icn3d 3.25.14 → 3.25.16

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Files changed (4) hide show
  1. package/icn3d.js +80 -50
  2. package/icn3d.min.js +2 -2
  3. package/icn3d.module.js +80 -50
  4. package/package.json +1 -1
package/icn3d.js CHANGED
@@ -35855,6 +35855,7 @@ class AnnoCddSite {
35855
35855
 
35856
35856
  for(let i = 0, il = dataArray.length; i < il; ++i) {
35857
35857
  //let data = (bSeq) ? dataArray[i][0] : dataArray[i];
35858
+ // somehow Node.js returned data in dataArray[i]
35858
35859
  let data = (me.bNode) ? dataArray[i] : dataArray[i].value;
35859
35860
 
35860
35861
  if(!data) continue;
@@ -46832,8 +46833,10 @@ class AlignParser {
46832
46833
  let dataArray = await allPromise;
46833
46834
 
46834
46835
  let data2 = data;
46835
- let data3 = (me.bNode) ? dataArray[0] : dataArray[0].value; //v3[0];
46836
- let data4 = (me.bNode) ? dataArray[1] : dataArray[1].value; //v4[0];
46836
+ // let data3 = (me.bNode) ? dataArray[0] : dataArray[0].value; //v3[0];
46837
+ // let data4 = (me.bNode) ? dataArray[1] : dataArray[1].value; //v4[0];
46838
+ let data3 = dataArray[0].value; //v3[0];
46839
+ let data4 = dataArray[1].value; //v4[0];
46837
46840
 
46838
46841
  if(data3.atoms !== undefined && data4.atoms !== undefined) {
46839
46842
  // ic.deferredOpm = $.Deferred(function() {
@@ -46995,7 +46998,8 @@ class AlignParser {
46995
46998
 
46996
46999
  let bFound = false;
46997
47000
  for(let i = 0, il = dataArray.length; i < il; ++i) {
46998
- let opmdata = (me.bNode) ? dataArray[i] : dataArray[i].value;
47001
+ //let opmdata = (me.bNode) ? dataArray[i] : dataArray[i].value;
47002
+ let opmdata = dataArray[i].value;
46999
47003
 
47000
47004
  if(!opmdata) continue;
47001
47005
 
@@ -47155,7 +47159,8 @@ class ChainalignParser {
47155
47159
 
47156
47160
  // modify the previous trans and rotation matrix
47157
47161
  for(let i = 0, il = dataArray.length; i < il; ++i) {
47158
- let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
47162
+ // let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
47163
+ let align = dataArray[i].value;//[0];
47159
47164
 
47160
47165
  let mmdbid_q = struArray[i];
47161
47166
  let index = indexArray[i];
@@ -47247,7 +47252,8 @@ class ChainalignParser {
47247
47252
 
47248
47253
  let bFoundAlignment = false;
47249
47254
  for(let i = 0, il = dataArray.length; i < il; ++i) {
47250
- let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
47255
+ // let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
47256
+ let align = dataArray[i].value;//[0];
47251
47257
 
47252
47258
  let bEqualMmdbid = false;
47253
47259
  let bEqualChain = false;
@@ -47639,7 +47645,8 @@ class ChainalignParser {
47639
47645
  // Each argument is an array with the following structure: [ data, statusText, jqXHR ]
47640
47646
  //var data2 = v2[0];
47641
47647
  // index = 0: the mmdb data of target
47642
- let targetData = (me.bNode) ? dataArray[0] : dataArray[0].value; //[0];
47648
+ // let targetData = (me.bNode) ? dataArray[0] : dataArray[0].value; //[0];
47649
+ let targetData = dataArray[0].value; //[0];
47643
47650
  let header = 'HEADER ' + mmdbid_t + '\n';
47644
47651
  if(isNaN(mmdbid_t) && mmdbid_t.length > 5) targetData = header + targetData;
47645
47652
 
@@ -47657,7 +47664,8 @@ class ChainalignParser {
47657
47664
  let queryDataArray = [];
47658
47665
 
47659
47666
  for(let index = 1, indexl = chainidArray.length; index < indexl; ++index) {
47660
- let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
47667
+ // let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
47668
+ let queryData = dataArray[index].value;//[0];
47661
47669
 
