icn3d 3.31.3 → 3.31.5

package/icn3d.js

@@ -8902,7 +8902,7 @@ class ClickMenu {
          let resid = residueArray[i];
 
          if(ic.resid2refnum) delete ic.resid2refnum[resid];
-         if(ic.resid2refnum_ori) delete ic.resid2refnum_ori[resid];
+         // if(ic.resid2refnum_ori) delete ic.resid2refnum_ori[resid];
          if(ic.resid2domainid) delete ic.resid2domainid[resid];
       }
 
@@ -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);
 
@@ -42516,13 +42516,11 @@ class Domain3d {
 	init3ddomain() { let ic = this.icn3d; ic.icn3dui;
         //this.dcut = 8; // threshold for C-alpha interactions
 
-		// It seemed the threshold 7 angstrom works better
-		//this.dcut = 7; // threshold for C-alpha interactions
 		this.dcut = 8; // threshold for C-alpha interactions
 
 		// added by Jiyao
-		// pdbid 1CD8 requires a min contact 4, not 5
-		this.min_contacts = 4; //5; //3;			// minimum number of contacts to be considered as neighbors
+		// Ig domain should not be separated into two parts, set min as 2
+		this.min_contacts = 2; //3;			// minimum number of contacts to be considered as neighbors
 
 		this.MAX_SSE = 512;
 
@@ -46238,8 +46236,10 @@ class Annotation {
                 }
             }
 
+            ic.bRunRefnumAgain = true;
             for(let chainid in ic.protein_chainid) {
                 await ic.annoIgCls.showIg(chainid, template);
+                ic.bRunRefnumAgain = false; // run it once for all chains
             }
         // }
         // ic.bIgShown = true;
@@ -54627,7 +54627,7 @@ class MmdbParser {
         if(Object.keys(data.atoms).length == 0) { // for large structures such as 3J3Q
             // use mmtfid
             let pdbid = data.pdbId;
-            await ic.bciffParserCls.downloadBcif(pdbid);
+            await ic.bcifParserCls.downloadBcif(pdbid);
 
             return;
         }
@@ -70547,6 +70547,7 @@ class Dssp {
         ic.domainid2pdb = {};
 
         let bNoMoreIg = true;
+        let bFoundDomain = false;
         for(let i = 0, il = struArray.length; i < il; ++i) {
             let struct = struArray[i];
             let chainidArray = ic.structures[struct];
@@ -70560,6 +70561,12 @@ class Dssp {
                 if(!ic.domainid2refpdbname) ic.domainid2refpdbname = {};
                 if(!ic.domainid2score) ic.domainid2score = {};
 
+                if(domainAtomsArray.length == 0) {
+                    continue;
+                }
+
+                bFoundDomain = true;
+
                 for(let k = 0, kl = domainAtomsArray.length; k < kl; ++k) {
                     bNoMoreIg = false;
 
@@ -70573,6 +70580,10 @@ class Dssp {
                     let resiSum = atomFirst.resi + ':' + atomLast.resi + ':' + Object.keys(domainAtomsArray[k]).length;
                     //let domainid = chainid + '-' + k + '_' + Object.keys(domainAtomsArray[k]).length;
                     let domainid = chainid + ',' + k + '_' + resiSum;
+
+                    // clear score
+                    delete ic.domainid2score[domainid];
+
                     ic.domainid2pdb[domainid] = pdb_target;
 
                     if(!template) {
@@ -70602,6 +70613,10 @@ class Dssp {
             }
         }
 
+        if(!bFoundDomain) {
+            return bNoMoreIg;
+        }
+
         //try {
             if(!template) {
                 let dataArray2 = [];
@@ -70737,27 +70752,13 @@ class Dssp {
                         // clear previous refnum assignment if any
                         // delete ic.resid2refnum[resid];
                         delete ic.residIgLoop[resid];
+                        delete ic.resid2domainid[resid];
                     }
                 }
 
                 if(resCnt < minResidues) continue;
 
                 domainAtomsArray.push(domainAtoms);
-/*
-                let atomFirst = ic.firstAtomObjCls.getFirstAtomObj(domainAtoms);
-                let atomLast = ic.firstAtomObjCls.getLastAtomObj(domainAtoms);
-                let resiSum = atomFirst.resi + ':' + atomLast.resi + ':' + Object.keys(domainAtoms).length;
-
-                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 - 1];
-                        //domainAtoms = me.hashUtilsCls.unionHash(domainAtoms, ic.residues[resid]);
-                        ic.resid2domainid[resid] = chainid + ',' + k + '_' + resiSum;
-                    }
-                }
-*/
             }
         }
 
