icn3d 3.30.5 → 3.30.7

package/icn3d.js

@@ -12017,7 +12017,7 @@ class SetDialog {
         tpl2strandsig['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = "A--- A-- A- A B C C' C'' D E F G";
         tpl2strandsig['FAB-HEAVY_5esv_C1-n2']                       = "A B C D E F G";
         tpl2strandsig['FAB-HEAVY_5esv_V-n1']                        = "A B C C' C'' D E F G";
-        tpl2strandsig['FAB-LIGHT_5esv_C1-n2']                       = "A B C C' E F G";
+        tpl2strandsig['FAB-LIGHT_5esv_C1-n2']                       = "A B C C' D E F G";
         tpl2strandsig['FAB-LIGHT_5esv_V-n1']                        = "A A' B C C' C'' D E F G";
         tpl2strandsig['GHR_1axiB_human_C1-n1']                     = "A B C C' D E F G";
         tpl2strandsig['ICOS_6x4gA_human_V']                         = "A B C C' C'' D E F G";
@@ -37993,7 +37993,7 @@ class AnnoIg {
             // titleArray.push(igType + confidance + ' (TM:' + parseFloat(tmscore).toFixed(2) + ')');
             // fullTitleArray.push(igType + confidance + ' (TM:' + parseFloat(tmscore).toFixed(2) + '), template: ' + info.refpdbname + ', Seq. identity: ' + parseFloat(info.seqid).toFixed(2) + ', aligned residues: ' + info.nresAlign);
 
-            let igType = (parseFloat(tmscore) < 0.75 ) ? 'Ig' : ic.ref2igtype[info.refpdbname];
+            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 + ', Seq. identity: ' + parseFloat(info.seqid).toFixed(2) + ', aligned residues: ' + info.nresAlign);
 
@@ -65828,6 +65828,8 @@ class Dssp {
  class Refnum {
     constructor(icn3d) {
         this.icn3d = icn3d;
+        this.TMThreshold = 0.85;
+        this.topClusters = 5;
     }
 
     async hideIgRefNum() { let ic = this.icn3d; ic.icn3dui;
@@ -66385,21 +66387,30 @@ class Dssp {
 
                     if(q_start > 2540 && q_start < 2560) {
                         bBstrand = true;
-                        let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
-                        if(atom.ss == 'helix') bBSheet = false;
                     }
                     else if(q_start > 3540 && q_start < 3560) {
                         bCstrand = true;
-                        let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
-                        if(atom.ss == 'helix') bCSheet = false;
                     }
                     else if(q_start > 7540 && q_start < 7560) {
                         bEstrand = true;
-                        let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
-                        if(atom.ss == 'helix') bESheet = false; 
                     }
                     else if(q_start > 8540 && q_start < 8560) {
                         bFstrand = true;
+                    }
+
+                    if(q_start == 2550) {
+                        let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                        if(atom.ss == 'helix') bBSheet = false;
+                    }
+                    else if(q_start == 3550) {
+                        let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                        if(atom.ss == 'helix') bCSheet = false;
+                    }
+                    else if(q_start == 7550) {
+                        let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                        if(atom.ss == 'helix') bESheet = false; 
+                    }
+                    else if(q_start == 8550) {
                         let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
                         if(atom.ss == 'helix') bFSheet = false;
                     }
@@ -66408,17 +66419,20 @@ class Dssp {
                     if(bBstrand && bCstrand && bEstrand && bFstrand) break;
                 }
 
-                if(!(bBstrand && bCstrand && bEstrand && bFstrand) || !(bBSheet && bCSheet && bESheet && bFSheet)) {
-                // if(!(bBstrand && bCstrand && bEstrand && bFstrand)) {
-                    if(!me.bNode && !(bBstrand && bCstrand && bEstrand && bFstrand)) console.log("Some of the Ig strands B, C, E, F are missing in the domain " + domainid + "...");
-                    if(!me.bNode && !(bBSheet && bCSheet && bESheet && bFSheet)) console.log("Some of the Ig strands B, C, E, F are not beta sheets...");
-                    // if(!me.bNode && (BCnt < 3 || CCnt < 3 || ECnt < 3 || FCnt < 3)) console.log("Some of the Ig strands B, C, E, F are missing in the domain " + domainid + "...");
-                    if(ic.domainid2refpdbname[domainid][0] == refpdbname) {
-                        delete ic.domainid2refpdbname[domainid];
-                        delete ic.domainid2score[domainid];
+                // if(refpdbname != 'CD19_6al5A_human-n1') { // relax for CD19
+                    if(!(bBstrand && bCstrand && bEstrand && bFstrand) || !(bBSheet && bCSheet && bESheet && bFSheet)) {
+                    // if(!(bBstrand && bCstrand && bEstrand && bFstrand)) {
+                        if(!me.bNode && !(bBstrand && bCstrand && bEstrand && bFstrand)) console.log("Some of the Ig strands B, C, E, F are missing in the domain " + domainid + "...");
+                        if(!me.bNode && !(bBSheet && bCSheet && bESheet && bFSheet)) console.log("Some of the Ig strands B, C, E, F are not beta sheets...");
+                        // if(!me.bNode && (BCnt < 3 || CCnt < 3 || ECnt < 3 || FCnt < 3)) console.log("Some of the Ig strands B, C, E, F are missing in the domain " + domainid + "...");
+                        if(ic.domainid2refpdbname[domainid][0] == refpdbname) {
+                            delete ic.domainid2refpdbname[domainid];
+                            delete ic.domainid2score[domainid];
+                        }
+                        // continue;
                     }
-                    continue;
-                }
+                // }
+
             }
 
             if(!bRound1) {
@@ -66447,7 +66461,9 @@ class Dssp {
                 ic.domainid2score[domainid] = queryData[0].score + '_' + queryData[0].frac_identical + '_' + queryData[0].num_res ;
 
                 if(bRound1) {
-                    ic.domainid2refpdbname[domainid] = score > 0.75 ? [refpdbname] : ['all_templates'];
+                    // ic.domainid2refpdbname[domainid] = score > 0.75 ? [refpdbname] : ['all_templates'];
+                    ic.domainid2refpdbname[domainid] = score >= this.TMThreshold ? [refpdbname] : ['all_templates'];
+                    // if(me.bNode) ic.domainid2refpdbname[domainid] = ['all_templates'];
                 }
                 else {
                     ic.domainid2refpdbname[domainid] = [refpdbname];
@@ -66466,7 +66482,7 @@ class Dssp {
             }
         }
 
