Merge pull request #225 in STRUC/icn3d from release2131 to master

* commit '0f41f196de69850ec4b20b469c7f205e970b459a':
  Showed membranes for transmembrane proteins in VAST+ alignment

CHANGELOG.md

@@ -1,5 +1,7 @@
 ## Change Log
-[icn3d-2.13.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.13.0.zip) was release on March 23, 2020. Added protein symmetry view.
+[icn3d-2.13.1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.13.1.zip) was release on March 26, 2020. Showed membranes for transmembrane proteins in VAST+ alignment.
+
+[icn3d-2.13.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.13.0.zip) was release on March 23, 2020. Added the "Symmetry" feature in the View menu.
 
 [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".
 

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-2.13.0.zip](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.13.0.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-2.13.1.zip](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.13.1.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.
 

icn3d.html

@@ -597,6 +597,12 @@ <h2>iCn3D gallery with live examples<span style="font-size:0.7em"> ("iCn3D PNG I
 </a>
 </div>
 
+<div class="gallery">
+<a href="https://icn3d.page.link/bGH1BfLsiGFhhTDn8" target="_blank">
+<img style="height:300px" src ="https://www.ncbi.nlm.nih.gov/Structure/icn3d/gallery/1KQ2-bGH1BfLsiGFhhTDn8.png"><br>Protein Symmetry Display (PDB 1KQ2)
+</a>
+</div>
+
 <div class="gallery">
 <a href="https://icn3d.page.link/1yydeU3ktdkPyptAA" target="_blank">
 <img style="height:300px" src ="https://www.ncbi.nlm.nih.gov/Structure/icn3d/gallery/1TUP-1yydeU3ktdkPyptAA.png"><br>3D Printing (PDB 1TUP)
@@ -2096,7 +2102,10 @@ <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-2.13.0.zip">icn3d-2.13.0</a> was release on March 23, 2020. Added protein symmetry view.
+<a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.13.1.zip">icn3d-2.13.1</a> was release on March 26, 2020. Showed membranes for transmembrane proteins in VAST+ alignment.
+<br><br>
+
+<a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.13.0.zip">icn3d-2.13.0</a> was release on March 23, 2020. Added the "Symmetry" feature in the View menu.
 <br><br>
 
 <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".

package.json

@@ -1,6 +1,6 @@
 {
   "name": "icn3d",
-  "version": "2.13.0",
+  "version": "2.13.1",
   "description": "iCn3D Structure Viewer",
   "main": "index.html",
   "scripts": {

src/icn3d/draw/drawing_full.js

@@ -432,17 +432,26 @@ iCn3D.prototype.applySymmetry = function (title) { var me = this; //"use strict"
         var colorAxis = dataArray[i][2];
         var colorPolygon = dataArray[i][3];
         var order = dataArray[i][4];
+        var chain = dataArray[i][5];
 
         me.createCylinder(start, end, axisRadius, colorAxis, 0);
 
         if(symmetryType == 'C' || (symmetryType == 'D' && order == nSide) ) {
-            // find the center and size of the first protein chain
-            var selectedChain = Object.keys(this.chains)[0];
-            for(var chainid in this.chains) {
-                var firstSerial = Object.keys(this.chains[chainid])[0];
-                if(this.proteins.hasOwnProperty(firstSerial)) {
-                    selectedChain = chainid;
-                    break;
+            // find the center and size of the selected protein chain
+            var selectedChain = Object.keys(this.structures)[0] + '_' + chain;
+
+            if(!this.chains.hasOwnProperty(selectedChain)) {
+                selectedChain = Object.keys(this.structures)[0] + '_' + chain.toLowerCase();
+            }
+
+            if(!this.chains.hasOwnProperty(selectedChain)) {
+                selectedChain = Object.keys(this.chains)[0];
+                for(var chainid in this.chains) {
+                    var firstSerial = Object.keys(this.chains[chainid])[0];
+                    if(this.proteins.hasOwnProperty(firstSerial)) {
+                        selectedChain = chainid;
+                        break;
+                    }
                 }
             }
 

