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<meta name="description" content="iCn3D Structure Viewer">
<meta name="keywords" content="NCBI, Structure, JavaScript, iCn3D, 3D, Viewer, WebGL, three.js, sequence, chemical">
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<meta name="ncbi_app" content="structure">
<meta name="ncbi_pdid" content="icn3d">
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<title>iCn3D: Web-based 3D Structure Viewer</title>
<script type="text/javascript">
    window.ncbi_startTime = new Date();
</script>
</head>
<body>
  <div id="div0"></div>

  <link rel="stylesheet" href="lib/jquery-ui-1.13.2.min.css">
  <link rel="stylesheet" href="icn3d.css">
  <script src="lib/jquery-3.5.0.min.js"></script>
  <script src="lib/jquery-ui-1.13.2.min.js"></script>
  <script src="lib/three_0.151.0.min.js"></script>
  <script src="icn3d.min.js"></script>

  <script type="text/javascript">

    $( document ).ready(async function() {
      if (navigator.userAgent.indexOf("MSIE ") > 0 || !!navigator.userAgent.match(/Trident.*rv\:11\./)) { // If Internet Explorer
          // iCn3D version 2.24.7 doesn't work with three_0.128.0.min.js
          //$.getScript('icn3d_full_ui_2.24.7.min.js', function() {
          //  var version = 2;
          //  await launchIcn3d(version);
          //});

          var fixedUrl = document.URL.replace('full.html', 'full_2.24.7.html');
          window.open(fixedUrl, '_self');

          alert("IE does NOT work with the current iCn3D version 3. The old iCn3D version 2 is used instead.");
      }
      else {
          //$.getScript('icn3d.min.js', function() {
            var version = 3;
            await launchIcn3d(version); //await 
          //});
      }

      async function launchIcn3d(version) {
          var cfg = getConfig();
          cfg.version = version;

          if(cfg.bcifid !== undefined) {
              await setupViewer('bcifid', cfg.bcifid, cfg);
          }
          else if(cfg.mmtfid !== undefined) {
              await setupViewer('mmtfid', cfg.mmtfid, cfg);
          }
          else if(cfg.pdbid !== undefined) {
              await setupViewer('pdbid', cfg.pdbid, cfg);
          }
          else if(cfg.afid !== undefined) {
              await setupViewer('afid', cfg.afid, cfg);
          }
          else if(cfg.opmid !== undefined) {
              await setupViewer('opmid', cfg.opmid, cfg);
          }
          else if(cfg.cid !== undefined) {
              await setupViewer('cid', cfg.cid, cfg);
          }
          else if(cfg.mmcifid !== undefined) {
              await setupViewer('mmcifid', cfg.mmcifid, cfg);
          }
          else if(cfg.mmdbid !== undefined) {
              await setupViewer('mmdbid', cfg.mmdbid, cfg);
          }
          else if(cfg.gi !== undefined) {
              await setupViewer('gi', cfg.gi, cfg);
          }
          else if(cfg.uniprotid !== undefined) {
              await setupViewer('uniprotid', cfg.uniprotid, cfg);
          }
          else if(cfg.blast_rep_id !== undefined) {
              if( (cfg.from === 'blast' || cfg.from === 'icn3d') && cfg.command == '') {
                command = 'view+annotations;+set+annotation+cdd;+set+annotation+site;+set+view+detailed+view;+select+chain+'
                  + cfg.blast_rep_id + ';+show+selection';
              }

              await setupViewer('blast_rep_id', cfg.blast_rep_id, cfg);
          }
          else if(cfg.urlname !== undefined) {
              var urlname = decodeURIComponent(cfg.urlname);

              await setupViewer('url', cfg.urltype + '|' + urlname, cfg);
          }
          // e.g., align=103701,1,4,68563,1,167 [mmdbid1,biounit,molecule,mmdbid2,biounit,molecule]
          else if(cfg.align !== undefined) {
              cfg.divid = 'div0';
              //cfg.align = cfg.align;
              //cfg.showalignseq = cfg.showalignseq;

              // VAST+ uses biological units
              cfg.bu = 1;

              cfg.idname = 'align';
              cfg.idvalue = cfg.align;

              var icn3dui = new icn3d.iCn3DUI(cfg);

              await icn3dui.show3DStructure();
          }
          else if(cfg.chainalign !== undefined || cfg.mmdbafid !== undefined) {
              cfg.divid = 'div0';

              if(cfg.chainalign !== undefined) {
                cfg.idname = 'chainalign';
                cfg.idvalue = cfg.chainalign;
              }
              else {
                cfg.idname = 'mmdbafid';
                cfg.idvalue = cfg.mmdbafid;
              }

              var icn3dui = new icn3d.iCn3DUI(cfg);

              await icn3dui.show3DStructure();
          }
          else {
              await setupViewer('', '', cfg);
          }
      }

      async function setupViewer(idName, idValue, cfg) {
        cfg.idname = idName;
        cfg.idvalue = idValue;
        
