icn3d 3.34.5 → 3.35.0

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Files changed (4) hide show
  1. package/icn3d.js +164 -64
  2. package/icn3d.min.js +2 -2
  3. package/icn3d.module.js +164 -64
  4. package/package.json +1 -1
package/icn3d.js CHANGED
@@ -40277,6 +40277,8 @@ class AnnoCddSite {
40277
40277
  let resiNCBI = resiNCBIArray[i] + 1; // zero-based
40278
40278
  let residNCBI = chainid + '_' + resiNCBI;
40279
40279
  let resid = ic.ncbi2resid[residNCBI];
40280
+ if(!resid) resid = residNCBI; // this happens sometimes, e.g., Q9Y4K1
40281
+
40280
40282
  let resi = resid.split('_')[2];
40281
40283
  if(i > 0) resiArrayStr += ',';
40282
40284
  resiArrayStr += resi;
@@ -42223,6 +42225,7 @@ class AnnoSnpClinVar {
42223
42225
  let altName = bClinvar ? 'clinvar' : 'snp';
42224
42226
  // determine whether the SNPis from virus directly
42225
42227
  let bVirus = false;
42228
+
42226
42229
  for(let resi in resi2rsnum) {
42227
42230
  for(let i = 0, il = resi2rsnum[resi].length; i < il; ++i) {
42228
42231
  if(resi2rsnum[resi][i] == 0) {
@@ -42235,7 +42238,8 @@ class AnnoSnpClinVar {
42235
42238
 
42236
42239
  if(bStartEndRes) {
42237
42240
  let title1 = 'ClinVar', title2 = 'SNP', warning = "", warning2 = "";
42238
- if(!bVirus && ic.organism !== undefined && ic.organism !== 'human' && ic.organism !== 'homo sapiens') {
42241
+
42242
+ if(!bVirus && ic.organism !== undefined && ic.organism.toLowerCase() !== 'human' && ic.organism.toLowerCase() !== 'homo sapiens') {
42239
42243
  warning = " <span style='color:#FFA500'>(from human)</span>";
42240
42244
  warning2 = " <span style='color:#FFA500'>(based on human sequences and mapped to this structure by sequence similarity)</span>";
42241
42245
  }
@@ -42258,7 +42262,11 @@ class AnnoSnpClinVar {
42258
42262
  let pre = altName;
42259
42263
  let snpCnt = 0, clinvarCnt = 0;
42260
42264
  let snpTypeHash = {}, currSnpTypeHash = {};
42261
- for(let i = 1, il = ic.giSeq[chnid].length; i <= il; ++i) {
42265
+ let residHash = ic.firstAtomObjCls.getResiduesFromAtoms(ic.chains[chnid]);
42266
+ // for(let i = 1, il = ic.giSeq[chnid].length; i <= il; ++i) {
42267
+ for(let resid in residHash) {
42268
+ let i = resid.split('_')[2];
42269
+
42262
42270
  if(resi2index[i] !== undefined) {
42263
42271
  ++snpCnt;
42264
42272
  let allDiseaseTitle = '';
@@ -42269,7 +42277,11 @@ class AnnoSnpClinVar {
42269
42277
  for(let k = 0, kl = diseaseArray.length; k < kl; ++k) {
42270
42278
  // relax the restriction to show all clinvar
42271
42279
  //if(diseaseArray[k] != '' && diseaseArray[k] != 'not specified' && diseaseArray[k] != 'not provided') {
42272
- diseaseTitle += diseaseArray[k] + '(' + sigArray[k] + '); ';
42280
+ diseaseTitle += diseaseArray[k];
42281
+ if(sigArray[k] != '') {
42282
+ diseaseTitle += '(' + sigArray[k] + ')';
42283
+ }
42284
+ diseaseTitle += '; ';
42273
42285
  //}
42274
42286
  }
42275
42287
 
@@ -42335,18 +42347,21 @@ class AnnoSnpClinVar {
42335
42347
  if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqStartLen[chnid], '-');
42336
42348
  }
42337
42349
 
