icn3d 3.45.7 → 3.46.1

package/css/icn3d.css

@@ -53,10 +53,15 @@
     background: #eee;
     color: #333;
 }
-
+/*
 .icn3d-menu .ui-menu-icons .ui-menu-item-wrapper, .ui-menu-icons .ui-menu-item {
     padding-left: 0.4em!important;
 }
+*/
+
+.ui-menu-icons .ui-menu-item-wrapper, .ui-menu-icons .ui-menu-item {
+    padding-left: 3px!important;
+}
 
 .icn3d-text {font-family: Verdana, Arial, Helvetica, sans-serif; font-size:12px!important;}
 

package/icn3d.js

@@ -56277,7 +56277,8 @@ class ClickMenu {
             else if(id == 'mn6_selectannotations') {
                 html += "</td><td valign='top'>";
             }
-            else if(id == 'abouticn3d') {
+            //!!!else if(id == 'abouticn3d') {
+            else if(id == 'ai_help') {
                 html += "</td><td valign='top'>";
             }
 
@@ -58900,6 +58901,8 @@ class SetMenu {
         html += tdStr + "<div style='position:relative; margin-left:6px;'>" + str1;
         html += "<div class='icn3d-commandTitle' style='min-width:40px; margin-top: 3px; white-space: nowrap;'>" + str2;
 
+        html += tdStr + '<div class="icn3d-commandTitle" style="white-space:nowrap; margin-top:10px; border-left:solid 1px #888888">' + me.htmlCls.space2 + '<a href="https://vizomics.org/ai-tutor" target="_blank" style="color:#f8b84e" title="AI Tutor shows step-by-step instructions about how to build a custom view">AI Tutor</a>' + me.htmlCls.space2 + '</div></td>';
+
         html += tdStr + '<div class="icn3d-commandTitle" style="white-space:nowrap; margin-top:10px; border-left:solid 1px #888888"><span id="' + me.pre +  'selection_expand" class="icn3d-expand icn3d-link" style="display:block;" title="Expand">' + me.htmlCls.space2 + 'Toolbar <span class="ui-icon ui-icon-plus" style="width:15px"></span>' + me.htmlCls.space2 + '</span><span id="' + me.pre +  'selection_shrink" class="icn3d-shrink icn3d-link" style="display:none;" title="Shrink">' + me.htmlCls.space2 + 'Toolbar <span class="ui-icon ui-icon-minus" style="width:15px"></span>' + me.htmlCls.space2 + '</span></div></td>';
 
         html += tdStr + '<div class="icn3d-commandTitle" style="white-space:nowrap; margin-top:8px; border-left:solid 1px #888888">' + me.htmlCls.space2 + '<input type="text" id="' + me.pre + 'search_seq" size="10" placeholder="one-letter seq."> <button style="white-space:nowrap;" id="' + me.pre + 'search_seq_button">Search</button> <a style="text-decoration: none;" href="' + me.htmlCls.baseUrl + 'icn3d/icn3d.html#selectb" target="_blank" title="Specification tips">?</a></div></td>';
@@ -59030,6 +59033,8 @@ class SetMenu {
         html += "<li><div style='position:relative; margin-top:-6px;'>" + str1;
         html += "<div class='icn3d-commandTitle' style='margin-top: 3px; white-space: nowrap;'>" + str2;
 
+        html += "<li><a href='https://vizomics.org/ai-tutor' target='_blank' id='" + me.pre + "ai_help' class='icn3d-menu-color' style='color:#f8b84e' title='shows step-by-step instructions about how to build a custom view'>AI Tutor</a>";
+
         //if(me.cfg.align !== undefined) {
             html += "<li><span id='" + me.pre + "alternate2' class='icn3d-menu-color' title='Alternate the structures'>Alternate</span>";
         //}
@@ -59911,7 +59916,7 @@ class SetMenu {
         }
         else {
             html += this.getRadio('mn3_lig', 'mn3_ligStick', 'Stick', undefined, 1, 2);
-            html += this.getRadio('mn3_lig', 'mn3_ligBallstick', 'BalHydrogensl and Stick', true, 1, 2);
+            html += this.getRadio('mn3_lig', 'mn3_ligBallstick', 'Ball and Stick', true, 1, 2);
         }
         html += this.getRadio('mn3_lig', 'mn3_ligSchematic', 'Schematic', undefined, 1, 2);
         html += this.getRadio('mn3_lig', 'mn3_ligSphere', 'Sphere', undefined, 1, 2);
@@ -60702,6 +60707,9 @@ class SetMenu {
 
         html += "<ul class='icn3d-mn-item'>";
 
