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.js CHANGED
@@ -27574,6 +27574,24 @@ class LoadScript {
27574
27574
 
27575
27575
  return;
27576
27576
  }
27577
+ else if(ic.commands[i].trim().indexOf('set annotation ptm') == 0 ) { // the command may have "|||{"factor"...
27578
+ let strArray = ic.commands[i].split("|||");
27579
+
27580
+ if(Object.keys(ic.proteins).length > 0 &&(ic.bAjaxPTM === undefined || !ic.bAjaxPTM) ) {
27581
+ $.when(thisClass.applyCommandPTM(strArray[0].trim())).then(function() {
27582
+ thisClass.execCommandsBase(i + 1, end, steps);
27583
+ });
27584
+ }
27585
+ else {
27586
+ if(Object.keys(ic.proteins).length > 0) {
27587
+ thisClass.applyCommandPTM(strArray[0].trim());
27588
+ }
27589
+
27590
+ this.execCommandsBase(i + 1, end, steps);
27591
+ }
27592
+
27593
+ return;
27594
+ }
27577
27595
  else if(ic.commands[i].trim().indexOf('set annotation 3ddomain') == 0) { // the command may have "|||{"factor"...
27578
27596
  let strArray = ic.commands[i].split("|||");
27579
27597
 
@@ -27804,6 +27822,8 @@ class LoadScript {
27804
27822
  ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
27805
27823
  }
27806
27824
 
27825
+ me.cfg.aligntool = 'vast';
27826
+
27807
27827
  $.when(thisClass.applyCommandRealignByStruct(command)).then(function() {
27808
27828
  thisClass.execCommandsBase(i + 1, end, steps);
27809
27829
  });
@@ -27964,6 +27984,9 @@ class LoadScript {
27964
27984
  else if(lastCommand.indexOf('set annotation snp') == 0) {
27965
27985
  thisClass.applyCommandSnp(lastCommand);
27966
27986
  }
27987
+ else if(lastCommand.indexOf('set annotation ptm') == 0) {
27988
+ thisClass.applyCommandPTM(lastCommand);
27989
+ }
27967
27990
  else if(lastCommand.indexOf('set annotation 3ddomain') == 0) {
27968
27991
  thisClass.applyCommand3ddomain(lastCommand);
27969
27992
  }
@@ -28014,6 +28037,9 @@ class LoadScript {
28014
28037
  let nameArray = paraArray[1].split(',');
28015
28038
  ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
28016
28039
  }
28040
+
28041
+ me.cfg.aligntool = 'vast';
28042
+
28017
28043
  thisClass.applyCommandRealignByStruct(lastCommand);
28018
28044
  }
28019
28045
  else if(lastCommand.indexOf('realign on tmalign') == 0) {
@@ -28419,6 +28445,25 @@ class LoadScript {
28419
28445
  return ic.deferredSnp.promise();
28420
28446
  }
28421
28447
 
28448
+ applyCommandPTMBase(command) { let ic = this.icn3d; ic.icn3dui;
28449
+ // chain functions together
28450
+ let pos = command.lastIndexOf(' '); // set annotation clinvar
28451
+ command.substr(pos + 1);
28452
+
28453
+ ic.annotationCls.setAnnoTabPTM();
28454
+ }
28455
+
28456
+ applyCommandPTM(command) { let ic = this.icn3d; ic.icn3dui;
28457
+ let thisClass = this;
28458
+
28459
+ // chain functions together
28460
+ ic.deferredPTM = $.Deferred(function() {
28461
+ thisClass.applyCommandPTMBase(command);
28462
+ }); // end of me.deferred = $.Deferred(function() {
28463
+
28464
+ return ic.deferredPTM.promise();
28465
+ }
28466
+
28422
28467
  applyCommand3ddomainBase(command) { let ic = this.icn3d; ic.icn3dui;
28423
28468
  // chain functions together
28424
28469
  let pos = command.lastIndexOf(' ');
@@ -29960,7 +30005,8 @@ class ShowSeq {
29960
30005
  if(seqLength > ic.maxAnnoLength) {
29961
30006
  ic.maxAnnoLength = seqLength;
29962
30007
  }
29963
- let itemArray = ['giseq', 'cddsite', 'clinvar', 'snp', 'domain', 'interaction', 'custom', 'ssbond', 'crosslink', 'transmem'];
30008
+ //let itemArray = ['giseq', 'cddsite', 'ptm', 'clinvar', 'snp', 'domain', 'interaction', 'custom', 'ssbond', 'crosslink', 'transmem'];
30009
+ let itemArray = ['giseq', 'cddsite', 'clinvar', 'snp', 'ptm', 'ssbond', 'crosslink', 'transmem', 'domain', 'custom', 'interaction'];
29964
30010
  for(let i in itemArray) {
29965
30011
  let item = itemArray[i];
29966
30012
  if($("#" + ic.pre + item + "_" + chnid).length) $("#" + ic.pre + item + "_" + chnid).width(divLength);
@@ -32922,6 +32968,9 @@ class ApplyCommand {
32922
32968
  else if(command == 'set annotation interaction') {
32923
32969
  ic.annotationCls.setAnnoTabInteraction();
32924
32970
  }
32971
+ else if(command == 'set annotation ptm') {
32972
+ ic.annotationCls.setAnnoTabPTM();
32973
+ }
32925
32974
  else if(command == 'set annotation cdd') {
32926
32975
  ic.annotationCls.setAnnoTabCdd();
32927
32976
  }
@@ -32968,6 +33017,9 @@ class ApplyCommand {
32968
33017
  else if(type == 'site') {
32969
33018
  ic.annotationCls.hideAnnoTabSite();
32970
33019
  }
33020
+ else if(type == 'ptm') {
33021
+ ic.annotationCls.hideAnnoTabPTM();
33022
+ }
32971
33023
  else if(type == 'interaction') {
32972
33024
  ic.annotationCls.hideAnnoTabInteraction();
32973
33025
  }
@@ -34166,6 +34218,7 @@ class ApplyCommand {
34166
34218
  else if(cmd== 'set view overview') return seqAnnoStr + ': "Summary" tab';
34167
34219
  else if(cmd == 'set annotation custom') return seqAnnoStr + ': "Custom" checkbox';
34168
34220
  else if(cmd == 'set annotation interaction') return seqAnnoStr + ': "Interactions" checkbox';
34221
+ else if(cmd == 'set annotation ptm') return seqAnnoStr + ': "PTM" checkbox';
34169
34222
  else if(cmd == 'set annotation cdd') return seqAnnoStr + ': "Conserved Domains" checkbox';
34170
34223
  else if(cmd == 'set annotation site') return seqAnnoStr + ': "Functional Sites" checkbox';
34171
34224
  else if(cmd == 'set annotation ssbond') return seqAnnoStr + ': "Disulfide Bonds" checkbox';
@@ -35468,7 +35521,8 @@ class SetSeqAlign {
35468
35521
  if(i > 0) {
35469
35522
  let index1 = alignIndex;
35470
35523
  for(let j = prevIndex1 + 1, jl = start1; j < jl; ++j) {
35471
- if(ic.chainsSeq[chainid1] === undefined) break;
35524
+ if(ic.chainsSeq[chainid1] === undefined || ic.chainsSeq[chainid1][j] === undefined) break;
35525
+
35472
35526
  let resi = ic.chainsSeq[chainid1][j].resi;
35473
35527
  let resn = ic.chainsSeq[chainid1][j].name.toLowerCase();
35474
35528
 
