icn3d 3.31.5 → 3.31.7

package/icn3d.js

@@ -9154,7 +9154,7 @@ class ClickMenu {
       });
 
       me.myEventCls.onIds("#" + me.pre + "mn1_exportKabat", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
-         ic.refnumCls.exportRefnum('kabat');
+      ic.refnumCls.exportRefnum('kabat');
          thisClass.setLogCmd("export refnum kabat", true);
       });
 
@@ -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 +53075,16 @@ 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();
+        }
+
         if(me.cfg.rotate !== undefined) ic.resizeCanvasCls.rotStruc(me.cfg.rotate, true);
 
         if(bQuery && me.cfg.matchedchains) {          
@@ -59421,7 +59430,9 @@ class ParserUtils {
 
             if(data && data.pdbid) {
               let question = "This is a single-spanning (bitopic) transmembrane protein according to the Membranome database. Do you want to align the protein with the model from Membranome? If you click \"OK\", you can press the letter \"a\" to alternate the structures.";
-             
+
+              if (me.bNode) return;
+
               if (me.cfg.afmem == 'off') {
                 // do nothing
                 /// if(ic.deferredOpm !== undefined) ic.deferredOpm.resolve();
@@ -64728,7 +64739,7 @@ class ApplyCommand {
       else if(command == 'clear selection') {
         ic.hlObjectsCls.removeHlObjects();
         ic.hlUpdateCls.removeHl2D();
-        ic.bShowHighlight = false;
+        // !!!ic.bShowHighlight = false;
 
         ic.bSelectResidue = false;
       }
@@ -66885,6 +66896,8 @@ class SelectCollections {
           true
         );
         ic.bSelectResidue = false;
+
+        ic.bShowHighlight = true; // reset
       }
     });
 
@@ -70313,7 +70326,8 @@ class Dssp {
  class Refnum {
     constructor(icn3d) {
         this.icn3d = icn3d;
-        this.TMThreshold = 0.85;
+        this.TMThresholdIgType = 0.85;
+        this.TMThresholdTemplate = 0.4;
         this.topClusters = 5;
     }
 
