icn3d 3.30.1 → 3.30.3

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Files changed (4) hide show
  1. package/icn3d.js +144 -37
  2. package/icn3d.min.js +5 -5
  3. package/icn3d.module.js +144 -37
  4. package/package.json +1 -1
package/icn3d.module.js CHANGED
@@ -12896,12 +12896,69 @@ class SetDialog {
12896
12896
 
12897
12897
  group2tpl['Other'] = ['CuZnSuperoxideDismutase_1hl5C_human', 'ECadherin_4zt1A_human_n2', 'LaminAC_1ifrA_human', 'ORF7a_1xakA_virus'];
12898
12898
 
12899
+ let tpl2strandsig = {};
12900
+ tpl2strandsig['ASF1A_2iijA_human'] = "A A' B C C' E F G G+";
12901
+ tpl2strandsig['B2Microglobulin_7phrL_human_C1'] = "A B C C' D E F G";
12902
+ tpl2strandsig['BArrestin1_4jqiA_rat_n1'] = "A- A A' B C C' E F G";
12903
+ tpl2strandsig['BTLA_2aw2A_human_Iset'] = "A A' B C C' D E F G";
12904
+ tpl2strandsig['C3_2qkiD_human_n1'] = "A A' B C C' E F G";
12905
+ tpl2strandsig['CD19_6al5A_human_C2orV-n1'] = "A' B C C' D E F G";
12906
+ tpl2strandsig['CD28_1yjdC_human_V'] = "A A' B C C' C'' D E F G";
12907
+ tpl2strandsig['CD2_1hnfA_human_C2-n2'] = "A B C C' E F G";
12908
+ tpl2strandsig['CD2_1hnfA_human_V-n1'] = "A' B C C' C'' D E F G";
12909
+ tpl2strandsig['CD3d_6jxrd_human_Iset'] = "A B C D E F G";
12910
+ tpl2strandsig['CD3e_6jxrf_human_Iset'] = "A B C C' D E F G";
12911
+ tpl2strandsig['CD3g_6jxrg_human_Iset'] = "A B C C' E F G G+";
12912
+ tpl2strandsig['CD8a_1cd8A_human_V'] = "A A' B C C' C'' D E F G";
12913
+ tpl2strandsig['CoAtomerGamma1_1r4xA_human'] = "A- A B C D E F G";
12914
+ tpl2strandsig['Contactin1_2ee2A_human_FN3-n9'] = "A A' B C C' E F G";
12915
+ tpl2strandsig['Contactin1_3s97C_human_C2-n2'] = "A A' B C D E F G";
12916
+ tpl2strandsig['CuZnSuperoxideDismutase_1hl5C_human'] = "A- A B C C' E F G";
12917
+ tpl2strandsig['ECadherin_4zt1A_human_n2'] = "A' B C D E F G";
12918
+ tpl2strandsig['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = "A--- A-- A- A B C C' C'' D E F G";
12919
+ tpl2strandsig['FAB-HEAVY_5esv_C1-n2'] = "A B C D E F G";
12920
+ tpl2strandsig['FAB-HEAVY_5esv_V-n1'] = "A B C C' C'' D E F G";
12921
+ tpl2strandsig['FAB-LIGHT_5esv_C1-n2'] = "A B C C' E F G";
12922
+ tpl2strandsig['FAB-LIGHT_5esv_V-n1'] = "A A' B C C' C'' D E F G";
12923
+ tpl2strandsig['GHR_1axiB_human_FN3-n1'] = "A B C C' D E F G";
12924
+ tpl2strandsig['ICOS_6x4gA_human_V'] = "A B C C' C'' D E F G";
12925
+ tpl2strandsig['IL6Rb_1bquB_human_FN3-n2'] = "A B C C' E F G";
12926
+ tpl2strandsig['IL6Rb_1bquB_human_FN3-n3'] = "A B C C' E F G";
12927
+ tpl2strandsig['InsulinR_8guyE_human_FN3-n1'] = "A B C C' E F G";
12928
+ tpl2strandsig['InsulinR_8guyE_human_FN3-n2'] = "A B C C' E F G";
12929
+ tpl2strandsig['IsdA_2iteA_bacteria'] = "A- A B C C' D E F G";
