icn3d 3.25.15 → 3.25.17

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Files changed (4) hide show
  1. package/icn3d.js +76 -35
  2. package/icn3d.min.js +2 -2
  3. package/icn3d.module.js +76 -35
  4. package/package.json +1 -1
package/icn3d.js CHANGED
@@ -32255,7 +32255,8 @@ class Alternate {
32255
32255
  ic.drawCls.draw();
32256
32256
 
32257
32257
  ic.bShowHighlight = true;
32258
- ic.opts['rotationcenter'] = 'molecule center';
32258
+ //ic.opts['rotationcenter'] = 'molecule center';
32259
+ ic.opts['rotationcenter'] = 'highlight center';
32259
32260
  }
32260
32261
 
32261
32262
  alternateWrapper() { let ic = this.icn3d; ic.icn3dui;
@@ -35855,6 +35856,7 @@ class AnnoCddSite {
35855
35856
 
35856
35857
  for(let i = 0, il = dataArray.length; i < il; ++i) {
35857
35858
  //let data = (bSeq) ? dataArray[i][0] : dataArray[i];
35859
+ // somehow Node.js returned data in dataArray[i]
35858
35860
  let data = (me.bNode) ? dataArray[i] : dataArray[i].value;
35859
35861
 
35860
35862
  if(!data) continue;
@@ -42211,6 +42213,8 @@ class ShowSeq {
42211
42213
  refnumStr = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
42212
42214
  currRefnum = parseInt(refnumStr);
42213
42215
  refnumLabelNoPostfix = currStrand + currRefnum;
42216
+
42217
+ currStrand = refnumLabel.replace(new RegExp(refnumStr,'g'), '');
42214
42218
 
42215
42219
  let firstChar = refnumLabel.substr(0,1);
42216
42220
  if(!bStart && (firstChar == ' ' || firstChar == 'A' || firstChar == 'B')) { // start of a new IG domain
@@ -42227,7 +42231,26 @@ class ShowSeq {
42227
42231
  refnumLabel = undefined;
42228
42232
  }
42229
42233
  else {
42230
- if(parseInt(currResi) < parseInt(strandArray[strandCnt].startResi)) {
42234
+ let bBefore = false, bInRange= false, bAfter = false;
42235
+ // 100, 100A
42236
+ if(parseInt(currResi) == parseInt(strandArray[strandCnt].startResi) && currResi != strandArray[strandCnt].startResi) {
42237
+ bBefore = currResi < strandArray[strandCnt].startResi;
42238
+ }
42239
+ else {
42240
+ bBefore = parseInt(currResi) < parseInt(strandArray[strandCnt].startResi);
42241
+ }
42242
+
42243
+ // 100, 100A
42244
+ if(parseInt(currResi) == parseInt(strandArray[strandCnt].endResi) && currResi != strandArray[strandCnt].endResi) {
42245
+ bAfter = currResi > strandArray[strandCnt].endResi;
42246
+ }
42247
+ else {
42248
+ bAfter = parseInt(currResi) > parseInt(strandArray[strandCnt].endResi);
42249
+ }
42250
+
42251
+ bInRange = (!bBefore && !bAfter) ? true : false;
42252
+
42253
+ if(bBefore) {
42231
42254
  ic.residIgLoop[residueid] = 1;
42232
42255
 
42233
42256
  if(bBeforeAstrand) { // make it continuous to the 1st strand
@@ -42288,7 +42311,7 @@ class ShowSeq {
42288
42311
  }
42289
42312
  }
42290
42313
  }
42291
- else if(parseInt(currResi) >= parseInt(strandArray[strandCnt].startResi) && parseInt(currResi) <= parseInt(strandArray[strandCnt].endResi)) {
42314
+ else if(bInRange) {
42292
42315
  // not in loop any more if you assign ref numbers multiple times
42293
42316
  //delete ic.residIgLoop[residueid];
42294
42317
 
