icn3d 3.47.3 → 3.48.1

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Files changed (4) hide show
  1. package/icn3d.js +200 -135
  2. package/icn3d.min.js +3 -3
  3. package/icn3d.module.js +200 -135
  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
@@ -80411,7 +80411,7 @@ class Strand {
80411
80411
  let bShowArray = [];
80412
80412
  let calphaIdArray = []; // used to store one of the final positions drawn in 3D
80413
80413
  let colors = [];
80414
- let currentChain, currentCA = null, currentO = null, currentColor = null, prevCoorCA = null, prevCoorO = null, prevColor = null;
80414
+ let currentChain, currentStyle, currentCA = null, currentO = null, currentColor = null, prevCoorCA = null, prevCoorO = null, prevColor = null;
80415
80415
  let prevCO = null, ss = null, ssend = false, atomid = null, prevAtomid = null, prevResi = null, calphaid = null, prevCalphaid = null;
80416
80416
  let strandWidth, bSheetSegment = false, bHelixSegment = false;
80417
80417
  let atom, tubeAtoms = {};
@@ -80464,15 +80464,15 @@ class Strand {
80464
80464
  }
80465
80465
  // smoothen each coil, helix and sheet separately. The joint residue has to be included both in the previous and next segment
80466
80466
  let bSameChain = true;
80467
- // if (currentChain !== atom.chain || currentResi + 1 !== atom.resi) {
80467
+
80468
80468
  if (currentChain !== atom.chain) {
80469
80469
  bSameChain = false;
80470
80470
  }
80471
80471
 
80472
- if(atom.ssend && atom.ss === 'sheet') {
80472
+ if((atom.ssend || currentStyle != atom.style)&& atom.ss === 'sheet') {
80473
80473
  bSheetSegment = true;
80474
80474
  }
80475
- else if(atom.ssend && atom.ss === 'helix') {
80475
+ else if((atom.ssend || currentStyle != atom.style) && atom.ss === 'helix') {
80476
80476
  bHelixSegment = true;
80477
80477
  }
80478
80478
 
@@ -80565,7 +80565,7 @@ class Strand {
80565
80565
  // bHelixSegment = true;
80566
80566
  // }
80567
80567
 
80568
- if ((atom.ssbegin || atom.ssend || (drawnResidueCount === totalResidueCount - 1) || bBrokenSs) && pnts[0].length > 0 && bSameChain) {
80568
+ if ((atom.ssbegin || atom.ssend || (drawnResidueCount === totalResidueCount - 1) || bBrokenSs || currentStyle != atom.style) && pnts[0].length > 0 && bSameChain) {
80569
80569
  let atomName = 'CA';
80570
80570
 
80571
80571
  let prevone = [], nexttwo = [];
@@ -80708,9 +80708,7 @@ class Strand {
80708
80708
  } // end if (atom.ssbegin || atom.ssend)
80709
80709
 
80710
80710
  // end of a chain
80711
- // if ((currentChain !== atom.chain || currentResi + 1 !== atom.resi) && pnts[0].length > 0) {
80712
- if ((currentChain !== atom.chain) && pnts[0].length > 0) {
80713
-
80711
+ if ((currentChain !== atom.chain || currentStyle != atom.style) && pnts[0].length > 0) {
80714
80712
  let atomName = 'CA';
80715
80713
 
80716
80714
  let prevone = [], nexttwo = [];
@@ -80762,7 +80760,7 @@ class Strand {
80762
80760
  }
80763
80761
 
80764
80762
  currentChain = atom.chain;
80765
- atom.resi;
80763
+ currentStyle = atom.style;
80766
80764
  ss = atom.ss;
80767
80765
  ssend = atom.ssend;
80768
80766
  prevAtomid = atom.serial;
@@ -84874,7 +84872,7 @@ class ApplyMissingRes {
84874
84872
  line.serial1 = ic.missingResResid2serial[resid0 + ',' + resid1];
84875
84873
  line.serial2 = ic.missingResResid2serial[resid1 + ',' + resid0];
84876
84874
 
84877
- line.color = "#" + ic.atoms[line.serial1].color.getHexString();
84875
+ line.color = (ic.atoms[line.serial1]) ? "#" + ic.atoms[line.serial1].color.getHexString() : undefined;
84878
84876
 
84879
84877
  line.radius = ic.coilWidth;
84880
84878
 
@@ -89729,6 +89727,9 @@ class SetStyle {
89729
89727
  setBackground(color) {var ic = this.icn3d, me = ic.icn3dui;
89730
89728
 
