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.module.js CHANGED
@@ -4298,7 +4298,8 @@ var saveAs = (function(view) {
4298
4298
  var reader = new FileReader();
4299
4299
  reader.onloadend = function() {
4300
4300
  var url = is_chrome_ios ? reader.result : reader.result.replace(/^data:[^;]*;/, 'data:attachment/file;');
4301
- var popup = view.open(url, '_blank');
4301
+ var urlTarget = '_blank';
4302
+ var popup = view.open(url, urlTarget);
4302
4303
  if(!popup) view.location.href = url;
4303
4304
  url=undefined; // release reference before dispatching
4304
4305
  filesaver.readyState = filesaver.DONE;
@@ -23858,13 +23859,18 @@ class PdbParser {
23858
23859
  //Ajax call was used to get the atom data from the "pdbid". This function was deferred so that
23859
23860
  //it can be chained together with other deferred functions for sequential execution. A wrapper
23860
23861
  //was added to support both http and https.
23861
- downloadPdb(pdbid, bAf) { let ic = this.icn3d; ic.icn3dui;
23862
+ downloadPdb(pdbid, bAf) { let ic = this.icn3d, me = ic.icn3dui;
23862
23863
  ic.deferredOpm = $.Deferred(function() {
23863
23864
  let url, dataType;
23864
23865
 
23865
23866
  if(bAf) {
23866
23867
  url = "https://alphafold.ebi.ac.uk/files/AF-" + pdbid + "-F1-model_" + ic.AFUniprotVersion + ".pdb";
23867
- ic.ParserUtilsCls.setYourNote(pdbid.toUpperCase() + '(AlphaFold) in iCn3D');
23868
+ if(me.cfg.refseqid) {
23869
+ ic.ParserUtilsCls.setYourNote(me.cfg.refseqid.toUpperCase() + '(RefSeq) in iCn3D');
23870
+ }
23871
+ else {
23872
+ ic.ParserUtilsCls.setYourNote(pdbid.toUpperCase() + '(AlphaFold) in iCn3D');
23873
+ }
23868
23874
  }
23869
23875
  else {
23870
23876
  url = "https://files.rcsb.org/view/" + pdbid + ".pdb";
@@ -25510,15 +25516,15 @@ class MmdbParser {
25510
25516
  }
25511
25517
  }
25512
25518
 
25513
- downloadUniprotid(uniprotid) { let ic = this.icn3d; ic.icn3dui;
25519
+ downloadRefseq(refseqid) { let ic = this.icn3d, me = ic.icn3dui;
25514
25520
  // get gis
25515
- let url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=protein&retmode=json&id=" + uniprotid;
25521
+ let url = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?refseq2uniprot=" + refseqid;
25516
25522
 
25517
25523
  ic.bCid = undefined;
25518
25524
 
25519
25525
  $.ajax({
25520
25526
  url: url,
25521
- dataType: 'json',
25527
+ dataType: 'jsonp',
25522
25528
  cache: true,
25523
25529
  tryCount : 0,
25524
25530
  retryLimit : 0, //1
@@ -25529,10 +25535,12 @@ class MmdbParser {
25529
25535
  //ic.ParserUtilsCls.hideLoading();
25530
25536
  },
25531
25537
  success: function(data) {
25532
- let giArray = data.result.uids;
25538
+ me.cfg.afid = data.uniprot;
25533
25539
 
25534
- let redirectUrl = "https://www.ncbi.nlm.nih.gov/structure?linkname=protein_structure&from_uid=" + giArray.join(',');
25535
- window.open(redirectUrl, '_self');
25540
+ let bAf = true;
25541
+ $.when(ic.pdbParserCls.downloadPdb(me.cfg.afid, bAf)).then(function() {
25542
+ ic.loadScriptCls.loadScript(me.cfg.command, undefined, true);
25543
+ });
25536
25544
  },
25537
25545
  error : function(xhr, textStatus, errorThrown ) {
25538
25546
  this.tryCount++;
@@ -29451,6 +29459,14 @@ class LoadScript {
29451
29459
  me.cfg.gi = id;
29452
29460
  ic.mmdbParserCls.downloadGi(id);
29453
29461
  }
29462
+ else if(command.indexOf('load refseq') !== -1) {
29463
+ me.cfg.refseqid = id;
29464
+ ic.mmdbParserCls.downloadRefseq(id);
29465
+ }
29466
+ // else if(command.indexOf('load proteinname') !== -1) {
29467
+ // me.cfg.proteinname = id;
29468
+ // ic.mmdbParserCls.downloadProteinname(id);
29469
+ // }
29454
29470
  else if(command.indexOf('load seq_struct_ids ') !== -1) {
29455
29471
  ic.bSmithwm = false;
29456
29472
  ic.bLocalSmithwm = false;
@@ -30150,7 +30166,7 @@ class ResizeCanvas {
30150
30166
  //let itemArray = ['dl_selectannotations', 'dl_alignment', 'dl_2ddgm', 'dl_definedsets', 'dl_graph',
30151
30167
  // 'dl_linegraph', 'dl_scatterplot', 'dl_contactmap', 'dl_allinteraction', 'dl_copyurl',
30152
30168
  // 'dl_symmetry', 'dl_symd', 'dl_rmsd', 'dl_legend', 'dl_disttable'];
30153
- 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'];
30169
+ 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'];
30154
30170
 
30155
30171
  for(let i in itemArray) {
30156
30172
  let item = itemArray[i];
@@ -35352,7 +35368,8 @@ class ApplyCommand {
35352
35368
  let paraArray = command.split(' | ');
35353
35369
  let url = paraArray[1];
35354
35370
 
35355
- window.open(url, '_blank');
35371
+ let urlTarget = '_blank';
35372
+ window.open(url, urlTarget);
35356
35373
  }
35357
35374
  else if(commandOri.indexOf('your note') == 0) {
35358
35375
  let paraArray = commandOri.split(' | ');
@@ -55482,13 +55499,14 @@ class SaveFile {
55482
55499
  }
55483
55500
  }
55484
55501
 
55485
- setStructureTitle(url, title, titlelinkColor) {var ic = this.icn3d; ic.icn3dui;
55502
+ setStructureTitle(url, title, titlelinkColor) {var ic = this.icn3d, me = ic.icn3dui;
55486
55503
  if(ic.molTitle.length > 40) title = ic.molTitle.substr(0, 40) + "...";
55487
55504
 
55488
55505
  //var asymmetricStr =(ic.bAssemblyUseAsu) ? "(Asymmetric Unit)" : "";
55489
55506
  let asymmetricStr = "";
55490
55507
 
55491
55508
  let idName = (isNaN(ic.inputid) && ic.inputid.length > 5) ? "AlphaFold ID" : "PDB ID";
55509
+ if(me.cfg.refseqid) idName = 'NCBI RefSeq ID';
55492
55510
 
55493
55511
  $("#" + ic.pre + "title").html(idName + " <a id='" + ic.pre + "titlelink' href='" + url + "' style='color:" + titlelinkColor + "' target='_blank'>" + ic.inputid.toUpperCase() + "</a>" + asymmetricStr + ": " + title);
55494
55512
  }
@@ -55499,6 +55517,9 @@ class SaveFile {
55499
55517
  if(me.cfg.cid !== undefined) {
55500
55518
  url = "https://www.ncbi.nlm.nih.gov/pccompound/?term=";
55501
55519
  }
55520
+ else if(me.cfg.refseqid !== undefined) {
55521
+ url = "https://www.ncbi.nlm.nih.gov/protein/";
55522
+ }
55502
55523
  else if(me.cfg.afid !== undefined) {
55503
55524
  url = "https://alphafold.ebi.ac.uk/search/text/";
55504
55525
  }
@@ -55544,12 +55565,14 @@ class SaveFile {
55544
55565
  if(structArray.length === 1) {
55545
55566
  url = "https://www.ncbi.nlm.nih.gov/" + db + "/?term=" + structArray[0];
55546
55567
  me.htmlCls.clickMenuCls.setLogCmd("Entrez " + db + " about PDB " + structArray[0] + ": " + url, false);
55547
- window.open(url, '_blank');
55568
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
55569
+ window.open(url, urlTarget);
55548
55570
  }
55549
55571
  else if(structArray.length === 2) {
55550
55572
  url = "https://www.ncbi.nlm.nih.gov/" + db + "/?term=" + structArray[0] + " OR " + structArray[1];
55551
55573
  me.htmlCls.clickMenuCls.setLogCmd("Entrez " + db + " about PDB " + structArray[0] + " OR " + structArray[1] + ": " + url, false);
55552
- window.open(url, '_blank');
55574
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
55575
+ window.open(url, urlTarget);
55553
55576
  }
55554
55577
  }
55555
55578
  }
@@ -55744,6 +55767,14 @@ class ClickMenu {
55744
55767
  me.htmlCls.dialogCls.openDlg('dl_afid', 'Please input AlphaFold UniProt ID');
55745
55768
  });
55746
55769
 
