icn3d 3.13.2 → 3.15.0

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Files changed (5) hide show
  1. package/css/icn3d.css +10 -2
  2. package/icn3d.js +1609 -876
  3. package/icn3d.min.js +1 -1
  4. package/icn3d.module.js +1609 -876
  5. package/package.json +1 -1
package/icn3d.js CHANGED
@@ -4174,6 +4174,10 @@ class UtilsCls {
4174
4174
  return window.sessionStorage;
4175
4175
  }
4176
4176
 
4177
+ isLocalStorageSupported() { this.icn3dui;
4178
+ return window.localStorage;
4179
+ }
4180
+
4177
4181
  // http://stackoverflow.com/questions/5623838/rgb-to-hex-and-hex-to-rgb
4178
4182
  hexToRgb(hex, a) { this.icn3dui;
4179
4183
  let result = /^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(hex);
@@ -7487,15 +7491,16 @@ class Strand {
7487
7491
  }
7488
7492
 
7489
7493
  let maxDist = 6.0;
7490
- //let bBrokenSs = (prevCoorCA && Math.abs(currentCA.x - prevCoorCA.x) > maxDist) || (prevCoorCA && Math.abs(currentCA.y - prevCoorCA.y) > maxDist) || (prevCoorCA && Math.abs(currentCA.z - prevCoorCA.z) > maxDist);
7491
- let bBrokenSs = !atoms.hasOwnProperty(atom.serial) || (prevCoorCA && Math.abs(currentCA.x - prevCoorCA.x) > maxDist) || (prevCoorCA && Math.abs(currentCA.y - prevCoorCA.y) > maxDist) || (prevCoorCA && Math.abs(currentCA.z - prevCoorCA.z) > maxDist);
7494
+ let bBrokenSs = (prevCoorCA && Math.abs(currentCA.x - prevCoorCA.x) > maxDist) || (prevCoorCA && Math.abs(currentCA.y - prevCoorCA.y) > maxDist) || (prevCoorCA && Math.abs(currentCA.z - prevCoorCA.z) > maxDist);
7495
+ // The following code didn't work to select one residue
7496
+ // let bBrokenSs = !atoms.hasOwnProperty(atom.serial) || (prevCoorCA && Math.abs(currentCA.x - prevCoorCA.x) > maxDist) || (prevCoorCA && Math.abs(currentCA.y - prevCoorCA.y) > maxDist) || (prevCoorCA && Math.abs(currentCA.z - prevCoorCA.z) > maxDist);
7492
7497
 
7493
- if(bBrokenSs && atom.ss === 'sheet') {
7494
- bSheetSegment = true;
7495
- }
7496
- else if(bBrokenSs && atom.ss === 'helix') {
7497
- bHelixSegment = true;
7498
- }
7498
+ // if(bBrokenSs && atom.ss === 'sheet') {
7499
+ // bSheetSegment = true;
7500
+ // }
7501
+ // else if(bBrokenSs && atom.ss === 'helix') {
7502
+ // bHelixSegment = true;
7503
+ // }
7499
7504
 
7500
7505
  if ((atom.ssbegin || atom.ssend || (drawnResidueCount === totalResidueCount - 1) || bBrokenSs) && pnts[0].length > 0 && bSameChain) {
7501
7506
  let atomName = 'CA';
@@ -11873,7 +11878,7 @@ class ShareLink {
11873
11878
  if(key === 'showtitle' && value === true) continue;
11874
11879
  if(key === 'showcommand' && value === true) continue;
11875
11880
 
11876
- if(key === 'simplemenu' && value === false) continue;
11881
+ //if(key === 'simplemenu' && value === false) continue;
11877
11882
  if(key === 'mobilemenu' && value === false) continue;
11878
11883
  //if(key === 'closepopup' && value === false) continue;
11879
11884
  if(key === 'showanno' && value === false) continue;
@@ -13782,7 +13787,10 @@ class DefinedSets {
13782
13787
  ic.hAtoms = {};
13783
13788
  this.setHAtomsFromSets(orArray, 'or');
13784
13789
 
13785
- if(Object.keys(ic.hAtoms).length == 0) ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
13790
+ if(Object.keys(ic.hAtoms).length == 0) {
13791
+ //ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
13792
+ ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
13793
+ }
13786
13794
  this.setHAtomsFromSets(andArray, 'and');
13787
13795
 
13788
13796
  this.setHAtomsFromSets(notArray, 'not');
@@ -17862,7 +17870,7 @@ class SetColor {
17862
17870
  break;
17863
17871
 
17864
17872
  case 'chain':
17865
- if(ic.chainsColor !== undefined && Object.keys(ic.chainsColor).length > 0) { // mmdb input
17873
+ if(ic.chainsColor !== undefined && Object.keys(ic.chainsColor).length > 0) { // mmdb input
17866
17874
  this.setMmdbChainColor();
17867
17875
  }
17868
17876
  else {
@@ -22656,7 +22664,7 @@ class Dssp {
22656
22664
 
22657
22665
  ic.pdbParserCls.loadPdbDataRender(bAppend);
22658
22666
 
22659
- if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
22667
+ //if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
22660
22668
  if(ic.deferredSecondary !== undefined) ic.deferredSecondary.resolve();
22661
22669
  });
22662
22670
  }
@@ -22775,7 +22783,7 @@ class Dssp {
22775
22783
 
22776
22784
  ic.pdbParserCls.loadPdbDataRender(bAppend);
22777
22785
 
22778
- if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
22786
+ //if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
22779
22787
  if(ic.deferredSecondary !== undefined) ic.deferredSecondary.resolve();
22780
22788
  }
22781
22789
  }
@@ -22796,7 +22804,7 @@ class PdbParser {
22796
22804
  let url, dataType;
22797
22805
 
22798
22806
  if(bAf) {
22799
- url = "https://alphafold.ebi.ac.uk/files/AF-" + pdbid + "-F1-model_v2.pdb";
22807
+ url = "https://alphafold.ebi.ac.uk/files/AF-" + pdbid + "-F1-model_v3.pdb";
22800
22808
  ic.ParserUtilsCls.setYourNote(pdbid.toUpperCase() + '(AlphaFold) in iCn3D');
22801
22809
  }
22802
22810
  else {
@@ -22940,9 +22948,6 @@ class PdbParser {
22940
22948
 
22941
22949
  ic.asuCnt = ic.biomtMatrices.length;
22942
22950
  }
22943
- else {
22944
- $("#" + ic.pre + "assemblyWrapper").hide();
22945
- }
22946
22951
 
22947
22952
  if(ic.emd !== undefined) {
22948
22953
  $("#" + ic.pre + "mapWrapper1").hide();
@@ -23121,9 +23126,6 @@ class MmtfParser {
23121
23126
 
23122
23127
  ic.asuCnt = ic.biomtMatrices.length;
23123
23128
  }
23124
- else {
23125
- $("#" + ic.pre + "assemblyWrapper").hide();
23126
- }
23127
23129
 
23128
23130
  let oriindex2serial = {};
23129
23131
 
@@ -24087,7 +24089,7 @@ class MmdbParser {
24087
24089
 
24088
24090
  let molid2rescount = data.moleculeInfor;
24089
24091
  let molid2color = {}, chain2molid = {}, molid2chain = {};
24090
- let chainNameHash = {};
24092
+ let chainNameHash = {};
24091
24093
  for(let i in molid2rescount) {
24092
24094
  if(Object.keys(molid2rescount[i]).length === 0) continue;
24093
24095
 
@@ -24107,7 +24109,7 @@ class MmdbParser {
24107
24109
  chain2molid[chain] = i;
24108
24110
  molid2chain[i] = chain;
24109
24111
 
24110
- ic.chainsColor[chain] =(type !== undefined) ? me.parasCls.thr(me.htmlCls.GREY8) : me.parasCls.thr(color);
24112
+ ic.chainsColor[chain] = (type !== undefined && !me.cfg.mmdbafid) ? me.parasCls.thr(me.htmlCls.GREY8) : me.parasCls.thr(color);
24111
24113
 
24112
24114
  let geneId =(molid2rescount[i].geneId === undefined) ? '' : molid2rescount[i].geneId;
24113
24115
  let geneSymbol =(molid2rescount[i].geneSymbol === undefined) ? '' : molid2rescount[i].geneSymbol;
@@ -24272,10 +24274,6 @@ class MmdbParser {
24272
24274
  $("#" + ic.pre + "assemblyWrapper").show();
24273
24275
  //ic.bAssembly = true;
24274
24276
  }
24275
- else {
24276
- $("#" + ic.pre + "assemblyWrapper").hide();
24277
- //ic.bAssembly = false;
24278
- }
24279
24277
 
24280
24278
  if(ic.emd !== undefined) {
24281
24279
  $("#" + ic.pre + "mapWrapper1").hide();
@@ -25679,7 +25677,7 @@ class ChainalignParser {
25679
25677
 
25680
25678
  let url_t;
25681
25679
  if(ic.mmdbid_t.length > 5) {
25682
- url_t = "https://alphafold.ebi.ac.uk/files/AF-" + ic.mmdbid_t + "-F1-model_v2.pdb";
25680
+ url_t = "https://alphafold.ebi.ac.uk/files/AF-" + ic.mmdbid_t + "-F1-model_v3.pdb";
25683
25681
 
25684
25682
  targetAjax = $.ajax({
25685
25683
  url: url_t,
@@ -25717,7 +25715,7 @@ class ChainalignParser {
25717
25715
 
25718
25716
  let url_q, queryAjax;
25719
25717
  if(ic.mmdbid_q.length > 5) {
25720
- url_q = "https://alphafold.ebi.ac.uk/files/AF-" + ic.mmdbid_q + "-F1-model_v2.pdb";
25718
+ url_q = "https://alphafold.ebi.ac.uk/files/AF-" + ic.mmdbid_q + "-F1-model_v3.pdb";
25721
25719
 
25722
25720
  queryAjax = $.ajax({
25723
25721
  url: url_q,
@@ -26020,7 +26018,7 @@ class ChainalignParser {
26020
26018
  let structure = ic.structArray[i];
26021
26019
 
26022
26020
  if(isNaN(structure) && structure.length > 5) {
26023
- url_t = "https://alphafold.ebi.ac.uk/files/AF-" + ic.structArray[i] + "-F1-model_v2.pdb";
26021
+ url_t = "https://alphafold.ebi.ac.uk/files/AF-" + ic.structArray[i] + "-F1-model_v3.pdb";
26024
26022
 
26025
26023
  targetAjax = $.ajax({
26026
26024
  url: url_t,
@@ -26085,6 +26083,8 @@ class ChainalignParser {
26085
26083
  let hAtoms = {}, hAtomsTmp = {};
26086
26084
  let bLastQuery = false;
26087
26085
 
26086
+ ic.opts['color'] = (structArray.length == 1) ? 'chain' : 'structure';
26087
+
26088
26088
  for(let i = 0, il = structArray.length; i < il; ++i) {
26089
26089
  if(i == structArray.length - 1) bLastQuery = true;
26090
26090
 
@@ -26097,10 +26097,11 @@ class ChainalignParser {
26097
26097
  targetOrQuery = 'query';
26098
26098
  bAppend = true;
26099
26099
  }
26100
-
26100
+
26101
26101
  //if(structArray[i].length > 4) {
26102
26102
  if(structArray[i].length > 5) { // PDB ID plus postfix could be 5
26103
- let bNoDssp = true;
26103
+ //let bNoDssp = true;
26104
+ let bNoDssp = false; // get secondary structure info
26104
26105
  hAtomsTmp = ic.pdbParserCls.loadPdbData(queryDataArray[i], structArray[i], false, bAppend, targetOrQuery, bLastQuery, bNoDssp);
26105
26106
  }
26106
26107
  else {
@@ -26113,7 +26114,7 @@ class ChainalignParser {
26113
26114
 
26114
26115
  // calculate secondary structures with applyCommandDssp
26115
26116
  if(bQuery && me.cfg.matchedchains) {
26116
- $.when(ic.pdbParserCls.applyCommandDssp(true)).then(function() {
26117
+ // $.when(ic.pdbParserCls.applyCommandDssp(true)).then(function() {
26117
26118
  let bRealign = true, bPredefined = true;
26118
26119
  ic.realignParserCls.realignChainOnSeqAlign(undefined, ic.chainidArray, bRealign, bPredefined);
26119
26120
  // reset annotations
@@ -26122,11 +26123,10 @@ class ChainalignParser {
26122
26123
  if($('#' + ic.pre + 'dl_selectannotations').dialog( 'isOpen' )) {
26123
26124
  $('#' + ic.pre + 'dl_selectannotations').dialog( 'close' );
26124
26125
  }
26125
- });
26126
- }
26127
- else {
26128
- ic.pdbParserCls.applyCommandDssp(true);
26126
+ //});
26129
26127
  }
26128
+
26129
+ if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
26130
26130
  }
26131
26131
  }
26132
26132
 
@@ -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
  }
@@ -34120,7 +34172,7 @@ class ApplyCommand {
34120
34172
  else if(cmd.indexOf('realign on seq align') == 0) return 'File > Realign Selection > on Sequence Alignment';
34121
34173
  else if(cmd.indexOf('realign') == 0) return 'File > Realign Selection > Residue by Residue';
34122
34174
  else if(cmd.indexOf('graph interaction pairs') == 0) return hbondIntStr + ' > 2D Graph(Force-Directed)';
34123
- else if(cmd.indexOf('export canvas') == 0) return 'File > Save Files > iCn3D PNG Image';
34175
+ else if(cmd.indexOf('export canvas') == 0) return 'File > Save File > iCn3D PNG Image';
34124
34176
  else if(cmd == 'export stl file') return printStr + 'STL';
34125
34177
  else if(cmd == 'export vrml file') return printStr + 'VRML(Color)';
34126
34178
  else if(cmd == 'export stl stabilizer file') return printStr + 'STL W/ Stabilizers';
@@ -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';
@@ -34454,7 +34507,9 @@ class SelectByCommand {
34454
34507
  bResidueId = true;
34455
34508
  }
34456
34509
  else {
34457
- if(residueStrArray[j][0] === '3' && residueStrArray[j].length > 1 &&(residueStrArray[j].length - 1) % 3 === 0) { // three letter residue string, such as :3LysArg
34510
+ //if(residueStrArray[j].length > 1 && residueStrArray[j][0] === '3' && (residueStrArray[j].length - 1) % 3 === 0) { // three letter residue string, such as :3LysArg
34511
+ if(residueStrArray[j].length > 1 && residueStrArray[j][0] === '3'
34512
+ && isNaN(residueStrArray[j][1]) && residueStrArray[j][0] !== '-') { // three letter residue string, such as :3LysArg or :3ZN, but not :30 neither :3-10
34458
34513
  let tmpStr = residueStrArray[j].toUpperCase();
34459
34514
  threeLetterResidueStr = tmpStr.substr(1);
34460
34515
  bResidueArrayThree = true;
@@ -34570,7 +34625,8 @@ class SelectByCommand {
34570
34625
  }
34571
34626
  else if(bResidueArrayThree) {
34572
34627
  let threeLetter = me.utilsCls.residueAbbr2Name(ic.chainsSeq[molecule_chain][s].name);
34573
- chainSeq +=(threeLetter.length == 3) ? threeLetter : ' ';
34628
+
34629
+ chainSeq +=(threeLetter.length == 3) ? threeLetter : threeLetter.padEnd(3, '_');
34574
34630
  }
34575
34631
  resiArray.push(ic.chainsSeq[molecule_chain][s].resi);
34576
34632
  }
@@ -35468,7 +35524,8 @@ class SetSeqAlign {
35468
35524
  if(i > 0) {
35469
35525
  let index1 = alignIndex;
35470
35526
  for(let j = prevIndex1 + 1, jl = start1; j < jl; ++j) {
35471
- if(ic.chainsSeq[chainid1] === undefined) break;
35527
+ if(ic.chainsSeq[chainid1] === undefined || ic.chainsSeq[chainid1][j] === undefined) break;
35528
+
35472
35529
  let resi = ic.chainsSeq[chainid1][j].resi;
35473
35530
  let resn = ic.chainsSeq[chainid1][j].name.toLowerCase();
35474
35531
 
@@ -35482,7 +35539,8 @@ class SetSeqAlign {
35482
35539
 
35483
35540
  let index2 = alignIndex;
35484
35541
  for(let j = prevIndex2 + 1, jl = start2; j < jl; ++j) {
35485
- if(ic.chainsSeq[chainid2] === undefined) break;
35542
+ if(ic.chainsSeq[chainid2] === undefined || ic.chainsSeq[chainid2] === undefined) break;
35543
+
35486
35544
  let resi = ic.chainsSeq[chainid2][j].resi;
35487
35545
  let resn = ic.chainsSeq[chainid2][j].name.toLowerCase();
35488
35546
 
@@ -37404,9 +37462,6 @@ class MmcifParser {
37404
37462
 
37405
37463
  ic.asuCnt = ic.biomtMatrices.length;
37406
37464
  }
37407
- else {
37408
- $("#" + ic.pre + "assemblyWrapper").hide();
37409
- }
37410
37465
 
37411
37466
  ic.setStyleCls.setAtomStyleByOptions(ic.opts);
37412
37467
  ic.setColorCls.setColorByOptions(ic.opts, ic.atoms);
@@ -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) {
@@ -42139,9 +42516,12 @@ class Selection {
42139
42516
 
42140
42517
  //Show the selection.
42141
42518
  showSelection() { let ic = this.icn3d, me = ic.icn3dui;
42142
- ic.dAtoms = {};
42519
+ //ic.dAtoms = {};
42143
42520
 
42144
- if(Object.keys(ic.hAtoms).length == 0) this.selectAll_base();
42521
+ if(Object.keys(ic.hAtoms).length == 0) {
42522
+ //this.selectAll_base();
42523
+ ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
42524
+ }
42145
42525
 
42146
42526
  ic.dAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
42147
42527
  ic.viewSelectionAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
@@ -42782,11 +43162,14 @@ class SetStyle {
42782
43162
  console.log("WebGL context was lost. Reset WebGLRenderer and launch iCn3D again.");
42783
43163
 
42784
43164
  ic.renderer = new THREE.WebGLRenderer({
42785
- canvas: ic.container.get(0),
42786
- antialias: true,
42787
- preserveDrawingBuffer: true,
42788
- alpha: true
43165
+ canvas: ic.oriContainer.get(0), //this.container.get(0),
43166
+ antialias: true,
43167
+ preserveDrawingBuffer: true,
43168
+ sortObjects: false,
43169
+ alpha: true
42789
43170
  });
43171
+ // Enable VR
43172
+ ic.renderer.xr.enabled = true;
42790
43173
 
42791
43174
  ic.drawCls.draw();
42792
43175
 
@@ -43995,7 +44378,8 @@ class ApplySymd {
43995
44378
  }
43996
44379
  else { // bSymd, subset, and one chain
43997
44380
  if(Object.keys(ic.hAtoms).length == 0) {
43998
- ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
44381
+ //ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
44382
+ ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
43999
44383
  }
44000
44384
 
44001
44385
  // pick the first 1/order of selection
@@ -53372,6 +53756,95 @@ class ClickMenu {
53372
53756
  $("#" + me.pre + id2).resizable();
53373
53757
  }
53374
53758
 
53759
+ applyShownMenus() { let me = this.icn3dui; me.icn3d;
53760
+ let idArray = [];
53761
+ for(let id in me.htmlCls.allMenus) {
53762
+ if(me.htmlCls.shownMenus.hasOwnProperty(id)) {
53763
+ $("#" + id).parent().show();
53764
+ idArray.push(id);
53765
+ }
53766
+ else {
53767
+ $("#" + id).parent().hide();
53768
+ }
53769
+ }
53770
+
53771
+ if(Object.keys(me.htmlCls.shownMenus).length == Object.keys(me.htmlCls.allMenus).length) {
53772
+ $(".icn3d-menusep").show();
53773
+ }
53774
+ else {
53775
+ $(".icn3d-menusep").hide();
53776
+ }
53777
+
53778
+ // save to localStorage
53779
+ if(localStorage) localStorage.setItem('menulist', JSON.stringify(idArray));
53780
+ }
53781
+
53782
+ getShownMenusFromCookie() { let me = this.icn3dui; me.icn3d;
53783
+ me.htmlCls.shownMenus = {};
53784
+
53785
+ let idArrayStr = (localStorage) ? localStorage.getItem('menulist') : '';
53786
+
53787
+ if(idArrayStr) {
53788
+ let idArray = JSON.parse(idArrayStr);
53789
+
53790
+ for(let i = 0, il = idArray.length; i < il; ++i) {
53791
+ me.htmlCls.shownMenus[idArray[i]] = 1;
53792
+ }
53793
+ }
53794
+ else {
53795
+ me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.allMenus);
53796
+ }
53797
+ }
53798
+
53799
+ displayShownMenus() { let me = this.icn3dui; me.icn3d;
53800
+ let html = "<form name='" + me.pre + "selmenu'>";
53801
+ html += "<table><tr><th>File</th><th>Select</th><th>View</th><th>Style</th><th>Color</th><th>Analysis</th><th>Help</th></tr>";
53802
+ html += "<tr>";
53803
+ for(let id in me.htmlCls.allMenusSel) {
53804
+ // skip all unicolor: too many
53805
+ let len = me.pre.length;
53806
+ if(id.substr(0, 6 + len) == me.pre + 'uniclr'
53807
+ || id.substr(0, 11 + len) == me.pre + 'mn5_opacity'
53808
+ || id.substr(0, 14 + len) == me.pre + 'mn6_labelscale'
53809
+ || id.substr(0, 4 + len) == me.pre + 'faq_'
53810
+ || id.substr(0, 4 + len) == me.pre + 'dev_') {
53811
+ continue;
53812
+ }
53813
+
53814
+ if(id == me.pre + 'mn1_searchstru') {
53815
+ html += "<td valign='top'>";
53816
+ }
53817
+ else if(id == me.pre + 'mn2_definedsets') {
53818
+ html += "</td><td valign='top'>";
53819
+ }
53820
+ else if(id == me.pre + 'mn2_show_selected') {
53821
+ html += "</td><td valign='top'>";
53822
+ }
53823
+ else if(id == me.pre + 'mn3_proteinwrap' || (me.cfg.cid && id == me.pre + 'mn3_ligwrap')) {
53824
+ html += "</td><td valign='top'>";
53825
+ }
53826
+ else if(id == me.pre + 'mn4_clrwrap') {
53827
+ html += "</td><td valign='top'>";
53828
+ }
53829
+ else if(id == me.pre + 'mn6_selectannotations') {
53830
+ html += "</td><td valign='top'>";
53831
+ }
53832
+ else if(id == me.pre + 'abouticn3d') {
53833
+ html += "</td><td valign='top'>";
53834
+ }
53835
+
53836
+ let checkStr = (me.htmlCls.shownMenus.hasOwnProperty(id)) ? "checked" : "";
53837
+
53838
+ let selType = me.htmlCls.allMenusSel[id];
53839
+ let styleStr = (selType == 3) ? " style='margin-left:30px'" : ((selType == 2) ? " style='margin-left:15px'" : "");
53840
+
53841
+ html += "<span style='white-space:nowrap'><input type='checkbox' name='" + id + "' value='" + id + "'" + checkStr + styleStr + ">" + me.htmlCls.allMenus[id] + "</span><br>";
53842
+ }
53843
+ html += "</td></tr></table></form>";
53844
+
53845
+ $("#" + me.pre + "menulist").html(html);
53846
+ }
53847
+
53375
53848
 
53376
53849
  clickMenu1() { let me = this.icn3dui; me.icn3d;
53377
53850
  if(me.bNode) return;
@@ -53753,6 +54226,98 @@ class ClickMenu {
53753
54226
  ic.resizeCanvasCls.replayoff();
53754
54227
  thisClass.setLogCmd("replay off", true);
53755
54228
  });
54229
+
54230
+ me.myEventCls.onIds("#" + me.pre + "mn1_menuall", "click", function(e) { me.icn3d;
54231
+ me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.allMenus);
54232
+
54233
+ thisClass.applyShownMenus();
54234
+ });
54235
+
54236
+ me.myEventCls.onIds("#" + me.pre + "mn1_menusimple", "click", function(e) { me.icn3d;
54237
+ me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.simpleMenus);
54238
+
54239
+ thisClass.applyShownMenus();
54240
+ });
54241
+
54242
+ me.myEventCls.onIds("#" + me.pre + "mn1_menupref", "click", function(e) { me.icn3d;
54243
+ me.htmlCls.dialogCls.openDlg('dl_menupref', 'Select Menus');
54244
+
54245
+ thisClass.getShownMenusFromCookie();
54246
+
54247
+ thisClass.displayShownMenus();
54248
+ });
54249
+
54250
+ me.myEventCls.onIds("#" + me.pre + "apply_menupref", "click", function(e) { me.icn3d;
54251
+ var checkboxes = document.querySelectorAll('form[name="' + me.pre + 'selmenu"] input:checked');
54252
+ me.htmlCls.shownMenus = {};
54253
+ for (var checkbox of checkboxes) {
54254
+ me.htmlCls.shownMenus[checkbox.value] = 1;
54255
+ }
54256
+
54257
+ thisClass.applyShownMenus();
54258
+ });
54259
+
54260
+ me.myEventCls.onIds("#" + me.pre + "reset_menupref", "click", function(e) { me.icn3d;
54261
+ me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.simpleMenus);
54262
+
54263
+ thisClass.applyShownMenus();
54264
+ thisClass.displayShownMenus();
54265
+ });
54266
+
54267
+ me.myEventCls.onIds("#" + me.pre + "reset_menupref_all", "click", function(e) { me.icn3d;
54268
+ me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.allMenus);
54269
+
54270
+ thisClass.applyShownMenus();
54271
+ thisClass.displayShownMenus();
54272
+ });
54273
+
54274
+ me.myEventCls.onIds("#" + me.pre + "savepref", "click", function(e) { let ic = me.icn3d;
54275
+ let menuStr = '[';
54276
+
54277
+ var checkboxes = document.querySelectorAll('form[name="' + me.pre + 'selmenu"] input:checked');
54278
+ let cnt = 0;
54279
+ for (var checkbox of checkboxes) {
54280
+ if(cnt > 0) menuStr += ', ';
54281
+ menuStr += '"' + checkbox.value + '"';
54282
+ ++cnt;
54283
+ }
54284
+
54285
+ menuStr += ']';
54286
+
54287
+ ic.saveFileCls.saveFile('icn3d_shown_menus.txt', 'text', [menuStr]);
54288
+ });
54289
+
54290
+ me.myEventCls.onIds("#" + me.pre + "reload_menupreffile", "click", function(e) { me.icn3d;
54291
+ e.preventDefault();
54292
+ if(!me.cfg.notebook) dialog.dialog( "close" );
54293
+ let file = $("#" + me.pre + "menupreffile")[0].files[0];
54294
+ if(!file) {
54295
+ var aaa = 1; //alert("Please select a file before clicking 'Load'");
54296
+ }
54297
+ else {
54298
+ me.htmlCls.setHtmlCls.fileSupport();
54299
+ let reader = new FileReader();
54300
+ reader.onload = function(e) {
54301
+ let dataStr = e.target.result; // or = reader.result;
54302
+ let idArray = JSON.parse(dataStr);
54303
+
54304
+ me.htmlCls.shownMenus = {};
54305
+ for(let i = 0, il = idArray.length; i < il; ++i) {
54306
+ me.htmlCls.shownMenus[idArray[i]] = 1;
54307
+ }
54308
+
54309
+ thisClass.applyShownMenus();
54310
+ thisClass.displayShownMenus();
54311
+ };
54312
+ reader.readAsText(file);
54313
+ }
54314
+ });
54315
+
54316
+ me.myEventCls.onIds("#" + me.pre + "mn1_menuloadpref", "click", function(e) { me.icn3d;
54317
+ me.htmlCls.dialogCls.openDlg('dl_menuloadpref', 'Please input the menu preference file');
54318
+ });
54319
+
54320
+
53756
54321
  // },
53757
54322
  // clkMn1_link_structure: function() {
53758
54323
  me.myEventCls.onIds("#" + me.pre + "mn1_link_structure", "click", function(e) { let ic = me.icn3d;
@@ -55396,8 +55961,9 @@ class ClickMenu {
55396
55961
  // },
55397
55962
  // clkmn5_setThickness: function() {
55398
55963
  me.myEventCls.onIds("#" + me.pre + "mn3_setThickness", "click", function(e) { me.icn3d;
55399
- me.htmlCls.dialogCls.openDlg('dl_thickness2', 'Preferences');
55964
+ me.htmlCls.dialogCls.openDlg('dl_thickness2', 'Style Preferences');
55400
55965
  });
55966
+
55401
55967
  // },
55402
55968
  // clkmn1_thicknessReset: function() {
55403
55969
  /*
@@ -55539,26 +56105,24 @@ class SetMenu {
55539
56105
  let tdStr = '<td valign="top">';
55540
56106
  html += tdStr + this.setMenu1() + '</td>';
55541
56107
 
