//Released under the GPL license
//http://www.gnu.org/copyleft/gpl.html
//-------------------------------------------------------------------------------------------------
// ==UserScript==
// @name 3DStructureView
// @author Harini Gopalakrishnan
// @namespace ChemicalBioGrid
// @desc View 3D Structures using Jmol
// @include http://pubchem.ncbi.nlm.nih.gov/summary/*
// @include http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pccompound*
// @include http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pccompound*
//-------------------------------------------------------------------------------------------------
// Update check
var d = new Date();
var curr_date = d.getDate();
var date_last_checked= GM_getValue("check_updates", 0);
if (date_last_checked != curr_date)
{
GM_setValue("check_updates", curr_date);
// Modified the code by Seifer at http://userscripts.org/users/33118
script_name = '3DStructureView.user.js';
script_num = '8033';
script_href = "http://blueobelisk.svn.sf.net/svnroot/blueobelisk/userscripts/trunk/3DStructureView.user.js";
script_as_text = "http://blueobelisk.svn.sourceforge.net/viewvc/*checkout*/blueobelisk/userscripts/trunk/3DStructureView.user.js?content-type=text%2Fplain";
script_version=1.0;
script_updatetext='ADD UPDATE TEXT HERE';
GM_xmlhttpRequest({
method: "GET",
url: script_as_text,
onload: function(responseDetails) {
var text = responseDetails.responseText;
var update_version = text.substring(text.indexOf("script_version=")+15,text.indexOf("\n",text.indexOf("script_version="))-2);
var update_text = text.substring(text.indexOf("script_updatetext=")+19,text.indexOf("\n",text.indexOf("script_updatetext="))-3);
if(update_version > script_version) {
newversion = document.createElement("div");
newversion.setAttribute("id", "gm_update_alert");
newversion.setAttribute("style", "background-color:yellow; width:100%; position:absolute; z-index:99; top:0px; left:0px; text-align:center; font-size:11px; font-family: Tahoma");
newversion.innerHTML = "<a href='#' onclick='document.body.removeChild(document.getElementById("gm_update_alert"))' style='color:red'>Close</a><font color='yellow'>--------</font><font color='red'>There is a new version of the ""+script_name+"" script. You are currently running version "+script_version+".</font><br><font color='yellow'>----------------</font>The latest version is "+update_version+". <a href='#' onclick='document.getElementById("gm_update_alert_info").setAttribute("style", "display:block")' style='color:green'>Click here for more info</a> or <a style='color:green' href='" + script_href + "'><b>Click here to download the latest version</b></a><span id='gm_update_alert_info' style='display:none'><b>Here's a short description of the latest update...</b><br>"+update_text+"</span>";
document.body.appendChild(newversion);
}
}
});
}
//URL Check
var gProxy = null;
var url=window.location+'';
if(url.indexOf("http://pubchem.ncbi.nlm.nih.gov/summary/")+1>0)
{
//alert(url);
//alert(url.indexOf("http://pubchem.ncbi.nlm.nih.gov/summary/"));
run_3DData();
}
else
{
if(url.indexOf("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pccompound")+1>0)
{
//alert(url.indexOf("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pccompound"));
run_3DSummary();
}
else
{
if(url.indexOf("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pccompound")+1>0)
{
//alert(url);
//alert(url.indexOf("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pccompound"));
run_3DSummary();
}
}
}
// programs to view 3Ddata in the individual molecule page
function run_3DData()
{
