icn3d 3.29.1 → 3.29.2

package/icn3d.js

@@ -8667,14 +8667,14 @@ class SetMenu {
         }
 
         //!!!
-
+/*
         html += this.getMenuText('m1_exportrefnum', 'Reference Numbers', undefined, undefined, 2);
         html += "<ul>";
         html += this.getLink('mn1_exportIgstrand', 'Ig Strand', undefined, 3);
         html += this.getLink('mn1_exportKabat', 'Kabat', undefined, 3);
         html += this.getLink('mn1_exportImgt', 'IMGT', undefined, 3);
         html += "</ul>";
-
+*/
 
         html += "<li><br/></li>";
 
@@ -9515,8 +9515,8 @@ class SetMenu {
             //}
 
             //!!!
-            html += this.getRadio('mn4_clr', 'mn4_clrIgstrand', 'Ig Strand', undefined, undefined, 2);
-            html += this.getRadio('mn4_clr', 'mn4_clrIgproto', 'Ig Protodomain', undefined, undefined, 2);
+            //html += this.getRadio('mn4_clr', 'mn4_clrIgstrand', 'Ig Strand', undefined, undefined, 2);
+            //html += this.getRadio('mn4_clr', 'mn4_clrIgproto', 'Ig Protodomain', undefined, undefined, 2);
         }
         else {
             //if(!me.cfg.hidelicense) html += this.getRadio('mn4_clr', 'mn1_delphi2', 'DelPhi<br><span style="padding-left:1.5em;">Potential ' + me.htmlCls.licenseStr + '</span>');
@@ -9647,7 +9647,7 @@ class SetMenu {
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelResidues', 'per Residue', undefined, 1, 2);
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelResnum', 'per Residue & Number', undefined, 1, 2);
             //!!!
-            html += this.getRadio('mn6_addlabel', 'mn6_addlabelRefnum', 'per Reference Number', undefined, 1, 2);
+            //html += this.getRadio('mn6_addlabel', 'mn6_addlabelRefnum', 'per Reference Number', undefined, 1, 2);
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelChains', 'per Chain', undefined, undefined, 2);
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelTermini', 'N- & C-Termini', undefined, 1, 2);
         }
@@ -9739,13 +9739,13 @@ class SetMenu {
 
             html += "<ul>";
 //!!!
-
+/*
             html += this.getLink('mn6_igrefYes', 'Show Ig Ref. Number', undefined, 2);
             html += this.getLink('mn6_igrefTpl', 'Ig w/ Specified Template', undefined, 2);
             html += this.getLink('mn6_igrefNo', 'Hide Ig Ref. Number', undefined, 2);
 
             html += this.getMenuSep();
-
+*/
             html += this.getLink('mn6_customref', 'Custom Ref. Number', undefined, 2);
             html += "</ul>";
             html += "</li>";
@@ -10971,12 +10971,14 @@ class SetDialog {
 
 
         html += me.htmlCls.divStr + "dl_selection' class='" + dialogClass + "'>";
-        html += this.addNotebookTitle('dl_selection', 'Load a selection file');
+        html += this.addNotebookTitle('dl_selection', 'Please input the selection file');
         html += "Selection file: " + me.htmlCls.inputFileStr + "id='" + me.pre + "selectionfile'><br/>";
         html += me.htmlCls.buttonStr + "reload_selectionfile' style='margin-top: 6px;'>Load</button>";
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_collection' class='" + dialogClass + "'>";
+        html += this.addNotebookTitle('dl_collection', 'Please input the collection file');
+        html += "You can load a collection of structures via a file. Here is <a href='https://github.com/ncbi/icn3d/blob/master/example/collection.json' target='_blank'>one example file</a><br><br>";
         html += "Collection file: " + me.htmlCls.inputFileStr + "id='" + me.pre + "collectionfile'><br/>";
         html += me.htmlCls.buttonStr + "reload_collectionfile' style='margin-top: 6px;'>Load</button>";
         html += "</div>";
@@ -13211,7 +13213,8 @@ class Events {
                 let dataStr = JSON.parse(e.target.result);
                 let collection = [dataStr["structures"].map(({ id }) => id), dataStr["structures"].map(({ title }) => title)];
                 let collectionHtml = ic.selectCollectionsCls.setAtomMenu(collection[0], collection[1]);
-                await ic.chainalignParserCls.downloadMmdbAf(collection[0][0]);
+                let bNoDuplicate = true;
+                await ic.chainalignParserCls.downloadMmdbAf(collection[0][0], undefined, undefined, bNoDuplicate);
     
