icn3d 3.13.2 → 3.14.0

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Files changed (5) hide show
  1. package/css/icn3d.css +8 -2
  2. package/icn3d.js +414 -32
  3. package/icn3d.min.js +1 -1
  4. package/icn3d.module.js +414 -32
  5. package/package.json +1 -1
package/icn3d.module.js CHANGED
@@ -28474,6 +28474,24 @@ class LoadScript {
28474
28474
 
28475
28475
  return;
28476
28476
  }
28477
+ else if(ic.commands[i].trim().indexOf('set annotation ptm') == 0 ) { // the command may have "|||{"factor"...
28478
+ let strArray = ic.commands[i].split("|||");
28479
+
28480
+ if(Object.keys(ic.proteins).length > 0 &&(ic.bAjaxPTM === undefined || !ic.bAjaxPTM) ) {
28481
+ $.when(thisClass.applyCommandPTM(strArray[0].trim())).then(function() {
28482
+ thisClass.execCommandsBase(i + 1, end, steps);
28483
+ });
28484
+ }
28485
+ else {
28486
+ if(Object.keys(ic.proteins).length > 0) {
28487
+ thisClass.applyCommandPTM(strArray[0].trim());
28488
+ }
28489
+
28490
+ this.execCommandsBase(i + 1, end, steps);
28491
+ }
28492
+
28493
+ return;
28494
+ }
28477
28495
  else if(ic.commands[i].trim().indexOf('set annotation 3ddomain') == 0) { // the command may have "|||{"factor"...
28478
28496
  let strArray = ic.commands[i].split("|||");
28479
28497
 
@@ -28704,6 +28722,8 @@ class LoadScript {
28704
28722
  ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
28705
28723
  }
28706
28724
 
28725
+ me.cfg.aligntool = 'vast';
28726
+
28707
28727
  $.when(thisClass.applyCommandRealignByStruct(command)).then(function() {
28708
28728
  thisClass.execCommandsBase(i + 1, end, steps);
28709
28729
  });
@@ -28864,6 +28884,9 @@ class LoadScript {
28864
28884
  else if(lastCommand.indexOf('set annotation snp') == 0) {
28865
28885
  thisClass.applyCommandSnp(lastCommand);
28866
28886
  }
28887
+ else if(lastCommand.indexOf('set annotation ptm') == 0) {
28888
+ thisClass.applyCommandPTM(lastCommand);
28889
+ }
28867
28890
  else if(lastCommand.indexOf('set annotation 3ddomain') == 0) {
28868
28891
  thisClass.applyCommand3ddomain(lastCommand);
28869
28892
  }
@@ -28914,6 +28937,9 @@ class LoadScript {
28914
28937
  let nameArray = paraArray[1].split(',');
28915
28938
  ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
28916
28939
  }
28940
+
28941
+ me.cfg.aligntool = 'vast';
28942
+
28917
28943
  thisClass.applyCommandRealignByStruct(lastCommand);
28918
28944
  }
28919
28945
  else if(lastCommand.indexOf('realign on tmalign') == 0) {
@@ -29319,6 +29345,25 @@ class LoadScript {
29319
29345
  return ic.deferredSnp.promise();
29320
29346
  }
29321
29347
 
29348
+ applyCommandPTMBase(command) { let ic = this.icn3d; ic.icn3dui;
29349
+ // chain functions together
29350
+ let pos = command.lastIndexOf(' '); // set annotation clinvar
29351
+ command.substr(pos + 1);
29352
+
29353
+ ic.annotationCls.setAnnoTabPTM();
29354
+ }
29355
+
29356
+ applyCommandPTM(command) { let ic = this.icn3d; ic.icn3dui;
29357
+ let thisClass = this;
29358
+
29359
+ // chain functions together
29360
+ ic.deferredPTM = $.Deferred(function() {
29361
+ thisClass.applyCommandPTMBase(command);
29362
+ }); // end of me.deferred = $.Deferred(function() {
29363
+
29364
+ return ic.deferredPTM.promise();
29365
+ }
29366
+
29322
29367
  applyCommand3ddomainBase(command) { let ic = this.icn3d; ic.icn3dui;
29323
29368
  // chain functions together
29324
29369
  let pos = command.lastIndexOf(' ');
@@ -30860,7 +30905,8 @@ class ShowSeq {
30860
30905
  if(seqLength > ic.maxAnnoLength) {
30861
30906
  ic.maxAnnoLength = seqLength;
30862
30907
  }
30863
- let itemArray = ['giseq', 'cddsite', 'clinvar', 'snp', 'domain', 'interaction', 'custom', 'ssbond', 'crosslink', 'transmem'];
30908
+ //let itemArray = ['giseq', 'cddsite', 'ptm', 'clinvar', 'snp', 'domain', 'interaction', 'custom', 'ssbond', 'crosslink', 'transmem'];
30909
+ let itemArray = ['giseq', 'cddsite', 'clinvar', 'snp', 'ptm', 'ssbond', 'crosslink', 'transmem', 'domain', 'custom', 'interaction'];
30864
30910
  for(let i in itemArray) {
30865
30911
  let item = itemArray[i];
30866
30912
  if($("#" + ic.pre + item + "_" + chnid).length) $("#" + ic.pre + item + "_" + chnid).width(divLength);
@@ -33822,6 +33868,9 @@ class ApplyCommand {
33822
33868
  else if(command == 'set annotation interaction') {
33823
33869
  ic.annotationCls.setAnnoTabInteraction();
33824
33870
  }
33871
+ else if(command == 'set annotation ptm') {
33872
+ ic.annotationCls.setAnnoTabPTM();
33873
+ }
33825
33874
  else if(command == 'set annotation cdd') {
33826
33875
  ic.annotationCls.setAnnoTabCdd();
33827
33876
  }
@@ -33868,6 +33917,9 @@ class ApplyCommand {
33868
33917
  else if(type == 'site') {
33869
33918
  ic.annotationCls.hideAnnoTabSite();
33870
33919
  }
33920
+ else if(type == 'ptm') {
33921
+ ic.annotationCls.hideAnnoTabPTM();
33922
+ }
33871
33923
  else if(type == 'interaction') {
33872
33924
  ic.annotationCls.hideAnnoTabInteraction();
33873
33925
  }
@@ -35066,6 +35118,7 @@ class ApplyCommand {
35066
35118
  else if(cmd== 'set view overview') return seqAnnoStr + ': "Summary" tab';
35067
35119
  else if(cmd == 'set annotation custom') return seqAnnoStr + ': "Custom" checkbox';
35068
35120
  else if(cmd == 'set annotation interaction') return seqAnnoStr + ': "Interactions" checkbox';
35121
+ else if(cmd == 'set annotation ptm') return seqAnnoStr + ': "PTM" checkbox';
35069
35122
  else if(cmd == 'set annotation cdd') return seqAnnoStr + ': "Conserved Domains" checkbox';
35070
35123
  else if(cmd == 'set annotation site') return seqAnnoStr + ': "Functional Sites" checkbox';
35071
35124
  else if(cmd == 'set annotation ssbond') return seqAnnoStr + ': "Disulfide Bonds" checkbox';
@@ -36368,7 +36421,8 @@ class SetSeqAlign {
36368
36421
  if(i > 0) {
36369
36422
  let index1 = alignIndex;
36370
36423
  for(let j = prevIndex1 + 1, jl = start1; j < jl; ++j) {
36371
- if(ic.chainsSeq[chainid1] === undefined) break;
36424
+ if(ic.chainsSeq[chainid1] === undefined || ic.chainsSeq[chainid1][j] === undefined) break;
36425
+
36372
36426
  let resi = ic.chainsSeq[chainid1][j].resi;
36373
36427
  let resn = ic.chainsSeq[chainid1][j].name.toLowerCase();
36374
36428
 
