icn3d 3.25.18 → 3.25.20

package/icn3d.js

@@ -41966,17 +41966,7 @@ class ShowSeq {
                 html3 += '</div></div>';
             }         
             else if(ic.bShowRefnum && ic.chainid2refpdbname.hasOwnProperty(chnid)) {              
-                let result = this.showRefNum(giSeq, chnid);
-                html += result.html;
-                html3 += result.html3;
-
-                let kabat_or_imgt = 1;
-                result = this.showRefNum(giSeq, chnid, kabat_or_imgt);
-                html += result.html;
-                html3 += result.html3;
-
-                kabat_or_imgt = 2;
-                result = this.showRefNum(giSeq, chnid, kabat_or_imgt);
+                let result = this.showAllRefNum(giSeq, chnid);
                 html += result.html;
                 html3 += result.html3;
             }
@@ -42004,7 +41994,27 @@ class ShowSeq {
         $("#" + ic.pre + 'tt_giseq_' + chnid).html(html3); // fixed title for scrolling
     }
 
-    showRefNum(giSeq, chnid, kabat_or_imgt, bCustom) {  let ic = this.icn3d; ic.icn3dui;
+    showAllRefNum(giSeq, chnid) {  let ic = this.icn3d; ic.icn3dui;
+        let html = '', html3 = '';
+
+        let result = this.showRefNum(giSeq, chnid);
+        html += result.html;
+        html3 += result.html3;
+
+        let kabat_or_imgt = 1;
+        result = this.showRefNum(giSeq, chnid, kabat_or_imgt);
+        html += result.html;
+        html3 += result.html3;
+
+        kabat_or_imgt = 2;
+        result = this.showRefNum(giSeq, chnid, kabat_or_imgt);
+        html += result.html;
+        html3 += result.html3;
+
+        return {'html': html, 'html3': html3};
+    }
+
+    showRefNum(giSeq, chnid, kabat_or_imgt, bCustom) {  let ic = this.icn3d, me = ic.icn3dui;
         let html = '', html3 = '';
 
         let chainList = '';
@@ -42036,11 +42046,12 @@ class ShowSeq {
 
         //check if Kabat refnum available
         let bKabatFound = false;
+
         for(let i = 0, il = giSeq.length; i < il; ++i) {
             let currResi = ic.ParserUtilsCls.getResi(chnid, i);
             let residueid = chnid + '_' + currResi;
             let domainid = (bCustom) ? 0 : ic.resid2domainid[residueid];
-
+            
             if(ic.domainid2ig2kabat[domainid] && Object.keys(ic.domainid2ig2kabat[domainid]).length > 0) {
                 bKabatFound = true;
                 break;
@@ -42073,7 +42084,7 @@ class ShowSeq {
         // sometimes one chain may have several Ig domains,set an index for each IgDomain
         let index = 1, bStart = false;
 
-        if(!bCustom && !kabat_or_imgt) {     
+        if(!bCustom && !kabat_or_imgt && !me.bNode) { // domnot overwrite loop in node  
             // reset ic.residIgLoop for the current selection, which could be the second round of ref num assignment
             let residHash = ic.firstAtomObjCls.getResiduesFromAtoms(ic.hAtoms);
             for(let resid in residHash) {
@@ -62536,8 +62547,8 @@ class Dssp {
 
         let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
 
-        // if(!ic.resid2domainid) ic.resid2domainid = {};
-        ic.resid2domainid = {};
+        if(!ic.resid2domainid) ic.resid2domainid = {};
+        //ic.resid2domainid = {};
         ic.domainid2pdb = {};
 
         let minResidues = 20;
@@ -62571,8 +62582,8 @@ class Dssp {
                     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';
-                    }   
+                        ic.resid2domainid[resid] = chainid + '-0' + '_' + Object.keys(currAtoms).length; 
+                    }
                 }
                 else {                 
                     for(let k = 0, kl = subdomains.length; k < kl; ++k) {
@@ -62583,15 +62594,23 @@ 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 resid = chainid + '_' + pos2resi[n];
                                 domainAtoms = me.hashUtilsCls.unionHash(domainAtoms, ic.residues[resid]);
-                                ic.resid2domainid[resid] = chainid + '-' + k;
+                                //ic.resid2domainid[resid] = chainid + '-' + k;
                             }
                         }
 
                         domainAtomsArray.push(domainAtoms);
+
+                        for(let m = 0, ml = segArray.length; m < ml; m += 2) {
+                            let startResi = segArray[m];
+                            let endResi = segArray[m+1];
+                            for(let n = parseInt(startResi); n <= parseInt(endResi); ++n) {
+                                let resid = chainid + '_' + pos2resi[n];
+                                //domainAtoms = me.hashUtilsCls.unionHash(domainAtoms, ic.residues[resid]);
+                                ic.resid2domainid[resid] = chainid + '-' + k + '_' + Object.keys(domainAtoms).length; 
+                            }
+                        }
                     }
                 }