icn3d 3.45.2 → 3.45.4

package/icn3d.module.js

@@ -92431,6 +92431,7 @@ class AnnoIg {
             html2 += htmlCnt + '<span class="icn3d-seqLine">';
 
             if(ic.seqStartLen && ic.seqStartLen[chnid]) html2 += ic.showSeqCls.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
+            // if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqStartLen[chnid], '-');
 
             let prevDomainindex, color;
             for(let i = 0, il = fromArray.length; i < il; ++i) {
@@ -96970,7 +96971,7 @@ class AddTrack {
 
         // adjust the total length
         if(ic.maxAnnoLength < ic.maxAnnoLengthOri + ic.seqStartLen[chainid] + ic.seqEndLen[chainid]) {
-                ic.maxAnnoLength = ic.maxAnnoLengthOri + ic.seqStartLen[chainid] + ic.seqEndLen[chainid];
+            ic.maxAnnoLength = ic.maxAnnoLengthOri + ic.seqStartLen[chainid] + ic.seqEndLen[chainid];
         }
 
         // do not remove other tracks
@@ -97271,6 +97272,9 @@ class AddTrack {
 
         me.htmlCls.clickMenuCls.setLogCmd("add exon track | chainid " + chainid + " | geneid " + geneid + " | startpos " + startpos + " | type " + type, true);
         me.htmlCls.clickMenuCls.setLogCmd("set annotation custom", true);
+        
+        // reset annotation tracks since exons may add extra space to the N-terminal
+        ic.annotationCls.resetAnnoTabAll();
     }
 
     async addMsaTracks(chainid, startpos, type, fastaList) { let ic = this.icn3d, me = ic.icn3dui;
@@ -106555,7 +106559,7 @@ class MmcifParser {
         ///// if(ic.deferredSymmetry !== undefined) ic.deferredSymmetry.resolve();
       }
       catch (err) {
-        if(!me.bNode) console.log("mmcifparser.cgi issues: " + err);
+        if(!me.bNode) console.log("downloadMmcifSymmetry issues: " + err);
         return;
       }
     }
@@ -106630,7 +106634,7 @@ class MmdbParser {
             this.getNoData(mmdbid, bGi);
             return;
         }
-        
+
         if(Object.keys(data.atoms).length == 0) { // for large structures such as 3J3Q
             // use mmtfid
             let pdbid = data.pdbId;
@@ -111922,7 +111926,7 @@ class ParserUtils {
     getResiNCBI(chainid, resi) { let ic = this.icn3d; ic.icn3dui;
         let residNCBI = ic.resid2ncbi[chainid + '_' + resi];
         let resiNCBI = (residNCBI) ? parseInt(residNCBI.substr(residNCBI.lastIndexOf('_') + 1)) : 0;
-            
+
         return resiNCBI;
     }
 }
@@ -113343,7 +113347,7 @@ class SetSeqAlign {
         // start and end of MSA
         let start_t = 9999, end_t = -1;
 
-        let baseResi = ic.chainsSeq[chainid1][0].resi - 1;
+        ic.chainsSeq[chainid1][0].resi - 1;
 
         for(let index = 1, indexl = chainidArray.length; index < indexl; ++index) { 
             let chainIndex = index - 1;
@@ -113353,34 +113357,25 @@ class SetSeqAlign {
             for(let i = 0, il = ic.qt_start_end[chainIndex].length; i < il; ++i) {
                 let start1, end1;
                 
-                // if(bRealign) { // real residue numbers are stored
-                //     start1 = ic.qt_start_end[chainIndex][i].t_start;
-                //     end1 = ic.qt_start_end[chainIndex][i].t_end;
-                // }
-                // else {
-                    //ic.qt_start_end is zero-based
-                    start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start) - 1;
-                    end1 = parseInt(ic.qt_start_end[chainIndex][i].t_end) - 1;
-                // }
+                // start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start) - 1;
+                // end1 = parseInt(ic.qt_start_end[chainIndex][i].t_end) - 1;
+
+                start1 = ic.ParserUtilsCls.getResiNCBI(chainid1, ic.qt_start_end[chainIndex][i].t_start) - 1;
+                end1 = ic.ParserUtilsCls.getResiNCBI(chainid1, ic.qt_start_end[chainIndex][i].t_end) - 1;
+
                 for(let j = start1; j <= end1; ++j) {
                     let resi, resid;
 
-                    // if(me.cfg.aligntool == 'tmalign') { // tmalign: just one residue in this for loop
-                    //     resi = ic.qt_start_end[chainIndex][i].t_start;
+                    // let resiPos;
+                    // if(me.cfg.aligntool == 'tmalign') {
+                    //     resiPos = j - baseResi;
                     // }
                     // else {
-                        // let resiPos = (bRealign || me.cfg.aligntool != 'tmalign') ? j : j - baseResi;
-                        let resiPos;
-                        if(me.cfg.aligntool == 'tmalign') {
-                            resiPos = j - baseResi;
-                        }
-                        else {
-                            // resiPos = (bRealign) ? j : j - baseResi;
-                            resiPos = j;
-                        }
-                        resi = ic.ParserUtilsCls.getResi(chainidArray[0], resiPos);
-                        resid = chainidArray[0] + '_' + resi;
+                    //     resiPos = j;
                     // }
+                    let resiPos = j;
+                    resi = ic.ParserUtilsCls.getResi(chainidArray[0], resiPos);
+                    resid = chainidArray[0] + '_' + resi;
 
                     resid2range_t[resid] = 1;
                     if(j < start_t) start_t = j;
@@ -113440,7 +113435,8 @@ class SetSeqAlign {
             let resi = ic.chainsSeq[chainid1][j].resi;
             let resid = chainid1 + '_' + resi;
 
