jmol.js

Jmol是一个使用java语言编写的开源的免费三维分子显示工具,用于分子模型的浏览和编辑

	}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.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 = []
 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 = []
 _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}
	}
}


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

//new 9:49 AM 3/6/2007:

//both w and h are optional. 
//if either is between 0 and 1, then it is taken as percent/100.
//if either is greater than 1, then it is taken as a size. 
function jmolResize(w,h) {
 _jmol.alerted = true;
 var percentW = (!w ? 100 : w <= 1  && w > 0 ? w * 100 : 0)
 var percentH = (!h ? percentW : h <= 1 && h > 0 ? h * 100 : 0)
 if (_jmol.browser=="msie") {
   var width=document.body.clientWidth;
   var height=document.body.clientHeight;
 } else {
   var netscapeScrollWidth=15;
   var width=window.innerWidth - netscapeScrollWidth;
   var height=window.innerHeight-netscapeScrollWidth;
 }
 var applet = _jmolGetApplet(0);
 if(!applet)return;
 applet.style.width = (percentW ? width * percentW/100 : w)+"px"
 applet.style.height = (percentH ? height * percentH/100 : h)+"px"
 title=width +  " " + height + " " + (new Date())
}