icn3d 3.33.1 → 3.33.2

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Files changed (4) hide show
  1. package/icn3d.js +152 -43
  2. package/icn3d.min.js +3 -3
  3. package/icn3d.module.js +152 -43
  4. package/package.json +1 -1
package/icn3d.js CHANGED
@@ -10400,8 +10400,8 @@ class ClickMenu {
10400
10400
  //if(!me.cfg.notebook) dialog.dialog( "close" );
10401
10401
  let sigma2fofc = parseFloat($("#" + me.pre + "sigma2fofc" ).val());
10402
10402
  let type = '2fofc';
10403
- await ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigma2fofc);
10404
- //ic.densityCifParserCls.densityCifParser(ic.inputid, type, sigma2fofc);
10403
+ //await ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigma2fofc);
10404
+ await ic.densityCifParserCls.densityCifParser(ic.inputid, type, sigma2fofc);
10405
10405
 
10406
10406
  //ic.setOptionCls.setOption('map', '2fofc');
10407
10407
  thisClass.setLogCmd('set map 2fofc sigma ' + sigma2fofc, true);
@@ -10413,7 +10413,8 @@ class ClickMenu {
10413
10413
  //if(!me.cfg.notebook) dialog.dialog( "close" );
10414
10414
  let sigmafofc = parseFloat($("#" + me.pre + "sigmafofc" ).val());
10415
10415
  let type = 'fofc';
10416
- await ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigmafofc);
10416
+ //await ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigmafofc);
10417
+ await ic.densityCifParserCls.densityCifParser(ic.inputid, type, sigma2fofc);
10417
10418
  //ic.setOptionCls.setOption('map', 'fofc');
10418
10419
  thisClass.setLogCmd('set map fofc sigma ' + sigmafofc, true);
10419
10420
  });
@@ -10962,6 +10963,18 @@ class ClickMenu {
10962
10963
  me.htmlCls.dialogCls.openDlg('dl_contact', 'Set contact map');
10963
10964
  });
10964
10965
 
10966
+ me.myEventCls.onIds(["#" + me.pre + "mn6_DSSP"], "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10967
+ thisClass.setLogCmd('set dssp sse', true);
10968
+ await ic.pdbParserCls.applyCommandDssp();
10969
+ ic.bResetAnno = true;
10970
+
10971
+ if(ic.bAnnoShown) {
10972
+ await ic.showAnnoCls.showAnnotations();
10973
+
10974
+ ic.annotationCls.resetAnnoTabAll();
10975
+ }
10976
+ });
10977
+
10965
10978
 
10966
10979
  me.myEventCls.onIds("#" + me.pre + "mn6_hbondsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10967
10980
  ic.showInterCls.hideHbondsContacts();
@@ -12882,6 +12895,8 @@ class SetMenu {
12882
12895
  html += "</ul>";
12883
12896
  html += "</li>";
12884
12897
 
12898
+ html += this.getLink('mn6_DSSP', 'DSSP Secondary', undefined, 1);
12899
+
12885
12900
  let bOnePdb = me.cfg.mmtfid !== undefined || me.cfg.pdbid !== undefined || me.cfg.opmid !== undefined || me.cfg.mmcifid !== undefined || me.cfg.mmdbid !== undefined || me.cfg.mmdbafid !== undefined || me.cfg.gi !== undefined || me.cfg.blast_rep_id !== undefined;
12886
12901
 
12887
12902
  if(bOnePdb) {
@@ -14182,14 +14197,14 @@ class SetDialog {
14182
14197
 
14183
14198
  html += "<span style='white-space:nowrap;font-weight:bold;'>2fofc contour at default threshold or at: "
14184
14199
  + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6sigma2fofc' value='' size=8> &sigma;</span><br/>";
14185
- //html += me.htmlCls.inputFileStr + "id='" + me.pre + "dsn6file2fofc'> " + me.htmlCls.buttonStr + "reload_dsn6file2fofc' style='margin: 6px 20px 0 0;'>Load DSN6</button><br><br><br/>";
14186
- html += me.htmlCls.inputFileStr + "id='" + me.pre + "dsn6file2fofc'><br>" + me.htmlCls.buttonStr + "reload_dsn6file2fofc' style='margin: 6px 20px 0 0;'>Load DSN6</button>" + me.htmlCls.buttonStr + "reload_ccp4file2fofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>" + me.htmlCls.buttonStr + "reload_mtzfile2fofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>" + me.htmlCls.buttonStr + "reload_rcsbmtzfile2fofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br/>";
14200
+ //html += me.htmlCls.inputFileStr + "id='" + me.pre + "dsn6file2fofc'><br>" + me.htmlCls.buttonStr + "reload_dsn6file2fofc' style='margin: 6px 20px 0 0;'>Load DSN6</button>" + me.htmlCls.buttonStr + "reload_ccp4file2fofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>" + me.htmlCls.buttonStr + "reload_mtzfile2fofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>" + me.htmlCls.buttonStr + "reload_rcsbmtzfile2fofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br/>";
14201
+ html += me.htmlCls.inputFileStr + "id='" + me.pre + "dsn6file2fofc'><br>" + me.htmlCls.buttonStr + "reload_ccp4file2fofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>" + me.htmlCls.buttonStr + "reload_mtzfile2fofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>" + me.htmlCls.buttonStr + "reload_rcsbmtzfile2fofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br/>";
14187
14202
 
