icn3d 3.29.9 → 3.29.11

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Files changed (4) hide show
  1. package/icn3d.js +284 -181
  2. package/icn3d.min.js +4 -4
  3. package/icn3d.module.js +284 -181
  4. package/package.json +1 -1
package/icn3d.module.js CHANGED
@@ -8279,6 +8279,8 @@ class ClickMenu {
8279
8279
  thisClass.setLogCmd('ig refnum on', true);
8280
8280
  // await ic.refnumCls.showIgRefNum();
8281
8281
  // thisClass.setLogCmd('set annotation ig', true);
8282
+ if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
8283
+
8282
8284
  let bSelection = true;
8283
8285
  await ic.annotationCls.setAnnoTabIg(bSelection);
8284
8286
 
@@ -8303,6 +8305,7 @@ class ClickMenu {
8303
8305
  thisClass.setLogCmd('ig template ' + template, true);
8304
8306
  let bSelection = true;
8305
8307
  // await ic.refnumCls.showIgRefNum(template);
8308
+ if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
8306
8309
  await ic.annotationCls.setAnnoTabIg(bSelection, template);
8307
8310
  });
8308
8311
 
@@ -10428,8 +10431,8 @@ class SetMenu {
10428
10431
  //}
10429
10432
 
10430
10433
  //!!!
10431
- //html += this.getRadio('mn4_clr', 'mn4_clrIgstrand', 'Ig Strand', undefined, undefined, 2);
10432
- //html += this.getRadio('mn4_clr', 'mn4_clrIgproto', 'Ig Protodomain', undefined, undefined, 2);
10434
+ // html += this.getRadio('mn4_clr', 'mn4_clrIgstrand', 'Ig Strand', undefined, undefined, 2);
10435
+ // html += this.getRadio('mn4_clr', 'mn4_clrIgproto', 'Ig Protodomain', undefined, undefined, 2);
10433
10436
  }
10434
10437
  else {
10435
10438
  //if(!me.cfg.hidelicense) html += this.getRadio('mn4_clr', 'mn1_delphi2', 'DelPhi<br><span style="padding-left:1.5em;">Potential ' + me.htmlCls.licenseStr + '</span>');
@@ -10560,7 +10563,7 @@ class SetMenu {
10560
10563
  html += this.getRadio('mn6_addlabel', 'mn6_addlabelResidues', 'per Residue', undefined, 1, 2);
10561
10564
  html += this.getRadio('mn6_addlabel', 'mn6_addlabelResnum', 'per Residue & Number', undefined, 1, 2);
10562
10565
  //!!!
10563
- //html += this.getRadio('mn6_addlabel', 'mn6_addlabelRefnum', 'per Reference Number', undefined, 1, 2);
10566
+ // html += this.getRadio('mn6_addlabel', 'mn6_addlabelRefnum', 'per Reference Number', undefined, 1, 2);
10564
10567
  html += this.getRadio('mn6_addlabel', 'mn6_addlabelChains', 'per Chain', undefined, undefined, 2);
10565
10568
  html += this.getRadio('mn6_addlabel', 'mn6_addlabelTermini', 'N- & C-Termini', undefined, 1, 2);
10566
10569
  }
@@ -10658,8 +10661,9 @@ class SetMenu {
10658
10661
  html += this.getLink('mn6_igrefYes', 'Show Ig for Selection', undefined, 2);
10659
10662
  html += this.getLink('mn6_igrefTpl', 'Ig w/ Specified Template', undefined, 2);
10660
10663
  html += this.getLink('mn6_igrefNo', 'Reset Ig Ref. Number', undefined, 2);
10661
- */
10664
+
10662
10665
  html += this.getMenuSep();
10666
+ */
10663
10667
 
10664
10668
  html += this.getLink('mn6_customref', 'Custom Ref. Number', undefined, 2);
10665
10669
  html += "</ul>";
@@ -12810,12 +12814,17 @@ class SetDialog {
12810
12814
 
12811
12815
  //html += me.htmlCls.setHtmlCls.getOptionHtml(['0', '10', '20', '30', '40', '50', '60', '70', '80', '90', '100'], 3);
12812
12816
  let group2tpl = {};
12813
- group2tpl['V'] = ['FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_V-n1', 'VNAR_1t6vN_shark_V', 'TCRa_6jxrm_human_V-n1', 'VISTA_6oilA_human_V', 'CD8a_1cd8A_human_V', 'PD1_4zqkB_human_V', 'ICOS_6x4gA_human_V', 'CD28_1yjdC_human_V', 'PDL1_4z18B_human_V-n1', 'CD2_1hnfA_human_V-n1', 'LAG3_7tzgD_human_V-n1'];
12814
- group2tpl['C1'] = ['FAB-LIGHT_5esv_C1-n2', 'GHR_1axiB_human_FN3-n1', 'VTCN1_Q7Z7D3_human_V-n2', 'B2Microglobulin_7phrL_human_C1', 'FAB-HEAVY_5esv_C1-n2', 'MHCIa_7phrH_human_C1', 'TCRa_6jxrm_human_C1-n2'];
12815
- group2tpl['C2'] = ['CD2_1hnfA_human_C2-n2', 'Siglec3_5j0bB_human_C2-n2', 'LAG3_7tzgD_human_C2-n2', 'Contactin1_3s97C_human_C2-n2'];
12816
- group2tpl['Iset'] = ['BTLA_2aw2A_human_Iset', 'Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Unk-n152', 'JAM1_1nbqA_human_VorIset-n2', 'CD19_6al5A_human_C2orV-n1'];
12817
- group2tpl['FN3'] = ['InsulinR_8guyE_human_FN3-n1', 'IL6Rb_1bquB_human_FN3-n3', 'Sidekick2_1wf5A_human_FN3-n7', 'InsulinR_8guyE_human_FN3-n2', 'Contactin1_2ee2A_human_FN3-n9', 'IL6Rb_1bquB_human_FN3-n2'];
12818
- group2tpl['Other'] = ['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'CoAtomerGamma1_1r4xA_human', 'TP34_2o6cA_bacteria', 'RBPJ_6py8C_human_Unk-n2', 'TP47_1o75A_bacteria', 'C3_2qkiD_human_n1', 'BArrestin1_4jqiA_rat_n1', 'RBPJ_6py8C_human_Unk-n1', 'CuZnSuperoxideDismutase_1hl5C_human', 'TEAD1_3kysC_human', 'ASF1A_2iijA_human', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'ORF7a_1xakA_virus', 'ECadherin_4zt1A_human_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'LaminAC_1ifrA_human', 'IsdA_2iteA_bacteria'];
12817
+ group2tpl['V'] = ['CD28_1yjdC_human_V', 'CD2_1hnfA_human_V-n1', 'CD8a_1cd8A_human_V', 'FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_V-n1', 'ICOS_6x4gA_human_V', 'LAG3_7tzgD_human_V-n1', 'PDL1_4z18B_human_V-n1', 'PD1_4zqkB_human_V', 'TCRa_6jxrm_human_V-n1', 'VISTA_6oilA_human_V', 'VNAR_1t6vN_shark_V'];
12818
+ group2tpl['C1'] = ['B2Microglobulin_7phrL_human_C1', 'FAB-LIGHT_5esv_C1-n2', 'FAB-HEAVY_5esv_C1-n2', 'GHR_1axiB_human_FN3-n1', 'MHCIa_7phrH_human_C1', 'TCRa_6jxrm_human_C1-n2', 'VTCN1_Q7Z7D3_human_V-n2'];
12819
+ group2tpl['C2'] = ['CD2_1hnfA_human_C2-n2', 'Contactin1_3s97C_human_C2-n2', 'LAG3_7tzgD_human_C2-n2', 'Siglec3_5j0bB_human_C2-n2'];
12820
+ group2tpl['I'] = ['BTLA_2aw2A_human_Iset', 'CD19_6al5A_human_C2orV-n1', 'JAM1_1nbqA_human_VorIset-n2', 'Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Unk-n152'];
12821
+ group2tpl['E'] = ['ASF1A_2iijA_human', 'CoAtomerGamma1_1r4xA_human', 'Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'IsdA_2iteA_bacteria', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'TP34_2o6cA_bacteria', 'TP47_1o75A_bacteria', 'TEAD1_3kysC_human'];
12822
+
12823
+ group2tpl['FN3'] = ['Contactin1_2ee2A_human_FN3-n9', 'IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3', 'InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2', 'Sidekick2_1wf5A_human_FN3-n7'];
12824
+
12825
+ group2tpl['FN3-like'] = ['BArrestin1_4jqiA_rat_n1', 'C3_2qkiD_human_n1', 'RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2'];
12826
+
12827
+ group2tpl['Other'] = ['CuZnSuperoxideDismutase_1hl5C_human', 'ECadherin_4zt1A_human_n2', 'LaminAC_1ifrA_human', 'ORF7a_1xakA_virus'];
12819
12828
 