+        //!!!
+        html += this.getMenuUrl('ai_help', "https://vizomics.org/ai-tutor", "AI Tutor" + me.htmlCls.wifiStr, 1, 1);
+
         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);
@@ -60757,7 +60765,7 @@ class SetMenu {
         html += "</ul>";
         html += "</li>";
 
-        html += this.getMenuUrl('helpdoc', me.htmlCls.baseUrl + "icn3d/docs/icn3d_help.html", "Help Doc " + me.htmlCls.wifiStr, 1, 1);
+        // html += this.getMenuUrl('helpdoc', me.htmlCls.baseUrl + "icn3d/docs/icn3d_help.html", "Help Doc " + me.htmlCls.wifiStr, 1, 1);
 
         html += this.getMenuSep();
 
@@ -66821,6 +66829,8 @@ class SetHtml {
         if(selType) me.htmlCls.allMenusSel[id] = selType;
         if(bSimpleMenu) me.htmlCls.simpleMenus[id] = 1;
 
+        if(id == 'ai_help') text = "<span style='color:#f8b84e'>" + text + "</span>";
+
         return "<li><a id='" + me.pre + id + "' href='" + url + "' target='_blank'>" + text + "</a></li>";
     }
 
@@ -67732,6 +67742,9 @@ class SetHtml {
             let file_pref = Object.keys(me.utilsCls.getHlStructures()).join(',');
             ic.saveFileCls.saveFile(file_pref + '_icn3d.pdb', 'text', [pdbStr]);
         }
+        else {
+            console.log(pdbStr);
+        }
         
         return pdbStr;
     }
@@ -67745,6 +67758,9 @@ class SetHtml {
             let file_pref = Object.keys(me.utilsCls.getHlStructures()).join(',');
             ic.saveFileCls.saveFile(file_pref + '_icn3d_ss.txt', 'text', [secondaryStr]);
         }
+        else {
+            console.log(secondaryStr);
+        }
         
         return secondaryStr;
     }
@@ -74149,20 +74165,20 @@ class Scene {
         if(options === undefined) options = ic.opts;
 
         // whether camera was set
-        me.bCamera = (ic.cam) ? true : false;
+        // me.bCamera = (ic.cam) ? true : false;
 
         this.rebuildSceneBase(options);
 
         ic.fogCls.setFog();
 
-        if(!ic.cam || ic.bChangeCamera) {
-            ic.cameraCls.setCamera();
+        // if(!ic.cam || ic.bChangeCamera) {
+            if(!ic.bNotSetCamera) ic.cameraCls.setCamera();
             // set the ratio for view point, which was set in ic.transformCls.resetOrientation_base
             if(!ic.container.whratio) {
                 ic.container.whratio = me.htmlCls.WIDTH / me.htmlCls.HEIGHT; 
                 ic.cam.aspect = ic.container.whratio;
             }
-        }
+        // }
 
         if(ic.opts['slab'] === 'yes') ic.cameraCls.setSlab();
 
@@ -74345,17 +74361,17 @@ class Scene {
             }
         }
 
-        if(!ic.perspectiveCamera) {
+        // if(!ic.perspectiveCamera) {
             ic.perspectiveCamera = new PerspectiveCamera$1(20, ic.container.whratio, 0.1, 10000);
             ic.perspectiveCamera.position.set(0, 0, ic.cam_z);
             ic.perspectiveCamera.lookAt(new Vector3$1(0, 0, 0));
-        }
+        // }
 
-        if(!ic.orthographicCamera) {
+        // if(!ic.orthographicCamera) {
             ic.orthographicCamera = new OrthographicCamera$1();
             ic.orthographicCamera.position.set(0, 0, ic.cam_z);
             ic.orthographicCamera.lookAt(new Vector3$1(0, 0, 0));
-        }
+        // }
 
         ic.cams = {
             perspective: ic.perspectiveCamera,
@@ -74538,10 +74554,10 @@ class Scene {
 
         if(!me.bNode) {
             $("#" + me.pre + "VRButton").remove();
-            $("#" + me.pre + "viewer").get(0).appendChild( ic.VRButtonCls.createButton( ic.renderer ) );
+            if($("#" + me.pre + "viewer").get(0)) $("#" + me.pre + "viewer").get(0).appendChild( ic.VRButtonCls.createButton( ic.renderer ) );
 
