icn3d 3.28.5 → 3.28.6

package/README.md

@@ -52,7 +52,7 @@ Usage
 		import * as icn3d from 'icn3d/module'
 		import "../node_modules/icn3d/css/icn3d.css"
 
-		function Icn3dViewer() {
+		async function Icn3dViewer() {
 			useEffect(() => {
 				const cfg = {
 					divid: 'viewer',
@@ -60,7 +60,7 @@ Usage
 				};
 				cfg['mmdbid'] = '1tup';
 				const icn3dui = new icn3d.iCn3DUI(cfg);
-				icn3dui.show3DStructure();
+				await icn3dui.show3DStructure();
 			}, []);
 			return <div id="viewer"></div>;
 		}
@@ -73,5 +73,5 @@ Usage
     
     	var cfg = {'mmdbid': '1tup'};
     	var icn3dui = new icn3d.iCn3DUI(cfg);
-    	icn3dui.show3DStructure();
+    	await icn3dui.show3DStructure();
 

package/icn3d.js

@@ -5765,7 +5765,7 @@ class ClickMenu {
                     continue;
             }
 
-            if(id == 'mn1_searchstru') {
+            if(id == 'mn1_searchgrooup') {
                 html += "<td valign='top'>";
             }
             else if(id == 'mn2_definedsets') {
@@ -8527,12 +8527,12 @@ class SetMenu {
         //html += this.getMenuText('mn1_fold', 'AlphaFold/ESM', undefined, undefined, 1);
         html += this.getMenuText('mn1_fold', 'Predict by Seq.', undefined, undefined, 1);
         html += "<ul>";
-        html += this.getLink('mn1_esmfold', 'ESMFold', undefined, 2);
-        html += this.getLink('mn1_alphafold', 'AlphaFold2 via ColabFold', undefined, 2);
+        //html += this.getLink('mn1_esmfold', 'ESMFold', undefined, 2);
+        html += this.getMenuUrl('mn1_esmfold_link', "https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/ESMFold.ipynb", "ESMFold via ColabFold" + me.htmlCls.wifiStr, undefined, 2);
+        html += this.getLink('mn1_alphafold', 'AlphaFold2 via ColabFold' + me.htmlCls.wifiStr, undefined, 2);
         html += "</ul>";
 
         
-
         html += this.getMenuText('mn1_alignwrap', 'Align', undefined, 1, 1);
         html += "<ul>";
         
@@ -9771,7 +9771,7 @@ class SetMenu {
         html += this.getMenuUrl('abouticn3d', me.htmlCls.baseUrl + "icn3d/icn3d.html#about", "About iCn3D<span style='font-size:0.9em'> " + me.REVISION + "</span>", 1, 1);
 
         html += this.getMenuUrl('gallery', me.htmlCls.baseUrl + "icn3d/icn3d.html#gallery", "Live Gallery " + me.htmlCls.wifiStr, 1, 1);
-        html += this.getMenuUrl('video', me.htmlCls.baseUrl + "icn3d/icn3d.html#videos", "iCn3D Videos", 1, 1);
+        html += this.getMenuUrl('video', me.htmlCls.baseUrl + "icn3d/icn3d.html#videos", "Videos & Tutorials", 1, 1);
 
         html += this.getMenuText('mn6_faq', 'FAQ', undefined, 1, 1);
 
@@ -10588,7 +10588,7 @@ class SetDialog {
         html += 'Note: <b>VAST</b> identifies 3D domains (substructures) within each protein structure in the Molecular Modeling Database (MMDB), and then finds other protein structures that have one or more similar 3D domains, using purely geometric criteria. You have two ways to do a VAST search.<br><br>'; 
 
