icn3d 3.47.3 → 3.48.0

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Files changed (4) hide show
  1. package/icn3d.js +179 -117
  2. package/icn3d.min.js +3 -3
  3. package/icn3d.module.js +179 -117
  4. package/package.json +1 -1
package/icn3d.module.js CHANGED
@@ -63994,20 +63994,20 @@ class SetDialog {
63994
63994
  group2tpl['IgC1'] = ['B2Microglobulin_7phrL_human_C1', 'CD3d_6jxrd_human_C1', 'CD3e_6jxrf_human_C1', 'FAB-LIGHT_5esv_C1-n2', 'FAB-HEAVY_5esv_C1-n2', 'GHR_1axiB_human_C1-n1', 'LAG3_7tzgD_human_C1-n2', 'MHCIa_7phrH_human_C1', 'Siglec3_5j0bB_human_C1-n2', 'TCRa_6jxrm_human_C1-n2', 'VTCN1_Q7Z7D3_human_C1-n2'];
63995
63995
  group2tpl['IgC2'] = ['CD2_1hnfA_human_C2-n2', 'CD3g_6jxrg_human_C2'];
63996
63996
  group2tpl['IgI'] = ['BTLA_2aw2A_human_Iset', 'Contactin1_3s97C_human_Iset-n2', 'JAM1_1nbqA_human_Iset-n2', 'Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Iset-n152'];
63997
- group2tpl['IgE'] = ['CoAtomerGamma1_1r4xA_human', 'Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'IsdA_2iteA_bacteria', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'TP34_2o6cA_bacteria', 'TP47_1o75A_bacteria'];
63997
+ //group2tpl['IgE'] = ['CoAtomerGamma1_1r4xA_human', 'Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'IsdA_2iteA_bacteria', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'TP34_2o6cA_bacteria', 'TP47_1o75A_bacteria'];
63998
63998
 
63999
63999
  group2tpl['IgFN3'] = ['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'];
64000
64000
 
64001
- group2tpl['IgFN3-like'] = ['ASF1A_2iijA_human', 'BArrestin1_4jqiA_rat_n1', 'C3_2qkiD_human_n1', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'RBPJ_6py8C_human_Unk-n1', 'TEAD1_3kysC_human'];
64001
+ //group2tpl['IgFN3-like'] = ['ASF1A_2iijA_human', 'BArrestin1_4jqiA_rat_n1', 'C3_2qkiD_human_n1', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'RBPJ_6py8C_human_Unk-n1', 'TEAD1_3kysC_human'];
64002
64002
 
64003
- group2tpl['Other Ig'] = ['CD19_6al5A_human-n1', 'CuZnSuperoxideDismutase_1hl5C_human', 'ECadherin_4zt1A_human_n2', 'LaminAC_1ifrA_human', 'ORF7a_1xakA_virus', 'RBPJ_6py8C_human_Unk-n2'];
64003
+ group2tpl['Other Ig'] = ['CD19_6al5A_human-n1', 'ECadherin_4zt1A_human_n2', 'LaminAC_1ifrA_human'];
64004
64004
 
64005
64005
  let tpl2strandsig = {};
64006
- tpl2strandsig['ASF1A_2iijA_human'] = "A A' B C C' E F G G+";
64006
+ //tpl2strandsig['ASF1A_2iijA_human'] = "A A' B C C' E F G G+";
64007
64007
  tpl2strandsig['B2Microglobulin_7phrL_human_C1'] = "A B C C' D E F G";
64008
- tpl2strandsig['BArrestin1_4jqiA_rat_n1'] = "A- A A' B C C' E F G";
64008
+ //tpl2strandsig['BArrestin1_4jqiA_rat_n1'] = "A- A A' B C C' E F G";
64009
64009
  tpl2strandsig['BTLA_2aw2A_human_Iset'] = "A A' B C C' D E F G";
64010
- tpl2strandsig['C3_2qkiD_human_n1'] = "A A' B C C' E F G";
64010
+ //tpl2strandsig['C3_2qkiD_human_n1'] = "A A' B C C' E F G";
64011
64011
  tpl2strandsig['CD19_6al5A_human-n1'] = "A' B C C' D E F G";
64012
64012
  tpl2strandsig['CD28_1yjdC_human_V'] = "A A' B C C' C'' D E F G";
64013
64013
  tpl2strandsig['CD2_1hnfA_human_C2-n2'] = "A B C C' E F G";
@@ -64016,12 +64016,12 @@ class SetDialog {
64016
64016
  tpl2strandsig['CD3e_6jxrf_human_C1'] = "A B C C' D E F G";
64017
64017
  tpl2strandsig['CD3g_6jxrg_human_C2'] = "A B C C' E F G G+";
64018
64018
  tpl2strandsig['CD8a_1cd8A_human_V'] = "A A' B C C' C'' D E F G";
64019
- tpl2strandsig['CoAtomerGamma1_1r4xA_human'] = "A- A B C D E F G";
64019
+ //tpl2strandsig['CoAtomerGamma1_1r4xA_human'] = "A- A B C D E F G";
64020
64020
  tpl2strandsig['Contactin1_2ee2A_human_FN3-n9'] = "A A' B C C' E F G";
64021
64021
  tpl2strandsig['Contactin1_3s97C_human_Iset-n2'] = "A A' B C D E F G";
64022
- tpl2strandsig['CuZnSuperoxideDismutase_1hl5C_human'] = "A- A B C C' E F G";
64022
+ //tpl2strandsig['CuZnSuperoxideDismutase_1hl5C_human'] = "A- A B C C' E F G";
64023
64023
  tpl2strandsig['ECadherin_4zt1A_human_n2'] = "A' B C D E F G";
64024
- tpl2strandsig['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = "A--- A-- A- A B C C' C'' D E F G";
64024
+ //tpl2strandsig['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = "A--- A-- A- A B C C' C'' D E F G";
64025
64025
  tpl2strandsig['FAB-HEAVY_5esv_C1-n2'] = "A B C D E F G";
64026
64026
  tpl2strandsig['FAB-HEAVY_5esv_V-n1'] = "A B C C' C'' D E F G";
64027
64027
  tpl2strandsig['FAB-LIGHT_5esv_C1-n2'] = "A B C C' D E F G";
@@ -64032,28 +64032,28 @@ class SetDialog {
64032
64032
  tpl2strandsig['IL6Rb_1bquB_human_FN3-n3'] = "A B C C' E F G";
64033
64033
  tpl2strandsig['InsulinR_8guyE_human_FN3-n1'] = "A B C C' E F G";
64034
64034
  tpl2strandsig['InsulinR_8guyE_human_FN3-n2'] = "A B C C' E F G";
64035
- tpl2strandsig['IsdA_2iteA_bacteria'] = "A- A B C C' D E F G";
64035
+ //tpl2strandsig['IsdA_2iteA_bacteria'] = "A- A B C C' D E F G";
64036
64036
  tpl2strandsig['JAM1_1nbqA_human_Iset-n2'] = "A A' B C C' D E F G";
64037
64037
  tpl2strandsig['LAG3_7tzgD_human_C1-n2'] = "A A' B C C' D E F G";
64038
64038
  tpl2strandsig['LAG3_7tzgD_human_V-n1'] = "A' B C C' D E F G";
64039
64039
  tpl2strandsig['LaminAC_1ifrA_human'] = "A- A B C C' E E+ F G";
64040
64040
  tpl2strandsig['MHCIa_7phrH_human_C1'] = "A B C C' D E F G";
64041
- tpl2strandsig['MPT63_1lmiA_bacteria'] = "A-- A- A BC C' E F G";
64042
- tpl2strandsig['NaCaExchanger_2fwuA_dog_n2'] = "A A' B C C' E F G";
64043
- tpl2strandsig['NaKATPaseTransporterBeta_2zxeB_spurdogshark']= "A A' B C D E F G";
64044
- tpl2strandsig['ORF7a_1xakA_virus'] = "A' B C D E F G";
64041
+ //tpl2strandsig['MPT63_1lmiA_bacteria'] = "A-- A- A BC C' E F G";
64042
+ //tpl2strandsig['NaCaExchanger_2fwuA_dog_n2'] = "A A' B C C' E F G";
64043
+ //tpl2strandsig['NaKATPaseTransporterBeta_2zxeB_spurdogshark']= "A A' B C D E F G";
64044
+ //tpl2strandsig['ORF7a_1xakA_virus'] = "A' B C D E F G";
64045
64045
  tpl2strandsig['PD1_4zqkB_human_V'] = "A A' B C C' D E F G";
64046
64046
  tpl2strandsig['PDL1_4z18B_human_V-n1'] = "A A' B C C' C'' D E F G";
64047
64047
  tpl2strandsig['Palladin_2dm3A_human_Iset-n1'] = "A A' B C C' D E F G";
64048
- tpl2strandsig['RBPJ_6py8C_human_Unk-n1'] = "A A' B C C' E F G";
64049
- tpl2strandsig['RBPJ_6py8C_human_Unk-n2'] = "A B C D E F G";
64048
+ //tpl2strandsig['RBPJ_6py8C_human_Unk-n1'] = "A A' B C C' E F G";
64049
+ //tpl2strandsig['RBPJ_6py8C_human_Unk-n2'] = "A B C D E F G";
64050
64050
  tpl2strandsig['Sidekick2_1wf5A_human_FN3-n7'] = "A B C C' E F G";
64051
64051
  tpl2strandsig['Siglec3_5j0bB_human_C1-n2'] = "A A' B C D E F G";
64052
64052
  tpl2strandsig['TCRa_6jxrm_human_C1-n2'] = "A B C D E F G";
64053
64053
  tpl2strandsig['TCRa_6jxrm_human_V-n1'] = "A A' B C C' C'' D E F G";
64054
- tpl2strandsig['TEAD1_3kysC_human'] = "A A+ A' B C C' E F G G+";
64055
- tpl2strandsig['TP34_2o6cA_bacteria'] = "A- A B C C' D E F G";
64056
- tpl2strandsig['TP47_1o75A_bacteria'] = "A B C C' D E F G";
64054
+ //tpl2strandsig['TEAD1_3kysC_human'] = "A A+ A' B C C' E F G G+";
64055
+ //tpl2strandsig['TP34_2o6cA_bacteria'] = "A- A B C C' D E F G";
64056
+ //tpl2strandsig['TP47_1o75A_bacteria'] = "A B C C' D E F G";
64057
64057
  tpl2strandsig['Titin_4uowM_human_Iset-n152'] = "A A' B C C' D E F G";
64058
64058
  tpl2strandsig['VISTA_6oilA_human_V'] = "A A' B C C' C'' D E F G G+";
64059
64059
  tpl2strandsig['VNAR_1t6vN_shark_V'] = "A A' B C C' D E F G";
@@ -75419,7 +75419,7 @@ class Scene {
75419
75419
  if(ic.opts['slab'] === 'yes') ic.cameraCls.setSlab();
75420
75420
 
