Fixed a bug on hydrogen bonds between residues with the same residue …

…number but different chain names. Removed duplicated names in the menu of "Defined Sets".
ncbi · Mar 12, 2020 · 253d6b4 · 253d6b4
1 parent 2eb8b6d
commit 253d6b4
Show file tree

Hide file tree

Showing 11 changed files with 89 additions and 50 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,4 +1,6 @@
 ## Change Log
+[icn3d-2.12.1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.12.1.zip) was release on March 12, 2020. Fixed a bug on hydrogen bonds between residues with the same residue number but different chain names. Removed duplicated names in the menu of "Defined Sets".
+
 [icn3d-2.12.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.12.0.zip) was release on March 2, 2020. Enabled to realign selected residues in VAST+ structure alignment. The option "Realign Selection" is in the View menu.
 
 [icn3d-2.11.5](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.11.5.zip) was release on February 11, 2020. Add colors to aligned sequence track based on Blosum62.

diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@
 
 ## About iCn3D
 
-"I see in 3D" (iCn3D) Structure Viewer is a WebGL-based 3D viewer using Three.js and jQuery. iCn3D synchronizes the display of 3D structure, 2D interaction, and 1D sequences and annotations. Users' custom display can be saved in a short URL or a PNG image. <b>Complete package</b> of iCn3D including Three.js and jQuery can be downloaded from [https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.12.0.zip](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.12.0.zip). The "Download ZIP" link in this page does not include third-party libraries. 
+"I see in 3D" (iCn3D) Structure Viewer is a WebGL-based 3D viewer using Three.js and jQuery. iCn3D synchronizes the display of 3D structure, 2D interaction, and 1D sequences and annotations. Users' custom display can be saved in a short URL or a PNG image. <b>Complete package</b> of iCn3D including Three.js and jQuery can be downloaded from [https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.12.1.zip](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.12.1.zip). The "Download ZIP" link in this page does not include third-party libraries. 
 * <b>View a 3D structure in iCn3D</b>: 
     Open the link https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html, input a PDB ID, and click "Load". You can also click "File" menu to "Open File" or input other IDs.
 

diff --git a/icn3d.html b/icn3d.html
@@ -2094,6 +2094,9 @@ <h3>Methods <a href="#Top"><span class="top">&nbsp;&nbsp;&nbsp;</span></a></h3>
 
 <a name="log"></a>
 <h2>Change Log:<img src="https://www.ncbi.nlm.nih.gov/Structure/IMG/spacer.gif" width="25" height="1" border="0"><a href="#Top"><img src="https://www.ncbi.nlm.nih.gov/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></a></h2>
+<a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.12.1.zip">icn3d-2.12.1</a> was release on March 12, 2020. Fixed a bug on hydrogen bonds between residues with the same residue number but different chain names. Removed duplicated names in the menu of "Defined Sets".
+<br><br>
+
 <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.12.0.zip">icn3d-2.12.0</a> was release on March 2, 2020. Enabled to realign selected residues in VAST+ structure alignment. The option "Realign Selection" is in the View menu.
 <br><br>
 

diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "icn3d",
-  "version": "2.12.0",
+  "version": "2.12.1",
   "description": "iCn3D Structure Viewer",
   "main": "index.html",
   "scripts": {

diff --git a/src/icn3d/other_full.js b/src/icn3d/other_full.js
@@ -240,7 +240,9 @@ iCn3D.prototype.isValidHbond = function (atom, atomHbond, threshold) { var me =
 
       //if (idealGeometry[donor.index] === AtomGeometry.Trigonal){ // 120
         var outOfPlane1 = this.calcPlaneAngle(donorAtom, acceptorAtom);
-        if (outOfPlane1 !== undefined && outOfPlane1 > maxHbondDonPlaneAngle) return false;
+        if (outOfPlane1 !== undefined && outOfPlane1 > maxHbondDonPlaneAngle) {
+            return false;
+        }
       //}
 
       var acceptorAngles = this.calcAngles(acceptorAtom, donorAtom);
@@ -356,7 +358,7 @@ iCn3D.prototype.calculateChemicalHbonds = function (startAtoms, targetAtoms, thr
             && (atom.name === 'N' || atom.name === 'O') && (atomHbond[j].name === 'O' || atomHbond[j].name === 'N') ) {
 
             if(atom.name === atomHbond[j].name) continue;
-            if(Math.abs(atom.resi - atomHbond[j].resi) <= 1) continue; // peptide bond
+            if(atom.structure == atomHbond[j].structure && atom.chain == atomHbond[j].chain && Math.abs(atom.resi - atomHbond[j].resi) <= 1) continue; // peptide bond
 
