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.module.js CHANGED
@@ -36756,6 +36756,7 @@ class AnnoCddSite {
36756
36756
 
36757
36757
  for(let i = 0, il = dataArray.length; i < il; ++i) {
36758
36758
  //let data = (bSeq) ? dataArray[i][0] : dataArray[i];
36759
+ // somehow Node.js returned data in dataArray[i]
36759
36760
  let data = (me.bNode) ? dataArray[i] : dataArray[i].value;
36760
36761
 
36761
36762
  if(!data) continue;
@@ -47733,8 +47734,10 @@ class AlignParser {
47733
47734
  let dataArray = await allPromise;
47734
47735
 
47735
47736
  let data2 = data;
47736
- let data3 = (me.bNode) ? dataArray[0] : dataArray[0].value; //v3[0];
47737
- let data4 = (me.bNode) ? dataArray[1] : dataArray[1].value; //v4[0];
47737
+ // let data3 = (me.bNode) ? dataArray[0] : dataArray[0].value; //v3[0];
47738
+ // let data4 = (me.bNode) ? dataArray[1] : dataArray[1].value; //v4[0];
47739
+ let data3 = dataArray[0].value; //v3[0];
47740
+ let data4 = dataArray[1].value; //v4[0];
47738
47741
 
47739
47742
  if(data3.atoms !== undefined && data4.atoms !== undefined) {
47740
47743
  // ic.deferredOpm = $.Deferred(function() {
@@ -47896,7 +47899,8 @@ class AlignParser {
47896
47899
 
47897
47900
  let bFound = false;
47898
47901
  for(let i = 0, il = dataArray.length; i < il; ++i) {
47899
- let opmdata = (me.bNode) ? dataArray[i] : dataArray[i].value;
47902
+ //let opmdata = (me.bNode) ? dataArray[i] : dataArray[i].value;
47903
+ let opmdata = dataArray[i].value;
47900
47904
 
47901
47905
  if(!opmdata) continue;
47902
47906
 
@@ -48056,7 +48060,8 @@ class ChainalignParser {
48056
48060
 
48057
48061
  // modify the previous trans and rotation matrix
48058
48062
  for(let i = 0, il = dataArray.length; i < il; ++i) {
48059
- let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
48063
+ // let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
48064
+ let align = dataArray[i].value;//[0];
48060
48065
 
48061
48066
  let mmdbid_q = struArray[i];
48062
48067
  let index = indexArray[i];
@@ -48148,7 +48153,8 @@ class ChainalignParser {
48148
48153
 
48149
48154
  let bFoundAlignment = false;
48150
48155
  for(let i = 0, il = dataArray.length; i < il; ++i) {
48151
- let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
48156
+ // let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
48157
+ let align = dataArray[i].value;//[0];
48152
48158
 
48153
48159
  let bEqualMmdbid = false;
48154
48160
  let bEqualChain = false;
@@ -48540,7 +48546,8 @@ class ChainalignParser {
48540
48546
  // Each argument is an array with the following structure: [ data, statusText, jqXHR ]
48541
48547
  //var data2 = v2[0];
48542
48548
  // index = 0: the mmdb data of target
48543
- let targetData = (me.bNode) ? dataArray[0] : dataArray[0].value; //[0];
48549
+ // let targetData = (me.bNode) ? dataArray[0] : dataArray[0].value; //[0];
48550
+ let targetData = dataArray[0].value; //[0];
48544
48551
  let header = 'HEADER ' + mmdbid_t + '\n';
48545
48552
  if(isNaN(mmdbid_t) && mmdbid_t.length > 5) targetData = header + targetData;
48546
48553
 
@@ -48558,7 +48565,8 @@ class ChainalignParser {
48558
48565
  let queryDataArray = [];
48559
48566
 
48560
48567
  for(let index = 1, indexl = chainidArray.length; index < indexl; ++index) {
48561
- let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
48568
+ // let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
48569
+ let queryData = dataArray[index].value;//[0];
48562
48570
 
