icn3d 3.24.6 → 3.25.1

package/icn3d.js

@@ -2302,7 +2302,7 @@ THREE.TrackballControls = function ( object, domElement, icn3d ) {
             this.screen.width = window.innerWidth;
             this.screen.height = window.innerHeight;
 
-        } else {
+        } else if(this.domElement) {
 
             var box = this.domElement.getBoundingClientRect();
             // adjustments come from similar code in the jquery offset() function
@@ -2872,7 +2872,7 @@ THREE.TrackballControls = function ( object, domElement, icn3d ) {
 
     }
 
-    if(Object.keys(window).length >= 2) {
+    if(Object.keys(window).length >= 2 && this.domElement) {
         this.domElement.addEventListener( 'contextmn', function ( event ) {
             //event.preventDefault();
         }, false );
@@ -2998,7 +2998,7 @@ THREE.OrthographicTrackballControls = function ( object, domElement, icn3d ) { v
             this.screen.width = window.innerWidth;
             this.screen.height = window.innerHeight;
 
-        } else {
+        } else if(this.domElement) {
 
             var box = this.domElement.getBoundingClientRect();
             // adjustments come from similar code in the jquery offset() function
@@ -3548,7 +3548,7 @@ THREE.OrthographicTrackballControls = function ( object, domElement, icn3d ) { v
 
     }
 
-    if(Object.keys(window).length >= 2) {
+    if(Object.keys(window).length >= 2 && this.domElement) {
         this.domElement.addEventListener( 'contextmn', function ( event ) {
             //event.preventDefault();
         }, false );
@@ -9396,8 +9396,8 @@ 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>');
@@ -38547,7 +38547,7 @@ class Domain3d {
 
 		//substruct: array of secondary structures, each of which has the keys: From (1-based), To (1-based), Sheet (0 or 1), also add these paras: x1, y1, z1, x2, y2, z2
 		let substruct = [];
-		// determine residue ranges for each subdomain
+		// determine residue position ranges for each subdomain
 		let subdomains = [];
 
 		// sheets: array of sheets, each of which has the key: sheet_num (beta sandwich has two sheets, e.g., 0 and 1), adj_strand1 (not used), adj_strand2
@@ -50156,10 +50156,15 @@ class RealignParser {
               //let chainTo = chainidArray[0];
               //let chainFrom = chainidArray[index + 1];
 
-              let bChainAlign = true;
+              let bChainAlign = true, result;
 
-
-              let result = ic.ParserUtilsCls.alignCoords(coordsFrom, coordsTo, fromStruct, undefined, chainTo, chainFrom, index + 1, bChainAlign);
+              if(ic.bAfMem) { // align to the query (membrane)
+                result = ic.ParserUtilsCls.alignCoords(coordsFrom, coordsTo, toStruct, undefined, chainTo, chainFrom, index + 1, bChainAlign);
+              }
+              else {
+                result = ic.ParserUtilsCls.alignCoords(coordsFrom, coordsTo, fromStruct, undefined, chainTo, chainFrom, index + 1, bChainAlign);
+              }
+              
               hAtoms = me.hashUtilsCls.unionHash(hAtoms, result.hAtoms);
 
     //          ic.opts['color'] = 'identity';
@@ -50247,13 +50252,13 @@ class RealignParser {
         }
         
         // use the model from Membranome as template
-        if(ic.bAfMem && chainidArray.length == 2) {
-            if(chainidArray[1].split('_')[0] == pdbidTemplate) {
-                let tmp = chainidArray[0];
-                chainidArray[0] = chainidArray[1]; 
-                chainidArray[1] = tmp;
-            }
-        }
+        // if(ic.bAfMem && chainidArray.length == 2) {
+        //     if(chainidArray[1].split('_')[0] == pdbidTemplate) {
+        //         let tmp = chainidArray[0];
+        //         chainidArray[0] = chainidArray[1]; 
+        //         chainidArray[1] = tmp;
+        //     }
+        // }
         
         let bRealign = true;
         ic.qt_start_end = []; // reset the alignment
@@ -51732,7 +51737,12 @@ class ParserUtils {
 
