icn3d 3.24.4 → 3.24.6

package/icn3d.js

@@ -9396,8 +9396,8 @@ class SetMenu {
             //}
 
             //!!!
-            html += this.getRadio('mn4_clr', 'mn4_clrIgstrand', 'Ig Strand', undefined, undefined, 2);
-            html += this.getRadio('mn4_clr', 'mn4_clrIgproto', 'Ig Protodomain', undefined, undefined, 2);
+            //html += this.getRadio('mn4_clr', 'mn4_clrIgstrand', 'Ig Strand', undefined, undefined, 2);
+            //html += this.getRadio('mn4_clr', 'mn4_clrIgproto', 'Ig Protodomain', undefined, undefined, 2);
         }
         else {
             //if(!me.cfg.hidelicense) html += this.getRadio('mn4_clr', 'mn1_delphi2', 'DelPhi<br><span style="padding-left:1.5em;">Potential ' + me.htmlCls.licenseStr + '</span>');
@@ -9528,7 +9528,7 @@ class SetMenu {
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelResidues', 'per Residue', undefined, 1, 2);
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelResnum', 'per Residue & Number', undefined, 1, 2);
             //!!!
-            html += this.getRadio('mn6_addlabel', 'mn6_addlabelRefnum', 'per Reference Number', undefined, 1, 2);
+            //html += this.getRadio('mn6_addlabel', 'mn6_addlabelRefnum', 'per Reference Number', undefined, 1, 2);
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelChains', 'per Chain', undefined, undefined, 2);
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelTermini', 'N- & C-Termini', undefined, 1, 2);
         }
@@ -9620,12 +9620,12 @@ class SetMenu {
 
             html += "<ul>";
 //!!!
-
+/*
             html += this.getLink('mn6_igrefYes', 'Show Ig Ref. Number', undefined, 2);
             html += this.getLink('mn6_igrefNo', 'Hide Ig Ref. Number', undefined, 2);
 
             html += this.getMenuSep();
-
+*/
             html += this.getLink('mn6_customref', 'Custom Ref. Number', undefined, 2);
             html += "</ul>";
             html += "</li>";
@@ -35390,7 +35390,6 @@ class SetOption {
      }
 
      showColorLegend(colorType) { let ic = this.icn3d, me = ic.icn3dui;
-        let bClose = false;
 
         let colorLabel = colorType.substr(0, 1).toUpperCase() + colorType.substr(1);
         if(colorType == 'confidence') {
@@ -35502,7 +35501,6 @@ class SetOption {
         }
         else {
             html = '';
-            bClose = true;
         }
 
         if(html) {
@@ -35510,9 +35508,9 @@ class SetOption {
             me.htmlCls.dialogCls.openDlg('dl_legend', 'Color Legend');
         }
 
-        if(bClose) {
-            if(window.dialog && window.dialog.hasClass('ui-dialog-content')) window.dialog.dialog( "close" );
-        }
+        // if(bClose) {
+        //     if(window.dialog && window.dialog.hasClass('ui-dialog-content')) window.dialog.dialog( "close" );
+        // }
      }
 
      getColorLegendForElem(category, atomHash) { let ic = this.icn3d, me = ic.icn3dui;
@@ -42194,24 +42192,7 @@ class ShowSeq {
                     }
                 }
                 else {
-                    let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[residueid]);
-
-                    // // skip non-protein residues
-                    // // after G strand and before A strand, just use the mapped reference number
-                    if((!atom || ic.proteins.hasOwnProperty(atom.serial)) && prevStrand && !bCustom && !kabat_or_imgt
-                      && (!currStrand_ori || currStrand_ori.substr(0,1) != 'G')) {
-                        if(currStrand != ' ') {
-                            bLoop = ic.residIgLoop[residueid];
-                            html += this.getRefnumHtml(residueid, refnumStr, refnumStr_ori, refnumLabel, currStrand, bLoop, bHidelabel);
-                            // if(bLoop) ic.residIgLoop[residueid] = 1;
-                        }
-                        else {
-                            html += '<span></span>';
-                        }
-                    }
-                    else {
-                        html += '<span></span>';
-                    }
+                    html += '<span></span>';
                 }
             //}
 