-        // combine the top four clusters for the 2nd round alignment
+        // combine the top  clusters for the 2nd round alignment
         if(bRound1) {
             for(let domainid in domainid2refpdbnamelist) {
                 if(!me.bNode && ic.domainid2refpdbname[domainid][0] == 'all_templates') {
@@ -66475,8 +66491,8 @@ class Dssp {
                     refpdbnameList.sort(function(a, b) {
                         return refpdbname2score[b] - refpdbname2score[a]
                     });
-                    // top 4 templates
-                    ic.domainid2refpdbname[domainid] = refpdbnameList.slice(0,4);
+                    // top templates
+                    ic.domainid2refpdbname[domainid] = refpdbnameList.slice(0, this.topClusters);
                 }
             }
         }
@@ -66713,8 +66729,8 @@ class Dssp {
                 let seg = segArray[i];
                 if(!seg) continue;
 
-                let qStart = seg.q_start;
-                parseInt(seg.q_start);
+                seg.q_start;
+                let qStartInt = parseInt(seg.q_start);
                 if(isNaN(seg.q_start)) seg.q_start.substr(seg.q_start.length - 1, 1);
 
                 // one item in "seq"
@@ -66727,7 +66743,8 @@ class Dssp {
                     let resid = chainid + '_' + seg.t_start;
                     //let refnum = qStartInt.toString() + postfix;
                     //let refnum = qStart + postfix;
-                    let refnum = qStart;
+                    //let refnum = qStart;
+                    let refnum = qStartInt;
 
                     let refnumLabel = this.getLabelFromRefnum(refnum);
                     currStrand = (refnumLabel) ? refnumLabel.replace(new RegExp(refnum,'g'), '') : undefined;
@@ -67142,7 +67159,7 @@ class Dssp {
         if(!ic.chainid2refpdbname[chnid]) return false;
 
         // auto-generate ref numbers for loops 
-        let currStrand = '', prevStrand = '';
+        let currStrand = '', prevStrand = '', prevValidStrand = '';
         let refnumLabel, refnumStr_ori, refnumStr, postfix, strandPostfix, refnum, refnum3c, refnum2c;
         let bExtendedStrand = false, bSecThird9 = false;
 
@@ -67206,7 +67223,8 @@ class Dssp {
                     if(!bSecThird9 || (bExtendedStrand && !bSecThird9)) {
                         let lastTwo = parseInt(refnum.toString().substr(refnum.toString().length - 2, 2));
                         
-                        if(currStrand != prevStrand) { // reset currCnt
+                        // reset currCnt
+                        if(currStrand != prevStrand && currStrand != prevValidStrand) { // sometimes the same resid appear several times, e.g, 7M7B_H_135
                             bFoundAnchor = false;
 
                             if(strandHash[currStrand + postfix]) {
@@ -67308,6 +67326,8 @@ class Dssp {
                             }
                         }
                     }
+
+                    prevValidStrand = currStrand;
                 }
             }
 
@@ -67395,6 +67415,7 @@ class Dssp {
         for(let il = strandArray.length, i = il - 1; i >= 0; --i) {
             // let strandTmp = strandArray[i].strand.substr(0, 1);
             let strandTmp = strandArray[i].strand;
+
             if(strandTmp != 'G' && strandArray[i].endRefnum - strandArray[i].startRefnum + 1 < 3) { // remove the strand
                 if(i != il - 1) { // modify 
                     strandArray[i + 1].loopResCnt += strandArray[i].loopResCnt + parseInt(strandArray[i].endResi) - parseInt(strandArray[i].startResi) + 1;
@@ -67411,7 +67432,7 @@ class Dssp {
                     let domainid = ic.resid2domainid[resid];
                     removeDomainidHash[domainid] = 1;
                     continue;
-                }
+                }                
             }
         }
 
@@ -67528,10 +67549,12 @@ class Dssp {
                                 let halfLen = parseInt(len / 2.0 + 0.5);
                     
                                 if(loopCnt <= halfLen) {
-                                    currRefnum = strandArray[prevStrandCnt].endRefnum + loopCnt;
-                                    refnumLabelNoPostfix = strandArray[prevStrandCnt].strand + currRefnum;
-                                    refnumLabel = refnumLabelNoPostfix  + strandArray[prevStrandCnt].strandPostfix; 
-                                    domainid = strandArray[prevStrandCnt].domainid;
+                                    if(strandArray[prevStrandCnt]) {
+                                        currRefnum = strandArray[prevStrandCnt].endRefnum + loopCnt;
+                                        refnumLabelNoPostfix = strandArray[prevStrandCnt].strand + currRefnum;
+                                        refnumLabel = refnumLabelNoPostfix  + strandArray[prevStrandCnt].strandPostfix; 
+                                        domainid = strandArray[prevStrandCnt].domainid;
+                                    }
                                 }
                                 else {
                                     currRefnum = strandArray[strandCnt].startRefnum - len + loopCnt - 1;