14188
14203
  html += "<span style='white-space:nowrap;font-weight:bold;'>fofc contour at default threshold or at: "
14189
14204
  + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6sigmafofc' value='' size=8> &sigma;</span><br/>";
14190
14205
 
14191
- //html += me.htmlCls.inputFileStr + "id='" + me.pre + "dsn6filefofc'> " + me.htmlCls.buttonStr + "reload_dsn6filefofc' style='margin: 6px 20px 0 0;'>Load DSN6</button><br><br><br>";
14192
- html += me.htmlCls.inputFileStr + "id='" + me.pre + "dsn6filefofc'><br>" + me.htmlCls.buttonStr + "reload_dsn6filefofc' style='margin: 6px 20px 0 0;'>Load DSN6</button>" + me.htmlCls.buttonStr + "reload_ccp4filefofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>" + me.htmlCls.buttonStr + "reload_mtzfilefofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>" + me.htmlCls.buttonStr + "reload_rcsbmtzfilefofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br>";
14206
+ //html += me.htmlCls.inputFileStr + "id='" + me.pre + "dsn6filefofc'><br>" + me.htmlCls.buttonStr + "reload_dsn6filefofc' style='margin: 6px 20px 0 0;'>Load DSN6</button>" + me.htmlCls.buttonStr + "reload_ccp4filefofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>" + me.htmlCls.buttonStr + "reload_mtzfilefofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>" + me.htmlCls.buttonStr + "reload_rcsbmtzfilefofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br>";
14207
+ html += me.htmlCls.inputFileStr + "id='" + me.pre + "dsn6filefofc'><br>" + me.htmlCls.buttonStr + "reload_ccp4filefofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>" + me.htmlCls.buttonStr + "reload_mtzfilefofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>" + me.htmlCls.buttonStr + "reload_rcsbmtzfilefofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br>";
14193
14208
 
14194
14209
 
14195
14210
  html += me.htmlCls.buttonStr + "elecmapNo4'>Remove Map</button><br>";
@@ -14203,12 +14218,16 @@ class SetDialog {
14203
14218
  html += "<span style='white-space:nowrap;font-weight:bold;'>2fofc contour at default threshold or at: "
14204
14219
  + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6sigmaurl2fofc' value='' size=8> &sigma;</span><br/>";
14205
14220
 
14206
- html += "URL in the same host: " + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6fileurl2fofc' size=20><br>" + me.htmlCls.buttonStr + "reload_dsn6fileurl2fofc' style='margin: 6px 20px 0 0;'>Load DSN6</button>" + me.htmlCls.buttonStr + "reload_ccp4fileurl2fofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>" + me.htmlCls.buttonStr + "reload_mtzfileurl2fofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>" + me.htmlCls.buttonStr + "reload_rcsbmtzfileurl2fofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br/>";
14221
+ //html += "URL in the same host: " + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6fileurl2fofc' size=20><br>" + me.htmlCls.buttonStr + "reload_dsn6fileurl2fofc' style='margin: 6px 20px 0 0;'>Load DSN6</button>" + me.htmlCls.buttonStr + "reload_ccp4fileurl2fofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>" + me.htmlCls.buttonStr + "reload_mtzfileurl2fofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>" + me.htmlCls.buttonStr + "reload_rcsbmtzfileurl2fofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br/>";
14222
+
14223
+ html += "URL in the same host: " + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6fileurl2fofc' size=20><br>" + me.htmlCls.buttonStr + "reload_ccp4fileurl2fofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>" + me.htmlCls.buttonStr + "reload_mtzfileurl2fofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>" + me.htmlCls.buttonStr + "reload_rcsbmtzfileurl2fofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br/>";
14207
14224
 
