icn3d 3.19.4 → 3.20.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (4) hide show
  1. package/icn3d.js +236 -147
  2. package/icn3d.min.js +2 -2
  3. package/icn3d.module.js +238 -148
  4. package/package.json +1 -1
package/icn3d.js CHANGED
@@ -22958,13 +22958,18 @@ class PdbParser {
22958
22958
  //Ajax call was used to get the atom data from the "pdbid". This function was deferred so that
22959
22959
  //it can be chained together with other deferred functions for sequential execution. A wrapper
22960
22960
  //was added to support both http and https.
22961
- downloadPdb(pdbid, bAf) { let ic = this.icn3d; ic.icn3dui;
22961
+ downloadPdb(pdbid, bAf) { let ic = this.icn3d, me = ic.icn3dui;
22962
22962
  ic.deferredOpm = $.Deferred(function() {
22963
22963
  let url, dataType;
22964
22964
 
22965
22965
  if(bAf) {
22966
22966
  url = "https://alphafold.ebi.ac.uk/files/AF-" + pdbid + "-F1-model_" + ic.AFUniprotVersion + ".pdb";
22967
- ic.ParserUtilsCls.setYourNote(pdbid.toUpperCase() + '(AlphaFold) in iCn3D');
22967
+ if(me.cfg.refseqid) {
22968
+ ic.ParserUtilsCls.setYourNote(me.cfg.refseqid.toUpperCase() + '(RefSeq) in iCn3D');
22969
+ }
22970
+ else {
22971
+ ic.ParserUtilsCls.setYourNote(pdbid.toUpperCase() + '(AlphaFold) in iCn3D');
22972
+ }
22968
22973
  }
22969
22974
  else {
22970
22975
  url = "https://files.rcsb.org/view/" + pdbid + ".pdb";
@@ -24610,15 +24615,15 @@ class MmdbParser {
24610
24615
  }
24611
24616
  }
24612
24617
 
24613
- downloadUniprotid(uniprotid) { let ic = this.icn3d; ic.icn3dui;
24618
+ downloadRefseq(refseqid) { let ic = this.icn3d, me = ic.icn3dui;
24614
24619
  // get gis
24615
- let url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=protein&retmode=json&id=" + uniprotid;
24620
+ let url = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?refseq2uniprot=" + refseqid;
24616
24621
 
24617
24622
  ic.bCid = undefined;
24618
24623
 
24619
24624
  $.ajax({
24620
24625
  url: url,
24621
- dataType: 'json',
24626
+ dataType: 'jsonp',
24622
24627
  cache: true,
24623
24628
  tryCount : 0,
24624
24629
  retryLimit : 0, //1
@@ -24629,10 +24634,12 @@ class MmdbParser {
24629
24634
  //ic.ParserUtilsCls.hideLoading();
24630
24635
  },
24631
24636
  success: function(data) {
24632
- let giArray = data.result.uids;
24637
+ me.cfg.afid = data.uniprot;
24633
24638
 
24634
- let redirectUrl = "https://www.ncbi.nlm.nih.gov/structure?linkname=protein_structure&from_uid=" + giArray.join(',');
24635
- window.open(redirectUrl, '_self');
24639
+ let bAf = true;
24640
+ $.when(ic.pdbParserCls.downloadPdb(me.cfg.afid, bAf)).then(function() {
24641
+ ic.loadScriptCls.loadScript(me.cfg.command, undefined, true);
24642
+ });
24636
24643
  },
24637
24644
  error : function(xhr, textStatus, errorThrown ) {
24638
24645
  this.tryCount++;
@@ -28551,6 +28558,14 @@ class LoadScript {
28551
28558
  me.cfg.gi = id;
28552
28559
  ic.mmdbParserCls.downloadGi(id);
28553
28560
  }
28561
+ else if(command.indexOf('load refseq') !== -1) {
28562
+ me.cfg.refseqid = id;
28563
+ ic.mmdbParserCls.downloadRefseq(id);
28564
+ }
28565
+ // else if(command.indexOf('load proteinname') !== -1) {
28566
+ // me.cfg.proteinname = id;
28567
+ // ic.mmdbParserCls.downloadProteinname(id);
28568
+ // }
28554
28569
  else if(command.indexOf('load seq_struct_ids ') !== -1) {
28555
28570
  ic.bSmithwm = false;
28556
28571
  ic.bLocalSmithwm = false;
@@ -29250,7 +29265,7 @@ class ResizeCanvas {
29250
29265
  //let itemArray = ['dl_selectannotations', 'dl_alignment', 'dl_2ddgm', 'dl_definedsets', 'dl_graph',
29251
29266
  // 'dl_linegraph', 'dl_scatterplot', 'dl_contactmap', 'dl_allinteraction', 'dl_copyurl',
29252
29267
  // 'dl_symmetry', 'dl_symd', 'dl_rmsd', 'dl_legend', 'dl_disttable'];
29253
- let itemArray = ['dl_2ddgm', 'dl_2dctn', 'dl_alignment', 'dl_sequence2', 'dl_definedsets', 'dl_setsmenu', 'dl_command', 'dl_setoperations', 'dl_vast', 'dl_foldseek', 'dl_mmtfid', 'dl_pdbid', 'dl_afid', 'dl_opmid', 'dl_pdbfile', 'dl_pdbfile_app', 'dl_rescolorfile', 'dl_customcolor', 'dl_align', 'dl_alignaf', 'dl_chainalign', 'dl_chainalign2', 'dl_chainalign3', 'dl_mutation', 'dl_mol2file', 'dl_sdffile', 'dl_xyzfile', 'dl_afmapfile', 'dl_urlfile', 'dl_mmciffile', 'dl_mmcifid', 'dl_mmdbid', 'dl_mmdbafid', 'dl_blast_rep_id', 'dl_yournote', 'dl_gi', 'dl_uniprotid', 'dl_cid', 'dl_pngimage', 'dl_state', 'dl_fixedversion', 'dl_selection', 'dl_dsn6', 'dl_dsn6url', 'dl_clr', 'dl_symmetry', 'dl_symd', 'dl_contact', 'dl_hbonds', 'dl_realign', 'dl_realignbystruct', 'dl_allinteraction', 'dl_interactionsorted', 'dl_linegraph', 'dl_linegraphcolor', 'dl_scatterplot', 'dl_scatterplotcolor', 'dl_contactmap', 'dl_alignerrormap', 'dl_elecmap2fofc', 'dl_elecmapfofc', 'dl_emmap', 'dl_aroundsphere', 'dl_adjustmem', 'dl_selectplane', 'dl_addlabel', 'dl_addlabelselection', 'dl_labelColor', 'dl_distance', 'dl_stabilizer', 'dl_disttwosets', 'dl_distmanysets', 'dl_stabilizer_rm', 'dl_thickness', 'dl_thickness2', 'dl_addtrack', 'dl_addtrack_tabs', 'dl_saveselection', 'dl_copyurl', 'dl_selectannotations', 'dl_annotations_tabs', 'dl_anno_view_tabs', 'dl_annotations', 'dl_graph', 'dl_svgcolor', 'dl_area', 'dl_colorbyarea', 'dl_rmsd', 'dl_buriedarea', 'dl_propbypercentout', 'dl_propbybfactor', 'dl_legend', 'dl_disttable'];
29268
+ let itemArray = ['dl_2ddgm', 'dl_2dctn', 'dl_alignment', 'dl_sequence2', 'dl_definedsets', 'dl_setsmenu', 'dl_command', 'dl_setoperations', 'dl_vast', 'dl_foldseek', 'dl_mmtfid', 'dl_pdbid', 'dl_afid', 'dl_opmid', 'dl_pdbfile', 'dl_pdbfile_app', 'dl_rescolorfile', 'dl_customcolor', 'dl_align', 'dl_alignaf', 'dl_chainalign', 'dl_chainalign2', 'dl_chainalign3', 'dl_mutation', 'dl_mol2file', 'dl_sdffile', 'dl_xyzfile', 'dl_afmapfile', 'dl_urlfile', 'dl_mmciffile', 'dl_mmcifid', 'dl_mmdbid', 'dl_mmdbafid', 'dl_blast_rep_id', 'dl_yournote', 'dl_gi', 'dl_refseqid', 'dl_cid', 'dl_pngimage', 'dl_state', 'dl_fixedversion', 'dl_selection', 'dl_dsn6', 'dl_dsn6url', 'dl_clr', 'dl_symmetry', 'dl_symd', 'dl_contact', 'dl_hbonds', 'dl_realign', 'dl_realignbystruct', 'dl_allinteracton', 'dl_interactionsorted', 'dl_linegraph', 'dl_linegraphcolor', 'dl_scatterplot', 'dl_scatterploitcolor', 'dl_contactmap', 'dl_alignerrormap', 'dl_elecmap2fofc', 'dl_elecmapfofc', 'dl_emmap', 'dl_aroundsphere', 'dl_adjustmem', 'dl_selectplane', 'dl_addlabel', 'dl_addlabelselection', 'dl_labelColor', 'dl_distance', 'dl_stabilizer', 'dl_disttwosets', 'dl_distmanysets', 'dl_stabilizer_rm', 'dl_thickness', 'dl_thickness2', 'dl_addtrack', 'dl_addtrack_tabs', 'dl_saveselection', 'dl_copyurl', 'dl_selectannotations', 'dl_annotations_tabs', 'dl_anno_view_tabs', 'dl_annotations', 'dl_graph', 'dl_svgcolor', 'dl_area', 'dl_colorbyarea', 'dl_rmsd', 'dl_buriedarea', 'dl_propbypercentout', 'dl_propbybfactor', 'dl_legend', 'dl_disttable'];
29254
29269
 