75421
75421
  // if(!ic.bSetVrArButtons) { // call once
75422
- if(!me.cfg.imageonly) this.setVrArButtons();
75422
+ if(!me.cfg.imageonly && ( 'xr' in navigator )) this.setVrArButtons();
75423
75423
  // }
75424
75424
 
75425
75425
  // if((ic.bVr || ic.bAr) && !ic.bSetVrAr) { // call once
@@ -84874,7 +84874,7 @@ class ApplyMissingRes {
84874
84874
  line.serial1 = ic.missingResResid2serial[resid0 + ',' + resid1];
84875
84875
  line.serial2 = ic.missingResResid2serial[resid1 + ',' + resid0];
84876
84876
 
84877
- line.color = "#" + ic.atoms[line.serial1].color.getHexString();
84877
+ line.color = (ic.atoms[line.serial1]) ? "#" + ic.atoms[line.serial1].color.getHexString() : undefined;
84878
84878
 
84879
84879
  line.radius = ic.coilWidth;
84880
84880
 
@@ -100331,7 +100331,7 @@ class HlUpdate {
100331
100331
  if(ic.mmdbid_q !== undefined && ic.mmdbid_q === ic.mmdbid_t) {
100332
100332
  html2ddgm += ic.diagram2dCls.draw2Ddgm(ic.interactionData2, ic.mmdbidArray[0].toUpperCase(), 1, true);
100333
100333
  }
100334
- else {
100334
+ else if(ic.mmdbidArray.length > 1) {
100335
100335
  html2ddgm += ic.diagram2dCls.draw2Ddgm(ic.interactionData2, ic.mmdbidArray[1].toUpperCase(), 1, true);
100336
100336
  }
100337
100337
  html2ddgm += ic.diagram2dCls.set2DdgmNote(true);
@@ -104613,16 +104613,31 @@ class ChainalignParser {
104613
104613
 
104614
104614
  // dynamically align pairs in all chainids
104615
104615
  // the resrange from VASTSrv or VAST search uses NCBI residue numbers!!!
104616
- let atomSet_t = (me.cfg.resrange) ? ic.realignParserCls.getSeqCoorResid([resRangeArray[0]], chainidArray[0], true).hAtoms : ic.chains[chainidArray[0]];
104616
+ let atomSet_t;
104617
+ if(me.cfg.resrange) {
104618
+ let result = ic.realignParserCls.getSeqCoorResid([resRangeArray[0]], chainidArray[0], true);
104619
+ atomSet_t = result.hAtoms;
104620
+ }
104621
+ else {
104622
+ atomSet_t = ic.chains[chainidArray[0]];
104623
+ }
104624
+
104617
104625
  for(let index = 1, indexl = chainidArray.length; index < indexl; ++index) {
104618
- let atomSet_q = (me.cfg.resrange) ? ic.realignParserCls.getSeqCoorResid([resRangeArray[index]], chainidArray[index], true).hAtoms : ic.chains[chainidArray[index]];
104626
+ let atomSet_q;
104627
+ if(me.cfg.resrange) {
104628
+ let result = ic.realignParserCls.getSeqCoorResid([resRangeArray[index]], chainidArray[index], true);
104629
+ atomSet_q = result.hAtoms;
104630
+ }
104631
+ else {
104632
+ atomSet_q = ic.chains[chainidArray[index]];
104633
+ }
104619
104634
  // end of new version to be done for VASTsrv ==============
104620
104635
 