55542
- //if(!me.cfg.simplemenu) {
55543
- html += tdStr + this.setMenu2() + '</td>';
55544
- //}
56108
+ html += tdStr + this.setMenu2() + '</td>';
55545
56109
 
55546
56110
  html += tdStr + this.setMenu2b() + '</td>';
55547
56111
  html += tdStr + this.setMenu3() + '</td>';
55548
56112
  html += tdStr + this.setMenu4() + '</td>';
55549
56113
 
55550
- //if(!me.cfg.simplemenu) {
55551
- html += tdStr + this.setMenu5() + '</td>';
55552
- //html += tdStr + this.setMenu5b() + '</td>';
55553
- html += tdStr + this.setMenu6() + '</td>';
56114
+ html += tdStr + this.setMenu5() + '</td>';
56115
+ //html += tdStr + this.setMenu5b() + '</td>';
56116
+ html += tdStr + this.setMenu6() + '</td>';
55554
56117
 
55555
- html += tdStr + "<div style='position:relative; margin-left:6px;'>" + str1;
55556
- html += "<div class='icn3d-commandTitle' style='min-width:40px; margin-top: 3px; white-space: nowrap;'>" + str2;
56118
+ me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.simpleMenus);
55557
56119
 
55558
- html += tdStr + '<div class="icn3d-commandTitle" style="white-space:nowrap; margin-top:10px; border-left:solid 1px #888888"><span id="' + me.pre + 'selection_expand" class="icn3d-expand icn3d-link" style="display:block;" title="Expand">' + me.htmlCls.space2 + 'Toolbar <span class="ui-icon ui-icon-plus" style="width:15px"></span>' + me.htmlCls.space2 + '</span><span id="' + me.pre + 'selection_shrink" class="icn3d-shrink icn3d-link" style="display:none;" title="Shrink">' + me.htmlCls.space2 + 'Toolbar <span class="ui-icon ui-icon-minus" style="width:15px"></span>' + me.htmlCls.space2 + '</span></div></td>';
56120
+ html += tdStr + "<div style='position:relative; margin-left:6px;'>" + str1;
56121
+ html += "<div class='icn3d-commandTitle' style='min-width:40px; margin-top: 3px; white-space: nowrap;'>" + str2;
55559
56122
 
55560
- html += tdStr + '<div class="icn3d-commandTitle" style="white-space:nowrap; margin-top:8px; border-left:solid 1px #888888">' + me.htmlCls.space2 + '<input type="text" id="' + me.pre + 'search_seq" size="10" placeholder="one-letter seq."> <button style="white-space:nowrap;" id="' + me.pre + 'search_seq_button">Search</button> <a style="text-decoration: none;" href="' + me.htmlCls.baseUrl + 'icn3d/icn3d.html#selectb" target="_blank" title="Specification tips">?</a></div></td>';
55561
- //}
56123
+ html += tdStr + '<div class="icn3d-commandTitle" style="white-space:nowrap; margin-top:10px; border-left:solid 1px #888888"><span id="' + me.pre + 'selection_expand" class="icn3d-expand icn3d-link" style="display:block;" title="Expand">' + me.htmlCls.space2 + 'Toolbar <span class="ui-icon ui-icon-plus" style="width:15px"></span>' + me.htmlCls.space2 + '</span><span id="' + me.pre + 'selection_shrink" class="icn3d-shrink icn3d-link" style="display:none;" title="Shrink">' + me.htmlCls.space2 + 'Toolbar <span class="ui-icon ui-icon-minus" style="width:15px"></span>' + me.htmlCls.space2 + '</span></div></td>';
56124
+
56125
+ html += tdStr + '<div class="icn3d-commandTitle" style="white-space:nowrap; margin-top:8px; border-left:solid 1px #888888">' + me.htmlCls.space2 + '<input type="text" id="' + me.pre + 'search_seq" size="10" placeholder="one-letter seq."> <button style="white-space:nowrap;" id="' + me.pre + 'search_seq_button">Search</button> <a style="text-decoration: none;" href="' + me.htmlCls.baseUrl + 'icn3d/icn3d.html#selectb" target="_blank" title="Specification tips">?</a></div></td>';
55562
56126
 
55563
56127
  html += "</tr>";
55564
56128
  html += "</table>";
@@ -55674,6 +56238,8 @@ class SetMenu {
55674
56238
  html += liStr + ">Help</span>";
55675
56239
  html += this.setMenu6_base();
55676
56240
 
56241
+ me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.simpleMenus);
56242
+
55677
56243
  html += "<li><div style='position:relative; margin-top:-6px;'>" + str1;
55678
56244
  html += "<div class='icn3d-commandTitle' style='margin-top: 3px; white-space: nowrap;'>" + str2;
55679
56245
 
@@ -55972,159 +56538,157 @@ class SetMenu {
55972
56538
  let html = "";
55973
56539
 
55974
56540
  html += "<ul class='icn3d-mn-item'>";
55975
- html += "<li><a href='https://www.ncbi.nlm.nih.gov/structure' target='_blank'>Search Structure " + me.htmlCls.wifiStr + "</a></li>";
56541
+ //html += "<li><a href='https://www.ncbi.nlm.nih.gov/structure' target='_blank'>Search Structure " + me.htmlCls.wifiStr + "</a></li>";
56542
+ html += me.htmlCls.setHtmlCls.getMenuUrl('mn1_searchstru', "https://www.ncbi.nlm.nih.gov/structure", "Search Structure " + me.htmlCls.wifiStr, 1, 1);
55976
56543
 
55977
- html += "<li><span>Search Similar</span>";
56544
+ //html += "<li><span>Search Similar</span>";
56545
+ html += me.htmlCls.setHtmlCls.getMenuText('mn1_searchsimilar', 'Search Similar', undefined, undefined, 1);
55978
56546
  html += "<ul>";
55979
- html += me.htmlCls.setHtmlCls.getLink('mn1_vastplus', 'NCBI VAST+ (PDB Assembly)' + me.htmlCls.wifiStr);
55980
- html += me.htmlCls.setHtmlCls.getLink('mn1_vast', 'NCBI VAST (PDB)' + me.htmlCls.wifiStr);
55981
- html += me.htmlCls.setHtmlCls.getLink('mn1_foldseek', 'Foldseek (PDB & AlphaFold)' + me.htmlCls.wifiStr);
56547
+ html += me.htmlCls.setHtmlCls.getLink('mn1_vastplus', 'NCBI VAST+ (PDB Assembly)' + me.htmlCls.wifiStr, undefined, 2);
56548
+ html += me.htmlCls.setHtmlCls.getLink('mn1_vast', 'NCBI VAST (PDB)' + me.htmlCls.wifiStr, undefined, 2);
56549
+ html += me.htmlCls.setHtmlCls.getLink('mn1_foldseek', 'Foldseek (PDB & AlphaFold)' + me.htmlCls.wifiStr, undefined, 2);
55982
56550
  html += "</ul>";
56551
+ html += "</li>";
55983
56552
 
55984
- html += "<li><span>Retrieve by ID</span>";
56553
+ //html += "<li><span>Retrieve by ID</span>";
56554
+ html += me.htmlCls.setHtmlCls.getMenuText('mn1_retrievebyid', 'Retrieve by ID', undefined, 1, 1);
55985
56555
  html += "<ul>";
55986
- html += me.htmlCls.setHtmlCls.getLink('mn1_mmdbid', 'MMDB ID ' + me.htmlCls.wifiStr);
55987
- html += me.htmlCls.setHtmlCls.getLink('mn1_mmtfid', 'MMTF ID ' + me.htmlCls.wifiStr);
55988
- html += me.htmlCls.setHtmlCls.getLink('mn1_pdbid', 'PDB ID ' + me.htmlCls.wifiStr);
55989
- html += me.htmlCls.setHtmlCls.getLink('mn1_afid', 'AlphaFold UniProt ID ' + me.htmlCls.wifiStr);
55990
- html += me.htmlCls.setHtmlCls.getLink('mn1_mmdbafid', 'MMDB or AlphaFold IDs' + me.htmlCls.wifiStr);
55991
- if(!me.cfg.simplemenu) {
55992
- html += me.htmlCls.setHtmlCls.getLink('mn1_opmid', 'OPM PDB ID ' + me.htmlCls.wifiStr);
55993
- html += me.htmlCls.setHtmlCls.getLink('mn1_mmcifid', 'mmCIF ID ' + me.htmlCls.wifiStr);
55994
- html += me.htmlCls.setHtmlCls.getLink('mn1_gi', 'NCBI gi ' + me.htmlCls.wifiStr);
55995
- }
56556
+
56557
+ html += me.htmlCls.setHtmlCls.getLink('mn1_mmdbafid', 'PDB/MMDB/AlphaFold IDs' + me.htmlCls.wifiStr, 1, 2);
56558
+ html += me.htmlCls.setHtmlCls.getLink('mn1_mmdbid', 'MMDB ID ' + me.htmlCls.wifiStr, undefined, 2);
56559
+ html += me.htmlCls.setHtmlCls.getLink('mn1_mmtfid', 'MMTF ID ' + me.htmlCls.wifiStr, undefined, 2);
56560
+ html += me.htmlCls.setHtmlCls.getLink('mn1_pdbid', 'PDB ID ' + me.htmlCls.wifiStr, undefined, 2);
56561
+ html += me.htmlCls.setHtmlCls.getLink('mn1_afid', 'AlphaFold UniProt ID ' + me.htmlCls.wifiStr, undefined, 2);
56562
+ html += me.htmlCls.setHtmlCls.getLink('mn1_opmid', 'OPM PDB ID ' + me.htmlCls.wifiStr, undefined, 2);
56563
+ html += me.htmlCls.setHtmlCls.getLink('mn1_mmcifid', 'mmCIF ID ' + me.htmlCls.wifiStr, undefined, 2);
56564
+ html += me.htmlCls.setHtmlCls.getLink('mn1_gi', 'NCBI gi ' + me.htmlCls.wifiStr, undefined, 2);
56565
+
55996
56566
  //html += me.htmlCls.setHtmlCls.getLink('mn1_uniprotid', 'UniProt ID ' + me.htmlCls.wifiStr);
55997
- html += me.htmlCls.setHtmlCls.getLink('mn1_cid', 'PubChem CID ' + me.htmlCls.wifiStr);
56567
+ html += me.htmlCls.setHtmlCls.getLink('mn1_cid', 'PubChem CID ' + me.htmlCls.wifiStr, 1, 2);
55998
56568
 
55999
56569
  html += "</ul>";
56000
56570
  html += "</li>";
56001
- html += "<li><span>Open File</span>";
56571
+
56572
+ //html += "<li><span>Open File</span>";
56573
+ html += me.htmlCls.setHtmlCls.getMenuText('mn1_openfile', 'Open File', undefined, 1, 1);
56002
56574
  html += "<ul>";
56003
56575
  // html += me.htmlCls.setHtmlCls.getLink('mn1_pdbfile', 'PDB File');
56004
56576
  // html += me.htmlCls.setHtmlCls.getLink('mn1_pdbfile_app', 'PDB File (append)');
56005
- html += me.htmlCls.setHtmlCls.getLink('mn1_pdbfile_app', 'PDB Files (appendable)');
56006
- if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getLink('mn1_mmciffile', 'mmCIF File');
56007
- html += me.htmlCls.setHtmlCls.getLink('mn1_mol2file', 'Mol2 File');
56008
- html += me.htmlCls.setHtmlCls.getLink('mn1_sdffile', 'SDF File');
56009
- html += me.htmlCls.setHtmlCls.getLink('mn1_xyzfile', 'XYZ File');
56010
- html += me.htmlCls.setHtmlCls.getLink('mn1_afmapfile', 'AlphaFold PAE File');
56011
-
56012
- if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getLink('mn1_urlfile', 'URL(Same Host) ' + me.htmlCls.wifiStr);
56013
- html += "<li>-</li>";
56014
- html += me.htmlCls.setHtmlCls.getLink('mn1_pngimage', 'iCn3D PNG Image');
56015
- html += me.htmlCls.setHtmlCls.getLink('mn1_state', 'State/Script File');
56016
- if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getLink('mn1_fixedversion', 'Share Link in Archived Ver. ' + me.htmlCls.wifiStr);
56017
- html += me.htmlCls.setHtmlCls.getLink('mn1_selection', 'Selection File');
56018
-
56019
- if(!me.cfg.simplemenu) {
56020
- html += "<li>-</li>";
56021
-
56022
- html += "<li><span>Electron Density(DSN6)</span>";
56023
- html += "<ul>";
56024
- html += me.htmlCls.setHtmlCls.getLink('mn1_dsn6', 'Local File');
56025
- html += me.htmlCls.setHtmlCls.getLink('mn1_dsn6url', 'URL(Same Host) ' + me.htmlCls.wifiStr);
56026
- html += "</ul>";
56027
- }
56577
+ html += me.htmlCls.setHtmlCls.getLink('mn1_pdbfile_app', 'PDB Files (appendable)', 1, 2);
56578
+ html += me.htmlCls.setHtmlCls.getLink('mn1_mmciffile', 'mmCIF File', undefined, 2);
56579
+ html += me.htmlCls.setHtmlCls.getLink('mn1_mol2file', 'Mol2 File', undefined, 2);
56580
+ html += me.htmlCls.setHtmlCls.getLink('mn1_sdffile', 'SDF File', undefined, 2);
56581
+ html += me.htmlCls.setHtmlCls.getLink('mn1_xyzfile', 'XYZ File', undefined, 2);
56582
+ html += me.htmlCls.setHtmlCls.getLink('mn1_afmapfile', 'AlphaFold PAE File', undefined, 2);
56583
+
56584
+ html += me.htmlCls.setHtmlCls.getLink('mn1_urlfile', 'URL(Same Host) ' + me.htmlCls.wifiStr, undefined, 2);
56585
+ html += me.htmlCls.setHtmlCls.getMenuSep();
56586
+ html += me.htmlCls.setHtmlCls.getLink('mn1_pngimage', 'iCn3D PNG Image', 1, 2);
56587
+ html += me.htmlCls.setHtmlCls.getLink('mn1_state', 'State/Script File', undefined, 2);
56588
+ html += me.htmlCls.setHtmlCls.getLink('mn1_fixedversion', 'Share Link in Archived Ver. ' + me.htmlCls.wifiStr, undefined, 2);
56589
+ html += me.htmlCls.setHtmlCls.getLink('mn1_selection', 'Selection File', undefined, 2);
56590
+
56591
+ html += me.htmlCls.setHtmlCls.getMenuSep();
56592
+
56593
+ //html += "<li><span>Electron Density(DSN6)</span>";
56594
+ html += me.htmlCls.setHtmlCls.getMenuText('mn1_dsn6wrap', 'Electron Density(DSN6)', undefined, undefined, 2);
56595
+ html += "<ul>";
56596
+ html += me.htmlCls.setHtmlCls.getLink('mn1_dsn6', 'Local File', undefined, 3);
56597
+ html += me.htmlCls.setHtmlCls.getLink('mn1_dsn6url', 'URL(Same Host) ' + me.htmlCls.wifiStr, undefined, 3);
56598
+ html += "</ul>";
56028
56599
 
56029
56600
  html += "</ul>";
56030
56601
  html += "</li>";
56031
- html += "<li><span>Align</span>";
56602
+
56603
+ //html += "<li><span>Align</span>";
56604
+ html += me.htmlCls.setHtmlCls.getMenuText('mn1_alignwrap', 'Align', undefined, 1, 1);
56032
56605
  html += "<ul>";
56033
56606
 
56034
- html += "<li><span>Multiple Chains</span>";
56607
+ //html += "<li><span>Multiple Chains</span>";
56608
+ html += me.htmlCls.setHtmlCls.getMenuText('mn1_chainalignwrap', 'Multiple Chains', undefined, 1, 2);
56035
56609
  html += "<ul>";
56036
- html += me.htmlCls.setHtmlCls.getRadio('mn1_chainalignRad', 'mn1_chainalign', 'by Structure Alignment ' + me.htmlCls.wifiStr);
56037
- html += me.htmlCls.setHtmlCls.getRadio('mn1_chainalignRad', 'mn1_chainalign2', 'by Sequence Alignment ' + me.htmlCls.wifiStr);
56038
- html += me.htmlCls.setHtmlCls.getRadio('mn1_chainalignRad', 'mn1_chainalign3', 'Residue by Residue');
56610
+ html += me.htmlCls.setHtmlCls.getRadio('mn1_chainalignRad', 'mn1_chainalign', 'by Structure Alignment ' + me.htmlCls.wifiStr, undefined, 1, 3);
56611
+ html += me.htmlCls.setHtmlCls.getRadio('mn1_chainalignRad', 'mn1_chainalign2', 'by Sequence Alignment ' + me.htmlCls.wifiStr, undefined, 1, 3);
56612
+ html += me.htmlCls.setHtmlCls.getRadio('mn1_chainalignRad', 'mn1_chainalign3', 'Residue by Residue', undefined, undefined, 3);
56039
56613
  html += "</ul>";
56040
56614
  html += "</li>";
56041
56615
 
56042
- html += "<li><span>Structure to Structure</span>";
56616
+ //html += "<li><span>Structure to Structure</span>";
56617
+ html += me.htmlCls.setHtmlCls.getMenuText('mn1_aligntwostru', 'Structure to Structure', undefined, undefined, 2);
56043
56618
  html += "<ul>";
56044
- html += me.htmlCls.setHtmlCls.getLink('mn1_align', 'Two PDB Structures ' + me.htmlCls.wifiStr);
56045
- html += me.htmlCls.setHtmlCls.getLink('mn1_alignaf', 'Two AlphaFold Structures ' + me.htmlCls.wifiStr);
56619
+ html += me.htmlCls.setHtmlCls.getLink('mn1_align', 'Two PDB Structures ' + me.htmlCls.wifiStr, undefined, 3);
56620
+ html += me.htmlCls.setHtmlCls.getLink('mn1_alignaf', 'Two AlphaFold Structures ' + me.htmlCls.wifiStr, undefined, 3);
56046
56621
  html += "</ul>";
56047
56622
 
56048
- html += me.htmlCls.setHtmlCls.getLink('mn1_blast_rep_id', 'Sequence to Structure');
56623
+ html += me.htmlCls.setHtmlCls.getLink('mn1_blast_rep_id', 'Sequence to Structure', undefined, 2);
56049
56624
 
56050
56625
  html += "</ul>";
56051
56626
  html += "</li>";
56052
56627
 
56053
- html += "<li id='" + me.pre + "mn2_realignWrap'><span>Realign Selection</span>";
56628
+ //html += "<li id='" + me.pre + "mn2_realignWrap'><span>Realign Selection</span>";
56629
+ html += me.htmlCls.setHtmlCls.getMenuText('mn2_realignWrap', 'Realign Selection', undefined, undefined, 1);
56054
56630
  html += "<ul>";
56055
56631
 
56056
- html += me.htmlCls.setHtmlCls.getRadio('mn2_realign', 'mn2_realignonstruct', 'by Structure Alignment ' + me.htmlCls.wifiStr);
56632
+ html += me.htmlCls.setHtmlCls.getRadio('mn2_realign', 'mn2_realignonstruct', 'by Structure Alignment ' + me.htmlCls.wifiStr, undefined, undefined, 2);
56057
56633
 
56058
- html += me.htmlCls.setHtmlCls.getRadio('mn2_realign', 'mn2_realignonseqalign', 'by Sequence Alignment ' + me.htmlCls.wifiStr);
56059
- html += me.htmlCls.setHtmlCls.getRadio('mn2_realign', 'mn2_realignresbyres', 'Residue by Residue');
56634
+ html += me.htmlCls.setHtmlCls.getRadio('mn2_realign', 'mn2_realignonseqalign', 'by Sequence Alignment ' + me.htmlCls.wifiStr, undefined, undefined, 2);
56635
+ html += me.htmlCls.setHtmlCls.getRadio('mn2_realign', 'mn2_realignresbyres', 'Residue by Residue', undefined, undefined, 2);
56060
56636
  html += "</ul>";
56061
56637
  html += "</li>";
56062
56638
 
56063
- html += "<li><span>3D Printing</span>";
56639
+ //html += "<li><span>3D Printing</span>";
56640
+ html += me.htmlCls.setHtmlCls.getMenuText('mn1_3dpprint', '3D Printing', undefined, 1, 1);
56064
56641
  html += "<ul>";
56065
56642
  if(me.cfg.cid === undefined) {
56066
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportVrmlStab', 'WRL/VRML(Color, W/ Stab.)');
56067
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportStlStab', 'STL(W/ Stabilizers)');
56068
- html += "<li>-</li>";
56069
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportVrml', 'WRL/VRML(Color)');
56070
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportStl', 'STL');
56071
-
56072
- if(!me.cfg.simplemenu) {
56073
- html += "<li>-</li>";
56074
- html += me.htmlCls.setHtmlCls.getLink('mn1_stabilizerYes', 'Add All Stabilizers');
56075
- html += me.htmlCls.setHtmlCls.getLink('mn1_stabilizerNo', 'Remove All Stabilizers');
56076
- html += "<li>-</li>";
56077
- html += me.htmlCls.setHtmlCls.getLink('mn1_stabilizerOne', 'Add One Stabilizer');
56078
- html += me.htmlCls.setHtmlCls.getLink('mn1_stabilizerRmOne', 'Remove One Stabilizer');
56079
- html += "<li>-</li>";
56080
- html += me.htmlCls.setHtmlCls.getLink('mn1_thicknessSet', 'Set Thickness');
56081
- //html += me.htmlCls.setHtmlCls.getLink('mn1_thicknessReset', 'Reset Thickness');
56082
- }
56643
+ html += me.htmlCls.setHtmlCls.getLink('mn1_exportVrmlStab', 'WRL/VRML(Color, W/ Stab.)', 1, 2);
56644
+ html += me.htmlCls.setHtmlCls.getLink('mn1_exportStlStab', 'STL(W/ Stabilizers)', 1, 2);
56645
+ html += me.htmlCls.setHtmlCls.getMenuSep();
56646
+ html += me.htmlCls.setHtmlCls.getLink('mn1_exportVrml', 'WRL/VRML(Color)', undefined, 2);
56647
+ html += me.htmlCls.setHtmlCls.getLink('mn1_exportStl', 'STL', undefined, 2);
56648
+
56649
+ html += me.htmlCls.setHtmlCls.getMenuSep();
56650
+ html += me.htmlCls.setHtmlCls.getLink('mn1_stabilizerYes', 'Add All Stabilizers', undefined, 2);
56651
+ html += me.htmlCls.setHtmlCls.getLink('mn1_stabilizerNo', 'Remove All Stabilizers', undefined, 2);
56652
+ html += me.htmlCls.setHtmlCls.getMenuSep();
56653
+ html += me.htmlCls.setHtmlCls.getLink('mn1_stabilizerOne', 'Add One Stabilizer', undefined, 2);
56654
+ html += me.htmlCls.setHtmlCls.getLink('mn1_stabilizerRmOne', 'Remove One Stabilizer', undefined, 2);
56655
+ html += me.htmlCls.setHtmlCls.getMenuSep();
56656
+ html += me.htmlCls.setHtmlCls.getLink('mn1_thicknessSet', 'Set Thickness', undefined, 2);
56083
56657
  }
56084
56658
  else {
56085
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportVrml', 'VRML(Color)');
56086
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportStl', 'STL');
56659
+ html += me.htmlCls.setHtmlCls.getLink('mn1_exportVrml', 'VRML(Color)', 1, 2);
56660
+ html += me.htmlCls.setHtmlCls.getLink('mn1_exportStl', 'STL', 1, 2);
56087
56661
  }
56088
56662
 
56089
56663
  html += "</ul>";
56090
56664
  html += "</li>";
56091
56665
 
56092
- html += "<li><span>Save Files</span>";
56666
+ //html += "<li><span>Save File</span>";
56667
+ html += me.htmlCls.setHtmlCls.getMenuText('mn1_savefile', 'Save File', undefined, 1, 1);
56093
56668
  html += "<ul>";
56094
- //html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas', 'iCn3D PNG Image');
56095
-
56096
- html += "<li><span>iCn3D PNG Image</span>";
56669
+ //html += "<li><span>iCn3D PNG Image</span>";
56670
+ html += me.htmlCls.setHtmlCls.getMenuText('mn1_savepngimage', 'iCn3D PNG Image', undefined, 1, 2);
56097
56671
  html += "<ul>";
56098
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas', 'Original Size & HTML');
56099
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas1', 'Original Size');
56100
- if(!me.cfg.simplemenu) {
56101
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas2', '2X Large');
56102
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas4', '4X Large');
56103
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas8', '8X Large');
56104
- }
56105
- html += "</ul>";
56106
- html += "</li>";
56672
+ html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas', 'Original Size & HTML', 1, 3);
56673
+ html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas1', 'Original Size', undefined, 3);
56107
56674
 
56108
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportState', 'State File');
56109
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportSelections', 'Selection File');
56110
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportSelDetails', 'Selection Details');
56111
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportCounts', 'Residue Counts');
56675
+ html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas2', '2X Large', undefined, 3);
56676
+ html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas4', '4X Large', undefined, 3);
56677
+ html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas8', '8X Large', undefined, 3);
56112
56678
 
56113
- /*
56114
- html += "<li><span>PDB</span>";
56115
- html += "<ul>";
56116
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportPdbRes', 'Selected Residues');
56117
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportPdbChain', 'Selected Chains');
56118
- html += "<li><br/></li>";
56119
56679
  html += "</ul>";
56120
56680
  html += "</li>";
56121
- */
56122
56681
 
56123
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportPdbRes', 'PDB');
56124
- html += me.htmlCls.setHtmlCls.getLink('delphipdbh', 'PDB with Hydrogens');
56682
+ html += me.htmlCls.setHtmlCls.getLink('mn1_exportState', 'State File', undefined, 2);
56683
+ html += me.htmlCls.setHtmlCls.getLink('mn1_exportSelections', 'Selection File', undefined, 2);
56684
+ html += me.htmlCls.setHtmlCls.getLink('mn1_exportSelDetails', 'Selection Details', undefined, 2);
56685
+ html += me.htmlCls.setHtmlCls.getLink('mn1_exportCounts', 'Residue Counts', undefined, 2);
56686
+
56687
+ html += me.htmlCls.setHtmlCls.getLink('mn1_exportPdbRes', 'PDB', 1, 2);
56688
+ html += me.htmlCls.setHtmlCls.getLink('delphipdbh', 'PDB with Hydrogens', undefined, 2);
56125
56689
 
