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.js CHANGED
@@ -63093,20 +63093,20 @@ class SetDialog {
63093
63093
  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'];
63094
63094
  group2tpl['IgC2'] = ['CD2_1hnfA_human_C2-n2', 'CD3g_6jxrg_human_C2'];
63095
63095
  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'];
63096
- group2tpl['IgE'] = ['CoAtomerGamma1_1r4xA_human', 'Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'IsdA_2iteA_bacteria', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'TP34_2o6cA_bacteria', 'TP47_1o75A_bacteria'];
63096
+ //group2tpl['IgE'] = ['CoAtomerGamma1_1r4xA_human', 'Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'IsdA_2iteA_bacteria', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'TP34_2o6cA_bacteria', 'TP47_1o75A_bacteria'];
63097
63097
 
63098
63098
  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'];
63099
63099
 
63100
- 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'];
63100
+ //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'];
63101
63101
 
63102
- 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'];
63102
+ group2tpl['Other Ig'] = ['CD19_6al5A_human-n1', 'ECadherin_4zt1A_human_n2', 'LaminAC_1ifrA_human'];
63103
63103
 
63104
63104
  let tpl2strandsig = {};
63105
- tpl2strandsig['ASF1A_2iijA_human'] = "A A' B C C' E F G G+";
63105
+ //tpl2strandsig['ASF1A_2iijA_human'] = "A A' B C C' E F G G+";
63106
63106
  tpl2strandsig['B2Microglobulin_7phrL_human_C1'] = "A B C C' D E F G";
63107
- tpl2strandsig['BArrestin1_4jqiA_rat_n1'] = "A- A A' B C C' E F G";
63107
+ //tpl2strandsig['BArrestin1_4jqiA_rat_n1'] = "A- A A' B C C' E F G";
63108
63108
  tpl2strandsig['BTLA_2aw2A_human_Iset'] = "A A' B C C' D E F G";
63109
- tpl2strandsig['C3_2qkiD_human_n1'] = "A A' B C C' E F G";
63109
+ //tpl2strandsig['C3_2qkiD_human_n1'] = "A A' B C C' E F G";
63110
63110
  tpl2strandsig['CD19_6al5A_human-n1'] = "A' B C C' D E F G";
63111
63111
  tpl2strandsig['CD28_1yjdC_human_V'] = "A A' B C C' C'' D E F G";
63112
63112
  tpl2strandsig['CD2_1hnfA_human_C2-n2'] = "A B C C' E F G";
@@ -63115,12 +63115,12 @@ class SetDialog {
63115
63115
  tpl2strandsig['CD3e_6jxrf_human_C1'] = "A B C C' D E F G";
63116
63116
  tpl2strandsig['CD3g_6jxrg_human_C2'] = "A B C C' E F G G+";
63117
63117
  tpl2strandsig['CD8a_1cd8A_human_V'] = "A A' B C C' C'' D E F G";
63118
- tpl2strandsig['CoAtomerGamma1_1r4xA_human'] = "A- A B C D E F G";
63118
+ //tpl2strandsig['CoAtomerGamma1_1r4xA_human'] = "A- A B C D E F G";
63119
63119
  tpl2strandsig['Contactin1_2ee2A_human_FN3-n9'] = "A A' B C C' E F G";
63120
63120
  tpl2strandsig['Contactin1_3s97C_human_Iset-n2'] = "A A' B C D E F G";
63121
- tpl2strandsig['CuZnSuperoxideDismutase_1hl5C_human'] = "A- A B C C' E F G";
63121
+ //tpl2strandsig['CuZnSuperoxideDismutase_1hl5C_human'] = "A- A B C C' E F G";
63122
63122
  tpl2strandsig['ECadherin_4zt1A_human_n2'] = "A' B C D E F G";
63123
- tpl2strandsig['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = "A--- A-- A- A B C C' C'' D E F G";
63123
+ //tpl2strandsig['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = "A--- A-- A- A B C C' C'' D E F G";
63124
63124
  tpl2strandsig['FAB-HEAVY_5esv_C1-n2'] = "A B C D E F G";
63125
63125
  tpl2strandsig['FAB-HEAVY_5esv_V-n1'] = "A B C C' C'' D E F G";
63126
63126
  tpl2strandsig['FAB-LIGHT_5esv_C1-n2'] = "A B C C' D E F G";
@@ -63131,28 +63131,28 @@ class SetDialog {
63131
63131
  tpl2strandsig['IL6Rb_1bquB_human_FN3-n3'] = "A B C C' E F G";
63132
63132
  tpl2strandsig['InsulinR_8guyE_human_FN3-n1'] = "A B C C' E F G";
63133
63133
  tpl2strandsig['InsulinR_8guyE_human_FN3-n2'] = "A B C C' E F G";
63134
- tpl2strandsig['IsdA_2iteA_bacteria'] = "A- A B C C' D E F G";
63134
+ //tpl2strandsig['IsdA_2iteA_bacteria'] = "A- A B C C' D E F G";
63135
63135
  tpl2strandsig['JAM1_1nbqA_human_Iset-n2'] = "A A' B C C' D E F G";
63136
63136
  tpl2strandsig['LAG3_7tzgD_human_C1-n2'] = "A A' B C C' D E F G";
63137
63137
  tpl2strandsig['LAG3_7tzgD_human_V-n1'] = "A' B C C' D E F G";
63138
63138
  tpl2strandsig['LaminAC_1ifrA_human'] = "A- A B C C' E E+ F G";
63139
63139
  tpl2strandsig['MHCIa_7phrH_human_C1'] = "A B C C' D E F G";
63140
- tpl2strandsig['MPT63_1lmiA_bacteria'] = "A-- A- A BC C' E F G";
63141
- tpl2strandsig['NaCaExchanger_2fwuA_dog_n2'] = "A A' B C C' E F G";
63142
- tpl2strandsig['NaKATPaseTransporterBeta_2zxeB_spurdogshark']= "A A' B C D E F G";
63143
- tpl2strandsig['ORF7a_1xakA_virus'] = "A' B C D E F G";
63140
+ //tpl2strandsig['MPT63_1lmiA_bacteria'] = "A-- A- A BC C' E F G";
63141
+ //tpl2strandsig['NaCaExchanger_2fwuA_dog_n2'] = "A A' B C C' E F G";
63142
+ //tpl2strandsig['NaKATPaseTransporterBeta_2zxeB_spurdogshark']= "A A' B C D E F G";
63143
+ //tpl2strandsig['ORF7a_1xakA_virus'] = "A' B C D E F G";
63144
63144
  tpl2strandsig['PD1_4zqkB_human_V'] = "A A' B C C' D E F G";
63145
63145
  tpl2strandsig['PDL1_4z18B_human_V-n1'] = "A A' B C C' C'' D E F G";
63146
63146
  tpl2strandsig['Palladin_2dm3A_human_Iset-n1'] = "A A' B C C' D E F G";
63147
- tpl2strandsig['RBPJ_6py8C_human_Unk-n1'] = "A A' B C C' E F G";
63148
- tpl2strandsig['RBPJ_6py8C_human_Unk-n2'] = "A B C D E F G";
63147
+ //tpl2strandsig['RBPJ_6py8C_human_Unk-n1'] = "A A' B C C' E F G";
63148
+ //tpl2strandsig['RBPJ_6py8C_human_Unk-n2'] = "A B C D E F G";
63149
63149
  tpl2strandsig['Sidekick2_1wf5A_human_FN3-n7'] = "A B C C' E F G";
63150
63150
  tpl2strandsig['Siglec3_5j0bB_human_C1-n2'] = "A A' B C D E F G";
63151
63151
  tpl2strandsig['TCRa_6jxrm_human_C1-n2'] = "A B C D E F G";
63152
63152
  tpl2strandsig['TCRa_6jxrm_human_V-n1'] = "A A' B C C' C'' D E F G";
63153
- tpl2strandsig['TEAD1_3kysC_human'] = "A A+ A' B C C' E F G G+";
63154
- tpl2strandsig['TP34_2o6cA_bacteria'] = "A- A B C C' D E F G";
63155
- tpl2strandsig['TP47_1o75A_bacteria'] = "A B C C' D E F G";
63153
+ //tpl2strandsig['TEAD1_3kysC_human'] = "A A+ A' B C C' E F G G+";
63154
+ //tpl2strandsig['TP34_2o6cA_bacteria'] = "A- A B C C' D E F G";
63155
+ //tpl2strandsig['TP47_1o75A_bacteria'] = "A B C C' D E F G";
63156
63156
  tpl2strandsig['Titin_4uowM_human_Iset-n152'] = "A A' B C C' D E F G";
63157
63157
  tpl2strandsig['VISTA_6oilA_human_V'] = "A A' B C C' C'' D E F G G+";
63158
63158
  tpl2strandsig['VNAR_1t6vN_shark_V'] = "A A' B C C' D E F G";
@@ -74518,7 +74518,7 @@ class Scene {
74518
74518
  if(ic.opts['slab'] === 'yes') ic.cameraCls.setSlab();
74519
74519
 
