icn3d 3.25.0 → 3.25.2

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Files changed (4) hide show
  1. package/icn3d.js +103 -63
  2. package/icn3d.min.js +3 -3
  3. package/icn3d.module.js +103 -63
  4. package/package.json +1 -1
package/icn3d.js CHANGED
@@ -2302,7 +2302,7 @@ THREE.TrackballControls = function ( object, domElement, icn3d ) {
2302
2302
  this.screen.width = window.innerWidth;
2303
2303
  this.screen.height = window.innerHeight;
2304
2304
 
2305
- } else {
2305
+ } else if(this.domElement) {
2306
2306
 
2307
2307
  var box = this.domElement.getBoundingClientRect();
2308
2308
  // adjustments come from similar code in the jquery offset() function
@@ -2872,7 +2872,7 @@ THREE.TrackballControls = function ( object, domElement, icn3d ) {
2872
2872
 
2873
2873
  }
2874
2874
 
2875
- if(Object.keys(window).length >= 2) {
2875
+ if(Object.keys(window).length >= 2 && this.domElement) {
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2876
  this.domElement.addEventListener( 'contextmn', function ( event ) {
2877
2877
  //event.preventDefault();
2878
2878
  }, false );
@@ -2998,7 +2998,7 @@ THREE.OrthographicTrackballControls = function ( object, domElement, icn3d ) { v
2998
2998
  this.screen.width = window.innerWidth;
2999
2999
  this.screen.height = window.innerHeight;
3000
3000
 
3001
- } else {
3001
+ } else if(this.domElement) {
3002
3002
 
3003
3003
  var box = this.domElement.getBoundingClientRect();
3004
3004
  // adjustments come from similar code in the jquery offset() function
@@ -3548,7 +3548,7 @@ THREE.OrthographicTrackballControls = function ( object, domElement, icn3d ) { v
3548
3548
 
3549
3549
  }
3550
3550
 
3551
- if(Object.keys(window).length >= 2) {
3551
+ if(Object.keys(window).length >= 2 && this.domElement) {
3552
3552
  this.domElement.addEventListener( 'contextmn', function ( event ) {
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3553
  //event.preventDefault();
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3554
  }, false );
@@ -21921,7 +21921,7 @@ class Scene {
21921
21921
 
21922
21922
  //This core function sets up the scene and display the structure according to the input
21923
21923
  //options (shown above), which is a hash containing values for different keys.
21924
- rebuildScene(options) { let ic = this.icn3d; ic.icn3dui;
21924
+ rebuildScene(options) { let ic = this.icn3d, me = ic.icn3dui;
21925
21925
  if(options === undefined) options = ic.opts;
21926
21926
 
21927
21927
  this.rebuildSceneBase(options);
@@ -21933,7 +21933,7 @@ class Scene {
21933
21933
  // }
21934
21934
 
21935
21935
  // if(!ic.bSetVrArButtons) { // call once
21936
- this.setVrArButtons();
21936
+ if(!me.cfg.imageonly) this.setVrArButtons();
21937
21937
  // }
21938
21938
 
21939
21939
  // if((ic.bVr || ic.bAr) && !ic.bSetVrAr) { // call once
@@ -42020,71 +42020,79 @@ class ShowSeq {
42020
42020
  }
42021
42021
  }
42022
42022
 
42023
- if(parseInt(currResi) < parseInt(strandArray[strandCnt].startResi)) {
42024
- ic.residIgLoop[residueid] = 1;
42023
+ let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[residueid]);
42025
42024
 
42026
- if(bNterminal) { // make it continuous to the 1st strand
42027
- if(bStart) {
42028
- currRefnum = strandArray[strandCnt].startRefnum - strandArray[strandCnt].loopResCnt + loopCnt;
42029
- refnumLabelNoPostfix = strandArray[strandCnt].strand + currRefnum;
42030
- refnumLabel = refnumLabelNoPostfix + strandArray[strandCnt].strandPostfix;
42031
- }
42032
- }
42033
- else {
42034
- //currStrand = strandArray[prevStrandCnt].strand;
42025
+ // skip non-protein residues
42026
+ if(!atom || !ic.proteins.hasOwnProperty(atom.serial)) {
42027
+ refnumLabel = undefined;
42028
+ }
42029
+ else {
42030
+ if(parseInt(currResi) < parseInt(strandArray[strandCnt].startResi)) {
42031
+ ic.residIgLoop[residueid] = 1;
42035
42032
 
