/plugin-jmol/src/main/resources/emma/plugin/jmol/files/Jmol.js

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/* Jmol 11.7 script library Jmol.js  12:17 AM 4/20/2009 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



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 allowJMOLJAR = true  





var undefined; // for IE 5 ... wherein undefined is undefined



////////////////////////////////////////////////////////////////

// Basic Scripting infrastruture

////////////////////////////////////////////////////////////////



function jmolInitialize(codebaseDirectory, fileNameOrUseSignedApplet) {

  if (_jmol.initialized)

    return;

  _jmol.initialized = true;

  if(allowJMOLJAR && document.location.search.indexOf("JMOLJAR=")>=0) {

    var f = document.location.search.split("JMOLJAR=")[1].split("&")[0];

    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

////////////////////////////////////////////////////////////////



function jmolButton(script, label, id, title) {

  _jmolInitCheck();

  if (id == undefined || id == null)

    id = "jmolButton" + _jmol.buttonCount;

  if (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(" + 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();

  if (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;

  }

  if (separatorHtml == undefined || separatorHtml == null)

    separatorHtml = "&nbsp; ";

  var len = arrayOfRadioButtons.length;

  jmolStartNewRadioGroup();

  if (!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();

  if (id == undefined || id == null)

    id = "jmolLink" + _jmol.linkCount;

  if (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(" + 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();

  if (id == undefined || id == null)

    id = "jmolCmd" + _jmol.cmdCount;

  if (label == undefined || label == null)

    label = "Execute";

  if (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) {

		jmolScript(document.getElementById(id).value, target)

	}

}







function jmolMenu(arrayOfMenuItems, size, id, title) {

  _jmolInitCheck();

  if (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;

      }

      if (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 + "\"" : "";

}



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"

  if (!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"

  if (!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();

    if (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: "",

  radioCssClass: null,

  radioCssText: "",

  linkCssClass: null,

  linkCssText: "",

  menuCssClass: null,

  menuCssText: "",

  

  targetSuffix: 0,

  targetText: "",

  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),

  

  os: "unknown",

  browser: "unknown",

  browserVersion: 0,

  hasGetElementById: !!document.getElementById,

  isJavaEnabled: navigator.javaEnabled(),

  isNetscape47Win: false,

  isIEWin: false,

  useIEObject: false,

  useHtml4Object: false,

  

  windowsClassId: "clsid:8AD9C840-044E-11D1-B3E9-00805F499D93",

  windowsCabUrl:

   "http://java.sun.com/update/1.5.0/jinstall-1_5_0_05-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,

  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("safari") ||

  _jmolTestUA("omniweb") ||

  _jmolTestUA("opera") ||

  _jmolTestUA("webtv") ||

  _jmolTestUA("icab") ||

  _jmolTestUA("msie") ||

  (_jmol.ua.indexOf("compatible") < 0 && _jmolTestUA("mozilla"));

  

  _jmolTestOS("linux") ||

  _jmolTestOS("unix") ||

  _jmolTestOS("mac") ||

  _jmolTestOS("win");



  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 == "safari" && 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;



  // IE5.5 works just fine ... but let's push them to Sun Java

  isIEWin = (os == "win" && browser == "msie" && browserVersion >= 5.5);

  useIEObject = isIEWin;

  useHtml4Object =

   (os != "mac" && browser == "mozilla" && browserVersion >= 5) ||

   (os == "win" && browser == "opera" && browserVersion >= 8) ||

   (os == "mac" && browser == "safari" && browserVersion >= 412.2);



 doTranslate = true;

 haveSetTranslate = false;

}





function jmolSetCallback(callbackName,funcName) {

  _jmol.params[callbackName] = funcName

}



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.		

	*/

  with (_jmol) {

    if (! nameSuffix)

      nameSuffix = appletCount;

    appletSuffixes.push(nameSuffix);

    ++appletCount;

    if (! script)

      script = "select *";

    var sz = _jmolGetAppletSize(size);

    var widthAndHeight = " width='" + sz[0] + "' height='" + sz[1] + "' ";

    var tHeader, tFooter;

    if (!codebase)

	jmolInitialize(".");

    if (useIEObject || useHtml4Object) {

      params.name = 'jmolApplet' + nameSuffix;

      params.archive = archivePath;

      params.mayscript = 'true';

      params.codebase = codebase;

    }

    if (useIEObject) { // use MSFT IE6 object tag with .cab file reference

      winCodebase = (windowsCabUrl ? " codebase='" + windowsCabUrl + "'\n" : "");

      params.code = 'JmolApplet';

      tHeader = 

        "<object name='jmolApplet" + nameSuffix +

        "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +

	" classid='" + windowsClassId + "'\n" + winCodebase + widthAndHeight + ">\n";

      tFooter = "</object>";

