icn3d 3.8.0 → 3.8.1

package/icn3d.js

@@ -7658,7 +7658,6 @@ class Strand {
                 }
 
                 currentChain = atom.chain;
-                atom.resi;
                 ss = atom.ss;
                 ssend = atom.ssend;
                 prevAtomid = atom.serial;
@@ -12045,7 +12044,6 @@ class HlObjects {
 
     //Show the highlight for the selected atoms: hAtoms.
     addHlObjects(color, bRender, atomsHash) { let ic = this.icn3d, me = ic.icn3dui;
-       if(color === undefined) color = ic.hColor;
        //if(atomsHash === undefined) atomsHash = ic.hAtoms;
        let atomsHashDisplay = (atomsHash) ? me.hashUtilsCls.intHash(atomsHash, ic.dAtoms) : me.hashUtilsCls.intHash(ic.hAtoms, ic.dAtoms);
 
@@ -13356,13 +13354,14 @@ class DefinedSets {
                 dAtoms = me.hashUtilsCls.unionHash(dAtoms, ic.alnChains[alignChain]);
             }
 
-            let residuesHash = {};
+            let  residuesHash = {}, chains = {};
             for(let i in dAtoms) {
                 let  atom = ic.atoms[i];
 
                 let  chainid = atom.structure + '_' + atom.chain;
                 let  resid = chainid + '_' + atom.resi;
                 residuesHash[resid] = 1;
+                chains[chainid] = 1;
             }
 
             let  commandname = 'protein_aligned';
@@ -16081,11 +16080,9 @@ class LineGraph {
             let id;
             if(bScatterplot) {
                 ic.scatterplotWidth = 2 * width;
-                ic.scatterplotWidth;
                 id = me.scatterplotid;
             } else {
                 ic.linegraphWidth = 2 * width;
-                ic.linegraphWidth;
                 id = me.linegraphid;
             }
             html =(strucArray.length == 0) ? "No interactions found for each structure<br><br>" :
@@ -20996,6 +20993,7 @@ class LoadAtomData {
         let  serial = serialBase;
 
         let  serial2structure = {}; // for "align" only
+        let  mmdbid2pdbid = {}; // for "align" only
 
         if(alignType === undefined || alignType === 'target') {
             ic.pmid = data.pubmedId;
@@ -21024,10 +21022,11 @@ class LoadAtomData {
               }
 
               let  pdbidTmp = structure.pdbId;
-              structure.mmdbId;
+              let  mmdbidTmp = structure.mmdbId;
 
               for(let j = structure.serialInterval[0], jl = structure.serialInterval[1]; j <= jl; ++j) {
                   serial2structure[j] = pdbidTmp.toString();
+                  mmdbid2pdbid[mmdbidTmp] = pdbidTmp;
               }
 
               for(let j = 0, jl = structure.molecules.length; j < jl; ++j) {
@@ -23827,7 +23826,7 @@ class MmdbParser {
         }
 
         let  molid2rescount = data.moleculeInfor;
-        let molid2chain = {};
+        let  molid2color = {}, chain2molid = {}, molid2chain = {};
         let  chainNameHash = {};
         for(let i in molid2rescount) {
           if(Object.keys(molid2rescount[i]).length === 0) continue;
@@ -23843,6 +23842,9 @@ class MmdbParser {
 
           let  chainNameFinal =(chainNameHash[chainName] === 1) ? chainName : chainName + chainNameHash[chainName].toString();
           let  chain = id + '_' + chainNameFinal;
+
+          molid2color[i] = color;
+          chain2molid[chain] = i;
           molid2chain[i] = chain;
 
           ic.chainsColor[chain] =(type !== undefined) ? me.parasCls.thr(me.htmlCls.GREY8) : me.parasCls.thr(color);
@@ -24005,13 +24007,13 @@ class MmdbParser {
     }
 
     downloadMmdbPart2(type) { let  ic = this.icn3d, me = ic.icn3dui;
-        if(ic.bAssemblyUseAsu) { // set up symmetric matrices
+        if(ic.bAssemblyUseAsu) { 
             $("#" + ic.pre + "assemblyWrapper").show();
-            ic.bAssembly = true;
+            //ic.bAssembly = true;
         }
         else {
             $("#" + ic.pre + "assemblyWrapper").hide();
-            ic.bAssembly = false;
+            //ic.bAssembly = false;
         }
 
