icn3d 3.31.5 → 3.31.6

package/icn3d.js

@@ -36179,7 +36179,7 @@ class Alternate {
         
         ic.drawCls.draw();
 
-        ic.bShowHighlight = true;
+        ic.bShowHighlight = true; //reset
     }
 
     async alternateWrapper() { let ic = this.icn3d; ic.icn3dui;
@@ -41169,7 +41169,7 @@ class AnnoIg {
 
             let tmscore = info.score;
 
-            let igType = (parseFloat(tmscore) < ic.refnumCls.TMThreshold ) ? 'Ig' : ic.ref2igtype[info.refpdbname];
+            let igType = (parseFloat(tmscore) < ic.refnumCls.TMThresholdIgType ) ? '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);
 
@@ -46218,36 +46218,32 @@ class Annotation {
     }
 
     async updateIg(bSelection, template) { let ic = this.icn3d, me = ic.icn3dui;
-        if(bSelection) { // clear previous refnum
-            let residueHash = ic.firstAtomObjCls.getResiduesFromAtoms(ic.hAtoms);
-            for(let resid in residueHash) {
-                if(ic.resid2refnum) delete ic.resid2refnum[resid];
-                if(ic.residIgLoop) delete ic.residIgLoop[resid];
-                if(ic.resid2domainid) delete ic.resid2domainid[resid];
+        ic.opts['color'] = 'ig strand';
+
+        // if(!bSelection && !template) {
+        if(!bSelection) {
+            // select all protein chains
+            ic.hAtoms = {};
+            for(let chainid in ic.protein_chainid) {
+                ic.hAtoms = me.hashUtilsCls.unionHash(ic.hAtoms, ic.chains[chainid]);
             }
         }
 
-        // if(!ic.bIgShown) {
-            if(!bSelection && !template) {
-                // select all protein chains
-                ic.hAtoms = {};
-                for(let chainid in ic.protein_chainid) {
-                    ic.hAtoms = me.hashUtilsCls.unionHash(ic.hAtoms, ic.chains[chainid]);
-                }
-            }
+        // clear previous refnum
+        let residueHash = ic.firstAtomObjCls.getResiduesFromAtoms(ic.hAtoms);
+        for(let resid in residueHash) {
+            if(ic.resid2refnum) delete ic.resid2refnum[resid];
+            if(ic.residIgLoop) delete ic.residIgLoop[resid];
+            if(ic.resid2domainid) delete ic.resid2domainid[resid];
+        }
 
-            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;
+        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
+        }
 
         if(ic.bShowRefnum) {
-            // ic.opts.color = 'ig strand';
-            // ic.setColorCls.setColorByOptions(ic.opts, ic.dAtoms);
-
             ic.hlUpdateCls.updateHlAll();
             ic.drawCls.draw();
         } 
@@ -47982,10 +47978,14 @@ class HlSeq {
                                     }
                                     */
                                     
-                                    if(($(that).attr('domain') !== undefined || $(that).attr('feat') !== undefined) || $(that).attr('3ddomain') !== undefined || $(that).attr('ig') !== undefined) {
+                                    if(($(that).attr('domain') !== undefined || $(that).attr('feat') !== undefined) || $(that).attr('ig') !== undefined) {
                                         let residNCBI = chainid + '_' + (j+1).toString();
                                         residueid = ic.ncbi2resid[residNCBI];
                                     }
+                                    else if($(that).attr('3ddomain') !== undefined) {
+                                        // the position of residues with coordinates
+                                        residueid = ic.posid2resid[chainid + '_' + (j+1).toString()];
+                                    }
                                     else {
                                         residueid = chainid + '_' + (j+1).toString();
                                     }
@@ -49961,7 +49961,7 @@ class ShowInter {
             }
         }
 