@@ -36382,7 +36436,8 @@ class SetSeqAlign {
36382
36436
 
36383
36437
  let index2 = alignIndex;
36384
36438
  for(let j = prevIndex2 + 1, jl = start2; j < jl; ++j) {
36385
- if(ic.chainsSeq[chainid2] === undefined) break;
36439
+ if(ic.chainsSeq[chainid2] === undefined || ic.chainsSeq[chainid2] === undefined) break;
36440
+
36386
36441
  let resi = ic.chainsSeq[chainid2][j].resi;
36387
36442
  let resn = ic.chainsSeq[chainid2][j].name.toLowerCase();
36388
36443
 
@@ -38332,8 +38387,8 @@ class HlSeq {
38332
38387
  if(me.bNode) return;
38333
38388
 
38334
38389
  let thisClass = this;
38335
- $("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "dt_giseq]").add("[id^=" + ic.pre + "dt_custom]").add("[id^=" + ic.pre + "dt_site]").add("[id^=" + ic.pre + "dt_snp]").add("[id^=" + ic.pre + "dt_clinvar]").add("[id^=" + ic.pre + "dt_cdd]").add("[id^=" + ic.pre + "dt_domain]").add("[id^=" + ic.pre + "dt_interaction]").add("[id^=" + ic.pre + "dt_ssbond]").add("[id^=" + ic.pre + "dt_crosslink]").add("[id^=" + ic.pre + "dt_transmem]")
38336
- .add("[id^=" + ic.pre + "tt_giseq]").add("[id^=" + ic.pre + "tt_custom]").add("[id^=" + ic.pre + "tt_site]").add("[id^=" + ic.pre + "tt_snp]").add("[id^=" + ic.pre + "tt_clinvar]").add("[id^=" + ic.pre + "tt_cdd]").add("[id^=" + ic.pre + "tt_domain]").add("[id^=" + ic.pre + "tt_interaction]").add("[id^=" + ic.pre + "tt_ssbond]").add("[id^=" + ic.pre + "tt_crosslink]").add("[id^=" + ic.pre + "tt_transmem]")
38390
+ $("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "dt_giseq]").add("[id^=" + ic.pre + "dt_custom]").add("[id^=" + ic.pre + "dt_site]").add("[id^=" + ic.pre + "dt_ptm]").add("[id^=" + ic.pre + "dt_snp]").add("[id^=" + ic.pre + "dt_clinvar]").add("[id^=" + ic.pre + "dt_cdd]").add("[id^=" + ic.pre + "dt_domain]").add("[id^=" + ic.pre + "dt_interaction]").add("[id^=" + ic.pre + "dt_ssbond]").add("[id^=" + ic.pre + "dt_crosslink]").add("[id^=" + ic.pre + "dt_transmem]")
38391
+ .add("[id^=" + ic.pre + "tt_giseq]").add("[id^=" + ic.pre + "tt_custom]").add("[id^=" + ic.pre + "tt_site]").add("[id^=" + ic.pre + "tt_ptm]").add("[id^=" + ic.pre + "tt_snp]").add("[id^=" + ic.pre + "tt_clinvar]").add("[id^=" + ic.pre + "tt_cdd]").add("[id^=" + ic.pre + "tt_domain]").add("[id^=" + ic.pre + "tt_interaction]").add("[id^=" + ic.pre + "tt_ssbond]").add("[id^=" + ic.pre + "tt_crosslink]").add("[id^=" + ic.pre + "tt_transmem]")
38337
38392
  .selectable({
38338
38393
  distance: 1, //Tolerance, in pixels, for when selecting should start. If specified, selecting will not start until the mouse has been dragged beyond the specified distance.
38339
38394
  stop: function() { let ic = thisClass.icn3d;
@@ -38386,11 +38441,11 @@ class HlSeq {
38386
38441
  }
38387
38442
  });
38388
38443
 
38389
- $("[id^=" + ic.pre + "ov_giseq]").add("[id^=" + ic.pre + "ov_custom]").add("[id^=" + ic.pre + "ov_site]").add("[id^=" + ic.pre + "ov_snp]").add("[id^=" + ic.pre + "ov_clinvar]").add("[id^=" + ic.pre + "ov_cdd]").add("[id^=" + ic.pre + "ov_domain]").add("[id^=" + ic.pre + "ov_interaction]").add("[id^=" + ic.pre + "ov_ssbond]").add("[id^=" + ic.pre + "ov_crosslink]").add("[id^=" + ic.pre + "ov_transmem]")
38390
- .add("[id^=" + ic.pre + "tt_giseq]").add("[id^=" + ic.pre + "tt_custom]").add("[id^=" + ic.pre + "tt_site]").add("[id^=" + ic.pre + "tt_snp]").add("[id^=" + ic.pre + "tt_clinvar]").add("[id^=" + ic.pre + "tt_cdd]").add("[id^=" + ic.pre + "tt_domain]").add("[id^=" + ic.pre + "tt_interaction]").add("[id^=" + ic.pre + "tt_ssbond]").add("[id^=" + ic.pre + "tt_crosslink]").add("[id^=" + ic.pre + "tt_transmem]")
38444
+ $("[id^=" + ic.pre + "ov_giseq]").add("[id^=" + ic.pre + "ov_custom]").add("[id^=" + ic.pre + "ov_site]").add("[id^=" + ic.pre + "ov_ptm]").add("[id^=" + ic.pre + "ov_snp]").add("[id^=" + ic.pre + "ov_clinvar]").add("[id^=" + ic.pre + "ov_cdd]").add("[id^=" + ic.pre + "ov_domain]").add("[id^=" + ic.pre + "ov_interaction]").add("[id^=" + ic.pre + "ov_ssbond]").add("[id^=" + ic.pre + "ov_crosslink]").add("[id^=" + ic.pre + "ov_transmem]")
38445
+ .add("[id^=" + ic.pre + "tt_giseq]").add("[id^=" + ic.pre + "tt_custom]").add("[id^=" + ic.pre + "tt_site]").add("[id^=" + ic.pre + "tt_ptm]").add("[id^=" + ic.pre + "tt_snp]").add("[id^=" + ic.pre + "tt_clinvar]").add("[id^=" + ic.pre + "tt_cdd]").add("[id^=" + ic.pre + "tt_domain]").add("[id^=" + ic.pre + "tt_interaction]").add("[id^=" + ic.pre + "tt_ssbond]").add("[id^=" + ic.pre + "tt_crosslink]").add("[id^=" + ic.pre + "tt_transmem]")
38391
38446
 