         if(ic.emd !== undefined) {
@@ -26695,7 +26697,7 @@ class LoadScript {
 
             return;
           }
-          else if(ic.commands[i].trim().indexOf('set af align error map') == 0) {
+          else if(ic.commands[i].trim().indexOf('set half pae map') == 0) {
             let  strArray = ic.commands[i].split("|||");
             let  command = strArray[0].trim();
 
@@ -26708,6 +26710,19 @@ class LoadScript {
 
             return;
           }
+          else if(ic.commands[i].trim().indexOf('set full pae map') == 0) {
+            let  strArray = ic.commands[i].split("|||");
+            let  command = strArray[0].trim();
+
+            $.when(thisClass.applyCommandAfmap(command, true)).then(function() {
+               //if(!me.cfg.notebook && dialog && dialog.hasClass("ui-dialog-content")) dialog.dialog( "close" );
+
+               //ic.drawCls.draw();
+               thisClass.execCommandsBase(i + 1, end, steps);
+            });
+
+            return;
+          }
           else {
               ic.applyCommandCls.applyCommand(ic.commands[i]);
           }
@@ -27041,18 +27056,18 @@ class LoadScript {
       return ic.deferredRealign.promise();
     }
 
-    applyCommandAfmapBase(command) { let ic = this.icn3d; ic.icn3dui;
+    applyCommandAfmapBase(command, bFull) { let ic = this.icn3d; ic.icn3dui;
         let afid = command.substr(command.lastIndexOf(' ') + 1);
      
-        ic.contactMapCls.afErrorMap(afid);
+        ic.contactMapCls.afErrorMap(afid, bFull);
     }
 
-    applyCommandAfmap(command) { let ic = this.icn3d; ic.icn3dui;
+    applyCommandAfmap(command, bFull) { let ic = this.icn3d; ic.icn3dui;
       let  thisClass = this;
 
       // chain functions together
       ic.deferredAfmap = new $.Deferred(function() {
-         thisClass.applyCommandAfmapBase(command);
+         thisClass.applyCommandAfmapBase(command, bFull);
       }); // end of me.deferred = $.Deferred(function() {
 
       return ic.deferredAfmap.promise();
@@ -28332,14 +28347,14 @@ class AddTrack {
 
                           let strand, itemRgb;
 
-                          if(fieldArray.length > 4) fieldArray[4];
+                          if(fieldArray.length > 4) ;
                           if(fieldArray.length > 5) strand = fieldArray[5]; // ., +, or -
-                          if(fieldArray.length > 6) fieldArray[6];
-                          if(fieldArray.length > 7) fieldArray[7];
+                          if(fieldArray.length > 6) ;
+                          if(fieldArray.length > 7) ;
                           if(fieldArray.length > 8) itemRgb = fieldArray[8];
-                          if(fieldArray.length > 9) fieldArray[9];
-                          if(fieldArray.length > 10) fieldArray[10];
-                          if(fieldArray.length > 11) fieldArray[11];
+                          if(fieldArray.length > 9) ;
+                          if(fieldArray.length > 10) ;
+                          if(fieldArray.length > 11) ;
 
                        let title = trackName;
 
@@ -34077,7 +34092,7 @@ class MmcifParser {
         }
     }
 
-    loadMmcifSymmetry(assembly) { let ic = this.icn3d; ic.icn3dui;
+    loadMmcifSymmetry(assembly) { let  ic = this.icn3d, me = ic.icn3dui;
         // load assembly info
         //var assembly = data.assembly;
         //var pmatrix = data.pmatrix;
@@ -34090,6 +34105,11 @@ class MmcifParser {
         }
 
         ic.asuCnt = ic.biomtMatrices.length;
+
+        // show bioassembly 
+        if(me.cfg.bu == 1 && Object.keys(ic.atoms).length * ic.asuCnt > ic.maxatomcnt) {
+            ic.bAssembly = true;
+        }
     }
 
     loadMmcifOpmDataPart2(data, pdbid) { let  ic = this.icn3d, me = ic.icn3dui;
@@ -39995,7 +40015,6 @@ class ApplyDisplay {
 
