icn3d 3.31.10 → 3.31.12

package/icn3d.js

@@ -46964,6 +46964,7 @@ class ShowAnno {
                   // the missing residues at the end of the seq will be filled up in the API showNewTrack()
                   let nGap = 0;
                   ic.alnChainsSeq[chnid] = [];
+
                   //let offset =(ic.chainid2offset[chnid]) ? ic.chainid2offset[chnid] : 0;                
                   for(let i = 0, il = targetSeq.length; i < il; ++i) {
                       //text += ic.showSeqCls.insertGap(chnid, i, '-', true);
@@ -57057,8 +57058,9 @@ class RealignParser {
       }
 
       // If rmsd from vastsrv is too large, realign the chains
-      //if(me.cfg.chainalign && !me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5) {   
-      if(!me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5) {     
+      //if(me.cfg.chainalign && !me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5) {  
+      // redo algnment only for VAST serv page 
+      if(!me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5) {    
         console.log("RMSD from VAST is larger than 5. Realign the chains with TM-align."); 
         //let nameArray = me.cfg.chainalign.split(',');
         let nameArray = Object.keys(chainidHash);
@@ -71640,7 +71642,7 @@ class Dssp {
     }
 
     rmStrandFromRefnumlabel(refnumLabel) { let ic = this.icn3d; ic.icn3dui;
-        if(isNaN(refnumLabel.substr(0,1))) {
+        if(refnumLabel && isNaN(refnumLabel.substr(0,1))) {
             return (!refnumLabel) ? refnumLabel : refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').replace(/\+/g, '').replace(/\-/g, '').substr(1); // C', C''
         }
         else { // custom ref numbers
@@ -71693,25 +71695,16 @@ class Dssp {
                 }
             }
 
-            // let bIgDomain = (ic.domainid2info && Object.keys(ic.domainid2info).length > 0) ? 1 : 0;
-            let stru2bIgDomain = {};
-            for(let domainid in ic.domainid2info) {
-                let stru = domainid.split('_')[0];
-                stru2bIgDomain[stru] = 1;
-            }
-
         // if(bIgDomain) {
             for(let structure in ic.structures) {
-                let bIgDomain = stru2bIgDomain.hasOwnProperty(structure) ? 1 : 0;
-
-                refData += '{"' + structure + '": {"Ig domain" : ' + bIgDomain + ', "igs": [\n';
-
+                let bIgDomain = 0;
+                let refDataTmp = '';
                 for(let m = 0, ml = ic.structures[structure].length; ic.bShowRefnum && m < ml; ++m) {
                     let chnid = ic.structures[structure][m]; 
                     let igArray = ic.chain2igArray[chnid];
 
                     if(igArray && igArray.length > 0) {
-                        refData += '{"' + chnid + '": {\n';
+                        refDataTmp += '{"' + chnid + '": {\n';
 
                         for(let i = 0, il = igArray.length; i < il; ++i) {
                             let startPosArray = igArray[i].startPosArray;
@@ -71720,26 +71713,32 @@ class Dssp {
                             let info = ic.domainid2info[domainid];
                             if(!info) continue;
 
-                            refData += '"' + domainid + '": {\n';
+                            refDataTmp += '"' + domainid + '": {\n';
 
-                            refData += '"refpdbname":"' + info.refpdbname + '", "score":' + info.score + ', "seqid":' + info.seqid + ', "nresAlign":' + info.nresAlign + ', "data": [';
+                            refDataTmp += '"refpdbname":"' + info.refpdbname + '", "score":' + info.score + ', "seqid":' + info.seqid + ', "nresAlign":' + info.nresAlign + ', "data": [';
                             for(let j = 0, jl = startPosArray.length; j < jl; ++j) {
                                 let startPos = startPosArray[j];
                                 let endPos = endPosArray[j];
                                 for(let k = startPos; k <= endPos; ++k) {
                                     const resid = chnid + '_' + ic.chainsSeq[chnid][k].resi + '_' + ic.chainsSeq[chnid][k].name;
-                                    refData += '{"' + resid + '": "' + resid2refnum[resid] + '"},\n';
+                                    refDataTmp += '{"' + resid + '": "' + resid2refnum[resid] + '"},\n';
                                 }
                             }
-                            refData += '],\n';
+                            refDataTmp += '],\n';
+
+                            refDataTmp += '},\n';
 
-                            refData += '},\n';
+                            bIgDomain = 1;
                         }
 
-                        refData += '}},\n';
+                        refDataTmp += '}},\n';
                     }
                 }
 
+                refData += '{"' + structure + '": {"Ig domain" : ' + bIgDomain + ', "igs": [\n';
+
+                if(bIgDomain) refData += refDataTmp;
+
                 refData += ']}},\n';
             }
         // }
@@ -72104,7 +72103,7 @@ class Dssp {
             let strandTmp = strandArray[i].strand;
 
             if(strandTmp != 'G' && strandArray[i].endRefnum - strandArray[i].startRefnum + 1 < 3) { // remove the strand
-                if(i != il - 1) { // modify 
+                if(strandArray[i + 1]) { // modify 
                     strandArray[i + 1].loopResCnt += strandArray[i].loopResCnt + parseInt(strandArray[i].endResi) - parseInt(strandArray[i].startResi) + 1;
                 }