@@ -35482,7 +35536,8 @@ class SetSeqAlign {
35482
35536
 
35483
35537
  let index2 = alignIndex;
35484
35538
  for(let j = prevIndex2 + 1, jl = start2; j < jl; ++j) {
35485
- if(ic.chainsSeq[chainid2] === undefined) break;
35539
+ if(ic.chainsSeq[chainid2] === undefined || ic.chainsSeq[chainid2] === undefined) break;
35540
+
35486
35541
  let resi = ic.chainsSeq[chainid2][j].resi;
35487
35542
  let resn = ic.chainsSeq[chainid2][j].name.toLowerCase();
35488
35543
 
@@ -37432,8 +37487,8 @@ class HlSeq {
37432
37487
  if(me.bNode) return;
37433
37488
 
37434
37489
  let thisClass = this;
37435
- $("#" + 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]")
37436
- .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]")
37490
+ $("#" + 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]")
37491
+ .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]")
37437
37492
  .selectable({
37438
37493
  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.
37439
37494
  stop: function() { let ic = thisClass.icn3d;
@@ -37486,11 +37541,11 @@ class HlSeq {
37486
37541
  }
37487
37542
  });
37488
37543
 
37489
- $("[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]")
37490
- .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]")
37544
+ $("[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]")
37545
+ .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]")
37491
37546
 
37492
- .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]")
37493
- .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]")
37547
+ .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]")
37548
+ .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]")
37494
37549
 
37495
37550
  .on('click', '.icn3d-seqTitle', function(e) { let ic = thisClass.icn3d;
37496
37551
  e.stopImmediatePropagation();
@@ -37531,7 +37586,7 @@ class HlSeq {
37531
37586
 
37532
37587
  let thisClass = this;
37533
37588
 
37534
- $("#" + 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;
37589
+ $("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "giseq]").add("[id^=" + ic.pre + "custom]").add("[id^=" + ic.pre + "site]").add("[id^=" + ic.pre + "ptm]").add("[id^=" + ic.pre + "clinvar]").add("[id^=" + ic.pre + "snp]").add("[id^=" + ic.pre + "cdd]").add("[id^=" + ic.pre + "domain]").add("[id^=" + ic.pre + "interaction]").add("[id^=" + ic.pre + "ssbond]").add("[id^=" + ic.pre + "crosslink]").add("[id^=" + ic.pre + "transmem]").on('click', '.icn3d-residue', function(e) { let ic = thisClass.icn3d;
37535
37590
  e.stopImmediatePropagation();
37536
37591
  /*
37537
37592
  //if($(this).attr('id') === ic.pre + "dl_sequence2") {
@@ -37580,7 +37635,7 @@ class HlSeq {
37580
37635
 
37581
37636
  let thisClass = this;
37582
37637
 
37583
- $("#" + 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;
37638
+ $("#" + 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;
37584
37639
  e.stopImmediatePropagation();
37585
37640
 
