/* Jmol 11.0 script library Jmol.js (aka Jmol-11.js) 12:54 AM 1/9/2007

 first pass at checkbox heirarchy -- see http://www.stolaf.edu/academics/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

// 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
	  	
var defaultdir = "."
var defaultjar = "JmolApplet.jar"

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

////////////////////////////////////////////////////////////////
// Basic Scripting infrastruture
////////////////////////////////////////////////////////////////

function jmolInitialize(codebaseDirectory, fileNameOrUseSignedApplet) {
  if (_jmol.initialized) {
    //alert("jmolInitialize() should only be called *ONCE* within a page");
    return;
  }
  if (! codebaseDirectory) {
    alert("codebaseDirectory is a required parameter to jmolInitialize");
    codebaseDirectory = ".";
  }

  if (codebaseDirectory.indexOf("http://") == 0 ||
      codebaseDirectory.indexOf("https://") == 0)
    alert("In general, an absolute URL is not recommended for codebaseDirectory.\n" +
	  "A directory- or docroot-relative reference is recommended.\n\n" +
	  "If you need to use an absolute URL (because, for example, the JAR and data\n" +
	  "files are on another server), then insert a space before\n" +
	  "\"http\" in your URL to avoid this warning message.");

  _jmolSetCodebase(codebaseDirectory);
  _jmolGetJarFilename(fileNameOrUseSignedApplet);
  _jmolOnloadResetForms();
  _jmol.initialized = true;
}

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 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 " : "") + _jmol.checkboxCssText + "/>" 
  if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
	t += eospan
	eospan = "";
  }
  t += labelHtml +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 jmolChangeStructureLink(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;' onClick='pdbid=text; ' onMouseout='_jmolMouseOut()' " +
          _jmol.linkCssText + ">" + label + "</a></span>";
  if (_jmol.debugAlert)
    alert(t);
  return _jmolDocumentWrite(t);
}


function jmolChangeStructureLoad(script, text, id) {
  
  _jmolInitCheck();
  pdbid=text;
  var scriptIndex = _jmolAddScript(script);
  jmolScript(script);
}

//gets pdb position from seq_str.pdbid.seq_pos global object
// and then calls jmolScript
function jmolSelectPosition(pos, labe, colour, targetSuffix) {
  
  var selPos = Number(seq_str[pdbid][pos]);
  if ( selPos == '') {
    alert("This amino acid is not defined in the structure, this could either mean i) the amino acid is missing in the structure or ii) we did not map the sequence position to structure")  ;
    return;
  }

  var chain = pdbid.substr(4,1);
  chain = (chain == '' ? '' : ":"+chain);
  colour = (colour == '' ? 'blue' : colour);

  var re = new RegExp ('\-', 'g') ;
  if(colour.match(re)) {
    var rgb = colour.replace(re, ',') ;
    colour = "["+rgb+"]";
  }

  var script = "save orientation init_orient; select within(10.0, "+selPos+chain+"); hbonds 0.1; ssbonds on; select "+selPos+chain+"; wireframe 0.5;colour  "+colour+";select "+selPos+chain+" and *.CA; label "+labe+":"+selPos+"; colour label black; ";
  script += "zoomto 2 (" + selPos+chain + ") 400; ";
  script += "moveto 2 0 1 0 180 400 (" + selPos+chain + "); ";
  script += "moveto 2 0 1 0 -359 400 (" + selPos+chain + "); ";
  script += "restore orientation init_orient 2; ";
  script += "select all;";
  jmolScript(script);
}