12930
+ tpl2strandsig['JAM1_1nbqA_human_VorIset-n2'] = "A A' B C C' D E F G";
12931
+ tpl2strandsig['LAG3_7tzgD_human_C2-n2'] = "A A' B C C' D E F G";
12932
+ tpl2strandsig['LAG3_7tzgD_human_V-n1'] = "A' B C C' D E F G";
12933
+ tpl2strandsig['LaminAC_1ifrA_human'] = "A- A B C C' E E+ F G";
12934
+ tpl2strandsig['MHCIa_7phrH_human_C1'] = "A B C C' D E F G";
12935
+ tpl2strandsig['MPT63_1lmiA_bacteria'] = "A-- A- A BC C' E F G";
12936
+ tpl2strandsig['NaCaExchanger_2fwuA_dog_n2'] = "A A' B C C' E F G";
12937
+ tpl2strandsig['NaKATPaseTransporterBeta_2zxeB_spurdogshark']= "A A' B C D E F G";
12938
+ tpl2strandsig['ORF7a_1xakA_virus'] = "A' B C D E F G";
12939
+ tpl2strandsig['PD1_4zqkB_human_V'] = "A A' B C C' D E F G";
12940
+ tpl2strandsig['PDL1_4z18B_human_V-n1'] = "A A' B C C' C'' D E F G";
12941
+ tpl2strandsig['Palladin_2dm3A_human_Iset-n1'] = "A A' B C C' D E F G";
12942
+ tpl2strandsig['RBPJ_6py8C_human_Unk-n1'] = "A A' B C C' E F G";
12943
+ tpl2strandsig['RBPJ_6py8C_human_Unk-n2'] = "A B C D E F G";
12944
+ tpl2strandsig['Sidekick2_1wf5A_human_FN3-n7'] = "A B C C' E F G";
12945
+ tpl2strandsig['Siglec3_5j0bB_human_C2-n2'] = "A A' B C D E F G";
12946
+ tpl2strandsig['TCRa_6jxrm_human_C1-n2'] = "A B C D E F G";
12947
+ tpl2strandsig['TCRa_6jxrm_human_V-n1'] = "A A' B C C' C'' D E F G";
12948
+ tpl2strandsig['TEAD1_3kysC_human'] = "A A+ A' B C C' E F G G+";
12949
+ tpl2strandsig['TP34_2o6cA_bacteria'] = "A- A B C C' D E F G";
12950
+ tpl2strandsig['TP47_1o75A_bacteria'] = "A B C C' D E F G";
12951
+ tpl2strandsig['Titin_4uowM_human_Unk-n152'] = "A A' B C C' D E F G";
12952
+ tpl2strandsig['VISTA_6oilA_human_V'] = "A A' B C C' C'' D E F G G+";
12953
+ tpl2strandsig['VNAR_1t6vN_shark_V'] = "A A' B C C' D E F G";
12954
+ tpl2strandsig['VTCN1_Q7Z7D3_human_V-n2'] = "A B C C' D E F G G+";
12955
+
12899
12956
  let html = '';
12900
12957
  for(let group in group2tpl) {
12901
12958
  html += "<optgroup label='" + group + "'>";
12902
12959
  for(let i = 0, il = group2tpl[group].length; i < il; ++i) {
12903
12960
  let template = group2tpl[group][i];
12904
- html += me.htmlCls.optionStr + "'" + template + "'>" + template + "</option>";
12961
+ html += me.htmlCls.optionStr + "'" + template + "'>" + template + ", Strands: " + tpl2strandsig[template] + "</option>";
12905
12962
  }
12906
12963
  html += "</optgroup>";
12907
12964
  }
@@ -13289,6 +13346,7 @@ class Events {
13289
13346
  me.htmlCls.HEIGHT = $( window ).height();
13290
13347
  ic.applyCenterCls.setWidthHeight(me.htmlCls.WIDTH, me.htmlCls.HEIGHT);
13291
13348
  ic.drawCls.draw();
13349
+
13292
13350
  ic.resizeCanvasCls.openFullscreen($("#" + me.pre + "canvas")[0]);
13293
13351
  });
13294
13352
 