74520
74520
  // if(!ic.bSetVrArButtons) { // call once
74521
- if(!me.cfg.imageonly) this.setVrArButtons();
74521
+ if(!me.cfg.imageonly && ( 'xr' in navigator )) this.setVrArButtons();
74522
74522
  // }
74523
74523
 
74524
74524
  // if((ic.bVr || ic.bAr) && !ic.bSetVrAr) { // call once
@@ -79510,7 +79510,7 @@ class Strand {
79510
79510
  let bShowArray = [];
79511
79511
  let calphaIdArray = []; // used to store one of the final positions drawn in 3D
79512
79512
  let colors = [];
79513
- let currentChain, currentCA = null, currentO = null, currentColor = null, prevCoorCA = null, prevCoorO = null, prevColor = null;
79513
+ let currentChain, currentStyle, currentCA = null, currentO = null, currentColor = null, prevCoorCA = null, prevCoorO = null, prevColor = null;
79514
79514
  let prevCO = null, ss = null, ssend = false, atomid = null, prevAtomid = null, prevResi = null, calphaid = null, prevCalphaid = null;
79515
79515
  let strandWidth, bSheetSegment = false, bHelixSegment = false;
79516
79516
  let atom, tubeAtoms = {};
@@ -79563,15 +79563,15 @@ class Strand {
79563
79563
  }
79564
79564
  // smoothen each coil, helix and sheet separately. The joint residue has to be included both in the previous and next segment
79565
79565
  let bSameChain = true;
79566
- // if (currentChain !== atom.chain || currentResi + 1 !== atom.resi) {
79566
+
79567
79567
  if (currentChain !== atom.chain) {
79568
79568
  bSameChain = false;
79569
79569
  }
79570
79570
 
79571
- if(atom.ssend && atom.ss === 'sheet') {
79571
+ if((atom.ssend || currentStyle != atom.style)&& atom.ss === 'sheet') {
79572
79572
  bSheetSegment = true;
79573
79573
  }
79574
- else if(atom.ssend && atom.ss === 'helix') {
79574
+ else if((atom.ssend || currentStyle != atom.style) && atom.ss === 'helix') {
79575
79575
  bHelixSegment = true;
79576
79576
  }
79577
79577
 
@@ -79664,7 +79664,7 @@ class Strand {
79664
79664
  // bHelixSegment = true;
79665
79665
  // }
79666
79666
 
79667
- if ((atom.ssbegin || atom.ssend || (drawnResidueCount === totalResidueCount - 1) || bBrokenSs) && pnts[0].length > 0 && bSameChain) {
79667
+ if ((atom.ssbegin || atom.ssend || (drawnResidueCount === totalResidueCount - 1) || bBrokenSs || currentStyle != atom.style) && pnts[0].length > 0 && bSameChain) {
79668
79668
  let atomName = 'CA';
79669
79669
 
79670
79670
  let prevone = [], nexttwo = [];
@@ -79807,9 +79807,7 @@ class Strand {
79807
79807
  } // end if (atom.ssbegin || atom.ssend)
79808
79808
 
79809
79809
  // end of a chain
79810
- // if ((currentChain !== atom.chain || currentResi + 1 !== atom.resi) && pnts[0].length > 0) {
79811
- if ((currentChain !== atom.chain) && pnts[0].length > 0) {
79812
-
79810
+ if ((currentChain !== atom.chain || currentStyle != atom.style) && pnts[0].length > 0) {
79813
79811
  let atomName = 'CA';
79814
79812
 
79815
79813
  let prevone = [], nexttwo = [];
@@ -79861,7 +79859,7 @@ class Strand {
79861
79859
  }
79862
79860
 
79863
79861
  currentChain = atom.chain;
79864
- atom.resi;
79862
+ currentStyle = atom.style;
79865
79863
  ss = atom.ss;
79866
79864
  ssend = atom.ssend;
79867
79865
  prevAtomid = atom.serial;
@@ -83973,7 +83971,7 @@ class ApplyMissingRes {
83973
83971
  line.serial1 = ic.missingResResid2serial[resid0 + ',' + resid1];
83974
83972
  line.serial2 = ic.missingResResid2serial[resid1 + ',' + resid0];
83975
83973
 
83976
- line.color = "#" + ic.atoms[line.serial1].color.getHexString();
83974
+ line.color = (ic.atoms[line.serial1]) ? "#" + ic.atoms[line.serial1].color.getHexString() : undefined;
83977
83975
 
83978
83976
  line.radius = ic.coilWidth;
83979
83977
 
@@ -88828,6 +88826,9 @@ class SetStyle {
88828
88826
  setBackground(color) {var ic = this.icn3d, me = ic.icn3dui;
88829
88827
 