37586
37641
  //if($(this).attr('id') === ic.pre + "dl_sequence2") {
@@ -37777,7 +37832,7 @@ class HlSeq {
37777
37832
  let residueid;
37778
37833
  let structure = chainid.substr(0, chainid.indexOf('_'));
37779
37834
  for(let i = 0, il = posArray.length; i < il; ++i) {
37780
- if($(that).attr('site') !== undefined) {
37835
+ if($(that).attr('site') !== undefined || $(that).attr('ptm') !== undefined) {
37781
37836
  if(ic.bNCBI) {
37782
37837
  let residNCBI = chainid + '_' +(parseInt(posArray[i])+1).toString();
37783
37838
  // AlphaFold domains calculated on-the-fly have no conversion
@@ -38179,6 +38234,8 @@ class ShowAnno {
38179
38234
  ++i;
38180
38235
  }
38181
38236
  ic.interactChainbase = me.hashUtilsCls.unionHash(ic.interactChainbase, chemical_chainid);
38237
+ ic.PTMChainbase = me.hashUtilsCls.unionHash(ic.PTMChainbase, ic.protein_chainid);
38238
+
38182
38239
  ic.ssbondChainbase = me.hashUtilsCls.unionHash(ic.ssbondChainbase, ic.protein_chainid);
38183
38240
  ic.ssbondChainbase = me.hashUtilsCls.unionHash(ic.ssbondChainbase, chemical_chainid);
38184
38241
  ic.crosslinkChainbase = me.hashUtilsCls.unionHash(ic.crosslinkChainbase, ic.protein_chainid);
@@ -38210,8 +38267,10 @@ class ShowAnno {
38210
38267
  //if(proteinName.length > 40) proteinName = proteinName.substr(0, 40) + "...";
38211
38268
  let categoryStr =(index == 0) ? "<span class='icn3d-annoLargeTitle'><b>Proteins</b>: </span><br><br>" : "";
38212
38269
  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>)" : '';
38270
+ let structure = chnid.substr(0, chnid.indexOf('_'));
38271
+ let chainLink = (structure.length > 5) ? '<a href="https://alphafold.ebi.ac.uk/entry/' + structure + '" target="_blank">' + chnid + '</a>' : chnid;
38213
38272
  let chainHtml = "<div id='" + ic.pre + "anno_" + chnid + "' class='icn3d-annotation'>" + categoryStr
38214
- + "<span style='font-weight:bold;'>Annotations of " + chnid
38273
+ + "<span style='font-weight:bold;'>Annotations of " + chainLink
38215
38274
  + "</span>: <a class='icn3d-blue' href='https://www.ncbi.nlm.nih.gov/protein?term="
38216
38275
  + chnid + "' target='_blank' title='" + fullProteinName + "'>" + proteinName + "</a>"
38217
38276
  + geneLink + "&nbsp;&nbsp;&nbsp;"
@@ -38224,7 +38283,8 @@ class ShowAnno {
38224
38283
  + 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;"
38225
38284
  + 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);
38226
38285
  $("#" + ic.pre + "dl_annotations").append(chainHtml);
38227
- let itemArray = ['giseq', 'cdd', 'clinvar', 'snp', 'domain', 'site', 'interaction', 'custom', 'ssbond', 'crosslink', 'transmem'];
38286
+ //let itemArray = ['giseq', 'cdd', 'clinvar', 'snp', 'domain', 'site', 'ptm', 'interaction', 'custom', 'ssbond', 'crosslink', 'transmem'];
38287
+ let itemArray = ['giseq', 'cdd', 'clinvar', 'snp', 'site', 'ptm', 'ssbond', 'crosslink', 'transmem', 'domain', 'custom', 'interaction'];
38228
38288
  // dt: detailed view, hide by default; ov: overview, show by default
38229
38289
  for(let i in itemArray) {
38230
38290
  let item = itemArray[i];
@@ -38652,6 +38712,286 @@ class ShowAnno {
38652
38712
 