@@ -27679,7 +27737,8 @@ class Axes {
27679
27737
  createArrow(dir, origin, axisLen, color, headLength, headWidth, bGlycan) { let ic = this.icn3d, me = ic.icn3dui;
27680
27738
  if(me.bNode) return;
27681
27739
 
27682
- let coneGeometry = new THREE.CylinderBufferGeometry( 0, 0.5, 1, 32, 1 );
27740
+ // let coneGeometry = new THREE.CylinderBufferGeometry( 0, 0.5, 1, 32, 1 );
27741
+ let coneGeometry = new THREE.CylinderGeometry( 0, 0.5, 1, 32, 1 );
27683
27742
  //coneGeometry.translate( 0, - 0.5, 0 );
27684
27743
  coneGeometry.translate( 0, 0.5, 0 );
27685
27744
  let material;
@@ -38832,10 +38891,15 @@ class AnnoIg {
38832
38891
  if(!info) continue;
38833
38892
 
38834
38893
  let tmscore = info.score;
38835
- let igType = ic.ref2igtype[info.refpdbname];
38836
- let confidance = (parseFloat(tmscore) < 0.75 ) ? '?' : '';
38837
- titleArray.push(igType + confidance + ' (TM:' + parseFloat(tmscore).toFixed(2) + ')');
38838
- fullTitleArray.push(igType + confidance + ' (TM:' + parseFloat(tmscore).toFixed(2) + '), template: ' + info.refpdbname + ', Seq. identity: ' + parseFloat(info.seqid).toFixed(2) + ', aligned residues: ' + info.nresAlign);
38894
+ // let igType = ic.ref2igtype[info.refpdbname];
38895
+ // let confidance = (parseFloat(tmscore) < 0.75 ) ? '?' : '';
38896
+ // titleArray.push(igType + confidance + ' (TM:' + parseFloat(tmscore).toFixed(2) + ')');
38897
+ // fullTitleArray.push(igType + confidance + ' (TM:' + parseFloat(tmscore).toFixed(2) + '), template: ' + info.refpdbname + ', Seq. identity: ' + parseFloat(info.seqid).toFixed(2) + ', aligned residues: ' + info.nresAlign);
38898
+
38899
+ let igType = (parseFloat(tmscore) < 0.75 ) ? 'Ig' : ic.ref2igtype[info.refpdbname];
38900
+ titleArray.push(igType + ' (TM:' + parseFloat(tmscore).toFixed(2) + ')');
38901
+ fullTitleArray.push(igType + ' (TM:' + parseFloat(tmscore).toFixed(2) + '), template: ' + info.refpdbname + ', Seq. identity: ' + parseFloat(info.seqid).toFixed(2) + ', aligned residues: ' + info.nresAlign);
38902
+
38839
38903
  domainArray.push(igType);
38840
38904
 
38841
38905
  let segs = [];
@@ -39190,15 +39254,13 @@ class AnnoDomain {
39190
39254
  let subdomainArray = domainArray[index].intervals;
39191
39255
  // remove duplicate, e.g., at https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdb_strview.cgi?v=2&program=icn3d&domain&molinfor&uid=1itw
39192
39256
  let domainFromHash = {}, domainToHash = {};
39193
- let fromArray = [], toArray = [];
39257
+ let fromArray = [], toArray = [], posFromArray = [], posToArray = [];
39194
39258
  let resiHash = {};
39195
39259
  let resCnt = 0;
39196
39260
 