55770
+ me.myEventCls.onIds("#" + me.pre + "mn1_refseqid", "click", function(e) { me.icn3d; e.preventDefault();
55771
+ me.htmlCls.dialogCls.openDlg('dl_refseqid', 'Please input NCBI RefSeq ID');
55772
+ });
55773
+
55774
+ // me.myEventCls.onIds("#" + me.pre + "mn1_proteinname", "click", function(e) { let ic = me.icn3d; e.preventDefault();
55775
+ // me.htmlCls.dialogCls.openDlg('dl_proteinname', 'Please input protein name to search');
55776
+ // });
55777
+
55747
55778
  // },
55748
55779
  // clkMn1_opmid: function() {
55749
55780
  me.myEventCls.onIds("#" + me.pre + "mn1_opmid", "click", function(e) { me.icn3d; e.preventDefault();
@@ -55816,11 +55847,12 @@ class ClickMenu {
55816
55847
  me.myEventCls.onIds("#" + me.pre + "mn1_fixedversion", "click", function(e) { me.icn3d; e.preventDefault();
55817
55848
  me.htmlCls.dialogCls.openDlg('dl_fixedversion', 'Open Share Link URL in the archived version of iCn3D');
55818
55849
  });
55819
- me.myEventCls.onIds("#" + me.pre + "reload_fixedversion", "click", function(e) { me.icn3d; e.preventDefault();
55850
+ me.myEventCls.onIds("#" + me.pre + "reload_fixedversion", "click", function(e) { let ic = me.icn3d; e.preventDefault();
55820
55851
  let url = $("#" + me.pre + "sharelinkurl").val();
55821
55852
  thisClass.setLogCmd("open " + url, false);
55822
55853
  localStorage.setItem('fixedversion', '1');
55823
- window.open(url, '_blank');
55854
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
55855
+ window.open(url, urlTarget);
55824
55856
  });
55825
55857
  // },
55826
55858
  // clkMn1_mmciffile: function() {
@@ -55852,13 +55884,6 @@ class ClickMenu {
55852
55884
  me.htmlCls.dialogCls.openDlg('dl_gi', 'Please input protein gi');
55853
55885
  });
55854
55886
 
55855
- me.myEventCls.onIds("#" + me.pre + "mn1_refseq", "click", function(e) { me.icn3d; e.preventDefault();
55856
- me.htmlCls.dialogCls.openDlg('dl_grefseq', 'Please input protein RefSeq');
55857
- });
55858
-
55859
- me.myEventCls.onIds("#" + me.pre + "mn1_uniprotid", "click", function(e) { me.icn3d; e.preventDefault();
55860
- me.htmlCls.dialogCls.openDlg('dl_uniprotid', 'Please input UniProt ID');
55861
- });
55862
55887
  // },
55863
55888
  // clkMn1_cid: function() {
55864
55889
  me.myEventCls.onIds("#" + me.pre + "mn1_cid", "click", function(e) { me.icn3d; e.preventDefault();
@@ -56199,14 +56224,16 @@ class ClickMenu {
56199
56224
  // clkMn1_link_structure: function() {
56200
56225
  me.myEventCls.onIds("#" + me.pre + "mn1_link_structure", "click", function(e) { let ic = me.icn3d; e.preventDefault();
56201
56226
  let url = ic.saveFileCls.getLinkToStructureSummary(true);
56202
- window.open(url, '_blank');
56227
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
56228
+ window.open(url, urlTarget);
56203
56229
  });
56204
56230
  // },
56205
56231
  // clkMn1_link_bind: function() {
56206
56232
  me.myEventCls.onIds("#" + me.pre + "mn1_link_bind", "click", function(e) { let ic = me.icn3d; e.preventDefault();
56207
56233
  url = "https://www.ncbi.nlm.nih.gov/pccompound?LinkName=pccompound_structure&from_uid=" + ic.inputid;
56208
56234
  thisClass.setLogCmd("link to 3D protein structures bound to CID " + ic.inputid + ": " + url, false);
56209
- window.open(url, '_blank');
56235
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
56236
+ window.open(url, urlTarget);
56210
56237
  });
56211
56238
  // },
56212
56239
  // clkMn1_link_vast: function() {
@@ -56233,8 +56260,10 @@ class ClickMenu {
56233
56260
  thisClass.setLogCmd("link to structures similar to " + idArray[0] + ": " + url, false);
56234
56261
  }
56235
56262
  }
56236
- window.open(url, '_blank');
56237
56263
  }
56264
+
56265
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
56266
+ window.open(url, urlTarget);
56238
56267
  });
56239
56268
  // },
56240
56269
  // clkMn1_link_pubmed: function() {
@@ -56243,7 +56272,8 @@ class ClickMenu {
56243
56272
  let url;
56244
56273
  url = "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + ic.molTitle;
56245
56274
  thisClass.setLogCmd("link to literature about " + ic.molTitle + ": " + url, false);
56246
- window.open(url, '_blank');
56275
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
56276
+ window.open(url, urlTarget);
56247
56277
  }
56248
56278
  else if(ic.pmid) {
56249
56279
  let idArray = ic.pmid.toString().split('_');
@@ -56256,7 +56286,8 @@ class ClickMenu {
56256
56286
  url = "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + idArray[0] + " OR " + idArray[1];
56257
56287
  thisClass.setLogCmd("link to PubMed IDs " + idArray[0] + ", " + idArray[1] + ": " + url, false);
56258
56288
  }
56259
- window.open(url, '_blank');
56289
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
56290
+ window.open(url, urlTarget);
56260
56291
  }
56261
56292
  else if(isNaN(ic.inputid)) {
56262
56293
  let idArray = ic.inputid.toString().split('_');
@@ -56269,7 +56300,8 @@ class ClickMenu {
56269
56300
  url = "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + idArray[0] + " OR " + idArray[1];
56270
56301
  thisClass.setLogCmd("link to literature about PDB " + idArray[0] + " OR " + idArray[1] + ": " + url, false);
56271
56302
  }
56272
- window.open(url, '_blank');
56303
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
56304
+ window.open(url, urlTarget);
56273
56305
  }
56274
56306
  else {
56275
56307
  if(me.cfg.cid !== undefined) {
@@ -56296,7 +56328,8 @@ class ClickMenu {
56296
56328
  if(text.length > 0) text = text.substr(0, text.length - 4);
56297
56329
  let url = "https://www.ncbi.nlm.nih.gov/protein/?term=" + text;
56298
56330
  thisClass.setLogCmd("link to Entrez protein about PDB " + structArray + ": " + url, false);
56299
- window.open(url, '_blank');
56331
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
56332
+ window.open(url, urlTarget);
56300
56333
  });
56301
56334
  // },
56302
56335
  }
@@ -57597,7 +57630,8 @@ class ClickMenu {
57597
57630
  //else {
57598
57631
  url = url.replace("full.html", "full2.html");
57599
57632
  url += '&closepopup=1';
57600
- window.open(url, '_blank');
57633
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
57634
+ window.open(url, urlTarget);
57601
57635
  thisClass.setLogCmd('side by side | ' + url, true);
57602
57636
  //}
57603
57637
  });
@@ -57987,7 +58021,8 @@ class ClickMenu {
57987
58021
 