48563
48571
  let pos = chainidArray[index].indexOf('_');
48564
48572
  let mmdbid_q = chainidArray[index].substr(0, pos).toUpperCase();
@@ -48604,7 +48612,8 @@ class ChainalignParser {
48604
48612
  ic.qt_start_end[index-1] = undefined;
48605
48613
  }
48606
48614
  else {
48607
- let align = (me.bNode) ? dataArray[index2 - missedChainCnt] : dataArray[index2 - missedChainCnt].value;//[0];
48615
+ // let align = (me.bNode) ? dataArray[index2 - missedChainCnt] : dataArray[index2 - missedChainCnt].value;//[0];
48616
+ let align = dataArray[index2 - missedChainCnt].value;//[0];
48608
48617
 
48609
48618
  let bEqualMmdbid = (mmdbid_q == mmdbid_t);
48610
48619
  let bEqualChain = (chain_q == chain_t);
@@ -48822,7 +48831,8 @@ class ChainalignParser {
48822
48831
 
48823
48832
  let queryDataArray = [];
48824
48833
  for(let index = 0, indexl = structArray.length; index < indexl; ++index) {
48825
- let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
48834
+ // let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
48835
+ let queryData = dataArray[index].value;//[0];
48826
48836
  let header = 'HEADER ' + structArray[index] + '\n';
48827
48837
  if(isNaN(structArray[index]) && structArray[index].length > 5) queryData = header + queryData;
48828
48838
 
@@ -51274,7 +51284,8 @@ class RealignParser {
51274
51284
  //var data2 = v2[0];
51275
51285
  for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
51276
51286
  // for(let index = 1, indexl = dataArray.length; index < indexl; ++index) {
51277
- let data = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
51287
+ // let data = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
51288
+ let data = dataArray[index].value;//[0];
51278
51289
  if(!data) continue;
51279
51290
 
51280
51291
  let fromStruct = chainidArray[index + 1].substr(0, chainidArray[index + 1].indexOf('_')); //.toUpperCase();
@@ -53124,13 +53135,15 @@ class ParserUtils {
53124
53135
  let allPromise = Promise.allSettled([prms1, prms2]);
53125
53136
  let dataArray = await allPromise;
53126
53137
 
53127
- ic.interactionData1 = (me.bNode) ? dataArray[0] : dataArray[0].value;
53138
+ // ic.interactionData1 = (me.bNode) ? dataArray[0] : dataArray[0].value;
53139
+ ic.interactionData1 = dataArray[0].value;
53128
53140
  ic.html2ddgm = '';
53129
53141
  ic.diagram2dCls.draw2Ddgm(ic.interactionData1, mmdbid1, 0);
53130
53142
  if(me.cfg.show2d) me.htmlCls.dialogCls.openDlg('dl_2ddgm', 'Interactions');
53131
53143
 
53132
53144
 
53133
- ic.interactionData2 = (me.bNode) ? dataArray[1] : dataArray[1].value;
53145
+ // ic.interactionData2 = (me.bNode) ? dataArray[1] : dataArray[1].value;
53146
+ ic.interactionData2 = dataArray[1].value;
53134
53147
  ic.diagram2dCls.draw2Ddgm(ic.interactionData2, mmdbid2, 1);
53135
53148
 
53136
53149
  ic.html2ddgm += "<br>" + ic.diagram2dCls.set2DdgmNote(true);
@@ -53178,7 +53191,8 @@ class ParserUtils {
53178
53191
  // Each argument is an array with the following structure: [ data, statusText, jqXHR ]
53179
53192
  //var data2 = v2[0];
53180
53193
  for(let index = 0, indexl = chainidArray.length; index < indexl; ++index) {
53181
- let data = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
53194
+ // let data = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
53195
+ let data = dataArray[index].value;//[0];
53182
53196
  let mmdbid = chainidArray[index].substr(0, chainidArray[index].indexOf('_'));
53183
53197
 
53184
53198
  ic.diagram2dCls.draw2Ddgm(data, mmdbid, 0);
@@ -56870,7 +56884,8 @@ class Vastplus {
56870
56884
 
56871
56885
  let queryDataArray = [];
56872
56886
  for(let index = 0, indexl = chainidpairArray.length; index < indexl; ++index) {
56873
- let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
56887
+ // let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
56888
+ let queryData = dataArray[index].value; //[0];
56874
56889
 
56875
56890
  queryDataArray.push(queryData);
56876
56891
  /*
@@ -63084,14 +63099,15 @@ class Dssp {
63084
63099
  }
63085
63100
  }
63086
63101
 