39197
39261
  for(let i = 0, il = subdomainArray.length; i < il; ++i) {
39198
- // let domainFrom = Math.round(subdomainArray[i][0]) - 1; // convert 1-based to 0-based
39199
- // let domainTo = Math.round(subdomainArray[i][1]) - 1;
39200
- let domainFrom = Math.round(subdomainArray[i][0]); // convert 1-based to 0-based
39201
- let domainTo = Math.round(subdomainArray[i][1]);
39262
+ let domainFrom = Math.round(subdomainArray[i][0]) - 1; // convert 1-based to 0-based
39263
+ let domainTo = Math.round(subdomainArray[i][1]) - 1;
39202
39264
 
39203
39265
  if(domainFromHash.hasOwnProperty(domainFrom) || domainToHash.hasOwnProperty(domainTo)) {
39204
39266
  continue; // do nothing for duplicated "from" or "to", e.g, PDBID 1ITW, 5FWI
@@ -39212,6 +39274,9 @@ class AnnoDomain {
39212
39274
  // if(ic.bNCBI || bCalcDirect) {
39213
39275
  fromArray.push(pos2resi[domainFrom]);
39214
39276
  toArray.push(pos2resi[domainTo]);
39277
+
39278
+ posFromArray.push(domainFrom);
39279
+ posToArray.push(domainTo);
39215
39280
  // }
39216
39281
  // else {
39217
39282
  // fromArray.push(domainFrom + ic.baseResi[chnid]);
@@ -39232,9 +39297,9 @@ class AnnoDomain {
39232
39297
 
39233
39298
  if(!ic.resid2domain) ic.resid2domain = {};
39234
39299
  if(!ic.resid2domain[chnid]) ic.resid2domain[chnid] = [];
39235
- for(let i = 0, il = fromArray.length; i < il; ++i) {
39236
- let from = parseInt(fromArray[i]);
39237
- let to = parseInt(toArray[i]);
39300
+ for(let i = 0, il = posFromArray.length; i < il; ++i) {
39301
+ let from = parseInt(posFromArray[i]);
39302
+ let to = parseInt(posToArray[i]);
39238
39303
  for(let j = from; j <= to; ++j) {
39239
39304
  // 0-based
39240
39305
  let obj = {};
@@ -39246,7 +39311,7 @@ class AnnoDomain {
39246
39311
  }
39247
39312
  }
39248
39313
 
39249
- let htmlTmp2 = '<div class="icn3d-seqTitle icn3d-link icn3d-blue" 3ddomain="' +(index+1).toString() + '" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + title + '" index="' + index + '" setname="' + chnid + '_3d_domain_' +(index+1).toString() + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">' + title + ' </div>';
39314
+ let htmlTmp2 = '<div class="icn3d-seqTitle icn3d-link icn3d-blue" 3ddomain="' +(index+1).toString() + '" from="' + posFromArray + '" to="' + posToArray + '" shorttitle="' + title + '" index="' + index + '" setname="' + chnid + '_3d_domain_' +(index+1).toString() + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">' + title + ' </div>';
39250
39315
  let htmlTmp3 = '<span class="icn3d-residueNum" title="residue count">' + resCnt.toString() + ' Res</span>';
39251
39316
  html3 += htmlTmp2 + htmlTmp3 + '<br>';
39252
39317
  let htmlTmp = '<span class="icn3d-seqLine">';
@@ -39286,12 +39351,12 @@ class AnnoDomain {
39286
39351
  if(ic.seqStartLen && ic.seqStartLen[chnid]) html2 += ic.showSeqCls.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
39287
39352
 
39288
39353
  if(me.cfg.blast_rep_id != chnid) { // regular
39289
- for(let i = 0, il = fromArray.length; i < il; ++i) {
39354
+ for(let i = 0, il = posFromArray.length; i < il; ++i) {
39290
39355
  // 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);
39291
- let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i]) / ic.maxAnnoLength) : Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
39356
+ let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(posFromArray[i]) / ic.maxAnnoLength) : Math.round(ic.seqAnnWidth *(posFromArray[i] - posToArray[i-1] - 1) / ic.maxAnnoLength);
39292
39357
 