       if(n < 4) var aaa = 1; //alert("Please select at least four residues in each structure...");
       if(n >= 4) {
-          ic.rmsd_suprTmp = me.rmsdSuprCls.getRmsdSuprCls(coordsFrom, coordsTo, n);
+          if(ic.bAfMem) { // align to the query (membrane)
+            ic.rmsd_suprTmp = me.rmsdSuprCls.getRmsdSuprCls(coordsTo, coordsFrom, n);
+          }
+          else {
+            ic.rmsd_suprTmp = me.rmsdSuprCls.getRmsdSuprCls(coordsFrom, coordsTo, n);
+          }
 
           // apply matrix for each atom
           if(ic.rmsd_suprTmp.rot !== undefined) {
@@ -52371,7 +52381,7 @@ class ParserUtils {
                    await ic.showAnnoCls.showAnnotations(); 
               }
 
-              if(me.cfg.closepopup) {
+              if(me.cfg.closepopup || me.cfg.imageonly) {
                   ic.resizeCanvasCls.closeDialogs();
               }
           }
@@ -52380,6 +52390,8 @@ class ParserUtils {
           }
           if($("#" + ic.pre + "atomsCustom").length > 0) $("#" + ic.pre + "atomsCustom")[0].blur();
           ic.bInitial = false;
+
+          if(me.cfg.imageonly) ic.saveFileCls.saveFile(undefined, 'png', undefined, true);
       }, 0);
     }
 
@@ -59109,9 +59121,10 @@ class LoadScript {
 
         // load pdb, mmcif, mmdb, cid
         let id = loadStr.substr(loadStr.lastIndexOf(' ') + 1);
+        if(id.length == 4) id = id.toUpperCase();
 
         // skip loading the structure if it was loaded before
-        if(ic.structures.hasOwnProperty(id)) return;
+        if(ic.structures && ic.structures.hasOwnProperty(id)) return;
 
         ic.inputid = id;
         if(command.indexOf('load mmtf') !== -1) {
@@ -59462,7 +59475,7 @@ class LoadScript {
             ic.drawCls.draw();
         }
 
-        if(me.cfg.closepopup) {
+        if(me.cfg.closepopup || me.cfg.imageonly) {
             setTimeout(function(){
                 ic.resizeCanvasCls.closeDialogs();
             }, 100);
@@ -59473,6 +59486,8 @@ class LoadScript {
         // an extra render to remove artifacts in transparent surface
         if(ic.bTransparentSurface && ic.bRender) ic.drawCls.render();
 
+        if(me.cfg.imageonly) ic.saveFileCls.saveFile(undefined, 'png', undefined, true);
+
         /// if(ic.deferred !== undefined) ic.deferred.resolve(); /// if(ic.deferred2 !== undefined) ic.deferred2.resolve();
         /// if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
     }
@@ -60367,7 +60382,7 @@ class Selection {
 
         ic.reinitAfterLoad();
 
-        ic.loadScriptCls.renderFinalStep(1);
+        //ic.loadScriptCls.renderFinalStep(1);
         ic.definedSetsCls.setMode('all');
 
         ic.selectionCls.selectAll();
@@ -60378,6 +60393,8 @@ class Selection {
         ic.hlUpdateCls.removeSeqResidueBkgd();
         ic.hlUpdateCls.removeHl2D();
         ic.hlUpdateCls.removeHlMenus();
+
+        ic.loadScriptCls.renderFinalStep(1);
     }
 
     async loadSelection(dataStr) { let ic = this.icn3d, me = ic.icn3dui;
@@ -61942,14 +61959,17 @@ class Dssp {
     async showIgRefNum() { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
-        if(ic.resid2refnum  && Object.keys(ic.resid2refnum).length > 0) {
-            ic.bShowRefnum = true;
+        // if(ic.resid2refnum  && Object.keys(ic.resid2refnum).length > 0) {
+        //     ic.bShowRefnum = true;
 