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 = '2.13.0';
+    this.REVISION = '2.13.1';
 
     me.bFullUi = true;
 
@@ -956,14 +956,27 @@ iCn3DUI.prototype = {
 
     renderStructure: function () {  var me = this; //"use strict";
       if(me.bInitial) {
+          jQuery.extend(me.icn3d.opts, me.opts);
+
+          if(me.icn3d.bOpm && me.cfg.align !== undefined) { // show membrane
+              var resid = me.selectedPdbid + '_MEM_1';
+              for(var i in me.icn3d.residues[resid]) {
+                  var atom = me.icn3d.atoms[i];
+                  atom.style = 'stick';
+                  atom.color = me.icn3d.atomColors[atom.name];
+                  me.icn3d.atomPrevColors[i] = atom.color;
+
+                  me.icn3d.dAtoms[i] = 1;
+              }
+          }
+
           if(me.cfg.command !== undefined && me.cfg.command !== '') {
               me.icn3d.bRender = false;
 
-              jQuery.extend(me.icn3d.opts, me.opts);
               me.icn3d.draw();
           }
           else {
-              jQuery.extend(me.icn3d.opts, me.opts);
+
               me.icn3d.draw();
           }
 

src/icn3dui/parsers/mmcif_mmdb_parser.js

@@ -206,7 +206,8 @@ iCn3DUI.prototype.loadMmcifData = function(data, mmcifid) { var me = this; //"us
 
         //me.loadAtomDataIn(data, data.mmcif, 'mmcifid');
         me.deferredOpm = $.Deferred(function() {
-              me.loadMmcifOpmData(data, mmcifid);
+              //me.loadMmcifOpmData(data, mmcifid);
+              me.loadOpmData(data, mmcifid, undefined, 'mmcif');
         });
 
         return me.deferredOpm.promise();
@@ -331,13 +332,13 @@ iCn3DUI.prototype.parseMmdbDataPart1 = function (data, type) { var me = this; //
 
 iCn3DUI.prototype.parseMmdbData = function (data, type) { var me = this; //"use strict";
         if(type === undefined) {
-            me.deferredOpm = $.Deferred(function() {
+            //me.deferredOpm = $.Deferred(function() {
                   var id = (data.pdbId !== undefined) ? data.pdbId : data.mmdbId;
 
                   me.loadMmdbOpmData(data, id, type);
-            });
+            //});
 
-            return me.deferredOpm.promise();
+            //return me.deferredOpm.promise();
         }
         else {
             me.parseMmdbDataPart1(data, type);
@@ -597,7 +598,7 @@ iCn3DUI.prototype.getMissingResidues = function (seqArray, type, chainid) { var
 
 //type: "mmdbid", "mmcifid", "align"
 //alignType: "query", "target" for chain to chain 3D alignment
-iCn3DUI.prototype.loadAtomDataIn = function (data, id, type, seqalign, alignType, chainCalphaHash2) { var me = this; //"use strict";
+iCn3DUI.prototype.loadAtomDataIn = function (data, id, type, seqalign, alignType) { var me = this; //"use strict";
     //me.icn3d.init();
     me.icn3d.pmin = new THREE.Vector3( 9999, 9999, 9999);
     me.icn3d.pmax = new THREE.Vector3(-9999,-9999,-9999);
@@ -1254,11 +1255,10 @@ iCn3DUI.prototype.loadAtomDataIn = function (data, id, type, seqalign, alignType
     }
 
     if(type === 'mmcifid') {
-        me.transformToOpmOri(id, chainCalphaHash2);
+        me.transformToOpmOri(id);
     }
     else if(type === 'mmdbid') {
-        var bResi_ori = false; // true
-        me.transformToOpmOri(id, chainCalphaHash2, bResi_ori);
+        me.transformToOpmOri(id);
     }
 