             $("#" + me.pre + "ARButton").remove();
-            $("#" + me.pre + "viewer").get(0).appendChild( ic.ARButtonCls.createButton( ic.renderer ) );
+            if($("#" + me.pre + "viewer").get(0)) $("#" + me.pre + "viewer").get(0).appendChild( ic.ARButtonCls.createButton( ic.renderer ) );
         }
     }
 
@@ -86369,7 +86385,7 @@ class Alternate {
             }
             
             ic.bShowHighlight = false;
-            ic.opts['rotationcenter'] = 'highlight center';
+//            ic.opts['rotationcenter'] = 'highlight center';
         }
 
         // also alternating the surfaces
@@ -86409,9 +86425,20 @@ class Alternate {
 
         //ic.glycanCls.showGlycans();
 
-        // ic.opts['rotationcenter'] = 'highlight center';
-        
+        // ic.opts['rotationcenter'] = 'highlight center';              
+
+        // zoomin at the beginning
+
+        if(ic.ALTERNATE_STRUCTURE == 0) { // default -1, so when it is 0, it is the first time
+            ic.transformCls.zoominSelection();
+        }
+
+        //ic.transformCls.resetOrientation(); // reset camera view point
+        // ic.drawCls.applyTransformation(ic._zoomFactor, ic.mouseChange, ic.quaternion);
+
+        // ic.bNotSetCamera = true;
         ic.drawCls.draw();
+        // ic.bNotSetCamera = false;
 
         ic.bShowHighlight = true; //reset
     }
@@ -90823,17 +90850,17 @@ class AnnoPTM {
         else if( structure.length > 5 ) {
             let url =  "https://www.ebi.ac.uk/proteins/api/features/" + structure; 
             let data;
-            try {
+            // try {
                 data = await me.getAjaxPromise(url, 'json');
 
                 thisClass.parsePTM(data, chnid, type);
                 /// if(ic.deferredPTM !== undefined) ic.deferredPTM.resolve();
-            }
-            catch {
-                thisClass.getNoPTM(chnid, type);
+            // }
+            // catch {
+            //     thisClass.getNoPTM(chnid, type);
 
-                return;
-            }
+            //     return;
+            // }
         }
         else { // PDB
             // get PDB to UniProt mapping
@@ -90843,15 +90870,13 @@ class AnnoPTM {
             let urlMap = "https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/" + structLower;
 
             let dataMap;
-            try {
+            // try {
                 dataMap = await me.getAjaxPromise(urlMap, 'json');
 
                 let UniProtID = '';
                 if(!ic.UPResi2ResiPosPerChain) ic.UPResi2ResiPosPerChain = {};
                 ic.UPResi2ResiPosPerChain[chnid] = {};
                 let mapping = dataMap[structLower].UniProt;
-
-                let bFound = false;
                 for(let up in mapping) {
                     let chainArray = mapping[up].mappings;
                     //if(bFound) break;
@@ -90874,7 +90899,6 @@ class AnnoPTM {
                             }
 
                             if(UniProtID == '' || UniProtID.length != 6) UniProtID = up;
-                            bFound = true;
                             //break;
                         }
                     }
@@ -90894,24 +90918,24 @@ class AnnoPTM {
                         
                         let url =  "https://www.ebi.ac.uk/proteins/api/features/" + UniProtID;     
                         let data;
-                        try {
+                        // try {
                             data = await me.getAjaxPromise(url, 'json');
                             ic.annoPtmData[UniProtID] = data;
 
                             thisClass.parsePTM(data, chnid, type);
                             /// if(ic.deferredPTM !== undefined) ic.deferredPTM.resolve();
-                        }
-                        catch(err) {
-                            thisClass.getNoPTM(chnid, type);
-                            return;
-                        }
+                        // }
+                        // catch(err) {
+                        //     thisClass.getNoPTM(chnid, type);
+                        //     return;
+                        // }
                     }
                 }
-            }
-            catch(err) {
-                thisClass.getNoPTM(chnid, type);
-                return;
-            }
+            // }
+            // catch(err) {
+            //     thisClass.getNoPTM(chnid, type);
+            //     return;
+            // }
         }
     }
 