42338
- for(let i = 1, il = ic.giSeq[chnid].length; i <= il; ++i) {
42350
+ for(let index = 1, indexl = ic.giSeq[chnid].length; index <= indexl; ++index) {
42351
+ let pos = ic.ParserUtilsCls.getResi(chnid, index - 1);
42352
+ let i = pos;
42353
+
42339
42354
  if(bOverview) {
42340
42355
  if(resi2index[i] !== undefined) {
42341
42356
 
42342
42357
  // get the mouse over text
42343
- let cFull = ic.giSeq[chnid][i-1];
42358
+ let cFull = ic.giSeq[chnid][index-1];
42344
42359
  let c = cFull;
42345
42360
  if(cFull.length > 1) {
42346
42361
  c = cFull[0] + '..';
42347
42362
  }
42348
42363
  // let pos =(i >= ic.matchedPos[chnid] && i-1 - ic.matchedPos[chnid] < ic.chainsSeq[chnid].length) ? ic.chainsSeq[chnid][i-1 - ic.matchedPos[chnid]].resi : ic.baseResi[chnid] + 1 + i-1;
42349
- let pos = ic.ParserUtilsCls.getResi(chnid, i - 1);
42364
+
42350
42365
  let snpTitle = pos + c + '>';
42351
42366
  for(let j = 0, jl = resi2snp[i].length; j < jl; ++j) {
42352
42367
  snpTitle += resi2snp[i][j];
@@ -42357,24 +42372,28 @@ class AnnoSnpClinVar {
42357
42372
  for(let k = 0, kl = diseaseArray.length; k < kl; ++k) {
42358
42373
  // relax the restriction to show all clinvar
42359
42374
  //if(diseaseArray[k] != '' && diseaseArray[k] != 'not specified' && diseaseArray[k] != 'not provided') {
42360
- diseaseTitle += diseaseArray[k] + '(' + sigArray[k] + '); ';
42375
+ diseaseTitle += diseaseArray[k];
42376
+ if(sigArray[k] != '') {
42377
+ diseaseTitle += '(' + sigArray[k] + ')';
42378
+ }
42379
+ diseaseTitle += '; ';
42361
42380
  //}
42362
42381
  }
42363
42382
  }
42364
42383
  }
42365
- html += ic.showSeqCls.insertGapOverview(chnid, i-1);
42366
- let emptyWidth = Math.round(ic.seqAnnWidth *(i-1) /(ic.maxAnnoLength + ic.nTotalGap) - prevEmptyWidth - prevLineWidth);
42384
+ html += ic.showSeqCls.insertGapOverview(chnid, index-1);
42385
+ let emptyWidth = Math.round(ic.seqAnnWidth *(index-1) /(ic.maxAnnoLength + ic.nTotalGap) - prevEmptyWidth - prevLineWidth);
42367
42386
  //let emptyWidth =(me.cfg.blast_rep_id == chnid) ? Math.round(ic.seqAnnWidth *(i-1) /(ic.maxAnnoLength + ic.nTotalGap) - prevEmptyWidth - prevLineWidth) : Math.round(ic.seqAnnWidth *(i-1) / ic.maxAnnoLength - prevEmptyWidth - prevLineWidth);
42368
42387
  //if(emptyWidth < 0) emptyWidth = 0;
42369
42388
  if(bClinvar) {
42370
- if(snpTypeHash[i] == 'icn3d-clinvar' || snpTypeHash[i] == 'icn3d-clinvar-path') {
42389
+ // if(snpTypeHash[i] == 'icn3d-clinvar' || snpTypeHash[i] == 'icn3d-clinvar-path') {
42371
42390
  if(emptyWidth >= 0) {
42372
42391
  html += '<div style="display:inline-block; width:' + emptyWidth + 'px;">&nbsp;</div>';
42373
42392
  html += '<div style="display:inline-block; background-color:#000; width:' + widthPerRes + 'px;" title="' + snpTitle + '">&nbsp;</div>';
42374
42393
  prevEmptyWidth += emptyWidth;
42375
42394
  prevLineWidth += widthPerRes;
42376
42395
  }
42377
- }
42396
+ // }
42378
42397
  }
42379
42398
  else {
42380
42399
  if(emptyWidth > 0) {
@@ -42387,20 +42406,20 @@ class AnnoSnpClinVar {
42387
42406
  }
42388
42407
  }
42389
42408
  else { // detailed view
42390
- html += ic.showSeqCls.insertGap(chnid, i-1, '-');
42409
+ html += ic.showSeqCls.insertGap(chnid, index-1, '-');
42391
42410
 