12820
12829
  for(let group in group2tpl) {
12821
12830
  html += "<optgroup label='" + group + "'>";
@@ -12869,10 +12878,10 @@ class SetDialog {
12869
12878
  html += "<td></td>";
12870
12879
  html += "</tr><tr>";
12871
12880
  html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_ig'>Ig Domains" + me.htmlCls.space2 + "</span></td>";
12872
- */
12881
+
12873
12882
  html += "<td></td>";
12874
12883
  html += "</tr></table></div></div>";
12875
-
12884
+ */
12876
12885
  return html;
12877
12886
  }
12878
12887
  }
@@ -15595,6 +15604,14 @@ class Events {
15595
15604
  thisClass.setLogCmd('define igloop sets | chain ' + chainid, true);
15596
15605
  });
15597
15606
 
15607
+ $(document).on("click", ".icn3d-igdomainsets", function(e) { let ic = me.icn3d;
15608
+ e.stopImmediatePropagation();
15609
+ //e.preventDefault();
15610
+ let chainid = $(this).attr('chainid');
15611
+ ic.addTrackCls.defineIgstrand(chainid, 'igdomain');
15612
+ thisClass.setLogCmd('define igdomain sets | chain ' + chainid, true);
15613
+ });
15614
+
15598
15615
  me.myEventCls.onIds("#" + me.pre + "deletesets", "click", function(e) { let ic = me.icn3d;
15599
15616
  ic.definedSetsCls.deleteSelectedSets();
15600
15617
  thisClass.setLogCmd("delete selected sets", true);
@@ -33374,7 +33391,7 @@ class Instancing {
33374
33391
  }
33375
33392
 
33376
33393
  if(ic.mdlImpostor !== undefined) {
33377
- // after three.js version 128, the cylinder impostor seemed to have a problem in cloning!!!
33394
+ // after three.js version 128, the cylinder impostor seemed to have a problem in cloning
33378
33395
  symmetryMate = ic.mdlImpostor.clone();
33379
33396
  //symmetryMate.applyMatrix(mat);
33380
33397
  this.applyMat(symmetryMate, mat);
@@ -37654,7 +37671,8 @@ class AnnoCddSite {
37654
37671
 
37655
37672
  //var setname = chnid + "_" + domain + "_" + index + "_" + r; //chnid + "_" + type + "_" + index + "_" + r;
37656
37673
  let setname = chnid + "_" + domain;
37657
- if(type != 'domain') setname += "_" + index + "_" + r; // + acc2domain[acc];
37674
+ // if(type != 'domain') setname += "_" + index + "_" + r;
37675
+ if(type != 'domain') setname = chnid + "_" + index + "_" + r + "_" + domain;
37658
37676
 
37659
37677
  if(type == 'domain') pssmid2fromArray[pssmid] = fromArray;
37660
37678
  if(type == 'domain') pssmid2toArray[pssmid] = toArray;
@@ -37733,7 +37751,13 @@ class AnnoCddSite {
37733
37751
 
37734
37752
  if(me.cfg.blast_rep_id != chnid) { // regular
37735
37753
  for(let i = 0, il = fromArray.length; i < il; ++i) {
37736
- let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i] - ic.baseResi[chnid] - 1) / ic.maxAnnoLength) : Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
37754
+ let emptyWidth;
37755
+ if(titleArray) {
37756
+ emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i]) / ic.maxAnnoLength) : Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
37757
+ }
37758
+ else {
37759
+ emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i] - ic.baseResi[chnid] - 1) / ic.maxAnnoLength) : Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
37760
+ }
37737
37761
 
37738
37762
  html2 += '<div style="display:inline-block; width:' + emptyWidth + 'px;">&nbsp;</div>';
37739
37763
  html2 += '<div style="display:inline-block; color:white!important; font-weight:bold; background-color:#' + color + '; width:' + Math.round(ic.seqAnnWidth *(toArray[i] - fromArray[i] + 1) / ic.maxAnnoLength) + 'px;" class="icn3d-seqTitle ' + linkStr + '" ' + type + '="' +(index+1).toString() + '" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + title + '" index="' + index + '" setname="' + setname + '" id="' + chnid + '_domain_' + index + '_' + r + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">' + domain + ' </div>';
@@ -38987,7 +39011,7 @@ class AnnoIg {
38987
39011
  refnumLabel = ic.resid2refnum[residueid];
38988
39012
  let bHidelabel = false;
38989
39013
 
38990
- if(refnumLabel) {
39014
+ if(refnumLabel) {
38991
39015
  refnumStr_ori = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
38992
39016
  currStrand = refnumLabel.replace(new RegExp(refnumStr_ori,'g'), '');
38993
39017
  currStrand_ori = currStrand;
@@ -39019,8 +39043,9 @@ class AnnoIg {
39019
39043
 
39020
39044
  igElem = {};
39021
39045
  igElem.startPos = i;
39022
- igElem.domainid = domainid;
39023
39046
  }
39047
+
39048
+ if(domainid) igElem.domainid = domainid;
39024
39049
 
39025
39050
  if(bCustom) {
39026
39051
  if(!refnumStr) {
@@ -39107,11 +39132,11 @@ class AnnoIg {
39107
39132
  htmlTmp += '<span class="icn3d-residueNum"></span>';
39108
39133
  }
39109
39134
  else if(kabat_or_imgt == 1) {
39110
- htmlTmp += '<div class="icn3d-annoTitle" anno="0" title="Kabat Reference Numbers ' + refStruTitle + '">Kabat Ref. No.</div>';
39135
+ htmlTmp += '<div class="icn3d-annoTitle" anno="0" title="Kabat Reference Numbers">Kabat Ref. No.</div>';
39111
39136
  htmlTmp += '<span class="icn3d-residueNum"></span>';
39112
39137
  }
39113
39138
  else if(kabat_or_imgt == 2) {
39114
- htmlTmp += '<div class="icn3d-annoTitle" anno="0" title="IMGT Reference Numbers ' + refStruTitle + '">IMGT Ref. No.</div>';
39139
+ htmlTmp += '<div class="icn3d-annoTitle" anno="0" title="IMGT Reference Numbers">IMGT Ref. No.</div>';
39115
39140
  htmlTmp += '<span class="icn3d-residueNum"></span>';
39116
39141
  }
39117
39142
  else {
@@ -39135,9 +39160,10 @@ class AnnoIg {
39135
39160
  html += '</div>';
39136
39161
  html += '</div>';
39137
39162
 
39138
- let igArray = ic.chain2igArray[chnid];
39163
+ let igArray = ic.chain2igArray[chnid];
39139
39164
  if(igArray.length == 0) return {html: '', html2: '', html3: ''};
39140
39165
  let rangeArray = [], titleArray = [], fullTitleArray = [], domainArray = [];
39166
+
39141
39167
  for(let i = 0, il = igArray.length; i < il; ++i) {
39142
39168
  let domainid = igArray[i].domainid;
39143
39169
  let info = ic.domainid2info[domainid];
@@ -39163,10 +39189,10 @@ class AnnoIg {
39163
39189
  let colorStr =(atom.color === undefined || atom.color.getHexString() === 'FFFFFF') ? 'DDDDDD' : atom.color.getHexString();
39164
39190
  let color =(atom.color !== undefined) ? colorStr : "CCCCCC";
39165
39191
 
39166
- let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i] - ic.baseResi[chnid] - 1) / ic.maxAnnoLength) :
39192
+ let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i]) / ic.maxAnnoLength) :
39167
39193
  Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
39168
39194
  html2 += '<div style="display:inline-block; width:' + emptyWidth + 'px;">&nbsp;</div>';
39169
- html2 += '<div style="display:inline-block; color:white!important; font-weight:bold; background-color:#' + color + '; width:' + Math.round(ic.seqAnnWidth *(toArray[i] - fromArray[i] + 1) / ic.maxAnnoLength) + 'px;" class="icn3d-seqTitle ' + linkStr + '" ig="0" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + domainArray[i] + '" index="0" setname="' + chnid + '_igs" id="' + chnid + '_igs" anno="sequence" chain="' + chnid + '" title="' + domainArray[i] + '">' + domainArray[i] + ' </div>';
39195
+ html2 += '<div style="display:inline-block; color:white!important; font-weight:bold; background-color:#' + color + '; width:' + Math.round(ic.seqAnnWidth *(toArray[i] - fromArray[i] + 1) / ic.maxAnnoLength) + 'px;" class="icn3d-seqTitle ' + linkStr + '" ig="0" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + domainArray[i] + '" index="0" setname="' + chnid + '_igs" id="' + chnid + '_igs" anno="sequence" chain="' + chnid + '" title="' + domainArray[i] + '">' + domainArray[i] + ' </div>';
39170
39196
  }
39171
39197
 
39172
39198
  html2 += htmlCnt;
@@ -40539,12 +40565,16 @@ class Domain3d {
40539
40565
 