38653
38713
  }
38654
38714
 
38715
+ /**
38716
+ * @author Jiyao Wang <wangjiy@ncbi.nlm.nih.gov> / https://github.com/ncbi/icn3d
38717
+ */
38718
+
38719
+ class AnnoPTM {
38720
+ constructor(icn3d) {
38721
+ this.icn3d = icn3d;
38722
+ }
38723
+
38724
+ //Show the annotations of CDD domains and binding sites.
38725
+ showPTM(chnid, chnidBase) { let ic = this.icn3d; ic.icn3dui;
38726
+ let thisClass = this;
38727
+
38728
+ // UniProt ID
38729
+ let structure = chnid.substr(0, chnid.indexOf('_'));
38730
+ let chain = chnid.substr(chnid.indexOf('_') + 1);
38731
+
38732
+ // UniProt ID
38733
+ if( structure.length > 5 ) {
38734
+ let url = "https://www.ebi.ac.uk/proteins/api/features/" + structure;
38735
+ $.ajax({
38736
+ url: url,
38737
+ dataType: 'json',
38738
+ cache: true,
38739
+ tryCount : 0,
38740
+ retryLimit : 0, //1
38741
+ success: function(data) {
38742
+ thisClass.parsePTM(data, chnid);
38743
+ if(ic.deferredPTM !== undefined) ic.deferredPTM.resolve();
38744
+ },
38745
+ error : function(xhr, textStatus, errorThrown ) {
38746
+ this.tryCount++;
38747
+ if(this.tryCount <= this.retryLimit) {
38748
+ //try again
38749
+ $.ajax(this);
38750
+ return;
38751
+ }
38752
+
38753
+ thisClass.getNoPTM(chnid);
38754
+
38755
+ return;
38756
+ }
38757
+ });
38758
+ }
38759
+ else { // PDB
38760
+ // get PDB to UniProt mapping
38761
+ // https://www.ebi.ac.uk/pdbe/api/doc/
38762
+ let structLower = structure.substr(0, 4).toLowerCase();
38763
+ let urlMap = "https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/" + structLower;
38764
+
38765
+ $.ajax({
38766
+ url: urlMap,
38767
+ dataType: 'json',
38768
+ cache: true,
38769
+ success: function(dataMap) {
38770
+ let UniProtID = '';
38771
+ if(!ic.UPResi2ResiPosPerChain) ic.UPResi2ResiPosPerChain = {};
38772
+ ic.UPResi2ResiPosPerChain[chnid] = {};
38773
+ let mapping = dataMap[structLower].UniProt;
38774
+
38775
+ let bFound = false;
38776
+ for(let up in mapping) {
38777
+ let chainArray = mapping[up].mappings;
38778
+ if(bFound) break;
38779
+
38780
+ for(let i = 0, il = chainArray.length; i < il; ++i) {
38781
+ //"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"
38782
+ let chainObj = chainArray[i];
38783
+ if(chainObj.chain_id == chain) {
38784
+ let start = chainObj.unp_start;
38785
+ let end = chainObj.unp_end;
38786
+ let posStart = chainObj.start.residue_number;
38787
+ let posEnd = chainObj.end.residue_number;
38788
+
38789
+ if(posEnd - posStart != end - start) {
38790
+ console.log("There might be some issues in the PDB to UniProt residue mapping.");
38791
+ }
38792
+
38793
+ for(let j = 0; j <= end - start; ++j) {
38794
+ ic.UPResi2ResiPosPerChain[chnid][j + start] = j + posStart - 1; // 0-based
38795
+ }
38796
+
38797
+ UniProtID = up;
38798
+ bFound = true;
38799
+ break;
38800
+ }
38801
+ }
38802
+ }
38803
+
38804
+ if(UniProtID == '') {
38805
+ thisClass.getNoPTM(chnid);
38806
+ }
38807
+ else {
38808
+ let url = "https://www.ebi.ac.uk/proteins/api/features/" + UniProtID;
38809
+ $.ajax({
38810
+ url: url,
38811
+ dataType: 'json',
38812
+ cache: true,
38813
+ tryCount : 0,
38814
+ retryLimit : 0, //1
38815
+ success: function(data) {
38816
+ thisClass.parsePTM(data, chnid);
38817
+ if(ic.deferredPTM !== undefined) ic.deferredPTM.resolve();
38818
+ },
38819
+ error : function(xhr, textStatus, errorThrown ) {
38820
+ this.tryCount++;
38821
+ if(this.tryCount <= this.retryLimit) {
38822
+ //try again
38823
+ $.ajax(this);
38824
+ return;
38825
+ }
38826
+
38827
+ thisClass.getNoPTM(chnid);
38828
+
38829
+ return;
38830
+ }
38831
+ });
38832
+ }
38833
+ },
38834
+ error : function(xhr, textStatus, errorThrown ) {
38835
+ thisClass.getNoPTM(chnid);
38836
+ }
38837
+ });
38838
+ }
38839
+ }
38840
+
38841
+ parsePTM(data, chnid) { let ic = this.icn3d, me = ic.icn3dui;
38842
+
38843
+ if(me.bNode) {
38844
+ //if(!ic.resid2ptm) ic.resid2ptm = {};
38845
+ ic.resid2ptm = {};
38846
+ ic.resid2ptm[chnid] = [];
38847
+ }
38848
+
38849
+ let ptmHash = {};
38850
+ for(let i = 0, il = data.features.length; i < il; ++i) {
38851
+ let feature = data.features[i];
38852
+
38853
+ if(feature.category == 'PTM' && feature.type != 'DISULFID' && feature.type != 'CROSSLNK') {
38854
+ let title = '';
38855
+ if(feature.type == 'CARBOHYD') {
38856
+ //title = 'Glycosylation, ' + feature.description;
38857
+ title = 'Glycosylation';
38858
+ }
38859
+ else if(feature.type == 'LIPID') {
38860
+ title = 'Lipidation, ' + feature.description;
38861
+ }
38862
+ else if(feature.description.indexOf('Phospho') == 0) {
38863
+ title = 'Phosphorylation';
38864
+ }
38865
+ else if(feature.description) {
38866
+ title = feature.description;
38867
+ }
38868
+ else {
38869
+ title = feature.type;
38870
+ }
38871
+
38872
+ if(!ptmHash[title]) ptmHash[title] = [];
38873
+ ptmHash[title].push(feature);
38874
+ }
38875
+ }
38876
+
38877
+ let index = 0;
38878
+ let html = '', html2 = '', html3 = '';
38879
+ html += '<div id="' + ic.pre + chnid + '_ptmseq_sequence" class="icn3d-cdd icn3d-dl_sequence">';
38880
+ html2 += html;
38881
+ html3 += html;
38882
+ let stucture = chnid.substr(0, chnid.indexOf('_'));
38883
+
38884
+ for(let ptm in ptmHash) {
38885
+ let ptmArray = ptmHash[ptm];
38886
+ //"type": "MOD_RES", "category": "PTM", "description": "4-hydroxyproline", "begin": "382", "end": "382",
38887
+ let resPosArray = [];
38888
+ let bCoordinates = false;
38889
+ for(let i = 0, il = ptmArray.length; i < il; ++i) {
38890
+ let begin = parseInt(ptmArray[i].begin);
38891
+ let end = parseInt(ptmArray[i].end);
38892
+
38893
+
38894
+ for(let j = begin; j <= end; ++j) {
38895
+ if(stucture.length > 5) { // UniProt
38896
+ resPosArray.push(j - 1); // 0-based
38897
+ }
38898
+ else { // PDB
38899
+ if(ic.UPResi2ResiPosPerChain[chnid][j]) resPosArray.push(ic.UPResi2ResiPosPerChain[chnid][j]);
38900
+ }
38901
+
38902
+ if(!bCoordinates && ic.residues.hasOwnProperty(chnid + '_' + j)) {
38903
+ bCoordinates = true;
38904
+ }
38905
+ }
38906
+ }
38907
+
38908
+ if(resPosArray.length == 0) continue;
38909
+
38910
+ let resCnt = resPosArray.length;
38911
+ let title = 'PTM: ' + ptm;
38912
+ if(title.length > 17) title = title.substr(0, 17) + '...';
38913
+ let fulltitle = ptm;
38914
+
38915
+ let linkStr = (bCoordinates) ? 'icn3d-link icn3d-blue' : '';
38916
+
38917
+ 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>';
38918
+ let htmlTmp3 = '<span class="icn3d-residueNum" title="residue count">' + resCnt.toString() + ' Res</span>';