-            // open sequence view
-            ic.hAtomsRefnum = {};
-            ic.bResetAnno = true;
-            await ic.showAnnoCls.showAnnotations();
-            ic.annotationCls.setAnnoViewAndDisplay('detailed view');
+        //     // open sequence view
+        //     ic.hAtomsRefnum = {};
+        //     ic.bResetAnno = true;
+        //     await ic.showAnnoCls.showAnnotations();
+        //     ic.annotationCls.setAnnoViewAndDisplay('detailed view');
+        // }
+        if(ic.pdbDataArray) {
+            await thisClass.parseRefPdbData(ic.pdbDataArray);
         }
         else {
             //ic.refpdbArray = ['1bqu_fn3', '1cd8_igv', '1t6v_vnar', '1wio_c2', '1wio_igv', '2atp_a', '2atp_b', '2dm3_iset', '5esv_vh', '5esv_vl', '6al5_cd19', '7bz5_cl1', '7bz5_vh', '7bz5_vl'];
@@ -62012,6 +62032,7 @@ class Dssp {
 
         let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
 
+        // if(!ic.resid2domainid) ic.resid2domainid = {};
         ic.resid2domainid = {};
 
         for(let i = 0, il = struArray.length; i < il; ++i) {
@@ -62025,20 +62046,33 @@ class Dssp {
                 && !ic.proteins.hasOwnProperty(ic.firstAtomObjCls.getMiddleAtomObj(ic.chains[chainid]).serial)) continue;
                 if(ic.chainsSeq[chainid].length < 50) continue; // peptide
 
+                let currAtoms = me.hashUtilsCls.intHash(ic.chains[chainid], ic.hAtoms);
+                if(Object.keys(currAtoms).length == 0) continue;
+
                 // align each 3D domain with reference structure
-                let result = ic.domain3dCls.c2b_NewSplitChain(ic.chains[chainid]);
+                //let result = ic.domain3dCls.c2b_NewSplitChain(ic.chains[chainid]);
+                // assign ref numbers to selected residues
+                let result = ic.domain3dCls.c2b_NewSplitChain(currAtoms);
                 let subdomains = result.subdomains;  
+                let pos2resi = result.pos2resi;
 
                 let domainAtomsArray = [];
                 if(subdomains.length <= 1) {
-                    domainAtomsArray.push(ic.chains[chainid]);
+                    //domainAtomsArray.push(ic.chains[chainid]);
+                    domainAtomsArray.push(currAtoms);
 
-                    for(let n = 0, nl = ic.chainsSeq[chainid].length; n < nl; ++n) {
-                        let resid = chainid + '_' + ic.chainsSeq[chainid][n].resi;
+                    // for(let n = 0, nl = ic.chainsSeq[chainid].length; n < nl; ++n) {
+                    //     let resid = chainid + '_' + ic.chainsSeq[chainid][n].resi;
+                    //     ic.resid2domainid[resid] = chainid + '-0';
+                    // }    
+                    
+                    let residueArray = ic.resid2specCls.atoms2residues(Object.keys(currAtoms));
+                    for(let n = 0, nl = residueArray.length; n < nl; ++n) {
+                        let resid = residueArray[n];
                         ic.resid2domainid[resid] = chainid + '-0';
-                    }             
+                    }   
                 }
-                else {
+                else {                 
                     for(let k = 0, kl = subdomains.length; k < kl; ++k) {
                         let domainAtoms = {};
                         let segArray = subdomains[k];
@@ -62047,8 +62081,9 @@ class Dssp {
                             let startResi = segArray[m];
                             let endResi = segArray[m+1];
                             for(let n = parseInt(startResi); n <= parseInt(endResi); ++n) {
-                                let residNCBI = chainid + '_' + n;
-                                let resid = ic.ncbi2resid[residNCBI];
+                                //let residNCBI = chainid + '_' + n;
+                                //let resid = ic.ncbi2resid[residNCBI];
+                                let resid = chainid + '_' + pos2resi[n];
                                 domainAtoms = me.hashUtilsCls.unionHash(domainAtoms, ic.residues[resid]);
                                 ic.resid2domainid[resid] = chainid + '-' + k;
                             }
@@ -62114,6 +62149,12 @@ class Dssp {
 
