icn3d 3.30.3 → 3.30.4

package/icn3d.module.js

@@ -6729,7 +6729,7 @@ 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;
@@ -8315,7 +8315,7 @@ 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();
@@ -15894,7 +15894,7 @@ class AlignSeq {
         alignChainArray = Object.keys(ic.alnChains);
 
         if (bReverse) alignChainArray = alignChainArray.reverse();
-
+        
         let maxSeqCnt = 0;
 
         let chainHash = {};
@@ -38621,8 +38621,6 @@ 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;
@@ -43410,7 +43408,7 @@ class Annotation {
 
         ic.bRunRefnumAgain = true;
         await this.updateIg();
-        // ic.bRunRefnumAgain = false;
+        ic.bRunRefnumAgain = false;
 
         this.updateInteraction();
     }
@@ -43492,8 +43490,9 @@ 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();
 
@@ -43606,6 +43605,7 @@ 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();
@@ -43768,7 +43768,7 @@ class Annotation {
                 await thisClass.setAnnoTabIg();
                 me.htmlCls.clickMenuCls.setLogCmd("set annotation ig", true);
 
-                // ic.bRunRefnumAgain = false;
+                ic.bRunRefnumAgain = false;
             }
             else {
                 thisClass.hideAnnoTabIg();
@@ -49992,7 +49992,7 @@ 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) {
@@ -50815,6 +50815,7 @@ 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);
         }
 
@@ -56583,7 +56584,8 @@ 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();
             //   }
@@ -58257,7 +58259,14 @@ 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);
                     // }
 
@@ -60051,6 +60060,7 @@ 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);
     }
 
@@ -60995,7 +61005,7 @@ 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;
@@ -61003,7 +61013,7 @@ 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();
@@ -63726,7 +63736,7 @@ 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);
@@ -67357,8 +67367,6 @@ class Dssp {
             }
         }
 
-        //!!!
-
         // combine the top four clusters for the 2nd round alignment
         if(bRound1) {
             for(let domainid in domainid2refpdbnamelist) {
@@ -68292,13 +68300,15 @@ 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;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "icn3d",
-  "version": "3.30.3",
+  "version": "3.30.4",
   "main": "./icn3d.js",
   "exports": {
     ".": {