@@ -42238,13 +42219,13 @@ class ShowSeq {
 
         let html = '';
 
-        if(lastTwo == 50 && !bLoop) {
+        if(refnumLabel && lastTwo == 50 && !bLoop) {
             // highlight the anchor residues
             ic.hAtomsRefnum = me.hashUtilsCls.unionHash(ic.hAtomsRefnum, ic.residues[residueid]);
 
             html += '<span ' + colorStr + ' title="' + refnumLabel + '"><b>' + refnumLabel.substr(0, 1) + '</b>' + refnumLabel.substr(1) + '</span>';
         }
-        else if(lastTwo % 2 == 0 && lastTwo != 52 && !bHidelabel) { // don't show label for the first, middle, and last loop residues
+        else if(refnumLabel && lastTwo % 2 == 0 && lastTwo != 52 && !bHidelabel) { // don't show label for the first, middle, and last loop residues
             // e.g., 2152a
             let lastTwoStr = isNaN(refnumStr) ? lastTwo + refnumStr.substr(refnumStr.length - 1, 1) : lastTwo;
             html += '<span ' + colorStr + ' title="' + refnumLabel + '">' + lastTwoStr + '</span>';
@@ -57115,7 +57096,9 @@ class ApplyCommand {
           let msa;
           if(paraArray.length >= 7) msa = paraArray[6].substr(4);
 
-          $("#" + ic.pre + "anno_custom")[0].checked = true;
+          if($("#" + ic.pre + "anno_custom")[0]) {
+            $("#" + ic.pre + "anno_custom")[0].checked = true;
+          }
           $("[id^=" + ic.pre + "custom]").show();
 
           if(color == '0') color = undefined;
@@ -60426,16 +60409,18 @@ class Selection {
         if(me.cfg.bSidebyside && structureArray.length == 2) {
             let dividArray = Object.keys(window.icn3duiHash);
             let pos = dividArray.indexOf(ic.divid);
-
             let structure = structureArray[pos];
             let chainArray = ic.structures[structure];
+            
             let structAtoms = {};
-            for(let i = 0, il = chainArray.length; i < il; ++i) {
-                structAtoms = me.hashUtilsCls.unionHash(structAtoms, ic.chains[chainArray[i]]);
-            }
+            if(chainArray) {
+                for(let i = 0, il = chainArray.length; i < il; ++i) {
+                    structAtoms = me.hashUtilsCls.unionHash(structAtoms, ic.chains[chainArray[i]]);
+                }
 
-            ic.dAtoms = me.hashUtilsCls.intHash(structAtoms, ic.dAtoms);
-            ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
+                ic.dAtoms = me.hashUtilsCls.intHash(structAtoms, ic.dAtoms);
+                ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
+            }
         }
     }
 
@@ -61962,6 +61947,7 @@ class Dssp {
 
             // open sequence view
             ic.hAtomsRefnum = {};
+            ic.bResetAnno = true;
             await ic.showAnnoCls.showAnnotations();
             ic.annotationCls.setAnnoViewAndDisplay('detailed view');
         }
@@ -62262,6 +62248,7 @@ if(!me.bNode) {
 
             // open sequence view
             ic.hAtomsRefnum = {};
+            ic.bResetAnno = true;
             await ic.showAnnoCls.showAnnotations();
             ic.annotationCls.setAnnoViewAndDisplay('detailed view');
         }
@@ -62540,10 +62527,12 @@ console.log("free energy: " + energy + " kcal/mol");
             if(struct == pdbid + '2') { // mutant
               let residWt = pdbid + resid.substr(resid.indexOf('_'));       
               let atomWt = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[residWt]);
-              for(let i in ic.residues[resid]) {
-                ic.atoms[i].ss = atomWt.ss;
-                ic.atoms[i].ssbegin = atomWt.ssbegin;
-                ic.atoms[i].ssend = atomWt.ssend;           
+              if(atomWt) {
+                for(let i in ic.residues[resid]) {
+                  ic.atoms[i].ss = atomWt.ss;
+                  ic.atoms[i].ssbegin = atomWt.ssbegin;
+                  ic.atoms[i].ssend = atomWt.ssend;           
+                }
               }
             }
           }