-        ic.bShowHighlight = false;
+        //!!!ic.bShowHighlight = false;
     }
 
     hideHydrogens() { let ic = this.icn3d; ic.icn3dui;
@@ -51541,8 +51541,10 @@ class ContactMap {
         // json format: [{"residue1": [1, ..., 1, ..., n, ..., n], "residue2": [1, 2, ..., n, ..., 1, 2, ..., n], 
         // "distance": [n*n matrix],"max_predicted_aligned_error":31.75}]
         //let distMatrix = dataJson[0].distance; // version 2, one dimension
-        let distMatrix = dataJson[0].predicted_aligned_error; // version 3, two dimensions 
-        let max = dataJson[0].max_predicted_aligned_error;
+        let data = (dataJson[0]) ? dataJson[0] : dataJson; // dataJson[0] is from AlphaFold UniProt database
+        let distMatrix = data.predicted_aligned_error || data.pae; // version 3, two dimensions 
+        let max = data.max_predicted_aligned_error || data.max_pae; // max_predicted_aligned_error is from AlphaFold UniProt database
+
         if(!distMatrix || !max) {
             var aaa = 1; //alert("The PAE file didn't have the right format...");
             return;
@@ -52943,7 +52945,7 @@ class ChainalignParser {
             ic.init();
         }
         else {
-            ic.resetConfig();
+            //ic.resetConfig();
         
             ic.bResetAnno = true;
             ic.bResetSets = true;
@@ -53039,7 +53041,9 @@ class ChainalignParser {
         let hAtoms = {}, hAtomsTmp = {};
         let bLastQuery = false;
 
-        ic.opts['color'] = (ic.structArray.length > 1) ? 'structure' : ((structArray[0].length > 5) ? 'confidence' : 'chain');
+        let opts = {};
+
+        opts['color'] = (structArray.length > 1) ? 'structure' : ((structArray[0].length > 5) ? 'confidence' : 'chain');
 
         for(let i = 0, il = structArray.length; i < il; ++i) {
             if(i == structArray.length - 1) bLastQuery = true;
@@ -53071,11 +53075,22 @@ class ChainalignParser {
             hAtoms = me.hashUtilsCls.unionHash(hAtoms, hAtomsTmp);
         }
 
-        // parseMmdbData() didn't render structures for mmdbafid input
-        if(ic.structArray.length > 1) ic.opts['color'] = 'structure';
-        ic.setColorCls.setColorByOptions(ic.opts, ic.atoms);
+        // add color only for the newly loaded structures
+        ic.setColorCls.setColorByOptions(opts, hAtoms);
         
-        await ic.ParserUtilsCls.renderStructure();
+        if(ic.bAnnoShown) {
+            await ic.showAnnoCls.showAnnotations();
+            ic.annotationCls.resetAnnoTabAll();
+        }
+
+        // await ic.ParserUtilsCls.renderStructure();
+        // ic.drawCls.draw();
+
+        // if(ic.bAnnoShown) {
+        //     await ic.showAnnoCls.showAnnotations();
+        //     ic.annotationCls.resetAnnoTabAll();
+        // }
+
         if(me.cfg.rotate !== undefined) ic.resizeCanvasCls.rotStruc(me.cfg.rotate, true);
 
         if(bQuery && me.cfg.matchedchains) {          
@@ -64728,7 +64743,7 @@ class ApplyCommand {
       else if(command == 'clear selection') {
         ic.hlObjectsCls.removeHlObjects();
         ic.hlUpdateCls.removeHl2D();
-        ic.bShowHighlight = false;
+        // !!!ic.bShowHighlight = false;
 
         ic.bSelectResidue = false;
       }
@@ -66885,6 +66900,8 @@ class SelectCollections {
           true
         );
         ic.bSelectResidue = false;
+
+        ic.bShowHighlight = true; // reset
       }
     });
 
@@ -70313,7 +70330,8 @@ class Dssp {
  class Refnum {
     constructor(icn3d) {
         this.icn3d = icn3d;
-        this.TMThreshold = 0.85;
+        this.TMThresholdIgType = 0.85;
+        this.TMThresholdTemplate = 0.4;
         this.topClusters = 5;
     }
 
@@ -70783,9 +70801,6 @@ class Dssp {
 
     parseAlignData_part1(dataArray, domainidpairArray, bRound1) { let ic = this.icn3d, me = ic.icn3dui;
     // async parseAlignData(dataArray, domainidpairArray, bRound1) { let ic = this.icn3d, me = ic.icn3dui;
-        let tmscoreThreshold = 0.45; // 0.4; //0.5;
-        //let rmsdThreshold = 10;
-
         // find the best alignment for each chain
         let domainid2segs = {};
         let domainid2refpdbnamelist = {};
@@ -70809,6 +70824,7 @@ class Dssp {
             }
 
             if(queryData[0].score === undefined) continue;
+            let score = parseFloat(queryData[0].score);
 