57988
58022
  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>";
57989
58023
 
57990
- let w = window.open('', '_blank');
58024
+ let urlTarget = '_blank';
58025
+ let w = window.open('', urlTarget);
57991
58026
  w.document.body.innerHTML = template;
57992
58027
 
57993
58028
  $.ajax({
@@ -58575,13 +58610,20 @@ class SetMenu {
58575
58610
  html += me.htmlCls.setHtmlCls.getLink('mn1_mmdbid', 'NCBI MMDB ID (annotation) ' + me.htmlCls.wifiStr, undefined, 2);
58576
58611
  html += me.htmlCls.setHtmlCls.getLink('mn1_mmtfid', 'RCSB MMTF ID (fast) ' + me.htmlCls.wifiStr, undefined, 2);
58577
58612
  html += me.htmlCls.setHtmlCls.getLink('mn1_pdbid', 'RCSB PDB ID ' + me.htmlCls.wifiStr, undefined, 2);
58578
- html += me.htmlCls.setHtmlCls.getLink('mn1_afid', 'AlphaFold UniProt ID ' + me.htmlCls.wifiStr, undefined, 2);
58613
+
58614
+ html += me.htmlCls.setHtmlCls.getMenuText('mn1_afwrap', 'AlphaFold Structures', undefined, undefined, 2);
58615
+ html += "<ul>";
58616
+
58617
+ html += me.htmlCls.setHtmlCls.getLink('mn1_afid', 'UniProt ID ' + me.htmlCls.wifiStr, undefined, 3);
58618
+ html += me.htmlCls.setHtmlCls.getLink('mn1_refseqid', 'NCBI RefSeq ID ' + me.htmlCls.wifiStr, undefined, 3);
58619
+ // html += me.htmlCls.setHtmlCls.getLink('mn1_proteinname', 'Protein Name ' + me.htmlCls.wifiStr, undefined, 3);
58620
+ html += "</ul>";
58621
+
58622
+
58579
58623
  html += me.htmlCls.setHtmlCls.getLink('mn1_opmid', 'OPM PDB ID ' + me.htmlCls.wifiStr, undefined, 2);
58580
58624
  html += me.htmlCls.setHtmlCls.getLink('mn1_mmcifid', 'RCSB mmCIF ID ' + me.htmlCls.wifiStr, undefined, 2);
58581
- html += me.htmlCls.setHtmlCls.getLink('mn1_gi', 'NCBI gi ' + me.htmlCls.wifiStr, undefined, 2);
58582
- //html += me.htmlCls.setHtmlCls.getLink('mn1_refseq', 'NCBI RefSeq ' + me.htmlCls.wifiStr, undefined, 2);
58625
+ //html += me.htmlCls.setHtmlCls.getLink('mn1_gi', 'NCBI gi ' + me.htmlCls.wifiStr, undefined, 2);
58583
58626
 
58584
- //html += me.htmlCls.setHtmlCls.getLink('mn1_uniprotid', 'UniProt ID ' + me.htmlCls.wifiStr);
58585
58627
  html += me.htmlCls.setHtmlCls.getLink('mn1_cid', 'PubChem CID ' + me.htmlCls.wifiStr, 1, 2);
58586
58628
 
58587
58629
  html += "</ul>";
@@ -60789,6 +60831,16 @@ class SetDialog {
60789
60831
  + me.htmlCls.buttonStr + "reload_afmapfull' style='margin-left:30px'>Load Full (slow)</button>";
60790
60832
  html += "</div>";
60791
60833
 
60834
+ html += me.htmlCls.divStr + "dl_refseqid' class='" + dialogClass + "'>";
60835
+ html += "NCBI RefSeq ID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "refseqid' value='0308234A' size=8> ";
60836
+ html += me.htmlCls.buttonStr + "reload_refseq'>Load</button>";
60837
+ html += "</div>";
60838
+
60839
+ // html += me.htmlCls.divStr + "dl_proteinname' class='" + dialogClass + "'>";
60840
+ // html += "PDB ID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "proteinname' value='kinase' size=8> ";
60841
+ // html += me.htmlCls.buttonStr + "reload_proteinname'>Load</button>";
60842
+ // html += "</div>";
60843
+
60792
60844
  html += me.htmlCls.divStr + "dl_opmid' class='" + dialogClass + "'>";
60793
60845
  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> ";
60794
60846
  html += me.htmlCls.buttonStr + "reload_opm'>Load</button>";
@@ -61007,17 +61059,6 @@ class SetDialog {
61007
61059
  html += me.htmlCls.buttonStr + "reload_gi'>Load</button>";
61008
61060
  html += "</div>";
61009
61061
 
61010
- html += me.htmlCls.divStr + "dl_refseq' class='" + dialogClass + "'>";
61011
- html += "Protein RefSeq: " + me.htmlCls.inputTextStr + "id='" + me.pre + "refseq' value='0308234A' size=8> ";
61012
- html += me.htmlCls.buttonStr + "reload_refseq'>Load</button>";
61013
- html += "</div>";
61014
-
61015
- html += me.htmlCls.divStr + "dl_uniprotid' class='" + dialogClass + "'>";
61016
- html += "Note: A list of structures will be shown. Click \"View in iCn3D\" to view each structure in 3D.<br><br>";
61017
- html += "UniProt ID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "uniprotid' value='P0DTC2' size=8> ";
61018
- html += me.htmlCls.buttonStr + "reload_uniprotid'>Load</button>";
61019
- html += "</div>";
61020
-
61021
61062
  html += me.htmlCls.divStr + "dl_cid' class='" + dialogClass + "'>";
61022
61063
  html += "PubChem CID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "cid' value='2244' size=8> ";
61023
61064
  html += me.htmlCls.buttonStr + "reload_cid'>Load</button>";
@@ -62021,7 +62062,7 @@ class Events {
62021
62062
  $("#" + me.pre + id).resizable();
62022
62063
  }
62023
62064
 
62024
- launchMmdb(ids, bBiounit, hostUrl) { let me = this.icn3dui; me.icn3d;
62065
+ launchMmdb(ids, bBiounit, hostUrl) { let me = this.icn3dui, ic = me.icn3d;
62025
62066
  let flag = bBiounit ? '1' : '0';
62026
62067
 
62027
62068
  ids = ids.replace(/,/g, ' ').replace(/\s+/g, ',').trim();
@@ -62034,11 +62075,13 @@ class Events {
62034
62075
  let idArray = ids.split(',');
62035
62076
  if(idArray.length == 1 && (idArray[0].length == 4 || !isNaN(idArray[0])) ) {
62036
62077
  me.htmlCls.clickMenuCls.setLogCmd("load mmdb" + flag + " " + ids, false);
62037
- window.open(hostUrl + '?mmdbid=' + ids + '&bu=' + flag, '_blank');
62078
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62079
+ window.open(hostUrl + '?mmdbid=' + ids + '&bu=' + flag, urlTarget);
62038
62080
  }
62039
62081
  else {
62040
62082
  me.htmlCls.clickMenuCls.setLogCmd("load mmdbaf" + flag + " " + ids, false);
62041
- window.open(hostUrl + '?mmdbafid=' + ids + '&bu=' + flag, '_blank');
62083
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62084
+ window.open(hostUrl + '?mmdbafid=' + ids + '&bu=' + flag, urlTarget);
62042
62085
  }
62043
62086
  }
62044
62087
 