@@ -42316,7 +42339,7 @@ class ShowSeq {
42316
42339
  }
42317
42340
  }
42318
42341
  }
42319
- else if(parseInt(currResi) > parseInt(strandArray[strandCnt].endResi)) {
42342
+ else if(bAfter) {
42320
42343
  ic.residIgLoop[residueid] = 1;
42321
42344
 
42322
42345
  if(!bAfterGstrand) {
@@ -46832,8 +46855,10 @@ class AlignParser {
46832
46855
  let dataArray = await allPromise;
46833
46856
 
46834
46857
  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];
46858
+ // let data3 = (me.bNode) ? dataArray[0] : dataArray[0].value; //v3[0];
46859
+ // let data4 = (me.bNode) ? dataArray[1] : dataArray[1].value; //v4[0];
46860
+ let data3 = dataArray[0].value; //v3[0];
46861
+ let data4 = dataArray[1].value; //v4[0];
46837
46862
 
46838
46863
  if(data3.atoms !== undefined && data4.atoms !== undefined) {
46839
46864
  // ic.deferredOpm = $.Deferred(function() {
@@ -46995,7 +47020,8 @@ class AlignParser {
46995
47020
 
46996
47021
  let bFound = false;
46997
47022
  for(let i = 0, il = dataArray.length; i < il; ++i) {
46998
- let opmdata = (me.bNode) ? dataArray[i] : dataArray[i].value;
47023
+ //let opmdata = (me.bNode) ? dataArray[i] : dataArray[i].value;
47024
+ let opmdata = dataArray[i].value;
46999
47025
 
47000
47026
  if(!opmdata) continue;
47001
47027
 
@@ -47155,7 +47181,8 @@ class ChainalignParser {
47155
47181
 
47156
47182
  // modify the previous trans and rotation matrix
47157
47183
  for(let i = 0, il = dataArray.length; i < il; ++i) {
47158
- let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
47184
+ // let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
47185
+ let align = dataArray[i].value;//[0];
47159
47186
 
47160
47187
  let mmdbid_q = struArray[i];
47161
47188
  let index = indexArray[i];
@@ -47247,7 +47274,8 @@ class ChainalignParser {
47247
47274
 
47248
47275
  let bFoundAlignment = false;
47249
47276
  for(let i = 0, il = dataArray.length; i < il; ++i) {
47250
- let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
47277
+ // let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
47278
+ let align = dataArray[i].value;//[0];
47251
47279
 
47252
47280
  let bEqualMmdbid = false;
47253
47281
  let bEqualChain = false;
@@ -47639,7 +47667,8 @@ class ChainalignParser {
47639
47667
  // Each argument is an array with the following structure: [ data, statusText, jqXHR ]
47640
47668
  //var data2 = v2[0];
47641
47669
  // index = 0: the mmdb data of target
47642
- let targetData = (me.bNode) ? dataArray[0] : dataArray[0].value; //[0];
47670
+ // let targetData = (me.bNode) ? dataArray[0] : dataArray[0].value; //[0];
47671
+ let targetData = dataArray[0].value; //[0];
47643
47672
  let header = 'HEADER ' + mmdbid_t + '\n';
47644
47673
  if(isNaN(mmdbid_t) && mmdbid_t.length > 5) targetData = header + targetData;
47645
47674
 
@@ -47657,7 +47686,8 @@ class ChainalignParser {
47657
47686
  let queryDataArray = [];
47658
47687
 
47659
47688
  for(let index = 1, indexl = chainidArray.length; index < indexl; ++index) {
47660
- let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
47689
+ // let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
47690
+ let queryData = dataArray[index].value;//[0];
47661
47691
 
47662
47692
  let pos = chainidArray[index].indexOf('_');
47663
47693
  let mmdbid_q = chainidArray[index].substr(0, pos).toUpperCase();
@@ -47703,7 +47733,8 @@ class ChainalignParser {
47703
47733
  ic.qt_start_end[index-1] = undefined;
47704
47734
  }
47705
47735
  else {
47706
- let align = (me.bNode) ? dataArray[index2 - missedChainCnt] : dataArray[index2 - missedChainCnt].value;//[0];
47736
+ // let align = (me.bNode) ? dataArray[index2 - missedChainCnt] : dataArray[index2 - missedChainCnt].value;//[0];
47737
+ let align = dataArray[index2 - missedChainCnt].value;//[0];
47707
47738
 