42392
42411
  if(resi2index[i] !== undefined) {
42393
42412
  if(!bClinvar && line == 1) {
42394
42413
  html += '<span>&dArr;</span>'; // or down triangle &#9660;
42395
42414
  }
42396
42415
  else {
42397
- let cFull = ic.giSeq[chnid][i-1];
42416
+ let cFull = ic.giSeq[chnid][index-1];
42398
42417
  let c = cFull;
42399
42418
  if(cFull.length > 1) {
42400
42419
  c = cFull[0] + '..';
42401
42420
  }
42402
42421
  // let pos =(i >= ic.matchedPos[chnid] && i-1 - ic.matchedPos[chnid] < ic.chainsSeq[chnid].length) ? ic.chainsSeq[chnid][i-1 - ic.matchedPos[chnid]].resi : ic.baseResi[chnid] + 1 + i-1;
42403
- let pos = ic.ParserUtilsCls.getResi(chnid, i - 1);
42422
+ // let pos = ic.ParserUtilsCls.getResi(chnid, index - 1);
42404
42423
  let snpStr = "", snpTitle = "<div class='snptip'>";
42405
42424
  //var snpType = '';
42406
42425
  let jl = resi2snp[i].length;
@@ -42445,7 +42464,10 @@ class AnnoSnpClinVar {
42445
42464
  else {
42446
42465
  if( j === 0 || j === 1) diseaseStr = 'disease="' + diseaseArray[k] + '"';
42447
42466
  }
42448
- diseaseTitle += diseaseArray[k] + '(' + sigArray[k] + ')';
42467
+ diseaseTitle += diseaseArray[k];
42468
+ if(sigArray[k] != '') {
42469
+ diseaseTitle += '(' + sigArray[k] + ')';
42470
+ }
42449
42471
  ++index;
42450
42472
  //}
42451
42473
  }
@@ -42515,23 +42537,26 @@ class AnnoSnpClinVar {
42515
42537
  let diseaseArray = resi2disease[i][j].split('; ');
42516
42538
  let sigArray = resi2sig[i][j].split('; ');
42517
42539
  let diseaseTitle = '';
42518
- let index = 0;
42540
+ let indexTmp = 0;
42519
42541
 
42520
42542
  for(let k = 0, kl = diseaseArray.length; k < kl; ++k) {
42521
42543
  // relax the restriction to show all clinvar
42522
42544
  //if(diseaseArray[k] != '' && diseaseArray[k] != 'not specified' && diseaseArray[k] != 'not provided') {
42523
- if(index > 0) {
42545
+ if(indexTmp > 0) {
42524
42546
  diseaseTitle += '; ';
42525
42547
  }
42526
42548
  else {
42527
42549
  if( j === 0 || j === 1) diseaseStr = 'disease="' + diseaseArray[k] + '"';
42528
42550
  }
42529
- diseaseTitle += diseaseArray[k] + '(' + sigArray[k] + ')';
42530
- ++index;
42551
+ diseaseTitle += diseaseArray[k];
42552
+ if(sigArray[k] != '') {
42553
+ diseaseTitle += '(' + sigArray[k] + ')';
42554
+ }
42555
+ ++indexTmp;
42531
42556
  //}
42532
42557
  }
42533
42558
 