89731
89729
  ic.setOptionCls.setOption('background', color);
89730
+ let exdays = 3650;
89731
+ me.htmlCls.setHtmlCls.setCookie('bkgdcolor', color, exdays);
89732
+
89732
89733
  me.htmlCls.clickMenuCls.setLogCmd('set background ' + color, true);
89733
89734
  //let titleColor =(color == 'black' || color == 'transparent') ? me.htmlCls.GREYD : 'black';
89734
89735
  let titleColor = (color == 'black') ? me.htmlCls.GREYD : 'black';
@@ -100331,7 +100332,7 @@ class HlUpdate {
100331
100332
  if(ic.mmdbid_q !== undefined && ic.mmdbid_q === ic.mmdbid_t) {
100332
100333
  html2ddgm += ic.diagram2dCls.draw2Ddgm(ic.interactionData2, ic.mmdbidArray[0].toUpperCase(), 1, true);
100333
100334
  }
100334
- else {
100335
+ else if(ic.mmdbidArray.length > 1) {
100335
100336
  html2ddgm += ic.diagram2dCls.draw2Ddgm(ic.interactionData2, ic.mmdbidArray[1].toUpperCase(), 1, true);
100336
100337
  }
100337
100338
  html2ddgm += ic.diagram2dCls.set2DdgmNote(true);
@@ -104613,16 +104614,31 @@ class ChainalignParser {
104613
104614
 
104614
104615
  // dynamically align pairs in all chainids
104615
104616
  // 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]];
104617
+ let atomSet_t;
104618
+ if(me.cfg.resrange) {
104619
+ let result = ic.realignParserCls.getSeqCoorResid([resRangeArray[0]], chainidArray[0], true);
104620
+ atomSet_t = result.hAtoms;
104621
+ }
104622
+ else {
104623
+ atomSet_t = ic.chains[chainidArray[0]];
104624
+ }
104625
+
104617
104626
  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]];
104627
+ let atomSet_q;
104628
+ if(me.cfg.resrange) {
104629
+ let result = ic.realignParserCls.getSeqCoorResid([resRangeArray[index]], chainidArray[index], true);
104630
+ atomSet_q = result.hAtoms;
104631
+ }
104632
+ else {
104633
+ atomSet_q = ic.chains[chainidArray[index]];
104634
+ }
104619
104635
  // end of new version to be done for VASTsrv ==============
104620
104636
 
104621
104637
  let alignAjax;
104622
104638
  if(me.cfg.aligntool != 'tmalign') {
104623
104639
  let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(atomSet_q);
104624
104640
  let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(atomSet_t);
104625
-
104641
+
104626
104642
  let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
104627
104643
  alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
104628
104644
  }
@@ -104658,6 +104674,7 @@ class ChainalignParser {
104658
104674
  //let bTargetTransformed = (ic.qt_start_end[0]) ? true : false;
104659
104675
 
104660
104676
  // modify the previous trans and rotation matrix
104677
+ let bAligned = false;
104661
104678
  for(let i = 0, il = dataArray.length; i < il; ++i) {
104662
104679
  // let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
104663
104680
  let align = dataArray[i].value;//[0];
@@ -104673,7 +104690,7 @@ class ChainalignParser {
104673
104690
 
104674
104691
  me.htmlCls.clickMenuCls.setLogCmd("Align " + mmdbid_t + " with " + mmdbid_q, false);
104675
104692
 
104676
- this.processAlign(align, index, queryData, bEqualMmdbid, bEqualChain);
104693
+ bAligned =await this.processAlign(align, index, queryData, bEqualMmdbid, bEqualChain, undefined);
104677
104694
  }
104678
104695
 
104679
104696
  // do not transform the target
@@ -104681,28 +104698,34 @@ class ChainalignParser {
104681
104698
  // this.transformStructure(mmdbid_t, indexArray[0], 'target');
104682
104699
  //}
104683
104700
 
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
- }
104701
+ if(bAligned) {
104702
+ // transform the rest
104703
+ for(let i = 0, il = dataArray.length; i < il; ++i) {
104704
+ let mmdbid_q = struArray[i];
104705
+ let index = indexArray[i];
104706
+ this.transformStructure(mmdbid_q, index, 'query');
104707
+ }
104690
104708
 
104691
- let hAtomsAll = {};
104709
+ let hAtomsAll = {};
104692
104710
 
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
- }
104711
+ if(ic.bFullUi && ic.q_rotation !== undefined && !me.cfg.resnum && !me.cfg.resdef) {
104712
+ // set multiple sequence alignment from ic.qt_start_end
104713
+ hAtomsAll = this.setMsa(chainidArray);
104714
+ }
104697
104715
 
104698
- // highlight all aligned atoms
104699
- //ic.hAtoms = me.hashUtilsCls.cloneHash(hAtomsTmp);
104700
- ic.hAtoms = me.hashUtilsCls.cloneHash(hAtomsAll);
104716
+ // highlight all aligned atoms
104717
+ //ic.hAtoms = me.hashUtilsCls.cloneHash(hAtomsTmp);
104718
+ ic.hAtoms = me.hashUtilsCls.cloneHash(hAtomsAll);
104701
104719
 
104702
- ic.transformCls.zoominSelection();
104720
+ ic.transformCls.zoominSelection();
104703
104721
 
104704
- // do the rest
104705
- await this.downloadChainalignmentPart3(chainresiCalphaHash2, chainidArray, ic.hAtoms);
104722
+ // do the rest
104723
+ await this.downloadChainalignmentPart3(chainresiCalphaHash2, chainidArray, ic.hAtoms);
104724
+ }
104725
+ else {
104726
+ me.cfg.aligntool = 'tmalign';
104727
+ await ic.chainalignParserCls.downloadChainalignment(me.cfg.chainalign);
104728
+ }
104706
104729
  }
104707
104730
 