38919
+ let htmlTmp = '<span class="icn3d-seqLine">';
38920
+ html3 += htmlTmp2 + htmlTmp3 + '<br>';
38921
+ html += htmlTmp2 + htmlTmp3 + htmlTmp;
38922
+ html2 += htmlTmp2 + htmlTmp3 + htmlTmp;
38923
+ let pre = 'ptm' + index.toString();
38924
+ //var widthPerRes = ic.seqAnnWidth / ic.maxAnnoLength;
38925
+ let prevEmptyWidth = 0;
38926
+ let prevLineWidth = 0;
38927
+ let widthPerRes = 1;
38928
+ for(let i = 0, il = ic.giSeq[chnid].length; i < il; ++i) {
38929
+ html += ic.showSeqCls.insertGap(chnid, i, '-');
38930
+ if(resPosArray.indexOf(i) != -1) {
38931
+ let cFull = ic.giSeq[chnid][i];
38932
+ let c = cFull;
38933
+ if(cFull.length > 1) {
38934
+ c = cFull[0] + '..';
38935
+ }
38936
+ let pos = ic.annoCddSiteCls.getAdjustedResi(i, chnid, ic.matchedPos, ic.chainsSeq, ic.baseResi);
38937
+
38938
+ html += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" title="' + c + pos + '" class="icn3d-residue">' + cFull + '</span>';
38939
+ if(me.bNode) {
38940
+ let obj = {};
38941
+ obj[chnid + '_' + pos] = 'PTM: ' + ptm;
38942
+ ic.resid2ptm[chnid].push(obj);
38943
+ }
38944
+
38945
+ html2 += ic.showSeqCls.insertGapOverview(chnid, i);
38946
+ 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);
38947
+ //if(emptyWidth < 0) emptyWidth = 0;
38948
+ if(emptyWidth >= 0) {
38949
+ html2 += '<div style="display:inline-block; width:' + emptyWidth + 'px;">&nbsp;</div>';
38950
+ html2 += '<div style="display:inline-block; background-color:#000; width:' + widthPerRes + 'px;" title="' + c + pos + '">&nbsp;</div>';
38951
+ prevEmptyWidth += emptyWidth;
38952
+ prevLineWidth += widthPerRes;
38953
+ }
38954
+ }
38955
+ else {
38956
+ html += '<span>-</span>'; //'<span>-</span>';
38957
+ }
38958
+ }
38959
+ htmlTmp = '<span class="icn3d-residueNum" title="residue count">&nbsp;' + resCnt.toString() + ' Residues</span>';
38960
+ htmlTmp += '</span>';
38961
+ htmlTmp += '<br>';
38962
+ html += htmlTmp;
38963
+ html2 += htmlTmp;
38964
+
38965
+ ++index;
38966
+ }
38967
+
38968
+ html += '</div>';
38969
+ html2 += '</div>';
38970
+ html3 += '</div>';
38971
+
38972
+ $("#" + ic.pre + "dt_ptm_" + chnid).html(html);
38973
+ $("#" + ic.pre + "ov_ptm_" + chnid).html(html2);
38974
+ $("#" + ic.pre + "tt_ptm_" + chnid).html(html3);
38975
+
38976
+ // add here after the ajax call
38977
+ ic.showAnnoCls.enableHlSeq();
38978
+ ic.bAjaxPTM = true;
38979
+ }
38980
+
38981
+ getNoPTM(chnid) { let ic = this.icn3d; ic.icn3dui;
38982
+ console.log( "No PTM data were found for the chain " + chnid + "..." );
38983
+
38984
+ $("#" + ic.pre + "dt_ptm_" + chnid).html('');
38985
+ $("#" + ic.pre + "ov_ptm_" + chnid).html('');
38986
+ $("#" + ic.pre + "tt_ptm_" + chnid).html('');
38987
+
38988
+ // add here after the ajax call
38989
+ ic.showAnnoCls.enableHlSeq();
38990
+ ic.bAjaxPTM = true;
38991
+ if(ic.deferredPTM !== undefined) ic.deferredPTM.resolve();
38992
+ }
38993
+ }
38994
+
38655
38995
  /**
38656
38996
  * @author Jiyao Wang <wangjiy@ncbi.nlm.nih.gov> / https://github.com/ncbi/icn3d
38657
38997
  */
@@ -39968,7 +40308,8 @@ class Annotation {
39968
40308
  this.setAnnoSeqBase(false);
39969
40309
  }
39970
40310
  setAnnoSeqBase(bShow) { let ic = this.icn3d; ic.icn3dui;
39971
- let itemArray = ['site', 'snp', 'clinvar', 'cdd', 'domain', 'interaction', 'ssbond', 'crosslink', 'transmem'];
40311
+ //let itemArray = ['site', 'ptm', 'snp', 'clinvar', 'cdd', 'domain', 'interaction', 'ssbond', 'crosslink', 'transmem'];
40312
+ let itemArray = ['cdd', 'clinvar', 'snp', 'site', 'ptm', 'ssbond', 'crosslink', 'transmem', 'domain', 'interaction'];
39972
40313
  for(let i in itemArray) {
39973
40314
  let item = itemArray[i];
39974
40315
  if(bShow) {
@@ -39980,7 +40321,8 @@ class Annotation {
39980
40321
  }
39981
40322
  }
39982
40323
  setAnnoTabBase(bChecked) { let ic = this.icn3d; ic.icn3dui;
39983
- let itemArray = ['all', 'binding', 'snp', 'clinvar', 'cdd', '3dd', 'interact', 'custom', 'ssbond', 'crosslink', 'transmem'];
40324
+ //let itemArray = ['all', 'binding', 'ptm', 'snp', 'clinvar', 'cdd', '3dd', 'interact', 'custom', 'ssbond', 'crosslink', 'transmem'];
40325
+ let itemArray = ['all', 'cdd', 'clinvar', 'snp', 'binding', 'ptm', 'ssbond', 'crosslink', 'transmem', '3dd', 'custom', 'interact'];
39984
40326
  for(let i in itemArray) {
39985
40327
  let item = itemArray[i];
39986
40328
  if($("#" + ic.pre + "anno_" + item).length) $("#" + ic.pre + "anno_" + item)[0].checked = bChecked;
@@ -39992,10 +40334,11 @@ class Annotation {
39992
40334
  this.updateClinvar();
39993
40335
  this.updateSnp();
39994
40336
  this.updateDomain();
39995
- this.updateInteraction();
40337
+ this.updatePTM();
39996
40338
  this.updateSsbond();
39997
40339
  this.updateCrosslink();
39998
40340
  this.updateTransmem();
40341
+ this.updateInteraction();
39999
40342
  }
40000
40343
  hideAnnoTabAll() { let ic = this.icn3d; ic.icn3dui;
40001
40344
  this.setAnnoTabBase(false);
@@ -40048,6 +40391,11 @@ class Annotation {
40048
40391
  ic.bInteractionShown = false;
40049
40392
  this.updateInteraction();
40050
40393
  }
40394
+ if($("#" + ic.pre + "anno_ptm").length && $("#" + ic.pre + "anno_ptm")[0].checked) {
40395
+ $("[id^=" + ic.pre + "ptm]").show();
40396
+ ic.bPTMShown = false;
40397
+ this.updatePTM();
40398
+ }
40051
40399
  if($("#" + ic.pre + "anno_custom").length && $("#" + ic.pre + "anno_custom")[0].checked) {
40052
40400
  $("[id^=" + ic.pre + "custom]").show();
40053
40401
  }
@@ -40129,6 +40477,15 @@ class Annotation {
40129
40477
  $("[id^=" + ic.pre + "interaction]").hide();
40130
40478
  if($("#" + ic.pre + "anno_interact").length) $("#" + ic.pre + "anno_interact")[0].checked = false;
40131
40479
  }
40480
+ setAnnoTabPTM() { let ic = this.icn3d; ic.icn3dui;
40481
+ $("[id^=" + ic.pre + "ptm]").show();
40482
+ if($("#" + ic.pre + "anno_ptm").length) $("#" + ic.pre + "anno_ptm")[0].checked = true;
40483
+ this.updatePTM();
40484
+ }
40485
+ hideAnnoTabPTM() { let ic = this.icn3d; ic.icn3dui;
40486
+ $("[id^=" + ic.pre + "ptm]").hide();
40487
+ if($("#" + ic.pre + "anno_ptm").length) $("#" + ic.pre + "anno_ptm")[0].checked = false;
40488
+ }
40132
40489
  setAnnoTabSsbond() { let ic = this.icn3d; ic.icn3dui;
40133
40490
  $("[id^=" + ic.pre + "ssbond]").show();
40134
40491
  if($("#" + ic.pre + "anno_ssbond").length) $("#" + ic.pre + "anno_ssbond")[0].checked = true;
@@ -40240,6 +40597,17 @@ class Annotation {
40240
40597
  }
40241
40598
  });
40242
40599
 