38392
- .add("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "dt_giseq]").add("[id^=" + ic.pre + "dt_custom]").add("[id^=" + ic.pre + "dt_site]").add("[id^=" + ic.pre + "dt_snp]").add("[id^=" + ic.pre + "dt_clinvar]").add("[id^=" + ic.pre + "dt_cdd]").add("[id^=" + ic.pre + "dt_domain]").add("[id^=" + ic.pre + "dt_interaction]").add("[id^=" + ic.pre + "dt_ssbond]").add("[id^=" + ic.pre + "dt_crosslink]").add("[id^=" + ic.pre + "dt_transmem]")
38393
- .add("[id^=" + ic.pre + "tt_giseq]").add("[id^=" + ic.pre + "tt_custom]").add("[id^=" + ic.pre + "tt_site]").add("[id^=" + ic.pre + "tt_snp]").add("[id^=" + ic.pre + "tt_clinvar]").add("[id^=" + ic.pre + "tt_cdd]").add("[id^=" + ic.pre + "tt_domain]").add("[id^=" + ic.pre + "tt_interaction]").add("[id^=" + ic.pre + "tt_ssbond]").add("[id^=" + ic.pre + "tt_crosslink]").add("[id^=" + ic.pre + "tt_transmem]")
38447
+ .add("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "dt_giseq]").add("[id^=" + ic.pre + "dt_custom]").add("[id^=" + ic.pre + "dt_site]").add("[id^=" + ic.pre + "dt_ptm]").add("[id^=" + ic.pre + "dt_snp]").add("[id^=" + ic.pre + "dt_clinvar]").add("[id^=" + ic.pre + "dt_cdd]").add("[id^=" + ic.pre + "dt_domain]").add("[id^=" + ic.pre + "dt_interaction]").add("[id^=" + ic.pre + "dt_ssbond]").add("[id^=" + ic.pre + "dt_crosslink]").add("[id^=" + ic.pre + "dt_transmem]")
38448
+ .add("[id^=" + ic.pre + "tt_giseq]").add("[id^=" + ic.pre + "tt_custom]").add("[id^=" + ic.pre + "tt_site]").add("[id^=" + ic.pre + "tt_ptm]").add("[id^=" + ic.pre + "tt_snp]").add("[id^=" + ic.pre + "tt_clinvar]").add("[id^=" + ic.pre + "tt_cdd]").add("[id^=" + ic.pre + "tt_domain]").add("[id^=" + ic.pre + "tt_interaction]").add("[id^=" + ic.pre + "tt_ssbond]").add("[id^=" + ic.pre + "tt_crosslink]").add("[id^=" + ic.pre + "tt_transmem]")
38394
38449
 
38395
38450
  .on('click', '.icn3d-seqTitle', function(e) { let ic = thisClass.icn3d;
38396
38451
  e.stopImmediatePropagation();
@@ -38431,7 +38486,7 @@ class HlSeq {
38431
38486
 
38432
38487
  let thisClass = this;
38433
38488
 
38434
- $("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "giseq]").add("[id^=" + ic.pre + "custom]").add("[id^=" + ic.pre + "site]").add("[id^=" + ic.pre + "clinvar]").add("[id^=" + ic.pre + "snp]").add("[id^=" + ic.pre + "cdd]").add("[id^=" + ic.pre + "domain]").add("[id^=" + ic.pre + "interaction]").add("[id^=" + ic.pre + "ssbond]").add("[id^=" + ic.pre + "crosslink]").add("[id^=" + ic.pre + "transmem]").on('click', '.icn3d-residue', function(e) { let ic = thisClass.icn3d;
38489
+ $("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "giseq]").add("[id^=" + ic.pre + "custom]").add("[id^=" + ic.pre + "site]").add("[id^=" + ic.pre + "ptm]").add("[id^=" + ic.pre + "clinvar]").add("[id^=" + ic.pre + "snp]").add("[id^=" + ic.pre + "cdd]").add("[id^=" + ic.pre + "domain]").add("[id^=" + ic.pre + "interaction]").add("[id^=" + ic.pre + "ssbond]").add("[id^=" + ic.pre + "crosslink]").add("[id^=" + ic.pre + "transmem]").on('click', '.icn3d-residue', function(e) { let ic = thisClass.icn3d;
38435
38490
  e.stopImmediatePropagation();
38436
38491
  /*
38437
38492
  //if($(this).attr('id') === ic.pre + "dl_sequence2") {
@@ -38480,7 +38535,7 @@ class HlSeq {
38480
38535
 
38481
38536
  let thisClass = this;
38482
38537
 
38483
- $("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "giseq]").add("[id^=" + ic.pre + "custom]").add("[id^=" + ic.pre + "site]").add("[id^=" + ic.pre + "feat]").add("[id^=" + ic.pre + "clinvar]").add("[id^=" + ic.pre + "snp]").add("[id^=" + ic.pre + "cdd]").add("[id^=" + ic.pre + "domain]").add("[id^=" + ic.pre + "interaction]").add("[id^=" + ic.pre + "ssbond]").add("[id^=" + ic.pre + "crosslink]").add("[id^=" + ic.pre + "transmem]").on('click', '.icn3d-seqTitle', function(e) { let ic = thisClass.icn3d;
38538
+ $("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "giseq]").add("[id^=" + ic.pre + "custom]").add("[id^=" + ic.pre + "site]").add("[id^=" + ic.pre + "ptm]").add("[id^=" + ic.pre + "feat]").add("[id^=" + ic.pre + "clinvar]").add("[id^=" + ic.pre + "snp]").add("[id^=" + ic.pre + "cdd]").add("[id^=" + ic.pre + "domain]").add("[id^=" + ic.pre + "interaction]").add("[id^=" + ic.pre + "ssbond]").add("[id^=" + ic.pre + "crosslink]").add("[id^=" + ic.pre + "transmem]").on('click', '.icn3d-seqTitle', function(e) { let ic = thisClass.icn3d;
38484
38539
  e.stopImmediatePropagation();
38485
38540
 