40540
40566
  // this.elements from the this.top of the this.stack
40541
40567
  //elts = &this.elements[this.stack[this.top - 1]];
40568
+
40542
40569
  for(i = this.stack[this.top - 1], il = this.elements.length; i < il; ++i) {
40543
40570
  elts.push(this.elements[i]);
40544
40571
  }
40545
40572
 
40546
40573
  // generate the partition based on the cut //
40547
- for (i = ne = ne0 = ne1 = 0, prt = prt0, t = -1; i < k; i++) {
40574
+ // for (i = ne = ne0 = ne1 = 0, prt = prt0, t = -1; i < k; i++) {
40575
+ let bAtZero = true;
40576
+ prt = prt0;
40577
+ for (i = ne = ne0 = ne1 = 0, t = -1; i < k; i++) {
40548
40578
  // write the this.elements into prt //
40549
40579
  for (j = t + 1; j <= cut[i]; j++)
40550
40580
  prt[ne++] = elts[j];
@@ -40552,15 +40582,20 @@ class Domain3d {
40552
40582
  t = cut[i];
40553
40583
 
40554
40584
  // switch the partition //
40555
- if (prt == prt0) {
40585
+ // if (prt == prt0) {
40586
+ if (bAtZero) {
40556
40587
  ne0 = ne;
40557
40588
  prt = prt1;
40558
40589
  ne = ne1;
40590
+
40591
+ bAtZero = false;
40559
40592
  }
40560
40593
  else {
40561
40594
  ne1 = ne;
40562
40595
  prt = prt0;
40563
40596
  ne = ne0;
40597
+
40598
+ bAtZero = true;
40564
40599
  }
40565
40600
  }
40566
40601
 
@@ -40568,7 +40603,8 @@ class Domain3d {
40568
40603
  for (j = t + 1; j < n; j++)
40569
40604
  prt[ne++] = elts[j];
40570
40605
 
40571
- if (prt == prt0)
40606
+ // if (prt == prt0)
40607
+ if (bAtZero)
40572
40608
  ne0 = ne;
40573
40609
  else
40574
40610
  ne1 = ne;
@@ -41237,6 +41273,8 @@ class Domain3d {
41237
41273
  let ss1 = parseInt(ssPair[0]);
41238
41274
  let ss2 = parseInt(ssPair[1]);
41239
41275
 
41276
+ if(ctable[pair] < this.min_contacts) ctable[pair] = 0;
41277
+
41240
41278
  // both are sheets
41241
41279
  // min number of contacts: this.min_contacts
41242
41280
  if(substruct[ss1 - 1].Sheet && substruct[ss2 - 1].Sheet && ctable[pair] >= this.min_contacts ) {
@@ -41247,7 +41285,7 @@ class Domain3d {
41247
41285
  sheetNeighbor[ss2][ss1] = 1;
41248
41286
  }
41249
41287
  }
41250
-
41288
+
41251
41289
  //https://www.geeksforgeeks.org/number-groups-formed-graph-friends/
41252
41290
  let existing_groups = 0;
41253
41291
  let sheet2sheetnum = {};
@@ -41270,12 +41308,13 @@ class Domain3d {
41270
41308
  // get sheet2sheetnum
41271
41309
  // each neighboring sheet will be represented by the sheet with the smallest sse
41272
41310
  for(let groupnum in this.groupnum2sheet) {
41273
- let ssArray = this.groupnum2sheet[groupnum].sort();
41311
+ let ssArray = this.groupnum2sheet[groupnum].sort(function(a, b){return a-b});
41274
41312
  for(let i = 0, il = ssArray.length; i < il; ++i) {
41275
41313
  sheet2sheetnum[ssArray[i]] = ssArray[0];
41276
41314
  }
41277
41315
  }
41278
41316
 
41317
+ let invalidSheethash = {};
41279
41318
  for (let i = 0; i < nsse; i++) {
41280
41319
  if(substruct[i].Sheet) {
41281
41320
  let sheetsItem = {};
@@ -41288,6 +41327,8 @@ class Domain3d {
41288
41327
  sheetsItem.sheet_num = 0;
41289
41328
  sheetsItem.adj_strand2 = 0;
41290
41329
  sheetsItem.sse = i + 1;
41330
+
41331
+ invalidSheethash[sheetsItem.sse] = 1;
41291
41332
  }
41292
41333
 
41293
41334
  sheets.push(sheetsItem);
@@ -41319,7 +41360,7 @@ class Domain3d {
41319
41360
  }
41320
41361
  }
41321
41362
 
41322
- let minStrand = 6;
41363
+ let minStrand = 6; // number of residues in a strand
41323
41364
 
41324
41365
  if (hasSheets) {
41325
41366
  //sheets: array of sheets, each of which has the key: sheet_num (number of strands), adj_strand1, adj_strand2
@@ -41343,7 +41384,8 @@ class Domain3d {
41343
41384
  if (cnt> 0) {
41344
41385
  for (let i = 0; i < sheets.length; i++) {
41345
41386
  let bsrec = sheets[i];
41346
- this.group_num[bsrec.sse - 1] = bsrec.sheet_num;
41387
+ // this.group_num[bsrec.sse - 1] = bsrec.sheet_num;
41388
+ if(bsrec.sheet_num != 0) this.group_num[bsrec.sse - 1] = bsrec.sheet_num;
41347
41389
  }
41348
41390
  }
41349
41391
  }
@@ -41399,11 +41441,25 @@ class Domain3d {
41399
41441
  }
41400
41442
  }
41401
41443
  }
41402
-
41444
+
41403
41445
  list_parts.sort(function(v1, v2) {
41404
41446
  return v1[0] - v2[0];
41405
41447
  });
41406
41448
 
41449
+ // remove sheets less than 3 residues
41450
+ let list_partsTmp = [];
41451
+ for(let i = 0, il = list_parts.length; i < il; ++i) {
41452
+ let list_parts_item = [];
41453
+ for(let j = 0, jl = list_parts[i].length; j < jl; ++j) {
41454
+ let sse = list_parts[i][j];
41455
+ if(!invalidSheethash.hasOwnProperty(sse)) {
41456
+ list_parts_item.push(sse);
41457
+ }
41458
+ }
41459
+ if(list_parts_item.length >= this.min_sse) list_partsTmp.push(list_parts[i]);
41460
+ }
41461
+ list_parts = list_partsTmp;
41462
+
41407
41463
  //for (lplet = list_parts.begin(); lplet != list_parts.end(); lpint++) {
41408
41464
  for (let index = 0, indexl = list_parts.length; index < indexl; ++index) {
41409
41465
  //vector<int> prts = *lpint;
@@ -42490,91 +42546,115 @@ class AddTrack {
42490
42546
  let selectedResidues = {};
42491
42547
  let bUnion = false, bUpdateHighlight = true;
42492
42548
 
42493
- let strandCnt = 0, loopCnt = 0;
42494
- let setName, currStrand, prevStrand, prevStrandReal = 'NT', currType, prevType;
42495
-
42496
42549
  // clear selection
42497
42550
  ic.hAtoms = {};
42498
42551
 
42499
- let bStart = false;
42500
-
42501
- for(let i = 0, il = ic.chainsSeq[chainid].length; i < il; ++i) {
42502
- let currResi = ic.chainsSeq[chainid][i].resi;
42503
- let resid = chainid + '_' + currResi;
42552
+ if(type == 'igdomain') {
42553
+ let igArray = ic.chain2igArray[chainid];
42504
42554
 
42505
- if(!ic.residues.hasOwnProperty(resid) ) continue;
42506
-
42507
- let refnumLabel, refnumStr, refnum;
42508
- refnumLabel = ic.resid2refnum[resid];
42509
- if(!refnumLabel) continue;
42555
+ if(igArray && igArray.length > 0) {
42556
+
42557
+ for(let i = 0, il = igArray.length; i < il; ++i) {
42558
+ let startPos = igArray[i].startPos;
42559
+ let endPos = igArray[i].endPos;
42560
+ let domainid = igArray[i].domainid;
42510
42561
 
42511
- refnumStr = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
42512
- currStrand = refnumLabel.replace(refnumStr, '');
42513
- refnum = parseInt(refnumStr);
42562
+ selectedResidues = {};
42563
+ for(let j = parseInt(startPos); j <= parseInt(endPos); ++j) {
42564
+ let currResi = ic.chainsSeq[chainid][j].resi;
42565
+ let resid = chainid + '_' + currResi;
42566
+ selectedResidues[resid] = 1;
42567
+ }
42514
42568
 