29255
29270
  for(let i in itemArray) {
29256
29271
  let item = itemArray[i];
@@ -34452,7 +34467,8 @@ class ApplyCommand {
34452
34467
  let paraArray = command.split(' | ');
34453
34468
  let url = paraArray[1];
34454
34469
 
34455
- window.open(url, '_blank');
34470
+ let urlTarget = '_blank';
34471
+ window.open(url, urlTarget);
34456
34472
  }
34457
34473
  else if(commandOri.indexOf('your note') == 0) {
34458
34474
  let paraArray = commandOri.split(' | ');
@@ -54582,13 +54598,14 @@ class SaveFile {
54582
54598
  }
54583
54599
  }
54584
54600
 
54585
- setStructureTitle(url, title, titlelinkColor) {var ic = this.icn3d; ic.icn3dui;
54601
+ setStructureTitle(url, title, titlelinkColor) {var ic = this.icn3d, me = ic.icn3dui;
54586
54602
  if(ic.molTitle.length > 40) title = ic.molTitle.substr(0, 40) + "...";
54587
54603
 
54588
54604
  //var asymmetricStr =(ic.bAssemblyUseAsu) ? "(Asymmetric Unit)" : "";
54589
54605
  let asymmetricStr = "";
54590
54606
 
54591
54607
  let idName = (isNaN(ic.inputid) && ic.inputid.length > 5) ? "AlphaFold ID" : "PDB ID";
54608
+ if(me.cfg.refseqid) idName = 'NCBI RefSeq ID';
54592
54609
 
54593
54610
  $("#" + ic.pre + "title").html(idName + " <a id='" + ic.pre + "titlelink' href='" + url + "' style='color:" + titlelinkColor + "' target='_blank'>" + ic.inputid.toUpperCase() + "</a>" + asymmetricStr + ": " + title);
54594
54611
  }
@@ -54599,6 +54616,9 @@ class SaveFile {
54599
54616
  if(me.cfg.cid !== undefined) {
54600
54617
  url = "https://www.ncbi.nlm.nih.gov/pccompound/?term=";
54601
54618
  }
54619
+ else if(me.cfg.refseqid !== undefined) {
54620
+ url = "https://www.ncbi.nlm.nih.gov/protein/";
54621
+ }
54602
54622
  else if(me.cfg.afid !== undefined) {
54603
54623
  url = "https://alphafold.ebi.ac.uk/search/text/";
54604
54624
  }
@@ -54644,12 +54664,14 @@ class SaveFile {
54644
54664
  if(structArray.length === 1) {
54645
54665
  url = "https://www.ncbi.nlm.nih.gov/" + db + "/?term=" + structArray[0];
54646
54666
  me.htmlCls.clickMenuCls.setLogCmd("Entrez " + db + " about PDB " + structArray[0] + ": " + url, false);
54647
- window.open(url, '_blank');
54667
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
54668
+ window.open(url, urlTarget);
54648
54669
  }
54649
54670
  else if(structArray.length === 2) {
54650
54671
  url = "https://www.ncbi.nlm.nih.gov/" + db + "/?term=" + structArray[0] + " OR " + structArray[1];
54651
54672
  me.htmlCls.clickMenuCls.setLogCmd("Entrez " + db + " about PDB " + structArray[0] + " OR " + structArray[1] + ": " + url, false);
54652
- window.open(url, '_blank');
54673
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
54674
+ window.open(url, urlTarget);
54653
54675
  }
54654
54676
  }
54655
54677
  }
@@ -54844,6 +54866,14 @@ class ClickMenu {
54844
54866
  me.htmlCls.dialogCls.openDlg('dl_afid', 'Please input AlphaFold UniProt ID');
54845
54867
  });
54846
54868
 
54869
+ me.myEventCls.onIds("#" + me.pre + "mn1_refseqid", "click", function(e) { me.icn3d; e.preventDefault();
54870
+ me.htmlCls.dialogCls.openDlg('dl_refseqid', 'Please input NCBI RefSeq ID');
54871
+ });
54872
+
54873
+ // me.myEventCls.onIds("#" + me.pre + "mn1_proteinname", "click", function(e) { let ic = me.icn3d; e.preventDefault();
54874
+ // me.htmlCls.dialogCls.openDlg('dl_proteinname', 'Please input protein name to search');
54875
+ // });
54876
+
54847
54877
  // },
54848
54878
  // clkMn1_opmid: function() {
54849
54879
  me.myEventCls.onIds("#" + me.pre + "mn1_opmid", "click", function(e) { me.icn3d; e.preventDefault();
@@ -54916,11 +54946,12 @@ class ClickMenu {
54916
54946
  me.myEventCls.onIds("#" + me.pre + "mn1_fixedversion", "click", function(e) { me.icn3d; e.preventDefault();
54917
54947
  me.htmlCls.dialogCls.openDlg('dl_fixedversion', 'Open Share Link URL in the archived version of iCn3D');
54918
54948
  });
54919
- me.myEventCls.onIds("#" + me.pre + "reload_fixedversion", "click", function(e) { me.icn3d; e.preventDefault();
54949
+ me.myEventCls.onIds("#" + me.pre + "reload_fixedversion", "click", function(e) { let ic = me.icn3d; e.preventDefault();
54920
54950
  let url = $("#" + me.pre + "sharelinkurl").val();
54921
54951
  thisClass.setLogCmd("open " + url, false);
54922
54952
  localStorage.setItem('fixedversion', '1');
54923
- window.open(url, '_blank');
54953
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
54954
+ window.open(url, urlTarget);
54924
54955
  });
54925
54956
  // },
54926
54957
  // clkMn1_mmciffile: function() {
@@ -54952,13 +54983,6 @@ class ClickMenu {
54952
54983
  me.htmlCls.dialogCls.openDlg('dl_gi', 'Please input protein gi');
54953
54984
  });
54954
54985
 
