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Enabled to show interactions using force-directed graph in the menu '…
…View > H-Bonds & Interactions > Force-Directed Graph'. Enabled to calculate Solvent Accessible Surface Area (SASA) in the menu 'View > Surface Area', or color by SASA in the menu 'Color > Solvent Accessibility'. Fixed ClinVar and SNP annotations.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,307 @@ | ||
| <!DOCTYPE html><html lang="en"><head> | ||
| <meta charset="utf-8"> | ||
| <meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1"> | ||
| <meta content="text/html; charset=utf-8" http-equiv="Content-Type"> | ||
| <meta name="description" content="iCn3D Structure Viewer"> | ||
| <meta name="ncbi_db" content="structure"><meta name="ncbi_app" content="iCn3D"><meta name="ncbi_pdid" content="advanced"> | ||
| <meta name="keywords" content="NCBI, Structure, JavaScript, iCn3D, 3D, Viewer, WebGL, three.js, sequence, chemical"> | ||
| <meta name="robots" content="index,follow,noarchive"> | ||
| <title>iCn3D: Web-based 3D Structure Viewer</title> | ||
| </head> | ||
| <body> | ||
| <div id="div0" style="float:left; padding-right:5px;"></div> | ||
| <div id="div1" style="float:left;"></div> | ||
|
|
||
| <link rel="stylesheet" href="lib/jquery-ui-1.12.1.min.css"> | ||
| <link rel="stylesheet" href="icn3d_full_ui.css"> | ||
| <script src="lib/jquery-3.5.0.min.js"></script> | ||
| <script src="lib/jquery-ui-1.12.1.min.js"></script> | ||
| <script src="lib/three_0.103.0.min.js"></script> | ||
| <script src="icn3d_full_ui.min.js"></script> | ||
|
|
||
| <script type="text/javascript"> | ||
| // separating the GET parameters from the current URL | ||
| // repalce "color #" with "color " in the url | ||
| var url = document.URL.replace(/\#/g, ''); | ||
|
|
||
| var bNopara = false; | ||
| var ampPos = url.indexOf("?"); | ||
| if(ampPos === -1) { | ||
| // alert("Please include '?pdbid=1GPK,2POR,...' in your url"); | ||
| bNopara = true; | ||
| } | ||
|
|
||
| var getParams = url.split("?"); | ||
| // transforming the GET parameters into a dictionnary | ||
| var search = getParams[getParams.length - 1]; | ||
| var params = {}; | ||
| var inpara = ""; | ||
|
|
||
| if(!bNopara) { | ||
| //params = JSON.parse('{"' + decodeURIComponent(search).replace(/"/g, '\\"').replace(/&/g, '","').replace(/=/g,'":"') + '"}'); | ||
|
|
||
| var decodeSearch = decodeURIComponent(search); | ||
|
|
||
| var hashes = decodeSearch.split('&'); | ||
| for (var i = 0; i < hashes.length; i++) { | ||
| hash = hashes[i].split('='); | ||
| params[hash[0].trim()] = (hash[1] !== undefined) ? hash[1].trim() : undefined; | ||
| } | ||
|
|
||
| // for mmdb structures, pass the parameters after the first "&" sign | ||
| inpara = "&" + url.substr(ampPos + 1); | ||
| } | ||
|
|
||
| var gi = params.gi; | ||
| var blast_rep_id = params.blast_rep_id; | ||
| var query_id = params.query_id; | ||
|
|
||
| var mmdbid = params.mmdbid; | ||
| var mmtfid = params.mmtfid; | ||
| var pdbid = params.pdbid; | ||
| var opmid = params.opmid; | ||
| var cid = params.cid; | ||
| var mmcifid = params.mmcifid; | ||
| var urlname = params.url; | ||
| var urltype = (params.type === undefined) ? 'pdb' : params.type; | ||
|
|
||
| var align = params.align; | ||
| var chainalign = params.chainalign; | ||
|
|
||
| var width = params.width; | ||
| var height = params.height; | ||
|
|
||
| var command = params.command; // ";" separated commands | ||