42515
- if(type == 'iganchor') {
42516
- if(refnum > 1000 && refnumStr.substr(refnumStr.length - 2, 2) == '50') {
42517
- selectedResidues[resid] = 1;
42518
- }
42519
- }
42520
- else {
42521
- if(ic.residIgLoop.hasOwnProperty(resid)) {
42522
- currType = 'igloop';
42569
+ let setName = domainid;
42570
+ ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
42523
42571
  }
42572
+ }
42573
+ }
42574
+ else {
42575
+ let strandCnt = 0, loopCnt = 0;
42576
+ let setName, currStrand, prevStrand, prevStrandReal = 'NT', currType, prevType;
42577
+
42578
+ let bStart = false;
42579
+
42580
+ for(let i = 0, il = ic.chainsSeq[chainid].length; i < il; ++i) {
42581
+ let currResi = ic.chainsSeq[chainid][i].resi;
42582
+ let resid = chainid + '_' + currResi;
42583
+
42584
+ if(!ic.residues.hasOwnProperty(resid) ) continue;
42585
+
42586
+ let refnumLabel, refnumStr, refnum;
42587
+ refnumLabel = ic.resid2refnum[resid];
42588
+ if(!refnumLabel) continue;
42589
+
42590
+ refnumStr = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
42591
+ currStrand = refnumLabel.replace(refnumStr, '');
42592
+ refnum = parseInt(refnumStr);
42593
+
42594
+ if(type == 'iganchor') {
42595
+ if(refnum > 1000 && refnumStr.substr(refnumStr.length - 2, 2) == '50') {
42596
+ selectedResidues[resid] = 1;
42597
+ }
42598
+ }
42524
42599
  else {
42525
- currType = 'igstrand';
42526
- }
42600
+ if(ic.residIgLoop.hasOwnProperty(resid)) {
42601
+ currType = 'igloop';
42602
+ }
42603
+ else {
42604
+ currType = 'igstrand';
42605
+ }
42527
42606
 
42528
- if(bStart && currType != prevType && Object.keys(selectedResidues).length > 0) {
42529
- if(prevType == 'igstrand') {
42530
- ++strandCnt;
42531
- setName = 'Strand-' + prevStrand + '-' + chainid + '-' + strandCnt.toString().padStart(3, '0');
42532
- setName = setName.replace(/'/g, '`');
42533
- if(type == 'igstrand') {
42534
- ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
42535
- if(!bUnion) bUnion = true;
42607
+ if(bStart && currType != prevType && Object.keys(selectedResidues).length > 0) {
42608
+ if(prevType == 'igstrand') {
42609
+ ++strandCnt;
42610
+ setName = 'Strand-' + prevStrand + '-' + chainid + '-' + strandCnt.toString().padStart(3, '0');
42611
+ setName = setName.replace(/'/g, '`');
42612
+ if(type == 'igstrand') {
42613
+ ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
42614
+ if(!bUnion) bUnion = true;
42615
+ }
42616
+ prevStrandReal = prevStrand;
42536
42617
  }
42537
- prevStrandReal = prevStrand;
42538
- }
42539
- else if(prevType == 'igloop') {
42540
- ++loopCnt;
42541
- setName = 'Loop-' + prevStrandReal + '_' + currStrand + '-' + chainid + '-' + loopCnt.toString().padStart(3, '0');
42542
- setName = setName.replace(/'/g, '`');
42543
- if(type == 'igloop') {
42544
- ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
42545
- if(!bUnion) bUnion = true;
42618
+ else if(prevType == 'igloop') {
42619
+ ++loopCnt;
42620
+ setName = 'Loop-' + prevStrandReal + '_' + currStrand + '-' + chainid + '-' + loopCnt.toString().padStart(3, '0');
42621
+ setName = setName.replace(/'/g, '`');
42622
+ if(type == 'igloop') {
42623
+ ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
42624
+ if(!bUnion) bUnion = true;
42625
+ }
42546
42626
  }
42547
- }
42548
42627
 
42549
- selectedResidues = {};
42550
- }
42628
+ selectedResidues = {};
42629
+ }
42551
42630
 
42552
- selectedResidues[resid] = 1;
42631
+ selectedResidues[resid] = 1;
42553
42632
 
42554
- prevStrand = currStrand;
42555
- prevType = currType;
42633
+ prevStrand = currStrand;
42634
+ prevType = currType;
42556
42635
 
42557
- bStart = true;
42558
- }
42559
- } // for loop
42636
+ bStart = true;
42637
+ }
42638
+ } // for loop
42560
42639
 
42561
- if(type == 'iganchor') {
42562
- setName = 'Anchor-' + chainid;
42563
- ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
42564
- }
42565
- else {
42566
- if(prevType == 'igstrand') {
42567
- ++strandCnt;
42568
- setName = 'Strand-' + prevStrand + '-' + chainid + '-' + strandCnt.toString().padStart(3, '0');
42569
- setName = setName.replace(/'/g, '`');
42570
- if(type == 'igstrand') ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
42640
+ if(type == 'iganchor') {
42641
+ setName = 'Anchor-' + chainid;
42642
+ ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
42571
42643
  }
42572
- else if(prevType == 'igloop') {
42573
- ++loopCnt;
42574
- currStrand = 'CT';
42575
- setName = 'Loop-' + prevStrandReal + '_' + currStrand + '-' + chainid + '-' + loopCnt.toString().padStart(3, '0');
42576
- setName = setName.replace(/'/g, '`');
42577
- if(type == 'igloop') ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
42644
+ else {
42645
+ if(prevType == 'igstrand') {
42646
+ ++strandCnt;
42647
+ setName = 'Strand-' + prevStrand + '-' + chainid + '-' + strandCnt.toString().padStart(3, '0');
42648
+ setName = setName.replace(/'/g, '`');
42649
+ if(type == 'igstrand') ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
42650
+ }
42651
+ else if(prevType == 'igloop') {
42652
+ ++loopCnt;
42653
+ currStrand = 'CT';
42654
+ setName = 'Loop-' + prevStrandReal + '_' + currStrand + '-' + chainid + '-' + loopCnt.toString().padStart(3, '0');
42655
+ setName = setName.replace(/'/g, '`');
42656
+ if(type == 'igloop') ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
42657
+ }
42578
42658
  }
42579
42659
  }
42580
42660
  }
@@ -44433,10 +44513,12 @@ class ShowAnno {
44433
44513
  + 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;"
44434
44514
  + 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);
44435
44515
 