14208
14225
  html += "<span style='white-space:nowrap;font-weight:bold;'>fofc contour at default threshold or at: "
14209
14226
  + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6sigmaurlfofc' value='' size=8> &sigma;</span><br/>";
14210
14227
 
14211
- html += "URL in the same host: " + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6fileurlfofc' size=20><br>" + me.htmlCls.buttonStr + "reload_dsn6fileurlfofc' style='margin: 6px 20px 0 0;'>Load DSN6</button>" + me.htmlCls.buttonStr + "reload_ccp4fileurlfofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>" + me.htmlCls.buttonStr + "reload_mtzfileurlfofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>" + me.htmlCls.buttonStr + "reload_rcsbmtzfileurlfofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br>";
14228
+ //html += "URL in the same host: " + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6fileurlfofc' size=20><br>" + me.htmlCls.buttonStr + "reload_dsn6fileurlfofc' style='margin: 6px 20px 0 0;'>Load DSN6</button>" + me.htmlCls.buttonStr + "reload_ccp4fileurlfofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>" + me.htmlCls.buttonStr + "reload_mtzfileurlfofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>" + me.htmlCls.buttonStr + "reload_rcsbmtzfileurlfofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br>";
14229
+
14230
+ html += "URL in the same host: " + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6fileurlfofc' size=20><br>" + me.htmlCls.buttonStr + "reload_ccp4fileurlfofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>" + me.htmlCls.buttonStr + "reload_mtzfileurlfofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>" + me.htmlCls.buttonStr + "reload_rcsbmtzfileurlfofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br>";
14212
14231
 
14213
14232
  html += me.htmlCls.buttonStr + "elecmapNo5'>Remove Map</button><br>";
14214
14233
 
@@ -14757,8 +14776,9 @@ class SetDialog {
14757
14776
  html += "</div>";
14758
14777
 
14759
14778
 
14760
- html += me.htmlCls.divStr + "dl_anglemanysets' class='" + dialogClass + "'>";
14779
+ html += me.htmlCls.divStr + "dl_anglemanysets' class='" + dialogClass + "' style='max-width:500px'>";
14761
14780
  html += this.addNotebookTitle('dl_anglemanysets', 'Measure angles among many sets');
14781
+ html += me.htmlCls.spanNowrapStr + "Note: Each set is represented by a vector, which is the X-axis of the principle axes. The angles between the vectors are then calculated.<br/><br/>";
14762
14782
  html += me.htmlCls.spanNowrapStr + "1. Select sets for pairwise angles</span><br/>";
14763
14783
  html += "<table border=0 width=400 cellspacing=10><tr><td>";
14764
14784
 
@@ -15080,8 +15100,8 @@ class SetDialog {
15080
15100
  html += "Z: " + me.htmlCls.inputTextStr + "id='" + me.pre + "v2Z' value='' size=6><br>";
15081
15101
  html += "<br>";
15082
15102
 
15083
- html += me.htmlCls.buttonStr + "measure_angle'>Measure Angle</button>";
15084
- html += "The angle is: " + me.htmlCls.inputTextStr + "id='" + me.pre + "angle_value' value='' size=6> degree.";
15103
+ html += me.htmlCls.buttonStr + "measure_angle'>Measure Angle</button><br><br>";
15104
+ html += "The angle is: " + me.htmlCls.inputTextStr + "id='" + me.pre + "angle_value' value='' size=6> degree.<br><br>";
15085
15105
  html += "</div>";
15086
15106
 
15087
15107
  html += me.htmlCls.divStr + "dl_matrix' class='" + dialogClass + "'>";
@@ -44526,7 +44546,7 @@ class AddTrack {
44526
44546
 
44527
44547
  }
44528
44548
 
44529
- showNewTrack(chnid, title, text, cssColorArray, inTarget2queryHash, type, color, bMsa, fromArray, toArray, seqStartLen, exonArray) { let ic = this.icn3d, me = ic.icn3dui;
44549
+ showNewTrack(chnid, title, text, cssColorArray, inTarget2queryHash, type, color, bMsa, fromArray, toArray, seqStartLen, exonArray, offsetArray) { let ic = this.icn3d, me = ic.icn3dui;
44530
44550
  //if(ic.customTracks[chnid] === undefined) {
44531
44551
  // ic.customTracks[chnid] = {}
44532
44552
  //}
@@ -44744,14 +44764,16 @@ class AddTrack {
44744
44764
 