56126
56690
  if(me.cfg.cid === undefined) {
56127
- html += me.htmlCls.setHtmlCls.getLink('mn1_exportSecondary', 'Secondary Structure');
56691
+ html += me.htmlCls.setHtmlCls.getLink('mn1_exportSecondary', 'Secondary Structure', undefined, 2);
56128
56692
  }
56129
56693
 
56130
56694
  html += "<li><br/></li>";
@@ -56132,9 +56696,21 @@ class SetMenu {
56132
56696
  html += "</ul>";
56133
56697
  html += "</li>";
56134
56698
 
56135
- html += me.htmlCls.setHtmlCls.getLink('mn1_sharelink', 'Share Link ' + me.htmlCls.wifiStr);
56699
+ html += me.htmlCls.setHtmlCls.getLink('mn1_sharelink', 'Share Link ' + me.htmlCls.wifiStr, 1, 1);
56700
+
56701
+ html += me.htmlCls.setHtmlCls.getLink('mn1_replayon', 'Replay Each Step', undefined, 1);
56136
56702
 
56137
- html += me.htmlCls.setHtmlCls.getLink('mn1_replayon', 'Replay Each Step');
56703
+ html += me.htmlCls.setHtmlCls.getMenuSep();
56704
+
56705
+ html += me.htmlCls.setHtmlCls.getMenuText('mn1_menuwrap', 'Customize Menus', undefined, 1, 1);
56706
+ html += "<ul>";
56707
+ html += me.htmlCls.setHtmlCls.getLink('mn1_menuall', 'All Menus', 1, 2);
56708
+ html += me.htmlCls.setHtmlCls.getLink('mn1_menusimple', 'Simple Menus', 1, 2);
56709
+ html += me.htmlCls.setHtmlCls.getMenuSep();
56710
+ html += me.htmlCls.setHtmlCls.getLink('mn1_menupref', 'Preferences', 1, 2);
56711
+ html += me.htmlCls.setHtmlCls.getLink('mn1_menuloadpref', 'Load Preferences', 1, 2);
56712
+ html += "</ul>";
56713
+ html += "</li>";
56138
56714
 
56139
56715
  html += "<li><br/></li>";
56140
56716
 
@@ -56170,87 +56746,86 @@ class SetMenu {
56170
56746
 
56171
56747
  html += "<ul class='icn3d-mn-item'>";
56172
56748
 
56173
- if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getLink('mn2_definedsets', 'Defined Sets');
56174
- html += me.htmlCls.setHtmlCls.getLink('mn2_selectall', 'All');
56175
- if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getLink('mn2_selectdisplayed', 'Displayed Set');
56176
- html += me.htmlCls.setHtmlCls.getLink('mn2_aroundsphere', 'by Distance');
56749
+ html += me.htmlCls.setHtmlCls.getLink('mn2_definedsets', 'Defined Sets', 1, 1);
56750
+ html += me.htmlCls.setHtmlCls.getLink('mn2_selectall', 'All', undefined, 1);
56751
+ html += me.htmlCls.setHtmlCls.getLink('mn2_selectdisplayed', 'Displayed Set', undefined, 1);
56752
+ html += me.htmlCls.setHtmlCls.getLink('mn2_aroundsphere', 'by Distance', 1, 1);
56177
56753
 
56178
- html += "<li><span>by Property</span>";
56754
+ //html += "<li><span>by Property</span>";
56755
+ html += me.htmlCls.setHtmlCls.getMenuText('mn2_selbyprop', 'by Property', undefined, undefined, 1);
56179
56756
  html += "<ul>";
56180
- html += me.htmlCls.setHtmlCls.getLink('mn2_propPos', 'Positive');
56181
- html += me.htmlCls.setHtmlCls.getLink('mn2_propNeg', 'Negative');
56182
- html += me.htmlCls.setHtmlCls.getLink('mn2_propHydro', 'Hydrophobic');
56183
- html += me.htmlCls.setHtmlCls.getLink('mn2_propPolar', 'Polar');
56184
- html += me.htmlCls.setHtmlCls.getLink('mn2_propBfactor', 'B-factor');
56185
- html += me.htmlCls.setHtmlCls.getLink('mn2_propSolAcc', 'Solvent Accessibility');
56757
+ html += me.htmlCls.setHtmlCls.getLink('mn2_propPos', 'Positive', undefined, 2);
56758
+ html += me.htmlCls.setHtmlCls.getLink('mn2_propNeg', 'Negative', undefined, 2);
56759
+ html += me.htmlCls.setHtmlCls.getLink('mn2_propHydro', 'Hydrophobic', undefined, 2);
56760
+ html += me.htmlCls.setHtmlCls.getLink('mn2_propPolar', 'Polar', undefined, 2);
56761
+ html += me.htmlCls.setHtmlCls.getLink('mn2_propBfactor', 'B-factor', undefined, 2);
56762
+ html += me.htmlCls.setHtmlCls.getLink('mn2_propSolAcc', 'Solvent Accessibility', undefined, 2);
56186
56763
  html += "</ul>";
56187
56764
  html += "</li>";
56188
56765
 
56189
- if(!me.cfg.simplemenu) {
56190
- html += me.htmlCls.setHtmlCls.getLink('mn2_selectcomplement', 'Inverse');
56191
- html += me.htmlCls.setHtmlCls.getLink('mn2_selectmainchains', 'Main Chains');
56192
- html += me.htmlCls.setHtmlCls.getLink('mn2_selectsidechains', 'Side Chains');
56193
- html += me.htmlCls.setHtmlCls.getLink('mn2_selectmainsidechains', 'Main & Side Chains');
56194
- html += me.htmlCls.setHtmlCls.getLink('mn2_command', 'Advanced');
56195
- }
56766
+ html += me.htmlCls.setHtmlCls.getLink('mn2_selectcomplement', 'Inverse', undefined, 1);
56767
+ html += me.htmlCls.setHtmlCls.getLink('mn2_selectmainchains', 'Main Chains', undefined, 1);
56768
+ html += me.htmlCls.setHtmlCls.getLink('mn2_selectsidechains', 'Side Chains', undefined, 1);
56769
+ html += me.htmlCls.setHtmlCls.getLink('mn2_selectmainsidechains', 'Main & Side Chains', undefined, 1);
56770
+ html += me.htmlCls.setHtmlCls.getLink('mn2_command', 'Advanced', undefined, 1);
56196
56771
 
56197
56772
  if(me.cfg.cid === undefined) {
56198
- html += "<li><span>Select on 3D</span>";
56773
+ //html += "<li><span>Select on 3D</span>";
56774
+ html += me.htmlCls.setHtmlCls.getMenuText('mn2_selon3d', 'Select on 3D', undefined, 1, 1);
56199
56775
  html += "<ul>";
56200
56776
 
56201
56777
  html += "<li>\"Alt\"+Click: start selection</li>";
56202
56778
  html += "<li>\"Ctrl\"+Click: union selection</li>";
56203
56779
  html += "<li>\"Shift\"+Click: range Selection</li>";
56204
- html += "<li>-</li>";
56205
- html += me.htmlCls.setHtmlCls.getRadio('mn2_pk', 'mn2_pkChain', 'Chain');
56780
+ html += me.htmlCls.setHtmlCls.getMenuSep();
56781
+ html += me.htmlCls.setHtmlCls.getRadio('mn2_pk', 'mn2_pkChain', 'Chain', undefined, 1, 2);
56206
56782
  if(me.cfg.mmdbid !== undefined || me.cfg.gi !== undefined) {
56207
- html += me.htmlCls.setHtmlCls.getRadio('mn2_pk', 'mn2_pkDomain', '3D Domain');
56783
+ html += me.htmlCls.setHtmlCls.getRadio('mn2_pk', 'mn2_pkDomain', '3D Domain', undefined, undefined, 2);
56208
56784
  }
56209
- html += me.htmlCls.setHtmlCls.getRadio('mn2_pk', 'mn2_pkStrand', 'Strand/Helix');
56210
- html += me.htmlCls.setHtmlCls.getRadio('mn2_pk', 'mn2_pkResidue', 'Residue', true);
56211
- html += me.htmlCls.setHtmlCls.getRadio('mn2_pk', 'mn2_pkYes', 'Atom');
56212
- html += me.htmlCls.setHtmlCls.getRadio('mn2_pk', 'mn2_pkNo', 'None');
56785
+ html += me.htmlCls.setHtmlCls.getRadio('mn2_pk', 'mn2_pkStrand', 'Strand/Helix', undefined, undefined, 2);
56786
+ html += me.htmlCls.setHtmlCls.getRadio('mn2_pk', 'mn2_pkResidue', 'Residue', true, 1, 2);
56787
+ html += me.htmlCls.setHtmlCls.getRadio('mn2_pk', 'mn2_pkYes', 'Atom', undefined, 1, 2);
56788
+ html += me.htmlCls.setHtmlCls.getRadio('mn2_pk', 'mn2_pkNo', 'None', undefined, undefined, 2);
56213
56789
  html += "</ul>";
56214
56790
  html += "</li>";
56215
56791
  }
56216
56792
  else {
56217
56793
  if(me.utilsCls.isMobile()) {
56218
- html += "<li><span>Touch to pick</span>";
56794
+ html += "<li><span>Touch to pick</span></li>";
56219
56795
  }
56220
56796
  else {
56221
- html += "<li><span>Picking with<br>\"Alt\" + Click</span>";
56797
+ html += "<li><span>Picking with<br>\"Alt\" + Click</span></li>";
56222
56798
  }
56223
56799
  }
56224
56800
 
56225
- html += "<li>-</li>";
56801
+ html += me.htmlCls.setHtmlCls.getMenuSep();
56226
56802
 
56227
- html += me.htmlCls.setHtmlCls.getLink('mn2_saveselection', 'Save Selection');
56228
- html += me.htmlCls.setHtmlCls.getLink('clearall', 'Clear Selection');
56803
+ html += me.htmlCls.setHtmlCls.getLink('mn2_saveselection', 'Save Selection', 1, 1);
56804
+ html += me.htmlCls.setHtmlCls.getLink('clearall', 'Clear Selection', undefined, 1);
56229
56805
 
56230
- html += "<li>-</li>";
56806
+ html += me.htmlCls.setHtmlCls.getMenuSep();
56231
56807
 
56232
- if(!me.cfg.simplemenu) {
56233
- html += "<li><span>Highlight Color</span>";
56234
- html += "<ul>";
56235
- html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_clr', 'mn2_hl_clrYellow', 'Yellow', true);
56236
- html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_clr', 'mn2_hl_clrGreen', 'Green');
56237
- html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_clr', 'mn2_hl_clrRed', 'Red');
56238
- html += "</ul>";
56239
- html += "</li>";
56240
- html += "<li><span>Highlight Style</span>";
56241
- html += "<ul>";
56808
+ //html += "<li><span>Highlight Color</span>";
56809
+ html += me.htmlCls.setHtmlCls.getMenuText('mn2_hlcolor', 'Highlight Color', undefined, undefined, 1);
56810
+ html += "<ul>";
56811
+ html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_clr', 'mn2_hl_clrYellow', 'Yellow', true, undefined, 2);
56812
+ html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_clr', 'mn2_hl_clrGreen', 'Green', undefined, undefined, 2);
56813
+ html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_clr', 'mn2_hl_clrRed', 'Red', undefined, undefined, 2);
56814
+ html += "</ul>";
56815
+ html += "</li>";
56816
+ //html += "<li><span>Highlight Style</span>";
56817
+ html += me.htmlCls.setHtmlCls.getMenuText('mn2_hlstyle', 'Highlight Style', undefined, undefined, 1);
56818
+ html += "<ul>";
56242
56819
 
56243
- html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_style', 'mn2_hl_styleOutline', 'Outline', true);
56244
- html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_style', 'mn2_hl_styleObject', '3D Objects');
56245
- //html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_style', 'mn2_hl_styleNone', 'No Highlight');
56820
+ html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_style', 'mn2_hl_styleOutline', 'Outline', true, undefined, 2);
56821
+ html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_style', 'mn2_hl_styleObject', '3D Objects', undefined, undefined, 2);
56246
56822
 
56247
- html += "</ul>";
56248
- html += "</li>";
56249
- }
56823
+ html += "</ul>";
56824
+ html += "</li>";
56250
56825
 
56251
56826
  //html += me.htmlCls.setHtmlCls.getLink('mn2_hl_styleNone', 'Clear Highlight');
56252
56827
 
56253
- html += me.htmlCls.setHtmlCls.getLink('toggleHighlight2', 'Toggle Highlight');
56828
+ html += me.htmlCls.setHtmlCls.getLink('toggleHighlight2', 'Toggle Highlight', 1, 1);
56254
56829
 
56255
56830
  html += "<li><br/></li>";
56256
56831
 
@@ -56284,108 +56859,104 @@ class SetMenu {
56284
56859
  let html = "";
56285
56860
  html += "<ul class='icn3d-mn-item'>";
56286
56861
 
56287
- html += me.htmlCls.setHtmlCls.getLink('mn2_show_selected', 'View Selection');
56288
- if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getLink('mn2_hide_selected', 'Hide Selection');
56289
- html += me.htmlCls.setHtmlCls.getLink('mn2_selectedcenter', 'Zoom in Selection');
56290
- html += me.htmlCls.setHtmlCls.getLink('mn6_center', 'Center Selection');
56862
+ html += me.htmlCls.setHtmlCls.getLink('mn2_show_selected', 'View Selection', 1, 1);
56863
+ html += me.htmlCls.setHtmlCls.getLink('mn2_hide_selected', 'Hide Selection', 1, 1);
56864
+ html += me.htmlCls.setHtmlCls.getLink('mn2_selectedcenter', 'Zoom in Selection', 1, 1);
56865
+ html += me.htmlCls.setHtmlCls.getLink('mn6_center', 'Center Selection', undefined, 1);
56291
56866
  html += me.htmlCls.setHtmlCls.getLink('mn2_fullstru', 'View Full Structure');
56292
- html += "<li id='" + me.pre + "mn2_alternateWrap'><span id='" + me.pre + "mn2_alternate' class='icn3d-link'>Alternate(Key \"a\")</span></li>";
56867
+ //html += "<li id='" + me.pre + "mn2_alternateWrap'><span id='" + me.pre + "mn2_alternate' class='icn3d-link'>Alternate(Key \"a\")</span></li>";
56868
+ html += me.htmlCls.setHtmlCls.getLinkWrapper('mn2_alternate', 'Alternate(Key "a")', 'mn2_alternateWrap', undefined, 1);
56293
56869
 
56294
56870
  if(me.cfg.opmid !== undefined) {
56295
- html += "<li id='" + me.pre + "togglememli'><span id='" + me.pre + "togglemem' class='icn3d-link'>Toggle Membrane</span></li>";
56296
- html += "<li id='" + me.pre + "adjustmemli'><span id='" + me.pre + "adjustmem' class='icn3d-link'>Adjust Membrane</span></li>";
56297
- html += "<li id='" + me.pre + "selectplaneli'><span id='" + me.pre + "selectplane' class='icn3d-link'>Select between<br>Two X-Y Planes</span></li>";
56298
- }
56299
- else {
56300
- html += "<li id='" + me.pre + "togglememli' style='display:none'><span id='" + me.pre + "togglemem' class='icn3d-link'>Toggle Membrane</span></li>";
56301
- html += "<li id='" + me.pre + "adjustmemli' style='display:none'><span id='" + me.pre + "adjustmem' class='icn3d-link'>Adjust Membrane</span></li>";
56302
- html += "<li id='" + me.pre + "selectplaneli' style='display:none'><span id='" + me.pre + "selectplane' class='icn3d-link'>Select between<br>Two X-Y Planes</span></li>";
56871
+ //html += "<li id='" + me.pre + "togglememli'><span id='" + me.pre + "togglemem' class='icn3d-link'>Toggle Membrane</span></li>";
56872
+ html += me.htmlCls.setHtmlCls.getLinkWrapper('togglemem', 'Toggle Membrane', 'togglememli', undefined, 1);
56873
+ //html += "<li id='" + me.pre + "adjustmemli'><span id='" + me.pre + "adjustmem' class='icn3d-link'>Adjust Membrane</span></li>";
56874
+ html += me.htmlCls.setHtmlCls.getLinkWrapper('adjustmem', 'Adjust Membrane', 'adjustmemli', undefined, 1);
56875
+ //html += "<li id='" + me.pre + "selectplaneli'><span id='" + me.pre + "selectplane' class='icn3d-link'>Select between<br>Two X-Y Planes</span></li>";
56876
+ html += me.htmlCls.setHtmlCls.getLinkWrapper('selectplane', 'Select between<br>Two X-Y Planes</span>', 'selectplaneli', undefined, 1);
56303
56877
  }
56304
56878
 
56305
- html += "<li>-</li>";
56306
-
56307
- let liStr = "<li><a href='";
56879
+ html += me.htmlCls.setHtmlCls.getMenuSep();
56308
56880
 
56309
- html += "<li><span>VR & AR Hints</span>";
56881
+ //html += "<li><span>VR & AR Hints</span>";
56882
+ html += me.htmlCls.setHtmlCls.getMenuText('mn2_vrarhints', 'VR & AR Hints', undefined, 1, 1);
56310
56883
  html += "<ul>";
56311
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#vr' target='_blank'>VR: VR Headsets</a></li>";
56312
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#ar' target='_blank'>AR: Chrome in Android</a></li>";
56884
+ html += me.htmlCls.setHtmlCls.getMenuUrl("vrhint", me.htmlCls.baseUrl + "icn3d/icn3d.html#vr", "VR: VR Headsets", 1, 2);
56885
+ html += me.htmlCls.setHtmlCls.getMenuUrl("arhint", me.htmlCls.baseUrl + "icn3d/icn3d.html#ar", "AR: Chrome in Android", 1, 2);
56313
56886
  html += "</ul>";
56314
- /*
56315
- let liStr = "<li><a href='";
56316
-
56317
- html += "<ul class='icn3d-mn-item'>";
56318
-
56319
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#about' target='_blank'>About iCn3D<span style='font-size:0.9em'> " + me.REVISION + "</span></a></li>";
56320
-
56321
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#gallery' target='_blank'>Live Gallery " + me.htmlCls.wifiStr + "</a></li>";
56322
- */
56887
+ html += "</li>";
56323
56888
 
56324
- html += me.htmlCls.setHtmlCls.getLink('mn6_sidebyside', 'Side by Side');
56889
+ html += me.htmlCls.setHtmlCls.getLink('mn6_sidebyside', 'Side by Side', 1, 1);
56325
56890
 
56326
- html += "<li><span>Rotate</span>";
56891
+ //html += "<li><span>Rotate</span>";
56892
+ html += me.htmlCls.setHtmlCls.getMenuText('mn2_rotate', 'Rotate', undefined, 1, 1);
56327
56893
  html += "<ul>";
56328
56894
 
56329
- html += "<li><span>Rotate 90&deg;</span>";
56895
+ //html += "<li><span>Rotate 90&deg;</span>";
56896
+ html += me.htmlCls.setHtmlCls.getMenuText('mn2_rotate90', 'Rotate 90&deg;', undefined, undefined, 2);
56330
56897
  html += "<ul>";
56331
- html += me.htmlCls.setHtmlCls.getRadio('mn6_rotate90', 'mn6_rotatex', 'X-axis(Shift + Key M)');
56332
- html += me.htmlCls.setHtmlCls.getRadio('mn6_rotate90', 'mn6_rotatey', 'Y-axis(Shift + Key J)');
56333
- html += me.htmlCls.setHtmlCls.getRadio('mn6_rotate90', 'mn6_rotatez', 'Z-axis');
56898
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_rotate90', 'mn6_rotatex', 'X-axis(Shift + Key M)', undefined, undefined, 2);
56899
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_rotate90', 'mn6_rotatey', 'Y-axis(Shift + Key J)', undefined, undefined, 2);
56900
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_rotate90', 'mn6_rotatez', 'Z-axis', undefined, undefined, 2);
56334
56901
  html += "</ul>";
56335
56902
  html += "</li>";
56336
- html += "<li><span>Auto Rotation</span>";
56903
+ //html += "<li><span>Auto Rotation</span>";
56904
+ html += me.htmlCls.setHtmlCls.getMenuText('mn2_rotateauto', 'Auto Rotation', undefined, 1, 2);
56337
56905
  html += "<ul>";
56338
- html += me.htmlCls.setHtmlCls.getRadio('mn6_rotate', 'mn6_rotateleft', 'Rotate Left');
56339
- html += me.htmlCls.setHtmlCls.getRadio('mn6_rotate', 'mn6_rotateright', 'Rotate Right');
56340
- html += me.htmlCls.setHtmlCls.getRadio('mn6_rotate', 'mn6_rotateup', 'Rotate Up');
56341
- html += me.htmlCls.setHtmlCls.getRadio('mn6_rotate', 'mn6_rotatedown', 'Rotate Down');
56906
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_rotate', 'mn6_rotateleft', 'Rotate Left', undefined, 1, 3);
56907
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_rotate', 'mn6_rotateright', 'Rotate Right', undefined, 1, 3);
56908
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_rotate', 'mn6_rotateup', 'Rotate Up', undefined, 1, 3);
56909
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_rotate', 'mn6_rotatedown', 'Rotate Down', undefined, 1, 3);
56342
56910
  html += "</ul>";
56343
56911
  html += "</li>";
56344
56912
 
56345
56913
  html += "</ul>";
56346
56914
  html += "</li>";
56347
56915
 
56348
- html += "<li><span>Camera</span>";
56916
+ //html += "<li><span>Camera</span>";
56917
+ html += me.htmlCls.setHtmlCls.getMenuText('mn2_camera', 'Camera', undefined, undefined, 1);
56349
56918
  html += "<ul>";
56350
- html += me.htmlCls.setHtmlCls.getRadio('mn6_camera', 'mn6_cameraPers', 'Perspective', true);
56351
- html += me.htmlCls.setHtmlCls.getRadio('mn6_camera', 'mn6_cameraOrth', 'Orthographic');
56919
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_camera', 'mn6_cameraPers', 'Perspective', true, undefined, 2);
56920
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_camera', 'mn6_cameraOrth', 'Orthographic', undefined, undefined, 2);
56352
56921
  html += "</ul>";
56353
56922
  html += "</li>";
56354
- html += "<li><span>Fog for Selection</span>";
56923
+ //html += "<li><span>Fog for Selection</span>";
56924
+ html += me.htmlCls.setHtmlCls.getMenuText('mn2_fog', 'Fog for Selection', undefined, undefined, 1);
56355
56925
  html += "<ul>";
56356
- html += me.htmlCls.setHtmlCls.getRadio('mn6_showfog', 'mn6_showfogYes', 'On');
56357
- html += me.htmlCls.setHtmlCls.getRadio('mn6_showfog', 'mn6_showfogNo', 'Off', true);
56926
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_showfog', 'mn6_showfogYes', 'On', undefined, undefined, 2);
56927
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_showfog', 'mn6_showfogNo', 'Off', true, undefined, 2);
56358
56928
  html += "</ul>";
56359
56929
  html += "</li>";
56360
- html += "<li><span>Slab for Selection</span>";
56930
+ //html += "<li><span>Slab for Selection</span>";
56931
+ html += me.htmlCls.setHtmlCls.getMenuText('mn2_slab', 'Slab for Selection', undefined, undefined, 1);
56361
56932
  html += "<ul>";
56362
- html += me.htmlCls.setHtmlCls.getRadio('mn6_showslab', 'mn6_showslabYes', 'On');
56363
- html += me.htmlCls.setHtmlCls.getRadio('mn6_showslab', 'mn6_showslabNo', 'Off', true);
56933
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_showslab', 'mn6_showslabYes', 'On', undefined, undefined, 2);
56934
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_showslab', 'mn6_showslabNo', 'Off', true, undefined, 2);
56364
56935
  html += "</ul>";
56365
56936
  html += "</li>";
56366
- html += "<li><span>XYZ-axes</span>";
56937
+ //html += "<li><span>XYZ-axes</span>";
56938
+ html += me.htmlCls.setHtmlCls.getMenuText('mn2_axes', 'XYZ-axes', undefined, 1);
56367
56939
  html += "<ul>";
56368
- html += me.htmlCls.setHtmlCls.getRadio('mn6_showaxis', 'mn6_showaxisYes', 'Original');
56369
- html += me.htmlCls.setHtmlCls.getRadio('mn6_showaxis', 'mn6_showaxisSel', 'Prin. Axes on Sel.');
56370
- html += me.htmlCls.setHtmlCls.getRadio('mn6_showaxis', 'mn6_showaxisNo', 'Hide', true);
56940
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_showaxis', 'mn6_showaxisYes', 'Original', undefined, undefined, 2);
56941
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_showaxis', 'mn6_showaxisSel', 'Prin. Axes on Sel.', undefined, undefined, 2);
56942
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_showaxis', 'mn6_showaxisNo', 'Hide', true, undefined, 2);
56371
56943
  html += "</ul>";
56372
56944
  html += "</li>";
56373
56945
 
56374
- html += "<li>-</li>";
56946
+ html += me.htmlCls.setHtmlCls.getMenuSep();
56375
56947
 
56376
- html += "<li><span>Reset</span>";
56948
+ //html += "<li><span>Reset</span>";
56949
+ html += me.htmlCls.setHtmlCls.getMenuText('mn2_resetwrap', 'Reset', undefined, 1, 1);
56377
56950
  html += "<ul>";
56378
- html += me.htmlCls.setHtmlCls.getRadio('mn6_reset', 'reset', 'All');
56379
- html += me.htmlCls.setHtmlCls.getRadio('mn6_reset', 'mn6_resetOrientation', 'Orientation');
56951
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_reset', 'reset', 'All', undefined, 1, 2);
56952
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_reset', 'mn6_resetOrientation', 'Orientation', undefined, 1, 2);
56380
56953
  html += "</ul>";
56381
56954
  html += "</li>";
56382
56955
 
56383
- if(!me.cfg.simplemenu) {
56384
- html += me.htmlCls.setHtmlCls.getLink('mn6_back', 'Undo');
56385
- html += me.htmlCls.setHtmlCls.getLink('mn6_forward', 'Redo');
56386
- }
56956
+ html += me.htmlCls.setHtmlCls.getLink('mn6_back', 'Undo', undefined, 1);
56957
+ html += me.htmlCls.setHtmlCls.getLink('mn6_forward', 'Redo', undefined, 1);
56387
56958
 
56388
- html += me.htmlCls.setHtmlCls.getLink('mn6_fullscreen', 'Full Screen');
56959
+ html += me.htmlCls.setHtmlCls.getLink('mn6_fullscreen', 'Full Screen', undefined, 1);
56389
56960
  // html += me.htmlCls.setHtmlCls.getLink('mn6_exitfullscreen', 'Exit Full Screen');
56390
56961
 
56391
56962
  html += "<li><br/></li>";
@@ -56423,243 +56994,248 @@ class SetMenu {
56423
56994
  html += "<ul class='icn3d-mn-item'>";
56424
56995
 
56425
56996
  if(me.cfg.cid === undefined) {
56426
- html += "<li><span>Proteins</span>";
56997
+ //html += "<li><span>Proteins</span>";
56998
+ html += me.htmlCls.setHtmlCls.getMenuText('mn3_proteinwrap', 'Proteins', undefined, 1, 1);
56427
56999
  html += "<ul>";
56428
57000
  if(me.cfg.align !== undefined || me.cfg.chainalign !== undefined) {
56429
- html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsRibbon', 'Ribbon');
57001
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsRibbon', 'Ribbon', undefined, 1, 2);
56430
57002
  }
56431
57003
  else {
56432
- html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsRibbon', 'Ribbon', true);
57004
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsRibbon', 'Ribbon', true, 1, 2);
56433
57005
  }
56434
57006
 