42036
- if(prevStrandCnt >= 0 && strandArray[prevStrandCnt].strand.substr(0, 1) == 'G') {
42037
- if(bStart && ic.resid2refnum[residueid]) {
42038
- currRefnum = strandArray[prevStrandCnt].endRefnum + loopCnt;
42039
- refnumLabelNoPostfix = strandArray[prevStrandCnt].strand + currRefnum;
42040
- refnumLabel = refnumLabelNoPostfix + strandArray[prevStrandCnt].strandPostfix;
42041
- }
42042
- else {
42043
- bStart = false;
42044
- bNterminal = true;
42045
- loopCnt = 0;
42046
- }
42033
+ if(bNterminal) { // make it continuous to the 1st strand
42034
+ if(bStart) {
42035
+ currRefnum = strandArray[strandCnt].startRefnum - strandArray[strandCnt].loopResCnt + loopCnt;
42036
+ refnumLabelNoPostfix = strandArray[strandCnt].strand + currRefnum;
42037
+ refnumLabel = refnumLabelNoPostfix + strandArray[strandCnt].strandPostfix;
42038
+ }
42047
42039
  }
42048
42040
  else {
42049
- let len = strandArray[strandCnt].loopResCnt;
42050
- let halfLen = parseInt(len / 2.0 + 0.5);
42051
-
42052
- if(loopCnt <= halfLen) {
42053
- currRefnum = strandArray[prevStrandCnt].endRefnum + loopCnt;
42054
- refnumLabelNoPostfix = strandArray[prevStrandCnt].strand + currRefnum;
42055
- refnumLabel = refnumLabelNoPostfix + strandArray[prevStrandCnt].strandPostfix;
42041
+ //currStrand = strandArray[prevStrandCnt].strand;
42042
+
42043
+ if(prevStrandCnt >= 0 && strandArray[prevStrandCnt].strand.substr(0, 1) == 'G') {
42044
+ if(bStart && ic.resid2refnum[residueid]) {
42045
+ currRefnum = strandArray[prevStrandCnt].endRefnum + loopCnt;
42046
+ refnumLabelNoPostfix = strandArray[prevStrandCnt].strand + currRefnum;
42047
+ refnumLabel = refnumLabelNoPostfix + strandArray[prevStrandCnt].strandPostfix;
42048
+ }
42049
+ else {
42050
+ bStart = false;
42051
+ bNterminal = true;
42052
+ loopCnt = 0;
42053
+ }
42056
42054
  }
42057
42055
  else {
42058
- currRefnum = strandArray[strandCnt].startRefnum - len + loopCnt - 1;
42059
- refnumLabelNoPostfix = strandArray[strandCnt].strand + currRefnum;
42060
- refnumLabel = refnumLabelNoPostfix + strandArray[strandCnt].strandPostfix;
42056
+ let len = strandArray[strandCnt].loopResCnt;
42057
+ let halfLen = parseInt(len / 2.0 + 0.5);
42058
+
42059
+ if(loopCnt <= halfLen) {
42060
+ currRefnum = strandArray[prevStrandCnt].endRefnum + loopCnt;
42061
+ refnumLabelNoPostfix = strandArray[prevStrandCnt].strand + currRefnum;
42062
+ refnumLabel = refnumLabelNoPostfix + strandArray[prevStrandCnt].strandPostfix;
42063
+ }
42064
+ else {
42065
+ currRefnum = strandArray[strandCnt].startRefnum - len + loopCnt - 1;
42066
+ refnumLabelNoPostfix = strandArray[strandCnt].strand + currRefnum;
42067
+ refnumLabel = refnumLabelNoPostfix + strandArray[strandCnt].strandPostfix;
42068
+ }
42061
42069
  }
42062
42070
  }
42063
42071
  }
42064
- }
42065
- else if(parseInt(currResi) >= parseInt(strandArray[strandCnt].startResi) && parseInt(currResi) <= parseInt(strandArray[strandCnt].endResi)) {
42066
- bNterminal = false;
42072
+ else if(parseInt(currResi) >= parseInt(strandArray[strandCnt].startResi) && parseInt(currResi) <= parseInt(strandArray[strandCnt].endResi)) {
42073
+ bNterminal = false;
42067
42074
 