44745
44765
  if(fromArray !== undefined) {
44746
44766
  htmlTmp2 = '';
44747
- let fromArray2 = [], toArray2 = [];
44767
+ let fromArray2 = [], toArray2 = [], offsetArray2 = [];
44748
44768
  for(let i = 0, il = fromArray.length; i < il; ++i) {
44749
44769
  fromArray2.push(fromArray[i]);
44770
+ offsetArray2.push(offsetArray[i]);
44750
44771
 
44751
44772
  for(let j = parseInt(fromArray[i]); j <= parseInt(toArray[i]); ++j) {
44752
44773
  if(ic.targetGapHash !== undefined && ic.targetGapHash.hasOwnProperty(j)) {
44753
44774
  toArray2.push(j - 1);
44754
44775
  fromArray2.push(j);
44776
+ offsetArray2.push(offsetArray[i]);
44755
44777
  }
44756
44778
  }
44757
44779
 
@@ -44785,6 +44807,7 @@ class AddTrack {
44785
44807
  // determine how this range sits in the exon ranges in exonArray
44786
44808
  let startExon, endExon;
44787
44809
 
44810
+ let offset = offsetArray2[i];
44788
44811
  cnt = toArray[i] - fromArray[i] + 1;
44789
44812
  let from = prevCntTotal, to = prevCntTotal + cnt - 1;
44790
44813
 
@@ -44813,26 +44836,26 @@ class AddTrack {
44813
44836
  endColorStr = this.getExonColor(startExon.rangeStart, startExon.rangeEnd, to);
44814
44837
 
44815
44838
  colorGradient = startColorStr + ' 0%, #FFF 50%, ' + endColorStr + ' 100%';
44816
- htmlTmp2 += this.getExonHtml(startExon.exonIndex, colorGradient, startExon.from, endExon.to, startExon.genomeRange, chnid, simpTitle);
44839
+ htmlTmp2 += this.getExonHtml(startExon.exonIndex, colorGradient, startExon.from, endExon.to, startExon.genomeRange, chnid, simpTitle, offset);
44817
44840
  }
44818
44841
  else {
44819
44842
  if(startExon) {
44820
44843
  startColorStr = this.getExonColor(startExon.rangeStart, startExon.rangeEnd, from);
44821
44844
 
44822
44845
  colorGradient = startColorStr + ' 0%, #FFF 50%, #00F 100%';
44823
- htmlTmp2 += this.getExonHtml(startExon.exonIndex, colorGradient, startExon.from, startExon.rangeEnd, startExon.genomeRange, chnid, simpTitle);
44846
+ htmlTmp2 += this.getExonHtml(startExon.exonIndex, colorGradient, startExon.from, startExon.rangeEnd, startExon.genomeRange, chnid, simpTitle, offset);
44824
44847
  }
44825
44848
 
44826
44849
  if(startExon && endExon) {
44827
44850
  for(let j = startExon.exonIndex + 1; j < endExon.exonIndex; ++j) {
44828
44851
  colorGradient = '#F00 0%, #FFF 50%, #00F 100%';
44829
- htmlTmp2 += this.getExonHtml(j, colorGradient, exonArray[j].resStart, exonArray[j].resEnd, exonArray[j].genomeRange, chnid, simpTitle);
44852
+ htmlTmp2 += this.getExonHtml(j, colorGradient, exonArray[j].resStart, exonArray[j].resEnd, exonArray[j].genomeRange, chnid, simpTitle, offset);
44830
44853
  }
44831
44854
 
44832
44855
  endColorStr = this.getExonColor(endExon.rangeStart, endExon.rangeEnd, to);
44833
44856
 
44834
44857
  colorGradient = '#F00 0%, #FFF 50%, ' + endColorStr + ' 100%';
44835
- htmlTmp2 += this.getExonHtml(endExon.exonIndex, colorGradient, endExon.rangeStart, endExon.to, endExon.genomeRange, chnid, simpTitle);
44858
+ htmlTmp2 += this.getExonHtml(endExon.exonIndex, colorGradient, endExon.rangeStart, endExon.to, endExon.genomeRange, chnid, simpTitle, offset);
44836
44859
  }
44837
44860
  }
44838
44861
 
@@ -44866,8 +44889,8 @@ class AddTrack {
44866
44889
  }
44867
44890
  }
44868
44891
 