56435
- html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsStrand', 'Strand');
56436
- html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsCylinder', 'Cylinder and Plate');
56437
- html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsSchematic', 'Schematic');
57007
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsStrand', 'Strand', undefined, undefined, 2);
57008
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsCylinder', 'Cylinder and Plate', undefined, undefined, 2);
57009
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsSchematic', 'Schematic', undefined, 1, 2);
56438
57010
 
56439
57011
  if(me.cfg.align !== undefined || me.cfg.chainalign !== undefined) {
56440
- html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsCalpha', 'C Alpha Trace', true);
57012
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsCalpha', 'C Alpha Trace', true, 1, 2);
56441
57013
  }
56442
57014
  else {
56443
- html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsCalpha', 'C Alpha Trace');
57015
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsCalpha', 'C Alpha Trace', undefined, 1, 2);
56444
57016
  }
56445
57017
 
56446
- html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsBackbone', 'Backbone');
56447
- html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsBfactor', 'B-factor Tube');
56448
- html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsLines', 'Lines');
56449
- html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsStick', 'Stick');
56450
- html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsBallstick', 'Ball and Stick');
56451
- html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsSphere', 'Sphere');
56452
- html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsNo', 'Hide');
57018
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsBackbone', 'Backbone', undefined, undefined, 2);
57019
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsBfactor', 'B-factor Tube', undefined, 1, 2);
57020
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsLines', 'Lines', undefined, 1, 2);
57021
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsStick', 'Stick', undefined, 1, 2);
57022
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsBallstick', 'Ball and Stick', undefined, 1, 2);
57023
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsSphere', 'Sphere', undefined, 1, 2);
57024
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_proteins', 'mn3_proteinsNo', 'Hide', undefined, 1, 2);
56453
57025
  html += "</ul>";
56454
57026
  html += "</li>";
56455
57027
 
56456
- html += "<li><span>Side Chains</span>";
57028
+ //html += "<li><span>Side Chains</span>";
57029
+ html += me.htmlCls.setHtmlCls.getMenuText('mn3_sidecwrap', 'Side Chains', undefined, 1, 1);
56457
57030
  html += "<ul>";
56458
57031
 
56459
- html += me.htmlCls.setHtmlCls.getRadio('mn3_sidec', 'mn3_sidecLines', 'Lines');
56460
- html += me.htmlCls.setHtmlCls.getRadio('mn3_sidec', 'mn3_sidecStick', 'Stick');
56461
- html += me.htmlCls.setHtmlCls.getRadio('mn3_sidec', 'mn3_sidecBallstick', 'Ball and Stick');
56462
- html += me.htmlCls.setHtmlCls.getRadio('mn3_sidec', 'mn3_sidecSphere', 'Sphere');
56463
- html += me.htmlCls.setHtmlCls.getRadio('mn3_sidec', 'mn3_sidecNo', 'Hide', true);
57032
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_sidec', 'mn3_sidecLines', 'Lines', undefined, 1, 2);
57033
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_sidec', 'mn3_sidecStick', 'Stick', undefined, 1, 2);
57034
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_sidec', 'mn3_sidecBallstick', 'Ball and Stick', undefined, 1, 2);
57035
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_sidec', 'mn3_sidecSphere', 'Sphere', undefined, 1, 2);
57036
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_sidec', 'mn3_sidecNo', 'Hide', true, 1, 2);
56464
57037
  html += "</ul>";
56465
57038
  html += "</li>";
56466
57039
 
56467
- html += "<li><span>Nucleotides</span>";
57040
+ //html += "<li><span>Nucleotides</span>";
57041
+ html += me.htmlCls.setHtmlCls.getMenuText('mn3_nuclwrap', 'Nucleotides', undefined, 1, 1);
56468
57042
  html += "<ul>";
56469
- html += me.htmlCls.setHtmlCls.getRadio('mn3_nucl', 'mn3_nuclCartoon', 'Cartoon', true);
56470
- html += me.htmlCls.setHtmlCls.getRadio('mn3_nucl', 'mn3_nuclPhos', "O3' Trace");
56471
- html += me.htmlCls.setHtmlCls.getRadio('mn3_nucl', 'mn3_nuclBackbone', 'Backbone');
56472
- html += me.htmlCls.setHtmlCls.getRadio('mn3_nucl', 'mn3_nuclSchematic', 'Schematic');
56473
- html += me.htmlCls.setHtmlCls.getRadio('mn3_nucl', 'mn3_nuclLines', 'Lines');
56474
- html += me.htmlCls.setHtmlCls.getRadio('mn3_nucl', 'mn3_nuclStick', 'Stick');
56475
- html += me.htmlCls.setHtmlCls.getRadio('mn3_nucl', 'mn3_nuclBallstick', 'Ball and Stick');
56476
- html += me.htmlCls.setHtmlCls.getRadio('mn3_nucl', 'mn3_nuclSphere', 'Sphere');
56477
- html += me.htmlCls.setHtmlCls.getRadio('mn3_nucl', 'mn3_nuclNo', 'Hide');
57043
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_nucl', 'mn3_nuclCartoon', 'Cartoon', true, 1, 2);
57044
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_nucl', 'mn3_nuclPhos', "O3' Trace", undefined, 1, 2);
57045
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_nucl', 'mn3_nuclBackbone', 'Backbone', undefined, undefined, 2);
57046
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_nucl', 'mn3_nuclSchematic', 'Schematic', undefined, 1, 2);
57047
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_nucl', 'mn3_nuclLines', 'Lines', undefined, 1, 2);
57048
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_nucl', 'mn3_nuclStick', 'Stick', undefined, 1, 2);
57049
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_nucl', 'mn3_nuclBallstick', 'Ball and Stick', undefined, 1, 2);
57050
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_nucl', 'mn3_nuclSphere', 'Sphere', undefined, 1, 2);
57051
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_nucl', 'mn3_nuclNo', 'Hide', undefined, 1, 2);
56478
57052
  html += "</ul>";
56479
57053
  html += "</li>";
56480
57054
 
56481
- html += "<li><span>Nucl. Bases</span>";
57055
+ //html += "<li><span>Nucl. Bases</span>";
57056
+ html += me.htmlCls.setHtmlCls.getMenuText('mn3_ntbasewrap', 'Nucl. Bases', undefined, 1, 1);
56482
57057
  html += "<ul>";
56483
57058
 
56484
- html += me.htmlCls.setHtmlCls.getRadio('mn3_ntbase', 'mn3_ntbaseLines', 'Lines');
56485
- html += me.htmlCls.setHtmlCls.getRadio('mn3_ntbase', 'mn3_ntbaseStick', 'Stick');
56486
- html += me.htmlCls.setHtmlCls.getRadio('mn3_ntbase', 'mn3_ntbaseBallstick', 'Ball and Stick');
56487
- html += me.htmlCls.setHtmlCls.getRadio('mn3_ntbase', 'mn3_ntbaseSphere', 'Sphere');
56488
- html += me.htmlCls.setHtmlCls.getRadio('mn3_ntbase', 'mn3_ntbaseNo', 'Hide', true);
57059
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_ntbase', 'mn3_ntbaseLines', 'Lines', undefined, 1, 2);
57060
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_ntbase', 'mn3_ntbaseStick', 'Stick', undefined, 1, 2);
57061
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_ntbase', 'mn3_ntbaseBallstick', 'Ball and Stick', undefined, 1, 2);
57062
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_ntbase', 'mn3_ntbaseSphere', 'Sphere', undefined, 1, 2);
57063
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_ntbase', 'mn3_ntbaseNo', 'Hide', true, 1, 2);
56489
57064
  html += "</ul>";
56490
57065
  html += "</li>";
56491
57066
  }
56492
57067
 
56493
- html += "<li><span>Chemicals</span>";
57068
+ //html += "<li><span>Chemicals</span>";
57069
+ html += me.htmlCls.setHtmlCls.getMenuText('mn3_ligwrap', 'Chemicals', undefined, 1, 1);
56494
57070
  html += "<ul>";
56495
- html += me.htmlCls.setHtmlCls.getRadio('mn3_lig', 'mn3_ligLines', 'Lines');
57071
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_lig', 'mn3_ligLines', 'Lines', undefined, 1, 2);
56496
57072
  if(me.cfg.cid === undefined) {
56497
- html += me.htmlCls.setHtmlCls.getRadio('mn3_lig', 'mn3_ligStick', 'Stick', true);
56498
- html += me.htmlCls.setHtmlCls.getRadio('mn3_lig', 'mn3_ligBallstick', 'Ball and Stick');
57073
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_lig', 'mn3_ligStick', 'Stick', true, 1, 2);
57074
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_lig', 'mn3_ligBallstick', 'Ball and Stick', undefined, 1, 2);
56499
57075
  }
56500
57076
  else {
56501
- html += me.htmlCls.setHtmlCls.getRadio('mn3_lig', 'mn3_ligStick', 'Stick');
56502
- html += me.htmlCls.setHtmlCls.getRadio('mn3_lig', 'mn3_ligBallstick', 'Ball and Stick', true);
57077
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_lig', 'mn3_ligStick', 'Stick', undefined, 1, 2);
57078
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_lig', 'mn3_ligBallstick', 'Ball and Stick', true, 1, 2);
56503
57079
  }
56504
- html += me.htmlCls.setHtmlCls.getRadio('mn3_lig', 'mn3_ligSchematic', 'Schematic');
56505
- html += me.htmlCls.setHtmlCls.getRadio('mn3_lig', 'mn3_ligSphere', 'Sphere');
56506
- html += me.htmlCls.setHtmlCls.getRadio('mn3_lig', 'mn3_ligNo', 'Hide');
57080
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_lig', 'mn3_ligSchematic', 'Schematic', undefined, 1, 2);
57081
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_lig', 'mn3_ligSphere', 'Sphere', undefined, 1, 2);
57082
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_lig', 'mn3_ligNo', 'Hide', undefined, 1, 2);
56507
57083
  html += "</ul>";
56508
57084
  html += "</li>";
56509
57085
 
56510
57086
  //if(me.cfg.cid !== undefined) {
56511
- html += "<li><span>Hydrogens</span>";
57087
+ //html += "<li><span>Hydrogens</span>";
57088
+ html += me.htmlCls.setHtmlCls.getMenuText('mn3_hydrogenswrap', 'Hydrogens', undefined, 1, 1);
56512
57089
  html += "<ul>";
56513
- html += me.htmlCls.setHtmlCls.getRadio('mn3_hydrogens', 'mn3_hydrogensYes', 'Show', true);
56514
- html += me.htmlCls.setHtmlCls.getRadio('mn3_hydrogens', 'mn3_hydrogensNo', 'Hide');
57090
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_hydrogens', 'mn3_hydrogensYes', 'Show', true, 1, 2);
57091
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_hydrogens', 'mn3_hydrogensNo', 'Hide', undefined, 1, 2);
56515
57092
  html += "</ul>";
56516
57093
  html += "</li>";
56517
57094
  //}
56518
57095
 
56519
57096
  if(me.cfg.cid === undefined) {
56520
- html += "<li><span>Glycans</span>";
57097
+ //html += "<li><span>Glycans</span>";
57098
+ html += me.htmlCls.setHtmlCls.getMenuText('mn3_glycanwrap', 'Glycans', undefined, undefined, 1);
56521
57099
  html += "<ul>";
56522
- html += me.htmlCls.setHtmlCls.getRadio('mn3_glycansCart', 'mn3_glycansCartYes', 'Show Cartoon');
56523
- html += me.htmlCls.setHtmlCls.getRadio('mn3_glycansCart', 'mn3_glycansCartNo', 'Hide Cartoon', true);
57100
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_glycansCart', 'mn3_glycansCartYes', 'Show Cartoon', undefined, undefined, 2);
57101
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_glycansCart', 'mn3_glycansCartNo', 'Hide Cartoon', true, undefined, 2);
56524
57102
  html += "</ul>";
56525
57103
  html += "</li>";
56526
57104
  }
56527
57105
 
56528
- html += "<li><span>Ions</span>";
57106
+ //html += "<li><span>Ions</span>";
57107
+ html += me.htmlCls.setHtmlCls.getMenuText('mn3_ionswrap', 'Ions', undefined, 1, 1);
56529
57108
  html += "<ul>";
56530
- html += me.htmlCls.setHtmlCls.getRadio('mn3_ions', 'mn3_ionsSphere', 'Sphere', true);
56531
- html += me.htmlCls.setHtmlCls.getRadio('mn3_ions', 'mn3_ionsDot', 'Dot');
56532
- html += me.htmlCls.setHtmlCls.getRadio('mn3_ions', 'mn3_ionsNo', 'Hide');
57109
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_ions', 'mn3_ionsSphere', 'Sphere', true, 1, 2);
57110
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_ions', 'mn3_ionsDot', 'Dot', undefined, 1, 2);
57111
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_ions', 'mn3_ionsNo', 'Hide', undefined, 1, 2);
56533
57112
  html += "</ul>";
56534
57113
  html += "</li>";
56535
57114
 
56536
- html += "<li><span>Water</span>";
57115
+ //html += "<li><span>Water</span>";
57116
+ html += me.htmlCls.setHtmlCls.getMenuText('mn3_waterwrap', 'Water', undefined, 1, 1);
56537
57117
  html += "<ul>";
56538
- html += me.htmlCls.setHtmlCls.getRadio('mn3_water', 'mn3_waterSphere', 'Sphere');
56539
- html += me.htmlCls.setHtmlCls.getRadio('mn3_water', 'mn3_waterDot', 'Dot');
56540
- html += me.htmlCls.setHtmlCls.getRadio('mn3_water', 'mn3_waterNo', 'Hide', true);
57118
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_water', 'mn3_waterSphere', 'Sphere', undefined, 1, 2);
57119
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_water', 'mn3_waterDot', 'Dot', undefined, 1, 2);
57120
+ html += me.htmlCls.setHtmlCls.getRadio('mn3_water', 'mn3_waterNo', 'Hide', true, 1, 2);
56541
57121
  html += "</ul>";
56542
57122
  html += "</li>";
56543
57123
 
56544
- html += me.htmlCls.setHtmlCls.getLink('mn3_setThickness', 'Preferences');
57124
+ html += me.htmlCls.setHtmlCls.getLink('mn3_setThickness', 'Preferences', undefined, 1);
56545
57125
 
56546
- if(!me.cfg.simplemenu) {
56547
- html += "<li>-</li>";
56548
- html += me.htmlCls.setHtmlCls.getLink('mn3_styleSave', 'Save Style');
56549
- html += me.htmlCls.setHtmlCls.getLink('mn3_styleApplySave', 'Apply Saved Style');
56550
- }
57126
+ html += me.htmlCls.setHtmlCls.getMenuSep();
57127
+ html += me.htmlCls.setHtmlCls.getLink('mn3_styleSave', 'Save Style', undefined, 2);
57128
+ html += me.htmlCls.setHtmlCls.getLink('mn3_styleApplySave', 'Apply Saved Style', undefined, 2);
56551
57129
 
56552
- html += "<li>-</li>";
57130
+ html += me.htmlCls.setHtmlCls.getMenuSep();
56553
57131
 
56554
- html += "<li><span>Surface Type</span>";
57132
+ //html += "<li><span>Surface Type</span>";
57133
+ html += me.htmlCls.setHtmlCls.getMenuText('mn5_surfacewrap', 'Surface Type', undefined, 1, 1);
56555
57134
  html += "<ul>";
56556
- html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceVDW', 'Van der Waals');
56557
- if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceVDWContext', 'VDW with Context');
56558
- html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceMolecular', 'Molecular Surface');
56559
- if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceMolecularContext', 'MS with Context');
56560
- html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceSAS', 'Solvent Accessible');
56561
- if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceSASContext', 'SA with Context');
57135
+ html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceVDW', 'Van der Waals', undefined, 1, 2);
57136
+ html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceVDWContext', 'VDW with Context', undefined, undefined, 2);
57137
+ html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceMolecular', 'Molecular Surface', undefined, 1, 2);
57138
+ html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceMolecularContext', 'MS with Context', undefined, undefined, 2);
57139
+ html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceSAS', 'Solvent Accessible', undefined, 1, 2);
57140
+ html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceSASContext', 'SA with Context', undefined, undefined, 2);
56562
57141
  html += "</ul>";
56563
57142
  html += "</li>";
56564
57143
 
56565
- html += me.htmlCls.setHtmlCls.getLink('mn5_surfaceNo', 'Remove Surface');
57144
+ html += me.htmlCls.setHtmlCls.getLink('mn5_surfaceNo', 'Remove Surface', 1, 1);
56566
57145
 
56567
- html += "<li><span>Surface Opacity</span>";
57146
+ //html += "<li><span>Surface Opacity</span>";
57147
+ html += me.htmlCls.setHtmlCls.getMenuText('mn5_surfaceop', 'Surface Opacity', undefined, 1, 1);
56568
57148
  html += "<ul>";
56569
57149
 
56570
- html += "<li><span>Fast Transparency</span>";
57150
+ //html += "<li><span>Fast Transparency</span>";
57151
+ html += me.htmlCls.setHtmlCls.getMenuText('mn5_surfaceopfast', 'Fast Transparency', undefined, 1, 2);
56571
57152
  html += "<ul>";
56572
- html += me.htmlCls.setHtmlCls.getRadio('mn5_opacity', 'mn5_opacity10', '1.0', true);
57153
+ html += me.htmlCls.setHtmlCls.getRadio('mn5_opacity', 'mn5_opacity10', '1.0', true, 1, 3);
56573
57154
 
56574
57155
  for(let i = 9; i > 0; --i) {
56575
- html += me.htmlCls.setHtmlCls.getRadio('mn5_opacity', 'mn5_opacity0' + i, '0.' + i);
57156
+ html += me.htmlCls.setHtmlCls.getRadio('mn5_opacity', 'mn5_opacity0' + i, '0.' + i, 1, 3);
56576
57157
  }
56577
57158
  html += "</ul>";
56578
57159
  html += "</li>";
56579
57160
 
56580
- html += "<li><span>Slow Transparency</span>";
57161
+ //html += "<li><span>Slow Transparency</span>";
57162
+ html += me.htmlCls.setHtmlCls.getMenuText('mn5_surfaceopslow', 'Slow Transparency', undefined, undefined, 2);
56581
57163
  html += "<ul>";
56582
- html += me.htmlCls.setHtmlCls.getRadio('mn5_opacityslow', 'mn5_opacityslow10', '1.0', true);
57164
+ html += me.htmlCls.setHtmlCls.getRadio('mn5_opacityslow', 'mn5_opacityslow10', '1.0', true, undefined, 3);
56583
57165
 
56584
57166
  for(let i = 9; i > 0; --i) {
56585
- html += me.htmlCls.setHtmlCls.getRadio('mn5_opacityslow', 'mn5_opacityslow0' + i, '0.' + i);
57167
+ html += me.htmlCls.setHtmlCls.getRadio('mn5_opacityslow', 'mn5_opacityslow0' + i, '0.' + i, undefined, undefined, 3);
56586
57168
  }
56587
57169
  html += "</ul>";
56588
57170
  html += "</li>";
56589
57171
 
56590
57172
  html += "</ul>"; // end of Surface Opacity
56591
57173
 
56592
- html += "<li><span>Surface Wireframe</span>";
57174
+ //html += "<li><span>Surface Wireframe</span>";
57175
+ html += me.htmlCls.setHtmlCls.getMenuText('mn5_wireframewrap', 'Surface Wireframe', undefined, 1, 1);
56593
57176
  html += "<ul>";
56594
- html += me.htmlCls.setHtmlCls.getRadio('mn5_wireframe', 'mn5_wireframeYes', 'Yes');
56595
- html += me.htmlCls.setHtmlCls.getRadio('mn5_wireframe', 'mn5_wireframeNo', 'No', true);
57177
+ html += me.htmlCls.setHtmlCls.getRadio('mn5_wireframe', 'mn5_wireframeYes', 'Yes', undefined, 1, 2);
57178
+ html += me.htmlCls.setHtmlCls.getRadio('mn5_wireframe', 'mn5_wireframeNo', 'No', true, 1, 2);
56596
57179
  html += "</ul>";
56597
57180
  html += "</li>";
56598
57181
 
56599
57182
  if(me.cfg.cid === undefined && me.cfg.align === undefined && me.cfg.chainalign === undefined && me.cfg.mmdbaf === undefined) {
56600
- if(!me.cfg.simplemenu) {
56601
- html += "<li>-</li>";
57183
+ html += me.htmlCls.setHtmlCls.getMenuSep();
56602
57184
 
56603
- html += "<li id='" + me.pre + "mapWrapper1'><span>Electron Density</span>";
56604
- html += "<ul>";
56605
- html += me.htmlCls.setHtmlCls.getRadio('mn5_elecmap', 'mn5_elecmap2fofc', '2Fo-Fc Map');
56606
- html += me.htmlCls.setHtmlCls.getRadio('mn5_elecmap', 'mn5_elecmapfofc', 'Fo-Fc Map');
56607
- html += "</ul>";
56608
- html += "</li>";
57185
+ //html += "<li id='" + me.pre + "mapWrapper1'><span>Electron Density</span>";
57186
+ html += me.htmlCls.setHtmlCls.getMenuText('mapWrapper1', 'Electron Density', undefined, undefined, 1);
57187
+ html += "<ul>";
57188
+ html += me.htmlCls.setHtmlCls.getRadio('mn5_elecmap', 'mn5_elecmap2fofc', '2Fo-Fc Map', undefined, undefined, 2);
57189
+ html += me.htmlCls.setHtmlCls.getRadio('mn5_elecmap', 'mn5_elecmapfofc', 'Fo-Fc Map', undefined, undefined, 2);
57190
+ html += "</ul>";
57191
+ html += "</li>";
56609
57192
 
56610
- html += me.htmlCls.setHtmlCls.getLinkWrapper('mn5_elecmapNo', 'Remove Map', 'mapWrapper2');
57193
+ html += me.htmlCls.setHtmlCls.getLinkWrapper('mn5_elecmapNo', 'Remove Map', 'mapWrapper2', undefined, 1);
56611
57194
 
56612
- html += "<li id='" + me.pre + "mapWrapper3'><span>Map Wireframe</span>";
56613
- html += "<ul>";
56614
- html += me.htmlCls.setHtmlCls.getRadio('mn5_mapwireframe', 'mn5_mapwireframeYes', 'Yes', true);
56615
- html += me.htmlCls.setHtmlCls.getRadio('mn5_mapwireframe', 'mn5_mapwireframeNo', 'No');
56616
- html += "</ul>";
56617
- html += "</li>";
57195
+ //html += "<li id='" + me.pre + "mapWrapper3'><span>Map Wireframe</span>";
57196
+ html += me.htmlCls.setHtmlCls.getMenuText('mapWrapper3', 'Map Wireframe', undefined, undefined, 1);
57197
+ html += "<ul>";
57198
+ html += me.htmlCls.setHtmlCls.getRadio('mn5_mapwireframe', 'mn5_mapwireframeYes', 'Yes', true, undefined, 2);
57199
+ html += me.htmlCls.setHtmlCls.getRadio('mn5_mapwireframe', 'mn5_mapwireframeNo', 'No', undefined, undefined, 2);
57200
+ html += "</ul>";
57201
+ html += "</li>";
56618
57202
 
56619
- if(me.cfg.mmtfid === undefined) {
56620
- //html += "<li>-</li>";
57203
+ if(me.cfg.mmtfid === undefined) {
57204
+ //html += me.htmlCls.setHtmlCls.getMenuSep();
56621
57205
 
56622
- html += me.htmlCls.setHtmlCls.getLinkWrapper('mn5_emmap', 'EM Density Map', 'emmapWrapper1');
56623
- html += me.htmlCls.setHtmlCls.getLinkWrapper('mn5_emmapNo', 'Remove EM Map', 'emmapWrapper2');
57206
+ html += me.htmlCls.setHtmlCls.getLinkWrapper('mn5_emmap', 'EM Density Map', 'emmapWrapper1', undefined, 1);
57207
+ html += me.htmlCls.setHtmlCls.getLinkWrapper('mn5_emmapNo', 'Remove EM Map', 'emmapWrapper2', undefined, 1);
56624
57208
 
56625
- html += "<li id='" + me.pre + "emmapWrapper3'><span>EM Map Wireframe</span>";
56626
- html += "<ul>";
56627
- html += me.htmlCls.setHtmlCls.getRadio('mn5_emmapwireframe', 'mn5_emmapwireframeYes', 'Yes', true);
56628
- html += me.htmlCls.setHtmlCls.getRadio('mn5_emmapwireframe', 'mn5_emmapwireframeNo', 'No');
56629
- html += "</ul>";
56630
- html += "</li>";
56631
- }
57209
+ //html += "<li id='" + me.pre + "emmapWrapper3'><span>EM Map Wireframe</span>";
57210
+ html += me.htmlCls.setHtmlCls.getLinkWrapper('mn5_emmapwfwrap', 'EM Map Wireframe', 'emmapWrapper3', undefined, 1);
57211
+ html += "<ul>";
57212
+ html += me.htmlCls.setHtmlCls.getRadio('mn5_emmapwireframe', 'mn5_emmapwireframeYes', 'Yes', true, undefined, 2);
57213
+ html += me.htmlCls.setHtmlCls.getRadio('mn5_emmapwireframe', 'mn5_emmapwireframeNo', 'No', undefined, undefined, 2);
57214
+ html += "</ul>";
57215
+ html += "</li>";
56632
57216
  }
56633
57217
  }
56634
57218
 
56635
- html += "<li>-</li>";
57219
+ html += me.htmlCls.setHtmlCls.getMenuSep();
56636
57220
 
56637
- html += "<li><span>Background</span>";
57221
+ //html += "<li><span>Background</span>";
57222
+ html += me.htmlCls.setHtmlCls.getMenuText('mn6_bkgdwrap', 'Background', undefined, 1, 1);
56638
57223
  html += "<ul>";
56639
- html += me.htmlCls.setHtmlCls.getRadio('mn6_bkgd', 'mn6_bkgdTransparent', 'Transparent');
56640
- html += me.htmlCls.setHtmlCls.getRadio('mn6_bkgd', 'mn6_bkgdBlack', 'Black', true);
56641
- html += me.htmlCls.setHtmlCls.getRadio('mn6_bkgd', 'mn6_bkgdGrey', 'Gray');
56642
- html += me.htmlCls.setHtmlCls.getRadio('mn6_bkgd', 'mn6_bkgdWhite', 'White');
57224
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_bkgd', 'mn6_bkgdTransparent', 'Transparent', undefined, 1, 2);
57225
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_bkgd', 'mn6_bkgdBlack', 'Black', true, 1, 2);
57226
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_bkgd', 'mn6_bkgdGrey', 'Gray', undefined, 1, 2);
57227
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_bkgd', 'mn6_bkgdWhite', 'White', undefined, 1, 2);
56643
57228
  html += "</ul>";
56644
57229
  html += "</li>";
56645
57230
 
