icn3d 3.37.0 → 3.37.1

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Files changed (4) hide show
  1. package/icn3d.js +54 -42
  2. package/icn3d.min.js +3 -3
  3. package/icn3d.module.js +54 -42
  4. package/package.json +1 -1
package/icn3d.module.js CHANGED
@@ -12003,9 +12003,9 @@ class ClickMenu {
12003
12003
 
12004
12004
  $("#" + me.pre + "newvs2").on('submit', function() {
12005
12005
  // fill the pdbstr
12006
- let pdbstr = ic.saveFileCls.getAtomPDB(ic.hAtoms);
12006
+ let bVastSearch = true;
12007
+ let pdbstr = ic.saveFileCls.getAtomPDB(ic.hAtoms, undefined, undefined, undefined, undefined, undefined, undefined, bVastSearch);
12007
12008
  $("#" + me.pre + "pdbstr").val(pdbstr);
12008
-
12009
12009
  return true;
12010
12010
  });
12011
12011
 
@@ -20170,8 +20170,8 @@ class SetHtml {
20170
20170
  });
20171
20171
  }
20172
20172
 
20173
- // async loadPng(imageStr, command) { let me = this.icn3dui, ic = me.icn3d;
20174
- async loadPng(imageStr) { let me = this.icn3dui, ic = me.icn3d;
20173
+ async loadPng(imageStr, command, bRender) { let me = this.icn3dui, ic = me.icn3d;
20174
+ // async loadPng(imageStr) { let me = this.icn3dui, ic = me.icn3d;
20175
20175
  let matchedStr = 'Share Link: ';
20176
20176
  let pos = imageStr.indexOf(matchedStr);
20177
20177
  let matchedStrState = "Start of state file======\n";
@@ -20192,8 +20192,8 @@ class SetHtml {
20192
20192
  let posData = imageStr.indexOf(matchedStrData);
20193
20193
  ic.bInputfile =(posData == -1) ? false : true;
20194
20194
  ic.bInputPNGWithData = ic.bInputfile;
20195
- // let commandStr = (command) ? command.replace(/;/g, "\n") : '';
20196
- let commandStr = '';
20195
+ let commandStr = (command) ? command.replace(/;/g, "\n") : '';
20196
+ // let commandStr = '';
20197
20197
 
20198
20198
  // let statefile;
20199
20199
  // if(ic.bInputfile) {
@@ -20214,31 +20214,37 @@ class SetHtml {
20214
20214
  //statefile = decodeURIComponent(statefile);
20215
20215
  statefile = decodeURIComponent(statefile + "\n" + commandStr);
20216
20216
 
20217
- /*
20218
- if(type === 'pdb') {
20219
- await ic.pdbParserCls.loadPdbData(data);
20217
+ if(bRender) {
20218
+ if(type === 'pdb') {
20219
+ await ic.pdbParserCls.loadPdbData(data);
20220
20220
 
20221
- ic.commands = [];
20222
- ic.optsHistory = [];
20223
- //await ic.loadScriptCls.loadScript(statefile, true);
20224
- }
20225
- else {
20226
- if(type === 'mol2') {
20227
- await ic.mol2ParserCls.loadMol2Data(data);
20221
+ ic.commands = [];
20222
+ ic.optsHistory = [];
20223
+ //await ic.loadScriptCls.loadScript(statefile, true);
20228
20224
  }
20229
- else if(type === 'sdf') {
20230
- await ic.sdfParserCls.loadSdfData(data);
20231
- }
20232
- else if(type === 'xyz') {
20233
- await ic.xyzParserCls.loadXyzData(data);
20234
- }
20235
- else if(type === 'mmcif') {
20236
- await ic.mmcifParserCls.loadMmcifData(data);
20225
+ else {
20226
+ if(type === 'mol2') {
20227
+ await ic.mol2ParserCls.loadMol2Data(data);
20228
+ }
20229
+ else if(type === 'sdf') {
20230
+ await ic.sdfParserCls.loadSdfData(data);
20231
+ }
20232
+ else if(type === 'xyz') {
20233
+ await ic.xyzParserCls.loadXyzData(data);
20234
+ }
20235
+ else if(type === 'mmcif') {
20236
+ await ic.mmcifParserCls.loadMmcifData(data);
20237
+ }
20238
+ ic.commands = [];
20239
+ ic.optsHistory = [];
20240
+ //await ic.loadScriptCls.loadScript(statefile, true);
20237
20241
  }
20238
- ic.commands = [];
20239
- ic.optsHistory = [];
20240
- //await ic.loadScriptCls.loadScript(statefile, true);
20241
- }
20242
+
20243
+ await ic.loadScriptCls.loadScript(statefile, true);
20244
+
20245
+ // me.htmlCls.clickMenuCls.setLogCmd('load iCn3D PNG image ' + $("#" + me.pre + "pngimage").val(), false);
20246
+ }
20247
+ /*
20242
20248
  }
20243
20249
  else { // url length > 4000
20244
20250
  //var matchedStrState = "Start of state file======\n";
@@ -43003,8 +43009,6 @@ class AnnoDomain {
43003
43009
  }
43004
43010
  }
43005
43011
 