104621
104636
  let alignAjax;
104622
104637
  if(me.cfg.aligntool != 'tmalign') {
104623
104638
  let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(atomSet_q);
104624
104639
  let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(atomSet_t);
104625
-
104640
+
104626
104641
  let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
104627
104642
  alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
104628
104643
  }
@@ -104658,6 +104673,7 @@ class ChainalignParser {
104658
104673
  //let bTargetTransformed = (ic.qt_start_end[0]) ? true : false;
104659
104674
 
104660
104675
  // modify the previous trans and rotation matrix
104676
+ let bAligned = false;
104661
104677
  for(let i = 0, il = dataArray.length; i < il; ++i) {
104662
104678
  // let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
104663
104679
  let align = dataArray[i].value;//[0];
@@ -104673,7 +104689,7 @@ class ChainalignParser {
104673
104689
 
104674
104690
  me.htmlCls.clickMenuCls.setLogCmd("Align " + mmdbid_t + " with " + mmdbid_q, false);
104675
104691
 
104676
- this.processAlign(align, index, queryData, bEqualMmdbid, bEqualChain);
104692
+ bAligned =await this.processAlign(align, index, queryData, bEqualMmdbid, bEqualChain, undefined);
104677
104693
  }
104678
104694
 
104679
104695
  // do not transform the target
@@ -104681,28 +104697,34 @@ class ChainalignParser {
104681
104697
  // this.transformStructure(mmdbid_t, indexArray[0], 'target');
104682
104698
  //}
104683
104699
 
104684
- // transform the rest
104685
- for(let i = 0, il = dataArray.length; i < il; ++i) {
104686
- let mmdbid_q = struArray[i];
104687
- let index = indexArray[i];
104688
- this.transformStructure(mmdbid_q, index, 'query');
104689
- }
104700
+ if(bAligned) {
104701
+ // transform the rest
104702
+ for(let i = 0, il = dataArray.length; i < il; ++i) {
104703
+ let mmdbid_q = struArray[i];
104704
+ let index = indexArray[i];
104705
+ this.transformStructure(mmdbid_q, index, 'query');
104706
+ }
104690
104707
 
104691
- let hAtomsAll = {};
104708
+ let hAtomsAll = {};
104692
104709
 
104693
- if(ic.bFullUi && ic.q_rotation !== undefined && !me.cfg.resnum && !me.cfg.resdef) {
104694
- // set multiple sequence alignment from ic.qt_start_end
104695
- hAtomsAll = this.setMsa(chainidArray);
104696
- }
104710
+ if(ic.bFullUi && ic.q_rotation !== undefined && !me.cfg.resnum && !me.cfg.resdef) {
104711
+ // set multiple sequence alignment from ic.qt_start_end
104712
+ hAtomsAll = this.setMsa(chainidArray);
104713
+ }
104697
104714
 
104698
- // highlight all aligned atoms
104699
- //ic.hAtoms = me.hashUtilsCls.cloneHash(hAtomsTmp);
104700
- ic.hAtoms = me.hashUtilsCls.cloneHash(hAtomsAll);
104715
+ // highlight all aligned atoms
104716
+ //ic.hAtoms = me.hashUtilsCls.cloneHash(hAtomsTmp);
104717
+ ic.hAtoms = me.hashUtilsCls.cloneHash(hAtomsAll);
104701
104718
 
104702
- ic.transformCls.zoominSelection();
104719
+ ic.transformCls.zoominSelection();
104703
104720
 
104704
- // do the rest
104705
- await this.downloadChainalignmentPart3(chainresiCalphaHash2, chainidArray, ic.hAtoms);
104721
+ // do the rest
104722
+ await this.downloadChainalignmentPart3(chainresiCalphaHash2, chainidArray, ic.hAtoms);
104723
+ }
104724
+ else {
104725
+ me.cfg.aligntool = 'tmalign';
104726
+ await ic.chainalignParserCls.downloadChainalignment(me.cfg.chainalign);
104727
+ }
104706
104728
  }
104707
104729
 
104708
104730
  setMsa(chainidArray, bVastplus, bRealign) { let ic = this.icn3d, me = ic.icn3dui;
@@ -104773,7 +104795,7 @@ class ChainalignParser {
104773
104795
 
104774
104796
  let bNoAlert = true;
104775
104797
 
104776
- let bAligned = this.processAlign(align, i, queryData, bEqualMmdbid, bEqualChain, bNoAlert);
104798
+ let bAligned = await this.processAlign(align, i, queryData, bEqualMmdbid, bEqualChain, bNoAlert);
104777
104799
 
104778
104800
  if(bAligned) {
104779
104801
  bFoundAlignment = true;
@@ -105265,7 +105287,7 @@ class ChainalignParser {
105265
105287
 
105266
105288
  me.htmlCls.clickMenuCls.setLogCmd("Align " + mmdbid_t + " with " + mmdbid_q, false);
105267
105289
 
105268
- this.processAlign(align, index-1, queryData, bEqualMmdbid, bEqualChain);
105290
+ await this.processAlign(align, index-1, queryData, bEqualMmdbid, bEqualChain, undefined);
105269
105291
  }
105270
105292
  }
105271
105293
  }
@@ -105275,13 +105297,13 @@ class ChainalignParser {
105275
105297
  await this.loadOpmDataForChainalign(targetData, queryDataArray, chainidArray, ic.mmdbidArray);
105276
105298
  }
105277
105299
 
105278
- processAlign(align, index, queryData, bEqualMmdbid, bEqualChain, bNoAlert) { let ic = this.icn3d, me = ic.icn3dui;
105300
+ async processAlign(align, index, queryData, bEqualMmdbid, bEqualChain, bNoAlert) { let ic = this.icn3d, me = ic.icn3dui;
105279
105301
  let bAligned = false;
105280
105302
 
105281
- if((!align || align.length == 0) && !bNoAlert) {
105282
- let serverName = (me.cfg.aligntool == 'tmalign') ? 'TM-align' : 'VAST';
105283
-
105284
- if(ic.bRender) var aaa = 1; //alert("These chains can not be aligned by " + serverName + ".");
105303
+ if((align === "error" || align === undefined || align.length == 0) && !bNoAlert) {
105304
+ // let serverName = (me.cfg.aligntool == 'tmalign') ? 'TM-align' : 'VAST';
105305
+
105306
+ // if(ic.bRender) var aaa = 1; //alert("These chains can not be aligned by " + serverName + ".");
105285
105307
  return bAligned;
105286
105308
  }
105287
105309
 
@@ -105430,7 +105452,6 @@ class ChainalignParser {
105430
105452
  let structArrayTmp = idlist.split(',');
105431
105453
 
105432
105454
  let structArray = [];
105433
-
105434
105455
  // only when bNoDuplicate is undefined/false, it's allowed to load multiple copies of the same structure
105435
105456
  if(!bNoDuplicate) {
105436
105457
  structArray = this.addPostfixForStructureids(structArrayTmp);
@@ -105443,7 +105464,7 @@ class ChainalignParser {
105443
105464
  if(!ic.structures.hasOwnProperty(id)) structArray.push(structArrayTmp[i]);
105444
105465
  }
105445
105466
  }
105446
-
105467
+
105447
105468
  if(structArray.length == 0) return;
105448
105469
 
105449
105470
  ic.structArray = ic.structArray.concat(structArray);
@@ -105543,6 +105564,8 @@ class ChainalignParser {
105543
105564
  let bNoSeqalign = true;
105544
105565
  let pdbid = structArray[i];
105545
105566
 