47708
47739
  let bEqualMmdbid = (mmdbid_q == mmdbid_t);
47709
47740
  let bEqualChain = (chain_q == chain_t);
@@ -47921,7 +47952,8 @@ class ChainalignParser {
47921
47952
 
47922
47953
  let queryDataArray = [];
47923
47954
  for(let index = 0, indexl = structArray.length; index < indexl; ++index) {
47924
- let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
47955
+ // let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
47956
+ let queryData = dataArray[index].value;//[0];
47925
47957
  let header = 'HEADER ' + structArray[index] + '\n';
47926
47958
  if(isNaN(structArray[index]) && structArray[index].length > 5) queryData = header + queryData;
47927
47959
 
@@ -50373,7 +50405,8 @@ class RealignParser {
50373
50405
  //var data2 = v2[0];
50374
50406
  for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
50375
50407
  // for(let index = 1, indexl = dataArray.length; index < indexl; ++index) {
50376
- let data = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
50408
+ // let data = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
50409
+ let data = dataArray[index].value;//[0];
50377
50410
  if(!data) continue;
50378
50411
 
50379
50412
  let fromStruct = chainidArray[index + 1].substr(0, chainidArray[index + 1].indexOf('_')); //.toUpperCase();
@@ -53912,7 +53945,10 @@ class SetSeqAlign {
53912
53945
  */
53913
53946
 
53914
53947
  let resid = chainid + '_' + resi;
53915
- return ic.residueId2Name[resid];
53948
+ let resn = ic.residueId2Name[resid];
53949
+ if(!resn) resn = '?';
53950
+
53951
+ return resn;
53916
53952
  }
53917
53953
 
53918
53954
  getResiAferAlign(chainid, bRealign, pos) { let ic = this.icn3d, me = ic.icn3dui;
@@ -62187,14 +62223,15 @@ class Dssp {
62187
62223
  }
62188
62224
  }
62189
62225
 
62190
- async parseDsspData(dataArray, struArray, bAppend) { let ic = this.icn3d, me = ic.icn3dui;
62226
+ async parseDsspData(dataArray, struArray, bAppend) { let ic = this.icn3d; ic.icn3dui;
62191
62227
  //var dataArray =(struArray.length == 1) ? [data] : data;
62192
62228
 
62193
62229
  // Each argument is an array with the following structure: [ data, statusText, jqXHR ]
62194
62230
  //var data2 = v2[0];
62195
62231
  for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
62196
62232
  //let ssHash = dataArray[index][0];
62197
- let ssHash = (me.bNode) ? dataArray[index] : dataArray[index].value;
62233
+ //let ssHash = (me.bNode) ? dataArray[index] : dataArray[index].value;
62234
+ let ssHash = dataArray[index].value;
62198
62235
 
62199
62236
  if(ssHash !== undefined && JSON.stringify(ssHash).indexOf('Oops there was a problem') === -1) {
62200
62237
  for(let chainNum in ic.chainsSeq) {
@@ -62476,16 +62513,17 @@ class Dssp {
62476
62513
  pdbAjaxArray.push(pdbAjax);
62477
62514
  }
62478
62515
 
