icn3d 3.30.0 → 3.30.2

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Files changed (4) hide show
  1. package/icn3d.js +159 -39
  2. package/icn3d.min.js +5 -5
  3. package/icn3d.module.js +159 -39
  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 = [];
@@ -39097,6 +39161,7 @@ class AnnoDomain {
39097
39161
 
39098
39162
  let result = ic.domain3dCls.c2b_NewSplitChain(atoms);
39099
39163
  let subdomains = result.subdomains;
39164
+ let pos2resi = result.pos2resi;
39100
39165
  //let substruct = result.substruct;
39101
39166
  //let jsonStr = ic.domain3dCls.getDomainJsonForAlign(atoms);
39102
39167
 
@@ -39111,6 +39176,8 @@ class AnnoDomain {
39111
39176
 
39112
39177
  data.domains[chainid].domains.push(domain);
39113
39178
  }
39179
+
39180
+ data.domains[chainid].pos2resi = pos2resi;
39114
39181
  }
39115
39182
  }
39116
39183
 
@@ -39147,7 +39214,7 @@ class AnnoDomain {
39147
39214
  let html = '<div id="' + ic.pre + chnid + '_domainseq_sequence" class="icn3d-dl_sequence">';
39148
39215
  let html2 = html;
39149
39216
  let html3 = html;
39150
- let domainArray, proteinname;
39217
+ let domainArray, pos2resi, proteinname;
39151
39218
  let pos = chnid.indexOf('_');
39152
39219
  let chain = chnid.substr(pos + 1);
39153
39220
  // MMDB symmetry chain has the form of 'A1'
@@ -39155,9 +39222,11 @@ class AnnoDomain {
39155
39222
  chain = chain.substr(0, chain.length - 1);
39156
39223
  }
39157
39224
 
39158
- if(bCalcDirect) {
39225
+ // if(bCalcDirect) {
39159
39226
  proteinname = chnid;
39160
39227
  domainArray = (data.domains[chnid]) ? data.domains[chnid].domains : [];
39228
+ pos2resi = data.domains[chnid].pos2resi;
39229
+ /*
39161
39230
  }
39162
39231
  else {
39163
39232
  let molinfo = data.moleculeInfor;
@@ -39176,6 +39245,7 @@ class AnnoDomain {
39176
39245
  domainArray = [];
39177
39246
  }
39178
39247
  }
39248
+ */
39179
39249
 
39180
39250
  for(let index = 0, indexl = domainArray.length; index < indexl; ++index) {
39181
39251
  //var fulltitle = '3D domain ' +(index+1).toString() + ' of ' + proteinname + '(PDB ID: ' + data.pdbId + ')';
@@ -39184,13 +39254,14 @@ class AnnoDomain {
39184
39254
  let subdomainArray = domainArray[index].intervals;
39185
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
39186
39256
  let domainFromHash = {}, domainToHash = {};
39187
- let fromArray = [], toArray = [];
39257
+ let fromArray = [], toArray = [], posFromArray = [], posToArray = [];
39188
39258
  let resiHash = {};
39189
39259
  let resCnt = 0;
39190
39260
 
39191
39261
  for(let i = 0, il = subdomainArray.length; i < il; ++i) {
39192
39262
  let domainFrom = Math.round(subdomainArray[i][0]) - 1; // convert 1-based to 0-based
39193
39263
  let domainTo = Math.round(subdomainArray[i][1]) - 1;
39264
+
39194
39265
  if(domainFromHash.hasOwnProperty(domainFrom) || domainToHash.hasOwnProperty(domainTo)) {
39195
39266
  continue; // do nothing for duplicated "from" or "to", e.g, PDBID 1ITW, 5FWI
39196
39267
  }
@@ -39201,8 +39272,11 @@ class AnnoDomain {
39201
39272
 