@@ -70435,13 +70449,13 @@ class Dssp {
         ic.ref2igtype['CD28_1yjdC_human_V'] = 'IgV';
         ic.ref2igtype['CD2_1hnfA_human_C2-n2'] = 'IgC2';
         ic.ref2igtype['CD2_1hnfA_human_V-n1'] = 'IgV';
-        ic.ref2igtype['CD3d_6jxrd_human_C1'] = 'IgI';
-        ic.ref2igtype['CD3e_6jxrf_human_C1'] = 'IgI';
-        ic.ref2igtype['CD3g_6jxrg_human_C2'] = 'IgI';
+        ic.ref2igtype['CD3d_6jxrd_human_C1'] = 'IgC1';
+        ic.ref2igtype['CD3e_6jxrf_human_C1'] = 'IgC1';
+        ic.ref2igtype['CD3g_6jxrg_human_C2'] = 'IgC2';
         ic.ref2igtype['CD8a_1cd8A_human_V'] = 'IgV';
         ic.ref2igtype['CoAtomerGamma1_1r4xA_human'] = 'IgE';
         ic.ref2igtype['Contactin1_2ee2A_human_FN3-n9'] = 'IgFN3';
-        ic.ref2igtype['Contactin1_3s97C_human_Iset-n2'] = 'IgC2';
+        ic.ref2igtype['Contactin1_3s97C_human_Iset-n2'] = 'IgI';
         ic.ref2igtype['CuZnSuperoxideDismutase_1hl5C_human'] = 'SOD';
         ic.ref2igtype['ECadherin_4zt1A_human_n2'] = 'Cadherin';
         ic.ref2igtype['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = 'IgE';
@@ -70449,7 +70463,7 @@ class Dssp {
         ic.ref2igtype['FAB-HEAVY_5esv_V-n1'] = 'IgV';
         ic.ref2igtype['FAB-LIGHT_5esv_C1-n2'] = 'IgC1';
         ic.ref2igtype['FAB-LIGHT_5esv_V-n1'] = 'IgV';
-        ic.ref2igtype['GHR_1axiB_human_C1-n1'] = 'IgFN3';
+        ic.ref2igtype['GHR_1axiB_human_C1-n1'] = 'IgC1';
         ic.ref2igtype['ICOS_6x4gA_human_V'] = 'IgV';
         ic.ref2igtype['IL6Rb_1bquB_human_FN3-n2'] = 'IgFN3';
         ic.ref2igtype['IL6Rb_1bquB_human_FN3-n3'] = 'IgFN3';
@@ -70457,7 +70471,7 @@ class Dssp {
         ic.ref2igtype['InsulinR_8guyE_human_FN3-n2'] = 'IgFN3';
         ic.ref2igtype['IsdA_2iteA_bacteria'] = 'IgE';
         ic.ref2igtype['JAM1_1nbqA_human_Iset-n2'] = 'IgI';
-        ic.ref2igtype['LAG3_7tzgD_human_C1-n2'] = 'IgC2';
+        ic.ref2igtype['LAG3_7tzgD_human_C1-n2'] = 'IgC1';
         ic.ref2igtype['LAG3_7tzgD_human_V-n1'] = 'IgV';
         ic.ref2igtype['LaminAC_1ifrA_human'] = 'Lamin';
         ic.ref2igtype['MHCIa_7phrH_human_C1'] = 'IgC1';
@@ -70471,7 +70485,7 @@ class Dssp {
         ic.ref2igtype['RBPJ_6py8C_human_Unk-n1'] = 'IgFN3-like';
         ic.ref2igtype['RBPJ_6py8C_human_Unk-n2'] = 'IgFN3-like';
         ic.ref2igtype['Sidekick2_1wf5A_human_FN3-n7'] = 'IgFN3';
-        ic.ref2igtype['Siglec3_5j0bB_human_C1-n2'] = 'IgC2';
+        ic.ref2igtype['Siglec3_5j0bB_human_C1-n2'] = 'IgC1';
         ic.ref2igtype['TCRa_6jxrm_human_C1-n2'] = 'IgC1';
         ic.ref2igtype['TCRa_6jxrm_human_V-n1'] = 'IgV';
         ic.ref2igtype['TEAD1_3kysC_human'] = 'IgE';
@@ -70480,7 +70494,7 @@ class Dssp {
         ic.ref2igtype['Titin_4uowM_human_Iset-n152'] = 'IgI';
         ic.ref2igtype['VISTA_6oilA_human_V'] = 'IgV';
         ic.ref2igtype['VNAR_1t6vN_shark_V'] = 'IgV';
-        ic.ref2igtype['VTCN1_Q7Z7D3_human_C1-n2'] = 'IgV';
+        ic.ref2igtype['VTCN1_Q7Z7D3_human_C1-n2'] = 'IgC1';
     }
 
     getPdbAjaxArray() {  let ic = this.icn3d, me = ic.icn3dui;
@@ -70783,9 +70797,6 @@ 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 +70820,7 @@ 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 +70829,13 @@ 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 +70846,9 @@ 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 +70908,7 @@ class Dssp {
                             delete ic.domainid2refpdbname[domainid];
                             delete ic.domainid2score[domainid];
                         }
-                        continue;
-                    }
+                        continue;                     }
                 // }
 
             }
@@ -70914,7 +70928,6 @@ 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 +70940,7 @@ 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 +70952,6 @@ 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
@@ -71179,7 +71185,7 @@ class Dssp {
 
                 if(seg.q_start.indexOf('8550') != -1) {
                     // check C' and D strands
-                    if(cntBtwCE == 1) {
+                    if(cntBtwCE == 1 && CAtom && EAtom && (CpAtom || DAtom)) {
                         let distToC = 999, distToE = 999;
                         for(let j = 0, jl = CAtomArray.length; j < jl; ++j) {
                             let dist = (bCpstrand) ? CpAtom.coord.distanceTo(CAtomArray[j].coord) : DAtom.coord.distanceTo(CAtomArray[j].coord);
@@ -71467,7 +71473,7 @@ class Dssp {
         // 1. show IgStrand ref numbers
         if(type == 'igstrand' || type == 'IgStrand') {
             // iGStrand reference numbers were adjusted when showing in sequences
-            // if(me.bNode) {            
+            // if(me.bNode) {        
             if(ic.bShowRefnum) {
                 for(let chnid in ic.chains) {
                     let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.chains[chnid]);
@@ -71506,50 +71512,56 @@ 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; ic.bShowRefnum && 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 +77540,8 @@ 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.