@@ -90978,7 +91002,7 @@ class AnnoPTM {
         html += '<div id="' + ic.pre + chnid + '_' + type + 'seq_sequence" class="icn3d-cdd icn3d-dl_sequence">';
         html2 += html;
         html3 += html;
-        chnid.substr(0, chnid.indexOf('_'));
+        let structure = chnid.substr(0, chnid.indexOf('_'));
 
         for(let ptm in ptmHash) {
             let ptmArray = ptmHash[ptm];
@@ -90990,7 +91014,7 @@ class AnnoPTM {
                 let end = parseInt(ptmArray[i].end);
 
                 for(let j = begin; j <= end; ++j) {
-                    if(stucture.length > 5) { // UniProt
+                    if(structure.length > 5) { // UniProt
                         resPosArray.push(j - 1); // 0-based
                     } 
                     else { // PDB                       
@@ -96104,6 +96128,7 @@ class AddTrack {
         for(let j = 0, jl = trackSeqArray.length; j < jl; ++j) {
             let resi = startpos;
             let text = '';
+  
             for(let k = 0; k < ic.startposGiSeq; ++k) {
                 if(ic.targetGapHash.hasOwnProperty(k)) {
                     for(let m = 0; m < ic.targetGapHash[k].to - ic.targetGapHash[k].from + 1; ++m) {
@@ -97199,6 +97224,8 @@ class ShowAnno {
         let chemical_chainid = result.chemical_chainid;
         let chemical_set = result.chemical_set;
 
+        let bAnnoShownPrev = ic.bAnnoShown;
+
         if(!ic.bAnnoShown || ic.bResetAnno) { // ic.bResetAnno when loading another structure
             // assign early to avoid load annotations twice
             ic.bAnnoShown = true;
@@ -97295,7 +97322,7 @@ class ShowAnno {
         }
         //ic.bAnnoShown = true;
 
-        if($("#" + ic.pre + "anno_ig").length && $("#" + ic.pre + "anno_ig")[0].checked) {
+        if($("#" + ic.pre + "anno_ig").length && $("#" + ic.pre + "anno_ig")[0].checked && !bAnnoShownPrev) {
             ic.bRunRefnumAgain = true;
             await ic.annotationCls.setAnnoTabIg();
 
@@ -101420,10 +101447,18 @@ class ViewInterPairs {
 
            $("#" + ic.pre + "dl_interactionsorted_html").html(html);
            me.htmlCls.dialogCls.openDlg('dl_interactionsorted', 'Show sorted interactions');
+
+           if(me.bNode) {
+            console.log(html);
+           }
        }
        else if(type == 'view') {
            $("#" + ic.pre + "dl_allinteraction_html").html(html);
            me.htmlCls.dialogCls.openDlg('dl_allinteraction', 'Show interactions');
+
+           if(me.bNode) {
+            console.log(html);
+           }
        }
        else if(type == 'linegraph') {
            me.htmlCls.dialogCls.openDlg('dl_linegraph', 'Show interactions between two lines of residue nodes');
@@ -101432,6 +101467,12 @@ class ViewInterPairs {
            // draw SVG
            let svgHtml = ic.lineGraphCls.drawLineGraph(ic.graphStr);
            $("#" + ic.pre + "linegraphDiv").html(svgHtml);
+
+            if(me.bNode) {
+                let graphStr2 = ic.lineGraphStr.substr(0, ic.lineGraphStr.lastIndexOf('}'));
+                graphStr2 += me.htmlCls.setHtmlCls.getLinkColor();
+                console.log(graphStr2);
+            }
        }
        else if(type == 'scatterplot') {
            me.htmlCls.dialogCls.openDlg('dl_scatterplot', 'Show interactions as scatterplot');
@@ -101440,6 +101481,12 @@ class ViewInterPairs {
            // draw SVG
            let svgHtml = ic.lineGraphCls.drawLineGraph(ic.graphStr, true);
            $("#" + ic.pre + "scatterplotDiv").html(svgHtml);
+
+            if(me.bNode) {
+                let graphStr2 = ic.scatterplotStr.substr(0, ic.scatterplotStr.lastIndexOf('}'));
+                graphStr2 += me.htmlCls.setHtmlCls.getLinkColor();
+                console.log(graphStr2);
+            }
        }
        else if(type == 'ligplot') {
             await ic.ligplotCls.drawLigplot(atomSet1);
@@ -104171,7 +104218,7 @@ class ChainalignParser {
                 targetOrQuery = 'query';
                 bAppend = true; 
             }
-console.log("### i " + i + " structArray[i] " + structArray[i]);
+
             //if(structArray[i].length > 4) {
             if(isNaN(structArray[i]) && structArray[i].length > 5) {  // PDB ID plus postfix could be 5 
                 //let bNoDssp = true;
@@ -104189,8 +104236,8 @@ console.log("### i " + i + " structArray[i] " + structArray[i]);
             // hAtoms = me.hashUtilsCls.unionHash(hAtoms, hAtomsTmp);
         }
 