39202
39273
  // use the NCBI residue number, and convert to PDB residue number during selection
39203
39274
  // if(ic.bNCBI || bCalcDirect) {
39204
- fromArray.push(domainFrom);
39205
- toArray.push(domainTo);
39275
+ fromArray.push(pos2resi[domainFrom]);
39276
+ toArray.push(pos2resi[domainTo]);
39277
+
39278
+ posFromArray.push(domainFrom);
39279
+ posToArray.push(domainTo);
39206
39280
  // }
39207
39281
  // else {
39208
39282
  // fromArray.push(domainFrom + ic.baseResi[chnid]);
@@ -39211,7 +39285,9 @@ class AnnoDomain {
39211
39285
 
39212
39286
  resCnt += domainTo - domainFrom + 1;
39213
39287
  for(let j = domainFrom; j <= domainTo; ++j) {
39214
- resiHash[j+1] = 1;
39288
+ // resiHash[j+1] = 1;
39289
+ let resi = pos2resi[j];
39290
+ resiHash[resi] = 1;
39215
39291
  }
39216
39292
  }
39217
39293
 
@@ -39221,20 +39297,21 @@ class AnnoDomain {
39221
39297
 
39222
39298
  if(!ic.resid2domain) ic.resid2domain = {};
39223
39299
  if(!ic.resid2domain[chnid]) ic.resid2domain[chnid] = [];
39224
- for(let i = 0, il = fromArray.length; i < il; ++i) {
39225
- let from = parseInt(fromArray[i]);
39226
- 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]);
39227
39303
  for(let j = from; j <= to; ++j) {
39228
39304
  // 0-based
39229
39305
  let obj = {};
39230
- let resi = ic.ParserUtilsCls.getResi(chnid, j);
39306
+ // let resi = ic.ParserUtilsCls.getResi(chnid, j);
39307
+ let resi = pos2resi[j];
39231
39308
  obj[chnid + '_' + resi] = domainName;
39232
39309
  ic.resid2domain[chnid].push(obj);
39233
39310
  }
39234
39311
  }
39235
39312
  }
39236
39313
 
39237
- 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>';
39238
39315
  let htmlTmp3 = '<span class="icn3d-residueNum" title="residue count">' + resCnt.toString() + ' Res</span>';
39239
39316
  html3 += htmlTmp2 + htmlTmp3 + '<br>';
39240
39317
  let htmlTmp = '<span class="icn3d-seqLine">';
@@ -39248,7 +39325,8 @@ class AnnoDomain {
39248
39325
  html += ic.showSeqCls.insertGap(chnid, i, '-');
39249
39326
  //if(i >= domainFrom && i <= domainTo) {
39250
39327
  let resi = ic.ParserUtilsCls.getResi(chnid, i);
39251
- if(resiHash.hasOwnProperty(i+1)) {
39328
+ // if(resiHash.hasOwnProperty(i+1)) {
39329
+ if(resiHash.hasOwnProperty(resi)) {
39252
39330
  let cFull = ic.giSeq[chnid][i];
39253
39331
  let c = cFull;
39254
39332
  if(cFull.length > 1) {
@@ -39273,12 +39351,12 @@ class AnnoDomain {
39273
39351
  if(ic.seqStartLen && ic.seqStartLen[chnid]) html2 += ic.showSeqCls.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
39274
39352
 
39275
39353
  if(me.cfg.blast_rep_id != chnid) { // regular
39276
- for(let i = 0, il = fromArray.length; i < il; ++i) {
39354
+ for(let i = 0, il = posFromArray.length; i < il; ++i) {
39277
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);
39278
- 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);
39279
39357
 
39280
39358
  html2 += '<div style="display:inline-block; width:' + emptyWidth + 'px;">&nbsp;</div>';
39281
- 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>';
39282
39360
  }
39283
39361
  }
39284
39362
  else { // with potential gaps
@@ -40812,7 +40890,7 @@ class Domain3d {
40812
40890
  if(!ic.posid2resid) ic.posid2resid = {};
40813
40891
 