         // find the best alignment for each chain
         let domainid2score = {}, domainid2segs = {}, chainid2segs = {};
+
+        // if(!ic.chainid2index) ic.chainid2index = {};
+        // if(!ic.domainid2index) ic.domainid2index = {};
+        // if(!ic.domainid2ig2kabat) ic.domainid2ig2kabat = {};
+        // if(!ic.domainid2ig2imgt) ic.domainid2ig2imgt = {};
+
         ic.chainid2index = {};
         ic.domainid2index = {};
         ic.domainid2ig2kabat = {};
@@ -66223,7 +66264,9 @@ class SaveFile {
     //The type "png" is used to save the current canvas image. The type "html" is used to save html file with the
     //"data". This can be used to save any text. The type "text" is used to save an array of text, where "data" is
     //actually an array. The type "binary" is used to save an array of binary, where "data" is actually an array.
-    saveFile(filename, type, text) { let ic = this.icn3d, me = ic.icn3dui;
+    saveFile(filename, type, text, bBlob) { let ic = this.icn3d, me = ic.icn3dui;
+        let thisClass = this;
+
         //Save file
         let blob;
 
@@ -66264,7 +66307,7 @@ class SaveFile {
             if(me.utilsCls.isIE()) {
                 blob = ic.renderer.domElement.msToBlob();
 
-                if(bAddURL) {
+                if(bAddURL && typeof(blob) == 'Blob') {
                     let reader = new FileReader();
                     reader.onload = function(e) {
                         let arrayBuffer = e.target.result; // or = reader.result;
@@ -66274,23 +66317,23 @@ class SaveFile {
                         blob = me.convertTypeCls.getBlobFromBufferAndText(arrayBuffer, text);
 
                         //if(window.navigator.msSaveBlob) navigator.msSaveBlob(blob, filename);
-                        saveAs(blob, filename);
+                        thisClass.saveBlob(blob, filename, bBlob, width, height);
 
-                        return;
+                        return blob;
                     };
 
                     reader.readAsArrayBuffer(blob);
                 }
                 else {
                     //ic.createLinkForBlob(blob, filename);
-                    saveAs(blob, filename);
+                    thisClass.saveBlob(blob, filename, bBlob, width, height);
 
-                    return;
+                    return blob;
                 }
             }
             else {
                 ic.renderer.domElement.toBlob(function(data) {
-                    if(bAddURL) {
+                    if(bAddURL && typeof(blob) == 'data') {
                         let reader = new FileReader();
                         reader.onload = function(e) {
                             let arrayBuffer = e.target.result; // or = reader.result;
@@ -66300,9 +66343,9 @@ class SaveFile {
                             blob = me.convertTypeCls.getBlobFromBufferAndText(arrayBuffer, text);
 
                             //ic.createLinkForBlob(blob, filename);
-                            saveAs(blob, filename);
+                            thisClass.saveBlob(blob, filename, bBlob, width, height);
 
-                            return;
+                            return blob;
                         };
 
                         reader.readAsArrayBuffer(data);
@@ -66311,9 +66354,9 @@ class SaveFile {
                         blob = data;
 
                         //ic.createLinkForBlob(blob, filename);
-                        saveAs(blob, filename);
+                        thisClass.saveBlob(blob, filename, bBlob, width, height);
 