44869
- getExonHtml(exonIndex, colorGradient, from, to, genomeRange, chainid, simpTitle) { let ic = this.icn3d; ic.icn3dui;
44870
- return '<div style="display:inline-block; color:white!important; width:' + Math.round(ic.seqAnnWidth *(to - from + 1) /(ic.maxAnnoLength + ic.nTotalGap)) + 'px;" class="icn3d-seqTitle icn3d-link icn3d-blue" domain="' + (exonIndex + 1) + '" from="' + from + '" to="' + to + '" setname="' + simpTitle + ', ' + (exonIndex + 1) + '" title="Exon: ' + genomeRange + ' genomic interval" anno="sequence" chain="' + chainid + '"><div style="height: 12px; border: 1px solid #000; background: linear-gradient(to right, ' + colorGradient + ');"></div></div>';
44892
+ getExonHtml(exonIndex, colorGradient, from, to, genomeRange, chainid, simpTitle, offset) { let ic = this.icn3d; ic.icn3dui;
44893
+ return '<div style="display:inline-block; color:white!important; width:' + Math.round(ic.seqAnnWidth *(to - from + 1) /(ic.maxAnnoLength + ic.nTotalGap)) + 'px;" class="icn3d-seqTitle icn3d-link icn3d-blue" domain="' + (exonIndex + 1) + '" from="' + (from + offset) + '" to="' + (to + offset) + '" setname="' + simpTitle + ', ' + (exonIndex + 1) + '" title="Exon: ' + genomeRange + ' genomic interval" anno="sequence" chain="' + chainid + '"><div style="height: 12px; border: 1px solid #000; background: linear-gradient(to right, ' + colorGradient + ');"></div></div>';
44871
44894
  }
44872
44895
 
44873
44896
  getExonColor(start, end, pos) { let ic = this.icn3d; ic.icn3dui;
@@ -45814,6 +45837,7 @@ class AddTrack {
45814
45837
  let fromArray = [], toArray = [];
45815
45838
  let bFound = false;
45816
45839
  let seqStartLen = 0;
45840
+ let offset = 0, offsetArray = [];
45817
45841
  // for(let k = seqStart; k <= seqEnd; ++k) {
45818
45842
  for(let k = 0; k < seqLength; ++k) {
45819
45843
  //if(seqFirst[k] == '-') continue;
@@ -45822,19 +45846,29 @@ class AddTrack {
45822
45846
 
45823
45847
  resn = trackSeqArray[j][k];
45824
45848
 
45849
+ if(resn != '-') {
45850
+ if(!bFound) {
45851
+ seqStartLen = k;
45852
+ bFound = true;
45853
+
45854
+ offset = ic.startposGiSeq - ic.seqStartLen[chainid] + seqStartLen;
45855
+ }
45856
+ }
45857
+
45825
45858
  if(prevResn == '-' && resn != '-') {
45826
45859
  fromArray.push(k);
45860
+ offsetArray.push(offset);
45827
45861
  }
45828
45862
 
45829
45863
  if(prevResn != '-' && resn == '-') {
45830
45864
  toArray.push(k - 1);
45831
45865
  }
45832
45866
 
45833
- if(resn != '-') {
45834
- if(!bFound) {
45835
- seqStartLen = k;
45836
- bFound = true;
45837
- }
45867
+ // use "offset" to adjut the residue numbers, e.g., P20138
45868
+ // some isoforms starts residues before the first residue in the template sequence
45869
+ if(k >= ic.seqStartLen[chainid]) {
45870
+ if(seqFirst[k] == '-') offset--;
45871
+ if(resn == '-') offset++;
45838
45872
  }
45839
45873
 
45840
45874
  text += resn; //ic.giSeq[chainid][i];
@@ -45855,7 +45889,7 @@ class AddTrack {
45855
45889
  let title =(trackTitleArray[j].length < 20) ? trackTitleArray[j] : trackTitleArray[j].substr(0, 20) + '...';
45856
45890
  let bMsa = true;
45857
45891
  let exonArray = (acc2exons) ? acc2exons[trackTitleArray[j]] : undefined;
45858
- this.showNewTrack(chainid, title, text, undefined, undefined, type, undefined, bMsa, fromArray, toArray, seqStartLen, exonArray);
45892
+ this.showNewTrack(chainid, title, text, undefined, undefined, type, undefined, bMsa, fromArray, toArray, seqStartLen, exonArray, offsetArray);
45859
45893
  }
45860
45894
 
45861
45895
  // update exon color
@@ -52663,8 +52697,10 @@ class ChainalignParser {
52663
52697
  //$.when(ic.pdbParserCls.applyCommandDssp(true)).then(function() {
52664
52698
  await ic.pdbParserCls.applyCommandDssp(true);
52665
52699
 
