icn3d 3.31.6 → 3.31.8

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);
       });
 
@@ -40933,6 +40933,7 @@ class AnnoIg {
         ic.chain2igArray[chnid] = [];
         this.setChain2igArray(chnid, giSeq, bCustom);
 
+
         // remove Igs without BCEF strands one more time
         let igArray = ic.chain2igArray[chnid];    
 
@@ -41005,6 +41006,7 @@ class AnnoIg {
             }
         }
 
+
         // reset ic.chain2igArray
         ic.chain2igArray[chnid] = [];
         this.setChain2igArray(chnid, giSeq, bCustom);
@@ -44422,7 +44424,8 @@ class AddTrack {
     }
 
     getExonHtml(exonIndex, colorGradient, from, to, genomeRange, chainid, simpTitle) { let ic = this.icn3d; ic.icn3dui;
-        return '<div style="display:inline-block; color:white!important; width:' + Math.round(ic.seqAnnWidth *(to - from + 1) /(ic.maxAnnoLength + ic.nTotalGap)) + 'px;" class="icn3d-seqTitle icn3d-link icn3d-blue" domain="' + (exonIndex + 1) + '" from="' + from + '" to="' + to + '" setname="' + simpTitle + ', Exon ' + (exonIndex + 1) + '" title="Exon ' + (exonIndex + 1) + ': ' + genomeRange + ' genomic interval" anno="sequence" chain="' + chainid + '"><div style="height: 12px; border: 1px solid #000; background: linear-gradient(to right, ' + colorGradient + ');"></div></div>';
+        // return '<div style="display:inline-block; color:white!important; width:' + Math.round(ic.seqAnnWidth *(to - from + 1) /(ic.maxAnnoLength + ic.nTotalGap)) + 'px;" class="icn3d-seqTitle icn3d-link icn3d-blue" domain="' + (exonIndex + 1) + '" from="' + from + '" to="' + to + '" setname="' + simpTitle + ', Exon ' + (exonIndex + 1) + '" title="Exon ' + (exonIndex + 1) + ': ' + genomeRange + ' genomic interval" anno="sequence" chain="' + chainid + '"><div style="height: 12px; border: 1px solid #000; background: linear-gradient(to right, ' + colorGradient + ');"></div></div>';
+        return '<div style="display:inline-block; color:white!important; width:' + Math.round(ic.seqAnnWidth *(to - from + 1) /(ic.maxAnnoLength + ic.nTotalGap)) + 'px;" class="icn3d-seqTitle icn3d-link icn3d-blue" domain="' + (exonIndex + 1) + '" from="' + from + '" to="' + to + '" setname="' + simpTitle + ', #' + (exonIndex + 1) + '" title="Exon: ' + genomeRange + ' genomic interval" anno="sequence" chain="' + chainid + '"><div style="height: 12px; border: 1px solid #000; background: linear-gradient(to right, ' + colorGradient + ');"></div></div>';
     }
 
     getExonColor(start, end, pos) { let ic = this.icn3d; ic.icn3dui;
@@ -51629,7 +51632,7 @@ class ContactMap {
                 let color2 = rHex + gHex + bHex;
 
                 if(bLink) linkStr += ', ';
-                linkStr += '{"source": "' + idStr + postA + '", "target": "' + idStr2 + postB + '", "v": 11, "c": "' + color2 + '"}\n';
+                linkStr += '{"source": "' + idStr + postA + '", "target": "' + idStr2 + postB + '", "v": 11, "c": "' + color2 + '", "pae": ' + parseInt(distMatrix[i][j]) + '}\n';
                 bLink = true;
             }
         }
@@ -53077,20 +53080,14 @@ class ChainalignParser {
 
         // 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) {          
@@ -55254,10 +55251,12 @@ class BcifParser {
             let conf_type_idArray = struct_conf.getColumn("conf_type_id");
 
             let chain1Array = struct_conf.getColumn("beg_auth_asym_id");
-            let resi1Array = struct_conf.getColumn("beg_label_seq_id");
+            // let resi1Array = struct_conf.getColumn("beg_label_seq_id");
+            let resi1Array = struct_conf.getColumn("beg_auth_seq_id");
 
             let chain2Array = struct_conf.getColumn("end_auth_asym_id");
-            let resi2Array = struct_conf.getColumn("end_label_seq_id");
+            // let resi2Array = struct_conf.getColumn("end_label_seq_id");
+            let resi2Array = struct_conf.getColumn("end_auth_seq_id");
 