             // protein backbone hydrogen
             // https://en.wikipedia.org/wiki/DSSP_(hydrogen_bond_estimation_algorithm)

diff --git a/src/icn3dui/full_ui.js b/src/icn3dui/full_ui.js
@@ -13,7 +13,7 @@ if (!$.ui.dialog.prototype._makeDraggableBase) {
 }
 
 var iCn3DUI = function(cfg) { var me = this; //"use strict";
-    this.REVISION = '2.12.0';
+    this.REVISION = '2.12.1';
 
     me.bFullUi = true;
 
@@ -1014,16 +1014,6 @@ iCn3DUI.prototype = {
                    me.setLogCmd(cmd, true);
 
                    me.showAnnotations();
-/*
-                   if(Object.keys(me.icn3d.proteins).length > 0) {
-                      $.when(me.applyCommandAnnotationsAndCddSite(cmd)).then(function() {
-                          // do something afterward
-                      });
-                   }
-                   else {
-                      me.applyCommandAnnotationsAndCddSiteBase(cmd);
-                   }
-*/
               }
 
               if(me.cfg.closepopup) {
@@ -6506,17 +6496,22 @@ iCn3DUI.prototype = {
         });
     },
 
-    clickSeqSaveSelection: function() { var me = this; //"use strict";
-        $(document).on("click", "#" + me.pre + "seq_saveselection", function(e) {
-           e.stopImmediatePropagation();
-           dialog.dialog( "close" );
-
+    saveSelectionPrep: function() { var me = this; //"use strict";
            if(!$('#' + me.pre + 'dl_definedsets').hasClass('ui-dialog-content') || !$('#' + me.pre + 'dl_definedsets').dialog( 'isOpen' )) {
              me.openDialog(me.pre + 'dl_definedsets', 'Select sets');
              $("#" + me.pre + "atomsCustom").resizable();
            }
 
            me.bSelectResidue = false;
+           me.bSelectAlignResidue = false;
+    },
+
+    clickSeqSaveSelection: function() { var me = this; //"use strict";
+        $(document).on("click", "#" + me.pre + "seq_saveselection", function(e) {
+           e.stopImmediatePropagation();
+           dialog.dialog( "close" );
+
+           me.saveSelectionPrep();
 
            var name = $("#" + me.pre + "seq_command_name").val().replace(/\s+/g, '_');
            //var description = $("#" + me.pre + "seq_command_desc").val();
@@ -6529,12 +6524,7 @@ iCn3DUI.prototype = {
         $(document).on("click", "#" + me.pre + "seq_saveselection2", function(e) {
            e.stopImmediatePropagation();
 
-           if(!$('#' + me.pre + 'dl_definedsets').hasClass('ui-dialog-content') || !$('#' + me.pre + 'dl_definedsets').dialog( 'isOpen' )) {
-             me.openDialog(me.pre + 'dl_definedsets', 'Select sets');
-             $("#" + me.pre + "atomsCustom").resizable();
-           }
-
-           me.bSelectResidue = false;
+           me.saveSelectionPrep();
 
            var name = $("#" + me.pre + "seq_command_name2").val().replace(/\s+/g, '_');
            //var description = $("#" + me.pre + "seq_command_desc2").val();
@@ -6547,19 +6537,14 @@ iCn3DUI.prototype = {
 
     clickAlignSeqSaveSelection: function() { var me = this; //"use strict";
         $(document).on("click", "#" + me.pre + "alignseq_saveselection", function(e) {
-            e.stopImmediatePropagation();
-
-           if(!$('#' + me.pre + 'dl_definedsets').hasClass('ui-dialog-content') || !$('#' + me.pre + 'dl_definedsets').dialog( 'isOpen' )) {
-             me.openDialog(me.pre + 'dl_definedsets', 'Select sets');
-             $("#" + me.pre + "atomsCustom").resizable();
-           }
+           e.stopImmediatePropagation();
 
-            me.bSelectAlignResidue = false;
+           me.saveSelectionPrep();
 
-            var name = $("#" + me.pre + "alignseq_command_name").val().replace(/\s+/g, '_');
-            //var description = $("#" + me.pre + "alignseq_command_desc").val();
+           var name = $("#" + me.pre + "alignseq_command_name").val().replace(/\s+/g, '_');
+           //var description = $("#" + me.pre + "alignseq_command_desc").val();
 
-            me.saveSelection(name, name);
+           me.saveSelection(name, name);
 