     // set up sequence alignment

src/icn3dui/parsers/mmcif_mmdb_parser_align.js

@@ -124,61 +124,71 @@ iCn3DUI.prototype.downloadAlignment = function (align) { var me = this; //"use s
 
     chained.done(function( data ) { // url
         if (data.atoms !== undefined) {
-            me.icn3d.init();
+            me.deferredOpm = $.Deferred(function() {
+                //var mmdbidArray = me.inputid.split('_');
+                me.mmdbidArray = [];
+                for(var i = 0, il = data.alignedStructures[0].length; i < il; ++i) {
+                    me.mmdbidArray.push(data.alignedStructures[0][i].pdbId);
+                }
 
-            me.loadAtomDataIn(data, undefined, 'align', seqalign);
+                me.loadOpmDataForAlign(data, seqalign, me.mmdbidArray);
+            });
 
-            if(me.cfg.align === undefined && Object.keys(me.icn3d.structures).length == 1) {
-                $("#" + me.pre + "alternateWrapper").hide();
-            }
+            return me.deferredOpm.promise();
+        }
+        else {
+            alert('invalid atoms data.');
+            return false;
+        }
+    });
+};
 
-            // show all
-            var allAtoms = {};
-            for(var i in me.icn3d.atoms) {
-                allAtoms[i] = 1;
-            }
-            me.icn3d.dAtoms = allAtoms;
-            me.icn3d.hAtoms = allAtoms;
+iCn3DUI.prototype.downloadAlignmentPart2 = function (data, seqalign, chainresiCalphaHash2) { var me = this; //"use strict";
+    //me.icn3d.init();
+    me.loadAtomDataIn(data, undefined, 'align', seqalign);
 
-            me.icn3d.setAtomStyleByOptions(me.opts);
-            // change the default color to "Identity"
-            me.icn3d.setColorByOptions(me.opts, me.icn3d.atoms);
+    if(me.cfg.align === undefined && Object.keys(me.icn3d.structures).length == 1) {
+        $("#" + me.pre + "alternateWrapper").hide();
+    }
 
-            //var mmdbidArray = me.inputid.split('_');
-            me.mmdbidArray = [];
-            for(var i = 0, il = data.alignedStructures[0].length; i < il; ++i) {
-                me.mmdbidArray.push(data.alignedStructures[0][i].pdbId);
-            }
+    // show all
+    var allAtoms = {};
+    for(var i in me.icn3d.atoms) {
+        allAtoms[i] = 1;
+    }
+    me.icn3d.dAtoms = allAtoms;
+    me.icn3d.hAtoms = allAtoms;
 
-            me.renderStructure();
+    me.icn3d.setAtomStyleByOptions(me.opts);
+    // change the default color to "Identity"
+    me.icn3d.setColorByOptions(me.opts, me.icn3d.atoms);
 
-            if(me.cfg.rotate !== undefined) me.rotStruc(me.cfg.rotate, true);
+    // memebrane is determined by one structure. But transform both structures
+    if(chainresiCalphaHash2 !== undefined) me.transformToOpmOriForAlign(me.selectedPdbid, chainresiCalphaHash2, true);
 
-            me.html2ddgm = '';
+    me.renderStructure();
 
-            //setTimeout(function(){
-            //    me.set2DDiagramsForAlign(me.mmdbidArray[0].toUpperCase(), me.mmdbidArray[1].toUpperCase());
-            //}, 0);
+    if(me.cfg.rotate !== undefined) me.rotStruc(me.cfg.rotate, true);
 
-            // by default, open the seq alignment window
-            //if(me.cfg.show2d !== undefined && me.cfg.show2d) me.openDialog(me.pre + 'dl_2ddgm', 'Interactions');
-            if(me.cfg.showalignseq !== undefined && me.cfg.showalignseq) {
-                me.openDialog(me.pre + 'dl_alignment', 'Select residues in aligned sequences');
-            }
+    me.html2ddgm = '';
 
-            if(me.cfg.show2d !== undefined && me.cfg.show2d && me.bFullUi) {
-                me.set2DDiagramsForAlign(me.mmdbidArray[0].toUpperCase(), me.mmdbidArray[1].toUpperCase());
-            }
+    //setTimeout(function(){
+    //    me.set2DDiagramsForAlign(me.mmdbidArray[0].toUpperCase(), me.mmdbidArray[1].toUpperCase());
+    //}, 0);
 