63087
- async parseDsspData(dataArray, struArray, bAppend) { let ic = this.icn3d, me = ic.icn3dui;
63102
+ async parseDsspData(dataArray, struArray, bAppend) { let ic = this.icn3d; ic.icn3dui;
63088
63103
  //var dataArray =(struArray.length == 1) ? [data] : data;
63089
63104
 
63090
63105
  // Each argument is an array with the following structure: [ data, statusText, jqXHR ]
63091
63106
  //var data2 = v2[0];
63092
63107
  for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
63093
63108
  //let ssHash = dataArray[index][0];
63094
- let ssHash = (me.bNode) ? dataArray[index] : dataArray[index].value;
63109
+ //let ssHash = (me.bNode) ? dataArray[index] : dataArray[index].value;
63110
+ let ssHash = dataArray[index].value;
63095
63111
 
63096
63112
  if(ssHash !== undefined && JSON.stringify(ssHash).indexOf('Oops there was a problem') === -1) {
63097
63113
  for(let chainNum in ic.chainsSeq) {
@@ -63373,16 +63389,17 @@ class Dssp {
63373
63389
  pdbAjaxArray.push(pdbAjax);
63374
63390
  }
63375
63391
 
63376
- // try {
63392
+ try {
63377
63393
  let allPromise = Promise.allSettled(pdbAjaxArray);
63378
63394
  ic.pdbDataArray = await allPromise;
63379
63395
  await thisClass.parseRefPdbData(ic.pdbDataArray);
63380
- // }
63381
- // catch(err) {
63382
- // if(!me.bNode) alert("Error in retrieveing reference PDB data...");
63383
- // //alert("Error in retrieveing reference PDB data...");
63384
- // return;
63385
- // }
63396
+ }
63397
+ catch(err) {
63398
+ if(!me.bNode) alert("Error in retrieveing reference PDB data...");
63399
+ //alert("Error in retrieveing reference PDB data...");
63400
+ return;
63401
+ }
63402
+
63386
63403
  // }
63387
63404
  // }
63388
63405
  }
@@ -63459,12 +63476,13 @@ class Dssp {
63459
63476
  for(let k = 0, kl = domainAtomsArray.length; k < kl; ++k) {
63460
63477
  let pdb_target = ic.saveFileCls.getAtomPDB(domainAtomsArray[k], undefined, undefined, undefined, undefined, struct);
63461
63478
  // ig strand for any subset will have the same k, use the number of residue to separate them
63462
- let domainid = chainid + '-' + k + '_' + domainAtomsArray[k].length;
63479
+ let domainid = chainid + '-' + k + '_' + Object.keys(domainAtomsArray[k]).length;
63463
63480
  ic.domainid2pdb[domainid] = pdb_target;
63464
63481
 
63465
63482
  for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
63466
63483
  let struct2 = ic.defaultPdbId + index;
63467
- let pdb_query = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
63484
+ //let pdb_query = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
63485
+ let pdb_query = dataArray[index].value; //[0];
63468
63486
  let header = 'HEADER ' + struct2 + '\n';
63469
63487
  pdb_query = header + pdb_query;
63470
63488
 
@@ -63478,7 +63496,7 @@ class Dssp {
63478
63496
  }
63479
63497
  }
63480
63498
 
63481
- // try {
63499
+ try {
63482
63500
  let dataArray2 = [];
63483
63501
  let allPromise = Promise.allSettled(ajaxArray);
63484
63502
  dataArray2 = await allPromise;
@@ -63487,12 +63505,12 @@ class Dssp {
63487
63505
  await thisClass.parseAlignData(dataArray2, domainidpairArray, bRound1);
63488
63506
 
63489
63507
  /// if(ic.deferredRefnum !== undefined) ic.deferredRefnum.resolve();
63490
- // }
63491
- // catch(err) {
63492
- // if(!me.bNode) console.log("Error in aligning with TM-align...");
63493
- // //console.log("Error in aligning with TM-align...");
63494
- // return;
63495
- // }
63508
+ }
63509
+ catch(err) {
63510
+ if(!me.bNode) console.log("Error in aligning with TM-align...");
63511
+ //console.log("Error in aligning with TM-align...");
63512
+ return;
63513
+ }
63496
63514
  }
63497
63515
 
63498
63516
  async parseAlignData(dataArray, domainidpairArray, bRound1) { let ic = this.icn3d, me = ic.icn3dui;
@@ -63516,7 +63534,8 @@ class Dssp {
63516
63534
  let minResidues = 20;
63517
63535
 
