icn3d 3.29.16 → 3.29.17

package/icn3d.js

@@ -36881,8 +36881,9 @@ class AnnoCddSite {
                 if(ic.seqStartLen && ic.seqStartLen[chnid]) html2 += ic.showSeqCls.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
 
                 if(me.cfg.blast_rep_id != chnid) { // regular
+                    let color;
                     for(let i = 0, il = fromArray.length; i < il; ++i) {
-                        let color = this.getColorFromPos(chnid, fromArray[i], titleArray);
+                        if(i == 0) color = this.getColorFromPos(chnid, fromArray[i], titleArray);
         
                         let emptyWidth;
                         // if(titleArray) {
@@ -37919,19 +37920,24 @@ class AnnoIg {
             html2 += htmlTitle; 
             html2 += htmlCnt + '<span class="icn3d-seqLine">';
 
+            let prevDomainindex, color;
             for(let i = 0, il = fromArray.length; i < il; ++i) {
                 let resi = ic.ParserUtilsCls.getResi(chnid, fromArray[i]);
                 let resid = chnid + "_" + resi;
-                let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
-                let colorStr =(!atom || atom.color === undefined || atom.color.getHexString() === 'FFFFFF') ? 'DDDDDD' : atom.color.getHexString();
-                let color =(atom && atom.color !== undefined) ? colorStr : "CCCCCC";
 
                 let domainindex = posindex2domainindex[fromArray[i]];
+                if(domainindex != prevDomainindex) {
+                    let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                    let colorStr =(!atom || atom.color === undefined || atom.color.getHexString() === 'FFFFFF') ? 'DDDDDD' : atom.color.getHexString();
+                    color =(atom && atom.color !== undefined) ? colorStr : "CCCCCC";
+                }
 
                 let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i]) / ic.maxAnnoLength) : 
                     Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
                 html2 += '<div style="display:inline-block; width:' + emptyWidth + 'px;">&nbsp;</div>';
                 html2 += '<div style="display:inline-block; color:white!important; font-weight:bold; background-color:#' + color + '; width:' + Math.round(ic.seqAnnWidth *(toArray[i] - fromArray[i] + 1) / ic.maxAnnoLength) + 'px;" class="icn3d-seqTitle ' + linkStr + '" ig="0" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + domainArray[domainindex] + '" index="0" setname="' + chnid + '_igs" id="' + chnid + '_igs" anno="sequence" chain="' + chnid + '" title="' + domainArray[domainindex] + '">' +  domainArray[domainindex] + ' </div>';
+
+                prevDomainindex = domainindex;
             }
 
             html2 += htmlCnt;
@@ -66024,9 +66030,9 @@ class Dssp {
 
         if(bRerunDomain) {
             let atomsAssigned = {};
-            //ic.resid2refnum_ori should be used
-            for(let resid in ic.resid2refnum_ori) {
-                atomsAssigned = me.hashUtilsCls.unionHash(atomsAssigned, ic.residues[resid]);
+            // for(let resid in ic.resid2refnum_ori) {
+            for(let resid in ic.resid2domainid) {
+                if(ic.resid2domainid[resid]) atomsAssigned = me.hashUtilsCls.unionHash(atomsAssigned, ic.residues[resid]);
             }
 
             currAtoms = me.hashUtilsCls.exclHash(currAtoms, atomsAssigned);
@@ -66283,11 +66289,10 @@ class Dssp {
         }
 
         //!!!
-/*
-        // combine the top three clusters for the 2nd round alignment
+
+        // combine the top four clusters for the 2nd round alignment
         if(bRound1) {
             for(let domainid in domainid2refpdbnamelist) {
-                if(!me.bNode) console.log("###score " + ic.domainid2score[domainid].split('_')[0] + " ic.domainid2refpdbname[domainid][0] " + ic.domainid2refpdbname[domainid][0])
                 if(!me.bNode && ic.domainid2refpdbname[domainid][0] == 'all_templates') {
                     let refpdbname2score = domainid2refpdbnamelist[domainid];
                     let refpdbnameList = Object.keys(refpdbname2score);
@@ -66295,12 +66300,11 @@ class Dssp {
                         return refpdbname2score[b] - refpdbname2score[a]
                     });
                     // top 3 templates
-                    ic.domainid2refpdbname[domainid] = refpdbnameList.slice(0,3);
+                    ic.domainid2refpdbname[domainid] = refpdbnameList.slice(0,4);
                 }
-                if(!me.bNode) console.log("###bb ic.domainid2refpdbname[domainid] " + ic.domainid2refpdbname[domainid])
             }
         }
-*/
+
         return domainid2segs; // only used in round 2
     }
 
@@ -67167,6 +67171,7 @@ class Dssp {
                             let currResid = chnid + '_' + currResi;
                             delete ic.residIgLoop[currResid];
                             ic.resid2domainid[currResid] = domainid;
+                            ic.resid2refnum_ori[currResid] = 1; // a hash to check which residues were assigned
                         }
 
                         break;
@@ -67200,6 +67205,7 @@ class Dssp {
                             let currResid = chnid + '_' + currResi;
                             delete ic.residIgLoop[currResid];
                             ic.resid2domainid[currResid] = domainid;
+                            ic.resid2refnum_ori[currResid] = 1; // a hash to check which residues were assigned
                         }
 
                         break;