@@ -62387,18 +62430,20 @@ class Events {
62387
62430
 
62388
62431
  // },
62389
62432
  // clickReload_mmtf: function() {
62390
- me.myEventCls.onIds("#" + me.pre + "reload_vastplus", "click", function(e) { me.icn3d;
62433
+ me.myEventCls.onIds("#" + me.pre + "reload_vastplus", "click", function(e) { let ic = me.icn3d;
62391
62434
  e.preventDefault();
62392
62435
  if(!me.cfg.notebook) dialog.dialog( "close" );
62393
62436
  me.htmlCls.clickMenuCls.setLogCmd("vast+ search " + $("#" + me.pre + "vastpluspdbid").val(), false);
62394
- window.open('https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi?uid=' + $("#" + me.pre + "vastpluspdbid").val(), '_blank');
62437
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62438
+ window.open('https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi?uid=' + $("#" + me.pre + "vastpluspdbid").val(), urlTarget);
62395
62439
  });
62396
62440
 
62397
- me.myEventCls.onIds("#" + me.pre + "reload_vast", "click", function(e) { me.icn3d;
62441
+ me.myEventCls.onIds("#" + me.pre + "reload_vast", "click", function(e) { let ic = me.icn3d;
62398
62442
  e.preventDefault();
62399
62443
  if(!me.cfg.notebook) dialog.dialog( "close" );
62400
62444
  me.htmlCls.clickMenuCls.setLogCmd("vast search " + $("#" + me.pre + "vastpdbid").val() + "_" + $("#" + me.pre + "vastchainid").val(), false);
62401
- window.open('https://www.ncbi.nlm.nih.gov/Structure/vast/vastsrv.cgi?pdbid=' + $("#" + me.pre + "vastpdbid").val() + '&chain=' + $("#" + me.pre + "vastchainid").val(), '_blank');
62445
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62446
+ window.open('https://www.ncbi.nlm.nih.gov/Structure/vast/vastsrv.cgi?pdbid=' + $("#" + me.pre + "vastpdbid").val() + '&chain=' + $("#" + me.pre + "vastchainid").val(), urlTarget);
62402
62447
  });
62403
62448
 
62404
62449
  me.myEventCls.onIds("#" + me.pre + "reload_foldseek", "click", function(e) { me.icn3d;
@@ -62416,50 +62461,55 @@ class Events {
62416
62461
  window.open(hostUrl + '?chainalign=' + alignment_final + '&aligntool=tmalign&showalignseq=1&bu=0', '_self');
62417
62462
  });
62418
62463
 
62419
- me.myEventCls.onIds("#" + me.pre + "reload_mmtf", "click", function(e) { me.icn3d;
62464
+ me.myEventCls.onIds("#" + me.pre + "reload_mmtf", "click", function(e) { let ic = me.icn3d;
62420
62465
  e.preventDefault();
62421
62466
  if(!me.cfg.notebook) dialog.dialog( "close" );
62422
62467
  me.htmlCls.clickMenuCls.setLogCmd("load mmtf " + $("#" + me.pre + "mmtfid").val(), false);
62423
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmtfid=' + $("#" + me.pre + "mmtfid").val(), '_blank');
62424
- window.open(hostUrl + '?mmtfid=' + $("#" + me.pre + "mmtfid").val(), '_blank');
62468
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmtfid=' + $("#" + me.pre + "mmtfid").val(), urlTarget);
62469
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62470
+ window.open(hostUrl + '?mmtfid=' + $("#" + me.pre + "mmtfid").val(), urlTarget);
62425
62471
  });
62426
62472
 
62427
- me.myEventCls.onIds("#" + me.pre + "mmtfid", "keyup", function(e) { me.icn3d;
62473
+ me.myEventCls.onIds("#" + me.pre + "mmtfid", "keyup", function(e) { let ic = me.icn3d;
62428
62474
  if (e.keyCode === 13) {
62429
62475
  e.preventDefault();
62430
62476
  if(!me.cfg.notebook) dialog.dialog( "close" );
62431
62477
  me.htmlCls.clickMenuCls.setLogCmd("load mmtf " + $("#" + me.pre + "mmtfid").val(), false);
62432
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmtfid=' + $("#" + me.pre + "mmtfid").val(), '_blank');
62433
- window.open(hostUrl + '?mmtfid=' + $("#" + me.pre + "mmtfid").val(), '_blank');
62478
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmtfid=' + $("#" + me.pre + "mmtfid").val(), urlTarget);
62479
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62480
+ window.open(hostUrl + '?mmtfid=' + $("#" + me.pre + "mmtfid").val(), urlTarget);
62434
62481
  }
62435
62482
  });
62436
62483
 
62437
62484
  // },
62438
62485
  // clickReload_pdb: function() {
62439
- me.myEventCls.onIds("#" + me.pre + "reload_pdb", "click", function(e) { me.icn3d;
62486
+ me.myEventCls.onIds("#" + me.pre + "reload_pdb", "click", function(e) { let ic = me.icn3d;
62440
62487
  e.preventDefault();
62441
62488
  if(!me.cfg.notebook) dialog.dialog( "close" );
62442
62489
  me.htmlCls.clickMenuCls.setLogCmd("load pdb " + $("#" + me.pre + "pdbid").val(), false);
62443
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?pdbid=' + $("#" + me.pre + "pdbid").val(), '_blank');
62444
- window.open(hostUrl + '?pdbid=' + $("#" + me.pre + "pdbid").val(), '_blank');
62490
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?pdbid=' + $("#" + me.pre + "pdbid").val(), urlTarget);
62491
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62492
+ window.open(hostUrl + '?pdbid=' + $("#" + me.pre + "pdbid").val(), urlTarget);
62445
62493
  });
62446
62494
 
62447
- me.myEventCls.onIds("#" + me.pre + "pdbid", "keyup", function(e) { me.icn3d;
62495
+ me.myEventCls.onIds("#" + me.pre + "pdbid", "keyup", function(e) { let ic = me.icn3d;
62448
62496
  if (e.keyCode === 13) {
62449
62497
  e.preventDefault();
62450
62498
  if(!me.cfg.notebook) dialog.dialog( "close" );
62451
62499
  me.htmlCls.clickMenuCls.setLogCmd("load pdb " + $("#" + me.pre + "pdbid").val(), false);
62452
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?pdbid=' + $("#" + me.pre + "pdbid").val(), '_blank');
62453
- window.open(hostUrl + '?pdbid=' + $("#" + me.pre + "pdbid").val(), '_blank');
62500
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?pdbid=' + $("#" + me.pre + "pdbid").val(), urlTarget);
62501
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62502
+ window.open(hostUrl + '?pdbid=' + $("#" + me.pre + "pdbid").val(), urlTarget);
62454
62503
  }
62455
62504
  });
62456
62505
 
62457
- me.myEventCls.onIds("#" + me.pre + "reload_af", "click", function(e) { me.icn3d;
62506
+ me.myEventCls.onIds("#" + me.pre + "reload_af", "click", function(e) { let ic = me.icn3d;
62458
62507
  e.preventDefault();
62459
62508
  if(!me.cfg.notebook) dialog.dialog( "close" );
62460
62509
  me.htmlCls.clickMenuCls.setLogCmd("load af " + $("#" + me.pre + "afid").val(), false);
62461
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?afid=' + $("#" + me.pre + "afid").val(), '_blank');
62462
- window.open(hostUrl + '?afid=' + $("#" + me.pre + "afid").val(), '_blank');
62510
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?afid=' + $("#" + me.pre + "afid").val(), urlTarget);
62511
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62512
+ window.open(hostUrl + '?afid=' + $("#" + me.pre + "afid").val(), urlTarget);
62463
62513
  });
62464
62514
 
62465
62515
  me.myEventCls.onIds("#" + me.pre + "reload_afmap", "click", function(e) { let ic = me.icn3d;
@@ -62481,79 +62531,87 @@ class Events {
62481
62531
  ic.contactMapCls.afErrorMap(afid, true);
62482
62532
  });
62483
62533
 