40600
+ me.myEventCls.onIds("#" + ic.pre + "anno_ptm", "click", function(e) {
40601
+ if($("#" + ic.pre + "anno_ptm")[0].checked) {
40602
+ thisClass.setAnnoTabPTM();
40603
+ me.htmlCls.clickMenuCls.setLogCmd("set annotation ptm", true);
40604
+ }
40605
+ else {
40606
+ thisClass.hideAnnoTabPTM();
40607
+ me.htmlCls.clickMenuCls.setLogCmd("hide annotation ptm", true);
40608
+ }
40609
+ });
40610
+
40243
40611
  //$("#" + ic.pre + "anno_custom", "click", function(e) {
40244
40612
  me.myEventCls.onIds("#" + ic.pre + "anno_custom", "click", function(e) {
40245
40613
  if($("#" + ic.pre + "anno_custom")[0].checked) {
@@ -40335,7 +40703,7 @@ class Annotation {
40335
40703
  }
40336
40704
  }
40337
40705
  setAnnoDisplay(display, prefix) { let ic = this.icn3d; ic.icn3dui;
40338
- let itemArray = ['giseq', 'custom', 'site', 'snp', 'clinvar', 'cdd', 'domain', 'interaction', 'ssbond', 'crosslink', 'transmem'];
40706
+ let itemArray = ['giseq', 'custom', 'site', 'ptm', 'snp', 'clinvar', 'cdd', 'domain', 'interaction', 'ssbond', 'crosslink', 'transmem'];
40339
40707
  for(let i in itemArray) {
40340
40708
  let item = itemArray[i];
40341
40709
  $("[id^=" + ic.pre + prefix + "_" + item + "]").attr('style', display);
@@ -40406,6 +40774,15 @@ class Annotation {
40406
40774
  }
40407
40775
  ic.bInteractionShown = true;
40408
40776
  }
40777
+ updatePTM() { let ic = this.icn3d; ic.icn3dui;
40778
+ if(ic.bPTMShown === undefined || !ic.bPTMShown) {
40779
+ for(let chainid in ic.PTMChainbase) {
40780
+ let chainidBase = ic.PTMChainbase[chainid];
40781
+ ic.annoPTMCls.showPTM(chainid, chainidBase);
40782
+ }
40783
+ }
40784
+ ic.bPTMShown = true;
40785
+ }
40409
40786
  updateSsbond() { let ic = this.icn3d; ic.icn3dui;
40410
40787
  if(ic.bSSbondShown === undefined || !ic.bSSbondShown) {
40411
40788
  for(let chainid in ic.ssbondChainbase) {
@@ -56695,7 +57072,7 @@ class SetMenu {
56695
57072
 