88830
88828
  ic.setOptionCls.setOption('background', color);
88829
+ let exdays = 3650;
88830
+ me.htmlCls.setHtmlCls.setCookie('bkgdcolor', color, exdays);
88831
+
88831
88832
  me.htmlCls.clickMenuCls.setLogCmd('set background ' + color, true);
88832
88833
  //let titleColor =(color == 'black' || color == 'transparent') ? me.htmlCls.GREYD : 'black';
88833
88834
  let titleColor = (color == 'black') ? me.htmlCls.GREYD : 'black';
@@ -99430,7 +99431,7 @@ class HlUpdate {
99430
99431
  if(ic.mmdbid_q !== undefined && ic.mmdbid_q === ic.mmdbid_t) {
99431
99432
  html2ddgm += ic.diagram2dCls.draw2Ddgm(ic.interactionData2, ic.mmdbidArray[0].toUpperCase(), 1, true);
99432
99433
  }
99433
- else {
99434
+ else if(ic.mmdbidArray.length > 1) {
99434
99435
  html2ddgm += ic.diagram2dCls.draw2Ddgm(ic.interactionData2, ic.mmdbidArray[1].toUpperCase(), 1, true);
99435
99436
  }
99436
99437
  html2ddgm += ic.diagram2dCls.set2DdgmNote(true);
@@ -103712,16 +103713,31 @@ class ChainalignParser {
103712
103713
 
103713
103714
  // dynamically align pairs in all chainids
103714
103715
  // the resrange from VASTSrv or VAST search uses NCBI residue numbers!!!
103715
- let atomSet_t = (me.cfg.resrange) ? ic.realignParserCls.getSeqCoorResid([resRangeArray[0]], chainidArray[0], true).hAtoms : ic.chains[chainidArray[0]];
103716
+ let atomSet_t;
103717
+ if(me.cfg.resrange) {
103718
+ let result = ic.realignParserCls.getSeqCoorResid([resRangeArray[0]], chainidArray[0], true);
103719
+ atomSet_t = result.hAtoms;
103720
+ }
103721
+ else {
103722
+ atomSet_t = ic.chains[chainidArray[0]];
103723
+ }
103724
+
103716
103725
  for(let index = 1, indexl = chainidArray.length; index < indexl; ++index) {
103717
- let atomSet_q = (me.cfg.resrange) ? ic.realignParserCls.getSeqCoorResid([resRangeArray[index]], chainidArray[index], true).hAtoms : ic.chains[chainidArray[index]];
103726
+ let atomSet_q;
103727
+ if(me.cfg.resrange) {
103728
+ let result = ic.realignParserCls.getSeqCoorResid([resRangeArray[index]], chainidArray[index], true);
103729
+ atomSet_q = result.hAtoms;
103730
+ }
103731
+ else {
103732
+ atomSet_q = ic.chains[chainidArray[index]];
103733
+ }
103718
103734
  // end of new version to be done for VASTsrv ==============
103719
103735
 
103720
103736
  let alignAjax;
103721
103737
  if(me.cfg.aligntool != 'tmalign') {
103722
103738
  let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(atomSet_q);
103723
103739
  let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(atomSet_t);
103724
-
103740
+
103725
103741
  let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
103726
103742
  alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
103727
103743
  }
@@ -103757,6 +103773,7 @@ class ChainalignParser {
103757
103773
  //let bTargetTransformed = (ic.qt_start_end[0]) ? true : false;
103758
103774
 
103759
103775
  // modify the previous trans and rotation matrix
103776
+ let bAligned = false;
103760
103777
  for(let i = 0, il = dataArray.length; i < il; ++i) {
103761
103778
  // let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
103762
103779
  let align = dataArray[i].value;//[0];
@@ -103772,7 +103789,7 @@ class ChainalignParser {
103772
103789
 
103773
103790
  me.htmlCls.clickMenuCls.setLogCmd("Align " + mmdbid_t + " with " + mmdbid_q, false);
103774
103791
 
103775
- this.processAlign(align, index, queryData, bEqualMmdbid, bEqualChain);
103792
+ bAligned =await this.processAlign(align, index, queryData, bEqualMmdbid, bEqualChain, undefined);
103776
103793
  }
103777
103794
 
103778
103795
  // do not transform the target
@@ -103780,28 +103797,34 @@ class ChainalignParser {
103780
103797
  // this.transformStructure(mmdbid_t, indexArray[0], 'target');
103781
103798
  //}
103782
103799
 
103783
- // transform the rest
103784
- for(let i = 0, il = dataArray.length; i < il; ++i) {
103785
- let mmdbid_q = struArray[i];
103786
- let index = indexArray[i];
103787
- this.transformStructure(mmdbid_q, index, 'query');
103788
- }
103800
+ if(bAligned) {
103801
+ // transform the rest
103802
+ for(let i = 0, il = dataArray.length; i < il; ++i) {
103803
+ let mmdbid_q = struArray[i];
103804
+ let index = indexArray[i];
103805
+ this.transformStructure(mmdbid_q, index, 'query');
103806
+ }
103789
103807
 
103790
- let hAtomsAll = {};
103808
+ let hAtomsAll = {};
103791
103809
 
103792
- if(ic.bFullUi && ic.q_rotation !== undefined && !me.cfg.resnum && !me.cfg.resdef) {
103793
- // set multiple sequence alignment from ic.qt_start_end
103794
- hAtomsAll = this.setMsa(chainidArray);
103795
- }
103810
+ if(ic.bFullUi && ic.q_rotation !== undefined && !me.cfg.resnum && !me.cfg.resdef) {
103811
+ // set multiple sequence alignment from ic.qt_start_end
103812
+ hAtomsAll = this.setMsa(chainidArray);
103813
+ }
103796
103814
 
103797
- // highlight all aligned atoms
103798
- //ic.hAtoms = me.hashUtilsCls.cloneHash(hAtomsTmp);
103799
- ic.hAtoms = me.hashUtilsCls.cloneHash(hAtomsAll);
103815
+ // highlight all aligned atoms
103816
+ //ic.hAtoms = me.hashUtilsCls.cloneHash(hAtomsTmp);
103817
+ ic.hAtoms = me.hashUtilsCls.cloneHash(hAtomsAll);
103800
103818
 
103801
- ic.transformCls.zoominSelection();
103819
+ ic.transformCls.zoominSelection();
103802
103820
 
103803
- // do the rest
103804
- await this.downloadChainalignmentPart3(chainresiCalphaHash2, chainidArray, ic.hAtoms);
103821
+ // do the rest
103822
+ await this.downloadChainalignmentPart3(chainresiCalphaHash2, chainidArray, ic.hAtoms);
103823
+ }
103824
+ else {
103825
+ me.cfg.aligntool = 'tmalign';
103826
+ await ic.chainalignParserCls.downloadChainalignment(me.cfg.chainalign);
103827
+ }
103805
103828
  }
103806
103829
 
103807
103830
  setMsa(chainidArray, bVastplus, bRealign) { let ic = this.icn3d, me = ic.icn3dui;
@@ -103872,7 +103895,7 @@ class ChainalignParser {
103872
103895
 
103873
103896
  let bNoAlert = true;
103874
103897
 
103875
- let bAligned = this.processAlign(align, i, queryData, bEqualMmdbid, bEqualChain, bNoAlert);
103898
+ let bAligned = await this.processAlign(align, i, queryData, bEqualMmdbid, bEqualChain, bNoAlert);
103876
103899
 
103877
103900
  if(bAligned) {
103878
103901
  bFoundAlignment = true;
@@ -104364,7 +104387,7 @@ class ChainalignParser {
104364
104387
 
