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.module.js CHANGED
@@ -33156,7 +33156,8 @@ class Alternate {
33156
33156
  ic.drawCls.draw();
33157
33157
 
33158
33158
  ic.bShowHighlight = true;
33159
- ic.opts['rotationcenter'] = 'molecule center';
33159
+ //ic.opts['rotationcenter'] = 'molecule center';
33160
+ ic.opts['rotationcenter'] = 'highlight center';
33160
33161
  }
33161
33162
 
33162
33163
  alternateWrapper() { let ic = this.icn3d; ic.icn3dui;
@@ -36756,6 +36757,7 @@ class AnnoCddSite {
36756
36757
 
36757
36758
  for(let i = 0, il = dataArray.length; i < il; ++i) {
36758
36759
  //let data = (bSeq) ? dataArray[i][0] : dataArray[i];
36760
+ // somehow Node.js returned data in dataArray[i]
36759
36761
  let data = (me.bNode) ? dataArray[i] : dataArray[i].value;
36760
36762
 
36761
36763
  if(!data) continue;
@@ -43112,6 +43114,8 @@ class ShowSeq {
43112
43114
  refnumStr = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
43113
43115
  currRefnum = parseInt(refnumStr);
43114
43116
  refnumLabelNoPostfix = currStrand + currRefnum;
43117
+
43118
+ currStrand = refnumLabel.replace(new RegExp(refnumStr,'g'), '');
43115
43119
 
43116
43120
  let firstChar = refnumLabel.substr(0,1);
43117
43121
  if(!bStart && (firstChar == ' ' || firstChar == 'A' || firstChar == 'B')) { // start of a new IG domain
@@ -43128,7 +43132,26 @@ class ShowSeq {
43128
43132
  refnumLabel = undefined;
43129
43133
  }
43130
43134
  else {
43131
- if(parseInt(currResi) < parseInt(strandArray[strandCnt].startResi)) {
43135
+ let bBefore = false, bInRange= false, bAfter = false;
43136
+ // 100, 100A
43137
+ if(parseInt(currResi) == parseInt(strandArray[strandCnt].startResi) && currResi != strandArray[strandCnt].startResi) {
43138
+ bBefore = currResi < strandArray[strandCnt].startResi;
43139
+ }
43140
+ else {
43141
+ bBefore = parseInt(currResi) < parseInt(strandArray[strandCnt].startResi);
43142
+ }
43143
+
43144
+ // 100, 100A
43145
+ if(parseInt(currResi) == parseInt(strandArray[strandCnt].endResi) && currResi != strandArray[strandCnt].endResi) {
43146
+ bAfter = currResi > strandArray[strandCnt].endResi;
43147
+ }
43148
+ else {
43149
+ bAfter = parseInt(currResi) > parseInt(strandArray[strandCnt].endResi);
43150
+ }
43151
+
43152
+ bInRange = (!bBefore && !bAfter) ? true : false;
43153
+
43154
+ if(bBefore) {
43132
43155
  ic.residIgLoop[residueid] = 1;
43133
43156
 
43134
43157
  if(bBeforeAstrand) { // make it continuous to the 1st strand
@@ -43189,7 +43212,7 @@ class ShowSeq {
43189
43212
  }
43190
43213
  }
43191
43214
  }
43192
- else if(parseInt(currResi) >= parseInt(strandArray[strandCnt].startResi) && parseInt(currResi) <= parseInt(strandArray[strandCnt].endResi)) {
43215
+ else if(bInRange) {
43193
43216
  // not in loop any more if you assign ref numbers multiple times
43194
43217
  //delete ic.residIgLoop[residueid];
43195
43218
 
@@ -43217,7 +43240,7 @@ class ShowSeq {
43217
43240
  }
43218
43241
  }
43219
43242
  }
43220
- else if(parseInt(currResi) > parseInt(strandArray[strandCnt].endResi)) {
43243
+ else if(bAfter) {
43221
43244
  ic.residIgLoop[residueid] = 1;
43222
43245
 