42534
- if(diseaseTitle != '') {
42559
+ // if(diseaseTitle != '') {
42535
42560
  if(diseaseCnt < shownResCnt) snpStr += resi2snp[i][j];
42536
42561
  snpTitle += pos + c + '>' + resi2snp[i][j];
42537
42562
  //snpType = 'icn3d-clinvar';
@@ -42544,19 +42569,22 @@ class AnnoSnpClinVar {
42544
42569
  }
42545
42570
 
42546
42571
  //snpTitle += "<br>Links: <span class='" + ic.pre + "snpin3d icn3d-snplink' snp='" + chnid + "_" + pos + "_" + resi2snp[i][j] + "'>SNP in 3D with scap</span>, <span class='" + ic.pre + "snpinter icn3d-snplink' snp='" + chnid + "_" + pos + "_" + resi2snp[i][j] + "'>SNP Interactions in 3D</span>, <span class='" + ic.pre + "snppdb icn3d-snplink' snp='" + chnid + "_" + pos + "_" + resi2snp[i][j] + "'>SNP PDB</span>, <a href='https://www.ncbi.nlm.nih.gov/clinvar/?term=" + resi2clinAllele[i][j] + "[AlleleID]' target='_blank'>ClinVar</a>, <a href='https://www.ncbi.nlm.nih.gov/snp/?term=" + resi2rsnum[i][j] + "' target='_blank'>dbSNP(rs" + resi2rsnum[i][j] + ")</a>";
42547
- snpTitle += "<br>Links: <a href='https://www.ncbi.nlm.nih.gov/clinvar/?term=" + resi2clinAllele[i][j] + "[AlleleID]' style='color:blue' target='_blank'>ClinVar</a>, <a href='https://www.ncbi.nlm.nih.gov/snp/?term=" + resi2rsnum[i][j] + "' style='color:blue' target='_blank'>dbSNP(rs" + resi2rsnum[i][j] + ")</a>";
42572
+ snpTitle += "<br>Links: <a href='https://www.ncbi.nlm.nih.gov/clinvar/?term=" + resi2clinAllele[i][j] + "[AlleleID]' style='color:blue' target='_blank'>ClinVar</a>";
42573
+ if(resi2rsnum[i][j] != 0) {
42574
+ snpTitle += ", <a href='https://www.ncbi.nlm.nih.gov/snp/?term=" + resi2rsnum[i][j] + "' style='color:blue' target='_blank'>dbSNP(rs" + resi2rsnum[i][j] + ")</a>";
42575
+ }
42548
42576
  if(j < jl - 1) {
42549
42577
  snpTitle += '<br><br>';
42550
42578
  }
42551
42579
  ++diseaseCnt;
42552
- } // if(diseaseTitle != '') {
42580
+ // } // if(diseaseTitle != '') {
42553
42581
  } // for(let j = start; j < jl && j < end; ++j) {
42554
42582
  //if(diseaseCnt > shownResCnt && line == 3) snpStr += '..';
42555
42583
  if(diseaseCnt > shownResCnt && line == 2) snpStr += '..';
42556
42584
  } // else { // if(bClinvar)
42557
42585
  snpTitle += '</div>';
42558
42586
  if(bClinvar) {
42559
- if(snpTypeHash[i] == 'icn3d-clinvar' || snpTypeHash[i] == 'icn3d-clinvar-path') {
42587
+ // if(snpTypeHash[i] == 'icn3d-clinvar' || snpTypeHash[i] == 'icn3d-clinvar-path') {
42560
42588
  if(line == 1) {
42561
42589
  html += '<span>&dArr;</span>'; // or down triangle &#9660;
42562
42590
  }
@@ -42565,13 +42593,14 @@ class AnnoSnpClinVar {
42565
42593
  html += '<span>-</span>';
42566
42594
  }
42567
42595
  else {
42568
- html += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" label title="' + snpTitle + '" ' + diseaseStr + ' class="icn3d-tooltip icn3d-residue ' + currSnpTypeHash[i] + '">' + snpStr + '</span>';
42596
+ // html += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" label title="' + snpTitle + '" ' + diseaseStr + ' class="icn3d-tooltip icn3d-residue ' + currSnpTypeHash[i] + '">' + snpStr + '</span>';
42597
+ html += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" label title="' + snpTitle + '" ' + diseaseStr + ' class="icn3d-tooltip icn3d-residue ' + snpTypeHash[i] + '">' + snpStr + '</span>';
42569
42598
  }
42570
42599
  }
42571
- }
42572
- else {
42573
- html += '<span>-</span>';
42574
- }
42600
+ // }
42601
+ // else {
42602
+ // html += '<span>-</span>';
42603
+ // }
42575
42604
  }
42576
42605
  else {
42577
42606
  if(snpStr == '' || snpStr == ' ') {
@@ -42579,10 +42608,12 @@ class AnnoSnpClinVar {
42579
42608
  }
42580
42609
  else {
42581
42610
  if(!bSnpOnly) {
42582
- html += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" label title="' + snpTitle + '" ' + diseaseStr + ' class="icn3d-tooltip icn3d-residue ' + currSnpTypeHash[i] + '">' + snpStr + '</span>';
42611
+ // html += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" label title="' + snpTitle + '" ' + diseaseStr + ' class="icn3d-tooltip icn3d-residue ' + currSnpTypeHash[i] + '">' + snpStr + '</span>';
42612
+ html += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" label title="' + snpTitle + '" ' + diseaseStr + ' class="icn3d-tooltip icn3d-residue ' + snpTypeHash[i] + '">' + snpStr + '</span>';
42583
42613
  }
42584
42614
  else {
42585
- html += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" label title="' + snpTitle + '" class="icn3d-tooltip icn3d-residue ' + currSnpTypeHash[i] + '">' + snpStr + '</span>';
42615
+ // html += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" label title="' + snpTitle + '" class="icn3d-tooltip icn3d-residue ' + currSnpTypeHash[i] + '">' + snpStr + '</span>';
42616
+ html += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" label title="' + snpTitle + '" class="icn3d-tooltip icn3d-residue ' + snpTypeHash[i] + '">' + snpStr + '</span>';
42586
42617
  }
42587
42618
  }
42588
42619
  }
@@ -42638,23 +42669,60 @@ class AnnoSnpClinVar {
42638
42669
  }
42639
42670
  }
42640
42671
 