42068
- if(currResi == strandArray[strandCnt].endResi) {
42069
- ++strandCnt; // next strand
42070
- loopCnt = 0;
42075
+ if(currResi == strandArray[strandCnt].endResi) {
42076
+ ++strandCnt; // next strand
42077
+ loopCnt = 0;
42071
42078
 
42072
- if(!strandArray[strandCnt]) { // last strand
42073
- --strandCnt;
42079
+ if(!strandArray[strandCnt]) { // last strand
42080
+ --strandCnt;
42081
+ }
42074
42082
  }
42075
42083
  }
42076
- }
42077
- else if(parseInt(currResi) > parseInt(strandArray[strandCnt].endResi)) {
42078
- ic.residIgLoop[residueid] = 1;
42084
+ else if(parseInt(currResi) > parseInt(strandArray[strandCnt].endResi)) {
42085
+ ic.residIgLoop[residueid] = 1;
42079
42086
 
42080
- // C-terminal
42081
- if(!ic.resid2refnum[residueid]) {
42082
- break;
42083
- }
42084
- else {
42085
- currRefnum = strandArray[strandCnt].endRefnum + loopCnt;
42086
- refnumLabelNoPostfix = strandArray[strandCnt].strand + currRefnum;
42087
- refnumLabel = refnumLabelNoPostfix + strandArray[strandCnt].strandPostfix;
42087
+ // C-terminal
42088
+ if(!ic.resid2refnum[residueid]) {
42089
+ break;
42090
+ }
42091
+ else {
42092
+ currRefnum = strandArray[strandCnt].endRefnum + loopCnt;
42093
+ refnumLabelNoPostfix = strandArray[strandCnt].strand + currRefnum;
42094
+ refnumLabel = refnumLabelNoPostfix + strandArray[strandCnt].strandPostfix;
42095
+ }
42088
42096
  }
42089
42097
  }
42090
42098
 
@@ -59121,9 +59129,10 @@ class LoadScript {
59121
59129
 
59122
59130
  // load pdb, mmcif, mmdb, cid
59123
59131
  let id = loadStr.substr(loadStr.lastIndexOf(' ') + 1);
59132
+ if(id.length == 4) id = id.toUpperCase();
59124
59133
 
59125
59134
  // skip loading the structure if it was loaded before
59126
- if(ic.structures.hasOwnProperty(id)) return;
59135
+ if(ic.structures && ic.structures.hasOwnProperty(id)) return;
59127
59136
 
59128
59137
  ic.inputid = id;
59129
59138
  if(command.indexOf('load mmtf') !== -1) {
@@ -66306,7 +66315,7 @@ class SaveFile {
66306
66315
  if(me.utilsCls.isIE()) {
66307
66316
  blob = ic.renderer.domElement.msToBlob();
66308
66317
 
66309
- if(bAddURL) {
66318
+ if(bAddURL && typeof(blob) == 'Blob') {
66310
66319
  let reader = new FileReader();
66311
66320
  reader.onload = function(e) {
66312
66321
  let arrayBuffer = e.target.result; // or = reader.result;
@@ -66332,7 +66341,7 @@ class SaveFile {
66332
66341
  }
66333
66342
  else {
66334
66343
  ic.renderer.domElement.toBlob(function(data) {
66335
- if(bAddURL) {
66344
+ if(bAddURL && typeof(blob) == 'data') {
66336
66345
  let reader = new FileReader();
66337
66346
  reader.onload = function(e) {
66338
66347
  let arrayBuffer = e.target.result; // or = reader.result;
@@ -66404,7 +66413,30 @@ class SaveFile {
66404
66413
 