         html += '<b>Option 1</b>, search with your selection (all residues are selected by default) in the loaded structures:<br>'; 
-        html += '<form method=post enctype=multipart/form-data action="https://www.ncbi.nlm.nih.gov/Structure/vast/VSMmdb.cgi" id="' + me.pre + 'newvs2" name="newvs2" target="_blank">';
+        html += '<form data-ncbi-sg-search="true" method=post enctype=multipart/form-data action="https://www.ncbi.nlm.nih.gov/Structure/vast/VSMmdb.cgi" id="' + me.pre + 'newvs2" name="newvs2" target="_blank">';
         html += '<input type=hidden id="' + me.pre + 'pdbstr" name="pdbstr">';
         html += "Searching against: <input type='radio' name='dataset' value='Non-redundant subset' checked> Medium-redundancy Subset of PDB <a href='https://www.ncbi.nlm.nih.gov/Structure/VAST/vasthelp.html#VASTNR' title='Medium-redundancy Subset' target='_blank'>?</a> <input type='radio' name='dataset' value='All'>All of PDB <br>";
         // the submit value has to be "Submit" in order to make the backend cgi works
@@ -10602,12 +10602,12 @@ class SetDialog {
         html += me.htmlCls.buttonStr + "reload_vast'>VAST</button><br><br>";
 
         html += '<b>Option 3</b>, search with a PDB file:<br>'; 
-        html += '<form method=post enctype=multipart/form-data action="https://www.ncbi.nlm.nih.gov/Structure/vast/VSMmdb.cgi" id="' + me.pre + 'newvs" name="newvs" target="_blank">';
+        html += '<form data-ncbi-sg-search="true" method=post enctype=multipart/form-data action="https://www.ncbi.nlm.nih.gov/Structure/vast/VSMmdb.cgi" id="' + me.pre + 'newvs" name="newvs" target="_blank">';
         html += "PDB File: " + me.htmlCls.inputFileStr + " name='pdbfile' size=8><br>";
         html += "Searching against: <input type='radio' name='dataset' value='Non-redundant subset' checked> Medium-redundancy Subset of PDB <a href='https://www.ncbi.nlm.nih.gov/Structure/VAST/vasthelp.html#VASTNR' title='Medium-redundancy Subset' target='_blank'>?</a> <input type='radio' name='dataset' value='All'>All of PDB <br>";
         // the submit value has to be "Submit" in order to make the backend cgi works
         //html += '<input type="submit" name="' + me.pre + 'cmdVSMmdb" value="VAST Search"></input>';
-        html += '<input type="submit" name="cmdVSMmdb" value="Submit"></input>';
+        html += '<input type="submit" id="' + me.pre + 'cmdVSMmdb" name="cmdVSMmdb" value="Submit"></input>';
         html += "</form><br>";
 
         html += "</div>";
@@ -10843,7 +10843,7 @@ class SetDialog {
         html += me.htmlCls.divStr + "dl_mmdbid' class='" + dialogClass + "' style='max-width:500px'>";
         html += this.addNotebookTitle('dl_mmdbid', 'Please input an MMDB ID');
         html += "MMDB or PDB ID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "mmdbid' value='1TUP' size=8> <br><br>";
-        html += me.htmlCls.buttonStr + "reload_mmdb_asym'>Load Asymmetric Unit (All Chains)</button>" + me.htmlCls.buttonStr + "reload_mmdb' style='margin-left:30px'>Load Biological Unit</button><br/><br/><br>";
+        html += me.htmlCls.buttonStr + "reload_mmdb'>Load Biological Unit</button>" + me.htmlCls.buttonStr + "reload_mmdb_asym' style='margin-left:30px'>Load Asymmetric Unit (All Chains)</button><br/><br/><br/>";
         html += '<b>Note</b>: The "<b>biological unit</b>" is the <b>biochemically active form of a biomolecule</b>, <div style="width:20px; margin:6px 0 0 20px; display:inline-block;"><span id="'
           + me.pre + 'asu_bu_expand" class="ui-icon ui-icon-plus icn3d-expand icn3d-link" style="width:15px;" title="Expand"></span><span id="'
           + me.pre + 'asu_bu_shrink" class="ui-icon ui-icon-minus icn3d-shrink icn3d-link" style="display:none; width:15px;" title="Shrink"></span></div>';
@@ -14803,7 +14803,7 @@ class SetHtml {
         if(selType) me.htmlCls.allMenusSel[id] = selType;
         if(bSimpleMenu) me.htmlCls.simpleMenus[id] = 1;
 