-            let jAdjusted = (me.cfg.aligntool != 'tmalign') ? j : j + baseResi;
+            // let jAdjusted = (me.cfg.aligntool != 'tmalign') ? j : j + baseResi;
+            let jAdjusted = ic.ParserUtilsCls.getResiNCBI(chainid1, resi) - 1;
 
             //if(j + baseResi < start_t || j + baseResi > end_t) {
             if(jAdjusted < start_t || jAdjusted > end_t) {    
@@ -113629,8 +113625,10 @@ class SetSeqAlign {
     insertNotAlignRes(chainid, start, len, bRealign) { let ic = this.icn3d; ic.icn3dui;
         // insert non-aligned residues in query seq
         for(let j = 0, jl = len; j < jl; ++j) {
-            let resi2 = ic.ParserUtilsCls.getResi(chainid, start + j);
-            let resn2 = this.getResn(chainid, start + j);
+            // let resi2 = ic.ParserUtilsCls.getResi(chainid, start + j);
+            // let resn2 = this.getResn(chainid, start + j);
+            let resi2 = start + j;
+            let resn2 = this.getResnFromResi(chainid, resi2);
             let resn1 = '-';
             let bAlign = false;
             let resObject = this.getResObject(chainid, false, bAlign, resi2, resn2, resn1);
@@ -113638,13 +113636,15 @@ class SetSeqAlign {
         }
     }
 
-    getTemplatePosFromOriPos(chainid1, start, end, bRealign) { let ic = this.icn3d; ic.icn3dui;
-        let startResi = ic.ParserUtilsCls.getResi(chainid1, start);
-        let endResi = ic.ParserUtilsCls.getResi(chainid1, end);
-            
+    getTemplatePosFromOriResi(chainid1, start, end, bRealign) { let ic = this.icn3d; ic.icn3dui;
+        // let startResi = ic.ParserUtilsCls.getResi(chainid1, start);
+        // let endResi = ic.ParserUtilsCls.getResi(chainid1, end);
+        let startResi = start;
+        let endResi = end;
+
         let result1 = this.getResiPosInTemplate(chainid1, startResi);
         let result2 = this.getResiPosInTemplate(chainid1, endResi);
-        
+ 
         return {"pos1": result1.pos, "pos2": result2.pos};
     }
 
@@ -113709,7 +113709,8 @@ class SetSeqAlign {
         let result;
 
         for(let i = 0, il = ic.qt_start_end[chainIndex].length; i < il; ++i) {
-            let start1, start2, end1, end2, resiStart1, start1Pos, end1Pos;
+            let start1, start2, end1, end2, resiStart1, start1Pos;
+            
             if(bRealign && me.cfg.aligntool == 'tmalign') { // real residue numbers are stored
                 start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start);
                 start2 = parseInt(ic.qt_start_end[chainIndex][i].q_start);
@@ -113724,7 +113725,7 @@ class SetSeqAlign {
                 // 1. before the mapped residues
                 resiStart1 = start1;
                 start1Pos = this.getPosFromResi(chainid1, ic.qt_start_end[chainIndex][i].t_start);
-                end1Pos = this.getPosFromResi(chainid1, ic.qt_start_end[chainIndex][i].t_end);
+                this.getPosFromResi(chainid1, ic.qt_start_end[chainIndex][i].t_end);
             }
             else {
                 start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start - 1);
@@ -113735,17 +113736,16 @@ class SetSeqAlign {
                 // 1. before the mapped residues
                 resiStart1 = ic.ParserUtilsCls.getResi(chainid1, start1);
                 start1Pos = start1;
-                end1Pos = end1;
             }
             //let range = resid2range_t[chainid1 + '_' + resiStart1];
-  
+
             // if the mapping does not start from start_t, add gaps to the query seq
             if(i == 0) {
-                //result = this.getTemplatePosFromOriPos(chainid1, start_t, start1, bRealign);
-                result = this.getTemplatePosFromOriPos(chainid1, start_t, start1Pos, bRealign);
+                //result = this.getTemplatePosFromOriResi(chainid1, start_t, start1, bRealign);
+                result = this.getTemplatePosFromOriResi(chainid1, start_t, start1Pos, bRealign);
                 pos1 = result.pos1;
                 pos2 = result.pos2;
-                
+
                 //if(start1 > start_t) {
                 if(start1Pos > start_t) {
                     for(let j = 0, jl = pos2 - pos1; j < jl; ++j) {
@@ -113755,7 +113755,7 @@ class SetSeqAlign {
             }
             else {
                 //let notAlnLen1 = start1 - (prevIndex1 + 1);
-                result = this.getTemplatePosFromOriPos(chainid1, prevIndex1, start1, bRealign);
+                result = this.getTemplatePosFromOriResi(chainid1, prevIndex1, start1, bRealign);
                 pos1 = result.pos1;
                 pos2 = result.pos2;
                 let notAlnLen1 = pos2 - (pos1 + 1);
@@ -113768,7 +113768,7 @@ class SetSeqAlign {
                     // add gaps before the query sequence
                     for(let j = 0, jl = notAlnLen1 - notAlnLen2; j < jl; ++j) {
                         ic.alnChainsSeq[chainid2].push(gapResObject2);
-                    }                       
+                    }
                 }
                 else {
                     // check the number of gaps before resiStart1 (n), and insert 'notAlnLen2 - notAlnLen1 - n' gaps
@@ -113777,8 +113777,8 @@ class SetSeqAlign {
             }
 