     //Apply style and label options to a certain set of atoms.
     applyDisplayOptions(options, atoms, bHighlight) { let ic = this.icn3d, me = ic.icn3dui;
-        if(options === undefined) options = ic.opts;
 
         // get parameters from cookies
         if(!me.bNode && me.htmlCls.setHtmlCls.getCookie('lineRadius') != '') {
@@ -42497,7 +42516,12 @@ class Draw {
         ic.setColorCls.applyPrevColor();
 
         if(ic.biomtMatrices !== undefined && ic.biomtMatrices.length > 1) {
-            if(ic.bAssembly && Object.keys(ic.structures).length == 1) {
+            // show bioassembly in two cases
+            // 1. asymmetric unit: me.cfg.bu == 0
+            // 2. biological unit with less than ic.maxatomcnt atom: 
+            // me.cfg.bu == 1 && Object.keys(ic.atoms).length * ic.biomtMatrices.length < ic.maxatomcnt
+            if(ic.bAssembly && Object.keys(ic.structures).length == 1 && (me.cfg.bu == 0 
+              || (me.cfg.bu == 1 && Object.keys(ic.atoms).length * ic.biomtMatrices.length > ic.maxatomcnt)) ) {
                 ic.instancingCls.drawSymmetryMates();
             }
             else {
@@ -43798,7 +43822,7 @@ class ClickMenu {
         });
 
         me.myEventCls.onIds("#" + me.pre + "mn1_afmapfile", "click", function(e) { me.icn3d;
-            me.htmlCls.dialogCls.openDlg('dl_afmapfile', 'Please input AlphaFold aligned error File');
+            me.htmlCls.dialogCls.openDlg('dl_afmapfile', 'Please input AlphaFold PAE File');
          });
     //    },
     //    clkMn1_urlfile: function() {
@@ -46173,7 +46197,8 @@ class SetMenu {
         html += me.htmlCls.setHtmlCls.getLink('mn1_mol2file', 'Mol2 File');
         html += me.htmlCls.setHtmlCls.getLink('mn1_sdffile', 'SDF File');
         html += me.htmlCls.setHtmlCls.getLink('mn1_xyzfile', 'XYZ File');
-        html += me.htmlCls.setHtmlCls.getLink('mn1_afmapfile', 'AlphaFold Aligned Error File');
+        html += me.htmlCls.setHtmlCls.getLink('mn1_afmapfile', 'AlphaFold PAE File');
+
         if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getLink('mn1_urlfile', 'URL(Same Host) ' + me.htmlCls.wifiStr);
         html += "<li>-</li>";
         html += me.htmlCls.setHtmlCls.getLink('mn1_pngimage', 'iCn3D PNG Image');
@@ -47286,8 +47311,14 @@ class SetMenu {
               html += "<li id='" + me.pre + "assemblyWrapper'><span>Assembly</span>";
               html += "<ul>";
 
-              html += me.htmlCls.setHtmlCls.getRadio('mn6_assembly', 'mn6_assemblyYes', 'Biological Assembly');
-              html += me.htmlCls.setHtmlCls.getRadio('mn6_assembly', 'mn6_assemblyNo', 'Asymmetric Unit', true);
+              if(me.cfg.bu == 0) {
+                html += me.htmlCls.setHtmlCls.getRadio('mn6_assembly', 'mn6_assemblyYes', 'Biological Assembly');
+                html += me.htmlCls.setHtmlCls.getRadio('mn6_assembly', 'mn6_assemblyNo', 'Asymmetric Unit', true);
+              }
+              else {
+                html += me.htmlCls.setHtmlCls.getRadio('mn6_assembly', 'mn6_assemblyYes', 'Biological Assembly', true);
+                html += me.htmlCls.setHtmlCls.getRadio('mn6_assembly', 'mn6_assemblyNo', 'Asymmetric Unit');
+              }
 