-        return "<li><span id='" + me.pre + id + "' class='icn3d-link'>" + text + "</span></li>";
+        return "<li><span data-pinger id='" + me.pre + id + "' class='icn3d-link'>" + text + "</span></li>";
     }
 
     // a group of menus
@@ -14815,7 +14815,7 @@ class SetHtml {
         let styleStr = (classname == 'icn3d-menupd') ? " style='padding-left:1.5em!important;'" : "";
 
         // no ending "</li>"" since this is usually the start of a group of menus
-        return "<li><span id='" + me.pre + id + "'" + styleStr + ">" + text + "</span>"; 
+        return "<li><span data-pinger id='" + me.pre + id + "'" + styleStr + ">" + text + "</span>"; 
     }
 
     getMenuUrl(id, url, text, bSimpleMenu, selType) { let me = this.icn3dui; me.icn3d;
@@ -14836,7 +14836,7 @@ class SetHtml {
         if(bSimpleMenu) me.htmlCls.simpleMenus[id] = 1;
 
         let hideStr = (bHide) ? ' style="display:none"' : '';
-        return "<li id='" + me.pre + wrapper + "'" + hideStr + "><span id='" + me.pre + id + "' class='icn3d-link'>" + text + "</span></li>";
+        return "<li id='" + me.pre + wrapper + "'" + hideStr + "><span data-pinger id='" + me.pre + id + "' class='icn3d-link'>" + text + "</span></li>";
     }
 
     getLinkWrapper2(id, text, wrapper, bSimpleMenu, selType) { let me = this.icn3dui; me.icn3d;
@@ -14844,7 +14844,7 @@ class SetHtml {
         if(selType) me.htmlCls.allMenusSel[id] = selType;
         if(bSimpleMenu) me.htmlCls.simpleMenus[id] = 1;
 
-        return "<li id='" + me.pre + wrapper + "'><span id='" + me.pre + id + "' class='icn3d-link'>" + text + "</span>";
+        return "<li id='" + me.pre + wrapper + "'><span data-pinger id='" + me.pre + id + "' class='icn3d-link'>" + text + "</span>";
     }
 
     getRadio(radioid, id, text, bChecked, bSimpleMenu, selType) { let me = this.icn3dui; me.icn3d;
@@ -14855,8 +14855,7 @@ class SetHtml {
         let checkedStr =(bChecked) ? ' checked' : '';
 
         //https://stackoverflow.com/questions/17541614/use-images-instead-of-radio-buttons/17541916
-        //return "<li><label for='" + me.pre + id + "' class='icn3d-rad'>" + me.htmlCls.inputRadioStr + "name='" + me.pre + radioid + "' " + "class='" + me.pre + radioid + "' " + "v='" + text + "' id='" + me.pre + id + "'" + checkedStr + "><span class='ui-icon ui-icon-blank'></span> <span class='icn3d-rad-text'>" + text + "</span></label></li>";
-        return "<li><label id='" + me.pre + id + "' class='icn3d-rad'>" + me.htmlCls.inputRadioStr + "name='" + me.pre + radioid + "' " + "class='" + me.pre + radioid + "' " + "v='" + text + "'" + checkedStr + "><span class='ui-icon ui-icon-blank'></span> <span class='icn3d-rad-text'>" + text + "</span></label></li>";
+        return "<li><label data-pinger id='" + me.pre + id + "' class='icn3d-rad'>" + me.htmlCls.inputRadioStr + "name='" + me.pre + radioid + "' " + "class='" + me.pre + radioid + "' " + "v='" + text + "'" + checkedStr + "><span class='ui-icon ui-icon-blank'></span> <span class='icn3d-rad-text'>" + text + "</span></label></li>";
     }
 
     getRadioColor(radioid, id, text, color, bChecked, bSimpleMenu, selType) { let me = this.icn3dui; me.icn3d;
@@ -14867,8 +14866,7 @@ class SetHtml {
         let checkedStr =(bChecked) ? ' checked' : '';
 