104708
104731
  setMsa(chainidArray, bVastplus, bRealign) { let ic = this.icn3d, me = ic.icn3dui;
@@ -104773,7 +104796,7 @@ class ChainalignParser {
104773
104796
 
104774
104797
  let bNoAlert = true;
104775
104798
 
104776
- let bAligned = this.processAlign(align, i, queryData, bEqualMmdbid, bEqualChain, bNoAlert);
104799
+ let bAligned = await this.processAlign(align, i, queryData, bEqualMmdbid, bEqualChain, bNoAlert);
104777
104800
 
104778
104801
  if(bAligned) {
104779
104802
  bFoundAlignment = true;
@@ -105265,7 +105288,7 @@ class ChainalignParser {
105265
105288
 
105266
105289
  me.htmlCls.clickMenuCls.setLogCmd("Align " + mmdbid_t + " with " + mmdbid_q, false);
105267
105290
 
105268
- this.processAlign(align, index-1, queryData, bEqualMmdbid, bEqualChain);
105291
+ await this.processAlign(align, index-1, queryData, bEqualMmdbid, bEqualChain, undefined);
105269
105292
  }
105270
105293
  }
105271
105294
  }
@@ -105275,13 +105298,13 @@ class ChainalignParser {
105275
105298
  await this.loadOpmDataForChainalign(targetData, queryDataArray, chainidArray, ic.mmdbidArray);
105276
105299
  }
105277
105300
 
105278
- processAlign(align, index, queryData, bEqualMmdbid, bEqualChain, bNoAlert) { let ic = this.icn3d, me = ic.icn3dui;
105301
+ async processAlign(align, index, queryData, bEqualMmdbid, bEqualChain, bNoAlert) { let ic = this.icn3d, me = ic.icn3dui;
105279
105302
  let bAligned = false;
105280
105303
 
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 + ".");
105304
+ if((align === "error" || align === undefined || align.length == 0) && !bNoAlert) {
105305
+ // let serverName = (me.cfg.aligntool == 'tmalign') ? 'TM-align' : 'VAST';
105306
+
105307
+ // if(ic.bRender) var aaa = 1; //alert("These chains can not be aligned by " + serverName + ".");
105285
105308
  return bAligned;
105286
105309
  }
105287
105310
 
@@ -105430,7 +105453,6 @@ class ChainalignParser {
105430
105453
  let structArrayTmp = idlist.split(',');
105431
105454
 
105432
105455
  let structArray = [];
105433
-
105434
105456
  // only when bNoDuplicate is undefined/false, it's allowed to load multiple copies of the same structure
105435
105457
  if(!bNoDuplicate) {
105436
105458
  structArray = this.addPostfixForStructureids(structArrayTmp);
@@ -105443,7 +105465,7 @@ class ChainalignParser {
105443
105465
  if(!ic.structures.hasOwnProperty(id)) structArray.push(structArrayTmp[i]);
105444
105466
  }
105445
105467
  }
105446
-
105468
+
105447
105469
  if(structArray.length == 0) return;
105448
105470
 
105449
105471
  ic.structArray = ic.structArray.concat(structArray);
@@ -105543,6 +105565,8 @@ class ChainalignParser {
105543
105565
  let bNoSeqalign = true;
105544
105566
  let pdbid = structArray[i];
105545
105567
 
105568
+ if(queryDataArray[i].pdbId) queryDataArray[i].pdbId = pdbid;
105569
+
105546
105570
  //hAtomsTmp contains all atoms
105547
105571
  await ic.mmdbParserCls.parseMmdbData(queryDataArray[i], targetOrQuery, undefined, undefined, bLastQuery, bNoSeqalign, pdbid);
105548
105572
  }
@@ -107119,7 +107143,7 @@ class MmdbParser {
107119
107143
  return;
107120
107144
  }
107121
107145
 
107122
- if(Object.keys(data.atoms).length == 0) { // for large structures such as 3J3Q
107146
+ if(!data.atoms || Object.keys(data.atoms).length == 0) { // for large structures such as 3J3Q
107123
107147
  // use mmtfid
107124
107148
  let pdbid = data.pdbId;
107125
107149
  await ic.bcifParserCls.downloadBcif(pdbid);
@@ -107129,6 +107153,7 @@ class MmdbParser {
107129
107153
 
107130
107154
  let bCalphaOnly = me.utilsCls.isCalphaPhosOnly(data.atoms); //, 'CA');
107131
107155
 
107156
+ //if(!data.pdbId) data.pdbId = mmdbid;
107132
107157
  if(bCalphaOnly || data.atomCount <= ic.maxatomcnt) {
107133
107158
  await this.parseMmdbData(data);
107134
107159
  }
@@ -107290,8 +107315,18 @@ class MmdbParser {
107290
107315
  async parseMmdbData(data, type, chainid, chainIndex, bLastQuery, bNoTransformNoSeqalign, pdbidIn) { let ic = this.icn3d, me = ic.icn3dui;
107291
107316
  let hAtoms;
107292
107317
  let pdbid = (data.pdbId !== undefined) ? data.pdbId : data.mmdbId;
107318
+ if(!pdbid && chainid) {
107319
+ pdbid = chainid.substr(0, chainid.lastIndexOf('_'));
107320
+ }
107321
+
107293
107322
  if(pdbidIn) pdbid = pdbidIn;
107294
107323
 