43006
- if(bNotShowDomain) continue;
43007
-
43008
43012
  // save 3D domain info for node.js script
43009
43013
  if(me.bNode) {
43010
43014
  let domainName = '3D domain ' +(index+1).toString();
@@ -43019,13 +43023,15 @@ class AnnoDomain {
43019
43023
  // 0-based
43020
43024
  let obj = {};
43021
43025
  // let resi = ic.ParserUtilsCls.getResi(chnid, j);
43022
- let resid = ic.ncbi2resid(chnid + '_' + j);
43026
+ let resid = ic.ncbi2resid[chnid + '_' + j];
43023
43027
  obj[resid] = domainName;
43024
43028
  ic.resid2domain[chnid].push(obj);
43025
43029
  }
43026
43030
  }
43027
43031
  }
43028
43032
 
43033
+ if(bNotShowDomain) continue;
43034
+
43029
43035
  let htmlTmp2 = '<div class="icn3d-seqTitle icn3d-link icn3d-blue" 3ddomain="' +(index+1).toString() + '" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + title + '" index="' + index + '" setname="' + chnid + '_3d_domain_' +(index+1).toString() + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">' + title + ' </div>';
43030
43036
  let htmlTmp3 = '<span class="icn3d-residueNum" title="residue count">' + resCnt.toString() + ' Res</span>';
43031
43037
  html3 += htmlTmp2 + htmlTmp3 + '<br>';
@@ -58504,8 +58510,7 @@ class PdbParser {
58504
58510
  await ic.mmcifParserCls.loadMmcifData(data);
58505
58511
  }
58506
58512
  else if(type === 'icn3dpng') {
58507
- // await me.htmlCls.setHtmlCls.loadPng(data, command);
58508
- await me.htmlCls.setHtmlCls.loadPng(data);
58513
+ await me.htmlCls.setHtmlCls.loadPng(data, command, true);
58509
58514
  }
58510
58515
  else if(type === 'pae') {
58511
58516
  me.htmlCls.dialogCls.openDlg('dl_alignerrormap', 'Show Predicted Aligned Error (PAE) map');
@@ -58635,7 +58640,7 @@ class PdbParser {
58635
58640
  }
58636
58641
 
58637
58642
  async execStatefile(structure, statefile) {let ic = this.icn3d, me = ic.icn3dui;
58638
- // if(!statefile) return;
58643
+ if(!statefile) return;
58639
58644
 
58640
58645
  let commandArray = statefile.trim().split('\n');
58641
58646
  commandArray = ['select $' + structure].concat(commandArray);
@@ -63991,7 +63996,8 @@ class LoadPDB {
63991
63996
  this.icn3d = icn3d;
63992
63997
  }
63993
63998
 
63994
- getStructureId(id, moleculeNum, bMutation) { let ic = this.icn3d; ic.icn3dui;
63999
+ getStructureId(id, moleculeNum, bMutation, bNMR) { let ic = this.icn3d; ic.icn3dui;
64000
+ id = (bNMR && ic.idNMR) ? ic.idNMR : id;
63995
64001
  let structure = id;
63996
64002
 
63997
64003
  if(id == ic.defaultPdbId || bMutation || ic.structures.hasOwnProperty(id)) { // bMutation: side chain prediction
@@ -64058,6 +64064,7 @@ class LoadPDB {
64058
64064
  //let chainMissingResidueArray = {}
64059
64065
 
64060
64066
  let id = (pdbid) ? pdbid : ic.defaultPdbId;
64067
+ let oriId = id;
64061
64068
 
64062
64069
  let structure = id;
64063
64070
 
@@ -64077,6 +64084,7 @@ class LoadPDB {
64077
64084
 
64078
64085
  ///id = line.substr(62, 4).trim();
64079
64086
  id = line.substr(62).trim();
64087
+ oriId = id;
64080
64088
 
64081
64089
  if(id == '') {
64082
64090
  if(bAppend) {
@@ -64088,7 +64096,7 @@ class LoadPDB {
64088
64096
  }
64089
64097
  }
64090
64098
 
64091
- structure = this.getStructureId(id, moleculeNum, bMutation);
64099
+ structure = this.getStructureId(id, moleculeNum, bMutation, bNMR);
64092
64100
 