|
|
||
| var from = params.from; | ||
|
|
||
| function getValue(input) { | ||
| if(input == 'true' || input == '1') { | ||
| input = true; | ||
| } | ||
| else if(input == 'false' || input == '0') { | ||
| input = false; | ||
| } | ||
|
|
||
| return input; | ||
| } | ||
|
|
||
| var resize = getValue(params.resize); | ||
|
|
||
| var showmenu = getValue(params.showmenu); | ||
|
|
||
| var showtitle = getValue(params.showtitle); | ||
|
|
||
| var showcommand = getValue(params.showcommand); | ||
|
|
||
| var simplemenu = getValue(params.simplemenu); | ||
|
|
||
| var mobilemenu = getValue(params.mobilemenu); | ||
|
|
||
| var closepopup = getValue(params.closepopup); | ||
|
|
||
| var showanno = getValue(params.showanno); | ||
|
|
||
| var showseq = getValue(params.showseq); | ||
|
|
||
| // backward compatible with showseq | ||
| showanno = showanno || showseq; | ||
|
|
||
| // for alignment | ||
| var showalignseq = getValue(params.showalignseq); | ||
|
|
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| var show2d = getValue(params.show2d); | ||
|
|
||
| var showsets = getValue(params.showsets); | ||
|
|
||
| var rotate = params.rotate; | ||
|
|
||
| var options = (params.options !== undefined) ? JSON.parse(params.options) : undefined; | ||
|
|
||
| $( document ).ready(function() { | ||
| // use the FIXED name "icn3duiHash", which is used in iCn3DUI | ||
| window.icn3duiHash = {}; | ||
|
|
||
| function setupViewer(idName, idValue) { | ||
| var maxStructure = 5; // show max 5 structures | ||
|
|
||
| var idArray = idValue.replace(/\s/g, '').split(','); | ||
|
|
||
| if(idArray.length > 1) { | ||
| resize = false; | ||
|
|
||
| if(width.indexOf('%') != -1) { | ||
| width = 400; | ||
| height = 400; | ||
| } | ||
| } | ||
|
|
||
| if(options === undefined || options === 'undefined') options = {}; | ||
|
|
||
| //Options are available at: https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#DisplayOptions | ||
| //options['chemicalbinding'] = 'show'; | ||
|
|
||
| //for(var i = 0, il = idArray.length; i < il && i < maxStructure; ++i) { | ||
| var i = 0; | ||
| var cfg = { | ||
| divid: 'div' + i, | ||
| inpara: inpara, | ||
| width: '49%', //width, | ||
| height: height, | ||
| resize: resize, | ||
| rotate: rotate, | ||
| showmenu: showmenu, | ||
| showtitle: showtitle, | ||
| showcommand: showcommand, | ||
| showanno: showanno, | ||
| show2d: show2d, | ||
| showsets: showsets, | ||
| simplemenu: simplemenu, | ||
| mobilemenu: true, //mobilemenu, | ||
| closepopup: true, //closepopup, | ||
| blast_rep_id: blast_rep_id, | ||
| query_id: query_id, | ||
| options: options, | ||
| controlGl: true, | ||
| command: command, | ||
| bSidebyside: true | ||
| }; | ||
| if(idName !== '') cfg[idName] = idArray[i]; | ||
|
|
||
| var icn3dui = new iCn3DUI(cfg); | ||
| icn3dui.show3DStructure(); | ||
| window.icn3duiHash['div0'] = icn3dui; | ||
| if(idName === '') $("#div" + i + "_wait").hide(); | ||
|
|
||
|
|
||
| i = 1; | ||
| var cfg2 = cfg; | ||
| cfg2.divid = 'div' + i; | ||
| var icn3dui2 = new iCn3DUI(cfg2); | ||
| icn3dui2.show3DStructure(); | ||
| window.icn3duiHash['div1'] = icn3dui2; | ||
| if(idName === '') $("#div" + i + "_wait").hide(); | ||
| //} | ||
| } | ||
|
|
||
| if(mmtfid !== undefined) { | ||
| setupViewer('mmtfid', mmtfid); | ||
| } | ||
| else if(pdbid !== undefined) { | ||
| setupViewer('pdbid', pdbid); | ||
| } | ||
| else if(opmid !== undefined) { | ||