107324
+ // if(!data.atoms || Object.keys(data.atoms).length == 0) { // for large structures such as 3J3Q
107325
+ // ic.bRender = false;
107326
+ // await ic.bcifParserCls.downloadBcif(pdbid);
107327
+ // return;
107328
+ // }
107329
+
107295
107330
  this.parseMmdbDataPart1(data, type);
107296
107331
 
107297
107332
  if(type === undefined) { // default mmdbid input
@@ -108958,7 +108993,7 @@ class PdbParser {
108958
108993
  }
108959
108994
 
108960
108995
  // if(!ic.bSecondaryStructure && Object.keys(ic.proteins).length > 0) {
108961
- if((!ic.bSecondaryStructure || bCalcSecondary) && Object.keys(ic.proteins).length > 0 && !bNoDssp) {
108996
+ if((!ic.bSecondaryStructure || bCalcSecondary) && Object.keys(ic.proteins).length > 0 && !bNoDssp) {
108962
108997
  await this.applyCommandDssp(bAppend);
108963
108998
  }
108964
108999
  else {
@@ -110933,8 +110968,7 @@ class RealignParser {
110933
110968
  // If rmsd from vastsrv is too large, realign the chains
110934
110969
  //if(me.cfg.chainalign && !me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5) {
110935
110970
  // 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.");
110971
+ if(!me.cfg.usepdbnum && (me.cfg.resdef || me.cfg.resrange) && rmsd > 5 && me.cfg.chainalign) {
110938
110972
  //let nameArray = me.cfg.chainalign.split(',');
110939
110973
  let nameArray = Object.keys(chainidHash);
110940
110974
  if(nameArray.length > 0) {
@@ -111186,15 +111220,30 @@ let resRangeArray = (me.cfg.resrange) ? decodeURIComponent(me.cfg.resrange).spli
111186
111220
  if(bVastsearch && me.cfg.resrange) {
111187
111221
  let resRangeArray = decodeURIComponent(me.cfg.resrange).split(' | ');
111188
111222
 
111189
- let atomSet_t = ic.realignParserCls.getSeqCoorResid([resRangeArray[0]], ic.chainidArray[0], true).hAtoms;
111223
+ let atomSet_t;
111224
+ if(me.cfg.resrange) {
111225
+ let result = ic.realignParserCls.getSeqCoorResid([resRangeArray[0]], ic.chainidArray[0], true);
111226
+ atomSet_t = result.hAtoms;
111227
+ }
111228
+ else {
111229
+ atomSet_t = ic.chains[ic.chainidArray[0]];
111230
+ }
111231
+
111190
111232
  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;
111233
+ let atomSet_q;
111234
+ if(me.cfg.resrange) {
111235
+ let result = ic.realignParserCls.getSeqCoorResid([resRangeArray[index]], ic.chainidArray[index], true);
111236
+ atomSet_q = result.hAtoms;
111237
+ }
111238
+ else {
111239
+ atomSet_q = ic.chains[ic.chainidArray[index]];
111240
+ }
111192
111241
 
111193
111242
  let alignAjax;
111194
111243
  if(me.cfg.aligntool != 'tmalign') {
111195
111244
  let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(atomSet_q);
111196
111245
  let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(atomSet_t);
111197
-
111246
+
111198
111247
  let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
111199
111248
  alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
111200
111249
  }
@@ -111255,9 +111304,7 @@ let resRangeArray = (me.cfg.resrange) ? decodeURIComponent(me.cfg.resrange).spli
111255
111304
  let alignAjax;
111256
111305
  if(me.cfg.aligntool != 'tmalign') {
111257
111306
  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);
111307
+
111261
111308
  let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
111262
111309
  alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
111263
111310
  }
@@ -111327,7 +111374,7 @@ console.log("@@@ jsonStr_t " + jsonStr_t);
111327
111374
 
111328
111375
  if(me.cfg.aligntool != 'tmalign') {
111329
111376
  let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(chainid2domain[chainid2]);
111330
-
111377
+
111331
111378
  let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
111332
111379
  alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
111333
111380
  }
@@ -111587,6 +111634,8 @@ console.log("@@@ jsonStr_t " + jsonStr_t);
111587
111634
  let hAtoms = {};
111588
111635
 
111589
111636
  for(let j = 0, jl = resiArray.length; j < jl; ++j) {
111637
+ if(!resiArray[j]) continue;
111638
+
111590
111639
  if(resiArray[j].indexOf('-') != -1) {
111591
111640
  let startEnd = resiArray[j].split('-');
111592
111641
  for(let k = parseInt(startEnd[0]); k <= parseInt(startEnd[1]); ++k) {
@@ -116757,7 +116806,8 @@ class LoadPDB {
116757
116806
  }
116758
116807
 
116759
116808
  isSecondary(resid, residArray, bNMR, bNonFull) { let ic = this.icn3d; ic.icn3dui;
116760
- if(bNonFull) return false;
116809
+ // still need to get the secondary info
116810
+ //if(bNonFull) return false;
116761
116811
 