44436
- if(ic.bShowRefnum && ic.chainid2refpdbname.hasOwnProperty(chnid) && ic.chainid2refpdbname[chnid].length > 0) {
44437
- chainHtml += "&nbsp;&nbsp;&nbsp;" + this.addButton(chnid, "icn3d-iganchorsets", "Ig Anchor Set", "Define the set for all Ig anchors in this chain and add them to the menu of \"Defined Sets\"", 80, buttonStyle) + "&nbsp;" + this.addButton(chnid, "icn3d-igstrandsets", "Ig Strand Sets", "Define sets for each Ig strand in this chain and add them to the menu of \"Defined Sets\"", 80, buttonStyle) + "&nbsp;"
44438
- + this.addButton(chnid, "icn3d-igloopsets", "Ig Loop Sets", "Define sets for each Ig loop in this chain and add them to the menu of \"Defined Sets\"", 80, buttonStyle);
44439
- }
44516
+ // if(ic.bShowRefnum && ic.chainid2refpdbname.hasOwnProperty(chnid) && ic.chainid2refpdbname[chnid].length > 0) {
44517
+ chainHtml += "&nbsp;&nbsp;&nbsp;" + this.addButton(chnid, "icn3d-iganchorsets", "Ig Anchor Set", "Define the set for all Ig anchors in this chain and add them to the menu of \"Defined Sets\"", 80, buttonStyle) + "&nbsp;"
44518
+ + this.addButton(chnid, "icn3d-igstrandsets", "Ig Strand Sets", "Define sets for each Ig strand in this chain and add them to the menu of \"Defined Sets\"", 80, buttonStyle) + "&nbsp;"
44519
+ + this.addButton(chnid, "icn3d-igloopsets", "Ig Loop Sets", "Define sets for each Ig loop in this chain and add them to the menu of \"Defined Sets\"", 80, buttonStyle) + "&nbsp;"
44520
+ + this.addButton(chnid, "icn3d-igdomainsets", "Ig Domain Sets", "Define sets for each Ig domain in this chain and add them to the menu of \"Defined Sets\"", 80, buttonStyle);
44521
+ // }
44440
44522
  $("#" + ic.pre + "dl_annotations").append(chainHtml);
44441
44523
  //let itemArray = ['giseq', 'cdd', 'clinvar', 'snp', 'domain', 'site', 'ptm', 'interaction', 'custom', 'ssbond', 'crosslink', 'transmem'];
44442
44524
  let itemArray = ['giseq', 'cdd', 'clinvar', 'snp', 'site', 'ptm', 'ssbond', 'crosslink', 'transmem', 'domain', 'custom', 'interaction', 'ig'];
@@ -61079,6 +61161,7 @@ class ApplyCommand {
61079
61161
  await ic.annotationCls.setAnnoTabIg();
61080
61162
  }
61081
61163
  else if(command == 'ig refnum on') {
61164
+ if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
61082
61165
  await ic.annotationCls.setAnnoTabIg(true);
61083
61166
  }
61084
61167
  else if(command == 'highlight level up') {
@@ -63568,6 +63651,7 @@ class LoadScript {
63568
63651
  else if(command.indexOf('ig template') == 0 ) {
63569
63652
  let template = command.substr(command.lastIndexOf(' ') + 1);
63570
63653
  // await ic.refnumCls.showIgRefNum(template);
63654
+ if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
63571
63655
  await ic.annotationCls.setAnnoTabIg(true, template);
63572
63656
  }
63573
63657
  else if(command.indexOf('set annotation 3ddomain') == 0) { // the command may have "|||{"factor"...
@@ -63771,6 +63855,7 @@ class LoadScript {
63771
63855
  }
63772
63856
  else if(lastCommand.indexOf('ig refnum on') == 0) {
63773
63857
  // await ic.refnumCls.showIgRefNum();
63858
+ if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
63774
63859
  await ic.annotationCls.setAnnoTabIg(true);
63775
63860
  }
63776
63861
  else if(lastCommand.indexOf('set annotation 3ddomain') == 0) {
@@ -63897,7 +63982,7 @@ class LoadScript {
63897
63982
  let idNew = '';
63898
63983
  for(let i = 0, il = idArray.length; i < il; ++i) {
63899
63984
  if(!(ic.structures && ic.structures.hasOwnProperty(idArray[i]))) {
63900
- if(!idNew) idNew += ',';
63985
+ if(idNew) idNew += ',';
63901
63986
  idNew += idArray[i];
63902
63987
  }
63903
63988
  }
@@ -66818,7 +66903,9 @@ class Dssp {
66818
66903
  ic.refpdbHash['1LaminAC_1ifrA_human'] = ['LaminAC_1ifrA_human', 'CD3d_6jxrd_human_Iset'];
66819
66904
  ic.refpdbHash['1CD3g_6jxrg_human_Iset'] = ['CD3g_6jxrg_human_Iset', 'TCRa_6jxrm_human_C1-n2', 'IsdA_2iteA_bacteria'];
66820
66905
  ic.refpdbHash['1CD28_1yjdC_human_V'] = ['CD28_1yjdC_human_V', 'MPT63_1lmiA_bacteria', 'CD3e_6jxrf_human_Iset'];
66821
- ic.refpdbHash['1CD19_6al5A_human_C2orV-n1'] = ['CD19_6al5A_human_C2orV-n1'];
66906
+ ic.refpdbHash['1CD19_6al5A_human_C2orV-n1'] = ['CD19_6al5A_human_C2orV-n1'];
66907
+
66908
+ ic.refpdbHash['all_templates'] = ['ASF1A_2iijA_human', 'B2Microglobulin_7phrL_human_C1', 'BArrestin1_4jqiA_rat_n1', 'BTLA_2aw2A_human_Iset', 'C3_2qkiD_human_n1', 'CD19_6al5A_human_C2orV-n1', 'CD28_1yjdC_human_V', 'CD2_1hnfA_human_C2-n2', 'CD2_1hnfA_human_V-n1', 'CD3d_6jxrd_human_Iset', 'CD3e_6jxrf_human_Iset', 'CD3g_6jxrg_human_Iset', 'CD8a_1cd8A_human_V', 'CoAtomerGamma1_1r4xA_human', 'Contactin1_2ee2A_human_FN3-n9', 'Contactin1_3s97C_human_C2-n2', 'CuZnSuperoxideDismutase_1hl5C_human', 'ECadherin_4zt1A_human_n2', 'Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'FAB-HEAVY_5esv_C1-n2', 'FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_C1-n2', 'FAB-LIGHT_5esv_V-n1', 'GHR_1axiB_human_FN3-n1', 'ICOS_6x4gA_human_V', 'IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3', 'InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2', 'IsdA_2iteA_bacteria', 'JAM1_1nbqA_human_VorIset-n2', 'LAG3_7tzgD_human_C2-n2', 'LAG3_7tzgD_human_V-n1', 'LaminAC_1ifrA_human', 'MHCIa_7phrH_human_C1', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'ORF7a_1xakA_virus', 'PD1_4zqkB_human_V', 'PDL1_4z18B_human_V-n1', 'Palladin_2dm3A_human_Iset-n1', 'RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2', 'Sidekick2_1wf5A_human_FN3-n7', 'Siglec3_5j0bB_human_C2-n2', 'TCRa_6jxrm_human_C1-n2', 'TCRa_6jxrm_human_V-n1', 'TEAD1_3kysC_human', 'TP34_2o6cA_bacteria', 'TP47_1o75A_bacteria', 'Titin_4uowM_human_Unk-n152', 'VISTA_6oilA_human_V', 'VNAR_1t6vN_shark_V', 'VTCN1_Q7Z7D3_human_V-n2'];
66822
66909
 
66823
66910
  // use known ref structure
66824
66911
  ic.refpdbHash['5ESV_C'] = ['FAB-HEAVY_5esv_V-n1', 'FAB-HEAVY_5esv_C1-n2'];
@@ -66875,9 +66962,9 @@ class Dssp {
66875
66962
 
66876
66963
  ic.ref2igtype['ASF1A_2iijA_human'] = 'IgE';
66877
66964
  ic.ref2igtype['B2Microglobulin_7phrL_human_C1'] = 'IgC1';
66878
- ic.ref2igtype['BArrestin1_4jqiA_rat_n1'] = 'IgFn3-like';
66965
+ ic.ref2igtype['BArrestin1_4jqiA_rat_n1'] = 'IgFN3-like';
66879
66966
  ic.ref2igtype['BTLA_2aw2A_human_Iset'] = 'IgI';
66880
- ic.ref2igtype['C3_2qkiD_human_n1'] = 'IgFn3-like';
66967
+ ic.ref2igtype['C3_2qkiD_human_n1'] = 'IgFN3-like';
66881
66968
  ic.ref2igtype['CD19_6al5A_human_C2orV-n1'] = 'other Ig'; //'CD19';
66882
66969
  ic.ref2igtype['CD28_1yjdC_human_V'] = 'IgV';
66883
66970
  ic.ref2igtype['CD2_1hnfA_human_C2-n2'] = 'IgC2';
@@ -66887,7 +66974,7 @@ class Dssp {
66887
66974
  ic.ref2igtype['CD3g_6jxrg_human_Iset'] = 'IgI';
66888
66975
  ic.ref2igtype['CD8a_1cd8A_human_V'] = 'IgV';
66889
66976
  ic.ref2igtype['CoAtomerGamma1_1r4xA_human'] = 'IgE';
66890
- ic.ref2igtype['Contactin1_2ee2A_human_FN3-n9'] = 'IgFn3';
66977
+ ic.ref2igtype['Contactin1_2ee2A_human_FN3-n9'] = 'IgFN3';
66891
66978
  ic.ref2igtype['Contactin1_3s97C_human_C2-n2'] = 'IgC2';
66892
66979
  ic.ref2igtype['CuZnSuperoxideDismutase_1hl5C_human'] = 'other Ig'; //'SOD';
66893
66980
  ic.ref2igtype['ECadherin_4zt1A_human_n2'] = 'other Ig'; //'Cadherin';
@@ -66896,12 +66983,12 @@ class Dssp {
66896
66983
  ic.ref2igtype['FAB-HEAVY_5esv_V-n1'] = 'IgV';
66897
66984
  ic.ref2igtype['FAB-LIGHT_5esv_C1-n2'] = 'IgC1';
66898
66985
  ic.ref2igtype['FAB-LIGHT_5esv_V-n1'] = 'IgV';
66899
- ic.ref2igtype['GHR_1axiB_human_FN3-n1'] = 'IgFn3';
66986
+ ic.ref2igtype['GHR_1axiB_human_FN3-n1'] = 'IgFN3';
66900
66987
  ic.ref2igtype['ICOS_6x4gA_human_V'] = 'IgV';
66901
- ic.ref2igtype['IL6Rb_1bquB_human_FN3-n2'] = 'IgFn3';
66902
- ic.ref2igtype['IL6Rb_1bquB_human_FN3-n3'] = 'IgFn3';
66903
- ic.ref2igtype['InsulinR_8guyE_human_FN3-n1'] = 'IgFn3';
66904
- ic.ref2igtype['InsulinR_8guyE_human_FN3-n2'] = 'IgFn3';
66988
+ ic.ref2igtype['IL6Rb_1bquB_human_FN3-n2'] = 'IgFN3';
66989
+ ic.ref2igtype['IL6Rb_1bquB_human_FN3-n3'] = 'IgFN3';
66990
+ ic.ref2igtype['InsulinR_8guyE_human_FN3-n1'] = 'IgFN3';
66991
+ ic.ref2igtype['InsulinR_8guyE_human_FN3-n2'] = 'IgFN3';
66905
66992
  ic.ref2igtype['IsdA_2iteA_bacteria'] = 'IgE';
66906
66993
  ic.ref2igtype['JAM1_1nbqA_human_VorIset-n2'] = 'IgI';
66907
66994
  ic.ref2igtype['LAG3_7tzgD_human_C2-n2'] = 'IgC2';
@@ -66915,9 +67002,9 @@ class Dssp {
66915
67002
  ic.ref2igtype['PD1_4zqkB_human_V'] = 'IgV';
66916
67003
  ic.ref2igtype['PDL1_4z18B_human_V-n1'] = 'IgV';
66917
67004
  ic.ref2igtype['Palladin_2dm3A_human_Iset-n1'] = 'IgI';
66918
- ic.ref2igtype['RBPJ_6py8C_human_Unk-n1'] = 'IgFn3-like';
66919
- ic.ref2igtype['RBPJ_6py8C_human_Unk-n2'] = 'IgFn3-like';
66920
- ic.ref2igtype['Sidekick2_1wf5A_human_FN3-n7'] = 'IgFn3';
67005
+ ic.ref2igtype['RBPJ_6py8C_human_Unk-n1'] = 'IgFN3-like';
67006
+ ic.ref2igtype['RBPJ_6py8C_human_Unk-n2'] = 'IgFN3-like';
67007
+ ic.ref2igtype['Sidekick2_1wf5A_human_FN3-n7'] = 'IgFN3';
66921
67008
  ic.ref2igtype['Siglec3_5j0bB_human_C2-n2'] = 'IgC2';
66922
67009
  ic.ref2igtype['TCRa_6jxrm_human_C1-n2'] = 'IgC1';
66923
67010
  ic.ref2igtype['TCRa_6jxrm_human_V-n1'] = 'IgV';
@@ -66982,7 +67069,7 @@ class Dssp {
66982
67069
  let thisClass = this;
66983
67070
 