105567
+ if(queryDataArray[i].pdbId) queryDataArray[i].pdbId = pdbid;
105568
+
105546
105569
  //hAtomsTmp contains all atoms
105547
105570
  await ic.mmdbParserCls.parseMmdbData(queryDataArray[i], targetOrQuery, undefined, undefined, bLastQuery, bNoSeqalign, pdbid);
105548
105571
  }
@@ -107119,7 +107142,7 @@ class MmdbParser {
107119
107142
  return;
107120
107143
  }
107121
107144
 
107122
- if(Object.keys(data.atoms).length == 0) { // for large structures such as 3J3Q
107145
+ if(!data.atoms || Object.keys(data.atoms).length == 0) { // for large structures such as 3J3Q
107123
107146
  // use mmtfid
107124
107147
  let pdbid = data.pdbId;
107125
107148
  await ic.bcifParserCls.downloadBcif(pdbid);
@@ -107129,6 +107152,7 @@ class MmdbParser {
107129
107152
 
107130
107153
  let bCalphaOnly = me.utilsCls.isCalphaPhosOnly(data.atoms); //, 'CA');
107131
107154
 
107155
+ //if(!data.pdbId) data.pdbId = mmdbid;
107132
107156
  if(bCalphaOnly || data.atomCount <= ic.maxatomcnt) {
107133
107157
  await this.parseMmdbData(data);
107134
107158
  }
@@ -107290,8 +107314,18 @@ class MmdbParser {
107290
107314
  async parseMmdbData(data, type, chainid, chainIndex, bLastQuery, bNoTransformNoSeqalign, pdbidIn) { let ic = this.icn3d, me = ic.icn3dui;
107291
107315
  let hAtoms;
107292
107316
  let pdbid = (data.pdbId !== undefined) ? data.pdbId : data.mmdbId;
107317
+ if(!pdbid && chainid) {
107318
+ pdbid = chainid.substr(0, chainid.lastIndexOf('_'));
107319
+ }
107320
+
107293
107321
  if(pdbidIn) pdbid = pdbidIn;
107294
107322
 
107323
+ // if(!data.atoms || Object.keys(data.atoms).length == 0) { // for large structures such as 3J3Q
107324
+ // ic.bRender = false;
107325
+ // await ic.bcifParserCls.downloadBcif(pdbid);
107326
+ // return;
107327
+ // }
107328
+
107295
107329
  this.parseMmdbDataPart1(data, type);
107296
107330
 
107297
107331
  if(type === undefined) { // default mmdbid input
@@ -108958,7 +108992,7 @@ class PdbParser {
108958
108992
  }
108959
108993
 
108960
108994
  // if(!ic.bSecondaryStructure && Object.keys(ic.proteins).length > 0) {
108961
- if((!ic.bSecondaryStructure || bCalcSecondary) && Object.keys(ic.proteins).length > 0 && !bNoDssp) {
108995
+ if((!ic.bSecondaryStructure || bCalcSecondary) && Object.keys(ic.proteins).length > 0 && !bNoDssp) {
108962
108996
  await this.applyCommandDssp(bAppend);
108963
108997
  }
108964
108998
  else {
@@ -110933,8 +110967,7 @@ class RealignParser {
110933
110967
  // If rmsd from vastsrv is too large, realign the chains
110934
110968
  //if(me.cfg.chainalign && !me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5) {
110935
110969
  // redo algnment only for VAST serv page
110936
- if(!me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5 && me.cfg.chainalign) {
110937
- console.log("RMSD from VAST is larger than 5. Realign the chains with TM-align.");
110970
+ if(!me.cfg.usepdbnum && (me.cfg.resdef || me.cfg.resrange) && rmsd > 5 && me.cfg.chainalign) {
110938
110971
  //let nameArray = me.cfg.chainalign.split(',');
110939
110972
  let nameArray = Object.keys(chainidHash);
110940
110973
  if(nameArray.length > 0) {
@@ -111186,15 +111219,30 @@ let resRangeArray = (me.cfg.resrange) ? decodeURIComponent(me.cfg.resrange).spli
111186
111219
  if(bVastsearch && me.cfg.resrange) {
111187
111220
  let resRangeArray = decodeURIComponent(me.cfg.resrange).split(' | ');
111188
111221
 
111189
- let atomSet_t = ic.realignParserCls.getSeqCoorResid([resRangeArray[0]], ic.chainidArray[0], true).hAtoms;
111222
+ let atomSet_t;
111223
+ if(me.cfg.resrange) {
111224
+ let result = ic.realignParserCls.getSeqCoorResid([resRangeArray[0]], ic.chainidArray[0], true);
111225
+ atomSet_t = result.hAtoms;
111226
+ }
111227
+ else {
111228
+ atomSet_t = ic.chains[ic.chainidArray[0]];
111229
+ }
111230
+
111190
111231
  for(let index = 1, indexl = ic.chainidArray.length; index < indexl; ++index) {
111191
- let atomSet_q = ic.realignParserCls.getSeqCoorResid([resRangeArray[index]], ic.chainidArray[index], true).hAtoms;
111232
+ let atomSet_q;
111233
+ if(me.cfg.resrange) {
111234
+ let result = ic.realignParserCls.getSeqCoorResid([resRangeArray[index]], ic.chainidArray[index], true);
111235
+ atomSet_q = result.hAtoms;
111236
+ }
111237
+ else {
111238
+ atomSet_q = ic.chains[ic.chainidArray[index]];
111239
+ }
111192
111240
 
111193
111241
  let alignAjax;
111194
111242
  if(me.cfg.aligntool != 'tmalign') {
111195
111243
  let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(atomSet_q);
111196
111244
  let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(atomSet_t);
111197
-
111245
+
111198
111246
  let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
111199
111247
  alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
111200
111248
  }
@@ -111255,9 +111303,7 @@ let resRangeArray = (me.cfg.resrange) ? decodeURIComponent(me.cfg.resrange).spli
111255
111303
  let alignAjax;
111256
111304
  if(me.cfg.aligntool != 'tmalign') {
111257
111305
  let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(struct2domain[struct2][chainid2]);
111258
- console.log("@@@ realign " + struct1 + " " + chainid1 + " and " + struct2 + " " + chainid2);
111259
- console.log("@@@ jsonStr_q " + jsonStr_q);
111260
- console.log("@@@ jsonStr_t " + jsonStr_t);
111306
+
111261
111307
  let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
111262
111308
  alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
111263
111309
  }
@@ -111327,7 +111373,7 @@ console.log("@@@ jsonStr_t " + jsonStr_t);
111327
111373
 
111328
111374
  if(me.cfg.aligntool != 'tmalign') {
111329
111375
  let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(chainid2domain[chainid2]);
111330
-
111376
+
111331
111377
  let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
111332
111378
  alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
111333
111379
  }
@@ -111587,6 +111633,8 @@ console.log("@@@ jsonStr_t " + jsonStr_t);
111587
111633
  let hAtoms = {};
111588
111634
 
111589
111635
  for(let j = 0, jl = resiArray.length; j < jl; ++j) {
111636
+ if(!resiArray[j]) continue;
111637
+
111590
111638
  if(resiArray[j].indexOf('-') != -1) {
111591
111639
  let startEnd = resiArray[j].split('-');
111592
111640
  for(let k = parseInt(startEnd[0]); k <= parseInt(startEnd[1]); ++k) {
@@ -116757,7 +116805,8 @@ class LoadPDB {
116757
116805
  }
116758
116806
 