//gets pdb positions from seq_str.pdbid.seq_pos global object
// and then calls jmolScript
function jmolSelectRegion(posone, postwo, labe, colour, targetSuffix) {

  while(seq_str[pdbid][posone] == null) {
    posone++;
  } 
  while(seq_str[pdbid][postwo] == null) {
    postwo--;
  }

  if(postwo - posone < 0) {
    alert("These amino acids are not defined in the structure, this could either mean i) the amino acids are missing in the structure or ii) we did not map the sequence positions to structure")  ;
    return;
  }
  var start = Number(seq_str[pdbid][posone]);
  var end = Number(seq_str[pdbid][postwo]);
  var chain = pdbid.substr(4,1);

  chain = (chain == '' ? '' : ":"+chain);
  colour = (colour == '' ? 'red' : colour);
  
  var re = new RegExp ('\-', 'g') ;
  if(colour.match(re)) {
    var rgb = colour.replace(re, ',') ;
    colour = "["+rgb+"]";
  }
  
  var label_pos = start + parseInt((end-start)/2);
  /*
  It's not clear why Kiran recolors the whole structure. This steps on other coloring, including any manual user coloring.
  var script = "select all; label off; colour cartoon yellow; select "+start+"-"+end+chain+"; colour cartoon "+colour+"; select "+label_pos+chain+" and *.CA; label "+labe+"; colour label white";
  */
  var script = "save orientation init_orient; select "+start+"-"+end+chain+"; colour cartoon "+colour+"; select "+label_pos+chain+" and *.CA; label "+labe+"; colour label black; ";
  script += "zoomto 2 (" + start+"-"+end+chain + ") 200; ";
  script += "moveto 2 0 1 0 180 200 (" + start+"-"+end+chain + "); ";
  script += "moveto 2 0 1 0 -359 200 (" + start+"-"+end+chain + "); ";
  script += "restore orientation init_orient 2; ";
  script += "select all;"
  jmolScript(script);
}

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+"'><input type=button value = '"+label+"' onClick='jmolScript(document.getElementById(\""+id+"\").value" + _jmol.targetText + ")'/></span>";
  if (_jmol.debugAlert)
    alert(t);
  return _jmolDocumentWrite(t);
}

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>" : "'>";
        t += "<option value='" + scriptIndex + selectedText + text + "</option>";
	  }
    }
    t += "</select></span>";
    if (_jmol.debugAlert)
      alert(t);
    return _jmolDocumentWrite(t);
  }
}
// the only difference with jmolMenu is that I call _jmolMenuSelected2 in addition to _jmolMenuSelected
function jmolChangeStructureMenu(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 + "); _jmolMenuSelected2(this.value,\""+arrayOfMenuItems+"\"); '" +
            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>" : "'>";
        t += "<option value='" + scriptIndex + selectedText + text + "</option>";
	  }
    }
    t += "</select></span>";
    if (_jmol.debugAlert)
      alert(t);
    return _jmolDocumentWrite(t);
  }
}

/* I know its pathetic that I have to get pdbid this way
 but the array I pass to jmol..Menu doesnot 
 accept more columns (the cols scripts and labels) see above function 
*/
function _jmolMenuSelected2(index,str) {
	myRe = /\(\d\w\w\w\w/g;
	myarr = str.match(myRe);
        pdbid = myarr[index-1].substr(1);
}

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
  var applet=_jmolGetApplet(targetSuffix);
  if (applet)applet.loadInline(model);
}

function jmolLoadInlineScript(model, script, targetSuffix) {
  if (!model)return
  var applet=_jmolGetApplet(targetSuffix);
  if (applet)applet.loadInline(model, script);
}

function jmolLoadInlineArray(ModelArray, script, targetSuffix) {
  if (!model)return
  if (!script)script=""
  var applet=_jmolGetApplet(targetSuffix);
  if (applet)applet.loadInlineArray(ModelArray, script);
}

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: [],
  
  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: {
	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 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.
	*/
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 />";
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 (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" : "");
      tHeader = 
        "<object name='jmolApplet" + nameSuffix +
        "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
	" classid='" + windowsClassId + "'\n" + winCodebase + widthAndHeight + ">\n";
        params.code = 'JmolApplet';
      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;" +
		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 + ">\n" +
		noJavaMsg2 +
        "</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 (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;
  if (_jmol.initialized)
    return;
  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 +
              "\n\n" + ua;
      alert(msg);
    }
  }
  return false;
}

function _jmolDocumentWrite(text) {
  if (_jmol.currentDocument)
    _jmol.currentDocument.write(text);
  return text;
}