-            //if(me.cfg.showseq !== undefined && me.cfg.showseq) me.openDialog(me.pre + 'dl_selectresidues', 'Select residues in sequences');
+    // by default, open the seq alignment window
+    //if(me.cfg.show2d !== undefined && me.cfg.show2d) me.openDialog(me.pre + 'dl_2ddgm', 'Interactions');
+    if(me.cfg.showalignseq !== undefined && me.cfg.showalignseq) {
+        me.openDialog(me.pre + 'dl_alignment', 'Select residues in aligned sequences');
+    }
 
-            if(me.deferred !== undefined) me.deferred.resolve(); if(me.deferred2 !== undefined) me.deferred2.resolve();
-        }
-        else {
-            alert('invalid atoms data.');
-            return false;
-        }
-    });
+    if(me.cfg.show2d !== undefined && me.cfg.show2d && me.bFullUi) {
+        me.set2DDiagramsForAlign(me.mmdbidArray[0].toUpperCase(), me.mmdbidArray[1].toUpperCase());
+    }
+
+    //if(me.cfg.showseq !== undefined && me.cfg.showseq) me.openDialog(me.pre + 'dl_selectresidues', 'Select residues in sequences');
+
+    if(me.deferred !== undefined) me.deferred.resolve(); if(me.deferred2 !== undefined) me.deferred2.resolve();
 };
 
 iCn3DUI.prototype.downloadChainAlignment = function (chainalign) { var me = this; //"use strict";

src/icn3dui/parsers/mmtf_parser.js

@@ -14,7 +14,8 @@ iCn3DUI.prototype.downloadMmtf = function (mmtfid) { var me = this; //"use stric
                 var bFull = false;
                 //me.parseMmtfData(mmtfData, bFull);
                 me.deferredOpm = $.Deferred(function() {
-                    me.loadMmtfOpmData(mmtfData, mmtfid, bFull);
+                    //me.loadMmtfOpmData(mmtfData, mmtfid, bFull);
+                    me.loadOpmData(mmtfData, mmtfid, bFull, 'mmtf');
                 });
 
                 return me.deferredOpm.promise();
@@ -29,7 +30,8 @@ iCn3DUI.prototype.downloadMmtf = function (mmtfid) { var me = this; //"use stric
                         var bFull = true;
                         //me.parseMmtfData(mmtfData2, bFull);
                         me.deferredOpm = $.Deferred(function() {
-                            me.loadMmtfOpmData(mmtfData2, mmtfid, bFull);
+                            //me.loadMmtfOpmData(mmtfData2, mmtfid, bFull);
+                            me.loadOpmData(mmtfData2, mmtfid, bFull, 'mmtf');
                         });
 
                         return me.deferredOpm.promise();
@@ -48,7 +50,7 @@ iCn3DUI.prototype.downloadMmtf = function (mmtfid) { var me = this; //"use stric
     );
 };
 
-iCn3DUI.prototype.parseMmtfData = function (mmtfData, mmtfid, bFull, chainCalphaHash2) { var me = this; //"use strict";
+iCn3DUI.prototype.parseMmtfData = function (mmtfData, mmtfid, bFull) { var me = this; //"use strict";
     var cnt = mmtfData.numAtoms;
 
     me.icn3d.init();
@@ -435,7 +437,7 @@ iCn3DUI.prototype.parseMmtfData = function (mmtfData, mmtfid, bFull, chainCalpha
     me.icn3d.oriMaxD = me.icn3d.maxD;
     me.icn3d.oriCenter = me.icn3d.center.clone();
 
-    me.transformToOpmOri(mmtfid, chainCalphaHash2);
+    me.transformToOpmOri(mmtfid);
 
     if(me.cfg.align === undefined && Object.keys(me.icn3d.structures).length == 1) {
         $("#" + me.pre + "alternateWrapper").hide();