116762
116812
  if(!bNMR) {
116763
116813
  return $.inArray(resid, residArray) != -1;
@@ -119127,16 +119177,18 @@ class ApplyCommand {
119127
119177
  }
119128
119178
  else if(command.indexOf('set background') == 0) {
119129
119179
  let value = command.substr(command.lastIndexOf(' ') + 1);
119130
- ic.opts['background'] = value;
119180
+ ic.setStyleCls.setBackground(value);
119131
119181
 
119132
- if(value == 'black') {
119133
- $("#" + ic.pre + "title").css("color", me.htmlCls.GREYD);
119134
- $("#" + ic.pre + "titlelink").css("color", me.htmlCls.GREYD);
119135
- }
119136
- else {
119137
- $("#" + ic.pre + "title").css("color", "black");
119138
- $("#" + ic.pre + "titlelink").css("color", "black");
119139
- }
119182
+ // ic.opts['background'] = value;
119183
+
119184
+ // if(value == 'black') {
119185
+ // $("#" + ic.pre + "title").css("color", me.htmlCls.GREYD);
119186
+ // $("#" + ic.pre + "titlelink").css("color", me.htmlCls.GREYD);
119187
+ // }
119188
+ // else {
119189
+ // $("#" + ic.pre + "title").css("color", "black");
119190
+ // $("#" + ic.pre + "titlelink").css("color", "black");
119191
+ // }
119140
119192
  }
119141
119193
  else if(command.indexOf('set label color') == 0) {
119142
119194
  ic.labelcolor = command.substr(command.lastIndexOf(' ') + 1);
@@ -124663,29 +124715,29 @@ class Dssp {
124663
124715
 
124664
124716
  setRefPdbs() { let ic = this.icn3d; ic.icn3dui;
124665
124717
  // 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'];
124718
+ 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
124719
 
124668
124720
  // round 2
124669
124721
  ic.refpdbHash = {};
124670
124722
  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'];
124723
+ ic.refpdbHash['1ICOS_6x4gA_human_V'] = ['ICOS_6x4gA_human_V'];
124724
+ //ic.refpdbHash['1CoAtomerGamma1_1r4xA_human'] = ['CoAtomerGamma1_1r4xA_human', 'TP34_2o6cA_bacteria'];
124725
+ //ic.refpdbHash['1C3_2qkiD_human_n1'] = ['C3_2qkiD_human_n1', 'RBPJ_6py8C_human_Unk-n1'];
124726
+ //ic.refpdbHash['1CuZnSuperoxideDismutase_1hl5C_human'] = ['TEAD1_3kysC_human'];
124727
+ //ic.refpdbHash['1ASF1A_2iijA_human'] = ['ASF1A_2iijA_human', 'TP47_1o75A_bacteria'];
124676
124728
  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
124729
  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'];
124730
+ ic.refpdbHash['1ECadherin_4zt1A_human_n2'] = ['ECadherin_4zt1A_human_n2'];
124731
+ //ic.refpdbHash['1NaKATPaseTransporterBeta_2zxeB_spurdogshark'] = ['NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
124680
124732
  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
124733
  ic.refpdbHash['1PDL1_4z18B_human_V-n1'] = ['PDL1_4z18B_human_V-n1', 'CD2_1hnfA_human_V-n1', 'LAG3_7tzgD_human_V-n1'];
124682
124734
  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
124735
  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'];
124736
+ ic.refpdbHash['1CD3g_6jxrg_human_C2'] = ['CD3g_6jxrg_human_C2', 'TCRa_6jxrm_human_C1-n2'];
124737
+ ic.refpdbHash['1CD28_1yjdC_human_V'] = ['CD28_1yjdC_human_V', 'CD3e_6jxrf_human_C1'];
124686
124738
  ic.refpdbHash['1CD19_6al5A_human-n1'] = ['CD19_6al5A_human-n1'];
124687
124739
 
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'];
124740
+ 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
124741
 
124690
124742
  // use known ref structure
124691
124743
  ic.refpdbHash['5ESV_C'] = ['FAB-HEAVY_5esv_V-n1', 'FAB-HEAVY_5esv_C1-n2'];
@@ -124694,36 +124746,36 @@ class Dssp {
124694
124746
  ic.refpdbHash['6JXR_m'] = ['TCRa_6jxrm_human_V-n1', 'TCRa_6jxrm_human_C1-n2'];
124695
124747
  ic.refpdbHash['1HNF_A'] = ['CD2_1hnfA_human_V-n1', 'CD2_1hnfA_human_C2-n2'];
124696
124748
  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'];
124749
+ //ic.refpdbHash['6PY8_C'] = ['RBPJ_6py8C_human_Unk-n1'];
124698
124750
  ic.refpdbHash['1BQU_B'] = ['IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3'];
124699
124751
 