-                        return;
+                        return blob;
                     }
                 });
             }
@@ -66351,6 +66394,44 @@ class SaveFile {
             //https://github.com/eligrey/FileSaver.js/
             saveAs(blob, filename);
         }
+
+        return blob;
+    }
+
+    saveBlob(blob, filename, bBlob, width, height) { let ic = this.icn3d; ic.icn3dui;
+        if(bBlob) {
+            let urlCreator = window.URL || window.webkitURL;
+            let imageUrl = urlCreator.createObjectURL(blob);
+
+            let url = ic.shareLinkCls.shareLinkUrl();
+
+            url = url.replace(/imageonly=1/g, '');
+
+            let bTooLong =(url.length > 4000 || url.indexOf('http') !== 0) ? true : false;
+
+            if(bTooLong || (ic.bInputfile && !ic.bInputUrlfile)) {
+                // $("#" + ic.pre + "viewer").html("<img src='" + imageUrl + "'/>");
+                $("#" + ic.pre + "mnlist").html("<img src='" + imageUrl + "'/>");
+            }
+            else {
+                // $("#" + ic.pre + "viewer").html("<a href='" + url + "' target='_blank'><img src='" + imageUrl + "'/></a>");
+                $("#" + ic.pre + "mnlist").html("<a href='" + url + "' target='_blank'><img src='" + imageUrl + "'/></a>");
+            }
+            
+            $("#" + ic.pre + "viewer").height(height);
+            $("#" + ic.pre + "cmdlog").hide();
+            $("#" + ic.pre + "title").hide();
+            //$("#" + ic.pre + "mnlist").hide();
+            $("#" + ic.pre + "canvas").hide(); // "load mmdbid ..." may cause problems if canvas was removed
+
+            if($("#" + ic.pre + "fullscreen").length > 0) $("#" + ic.pre + "fullscreen").hide();
+
+            // clear memory
+            ic = {};
+        }
+        else {
+            saveAs(blob, filename);
+        }
     }
 
     saveSvg(id, filename, bContactmap) { let ic = this.icn3d, me = ic.icn3dui;
@@ -66975,7 +67056,9 @@ class SaveFile {
                     $("#" + ic.pre + "title").html(title);
                 }
                 else if(structureArray.length == 1) {
-                    let url = this.getLinkToStructureSummary();
+                    //let url = this.getLinkToStructureSummary();
+                    let url = (isNaN(ic.inputid) && ic.inputid.length > 5) ? 'https://alphafold.ebi.ac.uk/entry/' + ic.inputid : 'https://www.ncbi.nlm.nih.gov/structure/?term=' + ic.inputid;
+
                     this.setStructureTitle(url, title, titlelinkColor);
                 }
             }
@@ -67290,6 +67373,10 @@ class ShareLink {
                    if(key_value.length == 2) paraHash[key_value[0]] = key_value[1];
                }
 
+               if(me.cfg.notebook && me.cfg.idname && !paraHash[me.cfg.idname]) { // somehow it is not included
+                    url += me.cfg.idname + '=' + me.cfg.idvalue + '&';
+               }
+
                for(let key in paraHash) {
                    if(key === 'v') continue;
 
@@ -67329,7 +67416,7 @@ class ShareLink {
            transformation.quaternion = ic.quaternion;
 
            let statefile = "";
-           let prevCommandStr = undefined;
+           let prevCommandStr = "";
 
            let toggleStr = 'toggle highlight';
            let cntToggle = 0;
@@ -67403,6 +67490,7 @@ class ShareLink {
            if(ic.structures !== undefined && Object.keys(ic.structures).length == 1 && ic.inputid !== undefined) {
                id = Object.keys(ic.structures)[0];
                url = url.replace(new RegExp(id + '_','g'), '!');
+               outputCmd = outputCmd.replace(new RegExp(id + '_','g'), '!');
            }
 
            if(me.cfg.blast_rep_id !== undefined) {
@@ -70268,7 +70356,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.24.2';
+    this.REVISION = '3.25.0';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -70282,6 +70370,7 @@ class iCn3DUI {
     if(this.cfg.showcommand === undefined) this.cfg.showcommand = true;
     //if(this.cfg.simplemenu === undefined) this.cfg.simplemenu = false;
     if(this.cfg.mobilemenu === undefined) this.cfg.mobilemenu = false;
+    if(this.cfg.imageonly === undefined) this.cfg.imageonly = false;
     if(this.cfg.closepopup === undefined) this.cfg.closepopup = false;
     if(this.cfg.showanno === undefined) this.cfg.showanno = false;
     if(this.cfg.showseq === undefined) this.cfg.showseq = false;