               html += "</ul>";
               html += "</li>";
@@ -48146,7 +48177,8 @@ class SetDialog {
 
         html += "<a href='https://alphafold.ebi.ac.uk/' target='_blank'>AlphaFold Uniprot</a> ID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "afid' value='" + afid + "' size=10><br><br>";
         html += me.htmlCls.buttonStr + "reload_af'>Load Structure</button>" 
-            + me.htmlCls.buttonStr + "reload_afmap' style='margin-left:30px'>Load Aligned Error Map (slow)</button>";
+            + me.htmlCls.buttonStr + "reload_afmap' style='margin-left:30px'>Load Half PAE Map</button>"
+            + me.htmlCls.buttonStr + "reload_afmapfull' style='margin-left:30px'>Load Full PAE Map (slow)</button>";
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_opmid' class='" + dialogClass + "'>";
@@ -48244,8 +48276,9 @@ class SetDialog {
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_afmapfile' class='" + dialogClass + "'>";
-        html += "AlphaFold Aligned Error File: " + me.htmlCls.inputFileStr + "id='" + me.pre + "afmapfile' size=8> ";
-        html += me.htmlCls.buttonStr + "reload_afmapfile'>Load</button>";
+        html += "AlphaFold PAE File: " + me.htmlCls.inputFileStr + "id='" + me.pre + "afmapfile' size=8> <br><br>";
+        html += me.htmlCls.buttonStr + "reload_afmapfile'>Load Half PAE Map</button>" 
+          + me.htmlCls.buttonStr + "reload_afmapfilefull' style='margin-left:30px'>Load Full PAE Map (slow)</button>";
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_urlfile' class='" + dialogClass + "'>";
@@ -48624,7 +48657,7 @@ class SetDialog {
         html += me.htmlCls.divNowrapStr + buttonStrTmp + me.alignerrormapid + '_svg">SVG</button>' + me.htmlCls.space2;
         html += buttonStrTmp + me.alignerrormapid + '_png">PNG (slow)</button>' + me.htmlCls.space2;
         html += buttonStrTmp + me.alignerrormapid + '_json">JSON</button>' + me.htmlCls.space4;
-        html += "<b>Scale</b>: <select id='" + me.alignerrormapid + "_scale'>";
+        html += '<b>Scale</b>: <select id="' + me.alignerrormapid + '_scale">';
 
         //let optArray5 = ['0.01', '0.02', '0.04', '0.06', '0.08', '0.1', '0.2', '0.4', '0.6', '0.8', '1'];
         html += me.htmlCls.setHtmlCls.getOptionHtml(optArray5, 2);
@@ -49382,10 +49415,19 @@ class Events {
             if(!me.cfg.notebook) dialog.dialog( "close" );
             let afid = me.cfg.afid ? me.cfg.afid : $("#" + me.pre + "afid").val();
 
-            me.htmlCls.clickMenuCls.setLogCmd("set af align error map " + afid, true);
+            me.htmlCls.clickMenuCls.setLogCmd("set half pae map " + afid, true);
             
             ic.contactMapCls.afErrorMap(afid);
         });
+        me.myEventCls.onIds("#" + me.pre + "reload_afmapfull", "click", function(e) { let ic = me.icn3d;
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+            let afid = me.cfg.afid ? me.cfg.afid : $("#" + me.pre + "afid").val();
+
+            me.htmlCls.clickMenuCls.setLogCmd("set full pae map " + afid, true);
+            
+            ic.contactMapCls.afErrorMap(afid, true);
+        });
 
