icn3d 3.50.0 → 3.50.1

package/icn3d.js

@@ -106863,6 +106863,7 @@ class MmdbParser {
         //ic.molid2color = molid2color;
         //ic.chain2molid = chain2molid;
         ic.molid2chain = molid2chain;
+
         // small structure with all atoms
         // show surface options
         $("#" + ic.pre + "accordion5").show();
@@ -115299,7 +115300,9 @@ class LoadPDB {
         
         let bHeader = false, bFirstAtom = true;
 
-        let segId, prevSegId;
+        let segId, prevSegId, entityid;
+
+        if(!ic.molid2chain) ic.molid2chain = {};
 
         for (let i in lines) {
             let line = lines[i];
@@ -115444,6 +115447,17 @@ class LoadPDB {
                 ic.organism = line.substr(28).toLowerCase().trim();
 
                 ic.organism = ic.organism.substr(0, ic.organism.length - 1);
+            } else if (record === 'COMPND') {
+                if(line.indexOf('MOL_ID: ') != -1) { // COMPND    MOL_ID: 1;
+                     let itemArray = line.trim().split(' ');
+                     let lastItem = itemArray[itemArray.length - 1];
+                     entityid = lastItem.substr(0, lastItem.length - 1);
+                }
+                else if(line.indexOf('CHAIN: ') != -1) { // COMPND   3 CHAIN: H;
+                     let itemArray = line.trim().split(' ');
+                     let lastItem = itemArray[itemArray.length - 1];
+                     ic.molid2chain[parseInt(entityid)] = structure + '_' + lastItem.substr(0, lastItem.length - 1);
+                }
             } else if (record === 'ENDMDL') {
                 if(ic.statefileArray) {
                     ic.struct_statefile.push({'structure': structure, 'statefile': ic.statefileArray[moleculeNum - 1]});
@@ -116520,6 +116534,7 @@ class LoadCIF {
             let resnArray = atom_site.getColumn("label_comp_id");
             let elemArray = atom_site.getColumn("type_symbol");
             let nameArray = atom_site.getColumn("label_atom_id");
+            let entiyidArray = atom_site.getColumn("label_entity_id");
 
             let chainArray = atom_site.getColumn("auth_asym_id");
 
@@ -116541,6 +116556,8 @@ class LoadCIF {
             let prevResn;
             let sChain = {};
             let prevModelNum = '';
+            if(!ic.molid2chain) ic.molid2chain = {};
+            
             for (let i = 0; i < atomSize; ++i) {
                 let modelNum = modelNumArray.getString(i);
                 if(i > 0 && modelNum != prevModelNum) {
@@ -116559,6 +116576,7 @@ class LoadCIF {
                 let resn = resnArray.getString(i);
                 let elem = elemArray.getString(i);
                 let atom = nameArray.getString(i);
+                let entityid = entiyidArray.getString(i);
                 let chain = chainArray.getString(i);
                 let resi = resiArray.getString(i);
                 let oriResi = resiOriArray.getString(i); 
@@ -116665,6 +116683,8 @@ class LoadCIF {
                 chainNum = structure + "_" + chain;
                 oriResidueNum = chainNum + "_" + oriResi;
 
+                ic.molid2chain[parseInt(entityid)] = chainNum;
+
                 residueNum = chainNum + "_" + resi;
 
                 //let chain_resi = chain + "_" + resi;
@@ -128633,19 +128653,14 @@ class Diagram2d {
 
 		//https://9c5d031c.na-hackathon-2026.pages.dev/api.json
 		//https://www.ebi.ac.uk/pdbe/static/entry/1ffk_2_9.json, or 1ffk_1_0.json [pdbid_molid_chain]
-        if(!ic.chainid2molid) {
-            ic.chainid2molid = {};
-
-            await ic.showAnnoCls.showAnnotations();
-            let molidTmp = 1;
-            for(let id in ic.nucleotide_chainid) {
-                ic.chainid2molid[id] = molidTmp;
-                ++molidTmp;
+        let molid = 1;
+        for(let i in ic.molid2chain) {
+            if(ic.molid2chain[i] == chainid) {
+                molid = i;
+                break;
             }
         }
 
-        let molid = ic.chainid2molid[chainid] ? ic.chainid2molid[chainid] : 1;
-
 		let url = "https://www.ebi.ac.uk/pdbe/static/entry/" + pdbid.toLowerCase() + "_" + molid + "_" + chain + ".json";
 		let apiData = await me.getAjaxPromise(url, 'json', undefined, 'The chain ' + chainid + ' with molid ' + molid + ' has no R2DT information in PDBe...');
 
@@ -128799,7 +128814,7 @@ class Diagram2d {
             if(from_type_to.length != 3) continue;
 
             let fromArray = from_type_to[0].split('|'), toArray = from_type_to[2].split('|');
-            if(fromArray.length != 5 || toArray.length != 5) continue;
+            if(fromArray.length < 5 || toArray.length < 5) continue;
             if(fromArray[2] != chain || toArray[2] != chain) continue;
             let resi1 = fromArray[4], resi2 = toArray[4]; 
             let ncbiResid1 = ic.resid2ncbi[chainid + '_' + resi1], ncbiResid2 = ic.resid2ncbi[chainid + '_' + resi2];
@@ -128999,12 +129014,12 @@ class Diagram2d {
 		html += "	rnaCanvas.drawingView.fitToContent();\n";
 		html += "	$('.UDedZ1UaiPZJsRmm1yxA').hide();\n"; // hide the "Powered by RNAcanvas" label
 
-		html += "var pos2node = {}, id2pos = {};\n";
+		html += "var pos2node = {};\n";
 		html += "var nodes = rnaCanvas.drawing.bases;\n";
 
 		html += "for (var i = 0, il = nodes.length; i < il; i++) {\n";
 		html += "  pos2node[i + 1] = nodes[i];\n";
-		html += "  id2pos[nodes[i].id] = i + 1;\n";
+        html += "  nodes[i].setAttribute('resi', i + 1);\n";
 		html += "}\n";
 
         html += "$(document).on('click', '#rnacanvasSvg svg text', function(e) {\n";
@@ -129015,19 +129030,17 @@ class Diagram2d {
 		html += "    }\n";
         html += "    $(this)[0].setAttribute('fill', '#f8b84e');\n";
 
-        html += "    var pos = id2pos[id];\n";
         html += "    var resn = $(this).text().split(' ')[0];\n"; //C Position 8
-        html += "    $(document).trigger('from_rnacanvas', pos + '_' + resn);\n";
+        html += "    $(document).trigger('from_rnacanvas', $(this).attr('resi') + '_' + resn);\n";
         html += "    document.dispatchEvent(event);\n";
         html += "});\n";
 
         html += "$(document).on('mouseover', '#rnacanvasSvg svg text', function(e) {\n";
         html += "   var id = $(this).attr('id');\n";
         html += "    $(this)[0].setAttribute('fill', '#f8b84e');\n";
-
         html += "   if(!$(this)[0].querySelector('title')) {\n";
         html += "       var title = document.createElementNS('http://www.w3.org/2000/svg', 'title');\n";
-        html += "       title.textContent = ' Position ' + id2pos[id];\n";
+        html += "       title.textContent = ' Position ' + $(this).attr('resi');\n";
         html += "       $(this)[0].appendChild(title);\n";
         html += "   }\n";
         html += "});\n";