38486
38541
  //if($(this).attr('id') === ic.pre + "dl_sequence2") {
@@ -38677,7 +38732,7 @@ class HlSeq {
38677
38732
  let residueid;
38678
38733
  let structure = chainid.substr(0, chainid.indexOf('_'));
38679
38734
  for(let i = 0, il = posArray.length; i < il; ++i) {
38680
- if($(that).attr('site') !== undefined) {
38735
+ if($(that).attr('site') !== undefined || $(that).attr('ptm') !== undefined) {
38681
38736
  if(ic.bNCBI) {
38682
38737
  let residNCBI = chainid + '_' +(parseInt(posArray[i])+1).toString();
38683
38738
  // AlphaFold domains calculated on-the-fly have no conversion
@@ -39079,6 +39134,8 @@ class ShowAnno {
39079
39134
  ++i;
39080
39135
  }
39081
39136
  ic.interactChainbase = me.hashUtilsCls.unionHash(ic.interactChainbase, chemical_chainid);
39137
+ ic.PTMChainbase = me.hashUtilsCls.unionHash(ic.PTMChainbase, ic.protein_chainid);
39138
+
39082
39139
  ic.ssbondChainbase = me.hashUtilsCls.unionHash(ic.ssbondChainbase, ic.protein_chainid);
39083
39140
  ic.ssbondChainbase = me.hashUtilsCls.unionHash(ic.ssbondChainbase, chemical_chainid);
39084
39141
  ic.crosslinkChainbase = me.hashUtilsCls.unionHash(ic.crosslinkChainbase, ic.protein_chainid);
@@ -39110,8 +39167,10 @@ class ShowAnno {
39110
39167
  //if(proteinName.length > 40) proteinName = proteinName.substr(0, 40) + "...";
39111
39168
  let categoryStr =(index == 0) ? "<span class='icn3d-annoLargeTitle'><b>Proteins</b>: </span><br><br>" : "";
39112
39169
  let geneLink =(ic.chainsGene[chnid] && ic.chainsGene[chnid].geneId) ? "(Gene: <a href='https://www.ncbi.nlm.nih.gov/gene/" + ic.chainsGene[chnid].geneId + "' target='_blank' title='" + ic.chainsGene[chnid].geneDesc + "'>" + ic.chainsGene[chnid].geneSymbol + "</a>)" : '';
39170
+ let structure = chnid.substr(0, chnid.indexOf('_'));
39171
+ let chainLink = (structure.length > 5) ? '<a href="https://alphafold.ebi.ac.uk/entry/' + structure + '" target="_blank">' + chnid + '</a>' : chnid;
39113
39172
  let chainHtml = "<div id='" + ic.pre + "anno_" + chnid + "' class='icn3d-annotation'>" + categoryStr
39114
- + "<span style='font-weight:bold;'>Annotations of " + chnid
39173
+ + "<span style='font-weight:bold;'>Annotations of " + chainLink
39115
39174
  + "</span>: <a class='icn3d-blue' href='https://www.ncbi.nlm.nih.gov/protein?term="
39116
39175
  + chnid + "' target='_blank' title='" + fullProteinName + "'>" + proteinName + "</a>"
39117
39176
  + geneLink + "&nbsp;&nbsp;&nbsp;"
@@ -39124,7 +39183,8 @@ class ShowAnno {
39124
39183
  + this.addButton(chnid, "icn3d-sheetsets", "Sheet Sets", "Define sets for each sheet in this chain and add them to the menu of \"Defined Sets\"", 60, buttonStyle) + "&nbsp;"
39125
39184
  + this.addButton(chnid, "icn3d-coilsets", "Coil Sets", "Define sets for each coil in this chain and add them to the menu of \"Defined Sets\"", 60, buttonStyle);
39126
39185
  $("#" + ic.pre + "dl_annotations").append(chainHtml);
39127
- let itemArray = ['giseq', 'cdd', 'clinvar', 'snp', 'domain', 'site', 'interaction', 'custom', 'ssbond', 'crosslink', 'transmem'];
39186
+ //let itemArray = ['giseq', 'cdd', 'clinvar', 'snp', 'domain', 'site', 'ptm', 'interaction', 'custom', 'ssbond', 'crosslink', 'transmem'];
39187
+ let itemArray = ['giseq', 'cdd', 'clinvar', 'snp', 'site', 'ptm', 'ssbond', 'crosslink', 'transmem', 'domain', 'custom', 'interaction'];
39128
39188
  // dt: detailed view, hide by default; ov: overview, show by default
39129
39189
  for(let i in itemArray) {
39130
39190
  let item = itemArray[i];
@@ -39552,6 +39612,286 @@ class ShowAnno {
39552
39612
 