@@ -70797,6 +70798,7 @@ class Dssp {
         if(!ic.domainid2ig2imgt) ic.domainid2ig2imgt = {};
 
         let minResidues = 20;
+
         for(let i = 0, il = domainidpairArray.length; i < il; ++i) {
             //let queryData = (me.bNode) ? dataArray[i] : dataArray[i].value; //[0];
             let queryData = (dataArray[i]) ? dataArray[i].value : undefined; //[0];
@@ -70816,15 +70818,12 @@ class Dssp {
 
             if(!bRound1) {
                 if(queryData[0].score < tmscoreThreshold || queryData[0].num_res < minResidues) {
-                    if(!me.bNode) console.log("domainid " + domainid + " and refpdbname " + refpdbname + " were skipped due to a TM-score less than " + tmscoreThreshold);
+                    if(!me.bNode) console.log("bRound1: " + bRound1 + ": domainid " + domainid + " and refpdbname " + refpdbname + " were skipped due to a TM-score less than " + tmscoreThreshold);
                     continue;
                 }
             }
             else {
-                // if(queryData[0].super_rmsd > rmsdThreshold || queryData[0].num_res < minResidues) {
-                //     continue;
-                // }
-                if(queryData[0].score < tmscoreThreshold || queryData[0].num_res < minResidues) {
+                if(queryData[0].score < tmscoreThreshold || queryData[0].num_res < minResidues / 2) {
                     continue;
                 }
             }
@@ -70894,7 +70893,7 @@ class Dssp {
                             delete ic.domainid2refpdbname[domainid];
                             delete ic.domainid2score[domainid];
                         }
-                        // continue;
+                        continue;
                     }
                 // }
 
@@ -70973,6 +70972,7 @@ class Dssp {
         let domainid2segs = this.parseAlignData_part1(dataArray, domainidpairArray, bRound1);
 
         // no more Igs to detect
+        // no need to rerun the rest residues any more
         if(Object.keys(domainid2segs).length == 0) {
             bNoMoreIg = true;
             return bNoMoreIg;
@@ -71044,7 +71044,7 @@ class Dssp {
 
             dataArray3 = await this.promiseWithFixedJobs(ajaxArray);
 
-            await this.parseAlignData(dataArray3, domainidpairArray3, false);
+            bNoMoreIg = await this.parseAlignData(dataArray3, domainidpairArray3, false);
 
             // end of round 2
             return bNoMoreIg;
@@ -71094,7 +71094,7 @@ class Dssp {
 
         // assign ic.resid2refnum, ic.refnum2residArray, ic.chainsMapping
         if(!ic.resid2refnum) ic.resid2refnum = {};
-        if(!ic.resid2refnum_ori) ic.resid2refnum_ori = {};
+        // if(!ic.resid2refnum_ori) ic.resid2refnum_ori = {};
         if(!ic.refnum2residArray) ic.refnum2residArray = {};
         if(!ic.chainsMapping) ic.chainsMapping = {};
 
@@ -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};
             }
@@ -71265,7 +71267,7 @@ class Dssp {
                     // only sheet or loop will be aligned
                     if(atom.ss != 'helix') {
                         ic.resid2refnum[resid] = refnumLabel;
-                        ic.resid2refnum_ori[resid] = refnumLabel;
+                        // ic.resid2refnum_ori[resid] = refnumLabel;
                         ic.resid2domainid[resid] = domainid;
                     }
                 //}
@@ -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;
@@ -71824,8 +71855,10 @@ 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
+                            // ic.resid2refnum_ori[currResid] = 1; // a hash to check which residues were assigned
                         }
 
                         break;
@@ -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) {
@@ -71858,8 +71892,10 @@ 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
+                            // ic.resid2refnum_ori[currResid] = 1; // a hash to check which residues were assigned
                         }
 
                         break;
@@ -71890,7 +71926,7 @@ class Dssp {
                     let domainid = ic.resid2domainid[resid];
                     removeDomainidHash[domainid] = 1;
                     continue;
-                }                
+                }   
             }
         }
 
@@ -72083,6 +72119,7 @@ class Dssp {
                 // remove domians without B,C,E,F strands
                 if(removeDomainidHash.hasOwnProperty(domainid)) {
                     delete ic.resid2refnum[residueid];
+                    delete ic.residIgLoop[residueid];
                     delete ic.resid2domainid[residueid];
 
                     continue;