62484
- me.myEventCls.onIds("#" + me.pre + "afid", "keyup", function(e) { me.icn3d;
62534
+ me.myEventCls.onIds("#" + me.pre + "afid", "keyup", function(e) { let ic = me.icn3d;
62485
62535
  if (e.keyCode === 13) {
62486
62536
  e.preventDefault();
62487
62537
  if(!me.cfg.notebook) dialog.dialog( "close" );
62488
62538
  me.htmlCls.clickMenuCls.setLogCmd("load af " + $("#" + me.pre + "afid").val(), false);
62489
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?afid=' + $("#" + me.pre + "afid").val(), '_blank');
62490
- window.open(hostUrl + '?afid=' + $("#" + me.pre + "afid").val(), '_blank');
62539
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?afid=' + $("#" + me.pre + "afid").val(), urlTarget);
62540
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62541
+ window.open(hostUrl + '?afid=' + $("#" + me.pre + "afid").val(), urlTarget);
62491
62542
  }
62492
62543
  });
62493
62544
 
62494
62545
  // },
62495
62546
  // clickReload_opm: function() {
62496
- me.myEventCls.onIds("#" + me.pre + "reload_opm", "click", function(e) { me.icn3d;
62547
+ me.myEventCls.onIds("#" + me.pre + "reload_opm", "click", function(e) { let ic = me.icn3d;
62497
62548
  e.preventDefault();
62498
62549
  if(!me.cfg.notebook) dialog.dialog( "close" );
62499
62550
  me.htmlCls.clickMenuCls.setLogCmd("load opm " + $("#" + me.pre + "opmid").val(), false);
62500
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?opmid=' + $("#" + me.pre + "opmid").val(), '_blank');
62501
- window.open(hostUrl + '?opmid=' + $("#" + me.pre + "opmid").val(), '_blank');
62551
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?opmid=' + $("#" + me.pre + "opmid").val(), urlTarget);
62552
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62553
+ window.open(hostUrl + '?opmid=' + $("#" + me.pre + "opmid").val(), urlTarget);
62502
62554
  });
62503
62555
 
62504
- me.myEventCls.onIds("#" + me.pre + "opmid", "keyup", function(e) { me.icn3d;
62556
+ me.myEventCls.onIds("#" + me.pre + "opmid", "keyup", function(e) { let ic = me.icn3d;
62505
62557
  if (e.keyCode === 13) {
62506
62558
  e.preventDefault();
62507
62559
  if(!me.cfg.notebook) dialog.dialog( "close" );
62508
62560
  me.htmlCls.clickMenuCls.setLogCmd("load opm " + $("#" + me.pre + "opmid").val(), false);
62509
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?opmid=' + $("#" + me.pre + "opmid").val(), '_blank');
62510
- window.open(hostUrl + '?opmid=' + $("#" + me.pre + "opmid").val(), '_blank');
62561
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?opmid=' + $("#" + me.pre + "opmid").val(), urlTarget);
62562
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62563
+ window.open(hostUrl + '?opmid=' + $("#" + me.pre + "opmid").val(), urlTarget);
62511
62564
  }
62512
62565
  });
62513
62566
 
62514
62567
  // },
62515
62568
  // clickReload_align_refined: function() {
62516
- me.myEventCls.onIds("#" + me.pre + "reload_align_refined", "click", function(e) { me.icn3d;
62569
+ me.myEventCls.onIds("#" + me.pre + "reload_align_refined", "click", function(e) { let ic = me.icn3d;
62517
62570
  e.preventDefault();
62518
62571
  if(!me.cfg.notebook) dialog.dialog( "close" );
62519
62572
  let alignment = $("#" + me.pre + "alignid1").val() + "," + $("#" + me.pre + "alignid2").val();
62520
62573
  me.htmlCls.clickMenuCls.setLogCmd("load alignment " + alignment + ' | parameters &atype=1&bu=1', false);
62521
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?align=' + alignment + '&showalignseq=1&atype=1', '_blank');
62522
- window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=1&bu=1', '_blank');
62574
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?align=' + alignment + '&showalignseq=1&atype=1', urlTarget);
62575
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62576
+ window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=1&bu=1', urlTarget);
62523
62577
  });
62524
62578
  // },
62525
62579
  // clickReload_align_ori: function() {
62526
- me.myEventCls.onIds("#" + me.pre + "reload_align_ori", "click", function(e) { me.icn3d;
62580
+ me.myEventCls.onIds("#" + me.pre + "reload_align_ori", "click", function(e) { let ic = me.icn3d;
62527
62581
  e.preventDefault();
62528
62582
  if(!me.cfg.notebook) dialog.dialog( "close" );
62529
62583
  let alignment = $("#" + me.pre + "alignid1").val() + "," + $("#" + me.pre + "alignid2").val();
62530
62584
  me.htmlCls.clickMenuCls.setLogCmd("load alignment " + alignment + ' | parameters &atype=0&bu=1', false);
62531
- //window.open( me.htmlCls.baseUrl + 'icn3d/full.html?align=' + alignment + '&showalignseq=1&atype=0', '_blank');
62532
- window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=0&bu=1', '_blank');
62585
+ //window.open( me.htmlCls.baseUrl + 'icn3d/full.html?align=' + alignment + '&showalignseq=1&atype=0', urlTarget);
62586
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62587
+ window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=0&bu=1', urlTarget);
62533
62588
  });
62534
62589
 
62535
- me.myEventCls.onIds("#" + me.pre + "reload_align_tmalign", "click", function(e) { me.icn3d;
62590
+ me.myEventCls.onIds("#" + me.pre + "reload_align_tmalign", "click", function(e) { let ic = me.icn3d;
62536
62591
  e.preventDefault();
62537
62592
  if(!me.cfg.notebook) dialog.dialog( "close" );
62538
62593
  let alignment = $("#" + me.pre + "alignid1").val() + "," + $("#" + me.pre + "alignid2").val();
62539
62594
  me.htmlCls.clickMenuCls.setLogCmd("load alignment " + alignment + ' | parameters &atype=2&bu=1', false);
62540
- window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=2&bu=1', '_blank');
62595
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62596
+ window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=2&bu=1', urlTarget);
62541
62597
  });
62542
62598
 
62543
- me.myEventCls.onIds("#" + me.pre + "reload_alignaf", "click", function(e) { me.icn3d;
62599
+ me.myEventCls.onIds("#" + me.pre + "reload_alignaf", "click", function(e) { let ic = me.icn3d;
62544
62600
  e.preventDefault();
62545
62601
  if(!me.cfg.notebook) dialog.dialog( "close" );
62546
62602
  let alignment = $("#" + me.pre + "alignafid1").val() + "_A," + $("#" + me.pre + "alignafid2").val() + "_A";
62547
62603
  me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment + " | residues | resdef ", false);
62548
- window.open(hostUrl + '?chainalign=' + alignment + '&resnum=&resdef=&showalignseq=1', '_blank');
62604
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62605
+ window.open(hostUrl + '?chainalign=' + alignment + '&resnum=&resdef=&showalignseq=1', urlTarget);
62549
62606
  });
62550
62607
 
62551
- me.myEventCls.onIds("#" + me.pre + "reload_alignaf_tmalign", "click", function(e) { me.icn3d;
62608
+ me.myEventCls.onIds("#" + me.pre + "reload_alignaf_tmalign", "click", function(e) { let ic = me.icn3d;
62552
62609
  e.preventDefault();
62553
62610
  if(!me.cfg.notebook) dialog.dialog( "close" );
62554
62611
  let alignment = $("#" + me.pre + "alignafid1").val() + "_A," + $("#" + me.pre + "alignafid2").val() + "_A";
62555
62612
  me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment + " | residues | resdef | align tmalign", false);
62556
- window.open(hostUrl + '?chainalign=' + alignment + '&aligntool=tmalign&resnum=&resdef=&showalignseq=1', '_blank');
62613
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62614
+ window.open(hostUrl + '?chainalign=' + alignment + '&aligntool=tmalign&resnum=&resdef=&showalignseq=1', urlTarget);
62557
62615
  });
62558
62616
  // },
62559
62617
  // clickReload_chainalign: function() {
@@ -62572,11 +62630,11 @@ class Events {
62572
62630
  }
62573
62631
 