52700
+ // original version =============
52666
52701
  // align PDB chains
52667
52702
  for(let index in ic.pdbChainIndexHash) {
52703
+ //ic.pdbChainIndexHash[index] = mmdbid_q_tmp + "_" + ic.chain_q + "_" + ic.mmdbid_t + "_" + ic.chain_t;
52668
52704
  let idArray = ic.pdbChainIndexHash[index].split('_');
52669
52705
  mmdbid_q = idArray[0];
52670
52706
  idArray[1];
@@ -52679,25 +52715,49 @@ class ChainalignParser {
52679
52715
  let urlalign = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi";
52680
52716
  let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
52681
52717
 
52718
+ let resRangeArray = (me.cfg.resrange) ? me.cfg.resrange.split(' | ') : [];
52719
+
52682
52720
  for(let index in ic.afChainIndexHash) {
52683
52721
  let idArray = ic.afChainIndexHash[index].split('_');
52684
52722
  mmdbid_q = idArray[0];
52685
52723
  let chain_q = idArray[1];
52724
+ let chainid_q = mmdbid_q + '_' + chain_q;
52725
+
52686
52726
  mmdbid_t = idArray[2];
52687
52727
  let chain_t = idArray[3];
52728
+ let chainid_t = mmdbid_t + '_' + chain_t;
52729
+
52730
+ let atomSet_t = (me.cfg.resrange) ? ic.realignParserCls.getSeqCoorResid(resRangeArray[0].split(','), chainid_t).hAtoms : ic.chains[chainid_t];
52731
+ let atomSet_q = (me.cfg.resrange) ? ic.realignParserCls.getSeqCoorResid(resRangeArray[index].split(','), chainid_q).hAtoms : ic.chains[chainid_q];
52732
+ // end of original version =============
52733
+
52734
+ /*
52735
+ // new version to be done for VASTsrv ==============
52736
+ // dynamically align pairs in all chainids
52737
+ let ajaxArray = [], indexArray = [], struArray = [];
52738
+ let urlalign = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi";
52739
+ let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
52740
+
52741
+ let resRangeArray = (me.cfg.resrange) ? me.cfg.resrange.split(' | ') : [];
52742
+
52743
+ // dynamically align pairs in all chainids
52744
+ let atomSet_t = (me.cfg.resrange) ? ic.realignParserCls.getSeqCoorResid(resRangeArray[0].split(','), chainidArray[0]).hAtoms : ic.chains[chainidArray[0]];
52745
+ for(let index = 1, indexl = chainidArray.length; index < indexl; ++index) {
52746
+ let atomSet_q = (me.cfg.resrange) ? ic.realignParserCls.getSeqCoorResid(resRangeArray[index].split(','), chainidArray[index]).hAtoms : ic.chains[chainidArray[index]];
52747
+ // end of new version to be done for VASTsrv ==============
52748
+ */
52688
52749
 
52689
52750
  let alignAjax;
52690
52751
  if(me.cfg.aligntool != 'tmalign') {
52691
- let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(ic.chains[mmdbid_q + '_' + chain_q]);
52692
- let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(ic.chains[mmdbid_t + '_' + chain_t]);
52752
+ let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(atomSet_q);
52753
+ let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(atomSet_t);
52693
52754
 
52694
52755
  let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
52695
52756
  alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
52696
52757
  }
52697
52758
  else {
52698
- let pdb_query = ic.saveFileCls.getAtomPDB(ic.chains[mmdbid_q + '_' + chain_q]);
52699
-
52700
- let pdb_target= ic.saveFileCls.getAtomPDB(ic.chains[mmdbid_t + '_' + chain_t]);
52759
+ let pdb_query = ic.saveFileCls.getAtomPDB(atomSet_q);
52760
+ let pdb_target= ic.saveFileCls.getAtomPDB(atomSet_t);
52701
52761
 
52702
52762
  let dataObj = {'pdb_query': pdb_query, 'pdb_target': pdb_target};
52703
52763
  alignAjax = me.getAjaxPostPromise(urltmalign, dataObj);
@@ -53100,7 +53160,7 @@ class ChainalignParser {
53100
53160
  return chainidArray;
53101
53161
  }
53102
53162
 
53103
- async downloadChainalignment(chainalign, resnum, resdef) { let ic = this.icn3d, me = ic.icn3dui;
53163
+ async downloadChainalignment(chainalign) { let ic = this.icn3d, me = ic.icn3dui;
53104
53164
  let thisClass = this;
53105
53165
 
53106
53166
  ic.opts['proteins'] = 'c alpha trace';
@@ -53377,7 +53437,7 @@ class ChainalignParser {
53377
53437
  async loadOpmDataForChainalign(data1, data2, chainidArray, mmdbidArray) { let ic = this.icn3d, me = ic.icn3dui;
53378
53438
  let thisClass = this;
53379
53439
 