116759
116807
  isSecondary(resid, residArray, bNMR, bNonFull) { let ic = this.icn3d; ic.icn3dui;
116760
- if(bNonFull) return false;
116808
+ // still need to get the secondary info
116809
+ //if(bNonFull) return false;
116761
116810
 
116762
116811
  if(!bNMR) {
116763
116812
  return $.inArray(resid, residArray) != -1;
@@ -124663,29 +124712,29 @@ class Dssp {
124663
124712
 
124664
124713
  setRefPdbs() { let ic = this.icn3d; ic.icn3dui;
124665
124714
  // round 1, 16 templates
124666
- ic.refpdbArray = ['1InsulinR_8guyE_human_FN3-n1', '1Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', '1CoAtomerGamma1_1r4xA_human', '1C3_2qkiD_human_n1', '1CuZnSuperoxideDismutase_1hl5C_human', '1ASF1A_2iijA_human', '1FAB-LIGHT_5esv_C1-n2', '1CD2_1hnfA_human_C2-n2', '1NaCaExchanger_2fwuA_dog_n2', '1NaKATPaseTransporterBeta_2zxeB_spurdogshark', '1FAB-HEAVY_5esv_V-n1', '1PDL1_4z18B_human_V-n1', '1BTLA_2aw2A_human_Iset', '1LaminAC_1ifrA_human', '1CD3g_6jxrg_human_C2', '1CD28_1yjdC_human_V', '1CD19_6al5A_human-n1'];
124715
+ ic.refpdbArray = ['1InsulinR_8guyE_human_FN3-n1', '1ICOS_6x4gA_human_V', '1FAB-LIGHT_5esv_C1-n2', '1CD2_1hnfA_human_C2-n2', '1ECadherin_4zt1A_human_n2', '1FAB-HEAVY_5esv_V-n1', '1PDL1_4z18B_human_V-n1', '1BTLA_2aw2A_human_Iset', '1LaminAC_1ifrA_human', '1CD3g_6jxrg_human_C2', '1CD28_1yjdC_human_V', '1CD19_6al5A_human-n1'];
124667
124716
 
124668
124717
  // round 2
124669
124718
  ic.refpdbHash = {};
124670
124719
  ic.refpdbHash['1InsulinR_8guyE_human_FN3-n1'] = ['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'];
124671
- ic.refpdbHash['1Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = ['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'ICOS_6x4gA_human_V'];
124672
- ic.refpdbHash['1CoAtomerGamma1_1r4xA_human'] = ['CoAtomerGamma1_1r4xA_human', 'TP34_2o6cA_bacteria'];
124673
- ic.refpdbHash['1C3_2qkiD_human_n1'] = ['C3_2qkiD_human_n1', 'BArrestin1_4jqiA_rat_n1', 'RBPJ_6py8C_human_Unk-n1'];
124674
- ic.refpdbHash['1CuZnSuperoxideDismutase_1hl5C_human'] = ['CuZnSuperoxideDismutase_1hl5C_human', 'TEAD1_3kysC_human'];
124675
- ic.refpdbHash['1ASF1A_2iijA_human'] = ['ASF1A_2iijA_human', 'RBPJ_6py8C_human_Unk-n2', 'TP47_1o75A_bacteria'];
124720
+ ic.refpdbHash['1ICOS_6x4gA_human_V'] = ['ICOS_6x4gA_human_V'];
124721
+ //ic.refpdbHash['1CoAtomerGamma1_1r4xA_human'] = ['CoAtomerGamma1_1r4xA_human', 'TP34_2o6cA_bacteria'];
124722
+ //ic.refpdbHash['1C3_2qkiD_human_n1'] = ['C3_2qkiD_human_n1', 'RBPJ_6py8C_human_Unk-n1'];
124723
+ //ic.refpdbHash['1CuZnSuperoxideDismutase_1hl5C_human'] = ['TEAD1_3kysC_human'];
124724
+ //ic.refpdbHash['1ASF1A_2iijA_human'] = ['ASF1A_2iijA_human', 'TP47_1o75A_bacteria'];
124676
124725
  ic.refpdbHash['1FAB-LIGHT_5esv_C1-n2'] = ['FAB-LIGHT_5esv_C1-n2', 'GHR_1axiB_human_C1-n1', 'VTCN1_Q7Z7D3_human_C1-n2', 'B2Microglobulin_7phrL_human_C1', 'FAB-HEAVY_5esv_C1-n2', 'MHCIa_7phrH_human_C1'];
124677
124726
  ic.refpdbHash['1CD2_1hnfA_human_C2-n2'] = ['CD2_1hnfA_human_C2-n2', 'Siglec3_5j0bB_human_C1-n2'];
124678
- ic.refpdbHash['1NaCaExchanger_2fwuA_dog_n2'] = ['NaCaExchanger_2fwuA_dog_n2', 'ORF7a_1xakA_virus', 'ECadherin_4zt1A_human_n2'];
124679
- ic.refpdbHash['1NaKATPaseTransporterBeta_2zxeB_spurdogshark'] = ['NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
124727
+ ic.refpdbHash['1ECadherin_4zt1A_human_n2'] = ['ECadherin_4zt1A_human_n2'];
124728
+ //ic.refpdbHash['1NaKATPaseTransporterBeta_2zxeB_spurdogshark'] = ['NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
124680
124729
  ic.refpdbHash['1FAB-HEAVY_5esv_V-n1'] = ['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'];
124681
124730
  ic.refpdbHash['1PDL1_4z18B_human_V-n1'] = ['PDL1_4z18B_human_V-n1', 'CD2_1hnfA_human_V-n1', 'LAG3_7tzgD_human_V-n1'];
124682
124731
  ic.refpdbHash['1BTLA_2aw2A_human_Iset'] = ['BTLA_2aw2A_human_Iset', 'Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Iset-n152', 'LAG3_7tzgD_human_C1-n2', 'JAM1_1nbqA_human_Iset-n2', 'Contactin1_3s97C_human_Iset-n2'];
124683
124732
  ic.refpdbHash['1LaminAC_1ifrA_human'] = ['LaminAC_1ifrA_human', 'CD3d_6jxrd_human_C1'];
124684
- ic.refpdbHash['1CD3g_6jxrg_human_C2'] = ['CD3g_6jxrg_human_C2', 'TCRa_6jxrm_human_C1-n2', 'IsdA_2iteA_bacteria'];
124685
- ic.refpdbHash['1CD28_1yjdC_human_V'] = ['CD28_1yjdC_human_V', 'MPT63_1lmiA_bacteria', 'CD3e_6jxrf_human_C1'];
124733
+ ic.refpdbHash['1CD3g_6jxrg_human_C2'] = ['CD3g_6jxrg_human_C2', 'TCRa_6jxrm_human_C1-n2'];
124734
+ ic.refpdbHash['1CD28_1yjdC_human_V'] = ['CD28_1yjdC_human_V', 'CD3e_6jxrf_human_C1'];
124686
124735
  ic.refpdbHash['1CD19_6al5A_human-n1'] = ['CD19_6al5A_human-n1'];
124687
124736
 