39293
39358
  html2 += '<div style="display:inline-block; width:' + emptyWidth + 'px;">&nbsp;</div>';
39294
- 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 icn3d-link icn3d-blue" 3ddomain="' +(index+1).toString() + '" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + title + '" index="' + index + '" setname="' + chnid + '_3d_domain_' +(index+1).toString() + '" id="' + chnid + '_3d_domain_' + index + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">3D domain ' +(index+1).toString() + '</div>';
39359
+ html2 += '<div style="display:inline-block; color:white!important; font-weight:bold; background-color:#' + color + '; width:' + Math.round(ic.seqAnnWidth *(posToArray[i] - posFromArray[i] + 1) / ic.maxAnnoLength) + 'px;" class="icn3d-seqTitle icn3d-link icn3d-blue" 3ddomain="' +(index+1).toString() + '" from="' + posFromArray + '" to="' + posToArray + '" shorttitle="' + title + '" index="' + index + '" setname="' + chnid + '_3d_domain_' +(index+1).toString() + '" id="' + chnid + '_3d_domain_' + index + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">3D domain ' +(index+1).toString() + '</div>';
39295
39360
  }
39296
39361
  }
39297
39362
  else { // with potential gaps
@@ -40825,7 +40890,7 @@ class Domain3d {
40825
40890
  if(!ic.posid2resid) ic.posid2resid = {};
40826
40891
 
40827
40892
  let substructItem = {};
40828
- let pos2resi = {};
40893
+ let pos2resi = {}; // 0-based
40829
40894
  for(let i = 0; i < residueArray.length; ++i) {
40830
40895
  let resid = residueArray[i];
40831
40896
 
@@ -40857,7 +40922,8 @@ class Domain3d {
40857
40922
 
40858
40923
  //resiArray.push(resi);
40859
40924
  resiArray.push(i+1);
40860
- pos2resi[i+1] = resi;
40925
+ // pos2resi[i+1] = resi;
40926
+ pos2resi[i] = resi;
40861
40927
 
40862
40928
  ic.posid2resid[atom.structure + '_' + atom.chain + '_' + (i+1).toString()] = resid;
40863
40929
  // let residNCBI = ic.resid2ncbi[resid];
@@ -41379,8 +41445,8 @@ class Domain3d {
41379
41445
  //ss: sstype ss_start ss_end x1 y1 z1 x2 y2 z2
41380
41446
  //sstype: 1 (helix), 2 (sheet)
41381
41447
  let sstype = (substruct[k].Sheet) ? 2 : 1;
41382
- let from = pos2resi[substruct[k].From];
41383
- let to = pos2resi[substruct[k].To];
41448
+ let from = pos2resi[substruct[k].From - 1]; // 1-based to 0-based
41449
+ let to = pos2resi[substruct[k].To - 1];
41384
41450
 
41385
41451
  // 1-based residue numbers
41386
41452
  let fromPos = substruct[k].From;
@@ -63329,6 +63395,27 @@ class LoadScript {
63329
63395
  return nameArray;
63330
63396
  }
63331
63397
 