47662
47670
  let pos = chainidArray[index].indexOf('_');
47663
47671
  let mmdbid_q = chainidArray[index].substr(0, pos).toUpperCase();
@@ -47703,7 +47711,8 @@ class ChainalignParser {
47703
47711
  ic.qt_start_end[index-1] = undefined;
47704
47712
  }
47705
47713
  else {
47706
- let align = (me.bNode) ? dataArray[index2 - missedChainCnt] : dataArray[index2 - missedChainCnt].value;//[0];
47714
+ // let align = (me.bNode) ? dataArray[index2 - missedChainCnt] : dataArray[index2 - missedChainCnt].value;//[0];
47715
+ let align = dataArray[index2 - missedChainCnt].value;//[0];
47707
47716
 
47708
47717
  let bEqualMmdbid = (mmdbid_q == mmdbid_t);
47709
47718
  let bEqualChain = (chain_q == chain_t);
@@ -47921,7 +47930,8 @@ class ChainalignParser {
47921
47930
 
47922
47931
  let queryDataArray = [];
47923
47932
  for(let index = 0, indexl = structArray.length; index < indexl; ++index) {
47924
- let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
47933
+ // let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
47934
+ let queryData = dataArray[index].value;//[0];
47925
47935
  let header = 'HEADER ' + structArray[index] + '\n';
47926
47936
  if(isNaN(structArray[index]) && structArray[index].length > 5) queryData = header + queryData;
47927
47937
 
@@ -50373,7 +50383,8 @@ class RealignParser {
50373
50383
  //var data2 = v2[0];
50374
50384
  for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
50375
50385
  // for(let index = 1, indexl = dataArray.length; index < indexl; ++index) {
50376
- let data = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
50386
+ // let data = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
50387
+ let data = dataArray[index].value;//[0];
50377
50388
  if(!data) continue;
50378
50389
 
50379
50390
  let fromStruct = chainidArray[index + 1].substr(0, chainidArray[index + 1].indexOf('_')); //.toUpperCase();
@@ -52223,13 +52234,15 @@ class ParserUtils {
52223
52234
  let allPromise = Promise.allSettled([prms1, prms2]);
52224
52235
  let dataArray = await allPromise;
52225
52236
 
52226
- ic.interactionData1 = (me.bNode) ? dataArray[0] : dataArray[0].value;
52237
+ // ic.interactionData1 = (me.bNode) ? dataArray[0] : dataArray[0].value;
52238
+ ic.interactionData1 = dataArray[0].value;
52227
52239
  ic.html2ddgm = '';
52228
52240
  ic.diagram2dCls.draw2Ddgm(ic.interactionData1, mmdbid1, 0);
52229
52241
  if(me.cfg.show2d) me.htmlCls.dialogCls.openDlg('dl_2ddgm', 'Interactions');
52230
52242
 
52231
52243
 
52232
- ic.interactionData2 = (me.bNode) ? dataArray[1] : dataArray[1].value;
52244
+ // ic.interactionData2 = (me.bNode) ? dataArray[1] : dataArray[1].value;
52245
+ ic.interactionData2 = dataArray[1].value;
52233
52246
  ic.diagram2dCls.draw2Ddgm(ic.interactionData2, mmdbid2, 1);
52234
52247
 
52235
52248
  ic.html2ddgm += "<br>" + ic.diagram2dCls.set2DdgmNote(true);
@@ -52277,7 +52290,8 @@ class ParserUtils {
52277
52290
  // Each argument is an array with the following structure: [ data, statusText, jqXHR ]
52278
52291
  //var data2 = v2[0];
52279
52292
  for(let index = 0, indexl = chainidArray.length; index < indexl; ++index) {
52280
- let data = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
52293
+ // let data = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
52294
+ let data = dataArray[index].value;//[0];
52281
52295
  let mmdbid = chainidArray[index].substr(0, chainidArray[index].indexOf('_'));
52282
52296
 
52283
52297
  ic.diagram2dCls.draw2Ddgm(data, mmdbid, 0);
@@ -55969,7 +55983,8 @@ class Vastplus {
55969
55983
 
55970
55984
  let queryDataArray = [];
55971
55985
  for(let index = 0, indexl = chainidpairArray.length; index < indexl; ++index) {
55972
- let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
55986
+ // let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
55987
+ let queryData = dataArray[index].value; //[0];
55973
55988
 
55974
55989
  queryDataArray.push(queryData);
55975
55990
  /*
@@ -62183,14 +62198,15 @@ class Dssp {
62183
62198
  }
62184
62199
  }
62185
62200
 
