icn3d 3.31.6 → 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);
       });
 
@@ -53077,20 +53077,14 @@ 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) {          
@@ -59436,7 +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();
@@ -70453,13 +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';
@@ -70467,7 +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';
@@ -70475,7 +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';
@@ -70489,7 +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';
@@ -70498,7 +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;
@@ -71189,7 +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);
@@ -71477,7 +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]);
@@ -71528,7 +71524,8 @@ 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];