icn3d 3.54.4 → 3.54.5

package/icn3d.js

@@ -81818,7 +81818,7 @@ class Axes {
 
     buildUnitcell() { let ic = this.icn3d, me = ic.icn3dui;
         if(!ic.cell) {
-            var aaa = 1; //alert("Unit cell information is available for structures from mmCIF files. Please load a structure from mmCIF file.");
+            var aaa = 1; //alert("Unit cell information is available for structures from mmCIF files. Please load a structure with 'mmcifid=', 'bcifid=', or from a mmCIF file.");
             return;
         }
 
@@ -115768,7 +115768,8 @@ class ShowAnno {
         }
 
         let nucleotide_chainid = {}, chemical_chainid = {}, chemical_set = {};
-        //ic.protein_chainid = {};
+        // ic.protein_chainid = {};
+
 
         if(ic.bAnnoShown === undefined || !ic.bAnnoShown || ic.bResetAnno) { // ic.bResetAnno when loading another structure
             ic.protein_chainid = {};
@@ -115795,7 +115796,7 @@ class ShowAnno {
                 dialogWidth =(me.cfg.notebook) ? me.htmlCls.WIDTH / 2 : $("#" + ic.pre + "dl_selectannotations").dialog( "option", "width" );
             }
             ic.seqAnnWidth = dialogWidth - 120 - 30*2 - 50; // title: 120px, start and end resi: 30px, extra space on the left and right: 50px
-            
+ 
             for(let i = 0, il = chainArray.length; i < il; ++i) {
                 if(!ic.chainsSeq[chainArray[i]]) continue; // skip empty chain
 
@@ -115905,8 +115906,8 @@ class ShowAnno {
 
                         await ic.mmcifParserCls.downloadMmcifSymmetry(id, 'mmtfid');
                     }
-                    
-                    await this.showAnnoSeqData(nucleotide_chainid, chemical_chainid, chemical_set);
+                  
+                    await this.showAnnoSeqData(nucleotide_chainid, chemical_chainid, chemical_set);               
                }
             }
             else if(me.cfg.blast_rep_id !== undefined && !ic.bSmithwm && !ic.bLocalSmithwm) { // align sequence to structure
@@ -134747,6 +134748,7 @@ class LoadCIF {
             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) {
@@ -134977,7 +134979,7 @@ class LoadCIF {
                 // if(oriResidueNum !== prevOriResidueNum) {
                 if(oriResidueNum !== prevOriResidueNum || chain + "_" + resn != prevResn || prevAutochain != autochain) {
                     let residue = me.utilsCls.residueName2Abbr(resn);
-                    
+                   
                     ic.residueId2Name[residueNum] = residue;
 
                     if(serial !== 1 && prevResidueNum !== '') {
@@ -135102,7 +135104,7 @@ class LoadCIF {
 
                 resiArray = oriResiArray = resnArray = chainArray = [];
             }
-            
+  
             this.setSeq(structure, sChain, mChainSeq, ligSeqHash);
         }
 
@@ -135304,17 +135306,22 @@ class LoadCIF {
     }
 
     setSeq(structure, sChain, mChainSeq, ligSeqHash) { let ic = this.icn3d; ic.icn3dui;
+        // sometimes a chain appears in both ligSeqHash and mChainSeq, e.g., mmcif data for 1TOP
+/*
         for(let chain in sChain) {
             let chainNum = structure + '_' + chain;
 
-            if(ligSeqHash.hasOwnProperty(chain)) {
+            if(mChainSeq.hasOwnProperty(chain)) {
+                ic.chainsSeq[chainNum] = mChainSeq[chain];
+            }
+            else if(ligSeqHash.hasOwnProperty(chain)) {
                 ic.chainsSeq[chainNum] = ligSeqHash[chain];
             }
             else {
                 ic.chainsSeq[chainNum] = mChainSeq[chain];
             }
         }
-
+*/
         ic.loadPDBCls.setResidMapping();
     }
 }
@@ -136255,9 +136262,11 @@ class ApplyCommand {
       }
       else if(command == 'set unitcell on') {
         ic.opts['unitcell'] = 'yes';
+        ic.drawCls.draw();
       }
       else if(command == 'set unitcell off') {
         ic.opts['unitcell'] = 'no';
+        ic.drawCls.draw();
       }
       else if(command == 'set fog on') {
         ic.opts['fog'] = 'yes';