if (!document.body || typeof(document.body.innerHTML) == "undefined")
{
return false;
}
var xPathResult = document.evaluate(
'.//text()[normalize-space(.) != ""]',
document.body,
null,
XPathResult.ORDERED_NODE_SNAPSHOT_TYPE,
null
);
var cid=document.getElementsByName('goentrezcid')[0].innerHTML;
Translate_3DData(cid);
}
function Translate_3DData(cid)
{
if (!gProxy) {
var listener = {
// gets called once the proxy has been instantiated
onLoad: function (aProxy)
{
gProxy = aProxy;
gProxy.setListener(listener);
requestTranslation(cid);
},
// gets called if an error occurs
onError: function (aError)
{
alert("An error has occured: " + aError);
},
// callback function is hardcoded to {methodname}Callback
getStructureByCIDCallback : function (aResult)
{
writeApplet_3DData(aResult);
}
};
createProxy(listener);
}
else
{
requestTranslation(cid);
}
}
function createProxy(aCreationListener)
{
try
{
var factory = new WebServiceProxyFactory();
factory.createProxyAsync("http://cheminfo.informatics.indiana.edu/Struct3D.xml", "Struct3D", "", true, aCreationListener);
}
catch (ex)
{
alert("Failed creating the proxy: "+ ex);
}
}
function requestTranslation(cid)
{
if (gProxy) {
try
{
var getStructureByCIDRequest = new Object();
gProxy.getStructureByCID(cid);
}
catch(ex)
{
alert('Error in service execution'+ex);
}
} else {
alert("Error: Proxy hasn't been set up correctly!");
}
}
function writeApplet_3DData(aResult)
{
try
{
//create script tag and refer Jmol.js to it
var scripttag=document.createElement('script');
//append script tag before head
var headElement=document.getElementsByTagName('head');
var newElement=headElement[0].firstCild;
headElement[0].insertBefore(scripttag,newElement);
var molecule='';
//loop to remove the '\n'
for(i=0;i<aResult.length;i++)
{
if(aResult[i]=='\n' || aResult[i]=='\r')
{
//encode so that it does not get corrupted while passing as a query string.
molecule=molecule+"\\\\n\\\" \+ \\n\"";
}
else
{
if(aResult[i]=='<' || aResult[i]=='>')
{
//alert('The incorrect symbol is:'+i+aResult[i]+":"+aResult[i+1] );
if(aResult[i]=='<')
{ molecule=molecule+"\<"; }
else
{ molecule=molecule+"\>"; }
}
else
{
molecule=molecule+aResult[i];
}
}
}
aResult=molecule;
//initialize javascript text for body element
var scripttag=document.createElement('script');
scripttag.setAttribute('type','text/javascript');
scripttag.innerHTML="\nfunction openwindow()\n{"+
"\n mywin=window.open(\"\",'3D Structure','width=415,height=450');\n"+
"\n mywin.document.write('<html><head>\\n<script type=\"text/javascript\" src=\" http://cheminfo.informatics.indiana.edu/JmolFolder/Jmol.js\"> </script></head>');"+
"\n mywin.document.write(\"<body>\\n<script type='text/javascript'> \\n jmolInitialize(' http://cheminfo.informatics.indiana.edu/JmolFolder/');\");"+
"\n mywin.document.write('\\n var molecule\=\" "+aResult+" \";\\n jmolAppletInline(400,molecule);');"+
"\n mywin.document.write('\\n document.write(\"<br><br><font size=2><b> 3D Structure Provided by<a href=http://www.chembiogrid.org/cheminfo/p3d/ target=_new>Pub3D</a>, part of <a href=http://www.chembiogrid.org target=_new>Chembiogrid.org</a></b></font>\");</script></body></html>');"+
"mywin.document.close();\n"+
"}";
var formElement=document.getElementsByTagName('body');
var newElement=formElement[0].firstChild;
formElement[0].insertBefore(scripttag,newElement);
var cidElement=document.getElementsByName('goentrezcid')[0].parentNode.parentNode;
var functionnode=document.createElement('span');
functionnode.setAttribute('id','appletholder');
var newNode=cidElement.parentNode;
newNode.insertBefore(functionnode,cidElement);