        var maxStructure = 5; // show max 5 structures

        var idArray = idValue.toString().replace(/\s/g, '').split(',');

        if(idArray.length > 1) {
          resize = false;

          if(cfg.width && cfg.width.indexOf('%') != -1) {
            cfg.width = 400;
            cfg.height = 400;
          }
        }

        for(var i = 0, il = idArray.length; i < il && i < maxStructure; ++i) {
          cfg.divid = 'div' + i;

          if(idName !== '') cfg[idName] = idArray[i];

          var icn3dui = new icn3d.iCn3DUI(cfg);

          await icn3dui.show3DStructure();
          //icn3dui.setOption('color', 'spectrum');

          if(idName === '') $("#div" + i + "_wait").hide();
        }
      }

      function getConfig() {
        // 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 params = url.split("?");
        // transforming the GET parameters into a dictionary
        var search = params[params.length - 1];

        var cfg = {};

        if(!bNopara) {
            var decodeSearch = decodeURIComponent(search).replace(/\+/g, ' ');

            // command could contains '&', for example when loading statefile 'load mmdb 1kq2 | parameters &atype=1'
            var commandPos = decodeSearch.indexOf('&command=');
            if(commandPos != -1) {
                cfg.command = decodeSearch.substr(commandPos + 9); // ";" separated commands
                decodeSearch = decodeSearch.substr(0, commandPos);

                var paraPos = decodeSearch.indexOf(' | parameters ');

                if(paraPos != -1) { //When loading statefile (e.g., 'load mmdb 1kq2 | parameters &atype=1'), the commands ends with '}}'.
                    var tmpPos = cfg.command.indexOf('}}&');
                    if(tmpPos != -1) { // more parameters after the command
                      decodeSearch += cfg.command.substr(tmpPos + 2);
                      cfg.command = cfg.command.substr(0, tmpPos + 2);
                    }
                }
                else {
                    var paraPos = cfg.command.indexOf(' | parameters ');

                    if(paraPos != -1) { // "&command=load mmdb 7DDD | parameters &mmdbid=7DDD; select..." the commands ends with '}}'.
                        var tmpPos = cfg.command.indexOf('}}&');
                        if(tmpPos != -1) { // more parameters after the command
                          decodeSearch += cfg.command.substr(tmpPos + 2);
                          cfg.command = cfg.command.substr(0, tmpPos + 2);
                        }
                    }
                    else {
                        var tmpPos = cfg.command.indexOf('&');
                        if(tmpPos != -1) {
                          decodeSearch += cfg.command.substr(tmpPos);
                          cfg.command = cfg.command.substr(0, tmpPos);
                        }
                    }
                }
            }
            else {
                cfg.command = '';
            }

            var hashes = decodeSearch.split('&');
            for (var i = 0; i < hashes.length; i++) {
                var hash = hashes[i].split('=');
                cfg[hash[0].trim()] = (hash[1] !== undefined) ? hash[1].trim() : undefined;
            }

            // for mmdb structures, pass the parameters after the first "&" sign
            cfg.inpara = "&" + url.substr(ampPos + 1);
        }

        // changed some parameter names
        cfg.rid = cfg.RID;

        cfg.urlname = cfg.url;
        if(cfg.urlname && cfg.urlname.indexOf('%3A%2F%2F') === -1) { // decoded URL
            // should encode it
            cfg.urlname = encodeURIComponent(cfg.urlname);
        }
        cfg.urltype = (cfg.type === undefined) ? 'pdb' : cfg.type;

        cfg.version = getValue(cfg.v);

        if(cfg.version !== undefined && window.localStorage && localStorage.getItem('fixedversion')) {
            var fixedUrl = url.replace('full.html', 'full_' + cfg.version + '.html');
            window.open(fixedUrl, '_self');

            localStorage.removeItem('fixedversion');
        }

        // standardize the input values
        for(var i in cfg) {
            if(i == 'bu') {
              cfg[i] = getInt(cfg[i]);
            }
            else {
               cfg[i] = getValue(cfg[i]);
            }
        }

        // backward compatible with showseq
        cfg.showanno = cfg.showanno || cfg.showseq;

        cfg.shownote = 1; //cfg.shownote;
        cfg.options = (cfg.options !== undefined) ? JSON.parse(cfg.options) : undefined;

        // default to show biological unit
        if(cfg.bu === undefined) cfg.bu = 1; //0;
        if(cfg.buidx !== undefined) cfg.bu = cfg.buidx;
        
        return cfg;
      }

      function getValue(input) {
        if(input == 'true' || input == '1') {
          input = true;
        }
        else if(input == 'false' || input == '0') {
          input = false;
        }

        return input;
      }

      function getInt(input) {
        if(input == 'true' || input == '1') {
          input = 1;
        }
        else if(input == 'false' || input == '0') {
          input = 0;
        }

        return input;
      }
    }); // document ready
  </script>

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