40814
40892
  let substructItem = {};
40815
- let pos2resi = {};
40893
+ let pos2resi = {}; // 0-based
40816
40894
  for(let i = 0; i < residueArray.length; ++i) {
40817
40895
  let resid = residueArray[i];
40818
40896
 
@@ -40844,7 +40922,8 @@ class Domain3d {
40844
40922
 
40845
40923
  //resiArray.push(resi);
40846
40924
  resiArray.push(i+1);
40847
- pos2resi[i+1] = resi;
40925
+ // pos2resi[i+1] = resi;
40926
+ pos2resi[i] = resi;
40848
40927
 
40849
40928
  ic.posid2resid[atom.structure + '_' + atom.chain + '_' + (i+1).toString()] = resid;
40850
40929
  // let residNCBI = ic.resid2ncbi[resid];
@@ -40893,7 +40972,7 @@ class Domain3d {
40893
40972
  // get a list of Calpha-Calpha contacts
40894
40973
  ///list< pair< pair< int, let >, let > >
40895
40974
  let cts = this.c2b_AlphaContacts(seqLen, x0, y0, z0, dcut, resiArray);
40896
-
40975
+
40897
40976
  //
40898
40977
  // Produce a "map" of the SSEs, i.e. vec_sse[i] = 0 means residue i + 1
40899
40978
  // is in a loop, and vec_sse[i] = k means residue i + 1 belongs to SSE
@@ -41366,8 +41445,8 @@ class Domain3d {
41366
41445
  //ss: sstype ss_start ss_end x1 y1 z1 x2 y2 z2
41367
41446
  //sstype: 1 (helix), 2 (sheet)
41368
41447
  let sstype = (substruct[k].Sheet) ? 2 : 1;
41369
- let from = pos2resi[substruct[k].From];
41370
- 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];
41371
41450
 
41372
41451
  // 1-based residue numbers
41373
41452
  let fromPos = substruct[k].From;
@@ -63316,6 +63395,27 @@ class LoadScript {
63316
63395
  return nameArray;
63317
63396
  }
63318
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
+
63319
63419
  async execCommandsBase(start, end, steps, bFinalStep) { let ic = this.icn3d, me = ic.icn3dui;
63320
63420
  let thisClass = this;
63321
63421
  let i;
@@ -63495,7 +63595,10 @@ class LoadScript {
63495
63595
  await thisClass.applyCommandGraphinteraction(command);
63496
63596
  }
63497
63597
  else if(command.indexOf('cartoon 2d domain') == 0) {
63598
+ ic.bRender = true;
63599
+ thisClass.updateTransformation(steps);
63498
63600
  await thisClass.applyCommandCartoon2d(command);
63601
+ ic.bRender = false;
63499
63602
  }
63500
63603
  else if(command.indexOf('set half pae map') == 0) {
63501
63604
  await thisClass.applyCommandAfmap(command);
@@ -63510,7 +63613,10 @@ class LoadScript {
63510
63613
  let pos = command.lastIndexOf(' ');
63511
63614
  let type = command.substr(pos + 1);
63512
63615
 
63616
+ ic.bRender = true;
63617
+ thisClass.updateTransformation(steps);
63513
63618
  await ic.cartoon2dCls.draw2Dcartoon(type);
63619
+ ic.bRender = false;
63514
63620
  }
63515
63621
  else if(command.indexOf('add msa track') == 0) {
63516
63622
  //add msa track | chainid " + chainid + " | startpos " + startpos + " | type " + type + " | fastaList " + fastaList
@@ -63548,7 +63654,7 @@ class LoadScript {
63548
63654
  await ic.applyCommandCls.applyCommand(ic.commands[i]);
63549
63655
  }
63550
63656
  }
63551
-
63657
+
63552
63658
  //if(i === steps - 1) {
63553
63659
  if(i === steps || bFinalStep) {
63554
63660
  this.renderFinalStep(i);
@@ -68178,19 +68284,25 @@ class Dssp {
68178
68284
  }
68179
68285
 