104365
104388
  me.htmlCls.clickMenuCls.setLogCmd("Align " + mmdbid_t + " with " + mmdbid_q, false);
104366
104389
 
104367
- this.processAlign(align, index-1, queryData, bEqualMmdbid, bEqualChain);
104390
+ await this.processAlign(align, index-1, queryData, bEqualMmdbid, bEqualChain, undefined);
104368
104391
  }
104369
104392
  }
104370
104393
  }
@@ -104374,13 +104397,13 @@ class ChainalignParser {
104374
104397
  await this.loadOpmDataForChainalign(targetData, queryDataArray, chainidArray, ic.mmdbidArray);
104375
104398
  }
104376
104399
 
104377
- processAlign(align, index, queryData, bEqualMmdbid, bEqualChain, bNoAlert) { let ic = this.icn3d, me = ic.icn3dui;
104400
+ async processAlign(align, index, queryData, bEqualMmdbid, bEqualChain, bNoAlert) { let ic = this.icn3d, me = ic.icn3dui;
104378
104401
  let bAligned = false;
104379
104402
 
104380
- if((!align || align.length == 0) && !bNoAlert) {
104381
- let serverName = (me.cfg.aligntool == 'tmalign') ? 'TM-align' : 'VAST';
104382
-
104383
- if(ic.bRender) var aaa = 1; //alert("These chains can not be aligned by " + serverName + ".");
104403
+ if((align === "error" || align === undefined || align.length == 0) && !bNoAlert) {
104404
+ // let serverName = (me.cfg.aligntool == 'tmalign') ? 'TM-align' : 'VAST';
104405
+
104406
+ // if(ic.bRender) var aaa = 1; //alert("These chains can not be aligned by " + serverName + ".");
104384
104407
  return bAligned;
104385
104408
  }
104386
104409
 
@@ -104529,7 +104552,6 @@ class ChainalignParser {
104529
104552
  let structArrayTmp = idlist.split(',');
104530
104553
 
104531
104554
  let structArray = [];
104532
-
104533
104555
  // only when bNoDuplicate is undefined/false, it's allowed to load multiple copies of the same structure
104534
104556
  if(!bNoDuplicate) {
104535
104557
  structArray = this.addPostfixForStructureids(structArrayTmp);
@@ -104542,7 +104564,7 @@ class ChainalignParser {
104542
104564
  if(!ic.structures.hasOwnProperty(id)) structArray.push(structArrayTmp[i]);
104543
104565
  }
104544
104566
  }
104545
-
104567
+
104546
104568
  if(structArray.length == 0) return;
104547
104569
 
104548
104570
  ic.structArray = ic.structArray.concat(structArray);
@@ -104642,6 +104664,8 @@ class ChainalignParser {
104642
104664
  let bNoSeqalign = true;
104643
104665
  let pdbid = structArray[i];
104644
104666
 
104667
+ if(queryDataArray[i].pdbId) queryDataArray[i].pdbId = pdbid;
104668
+
104645
104669
  //hAtomsTmp contains all atoms
104646
104670
  await ic.mmdbParserCls.parseMmdbData(queryDataArray[i], targetOrQuery, undefined, undefined, bLastQuery, bNoSeqalign, pdbid);
104647
104671
  }
@@ -106218,7 +106242,7 @@ class MmdbParser {
106218
106242
  return;
106219
106243
  }
106220
106244
 
106221
- if(Object.keys(data.atoms).length == 0) { // for large structures such as 3J3Q
106245
+ if(!data.atoms || Object.keys(data.atoms).length == 0) { // for large structures such as 3J3Q
106222
106246
  // use mmtfid
106223
106247
  let pdbid = data.pdbId;
106224
106248
  await ic.bcifParserCls.downloadBcif(pdbid);
@@ -106228,6 +106252,7 @@ class MmdbParser {
106228
106252
 
106229
106253
  let bCalphaOnly = me.utilsCls.isCalphaPhosOnly(data.atoms); //, 'CA');
106230
106254
 
106255
+ //if(!data.pdbId) data.pdbId = mmdbid;
106231
106256
  if(bCalphaOnly || data.atomCount <= ic.maxatomcnt) {
106232
106257
  await this.parseMmdbData(data);
106233
106258
  }
@@ -106389,8 +106414,18 @@ class MmdbParser {
106389
106414
  async parseMmdbData(data, type, chainid, chainIndex, bLastQuery, bNoTransformNoSeqalign, pdbidIn) { let ic = this.icn3d, me = ic.icn3dui;
106390
106415
  let hAtoms;
106391
106416
  let pdbid = (data.pdbId !== undefined) ? data.pdbId : data.mmdbId;
106417
+ if(!pdbid && chainid) {
106418
+ pdbid = chainid.substr(0, chainid.lastIndexOf('_'));
106419
+ }
106420
+
106392
106421
  if(pdbidIn) pdbid = pdbidIn;
106393
106422
 
106423
+ // if(!data.atoms || Object.keys(data.atoms).length == 0) { // for large structures such as 3J3Q
106424
+ // ic.bRender = false;
106425
+ // await ic.bcifParserCls.downloadBcif(pdbid);
106426
+ // return;
106427
+ // }
106428
+
106394
106429
  this.parseMmdbDataPart1(data, type);
106395
106430
 
106396
106431
  if(type === undefined) { // default mmdbid input
@@ -108057,7 +108092,7 @@ class PdbParser {
108057
108092
  }
108058
108093
 
108059
108094
  // if(!ic.bSecondaryStructure && Object.keys(ic.proteins).length > 0) {
108060
- if((!ic.bSecondaryStructure || bCalcSecondary) && Object.keys(ic.proteins).length > 0 && !bNoDssp) {
108095
+ if((!ic.bSecondaryStructure || bCalcSecondary) && Object.keys(ic.proteins).length > 0 && !bNoDssp) {
108061
108096
  await this.applyCommandDssp(bAppend);
108062
108097
  }
108063
108098
  else {
@@ -110032,8 +110067,7 @@ class RealignParser {
110032
110067
  // If rmsd from vastsrv is too large, realign the chains
110033
110068
  //if(me.cfg.chainalign && !me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5) {
110034
110069
  // redo algnment only for VAST serv page
110035
- if(!me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5 && me.cfg.chainalign) {
110036
- console.log("RMSD from VAST is larger than 5. Realign the chains with TM-align.");
110070
+ if(!me.cfg.usepdbnum && (me.cfg.resdef || me.cfg.resrange) && rmsd > 5 && me.cfg.chainalign) {
110037
110071
  //let nameArray = me.cfg.chainalign.split(',');
110038
110072
  let nameArray = Object.keys(chainidHash);
110039
110073
  if(nameArray.length > 0) {
@@ -110285,15 +110319,30 @@ let resRangeArray = (me.cfg.resrange) ? decodeURIComponent(me.cfg.resrange).spli
110285
110319
  if(bVastsearch && me.cfg.resrange) {
110286
110320
  let resRangeArray = decodeURIComponent(me.cfg.resrange).split(' | ');
110287
110321
 