63518
63536
  for(let i = 0, il = domainidpairArray.length; i < il; ++i) {
63519
- let queryData = (me.bNode) ? dataArray[i] : dataArray[i].value; //[0];
63537
+ //let queryData = (me.bNode) ? dataArray[i] : dataArray[i].value; //[0];
63538
+ let queryData = dataArray[i].value; //[0];
63520
63539
 
63521
63540
  if(!queryData) {
63522
63541
  if(!me.bNode) console.log("The alignment data for " + domainidpairArray[i] + " is unavailable...");
@@ -63608,7 +63627,8 @@ class Dssp {
63608
63627
  let pdb_target = ic.domainid2pdb[domainid];
63609
63628
  for(let index = 0, indexl = ic.pdbDataArray.length; index < indexl; ++index) {
63610
63629
  let struct2 = ic.defaultPdbId + index;
63611
- let pdb_query = (me.bNode) ? ic.pdbDataArray[index] : ic.pdbDataArray[index].value; //[0];
63630
+ //let pdb_query = (me.bNode) ? ic.pdbDataArray[index] : ic.pdbDataArray[index].value; //[0];
63631
+ let pdb_query = ic.pdbDataArray[index].value; //[0];
63612
63632
  let header = 'HEADER ' + struct2 + '\n';
63613
63633
  pdb_query = header + pdb_query;
63614
63634
 
@@ -72154,25 +72174,35 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
72154
72174
  let data = await me.getAjaxPromise(url, 'json', false, 'The RID ' + me.cfg.rid + ' may have expired...');
72155
72175
 
72156
72176
  for(let q = 0, ql = data.BlastOutput2.length; q < ql; ++q) {
72157
- if(data.BlastOutput2[q].report.results.search.query_id != me.cfg.query_id) continue;
72158
- let hitArray = data.BlastOutput2[q].report.results.search.hits;
72177
+
72178
+ let hitArray;
72179
+ if(data.BlastOutput2[q].report.results.iterations) { // psi-blast may have "iterations". Use the last iteration.
72180
+ let nIterations = data.BlastOutput2[q].report.results.iterations.length;
72181
+ if(data.BlastOutput2[q].report.results.iterations[nIterations - 1].search.query_id != me.cfg.query_id) continue;
72182
+ hitArray = data.BlastOutput2[q].report.results.iterations[nIterations - 1].search.hits;
72183
+ }
72184
+ else { // blastp may not have "iterations"
72185
+ if(data.BlastOutput2[q].report.results.search.query_id != me.cfg.query_id) continue;
72186
+ hitArray = data.BlastOutput2[q].report.results.search.hits;
72187
+ }
72188
+
72159
72189
  let qseq = undefined;
72160
72190
  for(let i = 0, il = hitArray.length; i < il; ++i) {
72161
- let hit = hitArray[i];
72162
- let bFound = false;
72163
- for(let j = 0, jl = hit.description.length; j < jl; ++j) {
72164
- let acc = hit.description[j].accession;
72165
- if(acc == me.cfg.blast_rep_id) {
72166
- bFound = true;
72167
- break;
72191
+ let hit = hitArray[i];
72192
+ let bFound = false;
72193
+ for(let j = 0, jl = hit.description.length; j < jl; ++j) {
72194
+ let acc = hit.description[j].accession;
72195
+ if(acc == me.cfg.blast_rep_id) {
72196
+ bFound = true;
72197
+ break;
72198
+ }
72199
+ }
72200
+ if(bFound) {
72201
+ qseq = hit.hsps[0].qseq;
72202
+ //remove gap '-'
72203
+ qseq = qseq.replace(/-/g, '');
72204
+ break;
72168
72205
  }
72169
- }
72170
- if(bFound) {
72171
- qseq = hit.hsps[0].qseq;
72172
- //remove gap '-'
72173
- qseq = qseq.replace(/-/g, '');
72174
- break;
72175
- }
72176
72206
  }
72177
72207
  if(qseq !== undefined) me.cfg.query_id = qseq;
72178
72208
  ic.inputid = me.cfg.query_id + '_' + me.cfg.blast_rep_id;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "icn3d",
3
- "version": "3.25.14",
3
+ "version": "3.25.16",
4
4
  "main": "./icn3d.js",
5
5
  "exports": {
6
6
  ".": {