124700
- ic.refpdbHash['1R4X_A'] = ['CoAtomerGamma1_1r4xA_human'];
124752
+ //ic.refpdbHash['1R4X_A'] = ['CoAtomerGamma1_1r4xA_human'];
124701
124753
  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'];
124754
+ //ic.refpdbHash['2ZXE_B'] = ['NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
124755
+ //ic.refpdbHash['1I8A_A'] = ['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'];
124756
+ //ic.refpdbHash['2FWU_A'] = ['NaCaExchanger_2fwuA_dog_n2'];
124757
+ //ic.refpdbHash['4JQI_A'] = ['BArrestin1_4jqiA_rat_n1'];
124706
124758
  ic.refpdbHash['1NBQ_A'] = ['JAM1_1nbqA_human_Iset-n2'];
124707
- ic.refpdbHash['1O75_A'] = ['TP47_1o75A_bacteria'];
124759
+ //ic.refpdbHash['1O75_A'] = ['TP47_1o75A_bacteria'];
124708
124760
  ic.refpdbHash['7PHR_H'] = ['MHCIa_7phrH_human_C1'];
124709
- ic.refpdbHash['2IIJ_A'] = ['ASF1A_2iijA_human'];
124761
+ //ic.refpdbHash['2IIJ_A'] = ['ASF1A_2iijA_human'];
124710
124762
  ic.refpdbHash['4Z18_B'] = ['PDL1_4z18B_human_V-n1'];
124711
124763
  ic.refpdbHash['1T6V_N'] = ['VNAR_1t6vN_shark_V'];
124712
- ic.refpdbHash['2O6C_A'] = ['TP34_2o6cA_bacteria'];
124713
- ic.refpdbHash['3KYS_C'] = ['TEAD1_3kysC_human'];
124764
+ //ic.refpdbHash['2O6C_A'] = ['TP34_2o6cA_bacteria'];
124765
+ //ic.refpdbHash['3KYS_C'] = ['TEAD1_3kysC_human'];
124714
124766
  ic.refpdbHash['7PHR_L'] = ['B2Microglobulin_7phrL_human_C1'];
124715
124767
  ic.refpdbHash['2AW2_A'] = ['BTLA_2aw2A_human_Iset'];
124716
- ic.refpdbHash['1HL5_C'] = ['CuZnSuperoxideDismutase_1hl5C_human'];
124768
+ //ic.refpdbHash['1HL5_C'] = ['CuZnSuperoxideDismutase_1hl5C_human'];
124717
124769
  ic.refpdbHash['1WF5_A'] = ['Sidekick2_1wf5A_human_FN3-n7'];
124718
124770
  ic.refpdbHash['5J0B_B'] = ['Siglec3_5j0bB_human_C1-n2'];
124719
124771
  ic.refpdbHash['1IFR_A'] = ['LaminAC_1ifrA_human'];
124720
124772
  ic.refpdbHash['Q7Z7D3_A'] = ['VTCN1_Q7Z7D3_human_C1-n2'];
124721
124773
  ic.refpdbHash['4ZQK_B'] = ['PD1_4zqkB_human_V'];
124722
124774
  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'];
124775
+ //ic.refpdbHash['2ITE_A'] = ['IsdA_2iteA_bacteria'];
124776
+ //ic.refpdbHash['1XAK_A'] = ['ORF7a_1xakA_virus'];
124725
124777
  ic.refpdbHash['4ZT1_A'] = ['ECadherin_4zt1A_human_n2'];
124726
- ic.refpdbHash['1LMI_A'] = ['MPT63_1lmiA_bacteria'];
124778
+ //ic.refpdbHash['1LMI_A'] = ['MPT63_1lmiA_bacteria'];
124727
124779
  ic.refpdbHash['1CD8_A'] = ['CD8a_1cd8A_human_V'];
124728
124780
  ic.refpdbHash['3S97_C'] = ['Contactin1_3s97C_human_Iset-n2'];
124729
124781
  ic.refpdbHash['1AXI_B'] = ['GHR_1axiB_human_C1-n1'];
@@ -124731,7 +124783,7 @@ class Dssp {
124731
124783
  ic.refpdbHash['2EE2_A'] = ['Contactin1_2ee2A_human_FN3-n9'];
124732
124784
  ic.refpdbHash['4UOW_M'] = ['Titin_4uowM_human_Iset-n152'];
124733
124785
  ic.refpdbHash['6A15_A'] = ['CD19_6al5A_human-n1'];
124734
- ic.refpdbHash['2QKI_D'] = ['C3_2qkiD_human_n1'];
124786
+ //ic.refpdbHash['2QKI_D'] = ['C3_2qkiD_human_n1'];
124735
124787
  ic.refpdbHash['1YJD_C'] = ['CD28_1yjdC_human_V'];
124736
124788
  ic.refpdbHash['6JXR_d'] = ['CD3d_6jxrd_human_C1'];
124737
124789
  ic.refpdbHash['6JXR_f'] = ['CD3e_6jxrf_human_C1'];
@@ -124740,11 +124792,11 @@ class Dssp {
124740
124792
  // assign Ig types
124741
124793
  ic.ref2igtype = {};
124742
124794
 