42672
+ let foundRealSnp = {};
42641
42673
  for(let i = 0, il = lineArray.length; i < il; ++i) {
42642
42674
  //bSnpOnly: false
42643
- //1310770 13 14 14Y>H 368771578 150500 Hereditary cancer-predisposing syndrome; Li-Fraumeni syndrome; not specified; Li-Fraumeni syndrome 1 Likely benign; Uncertain significance; Uncertain significance; Uncertain significance 1TSR_A 120407068 NP_000537.3
42644
- //Pdb_gi, Pos from, Pos to, Pos & Amino acid change, rs#, ClinVar Allele ID, Disease name, Clinical significance, master accession, master_gi, master_accession.version
42675
+ //1310770 13 14 14Y>H 368771578 150500 Hereditary cancer-predisposing syndrome; Li-Fraumeni syndrome; not specified; Li-Fraumeni syndrome 1 Likely benign; Uncertain significance; Uncertain significance; Uncertain significance 0
42676
+ //Pdb_gi, Pos from, Pos to, Pos & Amino acid change, rs#, ClinVar Allele ID, Disease name, Clinical significance, [whether data is directly from ClinVar database, 0 or 1]
42645
42677
  //bSnpOnly: true
42646
- //1310770 13 14 14Y>H 1111111
42678
+ //1310770 13 14 14Y>H 1111111 0
42647
42679
  if(lineArray[i] != '') {
42648
42680
  let fieldArray =(!bSnpOnly || bVirus) ? lineArray[i] : lineArray[i].split('\t');
42649
42681
  let snpStr = fieldArray[3];
42682
+ let rsnum = fieldArray[4];
42683
+ let bFromClinVarDb = false;
42684
+
42685
+ if(bSnpOnly) {
42686
+ if(fieldArray.length > 5) bFromClinVarDb = parseInt(fieldArray[5]);
42687
+ }
42688
+ else {
42689
+ if(fieldArray.length > 8) bFromClinVarDb = parseInt(fieldArray[8]);
42690
+ }
42650
42691
  if(snpStr == prevSnpStr) continue;
42651
42692
  prevSnpStr = snpStr;
42652
- let resiStr = snpStr.substr(0, snpStr.length - 3);
42693
+
42694
+ let posSymbol = snpStr.indexOf('>');
42695
+ // let resiStr = snpStr.substr(0, snpStr.length - 3);
42696
+ let resiStr = snpStr.substr(0, posSymbol - 1);
42653
42697
  let resi = Math.round(resiStr);
42654
42698
 