document.getElementById('appletholder').setAttribute('align','right');
document.getElementById('appletholder').innerHTML="<font color='white'>View</font><b>3D View: </b><a href='javascript:openwindow()'>3DView(Jmol)</a>";
//link to download the sdf file
var textdata=aResult;
var scripttag=document.createElement('script');
scripttag.setAttribute('type','text/javascript');
scripttag.innerHTML="\n function downloaddata()\n{"+
"\n mywin=window.open(\"\",'3D Structure Data','width=500,height=500');\n"+
"\n mywin.document.write('<html><body><span id=txtholder></span><script>var textnode=document.createElement(\"textarea\");');"+
"\n mywin.document.write('textnode.defaultValue\=\" "+textdata+" \" ;textnode.cols=\"55\";\\n textnode.rows=\"25\";');\n"+
"\n mywin.document.write('var parentnode=document.getElementById(\"txtholder\").appendChild(textnode);');\n"+
"\n mywin.document.write('\\n document.write(\"<br><br><font size=2><b> 3D Structure data Provided by<a href=http://www.chembiogrid.org/cheminfo/p3d/ target=_new>Pub3D</a>, part of <a href=http://www.chembiogrid.org target=_new>Chembiogrid.org</a></b></font>\");</script></body></html>');"+
"\n mywin.document.close();\n"+
"}";
var formElement=document.getElementsByTagName('body');
var newElement=formElement[0].firstChild;
formElement[0].insertBefore(scripttag,newElement);
var cidElement=document.getElementsByName('goentrezcid')[0].parentNode.parentNode;
var functionnode=document.createElement('span');
functionnode.setAttribute('id','downloadbox');
var newNode=cidElement.parentNode;
newNode.insertBefore(functionnode,cidElement);
document.getElementById('downloadbox').setAttribute('align','right');
document.getElementById('downloadbox').innerHTML=" <font size='2'><b>Get 3D Data:</b><a href='javascript:downloaddata()'>SDF Format</a></font>";
}
catch(ex)
{
alert('Error Writing Applet'+ex);
}
}
// individual molecule page link population program ends
// functions to view the data in the summary page for all the molecules
function run_3DSummary()
{
//alert("here");
if (!document.body || typeof(document.body.innerHTML) == "undefined") {
return false;
}
var xPathResult = document.evaluate(
'.//text()[normalize-space(.) != ""]',
document.body,
null,
XPathResult.ORDERED_NODE_SNAPSHOT_TYPE,
null
);
length_of_nodes=document.getElementsByName('uid').length;
for(var i=0;i<length_of_nodes;i++)
{
var cid=document.getElementsByName('uid')[i].value;
Translate_3DSummary(cid,i);
}
}
function Translate_3DSummary(cid,counter){
if (!gProxy) {
var listener = {
// gets called once the proxy has been instantiated
onLoad: function (aProxy)
{
// alert("Inside Onload");
gProxy = aProxy;
gProxy.setListener(listener);
requestTranslation(cid);
},
// gets called if an error occurs
onError: function (aError)
{
//alert("Inside Error");
alert("An error has occured: " + aError);
},
// callback function is hardcoded to {methodname}Callback
getStructureByCIDCallback : function (aResult)
{
if(aResult)
{
writeApplet_3DSummary(aResult,counter);
}
}
};
createProxy(listener);
} else {
requestTranslation(cid);
}
}
function writeApplet_3DSummary(aResult,counter)
{
try
{
//create script tag and refer Jmol.js to it
var scripttag=document.createElement('script');
//append script tag before head
var headElement=document.getElementsByTagName('head');
var newElement=headElement[0].firstCild;
headElement[0].insertBefore(scripttag,newElement);
var molecule='';
//loop to remove the '\n'
for(i=0;i<aResult.length;i++)
{
if(aResult[i]=='\n' || aResult[i]=='\r')
{
//encode so that it does not get corrupted while passing as a query string.