56646
- if(!me.cfg.simplemenu) {
56647
- html += "<li><span>Dialog Color</span>";
56648
- html += "<ul>";
56649
- html += me.htmlCls.setHtmlCls.getRadio('mn6_theme', 'mn6_themeBlue', 'Blue', true);
56650
- html += me.htmlCls.setHtmlCls.getRadio('mn6_theme', 'mn6_themeOrange', 'Orange');
56651
- html += me.htmlCls.setHtmlCls.getRadio('mn6_theme', 'mn6_themeBlack', 'Black');
56652
- html += "</ul>";
56653
- html += "</li>";
56654
- }
56655
-
56656
- // html += "<li><span>Two-color Helix</span>";
56657
- // html += "<ul>";
56658
- // html += me.htmlCls.setHtmlCls.getRadio('mn6_doublecolor', 'mn6_doublecolorYes', 'Yes');
56659
- // html += me.htmlCls.setHtmlCls.getRadio('mn6_doublecolor', 'mn6_doublecolorNo', 'No', true);
56660
- // html += "</ul>";
56661
- // html += "</li>";
56662
-
57231
+ html += "<li><span>Dialog Color</span>";
57232
+ html += me.htmlCls.setHtmlCls.getMenuText('mn6_themewrap', 'Dialog Color', undefined, undefined, 1);
57233
+ html += "<ul>";
57234
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_theme', 'mn6_themeBlue', 'Blue', true, undefined, 2);
57235
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_theme', 'mn6_themeOrange', 'Orange', undefined, undefined, 2);
57236
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_theme', 'mn6_themeBlack', 'Black', undefined, undefined, 2);
57237
+ html += "</ul>";
57238
+ html += "</li>";
56663
57239
 
56664
57240
  html += "<li><br/></li>";
56665
57241
 
@@ -56695,316 +57271,309 @@ class SetMenu {
56695
57271
 
56696
57272
  html += "<ul class='icn3d-mn-item'>";
56697
57273
 
56698
- html += "<li><span style='padding-left:1.5em;'>Unicolor</span>";
57274
+ //html += "<li><span style='padding-left:1.5em!important;'>Unicolor</span>";
57275
+ html += me.htmlCls.setHtmlCls.getMenuText('mn4_clrwrap', 'Unicolor', 'icn3d-menupd', 1, 1);
56699
57276
  html += "<ul>";
56700
57277
 
56701
57278
  html += "<li><span>Red</span>";
57279
+ html += me.htmlCls.setHtmlCls.getMenuText('uniclrRedwrap', 'Red', undefined, 1, 2);
56702
57280
  html += "<ul>";
56703
- //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrRed', 'Red');
56704
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrRed1', 'Red', 'F00');
56705
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrRed2', 'Indian Red', 'CD5C5C');
56706
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrRed3', 'Light Coral', 'F08080');
56707
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrRed4', 'Salmon', 'FA8072');
56708
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrRed5', 'Dark Salmon', 'E9967A');
56709
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrRed6', 'Light Salmon', 'FFA07A');
56710
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrRed7', 'Crimson', 'DC143C');
56711
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrRed8', 'Fire Brick', 'B22222');
56712
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrRed9', 'Dark Red', '8B0000');
57281
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrRed1', 'Red', 'F00', undefined, 1, 3);
57282
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrRed2', 'Indian Red', 'CD5C5C', undefined, 1, 3);
57283
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrRed3', 'Light Coral', 'F08080', undefined, 1, 3);
57284
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrRed4', 'Salmon', 'FA8072', undefined, 1, 3);
57285
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrRed5', 'Dark Salmon', 'E9967A', undefined, 1, 3);
57286
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrRed6', 'Light Salmon', 'FFA07A', undefined, 1, 3);
57287
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrRed7', 'Crimson', 'DC143C', undefined, 1, 3);
57288
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrRed8', 'Fire Brick', 'B22222', undefined, 1, 3);
57289
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrRed9', 'Dark Red', '8B0000', undefined, 1, 3);
56713
57290
  html += "</ul>";
56714
57291
 
56715
- html += "<li><span>Pink</span>";
57292
+ //html += "<li><span>Pink</span>";
57293
+ html += me.htmlCls.setHtmlCls.getMenuText('uniclrPinkwrap', 'Pink', undefined, 1, 2);
56716
57294
  html += "<ul>";
56717
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrPink1', 'Pink', 'FFC0CB');
56718
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrPink2', 'Light Pink', 'FFB6C1');
56719
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrPink3', 'Hot Pink', 'FF69B4');
56720
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrPink4', 'Deep Pink', 'FF1493');
56721
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrPink5', 'Medium Violet Red', 'C71585');
56722
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrPink6', 'Pale Violet Red', 'DB7093');
57295
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrPink1', 'Pink', 'FFC0CB', undefined, 1, 3);
57296
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrPink2', 'Light Pink', 'FFB6C1', undefined, 1, 3);
57297
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrPink3', 'Hot Pink', 'FF69B4', undefined, 1, 3);
57298
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrPink4', 'Deep Pink', 'FF1493', undefined, 1, 3);
57299
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrPink5', 'Medium Violet Red', 'C71585', undefined, 1, 3);
57300
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrPink6', 'Pale Violet Red', 'DB7093', undefined, 1, 3);
56723
57301
  html += "</ul>";
56724
57302
 
56725
- html += "<li><span>Orange</span>";
57303
+ //html += "<li><span>Orange</span>";
57304
+ html += me.htmlCls.setHtmlCls.getMenuText('uniclrOrangewrap', 'Orange', undefined, 1, 2);
56726
57305
  html += "<ul>";
56727
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrOran1', 'Orange', 'FFA500');
56728
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrOran2', 'Dark Orange', 'FF8C00');
56729
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrOran3', 'Orange Red', 'FF4500');
56730
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrOran4', 'Tomato', 'FF6347');
56731
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrOran5', 'Coral', 'FF7F50');
56732
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrOran6', 'Light Salmon', 'FFA07A');
57306
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrOran1', 'Orange', 'FFA500', undefined, 1, 3);
57307
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrOran2', 'Dark Orange', 'FF8C00', undefined, 1, 3);
57308
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrOran3', 'Orange Red', 'FF4500', undefined, 1, 3);
57309
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrOran4', 'Tomato', 'FF6347', undefined, 1, 3);
57310
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrOran5', 'Coral', 'FF7F50', undefined, 1, 3);
57311
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrOran6', 'Light Salmon', 'FFA07A', undefined, 1, 3);
56733
57312
  html += "</ul>";
56734
57313
 
56735
- html += "<li><span>Yellow</span>";
57314
+ //html += "<li><span>Yellow</span>";
57315
+ html += me.htmlCls.setHtmlCls.getMenuText('uniclrYellowwrap', 'Yellow', undefined, 1, 2);
56736
57316
  html += "<ul>";
56737
- //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrYllw', 'Yellow');
56738
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrYllw1', 'Yellow', 'FF0');
56739
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrYllw2', 'Gold', 'FFD700');
56740
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrYllw3', 'Light Yellow', 'FFFFE0');
56741
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrYllw4', 'Lemon Chiffon', 'FFFACD');
56742
- //html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrYllw5', 'Light Golden Rod Yellow', 'FAFAD2');
56743
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrYllw5', 'Light Golden Rod', 'FAFAD2');
56744
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrYllw6', 'Papaya Whip', 'FFEFD5');
56745
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrYllw7', 'Moccasin', 'FFE4B5');
56746
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrYllw8', 'Peach Puff', 'FFDAB9');
56747
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrYllw9', 'Pale Golden Rod', 'EEE8AA');
56748
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrYllw10', 'Khaki', 'F0E68C');
56749
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrYllw11', 'Dark Khaki', 'BDB76B');
57317
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrYllw1', 'Yellow', 'FF0', undefined, 1, 3);
57318
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrYllw2', 'Gold', 'FFD700', undefined, 1, 3);
57319
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrYllw3', 'Light Yellow', 'FFFFE0', undefined, 1, 3);
57320
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrYllw4', 'Lemon Chiffon', 'FFFACD', undefined, 1, 3);
57321
+ //html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrYllw5', 'Light Golden Rod Yellow', 'FAFAD2', undefined, 1, 3);
57322
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrYllw5', 'Light Golden Rod', 'FAFAD2', undefined, 1, 3);
57323
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrYllw6', 'Papaya Whip', 'FFEFD5', undefined, 1, 3);
57324
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrYllw7', 'Moccasin', 'FFE4B5', undefined, 1, 3);
57325
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrYllw8', 'Peach Puff', 'FFDAB9', undefined, 1, 3);
57326
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrYllw9', 'Pale Golden Rod', 'EEE8AA', undefined, 1, 3);
57327
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrYllw10', 'Khaki', 'F0E68C', undefined, 1, 3);
57328
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrYllw11', 'Dark Khaki', 'BDB76B', undefined, 1, 3);
56750
57329
  html += "</ul>";
56751
57330
 
56752
- html += "<li><span>Magenta</span>";
57331
+ //html += "<li><span>Magenta</span>";
57332
+ html += me.htmlCls.setHtmlCls.getMenuText('uniclrMagentawrap', 'Magenta', undefined, 1, 2);
56753
57333
  html += "<ul>";
56754
- //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrMgnt', 'Magenta');
56755
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrMgnt1', 'Magenta', 'F0F');
56756
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrMgnt2', 'Orchid', 'DA70D6');
56757
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrMgnt3', 'Violet', 'EE82EE');
56758
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrMgnt4', 'Plum', 'DDA0DD');
56759
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrMgnt5', 'Thistle', 'D8BFD8');
56760
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrMgnt6', 'Lavender', 'E6E6FA');
56761
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrMgnt7', 'Medium Orchid', 'BA55D3');
56762
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrMgnt8', 'Medium Purple', '9370DB');
56763
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrMgnt9', 'Rebecca Purple', '663399');
56764
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrMgnt10', 'Blue Violet', '8A2BE2');
56765
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrMgnt11', 'Dark Violet', '9400D3');
56766
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrMgnt12', 'Dark Orchid', '9932CC');
56767
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrMgnt13', 'Dark Magenta', '8B008B');
56768
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrMgnt14', 'Purple', '800080');
56769
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrMgnt15', 'Indigo', '4B0082');
56770
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrMgnt16', 'Slat Blue', '6A5ACD');
56771
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrMgnt17', 'Dark Slate Blue', '483D8B');
56772
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrMgnt18', 'Medium Slat Blue', '6A5ACD');
57334
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrMgnt1', 'Magenta', 'F0F', undefined, 1, 3);
57335
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrMgnt2', 'Orchid', 'DA70D6', undefined, 1, 3);
57336
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrMgnt3', 'Violet', 'EE82EE', undefined, 1, 3);
57337
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrMgnt4', 'Plum', 'DDA0DD', undefined, 1, 3);
57338
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrMgnt5', 'Thistle', 'D8BFD8', undefined, 1, 3);
57339
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrMgnt6', 'Lavender', 'E6E6FA', undefined, 1, 3);
57340
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrMgnt7', 'Medium Orchid', 'BA55D3', undefined, 1, 3);
57341
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrMgnt8', 'Medium Purple', '9370DB', undefined, 1, 3);
57342
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrMgnt9', 'Rebecca Purple', '663399', undefined, 1, 3);
57343
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrMgnt10', 'Blue Violet', '8A2BE2', undefined, 1, 3);
57344
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrMgnt11', 'Dark Violet', '9400D3', undefined, 1, 3);
57345
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrMgnt12', 'Dark Orchid', '9932CC', undefined, 1, 3);
57346
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrMgnt13', 'Dark Magenta', '8B008B', undefined, 1, 3);
57347
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrMgnt14', 'Purple', '800080', undefined, 1, 3);
57348
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrMgnt15', 'Indigo', '4B0082', undefined, 1, 3);
57349
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrMgnt16', 'Slat Blue', '6A5ACD', undefined, 1, 3);
57350
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrMgnt17', 'Dark Slate Blue', '483D8B', undefined, 1, 3);
57351
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrMgnt18', 'Medium Slat Blue', '6A5ACD', undefined, 1, 3);
56773
57352
  html += "</ul>";
56774
57353
 
56775
- html += "<li><span>Green</span>";
57354
+ //html += "<li><span>Green</span>";
57355
+ html += me.htmlCls.setHtmlCls.getMenuText('uniclrGreenwrap', 'Green', undefined, 1, 2);
56776
57356
  html += "<ul>";
56777
- //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrGrn', 'Green');
56778
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn1', 'Green', '0F0');
56779
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn2', 'Dark Green', '006400');
56780
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn3', 'Yellow Green', '9ACD32');
56781
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn4', 'Olive Drab', '6B8E23');
56782
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn5', 'Olive', '808000');
56783
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn6', 'Dark Olive Green', '556B2F');
56784
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn7', 'Medium Aquamarine', '66CDAA');
56785
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn8', 'Dark Sea Green', '8FBC8B');
56786
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn9', 'Lignt Sea Green', '20B2AA');
56787
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn10', 'Dark Cyan', '008B8B');
56788
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn11', 'Teal', '008080');
56789
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn12', 'Forest Green', '228B22');
56790
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn13', 'Sea Green', '2E8B57');
56791
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn14', 'Medium Sea Green', '3CB371');
56792
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn15', 'Spring Green', '00FF7F');
56793
- //html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn16', 'Medium Spring Green', '00FA9A');
56794
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn16', 'Medium Spring', '00FA9A');
56795
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn17', 'Light Green', '90EE90');
56796
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn18', 'Pale Green', '98FB98');
56797
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn19', 'Lime Green', '32CD32');
56798
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn20', 'Lawn Green', '7CFC00');
56799
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn21', 'Chartreuse', '7FFF00');
56800
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGrn22', 'Green Yellow', 'ADFF2F');
57357
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn1', 'Green', '0F0', undefined, 1, 3);
57358
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn2', 'Dark Green', '006400', undefined, 1, 3);
57359
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn3', 'Yellow Green', '9ACD32', undefined, 1, 3);
57360
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn4', 'Olive Drab', '6B8E23', undefined, 1, 3);
57361
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn5', 'Olive', '808000', undefined, 1, 3);
57362
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn6', 'Dark Olive Green', '556B2F', undefined, 1, 3);
57363
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn7', 'Medium Aquamarine', '66CDAA', undefined, 1, 3);
57364
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn8', 'Dark Sea Green', '8FBC8B', undefined, 1, 3);
57365
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn9', 'Lignt Sea Green', '20B2AA', undefined, 1, 3);
57366
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn10', 'Dark Cyan', '008B8B', undefined, 1, 3);
57367
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn11', 'Teal', '008080', undefined, 1, 3);
57368
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn12', 'Forest Green', '228B22', undefined, 1, 3);
57369
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn13', 'Sea Green', '2E8B57', undefined, 1, 3);
57370
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn14', 'Medium Sea Green', '3CB371', undefined, 1, 3);
57371
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn15', 'Spring Green', '00FF7F', undefined, 1, 3);
57372
+ //html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn16', 'Medium Spring Green', '00FA9A', undefined, 1, 3);
57373
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn16', 'Medium Spring', '00FA9A', undefined, 1, 3);
57374
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn17', 'Light Green', '90EE90', undefined, 1, 3);
57375
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn18', 'Pale Green', '98FB98', undefined, 1, 3);
57376
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn19', 'Lime Green', '32CD32', undefined, 1, 3);
57377
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn20', 'Lawn Green', '7CFC00', undefined, 1, 3);
57378
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn21', 'Chartreuse', '7FFF00', undefined, 1, 3);
57379
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGrn22', 'Green Yellow', 'ADFF2F', undefined, 1, 3);
56801
57380
  html += "</ul>";
56802
57381
 
56803
- html += "<li><span>Cyan</span>";
57382
+ //html += "<li><span>Cyan</span>";
57383
+ html += me.htmlCls.setHtmlCls.getMenuText('uniclrCyanwrap', 'Cyan', undefined, 1, 2);
56804
57384
  html += "<ul>";
56805
- //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrCyan', 'Cyan');
56806
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrCyan1', 'Cyan', '0FF');
56807
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrCyan2', 'Light Cyan', 'E0FFFF');
56808
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrCyan3', 'Pale Turquoise', 'AFEEEE');
56809
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrCyan4', 'Aquamarine', '7FFFD4');
56810
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrCyan5', 'Turquoise', '40E0D0');
56811
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrCyan6', 'Medium Turquoise', '48D1CC');
56812
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrCyan7', 'Dark Turquoise', '00CED1');
57385
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrCyan1', 'Cyan', '0FF', undefined, 1, 3);
57386
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrCyan2', 'Light Cyan', 'E0FFFF', undefined, 1, 3);
57387
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrCyan3', 'Pale Turquoise', 'AFEEEE', undefined, 1, 3);
57388
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrCyan4', 'Aquamarine', '7FFFD4', undefined, 1, 3);
57389
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrCyan5', 'Turquoise', '40E0D0', undefined, 1, 3);
57390
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrCyan6', 'Medium Turquoise', '48D1CC', undefined, 1, 3);
57391
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrCyan7', 'Dark Turquoise', '00CED1', undefined, 1, 3);
56813
57392
  html += "</ul>";
56814
57393
 
56815
- html += "<li><span>Blue</span>";
57394
+ //html += "<li><span>Blue</span>";
57395
+ html += me.htmlCls.setHtmlCls.getMenuText('uniclrBluewrap', 'Blue', undefined, 1, 2);
56816
57396
  html += "<ul>";
56817
- //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrBlue', 'Blue');
56818
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBlue1', 'Blue', '00F');
56819
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBlue2', 'Medium Blue', '0000CD');
56820
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBlue3', 'Dark Blue', '00008B');
56821
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBlue4', 'Navy', '000080');
56822
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBlue5', 'Midnight Blue', '191970');
56823
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBlue6', 'Royal Blue', '4169E1');
56824
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBlue7', 'Medium Slate Blue', '7B68EE');
56825
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBlue8', 'Corn Flower Blue', '6495ED');
56826
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBlue9', 'Dodger Blue', '1E90FF');
56827
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBlue10', 'Deep Sky Blue', '00BFFF');
56828
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBlue11', 'Light Sky Blue', '87CEFA');
56829
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBlue12', 'Sky Blue', '87CEEB');
56830
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBlue13', 'Light Blue', 'ADD8E6');
56831
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBlue14', 'Powder Blue', 'B0E0E6');
56832
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBlue15', 'Light Steel Blue', 'B0C4DE');
56833
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBlue16', 'Steel Blue', '4682B4');
56834
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBlue17', 'Cadet Blue', '5F9EA0');
57397
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBlue1', 'Blue', '00F', undefined, 1, 3);
57398
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBlue2', 'Medium Blue', '0000CD', undefined, 1, 3);
57399
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBlue3', 'Dark Blue', '00008B', undefined, 1, 3);
57400
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBlue4', 'Navy', '000080', undefined, 1, 3);
57401
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBlue5', 'Midnight Blue', '191970', undefined, 1, 3);
57402
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBlue6', 'Royal Blue', '4169E1', undefined, 1, 3);
57403
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBlue7', 'Medium Slate Blue', '7B68EE', undefined, 1, 3);
57404
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBlue8', 'Corn Flower Blue', '6495ED', undefined, 1, 3);
57405
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBlue9', 'Dodger Blue', '1E90FF', undefined, 1, 3);
57406
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBlue10', 'Deep Sky Blue', '00BFFF', undefined, 1, 3);
57407
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBlue11', 'Light Sky Blue', '87CEFA', undefined, 1, 3);
57408
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBlue12', 'Sky Blue', '87CEEB', undefined, 1, 3);
57409
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBlue13', 'Light Blue', 'ADD8E6', undefined, 1, 3);
57410
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBlue14', 'Powder Blue', 'B0E0E6', undefined, 1, 3);
57411
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBlue15', 'Light Steel Blue', 'B0C4DE', undefined, 1, 3);
57412
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBlue16', 'Steel Blue', '4682B4', undefined, 1, 3);
57413
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBlue17', 'Cadet Blue', '5F9EA0', undefined, 1, 3);
56835
57414
  html += "</ul>";
56836
57415
 
56837
- html += "<li><span>Brown</span>";
57416
+ //html += "<li><span>Brown</span>";
57417
+ html += me.htmlCls.setHtmlCls.getMenuText('uniclrBrownwrap', 'Brown', undefined, 1, 2);
56838
57418
  html += "<ul>";
56839
- //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrBrown', 'Brown');
56840
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBrown1', 'Brown', 'A52A2A');
56841
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBrown2', 'Maroon', '800000');
56842
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBrown3', 'Sienna', 'A0522D');
56843
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBrown4', 'Saddle Brown', '8B4513');
56844
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBrown5', 'Chocolate', 'D2691E');
56845
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBrown6', 'Peru', 'CD853F');
56846
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBrown7', 'Dark Golden Rod', 'B8860B');
56847
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBrown8', 'Golden Rod', 'DAA520');
56848
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBrown9', 'Sandy Brown', 'F4A460');
56849
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBrown10', 'Rosy Brown', 'BC8F8F');
56850
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBrown11', 'Tan', 'D2B48C');
56851
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBrown12', 'Burlywood', 'DEB887');
56852
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBrown13', 'Wheat', 'F5DEB3');
56853
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBrown14', 'Navajo White', 'FFDEAD');
56854
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBrown15', 'Bisque', 'FFE4C4');
56855
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBrown16', 'Blanched Almond', 'FFEBCD');
56856
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrBrown17', 'Corn Silk', 'FFF8DC');
57419
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBrown1', 'Brown', 'A52A2A', undefined, 1, 3);
57420
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBrown2', 'Maroon', '800000', undefined, 1, 3);
57421
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBrown3', 'Sienna', 'A0522D', undefined, 1, 3);
57422
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBrown4', 'Saddle Brown', '8B4513', undefined, 1, 3);
57423
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBrown5', 'Chocolate', 'D2691E', undefined, 1, 3);
57424
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBrown6', 'Peru', 'CD853F', undefined, 1, 3);
57425
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBrown7', 'Dark Golden Rod', 'B8860B', undefined, 1, 3);
57426
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBrown8', 'Golden Rod', 'DAA520', undefined, 1, 3);
57427
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBrown9', 'Sandy Brown', 'F4A460', undefined, 1, 3);
57428
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBrown10', 'Rosy Brown', 'BC8F8F', undefined, 1, 3);
57429
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBrown11', 'Tan', 'D2B48C', undefined, 1, 3);
57430
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBrown12', 'Burlywood', 'DEB887', undefined, 1, 3);
57431
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBrown13', 'Wheat', 'F5DEB3', undefined, 1, 3);
57432
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBrown14', 'Navajo White', 'FFDEAD', undefined, 1, 3);
57433
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBrown15', 'Bisque', 'FFE4C4', undefined, 1, 3);
57434
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBrown16', 'Blanched Almond', 'FFEBCD', undefined, 1, 3);
57435
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrBrown17', 'Corn Silk', 'FFF8DC', undefined, 1, 3);
56857
57436
  html += "</ul>";
56858
57437
 
56859
57438
  html += "<li><span>White</span>";
57439
+ html += me.htmlCls.setHtmlCls.getMenuText('uniclrWhitewrap', 'White', undefined, 1, 2);
56860
57440
  html += "<ul>";
56861
- //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrWhite', 'White');
56862
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrWhite1', 'White', 'FFF');
56863
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrWhite2', 'Snow', 'FFFAFA');
56864
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrWhite3', 'Honey Dew', 'F0FFF0');
56865
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrWhite4', 'Mint Cream', 'F5FFFA');
56866
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrWhite5', 'Azure', 'F0FFFF');
56867
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrWhite6', 'Alice Blue', 'F0F8FF');
56868
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrWhite7', 'Ghost White', 'F8F8FF');
56869
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrWhite8', 'White Smoke', 'F5F5F5');
56870
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrWhite9', 'Sea Shell', 'FFF5EE');
56871
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrWhite10', 'Beige', 'F5F5DC');
56872
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrWhite11', 'Old Lace', 'FDF5E6');
56873
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrWhite12', 'Floral White', 'FFFAF0');
56874
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrWhite13', 'Ivory', 'FFFFF0');
56875
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrWhite14', 'Antique White', 'FAEBD7');
56876
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrWhite15', 'Linen', 'FAF0E6');
56877
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrWhite16', 'Lavenderblush', 'FFF0F5');
56878
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrWhite17', 'Misty Rose', 'FFE4E1');
57441
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrWhite1', 'White', 'FFF', undefined, 1, 3);
57442
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrWhite2', 'Snow', 'FFFAFA', undefined, 1, 3);
57443
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrWhite3', 'Honey Dew', 'F0FFF0', undefined, 1, 3);
57444
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrWhite4', 'Mint Cream', 'F5FFFA', undefined, 1, 3);
57445
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrWhite5', 'Azure', 'F0FFFF', undefined, 1, 3);
57446
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrWhite6', 'Alice Blue', 'F0F8FF', undefined, 1, 3);
57447
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrWhite7', 'Ghost White', 'F8F8FF', undefined, 1, 3);
57448
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrWhite8', 'White Smoke', 'F5F5F5', undefined, 1, 3);
57449
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrWhite9', 'Sea Shell', 'FFF5EE', undefined, 1, 3);
57450
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrWhite10', 'Beige', 'F5F5DC', undefined, 1, 3);
57451
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrWhite11', 'Old Lace', 'FDF5E6', undefined, 1, 3);
57452
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrWhite12', 'Floral White', 'FFFAF0', undefined, 1, 3);
57453
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrWhite13', 'Ivory', 'FFFFF0', undefined, 1, 3);
57454
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrWhite14', 'Antique White', 'FAEBD7', undefined, 1, 3);
57455
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrWhite15', 'Linen', 'FAF0E6', undefined, 1, 3);
57456
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrWhite16', 'Lavenderblush', 'FFF0F5', undefined, 1, 3);
57457
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrWhite17', 'Misty Rose', 'FFE4E1', undefined, 1, 3);
56879
57458
  html += "</ul>";
56880
57459
 
56881
- html += "<li><span>Gray</span>";
57460
+ //html += "<li><span>Gray</span>";
57461
+ html += me.htmlCls.setHtmlCls.getMenuText('uniclrGraywrap', 'Gray', undefined, 1, 2);
56882
57462
  html += "<ul>";
56883
- //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrGray', 'Gray');
56884
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGray1', 'Gray', '808080');
56885
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGray2', 'Dim Gray', '696969');
56886
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGray3', 'Light Slate Gray', '778899');
56887
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGray4', 'Slate Gray', '708090');
56888
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGray5', 'Dark Slate Gray', '2F4F4F');
56889
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGray6', 'Black', '000000');
56890
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGray7', 'Dark Gray', 'A9A9A9');
56891
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGray8', 'Silver', 'C0C0C0');
56892
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGray9', 'Light Gray', 'D3D3D3');
56893
- html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'mn4_clrGray10', 'Gainsboro', 'DCDCDC');
57463
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGray1', 'Gray', '808080', undefined, 1, 3);
57464
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGray2', 'Dim Gray', '696969', undefined, 1, 3);
57465
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGray3', 'Light Slate Gray', '778899', undefined, 1, 3);
57466
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGray4', 'Slate Gray', '708090', undefined, 1, 3);
57467
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGray5', 'Dark Slate Gray', '2F4F4F', undefined, 1, 3);
57468
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGray6', 'Black', '000000', undefined, 1, 3);
57469
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGray7', 'Dark Gray', 'A9A9A9', undefined, 1, 3);
57470
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGray8', 'Silver', 'C0C0C0', undefined, 1, 3);
57471
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGray9', 'Light Gray', 'D3D3D3', undefined, 1, 3);
57472
+ html += me.htmlCls.setHtmlCls.getRadioColor('mn4_clr', 'uniclrGray10', 'Gainsboro', 'DCDCDC', undefined, 1, 3);
56894
57473
  html += "</ul>";
56895
57474
 
56896
57475
  html += "</ul>";
56897
57476
 
56898
- if(!me.cfg.simplemenu) {
56899
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrCustom', 'Color Picker');
56900
- html += "<li>-</li>";
56901
- }
57477
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrCustom', 'Color Picker', undefined, undefined, 1);
57478
+ html += me.htmlCls.setHtmlCls.getMenuSep();
56902
57479
 