124688
- 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-n1', 'CD28_1yjdC_human_V', 'CD2_1hnfA_human_C2-n2', 'CD2_1hnfA_human_V-n1', 'CD3d_6jxrd_human_C1', 'CD3e_6jxrf_human_C1', 'CD3g_6jxrg_human_C2', 'CD8a_1cd8A_human_V', 'CoAtomerGamma1_1r4xA_human', 'Contactin1_2ee2A_human_FN3-n9', 'Contactin1_3s97C_human_Iset-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_C1-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_Iset-n2', 'LAG3_7tzgD_human_C1-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_C1-n2', 'TCRa_6jxrm_human_C1-n2', 'TCRa_6jxrm_human_V-n1', 'TEAD1_3kysC_human', 'TP34_2o6cA_bacteria', 'TP47_1o75A_bacteria', 'Titin_4uowM_human_Iset-n152', 'VISTA_6oilA_human_V', 'VNAR_1t6vN_shark_V', 'VTCN1_Q7Z7D3_human_C1-n2'];
124737
+ ic.refpdbHash['all_templates'] = ['B2Microglobulin_7phrL_human_C1', 'BTLA_2aw2A_human_Iset', 'CD19_6al5A_human-n1', 'CD28_1yjdC_human_V', 'CD2_1hnfA_human_C2-n2', 'CD2_1hnfA_human_V-n1', 'CD3d_6jxrd_human_C1', 'CD3e_6jxrf_human_C1', 'CD3g_6jxrg_human_C2', 'CD8a_1cd8A_human_V', 'Contactin1_2ee2A_human_FN3-n9', 'Contactin1_3s97C_human_Iset-n2', 'ECadherin_4zt1A_human_n2', 'FAB-HEAVY_5esv_C1-n2', 'FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_C1-n2', 'FAB-LIGHT_5esv_V-n1', 'GHR_1axiB_human_C1-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', 'JAM1_1nbqA_human_Iset-n2', 'LAG3_7tzgD_human_C1-n2', 'LAG3_7tzgD_human_V-n1', 'LaminAC_1ifrA_human', 'MHCIa_7phrH_human_C1', 'PD1_4zqkB_human_V', 'PDL1_4z18B_human_V-n1', 'Palladin_2dm3A_human_Iset-n1', 'Sidekick2_1wf5A_human_FN3-n7', 'Siglec3_5j0bB_human_C1-n2', 'TCRa_6jxrm_human_C1-n2', 'TCRa_6jxrm_human_V-n1', 'Titin_4uowM_human_Iset-n152', 'VISTA_6oilA_human_V', 'VNAR_1t6vN_shark_V', 'VTCN1_Q7Z7D3_human_C1-n2'];
124689
124738
 
124690
124739
  // use known ref structure
124691
124740
  ic.refpdbHash['5ESV_C'] = ['FAB-HEAVY_5esv_V-n1', 'FAB-HEAVY_5esv_C1-n2'];
@@ -124694,36 +124743,36 @@ class Dssp {
124694
124743
  ic.refpdbHash['6JXR_m'] = ['TCRa_6jxrm_human_V-n1', 'TCRa_6jxrm_human_C1-n2'];
124695
124744
  ic.refpdbHash['1HNF_A'] = ['CD2_1hnfA_human_V-n1', 'CD2_1hnfA_human_C2-n2'];
124696
124745
  ic.refpdbHash['7TZG_D'] = ['LAG3_7tzgD_human_V-n1', 'LAG3_7tzgD_human_C1-n2'];
124697
- ic.refpdbHash['6PY8_C'] = ['RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2'];
124746
+ //ic.refpdbHash['6PY8_C'] = ['RBPJ_6py8C_human_Unk-n1'];
124698
124747
  ic.refpdbHash['1BQU_B'] = ['IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3'];
124699
124748
 
124700
- ic.refpdbHash['1R4X_A'] = ['CoAtomerGamma1_1r4xA_human'];
124749
+ //ic.refpdbHash['1R4X_A'] = ['CoAtomerGamma1_1r4xA_human'];
124701
124750
  ic.refpdbHash['6OIL_A'] = ['VISTA_6oilA_human_V'];
124702
- ic.refpdbHash['2ZXE_B'] = ['NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
124703
- ic.refpdbHash['1I8A_A'] = ['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'];
124704
- ic.refpdbHash['2FWU_A'] = ['NaCaExchanger_2fwuA_dog_n2'];
124705
- ic.refpdbHash['4JQI_A'] = ['BArrestin1_4jqiA_rat_n1'];
124751
+ //ic.refpdbHash['2ZXE_B'] = ['NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
124752
+ //ic.refpdbHash['1I8A_A'] = ['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'];
124753
+ //ic.refpdbHash['2FWU_A'] = ['NaCaExchanger_2fwuA_dog_n2'];
124754
+ //ic.refpdbHash['4JQI_A'] = ['BArrestin1_4jqiA_rat_n1'];
124706
124755
  ic.refpdbHash['1NBQ_A'] = ['JAM1_1nbqA_human_Iset-n2'];
124707
- ic.refpdbHash['1O75_A'] = ['TP47_1o75A_bacteria'];
124756
+ //ic.refpdbHash['1O75_A'] = ['TP47_1o75A_bacteria'];
124708
124757
  ic.refpdbHash['7PHR_H'] = ['MHCIa_7phrH_human_C1'];
124709
- ic.refpdbHash['2IIJ_A'] = ['ASF1A_2iijA_human'];
124758
+ //ic.refpdbHash['2IIJ_A'] = ['ASF1A_2iijA_human'];
124710
124759
  ic.refpdbHash['4Z18_B'] = ['PDL1_4z18B_human_V-n1'];
124711
124760
  ic.refpdbHash['1T6V_N'] = ['VNAR_1t6vN_shark_V'];
124712
- ic.refpdbHash['2O6C_A'] = ['TP34_2o6cA_bacteria'];
124713
- ic.refpdbHash['3KYS_C'] = ['TEAD1_3kysC_human'];
124761
+ //ic.refpdbHash['2O6C_A'] = ['TP34_2o6cA_bacteria'];
124762
+ //ic.refpdbHash['3KYS_C'] = ['TEAD1_3kysC_human'];
124714
124763
  ic.refpdbHash['7PHR_L'] = ['B2Microglobulin_7phrL_human_C1'];
124715
124764
  ic.refpdbHash['2AW2_A'] = ['BTLA_2aw2A_human_Iset'];
124716
- ic.refpdbHash['1HL5_C'] = ['CuZnSuperoxideDismutase_1hl5C_human'];
124765
+ //ic.refpdbHash['1HL5_C'] = ['CuZnSuperoxideDismutase_1hl5C_human'];
124717
124766
  ic.refpdbHash['1WF5_A'] = ['Sidekick2_1wf5A_human_FN3-n7'];
124718
124767
  ic.refpdbHash['5J0B_B'] = ['Siglec3_5j0bB_human_C1-n2'];
124719
124768
  ic.refpdbHash['1IFR_A'] = ['LaminAC_1ifrA_human'];
124720
124769
  ic.refpdbHash['Q7Z7D3_A'] = ['VTCN1_Q7Z7D3_human_C1-n2'];
124721
124770
  ic.refpdbHash['4ZQK_B'] = ['PD1_4zqkB_human_V'];
124722
124771
  ic.refpdbHash['2DM3_A'] = ['Palladin_2dm3A_human_Iset-n1'];
124723
- ic.refpdbHash['2ITE_A'] = ['IsdA_2iteA_bacteria'];
124724
- ic.refpdbHash['1XAK_A'] = ['ORF7a_1xakA_virus'];
124772
+ //ic.refpdbHash['2ITE_A'] = ['IsdA_2iteA_bacteria'];
124773
+ //ic.refpdbHash['1XAK_A'] = ['ORF7a_1xakA_virus'];
124725
124774
  ic.refpdbHash['4ZT1_A'] = ['ECadherin_4zt1A_human_n2'];
124726
- ic.refpdbHash['1LMI_A'] = ['MPT63_1lmiA_bacteria'];
124775
+ //ic.refpdbHash['1LMI_A'] = ['MPT63_1lmiA_bacteria'];
124727
124776
  ic.refpdbHash['1CD8_A'] = ['CD8a_1cd8A_human_V'];
124728
124777
  ic.refpdbHash['3S97_C'] = ['Contactin1_3s97C_human_Iset-n2'];
124729
124778
  ic.refpdbHash['1AXI_B'] = ['GHR_1axiB_human_C1-n1'];
@@ -124731,7 +124780,7 @@ class Dssp {
124731
124780
  ic.refpdbHash['2EE2_A'] = ['Contactin1_2ee2A_human_FN3-n9'];
124732
124781
  ic.refpdbHash['4UOW_M'] = ['Titin_4uowM_human_Iset-n152'];
124733
124782
  ic.refpdbHash['6A15_A'] = ['CD19_6al5A_human-n1'];
124734
- ic.refpdbHash['2QKI_D'] = ['C3_2qkiD_human_n1'];
124783
+ //ic.refpdbHash['2QKI_D'] = ['C3_2qkiD_human_n1'];
124735
124784
  ic.refpdbHash['1YJD_C'] = ['CD28_1yjdC_human_V'];
124736
124785
  ic.refpdbHash['6JXR_d'] = ['CD3d_6jxrd_human_C1'];
124737
124786
  ic.refpdbHash['6JXR_f'] = ['CD3e_6jxrf_human_C1'];
@@ -124740,11 +124789,11 @@ class Dssp {
124740
124789
  // assign Ig types
124741
124790
  ic.ref2igtype = {};
124742
124791
 
