icn3d 3.31.4 → 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];
       }
 
@@ -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;
                 }
             }
@@ -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 = {};
 
@@ -71267,7 +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;
                     }
                 //}
@@ -71858,7 +71858,7 @@ class Dssp {
                             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;
@@ -71895,7 +71895,7 @@ class Dssp {
                             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;
@@ -71926,7 +71926,7 @@ class Dssp {
                     let domainid = ic.resid2domainid[resid];
                     removeDomainidHash[domainid] = 1;
                     continue;
-                }                
+                }   
             }
         }
 
@@ -72119,6 +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;