                 ic.opts["color"] = "structure";
                 ic.setColorCls.setColorByOptions(ic.opts, ic.dAtoms);
@@ -37634,7 +37637,8 @@ class AnnoDomain {
                     for(let j = from; j <= to; ++j) {
                         // 0-based
                         let obj = {};
-                        obj[chnid + '_' + (j+1).toString()] = domainName;
+                        let resi = ic.ParserUtilsCls.getResi(chnid, j+1);
+                        obj[chnid + '_' + resi] = domainName;
                         ic.resid2domain[chnid].push(obj);
                     }
                 }
@@ -46194,7 +46198,7 @@ class LineGraph {
                 console.log("domainid: " + domainid);
             }
 
-            if(!ic.domainid2score.hasOwnProperty(domainid) || queryData[0].score >= ic.domainid2score[domainid].split('_')[0]) {
+            if(!domainid2segs.hasOwnProperty(domainid) || queryData[0].score >= ic.domainid2score[domainid].split('_')[0]) {
                 ic.domainid2score[domainid] = queryData[0].score + '_' + queryData[0].frac_identical + '_' + queryData[0].num_res ;  
     
                 ic.domainid2refpdbname[domainid] = refpdbname;
@@ -46274,6 +46278,7 @@ class LineGraph {
 
         // combine domainid into chainid
         let processedChainid = {};
+
         for(let domainid in ic.domainid2refpdbname) {
             // remove the first round template
             if(ic.domainid2refpdbname[domainid].substr(0,1) == '1') {
@@ -49746,6 +49751,7 @@ class ChainalignParser {
             me.htmlCls.clickMenuCls.setLogCmd("Align " + mmdbid1 + " with " + mmdbid2, false);
 
             let bNoAlert = true;
+
             let bAligned = this.processAlign(align, i, queryData, bEqualMmdbid, bEqualChain, bNoAlert);
 
             if(bAligned) {
@@ -50257,7 +50263,6 @@ class ChainalignParser {
                 ic.qt_start_end[index] = align[0].segs;
 
                 let rmsd = align[0].super_rmsd;
-console.log();
 
                 let logStr = "alignment RMSD: " + rmsd.toPrecision(4);
                 if(me.cfg.aligntool == 'tmalign') logStr += "; TM-score: " + align[0].score.toPrecision(4);
@@ -50342,7 +50347,7 @@ console.log();
         }
     }
 
-    async downloadMmdbAf(idlist, bQuery, vastplusAtype) { let ic = this.icn3d, me = ic.icn3dui;
+    async downloadMmdbAf(idlist, bQuery, vastplusAtype, bNoDuplicate) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
         ic.structArray = (ic.structures) ? Object.keys(ic.structures) : [];
@@ -50361,11 +50366,17 @@ console.log();
         let structArrayTmp = idlist.split(',');
 
         let structArray = [];
-        // remove redundant structures
+
         for(let i = 0, il = structArrayTmp.length; i < il; ++i) {
-            if(!ic.structures.hasOwnProperty(structArrayTmp[i].toUpperCase())) {
+            let id = structArrayTmp[i].toUpperCase();
+            // sometimes we want to load same structure multiple times
+            if(!ic.structures.hasOwnProperty(id) && structArray.indexOf(id) == -1) {
                 structArray.push(structArrayTmp[i]);
             }
+            else {
+                // only when bNoDuplicate is undefined/false, it's allowed to load multiple copies of the same structure
+                if(!bNoDuplicate) structArray.push(structArrayTmp[i] + me.htmlCls.postfix);
+            }
         }
         
         if(structArray.length == 0) return;
@@ -53839,6 +53850,7 @@ class RealignParser {
       // reinitialize
       ic.qt_start_end = [];
 
+      let chainidHash = {};
       for(let index = 0, indexl = chainidArray.length - 1; index < indexl; ++index) {         
           let fromStruct = chainidArray[index + 1].substr(0, chainidArray[index + 1].indexOf('_')); //.toUpperCase();
 