66984
67071
  let struArray = Object.keys(ic.structures);
66985
-
67072
+
66986
67073
  let ajaxArray = [];
66987
67074
  let domainidpairArray = [];
66988
67075
 
@@ -67001,7 +67088,7 @@ class Dssp {
67001
67088
  for(let j = 0, jl = chainidArray.length; j < jl; ++j) {
67002
67089
  let chainid = chainidArray[j];
67003
67090
 
67004
- // for selected atoms only
67091
+ // for selected atoms only, assign ic.resid2domainid[resid]
67005
67092
  let domainAtomsArray = this.getDomainAtomsArray(chainid, bRerun);
67006
67093
 
67007
67094
  if(!ic.domainid2refpdbname) ic.domainid2refpdbname = {};
@@ -67018,8 +67105,8 @@ class Dssp {
67018
67105
  let atomFirst = ic.firstAtomObjCls.getFirstAtomObj(domainAtomsArray[k]);
67019
67106
  let atomLast = ic.firstAtomObjCls.getLastAtomObj(domainAtomsArray[k]);
67020
67107
  let resiSum = atomFirst.resi + ':' + atomLast.resi + ':' + Object.keys(domainAtomsArray[k]).length;
67021
- //let domainid = chainid + '-' + k + '_' + Object.keys(domainAtomsArray[k]).length;
67022
- let domainid = chainid + ',' + k + '_' + resiSum;
67108
+ //let domainid = chainid + '-' + k + '_' + Object.keys(domainAtomsArray[k]).length;
67109
+ let domainid = chainid + ',' + k + '_' + resiSum;
67023
67110
  ic.domainid2pdb[domainid] = pdb_target;
67024
67111
 
67025
67112
  if(!template) {
@@ -67037,7 +67124,7 @@ class Dssp {
67037
67124
  // let alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
67038
67125
 
67039
67126
  ajaxArray.push(alignAjax);
67040
-
67127
+
67041
67128
  domainidpairArray.push(domainid + "|" + ic.refpdbArray[index]);
67042
67129
  }
67043
67130
  }
@@ -67057,14 +67144,14 @@ class Dssp {
67057
67144
  // dataArray2 = await allPromise;
67058
67145
 
67059
67146
  dataArray2 = await this.promiseWithFixedJobs(ajaxArray);
67060
-
67147
+
67061
67148
  let bRound1 = true;
67062
- await thisClass.parseAlignData(dataArray2, domainidpairArray, bRound1);
67149
+ bNoMoreIg = await thisClass.parseAlignData(dataArray2, domainidpairArray, bRound1);
67063
67150
 
67064
67151
  /// if(ic.deferredRefnum !== undefined) ic.deferredRefnum.resolve();
67065
67152
  }
67066
67153
  else {
67067
- if(!me.bNode) console.log("Start alignment with the reference culsters " + JSON.stringify(ic.domainid2refpdbname));
67154
+ if(!me.bNode) console.log("Start alignment with the reference culsters " + JSON.stringify(ic.domainid2refpdbname));
67068
67155
 
67069
67156
  // start round2
67070
67157
  let ajaxArray = [];
@@ -67079,36 +67166,36 @@ class Dssp {
67079
67166
  //let allPromise2 = Promise.allSettled(pdbAjaxArray);
67080
67167
  //ic.pdbDataArray = await allPromise2;
67081
67168
 
67082
- ic.pdbDataArray = await this.promiseWithFixedJobs(pdbAjaxArray);
67169
+ let pdbDataArray = await this.promiseWithFixedJobs(pdbAjaxArray);
67083
67170
 
67084
67171
  for(let domainid in ic.domainid2refpdbname) {
67085
67172
  ic.domainid2refpdbname[domainid];
67086
67173
  domainid.substr(0, domainid.indexOf(','));
67087
67174
 
67088
67175
  let pdb_target = ic.domainid2pdb[domainid];
67089
- for(let index = 0, indexl = ic.pdbDataArray.length; index < indexl; ++index) {
67176
+ for(let index = 0, indexl = pdbDataArray.length; index < indexl; ++index) {
67090
67177
  let struct2 = ic.defaultPdbId + index;
67091
- let pdb_query = ic.pdbDataArray[index].value; //[0];
67178
+ let pdb_query = pdbDataArray[index].value; //[0];
67092
67179
 
67093
67180
  let header = 'HEADER ' + struct2 + '\n';
67094
67181
  pdb_query = header + pdb_query;
67095
-
67182
+
67096
67183
  let dataObj = {'pdb_query': pdb_query, 'pdb_target': pdb_target, "queryid": template};
67097
67184
  let alignAjax = me.getAjaxPostPromise(urltmalign, dataObj);
67098
67185
  ajaxArray.push(alignAjax);
67099
-
67186
+
67100
67187
  //domainidpairArray3.push(domainid + "," + refpdbname);
67101
67188
  domainidpairArray3.push(domainid + "|" + template);
67102
67189
  }
67103
67190
  }
67104
-
67191
+
67105
67192
  let dataArray3 = [];
67106
67193
  //let allPromise = Promise.allSettled(ajaxArray);
67107
67194
  //dataArray3 = await allPromise;
67108
67195
 
67109
67196
  dataArray3 = await this.promiseWithFixedJobs(ajaxArray);
67110
-
67111
- await thisClass.parseAlignData(dataArray3, domainidpairArray3);
67197
+
67198
+ bNoMoreIg = await thisClass.parseAlignData(dataArray3, domainidpairArray3);
67112
67199
  }
67113
67200
 
67114
67201
  return bNoMoreIg;
@@ -67124,8 +67211,8 @@ class Dssp {
67124
67211
  }
67125
67212
  //console.log("Error in aligning with TM-align...");
67126
67213
  return;
67127
- }
67128
- */
67214
+ }
67215
+ */
67129
67216
  }
67130
67217
 
67131
67218
  getDomainAtomsArray(chainid, bRerunDomain) { let ic = this.icn3d, me = ic.icn3dui;
@@ -67168,21 +67255,22 @@ class Dssp {
67168
67255
  //let result = ic.domain3dCls.c2b_NewSplitChain(ic.chains[chainid]);
67169
67256
  // assign ref numbers to selected residues
67170
67257
  let result = ic.domain3dCls.c2b_NewSplitChain(currAtoms, undefined);
67171
- let subdomains = result.subdomains;
67258
+ let subdomains = result.subdomains;
67172
67259
  let pos2resi = result.pos2resi;
67173
67260
 
