Pull request #648: Users can use iCn3D to detect Ig domains for any structures and assign IgStrand reference numbers for each residue. The instruction is at https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#igrefnum.

Merge in STRUC/icn3d from release3330 to master

* commit 'b8fa42fa64f05d919bf021797c4d32035d871ddc':
  Users can use iCn3D to detect Ig domains for any structures and assign IgStrand reference numbers for each residue. The instruction is at https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#igrefnum.

Author: jiywang3

CHANGELOG.md

@@ -1,4 +1,6 @@
 ## Change Log
+[icn3d-3.33.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.0.zip) was release on June 12, 2024. Users can use iCn3D to detect Ig domains for any structures and assign IgStrand reference numbers for each residue. The instruction is at https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#igrefnum.  
+
 [icn3d-3.32.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.32.0.zip) was release on May 28, 2024. Allowed to load multiple mmCIF text files, which could contain multiple structures separated by "ENDMDL\n". 
 
 [icn3d-3.31.4](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.31.4.zip) was release on May 11, 2024. Release Ig templates for assigning reference numbers.

build/icn3d.js

@@ -11492,6 +11492,13 @@ var icn3d = (function (exports) {
              ic.drawCls.draw();
             });
 
+            me.myEventCls.onIds("#" + me.pre + "mn6_addlabelIg", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
+             ic.residueLabelsCls.addIgLabels(ic.hAtoms);
+             ic.selectionCls.saveSelectionIfSelected();
+             thisClass.setLogCmd('add ig labels', true);
+             ic.drawCls.draw();
+            });
+
             me.myEventCls.onIds("#" + me.pre + "mn6_addlabelChains", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
                ic.analysisCls.addChainLabels(ic.hAtoms);
                ic.selectionCls.saveSelectionIfSelected();
@@ -12716,15 +12723,12 @@ var icn3d = (function (exports) {
                 html += this.getLink('mn1_exportSecondary', 'Secondary Structure', undefined, 2);
             }
 
-            //!!!
-    /*
             html += this.getMenuText('m1_exportrefnum', 'Reference Numbers', undefined, undefined, 2);
             html += "<ul>";
             html += this.getLink('mn1_exportIgstrand', 'Ig Strand', undefined, 3);
             html += this.getLink('mn1_exportKabat', 'Kabat', undefined, 3);
             html += this.getLink('mn1_exportImgt', 'IMGT', undefined, 3);
             html += "</ul>";
-    */
 
             html += "<li><br/></li>";
 
@@ -13567,9 +13571,8 @@ var icn3d = (function (exports) {
                     html += this.getRadio('mn4_clr', 'mn4_clrConfidence', 'pLDDT', undefined, 1, 1);
                 //}
 
-                //!!!
-                // 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>');
@@ -13699,8 +13702,10 @@ var icn3d = (function (exports) {
             if(me.cfg.cid === undefined) {
                 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_addlabelIg', 'per Ig Domain', 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);
             }
@@ -13793,17 +13798,13 @@ var icn3d = (function (exports) {
                 html += this.getMenuText('mn6_igrefwrap', 'Ref. Number', undefined, undefined, 1);
 
                 html += "<ul>";
-    //!!!
-    /*
+
                 html += this.getLink('mn6_igrefYes', 'Show Ig for Selection', undefined, 2);
                 html += this.getLink('mn6_igrefTpl', 'Ig w/ Specified Template', undefined, 2);
                 html += this.getLink('mn6_alignrefTpl', 'Align w/ Specified Template', undefined, 2);
                 html += this.getLink('mn6_igrefNo', 'Reset Ig Ref. Number', undefined, 2);
 