63398
+ updateTransformation(steps) { let ic = this.icn3d; ic.icn3dui;
63399
+ let commandTransformation = (ic.commands[steps-1]) ? ic.commands[steps-1].split('|||') : [];
63400
+
63401
+ if(commandTransformation.length == 2) {
63402
+ let transformation = JSON.parse(commandTransformation[1]);
63403
+
63404
+ ic._zoomFactor = transformation.factor;
63405
+
63406
+ ic.mouseChange.x = transformation.mouseChange.x;
63407
+ ic.mouseChange.y = transformation.mouseChange.y;
63408
+
63409
+ ic.quaternion._x = transformation.quaternion._x;
63410
+ ic.quaternion._y = transformation.quaternion._y;
63411
+ ic.quaternion._z = transformation.quaternion._z;
63412
+ ic.quaternion._w = transformation.quaternion._w;
63413
+ }
63414
+
63415
+ // ic.bRender = true;
63416
+ ic.drawCls.draw();
63417
+ }
63418
+
63332
63419
  async execCommandsBase(start, end, steps, bFinalStep) { let ic = this.icn3d, me = ic.icn3dui;
63333
63420
  let thisClass = this;
63334
63421
  let i;
@@ -63508,7 +63595,10 @@ class LoadScript {
63508
63595
  await thisClass.applyCommandGraphinteraction(command);
63509
63596
  }
63510
63597
  else if(command.indexOf('cartoon 2d domain') == 0) {
63598
+ ic.bRender = true;
63599
+ thisClass.updateTransformation(steps);
63511
63600
  await thisClass.applyCommandCartoon2d(command);
63601
+ ic.bRender = false;
63512
63602
  }
63513
63603
  else if(command.indexOf('set half pae map') == 0) {
63514
63604
  await thisClass.applyCommandAfmap(command);
@@ -63523,7 +63613,10 @@ class LoadScript {
63523
63613
  let pos = command.lastIndexOf(' ');
63524
63614
  let type = command.substr(pos + 1);
63525
63615
 
63616
+ ic.bRender = true;
63617
+ thisClass.updateTransformation(steps);
63526
63618
  await ic.cartoon2dCls.draw2Dcartoon(type);
63619
+ ic.bRender = false;
63527
63620
  }
63528
63621
  else if(command.indexOf('add msa track') == 0) {
63529
63622
  //add msa track | chainid " + chainid + " | startpos " + startpos + " | type " + type + " | fastaList " + fastaList
@@ -63561,7 +63654,7 @@ class LoadScript {
63561
63654
  await ic.applyCommandCls.applyCommand(ic.commands[i]);
63562
63655
  }
63563
63656
  }
63564
-
63657
+
63565
63658
  //if(i === steps - 1) {
63566
63659
  if(i === steps || bFinalStep) {
63567
63660
  this.renderFinalStep(i);
@@ -67060,7 +67153,7 @@ class Dssp {
67060
67153
  let endResi = parseInt(segArray[m+1]);
67061
67154
 
67062
67155
  for(let n = startResi; n <= endResi; ++n) {
67063
- let resid = chainid + '_' + pos2resi[n];
67156
+ let resid = chainid + '_' + pos2resi[n - 1];
67064
67157
  ++resCnt;
67065
67158
  domainAtoms = me.hashUtilsCls.unionHash(domainAtoms, ic.residues[resid]);
67066
67159
 
@@ -67082,7 +67175,7 @@ class Dssp {
67082
67175
  let startResi = segArray[m];
67083
67176
  let endResi = segArray[m+1];
67084
67177
  for(let n = parseInt(startResi); n <= parseInt(endResi); ++n) {
67085
- let resid = chainid + '_' + pos2resi[n];
67178
+ let resid = chainid + '_' + pos2resi[n - 1];
67086
67179
  //domainAtoms = me.hashUtilsCls.unionHash(domainAtoms, ic.residues[resid]);
67087
67180
  ic.resid2domainid[resid] = chainid + ',' + k + '_' + resiSum;
67088
67181
  }
@@ -68191,19 +68284,25 @@ class Dssp {
68191
68284
  }
68192
68285
 
68193
68286
  // 2b. remove strands with less than 3 residues except G strand
68287
+ let removeDomainidHash = {};
68194
68288
  for(let il = strandArray.length, i = il - 1; i >= 0; --i) {
68195
- let strandTmp = strandArray[i].strand.substr(0, 1);
68289
+ // let strandTmp = strandArray[i].strand.substr(0, 1);
68290
+ let strandTmp = strandArray[i].strand;
68196
68291
  if(strandTmp != 'G' && strandArray[i].endRefnum - strandArray[i].startRefnum + 1 < 3) { // remove the strand
68197
- if(strandTmp == 'B' || strandTmp == 'C' || strandTmp == 'E' || strandTmp == 'F') {
68198
- if(!me.bNode) console.log("Some of the Ig strands B, C, E, F are removed since they are too short...");
68199
- return false;
68200
- }
68201
-
68202
68292
  if(i != il - 1) { // modify
68203
68293
  strandArray[i + 1].loopResCnt += strandArray[i].loopResCnt + parseInt(strandArray[i].endResi) - parseInt(strandArray[i].startResi) + 1;
68204
68294
  }
68205
68295
 