62186
- async parseDsspData(dataArray, struArray, bAppend) { let ic = this.icn3d, me = ic.icn3dui;
62201
+ async parseDsspData(dataArray, struArray, bAppend) { let ic = this.icn3d; ic.icn3dui;
62187
62202
  //var dataArray =(struArray.length == 1) ? [data] : data;
62188
62203
 
62189
62204
  // Each argument is an array with the following structure: [ data, statusText, jqXHR ]
62190
62205
  //var data2 = v2[0];
62191
62206
  for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
62192
62207
  //let ssHash = dataArray[index][0];
62193
- let ssHash = (me.bNode) ? dataArray[index] : dataArray[index].value;
62208
+ //let ssHash = (me.bNode) ? dataArray[index] : dataArray[index].value;
62209
+ let ssHash = dataArray[index].value;
62194
62210
 
62195
62211
  if(ssHash !== undefined && JSON.stringify(ssHash).indexOf('Oops there was a problem') === -1) {
62196
62212
  for(let chainNum in ic.chainsSeq) {
@@ -62472,16 +62488,17 @@ class Dssp {
62472
62488
  pdbAjaxArray.push(pdbAjax);
62473
62489
  }
62474
62490
 
62475
- // try {
62491
+ try {
62476
62492
  let allPromise = Promise.allSettled(pdbAjaxArray);
62477
62493
  ic.pdbDataArray = await allPromise;
62478
62494
  await thisClass.parseRefPdbData(ic.pdbDataArray);
62479
- // }
62480
- // catch(err) {
62481
- // if(!me.bNode) var aaa = 1; //alert("Error in retrieveing reference PDB data...");
62482
- // //var aaa = 1; //alert("Error in retrieveing reference PDB data...");
62483
- // return;
62484
- // }
62495
+ }
62496
+ catch(err) {
62497
+ if(!me.bNode) var aaa = 1; //alert("Error in retrieveing reference PDB data...");
62498
+ //var aaa = 1; //alert("Error in retrieveing reference PDB data...");
62499
+ return;
62500
+ }
62501
+
62485
62502
  // }
62486
62503
  // }
62487
62504
  }
@@ -62558,12 +62575,13 @@ class Dssp {
62558
62575
  for(let k = 0, kl = domainAtomsArray.length; k < kl; ++k) {
62559
62576
  let pdb_target = ic.saveFileCls.getAtomPDB(domainAtomsArray[k], undefined, undefined, undefined, undefined, struct);
62560
62577
  // ig strand for any subset will have the same k, use the number of residue to separate them
62561
- let domainid = chainid + '-' + k + '_' + domainAtomsArray[k].length;
62578
+ let domainid = chainid + '-' + k + '_' + Object.keys(domainAtomsArray[k]).length;
62562
62579
  ic.domainid2pdb[domainid] = pdb_target;
62563
62580
 
62564
62581
  for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
62565
62582
  let struct2 = ic.defaultPdbId + index;
62566
- let pdb_query = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
62583
+ //let pdb_query = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
62584
+ let pdb_query = dataArray[index].value; //[0];
62567
62585
  let header = 'HEADER ' + struct2 + '\n';
62568
62586
  pdb_query = header + pdb_query;
62569
62587
 
@@ -62577,7 +62595,7 @@ class Dssp {
62577
62595
  }
62578
62596
  }
62579
62597
 
62580
- // try {
62598
+ try {
62581
62599
  let dataArray2 = [];
62582
62600
  let allPromise = Promise.allSettled(ajaxArray);
62583
62601
  dataArray2 = await allPromise;
@@ -62586,12 +62604,12 @@ class Dssp {
62586
62604
  await thisClass.parseAlignData(dataArray2, domainidpairArray, bRound1);
62587
62605
 
62588
62606
  /// if(ic.deferredRefnum !== undefined) ic.deferredRefnum.resolve();
62589
- // }
62590
- // catch(err) {
62591
- // if(!me.bNode) console.log("Error in aligning with TM-align...");
62592
- // //console.log("Error in aligning with TM-align...");
62593
- // return;
62594
- // }
62607
+ }
62608
+ catch(err) {
62609
+ if(!me.bNode) console.log("Error in aligning with TM-align...");
62610
+ //console.log("Error in aligning with TM-align...");
62611
+ return;
62612
+ }
62595
62613
  }
62596
62614
 