                 html += this.getMenuSep();
-    */
-
-
 
                 html += this.getLink('mn6_customref', 'Custom Ref. Number', undefined, 2);
                 html += "</ul>";
@@ -13893,6 +13894,7 @@ var icn3d = (function (exports) {
             html += this.getMenuUrl('faq_simialphapdb', me.htmlCls.baseUrl + "icn3d/icn3d.html#simifoldseek", "Similar AlphaFold/PDB", 1, 2);
             html += this.getMenuUrl('faq_alnstru', me.htmlCls.baseUrl + "icn3d/icn3d.html#alignmul", "Align Multiple Structures", 1, 2);
             html += this.getMenuUrl('faq_batchanal', me.htmlCls.baseUrl + "icn3d/icn3d.html#batchanalysis", "Batch Analysis", 1, 2);
+            html += this.getMenuUrl('faq_batchanal', me.htmlCls.baseUrl + "icn3d/icn3d.html#igrefnum", "Assign Ig Ref. Numbers", 1, 2);
             html += this.getMenuUrl('faq_embedicn3d', me.htmlCls.baseUrl + "icn3d/icn3d.html#embedicn3d", "Embed iCn3D", 1, 2);
             html += "</ul>";
             html += "</li>";
@@ -16081,13 +16083,10 @@ var icn3d = (function (exports) {
             html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_interact'>Interactions" + me.htmlCls.space2 + "</span></td>";
             html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_crosslink'>Cross-Linkages" + me.htmlCls.space2 + "</span></td>";
             html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_transmem'>Transmembrane" + me.htmlCls.space2 + "</span></td>";
-    //!!!
-    /*
+
             html += "<td></td>";
             html += "</tr><tr>";
             html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_ig'>Ig Domains" + me.htmlCls.space2 + "</span></td>";
-    */
-
 
             html += "<td></td>";
             html += "</tr></table></div></div>";
@@ -35758,6 +35757,33 @@ var icn3d = (function (exports) {
             ic.hlObjectsCls.removeHlObjects();
         }
 
+        //Add labels for each Ig domain
+        addIgLabels(atoms) { let ic = this.icn3d, me = ic.icn3dui;
+            if(me.bNode) return;
+
+            let size = 60; //18;
+
+            ic.labels['ig'] = [];
+            let chainidHash = ic.firstAtomObjCls.getChainsFromAtoms(atoms);
+
+            for(let chainid in ic.igLabel2Pos) {
+                if(!chainidHash.hasOwnProperty(chainid)) continue;
+
+                for(let text in ic.igLabel2Pos[chainid]) {
+                    let label = {}; // Each label contains 'position', 'text', 'color', 'background'
+                    label.position = ic.igLabel2Pos[chainid][text];
+                    label.text = text;
+
+                    label.size = size;
+                    label.color = '#00FFFF';
+
+                    ic.labels['ig'].push(label);
+                }
+            }
+
+            ic.hlObjectsCls.removeHlObjects();
+        }
+
         addNonCarbonAtomLabels(atoms) { let ic = this.icn3d, me = ic.icn3dui;
             if(me.bNode) return;
 
@@ -42028,6 +42054,8 @@ var icn3d = (function (exports) {
             let igCnt = ic.chain2igArray[chnid].length;
             let fromArray = [], toArray = [];
             let posindex2domainindex = {};
+            if(!ic.igLabel2Pos) ic.igLabel2Pos = {};
+            ic.igLabel2Pos[chnid] = {};
             for(let i = 0; i < igCnt; ++i) {
                 let igElem = ic.chain2igArray[chnid][i];
                 fromArray = fromArray.concat(igElem.startPosArray);
@@ -42037,6 +42065,18 @@ var icn3d = (function (exports) {
                     let pos = igElem.startPosArray[j];
                     posindex2domainindex[pos] = i;
                 }
+
+                let resi1 = ic.ParserUtilsCls.getResi(chnid, igElem.startPosArray[0]);
+                let resid1 = chnid + "_" + resi1;
+                let calpha1 = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[resid1]);
+
+                let resi2 = ic.ParserUtilsCls.getResi(chnid, igElem.endPosArray[igElem.endPosArray.length - 1]);
+                let resid2 = chnid + "_" + resi2;
+                let calpha2 = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[resid2]);
+
+                let label = chnid.substr(chnid.lastIndexOf('_') + 1) + '-Ig' + (i+1).toString();
+
+                ic.igLabel2Pos[chnid][label] = calpha1.coord.clone().add(calpha2.coord).multiplyScalar(0.5);
             }
 