39553
39613
  }
39554
39614
 
39615
+ /**
39616
+ * @author Jiyao Wang <wangjiy@ncbi.nlm.nih.gov> / https://github.com/ncbi/icn3d
39617
+ */
39618
+
39619
+ class AnnoPTM {
39620
+ constructor(icn3d) {
39621
+ this.icn3d = icn3d;
39622
+ }
39623
+
39624
+ //Show the annotations of CDD domains and binding sites.
39625
+ showPTM(chnid, chnidBase) { let ic = this.icn3d; ic.icn3dui;
39626
+ let thisClass = this;
39627
+
39628
+ // UniProt ID
39629
+ let structure = chnid.substr(0, chnid.indexOf('_'));
39630
+ let chain = chnid.substr(chnid.indexOf('_') + 1);
39631
+
39632
+ // UniProt ID
39633
+ if( structure.length > 5 ) {
39634
+ let url = "https://www.ebi.ac.uk/proteins/api/features/" + structure;
39635
+ $.ajax({
39636
+ url: url,
39637
+ dataType: 'json',
39638
+ cache: true,
39639
+ tryCount : 0,
39640
+ retryLimit : 0, //1
39641
+ success: function(data) {
39642
+ thisClass.parsePTM(data, chnid);
39643
+ if(ic.deferredPTM !== undefined) ic.deferredPTM.resolve();
39644
+ },
39645
+ error : function(xhr, textStatus, errorThrown ) {
39646
+ this.tryCount++;
39647
+ if(this.tryCount <= this.retryLimit) {
39648
+ //try again
39649
+ $.ajax(this);
39650
+ return;
39651
+ }
39652
+
39653
+ thisClass.getNoPTM(chnid);
39654
+
39655
+ return;
39656
+ }
39657
+ });
39658
+ }
39659
+ else { // PDB
39660
+ // get PDB to UniProt mapping
39661
+ // https://www.ebi.ac.uk/pdbe/api/doc/
39662
+ let structLower = structure.substr(0, 4).toLowerCase();
39663
+ let urlMap = "https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/" + structLower;
39664
+
39665
+ $.ajax({
39666
+ url: urlMap,
39667
+ dataType: 'json',
39668
+ cache: true,
39669
+ success: function(dataMap) {
39670
+ let UniProtID = '';
39671
+ if(!ic.UPResi2ResiPosPerChain) ic.UPResi2ResiPosPerChain = {};
39672
+ ic.UPResi2ResiPosPerChain[chnid] = {};
39673
+ let mapping = dataMap[structLower].UniProt;
39674
+
39675
+ let bFound = false;
39676
+ for(let up in mapping) {
39677
+ let chainArray = mapping[up].mappings;
39678
+ if(bFound) break;
39679
+
39680
+ for(let i = 0, il = chainArray.length; i < il; ++i) {
39681
+ //"entity_id": 3, "end": { "author_residue_number": null, "author_insertion_code": "", "residue_number": 219 }, "chain_id": "A", "start": { "author_residue_number": 94, "author_insertion_code": "", "residue_number": 1 }, "unp_end": 312, "unp_start": 94, "struct_asym_id": "C"
39682
+ let chainObj = chainArray[i];
39683
+ if(chainObj.chain_id == chain) {
39684
+ let start = chainObj.unp_start;
39685
+ let end = chainObj.unp_end;
39686
+ let posStart = chainObj.start.residue_number;
39687
+ let posEnd = chainObj.end.residue_number;
39688
+
39689
+ if(posEnd - posStart != end - start) {
39690
+ console.log("There might be some issues in the PDB to UniProt residue mapping.");
39691
+ }
39692
+
39693
+ for(let j = 0; j <= end - start; ++j) {
39694
+ ic.UPResi2ResiPosPerChain[chnid][j + start] = j + posStart - 1; // 0-based
39695
+ }
39696
+
39697
+ UniProtID = up;
39698
+ bFound = true;
39699
+ break;
39700
+ }
39701
+ }
39702
+ }
39703
+
39704
+ if(UniProtID == '') {
39705
+ thisClass.getNoPTM(chnid);
39706
+ }
39707
+ else {
39708
+ let url = "https://www.ebi.ac.uk/proteins/api/features/" + UniProtID;
39709
+ $.ajax({
39710
+ url: url,
39711
+ dataType: 'json',
39712
+ cache: true,
39713
+ tryCount : 0,
39714
+ retryLimit : 0, //1
39715
+ success: function(data) {
39716
+ thisClass.parsePTM(data, chnid);
39717
+ if(ic.deferredPTM !== undefined) ic.deferredPTM.resolve();
39718
+ },
39719
+ error : function(xhr, textStatus, errorThrown ) {
39720
+ this.tryCount++;
39721
+ if(this.tryCount <= this.retryLimit) {
39722
+ //try again
39723
+ $.ajax(this);
39724
+ return;
39725
+ }
39726
+
39727
+ thisClass.getNoPTM(chnid);
39728
+
39729
+ return;
39730
+ }
39731
+ });
39732
+ }
39733
+ },
39734
+ error : function(xhr, textStatus, errorThrown ) {
39735
+ thisClass.getNoPTM(chnid);
39736
+ }
39737
+ });
39738
+ }
39739
+ }
39740
+
39741
+ parsePTM(data, chnid) { let ic = this.icn3d, me = ic.icn3dui;
39742
+
39743
+ if(me.bNode) {
39744
+ //if(!ic.resid2ptm) ic.resid2ptm = {};
39745
+ ic.resid2ptm = {};
39746
+ ic.resid2ptm[chnid] = [];
39747
+ }
39748
+
39749
+ let ptmHash = {};
39750
+ for(let i = 0, il = data.features.length; i < il; ++i) {
39751
+ let feature = data.features[i];
39752
+
39753
+ if(feature.category == 'PTM' && feature.type != 'DISULFID' && feature.type != 'CROSSLNK') {
39754
+ let title = '';
39755
+ if(feature.type == 'CARBOHYD') {
39756
+ //title = 'Glycosylation, ' + feature.description;
39757
+ title = 'Glycosylation';
39758
+ }
39759
+ else if(feature.type == 'LIPID') {
39760
+ title = 'Lipidation, ' + feature.description;
39761
+ }
39762
+ else if(feature.description.indexOf('Phospho') == 0) {
39763
+ title = 'Phosphorylation';
39764
+ }
39765
+ else if(feature.description) {
39766
+ title = feature.description;
39767
+ }
39768
+ else {
39769
+ title = feature.type;
39770
+ }
39771
+
39772
+ if(!ptmHash[title]) ptmHash[title] = [];
39773
+ ptmHash[title].push(feature);
39774
+ }
39775
+ }
39776
+
39777
+ let index = 0;
39778
+ let html = '', html2 = '', html3 = '';
39779
+ html += '<div id="' + ic.pre + chnid + '_ptmseq_sequence" class="icn3d-cdd icn3d-dl_sequence">';
39780
+ html2 += html;
39781
+ html3 += html;
39782
+ let stucture = chnid.substr(0, chnid.indexOf('_'));
39783
+
39784
+ for(let ptm in ptmHash) {
39785
+ let ptmArray = ptmHash[ptm];
39786
+ //"type": "MOD_RES", "category": "PTM", "description": "4-hydroxyproline", "begin": "382", "end": "382",
39787
+ let resPosArray = [];
39788
+ let bCoordinates = false;
39789
+ for(let i = 0, il = ptmArray.length; i < il; ++i) {
39790
+ let begin = parseInt(ptmArray[i].begin);
39791
+ let end = parseInt(ptmArray[i].end);
39792
+
39793
+
39794
+ for(let j = begin; j <= end; ++j) {
39795
+ if(stucture.length > 5) { // UniProt
39796
+ resPosArray.push(j - 1); // 0-based
39797
+ }
39798
+ else { // PDB
39799
+ if(ic.UPResi2ResiPosPerChain[chnid][j]) resPosArray.push(ic.UPResi2ResiPosPerChain[chnid][j]);
39800
+ }
39801
+
39802
+ if(!bCoordinates && ic.residues.hasOwnProperty(chnid + '_' + j)) {
39803
+ bCoordinates = true;
39804
+ }
39805
+ }
39806
+ }
39807
+
39808
+ if(resPosArray.length == 0) continue;
39809
+
39810
+ let resCnt = resPosArray.length;
39811
+ let title = 'PTM: ' + ptm;
39812
+ if(title.length > 17) title = title.substr(0, 17) + '...';
39813
+ let fulltitle = ptm;
39814
+
39815
+ let linkStr = (bCoordinates) ? 'icn3d-link icn3d-blue' : '';
39816
+
39817
+ let htmlTmp2 = '<div class="icn3d-seqTitle ' + linkStr + '" ptm="ptm" posarray="' + resPosArray.toString() + '" shorttitle="' + title + '" setname="' + chnid + '_ptm_' + index + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">' + title + ' </div>';