110288
- let atomSet_t = ic.realignParserCls.getSeqCoorResid([resRangeArray[0]], ic.chainidArray[0], true).hAtoms;
110322
+ let atomSet_t;
110323
+ if(me.cfg.resrange) {
110324
+ let result = ic.realignParserCls.getSeqCoorResid([resRangeArray[0]], ic.chainidArray[0], true);
110325
+ atomSet_t = result.hAtoms;
110326
+ }
110327
+ else {
110328
+ atomSet_t = ic.chains[ic.chainidArray[0]];
110329
+ }
110330
+
110289
110331
  for(let index = 1, indexl = ic.chainidArray.length; index < indexl; ++index) {
110290
- let atomSet_q = ic.realignParserCls.getSeqCoorResid([resRangeArray[index]], ic.chainidArray[index], true).hAtoms;
110332
+ let atomSet_q;
110333
+ if(me.cfg.resrange) {
110334
+ let result = ic.realignParserCls.getSeqCoorResid([resRangeArray[index]], ic.chainidArray[index], true);
110335
+ atomSet_q = result.hAtoms;
110336
+ }
110337
+ else {
110338
+ atomSet_q = ic.chains[ic.chainidArray[index]];
110339
+ }
110291
110340
 
110292
110341
  let alignAjax;
110293
110342
  if(me.cfg.aligntool != 'tmalign') {
110294
110343
  let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(atomSet_q);
110295
110344
  let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(atomSet_t);
110296
-
110345
+
110297
110346
  let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
110298
110347
  alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
110299
110348
  }
@@ -110354,9 +110403,7 @@ let resRangeArray = (me.cfg.resrange) ? decodeURIComponent(me.cfg.resrange).spli
110354
110403
  let alignAjax;
110355
110404
  if(me.cfg.aligntool != 'tmalign') {
110356
110405
  let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(struct2domain[struct2][chainid2]);
110357
- console.log("@@@ realign " + struct1 + " " + chainid1 + " and " + struct2 + " " + chainid2);
110358
- console.log("@@@ jsonStr_q " + jsonStr_q);
110359
- console.log("@@@ jsonStr_t " + jsonStr_t);
110406
+
110360
110407
  let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
110361
110408
  alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
110362
110409
  }
@@ -110426,7 +110473,7 @@ console.log("@@@ jsonStr_t " + jsonStr_t);
110426
110473
 
110427
110474
  if(me.cfg.aligntool != 'tmalign') {
110428
110475
  let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(chainid2domain[chainid2]);
110429
-
110476
+
110430
110477
  let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
110431
110478
  alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
110432
110479
  }
@@ -110686,6 +110733,8 @@ console.log("@@@ jsonStr_t " + jsonStr_t);
110686
110733
  let hAtoms = {};
110687
110734
 
110688
110735
  for(let j = 0, jl = resiArray.length; j < jl; ++j) {
110736
+ if(!resiArray[j]) continue;
110737
+
110689
110738
  if(resiArray[j].indexOf('-') != -1) {
110690
110739
  let startEnd = resiArray[j].split('-');
110691
110740
  for(let k = parseInt(startEnd[0]); k <= parseInt(startEnd[1]); ++k) {
@@ -115856,7 +115905,8 @@ class LoadPDB {
115856
115905
  }
115857
115906
 
115858
115907
  isSecondary(resid, residArray, bNMR, bNonFull) { let ic = this.icn3d; ic.icn3dui;
115859
- if(bNonFull) return false;
115908
+ // still need to get the secondary info
115909
+ //if(bNonFull) return false;
115860
115910
 
115861
115911
  if(!bNMR) {
115862
115912
  return $.inArray(resid, residArray) != -1;
@@ -118226,16 +118276,18 @@ class ApplyCommand {
118226
118276
  }
118227
118277
  else if(command.indexOf('set background') == 0) {
118228
118278
  let value = command.substr(command.lastIndexOf(' ') + 1);
118229
- ic.opts['background'] = value;
118279
+ ic.setStyleCls.setBackground(value);
118230
118280
 
118231
- if(value == 'black') {
118232
- $("#" + ic.pre + "title").css("color", me.htmlCls.GREYD);
118233
- $("#" + ic.pre + "titlelink").css("color", me.htmlCls.GREYD);
118234
- }
118235
- else {
118236
- $("#" + ic.pre + "title").css("color", "black");
118237
- $("#" + ic.pre + "titlelink").css("color", "black");
118238
- }
118281
+ // ic.opts['background'] = value;
118282
+
118283
+ // if(value == 'black') {
118284
+ // $("#" + ic.pre + "title").css("color", me.htmlCls.GREYD);
118285
+ // $("#" + ic.pre + "titlelink").css("color", me.htmlCls.GREYD);
118286
+ // }
118287
+ // else {
118288
+ // $("#" + ic.pre + "title").css("color", "black");
118289
+ // $("#" + ic.pre + "titlelink").css("color", "black");
118290
+ // }
118239
118291
  }
118240
118292
  else if(command.indexOf('set label color') == 0) {
118241
118293
  ic.labelcolor = command.substr(command.lastIndexOf(' ') + 1);
@@ -123762,29 +123814,29 @@ class Dssp {
123762
123814
 
123763
123815
  setRefPdbs() { let ic = this.icn3d; ic.icn3dui;
123764
123816
  // round 1, 16 templates
123765
- 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'];
123817
+ 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'];
123766
123818
 