56903
57480
  if(me.cfg.cid === undefined) {
56904
57481
  //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>";
57482
+ //html += "<li><span style='padding-left:1.5em!important;'>Rainbow (R-V)</span>";
57483
+ html += me.htmlCls.setHtmlCls.getMenuText('mn4_clrRainbowwrap', 'Rainbow (R-V)', 'icn3d-menupd', 1, 1);
56906
57484
  html += "<ul>";
56907
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrRainbow', 'for Selection');
56908
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrRainbowChain', 'for Chains');
56909
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrRainbowSets', 'for Sets');
57485
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrRainbow', 'for Selection', undefined, 1, 2);
57486
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrRainbowChain', 'for Chains', undefined, 1, 2);
57487
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrRainbowSets', 'for Sets', undefined, undefined, 2);
56910
57488
  html += "</ul>";
56911
57489
 
56912
- if(!me.cfg.simplemenu) {
56913
- //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>";
56915
- html += "<ul>";
56916
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrum', 'for Selection');
56917
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrumChain', 'for Chains');
56918
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrumSets', 'for Sets');
56919
- html += "</ul>";
56920
- }
56921
-
56922
- html += "<li><span style='padding-left:1.5em;'>Secondary</span>";
57490
+ html += me.htmlCls.setHtmlCls.getMenuText('mn4_clrSpectrumwrap', 'Spectrum (V-R)', 'icn3d-menupd', 1, 1);
56923
57491
  html += "<ul>";
56924
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSSGreen', 'Sheet in Green');
56925
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSSYellow', 'Sheet in Yellow');
56926
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSSSpectrum', 'Spectrum');
57492
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrum', 'for Selection', undefined, 1, 2);
57493
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrumChain', 'for Chains', undefined, 1, 2);
57494
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrumSets', 'for Sets', undefined, undefined, 2);
56927
57495
  html += "</ul>";
56928
57496
 
56929
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrCharge', 'Charge');
56930
-
56931
- // if(!me.cfg.notebook && !me.cfg.hidelicense) {
56932
- // html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn1_delphi2', 'DelPhi<br><span style="padding-left:1.5em;">Potential ' + me.htmlCls.licenseStr + '</span>');
56933
- // }
57497
+ //html += "<li><span style='padding-left:1.5em!important;'>Secondary</span>";
57498
+ html += me.htmlCls.setHtmlCls.getMenuText('mn4_clrSSwrap', 'Secondary', 'icn3d-menupd', 1, 1);
57499
+ html += "<ul>";
57500
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSSGreen', 'Sheet in Green', undefined, 1, 2);
57501
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSSYellow', 'Sheet in Yellow', undefined, 1, 2);
57502
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSSSpectrum', 'Spectrum', undefined, undefined, 2);
57503
+ html += "</ul>";
56934
57504
 
56935
- //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrHydrophobic', 'Wimley-White<br><span style="padding-left:1.5em;">Hydrophobicity</span>');
57505
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrCharge', 'Charge', undefined, 1, 1);
56936
57506
 
56937
- html += "<li><span style='padding-left:1.5em;'>Hydrophobicity</span>";
57507
+ //html += "<li><span style='padding-left:1.5em!important;'>Hydrophobicity</span>";
57508
+ html += me.htmlCls.setHtmlCls.getMenuText('mn4_hydrophobicwrap', 'Hydrophobicity', 'icn3d-menupd', 1, 1);
56938
57509
  html += "<ul>";
56939
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrNormalizedHP', 'Normalized');
56940
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrHydrophobic', 'Wimley-White');
57510
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrNormalizedHP', 'Normalized', undefined, 1, 2);
57511
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrHydrophobic', 'Wimley-White', undefined, undefined, 2);
56941
57512
  html += "</ul>";
56942
57513
 
56943
- html += "<li><span style='padding-left:1.5em;'>B-factor</span>";
57514
+ //html += "<li><span style='padding-left:1.5em!important;'>B-factor</span>";
57515
+ html += me.htmlCls.setHtmlCls.getMenuText('mn4_clrBfactorwrap', 'B-factor', 'icn3d-menupd', 1, 1);
56944
57516
  html += "<ul>";
56945
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrBfactor', 'Original');
56946
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrBfactorNorm', 'Percentile');
57517
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrBfactor', 'Original', undefined, 1, 2);
57518
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrBfactorNorm', 'Percentile', undefined, 1, 2);
56947
57519
  html += "</ul>";
56948
57520
 
56949
- if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrArea', 'Solvent<br><span style="padding-left:1.5em;">Accessibility</span>');
57521
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrArea', 'Solvent<br><span style="padding-left:1.5em;">Accessibility</span>', undefined, undefined, 1);
56950
57522
 
56951
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrStructure', 'Structure');
57523
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrStructure', 'Structure', undefined, 1, 1);
56952
57524
 
56953
57525
  if(me.cfg.align !== undefined || me.cfg.chainalign !== undefined || me.cfg.blast_rep_id !== undefined) {
56954
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrChain', 'Chain');
57526
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrChain', 'Chain', undefined, 1, 1);
56955
57527
  }
56956
57528
  else {
56957
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrChain', 'Chain', true);
57529
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrChain', 'Chain', true, 1, 1);
56958
57530
  }
56959
57531
 
56960
57532
  //if(me.cfg.mmdbid !== undefined || me.cfg.gi !== undefined) {
56961
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrdomain', '3D Domain');
57533
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrdomain', '3D Domain', undefined, undefined, 1);
56962
57534
  //}
56963
57535
 
56964
57536
  if(me.cfg.cid === undefined) {
56965
- if(!me.cfg.simplemenu) {
56966
- html += "<li><span style='padding-left:1.5em;'>Defined Sets</span>";
56967
- html += "<ul>";
56968
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrsets', 'Rainbow for Selected Sets<br>in "Analysis > Defined Sets"');
56969
- html += "</ul>";
56970
- }
57537
+ //html += "<li><span style='padding-left:1.5em!important;'>Defined Sets</span>";
57538
+ html += me.htmlCls.setHtmlCls.getMenuText('mn4_clrsetswrap', 'Defined Sets', 'icn3d-menupd', undefined, 1);
57539
+ html += "<ul>";
57540
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrsets', 'Rainbow for Selected Sets<br><span style="padding-left:1.5em;">in "Analysis > Defined Sets"</span>', undefined, undefined, 2);
57541
+ html += "</ul>";
57542
+ html += "</li>";
56971
57543
  }
56972
57544
 
56973
- //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrResidue', 'Residue');
56974
-
56975
- html += "<li><span style='padding-left:1.5em;'>Residue</span>";
57545
+ //html += "<li><span style='padding-left:1.5em!important;'>Residue</span>";
57546
+ html += me.htmlCls.setHtmlCls.getMenuText('mn4_clrResiduewrap', 'Residue', 'icn3d-menupd', 1, 1);
56976
57547
  html += "<ul>";
56977
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrResidue', 'Default');
56978
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrResidueCustom', 'Custom');
57548
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrResidue', 'Default', undefined, 1, 2);
57549
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrResidueCustom', 'Custom', undefined, undefined, 2);
56979
57550
  html += "</ul>";
56980
57551
 
56981
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrAtom', 'Atom');
57552
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrAtom', 'Atom', undefined, 1, 1);
56982
57553
 
56983
57554
  if(me.cfg.align !== undefined || me.cfg.chainalign !== undefined) {
56984
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrIdentity', 'Identity', true);
56985
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrConserved', 'Conservation');
57555
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrIdentity', 'Identity', true, undefined, 2);
57556
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrConserved', 'Conservation', undefined, undefined, 2);
56986
57557
  }
56987
57558
  else if(me.cfg.blast_rep_id !== undefined) {
56988
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrIdentity', 'Identity');
56989
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrConserved', 'Conservation', true);
57559
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrIdentity', 'Identity', undefined, undefined, 2);
57560
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrConserved', 'Conservation', true, undefined, 2);
56990
57561
  }
56991
57562
 
56992
57563
  //if(me.cfg.afid) html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrConfidence', 'AF Confidence');
56993
57564
  //if(!me.cfg.mmtfid && !me.cfg.pdbid && !me.cfg.opmid && !me.cfg.mmdbid && !me.cfg.gi && !me.cfg.uniprotid && !me.cfg.blast_rep_id && !me.cfg.cid && !me.cfg.mmcifid && !me.cfg.align && !me.cfg.chainalign) {
56994
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrConfidence', 'AlphaFold<br><span style="padding-left:1.5em;">Confidence</span>');
57565
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrConfidence', 'AlphaFold<br><span style="padding-left:1.5em;">Confidence</span>', undefined, 1, 1);
56995
57566
  //}
56996
57567
  }
56997
57568
  else {
56998
57569
  //if(!me.cfg.hidelicense) html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn1_delphi2', 'DelPhi<br><span style="padding-left:1.5em;">Potential ' + me.htmlCls.licenseStr + '</span>');
56999
- html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrAtom', 'Atom', true);
57570
+ html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrAtom', 'Atom', true, 1, 1);
57000
57571
  }
57001
57572
 
57002
- if(!me.cfg.simplemenu) {
57003
- html += "<li>-</li>";
57573
+ html += me.htmlCls.setHtmlCls.getMenuSep();
57004
57574
 
57005
- html += me.htmlCls.setHtmlCls.getLink('mn4_clrSave', 'Save Color');
57006
- html += me.htmlCls.setHtmlCls.getLink('mn4_clrApplySave', 'Apply Saved Color');
57007
- }
57575
+ html += me.htmlCls.setHtmlCls.getLink('mn4_clrSave', 'Save Color', undefined, 1);
57576
+ html += me.htmlCls.setHtmlCls.getLink('mn4_clrApplySave', 'Apply Saved Color', undefined, 1);
57008
57577
 
57009
57578
  html += "<li><br/></li>";
57010
57579
  html += "</ul>";
@@ -57040,197 +57609,194 @@ class SetMenu {
57040
57609
  html += "<ul class='icn3d-mn-item'>";
57041
57610
 
57042
57611
  if(me.cfg.cid === undefined) {
57043
- html += me.htmlCls.setHtmlCls.getLink('mn6_selectannotations', 'Seq. & Annotations ' + me.htmlCls.wifiStr);
57612
+ html += me.htmlCls.setHtmlCls.getLink('mn6_selectannotations', 'Seq. & Annotations ' + me.htmlCls.wifiStr, 1, 1);
57044
57613
 
57045
57614
  //if(me.cfg.align !== undefined || me.cfg.chainalign !== undefined) { // || ic.bRealign || ic.bSymd || ic.bInputfile) {
57046
- html += me.htmlCls.setHtmlCls.getLink('mn2_alignment', 'Aligned Seq. ' + me.htmlCls.wifiStr);
57615
+ html += me.htmlCls.setHtmlCls.getLink('mn2_alignment', 'Aligned Seq. ' + me.htmlCls.wifiStr, undefined, 1);
57047
57616
  //}
57048
57617
 
57049
57618
  if(me.cfg.mmdbid !== undefined || me.cfg.gi !== undefined || me.cfg.blast_rep_id !== undefined || me.cfg.align !== undefined || me.cfg.chainalign !== undefined) {
57050
- html += me.htmlCls.setHtmlCls.getLink('mn2_2ddgm', '2D Diagram ' + me.htmlCls.wifiStr);
57619
+ html += me.htmlCls.setHtmlCls.getLink('mn2_2ddgm', '2D Diagram ' + me.htmlCls.wifiStr, 1, 1);
57051
57620
  }
57052
57621
 
57053
- html += "<li><span>2D Cartoon</span>";
57622
+ //html += "<li><span>2D Cartoon</span>";
57623
+ html += me.htmlCls.setHtmlCls.getMenuText('2dctnwrap', '2D Cartoon', undefined, 1);
57054
57624
  html += "<ul>";
57055
- html += me.htmlCls.setHtmlCls.getLink('2dctn_chain', 'Chain Level');
57056
- html += me.htmlCls.setHtmlCls.getLink('2dctn_domain', 'Domain Level');
57057
- html += me.htmlCls.setHtmlCls.getLink('2dctn_secondary', 'Helix/Sheet Level');
57625
+ html += me.htmlCls.setHtmlCls.getLink('2dctn_chain', 'Chain Level', undefined, 2);
57626
+ html += me.htmlCls.setHtmlCls.getLink('2dctn_domain', 'Domain Level', undefined, 2);
57627
+ html += me.htmlCls.setHtmlCls.getLink('2dctn_secondary', 'Helix/Sheet Level', undefined, 2);
57058
57628
  html += "</ul>";
57059
57629
  html += "</li>";
57060
57630
 
57061
- html += me.htmlCls.setHtmlCls.getLink('definedsets2', 'Defined Sets');
57631
+ html += me.htmlCls.setHtmlCls.getLink('definedsets2', 'Defined Sets', 1, 1);
57062
57632
 
57063
- html += "<li>-</li>";
57633
+ html += me.htmlCls.setHtmlCls.getMenuSep();
57064
57634
 
57065
- html += me.htmlCls.setHtmlCls.getLink('mn6_hbondsYes', 'Interactions');
57635
+ html += me.htmlCls.setHtmlCls.getLink('mn6_hbondsYes', 'Interactions', 1, 1);
57066
57636
  //html += me.htmlCls.setHtmlCls.getLink('mn6_hbondsNo', 'Remove H-Bonds <br>& Interactions');
57067
57637
 
57068
- if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getLink('mn6_contactmap', 'Contact Map');
57069
- /*
57070
- html += "<li><span>Bring to Front</span>";
57071
- html += "<ul>";
57072
- html += me.htmlCls.setHtmlCls.getLink('mn1_window_table', 'Interaction Table');
57073
- html += me.htmlCls.setHtmlCls.getLink('mn1_window_linegraph', '2D Interaction Network');
57074
- html += me.htmlCls.setHtmlCls.getLink('mn1_window_scatterplot', '2D Interaction Map');
57075
- html += me.htmlCls.setHtmlCls.getLink('mn1_window_graph', '2D Graph(Force-Directed)');
57076
- html += "</ul>";
57077
- html += "</li>";
57078
- */
57638
+ html += me.htmlCls.setHtmlCls.getLink('mn6_contactmap', 'Contact Map', undefined, 1);
57079
57639
 
57080
57640
  if(!me.cfg.notebook) {
57081
- html += me.htmlCls.setHtmlCls.getLink('mn1_mutation', 'Mutation ' + me.htmlCls.wifiStr);
57641
+ html += me.htmlCls.setHtmlCls.getLink('mn1_mutation', 'Mutation ' + me.htmlCls.wifiStr, 1, 1);
57082
57642
  }
57083
57643
 
57084
- if(!me.cfg.simplemenu) html += "<li>-</li>";
57644
+ html += me.htmlCls.setHtmlCls.getMenuSep();
57085
57645
  }
57086
57646
 
57087
57647
  if(!me.cfg.notebook && !me.cfg.hidelicense) {
57088
- html += me.htmlCls.setHtmlCls.getLink('mn1_delphi', 'DelPhi Potential ' + me.htmlCls.licenseStr);
57648
+ html += me.htmlCls.setHtmlCls.getLink('mn1_delphi', 'DelPhi Potential ' + me.htmlCls.licenseStr, 1, 1);
57089
57649
 
57090
- if(!me.cfg.simplemenu) {
57091
- html += "<li><span>Load PQR/Phi</span>";
57092
- html += "<ul>";
57093
- html += me.htmlCls.setHtmlCls.getLink('mn1_phi', 'Local PQR/Phi/Cube File');
57094
- html += me.htmlCls.setHtmlCls.getLink('mn1_phiurl', 'URL PQR/Phi/Cube File');
57095
- html += "</ul>";
57096
- html += me.htmlCls.setHtmlCls.getLink('delphipqr', 'Download PQR');
57097
- }
57650
+ //html += "<li><span>Load PQR/Phi</span>";
57651
+ html += me.htmlCls.setHtmlCls.getMenuText('mn1_phiwrap', 'Load PQR/Phi', undefined, undefined, 1);
57652
+ html += "<ul>";
57653
+ html += me.htmlCls.setHtmlCls.getLink('mn1_phi', 'Local PQR/Phi/Cube File', undefined, 2);
57654
+ html += me.htmlCls.setHtmlCls.getLink('mn1_phiurl', 'URL PQR/Phi/Cube File', undefined, 2);
57655
+ html += "</ul>";
57656
+ html += "</li>";
57657
+ html += me.htmlCls.setHtmlCls.getLink('delphipqr', 'Download PQR', undefined, 1);
57098
57658
 
57099
- html += "<li>-</li>";
57659
+ html += me.htmlCls.setHtmlCls.getMenuSep();
57100
57660
  }
57101
57661
 
57102
- html += "<li><span>Distance</span>";
57662
+ //html += "<li><span>Distance</span>";
57663
+ html += me.htmlCls.setHtmlCls.getMenuText('mn6_distancewrap', 'Distance', undefined, 1, 1);
57103
57664
  html += "<ul>";
57104
- html += me.htmlCls.setHtmlCls.getRadio('mn6_distance', 'mn6_distanceYes', 'between Two Atoms');
57105
- html += me.htmlCls.setHtmlCls.getRadio('mn6_distance', 'mn6_distTwoSets', 'between Two Sets');
57106
- html += me.htmlCls.setHtmlCls.getRadio('mn6_distance', 'mn6_distManySets', 'Among Many Sets');
57107
- html += me.htmlCls.setHtmlCls.getRadio('mn6_distance', 'mn6_distanceNo', 'Hide', true);
57665
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_distance', 'mn6_distanceYes', 'between Two Atoms', undefined, 1, 2);
57666
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_distance', 'mn6_distTwoSets', 'between Two Sets', undefined, undefined, 2);
57667
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_distance', 'mn6_distManySets', 'Among Many Sets', undefined, undefined, 2);
57668
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_distance', 'mn6_distanceNo', 'Hide', true, 1, 2);
57108
57669
  html += "</ul>";
57109
57670
  html += "</li>";
57110
57671
 
57111
- html += me.htmlCls.setHtmlCls.getLink('mn6_area', 'Surface Area');
57672
+ html += me.htmlCls.setHtmlCls.getLink('mn6_area', 'Surface Area', 1, 1);
57112
57673
 
57113
- html += "<li><span>Label</span>";
57674
+ //html += "<li><span>Label</span>";
57675
+ html += me.htmlCls.setHtmlCls.getMenuText('mn6_addlabelwrap', 'Label', undefined, 1, 1);
57114
57676
  html += "<ul>";
57115
- html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelYes', 'by Picking Atoms');
57116
- html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelSelection', 'per Selection');
57117
- html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelAtoms', 'per Atom');
57118
- html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelElements', 'per Atom Element');
57677
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelYes', 'by Picking Atoms', undefined, undefined, 2);
57678
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelSelection', 'per Selection', undefined, undefined, 2);
57679
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelAtoms', 'per Atom', undefined, undefined, 2);
57680
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelElements', 'per Atom Element', undefined, 1, 2);
57119
57681
  if(me.cfg.cid === undefined) {
57120
- html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelResidues', 'per Residue');
57121
- html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelResnum', 'per Residue & Number');
57122
- html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelChains', 'per Chain');
57123
- html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelTermini', 'N- & C-Termini');
57682
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelResidues', 'per Residue', undefined, 1, 2);
57683
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelResnum', 'per Residue & Number', undefined, 1, 2);
57684
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelChains', 'per Chain', undefined, undefined, 2);
57685
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelTermini', 'N- & C-Termini', undefined, 1, 2);
57124
57686
  }
57125
57687
 
57126
- html += "<li>-</li>";
57127
- html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_labelColor', 'Change Label Color', true);
57128
- html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelNo', 'Remove', true);
57688
+ html += me.htmlCls.setHtmlCls.getMenuSep();
57689
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_labelColor', 'Change Label Color', undefined, 1, 2);
57690
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelNo', 'Remove', true, 1, 2);
57129
57691
  html += "</ul>";
57130
57692
  html += "</li>";
57131
57693
 
57132
- html += "<li><span>Label Scale</span>";
57694
+ //html += "<li><span>Label Scale</span>";
57695
+ html += me.htmlCls.setHtmlCls.getMenuText('labelscalewrap', 'Label Scale', undefined, 1, 1);
57133
57696
  html += "<ul>";
57134
57697
 
57135
57698
  for(let i = 1; i <= 4; ++i) {
57136
57699
  let twoi = 2 * i;
57137
- html += me.htmlCls.setHtmlCls.getRadio('mn6_labelscale', 'mn6_labelscale0' + twoi, '0.' + twoi);
57700
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_labelscale', 'mn6_labelscale0' + twoi, '0.' + twoi, undefined, 1, 2);
57138
57701
  }
57139
57702
 
57140
57703
  for(let i = 1; i <= 5; ++i) {
57141
57704
  if(i == 1) {
57142
- html += me.htmlCls.setHtmlCls.getRadio('mn6_labelscale', 'mn6_labelscale' + i + '0', i + '.0', true);
57705
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_labelscale', 'mn6_labelscale' + i + '0', i + '.0', true, 1, 2);
57143
57706
  }
57144
57707
  else {
57145
- html += me.htmlCls.setHtmlCls.getRadio('mn6_labelscale', 'mn6_labelscale' + i + '0', i + '.0');
57708
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_labelscale', 'mn6_labelscale' + i + '0', i + '.0', undefined, 1, 2);
57146
57709
  }
57147
57710
  }
57148
57711
 
57149
57712
  html += "</ul>";
57150
57713
  html += "</li>";
57151
57714
 
57152
- html += "<li>-</li>";
57715
+ html += me.htmlCls.setHtmlCls.getMenuSep();
57153
57716
 
57154
57717
  if(me.cfg.cid === undefined) {
57155
- if(!me.cfg.simplemenu) {
57156
- html += "<li><span>Chem. Binding</span>";
57157
- html += "<ul>";
57158
- html += me.htmlCls.setHtmlCls.getRadio('mn6_chemicalbinding', 'mn6_chemicalbindingshow', 'Show');
57159
- html += me.htmlCls.setHtmlCls.getRadio('mn6_chemicalbinding', 'mn6_chemicalbindinghide', 'Hide', true);
57160
- html += "</ul>";
57161
- html += "</li>";
57162
- }
57718
+ //html += "<li><span>Chem. Binding</span>";
57719
+ html += me.htmlCls.setHtmlCls.getMenuText('mn6_chemicalbindingwrap', 'Chem. Binding', undefined, undefined, 1);
57720
+ html += "<ul>";
57721
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_chemicalbinding', 'mn6_chemicalbindingshow', 'Show', undefined, undefined, 2);
57722
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_chemicalbinding', 'mn6_chemicalbindinghide', 'Hide', true, undefined, 2);
57723
+ html += "</ul>";
57724
+ html += "</li>";
57163
57725
 
57164
- html += "<li><span>Disulfide Bonds</span>";
57726
+ //html += "<li><span>Disulfide Bonds</span>";
57727
+ html += me.htmlCls.setHtmlCls.getMenuText('mn6_ssbondswrap', 'Disulfide Bonds', undefined, 1, 1);
57165
57728
  html += "<ul>";
57166
- html += me.htmlCls.setHtmlCls.getRadio('mn6_ssbonds', 'mn6_ssbondsYes', 'Show', true);
57167
- html += me.htmlCls.setHtmlCls.getRadio('mn6_ssbonds', 'mn6_ssbondsExport', 'Export Pairs');
57168
- html += me.htmlCls.setHtmlCls.getRadio('mn6_ssbonds', 'mn6_ssbondsNo', 'Hide');
57729
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_ssbonds', 'mn6_ssbondsYes', 'Show', true, 1, 2);
57730
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_ssbonds', 'mn6_ssbondsExport', 'Export Pairs', undefined, undefined, 2);
57731
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_ssbonds', 'mn6_ssbondsNo', 'Hide', undefined, 1, 2);
57169
57732
  html += "</ul>";
57170
57733
  html += "</li>";
57171
57734
 
57172
- if(!me.cfg.simplemenu) {
57173
- html += "<li><span>Cross-Linkages</span>";
57174
- html += "<ul>";
57175
- html += me.htmlCls.setHtmlCls.getRadio('mn6_clbonds', 'mn6_clbondsYes', 'Show', true);
57176
- html += me.htmlCls.setHtmlCls.getRadio('mn6_clbonds', 'mn6_clbondsExport', 'Export Pairs');
57177
- html += me.htmlCls.setHtmlCls.getRadio('mn6_clbonds', 'mn6_clbondsNo', 'Hide');
57178
- html += "</ul>";
57179
- html += "</li>";
57180
- }
57735
+ //html += "<li><span>Cross-Linkages</span>";
57736
+ html += me.htmlCls.setHtmlCls.getMenuText('mn6_clbondswrap', 'Cross-Linkages', undefined, undefined, 1);
57737
+ html += "<ul>";
57738
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_clbonds', 'mn6_clbondsYes', 'Show', true, undefined, 2);
57739
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_clbonds', 'mn6_clbondsExport', 'Export Pairs', undefined, undefined, 2);
57740
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_clbonds', 'mn6_clbondsNo', 'Hide', undefined, undefined, 2);
57741
+ html += "</ul>";
57742
+ html += "</li>";
57181
57743
 
57182
- let bOnePdb = me.cfg.mmtfid !== undefined || me.cfg.pdbid !== undefined || me.cfg.opmid !== undefined || me.cfg.mmcifid !== undefined || me.cfg.mmdbid !== undefined || me.cfg.gi !== undefined || me.cfg.blast_rep_id !== undefined;
57744
+ let bOnePdb = me.cfg.mmtfid !== undefined || me.cfg.pdbid !== undefined || me.cfg.opmid !== undefined || me.cfg.mmcifid !== undefined || me.cfg.mmdbid !== undefined || me.cfg.mmdbafid !== undefined || me.cfg.gi !== undefined || me.cfg.blast_rep_id !== undefined;
57183
57745
 
57184
57746
  if(bOnePdb) {
57185
- html += "<li id='" + me.pre + "assemblyWrapper'><span>Assembly</span>";
57747
+ //html += "<li id='" + me.pre + "assemblyWrapper'><span>Assembly</span>";
57748
+ html += me.htmlCls.setHtmlCls.getMenuText('assemblyWrapper', 'Assembly', undefined, 1, 1);
57186
57749
  html += "<ul>";
57187
57750
 
57188
57751
  if(!me.cfg.bu) {
57189
- html += me.htmlCls.setHtmlCls.getRadio('mn6_assembly', 'mn6_assemblyYes', 'Biological Assembly');
57190
- html += me.htmlCls.setHtmlCls.getRadio('mn6_assembly', 'mn6_assemblyNo', 'Asymmetric Unit', true);
57752
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_assembly', 'mn6_assemblyYes', 'Biological Assembly', undefined, 1, 2);
57753
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_assembly', 'mn6_assemblyNo', 'Asymmetric Unit', true, 1, 2);
57191
57754
  }
57192
57755
  else {
57193
- html += me.htmlCls.setHtmlCls.getRadio('mn6_assembly', 'mn6_assemblyYes', 'Biological Assembly', true);
57194
- html += me.htmlCls.setHtmlCls.getRadio('mn6_assembly', 'mn6_assemblyNo', 'Asymmetric Unit');
57756
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_assembly', 'mn6_assemblyYes', 'Biological Assembly', true, 1, 2);
57757
+ html += me.htmlCls.setHtmlCls.getRadio('mn6_assembly', 'mn6_assemblyNo', 'Asymmetric Unit', undefined, 1, 2);
57195
57758
  }
57196
57759
 
