icn3d 3.42.0 → 3.43.0

package/icn3d.js

@@ -14470,6 +14470,7 @@ class SetDialog {
 
         html += me.htmlCls.divStr + "dl_video' class='" + dialogClass + "'>";
         html += this.addNotebookTitle('dl_video', 'Save canvas changes in a video');
+        html += "State file: " + me.htmlCls.inputFileStr + "id='" + me.pre + "state'><br/>";
         html += me.htmlCls.buttonStr + "video_start' style='margin-top: 6px;'>Video Start</button>";
         html += me.htmlCls.buttonStr + "video_end' style='margin: 6px 0px 0px 30px;'>Video End</button>";
         html += "</div>";
@@ -20251,9 +20252,9 @@ class Html {
     this.MENU_WIDTH = 750;
     //The width (in px) that was left empty by the 3D viewer. The default is 20px.
     this.LESSWIDTH = 20;
-    this.LESSWIDTH_RESIZE = 20;
+    this.LESSWIDTH_RESIZE = 30; //20;
     //The height (in px) that was left empty by the 3D viewer. The default is 20px.
-    this.LESSHEIGHT = 20;
+    this.LESSHEIGHT = (me.cfg.showlogo) ? 60 : 20; //20; // NCBI log is 40px high
 
     // size of 2D cartoons
     this.width2d = 200;
@@ -61564,7 +61565,8 @@ class ParserUtils {
               ic.rmsd_supr = me.rmsdSuprCls.getRmsdSuprCls(coordsFrom, coordsTo, n);
 
               // apply matrix for each atom
-              if(ic.rmsd_supr.rot !== undefined && ic.rmsd_supr.rmsd < 0.1) {
+            //   if(ic.rmsd_supr.rot !== undefined && ic.rmsd_supr.rmsd < 0.1) {
+              if(ic.rmsd_supr.rot !== undefined && ic.rmsd_supr.rmsd < 1) { // 6M17 has some coordinates change and rmsd is 0.3
                   let rot = ic.rmsd_supr.rot;
                   let centerFrom = ic.rmsd_supr.trans1;
                   let centerTo = ic.rmsd_supr.trans2;
@@ -61840,6 +61842,10 @@ class ParserUtils {
               if(me.cfg.closepopup || me.cfg.imageonly) {
                   ic.resizeCanvasCls.closeDialogs();
               }
+
+              if(!me.cfg.showlogo) {
+                $("#ncbi_logo").hide();
+              }
           }
           else {
               ic.hlUpdateCls.updateHlAll();
@@ -70712,6 +70718,10 @@ class LoadScript {
             ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH, me.htmlCls.HEIGHT, true);
         }
 
+        if(!me.cfg.showlogo) {
+          $("#ncbi_logo").hide();
+        }
+
         // an extra render to remove artifacts in transparent surface
         if(ic.bTransparentSurface && ic.bRender) ic.drawCls.render();
 
@@ -80468,7 +80478,7 @@ class ShareLink {
                     let shortName = strArray[strArray.length - 1];
                     ic.saveFileCls.saveFile(inputid + '-' + shortName + '.png', 'png');
                     let text = '<div style="float:left; border: solid 1px #0000ff; padding: 5px; margin: 10px; text-align:center;">';
-                    text += '<a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/share.html?' + shortName + '" target="_blank">';
+                    text += '<a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/share2.html?' + shortName + '" target="_blank">';
                     text += '<img style="height:300px" src ="' + inputid + '-' + shortName + '.png"><br>\n';
                     text += '<!--Start of your comments==================-->\n';
                     let yournote =(ic.yournote) ? ': ' + ic.yournote.replace(/\n/g, "<br>").replace(/; /g, ", ") : '';
@@ -80483,13 +80493,14 @@ class ShareLink {
             if(bPngHtml && data.shortLink === undefined) {
                 ic.saveFileCls.saveFile(inputid + '_icn3d_loadable.png', 'png');
             }
-
+/*
             //shorturl: https://icn3d.page.link/NvbAh1Vmiwc4bgX87
             let urlArray = shorturl.split('page.link/');
-            //if(urlArray.length == 2) shorturl = me.htmlCls.baseUrl + 'icn3d/share.html?' + urlArray[1];
             // When the baseURL is structure.ncbi.nlm.nih.gov, mmcifparser.cgi has a problem to pass posted data in Mac/iphone
             // So the base URL is still www.ncbi.nlm.nih.gov/Structure,just use short URL here
             if(urlArray.length == 2) shorturl = 'https://www.ncbi.nlm.nih.gov/Structure/icn3d/share.html?' + urlArray[1];
+*/
+            shorturl = 'https://www.ncbi.nlm.nih.gov/Structure/icn3d/share2.html?' + shorturl;
 