             // Iterate through every row in the struct_conf category table, where each row delineates an interatomic connection
             let confSize = struct_conf.rowCount;
@@ -55302,10 +55301,12 @@ class BcifParser {
             let struct_sheet_range = block.getCategory("_struct_sheet_range");
 
             let chain1Array = struct_sheet_range.getColumn("beg_auth_asym_id");
-            let resi1Array = struct_sheet_range.getColumn("beg_label_seq_id");
+            // let resi1Array = struct_sheet_range.getColumn("beg_label_seq_id");
+            let resi1Array = struct_sheet_range.getColumn("beg_auth_seq_id");
 
             let chain2Array = struct_sheet_range.getColumn("end_auth_asym_id");
-            let resi2Array = struct_sheet_range.getColumn("end_label_seq_id");
+            // let resi2Array = struct_sheet_range.getColumn("end_label_seq_id");
+            let resi2Array = struct_sheet_range.getColumn("end_auth_seq_id");
 
             // Iterate through every row in the struct_sheet_range category table, where each row delineates an interatomic connection
             let sheetSize = struct_sheet_range.rowCount;
@@ -58810,9 +58811,13 @@ class ParserUtils {
 
         for(let i = 0, il = ic.realignResid[chainid_t].length; i < il && i < ic.realignResid[chainid_q].length; ++i) {
             let resid_t = ic.realignResid[chainid_t][i].resid;
+            if(!resid_t) continue;
+
             let pos_t = resid_t.lastIndexOf('_');
             let resi_t = parseInt(resid_t.substr(pos_t + 1));
             let resid_q = ic.realignResid[chainid_q][i].resid;
+            if(!resid_q) continue;
+
             let pos_q = resid_q.lastIndexOf('_');
             let resi_q = parseInt(resid_q.substr(pos_q + 1));
 
@@ -59436,7 +59441,9 @@ 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();
@@ -62823,10 +62830,12 @@ class LoadCIF {
             let conf_type_idArray = struct_conf.getColumn("conf_type_id");
         
             let chain1Array = struct_conf.getColumn("beg_auth_asym_id");
-            let resi1Array = struct_conf.getColumn("beg_label_seq_id");
+            // let resi1Array = struct_conf.getColumn("beg_label_seq_id");
+            let resi1Array = struct_conf.getColumn("beg_auth_seq_id");
         
             struct_conf.getColumn("end_auth_asym_id");
-            let resi2Array = struct_conf.getColumn("end_label_seq_id");
+            // let resi2Array = struct_conf.getColumn("end_label_seq_id");
+            let resi2Array = struct_conf.getColumn("end_auth_seq_id");
         
             // Iterate through every row in the struct_conf category table, where each row delineates an interatomic connection
             let confSize = struct_conf.rowCount;
@@ -62865,10 +62874,12 @@ class LoadCIF {
             let struct_sheet_range = block.getCategory("_struct_sheet_range");
         
             let chain1Array = struct_sheet_range.getColumn("beg_auth_asym_id");
-            let resi1Array = struct_sheet_range.getColumn("beg_label_seq_id");
+            // let resi1Array = struct_sheet_range.getColumn("beg_label_seq_id");
+            let resi1Array = struct_sheet_range.getColumn("beg_auth_seq_id");
         
             struct_sheet_range.getColumn("end_auth_asym_id");
-            let resi2Array = struct_sheet_range.getColumn("end_label_seq_id");
+            // let resi2Array = struct_sheet_range.getColumn("end_label_seq_id");
+            let resi2Array = struct_sheet_range.getColumn("end_auth_seq_id");
         
             // Iterate through every row in the struct_sheet_range category table, where each row delineates an interatomic connection
             let sheetSize = struct_sheet_range.rowCount;
@@ -62876,7 +62887,7 @@ class LoadCIF {
                 let startChain = chain1Array.getString(i);
                 let startResi = parseInt(resi1Array.getString(i));
                 let endResi = parseInt(resi2Array.getString(i));
-            
+
                 for(let j = startResi; j <= endResi; ++j) {
                     let resid = structure + "_" + startChain + "_" + j;
                     sheetArray.push(resid);
@@ -70453,13 +70464,13 @@ 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';
@@ -70467,7 +70478,7 @@ 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';
@@ -70475,7 +70486,7 @@ 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';
@@ -70489,7 +70500,7 @@ 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';
@@ -70498,7 +70509,7 @@ 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;
@@ -70907,12 +70918,13 @@ class Dssp {
                     // 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;  
+                  }
                 // }
 
             }
@@ -71189,7 +71201,7 @@ 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);
@@ -71477,7 +71489,7 @@ 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]);
@@ -71528,7 +71540,8 @@ class Dssp {
                 let bIgDomain = stru2bIgDomain.hasOwnProperty(structure) ? 1 : 0;
 
                 refData += '{"' + structure + '": {"Ig domain" : ' + bIgDomain + ', "igs": [\n';
-                for(let m = 0, ml = ic.structures[structure].length; m < ml; ++m) {
+
+                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];
 
@@ -80312,7 +80325,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.31.1';
+    this.REVISION = '3.31.2';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;