             // let htmlCnt = '<span class="icn3d-residueNum" title="Ig domain count">' + igCnt.toString() + ' Igs</span>';
@@ -42087,6 +42127,7 @@ var icn3d = (function (exports) {
             if(igArray.length == 0) return {html: html, html2: html2, html3: html3}
             let rangeArray = [], titleArray = [], fullTitleArray = [], domainArray = [];
 
+            let chain = chnid.substr(chnid.lastIndexOf('_') + 1);
             for(let i = 0, il = igArray.length; i < il; ++i) {
                 let domainid = igArray[i].domainid;
                 if(!ic.domainid2info) continue;
@@ -42098,7 +42139,7 @@ var icn3d = (function (exports) {
 
                 let igType = (parseFloat(tmscore) < ic.refnumCls.TMThresholdIgType ) ? 'Ig' : ic.ref2igtype[info.refpdbname];
                 titleArray.push(igType + ' (TM:' + parseFloat(tmscore).toFixed(2) + ')');
-                fullTitleArray.push(igType + ' (TM:' + parseFloat(tmscore).toFixed(2) + '), template: ' + info.refpdbname + ', type: ' + ic.ref2igtype[info.refpdbname] + ', Seq. identity: ' + parseFloat(info.seqid).toFixed(2) + ', aligned residues: ' + info.nresAlign);
+                fullTitleArray.push(igType + ' (TM:' + parseFloat(tmscore).toFixed(2) + '), template: ' + info.refpdbname + ', type: ' + ic.ref2igtype[info.refpdbname] + ', Seq. identity: ' + parseFloat(info.seqid).toFixed(2) + ', aligned residues: ' + info.nresAlign + ', label in 3D: ' + chain + '-Ig' + (i+1).toString());
 
                 domainArray.push(igType);
 
@@ -49368,7 +49409,7 @@ var icn3d = (function (exports) {
         }
 
         //Remove the highlight in the 2D interaction diagram.
-        removeHl2D() { let ic = this.icn3d; ic.icn3dui;
+        removeHl2D(bRemoveChainOnly) { let ic = this.icn3d; ic.icn3dui;
               // clear nodes in 2d dgm
               $("#" + ic.pre + "dl_2ddgm rect").attr('stroke', '#000000');
               $("#" + ic.pre + "dl_2ddgm circle").attr('stroke', '#000000');
@@ -49382,6 +49423,22 @@ var icn3d = (function (exports) {
                   $("#" + ic.pre + "dl_2ddgm svg line").attr('stroke', '#000000');
                   $("#" + ic.pre + "dl_2ddgm line").attr('stroke-width', 1);
               }
+
+              if(!bRemoveChainOnly) {
+                // clear nodes in 2d interaction network
+                // $("#" + ic.pre + "dl_linegraph rect").attr('stroke', '#000000');
+                $("#" + ic.pre + "dl_linegraph circle").attr('stroke', '#000000');
+        
+                // $("#" + ic.pre + "dl_linegraph rect").attr('stroke-width', 1);
+                $("#" + ic.pre + "dl_linegraph circle").attr('stroke-width', 1);
+
+                // clear nodes in 2d interaction graph
+                $("#" + ic.pre + "dl_scatterplot rect").attr('stroke', '#000000');
+                $("#" + ic.pre + "dl_scatterplot circle").attr('stroke', '#000000');
+        
+                $("#" + ic.pre + "dl_scatterplot rect").attr('stroke-width', 1);
+                $("#" + ic.pre + "dl_scatterplot circle").attr('stroke-width', 1);
+              }
         }
 
