icn3d 3.29.0 → 3.29.2

package/icn3d.js

@@ -5957,6 +5957,10 @@ class ClickMenu {
         me.myEventCls.onIds("#" + me.pre + "mn1_selection", "click", function(e) { me.icn3d; //e.preventDefault();
            me.htmlCls.dialogCls.openDlg('dl_selection', 'Please input the selection file');
         });
+       
+        me.myEventCls.onIds("#" + me.pre + "mn1_collection", "click", function (e) { me.icn3d; //e.preventDefault();
+         me.htmlCls.dialogCls.openDlg('dl_collection', 'Please input the collection file');
+       });
 
         me.myEventCls.onIds("#" + me.pre + "mn1_dsn6", "click", function(e) { me.icn3d; //e.preventDefault();
            me.htmlCls.dialogCls.openDlg('dl_dsn6', 'Please input the map file to display electron density map');
@@ -8546,6 +8550,7 @@ class SetMenu {
         html += this.getLink('mn1_state', 'State/Script File', undefined, 2);
         html += this.getLink('mn1_fixedversion', 'Share Link in Archived Ver. ' + me.htmlCls.wifiStr, undefined, 2);
         html += this.getLink('mn1_selection', 'Selection File', undefined, 2);
+        html += this.getLink("mn1_collection", "Collection File", undefined, 2);
 
         html += this.getMenuSep();
 
@@ -8662,14 +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>";
 
@@ -9510,8 +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>');
@@ -9642,7 +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);
         }
@@ -9734,13 +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>";
@@ -10966,11 +10971,26 @@ 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>";
+
+        html += me.htmlCls.divStr + "dl_selectCollections' class='" + dialogClass + "'>";
+        html += me.htmlCls.divStr + "dl_collectionsMenu'>";
+        html += "<b>Structures:</b> <br/>";
+        html += "<select id='" +  me.pre + "collections_menu' multiple size='6' style='min-width:130px;'>";
+        html += "</select>";
+        html += "</div>";
+        html += "</div>";
+
         html += me.htmlCls.divStr + "dl_menuloadpref' class='" + dialogClass + "'>";
         html += this.addNotebookTitle('dl_menuloadpref', 'Load a preference file');
         html += "Preference file: " + me.htmlCls.inputFileStr + "id='" + me.pre + "menupreffile'><br/>";
@@ -13175,6 +13195,46 @@ class Events {
            }
         });
 
+        me.myEventCls.onIds("#" + me.pre + "reload_collectionfile", "click", function (e) { let ic = me.icn3d;
+            e.preventDefault();
+            let file = $("#" + me.pre + "collectionfile")[0].files[0];
+            if (!file) {
+                var aaa = 1; //alert("Please select a file before clicking 'Load'");
+            } else {
+            if (!me.cfg.notebook) dialog.dialog("close");
+            if (!me.cfg.notebook) {
+                $(".ui-dialog-content").dialog("close");
+            } else {
+                ic.resizeCanvasCls.closeDialogs();
+            }
+            me.htmlCls.setHtmlCls.fileSupport();
+            let reader = new FileReader();
+            reader.onload = async function (e) {
+                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]);
+                let bNoDuplicate = true;
+                await ic.chainalignParserCls.downloadMmdbAf(collection[0][0], undefined, undefined, bNoDuplicate);
+    
+                ic.opts["color"] = "structure";
+                ic.setColorCls.setColorByOptions(ic.opts, ic.dAtoms);
+    
+                $("#" + ic.pre + "collections_menu").html(collectionHtml);
+                ic.selectCollectionsCls.clickStructure();
+    
+                $("#" + ic.pre + "collections_menu").trigger("change");
+    
+                me.htmlCls.clickMenuCls.setLogCmd(
+                "load collection file " +
+                    $("#" + me.pre + "collectionfile").val(),
+                false
+                );
+            };
+            reader.readAsText(file);
+            me.htmlCls.dialogCls.openDlg("dl_selectCollections", "Select Collections");
+            }
+        });
+
         me.myEventCls.onIds("#" + me.pre + "reload_dsn6file2fofc", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            //if(!me.cfg.notebook) dialog.dialog( "close" );
@@ -37577,7 +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);
                     }
                 }
@@ -46137,7 +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;
@@ -46217,6 +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') {
@@ -49689,6 +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) {
@@ -50200,7 +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);
@@ -50285,7 +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) : [];
@@ -50304,11 +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;
@@ -51743,7 +51811,6 @@ class MtzParser {
        else {
            sigma = await this.mtzParserBase(url, type, sigma, 'url');
 