62574
62632
  me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " | residues " + resalign + " | resdef " + predefinedres, false);
62575
- window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=' + resalign + '&resdef=' + predefinedres + '&showalignseq=1', '_blank');
62633
+ window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=' + resalign + '&resdef=' + predefinedres + '&showalignseq=1', urlTarget);
62576
62634
  });
62577
62635
  */
62578
62636
 
62579
- me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym", "click", function(e) { me.icn3d;
62637
+ me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym", "click", function(e) { let ic = me.icn3d;
62580
62638
  e.preventDefault();
62581
62639
  if(!me.cfg.notebook) dialog.dialog( "close" );
62582
62640
 
@@ -62584,10 +62642,11 @@ class Events {
62584
62642
  let alignment_final = thisClass.convertUniProtInChains(alignment);
62585
62643
 
62586
62644
  me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues | resdef ", false);
62587
- window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=&resdef=&showalignseq=1&bu=0', '_blank');
62645
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62646
+ window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=&resdef=&showalignseq=1&bu=0', urlTarget);
62588
62647
  });
62589
62648
 
62590
- me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym2", "click", function(e) { me.icn3d;
62649
+ me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym2", "click", function(e) { let ic = me.icn3d;
62591
62650
  e.preventDefault();
62592
62651
  if(!me.cfg.notebook) dialog.dialog( "close" );
62593
62652
 
@@ -62596,10 +62655,11 @@ class Events {
62596
62655
  let resalign = $("#" + me.pre + "resalignids").val();
62597
62656
 
62598
62657
  me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues " + resalign + " | resdef ", false);
62599
- window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=' + resalign + '&resdef=&showalignseq=1&bu=0', '_blank');
62658
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62659
+ window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=' + resalign + '&resdef=&showalignseq=1&bu=0', urlTarget);
62600
62660
  });
62601
62661
 
62602
- me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym3", "click", function(e) { me.icn3d;
62662
+ me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym3", "click", function(e) { let ic = me.icn3d;
62603
62663
  e.preventDefault();
62604
62664
  if(!me.cfg.notebook) dialog.dialog( "close" );
62605
62665
 
@@ -62613,7 +62673,8 @@ class Events {
62613
62673
  }
62614
62674
 
62615
62675
  me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues | resdef " + predefinedres, false);
62616
- window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=&resdef=' + predefinedres + '&showalignseq=1&bu=0', '_blank');
62676
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62677
+ window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=&resdef=' + predefinedres + '&showalignseq=1&bu=0', urlTarget);
62617
62678
  });
62618
62679
 
62619
62680
  me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym4", "click", function(e) { let ic = me.icn3d;
@@ -62638,7 +62699,7 @@ class Events {
62638
62699
  me.htmlCls.clickMenuCls.setLogCmd("realign predefined " + alignment_final + " " + predefinedres, true);
62639
62700
  });
62640
62701
 
62641
- me.myEventCls.onIds("#" + me.pre + "reload_chainalign_tmalign", "click", function(e) { me.icn3d;
62702
+ me.myEventCls.onIds("#" + me.pre + "reload_chainalign_tmalign", "click", function(e) { let ic = me.icn3d;
62642
62703
  e.preventDefault();
62643
62704
  if(!me.cfg.notebook) dialog.dialog( "close" );
62644
62705
 
@@ -62646,7 +62707,8 @@ class Events {
62646
62707
  let alignment_final = thisClass.convertUniProtInChains(alignment);
62647
62708
 
62648
62709
  me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues | resdef | align tmalign", false);
62649
- window.open(hostUrl + '?chainalign=' + alignment_final + '&aligntool=tmalign&resnum=&resdef=&showalignseq=1&bu=0', '_blank');
62710
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62711
+ window.open(hostUrl + '?chainalign=' + alignment_final + '&aligntool=tmalign&resnum=&resdef=&showalignseq=1&bu=0', urlTarget);
62650
62712
  });
62651
62713
 
62652
62714
  me.myEventCls.onIds("#" + me.pre + "reload_mutation_3d", "click", function(e) { let ic = me.icn3d;
@@ -62678,7 +62740,8 @@ class Events {
62678
62740
  else {
62679
62741
  let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));
62680
62742
  me.htmlCls.clickMenuCls.setLogCmd("3d of mutation " + mutationids, false);
62681
- window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap 3d ' + mutationids + '; select displayed set', '_blank');
62743
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62744
+ window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap 3d ' + mutationids + '; select displayed set', urlTarget);
62682
62745
  }
62683
62746
  });
62684
62747
 
@@ -62711,7 +62774,8 @@ class Events {
62711
62774
  else {
62712
62775
  let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));
62713
62776
  me.htmlCls.clickMenuCls.setLogCmd("pdb of mutation " + mutationids, false);
62714
- window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap pdb ' + mutationids + '; select displayed set', '_blank');
62777
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62778
+ window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap pdb ' + mutationids + '; select displayed set', urlTarget);
62715
62779
  }
62716
62780
  });
62717
62781
 
@@ -62768,44 +62832,49 @@ class Events {
62768
62832
  ic.resid2specCls.residueids2spec(residArray);
62769
62833
 
62770
62834
  me.htmlCls.clickMenuCls.setLogCmd("interaction change of mutation " + mutationids, false);
62771
- window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap interaction ' + mutationids, '_blank');
62835
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62836
+ window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap interaction ' + mutationids, urlTarget);
62772
62837
  }
62773
62838
  });
62774
62839
 
62775
62840
  // },
62776
62841
  // clickReload_mmcif: function() {
62777
- me.myEventCls.onIds("#" + me.pre + "reload_mmcif", "click", function(e) { me.icn3d;
62842
+ me.myEventCls.onIds("#" + me.pre + "reload_mmcif", "click", function(e) { let ic = me.icn3d;
62778
62843
  e.preventDefault();
62779
62844
  if(!me.cfg.notebook) dialog.dialog( "close" );
62780
62845
  me.htmlCls.clickMenuCls.setLogCmd("load mmcif " + $("#" + me.pre + "mmcifid").val(), false);
62781
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmcifid=' + $("#" + me.pre + "mmcifid").val(), '_blank');
62782
- window.open(hostUrl + '?mmcifid=' + $("#" + me.pre + "mmcifid").val(), '_blank');
62846
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmcifid=' + $("#" + me.pre + "mmcifid").val(), urlTarget);
62847
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62848
+ window.open(hostUrl + '?mmcifid=' + $("#" + me.pre + "mmcifid").val(), urlTarget);
62783
62849
  });
62784
62850
 
62785
- me.myEventCls.onIds("#" + me.pre + "mmcifid", "keyup", function(e) { me.icn3d;
62851
+ me.myEventCls.onIds("#" + me.pre + "mmcifid", "keyup", function(e) { let ic = me.icn3d;
62786
62852
  if (e.keyCode === 13) {
62787
62853
  e.preventDefault();
62788
62854
  if(!me.cfg.notebook) dialog.dialog( "close" );
62789
62855
  me.htmlCls.clickMenuCls.setLogCmd("load mmcif " + $("#" + me.pre + "mmcifid").val(), false);
62790
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmcifid=' + $("#" + me.pre + "mmcifid").val(), '_blank');
62791
- window.open(hostUrl + '?mmcifid=' + $("#" + me.pre + "mmcifid").val(), '_blank');
62856
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmcifid=' + $("#" + me.pre + "mmcifid").val(), urlTarget);
62857
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62858
+ window.open(hostUrl + '?mmcifid=' + $("#" + me.pre + "mmcifid").val(), urlTarget);
62792
62859
  }
62793
62860
  });
62794
62861
 