54955
- me.myEventCls.onIds("#" + me.pre + "mn1_refseq", "click", function(e) { me.icn3d; e.preventDefault();
54956
- me.htmlCls.dialogCls.openDlg('dl_grefseq', 'Please input protein RefSeq');
54957
- });
54958
-
54959
- me.myEventCls.onIds("#" + me.pre + "mn1_uniprotid", "click", function(e) { me.icn3d; e.preventDefault();
54960
- me.htmlCls.dialogCls.openDlg('dl_uniprotid', 'Please input UniProt ID');
54961
- });
54962
54986
  // },
54963
54987
  // clkMn1_cid: function() {
54964
54988
  me.myEventCls.onIds("#" + me.pre + "mn1_cid", "click", function(e) { me.icn3d; e.preventDefault();
@@ -55299,14 +55323,16 @@ class ClickMenu {
55299
55323
  // clkMn1_link_structure: function() {
55300
55324
  me.myEventCls.onIds("#" + me.pre + "mn1_link_structure", "click", function(e) { let ic = me.icn3d; e.preventDefault();
55301
55325
  let url = ic.saveFileCls.getLinkToStructureSummary(true);
55302
- window.open(url, '_blank');
55326
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
55327
+ window.open(url, urlTarget);
55303
55328
  });
55304
55329
  // },
55305
55330
  // clkMn1_link_bind: function() {
55306
55331
  me.myEventCls.onIds("#" + me.pre + "mn1_link_bind", "click", function(e) { let ic = me.icn3d; e.preventDefault();
55307
55332
  url = "https://www.ncbi.nlm.nih.gov/pccompound?LinkName=pccompound_structure&from_uid=" + ic.inputid;
55308
55333
  thisClass.setLogCmd("link to 3D protein structures bound to CID " + ic.inputid + ": " + url, false);
55309
- window.open(url, '_blank');
55334
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
55335
+ window.open(url, urlTarget);
55310
55336
  });
55311
55337
  // },
55312
55338
  // clkMn1_link_vast: function() {
@@ -55333,8 +55359,10 @@ class ClickMenu {
55333
55359
  thisClass.setLogCmd("link to structures similar to " + idArray[0] + ": " + url, false);
55334
55360
  }
55335
55361
  }
55336
- window.open(url, '_blank');
55337
55362
  }
55363
+
55364
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
55365
+ window.open(url, urlTarget);
55338
55366
  });
55339
55367
  // },
55340
55368
  // clkMn1_link_pubmed: function() {
@@ -55343,7 +55371,8 @@ class ClickMenu {
55343
55371
  let url;
55344
55372
  url = "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + ic.molTitle;
55345
55373
  thisClass.setLogCmd("link to literature about " + ic.molTitle + ": " + url, false);
55346
- window.open(url, '_blank');
55374
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
55375
+ window.open(url, urlTarget);
55347
55376
  }
55348
55377
  else if(ic.pmid) {
55349
55378
  let idArray = ic.pmid.toString().split('_');
@@ -55356,7 +55385,8 @@ class ClickMenu {
55356
55385
  url = "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + idArray[0] + " OR " + idArray[1];
55357
55386
  thisClass.setLogCmd("link to PubMed IDs " + idArray[0] + ", " + idArray[1] + ": " + url, false);
55358
55387
  }
55359
- window.open(url, '_blank');
55388
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
55389
+ window.open(url, urlTarget);
55360
55390
  }
55361
55391
  else if(isNaN(ic.inputid)) {
55362
55392
  let idArray = ic.inputid.toString().split('_');
@@ -55369,7 +55399,8 @@ class ClickMenu {
55369
55399
  url = "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + idArray[0] + " OR " + idArray[1];
55370
55400
  thisClass.setLogCmd("link to literature about PDB " + idArray[0] + " OR " + idArray[1] + ": " + url, false);
55371
55401
  }
55372
- window.open(url, '_blank');
55402
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
55403
+ window.open(url, urlTarget);
55373
55404
  }
55374
55405
  else {
55375
55406
  if(me.cfg.cid !== undefined) {
@@ -55396,7 +55427,8 @@ class ClickMenu {
55396
55427
  if(text.length > 0) text = text.substr(0, text.length - 4);
55397
55428
  let url = "https://www.ncbi.nlm.nih.gov/protein/?term=" + text;
55398
55429
  thisClass.setLogCmd("link to Entrez protein about PDB " + structArray + ": " + url, false);
55399
- window.open(url, '_blank');
55430
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
55431
+ window.open(url, urlTarget);
55400
55432
  });
55401
55433
  // },
55402
55434
  }
@@ -56697,7 +56729,8 @@ class ClickMenu {
56697
56729
  //else {
56698
56730
  url = url.replace("full.html", "full2.html");
56699
56731
  url += '&closepopup=1';
56700
- window.open(url, '_blank');
56732
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
56733
+ window.open(url, urlTarget);
56701
56734
  thisClass.setLogCmd('side by side | ' + url, true);
56702
56735
  //}
56703
56736
  });
@@ -57087,7 +57120,8 @@ class ClickMenu {
57087
57120
 
57088
57121
  let template = "<!doctype html>\n<head>\n<title>Loading Foldseek</title>\n<style>\n body {\n background-color: #121212;\n color: #fff;\n font-family: system-ui, -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, 'Open Sans', 'Helvetica Neue', sans-serif;\n height: 100vh;\n display: flex;\n flex-direction: column;\n flex-wrap: wrap;\n justify-content: center;\n align-items: center;\n }\n .loader {\n display: block;\n width: 80px;\n height: 80px;\n }\n .loader:after {\n content: \" \";\n display: block;\n width: 64px;\n height: 64px;\n margin: 8px;\n border-radius: 50%;\n border: 6px solid #fff;\n border-color: #fff transparent #fff transparent;\n animation: loader 1.2s linear infinite;\n }\n @keyframes loader {\n 0% {\n transform: rotate(0deg);\n }\n 100% {\n transform: rotate(360deg);\n }\n }\n</style>\n</head>\n<body>\n<div>Foldseek is loading...</div><div class=\"loader\"></div>\n</body>";
57089
57122
 
57090
- let w = window.open('', '_blank');
57123
+ let urlTarget = '_blank';
57124
+ let w = window.open('', urlTarget);
57091
57125
  w.document.body.innerHTML = template;
57092
57126
 
57093
57127
  $.ajax({
@@ -57675,13 +57709,20 @@ class SetMenu {
57675
57709
  html += me.htmlCls.setHtmlCls.getLink('mn1_mmdbid', 'NCBI MMDB ID (annotation) ' + me.htmlCls.wifiStr, undefined, 2);
57676
57710
  html += me.htmlCls.setHtmlCls.getLink('mn1_mmtfid', 'RCSB MMTF ID (fast) ' + me.htmlCls.wifiStr, undefined, 2);
57677
57711
  html += me.htmlCls.setHtmlCls.getLink('mn1_pdbid', 'RCSB PDB ID ' + me.htmlCls.wifiStr, undefined, 2);
57678
- html += me.htmlCls.setHtmlCls.getLink('mn1_afid', 'AlphaFold UniProt ID ' + me.htmlCls.wifiStr, undefined, 2);
57712
+
57713
+ html += me.htmlCls.setHtmlCls.getMenuText('mn1_afwrap', 'AlphaFold Structures', undefined, undefined, 2);
57714
+ html += "<ul>";
57715
+
57716
+ html += me.htmlCls.setHtmlCls.getLink('mn1_afid', 'UniProt ID ' + me.htmlCls.wifiStr, undefined, 3);
57717
+ html += me.htmlCls.setHtmlCls.getLink('mn1_refseqid', 'NCBI RefSeq ID ' + me.htmlCls.wifiStr, undefined, 3);
57718
+ // html += me.htmlCls.setHtmlCls.getLink('mn1_proteinname', 'Protein Name ' + me.htmlCls.wifiStr, undefined, 3);
57719
+ html += "</ul>";
57720
+
57721
+
57679
57722
  html += me.htmlCls.setHtmlCls.getLink('mn1_opmid', 'OPM PDB ID ' + me.htmlCls.wifiStr, undefined, 2);
57680
57723
  html += me.htmlCls.setHtmlCls.getLink('mn1_mmcifid', 'RCSB mmCIF ID ' + me.htmlCls.wifiStr, undefined, 2);
57681
- html += me.htmlCls.setHtmlCls.getLink('mn1_gi', 'NCBI gi ' + me.htmlCls.wifiStr, undefined, 2);
57682
- //html += me.htmlCls.setHtmlCls.getLink('mn1_refseq', 'NCBI RefSeq ' + me.htmlCls.wifiStr, undefined, 2);
57724
+ //html += me.htmlCls.setHtmlCls.getLink('mn1_gi', 'NCBI gi ' + me.htmlCls.wifiStr, undefined, 2);
57683
57725
 
57684
- //html += me.htmlCls.setHtmlCls.getLink('mn1_uniprotid', 'UniProt ID ' + me.htmlCls.wifiStr);
57685
57726
  html += me.htmlCls.setHtmlCls.getLink('mn1_cid', 'PubChem CID ' + me.htmlCls.wifiStr, 1, 2);
57686
57727
 
57687
57728
  html += "</ul>";
@@ -59889,6 +59930,16 @@ class SetDialog {
59889
59930
  + me.htmlCls.buttonStr + "reload_afmapfull' style='margin-left:30px'>Load Full (slow)</button>";
59890
59931
  html += "</div>";
59891
59932
 
59933
+ html += me.htmlCls.divStr + "dl_refseqid' class='" + dialogClass + "'>";
59934
+ html += "NCBI RefSeq ID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "refseqid' value='0308234A' size=8> ";
59935
+ html += me.htmlCls.buttonStr + "reload_refseq'>Load</button>";
59936
+ html += "</div>";
59937
+
59938
+ // html += me.htmlCls.divStr + "dl_proteinname' class='" + dialogClass + "'>";
59939
+ // html += "PDB ID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "proteinname' value='kinase' size=8> ";
59940
+ // html += me.htmlCls.buttonStr + "reload_proteinname'>Load</button>";
59941
+ // html += "</div>";
59942
+
59892
59943
  html += me.htmlCls.divStr + "dl_opmid' class='" + dialogClass + "'>";
59893
59944
  html += "<a href='https://opm.phar.umich.edu' target='_blank'>Orientations of Proteins in Membranes(OPM)</a> PDB ID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "opmid' value='6JXR' size=8> ";
59894
59945
  html += me.htmlCls.buttonStr + "reload_opm'>Load</button>";
@@ -60107,17 +60158,6 @@ class SetDialog {
60107
60158
  html += me.htmlCls.buttonStr + "reload_gi'>Load</button>";
60108
60159
  html += "</div>";
60109
60160
 