             // 2. In the mapped residues
-            //result = this.getTemplatePosFromOriPos(chainid1, start1, end1, bRealign);
-            result = this.getTemplatePosFromOriPos(chainid1, start1Pos, end1Pos, bRealign);
+            result = this.getTemplatePosFromOriResi(chainid1, start1, end1, bRealign);
+            //result = this.getTemplatePosFromOriResi(chainid1, start1Pos, end1Pos, bRealign);
             pos1 = result.pos1;
             pos2 = result.pos2;
             
@@ -113795,7 +113795,7 @@ class SetSeqAlign {
                     let resi2 = (bRealign) ? start2 + k : ic.ParserUtilsCls.getResi(chainid2, start2 + k);
                     let resn1 = this.getResnFromResi(chainid1, resi1); //this.getResn(chainid1, start1 + k);
                     let resn2 = this.getResnFromResi(chainid2, resi2); //this.getResn(chainid2, start2 + k);
-                    
+
                     let bAlign = true;
                     let resObject = this.getResObject(chainid2, false, bAlign, resi2, resn2, resn1);
                     ic.alnChainsSeq[chainid2].push(resObject);
@@ -113818,7 +113818,7 @@ class SetSeqAlign {
         } 
 
         // add gaps at the end
-        result = this.getTemplatePosFromOriPos(chainid1, prevIndex1, end_t, bRealign);
+        result = this.getTemplatePosFromOriResi(chainid1, prevIndex1, end_t, bRealign);
         pos1 = result.pos1;
         pos2 = result.pos2;
         for(let i = pos1; i < pos2; ++i) {
@@ -116130,7 +116130,7 @@ class Vastplus {
         }
 
         let allPromise = Promise.allSettled(ajaxArray);
-        try {
+        // try {
             let dataArray = await allPromise;
 
             // 2. cluster pairs
@@ -116142,10 +116142,10 @@ class Vastplus {
             await ic.pdbParserCls.loadPdbDataRender(true);
 
             /// if(ic.deferredRealignByVastplus !== undefined) ic.deferredRealignByVastplus.resolve();
-        }
-        catch(err) {
-            var aaa = 1; //alert("There are some problems in aligning the chains...");
-        }          
+        // }
+        // catch(err) {
+        //     var aaa = 1; //alert("There are some problems in aligning the chains...");
+        // }          
     }
 
     setAlignment(struct1, struct2, chainid1, chainid2, bRealign) { let ic = this.icn3d, me = ic.icn3dui;
@@ -123196,15 +123196,16 @@ class Dssp {
         let pdbAjaxArray = this.getPdbAjaxArray();
 
         // try {
+            let numRound = 0;
+            
             if(!template) {
                 //let allPromise = Promise.allSettled(pdbAjaxArray);
                 //ic.pdbDataArray = await allPromise;
 
                 ic.pdbDataArray = await this.promiseWithFixedJobs(pdbAjaxArray);
 
-                let numRound = 0;
                 let bNoMoreIg = await thisClass.parseRefPdbData(ic.pdbDataArray, template, undefined, numRound);
-                 ++numRound;
+                ++numRound;
 
                 //while(!bNoMoreIg) {
                 while(!bNoMoreIg && numRound < 15) {
@@ -133693,7 +133694,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.45.0';
+    this.REVISION = '3.45.2';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}", and added window = {navigator: {}, "__THREE__":"177"}
     this.bNode = (Object.keys(window).length < 3) ? true : false;
@@ -134273,7 +134274,7 @@ iCn3DUI.prototype.getXMLHttpRqstPromise = function(url, dataType, responseType,
                        var aaa = 1; //alert("RCSB server has no corresponding electron density map for this structure.");
                    }
                    else {
-                       var aaa = 1; //alert("The " + mapType + " file is unavailable...");
+                       console.log("The " + mapType + " file is unavailable...");
                    }
 
                    reject('error');

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "icn3d",
-  "version": "3.45.2",
+  "version": "3.45.4",
   "main": "./icn3d.js",
   "exports": {
     ".": {