icn3d 3.25.17 → 3.25.19

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;
             }
@@ -42004,6 +41994,26 @@ class ShowSeq {
         $("#" + ic.pre + 'tt_giseq_' + chnid).html(html3); // fixed title for scrolling
     }
 
+    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; ic.icn3dui;
         let html = '', html3 = '';
 
@@ -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;
@@ -42181,12 +42192,10 @@ class ShowSeq {
                 prevStrand = currStrand;
             }
 
-            // 2. remove strands with less than 3 residues
+            // 2. remove strands with less than 3 residues except G strand
             for(let il = strandArray.length, i = il - 1; i >= 0; --i) {
-                if(strandArray[i].endRefnum - strandArray[i].startRefnum + 1 < 3) { // remove the strand
+                if(strandArray[i].strand.substr(0, 1) != 'G' && strandArray[i].endRefnum - strandArray[i].startRefnum + 1 < 3) { // remove the strand
                     if(i != il - 1) { // modify 
-                        // strandArray[i + 1].loopResCnt += strandArray[i].loopResCnt + strandArray[i].endRefnum - strandArray[i].startRefnum + 1;
-
                         strandArray[i + 1].loopResCnt += strandArray[i].loopResCnt + parseInt(strandArray[i].endResi) - parseInt(strandArray[i].startResi) + 1;
                     }
 
@@ -62538,8 +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;
@@ -62573,8 +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) {
@@ -62585,15 +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; 
+                            }
+                        }
                     }
                 }