60110
- html += me.htmlCls.divStr + "dl_refseq' class='" + dialogClass + "'>";
60111
- html += "Protein RefSeq: " + me.htmlCls.inputTextStr + "id='" + me.pre + "refseq' value='0308234A' size=8> ";
60112
- html += me.htmlCls.buttonStr + "reload_refseq'>Load</button>";
60113
- html += "</div>";
60114
-
60115
- html += me.htmlCls.divStr + "dl_uniprotid' class='" + dialogClass + "'>";
60116
- html += "Note: A list of structures will be shown. Click \"View in iCn3D\" to view each structure in 3D.<br><br>";
60117
- html += "UniProt ID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "uniprotid' value='P0DTC2' size=8> ";
60118
- html += me.htmlCls.buttonStr + "reload_uniprotid'>Load</button>";
60119
- html += "</div>";
60120
-
60121
60161
  html += me.htmlCls.divStr + "dl_cid' class='" + dialogClass + "'>";
60122
60162
  html += "PubChem CID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "cid' value='2244' size=8> ";
60123
60163
  html += me.htmlCls.buttonStr + "reload_cid'>Load</button>";
@@ -61121,7 +61161,7 @@ class Events {
61121
61161
  $("#" + me.pre + id).resizable();
61122
61162
  }
61123
61163
 
61124
- launchMmdb(ids, bBiounit, hostUrl) { let me = this.icn3dui; me.icn3d;
61164
+ launchMmdb(ids, bBiounit, hostUrl) { let me = this.icn3dui, ic = me.icn3d;
61125
61165
  let flag = bBiounit ? '1' : '0';
61126
61166
 
61127
61167
  ids = ids.replace(/,/g, ' ').replace(/\s+/g, ',').trim();
@@ -61134,11 +61174,13 @@ class Events {
61134
61174
  let idArray = ids.split(',');
61135
61175
  if(idArray.length == 1 && (idArray[0].length == 4 || !isNaN(idArray[0])) ) {
61136
61176
  me.htmlCls.clickMenuCls.setLogCmd("load mmdb" + flag + " " + ids, false);
61137
- window.open(hostUrl + '?mmdbid=' + ids + '&bu=' + flag, '_blank');
61177
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61178
+ window.open(hostUrl + '?mmdbid=' + ids + '&bu=' + flag, urlTarget);
61138
61179
  }
61139
61180
  else {
61140
61181
  me.htmlCls.clickMenuCls.setLogCmd("load mmdbaf" + flag + " " + ids, false);
61141
- window.open(hostUrl + '?mmdbafid=' + ids + '&bu=' + flag, '_blank');
61182
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61183
+ window.open(hostUrl + '?mmdbafid=' + ids + '&bu=' + flag, urlTarget);
61142
61184
  }
61143
61185
  }
61144
61186
 
@@ -61487,18 +61529,20 @@ class Events {
61487
61529
 
61488
61530
  // },
61489
61531
  // clickReload_mmtf: function() {
61490
- me.myEventCls.onIds("#" + me.pre + "reload_vastplus", "click", function(e) { me.icn3d;
61532
+ me.myEventCls.onIds("#" + me.pre + "reload_vastplus", "click", function(e) { let ic = me.icn3d;
61491
61533
  e.preventDefault();
61492
61534
  if(!me.cfg.notebook) dialog.dialog( "close" );
61493
61535
  me.htmlCls.clickMenuCls.setLogCmd("vast+ search " + $("#" + me.pre + "vastpluspdbid").val(), false);
61494
- window.open('https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi?uid=' + $("#" + me.pre + "vastpluspdbid").val(), '_blank');
61536
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61537
+ window.open('https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi?uid=' + $("#" + me.pre + "vastpluspdbid").val(), urlTarget);
61495
61538
  });
61496
61539
 
61497
- me.myEventCls.onIds("#" + me.pre + "reload_vast", "click", function(e) { me.icn3d;
61540
+ me.myEventCls.onIds("#" + me.pre + "reload_vast", "click", function(e) { let ic = me.icn3d;
61498
61541
  e.preventDefault();
61499
61542
  if(!me.cfg.notebook) dialog.dialog( "close" );
61500
61543
  me.htmlCls.clickMenuCls.setLogCmd("vast search " + $("#" + me.pre + "vastpdbid").val() + "_" + $("#" + me.pre + "vastchainid").val(), false);
61501
- window.open('https://www.ncbi.nlm.nih.gov/Structure/vast/vastsrv.cgi?pdbid=' + $("#" + me.pre + "vastpdbid").val() + '&chain=' + $("#" + me.pre + "vastchainid").val(), '_blank');
61544
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61545
+ window.open('https://www.ncbi.nlm.nih.gov/Structure/vast/vastsrv.cgi?pdbid=' + $("#" + me.pre + "vastpdbid").val() + '&chain=' + $("#" + me.pre + "vastchainid").val(), urlTarget);
61502
61546
  });
61503
61547
 
61504
61548
  me.myEventCls.onIds("#" + me.pre + "reload_foldseek", "click", function(e) { me.icn3d;
@@ -61516,50 +61560,55 @@ class Events {
61516
61560
  window.open(hostUrl + '?chainalign=' + alignment_final + '&aligntool=tmalign&showalignseq=1&bu=0', '_self');
61517
61561
  });
61518
61562
 
61519
- me.myEventCls.onIds("#" + me.pre + "reload_mmtf", "click", function(e) { me.icn3d;
61563
+ me.myEventCls.onIds("#" + me.pre + "reload_mmtf", "click", function(e) { let ic = me.icn3d;
61520
61564
  e.preventDefault();
61521
61565
  if(!me.cfg.notebook) dialog.dialog( "close" );
61522
61566
  me.htmlCls.clickMenuCls.setLogCmd("load mmtf " + $("#" + me.pre + "mmtfid").val(), false);
61523
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmtfid=' + $("#" + me.pre + "mmtfid").val(), '_blank');
61524
- window.open(hostUrl + '?mmtfid=' + $("#" + me.pre + "mmtfid").val(), '_blank');
61567
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmtfid=' + $("#" + me.pre + "mmtfid").val(), urlTarget);
61568
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61569
+ window.open(hostUrl + '?mmtfid=' + $("#" + me.pre + "mmtfid").val(), urlTarget);
61525
61570
  });
61526
61571
 
61527
- me.myEventCls.onIds("#" + me.pre + "mmtfid", "keyup", function(e) { me.icn3d;
61572
+ me.myEventCls.onIds("#" + me.pre + "mmtfid", "keyup", function(e) { let ic = me.icn3d;
61528
61573
  if (e.keyCode === 13) {
61529
61574
  e.preventDefault();
61530
61575
  if(!me.cfg.notebook) dialog.dialog( "close" );
61531
61576
  me.htmlCls.clickMenuCls.setLogCmd("load mmtf " + $("#" + me.pre + "mmtfid").val(), false);
61532
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmtfid=' + $("#" + me.pre + "mmtfid").val(), '_blank');
61533
- window.open(hostUrl + '?mmtfid=' + $("#" + me.pre + "mmtfid").val(), '_blank');
61577
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmtfid=' + $("#" + me.pre + "mmtfid").val(), urlTarget);
61578
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61579
+ window.open(hostUrl + '?mmtfid=' + $("#" + me.pre + "mmtfid").val(), urlTarget);
61534
61580
  }
61535
61581
  });
61536
61582
 
61537
61583
  // },
61538
61584
  // clickReload_pdb: function() {
61539
- me.myEventCls.onIds("#" + me.pre + "reload_pdb", "click", function(e) { me.icn3d;
61585
+ me.myEventCls.onIds("#" + me.pre + "reload_pdb", "click", function(e) { let ic = me.icn3d;
61540
61586
  e.preventDefault();
61541
61587
  if(!me.cfg.notebook) dialog.dialog( "close" );
61542
61588
  me.htmlCls.clickMenuCls.setLogCmd("load pdb " + $("#" + me.pre + "pdbid").val(), false);
61543
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?pdbid=' + $("#" + me.pre + "pdbid").val(), '_blank');
61544
- window.open(hostUrl + '?pdbid=' + $("#" + me.pre + "pdbid").val(), '_blank');
61589
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?pdbid=' + $("#" + me.pre + "pdbid").val(), urlTarget);
61590
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61591
+ window.open(hostUrl + '?pdbid=' + $("#" + me.pre + "pdbid").val(), urlTarget);
61545
61592
  });
61546
61593
 