-           console.log("### sigma " + sigma);
            //me.htmlCls.clickMenuCls.setLogCmd('set map ' + type + ' sigma ' + sigma + ' file mtz | ' + encodeURIComponent(url), true);
        }
     }
@@ -53783,6 +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();
 
@@ -53790,6 +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;
@@ -53819,13 +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);
         }
@@ -54269,7 +54343,7 @@ class RealignParser {
                 struct2resid[chainid] = [];
             }
  
-            if(bPredefined) {
+            if(bPredefined) {             
                 //base = parseInt(ic.chainsSeq[chainid][0].resi);
 
                 if(i == 0) ;
@@ -54285,6 +54359,7 @@ class RealignParser {
 
                     // master
                     resiArray = predefinedResPair[0].split(",");        
+
                     result = thisClass.getSeqCoorResid(resiArray, chainid_t);
 
                     hAtoms = me.hashUtilsCls.unionHash(hAtoms, result.hAtoms);
@@ -54299,6 +54374,7 @@ class RealignParser {
 
                     // slave
                     resiArray = predefinedResPair[1].split(",");
+
                     result = thisClass.getSeqCoorResid(resiArray, chainid); 
                     hAtoms = me.hashUtilsCls.unionHash(hAtoms, result.hAtoms);
 
@@ -55524,6 +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();
@@ -56438,7 +56515,7 @@ class LoadAtomData {
           if(!bTitle) ic.molTitle = '';
         }
         else { // mmdbid or mmcifid
-            if(data.descr !== undefined) ic.molTitle += data.descr.name;
+            if(data.descr !== undefined) ic.molTitle = data.descr.name;
             if(type === 'mmdbid') {
               let pdbidTmp = (isNaN(id)) ? id : data.pdbId;
               let chainHash = {};
@@ -62069,7 +62146,7 @@ class DefinedSets {
     }
 
     //Set the menu of defined sets with an array of defined names "commandnameArray".
-    setAtomMenu(commandnameArray) { let ic = this.icn3d; ic.icn3dui;
+    setAtomMenu(commandnameArray) { let ic = this.icn3d, me = ic.icn3dui;
       let html = "";
 
       let nameArray1 =(ic.defNames2Residues !== undefined) ? Object.keys(ic.defNames2Residues) : [];
@@ -62078,12 +62155,22 @@ class DefinedSets {
       let nameArrayTmp = nameArray1.concat(nameArray2).sort();
 
       let nameArray = [];
-    //  $.each(nameArrayTmp, function(i, el){
-    //       if($.inArray(el, nameArray) === -1) nameArray.push(el);
-    //  });
-      nameArrayTmp.forEach(elem => {
-           if($.inArray(elem, nameArray) === -1) nameArray.push(elem);
-      });
+        //  $.each(nameArrayTmp, function(i, el){
+        //       if($.inArray(el, nameArray) === -1) nameArray.push(el);
+        //  });
+        //   nameArrayTmp.forEach(elem => {
+        //        if($.inArray(elem, nameArray) === -1) nameArray.push(elem);
+        //   });
+        
+        let structureArray = Object.keys(me.utilsCls.getStructures(ic.dAtoms));
+
+        nameArrayTmp.forEach((elem) => {
+            structureArray.forEach((structure) => {
+                if (ic.defNames2Residues[elem] && ic.defNames2Residues[elem][0] && ic.defNames2Residues[elem][0].split("_")[0].includes(structure.split("_")[0])){
+                    if ($.inArray(elem, nameArray) === -1) nameArray.push(elem);
+                }
+            });
+        });
 
       //for(let i in ic.defNames2Atoms) {
       for(let i = 0, il = nameArray.length; i < il; ++i) {
@@ -62649,6 +62736,129 @@ class DefinedSets {
 
