icn3d 3.30.2 → 3.30.4

package/icn3d.js

@@ -5828,7 +5828,7 @@ class ClickMenu {
       if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
       await ic.annotationCls.setAnnoTabIg(bSelection, template);
 
-      // ic.bRunRefnumAgain = false;
+      ic.bRunRefnumAgain = false;
     }
 
     clickMenu1() { let me = this.icn3dui; me.icn3d;
@@ -7414,7 +7414,7 @@ class ClickMenu {
             //    ic.drawCls.draw();
             // }
 
-            // ic.bRunRefnumAgain = false;
+            ic.bRunRefnumAgain = false;
          });
 
         me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl", "click", async function(e) { me.icn3d; //e.preventDefault();
@@ -14993,7 +14993,7 @@ class AlignSeq {
         alignChainArray = Object.keys(ic.alnChains);
 
         if (bReverse) alignChainArray = alignChainArray.reverse();
-
+        
         let maxSeqCnt = 0;
 
         let chainHash = {};
@@ -37720,8 +37720,6 @@ class AnnoIg {
         $("#" + ic.pre + "dt_" + type + "_" + chnid).html(html);
         $("#" + ic.pre + "ov_" + type + "_" + chnid).html(html2);
         $("#" + ic.pre + "tt_" + type + "_" + chnid).html(html3);
-
-        ic.bRunRefnumAgain = false;
     }
 
     showAllRefNum(giSeq, chnid) {  let ic = this.icn3d; ic.icn3dui;
@@ -42509,7 +42507,7 @@ class Annotation {
 
         ic.bRunRefnumAgain = true;
         await this.updateIg();
-        // ic.bRunRefnumAgain = false;
+        ic.bRunRefnumAgain = false;
 
         this.updateInteraction();
     }
@@ -42591,8 +42589,9 @@ class Annotation {
 
             $("[id^=" + ic.pre + "transmem]").show();
         }
-        if($("#" + ic.pre + "anno_ig").length && $("#" + ic.pre + "anno_ig")[0].checked) {
-            // ic.bRunRefnumAgain = true;
+        if($("#" + ic.pre + "anno_ig").length && $("#" + ic.pre + "anno_ig")[0].checked || ic.bShowRefnum) {
+            // no need to redo ref num calculation
+            ic.bRunRefnumAgain = false;
 
             await this.updateIg();
 
@@ -42705,6 +42704,7 @@ class Annotation {
         if($("#" + ic.pre + "anno_transmem").length) $("#" + ic.pre + "anno_transmem")[0].checked = false;
     }
     async setAnnoTabIg(bSelection, template) {  let ic = this.icn3d; ic.icn3dui;
+
         await this.updateIg(bSelection, template);
 
         $("[id^=" + ic.pre + "ig]").show();
@@ -42867,7 +42867,7 @@ class Annotation {
                 await thisClass.setAnnoTabIg();
                 me.htmlCls.clickMenuCls.setLogCmd("set annotation ig", true);
 
-                // ic.bRunRefnumAgain = false;
+                ic.bRunRefnumAgain = false;
             }
             else {
                 thisClass.hideAnnoTabIg();
@@ -49091,7 +49091,7 @@ class ChainalignParser {
         await this.downloadChainalignmentPart3(chainresiCalphaHash2, chainidArray, ic.hAtoms);
     }
 
-    setMsa(chainidArray, bVastplus, bRealign) { let ic = this.icn3d, me = ic.icn3dui;
+    setMsa(chainidArray, bVastplus, bRealign) { let ic = this.icn3d, me = ic.icn3dui;        
         // get aligned length for each pair
         let index_alignLen = [];
         for(let index = 1, indexl = chainidArray.length; index < indexl; ++index) {
@@ -49914,6 +49914,7 @@ class ChainalignParser {
             // vastplusAtype: 0: VAST, global, 1: VAST, invarant core, 2: TM-align, global
             // VAST+ on the fly
             let structArray = Object.keys(ic.structures);
+            if(vastplusAtype == 2) me.cfg.aligntool = 'tmalign';
             await ic.vastplusCls.vastplusAlign(structArray, vastplusAtype);
         }
 