39818
+ let htmlTmp3 = '<span class="icn3d-residueNum" title="residue count">' + resCnt.toString() + ' Res</span>';
39819
+ let htmlTmp = '<span class="icn3d-seqLine">';
39820
+ html3 += htmlTmp2 + htmlTmp3 + '<br>';
39821
+ html += htmlTmp2 + htmlTmp3 + htmlTmp;
39822
+ html2 += htmlTmp2 + htmlTmp3 + htmlTmp;
39823
+ let pre = 'ptm' + index.toString();
39824
+ //var widthPerRes = ic.seqAnnWidth / ic.maxAnnoLength;
39825
+ let prevEmptyWidth = 0;
39826
+ let prevLineWidth = 0;
39827
+ let widthPerRes = 1;
39828
+ for(let i = 0, il = ic.giSeq[chnid].length; i < il; ++i) {
39829
+ html += ic.showSeqCls.insertGap(chnid, i, '-');
39830
+ if(resPosArray.indexOf(i) != -1) {
39831
+ let cFull = ic.giSeq[chnid][i];
39832
+ let c = cFull;
39833
+ if(cFull.length > 1) {
39834
+ c = cFull[0] + '..';
39835
+ }
39836
+ let pos = ic.annoCddSiteCls.getAdjustedResi(i, chnid, ic.matchedPos, ic.chainsSeq, ic.baseResi);
39837
+
39838
+ html += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" title="' + c + pos + '" class="icn3d-residue">' + cFull + '</span>';
39839
+ if(me.bNode) {
39840
+ let obj = {};
39841
+ obj[chnid + '_' + pos] = 'PTM: ' + ptm;
39842
+ ic.resid2ptm[chnid].push(obj);
39843
+ }
39844
+
39845
+ html2 += ic.showSeqCls.insertGapOverview(chnid, i);
39846
+ let emptyWidth =(me.cfg.blast_rep_id == chnid) ? Math.round(ic.seqAnnWidth * i /(ic.maxAnnoLength + ic.nTotalGap) - prevEmptyWidth - prevLineWidth) : Math.round(ic.seqAnnWidth * i / ic.maxAnnoLength - prevEmptyWidth - prevLineWidth);
39847
+ //if(emptyWidth < 0) emptyWidth = 0;
39848
+ if(emptyWidth >= 0) {
39849
+ html2 += '<div style="display:inline-block; width:' + emptyWidth + 'px;">&nbsp;</div>';
39850
+ html2 += '<div style="display:inline-block; background-color:#000; width:' + widthPerRes + 'px;" title="' + c + pos + '">&nbsp;</div>';
39851
+ prevEmptyWidth += emptyWidth;
39852
+ prevLineWidth += widthPerRes;
39853
+ }
39854
+ }
39855
+ else {
39856
+ html += '<span>-</span>'; //'<span>-</span>';
39857
+ }
39858
+ }
39859
+ htmlTmp = '<span class="icn3d-residueNum" title="residue count">&nbsp;' + resCnt.toString() + ' Residues</span>';
39860
+ htmlTmp += '</span>';
39861
+ htmlTmp += '<br>';
39862
+ html += htmlTmp;
39863
+ html2 += htmlTmp;
39864
+
39865
+ ++index;
39866
+ }
39867
+
39868
+ html += '</div>';
39869
+ html2 += '</div>';
39870
+ html3 += '</div>';
39871
+
39872
+ $("#" + ic.pre + "dt_ptm_" + chnid).html(html);
39873
+ $("#" + ic.pre + "ov_ptm_" + chnid).html(html2);
39874
+ $("#" + ic.pre + "tt_ptm_" + chnid).html(html3);
39875
+
39876
+ // add here after the ajax call
39877
+ ic.showAnnoCls.enableHlSeq();
39878
+ ic.bAjaxPTM = true;
39879
+ }
39880
+
39881
+ getNoPTM(chnid) { let ic = this.icn3d; ic.icn3dui;
39882
+ console.log( "No PTM data were found for the chain " + chnid + "..." );
39883
+
39884
+ $("#" + ic.pre + "dt_ptm_" + chnid).html('');
39885
+ $("#" + ic.pre + "ov_ptm_" + chnid).html('');
39886
+ $("#" + ic.pre + "tt_ptm_" + chnid).html('');
39887
+
39888
+ // add here after the ajax call
39889
+ ic.showAnnoCls.enableHlSeq();
39890
+ ic.bAjaxPTM = true;
39891
+ if(ic.deferredPTM !== undefined) ic.deferredPTM.resolve();
39892
+ }
39893
+ }
39894
+
39555
39895
  /**
39556
39896
  * @author Jiyao Wang <wangjiy@ncbi.nlm.nih.gov> / https://github.com/ncbi/icn3d
39557
39897
  */
@@ -40868,7 +41208,8 @@ class Annotation {
40868
41208
  this.setAnnoSeqBase(false);
40869
41209
  }
40870
41210
  setAnnoSeqBase(bShow) { let ic = this.icn3d; ic.icn3dui;
40871
- let itemArray = ['site', 'snp', 'clinvar', 'cdd', 'domain', 'interaction', 'ssbond', 'crosslink', 'transmem'];
41211
+ //let itemArray = ['site', 'ptm', 'snp', 'clinvar', 'cdd', 'domain', 'interaction', 'ssbond', 'crosslink', 'transmem'];
41212
+ let itemArray = ['cdd', 'clinvar', 'snp', 'site', 'ptm', 'ssbond', 'crosslink', 'transmem', 'domain', 'interaction'];
40872
41213
  for(let i in itemArray) {
40873
41214
  let item = itemArray[i];
40874
41215
  if(bShow) {
@@ -40880,7 +41221,8 @@ class Annotation {
40880
41221
  }
40881
41222
  }
40882
41223
  setAnnoTabBase(bChecked) { let ic = this.icn3d; ic.icn3dui;
40883
- let itemArray = ['all', 'binding', 'snp', 'clinvar', 'cdd', '3dd', 'interact', 'custom', 'ssbond', 'crosslink', 'transmem'];
41224
+ //let itemArray = ['all', 'binding', 'ptm', 'snp', 'clinvar', 'cdd', '3dd', 'interact', 'custom', 'ssbond', 'crosslink', 'transmem'];
41225
+ let itemArray = ['all', 'cdd', 'clinvar', 'snp', 'binding', 'ptm', 'ssbond', 'crosslink', 'transmem', '3dd', 'custom', 'interact'];
40884
41226
  for(let i in itemArray) {
40885
41227
  let item = itemArray[i];
40886
41228
  if($("#" + ic.pre + "anno_" + item).length) $("#" + ic.pre + "anno_" + item)[0].checked = bChecked;
@@ -40892,10 +41234,11 @@ class Annotation {
40892
41234
  this.updateClinvar();
40893
41235
  this.updateSnp();
40894
41236
  this.updateDomain();
40895
- this.updateInteraction();
41237
+ this.updatePTM();
40896
41238
  this.updateSsbond();
40897
41239
  this.updateCrosslink();
40898
41240
  this.updateTransmem();
41241
+ this.updateInteraction();
40899
41242
  }
40900
41243
  hideAnnoTabAll() { let ic = this.icn3d; ic.icn3dui;
40901
41244
  this.setAnnoTabBase(false);
@@ -40948,6 +41291,11 @@ class Annotation {
40948
41291
  ic.bInteractionShown = false;
40949
41292
  this.updateInteraction();
40950
41293
  }
41294
+ if($("#" + ic.pre + "anno_ptm").length && $("#" + ic.pre + "anno_ptm")[0].checked) {
41295
+ $("[id^=" + ic.pre + "ptm]").show();
41296
+ ic.bPTMShown = false;
41297
+ this.updatePTM();
41298
+ }
40951
41299
  if($("#" + ic.pre + "anno_custom").length && $("#" + ic.pre + "anno_custom")[0].checked) {
40952
41300
  $("[id^=" + ic.pre + "custom]").show();
40953
41301
  }
@@ -41029,6 +41377,15 @@ class Annotation {
41029
41377
  $("[id^=" + ic.pre + "interaction]").hide();
41030
41378
  if($("#" + ic.pre + "anno_interact").length) $("#" + ic.pre + "anno_interact")[0].checked = false;
41031
41379
  }
41380
+ setAnnoTabPTM() { let ic = this.icn3d; ic.icn3dui;
41381
+ $("[id^=" + ic.pre + "ptm]").show();
41382
+ if($("#" + ic.pre + "anno_ptm").length) $("#" + ic.pre + "anno_ptm")[0].checked = true;
41383
+ this.updatePTM();
41384
+ }
41385
+ hideAnnoTabPTM() { let ic = this.icn3d; ic.icn3dui;
41386
+ $("[id^=" + ic.pre + "ptm]").hide();
41387
+ if($("#" + ic.pre + "anno_ptm").length) $("#" + ic.pre + "anno_ptm")[0].checked = false;
41388
+ }
41032
41389
  setAnnoTabSsbond() { let ic = this.icn3d; ic.icn3dui;
41033
41390
  $("[id^=" + ic.pre + "ssbond]").show();
41034
41391
  if($("#" + ic.pre + "anno_ssbond").length) $("#" + ic.pre + "anno_ssbond")[0].checked = true;
@@ -41140,6 +41497,17 @@ class Annotation {
41140
41497
  }
41141
41498
  });
41142
41499
 