 }
 
+/**
+ * @author Jack Lin <th3linja@yahoo.com> / https://github.com/ncbi/icn3d
+ */
+
+class SelectCollections {
+  constructor(icn3d) {
+    this.icn3d = icn3d;
+  }
+
+  //Set the menu of defined sets with an array of defined names "commandnameArray".
+  setAtomMenu(nameArray, titleArray) {
+    let ic = this.icn3d;
+    ic.icn3dui;
+    let html = "";
+    let commandnameArray = [nameArray[0]];
+    //for(let i in ic.defNames2Atoms) {
+    for (let i = 0, il = nameArray.length; i < il; ++i) {
+      let name = nameArray[i];
+      let title = titleArray[i];
+
+      let atomHash;
+      if (
+        ic.defNames2Atoms !== undefined &&
+        ic.defNames2Atoms.hasOwnProperty(name)
+      ) {
+        let atomArray = ic.defNames2Atoms[name];
+
+        if (atomArray.length > 0) ic.atoms[atomArray[0]];
+      } else if (
+        ic.defNames2Residues !== undefined &&
+        ic.defNames2Residues.hasOwnProperty(name)
+      ) {
+        let residueArray = ic.defNames2Residues[name];
+        if (residueArray.length > 0) {
+          atomHash = ic.residues[residueArray[0]];
+          if (atomHash) {
+            ic.atoms[Object.keys(atomHash)[0]];
+          }
+        }
+      }
+
+      if (commandnameArray.indexOf(name) != -1) {
+        html +=
+          "<option value='" +
+          name +
+          "' selected='selected'>" +
+          title +
+          "</option>";
+      } else {
+        html += "<option value='" + name + "'>" + title + "</option>";
+      }
+    }
+
+    return html;
+  }
+
+  clickStructure() {
+    let ic = this.icn3d,
+      me = ic.icn3dui;
+    let thisClass = this;
+
+    //me.myEventCls.onIds("#" + ic.pre + "atomsCustom", "change", function(e) { let  ic = thisClass.icn3d;
+    $("#" + ic.pre + "collections_menu").change(async function (e) {
+      let ic = thisClass.icn3d;
+      //    ic.init()
+      let nameArray = $(this).val();
+      let nameStructure = $(this).find("option:selected").text();
+
+      ic.nameArray = nameArray;
+      if (nameArray !== null) {
+        ic.bShowHighlight = false;
+        let bNoDuplicate = true;
+        await ic.chainalignParserCls.downloadMmdbAf(nameArray.toString(), undefined, undefined, bNoDuplicate);
+
+        ic.dAtoms = {};
+        ic.hAtoms = {};
+        //  ic.ssbondpnts = {};
+        let chainIdHash = {};
+
+        for (const name in nameArray) {
+          for (const key in ic.chains) {
+            if (key.includes(nameArray[name])) {
+              chainIdHash[key] = 1;
+              if (ic.chains.hasOwnProperty(key)) {
+                const innerDict = ic.chains[key];
+                for (const innerKey in innerDict) {
+                  if (innerDict.hasOwnProperty(innerKey)) {
+                    ic.dAtoms[innerKey] = innerDict[innerKey];
+                    ic.hAtoms[innerKey] = innerDict[innerKey];
+                  }
+                }
+              }
+            }
+          }
+        }
+
+        ic.transformCls.zoominSelection();
+        ic.definedSetsCls.showSets();
+
+
+        await ic.drawCls.draw();
+        ic.saveFileCls.showTitle();
+
+        me.htmlCls.clickMenuCls.setLogCmd(
+          "select structure " + "[" + nameStructure + "]",
+          true
+        );
+        ic.bSelectResidue = false;
+      }
+    });
+
+    me.myEventCls.onIds(
+      "#" + ic.pre + "collections_menu",
+      "focus",
+      function (e) {
+        let ic = thisClass.icn3d;
+        if (me.utilsCls.isMobile())
+          $("#" + ic.pre + "collections_menu").val("");
+      }
+    );
+  }
+}
+
 /**
  * @author Jiyao Wang <wangjiy@ncbi.nlm.nih.gov> / https://github.com/ncbi/icn3d
  */
@@ -73853,7 +74063,8 @@ class iCn3D {
     this.setSeqAlignCls = new SetSeqAlign(this);
 
     this.applyCommandCls = new ApplyCommand(this);
-    this.definedSetsCls = new DefinedSets(this);
+      this.definedSetsCls = new DefinedSets(this);
+      this.selectCollectionsCls = new SelectCollections(this);
     this.legendTableCls = new LegendTable(this);
     this.loadScriptCls = new LoadScript(this);
     this.selByCommCls = new SelectByCommand(this);
@@ -74100,7 +74311,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.29.0';
+    this.REVISION = '3.29.1';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -74326,7 +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);
         }