123767
123819
  // round 2
123768
123820
  ic.refpdbHash = {};
123769
123821
  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'];
123770
- ic.refpdbHash['1Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = ['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'ICOS_6x4gA_human_V'];
123771
- ic.refpdbHash['1CoAtomerGamma1_1r4xA_human'] = ['CoAtomerGamma1_1r4xA_human', 'TP34_2o6cA_bacteria'];
123772
- ic.refpdbHash['1C3_2qkiD_human_n1'] = ['C3_2qkiD_human_n1', 'BArrestin1_4jqiA_rat_n1', 'RBPJ_6py8C_human_Unk-n1'];
123773
- ic.refpdbHash['1CuZnSuperoxideDismutase_1hl5C_human'] = ['CuZnSuperoxideDismutase_1hl5C_human', 'TEAD1_3kysC_human'];
123774
- ic.refpdbHash['1ASF1A_2iijA_human'] = ['ASF1A_2iijA_human', 'RBPJ_6py8C_human_Unk-n2', 'TP47_1o75A_bacteria'];
123822
+ ic.refpdbHash['1ICOS_6x4gA_human_V'] = ['ICOS_6x4gA_human_V'];
123823
+ //ic.refpdbHash['1CoAtomerGamma1_1r4xA_human'] = ['CoAtomerGamma1_1r4xA_human', 'TP34_2o6cA_bacteria'];
123824
+ //ic.refpdbHash['1C3_2qkiD_human_n1'] = ['C3_2qkiD_human_n1', 'RBPJ_6py8C_human_Unk-n1'];
123825
+ //ic.refpdbHash['1CuZnSuperoxideDismutase_1hl5C_human'] = ['TEAD1_3kysC_human'];
123826
+ //ic.refpdbHash['1ASF1A_2iijA_human'] = ['ASF1A_2iijA_human', 'TP47_1o75A_bacteria'];
123775
123827
  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'];
123776
123828
  ic.refpdbHash['1CD2_1hnfA_human_C2-n2'] = ['CD2_1hnfA_human_C2-n2', 'Siglec3_5j0bB_human_C1-n2'];
123777
- ic.refpdbHash['1NaCaExchanger_2fwuA_dog_n2'] = ['NaCaExchanger_2fwuA_dog_n2', 'ORF7a_1xakA_virus', 'ECadherin_4zt1A_human_n2'];
123778
- ic.refpdbHash['1NaKATPaseTransporterBeta_2zxeB_spurdogshark'] = ['NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
123829
+ ic.refpdbHash['1ECadherin_4zt1A_human_n2'] = ['ECadherin_4zt1A_human_n2'];
123830
+ //ic.refpdbHash['1NaKATPaseTransporterBeta_2zxeB_spurdogshark'] = ['NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
123779
123831
  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'];
123780
123832
  ic.refpdbHash['1PDL1_4z18B_human_V-n1'] = ['PDL1_4z18B_human_V-n1', 'CD2_1hnfA_human_V-n1', 'LAG3_7tzgD_human_V-n1'];
123781
123833
  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'];
123782
123834
  ic.refpdbHash['1LaminAC_1ifrA_human'] = ['LaminAC_1ifrA_human', 'CD3d_6jxrd_human_C1'];
123783
- ic.refpdbHash['1CD3g_6jxrg_human_C2'] = ['CD3g_6jxrg_human_C2', 'TCRa_6jxrm_human_C1-n2', 'IsdA_2iteA_bacteria'];
123784
- ic.refpdbHash['1CD28_1yjdC_human_V'] = ['CD28_1yjdC_human_V', 'MPT63_1lmiA_bacteria', 'CD3e_6jxrf_human_C1'];
123835
+ ic.refpdbHash['1CD3g_6jxrg_human_C2'] = ['CD3g_6jxrg_human_C2', 'TCRa_6jxrm_human_C1-n2'];
123836
+ ic.refpdbHash['1CD28_1yjdC_human_V'] = ['CD28_1yjdC_human_V', 'CD3e_6jxrf_human_C1'];
123785
123837
  ic.refpdbHash['1CD19_6al5A_human-n1'] = ['CD19_6al5A_human-n1'];
123786
123838
 
123787
- 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'];
123839
+ 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'];
123788
123840
 
123789
123841
  // use known ref structure
123790
123842
  ic.refpdbHash['5ESV_C'] = ['FAB-HEAVY_5esv_V-n1', 'FAB-HEAVY_5esv_C1-n2'];
@@ -123793,36 +123845,36 @@ class Dssp {
123793
123845
  ic.refpdbHash['6JXR_m'] = ['TCRa_6jxrm_human_V-n1', 'TCRa_6jxrm_human_C1-n2'];
123794
123846
  ic.refpdbHash['1HNF_A'] = ['CD2_1hnfA_human_V-n1', 'CD2_1hnfA_human_C2-n2'];
123795
123847
  ic.refpdbHash['7TZG_D'] = ['LAG3_7tzgD_human_V-n1', 'LAG3_7tzgD_human_C1-n2'];
123796
- ic.refpdbHash['6PY8_C'] = ['RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2'];
123848
+ //ic.refpdbHash['6PY8_C'] = ['RBPJ_6py8C_human_Unk-n1'];
123797
123849
  ic.refpdbHash['1BQU_B'] = ['IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3'];
123798
123850
 
123799
- ic.refpdbHash['1R4X_A'] = ['CoAtomerGamma1_1r4xA_human'];
123851
+ //ic.refpdbHash['1R4X_A'] = ['CoAtomerGamma1_1r4xA_human'];
123800
123852
  ic.refpdbHash['6OIL_A'] = ['VISTA_6oilA_human_V'];
123801
- ic.refpdbHash['2ZXE_B'] = ['NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
123802
- ic.refpdbHash['1I8A_A'] = ['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'];
123803
- ic.refpdbHash['2FWU_A'] = ['NaCaExchanger_2fwuA_dog_n2'];
123804
- ic.refpdbHash['4JQI_A'] = ['BArrestin1_4jqiA_rat_n1'];
123853
+ //ic.refpdbHash['2ZXE_B'] = ['NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
123854
+ //ic.refpdbHash['1I8A_A'] = ['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'];
123855
+ //ic.refpdbHash['2FWU_A'] = ['NaCaExchanger_2fwuA_dog_n2'];
123856
+ //ic.refpdbHash['4JQI_A'] = ['BArrestin1_4jqiA_rat_n1'];
123805
123857
  ic.refpdbHash['1NBQ_A'] = ['JAM1_1nbqA_human_Iset-n2'];
123806
- ic.refpdbHash['1O75_A'] = ['TP47_1o75A_bacteria'];
123858
+ //ic.refpdbHash['1O75_A'] = ['TP47_1o75A_bacteria'];
123807
123859
  ic.refpdbHash['7PHR_H'] = ['MHCIa_7phrH_human_C1'];
123808
- ic.refpdbHash['2IIJ_A'] = ['ASF1A_2iijA_human'];
123860
+ //ic.refpdbHash['2IIJ_A'] = ['ASF1A_2iijA_human'];
123809
123861
  ic.refpdbHash['4Z18_B'] = ['PDL1_4z18B_human_V-n1'];
123810
123862
  ic.refpdbHash['1T6V_N'] = ['VNAR_1t6vN_shark_V'];
123811
- ic.refpdbHash['2O6C_A'] = ['TP34_2o6cA_bacteria'];
123812
- ic.refpdbHash['3KYS_C'] = ['TEAD1_3kysC_human'];
123863
+ //ic.refpdbHash['2O6C_A'] = ['TP34_2o6cA_bacteria'];
123864
+ //ic.refpdbHash['3KYS_C'] = ['TEAD1_3kysC_human'];
123813
123865
  ic.refpdbHash['7PHR_L'] = ['B2Microglobulin_7phrL_human_C1'];
123814
123866
  ic.refpdbHash['2AW2_A'] = ['BTLA_2aw2A_human_Iset'];
123815
- ic.refpdbHash['1HL5_C'] = ['CuZnSuperoxideDismutase_1hl5C_human'];
123867
+ //ic.refpdbHash['1HL5_C'] = ['CuZnSuperoxideDismutase_1hl5C_human'];
123816
123868
  ic.refpdbHash['1WF5_A'] = ['Sidekick2_1wf5A_human_FN3-n7'];
123817
123869
  ic.refpdbHash['5J0B_B'] = ['Siglec3_5j0bB_human_C1-n2'];
123818
123870
  ic.refpdbHash['1IFR_A'] = ['LaminAC_1ifrA_human'];
123819
123871
  ic.refpdbHash['Q7Z7D3_A'] = ['VTCN1_Q7Z7D3_human_C1-n2'];
123820
123872
  ic.refpdbHash['4ZQK_B'] = ['PD1_4zqkB_human_V'];
123821
123873
  ic.refpdbHash['2DM3_A'] = ['Palladin_2dm3A_human_Iset-n1'];
123822
- ic.refpdbHash['2ITE_A'] = ['IsdA_2iteA_bacteria'];
123823
- ic.refpdbHash['1XAK_A'] = ['ORF7a_1xakA_virus'];
123874
+ //ic.refpdbHash['2ITE_A'] = ['IsdA_2iteA_bacteria'];
123875
+ //ic.refpdbHash['1XAK_A'] = ['ORF7a_1xakA_virus'];
123824
123876
  ic.refpdbHash['4ZT1_A'] = ['ECadherin_4zt1A_human_n2'];
123825
- ic.refpdbHash['1LMI_A'] = ['MPT63_1lmiA_bacteria'];
123877
+ //ic.refpdbHash['1LMI_A'] = ['MPT63_1lmiA_bacteria'];
123826
123878
  ic.refpdbHash['1CD8_A'] = ['CD8a_1cd8A_human_V'];
123827
123879
  ic.refpdbHash['3S97_C'] = ['Contactin1_3s97C_human_Iset-n2'];
123828
123880
  ic.refpdbHash['1AXI_B'] = ['GHR_1axiB_human_C1-n1'];
@@ -123830,7 +123882,7 @@ class Dssp {
123830
123882
  ic.refpdbHash['2EE2_A'] = ['Contactin1_2ee2A_human_FN3-n9'];
123831
123883
  ic.refpdbHash['4UOW_M'] = ['Titin_4uowM_human_Iset-n152'];
123832
123884
  ic.refpdbHash['6A15_A'] = ['CD19_6al5A_human-n1'];
123833
- ic.refpdbHash['2QKI_D'] = ['C3_2qkiD_human_n1'];
123885
+ //ic.refpdbHash['2QKI_D'] = ['C3_2qkiD_human_n1'];
123834
123886
  ic.refpdbHash['1YJD_C'] = ['CD28_1yjdC_human_V'];
123835
123887
  ic.refpdbHash['6JXR_d'] = ['CD3d_6jxrd_human_C1'];
123836
123888
  ic.refpdbHash['6JXR_f'] = ['CD3e_6jxrf_human_C1'];
@@ -123839,11 +123891,11 @@ class Dssp {
123839
123891
  // assign Ig types
123840
123892
  ic.ref2igtype = {};
123841
123893
 