57197
57760
  html += "</ul>";
57198
57761
  html += "</li>";
57199
-
57200
57762
  }
57201
57763
 
57202
- html += "<li><span>Symmetry</span>";
57764
+ //html += "<li><span>Symmetry</span>";
57765
+ html += me.htmlCls.setHtmlCls.getMenuText('mn6_symmetrywrap', 'Symmetry', undefined, undefined, 1);
57203
57766
  html += "<ul>";
57204
- if(bOnePdb) html += me.htmlCls.setHtmlCls.getLink('mn6_symmetry', 'from PDB(precalculated) ' + me.htmlCls.wifiStr);
57205
- if(!me.cfg.simplemenu) {
57206
- html += me.htmlCls.setHtmlCls.getLink('mn6_symd', 'from SymD(Dynamic) ' + me.htmlCls.wifiStr);
57207
- html += me.htmlCls.setHtmlCls.getLink('mn6_clear_sym', 'Clear SymD Symmetry');
57208
- html += me.htmlCls.setHtmlCls.getLink('mn6_axes_only', 'Show Axes Only');
57209
- }
57767
+ if(bOnePdb) html += me.htmlCls.setHtmlCls.getLink('mn6_symmetry', 'from PDB(precalculated) ' + me.htmlCls.wifiStr, undefined, 2);
57768
+
57769
+ html += me.htmlCls.setHtmlCls.getLink('mn6_symd', 'from SymD(Dynamic) ' + me.htmlCls.wifiStr, undefined, 2);
57770
+ html += me.htmlCls.setHtmlCls.getLink('mn6_clear_sym', 'Clear SymD Symmetry', undefined, 2);
57771
+ html += me.htmlCls.setHtmlCls.getLink('mn6_axes_only', 'Show Axes Only', undefined, 2);
57772
+
57210
57773
  html += "</ul>";
57211
57774
  html += "</li>";
57212
57775
 
57213
- html += "<li>-</li>";
57776
+ html += me.htmlCls.setHtmlCls.getMenuSep();
57214
57777
  }
57215
57778
 
57216
- if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getLink('mn6_yournote', 'Window Title');
57779
+ html += me.htmlCls.setHtmlCls.getLink('mn6_yournote', 'Window Title', undefined, 1);
57217
57780
 
57218
57781
  if(me.cfg.cid !== undefined) {
57219
- html += "<li><span>Links</span>";
57782
+ //html += "<li><span>Links</span>";
57783
+ html += me.htmlCls.setHtmlCls.getMenuText('mn1_linkwrap', 'Links', undefined, undefined, 1);
57784
+
57220
57785
  html += "<ul>";
57221
- html += me.htmlCls.setHtmlCls.getLink('mn1_link_structure', 'Compound Summary ' + me.htmlCls.wifiStr);
57222
- html += me.htmlCls.setHtmlCls.getLink('mn1_link_vast', 'Similar Compounds ' + me.htmlCls.wifiStr);
57223
- html += me.htmlCls.setHtmlCls.getLink('mn1_link_bind', 'Structures Bound ' + me.htmlCls.wifiStr);
57786
+ html += me.htmlCls.setHtmlCls.getLink('mn1_link_structure', 'Compound Summary ' + me.htmlCls.wifiStr, undefined, 2);
57787
+ html += me.htmlCls.setHtmlCls.getLink('mn1_link_vast', 'Similar Compounds ' + me.htmlCls.wifiStr, undefined, 2);
57788
+ html += me.htmlCls.setHtmlCls.getLink('mn1_link_bind', 'Structures Bound ' + me.htmlCls.wifiStr, undefined, 2);
57224
57789
  html += "</ul>";
57225
57790
  html += "</li>";
57226
57791
  }
57227
57792
  else {
57228
- html += "<li><span>Links</span>";
57793
+ //html += "<li><span>Links</span>";
57794
+ html += me.htmlCls.setHtmlCls.getMenuText('mn1_linkwrap', 'Links', undefined, undefined, 1);
57229
57795
  html += "<ul>";
57230
- html += me.htmlCls.setHtmlCls.getLink('mn1_link_structure', 'Structure Summary ' + me.htmlCls.wifiStr);
57231
- html += me.htmlCls.setHtmlCls.getLink('mn1_link_vast', 'Similar Structures ' + me.htmlCls.wifiStr);
57232
- html += me.htmlCls.setHtmlCls.getLink('mn1_link_pubmed', 'Literature ' + me.htmlCls.wifiStr);
57233
- html += me.htmlCls.setHtmlCls.getLink('mn1_link_protein', 'Protein ' + me.htmlCls.wifiStr);
57796
+ html += me.htmlCls.setHtmlCls.getLink('mn1_link_structure', 'Structure Summary ' + me.htmlCls.wifiStr, undefined, 2);
57797
+ html += me.htmlCls.setHtmlCls.getLink('mn1_link_vast', 'Similar Structures ' + me.htmlCls.wifiStr, undefined, 2);
57798
+ html += me.htmlCls.setHtmlCls.getLink('mn1_link_pubmed', 'Literature ' + me.htmlCls.wifiStr, undefined, 2);
57799
+ html += me.htmlCls.setHtmlCls.getLink('mn1_link_protein', 'Protein ' + me.htmlCls.wifiStr, undefined, 2);
57234
57800
  //html += me.htmlCls.setHtmlCls.getLink('mn1_link_gene', 'Gene');
57235
57801
  //html += me.htmlCls.setHtmlCls.getLink('mn1_link_chemicals', 'Chemicals');
57236
57802
  html += "</ul>";
@@ -57269,55 +57835,77 @@ class SetMenu {
57269
57835
 
57270
57836
  let html = "";
57271
57837
 
57272
- let liStr = "<li><a href='";
57273
-
57274
57838
  html += "<ul class='icn3d-mn-item'>";
57275
57839
 
57276
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#about' target='_blank'>About iCn3D<span style='font-size:0.9em'> " + me.REVISION + "</span></a></li>";
57840
+ //html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#about' target='_blank'>About iCn3D<span style='font-size:0.9em'> " + me.REVISION + "</span></a></li>";
57841
+ html += me.htmlCls.setHtmlCls.getMenuUrl('abouticn3d', me.htmlCls.baseUrl + "icn3d/icn3d.html#about", "About iCn3D<span style='font-size:0.9em'> " + me.REVISION + "</span>", 1, 1);
57842
+
57843
+ //html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#gallery' target='_blank'>Live Gallery " + me.htmlCls.wifiStr + "</a></li>";
57844
+ html += me.htmlCls.setHtmlCls.getMenuUrl('gallery', me.htmlCls.baseUrl + "icn3d/icn3d.html#gallery", "Live Gallery " + me.htmlCls.wifiStr, 1, 1);
57845
+ //html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#videos' target='_blank'>iCn3D Videos</a></li>";
57846
+ html += me.htmlCls.setHtmlCls.getMenuUrl('video', me.htmlCls.baseUrl + "icn3d/icn3d.html#videos", "iCn3D Videos", 1, 1);
57277
57847
 
57278
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#gallery' target='_blank'>Live Gallery " + me.htmlCls.wifiStr + "</a></li>";
57848
+ //html += "<li><span>FAQ</span>";
57849
+ html += me.htmlCls.setHtmlCls.getMenuText('mn6_faq', 'FAQ', undefined, 1, 1);
57279
57850
 
57280
- html += "<li><span>Tutorial</span>";
57281
57851
  html += "<ul>";
57282
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#useicn3d' target='_blank'>Use iCn3D</a></li>";
57283
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#videos' target='_blank'>iCn3D Videos</a></li>";
57284
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#parameters' target='_blank'>URL Parameters</a></li>";
57285
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#commands' target='_blank'>Commands</a></li>";
57852
+ html += me.htmlCls.setHtmlCls.getMenuUrl('faq_viewstru', me.htmlCls.baseUrl + "icn3d/icn3d.html#viewstru", "View structure", 1, 2);
57853
+ html += me.htmlCls.setHtmlCls.getMenuUrl('faq_tfstru', me.htmlCls.baseUrl + "icn3d/icn3d.html#tfstru", "Transform Structure", 1, 2);
57854
+ html += me.htmlCls.setHtmlCls.getMenuUrl('faq_selsubset', me.htmlCls.baseUrl + "icn3d/icn3d.html#selsubset", "Select Subsets", 1, 2);
57855
+ html += me.htmlCls.setHtmlCls.getMenuUrl('faq_stylecolor', me.htmlCls.baseUrl + "icn3d/icn3d.html#changestylecolor", "Change Style/Color", 1, 2);
57856
+ html += me.htmlCls.setHtmlCls.getMenuUrl('faq_savework', me.htmlCls.baseUrl + "icn3d/icn3d.html#saveview", "Save Work", 1, 2);
57857
+ html += me.htmlCls.setHtmlCls.getMenuUrl('faq_showanno', me.htmlCls.baseUrl + "icn3d/icn3d.html#showanno", "Show Annotations", 1, 2);
57858
+ html += me.htmlCls.setHtmlCls.getMenuUrl('faq_exportanno', me.htmlCls.baseUrl + "icn3d/icn3d.html#exportanno", "Export Annotations", 1, 2);
57859
+ html += me.htmlCls.setHtmlCls.getMenuUrl('faq_interanal', me.htmlCls.baseUrl + "icn3d/icn3d.html#interanalysis", "Interactions Analysis", 1, 2);
57860
+ html += me.htmlCls.setHtmlCls.getMenuUrl('faq_mutanal', me.htmlCls.baseUrl + "icn3d/icn3d.html#mutationanalysis", "Mutation Analysis", 1, 2);
57861
+ html += me.htmlCls.setHtmlCls.getMenuUrl('faq_elecpot', me.htmlCls.baseUrl + "icn3d/icn3d.html#elecpot", "Electrostatic Pot.", 1, 2);
57862
+ html += me.htmlCls.setHtmlCls.getMenuUrl('faq_simipdb', me.htmlCls.baseUrl + "icn3d/icn3d.html#simivast", "Similar PDB", 1, 2);
57863
+ html += me.htmlCls.setHtmlCls.getMenuUrl('faq_simialphapdb', me.htmlCls.baseUrl + "icn3d/icn3d.html#simifoldseek", "Similar AlphaFold/PDB", 1, 2);
57864
+ html += me.htmlCls.setHtmlCls.getMenuUrl('faq_alnstru', me.htmlCls.baseUrl + "icn3d/icn3d.html#alignmul", "Align Multiple Structures", 1, 2);
57865
+ html += me.htmlCls.setHtmlCls.getMenuUrl('faq_batchanal', me.htmlCls.baseUrl + "icn3d/icn3d.html#batchanalysis", "Batch Analysis", 1, 2);
57866
+ html += me.htmlCls.setHtmlCls.getMenuUrl('faq_embedicn3d', me.htmlCls.baseUrl + "icn3d/icn3d.html#embedicn3d", "Embed iCn3D", 1, 2);
57286
57867
  html += "</ul>";
57287
57868
  html += "</li>";
57288
57869
 
57289
- html += liStr + "https://www.ncbi.nlm.nih.gov/structure' target='_blank'>Search Structure " + me.htmlCls.wifiStr + "</a></li>";
57290
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#citing' target='_blank'>Citing iCn3D</a></li>";
57870
+ //html += liStr + "https://www.ncbi.nlm.nih.gov/structure' target='_blank'>Search Structure " + me.htmlCls.wifiStr + "</a></li>";
57871
+ //html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#citing' target='_blank'>Citing iCn3D</a></li>";
57872
+ html += me.htmlCls.setHtmlCls.getMenuUrl('citing', me.htmlCls.baseUrl + "icn3d/icn3d.html#citing", "Citing iCn3D", undefined, 1);
57291
57873
 
57292
- html += "<li><span>Source Code</span>";
57874
+ //html += "<li><span>Source Code</span>";
57875
+ html += me.htmlCls.setHtmlCls.getMenuText('mn6_source', 'Source Code', undefined, 1, 1);
57293
57876
  html += "<ul>";
57294
- html += liStr + "https://github.com/ncbi/icn3d' target='_blank'>GitHub (browser) " + me.htmlCls.wifiStr + "</a></li>";
57295
- html += liStr + "https://www.npmjs.com/package/icn3d' target='_blank'>npm (Node.js) " + me.htmlCls.wifiStr + "</a></li>";
57296
- html += liStr + "https://pypi.org/project/icn3dpy' target='_blank'>Jupyter Notebook " + me.htmlCls.wifiStr + "</a></li>";
57877
+ html += me.htmlCls.setHtmlCls.getMenuUrl('github', "https://github.com/ncbi/icn3d", "GitHub (browser) " + me.htmlCls.wifiStr, 1, 2);
57878
+ html += me.htmlCls.setHtmlCls.getMenuUrl('npm', "https://www.npmjs.com/package/icn3d", "npm (Node.js) " + me.htmlCls.wifiStr, 1, 2);
57879
+ html += me.htmlCls.setHtmlCls.getMenuUrl('notebook', "https://pypi.org/project/icn3dpy", "Jupyter Notebook " + me.htmlCls.wifiStr, 1, 2);
57297
57880
  html += "</ul>";
57298
57881
  html += "</li>";
57299
57882
 
57300
- if(!me.cfg.simplemenu) {
57301
- html += "<li><span>Develop</span>";
57302
- html += "<ul>";
57303
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#HowToUse' target='_blank'>How to Embed</a></li>";
57304
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#datastructure' target='_blank'>Data Structure</a></li>";
57305
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#classstructure' target='_blank'>Class Structure</a></li>";
57306
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#addclass' target='_blank'>Add New Classes</a></li>";
57307
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#modifyfunction' target='_blank'>Modify Functions</a></li>";
57308
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#restfulapi' target='_blank'>RESTful APIs</a></li>";
57309
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#contributors' target='_blank'>Codeathon Contributors</a></li>";
57310
- html += "</ul>";
57311
- html += "</li>";
57312
- }
57883
+ //html += "<li><span>Develop</span>";
57884
+ html += me.htmlCls.setHtmlCls.getMenuText('mn6_develop', 'Develop', undefined, undefined, 1);
57885
+ html += "<ul>";
57886
+ html += me.htmlCls.setHtmlCls.getMenuUrl('dev_embedicn3d2', me.htmlCls.baseUrl + "icn3d/icn3d.html#HowToUse", "Embed iCn3D", undefined, 2);
57887
+ html += me.htmlCls.setHtmlCls.getMenuUrl('dev_urlpara', me.htmlCls.baseUrl + "icn3d/icn3d.html#parameters", "URL Parameters", undefined, 2);
57888
+ html += me.htmlCls.setHtmlCls.getMenuUrl('dev_command', me.htmlCls.baseUrl + "icn3d/icn3d.html#commands", "Commands", undefined, 2);
57889
+
57890
+ html += me.htmlCls.setHtmlCls.getMenuUrl('dev_datastru', me.htmlCls.baseUrl + "icn3d/icn3d.html#datastructure", "Data Structure", undefined, 2);
57891
+ html += me.htmlCls.setHtmlCls.getMenuUrl('dev_classstru', me.htmlCls.baseUrl + "icn3d/icn3d.html#classstructure", "Class Structure", undefined, 2);
57892
+ html += me.htmlCls.setHtmlCls.getMenuUrl('dev_addclass', me.htmlCls.baseUrl + "icn3d/icn3d.html#addclass", "Add New Classes", undefined, 2);
57893
+ html += me.htmlCls.setHtmlCls.getMenuUrl('dev_modfunc', me.htmlCls.baseUrl + "icn3d/icn3d.html#modifyfunction", "Modify Functions", undefined, 2);
57894
+ html += me.htmlCls.setHtmlCls.getMenuUrl('dev_restful', me.htmlCls.baseUrl + "icn3d/icn3d.html#restfulapi", "RESTful APIs", undefined, 2);
57895
+ html += me.htmlCls.setHtmlCls.getMenuUrl('dev_contributor', me.htmlCls.baseUrl + "icn3d/icn3d.html#contributors", "Codeathon Contributors", undefined, 2);
57896
+ html += "</ul>";
57897
+ html += "</li>";
57313
57898
 
57314
- html += liStr + me.htmlCls.baseUrl + "icn3d/docs/icn3d_help.html' target='_blank'>Help Doc " + me.htmlCls.wifiStr + "</a></li>";
57899
+ //html += liStr + me.htmlCls.baseUrl + "icn3d/docs/icn3d_help.html' target='_blank'>Help Doc " + me.htmlCls.wifiStr + "</a></li>";
57900
+ html += me.htmlCls.setHtmlCls.getMenuUrl('helpdoc', me.htmlCls.baseUrl + "icn3d/docs/icn3d_help.html", "Help Doc " + me.htmlCls.wifiStr, 1, 1);
57315
57901
 
57316
- html += "<li>-</li>";
57902
+ html += me.htmlCls.setHtmlCls.getMenuSep();
57317
57903
 
57318
- html += "<li><span>Transform Hints</span>";
57904
+ //html += "<li><span>Transform Hints</span>";
57905
+ html += me.htmlCls.setHtmlCls.getMenuText('mn6_tfhint', 'Transform Hints', undefined, 1, 1);
57319
57906
  html += "<ul>";
57320
- html += "<li><span>Rotate</span>";
57907
+ //html += "<li><span>Rotate</span>";
57908
+ html += me.htmlCls.setHtmlCls.getMenuText('mn6_rotate', 'Rotate', undefined, 1, 2);
57321
57909
  html += "<ul>";
57322
57910
  html += "<li>Left Mouse (Click & Drag)</li>";
57323
57911
  html += "<li>Key l: Left</li>";
@@ -57330,14 +57918,16 @@ class SetMenu {
57330
57918
  html += "<li>Shift + Key m: Down 90&deg;</li>";
57331
57919
  html += "</ul>";
57332
57920
  html += "</li>";
57333
- html += "<li><span>Zoom</span>";
57921
+ //html += "<li><span>Zoom</span>";
57922
+ html += me.htmlCls.setHtmlCls.getMenuText('mn6_zoom', 'Zoom', undefined, 1, 2);
57334
57923
  html += "<ul>";
57335
57924
  html += "<li>Middle Mouse <br>(Pinch & Spread)</li>";
57336
57925
  html += "<li>Key z: Zoom in</li>";
57337
57926
  html += "<li>Key x: Zoom out</li>";
57338
57927
  html += "</ul>";
57339
57928
  html += "</li>";
57340
- html += "<li><span>Translate</span>";
57929
+ //html += "<li><span>Translate</span>";
57930
+ html += me.htmlCls.setHtmlCls.getMenuText('mn6_translate', 'Translate', undefined, 1, 2);
57341
57931
  html += "<ul>";
57342
57932
  html += "<li>Right Mouse <br>(Two Finger Click & Drag)</li>";
57343
57933
  html += "</ul>";
@@ -57345,11 +57935,10 @@ class SetMenu {
57345
57935
  html += "</ul>";
57346
57936
  html += "</li>";
57347
57937
 
57348
- if(!me.cfg.simplemenu) {
57349
- html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#HowToUseStep5' target='_blank'>Selection Hints</a></li>";
57350
-
57351
- html += liStr + "https://support.nlm.nih.gov/support/create-case/' target='_blank'>Write to Help Desk</a></li>";
57352
- }
57938
+ //html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#HowToUseStep5' target='_blank'>Selection Hints</a></li>";
57939
+ html += me.htmlCls.setHtmlCls.getMenuUrl('selhints', me.htmlCls.baseUrl + "icn3d/icn3d.html#HowToUseStep5", "Selection Hints", undefined, 1);
57940
+ //html += liStr + "https://support.nlm.nih.gov/support/create-case/' target='_blank'>Write to Help Desk</a></li>";
57941
+ html += me.htmlCls.setHtmlCls.getMenuUrl('helpdesk', "https://support.nlm.nih.gov/support/create-case/", "Write to Help Desk", 1, 1);
57353
57942
 
57354
57943
  html += "<li><br/></li>";
57355
57944
  html += "</ul>";
@@ -58068,8 +58657,8 @@ class SetDialog {
58068
58657
  html += "</div>";
58069
58658
 
58070
58659
  html += me.htmlCls.divStr + "dl_foldseek' class='" + dialogClass + "' style='max-width:500px'>";
58071
- html += 'Note: You can search similar PDB or AlphaFold structures for any structure at the fast <a href="https://search.foldseek.com/search" target="_blank">Foldseek</a> web server. <br><br>Once you see the structure neighbors, you can view the alignment in iCn3D by inputing a list of chain IDs below. <br><br>The PDB chain IDs are the same as the record names such as "1hho_A". The AlphaFold chain IDs are the UniProt ID plus "_A". For example, the UniProt ID for the record name "AF-P69905-F1-model_v2" is "P69905".<br><br>';
58072
- html += "Chain ID List: " + me.htmlCls.inputTextStr + "id='" + me.pre + "foldseekchainids' value='P69905_A,P01942_A,1HHO_A' size=30> ";
58660
+ html += 'Note: You can search similar PDB or AlphaFold structures for any structure at the fast <a href="https://search.foldseek.com/search" target="_blank">Foldseek</a> web server. <br><br>Once you see the structure neighbors, you can view the alignment in iCn3D by inputing a list of PDB chain IDs or AlphaFold UniProt IDs below. <br><br>The PDB chain IDs are the same as the record names such as "1hho_A". The UniProt ID is the text between "AF-" and "-F1". For example, the UniProt ID for the record name "AF-P69905-F1-model_v3" is "P69905".<br><br>';
58661
+ html += "Chain ID List: " + me.htmlCls.inputTextStr + "id='" + me.pre + "foldseekchainids' value='P69905,P01942,1hho_A' size=30> ";
58073
58662
  html += me.htmlCls.buttonStr + "reload_foldseek'>Align</button>";
58074
58663
  html += "</div>";
58075
58664
 
@@ -58191,11 +58780,19 @@ class SetDialog {
58191
58780
  html += 'Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[PDB ID or AlphaFold UniProt ID]_[Chain ID]_[Residue Number]_[One Letter Mutatnt Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A".<br/><br/>';
58192
58781
  html += "<div style='display:inline-block; width:110px'>Mutations: </div>" + me.htmlCls.inputTextStr + "id='" + me.pre + "mutationids' value='6M0J_E_484_K,6M0J_E_501_Y,6M0J_E_417_N' size=50><br/><br/>";
58193
58782
 
58194
- html += "<b>Data Source</b>: <select id='" + me.pre + "idsource'>";
58195
- html += "<option value='mmdbid' selected>PDB ID</option>";
58196
- html += "<option value='afid'>AlphaFold UniProt ID</option>";
58197
- html += "</select><br/><br/>";
58198
-
58783
+ // html += "<b>Data Source</b>: <select id='" + me.pre + "idsource'>";
58784
+ // html += "<option value='mmdbid' selected>PDB ID</option>";
58785
+ // html += "<option value='afid'>AlphaFold UniProt ID</option>";
58786
+ // html += "</select><br/><br/>";
58787
+
58788
+ html += '<b>ID Type</b>: ';
58789
+ html += '<input type="radio" name="' + me.pre + 'idsource" id="' + me.pre + 'type_mmdbid" value="mmdbid" checked>PDB ID';
58790
+ html += '<input type="radio" name="' + me.pre + 'idsource" id="' + me.pre + 'type_afid" value="afid" style="margin-left:20px">AlphaFold UniProt ID<br><br>';
58791
+
58792
+ html += '<b>Show Mutation in</b>: ';
58793
+ html += '<input type="radio" name="' + me.pre + 'pdbsource" id="' + me.pre + 'showin_currentpage" value="currentpage">Current Page';
58794
+ html += '<input type="radio" name="' + me.pre + 'pdbsource" id="' + me.pre + 'showin_newpage" value="newpage" style="margin-left:20px" checked>New Page<br><br>';
58795
+
58199
58796
  html += me.htmlCls.buttonStr + "reload_mutation_3d' title='Show the mutations in 3D using the scap program'>3D with scap</button>";
58200
58797
  html += me.htmlCls.buttonStr + "reload_mutation_inter' style='margin-left:20px' title='Show the mutations in 3D and the change of interactions'>Interactions</button>";
58201
58798
  html += me.htmlCls.buttonStr + "reload_mutation_pdb' style='margin-left:20px' title='Show the mutations in 3D and export the PDB of the mutant within 10 angstrom'>PDB</button>";
@@ -58279,7 +58876,7 @@ class SetDialog {
58279
58876
  html += "</div>";
58280
58877
 
58281
58878
  html += me.htmlCls.divStr + "dl_yournote' class='" + dialogClass + "'>";
58282
- html += "Your note will be saved in the HTML file when you click \"File > Save Files > iCn3D PNG Image\".<br><br>";
58879
+ html += "Your note will be saved in the HTML file when you click \"File > Save File > iCn3D PNG Image\".<br><br>";
58283
58880
  html += "<textarea id='" + me.pre + "yournote' rows='5' style='width: 100%; height: " +(me.htmlCls.LOG_HEIGHT) + "px; padding: 0px; border: 0px;' placeholder='Enter your note here'></textarea><br>";
58284
58881
  html += me.htmlCls.buttonStr + "applyyournote'>Save</button>";
58285
58882
  html += "</div>";
@@ -58322,6 +58919,11 @@ class SetDialog {
58322
58919
  html += me.htmlCls.buttonStr + "reload_selectionfile' style='margin-top: 6px;'>Load</button>";
58323
58920
  html += "</div>";
58324
58921
 
58922
+ html += me.htmlCls.divStr + "dl_menuloadpref' class='" + dialogClass + "'>";
58923
+ html += "Preference file: " + me.htmlCls.inputFileStr + "id='" + me.pre + "menupreffile'><br/>";
58924
+ html += me.htmlCls.buttonStr + "reload_menupreffile' style='margin-top: 6px;'>Load</button>";
58925
+ html += "</div>";
58926
+
58325
58927
  html += me.htmlCls.divStr + "dl_dsn6' class='" + dialogClass + "'>";
58326
58928
  html += "<b>Note</b>: Always load a PDB file before loading DSN6 files. <br/><br/><br/>";
58327
58929
 
@@ -58816,6 +59418,15 @@ class SetDialog {
58816
59418
  html += me.htmlCls.setHtmlCls.setThicknessHtml('style');
58817
59419
  html += "</div>";
58818
59420
 
59421
+ html += me.htmlCls.divStr + "dl_menupref' class='" + dialogClass + "'>";
59422
+ html += "<b>Note</b>: The following parameters will be saved in cache. You just need to set them once. <br><br>";
59423
+ html += "<div id='" + me.pre + "menulist' style='max-width:500px; max-height:300px; overflow:scroll'></div><br><br>";
59424
+ html += me.htmlCls.spanNowrapStr + "" + me.htmlCls.buttonStr + "apply_menupref'>Apply</button></span>";
59425
+ html += me.htmlCls.spanNowrapStr + "" + me.htmlCls.buttonStr + "reset_menupref' style='margin-left:30px'>Reset to Simple Menus</button></span>";
59426
+ html += me.htmlCls.spanNowrapStr + "" + me.htmlCls.buttonStr + "reset_menupref_all' style='margin-left:30px'>Reset to All Menus</button></span>";
59427
+ html += me.htmlCls.spanNowrapStr + "" + me.htmlCls.buttonStr + "savepref' style='margin-left:30px'>Save Preferences</button></span>";
59428
+ html += "</div>";
59429
+
58819
59430
  html += me.htmlCls.divStr + "dl_addtrack' class='" + dialogClass + "'>";
58820
59431
  html += " <input type='hidden' id='" + me.pre + "track_chainid' value=''>";
58821
59432
 