         //https://stackoverflow.com/questions/17541614/use-images-instead-of-radio-buttons/17541916
-        //return "<li><label for='" + me.pre + id + "' class='icn3d-rad'>" + me.htmlCls.inputRadioStr + "name='" + me.pre + radioid + "' id='" + me.pre + id + "'" + checkedStr + "><span class='ui-icon ui-icon-blank'></span> <span class='icn3d-color-rad-text' color='" + color + "'><span style='background-color:#" + color + "'>" + me.htmlCls.space3 + "</span> " + text + "</span></label></li>";
-        return "<li><label id='" + me.pre + id + "' class='icn3d-rad'>" + me.htmlCls.inputRadioStr + "name='" + me.pre + radioid + "'" + checkedStr + "><span class='ui-icon ui-icon-blank'></span> <span class='icn3d-color-rad-text' color='" + color + "'><span style='background-color:#" + color + "'>" + me.htmlCls.space3 + "</span> " + text + "</span></label></li>";
+        return "<li><label data-pinger id='" + me.pre + id + "' class='icn3d-rad'>" + me.htmlCls.inputRadioStr + "name='" + me.pre + radioid + "'" + checkedStr + "><span class='ui-icon ui-icon-blank'></span> <span class='icn3d-color-rad-text' color='" + color + "'><span style='background-color:#" + color + "'>" + me.htmlCls.space3 + "</span> " + text + "</span></label></li>";
     }
 
     setAdvanced(index) { let me = this.icn3dui; me.icn3d;
@@ -35922,7 +35920,7 @@ class AnnoCddSite {
         //if(me.cfg.afid) {
 
         // use precalculated CDD annotation if
-        if( (Object.keys(ic.structures).length == 1 && (me.cfg.mmtfid || me.cfg.pdbid || me.cfg.opmid || me.cfg.mmdbid || me.cfg.gi || me.cfg.uniprotid || me.cfg.blast_rep_id || me.cfg.cid || me.cfg.mmcifid))
+        if( (Object.keys(ic.structures).length == 1 && !me.cfg.afid && (me.cfg.mmtfid || me.cfg.pdbid || me.cfg.opmid || me.cfg.mmdbid || me.cfg.gi || me.cfg.uniprotid || me.cfg.blast_rep_id || me.cfg.cid || me.cfg.mmcifid))
             || (Object.keys(ic.structures).length == 2 && me.cfg.align) ) {
                 let data = {};
                 try {
@@ -39759,7 +39757,7 @@ class AddTrack {
         if(exonArray) {
             for(let j = 0, jl = exonArray.length; j < jl; ++j) {
                 let start = exonArray[j].resStart, end = exonArray[j].resEnd;
-                let genStart = exonArray[j].genomeRange.split('-')[0];
+                let genStart = parseInt(exonArray[j].genomeRange.split('-')[0]);
 
                 for(let k = 0, kl = end - start + 1; k < kl; ++k) {
                     let colorStr = this.getExonColor(start, end, cnt);
@@ -42024,7 +42022,7 @@ class ShowAnno {
                 url = "https://rest.uniprot.org/uniprotkb/search?format=json&fields=xref_geneid,gene_names&query=" + structure;
                 let geneData = await me.getAjaxPromise(url, 'json');
                 let geneId = (geneData.results[0] && geneData.results[0].uniProtKBCrossReferences && geneData.results[0].uniProtKBCrossReferences[0]) ? geneData.results[0].uniProtKBCrossReferences[0].id : undefined;
-                let geneSymbol = (geneData.results[0] && geneData.results[0].genes && geneData.results[0].genes[0] && geneData.results[0].genes[0].geneName) ? geneData.results[0].genes[0].geneName.value : undefined;
+                let geneSymbol = (geneData.results[0] && geneData.results[0].genes && geneData.results[0].genes[0] && geneData.results[0].genes[0].geneName) ? geneData.results[0].genes[0].geneName.value : 'ID ' + geneId;
                 ic.chainsGene[chnid] = {geneId: geneId, geneSymbol: geneSymbol};
             }
         }
@@ -50386,7 +50384,7 @@ class MmdbParser {
         if(Object.keys(data.atoms).length == 0) { // for large structures such as 3J3Q
             // use mmtfid
             let pdbid = data.pdbId;
-            ic.mmtfParserCls.downloadMmtf(pdbid);
+            await ic.mmtfParserCls.downloadMmtf(pdbid);
 