61547
- me.myEventCls.onIds("#" + me.pre + "pdbid", "keyup", function(e) { me.icn3d;
61594
+ me.myEventCls.onIds("#" + me.pre + "pdbid", "keyup", function(e) { let ic = me.icn3d;
61548
61595
  if (e.keyCode === 13) {
61549
61596
  e.preventDefault();
61550
61597
  if(!me.cfg.notebook) dialog.dialog( "close" );
61551
61598
  me.htmlCls.clickMenuCls.setLogCmd("load pdb " + $("#" + me.pre + "pdbid").val(), false);
61552
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?pdbid=' + $("#" + me.pre + "pdbid").val(), '_blank');
61553
- window.open(hostUrl + '?pdbid=' + $("#" + me.pre + "pdbid").val(), '_blank');
61599
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?pdbid=' + $("#" + me.pre + "pdbid").val(), urlTarget);
61600
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61601
+ window.open(hostUrl + '?pdbid=' + $("#" + me.pre + "pdbid").val(), urlTarget);
61554
61602
  }
61555
61603
  });
61556
61604
 
61557
- me.myEventCls.onIds("#" + me.pre + "reload_af", "click", function(e) { me.icn3d;
61605
+ me.myEventCls.onIds("#" + me.pre + "reload_af", "click", function(e) { let ic = me.icn3d;
61558
61606
  e.preventDefault();
61559
61607
  if(!me.cfg.notebook) dialog.dialog( "close" );
61560
61608
  me.htmlCls.clickMenuCls.setLogCmd("load af " + $("#" + me.pre + "afid").val(), false);
61561
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?afid=' + $("#" + me.pre + "afid").val(), '_blank');
61562
- window.open(hostUrl + '?afid=' + $("#" + me.pre + "afid").val(), '_blank');
61609
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?afid=' + $("#" + me.pre + "afid").val(), urlTarget);
61610
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61611
+ window.open(hostUrl + '?afid=' + $("#" + me.pre + "afid").val(), urlTarget);
61563
61612
  });
61564
61613
 
61565
61614
  me.myEventCls.onIds("#" + me.pre + "reload_afmap", "click", function(e) { let ic = me.icn3d;
@@ -61581,79 +61630,87 @@ class Events {
61581
61630
  ic.contactMapCls.afErrorMap(afid, true);
61582
61631
  });
61583
61632
 
61584
- me.myEventCls.onIds("#" + me.pre + "afid", "keyup", function(e) { me.icn3d;
61633
+ me.myEventCls.onIds("#" + me.pre + "afid", "keyup", function(e) { let ic = me.icn3d;
61585
61634
  if (e.keyCode === 13) {
61586
61635
  e.preventDefault();
61587
61636
  if(!me.cfg.notebook) dialog.dialog( "close" );
61588
61637
  me.htmlCls.clickMenuCls.setLogCmd("load af " + $("#" + me.pre + "afid").val(), false);
61589
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?afid=' + $("#" + me.pre + "afid").val(), '_blank');
61590
- window.open(hostUrl + '?afid=' + $("#" + me.pre + "afid").val(), '_blank');
61638
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?afid=' + $("#" + me.pre + "afid").val(), urlTarget);
61639
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61640
+ window.open(hostUrl + '?afid=' + $("#" + me.pre + "afid").val(), urlTarget);
61591
61641
  }
61592
61642
  });
61593
61643
 
61594
61644
  // },
61595
61645
  // clickReload_opm: function() {
61596
- me.myEventCls.onIds("#" + me.pre + "reload_opm", "click", function(e) { me.icn3d;
61646
+ me.myEventCls.onIds("#" + me.pre + "reload_opm", "click", function(e) { let ic = me.icn3d;
61597
61647
  e.preventDefault();
61598
61648
  if(!me.cfg.notebook) dialog.dialog( "close" );
61599
61649
  me.htmlCls.clickMenuCls.setLogCmd("load opm " + $("#" + me.pre + "opmid").val(), false);
61600
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?opmid=' + $("#" + me.pre + "opmid").val(), '_blank');
61601
- window.open(hostUrl + '?opmid=' + $("#" + me.pre + "opmid").val(), '_blank');
61650
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?opmid=' + $("#" + me.pre + "opmid").val(), urlTarget);
61651
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61652
+ window.open(hostUrl + '?opmid=' + $("#" + me.pre + "opmid").val(), urlTarget);
61602
61653
  });
61603
61654
 
61604
- me.myEventCls.onIds("#" + me.pre + "opmid", "keyup", function(e) { me.icn3d;
61655
+ me.myEventCls.onIds("#" + me.pre + "opmid", "keyup", function(e) { let ic = me.icn3d;
61605
61656
  if (e.keyCode === 13) {
61606
61657
  e.preventDefault();
61607
61658
  if(!me.cfg.notebook) dialog.dialog( "close" );
61608
61659
  me.htmlCls.clickMenuCls.setLogCmd("load opm " + $("#" + me.pre + "opmid").val(), false);
61609
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?opmid=' + $("#" + me.pre + "opmid").val(), '_blank');
61610
- window.open(hostUrl + '?opmid=' + $("#" + me.pre + "opmid").val(), '_blank');
61660
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?opmid=' + $("#" + me.pre + "opmid").val(), urlTarget);
61661
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61662
+ window.open(hostUrl + '?opmid=' + $("#" + me.pre + "opmid").val(), urlTarget);
61611
61663
  }
61612
61664
  });
61613
61665
 
61614
61666
  // },
61615
61667
  // clickReload_align_refined: function() {
61616
- me.myEventCls.onIds("#" + me.pre + "reload_align_refined", "click", function(e) { me.icn3d;
61668
+ me.myEventCls.onIds("#" + me.pre + "reload_align_refined", "click", function(e) { let ic = me.icn3d;
61617
61669
  e.preventDefault();
61618
61670
  if(!me.cfg.notebook) dialog.dialog( "close" );
61619
61671
  let alignment = $("#" + me.pre + "alignid1").val() + "," + $("#" + me.pre + "alignid2").val();
61620
61672
  me.htmlCls.clickMenuCls.setLogCmd("load alignment " + alignment + ' | parameters &atype=1&bu=1', false);
61621
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?align=' + alignment + '&showalignseq=1&atype=1', '_blank');
61622
- window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=1&bu=1', '_blank');
61673
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?align=' + alignment + '&showalignseq=1&atype=1', urlTarget);
61674
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61675
+ window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=1&bu=1', urlTarget);
61623
61676
  });
61624
61677
  // },
61625
61678
  // clickReload_align_ori: function() {
61626
- me.myEventCls.onIds("#" + me.pre + "reload_align_ori", "click", function(e) { me.icn3d;
61679
+ me.myEventCls.onIds("#" + me.pre + "reload_align_ori", "click", function(e) { let ic = me.icn3d;
61627
61680
  e.preventDefault();
61628
61681
  if(!me.cfg.notebook) dialog.dialog( "close" );
61629
61682
  let alignment = $("#" + me.pre + "alignid1").val() + "," + $("#" + me.pre + "alignid2").val();
61630
61683
  me.htmlCls.clickMenuCls.setLogCmd("load alignment " + alignment + ' | parameters &atype=0&bu=1', false);
61631
- //window.open( me.htmlCls.baseUrl + 'icn3d/full.html?align=' + alignment + '&showalignseq=1&atype=0', '_blank');
61632
- window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=0&bu=1', '_blank');
61684
+ //window.open( me.htmlCls.baseUrl + 'icn3d/full.html?align=' + alignment + '&showalignseq=1&atype=0', urlTarget);
61685
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61686
+ window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=0&bu=1', urlTarget);
61633
61687
  });
61634
61688
 
61635
- me.myEventCls.onIds("#" + me.pre + "reload_align_tmalign", "click", function(e) { me.icn3d;
61689
+ me.myEventCls.onIds("#" + me.pre + "reload_align_tmalign", "click", function(e) { let ic = me.icn3d;
61636
61690
  e.preventDefault();
61637
61691
  if(!me.cfg.notebook) dialog.dialog( "close" );
61638
61692
  let alignment = $("#" + me.pre + "alignid1").val() + "," + $("#" + me.pre + "alignid2").val();
61639
61693
  me.htmlCls.clickMenuCls.setLogCmd("load alignment " + alignment + ' | parameters &atype=2&bu=1', false);
61640
- window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=2&bu=1', '_blank');
61694
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61695
+ window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=2&bu=1', urlTarget);
61641
61696
  });
61642
61697
 