124743
- ic.ref2igtype['ASF1A_2iijA_human'] = 'IgFN3-like';
124792
+ //ic.ref2igtype['ASF1A_2iijA_human'] = 'IgFN3-like';
124744
124793
  ic.ref2igtype['B2Microglobulin_7phrL_human_C1'] = 'IgC1';
124745
- ic.ref2igtype['BArrestin1_4jqiA_rat_n1'] = 'IgFN3-like';
124794
+ //ic.ref2igtype['BArrestin1_4jqiA_rat_n1'] = 'IgFN3-like';
124746
124795
  ic.ref2igtype['BTLA_2aw2A_human_Iset'] = 'IgI';
124747
- ic.ref2igtype['C3_2qkiD_human_n1'] = 'IgFN3-like';
124796
+ //ic.ref2igtype['C3_2qkiD_human_n1'] = 'IgFN3-like';
124748
124797
  ic.ref2igtype['CD19_6al5A_human-n1'] = 'CD19';
124749
124798
  ic.ref2igtype['CD28_1yjdC_human_V'] = 'IgV';
124750
124799
  ic.ref2igtype['CD2_1hnfA_human_C2-n2'] = 'IgC2';
@@ -124753,12 +124802,12 @@ class Dssp {
124753
124802
  ic.ref2igtype['CD3e_6jxrf_human_C1'] = 'IgC1';
124754
124803
  ic.ref2igtype['CD3g_6jxrg_human_C2'] = 'IgC2';
124755
124804
  ic.ref2igtype['CD8a_1cd8A_human_V'] = 'IgV';
124756
- ic.ref2igtype['CoAtomerGamma1_1r4xA_human'] = 'IgE';
124805
+ //ic.ref2igtype['CoAtomerGamma1_1r4xA_human'] = 'IgE';
124757
124806
  ic.ref2igtype['Contactin1_2ee2A_human_FN3-n9'] = 'IgFN3';
124758
124807
  ic.ref2igtype['Contactin1_3s97C_human_Iset-n2'] = 'IgI';
124759
- ic.ref2igtype['CuZnSuperoxideDismutase_1hl5C_human'] = 'SOD';
124808
+ //ic.ref2igtype['CuZnSuperoxideDismutase_1hl5C_human'] = 'SOD';
124760
124809
  ic.ref2igtype['ECadherin_4zt1A_human_n2'] = 'Cadherin';
124761
- ic.ref2igtype['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = 'IgE';
124810
+ //ic.ref2igtype['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = 'IgE';
124762
124811
  ic.ref2igtype['FAB-HEAVY_5esv_C1-n2'] = 'IgC1';
124763
124812
  ic.ref2igtype['FAB-HEAVY_5esv_V-n1'] = 'IgV';
124764
124813
  ic.ref2igtype['FAB-LIGHT_5esv_C1-n2'] = 'IgC1';
@@ -124769,28 +124818,28 @@ class Dssp {
124769
124818
  ic.ref2igtype['IL6Rb_1bquB_human_FN3-n3'] = 'IgFN3';
124770
124819
  ic.ref2igtype['InsulinR_8guyE_human_FN3-n1'] = 'IgFN3';
124771
124820
  ic.ref2igtype['InsulinR_8guyE_human_FN3-n2'] = 'IgFN3';
124772
- ic.ref2igtype['IsdA_2iteA_bacteria'] = 'IgE';
124821
+ //ic.ref2igtype['IsdA_2iteA_bacteria'] = 'IgE';
124773
124822
  ic.ref2igtype['JAM1_1nbqA_human_Iset-n2'] = 'IgI';
124774
124823
  ic.ref2igtype['LAG3_7tzgD_human_C1-n2'] = 'IgC1';
124775
124824
  ic.ref2igtype['LAG3_7tzgD_human_V-n1'] = 'IgV';
124776
124825
  ic.ref2igtype['LaminAC_1ifrA_human'] = 'Lamin';
124777
124826
  ic.ref2igtype['MHCIa_7phrH_human_C1'] = 'IgC1';
124778
- ic.ref2igtype['MPT63_1lmiA_bacteria'] = 'IgFN3-like';
124779
- ic.ref2igtype['NaCaExchanger_2fwuA_dog_n2'] = 'IgFN3-like';
124780
- ic.ref2igtype['NaKATPaseTransporterBeta_2zxeB_spurdogshark'] = 'IgE';
124781
- ic.ref2igtype['ORF7a_1xakA_virus'] = 'ORF';
124827
+ //ic.ref2igtype['MPT63_1lmiA_bacteria'] = 'IgFN3-like';
124828
+ //ic.ref2igtype['NaCaExchanger_2fwuA_dog_n2'] = 'IgFN3-like';
124829
+ //ic.ref2igtype['NaKATPaseTransporterBeta_2zxeB_spurdogshark'] = 'IgE';
124830
+ //ic.ref2igtype['ORF7a_1xakA_virus'] = 'ORF';
124782
124831
  ic.ref2igtype['PD1_4zqkB_human_V'] = 'IgV';
124783
124832
  ic.ref2igtype['PDL1_4z18B_human_V-n1'] = 'IgV';
124784
124833
  ic.ref2igtype['Palladin_2dm3A_human_Iset-n1'] = 'IgI';
124785
- ic.ref2igtype['RBPJ_6py8C_human_Unk-n1'] = 'IgFN3-like';
124834
+ //ic.ref2igtype['RBPJ_6py8C_human_Unk-n1'] = 'IgFN3-like';
124786
124835
  //ic.ref2igtype['RBPJ_6py8C_human_Unk-n2'] = 'IgFN3-like';
124787
124836
  ic.ref2igtype['Sidekick2_1wf5A_human_FN3-n7'] = 'IgFN3';
124788
124837
  ic.ref2igtype['Siglec3_5j0bB_human_C1-n2'] = 'IgC1';
124789
124838
  ic.ref2igtype['TCRa_6jxrm_human_C1-n2'] = 'IgC1';
124790
124839
  ic.ref2igtype['TCRa_6jxrm_human_V-n1'] = 'IgV';
124791
- ic.ref2igtype['TEAD1_3kysC_human'] = 'IgFN3-like';
124792
- ic.ref2igtype['TP34_2o6cA_bacteria'] = 'IgE';
124793
- ic.ref2igtype['TP47_1o75A_bacteria'] = 'IgE';
124840
+ //ic.ref2igtype['TEAD1_3kysC_human'] = 'IgFN3-like';
124841
+ //ic.ref2igtype['TP34_2o6cA_bacteria'] = 'IgE';
124842
+ //ic.ref2igtype['TP47_1o75A_bacteria'] = 'IgE';
124794
124843
  ic.ref2igtype['Titin_4uowM_human_Iset-n152'] = 'IgI';
124795
124844
  ic.ref2igtype['VISTA_6oilA_human_V'] = 'IgV';
124796
124845
  ic.ref2igtype['VNAR_1t6vN_shark_V'] = 'IgV';
@@ -126341,6 +126390,7 @@ class Dssp {
126341
126390
  }
126342
126391
  else {
126343
126392
  let bBefore = false, bInRange= false, bAfter = false;
126393
+ /*
126344
126394
  // 100, 100A
126345
126395
  if(parseInt(currResi) == parseInt(strandArray[strandCnt].startResi) && currResi != strandArray[strandCnt].startResi) {
126346
126396
  bBefore = currResi < strandArray[strandCnt].startResi;
@@ -126356,6 +126406,14 @@ class Dssp {
126356
126406
  else {
126357
126407
  bAfter = parseInt(currResi) > parseInt(strandArray[strandCnt].endResi);
126358
126408
  }
126409
+ */
126410
+
126411
+ let currResiNcbi = ic.ParserUtilsCls.getResiNCBI(chnid, currResi);
126412
+ let startResiNcbi = ic.ParserUtilsCls.getResiNCBI(chnid, strandArray[strandCnt].startResi);
126413
+ let endResiNcbi = ic.ParserUtilsCls.getResiNCBI(chnid, strandArray[strandCnt].endResi);
126414
+
126415
+ bBefore = parseInt(currResiNcbi) < parseInt(startResiNcbi);
126416
+ bAfter = parseInt(currResiNcbi) > parseInt(endResiNcbi);
126359
126417
 