             return;
         }
@@ -50778,7 +50776,7 @@ class MmdbParser {
             url = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&bu=" + me.cfg.bu + "&simple=1&uid=" + mmdbid;
         }
 
-        // use asymmetric unit for BLAST search, e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?from=blast&blast_rep_id=5XZC_B&query_id=1TUP_A&command=view+annotations;set+annotation+cdd;set+annotation+site;set+view+detailed+view;select+chain+5XZC_B;show+selection&log$=align&blast_rank=1&RID=EPUCYNVV014&bu=0
+        // use asymmetric unit for BLAST search, e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/?from=blast&blast_rep_id=5XZC_B&query_id=1TUP_A&command=view+annotations;set+annotation+cdd;set+annotation+site;set+view+detailed+view;select+chain+5XZC_B;show+selection&log$=align&blast_rank=1&RID=EPUCYNVV014&bu=0
         if(me.cfg.blast_rep_id !== undefined) url += '&bu=0';
 
         //ic.bCid = undefined;
@@ -50810,57 +50808,31 @@ class MmtfParser {
 
     //MMTF is a new binary data format besides the previous PDB and mmCIF formats for 3D structures.
     //The JavaScript Methods at http://mmtf.rcsb.org/ was used to load and parse the data.
-    downloadMmtf(mmtfid) { let ic = this.icn3d; ic.icn3dui;
+    async downloadMmtf(mmtfid) { let ic = this.icn3d, me = ic.icn3dui;
         ic.ParserUtilsCls.setYourNote(mmtfid.toUpperCase() + '(MMTF) in iCn3D');
         //ic.bCid = undefined;
 
-        MMTF.fetchReduced(
-            mmtfid,
-            // onLoad callback
-            async function( mmtfData ){
-                if(mmtfData.numAtoms * 10 > ic.maxatomcnt) {
-                    let bFull = false;
-                    if(Object.keys(mmtfData).length == 0) {
-                        var aaa = 1; //alert('This PDB structure is not found at RCSB...');
-                        return;
-                    }
+        let mmtfData = await me.getMmtfReducedPromise(mmtfid);
+        if(mmtfData.numAtoms * 10 > ic.maxatomcnt) {
+            let bFull = false;
+            if(Object.keys(mmtfData).length == 0) {
+                var aaa = 1; //alert('This PDB structure is not found at RCSB...');
+                return;
+            }
 
-                    await ic.opmParserCls.loadOpmData(mmtfData, mmtfid, bFull, 'mmtf');
-                }
-                else {
-                    mmtfData = null;
-
-                    MMTF.fetch(
-                        mmtfid,
-                        // onLoad callback
-                        async function( mmtfData2 ){
-                            let bFull = true;
-                            if(Object.keys(mmtfData2).length == 0) {
-                                var aaa = 1; //alert('This PDB structure is not found at RCSB...');
-                                return;
-                            }
-                            // ic.deferredOpm = $.Deferred(function() {
-                            //     ic.opmParserCls.loadOpmData(mmtfData2, mmtfid, bFull, 'mmtf');
-                            // });
-
-                            // return ic.deferredOpm.promise();
-
-                            await ic.opmParserCls.loadOpmData(mmtfData2, mmtfid, bFull, 'mmtf');
-                        },
-                        // onError callback
-                        function( error ){
-                            //var aaa = 1; //alert('This PDB structure is not found at RCSB...');
-                            //console.error( error )
-                        }
-                    );
-                }
-            },
-            // onError callback
-            function( error ){
-                //var aaa = 1; //alert('This PDB structure is not found at RCSB...');
-                //console.error( error )
+            await ic.opmParserCls.loadOpmData(mmtfData, mmtfid, bFull, 'mmtf');
+        }
+        else {
+            let mmtfData2 = await me.getMmtfPromise(mmtfid);
+
+            let bFull = true;
+            if(Object.keys(mmtfData2).length == 0) {
+                var aaa = 1; //alert('This PDB structure is not found at RCSB...');
+                return;
             }
-        );
+
+            await ic.opmParserCls.loadOpmData(mmtfData2, mmtfid, bFull, 'mmtf');
+        }
     }
 