43223
43246
  if(!bAfterGstrand) {
@@ -47733,8 +47756,10 @@ class AlignParser {
47733
47756
  let dataArray = await allPromise;
47734
47757
 
47735
47758
  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];
47759
+ // let data3 = (me.bNode) ? dataArray[0] : dataArray[0].value; //v3[0];
47760
+ // let data4 = (me.bNode) ? dataArray[1] : dataArray[1].value; //v4[0];
47761
+ let data3 = dataArray[0].value; //v3[0];
47762
+ let data4 = dataArray[1].value; //v4[0];
47738
47763
 
47739
47764
  if(data3.atoms !== undefined && data4.atoms !== undefined) {
47740
47765
  // ic.deferredOpm = $.Deferred(function() {
@@ -47896,7 +47921,8 @@ class AlignParser {
47896
47921
 
47897
47922
  let bFound = false;
47898
47923
  for(let i = 0, il = dataArray.length; i < il; ++i) {
47899
- let opmdata = (me.bNode) ? dataArray[i] : dataArray[i].value;
47924
+ //let opmdata = (me.bNode) ? dataArray[i] : dataArray[i].value;
47925
+ let opmdata = dataArray[i].value;
47900
47926
 
47901
47927
  if(!opmdata) continue;
47902
47928
 
@@ -48056,7 +48082,8 @@ class ChainalignParser {
48056
48082
 
48057
48083
  // modify the previous trans and rotation matrix
48058
48084
  for(let i = 0, il = dataArray.length; i < il; ++i) {
48059
- let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
48085
+ // let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
48086
+ let align = dataArray[i].value;//[0];
48060
48087
 
48061
48088
  let mmdbid_q = struArray[i];
48062
48089
  let index = indexArray[i];
@@ -48148,7 +48175,8 @@ class ChainalignParser {
48148
48175
 
48149
48176
  let bFoundAlignment = false;
48150
48177
  for(let i = 0, il = dataArray.length; i < il; ++i) {
48151
- let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
48178
+ // let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
48179
+ let align = dataArray[i].value;//[0];
48152
48180
 
48153
48181
  let bEqualMmdbid = false;
48154
48182
  let bEqualChain = false;
@@ -48540,7 +48568,8 @@ class ChainalignParser {
48540
48568
  // Each argument is an array with the following structure: [ data, statusText, jqXHR ]
48541
48569
  //var data2 = v2[0];
48542
48570
  // index = 0: the mmdb data of target
48543
- let targetData = (me.bNode) ? dataArray[0] : dataArray[0].value; //[0];
48571
+ // let targetData = (me.bNode) ? dataArray[0] : dataArray[0].value; //[0];
48572
+ let targetData = dataArray[0].value; //[0];
48544
48573
  let header = 'HEADER ' + mmdbid_t + '\n';
48545
48574
  if(isNaN(mmdbid_t) && mmdbid_t.length > 5) targetData = header + targetData;
48546
48575
 
@@ -48558,7 +48587,8 @@ class ChainalignParser {
48558
48587
  let queryDataArray = [];
48559
48588
 
48560
48589
  for(let index = 1, indexl = chainidArray.length; index < indexl; ++index) {
48561
- let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
48590
+ // let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
48591
+ let queryData = dataArray[index].value;//[0];
48562
48592
 
48563
48593
  let pos = chainidArray[index].indexOf('_');
48564
48594
  let mmdbid_q = chainidArray[index].substr(0, pos).toUpperCase();
@@ -48604,7 +48634,8 @@ class ChainalignParser {
48604
48634
  ic.qt_start_end[index-1] = undefined;
48605
48635
  }
48606
48636
  else {
48607
- let align = (me.bNode) ? dataArray[index2 - missedChainCnt] : dataArray[index2 - missedChainCnt].value;//[0];
48637
+ // let align = (me.bNode) ? dataArray[index2 - missedChainCnt] : dataArray[index2 - missedChainCnt].value;//[0];
48638
+ let align = dataArray[index2 - missedChainCnt].value;//[0];
48608
48639
 