53380
- if(me.cfg.resnum || me.cfg.resdef) {
53440
+ if(me.cfg.resnum || me.cfg.resdef || me.cfg.resrange) {
53381
53441
  if(!ic.bCommandLoad) ic.init(); // remove all previously loaded data
53382
53442
  await this.downloadChainalignmentPart2(data1, data2, undefined, chainidArray);
53383
53443
 
@@ -58254,6 +58314,7 @@ class DensityCifParser {
58254
58314
 
58255
58315
  //https://www.ebi.ac.uk/pdbe/densities/doc.html
58256
58316
  if(type == '2fofc' || type == 'fofc') {
58317
+ detail = 0;
58257
58318
  url = "https://www.ebi.ac.uk/pdbe/densities/x-ray/" + pdbid.toLowerCase() + "/cell?detail=" + detail;
58258
58319
  }
58259
58320
  else if(type == 'em') {
@@ -58294,6 +58355,39 @@ class DensityCifParser {
58294
58355
  }
58295
58356
  }
58296
58357
 
58358
+ async densityCifParserBase(url, type, sigma, location, bInputSigma) { let ic = this.icn3d, me = ic.icn3dui;
58359
+ let thisClass = this;
58360
+
58361
+ //https://stackoverflow.com/questions/33902299/using-jquery-ajax-to-download-a-binary-file
58362
+ if(type == '2fofc' && ic.bAjax2fofc) {
58363
+ ic.mapData.sigma2 = sigma;
58364
+ ic.setOptionCls.setOption('map', type);
58365
+ }
58366
+ else if(type == 'fofc' && ic.bAjaxfofc) {
58367
+ ic.mapData.sigma = sigma;
58368
+ ic.setOptionCls.setOption('map', type);
58369
+ }
58370
+ else {
58371
+ let arrayBuffer = await me.getXMLHttpRqstPromise(url, 'GET', 'arraybuffer', type);
58372
+
58373
+ thisClass.parseChannels(arrayBuffer, type, sigma);
58374
+
58375
+ if(type == '2fofc' || type == 'fofc') {
58376
+ ic.bAjax2fofc = true;
58377
+ ic.bAjaxfofc = true;
58378
+
58379
+ ic.setOptionCls.setOption('map', type);
58380
+ }
58381
+ else if(type == 'em') {
58382
+ ic.bAjaxEm = true;
58383
+
58384
+ ic.setOptionCls.setOption('emmap', type);
58385
+ }
58386
+ }
58387
+
58388
+ // return sigma;
58389
+ }
58390
+
58297
58391
  parseChannels(densitydata, type, sigma) { let ic = this.icn3d; ic.icn3dui;
58298
58392
  let cif = this.BinaryParse(densitydata);
58299
58393
 
@@ -63286,7 +63380,7 @@ class LoadCIF {
63286
63380
 
63287
63381
  let bFirstAtom = true;
63288
63382
 
63289
- let cifArray = bcifData.split('ENDMDL\n');
63383
+ let cifArray = (bText) ? bcifData.split('ENDMDL\n') : [bcifData];
63290
63384
 
63291
63385
  for(let index = 0, indexl = cifArray.length; index < indexl; ++index) {
63292
63386
  ++moleculeNum;
@@ -66277,6 +66371,16 @@ class ApplyCommand {
66277
66371
  ic.transformCls.rotateCoord(ic.hAtoms, mArrayFloat);
66278
66372
  ic.drawCls.draw();
66279
66373
  }
66374
+ else if(command.indexOf('set dssp sse') == 0) {
66375
+ await ic.pdbParserCls.applyCommandDssp();
66376
+ ic.bResetAnno = true;
66377
+
66378
+ if(ic.bAnnoShown) {
66379
+ await ic.showAnnoCls.showAnnotations();
66380
+
66381
+ ic.annotationCls.resetAnnoTabAll();
66382
+ }
66383
+ }
66280
66384
 