123842
- ic.ref2igtype['ASF1A_2iijA_human'] = 'IgFN3-like';
123894
+ //ic.ref2igtype['ASF1A_2iijA_human'] = 'IgFN3-like';
123843
123895
  ic.ref2igtype['B2Microglobulin_7phrL_human_C1'] = 'IgC1';
123844
- ic.ref2igtype['BArrestin1_4jqiA_rat_n1'] = 'IgFN3-like';
123896
+ //ic.ref2igtype['BArrestin1_4jqiA_rat_n1'] = 'IgFN3-like';
123845
123897
  ic.ref2igtype['BTLA_2aw2A_human_Iset'] = 'IgI';
123846
- ic.ref2igtype['C3_2qkiD_human_n1'] = 'IgFN3-like';
123898
+ //ic.ref2igtype['C3_2qkiD_human_n1'] = 'IgFN3-like';
123847
123899
  ic.ref2igtype['CD19_6al5A_human-n1'] = 'CD19';
123848
123900
  ic.ref2igtype['CD28_1yjdC_human_V'] = 'IgV';
123849
123901
  ic.ref2igtype['CD2_1hnfA_human_C2-n2'] = 'IgC2';
@@ -123852,12 +123904,12 @@ class Dssp {
123852
123904
  ic.ref2igtype['CD3e_6jxrf_human_C1'] = 'IgC1';
123853
123905
  ic.ref2igtype['CD3g_6jxrg_human_C2'] = 'IgC2';
123854
123906
  ic.ref2igtype['CD8a_1cd8A_human_V'] = 'IgV';
123855
- ic.ref2igtype['CoAtomerGamma1_1r4xA_human'] = 'IgE';
123907
+ //ic.ref2igtype['CoAtomerGamma1_1r4xA_human'] = 'IgE';
123856
123908
  ic.ref2igtype['Contactin1_2ee2A_human_FN3-n9'] = 'IgFN3';
123857
123909
  ic.ref2igtype['Contactin1_3s97C_human_Iset-n2'] = 'IgI';
123858
- ic.ref2igtype['CuZnSuperoxideDismutase_1hl5C_human'] = 'SOD';
123910
+ //ic.ref2igtype['CuZnSuperoxideDismutase_1hl5C_human'] = 'SOD';
123859
123911
  ic.ref2igtype['ECadherin_4zt1A_human_n2'] = 'Cadherin';
123860
- ic.ref2igtype['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = 'IgE';
123912
+ //ic.ref2igtype['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = 'IgE';
123861
123913
  ic.ref2igtype['FAB-HEAVY_5esv_C1-n2'] = 'IgC1';
123862
123914
  ic.ref2igtype['FAB-HEAVY_5esv_V-n1'] = 'IgV';
123863
123915
  ic.ref2igtype['FAB-LIGHT_5esv_C1-n2'] = 'IgC1';
@@ -123868,28 +123920,28 @@ class Dssp {
123868
123920
  ic.ref2igtype['IL6Rb_1bquB_human_FN3-n3'] = 'IgFN3';
123869
123921
  ic.ref2igtype['InsulinR_8guyE_human_FN3-n1'] = 'IgFN3';
123870
123922
  ic.ref2igtype['InsulinR_8guyE_human_FN3-n2'] = 'IgFN3';
123871
- ic.ref2igtype['IsdA_2iteA_bacteria'] = 'IgE';
123923
+ //ic.ref2igtype['IsdA_2iteA_bacteria'] = 'IgE';
123872
123924
  ic.ref2igtype['JAM1_1nbqA_human_Iset-n2'] = 'IgI';
123873
123925
  ic.ref2igtype['LAG3_7tzgD_human_C1-n2'] = 'IgC1';
123874
123926
  ic.ref2igtype['LAG3_7tzgD_human_V-n1'] = 'IgV';
123875
123927
  ic.ref2igtype['LaminAC_1ifrA_human'] = 'Lamin';
123876
123928
  ic.ref2igtype['MHCIa_7phrH_human_C1'] = 'IgC1';
123877
- ic.ref2igtype['MPT63_1lmiA_bacteria'] = 'IgFN3-like';
123878
- ic.ref2igtype['NaCaExchanger_2fwuA_dog_n2'] = 'IgFN3-like';
123879
- ic.ref2igtype['NaKATPaseTransporterBeta_2zxeB_spurdogshark'] = 'IgE';
123880
- ic.ref2igtype['ORF7a_1xakA_virus'] = 'ORF';
123929
+ //ic.ref2igtype['MPT63_1lmiA_bacteria'] = 'IgFN3-like';
123930
+ //ic.ref2igtype['NaCaExchanger_2fwuA_dog_n2'] = 'IgFN3-like';
123931
+ //ic.ref2igtype['NaKATPaseTransporterBeta_2zxeB_spurdogshark'] = 'IgE';
123932
+ //ic.ref2igtype['ORF7a_1xakA_virus'] = 'ORF';
123881
123933
  ic.ref2igtype['PD1_4zqkB_human_V'] = 'IgV';
123882
123934
  ic.ref2igtype['PDL1_4z18B_human_V-n1'] = 'IgV';
123883
123935
  ic.ref2igtype['Palladin_2dm3A_human_Iset-n1'] = 'IgI';
123884
- ic.ref2igtype['RBPJ_6py8C_human_Unk-n1'] = 'IgFN3-like';
123936
+ //ic.ref2igtype['RBPJ_6py8C_human_Unk-n1'] = 'IgFN3-like';
123885
123937
  //ic.ref2igtype['RBPJ_6py8C_human_Unk-n2'] = 'IgFN3-like';
123886
123938
  ic.ref2igtype['Sidekick2_1wf5A_human_FN3-n7'] = 'IgFN3';
123887
123939
  ic.ref2igtype['Siglec3_5j0bB_human_C1-n2'] = 'IgC1';
123888
123940
  ic.ref2igtype['TCRa_6jxrm_human_C1-n2'] = 'IgC1';
123889
123941
  ic.ref2igtype['TCRa_6jxrm_human_V-n1'] = 'IgV';
123890
- ic.ref2igtype['TEAD1_3kysC_human'] = 'IgFN3-like';
123891
- ic.ref2igtype['TP34_2o6cA_bacteria'] = 'IgE';
123892
- ic.ref2igtype['TP47_1o75A_bacteria'] = 'IgE';
123942
+ //ic.ref2igtype['TEAD1_3kysC_human'] = 'IgFN3-like';
123943
+ //ic.ref2igtype['TP34_2o6cA_bacteria'] = 'IgE';
123944
+ //ic.ref2igtype['TP47_1o75A_bacteria'] = 'IgE';
123893
123945
  ic.ref2igtype['Titin_4uowM_human_Iset-n152'] = 'IgI';
123894
123946
  ic.ref2igtype['VISTA_6oilA_human_V'] = 'IgV';
123895
123947
  ic.ref2igtype['VNAR_1t6vN_shark_V'] = 'IgV';
@@ -125440,6 +125492,7 @@ class Dssp {
125440
125492
  }
125441
125493
  else {
125442
125494
  let bBefore = false, bInRange= false, bAfter = false;
125495
+ /*
125443
125496
  // 100, 100A
125444
125497
  if(parseInt(currResi) == parseInt(strandArray[strandCnt].startResi) && currResi != strandArray[strandCnt].startResi) {
125445
125498
  bBefore = currResi < strandArray[strandCnt].startResi;
@@ -125455,6 +125508,14 @@ class Dssp {
125455
125508
  else {
125456
125509
  bAfter = parseInt(currResi) > parseInt(strandArray[strandCnt].endResi);
125457
125510
  }
125511
+ */
125512
+
125513
+ let currResiNcbi = ic.ParserUtilsCls.getResiNCBI(chnid, currResi);
125514
+ let startResiNcbi = ic.ParserUtilsCls.getResiNCBI(chnid, strandArray[strandCnt].startResi);
125515
+ let endResiNcbi = ic.ParserUtilsCls.getResiNCBI(chnid, strandArray[strandCnt].endResi);
125516
+
125517
+ bBefore = parseInt(currResiNcbi) < parseInt(startResiNcbi);
125518
+ bAfter = parseInt(currResiNcbi) > parseInt(endResiNcbi);
125458
125519
 