| setupViewer('opmid', opmid); | ||
| } | ||
| else if(cid !== undefined) { | ||
| setupViewer('cid', cid); | ||
| } | ||
| else if(mmcifid !== undefined) { | ||
| setupViewer('mmcifid', mmcifid); | ||
| } | ||
| else if(mmdbid !== undefined) { | ||
| setupViewer('mmdbid', mmdbid); | ||
| } | ||
| else if(gi !== undefined) { | ||
| setupViewer('gi', gi); | ||
| } | ||
| else if(blast_rep_id !== undefined) { | ||
| if( (from === 'blast' || from === 'icn3d') && command == '') { | ||
| command = 'view+annotations;+set+annotation+cdd;+set+annotation+site;+set+view+detailed+view;+select+chain+' | ||
| + blast_rep_id + ';+show+selection'; | ||
| } | ||
|
|
||
| setupViewer('blast_rep_id', blast_rep_id); | ||
| } | ||
| else if(urlname !== undefined) { | ||
| urlname = decodeURIComponent(urlname); | ||
| setupViewer('url', urltype + '|' + urlname); | ||
| } | ||
| // e.g., align=103701,1,4,68563,1,167 [mmdbid1,biounit,molecule,mmdbid2,biounit,molecule] | ||
| else if(align !== undefined) { | ||
| var cfg = { | ||
| divid: 'div0', | ||
| inpara: inpara, | ||
| width: '49%', //width, | ||
| height: height, | ||
| resize: resize, | ||
| rotate: rotate, | ||
| showmenu: showmenu, | ||
| showtitle: showtitle, | ||
| showcommand: showcommand, | ||
| showanno: showanno, | ||
| showalignseq: showalignseq, | ||
| show2d: show2d, | ||
| showsets: showsets, | ||
| simplemenu: simplemenu, | ||
| mobilemenu: true, //mobilemenu, | ||
| closepopup: true, //closepopup, | ||
| align: align, | ||
| controlGl: true, | ||
| command: command, | ||
| bSidebyside: true | ||
| }; | ||
|
|
||
| var icn3dui = new iCn3DUI(cfg); | ||
| icn3dui.show3DStructure(); | ||
| window.icn3duiHash['div0'] = icn3dui; | ||
|
|
||
| var cfg2 = cfg; | ||
| cfg2.divid = 'div1'; | ||
| var icn3dui2 = new iCn3DUI(cfg2); | ||
| icn3dui2.show3DStructure(); | ||
| window.icn3duiHash['div1'] = icn3dui2; | ||
| } | ||
| else if(chainalign !== undefined) { | ||
| var cfg = { | ||
| divid: 'div0', | ||
| inpara: inpara, | ||
| width: '49%', //width, | ||
| height: height, | ||
| resize: resize, | ||
| rotate: rotate, | ||
| showmenu: showmenu, | ||
| showtitle: showtitle, | ||
| showcommand: showcommand, | ||
| showanno: showanno, | ||
| showalignseq: showalignseq, | ||
| show2d: show2d, | ||
| showsets: showsets, | ||
| simplemenu: simplemenu, | ||
| mobilemenu: true, //mobilemenu, | ||
| closepopup: true, //closepopup, | ||
| chainalign: chainalign, | ||
| controlGl: true, | ||
| command: command, | ||
| bSidebyside: true | ||
| }; | ||
|
|
||
| var icn3dui = new iCn3DUI(cfg); | ||
| icn3dui.show3DStructure(); | ||
| window.icn3duiHash['div0'] = icn3dui; | ||
|
|
||
| var cfg2 = cfg; | ||
| cfg2.divid = 'div1'; | ||
| var icn3dui2 = new iCn3DUI(cfg2); | ||
| icn3dui2.show3DStructure(); | ||
| window.icn3duiHash['div1'] = icn3dui2; | ||
| } | ||
| else { | ||
| setupViewer('', ''); | ||
| } | ||
|
|
||
| }); // document ready | ||
|
|
||
| </script> | ||
|
|
||
| <!-- Google Analytics --> | ||
| <script type="text/javascript"> | ||
| var _gaq = _gaq || []; | ||
| _gaq.push(['_setAccount', 'UA-68648221-3']); | ||
| _gaq.push(['_setDomainName', '.ncbi.nlm.nih.gov']); | ||
| _gaq.push(['_trackPageview']); | ||
| setTimeout("_gaq.push(['_trackEvent', '10_seconds', 'read'])",10000); | ||
| (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); | ||
| </script> | ||
| </body></html> | ||
|
|
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