             //let domainid_index = domainidpairArray[i].split(',');
             //let domainid = domainid_index[0];
@@ -70817,13 +70833,13 @@ class Dssp {
             //let chainid = domainid.split('-')[0];
 
             if(!bRound1) {
-                if(queryData[0].score < tmscoreThreshold || queryData[0].num_res < minResidues) {
-                    if(!me.bNode) console.log("bRound1: " + bRound1 + ": domainid " + domainid + " and refpdbname " + refpdbname + " were skipped due to a TM-score less than " + tmscoreThreshold);
+                if(queryData[0].score < this.TMThresholdTemplate || queryData[0].num_res < minResidues) {
+                    if(!me.bNode) console.log("bRound1: " + bRound1 + ": domainid " + domainid + " and refpdbname " + refpdbname + " were skipped due to a TM-score less than " + this.TMThresholdTemplate);
                     continue;
                 }
             }
             else {
-                if(queryData[0].score < tmscoreThreshold || queryData[0].num_res < minResidues / 2) {
+                if(queryData[0].score < this.TMThresholdTemplate || queryData[0].num_res < minResidues / 2) {
                     continue;
                 }
             }
@@ -70834,6 +70850,9 @@ class Dssp {
             else {
                 // if(!me.bNode) console.log("domainid: " + domainid + " refpdbname " + refpdbname + " RMSD: " + queryData[0].super_rmsd + ", num_seg: " + queryData[0].num_seg + ",  10/RMSD + num_seg/5: " + (10 / queryData[0].super_rmsd + queryData[0].num_seg / 5).toFixed(1));
                 if(!me.bNode) console.log("domainid: " + domainid + " refpdbname " + refpdbname + " TM-score: " + queryData[0].score);
+
+                if(!domainid2refpdbnamelist[domainid]) domainid2refpdbnamelist[domainid] = {};
+                domainid2refpdbnamelist[domainid][refpdbname] = score;
             }
 
             // Ig-like domains: B (2150, 2150a, 2150b), C (3150, 3250), E (7150, 7250), F (8150, 8250) strands
@@ -70893,8 +70912,7 @@ class Dssp {
                             delete ic.domainid2refpdbname[domainid];
                             delete ic.domainid2score[domainid];
                         }
-                        continue;
-                    }
+                        continue;                     }
                 // }
 
             }
@@ -70914,7 +70932,6 @@ class Dssp {
             // }
 
             // let tmAdjust = 0.1; 
-            let score = parseFloat(queryData[0].score);
 
             // if the TM score difference is within 0.1 and more strands are found, use the template with more strands
             // if(!domainid2segs.hasOwnProperty(domainid) || 
@@ -70927,9 +70944,7 @@ 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 >= this.TMThreshold ? [refpdbname] : ['all_templates'];
-                    // if(me.bNode) ic.domainid2refpdbname[domainid] = ['all_templates'];
+                    ic.domainid2refpdbname[domainid] = score >= this.TMThresholdIgType ? [refpdbname] : ['all_templates'];
                 }
                 else {
                     ic.domainid2refpdbname[domainid] = [refpdbname];
@@ -70941,11 +70956,6 @@ class Dssp {
                 ic.domainid2ig2kabat[domainid] = queryData[0].ig2kabat;
                 ic.domainid2ig2imgt[domainid] = queryData[0].ig2imgt;
             }
-
-            if(bRound1) {
-                if(!domainid2refpdbnamelist[domainid]) domainid2refpdbnamelist[domainid] = {};
-                domainid2refpdbnamelist[domainid][refpdbname] = score;
-            }
         }
 
         // combine the top  clusters for the 2nd round alignment
@@ -71506,50 +71516,55 @@ class Dssp {
                 }
             }
 
-            let bIgDomain = (ic.domainid2info && Object.keys(ic.domainid2info).length > 0) ? 1 : 0;
+            // let bIgDomain = (ic.domainid2info && Object.keys(ic.domainid2info).length > 0) ? 1 : 0;
+            let stru2bIgDomain = {};
+            for(let domainid in ic.domainid2info) {
+                let stru = domainid.split('_')[0];
+                stru2bIgDomain[stru] = 1;
+            }
 