            //$( ".icn3d-accordion" ).accordion(me.closeAc);
         });

diff --git a/src/icn3dui/highlight/hl_update.js b/src/icn3dui/highlight/hl_update.js
@@ -75,6 +75,7 @@ iCn3DUI.prototype.removeHl2D = function() { var me = this; //"use strict";
 // remove highlight in the menu of defined sets
 iCn3DUI.prototype.removeHlMenus = function() { var me = this; //"use strict";
     $("#" + me.pre + "atomsCustom").val("");
+    $("#" + me.pre + "atomsCustom")[0].blur();
 };
 
 iCn3DUI.prototype.updateHlAll = function(commandnameArray, bSetMenu, bUnion, bForceHighlight) { var me = this; //"use strict";
@@ -226,6 +227,7 @@ iCn3DUI.prototype.updateHlMenus = function(commandnameArray) { var me = this; //
 
     if($("#" + me.pre + "atomsCustom").length) {
         $("#" + me.pre + "atomsCustom").html(definedAtomsHtml);
+        $("#" + me.pre + "atomsCustom")[0].blur();
     }
 };
 
@@ -235,7 +237,26 @@ iCn3DUI.prototype.setAtomMenu = function (commandnameArray) { var me = this; //"
   var nameArray1 = (me.icn3d.defNames2Residues !== undefined) ? Object.keys(me.icn3d.defNames2Residues) : [];
   var nameArray2 = (me.icn3d.defNames2Atoms !== undefined) ? Object.keys(me.icn3d.defNames2Atoms) : [];
 
-  var nameArray = nameArray1.concat(nameArray2).sort();
+/*
+  var nameHash = {};
+
+  for(var i = 0, il = nameArray1.length; i < il; ++i) {
+      nameHash[nameArray1[i]] = 1;
+  }
+
+  for(var i = 0, il = nameArray2.length; i < il; ++i) {
+      nameHash[nameArray2[i]] = 1;
+  }
+
+  var nameArray = Object.keys(nameHash);
+*/
+
+  var nameArrayTmp = nameArray1.concat(nameArray2).sort();
+
+  var nameArray = [];
+  $.each(nameArrayTmp, function(i, el){
+       if($.inArray(el, nameArray) === -1) nameArray.push(el);
+  });
 
   //for(var i in me.icn3d.defNames2Atoms) {
   for(var i = 0, il = nameArray.length; i < il; ++i) {

diff --git a/src/icn3dui/parsers/mmcif_mmdb_parser_align.js b/src/icn3dui/parsers/mmcif_mmdb_parser_align.js
@@ -334,7 +334,7 @@ iCn3DUI.prototype.downloadChainAlignment = function (chainalign) { var me = this
 iCn3DUI.prototype.set2DDiagramsForAlign = function (mmdbid1, mmdbid2) { var me = this; //"use strict";
    me.openDialog(me.pre + 'dl_2ddgm', 'Interactions');
 
-   var url1 = me.baseUrl + "mmdb_strview.cgi?v=2&program=icn3d&uid="+mmdbid1+"&intrac=1";
+   var url1 = me.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&uid="+mmdbid1+"&intrac=1";
    var url2 = me.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&uid="+mmdbid2+"&intrac=1";
 
    if(me.cfg.inpara !== undefined) {

diff --git a/src/icn3dui/parsers/pdb_parser.js b/src/icn3dui/parsers/pdb_parser.js
@@ -231,25 +231,29 @@ iCn3DUI.prototype.transformToOpmOri = function(pdbid, chainresiCalphaHash2, bRes
       var chainresiCalphaHash1 = me.icn3d.getChainCalpha(me.icn3d.chains, me.icn3d.atoms, bResi_ori);
 
       var coordsFrom = [], coordsTo = [];
+      var bOneChain = (Object.keys(chainresiCalphaHash1.chainresiCalphaHash).length == 1 || Object.keys(chainresiCalphaHash2.chainresiCalphaHash).length == 1) ? true : false;
       for(var chainresi in chainresiCalphaHash1.chainresiCalphaHash) {
           if(chainresiCalphaHash2.chainresiCalphaHash.hasOwnProperty(chainresi)) {
               var coord1 = chainresiCalphaHash1.chainresiCalphaHash[chainresi];
               var coord2 = chainresiCalphaHash2.chainresiCalphaHash[chainresi];
 
-              coordsFrom.push(coord1);
-              coordsTo.push(coord2);
+              if(coord1.length == coord2.length || bOneChain) {
+                  coordsFrom = coordsFrom.concat(coord1);
+                  coordsTo = coordsTo.concat(coord2);
+              }
 
               if(coordsFrom.length > 500) break; // no need to use all c-alpha
           }
       }
 
-      var n = coordsFrom.length;
+      //var n = coordsFrom.length;
+      var n = (coordsFrom.length < coordsTo.length) ? coordsFrom.length : coordsTo.length;
 