    } else if (useHtml4Object) { // use HTML4 object tag

      tHeader = 

        "<object name='jmolApplet" + nameSuffix +

        "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +

	" classid='java:JmolApplet'\n" +

        " type='application/x-java-applet'\n" +

        widthAndHeight + ">\n";

      tFooter = "</object>";

    } else { // use applet tag

      tHeader = 

        "<applet name='jmolApplet" + nameSuffix +

        "' id='jmolApplet" + nameSuffix +

        "' " + appletCssText +

        " code='JmolApplet'" +

        " archive='" + archivePath + "' codebase='" + codebase + "'\n" +

		widthAndHeight +

        " mayscript='true'>\n";

      tFooter = "</applet>";

    }

    var visitJava;

    if (isIEWin || 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?



	if (!closetag)closetag = ""

	if (!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) {

  var inlineScript = script.replace(/'/g, "&#39;");

  if (_jmol.debugAlert)

    alert("script:\n" + inlineScript);

  return inlineScript;

}



function _jmolSterilizeInline(model) {

  var inlineModel =

    model.replace(/\r|\n|\r\n/g, "|").replace(/'/g, "&#39;");

  if (_jmol.debugAlert)

    alert("inline model:\n" + inlineModel);

  return inlineModel;

}



function _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {

  ++_jmol.radioCount;

  if (groupName == undefined || groupName == null)

    groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1);

  if (!script)

    return "";

  if (labelHtml == undefined || labelHtml == null)

    labelHtml = script.substring(0, 32);

  if (! 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(" +

         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

 if(!_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;

    // getElementById fails on MacOSX Safari & Mozilla	

    if (_jmol.useHtml4Object || _jmol.useIEObject)

      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(scriptIndex, targetSuffix, elementClicked) {

  _jmol.element = elementClicked;

  jmolScript(_jmol.scripts[scriptIndex], targetSuffix);

}



function _jmolMenuSelected(menuObject, targetSuffix) {

  var scriptIndex = menuObject.value;

  if (scriptIndex != undefined) {

    jmolScript(_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].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.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

 if(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);

 if(!sValue)sValue=""

 return (applet ? applet.getPropertyAsString(sKey,sValue) + "" : "")

}



function jmolGetPropertyAsJSON(sKey,sValue,targetSuffix) {

 if(!sValue)sValue = ""

 var applet = _jmolGetApplet(targetSuffix);

 try {

  return (applet ? applet.getPropertyAsJSON(sKey,sValue) + "" : "")

 } catch(e) {

  return ""

 }

}



function jmolGetPropertyAsJavaObject(sKey,sValue,targetSuffix) {

 if(!sValue)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) {

  if(!targetSuffix)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) {

  if(!targetSuffix)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



  if(!targetSuffix)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

  if(!targetSuffix)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"

  if(!targetSuffix)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) {  

 if(!targetSuffix)targetSuffix="0"

  return _jmol["savedOrientation"+id] = jmolGetPropertyAsArray("orientationInfo","info",targetSuffix).moveTo

}



function jmolRestoreOrientation(id, targetSuffix) {

 if(!targetSuffix)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) {

 if(arguments.length < 2)delay=1;

 if(!targetSuffix)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){

  if(value == "")return appletCode

  return 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){



 if(!_jmol.thismodel)_jmol.thismodel = "1crn"

 if(!_jmol.serverURL)_jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm"

 if(!_jmol.RCSBserver)_jmol.RCSBserver="http://www.rcsb.org"

 if(!_jmol.defaultURL_RCSB)_jmol.defaultURL_RCSB=_jmol.RCSBserver+"/pdb/files/1CRN.CIF"

 if(!fileformat)fileformat="PDB"

 if(!pdbid)pdbid=prompt("Enter a 4-digit PDB ID:",_jmol.thismodel)

 if(!pdbid || pdbid.length != 4)return ""

 if(!targetSuffix)targetSuffix="0"

 if(!optionalscript)optionalscript=""

 var url=_jmol.defaultURL_RCSB.replace(/1CRN/g,pdbid.toUpperCase())

 if(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

}



/////////////// 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"

 if(!_jmol.thisurlANY)_jmol.thisurlANY = "http://www.stolaf.edu/depts/chemistry/mo/struc/data/ycp3-1.mol"

 if(!url)url=prompt("Enter any (uncompressed file) URL:", _jmol.thisurlANY)

 if(!userid)userid="0"

 if(!targetSuffix)targetSuffix="0"

 if(!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){



 if(!_jmol.thiskeyMSA)_jmol.thiske…