icn3d 3.25.14 → 3.25.15

package/icn3d.js

@@ -52223,13 +52223,15 @@ class ParserUtils {
         let allPromise = Promise.allSettled([prms1, prms2]);
         let dataArray = await allPromise;
         
-        ic.interactionData1 = (me.bNode) ? dataArray[0] : dataArray[0].value;
+        // ic.interactionData1 = (me.bNode) ? dataArray[0] : dataArray[0].value;
+        ic.interactionData1 = dataArray[0].value;
         ic.html2ddgm = '';
         ic.diagram2dCls.draw2Ddgm(ic.interactionData1, mmdbid1, 0);
         if(me.cfg.show2d) me.htmlCls.dialogCls.openDlg('dl_2ddgm', 'Interactions');
 
 
-        ic.interactionData2 = (me.bNode) ? dataArray[1] : dataArray[1].value;
+        // ic.interactionData2 = (me.bNode) ? dataArray[1] : dataArray[1].value;
+        ic.interactionData2 = dataArray[1].value;
         ic.diagram2dCls.draw2Ddgm(ic.interactionData2, mmdbid2, 1);
 
         ic.html2ddgm += "<br>" + ic.diagram2dCls.set2DdgmNote(true);
@@ -52277,7 +52279,8 @@ class ParserUtils {
         // Each argument is an array with the following structure: [ data, statusText, jqXHR ]
         //var data2 = v2[0];
         for(let index = 0, indexl = chainidArray.length; index < indexl; ++index) {
-            let data = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
+            // let data = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
+            let data = dataArray[index].value;//[0];
             let mmdbid = chainidArray[index].substr(0, chainidArray[index].indexOf('_'));
 
             ic.diagram2dCls.draw2Ddgm(data, mmdbid, 0);
@@ -55969,7 +55972,8 @@ class Vastplus {
 
         let queryDataArray = [];
         for(let index = 0, indexl = chainidpairArray.length; index < indexl; ++index) {
-            let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
+            // let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
+            let queryData = dataArray[index].value; //[0];
 
             queryDataArray.push(queryData);
 /*
@@ -71253,25 +71257,35 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
             let data = await me.getAjaxPromise(url, 'json', false, 'The RID ' + me.cfg.rid + ' may have expired...');
 
             for(let q = 0, ql = data.BlastOutput2.length; q < ql; ++q) {
-                if(data.BlastOutput2[q].report.results.search.query_id != me.cfg.query_id) continue;
-                let hitArray = data.BlastOutput2[q].report.results.search.hits;
+                
+                let hitArray;
+                if(data.BlastOutput2[q].report.results.iterations) { // psi-blast may have "iterations". Use the last iteration.
+                    let nIterations = data.BlastOutput2[q].report.results.iterations.length;
+                    if(data.BlastOutput2[q].report.results.iterations[nIterations - 1].search.query_id != me.cfg.query_id) continue;
+                    hitArray = data.BlastOutput2[q].report.results.iterations[nIterations - 1].search.hits;
+                }
+                else { // blastp may not have "iterations"
+                    if(data.BlastOutput2[q].report.results.search.query_id != me.cfg.query_id) continue;
+                    hitArray = data.BlastOutput2[q].report.results.search.hits;
+                }
+                
                 let qseq = undefined;
                 for(let i = 0, il = hitArray.length; i < il; ++i) {
-                let hit = hitArray[i];
-                let bFound = false;
-                for(let j = 0, jl = hit.description.length; j < jl; ++j) {
-                    let acc = hit.description[j].accession;
-                    if(acc == me.cfg.blast_rep_id) {
-                    bFound = true;
-                    break;
+                    let hit = hitArray[i];
+                    let bFound = false;
+                    for(let j = 0, jl = hit.description.length; j < jl; ++j) {
+                        let acc = hit.description[j].accession;
+                        if(acc == me.cfg.blast_rep_id) {
+                            bFound = true;
+                            break;
+                        }
+                    }
+                    if(bFound) {
+                        qseq = hit.hsps[0].qseq;
+                        //remove gap '-'
+                        qseq = qseq.replace(/-/g, '');
+                        break;
                     }
-                }
-                if(bFound) {
-                    qseq = hit.hsps[0].qseq;
-                    //remove gap '-'
-                    qseq = qseq.replace(/-/g, '');
-                    break;
-                }
                 }
                 if(qseq !== undefined) me.cfg.query_id = qseq;
                 ic.inputid = me.cfg.query_id + '_' + me.cfg.blast_rep_id;