62795
62862
  // },
62796
62863
  // clickReload_mmdb: function() {
62797
- me.myEventCls.onIds("#" + me.pre + "reload_mmdb", "click", function(e) { me.icn3d;
62864
+ me.myEventCls.onIds("#" + me.pre + "reload_mmdb", "click", function(e) { let ic = me.icn3d;
62798
62865
  e.preventDefault();
62799
62866
  //if(!me.cfg.notebook) dialog.dialog( "close" );
62800
62867
  me.htmlCls.clickMenuCls.setLogCmd("load mmdb1 " + $("#" + me.pre + "mmdbid").val(), false);
62801
- window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&bu=1', '_blank');
62868
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62869
+ window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&bu=1', urlTarget);
62802
62870
  });
62803
62871
 
62804
- me.myEventCls.onIds("#" + me.pre + "reload_mmdb_asym", "click", function(e) { me.icn3d;
62872
+ me.myEventCls.onIds("#" + me.pre + "reload_mmdb_asym", "click", function(e) { let ic = me.icn3d;
62805
62873
  e.preventDefault();
62806
62874
  //if(!me.cfg.notebook) dialog.dialog( "close" );
62807
62875
  me.htmlCls.clickMenuCls.setLogCmd("load mmdb0 " + $("#" + me.pre + "mmdbid").val(), false);
62808
- window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&bu=0', '_blank');
62876
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62877
+ window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&bu=0', urlTarget);
62809
62878
  });
62810
62879
 
62811
62880
  me.myEventCls.onIds("#" + me.pre + "reload_mmdbaf", "click", function(e) { me.icn3d;
@@ -62827,12 +62896,13 @@ class Events {
62827
62896
  thisClass.launchMmdb(ids, 0, hostUrl);
62828
62897
  });
62829
62898
 
62830
- me.myEventCls.onIds("#" + me.pre + "mmdbid", "keyup", function(e) { me.icn3d;
62899
+ me.myEventCls.onIds("#" + me.pre + "mmdbid", "keyup", function(e) { let ic = me.icn3d;
62831
62900
  if (e.keyCode === 13) {
62832
62901
  e.preventDefault();
62833
62902
  //if(!me.cfg.notebook) dialog.dialog( "close" );
62834
62903
  me.htmlCls.clickMenuCls.setLogCmd("load mmdb1 " + $("#" + me.pre + "mmdbid").val(), false);
62835
- window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&bu=1', '_blank');
62904
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62905
+ window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&bu=1', urlTarget);
62836
62906
  }
62837
62907
  });
62838
62908
 
@@ -62847,7 +62917,7 @@ class Events {
62847
62917
 
62848
62918
  // },
62849
62919
  // clickReload_blast_rep_id: function() {
62850
- me.myEventCls.onIds("#" + me.pre + "reload_blast_rep_id", "click", function(e) { me.icn3d;
62920
+ me.myEventCls.onIds("#" + me.pre + "reload_blast_rep_id", "click", function(e) { let ic = me.icn3d;
62851
62921
  e.preventDefault();
62852
62922
  if(!me.cfg.notebook) dialog.dialog( "close" );
62853
62923
  let query_id = $("#" + me.pre + "query_id").val();
@@ -62856,13 +62926,14 @@ class Events {
62856
62926
  me.htmlCls.clickMenuCls.setLogCmd("load seq_struct_ids " + query_id + "," + blast_rep_id, false);
62857
62927
  query_id =(query_id !== '' && query_id !== undefined) ? query_id : query_fasta;
62858
62928
  //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?from=icn3d&blast_rep_id=' + blast_rep_id
62929
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62859
62930
  window.open(hostUrl + '?from=icn3d&alg=blast&blast_rep_id=' + blast_rep_id
62860
62931
  + '&query_id=' + query_id
62861
62932
  + '&command=view annotations; set annotation cdd; set annotation site; set view detailed view; select chain '
62862
- + blast_rep_id + '; show selection', '_blank');
62933
+ + blast_rep_id + '; show selection', urlTarget);
62863
62934
  });
62864
62935
 
62865
- me.myEventCls.onIds("#" + me.pre + "reload_alignsw", "click", function(e) { me.icn3d;
62936
+ me.myEventCls.onIds("#" + me.pre + "reload_alignsw", "click", function(e) { let ic = me.icn3d;
62866
62937
  e.preventDefault();
62867
62938
  if(!me.cfg.notebook) dialog.dialog( "close" );
62868
62939
  let query_id = $("#" + me.pre + "query_id").val();
@@ -62871,13 +62942,14 @@ class Events {
62871
62942
  me.htmlCls.clickMenuCls.setLogCmd("load seq_struct_ids_smithwm " + query_id + "," + blast_rep_id, false);
62872
62943
  query_id =(query_id !== '' && query_id !== undefined) ? query_id : query_fasta;
62873
62944
 
62945
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62874
62946
  window.open(hostUrl + '?from=icn3d&alg=smithwm&blast_rep_id=' + blast_rep_id
62875
62947
  + '&query_id=' + query_id
62876
62948
  + '&command=view annotations; set annotation cdd; set annotation site; set view detailed view; select chain '
62877
- + blast_rep_id + '; show selection', '_blank');
62949
+ + blast_rep_id + '; show selection', urlTarget);
62878
62950
  });
62879
62951
 
62880
- me.myEventCls.onIds("#" + me.pre + "reload_alignswlocal", "click", function(e) { me.icn3d;
62952
+ me.myEventCls.onIds("#" + me.pre + "reload_alignswlocal", "click", function(e) { let ic = me.icn3d;
62881
62953
  e.preventDefault();
62882
62954
  if(!me.cfg.notebook) dialog.dialog( "close" );
62883
62955
  let query_id = $("#" + me.pre + "query_id").val();
@@ -62886,75 +62958,84 @@ class Events {
62886
62958
  me.htmlCls.clickMenuCls.setLogCmd("load seq_struct_ids_local_smithwm " + query_id + "," + blast_rep_id, false);
62887
62959
  query_id =(query_id !== '' && query_id !== undefined) ? query_id : query_fasta;
62888
62960
 
62961
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62889
62962
  window.open(hostUrl + '?from=icn3d&alg=local_smithwm&blast_rep_id=' + blast_rep_id
62890
62963
  + '&query_id=' + query_id
62891
62964
  + '&command=view annotations; set annotation cdd; set annotation site; set view detailed view; select chain '
62892
- + blast_rep_id + '; show selection', '_blank');
62965
+ + blast_rep_id + '; show selection', urlTarget);
62893
62966
  });
62894
62967
 
62895
62968
  // },
62896
62969
  // clickReload_gi: function() {
62897
- me.myEventCls.onIds("#" + me.pre + "reload_gi", "click", function(e) { me.icn3d;
62970
+ me.myEventCls.onIds("#" + me.pre + "reload_gi", "click", function(e) { let ic = me.icn3d;
62898
62971
  e.preventDefault();
62899
62972
  if(!me.cfg.notebook) dialog.dialog( "close" );
62900
62973
  me.htmlCls.clickMenuCls.setLogCmd("load gi " + $("#" + me.pre + "gi").val(), false);
62901
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?gi=' + $("#" + me.pre + "gi").val(), '_blank');
62902
- window.open(hostUrl + '?gi=' + $("#" + me.pre + "gi").val(), '_blank');
62974
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?gi=' + $("#" + me.pre + "gi").val(), urlTarget);
62975
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62976
+ window.open(hostUrl + '?gi=' + $("#" + me.pre + "gi").val(), urlTarget);
62903
62977
  });
62904
62978
 