         //Remove the selection in the menu of defined sets.
@@ -49479,7 +49536,7 @@ var icn3d = (function (exports) {
         // update highlight in 2D window
         //Update the highlight of 2D interaction diagram according to the current highlighted atoms.
         updateHl2D(chainArray2d) { let ic = this.icn3d, me = ic.icn3dui;
-          this.removeHl2D();
+          this.removeHl2D(true);
 
           if(ic.hAtoms && ic.atoms && Object.keys(ic.hAtoms).length == Object.keys(ic.atoms).length) return;
 
@@ -49906,6 +49963,8 @@ var icn3d = (function (exports) {
                             && ic.chainsMapping[chainid2] && ic.chainsMapping[chainid2][resid2]) { 
                               mapping1 = (nodeA.s == "a") ? ic.chainsMapping[chainid1][resid1] : ic.chainsMapping[chainid2][resid2];
                               mapping2 = (nodeA.s == "a") ? ic.chainsMapping[chainid2][resid2] : ic.chainsMapping[chainid1][resid1];
+
+                              let bIgRef = (mapping1.length > 4 && !isNaN(parseInt(mapping1.substr(-4, 4)))) || (mapping2.length > 4 && !isNaN(parseInt(mapping2.substr(-4, 4))));
 
                               let mappingid = mapping1 + '_' + mapping2 + '_' + link.c; // link.c determines the interaction type
 
@@ -49917,7 +49976,7 @@ var icn3d = (function (exports) {
                               linkDiff.source += separatorDiff + ic.chainsMapping[chainid1][resid1];
                               linkDiff.target += separatorDiff + ic.chainsMapping[chainid2][resid2];
 
-                              if(linkedNodeCnt[mappingid] == structureArray.length && linkedNodeInterDiffBool[mappingid] == 0) {
+                              if(linkedNodeCnt[mappingid] == structureArray.length && (bIgRef || linkedNodeInterDiffBool[mappingid] == 0)) {
                                   linkArraySplitCommon[index].push(linkCommon);
                               }  
                               else {
@@ -64840,7 +64899,7 @@ var icn3d = (function (exports) {
                     let chainid = chainidArray[i];
                     let atoms = me.hashUtilsCls.intHash(ic.hAtoms, ic.chains[chainid]);               
                     let firstAtom = ic.firstAtomObjCls.getFirstAtomObj(atoms);
-                    structHash[firstAtom.structure] = 1;
+                    if(firstAtom) structHash[firstAtom.structure] = 1;
                 }
             }
 
@@ -65862,6 +65921,11 @@ var icn3d = (function (exports) {
 
             ic.drawCls.draw();
           }
+          else if(command == 'add ig labels') {
+            ic.residueLabelsCls.addIgLabels(ic.hAtoms);
+
+            ic.drawCls.draw();
+          }
           else if(command == 'add atom labels') {
             ic.residueLabelsCls.addAtomLabels(ic.hAtoms);
 
@@ -67188,6 +67252,7 @@ var icn3d = (function (exports) {
             else if(cmd.indexOf('hide annotation') == 0) return seqAnnoStr + ': checkboxes off';
             else if(cmd == 'add residue labels') return labelStr + 'per Residue';
             else if(cmd == 'add residue number labels') return labelStr + 'per Residue & Number';
+            else if(cmd == 'add Ig domain labels') return labelStr + 'per Ig Domain';
             else if(cmd == 'add atom labels') return labelStr + 'per Atom';
             else if(cmd == 'add chain labels') return labelStr + 'per Chain';
             else if(cmd == 'add terminal labels') return labelStr + 'N- & C- Termini';
@@ -81692,7 +81757,7 @@ var icn3d = (function (exports) {
         //even when multiple iCn3D viewers are shown together.
         this.pre = this.cfg.divid + "_";
 
-        this.REVISION = '3.32.0';
+        this.REVISION = '3.33.0';
 
         // In nodejs, iCn3D defines "window = {navigator: {}}"
         this.bNode = (Object.keys(window).length < 2) ? true : false;