         me.myEventCls.onIds("#" + me.pre + "afid", "keyup", function(e) { me.icn3d;
            if (e.keyCode === 13) {
@@ -49420,23 +49462,23 @@ class Events {
     //    },
     //    clickReload_align_refined: function() {
         me.myEventCls.onIds("#" + me.pre + "reload_align_refined", "click", function(e) { me.icn3d;
-           e.preventDefault();
-           if(!me.cfg.notebook) dialog.dialog( "close" );
-           let alignment = $("#" + me.pre + "alignid1").val() + "," + $("#" + me.pre + "alignid2").val();
-           me.htmlCls.clickMenuCls.setLogCmd("load alignment " + alignment + ' | parameters &atype=1', false);
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?align=' + alignment + '&showalignseq=1&atype=1', '_blank');
-           window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=1', '_blank');
-        });
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+            let alignment = $("#" + me.pre + "alignid1").val() + "," + $("#" + me.pre + "alignid2").val();
+            me.htmlCls.clickMenuCls.setLogCmd("load alignment " + alignment + ' | parameters &atype=1&bu=1', false);
+            //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?align=' + alignment + '&showalignseq=1&atype=1', '_blank');
+            window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=1&bu=1', '_blank');
+         });
     //    },
     //    clickReload_align_ori: function() {
         me.myEventCls.onIds("#" + me.pre + "reload_align_ori", "click", function(e) { me.icn3d;
-           e.preventDefault();
-           if(!me.cfg.notebook) dialog.dialog( "close" );
-           let alignment = $("#" + me.pre + "alignid1").val() + "," + $("#" + me.pre + "alignid2").val();
-           me.htmlCls.clickMenuCls.setLogCmd("load alignment " + alignment + ' | parameters &atype=0', false);
-           //window.open( me.htmlCls.baseUrl + 'icn3d/full.html?align=' + alignment + '&showalignseq=1&atype=0', '_blank');
-           window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=0', '_blank');
-        });
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+            let alignment = $("#" + me.pre + "alignid1").val() + "," + $("#" + me.pre + "alignid2").val();
+            me.htmlCls.clickMenuCls.setLogCmd("load alignment " + alignment + ' | parameters &atype=0&bu=1', false);
+            //window.open( me.htmlCls.baseUrl + 'icn3d/full.html?align=' + alignment + '&showalignseq=1&atype=0', '_blank');
+            window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=0&bu=1', '_blank');
+         });
     //    },
     //    clickReload_chainalign: function() {
         me.myEventCls.onIds("#" + me.pre + "reload_chainalign", "click", function(e) { me.icn3d;
@@ -49970,14 +50012,43 @@ class Events {
               let reader = new FileReader();
               reader.onload = function(e) {
                 let dataStr = e.target.result; // or = reader.result;
-                me.htmlCls.clickMenuCls.setLogCmd('load AlphaFold aligned error file ' + $("#" + me.pre + "afmapfile").val(), false);
+                me.htmlCls.clickMenuCls.setLogCmd('load AlphaFold PAE file ' + $("#" + me.pre + "afmapfile").val(), false);
                 
-                me.htmlCls.dialogCls.openDlg('dl_alignerrormap', 'Show predicted aligned error map');
+                me.htmlCls.dialogCls.openDlg('dl_alignerrormap', 'Show Predicted Aligned Error (PAE) map');
                 ic.contactMapCls.processAfErrorMap(JSON.parse(dataStr));
               };
               reader.readAsText(file);
             }
          });
+
+         me.myEventCls.onIds("#" + me.pre + "reload_afmapfilefull", "click", function(e) { let ic = me.icn3d;
+            e.preventDefault();
+            ic.bInitial = true;
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+            //close all dialog
+            if(!me.cfg.notebook) {
+                $(".ui-dialog-content").dialog("close");
+            }
+            else {
+                ic.resizeCanvasCls.closeDialogs();
+            }
+            let file = $("#" + me.pre + "afmapfile")[0].files[0];
+            if(!file) {
+              var aaa = 1; //alert("Please select a file before clicking 'Load'");
+            }
+            else {
+              me.htmlCls.setHtmlCls.fileSupport();
+              let reader = new FileReader();
+              reader.onload = function(e) {
+                let dataStr = e.target.result; // or = reader.result;
+                me.htmlCls.clickMenuCls.setLogCmd('load AlphaFold PAE file ' + $("#" + me.pre + "afmapfile").val(), false);
+                
+                me.htmlCls.dialogCls.openDlg('dl_alignerrormap', 'Show Predicted Aligned Error (PAE) map');
+                ic.contactMapCls.processAfErrorMap(JSON.parse(dataStr), true);
+              };
+              reader.readAsText(file);
+            }
+         });
     //    },
     //    clickReload_urlfile: function() {
         me.myEventCls.onIds("#" + me.pre + "reload_urlfile", "click", function(e) { let ic = me.icn3d;
@@ -50356,9 +50427,17 @@ class Events {
             e.preventDefault();
             //if(!me.cfg.notebook) dialog.dialog( "close" );
             ic.saveFileCls.savePng(me.alignerrormapid, ic.inputid + "_alignerrormap.png", true);
+         });
+         me.myEventCls.onIds("#" + me.alignerrormapid + "_full", "click", function(e) { let ic = me.icn3d;
+            e.preventDefault();
+            //if(!me.cfg.notebook) dialog.dialog( "close" );
+            ic.contactMapCls.afErrorMap(afid, true);
+
+            
          });
          me.myEventCls.onIds("#" + me.alignerrormapid + "_json", "click", function(e) { let ic = me.icn3d;
              e.preventDefault();
+             
              //if(!me.cfg.notebook) dialog.dialog( "close" );
              let graphStr2 = ic.alignerrormapStr.substr(0, ic.alignerrormapStr.lastIndexOf('}'));
  