66405
66414
  let url = ic.shareLinkCls.shareLinkUrl();
66406
66415
 
66416
+ url = url.replace(/imageonly=1/g, '');
66417
+
66407
66418
  let bTooLong =(url.length > 4000 || url.indexOf('http') !== 0) ? true : false;
66419
+ /*
66420
+ if(bTooLong || (ic.bInputfile && !ic.bInputUrlfile)) {
66421
+ // $("#" + ic.pre + "viewer").html("<img src='" + imageUrl + "'/>");
66422
+ $("#" + ic.pre + "mnlist").html("<img src='" + imageUrl + "'/>");
66423
+ }
66424
+ else {
66425
+ // $("#" + ic.pre + "viewer").html("<a href='" + url + "' target='_blank'><img src='" + imageUrl + "'/></a>");
66426
+ $("#" + ic.pre + "mnlist").html("<a href='" + url + "' target='_blank'><img src='" + imageUrl + "'/></a>");
66427
+ }
66428
+
66429
+ // $("#" + ic.pre + "viewer").width(width);
66430
+ // $("#" + ic.pre + "viewer").height(height);
66431
+ $("#" + ic.pre + "mnlist").width(width);
66432
+ $("#" + ic.pre + "mnlist").height(height);
66433
+
66434
+ $("#" + ic.pre + "cmdlog").hide();
66435
+ $("#" + ic.pre + "title").hide();
66436
+
66437
+ //$("#" + ic.pre + "mnlist").hide();
66438
+ $("#" + ic.pre + "canvas").hide(); // "load mmdbid ..." may cause problems if canvas was removed
66439
+ */
66408
66440
 
66409
66441
  if(bTooLong || (ic.bInputfile && !ic.bInputUrlfile)) {
66410
66442
  $("#" + ic.pre + "viewer").html("<img src='" + imageUrl + "'/>");
@@ -66412,11 +66444,15 @@ class SaveFile {
66412
66444
  else {
66413
66445
  $("#" + ic.pre + "viewer").html("<a href='" + url + "' target='_blank'><img src='" + imageUrl + "'/></a>");
66414
66446
  }
66415
-
66447
+
66448
+ $("#" + ic.pre + "viewer").width(width);
66416
66449
  $("#" + ic.pre + "viewer").height(height);
66417
- $("#" + ic.pre + "mnlist").hide();
66450
+
66418
66451
  $("#" + ic.pre + "cmdlog").hide();
66419
66452
  $("#" + ic.pre + "title").hide();
66453
+ $("#" + ic.pre + "mnlist").hide();
66454
+
66455
+ if($("#" + ic.pre + "fullscreen").length > 0) $("#" + ic.pre + "fullscreen").hide();
66420
66456
 
66421
66457
  // clear memory
66422
66458
  ic = {};
@@ -67365,6 +67401,10 @@ class ShareLink {
67365
67401
  if(key_value.length == 2) paraHash[key_value[0]] = key_value[1];
67366
67402
  }
67367
67403
 
67404
+ if(me.cfg.idname && !paraHash[me.cfg.idname]) { // somehow it is not included
67405
+ url += me.cfg.idname + '=' + me.cfg.idvalue + '&';
67406
+ }
67407
+
67368
67408
  for(let key in paraHash) {
67369
67409
  if(key === 'v') continue;
67370
67410
 
@@ -67404,7 +67444,7 @@ class ShareLink {
67404
67444
  transformation.quaternion = ic.quaternion;
67405
67445
 
67406
67446
  let statefile = "";
67407
- let prevCommandStr = undefined;
67447
+ let prevCommandStr = "";
67408
67448
 
67409
67449
  let toggleStr = 'toggle highlight';
67410
67450
  let cntToggle = 0;