42699
+ // if the data is From ClinVar Db directly, the residue numbers are PDB residue numbers. Otherwise, the residue numbers are NCBI residue numbers.
42700
+ let realResi = (bFromClinVarDb) ? resi : ic.ParserUtilsCls.getResi(chnid, resi - 1);
42701
+
42702
+ let realSnp = realResi + snpStr.substr(posSymbol - 1);
42703
+ if(foundRealSnp.hasOwnProperty(realSnp)) {
42704
+ continue;
42705
+ }
42706
+ else {
42707
+ foundRealSnp[realSnp] = 1;
42708
+ }
42709
+
42710
+ let snpResn = snpStr.substr(posSymbol - 1, 1);
42711
+ let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[chnid + '_' + realResi]);
42712
+ let oneLetterRes = (atom) ? me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3)) : '';
42713
+ if(!bFromClinVarDb) {
42714
+ oneLetterRes = ic.chainsSeq[chnid][resi - 1].name;
42715
+ }
42716
+
42717
+ if(snpResn != oneLetterRes) {
42718
+ // console.error("The snp " + snpStr + " didn't match the residue name " + oneLetterRes);
42719
+ continue;
42720
+ }
42721
+
42655
42722
  if(me.bNode) {
42656
42723
  let obj = {};
42657
- obj[chnid + '_' + resi] = snpStr;
42724
+ // obj[chnid + '_' + resi] = snpStr;
42725
+ obj[chnid + '_' + realResi] = realSnp;
42658
42726
 
42659
42727
  if(bSnpOnly) {
42660
42728
  ic.resid2snp[chnid].push(obj);
@@ -42664,52 +42732,53 @@ class AnnoSnpClinVar {
42664
42732
  }
42665
42733
  }
42666
42734
 