64093
64101
  ic.molTitle = '';
64094
64102
  ic.molTitleHash = {};
@@ -64159,6 +64167,7 @@ class LoadPDB {
64159
64167
  else if (remarkType == 210) {
64160
64168
  if((line.substr(11, 32).trim() == 'EXPERIMENT TYPE') && line.substr(45).trim() == 'NMR') {
64161
64169
  bNMR = true;
64170
+ ic.idNMR = oriId;
64162
64171
  }
64163
64172
  }
64164
64173
  else if (remarkType == 350 && line.substr(13, 5) == 'BIOMT') {
@@ -64212,7 +64221,7 @@ class LoadPDB {
64212
64221
  ++moleculeNum;
64213
64222
  id = ic.defaultPdbId;
64214
64223
 
64215
- structure = this.getStructureId(id, moleculeNum, bMutation);
64224
+ structure = this.getStructureId(id, moleculeNum, bMutation, bNMR);
64216
64225
  //helices = [];
64217
64226
  //sheets = [];
64218
64227
  if(!bNMR) {
@@ -64235,7 +64244,7 @@ class LoadPDB {
64235
64244
  segId = line.substr(72, 4).trim();
64236
64245
 
64237
64246
  if(bFirstAtom) {
64238
- structure = this.getStructureId(id, moleculeNum, bMutation);
64247
+ structure = this.getStructureId(id, moleculeNum, bMutation, bNMR);
64239
64248
 
64240
64249
  bFirstAtom = false;
64241
64250
  }
@@ -64243,7 +64252,7 @@ class LoadPDB {
64243
64252
  ++moleculeNum;
64244
64253
  id = ic.defaultPdbId;
64245
64254
 
64246
- structure = this.getStructureId(id, moleculeNum, bMutation);
64255
+ structure = this.getStructureId(id, moleculeNum, bMutation, bNMR);
64247
64256
 
64248
64257
  //helices = [];
64249
64258
  //sheets = [];
@@ -79398,7 +79407,7 @@ class SaveFile {
79398
79407
  }
79399
79408
 
79400
79409
  //getAtomPDB: function(atomHash, bPqr, bPdb, bNoChem) { let ic = this.icn3d, me = ic.icn3dui;
79401
- getAtomPDB(atomHash, bPqr, bNoChem, bNoHeader, chainResi2pdb, pdbid, bMergeIntoOne) { let ic = this.icn3d, me = ic.icn3dui;
79410
+ getAtomPDB(atomHash, bPqr, bNoChem, bNoHeader, chainResi2pdb, pdbid, bMergeIntoOne, bVastSearch) { let ic = this.icn3d, me = ic.icn3dui;
79402
79411
  let pdbStr = '';
79403
79412
 
79404
79413
  // get all phosphate groups in lipids
@@ -79475,7 +79484,7 @@ class SaveFile {
79475
79484
  for(let i = 0, il = ssArray.length; i < il; ++i) {
79476
79485
  let ssObj = ssArray[i];
79477
79486
 
79478
- if(ssObj.ss != prevSs) {
79487
+ if(ssObj.ss != prevSs || ssObj.ssbegin) {
79479
79488
  // print prev
79480
79489
  stru2header[stru] += this.printPrevSecondary(bHelix, bSheet, prevRealSsObj, ssCnt);
79481
79490
 
@@ -79673,6 +79682,7 @@ class SaveFile {
79673
79682
  //line +=(atom.chain.length <= 1) ? atom.chain.padStart(1, ' ') : atom.chain.substr(0, 1);
79674
79683
  if(atom.chain.length >= 2) {
79675
79684
  let chainTmp = atom.chain.replace(/_/gi, '').substr(0, 2);
79685
+ if(bVastSearch) chainTmp = ' ' + chainTmp.substr(0,1); // VAST search only support one lettter chain ID
79676
79686
  line += chainTmp;
79677
79687
  }
79678
79688
  else if(atom.chain.length == 1) {
@@ -79751,7 +79761,9 @@ class SaveFile {
79751
79761
  }
79752
79762
  else {
79753
79763
  line += "1.00".padStart(6, ' ');
79754
- line +=(atom.b) ? parseFloat(atom.b).toFixed(2).toString().padStart(6, ' ') : ' '.padStart(6, ' ');
79764
+ // line +=(atom.b) ? parseFloat(atom.b).toFixed(2).toString().padStart(6, ' ') : ' '.padStart(6, ' ');
79765
+ let defaultBFactor = (bVastSearch) ? "1.0" : " ";
79766
+ line +=(atom.b) ? parseFloat(atom.b).toFixed(2).toString().padStart(6, ' ') : defaultBFactor.padStart(6, ' ');
79755
79767
  line += ' '.padStart(10, ' ');
79756
79768
  line += atom.elem.padStart(2, ' ');
79757
79769
  line += ' '.padStart(2, ' ');
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "icn3d",
3
- "version": "3.37.0",
3
+ "version": "3.37.1",
4
4
  "main": "./icn3d.js",
5
5
  "exports": {
6
6
  ".": {