68206
68296
  strandArray.splice(i, 1);
68297
+
68298
+ if(strandTmp == 'B' || strandTmp == 'C' || strandTmp == 'E' || strandTmp == 'F') {
68299
+ if(!me.bNode) console.log("Ig strand " + strandTmp + " is removed since it is too short...");
68300
+
68301
+ let resid = chnid + '_' + strandArray[i].startResi;
68302
+ let domainid = ic.resid2domainid[resid];
68303
+ removeDomainidHash[domainid] = 1;
68304
+ continue;
68305
+ }
68207
68306
  }
68208
68307
  }
68209
68308
 
@@ -68393,6 +68492,14 @@ class Dssp {
68393
68492
  prevStrand = currStrand;
68394
68493
  prevStrandCnt = strandCnt - 1;
68395
68494
 
68495
+ // remove domians without B,C,E,F strands
68496
+ if(removeDomainidHash.hasOwnProperty(domainid)) {
68497
+ delete ic.resid2refnum[residueid];
68498
+ delete ic.resid2domainid[residueid];
68499
+
68500
+ continue;
68501
+ }
68502
+
68396
68503
  // assign the adjusted reference numbers
68397
68504
  ic.resid2refnum[residueid] = refnumLabel;
68398
68505
  ic.resid2domainid[residueid] = domainid;
@@ -71174,7 +71281,7 @@ class Cartoon2d {
71174
71281
  idStr = idStr.substr(0, idStr.indexOf('-'));
71175
71282
  }
71176
71283
  else {
71177
- idStr = idStr.substr(idStr.lastIndexOf('_') + 1);
71284
+ idStr = idStr; //idStr.substr(idStr.lastIndexOf('_') + 1);
71178
71285
  }
71179
71286
 
71180
71287
  return idStr;
@@ -71871,14 +71978,14 @@ class ResizeCanvas {
71871
71978
  !document.webkitFullscreenElement && !document.msFullscreenElement) {
71872
71979
  if(elem.requestFullscreen) {
71873
71980
  elem.requestFullscreen();
71874
- } else if(elem.mozRequestFullScreen) { /* Firefox */
71981
+ } else if(elem.mozRequestFullScreen) { // Firefox
71875
71982
  elem.mozRequestFullScreen();
71876
- } else if(elem.webkitRequestFullscreen) { /* Chrome, Safari and Opera */
71983
+ } else if(elem.webkitRequestFullscreen) { // Chrome, Safari and Opera
71877
71984
  elem.webkitRequestFullscreen();
71878
- } else if(elem.msRequestFullscreen) { /* IE/Edge */
71985
+ } else if(elem.msRequestFullscreen) { // IE/Edge
71879
71986
  elem.msRequestFullscreen();
71880
71987
  }
71881
- }
71988
+ }
71882
71989
  }
71883
71990
 
71884
71991
  //Rotate the structure in one of the directions: "left", "right", "up", and "down".
@@ -76569,7 +76676,7 @@ class iCn3DUI {
76569
76676
  //even when multiple iCn3D viewers are shown together.
76570
76677
  this.pre = this.cfg.divid + "_";
76571
76678
 
76572
- this.REVISION = '3.30.0';
76679
+ this.REVISION = '3.30.1';
76573
76680
 
76574
76681
  // In nodejs, iCn3D defines "window = {navigator: {}}"
76575
76682
  this.bNode = (Object.keys(window).length < 2) ? true : false;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "icn3d",
3
- "version": "3.30.1",
3
+ "version": "3.30.3",
4
4
  "main": "./icn3d.js",
5
5
  "exports": {
6
6
  ".": {