- _jmol.thiskeyMSA=key
- _jmol.thismodelMSA=value
- _jmol.thistargetsuffix=targetSuffix
- _jmol.thisurl=url
- _jmol.modelArray = []
- loadModel=_jmolLoadModel
- _jmolDomScriptLoad(url)
- return url
-}
-
-
-
-function jmolLoadAjaxJS(url, userid, optionalscript,targetSuffix){
- userid || (userid="0")
- targetSuffix || (targetSuffix="0")
- optionalscript || (optionalscript="")
- _jmol.optionalscript=optionalscript
- _jmol.thismodel=userid
- _jmol.thistargetsuffix=targetSuffix
- _jmol.modelArray = []
- _jmol.thisurl = url
- url+="&returnFunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix
- _jmolDomScriptLoad(url)
-}
-
-
-//// in case Jmol library has already been loaded:
-
-}catch(e){}
-
-///////////////moving atoms //////////////
-
-// HIGHLY experimental!!
-
-function jmolSetAtomCoord(i,x,y,z,targetSuffix){
-    _jmolCheckBrowser();
-      var applet=_jmolGetApplet(targetSuffix);
-      if (applet) applet.getProperty('jmolViewer').setAtomCoord(i,x,y,z)
-}
-
-function jmolSetAtomCoordRelative(i,x,y,z,targetSuffix){
-    _jmolCheckBrowser();
-      var applet=_jmolGetApplet(targetSuffix);
-      if (applet) applet.getProperty('jmolViewer').setAtomCoordRelative(i,x,y,z)
-}
-
-
-///////////////applet fake for testing buttons/////////////
-
-
-if(_jmol.useNoApplet){
-	jmolApplet = function(w){
-		var s="<table style='background-color:black' width="+w+"><tr height="+w+">"
-		+"<td align=center valign=center style='background-color:white'>"
-		+"Applet would be here"
-		+"<p><textarea id=fakeApplet rows=5 cols=50></textarea>"
-		+"</td></tr></table>"
-		return _jmolDocumentWrite(s)
-	}
-
-	_jmolFindApplet = function(){return jmolApplet0}
-
-	jmolApplet0 = {
-	 script: function(script){document.getElementById("fakeApplet").value="\njmolScript:\n"+script}
-	,scriptWait: function(script){document.getElementById("fakeApplet").value="\njmolScriptWait:\n"+script}	
-	,loadInline: function(data,script){document.getElementById("fakeApplet").value="\njmolLoadInline data:\n"+data+"\n\nscript:\n"+script}
-	}
-}
-
-
-///////////////////////////////////////////
-
-  //  This should no longer be needed, jmolResizeApplet() is better; kept for backwards compatibility
-  /*
-	Resizes absolutely (pixels) or by percent of window (w or h 0.5 means 50%).
-	targetSuffix is optional and defaults to zero (first applet in page).
-	Both w and h are optional, but needed if you want to use targetSuffix.
-		h defaults to w
-		w defaults to 100% of window
-	If either w or h is between 0 and 1, then it is taken as percent/100.
-	If either w or h is greater than 1, then it is taken as a size (pixels). 
-	*/
-function jmolResize(w,h,targetSuffix) {
- _jmol.alerted = true;
- var percentW = (!w ? 100 : w <= 1  && w > 0 ? w * 100 : 0);
- var percentH = (!h ? percentW : h <= 1 && h > 0 ? h * 100 : 0);
- if (_jmol.browser=="msie") {
-   var width=document.body.clientWidth;
-   var height=document.body.clientHeight;
- } else {
-   var netscapeScrollWidth=15;
-   var width=window.innerWidth - netscapeScrollWidth;
-   var height=window.innerHeight-netscapeScrollWidth;
- }
- var applet = _jmolGetApplet(targetSuffix);
- if(!applet)return;
- applet.style.width = (percentW ? width * percentW/100 : w)+"px";
- applet.style.height = (percentH ? height * percentH/100 : (h ? h : w))+"px";
- //title=width +  " " + height + " " + (new Date());
-}
-
-// 13 Jun 09 -- makes jmolResize() obsolete  (kept for backwards compatibility)
-function jmolResizeApplet(size,targetSuffix) {
- // See _jmolGetAppletSize() for the formats accepted as size [same used by jmolApplet()]
- //  Special case: an empty value for width or height is accepted, meaning no change in that dimension.
- _jmol.alerted = true;
- var applet = _jmolGetApplet(targetSuffix);
- if(!applet)return;
- var sz = _jmolGetAppletSize(size, "px");
- sz[0] && (applet.style.width = sz[0]);
- sz[1] && (applet.style.height = sz[1]);
-}
-
-function _jmolGetAppletSize(size, units) {
-	/* Accepts single number or 2-value array, each one can be one of:
-	   percent (text string ending %), decimal 0 to 1 (percent/100), number, or text string (interpreted as nr.)
-	   [width, height] array of strings is returned, with units added if specified.
-	   Percent is relative to container div or element (which should have explicitly set size).
-	*/
-  var width, height;
-  if ( (typeof size) == "object" && size != null ) {
-    width = size[0]; height = size[1];
-  } else {
-    width = height = size;
-  }
-  return [_jmolFixDim(width, units), _jmolFixDim(height, units)];
-}
-
-function _jmolFixDim(x, units) {
-  var sx = "" + x;
-  return (sx.length == 0 ? (units ? "" : _jmol.allowedJmolSize[2])
-	: sx.indexOf("%") == sx.length-1 ? sx 
-  	: (x = parseFloat(x)) <= 1 && x > 0 ? x * 100 + "%"
-  	: (isNaN(x = Math.floor(x)) ? _jmol.allowedJmolSize[2]
-  		: x < _jmol.allowedJmolSize[0] ? _jmol.allowedJmolSize[0]
-  	    : x > _jmol.allowedJmolSize[1] ? _jmol.allowedJmolSize[1] 
-        : x) + (units ? units : ""));
-}
-
-
-
-