42667
- snpStr.substr(snpStr.length - 3, 1);
42668
- let snpRes = snpStr.substr(snpStr.indexOf('>') + 1); //snpStr.substr(snpStr.length - 1, 1);
42735
+ // let currRes = snpStr.substr(snpStr.length - 3, 1);
42736
+ // let snpRes = snpStr.substr(snpStr.indexOf('>') + 1); //snpStr.substr(snpStr.length - 1, 1);
42737
+ let snpRes = realSnp.substr(realSnp.indexOf('>') + 1); //realSnp.substr(realSnp.length - 1, 1);
42669
42738
  //var rsnum = bSnpOnly ? '' : fieldArray[4];
42670
- let rsnum = fieldArray[4];
42739
+
42671
42740
  let clinAllele = bSnpOnly ? '' : fieldArray[5];
42672
42741
  let disease = bSnpOnly ? '' : fieldArray[6]; // When more than 2+ diseases, they are separated by "; "
42673
42742
  // Some are "not specified", "not provided"
42674
42743
  let clinSig = bSnpOnly ? '' : fieldArray[7]; // Clinical significance, When more than 2+ diseases, they are separated by "; "
42675
42744
  // "*" means terminating codon, "-" means deleted codon
42676
42745
  //if(currRes !== '-' && currRes !== '*' && snpRes !== '-' && snpRes !== '*') {
42677
- let realResi = ic.ParserUtilsCls.getResi(chnid, resi - 1);
42746
+
42678
42747
  // posHash[resi + ic.baseResi[chnid]] = 1;
42679
42748
  // if(disease != '') posClinHash[resi + ic.baseResi[chnid]] = 1;
42680
42749
  posHash[realResi] = 1;
42681
42750
  if(disease != '') posClinHash[realResi] = 1;
42682
- resi2index[resi] = i + 1;
42683
- if(resi2snp[resi] === undefined) {
42684
- resi2snp[resi] = [];
42751
+ resi2index[realResi] = i + 1;
42752
+ if(resi2snp[realResi] === undefined) {
42753
+ resi2snp[realResi] = [];
42685
42754
  }
42686
- resi2snp[resi].push(snpRes);
42687
- if(resi2rsnum[resi] === undefined) {
42688
- resi2rsnum[resi] = [];
42755
+ resi2snp[realResi].push(snpRes);
42756
+ if(resi2rsnum[realResi] === undefined) {
42757
+ resi2rsnum[realResi] = [];
42689
42758
  }
42690
- resi2rsnum[resi].push(rsnum);
42691
- if(resi2clinAllele[resi] === undefined) {
42692
- resi2clinAllele[resi] = [];
42759
+ resi2rsnum[realResi].push(rsnum);
42760
+ if(resi2clinAllele[realResi] === undefined) {
42761
+ resi2clinAllele[realResi] = [];
42693
42762
  }
42694
- resi2clinAllele[resi].push(clinAllele);
42695
- if(resi2disease[resi] === undefined) {
42696
- resi2disease[resi] = [];
42763
+ resi2clinAllele[realResi].push(clinAllele);
42764
+ if(resi2disease[realResi] === undefined) {
42765
+ resi2disease[realResi] = [];
42697
42766
  }
42698
- resi2disease[resi].push(disease);
42767
+ resi2disease[realResi].push(disease);
42699
42768
  if(disease != '') {
42700
- if(ic.resi2disease_nonempty[chnid][resi] === undefined) {
42701
- ic.resi2disease_nonempty[chnid][resi] = [];
42769
+ if(ic.resi2disease_nonempty[chnid][realResi] === undefined) {
42770
+ ic.resi2disease_nonempty[chnid][realResi] = [];
42702
42771
  }
42703
- ic.resi2disease_nonempty[chnid][resi].push(disease);
42772
+ ic.resi2disease_nonempty[chnid][realResi].push(disease);
42704
42773
  }
42705
- if(resi2sig[resi] === undefined) {
42706
- resi2sig[resi] = [];
42774
+ if(resi2sig[realResi] === undefined) {
42775
+ resi2sig[realResi] = [];
42707
42776
  }
42708
- resi2sig[resi].push(clinSig);
42777
+ resi2sig[realResi].push(clinSig);
42709
42778
  //}
42710
42779
  }
42711
42780
  }
42712
-
42781
+
42713
42782
  let posarray = Object.keys(posHash);
42714
42783
  let posClinArray = Object.keys(posClinHash);
42715
42784
  if(bSnpOnly) {
@@ -42728,7 +42797,7 @@ class AnnoSnpClinVar {
42728
42797
  $("#" + ic.pre + 'ov_snp_' + chnid).html(html2);
42729
42798
  $("#" + ic.pre + 'tt_snp_' + chnid).html(html3);
42730
42799
  }
42731
- else {
42800
+ else {
42732
42801
  //if(!bSnpOnly && ic.bClinvarCnt) {
42733
42802
  let bClinvar = true;
42734
42803
  htmlClinvar += this.getSnpLine(1, 2, resi2snp, resi2rsnum, resi2clinAllele, resi2disease, resi2index, resi2sig, posarray, posClinArray, 1, chnid, false, bClinvar, undefined, bSnpOnly);
@@ -42761,9 +42830,12 @@ class AnnoSnpClinVar {
42761
42830
  }
42762
42831
  async showClinvarPart2(chnid, chnidBase, gi) { let ic = this.icn3d, me = ic.icn3dui;
42763
42832
  let thisClass = this;
42833
+
42834
+ if(!ic.chainid2uniport) await this.getUniprotForAllStructures();
42835
+
42764
42836
  //var url = "https://www.ncbi.nlm.nih.gov/projects/SNP/beVarSearch_mt.cgi?appname=iCn3D&format=bed&report=pdb2bed&acc=" + chnidBase;
42765
42837
  //var url = "https://www.ncbi.nlm.nih.gov/Structure/icn3d/clinvar.txt";
42766
- let url = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?chainid_clinvar=" + chnidBase;
42838
+ let url = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?chainid_clinvar=" + chnidBase + "&uniprot=" + ic.chainid2uniport[chnidBase];
42767
42839
  if(ic.chainsGene[chnid] && ic.chainsGene[chnid].geneSymbol) {
42768
42840
  url += "&gene=" + ic.chainsGene[chnid].geneSymbol;
42769
42841
  }
@@ -42783,15 +42855,43 @@ class AnnoSnpClinVar {
42783
42855
  }
42784
42856
  catch(err) {
42785
42857
  thisClass.processNoClinvar(chnid);
42786
- ///// if(ic.deferredClinvar !== undefined) ic.deferredClinvar.resolve();
42787
42858
  return;
42788
42859
  }
42789
42860
  }
42790
42861
 