61643
- me.myEventCls.onIds("#" + me.pre + "reload_alignaf", "click", function(e) { me.icn3d;
61698
+ me.myEventCls.onIds("#" + me.pre + "reload_alignaf", "click", function(e) { let ic = me.icn3d;
61644
61699
  e.preventDefault();
61645
61700
  if(!me.cfg.notebook) dialog.dialog( "close" );
61646
61701
  let alignment = $("#" + me.pre + "alignafid1").val() + "_A," + $("#" + me.pre + "alignafid2").val() + "_A";
61647
61702
  me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment + " | residues | resdef ", false);
61648
- window.open(hostUrl + '?chainalign=' + alignment + '&resnum=&resdef=&showalignseq=1', '_blank');
61703
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61704
+ window.open(hostUrl + '?chainalign=' + alignment + '&resnum=&resdef=&showalignseq=1', urlTarget);
61649
61705
  });
61650
61706
 
61651
- me.myEventCls.onIds("#" + me.pre + "reload_alignaf_tmalign", "click", function(e) { me.icn3d;
61707
+ me.myEventCls.onIds("#" + me.pre + "reload_alignaf_tmalign", "click", function(e) { let ic = me.icn3d;
61652
61708
  e.preventDefault();
61653
61709
  if(!me.cfg.notebook) dialog.dialog( "close" );
61654
61710
  let alignment = $("#" + me.pre + "alignafid1").val() + "_A," + $("#" + me.pre + "alignafid2").val() + "_A";
61655
61711
  me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment + " | residues | resdef | align tmalign", false);
61656
- window.open(hostUrl + '?chainalign=' + alignment + '&aligntool=tmalign&resnum=&resdef=&showalignseq=1', '_blank');
61712
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61713
+ window.open(hostUrl + '?chainalign=' + alignment + '&aligntool=tmalign&resnum=&resdef=&showalignseq=1', urlTarget);
61657
61714
  });
61658
61715
  // },
61659
61716
  // clickReload_chainalign: function() {
@@ -61672,11 +61729,11 @@ class Events {
61672
61729
  }
61673
61730
 
61674
61731
  me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " | residues " + resalign + " | resdef " + predefinedres, false);
61675
- window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=' + resalign + '&resdef=' + predefinedres + '&showalignseq=1', '_blank');
61732
+ window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=' + resalign + '&resdef=' + predefinedres + '&showalignseq=1', urlTarget);
61676
61733
  });
61677
61734
  */
61678
61735
 
61679
- me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym", "click", function(e) { me.icn3d;
61736
+ me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym", "click", function(e) { let ic = me.icn3d;
61680
61737
  e.preventDefault();
61681
61738
  if(!me.cfg.notebook) dialog.dialog( "close" );
61682
61739
 
@@ -61684,10 +61741,11 @@ class Events {
61684
61741
  let alignment_final = thisClass.convertUniProtInChains(alignment);
61685
61742
 
61686
61743
  me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues | resdef ", false);
61687
- window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=&resdef=&showalignseq=1&bu=0', '_blank');
61744
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61745
+ window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=&resdef=&showalignseq=1&bu=0', urlTarget);
61688
61746
  });
61689
61747
 
61690
- me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym2", "click", function(e) { me.icn3d;
61748
+ me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym2", "click", function(e) { let ic = me.icn3d;
61691
61749
  e.preventDefault();
61692
61750
  if(!me.cfg.notebook) dialog.dialog( "close" );
61693
61751
 
@@ -61696,10 +61754,11 @@ class Events {
61696
61754
  let resalign = $("#" + me.pre + "resalignids").val();
61697
61755
 
61698
61756
  me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues " + resalign + " | resdef ", false);
61699
- window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=' + resalign + '&resdef=&showalignseq=1&bu=0', '_blank');
61757
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61758
+ window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=' + resalign + '&resdef=&showalignseq=1&bu=0', urlTarget);
61700
61759
  });
61701
61760
 
61702
- me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym3", "click", function(e) { me.icn3d;
61761
+ me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym3", "click", function(e) { let ic = me.icn3d;
61703
61762
  e.preventDefault();
61704
61763
  if(!me.cfg.notebook) dialog.dialog( "close" );
61705
61764
 
@@ -61713,7 +61772,8 @@ class Events {
61713
61772
  }
61714
61773
 
61715
61774
  me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues | resdef " + predefinedres, false);
61716
- window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=&resdef=' + predefinedres + '&showalignseq=1&bu=0', '_blank');
61775
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61776
+ window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=&resdef=' + predefinedres + '&showalignseq=1&bu=0', urlTarget);
61717
61777
  });
61718
61778
 
61719
61779
  me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym4", "click", function(e) { let ic = me.icn3d;
@@ -61738,7 +61798,7 @@ class Events {
61738
61798
  me.htmlCls.clickMenuCls.setLogCmd("realign predefined " + alignment_final + " " + predefinedres, true);
61739
61799
  });
61740
61800
 
61741
- me.myEventCls.onIds("#" + me.pre + "reload_chainalign_tmalign", "click", function(e) { me.icn3d;
61801
+ me.myEventCls.onIds("#" + me.pre + "reload_chainalign_tmalign", "click", function(e) { let ic = me.icn3d;
61742
61802
  e.preventDefault();
61743
61803
  if(!me.cfg.notebook) dialog.dialog( "close" );
61744
61804
 
@@ -61746,7 +61806,8 @@ class Events {
61746
61806
  let alignment_final = thisClass.convertUniProtInChains(alignment);
61747
61807
 
61748
61808
  me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues | resdef | align tmalign", false);
61749
- window.open(hostUrl + '?chainalign=' + alignment_final + '&aligntool=tmalign&resnum=&resdef=&showalignseq=1&bu=0', '_blank');
61809
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61810
+ window.open(hostUrl + '?chainalign=' + alignment_final + '&aligntool=tmalign&resnum=&resdef=&showalignseq=1&bu=0', urlTarget);
61750
61811
  });
61751
61812
 
61752
61813
  me.myEventCls.onIds("#" + me.pre + "reload_mutation_3d", "click", function(e) { let ic = me.icn3d;
@@ -61778,7 +61839,8 @@ class Events {
61778
61839
  else {
61779
61840
  let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));
61780
61841
  me.htmlCls.clickMenuCls.setLogCmd("3d of mutation " + mutationids, false);
61781
- window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap 3d ' + mutationids + '; select displayed set', '_blank');
61842
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61843
+ window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap 3d ' + mutationids + '; select displayed set', urlTarget);
61782
61844
  }
61783
61845
  });
61784
61846
 
@@ -61811,7 +61873,8 @@ class Events {
61811
61873
  else {
61812
61874
  let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));
61813
61875
  me.htmlCls.clickMenuCls.setLogCmd("pdb of mutation " + mutationids, false);
61814
- window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap pdb ' + mutationids + '; select displayed set', '_blank');
61876
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61877
+ window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap pdb ' + mutationids + '; select displayed set', urlTarget);
61815
61878
  }
61816
61879
  });
61817
61880
 
@@ -61868,44 +61931,49 @@ class Events {
61868
61931
  ic.resid2specCls.residueids2spec(residArray);
61869
61932
 
61870
61933
  me.htmlCls.clickMenuCls.setLogCmd("interaction change of mutation " + mutationids, false);
61871
- window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap interaction ' + mutationids, '_blank');
61934
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61935
+ window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap interaction ' + mutationids, urlTarget);
61872
61936
  }
61873
61937
  });
61874
61938
 
61875
61939
  // },
61876
61940
  // clickReload_mmcif: function() {
61877
- me.myEventCls.onIds("#" + me.pre + "reload_mmcif", "click", function(e) { me.icn3d;
61941
+ me.myEventCls.onIds("#" + me.pre + "reload_mmcif", "click", function(e) { let ic = me.icn3d;
61878
61942
  e.preventDefault();
61879
61943
  if(!me.cfg.notebook) dialog.dialog( "close" );
61880
61944
  me.htmlCls.clickMenuCls.setLogCmd("load mmcif " + $("#" + me.pre + "mmcifid").val(), false);
61881
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmcifid=' + $("#" + me.pre + "mmcifid").val(), '_blank');
61882
- window.open(hostUrl + '?mmcifid=' + $("#" + me.pre + "mmcifid").val(), '_blank');
61945
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmcifid=' + $("#" + me.pre + "mmcifid").val(), urlTarget);
61946
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61947
+ window.open(hostUrl + '?mmcifid=' + $("#" + me.pre + "mmcifid").val(), urlTarget);
61883
61948
  });
61884
61949
 