@@ -59034,10 +59645,17 @@ class SetDialog {
59034
59645
  html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_custom'>Custom" + me.htmlCls.space2 + "</span></td>";
59035
59646
  html += tmpStr2 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_3dd'>3D Domains" + me.htmlCls.space2 + "</span></td>";
59036
59647
  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>";
59648
+
59649
+ // if(me.cfg.mmdbid != undefined || me.cfg.pdbid != undefined || me.cfg.mmtfid != undefined || me.cfg.mmcifid != undefined) { // PDB
59650
+ // html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_ptm' disabled>PTM (UniProt)" + me.htmlCls.space2 + "</span></td>";
59651
+ // }
59652
+ // else {
59653
+ html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_ptm'>PTM (UniProt)" + me.htmlCls.space2 + "</span></td>";
59654
+ // }
59038
59655
  html += "<td></td>";
59039
59656
  html += "</tr><tr>";
59040
59657
  html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_ssbond'>Disulfide Bonds" + me.htmlCls.space2 + "</span></td>";
59658
+ html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_interact'>Interactions" + me.htmlCls.space2 + "</span></td>";
59041
59659
  html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_crosslink'>Cross-Linkages" + me.htmlCls.space2 + "</span></td>";
59042
59660
  if(me.cfg.opmid !== undefined) {
59043
59661
  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>";
@@ -59076,6 +59694,17 @@ class Events {
59076
59694
  }
59077
59695
  }
59078
59696
 
59697
+ convertUniProtInChains(alignment) { let me = this.icn3dui; me.icn3d;
59698
+ let idArray = alignment.split(',');
59699
+ let alignment_final = '';
59700
+ for(let i = 0, il = idArray.length; i < il; ++i) {
59701
+ alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
59702
+ if(i < il - 1) alignment_final += ',';
59703
+ }
59704
+
59705
+ return alignment_final;
59706
+ }
59707
+
59079
59708
  searchSeq() { let me = this.icn3dui, ic = me.icn3d;
59080
59709
  let select = $("#" + me.pre + "search_seq").val();
59081
59710
  if(isNaN(select) && select.indexOf('$') == -1 && select.indexOf('.') == -1 && select.indexOf(':') == -1 && select.indexOf('@') == -1) {
@@ -59414,10 +60043,7 @@ class Events {
59414
60043
  ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
59415
60044
  }
59416
60045
 
59417
- // save the current selection
59418
- //ic.selectionCls.saveSelectionPrep();
59419
- //let name = 'realignSetsByStruct';
59420
- //ic.selectionCls.saveSelection(name, name);
60046
+ me.cfg.aligntool = 'vast';
59421
60047
 
59422
60048
  ic.realignParserCls.realignOnStructAlign();
59423
60049
  if(nameArray.length > 0) {
@@ -59549,8 +60175,16 @@ class Events {
59549
60175
  me.myEventCls.onIds("#" + me.pre + "reload_foldseek", "click", function(e) { me.icn3d;
59550
60176
  e.preventDefault();
59551
60177
  if(!me.cfg.notebook) dialog.dialog( "close" );
59552
- me.htmlCls.clickMenuCls.setLogCmd("load chainalignment " + $("#" + me.pre + "foldseekchainids").val(), true);
59553
- window.open(hostUrl + '?chainalign=' + $("#" + me.pre + "foldseekchainids").val(), '_self');
60178
+
60179
+ // me.htmlCls.clickMenuCls.setLogCmd("load chainalignment " + $("#" + me.pre + "foldseekchainids").val(), true);
60180
+ // window.open(hostUrl + '?chainalign=' + $("#" + me.pre + "foldseekchainids").val(), '_self');
60181
+
60182
+
60183
+ let alignment = $("#" + me.pre + "foldseekchainids").val();
60184
+ let alignment_final = thisClass.convertUniProtInChains(alignment);
60185
+
60186
+ me.htmlCls.clickMenuCls.setLogCmd("load chainalignment " + alignment_final, true);
60187
+ window.open(hostUrl + '?chainalign=' + alignment_final + '&aligntool=tmalign&showalignseq=1&bu=0', '_self');
59554
60188
  });
59555
60189
 
59556
60190
  me.myEventCls.onIds("#" + me.pre + "reload_mmtf", "click", function(e) { me.icn3d;
@@ -59692,12 +60326,7 @@ class Events {
59692
60326
  if(!me.cfg.notebook) dialog.dialog( "close" );
59693
60327
 
59694
60328
  let alignment = $("#" + me.pre + "chainalignids").val();
59695
- let idArray = alignment.split(',');
59696
- let alignment_final = '';
59697
- for(let i = 0, il = idArray.length; i < il; ++i) {
59698
- alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
59699
- if(i < il - 1) alignment_final += ',';
59700
- }
60329
+ let alignment_final = thisClass.convertUniProtInChains(alignment);
59701
60330
  let resalign = $("#" + me.pre + "resalignids").val();
59702
60331
  let predefinedres = $("#" + me.pre + "predefinedres").val().trim().replace(/\n/g, '; ');
59703
60332
  if(predefinedres && alignment_final.split(',').length - 1 != predefinedres.split('; ').length) {
@@ -59715,12 +60344,7 @@ class Events {
59715
60344
  if(!me.cfg.notebook) dialog.dialog( "close" );
59716
60345
 
59717
60346
  let alignment = $("#" + me.pre + "chainalignids").val();
59718
- let idArray = alignment.split(',');
59719
- let alignment_final = '';
59720
- for(let i = 0, il = idArray.length; i < il; ++i) {
59721
- alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
59722
- if(i < il - 1) alignment_final += ',';
59723
- }
60347
+ let alignment_final = thisClass.convertUniProtInChains(alignment);
59724
60348
 
59725
60349
  me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues | resdef ", false);
59726
60350
  window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=&resdef=&showalignseq=1&bu=0', '_blank');
@@ -59731,12 +60355,7 @@ class Events {
59731
60355
  if(!me.cfg.notebook) dialog.dialog( "close" );
59732
60356
 
59733
60357
  let alignment = $("#" + me.pre + "chainalignids2").val();
59734
- let idArray = alignment.split(',');
59735
- let alignment_final = '';
59736
- for(let i = 0, il = idArray.length; i < il; ++i) {
59737
- alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
59738
- if(i < il - 1) alignment_final += ',';
59739
- }
60358
+ let alignment_final = thisClass.convertUniProtInChains(alignment);
59740
60359
  let resalign = $("#" + me.pre + "resalignids").val();
59741
60360
 
59742
60361
  me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues " + resalign + " | resdef ", false);
@@ -59748,12 +60367,7 @@ class Events {
59748
60367
  if(!me.cfg.notebook) dialog.dialog( "close" );
59749
60368
 
59750
60369
  let alignment = $("#" + me.pre + "chainalignids3").val();
59751
- let idArray = alignment.split(',');
59752
- let alignment_final = '';
59753
- for(let i = 0, il = idArray.length; i < il; ++i) {
59754
- alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
59755
- if(i < il - 1) alignment_final += ',';
59756
- }
60370
+ let alignment_final = thisClass.convertUniProtInChains(alignment);
59757
60371
 
59758
60372
  let predefinedres = $("#" + me.pre + "predefinedres").val().trim().replace(/\n/g, '; ');
59759
60373
  if(predefinedres && alignment_final.split(',').length - 1 != predefinedres.split('; ').length) {
@@ -59770,66 +60384,133 @@ class Events {
59770
60384
  if(!me.cfg.notebook) dialog.dialog( "close" );
59771
60385
 
59772
60386
  let alignment = $("#" + me.pre + "chainalignids").val();
59773
- let idArray = alignment.split(',');
59774
- let alignment_final = '';
59775
- for(let i = 0, il = idArray.length; i < il; ++i) {
59776
- alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
59777
- if(i < il - 1) alignment_final += ',';
59778
- }
60387
+ let alignment_final = thisClass.convertUniProtInChains(alignment);
59779
60388
 
59780
60389
  me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues | resdef | align tmalign", false);
59781
60390
  window.open(hostUrl + '?chainalign=' + alignment_final + '&aligntool=tmalign&resnum=&resdef=&showalignseq=1&bu=0', '_blank');
59782
60391
  });
59783
60392
 
59784
- me.myEventCls.onIds("#" + me.pre + "reload_mutation_3d", "click", function(e) { me.icn3d;
60393
+ me.myEventCls.onIds("#" + me.pre + "reload_mutation_3d", "click", function(e) { let ic = me.icn3d;
59785
60394
  e.preventDefault();
59786
60395
  if(!me.cfg.notebook) dialog.dialog( "close" );
59787
60396
  let mutationids = $("#" + me.pre + "mutationids").val();
59788
- let idsource = $("#" + me.pre + "idsource").val();
59789
- let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));
59790
- me.htmlCls.clickMenuCls.setLogCmd("3d of mutation " + mutationids, false);
59791
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmdbid=' + mmdbid + '&command=scap 3d ' + mutationids + '; select displayed set', '_blank');
59792
- window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap 3d ' + mutationids + '; select displayed set', '_blank');
60397
+ //let idsource = $("#" + me.pre + "idsource").val();
60398
+ let idsource, pdbsource;
60399
+ if($("#" + me.pre + "type_mmdbid").is(":checked")) {
60400
+ idsource = 'mmdbid';
60401
+ }
60402
+ else {
60403
+ idsource = 'afid';
60404
+ }
60405
+ if($("#" + me.pre + "showin_currentpage").is(":checked")) {
60406
+ pdbsource = 'currentpage';
60407
+ }
60408
+ else {
60409
+ pdbsource = 'newpage';
60410
+ }
60411
+
60412
+ if(pdbsource == 'currentpage') {
60413
+ let snp = mutationids;
60414
+
60415
+ ic.scapCls.retrieveScap(snp);
60416
+ me.htmlCls.clickMenuCls.setLogCmd('scap 3d ' + snp, true);
60417
+ me.htmlCls.clickMenuCls.setLogCmd("select displayed set", true);
60418
+ }
60419
+ else {
60420
+ let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));
60421
+ me.htmlCls.clickMenuCls.setLogCmd("3d of mutation " + mutationids, false);
60422
+ window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap 3d ' + mutationids + '; select displayed set', '_blank');
60423
+ }
59793
60424
  });
59794
60425
 
59795
- me.myEventCls.onIds("#" + me.pre + "reload_mutation_pdb", "click", function(e) { me.icn3d;
60426
+ me.myEventCls.onIds("#" + me.pre + "reload_mutation_pdb", "click", function(e) { let ic = me.icn3d;
59796
60427
  e.preventDefault();
59797
60428
  if(!me.cfg.notebook) dialog.dialog( "close" );
59798
60429
  let mutationids = $("#" + me.pre + "mutationids").val();
59799
- let idsource = $("#" + me.pre + "idsource").val();
59800
- let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));
59801
- me.htmlCls.clickMenuCls.setLogCmd("pdb of mutation " + mutationids, false);
59802
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmdbid=' + mmdbid + '&command=scap pdb ' + mutationids + '; select displayed set', '_blank');
59803
- window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap pdb ' + mutationids + '; select displayed set', '_blank');
60430
+ //let idsource = $("#" + me.pre + "idsource").val();
60431
+ let idsource, pdbsource;
60432
+ if($("#" + me.pre + "type_mmdbid").is(":checked")) {
60433
+ idsource = 'mmdbid';
60434
+ }
60435
+ else {
60436
+ idsource = 'afid';
60437
+ }
60438
+ if($("#" + me.pre + "showin_currentpage").is(":checked")) {
60439
+ pdbsource = 'currentpage';
60440
+ }
60441
+ else {
60442
+ pdbsource = 'newpage';
60443
+ }
60444
+
60445
+ if(pdbsource == 'currentpage') {
60446
+ let snp = mutationids;
60447
+
60448
+ let bPdb = true;
60449
+ ic.scapCls.retrieveScap(snp, undefined, bPdb);
60450
+ me.htmlCls.clickMenuCls.setLogCmd('scap pdb ' + snp, true);
60451
+ }
60452
+ else {
60453
+ let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));
60454
+ me.htmlCls.clickMenuCls.setLogCmd("pdb of mutation " + mutationids, false);
60455
+ window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap pdb ' + mutationids + '; select displayed set', '_blank');
60456
+ }
59804
60457
  });
59805
60458
 
59806
60459
  me.myEventCls.onIds("#" + me.pre + "reload_mutation_inter", "click", function(e) { let ic = me.icn3d;
59807
60460
  e.preventDefault();
59808
60461
  if(!me.cfg.notebook) dialog.dialog( "close" );
59809
60462
  let mutationids = $("#" + me.pre + "mutationids").val();
59810
- let idsource = $("#" + me.pre + "idsource").val();
59811
-
59812
- let mutationArray = mutationids.split(',');
59813
- let residArray = [];
59814
- for(let i = 0, il = mutationArray.length; i < il; ++i) {
59815
- let pos = mutationArray[i].lastIndexOf('_');
59816
- let resid = mutationArray[i].substr(0, pos);
59817
- residArray.push(resid);
60463
+ //let idsource = $("#" + me.pre + "idsource").val();
60464
+ let idsource, pdbsource;
60465
+ if($("#" + me.pre + "type_mmdbid").is(":checked")) {
60466
+ idsource = 'mmdbid';
60467
+ }
60468
+ else {
60469
+ idsource = 'afid';
59818
60470
  }
60471
+ if($("#" + me.pre + "showin_currentpage").is(":checked")) {
60472
+ pdbsource = 'currentpage';
60473
+ }
60474
+ else {
60475
+ pdbsource = 'newpage';
60476
+ }
59819
60477
 
59820
- let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));
60478
+ if(pdbsource == 'currentpage') {
60479
+ let snp = mutationids;
59821
60480
 
59822
- // if no structures are loaded yet
59823
- if(!ic.structures) {
59824
- ic.structures = {};
59825
- ic.structures[mmdbid] = 1;
60481
+ let bInteraction = true;
60482
+ ic.scapCls.retrieveScap(snp, bInteraction);
60483
+ me.htmlCls.clickMenuCls.setLogCmd('scap interaction ' + snp, true);
60484
+
60485
+ let idArray = snp.split('_'); //stru_chain_resi_snp
60486
+ let select = '.' + idArray[1] + ':' + idArray[2];
60487
+ let name = 'snp_' + idArray[1] + '_' + idArray[2];
60488
+ me.htmlCls.clickMenuCls.setLogCmd("select " + select + " | name " + name, true);
60489
+ me.htmlCls.clickMenuCls.setLogCmd("line graph interaction pairs | selected non-selected | hbonds,salt bridge,interactions,halogen,pi-cation,pi-stacking | false | threshold 3.8 6 4 3.8 6 5.5", true);
60490
+ me.htmlCls.clickMenuCls.setLogCmd("adjust dialog dl_linegraph", true);
60491
+ me.htmlCls.clickMenuCls.setLogCmd("select displayed set", true);
59826
60492
  }
59827
- ic.resid2specCls.residueids2spec(residArray);
60493
+ else {
60494
+ let mutationArray = mutationids.split(',');
60495
+ let residArray = [];
60496
+ for(let i = 0, il = mutationArray.length; i < il; ++i) {
60497
+ let pos = mutationArray[i].lastIndexOf('_');
60498
+ let resid = mutationArray[i].substr(0, pos);
60499
+ residArray.push(resid);
60500
+ }
60501
+
60502
+ let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));
60503
+
60504
+ // if no structures are loaded yet
60505
+ if(!ic.structures) {
60506
+ ic.structures = {};
60507
+ ic.structures[mmdbid] = 1;
60508
+ }
60509
+ ic.resid2specCls.residueids2spec(residArray);
59828
60510
 
59829
- me.htmlCls.clickMenuCls.setLogCmd("interaction change of mutation " + mutationids, false);
59830
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmdbid=' + mmdbid + '&command=scap interaction ' + mutationids + '; select ' + selectSpec + ' | name test; line graph interaction pairs | selected non-selected | hbonds,salt bridge,interactions,halogen,pi-cation,pi-stacking | false | threshold 3.8 6 4 3.8 6 5.5; adjust dialog dl_linegraph; select displayed set', '_blank');
59831
- //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmdbid=' + mmdbid + '&command=scap interaction ' + mutationids, '_blank');
59832
- window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap interaction ' + mutationids, '_blank');
60511
+ me.htmlCls.clickMenuCls.setLogCmd("interaction change of mutation " + mutationids, false);
60512
+ window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap interaction ' + mutationids, '_blank');
60513
+ }
59833
60514
  });
59834
60515
 
59835
60516
  // },
@@ -61660,26 +62341,68 @@ class SetHtml {
61660
62341
  this.icn3dui = icn3dui;
61661
62342
  }
61662
62343
 
61663
- getLink(id, text) { let me = this.icn3dui; me.icn3d;
62344
+ getLink(id, text, bSimpleMenu, selType) { let me = this.icn3dui; me.icn3d;
62345
+ me.htmlCls.allMenus[me.pre + id] = text;
62346
+ if(selType) me.htmlCls.allMenusSel[me.pre + id] = selType;
62347
+ if(bSimpleMenu) me.htmlCls.simpleMenus[me.pre + id] = 1;
62348
+
61664
62349
  return "<li><span id='" + me.pre + id + "' class='icn3d-link'>" + text + "</span></li>";
61665
62350
  }
61666
62351
 
61667
- getLinkWrapper(id, text, wrapper) { let me = this.icn3dui; me.icn3d;
62352
+ // a group of menus
62353
+ getMenuText(id, text, classname, bSimpleMenu, selType) { let me = this.icn3dui; me.icn3d;
62354
+ me.htmlCls.allMenus[me.pre + id] = text;
62355
+ if(selType) me.htmlCls.allMenusSel[me.pre + id] = selType;
62356
+ if(bSimpleMenu) me.htmlCls.simpleMenus[me.pre + id] = 1;
62357
+
62358
+ let styleStr = (classname == 'icn3d-menupd') ? " style='padding-left:1.5em!important;'" : "";
62359
+
62360
+ // no ending "</li>"" since this is usually the start of a group of menus
62361
+ return "<li><span id='" + me.pre + id + "'" + styleStr + ">" + text + "</span>";
62362
+ }
62363
+
62364
+ getMenuUrl(id, url, text, bSimpleMenu, selType) { let me = this.icn3dui; me.icn3d;
62365
+ me.htmlCls.allMenus[me.pre + id] = text;
62366
+ if(selType) me.htmlCls.allMenusSel[me.pre + id] = selType;
62367
+ if(bSimpleMenu) me.htmlCls.simpleMenus[me.pre + id] = 1;
62368
+
62369
+ return "<li><a id='" + me.pre + id + "' href='" + url + "' target='_blank'>" + text + "</a></li>";
62370
+ }
62371
+
62372
+ getMenuSep() { let me = this.icn3dui; me.icn3d;
62373
+ return "<li class='icn3d-menusep'>-</li>";
62374
+ }
62375
+
62376
+ getLinkWrapper(id, text, wrapper, bSimpleMenu, selType) { let me = this.icn3dui; me.icn3d;
62377
+ me.htmlCls.allMenus[me.pre + id] = text;
62378
+ if(selType) me.htmlCls.allMenusSel[me.pre + id] = selType;
62379
+ if(bSimpleMenu) me.htmlCls.simpleMenus[me.pre + id] = 1;
62380
+
61668
62381
  return "<li id='" + me.pre + wrapper + "'><span id='" + me.pre + id + "' class='icn3d-link'>" + text + "</span></li>";
61669
62382
  }
61670
62383
 
61671
- getRadio(radioid, id, text, bChecked) { let me = this.icn3dui; me.icn3d;
62384
+ getRadio(radioid, id, text, bChecked, bSimpleMenu, selType) { let me = this.icn3dui; me.icn3d;
62385
+ me.htmlCls.allMenus[me.pre + id] = text;
62386
+ if(selType) me.htmlCls.allMenusSel[me.pre + id] = selType;
62387
+ if(bSimpleMenu) me.htmlCls.simpleMenus[me.pre + id] = 1;
62388
+
61672
62389
  let checkedStr =(bChecked) ? ' checked' : '';
61673
62390
 
61674
62391
  //https://stackoverflow.com/questions/17541614/use-images-instead-of-radio-buttons/17541916
61675
- return "<li><label for='" + me.pre + id + "' class='icn3d-rad'>" + me.htmlCls.inputRadioStr + "name='" + me.pre + radioid + "' " + "class='" + me.pre + radioid + "' " + "v='" + text + "' id='" + me.pre + id + "'" + checkedStr + "><span class='ui-icon ui-icon-blank'></span> <span class='icn3d-rad-text'>" + text + "</span></label></li>";
62392
+ //return "<li><label for='" + me.pre + id + "' class='icn3d-rad'>" + me.htmlCls.inputRadioStr + "name='" + me.pre + radioid + "' " + "class='" + me.pre + radioid + "' " + "v='" + text + "' id='" + me.pre + id + "'" + checkedStr + "><span class='ui-icon ui-icon-blank'></span> <span class='icn3d-rad-text'>" + text + "</span></label></li>";
62393
+ return "<li><label id='" + me.pre + id + "' class='icn3d-rad'>" + me.htmlCls.inputRadioStr + "name='" + me.pre + radioid + "' " + "class='" + me.pre + radioid + "' " + "v='" + text + "'" + checkedStr + "><span class='ui-icon ui-icon-blank'></span> <span class='icn3d-rad-text'>" + text + "</span></label></li>";
61676
62394
  }
61677
62395
 
61678
- getRadioColor(radioid, id, text, color, bChecked) { let me = this.icn3dui; me.icn3d;
62396
+ getRadioColor(radioid, id, text, color, bChecked, bSimpleMenu, selType) { let me = this.icn3dui; me.icn3d;
62397
+ me.htmlCls.allMenus[me.pre + id] = text;
62398
+ if(selType) me.htmlCls.allMenusSel[me.pre + id] = selType;
62399
+ if(bSimpleMenu) me.htmlCls.simpleMenus[me.pre + id] = 1;
62400
+
61679
62401
  let checkedStr =(bChecked) ? ' checked' : '';
61680
62402
 
61681
62403
  //https://stackoverflow.com/questions/17541614/use-images-instead-of-radio-buttons/17541916
61682
- return "<li><label for='" + me.pre + id + "' class='icn3d-rad'>" + me.htmlCls.inputRadioStr + "name='" + me.pre + radioid + "' id='" + me.pre + id + "'" + checkedStr + "><span class='ui-icon ui-icon-blank'></span> <span class='icn3d-color-rad-text' color='" + color + "'><span style='background-color:#" + color + "'>" + me.htmlCls.space3 + "</span> " + text + "</span></label></li>";
62404
+ //return "<li><label for='" + me.pre + id + "' class='icn3d-rad'>" + me.htmlCls.inputRadioStr + "name='" + me.pre + radioid + "' id='" + me.pre + id + "'" + checkedStr + "><span class='ui-icon ui-icon-blank'></span> <span class='icn3d-color-rad-text' color='" + color + "'><span style='background-color:#" + color + "'>" + me.htmlCls.space3 + "</span> " + text + "</span></label></li>";
62405
+ return "<li><label id='" + me.pre + id + "' class='icn3d-rad'>" + me.htmlCls.inputRadioStr + "name='" + me.pre + radioid + "'" + checkedStr + "><span class='ui-icon ui-icon-blank'></span> <span class='icn3d-color-rad-text' color='" + color + "'><span style='background-color:#" + color + "'>" + me.htmlCls.space3 + "</span> " + text + "</span></label></li>";
61683
62406
  }
61684
62407
 
61685
62408
  setAdvanced(index) { let me = this.icn3dui; me.icn3d;
@@ -62576,6 +63299,11 @@ class Html {
62576
63299
  this.opts = {};
62577
63300
  this.opts['background'] = 'black'; //transparent, black, grey, white
62578
63301
 
63302
+ this.allMenus = {};
63303
+ this.allMenusSel= {}; // Selectable menus
63304
+ this.simpleMenus = {};
63305
+ this.shownMenus = {};
63306
+
62579
63307
  this.WIDTH = 400; // total width of view area
62580
63308
  this.HEIGHT = 400; // total height of view area
62581
63309
  this.RESIDUE_WIDTH = 10; // sequences
@@ -65512,7 +66240,7 @@ class iCn3D {
65512
66240
  if(bWebGL){
65513
66241
  //https://discourse.threejs.org/t/three-js-r128-ext-frag-depth-and-angle-instanced-arrays-extensions-are-not-supported/26037
65514
66242
  //this.renderer = new THREE.WebGL1Renderer({
65515
- if ( bWebGL2 && bVR) {
66243
+ if ( bWebGL2 && bVR) {
65516
66244
  this.renderer = new THREE.WebGLRenderer({
65517
66245
  canvas: this.oriContainer.get(0), //this.container.get(0),
65518
66246
  antialias: true,
@@ -65879,6 +66607,7 @@ class iCn3D {
65879
66607
 
65880
66608
  this.annoCddSiteCls = new AnnoCddSite(this);
65881
66609
  this.annoContactCls = new AnnoContact(this);
66610
+ this.annoPTMCls = new AnnoPTM(this);
65882
66611
  this.annoCrossLinkCls = new AnnoCrossLink(this);
65883
66612
  this.annoDomainCls = new AnnoDomain(this);
65884
66613
  this.annoSnpClinVarCls = new AnnoSnpClinVar(this);
@@ -66126,7 +66855,7 @@ iCn3D.prototype.resetConfig = function () { let ic = this, me = ic.icn3dui;
66126
66855
  }
66127
66856
 
66128
66857
  if(me.cfg.blast_rep_id !== undefined) this.opts['color'] = 'conservation';
66129
- if(me.cfg.mmdbafid !== undefined) this.opts['color'] = 'structure';
66858
+ if(me.cfg.mmdbafid !== undefined && ic.structures) ic.opts['color'] = (Object.keys(ic.structures).length == 1) ? 'chain' : 'structure';
66130
66859
 
66131
66860
  if(me.cfg.options !== undefined) $.extend(this.opts, me.cfg.options);
66132
66861
  };
@@ -66143,7 +66872,7 @@ class iCn3DUI {
66143
66872
  //even when multiple iCn3D viewers are shown together.
66144
66873
  this.pre = this.cfg.divid + "_";
66145
66874
 
66146
- this.REVISION = '3.13.2';
66875
+ this.REVISION = '3.15.0';
66147
66876
 
66148
66877
  // In nodejs, iCn3D defines "window = {navigator: {}}"
66149
66878
  this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -66155,7 +66884,7 @@ class iCn3DUI {
66155
66884
  if(this.cfg.showmenu === undefined) this.cfg.showmenu = true;
66156
66885
  if(this.cfg.showtitle === undefined) this.cfg.showtitle = true;
66157
66886
  if(this.cfg.showcommand === undefined) this.cfg.showcommand = true;
66158
- if(this.cfg.simplemenu === undefined) this.cfg.simplemenu = false;
66887
+ //if(this.cfg.simplemenu === undefined) this.cfg.simplemenu = false;
66159
66888
  if(this.cfg.mobilemenu === undefined) this.cfg.mobilemenu = false;
66160
66889
  if(this.cfg.closepopup === undefined) this.cfg.closepopup = false;
66161
66890
  if(this.cfg.showanno === undefined) this.cfg.showanno = false;
@@ -66309,6 +67038,10 @@ iCn3DUI.prototype.show3DStructure = function(pdbStr) { let me = this;
66309
67038
  ic.molTitle = '';
66310
67039
  ic.loadCmd;
66311
67040
 
67041
+ // set menus
67042
+ me.htmlCls.clickMenuCls.getShownMenusFromCookie();
67043
+ me.htmlCls.clickMenuCls.applyShownMenus();
67044
+
66312
67045
  if(pdbStr) { // input pdbStr
66313
67046
  ic.init();
66314
67047