124743
- ic.ref2igtype['ASF1A_2iijA_human'] = 'IgFN3-like';
124795
+ //ic.ref2igtype['ASF1A_2iijA_human'] = 'IgFN3-like';
124744
124796
  ic.ref2igtype['B2Microglobulin_7phrL_human_C1'] = 'IgC1';
124745
- ic.ref2igtype['BArrestin1_4jqiA_rat_n1'] = 'IgFN3-like';
124797
+ //ic.ref2igtype['BArrestin1_4jqiA_rat_n1'] = 'IgFN3-like';
124746
124798
  ic.ref2igtype['BTLA_2aw2A_human_Iset'] = 'IgI';
124747
- ic.ref2igtype['C3_2qkiD_human_n1'] = 'IgFN3-like';
124799
+ //ic.ref2igtype['C3_2qkiD_human_n1'] = 'IgFN3-like';
124748
124800
  ic.ref2igtype['CD19_6al5A_human-n1'] = 'CD19';
124749
124801
  ic.ref2igtype['CD28_1yjdC_human_V'] = 'IgV';
124750
124802
  ic.ref2igtype['CD2_1hnfA_human_C2-n2'] = 'IgC2';
@@ -124753,12 +124805,12 @@ class Dssp {
124753
124805
  ic.ref2igtype['CD3e_6jxrf_human_C1'] = 'IgC1';
124754
124806
  ic.ref2igtype['CD3g_6jxrg_human_C2'] = 'IgC2';
124755
124807
  ic.ref2igtype['CD8a_1cd8A_human_V'] = 'IgV';
124756
- ic.ref2igtype['CoAtomerGamma1_1r4xA_human'] = 'IgE';
124808
+ //ic.ref2igtype['CoAtomerGamma1_1r4xA_human'] = 'IgE';
124757
124809
  ic.ref2igtype['Contactin1_2ee2A_human_FN3-n9'] = 'IgFN3';
124758
124810
  ic.ref2igtype['Contactin1_3s97C_human_Iset-n2'] = 'IgI';
124759
- ic.ref2igtype['CuZnSuperoxideDismutase_1hl5C_human'] = 'SOD';
124811
+ //ic.ref2igtype['CuZnSuperoxideDismutase_1hl5C_human'] = 'SOD';
124760
124812
  ic.ref2igtype['ECadherin_4zt1A_human_n2'] = 'Cadherin';
124761
- ic.ref2igtype['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = 'IgE';
124813
+ //ic.ref2igtype['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = 'IgE';
124762
124814
  ic.ref2igtype['FAB-HEAVY_5esv_C1-n2'] = 'IgC1';
124763
124815
  ic.ref2igtype['FAB-HEAVY_5esv_V-n1'] = 'IgV';
124764
124816
  ic.ref2igtype['FAB-LIGHT_5esv_C1-n2'] = 'IgC1';
@@ -124769,28 +124821,28 @@ class Dssp {
124769
124821
  ic.ref2igtype['IL6Rb_1bquB_human_FN3-n3'] = 'IgFN3';
124770
124822
  ic.ref2igtype['InsulinR_8guyE_human_FN3-n1'] = 'IgFN3';
124771
124823
  ic.ref2igtype['InsulinR_8guyE_human_FN3-n2'] = 'IgFN3';
124772
- ic.ref2igtype['IsdA_2iteA_bacteria'] = 'IgE';
124824
+ //ic.ref2igtype['IsdA_2iteA_bacteria'] = 'IgE';
124773
124825
  ic.ref2igtype['JAM1_1nbqA_human_Iset-n2'] = 'IgI';
124774
124826
  ic.ref2igtype['LAG3_7tzgD_human_C1-n2'] = 'IgC1';
124775
124827
  ic.ref2igtype['LAG3_7tzgD_human_V-n1'] = 'IgV';
124776
124828
  ic.ref2igtype['LaminAC_1ifrA_human'] = 'Lamin';
124777
124829
  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';
124830
+ //ic.ref2igtype['MPT63_1lmiA_bacteria'] = 'IgFN3-like';
124831
+ //ic.ref2igtype['NaCaExchanger_2fwuA_dog_n2'] = 'IgFN3-like';
124832
+ //ic.ref2igtype['NaKATPaseTransporterBeta_2zxeB_spurdogshark'] = 'IgE';
124833
+ //ic.ref2igtype['ORF7a_1xakA_virus'] = 'ORF';
124782
124834
  ic.ref2igtype['PD1_4zqkB_human_V'] = 'IgV';
124783
124835
  ic.ref2igtype['PDL1_4z18B_human_V-n1'] = 'IgV';
124784
124836
  ic.ref2igtype['Palladin_2dm3A_human_Iset-n1'] = 'IgI';
124785
- ic.ref2igtype['RBPJ_6py8C_human_Unk-n1'] = 'IgFN3-like';
124837
+ //ic.ref2igtype['RBPJ_6py8C_human_Unk-n1'] = 'IgFN3-like';
124786
124838
  //ic.ref2igtype['RBPJ_6py8C_human_Unk-n2'] = 'IgFN3-like';
124787
124839
  ic.ref2igtype['Sidekick2_1wf5A_human_FN3-n7'] = 'IgFN3';
124788
124840
  ic.ref2igtype['Siglec3_5j0bB_human_C1-n2'] = 'IgC1';
124789
124841
  ic.ref2igtype['TCRa_6jxrm_human_C1-n2'] = 'IgC1';
124790
124842
  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';
124843
+ //ic.ref2igtype['TEAD1_3kysC_human'] = 'IgFN3-like';
124844
+ //ic.ref2igtype['TP34_2o6cA_bacteria'] = 'IgE';
124845
+ //ic.ref2igtype['TP47_1o75A_bacteria'] = 'IgE';
124794
124846
  ic.ref2igtype['Titin_4uowM_human_Iset-n152'] = 'IgI';
124795
124847
  ic.ref2igtype['VISTA_6oilA_human_V'] = 'IgV';
124796
124848
  ic.ref2igtype['VNAR_1t6vN_shark_V'] = 'IgV';
@@ -126341,6 +126393,7 @@ class Dssp {
126341
126393
  }
126342
126394
  else {
126343
126395
  let bBefore = false, bInRange= false, bAfter = false;
126396
+ /*
126344
126397
  // 100, 100A
126345
126398
  if(parseInt(currResi) == parseInt(strandArray[strandCnt].startResi) && currResi != strandArray[strandCnt].startResi) {
126346
126399
  bBefore = currResi < strandArray[strandCnt].startResi;
@@ -126356,6 +126409,14 @@ class Dssp {
126356
126409
  else {
126357
126410
  bAfter = parseInt(currResi) > parseInt(strandArray[strandCnt].endResi);
126358
126411
  }
126412
+ */
126413
+
126414
+ let currResiNcbi = ic.ParserUtilsCls.getResiNCBI(chnid, currResi);
126415
+ let startResiNcbi = ic.ParserUtilsCls.getResiNCBI(chnid, strandArray[strandCnt].startResi);
126416
+ let endResiNcbi = ic.ParserUtilsCls.getResiNCBI(chnid, strandArray[strandCnt].endResi);
126417
+
126418
+ bBefore = parseInt(currResiNcbi) < parseInt(startResiNcbi);
126419
+ bAfter = parseInt(currResiNcbi) > parseInt(endResiNcbi);
126359
126420
 