41500
+ me.myEventCls.onIds("#" + ic.pre + "anno_ptm", "click", function(e) {
41501
+ if($("#" + ic.pre + "anno_ptm")[0].checked) {
41502
+ thisClass.setAnnoTabPTM();
41503
+ me.htmlCls.clickMenuCls.setLogCmd("set annotation ptm", true);
41504
+ }
41505
+ else {
41506
+ thisClass.hideAnnoTabPTM();
41507
+ me.htmlCls.clickMenuCls.setLogCmd("hide annotation ptm", true);
41508
+ }
41509
+ });
41510
+
41143
41511
  //$("#" + ic.pre + "anno_custom", "click", function(e) {
41144
41512
  me.myEventCls.onIds("#" + ic.pre + "anno_custom", "click", function(e) {
41145
41513
  if($("#" + ic.pre + "anno_custom")[0].checked) {
@@ -41235,7 +41603,7 @@ class Annotation {
41235
41603
  }
41236
41604
  }
41237
41605
  setAnnoDisplay(display, prefix) { let ic = this.icn3d; ic.icn3dui;
41238
- let itemArray = ['giseq', 'custom', 'site', 'snp', 'clinvar', 'cdd', 'domain', 'interaction', 'ssbond', 'crosslink', 'transmem'];
41606
+ let itemArray = ['giseq', 'custom', 'site', 'ptm', 'snp', 'clinvar', 'cdd', 'domain', 'interaction', 'ssbond', 'crosslink', 'transmem'];
41239
41607
  for(let i in itemArray) {
41240
41608
  let item = itemArray[i];
41241
41609
  $("[id^=" + ic.pre + prefix + "_" + item + "]").attr('style', display);
@@ -41306,6 +41674,15 @@ class Annotation {
41306
41674
  }
41307
41675
  ic.bInteractionShown = true;
41308
41676
  }
41677
+ updatePTM() { let ic = this.icn3d; ic.icn3dui;
41678
+ if(ic.bPTMShown === undefined || !ic.bPTMShown) {
41679
+ for(let chainid in ic.PTMChainbase) {
41680
+ let chainidBase = ic.PTMChainbase[chainid];
41681
+ ic.annoPTMCls.showPTM(chainid, chainidBase);
41682
+ }
41683
+ }
41684
+ ic.bPTMShown = true;
41685
+ }
41309
41686
  updateSsbond() { let ic = this.icn3d; ic.icn3dui;
41310
41687
  if(ic.bSSbondShown === undefined || !ic.bSSbondShown) {
41311
41688
  for(let chainid in ic.ssbondChainbase) {
@@ -57595,7 +57972,7 @@ class SetMenu {
57595
57972
 
57596
57973
  html += "<ul class='icn3d-mn-item'>";
57597
57974
 
57598
- html += "<li><span style='padding-left:1.5em;'>Unicolor</span>";
57975
+ html += "<li><span style='padding-left:1.5em!important;'>Unicolor</span>";
57599
57976
  html += "<ul>";
57600
57977
 
57601
57978
  html += "<li><span>Red</span>";
@@ -57802,7 +58179,7 @@ class SetMenu {
57802
58179
 