67174
67261
  if(subdomains.length <= 1) {
67175
67262
  let residueArray = ic.resid2specCls.atoms2residues(Object.keys(currAtoms));
67176
67263
  if(residueArray.length < minResidues) return domainAtomsArray;
67177
-
67264
+ /*
67178
67265
  let atomFirst = ic.firstAtomObjCls.getFirstAtomObj(currAtoms);
67179
67266
  let atomLast = ic.firstAtomObjCls.getLastAtomObj(currAtoms);
67180
67267
  let resiSum = atomFirst.resi + ':' + atomLast.resi + ':' + Object.keys(currAtoms).length;
67181
-
67268
+ */
67182
67269
  for(let n = 0, nl = residueArray.length; n < nl; ++n) {
67183
67270
  let resid = residueArray[n];
67184
- ic.resid2domainid[resid] = chainid + ',0' + '_' + resiSum;
67185
-
67271
+ /*
67272
+ ic.resid2domainid[resid] = chainid + ',0' + '_' + resiSum;
67273
+ */
67186
67274
  // clear previous refnum assignment if any
67187
67275
  // if(!bRerunDomain && ic.resid2refnum && ic.resid2refnum[resid]) {
67188
67276
  // if(ic.resid2refnum && ic.resid2refnum[resid]) {
@@ -67193,7 +67281,7 @@ class Dssp {
67193
67281
 
67194
67282
  domainAtomsArray.push(currAtoms);
67195
67283
  }
67196
- else {
67284
+ else {
67197
67285
  for(let k = 0, kl = subdomains.length; k < kl; ++k) {
67198
67286
  let domainAtoms = {};
67199
67287
  let segArray = subdomains[k];
@@ -67220,7 +67308,7 @@ class Dssp {
67220
67308
  if(resCnt < minResidues) continue;
67221
67309
 
67222
67310
  domainAtomsArray.push(domainAtoms);
67223
-
67311
+ /*
67224
67312
  let atomFirst = ic.firstAtomObjCls.getFirstAtomObj(domainAtoms);
67225
67313
  let atomLast = ic.firstAtomObjCls.getLastAtomObj(domainAtoms);
67226
67314
  let resiSum = atomFirst.resi + ':' + atomLast.resi + ':' + Object.keys(domainAtoms).length;
@@ -67231,15 +67319,16 @@ class Dssp {
67231
67319
  for(let n = parseInt(startResi); n <= parseInt(endResi); ++n) {
67232
67320
  let resid = chainid + '_' + pos2resi[n];
67233
67321
  //domainAtoms = me.hashUtilsCls.unionHash(domainAtoms, ic.residues[resid]);
67234
- ic.resid2domainid[resid] = chainid + ',' + k + '_' + resiSum;
67322
+ ic.resid2domainid[resid] = chainid + ',' + k + '_' + resiSum;
67235
67323
  }
67236
67324
  }
67325
+ */
67237
67326
  }
67238
67327
  }
67239
67328
 
67240
67329
  return domainAtomsArray;
67241
67330
  }
67242
-
67331
+
67243
67332
  getTemplateList(domainid) { let ic = this.icn3d; ic.icn3dui;
67244
67333
  let refpdbname = '', score = '', seqid = '', nresAlign = '';
67245
67334
 
@@ -67272,7 +67361,6 @@ class Dssp {
67272
67361
  if(!ic.domainid2ig2imgt) ic.domainid2ig2imgt = {};
67273
67362
 
67274
67363
  let minResidues = 20;
67275
-
67276
67364
  for(let i = 0, il = domainidpairArray.length; i < il; ++i) {
67277
67365
  //let queryData = (me.bNode) ? dataArray[i] : dataArray[i].value; //[0];
67278
67366
  let queryData = (dataArray[i]) ? dataArray[i].value : undefined; //[0];
@@ -67283,7 +67371,7 @@ class Dssp {
67283
67371
  }
67284
67372
 
67285
67373
  if(queryData[0].score === undefined) continue;
67286
-
67374
+
67287
67375
  //let domainid_index = domainidpairArray[i].split(',');
67288
67376
  //let domainid = domainid_index[0];
67289
67377
  let domainid = domainidpairArray[i].substr(0, domainidpairArray[i].indexOf('|'));
@@ -67304,7 +67392,7 @@ class Dssp {
67304
67392
  continue;
67305
67393
  }
67306
67394
  }
67307
-
67395
+
67308
67396
  if(!bRound1) {
67309
67397
  if(!me.bNode) console.log("refpdbname " + refpdbname + " TM-score: " + queryData[0].score);
67310
67398
  }
@@ -67367,8 +67455,13 @@ class Dssp {
67367
67455
  }
67368
67456
 
67369
67457
  if(!domainid2segs.hasOwnProperty(domainid) || queryData[0].score >= ic.domainid2score[domainid].split('_')[0]) {
67370
- ic.domainid2score[domainid] = queryData[0].score + '_' + queryData[0].frac_identical + '_' + queryData[0].num_res ;
67371
- ic.domainid2refpdbname[domainid] = refpdbname;
67458
+ ic.domainid2score[domainid] = queryData[0].score + '_' + queryData[0].frac_identical + '_' + queryData[0].num_res ;
67459
+ if(bRound1) {
67460
+ ic.domainid2refpdbname[domainid] = parseFloat(queryData[0].score) > 0.75 ? refpdbname : 'all_templates';
67461
+ }
67462
+ else {
67463
+ ic.domainid2refpdbname[domainid] = refpdbname;
67464
+ }
67372
67465
  domainid2segs[domainid] = queryData[0].segs;
67373
67466
  ic.domainid2ig2kabat[domainid] = queryData[0].ig2kabat;
67374
67467
  ic.domainid2ig2imgt[domainid] = queryData[0].ig2imgt;
@@ -67379,10 +67472,17 @@ class Dssp {
67379
67472
  }
67380
67473
 
67381
67474
  async parseAlignData(dataArray, domainidpairArray, bRound1) { let ic = this.icn3d, me = ic.icn3dui;
67475
+ let bNoMoreIg = false;
67476
+
67382
67477
  let domainid2segs = this.parseAlignData_part1(dataArray, domainidpairArray, bRound1);
67383
67478
 
67479
+ if(Object.keys(domainid2segs).length == 0) {
67480
+ bNoMoreIg = true;
67481
+ return bNoMoreIg;
67482
+ }
67483
+
67384
67484
  if(bRound1) {
67385
- if(!me.bNode) console.log("Start round 2 alignment with the reference culsters " + JSON.stringify(ic.domainid2refpdbname));
67485
+ if(!me.bNode) console.log("Start round 2 alignment with the reference culsters " + JSON.stringify(ic.domainid2refpdbname));
67386
67486
 
67387
67487
  // start round2
67388
67488
  let ajaxArray = [];
@@ -67400,7 +67500,7 @@ class Dssp {
67400
67500
  //refpdbname = pdbid;
67401
67501
  refpdbname = chainid;
67402
67502
 
67403
- if(!me.bNode) console.log("Adjusted refpdbname for domainid " + domainid + ": " + refpdbname);
67503
+ if(!me.bNode) console.log("Adjusted refpdbname for domainid " + domainid + ": " + refpdbname);
67404
67504
  }
67405
67505
 
67406
67506
  if(!ic.refpdbHash[refpdbname]) {
@@ -67418,20 +67518,20 @@ class Dssp {
67418
67518
  //let allPromise2 = Promise.allSettled(pdbAjaxArray);
67419
67519
  //ic.pdbDataArray = await allPromise2;
67420
67520
 
67421
- ic.pdbDataArray = await this.promiseWithFixedJobs(pdbAjaxArray);
67521
+ let pdbDataArray = await this.promiseWithFixedJobs(pdbAjaxArray);
67422
67522
 
67423
67523
  let pdb_target = ic.domainid2pdb[domainid];
67424
- for(let index = 0, indexl = ic.pdbDataArray.length; index < indexl; ++index) {
67524
+ for(let index = 0, indexl = pdbDataArray.length; index < indexl; ++index) {
67425
67525
  let struct2 = ic.defaultPdbId + index;
67426
- //let pdb_query = (me.bNode) ? ic.pdbDataArray[index] : ic.pdbDataArray[index].value; //[0];
67427
- let pdb_query = ic.pdbDataArray[index].value; //[0];
67526
+ //let pdb_query = (me.bNode) ? pdbDataArray[index] : pdbDataArray[index].value; //[0];
67527
+ let pdb_query = pdbDataArray[index].value; //[0];
67428
67528
  let header = 'HEADER ' + struct2 + '\n';
67429
67529
  pdb_query = header + pdb_query;
67430
67530
 
67431
67531
  let dataObj = {'pdb_query': pdb_query, 'pdb_target': pdb_target, "queryid": ic.refpdbHash[refpdbname][index]};
67432
67532
  let alignAjax = me.getAjaxPostPromise(urltmalign, dataObj);
67433
67533
  ajaxArray.push(alignAjax);
67434
-
67534
+
67435
67535
  //domainidpairArray3.push(domainid + "," + refpdbname);
67436
67536
  domainidpairArray3.push(domainid + "|" + ic.refpdbHash[refpdbname][index]);
67437
67537
  }
@@ -67444,12 +67544,14 @@ class Dssp {
67444
67544
  dataArray3 = await this.promiseWithFixedJobs(ajaxArray);
67445
67545
 
67446
67546
  await this.parseAlignData(dataArray3, domainidpairArray3, false);
67447
-
67547
+
67448
67548
  // end of round 2
67449
- return;
67549
+ return bNoMoreIg;
67450
67550
  }
67451
67551
 