125459
125520
  bInRange = (!bBefore && !bAfter) ? true : false;
125460
125521
 
@@ -131273,8 +131334,9 @@ class ShareLink {
131273
131334
  }
131274
131335
 
131275
131336
  let paraHash = {};
131276
- for(let key in ic.cfg) {
131277
- let value = ic.cfg[key];
131337
+ /*
131338
+ for(let key in me.cfg) {
131339
+ let value = me.cfg[key];
131278
131340
  //if(key === 'inpara' || ic.key === 'command' || value === undefined) continue;
131279
131341
  if(key === 'inpara' || key === 'command' || key === 'usepdbnum'
131280
131342
  || key === 'date' || key === 'v' || value === undefined) continue;
@@ -131324,7 +131386,7 @@ class ShareLink {
131324
131386
  paraHash[key] = value;
131325
131387
  }
131326
131388
  }
131327
-
131389
+ */
131328
131390
  if(ic.bAfMem) {
131329
131391
  paraHash['afmem'] = 'on';
131330
131392
  }
@@ -131346,6 +131408,12 @@ class ShareLink {
131346
131408
  if(key_value.length == 2) paraHash[key_value[0]] = key_value[1];
131347
131409
  }
131348
131410
 
131411
+ // BLAST RID is usually added at the end of the URL. It should be included.
131412
+ if(me.cfg.rid && !paraHash['RID']) {
131413
+ url += 'RID=' + me.cfg.rid + '&';
131414
+ }
131415
+
131416
+ // sometimes idname is not part of the URL
131349
131417
  if(me.cfg.idname && !paraHash[me.cfg.idname]) { // somehow it is not included
131350
131418
  url += me.cfg.idname + '=' + me.cfg.idvalue + '&';
131351
131419
  }
@@ -134459,7 +134527,7 @@ class iCn3DUI {
134459
134527
  //even when multiple iCn3D viewers are shown together.
134460
134528
  this.pre = this.cfg.divid + "_";
134461
134529
 
134462
- this.REVISION = '3.47.1';
134530
+ this.REVISION = '3.48.1';
134463
134531
 
134464
134532
  // In nodejs, iCn3D defines "window = {navigator: {}}", and added window = {navigator: {}, "__THREE__":"177"}
134465
134533
  this.bNode = (Object.keys(window).length < 3) ? true : false;
@@ -134661,14 +134729,8 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
134661
134729
  let domainidArray = me.cfg.matchedchains.split(',');
134662
134730
  let chainidArray = [];
134663
134731
  for(let i = 0, il = domainidArray.length; i < il; ++i) {
134664
- let pos = domainidArray[i].lastIndexOf('_');
134665
- let lastId = domainidArray[i].substr(pos + 1);
134666
- if(!isNaN(lastId)) { // lastId is domain id
134667
- chainidArray.push(domainidArray[i].substr(0, pos));
134668
- }
134669
- else {
134670
- chainidArray.push(domainidArray[i]);
134671
- }
134732
+ let idArray = domainidArray[i].split('_');
134733
+ chainidArray.push(idArray[0] + '_' + idArray[1]);
134672
134734
  }
134673
134735
 
134674
134736
  // get the matched structures, do not include the template
@@ -134897,6 +134959,9 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
134897
134959
  if(me.cfg.align.indexOf('185055,') != -1) {
134898
134960
  me.cfg.align = me.cfg.align.replace('185055,', '199731,'); //the mmdbid of PDB 6M17 was changed from 185055 to 199731
134899
134961
  }
134962
+ else if(me.cfg.align == '54567,1,12161,1,2,1') {
134963
+ me.cfg.align = '3HHR,1BQU'; // somehow the VAST+ data for this published alignment were not there anymore
134964
+ }
134900
134965
 
134901
134966
  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]
134902
134967