61885
- me.myEventCls.onIds("#" + me.pre + "mmcifid", "keyup", function(e) { me.icn3d;
61950
+ me.myEventCls.onIds("#" + me.pre + "mmcifid", "keyup", function(e) { let ic = me.icn3d;
61886
61951
  if (e.keyCode === 13) {
61887
61952
  e.preventDefault();
61888
61953
  if(!me.cfg.notebook) dialog.dialog( "close" );
61889
61954
  me.htmlCls.clickMenuCls.setLogCmd("load mmcif " + $("#" + me.pre + "mmcifid").val(), false);
61890
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmcifid=' + $("#" + me.pre + "mmcifid").val(), '_blank');
61891
- window.open(hostUrl + '?mmcifid=' + $("#" + me.pre + "mmcifid").val(), '_blank');
61955
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmcifid=' + $("#" + me.pre + "mmcifid").val(), urlTarget);
61956
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61957
+ window.open(hostUrl + '?mmcifid=' + $("#" + me.pre + "mmcifid").val(), urlTarget);
61892
61958
  }
61893
61959
  });
61894
61960
 
61895
61961
  // },
61896
61962
  // clickReload_mmdb: function() {
61897
- me.myEventCls.onIds("#" + me.pre + "reload_mmdb", "click", function(e) { me.icn3d;
61963
+ me.myEventCls.onIds("#" + me.pre + "reload_mmdb", "click", function(e) { let ic = me.icn3d;
61898
61964
  e.preventDefault();
61899
61965
  //if(!me.cfg.notebook) dialog.dialog( "close" );
61900
61966
  me.htmlCls.clickMenuCls.setLogCmd("load mmdb1 " + $("#" + me.pre + "mmdbid").val(), false);
61901
- window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&bu=1', '_blank');
61967
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61968
+ window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&bu=1', urlTarget);
61902
61969
  });
61903
61970
 
61904
- me.myEventCls.onIds("#" + me.pre + "reload_mmdb_asym", "click", function(e) { me.icn3d;
61971
+ me.myEventCls.onIds("#" + me.pre + "reload_mmdb_asym", "click", function(e) { let ic = me.icn3d;
61905
61972
  e.preventDefault();
61906
61973
  //if(!me.cfg.notebook) dialog.dialog( "close" );
61907
61974
  me.htmlCls.clickMenuCls.setLogCmd("load mmdb0 " + $("#" + me.pre + "mmdbid").val(), false);
61908
- window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&bu=0', '_blank');
61975
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61976
+ window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&bu=0', urlTarget);
61909
61977
  });
61910
61978
 
61911
61979
  me.myEventCls.onIds("#" + me.pre + "reload_mmdbaf", "click", function(e) { me.icn3d;
@@ -61927,12 +61995,13 @@ class Events {
61927
61995
  thisClass.launchMmdb(ids, 0, hostUrl);
61928
61996
  });
61929
61997
 
61930
- me.myEventCls.onIds("#" + me.pre + "mmdbid", "keyup", function(e) { me.icn3d;
61998
+ me.myEventCls.onIds("#" + me.pre + "mmdbid", "keyup", function(e) { let ic = me.icn3d;
61931
61999
  if (e.keyCode === 13) {
61932
62000
  e.preventDefault();
61933
62001
  //if(!me.cfg.notebook) dialog.dialog( "close" );
61934
62002
  me.htmlCls.clickMenuCls.setLogCmd("load mmdb1 " + $("#" + me.pre + "mmdbid").val(), false);
61935
- window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&bu=1', '_blank');
62003
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62004
+ window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&bu=1', urlTarget);
61936
62005
  }
61937
62006
  });
61938
62007
 
@@ -61947,7 +62016,7 @@ class Events {
61947
62016
 
61948
62017
  // },
61949
62018
  // clickReload_blast_rep_id: function() {
61950
- me.myEventCls.onIds("#" + me.pre + "reload_blast_rep_id", "click", function(e) { me.icn3d;
62019
+ me.myEventCls.onIds("#" + me.pre + "reload_blast_rep_id", "click", function(e) { let ic = me.icn3d;
61951
62020
  e.preventDefault();
61952
62021
  if(!me.cfg.notebook) dialog.dialog( "close" );
61953
62022
  let query_id = $("#" + me.pre + "query_id").val();
@@ -61956,13 +62025,14 @@ class Events {
61956
62025
  me.htmlCls.clickMenuCls.setLogCmd("load seq_struct_ids " + query_id + "," + blast_rep_id, false);
61957
62026
  query_id =(query_id !== '' && query_id !== undefined) ? query_id : query_fasta;
61958
62027
  //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?from=icn3d&blast_rep_id=' + blast_rep_id
62028
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61959
62029
  window.open(hostUrl + '?from=icn3d&alg=blast&blast_rep_id=' + blast_rep_id
61960
62030
  + '&query_id=' + query_id
61961
62031
  + '&command=view annotations; set annotation cdd; set annotation site; set view detailed view; select chain '
61962
- + blast_rep_id + '; show selection', '_blank');
62032
+ + blast_rep_id + '; show selection', urlTarget);
61963
62033
  });
61964
62034
 
61965
- me.myEventCls.onIds("#" + me.pre + "reload_alignsw", "click", function(e) { me.icn3d;
62035
+ me.myEventCls.onIds("#" + me.pre + "reload_alignsw", "click", function(e) { let ic = me.icn3d;
61966
62036
  e.preventDefault();
61967
62037
  if(!me.cfg.notebook) dialog.dialog( "close" );
61968
62038
  let query_id = $("#" + me.pre + "query_id").val();
@@ -61971,13 +62041,14 @@ class Events {
61971
62041
  me.htmlCls.clickMenuCls.setLogCmd("load seq_struct_ids_smithwm " + query_id + "," + blast_rep_id, false);
61972
62042
  query_id =(query_id !== '' && query_id !== undefined) ? query_id : query_fasta;
61973
62043
 
62044
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61974
62045
  window.open(hostUrl + '?from=icn3d&alg=smithwm&blast_rep_id=' + blast_rep_id
61975
62046
  + '&query_id=' + query_id
61976
62047
  + '&command=view annotations; set annotation cdd; set annotation site; set view detailed view; select chain '
61977
- + blast_rep_id + '; show selection', '_blank');
62048
+ + blast_rep_id + '; show selection', urlTarget);
61978
62049
  });
61979
62050
 
61980
- me.myEventCls.onIds("#" + me.pre + "reload_alignswlocal", "click", function(e) { me.icn3d;
62051
+ me.myEventCls.onIds("#" + me.pre + "reload_alignswlocal", "click", function(e) { let ic = me.icn3d;
61981
62052
  e.preventDefault();
61982
62053
  if(!me.cfg.notebook) dialog.dialog( "close" );
61983
62054
  let query_id = $("#" + me.pre + "query_id").val();
@@ -61986,75 +62057,84 @@ class Events {
61986
62057
  me.htmlCls.clickMenuCls.setLogCmd("load seq_struct_ids_local_smithwm " + query_id + "," + blast_rep_id, false);
61987
62058
  query_id =(query_id !== '' && query_id !== undefined) ? query_id : query_fasta;
61988
62059
 
62060
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
61989
62061
  window.open(hostUrl + '?from=icn3d&alg=local_smithwm&blast_rep_id=' + blast_rep_id
61990
62062
  + '&query_id=' + query_id
61991
62063
  + '&command=view annotations; set annotation cdd; set annotation site; set view detailed view; select chain '
61992
- + blast_rep_id + '; show selection', '_blank');
62064
+ + blast_rep_id + '; show selection', urlTarget);
61993
62065
  });
61994
62066
 
61995
62067
  // },
61996
62068
  // clickReload_gi: function() {
61997
- me.myEventCls.onIds("#" + me.pre + "reload_gi", "click", function(e) { me.icn3d;
62069
+ me.myEventCls.onIds("#" + me.pre + "reload_gi", "click", function(e) { let ic = me.icn3d;
61998
62070
  e.preventDefault();
61999
62071
  if(!me.cfg.notebook) dialog.dialog( "close" );
62000
62072
  me.htmlCls.clickMenuCls.setLogCmd("load gi " + $("#" + me.pre + "gi").val(), false);
62001
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?gi=' + $("#" + me.pre + "gi").val(), '_blank');
62002
- window.open(hostUrl + '?gi=' + $("#" + me.pre + "gi").val(), '_blank');
62073
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?gi=' + $("#" + me.pre + "gi").val(), urlTarget);
62074
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62075
+ window.open(hostUrl + '?gi=' + $("#" + me.pre + "gi").val(), urlTarget);
62003
62076
  });
62004
62077
 