56696
57073
  html += "<ul class='icn3d-mn-item'>";
56697
57074
 
56698
- html += "<li><span style='padding-left:1.5em;'>Unicolor</span>";
57075
+ html += "<li><span style='padding-left:1.5em!important;'>Unicolor</span>";
56699
57076
  html += "<ul>";
56700
57077
 
56701
57078
  html += "<li><span>Red</span>";
@@ -56902,7 +57279,7 @@ class SetMenu {
56902
57279
 
56903
57280
  if(me.cfg.cid === undefined) {
56904
57281
  //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrRainbow', 'Rainbow (R-V)');
56905
- html += "<li><span style='padding-left:1.5em;'>Rainbow (R-V)</span>";
57282
+ html += "<li><span style='padding-left:1.5em!important;'>Rainbow (R-V)</span>";
56906
57283
  html += "<ul>";
56907
57284
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrRainbow', 'for Selection');
56908
57285
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrRainbowChain', 'for Chains');
@@ -56911,7 +57288,7 @@ class SetMenu {
56911
57288
 
56912
57289
  if(!me.cfg.simplemenu) {
56913
57290
  //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrum', 'Spectrum (V-R)');
56914
- html += "<li><span style='padding-left:1.5em;'>Spectrum (V-R)</span>";
57291
+ html += "<li><span style='padding-left:1.5em!important;'>Spectrum (V-R)</span>";
56915
57292
  html += "<ul>";
56916
57293
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrum', 'for Selection');
56917
57294
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrumChain', 'for Chains');
@@ -56919,7 +57296,7 @@ class SetMenu {
56919
57296
  html += "</ul>";
56920
57297
  }
56921
57298
 
56922
- html += "<li><span style='padding-left:1.5em;'>Secondary</span>";
57299
+ html += "<li><span style='padding-left:1.5em!important;'>Secondary</span>";
56923
57300
  html += "<ul>";
56924
57301
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSSGreen', 'Sheet in Green');
56925
57302
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSSYellow', 'Sheet in Yellow');
@@ -56934,13 +57311,13 @@ class SetMenu {
56934
57311
 