     async parseMmtfData(mmtfData, mmtfid, bFull) { let ic = this.icn3d, me = ic.icn3dui;
@@ -58745,7 +58717,6 @@ class ApplyCommand {
       let command = commandOri.toLowerCase();
 
     // exact match =============
-
       //var file_pref =(ic.inputid) ? ic.inputid : "custom";
       if(command == 'share link') {
         await ic.shareLinkCls.shareLink();
@@ -61659,6 +61630,7 @@ class LoadScript {
         ic.inputid = id;
         if(command.indexOf('load mmtf') !== -1) {
           me.cfg.mmtfid = id;
+          
           await ic.mmtfParserCls.downloadMmtf(id);
         }
         else if(command.indexOf('load pdb') !== -1) {
@@ -69405,7 +69377,8 @@ class ShareLink {
         let url = this.shareLinkUrl();
 
         let bTooLong =(url.length > 4000 || url.indexOf('http') !== 0) ? true : false;
-        if(bPngHtml) url += "&random=" + parseInt(Math.random() * 1000); // generate a new shorten URL and thus image name everytime
+        //if(bPngHtml) url += "&random=" + parseInt(Math.random() * 1000); // generate a new shorten URL and thus image name everytime
+        
         //var inputid =(ic.inputid) ? ic.inputid : "custom";
         let inputid = Object.keys(ic.structures).join('_');
         if(inputid == ic.defaultPdbId) {
@@ -69513,7 +69486,7 @@ class ShareLink {
     }
 
     shareLinkUrl(bAllCommands, bOutputCmd) { let ic = this.icn3d, me = ic.icn3dui;
-           let url = me.htmlCls.baseUrl + "icn3d/full.html?";
+           let url = me.htmlCls.baseUrl + "icn3d/?";
            let outputCmd = '';
            if(me.cfg.bSidebyside) url = me.htmlCls.baseUrl + "icn3d/full2.html?";
 
@@ -72578,7 +72551,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.28.0';
+    this.REVISION = '3.28.1';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -73065,6 +73038,40 @@ iCn3DUI.prototype.setIcn3d = function() { let me = this;
     me.setDialogAjax();
 };
 
+iCn3DUI.prototype.getMmtfPromise = function(mmtfid) {    return new Promise(function(resolve, reject) {
+        MMTF.fetch(
+            mmtfid,
+            // onLoad callback
+            async function( mmtfData ){
+                resolve(mmtfData);
+            },
+            // onError callback
+            function( error ){
+                //var aaa = 1; //alert('This PDB structure is not found at RCSB...');
+                //console.error( error )
+                reject('error');
+            }
+        );
+    });
+};
+
+iCn3DUI.prototype.getMmtfReducedPromise = function(mmtfid) {    return new Promise(function(resolve, reject) {
+        MMTF.fetchReduced(
+            mmtfid,
+            // onLoad callback
+            async function( mmtfData ){
+                resolve(mmtfData);
+            },
+            // onError callback
+            function( error ){
+                //var aaa = 1; //alert('This PDB structure is not found at RCSB...');
+                //console.error( error )
+                reject('error');
+            }
+        );
+    });
+};
+
 iCn3DUI.prototype.getAjaxPromise = function(url, dataType, beforeSend, alertMess, logMess, complete, bNode) { let me = this;
     // if(!bNode || dataType != 'json') {
         return new Promise(function(resolve, reject) {