-            
+        // if(bIgDomain) {
+            for(let structure in ic.structures) {
+                let bIgDomain = stru2bIgDomain.hasOwnProperty(structure) ? 1 : 0;
 
-            if(bIgDomain) {
-                for(let structure in ic.structures) {
-                    refData += '{"' + structure + '": {"Ig domain" : ' + bIgDomain + ', "igs": [\n';
-                    for(let m = 0, ml = ic.structures[structure].length; m < ml; ++m) {
-                        let chnid = ic.structures[structure][m]; 
-                        let igArray = ic.chain2igArray[chnid];
-
-                        if(igArray && igArray.length > 0) {
-                            refData += '{"' + chnid + '": {\n';
-
-                            for(let i = 0, il = igArray.length; i < il; ++i) {
-                                let startPosArray = igArray[i].startPosArray;
-                                let endPosArray = igArray[i].endPosArray;
-                                let domainid = igArray[i].domainid;
-                                let info = ic.domainid2info[domainid];
-                                if(!info) continue;
-
-                                refData += '"' + domainid + '": {\n';
-
-                                refData += '"refpdbname":"' + info.refpdbname + '", "score":' + info.score + ', "seqid":' + info.seqid + ', "nresAlign":' + info.nresAlign + ', "data": [';
-                                for(let j = 0, jl = startPosArray.length; j < jl; ++j) {
-                                    let startPos = startPosArray[j];
-                                    let endPos = endPosArray[j];
-                                    for(let k = startPos; k <= endPos; ++k) {
-                                        const resid = chnid + '_' + ic.chainsSeq[chnid][k].resi + '_' + ic.chainsSeq[chnid][k].name;
-                                        refData += '{"' + resid + '": "' + resid2refnum[resid] + '"},\n';
-                                    }
-                                }
-                                refData += '],\n';
+                refData += '{"' + structure + '": {"Ig domain" : ' + bIgDomain + ', "igs": [\n';
+                for(let m = 0, ml = ic.structures[structure].length; m < ml; ++m) {
+                    let chnid = ic.structures[structure][m]; 
+                    let igArray = ic.chain2igArray[chnid];
+
+                    if(igArray && igArray.length > 0) {
+                        refData += '{"' + chnid + '": {\n';
+
+                        for(let i = 0, il = igArray.length; i < il; ++i) {
+                            let startPosArray = igArray[i].startPosArray;
+                            let endPosArray = igArray[i].endPosArray;
+                            let domainid = igArray[i].domainid;
+                            let info = ic.domainid2info[domainid];
+                            if(!info) continue;
 
-                                refData += '},\n';
+                            refData += '"' + domainid + '": {\n';
+
+                            refData += '"refpdbname":"' + info.refpdbname + '", "score":' + info.score + ', "seqid":' + info.seqid + ', "nresAlign":' + info.nresAlign + ', "data": [';
+                            for(let j = 0, jl = startPosArray.length; j < jl; ++j) {
+                                let startPos = startPosArray[j];
+                                let endPos = endPosArray[j];
+                                for(let k = startPos; k <= endPos; ++k) {
+                                    const resid = chnid + '_' + ic.chainsSeq[chnid][k].resi + '_' + ic.chainsSeq[chnid][k].name;
+                                    refData += '{"' + resid + '": "' + resid2refnum[resid] + '"},\n';
+                                }
                             }
+                            refData += '],\n';
 
-                            refData += '}},\n';
+                            refData += '},\n';
                         }
-                    }
 
-                    refData += ']}},\n';
+                        refData += '}},\n';
+                    }
                 }
+
+                refData += ']}},\n';
             }
+        // }
         }
         // 2. show Kabat ref numbers
         else if(type == 'kabat' || type == 'Kabat') {
@@ -77528,6 +77543,8 @@ class ThreeDPrint {
         }
 
         ic.drawCls.draw();
+
+        ic.bShowHighlight = true; // reset
     }
 
     //Reset the hydrogen bonds, distance lines to dashed lines. Reset the thickness to the default values.