57803
58180
  if(me.cfg.cid === undefined) {
57804
58181
  //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrRainbow', 'Rainbow (R-V)');
57805
- html += "<li><span style='padding-left:1.5em;'>Rainbow (R-V)</span>";
58182
+ html += "<li><span style='padding-left:1.5em!important;'>Rainbow (R-V)</span>";
57806
58183
  html += "<ul>";
57807
58184
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrRainbow', 'for Selection');
57808
58185
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrRainbowChain', 'for Chains');
@@ -57811,7 +58188,7 @@ class SetMenu {
57811
58188
 
57812
58189
  if(!me.cfg.simplemenu) {
57813
58190
  //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrum', 'Spectrum (V-R)');
57814
- html += "<li><span style='padding-left:1.5em;'>Spectrum (V-R)</span>";
58191
+ html += "<li><span style='padding-left:1.5em!important;'>Spectrum (V-R)</span>";
57815
58192
  html += "<ul>";
57816
58193
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrum', 'for Selection');
57817
58194
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrumChain', 'for Chains');
@@ -57819,7 +58196,7 @@ class SetMenu {
57819
58196
  html += "</ul>";
57820
58197
  }
57821
58198
 
57822
- html += "<li><span style='padding-left:1.5em;'>Secondary</span>";
58199
+ html += "<li><span style='padding-left:1.5em!important;'>Secondary</span>";
57823
58200
  html += "<ul>";
57824
58201
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSSGreen', 'Sheet in Green');
57825
58202
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSSYellow', 'Sheet in Yellow');
@@ -57834,13 +58211,13 @@ class SetMenu {
57834
58211
 
57835
58212
  //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrHydrophobic', 'Wimley-White<br><span style="padding-left:1.5em;">Hydrophobicity</span>');
57836
58213
 
57837
- html += "<li><span style='padding-left:1.5em;'>Hydrophobicity</span>";
58214
+ html += "<li><span style='padding-left:1.5em!important;'>Hydrophobicity</span>";
57838
58215
  html += "<ul>";
57839
58216
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrNormalizedHP', 'Normalized');
57840
58217
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrHydrophobic', 'Wimley-White');
57841
58218
  html += "</ul>";
57842
58219
 
57843
- html += "<li><span style='padding-left:1.5em;'>B-factor</span>";
58220
+ html += "<li><span style='padding-left:1.5em!important;'>B-factor</span>";
57844
58221
  html += "<ul>";
57845
58222
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrBfactor', 'Original');
57846
58223
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrBfactorNorm', 'Percentile');
@@ -57863,7 +58240,7 @@ class SetMenu {
57863
58240
 
57864
58241
  if(me.cfg.cid === undefined) {
57865
58242
  if(!me.cfg.simplemenu) {
57866
- html += "<li><span style='padding-left:1.5em;'>Defined Sets</span>";
58243
+ html += "<li><span style='padding-left:1.5em!important;'>Defined Sets</span>";
57867
58244
  html += "<ul>";
57868
58245
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrsets', 'Rainbow for Selected Sets<br>in "Analysis > Defined Sets"');
57869
58246
  html += "</ul>";
@@ -57872,7 +58249,7 @@ class SetMenu {
57872
58249
 
57873
58250
  //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrResidue', 'Residue');
57874
58251
 
57875
- html += "<li><span style='padding-left:1.5em;'>Residue</span>";
58252
+ html += "<li><span style='padding-left:1.5em!important;'>Residue</span>";
57876
58253
  html += "<ul>";
57877
58254
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrResidue', 'Default');
57878
58255
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrResidueCustom', 'Custom');
@@ -59934,10 +60311,17 @@ class SetDialog {
59934
60311
  html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_custom'>Custom" + me.htmlCls.space2 + "</span></td>";
59935
60312
  html += tmpStr2 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_3dd'>3D Domains" + me.htmlCls.space2 + "</span></td>";
59936
60313
  html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_snp'>SNPs" + me.htmlCls.space2 + "</span></td>";
59937
- html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_interact'>Interactions" + me.htmlCls.space2 + "</span></td>";
60314
+
60315
+ // if(me.cfg.mmdbid != undefined || me.cfg.pdbid != undefined || me.cfg.mmtfid != undefined || me.cfg.mmcifid != undefined) { // PDB
60316
+ // html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_ptm' disabled>PTM (UniProt)" + me.htmlCls.space2 + "</span></td>";
60317
+ // }
60318
+ // else {
60319
+ html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_ptm'>PTM (UniProt)" + me.htmlCls.space2 + "</span></td>";
60320
+ // }
59938
60321
  html += "<td></td>";
59939
60322
  html += "</tr><tr>";
59940
60323
  html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_ssbond'>Disulfide Bonds" + me.htmlCls.space2 + "</span></td>";
60324
+ html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_interact'>Interactions" + me.htmlCls.space2 + "</span></td>";
59941
60325
  html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_crosslink'>Cross-Linkages" + me.htmlCls.space2 + "</span></td>";
59942
60326
  if(me.cfg.opmid !== undefined) {
59943
60327
  html += "<td style='min-width:110px;'><span id='" + me.pre + "anno_transmemli' style='white-space:nowrap'>" + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_transmem'>Transmembrane" + me.htmlCls.space2 + "</span></td>";
@@ -60314,10 +60698,7 @@ class Events {
60314
60698
  ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
60315
60699
  }
60316
60700
 
60317
- // save the current selection
60318
- //ic.selectionCls.saveSelectionPrep();
60319
- //let name = 'realignSetsByStruct';
60320
- //ic.selectionCls.saveSelection(name, name);
60701
+ me.cfg.aligntool = 'vast';
60321
60702
 
60322
60703
  ic.realignParserCls.realignOnStructAlign();
60323
60704
  if(nameArray.length > 0) {
@@ -66779,6 +67160,7 @@ class iCn3D {
66779
67160
 
66780
67161
  this.annoCddSiteCls = new AnnoCddSite(this);
66781
67162
  this.annoContactCls = new AnnoContact(this);
67163
+ this.annoPTMCls = new AnnoPTM(this);
66782
67164
  this.annoCrossLinkCls = new AnnoCrossLink(this);
66783
67165
  this.annoDomainCls = new AnnoDomain(this);
66784
67166
  this.annoSnpClinVarCls = new AnnoSnpClinVar(this);
@@ -67043,7 +67425,7 @@ class iCn3DUI {
67043
67425
  //even when multiple iCn3D viewers are shown together.
67044
67426
  this.pre = this.cfg.divid + "_";
67045
67427
 
67046
- this.REVISION = '3.13.2';
67428
+ this.REVISION = '3.14.0';
67047
67429
 
67048
67430
  // In nodejs, iCn3D defines "window = {navigator: {}}"
67049
67431
  this.bNode = (Object.keys(window).length < 2) ? true : false;