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;
}

	/*  AngelH, mar2007:
		By (re)setting this variable in the webpage before calling jmolApplet(), limits for applet size can be overriden.
	*/
var allowedJmolSize = [25, 2000, 300]   // min, max, default (pixels)
function _jmolGetAppletSize(size) {
	/*  AngelH, mar2007
		Accepts single number or 2-value array, each one can be either:
	   percent (text string ending %), decimal 0 to 1 (percent/100), number, or text string (interpreted as nr.)
	   Size is now returned as string or number, no "px".
	*/
  var width, height;
  if ( (typeof size) == "object" && size != null ) {
    width = size[0]; height = size[1];
  } else {
    width = height = size;
  }
  // if percent, leave it as it is:
  if ( width.toString().charAt(width.toString().length-1) != "%" ) {
    width = parseFloat(width);	// convert to nr., or strip text, or make zero
	if ( width <= 1 && width > 0 ) { width = (width*100)+"%" }	// decimal: convert to percent and quit
	else if ( width >= allowedJmolSize[0] && width <= allowedJmolSize[1] ) { width = parseInt(width) }	// accept only that range (pixels)
	else { width = allowedJmolSize[2] }	// default size 300 pixels
  }
  if ( height.toString().charAt(height.toString().length-1) != "%" ) {
    height = parseFloat(height);
	if ( height <= 1 && height > 0 ) { height = (height*100)+"%" }
	else if ( height >= allowedJmolSize[0] && height <= allowedJmolSize[1] ) { height = parseInt(height) }
	else { height = allowedJmolSize[2] }
  }
  return [width, height];
}

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 " : "") + _jmol.radioCssText + "/>"
  if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
	t += eospan
	eospan = "";
  }
  t += labelHtml +eospan + separatorHtml;
  return t;
}

function _jmolFindApplet(target) {
  // first look for the target in the current window
  var applet = _jmolFindAppletInWindow(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
    for (var i = 0; i < frames.length; ++i) {
      applet = _jmolSearchFrames(frames[i], target);
      if (applet)
        break;
    }
  } else { // look for the applet in this window
   applet = _jmolFindAppletInWindow(win, target)
  }
  return applet;
}

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) {
  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 = new Array();
_jmol.checkboxItems = new Array();

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] = new Array();
	m.chkMaster = chkMaster;
	m.chkGroup = new Array();
	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) {
  _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() {
  _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+"=new Array()"
    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+"=new Array()"
	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 = new Array()
 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(i=Ret.length;--i>=0;)
  for(j=0;j< Ret[i].length;j++)
	s+=Ret[i][j]+"\n"
  return s
}

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 = new Array()
 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 = new Array()
 _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.thiskeyMSA = "mineral"
 if(!_jmol.thismodelMSA)_jmol.thismodelMSA = "quartz"
 if(!_jmol.ajaxURL_MSA)_jmol.ajaxURL_MSA="http://rruff.geo.arizona.edu/AMS/result.php?mineral=quartz&viewing=ajaxjs"
 if(!key)key=prompt("Enter a field:", _jmol.thiskeyMSA)
 if(!key)return ""
 if(!value)value=prompt("Enter a "+key+":", _jmol.thismodelMSA)
 if(!value)return ""
 if(!targetSuffix)targetSuffix="0"
 if(!optionalscript)optionalscript=""
 if(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 = new Array()
 loadModel=_jmolLoadModel
 _jmolDomScriptLoad(url)
 return url
}



function jmolLoadAjaxJS(url, userid, optionalscript,targetSuffix){
 if(!userid)userid="0"
 if(!targetSuffix)targetSuffix="0"
 if(!optionalscript)optionalscript=""
 _jmol.optionalscript=optionalscript
 _jmol.thismodel=userid
 _jmol.thistargetsuffix=targetSuffix
 _jmol.modelArray = new Array()
 _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(document.location.search.indexOf("NOAPPLET")>=0){
	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}
	}
}


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