@@ -52789,10 +52868,10 @@ class ContactMap {
        }
     }
 
-    afErrorMap(afid) { let  ic = this.icn3d, me = ic.icn3dui;
+    afErrorMap(afid, bFull) { let  ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
-        me.htmlCls.dialogCls.openDlg('dl_alignerrormap', 'Show predicted aligned error map');
+        me.htmlCls.dialogCls.openDlg('dl_alignerrormap', 'Show Predicted Aligned Error (PAE) map');
 
         let  url, dataType;
     
@@ -52807,7 +52886,7 @@ class ContactMap {
             tryCount : 0,
             retryLimit : 1,
             success: function(data) {
-                thisClass.processAfErrorMap(data);
+                thisClass.processAfErrorMap(data, bFull);
             },
             error : function(xhr, textStatus, errorThrown ) {
                 this.tryCount++;
@@ -52816,19 +52895,19 @@ class ContactMap {
                     $.ajax(this);
                     return;
                 }
-                var aaa = 1; //alert("There are some problems in loading the predicted aligned error file...");
+                var aaa = 1; //alert("There are some problems in loading the PAE file...");
                 return;
             }
         });      
     }
 
-    processAfErrorMap(dataJson) { let ic = this.icn3d, me = ic.icn3dui;
+    processAfErrorMap(dataJson, bFull) { let ic = this.icn3d, me = ic.icn3dui;
         // json format: [{"residue1": [1, ..., 1, ..., n, ..., n], "residue2": [1, 2, ..., n, ..., 1, 2, ..., n], 
         // "distance": [n*n matrix],"max_predicted_aligned_error":31.75}]
         let distMatrix = dataJson[0].distance;
         let max = dataJson[0].max_predicted_aligned_error;
         if(!distMatrix || !max) {
-            var aaa = 1; //alert("The predicted aligned error file didn't have the right format...");
+            var aaa = 1; //alert("The PAE file didn't have the right format...");
             return;
         }
 
@@ -52840,18 +52919,39 @@ class ContactMap {
         let postA = '', postB = '.';
 
         // initialize some parameters if no structure wasloaded yet
-        if(!ic.chains) ic.init_base();
+        let bStruData;
+        if(!ic.chains || Object.keys(ic.chains).length == 0) {
+            bStruData = false;
+            ic.init_base();
+        }
+        else {
+            bStruData = true;
+        }
 
-        let chainidArray = Object.keys(ic.chains);
-        let chainid = (chainidArray.length == 1) ? chainidArray[0] : 'stru_A';
+        //let chainidArray = Object.keys(ic.chains);
+        //let chainid = (chainidArray.length == 1) ? chainidArray[0] : 'stru_A';
 
         let dim = parseInt(Math.sqrt(distMatrix.length));
 