48609
48640
  let bEqualMmdbid = (mmdbid_q == mmdbid_t);
48610
48641
  let bEqualChain = (chain_q == chain_t);
@@ -48822,7 +48853,8 @@ class ChainalignParser {
48822
48853
 
48823
48854
  let queryDataArray = [];
48824
48855
  for(let index = 0, indexl = structArray.length; index < indexl; ++index) {
48825
- let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
48856
+ // let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
48857
+ let queryData = dataArray[index].value;//[0];
48826
48858
  let header = 'HEADER ' + structArray[index] + '\n';
48827
48859
  if(isNaN(structArray[index]) && structArray[index].length > 5) queryData = header + queryData;
48828
48860
 
@@ -51274,7 +51306,8 @@ class RealignParser {
51274
51306
  //var data2 = v2[0];
51275
51307
  for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
51276
51308
  // for(let index = 1, indexl = dataArray.length; index < indexl; ++index) {
51277
- let data = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
51309
+ // let data = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
51310
+ let data = dataArray[index].value;//[0];
51278
51311
  if(!data) continue;
51279
51312
 
51280
51313
  let fromStruct = chainidArray[index + 1].substr(0, chainidArray[index + 1].indexOf('_')); //.toUpperCase();
@@ -54813,7 +54846,10 @@ class SetSeqAlign {
54813
54846
  */
54814
54847
 
54815
54848
  let resid = chainid + '_' + resi;
54816
- return ic.residueId2Name[resid];
54849
+ let resn = ic.residueId2Name[resid];
54850
+ if(!resn) resn = '?';
54851
+
54852
+ return resn;
54817
54853
  }
54818
54854
 
54819
54855
  getResiAferAlign(chainid, bRealign, pos) { let ic = this.icn3d, me = ic.icn3dui;
@@ -63088,14 +63124,15 @@ class Dssp {
63088
63124
  }
63089
63125
  }
63090
63126
 
63091
- async parseDsspData(dataArray, struArray, bAppend) { let ic = this.icn3d, me = ic.icn3dui;
63127
+ async parseDsspData(dataArray, struArray, bAppend) { let ic = this.icn3d; ic.icn3dui;
63092
63128
  //var dataArray =(struArray.length == 1) ? [data] : data;
63093
63129
 
63094
63130
  // Each argument is an array with the following structure: [ data, statusText, jqXHR ]
63095
63131
  //var data2 = v2[0];
63096
63132
  for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
63097
63133
  //let ssHash = dataArray[index][0];
63098
- let ssHash = (me.bNode) ? dataArray[index] : dataArray[index].value;
63134
+ //let ssHash = (me.bNode) ? dataArray[index] : dataArray[index].value;
63135
+ let ssHash = dataArray[index].value;
63099
63136
 
63100
63137
  if(ssHash !== undefined && JSON.stringify(ssHash).indexOf('Oops there was a problem') === -1) {
63101
63138
  for(let chainNum in ic.chainsSeq) {
@@ -63377,16 +63414,17 @@ class Dssp {
63377
63414
  pdbAjaxArray.push(pdbAjax);
63378
63415
  }
63379
63416
 
63380
- // try {
63417
+ try {
63381
63418
  let allPromise = Promise.allSettled(pdbAjaxArray);
63382
63419
  ic.pdbDataArray = await allPromise;
63383
63420
  await thisClass.parseRefPdbData(ic.pdbDataArray);
63384
- // }
63385
- // catch(err) {
63386
- // if(!me.bNode) alert("Error in retrieveing reference PDB data...");
63387
- // //alert("Error in retrieveing reference PDB data...");
63388
- // return;
63389
- // }
63421
+ }
63422
+ catch(err) {
63423
+ if(!me.bNode) alert("Error in retrieveing reference PDB data...");
63424
+ //alert("Error in retrieveing reference PDB data...");
63425
+ return;
63426
+ }
63427
+
63390
63428
  // }
63391
63429
  // }
63392
63430
  }
@@ -63463,12 +63501,13 @@ class Dssp {
63463
63501
  for(let k = 0, kl = domainAtomsArray.length; k < kl; ++k) {
63464
63502
  let pdb_target = ic.saveFileCls.getAtomPDB(domainAtomsArray[k], undefined, undefined, undefined, undefined, struct);
63465
63503
  // ig strand for any subset will have the same k, use the number of residue to separate them
63466
- let domainid = chainid + '-' + k + '_' + domainAtomsArray[k].length;
63504
+ let domainid = chainid + '-' + k + '_' + Object.keys(domainAtomsArray[k]).length;
63467
63505
  ic.domainid2pdb[domainid] = pdb_target;
63468
63506
 
