icn3d 3.31.3 → 3.31.4

package/icn3d.js

@@ -41171,7 +41171,7 @@ class AnnoIg {
 
             let igType = (parseFloat(tmscore) < ic.refnumCls.TMThreshold ) ? 'Ig' : ic.ref2igtype[info.refpdbname];
             titleArray.push(igType + ' (TM:' + parseFloat(tmscore).toFixed(2) + ')');
-            fullTitleArray.push(igType + ' (TM:' + parseFloat(tmscore).toFixed(2) + '), template: ' + info.refpdbname + ', type: ' + ic.ref2igtype[info.refpdbname] + ' Seq. identity: ' + parseFloat(info.seqid).toFixed(2) + ', aligned residues: ' + info.nresAlign);
+            fullTitleArray.push(igType + ' (TM:' + parseFloat(tmscore).toFixed(2) + '), template: ' + info.refpdbname + ', type: ' + ic.ref2igtype[info.refpdbname] + ', Seq. identity: ' + parseFloat(info.seqid).toFixed(2) + ', aligned residues: ' + info.nresAlign);
 
             domainArray.push(igType);
 
@@ -70894,7 +70894,7 @@ class Dssp {
                             delete ic.domainid2refpdbname[domainid];
                             delete ic.domainid2score[domainid];
                         }
-                        // continue;
+                        continue;
                     }
                 // }
 
@@ -71115,10 +71115,12 @@ class Dssp {
 
             if(refpdbname) {
                 let message = "The reference PDB for domain " + domainid + " is " + refpdbname + ". The TM-score is " + score  + ". The sequence identity is " + seqid  + ". The number of aligned residues is " + nresAlign + ".";
+
                 if(!me.bNode) {
                     console.log(message);
                     me.htmlCls.clickMenuCls.setLogCmd(message, false, true);
                 }
+
                 // ic.refPdbList.push(message);
                 ic.domainid2info[domainid] = {'refpdbname': refpdbname, 'score': score, 'seqid': seqid, 'nresAlign': nresAlign};
             }
@@ -71322,7 +71324,7 @@ class Dssp {
         // loops may have numbers such as 1310, 1410
 
         let strand;
-
+/*
         if(refnum < 1000) strand = undefined;
         else if(refnum >= 1200 && refnum < 1290) strand = "A---";
         else if(refnum >= 1320 && refnum < 1390) strand = "A--";
@@ -71345,6 +71347,34 @@ class Dssp {
         else if(refnum >= 9720 && refnum < 9790) strand = "G++";
         else if(refnum > 9900) strand = undefined;
         else strand = " ";
+*/
+
+        // cover all ranges
+        if(refnum < 1000) strand = undefined;
+        else if(refnum >= 1200 && refnum < 1320) strand = "A---";
+        else if(refnum >= 1320 && refnum < 1420) strand = "A--";
+        else if(refnum >= 1420 && refnum < 1520) strand = "A-";
+        else if(refnum >= 1520 && refnum < 1620) strand = "A";
+        else if(refnum >= 1620 && refnum < 1720) strand = "A+";
+        else if(refnum >= 1720 && refnum < 1820) strand = "A++";
+        else if(refnum >= 1820 && refnum < 2000) strand = "A'";
+        else if(refnum >= 2000 && refnum < 3000) strand = "B";
+        else if(refnum >= 3000 && refnum < 3420) strand = "C--";
+        else if(refnum >= 3420 && refnum < 3520) strand = "C-";
+        else if(refnum >= 3520 && refnum < 4000) strand = "C";
+        else if(refnum >= 4000 && refnum < 5000) strand = "C'";
+        else if(refnum >= 5000 && refnum < 6000) strand = "C''";
+        else if(refnum >= 6000 && refnum < 7000) strand = "D";
+        else if(refnum >= 7000 && refnum < 7620) strand = "E";
+        else if(refnum >= 7620 && refnum < 8000) strand = "E+";
+        else if(refnum >= 8000 && refnum < 9000) strand = "F";
+        else if(refnum >= 9000 && refnum < 9620) strand = "G";
+        else if(refnum >= 9620 && refnum < 9720) strand = "G+";
+        else if(refnum >= 9720 && refnum < 9820) strand = "G++";
+        else if(refnum >= 9820 && refnum < 9900) strand = "G+++";
+        else if(refnum > 9900) strand = undefined;
+        else strand = " ";
+
         if(prevStrand) strand = prevStrand;
 
         return strand
@@ -71666,7 +71696,7 @@ class Dssp {
                 refnum3c = (refnum - parseInt(refnum/1000) * 1000).toString();
                 refnum2c = (refnum - parseInt(refnum/100) * 100).toString();
 
-                // for extended strands, since A is 1550 and A+ is 1650, then the AA+ loop will be 1591, 1592, ... 1610, 1611, etc
+                // for extended strands, since A is 1550 and A+ is 1650, then the AA+ loop will be 1591, 1592, ... 1618, 1619, etc
                 bSecThird9 = refnum3c.substr(0,1) == '9' || refnum2c.substr(0,1) == '9' || refnum2c.substr(0,1) == '0' || refnum2c.substr(0,1) == '1';
                 if(bSecThird9) ic.residIgLoop[residueid] = 1;
 
@@ -71812,6 +71842,7 @@ class Dssp {
                     let domainid = ic.resid2domainid[currResid];
                     if(currAtom.ssbegin) { // find the start of the sheet
                         // update the following: startResi,startRefnum,endResi,endRefnum,loopResCnt,resCntBfAnchor,resCntAtAnchor
+                        let oriStartRefnum = strandArray[i].startRefnum;
                         strandArray[i].startResi = currResi;
                         strandArray[i].startRefnum -= j;
                         strandArray[i].loopResCnt -= j;
@@ -71824,6 +71855,8 @@ class Dssp {
                             currResi = ic.ParserUtilsCls.getResi(chnid, currPos);
                             let currResid = chnid + '_' + currResi;
                             delete ic.residIgLoop[currResid];
+                            ic.resid2refnum[currResid] = strandArray[i].strand + (oriStartRefnum - k).toString();
+
                             ic.resid2domainid[currResid] = domainid;
                             ic.resid2refnum_ori[currResid] = 1; // a hash to check which residues were assigned
                         }
@@ -71844,6 +71877,7 @@ class Dssp {
                     let domainid = ic.resid2domainid[currResid];
                     if(currAtom.ssend) { // find the end of the sheet
                         // update the following: startResi,startRefnum,endResi,endRefnum,loopResCnt,resCntBfAnchor,resCntAtAnchor
+                        let oriEndRefnum = strandArray[i].endRefnum;
                         strandArray[i].endResi = currResi;
                         strandArray[i].endRefnum += j;
                         if(i < il - 1) {
@@ -71858,6 +71892,8 @@ class Dssp {
                             currResi = ic.ParserUtilsCls.getResi(chnid, currPos);
                             let currResid = chnid + '_' + currResi;
                             delete ic.residIgLoop[currResid];
+                            ic.resid2refnum[currResid] = strandArray[i].strand + (oriEndRefnum + k).toString();
+
                             ic.resid2domainid[currResid] = domainid;
                             ic.resid2refnum_ori[currResid] = 1; // a hash to check which residues were assigned
                         }