@@ -55682,7 +55683,8 @@ class ParserUtils {
  
       // display the structure right away. load the mns and sequences later
       setTimeout(async function(){
-          if(ic.bInitial) {
+            if(ic.bInitial) {
+        //   if(!ic.bAnnoShown || ic.bResetAnno) {
             //   if(me.cfg.showsets) {
             //        ic.definedSetsCls.showSets();
             //   }
@@ -57356,7 +57358,14 @@ class SetSeqAlign {
                     //     resi = ic.qt_start_end[chainIndex][i].t_start;
                     // }
                     // else {
-                        let resiPos = (bRealign || me.cfg.aligntool != 'tmalign') ? j : j - baseResi;
+                        // 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;
+                        }
                         resi = ic.ParserUtilsCls.getResi(chainidArray[0], resiPos);
                     // }
 
@@ -59150,6 +59159,7 @@ class Vastplus {
         }
 
         let bRealign = true, atype = 2; // VAST+ based on TM-align
+        me.cfg.aligntool = 'tmalign';
         await ic.vastplusCls.vastplusAlign(Object.keys(structHash), atype, bRealign);
     }
 
@@ -60094,7 +60104,7 @@ class ApplyCommand {
       else if(command == 'set annotation ig') {
           ic.bRunRefnumAgain = true;
           await ic.annotationCls.setAnnoTabIg();
-          // ic.bRunRefnumAgain = false;
+          ic.bRunRefnumAgain = false;
       }
       else if(command == 'ig refnum on') {
         ic.bRunRefnumAgain = true;
@@ -60102,7 +60112,7 @@ class ApplyCommand {
         if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
         await ic.annotationCls.setAnnoTabIg(true);
 
-        // ic.bRunRefnumAgain = false;
+        ic.bRunRefnumAgain = false;
     }
       else if(command == 'highlight level up') {
           ic.resid2specCls.switchHighlightLevelUp();
@@ -62825,7 +62835,7 @@ class LoadScript {
                         if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
                         await ic.annotationCls.setAnnoTabIg(true);
 
-                        // ic.bRunRefnumAgain = false;
+                        ic.bRunRefnumAgain = false;
                     }
                     else if(lastCommand.indexOf('set annotation 3ddomain') == 0) {
                         thisClass.applyCommand3ddomain(lastCommand);
@@ -66252,7 +66262,7 @@ class Dssp {
                     let endResi = parseInt(segArray[m+1]);
 
                     for(let n = startResi; n <= endResi; ++n) {
-                        let resid = chainid + '_' + pos2resi[n];
+                        let resid = chainid + '_' + pos2resi[n - 1];
                         ++resCnt;
                         domainAtoms = me.hashUtilsCls.unionHash(domainAtoms, ic.residues[resid]);
 
@@ -66274,7 +66284,7 @@ class Dssp {
                     let startResi = segArray[m];
                     let endResi = segArray[m+1];
                     for(let n = parseInt(startResi); n <= parseInt(endResi); ++n) {
-                        let resid = chainid + '_' + pos2resi[n];
+                        let resid = chainid + '_' + pos2resi[n - 1];
                         //domainAtoms = me.hashUtilsCls.unionHash(domainAtoms, ic.residues[resid]);
                         ic.resid2domainid[resid] = chainid + ',' + k + '_' + resiSum;
                     }
@@ -66456,8 +66466,6 @@ class Dssp {
             }
         }
 
-        //!!!
-
         // combine the top four clusters for the 2nd round alignment
         if(bRound1) {
             for(let domainid in domainid2refpdbnamelist) {
@@ -67391,13 +67399,15 @@ class Dssp {
                 if(i != il - 1) { // modify 
                     strandArray[i + 1].loopResCnt += strandArray[i].loopResCnt + parseInt(strandArray[i].endResi) - parseInt(strandArray[i].startResi) + 1;
                 }
+                
+                // assign before removing
+                let resid = chnid + '_' + strandArray[i].startResi;
 
                 strandArray.splice(i, 1);
 
                 if(strandTmp == 'B' || strandTmp == 'C' || strandTmp == 'E' || strandTmp == 'F') {
                     if(!me.bNode) console.log("Ig strand " + strandTmp + " is removed since it is too short...");
                     
-                    let resid = chnid + '_' + strandArray[i].startResi;
                     let domainid = ic.resid2domainid[resid];
                     removeDomainidHash[domainid] = 1;
                     continue;