56935
57312
  //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrHydrophobic', 'Wimley-White<br><span style="padding-left:1.5em;">Hydrophobicity</span>');
56936
57313
 
56937
- html += "<li><span style='padding-left:1.5em;'>Hydrophobicity</span>";
57314
+ html += "<li><span style='padding-left:1.5em!important;'>Hydrophobicity</span>";
56938
57315
  html += "<ul>";
56939
57316
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrNormalizedHP', 'Normalized');
56940
57317
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrHydrophobic', 'Wimley-White');
56941
57318
  html += "</ul>";
56942
57319
 
56943
- html += "<li><span style='padding-left:1.5em;'>B-factor</span>";
57320
+ html += "<li><span style='padding-left:1.5em!important;'>B-factor</span>";
56944
57321
  html += "<ul>";
56945
57322
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrBfactor', 'Original');
56946
57323
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrBfactorNorm', 'Percentile');
@@ -56963,7 +57340,7 @@ class SetMenu {
56963
57340
 
56964
57341
  if(me.cfg.cid === undefined) {
56965
57342
  if(!me.cfg.simplemenu) {
56966
- html += "<li><span style='padding-left:1.5em;'>Defined Sets</span>";
57343
+ html += "<li><span style='padding-left:1.5em!important;'>Defined Sets</span>";
56967
57344
  html += "<ul>";
56968
57345
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrsets', 'Rainbow for Selected Sets<br>in "Analysis > Defined Sets"');
56969
57346
  html += "</ul>";
@@ -56972,7 +57349,7 @@ class SetMenu {
56972
57349
 
56973
57350
  //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrResidue', 'Residue');
56974
57351
 
56975
- html += "<li><span style='padding-left:1.5em;'>Residue</span>";
57352
+ html += "<li><span style='padding-left:1.5em!important;'>Residue</span>";
56976
57353
  html += "<ul>";
56977
57354
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrResidue', 'Default');
56978
57355
  html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrResidueCustom', 'Custom');
@@ -59034,10 +59411,17 @@ class SetDialog {
59034
59411
  html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_custom'>Custom" + me.htmlCls.space2 + "</span></td>";
59035
59412
  html += tmpStr2 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_3dd'>3D Domains" + me.htmlCls.space2 + "</span></td>";
59036
59413
  html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_snp'>SNPs" + me.htmlCls.space2 + "</span></td>";
59037
- html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_interact'>Interactions" + me.htmlCls.space2 + "</span></td>";
59414
+
59415
+ // if(me.cfg.mmdbid != undefined || me.cfg.pdbid != undefined || me.cfg.mmtfid != undefined || me.cfg.mmcifid != undefined) { // PDB
59416
+ // html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_ptm' disabled>PTM (UniProt)" + me.htmlCls.space2 + "</span></td>";
59417
+ // }
59418
+ // else {
59419
+ html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_ptm'>PTM (UniProt)" + me.htmlCls.space2 + "</span></td>";
59420
+ // }
59038
59421
  html += "<td></td>";
59039
59422
  html += "</tr><tr>";
59040
59423
  html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_ssbond'>Disulfide Bonds" + me.htmlCls.space2 + "</span></td>";
59424
+ html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_interact'>Interactions" + me.htmlCls.space2 + "</span></td>";
59041
59425
  html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_crosslink'>Cross-Linkages" + me.htmlCls.space2 + "</span></td>";
59042
59426
  if(me.cfg.opmid !== undefined) {
59043
59427
  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>";
@@ -59414,10 +59798,7 @@ class Events {
59414
59798
  ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
59415
59799
  }
59416
59800
 
59417
- // save the current selection
59418
- //ic.selectionCls.saveSelectionPrep();
59419
- //let name = 'realignSetsByStruct';
59420
- //ic.selectionCls.saveSelection(name, name);
59801
+ me.cfg.aligntool = 'vast';
59421
59802
 
59422
59803
  ic.realignParserCls.realignOnStructAlign();
59423
59804
  if(nameArray.length > 0) {
@@ -65879,6 +66260,7 @@ class iCn3D {
65879
66260
 
65880
66261
  this.annoCddSiteCls = new AnnoCddSite(this);
65881
66262
  this.annoContactCls = new AnnoContact(this);
66263
+ this.annoPTMCls = new AnnoPTM(this);
65882
66264
  this.annoCrossLinkCls = new AnnoCrossLink(this);
65883
66265
  this.annoDomainCls = new AnnoDomain(this);
65884
66266
  this.annoSnpClinVarCls = new AnnoSnpClinVar(this);
@@ -66143,7 +66525,7 @@ class iCn3DUI {
66143
66525
  //even when multiple iCn3D viewers are shown together.
66144
66526
  this.pre = this.cfg.divid + "_";
66145
66527
 
66146
- this.REVISION = '3.13.2';
66528
+ this.REVISION = '3.14.0';
66147
66529
 
66148
66530
  // In nodejs, iCn3D defines "window = {navigator: {}}"
66149
66531
  this.bNode = (Object.keys(window).length < 2) ? true : false;