-        let structArrayAll = structArray; //Object.keys(ic.structures);
-console.log("### ic.chains: " + JSON.stringify(ic.chains) + " ic.structures " + JSON.stringify(ic.structures));
+        let structArrayAll = Object.keys(ic.structures);
+
         ic.opts['color'] = (structArrayAll.length > 1) ? 'structure' : ((structArrayAll[0].length > 5) ? 'confidence' : 'chain');
 
         // add color for all structures
@@ -112976,7 +113023,7 @@ class SetSeqAlign {
 
         for(let i = 0, il = ic.qt_start_end[index].length; i < il; ++i) {
             let start1, start2, end1, end2, resiStart1, start1Pos, end1Pos;
-            
+
             start1 = ic.qt_start_end[index][i].t_start;
             start2 = ic.qt_start_end[index][i].q_start;
             end1 = ic.qt_start_end[index][i].t_end;
@@ -119189,16 +119236,16 @@ class LoadScript {
                     if(lastCommand.indexOf('load') !== -1) {
                         await thisClass.applyCommandLoad(lastCommand);
                     }
-                    else if(lastCommand.indexOf('set map') !== -1 && lastCommand.indexOf('set map wireframe') === -1) {
+                    else if(lastCommand.indexOf('set map') == 0 && lastCommand.indexOf('set map wireframe') == 0) {
                         await thisClass.applyCommandMap(lastCommand);
                     }
-                    else if(lastCommand.indexOf('set emmap') !== -1 && lastCommand.indexOf('set emmap wireframe') === -1) {
+                    else if(lastCommand.indexOf('set emmap') == 0 && lastCommand.indexOf('set emmap wireframe') == 0) {
                         await thisClass.applyCommandEmmap(lastCommand);
                     }
-                    else if(lastCommand.indexOf('set phi') !== -1) {
+                    else if(lastCommand.indexOf('set phi') == 0) {
                         await ic.delphiCls.applyCommandPhi(lastCommand);
                     }
-                    else if(lastCommand.indexOf('set delphi') !== -1) {
+                    else if(lastCommand.indexOf('set delphi') == 0) {
                         await ic.delphiCls.applyCommandDelphi(lastCommand);
                     }
                     else if(lastCommand.indexOf('view annotations') == 0
@@ -119903,6 +119950,14 @@ class SelectByCommand {
            // wild card * can be used to select all
            //var currHighlightAtoms = {}
 
+           // convert 1TOP_A:20 to $1TOP.A:20
+           if(commandArray[i].indexOf('_') !== -1) {
+             let itemArray = commandArray[i].split('_');
+             if(itemArray.length ==2 ) {
+              commandArray[i] = '$' + itemArray[0] + '.' + itemArray[1];
+             }
+           }
+
            let dollarPos = commandArray[i].indexOf('$');
            let periodPos = commandArray[i].indexOf('.');
            let colonPos = commandArray[i].indexOf(':');
@@ -124377,6 +124432,7 @@ console.log("free energy: " + energy + " kcal/mol");
         ic.saveFileCls.saveFile(file_pref + '_icn3d_' + postfix + '.pdb', 'text', [data]);
       }
       else {
+        console.log(data);
         return data;
       }
    }
@@ -127939,6 +127995,7 @@ class ResizeCanvas {
 
         if(ic.structures && Object.keys(ic.structures).length > 0 && (bDraw === undefined || bDraw)) {
             ic.drawCls.draw();
+            // ic.drawCls.render();
         }
       }
     }
@@ -128168,7 +128225,8 @@ class Transform {
     //Set the orientation to the original one, but leave the style, color, etc alone.
     resetOrientation() { let ic = this.icn3d; ic.icn3dui;
         if(ic.commands.length > 0) {
-            let commandTransformation = ic.commands[0].split('|||');
+            // let commandTransformation = ic.commands[0].split('|||');
+            let commandTransformation = ic.commands[ic.commands.length-1].split('|||');
 
             this.resetOrientation_base(commandTransformation);
         }
@@ -132854,7 +132912,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.45.4';
+    this.REVISION = '3.46.0';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}", and added window = {navigator: {}, "__THREE__":"177"}
     this.bNode = (Object.keys(window).length < 3) ? true : false;