             $("#" + ic.pre + "short_url").val(shorturl);
             $("#" + ic.pre + "short_url_title").val(shorturl + '&t=' + ic.yournote);
@@ -80508,6 +80519,7 @@ class ShareLink {
     }
 
     getShareLinkPrms(url, bPngHtml) { let ic = this.icn3d, me = ic.icn3dui;
+        /*
         //https://firebase.google.com/docs/dynamic-links/rest
         //Web API Key: AIzaSyBxl9CgM0dY5lagHL4UOhEpLWE1fuwdnvc
         let fdlUrl = "https://firebasedynamiclinks.googleapis.com/v1/shortLinks?key=AIzaSyBxl9CgM0dY5lagHL4UOhEpLWE1fuwdnvc";
@@ -80531,6 +80543,26 @@ class ShareLink {
                 }
             });
         });
+        */
+
+        let serviceUrl = "https://icn3d.link/?longurl=" + encodeURIComponent(url);
+        return new Promise(function(resolve, reject) {
+            $.ajax({
+                url: serviceUrl,
+                dataType: 'json',
+                cache: true,
+                success: function(data) {
+                    resolve(data);
+                },
+                error : function(xhr, textStatus, errorThrown ) {
+                    let shorturl = 'Problem in getting shortened URL';
+                    $("#" + ic.pre + "ori_url").val(url);
+                    $("#" + ic.pre + "short_url").val(shorturl);
+                    $("#" + ic.pre + "short_url_title").val(shorturl + '&t=' + ic.yournote);
+                    if(!bPngHtml) me.htmlCls.dialogCls.openDlg('dl_copyurl', 'Copy a Share Link URL');
+                }
+            });
+        });
     }
 
     shareLinkUrl(bAllCommands, bOutputCmd, bStatefile) { let ic = this.icn3d, me = ic.icn3dui;
@@ -80557,6 +80589,7 @@ class ShareLink {
                 if(key === 'height' && value === '100%') continue;
 
                 if(key === 'resize' && value === true) continue;
+                if(key === 'showlogo' && value === true) continue;
                 if(key === 'showmenu' && value === true) continue;
                 if(key === 'showtitle' && value === true) continue;
                 if(key === 'showcommand' && value === true) continue;
@@ -83650,7 +83683,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.42.0';
+    this.REVISION = '3.43.0';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -83659,6 +83692,7 @@ class iCn3DUI {
     if(this.cfg.width === undefined) this.cfg.width = '100%';
     if(this.cfg.height === undefined) this.cfg.height = '100%';
     if(this.cfg.resize === undefined) this.cfg.resize = true;
+    if(this.cfg.showlogo === undefined) this.cfg.showlogo = true;
     if(this.cfg.showmenu === undefined) this.cfg.showmenu = true;
     if(this.cfg.showtitle === undefined) this.cfg.showtitle = true;
     if(this.cfg.showcommand === undefined) this.cfg.showcommand = true;
@@ -84079,8 +84113,12 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
     }
     else if(me.cfg.align !== undefined) {
         // ic.bNCBI = true;
-
+        if(me.cfg.align.indexOf('185055,') != -1) {
+            me.cfg.align = me.cfg.align.replace('185055,', '199731,'); //the mmdbid of PDB 6M17 was changed from 185055 to 199731
+        }
+ 
         let alignArray = me.cfg.align.split(','); // e.g., 6 IDs: 103701,1,4,68563,1,167 [mmdbid1,biounit,molecule,mmdbid2,biounit,molecule], or 2IDs: 103701,68563 [mmdbid1,mmdbid2]
+        
         if(alignArray.length === 6) {
             ic.inputid = alignArray[0] + "_" + alignArray[3];
         }