62005
- me.myEventCls.onIds("#" + me.pre + "reload_refseq", "click", function(e) { me.icn3d;
62078
+ me.myEventCls.onIds("#" + me.pre + "reload_refseq", "click", function(e) { let ic = me.icn3d;
62006
62079
  e.preventDefault();
62007
62080
  if(!me.cfg.notebook) dialog.dialog( "close" );
62008
- me.htmlCls.clickMenuCls.setLogCmd("load refseq " + $("#" + me.pre + "refseq").val(), false);
62009
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?gi=' + $("#" + me.pre + "gi").val(), '_blank');
62010
- window.open(hostUrl + '?refseq=' + $("#" + me.pre + "refseq").val(), '_blank');
62081
+ me.htmlCls.clickMenuCls.setLogCmd("load refseq " + $("#" + me.pre + "refseqid").val(), false);
62082
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?gi=' + $("#" + me.pre + "gi").val(), urlTarget);
62083
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62084
+ window.open(hostUrl + '?refseqid=' + $("#" + me.pre + "refseqid").val(), urlTarget);
62011
62085
  });
62012
62086
 
62013
- me.myEventCls.onIds("#" + me.pre + "gi", "keyup", function(e) { me.icn3d;
62087
+ me.myEventCls.onIds("#" + me.pre + "gi", "keyup", function(e) { let ic = me.icn3d;
62014
62088
  if (e.keyCode === 13) {
62015
62089
  e.preventDefault();
62016
62090
  if(!me.cfg.notebook) dialog.dialog( "close" );
62017
62091
  me.htmlCls.clickMenuCls.setLogCmd("load gi " + $("#" + me.pre + "gi").val(), false);
62018
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?gi=' + $("#" + me.pre + "gi").val(), '_blank');
62019
- window.open(hostUrl + '?gi=' + $("#" + me.pre + "gi").val(), '_blank');
62092
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?gi=' + $("#" + me.pre + "gi").val(), urlTarget);
62093
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62094
+ window.open(hostUrl + '?gi=' + $("#" + me.pre + "gi").val(), urlTarget);
62020
62095
  }
62021
62096
  });
62022
62097
 
62023
- me.myEventCls.onIds("#" + me.pre + "reload_uniprotid", "click", function(e) { me.icn3d;
62098
+ me.myEventCls.onIds("#" + me.pre + "reload_uniprotid", "click", function(e) { let ic = me.icn3d;
62024
62099
  e.preventDefault();
62025
62100
  if(!me.cfg.notebook) dialog.dialog( "close" );
62026
62101
  me.htmlCls.clickMenuCls.setLogCmd("load uniprotid " + $("#" + me.pre + "uniprotid").val(), false);
62027
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?uniprotid=' + $("#" + me.pre + "uniprotid").val(), '_blank');
62028
- window.open(hostUrl + '?uniprotid=' + $("#" + me.pre + "uniprotid").val(), '_blank');
62102
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?uniprotid=' + $("#" + me.pre + "uniprotid").val(), urlTarget);
62103
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62104
+ window.open(hostUrl + '?uniprotid=' + $("#" + me.pre + "uniprotid").val(), urlTarget);
62029
62105
  });
62030
62106
 
62031
- me.myEventCls.onIds("#" + me.pre + "uniprotid", "keyup", function(e) { me.icn3d;
62107
+ me.myEventCls.onIds("#" + me.pre + "uniprotid", "keyup", function(e) { let ic = me.icn3d;
62032
62108
  if (e.keyCode === 13) {
62033
62109
  e.preventDefault();
62034
62110
  if(!me.cfg.notebook) dialog.dialog( "close" );
62035
62111
  me.htmlCls.clickMenuCls.setLogCmd("load uniprotid " + $("#" + me.pre + "uniprotid").val(), false);
62036
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?uniprotid=' + $("#" + me.pre + "uniprotid").val(), '_blank');
62037
- window.open(hostUrl + '?uniprotid=' + $("#" + me.pre + "uniprotid").val(), '_blank');
62112
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?uniprotid=' + $("#" + me.pre + "uniprotid").val(), urlTarget);
62113
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62114
+ window.open(hostUrl + '?uniprotid=' + $("#" + me.pre + "uniprotid").val(), urlTarget);
62038
62115
  }
62039
62116
  });
62040
62117
 
62041
62118
  // },
62042
62119
  // clickReload_cid: function() {
62043
- me.myEventCls.onIds("#" + me.pre + "reload_cid", "click", function(e) { me.icn3d;
62120
+ me.myEventCls.onIds("#" + me.pre
62121
+ + "reload_cid", "click", function(e) { let ic = me.icn3d;
62044
62122
  e.preventDefault();
62045
62123
  if(!me.cfg.notebook) dialog.dialog( "close" );
62046
62124
  me.htmlCls.clickMenuCls.setLogCmd("load cid " + $("#" + me.pre + "cid").val(), false);
62047
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?cid=' + $("#" + me.pre + "cid").val(), '_blank');
62048
- window.open(hostUrl + '?cid=' + $("#" + me.pre + "cid").val(), '_blank');
62125
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?cid=' + $("#" + me.pre + "cid").val(), urlTarget);
62126
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62127
+ window.open(hostUrl + '?cid=' + $("#" + me.pre + "cid").val(), urlTarget);
62049
62128
  });
62050
62129
 
62051
- me.myEventCls.onIds("#" + me.pre + "cid", "keyup", function(e) { me.icn3d;
62130
+ me.myEventCls.onIds("#" + me.pre + "cid", "keyup", function(e) { let ic = me.icn3d;
62052
62131
  if (e.keyCode === 13) {
62053
62132
  e.preventDefault();
62054
62133
  if(!me.cfg.notebook) dialog.dialog( "close" );
62055
62134
  me.htmlCls.clickMenuCls.setLogCmd("load cid " + $("#" + me.pre + "cid").val(), false);
62056
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?cid=' + $("#" + me.pre + "cid").val(), '_blank');
62057
- window.open(hostUrl + '?cid=' + $("#" + me.pre + "cid").val(), '_blank');
62135
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?cid=' + $("#" + me.pre + "cid").val(), urlTarget);
62136
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62137
+ window.open(hostUrl + '?cid=' + $("#" + me.pre + "cid").val(), urlTarget);
62058
62138
  }
62059
62139
  });
62060
62140
 
@@ -69830,7 +69910,7 @@ class iCn3DUI {
69830
69910
  //even when multiple iCn3D viewers are shown together.
69831
69911
  this.pre = this.cfg.divid + "_";
69832
69912
 
69833
- this.REVISION = '3.19.1';
69913
+ this.REVISION = '3.20.0';
69834
69914
 
69835
69915
  // In nodejs, iCn3D defines "window = {navigator: {}}"
69836
69916
  this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -70119,11 +70199,20 @@ iCn3DUI.prototype.show3DStructure = function(pdbStr) { let me = this;
70119
70199
  me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
70120
70200
  ic.mmdbParserCls.downloadGi(me.cfg.gi);
70121
70201
  }
70122
- else if(me.cfg.uniprotid !== undefined) {
70123
- ic.loadCmd = 'load uniprotid ' + me.cfg.uniprotid;
70124
- me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
70125
- ic.mmdbParserCls.downloadUniprotid(me.cfg.uniprotid);
70126
- }
70202
+ else if(me.cfg.refseqid !== undefined) {
70203
+ ic.inputid = me.cfg.refseqid;
70204
+
70205
+ ic.bNCBI = true;
70206
+ ic.loadCmd = 'load refseq ' + me.cfg.refseqid;
70207
+ me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
70208
+ ic.mmdbParserCls.downloadRefseq(me.cfg.refseqid);
70209
+ }
70210
+ // else if(me.cfg.proteinname !== undefined) {
70211
+ // ic.bNCBI = true;
70212
+ // ic.loadCmd = 'load proteinname ' + me.cfg.gi;
70213
+ // me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
70214
+ // ic.mmdbParserCls.downloadProteinname(me.cfg.proteinname);
70215
+ // }
70127
70216
  else if(me.cfg.blast_rep_id !== undefined) {
70128
70217
  ic.bNCBI = true;
70129
70218