126360
126418
  bInRange = (!bBefore && !bAfter) ? true : false;
126361
126419
 
@@ -132174,8 +132232,9 @@ class ShareLink {
132174
132232
  }
132175
132233
 
132176
132234
  let paraHash = {};
132177
- for(let key in ic.cfg) {
132178
- let value = ic.cfg[key];
132235
+ /*
132236
+ for(let key in me.cfg) {
132237
+ let value = me.cfg[key];
132179
132238
  //if(key === 'inpara' || ic.key === 'command' || value === undefined) continue;
132180
132239
  if(key === 'inpara' || key === 'command' || key === 'usepdbnum'
132181
132240
  || key === 'date' || key === 'v' || value === undefined) continue;
@@ -132225,7 +132284,7 @@ class ShareLink {
132225
132284
  paraHash[key] = value;
132226
132285
  }
132227
132286
  }
132228
-
132287
+ */
132229
132288
  if(ic.bAfMem) {
132230
132289
  paraHash['afmem'] = 'on';
132231
132290
  }
@@ -132247,6 +132306,12 @@ class ShareLink {
132247
132306
  if(key_value.length == 2) paraHash[key_value[0]] = key_value[1];
132248
132307
  }
132249
132308
 
132309
+ // BLAST RID is usually added at the end of the URL. It should be included.
132310
+ if(me.cfg.rid && !paraHash['RID']) {
132311
+ url += 'RID=' + me.cfg.rid + '&';
132312
+ }
132313
+
132314
+ // sometimes idname is not part of the URL
132250
132315
  if(me.cfg.idname && !paraHash[me.cfg.idname]) { // somehow it is not included
132251
132316
  url += me.cfg.idname + '=' + me.cfg.idvalue + '&';
132252
132317
  }
@@ -135360,7 +135425,7 @@ class iCn3DUI {
135360
135425
  //even when multiple iCn3D viewers are shown together.
135361
135426
  this.pre = this.cfg.divid + "_";
135362
135427
 
135363
- this.REVISION = '3.47.1';
135428
+ this.REVISION = '3.48.0';
135364
135429
 
135365
135430
  // In nodejs, iCn3D defines "window = {navigator: {}}", and added window = {navigator: {}, "__THREE__":"177"}
135366
135431
  this.bNode = (Object.keys(window).length < 3) ? true : false;
@@ -135562,14 +135627,8 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
135562
135627
  let domainidArray = me.cfg.matchedchains.split(',');
135563
135628
  let chainidArray = [];
135564
135629
  for(let i = 0, il = domainidArray.length; i < il; ++i) {
135565
- let pos = domainidArray[i].lastIndexOf('_');
135566
- let lastId = domainidArray[i].substr(pos + 1);
135567
- if(!isNaN(lastId)) { // lastId is domain id
135568
- chainidArray.push(domainidArray[i].substr(0, pos));
135569
- }
135570
- else {
135571
- chainidArray.push(domainidArray[i]);
135572
- }
135630
+ let idArray = domainidArray[i].split('_');
135631
+ chainidArray.push(idArray[0] + '_' + idArray[1]);
135573
135632
  }
135574
135633
 
135575
135634
  // get the matched structures, do not include the template
@@ -135798,6 +135857,9 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
135798
135857
  if(me.cfg.align.indexOf('185055,') != -1) {
135799
135858
  me.cfg.align = me.cfg.align.replace('185055,', '199731,'); //the mmdbid of PDB 6M17 was changed from 185055 to 199731
135800
135859
  }
135860
+ else if(me.cfg.align == '54567,1,12161,1,2,1') {
135861
+ me.cfg.align = '3HHR,1BQU'; // somehow the VAST+ data for this published alignment were not there anymore
135862
+ }
135801
135863
 
135802
135864
  let alignArray = me.cfg.align.split(','); // e.g., 6 IDs: 103701,1,4,68563,1,167 [mmdbid1,biounit,molecule,mmdbid2,biounit,molecule], or 2IDs: 103701,68563 [mmdbid1,mmdbid2]
135803
135865