66281
66385
  // special, select ==========
66282
66386
 
@@ -68259,20 +68363,23 @@ class LoadScript {
68259
68363
  }
68260
68364
  }
68261
68365
  else if(command.indexOf('load chainalignment') !== -1) {
68262
- //load chainalignment [id] | resnum [resnum] | resdef [resnum] | aligntool [aligntool] | parameters [inpara]
68366
+ //load chainalignment [id] | resnum [resnum] | resdef [resdef] | aligntool [aligntool] | parameters [inpara] | resrange [resrange]
68263
68367
  let urlArray = command.split(" | ");
68264
68368
  if(urlArray.length > 1 && urlArray[1].indexOf('resnum') != -1) {
68265
68369
  me.cfg.resnum = urlArray[1].substr(urlArray[1].indexOf('resnum') + 7);
68266
68370
  }
68267
68371
  if(urlArray.length > 2 && urlArray[2].indexOf('resdef') != -1) {
68268
- me.cfg.resdef = urlArray[2].substr(urlArray[1].indexOf('resdef') + 7);
68372
+ me.cfg.resdef = urlArray[2].substr(urlArray[2].indexOf('resdef') + 7);
68269
68373
  }
68270
68374
  if(urlArray.length > 3 && urlArray[3].indexOf('aligntool') != -1) {
68271
- me.cfg.aligntool = urlArray[3].substr(urlArray[1].indexOf('aligntool') + 10);
68375
+ me.cfg.aligntool = urlArray[3].substr(urlArray[3].indexOf('aligntool') + 10);
68376
+ }
68377
+ if(urlArray.length > 5 && urlArray[5].indexOf('resrange') != -1) {
68378
+ me.cfg.resrange = urlArray[5].substr(urlArray[5].indexOf('resrange') + 9);
68272
68379
  }
68273
68380
 
68274
68381
  me.cfg.chainalign = id;
68275
- await ic.chainalignParserCls.downloadChainalignment(id, me.cfg.resnum, me.cfg.resdef);
68382
+ await ic.chainalignParserCls.downloadChainalignment(id);
68276
68383
  }
68277
68384
  else if(command.indexOf('load url') !== -1) {
68278
68385
  let typeStr = load_parameters[1]; // type pdb
@@ -68321,7 +68428,8 @@ class LoadScript {
68321
68428
  if(urlArray.length == 2) {
68322
68429
  let bInputSigma = true;
68323
68430
  if(fileType == 'dsn6') {
68324
- await ic.dsn6ParserCls.dsn6ParserBase(urlArray[1], type, sigma, 'url', bInputSigma);
68431
+ // await ic.dsn6ParserCls.dsn6ParserBase(urlArray[1], type, sigma, 'url', bInputSigma);
68432
+ await ic.densityCifParserCls.densityCifParserBase(urlArray[1], type, sigma, 'url', bInputSigma);
68325
68433
  }
68326
68434
  else if(fileType == 'ccp4') {
68327
68435
  await ic.ccp4ParserCls.ccp4ParserBase(urlArray[1], type, sigma, 'url', bInputSigma);
@@ -68334,7 +68442,8 @@ class LoadScript {
68334
68442
  }
68335
68443
  }
68336
68444
  else {
68337
- await ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigma);
68445
+ // await ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigma);
68446
+ await ic.densityCifParserCls.densityCifParser(ic.inputid, type, sigma);
68338
68447
  }
68339
68448
  }
68340
68449
  // }); // end of me.deferred = $.Deferred(function() {
@@ -81136,7 +81245,7 @@ class iCn3DUI {
81136
81245
  //even when multiple iCn3D viewers are shown together.
81137
81246
  this.pre = this.cfg.divid + "_";
81138
81247
 
81139
- this.REVISION = '3.33.2';
81248
+ this.REVISION = '3.33.3';
81140
81249
 
81141
81250
  // In nodejs, iCn3D defines "window = {navigator: {}}"
81142
81251
  this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -81579,9 +81688,9 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
81579
81688
 
81580
81689
  ic.bChainAlign = true;
81581
81690
  ic.inputid = me.cfg.chainalign;
81582
- ic.loadCmd = 'load chainalignment ' + me.cfg.chainalign + ' | resnum ' + me.cfg.resnum + ' | resdef ' + me.cfg.resdef + ' | aligntool ' + me.cfg.aligntool + ' | parameters ' + me.cfg.inpara;
81691
+ ic.loadCmd = 'load chainalignment ' + me.cfg.chainalign + ' | resnum ' + me.cfg.resnum + ' | resdef ' + me.cfg.resdef + ' | aligntool ' + me.cfg.aligntool + ' | parameters ' + me.cfg.inpara + ' | resrange ' + me.cfg.resrange;
81583
81692
  me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
81584
- await ic.chainalignParserCls.downloadChainalignment(me.cfg.chainalign, me.cfg.resnum, me.cfg.resdef);
81693
+ await ic.chainalignParserCls.downloadChainalignment(me.cfg.chainalign);
81585
81694
  }
81586
81695
  else if(me.cfg.mmdbafid !== undefined) {
81587
81696
  // ic.bNCBI = true;