63469
63507
  for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
63470
63508
  let struct2 = ic.defaultPdbId + index;
63471
- let pdb_query = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
63509
+ //let pdb_query = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
63510
+ let pdb_query = dataArray[index].value; //[0];
63472
63511
  let header = 'HEADER ' + struct2 + '\n';
63473
63512
  pdb_query = header + pdb_query;
63474
63513
 
@@ -63482,7 +63521,7 @@ class Dssp {
63482
63521
  }
63483
63522
  }
63484
63523
 
63485
- // try {
63524
+ try {
63486
63525
  let dataArray2 = [];
63487
63526
  let allPromise = Promise.allSettled(ajaxArray);
63488
63527
  dataArray2 = await allPromise;
@@ -63491,12 +63530,12 @@ class Dssp {
63491
63530
  await thisClass.parseAlignData(dataArray2, domainidpairArray, bRound1);
63492
63531
 
63493
63532
  /// if(ic.deferredRefnum !== undefined) ic.deferredRefnum.resolve();
63494
- // }
63495
- // catch(err) {
63496
- // if(!me.bNode) console.log("Error in aligning with TM-align...");
63497
- // //console.log("Error in aligning with TM-align...");
63498
- // return;
63499
- // }
63533
+ }
63534
+ catch(err) {
63535
+ if(!me.bNode) console.log("Error in aligning with TM-align...");
63536
+ //console.log("Error in aligning with TM-align...");
63537
+ return;
63538
+ }
63500
63539
  }
63501
63540
 
63502
63541
  async parseAlignData(dataArray, domainidpairArray, bRound1) { let ic = this.icn3d, me = ic.icn3dui;
@@ -63520,7 +63559,8 @@ class Dssp {
63520
63559
  let minResidues = 20;
63521
63560
 
63522
63561
  for(let i = 0, il = domainidpairArray.length; i < il; ++i) {
63523
- let queryData = (me.bNode) ? dataArray[i] : dataArray[i].value; //[0];
63562
+ //let queryData = (me.bNode) ? dataArray[i] : dataArray[i].value; //[0];
63563
+ let queryData = dataArray[i].value; //[0];
63524
63564
 
63525
63565
  if(!queryData) {
63526
63566
  if(!me.bNode) console.log("The alignment data for " + domainidpairArray[i] + " is unavailable...");
@@ -63612,7 +63652,8 @@ class Dssp {
63612
63652
  let pdb_target = ic.domainid2pdb[domainid];
63613
63653
  for(let index = 0, indexl = ic.pdbDataArray.length; index < indexl; ++index) {
63614
63654
  let struct2 = ic.defaultPdbId + index;
63615
- let pdb_query = (me.bNode) ? ic.pdbDataArray[index] : ic.pdbDataArray[index].value; //[0];
63655
+ //let pdb_query = (me.bNode) ? ic.pdbDataArray[index] : ic.pdbDataArray[index].value; //[0];
63656
+ let pdb_query = ic.pdbDataArray[index].value; //[0];
63616
63657
  let header = 'HEADER ' + struct2 + '\n';
63617
63658
  pdb_query = header + pdb_query;
63618
63659
 
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "icn3d",
3
- "version": "3.25.15",
3
+ "version": "3.25.17",
4
4
  "main": "./icn3d.js",
5
5
  "exports": {
6
6
  ".": {