molecule=molecule+"\\\\n\\\" \+ \\n\"";
}
else
{
if(aResult[i]=='<' || aResult[i]=='>')
{
//alert('The incorrect symbol is:'+i+aResult[i]+":"+aResult[i+1] );
if(aResult[i]=='<')
{ //molecule=molecule+"<";
molecule=molecule+"\<";
}
else
{ //molecule=molecule+">";
molecule=molecule+"\>";
}
}
else
{
molecule=molecule+aResult[i];
}
}
}
aResult=molecule;
var datanode=document.createElement('input');
datanode.setAttribute('id','dataholder');
datanode.setAttribute('type','hidden');
// document.getElementById('dataholder').setAttribute('value','hello');
datanode.value='hello';
var formElement=document.getElementsByTagName('body');
var newElement=formElement[0].firstChild;
formElement[0].insertBefore(datanode,newElement);
document.getElementById('dataholder').value=aResult;
create_view_link(counter);
// return(aResult);
}
catch(ex)
{
alert('Error Writing Applet'+ex);
}
}
// function that writes the 3DView link
function create_view_link(counter)
{
//building string for populating the pop-up window with the 3D data
var textmessage='hello';
var scripttag=document.createElement('script');
scripttag.setAttribute('type','text/javascript');
//var linkString="<script>function downloaddata(data)\\n{\\n var molecule\=\"+data+\";alert(molecule);}</script>"+
// "<a onclick\=return downloaddata(\'"+textmessage+" \')>Click to download 3D data</a></body></html>";
scripttag.innerHTML="\nfunction openwindow()\n{"+
"\n mywin=window.open(\"\",'3D Structure','width=415,height=450');\n"+
"\n mywin.document.write('<html><head>\\n<script type=\"text/javascript\" src=\" http://cheminfo.informatics.indiana.edu/JmolFolder/Jmol.js\"></script></head>');"+
"\n mywin.document.write(\"<body>\\n<script type='text/javascript'> \\n jmolInitialize(' http://cheminfo.informatics.indiana.edu/JmolFolder');\");"+
"\n mywin.document.write('\\n var molecule\=\" "+ document.getElementById('dataholder').value+" \";\\n jmolAppletInline(400,molecule);');"+
"\n mywin.document.write('\\n document.write(\"<br><br><font size=2><b> 3D Structure Provided by<a href=http://www.chembiogrid.org/cheminfo/p3d/ target=_new>Pub3D</a>, part of <a href=http://www.chembiogrid.org target=_new>Chembiogrid.org</a></b></font>\");</script></body></html>');"+
"mywin.document.close();\n"+
"}";
var formElement=document.getElementsByTagName('body');
var newElement=formElement[0].firstChild;
formElement[0].insertBefore(scripttag,newElement);
var cidElement=document.getElementsByName('uid')[counter].parentNode.parentNode;
var functionnode=document.createElement('span');
functionnode.setAttribute('id','appletholder');
var newNode=cidElement.parentNode;
newNode.insertBefore(functionnode,cidElement);
document.getElementById('appletholder').setAttribute('align','right');
document.getElementById('appletholder').innerHTML="<font ><b>3D View: </b><a href='javascript:openwindow()'>3DView(Jmol)</a></font>";
//link to download the sdf file
var textdata=document.getElementById('dataholder').value;
var scripttag=document.createElement('script');
scripttag.setAttribute('type','text/javascript');
scripttag.innerHTML="\n function downloaddata()\n{"+
"\n mywin=window.open(\"\",'3D Structure Data','width=500,height=500');\n"+
"\n mywin.document.write('<html><body><span id=txtholder></span><script>var textnode=document.createElement(\"textarea\");');"+
"\n mywin.document.write('textnode.defaultValue\=\" "+textdata+" \" ;textnode.cols=\"55\";\\n textnode.rows=\"25\";');\n"+
"\n mywin.document.write('var parentnode=document.getElementById(\"txtholder\").appendChild(textnode);');\n"+
"\n mywin.document.write('\\n document.write(\"<br><br><font size=2><b> 3D Structure data Provided by<a href=http://www.chembiogrid.org/cheminfo/p3d/ target=_new>Pub3D</a>, part of <a href=http://www.chembiogrid.org target=_new>Chembiogrid.org</a></b></font>\");</script></body></html>');"+
"\n mywin.document.close();\n"+
"}";
var formElement=document.getElementsByTagName('body');
var newElement=formElement[0].firstChild;
formElement[0].insertBefore(scripttag,newElement);
var cidElement=document.getElementsByName('uid')[counter].parentNode.parentNode;
var functionnode=document.createElement('span');
functionnode.setAttribute('id','downloadbox');
var newNode=cidElement.parentNode;
newNode.insertBefore(functionnode,cidElement);
document.getElementById('downloadbox').setAttribute('align','right');
document.getElementById('downloadbox').innerHTML=" <font color='black' size='2'><b>Get 3D Data:</b><a href='javascript:downloaddata()'>SDF Format</a></font>";
}