62479
- // try {
62516
+ try {
62480
62517
  let allPromise = Promise.allSettled(pdbAjaxArray);
62481
62518
  ic.pdbDataArray = await allPromise;
62482
62519
  await thisClass.parseRefPdbData(ic.pdbDataArray);
62483
- // }
62484
- // catch(err) {
62485
- // if(!me.bNode) var aaa = 1; //alert("Error in retrieveing reference PDB data...");
62486
- // //var aaa = 1; //alert("Error in retrieveing reference PDB data...");
62487
- // return;
62488
- // }
62520
+ }
62521
+ catch(err) {
62522
+ if(!me.bNode) var aaa = 1; //alert("Error in retrieveing reference PDB data...");
62523
+ //var aaa = 1; //alert("Error in retrieveing reference PDB data...");
62524
+ return;
62525
+ }
62526
+
62489
62527
  // }
62490
62528
  // }
62491
62529
  }
@@ -62562,12 +62600,13 @@ class Dssp {
62562
62600
  for(let k = 0, kl = domainAtomsArray.length; k < kl; ++k) {
62563
62601
  let pdb_target = ic.saveFileCls.getAtomPDB(domainAtomsArray[k], undefined, undefined, undefined, undefined, struct);
62564
62602
  // ig strand for any subset will have the same k, use the number of residue to separate them
62565
- let domainid = chainid + '-' + k + '_' + domainAtomsArray[k].length;
62603
+ let domainid = chainid + '-' + k + '_' + Object.keys(domainAtomsArray[k]).length;
62566
62604
  ic.domainid2pdb[domainid] = pdb_target;
62567
62605
 
62568
62606
  for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
62569
62607
  let struct2 = ic.defaultPdbId + index;
62570
- let pdb_query = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
62608
+ //let pdb_query = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
62609
+ let pdb_query = dataArray[index].value; //[0];
62571
62610
  let header = 'HEADER ' + struct2 + '\n';
62572
62611
  pdb_query = header + pdb_query;
62573
62612
 
@@ -62581,7 +62620,7 @@ class Dssp {
62581
62620
  }
62582
62621
  }
62583
62622
 
62584
- // try {
62623
+ try {
62585
62624
  let dataArray2 = [];
62586
62625
  let allPromise = Promise.allSettled(ajaxArray);
62587
62626
  dataArray2 = await allPromise;
@@ -62590,12 +62629,12 @@ class Dssp {
62590
62629
  await thisClass.parseAlignData(dataArray2, domainidpairArray, bRound1);
62591
62630
 
62592
62631
  /// if(ic.deferredRefnum !== undefined) ic.deferredRefnum.resolve();
62593
- // }
62594
- // catch(err) {
62595
- // if(!me.bNode) console.log("Error in aligning with TM-align...");
62596
- // //console.log("Error in aligning with TM-align...");
62597
- // return;
62598
- // }
62632
+ }
62633
+ catch(err) {
62634
+ if(!me.bNode) console.log("Error in aligning with TM-align...");
62635
+ //console.log("Error in aligning with TM-align...");
62636
+ return;
62637
+ }
62599
62638
  }
62600
62639
 
62601
62640
  async parseAlignData(dataArray, domainidpairArray, bRound1) { let ic = this.icn3d, me = ic.icn3dui;
@@ -62619,7 +62658,8 @@ class Dssp {
62619
62658
  let minResidues = 20;
62620
62659
 
62621
62660
  for(let i = 0, il = domainidpairArray.length; i < il; ++i) {
62622
- let queryData = (me.bNode) ? dataArray[i] : dataArray[i].value; //[0];
62661
+ //let queryData = (me.bNode) ? dataArray[i] : dataArray[i].value; //[0];
62662
+ let queryData = dataArray[i].value; //[0];
62623
62663
 
62624
62664
  if(!queryData) {
62625
62665
  if(!me.bNode) console.log("The alignment data for " + domainidpairArray[i] + " is unavailable...");
@@ -62711,7 +62751,8 @@ class Dssp {
62711
62751
  let pdb_target = ic.domainid2pdb[domainid];
62712
62752
  for(let index = 0, indexl = ic.pdbDataArray.length; index < indexl; ++index) {
62713
62753
  let struct2 = ic.defaultPdbId + index;
62714
- let pdb_query = (me.bNode) ? ic.pdbDataArray[index] : ic.pdbDataArray[index].value; //[0];
62754
+ //let pdb_query = (me.bNode) ? ic.pdbDataArray[index] : ic.pdbDataArray[index].value; //[0];
62755
+ let pdb_query = ic.pdbDataArray[index].value; //[0];
62715
62756
  let header = 'HEADER ' + struct2 + '\n';
62716
62757
  pdb_query = header + pdb_query;
62717
62758