62905
- me.myEventCls.onIds("#" + me.pre + "reload_refseq", "click", function(e) { me.icn3d;
62979
+ me.myEventCls.onIds("#" + me.pre + "reload_refseq", "click", function(e) { let ic = me.icn3d;
62906
62980
  e.preventDefault();
62907
62981
  if(!me.cfg.notebook) dialog.dialog( "close" );
62908
- me.htmlCls.clickMenuCls.setLogCmd("load refseq " + $("#" + me.pre + "refseq").val(), false);
62909
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?gi=' + $("#" + me.pre + "gi").val(), '_blank');
62910
- window.open(hostUrl + '?refseq=' + $("#" + me.pre + "refseq").val(), '_blank');
62982
+ me.htmlCls.clickMenuCls.setLogCmd("load refseq " + $("#" + me.pre + "refseqid").val(), false);
62983
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?gi=' + $("#" + me.pre + "gi").val(), urlTarget);
62984
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62985
+ window.open(hostUrl + '?refseqid=' + $("#" + me.pre + "refseqid").val(), urlTarget);
62911
62986
  });
62912
62987
 
62913
- me.myEventCls.onIds("#" + me.pre + "gi", "keyup", function(e) { me.icn3d;
62988
+ me.myEventCls.onIds("#" + me.pre + "gi", "keyup", function(e) { let ic = me.icn3d;
62914
62989
  if (e.keyCode === 13) {
62915
62990
  e.preventDefault();
62916
62991
  if(!me.cfg.notebook) dialog.dialog( "close" );
62917
62992
  me.htmlCls.clickMenuCls.setLogCmd("load gi " + $("#" + me.pre + "gi").val(), false);
62918
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?gi=' + $("#" + me.pre + "gi").val(), '_blank');
62919
- window.open(hostUrl + '?gi=' + $("#" + me.pre + "gi").val(), '_blank');
62993
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?gi=' + $("#" + me.pre + "gi").val(), urlTarget);
62994
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
62995
+ window.open(hostUrl + '?gi=' + $("#" + me.pre + "gi").val(), urlTarget);
62920
62996
  }
62921
62997
  });
62922
62998
 
62923
- me.myEventCls.onIds("#" + me.pre + "reload_uniprotid", "click", function(e) { me.icn3d;
62999
+ me.myEventCls.onIds("#" + me.pre + "reload_uniprotid", "click", function(e) { let ic = me.icn3d;
62924
63000
  e.preventDefault();
62925
63001
  if(!me.cfg.notebook) dialog.dialog( "close" );
62926
63002
  me.htmlCls.clickMenuCls.setLogCmd("load uniprotid " + $("#" + me.pre + "uniprotid").val(), false);
62927
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?uniprotid=' + $("#" + me.pre + "uniprotid").val(), '_blank');
62928
- window.open(hostUrl + '?uniprotid=' + $("#" + me.pre + "uniprotid").val(), '_blank');
63003
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?uniprotid=' + $("#" + me.pre + "uniprotid").val(), urlTarget);
63004
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
63005
+ window.open(hostUrl + '?uniprotid=' + $("#" + me.pre + "uniprotid").val(), urlTarget);
62929
63006
  });
62930
63007
 
62931
- me.myEventCls.onIds("#" + me.pre + "uniprotid", "keyup", function(e) { me.icn3d;
63008
+ me.myEventCls.onIds("#" + me.pre + "uniprotid", "keyup", function(e) { let ic = me.icn3d;
62932
63009
  if (e.keyCode === 13) {
62933
63010
  e.preventDefault();
62934
63011
  if(!me.cfg.notebook) dialog.dialog( "close" );
62935
63012
  me.htmlCls.clickMenuCls.setLogCmd("load uniprotid " + $("#" + me.pre + "uniprotid").val(), false);
62936
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?uniprotid=' + $("#" + me.pre + "uniprotid").val(), '_blank');
62937
- window.open(hostUrl + '?uniprotid=' + $("#" + me.pre + "uniprotid").val(), '_blank');
63013
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?uniprotid=' + $("#" + me.pre + "uniprotid").val(), urlTarget);
63014
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
63015
+ window.open(hostUrl + '?uniprotid=' + $("#" + me.pre + "uniprotid").val(), urlTarget);
62938
63016
  }
62939
63017
  });
62940
63018
 
62941
63019
  // },
62942
63020
  // clickReload_cid: function() {
62943
- me.myEventCls.onIds("#" + me.pre + "reload_cid", "click", function(e) { me.icn3d;
63021
+ me.myEventCls.onIds("#" + me.pre
63022
+ + "reload_cid", "click", function(e) { let ic = me.icn3d;
62944
63023
  e.preventDefault();
62945
63024
  if(!me.cfg.notebook) dialog.dialog( "close" );
62946
63025
  me.htmlCls.clickMenuCls.setLogCmd("load cid " + $("#" + me.pre + "cid").val(), false);
62947
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?cid=' + $("#" + me.pre + "cid").val(), '_blank');
62948
- window.open(hostUrl + '?cid=' + $("#" + me.pre + "cid").val(), '_blank');
63026
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?cid=' + $("#" + me.pre + "cid").val(), urlTarget);
63027
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
63028
+ window.open(hostUrl + '?cid=' + $("#" + me.pre + "cid").val(), urlTarget);
62949
63029
  });
62950
63030
 
62951
- me.myEventCls.onIds("#" + me.pre + "cid", "keyup", function(e) { me.icn3d;
63031
+ me.myEventCls.onIds("#" + me.pre + "cid", "keyup", function(e) { let ic = me.icn3d;
62952
63032
  if (e.keyCode === 13) {
62953
63033
  e.preventDefault();
62954
63034
  if(!me.cfg.notebook) dialog.dialog( "close" );
62955
63035
  me.htmlCls.clickMenuCls.setLogCmd("load cid " + $("#" + me.pre + "cid").val(), false);
62956
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?cid=' + $("#" + me.pre + "cid").val(), '_blank');
62957
- window.open(hostUrl + '?cid=' + $("#" + me.pre + "cid").val(), '_blank');
63036
+ //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?cid=' + $("#" + me.pre + "cid").val(), urlTarget);
63037
+ let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
63038
+ window.open(hostUrl + '?cid=' + $("#" + me.pre + "cid").val(), urlTarget);
62958
63039
  }
62959
63040
  });
62960
63041
 
@@ -70730,7 +70811,7 @@ class iCn3DUI {
70730
70811
  //even when multiple iCn3D viewers are shown together.
70731
70812
  this.pre = this.cfg.divid + "_";
70732
70813
 
70733
- this.REVISION = '3.19.1';
70814
+ this.REVISION = '3.20.0';
70734
70815
 
70735
70816
  // In nodejs, iCn3D defines "window = {navigator: {}}"
70736
70817
  this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -71019,11 +71100,20 @@ iCn3DUI.prototype.show3DStructure = function(pdbStr) { let me = this;
71019
71100
  me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
71020
71101
  ic.mmdbParserCls.downloadGi(me.cfg.gi);
71021
71102
  }
71022
- else if(me.cfg.uniprotid !== undefined) {
71023
- ic.loadCmd = 'load uniprotid ' + me.cfg.uniprotid;
71024
- me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
71025
- ic.mmdbParserCls.downloadUniprotid(me.cfg.uniprotid);
71026
- }
71103
+ else if(me.cfg.refseqid !== undefined) {
71104
+ ic.inputid = me.cfg.refseqid;
71105
+
71106
+ ic.bNCBI = true;
71107
+ ic.loadCmd = 'load refseq ' + me.cfg.refseqid;
71108
+ me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
71109
+ ic.mmdbParserCls.downloadRefseq(me.cfg.refseqid);
71110
+ }
71111
+ // else if(me.cfg.proteinname !== undefined) {
71112
+ // ic.bNCBI = true;
71113
+ // ic.loadCmd = 'load proteinname ' + me.cfg.gi;
71114
+ // me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
71115
+ // ic.mmdbParserCls.downloadProteinname(me.cfg.proteinname);
71116
+ // }
71027
71117
  else if(me.cfg.blast_rep_id !== undefined) {
71028
71118
  ic.bNCBI = true;
71029
71119