62597
62615
  async parseAlignData(dataArray, domainidpairArray, bRound1) { let ic = this.icn3d, me = ic.icn3dui;
@@ -62615,7 +62633,8 @@ class Dssp {
62615
62633
  let minResidues = 20;
62616
62634
 
62617
62635
  for(let i = 0, il = domainidpairArray.length; i < il; ++i) {
62618
- let queryData = (me.bNode) ? dataArray[i] : dataArray[i].value; //[0];
62636
+ //let queryData = (me.bNode) ? dataArray[i] : dataArray[i].value; //[0];
62637
+ let queryData = dataArray[i].value; //[0];
62619
62638
 
62620
62639
  if(!queryData) {
62621
62640
  if(!me.bNode) console.log("The alignment data for " + domainidpairArray[i] + " is unavailable...");
@@ -62707,7 +62726,8 @@ class Dssp {
62707
62726
  let pdb_target = ic.domainid2pdb[domainid];
62708
62727
  for(let index = 0, indexl = ic.pdbDataArray.length; index < indexl; ++index) {
62709
62728
  let struct2 = ic.defaultPdbId + index;
62710
- let pdb_query = (me.bNode) ? ic.pdbDataArray[index] : ic.pdbDataArray[index].value; //[0];
62729
+ //let pdb_query = (me.bNode) ? ic.pdbDataArray[index] : ic.pdbDataArray[index].value; //[0];
62730
+ let pdb_query = ic.pdbDataArray[index].value; //[0];
62711
62731
  let header = 'HEADER ' + struct2 + '\n';
62712
62732
  pdb_query = header + pdb_query;
62713
62733
 
@@ -71253,25 +71273,35 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
71253
71273
  let data = await me.getAjaxPromise(url, 'json', false, 'The RID ' + me.cfg.rid + ' may have expired...');
71254
71274
 
71255
71275
  for(let q = 0, ql = data.BlastOutput2.length; q < ql; ++q) {
71256
- if(data.BlastOutput2[q].report.results.search.query_id != me.cfg.query_id) continue;
71257
- let hitArray = data.BlastOutput2[q].report.results.search.hits;
71276
+
71277
+ let hitArray;
71278
+ if(data.BlastOutput2[q].report.results.iterations) { // psi-blast may have "iterations". Use the last iteration.
71279
+ let nIterations = data.BlastOutput2[q].report.results.iterations.length;
71280
+ if(data.BlastOutput2[q].report.results.iterations[nIterations - 1].search.query_id != me.cfg.query_id) continue;
71281
+ hitArray = data.BlastOutput2[q].report.results.iterations[nIterations - 1].search.hits;
71282
+ }
71283
+ else { // blastp may not have "iterations"
71284
+ if(data.BlastOutput2[q].report.results.search.query_id != me.cfg.query_id) continue;
71285
+ hitArray = data.BlastOutput2[q].report.results.search.hits;
71286
+ }
71287
+
71258
71288
  let qseq = undefined;
71259
71289
  for(let i = 0, il = hitArray.length; i < il; ++i) {
71260
- let hit = hitArray[i];
71261
- let bFound = false;
71262
- for(let j = 0, jl = hit.description.length; j < jl; ++j) {
71263
- let acc = hit.description[j].accession;
71264
- if(acc == me.cfg.blast_rep_id) {
71265
- bFound = true;
71266
- break;
71290
+ let hit = hitArray[i];
71291
+ let bFound = false;
71292
+ for(let j = 0, jl = hit.description.length; j < jl; ++j) {
71293
+ let acc = hit.description[j].accession;
71294
+ if(acc == me.cfg.blast_rep_id) {
71295
+ bFound = true;
71296
+ break;
71297
+ }
71298
+ }
71299
+ if(bFound) {
71300
+ qseq = hit.hsps[0].qseq;
71301
+ //remove gap '-'
71302
+ qseq = qseq.replace(/-/g, '');
71303
+ break;
71267
71304
  }
71268
- }
71269
- if(bFound) {
71270
- qseq = hit.hsps[0].qseq;
71271
- //remove gap '-'
71272
- qseq = qseq.replace(/-/g, '');
71273
- break;
71274
- }
71275
71305
  }
71276
71306
  if(qseq !== undefined) me.cfg.query_id = qseq;
71277
71307
  ic.inputid = me.cfg.query_id + '_' + me.cfg.blast_rep_id;