126360
126421
  bInRange = (!bBefore && !bAfter) ? true : false;
126361
126422
 
@@ -132174,8 +132235,9 @@ class ShareLink {
132174
132235
  }
132175
132236
 
132176
132237
  let paraHash = {};
132177
- for(let key in ic.cfg) {
132178
- let value = ic.cfg[key];
132238
+ /*
132239
+ for(let key in me.cfg) {
132240
+ let value = me.cfg[key];
132179
132241
  //if(key === 'inpara' || ic.key === 'command' || value === undefined) continue;
132180
132242
  if(key === 'inpara' || key === 'command' || key === 'usepdbnum'
132181
132243
  || key === 'date' || key === 'v' || value === undefined) continue;
@@ -132225,7 +132287,7 @@ class ShareLink {
132225
132287
  paraHash[key] = value;
132226
132288
  }
132227
132289
  }
132228
-
132290
+ */
132229
132291
  if(ic.bAfMem) {
132230
132292
  paraHash['afmem'] = 'on';
132231
132293
  }
@@ -132247,6 +132309,12 @@ class ShareLink {
132247
132309
  if(key_value.length == 2) paraHash[key_value[0]] = key_value[1];
132248
132310
  }
132249
132311
 
132312
+ // BLAST RID is usually added at the end of the URL. It should be included.
132313
+ if(me.cfg.rid && !paraHash['RID']) {
132314
+ url += 'RID=' + me.cfg.rid + '&';
132315
+ }
132316
+
132317
+ // sometimes idname is not part of the URL
132250
132318
  if(me.cfg.idname && !paraHash[me.cfg.idname]) { // somehow it is not included
132251
132319
  url += me.cfg.idname + '=' + me.cfg.idvalue + '&';
132252
132320
  }
@@ -135360,7 +135428,7 @@ class iCn3DUI {
135360
135428
  //even when multiple iCn3D viewers are shown together.
135361
135429
  this.pre = this.cfg.divid + "_";
135362
135430
 
135363
- this.REVISION = '3.47.1';
135431
+ this.REVISION = '3.48.1';
135364
135432
 
135365
135433
  // In nodejs, iCn3D defines "window = {navigator: {}}", and added window = {navigator: {}, "__THREE__":"177"}
135366
135434
  this.bNode = (Object.keys(window).length < 3) ? true : false;
@@ -135562,14 +135630,8 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
135562
135630
  let domainidArray = me.cfg.matchedchains.split(',');
135563
135631
  let chainidArray = [];
135564
135632
  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
- }
135633
+ let idArray = domainidArray[i].split('_');
135634
+ chainidArray.push(idArray[0] + '_' + idArray[1]);
135573
135635
  }
135574
135636
 
135575
135637
  // get the matched structures, do not include the template
@@ -135798,6 +135860,9 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
135798
135860
  if(me.cfg.align.indexOf('185055,') != -1) {
135799
135861
  me.cfg.align = me.cfg.align.replace('185055,', '199731,'); //the mmdbid of PDB 6M17 was changed from 185055 to 199731
135800
135862
  }
135863
+ else if(me.cfg.align == '54567,1,12161,1,2,1') {
135864
+ me.cfg.align = '3HHR,1BQU'; // somehow the VAST+ data for this published alignment were not there anymore
135865
+ }
135801
135866
 
135802
135867
  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
135868