67452
67552
  await this.parseAlignData_part3(domainid2segs);
67553
+
67554
+ return bNoMoreIg;
67453
67555
  }
67454
67556
 
67455
67557
  async parseAlignData_part3(domainid2segs) { let ic = this.icn3d, me = ic.icn3dui;
@@ -67595,7 +67697,7 @@ class Dssp {
67595
67697
  for(let i = 0, il = segArray.length; i < il; ++i) {
67596
67698
  let seg = segArray[i];
67597
67699
  if(!seg) continue;
67598
-
67700
+
67599
67701
  let qStart = seg.q_start;
67600
67702
  parseInt(seg.q_start);
67601
67703
  if(isNaN(seg.q_start)) seg.q_start.substr(seg.q_start.length - 1, 1);
@@ -67636,9 +67738,10 @@ class Dssp {
67636
67738
  if(currStrand != currStrandFinal) {
67637
67739
  refnumLabel = this.getLabelFromRefnum(refnum, currStrandFinal);
67638
67740
  }
67639
-
67640
- ic.resid2refnum[resid] = refnumLabel;
67741
+
67742
+ ic.resid2refnum[resid] = refnumLabel;
67641
67743
  ic.resid2refnum_ori[resid] = refnumLabel;
67744
+ ic.resid2domainid[resid] = domainid;
67642
67745
 
67643
67746
  // final reference numbers will be assign in ic.annoIgCls.showRefNum()
67644
67747
 
@@ -67685,7 +67788,7 @@ class Dssp {
67685
67788
  else {
67686
67789
  await ic.showAnnoCls.showAnnotations();
67687
67790
  }
67688
-
67791
+
67689
67792
  ic.annotationCls.setAnnoViewAndDisplay('detailed view');
67690
67793
  }
67691
67794
  else if(!me.bNode) {
@@ -67726,13 +67829,13 @@ class Dssp {
67726
67829
  // loops may have numbers such as 1310, 1410
67727
67830
 
67728
67831
  let refnumLabel;
67729
-
67832
+
67730
67833
  if(refnum < 1000) refnumLabel = undefined;
67731
67834
  else if(refnum >= 1200 && refnum < 1290) refnumLabel = "A---" + oriRefnum;
67732
67835
  else if(refnum >= 1320 && refnum < 1390) refnumLabel = "A--" + oriRefnum;
67733
67836
  else if(refnum >= 1420 && refnum < 1490) refnumLabel = "A-" + oriRefnum;
67734
- else if(refnum >= 1520 && refnum < 1590) refnumLabel = "A" + oriRefnum;
67735
- else if(refnum >= 1620 && refnum < 1690) refnumLabel = "A+" + oriRefnum;
67837
+ else if(refnum >= 1520 && refnum < 1590) refnumLabel = "A" + oriRefnum;
67838
+ else if(refnum >= 1620 && refnum < 1690) refnumLabel = "A+" + oriRefnum;
67736
67839
  else if(refnum >= 1820 && refnum < 1890) refnumLabel = "A'" + oriRefnum;
67737
67840
  else if(refnum >= 2000 && refnum < 2900) refnumLabel = "B" + oriRefnum;
67738
67841
  else if(refnum >= 3300 && refnum < 3390) refnumLabel = "C--" + oriRefnum;
@@ -67741,8 +67844,8 @@ class Dssp {
67741
67844
  else if(refnum >= 4000 && refnum < 4900) refnumLabel = "C'" + oriRefnum;
67742
67845
  else if(refnum >= 5000 && refnum < 5900) refnumLabel = "C''" + oriRefnum;
67743
67846
  else if(refnum >= 6000 && refnum < 6900) refnumLabel = "D" + oriRefnum;
67744
- else if(refnum >= 7500 && refnum < 7590) refnumLabel = "E" + oriRefnum;
67745
- else if(refnum >= 7620 && refnum < 7900) refnumLabel = "E+" + oriRefnum;
67847
+ else if(refnum >= 7500 && refnum < 7590) refnumLabel = "E" + oriRefnum;
67848
+ else if(refnum >= 7620 && refnum < 7900) refnumLabel = "E+" + oriRefnum;
67746
67849
  else if(refnum >= 8000 && refnum < 8900) refnumLabel = "F" + oriRefnum;
67747
67850
  else if(refnum >= 9500 && refnum < 9590) refnumLabel = "G" + oriRefnum;
67748
67851
  else if(refnum >= 9620 && refnum < 9690) refnumLabel = "G+" + oriRefnum;
@@ -67831,7 +67934,7 @@ class Dssp {
67831
67934
  if(type == 'igstrand' || type == 'IgStrand') {
67832
67935
  // iGStrand reference numbers were adjusted when showing in sequences
67833
67936
  if(me.bNode) {
67834
- for(let chnid in ic.chains) {
67937
+ for(let chnid in ic.chains) {
67835
67938
  let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.chains[chnid]);
67836
67939
  if(ic.proteins.hasOwnProperty(atom.serial)) {
67837
67940
  let giSeq = [];
@@ -67842,22 +67945,22 @@ class Dssp {
67842
67945
  }
67843
67946
  }
67844
67947
  }
67845
-
67948
+
67846
67949
  let resid2refnum = {};
67847
67950
  for(let resid in ic.resid2refnum) {
67848
67951
  let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
67849
67952
  if(!atom) continue;
67850
-
67953
+
67851
67954
  let resn = me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3));
67852
-
67955
+
67853
67956
  let domainid = ic.resid2domainid[resid];
67854
67957
  let refnumLabel = ic.resid2refnum[resid];
67855
-
67958
+
67856
67959
  if(refnumLabel) {
67857
67960
  let refnumStr_ori = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
67858
67961
  (ic.domainid2ig2kabat[domainid]) ? ic.domainid2ig2kabat[domainid][refnumStr_ori] : undefined;
67859
67962
  }
67860
-
67963
+
67861
67964
  if(ic.resid2refnum[resid]) {
67862
67965
  if(ic.residIgLoop.hasOwnProperty(resid)) { // loop
67863
67966
  resid2refnum[resid + '_' + resn] = ic.resid2refnum[resid] + '_loop';
@@ -67938,18 +68041,18 @@ class Dssp {
67938
68041
  for(let resid in ic.resid2refnum) {
67939
68042
  let domainid = ic.resid2domainid[resid];
67940
68043
  let refnumStr, refnumLabel = ic.resid2refnum[resid];
67941
-
68044
+
67942
68045
  let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
67943
68046
  let resn = me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3));
67944
-
68047
+
67945
68048
  if(refnumLabel) {
67946
68049
  let refnumStr_ori = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
67947
68050
  refnumStr = (ic.domainid2ig2kabat[domainid]) ? ic.domainid2ig2kabat[domainid][refnumStr_ori] : undefined;
67948
68051
  }
67949
-
68052
+
67950
68053
  resid2kabat[resid + '_' + resn] = refnumStr;
67951
68054
  }
67952
-
68055
+
67953
68056
  refData += JSON.stringify(resid2kabat);
67954
68057
  }
67955
68058
  // 3. show IMGT ref numbers
@@ -67958,25 +68061,25 @@ class Dssp {
67958
68061
  for(let resid in ic.resid2refnum) {
67959
68062
  let domainid = ic.resid2domainid[resid];
67960
68063
  let refnumStr, refnumLabel = ic.resid2refnum[resid];
67961
-
68064
+
67962
68065
  let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
67963
68066
  let resn = me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3));
67964
-
68067
+
67965
68068
  if(refnumLabel) {
67966
68069
  let refnumStr_ori = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
67967
68070
  refnumStr = (ic.domainid2ig2imgt[domainid]) ? ic.domainid2ig2imgt[domainid][refnumStr_ori] : undefined;
67968
68071
  }
67969
-
68072
+
67970
68073
  resid2imgt[resid + '_' + resn] = refnumStr;
67971
68074
  }
67972
-
68075
+
67973
68076
  refData += JSON.stringify(resid2imgt);
67974
68077
  }
67975
68078
 
67976
68079
 
67977
68080
  if(!me.bNode) {
67978
68081
  let file_pref = Object.keys(me.utilsCls.getHlStructures()).join(',');
67979
-
68082
+
67980
68083
  ic.saveFileCls.saveFile(file_pref + '_refnum_' + type + '.txt', 'text', [refData]);
67981
68084
  }
67982
68085
  else {
@@ -67994,7 +68097,7 @@ class Dssp {
67994
68097
 
67995
68098
  for(let i = 0, il = parseInt((ajaxArray.length - 1) / n + 1); i < il; ++i) {
67996
68099
  let currAjaxArray = [];
67997
- if(i == il - 1) { // last one
68100
+ if(i == il - 1) { // last one
67998
68101
  currAjaxArray = ajaxArray.slice(i * n, ajaxArray.length);
67999
68102
  }
68000
68103
  else {