@@ -53846,6 +53858,8 @@ class RealignParser {
 
           let chainTo = toStruct + chainidArray[0].substr(chainidArray[0].indexOf('_'));
           let chainFrom = fromStruct + chainidArray[index + 1].substr(chainidArray[index + 1].indexOf('_'));
+          chainidHash[chainTo] = 1;
+          chainidHash[chainFrom] = 1;
 
           chainidArray[0] = chainTo;
           chainidArray[index + 1] = chainFrom;
@@ -53875,13 +53889,17 @@ class RealignParser {
           // set ic.qt_start_end in alignCoords()
 
           let result = ic.ParserUtilsCls.alignCoords(coord2, coord1, fromStruct, undefined, chainTo, chainFrom, index + 1, bChainAlign);
+
           hAtoms = me.hashUtilsCls.unionHash(hAtoms, result.hAtoms);
           rmsd = parseFloat(result.rmsd);
       }
 
       // If rmsd from vastsrv is too large, realign the chains
-      if(me.cfg.chainalign && !me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5) {      
-        let nameArray = me.cfg.chainalign.split(',');
+      //if(me.cfg.chainalign && !me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5) {   
+      if(!me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5) {     
+        console.log("RMSD from VAST is larger than 5. Realign the chains with TM-align."); 
+        //let nameArray = me.cfg.chainalign.split(',');
+        let nameArray = Object.keys(chainidHash);
         if(nameArray.length > 0) {
             ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
         }
@@ -54325,7 +54343,7 @@ class RealignParser {
                 struct2resid[chainid] = [];
             }
  
-            if(bPredefined) {
+            if(bPredefined) {             
                 //base = parseInt(ic.chainsSeq[chainid][0].resi);
 
                 if(i == 0) ;
@@ -54341,6 +54359,7 @@ class RealignParser {
 
                     // master
                     resiArray = predefinedResPair[0].split(",");        
+
                     result = thisClass.getSeqCoorResid(resiArray, chainid_t);
 
                     hAtoms = me.hashUtilsCls.unionHash(hAtoms, result.hAtoms);
@@ -54355,6 +54374,7 @@ class RealignParser {
 
                     // slave
                     resiArray = predefinedResPair[1].split(",");
+
                     result = thisClass.getSeqCoorResid(resiArray, chainid); 
                     hAtoms = me.hashUtilsCls.unionHash(hAtoms, result.hAtoms);
 
@@ -55580,6 +55600,7 @@ class ParserUtils {
               if(rmsd) {
                   me.htmlCls.clickMenuCls.setLogCmd("realignment RMSD: " + rmsd.toPrecision(4), false);
                   let html = "<br><b>Realignment RMSD</b>: " + rmsd.toPrecision(4) + " &#8491;<br><br>";
+
                   if(ic.bAfMem && !me.cfg.chainalign) {
                     //if(window.dialog && window.dialog.hasClass('ui-dialog-content')) window.dialog.dialog( "close" );
                     html += me.utilsCls.getMemDesc();
@@ -62145,7 +62166,7 @@ class DefinedSets {
 
         nameArrayTmp.forEach((elem) => {
             structureArray.forEach((structure) => {
-                if (ic.defNames2Residues[elem][0].split("_")[0].includes(structure.split("_")[0])){
+                if (ic.defNames2Residues[elem] && ic.defNames2Residues[elem][0] && ic.defNames2Residues[elem][0].split("_")[0].includes(structure.split("_")[0])){
                     if ($.inArray(elem, nameArray) === -1) nameArray.push(elem);
                 }
             });
@@ -62715,6 +62736,10 @@ class DefinedSets {
 
 }
 
+/**
+ * @author Jack Lin <th3linja@yahoo.com> / https://github.com/ncbi/icn3d
+ */
+
 class SelectCollections {
   constructor(icn3d) {
     this.icn3d = icn3d;
@@ -62782,7 +62807,8 @@ class SelectCollections {
       ic.nameArray = nameArray;
       if (nameArray !== null) {
         ic.bShowHighlight = false;
-        await ic.chainalignParserCls.downloadMmdbAf(nameArray.toString());
+        let bNoDuplicate = true;
+        await ic.chainalignParserCls.downloadMmdbAf(nameArray.toString(), undefined, undefined, bNoDuplicate);
 
         ic.dAtoms = {};
         ic.hAtoms = {};
@@ -74511,7 +74537,7 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
             // load multiple PDBs
             // ic.bNCBI = true;
             ic.bMmdbafid = true;
-            
+
             let bQuery = true;
             await ic.chainalignParserCls.downloadMmdbAf(mmdbafid, bQuery);
         }