-      if(n > 2) {
+      if(n >= 4) {
           me.icn3d.rmsd_supr = me.rmsd_supr(coordsFrom, coordsTo, n);
 
           // apply matrix for each atom
-          if(me.icn3d.rmsd_supr.rot !== undefined) {
+          if(me.icn3d.rmsd_supr.rot !== undefined && me.icn3d.rmsd_supr.rsmd < 0.1) {
               var rot = me.icn3d.rmsd_supr.rot;
               var centerFrom = me.icn3d.rmsd_supr.trans1;
               var centerTo = me.icn3d.rmsd_supr.trans2;
@@ -294,42 +298,56 @@ iCn3DUI.prototype.transformToOpmOri = function(pdbid, chainresiCalphaHash2, bRes
 };
 
 iCn3DUI.prototype.realign = function() { var me = this; //"use strict";
+    me.saveSelectionPrep();
+
+    var index = Object.keys(me.icn3d.defNames2Atoms).length;
+    var name = 'alseq_' + index;
+
+    me.saveSelection(name, name);
+
     var structHash = {};
-    var lastResi = 0;
+    var lastStruResi = '';
     for(var serial in me.icn3d.hAtoms) {
         var atom = me.icn3d.atoms[serial];
         if( (me.icn3d.proteins.hasOwnProperty(serial) && atom.name == "CA")
           || (me.icn3d.nucleotides.hasOwnProperty(serial) && (atom.name == "O3'" || atom.name == "O3*")) ) {
-            if(atom.resi == lastResi) continue; // e.g., Alt A and B
+            if(atom.structure + '_' + atom.resi == lastStruResi) continue; // e.g., Alt A and B
 
             if(!structHash.hasOwnProperty(atom.structure)) {
                 structHash[atom.structure] = [];
             }
 
             structHash[atom.structure].push(atom.coord.clone());
 
-            lastResi = atom.resi;
+            lastStruResi = atom.structure + '_' + atom.resi;
         }
     }
 
     var structArray = Object.keys(structHash);
 
-    if(structArray.length >= 2 && structHash[structArray[0]].length == structHash[structArray[1]].length) {
+//    if(structHash[structArray[0]].length != structHash[structArray[1]].length) alert("The number of selected residues in each structure should be the same...");
+
+//    if(structArray.length >= 2 && structHash[structArray[0]].length == structHash[structArray[1]].length) {
+    if(structArray.length >= 2) {
       var firstStruct = structArray[0];
       var secondStruct = structArray[1];
 
       // transform from the second structure to the first structure
       var coordsFrom = structHash[secondStruct];
       var coordsTo = structHash[firstStruct];
 
-      var n = coordsFrom.length;
+      //var n = coordsFrom.length;
+      var n = (coordsFrom.length < coordsTo.length) ? coordsFrom.length : coordsTo.length;
 
-      if(n > 2) {
+      if(n < 4) alert("Please select at least four residues in each structure...");
+      if(n >= 4) {
           me.icn3d.rmsd_supr = me.rmsd_supr(coordsFrom, coordsTo, n);
 
           // apply matrix for each atom
           if(me.icn3d.rmsd_supr.rot !== undefined) {
               var rot = me.icn3d.rmsd_supr.rot;
+              if(rot[0] === null) alert("Please select more residues in each structure...");
+
               var centerFrom = me.icn3d.rmsd_supr.trans1;
               var centerTo = me.icn3d.rmsd_supr.trans2;
               //var rsmd = me.icn3d.rmsd_supr.rsmd;

diff --git a/src/icn3dui/selection/sets.js b/src/icn3dui/selection/sets.js
@@ -70,6 +70,13 @@ iCn3DUI.prototype.deleteSelectedSets = function() { var me = this; //"use strict
 iCn3DUI.prototype.changeCustomAtoms = function (nameArray, bUpdateHlMenus) { var me = this; //"use strict";
    me.icn3d.hAtoms = {};
 
+/*
+   var nameArray = [];
+   $.each(inNameArray, function(i, el){
+       if($.inArray(el, nameArray) === -1) nameArray.push(el);
+   });
+*/
+
    for(var i = 0; i < nameArray.length; ++i) {
      var selectedSet = nameArray[i];
 

diff --git a/src/utils/rmsd_supr.js b/src/utils/rmsd_supr.js
@@ -511,7 +511,8 @@ iCn3DUI.prototype.null_basis = function(a0, v1, v2, v3, epsi) { var me = this; /
                 // the null space contains only the zero vector
                 k0 = 0;
                 v1[0] = 0.0; v1[1] = 0.0; v1[2] = 0.0;
-                return;
+                //return;
+                return {'k': k0, 'v1': v1, 'v2': v2, 'v3': v3};
             }
         }
     }