+        // map index with residue number when the structure has multiple chains
+        let index = 0;
+        let index2resObj = {};
+        for(let chainid in ic.chains) {
+            for(let j = 0, jl = ic.chainsSeq[chainid].length; j < jl; ++j) {
+                index2resObj[index] = ic.chainsSeq[chainid][j];
+                index2resObj[index].chainid = chainid;
+                ++index;
+            }
+        }
+
         //for(let chainid in ic.chains) {
         //for(let i = 0, il = ic.chainsSeq[chainid].length; i < il; ++i) {
+        index = 0;
         for(let i = 0; i < dim; ++i) {
-            let resi = (ic.chainsSeq[chainid]) ? ic.chainsSeq[chainid][i].resi : i + 1;
-            let resn = (ic.chainsSeq[chainid]) ? ic.chainsSeq[chainid][i].name : '*';
+            let resi = (bStruData) ? index2resObj[i].resi : i + 1;
+            let resn = (bStruData) ? index2resObj[i].name : '*';
+            let chainid = (bStruData) ? index2resObj[i].chainid : 'stru_A';
+
             let resid = chainid + '_' + resi;
             let atom = (ic.residues[resid]) ? ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]) 
                 : {color: me.parasCls.thr(0x888888)};
@@ -52864,13 +52964,19 @@ class ContactMap {
             nodeStr += ', {"id":"' + idStr + postB + '","r":"1_1_' + resid + '","s":"b","c":"' + color + '"}';
             bNode = true;
 
+            let start = (bFull) ? 0 : i; // full map, or half map
+
             //for(let j = 0, jl = ic.chainsSeq[chainid].length; j < jl; ++j) {
             //for(let j = 0; j < dim; ++j) {
-            for(let j = i; j < dim; ++j) { // half map
-                let resi2 = (ic.chainsSeq[chainid]) ? ic.chainsSeq[chainid][j].resi : j + 1;
-                let resn2 = (ic.chainsSeq[chainid]) ? ic.chainsSeq[chainid][j].name : '*';
-                let idStr2 = resn2 + resi2 + '.' + chain;
-                let index = i * dim + j;
+            for(let j = start; j < dim; ++j) { 
+                index = i * dim + j;
+                let resi2 = (bStruData) ? index2resObj[j].resi : j + 1;
+                let resn2 = (bStruData) ? index2resObj[j].name : '*';
+                let chainid2 = (bStruData) ? index2resObj[j].chainid : 'stru_A';
+                let chain2 = chainid2.substr(chainid2.indexOf('_') + 1);
+
+                let idStr2 = resn2 + resi2 + '.' + chain2;
+                
                 // max dark green color 004d00, 0x4d = 77, 77/255 = 0.302
                 // 0: 004d00, max: FFFFFF
                 let ratio = (distMatrix[index]) ? distMatrix[index] / max : 0;
@@ -55394,7 +55500,7 @@ iCn3D.prototype.init = function (bKeepCmd) {
     //this.inputid = {"idtype": undefined, "id":undefined}; // support pdbid, mmdbid
 
     this.biomtMatrices = [];
-    this.bAssembly = true;
+    this.bAssembly = false; //true;
 
     this.bDrawn = false;
     this.bSecondaryStructure = false;
@@ -55532,7 +55638,7 @@ iCn3D.prototype.reinitAfterLoad = function () { let ic = this, me = ic.icn3dui;
     ic.lines = {};    // hash of name -> a list of solid or dashed lines. Each line contains 'position1', 'position2', 'color', and a boolean of 'dashed'
                         // line name could be custom, hbond, ssbond, distance
 
-    ic.bAssembly = true;
+    ic.bAssembly = false; //true;
 };
 
 iCn3D.prototype.resetConfig = function () { let ic = this, me = ic.icn3dui;
@@ -55571,7 +55677,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.8.0';
+    this.REVISION = '3.8.1';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "icn3d",
-  "version": "3.8.0",
+  "version": "3.8.1",
   "main": "icn3d.js",
   "description": "iCn3D Structure Viewer",
   "repository": {
@@ -15,6 +15,6 @@
   "dependencies": {
     "jquery": "^3.5.0",
     "jsdom": "^16.5.3",
-    "three": "~0.128.0"
+    "three": "~0.137.0"
   }
 }