68180
68286
  // 2b. remove strands with less than 3 residues except G strand
68287
+ let removeDomainidHash = {};
68181
68288
  for(let il = strandArray.length, i = il - 1; i >= 0; --i) {
68182
- let strandTmp = strandArray[i].strand.substr(0, 1);
68289
+ // let strandTmp = strandArray[i].strand.substr(0, 1);
68290
+ let strandTmp = strandArray[i].strand;
68183
68291
  if(strandTmp != 'G' && strandArray[i].endRefnum - strandArray[i].startRefnum + 1 < 3) { // remove the strand
68184
- if(strandTmp == 'B' || strandTmp == 'C' || strandTmp == 'E' || strandTmp == 'F') {
68185
- if(!me.bNode) console.log("Some of the Ig strands B, C, E, F are removed since they are too short...");
68186
- return false;
68187
- }
68188
-
68189
68292
  if(i != il - 1) { // modify
68190
68293
  strandArray[i + 1].loopResCnt += strandArray[i].loopResCnt + parseInt(strandArray[i].endResi) - parseInt(strandArray[i].startResi) + 1;
68191
68294
  }
68192
68295
 
68193
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
+ }
68194
68306
  }
68195
68307
  }
68196
68308
 
@@ -68380,6 +68492,14 @@ class Dssp {
68380
68492
  prevStrand = currStrand;
68381
68493
  prevStrandCnt = strandCnt - 1;
68382
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
+
68383
68503
  // assign the adjusted reference numbers
68384
68504
  ic.resid2refnum[residueid] = refnumLabel;
68385
68505
  ic.resid2domainid[residueid] = domainid;
@@ -71161,7 +71281,7 @@ class Cartoon2d {
71161
71281
  idStr = idStr.substr(0, idStr.indexOf('-'));
71162
71282
  }
71163
71283
  else {
71164
- idStr = idStr.substr(idStr.lastIndexOf('_') + 1);
71284
+ idStr = idStr; //idStr.substr(idStr.lastIndexOf('_') + 1);
71165
71285
  }
71166
71286
 
71167
71287
  return idStr;
@@ -71858,14 +71978,14 @@ class ResizeCanvas {
71858
71978
  !document.webkitFullscreenElement && !document.msFullscreenElement) {
71859
71979
  if(elem.requestFullscreen) {
71860
71980
  elem.requestFullscreen();
71861
- } else if(elem.mozRequestFullScreen) { /* Firefox */
71981
+ } else if(elem.mozRequestFullScreen) { // Firefox
71862
71982
  elem.mozRequestFullScreen();
71863
- } else if(elem.webkitRequestFullscreen) { /* Chrome, Safari and Opera */
71983
+ } else if(elem.webkitRequestFullscreen) { // Chrome, Safari and Opera
71864
71984
  elem.webkitRequestFullscreen();
71865
- } else if(elem.msRequestFullscreen) { /* IE/Edge */
71985
+ } else if(elem.msRequestFullscreen) { // IE/Edge
71866
71986
  elem.msRequestFullscreen();
71867
71987
  }
71868
- }
71988
+ }
71869
71989
  }
71870
71990
 
71871
71991
  //Rotate the structure in one of the directions: "left", "right", "up", and "down".
@@ -76556,7 +76676,7 @@ class iCn3DUI {
76556
76676
  //even when multiple iCn3D viewers are shown together.
76557
76677
  this.pre = this.cfg.divid + "_";
76558
76678
 
76559
- this.REVISION = '3.30.0';
76679
+ this.REVISION = '3.30.1';
76560
76680
 
76561
76681
  // In nodejs, iCn3D defines "window = {navigator: {}}"
76562
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": "3.30.0",
3
+ "version": "3.30.2",
4
4
  "main": "./icn3d.js",
5
5
  "exports": {
6
6
  ".": {