42862
+ async getUniprotForAllStructures() { let ic = this.icn3d, me = ic.icn3dui;
42863
+ ic.chainid2uniport = {};
42864
+
42865
+ // get UniProt ID ffrom chainid
42866
+ for(let structure in ic.structures) {
42867
+ if(structure.length > 5) {
42868
+ let chainidArray = ic.structures[structure];
42869
+ for(let i = 0, il = chainidArray.length; i < il; ++i) {
42870
+ ic.chainid2uniport[chainidArray[i]] = structure;
42871
+ }
42872
+ }
42873
+ else {
42874
+ let structLower = structure.toLowerCase();
42875
+ let url = "https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/" + structLower;
42876
+ let dataJson = await me.getAjaxPromise(url, 'json');
42877
+ let data= dataJson[structLower]['UniProt'];
42878
+ for(let uniprot in data) {
42879
+ let chainDataArray = data[uniprot].mappings;
42880
+ for(let i = 0, il = chainDataArray.length; i < il; ++i) {
42881
+ let chain = chainDataArray[i].chain_id;
42882
+ ic.chainid2uniport[structure + '_' + chain] = uniprot;
42883
+ }
42884
+ }
42885
+ }
42886
+ }
42887
+ }
42888
+
42791
42889
  async showSnpPart2(chnid, chnidBase, gi) { let ic = this.icn3d, me = ic.icn3dui;
42792
42890
  let thisClass = this;
42891
+ if(!ic.chainid2uniport) await this.getUniprotForAllStructures();
42892
+
42793
42893
  if(gi !== undefined) {
42794
- let url4 = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?chainid_snp=" + chnidBase;
42894
+ let url4 = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?chainid_snp=" + chnidBase + "&uniprot=" + ic.chainid2uniport[chnidBase];
42795
42895
  if(ic.chainsGene[chnid] && ic.chainsGene[chnid].geneSymbol) {
42796
42896
  url4 += "&gene=" + ic.chainsGene[chnid].geneSymbol;
42797
42897
  }
@@ -81990,7 +82090,7 @@ class iCn3DUI {
81990
82090
  //even when multiple iCn3D viewers are shown together.
81991
82091
  this.pre = this.cfg.divid + "_";
81992
82092
 
81993
- this.REVISION = '3.34.1';
82093
+ this.REVISION = '3.35.0';
81994
82094
 
81995
82095
  // In nodejs, iCn3D defines "window = {navigator: {}}"
81996
82096
  this.bNode = (Object.keys(window).length < 2) ? true : false;